GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in KIRC-TP

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in KIRC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1J38RKT

Overview

Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes in KIRC-TP. This pipeline has the following features:

For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.
Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).
Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).
Checks if the top core genes are up-regulated or down-regulated.
Checks if the top core genes are high expressed or low expressed.
Checks if the top core genes are significantly differently expressed genes.

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 194
Number of samples: 533
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 116
pheno.type: 2 - 3 :[ clus2 ] 223
pheno.type: 3 - 3 :[ clus3 ] 194

For the expression subtypes of 18278 genes in 534 samples, GSEA found enriched gene sets in each cluster using 533 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA RHO PATHWAY, BIOCARTA GPCR PATHWAY, BIOCARTA CREB PATHWAY, KEGG OXIDATIVE PHOSPHORYLATION, KEGG O GLYCAN BIOSYNTHESIS, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG CARDIAC MUSCLE CONTRACTION, KEGG WNT SIGNALING PATHWAY

And common core enriched genes are PRKCA, CTNNB1, CXXC4, DAAM1, DKK1, FRAT1, FZD2, FZD3, FZD6, FZD7

clus2

Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA VEGF PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG GALACTOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION

And common core enriched genes are EHHADH, ACADM, ALDH3A2, ACSL1, HMGCS2, SLC27A2, ABAT, ACAT1, ALDH6A1, ALDH7A1

clus3

Top enriched gene sets are BIOCARTA INFLAM PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA WNT PATHWAY, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG DNA REPLICATION, KEGG BASE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG CELL CYCLE, KEGG OOCYTE MEIOSIS

And common core enriched genes are CCL5, IL1B, IL6, IL18, PYCARD, CCNB1, CCNB2, CCNE1, CCNE2, CDK1

Results

Subtype clus1 enriched pathways

Table 3. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA NO1 PATHWAY	28	genes.ES.table	0.57	1.4	0.064	0.68	0.93	0.46	0.18	0.38	0.52	0.22
BIOCARTA AGR PATHWAY	34	genes.ES.table	0.58	1.7	0.0021	0.57	0.49	0.26	0.14	0.23	0	0.19
BIOCARTA RHO PATHWAY	31	genes.ES.table	0.43	1.6	0.024	0.79	0.78	0.19	0.16	0.16	0.5	0.26
BIOCARTA GPCR PATHWAY	32	genes.ES.table	0.48	1.5	0.061	0.56	0.86	0.47	0.26	0.35	0.37	0.18
BIOCARTA CREB PATHWAY	25	genes.ES.table	0.46	1.5	0.069	0.56	0.88	0.44	0.26	0.32	0.38	0.16
KEGG OXIDATIVE PHOSPHORYLATION	113	genes.ES.table	0.5	1.5	0.16	0.63	0.91	0.6	0.32	0.41	0.46	0.2
KEGG O GLYCAN BIOSYNTHESIS	28	genes.ES.table	0.48	1.3	0.086	0.73	0.97	0.46	0.19	0.38	0.61	0.24
KEGG INOSITOL PHOSPHATE METABOLISM	53	genes.ES.table	0.37	1.3	0.15	0.63	0.98	0.36	0.23	0.28	0.53	0.19
KEGG CARDIAC MUSCLE CONTRACTION	66	genes.ES.table	0.45	1.3	0.09	0.6	0.98	0.3	0.14	0.26	0.51	0.17
KEGG WNT SIGNALING PATHWAY	145	genes.ES.table	0.46	1.5	0.037	0.76	0.82	0.37	0.21	0.3	0.49	0.26

genes ES table in pathway: BIOCARTA NO1 PATHWAY

Table S1. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ATP6V0A4	ATP6V0A4	ATP6V0A4	8	0.69	0.12	YES
2	ATP6V1B1	ATP6V1B1	ATP6V1B1	40	0.59	0.22	YES
3	CFTR	CFTR	CFTR	54	0.58	0.32	YES
4	ATP6V0D2	ATP6V0D2	ATP6V0D2	139	0.48	0.4	YES
5	PLCG2	PLCG2	PLCG2	1071	0.23	0.38	YES
6	KCNQ1	KCNQ1	KCNQ1	1101	0.22	0.42	YES
7	ATP6V1C2	ATP6V1C2	ATP6V1C2	1102	0.22	0.46	YES
8	ATP6V1G2	ATP6V1G2	ATP6V1G2	1115	0.22	0.5	YES
9	SLC12A2	SLC12A2	SLC12A2	1997	0.14	0.47	YES
10	ATP6V1A	ATP6V1A	ATP6V1A	2299	0.12	0.48	YES
11	ATP6V1D	ATP6V1D	ATP6V1D	2454	0.11	0.49	YES
12	ATP6V1H	ATP6V1H	ATP6V1H	2724	0.1	0.49	YES
13	PRKCA	PRKCA	PRKCA	2922	0.092	0.5	YES
14	ATP6V0B	ATP6V0B	ATP6V0B	3032	0.088	0.5	YES
15	ATP6V0A2	ATP6V0A2	ATP6V0A2	3047	0.088	0.52	YES
16	TJP1	TJP1	TJP1	3400	0.076	0.51	NO
17	ATP6V0E2	ATP6V0E2	ATP6V0E2	3670	0.068	0.51	NO
18	ATP6V0D1	ATP6V0D1	ATP6V0D1	4097	0.059	0.5	NO
19	ATP6V0C	ATP6V0C	ATP6V0C	4127	0.058	0.5	NO
20	ATP6V1G1	ATP6V1G1	ATP6V1G1	4243	0.056	0.51	NO
21	ATP6AP1	ATP6AP1	ATP6AP1	4491	0.051	0.5	NO
22	GNAS	GNAS	GNAS	4530	0.05	0.51	NO
23	ATP6V1E1	ATP6V1E1	ATP6V1E1	4740	0.046	0.51	NO
24	PRKACB	PRKACB	PRKACB	4823	0.045	0.51	NO
25	TJP2	TJP2	TJP2	5652	0.032	0.47	NO
26	PRKACA	PRKACA	PRKACA	5827	0.03	0.46	NO
27	ATP6V1F	ATP6V1F	ATP6V1F	5830	0.03	0.47	NO
28	ACTG1	ACTG1	ACTG1	6293	0.024	0.45	NO
29	KDELR1	KDELR1	KDELR1	6742	0.019	0.43	NO
30	ATP6V0E1	ATP6V0E1	ATP6V0E1	7328	0.012	0.4	NO
31	ATP6V1C1	ATP6V1C1	ATP6V1C1	7633	0.0092	0.38	NO
32	ACTB	ACTB	ACTB	7964	0.0061	0.37	NO
33	PRKX	PRKX	PRKX	8539	0.0004	0.33	NO
34	PLCG1	PLCG1	PLCG1	9144	-0.0056	0.3	NO
35	SEC61B	SEC61B	SEC61B	9394	-0.0081	0.29	NO
36	ARF1	ARF1	ARF1	9606	-0.01	0.28	NO
37	MUC2	MUC2	MUC2	9991	-0.014	0.26	NO
38	KDELR2	KDELR2	KDELR2	10537	-0.02	0.24	NO
39	SEC61A1	SEC61A1	SEC61A1	10820	-0.024	0.22	NO
40	ERO1L	ERO1L	ERO1L	11918	-0.038	0.17	NO
41	ADCY9	ADCY9	ADCY9	11963	-0.039	0.17	NO
42	ATP6V1B2	ATP6V1B2	ATP6V1B2	12650	-0.051	0.14	NO
43	PDIA4	PDIA4	PDIA4	13627	-0.072	0.1	NO
44	SEC61G	SEC61G	SEC61G	13650	-0.073	0.12	NO
45	ATP6V0A1	ATP6V0A1	ATP6V0A1	13734	-0.075	0.12	NO
46	KDELR3	KDELR3	KDELR3	14435	-0.096	0.1	NO
47	SEC61A2	SEC61A2	SEC61A2	14609	-0.1	0.11	NO
48	TCIRG1	TCIRG1	TCIRG1	14615	-0.1	0.13	NO
49	ATP6V1E2	ATP6V1E2	ATP6V1E2	14777	-0.11	0.14	NO
50	PRKCG	PRKCG	PRKCG	14786	-0.11	0.16	NO
51	PRKCB	PRKCB	PRKCB	16685	-0.2	0.086	NO

Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA AGR PATHWAY

Table S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	LAMA2	LAMA2	LAMA2	32	0.6	0.17	YES
2	PAK6	PAK6	PAK6	48	0.58	0.33	YES
3	PAK7	PAK7	PAK7	401	0.36	0.41	YES
4	CHRM1	CHRM1	CHRM1	1076	0.23	0.44	YES
5	ACTA1	ACTA1	ACTA1	1193	0.21	0.49	YES
6	NRG2	NRG2	NRG2	1221	0.21	0.55	YES
7	DMD	DMD	DMD	1942	0.14	0.55	YES
8	DAG1	DAG1	DAG1	2222	0.12	0.56	YES
9	LAMA3	LAMA3	LAMA3	2552	0.11	0.58	YES
10	MAPK8	MAPK8	MAPK8	4785	0.046	0.47	NO
11	PTK2	PTK2	PTK2	5172	0.039	0.46	NO
12	PAK4	PAK4	PAK4	5807	0.03	0.43	NO
13	CDC42	CDC42	CDC42	6780	0.018	0.38	NO
14	UTRN	UTRN	UTRN	6948	0.017	0.38	NO
15	ITGB1	ITGB1	ITGB1	7161	0.014	0.37	NO
16	CHRNA1	CHRNA1	CHRNA1	7700	0.0087	0.34	NO
17	RAC1	RAC1	RAC1	7856	0.0071	0.34	NO
18	CTTN	CTTN	CTTN	8870	-0.003	0.28	NO
19	MAPK3	MAPK3	MAPK3	9071	-0.005	0.27	NO
20	PXN	PXN	PXN	9426	-0.0084	0.26	NO
21	ITGA1	ITGA1	ITGA1	9512	-0.0093	0.25	NO
22	PAK2	PAK2	PAK2	9603	-0.01	0.25	NO
23	DVL1	DVL1	DVL1	9928	-0.013	0.24	NO
24	LAMA4	LAMA4	LAMA4	10475	-0.019	0.21	NO
25	MAPK1	MAPK1	MAPK1	11822	-0.037	0.15	NO
26	SP1	SP1	SP1	12235	-0.043	0.14	NO
27	SRC	SRC	SRC	12472	-0.048	0.14	NO
28	PAK1	PAK1	PAK1	12783	-0.054	0.14	NO
29	PAK3	PAK3	PAK3	13640	-0.073	0.11	NO
30	EGFR	EGFR	EGFR	13768	-0.076	0.12	NO
31	JUN	JUN	JUN	13855	-0.079	0.14	NO
32	NRG1	NRG1	NRG1	14797	-0.11	0.12	NO
33	RAPSN	RAPSN	RAPSN	15023	-0.12	0.14	NO
34	GIT2	GIT2	GIT2	15488	-0.14	0.15	NO

Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AGR PATHWAY.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AGR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RHO PATHWAY

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SFRP1	SFRP1	SFRP1	82	0.54	0.057	YES
2	PYGO1	PYGO1	PYGO1	205	0.45	0.1	YES
3	NKD1	NKD1	NKD1	294	0.4	0.14	YES
4	WNT4	WNT4	WNT4	374	0.37	0.18	YES
5	WNT7A	WNT7A	WNT7A	473	0.34	0.22	YES
6	WNT11	WNT11	WNT11	479	0.34	0.25	YES
7	WNT2	WNT2	WNT2	529	0.33	0.29	YES
8	TLE2	TLE2	TLE2	622	0.3	0.32	YES
9	FZD7	FZD7	FZD7	869	0.26	0.33	YES
10	WNT7B	WNT7B	WNT7B	881	0.26	0.36	YES
11	DAAM1	DAAM1	DAAM1	901	0.25	0.39	YES
12	FZD2	FZD2	FZD2	1235	0.21	0.4	YES
13	WISP1	WISP1	WISP1	1346	0.2	0.41	YES
14	WNT5A	WNT5A	WNT5A	1750	0.16	0.41	YES
15	CXXC4	CXXC4	CXXC4	1853	0.15	0.42	YES
16	FZD3	FZD3	FZD3	1867	0.15	0.44	YES
17	HPRT1	HPRT1	HPRT1	2067	0.13	0.44	YES
18	PORCN	PORCN	PORCN	2124	0.13	0.45	YES
19	TCF7L1	TCF7L1	TCF7L1	2223	0.12	0.46	YES
20	TLE1	TLE1	TLE1	2416	0.11	0.46	YES
21	WNT6	WNT6	WNT6	2428	0.11	0.48	YES
22	FRAT1	FRAT1	FRAT1	2550	0.11	0.48	YES
23	LEF1	LEF1	LEF1	2713	0.1	0.48	YES
24	WIF1	WIF1	WIF1	3046	0.088	0.48	YES
25	WNT5B	WNT5B	WNT5B	3265	0.08	0.47	YES
26	LRP6	LRP6	LRP6	3351	0.078	0.48	YES
27	FZD6	FZD6	FZD6	3366	0.077	0.48	YES
28	BCL9	BCL9	BCL9	3373	0.077	0.49	YES
29	WNT9A	WNT9A	WNT9A	3451	0.074	0.5	YES
30	DKK1	DKK1	DKK1	3532	0.072	0.5	YES
31	CTNNB1	CTNNB1	CTNNB1	3624	0.069	0.5	YES
32	TCF7	TCF7	TCF7	3722	0.067	0.51	YES
33	GSK3B	GSK3B	GSK3B	3846	0.065	0.51	YES
34	FBXW2	FBXW2	FBXW2	4267	0.055	0.49	NO
35	FZD8	FZD8	FZD8	4475	0.051	0.49	NO
36	CTNNBIP1	CTNNBIP1	CTNNBIP1	4946	0.043	0.46	NO
37	FOXN1	FOXN1	FOXN1	5052	0.041	0.46	NO
38	AES	AES	AES	5328	0.037	0.45	NO
39	FBXW11	FBXW11	FBXW11	5534	0.034	0.45	NO
40	CSNK2A1	CSNK2A1	CSNK2A1	6036	0.027	0.42	NO
41	SOX17	SOX17	SOX17	6841	0.018	0.38	NO
42	BTRC	BTRC	BTRC	7082	0.015	0.37	NO
43	RHOU	RHOU	RHOU	7219	0.014	0.36	NO
44	KREMEN1	KREMEN1	KREMEN1	7243	0.013	0.36	NO
45	EP300	EP300	EP300	7375	0.012	0.36	NO
46	PPP2R1A	PPP2R1A	PPP2R1A	7410	0.012	0.36	NO
47	DVL2	DVL2	DVL2	7756	0.008	0.34	NO
48	GSK3A	GSK3A	GSK3A	7769	0.008	0.34	NO
49	LRP5	LRP5	LRP5	7838	0.0072	0.34	NO
50	PPP2CA	PPP2CA	PPP2CA	7844	0.0072	0.34	NO
51	ACTB	ACTB	ACTB	7964	0.0061	0.33	NO
52	CSNK1G1	CSNK1G1	CSNK1G1	7990	0.0059	0.33	NO
53	RPL13A	RPL13A	RPL13A	8052	0.0054	0.33	NO
54	SENP2	SENP2	SENP2	8266	0.0032	0.32	NO
55	CSNK1D	CSNK1D	CSNK1D	8383	0.0019	0.31	NO
56	APC	APC	APC	8501	0.00067	0.3	NO
57	CTBP1	CTBP1	CTBP1	8673	-0.001	0.29	NO
58	AXIN1	AXIN1	AXIN1	9215	-0.0063	0.26	NO
59	CTBP2	CTBP2	CTBP2	9452	-0.0087	0.25	NO
60	CCND3	CCND3	CCND3	9559	-0.0098	0.25	NO
61	CCND2	CCND2	CCND2	9809	-0.012	0.24	NO
62	FRZB	FRZB	FRZB	9810	-0.012	0.24	NO
63	NLK	NLK	NLK	9827	-0.012	0.24	NO
64	DVL1	DVL1	DVL1	9928	-0.013	0.23	NO
65	FBXW4	FBXW4	FBXW4	10095	-0.015	0.22	NO
66	CSNK1A1	CSNK1A1	CSNK1A1	10525	-0.02	0.2	NO
67	B2M	B2M	B2M	11404	-0.031	0.16	NO
68	SFRP4	SFRP4	SFRP4	11774	-0.036	0.14	NO
69	FZD4	FZD4	FZD4	12617	-0.05	0.1	NO
70	FOSL1	FOSL1	FOSL1	13077	-0.059	0.084	NO
71	GAPDH	GAPDH	GAPDH	13153	-0.061	0.087	NO
72	WNT16	WNT16	WNT16	13175	-0.062	0.093	NO
73	WNT2B	WNT2B	WNT2B	13310	-0.064	0.093	NO
74	JUN	JUN	JUN	13855	-0.079	0.072	NO
75	DIXDC1	DIXDC1	DIXDC1	13935	-0.081	0.077	NO
76	WNT10A	WNT10A	WNT10A	13945	-0.081	0.086	NO
77	CCND1	CCND1	CCND1	14009	-0.083	0.092	NO
78	SLC9A3R1	SLC9A3R1	SLC9A3R1	15432	-0.13	0.029	NO
79	FZD1	FZD1	FZD1	15552	-0.14	0.038	NO
80	PITX2	PITX2	PITX2	15717	-0.14	0.046	NO
81	MYC	MYC	MYC	15790	-0.15	0.059	NO
82	WNT3	WNT3	WNT3	15824	-0.15	0.074	NO
83	FZD5	FZD5	FZD5	16822	-0.21	0.044	NO
84	WNT1	WNT1	WNT1	17674	-0.31	0.032	NO

Figure S5. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA RHO PATHWAY.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA RHO PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GPCR PATHWAY

Table S4. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PIP5K1B	PIP5K1B	PIP5K1B	153	0.48	0.22	YES
2	PPP1R12B	PPP1R12B	PPP1R12B	1424	0.19	0.24	YES
3	ARHGAP6	ARHGAP6	ARHGAP6	1448	0.19	0.33	YES
4	OPHN1	OPHN1	OPHN1	1687	0.16	0.39	YES
5	ARHGAP5	ARHGAP5	ARHGAP5	2449	0.11	0.4	YES
6	VCL	VCL	VCL	2901	0.093	0.42	YES
7	RHOA	RHOA	RHOA	3584	0.07	0.42	NO
8	GSN	GSN	GSN	4218	0.056	0.41	NO
9	ARPC4	ARPC4	ARPC4	4736	0.046	0.41	NO
10	ROCK1	ROCK1	ROCK1	5280	0.038	0.4	NO
11	ARHGEF5	ARHGEF5	ARHGEF5	6673	0.02	0.33	NO
12	MYLK	MYLK	MYLK	7163	0.014	0.31	NO
13	CFL1	CFL1	CFL1	7406	0.012	0.3	NO
14	ARHGAP1	ARHGAP1	ARHGAP1	7956	0.0062	0.27	NO
15	ARHGEF11	ARHGEF11	ARHGEF11	7969	0.0061	0.28	NO
16	ARPC1A	ARPC1A	ARPC1A	8094	0.0051	0.27	NO
17	PIP5K1A	PIP5K1A	PIP5K1A	9120	-0.0055	0.22	NO
18	LIMK1	LIMK1	LIMK1	9521	-0.0095	0.2	NO
19	ACTR2	ACTR2	ACTR2	10211	-0.016	0.17	NO
20	BAIAP2	BAIAP2	BAIAP2	10248	-0.017	0.18	NO
21	ACTR3	ACTR3	ACTR3	10509	-0.02	0.17	NO
22	ARPC2	ARPC2	ARPC2	10643	-0.021	0.18	NO
23	ARPC3	ARPC3	ARPC3	10761	-0.023	0.18	NO
24	DIAPH1	DIAPH1	DIAPH1	11468	-0.032	0.16	NO
25	ARPC5	ARPC5	ARPC5	11502	-0.032	0.17	NO
26	PFN1	PFN1	PFN1	11981	-0.04	0.16	NO
27	SRC	SRC	SRC	12472	-0.048	0.16	NO
28	ARPC1B	ARPC1B	ARPC1B	13225	-0.063	0.15	NO
29	ARHGAP4	ARHGAP4	ARHGAP4	13538	-0.07	0.16	NO
30	MYL2	MYL2	MYL2	14368	-0.094	0.16	NO
31	ARHGEF1	ARHGEF1	ARHGEF1	14741	-0.11	0.19	NO

Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GPCR PATHWAY.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GPCR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CREB PATHWAY

Table S5. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SFRP1	SFRP1	SFRP1	82	0.54	0.034	YES
2	NKD1	NKD1	NKD1	294	0.4	0.052	YES
3	WNT4	WNT4	WNT4	374	0.37	0.074	YES
4	AXIN2	AXIN2	AXIN2	434	0.35	0.097	YES
5	WNT7A	WNT7A	WNT7A	473	0.34	0.12	YES
6	WNT11	WNT11	WNT11	479	0.34	0.14	YES
7	WNT2	WNT2	WNT2	529	0.33	0.16	YES
8	FZD9	FZD9	FZD9	576	0.32	0.18	YES
9	CAMK2A	CAMK2A	CAMK2A	697	0.29	0.2	YES
10	DKK2	DKK2	DKK2	808	0.27	0.21	YES
11	CAMK2B	CAMK2B	CAMK2B	847	0.26	0.23	YES
12	FZD7	FZD7	FZD7	869	0.26	0.25	YES
13	WNT7B	WNT7B	WNT7B	881	0.26	0.26	YES
14	DAAM1	DAAM1	DAAM1	901	0.25	0.28	YES
15	FZD10	FZD10	FZD10	923	0.25	0.3	YES
16	WNT9B	WNT9B	WNT9B	1213	0.21	0.3	YES
17	FZD2	FZD2	FZD2	1235	0.21	0.31	YES
18	SFRP2	SFRP2	SFRP2	1276	0.2	0.32	YES
19	TBL1Y	TBL1Y	TBL1Y	1387	0.19	0.33	YES
20	VANGL2	VANGL2	VANGL2	1492	0.18	0.34	YES
21	PRICKLE1	PRICKLE1	PRICKLE1	1548	0.18	0.35	YES
22	MMP7	MMP7	MMP7	1698	0.16	0.35	YES
23	WNT5A	WNT5A	WNT5A	1750	0.16	0.36	YES
24	CXXC4	CXXC4	CXXC4	1853	0.15	0.37	YES
25	FZD3	FZD3	FZD3	1867	0.15	0.38	YES
26	CHP2	CHP2	CHP2	1970	0.14	0.38	YES
27	RAC3	RAC3	RAC3	2111	0.13	0.38	YES
28	PORCN	PORCN	PORCN	2124	0.13	0.39	YES
29	FRAT2	FRAT2	FRAT2	2160	0.13	0.4	YES
30	TCF7L1	TCF7L1	TCF7L1	2223	0.12	0.4	YES
31	NFATC4	NFATC4	NFATC4	2354	0.12	0.4	YES
32	WNT6	WNT6	WNT6	2428	0.11	0.41	YES
33	FRAT1	FRAT1	FRAT1	2550	0.11	0.41	YES
34	PPP2R5A	PPP2R5A	PPP2R5A	2659	0.1	0.41	YES
35	LEF1	LEF1	LEF1	2713	0.1	0.42	YES
36	PRKCA	PRKCA	PRKCA	2922	0.092	0.41	YES
37	MAPK10	MAPK10	MAPK10	2972	0.09	0.42	YES
38	PPP3CA	PPP3CA	PPP3CA	3017	0.089	0.42	YES
39	WIF1	WIF1	WIF1	3046	0.088	0.42	YES
40	PPP2R5E	PPP2R5E	PPP2R5E	3078	0.087	0.43	YES
41	WNT5B	WNT5B	WNT5B	3265	0.08	0.42	YES
42	LRP6	LRP6	LRP6	3351	0.078	0.42	YES
43	FZD6	FZD6	FZD6	3366	0.077	0.43	YES
44	PSEN1	PSEN1	PSEN1	3392	0.076	0.43	YES
45	WNT9A	WNT9A	WNT9A	3451	0.074	0.44	YES
46	DKK1	DKK1	DKK1	3532	0.072	0.44	YES
47	PPP2R5C	PPP2R5C	PPP2R5C	3539	0.072	0.44	YES
48	RHOA	RHOA	RHOA	3584	0.07	0.44	YES
49	CTNNB1	CTNNB1	CTNNB1	3624	0.069	0.45	YES
50	PPP3CB	PPP3CB	PPP3CB	3652	0.069	0.45	YES
51	TCF7	TCF7	TCF7	3722	0.067	0.45	YES
52	SMAD4	SMAD4	SMAD4	3739	0.067	0.46	YES
53	WNT3A	WNT3A	WNT3A	3793	0.066	0.46	YES
54	GSK3B	GSK3B	GSK3B	3846	0.065	0.46	YES
55	NFAT5	NFAT5	NFAT5	4102	0.059	0.45	NO
56	SMAD2	SMAD2	SMAD2	4140	0.058	0.45	NO
57	CHP	CHP	CHP	4294	0.055	0.45	NO
58	SFRP5	SFRP5	SFRP5	4448	0.052	0.44	NO
59	FZD8	FZD8	FZD8	4475	0.051	0.44	NO
60	MAPK8	MAPK8	MAPK8	4785	0.046	0.43	NO
61	PRKACB	PRKACB	PRKACB	4823	0.045	0.43	NO
62	CTNNBIP1	CTNNBIP1	CTNNBIP1	4946	0.043	0.43	NO
63	DAAM2	DAAM2	DAAM2	5227	0.039	0.42	NO
64	SIAH1	SIAH1	SIAH1	5273	0.038	0.42	NO
65	ROCK1	ROCK1	ROCK1	5280	0.038	0.42	NO
66	PPP2R1B	PPP2R1B	PPP2R1B	5432	0.036	0.41	NO
67	CSNK1A1L	CSNK1A1L	CSNK1A1L	5484	0.035	0.41	NO
68	CHD8	CHD8	CHD8	5523	0.034	0.41	NO
69	FBXW11	FBXW11	FBXW11	5534	0.034	0.42	NO
70	MAP3K7	MAP3K7	MAP3K7	5657	0.032	0.41	NO
71	ROCK2	ROCK2	ROCK2	5664	0.032	0.41	NO
72	SKP1	SKP1	SKP1	5816	0.03	0.41	NO
73	PRKACA	PRKACA	PRKACA	5827	0.03	0.41	NO
74	WNT8B	WNT8B	WNT8B	5931	0.029	0.4	NO
75	CSNK2A1	CSNK2A1	CSNK2A1	6036	0.027	0.4	NO
76	CSNK2A2	CSNK2A2	CSNK2A2	6144	0.026	0.4	NO
77	PPP2R5D	PPP2R5D	PPP2R5D	6358	0.023	0.39	NO
78	PRICKLE2	PRICKLE2	PRICKLE2	6561	0.021	0.38	NO
79	RUVBL1	RUVBL1	RUVBL1	6686	0.02	0.37	NO
80	PPP3CC	PPP3CC	PPP3CC	6750	0.019	0.37	NO
81	SOX17	SOX17	SOX17	6841	0.018	0.37	NO
82	BTRC	BTRC	BTRC	7082	0.015	0.35	NO
83	CAMK2D	CAMK2D	CAMK2D	7114	0.015	0.35	NO
84	PPP2CB	PPP2CB	PPP2CB	7143	0.014	0.35	NO
85	CUL1	CUL1	CUL1	7320	0.012	0.34	NO
86	DVL3	DVL3	DVL3	7351	0.012	0.34	NO
87	EP300	EP300	EP300	7375	0.012	0.34	NO
88	PPP2R1A	PPP2R1A	PPP2R1A	7410	0.012	0.34	NO
89	CREBBP	CREBBP	CREBBP	7421	0.012	0.34	NO
90	PPARD	PPARD	PPARD	7532	0.01	0.34	NO
91	DVL2	DVL2	DVL2	7756	0.008	0.32	NO
92	LRP5	LRP5	LRP5	7838	0.0072	0.32	NO
93	PPP2CA	PPP2CA	PPP2CA	7844	0.0072	0.32	NO
94	RAC1	RAC1	RAC1	7856	0.0071	0.32	NO
95	TCF7L2	TCF7L2	TCF7L2	8131	0.0046	0.31	NO
96	SENP2	SENP2	SENP2	8266	0.0032	0.3	NO
97	APC	APC	APC	8501	0.00067	0.29	NO
98	PRKX	PRKX	PRKX	8539	0.0004	0.28	NO
99	SMAD3	SMAD3	SMAD3	8644	-0.00078	0.28	NO
100	CTBP1	CTBP1	CTBP1	8673	-0.001	0.28	NO
101	AXIN1	AXIN1	AXIN1	9215	-0.0063	0.25	NO
102	PPP3R1	PPP3R1	PPP3R1	9272	-0.0068	0.24	NO
103	CAMK2G	CAMK2G	CAMK2G	9293	-0.007	0.24	NO
104	VANGL1	VANGL1	VANGL1	9352	-0.0077	0.24	NO
105	CTBP2	CTBP2	CTBP2	9452	-0.0087	0.24	NO
106	RBX1	RBX1	RBX1	9516	-0.0094	0.23	NO
107	CCND3	CCND3	CCND3	9559	-0.0098	0.23	NO
108	CSNK1E	CSNK1E	CSNK1E	9786	-0.012	0.22	NO
109	CCND2	CCND2	CCND2	9809	-0.012	0.22	NO
110	NLK	NLK	NLK	9827	-0.012	0.22	NO
111	DVL1	DVL1	DVL1	9928	-0.013	0.22	NO
112	CSNK2B	CSNK2B	CSNK2B	10190	-0.016	0.2	NO
113	NFATC3	NFATC3	NFATC3	10243	-0.017	0.2	NO
114	TBL1X	TBL1X	TBL1X	10295	-0.017	0.2	NO
115	CSNK1A1	CSNK1A1	CSNK1A1	10525	-0.02	0.19	NO
116	MAPK9	MAPK9	MAPK9	10740	-0.023	0.18	NO
117	TP53	TP53	TP53	10780	-0.023	0.18	NO
118	PLCB3	PLCB3	PLCB3	11190	-0.028	0.16	NO
119	CACYBP	CACYBP	CACYBP	11742	-0.036	0.13	NO
120	SFRP4	SFRP4	SFRP4	11774	-0.036	0.13	NO
121	NFATC2	NFATC2	NFATC2	11938	-0.039	0.12	NO
122	NFATC1	NFATC1	NFATC1	12103	-0.041	0.12	NO
123	FZD4	FZD4	FZD4	12617	-0.05	0.094	NO
124	APC2	APC2	APC2	12767	-0.054	0.089	NO
125	FOSL1	FOSL1	FOSL1	13077	-0.059	0.076	NO
126	WNT16	WNT16	WNT16	13175	-0.062	0.076	NO
127	TBL1XR1	TBL1XR1	TBL1XR1	13218	-0.062	0.078	NO
128	WNT2B	WNT2B	WNT2B	13310	-0.064	0.077	NO
129	PLCB4	PLCB4	PLCB4	13605	-0.072	0.066	NO
130	JUN	JUN	JUN	13855	-0.079	0.058	NO
131	WNT10A	WNT10A	WNT10A	13945	-0.081	0.059	NO
132	CCND1	CCND1	CCND1	14009	-0.083	0.062	NO
133	NKD2	NKD2	NKD2	14675	-0.1	0.032	NO
134	PRKCG	PRKCG	PRKCG	14786	-0.11	0.034	NO
135	PPP3R2	PPP3R2	PPP3R2	15055	-0.12	0.028	NO
136	FZD1	FZD1	FZD1	15552	-0.14	0.011	NO
137	MYC	MYC	MYC	15790	-0.15	0.0083	NO
138	WNT3	WNT3	WNT3	15824	-0.15	0.017	NO
139	WNT10B	WNT10B	WNT10B	15843	-0.15	0.027	NO
140	PRKCB	PRKCB	PRKCB	16685	-0.2	-0.0044	NO
141	PLCB1	PLCB1	PLCB1	16818	-0.21	0.0037	NO
142	FZD5	FZD5	FZD5	16822	-0.21	0.019	NO
143	RAC2	RAC2	RAC2	17187	-0.25	0.017	NO
144	PLCB2	PLCB2	PLCB2	17454	-0.28	0.022	NO
145	WNT1	WNT1	WNT1	17674	-0.31	0.032	NO

Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CREB PATHWAY.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CREB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

Table S6. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FGF9	FGF9	FGF9	1	0.72	0.11	YES
2	PDGFRA	PDGFRA	PDGFRA	131	0.49	0.17	YES
3	FGF7	FGF7	FGF7	189	0.45	0.24	YES
4	FGF1	FGF1	FGF1	320	0.39	0.29	YES
5	FGF13	FGF13	FGF13	389	0.37	0.34	YES
6	FGF12	FGF12	FGF12	482	0.34	0.38	YES
7	FGF14	FGF14	FGF14	775	0.27	0.41	YES
8	IGF1	IGF1	IGF1	907	0.25	0.44	YES
9	FGF18	FGF18	FGF18	987	0.24	0.47	YES
10	EGF	EGF	EGF	1856	0.15	0.44	NO
11	BRAF	BRAF	BRAF	3062	0.087	0.39	NO
12	FGFR1	FGFR1	FGFR1	3154	0.084	0.4	NO
13	MITF	MITF	MITF	3266	0.08	0.4	NO
14	IGF1R	IGF1R	IGF1R	3519	0.072	0.4	NO
15	RAF1	RAF1	RAF1	3843	0.065	0.39	NO
16	PDGFC	PDGFC	PDGFC	3908	0.063	0.4	NO
17	AKT1	AKT1	AKT1	4126	0.059	0.39	NO
18	PIK3CA	PIK3CA	PIK3CA	4213	0.056	0.4	NO
19	PIK3R3	PIK3R3	PIK3R3	4584	0.049	0.38	NO
20	ARAF	ARAF	ARAF	4791	0.046	0.38	NO
21	CDH1	CDH1	CDH1	4809	0.045	0.39	NO
22	AKT3	AKT3	AKT3	5114	0.04	0.38	NO
23	KRAS	KRAS	KRAS	5274	0.038	0.37	NO
24	PTEN	PTEN	PTEN	5552	0.034	0.36	NO
25	AKT2	AKT2	AKT2	6078	0.027	0.34	NO
26	CDK4	CDK4	CDK4	6104	0.026	0.34	NO
27	PDGFRB	PDGFRB	PDGFRB	6252	0.025	0.34	NO
28	MAP2K1	MAP2K1	MAP2K1	6602	0.02	0.32	NO
29	CDK6	CDK6	CDK6	6926	0.017	0.3	NO
30	FGF23	FGF23	FGF23	7154	0.014	0.29	NO
31	PDGFD	PDGFD	PDGFD	8065	0.0053	0.24	NO
32	CDKN1A	CDKN1A	CDKN1A	8102	0.005	0.24	NO
33	PIK3R2	PIK3R2	PIK3R2	8205	0.0037	0.24	NO
34	MAP2K2	MAP2K2	MAP2K2	8354	0.0022	0.23	NO
35	FGF2	FGF2	FGF2	8769	-0.0019	0.21	NO
36	MAPK3	MAPK3	MAPK3	9071	-0.005	0.19	NO
37	HRAS	HRAS	HRAS	9562	-0.0099	0.17	NO
38	HGF	HGF	HGF	9895	-0.013	0.15	NO
39	BAD	BAD	BAD	10023	-0.014	0.14	NO
40	PDGFA	PDGFA	PDGFA	10103	-0.015	0.14	NO
41	FGF8	FGF8	FGF8	10294	-0.017	0.14	NO
42	TP53	TP53	TP53	10780	-0.023	0.11	NO
43	PDGFB	PDGFB	PDGFB	11761	-0.036	0.063	NO
44	MAPK1	MAPK1	MAPK1	11822	-0.037	0.065	NO
45	NRAS	NRAS	NRAS	11870	-0.038	0.068	NO
46	RB1	RB1	RB1	12567	-0.049	0.038	NO
47	PIK3CB	PIK3CB	PIK3CB	12586	-0.05	0.044	NO
48	E2F3	E2F3	E2F3	12723	-0.052	0.044	NO
49	MET	MET	MET	12800	-0.054	0.048	NO
50	MDM2	MDM2	MDM2	13396	-0.067	0.025	NO
51	FGF17	FGF17	FGF17	13462	-0.068	0.032	NO
52	PIK3R1	PIK3R1	PIK3R1	13632	-0.073	0.033	NO
53	EGFR	EGFR	EGFR	13768	-0.076	0.037	NO
54	CCND1	CCND1	CCND1	14009	-0.083	0.036	NO
55	PIK3CD	PIK3CD	PIK3CD	14676	-0.1	0.015	NO
56	FGF5	FGF5	FGF5	14723	-0.11	0.028	NO
57	FGF20	FGF20	FGF20	15402	-0.13	0.01	NO
58	FGF11	FGF11	FGF11	15892	-0.15	0.0062	NO
59	PIK3CG	PIK3CG	PIK3CG	16171	-0.17	0.016	NO
60	CDKN2A	CDKN2A	CDKN2A	16564	-0.19	0.023	NO
61	PIK3R5	PIK3R5	PIK3R5	16760	-0.21	0.043	NO
62	E2F2	E2F2	E2F2	17347	-0.26	0.05	NO

Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

Table S7. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	KCNJ1	KCNJ1	KCNJ1	86	0.53	0.1	YES
2	FXYD4	FXYD4	FXYD4	158	0.47	0.19	YES
3	SCNN1A	SCNN1A	SCNN1A	178	0.46	0.28	YES
4	NR3C2	NR3C2	NR3C2	550	0.32	0.32	YES
5	IGF1	IGF1	IGF1	907	0.25	0.35	YES
6	HSD11B2	HSD11B2	HSD11B2	1183	0.21	0.38	YES
7	IRS1	IRS1	IRS1	1223	0.21	0.42	YES
8	HSD11B1	HSD11B1	HSD11B1	1256	0.2	0.46	YES
9	SCNN1G	SCNN1G	SCNN1G	1337	0.2	0.49	YES
10	ATP1A2	ATP1A2	ATP1A2	1427	0.19	0.52	YES
11	NEDD4L	NEDD4L	NEDD4L	1887	0.15	0.52	YES
12	IRS2	IRS2	IRS2	1940	0.14	0.55	YES
13	PRKCA	PRKCA	PRKCA	2922	0.092	0.51	NO
14	ATP1A1	ATP1A1	ATP1A1	2947	0.092	0.53	NO
15	SCNN1B	SCNN1B	SCNN1B	3012	0.089	0.55	NO
16	PIK3CA	PIK3CA	PIK3CA	4213	0.056	0.49	NO
17	PIK3R3	PIK3R3	PIK3R3	4584	0.049	0.48	NO
18	ATP1B2	ATP1B2	ATP1B2	4940	0.043	0.47	NO
19	SFN	SFN	SFN	4995	0.042	0.47	NO
20	KRAS	KRAS	KRAS	5274	0.038	0.47	NO
21	SLC9A3R2	SLC9A3R2	SLC9A3R2	5705	0.032	0.45	NO
22	ATP1B3	ATP1B3	ATP1B3	5990	0.028	0.44	NO
23	ATP1A4	ATP1A4	ATP1A4	6232	0.025	0.43	NO
24	PDPK1	PDPK1	PDPK1	8176	0.0041	0.32	NO
25	PIK3R2	PIK3R2	PIK3R2	8205	0.0037	0.32	NO
26	MAPK3	MAPK3	MAPK3	9071	-0.005	0.28	NO
27	INSR	INSR	INSR	11069	-0.026	0.17	NO
28	ATP1B1	ATP1B1	ATP1B1	11626	-0.034	0.15	NO
29	MAPK1	MAPK1	MAPK1	11822	-0.037	0.15	NO
30	PIK3CB	PIK3CB	PIK3CB	12586	-0.05	0.11	NO
31	ATP1A3	ATP1A3	ATP1A3	13011	-0.058	0.1	NO
32	PIK3R1	PIK3R1	PIK3R1	13632	-0.073	0.082	NO
33	SGK1	SGK1	SGK1	13946	-0.081	0.081	NO
34	PIK3CD	PIK3CD	PIK3CD	14676	-0.1	0.061	NO
35	PRKCG	PRKCG	PRKCG	14786	-0.11	0.076	NO
36	PIK3CG	PIK3CG	PIK3CG	16171	-0.17	0.033	NO
37	PRKCB	PRKCB	PRKCB	16685	-0.2	0.045	NO
38	PIK3R5	PIK3R5	PIK3R5	16760	-0.21	0.082	NO

Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG O GLYCAN BIOSYNTHESIS.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG O GLYCAN BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG INOSITOL PHOSPHATE METABOLISM

Table S8. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ADCY1	ADCY1	ADCY1	355	0.38	0.17	YES
2	PRKAR2A	PRKAR2A	PRKAR2A	1578	0.17	0.18	YES
3	NFATC4	NFATC4	NFATC4	2354	0.12	0.2	YES
4	PRKAR2B	PRKAR2B	PRKAR2B	2492	0.11	0.24	YES
5	PRKAR1B	PRKAR1B	PRKAR1B	2794	0.097	0.28	YES
6	PRKCA	PRKCA	PRKCA	2922	0.092	0.31	YES
7	PPP3CA	PPP3CA	PPP3CA	3017	0.089	0.35	YES
8	GNAI1	GNAI1	GNAI1	3629	0.069	0.35	YES
9	PPP3CB	PPP3CB	PPP3CB	3652	0.069	0.39	YES
10	RAF1	RAF1	RAF1	3843	0.065	0.41	YES
11	GNAQ	GNAQ	GNAQ	4157	0.058	0.42	YES
12	GNAS	GNAS	GNAS	4530	0.05	0.42	YES
13	CALM2	CALM2	CALM2	4576	0.049	0.44	YES
14	PRKAR1A	PRKAR1A	PRKAR1A	4691	0.047	0.46	YES
15	PRKACB	PRKACB	PRKACB	4823	0.045	0.48	YES
16	CALM1	CALM1	CALM1	5702	0.032	0.44	NO
17	MAP2K1	MAP2K1	MAP2K1	6602	0.02	0.4	NO
18	PPP3CC	PPP3CC	PPP3CC	6750	0.019	0.4	NO
19	CREB1	CREB1	CREB1	7413	0.012	0.37	NO
20	ELK1	ELK1	ELK1	7962	0.0061	0.35	NO
21	GNB1	GNB1	GNB1	8337	0.0025	0.33	NO
22	GNGT1	GNGT1	GNGT1	8583	-0.000015	0.31	NO
23	FOS	FOS	FOS	9031	-0.0046	0.29	NO
24	MAPK3	MAPK3	MAPK3	9071	-0.005	0.29	NO
25	PLCG1	PLCG1	PLCG1	9144	-0.0056	0.29	NO
26	NFATC3	NFATC3	NFATC3	10243	-0.017	0.24	NO
27	RPS6KA3	RPS6KA3	RPS6KA3	10715	-0.022	0.22	NO
28	CALM3	CALM3	CALM3	11035	-0.026	0.22	NO
29	NFATC2	NFATC2	NFATC2	11938	-0.039	0.19	NO
30	NFATC1	NFATC1	NFATC1	12103	-0.041	0.2	NO
31	JUN	JUN	JUN	13855	-0.079	0.14	NO
32	PRKCB	PRKCB	PRKCB	16685	-0.2	0.086	NO

Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG INOSITOL PHOSPHATE METABOLISM.

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG INOSITOL PHOSPHATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CARDIAC MUSCLE CONTRACTION

Table S9. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CAMK2A	CAMK2A	CAMK2A	697	0.29	0.13	YES
2	CAMK2B	CAMK2B	CAMK2B	847	0.26	0.26	YES
3	PRKAR2A	PRKAR2A	PRKAR2A	1578	0.17	0.32	YES
4	PRKAR2B	PRKAR2B	PRKAR2B	2492	0.11	0.34	YES
5	PRKAR1B	PRKAR1B	PRKAR1B	2794	0.097	0.38	YES
6	PRKCA	PRKCA	PRKCA	2922	0.092	0.42	YES
7	AKT1	AKT1	AKT1	4126	0.059	0.39	YES
8	PIK3CA	PIK3CA	PIK3CA	4213	0.056	0.42	YES
9	GNAS	GNAS	GNAS	4530	0.05	0.43	YES
10	PRKAR1A	PRKAR1A	PRKAR1A	4691	0.047	0.44	YES
11	PRKACB	PRKACB	PRKACB	4823	0.045	0.46	YES
12	CAMK2D	CAMK2D	CAMK2D	7114	0.015	0.35	NO
13	CREB1	CREB1	CREB1	7413	0.012	0.34	NO
14	RAC1	RAC1	RAC1	7856	0.0071	0.32	NO
15	MAPK3	MAPK3	MAPK3	9071	-0.005	0.25	NO
16	CAMK2G	CAMK2G	CAMK2G	9293	-0.007	0.24	NO
17	SOS1	SOS1	SOS1	9555	-0.0098	0.24	NO
18	HRAS	HRAS	HRAS	9562	-0.0099	0.24	NO
19	MAPK14	MAPK14	MAPK14	10093	-0.015	0.22	NO
20	RPS6KA5	RPS6KA5	RPS6KA5	10268	-0.017	0.22	NO
21	GRB2	GRB2	GRB2	11603	-0.034	0.17	NO
22	RPS6KA1	RPS6KA1	RPS6KA1	11644	-0.034	0.18	NO
23	MAPK1	MAPK1	MAPK1	11822	-0.037	0.2	NO
24	PIK3R1	PIK3R1	PIK3R1	13632	-0.073	0.14	NO
25	PRKCB	PRKCB	PRKCB	16685	-0.2	0.086	NO

Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CARDIAC MUSCLE CONTRACTION.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CARDIAC MUSCLE CONTRACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

Table S10. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ATP6V0A4	ATP6V0A4	ATP6V0A4	8	0.69	0.08	YES
2	ATP6V1B1	ATP6V1B1	ATP6V1B1	40	0.59	0.15	YES
3	ATP6V0D2	ATP6V0D2	ATP6V0D2	139	0.48	0.2	YES
4	ATP12A	ATP12A	ATP12A	251	0.42	0.24	YES
5	COX7A1	COX7A1	COX7A1	721	0.28	0.25	YES
6	ATP4B	ATP4B	ATP4B	838	0.26	0.27	YES
7	ATP6V1C2	ATP6V1C2	ATP6V1C2	1102	0.22	0.28	YES
8	ATP6V1G2	ATP6V1G2	ATP6V1G2	1115	0.22	0.31	YES
9	COX6B2	COX6B2	COX6B2	1785	0.16	0.29	YES
10	UQCRHL	UQCRHL	UQCRHL	1858	0.15	0.3	YES
11	UQCRH	UQCRH	UQCRH	2066	0.13	0.31	YES
12	NDUFA4	NDUFA4	NDUFA4	2221	0.12	0.31	YES
13	ATP6V1A	ATP6V1A	ATP6V1A	2299	0.12	0.32	YES
14	UQCRFS1	UQCRFS1	UQCRFS1	2367	0.12	0.33	YES
15	UQCRC1	UQCRC1	UQCRC1	2391	0.12	0.34	YES
16	ATP6V1D	ATP6V1D	ATP6V1D	2454	0.11	0.36	YES
17	ATP6V1H	ATP6V1H	ATP6V1H	2724	0.1	0.35	YES
18	ATP5A1	ATP5A1	ATP5A1	2943	0.092	0.35	YES
19	ATP6V0B	ATP6V0B	ATP6V0B	3032	0.088	0.36	YES
20	ATP6V0A2	ATP6V0A2	ATP6V0A2	3047	0.088	0.36	YES
21	NDUFA6	NDUFA6	NDUFA6	3055	0.088	0.38	YES
22	COX5A	COX5A	COX5A	3205	0.082	0.38	YES
23	PPA2	PPA2	PPA2	3211	0.082	0.39	YES
24	NDUFB1	NDUFB1	NDUFB1	3353	0.078	0.39	YES
25	NDUFC2	NDUFC2	NDUFC2	3523	0.072	0.39	YES
26	COX7A2	COX7A2	COX7A2	3603	0.07	0.39	YES
27	ATP5B	ATP5B	ATP5B	3610	0.07	0.4	YES
28	ATP6V0E2	ATP6V0E2	ATP6V0E2	3670	0.068	0.4	YES
29	ATP5L	ATP5L	ATP5L	3686	0.068	0.41	YES
30	COX7B	COX7B	COX7B	3687	0.068	0.42	YES
31	NDUFA8	NDUFA8	NDUFA8	3758	0.067	0.42	YES
32	NDUFS8	NDUFS8	NDUFS8	3769	0.066	0.43	YES
33	UQCRC2	UQCRC2	UQCRC2	3852	0.064	0.43	YES
34	COX10	COX10	COX10	3930	0.063	0.44	YES
35	ATP6V0D1	ATP6V0D1	ATP6V0D1	4097	0.059	0.43	YES
36	ATP6V0C	ATP6V0C	ATP6V0C	4127	0.058	0.44	YES
37	SDHD	SDHD	SDHD	4164	0.058	0.44	YES
38	COX6C	COX6C	COX6C	4235	0.056	0.44	YES
39	ATP6V1G1	ATP6V1G1	ATP6V1G1	4243	0.056	0.45	YES
40	NDUFB5	NDUFB5	NDUFB5	4274	0.055	0.46	YES
41	NDUFA3	NDUFA3	NDUFA3	4413	0.052	0.46	YES
42	NDUFB9	NDUFB9	NDUFB9	4441	0.052	0.46	YES
43	ATP6AP1	ATP6AP1	ATP6AP1	4491	0.051	0.46	YES
44	NDUFB2	NDUFB2	NDUFB2	4521	0.05	0.47	YES
45	NDUFS3	NDUFS3	NDUFS3	4524	0.05	0.47	YES
46	COX8A	COX8A	COX8A	4590	0.049	0.47	YES
47	ATP6V1E1	ATP6V1E1	ATP6V1E1	4740	0.046	0.47	YES
48	UQCR11	UQCR11	UQCR11	4761	0.046	0.48	YES
49	UQCR10	UQCR10	UQCR10	4926	0.043	0.47	YES
50	NDUFS1	NDUFS1	NDUFS1	4927	0.043	0.48	YES
51	UQCRB	UQCRB	UQCRB	4937	0.043	0.48	YES
52	NDUFV1	NDUFV1	NDUFV1	4985	0.042	0.48	YES
53	COX4I1	COX4I1	COX4I1	5027	0.042	0.49	YES
54	ATP5E	ATP5E	ATP5E	5071	0.041	0.49	YES
55	NDUFA9	NDUFA9	NDUFA9	5112	0.04	0.49	YES
56	COX6B1	COX6B1	COX6B1	5135	0.04	0.5	YES
57	COX4I2	COX4I2	COX4I2	5157	0.04	0.5	YES
58	ATP5D	ATP5D	ATP5D	5346	0.037	0.49	YES
59	COX6A1	COX6A1	COX6A1	5413	0.036	0.49	YES
60	NDUFA5	NDUFA5	NDUFA5	5430	0.036	0.5	YES
61	NDUFB6	NDUFB6	NDUFB6	5498	0.035	0.5	YES
62	ATP5G1	ATP5G1	ATP5G1	5504	0.035	0.5	YES
63	ATP5J	ATP5J	ATP5J	5536	0.034	0.5	YES
64	NDUFB7	NDUFB7	NDUFB7	5668	0.032	0.5	YES
65	ATP5F1	ATP5F1	ATP5F1	5679	0.032	0.5	YES
66	COX7A2L	COX7A2L	COX7A2L	5732	0.032	0.5	YES
67	ATP6V1F	ATP6V1F	ATP6V1F	5830	0.03	0.5	YES
68	ATP5J2	ATP5J2	ATP5J2	5855	0.03	0.5	YES
69	NDUFA11	NDUFA11	NDUFA11	6313	0.024	0.48	NO
70	ATP5I	ATP5I	ATP5I	6346	0.023	0.48	NO
71	ATP5O	ATP5O	ATP5O	6414	0.022	0.48	NO
72	COX7C	COX7C	COX7C	6505	0.021	0.48	NO
73	NDUFB8	NDUFB8	NDUFB8	6532	0.021	0.48	NO
74	ATP5H	ATP5H	ATP5H	6560	0.021	0.48	NO
75	COX5B	COX5B	COX5B	6606	0.02	0.48	NO
76	NDUFA1	NDUFA1	NDUFA1	6685	0.02	0.48	NO
77	NDUFS2	NDUFS2	NDUFS2	6717	0.019	0.48	NO
78	NDUFAB1	NDUFAB1	NDUFAB1	6761	0.019	0.48	NO
79	COX17	COX17	COX17	6800	0.018	0.48	NO
80	NDUFS7	NDUFS7	NDUFS7	6813	0.018	0.48	NO
81	NDUFS6	NDUFS6	NDUFS6	6883	0.017	0.48	NO
82	CYC1	CYC1	CYC1	6898	0.017	0.48	NO
83	ATP5C1	ATP5C1	ATP5C1	6920	0.017	0.48	NO
84	NDUFA10	NDUFA10	NDUFA10	7257	0.013	0.46	NO
85	ATP6V0E1	ATP6V0E1	ATP6V0E1	7328	0.012	0.46	NO
86	NDUFB10	NDUFB10	NDUFB10	7453	0.011	0.46	NO
87	NDUFV2	NDUFV2	NDUFV2	7512	0.011	0.45	NO
88	NDUFS4	NDUFS4	NDUFS4	7551	0.01	0.45	NO
89	ATP6V1C1	ATP6V1C1	ATP6V1C1	7633	0.0092	0.45	NO
90	NDUFS5	NDUFS5	NDUFS5	8024	0.0056	0.43	NO
91	SDHA	SDHA	SDHA	8032	0.0056	0.43	NO
92	COX11	COX11	COX11	8046	0.0055	0.43	NO
93	SDHC	SDHC	SDHC	8418	0.0016	0.41	NO
94	NDUFA7	NDUFA7	NDUFA7	8438	0.0014	0.41	NO
95	ATP5G3	ATP5G3	ATP5G3	8476	0.00098	0.4	NO
96	SDHB	SDHB	SDHB	8493	0.00078	0.4	NO
97	NDUFB3	NDUFB3	NDUFB3	8804	-0.0022	0.39	NO
98	NDUFB4	NDUFB4	NDUFB4	9664	-0.011	0.34	NO
99	UQCRQ	UQCRQ	UQCRQ	9813	-0.012	0.34	NO
100	LHPP	LHPP	LHPP	10114	-0.015	0.32	NO
101	ATP5G2	ATP5G2	ATP5G2	10512	-0.02	0.3	NO
102	NDUFV3	NDUFV3	NDUFV3	10721	-0.022	0.29	NO
103	COX15	COX15	COX15	10933	-0.025	0.28	NO
104	PPA1	PPA1	PPA1	11679	-0.035	0.25	NO
105	NDUFA2	NDUFA2	NDUFA2	12209	-0.043	0.22	NO
106	ATP6V1B2	ATP6V1B2	ATP6V1B2	12650	-0.051	0.2	NO
107	COX8C	COX8C	COX8C	12898	-0.056	0.2	NO
108	NDUFC1	NDUFC1	NDUFC1	13031	-0.058	0.2	NO
109	ATP6V0A1	ATP6V0A1	ATP6V0A1	13734	-0.075	0.17	NO
110	TCIRG1	TCIRG1	TCIRG1	14615	-0.1	0.13	NO
111	ATP6V1E2	ATP6V1E2	ATP6V1E2	14777	-0.11	0.13	NO
112	COX6A2	COX6A2	COX6A2	16805	-0.21	0.046	NO
113	NDUFA4L2	NDUFA4L2	NDUFA4L2	17561	-0.29	0.038	NO

Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG WNT SIGNALING PATHWAY.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG WNT SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

up-regulated, please check the list of up-regulated genes
down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

highly expressed genes, please check the list of high (top 30%) expressed genes
low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Subtype clus2 enriched pathways

Table 4. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus2. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA AT1R PATHWAY	32	genes.ES.table	0.34	1.3	0.18	0.72	0.98	0.094	0.1	0.084	0.6	0.23
BIOCARTA DEATH PATHWAY	32	genes.ES.table	0.32	1.2	0.29	0.82	1	0.56	0.37	0.36	0.74	0.28
BIOCARTA VEGF PATHWAY	28	genes.ES.table	0.41	1.3	0.23	0.71	0.99	0.18	0.14	0.15	0.62	0.22
KEGG GLYCOLYSIS GLUCONEOGENESIS	57	genes.ES.table	0.39	1.2	0.21	0.78	1	0.14	0.047	0.13	0.69	0.26
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS	26	genes.ES.table	0.67	1.4	0.11	0.99	0.96	0.42	0.1	0.38	0.8	0.38
KEGG GALACTOSE METABOLISM	25	genes.ES.table	0.41	1.3	0.18	0.72	0.99	0.12	0.025	0.12	0.63	0.22
KEGG FATTY ACID METABOLISM	40	genes.ES.table	0.52	1.4	0.14	0.87	0.96	0.32	0.12	0.29	0.7	0.32
KEGG GLYCINE SERINE AND THREONINE METABOLISM	30	genes.ES.table	0.52	1.2	0.23	0.79	1	0.4	0.12	0.35	0.7	0.26
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	43	genes.ES.table	0.59	1.6	0.074	1	0.75	0.7	0.28	0.5	0.68	0.38
KEGG LYSINE DEGRADATION	43	genes.ES.table	0.34	1.3	0.16	0.67	0.98	0.33	0.26	0.24	0.57	0.2

genes ES table in pathway: BIOCARTA AT1R PATHWAY

Table S11. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CYP4A11	CYP4A11	CYP4A11	2	0.83	0.082	YES
2	CYP4A22	CYP4A22	CYP4A22	40	0.59	0.14	YES
3	SLC27A2	SLC27A2	SLC27A2	48	0.57	0.2	YES
4	PCK1	PCK1	PCK1	60	0.55	0.25	YES
5	AQP7	AQP7	AQP7	104	0.48	0.29	YES
6	FABP4	FABP4	FABP4	140	0.45	0.34	YES
7	ACADL	ACADL	ACADL	192	0.42	0.38	YES
8	HMGCS2	HMGCS2	HMGCS2	208	0.41	0.42	YES
9	CD36	CD36	CD36	416	0.32	0.44	YES
10	EHHADH	EHHADH	EHHADH	589	0.28	0.45	YES
11	RXRG	RXRG	RXRG	850	0.22	0.46	YES
12	CYP27A1	CYP27A1	CYP27A1	930	0.21	0.48	YES
13	PLIN1	PLIN1	PLIN1	1158	0.18	0.48	YES
14	LPL	LPL	LPL	1170	0.18	0.5	YES
15	GK	GK	GK	1189	0.18	0.52	YES
16	FABP1	FABP1	FABP1	1290	0.17	0.53	YES
17	ANGPTL4	ANGPTL4	ANGPTL4	1521	0.15	0.53	YES
18	ACADM	ACADM	ACADM	1565	0.15	0.55	YES
19	CPT2	CPT2	CPT2	1600	0.15	0.56	YES
20	PCK2	PCK2	PCK2	1805	0.14	0.56	YES
21	ACSL1	ACSL1	ACSL1	1830	0.13	0.57	YES
22	FABP7	FABP7	FABP7	1967	0.13	0.58	YES
23	PPARG	PPARG	PPARG	2095	0.12	0.58	YES
24	CPT1A	CPT1A	CPT1A	2171	0.12	0.59	YES
25	PPARA	PPARA	PPARA	2804	0.092	0.56	NO
26	FABP3	FABP3	FABP3	3888	0.062	0.51	NO
27	ACOX1	ACOX1	ACOX1	4519	0.05	0.48	NO
28	FABP2	FABP2	FABP2	4549	0.049	0.48	NO
29	PDPK1	PDPK1	PDPK1	4977	0.042	0.46	NO
30	SCP2	SCP2	SCP2	5236	0.038	0.45	NO
31	SCD5	SCD5	SCD5	5326	0.037	0.45	NO
32	CPT1B	CPT1B	CPT1B	5677	0.032	0.44	NO
33	RXRB	RXRB	RXRB	5814	0.03	0.43	NO
34	SCD	SCD	SCD	6237	0.024	0.41	NO
35	ILK	ILK	ILK	6403	0.023	0.4	NO
36	ACAA1	ACAA1	ACAA1	6952	0.016	0.38	NO
37	SORBS1	SORBS1	SORBS1	7859	0.0057	0.33	NO
38	PPARD	PPARD	PPARD	8237	0.0011	0.31	NO
39	NR1H3	NR1H3	NR1H3	8541	-0.0023	0.29	NO
40	UBC	UBC	UBC	8864	-0.006	0.27	NO
41	FADS2	FADS2	FADS2	8886	-0.0064	0.27	NO
42	RXRA	RXRA	RXRA	9230	-0.01	0.25	NO
43	ACSL3	ACSL3	ACSL3	9963	-0.019	0.22	NO
44	ACSL6	ACSL6	ACSL6	10111	-0.021	0.21	NO
45	SLC27A1	SLC27A1	SLC27A1	10185	-0.022	0.21	NO
46	CYP7A1	CYP7A1	CYP7A1	10407	-0.024	0.2	NO
47	CPT1C	CPT1C	CPT1C	11021	-0.032	0.17	NO
48	OLR1	OLR1	OLR1	11762	-0.043	0.13	NO
49	FABP6	FABP6	FABP6	12675	-0.058	0.087	NO
50	FABP5	FABP5	FABP5	12948	-0.063	0.078	NO
51	ACSL5	ACSL5	ACSL5	13195	-0.069	0.072	NO
52	APOA2	APOA2	APOA2	13380	-0.074	0.069	NO
53	CYP8B1	CYP8B1	CYP8B1	13455	-0.076	0.072	NO
54	SLC27A4	SLC27A4	SLC27A4	13578	-0.079	0.073	NO
55	DBI	DBI	DBI	13651	-0.081	0.077	NO
56	ADIPOQ	ADIPOQ	ADIPOQ	13792	-0.084	0.078	NO
57	ACSL4	ACSL4	ACSL4	14134	-0.095	0.069	NO
58	MMP1	MMP1	MMP1	14280	-0.1	0.07	NO
59	ACOX3	ACOX3	ACOX3	14632	-0.11	0.062	NO
60	SLC27A5	SLC27A5	SLC27A5	15757	-0.18	0.018	NO
61	APOA1	APOA1	APOA1	15978	-0.19	0.025	NO
62	APOC3	APOC3	APOC3	16695	-0.25	0.011	NO
63	ME1	ME1	ME1	17052	-0.29	0.02	NO
64	PLTP	PLTP	PLTP	17916	-0.46	0.019	NO

Figure S21. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AT1R PATHWAY.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA DEATH PATHWAY

Table S12. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HMGCS2	HMGCS2	HMGCS2	208	0.41	0.08	YES
2	ALDH6A1	ALDH6A1	ALDH6A1	346	0.34	0.15	YES
3	AOX1	AOX1	AOX1	456	0.31	0.21	YES
4	EHHADH	EHHADH	EHHADH	589	0.28	0.26	YES
5	ALDH3A2	ALDH3A2	ALDH3A2	862	0.22	0.3	YES
6	ACAA2	ACAA2	ACAA2	906	0.22	0.35	YES
7	HIBCH	HIBCH	HIBCH	982	0.2	0.39	YES
8	ABAT	ABAT	ABAT	1040	0.2	0.43	YES
9	ACAT1	ACAT1	ACAT1	1266	0.18	0.46	YES
10	ACADM	ACADM	ACADM	1565	0.15	0.47	YES
11	PCCA	PCCA	PCCA	1576	0.15	0.51	YES
12	AUH	AUH	AUH	1675	0.14	0.53	YES
13	ACADSB	ACADSB	ACADSB	1806	0.14	0.56	YES
14	MUT	MUT	MUT	2315	0.11	0.55	YES
15	ALDH9A1	ALDH9A1	ALDH9A1	2638	0.097	0.56	YES
16	ALDH7A1	ALDH7A1	ALDH7A1	3122	0.082	0.55	YES
17	IVD	IVD	IVD	3749	0.065	0.53	YES
18	ALDH2	ALDH2	ALDH2	3788	0.064	0.54	YES
19	ACADS	ACADS	ACADS	3860	0.063	0.55	YES
20	MCEE	MCEE	MCEE	4359	0.052	0.54	YES
21	BCKDHB	BCKDHB	BCKDHB	4392	0.052	0.55	YES
22	MCCC1	MCCC1	MCCC1	4544	0.049	0.55	YES
23	DBT	DBT	DBT	4632	0.048	0.56	YES
24	HMGCL	HMGCL	HMGCL	4708	0.047	0.56	YES
25	HADHB	HADHB	HADHB	4720	0.047	0.57	YES
26	HADHA	HADHA	HADHA	4730	0.047	0.58	YES
27	HIBADH	HIBADH	HIBADH	4886	0.044	0.58	YES
28	HMGCS1	HMGCS1	HMGCS1	4899	0.044	0.59	YES
29	ACAD8	ACAD8	ACAD8	5148	0.04	0.59	YES
30	BCKDHA	BCKDHA	BCKDHA	5197	0.039	0.59	YES
31	ALDH1B1	ALDH1B1	ALDH1B1	5616	0.032	0.58	NO
32	OXCT1	OXCT1	OXCT1	6260	0.024	0.55	NO
33	ECHS1	ECHS1	ECHS1	6506	0.022	0.54	NO
34	ACAA1	ACAA1	ACAA1	6952	0.016	0.52	NO
35	MCCC2	MCCC2	MCCC2	7312	0.012	0.5	NO
36	DLD	DLD	DLD	8567	-0.0026	0.43	NO
37	HADH	HADH	HADH	8673	-0.0038	0.43	NO
38	IL4I1	IL4I1	IL4I1	9171	-0.0095	0.4	NO
39	BCAT2	BCAT2	BCAT2	10122	-0.021	0.36	NO
40	HSD17B10	HSD17B10	HSD17B10	12118	-0.049	0.26	NO
41	ACAT2	ACAT2	ACAT2	12516	-0.055	0.25	NO
42	PCCB	PCCB	PCCB	13086	-0.067	0.23	NO
43	OXCT2	OXCT2	OXCT2	16486	-0.24	0.097	NO

Figure S23. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA DEATH PATHWAY.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA DEATH PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA VEGF PATHWAY

Table S13. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	AMDHD1	AMDHD1	AMDHD1	28	0.62	0.13	YES
2	DDC	DDC	DDC	82	0.51	0.24	YES
3	ASPA	ASPA	ASPA	168	0.43	0.32	YES
4	FTCD	FTCD	FTCD	170	0.43	0.42	YES
5	ACY3	ACY3	ACY3	567	0.28	0.45	YES
6	ABP1	ABP1	ABP1	689	0.26	0.5	YES
7	HDC	HDC	HDC	726	0.25	0.55	YES
8	ALDH3A2	ALDH3A2	ALDH3A2	862	0.22	0.59	YES
9	MAOB	MAOB	MAOB	1080	0.19	0.62	YES
10	HNMT	HNMT	HNMT	1716	0.14	0.62	NO
11	ALDH9A1	ALDH9A1	ALDH9A1	2638	0.097	0.59	NO
12	ALDH7A1	ALDH7A1	ALDH7A1	3122	0.082	0.58	NO
13	LCMT2	LCMT2	LCMT2	3714	0.066	0.56	NO
14	ALDH2	ALDH2	ALDH2	3788	0.064	0.57	NO
15	HAL	HAL	HAL	4303	0.054	0.55	NO
16	ALDH1B1	ALDH1B1	ALDH1B1	5616	0.032	0.49	NO
17	ALDH3A1	ALDH3A1	ALDH3A1	5855	0.029	0.48	NO
18	TRMT11	TRMT11	TRMT11	6152	0.025	0.47	NO
19	HEMK1	HEMK1	HEMK1	7412	0.011	0.4	NO
20	ALDH3B1	ALDH3B1	ALDH3B1	7707	0.0076	0.39	NO
21	METTL2B	METTL2B	METTL2B	8232	0.0012	0.36	NO
22	UROC1	UROC1	UROC1	10124	-0.021	0.26	NO
23	MAOA	MAOA	MAOA	10573	-0.026	0.24	NO
24	LCMT1	LCMT1	LCMT1	11018	-0.032	0.22	NO
25	WBSCR22	WBSCR22	WBSCR22	13246	-0.07	0.12	NO
26	METTL6	METTL6	METTL6	13876	-0.087	0.1	NO
27	ALDH3B2	ALDH3B2	ALDH3B2	15603	-0.17	0.041	NO
28	ALDH1A3	ALDH1A3	ALDH1A3	17979	-0.49	0.015	NO

Figure S25. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA VEGF PATHWAY.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA VEGF PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

Table S14. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ALDH6A1	ALDH6A1	ALDH6A1	346	0.34	0.085	YES
2	EHHADH	EHHADH	EHHADH	589	0.28	0.16	YES
3	ALDH3A2	ALDH3A2	ALDH3A2	862	0.22	0.21	YES
4	HIBCH	HIBCH	HIBCH	982	0.2	0.27	YES
5	ABAT	ABAT	ABAT	1040	0.2	0.33	YES
6	ACAT1	ACAT1	ACAT1	1266	0.18	0.37	YES
7	ACADM	ACADM	ACADM	1565	0.15	0.4	YES
8	PCCA	PCCA	PCCA	1576	0.15	0.44	YES
9	MLYCD	MLYCD	MLYCD	2254	0.11	0.44	YES
10	MUT	MUT	MUT	2315	0.11	0.47	YES
11	ALDH9A1	ALDH9A1	ALDH9A1	2638	0.097	0.48	YES
12	LDHAL6A	LDHAL6A	LDHAL6A	2745	0.094	0.51	YES
13	ALDH7A1	ALDH7A1	ALDH7A1	3122	0.082	0.51	YES
14	ACSS3	ACSS3	ACSS3	3136	0.081	0.54	YES
15	ACSS1	ACSS1	ACSS1	3287	0.077	0.55	YES
16	SUCLA2	SUCLA2	SUCLA2	3371	0.074	0.57	YES
17	ALDH2	ALDH2	ALDH2	3788	0.064	0.57	NO
18	MCEE	MCEE	MCEE	4359	0.052	0.55	NO
19	HADHA	HADHA	HADHA	4730	0.047	0.55	NO
20	ACACB	ACACB	ACACB	5401	0.035	0.52	NO
21	ALDH1B1	ALDH1B1	ALDH1B1	5616	0.032	0.52	NO
22	LDHA	LDHA	LDHA	5933	0.028	0.51	NO
23	ECHS1	ECHS1	ECHS1	6506	0.022	0.49	NO
24	SUCLG1	SUCLG1	SUCLG1	8368	-0.00036	0.38	NO
25	ACSS2	ACSS2	ACSS2	9894	-0.018	0.31	NO
26	SUCLG2	SUCLG2	SUCLG2	11049	-0.033	0.25	NO
27	LDHB	LDHB	LDHB	12499	-0.055	0.19	NO
28	ACAT2	ACAT2	ACAT2	12516	-0.055	0.21	NO
29	PCCB	PCCB	PCCB	13086	-0.067	0.2	NO
30	ACACA	ACACA	ACACA	14505	-0.11	0.15	NO
31	LDHAL6B	LDHAL6B	LDHAL6B	15780	-0.18	0.14	NO

Figure S27. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

Table S15. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HAO2	HAO2	HAO2	15	0.74	0.095	YES
2	SLC27A2	SLC27A2	SLC27A2	48	0.57	0.17	YES
3	DAO	DAO	DAO	297	0.36	0.2	YES
4	EHHADH	EHHADH	EHHADH	589	0.28	0.22	YES
5	PXMP2	PXMP2	PXMP2	723	0.25	0.25	YES
6	AGXT	AGXT	AGXT	738	0.24	0.28	YES
7	EPHX2	EPHX2	EPHX2	878	0.22	0.3	YES
8	NOS2	NOS2	NOS2	1031	0.2	0.32	YES
9	DDO	DDO	DDO	1131	0.19	0.34	YES
10	FAR2	FAR2	FAR2	1293	0.17	0.35	YES
11	PECR	PECR	PECR	1299	0.17	0.37	YES
12	PEX11A	PEX11A	PEX11A	1327	0.17	0.39	YES
13	ACSL1	ACSL1	ACSL1	1830	0.13	0.38	YES
14	DECR2	DECR2	DECR2	2015	0.12	0.39	YES
15	NUDT12	NUDT12	NUDT12	2131	0.12	0.4	YES
16	MLYCD	MLYCD	MLYCD	2254	0.11	0.4	YES
17	PEX11G	PEX11G	PEX11G	2329	0.11	0.42	YES
18	PAOX	PAOX	PAOX	2420	0.1	0.42	YES
19	PHYH	PHYH	PHYH	2555	0.1	0.43	YES
20	DHRS4	DHRS4	DHRS4	2654	0.097	0.44	YES
21	CRAT	CRAT	CRAT	2665	0.096	0.45	YES
22	AGPS	AGPS	AGPS	2714	0.095	0.46	YES
23	CAT	CAT	CAT	2786	0.092	0.47	YES
24	ECH1	ECH1	ECH1	2840	0.091	0.48	YES
25	PEX1	PEX1	PEX1	2970	0.086	0.48	YES
26	ABCD3	ABCD3	ABCD3	3084	0.083	0.48	YES
27	PECI	PECI	PECI	3432	0.073	0.47	NO
28	MPV17L	MPV17L	MPV17L	3601	0.069	0.47	NO
29	ABCD4	ABCD4	ABCD4	3751	0.065	0.47	NO
30	AMACR	AMACR	AMACR	3844	0.063	0.48	NO
31	PEX3	PEX3	PEX3	3949	0.061	0.48	NO
32	PEX7	PEX7	PEX7	4410	0.052	0.46	NO
33	PEX10	PEX10	PEX10	4467	0.051	0.46	NO
34	ACOX1	ACOX1	ACOX1	4519	0.05	0.47	NO
35	PMVK	PMVK	PMVK	4567	0.049	0.47	NO
36	HMGCL	HMGCL	HMGCL	4708	0.047	0.47	NO
37	ABCD2	ABCD2	ABCD2	5027	0.042	0.46	NO
38	PEX5	PEX5	PEX5	5052	0.041	0.46	NO
39	SCP2	SCP2	SCP2	5236	0.038	0.46	NO
40	PEX11B	PEX11B	PEX11B	5460	0.035	0.45	NO
41	PEX19	PEX19	PEX19	6569	0.021	0.39	NO
42	PEX26	PEX26	PEX26	6590	0.021	0.39	NO
43	PEX12	PEX12	PEX12	6891	0.017	0.38	NO
44	ACAA1	ACAA1	ACAA1	6952	0.016	0.38	NO
45	PIPOX	PIPOX	PIPOX	7085	0.015	0.37	NO
46	PEX13	PEX13	PEX13	7090	0.015	0.37	NO
47	SLC25A17	SLC25A17	SLC25A17	7477	0.01	0.35	NO
48	SOD1	SOD1	SOD1	8555	-0.0025	0.3	NO
49	CROT	CROT	CROT	8832	-0.0056	0.28	NO
50	GNPAT	GNPAT	GNPAT	9056	-0.0082	0.27	NO
51	HSD17B4	HSD17B4	HSD17B4	9175	-0.0096	0.26	NO
52	PEX14	PEX14	PEX14	9435	-0.013	0.25	NO
53	PEX6	PEX6	PEX6	9912	-0.018	0.23	NO
54	ACSL3	ACSL3	ACSL3	9963	-0.019	0.23	NO
55	ACSL6	ACSL6	ACSL6	10111	-0.021	0.22	NO
56	GSTK1	GSTK1	GSTK1	10609	-0.027	0.2	NO
57	IDH2	IDH2	IDH2	10659	-0.027	0.2	NO
58	ABCD1	ABCD1	ABCD1	10747	-0.029	0.2	NO
59	PEX2	PEX2	PEX2	11255	-0.036	0.18	NO
60	FAR1	FAR1	FAR1	11319	-0.036	0.18	NO
61	MPV17	MPV17	MPV17	11841	-0.044	0.15	NO
62	PRDX5	PRDX5	PRDX5	12146	-0.049	0.14	NO
63	PRDX1	PRDX1	PRDX1	12312	-0.052	0.14	NO
64	PEX16	PEX16	PEX16	12334	-0.052	0.15	NO
65	HACL1	HACL1	HACL1	12355	-0.053	0.15	NO
66	ACSL5	ACSL5	ACSL5	13195	-0.069	0.12	NO
67	NUDT19	NUDT19	NUDT19	13396	-0.074	0.11	NO
68	SOD2	SOD2	SOD2	13549	-0.078	0.12	NO
69	MVK	MVK	MVK	13559	-0.078	0.12	NO
70	ACOT8	ACOT8	ACOT8	13789	-0.084	0.12	NO
71	PXMP4	PXMP4	PXMP4	13805	-0.085	0.13	NO
72	ACSL4	ACSL4	ACSL4	14134	-0.095	0.13	NO
73	ACOX3	ACOX3	ACOX3	14632	-0.11	0.12	NO
74	IDH1	IDH1	IDH1	14782	-0.12	0.12	NO
75	BAAT	BAAT	BAAT	14874	-0.12	0.13	NO
76	XDH	XDH	XDH	17674	-0.4	0.032	NO

Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG GALACTOSE METABOLISM

Table S16. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	G6PC	G6PC	G6PC	27	0.64	0.1	YES
2	PCK1	PCK1	PCK1	60	0.55	0.19	YES
3	CD36	CD36	CD36	416	0.32	0.22	YES
4	G6PC2	G6PC2	G6PC2	458	0.31	0.26	YES
5	RXRG	RXRG	RXRG	850	0.22	0.28	YES
6	PRKAA2	PRKAA2	PRKAA2	1485	0.16	0.27	YES
7	SLC2A4	SLC2A4	SLC2A4	1712	0.14	0.28	YES
8	PCK2	PCK2	PCK2	1805	0.14	0.3	YES
9	ACSL1	ACSL1	ACSL1	1830	0.13	0.32	YES
10	MAPK8	MAPK8	MAPK8	1836	0.13	0.34	YES
11	PPARGC1A	PPARGC1A	PPARGC1A	1847	0.13	0.36	YES
12	AKT3	AKT3	AKT3	2165	0.12	0.36	YES
13	CPT1A	CPT1A	CPT1A	2171	0.12	0.38	YES
14	MAPK10	MAPK10	MAPK10	2413	0.1	0.38	YES
15	NFKBIA	NFKBIA	NFKBIA	2614	0.098	0.39	YES
16	PPARA	PPARA	PPARA	2804	0.092	0.39	YES
17	PRKAB1	PRKAB1	PRKAB1	3576	0.07	0.36	NO
18	LEPR	LEPR	LEPR	4069	0.058	0.34	NO
19	CAMKK1	CAMKK1	CAMKK1	4122	0.057	0.35	NO
20	NFKB1	NFKB1	NFKB1	4513	0.05	0.34	NO
21	NFKBIE	NFKBIE	NFKBIE	4780	0.046	0.33	NO
22	TRADD	TRADD	TRADD	4848	0.045	0.33	NO
23	PRKAA1	PRKAA1	PRKAA1	5315	0.037	0.31	NO
24	JAK2	JAK2	JAK2	5316	0.037	0.32	NO
25	ACACB	ACACB	ACACB	5401	0.035	0.32	NO
26	CPT1B	CPT1B	CPT1B	5677	0.032	0.31	NO
27	RXRB	RXRB	RXRB	5814	0.03	0.31	NO
28	CHUK	CHUK	CHUK	5920	0.028	0.3	NO
29	TRAF2	TRAF2	TRAF2	6275	0.024	0.29	NO
30	PRKAB2	PRKAB2	PRKAB2	7185	0.014	0.24	NO
31	IKBKB	IKBKB	IKBKB	7991	0.0042	0.2	NO
32	NFKBIB	NFKBIB	NFKBIB	8133	0.0023	0.19	NO
33	MAPK9	MAPK9	MAPK9	8630	-0.0034	0.16	NO
34	ADIPOR1	ADIPOR1	ADIPOR1	8663	-0.0037	0.16	NO
35	RELA	RELA	RELA	8793	-0.0052	0.16	NO
36	STAT3	STAT3	STAT3	8849	-0.0058	0.16	NO
37	RXRA	RXRA	RXRA	9230	-0.01	0.14	NO
38	ADIPOR2	ADIPOR2	ADIPOR2	9590	-0.015	0.12	NO
39	AKT2	AKT2	AKT2	9906	-0.018	0.1	NO
40	ACSL3	ACSL3	ACSL3	9963	-0.019	0.1	NO
41	STK11	STK11	STK11	10042	-0.02	0.1	NO
42	ACSL6	ACSL6	ACSL6	10111	-0.021	0.1	NO
43	PRKAG1	PRKAG1	PRKAG1	10133	-0.021	0.1	NO
44	TNFRSF1B	TNFRSF1B	TNFRSF1B	10148	-0.021	0.11	NO
45	MTOR	MTOR	MTOR	10232	-0.022	0.11	NO
46	CAMKK2	CAMKK2	CAMKK2	10283	-0.023	0.11	NO
47	AKT1	AKT1	AKT1	10352	-0.024	0.11	NO
48	CPT1C	CPT1C	CPT1C	11021	-0.032	0.076	NO
49	PTPN11	PTPN11	PTPN11	11033	-0.032	0.08	NO
50	TNFRSF1A	TNFRSF1A	TNFRSF1A	11406	-0.038	0.066	NO
51	PRKAG2	PRKAG2	PRKAG2	11691	-0.042	0.057	NO
52	PRKCQ	PRKCQ	PRKCQ	12116	-0.049	0.042	NO
53	SLC2A1	SLC2A1	SLC2A1	12418	-0.054	0.034	NO
54	TNF	TNF	TNF	13078	-0.066	0.0081	NO
55	IKBKG	IKBKG	IKBKG	13157	-0.068	0.015	NO
56	ACSL5	ACSL5	ACSL5	13195	-0.069	0.024	NO
57	ADIPOQ	ADIPOQ	ADIPOQ	13792	-0.084	0.0047	NO
58	ACSL4	ACSL4	ACSL4	14134	-0.095	0.0012	NO
59	SOCS3	SOCS3	SOCS3	14708	-0.12	-0.012	NO
60	IRS1	IRS1	IRS1	15689	-0.17	-0.038	NO
61	POMC	POMC	POMC	15694	-0.17	-0.01	NO
62	AGRP	AGRP	AGRP	16498	-0.24	-0.017	NO
63	IRS2	IRS2	IRS2	17433	-0.35	-0.012	NO
64	LEP	LEP	LEP	17496	-0.36	0.042	NO

Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GALACTOSE METABOLISM.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GALACTOSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table S17. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	DHDH	DHDH	DHDH	67	0.53	0.14	YES
2	UGT2A3	UGT2A3	UGT2A3	327	0.35	0.22	YES
3	UGT1A9	UGT1A9	UGT1A9	331	0.34	0.32	YES
4	XYLB	XYLB	XYLB	436	0.31	0.4	YES
5	UGT2B7	UGT2B7	UGT2B7	636	0.27	0.46	YES
6	UGT2B11	UGT2B11	UGT2B11	640	0.27	0.53	YES
7	UGT1A6	UGT1A6	UGT1A6	1406	0.16	0.54	YES
8	UGT1A8	UGT1A8	UGT1A8	1479	0.16	0.57	YES
9	UGT2B10	UGT2B10	UGT2B10	1599	0.15	0.61	YES
10	CRYL1	CRYL1	CRYL1	1649	0.15	0.65	YES
11	UGT1A1	UGT1A1	UGT1A1	1899	0.13	0.67	YES
12	UGT1A3	UGT1A3	UGT1A3	5066	0.041	0.51	NO
13	UGT2A1	UGT2A1	UGT2A1	5231	0.038	0.51	NO
14	UGT1A4	UGT1A4	UGT1A4	5609	0.032	0.5	NO
15	UGT1A7	UGT1A7	UGT1A7	6219	0.024	0.47	NO
16	LOC729020	LOC729020	LOC729020	6398	0.023	0.47	NO
17	UGT1A5	UGT1A5	UGT1A5	8729	-0.0045	0.34	NO
18	UGT2B15	UGT2B15	UGT2B15	10169	-0.022	0.27	NO
19	RPE	RPE	RPE	10333	-0.024	0.26	NO
20	UGT2B28	UGT2B28	UGT2B28	11882	-0.045	0.19	NO
21	GUSB	GUSB	GUSB	12691	-0.058	0.16	NO
22	UGT2B4	UGT2B4	UGT2B4	12854	-0.062	0.17	NO
23	UGP2	UGP2	UGP2	13169	-0.068	0.17	NO
24	DCXR	DCXR	DCXR	13226	-0.07	0.19	NO
25	AKR1B1	AKR1B1	AKR1B1	13641	-0.08	0.19	NO
26	UGT1A10	UGT1A10	UGT1A10	16475	-0.23	0.098	NO

Figure S33. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FATTY ACID METABOLISM.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FATTY ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM

Table S18. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CYP4A11	CYP4A11	CYP4A11	2	0.83	0.14	YES
2	CYP4A22	CYP4A22	CYP4A22	40	0.59	0.23	YES
3	ADH6	ADH6	ADH6	121	0.47	0.3	YES
4	ACADL	ACADL	ACADL	192	0.42	0.37	YES
5	EHHADH	EHHADH	EHHADH	589	0.28	0.39	YES
6	ALDH3A2	ALDH3A2	ALDH3A2	862	0.22	0.41	YES
7	ACAA2	ACAA2	ACAA2	906	0.22	0.44	YES
8	ACAT1	ACAT1	ACAT1	1266	0.18	0.45	YES
9	ACADM	ACADM	ACADM	1565	0.15	0.46	YES
10	CPT2	CPT2	CPT2	1600	0.15	0.48	YES
11	ACADSB	ACADSB	ACADSB	1806	0.14	0.5	YES
12	ACSL1	ACSL1	ACSL1	1830	0.13	0.52	YES
13	CPT1A	CPT1A	CPT1A	2171	0.12	0.52	YES
14	ALDH9A1	ALDH9A1	ALDH9A1	2638	0.097	0.51	NO
15	ALDH7A1	ALDH7A1	ALDH7A1	3122	0.082	0.49	NO
16	PECI	PECI	PECI	3432	0.073	0.49	NO
17	ADH5	ADH5	ADH5	3512	0.071	0.5	NO
18	ALDH2	ALDH2	ALDH2	3788	0.064	0.49	NO
19	ACADS	ACADS	ACADS	3860	0.063	0.5	NO
20	ACADVL	ACADVL	ACADVL	4284	0.054	0.48	NO
21	HADHB	HADHB	HADHB	4720	0.047	0.47	NO
22	HADHA	HADHA	HADHA	4730	0.047	0.48	NO
23	DCI	DCI	DCI	5194	0.039	0.46	NO
24	ALDH1B1	ALDH1B1	ALDH1B1	5616	0.032	0.44	NO
25	CPT1B	CPT1B	CPT1B	5677	0.032	0.44	NO
26	ECHS1	ECHS1	ECHS1	6506	0.022	0.4	NO
27	ACAA1	ACAA1	ACAA1	6952	0.016	0.38	NO
28	HADH	HADH	HADH	8673	-0.0038	0.28	NO
29	ACSL3	ACSL3	ACSL3	9963	-0.019	0.22	NO
30	ACSL6	ACSL6	ACSL6	10111	-0.021	0.21	NO
31	CPT1C	CPT1C	CPT1C	11021	-0.032	0.16	NO
32	GCDH	GCDH	GCDH	12035	-0.047	0.12	NO
33	ACAT2	ACAT2	ACAT2	12516	-0.055	0.1	NO
34	ACSL5	ACSL5	ACSL5	13195	-0.069	0.074	NO
35	ACSL4	ACSL4	ACSL4	14134	-0.095	0.038	NO
36	ACOX3	ACOX3	ACOX3	14632	-0.11	0.03	NO
37	ADH1B	ADH1B	ADH1B	15704	-0.17	-0.0011	NO
38	ADH1A	ADH1A	ADH1A	16469	-0.23	-0.005	NO
39	ADH4	ADH4	ADH4	16779	-0.26	0.021	NO
40	ADH1C	ADH1C	ADH1C	17552	-0.37	0.039	NO

Figure S35. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION

Table S19. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	AGPAT9	AGPAT9	AGPAT9	469	0.3	0.031	YES
2	DGKB	DGKB	DGKB	662	0.26	0.069	YES
3	DGKI	DGKI	DGKI	692	0.25	0.11	YES
4	DGKH	DGKH	DGKH	755	0.24	0.16	YES
5	ALDH3A2	ALDH3A2	ALDH3A2	862	0.22	0.19	YES
6	LIPC	LIPC	LIPC	904	0.22	0.23	YES
7	LPL	LPL	LPL	1170	0.18	0.25	YES
8	GK	GK	GK	1189	0.18	0.28	YES
9	PPAP2B	PPAP2B	PPAP2B	1206	0.18	0.31	YES
10	DGKE	DGKE	DGKE	1267	0.18	0.34	YES
11	PPAP2A	PPAP2A	PPAP2A	1313	0.17	0.37	YES
12	PNPLA3	PNPLA3	PNPLA3	1461	0.16	0.39	YES
13	ALDH9A1	ALDH9A1	ALDH9A1	2638	0.097	0.35	NO
14	ALDH7A1	ALDH7A1	ALDH7A1	3122	0.082	0.34	NO
15	DGKD	DGKD	DGKD	3207	0.079	0.35	NO
16	DAK	DAK	DAK	3399	0.074	0.35	NO
17	AGPAT3	AGPAT3	AGPAT3	3579	0.07	0.35	NO
18	ALDH2	ALDH2	ALDH2	3788	0.064	0.35	NO
19	LCLAT1	LCLAT1	LCLAT1	4147	0.056	0.34	NO
20	AKR1A1	AKR1A1	AKR1A1	4798	0.046	0.32	NO
21	ALDH1B1	ALDH1B1	ALDH1B1	5616	0.032	0.28	NO
22	DGKZ	DGKZ	DGKZ	6086	0.026	0.26	NO
23	AGPAT1	AGPAT1	AGPAT1	6452	0.022	0.24	NO
24	GLYCTK	GLYCTK	GLYCTK	7373	0.011	0.19	NO
25	MGLL	MGLL	MGLL	7583	0.0091	0.18	NO
26	AGPAT4	AGPAT4	AGPAT4	9319	-0.012	0.09	NO
27	AGPAT6	AGPAT6	AGPAT6	9404	-0.012	0.088	NO
28	MBOAT2	MBOAT2	MBOAT2	10902	-0.031	0.011	NO
29	GPAM	GPAM	GPAM	11594	-0.04	-0.019	NO
30	DGKQ	DGKQ	DGKQ	12113	-0.048	-0.038	NO
31	LIPG	LIPG	LIPG	12190	-0.05	-0.033	NO
32	AGK	AGK	AGK	12543	-0.056	-0.042	NO
33	MBOAT1	MBOAT1	MBOAT1	12586	-0.057	-0.034	NO
34	DGAT1	DGAT1	DGAT1	13040	-0.066	-0.047	NO
35	AGPAT2	AGPAT2	AGPAT2	13453	-0.076	-0.055	NO
36	AKR1B1	AKR1B1	AKR1B1	13641	-0.08	-0.051	NO
37	LIPF	LIPF	LIPF	13645	-0.08	-0.036	NO
38	GPAT2	GPAT2	GPAT2	13679	-0.081	-0.022	NO
39	DGKA	DGKA	DGKA	14218	-0.098	-0.034	NO
40	AWAT2	AWAT2	AWAT2	14612	-0.11	-0.034	NO
41	GLA	GLA	GLA	15256	-0.14	-0.043	NO
42	PPAP2C	PPAP2C	PPAP2C	16140	-0.2	-0.054	NO
43	CEL	CEL	CEL	16371	-0.22	-0.025	NO
44	DGAT2	DGAT2	DGAT2	16902	-0.28	-0.0031	NO
45	DGKG	DGKG	DGKG	17764	-0.42	0.027	NO

Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG LYSINE DEGRADATION

Table S20. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CREB3L3	CREB3L3	CREB3L3	258	0.38	0.1	YES
2	AQP4	AQP4	AQP4	417	0.32	0.19	YES
3	AVPR2	AVPR2	AVPR2	1028	0.2	0.21	YES
4	DYNC2H1	DYNC2H1	DYNC2H1	1309	0.17	0.25	YES
5	ADCY9	ADCY9	ADCY9	1441	0.16	0.29	YES
6	CREB5	CREB5	CREB5	1941	0.13	0.3	YES
7	DCTN6	DCTN6	DCTN6	2627	0.097	0.29	YES
8	DYNC2LI1	DYNC2LI1	DYNC2LI1	2712	0.095	0.32	YES
9	AQP3	AQP3	AQP3	2964	0.086	0.33	YES
10	CREB3L4	CREB3L4	CREB3L4	3166	0.08	0.34	YES
11	VAMP2	VAMP2	VAMP2	3196	0.079	0.36	YES
12	DYNLL2	DYNLL2	DYNLL2	3722	0.066	0.35	NO
13	DCTN1	DCTN1	DCTN1	4380	0.052	0.33	NO
14	CREB3	CREB3	CREB3	5007	0.042	0.31	NO
15	DYNC1I2	DYNC1I2	DYNC1I2	5256	0.038	0.31	NO
16	CREB1	CREB1	CREB1	5992	0.027	0.28	NO
17	PRKACB	PRKACB	PRKACB	7170	0.014	0.22	NO
18	DYNC1LI2	DYNC1LI2	DYNC1LI2	7906	0.0051	0.18	NO
19	ADCY6	ADCY6	ADCY6	8034	0.0035	0.17	NO
20	ARHGDIB	ARHGDIB	ARHGDIB	8045	0.0034	0.17	NO
21	DYNC1H1	DYNC1H1	DYNC1H1	8266	0.00072	0.16	NO
22	RAB5C	RAB5C	RAB5C	8527	-0.0021	0.15	NO
23	DCTN4	DCTN4	DCTN4	8569	-0.0026	0.14	NO
24	ARHGDIA	ARHGDIA	ARHGDIA	8808	-0.0054	0.13	NO
25	RAB5B	RAB5B	RAB5B	8983	-0.0074	0.12	NO
26	RAB11A	RAB11A	RAB11A	9140	-0.0092	0.12	NO
27	STX4	STX4	STX4	9267	-0.011	0.12	NO
28	CREB3L2	CREB3L2	CREB3L2	9469	-0.013	0.11	NO
29	DCTN5	DCTN5	DCTN5	10096	-0.021	0.081	NO
30	RAB11B	RAB11B	RAB11B	10453	-0.025	0.068	NO
31	PRKACA	PRKACA	PRKACA	10539	-0.026	0.072	NO
32	DYNC1LI1	DYNC1LI1	DYNC1LI1	10756	-0.029	0.068	NO
33	NSF	NSF	NSF	10888	-0.03	0.07	NO
34	DCTN2	DCTN2	DCTN2	11600	-0.04	0.043	NO
35	RAB5A	RAB5A	RAB5A	11834	-0.044	0.044	NO
36	PRKX	PRKX	PRKX	11958	-0.046	0.05	NO
37	DYNLL1	DYNLL1	DYNLL1	12254	-0.051	0.05	NO
38	DYNC1I1	DYNC1I1	DYNC1I1	13525	-0.078	0.0031	NO
39	GNAS	GNAS	GNAS	14553	-0.11	-0.021	NO
40	AQP2	AQP2	AQP2	15604	-0.17	-0.028	NO
41	CREB3L1	CREB3L1	CREB3L1	18136	-0.58	0.0067	NO

Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG LYSINE DEGRADATION.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

up-regulated, please check the list of up-regulated genes
down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

highly expressed genes, please check the list of high (top 30%) expressed genes
low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Subtype clus3 enriched pathways

Table 5. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA INFLAM PATHWAY	25	genes.ES.table	0.66	1.5	0.063	0.6	0.92	0.76	0.28	0.55	0.47	0.18
BIOCARTA GSK3 PATHWAY	26	genes.ES.table	0.53	1.6	0.028	0.56	0.7	0.15	0.054	0.15	0.34	0.18
BIOCARTA WNT PATHWAY	25	genes.ES.table	0.41	1.4	0.084	0.58	0.93	0.08	0.054	0.076	0.46	0.17
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.47	1.6	0.076	0.54	0.73	0.51	0.35	0.33	0.33	0.17
KEGG DNA REPLICATION	35	genes.ES.table	0.53	1.6	0.075	0.51	0.74	0.66	0.38	0.41	0.33	0.15
KEGG BASE EXCISION REPAIR	32	genes.ES.table	0.44	1.4	0.14	0.59	0.93	0.47	0.36	0.3	0.46	0.17
KEGG HOMOLOGOUS RECOMBINATION	27	genes.ES.table	0.62	1.6	0.061	0.55	0.82	0.41	0.23	0.31	0.38	0.18
KEGG CHEMOKINE SIGNALING PATHWAY	181	genes.ES.table	0.51	1.5	0.089	0.68	0.9	0.44	0.25	0.34	0.52	0.23
KEGG CELL CYCLE	123	genes.ES.table	0.53	1.7	0.043	0.67	0.56	0.23	0.12	0.2	0.34	0.23
KEGG OOCYTE MEIOSIS	106	genes.ES.table	0.42	1.5	0.094	0.68	0.91	0.21	0.14	0.18	0.52	0.23

genes ES table in pathway: BIOCARTA INFLAM PATHWAY

Table S21. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IL6	IL6	IL6	260	0.45	0.094	YES
2	C8G	C8G	C8G	557	0.38	0.17	YES
3	NCAM1	NCAM1	NCAM1	824	0.33	0.23	YES
4	NCAM2	NCAM2	NCAM2	949	0.32	0.3	YES
5	C9	C9	C9	1062	0.3	0.37	YES
6	IL1A	IL1A	IL1A	1186	0.28	0.43	YES
7	CCL5	CCL5	CCL5	1522	0.25	0.47	YES
8	C1QB	C1QB	C1QB	1894	0.22	0.5	YES
9	C1QC	C1QC	C1QC	2119	0.2	0.54	YES
10	IL1B	IL1B	IL1B	2148	0.2	0.58	YES
11	C1QA	C1QA	C1QA	2164	0.2	0.63	YES
12	BAX	BAX	BAX	4091	0.11	0.55	NO
13	ELK1	ELK1	ELK1	4856	0.084	0.53	NO
14	MAP2K2	MAP2K2	MAP2K2	6021	0.059	0.48	NO
15	PRKX	PRKX	PRKX	6689	0.047	0.46	NO
16	PRNP	PRNP	PRNP	7173	0.04	0.44	NO
17	C5	C5	C5	7278	0.038	0.44	NO
18	HSPA5	HSPA5	HSPA5	7317	0.038	0.45	NO
19	SOD1	SOD1	SOD1	7875	0.029	0.42	NO
20	STIP1	STIP1	STIP1	8061	0.027	0.42	NO
21	MAP2K1	MAP2K1	MAP2K1	8955	0.015	0.38	NO
22	HSPA1A	HSPA1A	HSPA1A	9585	0.0069	0.34	NO
23	PRKACA	PRKACA	PRKACA	9732	0.0048	0.34	NO
24	LAMC1	LAMC1	LAMC1	10575	-0.0057	0.29	NO
25	MAPK3	MAPK3	MAPK3	13069	-0.039	0.16	NO
26	PRKACB	PRKACB	PRKACB	13598	-0.048	0.15	NO
27	NOTCH1	NOTCH1	NOTCH1	13625	-0.048	0.16	NO
28	MAPK1	MAPK1	MAPK1	13695	-0.05	0.16	NO
29	FYN	FYN	FYN	15334	-0.087	0.096	NO
30	EGR1	EGR1	EGR1	15866	-0.1	0.093	NO
31	C6	C6	C6	16822	-0.16	0.079	NO

Figure S41. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA INFLAM PATHWAY.

Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INFLAM PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GSK3 PATHWAY

Table S22. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	AIM2	AIM2	AIM2	96	0.55	0.099	YES
2	IL6	IL6	IL6	260	0.45	0.18	YES
3	ZBP1	ZBP1	ZBP1	370	0.42	0.25	YES
4	IKBKE	IKBKE	IKBKE	390	0.41	0.32	YES
5	PYCARD	PYCARD	PYCARD	762	0.34	0.37	YES
6	IFNB1	IFNB1	IFNB1	892	0.32	0.42	YES
7	CCL5	CCL5	CCL5	1522	0.25	0.43	YES
8	CCL4	CCL4	CCL4	1702	0.23	0.47	YES
9	IRF7	IRF7	IRF7	2050	0.2	0.49	YES
10	IL1B	IL1B	IL1B	2148	0.2	0.52	YES
11	POLR3G	POLR3G	POLR3G	2152	0.2	0.56	YES
12	CCL4L2	CCL4L2	CCL4L2	2187	0.2	0.59	YES
13	IL18	IL18	IL18	2297	0.19	0.62	YES
14	CASP1	CASP1	CASP1	3214	0.14	0.6	NO
15	RIPK3	RIPK3	RIPK3	3573	0.12	0.6	NO
16	TMEM173	TMEM173	TMEM173	4181	0.1	0.59	NO
17	CXCL10	CXCL10	CXCL10	5000	0.08	0.56	NO
18	IKBKG	IKBKG	IKBKG	5016	0.08	0.57	NO
19	IRF3	IRF3	IRF3	5240	0.074	0.57	NO
20	POLR3K	POLR3K	POLR3K	5243	0.074	0.59	NO
21	TBK1	TBK1	TBK1	6725	0.047	0.51	NO
22	POLR3D	POLR3D	POLR3D	8349	0.023	0.43	NO
23	TREX1	TREX1	TREX1	8395	0.022	0.43	NO
24	NFKBIB	NFKBIB	NFKBIB	8541	0.021	0.43	NO
25	POLR3H	POLR3H	POLR3H	8832	0.016	0.41	NO
26	POLR3C	POLR3C	POLR3C	9033	0.014	0.41	NO
27	IKBKB	IKBKB	IKBKB	9331	0.01	0.39	NO
28	ADAR	ADAR	ADAR	9448	0.0086	0.39	NO
29	POLR1C	POLR1C	POLR1C	9589	0.0069	0.38	NO
30	RELA	RELA	RELA	9833	0.0034	0.37	NO
31	POLR3A	POLR3A	POLR3A	9898	0.0025	0.36	NO
32	DDX58	DDX58	DDX58	9989	0.0015	0.36	NO
33	RIPK1	RIPK1	RIPK1	10704	-0.0071	0.32	NO
34	POLR3GL	POLR3GL	POLR3GL	10808	-0.0084	0.32	NO
35	POLR3F	POLR3F	POLR3F	11188	-0.013	0.3	NO
36	MAVS	MAVS	MAVS	11263	-0.014	0.3	NO
37	POLR1D	POLR1D	POLR1D	11268	-0.014	0.3	NO
38	NFKB1	NFKB1	NFKB1	12805	-0.035	0.22	NO
39	IL33	IL33	IL33	13032	-0.039	0.22	NO
40	POLR3B	POLR3B	POLR3B	13137	-0.041	0.22	NO
41	CHUK	CHUK	CHUK	13895	-0.053	0.19	NO
42	NFKBIA	NFKBIA	NFKBIA	14643	-0.069	0.16	NO
43	IFNA13	IFNA13	IFNA13	15751	-0.1	0.12	NO
44	IFNA5	IFNA5	IFNA5	15835	-0.1	0.13	NO

Figure S43. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GSK3 PATHWAY.

Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GSK3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA WNT PATHWAY

Table S23. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CDC25C	CDC25C	CDC25C	156	0.51	0.028	YES
2	BUB1	BUB1	BUB1	190	0.49	0.06	YES
3	CCNE1	CCNE1	CCNE1	265	0.45	0.088	YES
4	PTTG1	PTTG1	PTTG1	277	0.44	0.12	YES
5	PLK1	PLK1	PLK1	300	0.44	0.15	YES
6	CCNB2	CCNB2	CCNB2	377	0.42	0.17	YES
7	CDC20	CDC20	CDC20	407	0.41	0.2	YES
8	PKMYT1	PKMYT1	PKMYT1	459	0.4	0.23	YES
9	ORC6L	ORC6L	ORC6L	536	0.38	0.25	YES
10	BUB1B	BUB1B	BUB1B	566	0.37	0.27	YES
11	TTK	TTK	TTK	603	0.37	0.3	YES
12	SFN	SFN	SFN	769	0.34	0.31	YES
13	CDC45	CDC45	CDC45	771	0.34	0.34	YES
14	E2F2	E2F2	E2F2	831	0.33	0.36	YES
15	ORC1L	ORC1L	ORC1L	1000	0.31	0.37	YES
16	CCNA1	CCNA1	CCNA1	1011	0.3	0.39	YES
17	CHEK2	CHEK2	CHEK2	1145	0.29	0.4	YES
18	CCNA2	CCNA2	CCNA2	1149	0.29	0.42	YES
19	ESPL1	ESPL1	ESPL1	1228	0.28	0.44	YES
20	CDKN2A	CDKN2A	CDKN2A	1278	0.27	0.46	YES
21	CCNB1	CCNB1	CCNB1	1380	0.26	0.47	YES
22	CDK1	CDK1	CDK1	1429	0.26	0.48	YES
23	CDC6	CDC6	CDC6	1595	0.24	0.49	YES
24	SMC1B	SMC1B	SMC1B	2010	0.21	0.48	YES
25	CCNE2	CCNE2	CCNE2	2026	0.21	0.5	YES
26	CDC25A	CDC25A	CDC25A	2053	0.2	0.51	YES
27	CDC7	CDC7	CDC7	2185	0.2	0.52	YES
28	MAD2L1	MAD2L1	MAD2L1	2284	0.19	0.53	YES
29	E2F1	E2F1	E2F1	2905	0.16	0.5	NO
30	CDC25B	CDC25B	CDC25B	2988	0.15	0.51	NO
31	MAD2L2	MAD2L2	MAD2L2	3709	0.12	0.48	NO
32	E2F3	E2F3	E2F3	4130	0.1	0.46	NO
33	CHEK1	CHEK1	CHEK1	4160	0.1	0.47	NO
34	MCM6	MCM6	MCM6	4264	0.1	0.47	NO
35	TGFB1	TGFB1	TGFB1	4266	0.1	0.48	NO
36	MCM2	MCM2	MCM2	4479	0.094	0.47	NO
37	CDK7	CDK7	CDK7	4744	0.086	0.46	NO
38	MAD1L1	MAD1L1	MAD1L1	4864	0.084	0.46	NO
39	PTTG2	PTTG2	PTTG2	4873	0.083	0.47	NO
40	ANAPC11	ANAPC11	ANAPC11	5130	0.077	0.46	NO
41	MCM4	MCM4	MCM4	5162	0.076	0.46	NO
42	ANAPC5	ANAPC5	ANAPC5	5238	0.074	0.46	NO
43	YWHAG	YWHAG	YWHAG	5383	0.071	0.46	NO
44	RBX1	RBX1	RBX1	5560	0.068	0.46	NO
45	PCNA	PCNA	PCNA	5756	0.064	0.45	NO
46	CDK4	CDK4	CDK4	5814	0.063	0.45	NO
47	TGFB3	TGFB3	TGFB3	5839	0.062	0.45	NO
48	ORC5L	ORC5L	ORC5L	5900	0.061	0.46	NO
49	MDM2	MDM2	MDM2	5987	0.059	0.45	NO
50	TP53	TP53	TP53	6107	0.057	0.45	NO
51	MCM5	MCM5	MCM5	6226	0.055	0.45	NO
52	ATR	ATR	ATR	6267	0.055	0.45	NO
53	CDK2	CDK2	CDK2	6339	0.054	0.45	NO
54	CCNH	CCNH	CCNH	6559	0.05	0.44	NO
55	MYC	MYC	MYC	6757	0.046	0.44	NO
56	GADD45G	GADD45G	GADD45G	6915	0.044	0.43	NO
57	CUL1	CUL1	CUL1	7041	0.042	0.42	NO
58	YWHAZ	YWHAZ	YWHAZ	7119	0.04	0.42	NO
59	ANAPC7	ANAPC7	ANAPC7	7298	0.038	0.42	NO
60	CDKN2D	CDKN2D	CDKN2D	7395	0.036	0.41	NO
61	CDK6	CDK6	CDK6	7442	0.036	0.41	NO
62	CCNB3	CCNB3	CCNB3	7579	0.034	0.41	NO
63	E2F4	E2F4	E2F4	7651	0.032	0.41	NO
64	CCND2	CCND2	CCND2	7685	0.032	0.41	NO
65	BUB3	BUB3	BUB3	7688	0.032	0.41	NO
66	ANAPC4	ANAPC4	ANAPC4	7798	0.03	0.41	NO
67	GADD45B	GADD45B	GADD45B	7840	0.03	0.41	NO
68	YWHAQ	YWHAQ	YWHAQ	8196	0.025	0.39	NO
69	E2F5	E2F5	E2F5	8213	0.025	0.39	NO
70	CCND3	CCND3	CCND3	8237	0.024	0.39	NO
71	SKP2	SKP2	SKP2	8303	0.024	0.39	NO
72	PRKDC	PRKDC	PRKDC	8462	0.022	0.38	NO
73	CDKN2C	CDKN2C	CDKN2C	8572	0.02	0.38	NO
74	RBL1	RBL1	RBL1	8592	0.02	0.38	NO
75	TFDP2	TFDP2	TFDP2	8599	0.02	0.38	NO
76	ZBTB17	ZBTB17	ZBTB17	8614	0.02	0.38	NO
77	CDC16	CDC16	CDC16	8631	0.019	0.38	NO
78	MCM7	MCM7	MCM7	9239	0.011	0.34	NO
79	FZR1	FZR1	FZR1	9531	0.0075	0.33	NO
80	ANAPC1	ANAPC1	ANAPC1	10004	0.0014	0.3	NO
81	HDAC1	HDAC1	HDAC1	10082	0.00028	0.3	NO
82	ANAPC10	ANAPC10	ANAPC10	10482	-0.0046	0.28	NO
83	GADD45A	GADD45A	GADD45A	10559	-0.0056	0.27	NO
84	YWHAB	YWHAB	YWHAB	10613	-0.0062	0.27	NO
85	MCM3	MCM3	MCM3	10624	-0.0063	0.27	NO
86	RB1	RB1	RB1	10739	-0.0076	0.27	NO
87	CDKN1A	CDKN1A	CDKN1A	11031	-0.011	0.25	NO
88	CDC27	CDC27	CDC27	11202	-0.013	0.24	NO
89	YWHAH	YWHAH	YWHAH	11315	-0.015	0.24	NO
90	ATM	ATM	ATM	11407	-0.016	0.23	NO
91	RAD21	RAD21	RAD21	11652	-0.019	0.22	NO
92	SKP1	SKP1	SKP1	11804	-0.021	0.21	NO
93	GSK3B	GSK3B	GSK3B	11889	-0.022	0.21	NO
94	ORC3L	ORC3L	ORC3L	12250	-0.027	0.19	NO
95	YWHAE	YWHAE	YWHAE	12383	-0.029	0.19	NO
96	SMC1A	SMC1A	SMC1A	12430	-0.03	0.19	NO
97	CDKN1B	CDKN1B	CDKN1B	12524	-0.031	0.18	NO
98	ORC2L	ORC2L	ORC2L	12553	-0.031	0.18	NO
99	ABL1	ABL1	ABL1	12580	-0.032	0.19	NO
100	SMAD2	SMAD2	SMAD2	12777	-0.035	0.18	NO
101	SMAD3	SMAD3	SMAD3	12834	-0.036	0.18	NO
102	CDC23	CDC23	CDC23	12903	-0.037	0.18	NO
103	HDAC2	HDAC2	HDAC2	12909	-0.037	0.18	NO
104	CREBBP	CREBBP	CREBBP	13220	-0.042	0.16	NO
105	RBL2	RBL2	RBL2	13384	-0.044	0.16	NO
106	TFDP1	TFDP1	TFDP1	13675	-0.049	0.15	NO
107	ANAPC13	ANAPC13	ANAPC13	13907	-0.053	0.14	NO
108	SMC3	SMC3	SMC3	13973	-0.054	0.14	NO
109	ORC4L	ORC4L	ORC4L	13997	-0.055	0.14	NO
110	EP300	EP300	EP300	14084	-0.056	0.14	NO
111	TGFB2	TGFB2	TGFB2	14162	-0.058	0.14	NO
112	STAG1	STAG1	STAG1	14331	-0.062	0.13	NO
113	STAG2	STAG2	STAG2	14392	-0.063	0.14	NO
114	WEE1	WEE1	WEE1	14886	-0.075	0.11	NO
115	ANAPC2	ANAPC2	ANAPC2	14900	-0.075	0.12	NO
116	WEE2	WEE2	WEE2	15232	-0.084	0.11	NO
117	CDKN2B	CDKN2B	CDKN2B	15336	-0.087	0.11	NO
118	SMAD4	SMAD4	SMAD4	15618	-0.096	0.097	NO
119	CDC26	CDC26	CDC26	15759	-0.1	0.097	NO
120	CDKN1C	CDKN1C	CDKN1C	15977	-0.11	0.093	NO
121	CCND1	CCND1	CCND1	16145	-0.12	0.092	NO
122	CDC14A	CDC14A	CDC14A	16669	-0.15	0.073	NO
123	CDC14B	CDC14B	CDC14B	17287	-0.2	0.054	NO

Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA WNT PATHWAY.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA WNT PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

Table S24. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCNE1	CCNE1	CCNE1	265	0.45	0.043	YES
2	GTSE1	GTSE1	GTSE1	350	0.42	0.092	YES
3	CCNB2	CCNB2	CCNB2	377	0.42	0.14	YES
4	BAI1	BAI1	BAI1	462	0.4	0.19	YES
5	RRM2	RRM2	RRM2	575	0.37	0.23	YES
6	SFN	SFN	SFN	769	0.34	0.26	YES
7	TP73	TP73	TP73	987	0.31	0.29	YES
8	CHEK2	CHEK2	CHEK2	1145	0.29	0.32	YES
9	SERPINE1	SERPINE1	SERPINE1	1183	0.28	0.35	YES
10	CD82	CD82	CD82	1231	0.28	0.39	YES
11	PMAIP1	PMAIP1	PMAIP1	1262	0.27	0.42	YES
12	CDKN2A	CDKN2A	CDKN2A	1278	0.27	0.45	YES
13	CCNB1	CCNB1	CCNB1	1380	0.26	0.48	YES
14	CDK1	CDK1	CDK1	1429	0.26	0.51	YES
15	CCNE2	CCNE2	CCNE2	2026	0.21	0.51	YES
16	BID	BID	BID	2506	0.18	0.5	YES
17	BBC3	BBC3	BBC3	3565	0.12	0.46	YES
18	LRDD	LRDD	LRDD	3619	0.12	0.47	YES
19	CASP3	CASP3	CASP3	3639	0.12	0.49	YES
20	CASP8	CASP8	CASP8	4019	0.11	0.48	YES
21	BAX	BAX	BAX	4091	0.11	0.49	YES
22	IGFBP3	IGFBP3	IGFBP3	4112	0.11	0.5	YES
23	CHEK1	CHEK1	CHEK1	4160	0.1	0.51	YES
24	TP53I3	TP53I3	TP53I3	5458	0.07	0.45	NO
25	TNFRSF10B	TNFRSF10B	TNFRSF10B	5476	0.069	0.46	NO
26	IGF1	IGF1	IGF1	5598	0.067	0.46	NO
27	FAS	FAS	FAS	5615	0.067	0.47	NO
28	PERP	PERP	PERP	5721	0.065	0.47	NO
29	CDK4	CDK4	CDK4	5814	0.063	0.47	NO
30	MDM2	MDM2	MDM2	5987	0.059	0.47	NO
31	APAF1	APAF1	APAF1	5991	0.059	0.48	NO
32	TP53	TP53	TP53	6107	0.057	0.48	NO
33	SHISA5	SHISA5	SHISA5	6197	0.056	0.48	NO
34	DDB2	DDB2	DDB2	6263	0.055	0.49	NO
35	ATR	ATR	ATR	6267	0.055	0.49	NO
36	CDK2	CDK2	CDK2	6339	0.054	0.5	NO
37	RPRM	RPRM	RPRM	6420	0.052	0.5	NO
38	ZMAT3	ZMAT3	ZMAT3	6595	0.049	0.49	NO
39	SESN3	SESN3	SESN3	6721	0.047	0.49	NO
40	CASP9	CASP9	CASP9	6841	0.045	0.49	NO
41	GADD45G	GADD45G	GADD45G	6915	0.044	0.49	NO
42	RFWD2	RFWD2	RFWD2	6960	0.043	0.5	NO
43	SESN2	SESN2	SESN2	7141	0.04	0.49	NO
44	CDK6	CDK6	CDK6	7442	0.036	0.48	NO
45	CCNB3	CCNB3	CCNB3	7579	0.034	0.48	NO
46	CCND2	CCND2	CCND2	7685	0.032	0.48	NO
47	GADD45B	GADD45B	GADD45B	7840	0.03	0.47	NO
48	CCND3	CCND3	CCND3	8237	0.024	0.45	NO
49	RRM2B	RRM2B	RRM2B	8318	0.023	0.45	NO
50	CYCS	CYCS	CYCS	8517	0.021	0.44	NO
51	EI24	EI24	EI24	9586	0.0069	0.38	NO
52	SERPINB5	SERPINB5	SERPINB5	9793	0.0039	0.37	NO
53	MDM4	MDM4	MDM4	10234	-0.0015	0.35	NO
54	GADD45A	GADD45A	GADD45A	10559	-0.0056	0.33	NO
55	TSC2	TSC2	TSC2	11004	-0.011	0.31	NO
56	CDKN1A	CDKN1A	CDKN1A	11031	-0.011	0.31	NO
57	ATM	ATM	ATM	11407	-0.016	0.29	NO
58	SIAH1	SIAH1	SIAH1	12035	-0.024	0.26	NO
59	SESN1	SESN1	SESN1	12461	-0.03	0.24	NO
60	PTEN	PTEN	PTEN	12629	-0.032	0.24	NO
61	THBS1	THBS1	THBS1	13841	-0.052	0.18	NO
62	CCNG2	CCNG2	CCNG2	14301	-0.061	0.16	NO
63	CCNG1	CCNG1	CCNG1	14816	-0.073	0.14	NO
64	TP53AIP1	TP53AIP1	TP53AIP1	14974	-0.077	0.14	NO
65	PPM1D	PPM1D	PPM1D	15479	-0.091	0.12	NO
66	RCHY1	RCHY1	RCHY1	15787	-0.1	0.12	NO
67	CCND1	CCND1	CCND1	16145	-0.12	0.12	NO

Figure S47. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DNA REPLICATION

Table S25. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IL6	IL6	IL6	260	0.45	0.04	YES
2	CASP5	CASP5	CASP5	293	0.44	0.09	YES
3	NOD2	NOD2	NOD2	402	0.41	0.13	YES
4	MEFV	MEFV	MEFV	591	0.37	0.17	YES
5	CARD9	CARD9	CARD9	672	0.36	0.2	YES
6	PYCARD	PYCARD	PYCARD	762	0.34	0.24	YES
7	PSTPIP1	PSTPIP1	PSTPIP1	956	0.31	0.27	YES
8	CCL11	CCL11	CCL11	1057	0.3	0.3	YES
9	IL8	IL8	IL8	1086	0.3	0.33	YES
10	PYDC1	PYDC1	PYDC1	1230	0.28	0.36	YES
11	CCL13	CCL13	CCL13	1268	0.27	0.39	YES
12	NLRC4	NLRC4	NLRC4	1342	0.27	0.41	YES
13	CCL7	CCL7	CCL7	1366	0.26	0.44	YES
14	CXCL1	CXCL1	CXCL1	1427	0.26	0.47	YES
15	BIRC3	BIRC3	BIRC3	1435	0.26	0.5	YES
16	CXCL2	CXCL2	CXCL2	1503	0.25	0.53	YES
17	CCL5	CCL5	CCL5	1522	0.25	0.56	YES
18	NAIP	NAIP	NAIP	1880	0.22	0.56	YES
19	IL1B	IL1B	IL1B	2148	0.2	0.57	YES
20	IL18	IL18	IL18	2297	0.19	0.58	YES
21	CCL8	CCL8	CCL8	2434	0.18	0.6	YES
22	RIPK2	RIPK2	RIPK2	2488	0.18	0.62	YES
23	NLRP3	NLRP3	NLRP3	2928	0.15	0.61	NO
24	CASP1	CASP1	CASP1	3214	0.14	0.61	NO
25	TNF	TNF	TNF	3603	0.12	0.61	NO
26	CASP8	CASP8	CASP8	4019	0.11	0.6	NO
27	HSP90B1	HSP90B1	HSP90B1	4638	0.09	0.57	NO
28	IKBKG	IKBKG	IKBKG	5016	0.08	0.56	NO
29	TRIP6	TRIP6	TRIP6	5290	0.073	0.56	NO
30	MAPK11	MAPK11	MAPK11	5548	0.068	0.55	NO
31	TNFAIP3	TNFAIP3	TNFAIP3	6285	0.055	0.52	NO
32	MAPK13	MAPK13	MAPK13	6640	0.048	0.5	NO
33	NLRP1	NLRP1	NLRP1	7749	0.031	0.44	NO
34	NFKBIB	NFKBIB	NFKBIB	8541	0.021	0.4	NO
35	MAPK9	MAPK9	MAPK9	8589	0.02	0.4	NO
36	NOD1	NOD1	NOD1	8680	0.019	0.4	NO
37	BIRC2	BIRC2	BIRC2	9091	0.013	0.38	NO
38	MAPK14	MAPK14	MAPK14	9234	0.011	0.37	NO
39	IKBKB	IKBKB	IKBKB	9331	0.01	0.37	NO
40	ERBB2IP	ERBB2IP	ERBB2IP	9405	0.0092	0.37	NO
41	CARD8	CARD8	CARD8	9574	0.0071	0.36	NO
42	RELA	RELA	RELA	9833	0.0034	0.34	NO
43	SUGT1	SUGT1	SUGT1	10073	0.0004	0.33	NO
44	TAB1	TAB1	TAB1	10118	-0.000062	0.33	NO
45	XIAP	XIAP	XIAP	10159	-0.00064	0.33	NO
46	MAP3K7	MAP3K7	MAP3K7	10980	-0.01	0.28	NO
47	TAB3	TAB3	TAB3	10983	-0.011	0.28	NO
48	TAB2	TAB2	TAB2	11362	-0.016	0.26	NO
49	HSP90AA1	HSP90AA1	HSP90AA1	12550	-0.031	0.2	NO
50	NFKB1	NFKB1	NFKB1	12805	-0.035	0.19	NO
51	MAPK3	MAPK3	MAPK3	13069	-0.039	0.18	NO
52	CARD6	CARD6	CARD6	13331	-0.043	0.18	NO
53	MAPK1	MAPK1	MAPK1	13695	-0.05	0.16	NO
54	CHUK	CHUK	CHUK	13895	-0.053	0.16	NO
55	CCL2	CCL2	CCL2	14285	-0.061	0.14	NO
56	MAPK12	MAPK12	MAPK12	14300	-0.061	0.15	NO
57	NFKBIA	NFKBIA	NFKBIA	14643	-0.069	0.14	NO
58	TRAF6	TRAF6	TRAF6	16737	-0.15	0.041	NO
59	MAPK8	MAPK8	MAPK8	17022	-0.18	0.046	NO
60	MAPK10	MAPK10	MAPK10	17066	-0.18	0.066	NO

Figure S49. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DNA REPLICATION.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DNA REPLICATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG BASE EXCISION REPAIR

Table S26. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	LBP	LBP	LBP	18	0.75	0.22	YES
2	LEF1	LEF1	LEF1	237	0.47	0.35	YES
3	LY96	LY96	LY96	339	0.42	0.47	YES
4	WNT1	WNT1	WNT1	980	0.31	0.53	YES
5	CD14	CD14	CD14	2220	0.19	0.52	NO
6	IRAK1	IRAK1	IRAK1	4288	0.1	0.44	NO
7	MYD88	MYD88	MYD88	5007	0.08	0.42	NO
8	PIK3R1	PIK3R1	PIK3R1	6554	0.05	0.35	NO
9	AXIN1	AXIN1	AXIN1	7714	0.032	0.3	NO
10	EIF2AK2	EIF2AK2	EIF2AK2	9192	0.012	0.22	NO
11	RELA	RELA	RELA	9833	0.0034	0.19	NO
12	PPP2CA	PPP2CA	PPP2CA	10526	-0.0052	0.15	NO
13	DVL1	DVL1	DVL1	10599	-0.006	0.15	NO
14	AKT1	AKT1	AKT1	11589	-0.018	0.098	NO
15	GSK3B	GSK3B	GSK3B	11889	-0.022	0.089	NO
16	NFKB1	NFKB1	NFKB1	12805	-0.035	0.049	NO
17	PDPK1	PDPK1	PDPK1	13588	-0.048	0.021	NO
18	TLR4	TLR4	TLR4	14645	-0.069	-0.017	NO
19	APC	APC	APC	14740	-0.071	-0.00076	NO
20	PIK3CA	PIK3CA	PIK3CA	14835	-0.073	0.016	NO
21	FZD1	FZD1	FZD1	14873	-0.074	0.036	NO
22	TIRAP	TIRAP	TIRAP	14904	-0.075	0.057	NO
23	CTNNB1	CTNNB1	CTNNB1	15277	-0.086	0.062	NO
24	GNAI1	GNAI1	GNAI1	15742	-0.1	0.067	NO
25	CCND1	CCND1	CCND1	16145	-0.12	0.08	NO
26	GJA1	GJA1	GJA1	16201	-0.12	0.11	NO

Figure S51. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASE EXCISION REPAIR.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASE EXCISION REPAIR, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

Table S27. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GFPT2	GFPT2	GFPT2	4	0.89	0.2	YES
2	HK3	HK3	HK3	683	0.35	0.24	YES
3	NPL	NPL	NPL	1096	0.29	0.28	YES
4	CHIT1	CHIT1	CHIT1	1324	0.27	0.32	YES
5	GCK	GCK	GCK	1912	0.22	0.34	YES
6	GALK1	GALK1	GALK1	2272	0.19	0.36	YES
7	HK2	HK2	HK2	2323	0.19	0.4	YES
8	PMM2	PMM2	PMM2	3026	0.15	0.39	YES
9	TSTA3	TSTA3	TSTA3	3269	0.14	0.41	YES
10	GALE	GALE	GALE	3295	0.14	0.44	YES
11	GMPPB	GMPPB	GMPPB	3779	0.12	0.44	YES
12	UGDH	UGDH	UGDH	4077	0.11	0.45	YES
13	GMPPA	GMPPA	GMPPA	4216	0.1	0.46	YES
14	CMAS	CMAS	CMAS	4780	0.086	0.45	YES
15	NAGK	NAGK	NAGK	4920	0.082	0.46	YES
16	GMDS	GMDS	GMDS	5354	0.072	0.45	YES
17	HEXA	HEXA	HEXA	5660	0.066	0.45	YES
18	UGP2	UGP2	UGP2	5812	0.063	0.46	YES
19	HK1	HK1	HK1	5967	0.06	0.46	YES
20	NANS	NANS	NANS	6072	0.058	0.47	YES
21	GNPDA1	GNPDA1	GNPDA1	6347	0.053	0.46	YES
22	PGM1	PGM1	PGM1	6385	0.052	0.47	YES
23	HEXB	HEXB	HEXB	7160	0.04	0.44	NO
24	PGM3	PGM3	PGM3	7346	0.037	0.44	NO
25	AMDHD2	AMDHD2	AMDHD2	7570	0.034	0.43	NO
26	UAP1	UAP1	UAP1	7697	0.032	0.43	NO
27	GPI	GPI	GPI	8560	0.02	0.39	NO
28	FUK	FUK	FUK	9758	0.0045	0.32	NO
29	GFPT1	GFPT1	GFPT1	9922	0.0022	0.32	NO
30	RENBP	RENBP	RENBP	10493	-0.0047	0.29	NO
31	CYB5R1	CYB5R1	CYB5R1	11387	-0.016	0.24	NO
32	NANP	NANP	NANP	11458	-0.017	0.24	NO
33	UXS1	UXS1	UXS1	11562	-0.018	0.24	NO
34	PGM2	PGM2	PGM2	11756	-0.021	0.23	NO
35	MPI	MPI	MPI	12483	-0.03	0.2	NO
36	GNPDA2	GNPDA2	GNPDA2	13244	-0.042	0.17	NO
37	FPGT	FPGT	FPGT	13319	-0.043	0.17	NO
38	GALK2	GALK2	GALK2	13500	-0.046	0.17	NO
39	GNPNAT1	GNPNAT1	GNPNAT1	13530	-0.047	0.18	NO
40	CHIA	CHIA	CHIA	13872	-0.053	0.17	NO
41	GALT	GALT	GALT	15035	-0.078	0.13	NO
42	PMM1	PMM1	PMM1	15535	-0.093	0.12	NO
43	GNE	GNE	GNE	16424	-0.13	0.1	NO

Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HOMOLOGOUS RECOMBINATION.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HOMOLOGOUS RECOMBINATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table S28. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	DNA2	DNA2	DNA2	1881	0.22	-0.0081	YES
2	POLD4	POLD4	POLD4	2763	0.16	0.015	YES
3	RPA4	RPA4	RPA4	3298	0.14	0.045	YES
4	RFC4	RFC4	RFC4	3586	0.12	0.084	YES
5	RNASEH2A	RNASEH2A	RNASEH2A	3752	0.12	0.13	YES
6	POLD1	POLD1	POLD1	3882	0.11	0.17	YES
7	MCM6	MCM6	MCM6	4264	0.1	0.19	YES
8	POLA2	POLA2	POLA2	4295	0.1	0.24	YES
9	MCM2	MCM2	MCM2	4479	0.094	0.27	YES
10	RFC2	RFC2	RFC2	4524	0.093	0.31	YES
11	RNASEH2B	RNASEH2B	RNASEH2B	4634	0.09	0.34	YES
12	POLE	POLE	POLE	4934	0.082	0.36	YES
13	LIG1	LIG1	LIG1	5030	0.08	0.39	YES
14	MCM4	MCM4	MCM4	5162	0.076	0.42	YES
15	RFC5	RFC5	RFC5	5384	0.071	0.43	YES
16	PCNA	PCNA	PCNA	5756	0.064	0.44	YES
17	POLD3	POLD3	POLD3	5948	0.06	0.46	YES
18	SSBP1	SSBP1	SSBP1	6110	0.057	0.47	YES
19	MCM5	MCM5	MCM5	6226	0.055	0.49	YES
20	RNASEH1	RNASEH1	RNASEH1	6522	0.05	0.5	YES
21	RPA3	RPA3	RPA3	6804	0.046	0.5	YES
22	PRIM2	PRIM2	PRIM2	6958	0.043	0.51	YES
23	POLD2	POLD2	POLD2	6979	0.043	0.53	YES
24	FEN1	FEN1	FEN1	7482	0.035	0.52	NO
25	RNASEH2C	RNASEH2C	RNASEH2C	8472	0.021	0.47	NO
26	MCM7	MCM7	MCM7	9239	0.011	0.44	NO
27	POLE2	POLE2	POLE2	9550	0.0073	0.42	NO
28	RPA2	RPA2	RPA2	9564	0.0072	0.42	NO
29	POLE4	POLE4	POLE4	9729	0.0049	0.42	NO
30	PRIM1	PRIM1	PRIM1	10450	-0.0042	0.38	NO
31	MCM3	MCM3	MCM3	10624	-0.0063	0.37	NO
32	RPA1	RPA1	RPA1	10779	-0.0081	0.37	NO
33	RFC1	RFC1	RFC1	12456	-0.03	0.29	NO
34	POLE3	POLE3	POLE3	12508	-0.031	0.3	NO
35	RFC3	RFC3	RFC3	12655	-0.033	0.31	NO

Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CELL CYCLE

Table S29. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	F2	F2	F2	6	0.87	0.063	YES
2	FGA	FGA	FGA	200	0.48	0.088	YES
3	C1S	C1S	C1S	251	0.46	0.12	YES
4	C1R	C1R	C1R	276	0.44	0.15	YES
5	C2	C2	C2	384	0.41	0.17	YES
6	FGG	FGG	FGG	453	0.4	0.2	YES
7	C8G	C8G	C8G	557	0.38	0.22	YES
8	FGB	FGB	FGB	571	0.37	0.25	YES
9	MBL2	MBL2	MBL2	674	0.36	0.27	YES
10	PLAUR	PLAUR	PLAUR	710	0.35	0.29	YES
11	C4BPA	C4BPA	C4BPA	852	0.33	0.31	YES
12	CR1	CR1	CR1	858	0.33	0.33	YES
13	CFH	CFH	CFH	917	0.32	0.35	YES
14	BDKRB1	BDKRB1	BDKRB1	990	0.31	0.37	YES
15	CFB	CFB	CFB	1001	0.31	0.39	YES
16	C9	C9	C9	1062	0.3	0.41	YES
17	CFD	CFD	CFD	1067	0.3	0.43	YES
18	C3	C3	C3	1118	0.29	0.45	YES
19	SERPINE1	SERPINE1	SERPINE1	1183	0.28	0.47	YES
20	F3	F3	F3	1218	0.28	0.48	YES
21	PLAU	PLAU	PLAU	1321	0.27	0.5	YES
22	CR2	CR2	CR2	1714	0.23	0.49	YES
23	F12	F12	F12	1782	0.23	0.51	YES
24	SERPINA5	SERPINA5	SERPINA5	1817	0.22	0.52	YES
25	C1QB	C1QB	C1QB	1894	0.22	0.53	YES
26	BDKRB2	BDKRB2	BDKRB2	1968	0.21	0.54	YES
27	C1QC	C1QC	C1QC	2119	0.2	0.55	YES
28	C1QA	C1QA	C1QA	2164	0.2	0.56	YES
29	SERPINF2	SERPINF2	SERPINF2	2215	0.19	0.57	YES
30	C5AR1	C5AR1	C5AR1	2240	0.19	0.59	YES
31	SERPINA1	SERPINA1	SERPINA1	2288	0.19	0.6	YES
32	SERPING1	SERPING1	SERPING1	2365	0.18	0.61	YES
33	CPB2	CPB2	CPB2	2414	0.18	0.62	YES
34	C3AR1	C3AR1	C3AR1	2694	0.16	0.61	YES
35	F13A1	F13A1	F13A1	2752	0.16	0.62	YES
36	F5	F5	F5	2782	0.16	0.63	YES
37	CFI	CFI	CFI	3178	0.14	0.62	NO
38	PROS1	PROS1	PROS1	4411	0.096	0.56	NO
39	SERPINC1	SERPINC1	SERPINC1	4879	0.083	0.54	NO
40	C4A	C4A	C4A	5042	0.079	0.54	NO
41	F10	F10	F10	6029	0.059	0.49	NO
42	SERPIND1	SERPIND1	SERPIND1	6447	0.051	0.47	NO
43	CD55	CD55	CD55	6949	0.044	0.44	NO
44	THBD	THBD	THBD	7272	0.038	0.43	NO
45	C5	C5	C5	7278	0.038	0.43	NO
46	F2R	F2R	F2R	9771	0.0043	0.3	NO
47	TFPI	TFPI	TFPI	10658	-0.0067	0.25	NO
48	KNG1	KNG1	KNG1	12147	-0.026	0.17	NO
49	C7	C7	C7	12739	-0.034	0.14	NO
50	F8	F8	F8	13945	-0.054	0.075	NO
51	CD46	CD46	CD46	14015	-0.055	0.075	NO
52	CD59	CD59	CD59	14089	-0.056	0.076	NO
53	C4BPB	C4BPB	C4BPB	14533	-0.066	0.056	NO
54	PROC	PROC	PROC	16111	-0.12	-0.022	NO
55	VWF	VWF	VWF	16181	-0.12	-0.017	NO
56	F7	F7	F7	16320	-0.13	-0.016	NO
57	KLKB1	KLKB1	KLKB1	16420	-0.13	-0.012	NO
58	C6	C6	C6	16822	-0.16	-0.022	NO
59	PLAT	PLAT	PLAT	16936	-0.17	-0.016	NO
60	MASP2	MASP2	MASP2	17564	-0.24	-0.033	NO
61	MASP1	MASP1	MASP1	17783	-0.28	-0.025	NO
62	F11	F11	F11	17821	-0.28	-0.0064	NO
63	PLG	PLG	PLG	18121	-0.42	0.0075	NO

Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CELL CYCLE.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG OOCYTE MEIOSIS

Table S30. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	EME1	EME1	EME1	299	0.44	0.12	YES
2	RAD54B	RAD54B	RAD54B	312	0.44	0.25	YES
3	RAD54L	RAD54L	RAD54L	423	0.4	0.36	YES
4	BLM	BLM	BLM	708	0.35	0.45	YES
5	RAD51	RAD51	RAD51	1115	0.29	0.52	YES
6	XRCC2	XRCC2	XRCC2	1430	0.26	0.58	YES
7	POLD4	POLD4	POLD4	2763	0.16	0.56	YES
8	RPA4	RPA4	RPA4	3298	0.14	0.57	YES
9	SHFM1	SHFM1	SHFM1	3690	0.12	0.58	YES
10	POLD1	POLD1	POLD1	3882	0.11	0.61	YES
11	BRCA2	BRCA2	BRCA2	4277	0.1	0.62	YES
12	POLD3	POLD3	POLD3	5948	0.06	0.54	NO
13	NBN	NBN	NBN	6094	0.058	0.55	NO
14	SSBP1	SSBP1	SSBP1	6110	0.057	0.57	NO
15	RPA3	RPA3	RPA3	6804	0.046	0.54	NO
16	RAD51L3	RAD51L3	RAD51L3	6918	0.044	0.55	NO
17	RAD52	RAD52	RAD52	6953	0.044	0.56	NO
18	POLD2	POLD2	POLD2	6979	0.043	0.57	NO
19	XRCC3	XRCC3	XRCC3	7543	0.034	0.55	NO
20	RAD51L1	RAD51L1	RAD51L1	7800	0.03	0.55	NO
21	TOP3B	TOP3B	TOP3B	8936	0.015	0.49	NO
22	RPA2	RPA2	RPA2	9564	0.0072	0.46	NO
23	MUS81	MUS81	MUS81	10101	0.00014	0.43	NO
24	RPA1	RPA1	RPA1	10779	-0.0081	0.39	NO
25	TOP3A	TOP3A	TOP3A	11096	-0.012	0.38	NO
26	RAD50	RAD50	RAD50	11583	-0.018	0.36	NO
27	MRE11A	MRE11A	MRE11A	11908	-0.023	0.35	NO

Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OOCYTE MEIOSIS.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OOCYTE MEIOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

up-regulated, please check the list of up-regulated genes
down-regulated, please check the list of down-regulated genes

Expression level

For the top enriched genes, if you want to check whether they are

highly expressed genes, please check the list of high (top 30%) expressed genes
low expressed genes, please check the list of low (bottom 30%) expressed genes

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Methods & Data

Input

Gene set database = c2.cp.v3.0-2.symbols.gmt
Expression data file = KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = KIRC-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Subramanian, A. et al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles., Proc. Natl. Acad. Sci. USA 102(43) (2005)

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