WO2016004387A1

WO2016004387A1 - Gene expression signature for cancer prognosis

Info

Publication number: WO2016004387A1
Application number: PCT/US2015/039108
Authority: WO
Inventors: Jesus Gonzalez BOSQUET; Johnathan Mark Lancaster
Original assignee: H. Lee Moffitt Cancer Center And Research Institute, Inc.
Priority date: 2014-07-02
Filing date: 2015-07-02
Publication date: 2016-01-07

Abstract

The current invention pertains to a method for determining whether a subject suffering from a cancer is a good candidate for a chemotherapy for the cancer, and a method of treating a subject suffering from a cancer based on the identification of the subject as a good candidate or a bad candidate for the chemotherapy. The methods comprise the steps of identifying the subject as a good candidate for a chemotherapy or a bad candidate for the chemotherapy. The methods may further include administering the chemotherapy to the subject if the subject is identified as a good candidate for the chemotherapy, or withholding the administration of the chemotherapy to the subject identified as the bad candidate for the chemotherapy. In addition to withholding the chemotherapy from the bad candidate, an alternative treatment may be administered. The current invention also provides microarray chips useful in practicing the claimed invention of identifying a subject suffering from a cancer as a good candidate for a chemotherapy.

Description

GENE EXPRESSION SIGNATURE FOR CANCER PROGNOSIS

DESCRIPTION

CROSS-REFERENCE TO RELATED APPLICATION

The present application claims the benefit of U.S. Provisional Application Serial No. 62/020,310, filed July 2, 2014, which is hereby incorporated by reference herein in its entirety, including any figures, tables, nucleic acid sequences, amino acid sequences, or drawings.

GOVERNMENT SUPPORT

This invention was made with government support under grant number W81XWH- 08-2-0101 awarded by the US Army Medical Research and Materiel Command. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Epithelial ovarian cancer (OVCA) has the highest mortality rate of all gynecologic cancers¹, mainly because more than 70% of patients present with advanced stage and will have disseminated intra-peritoneal disease at diagnosis². But also because between 20-30% will not respond to the initial treatment consisting of a combination of cytoreductive surgery and a platinum-based chemotherapy³. Even in some patients with a complete initial response to chemotherapy, the disease will recur and eventually develop resistance to multiple drugs⁴. Several mechanisms have been described to contribute to chemo-response including drug efflux, increased cellular glutathione levels, increased DNA repair, and drug tolerance, but the exact mechanisms are not fully defined^5"7, and there are no valid clinical biomarkers or molecular signatures that effectively predict response to chemotherapy⁸'⁹. Understanding the underlying processes could lead to the identification of prognostic signatures, which in turn, could be used to stratify patients who are likely to develop resistance to standard chemotherapy and thus could benefit from alternative strategies⁹. BRIEF SUMMARY OF THE INVENTION

The current invention provides a method of treating a subject suffering from a cancer, the method comprising the steps of:

a) comparing the expression of mRNAs corresponding to the proteins identified in Table 9 or Table 12 in a sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy,

b) identifying the subject as a good candidate for a chemotherapy or a bad candidate for the chemotherapy, and

i) administering the chemotherapy to the subject if the subject is identified as the good candidate for the chemotherapy, or

ii) withholding the administration of the chemotherapy to the subject identified as the bad candidate for the chemotherapy, and optionally, administering a cancer treatment other than the chemotherapy to the subject identified as the bad candidate for the chemotherapy,

wherein, the subject is the good candidate for the chemotherapy if the expression in the sample of the subject of at least 75% of the mRNAs corresponding to the proteins identified in Table 9 or Table 12 are not significantly different than the corresponding reference values for the good responder, and/or

the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 25% of the mRNAs corresponding to the proteins identified in Table 9 or Table 12 are significantly different than the corresponding reference value for a bad responder.

Prior to the comparison step, the method may further comprise the step of obtaining the sample from the subject. Prior to the comparison step, and after a sample is obtained from the subject, the method may further comprise measuring (quantifying) the expression of mRNAs corresponding to the proteins identified in Table 9 or Table 12 in the sample obtained from the subject.

The current invention also provides microarray chip comprising mRNAs corresponding to proteins involved in cellular signaling pathways directly associated with responsiveness to chemotherapy for treatment of a cancer, the microarray chip consisting essentially of oligonucleotides corresponding to the mRNAs corresponding to the proteins identified in Table 9 or Table 12. The microarray chips of the current invention are useful in practicing the claimed invention of identifying a subject suffering from a cancer as a good candidate for chemotherapy.

BRIEF DESCRIPTION OF THE DRAWINGS The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Patent and Trademark Office upon request and payment of the necessary fee.

Figures 1A-1C show consensus matrices of the final signature model. Figure 1A: Consensus matrix of the final model including 422 genes, suggesting and optimal and more robust result, with limited overlap between clusters, for clustering with k- factor = 2. Figure IB: Cophenetic correlation coefficients representation, with an optimal result for k=2. Figure 1C: Other consensus matrices for k=3 to k=6 showing less harmonious models.

Figures 2A-2E show validation of the NMF consensus clustering in independent publicly available databases. In all of them we used 422 genes included the final model. All of them also showed robust clustering with k = 2, and very limited overlap between clusters. Other consensus matrices for k=3 to k=6 were less harmonious (not shown). All cophenetic correlation coefficients had optimal results for k=2 (not shown). The level of agreement (kappa coefficient) for placement of an individual gene in the same cluster than in TCGA analysis are also shown for each dataset. Figure 2A: GSE9891 database¹⁵. Figure 2B: GSE3149 database¹⁴. Figure 2C: GSE26712 database¹⁸. Figure 2D: GSE23554 database¹². Figure 2E: GSE17260 database¹⁷.

Figure 3 shows gene expression correlation matrix of the 422 and association with pathway analysis. Pathway analysis of both clusters showed an overrepresentation of cellular signaling and immune response pathways in cluster #1 (blue), and DNA repair/replication within the context of cell cycle pathways in cluster #2 (yellow).

Figure 4 shows gene expression profile of genes included in cluster #1 and #2 and their association with significant pathways identified with enrichment pathway analyses. Cluster 1 : significantly associated with cell signaling (blue), immune response (yellow) and a variety of metabolic pathways (purple). Cluster 2: significantly associated with DNA repair/replication and cell cycle (green), pathways in cancer (red) and a cell adhesion/cytoskeleton pathways (maroon). Figure 5. Multivariate analysis of clinical factors affecting survival in TCGA database. Kaplan-Meier curve representing survival of patients with CR versus patients with IR (graph). Table with independent clinical variables for survival in TCGA: chemo-response is the most significant of all of them with a p-value <10-15 (table).

Figure 6. Differentially expressed genes between patients with complete response

(CR) and patients with incomplete response (IR) in the 3 clinical databases (GSE9891, TCGA, GSE23554); and in OVCA cell lines after in vitro chemo-sensitivity analysis. Only common significant genes between analyses, marked with colored arrows, were included in the enrichment analysis with GeneGo (METACORE™, Carlsbad, CA).

Figure 7. Representation of genomic somatic gains and losses determined by the genomic identification of significant targets in cancer (GISTIC) analysis. Losses (blue) and gains (red) are represented with respect to their position in each chromosome. Depiction of X and Y chromosomes are the result of all individuals being female.

Figures 8A-8D: TCGA analyses of gene expression, mutations, DNA methylation and miRNA expression between CR samples and IR samples. Figure 8 A: Heat map of a 69 gene expression signature predictive of CR versus IR in the correlated CNA-gene expression (CCP) subset of genes. Figure 8B: Mutated genes associated with chemo-response, CR versus IR (in the first column) and their significant correlation with expressed genes (second column) in the CCP gene subset, p-value <10^"4. Figure 8C: Heat map of the 69 genes differentially methylated between the CR and IR groups at 0.001 level of the univariate test. Figure 8D: Heat map of the 38 miRNA differentially expressed between the CR and IR groups (p-value <0.05, as there were only 619 unique miRNA entering the analysis).

Figure 9. Validation of TCGA gene expression signature in independent available databases. Same study design (definitions of variables, normalization procedures, statistics), same software and analysis tools (BRB Array Tools) were used for validation. GEO# GSE9891¹⁵, with a p-value < 0.001. GSE23554¹², with a p-value of 0.02. GSE28739¹⁶, with a p-value of 0.01.

Figures 10A-10B. Transcription factor (TF) binding site analysis. Figure 10A: Heat map of the 59 differentially expressed genes between CR and IR that were identified to have TF binding sites at the CCP gene subset (p-value <0.01). Figure 10B: UCSC Genome Browser of one of the significant genes, RHOT1, with representation of its TF binding sites (above) and conserved gene structure across species (below). Figures 11A-11E. Detail of level of agreement (kappa coefficient) for placement of an individual gene in the same cluster than in TCGA analysis represented in contingency tables. Figure 11A: GSE9891 database¹⁵. Figure 11B: GSE3149 database¹⁴. Figure 1 1C: GSE26712 database¹⁸. Figure 11D: GSE23554 database¹². Figure HE: GSE17260 database¹⁷.

DETAILED DESCRIPTION OF THE INVENTION

A third of patients with epithelial ovarian cancer (OVCA) do not respond to standard treatment. The determination of a robust signature that predicts chemo-response could lead to the identification of molecular markers for response as well as possible clinical implementation in the future to identify patients at risk of failing therapy. The claimed invention was designed to identify biological processes affecting candidate pathways associated with chemo-response and to create a robust gene signature. After identifying common pathways associated with chemo-response in serous OVCA in 3 independent gene expression experiments, the biological processes associated with them was assessed using The Cancer Genome Atlas (TCGA) dataset for serous OVCA. The differential copy number alterations (CNA), mutations, DNA methylation, and miRNA expression between patients that responded to standard treatment and those who did not or recurred prematurely was also identified. These significant parameters were correlated to gene expression to create a signature of genes associated with chemo-response. A consensus clustering of this signature identified differentiated clusters with unique molecular patterns: for example, a cluster was significant for cellular signaling and immune response (mainly cell-mediated); whereas, another cluster was significant for pathways involving DNA damage repair and replication, cell cycle and apoptosis. Validation through consensus clustering was performed in 5 independent OVCA gene expression experiments. Genes were located in the same cluster with consistent agreement in all 5 studies (Kappa coefficient > 0.6 in 4). As such, integrating high throughput biological data provides a robust molecular signature that predicts chemo- response in OVCA.

Previous studies have identified a series of molecular signaling pathways associated with OVCA response to chemotherapy in vitro as well as in clinical settings^10"13. The current invention is based on identifying pathways associated with chemo-response to identify biological processes that influence expression. Accordingly, the current invention provides a method for determining whether a subject suffering from a cancer is a good candidate or a bad candidate for a chemotherapy for the cancer, the method comprising the steps of:

b) identifying the subject as the good candidate for the chemotherapy or the bad candidate for the chemotherapy,

The method of the claimed invention can further comprise treating the subject suffering from a cancer, the method comprising the steps of:

ii) withholding the administration of the chemotherapy to the subject identified as the bad candidate for the chemotherapy, and optionally, administering a cancer treatment other than the chemotherapy to the subject identified as the bad candidate for the chemotherapy.

In an embodiment of the invention, the subject is the good candidate for the chemotherapy if the expression in the tissue sample of the subject of at least 80%>, 85%, 90%, 95% or 99% of the mRNAs corresponding to the proteins identified in Table 9 or Table 12 are not significantly different than the corresponding reference values for the good responder and/or the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 20%, 15%, 10%, 5% or 1% of the mRNAs corresponding to the proteins identified in Table 9 or Table 12 are significantly different than the corresponding reference value for a bad responder.

In certain embodiments of the current invention, the good responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 9 or Table 12 in a sample from a person known to be responsive to the chemotherapy, wherein the sample from the person known to be responsive to the chemotherapy is obtained from the person before the administration of the chemotherapy. In certain other embodiments of the current invention, the bad responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 9 or Table 12 in a sample from a person known to be non-responsive to the chemotherapy, wherein the sample from the person known to be non-responsive to the chemotherapy is obtained before the administration of the chemotherapy.

For the purposes of the current invention, a good responder (i.e., a complete responder

(CR)) to a chemotherapy for treatment of a cancer is a patient who shows a complete disappearance of all disease for a duration of time, for example, 3 months, 4 months, 5 months, 6 months, or longer after treatment. Similarly, a bad responder (i.e. an incomplete responder (IR)) is a patient who either has not responded or progressed during treatment (refractory) or the disease recurred within a duration of time, for example, 3 months, 4 months, 5 months, 6 months, or longer after of treatment completion (resistant)³'¹⁹'²⁰.

In one embodiment of the current invention, the chemotherapy comprises administering a platinum based drug, a taxane, or both (such as Taxol/Carbo) to a subject. Non-limiting examples of a platinum based drug include cisplatin, carboplatin, oxalaplatin, satraplatin, picoplatin, nedaplatin, triplatin, or a combination of two or more of the foregoing. Optionally, the platinum-based drug may be a liposomal version, such as lipoplatin. Non- limiting examples of taxanes include paclitaxel, docetaxel, cabazitaxel, or a combination of two or more of the foregoing. Additional examples of platinum based drugs and/or taxanes are well known to a person of ordinary skill in the art and such embodiments are within the purview of the current invention.

As used herein, the term "cancer" or "tumor" refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. For example, a particular cancer may be characterized by a solid mass tumor. The solid tumor mass, if present, may be a primary tumor mass. A primary tumor mass refers to a growth of cancer cells in a tissue resulting from the transformation of a normal cell of that tissue. In most cases, the primary tumor mass is identified by the presence of a cyst, which can be found through visual or palpation methods, or by irregularity in shape, texture or weight of the tissue. However, some primary tumors are not palpable and can be detected only through medical imaging techniques such as X-rays (e.g., mammography), or by needle aspirations. The use of these latter techniques is more common in early detection. Molecular and phenotypic analysis of cancer cells within a tissue will usually confirm if the cancer is endogenous to the tissue or if the lesion is due to metastasis from another site. The term cancer or tumor is inclusive of solid tumors and non-solid tumors.

Cancers suitable for practicing the methods of the claimed invention include, but are not limited to, cancer and/or tumors of the anus, bile duct, bladder, bone, bone marrow, bowel (including colon and rectum), breast, eye, gall bladder, kidney, mouth, larynx, esophagus, stomach, testis, cervix, head, neck, ovary, lung, mesothelioma, neuroendocrine, penis, skin, spinal cord, thyroid, vagina, vulva, uterus, liver, muscle, pancreas, prostate, blood cells (including lymphocytes and other immune system cells), and brain. Specific cancers contemplated with the methods of the present invention include, but are not limited to, carcinomas, Karposi's sarcoma, melanoma, mesothelioma, soft tissue sarcoma, ovarian cancer, uterine cancer, endometrial cancer, breast cancer, pancreatic cancer, lung cancer, leukemia (acute lymphoblastic, acute myeloid, chronic lymphocytic, chronic myeloid, and other), and lymphoma (Hodgkin's and non-Hodgkin's), and multiple myeloma.

Examples of cancers that can be treated according to the present invention are:

Acute Lymphoblastic Leukemia, Hairy Cell Leukemia

Adult Head and Neck Cancer

Acute Lymphoblastic Leukemia, Hepatocellular (Liver) Cancer, Adult

Childhood (Primary)

Acute Myeloid Leukemia, Adult Hepatocellular (Liver) Cancer, Childhood

Acute Myeloid Leukemia, Childhood (Primary)

Adrenocortical Carcinoma Hodgkin's Lymphoma, Adult

Adrenocortical Carcinoma, Childhood Hodgkin's Lymphoma, Childhood

AIDS-Related Cancers Hodgkin's Lymphoma During Pregnancy

AIDS -Related Lymphoma Hypopharyngeal Cancer

Anal Cancer Hypothalamic and Visual Pathway Glioma,

Astrocytoma, Childhood Cerebellar Childhood Astrocytoma, Childhood Cerebral Intraocular Melanoma

Islet Cell Carcinoma (Endocrine Pancreas)

Basal Cell Carcinoma

Bile Duct Cancer, Extrahepatic Kaposi's Sarcoma

Bladder Cancer Kidney (Renal Cell) Cancer

Bladder Cancer, Childhood Kidney Cancer, Childhood

Bone Cancer,

Osteosarcoma/Malignant Fibrous Laryngeal Cancer

Histiocytoma Laryngeal Cancer, Childhood

Brain Stem Glioma, Childhood Leukemia, Acute Lymphoblastic, Adult

Brain Tumor, Adult Leukemia, Acute Lymphoblastic, Childhood

Brain Tumor, Brain Stem Glioma, Leukemia, Acute Myeloid, Adult

Childhood Leukemia, Acute Myeloid, Childhood

Brain Tumor, Cerebellar Leukemia, Chronic Lymphocytic

Astrocytoma, Childhood Leukemia, Chronic Myelogenous

Brain Tumor, Cerebral Leukemia, Hairy Cell

Astrocytoma/Malignant Glioma, Lip and Oral Cavity Cancer

Childhood Liver Cancer, Adult (Primary)

Brain Tumor, Ependymoma, Liver Cancer, Childhood (Primary)

Childhood Lung Cancer, Non-Small Cell

Brain Tumor, Medulloblastoma, Lung Cancer, Small Cell

Childhood Lymphoma, AIDS-Related

Brain Tumor, Supratentorial Primitive Lymphoma, Burkitt's

Neuroectodermal Tumors, Childhood Lymphoma, Cutaneous T-Cell, see Mycosis

Brain Tumor, Visual Pathway and Fungoides and Sezary Syndrome

Hypothalamic Glioma, Childhood Lymphoma, Hodgkin's, Adult

Brain Tumor, Childhood Lymphoma, Hodgkin's, Childhood

Breast Cancer Lymphoma, Hodgkin's During Pregnancy

Breast Cancer, Childhood Lymphoma, Non-Hodgkin's, Adult

Breast Cancer, Male Lymphoma, Non-Hodgkin's, Childhood

Bronchial Adenomas/Carcinoids, Lymphoma, Non-Hodgkin's During

Childhood Pregnancy

Burkitt's Lymphoma Lymphoma, Primary Central Nervous

System

Carcinoid Tumor, Childhood

Carcinoid Tumor, Gastrointestinal Macroglobulinemia, Waldenstrom's Carcinoma of Unknown Primary Malignant Fibrous Histiocytoma of Central Nervous System Lymphoma, Bone/Osteosarcoma

Primary Medulloblastoma, Childhood

Cerebellar Astrocytoma, Childhood Melanoma

Cerebral Astrocytoma/Malignant Melanoma, Intraocular (Eye)

Glioma, Childhood Merkel Cell Carcinoma

Cervical Cancer Mesothelioma, Adult Malignant

Childhood Cancers Mesothelioma, Childhood

Chronic Lymphocytic Leukemia Metastatic Squamous Neck Cancer with Chronic Myelogenous Leukemia Occult Primary

Chronic Myeloproliferative Disorders Multiple Endocrine Neoplasia Syndrome, Colon Cancer Childhood Colorectal Cancer, Childhood Multiple Myeloma/Plasma Cell Neoplasm Cutaneous T-Cell Lymphoma, see Mycosis Fungoides

Mycosis Fungoides and Sezary Myelodysplasia Syndromes

Syndrome Myelodysplastic/Myeloproliferative

Diseases

Endometrial Cancer Myelogenous Leukemia, Chronic

Ependymoma, Childhood Myeloid Leukemia, Adult Acute

Esophageal Cancer Myeloid Leukemia, Childhood Acute Esophageal Cancer, Childhood Myeloma, Multiple

Ewing's Family of Tumors Myeloproliferative Disorders, Chronic Extracranial Germ Cell Tumor,

Childhood Nasal Cavity and Paranasal Sinus Cancer

Extragonadal Germ Cell Tumor Nasopharyngeal Cancer

Extrahepatic Bile Duct Cancer Nasopharyngeal Cancer, Childhood Eye Cancer, Intraocular Melanoma Neuroblastoma

Eye Cancer, Retinoblastoma Non-Hodgkin's Lymphoma, Adult

Non-Hodgkin's Lymphoma, Childhood

Gallbladder Cancer Non-Hodgkin's Lymphoma During

Gastric (Stomach) Cancer Pregnancy

Gastric (Stomach) Cancer, Childhood Non-Small Cell Lung Cancer

Gastrointestinal Carcinoid Tumor

Germ Cell Tumor, Extracranial, Oral Cancer, Childhood

Childhood Oral Cavity Cancer, Lip and

Germ Cell Tumor, Extragonadal Oropharyngeal Cancer

Germ Cell Tumor, Ovarian Osteosarcoma/Malignant Fibrous

Gestational Trophoblastic Tumor Histiocytoma of Bone

Glioma, Adult Ovarian Cancer, Childhood

Glioma, Childhood Brain Stem Ovarian Epithelial Cancer

Glioma, Childhood Cerebral Ovarian Germ Cell Tumor

Astrocytoma Ovarian Low Malignant Potential Tumor

Glioma, Childhood Visual Pathway

and Hypothalamic Pancreatic Cancer

Pancreatic Cancer, Childhood

Skin Cancer (Melanoma) Pancreatic Cancer, Islet Cell

Skin Carcinoma, Merkel Cell Paranasal Sinus and Nasal Cavity Cancer Small Cell Lung Cancer Parathyroid Cancer

Small Intestine Cancer Penile Cancer

Soft Tissue Sarcoma, Adult Pheochromocytoma

Soft Tissue Sarcoma, Childhood Pineoblastoma and Supratentorial Primitive Squamous Cell Carcinoma, see Skin Neuroectodermal Tumors, Childhood Cancer (non-Melanoma) Pituitary Tumor

Squamous Neck Cancer with Occult Plasma Cell Neoplasm/Multiple Myeloma Primary, Metastatic Pleuropulmonary Blastoma

Stomach (Gastric) Cancer Pregnancy and Breast Cancer

Stomach (Gastric) Cancer, Childhood Pregnancy and Hodgkin's Lymphoma Supratentorial Primitive Pregnancy and Non-Hodgkin's Lymphoma Neuroectodermal Tumors, Childhood Primary Central Nervous System

Lymphoma T-Cell Lymphoma, Cutaneous, see Prostate Cancer

Mycosis Fungoides and Sezary

Syndrome Rectal Cancer

Testicular Cancer Renal Cell (Kidney) Cancer

Thymoma, Childhood Renal Cell (Kidney) Cancer, Childhood

Thymoma and Thymic Carcinoma Renal Pelvis and Ureter, Transitional Cell

Thyroid Cancer Cancer

Thyroid Cancer, Childhood Retinoblastoma

Transitional Cell Cancer of the Renal Rhabdomyosarcoma, Childhood

Pelvis and Ureter

Trophoblastic Tumor, Gestational Salivary Gland Cancer

Salivary Gland Cancer, Childhood

Unknown Primary Site, Carcinoma of, Sarcoma, Ewing's Family of Tumors

Adult Sarcoma, Kaposi's

Unknown Primary Site, Cancer of, Sarcoma, Soft Tissue, Adult

Childhood Sarcoma, Soft Tissue, Childhood

Unusual Cancers of Childhood Sarcoma, Uterine

Ureter and Renal Pelvis, Transitional Sezary Syndrome

Cell Cancer Skin Cancer (non-Melanoma)

Urethral Cancer Skin Cancer, Childhood

Uterine Cancer, Endometrial

Uterine Sarcoma

Vaginal Cancer

Visual Pathway and Hypothalamic

Glioma, Childhood

Vulvar Cancer

Waldenstrom's Macroglobulinemia

Wilms' Tumor

In one embodiment of the methods of the invention, the cancer is a gynecologic cancer. In one embodiment of the current invention, the cancer is ovarian cancer (e.g., epithelial ovarian cancer or serous ovarian cancer), endometrial cancer, uterine cancer, or breast cancer. In one embodiment, the cancer is breast cancer of the triple-negative type (TNBC; any breast cancer that does not express the genes for estrogen receptor (ER), progesterone receptor (PR), and Her2/neu.

The cancer may be primary or metastatic. The cancer may be any grade or stage. For example, in the case of ovarian cancer, the cancer may be stage I, IA, IB, IC, II, IA, IIB, IIC, III, IA, IIIB, IIIC, or IV.

As used herein, the terms "treat" or "treatment" refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down a cancer, such as the development and/or spread of a cancer. For purposes of this invention, beneficial or desired clinical results include, but are not limited to, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. "Treatment" can also mean prolonging survival as compared to expected survival if not receiving treatment. Those in need of treatment include those with the condition or disorder.

Various well known methods can be used to estimate and compare the expression of mR As for practicing the claimed invention. These methods include, but are not limited to detecting and quantifying the expression of mRNAs by northern blot analysis, micro-array based method, real-time quantitative PCR, or semi-quantitative RT-PCR.

In one embodiment, the method of the current invention is practiced in a mammal. Non-limiting examples of a mammal include a human, ape, canine, pig, bovine, rodent, or feline.

The sample used for practicing the methods of the current invention can be a tissue sample or a body fluid sample. Non- limiting examples of the tissue sample include brain, eyes, Pineal gland, Pituitary gland, Thyroid gland, Parathyroid glands, thorax, heart, lungs, esophagus, Thymus gland, pleura, Adrenal glands, Appendix, Gall bladder, urinary bladder, large intestine, small intestine, kidneys, liver, pancreas, spleen, stoma, Prostate gland, Testes, ovaries, or uterus. Non-limiting examples of a body fluid sample include amniotic fluid, aqueous humor, vitreous humor, bile, cerebrospinal fluid, chyle, endolymph, perilymph, female ejaculate, male ejaculate, lymph, mucus (including nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sputum, synovial fluid, vaginal secretion, pancreatic juice or aspirate, pancreatic cyst fluid, serum, plasma, and blood.

It will be understood that the treatments of the invention include certain steps that are also a separate aspect of the invention: a method for determining whether a subject suffering from a cancer is a good candidate or bad candidate for a chemotherapy for the cancer, the method comprising the steps of:

a) comparing the expression of mRNAs corresponding to the proteins identified in

Table 9 or Table 12 in a sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy,

the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 25% of the mRNAs corresponding to the proteins identified in Table 9 or Table 12 are significantly different than the corresponding reference value for a bad responder. Optionally, the method further includes administering the chemotherapy to the subject identified as a good candidate; or withholding chemotherapy and, optionally, administering a cancer treatment other than chemotherapy (e.g., an immunotherapy) to the subject identified as a bad candidate for chemotherapy.

Another aspect of the invention includes a method for gene expression analysis, comprising:

a) measuring the expression of mRNAs corresponding to the proteins identified in Table 9 or Table 12 in a sample obtained from a subject having cancer; and

b) optionally, comparing the measured expression to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy. In some embodiments, the method further comprises providing a report of the outcome of a). In some embodiments, when b), is carried out, the method may further comprise providing a report of the outcome of b), such as to a healthcare provider or to the subject.

A report may be generated and provided to a healthcare provider or to the subject. The report can be in electronic, verbal, or in paper format, for example. Thus, the report can be provided electronically, telephonically (e.g., by facsimile, using devices such as fax back), or by mail or courier, or in person, for example. In some embodiments, the report includes an icon or other indicator indicating the classification of a sample as being above or below a reference value as described with the methods of treatment of the invention. In some embodiments, the report includes an indicator of whether the subject is a good candidate or a bad candidate for chemotherapy as described with the methods of the treatment of the invention.

The current invention further provides a microarray chip useful for carrying out the methods of the invention, comprising or consisting essentially of the oligonucleotides corresponding to mR As corresponding to proteins directly associated with cellular signaling pathways that impact responsiveness to a chemotherapy for the treatment of cancer. For the purposes of this invention, a microarray chip "consisting essentially of oligonucleotides corresponding to mRNAs corresponding to proteins directly associated with cellular signaling pathways that impact responsiveness to a chemotherapy for the treatment of cancer indicates that the microarray chip contains only those oligonucleotides which correspond to mRNAs corresponding to proteins directly associated with cellular signaling pathways that impact responsiveness to a chemotherapy for the treatment of cancer and do not contain oligonucleotides corresponding to mRNAs corresponding to proteins that are not so associated.

In further embodiments, the microarray chips of the claimed invention consist of about 500, about 600, about 700, about 800, about 900 or about 1000 oligonucleotides.

In certain embodiments, the microarray chips of the claimed invention consist essentially of oligonucleotides corresponding to mRNAs corresponding to proteins directly associated with cellular signaling pathways that impact responsiveness to a chemotherapy which comprises administering a platinum based drug and/or taxane to the subject. The platinum based drug can be cisplatin, carboplatin, oxalaplatin or a combination thereof and the taxane can be paclitaxel and/or docetaxel. Accordingly, in certain embodiments, the current invention provides microarray chips consisting essentially of oligonucleotides corresponding to mRNAs corresponding to proteins identified in Table 9 or Table 12.

Preferably, the oligonucleotides, which act as capture probes, are immobilized on a solid surface (e.g., plate, flow channel, bead or other particle, etc.). The oligonucleotides may be systematically arranged in different positions (e.g., by spatial mapping or by differential tagging).

The arrayed arrayed oligonucleotide sequences are then hybridized with isolated nucleic acids (such as cDNA, miRNA or mRNA) from the test sample obtained from a subject. In some embodiments, the isolated nucleic acids from the test sample are labeled, such that their hybridization with the specific complementary oligonucleotide on the array (e.g., from Table 9, Table 12, or both) can be determined. Alternatively, the test sample nucleic acids are not labeled, and hybridization between the oligonucleotides on the array and the target nucleic acid is detected using a sandwich assay, for example using additional oligonucleotides complementary to the target that are labeled.

In one embodiment, the hybridized nucleic acids are detected by detecting one or more labels attached to the sample nucleic acids or attached to a nucleic acid probe that hybridizes directly or indirectly to the target nucleic acids. The labels can be incorporated by any of a number of methods. In one example, the label is simultaneously incorporated during the amplification step in the preparation of the sample nucleic acids. Thus, for example, polymerase chain reaction (PCR) with labeled primers or labeled nucleotides will provide a labeled amplification product. In one embodiment, transcription amplification using a labeled nucleotide (such as fluorescein-labeled UTP and/or CTP) incorporates a label into the transcribed nucleic acids).

Detectable labels suitable for use in embodiments throughout this disclosure include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels include biotin for staining with labeled streptavidin conjugate, magnetic beads (for example DYNABEADS), fluorescent dyes (for example, fluorescein, Texas red, rhodamine, green fluorescent protein, and the like), chemiluminescent markers, radiolabels, enzymes (for example, horseradish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (for example, polystyrene, polypropylene, latex, etc.) beads. Patents teaching the use of such labels include U.S. Patent No. 3,817,837; U.S. Patent No. 3,850,752; U.S. Patent No. 3,939,350; U.S. Patent No. 3,996,345; U.S. Patent No. 4,277,437; U.S. Patent No. 4,275,149; and U.S. Patent No. 4,366,241. In some embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance.

Means of detecting such labels are also well known. Thus, for example, radiolabels may be detected using photographic film or scintillation counters, fluorescent markers may be detected using a photodetector to detect emitted light. Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label. The label may be added to the target (sample) nucleic acid(s) prior to, or after, the hybridization. So-called "direct labels" are detectable labels that are directly attached to or incorporated into the target (sample) nucleic acid prior to hybridization. In contrast, so-called "indirect labels" are joined to the hybrid duplex after hybridization. Often, the indirect label is attached to a binding moiety that has been attached to the target nucleic acid prior to the hybridization. Thus, for example, the target nucleic acid may be biotinylated before the hybridization. After hybridization, an avidin-conjugated fluorophore will bind the biotin bearing hybrid duplexes providing a label that is easily detected (see Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24: Hybridization With Nucleic Acid Probes, P. Tijssen, ed. Elsevier, N.Y., 1993).

Exemplified Embodiments:

Examples of embodiments of the invention include, but are not limited to:

Embodiment 1. A method of treating a subject suffering from a cancer, the method comprising the steps of:

a) comparing the expression of mRNAs corresponding to the proteins identified in Table 9 in a sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy,

b) identifying the subject as a good candidate for a chemotherapy or a bad candidate for the chemotherapy, wherein, the subject is the good candidate for the chemotherapy if the expression in the sample of the subject of at least 75% of the mRNAs corresponding to the proteins identified in Table 9 are not significantly different than the corresponding reference values for the good responder, and/or

the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 25% of the mRNAs corresponding to the proteins identified in Table 9 are significantly different than the corresponding reference value for a bad responder, and

c) administering the chemotherapy to the subject if the subject is identified as the good candidate for the chemotherapy or withholding the administration of the chemotherapy to the subject identified as the bad candidate for the chemotherapy, and optionally, administering a cancer treatment other than the chemotherapy to the subject identified as the bad candidate for the chemotherapy. Embodiment 2. The method of embodiment 1, wherein the subject is the good candidate for the chemotherapy if the expression in the sample of the subject of at least 80%, 85%o, 90%), 95%o or 99% of the mRNAs corresponding to the proteins identified in Table 9 are not significantly different than the corresponding reference values for the good responder and/or the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 20%>, 15%, 10%>, 5% or 1% of the mRNAs corresponding to the proteins identified in Table 9 are significantly different than the corresponding reference value for a bad responder.

Embodiment 3. The method of any preceding embodiment, wherein the good responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 9 in a sample from a person known to be responsive to the chemotherapy, wherein the sample from the person known to be responsive to the chemotherapy is obtained before the administration of the chemotherapy.

Embodiment 4. The method of any preceding embodiment, wherein the bad responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 9 in a sample from a person known to be non-responsive to the chemotherapy, wherein the sample from the person known to be non- responsive to the chemotherapy is obtained before the administration of the chemotherapy.

Embodiment 5. The method of any preceding embodiment, wherein the chemotherapy comprises administering a platinum based drug and/or taxane to the subject.

Embodiment 6. The method of any preceding embodiment, wherein the platinum based drug is cisplatin, carboplatin, oxaliplatin or a combination of two or more of the foregoing.

Embodiment 7. The method of any preceding embodiment, wherein the taxane is paclitaxel and/or docetaxel.

Embodiment 8. The method of any preceding embodiment, wherein the cancer is epithelial ovarian cancer, serous ovarian cancer, endometrial ovarian cancer, uterine cancer or breast cancer.

Embodiment 9. The method of any preceding embodiment, wherein said method comprises identifying the subject as a good candidate for a chemotherapy; and administering the chemotherapy to the subject identified as the good candidate for the chemotherapy. Embodiment 10. The method of any one of embodiments 1 to 8, wherein said method comprises identifying the subject as a bad candidate for a chemotherapy; and administering a cancer treatment other than the chemotherapy to the subject identified as the bad candidate for the chemotherapy.

Embodiment 11. The method of any preceding embodiment, wherein the step of comparing the expression of mRNAs corresponding to the proteins identified in Table 9 in the sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy comprises:

a) obtaining the sample the subject,

b) detecting and quantifying the expression of mRNAs by northern blot analysis, micro-array based method, real-time quantitative PCR, or semi-quantitative RT-PCR

d) comparing the expression of mRNAs corresponding to the proteins identified in Table 9 in the sample obtained from the subject to the reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to the reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy.

Embodiment 12. The method of any preceding embodiment, wherein the sample is a tissue sample or a body fluid sample.

Embodiment 13. The method of embodiment 12, wherein the sample is a body fluid sample that is amniotic fluid, aqueous humor, vitreous humor, bile, cerebrospinal fluid, chyle, endolymph, perilymph, female ejaculate, male ejaculate, lymph, mucus (including nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sputum, synovial fluid, vaginal secretion, pancreatic juice or aspirate, pancreatic cyst fluid, serum, plasma, or blood.

Embodiment 14. The method of embodiment 12, wherein the sample is a tissue sample comprising or consisting of tissue of the brain, eyes, Pineal gland, Pituitary gland, Thyroid gland, Parathyroid glands, thorax, heart, lungs, esophagus, Thymus gland, pleura, Adrenal glands, Appendix, Gall blader, urinary blader, large intestine, small intestine, kidneys, liver, pancrease, spleen, stoma, Prostate gland, Testes, ovaries, or uterus. Embodiment 15. The method of any preceding embodiment, wherein the subject is human.

Embodiment 16. A method of treating a subject suffering from a cancer, the method comprising the steps of:

Table 12 in a sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy,

b) identifying the subject as a good candidate for a chemotherapy or a bad candidate for the chemotherapy, wherein, the subject is the good candidate for the chemotherapy if the expression in the sample of the subject of at least 75% of the mRNAs corresponding to the proteins identified in Table 12 are not significantly different than the corresponding reference values for the good responder, and/or

the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 25% of the mRNAs corresponding to the proteins identified in Table 12 are significantly different than the corresponding reference value for a bad responder, and

c) administering the chemotherapy to the subject if the subject is identified as the good candidate for the chemotherapy or withholding the administration of the chemotherapy to the subject identified as the bad candidate for the chemotherapy, and optionally, administering a cancer treatment other than the chemotherapy to the subject identified as the bad candidate for the chemotherapy.

Embodiment 17. The method of embodiment 16, wherein the subject is the good candidate for the chemotherapy if the expression in the sample of the subject of at least 80%, 85%o, 90%), 95%o or 99% of the mRNAs corresponding to the proteins identified in Table 12 are not significantly different than the corresponding reference values for the good responder and/or the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 20%>, 15%, 10%>, 5% or 1% of the mRNAs corresponding to the proteins identified in Table 12 are significantly different than the corresponding reference value for a bad responder.

Embodiment 18. The method of any preceding embodiment, wherein the good responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 12 in a sample from a person known to be responsive to the chemotherapy, wherein the sample from the person known to be responsive to the chemotherapy is obtained before the administration of the chemotherapy.

Embodiment 19. The method of any preceding embodiment, wherein the bad responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 12 in a sample from a person known to be non-responsive to the chemotherapy, wherein the sample from the person known to be non- responsive to the chemotherapy is obtained before the administration of the chemotherapy.

Embodiment 20. The method of any preceding embodiment, wherein the chemotherapy comprises administering a platinum based drug and/or taxane to the subject.

Embodiment 21. The method of embodiment 20, wherein the platinum based drug is cisplatin, carboplatin, oxalaplatin or a combination of two or more of the foregoing.

Embodiment 22. The method of embodiment 21, wherein the taxane is paclitaxel and/or docetaxel.

Embodiment 23. The method of any preceding embodiment, wherein the cancer is epithelial ovarian cancer, serous ovarian cancer, endometrial ovarian cancer, uterine cancer or breast cancer.

Embodiment 24. The method of any preceding embodiment, wherein the step of comparing the expression of mRNAs corresponding to the proteins identified in Table 12 in the sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy comprises:

a) obtaining the sample the subject,

b) detecting and quantifying the expression of mRNAs by northern blot analysis, micro-array based method, real-time quantitative PCR, or semi-quantitative

RT-PCR

d) comparing the expression of mRNAs corresponding to the proteins identified in Table 12 in the sample obtained from the subject to the reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to the reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy.

Embodiment 25. The method of any preceding embodiment, wherein the subject is human.

Embodiment 26. The method of any preceding embodiment, wherein the sample is a tissue sample or a body fluid sample.

Embodiment 27. The method of embodiment 26, wherein the same is a tissue sample comprising or consisting of a tissue of the brain, eyes, Pineal gland, Pituitary gland, Thyroid gland, Parathyroid glands, thorax, heart, lungs, esophagus, Thymus gland, pleura, Adrenal glands, Appendix, Gall blader, urinary blader, large intestine, small intestine, kidneys, liver, pancrease, spleen, stoma, Prostate gland, Testes, ovaries, or uterus.

Embodiment 28. The method of embodiment 26, wherein the sample is a body fluid sample that is amniotic fluid, aqueous humor, vitreous humor, bile, cerebrospinal fluid, chyle, endolymph, perilymph, female ejaculate, male ejaculate, lymph, mucus (including nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sputum, synovial fluid, vaginal secretion, pancreatic juice or aspirate, pancreatic cyst fluid, serum, plasma, or blood.

Embodiment 29. A microarray chip comprising mRNAs corresponding to proteins involved in cellular signaling pathways directly associated with responsiveness to chemotherapy for treatment of a cancer, the microarray chip comprises oligonucleotides corresponding to the mRNAs corresponding to the proteins identified in Table 9 or Table 12, or both.

Embodiment 30. The microarray chip of embodiment 29, wherein the chemotherapy comprises administering a platinum based drug and/or taxane to the subject.

Embodiment 31. The microarray chip of embodiment 30, wherein the platinum based drug is cisplatin, carboplatin, oxaliplatin or a combination thereof.

Embodiment 32. The microarray chip of embodiment 30, wherein the taxane is paclitaxel and/or docetaxel.

Embodiment 33. The microarray chip of any preceding embodiment, wherein the cancer is epithelial ovarian cancer, serous ovarian cancer, endometrial ovarian cancer, uterine cancer or breast cancer.

Embodiment 34. The microarray chip of embodiment 29, wherein the microarray chip has no more than one thousand different oligonucleotides (i.e., no more than one thousand oligonucleotides with different sequences). Embodiment 35. The microarray chip of emnbodiment 29, wherein the microarray chip has no more than nine hundred different oligonucleotides.

Embodiment 36. The microarray chip of embodiment 29, wherein the microarray chip has no more than eight hundred different oligonucleotides.

Embodiment 37. The microarray chip of embodiment 29, wherein the microarray chip has no more than seven hundred different oligonucleotides.

Embodiment 38. The microarray chip of embodiment 29, wherein the microarray chip has no more than six hundred different oligonucleotides.

Embodiment 39. The microarray chip of embodiment 29, wherein the microarray chip has no more than five hundred different oligonucleotides.

Embodiment 40. The microarray chip of embodiment 29, wherein the microarray chip consists essentially of oligonucleotides corresponding to the mRNAs corresponding to the proteins identified in Table 9 or Table 12, or both

Embodiment 41. A method for determining whether a subject suffering from a cancer is a good candidate or bad candidate for a chemotherapy for the cancer, the method comprising the steps of:

Embodiment 42. A method for gene expression analysis, comprising:

a) measuring the expression of mRNAs corresponding to the proteins identified in Table 9 or Table 12 in a sample obtained from a subject having cancer; and b) optionally, comparing the measured expression to reference values corresponding to the mR As expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy.

Embodiment 43. The method of embodiment 42, further comprising providing a report of the outcome of a).

Embodiment 44. The method of embodiment 43, further comprising providing a report of the outcome of b).

MATERIALS AND METHODS

Sources of data

Only serous OVCA specimens were used for these comparisons. The study included the following sets:

1. OVCA cultured cell lines used were A2008, A2780CP, A2780S, C13, IGROV1, OV2008, OVCAR5, and T8¹². Cells were subjected to sequential treatment with increasing doses of cisplatin. Both cisplatin resistance and genome-wide expression changes were measured serially at baseline and after 3 and 6 cisplatin-treatment/expansion cycles. Gene expression using Affymetrix Human U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) was uploaded at the Gene Expression Omnibus (GEO), accession number GSE23553.

2. GEO clinical datasets: 127 serous OVCA with chemo-response information from the dataset GSE23554¹² and dataset GSE3149¹⁴ with Affymetrix Human Genome U133 Plus

2.0 and U133A arrays; 240 serous OVCA with chemo-response information from the dataset GSE9891¹⁵ with Affymetrix Human Genome U133 Plus 2.0 arrays; 50 serous OVCA with chemo-response information from the dataset GSE28739¹⁶ with Agilent-012097 Human 1A arrays (V2) (Agilent Technologies, Santa Clara, CA); 110 serous OVCA with chemo- response information from the dataset GSE17260¹⁷ with Agilent-014850 Whole Human Genome 4x44K arrays; 185 serous OVCA from the dataset GSE26712¹⁸ with Affymetrix human U133A arrays.

3. TCGA (wee world- wide-website: cancergenome.nih.gov): Over 20 different cancer types are included in this initiative, including more than 560 serous epithelial ovarian cancers, the most common histological subtype of OVCA. TCGA comprehensive genomic information includes copy number variation, SNPs, miRNA expression, gene expression (mRNA), and DNA methylation as well as clinical and outcome information. Data from TCGA was downloaded, normalized, formatted and organized for the integration and analysis with other biological datasets in accordance with the precepts of the TCGA data sharing agreements.

All data collection and processing, including the consenting process, were performed after approval by a local institutional review board and in accord with the TCGA Human Subjects Protection and Data Access Policies, adopted by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI).

Clinical Outcomes

Complete response (CR) was defined as complete disappearance of all disease up to 6 months after treatment. In patients with incomplete response (IR) the disease either not responded or progressed during treatment (refractory) or recurred within 6 months of treatment completion (resistant)³'¹⁹'²⁰. Data analysis

Copy number alteration (CNA): Samples from Agilent Human Genome CGH Microarray 244A (Agilent Technologies, Santa Clara, CA) were processed and DNA sequences were aligned to NCBI Build 36 of the human genome. Circular Binary Segmentation was used to identify regions with altered copy number in each chromosome²¹. The copy number at a particular genomic location was computed based on the segmentation mean log ratio data. We found regions with frequent CNA among all samples by performing genomic identification of significant targets in cancer (or GISTIC) analysis²². The significance of CNA at a particular genomic location is determined based on false discovery rate (FDR), as previously described²³. To determine the performance of our strategy, we initially proceed with the analysis of the whole sample set, and then repeated the methodology with only samples from patients that demonstrated CR (n=294) and IR (n=158). CNA in both scenarios was consistent.

Mutation analysis: Somatic mutation detection, calling, annotation and validation have been extensively discussed previously²³. Somatic mutation information resulting from Illumina Genome Analyzer DNA Sequencing GAIIx platform (Illumina Inc., San Diego, CA) was downloaded and formatted for analysis. Mutation information was downloaded as Level 3, or validated somatic mutations. Somatic mutation information was available from 137 samples from patients with CR and 55 with IR. For those patients, there were 6,716 unique genes presenting some type of validated somatic mutation. These included: frame shift insertions and deletions, in-frame insertions or deletions, missense, nonsense and nonstop mutations, silence, splice site and translation start site mutations. All independent significant mutated genes were correlated with gene expression of the candidate pathways genes to determine if mutated genes were associated or influenced expression of those pathways. To correlate mutated genes with gene expression we used Spearman's rank correlation test, as both variables are not completely independent one from another. We assessed statistical significance of the correlation by computing q-value for FDR (qFDR) and p-value, corrected for multiple analyses²⁴.

Gene expression and correlation with CNA: Raw gene expression data was downloaded from the TCGA Data Portal (Level 1), extracted, loaded, and normalized with the analytical software, BRB-ArrayTools. In total 594 microarrays samples analyzed with Affymetrix HT Human Genome U133 Array: 584 coming from cancer tissue and 10 coming from ovarian normal samples. DNA sequences were aligned to NCBI Build 36 of the human genome. There were 452 arrays with clinical information about chemo-response. During the Circular Binary Segmentation analysis of the CNA, a gene-centric table is created, which contains a value for each gene covered in the genomic array. This value is assigned based on the segmentation mean log ratios. The gene-centric table is required for the correlation analysis between copy number and gene expression. Positive correlation between gene expression and CNA (increased CNA/increased gene expression, and decreased CNA/decreased gene expression) was performed using Spearman's rank correlation test, as the expression between genes is not completely independent one from another. Statistical significance was assessed with qFDR and p-value, and corrected for multiple analyses²⁴.

To construct a gene signature profile that would classify patients between complete responders and incomplete responders, we used the Class Prediction Tool of BRB- ArrayTools. Genes differentially expressed between both classes at significance level p<0.001 were included in the predictor and evaluated with several methods. To assess how accurately the groups are predicted by this multivariate class predictor, a cross-validated misclassification rate is computed, usually in the form of Leave -one-out cross-validation method. For TCGA gene expression analysis, 40 samples in each group (CR versus IR) had 90% power of detect differentially expressed gene, with a type 1 error of 0.001. A similar experiment, using the same software (BRB Array Tools), same statistics, same outcomes definitions (CR versus IR), and list of genes from the gene signature identified in the testing set (TCGA), was designed to validate the results of the signature profile in independent available databases: GEO# GSE9891¹⁵, GSE28739¹⁶, and GSE23554¹².

Methylation analysis and correlation with gene expression: DNA methylation data with beta-values, methylated (M) and unmethylated (U) intensities were downloaded from the TCGA Data Portal (Level 2), extracted, loaded, and normalized. In total 574 arrays samples of Illumina Infinium Human DNA Methylation 27 (Illumina Inc., San Diego, CA): 572 cancer, 2 normal. There were 453 unique DNA-methylation arrays from serous OVCA with clinical information about chemo-response. Differential DNA methylation of gene promoters was computed based on beta-values. Beta-values for each sample and locus were calculated as (M/(M+U))²³. Differences of gene's beta-values between the classes (CR vs. IR) at the univariate significance level of p<0.001 were considered significant. Rank-based Spearman correlation was used to allow for non-linear relationships between DNA methylation and gene expression, along with p-values. To control the false discovery rate (FDR) we used the q-value for statistical significance (qFDR)²⁴ and Bonferroni correction for multiple comparisons.

miRNA expression analysis and its correlation with gene expression: Raw miRNA expression data was downloaded from the TCGA Data Portal (Level 1), extracted, loaded, and normalized with the analytical software, BRB- Array Tools. In total 595 microarrays samples of Agilent Human miRNA Microarray Rell2.0 (Agilent Technologies Inc., Santa Clara, CA): 585 cancer, 10 normal. There were 455 unique miRNA expression arrays from serous OVCA with clinical information about chemo-response²³. Differences of miRNA expression between the classes (CR vs. IR) at the univariate significance level of p<0.05 were considered significant, as there were 619 unique miRNA tested. Rank-based Spearman correlation was used to allow for non-linear relationships between miRNA expression and gene expression, along with p-values. To control the false discovery rate (FDR) we used the q-value for statistical significance (qFDR)²⁴ and Bonferroni correction for multiple comparisons.

Transcription factor (TF) binding sites and their association with gene expression: To identify TF and their binding sites within the CNA-Correlated-Pathway (CCP) gene subset, we used publicly available search tools, The Transcription Factor Database (TRANSFAC®)²⁵. TRANSFAC is a knowledge-base containing published data on eukaryotic transcription factors, their experimentally-proven binding sites, and regulated genes²⁶ that utilizes a range of tools and algorithms to search DNA sequences for predicted TF binding sites through high-throughput promoter analysis. Differential gene expression between CR and IR were performed on those genes within the CCP set found to have TF binding sites by TRANSFAC database. Differences of gene expression between the classes (CR vs. IR) at the univariate significance level of p<0.01 were considered significant, as ~ 1,700 genes were introduced in the analysis.

Non-negative matrix factorization (NMF) consensus clustering of final model: NMF is an unsupervised learning algorithm that has been shown to identify molecular patterns when applied to gene expression data. NMF detects context dependent patterns of gene expression in complex biological systems¹⁵' ²³. This method computes multiple k-factor factorization decompositions of the expression matrix and evaluates the stability of the solutions using a cophenetic coefficient. The final subclasses of genes were defined based on the most stable k-factor decomposition and visual inspection of gene by gene correlation matrices.

Software

The majority of analyses were performed using R statistical package for statistical computing and graphics (see, world-wide website: r-project.org) as background, using Bioconductor packages as open source software for bioinformatics (bioconductor.org). Analysis of comparative genomic hybridization (CGH) to assess CNA and analysis of gene expression were performed using Biometric Research Branch (BRB) ArrayTools, an integrated package for the visualization and statistical analysis that utilizes Excel (Microsoft, Redmond, WA) as front end, and with tools developed in the R statistical system. BRB- Array Tools were developed by Dr. Richard Simon and the BRB-Array Tools development team.

MultiExperiment Viewer was used to implement the NMF consensus clustering and is part of the TM4 suite of tools (see world-wide website: tm4.org) developed in Java, an open- source, and freely available collection of tools of use to a wide range of laboratories conducting microarray experiments. Pathway enrichment analysis: To identify over-represented and significant pathways among the selected list of genes we used MetaCore™ (GeneGo, Inc., Carlsbad, CA), an integrated and curated "knowledge-based" platform for pathway analysis. The p- value of significant associated pathways represents the probability that a particular gene of an experiment is placed into a pathway by chance, considering the numbers of genes in the experiment, and total genes across all pathways.

Following are examples which illustrate procedures for practicing the invention. These examples should not be construed as limiting. All percentages are by weight and all solvent mixture proportions are by volume unless otherwise noted. It should be understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and the scope of the appended claims. In addition, any elements or limitations of any invention or embodiment thereof disclosed herein can be combined with any and/or all other elements or limitations (individually or in any combination) or any other invention or embodiment thereof disclosed herein, and all such combinations are contemplated with the scope of the invention without limitation thereto. EXAMPLE 1 - SELECTION OF CANDIDATE PATHWAYS DIRECTLY ASSOCIATED

WITH RESPONSIVENESS TO CHEMOTHERAPY IN OVCA

The findings described in the journal article Gonzalez Bosquet et al., Analysis of Chemotherapeutic Response in Ovarian Cancers Using Publicly Available High-Throughput Data, Cancer Res. 2014 May 21, pii: canres.0186.2014. [Epub ahead of print], doi: 10.1158/0008-5472. CAN-14-0186 are incorporated herein by reference in their entirety, including, but not limited to, the Figures 1-4, Tables 1-2, Supplementary Figures 1-6 and Supplementary Tables 1-9.

Our analysis focused on gene expression data from different sources to identify genes and pathways involved in OVCA chemo-resistance. Sources included OVCA cultured cell lines that underwent progressive higher doses of chemotherapy and tested with a chemo- sensitivity analysis measured by IC₅₀. Then gene expression of 48 samples was compared before and after the treatment¹². Also, we included clinical samples gathered from our own institution, 127 samples, available at the Gene Expression Omnibus repository (GEO) with accession number GSE23554¹⁰' ¹²' ¹³, OVCA samples from 240 patients from the GEO database GSE9891¹⁵, and data from TCGA, with 465 OVCA samples²³. Only serous OVCA specimens with information of response to chemotherapy were used for comparison. Chemo- response, as defined in methods, was a significant independent survival factor in TCGA dataset survival analysis (Cox proportional hazard ratio), even after control for age, stage and optimal surgery (p-value <10^~15, Figure 5). We determined genes that were differentially expressed between patients with CR and patients with IR in the 3 clinical databases; furthermore, we evaluated genes differentially expressed in the OVCA cell lines based on in vitro chemo-sensitivity analysis. A series of genes were common between these comparison analyses: TIMP3, OLFML3, C10orf26, COPZ2, PDGFD, OMD, PKD2, SNRPA, COL8A1, GCNT1, CDK5RAP3, PRPF40A, RAB35, MAPK14, PARN, NCRNA00184, ERCC5, Cl3orfl3, LHFP, KIAA1033, GJBI, SVEPI, TPMI, and IMPACT (Figure 6). We introduced these common differentially expressed genes in the pathway enrichment analysis by GeneGO (MetaCore ™) and only those significant pathways that were previously described as associated with chemo response in OVCA were used as candidates pathways: the O-glycan biosynthesis pathway (p-value=7xl0^~3), described in our previous in vitro studies of chemo- sensitivity¹⁰, the Transport RABIA regulation pathway (p-value=5xl0^~3) that controls vesicle

27 11 28

traffic within the cell and members of the RAS oncogene family ' , MAPK14 and PDGFD²⁹ part of the MAPK signaling pathway (p-value=10^~4), involved in the in the initiation of a G2 delay after ultraviolet radiation³⁰ and also identified in in vitro studies¹¹. Only these candidate pathways, previously associated with chemo-response, were used in the rest of the study. Identification of elements influencing expression of candidate pathways genes

TCGA datasets for genomic copy number alterations (CNA), mutation and methylation analysis, and miRNA expression were used to identify the elements that could potentially influence the expression of our candidate pathways. Main clinical and biological data from TCGA patients included in our study are summarized in Table 1. The Transcription

25 31 32

Factor (TRANSFAC) database ' ' was used to predict TF binding sites in our analysis. Tislsk 1 : CiJsskal ami Mi½gk.a dais frosts 1^'CGA psti su-s i n luded in iiie s d

CNA analysis and correlation with gene expression:

Of the 452 patients with clinical information about chemo-response (294 CR and 158 IR) and gene expression data from specimens collected at diagnosis, 435 underwent comparative genomic hybridization to determine CNA. Figure 7 and Table 3 summarize whole genome significant somatic gains and losses determined by the genomic identification of significant targets in cancer (GISTIC) analysis²². CNA could be divided into regional alterations, when gain or loss of genetic material affects more than 50% of the chromosomal arm and focal alterations when gains/losses are smaller . In a genome-wide assessment, there were 4 significant regional alterations with gains, 3q22.1-q29, 8pl 1.21-q24.3, 12pl3.33- pl 1.21, and 20ql 1.21-ql3.33, and 8 with losses, 4ql3.3-q35.2, 6ql5-q27, 8p23.3-pl2, 13ql l-q34, 16ql2.2-q24.3, 17pl3.3-q21.2), 18ql2.2-q23, and 22ql l .22-ql3.33. Apart from the candidate pathways genes, these altered regions contained other genes that may be important or associated with unknown mechanisms of chemo-response in OVCA. Details of regional and focal CNA somatic gains and losses affecting genes of the candidate pathways are summarized in Table 2.

Table 2x CNA Aedsi cajidldsste pathway gt-iics

Of the genes included in these candidate regions with CNA (6,622 genes) only 2,364 showed statistically significant positive correlation with gene expression, determined by Spearman's rank correlation (Table 4). Positive statistical correlation was defined as CNA gain with increased gene expression, or CNA loss with decreased gene expression, with a p- value <10^~4 to account for multiple comparisons²³. These 2,364 genes with CNA and correlated gene expression, including 68 genes from the 3 candidate pathways, may influence or be associated with chemo-response through our candidate pathways, and will be used for the remainder of our analyses and referred as the CNA-Correlated-Pathway (CCP) gene subset.

Differential gene expression at the univariate significance level p<0.001 was used to create a 69 gene expression signature predictive of CR versus IR in the CCP subset of genes (Figure 8A, Table 5). Validation of the gene signature was performed in previously published gene expression studies, including one from our own institution¹²' ¹⁵' ¹⁶. For this validation we used the same study design used in the testing set (TCGA), a retrospective design of micro-array gene expression with additional information about chemo-response, the same software used in the testing set (BRB ArrayTools), same statistics (t-test at significance level p<0.001), same outcomes definitions (CR versus IR), and the same list of genes from the gene signature in the testing set. The gene signature profile was validated in all independent databases with a p-value < 0.001 for GEO# GSE9891¹⁵, p-value of 0.01 for GSE28739¹⁶, and p-value of 0.02 for GSE23554¹²(Figure 9).

Somatic mutations and their correlation with gene expression:

Somatic mutations in genes have been shown to influence gene expression patterns, of both individual genes and distinct pathways^33"35. Only validated mutations were used for these series of analyses²³. Mutations of 6,716 genes were available for 192 patient's samples with information about chemo-response at TCGA data site. We performed a logistic regression analysis to determine which mutations were associated with chemo-response (CR versus IR). KRT72, MY05C, ODZ1, SMARCA4, and TP53 were statistically associated with the outcome. SMARCA4 had mutations in 0.7% of CR samples and in 7.3% of IR samples (p-value=0.04); and TP53 had mutations in 88.3% of CR samples and in 72.7% of IR samples (p-value=0.01). Spearman's rank correlation, with correction for multiple comparisons, was used to assess the correlation between significant mutated genes and gene expression of CCP gene subset (p-value and qFDR < 10^"4) (Figure 8B). Significant mutated genes as well as their 22 correlated genes with significant change in gene expression were included in the model and added to the significant gene signature identified from the CCP gene subset.

Methylation analysis and its correlation with gene expression:

Epigenetic gene regulation also may affect expression of candidate pathways by inactivating gene function³⁶. As we did with mutations, an analysis of DNA methylation status was performed in 440 patients with high-throughput data and information about chemo-response available. 69 genes were differentially methylated between the CR and IR groups (Figure 8C). A list of these genes could be reviewed at Table 6. In order to explore possible interactions between differentially methylated genes and their possible influence in the expression of our candidate pathways we performed a correlation, with correction for multiple comparisons, between these differentially methylated genes and the expression of the CCP gene subset (p-value and qFDR < 10^"6). Differentially methylated genes and their correlated expressed genes were also added to significant gene signature and mutations found previously to improve the molecular model.

miRNA expression analysis and its correlation with gene expression:

Gene expression is also regulated by miRNAs. As previously, differentially miRNA expression was performed in 455 patients with available high-throughput data and information about chemo-response. A heat map of the 38 miRNA differentially expressed between the CR and IR groups is represented in Figure 8D. A list of these miRNA could be reviewed at Table 7. Possible interactions between differentially expressed miRNA and their possible influence in the expression of our candidate pathways were explored with a corrected correlation between miRNA expression and gene expression of the CCP subset (p- value and qFDR < 10^"6). Differentially expressed miRNAs and their correlated genes were also included to the model or signature.

Transcription factor (TF) binding sites and their association with gene expression:

Since gene expression is regulated at the transcriptional level, we examined web- based tools that utilize algorithms to search DNA sequences for predicted TF binding sites through high-throughput promoter analysis. TRANSFAC® was used to predict TF binding sites in genes of the candidate pathways associated with OVCA chemo-response³¹. Of the 2,364 gene of the CCP subset, 1,772 genes were identified to have TF binding sites in their promoter area; 59 of these genes had a differential gene expression between CR and IR (Figure 10A, Table 8). Only these 59 genes harboring TF binding sites that presented both copy number alterations and differentially gene expression were also introduced in the final model.

External validation of final model with non-negative matrix factorization (NMF) consensus clustering:

The combined data from all significant and correlated genes included 422 unique different genes introduced in the final model (Table 9). A cluster analysis of these final model was performed with the non-negative matrix factorization consensus clustering, a type of unsupervised learning algorithm that has been shown to identify molecular patterns when applied to gene expression data¹⁵. This analysis yielded two clusters with differentiated gene patterns (Figure 1A). Attempts to create models with more than 2 clusters resulted in lower cophenetic correlation coefficients (Figure IB), and less harmonic consensus matrices (Figure 1C).

Validation of this molecular pattern with 2 defined clusters observed in the final signature model of TCGA data were performed in 5 publicly available independent OVCA gene expression datasets with the same analytical tool, NMF consensus clustering. All these independent gene experiments also showed two differentiated clusters with the highest cophenetic correlation coefficients and the most harmonious consensus matrices¹²'¹⁴'¹⁵'¹⁷'¹⁸. Comparison of these 6 sets of two clusters (TCGA and 5 validation sets) showed an unprecedented external validation of molecular signatures associated with chemo-response in OVCA (Figures 2A-2E).

We also determined if the individual genes were placed by the NMF consensus clustering within the same cluster in all databases used for validation. The level of agreement measured with kappa coefficient was considered 'good or substantial' for 3 of them (0.61- 0.80)¹²' ¹⁴' ¹¹ , 'almost perfect' for another one (0.8 l-l)¹⁵ and 'moderate' in only one of them (0.41-0.60)¹⁸ (Figure 2, and Figures 1 lA-1 IE).

Pathway enrichment analysis:

To identify which pathways and biological processes were overrepresented in both gene clusters identified within the final gene model, further analysis was conducted with MetaCore™ and clusterProfiler³⁷, from the R statistical package, which mines the KEGG database (Kyoto Encyclopedia of Genes and Genomes, www.genome.jp/kegg). The correlation matrix of each cluster denotes overrepresented predominant pathways (Figure 3). Cluster #1 showed a significant representation of cellular signaling and immune response (mainly cell-mediated) pathways, but also several types of metabolic pathways (Figure 4, and Table 10). Three fourths (75%) of all signaling and metabolic pathways genes in cluster #1 were overexpressed in the IR tumors with respect to the CR samples, with the general perception that IR tumors were engaged in higher metabolic rates through external and internal stimuli. Cluster #2 was significant for pathways involving DNA damage repair and replication as well as cell cycle and apoptosis, all of them with strong influence by mutated TP53. Cluster #2 also presented significant pathways related to cancer and cytoskeleton configuration and structure (Figure 4, and Table 11). Two thirds of all cell cycle and DNA repair genes presented elevated expression in CR tumors when compared to IR tumors, probably driven by mutated key elements of these pathways, like TP53, and increased expression of transcription factors, like ATF6B, CRTC1, E2F1, SIN3B and NFIX.

Discussion:

Patients suffering from platinum-refractory or resistant ovarian cancer have a median overall survival around 12-13 months³. Furthermore, these patients become resistant to multiple drugs early on the course of treatment of their disease and thus, it is challenging to establish efficacious treatment strategies³⁸. The objective of our study was to identify biological processes associated with chemo-response so we may, in the future, identify patients at risk for standard chemotherapy resistance, thus eligible for novel strategies. Also, knowledge of mechanisms involved in chemo-response may help design new strategies as molecular-targeted therapy is gaining traction³⁹. Our study determined chemo-response as the most significant independent clinical factor for survival (p-value <10^"15) in the TCGA database, agreeing with daily clinical practice and published clinical trials²⁰.

Despite increasing knowledge about mechanisms of chemo-response in tumor cells there are no valid clinical biomarkers or molecular signatures that could effectively predict response to chemotherapy^8"9. Initial analysis of gene profiling aiming to identify functional processes associated with chemo-response in OVCA had showed little overlap between studies looking for expression signatures or pathways associated with response to therapy⁴⁰. Previously, several groups have used integration of Omics data in OVCA to predict other clinical outcomes^41"43. By integrating the comprehensive characterization of TCGA data, namely, CNA, gene mutations, DNA methylation, miRNA expression, and TF binding sites location, into an analytical framework for gene expression, we have created a robust molecular signature that predicts chemo-response in OVCA. This model, with 2 clusters involving previous known mechanisms of chemo-response⁹, was the most robust in TCGA database; but what is even more important and unprecedented in our study is the external validation of the TCGA model with other 5 independent gene expression studies of

These findings demonstrate consistency of this signature across diverse studies and platforms that we believe is due to the selection of micro-array experiments with the same tumor type of OVCA (serous), statistical design of analyses, and adequately powered. Furthermore, both clusters in the model included the same individual genes with substantial agreement in all but one of the 5 independent gene expression sets, where the agreement was moderate (Figure 2). We think that adding elements to the model that did not result exclusively from the differential gene expression of micro-arrays (CNA, mutations, methylation, miRNA, TF binding sites) added stability to the molecular signature and provided enough range to overcome validation difficulties observed by gene expression experiments alone due to tumor heterogeneity^8"9.

Most genes included in our molecular signature for chemo-response are drawn from cellular functions previously associated with response to chemotherapy⁹. These biological processes include cell signaling pathways, immune response pathways, and several types of metabolic pathways that are involved in DNA damage repair and replication, cell cycle and apoptosis, all of them also have been associated with cancer transformation and proliferation⁴⁴. In ovarian cancers, signaling transduction cascades from the pathways PBKIAKTI m TOR and RaslRaflMEKIMAPKIERK (with representation in our molecular model, Table 9) may result in diverse effects, including cell proliferation, invasion, angiogenesis, apoptosis evasion, and response to chemotherapy^44"45. The MAPK signaling pathway is also connected to the Ras pathway (which includes PAK4), that also regulates cell morphology, cytoskeletal organization, and cell proliferation and migration; PAK4 can also function as an anti-apoptotic protein⁴⁶. PAK proteins are critical effectors that link Rho GTPases to cytoskeleton reorganization and nuclear signaling. Both PAK4 and RHOT1 are included in cluster #2. The Ras gene family (which RASAl is part) encodes membrane- associated, guanine nucleotide-binding proteins that are involved also in the control of cellular proliferation and differentiation, and have a weak intrinsic GTPase activity, effectors of Ras oncogene action⁴⁷. MAP kinases may also have a role in early gene expression by modifying the chromatin environment of target genes⁴⁸, an action regulated through phosphorylation of various substrates, including transcription factors and chromatin constituents. NCAPG, a component of the condensin complex that is required for both interphase and mitotic condensation, is present in cluster #2 of the chemo-response model. Animal models with condensin mutations, DNA damage induced by ultraviolet radiation is not repaired and cells arrested by hydroxyurea do not recover⁴⁹. In our gene signature, it is notable that a set of genes map to DNA repair pathway (mainly through homologous recombination), like RAD52, and elements of the PARP family, like PARP12. PARPs inhibitors have been proven to be efficacious in the treatment of OVCA in carriers of BRCA1 or BRCA2 mutations⁵⁰. Also notable are the results of bevacizumab, a humanized antibody against VEGF, in the adjuvant treatment of OVCA⁵¹. PDGFB, a component of the VEGF signaling pathway, is present in cluster #1, with other numerous components of cell signaling pathways. With all these interconnections between signaling pathways, DNA damage repair, and cell cycle, alternative strategies to standard therapies may have to involve a combination of cross-specific drugs to avoid by-pass of the blocked path⁵².

The claimed invention based on a large genomic dataset, which has high benchmarks for quality control and processing (TCGA). The large sample size confers adequate power to detect important patterns while at the same time, it overcomes possible bias introduced by outliers; moreover, it permits better selection of the histological type (serous) and outcome of interest (chemo-response) to improve homogeneity. We believe that those are major factors influencing in the important external validation of the molecular signature in 5 independent gene expression experiments, which is unprecedented in micro-array analysis⁴⁰. Other major factor influencing a significant validation is the integration of diverse biological data, other than gene expression, in the final model. For the validation process we used two OVCA datasets that were used initially to identify candidate pathways¹²'¹⁵. These datasets had the closest clinical information, including chemo-response, and study design to TCGA. To avoid data over fitting in the validation process, though, we added 3 independent gene expression experiments not used before, despite presenting minor differences in study design and platform content¹⁴'¹⁷'¹⁸.

Nearly all patients received standard treatment, with over 99% of them getting a platinum-based chemotherapy (Table 1). Initial treatment with platinum may select for some of molecular patterns observed in our signature, like cell cycle or DNA repair pathways, due to the DNA adducts induced by platinum⁵³. Consequently, the current invention is applicable to OVCA that would receive initial platinum-based treatment, and may also be suited for other scenarios with different initial therapeutic strategies.

Integration of diverse biological data into gene expression may strengthen gene signature models for prediction of OVCA chemo-response. Robust validation over 5 independent publicly available gene expression experiments supports these findings.

All patents, patent applications, provisional applications, and publications referred to or cited herein are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification.

Table 3: Whole genome CNA

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

Copy Number Gains

37888254 120807 0.10 lp34.3 Clorfl09, CDCA8, EPHA10

RRAGC, MYCBP, GJA9-MYCBP, GJA9, RHBDL2, AKIRIN1, NDUFS5, MACF1, lp34.3- KIAA0754, BMP8A, PPIEL, PABPC4, SNORA55, HEYL, NT5C1A, HPCAL4, PPIE,

38728744 3008098 2.42 44 BMP8B, OXCT2, TRIT1, MYCL1, MFSD2A, CAP1, PPT1, RLF, TMC02, ZMPSTE24, p34.2 COL9A2, SMAP2, ZNF643, ZNF642, DEMI, ZNF684, RIMS3, LOC100130557, NFYC,

MIR30E, MIR30C1, KCNQ4, CITED4, CTPS, SLFNL1, SCMH1, EDN2

110033018 8694 0.01 lpl3.3 GSTMl

SEC22B, NOTCH2NL, NBPF10, HFE2, TXNIP, POLR3GL, ANKRD34A, LIX1L, RBM8A, GNRHR2, PEX11B, ITGA10, ANKRD35, PIAS3, NUDT17, POLR3C, RNF115, CD160, PDZK1, GPR89A, GPR89C, PDZK1P1, NBPF11, NBPF24, LOC728989, PRKAB2, PDIA3P, FM05, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, NBPF14, PPIAL4E, PPIAL4D, PPIAL4F, NBPF15, NBPF16, LOC645166, LOC388692, FCGR1C, HIST2H2BF, FCGR1A, HIST2H3D, HIST2H4B, HIST2H4A, HIST2H3C, HIST2H3A, HIST2H2AA4, HIST2H2AA3, HIST2H2BC, HIST2H2BE, HIST2H2AC, HIST2H2AB, BOLA1, SV2A, SF3B4, MTMR11, OTUD7B, VPS45, PLEKHOl, ANP32E, CA14, APHIA, Clorf54, Clorf51, MRPS21, PRPF3, RPRD2, TARS2, ECM1, ADAMTSL4, MIR4257, MCL1, ENSA, GOLPH3L, HORMAD1, CTSS, CTSK, ARNT, SETDB1, LASS2, ANXA9, FAM63A, PRUNE, BNIPL, Clorf56, CDC42SE1, MLLT11, GABPB2, SEMA6C, TNFAIP8L2, LYSMD1, SCNM1, TMOD4, VPS72, PIP5K1A, PSMD4, ZNF687, PI4KB, RFX5, SELENBP1, PSMB4, POGZ, CGN, TUFT1, MIR554, SNX27, CELF3, RIIAD1, MRPL9, OAZ3, TDRKH, LING04, RORC, C2CD4D, LOC100132111, THEM5, THEM4, S100A10, S100A11, TCHHL1, TCHH, RPTN, lq21.1- HRNR, FLG, FLG2, CRNN, LCE5A, CRCT1, LCE3E, LCE3D, LCE3C, LCE3B, LCE3A,

143809389 13468627 10.98 338 LCE2D, LCE2C, LCE2B, LCE2A, LCE4A, Clorf68, KPRP, LCEIF, LCEIE, LCEID, LCEIC, q23.1 LCE1B, LCE1A, LCE6A, SMCP, IVL, SPRR4, SPRR1A, SPRR3, SPRR1B, SPRR2D,

SPRR2A, SPRR2B, SPRR2E, SPRR2F, SPRR2C, SPRR2G, LELP1, PRR9, LOR, PGLYRP3, PGLYRP4, S100A9, S100A12, S100A8, S100A7A, S100A7L2, S100A7, S100A6, S100A5, S100A4, S100A3, S100A2, S100A16, S100A14, S100A13, S100A1, Clorf77, SNAPIN, ILF2, NPR1, INTS3, SLC27A3, GATAD2B, DENND4B, CRTC2, SLC39A1, CREB3L4, JTB, RAB13, RPS27, NUP210L, TPM3, MIR190B, Clorfl89, Clorf43, UBAP2L, HAX1, AQP10, ATP8B2, IL6R, SHE, TDRD10, UBE2Q1, CHRNB2, ADAR, KCNN3, PMVK, PBXIP1, PYG02, SHC1, CKS1B, MIR4258, FLAD1, LENEP, ZBTB7B, DCST2, DCST1, ADAM 15, EFNA4, EFNA3, EFNA1, SLC50A1, DPM3, KRTCAP2, TRIM46, MUC1, MIR92B, THBS3, MTXl, GBAPl, GBA, FAM189B, SCAMP3, CLK2, HCN3, PKLR, FDPS, Clorfl04, RUSCl, ASH1L, MIR555, POU5F1P4, LOC645676, MSTOl, YY1AP1, DAP3, MST02P, GON4L, SYT11, RIT1, KIAA0907, SNORA42, SCARNA4, RXFP4, ARHGEF2, SSR2, UBQLN4, ROBLD3, RAB25, MEX3A, LMNA, SEMA4A, SLC25A44, PMF1, PMF1-BGLAP, BGLAP, PAQR6, SMG5, TMEM79, Clorf85, VHLL, CCT3, Clorfl82, RHBG, Clorf61, MIR9-1, MEF2D, IQGAP3, TTC24, APQAIBP, GPATCH4, HAPLN2, BCAN, NES, CRABP2,

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

ISG20L2, RRNAD1, MRPL24, HDGF, PRCC, SH2D2A, NTRK1, INSRR, PEAR1, Clorf92, ARHGEF11, MIR765, ETV3L, ETV3, CYCSP52, FCRL5, FCRL4, FCRL3, FCRL2, FCRL1, CD5L, KIRREL, LOC646268, CD1D, CD1A, CD1C, CD1B, CD1E, OR10T2, OR10K2, OR10K1, OR10R2, OR6Y1, OR6P1, OR10X1, OR10Z1, SPTA1, OR6K2, OR6K3, OR6K6, OR6N1, OR6N2, MNDA, PYHIN1, IFI16

IFI16, AIM2, CADM3, DARC, FCER1A, OR10J3, OR10J1, OR10J5, APCS, CRP, DUSP23, FCRL6, SLAMF8, Clorf204, VSIG8, CCDC19, TAGLN2, IGSF9, SLAMF9, PIGM, KCNJIO, KCNJ9, IGSF8, ATP1A2, ATP1A4, CASQ1, PEA15, DCAF8, PEX19, COP A, SUM01P3, lq23.1- NCSTN, NHLH1, VANGL2, SLAMF6, CD84, SLAMF1, CD48, SLAMF7, LY9, CD244,

1 q 157287924 3811143 3.11 89 ITLNl, ITLN2, FUR, TSTDl, USFl, ARHGAP30, PVRL4, KLHDC9, PFDN2, NITl, DEDD, q23.3 UFC1, USP21, PPOX, B4GALT3, ADAMTS4, NDUFS2, FCER1G, APOA2, TOMM40L,

NR1I3, PCP4L1, MPZ, SDHC, Clorfl92, FCGR2A, HSPA6, FCGR3A, FCGR2C, HSPA7, FCGR3B, FCGR2B, RPL31P11, FCRLA, FCRLB, DUSP12, ATF6, OLFML2B, NOS1AP, MIR556, Clorfl l l, Clorf226, SH2D1B, UHMK1, UAP1, DDR2, HSD17B7, Clorfl lO

1 q 226200980 2625 0.00 lq42.13 1 WNT9A

lq42.13- GALNT2, PGBD5, COG2, AGT, CAPN9, Clorfl98, TTC13, ARV1, FAM89A, MIR1182, i q 228261810 1847426 1.51 22 TRIM67, Clorfl31, GNPAT, EXOC8, Clorfl24, EGLN1, SNRPD2P2, TSNAX, TSNAX- q42.2 DISC1, LOC100287814, DISCI, DISC2

DISCI, SIPA1L2, KIAA1383, NTPCR, PCNXL2, KIAA1804, KCNK1, SLC35F3, Clorf31, lq42.2- TARBP1, IRF2BP2, NCRNA00184, TOMM20, SNORA14B, RBM34, ARID4B, GGPS1, q 230118582 8427149 6.87 38 TBCE, B3GALNT2, GNG4, LYST, MIR1537, NIDI, GPR137B, EROILB, EDARADD, q43 LGALS8, LOC100287902, HEATR1, ACTN2, MTR, RYR2, LOC100130331, ZP4,

LOC339535, CHRM3, RPS7P5, FMN2

1 q 238553479 569652 0.46 lq43 3 FMN2, GREM2, RGS7

1 q 239365946 878760 0.72 lq43 8 RGS7, FH, KMO, OPN3, CHML, WDR64, EXOl, MAP1LC3C

1 q 240263553 841298 0.69 lq43 1 PLD5

1 q 241366280 1602740 1.31 Iq43-q44 9 CEP170, SDCCAG8, AKT3, LOC339529, ZNF238, ClorflOO, ADSS, ClorflOl, PPPDE1

FAM36A, NCRNA00201, HNRNPU, EFCAB2, KIF26B, SMYD3, TFB2M, CNST, SCCPDH, i q 242989278 2757076 2.25 lq44 22 LOC149134, AHCTF1, ZNF695, ZNF670, ZNF669, Clorf229, ZNF124, MIR3916, VN1R5,

ZNF496, NLRP3, OR2B11, OR2W5

OR2L13, OR2L8, OR2AK2, OR2L1P, OR2L2, OR2L3, OR2M1P, OR2M5, OR2M2, OR2M3, i q 246176580 592438 0.48 lq44 22 OR2M4, OR2T33, OR2T12, OR2M7, OR14C36, OR2T4, OR2T6, OR2T1, OR2T2, OR2T3,

OR2T5, OR2G6

1 q 246863179 323335 0.26 lq44 9 OR2T35, OR2T27, OR14I1, LOC646627, SH3BP5L, MIR3124, ZNF672, ZNF692, PGBD2

2 P 33078005 2432 0.00 2p22.3 1 LTBP1

2 q 154605621 1322 0.00 2q24.1 1 GALNT13

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

2 q 179777850 1069 0.00 2q31.2 1 SESTDl

3 q 133191877 2808 0.00 3q22.1 1 CPNE4

CPNE4, ACPP, DNAJC13, ACAD11, NPHP3-ACAD11, CCRL1, UBA5, NPHP3, NCRNA00119, TMEM108, BFSP2, CDV3, TOPBP1, TF, SRPRB, RAB6B, C3orf36, SLC02A1, RYK, AMOTL2, ANAPC13, CEP63, KY, EPHB1, PPP2R3A, MSL2, PCCB, STAG1, TMEM22, NCK1, IL20RB, SOX14, CLDNl 8, DZIP1L, A4GNT, DBR1, ARMC8, TXNDC6, MRAS, ESYT3, CEP70, FAIM, PIK3CB, FOXL2, C3orf72, PRR23A, PRR23B, PRR23C, BPESC1, PISRT1, MRPS22, COPB2, RBP2, RBP1, NMNAT3, CLSTN2, TRIM42, SLC25A36, SPSB4, ACPL2, ZBTB38, RASA2, RNF7, GRK7, ATP1B3, TFDP2, GK5, XRN1, ATR, PLS1, TRPC1, PCOLCE2, PAQR9, LOC100289361, U2SURP, CHST2, SLC9A9, C3orf58, PLOD2, PLSCR4, PLSCR2, PLSCR1, PLSCR5, ZIC4, ZIC1, AGTR1, CPB1, CPA3, GYG1, HLTF, HP S3, CP, TM4SF18, TM4SF1, TM4SF4, WWTR1, COMMD2, C3orfl6, RNF13, PFN2, LOC646903, TSC22D2, SERP1, EIF2A, SELT, FAM194A, SIAH2, CLRN1, CLRNIOS, MED12L, GPR171, P2RY14, GPR87, P2RY13, P2RY12, IGSF10, MIR548H2, AADACL2, LOC201651, AADAC, SUCNR1, LOC401093, MBNL1, TMEM14E, P2RY1, RAP2B, C3orf79, ARHGEF26, DHX36, GPR149, MME, PLCH1, C3orf33, SLC33A1, GMPS, KCNABl, SSR3, LOC100287227, TIPARP, PA2G4P4, LEKRl, LOC339894, LOC100498859, CCNL1, VEPH1, PTX3, C3orf55, SHOX2, RSRC1, MLF1, GFM1, LXN, RARRES1, MFSD1, IQCJ, IQCJ-SCHIP1, SCHIP1, MIR3919, IL12A, LOC401097, IFT80, SMC4, MIR15B, MIR16-2, TRIM59, KPNA4, SCARNA7, ARL14, PPM1L, B3GALNT1, NMD3, C3orf57, OTOLl, LOC647107, SI, SLITRK3, BCHE, ZBBX, SERPINI2, WDR49, PDCD10, SERPINIl,

3q22.1- LOC646168, GOLIM4, EGFEM1P, MIR551B, MECOM, TERC, ARPM1, MYNN, LRRC34,

3 q 133198618 66130974 61.06 386

q29 LRRIQ4, LRRC31, SAMD7, LOC100128164, SEC62, GPR160, PHC3, PRKCI, SKIL,

CLDNl 1, SLC7A14, RPL22L1, EIF5A2, SLC2A2, TNIK, MIR569, PLD1, TMEM212, FNDC3B, GHSR, TNFSF10, NCEH1, ECT2, SPATA16, NLGN1, NAALADL2, TBL1XR1, KCNMB2, ZMAT3, PIK3CA, KCNMB3, ZNF639, MFN1, GNB4, ACTL6A, MRPL47, NDUFB5, USP13, PEX5L, TTC14, CCDC39, FXR1, DNAJC19, SOX20T, SOX2, ATP11B, DCUN1D1, MCCC1, LAMP3, MCF2L2, B3GNT5, KLHL6, KLHL24, YEATS2, MAP6D1, PARL, ABCC5, HTR3D, HTR3C, HTR3E, EIF2B5, DVL3, AP2M1, ABCF3, VWA5B2, MIR1224, ALG3, ECE2, CAMK2N2, PSMD2, EIF4G1, SNORD66, FAM131A, CLCN2, POLR2H, THPO, CHRD, EPHB3, MAGEF1, VPS8, C3orf70, EHHADH, MAP3K13, TMEM41A, LIPH, SENP2, IGF2BP2, C3orf65, TRA2B, LOC344887, ETV5, DGKG, LOC253573, CRYGS, TBCCD1, DNAJB11, AHSG, FETUB, HRG, KNG1, EIF4A2, SNORD2, MIR1248, SNORA81, SNORA63, SNORA4, RFC4, ADIPOQ, ST6GAL1, RPL39L, RTP1, MASP1, RTP4, SST, RTP2, LOC100131635, BCL6, LOC339929, LPP, FLJ42393, TPRGl, TP63, MIR944, LEPRELl, CLDNl, CLDN16, TMEM207, ILIRAP, GEMCl, SNAR- I, OSTN, UTS2D, CCDC50, PYDC2, FGF12, C3orf59, HRASLS, MGC2889, ATP13A5, ATP13A4, OPAl, LOC647323, LOC100128023, HES1, LOC100131551, CPN2, LRRC15, GP5, ATP 13 A3, FLJ34208, TMEM44, LSG1, FAM43A, C3orf21, ACAP2, PPP1R2, APOD, SDHAP2, MIR570, MUC20, MUC4, TNK2, SDHAP1, TFRC, LOC401109, ZDHHC19, OSTalp a, PCYT1A, TCTEX1D2, TM4SF19, UBXN7, RNF168, C3orf43, WDR53, FBX045, LRRC33, C3orf34, PIGX, PAK2, SENP5, NCBP2, LOC152217, PIGZ, MFI2, DLG1, BDH1,

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W:\DOCS\1877\MOF.₁55XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

p22.2 NRSNl, DCDC2, KAAG1, MRS2, GPLD1, ALDH5A1, KIAA0319, TDP2, ACOT13,

C6orf62, GMNN, FAM65B, CMAH, LRRC16A, SCGN

6 P 26125251 16061 0.03 6p22.1 6 HIST1H1A, HIST1H3A, HIST1H4A, HIST1H4B, HIST1H3B, HIST1H2AB

GUSBL1, NCRNA00240, LOC100270746, HIST1H2BJ, HIST1H2AG, HIST1H2BK, HIST1H4I, HIST1H2AH, MIR3143, PRSS16, POM121L2, FKSG83, ZNF204P, ZNF391, ZNF184, HIST1H2BL, HIST1H2AI, HIST1H3H, HIST1H2AJ, HIST1H2BM, HIST1H4J,

6 P 26863540 1843125 3.05 6p22.1 51 HIST1H4K, HIST1H2AK, HIST1H2BN, HIST1H2AL, HIST1H1B, HIST1H3I, HIST1H4L,

HIST1H3J, HIST1H2AM, HIST1H2BO, OR2B2, OR2B6, ZNF165, ZSCAN12P1, ZSCAN16, ZNF192, ZNF389, LOC222699, ZNF193, ZKSCAN4, NKAPL, ZNF187, PGBD1, ZNF323, ZKSCAN3, ZSCAN12, ZSCAN23, GPX6, GPX5, SCAND3

OR2H1, MAS1L, LOC100507362, UBD, SNORD32B, OR2H2, GABBR1, MOG, ZFP57,

6 P 29535783 291869 0.48 6p22.1 12 HLA-F, LOC285830, IFITM4P

6 P 29972382 20564 0.03 6p21.33 1 HCG2P7

6 P 30000990 20918 0.03 6p21.33 2 HCG4P6, HLA-A

ABCF1, MIR877, PPP1R10, MRPS18B, ATAT1, C6orfl36, DHX16, KIAA1949, NRM,

6 P 30653994 590781 0.98 6p21.33 28 MDC1, TUBB, FLOT1, IER3, DDR1, GTF2H4, VARS2, SFTA2, DPCR1, MUC21,

PBMUCL1, HCG22, C6orfl5, PSORS1C1, CDSN, PSORS1C2, CCHCR1, TCF19, POU5F1

MICB, MCCD1, DDX39B, ATP6V1G2-DDX39B, SNORD117, SNORD84, ATP6V1G2, NFKBIL1, LTA, TNF, LTB, LST1, NCR3, AIF1, PRRC2A, SNORA38, BAG6, APOM, C6orf47, GPANKl, CSNK2B, LY6G5B, LY6G5C, ABHD16A, LY6G6F, LY6G6E, LY6G6D,

6p21.33- LY6G6C, C6orf25, DDAH2, CLIC1, MSH5, MSH5-C60RF26, C6orf26, C6orf27, VARS,

6 P 31563829 1041471 1.72 77 LSM2, HSPA1L, HSPA1A, HSPA1B, C6orf48, SNORD48, SNORD52, NEU1, SLC44A4, p21.32 EHMT2, ZBTB12, C2, CFB, RDBP, MIR1236, SKIV2L, DOM3Z, STK19, C4B, C4A, TNXA,

CYP21A2, TNXB, ATF6B, FKBPL, PRRT1, LOC100507547, PPT2, PPT2-EGFL8, EGFL8, AGP ATI, RNF5, RNF5P1, AGER, PBX2, GPSM3, NOTCH4, C6orfl0, BTNL2, HLA-DRA, HLA-DRB5

6 P 32713363 15124 0.02 6p21.32 1 HLA-DQA1

6 P 54037199 5535 0.01 6pl2.1 1 C6orfl42

7 q 1047636 71 0.00 7p22.3 1 C7orf50

7 q 127458264 1148 0.00 7q32.1 1 SND1

7 q 127508735 3952 0.00 7q32.1 2 SND1, MIR593

7 q 127633668 9801 0.01 7q32.1 1 MIR129-1

7q32.1- CALU, OPN1SW, CCDC136, FLNC, ATP6V1F, LOC100130705, KCP, IRF5, TNP03,

7 q 128194352 30626911 30.66 265 TPI1P2, LOC407835, TSPAN33, SMO, AHCYL2, FAM40B, LOC100287482, NRF1,

q36.3 MIR182, MIR96, MIR183, UBE2H, ZC3HC1, KLHDCIO, TMEM209, C7orf45, CPA2, CPA4,

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W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

SNORD87, TCF24, LRRC67, COPS5, CSPP1, ARFGEF1, CPA6, PREX2, C8orf34, SULF1, SLC05A1, PRDM14, NCOA2, TRAM1, LACTB2, XKR9, EYA1, MSC, LOC100132891, TRPA1, LOC392232, KCNB2, TERF1, C8orf84, LOC100130301, RPL7, RDH10, STAU2, UBE2W, TCEB1, TMEM70, LY96, JPH1, GDAP1, FLJ39080, MIR2052, PI15, CRISPLD1, HNF4G, LOC100192378, ZFHX4, PEX2, PKIA, FAM164A, IL7, STMN2, HEY1, MRPS28, TPD52, ZBTB10, ZNF704, PAG1, FABP5, PMP2, FABP9, FABP4, FABP12, IMPA1, SLC10A5, ZFAND1, CHMP4C, SNX16, RALYL, LRRCC1, E2F5, C8orf59, CA13, CA1, CA3, CA2, REX01L2P, REX01L1, PSKH2, ATP6V0D2, SLC7A13, WWP1, FAM82B, CPNE3, CNGB3, CNBD1, DCAF4L2, MMP16, RIPK2, OSGIN2, NBN, DECR1, CALB1, TMEM64, NECAB1, LOC100127983, TMEM55A, OTUD6B, LRRC69, SLC26A7, RUNXITI, C8orf83, LOC642924, FAM92A1, RBM12B, C8orf39, TMEM67, PDPl, CDH17, GEM, RAD54B, KIAA1429, LOC100288748, ESRPl, DPY19L4, INTS8, CCNE2, TP53INP1, C8orf38, MIR3150B, MIR3150, PLEKHF2, C8orf37, LOC100500773, GDF6, UQCRB, MTERFD1, PTDSS1, SDC2, PGCP, TSPYL5, MTDH, LAPTM4B, MATN2, RPL30, SNORA72, C8orf47, HRSP12, POP1, NIPAL2, KCNS2, STK3, OSR2, VPS13B, MIR599, MIR875, COX6C, RGS22, FBX043, POLR2K, SPAG1, RNF19A, ANKRD46, SNX31, PABPCl, YWHAZ, FLJ42969, ZNF706, NACAPl, GRHL2, NCALD, RRM2B, UBR5, ODFl, KLF10, AZIN1, ATP6V1C1, C8orf56, BAALC, MIR3151, LOC100499183, FZD6, CTHRC1, SLC25A32, DCAF13, RIMS2, TM7SF4, DPYS, LRP12, ZFPM2, OXR1, ABRA, ANGPT1, RSP02, EIF3E, TTC35, TMEM74, TRHR, NUDCD1, ENY2, PKHD1L1, EBAG9, SYBU, KCNV1, CSMD3, MIR2053, TRPS1, EIF3H, UTP23, RAD21, NCRNA00255, MIR3610, C8orf85, SLC30A8, MED30, EXT1, SAMD12, TNFRSF11B, COLECIO, MAL2, NOV, ENPP2, TAF2, DSCC1, DEPTOR, COL14A1, MRPL13, MTBP, SNTB1, HAS2, HAS2-AS1, ZHX2, DERL1, WDR67, FAM83A, LOC100131726, C8orf76, ZHX1, ATAD2, WDYHV1, FBX032, KLHL38, ANXA13, FAM91A1, FER1L6, TMEM65, TRMT12, RNF139, TATDNl, NDUFB9, MTSS1, LOC157381, ZNF572, SQLE, KIAA0196, NSMCE2, TRIB 1, FAM84B, POU5F1B, LOC727677, MYC, PVT1, MIR1204, MIR1205, MIR1206, MIR1207, MIR1208, LOC728724, GSDMC, FAM49B, ASAP1, ASAP1-IT, ADCY8, EFR3A, OC90, HHLA1, KCNQ3, HPYR1, LRRC6, TMEM71, PHF20L1, TG, SLA, WISP1, NDRG1, ST3GAL1, ZFAT, ZFAT-AS1, MIR30B, MIR30D, LOC286094, KHDRBS3, FAM135B, COL22A1, KCNK9, TRAPPC9, CHRAC1, EIF2C2, PTK2, DENND3, SLC45A4, LOC731779, GPR20, PTP4A3, FLJ43860, NCRNA00051, TSNARE1, BAI1, ARC, JRK, PSCA, LY6K, C8orf55, SLURP1, LYPD2, LYNX1, LY6D, GML, CYP11B 1, CYP11B2, LOC100133669, LY6E, C8orf31, LY6H, GPIHBP1, ZFP41, GLI4, ZNF696, TOP1MT, C8orf51, RHPN1, MAFA, ZC3H3, GSDMD, C8orf73, NAPRT1, EEF1D, TIGD5, PYCRL, TSTA3, ZNF623, ZNF707, BREA2, LOC100130274, MAPK15, FAM83H, LOC100128338, SCRIB, MIR937, PUF60, NRBP2, EPPK1, PLEC, MIR661, PARP10, GRINA, SPATC1, OPLAH, EXOSC4, GPAAl, CYC1, SHARPIN, MAF1, KIAA1875, C8orf30A, HEATR7A, SCXA, SCXB, BOP1, HSF1, DGAT1, SCRT1, C80RFK29, FBXL6, GPR172A, ADCK5, CPSF1, MIR939, MIR1234, SLC39A4, VPS28, TONSL, CYHR1, KIFC2, FOXH1, PPP1R16A, GPT, MFSD3, RECQL4, LRRC14, LRRC24, C8orf82, ARHGAP39, ZNF251, ZNF34, RPL8, ZNF517, ZNF7, COMMD5, ZNF250, ZNF16, ZNF252, TMED10P1, C8orf77, C8orf33

9 P 15805300 1823 0.00 9p22.3 1 C9orf93

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

9 q 70928471 2057 0.00 9q21.11 1 TJP2

10 P 27040181 1631 0.00 10pl2.1 1 PDSS1

10 q 77926390 2348 0.00 10q22.3 1 ClOorfl l

l lql3.5- GUCY2E, TSKU, ACER3, B3GNT6, CAPN5, OMP, MY07A, GDPD4, PAK1, AQP11,

11 q 76074403 2562103 3.16 24 CLNS1A, RSF1, Cl lorf67, INTS4, KCTD14, NDUFC2-KCTD14, THRSP, NDUFC2, ALG8, ql4.1 KCTD21, USP35, GAB2, NARS2, ODZ4

IQSEC3, LOC574538, SLC6A12, SLC6A13, KDM5A, CCDC77, B4GALNT3, NINJ2, WNKl, RAD52, ERC1, LOC100292680, FBXL14, WNT5B, MIR3649, ADIPOR2, CACNA2D4, LRTM2, LOC100271702, DCPIB, CACNAIC, LOC283440, FKBP4, ITFG2, NRIP2, FOXMl, C12orf32, TULP3, TEAD4, TSPAN9, PRMT8, EFCAB4B, PARP11, CCND2, C12orf5, FGF23, FGF6, C12orf4, RAD51AP1, DYRK4, AKAP3, NDUFA9, GALNT8, KCNA6, KCNA1, KCNA5, NTF3, AN02, VWF, CD9, PLEKHG6, TNFRSF1A, SCNN1A, LTBR, LOC678655, CD27, TAPBPL, VAMP1, MRPL51, NCAPD2, SCARNA10, GAPDH, IFFOl, NOP2, CHD4, SCARNA11, LPAR5, ACRBP, ING4, ZNF384, C12orf53, COPS7A, MLF2, PTMS, LAG3, CD4, GPR162, LEPREL2, GNB3, CDC A3, USP5, TPI1, SPSB2, RPL13P5, DSTNP2, LRRC23, EN02, ATN1, C12orf57, PTPN6, MIR200C, MIR141, PHB2,

SCARNA12, EMG1, LPCAT3, CIS, C1R, C1RL, LOC283314, RBP5, CLSTN3, PEX5, ACSM4, CD163L1, CD163, APOBEC1, GDF3, DPP A3, CLEC4C, NANOGNB, NANOG, SLC2A14, SLC2A3, FOXJ2, C3AR1, NECAP1, CLEC4A, POU5F1P3, ZNF705A, FAM66C, FAM90A1, LOC653113, LOC389634, CLEC6A, CLEC4D, CLEC4E, AICDA, MFAP5, RIMKLB, A2ML1, PHC1, M6PR, KLRG1, C12orG3, LOC144571, A2M, PZP,

LOC100499405, LOC642846, DDX12, KLRB 1, LOC374443, CLEC2D, CLECL1, CD69,

12pl3.33- KLRF1, CLEC2B, KLRF2, CLEC2A, CLEC12A, CLEC1B, CLEC12B, CLEC9A, CLEC1A,

12 P 33854 32885882 92.90 314 CLEC7A, OLRl, C12orf59, GABARAPL1, KLRD1, KLRK1, KLRC4-KLRK1, KLRC4, pl l .21 KLRC3, KLRC2, KLRC1, KLRAP1, MAGOHB, STYK1, CSDA, TAS2R7, TAS2R8,

TAS2R9, TAS2R10, PRR4, PRH1, TAS2R13, PRH2, TAS2R14, TAS2R50, TAS2R20, TAS2R19, TAS2R31, TAS2R46, TAS2R43, TAS2R30, LOC100129361, TAS2R42, PRB3, PRB4, PRB1, PRB2, LOC338817, ETV6, BCL2L14, LRP6, MANSC1, LOH12CR2, LOH12CR1, DUSP16, CREBL2, GPR19, CDKN1B, APOLD1, MIR613, DDX47,

RPL13AP20, GPRC5A, MIR614, GPRC5D, HEBP1, HTR7P1, KIAA1467, GSG1, EMP1, C12orf36, GRIN2B, ATF7IP, PLBD1, GUCY2C, HIST4H4, H2AFJ, WBP11, C12orf60, C12orf69, ART4, MGP, ERP27, ARHGDIB, PDE6H, RERG, PTPRO, EPS8, STRAP, DERA, SLC15A5, MGST1, LM03, LOC728622, RERGL, PIK3C2G, PLCZ1, CAPZA3, PLEKHA5, AEBP2, PDE3A, SLCOICI, SLC01B3, LST-3TM12, SLCOIB I, SLC01A2, IAPP, PYROXDl, RECQL, GOLTIB, C12orf39, GYS2, LDHB, KCNJ8, ABCC9, CMAS, ST8SIA1, KIAA0528, ETNKl, SOX5, MIR920, C12orf67, BCATl, C12orf77, LRMP, CASCl, LYRM5, KRAS, IFLTD1, MIR4302, RASSF8, BHLHE41, SSPN, ITPR2, C12orfl l, FGFR10P2, TM7SF3, MED21, C12orf71, STK38L, ARNTL2, C12orf70, PPFIBP1, REP 15, MRPS35, LOC100287284, KLHDC5, PTHLH, CCDC91, FAR2, ERGIC2, OVCHl, TMTC1, IP08, CAPRIN2, TSPAN11, DDX11, FAM60A, FLJ13224, DENND5B, C12orf72, AMN1, H3F3C, C12orf35, BICDl, FGD4, DNM1L, YARS2, PKP2

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

12 P 130944468 1780 0.00 12q24.33 1 ULKl

13 q 100692746 1146 0.00 13q33.1 1 NALCN

13 q 113792974 1695 0.00 13q34 1 RASA3

14 q 34676390 7420 0.01 14ql3.2 1 KIAA0391

14 q 73072457 19655 0.02 14q24.3 HEATR4, ACOT1

15 q 74678353 2086 0.00 15q24.3 1 SCAPER

15 q 99634434 1267 0.00 15q26.3 1 SELS

16 P 1299180 1161 0.00 16pl3.3 1 UBE2I

16 q 57204859 1913 0.00 16q21 1 CNOT1

16 q 75097331 3534 0.01 16q23.1 1 CNTNAP4

16 q 76929598 10620 0.02 16q23.1 1 WWOX

17 P 1906319 72 0.00 17pl3.3 1 HICl

19 P 241442 1584 0.01 19pl3.3 1 PPAP2C

19 P 9351476 73900 0.26 19pl3.2 3 ZNF559-ZNF177, ZNF177, ZNF266

ZNF560, ZNF426, ZNF121, ZNF561, ZNF562, ZNF812, ZNF846, FBXL12, UBL5, PIN1, OLFM2, COL5A3, RDH8, C3P1, C19orf66, ANGPTL6, PPAN, PPAN-P2RY11, SNORD105, SNORD105B, P2RY11, EIF3G, DNMT1, S1PR2, MIR4322, MRPL4, ICAM1, ICAM4, ICAM5, ZGLP1, FDX1L, RAVER 1, ICAM3, TYK2, CDC37, MIR1181, PDE4A, KEAP1, S1PR5, ATG4D, MIR1238, KRIl, CDKN2D, AP1M2, SLC44A2, LOC147727, ILF3, QTRTl, DNM2, MIR638, MIR1 A1, TMED1, C19orf38, CARM1, YIPF2, C19orf52, SMARCA4, LDLR, SPC24, KANK2, DOCK6, LOC55908, TSPAN16, RAB3D, TMEM205, CCDC159,

19pl3.2- LPPR2, C19orf39, EPOR, RGL3, CCDC151, PRKCSH, ELAVL3, ZNF653, ECSIT, CNN1,

19 P 9457512 10236513 35.92 323 ELOF1, ACP5, ZNF627, ZNF833P, ZNF823, ZNF441, ZNF491, ZNF440, ZNF439, ZNF69, pl3.11 ZNF700, ZNF763, ZNF433, ZNF878, ZNF844, ZNF788, ZNF20, ZNF625-ZNF20, ZNF625,

ZNF136, ZNF44, ZNF563, ZNF442, ZNF799, ZNF443, ZNF709, ZNF564, ZNF490, ZNF791, MAN2B1, WDR83, C19orf56, DHPS, FBXW9, TNP02, SNORD41, C19orf43, ASNA1, BEST2, HOOK2, JUNB, PRDX2, RNASEH2A, RTBDN, MAST1, DNASE2, KLF1, GCDH, SYCE2, FARSA, CALR, RAD23A, GADD45GIP1, DAND5, NFIX, LYLl, TRMTl, NACCl, STX10, IER2, CACNA1A, CCDC130, MRU, C19orf53, ZSWIM4, LOC284454, MIR24-2, MIR27A, MIR23A, MIR181C, MIR181D, NANOS3, C19orf57, CC2D1A, PODNLl, DCAF15, RFX1, RLN3, IL27RA, PALM3, LOCI 13230, SAMD1, PRKACA, ASF1B, LPHN1, CD97,

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

DDX39A, PKN1, PTGER1, GIPCl, LOC100130932, DNAJB1, MIR639, TECR, NDUFB7, CLEC17A, EMR3, ZNF333, EMR2, OR7C1, OR7A5, OR7A10, OR7A17, OR7C2, SLC1A6, CCDC105, CASP14, OR1I1, SYDE1, ILVBL, NOTCH3, EPHX3, BRD4, AKAP8, AKAP8L, WIZ, MIR1470, RASAL3, PGLYRP2, CYP4F22, CYP4F8, CYP4F3, CYP4F12, OR10H2, OR10H3, CYP4F24P, OR10H5, ORIOHI, UCAl, CYP4F2, CYP4F11, OR10H4, LOC126536, FLJ25328, TPM4, RAB8A, HSH2D, CIB3, FAM32A, AP1M1, KLF2, EPS15L1, CALR3, C19orf44, CHERP, SLC35E1, MED26, C19orf42, TMEM38A, NWD1, SIN3B, F2RL3, CPAMD8, HAUS8, MY09B, USE1, OCEL1, NR2F6, USHBP1, BABAM1, ANKLE 1, ABHD8, MRPL34, DDAl, AN08, GTPBP3, PLVAP, BST2, FAM125A, TMEM221, NXNLl, SLC27A1, PGLS, FAM129C, GLT25D1, UNCI 3 A, MAP1S, FCHOl, B3GNT3, INSL3, JAK3, RPL18AP3, RPL18A, SNORA68, SLC5A5, CCDC124, KCNN1, ARRDC2, IL12RB1, MAST3, PIK3R2, IFI30, MPV17L2, RAB3A, PDE4C, LOC729966, KIAA1683, JUND, MIR3188, LSM4, PGPEP1, GDF15, MIR3189, LRRC25, SSBP4, ISYNA1, ELL, FKBP8, C19orf50, UBA52, C19orf60, CRLF1, TMEM59L, KLHL26, CRTC1, COMP, UPF1, GDF1, LASS1, COPE, DDX49, HOMER3, SUGP2, ARMC6, SLC25A42, TMEM161A, MEF2B, LOC729991-MEF2B, LOC729991, RFXANK, NR2C2AP, NCAN, HAPLN4, TM6SF2, SUGP1, MAU2, GATAD2A, TSSK6, NDUFA13, YJEFN3, CILP2, PBX4, LPAR2, GMIP, ATP13A1, ZNF101, ZNF14

19pl3.11- ZNF14, LOC284440, ZNF506, ZNF253, ZNF93, ZNF682, ZNF90, ZNF486, ZNF826P,

19 P 19702214 2191477 7.69 25 MIR1270-1, MIR1270-2, ZNF737, ZNF626, ZNF85, ZNF430, ZNF714, ZNF431, ZNF708, pl2 ZNF738, ZNF493, LOC400680, ZNF429, ZNF100, LOC641367, ZNF43

LOC148189, LOC148145, UQCRFS1, VSTM2B, POP4, PLEKHF1, C19orfl2, CCNE1, C19orf2, ZNF536, DKFZp566F0947, TSHZ3, ZNF507, DPY19L3, PDCD5, ANKRD27, RGS9BP, NUDT19, TDRD12, SLC7A9, CCDC123, C19orf40, RHPN2, GPATCH1, WDR88, LRP3, SLC7A10, CEBPA, LOC80054, CEBPG, PEPD, CHST8, KCTD15, LSM14A, KIAA0355, GPI, PDCD2L, UBA2, WTIP, LOC643719, SCGBL, ZNF302, ZNF181, ZNF599, LOC400685, ZNF30, ZNF792, GRAMD1A, SCN1B, HPN, LOC100128675, FXYD3, LGI4, FXYD1, FXYD7, FXYD5, FAM187B, LSR, USF2, HAMP, MAG, CD22, FFAR1, FFAR3, FFAR2, KRTDAP, DMKN, SBSN, GAPDHS, TMEM147, ATP4A, HAUS5, RBM42, ETV2, COX6B1, UPK1A, ZBTB32, MLL4, TMEM149, U2AF1L4, PSENEN, LIN37, HSPB6, C19orf55, ARHGAP33, PRODH2, NPHS1, KIRREL2, APLP1, NFKBID, HCST, TYROBP,

19ql2- LRFN3, SDHAF1, C19orf46, ALKBH6, CLIP3, THAP8, WDR62, POLR2I, TBCB, CAPNS1,

19 q 32545047 13265170 37.37 219 COX7A1, ZNF565, ZNF146, LOC100134317, ZFP14, ZFP82, LOC644189, ZNF566,

ql3.2 LOC728752, ZNF260, ZNF529, ZNF382, ZNF461, ZNF567, ZNF850, ZNF790, ZNF345,

ZNF829, ZNF568, ZNF420, ZNF585A, ZNF585B, ZNF383, LOC284412, HKR1, ZNF527, ZNF569, ZNF570, ZNF793, ZNF540, ZNF571, ZFP30, ZNF781, ZNF607, ZNF573, LOC728853, WDR87, SIPA1L3, DPF1, PPP1R14A, SPINT2, YIF1B, C19orf33, KCNK6, CATSPERG, PSMD8, GGN, SPRED3, FAM98C, RASGRP4, RYR1, MAP4K1, EIF3K, ACTN4, CAPN12, LGALS7, LGALS7B, LGALS4, ECHl, HNRNPL, RINL, SIRT2, NFKBIB, SARS2, MRPS12, FBX017, FBX027, PAPL, PAK4, NCCRP1, SYCN, IL28B, IL28A, IL29, LRFN1, GMFG, SAMD4B, PAF1, MED29, ZFP36, PLEKHG2, RPS16, SUPT5H, TIMM50, DLL3, SELV, EID2B, EID2, LGALS13, LOC100129935, LGALS16, LGALS17A, LGALS14, CLC, LEUTX, DYRK1B, FBL, FCGBP, PSMC4, ZNF546, ZNF780B, ZNF780A, MAP3K10, TTC9B, CNTD2, AKT2, MIR641, C19orf47, PLD3, HIPK4, PRX, SERTAD1, SERTAD3,

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

RBM39, PHF20, SCAND1, C20orfl52, LOC647979, EPB41L1, C20orf4, DLGAP4, MYL9, TGIF2, TGIF2-C20ORF24, C20orf24, SLA2, NDRG3, DSN1, C20orfl l7, C20orfl l8, SAMHD1, RBL1, C20orfl32, RPN2, GHRH, MANBAL, SRC, BLCAP, NNAT, CTNNBLl, VSTM2L, TTI1, RPRD1B, TGM2, KIAA1755, BPI, LBP, LOC388796, SNORA71B, SNORA71 A, SNORA71C, SNORA71D, SNHGl l, SNORA39, SNORA60, RALGAPB, ADIG, ARHGAP40, SLC32A1, ACTR5, PPP1R16B, FAM83D, DHX35, LOC339568, MAFB, TOPI, PLCG1, ZHX3, LPIN3, EMILIN3, CHD6, PTPRT, SRSF6, L3MBTL1, SGK2, IFT52, MYBL2, GTSF1L, TOX2, JPH2, C20orfl l l, GDAP1L1, FITM2, R3HDML, HNF4A, MIR3646, TTPAL, SERINC3, PKIG, ADA, LOC79015, WISP2, KCNK15, RIMS4, YWHAB, PABPC1L, TOMM34, STK4, KCNS1, WFDC5, WFDC12, PI3, SEMG1, SEMG2, SLPI, MATN4, RBPJL, SDC4, SYS1, SYS1-DBNDD2, TP53TG5, DBNDD2, PIGT, WFDC2, SPINT3, WFDC6, SPINLW1-WFDC6, SPINLW1, WFDC8, WFDC9, WFDCIOA, WFDC11, WFDCIOB, WFDC13, SPINT4, WFDC3, DNTTIP1, UBE2C, TNNC2, SNX21, ACOT8, ZSWIM3, ZSWIM1, C20orfl65, NEURL2, CTSA, PLTP, PCIF1, ZNF335, MMP9, SLC12A5, NCOA5, CD40, CDH22, SLC35C2, ELM02, LOC100240726, ZNF334, C20orfl23, SLC13A3, TP53RK, SLC2A10, EYA2, MIR3616, ZMYND8, LOC100131496, NCOA3, SULF2, LOC284749, PREX1, ARFGEF2, CSE1L, STAU1, DDX27, ZNFX1, NCRNA00275, SNORD12C, SNORD12B, SNORD12, KCNB1, PTGIS, B4GALT5, SLC9A8, SPATA2, RNF114, SNAI1, UBE2V1, TMEM189-UBE2V1, TMEM189, CEBPB, LOC284751, PTPN1, MIR645, FAM65C, PARD6B, BCAS4, ADNP, DPMI, MOCS3, KCNGl, NFATC2, MIR3194, ATP9A, SALL4, ZFP64, TSHZ2, ZNF217, SUM01P1, BCAS1, CYP24A1, PFDN4, DOK5, CBLN4, MC3R, C20orf 08, AURKA, CSTF1, CASS4, C20orf43, GCNT7, C20orfl06, C20orfl07, TFAP2C, BMP7, MIR4325, SPOl l, RAEl, MTRNR2L3, RBM38, CTCFL, PCKl, ZBP1, PMEPA1, C20orf85, PPP4R1L, RAB22A, VAPB, APCDD1L, LOC149773, STX16, NPEPL1, MIR296, MIR298, GNAS-AS1, GNAS, TH1L, CTSZ, TUBB1, ATP5E, SLM02, ZNF831, EDN3, PHACTR3, SYCP2, C20orfl77, PPP1R3D, CDH26, C20orfl97, MIR646, CDH4, MIR1257, TAF4, LSM14B, PSMA7, SS18L1, GTPBP5, HRH3, OSBPL2, ADRM1, LAMA5, RPS21, CABLES2, C20orfl51, GATA5, C20orf200, C20orfl66, MIRl-1, MIR133A2, SLC04A1, LOC100127888, NTSR1, C20orf20, OGFR, COL9A3, TCFL5, DPH3P1, DIDOl, C20orfl l, SLC17A9, BHLHE23, LOC63930, NCRNA00029,

LOC100144597, HAR1B, HAR1A, MIR124-3, YTHDF1, BIRC7, MIR3196, NKAIN4, FLJ16779, ARFGAP1, MIR4326, COL20A1, CHRNA4, KCNQ2, EEF1A2, PPDPF, PTK6, SRMS, C20orfl95, PRIC285, GMEB2, STMN3, RTEL1, TNFRSF6B, ARFRP1, ZGPAT, LIME1, SLC2A4RG, ZBTB46, ABHD16B, TPD52L2, DNAJC5, MIR941-1, MIR941-3, MIR941-2, UCKL1, MIR1914, MIR647, UCKL1-AS1, ZNF512B, SAMD10, PRPF6, NCRNA00176, SOX18, TCEA2, RGS19, OPRL1, C20orf201, NPBWR2, MYT1, PCMTD2

22 18127933 1261 0.00 22ql l .21 TBXl

Copy Number Losses

numbe

size/arm

chromosome arm start size cytoband r of gene symbol

(%) genes

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of arm start size cytoband gene symbol some (%) genes

1611047

1 q 39 0.00 lq23.3

52 1 Clorfl lO

1 P 1652866 1160 0.00 lp36.33 1 SLC35E2

1093747

1 P 1459 0.00 lpl3.3 WDR47

90 1

1138474

1 P 1506 0.00 lpl3.2 I3

79 1 MAG

1160316

1 P 1732 0.00 lpl3.1

70 1 VANGL1

1085358

1 P 2848 0.00 lpl3.3

14 1 SLC25A24

1730635

1 q 3800 0.00 lq25.1

37 1 RABGAPIL

1100330

1 P 6370 0.01 lpl3.3

18 1 GSTM1

1510287

1 q 7735 0.01 lq21.3

00 1 LCE1D

1674937

1 q 14130 0.01 lq24.2

68 1 NME7

1508230

1 q 28366 0.02 lq21.3

73 1 LCE3C

2468055

1 q 56508 0.05 lq44 2 OR2T10, OR2T11

21

1950093

1 q 56509 0.05 lq31.3 2 CFHR3, CFHR1

58

1546056

2 q 1322 0.00 2q24.1 1 GALNT13

21

1797778

2 q 1069 0.00 2q31.2 1 SESTD1

50

3307800

2 P 2432 0.00 2p22.3 1 LTBP1

5

2128928

2 q 5991 0.00 2q34 1 ERBB4

84

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

4746642

3 P 498 0.00 3p21.31

3 1 SCAP

1912217

3 q 1133 0.00 3q28

58 1 LEPREL1

3 P 7375107 1410 0.00 3p26.1 1 GRM7

1331918

3 q 2808 0.00 3q22.1

77 1 CPNE4

1138689

3 P 2732 0.00 3p25.3

2 1 ATG7

1925481

3 q 4599 0.00 3q28

35 1 CCDC50

3795481

3 P 6291 0.01 3p22.2

9 1 CTDSPL

5300313

3 P 8749 0.01 3p21.1

6 1 SFMBT1

GC, NPFFR2, ADAMTS3, COX18, ANKRD17, ALB, AFP, AFM, RASSF6, IL8, CXCL6, PF4V1, CXCL1, PF4, PPBP, CXCL5, CXCL3, PPBPL2, CXCL2, MTHFD2L, EPGN, EREG, AREG, BTC, PARM1, LOC441025, RCHY1, THAP6, C4orf26, CDKL2, G3BP2, USOl, PPEF2, NAAA, SDAD1, CXCL9, ART3, CXCL10, CXCL11, NUP54, SCARB2, FAM47E, STBD1, CCDC158, SHROOM3, ANKRD56, SEPT11, CCNI, CCNG2, CXCL13, CNOT6L, MRPL1, FRAS1, ANXA3, BMP2K, PAQR3, NAA11, GK2, GDEP, ANTXR2, PRDM8, FGF5, C4orf22, BMP3, PRKG2, RASGEF1B, HNRNPD, HNRPDL, ENOPH1, TMEM150C, C4orfl l, SCD5, MIR575, SEC31A, LOC100499177, THAP9, LIN54, COPS4, PLAC8, COQ2, HPSE, HELQ, MRPS18C, FAM175A, AGPAT9, NKX6-1, CDS1, WDFY3, NCRNA00247, ARHGAP24, MAPK10, PTPN13, SLC10A6, C4orf36, AFF1, KLHL8, HSD17B13, HSD17B11, NUDT9, SPARCL1, DSPP, DMP1, IBSP, MEPE, HSP90AB3P, SPP1, PKD2,

7272022 11843338 4ql3.3- ABCG2, PPMIK, HERC6, HERC5, PIGY, HERC3, NAP1L5, FAM13AOS, FAM13A, TIGD2,

4 q 84.47 479

8 5 q35.2 GPRIN3, SNCA, MMRN1, FAM190A, TMSL3, GRID2, ATOH1, SMARCADl, HPGDS,

PDLIM5, BMPR1B, UNC5C, PDHA2, C4orf37, RAP1GDS1, TSPAN5, EIF4E, METAP1, MIR3684, ADH5, ADH4, PCNAP1, ADH6, ADH1A, ADH1B, ADH1C, ADH7, C4orfl7, RG9MTD2, MTTP, DAPP1, MAPKSPl, DNAJB 14, H2AFZ, LOC256880, DDIT4L, EMCN, PPP3CA, FLJ20021, BANK1, SLC39A8, NFKB 1, MANBA, UBE2D3, CISD2, NHEDC1, NHEDC2, BDH2, CENPE, TACR3, CXXC4, TET2, PPA2, EEF1A1P9, ARHGEF38, INTS12, GSTCD, NPNT, TBCK, AIMP1, LOC100507096, DKK2, PAPSS1, SGMS2, CYP2U1, HADH, LEF1, LOC641518, LOC285456, RPL34, OSTC, AGXT2L1, COL25A1, SEC24B, CCDC109B, CASP6, PLA2G12A, CFI, GARi, RRH, LRIT3, EGF, ELOVL6, ENPEP, PITX2, C4orf32, APiAR, TIFA, ALPKi, NEUROG2, C4orm, LARP7, MIR367, MIR302D, MIR302A, MIR302C, MIR302B, ANK2, MHU243, CAMK2D, ARSJ, UGT8, MIR577, NDST4, MIR!973, TRAM!L!, NDST3, SNHG8, SNORA24, PRSS12, CEPHOP!, METTL!4,

W:\DOCS\1877\MOF.₁55XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

SEC24D, SYNP02, MYOZ2, USP53, C4orf3, FABP2, FLJ14186, LOC645513, PDE5A, MAD2L1, PRDM5, C4orf31, TNIP3, QRFPR, ANXA5, TMEM155, LOC100192379, EXOSC9, CCNA2, BBS7, TRPC3, KIAA1109, ADAD1, IL2, IL21, CETN4P, BBS12, FGF2, NUDT6, SPATA5, SPRY1, LOC285419, ANKRD50, FAT4, INTU, SLC25A31, HSPA4L, PLK4, MFSD8, C4orf29, LARPIB, PGRMC2, PHF17, SCLTl, C4orf33, PCDHIO, PABPC4L, PCDH18, SLC7A11, CCRN4L, ELF2, C4orf49, NDUFC1, NAA15, RAB33B, SETD7, MGST2, MAML3, SCOC, LOC100129858, CLGN, ELMOD2, UCP1, TBC1D9, RNF150, ZNF330, IL15, INPP4B, USP38, GAB1, MIR3139, SMARCA5, LOC441046, FREM3, GYPE, GYPB, GYP A, HHIP, ANAPC10, ABCE1, OTUD4, SMAD1, MMAA, C4orf51, ZNF827, LSM6, SLC10A7, POU4F2, TTC29, EDNRA, TMEM184C, PRMT10, ARHGAP10, NR3C2, DCLK2, LRBA, MAB21L2, RPS3A, SNORD73A, SH3D19, PRSS48, FAM160A1, PET112L, FBXW7, MIR3140, DKFZP434I0714, TMEM154, TIGD4, ARFIP1, FHDC1, TRIM2, ANXA2P1, MND1, KIAA0922, TLR2, RNF175, SFRP2, DCHS2, PLRG1, FGB, FGA, FGG, LRAT, RBM46, NPY2R, MAP9, GUCY1A3, GUCY1B3, ACCN5, TD02, CTSO, PDGFC, GLRB, GRIA2, LOC340017, FAM198B, TMEM144, RXFPl, C4orf46, ETFDH, PPID, FNIP2, C4orf45, MIR3688, RAPGEF2, FSTL5, NAF1, NPY1R, NPY5R, TKTL2, C4orf43, MARCH 1, ANP32C, TRIM61, C4orG9, TRIM60, TMEM192, KLHL2, GK3P, SC4MOL, CPE, MIR578, TLL1, SPOCK3, ANXA10, DDX60, DDX60L, PALLD, CBR4, SH3RF1, NEK1, CLCN3, C4orf27, MFAP3L, AADAT, HSP90AA6P, GALNTL6, GALNT7, HMGB2, SAP30, SCRG1, HAND2, NBLA00301, MORF4, FBX08, KIAA1712, MIR4276, HPGD, GLRA3, ADAM29, GPM6A, MIR1267, WDR17, SPATA4, ASB5, SPCS3, VEGFC, NEIL3, AGA, LOC285501, NCRNA00290, MGC45800, MIR1305, ODZ3, DCTD, FAM92A3, C4orf38, WWC2, CLDN22, CLDN24, CDKN2AIP, LOC389247, ING2, RWDD4, C4orf41, STOX2, ENPP6, IRF2, CASP3, CCDC111, MLF1IP, ACSL1, SLED1, MIR3945, HELT, SLC25A4, KIAA1430, SNX25, LRP2BP, ANKRD37, UFSP2, C4orf47, CCDC110, PDLIM3, SORBS2, TLR3, FAM149A, CYP4V2, KLKB1, Fl l, LOC285441, MTNR1A, FAT1, ZFP42, TRIML2, TRIML1, LOC401164, HSP90AA4P, FRG1, TUBB4Q

7251873

4 q 3272 0.00 4ql3.3

7 1 SLC4A4

3886979

4 P 2571 0.01 4pl4

6 1 WDR19

1719950

4 P 6065 0.01 4pl5.32

2 1 LAP3

6998008

4 q 18477 0.01 4ql3.2 UGT2B7

0 1

6972080

4 q 21644 0.02 4ql3.2

5 1 UGT2B10

7019068

4 q 103630 0.07 4ql3.2

2 1 UGT2B28

4 q 6890567 260144 0.19 4ql3.2 2 TMPRSS11E, UGT2B17

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

0

3836037

4 P 232761 0.46 4pl4 6 KLF3, TLR10, TLR1, TLR6, FAM114A1, MIR574

5

3938243

4 P 328209 0.65 4pl4 2 UBE2K, PDS5A

5

3983266

4 P 525382 1.03 4pl4 4 N4BP2, RHOH, CHRNA9, RBM47

5

3737488

4 P 846993 1.67 4pl4 3 PGM2, TBC1D1, PTTG2

7

SLIT2, MIR218-1, PACRGL, KCNIP4, NCRNA00099, GPR125, GBA3, PPARGC1A,

1865341 4pl5.31- MIR573, DHX15, SOD3, CCDC149, LGI2, SEPSECS, PI4K2B, ZCCHC4, ANAPC4,

4 P 18702180 36.82 31

8 pl4 SLC34A2, SEL1L3, C4orf52, RBPJ, CCKAR, TBC1D19, STIM2, MIR4275, PCDH7, ARAP2,

DTHD1, KIAA1239, C4orfl9, RELL1

PELO, ITGA1, ITGA2, MOCS2, LOC257396, FST, NDUFS4, ARL15, MIR581, HSPB3, SNX18, ESM1, GZMK, GZMA, CDC20B, GPX8, MIR449A, MIR449B, MIR449C, LOC345643, CCNO, DHX29, SKIV2L2, PPAP2A, RNF138P1, SLC38A9, DDX4, IL31RA, IL6ST, ANKRD55, MAP3K1, C5orf35, MIER3, GPBP1, ACTBL2, PLK2, GAPT, RAB3C, PDE4D, PARTI, DEPDC1B, ELOVL7, ERCC8, NDUFAF2, C5orf43, ZSWIM6, FLJ37543, KIF2A, DIMT1L, IPOl l, LRRC70, HTR1A, RNF180, RGS7BP, FAM159B, SREK1IP1, CWC27, ADAMTS6, CENPK, PPWD1, TRIM23, C5orf44, SGTB, NLN, ERBB2IP, LOC100303749, SREK1, MAST4, CD180, PIK3R1, SLC30A5, CCNB 1, CENPH, MRPS36, CDK7, CCDC125, TAF9, RAD17, MARVELD2, OCLN, LOC647859, GTF2H2B, GTF2H2C, GTF2H2, GTF2H2D, LOC100272216, GUSBP3, LOC100049076, SERFIA, SERFIB, SMN2, SMN1, LOC100170939, SMA5, NAIP, PMCHL2, BDP1, MCCC2, CARTPT, MAP IB,

5163255 5ql l .2- MRPS27, PTCD2, ZNF366, TNPOl, FCH02, TMEM171, TMEM174, FOXD1, BTF3,

5 q 47776009 35.84 225 ANKRA2, UTP15, RGNEF, ENC1, HEXB, GFM2, NSA2, FAM169A, GCNT4, ANKRD31,

4 q21.1 HMGCR, COL4A3BP, POLK, POC5, SV2C, IQGAP2, F2RL2, NCRUPAR, F2R, F2RL1,

S100Z, CRHBP, AGGF1, ZBED3, SNORA47, LOC728723, PDE8B, WDR41, OTP, TBCA, AP3B1, SCAMPI, LHFPL2, ARSB, DMGDH, BHMT2, BHMT, JMY, HOMER 1, PAPD4, CMYA5, MTX3, THBS4, SERINC5, LOC644936, SPZ1, CRSP8P, ZFYVE16, FAM151B, ANKRD34B, DHFR, MTRNR2L2, MSH3, RASGRF2, CKMT2, LOC100131067, ZCCHC9, ACOT12, SSBP2, ATG10, RPS23, ATP6AP1L, TMEM167A, SCARNA18, XRCC4, VCAN, HAPLN1, EDIL3, NBPF22P, COX7C, MIR3607, MIR4280, RASA1, CCNH, TMEM161B, LOC645323, MIR9-2, MEF2C, MIR3660, CETN3, MBLAC2, POLR3G, LYSMD3, GPR98, ARRDC3, LOC100129716, FLJ42709, NR2F1, FAM172A, MIR2277, POU5F2, C5orf36, ANKRD32, MCTP1, FAM81B, TTC37, ARSK, GPR150, RFESD, SPATA9, RHOBTB3, GLRX, C5orf27, ELL2, MIR583, PCSK1, CAST, ERAP1, ERAP2, LNPEP, LIX1, RIOK2, RGMB, FLJ35946, CHD1, LOC100289230

1723482

5 q 1701 0.00 5q35.2 1 ATP6V0E1

16

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

TAAR3, TAAR2, TAAR1, VNN1, VNN3, VNN2, C6orfl92, RPS12, SNORD101, SNORDIOO, SNORA33, LOC285735, EYA4, MGC34034, TCF21, TBPLl, SLC2A12, SGKl, ALDH8A1, HBS1L, MIR3662, MYB, AHI1, MIR548H4, NCRNA00271, PDE7B, FAM54A, BCLAFl, MAP7, MAP3K5, PEX7, SLC35D3, NHEGl, IL20RA, IL22RA2, IFNGRl, OLIG3, TNFAIP3, PERP, KIAA1244, PBOV1, HEBP2, NHSL1, MIR3145, FLJ46906, CCDC28A, ECT2L, REPSl, C6orfl l5, HECA, TXLNB, CITED2, LOC645434, MIR3668, NMBR, VTAl, GPR126, LOC153910, HIVEP2, AIG1, ADAT2, PEX3, FUCA2, LOC285740, PHACTR2, LTV1, C6orf94, PLAGL1, HYMAI, SF3B5, STX11, UTRN, EPM2A, FBXO30, SHPRH, GRM1, RAB32, C6orfl03, LOC729176, LOC729178, STXBP5, SAMD5, SASH1, UST, TAB2, SUM04, ZC3H12D, PPIL4, C6orf72, KATNA1, LATS1, NUP43, PCMT1, LRP11, RAET1E, RAETIG, ULBP2, ULBP1, RAET1K, RAET1L, ULBP3, PPP1R14C, I YD, PLEKHG1, MTHFD1L, AKAP12, ZBTB2, RMND1, C6orf211, C6orf97, ESR1, SYNE1, MYCT1, VIP, FBX05, MTRF1L, RGS17, OPRM1, IPCEF1, CNKSR3, SCAF8, TIAM2, TFB1M, CLDN20, NOX3, ARID IB, ZDHHC14, MIR3692, SNX9, SYNJ2, SERAC1, GTF2H5, TULP4, TMEM181, DYNLT1, SYTL3, MIR3918, EZR, OSTCL, C6orf99, RSPH3, TAGAP, FNDC1, SOD2, WTAP, LOC100129518, ACAT2, TCP1, SNORA20, SNORA29, MRPL18, PNLDC1, MASl, IGF2R, LOC729603, SLC22A1, SLC22A2, SLC22A3, LPAL2, LPA, PLG, MAP3K4, AGPAT4, NCRNA00241, PARK2, PACRG, LOC285796,

DKFZp451B082, LOC100526820, QKI, C6orfl l8, PDE10A, C6orfl76, LOC441177, T, PRR18, SFT2D1, BRP44L, RPS6KA2, MIR1913, RNASET2, MIR3939, FGFRIOP, CCR6, GPR31, TCP10L2, UNC93A, TTLL2, TCP10, C6orfl23, C6orfl24, MLLT4, HGC6.3, KIF25, FRMD1, DACT2, SMOC2, THBS2, WDR27, C6orfl20, PHF10, TCTE3, C6orf70, NCRNA00242, C6orf208, LOC154449, DLL1, FAM120B, PSMB 1, TBP, PDCD2

7292089

6 q 3546 0.00 6ql3 1 RIMS1

4

6645625

6 q 4298 0.00 6ql2 1 EYS

0

5403719

6 P 5535 0.01 6pl2.1 1 C6orfl42

9

3271625

6 P 12232 0.02 6p21.32 1 HLA-DQA1

5

8983798

6 q 27339 0.02 6ql5 2 PNRC1, SRSF12

7

2997238

6 P 28608 0.05 6p21.33 2 HCG2P7, HCG4P6

2

3255867

6 P 75014 0.12 6p21.32 2 HLA-DRB5, HLA-DRB6

7

8926423

6 q 549324 0.50 6ql5 1 RNGTT

3

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

7191194

7 q 125 0.00 7ql l .23

0 1 TYW1B

1613857

7 P 1439 0.00 7p21.1 ISPD

9 1

1477042

7 q 4182 0.00 7q36.1

00 1 CNTNAP2

1001662

7 q 8734 0.01 7q22.1

57 1 ZAN

1421591

7 q 8735 0.01 7q34

73 1 TRY6

1414133

7 q 26832 0.03 7q34

52 1 MGAM

RPL23AP53, ZNF596, FBX025, C8orf42, ERICHl, LOC286083, DLGAP2, CLN8, MIR596, ARHGEF10, KBTBD11, MYOM2, CSMD1, MCPH1, ANGPT2, AGPAT5, XKR5, DEFB1, DEFA6, DEFA4, DEFA10P, DEFA1B, DEFA1, DEFT1P, DEFT1P2, DEFA3, DEFA5, FAM90A14, FAM90A13, LOC349196, FAM90A5, FAM90A20, FAM66B, DEFB109P1B, ZNF705G, DEFB103B, DEFB103A, SPAG11B, DEFB104B, DEFB104A, DEFB106B, DEFB 106A, DEFB 105B, DEFB 105A, DEFB107B, DEFB 107A, FAM90A7, FAM90A19, FAM90A18, FAM90A8, FAM90A9, FAM90A10, SPAG11A, DEFB4A, LOC100132396, FAM66E, MIR548I3, FLJ10661, SGK223, CLDN23, MFHAS1, ERI1, PPP1R3B, TNKS, MIR597, LOC157627, MIR124-1, MSRA, PRSS55, RP1L1, MIR4286, C8orf74, SOX7, PINX1, MIR1322, XKR6, MIR598, MTMR9, AMAC1L2, TDH, C8orfl2, FAM167A, BLK, GATA4, NEIL2, FDFTl, CTSB, DEFB136, DEFB 135, DEFB134, DEFB 130, LOC100133267, ZNF705D, FAM66D, LOC392196, USP17L2, FAM86B 1, FAM66A, DEFB 109P1, FAM90A25P, FAM86B2, LONRF1, MIR3926-1, MIR3926-2, LOC340357, C8orf79, DLC1,

8p23.3- C8orf48, SGCZ, MIR383, TUSC3, MSR1, FGF20, EFHA2, ZDHHC2, CNOT7, VP S37 A,

8 P 151472 37851200 83.74 249

pl2 MTMR7, SLC7A2, PDGFRL, MTUS1, FGL1, PCM1, ASAH1, NAT1, NAT2, PSD3,

SH2D4A, CSGALNACT1, INTS10, LPL, SLC18A1, ATP6V1B2, LZTS1, LOC286114, GFRA2, DOK2, XP07, NPM2, FGF17, EPB49, FAM160B2, NUDT18, HR, REEP4, LGI3, SFTPC, BMP1, PHYHIP, MIR320A, POLR3D, PIWIL2, SLC39A14, PPP3CC, SORB S3, PDLIM2, C8orf58, KIAA1967, BIN3, FLJ14107, EGR3, PEBP4, RHOBTB2, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF10A, LOC389641, CHMP7, R3HCC1, LOXL2, ENTPD4, SLC25A37, NKX3-1, NKX2-6, STCl, ADAM28, ADAMDECl, ADAM7, NEFM, NEFL, DOCK5, GNRH1, KCTD9, CDCA2, EBF2, PPP2R2A, BNIP3L, PNMA2, DPYSL2, ADRA1A, STMN4, TRIM35, PTK2B, CHRNA2, EPHX2, CLU, SCARA3, MIR3622B, MIR3622A, CCDC25, ESC02, PBK, SCARA5, MIR4287, C8orf80, ELP3, PNOC, ZNF395, FBX016, FZD3, MIR4288, EXTL3, INTS9, HMBOX1, KIF13B, DUSP4, C8orf75, LOC286135, MIR3148, TMEM66, LEPROTLl, MBOAT4, DCTN6, RBPMS, GTF2E2, GSR, UBXN8, PPP2CB, TEX15, PURG, WRN, NRG1, FUT10, MAK16, C8orf41, RNF122, DUSP26, UNC5D, KCNU1, ZNF703, ERLIN2, LOC728024, PROSC, GPR124, BRF2,

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

LOC389705, TTC39B, SNAPC3, PSIP1, C9orf93

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

8962668

10 q 0 0.00 10q23.31

4 1 PTEN

5368651

10 q 1365 0.00 10q21.1

5 1 PRKG1

1327992

10 q 2251 0.00 10q26.3

12 1 TCERG1L

7792639

10 q 2348 0.00 10q22.3

0 1 ClOorfl l

1243378

10 q 2496 0.00 10q26.13

60 1 DMBT1

1141035

10 q 2913 0.00 10q25.2

47 1 GUCY2GP

2704018

10 P 1631 0.00 10pl2.1

1 1 PDSS1

1006788

10 q 7970 0.01 10q24.2

17 1 HPSE2

3128710

10 P 4424 0.01 10pl l .23

1 1 ZNF438

1067443

11 q 3583 0.00 l lq22.3 CWF19L2

37 1

2080197

11 P 4121 0.01 l lpl5.1

3 1 NELL1

11 P 5834025 5899 0.01 l lpl5.4 1 OR52E8

1890650

11 P 10686 0.02 l lpl5.1

5 1 MRGPRX1

11 P 7771593 11899 0.02 l lpl5.4 1 OR5P2

5512371

11 q 85907 0.11 l lql l 4 OR4C11, OR4P4, OR4S2, OR4C6

9

OR51A2, MMP26, OR51L1, OR52J3, OR52E2, OR52A4, OR52A5, OR52A1, OR51V1, HBB, HBD, HBBPl, HBGl, HBG2, HBEl, OR51B4, OR51B2, OR51B5, OR51B6, OR51M1,

11 P 4926583 838855 1.59 l lpl5.4 37 OR51Q1, OR51I1, OR51I2, OR52D1, UBQLN3, UBQLNL, OR52H1, OR52B6, TRIM6,

TRIM6-TRIM34, TRIM34, TRIM78P, TRIM5, TRIM22, OR56B 1, OR52N4, OR52N5

12 P 738240 4983 0.01 12pl3.33 1 WNK1

12 q 8066392 2828 0.00 12q21.31 1 PPFIA2

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

3

1006268

12 q 2995 0.00 12q23.2 1 CHPTl

37

1047482

12 P 11023 0.03 12pl3.2 1 KLRC2

5

1112120

12 P 19217 0.05 12pl3.2 2 PRH1, TAS2R43

4

LOC284232, LOC348021, PHF2P1, TUBA3C, LOC100101938, LOC100287114, TPTE2, MPHOSPH8, PSPC1, ZMYM5, ZMYM2, GJA3, GJB2, GJB6, CRYL1, IFT88, IL17D, N6AMT2, XP04, LATS2, SAP 18, SKA3, MRP63, ZDHHC20, EFHA1, FGF9, BASP1P1, SGCG, SACS, TNFRSF19, MIPEP, PCOTH, C1QTNF9B, SPATA13, MIR2276, C1QTNF9, PARP4, LOC374491, ATP 12 A, RNF17, CENPJ, TPTE2P1, PABPC3, FAM123A, MTMR6, NUPL1, ATP8A2, SHISA2, RNF6, CDK8, WASF3, GPR12, USP12, RPL21, RPL21P28, SNORD102, SNORA27, RASL11A, GTF3A, MTIF3, LNX2, POLR1D, GSX1, PDX1, ATP5EP2, CDX2, PRHOXNB, FLT3, LOC100288730, PAN3, FLT1, POMP, SLC46A3, MTUS2, SLC7A1, UBL3, LOC440131, KATNAL1, LOC100188949, HMGB1, USPL1, ALOX5AP, C13orf33, C13orf26, HSPH1, B3GALTL, RXFP2, EEF1DP3, FRY, ZAR1L, BRCA2, N4BP2L1, N4BP2L2, CG030, PDS5B, KL, STARD13, RFC3, NBEA, MAB21L1, MIR548F5, DCLK1, SOHLH2, C13orf38-SOHLH2, C13orf38, SPG20, CCNA1, C13orf36, RFXAP, SMAD9, ALG5, EXOSC8, FAM48A, CSNKIAIL, POSTN, TRPC4, UFMl, FREM2, STOML3, C13orf23, NHLRC3, LHFP, COG6, MIR4305, FLJ42392, LOC646982, FOXOl, MIR320D1, MRPS31, SLC25A15, SUGT1P3, MIR621, ELF1, WBP4, KBTBD6, KBTBD7, MTRF1, NAA16, OR7E37P, C13orfl5, KIAA0564, DGKH, AKAP11, TNFSF11, C13orf30,

1819454 13ql l- EPSTI1, DNAJC15, ENOX1, CCDC122, C13orf31, NCRNA00284, SERP2, TSC22D1,

13 q 95928796 97.89 382

4 q34 NUFIP1, KIAA1704, GTF2F2, KCTD4, TPT1, SNORA31, LOC100190939, SLC25A30,

COG3, FAM194B, SPERT, SIAH3, ZC3H13, CPB2, LCPl, C13orfl8, LRCHl, ESD, HTR2A, SUCLA2, NUDT15, MED4, ITM2B, RBI, LPAR6, RCBTB2, CYSLTR2, FNDC3A, MLNR, CDADC1, CAB39L, SETDB2, PHF11, RCBTB1, ARL11, EBPL, KPNA3, CTAGE10P, C13orfl, DLEU2, MIR3613, TRIM13, KCNRG, MIR16-1, MIR15A, DLEU1, ST13P4, DLEU7, RNASEH2B, GUCY1B2, FAM124A, SERPINE3, INTS6, WDFY2, DHRS12, NCRNA00282, CCDC70, ATP7B, ALG11, UTP14C, NEK5, NEK3, THSD1P1, TPTE2P2, THSD1, VPS36, CKAP2, TPTE2P3, HNRNPA1L2, SUGT1, LECT1, MIR759, PCDH8, OLFM4, MIR1297, PRR20B, PRR20C, PRR20D, PRR20E, PRR20A, PCDH17, DIAPH3, TDRD3, MIR3169, PCDH20, OR7E156P, PCDH9, KLHLl, ATXN80S, DACHl, MIR548I4, MZT1, C13orG4, DIS3, PIBF1, KLF5, KLF12, LOC338864, CTAGE11P, TBC1D4, COMMD6, UCHL3, LM07, KCTD12, BTF3P11, CLN5, FBXL3, MYCBP2, SCEL, MIR3665, SLAIN1, EDNRB, POU4F1, RNF219, MIR548A2, RBM26, NDFIP2, SPRY2, SLITRK1, MIR548F1, SLITRK6, LOC642345, SLITRK5, MIR622, LOC144776, MIR17HG, MIR17, MIR18A, MIR19A, MIR20A, MIR19B1, MIR92A1, GPC5, GPC6, DCT, TGDS, GPR180, SOX21, ABCC4, CLDN10, DZIP1, DNAJC3, UGGT2, HS6ST3, OXGR1, MBNL2, RAP2A, IP05, FARP1, RNF113B, MIR3170, STK24, SLC15A1, DOCK9, LOC100289373, UBAC2,

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Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

LOC100289656, LOC646278, APBA2, FAM189A1, NDNL2, TJP1, FAM7A1, FAM7A2, FAM7A3, LOC653075, DKFZP434L187, CHRFAM7A, ARHGAP11B, FAN1, MTMR10, TRPM1, MIR211, KLF13, OTUD7A, CHRNA7, LOC100288615, ARHGAP11A, SCG5, GREMl, FMNl, RYR3, AVEN, CHRM5, C15orf24, PGBD4, C15orf29, TMEM85, SLC12A6, NOP10, C15orf55, LPCAT4, GOLGA8A, MIR1233-1, MIR1233-2, GOLGA8B, GJD2, ACTC1, AQR, ZNF770, LOC723972, ATPBD4, MIR3942, C15orf41, CSNK1A1P1, LOC145845, MEIS2, TMC05A, SPRED1, FAM98B, RASGRP1, C15orf53, C15orf54, THBSl, FSIPl, GPR176, EIF2AK4, SRP14, BMF, BUB IB, PAK6, C15orf56, LOC100131244, PLCB2, C15orf52, PHGRl, DISP2, C15orf23, IVD, BAHDl, CHST14, MRPL42P5, C15orf57, RPUSD2, CASC5, RAD51, FAM82A2, GCHFR, DNAJC17, C15orf62, ZFYVE19, PPP1R14D, SPINT1, RHOV, VPS18, DLL4, CHAC1, INO80, EXD1, CHP, LOC729082, OIP5, NUSAP1, NDUFAF1, RTF1, ITPKA, LTK, RPAP1, TYR03, MGA, MIR626, MAPKBP1, JMJD7, JMJD7-PLA2G4B, PLA2G4B, SPTBN5, MIR4310, EHD4, PLA2G4E, PLA2G4D, PLA2G4F, VPS39, MIR627, TMEM87A, GANC, CAPN3, ZFP106, SNAP23, LRRC57, HAUS2, STARD9, CDANl, TTBK2, UBRl, TMEM62, CCNDBPl, EPB42, TGM5, TGM7, LCMT2, ADAL, ZSCAN29, TUBGCP4, TP53BP1, MAPI A, PPIP5K1, CKMT1B, STRC, CATSPER2, CKMT1A, CATSPER2P1, PDIA3, ELL3, SERF2, SERF2-C150RF63, MIR1282, SERINC4, C15orf63, MFAP1, WDR76, FRMD5, LOC728758, CASC4, CTDSPL2, LOC645212, EIF3J, SPG11, PATL2, B2M, TRIM69, C15orf43, SORD, DUOX2, DUOXA2, DUOXA1, DUOX1, SHF, SLC28A2, GATM, LOC145663, SPATA5L1, C15orf48, MIR147B, SLC30A4, HMGN2P46, PLDN, SQRDL, MIR548A3

5344288

15 q 859 0.00 15q21.3

3 1 CCPG1

7551969

15 q 981 0.00 15q24.3

1 1 HMG20A

8233369

15 q 1006 0.00 15q25.2

8 1 ADAMTSL3

4809675

15 q 1598 0.00 15q21.2

8 1 ATP8B4

4760950

15 q 2798 0.00 15q21.2

2 1 C15orf33

4530321

15 q 5532 0.01 15q21.1

0 1 SEMA6D

7467162

15 q 8813 0.01 15q24.3

6 1 SCAPER

5251907

15 q 14153 0.02 15q21.3

4 1 UNC13C

4619900

15 q 17431 0.02 15q21.1

6 1 SLC24A5

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W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromosize/arm # of

arm start size cytoband gene symbol

some (%) genes

q21.2 OR1A2, OR1A1, OR1D4, OR3A2, OR3A1, OR3A4, OR1E1, OR3A3, OR1E2, SPATA22,

ASPA, TRPV3, TRPV1, SHPK, CTNS, TAX1BP3, TMEM93, P2RX5, ITGAE, GSG2, C17orf85, CAMKK1, P2RX1, ATP2A3, ZZEF1, CYB5D2, ANKFY1, UBE2G1, SPNS3, SPNS2, MYBBP1A, GGT6, SMTNL2, ALOX15, PELP1, ARRB2, MED11, CXCL16, ZMYND15, TM4SF5, VMOl, GLTPD2, PSMB6, PLD2, MINK1, CHRNE, C17orfl07, GP1BA, SLC25A11, RNF167, PFN1, EN03, SPAG7, CAMTA2, INCA1, KIF1C, GPR172B, ZFP3, ZNF232, USP6, ZNF594, LOC100130950, C17orf87, RABEP1, NUP88, RPAIN, C1QBP, DHX33, DERL2, MIS12, LOC728392, NLRP1, WSCD1, AIPL1, FAM64A, PITPNM3, KIAA0753, TXNDC17, MED31, C17orfl00, SLC13A5, XAF1, FBX039, TEKT1, ALOX12P2, ALOX12, RNASEK, RNASEK-C 170RF49, C17orf49, MIR195, MIR497, BCL6B, SLC16A13, SLC16A11, CLECIOA, ASGR2, ASGR1, DLG4, ACADVL, MIR324, DVL2, PHF23, GABARAP, CTDNEP1, C17orf81, CLDN7, SLC2A4, YBX2, EIF5A, GPS2, NEURL4, ACAP1, KCTD11, TMEM95, TNK1, PLSCR3, C17orf61-PLSCR3, C17orf61, NLGN2, SPEM1, C17orf74, TMEM102, FGF11, CHRNB1, ZBTB4, AMAC1L3, POLR2A, TNFSF12, TNFSF12-TNFSF13, TNFSF13, SENP3, EIF4A1, SNORA48, SNORD10, SNORA67, CD68, MPDUl, SOX15, FXR2, SHBG, SAT2, ATP1B2, TP53, WRAP53, EFNB3, DNAH2, RPL29P2, KDM6B, TMEM88, LSMD1, CYB5D1, CHD3, SCARNA21 , LOC284023, KCNAB3, TRAPPC1, CNTROB, GUCY2D, ALOX15B, ALOX12B, MIR4314, ALOXE3, HES7, PERI, VAMP2, TMEM107, MIR3676, C17orf59, AURKB, C17orf44, C17orf68, PFAS, SLC25A35, RANGRF, ARHGEF15, ODF4, LOC100128288, KRBA2, RPL26, RNF222, NDEL1, MYH10, CCDC42, SPDYE4, MFSD6L, PIK3R6, PIK3R5, NTN1, STX8, WDR16, USP43, DHRS7C, GLP2R, RCVRN, GAS7, MYH13, MYH8, MYH4, MYHl, MYH2, MYH3, SCOl, C17orf48, TMEM220, LOC100289255, PIRT, SHISA6, DNAH9, ZNF18, MAP2K4, MIR744, FLJ34690, MYOCD, ARHGAP44, ELAC2, HS3ST3A1, CDRT15P, COX10, CDRT15, HS3ST3B1, MGC12916, CDRT7, PMP22, TEKT3, CDRT4, FAM18B2, CDRT1, TRIM16, ZNF286A, TBC1D26, CDRT15L1, MEIS3P1, ADORA2B, ZSWIM7, TTC19, NCOR1, PIGL, MIR1288, CENPV, UBB, TRPV2, NCRNA00188, SNORD49B, SNORD49A, SNORD65, C17orf76, ZNF287, ZNF624, CCDC144A, LOC162632, FAM106C, KRT16P2, TNFRSF13B, MPRIP, PLD6, FLCN, COP S3, NT5M, MED9, RASD1, PEMT, RAI1, SMCR5, SREBF1, MIR33B, TOM1L2, LRRC48, ATPAF2, C17orf39, DRG2, MY015A, ALKBH5, LLGL1, FLU, SMCR7, TOP3A, SMCR8, SHMT1, EVPLL, LOC339240, LGALS9C, LOC220594, FAM106A, CCDC144B, TBC1D28, ZNF286B, FOX03B, TRIM16L, FBXW10, FAM18B1, PRPSAP2, SLC5A10, FAM83G, GRAP, GRAPL, EPN2, B9D1, MIR1180, MAPK7, MFAP4, RNF112, SLC47A1, ALDH3A2, SLC47A2, ALDH3A1, ULK2, AKAP10, SPECC1, CCDC144C, LGALS9B, KRT16P3, CDRT15L2, CCDC144NL, USP22, DHRS7B, TMEM11, C17orfl03, MAP2K3, KCNJ12, KCNJ18, C17orf51, FAM27L, FLJ36000, MTRNR2L1, WSB l, LOC440419, KSRl, LGALS9, NOS2, C17orfl08, NLK, PYY2, PPY2, FLJ40504, TMEM97, IFT20, TNFAIP1, POLDIP2, TMEM199, SEBOX, VTN, SARMl, SLC46A1, SLC13A2, FOXNl, UNCI 19, PIGS, ALDOC, SPAG5, SGK494, KIAAOIOO, SDF2, SUPT6H, PROCAl, RAB34, RPL23A, SNORD42B, SNORD4A, SNORD42A, SNORD4B, TLCD1, NEK8, TRAF4, C17orf63, ERAL1, MIR451, MIR144, FLOT2, DHRS13, PHF12, SEZ6, PIPOX, MY018A, TIAF1, CRYBA1, NUFIP2, TAOKl, ABHD15, TP53I13, GIT1, ANKRD13B, COR06, SSH2, EFCAB5, CCDC55, MIR423, MIR3184, SLC6A4, BLMH, TMIGD1, CPD, GOSR1, TBC1D29, LRRC37BP1,

W:\DOCS\1877\MOF.155XPCT\APPL\2FB7243.DOC/maj

Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

SH3GL1P2, SUZ12P, CRLF3, ATAD5, C17orf42, ADAP2, RNF135, DPRXP4, NF1, OMG, EVI2B, EVI2A, RAB11FIP4, MIR193A, MIR365-2, C17orf79, UTP6, SUZ12, LRRC37B, SH3GL1P1, RHOTl, ARGFXP2, RHBDL3, C17orf75, MIR632, ZNF207, PSMDl l, CDK5R1, MYOID, TMEM98, SPACA3, ACCN1, AA06, CCL2, CCL7, CCL11, CCL8, CCL13, CCL1, C17orfl02, TMEM132E, CCT6B, ZNF830, LIG3, RFFL, RAD51L3-RFFL, RAD51L3, FNDC8, NLEl, UNC45B, AMACl, SLFN5, SLFNl l, SLFN12, SLFN13, SLFN12L, SLFN14, SNORD7, PEX12, AP2B1, RASLIOB, GAS2L2, C17orf50, MMP28, TAF15, C17orf66, CCL5, RDM1, LYZL6, CCL16, CCL14, CCL14-CCL15, CCL15, CCL23, CCL18, CCL3, CCL4, TBC1D3B, CCL3L3, CCL3L1, CCL4L2, CCL4L1, TBC1D3C, TBC1D3F, TBC1D3H, TBC1D3G, ZNHIT3, MY019, PIGW, GGNBP2, DHRS11, MRM1, LHX1, AATF, MIR2909, ACACA, C17orf78, TADA2A, DUSP14, SYNRG, DDX52, HNF1B, LOC284100, TBC1D3, LOC440434, MRPL45, GPR179, SOCS7, ARHGAP23, SRCIN1, C17orf96, MLLT6, CISD3, PCGF2, PSMB3, PIP4K2B, CWC25, C17orf98, RPL23, SNORA21, LASP1, FBX047, FLJ43826, LOC100131347, PLXDC1, ARL5C, CACNB1, RPL19, STAC2, FBXL20, MED1, CDK12, NEUROD2, PPPIRIB, STARD3, TCAP, PNMT, PGAP3, ERBB2, C17orf37, GRB7, IKZF3, ZPBP2, GSDMB, ORMDL3, LOC728129, GSDMA, PSMD3, CSF3, MED24, SNORD124, THRA, NR1D1, MSL1, CASC3, RAPGEFL1, WIPF2, CDC6, RARA, GJD3, TOP2A, IGFBP4, TNS4, CCR7, SMARCE1, KRT222, KRT24, KRT25, KRT26, KRT27, KRT28, KRT10, TMEM99, KRT12, KRT20, KRT23, KRT39, KRT40, KRTAP3-3, KRTAP3- 2, KRTAP3-1, KRTAP1-5, KRTAP1-3, KRTAPl-1, KRTAP2-1, LOC730755, KRTAP2-4, KRTAP4-7, KRTAP4-8, KRTAP4-9, KRTAP4-11, KRTAP4-12, KRTAP4-5, KRTAP4-4, KRTAP4-3, KRTAP4-2, KRTAP4-1, KRTAP9-1, KRTAP9-2, KRTAP9-3, KRTAP9-8, KRTAP9-4, KRTAP9-9

3830810

17 q 0 0.00 17q21.31

9 1 G6PC

4024544

17 q 1434 0.00 17q21.31

4 1 GJC1

3828557

17 q 1444 0.00 17q21.31 LOC388387

7 1

3738639

17 q 2669 0.00 17q21.2

8 1 DNAJC7

6832735

17 q 4277 0.01 17q24.3

2 1 SLC39A11

3844323

17 q 7674 0.01 17q21.31

1 1 BRCA1

3786134

17 q 9114 0.02 17q21.31

0 1 ATP6V0A1

3672635

17 q 58936 0.10 17q21.2 2 KRT33A, KRT33B

0

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Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

4152154

17 q 188856 0.33 17q21.31 2 KIAA1267, LOC644246

4

BHLHA9, TUSC5, YWHAE, CRK, MYOIC, INPP5K, LOC100306951, PITPNA, SLC43A2,

17 P 1031233 873218 3.93 17pl3.3 25 SCARF1, RILP, PRPF8, TLCD2, C17orf91, MIR22, WDR81, SERPINF2, SERPINF1,

SMYD4, RPA1, RTN4RL1, DPH1, OVCA2, MIR132, MIR212

RPH3AL, C17orf97, FAM101B, VPS53, FAM57A, GEMIN4, DBIL5P, GLOD4, RNMTL1,

17 P 47546 981433 4.42 17pl3.3 13 NXN, TIMM22, ABR, MIR3183

LOC647946, KC6, PIK3C3, RIT2, SYT4, SETBP1, MIR4319, SLC14A2, SLC14A1, SIGLEC15, KIAA1632, PSTPIP2, ATP5A1, HAUS1, C18orf25, RNF165, LOXHD1, ST8SIA5, PIAS2, KATNAL2, TCEB3CL, TCEB3C, TCEB3B, HDHD2, IER3IP1, SMAD2, ZBTB7C, CTIF, SMAD7, DYM, C18orf32, RPL17-C180RF32, MIR1539, RPL17, SNORD58C, U58, SNORD58A, SNORD58B, LIPG, ACAA2, SCARNA17, MY05B, MIR4320, CCDC11, MBD1, CXXC1, SKA1, MAPK4, MRO, ME2, ELAC1, SMAD4, MEX3C, DCC, MBD2, SNORA37, POLI, STARD6, C18orf54, C18orf26, RAB27B, CCDC68, TCF4, TXNL1, WDR7, BOD1P, ST8SIA3, ONECUT2, FECH, NARS, ATP8B 1, NEDD4L,

3365986 18ql2.2- MIR122, ALPK2, MALT1, ZNF532, LOC390858, SEC11C, GRP, RAX, CPLX4, LMAN1,

18 q 42456164 70.88 151

2 q23 CCBE1, PMAIP1, MC4R, CDH20, RNF152, PIGN, KIAA1468, TNFRSF11A, ZCCHC2,

PHLPP1, BCL2, KDSR, VPS4B, SERPINB5, SERPINB12, SERPINB13, SERPINB4, SERPINB3, SERPINB 11, SERPINB7, SERPINB2, SERPINB 10, HMSD, SERPINB8, C18orf20, LOC284294, LOC400654, CDH7, CDH19, DSEL, LOC643542, TMX3, CCDC102B, DOK6, CD226, RTTN, SOCS6, CBLN2, NETOl, LOC400655, FBX015, C18orf55, CYB5A, DKFZP781G0119, FAM69C, CNDP2, CNDP1, LOC400657, ZNF407, ZADH2, TSHZl, C18orf62, ZNF516, LOC284276, ZNF236, MBP, GALRl, SALL3, ATP9B, NFATCl, CTDPl, KCNG2, PQLCl, HSBPILI, TXNL4A, RBFA, ADNP2, LOC100130522, PARD6G

3246071

18 q 1868 0.00 18ql2.2

8 1 FHOD3

3279120

18 q 7691 0.01 18ql2.2

6 1 KIAA1328

19 P 3592564 1082 0.00 19pl3.3 1 PIP5K1C

1969902

19 P 1596 0.01 19pl3.11 ZNF14

4 1

5924927

19 q 2552 0.01 19ql3.42

9 1 VSTM1

5949265

19 q 4399 0.01 19ql3.42

0 1 LILRA3

4153340

19 q 5244 0.01 19ql3.12

5 1 ZFP14

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Chromo- . . size/arm # of

arm start size cytoband gene symbol

some (%) genes

5942119

19 q 13005 0.04 19ql3.42 1 LILRA6

7

5682579

19 q 14552 0.04 19ql3.33 1 SIGLEC14

4

20 P 1511632 20801 0.08 20 l3 1 SIRPB1

RTDR1, GNAZ, RAB36, BCR, FBXW4P1, CES5AP1, ZDHHC8P1, IGLL1, C22orf43, LOC91316, RGL4, ZNF70, VPREB3, C22orfl5, CHCHD10, MMP11, SMARCB1, DERL3, SLC2A11, MIF, GSTT2B, GSTT2, DDTL, DDT, GSTTP1, LOC391322, GSTT1, GSTTP2, CABIN1, SUSD2, GGT5, POM121L9P, SPECC1L, ADORA2A, C22orf45, UPB1, C22orfl3, SNRPD3, GGT1, C22orf36, BCRP3, POM121L10P, PIWIL3, TOP1P2, SGSM1, TMEM211, KIAA1671, CRYBB3, CRYBB2, IGLL3P, LRP5L, CRYBB2P1, ADRBK2, MY018B, MIR1302-1, SEZ6L, ASPHD2, HPS4, SRRD, TFIPl l, TPST2, MIR548J, CRYBBl, CRYBA4, MIAT, MN1, PITPNB, TTC28-AS1, MIR3199-1, MIR3199-2, TTC28, CHEK2, HSCB, CCDC117, XBP1, ZNRF3, C22orf31, KREMEN1, EMID1, RHBDD3, EWSR1, GAS2L1, RASL10A, AP1B1, MIR3653, SNORD125, RFPL1S, RFPL1, NEFH, THOC5, NIPSNAP1, NF2, CABP7, ZMAT5, UQCR10, ASCC2, MTMR3, HORMAD2, LIF, OSM, GATSL3, TBC1D10A, SF3A1, CCDC157, RNF215, SEC14L2, MTFP1, SEC14L3, SDC4P, SEC14L4, LOC730005, GAL3ST1, PES1, TCN2, SLC35E4, DUSP18, OSBP2, MIR3200, C22orf27, MORC2, TUG1, SMTN, SELM, INPP5J, PLA2G3, MIR3928, RNF185, LIMK2, PIK3IP1, PATZ1, DRG1, EIF4ENIF1, SFI1, PISD, PRR14L, DEPDC5, C22orf24, YWHAH, SLC5A1, C22orf42, RFPL2, SLC5A4, RFPL3, RFPL3S, C22orf28, BPIL2, FBX07, SYN3, TIMP3, LARGE, ISX, HMGXB4, TOMl, MIR3909, HMOXl, MCM5, RASD2, MB, APOL6, APOL5,

2157964 22ql l.22- RBFOX2, APOL3, APOL4, APOL2, APOL1, MYH9, TXN2, FOXRED2, EIF3D, CACNG2,

22 q 27991419 73.28 402 IFT27, PVALB, NCF4, CSF2RB, C22orf33, TST, MPST, KCTD17, TMPRSS6, IL2RB,

9 ql3.33 C1QTNF6, SSTR3, RAC2, CYTH4, ELFN2, MFNG, CARDIO, CDC42EP1, LGALS2, GGAl,

SH3BP1, PDXP, LGALS1, NOL12, TRIOBP, H1F0, GCAT, GALR3, ANKRD54, MIR658, MIR659, EIF3L, MIC ALL 1, C22orf23, POLR2F, SOX10, PICKl, SLC16A8, BAIAP2L2, PLA2G6, MAFF, TMEM184B, CSNK1E, LOC400927, KCNJ4, KDELR3, DDX17, DMC1, LOC646851, CBY1, TOMM22, JOSD1, GTPBP1, SUN2, DNAL4, NPTXR, CBX6, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, APOBEC3H, CBX7, PDGFB, RPL3, SNORD83B, SNORD83A, RNU86, SNORD43, SYNGR1, TAB1, MGAT3, SMCR7L, ATF4, RPS19BP1, CACNA1I, ENTHD1, GRAP2, FAM83F, TNRC6B, ADSL, SGSM3, MKL1, MCHR1, SLC25A17, ST13, XPNPEP3, DNAJB7, RBX1, MIR1281, EP300, L3MBTL2, CHADL, RANGAP1, ZC3H7B, TEF, TOB2, PHF5A, AC02, POLR3H, CSDC2, PMM1, PPPDE2, XRCC6, NHP2L1, C22orf46, MEI1, CCDC134, SREBF2, MIR33A, TNFRSF13C, CENPM, LOC339674, SEPT3, WBP2NL, NAGA, FAM109B, C22orG2, NDUFA6, LOC100132273, CYP2D6, CYP2D7P1, TCF20, LOC388906, NFAM1, SERHL, RRP7A, SERHL2, RRP7B, POLDIP3, RNU12, CYB5R3, ATP5L2, A4GALT, ARFGAP3, PACSIN2, TTLL1, BIK, MCAT, TSPO, TTLL12, SCUBE1, MPPEDl, EFCAB6, SULT4A1, PNPLA5, PNPLA3, SAMM50, PARVB, PARVG, KIAA1644, LDOCIL, NCRNA00207, PRR5, PRR5-ARHGAP8, ARHGAP8, PHF21B, NUP50, C22orf9, MIR1249, UPK3A, FAM118A, SMC1B, RIBC2, FBLN1, ATXN10, WNT7B, LOC730668,

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Table 4: Genes with significant correlation between copy number and gene expression

Correlation

Gene Symbol Location p-value qFDR

Coefficient

AARS Chrl6q 0.4619 <0.0001 <0.0001

AATF Chrl7q 0.3449 <0.0001 <0.0001

ABCB8 Chr7q 0.3092 <0.0001 <0.0001

ABCC4 Chrl3q 0.2712 <0.0001 <0.0001

ABCC5 Chr3q 0.3705 <0.0001 <0.0001

ABCE1 Chr4q 0.6457 <0.0001 <0.0001

ABCF2 Chr7q 0.6552 <0.0001 <0.0001

ABCF3 Chr3q 0.5184 <0.0001 <0.0001

ABHD8 Chrl9p 0.3976 <0.0001 <0.0001

ACAA2 Chrl 8q 0.3178 <0.0001 <0.0001

ACACA Chrl7q 0.2391 <0.0001 <0.0001

ACADVL Chrl7p 0.4644 <0.0001 <0.0001

ACAP2 Chr3q 0.5527 <0.0001 <0.0001

ACAT2 Chr6q 0.3644 <0.0001 <0.0001

ACD Chrl6q 0.4438 <0.0001 <0.0001

AC02 Chr22q 0.4073 <0.0001 <0.0001

ACOT8 Chr20q 0.4373 <0.0001 <0.0001

ACP5 Chrl9p 0.214 <0.0001 <0.0001

ACP6 Chrlq 0.2179 <0.0001 <0.0001

ACPP Chr3q 0.189 <0.0001 <0.0001

ACSL1 Chr4q 0.3251 <0.0001 <0.0001

ACTL6A Chr3q 0.5644 <0.0001 <0.0001

ACTN4 Chrl9q 0.52 <0.0001 <0.0001

ACTR3B Chr7q 0.4442 <0.0001 <0.0001

ACTR5 Chr20q 0.4324 <0.0001 <0.0001

ADA Chr20q 0.2801 <0.0001 <0.0001

ADAM28 Chr8p 0.2265 <0.0001 <0.0001

ADAMTS3 Chr4q 0.2091 <0.0001 <0.0001

ADAR Chrlq 0.3479 <0.0001 <0.0001

AD ATI Chrl6q 0.5053 <0.0001 <0.0001

ADCK2 Chr7q 0.5075 <0.0001 <0.0001

ADH5 Chr4q 0.4747 <0.0001 <0.0001

ADIPOR2 Chrl2p 0.6525 <0.0001 <0.0001

ADNP Chr20q 0.4587 <0.0001 <0.0001

ADNP2 Chrl 8q 0.4196 <0.0001 <0.0001

ADRBK2 Chr22q 0.2857 <0.0001 <0.0001

ADRM1 Chr20q 0.448 <0.0001 <0.0001

ADSL Chr22q 0.4728 <0.0001 <0.0001

AFF1 Chr4q 0.359 <0.0001 <0.0001

AGA Chr4q 0.4572 <0.0001 <0.0001

AGGF1 Chr5q 0.5457 <0.0001 <0.0001

AGK Chr7q 0.6475 <0.0001 <0.0001

AGPAT1 Chr6p 0.4683 <0.0001 <0.0001

AGPAT4 Chr6q 0.3856 <0.0001 <0.0001

AGPAT5 Chr8p 0.5659 <0.0001 <0.0001

AHCY Chr20q 0.3404 <0.0001 <0.0001

AHCYL2 Chr7q 0.4234 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

AHI1 Chr6q 0.4554 <0.0001 <0.0001

AIM1 Chr6q 0.3584 <0.0001 <0.0001

AIMP1 Chr4q 0.5422 <0.0001 <0.0001

AKAP10 Chrl7p 0.3294 <0.0001 <0.0001

AKAP11 Chrl3q 0.5966 <0.0001 <0.0001

AKAP12 Chr6q 0.1851 <0.0001 <0.0001

AKAP3 Chrl2p 0.2036 <0.0001 <0.0001

AKAP7 Chr6q 0.3398 <0.0001 <0.0001

AKAP8 Chrl9p 0.605 <0.0001 <0.0001

AKAP8L Chrl9p 0.4093 <0.0001 <0.0001

AKR1B1 Chr7q 0.1769 <0.0001 <0.0001

AKT2 Chrl9q 0.3224 <0.0001 <0.0001

ALDH3A2 Chrl7p 0.3281 <0.0001 <0.0001

ALDH8A1 Chr6q 0.1714 <0.0001 <0.0001

ALG12 Chr22q 0.4343 <0.0001 <0.0001

ALG3 Chr3q 0.5702 <0.0001 <0.0001

ALG5 Chrl3q 0.5157 <0.0001 <0.0001

ALG8 Chrl lq 0.549 <0.0001 <0.0001

AMD1 Chr6q 0.4768 <0.0001 <0.0001

AMFR Chrl6q 0.4191 <0.0001 <0.0001

AMOTL2 Chr3q 0.2451 <0.0001 <0.0001

ANAPC10 Chr4q 0.5973 <0.0001 <0.0001

ANAPC13 Chr3q 0.218 <0.0001 <0.0001

ANKFY1 Chrl7p 0.3135 <0.0001 <0.0001

ANKRA2 Chr5q 0.4791 <0.0001 <0.0001

ANKRD10 Chrl3q 0.4811 <0.0001 <0.0001

ANKRD11 Chrl6q 0.3372 <0.0001 <0.0001

ANKRD17 Chr4q 0.5592 <0.0001 <0.0001

ANKRD27 Chrl9q 0.5348 <0.0001 <0.0001

ANKRD46 Chr8q 0.4272 <0.0001 <0.0001

ANKRD6 Chr6q 0.1939 <0.0001 <0.0001

AN02 Chrl2p 0.3104 <0.0001 <0.0001

ANP32E Chrlq 0.2936 <0.0001 <0.0001

ANXA13 Chr8q 0.178 <0.0001 <0.0001

ANXA3 Chr4q 0.2619 <0.0001 <0.0001

ANXA5 Chr4q 0.3499 <0.0001 <0.0001

AP1AR Chr4q 0.6057 <0.0001 <0.0001

AP1B1 Chr22q 0.5454 <0.0001 <0.0001

AP1G1 Chrl6q 0.5115 <0.0001 <0.0001

AP1M2 Chrl9p 0.5202 <0.0001 <0.0001

AP2B1 Chrl7q 0.4048 <0.0001 <0.0001

AP2M1 Chr3q 0.557 <0.0001 <0.0001

AP3B1 Chr5q 0.4454 <0.0001 <0.0001

AP3M2 Chr8p 0.4095 <0.0001 <0.0001

APH1A Chrlq 0.2978 <0.0001 <0.0001

APLP1 Chrl9q 0.2344 <0.0001 <0.0001

APOBEC3B Chr22q 0.1874 <0.0001 <0.0001

APOBEC3C Chr22q 0.2078 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

APOBEC3F Chr22q 0.2401 <0.0001 <0.0001

APOBEC3G Chr22q 0.2554 <0.0001 <0.0001

APOL1 Chr22q 0.3459 <0.0001 <0.0001

APOL2 Chr22q 0.411 <0.0001 <0.0001

APOL3 Chr22q 0.2675 <0.0001 <0.0001

APOL6 Chr22q 0.3472 <0.0001 <0.0001

APOM Chr6p 0.1936 <0.0001 <0.0001

APRT Chrl6q 0.5262 <0.0001 <0.0001

AQR Chrl5q 0.6553 <0.0001 <0.0001

AREG Chr4q 0.2698 <0.0001 <0.0001

ARFGAP1 Chr20q 0.4174 <0.0001 <0.0001

ARFGAP3 Chr22q 0.5268 <0.0001 <0.0001

ARFGEF1 Chr8q 0.4584 <0.0001 <0.0001

ARFGEF2 Chr20q 0.4457 <0.0001 <0.0001

ARFIP1 Chr4q 0.5941 <0.0001 <0.0001

ARFRP1 Chr20q 0.3209 <0.0001 <0.0001

ARGLU1 Chrl3q 0.5121 <0.0001 <0.0001

ARHGAP11A Chrl5q 0.2363 <0.0001 <0.0001

ARHGAP33 Chrl9q 0.307 <0.0001 <0.0001

ARHGEF10 Chr8p 0.5529 <0.0001 <0.0001

ARHGEF11 Chrlq 0.4231 <0.0001 <0.0001

ARHGEF2 Chrlq 0.4052 <0.0001 <0.0001

ARHGEF5 Chr7q 0.51 <0.0001 <0.0001

ARHGEF7 Chrl3q 0.6847 <0.0001 <0.0001

ARL15 Chr5q 0.2727 <0.0001 <0.0001

ARL2BP Chrl6q 0.5243 <0.0001 <0.0001

ARMC1 Chr8q 0.4766 <0.0001 <0.0001

ARMC6 Chrl9p 0.4769 <0.0001 <0.0001

ARMC8 Chr3q 0.5123 <0.0001 <0.0001

ARNT Chrlq 0.3439 <0.0001 <0.0001

ARNTL2 Chrl2p 0.2835 <0.0001 <0.0001

ARRB2 Chrl7p 0.3072 <0.0001 <0.0001

ARSA Chr22q 0.3024 <0.0001 <0.0001

ASAH1 Chr8p 0.5582 <0.0001 <0.0001

ASAP1 Chr8q 0.4013 <0.0001 <0.0001

ASAP 1 -IT Chr8q 0.1929 <0.0001 <0.0001

ASCC2 Chr22q 0.5655 <0.0001 <0.0001

ASCC3 Chr6q 0.5611 <0.0001 <0.0001

ASF1A Chr6q 0.5883 <0.0001 <0.0001

ASF1B Chrl9p 0.4603 <0.0001 <0.0001

ASH1L Chrlq 0.1813 <0.0001 <0.0001

ASNA1 Chrl9p 0.4948 <0.0001 <0.0001

ASPH Chr8q 0.2332 <0.0001 <0.0001

ASXL1 Chr20q 0.4453 <0.0001 <0.0001

ATAD2 Chr8q 0.4986 <0.0001 <0.0001

ATAD5 Chrl7q 0.1969 <0.0001 <0.0001

ATF4 Chr22q 0.3676 <0.0001 <0.0001

ATF6 Chrlq 0.4663 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

ATF6B Chr6p 0.3333 <0.0001 <0.0001

ATF7IP Chrl2p 0.3739 <0.0001 <0.0001

ATG5 Chr6q 0.6146 <0.0001 <0.0001

ATMIN Chrl6q 0.6514 <0.0001 <0.0001

ATN1 Chrl2p 0.3697 <0.0001 <0.0001

ATP11A Chrl3q 0.2916 <0.0001 <0.0001

ATP 1 IB Chr3q 0.3486 <0.0001 <0.0001

ATP13A1 Chrl9p 0.4966 <0.0001 <0.0001

ATP13A3 Chr3q 0.5146 <0.0001 <0.0001

ATP1B3 Chr3q 0.2494 <0.0001 <0.0001

ATP5A1 Chrl 8q 0.6072 <0.0001 <0.0001

ATP5E Chr20q 0.484 <0.0001 <0.0001

ATP6V0D1 Chrl6q 0.4633 <0.0001 <0.0001

ATP6V0E2 Chr7q 0.4478 <0.0001 <0.0001

ATP6V1B2 Chr8p 0.4713 <0.0001 <0.0001

ATP6V1C1 Chr8q 0.5859 <0.0001 <0.0001

ATP6V1F Chr7q 0.5082 <0.0001 <0.0001

ATP6V1H Chr8q 0.4899 <0.0001 <0.0001

ATP7B Chrl3q 0.2776 <0.0001 <0.0001

ATP8A2 Chrl3q 0.1653 <0.0001 1.00E-04

ATP9A Chr20q 0.3725 <0.0001 <0.0001

ATP9B Chrl 8q 0.5118 <0.0001 <0.0001

ATPAF2 Chrl7p 0.4131 <0.0001 <0.0001

ATR Chr3q 0.4911 <0.0001 <0.0001

ATRN Chr20p 0.5045 <0.0001 <0.0001

ATXN1 Chr6p 0.2275 <0.0001 <0.0001

ATXN10 Chr22q 0.4536 <0.0001 <0.0001

AURKA Chr20q 0.398 <0.0001 <0.0001

AURKB Chrl7p 0.2362 <0.0001 <0.0001

AVEN Chrl5q 0.4614 <0.0001 <0.0001

AZIN1 Chr8q 0.6147 <0.0001 <0.0001

B2M Chrl5q 0.2286 <0.0001 <0.0001

B3GALNT1 Chr3q 0.2928 <0.0001 <0.0001

B4GALT3 Chrlq 0.4241 <0.0001 <0.0001

B4GALT5 Chr20q 0.3738 <0.0001 <0.0001

BABAM1 Chrl9p 0.6165 <0.0001 <0.0001

BACH 2 Chr6q 0.3155 <0.0001 <0.0001

BAG6 Chr6p 0.5952 <0.0001 <0.0001

BAHD1 Chrl5q 0.342 <0.0001 <0.0001

BANK1 Chr4q 0.2128 <0.0001 <0.0001

BANP Chrl6q 0.359 <0.0001 <0.0001

BBS7 Chr4q 0.2843 <0.0001 <0.0001

BCAS4 Chr20q 0.3379 <0.0001 <0.0001

BCL2 Chrl 8q 0.2084 <0.0001 <0.0001

BCL2L1 Chr20q 0.2521 <0.0001 <0.0001

BCL2L14 Chrl2p 0.2227 <0.0001 <0.0001

BCL9 Chrlq 0.22 <0.0001 <0.0001

BCLAF1 Chr6q 0.3929 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

BCMOl Chrl6q 0.1986 <0.0001 <0.0001

BCR Chr22q 0.5047 <0.0001 <0.0001

BDH1 Chr3q 0.399 <0.0001 <0.0001

BDH2 Chr4q 0.3594 <0.0001 <0.0001

BGLAP Chrlq 0.2624 <0.0001 <0.0001

BHLHE41 Chrl2p 0.2052 <0.0001 <0.0001

BICDl Chrl2p 0.2885 <0.0001 <0.0001

BIK Chr22q 0.2217 <0.0001 <0.0001

BIN3 Chr8p 0.6667 <0.0001 <0.0001

BLCAP Chr20q 0.3476 <0.0001 <0.0001

BLMH Chrl7q 0.4554 <0.0001 <0.0001

BLVRB Chrl9q 0.3552 <0.0001 <0.0001

BMP1 Chr8p 0.3439 <0.0001 <0.0001

BMP2K Chr4q 0.4342 <0.0001 <0.0001

BMP7 Chr20q 0.213 <0.0001 <0.0001

BNIP3L Chr8p 0.5836 <0.0001 <0.0001

BOLA1 Chrlq 0.2615 <0.0001 <0.0001

BOP1 Chr8q 0.6495 <0.0001 <0.0001

BPGM Chr7q 0.4023 <0.0001 <0.0001

BRAF Chr7q 0.3788 <0.0001 <0.0001

BRCA2 Chrl3q 0.364 <0.0001 <0.0001

BRD1 Chr22q 0.4168 <0.0001 <0.0001

BRD4 Chrl9p 0.5353 <0.0001 <0.0001

BRF2 Chr8p 0.5096 <0.0001 <0.0001

BRP44L Chr6q 0.4235 <0.0001 <0.0001

BST2 Chrl9p 0.1986 <0.0001 <0.0001

BTC Chr4q 0.3195 <0.0001 <0.0001

BTF3 Chr5q 0.5007 <0.0001 <0.0001

BUB1B Chrl5q 0.2166 <0.0001 <0.0001

Cl lorf67 Chrl lq 0.4625 <0.0001 <0.0001

CUorfll Chrl2p 0.4928 <0.0001 <0.0001

C12orfi5 Chrl2p 0.1851 <0.0001 <0.0001

C12orf4 Chrl2p 0.5372 <0.0001 <0.0001

C12orf5 Chrl2p 0.4429 <0.0001 <0.0001

C13orfl Chrl3q 0.3951 <0.0001 <0.0001

C13orfl5 Chrl3q 0.202 <0.0001 <0.0001

C13orf23 Chrl3q 0.5443 <0.0001 <0.0001

C13orf27 Chrl3q 0.506 <0.0001 <0.0001

C13orfi4 Chrl3q 0.4106 <0.0001 <0.0001

C15orf24 Chrl5q 0.5746 <0.0001 <0.0001

C15orf29 Chrl5q 0.3772 <0.0001 <0.0001

C16orf57 Chrl6q 0.3723 <0.0001 <0.0001

C16orf61 Chrl6q 0.4661 <0.0001 <0.0001

C16orf7 Chrl6q 0.2716 <0.0001 <0.0001

C16orf80 Chrl6q 0.492 <0.0001 <0.0001

C17orfl08 Chrl7q 0.2128 <0.0001 <0.0001

CI 7ο 9 Chrl7p 0.1908 <0.0001 <0.0001

CI 7orf42 Chrl7q 0.3854 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

CI 7orf48 Chrl7p 0.368 <0.0001 <0.0001

CI 7orf63 Chrl7q 0.4661 <0.0001 <0.0001

CI 7orf75 Chrl7q 0.2984 <0.0001 <0.0001

CI 7ονβ1 Chrl7p 0.2249 <0.0001 <0.0001

CI 7ονβ5 Chrl7p 0.4401 <0.0001 <0.0001

C18orf25 Chrl 8q 0.4242 <0.0001 <0.0001

C19orf2 Chrl9q 0.5609 <0.0001 <0.0001

C19orf40 Chrl9q 0.3101 <0.0001 <0.0001

C19orf42 Chrl9p 0.5739 <0.0001 <0.0001

C19orf50 Chrl9p 0.6062 <0.0001 <0.0001

C19orf53 Chrl9p 0.5636 <0.0001 <0.0001

C19orf56 Chrl9p 0.5699 <0.0001 <0.0001

C19orf57 Chrl9p 0.3667 <0.0001 <0.0001

C19orf60 Chrl9p 0.41 <0.0001 <0.0001

C19orf66 Chrl9p 0.4162 <0.0001 <0.0001

Clorf56 Chrlq 0.2594 <0.0001 <0.0001

Clorf77 Chrlq 0.314 <0.0001 <0.0001

C1QBP Chrl7p 0.4791 <0.0001 <0.0001

C1RL Chrl2p 0.2799 <0.0001 <0.0001

C20orfll Chr20q 0.4635 <0.0001 <0.0001

C20orflll Chr20q 0.4252 <0.0001 <0.0001

C20orf20 Chr20q 0.5314 <0.0001 <0.0001

C20orf24 Chr20q 0.3478 <0.0001 <0.0001

C20orf27 Chr20p 0.4156 <0.0001 <0.0001

C20orf29 Chr20p 0.4113 <0.0001 <0.0001

C20orf4 Chr20q 0.5289 <0.0001 <0.0001

C20orf43 Chr20q 0.5479 <0.0001 <0.0001

C22orf28 Chr22q 0.6209 <0.0001 <0.0001

C22orf46 Chr22q 0.1866 <0.0001 <0.0001

C4orf27 Chr4q 0.4985 <0.0001 <0.0001

C4orf29 Chr4q 0.3127 <0.0001 <0.0001

C4orf41 Chr4q 0.6588 <0.0001 <0.0001

C4orf43 Chr4q 0.5388 <0.0001 <0.0001

C5orf44 Chr5q 0.3835 <0.0001 <0.0001

C6orfl20 Chr6q 0.5876 <0.0001 <0.0001

C6orfl24 Chr6q 0.2034 <0.0001 <0.0001

C6orf211 Chr6q 0.46 <0.0001 <0.0001

C6orf26 Chr6p 0.2344 <0.0001 <0.0001

C6orf47 Chr6p 0.3802 <0.0001 <0.0001

C6orf48 Chr6p 0.2824 <0.0001 <0.0001

C7orf49 Chr7q 0.4512 <0.0001 <0.0001

C8orfl3 Chr8q 0.5673 <0.0001 <0.0001

C8orf41 Chr8p 0.5889 <0.0001 <0.0001

C8orf44 Chr8q 0.2471 <0.0001 <0.0001

C8orf51 Chr8q 0.3607 <0.0001 <0.0001

C8orf55 Chr8q 0.5902 <0.0001 <0.0001

C8orfi4 Chr8q 0.2263 <0.0001 <0.0001

CA2 Chr8q 0.2057 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

CAS Chr8q 0.2072 <0.0001 <0.0001

CAB39L Chrl3q 0.1703 <0.0001 <0.0001

CABIN1 Chr22q 0.52 <0.0001 <0.0001

CACNA1A Chrl9p 0.4293 <0.0001 <0.0001

CALR Chrl9p 0.4227 <0.0001 <0.0001

CALU Chr7q 0.2851 <0.0001 <0.0001

CAMTA2 Chrl7p 0.3765 <0.0001 <0.0001

CAPN3 Chrl5q 0.2384 <0.0001 <0.0001

CAPN5 Chrl lq 0.327 <0.0001 <0.0001

CAPNS1 Chrl9q 0.5079 <0.0001 <0.0001

CAPRIN2 Chrl2p 0.3512 <0.0001 <0.0001

CARD10 Chr22q 0.28 <0.0001 <0.0001

CAKKD Chrl3q 0.7139 <0.0001 <0.0001

CARM1 Chrl9p 0.613 <0.0001 <0.0001

CARS2 Chrl3q 0.5911 <0.0001 <0.0001

CASC1 Chrl2p 0.3348 <0.0001 <0.0001

CASC3 Chrl7q 0.4183 <0.0001 <0.0001

CASP2 Chr7q 0.2678 <0.0001 <0.0001

CASP3 Chr4q 0.5403 <0.0001 <0.0001

CASP6 Chr4q 0.4481 <0.0001 <0.0001

CASP8AP2 Chr6q 0.6294 <0.0001 <0.0001

CAST Chr5q 0.5568 <0.0001 <0.0001

CBFA2T2 Chr20q 0.4499 <0.0001 <0.0001

CBFB Chrl6q 0.5611 <0.0001 <0.0001

CBR4 Chr4q 0.4776 <0.0001 <0.0001

CBX6 Chr22q 0.2621 <0.0001 <0.0001

CBX7 Chr22q 0.3636 <0.0001 <0.0001

CBY1 Chr22q 0.4007 <0.0001 <0.0001

CC2D1A Chrl9p 0.513 <0.0001 <0.0001

CCDC109B Chr4q 0.3906 <0.0001 <0.0001

CCDC130 Chrl9p 0.6303 <0.0001 <0.0001

CCDC25 Chr8p 0.5875 <0.0001 <0.0001

CCDC28A Chr6q 0.4722 <0.0001 <0.0001

CCDC68 Chrl 8q 0.2303 <0.0001 <0.0001

CCDC90A Chr6p 0.526 <0.0001 <0.0001

CCDC91 Chrl2p 0.4547 <0.0001 <0.0001

CCL11 Chrl7q 0.1853 <0.0001 <0.0001

CCNA2 Chr4q 0.3178 <0.0001 <0.0001

CCNB1 Chr5q 0.253 <0.0001 <0.0001

CCNC Chr6q 0.5992 <0.0001 <0.0001

CCNE1 Chrl9q 0.5179 <0.0001 <0.0001

CCNE2 Chr8q 0.2902 <0.0001 <0.0001

CCNG2 Chr4q 0.4489 <0.0001 <0.0001

CCNH Chr5q 0.5195 <0.0001 <0.0001

CCNI Chr4q 0.419 <0.0001 <0.0001

CCNL1 Chr3q 0.3298 <0.0001 <0.0001

CCNO Chr5q 0.1808 <0.0001 <0.0001

CCR7 Chrl7q 0.1857 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

CCT3 Chrlq 0.4266 <0.0001 <0.0001

CD164 Chr6q 0.5646 <0.0001 <0.0001

CD83 Chr6p 0.2457 <0.0001 <0.0001

CD9 Chrl2p 0.3511 <0.0001 <0.0001

CD97 Chrl9p 0.247 <0.0001 <0.0001

CDADC1 Chrl3q 0.2327 <0.0001 <0.0001

CDC 16 Chrl3q 0.6866 <0.0001 <0.0001

CDC25B Chr20p 0.1951 <0.0001 <0.0001

CDC37 Chrl9p 0.574 <0.0001 <0.0001

CDC40 Chr6q 0.6916 <0.0001 <0.0001

CDC42EP1 Chr22q 0.3071 <0.0001 <0.0001

CDC42SE1 Chrlq 0.1947 <0.0001 <0.0001

CDC6 Chrl7q 0.2488 <0.0001 <0.0001

CDCA3 Chrl2p 0.4058 <0.0001 <0.0001

CDH1 Chrl6q 0.361 <0.0001 <0.0001

CDH3 Chrl6q 0.1794 <0.0001 <0.0001

CDK10 Chrl6q 0.3511 <0.0001 <0.0001

CDK12 Chrl7q 0.4196 <0.0001 <0.0001

CDK19 Chr6q 0.6173 <0.0001 <0.0001

CDK5 Chr7q 0.5275 <0.0001 <0.0001

CDK5RAP1 Chr20q 0.4556 <0.0001 <0.0001

CDK7 Chr5q 0.469 <0.0001 <0.0001

CDK8 Chrl3q 0.5222 <0.0001 <0.0001

CDKN1B Chrl2p 0.3696 <0.0001 <0.0001

CDKN2AIP Chr4q 0.6029 <0.0001 <0.0001

CDKN2D Chrl9p 0.2916 <0.0001 <0.0001

CDS1 Chr4q 0.4064 <0.0001 <0.0001

CDT1 Chrl6q 0.1682 <0.0001 <0.0001

CDV3 Chr3q 0.3856 <0.0001 <0.0001

CEBPA Chrl9q 0.176 <0.0001 <0.0001

CEBPB Chr20q 0.2489 <0.0001 <0.0001

CEBPG Chrl9q 0.4618 <0.0001 <0.0001

CELSR1 Chr22q 0.3299 <0.0001 <0.0001

CENPB Chr20p 0.2563 <0.0001 <0.0001

CENPE Chr4q 0.231 <0.0001 <0.0001

CENPJ Chrl3q 0.4084 <0.0001 <0.0001

CENPM Chr22q 0.2539 <0.0001 <0.0001

CENPN Chrl6q 0.2834 <0.0001 <0.0001

CENPT Chrl6q 0.3344 <0.0001 <0.0001

CEP250 Chr20q 0.2632 <0.0001 <0.0001

CEP63 Chr3q 0.4185 <0.0001 <0.0001

CEP70 Chr3q 0.3122 <0.0001 <0.0001

CEKK Chr22q 0.3222 <0.0001 <0.0001

CES2 Chrl6q 0.4714 <0.0001 <0.0001

CETN3 Chr5q 0.4357 <0.0001 <0.0001

CFDP1 Chrl6q 0.4743 <0.0001 <0.0001

CFI Chr4q 0.2586 <0.0001 <0.0001

CHCHD3 Chr7q 0.4911 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

CHCHD7 Chr8q 0.4487 <0.0001 <0.0001

CHD1 Chr5q 0.6029 <0.0001 <0.0001

CHD1L Chrlq 0.3067 <0.0001 <0.0001

CHD3 Chrl7p 0.3144 <0.0001 <0.0001

CHD4 Chrl2p 0.304 <0.0001 <0.0001

CHD7 Chr8q 0.3419 <0.0001 <0.0001

CHEK2 Chr22q 0.2965 <0.0001 <0.0001

CHERP Chrl9p 0.5588 <0.0001 <0.0001

CHKB Chr22q 0.3477 <0.0001 <0.0001

CHMP1A Chrl6q 0.5452 <0.0001 <0.0001

CHMP7 Chr8p 0.6451 <0.0001 <0.0001

CHP Chrl5q 0.5027 <0.0001 <0.0001

CHPF2 Chr7q 0.5259 <0.0001 <0.0001

CHRNB1 Chrl7p 0.4379 <0.0001 <0.0001

CHST4 Chrl6q 0.195 <0.0001 <0.0001

CIAPIN1 Chrl6q 0.5191 <0.0001 <0.0001

CITED2 Chr6q 0.3427 <0.0001 <0.0001

CKAP2 Chrl3q 0.4677 <0.0001 <0.0001

CKLF Chrl6q 0.4366 <0.0001 <0.0001

CKMT2 Chr5q 0.2002 <0.0001 <0.0001

CKS1B Chrlq 0.2033 <0.0001 <0.0001

CLCN2 Chr3q 0.2944 <0.0001 <0.0001

CLCN3 Chr4q 0.5822 <0.0001 <0.0001

CLDN7 Chrl7p 0.2993 <0.0001 <0.0001

CLGN Chr4q 0.2901 <0.0001 <0.0001

CLIC1 Chr6p 0.4104 <0.0001 <0.0001

CLIP3 Chrl9q 0.3014 <0.0001 <0.0001

CLK2 Chrlq 0.442 <0.0001 <0.0001

CLN5 Chrl3q 0.4799 <0.0001 <0.0001

CLN8 Chr8p 0.5411 <0.0001 <0.0001

CLNS1A Chrl lq 0.5216 <0.0001 <0.0001

CLSTN3 Chrl2p 0.3028 <0.0001 <0.0001

CLU Chr8p 0.237 <0.0001 <0.0001

CMAS Chrl2p 0.4467 <0.0001 <0.0001

CNDP2 Chrl 8q 0.4528 <0.0001 <0.0001

CNOT1 Chrl6q 0.5126 <0.0001 <0.0001

CNOT4 Chr7q 0.5341 <0.0001 <0.0001

CNOT7 Chr8p 0.6982 <0.0001 <0.0001

COG4 Chrl6q 0.4878 <0.0001 <0.0001

COL4A2 Chrl3q 0.2366 <0.0001 <0.0001

COL4A3BP Chr5q 0.3034 <0.0001 <0.0001

COL9A3 Chr20q 0.2194 <0.0001 <0.0001

COPA Chrlq 0.3618 <0.0001 <0.0001

COPB2 Chr3q 0.4688 <0.0001 <0.0001

COPE Chrl9p 0.476 <0.0001 <0.0001

COPS3 Chrl7p 0.3156 <0.0001 <0.0001

COPS4 Chr4q 0.4707 <0.0001 <0.0001

COPS5 Chr8q 0.5598 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

COPS7A Chrl2p 0.4816 <0.0001 <0.0001

COQ2 Chr4q 0.4046 <0.0001 <0.0001

COQ3 Chr6q 0.4972 <0.0001 <0.0001

COQ9 Chrl6q 0.4997 <0.0001 <0.0001

COX10 Chrl7p 0.3853 <0.0001 <0.0001

COX4I1 Chrl6q 0.5402 <0.0001 <0.0001

COX4NB Chrl6q 0.5425 <0.0001 <0.0001

COX6B1 Chrl9q 0.5543 <0.0001 <0.0001

COX6C Chr8q 0.6505 <0.0001 <0.0001

COX7C Chr5q 0.5379 <0.0001 <0.0001

CP Chr3q 0.1767 <0.0001 <0.0001

CPD Chrl7q 0.1968 <0.0001 <0.0001

CPE Chr4q 0.1857 <0.0001 <0.0001

CPNE1 Chr20q 0.4919 <0.0001 <0.0001

CPNE3 Chr8q 0.5044 <0.0001 <0.0001

CPSF1 Chr8q 0.5715 <0.0001 <0.0001

CREB3L2 Chr7q 0.2582 <0.0001 <0.0001

CKEBL2 Chrl2p 0.427 <0.0001 <0.0001

CKELD2 Chr22q 0.5261 <0.0001 <0.0001

CKLF3 Chrl7q 0.4253 <0.0001 <0.0001

CRTC1 Chrl9p 0.4058 <0.0001 <0.0001

CRYBB2P1 Chr22q 0.2516 <0.0001 <0.0001

CRYL1 Chrl3q 0.2283 <0.0001 <0.0001

CSDA Chrl2p 0.4359 <0.0001 <0.0001

CSE1L Chr20q 0.5525 <0.0001 <0.0001

CSF2RB Chr22q 0.2506 <0.0001 <0.0001

CSGALNACTl Chr8p 0.334 <0.0001 <0.0001

CSNK1E Chr22q 0.4182 <0.0001 <0.0001

CSNK2A1 Chr20p 0.6334 <0.0001 <0.0001

CSNK2A2 Chrl6q 0.4165 <0.0001 <0.0001

CSNK2B Chr6p 0.6262 <0.0001 <0.0001

CSPP1 Chr8q 0.4515 <0.0001 <0.0001

CSTF1 Chr20q 0.5106 <0.0001 <0.0001

CTCF Chrl6q 0.4371 <0.0001 <0.0001

CTDNEP1 Chrl7p 0.463 <0.0001 <0.0001

CTDP1 Chrl 8q 0.3984 <0.0001 <0.0001

CTIF Chrl 8q 0.3249 <0.0001 <0.0001

CTNNBL1 Chr20q 0.513 <0.0001 <0.0001

CTNS Chrl7p 0.5192 <0.0001 <0.0001

CTSA Chr20q 0.2807 <0.0001 <0.0001

CTSB Chr8p 0.4214 <0.0001 <0.0001

CTSO Chr4q 0.5636 <0.0001 <0.0001

CUL1 Chr7q 0.6023 <0.0001 <0.0001

CUL4A Chrl3q 0.6859 <0.0001 <0.0001

CWC25 Chrl7q 0.4247 <0.0001 <0.0001

CX3CL1 Chrl6q 0.2146 <0.0001 <0.0001

CXCL10 Chr4q 0.3034 <0.0001 <0.0001

CXCL11 Chr4q 0.274 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

CXCL9 Chr4q 0.1916 <0.0001 <0.0001

CXXC1 Chrl 8q 0.6706 <0.0001 <0.0001

CYB5A Chrl 8q 0.4454 <0.0001 <0.0001

CYB5B Chrl6q 0.4584 <0.0001 <0.0001

CYB5R3 Chr22q 0.5343 <0.0001 <0.0001

CYBA Chrl6q 0.3409 <0.0001 <0.0001

CYC1 Chr8q 0.5986 <0.0001 <0.0001

CYFIP1 Chrl5q 0.5566 <0.0001 <0.0001

CYHR1 Chr8q 0.5652 <0.0001 <0.0001

DACH1 Chrl3q 0.1947 <0.0001 <0.0001

DAP3 Chrlq 0.3884 <0.0001 <0.0001

DAPP1 Chr4q 0.2043 <0.0001 <0.0001

DBNDD1 Chrl6q 0.3126 <0.0001 <0.0001

DBR1 Chr3q 0.2861 <0.0001 <0.0001

DCAF13 Chr8q 0.2134 <0.0001 <0.0001

DCAF15 Chrl9p 0.5484 <0.0001 <0.0001

DCAF8 Chrlq 0.3908 <0.0001 <0.0001

DCLK1 Chrl3q 0.2099 <0.0001 <0.0001

DCTD Chr4q 0.5704 <0.0001 <0.0001

DCTN6 Chr8p 0.6624 <0.0001 <0.0001

DCUN1D1 Chr3q 0.5656 <0.0001 <0.0001

DCUN1D2 Chrl3q 0.5001 <0.0001 <0.0001

DDA1 Chrl9p 0.4629 <0.0001 <0.0001

DDAH2 Chr6p 0.4276 <0.0001 <0.0001

DDRGK1 Chr20p 0.3355 <0.0001 <0.0001

DDT Chr22q 0.5934 <0.0001 <0.0001

DDX11 Chrl2p 0.3596 <0.0001 <0.0001

DDX17 Chr22q 0.3549 <0.0001 <0.0001

DDX19A Chrl6q 0.5416 <0.0001 <0.0001

DDX27 Chr20q 0.4758 <0.0001 <0.0001

DDX28 Chrl6q 0.4311 <0.0001 <0.0001

DDX39A Chrl9p 0.5791 <0.0001 <0.0001

DDX39B Chr6p 0.3962 <0.0001 <0.0001

DDX47 Chrl2p 0.601 <0.0001 <0.0001

DDX49 Chrl9p 0.5969 <0.0001 <0.0001

DDX52 Chrl7q 0.4754 <0.0001 <0.0001

DDX60 Chr4q 0.3312 <0.0001 <0.0001

DECR1 Chr8q 0.3877 <0.0001 <0.0001

DEDD Chrlq 0.403 <0.0001 <0.0001

DEF8 Chrl6q 0.3803 <0.0001 <0.0001

DEFB1 Chr8p 0.1657 <0.0001 1.00E-04

DENND3 Chr8q 0.255 <0.0001 <0.0001

DENND4B Chrlq 0.3401 <0.0001 <0.0001

DENND5B Chrl2p 0.2385 <0.0001 <0.0001

DEPDC5 Chr22q 0.3877 <0.0001 <0.0001

DEPTOR Chr8q 0.3214 <0.0001 <0.0001

DERA Chrl2p 0.4628 <0.0001 <0.0001

DERL1 Chr8q 0.6801 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

DERL2 Chrl7p 0.5006 <0.0001 <0.0001

DGAT1 Chr8q 0.63 <0.0001 <0.0001

DHFR Chr5q 0.3519 <0.0001 <0.0001

DHODH Chrl6q 0.2738 <0.0001 <0.0001

DHPS Chrl9p 0.5488 <0.0001 <0.0001

DHRS11 Chrl7q 0.2244 <0.0001 <0.0001

DHRS12 Chrl3q 0.3888 <0.0001 <0.0001

DHRS7B Chrl7p 0.2373 <0.0001 <0.0001

DHX29 Chr5q 0.5573 <0.0001 <0.0001

DHX35 Chr20q 0.522 <0.0001 <0.0001

DHX38 Chrl6q 0.4367 <0.0001 <0.0001

DIDOl Chr20q 0.3328 <0.0001 <0.0001

DIMT1L Chr5q 0.4511 <0.0001 <0.0001

DIS3 Chrl3q 0.5239 <0.0001 <0.0001

DLC1 Chr8p 0.1943 <0.0001 <0.0001

DLEU1 Chrl3q 0.3349 <0.0001 <0.0001

DLEU2 Chrl3q 0.1944 <0.0001 <0.0001

DLG1 Chr3q 0.6742 <0.0001 <0.0001

DLGAP4 Chr20q 0.383 <0.0001 <0.0001

DLL3 Chrl9q 0.3029 <0.0001 <0.0001

DNAJBl Chrl9p 0.512 <0.0001 <0.0001

DNAJB14 Chr4q 0.5658 <0.0001 <0.0001

DNAJB6 Chr7q 0.4905 <0.0001 <0.0001

DNAJC13 Chr3q 0.4803 <0.0001 <0.0001

DNAJC15 Chrl3q 0.1793 <0.0001 <0.0001

DNAJC17 Chrl5q 0.3813 <0.0001 <0.0001

DNAJC3 Chrl3q 0.4759 <0.0001 <0.0001

DNAL4 Chr22q 0.4045 <0.0001 <0.0001

DNASE2 Chrl9p 0.4439 <0.0001 <0.0001

DNM1L Chrl2p 0.4038 <0.0001 <0.0001

DNM2 Chrl9p 0.5525 <0.0001 <0.0001

DNMT1 Chrl9p 0.4671 <0.0001 <0.0001

DNMT3B Chr20q 0.259 <0.0001 <0.0001

DOCK6 Chrl9p 0.3791 <0.0001 <0.0001

DOCK9 Chrl3q 0.3754 <0.0001 <0.0001

DOK4 Chrl6q 0.2997 <0.0001 <0.0001

DOM3Z Chr6p 0.4571 <0.0001 <0.0001

DPMI Chr20q 0.477 <0.0001 <0.0001

DPM3 Chrlq 0.1999 <0.0001 <0.0001

DPY19L4 Chr8q 0.4351 <0.0001 <0.0001

DPYSL2 Chr8p 0.3641 <0.0001 <0.0001

DRG1 Chr22q 0.6343 <0.0001 <0.0001

DRG2 Chrl7p 0.3331 <0.0001 <0.0001

DSCC1 Chr8q 0.4489 <0.0001 <0.0001

DSE Chr6q 0.2381 <0.0001 <0.0001

DSN1 Chr20q 0.3822 <0.0001 <0.0001

DSTNP2 Chrl2p 0.1843 <0.0001 <0.0001

DUS2L Chrl6q 0.4259 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

DUSP12 Chrlq 0.3756 <0.0001 <0.0001

DUSP14 Chrl7q 0.382 <0.0001 <0.0001

DUSP4 Chr8p 0.2214 <0.0001 <0.0001

DVL2 Chrl7p 0.5142 <0.0001 <0.0001

DVL3 Chr3q 0.5462 <0.0001 <0.0001

DYM Chrl 8q 0.2211 <0.0001 <0.0001

DYNC1LI2 Chrl6q 0.4859 <0.0001 <0.0001

DYNLKB1 Chr20q 0.4663 <0.0001 <0.0001

DYNLT1 Chr6q 0.542 <0.0001 <0.0001

DYRK1B Chrl9q 0.2773 <0.0001 <0.0001

DYRK4 Chrl2p 0.5228 <0.0001 <0.0001

DZIP1 Chrl3q 0.2796 <0.0001 <0.0001

E2F1 Chr20q 0.2641 <0.0001 <0.0001

E2F4 Chrl6q 0.2622 <0.0001 <0.0001

E2F5 Chr8q 0.355 <0.0001 <0.0001

EBAG9 Chr8q 0.7124 <0.0001 <0.0001

ECH1 Chrl9q 0.5774 <0.0001 <0.0001

ECHDC1 Chr6q 0.537 <0.0001 <0.0001

ECSIT Chrl9p 0.5399 <0.0001 <0.0001

ECT2 Chr3q 0.5011 <0.0001 <0.0001

EDC4 Chrl6q 0.4352 <0.0001 <0.0001

EDEM2 Chr20q 0.418 <0.0001 <0.0001

EDNRA Chr4q 0.228 <0.0001 <0.0001

EEF1D Chr8q 0.5553 <0.0001 <0.0001

EFHA1 Chrl3q 0.6179 <0.0001 <0.0001

EFNA1 Chrlq 0.203 <0.0001 <0.0001

EFNA3 Chrlq 0.2427 <0.0001 <0.0001

EFNA4 Chrlq 0.2401 <0.0001 <0.0001

EFNB2 Chrl3q 0.3861 <0.0001 <0.0001

EFNB3 Chrl7p 0.2272 <0.0001 <0.0001

EFR3A Chr8q 0.6146 <0.0001 <0.0001

EHD4 Chrl5q 0.4402 <0.0001 <0.0001

EHHADH Chr3q 0.3418 <0.0001 <0.0001

EHMT2 Chr6p 0.5652 <0.0001 <0.0001

EIF2B5 Chr3q 0.5671 <0.0001 <0.0001

EIF2C2 Chr8q 0.5696 <0.0001 <0.0001

EIF2S2 Chr20q 0.4058 <0.0001 <0.0001

EIF3D Chr22q 0.4336 <0.0001 <0.0001

EIF3E Chr8q 0.5294 <0.0001 <0.0001

EIF3G Chrl9p 0.5852 <0.0001 <0.0001

EIF3H Chr8q 0.5936 <0.0001 <0.0001

EIF3J Chrl5q 0.6286 <0.0001 <0.0001

EIF3K Chrl9q 0.5546 <0.0001 <0.0001

EIF3L Chr22q 0.423 <0.0001 <0.0001

EIF4A1 Chrl7p 0.4765 <0.0001 <0.0001

EIF4A2 Chr3q 0.3811 <0.0001 <0.0001

EIF4E Chr4q 0.5149 <0.0001 <0.0001

EIF4ENIF1 Chr22q 0.59 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

EIF4G1 Chr3q 0.4719 <0.0001 <0.0001

EIF5A Chrl7p 0.3975 <0.0001 <0.0001

EIF5A2 Chr3q 0.2075 <0.0001 <0.0001

EIF6 Chr20q 0.3821 <0.0001 <0.0001

ELAC1 Chrl 8q 0.3321 <0.0001 <0.0001

EL AC 2 Chrl7p 0.3446 <0.0001 <0.0001

ELF1 Chrl3q 0.5919 <0.0001 <0.0001

ELF2 Chr4q 0.5671 <0.0001 <0.0001

ELL Chrl9p 0.3286 <0.0001 <0.0001

ELL2 Chr5q 0.1712 <0.0001 <0.0001

ELM02 Chr20q 0.5534 <0.0001 <0.0001

ELM03 Chrl6q 0.394 <0.0001 <0.0001

ELOVL6 Chr4q 0.3053 <0.0001 <0.0001

ELP3 Chr8p 0.5416 <0.0001 <0.0001

EMG1 Chrl2p 0.5385 <0.0001 <0.0001

ENC1 Chr5q 0.2045 <0.0001 <0.0001

EN02 Chrl2p 0.2828 <0.0001 <0.0001

EN03 Chrl7p 0.1903 <0.0001 <0.0001

ENOPH1 Chr4q 0.5631 <0.0001 <0.0001

ENOX1 Chrl3q 0.1862 <0.0001 <0.0001

ENPEP Chr4q 0.185 <0.0001 <0.0001

ENPP1 Chr6q 0.1911 <0.0001 <0.0001

ENSA Chrlq 0.4234 <0.0001 <0.0001

ENTPD4 Chr8p 0.6046 <0.0001 <0.0001

ENY2 Chr8q 0.5903 <0.0001 <0.0001

EP300 Chr22q 0.3232 <0.0001 <0.0001

EPB41L1 Chr20q 0.185 <0.0001 <0.0001

EPB41L2 Chr6q 0.268 <0.0001 <0.0001

EPB49 Chr8p 0.3504 <0.0001 <0.0001

EPHA1 Chr7q 0.4344 <0.0001 <0.0001

EPHB3 Chr3q 0.3191 <0.0001 <0.0001

EPHB6 Chr7q 0.3347 <0.0001 <0.0001

EPHX2 Chr8p 0.5066 <0.0001 <0.0001

EPM2A Chr6q 0.3632 <0.0001 <0.0001

EPN2 Chrl7p 0.3657 <0.0001 <0.0001

EPOR Chrl9p 0.3587 <0.0001 <0.0001

EPPK1 Chr8q 0.3434 <0.0001 <0.0001

EPS15L1 Chrl9p 0.4869 <0.0001 <0.0001

EPS8 Chrl2p 0.1994 <0.0001 <0.0001

ERAL1 Chrl7q 0.4568 <0.0001 <0.0001

ERAP1 Chr5q 0.4791 <0.0001 <0.0001

ERAP2 Chr5q 0.2217 <0.0001 <0.0001

ERBB2 Chrl7q 0.3963 <0.0001 <0.0001

ERBB2IP Chr5q 0.5111 <0.0001 <0.0001

ERC1 Chrl2p 0.5116 <0.0001 <0.0001

ERCC5 Chrl3q 0.5123 <0.0001 <0.0001

ERCC8 Chr5q 0.3312 <0.0001 <0.0001

ERGIC2 Chrl2p 0.4145 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

ERGIC3 Chr20q 0.4536 <0.0001 <0.0001

ERICH1 Chr8p 0.1985 <0.0001 <0.0001

ERLIN2 Chr8p 0.4963 <0.0001 <0.0001

ESD Chrl3q 0.6589 <0.0001 <0.0001

ESR1 Chr6q 0.1684 <0.0001 1.00E-04

ESRP1 Chr8q 0.583 <0.0001 <0.0001

ESRP2 Chrl6q 0.3633 <0.0001 <0.0001

ETFDH Chr4q 0.4412 <0.0001 <0.0001

ETNK1 Chrl2p 0.4352 <0.0001 <0.0001

ETV6 Chrl2p 0.3377 <0.0001 <0.0001

EVI2A Chrl7q 0.1749 <0.0001 <0.0001

EWSR1 Chr22q 0.2923 <0.0001 <0.0001

EXOSC4 Chr8q 0.6509 <0.0001 <0.0001

EXOSC8 Chrl3q 0.4829 <0.0001 <0.0001

EXOSC9 Chr4q 0.4666 <0.0001 <0.0001

EXT1 Chr8q 0.4741 <0.0001 <0.0001

EXTL3 Chr8p 0.4047 <0.0001 <0.0001

EZH2 Chr7q 0.3574 <0.0001 <0.0001

EZR Chr6q 0.5028 <0.0001 <0.0001

F10 Chrl3q 0.1987 <0.0001 <0.0001

FUR Chrlq 0.2586 <0.0001 <0.0001

F2R Chr5q 0.2392 <0.0001 <0.0001

F2RL1 Chr5q 0.294 <0.0001 <0.0001

FAIM Chr3q 0.3183 <0.0001 <0.0001

FAM115A Chr7q 0.2192 <0.0001 <0.0001

FAM118A Chr22q 0.2153 <0.0001 <0.0001

FAM131A Chr3q 0.5027 <0.0001 <0.0001

FAM13A Chr4q 0.2987 <0.0001 <0.0001

FAM149A Chr4q 0.2415 <0.0001 <0.0001

FAM160B2 Chr8p 0.5373 <0.0001 <0.0001

F AM 164 A Chr8q 0.2961 <0.0001 <0.0001

FAM172A Chr5q 0.5272 <0.0001 <0.0001

FAM184A Chr6q 0.2812 <0.0001 <0.0001

FAM189B Chrlq 0.3715 <0.0001 <0.0001

FAM18B1 Chrl7p 0.3734 <0.0001 <0.0001

FAM192A Chrl6q 0.5083 <0.0001 <0.0001

FAM32A Chrl9p 0.5955 <0.0001 <0.0001

FAM38A Chrl6q 0.186 <0.0001 <0.0001

FAM48A Chrl3q 0.5951 <0.0001 <0.0001

FAM49B Chr8q 0.5404 <0.0001 <0.0001

FAM60A Chrl2p 0.3936 <0.0001 <0.0001

FAM63A Chrlq 0.2222 <0.0001 <0.0001

FAM64A Chrl7p 0.2503 <0.0001 <0.0001

FAM65A Chrl6q 0.4441 <0.0001 <0.0001

FAM82A2 Chrl5q 0.5989 <0.0001 <0.0001

FAM82B Chr8q 0.4813 <0.0001 <0.0001

FAM86B1 Chr8p 0.1762 <0.0001 <0.0001

FAM90A1 Chrl2p 0.4142 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

FAM96B Chrl6q 0.5365 <0.0001 <0.0001

FAN1 Chrl5q 0.5254 <0.0001 <0.0001

FANCA Chrl6q 0.2324 <0.0001 <0.0001

FARP1 Chrl3q 0.5648 <0.0001 <0.0001

FARSA Chrl9p 0.6027 <0.0001 <0.0001

FASTK Chr7q 0.6162 <0.0001 <0.0001

FASTKD5 Chr20p 0.4914 <0.0001 <0.0001

FAT1 Chr4q 0.2951 <0.0001 <0.0001

FBI Chrl9q 0.536 <0.0001 <0.0001

FBLN1 Chr22q 0.186 <0.0001 <0.0001

FBXL12 Chrl9p 0.6686 <0.0001 <0.0001

FBXL14 Chrl2p 0.6397 <0.0001 <0.0001

FBXL4 Chr6q 0.5876 <0.0001 <0.0001

FBXL6 Chr8q 0.5281 <0.0001 <0.0001

FBX031 Chrl6q 0.3533 <0.0001 <0.0001

FBX05 Chr6q 0.4162 <0.0001 <0.0001

FBX07 Chr22q 0.6677 <0.0001 <0.0001

FBXW4P1 Chr22q 0.196 <0.0001 <0.0001

FBXW7 Chr4q 0.3558 <0.0001 <0.0001

FCHOl Chrl9p 0.2918 <0.0001 <0.0001

FDFT1 Chr8p 0.5497 <0.0001 <0.0001

FDPS Chrlq 0.1841 <0.0001 <0.0001

FECH Chrl 8q 0.5676 <0.0001 <0.0001

FGF12 Chr3q 0.1785 <0.0001 <0.0001

FGF9 Chrl3q 0.2505 <0.0001 <0.0001

FGFRIOP Chr6q 0.5684 <0.0001 <0.0001

FHOD1 Chrl6q 0.2478 <0.0001 <0.0001

FIG4 Chr6q 0.6349 <0.0001 <0.0001

FKBP1A Chr20p 0.479 <0.0001 <0.0001

FKBP4 Chrl2p 0.5991 <0.0001 <0.0001

FKBP8 Chrl9p 0.4521 <0.0001 <0.0001

FKBPL Chr6p 0.4958 <0.0001 <0.0001

FLAD1 Chrlq 0.3663 <0.0001 <0.0001

FLCN Chrl7p 0.2018 <0.0001 <0.0001

FLU Chrl7p 0.4327 <0.0001 <0.0001

FLOT2 Chrl7q 0.4146 <0.0001 <0.0001

FNDC3A Chrl3q 0.5577 <0.0001 <0.0001

FNDC3B Chr3q 0.3804 <0.0001 <0.0001

FNTA Chr8p 0.4589 <0.0001 <0.0001

FOXJ2 Chrl2p 0.3441 <0.0001 <0.0001

FOXM1 Chrl2p 0.3956 <0.0001 <0.0001

FOXOl Chrl3q 0.4523 <0.0001 <0.0001

FOX03 Chr6q 0.5382 <0.0001 <0.0001

FOXRED2 Chr22q 0.2107 <0.0001 <0.0001

FRG1 Chr4q 0.541 <0.0001 <0.0001

FRK Chr6q 0.4088 <0.0001 <0.0001

FRY Chrl3q 0.2748 <0.0001 <0.0001

FXR1 Chr3q 0.532 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

FXR2 Chrl7p 0.4538 <0.0001 <0.0001

FXYD1 Chrl9q 0.2057 <0.0001 <0.0001

FXYD3 Chrl9q 0.1992 <0.0001 <0.0001

FXYD7 Chrl9q 0.1935 <0.0001 <0.0001

FYN Chr6q 0.2763 <0.0001 <0.0001

FZD3 Chr8p 0.4385 <0.0001 <0.0001

FZD6 Chr8q 0.3918 <0.0001 <0.0001

G3BP2 Chr4q 0.5735 <0.0001 <0.0001

GAB1 Chr4q 0.2851 <0.0001 <0.0001

GAB2 Chrl lq 0.3766 <0.0001 <0.0001

GABARAP Chrl7p 0.5133 <0.0001 <0.0001

GABARAPL1 Chrl2p 0.2994 <0.0001 <0.0001

GABARAPL2 Chrl6q 0.5358 <0.0001 <0.0001

GADD45GIP1 Chrl9p 0.5352 <0.0001 <0.0001

GALNS Chrl6q 0.377 <0.0001 <0.0001

G ALNT 11 Chr7q 0.5617 <0.0001 <0.0001

GALNT7 Chr4q 0.4663 <0.0001 <0.0001

GALNT8 Chrl2p 0.1739 <0.0001 <0.0001

GAPDH Chrl2p 0.4911 <0.0001 <0.0001

GAR1 Chr4q 0.4956 <0.0001 <0.0001

GAS2L1 Chr22q 0.4669 <0.0001 <0.0001

GAS6 Chrl3q 0.3141 <0.0001 <0.0001

GAS7 Chrl7p 0.2428 <0.0001 <0.0001

GAS8 Chrl6q 0.3694 <0.0001 <0.0001

GATAD2A Chrl9p 0.5069 <0.0001 <0.0001

GBAP1 Chrlq 0.3227 <0.0001 <0.0001

GCAT Chr22q 0.3079 <0.0001 <0.0001

GCDH Chrl9p 0.5693 <0.0001 <0.0001

GCHFR Chrl5q 0.1847 <0.0001 <0.0001

GCNT2 Chr6p 0.1722 <0.0001 <0.0001

GDF15 Chrl9p 0.182 <0.0001 <0.0001

GFOD2 Chrl6q 0.4517 <0.0001 <0.0001

GGA1 Chr22q 0.4676 <0.0001 <0.0001

GGH Chr8q 0.2593 <0.0001 <0.0001

GGNBP2 Chrl7q 0.443 <0.0001 <0.0001

GGT1 Chr22q 0.2477 <0.0001 <0.0001

GGT5 Chr22q 0.2767 <0.0001 <0.0001

GINS2 Chrl6q 0.2021 <0.0001 <0.0001

GINS3 Chrl6q 0.2853 <0.0001 <0.0001

GINS4 Chr8p 0.24 <0.0001 <0.0001

GIPCl Chrl9p 0.5091 <0.0001 <0.0001

GJA1 Chr6q 0.294 <0.0001 <0.0001

GLG1 Chrl6q 0.5272 <0.0001 <0.0001

GLRB Chr4q 0.271 <0.0001 <0.0001

GLRX Chr5q 0.166 <0.0001 1.00E-04

GLT25D1 Chrl9p 0.4504 <0.0001 <0.0001

GMEB2 Chr20q 0.4077 <0.0001 <0.0001

GMIP Chrl9p 0.3425 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

GMPR Chr6p 0.2417 <0.0001 <0.0001

GMPS Chr3q 0.4704 <0.0001 <0.0001

GNAS Chr20q 0.4733 <0.0001 <0.0001

GNAZ Chr22q 0.2359 <0.0001 <0.0001

GNRH1 Chr8p 0.2413 <0.0001 <0.0001

GOLGA 7 Chr8p 0.3998 <0.0001 <0.0001

GOLGA8A Chrl5q 0.1975 <0.0001 <0.0001

GOLGA8B Chrl5q 0.2468 <0.0001 <0.0001

GOLIM4 Chr3q 0.2841 <0.0001 <0.0001

GOLPH3L Chrlq 0.383 <0.0001 <0.0001

GOLT1B Chrl2p 0.3816 <0.0001 <0.0001

GON4L Chrlq 0.3635 <0.0001 <0.0001

GOSR1 Chrl7q 0.4657 <0.0001 <0.0001

GOT2 Chrl6q 0.5558 <0.0001 <0.0001

GPAA1 Chr8q 0.6865 <0.0001 <0.0001

GPATCH1 Chrl9q 0.5421 <0.0001 <0.0001

GPC5 Chrl3q 0.1699 <0.0001 <0.0001

GPI Chrl9q 0.4389 <0.0001 <0.0001

GPR126 Chr6q 0.1647 <0.0001 1.00E-04

GPR172A Chr8q 0.6508 <0.0001 <0.0001

GPR19 Chrl2p 0.3479 <0.0001 <0.0001

GPR56 Chrl6q 0.3755 <0.0001 <0.0001

GPS2 Chrl7p 0.5236 <0.0001 <0.0001

GPT Chr8q 0.2303 <0.0001 <0.0001

GRAMD4 Chr22q 0.36 <0.0001 <0.0001

GRB7 Chrl7q 0.3213 <0.0001 <0.0001

GRHL2 Chr8q 0.3554 <0.0001 <0.0001

GRINA Chr8q 0.5955 <0.0001 <0.0001

GSDMB Chrl7q 0.1986 <0.0001 <0.0001

GSDMD Chr8q 0.6047 <0.0001 <0.0001

GSR Chr8p 0.4522 <0.0001 <0.0001

GSS Chr20q 0.258 <0.0001 <0.0001

GSTK1 Chr7q 0.5749 <0.0001 <0.0001

GSTT1 Chr22q 0.7096 <0.0001 <0.0001

GSTT2 Chr22q 0.1658 <0.0001 1.00E-04

GTF2E2 Chr8p 0.6764 <0.0001 <0.0001

GTF2F2 Chrl3q 0.5724 <0.0001 <0.0001

GTF2H5 Chr6q 0.5314 <0.0001 <0.0001

GTF3A Chrl3q 0.5648 <0.0001 <0.0001

GTPBP1 Chr22q 0.3067 <0.0001 <0.0001

GTPBP3 Chrl9p 0.485 <0.0001 <0.0001

GTSE1 Chr22q 0.2797 <0.0001 <0.0001

GUCY1A3 Chr4q 0.2947 <0.0001 <0.0001

GUCY1B2 Chrl3q 0.2298 <0.0001 <0.0001

GUCY1B3 Chr4q 0.3651 <0.0001 <0.0001

GYG1 Chr3q 0.3483 <0.0001 <0.0001

H2AFJ Chrl2p 0.1999 <0.0001 <0.0001

H2AFZ Chr4q 0.3817 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

HADH Chr4q 0.4034 <0.0001 <0.0001

HAUS5 Chrl9q 0.3978 <0.0001 <0.0001

HAX1 Chrlq 0.4164 <0.0001 <0.0001

HBS1L Chr6q 0.6717 <0.0001 <0.0001

HDAC2 Chr6q 0.5867 <0.0001 <0.0001

HDDC2 Chr6q 0.5347 <0.0001 <0.0001

HDGF Chrlq 0.4055 <0.0001 <0.0001

HEBP1 Chrl2p 0.418 <0.0001 <0.0001

HEBP2 Chr6q 0.5081 <0.0001 <0.0001

HECA Chr6q 0.5392 <0.0001 <0.0001

HERC2 Chrl5q 0.5101 <0.0001 <0.0001

HERC3 Chr4q 0.1751 <0.0001 <0.0001

HERC5 Chr4q 0.2442 <0.0001 <0.0001

HERC6 Chr4q 0.2566 <0.0001 <0.0001

HERPUD1 Chrl6q 0.5038 <0.0001 <0.0001

HEXB Chr5q 0.45 <0.0001 <0.0001

HEY2 Chr6q 0.1954 <0.0001 <0.0001

HGSNAT Chr8p 0.3347 <0.0001 <0.0001

HIPK2 Chr7q 0.2964 <0.0001 <0.0001

HIVEP1 Chr6p 0.4124 <0.0001 <0.0001

HIVEP2 Chr6q 0.362 <0.0001 <0.0001

HLTF Chr3q 0.4849 <0.0001 <0.0001

HMBOX1 Chr8p 0.509 <0.0001 <0.0001

HMGB1 Chrl3q 0.5749 <0.0001 <0.0001

HMGB2 Chr4q 0.3572 <0.0001 <0.0001

HMGCR Chr5q 0.3982 <0.0001 <0.0001

HMGXB4 Chr22q 0.5626 <0.0001 <0.0001

HMOX1 Chr22q 0.2729 <0.0001 <0.0001

HNRNPD Chr4q 0.364 <0.0001 <0.0001

HNRNPL Chrl9q 0.3598 <0.0001 <0.0001

HNRPDL Chr4q 0.2078 <0.0001 <0.0001

HOMER1 Chr5q 0.2873 <0.0001 <0.0001

HOMER3 Chrl9p 0.2606 <0.0001 <0.0001

HOOK2 Chrl9p 0.4848 <0.0001 <0.0001

HPN Chrl9q 0.1899 <0.0001 <0.0001

HPS4 Chr22q 0.5675 <0.0001 <0.0001

HPSE Chr4q 0.1794 <0.0001 <0.0001

HRASLS Chr3q 0.401 <0.0001 <0.0001

HRSP12 Chr8q 0.4804 <0.0001 <0.0001

HSBP1 Chrl6q 0.5543 <0.0001 <0.0001

HSD11B2 Chrl6q 0.1841 <0.0001 <0.0001

HSD17B11 Chr4q 0.2413 <0.0001 <0.0001

HSD17B7 Chrlq 0.2058 <0.0001 <0.0001

HSF1 Chr8q 0.7013 <0.0001 <0.0001

HSF2 Chr6q 0.5726 <0.0001 <0.0001

HSPA1L Chr6p 0.1782 <0.0001 <0.0001

HSPA4L Chr4q 0.2203 <0.0001 <0.0001

HSPB6 Chrl9q 0.215 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

HSPH1 Chrl3q 0.4666 <0.0001 <0.0001

ICAM1 Chrl9p 0.1813 <0.0001 <0.0001

ICAM3 Chrl9p 0.4418 <0.0001 <0.0001

ICAM5 Chrl9p 0.1772 <0.0001 <0.0001

IDH3B Chr20p 0.4961 <0.0001 <0.0001

IER2 Chrl9p 0.425 <0.0001 <0.0001

IER3IP1 Chrl 8q 0.5332 <0.0001 <0.0001

IFNGR1 Chr6q 0.3686 <0.0001 <0.0001

IFT20 Chrl7q 0.419 <0.0001 <0.0001

IFT27 Chr22q 0.2794 <0.0001 <0.0001

IFT52 Chr20q 0.5429 <0.0001 <0.0001

IFT88 Chrl3q 0.3929 <0.0001 <0.0001

IGF2BP2 Chr3q 0.2178 <0.0001 <0.0001

IGF2R Chr6q 0.571 <0.0001 <0.0001

IGFBP4 Chrl7q 0.3091 <0.0001 <0.0001

IGLL3P Chr22q 0.1858 <0.0001 <0.0001

IKBKB Chr8p 0.428 <0.0001 <0.0001

IL12A Chr3q 0.2025 <0.0001 <0.0001

III 5 Chr4q 0.3995 <0.0001 <0.0001

ILIRAP Chr3q 0.3068 <0.0001 <0.0001

IL27RA Chrl9p 0.2779 <0.0001 <0.0001

IL2RB Chr22q 0.1933 <0.0001 <0.0001

IL6ST Chr5q 0.4896 <0.0001 <0.0001

ILF2 Chrlq 0.3322 <0.0001 <0.0001

ILF3 Chrl9p 0.457 <0.0001 <0.0001

ILVBL Chrl9p 0.5091 <0.0001 <0.0001

IMPA1 Chr8q 0.4294 <0.0001 <0.0001

IMPAD1 Chr8q 0.394 <0.0001 <0.0001

ING1 Chrl3q 0.6201 <0.0001 <0.0001

ING2 Chr4q 0.4712 <0.0001 <0.0001

ING4 Chrl2p 0.4296 <0.0001 <0.0001

INPP4B Chr4q 0.3856 <0.0001 <0.0001

INPP5J Chr22q 0.262 <0.0001 <0.0001

INSIG1 Chr7q 0.333 <0.0001 <0.0001

INTS12 Chr4q 0.5044 <0.0001 <0.0001

INTS3 Chrlq 0.1979 <0.0001 <0.0001

INTS6 Chrl3q 0.5829 <0.0001 <0.0001

INTS8 Chr8q 0.6066 <0.0001 <0.0001

INTS9 Chr8p 0.6736 <0.0001 <0.0001

IP05 Chrl3q 0.6486 <0.0001 <0.0001

IPOS Chrl2p 0.2435 <0.0001 <0.0001

IPW Chrl5q 0.2072 <0.0001 <0.0001

IQCG Chr3q 0.2155 <0.0001 <0.0001

IQSEC3 Chrl2p 0.2449 <0.0001 <0.0001

IRF2 Chr4q 0.504 <0.0001 <0.0001

IRF5 Chr7q 0.1783 <0.0001 <0.0001

IRS2 Chrl3q 0.4844 <0.0001 <0.0001

ISG20L2 Chrlq 0.46 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

ISYNA1 Chrl9p 0.4197 <0.0001 <0.0001

ITCH Chr20q 0.2973 <0.0001 <0.0001

ITFG2 Chrl2p 0.3804 <0.0001 <0.0001

ITGA2 Chr5q 0.1898 <0.0001 <0.0001

ITGAE Chrl7p 0.3992 <0.0001 <0.0001

ITM2B Chrl3q 0.4627 <0.0001 <0.0001

ITPA Chr20p 0.4528 <0.0001 <0.0001

ITPR2 Chrl2p 0.261 <0.0001 <0.0001

IVD Chrl5q 0.5418 <0.0001 <0.0001

JARID2 Chr6p 0.5044 <0.0001 <0.0001

JHDM1D Chr7q 0.3155 <0.0001 <0.0001

JOSD1 Chr22q 0.493 <0.0001 <0.0001

JRK Chr8q 0.3548 <0.0001 <0.0001

JTB Chrlq 0.3523 <0.0001 <0.0001

JUNB Chrl9p 0.2803 <0.0001 <0.0001

JUND Chrl9p 0.4545 <0.0001 <0.0001

KANK2 Chrl9p 0.414 <0.0001 <0.0001

KARS Chrl6q 0.5892 <0.0001 <0.0001

KATNA1 Chr6q 0.5768 <0.0001 <0.0001

KATNB1 Chrl6q 0.4498 <0.0001 <0.0001

KBTBD11 Chr8p 0.1752 <0.0001 <0.0001

KCNB2 Chr8q 0.1655 <0.0001 1.00E-04

KCNG1 Chr20q 0.3416 <0.0001 <0.0001

KCNH2 Chr7q 0.2067 <0.0001 <0.0001

KCNMB3 Chr3q 0.334 <0.0001 <0.0001

KCNN3 Chrlq 0.1887 <0.0001 <0.0001

KCNS1 Chr20q 0.1931 <0.0001 <0.0001

KCTD12 Chrl3q 0.264 <0.0001 <0.0001

KCTD14 Chrl lq 0.2671 <0.0001 <0.0001

KCTD15 Chrl9q 0.1928 <0.0001 <0.0001

KCTD9 Chr8p 0.5953 <0.0001 <0.0001

KDELC1 Chrl3q 0.4151 <0.0001 <0.0001

KDELR3 Chr22q 0.3215 <0.0001 <0.0001

KDM5A Chrl2p 0.5949 <0.0001 <0.0001

KDM6B Chrl7p 0.3465 <0.0001 <0.0001

KDSR Chrl 8q 0.6781 <0.0001 <0.0001

KEAP1 Chrl9p 0.6473 <0.0001 <0.0001

KHDRBS3 Chr8q 0.2482 <0.0001 <0.0001

KIAA0100 Chrl7q 0.5177 <0.0001 <0.0001

KIAA0146 Chr8q 0.314 <0.0001 <0.0001

KIAA0174 Chrl6q 0.6032 <0.0001 <0.0001

KIAA0182 Chrl6q 0.4242 <0.0001 <0.0001

KIAA0196 Chr8q 0.6256 <0.0001 <0.0001

KIAA0226 Chr3q 0.5622 <0.0001 <0.0001

KIAA0355 Chrl9q 0.4918 <0.0001 <0.0001

KIAA0528 Chrl2p 0.5195 <0.0001 <0.0001

KIAA0564 Chrl3q 0.5885 <0.0001 <0.0001

KIAA0664 Chrl7p 0.299 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

KIAA0753 Chrl7p 0.3524 <0.0001 <0.0001

KIAA0776 Chr6q 0.6389 <0.0001 <0.0001

KIAA0907 Chrlq 0.3407 <0.0001 <0.0001

KIAA0922 Chr4q 0.293 <0.0001 <0.0001

KIAA1109 Chr4q 0.4828 <0.0001 <0.0001

KIAA1467 Chrl2p 0.3422 <0.0001 <0.0001

KIAA1609 Chrl6q 0.4801 <0.0001 <0.0001

KIAA1644 Chr22q 0.1792 <0.0001 <0.0001

KIAA1704 Chrl3q 0.4745 <0.0001 <0.0001

KIF13B Chr8p 0.4579 <0.0001 <0.0001

KIF1C Chrl7p 0.2837 <0.0001 <0.0001

KIF2A Chr5q 0.4117 <0.0001 <0.0001

KIF3B Chr20q 0.3392 <0.0001 <0.0001

KLF1 Chrl9p 0.1729 <0.0001 <0.0001

KLF10 Chr8q 0.3744 <0.0001 <0.0001

KLF12 Chrl3q 0.4141 <0.0001 <0.0001

KLF13 Chrl5q 0.3322 <0.0001 <0.0001

KLF5 Chrl3q 0.4469 <0.0001 <0.0001

KLHDC10 Chr7q 0.3959 <0.0001 <0.0001

KLHDC4 Chrl6q 0.3758 <0.0001 <0.0001

KLHL2 Chr4q 0.3952 <0.0001 <0.0001

KLHL24 Chr3q 0.485 <0.0001 <0.0001

KLHL26 Chrl9p 0.525 <0.0001 <0.0001

KLHL36 Chrl6q 0.3179 <0.0001 <0.0001

KLRAP1 Chrl2p 0.1827 <0.0001 <0.0001

KLKF1 Chrl2p 0.3205 <0.0001 <0.0001

KLRG1 Chrl2p 0.2491 <0.0001 <0.0001

KPNA3 Chrl3q 0.62 <0.0001 <0.0001

KPNA4 Chr3q 0.3352 <0.0001 <0.0001

KPNA5 Chr6q 0.3726 <0.0001 <0.0001

KRAS Chrl2p 0.6034 <0.0001 <0.0001

KRI1 Chrl9p 0.5895 <0.0001 <0.0001

KRT10 Chrl7q 0.3625 <0.0001 <0.0001

L3MBTL1 Chr20q 0.2534 <0.0001 <0.0001

LACTB2 Chr8q 0.3328 <0.0001 <0.0001

LAMA5 Chr20q 0.3184 <0.0001 <0.0001

LAMP1 Chrl3q 0.5399 <0.0001 <0.0001

LAMP3 Chr3q 0.2087 <0.0001 <0.0001

LAPTM4B Chr8q 0.5908 <0.0001 <0.0001

LARGE Chr22q 0.2917 <0.0001 <0.0001

LARP7 Chr4q 0.451 <0.0001 <0.0001

LASP1 Chrl7q 0.4256 <0.0001 <0.0001

LASS2 Chrlq 0.2874 <0.0001 <0.0001

LCMT2 Chrl5q 0.5582 <0.0001 <0.0001

LDHB Chrl2p 0.4754 <0.0001 <0.0001

LDLR Chrl9p 0.2458 <0.0001 <0.0001

LEPROTL1 Chr8p 0.6381 <0.0001 <0.0001

LGALS1 Chr22q 0.3035 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

LHFP Chrl3q 0.2077 <0.0001 <0.0001

LHFPL2 Chr5q 0.2289 <0.0001 <0.0001

LIF Chr22q 0.2516 <0.0001 <0.0001

LIG3 Chrl7q 0.3132 <0.0001 <0.0001

LIG4 Chrl3q 0.2464 <0.0001 <0.0001

LIMK2 Chr22q 0.5815 <0.0001 <0.0001

LIN 37 Chrl9q 0.5696 <0.0001 <0.0001

LIPG Chrl 8q 0.2441 <0.0001 <0.0001

LMAN1 Chrl 8q 0.3529 <0.0001 <0.0001

LMF2 Chr22q 0.4487 <0.0001 <0.0001

LM07 Chrl3q 0.3697 <0.0001 <0.0001

LNPEP Chr5q 0.3639 <0.0001 <0.0001

LOCI 00129361 Chrl2p 0.5527 <0.0001 <0.0001

LOC100134713 Chr7q 0.421 <0.0001 <0.0001

LOCI 00170939 Chr5q 0.2138 <0.0001 <0.0001

LOCI 00289410 Chrl3q 0.2214 <0.0001 <0.0001

LOCI 55060 Chr7q 0.4553 <0.0001 <0.0001

LOC220594 Chrl7p 0.1688 <0.0001 <0.0001

LOC388796 Chr20q 0.2112 <0.0001 <0.0001

LOC440434 Chrl7q 0.2006 <0.0001 <0.0001

LOC729991 Chrl9p 0.3522 <0.0001 <0.0001

LOC91316 Chr22q 0.2165 <0.0001 <0.0001

LPAR2 Chrl9p 0.4331 <0.0001 <0.0001

LPCAT3 Chrl2p 0.5614 <0.0001 <0.0001

LPCAT4 Chrl5q 0.4685 <0.0001 <0.0001

LPHN1 Chrl9p 0.2751 <0.0001 <0.0001

LPP Chr3q 0.4005 <0.0001 <0.0001

LPPR2 Chrl9p 0.2794 <0.0001 <0.0001

LRBA Chr4q 0.5369 <0.0001 <0.0001

LRCH3 Chr3q 0.5211 <0.0001 <0.0001

LRFN3 Chrl9q 0.357 <0.0001 <0.0001

LRP12 Chr8q 0.3029 <0.0001 <0.0001

LRP2BP Chr4q 0.3148 <0.0001 <0.0001

LRP3 Chrl9q 0.2789 <0.0001 <0.0001

LRP5L Chr22q 0.2913 <0.0001 <0.0001

LRP6 Chrl2p 0.5054 <0.0001 <0.0001

LRRC14 Chr8q 0.4561 <0.0001 <0.0001

LRRC23 Chrl2p 0.3769 <0.0001 <0.0001

LRRC6 Chr8q 0.3806 <0.0001 <0.0001

LRRC61 Chr7q 0.3847 <0.0001 <0.0001

LSG1 Chr3q 0.6657 <0.0001 <0.0001

LSM14A Chrl9q 0.5469 <0.0001 <0.0001

LSM14B Chr20q 0.445 <0.0001 <0.0001

LSM2 Chr6p 0.4774 <0.0001 <0.0001

LSM4 Chrl9p 0.4973 <0.0001 <0.0001

LSM6 Chr4q 0.5652 <0.0001 <0.0001

LSR Chrl9q 0.4138 <0.0001 <0.0001

LTBP4 Chrl9q 0.2069 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

LTBR Chrl2p 0.4216 <0.0001 <0.0001

LUC7L2 Chr7q 0.4573 <0.0001 <0.0001

LY6E Chr8q 0.4615 <0.0001 <0.0001

LY6G5C Chr6p 0.1885 <0.0001 <0.0001

LYN Chr8q 0.2316 <0.0001 <0.0001

LYPLA1 Chr8q 0.3653 <0.0001 <0.0001

LYRM2 Chr6q 0.6427 <0.0001 <0.0001

M6PR Chrl2p 0.5859 <0.0001 <0.0001

MAD2L1 Chr4q 0.3642 <0.0001 <0.0001

MAF Chrl6q 0.1694 <0.0001 <0.0001

MAFF Chr22q 0.3535 <0.0001 <0.0001

MAGEF1 Chr3q 0.4946 <0.0001 <0.0001

MAGOHB Chrl2p 0.4889 <0.0001 <0.0001

MAK Chr6p 0.2356 <0.0001 <0.0001

MAK16 Chr8p 0.6691 <0.0001 <0.0001

MALT1 Chrl 8q 0.4562 <0.0001 <0.0001

MAN1A1 Chr6q 0.1789 <0.0001 <0.0001

MAN2B1 Chrl9p 0.3983 <0.0001 <0.0001

MANBA Chr4q 0.3787 <0.0001 <0.0001

MANEA Chr6q 0.5058 <0.0001 <0.0001

MANSC1 Chrl2p 0.3564 <0.0001 <0.0001

MAP1B Chr5q 0.2231 <0.0001 <0.0001

MAP1LC3B Chrl6q 0.6239 <0.0001 <0.0001

MAP1S Chrl9p 0.5157 <0.0001 <0.0001

MAP2K3 Chrl7p 0.2655 <0.0001 <0.0001

MAP2K4 Chrl7p 0.4097 <0.0001 <0.0001

MAP3K1 Chr5q 0.2397 <0.0001 <0.0001

MAP3K13 Chr3q 0.1899 <0.0001 <0.0001

MAP3K4 Chr6q 0.5125 <0.0001 <0.0001

MAP3K5 Chr6q 0.336 <0.0001 <0.0001

MAP3K7 Chr6q 0.5956 <0.0001 <0.0001

MAP4K1 Chrl9q 0.3068 <0.0001 <0.0001

MAP6D1 Chr3q 0.3095 <0.0001 <0.0001

MAP7 Chr6q 0.6255 <0.0001 <0.0001

MAP9 Chr4q 0.4715 <0.0001 <0.0001

MAPK11 Chr22q 0.1779 <0.0001 <0.0001

MAPK7 Chrl7p 0.2955 <0.0001 <0.0001

MAPKBP1 Chrl5q 0.4061 <0.0001 <0.0001

MAPRE1 Chr20q 0.4061 <0.0001 <0.0001

MARCKS Chr6q 0.266 <0.0001 <0.0001

MAST1 Chrl9p 0.2231 <0.0001 <0.0001

MAST3 Chrl9p 0.4565 <0.0001 <0.0001

MAST4 Chr5q 0.2104 <0.0001 <0.0001

MAW 2 Chr8q 0.2897 <0.0001 <0.0001

MAU2 Chrl9p 0.5606 <0.0001 <0.0001

MA YS Chr20p 0.32 <0.0001 <0.0001

MB Chr22q 0.1633 <0.0001 1.00E-04

MBD1 Chrl 8q 0.6503 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

MBD2 Chrl 8q 0.5684 <0.0001 <0.0001

MBNL1 Chr3q 0.3461 <0.0001 <0.0001

MBNL2 Chrl3q 0.5378 <0.0001 <0.0001

MBP Chrl 8q 0.4282 <0.0001 <0.0001

MBTPS1 Chrl6q 0.5079 <0.0001 <0.0001

MC1R Chrl6q 0.1678 <0.0001 <0.0001

MCAT Chr22q 0.3905 <0.0001 <0.0001

MCCC1 Chr3q 0.4982 <0.0001 <0.0001

MCCC2 Chr5q 0.4269 <0.0001 <0.0001

MCF2L Chrl3q 0.2584 <0.0001 <0.0001

MCL1 Chrlq 0.2254 <0.0001 <0.0001

MCM4 Chr8q 0.2814 <0.0001 <0.0001

MCM5 Chr22q 0.3577 <0.0001 <0.0001

MCM9 Chr6q 0.5497 <0.0001 <0.0001

MCPH1 Chr8p 0.3344 <0.0001 <0.0001

MCTP1 Chr5q 0.1679 <0.0001 1.00E-04

MDN1 Chr6q 0.5448 <0.0001 <0.0001

ME2 Chrl 8q 0.4321 <0.0001 <0.0001

MECOM Chr3q 0.286 <0.0001 <0.0001

MED1 Chrl7q 0.3761 <0.0001 <0.0001

MED21 Chrl2p 0.5062 <0.0001 <0.0001

MED23 Chr6q 0.5995 <0.0001 <0.0001

MED24 Chrl7q 0.38 <0.0001 <0.0001

MED4 Chrl3q 0.5222 <0.0001 <0.0001

MED9 Chrl7p 0.2837 <0.0001 <0.0001

MEF2C Chr5q 0.1701 <0.0001 <0.0001

MEF2D Chrlq 0.3098 <0.0001 <0.0001

MEIS2 Chrl5q 0.2329 <0.0001 <0.0001

MEIS3P1 Chrl7p 0.3455 <0.0001 <0.0001

METAP1 Chr4q 0.568 <0.0001 <0.0001

MEX3C Chrl 8q 0.586 <0.0001 <0.0001

MFAP1 Chrl5q 0.5473 <0.0001 <0.0001

MFAP3L Chr4q 0.1926 <0.0001 <0.0001

MFHAS1 Chr8p 0.4546 <0.0001 <0.0001

MFN1 Chr3q 0.5356 <0.0001 <0.0001

MFNG Chr22q 0.2455 <0.0001 <0.0001

MFSD1 Chr3q 0.3033 <0.0001 <0.0001

MGA Chrl5q 0.3607 <0.0001 <0.0001

MGC2889 Chr3q 0.2359 <0.0001 <0.0001

MGST2 Chr4q 0.4789 <0.0001 <0.0001

MICALl Chr6q 0.2987 <0.0001 <0.0001

MICALL1 Chr22q 0.419 <0.0001 <0.0001

MIF Chr22q 0.5178 <0.0001 <0.0001

MINK1 Chrl7p 0.3177 <0.0001 <0.0001

MIPEP Chrl3q 0.5282 <0.0001 <0.0001

MSI 2 Chrl7p 0.4724 <0.0001 <0.0001

MKL1 Chr22q 0.4283 <0.0001 <0.0001

MKLN1 Chr7q 0.3791 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

MKRN1 Chr7q 0.6388 <0.0001 <0.0001

MLF1 Chr3q 0.3595 <0.0001 <0.0001

MLF1IP Chr4q 0.2847 <0.0001 <0.0001

MLF2 Chrl2p 0.6234 <0.0001 <0.0001

MLL4 Chrl9q 0.3779 <0.0001 <0.0001

MLLT4 Chr6q 0.2156 <0.0001 <0.0001

MLYCD Chrl6q 0.477 <0.0001 <0.0001

MMP15 Chrl6q 0.1753 <0.0001 <0.0001

MMP24 Chr20q 0.2293 <0.0001 <0.0001

MN1 Chr22q 0.1927 <0.0001 <0.0001

MNT Chrl7p 0.3635 <0.0001 <0.0001

MNX1 Chr7q 0.2357 <0.0001 <0.0001

MOCS2 Chr5q 0.5717 <0.0001 <0.0001

MOCS3 Chr20q 0.3225 <0.0001 <0.0001

MON1B Chrl6q 0.5206 <0.0001 <0.0001

MORC2 Chr22q 0.2869 <0.0001 <0.0001

MPDU1 Chrl7p 0.3452 <0.0001 <0.0001

MPHOSPH6 Chrl6q 0.5197 <0.0001 <0.0001

MPHOSPH8 Chrl3q 0.5718 <0.0001 <0.0001

MPRIP Chrl7p 0.3257 <0.0001 <0.0001

MPST Chr22q 0.3444 <0.0001 <0.0001

MRAS Chr3q 0.2037 <0.0001 <0.0001

MRP63 Chrl3q 0.4371 <0.0001 <0.0001

MRPL13 Chr8q 0.5403 <0.0001 <0.0001

MRPL15 Chr8q 0.487 <0.0001 <0.0001

MRPL18 Chr6q 0.6017 <0.0001 <0.0001

MRPL24 Chrlq 0.2716 <0.0001 <0.0001

MRPL34 Chrl9p 0.4989 <0.0001 <0.0001

MRPL4 Chrl9p 0.5953 <0.0001 <0.0001

MRPL9 Chrlq 0.4282 <0.0001 <0.0001

MRPS12 Chrl9q 0.5446 <0.0001 <0.0001

MRPS18C Chr4q 0.2901 <0.0001 <0.0001

MRPS22 Chr3q 0.502 <0.0001 <0.0001

MRPS27 Chr5q 0.458 <0.0001 <0.0001

MRPS28 Chr8q 0.4486 <0.0001 <0.0001

MRPS31 Chrl3q 0.683 <0.0001 <0.0001

MRPS33 Chr7q 0.4989 <0.0001 <0.0001

MRPS35 Chrl2p 0.4822 <0.0001 <0.0001

MSH3 Chr5q 0.5298 <0.0001 <0.0001

MSL1 Chrl7q 0.3725 <0.0001 <0.0001

MSL2 Chr3q 0.3431 <0.0001 <0.0001

MSRA Chr8p 0.43 <0.0001 <0.0001

MT1E Chrl6q 0.1644 <0.0001 1.00E-04

MT1X Chrl6q 0.1923 <0.0001 <0.0001

MT2A Chrl6q 0.1952 <0.0001 <0.0001

MTDH Chr8q 0.6719 <0.0001 <0.0001

MTERFD1 Chr8q 0.5966 <0.0001 <0.0001

MTFR1 Chr8q 0.3825 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

MTHFD2L Chr4q 0.4244 <0.0001 <0.0001

MTHFSD Chrl6q 0.4354 <0.0001 <0.0001

MTMR3 Chr22q 0.5415 <0.0001 <0.0001

MTMR6 Chrl3q 0.4877 <0.0001 <0.0001

MTMR9 Chr8p 0.6372 <0.0001 <0.0001

MTRF1 Chrl3q 0.5222 <0.0001 <0.0001

MTSS1 Chr8q 0.1983 <0.0001 <0.0001

MTUS1 Chr8p 0.4115 <0.0001 <0.0001

MTX1 Chrlq 0.4113 <0.0001 <0.0001

MVD Chrl6q 0.1699 <0.0001 <0.0001

MYB Chr6q 0.2285 <0.0001 <0.0001

MYBBP1A Chrl7p 0.3502 <0.0001 <0.0001

MYBL1 Chr8q 0.2934 <0.0001 <0.0001

MYBL2 Chr20q 0.3004 <0.0001 <0.0001

MYC Chr8q 0.2347 <0.0001 <0.0001

MYCBP2 Chrl3q 0.5478 <0.0001 <0.0001

MYH10 Chrl7p 0.2754 <0.0001 <0.0001

MYH9 Chr22q 0.4428 <0.0001 <0.0001

MYLIP Chr6p 0.3906 <0.0001 <0.0001

MYNN Chr3q 0.5063 <0.0001 <0.0001 mow Chrl7q 0.2864 <0.0001 <0.0001

MY07A Chrl lq 0.2286 <0.0001 <0.0001

MY09B Chrl9p 0.5137 <0.0001 <0.0001

MYST3 Chr8p 0.4292 <0.0001 <0.0001

N4BP2L1 Chrl3q 0.3118 <0.0001 <0.0001

N4BP2L2 Chrl3q 0.5826 <0.0001 <0.0001

NAA15 Chr4q 0.5664 <0.0001 <0.0001

NAA16 Chrl3q 0.4969 <0.0001 <0.0001

NAAA Chr4q 0.3155 <0.0001 <0.0001

NAE1 Chrl6q 0.486 <0.0001 <0.0001

NAGA Chr22q 0.5233 <0.0001 <0.0001

NAIP Chr5q 0.2677 <0.0001 <0.0001

NARS Chrl 8q 0.6997 <0.0001 <0.0001

NARS2 Chrl lq 0.5305 <0.0001 <0.0001

NAT1 Chr8p 0.4568 <0.0001 <0.0001

NBEA Chrl3q 0.218 <0.0001 <0.0001

NBN Chr8q 0.5347 <0.0001 <0.0001

NCALD Chr8q 0.3617 <0.0001 <0.0001

NCAPD2 Chrl2p 0.4966 <0.0001 <0.0001

NCAPG2 Chr7q 0.4213 <0.0001 <0.0001

NCAPH2 Chr22q 0.303 <0.0001 <0.0001

NCBP2 Chr3q 0.6609 <0.0001 <0.0001

NCF4 Chr22q 0.2155 <0.0001 <0.0001

NCK1 Chr3q 0.3178 <0.0001 <0.0001

NCOA2 Chr8q 0.4563 <0.0001 <0.0001

NCOA3 Chr20q 0.3563 <0.0001 <0.0001

NCOA6 Chr20q 0.4313 <0.0001 <0.0001

NCOR1 Chrl7p 0.4443 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

NCSTN Chrlq 0.4239 <0.0001 <0.0001

NDEL1 Chrl7p 0.5236 <0.0001 <0.0001

NDRG1 Chr8q 0.423 <0.0001 <0.0001

NDRG3 Chr20q 0.5229 <0.0001 <0.0001

NDUFA6 Chr22q 0.4273 <0.0001 <0.0001

NDUFA9 Chrl2p 0.6021 <0.0001 <0.0001

NDUFAF1 Chrl5q 0.5392 <0.0001 <0.0001

NDUFAF4 Chr6q 0.5275 <0.0001 <0.0001

NDUFB2 Chr7q 0.5247 <0.0001 <0.0001

NDUFB5 Chr3q 0.4277 <0.0001 <0.0001

NDUFB7 Chrl9p 0.4955 <0.0001 <0.0001

NDUFC1 Chr4q 0.5791 <0.0001 <0.0001

NDUFC2 Chrl lq 0.5126 <0.0001 <0.0001

NDUFS2 Chrlq 0.4123 <0.0001 <0.0001

NDUFS4 Chr5q 0.5438 <0.0001 <0.0001

NECAB3 Chr20q 0.3341 <0.0001 <0.0001

NECAP1 Chrl2p 0.5573 <0.0001 <0.0001

NEDD4L Chrl 8q 0.5003 <0.0001 <0.0001

NEDD9 Chr6p 0.1977 <0.0001 <0.0001

NEIL3 Chr4q 0.2607 <0.0001 <0.0001

NEK1 Chr4q 0.5092 <0.0001 <0.0001

NEK3 Chrl3q 0.4717 <0.0001 <0.0001

NEW Chr6p 0.2601 <0.0001 <0.0001

NF1 Chrl7q 0.4698 <0.0001 <0.0001

NF2 Chr22q 0.5446 <0.0001 <0.0001

NFAT5 Chrl6q 0.3348 <0.0001 <0.0001

NFATC1 Chrl 8q 0.2294 <0.0001 <0.0001

NFATC3 Chrl6q 0.4407 <0.0001 <0.0001

NFIX Chrl9p 0.2706 <0.0001 <0.0001

NFKB1 Chr4q 0.4023 <0.0001 <0.0001

NFKBIB Chrl9q 0.4687 <0.0001 <0.0001

NFKBIL1 Chr6p 0.4655 <0.0001 <0.0001

NFS1 Chr20q 0.4368 <0.0001 <0.0001

NHP2L1 Chr22q 0.378 <0.0001 <0.0001

NINJ2 Chrl2p 0.1642 <0.0001 1.00E-04

NIP7 Chrl6q 0.4864 <0.0001 <0.0001

NIPA2 Chrl5q 0.5702 <0.0001 <0.0001

NIPAL2 Chr8q 0.2797 <0.0001 <0.0001

NIPSNAP1 Chr22q 0.5072 <0.0001 <0.0001

NIT1 Chrlq 0.4125 <0.0001 <0.0001

NKX3-1 Chr8p 0.1982 <0.0001 <0.0001

NLE1 Chrl7q 0.2939 <0.0001 <0.0001

NLK Chrl7q 0.4133 <0.0001 <0.0001

NMD3 Chr3q 0.2533 <0.0001 <0.0001

NOL12 Chr22q 0.1828 <0.0001 <0.0001

NOL3 Chrl6q 0.3555 <0.0001 <0.0001

NOL7 Chr6p 0.5984 <0.0001 <0.0001

NOP 10 Chrl5q 0.4931 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

NOP2 Chrl2p 0.5794 <0.0001 <0.0001

NOP56 Chr20p 0.4519 <0.0001 <0.0001

NOTCH3 Chrl9p 0.3908 <0.0001 <0.0001

NOTCH4 Chr6p 0.2214 <0.0001 <0.0001

NOV Chr8q 0.2 <0.0001 <0.0001

NPTXR Chr22q 0.2704 <0.0001 <0.0001

NQOl Chrl6q 0.1917 <0.0001 <0.0001

NR2F6 Chrl9p 0.5169 <0.0001 <0.0001

NR3C2 Chr4q 0.2504 <0.0001 <0.0001

NRF1 Chr7q 0.2064 <0.0001 <0.0001

NRSN2 Chr20p 0.3873 <0.0001 <0.0001

NSA2 Chr5q 0.5155 <0.0001 <0.0001

NSFL1C Chr20p 0.6112 <0.0001 <0.0001

NSMAF Chr8q 0.3423 <0.0001 <0.0001

NTF3 Chrl2p 0.2922 <0.0001 <0.0001

NUDT15 Chrl3q 0.5109 <0.0001 <0.0001

NUDT18 Chr8p 0.3274 <0.0001 <0.0001

NUDT21 Chrl6q 0.4768 <0.0001 <0.0001

NUDT6 Chr4q 0.3954 <0.0001 <0.0001

NUDT9 Chr4q 0.5363 <0.0001 <0.0001

NUFIP1 Chrl3q 0.6523 <0.0001 <0.0001

NUP205 Chr7q 0.5086 <0.0001 <0.0001

NUP43 Chr6q 0.6423 <0.0001 <0.0001

NUP50 Chr22q 0.4373 <0.0001 <0.0001

NUP54 Chr4q 0.5797 <0.0001 <0.0001

NUP88 Chrl7p 0.471 <0.0001 <0.0001

NUP93 Chrl6q 0.4523 <0.0001 <0.0001

NUPL1 Chrl3q 0.4098 <0.0001 <0.0001

NUSAP1 Chrl5q 0.1756 <0.0001 <0.0001

NUTF2 Chrl6q 0.3861 <0.0001 <0.0001

OCEL1 Chrl9p 0.4679 <0.0001 <0.0001

OCLN Chr5q 0.2971 <0.0001 <0.0001

OGFOD1 Chrl6q 0.4935 <0.0001 <0.0001

OGFR Chr20q 0.2052 <0.0001 <0.0001

OIP5 Chrl5q 0.2293 <0.0001 <0.0001

OPA1 Chr3q 0.5467 <0.0001 <0.0001

OPLAH Chr8q 0.4851 <0.0001 <0.0001

OR7C2 Chrl9p 0.172 <0.0001 <0.0001

OSBPL2 Chr20q 0.5344 <0.0001 <0.0001

OSGIN2 Chr8q 0.4125 <0.0001 <0.0001

OSTM1 Chr6q 0.3232 <0.0001 <0.0001

OTUD4 Chr4q 0.5934 <0.0001 <0.0001

OXR1 Chr8q 0.5207 <0.0001 <0.0001

PABPC1 Chr8q 0.584 <0.0001 <0.0001

PACSIN2 Chr22q 0.4948 <0.0001 <0.0001

PAF1 Chrl9q 0.6163 <0.0001 <0.0001

PAFAH1B1 Chrl7p 0.5739 <0.0001 <0.0001

PARI Chrl lq 0.4015 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

PAK1IP1 Chr6p 0.613 <0.0001 <0.0001

PAK2 Chr3q 0.6687 <0.0001 <0.0001

PAK4 Chrl9q 0.5868 <0.0001 <0.0001

PAK6 Chrl5q 0.2328 <0.0001 <0.0001

PALLD Chr4q 0.2971 <0.0001 <0.0001

PANK2 Chr20p 0.4834 <0.0001 <0.0001

PAPSS1 Chr4q 0.4092 <0.0001 <0.0001

PAQR3 Chr4q 0.3434 <0.0001 <0.0001

PAQR6 Chrlq 0.1887 <0.0001 <0.0001

PAR5 Chrl5q 0.1884 <0.0001 <0.0001

PARD6A Chrl6q 0.2481 <0.0001 <0.0001

PARI Chr3q 0.6202 <0.0001 <0.0001

PARP11 Chrl2p 0.3047 <0.0001 <0.0001

PARP12 Chr7q 0.3003 <0.0001 <0.0001

PARP4 Chrl3q 0.5499 <0.0001 <0.0001

PARTI Chr5q 0.2126 <0.0001 <0.0001

PARVB Chr22q 0.228 <0.0001 <0.0001

PATZ1 Chr22q 0.4561 <0.0001 <0.0001

PAXIP1 Chr7q 0.5303 <0.0001 <0.0001

PBK Chr8p 0.3669 <0.0001 <0.0001

PBX2 Chr6p 0.4954 <0.0001 <0.0001

PBXIP1 Chrlq 0.3255 <0.0001 <0.0001

PCCA Chrl3q 0.5204 <0.0001 <0.0001

PCCB Chr3q 0.3071 <0.0001 <0.0001

PCDH9 Chrl3q 0.2601 <0.0001 <0.0001

PCGF2 Chrl7q 0.2286 <0.0001 <0.0001

PCID2 Chrl3q 0.5809 <0.0001 <0.0001

PCIF1 Chr20q 0.3466 <0.0001 <0.0001

PCM1 Chr8p 0.6643 <0.0001 <0.0001

PCMT1 Chr6q 0.5975 <0.0001 <0.0001

PCMTD2 Chr20q 0.5092 <0.0001 <0.0001

PCOTH Chrl3q 0.2276 <0.0001 <0.0001

PCYT1A Chr3q 0.5117 <0.0001 <0.0001

PDCD10 Chr3q 0.5108 <0.0001 <0.0001

PDCD2 Chr6q 0.5869 <0.0001 <0.0001

PDCD5 Chrl9q 0.5066 <0.0001 <0.0001

PDE3A Chrl2p 0.215 <0.0001 <0.0001

PDE4A Chrl9p 0.2731 <0.0001 <0.0001

PDE4D Chr5q 0.2416 <0.0001 <0.0001

PDGFB Chr22q 0.2367 <0.0001 <0.0001

PDGFC Chr4q 0.3737 <0.0001 <0.0001

PDGFRL Chr8p 0.2992 <0.0001 <0.0001

PDIA3 Chrl5q 0.4991 <0.0001 <0.0001

PDIA4 Chr7q 0.4305 <0.0001 <0.0001

PDLIM2 Chr8p 0.2972 <0.0001 <0.0001

PDLIM3 Chr4q 0.263 <0.0001 <0.0001

PDLIM5 Chr4q 0.3398 <0.0001 <0.0001

PDP1 Chr8q 0.482 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

PDPR Chrl6q 0.1871 <0.0001 <0.0001

PDS5B Chrl3q 0.5414 <0.0001 <0.0001

PDSS2 Chr6q 0.5887 <0.0001 <0.0001

PEA15 Chrlq 0.1847 <0.0001 <0.0001

PELO Chr5q 0.4872 <0.0001 <0.0001

PELP1 Chrl7p 0.4458 <0.0001 <0.0001

PEMT Chrl7p 0.2927 <0.0001 <0.0001

PEPD Chrl9q 0.4458 <0.0001 <0.0001

PERI Chrl7p 0.221 <0.0001 <0.0001

PERP Chr6q 0.3544 <0.0001 <0.0001

PES1 Chr22q 0.5859 <0.0001 <0.0001

PET112L Chr4q 0.5586 <0.0001 <0.0001

PEX11B Chrlq 0.2717 <0.0001 <0.0001

PEX12 Chrl7q 0.2733 <0.0001 <0.0001

PEX19 Chrlq 0.3862 <0.0001 <0.0001

PEX2 Chr8q 0.3574 <0.0001 <0.0001

PEX3 Chr6q 0.6144 <0.0001 <0.0001

PEX5 Chrl2p 0.6405 <0.0001 <0.0001

PEX7 Chr6q 0.5015 <0.0001 <0.0001

PFAS Chrl7p 0.3757 <0.0001 <0.0001

PFDN2 Chrlq 0.44 <0.0001 <0.0001

PFDN4 Chr20q 0.3499 <0.0001 <0.0001

PFN1 Chrl7p 0.4471 <0.0001 <0.0001

PGAP3 Chrl7q 0.3799 <0.0001 <0.0001

PGCP Chr8q 0.3561 <0.0001 <0.0001

PGLS Chrl9p 0.5396 <0.0001 <0.0001

PGPEP1 Chrl9p 0.1986 <0.0001 <0.0001

PGRMC2 Chr4q 0.5956 <0.0001 <0.0001

PHACTR2 Chr6q 0.4431 <0.0001 <0.0001

PHB2 Chrl2p 0.5572 <0.0001 <0.0001

PHC1 Chrl2p 0.4728 <0.0001 <0.0001

PHC3 Chr3q 0.2055 <0.0001 <0.0001

PHF10 Chr6q 0.5571 <0.0001 <0.0001

PHF11 Chrl3q 0.3687 <0.0001 <0.0001

PHF17 Chr4q 0.3956 <0.0001 <0.0001

PHF20 Chr20q 0.3294 <0.0001 <0.0001

PHF20L1 Chr8q 0.4719 <0.0001 <0.0001

PHLPP1 Chrl 8q 0.4403 <0.0001 <0.0001

PHLPP2 Chrl6q 0.2697 <0.0001 <0.0001

PI3 Chr20q 0.1689 <0.0001 <0.0001

PI4KB Chrlq 0.4086 <0.0001 <0.0001

PIAS2 Chrl 8q 0.4887 <0.0001 <0.0001

PIAS3 Chrlq 0.2558 <0.0001 <0.0001

PIBF1 Chrl3q 0.6359 <0.0001 <0.0001

PICKl Chr22q 0.1756 <0.0001 <0.0001

PIGN Chrl 8q 0.5365 <0.0001 <0.0001

PIGT Chr20q 0.5742 <0.0001 <0.0001

PIGZ Chr3q 0.2805 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

PIK3C3 Chrl 8q 0.6232 <0.0001 <0.0001

PIK3CA Chr3q 0.4862 <0.0001 <0.0001

PIK3CB Chr3q 0.3858 <0.0001 <0.0001

PIK3IP1 Chr22q 0.436 <0.0001 <0.0001

PIK3R1 Chr5q 0.1709 <0.0001 <0.0001

PIK3R2 Chrl9p 0.3736 <0.0001 <0.0001

PIN1 Chrl9p 0.6191 <0.0001 <0.0001

PIP4K2B Chrl7q 0.368 <0.0001 <0.0001

PIP5K1A Chrlq 0.3314 <0.0001 <0.0001

PISD Chr22q 0.4917 <0.0001 <0.0001

PITPNB Chr22q 0.6746 <0.0001 <0.0001

PKD2 Chr4q 0.3412 <0.0001 <0.0001

PKIG Chr20q 0.4412 <0.0001 <0.0001

PKN1 Chrl9p 0.4088 <0.0001 <0.0001

PKP2 Chrl2p 0.3477 <0.0001 <0.0001

PLA2G12A Chr4q 0.3509 <0.0001 <0.0001

PLA2G15 Chrl6q 0.369 <0.0001 <0.0001

PL AC 8 Chr4q 0.192 <0.0001 <0.0001

PLAG1 Chr8q 0.2759 <0.0001 <0.0001

PLAGL1 Chr6q 0.2608 <0.0001 <0.0001

PLAGL2 Chr20q 0.2792 <0.0001 <0.0001

PLBD1 Chrl2p 0.2177 <0.0001 <0.0001

PLCG1 Chr20q 0.4128 <0.0001 <0.0001

PLCG2 Chrl6q 0.3445 <0.0001 <0.0001

PLD1 Chr3q 0.2967 <0.0001 <0.0001

PLD2 Chrl7p 0.2316 <0.0001 <0.0001

PLD3 Chrl9q 0.3334 <0.0001 <0.0001

PLEC Chr8q 0.4556 <0.0001 <0.0001

PLEKHA5 Chrl2p 0.4615 <0.0001 <0.0001

PLEKHF1 Chrl9q 0.3238 <0.0001 <0.0001

PLEKHF2 Chr8q 0.5203 <0.0001 <0.0001

PLEKHG6 Chrl2p 0.3319 <0.0001 <0.0001

PLK2 Chr5q 0.2727 <0.0001 <0.0001

PLK4 Chr4q 0.2914 <0.0001 <0.0001

PLLP Chrl6q 0.21 <0.0001 <0.0001

PLOD2 Chr3q 0.1902 <0.0001 <0.0001

PLS1 Chr3q 0.1751 <0.0001 <0.0001

PLSCR1 Chr3q 0.2072 <0.0001 <0.0001

PLSCR2 Chr3q 0.1853 <0.0001 <0.0001

PLSCR3 Chrl7p 0.4591 <0.0001 <0.0001

PLTP Chr20q 0.273 <0.0001 <0.0001

PLXNB2 Chr22q 0.4677 <0.0001 <0.0001

PMAIP1 Chrl 8q 0.3016 <0.0001 <0.0001

PMF1 Chrlq 0.3549 <0.0001 <0.0001

PMM1 Chr22q 0.2863 <0.0001 <0.0001

PMP22 Chrl7p 0.213 <0.0001 <0.0001

PMVK Chrlq 0.2621 <0.0001 <0.0001

PNMA2 Chr8p 0.2172 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

PNPLA3 Chr22q 0.2027 <0.0001 <0.0001

PODXL Chr7q 0.2659 <0.0001 <0.0001

POFUT1 Chr20q 0.3039 <0.0001 <0.0001

POGZ Chrlq 0.2692 <0.0001 <0.0001

POLB Chr8p 0.4381 <0.0001 <0.0001

POLDIP2 Chrl7q 0.4253 <0.0001 <0.0001

POLDIP3 Chr22q 0.4131 <0.0001 <0.0001

POLI Chrl 8q 0.491 <0.0001 <0.0001

POLR1D Chrl3q 0.455 <0.0001 <0.0001

POLR2A Chrl7p 0.181 <0.0001 <0.0001

POLR2C Chrl6q 0.5767 <0.0001 <0.0001

POLR2F Chr22q 0.4554 <0.0001 <0.0001

POLR2H Chr3q 0.6037 <0.0001 <0.0001

POLR2I Chrl9q 0.5519 <0.0001 <0.0001

POLR2K Chr8q 0.6035 <0.0001 <0.0001

POLR3C Chrlq 0.4397 <0.0001 <0.0001

POLR3D Chr8p 0.5014 <0.0001 <0.0001

POLR3G Chr5q 0.2161 <0.0001 <0.0001

POMP Chrl3q 0.6219 <0.0001 <0.0001

POP1 Chr8q 0.2701 <0.0001 <0.0001

POP4 Chrl9q 0.5135 <0.0001 <0.0001

PPA2 Chr4q 0.447 <0.0001 <0.0001

PPAN Chrl9p 0.5684 <0.0001 <0.0001

PPAP2A Chr5q 0.2339 <0.0001 <0.0001

PPARA Chr22q 0.2413 <0.0001 <0.0001

PPDPF Chr20q 0.2461 <0.0001 <0.0001

PPFIBP1 Chrl2p 0.297 <0.0001 <0.0001

PPID Chr4q 0.5028 <0.0001 <0.0001

PPIP5K1 Chrl5q 0.391 <0.0001 <0.0001

PPOX Chrlq 0.3716 <0.0001 <0.0001

PPP1R2 Chr3q 0.6213 <0.0001 <0.0001

PPP1R3D Chr20q 0.3767 <0.0001 <0.0001

PPP2CB Chr8p 0.5779 <0.0001 <0.0001

PPP2R2A Chr8p 0.6874 <0.0001 <0.0001

PPP2R3A Chr3q 0.3955 <0.0001 <0.0001

PPP3CA Chr4q 0.4033 <0.0001 <0.0001

PPP3CC Chr8p 0.4056 <0.0001 <0.0001

PPP6R2 Chr22q 0.3953 <0.0001 <0.0001

PPPDE2 Chr22q 0.5186 <0.0001 <0.0001

PPT2 Chr6p 0.3421 <0.0001 <0.0001

PPWD1 Chr5q 0.52 <0.0001 <0.0001

PQLC1 Chrl 8q 0.5789 <0.0001 <0.0001

PRCC Chrlq 0.4194 <0.0001 <0.0001

PRDX2 Chrl9p 0.5604 <0.0001 <0.0001

PREP Chr6q 0.6296 <0.0001 <0.0001

PRKAB2 Chrlq 0.2975 <0.0001 <0.0001

PRKACA Chrl9p 0.5489 <0.0001 <0.0001

PRKAG2 Chr7q 0.4727 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

PRKCI Chr3q 0.3183 <0.0001 <0.0001

PRKCSH Chrl9p 0.5832 <0.0001 <0.0001

PRKDC Chr8q 0.2949 <0.0001 <0.0001

PRMT7 Chrl6q 0.3688 <0.0001 <0.0001

PRNP Chr20p 0.1804 <0.0001 <0.0001

ProSAPiPl Chr20p 0.3245 <0.0001 <0.0001

PROSC Chr8p 0.5566 <0.0001 <0.0001

PRPF3 Chrlq 0.2934 <0.0001 <0.0001

PRPF6 Chr20q 0.3761 <0.0001 <0.0001

PRPSAP2 Chrl7p 0.3221 <0.0001 <0.0001

PRR14L Chr22q 0.306 <0.0001 <0.0001

PRR4 Chrl2p 0.3574 <0.0001 <0.0001

PRR5 Chr22q 0.3416 <0.0001 <0.0001

PRRC2A Chr6p 0.3463 <0.0001 <0.0001

PRSS1 Chr7q 0.2403 <0.0001 <0.0001

PRSS2 Chr7q 0.2671 <0.0001 <0.0001

PRUNE Chrlq 0.4089 <0.0001 <0.0001

PSCA Chr8q 0.2344 <0.0001 <0.0001

PSD3 Chr8p 0.3984 <0.0001 <0.0001

PSENEN Chrl9q 0.4657 <0.0001 <0.0001

PSKH1 Chrl6q 0.3659 <0.0001 <0.0001

PSMA7 Chr20q 0.4618 <0.0001 <0.0001

PSMB1 Chr6q 0.6927 <0.0001 <0.0001

PSMB10 Chrl6q 0.2965 <0.0001 <0.0001

PSMB3 Chrl7q 0.4113 <0.0001 <0.0001

PSMB4 Chrlq 0.422 <0.0001 <0.0001

PSMB6 Chrl7p 0.5424 <0.0001 <0.0001

PSMC4 Chrl9q 0.5732 <0.0001 <0.0001

PSMD11 Chrl7q 0.3926 <0.0001 <0.0001

PSMD2 Chr3q 0.6598 <0.0001 <0.0001

PSMD3 Chrl7q 0.4035 <0.0001 <0.0001

PSMD4 Chrlq 0.453 <0.0001 <0.0001

PSMD7 Chrl6q 0.5401 <0.0001 <0.0001

PSMD8 Chrl9q 0.5579 <0.0001 <0.0001

PSMF1 Chr20p 0.6065 <0.0001 <0.0001

PSPC1 Chrl3q 0.5517 <0.0001 <0.0001

PSTPIP2 Chrl 8q 0.2677 <0.0001 <0.0001

PTCD2 Chr5q 0.3798 <0.0001 <0.0001

PTDSS1 Chr8q 0.5292 <0.0001 <0.0001

PTGER1 Chrl9p 0.1889 <0.0001 <0.0001

PTK2 Chr8q 0.5862 <0.0001 <0.0001

PTK2B Chr8p 0.2723 <0.0001 <0.0001

PTMS Chrl2p 0.4117 <0.0001 <0.0001

PTP4A3 Chr8q 0.4293 <0.0001 <0.0001

PTPN1 Chr20q 0.3784 <0.0001 <0.0001

PTPN6 Chrl2p 0.3178 <0.0001 <0.0001

PTPRA Chr20p 0.5384 <0.0001 <0.0001

PTPRK Chr6q 0.4337 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

PTX3 Chr3q 0.192 <0.0001 <0.0001

PUF60 Chr8q 0.6827 <0.0001 <0.0001

PVT1 Chr8q 0.1707 <0.0001 <0.0001

PYCRL Chr8q 0.6345 <0.0001 <0.0001

PYROXD1 Chrl2p 0.4272 <0.0001 <0.0001

QKI Chr6q 0.4397 <0.0001 <0.0001

QRSL1 Chr6q 0.517 <0.0001 <0.0001

QTRT1 Chrl9p 0.5272 <0.0001 <0.0001

R3HCC1 Chr8p 0.648 <0.0001 <0.0001

RABllFIPl Chr8p 0.425 <0.0001 <0.0001

RAB13 Chrlq 0.2663 <0.0001 <0.0001

RAB20 Chrl3q 0.4296 <0.0001 <0.0001

RAB22A Chr20q 0.5608 <0.0001 <0.0001

RAB2A Chr8q 0.5461 <0.0001 <0.0001

RAB32 Chr6q 0.315 <0.0001 <0.0001

RAB33B Chr4q 0.4031 <0.0001 <0.0001

RAB36 Chr22q 0.2992 <0.0001 <0.0001

RAB3A Chrl9p 0.2698 <0.0001 <0.0001

RAB3D Chrl9p 0.1771 <0.0001 <0.0001

RAB8A Chrl9p 0.484 <0.0001 <0.0001

RABEPl Chrl7p 0.3126 <0.0001 <0.0001

RAC2 Chr22q 0.2385 <0.0001 <0.0001

RAD 17 Chr5q 0.4909 <0.0001 <0.0001

RAD21 Chr8q 0.6355 <0.0001 <0.0001

RAD23A Chrl9p 0.6252 <0.0001 <0.0001

RAD51 Chrl5q 0.2075 <0.0001 <0.0001

RAD51AP1 Chrl2p 0.4472 <0.0001 <0.0001

RAD51L3 Chrl7q 0.287 <0.0001 <0.0001

RAD52 Chrl2p 0.4306 <0.0001 <0.0001

RAD54B Chr8q 0.2613 <0.0001 <0.0001

RAEl Chr20q 0.5473 <0.0001 <0.0001

RALGAPB Chr20q 0.5567 <0.0001 <0.0001

RALY Chr20q 0.3873 <0.0001 <0.0001

RANBPIO Chrl6q 0.4811 <0.0001 <0.0001

RANBP9 Chr6p 0.4725 <0.0001 <0.0001

RANGAPl Chr22q 0.3139 <0.0001 <0.0001

RANGRF Chrl7p 0.4173 <0.0001 <0.0001

RAP1GAP2 Chrl7p 0.2793 <0.0001 <0.0001

RAP 1 CDS 1 Chr4q 0.3906 <0.0001 <0.0001

RAP2A Chrl3q 0.5808 <0.0001 <0.0001

RAP2B Chr3q 0.3138 <0.0001 <0.0001

RAPGEF2 Chr4q 0.449 <0.0001 <0.0001

RARA Chrl7q 0.205 <0.0001 <0.0001

RARRESl Chr3q 0.18 <0.0001 <0.0001

RASAl Chr5q 0.4912 <0.0001 <0.0001

RASA2 Chr3q 0.2207 <0.0001 <0.0001

RASGRP1 Chrl5q 0.3082 <0.0001 <0.0001

RBI Chrl3q 0.4121 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

KB1CC1 Chr8q 0.491 <0.0001 <0.0001

KBCK1 Chr20p 0.4608 <0.0001 <0.0001

RBFA Chrl 8q 0.4752 <0.0001 <0.0001

KBFOX2 Chr22q 0.3369 <0.0001 <0.0001

RBLl Chr20q 0.2381 <0.0001 <0.0001

KBM12 Chr20q 0.2859 <0.0001 <0.0001

KBM12B Chr8q 0.3514 <0.0001 <0.0001

RBM26 Chrl3q 0.6122 <0.0001 <0.0001

KBM38 Chr20q 0.3392 <0.0001 <0.0001

KBM39 Chr20q 0.3352 <0.0001 <0.0001

KBM42 Chrl9q 0.5622 <0.0001 <0.0001

KBM8A Chrlq 0.2456 <0.0001 <0.0001

RBPMS Chr8p 0.3678 <0.0001 <0.0001

RBXl Chr22q 0.3919 <0.0001 <0.0001

RCBTB1 Chrl3q 0.4438 <0.0001 <0.0001

RCBTB2 Chrl3q 0.428 <0.0001 <0.0001

RCHY1 Chr4q 0.4641 <0.0001 <0.0001

RDBP Chr6p 0.5771 <0.0001 <0.0001

RECQL Chrl2p 0.5072 <0.0001 <0.0001

RECQL4 Chr8q 0.4156 <0.0001 <0.0001

REEP4 Chr8p 0.4368 <0.0001 <0.0001

REPIN1 Chr7q 0.5943 <0.0001 <0.0001

REPS1 Chr6q 0.3229 <0.0001 <0.0001

REV3L Chr6q 0.4972 <0.0001 <0.0001

RFC3 Chrl3q 0.4125 <0.0001 <0.0001

RFC4 Chr3q 0.5576 <0.0001 <0.0001

RFWD3 Chrl6q 0.3707 <0.0001 <0.0001

RFX5 Chrlq 0.1891 <0.0001 <0.0001

RFXANK Chrl9p 0.4644 <0.0001 <0.0001

RFXAP Chrl3q 0.1905 <0.0001 <0.0001

RGNEF Chr5q 0.2476 <0.0001 <0.0001

RGS19 Chr20q 0.2891 <0.0001 <0.0001

RHBDD3 Chr22q 0.3797 <0.0001 <0.0001

RHEB Chr7q 0.5809 <0.0001 <0.0001

RHOBTB2 Chr8p 0.4091 <0.0001 <0.0001

RHOBTB3 Chr5q 0.1812 <0.0001 <0.0001

RHOT1 Chrl7q 0.5077 <0.0001 <0.0001

RIOK2 Chr5q 0.5894 <0.0001 <0.0001

RIPK2 Chr8q 0.4828 <0.0001 <0.0001

RIT1 Chrlq 0.2473 <0.0001 <0.0001

RMNDl Chr6q 0.4773 <0.0001 <0.0001

RNASEH2A Chrl9p 0.531 <0.0001 <0.0001

RNASEH2B Chrl3q 0.4045 <0.0001 <0.0001

RNASET2 Chr6q 0.3358 <0.0001 <0.0001

RNF114 Chr20q 0.4057 <0.0001 <0.0001

RNF115 Chrlq 0.4053 <0.0001 <0.0001

RNF122 Chr8p 0.2803 <0.0001 <0.0001

RNF13 Chr3q 0.2854 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

RNF139 Chr8q 0.6463 <0.0001 <0.0001

RNF146 Chr6q 0.4386 <0.0001 <0.0001

RNF167 Chrl7p 0.342 <0.0001 <0.0001

RNF170 Chr8p 0.3713 <0.0001 <0.0001

RNF19A Chr8q 0.4788 <0.0001 <0.0001

RNF219 Chrl3q 0.6383 <0.0001 <0.0001

RNF24 Chr20p 0.3461 <0.0001 <0.0001

RNF32 Chr7q 0.1839 <0.0001 <0.0001

RNF5 Chr6p 0.4786 <0.0001 <0.0001

RNF6 Chrl3q 0.5814 <0.0001 <0.0001

RNF7 Chr3q 0.4496 <0.0001 <0.0001

RPAIN Chrl7p 0.3027 <0.0001 <0.0001

RPAP1 Chrl5q 0.4597 <0.0001 <0.0001

RPL13 Chrl6q 0.4828 <0.0001 <0.0001

RPL13P5 Chrl2p 0.3327 <0.0001 <0.0001

RPL17 Chrl 8q 0.5407 <0.0001 <0.0001

RPL19 Chrl7q 0.4444 <0.0001 <0.0001

RPL21 Chrl3q 0.5377 <0.0001 <0.0001

RPL23 Chrl7q 0.2893 <0.0001 <0.0001

RPL23A Chrl7q 0.3906 <0.0001 <0.0001

RPL26 Chrl7p 0.3744 <0.0001 <0.0001

RPL3 Chr22q 0.3196 <0.0001 <0.0001

RPL30 Chr8q 0.6326 <0.0001 <0.0001

RPL34 Chr4q 0.4588 <0.0001 <0.0001

RPL35A Chr3q 0.2784 <0.0001 <0.0001

RPL39L Chr3q 0.5212 <0.0001 <0.0001

RPL7 Chr8q 0.4097 <0.0001 <0.0001

RPL8 Chr8q 0.6422 <0.0001 <0.0001

RPN2 Chr20q 0.5579 <0.0001 <0.0001

RPKD2 Chrlq 0.3094 <0.0001 <0.0001

RPS12 Chr6q 0.2583 <0.0001 <0.0001

RPS16 Chrl9q 0.543 <0.0001 <0.0001

RPS20 Chr8q 0.4247 <0.0001 <0.0001

RPS21 Chr20q 0.2093 <0.0001 <0.0001

RPS23 Chr5q 0.4948 <0.0001 <0.0001

RPS27 Chrlq 0.274 <0.0001 <0.0001

RPS3A Chr4q 0.3823 <0.0001 <0.0001

RPS6KA2 Chr6q 0.3177 <0.0001 <0.0001

RPUSD2 Chrl5q 0.4659 <0.0001 <0.0001

KRAGD Chr6q 0.2328 <0.0001 <0.0001

RRNAD1 Chrlq 0.2282 <0.0001 <0.0001

RRP7A Chr22q 0.418 <0.0001 <0.0001

RRS1 Chr8q 0.4558 <0.0001 <0.0001

RSF1 Chrl lq 0.4383 <0.0001 <0.0001

RSRC1 Chr3q 0.4851 <0.0001 <0.0001

RTF1 Chrl5q 0.577 <0.0001 <0.0001

RUSC1 Chrlq 0.3775 <0.0001 <0.0001

RWDD1 Chr6q 0.5977 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

RYK Chr3q 0.2999 <0.0001 <0.0001

RYR1 Chrl9q 0.3503 <0.0001 <0.0001

SACS Chrl3q 0.4176 <0.0001 <0.0001

SAMM50 Chr22q 0.3696 <0.0001 <0.0001

SAP18 Chrl3q 0.6132 <0.0001 <0.0001

SAP30 Chr4q 0.3867 <0.0001 <0.0001

SARS2 Chrl9q 0.479 <0.0001 <0.0001

SASH1 Chr6q 0.4877 <0.0001 <0.0001

SBF1 Chr22q 0.3577 <0.0001 <0.0001

SC4MOL Chr4q 0.505 <0.0001 <0.0001

SCAF8 Chr6q 0.5308 <0.0001 <0.0001

SCAMPI Chr5q 0.4996 <0.0001 <0.0001

SCAMP3 Chrlq 0.4209 <0.0001 <0.0001

SCAND1 Chr20q 0.3348 <0.0001 <0.0001

SCARA3 Chr8p 0.3152 <0.0001 <0.0001

SCARB2 Chr4q 0.4387 <0.0001 <0.0001

SCEL Chrl3q 0.2592 <0.0001 <0.0001

SCHIP1 Chr3q 0.1982 <0.0001 <0.0001

SCNM1 Chrlq 0.4216 <0.0001 <0.0001

SCNN1A Chrl2p 0.3397 <0.0001 <0.0001

SC02 Chr22q 0.4486 <0.0001 <0.0001

SCRIB Chr8q 0.5093 <0.0001 <0.0001

SDAD1 Chr4q 0.4856 <0.0001 <0.0001

SDCBP Chr8q 0.3303 <0.0001 <0.0001

SDF2 Chrl7q 0.4009 <0.0001 <0.0001

SDHAF1 Chrl9q 0.5516 <0.0001 <0.0001

SDHC Chrlq 0.3728 <0.0001 <0.0001

SEC14L2 Chr22q 0.2714 <0.0001 <0.0001

SEC22B Chrlq 0.2603 <0.0001 <0.0001

SEC24B Chr4q 0.6527 <0.0001 <0.0001

SEC24D Chr4q 0.3888 <0.0001 <0.0001

SEC31A Chr4q 0.4701 <0.0001 <0.0001

SEC62 Chr3q 0.5459 <0.0001 <0.0001

SEC63 Chr6q 0.602 <0.0001 <0.0001

SELENBP1 Chrlq 0.1639 <0.0001 1.00E-04

SELT Chr3q 0.2675 <0.0001 <0.0001

SENP2 Chr3q 0.3501 <0.0001 <0.0001

SENP3 Chrl7p 0.5339 <0.0001 <0.0001

SENP5 Chr3q 0.6995 <0.0001 <0.0001

SERF2 Chrl5q 0.5255 <0.0001 <0.0001

SERHL2 Chr22q 0.1918 <0.0001 <0.0001

SERINC1 Chr6q 0.5068 <0.0001 <0.0001

SERINC3 Chr20q 0.3845 <0.0001 <0.0001

SERINC5 Chr5q 0.3101 <0.0001 <0.0001

SERP1 Chr3q 0.4251 <0.0001 <0.0001

SERPINB7 Chrl 8q 0.1789 <0.0001 <0.0001

SERPINB8 Chrl 8q 0.3425 <0.0001 <0.0001

SERPINU Chr3q 0.237 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

SERTAD3 Chrl9q 0.3632 <0.0001 <0.0001

SESN1 Chr6q 0.3684 <0.0001 <0.0001

SETBP1 Chrl 8q 0.2786 <0.0001 <0.0001

SETD6 Chrl6q 0.3705 <0.0001 <0.0001

SETDB1 Chrlq 0.4283 <0.0001 <0.0001

SF3A1 Chr22q 0.5057 <0.0001 <0.0001

SF3B3 Chrl6q 0.4744 <0.0001 <0.0001

SF3B4 Chrlq 0.3794 <0.0001 <0.0001

SF3B5 Chr6q 0.5703 <0.0001 <0.0001

SFI1 Chr22q 0.2366 <0.0001 <0.0001

SFRS18 Chr6q 0.4672 <0.0001 <0.0001

SGCG Chrl3q 0.1822 <0.0001 <0.0001

SGK1 Chr6q 0.2347 <0.0001 <0.0001

SGSM2 Chrl7p 0.3649 <0.0001 <0.0001

SGSM3 Chr22q 0.3757 <0.0001 <0.0001

SH2D2A Chrlq 0.2049 <0.0001 <0.0001

SH2D4A Chr8p 0.4151 <0.0001 <0.0001

SHARPIN Chr8q 0.6747 <0.0001 <0.0001

SHC1 Chrlq 0.3089 <0.0001 <0.0001

SHPK Chrl7p 0.2919 <0.0001 <0.0001

SIAH2 Chr3q 0.3963 <0.0001 <0.0001

SIN3B Chrl9p 0.5201 <0.0001 <0.0001

SIPA1L3 Chrl9q 0.4616 <0.0001 <0.0001

SIRT2 Chrl9q 0.4577 <0.0001 <0.0001

SIRT5 Chr6p 0.4706 <0.0001 <0.0001

SKA1 Chrl 8q 0.2406 <0.0001 <0.0001

SKIL Chr3q 0.2695 <0.0001 <0.0001

SKIV2L Chr6p 0.4902 <0.0001 <0.0001

SKIV2L2 Chr5q 0.5952 <0.0001 <0.0001

SLC16A10 Chr6q 0.2886 <0.0001 <0.0001

SLC20A2 Chr8p 0.2887 <0.0001 <0.0001

SLC23A2 Chr20p 0.3019 <0.0001 <0.0001

SLC25A11 Chrl7p 0.4561 <0.0001 <0.0001

SLC25A15 Chrl3q 0.4455 <0.0001 <0.0001

SLC25A17 Chr22q 0.4656 <0.0001 <0.0001

SLC25A32 Chr8q 0.6547 <0.0001 <0.0001

SLC25A36 Chr3q 0.4725 <0.0001 <0.0001

SLC25A37 Chr8p 0.4503 <0.0001 <0.0001

SLC25A4 Chr4q 0.4397 <0.0001 <0.0001

SLC25A44 Chrlq 0.4557 <0.0001 <0.0001

SLC27A3 Chrlq 0.224 <0.0001 <0.0001

SLC2A10 Chr20q 0.3114 <0.0001 <0.0001

SLC2A11 Chr22q 0.2735 <0.0001 <0.0001

SLC2A4RG Chr20q 0.3451 <0.0001 <0.0001

SLC30A5 Chr5q 0.5077 <0.0001 <0.0001

SLC33A1 Chr3q 0.4596 <0.0001 <0.0001

SLC35C2 Chr20q 0.3718 <0.0001 <0.0001

SLC35E1 Chrl9p 0.4198 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

SLC38A 7 Chrl6q 0.4306 <0.0001 <0.0001

SLC39A1 Chrlq 0.261 <0.0001 <0.0001

SLC39A14 Chr8p 0.4207 <0.0001 <0.0001

SLC39A4 Chr8q 0.5691 <0.0001 <0.0001

SLC39A8 Chr4q 0.1953 <0.0001 <0.0001

SLC46A3 Chrl3q 0.3656 <0.0001 <0.0001

SLC4A2 Chr7q 0.4475 <0.0001 <0.0001

SLC50A1 Chrlq 0.2467 <0.0001 <0.0001

SLC5A5 Chrl9p 0.2004 <0.0001 <0.0001

SLC6A12 Chrl2p 0.2397 <0.0001 <0.0001

SLC6A13 Chrl2p 0.1739 <0.0001 <0.0001

SLC7A1 Chrl3q 0.5129 <0.0001 <0.0001

SLC7A11 Chr4q 0.3082 <0.0001 <0.0001

SLC7A5 Chrl6q 0.2818 <0.0001 <0.0001

SLC7A6 Chrl6q 0.3674 <0.0001 <0.0001

SLC7A9 Chrl9q 0.3615 <0.0001 <0.0001

SLC9A8 Chr20q 0.2062 <0.0001 <0.0001

SLC01A2 Chrl2p 0.3173 <0.0001 <0.0001

SLFN12 Chrl7q 0.1658 <0.0001 1.00E-04

SLM02 Chr20q 0.4337 <0.0001 <0.0001

SLPI Chr20q 0.1677 <0.0001 <0.0001

SMAD1 Chr4q 0.5348 <0.0001 <0.0001

SMAD2 Chrl 8q 0.6769 <0.0001 <0.0001

SMAD4 Chrl 8q 0.5534 <0.0001 <0.0001

SMAD7 Chrl 8q 0.3308 <0.0001 <0.0001

SMARCA4 Chrl9p 0.5559 <0.0001 <0.0001

SMARCA5 Chr4q 0.6295 <0.0001 <0.0001

SMARCB1 Chr22q 0.51 <0.0001 <0.0001

SMARCD3 Chr7q 0.1731 <0.0001 <0.0001

SMARCE1 Chrl7q 0.5252 <0.0001 <0.0001

SMC4 Chr3q 0.4608 <0.0001 <0.0001

SMCR7L Chr22q 0.5027 <0.0001 <0.0001

SMG5 Chrlq 0.3243 <0.0001 <0.0001

SMG6 Chrl7p 0.197 <0.0001 <0.0001

SMO Chr7q 0.2386 <0.0001 <0.0001

SMPD2 Chr6q 0.3585 <0.0001 <0.0001

SMPDL3A Chr6q 0.1687 <0.0001 <0.0001

SMTN Chr22q 0.3341 <0.0001 <0.0001

SNAP23 Chrl5q 0.4726 <0.0001 <0.0001

SNCA Chr4q 0.1689 <0.0001 <0.0001

SNORA21 Chrl7q 0.2278 <0.0001 <0.0001

SNPH Chr20p 0.1754 <0.0001 <0.0001

SNRPB Chr20p 0.4415 <0.0001 <0.0001

SNRPD3 Chr22q 0.6616 <0.0001 <0.0001

SNTA1 Chr20q 0.2126 <0.0001 <0.0001

SNTB1 Chr8q 0.344 <0.0001 <0.0001

SNTB2 Chrl6q 0.4131 <0.0001 <0.0001

SNX16 Chr8q 0.4068 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

SNX27 Chrlq 0.3688 <0.0001 <0.0001

SNX3 Chr6q 0.5593 <0.0001 <0.0001

SOCS6 Chrl 8q 0.4631 <0.0001 <0.0001

SOD2 Chr6q 0.2216 <0.0001 <0.0001

SORBS3 Chr8p 0.3661 <0.0001 <0.0001

SORD Chrl5q 0.4457 <0.0001 <0.0001

SOX12 Chr20p 0.443 <0.0001 <0.0001

SPAG1 Chr8q 0.3432 <0.0001 <0.0001

SPAG5 Chrl7q 0.2657 <0.0001 <0.0001

SPAG7 Chrl7p 0.4111 <0.0001 <0.0001

SPATA2 Chr20q 0.5022 <0.0001 <0.0001

SPATA2L Chrl6q 0.4331 <0.0001 <0.0001

SPATA5L1 Chrl5q 0.5685 <0.0001 <0.0001

SPCS3 Chr4q 0.4887 <0.0001 <0.0001

SPECC1L Chr22q 0.5335 <0.0001 <0.0001

SPG 11 Chrl5q 0.6094 <0.0001 <0.0001

SPG20 Chrl3q 0.3605 <0.0001 <0.0001

SPG7 Chrl6q 0.5101 <0.0001 <0.0001

SPINT1 Chrl5q 0.5413 <0.0001 <0.0001

SPINT2 Chrl9q 0.5441 <0.0001 <0.0001

SPRY1 Chr4q 0.2088 <0.0001 <0.0001

SPRY 2 Chrl3q 0.2585 <0.0001 <0.0001

SQLE Chr8q 0.5045 <0.0001 <0.0001

SQRDL Chrl5q 0.2797 <0.0001 <0.0001

SRC Chr20q 0.3333 <0.0001 <0.0001

SREBF1 Chrl7p 0.1733 <0.0001 <0.0001

SREBF2 Chr22q 0.4597 <0.0001 <0.0001

SREK1 Chr5q 0.4719 <0.0001 <0.0001

SREK1IP1 Chr5q 0.3893 <0.0001 <0.0001

SRP14 Chrl5q 0.5167 <0.0001 <0.0001

SRPRB Chr3q 0.2837 <0.0001 <0.0001

SRR Chrl7p 0.237 <0.0001 <0.0001

SRRD Chr22q 0.5683 <0.0001 <0.0001

SRSF6 Chr20q 0.2344 <0.0001 <0.0001

SS18L1 Chr20q 0.4892 <0.0001 <0.0001

SSBP1 Chr7q 0.5541 <0.0001 <0.0001

SSBP2 Chr5q 0.3386 <0.0001 <0.0001

SSPN Chrl2p 0.2931 <0.0001 <0.0001

SSR2 Chrlq 0.3827 <0.0001 <0.0001

SSR3 Chr3q 0.2957 <0.0001 <0.0001

ST13 Chr22q 0.4269 <0.0001 <0.0001

ST3GAL1 Chr8q 0.2989 <0.0001 <0.0001

ST3GAL2 Chrl6q 0.2278 <0.0001 <0.0001

ST6GAL1 Chr3q 0.2896 <0.0001 <0.0001

STAG1 Chr3q 0.3391 <0.0001 <0.0001

STARD13 Chrl3q 0.2874 <0.0001 <0.0001

STARD3 Chrl7q 0.293 <0.0001 <0.0001

ST AVI Chr20q 0.5549 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

STAU2 Chr8q 0.3636 <0.0001 <0.0001

STBD1 Chr4q 0.3611 <0.0001 <0.0001

STC1 Chr8p 0.2001 <0.0001 <0.0001

STK19 Chr6p 0.3834 <0.0001 <0.0001

STK24 Chrl3q 0.6656 <0.0001 <0.0001

STK3 Chr8q 0.6555 <0.0001 <0.0001

STK38L Chrl2p 0.4266 <0.0001 <0.0001

STK4 Chr20q 0.3925 <0.0001 <0.0001

STRAP Chrl2p 0.6159 <0.0001 <0.0001

STX10 Chrl9p 0.57 <0.0001 <0.0001

STX16 Chr20q 0.3686 <0.0001 <0.0001

STX7 Chr6q 0.5655 <0.0001 <0.0001

STX8 Chrl7p 0.413 <0.0001 <0.0001

SUCLA2 Chrl3q 0.5857 <0.0001 <0.0001

SUGP1 Chrl9p 0.5438 <0.0001 <0.0001

SUGP2 Chrl9p 0.3807 <0.0001 <0.0001

SUN2 Chr22q 0.4059 <0.0001 <0.0001

SUPT5H Chrl9q 0.5707 <0.0001 <0.0001

SUPT6H Chrl7q 0.4849 <0.0001 <0.0001

SUZ12 Chrl7q 0.4699 <0.0001 <0.0001

SYBU Chr8q 0.3181 <0.0001 <0.0001

SYCP2 Chr20q 0.1842 <0.0001 <0.0001

SYDE1 Chrl9p 0.2761 <0.0001 <0.0001

SYNE1 Chr6q 0.1649 <0.0001 1.00E-04

SYNGR1 Chr22q 0.2984 <0.0001 <0.0001

SYNJ2 Chr6q 0.3259 <0.0001 <0.0001

SYNRG Chrl7q 0.4966 <0.0001 <0.0001

SYT11 Chrlq 0.2827 <0.0001 <0.0001

TAB1 Chr22q 0.2654 <0.0001 <0.0001

TAB2 Chr6q 0.5887 <0.0001 <0.0001

TADA2A Chrl7q 0.2745 <0.0001 <0.0001

TAF1C Chrl6q 0.3625 <0.0001 <0.0001

TAF2 Chr8q 0.6289 <0.0001 <0.0001

TAF4 Chr20q 0.4811 <0.0001 <0.0001

TAF9 Chr5q 0.5125 <0.0001 <0.0001

TAGLN2 Chrlq 0.1832 <0.0001 <0.0001

TAPBPL Chrl2p 0.1723 <0.0001 <0.0001

TARS2 Chrlq 0.3789 <0.0001 <0.0001

TAS2R14 Chrl2p 0.1847 <0.0001 <0.0001

TAX1BP3 Chrl7p 0.4722 <0.0001 <0.0001

TBC1D22A Chr22q 0.5641 <0.0001 <0.0001

TBC1D4 Chrl3q 0.2713 <0.0001 <0.0001

TBC1D9 Chr4q 0.5069 <0.0001 <0.0001

TBCA Chr5q 0.54 <0.0001 <0.0001

TBCB Chrl9q 0.5864 <0.0001 <0.0001

TBCCD1 Chr3q 0.5179 <0.0001 <0.0001

TBL1XR1 Chr3q 0.3401 <0.0001 <0.0001

TBP Chr6q 0.5954 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

TBPL1 Chr6q 0.5711 <0.0001 <0.0001

TCEA1 Chr8q 0.4624 <0.0001 <0.0001

TCEA2 Chr20q 0.3342 <0.0001 <0.0001

TCEB1 Chr8q 0.5089 <0.0001 <0.0001

TCF20 Chr22q 0.3651 <0.0001 <0.0001

TCF25 Chrl6q 0.5792 <0.0001 <0.0001

TCF4 Chrl 8q 0.1753 <0.0001 <0.0001

TCFL5 Chr20q 0.3502 <0.0001 <0.0001

TCN2 Chr22q 0.396 <0.0001 <0.0001

TCP1 Chr6q 0.6722 <0.0001 <0.0001

TD02 Chr4q 0.2535 <0.0001 <0.0001

TDKD12 Chrl9q 0.2319 <0.0001 <0.0001

TDRD3 Chrl3q 0.6046 <0.0001 <0.0001

TDRKH Chrlq 0.2803 <0.0001 <0.0001

TEAD4 Chrl2p 0.4707 <0.0001 <0.0001

TECR Chrl9p 0.5819 <0.0001 <0.0001

TERF1 Chr8q 0.5711 <0.0001 <0.0001

TERF2 Chrl6q 0.4386 <0.0001 <0.0001

TERF2IP Chrl6q 0.5911 <0.0001 <0.0001

TFB1M Chr6q 0.495 <0.0001 <0.0001

TFDP1 Chrl3q 0.5316 <0.0001 <0.0001

TFDP2 Chr3q 0.4275 <0.0001 <0.0001

TFIP11 Chr22q 0.6042 <0.0001 <0.0001

TFRC Chr3q 0.3511 <0.0001 <0.0001

TGDS Chrl3q 0.6193 <0.0001 <0.0001

TGIF2 Chr20q 0.389 <0.0001 <0.0001

TGS1 Chr8q 0.4724 <0.0001 <0.0001 mil Chr20q 0.4961 <0.0001 <0.0001

THAPl Chr8p 0.2837 <0.0001 <0.0001

THAP11 Chrl6q 0.4764 <0.0001 <0.0001

THAP9 Chr4q 0.2191 <0.0001 <0.0001

THBS1 Chrl5q 0.1816 <0.0001 <0.0001

THBS3 Chrlq 0.2483 <0.0001 <0.0001

THOC5 Chr22q 0.5266 <0.0001 <0.0001

THRA Chrl7q 0.1955 <0.0001 <0.0001

TIAM2 Chr6q 0.2276 <0.0001 <0.0001

TIMM50 Chrl9q 0.3635 <0.0001 <0.0001

TIMP3 Chr22q 0.1931 <0.0001 <0.0001

TIPARP Chr3q 0.2814 <0.0001 <0.0001

TJP1 Chrl5q 0.3839 <0.0001 <0.0001

TK2 Chrl6q 0.3971 <0.0001 <0.0001

TLR2 Chr4q 0.2371 <0.0001 <0.0001

TLR3 Chr4q 0.3835 <0.0001 <0.0001

TM4SF1 Chr3q 0.1944 <0.0001 <0.0001

TM7SF3 Chrl2p 0.4011 <0.0001 <0.0001

TM7SF4 Chr8q 0.1678 <0.0001 1.00E-04

TM9SF2 Chrl3q 0.5657 <0.0001 <0.0001

TM9SF4 Chr20q 0.3308 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

TMC03 Chrl3q 0.4782 <0.0001 <0.0001

TMED1 Chrl9p 0.5378 <0.0001 <0.0001

TMEM11 Chrl7p 0.37 <0.0001 <0.0001

TMEM144 Chr4q 0.2082 <0.0001 <0.0001

TMEM147 Chrl9q 0.5776 <0.0001 <0.0001

TMEM149 Chrl9q 0.2408 <0.0001 <0.0001

TMEM14B Chr6p 0.4981 <0.0001 <0.0001

TMEM161A Chrl9p 0.5463 <0.0001 <0.0001

TMEM184B Chr22q 0.492 <0.0001 <0.0001

TMEM184C Chr4q 0.5373 <0.0001 <0.0001

TMEM208 Chrl6q 0.5175 <0.0001 <0.0001

TMEM209 Chr7q 0.4157 <0.0001 <0.0001

TMEM231 Chrl6q 0.3354 <0.0001 <0.0001

TMEM62 Chrl5q 0.3595 <0.0001 <0.0001

TMEM66 Chr8p 0.5704 <0.0001 <0.0001

TMEM70 Chr8q 0.4634 <0.0001 <0.0001

TMEM87A Chrl5q 0.5831 <0.0001 <0.0001

TMEM93 Chrl7p 0.518 <0.0001 <0.0001

TMEM97 Chrl7q 0.2023 <0.0001 <0.0001

TNFAIP1 Chrl7q 0.5425 <0.0001 <0.0001

TNFRSF10B Chr8p 0.5735 <0.0001 <0.0001

TNFRSF11B Chr8q 0.319 <0.0001 <0.0001

TNFRSF1A Chrl2p 0.3109 <0.0001 <0.0001

TNFSF10 Chr3q 0.24 <0.0001 <0.0001

TNFSF12 Chrl7p 0.233 <0.0001 <0.0001

TNFSF13 Chrl7p 0.2252 <0.0001 <0.0001

TNK1 Chrl7p 0.2838 <0.0001 <0.0001

TNK2 Chr3q 0.3202 <0.0001 <0.0001

TNKS Chr8p 0.6283 <0.0001 <0.0001

TNPOl Chr5q 0.4776 <0.0001 <0.0001

TNP02 Chrl9p 0.5516 <0.0001 <0.0001

TNP03 Chr7q 0.5213 <0.0001 <0.0001

TNRC6B Chr22q 0.4574 <0.0001 <0.0001

TOB2 Chr22q 0.3377 <0.0001 <0.0001

TOM1 Chr22q 0.4228 <0.0001 <0.0001

TOMM22 Chr22q 0.3727 <0.0001 <0.0001

TOMM34 Chr20q 0.4463 <0.0001 <0.0001

TOPI Chr20q 0.3582 <0.0001 <0.0001

TOP2A Chrl7q 0.2327 <0.0001 <0.0001

TOP3A Chrl7p 0.1664 <0.0001 1.00E-04

TOPBP1 Chr3q 0.4965 <0.0001 <0.0001

TOX Chr8q 0.1697 <0.0001 <0.0001

TP53 Chrl7p 0.1719 <0.0001 <0.0001

TP53BP1 Chrl5q 0.4204 <0.0001 <0.0001

TPD52 Chr8q 0.5477 <0.0001 <0.0001

TPD52L1 Chr6q 0.4086 <0.0001 <0.0001

TPD52L2 Chr20q 0.4955 <0.0001 <0.0001

TPI1 Chrl2p 0.5523 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

TPM4 Chrl9p 0.3406 <0.0001 <0.0001

TPP2 Chrl3q 0.6531 <0.0001 <0.0001

TPPP3 Chrl6q 0.1695 <0.0001 <0.0001

TPST2 Chr22q 0.4795 <0.0001 <0.0001

TPT1 Chrl3q 0.5543 <0.0001 <0.0001

TPX2 Chr20q 0.3211 <0.0001 <0.0001

TRA2B Chr3q 0.4576 <0.0001 <0.0001

TRABD Chr22q 0.3889 <0.0001 <0.0001

TRADD Chrl6q 0.4826 <0.0001 <0.0001

TRAF3IP2 Chr6q 0.3462 <0.0001 <0.0001

TRAF4 Chrl7q 0.2908 <0.0001 <0.0001

TRAM1 Chr8q 0.4474 <0.0001 <0.0001

TRAPPC2L Chrl6q 0.4988 <0.0001 <0.0001

TRAPPC9 Chr8q 0.533 <0.0001 <0.0001

TRIB1 Chr8q 0.3517 <0.0001 <0.0001

TRIB3 Chr20p 0.2215 <0.0001 <0.0001

TRIM13 Chrl3q 0.4754 <0.0001 <0.0001

TRIM 16 Chrl7p 0.2626 <0.0001 <0.0001

TRIM2 Chr4q 0.2882 <0.0001 <0.0001

TRIM23 Chr5q 0.5109 <0.0001 <0.0001

TRIM24 Chr7q 0.4512 <0.0001 <0.0001

TRIOBP Chr22q 0.4292 <0.0001 <0.0001

TRMT1 Chrl9p 0.5993 <0.0001 <0.0001

TRMT11 Chr6q 0.4649 <0.0001 <0.0001

TRMT12 Chr8q 0.6408 <0.0001 <0.0001

TRMU Chr22q 0.2429 <0.0001 <0.0001

TRPC4AP Chr20q 0.4372 <0.0001 <0.0001

TRPSl Chr8q 0.3923 <0.0001 <0.0001

TRPVl Chrl7p 0.226 <0.0001 <0.0001

TSC22D1 Chrl3q 0.3893 <0.0001 <0.0001

TSC22D2 Chr3q 0.2996 <0.0001 <0.0001

TSGA14 Chr7q 0.178 <0.0001 <0.0001

TSKU Chrl lq 0.2154 <0.0001 <0.0001

TSPAN9 Chrl2p 0.2785 <0.0001 <0.0001

TSPO Chr22q 0.4371 <0.0001 <0.0001

TSPYL1 Chr6q 0.495 <0.0001 <0.0001

TSPYL4 Chr6q 0.4703 <0.0001 <0.0001

TSPYL5 Chr8q 0.1833 <0.0001 <0.0001

TSR1 Chrl7p 0.4834 <0.0001 <0.0001

TST Chr22q 0.2846 <0.0001 <0.0001

TSTA3 Chr8q 0.5699 <0.0001 <0.0001

TTBK2 Chrl5q 0.3696 <0.0001 <0.0001

TTC19 Chrl7p 0.2931 <0.0001 <0.0001

TTC26 Chr7q 0.2629 <0.0001 <0.0001

TTC28 Chr22q 0.2718 <0.0001 <0.0001

TTC35 Chr8q 0.6547 <0.0001 <0.0001

TTC37 Chr5q 0.5828 <0.0001 <0.0001

TTC38 Chr22q 0.2814 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

TTI1 Chr20q 0.5227 <0.0001 <0.0001

TTLL1 Chr22q 0.3494 <0.0001 <0.0001

TTLL12 Chr22q 0.3514 <0.0001 <0.0001

TTPAL Chr20q 0.4204 <0.0001 <0.0001

TUBGCP3 Chrl3q 0.6454 <0.0001 <0.0001

TUBGCP4 Chrl5q 0.4712 <0.0001 <0.0001

TUBGCP5 Chrl5q 0.3681 <0.0001 <0.0001

TUFT1 Chrlq 0.314 <0.0001 <0.0001

TUG1 Chr22q 0.4867 <0.0001 <0.0001

TULP3 Chrl2p 0.62 <0.0001 <0.0001

TULP4 Chr6q 0.5068 <0.0001 <0.0001

TUSC3 Chr8p 0.5272 <0.0001 <0.0001

TXN2 Chr22q 0.5151 <0.0001 <0.0001

TXNL1 Chrl 8q 0.7011 <0.0001 <0.0001

TXNL4A Chrl 8q 0.574 <0.0001 <0.0001

TXNL4B Chrl6q 0.3329 <0.0001 <0.0001

TYK2 Chrl9p 0.6295 <0.0001 <0.0001

TYMP Chr22q 0.2915 <0.0001 <0.0001

TYRO 3 Chrl5q 0.2821 <0.0001 <0.0001

U2SURP Chr3q 0.3552 <0.0001 <0.0001

UAP1 Chrlq 0.4456 <0.0001 <0.0001

UBA2 Chrl9q 0.5027 <0.0001 <0.0001

UBA5 Chr3q 0.3834 <0.0001 <0.0001

UBA52 Chrl9p 0.5947 <0.0001 <0.0001

UBAP2L Chrlq 0.4148 <0.0001 <0.0001

UBE2C Chr20q 0.4077 <0.0001 <0.0001

UBE2D3 Chr4q 0.6164 <0.0001 <0.0001

UBE2G1 Chrl7p 0.5241 <0.0001 <0.0001

UBE2H Chr7q 0.3398 <0.0001 <0.0001

UBE2J1 Chr6q 0.5624 <0.0001 <0.0001

UBE2Q1 Chrlq 0.5289 <0.0001 <0.0001

UBE2V2 Chr8q 0.4185 <0.0001 <0.0001

UBE2W Chr8q 0.5539 <0.0001 <0.0001

UBE3A Chrl5q 0.6126 <0.0001 <0.0001

UBE3C Chr7q 0.6314 <0.0001 <0.0001

UBL3 Chrl3q 0.5944 <0.0001 <0.0001

UBL5 Chrl9p 0.583 <0.0001 <0.0001

UBOX5 Chr20p 0.3959 <0.0001 <0.0001

UBR5 Chr8q 0.6444 <0.0001 <0.0001

UBXN2B Chr8q 0.4613 <0.0001 <0.0001

UBXN7 Chr3q 0.5464 <0.0001 <0.0001

UBXN8 Chr8p 0.4402 <0.0001 <0.0001

UCHL3 Chrl3q 0.5361 <0.0001 <0.0001

UCKL1 Chr20q 0.4794 <0.0001 <0.0001

UFC1 Chrlq 0.4207 <0.0001 <0.0001

UFM1 Chrl3q 0.6254 <0.0001 <0.0001

UFSP2 Chr4q 0.5945 <0.0001 <0.0001

UGGT2 Chrl3q 0.5486 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

UGT8 Chr4q 0.2328 <0.0001 <0.0001

ULK2 Chrl7p 0.2465 <0.0001 <0.0001

UNCI 19 Chrl7q 0.3329 <0.0001 <0.0001

UPF1 Chrl9p 0.4698 <0.0001 <0.0001

UPF3A Chrl3q 0.5867 <0.0001 <0.0001

UQCC Chr20q 0.4656 <0.0001 <0.0001

UQCR10 Chr22q 0.5748 <0.0001 <0.0001

UQCKB Chr8q 0.5379 <0.0001 <0.0001

UQCRFS1 Chrl9q 0.4455 <0.0001 <0.0001

USE1 Chrl9p 0.5385 <0.0001 <0.0001

USF2 Chrl9q 0.5393 <0.0001 <0.0001

USOl Chr4q 0.5988 <0.0001 <0.0001

USP10 Chrl6q 0.6084 <0.0001 <0.0001

USP12 Chrl3q 0.4944 <0.0001 <0.0001

USP13 Chr3q 0.2438 <0.0001 <0.0001

USP21 Chrlq 0.4071 <0.0001 <0.0001

USP22 Chrl7p 0.3176 <0.0001 <0.0001

USP5 Chrl2p 0.485 <0.0001 <0.0001

USP53 Chr4q 0.2087 <0.0001 <0.0001

USPL1 Chrl3q 0.5707 <0.0001 <0.0001

UTP14C Chrl3q 0.6694 <0.0001 <0.0001

UTP6 Chrl7q 0.4574 <0.0001 <0.0001

UTRN Chr6q 0.3347 <0.0001 <0.0001

VAC14 Chrl6q 0.3979 <0.0001 <0.0001

VAMP1 Chrl2p 0.2838 <0.0001 <0.0001

VAMP2 Chrl7p 0.32 <0.0001 <0.0001

VAPB Chr20q 0.4928 <0.0001 <0.0001

VARS Chr6p 0.4842 <0.0001 <0.0001

VCAN Chr5q 0.1802 <0.0001 <0.0001

VCPIP1 Chr8q 0.3168 <0.0001 <0.0001

VDAC3 Chr8p 0.4275 <0.0001 <0.0001

VEGFC Chr4q 0.1867 <0.0001 <0.0001

VPS13B Chr8q 0.5452 <0.0001 <0.0001

VPS 16 Chr20p 0.478 <0.0001 <0.0001

VPS28 Chr8q 0.6385 <0.0001 <0.0001

VPS39 Chrl5q 0.5146 <0.0001 <0.0001

VPS45 Chrlq 0.3814 <0.0001 <0.0001

VPS4A Chrl6q 0.5448 <0.0001 <0.0001

VPS4B Chrl 8q 0.6674 <0.0001 <0.0001

VPS72 Chrlq 0.4783 <0.0001 <0.0001

VPS8 Chr3q 0.5814 <0.0001 <0.0001

WASF1 Chr6q 0.4607 <0.0001 <0.0001

WASF3 Chrl3q 0.2951 <0.0001 <0.0001

WBP11 Chrl2p 0.6238 <0.0001 <0.0001

WBP4 Chrl3q 0.6713 <0.0001 <0.0001

WDFY3 Chr4q 0.4924 <0.0001 <0.0001

WDR41 Chr5q 0.3739 <0.0001 <0.0001

WDR59 Chrl6q 0.5045 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

WDR60 Chr7q 0.4442 <0.0001 <0.0001

WDR62 Chrl9q 0.2129 <0.0001 <0.0001

WDR67 Chr8q 0.461 <0.0001 <0.0001

WDR7 Chrl 8q 0.6214 <0.0001 <0.0001

WDR76 Chrl5q 0.1773 <0.0001 <0.0001

WDR91 Chr7q 0.4291 <0.0001 <0.0001

WDYHV1 Chr8q 0.5211 <0.0001 <0.0001

WFDC2 Chr20q 0.2589 <0.0001 <0.0001

WIPF2 Chrl7q 0.4474 <0.0001 <0.0001

WISP3 Chr6q 0.1667 <0.0001 1.00E-04

WIZ Chrl9p 0.6238 <0.0001 <0.0001

WNK1 Chrl2p 0.4556 <0.0001 <0.0001

WNT5B Chrl2p 0.1935 <0.0001 <0.0001

WRAP53 Chrl7p 0.3466 <0.0001 <0.0001

WRN Chr8p 0.5364 <0.0001 <0.0001

WSB1 Chrl7q 0.3452 <0.0001 <0.0001

WTAP Chr6q 0.5334 <0.0001 <0.0001

WWC2 Chr4q 0.2881 <0.0001 <0.0001

WWOX Chrl6q 0.3208 <0.0001 <0.0001

WWP1 Chr8q 0.5381 <0.0001 <0.0001

WWP2 Chrl6q 0.4782 <0.0001 <0.0001

WWTR1 Chr3q 0.3898 <0.0001 <0.0001

XBP1 Chr22q 0.432 <0.0001 <0.0001

XPNPEP3 Chr22q 0.3516 <0.0001 <0.0001

XP04 Chrl3q 0.2953 <0.0001 <0.0001

XP07 Chr8p 0.5924 <0.0001 <0.0001

XRCC2 Chr7q 0.2351 <0.0001 <0.0001

XRCC4 Chr5q 0.4534 <0.0001 <0.0001

XRCC6 Chr22q 0.5122 <0.0001 <0.0001

YARS2 Chrl2p 0.4505 <0.0001 <0.0001

YEATS 2 Chr3q 0.5349 <0.0001 <0.0001

YIPF2 Chrl9p 0.4891 <0.0001 <0.0001

YTHDF1 Chr20q 0.5344 <0.0001 <0.0001

YTHDF3 Chr8q 0.5712 <0.0001 <0.0001

YWHAB Chr20q 0.502 <0.0001 <0.0001

YWHAH Chr22q 0.4971 <0.0001 <0.0001

YWHAZ Chr8q 0.559 <0.0001 <0.0001

YY1AP1 Chrlq 0.4193 <0.0001 <0.0001

ZBED4 Chr22q 0.2944 <0.0001 <0.0001

ZBTB10 Chr8q 0.4354 <0.0001 <0.0001

ZBTB24 Chr6q 0.5802 <0.0001 <0.0001

ZBTB38 Chr3q 0.3691 <0.0001 <0.0001

ZC3H13 Chrl3q 0.5899 <0.0001 <0.0001

ZC3H3 Chr8q 0.6158 <0.0001 <0.0001

ZC3HAV1 Chr7q 0.2625 <0.0001 <0.0001

ZCCHC14 Chrl6q 0.4267 <0.0001 <0.0001

ZCCHC2 Chrl 8q 0.5389 <0.0001 <0.0001

ZDHHC14 Chr6q 0.2474 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

ZDHHC7 Chrl6q 0.5933 <0.0001 <0.0001

ZFAND1 Chr8q 0.4245 <0.0001 <0.0001

ZFHX3 Chrl6q 0.294 <0.0001 <0.0001

ZFP106 Chrl5q 0.5551 <0.0001 <0.0001

ZFP30 Chrl9q 0.4802 <0.0001 <0.0001

ZFP64 Chr20q 0.4918 <0.0001 <0.0001

ZFPM2 Chr8q 0.1689 <0.0001 <0.0001

ZFYVE16 Chr5q 0.4906 <0.0001 <0.0001

ZGPAT Chr20q 0.4484 <0.0001 <0.0001

ZHX3 Chr20q 0.1827 <0.0001 <0.0001

ZMAT5 Chr22q 0.4939 <0.0001 <0.0001

ZMYM2 Chrl3q 0.4452 <0.0001 <0.0001

ZMYM5 Chrl3q 0.5217 <0.0001 <0.0001

ZMYND8 Chr20q 0.2691 <0.0001 <0.0001

ZNF136 Chrl9p 0.5829 <0.0001 <0.0001

ZNF14 Chrl9p 0.4582 <0.0001 <0.0001

ZNF146 Chrl9q 0.4841 <0.0001 <0.0001

ZNF16 Chr8q 0.6829 <0.0001 <0.0001

ZNF207 Chrl7q 0.2614 <0.0001 <0.0001

ZNF212 Chr7q 0.5951 <0.0001 <0.0001

ZNF23 Chrl6q 0.5098 <0.0001 <0.0001

ZNF232 Chrl7p 0.3628 <0.0001 <0.0001

ZNF236 Chrl 8q 0.4293 <0.0001 <0.0001

ZNF250 Chr8q 0.5683 <0.0001 <0.0001

ZNF276 Chrl6q 0.3657 <0.0001 <0.0001

ZNF282 Chr7q 0.5685 <0.0001 <0.0001

ZNF302 Chrl9q 0.4301 <0.0001 <0.0001

ZNF330 Chr4q 0.5836 <0.0001 <0.0001

ZNF334 Chr20q 0.22 <0.0001 <0.0001

ZNF335 Chr20q 0.1821 <0.0001 <0.0001

ZNF34 Chr8q 0.6149 <0.0001 <0.0001

ZNF345 Chrl9q 0.3625 <0.0001 <0.0001

ZNF384 Chrl2p 0.567 <0.0001 <0.0001

ZNF395 Chr8p 0.5423 <0.0001 <0.0001

ZNF426 Chrl9p 0.5451 <0.0001 <0.0001

ZNF44 Chrl9p 0.4874 <0.0001 <0.0001

ZNF440 Chrl9p 0.257 <0.0001 <0.0001

ZNF442 Chrl9p 0.2641 <0.0001 <0.0001

ZNF443 Chrl9p 0.4554 <0.0001 <0.0001

ZNF467 Chr7q 0.3142 <0.0001 <0.0001

ZNF512B Chr20q 0.3907 <0.0001 <0.0001

ZNF516 Chrl 8q 0.333 <0.0001 <0.0001

ZNF529 Chrl9q 0.388 <0.0001 <0.0001

ZNF532 Chrl 8q 0.3647 <0.0001 <0.0001

ZNF562 Chrl9p 0.5805 <0.0001 <0.0001

ZNF571 Chrl9q 0.5094 <0.0001 <0.0001

ZNF573 Chrl9q 0.3888 <0.0001 <0.0001

ZNF623 Chr8q 0.6133 <0.0001 <0.0001 Correlation

Gene Symbol Location p-value qFDR

Coefficient

ZNF639 Chr3q 0.316 <0.0001 <0.0001

ZNF696 Chr8q 0.4866 <0.0001 <0.0001

ZNF7 Chr8q 0.6699 <0.0001 <0.0001

ZNF706 Chr8q 0.66 <0.0001 <0.0001

ZNF767 Chr7q 0.3539 <0.0001 <0.0001

ZNF770 Chrl5q 0.2485 <0.0001 <0.0001

ZNF778 Chrl6q 0.172 <0.0001 <0.0001

ZNF821 Chrl6q 0.2157 <0.0001 <0.0001

ZNF862 Chr7q 0.3799 <0.0001 <0.0001

ZNHIT3 Chrl7q 0.3299 <0.0001 <0.0001

ZSWIM1 Chr20q 0.2247 <0.0001 <0.0001

ZYX Chr7q 0.36 <0.0001 <0.0001

ZZEF1 Chrl7p 0.3768 <0.0001 <0.0001

Table 5: Gene expression signature predictive of complete response (CR) versus incomplete response (IR) using the CI VA-Correlated-Pathway (CCP) gene subset.

Fold- p-value Symbol Name

change

.91E-05 0.88 RHOT1 ras homolog gene family, member Tl

.92E-04 0.67 TIMP3 TIMP metallopeptidase inhibitor 3

.92E-04 0.82 PPP3CA protein phosphatase 3, catalytic subunit, alpha isozyme

.41E-04 0.87 DNAJB14 DnaJ (Hsp40) homolog, subfamily B, member 14

.88E-04 0.88 PKD2 polycystic kidney disease 2 (autosomal dominant)

.41E-04 0.85 UBL3 ubiquitin-like 3

.45E-04 0.84 WDR41 WD repeat domain 41

.16E-03 0.88 NUDT9 nudix (nucleoside diphosphate linked moiety X)-type motif 9 .51E-03 0.84 PGCP plasma glutamate carboxypeptidase

.64E-03 0.87 RASA1 RAS p21 protein activator (GTPase activating protein) 1

COP9 constitutive photomorphogenic homolog subunit 4 .12E-03 0.87 COPS4 (Arabidopsis)

.51E-03 0.77 PDLIM3 PDZ and LIM domain 3

.62E-03 0.89 AGGF1 angiogenic factor with G patch and FHA domains 1

.74E-03 0.94 RPL34 ribosomal protein L34

.76E-03 0.93 RPL23 ribosomal protein L23

.80E-03 0.91 UBE2D3 ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast) .00E-03 0.91 EIF3E eukaryotic translation initiation factor 3, subunit E

.09E-03 0.89 SLC30A5 solute carrier family 30 (zinc transporter), member 5

.23E-03 0.9 DUSP14 dual specificity phosphatase 14

.37E-03 0.84 KDELC1 KDEL (Lys-Asp-Glu-Leu) containing 1

.44E-03 0.89 NSA2 NSA2 ribosome biogenesis homolog (S. cerevisiae)

.44E-03 0.88 SLC25A32 solute carrier family 25, member 32

.62E-03 0.91 RPL26 ribosomal protein L26

.80E-03 0.93 TTBK2 tau tubulin kinase 2

.95E-03 0.85 RBI retinoblastoma 1

.08E-03 0.92 SCAMP3 secretory carrier membrane protein 3

.48E-03 0.88 THAP1 THAP domain containing, apoptosis associated protein 1 Fold- p-value Symbol Name

change

.53E-03 0.93 SLC25A44 solute carrier family 25, member 44

.89E-03 0.87 FAM18B1 family with sequence similarity 18, member Bl

.20E-03 0.8 SNCA synuclein, alpha (non A4 component of amyloid precursor) .26E-03 0.9 MANBA mannosidase, beta A, lysosomal

.30E-03 0.89 CCNH cyclin H

.81E-03 0.88 FECH ferrochelatase

.85E-03 0.89 PGRMC2 progesterone receptor membrane component 2

.85E-03 0.92 TBCA tubulin folding cofactor A

.18E-03 0.83 HSD17B11 hydroxysteroid (17-beta) dehydrogenase 11

.44E-03 0.84 ERLIN2 ER lipid raft associated 2

.45E-03 0.91 MAPKBP1 mitogen-activated protein kinase binding protein 1

.28E-03 0.9 SERINC3 serine incorporator 3

.39E-03 0.91 ENOPH1 enolase-phosphatase 1

.65E-03 0.89 SLFN12 schlafen family member 12

.74E-03 0.96 RPS23 ribosomal protein S23

.96E-03 0.93 C20orf4 chromosome 20 open reading frame 4

.34E-03 0.9 HEXB hexosaminidase B (beta polypeptide)

.93E-03 0.89 USP22 ubiquitin specific peptidase 22

.02E-03 0.92 SEC31A SEC31 homolog A (S. cerevisiae)

.79E-03 0.89 SERINC1 serine incorporator 1

.96E-03 1.1 1 MRPL15 mitochondrial ribosomal protein LI 5

.53E-03 1.15 SARS2 seryl-tRNA synthetase 2, mitochondrial

.34E-03 1.23 CDH3 cadherin 3, type 1, P-cadherin (placental)

.50E-03 1.18 RNASEH2A ribonuclease H2, subunit A

.49E-03 1.14 SPINT2 serine peptidase inhibitor, Kunitz type, 2

.26E-03 1.08 NOTCH4 notch 4

.17E-03 1.1 U2SURP U2 snRNP-associated SURP domain containing

.82E-03 1.08 E2F1 E2F transcription factor 1

.76E-03 1.14 NUDT15 nudix (nucleoside diphosphate linked moiety X)-type motif 15 .19E-03 1.12 AARS alanyl-tRNA synthetase

.30E-03 1.19 GPR19 G protein-coupled receptor 19

.16E-03 1.21 EZH2 enhancer of zeste homolog 2 (Drosophila)

.10E-03 1.13 DDX11 DEAD/H (Asp-Glu- Ala- Asp/His) box polypeptide 11

.86E-03 1.16 HIPK2 homeodomain interacting protein kinase 2

.85E-03 1.39 PRSS2 protease, serine, 2 (trypsin 2)

.78E-03 1.1 1 GINS3 GINS complex subunit 3 (PsG homolog)

.71E-03 1.13 PAK4 p21 protein (Cdc42/Rac)-activated kinase 4

.61E-03 1.21 PARP12 poly (ADP-ribose) polymerase family, member 12

.58E-03 1.22 MECOM MDS1 and EVI1 complex locus

.86E-03 1.19 EPHA1 EPH receptor Al

.75E-03 1.14 ZNF767 zinc finger family member 767

.43E-03 1.19 SLC27A3 solute carrier family 27 (fatty acid transporter), member 3 .30E-03 1.21 RAD54B RAD54 homolog B (S. cerevisiae)

.58E-03 1.17 NCAPG2 non- SMC condensin II complex, subunit G2 Fold- p-value Symbol Name

change

.69E-04 1.16 WDR91 WD repeat domain 91

.13E-04 1.36 PRSS1 protease, serine, 1 (trypsin 1)

.83E-04 1.21 MCM5 mmichromosome maintenance complex component 5 .15E-04 1.23 MCM4 mmichromosome maintenance complex component 4

Table 6: Differentially methylated genes between the CR and IR groups

Parametric Fold-

Unique-ID Accession Symbol p-value change

3.10E-06 0.74 cg26873164 NM 005985 SNAI1

9.40E-06 1.24 cg06006444 NM 003340 UBE2D3

1.93E-05 1.24 cgl2411068 NM 003072 SMARCA4

3.02E-05 1.21 cg02832245 NM 005033 EXOSC9

3.71E-05 1.2 cg02675896 NM 033211 LOC90355

4.65E-05 1.19 cg22968727 NM 000975 RPL11

4.85E-05 1.2 cg02782630 NM 139076 FLJ13614

5.54E-05 0.77 cgl 1086066 NM 173091 NFATC2

6.18E-05 1.2 cg03761560 NM 017626 DNAJB12

7.54E-05 1.15 cg26413355 NM 205548 UNQ9217

8.75E-05 1.25 cgO 1620569 NM 001625 AK2

1.07E-04 1.16 cg21559783 NM 152571 FLJ36779

1.12E-04 0.78 cg09017174 NM 004171 SLC1A2

1.15E-04 1.22 cg01254459 NM 002806 PSMC6

1.24E-04 1.17 cg24974477 NM 030821 PLA2G12A

1.72E-04 1.23 cg24323434 NM 001018108 SERF2

1.81E-04 0.8 cg06911113 NM 152376 UBXD3

2.06E-04 1.25 cg23248587 NM 003401 XRCC4

2.40E-04 1.23 cgl7506742 NM 000628 IL10RB

2.55E-04 1.21 cgl2099357 NM 152660 FAM76A

2.69E-04 1.23 cgl 1821147 NM 031435 THAP2

2.71E-04 1.19 cgl2477119 NM 016507 CRKRS

2.78E-04 1.19 cgl5507817 NM 058238 WNT7B

3.23E-04 0.82 cg00564163 NM 024636 STEAP4

3.28E-04 1.19 cgl7881637 NM 003776 MRPL40

3.31E-04 1.18 cgl5757271 NM 003392 WNT5A

3.42E-04 1.21 cg21284880 NM 005780 LHFP

3.60E-04 0.82 cg25457331 NM 006877 GMPR

3.79E-04 1.15 cgl 8497960 NM 006047 RBM12

3.83E-04 1.18 cg00948524 NM 032322 RNF135

3.94E-04 1.13 cg00763679 NM 001008491 SEPT2

3.98E-04 1.17 cgl 8042079 NM 018428 C17orf40 Parametric Fold-

Unique-ID Accession Symbol p-value change

3.98E-04 0.75 cg06038133 NM 032854 COR06

4.04E-04 1.21 cg27441551 NM 005700 DPP3

4.07E-04 1.2 cgO 1522721 NM 007065 CDC37

4.22E-04 1.19 cgl5785580 NM 005881 BCKDK

4.74E-04 1.19 cg01222684 NM 003314 TTC1

4.86E-04 1.2 cgO 1990225 NM 030805 LMAN2L

4.99E-04 1.18 cg22816171 NM 024045 DDX50

5.17E-04 1.21 cgl7895873 NM 006062 SMYD5

6.00E-04 1.15 cgl5484019 NM 014673 KIAA0103

6.12E-04 1.19 cgl 1603096 NM 003753 EIF3S7

6.23E-04 0.78 cg06834875 NM 032425 KIAA1822

6.28E-04 0.77 cgl 1521965 NM 002825 PTN

6.30E-04 1.2 cg06470552 NM 005445 CSPG6

6.50E-04 1.2 cgl 1220635 NM 016026 RDH11

6.62E-04 1.18 cg06999776 NM 004263 SEMA4F

6.64E-04 1.21 cg05401645 NM 178126 LOCI 62427

6.77E-04 1.19 cg27323780 NM 152912 MTIF3

7.04E-04 0.79 cg25947945 NM 005558 LAD1

7.12E-04 1.17 cg25853833 NM 017546 C2orf29

7.47E-04 1.16 cgl8181070 NM 013247 HTRA2

7.49E-04 1.18 cg01618083 NM 021117 CRY2

7.56E-04 1.13 cgl2448934 NM 014718 CLSTN3

7.67E-04 1.21 cgl6091845 NM 003601 SMARCA5

7.70E-04 1.17 cg05389183 NM 000943 PPIC

7.98E-04 1.14 cg03805364 NM 002572 PAFAH1B2

8.01E-04 1.2 cg00636639 NM 138777 MRRF

8.01E-04 1.16 cg06242000 NM 032331 MGC2408

8.24E-04 1.19 cg01634119 NM 003875 GMPS

8.67E-04 1.2 cg25232934 NM 153332 THEX1

8.90E-04 1.21 cg24403722 NM 004430 EGR3

9.01E-04 0.82 cg04219321 NM 002126 HLF

9.08E-04 1.25 cg02147791 NM 005870 SAP18

9.18E-04 0.88 cgl7009433 NM 000170 GLDC

9.26E-04 1.15 cg01465641 NM 003024 ITSN1

9.44E-04 1.16 cg06565684 NM 001033025 EXTL2

9.54E-04 1.17 cg24587268 NM 014835 OSBPL2

9.84E-04 1.16 cgl 1108432 NM 017884 PINX1 7: Different ially expressed miRNA between the CR and IR groups

Parametric

Fold-change Symbol Chromosomal Location p-value

1.72E-04 1.35 hsa-miR-lOb* chr2: 176723363-176723345

7.92E-04 1.36 hsa-miR-lOb chr2: 176723325-176723305

3.43E-03 1.4 hsa-miR-592 chr7: 126485438-126485457

4.61E-03 1.24 hsa-miR-129-3p chrl 1 :043559597-043559579

7.42E-03 1.19 hsa-miR-424 chrX: 133508376-133508397

8.27E-03 1.24 hsa-miR-302b chr4: l 13789094-113789113

8.32E-03 1.22 hsa-miR-135b chrl :203684112-203684134

8.91E-03 1.22 hsa-miR-182 chr7: 129197523-129197539

9.45E-03 1.3 ebv-miR-B ART 15 unmapped

1.06E-02 1.68 hsa-miR-509-3-5p chrX: 146148906-146148922

1.15E-02 1.38 hsa-miR-488 chrl : 175265133-175265152

1.30E-02 1.15 hsa-miR-371-5p chrl9:058982765-058982755

1.87E-02 1.26 hsa-miR-34b chrl l : 110888943-110888927

1.94E-02 1.22 hsa-miR-641 chrl9:045480350-045480368

2.04E-02 1.16 hsa-miR-498 chrl9:058869318-058869303

2.07E-02 1.25 hsa-miR-431 * chrl4: 100417180-100417167

2.14E-02 0.93 hsa-miR- 193a-3p chrl7:026911203-026911187

2.18E-02 0.8 hsa-miR-22 chrl7:001563958-001563976

2.45E-02 1.15 hsa-miR- 148a chr7:025956067-025956086

2.64E-02 1.19 hsa-miR-513a-5p chrX: 146102748-146102763

2.64E-02 1.31 hsa-miR-517b chrl9:058907409-058907390

2.68E-02 1.17 hsa-miR-7 chrl5:086956113-086956092

2.79E-02 1.17 hsa-miR-96 chr7: 129201815-129201836

2.88E-02 1.22 hsa-miR-200b chrl :001092424-001092408

3.01E-02 1.2 hsa-miR-708 chrl 1 :078790769-078790784

3.27E-02 0.78 hsa-miR- 1233 chrl 5:032461562-032461574 Parametric

Fold-change Symbol Chromosomal Location p-value

3.30E-02 1.09 hsa-miR-30a* chr6 :072169978-072169994

3.37E-02 1.16 hsa-miR-491-5p chr9:020706140-020706125

3.40E-02 0.87 NC2 00092197

3.53E-02 1.16 hsa-miR-7-1 * chr9:085774506-085774524

3.57E-02 1.14 hsa-miR-625* chrl4:065007645-065007627

3.61E-02 1.13 hsa-miR-545 chrX:073423686-073423707

3.91E-02 1.16 hsa-miR-628-5p chrl5:053452481-053452501

3.92E-02 1.15 hsa-miR-183 chr7: 129202043-129202062

3.99E-02 0.83 hsa-miR-33b chrl7:017657936-017657955

4.69E-02 1.17 hsa-miR-597 chr8:009636628-009636612

4.78E-02 1.16 hsa-miR-492 chrl2:093752356-093752339

4.89E-02 1.11 hsa-miR-629* chrl5:068158780-068158795

Table 8: Differentially expressed genes (CR versus IR) from the 1,772 genes identified to

Parametric Fold-

Symbol Name

p-value change

1.00E-06 0.87 RHOT1 ras homo log gene family, member Tl

1.81E-04 0.75 OLFML3 olfactomedin-like 3

2.17E-04 0.81 OLFML1 olfactomedin-like 1

2.98E-04 0.88 DUSP14 dual specificity phosphatase 14

3.43E-04 1.20 MCM4 minichromosome maintenance complex

component 4

3.55E-04 1.34 PRSS1 protease, serine, 1 (trypsin 1)

4.73E-04 0.70 TIMP3 TIMP metallopeptidase inhibitor 3

4.88E-04 0.88 RIN2 Ras and Rab interactor 2

5.99E-04 1.18 C19orf54 chromosome 19 open reading frame 54

6.21E-04 1.15 MCM7 minichromosome maintenance complex

component 7

6.93E-04 0.86 PGAP3 post-GPI attachment to proteins 3

7.65E-04 0.83 KDELC1 KDEL (Lys-Asp-Glu-Leu) containing 1

7.69E-04 0.85 PPP3CA protein phosphatase 3, catalytic subunit, alpha

isozyme

7.89E-04 0.86 UBL3 ubiquitin-like 3

1.10E-03 1.17 HIPK2 homeodomain interacting protein kinase 2

1.56E-03 1.16 NCAPG2 non-SMC condensin II complex, subunit G2 Parametric Fold-

Symbol Name

p-value change

1.77E-03 1.21 ZBTB10 zinc finger and BTB domain containing 10

1.83E-03 0.78 PDLIM3 PDZ and LIM domain 3

2.84E-03 0.91 RPL26 ribosomal protein L26

2.93E-03 1.26 CDH3 cadherin 3, type 1, P-cadherin (placental)

3.12E-03 0.95 RPL19 ribosomal protein LI 9

3.22E-03 0.93 RPL23 ribosomal protein L23

3.35E-03 0.90 YTHDF1 YTH domain family, member 1

3.62E-03 1.12 AARS alanyl-tRNA synthetase

4.19E-03 0.88 FECH ferrochelatase

4.83E-03 1.08 NOTCH4 notch 4

4.91E-03 0.90 SYNRG synergin, gamma

5.57E-03 0.92 TNFSF12 tumor necrosis factor (ligand) superfamily, member 12

5.67E-03 0.91 TPD52L2 tumor protein D52-like 2

5.73E-03 0.90 NDRG3 NDRG family member 3

6.02E-03 1.04 PDPR pyruvate dehydrogenase phosphatase regulatory subunit

6.07E-03 0.88 BGLAP bone gamma-carboxyglutamate (gla) protein

6.24E-03 0.88 SLM02 slowmo homolog 2 (Drosophila)

6.31E-03 0.89 RASA1 RAS p21 protein activator (GTPase activating protein) 1

6.42E-03 0.89 STX8 syntaxin 8

6.44E-03 1.19 PARP12 poly (ADP-ribose) polymerase family, member

12

6.76E-03 0.88 BLMH bleomycin hydrolase

6.83E-03 1.19 MECOM MDS1 and EVI1 complex locus

6.94E-03 0.89 COPS4 COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)

6.94E-03 0.90 DNAJB14 DnaJ (Hsp40) homolog, subfamily B, member

14

7.01E-03 1.09 COG4 component of oligomeric golgi complex 4

7.12E-03 1.36 PRSS2 protease, serine, 2 (trypsin 2)

7.37E-03 0.96 RPS23 ribosomal protein S23

7.50E-03 0.90 KRT10 keratin 10

7.57E-03 0.89 ALG5 asparagine-linked glycosylation 5, dolichyl- phosphate beta-glucosyltransferase homolog (S. cerevisiae)

7.65E-03 0.88 FAM172A family with sequence similarity 172, member A

7.83E-03 1.10 GINS3 GINS complex subunit 3 (Psf3 homolog)

8.16E-03 0.93 C20orf4 chromosome 20 open reading frame 4

8.18E-03 0.90 PPP1R3D protein phosphatase 1 , regulatory (inhibitor) subunit 3D

8.30E-03 1.11 TRIM24 tripartite motif containing 24 Parametric Fold-

Symbol Name

p-value change

8.39E-03 0.88 PPAP2A phosphatidic acid phosphatase type 2A

8.41E-03 1.08 MY07A myosin VIIA

8.41E-03 1.07 GAS 8 growth arrest-specific 8

8.43E-03 0.92 PTPN1 protein tyrosine phosphatase, non-receptor type

1

8.51E-03 1.19 EZH2 enhancer of zeste homolog 2 (Drosophila)

9.15E-03 1.23 SLC7A11 solute carrier family 7, (cationic amino acid

transporter, y+ system) member 1 1

9.41E-03 0.87 ENPP1 ectonucleotide

pyrophosphatase/phosphodiesterase 1

9.75E-03 0.91 RWDD1 RWD domain containing 1

9.96E-03 0.93 TDRKH tudor and KH domain containing

Table 9: 422 significant genes included in the final model or signature. CR/IR value indicates the ratio of the natural logarithm of the average of the expression level of an mRNA in good responders (ie. complete responders (CR)) to the natural logarithm of the average of the expression level of the mRNA in bad responders (i.e. incomplete

Symbol CR/IR Name Entrez ID

MYB 1.17 v-myb myeloblastosis viral oncogene homolog (avian) 4602

DROSHA 1.16 drosha, ribonuclease type III 29102

MCM7 1.16 minichromosome maintenance complex component 7 4176

ZNF85 1.16 zinc finger protein 85 7639

GPR19 1.16 G protein-coupled receptor 19 2842

PTN 1.16 pleiotrophin 5764

MARCH6 1.15 membrane-associated ring finger (C3HC4) 6 10299

ISYNA1 1.15 inositol-3 -phosphate synthase 1 51477

POLE 1.14 polymerase (DNA directed), epsilon 5426

PLAGL2 1.14 pleomorphic adenoma gene-like 2 5326

ENTPD5 1.13 ectonucleoside triphosphate diphosphohydrolase 5 957

LRRC8D 1.13 leucine rich repeat containing 8 family, member D 55144

BRD9 1.13 bromodomain containing 9 65980

WDR91 1.13 WD repeat domain 91 29062

MTAP 1.12 methylthioadenosine phosphorylase 4507

TRIM24 1.12 tripartite motif containing 24 8805

AARS 1.12 alanyl-tRNA synthetase 16

ZNF467 1.12 zinc finger protein 467 168544

CHD7 1.12 chromodomain helicase DNA binding protein 7 55636

STX17 1.11 syntaxin 17 55014

RFWD3 1.11 ring finger and WD repeat domain 3 55159

ZNF767 1.11 zinc finger family member 767 79970

PRRC2A 1.11 proline-rich coiled-coil 2A 7916

Cl lorf67 1.11 chromosome 11 open reading frame 67 28971

NARS2 1.11 asparaginyl-tRNA synthetase 2, mitochondrial (putative) 79731

JARID2 1.11 jumonji, AT rich interactive domain 2 3720

GINS3 1.1 GINS complex subunit 3 (Psf3 homolog) 64785

AKAP8L 1.1 A kinase (PRKA) anchor protein 8 -like 26993

MAK 1.1 male germ cell-associated kinase 4117

COG4 1.09 component of oligomeric golgi complex 4 25839

UBAP2L 1.09 ubiquitin associated protein 2-like 9898

PAK4 1.09 p21 protein (Cdc42/Rac)-activated kinase 4 10298

DDX11 1.09 DEAD/H (Asp-Glu- Ala- Asp/His) box polypeptide 11 1663

ODZ1 1.09 odz, odd Oz/ten-m homolog l(Drosophila) 10178

C6orf26 1.09 chromosome 6 open reading frame 26 401251

RBM38 1.09 RNA binding motif protein 38 55544 v-myb myeloblastosis viral oncogene homolog (avian)-like

MYBL2 1.09 4605

2

TPX2 1.09 TPX2, microtubule-associated, homolog (Xenopus laevis) 22974

PLSCR1 1.09 phospholipid scramblase 1 5359 Symbol CR/IR Name Entrez ID

NOTCH4 1.08 notch 4 4855

MY07A 1.08 myosin VIIA 4647

WIZ 1.08 widely interspaced zinc finger motifs 58525

EHMT2 1.08 euchromatic histone-lysine N-methyltransferase 2 10919

ZC3HAV1 1.08 zinc finger CCCH-type, antiviral 1 56829

BRAF 1.08 v-raf murine sarcoma viral oncogene homo log Bl 673

WDR59 1.08 WD repeat domain 59 79726

PBX2 1.08 pre-B-cell leukemia homeobox 2 5089

ZNF395 1.08 zinc finger protein 395 55893

CEBPA 1.08 CCAAT/enhancer binding protein (C/EBP), alpha 1050

FXYD1 1.08 FXYD domain containing ion transport regulator 1 5348

TP53 1.08 tumor protein p53 7157

GAS 8 1.07 growth arrest-specific 8 2622

MMP15 1.07 matrix metallopeptidase 15 (membrane -inserted) 4324

FASTK 1.07 Fas-activated serine/threonine kinase 10922

FAM86B1 1.07 family with sequence similarity 86, member Bl 85002

SPAG5 1.07 sperm associated antigen 5 10615

TATA box binding protein (TBP)-associated factor, RNA

TAF1C 1.06 9013 polymerase I, C, 1 lOkDa

LIPG 1.06 lipase, endothelial 9388

CASP2 1.06 caspase 2, apopto sis-related cysteine peptidase 835

ZNF282 1.06 zinc finger protein 282 8427

DNASE2 1.06 deoxyribonuclease II, lysosomal 1777

TCN2 1.06 transcobalamin II 6948 human immunodeficiency virus type I enhancer binding

HIVEP2 1.06 3097 protein 2

DPM3 1.06 dolichyl-phosphate mannosyltransferase polypeptide 3 54344

WNT5A 1.06 wingless-type MMTV integration site family, member 5A 7474

CLSTN3 1.05 calsyntenin 3 9746

LRRC61 1.05 leucine rich repeat containing 61 65999

RAD52 1.05 RAD52 homo log (S. cerevisiae) 5893

CHD4 1.05 chromodomain helicase DNA binding protein 4 1108

PTMS 1.05 parathymosin 5763

KIAA0753 1.05 KIAA0753 9851 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase

YWHAH 1.05 7533 activation protein, eta polypeptide

LAD1 1.05 ladinin 1 3898

ARGLU1 1.05 arginine and glutamate rich 1 55082

SETBP1 1.05 SET binding protein 1 26040

LSR 1.05 lipolysis stimulated lipoprotein receptor 51599

ZNF334 1.05 zinc finger protein 334 55713 Symbol CR/IR Name Entrez ID

BCL2 1.05 B-cell CLL/lymphoma 2 596

CASC1 1.05 cancer susceptibility candidate 1 55259

WISP3 1.05 WNT1 inducible signaling pathway protein 3 8838

CXCL9 1.05 chemokine (C-X-C motif) ligand 9 4283

ZNF695 1.04 zinc finger protein 695 57116

PDPR 1.04 pyruvate dehydrogenase phosphatase regulatory subunit 55066

E2F1 1.04 E2F transcription factor 1 1869

PLD1 1.04 phospho lipase Dl, phosphatidylcho line-specific 5337

AKT2 1.04 v-akt murine thymoma viral oncogene homolog 2 208

NRF 1 1.04 nuclear respiratory factor 1 4899

ZNF384 1.04 zinc finger protein 384 171017

BANP 1.04 BTG3 associated nuclear protein 54971

MDN1 1.04 MDN1, midasin homolog (yeast) 23195

GTPBP3 1.04 GTP binding protein 3 (mitochondrial) 84705

PRP3 pre-mRNA processing factor 3 homolog (S.

PRPF3 1.04 9129 cerevisiae)

KIAA0907 1.04 KIAA0907 22889

POGZ 1.04 pogo transposable element with ZNF domain 23126

ECH1 1.04 enoyl CoA hydratase 1 , peroxisomal 1891

CHERP 1.04 calcium homeostasis endoplasmic reticulum protein 10523

DENND5B 1.04 DENN/MADD domain containing 5B 160518

NAA16 1.04 N(alpha)-acetyltransferase 16, NatA auxiliary subunit 79612

SIAH2 1.04 seven in absentia homolog 2 (Drosophila) 6478

PSTPIP2 1.04 proline-serine-threonine phosphatase interacting protein 2 9050

TYRO 3 1.04 TYR03 protein tyrosine kinase 7301

SWI/SNF related, matrix associated, actin dependent

SMARCA4 1.04 6597 regulator of chromatin, subfamily a, member 4

SPRY2 1.04 sprouty homolog 2 (Drosophila) 10253

FAM76A 1.03 family with sequence similarity 76, member A 199870

ZNF778 1.03 zinc finger protein 778 197320 solute carrier family 1 (glial high affinity glutamate

SLC1A2 1.03 6506 transporter), member 2

CRTC1 1.03 CREB regulated transcription coactivator 1 23373

TMEM209 1.03 transmembrane protein 209 84928 solute carrier organic anion transporter family, member

SLC01A2 1.03 6579

1A2

SMO 1.03 smoothened homolog (Drosophila) 6608

PAFAH1B platelet-activating factor acetylhydrolase lb, catalytic

1.03 5049 2 subunit 2 (30kDa)

RNA binding protein, autoantigenic (hnRNP-associated

RALY 1.03 22913 with lethal yellow homolog (mouse)) Symbol CR/IR Name Entrez ID

AKAP3 1.03 A kinase (PRKA) anchor protein 3 10566

COX4I1 1.03 cytochrome c oxidase subunit IV isoform 1 1327

TARS2 1.03 threonyl-tRNA synthetase 2, mitochondrial (putative) 80222 microtubule associated monoxygenase, calponin and LIM

MICALl 1.03 64780 domain containing 1

DPP3 1.03 dipeptidyl-peptidase 3 10072

USP21 1.03 ubiquitin specific peptidase 21 27005

SETDB1 1.03 SET domain, bifurcated 1 9869

WDR60 1.03 WD repeat domain 60 55112

VPS72 1.03 vacuolar protein sorting 72 homo log (S. cerevisiae) 6944

MYH9 1.03 myosin, heavy chain 9, non-muscle 4627

PTK2 1.03 PTK2 protein tyrosine kinase 2 5747

PGLS 1.03 6-phosphogluconolactonase 25796

DCAF15 1.03 DDB1 and CUL4 associated factor 15 90379

APOL2 1.03 apolipoprotein L, 2 23780

ZNF44 1.03 zinc finger protein 44 51710

TRMT1 1.03 TRMl tRNA methyltransferase 1 homo log (S. cerevisiae) 55621

AURKB 1.03 aurora kinase B 9212

ADAM metallopeptidase with thrombospondin type 1

ADAMTS3 1.03 9508 motif, 3

TMEM231 1.03 transmembrane protein 231 79583

APOL1 1.03 apolipoprotein L, 1 8542

KLRAP 1 1.02 killer cell lectin-like receptor subfamily A pseudogene 1 10748

RPS20 1.02 ribosomal protein S20 6224

PIP5K1A 1.02 phosphatidylinositol-4-phosphate 5-kinase, type I, alpha 8394

RBM12 1.02 RNA binding motif protein 12 10137

SEC62 1.02 SEC62 homo log (S. cerevisiae) 7095

ZNF212 1.02 zinc finger protein 212 7988

CLK2 1.02 CDC-like kinase 2 1196

PFDN2 1.02 prefoldin subunit 2 5202

ACTR3B 1.02 ARP3 actin-related protein 3 homolog B (yeast) 57180

PCM1 1.02 pericentriolar material 1 5108

SYNE1 1.02 spectrin repeat containing, nuclear envelope 1 23345 leukemia inhibitory factor (cholinergic differentiation

LIF 1.02 3976 factor)

JUNB 1.02 jun B proto-oncogene 3726

HMBOX1 1.02 homeobox containing 1 79618

AURKA 1.02 aurora kinase A 6790

DERL1 1.02 Deri -like domain family, member 1 79139

LRRC23 1.02 leucine rich repeat containing 23 10233

DUSP4 1.02 dual specificity phosphatase 4 1846 Symbol CR/IR Name Entrez ID

SNAI1 1.01 snail homolog 1 (Drosophila) 6615

OR7C2 1.01 olfactory receptor, family 7, subfamily C, member 2 26658

TSGA14 1.01 testis specific, 14 95681

HAUS5 1.01 HAUS augmin-like complex, subunit 5 23354

APOM 1.01 apolipoprotein M 55937

JR 1.01 jerky homolog (mouse) 8629

LPPR2 1.01 lipid phosphate phosphatase-related protein type 2 64748

ZNF236 1.01 zinc finger protein 236 7776

SUGP2 1.01 SURP and G patch domain containing 2 10147

NFIX 1.01 nuclear factor I/X (CCAAT -binding transcription factor) 4784

MGA 1.01 MAX gene associated 23269

HLF 1.01 hepatic leukemia factor 3131

AKAP8 1.01 A kinase (PRKA) anchor protein 8 10270

RAP2B 1.01 RAP2B, member of RAS oncogene family 5912

TYMP 1.01 thymidine phosphorylase 1890

CCDC130 1.01 coiled-coil domain containing 130 81576

SIN3B 1.01 SIN3 homolog B, transcription regulator (yeast) 23309

MARCH6 1.01 membrane-associated ring finger (C3HC4) 7 64844

ATF6B 1.01 activating transcription factor 6 beta 1388

DLGAP4 1.01 discs, large (Drosophila) homolog-associated protein 4 22839

DCLK1 1.01 doublecortin-like kinase 1 9201

SFRS18 1.01 splicing factor, arginine/serine-rich 18 25957

LHFPL2 1.01 lipoma HMGIC fusion partner-like 2 10184

PHC1 1.01 polyhomeotic homolog 1 (Drosophila) 1911

MTERFD1 1.01 MTERF domain containing 1 51001

MRPL40 1.01 mitochondrial ribosomal protein L40 64976

CCDC109

1.01 coiled-coil domain containing 109B 55013 B

WRAP53 1 WD repeat containing, antisense to TP53 55135

UBOX5 1 U-box domain containing 5 22888

AP1B1 1 adaptor-related protein complex 1 , beta 1 subunit 162 guanine nucleotide binding protein (G protein), alpha z

GNAZ 1 2781 polypeptide

MAU2 1 MAU2 chromatid cohesion factor homolog (C. elegans) 23383

RNF13 1 ring finger protein 13 11342

EFNA3 1 ephrin-A3 1944

PPP3CC 1 protein phosphatase 3, catalytic subunit, gamma isozyme 5533

GGT5 1 gamma-glutamyltransferase 5 2687

ZNF516 1 zinc finger protein 516 9658

PEPD 1 peptidase D 5184 Symbol CR/IR Name Entrez ID

HMOX1 1 heme oxygenase (decycling) 1 3162

CAPRIN2 1 caprin family member 2 65981

LRP6 1 low density lipoprotein receptor-related protein 6 4040

AN02 1 anoctamin 2 57101

CCR7 1 chemokine (C-C motif) receptor 7 1236

DCN1, defective in cullin neddylation 1, domain

DCUN1D2 1 55208 containing 2 (S. cerevisiae)

MFAP3L 1 micro fibrillar-associated protein 3 -like 9848

TULP3 1 tubby like protein 3 7289

NCF4 1 neutrophil cytosolic factor 4, 40kDa 4689

SWI/SNF related, matrix associated, actin dependent

SMARCA5 1 8467 regulator of chromatin, subfamily a, member 5

FAM65A 1 family with sequence similarity 65, member A 79567

DNAJC3 1 DnaJ (Hsp40) homolog, subfamily C, member 3 5611

TPT1 0.99 tumor protein, translationally-controlled 1 7178

ELL2 0.99 elongation factor, RNA polymerase II, 2 22936

SERF2 0.99 small EDR -rich factor 2 10169 platelet-derived growth factor beta polypeptide (simian

PDGFB 0.99 5155 sarcoma viral (v-sis) oncogene homolog)

SCNM1 0.99 sodium channel modifier 1 79005

L3MBTL1 0.99 l(3)mbt-like 1 (Drosophila) 26013

LAPTM4B 0.99 lysosomal protein transmembrane 4 beta 55353 translocase of outer mitochondrial membrane 22 homolog

TOMM22 0.99 56993

(yeast)

CHD1 0.99 chromodomain helicase DNA binding protein 1 1105

MRAS 0.99 muscle RAS oncogene homolog 22808

BCKDK 0.99 branched chain ketoacid dehydrogenase kinase 10295

SMYD5 0.99 SMYD family member 5 10322

NSFL1C 0.99 NSFL1 (p97) cofactor (p47) 55968

PPOX 0.99 protoporphyrinogen oxidase 5498

IL2RB 0.99 interleukin 2 receptor, beta 3560

QTRT1 0.99 queuine tRNA-ribosyltransferase 1 81890

PSD3 0.99 pleckstrin and Sec7 domain containing 3 23362

NAGA 0.99 N-acetylgalactosaminidase, alpha- 4668

KIAA0528 0.99 KIAA0528 9847

INPP4B 0.99 inositol polyphosphate-4-phosphatase, type II, 105kDa 8821

SCHIP1 0.99 schwannomin interacting protein 1 29970

PEX5 0.99 peroxisomal biogenesis factor 5 5830 glucuronidase, beta/immunoglobulin lambda-like

LOC91316 0.99 91316 polypeptide 1 pseudogene

ZSWIM1 0.98 zinc finger, SWIM-type containing 1 90204 Symbol CR/IR Name Entrez ID

LOC72999

0.98 hypothetical protein LOC729991 729991 1

PTCD2 0.98 pentatricopeptide repeat domain 2 79810

KLHL26 0.98 kelch-like 26 (Drosophila) 55295

ASXL1 0.98 additional sex combs like 1 (Drosophila) 171023

OSBPL2 0.98 oxysterol binding protein-like 2 9885

TBC1D22

0.98 TBC 1 domain family, member 22A 25771 A

SYDE1 0.98 synapse defective 1, Rho GTPase, homo log 1 (C. elegans) 85360

EFNA4 0.98 ephrin-A4 1945 core-binding factor, runt domain, alpha subunit 2;

CBFA2T2 0.98 9139 translocated to, 2

SC4MOL 0.98 sterol-C4-methyl oxidase-like 6307

CTSO 0.98 cathepsin O 1519

EPS8 0.98 epidermal growth factor receptor pathway substrate 8 2059

C6orfl24 0.98 chromosome 6 open reading frame 124 653483

PLLP 0.98 plasmolipin 51090 colony stimulating factor 2 receptor, beta, low-affinity

CSF2RB 0.98 1439

(granulocyte-macrophage)

SLC39A8 0.98 solute carrier family 39 (zinc transporter), member 8 64116 suppression of tumorigenicity 18 (breast carcinoma) (zinc

ST18 0.97 9705 finger protein)

STEAP4 0.97 STEAP family member 4 79689

ARL15 0.97 ADP-ribosylation factor- like 15 54622

SIRT2 0.97 sirtuin 2 22933

SERHL2 0.97 serine hydrolase-like 2 253190

RGNEF 0.97 190 kDa guanine nucleotide exchange factor 64283

DNAJC13 0.97 DnaJ (Hsp40) homolog, subfamily C, member 13 23317 proteasome (prosome, macropain) 26S subunit, non-

PSMD3 0.97 5709

ATPase, 3

ANKRD27 0.97 ankyrin repeat domain 27 (VPS9 domain) 84079

SYNGR1 0.97 synaptogyrin 1 9145

ARFGAP3 0.97 ADP-ribosylation factor GTPase activating protein 3 26286

CDC40 0.97 cell division cycle 40 homolog (S. cerevisiae) 51362

MEF2C 0.97 myocyte enhancer factor 2C 4208

GOLT1B 0.97 golgi transport IB 51026

GAS2L1 0.97 growth arrest-specific 2 like 1 10634 sprouty homolog 1, antagonist of FGF signaling

SPRY1 0.97 10252

(Drosophila)

SMPDL3A 0.97 sphingomyelin phosphodiesterase, acid-like 3 A 10924

DLC1 0.97 deleted in liver cancer 1 10395

KDELR3 0.97 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein 1 1015 Symbol CR/IR Name Entrez ID

retention receptor 3

RPS23 0.96 ribosomal protein S23 6228

ENOX1 0.96 ecto-NOX disulfide-thiol exchanger 1 55068 eukaryotic translation initiation factor 2B, subunit 5

EIF2B5 0.96 8893 epsilon, 82kDa

B2M 0.96 beta-2 -microglobulin 567

Clorf77 0.96 chromosome 1 open reading frame 77 26097

ARL2BP 0.96 ADP-ribosylation factor-like 2 binding protein 23568

AP3M2 0.96 adaptor-related protein complex 3, mu 2 subunit 10947

TUBGCP4 0.96 tubulin, gamma complex associated protein 4 27229

MAVS 0.96 mitochondrial antiviral signaling protein 57506

NQOl 0.96 NAD(P)H dehydrogenase, quinone 1 1728

ZFPM2 0.96 zinc finger protein, multitype 2 23414

RPL19 0.95 ribosomal protein LI 9 6143

SHC (Src homology 2 domain containing) transforming

SHC1 0.95 6464 protein 1

EIF3J 0.95 eukaryotic translation initiation factor 3, subunit J 8669

FGFRIOP 0.95 FGFR1 oncogene partner 11116

ADP-ribosylation factor guanine nucleotide-exchange

ARFGEF2 0.95 10564 factor 2 (brefeldin A-inhibited)

ITM2B 0.95 integral membrane protein 2B 9445

TRIM 13 0.95 tripartite motif containing 13 10206

MSL1 0.95 male-specific lethal 1 homolog (Drosophila) 339287

SRSF6 0.95 serine/arginine-rich splicing factor 6 6431

SREBF1 0.95 sterol regulatory element binding transcription factor 1 6720

CSNK2A2 0.95 casein kinase 2, alpha prime polypeptide 1459

TTC37 0.95 tetratricopeptide repeat domain 37 9652

MARCKS 0.95 myristoylated alanine-rich protein kinase C substrate 4082

PLOD2 0.95 procollagen- lysine, 2-oxoglutarate 5-dioxygenase 2 5352

TOM1 0.94 target of mybl (chicken) 10043

TDRKH 0.94 tudor and KH domain containing 11022

MCTP1 0.94 multiple C2 domains, transmembrane 1 79772

CTSA 0.94 cathepsin A 5476

IFT52 0.94 intraflagellar transport 52 homolog (Chlamydomonas) 51098 signal sequence receptor, gamma (translocon-associated

SSR3 0.94 6747 protein gamma)

GAS7 0.94 growth arrest-specific 7 8522

GLRX 0.94 glutaredoxin (thioltransferase) 2745

GUCY1A3 0.94 guanylate cyclase 1 , soluble, alpha 3 2982

PDGFRL 0.94 platelet-derived growth factor receptor-like 5157

MATK 0.93 megakaryocyte-associated tyrosine kinase 4145 Symbol CR/IR Name Entrez ID

RPL23 0.93 ribosomal protein L23 9349

TNFSF12 0.93 tumor necrosis factor (ligand) superfamily, member 12 8742

C20orf4 0.93 chromosome 20 open reading frame 4 25980

C15orf24 0.93 chromosome 15 open reading frame 24 56851

PEX11B 0.93 peroxisomal biogenesis factor 11 beta 8799

MN1 0.93 meningioma (disrupted in balanced translocation) 1 4330

C6orfl20 0.93 chromosome 6 open reading frame 120 387263

ANAPC10 0.93 anaphase promoting complex subunit 10 10393

AP1M2 0.93 adaptor-related protein complex 1 , mu 2 subunit 10053

SLC46A3 0.93 solute carrier family 46, member 3 283537

MEIS3P1 0.93 Meis homeobox 3 pseudogene 1 4213

ICAM1 0.93 intercellular adhesion molecule 1 3383

AKAP12 0.93 A kinase (PRKA) anchor protein 12 9590

IGLL3P 0.93 immunoglobulin lambda-like polypeptide 3, pseudogene 91353

PTPN1 0.92 protein tyrosine phosphatase, non-receptor type 1 5770

SNAP23 0.92 synaptosomal-associated protein, 23kDa 8773

DNAJB12 0.92 DnaJ (Hsp40) homo log, subfamily B, member 12 54788

HEXB 0.92 hexosaminidase B (beta polypeptide) 3074

UFM1 0.92 ubiquitin-fold modifier 1 51569

ATP6V1B ATPase, H+ transporting, lysosomal 56/58kDa, VI subunit

0.92 526 2 B2

SEC24D 0.92 SEC24 family, member D (S. cerevisiae) 9871

PDLIM5 0.92 PDZ and LIM domain 5 10611

OSTM1 0.92 osteopetrosis associated transmembrane protein 1 28962

PDLIM2 0.92 PDZ and LIM domain 2 (mystique) 64236

TSPO 0.92 translocator protein (18kDa) 706

NAAA 0.92 N-acylethanolamine acid amidase 27163

ATP6V1C ATPase, H+ transporting, lysosomal 42kDa, VI subunit

0.92 528 1 CI

TLR2 0.92 toll-like receptor 2 7097

LHFP 0.92 lipoma HMGIC fusion partner 10186

DSE 0.92 dermatan sulfate epimerase 29940

ATP6V1A 0.91 ATPase, H+ transporting, lysosomal 70kDa, VI subunit A 523

RPL26 0.91 ribosomal protein L26 6154

MAPKBP1 0.91 mitogen-activated protein kinase binding protein 1 23005

TPD52L2 0.91 tumor protein D52-like 2 7165

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex,

NDUFAF1 0.91 51103 assembly factor 1

AGGF1 0.91 angiogenic factor with G patch and FHA domains 1 55109

NDRG3 0.91 NDRG family member 3 57446

PDE4A 0.91 phosphodiesterase 4A, cAMP-specific 5141 Symbol CR/IR Name Entrez ID

RWDD1 0.91 RWD domain containing 1 51389

PPP1R3D 0.91 protein phosphatase 1, regulatory (inhibitor) subunit 3D 5509

PGRMC2 0.91 progesterone receptor membrane component 2 10424

MFSD1 0.91 major facilitator superfamily domain containing 1 64747

SERINC1 0.91 serine incorporator 1 57515 interleukin 6 signal transducer (gpl30, oncostatin M

IL6ST 0.91 3572 receptor)

SUCLA2 0.91 succinate-CoA ligase, ADP-forming, beta subunit 8803

PLK2 0.91 polo-like kinase 2 10769

DPT 0.9 dermatopontin 1805

PKD2 0.9 polycystic kidney disease 2 (autosomal dominant) 5311

YTHDF1 0.9 YTH domain family, member 1 54915

SYNRG 0.9 synergin, gamma 11276

NSA2 0.9 NSA2 ribosome biogenesis homolog (S. cerevisiae) 10412

DNAJB14 0.9 DnaJ (Hsp40) homolog, subfamily B, member 14 79982

STX8 0.9 syntaxin 8 9482

KRT10 0.9 keratin 10 3858

PGCP 0.9 plasma glutamate carboxypeptidase 10404 ras-related C3 botulinum toxin substrate 2 (rho family,

RAC2 0.9 5880 small GTP binding protein Rac2)

F2R 0.9 coagulation factor II (thrombin) receptor 2149

MAN1A1 0.9 mannosidase, alpha, class 1A, member 1 4121

CCNH 0.89 cyclin H 902

FECH 0.89 ferrochelatase 2235

RASA1 0.89 RAS p21 protein activator (GTPase activating protein) 1 5921 asparagine-linked glycosylation 5, dolichyl-phosphate

ALG5 0.89 29880 beta-glucosyltransferase homolog (S. cerevisiae)

COP9 constitutive photomorphogenic homolog subunit 4

COPS4 0.89 51138

(Arabidopsis)

BGLAP 0.89 bone gamma-carboxyglutamate (gla) protein 632

WTAP 0.89 Wilms tumor 1 associated protein 9589

MLX 0.88 MAX-like protein X 6945

DUSP14 0.88 dual specificity phosphatase 14 11072

RIN2 0.88 Ras and Rab interactor 2 54453

MFAP3 0.88 microfibrillar-associated protein 3 4238

SLM02 0.88 slowmo homolog 2 (Drosophila) 51012

PPAP2A 0.88 phosphatidic acid phosphatase type 2A 8611

FAM172A 0.88 family with sequence similarity 172, member A 83989

TPST2 0.88 tyrosylprotein sulfotransferase 2 8459 v-maf musculoaponeurotic fibrosarcoma oncogene

MAF 0.88 4094 homolog (avian) Symbol CR/IR Name Entrez ID

IGFBP4 0.88 insulin-like growth factor binding protein 4 3487

ACSL1 0.88 acyl-CoA synthetase long-chain family member 1 2180

C13orfl5 0.88 chromosome 13 open reading frame 15 28984

RHOBTB3 0.88 Rho-related BTB domain containing 3 22836

THBS1 0.88 thrombospondin 1 7057

RHOT1 0.87 ras homo log gene family, member Tl 55288

C10orf26 0.87 chromosome 10 open reading frame 26 54838

BLMH 0.87 bleomycin hydrolase 642

RAB32 0.87 RAB32, member RAS oncogene family 10981

UBL3 0.86 ubiquitin-like 3 5412

PGAP3 0.86 post-GPI attachment to proteins 3 93210

ENPP1 0.86 ectonucleotide pyrophosphatase/phosphodiesterase 1 5167

EVI2A 0.86 ecotropic viral integration site 2A 2123

FBLN1 0.86 fibulin 1 2192

PPP3CA 0.85 protein phosphatase 3, catalytic subunit, alpha isozyme 5530

CCL11 0.85 chemokine (C-C motif) ligand 11 6356

TD02 0.85 tryptophan 2,3-dioxygenase 6999

CCPG1 0.84 cell cycle progression 1 9236

RBI 0.84 retinoblastoma 1 5925

PPIC 0.84 peptidylprolyl isomerase C (cyclophilin C) 5480

PMP22 0.84 peripheral myelin protein 22 5376

KDELC1 0.83 KDEL (Lys-Asp-Glu-Leu) containing 1 79070

EDNRA 0.83 endothelin receptor type A 1909

OLFML1 0.82 olfactomedin-like 1 283298

FZD1 0.81 frizzled homolog 1 (Drosophila) 8321

OMD 0.79 osteomodulin 4958

COPZ2 0.78 coatomer protein complex, subunit zeta 2 51226

PDLIM3 0.78 PDZ and LIM domain 3 27295

OLFML3 0.76 olfactomedin-like 3 56944

PDGFD 0.76 platelet derived growth factor D 80310

NUAK1 0.75 NUAK family, SNFl-like kinase, 1 9891

TIMP3 0.7 TIMP metallopeptidase inhibitor 3 7078

FAP 0.7 fibroblast activation protein, alpha 2191

Table 10: Pathways and biological processes identified with the software for enrichment analysis GeneGo. These pathways were overrepresented in cluster #1 of the NMF consensus clustering

Maps p-value FDR Network Objects

Immune response Oncostatin M 3.755E-05 6.709E-03 Eotaxin, LIFR, gpl30, LIF signaling via JAK-Stat in human receptor

cells

Table 11: Pathways and biological processes identified with the software for enrichment analysis GeneGo. These pathways overrepresented in cluster #2 of the NMF consensus

Maps p-value FDR Network Objects from

Active Data

Cell cycle_Chromosome 3.101E-05 8.735E-03 Aurora-B, AKAP8, CAP-G/G2, condensation in prometaphase Aurora-A

G-protein signaling_Cross-talk 4.526E-05 8.735E-03 B-Raf, PLD1, AKT(PKB), between Ras-family GTPases pl20GAP Maps p-value FDR Network Objects from

Active Data

Immune response_C5a signaling 7.605E-05 9.785E-03 G-protein alpha-i family, B-Raf,

Bcl-2, PLD1, AKT(PKB)

Cell adhesion_Ephrin signaling 6.566E-04 4.989E-02 Ephrin-A, G-protein alpha-i family, FAK1, pl20GAP

DNA damagejnhibition of 6.941E-04 4.989E-02 p53, AKT(PKB), E2F1 telomerase activity and cellular

senescence

Development_Leptin signaling via 7.755E-04 4.989E-02 PTP-1B, C/EBPalpha,

PI3K-dependent pathway AKT(PKB), AKT2

Chemotaxis_Inhibitory action of 1.058E-03 5.346E-02 G-protein alpha-i family, lipoxins on IL-8- and Leukotriene PIP5KI, PLD1, AKT(PKB) B4-induced neutrophil migration

Development_WNT signaling 1.223E-03 5.346E-02 Casein kinase II, alpha chains, pathway. Part 2 SNAIL1, BRG1, WNT

Apoptosis and survival_Apoptotic 1.356E-03 5.346E-02 p53, AKT(PKB), pl20GAP Activin A signaling

Impaired inhibitory action of 1.503E-03 5.346E-02 G-protein alpha-i family, lipoxins on neutrophil migration PIP5KI, PLD1, AKT(PKB) in CF

Cell adhesion_Cadherin-mediated 1.524E-03 5.346E-02 P-cadherin, M-cadherin, FAK1 cell adhesion

Cell adhesion_Chemokines and 1.913E-03 5.846E-02 TRIO, G-protein alpha-i family, adhesion B-Raf, AKT(PKB), FAK1

Apoptosis and survival_p53- 2.101E-03 5.846E-02 p53, Bcl-2, E2F1

dependent apoptosis

Immune response_IL-15 signaling 2.465E-03 5.846E-02 Bcl-2, c-Myb, AKT(PKB), FAK1

Development_Regulation of 2.465E-03 5.846E-02 SNAIL1, NOTCH4, Bcl-2, WNT epithelial-to-mesenchymal

transition (ΈΜΤ)

Development_Transcription 2.797E-03 5.846E-02 c-Myb, C/EBPalpha, E2F1 regulation of granulocyte

development

Cell cycle_Start of DNA replication 2.797E-03 5.846E-02 MCM4, MCM5, E2F1 in early S phase

Cytoskeleton remodeling_TGF, 3.019E-03 5.846E-02 Casein kinase II, alpha chains, WNT and cytoskeletal remodeling p53, AKT(PKB), FAK1, WNT

Cell cycle_Spindle assembly and 3.057E-03 5.846E-02 Aurora-B, TPX2, Aurora-A chromosome separation

Apoptosis and survival_Role of 3.332E-03 5.846E-02 p53, Bcl-2, AKT(PKB)

CDK5 in neuronal death and

survival

G-protein signaling_RhoA 3.332E-03 5.846E-02 Ephrin-A, PLD1, FAK1 regulation pathway Maps p-value FDR Network Objects from

Active Data

Chemotaxis_CXCR4 signaling 3.332E-03 5.846E-02 G-protein alpha-i family, FAK1, pathway pl20GAP

G-protein signaling_SlP2 receptor 3.621E-03 6.077E-02 G-protein alpha-i family, signaling AKT(PKB), FAK1

Development_SSTR2 in regulation 3.925E-03 6.313E-02 G-protein alpha-i family, B-Raf, of cell proliferation AKT(PKB)

Chemotaxis_Leukocyte 4.381E-03 6.561E-02 G-protein alpha-i family, chemotaxis PIP5KI, PLD1, PIP5K1A

Transcription_Sin3 and NuRD in 4.579E-03 6.561E-02 Sin3B, Mi-2 beta, Mi-2 alpha transcription regulation

Transcription_P53 signaling 4.929E-03 6.561E-02 p53, Bcl-2, E2F1

pathway

Translation _.Regulation of EIF2 4.929E-03 6.561E-02 Casein kinase II, alpha chains, activity eIF2B5, AKT(PKB)

Cell adhesion_PLAU signaling 4.929E-03 6.561E-02 Casein kinase II, alpha chains,

AKT(PKB), FAK1

G-protein signaling_RaplA 5.295E-03 6.593E-02 G-protein alpha-i family, B-Raf, regulation pathway pl20GAP

Development_Neurotrophin 5.295E-03 6.593E-02 B-Raf, p53, AKT(PKB) family signaling

Apoptosis and survival_Anti- 6.489E-03 7.367E-02 Bcl-2, AKT(PKB), FAK1 apoptotic action of Gastrin

Apoptosis and survival_TNF- 6.489E-03 7.367E-02 Caspase-2, AKT(PKB), AKT2 alpha-induced Caspase-8

signaling

Chemotaxis_C5a-induced 6.489E-03 7.367E-02 G-protein alpha-i family, B-Raf, chemotaxis PLD1

Neurophysiological 7.368E-03 7.751E-02 Ephrin-A, Pleiotrophin (OSF1), process_Receptor-mediated axon B-Raf

growth repulsion

Apoptosis and survival_DNA- 7.626E-03 7.751E-02 p53, E2F1

damage-induced apoptosis

Development_G-Proteins 7.832E-03 7.751E-02 SynGAP, G-protein alpha-i mediated regulation MAPK-ERK family, B-Raf

signaling

Chemotaxis_Lipoxin inhibitory 7.832E-03 7.751E-02 G-protein alpha-i family, PLD1, action on fMLP-induced AKT(PKB)

neutrophil chemotaxis

Signal transduction_PTEN 7.832E-03 7.751E-02 p53, AKT(PKB), FAK1 pathway

Regulation of lipid 8.313E-03 8.022E-02 eIF2B5, AKT(PKB), AKT2 metabolism_Insulin

signaling:generic cascades Maps p-value FDR Network Objects from

Active Data

Muscle contraction_Relaxin 8.811E-03 8.273E-02 G-protein alpha-i family, B-Raf, signaling pathway AKT(PKB)

Development_Thromboxane A2 9.326E-03 8.273E-02 G-protein alpha-i family, B-Raf, pathway signaling AKT(PKB)

Cytoskeleton remodelingjntegrin 9.326E-03 8.273E-02 TRIO, AKT(PKB), FAK1 outside-in signaling

DNA damage_Role of SUMO in p53 9.765E-03 8.273E-02 p53, AKT(PKB)

regulation

Apoptosis and survival_HTRlA 9.859E-03 8.273E-02 G-protein alpha-i family, Bcl-2, signaling AKT(PKB)

Development_EDNRB signaling 9.859E-03 8.273E-02 G-protein alpha-i family, B-Raf,

AKT(PKB)

Signal transduction_PKA signaling 1.041E-02 8.371E-02 G-protein alpha-i family,

AKAP3, AKAP8

Some pathways of EMT in cancer 1.041E-02 8.371E-02 SNAIL1, Bcl-2, AKT(PKB) cells

G-protein signaling_Proinsulin C- 1.098E-02 8.647E-02 G-protein alpha-i family, Bcl-2, peptide signaling AKT(PKB)

Cell cyclejnfluence of Ras and 1.156E-02 8.926E-02 AKT(PKB), FAK1, E2F1 Rho proteins on Gl/S Transition

DNA damage_NHEJ mechanisms 1.214E-02 9.010E-02 Casein kinase II, alpha chains, of DSBs repair Sirtuin

Development_NOTCH-induced 1.214E-02 9.010E-02 SNAIL1, NOTCH4

EMT

Neurophysiological 1.341E-02 9.766E-02 AN02, Olfactory receptor process_01factory transduction

Table 12: 233 significant genes included in the final model or signature. CR/IR value indicates the ratio of the natural logarithm of the average of the expression level of an mRNA in good responders (le. complete responders (CR)) to the natural logarithm of the average of the expression level of the mRNA in bad responders (Le. incomplete responders (] [R)).

Entrez

Symbol CR/IR Name

ID

PRSS2 1.34 protease, serine, 2 (trypsin 2) 5645

PRSS1 1.32 protease, serine, 1 (trypsin 1) 5644

CDH3 1.26 cadherin 3, type 1 , P-cadherin (placental) 1001 solute carrier family 7, (cationic amino acid

SLC7A1 1 1.21 23657 transporter, y+ system) member 1 1

MCM4 1.2 minichromosome maintenance complex component 4 4173

ZBTB 10 1.2 zinc finger and BTB domain containing 10 65986 Entrez

Symbol CR/IR Name

ID

MECOM 1.2 MDS1 and EVI1 complex locus 2122 prostate androgen-regulated transcript 1 (non-protein

PARTI 1.2 25859 coding)

KIAA0020 1.19 KIAA0020 9933

MCM5 1.19 minichromosome maintenance complex component 5 4174

EZH2 1.19 enhancer of zeste homolog 2 (Drosophila) 2146

GMPR 1.19 guanosine monophosphate reductase 2766

TRIO 1.18 triple functional domain (PTPRF interacting) 7204

C19orf54 1.18 chromosome 19 open reading frame 54 284325

HIPK2 1.18 homeodomain interacting protein kinase 2 28996

PARP12 1.18 poly (ADP-ribose) polymerase family, member 12 64761

GCNT1 1.17 glucosaminyl (N-acetyl) transferase 1 , core 2 2650

C9orf82 1.17 chromosome 9 open reading frame 82 79886

NCAPG2 1.17 non-SMC condensin II complex, subunit G2 54892

SIRT5 1.17 sirtuin 5 23408 v-myb myeloblastosis viral oncogene homolog

MYB 1.17 4602

(avian)

DROSHA 1.16 drosha, ribonuclease type III 29102

MCM7 1.16 minichromosome maintenance complex component 7 4176

ZNF85 1.16 zinc finger protein 85 7639

GPR19 1.16 G protein-coupled receptor 19 2842

PTN 1.16 pleiotrophin 5764

MARCH6 1.15 membrane-associated ring finger (C3HC4) 6 10299

ISYNA1 1.15 inositol-3 -phosphate synthase 1 51477

POLE 1.14 polymerase (DNA directed), epsilon 5426

PLAGL2 1.14 pleomorphic adenoma gene-like 2 5326

ENTPD5 1.13 ectonucleoside triphosphate diphosphohydrolase 5 957

LRRC8D 1.13 leucine rich repeat containing 8 family, member D 55144

BRD9 1.13 bromodomain containing 9 65980

WDR91 1.13 WD repeat domain 91 29062

MTAP 1.12 methylthioadenosine phosphorylase 4507

TRIM24 1.12 tripartite motif containing 24 8805

AARS 1.12 alanyl-tRNA synthetase 16

ZNF467 1.12 zinc finger protein 467 168544

CHD7 1.12 chromodomain helicase DNA binding protein 7 55636

STX17 1.11 syntaxin 17 55014

RFWD3 1.11 ring finger and WD repeat domain 3 55159

ZNF767 1.11 zinc finger family member 767 79970

PRRC2A 1.11 proline-rich coiled-coil 2A 7916

Cl lorf67 1.11 chromosome 11 open reading frame 67 28971 Entrez

Symbol CR/IR Name

ID

asparaginyl-tRNA synthetase 2, mitochondrial

NARS2 1.11 79731

(putative)

JARID2 1.11 jumonji, AT rich interactive domain 2 3720

GINS3 1.1 GINS complex subunit 3 (Psf3 homolog) 64785

AKAP8L 1.1 A kinase (PRKA) anchor protein 8 -like 26993

MAK 1.1 male germ cell-associated kinase 4117

COG4 1.09 component of oligomeric golgi complex 4 25839

UBAP2L 1.09 ubiquitin associated protein 2-like 9898

PAK4 1.09 p21 protein (Cdc42/Rac)-activated kinase 4 10298

DDX11 1.09 DEAD/H (Asp-Glu- Ala-Asp/His) box polypeptide 11 1663

ODZ1 1.09 odz, odd Oz/ten-m homolog l(Drosophila) 10178

C6orf26 1.09 chromosome 6 open reading frame 26 401251

RBM38 1.09 RNA binding motif protein 38 55544 v-myb myeloblastosis viral oncogene homolog

MYBL2 1.09 4605

(avian)-like 2

TPX2, microtubule-associated, homolog (Xenopus

TPX2 1.09 22974 laevis)

PLSCR1 1.09 phospholipid scramblase 1 5359

NOTCH4 1.08 notch 4 4855

MY07A 1.08 myosin VIIA 4647

WIZ 1.08 widely interspaced zinc finger motifs 58525

EHMT2 1.08 euchromatic histone-lysine N-methyltransferase 2 10919

ZC3HAV1 1.08 zinc finger CCCH-type, antiviral 1 56829

BRAF 1.08 v-raf murine sarcoma viral oncogene homolog Bl 673

WDR59 1.08 WD repeat domain 59 79726

PBX2 1.08 pre-B-cell leukemia homeobox 2 5089

ZNF395 1.08 zinc finger protein 395 55893

CEBPA 1.08 CCAAT/enhancer binding protein (C/EBP), alpha 1050

FXYD1 1.08 FXYD domain containing ion transport regulator 1 5348

TP53 1.08 tumor protein p53 7157

GAS 8 1.07 growth arrest-specific 8 2622

MMP15 1.07 matrix metallopeptidase 15 (membrane-inserted) 4324

FASTK 1.07 Fas-activated serine/threonine kinase 10922

FAM86B1 1.07 family with sequence similarity 86, member Bl 85002

SPAG5 1.07 sperm associated antigen 5 10615

TATA box binding protein (TBP)-associated factor,

TAF1C 1.06 9013

RNA polymerase I, C, 1 lOkDa

LIPG 1.06 lipase, endothelial 9388

CASP2 1.06 caspase 2, apoptosis-related cysteine peptidase 835

ZNF282 1.06 zinc finger protein 282 8427 Entrez

Symbol CR/IR Name

ID

DNASE2 1.06 deoxyribonuclease II, lysosomal 1777

TCN2 1.06 transcobalamin II 6948 human immunodeficiency virus type I enhancer

HIVEP2 1.06 3097 binding protein 2

dolichyl-phosphate mannosyltransferase polypeptide

DPM3 1.06 54344

3

wingless-type MMTV integration site family,

WNT5A 1.06 7474 member 5A

CLSTN3 1.05 calsyntenin 3 9746

LRRC61 1.05 leucine rich repeat containing 61 65999

RAD52 1.05 RAD52 homo log (S. cerevisiae) 5893

CHD4 1.05 chromodomain helicase DNA binding protein 4 1108

PTMS 1.05 parathymosin 5763

KIAA0753 1.05 KIAA0753 9851 tyrosine 3-monooxygenase/tryptophan 5-

YWHAH 1.05 7533 monooxygenase activation protein, eta polypeptide

LAD1 1.05 ladinin 1 3898

ARGLU1 1.05 arginine and glutamate rich 1 55082

SETBP1 1.05 SET binding protein 1 26040

LSR 1.05 lipolysis stimulated lipoprotein receptor 51599

ZNF334 1.05 zinc finger protein 334 55713

BCL2 1.05 B-cell CLL/lymphoma 2 596

CASC1 1.05 cancer susceptibility candidate 1 55259

WISP3 1.05 WNT1 inducible signaling pathway protein 3 8838

CXCL9 1.05 chemokine (C-X-C motif) ligand 9 4283

RPL19 0.95 ribosomal protein L19 6143

SHC (Src homology 2 domain containing)

SHC1 0.95 6464 transforming protein 1

EIF3J 0.95 eukaryotic translation initiation factor 3, subunit J 8669

FGFR10P 0.95 FGFR1 oncogene partner 11116

ADP-ribosylation factor guanine nucleotide-

ARFGEF2 0.95 10564 exchange factor 2 (brefeldin A-inhibited)

ITM2B 0.95 integral membrane protein 2B 9445

TRIM 13 0.95 tripartite motif containing 13 10206

MSL1 0.95 male-specific lethal 1 homolog (Drosophila) 339287

SRSF6 0.95 serine/arginine-rich splicing factor 6 6431 sterol regulatory element binding transcription factor

SREBFl 0.95 6720

1

CSNK2A2 0.95 casein kinase 2, alpha prime polypeptide 1459

TTC37 0.95 tetratricopeptide repeat domain 37 9652

MARCKS 0.95 myristoylated alanine-rich protein kinase C substrate 4082 Entrez

Symbol CR/IR Name

ID

PLOD2 0.95 procollagen- lysine, 2-oxoglutarate 5-dioxygenase 2 5352

TOM1 0.94 target of mybl (chicken) 10043

TDRKH 0.94 tudor and KH domain containing 11022

MCTP1 0.94 multiple C2 domains, transmembrane 1 79772

CTSA 0.94 cathepsin A 5476 intrafiagellar transport 52 homolog

IFT52 0.94 51098

(Chlamydomonas)

signal sequence receptor, gamma (translocon-

SSR3 0.94 6747 associated protein gamma)

GAS 7 0.94 growth arrest-specific 7 8522

GLPvX 0.94 glutaredoxin (thioltransferase) 2745

GUCY1A3 0.94 guanylate cyclase 1 , soluble, alpha 3 2982

PDGFRL 0.94 platelet-derived growth factor receptor-like 5157

MATK 0.93 megakaryocyte-associated tyrosine kinase 4145

RPL23 0.93 ribosomal protein L23 9349 tumor necrosis factor (ligand) superfamily, member

TNFSF12 0.93 8742

12

C20orf4 0.93 chromosome 20 open reading frame 4 25980

C15orf24 0.93 chromosome 15 open reading frame 24 56851

PEX11B 0.93 peroxisomal biogenesis factor 11 beta 8799

MN1 0.93 meningioma (disrupted in balanced translocation) 1 4330

C6orfl20 0.93 chromosome 6 open reading frame 120 387263

ANAPC10 0.93 anaphase promoting complex subunit 10 10393

AP1M2 0.93 adaptor-related protein complex 1 , mu 2 subunit 10053

SLC46A3 0.93 solute carrier family 46, member 3 283537

MEIS3P1 0.93 Meis homeobox 3 pseudogene 1 4213

ICAM1 0.93 intercellular adhesion molecule 1 3383

AKAP12 0.93 A kinase (PRKA) anchor protein 12 9590 immunoglobulin lambda- like polypeptide 3,

IGLL3P 0.93 91353 pseudogene

PTPN1 0.92 protein tyrosine phosphatase, non-receptor type 1 5770

SNAP23 0.92 synaptosomal-associated protein, 23kDa 8773

DNAJB12 0.92 DnaJ (Hsp40) homolog, subfamily B, member 12 54788

HEXB 0.92 hexosaminidase B (beta polypeptide) 3074

UFM1 0.92 ubiquitin-fold modifier 1 51569

ATP6V1B ATPase, H+ transporting, lysosomal 56/58kDa, VI

0.92 526 2 subunit B2

SEC24D 0.92 SEC24 family, member D (S. cerevisiae) 9871

PDLIM5 0.92 PDZ and LIM domain 5 10611

OSTM1 0.92 osteopetrosis associated transmembrane protein 1 28962 Entrez

Symbol CR/IR Name

ID

PDLIM2 0.92 PDZ and LIM domain 2 (mystique) 64236

TSPO 0.92 translocator protein (18kDa) 706

NAAA 0.92 N-acylethanolamine acid amidase 27163

ATP6V1C ATPase, H+ transporting, lysosomal 42kDa, VI

0.92 528 1 subunit CI

TLR2 0.92 toll-like receptor 2 7097

LHFP 0.92 lipoma HMGIC fusion partner 10186

DSE 0.92 dermatan sulfate epimerase 29940

ATPase, H+ transporting, lysosomal 70kDa, VI

ATP6V1A 0.91 523 subunit A

RPL26 0.91 ribosomal protein L26 6154

MAPKBP1 0.91 mitogen-activated protein kinase binding protein 1 23005

TPD52L2 0.91 tumor protein D52-like 2 7165

NADH dehydrogenase (ubiquinone) 1 alpha

NDUFAF1 0.91 51103 subcomplex, assembly factor 1

AGGF1 0.91 angiogenic factor with G patch and FHA domains 1 55109

NDRG3 0.91 NDRG family member 3 57446

PDE4A 0.91 phosphodiesterase 4A, cAMP-specific 5141

RWDD1 0.91 RWD domain containing 1 51389 protein phosphatase 1 , regulatory (inhibitor) subunit

PPP1R3D 0.91 5509

3D

PGRMC2 0.91 progesterone receptor membrane component 2 10424

MFSD1 0.91 major facilitator superfamily domain containing 1 64747

IL6ST 0.91 3572 receptor)

SUCLA2 0.91 succinate-CoA ligase, ADP-forming, beta subunit 8803

PLK2 0.91 polo-like kinase 2 10769

DPT 0.9 dermatopontin 1805

PKD2 0.9 polycystic kidney disease 2 (autosomal dominant) 5311

YTHDF1 0.9 YTH domain family, member 1 54915

SYNRG 0.9 synergin, gamma 11276

NSA2 0.9 NSA2 ribosome biogenesis homo log (S. cerevisiae) 10412

DNAJB14 0.9 DnaJ (Hsp40) homo log, subfamily B, member 14 79982

STX8 0.9 syntaxin 8 9482

KRT10 0.9 keratin 10 3858

PGCP 0.9 plasma glutamate carboxypeptidase 10404 ras-related C3 botulinum toxin substrate 2 (rho

RAC2 0.9 5880 family, small GTP binding protein Rac2)

F2R 0.9 coagulation factor II (thrombin) receptor 2149

MAN1A1 0.9 mannosidase, alpha, class 1A, member 1 4121 Entrez

Symbol CR/IR Name

ID

CCNH 0.89 cyclin H 902

FECH 0.89 ferrochelatase 2235

RAS p21 protein activator (GTPase activating

RASA1 0.89 5921 protein) 1

asparagine-linked glycosylation 5, dolichyl-

ALG5 0.89 phosphate beta-glucosyltransferase homo log (S. 29880 cerevisiae)

COP9 constitutive photomorphogenic homolog

COPS4 0.89 51138 subunit 4 (Arabidopsis)

BGLAP 0.89 bone gamma-carboxyglutamate (gla) protein 632

WTAP 0.89 Wilms tumor 1 associated protein 9589

MLX 0.88 MAX-like protein X 6945

DUSP14 0.88 dual specificity phosphatase 14 11072

RIN2 0.88 Ras and Rab interactor 2 54453

MFAP3 0.88 microfibrillar-associated protein 3 4238

SLM02 0.88 slowmo homolog 2 (Drosophila) 51012

PPAP2A 0.88 phosphatidic acid phosphatase type 2A 8611

FAM172A 0.88 family with sequence similarity 172, member A 83989

MAF 0.88 4094 homolog (avian)

IGFBP4 0.88 insulin-like growth factor binding protein 4 3487

ACSL1 0.88 acyl-CoA synthetase long-chain family member 1 2180

C13orfl5 0.88 chromosome 13 open reading frame 15 28984

RHOBTB3 0.88 Rho-related BTB domain containing 3 22836

THBS1 0.88 thrombospondin 1 7057

RHOT1 0.87 ras homolog gene family, member Tl 55288

C10orf26 0.87 chromosome 10 open reading frame 26 54838

BLMH 0.87 bleomycin hydrolase 642

RAB32 0.87 RAB32, member RAS oncogene family 10981

UBL3 0.86 ubiquitin-like 3 5412

PGAP3 0.86 post-GPI attachment to proteins 3 93210

ENPP1 0.86 ectonucleotide pyrophosphatase/phosphodiesterase 1 5167

EVI2A 0.86 ecotropic viral integration site 2A 2123

FBLN1 0.86 fibulin 1 2192 protein phosphatase 3, catalytic subunit, alpha

PPP3CA 0.85 5530 isozyme

CCL11 0.85 chemokine (C-C motif) ligand 11 6356

TD02 0.85 tryptophan 2,3-dioxygenase 6999

CCPG1 0.84 cell cycle progression 1 9236 Entrez

Symbol CR/IR Name

ID

RBI 0.84 retinoblastoma 1 5925

PPIC 0.84 peptidylprolyl isomerase C (cyclophilin C) 5480

PMP22 0.84 peripheral myelin protein 22 5376

KDELC1 0.83 KDEL (Lys-Asp-Glu-Leu) containing 1 79070

EDNRA 0.83 endothelin receptor type A 1909

OLFML1 0.82 olfactomedin-like 1 283298

FZD1 0.81 frizzled homolog 1 (Drosophila) 8321

OMD 0.79 osteomodulin 4958

COPZ2 0.78 coatomer protein complex, subunit zeta 2 51226

PDLIM3 0.78 PDZ and LIM domain 3 27295

OLFML3 0.76 olfactomedin-like 3 56944

PDGFD 0.76 platelet derived growth factor D 80310

NUAK1 0.75 NUAK family, SNFl-like kinase, 1 9891

TIMP3 0.7 TIMP metallopeptidase inhibitor 3 7078

FAP 0.7 fibroblast activation protein, alpha 2191

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Claims

CLAIMS We claim:

1. A method of treating a subject suffering from a cancer, the method comprising the steps of:

2. The method of claim 1, wherein the subject is the good candidate for the chemotherapy if the expression in the sample of the subject of at least 80%>, 85%, 90%, 95% or 99% of the mRNAs corresponding to the proteins identified in Table 9 are not significantly different than the corresponding reference values for the good responder and/or the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 20%, 15%), 10%), 5%) or 1%) of the mRNAs corresponding to the proteins identified in Table 9 are significantly different than the corresponding reference value for a bad responder.

3. The method of claim 1 or 2, wherein the good responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 9 in a sample from a person known to be responsive to the chemotherapy, wherein the sample from the person known to be responsive to the chemotherapy is obtained before the administration of the chemotherapy.

4. The method of claim 1 or 2, wherein the bad responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 9 in a sample from a person known to be non-responsive to the chemotherapy, wherein the sample from the person known to be non-responsive to the chemotherapy is obtained before the administration of the chemotherapy.

5. The method of claim 1 or 2, wherein the chemotherapy comprises administering a platinum based drug and/or taxane to the subject.

6. The method of claim 5, wherein the platinum based drug is cisplatin, carboplatin, oxaliplatin or a combination of two or more of the foregoing.

7. The method of claim 5, wherein the taxane is paclitaxel and/or docetaxel.

8. The method of claim 1 or 2, wherein the cancer is epithelial ovarian cancer, serous ovarian cancer, endometrial ovarian cancer, uterine cancer or breast cancer.

9. The method of claim 1 or 2, wherein said method comprises identifying the subject as a good candidate for a chemotherapy; and administering the chemotherapy to the subject identified as the good candidate for the chemotherapy.

10. The method of claim 1 or 2, wherein said method comprises identifying the subject as a bad candidate for a chemotherapy; and administering a cancer treatment other than the chemotherapy to the subject identified as the bad candidate for the chemotherapy.

11. The method of claim 1, wherein the step of comparing the expression of mRNAs corresponding to the proteins identified in Table 9 in the sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy comprises:

a) obtaining the sample the subject,

12. The method of claim 1, wherein the sample is a tissue sample or a body fluid sample.

13. The method of claim 12, wherein the sample is a body fluid sample that is amniotic fluid, aqueous humor, vitreous humor, bile, cerebrospinal fluid, chyle, endolymph, perilymph, female ejaculate, male ejaculate, lymph, mucus (including nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sputum, synovial fluid, vaginal secretion, pancreatic juice or aspirate, pancreatic cyst fluid, serum, plasma, or blood.

14. The method of claim 12, wherein the sample is a tissue sample comprising or consisting of tissue of the brain, eyes, Pineal gland, Pituitary gland, Thyroid gland, Parathyroid glands, thorax, heart, lungs, esophagus, Thymus gland, pleura, Adrenal glands, Appendix, Gall bladder, urinary bladder, large intestine, small intestine, kidneys, liver, pancreas, spleen, stoma, Prostate gland, Testes, ovaries, or uterus.

15. The method of claim 1 or 2, wherein the subject is human.

16. A method of treating a subject suffering from a cancer, the method comprising the steps of:

a) comparing the expression of mRNAs corresponding to the proteins identified in Table 12 in a sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy,

17. The method of claim 16, wherein the subject is the good candidate for the chemotherapy if the expression in the sample of the subject of at least 80%>, 85%, 90%, 95% or 99% of the mRNAs corresponding to the proteins identified in Table 12 are not significantly different than the corresponding reference values for the good responder and/or the subject is the bad candidate for the chemotherapy if the expression in the subject of more than 20%), 15%, 10%>, 5% or 1% of the mRNAs corresponding to the proteins identified in Table 12 are significantly different than the corresponding reference value for a bad responder.

18. The method of claim 16 or 17, wherein the good responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 12 in a sample from a person known to be responsive to the chemotherapy, wherein the sample from the person known to be responsive to the chemotherapy is obtained before the administration of the chemotherapy.

19. The method of claim 16 or 17, wherein the bad responder reference values are obtained by estimating the expression of the mRNAs corresponding to the proteins identified in Table 12 in a sample from a person known to be non-responsive to the chemotherapy, wherein the sample from the person known to be non-responsive to the chemotherapy is obtained before the administration of the chemotherapy.

20. The method of claim 16 or 17, wherein the chemotherapy comprises administering a platinum based drug and/or taxane to the subject.

21. The method of claim 20, wherein the platinum based drug is cisp latin, carboplatin, oxalaplatin or a combination of two or more of the foregoing.

22. The method of claim 21, wherein the taxane is paclitaxel and/or docetaxel.

23. The method of claim 16 or 17, wherein the cancer is epithelial ovarian cancer, serous ovarian cancer, endometrial ovarian cancer, uterine cancer or breast cancer.

24. The method of claim 16, wherein the step of comparing the expression of mRNAs corresponding to the proteins identified in Table 12 in the sample obtained from the subject to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy comprises:

a) obtaining the sample the subject,

25. The method claim 16 or 17, wherein the subject is human.

26. The method of claim 16 or 17, wherein the sample is a tissue sample or a body fluid sample.

27. The method of claim 26, wherein the same is a tissue sample comprising or consisting of a tissue of the brain, eyes, Pineal gland, Pituitary gland, Thyroid gland, Parathyroid glands, thorax, heart, lungs, esophagus, Thymus gland, pleura, Adrenal glands, Appendix, Gall bladder, urinary bladder, large intestine, small intestine, kidneys, liver, pancreas, spleen, stoma, Prostate gland, Testes, ovaries, or uterus.

28. The method of claim 26, wherein the sample is a body fluid sample that is amniotic fluid, aqueous humor, vitreous humor, bile, cerebrospinal fluid, chyle, endolymph, perilymph, female ejaculate, male ejaculate, lymph, mucus (including nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sputum, synovial fluid, vaginal secretion, pancreatic juice or aspirate, pancreatic cyst fluid, serum, plasma, or blood.

29. A microarray chip comprising mRNAs corresponding to proteins involved in cellular signaling pathways directly associated with responsiveness to chemotherapy for treatment of a cancer, the microarray chip comprises oligonucleotides corresponding to the mRNAs corresponding to the proteins identified in Table 9 or Table 12, or both.

30. The microarray chip of claim 29, wherein the chemotherapy comprises administering a platinum based drug and/or taxane to the subject.

31. The microarray chip of claim 30, wherein the platinum based drug is cisplatin, carboplatin, oxaliplatin or a combination thereof.

32. The microarray chip of claim 30, wherein the taxane is paclitaxel and/or docetaxel.

33. The microarray chip of claim 29, wherein the cancer is epithelial ovarian cancer, serous ovarian cancer, endometrial ovarian cancer, uterine cancer or breast cancer.

34. The microarray chip of claim 29, wherein the microarray chip has no more than one thousand different oligonucleotides.

35. The microarray chip of claim 29, wherein the microarray chip has no more than nine hundred different oligonucleotides.

36. The microarray chip of claim 29, wherein the microarray chip has no more than eight hundred different oligonucleotides.

37. The microarray chip of claim 29, wherein the microarray chip has no more than seven hundred different oligonucleotides.

38. The microarray chip of claim 29, wherein the microarray chip has no more than six hundred different oligonucleotides.

39. The microarray chip of claim 29, wherein the microarray chip has no more than five hundred different oligonucleotides.

40. The microarray chip of claim 29, wherein the microarray chip consists essentially of oligonucleotides corresponding to the mRNAs corresponding to the proteins identified in Table 9 or Table 12, or both

41. A method for determining whether a subject suffering from a cancer is a good candidate or bad candidate for a chemotherapy for the cancer, the method comprising the steps of:

42. A method for gene expression analysis, comprising:

b) optionally, comparing the measured expression to reference values corresponding to the mRNAs expression in a good responder to the chemotherapy and/or to reference values corresponding to the mRNAs expression in a bad responder to the chemotherapy.

43. The method of claim 42, further comprising providing a report of the outcome of a).

44. The method of claim 43, further comprising providing a report of the outcome of b).