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

Stomach and Esophageal 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 STES-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1HQ3Z14

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 STES-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: 195
Number of samples: 458
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 ] 236
pheno.type: 2 - 3 :[ clus2 ] 129
pheno.type: 3 - 3 :[ clus3 ] 93

For the expression subtypes of 23517 genes in 459 samples, GSEA found enriched gene sets in each cluster using 458 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are BIOCARTA DEATH PATHWAY, BIOCARTA PPARA PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM

And common core enriched genes are ALDOB, FBP1, FBP2, ABCD1, ABCD3, ACAA1, ACOT8, ACOX1, ACSL5, AGXT

clus2

Top enriched gene sets are BIOCARTA CARM ER PATHWAY, BIOCARTA G1 PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA MAPK PATHWAY, BIOCARTA MYOSIN PATHWAY, BIOCARTA IL1R PATHWAY, KEGG SPLICEOSOME, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG CELL CYCLE

And common core enriched genes are CCND1, TP73, MAPK10, MAPK11, MAPK12, MAPK7, MYC, BAI1, PERP, PMAIP1

clus3

Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA IL2RB PATHWAY

And common core enriched genes are NFATC1, NFATC2, CAMK1, CAMK1G, IGF1, PIK3CG, PRKACB, PRKAR2B, AGT, HDAC5

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 DEATH PATHWAY	31	genes.ES.table	0.53	1.8	0.013	0.096	0.24	0.39	0.19	0.32	0	0.019
BIOCARTA PPARA PATHWAY	55	genes.ES.table	0.46	1.7	0.012	0.14	0.49	0.16	0.1	0.15	0	0.015
KEGG GLYCOLYSIS GLUCONEOGENESIS	59	genes.ES.table	0.48	1.7	0.018	0.15	0.54	0.27	0.11	0.24	0.06	0.017
KEGG CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.49	1.6	0.055	0.2	0.69	0.76	0.31	0.53	0.11	0.02
KEGG PENTOSE PHOSPHATE PATHWAY	25	genes.ES.table	0.63	2	0	0.049	0.068	0.28	0.14	0.24	0	0.016
KEGG FRUCTOSE AND MANNOSE METABOLISM	32	genes.ES.table	0.61	2	0.002	0.046	0.094	0.38	0.13	0.33	0	0.009
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	31	genes.ES.table	0.6	1.8	0.006	0.099	0.34	0.26	0.074	0.24	0	0.015
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	43	genes.ES.table	0.5	1.8	0.02	0.11	0.32	0.51	0.24	0.39	0	0.015
KEGG ARGININE AND PROLINE METABOLISM	53	genes.ES.table	0.48	1.6	0.027	0.21	0.68	0.32	0.12	0.28	0.12	0.027
KEGG HISTIDINE METABOLISM	28	genes.ES.table	0.54	1.5	0.063	0.22	0.77	0.25	0.11	0.22	0.14	0.017

genes ES table in pathway: BIOCARTA DEATH 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	AGXT	AGXT	AGXT	327	0.46	0.053	YES
2	NOS2	NOS2	NOS2	436	0.4	0.11	YES
3	SLC27A2	SLC27A2	SLC27A2	463	0.4	0.16	YES
4	ACSL5	ACSL5	ACSL5	504	0.38	0.22	YES
5	BAAT	BAAT	BAAT	621	0.35	0.26	YES
6	FAR2	FAR2	FAR2	715	0.32	0.31	YES
7	EPHX2	EPHX2	EPHX2	1517	0.2	0.3	YES
8	HAO2	HAO2	HAO2	1543	0.19	0.33	YES
9	DECR2	DECR2	DECR2	1798	0.17	0.34	YES
10	PEX11A	PEX11A	PEX11A	2050	0.15	0.36	YES
11	PXMP2	PXMP2	PXMP2	2069	0.15	0.38	YES
12	PIPOX	PIPOX	PIPOX	2173	0.14	0.39	YES
13	AMACR	AMACR	AMACR	2215	0.14	0.41	YES
14	PHYH	PHYH	PHYH	2394	0.13	0.42	YES
15	IDH1	IDH1	IDH1	2411	0.13	0.44	YES
16	PEX7	PEX7	PEX7	2506	0.12	0.46	YES
17	DAO	DAO	DAO	2509	0.12	0.47	YES
18	XDH	XDH	XDH	2634	0.12	0.48	YES
19	ABCD3	ABCD3	ABCD3	2693	0.12	0.5	YES
20	PEX11G	PEX11G	PEX11G	2964	0.1	0.5	YES
21	PECR	PECR	PECR	3034	0.1	0.52	YES
22	CAT	CAT	CAT	3086	0.1	0.53	YES
23	HMGCL	HMGCL	HMGCL	3231	0.095	0.54	YES
24	IDH2	IDH2	IDH2	3386	0.09	0.54	YES
25	GSTK1	GSTK1	GSTK1	3394	0.09	0.55	YES
26	NUDT12	NUDT12	NUDT12	3402	0.09	0.57	YES
27	HAO1	HAO1	HAO1	3478	0.088	0.58	YES
28	ACAA1	ACAA1	ACAA1	3521	0.086	0.59	YES
29	SCP2	SCP2	SCP2	3602	0.084	0.6	YES
30	DDO	DDO	DDO	3927	0.076	0.59	YES
31	MLYCD	MLYCD	MLYCD	4128	0.071	0.6	YES
32	ABCD1	ABCD1	ABCD1	4159	0.07	0.6	YES
33	PEX11B	PEX11B	PEX11B	4473	0.064	0.6	YES
34	HACL1	HACL1	HACL1	4587	0.062	0.6	YES
35	PEX16	PEX16	PEX16	4594	0.062	0.61	YES
36	ACOX1	ACOX1	ACOX1	4865	0.057	0.61	YES
37	PXMP4	PXMP4	PXMP4	4973	0.055	0.61	YES
38	PEX1	PEX1	PEX1	5072	0.054	0.62	YES
39	SOD1	SOD1	SOD1	5080	0.054	0.62	YES
40	HSD17B4	HSD17B4	HSD17B4	5166	0.052	0.63	YES
41	PEX2	PEX2	PEX2	5222	0.052	0.63	YES
42	ACOT8	ACOT8	ACOT8	5372	0.049	0.63	YES
43	EHHADH	EHHADH	EHHADH	5462	0.048	0.64	YES
44	ABCD4	ABCD4	ABCD4	5632	0.046	0.64	NO
45	GNPAT	GNPAT	GNPAT	5765	0.044	0.64	NO
46	CRAT	CRAT	CRAT	6126	0.039	0.63	NO
47	PEX26	PEX26	PEX26	6388	0.036	0.62	NO
48	ACSL3	ACSL3	ACSL3	6622	0.033	0.61	NO
49	PRDX5	PRDX5	PRDX5	7828	0.02	0.56	NO
50	PEX6	PEX6	PEX6	8425	0.014	0.54	NO
51	PEX13	PEX13	PEX13	9322	0.0059	0.5	NO
52	PEX14	PEX14	PEX14	9429	0.005	0.5	NO
53	PRDX1	PRDX1	PRDX1	9640	0.0031	0.49	NO
54	FAR1	FAR1	FAR1	9913	0.00075	0.48	NO
55	PEX10	PEX10	PEX10	9920	0.00064	0.48	NO
56	AGPS	AGPS	AGPS	9997	0.000074	0.47	NO
57	ACSL4	ACSL4	ACSL4	10242	-0.0021	0.46	NO
58	ACOX3	ACOX3	ACOX3	10678	-0.0059	0.44	NO
59	PEX3	PEX3	PEX3	11137	-0.01	0.42	NO
60	PMVK	PMVK	PMVK	11257	-0.011	0.42	NO
61	MVK	MVK	MVK	11303	-0.012	0.42	NO
62	PEX12	PEX12	PEX12	11334	-0.012	0.42	NO
63	PEX5	PEX5	PEX5	11774	-0.017	0.4	NO
64	MPV17L	MPV17L	MPV17L	11833	-0.017	0.4	NO
65	DHRS4	DHRS4	DHRS4	12205	-0.021	0.39	NO
66	NUDT19	NUDT19	NUDT19	12841	-0.028	0.37	NO
67	SLC25A17	SLC25A17	SLC25A17	12871	-0.028	0.37	NO
68	ABCD2	ABCD2	ABCD2	12980	-0.029	0.37	NO
69	PAOX	PAOX	PAOX	13914	-0.04	0.34	NO
70	MPV17	MPV17	MPV17	13984	-0.041	0.34	NO
71	SOD2	SOD2	SOD2	14125	-0.042	0.34	NO
72	ACSL6	ACSL6	ACSL6	14473	-0.048	0.33	NO
73	ACSL1	ACSL1	ACSL1	17109	-0.098	0.23	NO
74	CROT	CROT	CROT	18689	-0.14	0.18	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 DEATH PATHWAY.

Figure S2. 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 PPARA 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	ALDOB	ALDOB	ALDOB	90	0.64	0.26	YES
2	FBP1	FBP1	FBP1	402	0.42	0.42	YES
3	FBP2	FBP2	FBP2	765	0.31	0.53	YES
4	RPIA	RPIA	RPIA	2085	0.15	0.54	YES
5	LOC729020	LOC729020	LOC729020	2645	0.12	0.56	YES
6	TKTL1	TKTL1	TKTL1	2748	0.11	0.6	YES
7	RBKS	RBKS	RBKS	3075	0.1	0.63	YES
8	TKTL2	TKTL2	TKTL2	5925	0.042	0.52	NO
9	PFKL	PFKL	PFKL	6382	0.036	0.52	NO
10	RPE	RPE	RPE	7145	0.027	0.49	NO
11	PRPS2	PRPS2	PRPS2	8042	0.018	0.46	NO
12	GPI	GPI	GPI	8249	0.016	0.46	NO
13	TKT	TKT	TKT	10291	-0.0025	0.37	NO
14	PFKP	PFKP	PFKP	10608	-0.0054	0.36	NO
15	PGM1	PGM1	PGM1	10670	-0.0059	0.36	NO
16	TALDO1	TALDO1	TALDO1	11146	-0.01	0.34	NO
17	PRPS1	PRPS1	PRPS1	12269	-0.022	0.3	NO
18	DERA	DERA	DERA	12533	-0.024	0.3	NO
19	PGLS	PGLS	PGLS	12583	-0.025	0.31	NO
20	H6PD	H6PD	H6PD	12826	-0.027	0.31	NO
21	PGM2	PGM2	PGM2	14132	-0.042	0.27	NO
22	PFKM	PFKM	PFKM	14327	-0.045	0.28	NO
23	PGD	PGD	PGD	14403	-0.047	0.3	NO
24	ALDOC	ALDOC	ALDOC	15456	-0.064	0.28	NO
25	G6PD	G6PD	G6PD	17554	-0.11	0.23	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 PPARA PATHWAY.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PPARA 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 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	ALDOB	ALDOB	ALDOB	90	0.64	0.16	YES
2	FBP1	FBP1	FBP1	402	0.42	0.26	YES
3	FBP2	FBP2	FBP2	765	0.31	0.32	YES
4	GMDS	GMDS	GMDS	773	0.31	0.4	YES
5	KHK	KHK	KHK	1446	0.2	0.43	YES
6	PFKFB2	PFKFB2	PFKFB2	1480	0.2	0.48	YES
7	TSTA3	TSTA3	TSTA3	1813	0.17	0.51	YES
8	SORD	SORD	SORD	2443	0.13	0.52	YES
9	GMPPB	GMPPB	GMPPB	2459	0.13	0.55	YES
10	GMPPA	GMPPA	GMPPA	2799	0.11	0.56	YES
11	FUK	FUK	FUK	2830	0.11	0.59	YES
12	PMM2	PMM2	PMM2	3023	0.1	0.61	YES
13	HK3	HK3	HK3	5405	0.049	0.52	NO
14	AKR1B10	AKR1B10	AKR1B10	6257	0.037	0.49	NO
15	PFKL	PFKL	PFKL	6382	0.036	0.49	NO
16	MPI	MPI	MPI	7038	0.028	0.47	NO
17	HK2	HK2	HK2	7925	0.019	0.44	NO
18	PHPT1	PHPT1	PHPT1	8024	0.018	0.44	NO
19	MTMR6	MTMR6	MTMR6	8046	0.018	0.44	NO
20	PFKFB3	PFKFB3	PFKFB3	9361	0.0056	0.39	NO
21	TPI1	TPI1	TPI1	10130	-0.0012	0.35	NO
22	PFKP	PFKP	PFKP	10608	-0.0054	0.33	NO
23	MTMR7	MTMR7	MTMR7	11657	-0.015	0.29	NO
24	PFKFB4	PFKFB4	PFKFB4	12545	-0.024	0.26	NO
25	MTMR2	MTMR2	MTMR2	12620	-0.025	0.26	NO
26	PMM1	PMM1	PMM1	13921	-0.04	0.22	NO
27	PFKM	PFKM	PFKM	14327	-0.045	0.21	NO
28	ALDOC	ALDOC	ALDOC	15456	-0.064	0.18	NO
29	MTMR1	MTMR1	MTMR1	16001	-0.074	0.17	NO
30	AKR1B1	AKR1B1	AKR1B1	18459	-0.14	0.099	NO
31	HK1	HK1	HK1	18913	-0.15	0.12	NO
32	PFKFB1	PFKFB1	PFKFB1	19664	-0.19	0.14	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: KEGG GLYCOLYSIS GLUCONEOGENESIS.

Figure S6. 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 CITRATE CYCLE TCA CYCLE

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	CFTR	CFTR	CFTR	116	0.61	0.11	YES
2	MUC2	MUC2	MUC2	325	0.46	0.19	YES
3	KCNQ1	KCNQ1	KCNQ1	403	0.42	0.26	YES
4	PRKACG	PRKACG	PRKACG	663	0.34	0.31	YES
5	PRKCG	PRKCG	PRKCG	833	0.3	0.36	YES
6	SLC12A2	SLC12A2	SLC12A2	1081	0.25	0.4	YES
7	KDELR3	KDELR3	KDELR3	1385	0.21	0.42	YES
8	ATP6V0D2	ATP6V0D2	ATP6V0D2	1838	0.17	0.43	YES
9	PRKCA	PRKCA	PRKCA	2328	0.13	0.44	YES
10	KDELR2	KDELR2	KDELR2	2969	0.1	0.43	YES
11	TJP2	TJP2	TJP2	3556	0.086	0.42	YES
12	PDIA4	PDIA4	PDIA4	3571	0.085	0.44	YES
13	KDELR1	KDELR1	KDELR1	3739	0.08	0.44	YES
14	TCIRG1	TCIRG1	TCIRG1	3950	0.075	0.45	YES
15	ATP6V0B	ATP6V0B	ATP6V0B	5383	0.049	0.39	NO
16	ATP6V1C2	ATP6V1C2	ATP6V1C2	5426	0.049	0.4	NO
17	ARF1	ARF1	ARF1	5758	0.044	0.39	NO
18	ATP6V0E2	ATP6V0E2	ATP6V0E2	6549	0.034	0.37	NO
19	ATP6V0A2	ATP6V0A2	ATP6V0A2	6651	0.032	0.37	NO
20	ATP6AP1	ATP6AP1	ATP6AP1	7269	0.026	0.34	NO
21	SEC61B	SEC61B	SEC61B	7455	0.024	0.34	NO
22	ATP6V0D1	ATP6V0D1	ATP6V0D1	8210	0.016	0.31	NO
23	ATP6V1C1	ATP6V1C1	ATP6V1C1	8560	0.013	0.3	NO
24	ATP6V0A1	ATP6V0A1	ATP6V0A1	8574	0.013	0.3	NO
25	SEC61A1	SEC61A1	SEC61A1	8750	0.011	0.3	NO
26	ERO1L	ERO1L	ERO1L	8955	0.0092	0.29	NO
27	ATP6V1B2	ATP6V1B2	ATP6V1B2	9035	0.0084	0.28	NO
28	SEC61A2	SEC61A2	SEC61A2	9336	0.0058	0.27	NO
29	SEC61G	SEC61G	SEC61G	9572	0.0037	0.26	NO
30	ATP6V0C	ATP6V0C	ATP6V0C	10340	-0.003	0.23	NO
31	ACTG1	ACTG1	ACTG1	10388	-0.0033	0.23	NO
32	ATP6V1G1	ATP6V1G1	ATP6V1G1	11002	-0.0088	0.2	NO
33	ATP6V0E1	ATP6V0E1	ATP6V0E1	11178	-0.01	0.2	NO
34	ATP6V1D	ATP6V1D	ATP6V1D	11819	-0.017	0.17	NO
35	ATP6V1F	ATP6V1F	ATP6V1F	12167	-0.02	0.16	NO
36	GNAS	GNAS	GNAS	12452	-0.023	0.15	NO
37	ACTB	ACTB	ACTB	12699	-0.026	0.15	NO
38	ATP6V1E1	ATP6V1E1	ATP6V1E1	13138	-0.03	0.13	NO
39	ATP6V1H	ATP6V1H	ATP6V1H	13292	-0.032	0.13	NO
40	ATP6V1A	ATP6V1A	ATP6V1A	13761	-0.038	0.12	NO
41	PRKACA	PRKACA	PRKACA	13884	-0.04	0.12	NO
42	TJP1	TJP1	TJP1	14414	-0.047	0.11	NO
43	ADCY9	ADCY9	ADCY9	15146	-0.058	0.086	NO
44	PRKCB	PRKCB	PRKCB	15469	-0.064	0.084	NO
45	PLCG1	PLCG1	PLCG1	15888	-0.072	0.079	NO
46	PRKX	PRKX	PRKX	16664	-0.087	0.061	NO
47	ATP6V1E2	ATP6V1E2	ATP6V1E2	17134	-0.098	0.059	NO
48	PRKACB	PRKACB	PRKACB	17450	-0.11	0.065	NO
49	PLCG2	PLCG2	PLCG2	17645	-0.11	0.077	NO
50	ATP6V1B1	ATP6V1B1	ATP6V1B1	20500	-0.24	-0.0047	NO
51	ATP6V1G2	ATP6V1G2	ATP6V1G2	20735	-0.25	0.032	NO
52	ATP6V0A4	ATP6V0A4	ATP6V0A4	21342	-0.3	0.062	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: KEGG CITRATE CYCLE TCA CYCLE.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CITRATE CYCLE TCA 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 PENTOSE PHOSPHATE 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	GAS2	GAS2	GAS2	649	0.34	0.11	YES
2	CASP10	CASP10	CASP10	1095	0.25	0.19	YES
3	BIRC3	BIRC3	BIRC3	1520	0.2	0.24	YES
4	CASP6	CASP6	CASP6	1542	0.19	0.32	YES
5	DFFB	DFFB	DFFB	1597	0.19	0.39	YES
6	APAF1	APAF1	APAF1	2517	0.12	0.4	YES
7	CASP7	CASP7	CASP7	2896	0.11	0.43	YES
8	CASP8	CASP8	CASP8	3264	0.093	0.45	YES
9	CASP3	CASP3	CASP3	3459	0.088	0.48	YES
10	TNFRSF10A	TNFRSF10A	TNFRSF10A	3473	0.088	0.51	YES
11	CYCS	CYCS	CYCS	3842	0.078	0.52	YES
12	TNFRSF10B	TNFRSF10B	TNFRSF10B	4237	0.068	0.53	YES
13	TRAF2	TRAF2	TRAF2	5610	0.046	0.49	NO
14	CHUK	CHUK	CHUK	5898	0.042	0.5	NO
15	CASP9	CASP9	CASP9	6137	0.039	0.5	NO
16	SPTAN1	SPTAN1	SPTAN1	7279	0.026	0.46	NO
17	XIAP	XIAP	XIAP	7464	0.024	0.46	NO
18	RIPK1	RIPK1	RIPK1	8798	0.011	0.41	NO
19	CFLAR	CFLAR	CFLAR	10264	-0.0023	0.34	NO
20	DFFA	DFFA	DFFA	10710	-0.0062	0.33	NO
21	MAP3K14	MAP3K14	MAP3K14	10728	-0.0064	0.33	NO
22	BIRC2	BIRC2	BIRC2	10837	-0.0073	0.33	NO
23	NFKB1	NFKB1	NFKB1	11203	-0.011	0.32	NO
24	RELA	RELA	RELA	11569	-0.014	0.3	NO
25	TNFRSF25	TNFRSF25	TNFRSF25	12259	-0.021	0.28	NO
26	LMNA	LMNA	LMNA	13108	-0.03	0.26	NO
27	TRADD	TRADD	TRADD	14067	-0.042	0.23	NO
28	NFKBIA	NFKBIA	NFKBIA	15718	-0.068	0.19	NO
29	TNFSF10	TNFSF10	TNFSF10	16242	-0.078	0.2	NO
30	FADD	FADD	FADD	16340	-0.08	0.22	NO
31	BCL2	BCL2	BCL2	18832	-0.15	0.17	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: KEGG PENTOSE PHOSPHATE PATHWAY.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE PHOSPHATE 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 FRUCTOSE AND MANNOSE METABOLISM

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	HMGCS2	HMGCS2	HMGCS2	148	0.58	0.2	YES
2	ACSM3	ACSM3	ACSM3	640	0.34	0.3	YES
3	ACSM1	ACSM1	ACSM1	934	0.28	0.38	YES
4	ACADS	ACADS	ACADS	1667	0.18	0.42	YES
5	ALDH2	ALDH2	ALDH2	2324	0.14	0.43	YES
6	GAD1	GAD1	GAD1	2741	0.11	0.46	YES
7	HADH	HADH	HADH	2960	0.1	0.48	YES
8	ECHS1	ECHS1	ECHS1	3130	0.098	0.51	YES
9	HMGCL	HMGCL	HMGCL	3231	0.095	0.54	YES
10	ABAT	ABAT	ABAT	3327	0.092	0.57	YES
11	PDHA1	PDHA1	PDHA1	3669	0.082	0.58	YES
12	BDH1	BDH1	BDH1	4636	0.061	0.56	YES
13	GAD2	GAD2	GAD2	5297	0.05	0.55	YES
14	ACAT1	ACAT1	ACAT1	5430	0.048	0.56	YES
15	PDHB	PDHB	PDHB	5630	0.046	0.57	YES
16	ALDH5A1	ALDH5A1	ALDH5A1	6082	0.04	0.56	YES
17	BDH2	BDH2	BDH2	6179	0.038	0.57	YES
18	AKR1B10	AKR1B10	AKR1B10	6257	0.037	0.58	YES
19	HMGCS1	HMGCS1	HMGCS1	6550	0.034	0.58	YES
20	ACAT2	ACAT2	ACAT2	6739	0.032	0.58	YES
21	HADHA	HADHA	HADHA	6942	0.029	0.58	YES
22	ALDH9A1	ALDH9A1	ALDH9A1	7439	0.024	0.57	NO
23	ALDH1B1	ALDH1B1	ALDH1B1	8559	0.013	0.52	NO
24	ACSM5	ACSM5	ACSM5	8675	0.012	0.52	NO
25	L2HGDH	L2HGDH	L2HGDH	8945	0.0094	0.52	NO
26	ACSM4	ACSM4	ACSM4	11232	-0.011	0.42	NO
27	AACS	AACS	AACS	11861	-0.017	0.4	NO
28	ALDH7A1	ALDH7A1	ALDH7A1	12118	-0.02	0.39	NO
29	ACSM2A	ACSM2A	ACSM2A	12515	-0.024	0.38	NO
30	ALDH3A2	ALDH3A2	ALDH3A2	12737	-0.026	0.38	NO
31	OXCT2	OXCT2	OXCT2	13259	-0.032	0.37	NO
32	OXCT1	OXCT1	OXCT1	18272	-0.13	0.2	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 FRUCTOSE AND MANNOSE METABOLISM.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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	HMGCS2	HMGCS2	HMGCS2	148	0.58	0.16	YES
2	ACAA2	ACAA2	ACAA2	1185	0.23	0.18	YES
3	ACADS	ACADS	ACADS	1667	0.18	0.22	YES
4	ALDH2	ALDH2	ALDH2	2324	0.14	0.23	YES
5	HIBADH	HIBADH	HIBADH	2795	0.11	0.24	YES
6	HADH	HADH	HADH	2960	0.1	0.26	YES
7	BCKDHB	BCKDHB	BCKDHB	2976	0.1	0.29	YES
8	ECHS1	ECHS1	ECHS1	3130	0.098	0.31	YES
9	HMGCL	HMGCL	HMGCL	3231	0.095	0.34	YES
10	ABAT	ABAT	ABAT	3327	0.092	0.36	YES
11	MCCC2	MCCC2	MCCC2	3442	0.089	0.38	YES
12	ACAA1	ACAA1	ACAA1	3521	0.086	0.4	YES
13	HIBCH	HIBCH	HIBCH	3555	0.086	0.42	YES
14	PCCA	PCCA	PCCA	3680	0.082	0.44	YES
15	IVD	IVD	IVD	4088	0.072	0.44	YES
16	ACAD8	ACAD8	ACAD8	4317	0.067	0.45	YES
17	MCEE	MCEE	MCEE	4432	0.065	0.47	YES
18	ACADSB	ACADSB	ACADSB	4518	0.063	0.48	YES
19	AUH	AUH	AUH	4872	0.057	0.48	YES
20	BCAT2	BCAT2	BCAT2	5135	0.053	0.49	YES
21	ACAT1	ACAT1	ACAT1	5430	0.048	0.49	YES
22	EHHADH	EHHADH	EHHADH	5462	0.048	0.5	YES
23	ALDH6A1	ALDH6A1	ALDH6A1	5866	0.043	0.5	NO
24	DLD	DLD	DLD	6513	0.034	0.48	NO
25	HMGCS1	HMGCS1	HMGCS1	6550	0.034	0.48	NO
26	ACAT2	ACAT2	ACAT2	6739	0.032	0.49	NO
27	HADHA	HADHA	HADHA	6942	0.029	0.49	NO
28	HSD17B10	HSD17B10	HSD17B10	7341	0.025	0.48	NO
29	ALDH9A1	ALDH9A1	ALDH9A1	7439	0.024	0.48	NO
30	PCCB	PCCB	PCCB	8456	0.014	0.44	NO
31	ALDH1B1	ALDH1B1	ALDH1B1	8559	0.013	0.44	NO
32	MUT	MUT	MUT	8613	0.012	0.44	NO
33	IL4I1	IL4I1	IL4I1	8943	0.0094	0.43	NO
34	ACADM	ACADM	ACADM	9180	0.0071	0.42	NO
35	MCCC1	MCCC1	MCCC1	9720	0.0024	0.4	NO
36	HADHB	HADHB	HADHB	10384	-0.0033	0.37	NO
37	ALDH7A1	ALDH7A1	ALDH7A1	12118	-0.02	0.3	NO
38	ALDH3A2	ALDH3A2	ALDH3A2	12737	-0.026	0.28	NO
39	OXCT2	OXCT2	OXCT2	13259	-0.032	0.26	NO
40	BCKDHA	BCKDHA	BCKDHA	15088	-0.057	0.2	NO
41	DBT	DBT	DBT	15129	-0.058	0.22	NO
42	OXCT1	OXCT1	OXCT1	18272	-0.13	0.11	NO
43	AOX1	AOX1	AOX1	21168	-0.29	0.07	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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE 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 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	GPT	GPT	GPT	149	0.58	0.13	YES
2	ACY3	ACY3	ACY3	173	0.56	0.26	YES
3	AGXT	AGXT	AGXT	327	0.46	0.37	YES
4	CPS1	CPS1	CPS1	711	0.32	0.43	YES
5	ASL	ASL	ASL	938	0.28	0.48	YES
6	ASS1	ASS1	ASS1	1144	0.24	0.53	YES
7	AGXT2	AGXT2	AGXT2	1525	0.2	0.56	YES
8	GFPT1	GFPT1	GFPT1	1680	0.18	0.6	YES
9	GAD1	GAD1	GAD1	2741	0.11	0.58	NO
10	ABAT	ABAT	ABAT	3327	0.092	0.57	NO
11	DDO	DDO	DDO	3927	0.076	0.57	NO
12	GOT1	GOT1	GOT1	4755	0.059	0.54	NO
13	GAD2	GAD2	GAD2	5297	0.05	0.53	NO
14	ALDH5A1	ALDH5A1	ALDH5A1	6082	0.04	0.51	NO
15	PPAT	PPAT	PPAT	6716	0.032	0.49	NO
16	GPT2	GPT2	GPT2	8670	0.012	0.4	NO
17	IL4I1	IL4I1	IL4I1	8943	0.0094	0.4	NO
18	ASNS	ASNS	ASNS	10112	-0.001	0.34	NO
19	NIT2	NIT2	NIT2	10623	-0.0056	0.32	NO
20	ADSL	ADSL	ADSL	10773	-0.0068	0.32	NO
21	GLS	GLS	GLS	11383	-0.012	0.29	NO
22	GLS2	GLS2	GLS2	12129	-0.02	0.27	NO
23	GOT2	GOT2	GOT2	12529	-0.024	0.25	NO
24	CAD	CAD	CAD	12535	-0.024	0.26	NO
25	ASPA	ASPA	ASPA	13526	-0.035	0.22	NO
26	GLUD1	GLUD1	GLUD1	13726	-0.038	0.22	NO
27	GLUD2	GLUD2	GLUD2	15044	-0.057	0.18	NO
28	ADSSL1	ADSSL1	ADSSL1	16566	-0.085	0.13	NO
29	ALDH4A1	ALDH4A1	ALDH4A1	17460	-0.11	0.12	NO
30	GLUL	GLUL	GLUL	17764	-0.12	0.13	NO
31	GFPT2	GFPT2	GFPT2	21798	-0.36	0.042	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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S16. 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 ARGININE AND PROLINE METABOLISM

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	GAL3ST1	GAL3ST1	GAL3ST1	129	0.6	0.099	YES
2	SMPD3	SMPD3	SMPD3	163	0.57	0.2	YES
3	DEGS2	DEGS2	DEGS2	312	0.46	0.27	YES
4	NEU4	NEU4	NEU4	517	0.38	0.33	YES
5	ASAH2	ASAH2	ASAH2	699	0.33	0.38	YES
6	UGT8	UGT8	UGT8	772	0.31	0.43	YES
7	ACER2	ACER2	ACER2	1174	0.23	0.45	YES
8	GALC	GALC	GALC	1347	0.21	0.48	YES
9	SGPP2	SGPP2	SGPP2	1834	0.17	0.49	YES
10	PPAP2C	PPAP2C	PPAP2C	2195	0.14	0.5	YES
11	GLB1	GLB1	GLB1	2382	0.13	0.52	YES
12	SMPD2	SMPD2	SMPD2	2430	0.13	0.54	YES
13	SPHK2	SPHK2	SPHK2	2916	0.11	0.53	NO
14	ASAH1	ASAH1	ASAH1	4336	0.067	0.48	NO
15	NEU3	NEU3	NEU3	4445	0.064	0.49	NO
16	SPTLC2	SPTLC2	SPTLC2	4831	0.058	0.48	NO
17	B4GALT6	B4GALT6	B4GALT6	5348	0.05	0.47	NO
18	GLA	GLA	GLA	5543	0.047	0.47	NO
19	SGMS2	SGMS2	SGMS2	5945	0.042	0.46	NO
20	GBA	GBA	GBA	6192	0.038	0.45	NO
21	SGMS1	SGMS1	SGMS1	8375	0.015	0.36	NO
22	ARSA	ARSA	ARSA	10522	-0.0046	0.27	NO
23	CERK	CERK	CERK	10599	-0.0054	0.26	NO
24	SMPD4	SMPD4	SMPD4	10687	-0.006	0.26	NO
25	PPAP2A	PPAP2A	PPAP2A	11043	-0.0092	0.25	NO
26	SPTLC1	SPTLC1	SPTLC1	11335	-0.012	0.24	NO
27	ACER3	ACER3	ACER3	11456	-0.013	0.23	NO
28	SMPD1	SMPD1	SMPD1	13132	-0.03	0.16	NO
29	SGPL1	SGPL1	SGPL1	13285	-0.032	0.16	NO
30	NEU1	NEU1	NEU1	13488	-0.034	0.16	NO
31	PPAP2B	PPAP2B	PPAP2B	14382	-0.046	0.13	NO
32	SGPP1	SGPP1	SGPP1	15080	-0.057	0.11	NO
33	KDSR	KDSR	KDSR	15509	-0.065	0.1	NO
34	UGCG	UGCG	UGCG	15594	-0.066	0.11	NO
35	DEGS1	DEGS1	DEGS1	16215	-0.078	0.096	NO
36	SPHK1	SPHK1	SPHK1	20885	-0.26	-0.064	NO
37	NEU2	NEU2	NEU2	21849	-0.37	-0.042	NO
38	ACER1	ACER1	ACER1	22362	-0.46	0.017	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 ARGININE AND PROLINE METABOLISM.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARGININE AND PROLINE 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 HISTIDINE METABOLISM

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	UGT2B7	UGT2B7	UGT2B7	125	0.6	0.16	YES
2	UGT2B15	UGT2B15	UGT2B15	171	0.56	0.31	YES
3	UGT2A3	UGT2A3	UGT2A3	205	0.52	0.46	YES
4	UGT2B11	UGT2B11	UGT2B11	1076	0.25	0.49	YES
5	UGT2B17	UGT2B17	UGT2B17	1422	0.21	0.53	YES
6	ALAS1	ALAS1	ALAS1	2675	0.12	0.51	YES
7	UGT1A1	UGT1A1	UGT1A1	2900	0.11	0.53	YES
8	ALAS2	ALAS2	ALAS2	3030	0.1	0.55	YES
9	GUSB	GUSB	GUSB	3238	0.094	0.57	YES
10	HMBS	HMBS	HMBS	3415	0.089	0.59	YES
11	UGT2B4	UGT2B4	UGT2B4	4360	0.066	0.56	YES
12	BLVRB	BLVRB	BLVRB	4418	0.065	0.58	YES
13	UGT2B28	UGT2B28	UGT2B28	4565	0.062	0.59	YES
14	HMOX1	HMOX1	HMOX1	4930	0.056	0.59	YES
15	EARS2	EARS2	EARS2	5054	0.054	0.6	YES
16	EPRS	EPRS	EPRS	6021	0.04	0.57	NO
17	COX15	COX15	COX15	6542	0.034	0.55	NO
18	COX10	COX10	COX10	6701	0.032	0.56	NO
19	UROS	UROS	UROS	6832	0.031	0.56	NO
20	ALAD	ALAD	ALAD	7612	0.022	0.53	NO
21	HMOX2	HMOX2	HMOX2	7756	0.021	0.53	NO
22	CP	CP	CP	7888	0.019	0.53	NO
23	MMAB	MMAB	MMAB	8246	0.016	0.52	NO
24	FTH1	FTH1	FTH1	8757	0.011	0.5	NO
25	PPOX	PPOX	PPOX	9964	0.0003	0.45	NO
26	CPOX	CPOX	CPOX	10791	-0.007	0.41	NO
27	UROD	UROD	UROD	14362	-0.046	0.27	NO
28	FECH	FECH	FECH	16330	-0.08	0.2	NO
29	UGT2A1	UGT2A1	UGT2A1	16944	-0.093	0.2	NO
30	BLVRA	BLVRA	BLVRA	19744	-0.19	0.13	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 HISTIDINE METABOLISM.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HISTIDINE METABOLISM, 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 CARM ER PATHWAY	33	genes.ES.table	0.42	1.5	0.061	1	0.74	0.61	0.44	0.34	0.94	0.48
BIOCARTA G1 PATHWAY	27	genes.ES.table	0.48	1.5	0.061	0.5	0.75	0.41	0.27	0.3	0.3	0.16
BIOCARTA ERK PATHWAY	26	genes.ES.table	0.41	1.4	0.12	0.45	0.87	0.19	0.1	0.17	0.34	0.11
BIOCARTA INTEGRIN PATHWAY	37	genes.ES.table	0.38	1.4	0.13	0.48	0.86	0.081	0.1	0.073	0.35	0.14
BIOCARTA MAPK PATHWAY	85	genes.ES.table	0.34	1.5	0.077	1	0.74	0.55	0.43	0.32	0.63	0.37
BIOCARTA MYOSIN PATHWAY	29	genes.ES.table	0.41	1.4	0.13	0.44	0.9	0.14	0.096	0.12	0.34	0.097
BIOCARTA IL1R PATHWAY	32	genes.ES.table	0.46	1.4	0.13	0.46	0.87	0.12	0.051	0.12	0.35	0.12
KEGG SPLICEOSOME	111	genes.ES.table	0.41	1.4	0.11	0.48	0.84	0.65	0.48	0.34	0.34	0.14
KEGG NUCLEOTIDE EXCISION REPAIR	42	genes.ES.table	0.43	1.4	0.13	0.52	0.84	0.79	0.46	0.42	0.37	0.16
KEGG CELL CYCLE	117	genes.ES.table	0.41	1.5	0.11	0.58	0.75	0.67	0.41	0.4	0.35	0.19

genes ES table in pathway: BIOCARTA CARM ER 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	TP53AIP1	TP53AIP1	TP53AIP1	64	1.2	0.13	YES
2	TP73	TP73	TP73	500	0.6	0.18	YES
3	SFN	SFN	SFN	587	0.56	0.24	YES
4	SESN3	SESN3	SESN3	815	0.47	0.28	YES
5	SERPINB5	SERPINB5	SERPINB5	833	0.46	0.33	YES
6	BAI1	BAI1	BAI1	956	0.43	0.37	YES
7	PERP	PERP	PERP	1001	0.42	0.42	YES
8	PMAIP1	PMAIP1	PMAIP1	1325	0.35	0.44	YES
9	SERPINE1	SERPINE1	SERPINE1	2318	0.24	0.43	YES
10	RPRM	RPRM	RPRM	2367	0.24	0.45	YES
11	CCND1	CCND1	CCND1	3329	0.18	0.43	NO
12	CCNE2	CCNE2	CCNE2	4086	0.15	0.41	NO
13	ATR	ATR	ATR	4366	0.14	0.41	NO
14	CCNB2	CCNB2	CCNB2	4784	0.13	0.41	NO
15	CDK6	CDK6	CDK6	4820	0.12	0.42	NO
16	CDK1	CDK1	CDK1	5271	0.11	0.42	NO
17	CDKN1A	CDKN1A	CDKN1A	5453	0.11	0.42	NO
18	CCNB1	CCNB1	CCNB1	5709	0.1	0.42	NO
19	DDB2	DDB2	DDB2	5711	0.1	0.43	NO
20	SIAH1	SIAH1	SIAH1	5951	0.098	0.43	NO
21	GTSE1	GTSE1	GTSE1	6614	0.086	0.41	NO
22	RRM2	RRM2	RRM2	6651	0.085	0.42	NO
23	GADD45A	GADD45A	GADD45A	7136	0.077	0.41	NO
24	CHEK2	CHEK2	CHEK2	7334	0.074	0.41	NO
25	CHEK1	CHEK1	CHEK1	7702	0.069	0.4	NO
26	RRM2B	RRM2B	RRM2B	7879	0.066	0.4	NO
27	TSC2	TSC2	TSC2	8476	0.058	0.38	NO
28	CCNG2	CCNG2	CCNG2	9619	0.043	0.33	NO
29	CCNE1	CCNE1	CCNE1	9705	0.042	0.33	NO
30	RFWD2	RFWD2	RFWD2	10009	0.038	0.32	NO
31	CDK2	CDK2	CDK2	10039	0.038	0.33	NO
32	MDM2	MDM2	MDM2	10847	0.029	0.29	NO
33	CDK4	CDK4	CDK4	11233	0.024	0.28	NO
34	MDM4	MDM4	MDM4	11700	0.018	0.26	NO
35	PTEN	PTEN	PTEN	11999	0.014	0.25	NO
36	CD82	CD82	CD82	12251	0.011	0.24	NO
37	CYCS	CYCS	CYCS	12681	0.005	0.22	NO
38	ZMAT3	ZMAT3	ZMAT3	12841	0.0029	0.22	NO
39	TNFRSF10B	TNFRSF10B	TNFRSF10B	13036	0.000014	0.21	NO
40	GADD45B	GADD45B	GADD45B	13074	-0.00054	0.2	NO
41	BID	BID	BID	13111	-0.001	0.2	NO
42	SHISA5	SHISA5	SHISA5	13268	-0.0035	0.2	NO
43	THBS1	THBS1	THBS1	13471	-0.0064	0.19	NO
44	RCHY1	RCHY1	RCHY1	13902	-0.013	0.17	NO
45	TP53	TP53	TP53	14055	-0.015	0.17	NO
46	EI24	EI24	EI24	14068	-0.015	0.17	NO
47	ATM	ATM	ATM	14102	-0.016	0.17	NO
48	FAS	FAS	FAS	14169	-0.016	0.17	NO
49	CASP3	CASP3	CASP3	14358	-0.019	0.16	NO
50	IGFBP3	IGFBP3	IGFBP3	15337	-0.037	0.12	NO
51	CASP9	CASP9	CASP9	15723	-0.045	0.11	NO
52	PPM1D	PPM1D	PPM1D	15982	-0.05	0.1	NO
53	TP53I3	TP53I3	TP53I3	16048	-0.052	0.11	NO
54	SESN2	SESN2	SESN2	16292	-0.058	0.1	NO
55	CCND3	CCND3	CCND3	16400	-0.06	0.1	NO
56	CASP8	CASP8	CASP8	16636	-0.066	0.1	NO
57	BAX	BAX	BAX	17340	-0.086	0.079	NO
58	GADD45G	GADD45G	GADD45G	17592	-0.095	0.079	NO
59	CCNG1	CCNG1	CCNG1	18275	-0.12	0.062	NO
60	APAF1	APAF1	APAF1	18289	-0.12	0.076	NO
61	CDKN2A	CDKN2A	CDKN2A	18407	-0.13	0.085	NO
62	SESN1	SESN1	SESN1	18587	-0.14	0.092	NO
63	CCND2	CCND2	CCND2	19501	-0.18	0.072	NO
64	BBC3	BBC3	BBC3	19650	-0.19	0.087	NO
65	CCNB3	CCNB3	CCNB3	19851	-0.2	0.1	NO
66	IGF1	IGF1	IGF1	20335	-0.24	0.11	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 CARM ER PATHWAY.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CARM ER 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 G1 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	GRIP1	GRIP1	GRIP1	604	0.56	0.18	YES
2	NR0B1	NR0B1	NR0B1	1812	0.29	0.24	YES
3	CCND1	CCND1	CCND1	3329	0.18	0.24	YES
4	NRIP1	NRIP1	NRIP1	4621	0.13	0.23	YES
5	ESR1	ESR1	ESR1	4962	0.12	0.26	YES
6	GTF2E1	GTF2E1	GTF2E1	5219	0.11	0.29	YES
7	POLR2A	POLR2A	POLR2A	5371	0.11	0.32	YES
8	HDAC4	HDAC4	HDAC4	5590	0.11	0.35	YES
9	BRCA1	BRCA1	BRCA1	5972	0.098	0.37	YES
10	SPEN	SPEN	SPEN	6612	0.086	0.38	YES
11	PELP1	PELP1	PELP1	7470	0.072	0.36	YES
12	ERCC3	ERCC3	ERCC3	7920	0.065	0.37	YES
13	HDAC2	HDAC2	HDAC2	8255	0.061	0.38	YES
14	CARM1	CARM1	CARM1	8537	0.057	0.39	YES
15	HDAC5	HDAC5	HDAC5	8540	0.057	0.41	YES
16	NCOR2	NCOR2	NCOR2	9181	0.048	0.4	YES
17	HDAC3	HDAC3	HDAC3	9570	0.044	0.4	YES
18	EP300	EP300	EP300	9721	0.042	0.4	YES
19	CREBBP	CREBBP	CREBBP	9875	0.04	0.41	YES
20	HDAC8	HDAC8	HDAC8	10053	0.038	0.42	YES
21	GTF2F1	GTF2F1	GTF2F1	10713	0.03	0.4	NO
22	HDAC9	HDAC9	HDAC9	11098	0.025	0.39	NO
23	TBP	TBP	TBP	11432	0.022	0.39	NO
24	HDAC10	HDAC10	HDAC10	11707	0.018	0.38	NO
25	PHB2	PHB2	PHB2	11782	0.017	0.38	NO
26	GTF2A1	GTF2A1	GTF2A1	12176	0.012	0.37	NO
27	HDAC6	HDAC6	HDAC6	12309	0.0098	0.37	NO
28	HDAC11	HDAC11	HDAC11	12818	0.0032	0.35	NO
29	HDAC1	HDAC1	HDAC1	13100	-0.00085	0.34	NO
30	MED1	MED1	MED1	13114	-0.0011	0.34	NO
31	HDAC7	HDAC7	HDAC7	13511	-0.007	0.32	NO
32	SRA1	SRA1	SRA1	14477	-0.021	0.29	NO
33	PPARGC1A	PPARGC1A	PPARGC1A	19899	-0.21	0.12	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 G1 PATHWAY.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 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 ERK 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	MAP3K6	MAP3K6	MAP3K6	2174	0.26	-0.056	YES
2	HRAS	HRAS	HRAS	2188	0.25	-0.017	YES
3	MAPK6	MAPK6	MAPK6	2281	0.25	0.018	YES
4	MAP3K9	MAP3K9	MAP3K9	2393	0.24	0.05	YES
5	MAPK10	MAPK10	MAPK10	2663	0.22	0.072	YES
6	MAPK11	MAPK11	MAPK11	3483	0.17	0.063	YES
7	MAP3K4	MAP3K4	MAP3K4	3521	0.17	0.088	YES
8	MAPK12	MAPK12	MAPK12	3695	0.16	0.11	YES
9	TGFB1	TGFB1	TGFB1	3855	0.16	0.12	YES
10	MAP4K5	MAP4K5	MAP4K5	4248	0.14	0.13	YES
11	MAP2K4	MAP2K4	MAP2K4	4439	0.14	0.14	YES
12	MAP4K4	MAP4K4	MAP4K4	4661	0.13	0.15	YES
13	MAPK7	MAPK7	MAPK7	4947	0.12	0.16	YES
14	MYC	MYC	MYC	4958	0.12	0.18	YES
15	MAP4K2	MAP4K2	MAP4K2	4976	0.12	0.2	YES
16	PAK2	PAK2	PAK2	5296	0.11	0.2	YES
17	MKNK2	MKNK2	MKNK2	5344	0.11	0.22	YES
18	MAP3K10	MAP3K10	MAP3K10	5473	0.11	0.23	YES
19	TGFB2	TGFB2	TGFB2	5994	0.097	0.22	YES
20	BRAF	BRAF	BRAF	6211	0.093	0.22	YES
21	SHC1	SHC1	SHC1	6285	0.092	0.24	YES
22	MAP2K1	MAP2K1	MAP2K1	6407	0.09	0.24	YES
23	NFKBIA	NFKBIA	NFKBIA	6518	0.088	0.25	YES
24	MKNK1	MKNK1	MKNK1	6594	0.086	0.26	YES
25	RPS6KB1	RPS6KB1	RPS6KB1	6896	0.081	0.26	YES
26	MEF2A	MEF2A	MEF2A	7013	0.079	0.27	YES
27	TGFBR1	TGFBR1	TGFBR1	7343	0.074	0.27	YES
28	MAP3K7	MAP3K7	MAP3K7	7413	0.073	0.28	YES
29	RPS6KA4	RPS6KA4	RPS6KA4	7433	0.073	0.29	YES
30	MAPK1	MAPK1	MAPK1	7770	0.068	0.28	YES
31	MAPK13	MAPK13	MAPK13	7875	0.066	0.29	YES
32	IKBKB	IKBKB	IKBKB	7881	0.066	0.3	YES
33	RPS6KA5	RPS6KA5	RPS6KA5	7882	0.066	0.31	YES
34	TRADD	TRADD	TRADD	7988	0.064	0.31	YES
35	TGFB3	TGFB3	TGFB3	8038	0.064	0.32	YES
36	CREB1	CREB1	CREB1	8642	0.055	0.3	YES
37	MAP3K2	MAP3K2	MAP3K2	8669	0.055	0.31	YES
38	STAT1	STAT1	STAT1	8681	0.054	0.32	YES
39	RPS6KB2	RPS6KB2	RPS6KB2	8890	0.052	0.32	YES
40	MAP3K5	MAP3K5	MAP3K5	8951	0.051	0.32	YES
41	MAP3K1	MAP3K1	MAP3K1	9058	0.05	0.33	YES
42	MAPK14	MAPK14	MAPK14	9105	0.049	0.33	YES
43	MAP2K7	MAP2K7	MAP2K7	9373	0.046	0.33	YES
44	RAC1	RAC1	RAC1	9427	0.045	0.33	YES
45	JUN	JUN	JUN	9465	0.045	0.34	YES
46	MAP2K2	MAP2K2	MAP2K2	9646	0.043	0.34	YES
47	RELA	RELA	RELA	9736	0.042	0.34	YES
48	DAXX	DAXX	DAXX	10151	0.037	0.33	NO
49	NFKB1	NFKB1	NFKB1	10161	0.036	0.33	NO
50	RAF1	RAF1	RAF1	10265	0.035	0.33	NO
51	MAP3K11	MAP3K11	MAP3K11	10623	0.031	0.32	NO
52	SP1	SP1	SP1	11186	0.024	0.3	NO
53	MAPKAPK2	MAPKAPK2	MAPKAPK2	11827	0.016	0.28	NO
54	PAK1	PAK1	PAK1	11992	0.014	0.27	NO
55	ATF2	ATF2	ATF2	12262	0.01	0.26	NO
56	CHUK	CHUK	CHUK	12489	0.0075	0.25	NO
57	MAP3K8	MAP3K8	MAP3K8	12783	0.0037	0.24	NO
58	MAPK4	MAPK4	MAPK4	12844	0.0028	0.24	NO
59	MAP3K13	MAP3K13	MAP3K13	12966	0.001	0.23	NO
60	TRAF2	TRAF2	TRAF2	12977	0.00092	0.23	NO
61	RIPK1	RIPK1	RIPK1	13080	-0.0006	0.23	NO
62	MAPK8	MAPK8	MAPK8	13283	-0.0037	0.22	NO
63	MAPK9	MAPK9	MAPK9	13324	-0.0043	0.22	NO
64	MAP4K3	MAP4K3	MAP4K3	13412	-0.0055	0.21	NO
65	MAP2K5	MAP2K5	MAP2K5	13524	-0.0071	0.21	NO
66	FOS	FOS	FOS	13530	-0.0072	0.21	NO
67	MAP3K3	MAP3K3	MAP3K3	13658	-0.0089	0.21	NO
68	MAPKAPK5	MAPKAPK5	MAPKAPK5	13769	-0.01	0.2	NO
69	MAX	MAX	MAX	13785	-0.011	0.2	NO
70	GRB2	GRB2	GRB2	14210	-0.017	0.19	NO
71	MAPKAPK3	MAPKAPK3	MAPKAPK3	14897	-0.029	0.16	NO
72	ELK1	ELK1	ELK1	15012	-0.031	0.16	NO
73	MAP2K3	MAP2K3	MAP2K3	15410	-0.038	0.15	NO
74	RPS6KA1	RPS6KA1	RPS6KA1	15652	-0.043	0.15	NO
75	MEF2D	MEF2D	MEF2D	15841	-0.047	0.15	NO
76	ARAF	ARAF	ARAF	15977	-0.05	0.15	NO
77	MAP3K14	MAP3K14	MAP3K14	15995	-0.05	0.16	NO
78	CEBPA	CEBPA	CEBPA	16177	-0.055	0.16	NO
79	RPS6KA3	RPS6KA3	RPS6KA3	16182	-0.055	0.16	NO
80	MAP3K12	MAP3K12	MAP3K12	16444	-0.061	0.16	NO
81	RAPGEF2	RAPGEF2	RAPGEF2	17233	-0.083	0.14	NO
82	MAPK3	MAPK3	MAPK3	17731	-0.1	0.14	NO
83	RPS6KA2	RPS6KA2	RPS6KA2	18373	-0.13	0.13	NO
84	MAP2K6	MAP2K6	MAP2K6	19697	-0.2	0.098	NO
85	MAP4K1	MAP4K1	MAP4K1	20243	-0.23	0.11	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 ERK PATHWAY.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ERK 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 INTEGRIN PATHWAY

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	FOXN1	FOXN1	FOXN1	92	1.1	0.062	YES
2	WNT7A	WNT7A	WNT7A	126	1	0.12	YES
3	WNT7B	WNT7B	WNT7B	148	0.94	0.18	YES
4	PITX2	PITX2	PITX2	315	0.72	0.21	YES
5	WNT9A	WNT9A	WNT9A	851	0.46	0.22	YES
6	WNT10A	WNT10A	WNT10A	877	0.45	0.24	YES
7	DKK1	DKK1	DKK1	879	0.45	0.27	YES
8	FZD6	FZD6	FZD6	1039	0.41	0.29	YES
9	FOSL1	FOSL1	FOSL1	1071	0.4	0.31	YES
10	KREMEN1	KREMEN1	KREMEN1	1254	0.36	0.33	YES
11	WNT6	WNT6	WNT6	1406	0.34	0.34	YES
12	WNT4	WNT4	WNT4	1450	0.34	0.36	YES
13	WIF1	WIF1	WIF1	1578	0.32	0.37	YES
14	WNT3	WNT3	WNT3	1722	0.3	0.38	YES
15	WNT5A	WNT5A	WNT5A	1871	0.28	0.4	YES
16	TCF7L1	TCF7L1	TCF7L1	1998	0.27	0.41	YES
17	CTNNBIP1	CTNNBIP1	CTNNBIP1	2246	0.25	0.41	YES
18	WNT16	WNT16	WNT16	2829	0.21	0.4	YES
19	PORCN	PORCN	PORCN	2946	0.2	0.4	YES
20	WNT2B	WNT2B	WNT2B	3092	0.19	0.41	YES
21	CCND1	CCND1	CCND1	3329	0.18	0.41	YES
22	DVL2	DVL2	DVL2	3560	0.17	0.41	YES
23	FZD7	FZD7	FZD7	3570	0.17	0.42	YES
24	FZD1	FZD1	FZD1	3663	0.16	0.43	YES
25	DAAM1	DAAM1	DAAM1	3829	0.16	0.43	YES
26	WNT11	WNT11	WNT11	3908	0.16	0.43	YES
27	CSNK1A1	CSNK1A1	CSNK1A1	4311	0.14	0.42	YES
28	T	T	T	4413	0.14	0.43	YES
29	SENP2	SENP2	SENP2	4489	0.14	0.43	YES
30	CSNK1G1	CSNK1G1	CSNK1G1	4741	0.13	0.43	YES
31	MYC	MYC	MYC	4958	0.12	0.43	YES
32	SFRP1	SFRP1	SFRP1	4968	0.12	0.44	YES
33	NKD1	NKD1	NKD1	5008	0.12	0.44	YES
34	SLC9A3R1	SLC9A3R1	SLC9A3R1	5169	0.12	0.44	NO
35	DVL1	DVL1	DVL1	5783	0.1	0.42	NO
36	BTRC	BTRC	BTRC	6020	0.097	0.42	NO
37	GSK3B	GSK3B	GSK3B	6202	0.093	0.41	NO
38	LEF1	LEF1	LEF1	6525	0.087	0.4	NO
39	HPRT1	HPRT1	HPRT1	6613	0.086	0.41	NO
40	FGF4	FGF4	FGF4	7056	0.078	0.39	NO
41	PYGO1	PYGO1	PYGO1	7578	0.071	0.37	NO
42	GAPDH	GAPDH	GAPDH	7844	0.067	0.36	NO
43	FBXW2	FBXW2	FBXW2	7983	0.064	0.36	NO
44	FBXW4	FBXW4	FBXW4	8050	0.063	0.36	NO
45	WNT5B	WNT5B	WNT5B	8094	0.063	0.36	NO
46	APC	APC	APC	9124	0.049	0.32	NO
47	JUN	JUN	JUN	9465	0.045	0.31	NO
48	EP300	EP300	EP300	9721	0.042	0.3	NO
49	CSNK2A1	CSNK2A1	CSNK2A1	10493	0.033	0.27	NO
50	AXIN1	AXIN1	AXIN1	10559	0.032	0.27	NO
51	ACTB	ACTB	ACTB	11207	0.024	0.24	NO
52	FBXW11	FBXW11	FBXW11	11766	0.017	0.22	NO
53	GSK3A	GSK3A	GSK3A	11906	0.015	0.21	NO
54	PPP2R1A	PPP2R1A	PPP2R1A	12126	0.012	0.2	NO
55	CTNNB1	CTNNB1	CTNNB1	12869	0.0024	0.17	NO
56	CSNK1D	CSNK1D	CSNK1D	12922	0.0018	0.17	NO
57	NLK	NLK	NLK	12971	0.00098	0.17	NO
58	FZD3	FZD3	FZD3	13212	-0.0028	0.16	NO
59	AES	AES	AES	13436	-0.0059	0.15	NO
60	FZD2	FZD2	FZD2	13537	-0.0074	0.14	NO
61	CTBP1	CTBP1	CTBP1	14415	-0.02	0.11	NO
62	CTBP2	CTBP2	CTBP2	15123	-0.033	0.077	NO
63	LRP6	LRP6	LRP6	15173	-0.034	0.077	NO
64	BCL9	BCL9	BCL9	15292	-0.036	0.074	NO
65	LRP5	LRP5	LRP5	15445	-0.039	0.069	NO
66	B2M	B2M	B2M	15573	-0.041	0.066	NO
67	RPL13A	RPL13A	RPL13A	15742	-0.045	0.062	NO
68	WISP1	WISP1	WISP1	15770	-0.045	0.063	NO
69	TLE1	TLE1	TLE1	15938	-0.049	0.059	NO
70	CCND3	CCND3	CCND3	16400	-0.06	0.042	NO
71	DIXDC1	DIXDC1	DIXDC1	19193	-0.17	-0.071	NO
72	TCF7	TCF7	TCF7	19319	-0.17	-0.066	NO
73	CCND2	CCND2	CCND2	19501	-0.18	-0.063	NO
74	FZD4	FZD4	FZD4	19674	-0.19	-0.059	NO
75	WNT2	WNT2	WNT2	19716	-0.2	-0.048	NO
76	FRAT1	FRAT1	FRAT1	19779	-0.2	-0.039	NO
77	FZD8	FZD8	FZD8	19976	-0.21	-0.035	NO
78	CXXC4	CXXC4	CXXC4	20230	-0.23	-0.032	NO
79	SFRP4	SFRP4	SFRP4	20234	-0.23	-0.018	NO
80	TLE2	TLE2	TLE2	20251	-0.23	-0.0047	NO
81	WNT1	WNT1	WNT1	20659	-0.26	-0.0066	NO
82	SOX17	SOX17	SOX17	20944	-0.29	-0.0014	NO
83	FZD5	FZD5	FZD5	21356	-0.34	0.0011	NO
84	RHOU	RHOU	RHOU	21969	-0.45	0.0013	NO
85	FRZB	FRZB	FRZB	22324	-0.54	0.019	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: BIOCARTA INTEGRIN PATHWAY.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INTEGRIN 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 MAPK PATHWAY

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	CALML3	CALML3	CALML3	2	1.7	0.11	YES
2	CALML5	CALML5	CALML5	54	1.2	0.18	YES
3	NTF4	NTF4	NTF4	59	1.2	0.26	YES
4	NTRK2	NTRK2	NTRK2	454	0.62	0.28	YES
5	TP73	TP73	TP73	500	0.6	0.31	YES
6	NGFR	NGFR	NGFR	768	0.48	0.33	YES
7	CALML6	CALML6	CALML6	1907	0.28	0.3	YES
8	NGFRAP1	NGFRAP1	NGFRAP1	1923	0.28	0.32	YES
9	CAMK2B	CAMK2B	CAMK2B	2105	0.26	0.32	YES
10	NGF	NGF	NGF	2288	0.25	0.33	YES
11	MAPK10	MAPK10	MAPK10	2663	0.22	0.33	YES
12	BDNF	BDNF	BDNF	2741	0.21	0.34	YES
13	CAMK2A	CAMK2A	CAMK2A	2863	0.2	0.34	YES
14	IRS4	IRS4	IRS4	3113	0.19	0.35	YES
15	MAPK11	MAPK11	MAPK11	3483	0.17	0.34	YES
16	PIK3CA	PIK3CA	PIK3CA	3545	0.17	0.35	YES
17	MAPK12	MAPK12	MAPK12	3695	0.16	0.35	YES
18	CRKL	CRKL	CRKL	3981	0.15	0.35	YES
19	PDK1	PDK1	PDK1	4094	0.15	0.35	YES
20	PIK3CD	PIK3CD	PIK3CD	4361	0.14	0.35	YES
21	YWHAQ	YWHAQ	YWHAQ	4437	0.14	0.36	YES
22	ZNF274	ZNF274	ZNF274	4809	0.12	0.35	YES
23	SHC3	SHC3	SHC3	4815	0.12	0.35	YES
24	MAPK7	MAPK7	MAPK7	4947	0.12	0.36	YES
25	KIDINS220	KIDINS220	KIDINS220	5606	0.11	0.33	NO
26	YWHAZ	YWHAZ	YWHAZ	5772	0.1	0.33	NO
27	YWHAG	YWHAG	YWHAG	5977	0.098	0.33	NO
28	SOS2	SOS2	SOS2	6141	0.094	0.33	NO
29	GSK3B	GSK3B	GSK3B	6202	0.093	0.33	NO
30	BRAF	BRAF	BRAF	6211	0.093	0.34	NO
31	SHC1	SHC1	SHC1	6285	0.092	0.34	NO
32	MAP2K1	MAP2K1	MAP2K1	6407	0.09	0.34	NO
33	NFKBIA	NFKBIA	NFKBIA	6518	0.088	0.34	NO
34	AKT3	AKT3	AKT3	6785	0.083	0.33	NO
35	IRS1	IRS1	IRS1	6925	0.081	0.33	NO
36	YWHAE	YWHAE	YWHAE	6932	0.08	0.34	NO
37	RPS6KA4	RPS6KA4	RPS6KA4	7433	0.073	0.32	NO
38	NRAS	NRAS	NRAS	7613	0.07	0.32	NO
39	PLCG1	PLCG1	PLCG1	7619	0.07	0.32	NO
40	MAPK1	MAPK1	MAPK1	7770	0.068	0.32	NO
41	MAPK13	MAPK13	MAPK13	7875	0.066	0.32	NO
42	IKBKB	IKBKB	IKBKB	7881	0.066	0.32	NO
43	RPS6KA5	RPS6KA5	RPS6KA5	7882	0.066	0.32	NO
44	SHC4	SHC4	SHC4	8337	0.06	0.31	NO
45	PRDM4	PRDM4	PRDM4	8430	0.058	0.31	NO
46	CRK	CRK	CRK	8796	0.053	0.3	NO
47	FRS2	FRS2	FRS2	8898	0.052	0.29	NO
48	MAP3K5	MAP3K5	MAP3K5	8951	0.051	0.3	NO
49	IRS2	IRS2	IRS2	8984	0.051	0.3	NO
50	IRAK1	IRAK1	IRAK1	9052	0.05	0.3	NO
51	MAP3K1	MAP3K1	MAP3K1	9058	0.05	0.3	NO
52	MAPK14	MAPK14	MAPK14	9105	0.049	0.3	NO
53	RPS6KA6	RPS6KA6	RPS6KA6	9240	0.047	0.3	NO
54	GAB1	GAB1	GAB1	9340	0.046	0.3	NO
55	MAP2K7	MAP2K7	MAP2K7	9373	0.046	0.3	NO
56	RAC1	RAC1	RAC1	9427	0.045	0.3	NO
57	JUN	JUN	JUN	9465	0.045	0.3	NO
58	CAMK2D	CAMK2D	CAMK2D	9574	0.044	0.3	NO
59	MAP2K2	MAP2K2	MAP2K2	9646	0.043	0.3	NO
60	SOS1	SOS1	SOS1	9716	0.042	0.3	NO
61	RELA	RELA	RELA	9736	0.042	0.3	NO
62	IRAK4	IRAK4	IRAK4	10149	0.037	0.28	NO
63	NFKB1	NFKB1	NFKB1	10161	0.036	0.28	NO
64	RAF1	RAF1	RAF1	10265	0.035	0.28	NO
65	AKT2	AKT2	AKT2	10312	0.035	0.28	NO
66	PTPN11	PTPN11	PTPN11	10442	0.033	0.28	NO
67	ARHGDIA	ARHGDIA	ARHGDIA	10446	0.033	0.28	NO
68	CSK	CSK	CSK	10447	0.033	0.28	NO
69	AKT1	AKT1	AKT1	10537	0.032	0.28	NO
70	SH2B2	SH2B2	SH2B2	10918	0.028	0.27	NO
71	FOXO3	FOXO3	FOXO3	10946	0.027	0.27	NO
72	ABL1	ABL1	ABL1	11108	0.025	0.26	NO
73	RAPGEF1	RAPGEF1	RAPGEF1	11573	0.02	0.24	NO
74	MAPKAPK2	MAPKAPK2	MAPKAPK2	11827	0.016	0.23	NO
75	TRAF6	TRAF6	TRAF6	11867	0.016	0.23	NO
76	ATF4	ATF4	ATF4	11954	0.015	0.23	NO
77	PIK3CB	PIK3CB	PIK3CB	12185	0.012	0.22	NO
78	SH2B1	SH2B1	SH2B1	12322	0.0096	0.21	NO
79	PSEN1	PSEN1	PSEN1	12477	0.0076	0.21	NO
80	KRAS	KRAS	KRAS	12510	0.0072	0.2	NO
81	YWHAB	YWHAB	YWHAB	12918	0.0018	0.19	NO
82	MAGED1	MAGED1	MAGED1	13148	-0.0015	0.18	NO
83	CALM1	CALM1	CALM1	13187	-0.0023	0.18	NO
84	BAD	BAD	BAD	13244	-0.0032	0.17	NO
85	MAPK8	MAPK8	MAPK8	13283	-0.0037	0.17	NO
86	MAPK9	MAPK9	MAPK9	13324	-0.0043	0.17	NO
87	MAP2K5	MAP2K5	MAP2K5	13524	-0.0071	0.16	NO
88	MAP3K3	MAP3K3	MAP3K3	13658	-0.0089	0.16	NO
89	CAMK2G	CAMK2G	CAMK2G	13874	-0.012	0.15	NO
90	RAP1B	RAP1B	RAP1B	13988	-0.014	0.14	NO
91	CDC42	CDC42	CDC42	14053	-0.015	0.14	NO
92	TP53	TP53	TP53	14055	-0.015	0.14	NO
93	GRB2	GRB2	GRB2	14210	-0.017	0.14	NO
94	NFKBIB	NFKBIB	NFKBIB	14220	-0.017	0.14	NO
95	PLCG2	PLCG2	PLCG2	14832	-0.028	0.11	NO
96	CALM2	CALM2	CALM2	15144	-0.033	0.1	NO
97	CAMK4	CAMK4	CAMK4	15190	-0.034	0.1	NO
98	YWHAH	YWHAH	YWHAH	15264	-0.036	0.1	NO
99	RPS6KA1	RPS6KA1	RPS6KA1	15652	-0.043	0.086	NO
100	PIK3R2	PIK3R2	PIK3R2	15734	-0.045	0.085	NO
101	RIPK2	RIPK2	RIPK2	15912	-0.048	0.08	NO
102	RHOA	RHOA	RHOA	16026	-0.051	0.078	NO
103	RPS6KA3	RPS6KA3	RPS6KA3	16182	-0.055	0.075	NO
104	BCL2	BCL2	BCL2	16300	-0.058	0.073	NO
105	SORT1	SORT1	SORT1	16508	-0.062	0.068	NO
106	RAP1A	RAP1A	RAP1A	16532	-0.063	0.071	NO
107	PRKCD	PRKCD	PRKCD	16647	-0.066	0.07	NO
108	PIK3R1	PIK3R1	PIK3R1	17213	-0.082	0.05	NO
109	PIK3R3	PIK3R3	PIK3R3	17227	-0.083	0.055	NO
110	BAX	BAX	BAX	17340	-0.086	0.055	NO
111	MAPK3	MAPK3	MAPK3	17731	-0.1	0.044	NO
112	ARHGDIB	ARHGDIB	ARHGDIB	18350	-0.13	0.025	NO
113	NFKBIE	NFKBIE	NFKBIE	18366	-0.13	0.032	NO
114	RPS6KA2	RPS6KA2	RPS6KA2	18373	-0.13	0.04	NO
115	SH2B3	SH2B3	SH2B3	18376	-0.13	0.048	NO
116	CALM3	CALM3	CALM3	18518	-0.13	0.05	NO
117	IRAK2	IRAK2	IRAK2	18634	-0.14	0.053	NO
118	IRAK3	IRAK3	IRAK3	18763	-0.14	0.057	NO
119	NTRK1	NTRK1	NTRK1	19941	-0.21	0.018	NO
120	PIK3R5	PIK3R5	PIK3R5	20392	-0.24	0.013	NO
121	NTF3	NTF3	NTF3	20555	-0.26	0.022	NO
122	SHC2	SHC2	SHC2	20560	-0.26	0.037	NO
123	NTRK3	NTRK3	NTRK3	20665	-0.26	0.049	NO
124	FASLG	FASLG	FASLG	20717	-0.27	0.064	NO
125	PIK3CG	PIK3CG	PIK3CG	21847	-0.42	0.04	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: BIOCARTA MAPK PATHWAY.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MAPK 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 MYOSIN PATHWAY

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	CCNA1	CCNA1	CCNA1	252	0.79	0.06	YES
2	SFN	SFN	SFN	587	0.56	0.096	YES
3	ESPL1	ESPL1	ESPL1	3083	0.19	0.0029	YES
4	ANAPC1	ANAPC1	ANAPC1	3293	0.18	0.0099	YES
5	CDC45	CDC45	CDC45	3324	0.18	0.025	YES
6	CCND1	CCND1	CCND1	3329	0.18	0.04	YES
7	CDKN2D	CDKN2D	CDKN2D	3391	0.18	0.054	YES
8	SMC1B	SMC1B	SMC1B	3539	0.17	0.062	YES
9	SMAD3	SMAD3	SMAD3	3717	0.16	0.069	YES
10	BUB1B	BUB1B	BUB1B	3771	0.16	0.081	YES
11	TGFB1	TGFB1	TGFB1	3855	0.16	0.092	YES
12	PKMYT1	PKMYT1	PKMYT1	3900	0.16	0.1	YES
13	MCM2	MCM2	MCM2	3970	0.15	0.11	YES
14	PTTG1	PTTG1	PTTG1	4028	0.15	0.12	YES
15	TTK	TTK	TTK	4047	0.15	0.14	YES
16	CCNE2	CCNE2	CCNE2	4086	0.15	0.15	YES
17	WEE1	WEE1	WEE1	4270	0.14	0.15	YES
18	ATR	ATR	ATR	4366	0.14	0.16	YES
19	YWHAQ	YWHAQ	YWHAQ	4437	0.14	0.17	YES
20	ANAPC7	ANAPC7	ANAPC7	4749	0.13	0.17	YES
21	CCNB2	CCNB2	CCNB2	4784	0.13	0.18	YES
22	MAD2L2	MAD2L2	MAD2L2	4804	0.12	0.19	YES
23	CDK6	CDK6	CDK6	4820	0.12	0.2	YES
24	E2F2	E2F2	E2F2	4881	0.12	0.21	YES
25	SKP2	SKP2	SKP2	4943	0.12	0.22	YES
26	MYC	MYC	MYC	4958	0.12	0.23	YES
27	FZR1	FZR1	FZR1	4986	0.12	0.24	YES
28	MCM4	MCM4	MCM4	5022	0.12	0.24	YES
29	CDC7	CDC7	CDC7	5150	0.12	0.25	YES
30	MCM5	MCM5	MCM5	5161	0.12	0.26	YES
31	CDK1	CDK1	CDK1	5271	0.11	0.26	YES
32	CDC20	CDC20	CDC20	5323	0.11	0.27	YES
33	RBL1	RBL1	RBL1	5407	0.11	0.28	YES
34	CDKN1A	CDKN1A	CDKN1A	5453	0.11	0.29	YES
35	MAD2L1	MAD2L1	MAD2L1	5493	0.11	0.3	YES
36	PRKDC	PRKDC	PRKDC	5549	0.11	0.3	YES
37	CCNB1	CCNB1	CCNB1	5709	0.1	0.3	YES
38	ZBTB17	ZBTB17	ZBTB17	5761	0.1	0.31	YES
39	YWHAZ	YWHAZ	YWHAZ	5772	0.1	0.32	YES
40	STAG1	STAG1	STAG1	5937	0.098	0.32	YES
41	YWHAG	YWHAG	YWHAG	5977	0.098	0.33	YES
42	TGFB2	TGFB2	TGFB2	5994	0.097	0.34	YES
43	CCNA2	CCNA2	CCNA2	6061	0.096	0.34	YES
44	RBX1	RBX1	RBX1	6095	0.095	0.35	YES
45	GSK3B	GSK3B	GSK3B	6202	0.093	0.35	YES
46	STAG2	STAG2	STAG2	6679	0.085	0.34	YES
47	SMAD2	SMAD2	SMAD2	6885	0.081	0.34	YES
48	YWHAE	YWHAE	YWHAE	6932	0.08	0.34	YES
49	GADD45A	GADD45A	GADD45A	7136	0.077	0.34	YES
50	CHEK2	CHEK2	CHEK2	7334	0.074	0.34	YES
51	CDC6	CDC6	CDC6	7384	0.073	0.34	YES
52	MAD1L1	MAD1L1	MAD1L1	7460	0.072	0.35	YES
53	RAD21	RAD21	RAD21	7478	0.072	0.35	YES
54	MCM7	MCM7	MCM7	7553	0.071	0.36	YES
55	CDC27	CDC27	CDC27	7555	0.071	0.36	YES
56	CHEK1	CHEK1	CHEK1	7702	0.069	0.36	YES
57	BUB1	BUB1	BUB1	7717	0.069	0.37	YES
58	SMC3	SMC3	SMC3	7936	0.065	0.36	YES
59	ANAPC11	ANAPC11	ANAPC11	7956	0.065	0.37	YES
60	CDC23	CDC23	CDC23	8027	0.064	0.37	YES
61	TGFB3	TGFB3	TGFB3	8038	0.064	0.38	YES
62	ANAPC2	ANAPC2	ANAPC2	8040	0.064	0.38	YES
63	CDKN2B	CDKN2B	CDKN2B	8071	0.063	0.39	YES
64	TFDP1	TFDP1	TFDP1	8130	0.062	0.39	YES
65	PLK1	PLK1	PLK1	8144	0.062	0.39	YES
66	HDAC2	HDAC2	HDAC2	8255	0.061	0.4	YES
67	RB1	RB1	RB1	8284	0.06	0.4	YES
68	E2F4	E2F4	E2F4	8607	0.056	0.39	YES
69	RBL2	RBL2	RBL2	8611	0.056	0.4	YES
70	E2F3	E2F3	E2F3	8663	0.055	0.4	YES
71	CDKN2C	CDKN2C	CDKN2C	8668	0.055	0.4	YES
72	CDK7	CDK7	CDK7	8744	0.053	0.4	YES
73	CDC25B	CDC25B	CDC25B	8777	0.053	0.41	YES
74	MCM6	MCM6	MCM6	9042	0.05	0.4	YES
75	CUL1	CUL1	CUL1	9046	0.05	0.4	YES
76	CDC25A	CDC25A	CDC25A	9198	0.048	0.4	YES
77	PCNA	PCNA	PCNA	9205	0.048	0.41	YES
78	E2F1	E2F1	E2F1	9229	0.048	0.41	YES
79	CCNE1	CCNE1	CCNE1	9705	0.042	0.39	NO
80	EP300	EP300	EP300	9721	0.042	0.4	NO
81	CREBBP	CREBBP	CREBBP	9875	0.04	0.39	NO
82	ANAPC10	ANAPC10	ANAPC10	10031	0.038	0.39	NO
83	CDK2	CDK2	CDK2	10039	0.038	0.39	NO
84	CDC25C	CDC25C	CDC25C	10171	0.036	0.39	NO
85	MCM3	MCM3	MCM3	10289	0.035	0.39	NO
86	ANAPC4	ANAPC4	ANAPC4	10460	0.033	0.38	NO
87	ANAPC5	ANAPC5	ANAPC5	10508	0.033	0.38	NO
88	MDM2	MDM2	MDM2	10847	0.029	0.37	NO
89	ANAPC13	ANAPC13	ANAPC13	10975	0.027	0.37	NO
90	BUB3	BUB3	BUB3	11042	0.026	0.37	NO
91	ABL1	ABL1	ABL1	11108	0.025	0.37	NO
92	CDK4	CDK4	CDK4	11233	0.024	0.36	NO
93	CDKN1C	CDKN1C	CDKN1C	11286	0.023	0.36	NO
94	SKP1	SKP1	SKP1	11292	0.023	0.36	NO
95	SMC1A	SMC1A	SMC1A	11606	0.019	0.35	NO
96	SMAD4	SMAD4	SMAD4	12582	0.0062	0.31	NO
97	YWHAB	YWHAB	YWHAB	12918	0.0018	0.3	NO
98	GADD45B	GADD45B	GADD45B	13074	-0.00054	0.29	NO
99	HDAC1	HDAC1	HDAC1	13100	-0.00085	0.29	NO
100	TFDP2	TFDP2	TFDP2	13269	-0.0035	0.28	NO
101	CDC16	CDC16	CDC16	13760	-0.01	0.26	NO
102	CCNH	CCNH	CCNH	14009	-0.014	0.25	NO
103	TP53	TP53	TP53	14055	-0.015	0.25	NO
104	ATM	ATM	ATM	14102	-0.016	0.25	NO
105	CDC14A	CDC14A	CDC14A	14467	-0.021	0.24	NO
106	YWHAH	YWHAH	YWHAH	15264	-0.036	0.2	NO
107	CCND3	CCND3	CCND3	16400	-0.06	0.16	NO
108	WEE2	WEE2	WEE2	16490	-0.062	0.16	NO
109	CDC26	CDC26	CDC26	16542	-0.063	0.16	NO
110	CDKN1B	CDKN1B	CDKN1B	17055	-0.078	0.15	NO
111	GADD45G	GADD45G	GADD45G	17592	-0.095	0.13	NO
112	CDC14B	CDC14B	CDC14B	18015	-0.11	0.12	NO
113	CDKN2A	CDKN2A	CDKN2A	18407	-0.13	0.12	NO
114	CCND2	CCND2	CCND2	19501	-0.18	0.086	NO
115	PTTG2	PTTG2	PTTG2	19761	-0.2	0.092	NO
116	CCNB3	CCNB3	CCNB3	19851	-0.2	0.11	NO
117	E2F5	E2F5	E2F5	20320	-0.24	0.11	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: BIOCARTA MYOSIN PATHWAY.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MYOSIN 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 IL1R PATHWAY

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	CCNA1	CCNA1	CCNA1	252	0.79	0.28	YES
2	CCND1	CCND1	CCND1	3329	0.18	0.2	YES
3	SMAD3	SMAD3	SMAD3	3717	0.16	0.25	YES
4	TGFB1	TGFB1	TGFB1	3855	0.16	0.3	YES
5	ATR	ATR	ATR	4366	0.14	0.32	YES
6	CDK6	CDK6	CDK6	4820	0.12	0.35	YES
7	SKP2	SKP2	SKP2	4943	0.12	0.39	YES
8	CDK1	CDK1	CDK1	5271	0.11	0.42	YES
9	CDKN1A	CDKN1A	CDKN1A	5453	0.11	0.45	YES
10	TGFB2	TGFB2	TGFB2	5994	0.097	0.46	YES
11	GSK3B	GSK3B	GSK3B	6202	0.093	0.48	YES
12	TGFB3	TGFB3	TGFB3	8038	0.064	0.42	NO
13	CDKN2B	CDKN2B	CDKN2B	8071	0.063	0.44	NO
14	TFDP1	TFDP1	TFDP1	8130	0.062	0.46	NO
15	RB1	RB1	RB1	8284	0.06	0.48	NO
16	CDC25A	CDC25A	CDC25A	9198	0.048	0.46	NO
17	CCNE1	CCNE1	CCNE1	9705	0.042	0.45	NO
18	CDK2	CDK2	CDK2	10039	0.038	0.45	NO
19	ABL1	ABL1	ABL1	11108	0.025	0.41	NO
20	CDK4	CDK4	CDK4	11233	0.024	0.42	NO
21	SMAD4	SMAD4	SMAD4	12582	0.0062	0.36	NO
22	HDAC1	HDAC1	HDAC1	13100	-0.00085	0.34	NO
23	DHFR	DHFR	DHFR	13758	-0.01	0.31	NO
24	TP53	TP53	TP53	14055	-0.015	0.3	NO
25	ATM	ATM	ATM	14102	-0.016	0.31	NO
26	CDKN1B	CDKN1B	CDKN1B	17055	-0.078	0.2	NO
27	CDKN2A	CDKN2A	CDKN2A	18407	-0.13	0.19	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: BIOCARTA IL1R PATHWAY.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R 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 SPLICEOSOME

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	CALML3	CALML3	CALML3	2	1.7	0.12	YES
2	CALML5	CALML5	CALML5	54	1.2	0.2	YES
3	CDK5R1	CDK5R1	CDK5R1	498	0.6	0.22	YES
4	NOS1	NOS1	NOS1	716	0.5	0.24	YES
5	NDUFA4L2	NDUFA4L2	NDUFA4L2	1015	0.42	0.26	YES
6	COX6B2	COX6B2	COX6B2	1666	0.31	0.25	YES
7	SNCA	SNCA	SNCA	1902	0.28	0.26	YES
8	CALML6	CALML6	CALML6	1907	0.28	0.28	YES
9	ADAM17	ADAM17	ADAM17	2157	0.26	0.29	YES
10	RYR3	RYR3	RYR3	2502	0.23	0.29	YES
11	FADD	FADD	FADD	2666	0.22	0.3	YES
12	COX8C	COX8C	COX8C	3990	0.15	0.25	NO
13	TNF	TNF	TNF	4355	0.14	0.24	NO
14	CAPN1	CAPN1	CAPN1	4876	0.12	0.23	NO
15	BACE1	BACE1	BACE1	5374	0.11	0.21	NO
16	ATP2A2	ATP2A2	ATP2A2	5869	0.1	0.2	NO
17	ATP2A1	ATP2A1	ATP2A1	6101	0.095	0.19	NO
18	GSK3B	GSK3B	GSK3B	6202	0.093	0.19	NO
19	MAPT	MAPT	MAPT	6264	0.092	0.2	NO
20	MME	MME	MME	7242	0.076	0.16	NO
21	NAE1	NAE1	NAE1	7445	0.072	0.16	NO
22	CAPN2	CAPN2	CAPN2	7682	0.069	0.15	NO
23	MAPK1	MAPK1	MAPK1	7770	0.068	0.15	NO
24	GAPDH	GAPDH	GAPDH	7844	0.067	0.15	NO
25	ITPR3	ITPR3	ITPR3	8002	0.064	0.15	NO
26	TNFRSF1A	TNFRSF1A	TNFRSF1A	8145	0.062	0.15	NO
27	NDUFB5	NDUFB5	NDUFB5	8528	0.057	0.14	NO
28	COX7B2	COX7B2	COX7B2	9483	0.044	0.096	NO
29	NDUFS6	NDUFS6	NDUFS6	9495	0.044	0.098	NO
30	PPP3R1	PPP3R1	PPP3R1	9809	0.041	0.087	NO
31	NDUFS5	NDUFS5	NDUFS5	9810	0.041	0.09	NO
32	NDUFB4	NDUFB4	NDUFB4	10139	0.037	0.078	NO
33	PPP3CC	PPP3CC	PPP3CC	10421	0.034	0.068	NO
34	COX6C	COX6C	COX6C	10662	0.031	0.059	NO
35	NDUFS8	NDUFS8	NDUFS8	11079	0.026	0.043	NO
36	APP	APP	APP	11093	0.026	0.044	NO
37	PPP3CB	PPP3CB	PPP3CB	11099	0.025	0.045	NO
38	HSD17B10	HSD17B10	HSD17B10	11202	0.024	0.042	NO
39	ADAM10	ADAM10	ADAM10	11393	0.022	0.036	NO
40	NCSTN	NCSTN	NCSTN	11442	0.021	0.035	NO
41	LRP1	LRP1	LRP1	11540	0.02	0.032	NO
42	NDUFB9	NDUFB9	NDUFB9	11733	0.018	0.025	NO
43	NDUFB1	NDUFB1	NDUFB1	11774	0.017	0.024	NO
44	PLCB3	PLCB3	PLCB3	11921	0.015	0.019	NO
45	ATP5H	ATP5H	ATP5H	11966	0.015	0.018	NO
46	NDUFV1	NDUFV1	NDUFV1	11985	0.014	0.018	NO
47	ATP5A1	ATP5A1	ATP5A1	12246	0.011	0.0071	NO
48	NDUFB3	NDUFB3	NDUFB3	12390	0.0089	0.0014	NO
49	PSEN1	PSEN1	PSEN1	12477	0.0076	-0.0019	NO
50	IDE	IDE	IDE	12546	0.0067	-0.0044	NO
51	NDUFAB1	NDUFAB1	NDUFAB1	12567	0.0064	-0.0049	NO
52	PPP3CA	PPP3CA	PPP3CA	12664	0.0052	-0.0088	NO
53	CYCS	CYCS	CYCS	12681	0.005	-0.0091	NO
54	COX8A	COX8A	COX8A	12827	0.0031	-0.015	NO
55	NDUFA10	NDUFA10	NDUFA10	12875	0.0024	-0.017	NO
56	BID	BID	BID	13111	-0.001	-0.028	NO
57	ATP5G3	ATP5G3	ATP5G3	13147	-0.0015	-0.029	NO
58	CALM1	CALM1	CALM1	13187	-0.0023	-0.031	NO
59	BAD	BAD	BAD	13244	-0.0032	-0.033	NO
60	SDHA	SDHA	SDHA	13328	-0.0044	-0.036	NO
61	NDUFS1	NDUFS1	NDUFS1	13361	-0.0048	-0.037	NO
62	COX4I1	COX4I1	COX4I1	13503	-0.0069	-0.043	NO
63	NDUFS4	NDUFS4	NDUFS4	13618	-0.0084	-0.048	NO
64	UQCRH	UQCRH	UQCRH	13639	-0.0088	-0.048	NO
65	COX5B	COX5B	COX5B	13650	-0.0088	-0.048	NO
66	NDUFA8	NDUFA8	NDUFA8	13655	-0.0089	-0.047	NO
67	NDUFA9	NDUFA9	NDUFA9	13671	-0.0091	-0.047	NO
68	PLCB1	PLCB1	PLCB1	13677	-0.0091	-0.047	NO
69	UQCRHL	UQCRHL	UQCRHL	13753	-0.01	-0.05	NO
70	COX6A1	COX6A1	COX6A1	13813	-0.011	-0.051	NO
71	NDUFS7	NDUFS7	NDUFS7	13922	-0.013	-0.055	NO
72	ATP5E	ATP5E	ATP5E	13926	-0.013	-0.054	NO
73	EIF2AK3	EIF2AK3	EIF2AK3	13993	-0.014	-0.056	NO
74	ATP5B	ATP5B	ATP5B	14073	-0.015	-0.059	NO
75	ATF6	ATF6	ATF6	14085	-0.015	-0.058	NO
76	UQCRC1	UQCRC1	UQCRC1	14125	-0.016	-0.059	NO
77	NDUFB7	NDUFB7	NDUFB7	14162	-0.016	-0.059	NO
78	FAS	FAS	FAS	14169	-0.016	-0.059	NO
79	ATP5C1	ATP5C1	ATP5C1	14180	-0.017	-0.058	NO
80	NDUFC1	NDUFC1	NDUFC1	14183	-0.017	-0.057	NO
81	CYC1	CYC1	CYC1	14222	-0.017	-0.057	NO
82	NDUFA6	NDUFA6	NDUFA6	14320	-0.019	-0.06	NO
83	CASP3	CASP3	CASP3	14358	-0.019	-0.061	NO
84	ITPR2	ITPR2	ITPR2	14414	-0.02	-0.062	NO
85	COX7B	COX7B	COX7B	14442	-0.021	-0.062	NO
86	COX7A2L	COX7A2L	COX7A2L	14453	-0.021	-0.06	NO
87	ATP5D	ATP5D	ATP5D	14512	-0.022	-0.062	NO
88	NDUFB10	NDUFB10	NDUFB10	14519	-0.022	-0.06	NO
89	NDUFS3	NDUFS3	NDUFS3	14573	-0.023	-0.061	NO
90	SDHC	SDHC	SDHC	14579	-0.023	-0.06	NO
91	SDHD	SDHD	SDHD	14679	-0.025	-0.062	NO
92	IL1B	IL1B	IL1B	14682	-0.025	-0.061	NO
93	NDUFA1	NDUFA1	NDUFA1	14692	-0.025	-0.06	NO
94	ATP5F1	ATP5F1	ATP5F1	14705	-0.025	-0.058	NO
95	NDUFB8	NDUFB8	NDUFB8	14751	-0.026	-0.058	NO
96	COX7A2	COX7A2	COX7A2	14757	-0.026	-0.057	NO
97	UQCR10	UQCR10	UQCR10	14785	-0.027	-0.056	NO
98	NDUFB6	NDUFB6	NDUFB6	14844	-0.028	-0.057	NO
99	ATP5G2	ATP5G2	ATP5G2	14849	-0.028	-0.055	NO
100	SDHB	SDHB	SDHB	15053	-0.032	-0.062	NO
101	UQCR11	UQCR11	UQCR11	15062	-0.032	-0.06	NO
102	UQCRC2	UQCRC2	UQCRC2	15095	-0.032	-0.059	NO
103	NDUFS2	NDUFS2	NDUFS2	15131	-0.033	-0.059	NO
104	CALM2	CALM2	CALM2	15144	-0.033	-0.057	NO
105	UQCRB	UQCRB	UQCRB	15186	-0.034	-0.056	NO
106	ATP5J	ATP5J	ATP5J	15234	-0.035	-0.056	NO
107	COX6B1	COX6B1	COX6B1	15273	-0.036	-0.055	NO
108	CDK5	CDK5	CDK5	15310	-0.036	-0.054	NO
109	PSENEN	PSENEN	PSENEN	15345	-0.037	-0.053	NO
110	NDUFV3	NDUFV3	NDUFV3	15365	-0.038	-0.052	NO
111	GNAQ	GNAQ	GNAQ	15539	-0.041	-0.056	NO
112	NDUFB2	NDUFB2	NDUFB2	15561	-0.041	-0.055	NO
113	NDUFA5	NDUFA5	NDUFA5	15672	-0.044	-0.056	NO
114	CASP9	CASP9	CASP9	15723	-0.045	-0.056	NO
115	NDUFV2	NDUFV2	NDUFV2	15737	-0.045	-0.053	NO
116	APH1A	APH1A	APH1A	15830	-0.047	-0.054	NO
117	CACNA1S	CACNA1S	CACNA1S	15923	-0.049	-0.055	NO
118	COX5A	COX5A	COX5A	16028	-0.051	-0.056	NO
119	GRIN2C	GRIN2C	GRIN2C	16179	-0.055	-0.059	NO
120	CASP7	CASP7	CASP7	16188	-0.055	-0.055	NO
121	COX7C	COX7C	COX7C	16251	-0.057	-0.054	NO
122	ATP5G1	ATP5G1	ATP5G1	16337	-0.058	-0.054	NO
123	NDUFA4	NDUFA4	NDUFA4	16364	-0.059	-0.051	NO
124	COX6A2	COX6A2	COX6A2	16397	-0.06	-0.048	NO
125	UQCRQ	UQCRQ	UQCRQ	16438	-0.061	-0.046	NO
126	UQCRFS1	UQCRFS1	UQCRFS1	16448	-0.061	-0.042	NO
127	CHP2	CHP2	CHP2	16635	-0.066	-0.046	NO
128	CASP8	CASP8	CASP8	16636	-0.066	-0.041	NO
129	NDUFA2	NDUFA2	NDUFA2	16730	-0.068	-0.041	NO
130	NDUFA7	NDUFA7	NDUFA7	16918	-0.073	-0.044	NO
131	APBB1	APBB1	APBB1	17347	-0.087	-0.057	NO
132	PPP3R2	PPP3R2	PPP3R2	17392	-0.088	-0.053	NO
133	GRIN1	GRIN1	GRIN1	17425	-0.089	-0.048	NO
134	ERN1	ERN1	ERN1	17488	-0.091	-0.045	NO
135	PSEN2	PSEN2	PSEN2	17662	-0.097	-0.046	NO
136	ITPR1	ITPR1	ITPR1	17665	-0.097	-0.039	NO
137	MAPK3	MAPK3	MAPK3	17731	-0.1	-0.035	NO
138	NDUFA3	NDUFA3	NDUFA3	17862	-0.1	-0.034	NO
139	APAF1	APAF1	APAF1	18289	-0.12	-0.044	NO
140	CACNA1F	CACNA1F	CACNA1F	18304	-0.12	-0.036	NO
141	CALM3	CALM3	CALM3	18518	-0.13	-0.037	NO
142	COX7A1	COX7A1	COX7A1	18595	-0.14	-0.031	NO
143	COX4I2	COX4I2	COX4I2	18910	-0.15	-0.034	NO
144	APOE	APOE	APOE	19344	-0.18	-0.041	NO
145	BACE2	BACE2	BACE2	19586	-0.19	-0.039	NO
146	CACNA1C	CACNA1C	CACNA1C	19672	-0.19	-0.03	NO
147	LPL	LPL	LPL	19877	-0.21	-0.025	NO
148	GRIN2D	GRIN2D	GRIN2D	20312	-0.24	-0.028	NO
149	PLCB2	PLCB2	PLCB2	20372	-0.24	-0.014	NO
150	GRIN2A	GRIN2A	GRIN2A	20401	-0.24	0.0017	NO
151	GRIN2B	GRIN2B	GRIN2B	20409	-0.24	0.018	NO
152	PLCB4	PLCB4	PLCB4	21287	-0.33	0.0019	NO
153	ATP2A3	ATP2A3	ATP2A3	21705	-0.39	0.01	NO
154	CACNA1D	CACNA1D	CACNA1D	22263	-0.52	0.022	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 SPLICEOSOME.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPLICEOSOME, 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 NUCLEOTIDE EXCISION REPAIR

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	CALML3	CALML3	CALML3	2	1.7	0.13	YES
2	CALML5	CALML5	CALML5	54	1.2	0.23	YES
3	FBXO43	FBXO43	FBXO43	669	0.52	0.24	YES
4	CALML6	CALML6	CALML6	1907	0.28	0.21	YES
5	CAMK2B	CAMK2B	CAMK2B	2105	0.26	0.22	YES
6	IGF1R	IGF1R	IGF1R	2216	0.25	0.23	YES
7	ADCY8	ADCY8	ADCY8	2681	0.22	0.23	YES
8	CAMK2A	CAMK2A	CAMK2A	2863	0.2	0.24	YES
9	ESPL1	ESPL1	ESPL1	3083	0.19	0.24	YES
10	SPDYA	SPDYA	SPDYA	3226	0.18	0.25	YES
11	ANAPC1	ANAPC1	ANAPC1	3293	0.18	0.26	YES
12	SMC1B	SMC1B	SMC1B	3539	0.17	0.26	YES
13	MAPK12	MAPK12	MAPK12	3695	0.16	0.27	YES
14	PKMYT1	PKMYT1	PKMYT1	3900	0.16	0.27	YES
15	PRKX	PRKX	PRKX	3976	0.15	0.28	YES
16	PTTG1	PTTG1	PTTG1	4028	0.15	0.29	YES
17	CCNE2	CCNE2	CCNE2	4086	0.15	0.3	YES
18	PPP1CB	PPP1CB	PPP1CB	4244	0.14	0.3	YES
19	YWHAQ	YWHAQ	YWHAQ	4437	0.14	0.31	YES
20	ANAPC7	ANAPC7	ANAPC7	4749	0.13	0.3	YES
21	ADCY7	ADCY7	ADCY7	4750	0.13	0.31	YES
22	CCNB2	CCNB2	CCNB2	4784	0.13	0.32	YES
23	MAD2L2	MAD2L2	MAD2L2	4804	0.12	0.33	YES
24	CDK1	CDK1	CDK1	5271	0.11	0.32	YES
25	CDC20	CDC20	CDC20	5323	0.11	0.32	YES
26	MAD2L1	MAD2L1	MAD2L1	5493	0.11	0.32	YES
27	CCNB1	CCNB1	CCNB1	5709	0.1	0.32	YES
28	YWHAZ	YWHAZ	YWHAZ	5772	0.1	0.33	YES
29	SLK	SLK	SLK	5975	0.098	0.33	YES
30	YWHAG	YWHAG	YWHAG	5977	0.098	0.34	YES
31	BTRC	BTRC	BTRC	6020	0.097	0.34	YES
32	RBX1	RBX1	RBX1	6095	0.095	0.34	YES
33	PPP2R5E	PPP2R5E	PPP2R5E	6160	0.094	0.35	YES
34	MAP2K1	MAP2K1	MAP2K1	6407	0.09	0.34	NO
35	YWHAE	YWHAE	YWHAE	6932	0.08	0.33	NO
36	CDC27	CDC27	CDC27	7555	0.071	0.31	NO
37	BUB1	BUB1	BUB1	7717	0.069	0.3	NO
38	MAPK1	MAPK1	MAPK1	7770	0.068	0.31	NO
39	SMC3	SMC3	SMC3	7936	0.065	0.3	NO
40	ANAPC11	ANAPC11	ANAPC11	7956	0.065	0.31	NO
41	ITPR3	ITPR3	ITPR3	8002	0.064	0.31	NO
42	CDC23	CDC23	CDC23	8027	0.064	0.32	NO
43	ANAPC2	ANAPC2	ANAPC2	8040	0.064	0.32	NO
44	FBXO5	FBXO5	FBXO5	8108	0.063	0.32	NO
45	PLK1	PLK1	PLK1	8144	0.062	0.33	NO
46	PPP2R5C	PPP2R5C	PPP2R5C	8635	0.055	0.31	NO
47	CUL1	CUL1	CUL1	9046	0.05	0.29	NO
48	RPS6KA6	RPS6KA6	RPS6KA6	9240	0.047	0.29	NO
49	CAMK2D	CAMK2D	CAMK2D	9574	0.044	0.28	NO
50	CCNE1	CCNE1	CCNE1	9705	0.042	0.28	NO
51	PPP3R1	PPP3R1	PPP3R1	9809	0.041	0.27	NO
52	ANAPC10	ANAPC10	ANAPC10	10031	0.038	0.27	NO
53	CDK2	CDK2	CDK2	10039	0.038	0.27	NO
54	CDC25C	CDC25C	CDC25C	10171	0.036	0.27	NO
55	PPP2R5A	PPP2R5A	PPP2R5A	10231	0.036	0.27	NO
56	PPP2R5B	PPP2R5B	PPP2R5B	10353	0.034	0.26	NO
57	PPP3CC	PPP3CC	PPP3CC	10421	0.034	0.26	NO
58	ANAPC4	ANAPC4	ANAPC4	10460	0.033	0.26	NO
59	ANAPC5	ANAPC5	ANAPC5	10508	0.033	0.27	NO
60	ANAPC13	ANAPC13	ANAPC13	10975	0.027	0.25	NO
61	PPP2R5D	PPP2R5D	PPP2R5D	11045	0.026	0.25	NO
62	PPP3CB	PPP3CB	PPP3CB	11099	0.025	0.25	NO
63	SKP1	SKP1	SKP1	11292	0.023	0.24	NO
64	PPP2CB	PPP2CB	PPP2CB	11463	0.021	0.23	NO
65	SMC1A	SMC1A	SMC1A	11606	0.019	0.23	NO
66	FBXW11	FBXW11	FBXW11	11766	0.017	0.22	NO
67	PRKACA	PRKACA	PRKACA	12035	0.014	0.21	NO
68	PPP1CA	PPP1CA	PPP1CA	12125	0.012	0.21	NO
69	PPP2R1A	PPP2R1A	PPP2R1A	12126	0.012	0.21	NO
70	SGOL1	SGOL1	SGOL1	12200	0.011	0.21	NO
71	PRKACB	PRKACB	PRKACB	12494	0.0074	0.2	NO
72	PPP1CC	PPP1CC	PPP1CC	12532	0.007	0.19	NO
73	AURKA	AURKA	AURKA	12639	0.0054	0.19	NO
74	PPP3CA	PPP3CA	PPP3CA	12664	0.0052	0.19	NO
75	YWHAB	YWHAB	YWHAB	12918	0.0018	0.18	NO
76	CALM1	CALM1	CALM1	13187	-0.0023	0.17	NO
77	PPP2R1B	PPP2R1B	PPP2R1B	13365	-0.0048	0.16	NO
78	CDC16	CDC16	CDC16	13760	-0.01	0.14	NO
79	CAMK2G	CAMK2G	CAMK2G	13874	-0.012	0.14	NO
80	ADCY9	ADCY9	ADCY9	13965	-0.014	0.14	NO
81	ADCY1	ADCY1	ADCY1	13984	-0.014	0.14	NO
82	STAG3	STAG3	STAG3	14104	-0.016	0.13	NO
83	ITPR2	ITPR2	ITPR2	14414	-0.02	0.12	NO
84	PLCZ1	PLCZ1	PLCZ1	14624	-0.024	0.11	NO
85	CALM2	CALM2	CALM2	15144	-0.033	0.092	NO
86	YWHAH	YWHAH	YWHAH	15264	-0.036	0.09	NO
87	RPS6KA1	RPS6KA1	RPS6KA1	15652	-0.043	0.076	NO
88	RPS6KA3	RPS6KA3	RPS6KA3	16182	-0.055	0.057	NO
89	CDC26	CDC26	CDC26	16542	-0.063	0.046	NO
90	CHP2	CHP2	CHP2	16635	-0.066	0.047	NO
91	CPEB1	CPEB1	CPEB1	16811	-0.07	0.044	NO
92	PPP3R2	PPP3R2	PPP3R2	17392	-0.088	0.026	NO
93	ITPR1	ITPR1	ITPR1	17665	-0.097	0.021	NO
94	MAPK3	MAPK3	MAPK3	17731	-0.1	0.026	NO
95	AR	AR	AR	18186	-0.12	0.015	NO
96	ADCY2	ADCY2	ADCY2	18189	-0.12	0.024	NO
97	RPS6KA2	RPS6KA2	RPS6KA2	18373	-0.13	0.026	NO
98	CALM3	CALM3	CALM3	18518	-0.13	0.03	NO
99	SPDYC	SPDYC	SPDYC	18857	-0.15	0.027	NO
100	REC8	REC8	REC8	19260	-0.17	0.022	NO
101	ADCY5	ADCY5	ADCY5	19568	-0.19	0.023	NO
102	PTTG2	PTTG2	PTTG2	19761	-0.2	0.03	NO
103	PGR	PGR	PGR	19784	-0.2	0.045	NO
104	ADCY4	ADCY4	ADCY4	19804	-0.2	0.06	NO
105	ADCY6	ADCY6	ADCY6	19810	-0.2	0.075	NO
106	IGF1	IGF1	IGF1	20335	-0.24	0.071	NO
107	PRKACG	PRKACG	PRKACG	22028	-0.46	0.032	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 NUCLEOTIDE EXCISION REPAIR.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NUCLEOTIDE 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 CELL CYCLE

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	CALML3	CALML3	CALML3	2	1.7	0.16	YES
2	CALML5	CALML5	CALML5	54	1.2	0.26	YES
3	EGF	EGF	EGF	622	0.54	0.29	YES
4	TGFA	TGFA	TGFA	1345	0.35	0.29	YES
5	EGFR	EGFR	EGFR	1446	0.34	0.32	YES
6	CALML6	CALML6	CALML6	1907	0.28	0.32	YES
7	CAMK2B	CAMK2B	CAMK2B	2105	0.26	0.34	YES
8	HRAS	HRAS	HRAS	2188	0.25	0.35	YES
9	IGF1R	IGF1R	IGF1R	2216	0.25	0.38	YES
10	CAMK2A	CAMK2A	CAMK2A	2863	0.2	0.37	NO
11	CCND1	CCND1	CCND1	3329	0.18	0.36	NO
12	PIK3CA	PIK3CA	PIK3CA	3545	0.17	0.37	NO
13	PIK3CD	PIK3CD	PIK3CD	4361	0.14	0.34	NO
14	SHC3	SHC3	SHC3	4815	0.12	0.34	NO
15	CDK6	CDK6	CDK6	4820	0.12	0.35	NO
16	E2F2	E2F2	E2F2	4881	0.12	0.36	NO
17	CDKN1A	CDKN1A	CDKN1A	5453	0.11	0.34	NO
18	SOS2	SOS2	SOS2	6141	0.094	0.32	NO
19	BRAF	BRAF	BRAF	6211	0.093	0.32	NO
20	SHC1	SHC1	SHC1	6285	0.092	0.33	NO
21	MAP2K1	MAP2K1	MAP2K1	6407	0.09	0.33	NO
22	AKT3	AKT3	AKT3	6785	0.083	0.32	NO
23	NRAS	NRAS	NRAS	7613	0.07	0.29	NO
24	PLCG1	PLCG1	PLCG1	7619	0.07	0.3	NO
25	MAPK1	MAPK1	MAPK1	7770	0.068	0.3	NO
26	RB1	RB1	RB1	8284	0.06	0.28	NO
27	SHC4	SHC4	SHC4	8337	0.06	0.28	NO
28	MTOR	MTOR	MTOR	8574	0.056	0.28	NO
29	E2F3	E2F3	E2F3	8663	0.055	0.28	NO
30	CAMK2D	CAMK2D	CAMK2D	9574	0.044	0.24	NO
31	MAP2K2	MAP2K2	MAP2K2	9646	0.043	0.24	NO
32	SOS1	SOS1	SOS1	9716	0.042	0.25	NO
33	RAF1	RAF1	RAF1	10265	0.035	0.22	NO
34	AKT2	AKT2	AKT2	10312	0.035	0.23	NO
35	AKT1	AKT1	AKT1	10537	0.032	0.22	NO
36	MDM2	MDM2	MDM2	10847	0.029	0.21	NO
37	CDK4	CDK4	CDK4	11233	0.024	0.19	NO
38	PDGFB	PDGFB	PDGFB	11388	0.022	0.19	NO
39	PTEN	PTEN	PTEN	11999	0.014	0.16	NO
40	PIK3CB	PIK3CB	PIK3CB	12185	0.012	0.16	NO
41	KRAS	KRAS	KRAS	12510	0.0072	0.14	NO
42	CALM1	CALM1	CALM1	13187	-0.0023	0.11	NO
43	CAMK2G	CAMK2G	CAMK2G	13874	-0.012	0.083	NO
44	TP53	TP53	TP53	14055	-0.015	0.077	NO
45	GRB2	GRB2	GRB2	14210	-0.017	0.071	NO
46	PLCG2	PLCG2	PLCG2	14832	-0.028	0.046	NO
47	CALM2	CALM2	CALM2	15144	-0.033	0.036	NO
48	PIK3R2	PIK3R2	PIK3R2	15734	-0.045	0.014	NO
49	ARAF	ARAF	ARAF	15977	-0.05	0.0078	NO
50	PDGFRB	PDGFRB	PDGFRB	17122	-0.08	-0.035	NO
51	PIK3R1	PIK3R1	PIK3R1	17213	-0.082	-0.032	NO
52	PIK3R3	PIK3R3	PIK3R3	17227	-0.083	-0.025	NO
53	PDGFRA	PDGFRA	PDGFRA	17472	-0.091	-0.027	NO
54	MAPK3	MAPK3	MAPK3	17731	-0.1	-0.03	NO
55	PDGFA	PDGFA	PDGFA	17743	-0.1	-0.021	NO
56	CDKN2A	CDKN2A	CDKN2A	18407	-0.13	-0.039	NO
57	CALM3	CALM3	CALM3	18518	-0.13	-0.031	NO
58	PRKCA	PRKCA	PRKCA	20086	-0.22	-0.08	NO
59	IGF1	IGF1	IGF1	20335	-0.24	-0.07	NO
60	PIK3R5	PIK3R5	PIK3R5	20392	-0.24	-0.05	NO
61	SHC2	SHC2	SHC2	20560	-0.26	-0.034	NO
62	PRKCB	PRKCB	PRKCB	21511	-0.36	-0.044	NO
63	PIK3CG	PIK3CG	PIK3CG	21847	-0.42	-0.021	NO
64	PRKCG	PRKCG	PRKCG	22528	-0.67	0.0097	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 CELL CYCLE.

Figure S40. 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

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 NO1 PATHWAY	29	genes.ES.table	0.46	1.4	0.13	0.24	0.88	0.38	0.23	0.29	0.18	0.005
BIOCARTA AGR PATHWAY	35	genes.ES.table	0.42	1.4	0.13	0.24	0.88	0.17	0.077	0.16	0.18	0.005
BIOCARTA ALK PATHWAY	35	genes.ES.table	0.43	1.4	0.11	0.23	0.86	0.49	0.31	0.34	0.17	0.006
BIOCARTA AT1R PATHWAY	31	genes.ES.table	0.47	1.8	0.0079	0.094	0.26	0.097	0.08	0.089	0	0.015
BIOCARTA BCR PATHWAY	33	genes.ES.table	0.6	1.9	0.01	0.088	0.22	0.21	0.14	0.18	0	0.014
BIOCARTA BIOPEPTIDES PATHWAY	41	genes.ES.table	0.52	1.9	0.008	0.14	0.21	0.2	0.15	0.16	0	0.038
BIOCARTA HDAC PATHWAY	25	genes.ES.table	0.63	2	0	0.16	0.071	0.52	0.3	0.37	0	0.057
BIOCARTA FCER1 PATHWAY	37	genes.ES.table	0.55	1.8	0.0062	0.095	0.28	0.27	0.21	0.21	0	0.013
BIOCARTA GH PATHWAY	26	genes.ES.table	0.61	1.9	0	0.097	0.22	0.19	0.071	0.18	0	0.017
BIOCARTA IL2RB PATHWAY	37	genes.ES.table	0.45	1.4	0.16	0.21	0.84	0.3	0.23	0.23	0.15	0.008

genes ES table in pathway: BIOCARTA NO1 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	IGF1	IGF1	IGF1	157	0.68	0.26	YES
2	PIK3CG	PIK3CG	PIK3CG	1625	0.35	0.33	YES
3	NFATC2	NFATC2	NFATC2	3123	0.22	0.35	YES
4	CAMK1G	CAMK1G	CAMK1G	3423	0.2	0.41	YES
5	CAMK1	CAMK1	CAMK1	3466	0.19	0.49	YES
6	NFATC1	NFATC1	NFATC1	4427	0.14	0.5	YES
7	PIK3R1	PIK3R1	PIK3R1	4826	0.12	0.53	YES
8	PPP3CC	PPP3CC	PPP3CC	5549	0.095	0.54	YES
9	MEF2D	MEF2D	MEF2D	5873	0.084	0.56	YES
10	MEF2A	MEF2A	MEF2A	6155	0.075	0.57	YES
11	INSR	INSR	INSR	6303	0.071	0.59	YES
12	HDAC5	HDAC5	HDAC5	6313	0.071	0.62	YES
13	PPP3CB	PPP3CB	PPP3CB	6710	0.059	0.63	YES
14	CALM3	CALM3	CALM3	8654	0.016	0.55	NO
15	CALM1	CALM1	CALM1	8754	0.015	0.55	NO
16	CABIN1	CABIN1	CABIN1	9336	0.0059	0.52	NO
17	PPP3CA	PPP3CA	PPP3CA	9377	0.0053	0.52	NO
18	YWHAH	YWHAH	YWHAH	9934	-0.0022	0.5	NO
19	IGF1R	IGF1R	IGF1R	10097	-0.0044	0.5	NO
20	PIK3CA	PIK3CA	PIK3CA	10523	-0.0096	0.48	NO
21	CALM2	CALM2	CALM2	11066	-0.016	0.46	NO
22	MAPK7	MAPK7	MAPK7	11328	-0.019	0.46	NO
23	AKT1	AKT1	AKT1	11984	-0.027	0.44	NO
24	MAPK14	MAPK14	MAPK14	12589	-0.033	0.43	NO
25	MAP2K6	MAP2K6	MAP2K6	14163	-0.05	0.38	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 NO1 PATHWAY.

Figure S42. 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 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	VIPR2	VIPR2	VIPR2	8	0.88	0.33	YES
2	PRKAR2B	PRKAR2B	PRKAR2B	1436	0.37	0.4	YES
3	NFATC2	NFATC2	NFATC2	3123	0.22	0.41	YES
4	EGR2	EGR2	EGR2	3279	0.21	0.48	YES
5	PRKACB	PRKACB	PRKACB	4212	0.15	0.5	YES
6	EGR3	EGR3	EGR3	4386	0.14	0.54	YES
7	NFATC1	NFATC1	NFATC1	4427	0.14	0.59	YES
8	PPP3CC	PPP3CC	PPP3CC	5549	0.095	0.58	NO
9	PPP3CB	PPP3CB	PPP3CB	6710	0.059	0.55	NO
10	PLCG1	PLCG1	PLCG1	8325	0.022	0.49	NO
11	PRKAR2A	PRKAR2A	PRKAR2A	8385	0.021	0.49	NO
12	GNAQ	GNAQ	GNAQ	8620	0.017	0.49	NO
13	CALM3	CALM3	CALM3	8654	0.016	0.49	NO
14	CALM1	CALM1	CALM1	8754	0.015	0.5	NO
15	PRKAR1A	PRKAR1A	PRKAR1A	9298	0.0064	0.47	NO
16	PPP3CA	PPP3CA	PPP3CA	9377	0.0053	0.47	NO
17	PRKACG	PRKACG	PRKACG	9382	0.0052	0.47	NO
18	NFKBIA	NFKBIA	NFKBIA	10107	-0.0046	0.44	NO
19	CALM2	CALM2	CALM2	11066	-0.016	0.41	NO
20	MAP3K1	MAP3K1	MAP3K1	11198	-0.018	0.41	NO
21	NFKB1	NFKB1	NFKB1	12213	-0.029	0.37	NO
22	RELA	RELA	RELA	12279	-0.03	0.38	NO
23	PRKAR1B	PRKAR1B	PRKAR1B	13615	-0.044	0.34	NO
24	CHUK	CHUK	CHUK	16409	-0.075	0.24	NO
25	MYC	MYC	MYC	17484	-0.09	0.23	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 AGR PATHWAY.

Figure S44. 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 ALK 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	HAND2	HAND2	HAND2	14	0.86	0.12	YES
2	IGF1	IGF1	IGF1	157	0.68	0.21	YES
3	PRKAR2B	PRKAR2B	PRKAR2B	1436	0.37	0.2	YES
4	MYH2	MYH2	MYH2	1516	0.36	0.25	YES
5	PIK3CG	PIK3CG	PIK3CG	1625	0.35	0.3	YES
6	FGF2	FGF2	FGF2	1648	0.35	0.34	YES
7	CAMK4	CAMK4	CAMK4	1690	0.34	0.39	YES
8	ACTA1	ACTA1	ACTA1	1751	0.34	0.43	YES
9	AGT	AGT	AGT	1828	0.33	0.48	YES
10	CTF1	CTF1	CTF1	2239	0.29	0.5	YES
11	NFATC4	NFATC4	NFATC4	2403	0.27	0.53	YES
12	NFATC2	NFATC2	NFATC2	3123	0.22	0.53	YES
13	CAMK1G	CAMK1G	CAMK1G	3423	0.2	0.54	YES
14	CAMK1	CAMK1	CAMK1	3466	0.19	0.57	YES
15	PRKACB	PRKACB	PRKACB	4212	0.15	0.56	YES
16	GATA4	GATA4	GATA4	4245	0.15	0.57	YES
17	NFATC1	NFATC1	NFATC1	4427	0.14	0.59	YES
18	PIK3R1	PIK3R1	PIK3R1	4826	0.12	0.59	NO
19	HAND1	HAND1	HAND1	5484	0.097	0.57	NO
20	PPP3CC	PPP3CC	PPP3CC	5549	0.095	0.58	NO
21	EDN1	EDN1	EDN1	6444	0.067	0.55	NO
22	PPP3CB	PPP3CB	PPP3CB	6710	0.059	0.55	NO
23	NKX2-5	NKX2-5	NKX2-5	8016	0.028	0.49	NO
24	PRKAR2A	PRKAR2A	PRKAR2A	8385	0.021	0.48	NO
25	CALM3	CALM3	CALM3	8654	0.016	0.47	NO
26	CALM1	CALM1	CALM1	8754	0.015	0.47	NO
27	CREBBP	CREBBP	CREBBP	8784	0.014	0.47	NO
28	PRKAR1A	PRKAR1A	PRKAR1A	9298	0.0064	0.45	NO
29	ELSPBP1	ELSPBP1	ELSPBP1	9317	0.0062	0.45	NO
30	PPP3CA	PPP3CA	PPP3CA	9377	0.0053	0.45	NO
31	PRKACG	PRKACG	PRKACG	9382	0.0052	0.45	NO
32	PIK3CA	PIK3CA	PIK3CA	10523	-0.0096	0.4	NO
33	LIF	LIF	LIF	10709	-0.012	0.39	NO
34	CALM2	CALM2	CALM2	11066	-0.016	0.38	NO
35	RAF1	RAF1	RAF1	11617	-0.022	0.36	NO
36	NFATC3	NFATC3	NFATC3	11826	-0.025	0.35	NO
37	FKBP1A	FKBP1A	FKBP1A	11875	-0.025	0.35	NO
38	AKT1	AKT1	AKT1	11984	-0.027	0.35	NO
39	MAPK1	MAPK1	MAPK1	12386	-0.031	0.34	NO
40	MAPK14	MAPK14	MAPK14	12589	-0.033	0.33	NO
41	F2	F2	F2	12667	-0.034	0.34	NO
42	MAPK3	MAPK3	MAPK3	12775	-0.035	0.34	NO
43	PRKAR1B	PRKAR1B	PRKAR1B	13615	-0.044	0.3	NO
44	RPS6KB1	RPS6KB1	RPS6KB1	13740	-0.046	0.31	NO
45	CALR	CALR	CALR	13888	-0.048	0.31	NO
46	MAPK8	MAPK8	MAPK8	14881	-0.057	0.27	NO
47	CSNK1A1	CSNK1A1	CSNK1A1	15324	-0.062	0.26	NO
48	MAP2K1	MAP2K1	MAP2K1	15891	-0.069	0.24	NO
49	GSK3B	GSK3B	GSK3B	16271	-0.073	0.24	NO
50	NPPA	NPPA	NPPA	17064	-0.084	0.21	NO
51	HBEGF	HBEGF	HBEGF	19083	-0.12	0.14	NO
52	HRAS	HRAS	HRAS	19689	-0.14	0.14	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 ALK PATHWAY.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ALK 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 AT1R PATHWAY

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	MAPT	MAPT	MAPT	385	0.58	0.12	YES
2	PRKCB	PRKCB	PRKCB	629	0.5	0.22	YES
3	AGTR2	AGTR2	AGTR2	844	0.46	0.31	YES
4	MYLK	MYLK	MYLK	1054	0.42	0.4	YES
5	AGT	AGT	AGT	1828	0.33	0.44	YES
6	CAMK2A	CAMK2A	CAMK2A	2209	0.29	0.49	YES
7	STAT4	STAT4	STAT4	3271	0.21	0.49	YES
8	FYN	FYN	FYN	3502	0.19	0.52	YES
9	STAT5A	STAT5A	STAT5A	5012	0.12	0.48	NO
10	STAT5B	STAT5B	STAT5B	5208	0.11	0.5	NO
11	CAMK2B	CAMK2B	CAMK2B	6182	0.074	0.47	NO
12	PRKCA	PRKCA	PRKCA	6570	0.063	0.47	NO
13	JAK2	JAK2	JAK2	6971	0.053	0.46	NO
14	CAMK2G	CAMK2G	CAMK2G	7257	0.045	0.46	NO
15	GNAI1	GNAI1	GNAI1	7712	0.034	0.45	NO
16	PLCG1	PLCG1	PLCG1	8325	0.022	0.43	NO
17	CALM3	CALM3	CALM3	8654	0.016	0.42	NO
18	CALM1	CALM1	CALM1	8754	0.015	0.41	NO
19	STAT2	STAT2	STAT2	9056	0.01	0.4	NO
20	STAT3	STAT3	STAT3	9858	-0.0014	0.37	NO
21	SOS1	SOS1	SOS1	10099	-0.0044	0.36	NO
22	STAT6	STAT6	STAT6	10843	-0.014	0.33	NO
23	GRB2	GRB2	GRB2	10878	-0.014	0.33	NO
24	CALM2	CALM2	CALM2	11066	-0.016	0.33	NO
25	GNB1	GNB1	GNB1	11352	-0.02	0.32	NO
26	RAF1	RAF1	RAF1	11617	-0.022	0.31	NO
27	STAT1	STAT1	STAT1	11891	-0.026	0.31	NO
28	PTK2B	PTK2B	PTK2B	11922	-0.026	0.31	NO
29	CDK5	CDK5	CDK5	12311	-0.03	0.3	NO
30	MAPK1	MAPK1	MAPK1	12386	-0.031	0.3	NO
31	SHC1	SHC1	SHC1	12436	-0.032	0.31	NO
32	MAPK14	MAPK14	MAPK14	12589	-0.033	0.31	NO
33	F2	F2	F2	12667	-0.034	0.31	NO
34	MAPK3	MAPK3	MAPK3	12775	-0.035	0.32	NO
35	MAP2K2	MAP2K2	MAP2K2	13089	-0.039	0.31	NO
36	CAMK2D	CAMK2D	CAMK2D	13233	-0.04	0.32	NO
37	GNA11	GNA11	GNA11	13235	-0.04	0.32	NO
38	MAPK8	MAPK8	MAPK8	14881	-0.057	0.26	NO
39	MAP2K1	MAP2K1	MAP2K1	15891	-0.069	0.24	NO
40	KNG1	KNG1	KNG1	17822	-0.095	0.17	NO
41	GNGT1	GNGT1	GNGT1	20873	-0.2	0.083	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: BIOCARTA AT1R PATHWAY.

Figure S48. 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 BCR PATHWAY

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	SLC2A4	SLC2A4	SLC2A4	236	0.64	0.065	YES
2	ADIPOQ	ADIPOQ	ADIPOQ	268	0.62	0.14	YES
3	RXRG	RXRG	RXRG	749	0.48	0.17	YES
4	NPY	NPY	NPY	809	0.46	0.22	YES
5	MAPK10	MAPK10	MAPK10	847	0.45	0.28	YES
6	PRKAA2	PRKAA2	PRKAA2	927	0.44	0.33	YES
7	ACSL6	ACSL6	ACSL6	1139	0.41	0.36	YES
8	POMC	POMC	POMC	1993	0.31	0.36	YES
9	CD36	CD36	CD36	2124	0.3	0.39	YES
10	LEPR	LEPR	LEPR	2325	0.28	0.42	YES
11	PRKCQ	PRKCQ	PRKCQ	2442	0.27	0.45	YES
12	CPT1C	CPT1C	CPT1C	2604	0.26	0.47	YES
13	ACACB	ACACB	ACACB	2820	0.24	0.49	YES
14	AKT3	AKT3	AKT3	2880	0.24	0.51	YES
15	IRS4	IRS4	IRS4	3959	0.17	0.48	NO
16	LEP	LEP	LEP	4866	0.12	0.46	NO
17	IRS2	IRS2	IRS2	4993	0.12	0.47	NO
18	AGRP	AGRP	AGRP	5188	0.11	0.47	NO
19	TNFRSF1B	TNFRSF1B	TNFRSF1B	5381	0.1	0.48	NO
20	PRKAG2	PRKAG2	PRKAG2	6026	0.08	0.46	NO
21	IRS1	IRS1	IRS1	6722	0.059	0.43	NO
22	PPARGC1A	PPARGC1A	PPARGC1A	6787	0.058	0.44	NO
23	JAK2	JAK2	JAK2	6971	0.053	0.44	NO
24	SOCS3	SOCS3	SOCS3	8190	0.025	0.38	NO
25	ACSL5	ACSL5	ACSL5	8348	0.022	0.38	NO
26	AKT2	AKT2	AKT2	9058	0.01	0.35	NO
27	PRKAB2	PRKAB2	PRKAB2	9509	0.0034	0.33	NO
28	STAT3	STAT3	STAT3	9858	-0.0014	0.32	NO
29	PRKAB1	PRKAB1	PRKAB1	9876	-0.0016	0.32	NO
30	NFKBIA	NFKBIA	NFKBIA	10107	-0.0046	0.3	NO
31	RXRB	RXRB	RXRB	10121	-0.0047	0.3	NO
32	ACSL4	ACSL4	ACSL4	10260	-0.0064	0.3	NO
33	CPT1A	CPT1A	CPT1A	10321	-0.0071	0.3	NO
34	PTPN11	PTPN11	PTPN11	10453	-0.0087	0.29	NO
35	TRADD	TRADD	TRADD	11099	-0.016	0.27	NO
36	CAMKK2	CAMKK2	CAMKK2	11163	-0.017	0.27	NO
37	TNFRSF1A	TNFRSF1A	TNFRSF1A	11769	-0.024	0.24	NO
38	PRKAG1	PRKAG1	PRKAG1	11866	-0.025	0.24	NO
39	AKT1	AKT1	AKT1	11984	-0.027	0.24	NO
40	NFKB1	NFKB1	NFKB1	12213	-0.029	0.23	NO
41	RELA	RELA	RELA	12279	-0.03	0.23	NO
42	PRKAA1	PRKAA1	PRKAA1	12525	-0.033	0.23	NO
43	IKBKG	IKBKG	IKBKG	12771	-0.035	0.22	NO
44	PCK1	PCK1	PCK1	13305	-0.041	0.2	NO
45	MAPK9	MAPK9	MAPK9	13336	-0.041	0.2	NO
46	PPARA	PPARA	PPARA	13358	-0.042	0.21	NO
47	STK11	STK11	STK11	13492	-0.043	0.21	NO
48	ACSL1	ACSL1	ACSL1	13750	-0.046	0.2	NO
49	G6PC	G6PC	G6PC	14118	-0.05	0.19	NO
50	IKBKB	IKBKB	IKBKB	14255	-0.051	0.19	NO
51	NFKBIE	NFKBIE	NFKBIE	14450	-0.053	0.19	NO
52	RXRA	RXRA	RXRA	14573	-0.054	0.19	NO
53	MTOR	MTOR	MTOR	14765	-0.056	0.19	NO
54	NFKBIB	NFKBIB	NFKBIB	14858	-0.057	0.19	NO
55	MAPK8	MAPK8	MAPK8	14881	-0.057	0.2	NO
56	ADIPOR1	ADIPOR1	ADIPOR1	15292	-0.062	0.19	NO
57	TRAF2	TRAF2	TRAF2	16243	-0.073	0.15	NO
58	CHUK	CHUK	CHUK	16409	-0.075	0.16	NO
59	ADIPOR2	ADIPOR2	ADIPOR2	16420	-0.075	0.16	NO
60	CPT1B	CPT1B	CPT1B	16478	-0.076	0.17	NO
61	CAMKK1	CAMKK1	CAMKK1	17238	-0.086	0.15	NO
62	ACSL3	ACSL3	ACSL3	17628	-0.092	0.14	NO
63	PCK2	PCK2	PCK2	18727	-0.11	0.11	NO
64	TNF	TNF	TNF	19172	-0.12	0.1	NO
65	G6PC2	G6PC2	G6PC2	20049	-0.15	0.08	NO
66	SLC2A1	SLC2A1	SLC2A1	22263	-0.33	0.021	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: BIOCARTA BCR PATHWAY.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BCR 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 BIOPEPTIDES PATHWAY

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	SLC2A4	SLC2A4	SLC2A4	236	0.64	0.18	YES
2	PRKCB	PRKCB	PRKCB	629	0.5	0.3	YES
3	GHR	GHR	GHR	711	0.48	0.44	YES
4	GH1	GH1	GH1	1461	0.37	0.51	YES
5	PIK3CG	PIK3CG	PIK3CG	1625	0.35	0.61	YES
6	PIK3R1	PIK3R1	PIK3R1	4826	0.12	0.5	NO
7	STAT5A	STAT5A	STAT5A	5012	0.12	0.53	NO
8	STAT5B	STAT5B	STAT5B	5208	0.11	0.55	NO
9	INSR	INSR	INSR	6303	0.071	0.52	NO
10	PRKCA	PRKCA	PRKCA	6570	0.063	0.53	NO
11	HNF1A	HNF1A	HNF1A	6594	0.063	0.55	NO
12	IRS1	IRS1	IRS1	6722	0.059	0.56	NO
13	SRF	SRF	SRF	6774	0.058	0.57	NO
14	JAK2	JAK2	JAK2	6971	0.053	0.58	NO
15	PLCG1	PLCG1	PLCG1	8325	0.022	0.53	NO
16	SOCS1	SOCS1	SOCS1	8522	0.019	0.52	NO
17	PTPN6	PTPN6	PTPN6	8985	0.011	0.51	NO
18	SOS1	SOS1	SOS1	10099	-0.0044	0.46	NO
19	PIK3CA	PIK3CA	PIK3CA	10523	-0.0096	0.44	NO
20	GRB2	GRB2	GRB2	10878	-0.014	0.43	NO
21	RAF1	RAF1	RAF1	11617	-0.022	0.41	NO
22	MAPK1	MAPK1	MAPK1	12386	-0.031	0.38	NO
23	SHC1	SHC1	SHC1	12436	-0.032	0.39	NO
24	MAPK3	MAPK3	MAPK3	12775	-0.035	0.38	NO
25	MAP2K1	MAP2K1	MAP2K1	15891	-0.069	0.27	NO
26	RPS6KA1	RPS6KA1	RPS6KA1	18988	-0.12	0.16	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: BIOCARTA BIOPEPTIDES PATHWAY.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BIOPEPTIDES 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 HDAC PATHWAY

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	CD79B	CD79B	CD79B	331	0.6	0.15	YES
2	CD79A	CD79A	CD79A	623	0.5	0.27	YES
3	PRKCB	PRKCB	PRKCB	629	0.5	0.4	YES
4	BTK	BTK	BTK	1351	0.38	0.47	YES
5	NFATC4	NFATC4	NFATC4	2403	0.27	0.5	YES
6	VAV1	VAV1	VAV1	2622	0.25	0.56	YES
7	NFATC2	NFATC2	NFATC2	3123	0.22	0.6	YES
8	NFATC1	NFATC1	NFATC1	4427	0.14	0.58	NO
9	PPP3CC	PPP3CC	PPP3CC	5549	0.095	0.55	NO
10	PRKCA	PRKCA	PRKCA	6570	0.063	0.52	NO
11	PPP3CB	PPP3CB	PPP3CB	6710	0.059	0.54	NO
12	BLNK	BLNK	BLNK	6957	0.053	0.54	NO
13	JUN	JUN	JUN	7911	0.03	0.5	NO
14	PLCG1	PLCG1	PLCG1	8325	0.022	0.49	NO
15	CALM3	CALM3	CALM3	8654	0.016	0.48	NO
16	CALM1	CALM1	CALM1	8754	0.015	0.48	NO
17	ELK1	ELK1	ELK1	8967	0.012	0.48	NO
18	PPP3CA	PPP3CA	PPP3CA	9377	0.0053	0.46	NO
19	SOS1	SOS1	SOS1	10099	-0.0044	0.43	NO
20	GRB2	GRB2	GRB2	10878	-0.014	0.4	NO
21	CALM2	CALM2	CALM2	11066	-0.016	0.39	NO
22	MAP3K1	MAP3K1	MAP3K1	11198	-0.018	0.39	NO
23	SYK	SYK	SYK	11374	-0.02	0.39	NO
24	RAF1	RAF1	RAF1	11617	-0.022	0.39	NO
25	NFATC3	NFATC3	NFATC3	11826	-0.025	0.38	NO
26	FOS	FOS	FOS	11836	-0.025	0.39	NO
27	SHC1	SHC1	SHC1	12436	-0.032	0.37	NO
28	LYN	LYN	LYN	12559	-0.033	0.38	NO
29	MAPK14	MAPK14	MAPK14	12589	-0.033	0.38	NO
30	MAPK3	MAPK3	MAPK3	12775	-0.035	0.38	NO
31	MAPK8	MAPK8	MAPK8	14881	-0.057	0.31	NO
32	MAP2K1	MAP2K1	MAP2K1	15891	-0.069	0.28	NO
33	RAC1	RAC1	RAC1	16487	-0.076	0.28	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: BIOCARTA HDAC PATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HDAC 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 FCER1 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	AGTR1	AGTR1	AGTR1	33	0.83	0.27	YES
2	PRKCB	PRKCB	PRKCB	629	0.5	0.42	YES
3	AGT	AGT	AGT	1828	0.33	0.47	YES
4	MEF2D	MEF2D	MEF2D	5873	0.084	0.32	NO
5	MEF2A	MEF2A	MEF2A	6155	0.075	0.34	NO
6	PRKCA	PRKCA	PRKCA	6570	0.063	0.34	NO
7	JUN	JUN	JUN	7911	0.03	0.29	NO
8	GNAQ	GNAQ	GNAQ	8620	0.017	0.26	NO
9	CALM3	CALM3	CALM3	8654	0.016	0.27	NO
10	CALM1	CALM1	CALM1	8754	0.015	0.27	NO
11	ELK1	ELK1	ELK1	8967	0.012	0.26	NO
12	ATF2	ATF2	ATF2	9330	0.006	0.25	NO
13	SOS1	SOS1	SOS1	10099	-0.0044	0.22	NO
14	GRB2	GRB2	GRB2	10878	-0.014	0.19	NO
15	CALM2	CALM2	CALM2	11066	-0.016	0.18	NO
16	MAP3K1	MAP3K1	MAP3K1	11198	-0.018	0.18	NO
17	RAF1	RAF1	RAF1	11617	-0.022	0.17	NO
18	PTK2B	PTK2B	PTK2B	11922	-0.026	0.17	NO
19	MAPK1	MAPK1	MAPK1	12386	-0.031	0.16	NO
20	SHC1	SHC1	SHC1	12436	-0.032	0.17	NO
21	MAPK3	MAPK3	MAPK3	12775	-0.035	0.16	NO
22	MAP2K2	MAP2K2	MAP2K2	13089	-0.039	0.16	NO
23	MAPK8	MAPK8	MAPK8	14881	-0.057	0.1	NO
24	MAP2K4	MAP2K4	MAP2K4	15503	-0.064	0.097	NO
25	MAP2K1	MAP2K1	MAP2K1	15891	-0.069	0.1	NO
26	SRC	SRC	SRC	16326	-0.074	0.11	NO
27	RAC1	RAC1	RAC1	16487	-0.076	0.13	NO
28	PTK2	PTK2	PTK2	16833	-0.08	0.14	NO
29	PAK1	PAK1	PAK1	18191	-0.1	0.11	NO
30	EGFR	EGFR	EGFR	19222	-0.12	0.11	NO
31	HRAS	HRAS	HRAS	19689	-0.14	0.14	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: BIOCARTA FCER1 PATHWAY.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 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 GH PATHWAY

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	PRKCB	PRKCB	PRKCB	629	0.5	0.11	YES
2	FCER1A	FCER1A	FCER1A	950	0.44	0.21	YES
3	BTK	BTK	BTK	1351	0.38	0.3	YES
4	PIK3CG	PIK3CG	PIK3CG	1625	0.35	0.38	YES
5	NFATC4	NFATC4	NFATC4	2403	0.27	0.42	YES
6	VAV1	VAV1	VAV1	2622	0.25	0.48	YES
7	NFATC2	NFATC2	NFATC2	3123	0.22	0.52	YES
8	NFATC1	NFATC1	NFATC1	4427	0.14	0.5	YES
9	FCER1G	FCER1G	FCER1G	4653	0.13	0.52	YES
10	PIK3R1	PIK3R1	PIK3R1	4826	0.12	0.55	YES
11	PPP3CC	PPP3CC	PPP3CC	5549	0.095	0.54	NO
12	PPP3CB	PPP3CB	PPP3CB	6710	0.059	0.5	NO
13	JUN	JUN	JUN	7911	0.03	0.46	NO
14	PLCG1	PLCG1	PLCG1	8325	0.022	0.45	NO
15	CALM3	CALM3	CALM3	8654	0.016	0.44	NO
16	CALM1	CALM1	CALM1	8754	0.015	0.44	NO
17	ELK1	ELK1	ELK1	8967	0.012	0.43	NO
18	MAP2K7	MAP2K7	MAP2K7	9224	0.0075	0.42	NO
19	PPP3CA	PPP3CA	PPP3CA	9377	0.0053	0.42	NO
20	SOS1	SOS1	SOS1	10099	-0.0044	0.39	NO
21	PIK3CA	PIK3CA	PIK3CA	10523	-0.0096	0.37	NO
22	GRB2	GRB2	GRB2	10878	-0.014	0.36	NO
23	CALM2	CALM2	CALM2	11066	-0.016	0.36	NO
24	MAP3K1	MAP3K1	MAP3K1	11198	-0.018	0.35	NO
25	SYK	SYK	SYK	11374	-0.02	0.35	NO
26	RAF1	RAF1	RAF1	11617	-0.022	0.35	NO
27	NFATC3	NFATC3	NFATC3	11826	-0.025	0.34	NO
28	FOS	FOS	FOS	11836	-0.025	0.35	NO
29	MAPK1	MAPK1	MAPK1	12386	-0.031	0.34	NO
30	SHC1	SHC1	SHC1	12436	-0.032	0.34	NO
31	LYN	LYN	LYN	12559	-0.033	0.34	NO
32	MAPK3	MAPK3	MAPK3	12775	-0.035	0.34	NO
33	MAPK8	MAPK8	MAPK8	14881	-0.057	0.27	NO
34	MAP2K4	MAP2K4	MAP2K4	15503	-0.064	0.26	NO
35	PAK2	PAK2	PAK2	15768	-0.067	0.26	NO
36	MAP2K1	MAP2K1	MAP2K1	15891	-0.069	0.28	NO
37	PLA2G4A	PLA2G4A	PLA2G4A	17402	-0.089	0.24	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: BIOCARTA GH PATHWAY.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GH 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 IL2RB PATHWAY

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	PRKCB	PRKCB	PRKCB	629	0.5	0.068	YES
2	CD3G	CD3G	CD3G	1385	0.38	0.11	YES
3	TRA@	TRA@	TRA@	1558	0.36	0.17	YES
4	PIK3CG	PIK3CG	PIK3CG	1625	0.35	0.23	YES
5	ZAP70	ZAP70	ZAP70	1970	0.32	0.28	YES
6	CD3D	CD3D	CD3D	2061	0.3	0.33	YES
7	CD247	CD247	CD247	2164	0.29	0.38	YES
8	NFATC4	NFATC4	NFATC4	2403	0.27	0.42	YES
9	VAV1	VAV1	VAV1	2622	0.25	0.46	YES
10	CD3E	CD3E	CD3E	2666	0.25	0.51	YES
11	NFATC2	NFATC2	NFATC2	3123	0.22	0.53	YES
12	LCK	LCK	LCK	3358	0.2	0.56	YES
13	PTPN7	PTPN7	PTPN7	3399	0.2	0.6	YES
14	FYN	FYN	FYN	3502	0.19	0.63	YES
15	NFATC1	NFATC1	NFATC1	4427	0.14	0.61	NO
16	PIK3R1	PIK3R1	PIK3R1	4826	0.12	0.62	NO
17	PPP3CC	PPP3CC	PPP3CC	5549	0.095	0.6	NO
18	PRKCA	PRKCA	PRKCA	6570	0.063	0.57	NO
19	PPP3CB	PPP3CB	PPP3CB	6710	0.059	0.58	NO
20	JUN	JUN	JUN	7911	0.03	0.53	NO
21	LAT	LAT	LAT	8257	0.024	0.52	NO
22	PLCG1	PLCG1	PLCG1	8325	0.022	0.52	NO
23	CALM3	CALM3	CALM3	8654	0.016	0.51	NO
24	CALM1	CALM1	CALM1	8754	0.015	0.51	NO
25	ELK1	ELK1	ELK1	8967	0.012	0.5	NO
26	PPP3CA	PPP3CA	PPP3CA	9377	0.0053	0.48	NO
27	SOS1	SOS1	SOS1	10099	-0.0044	0.45	NO
28	NFKBIA	NFKBIA	NFKBIA	10107	-0.0046	0.45	NO
29	PIK3CA	PIK3CA	PIK3CA	10523	-0.0096	0.44	NO
30	RASA1	RASA1	RASA1	10715	-0.012	0.43	NO
31	GRB2	GRB2	GRB2	10878	-0.014	0.43	NO
32	CALM2	CALM2	CALM2	11066	-0.016	0.42	NO
33	MAP3K1	MAP3K1	MAP3K1	11198	-0.018	0.42	NO
34	RAF1	RAF1	RAF1	11617	-0.022	0.4	NO
35	NFATC3	NFATC3	NFATC3	11826	-0.025	0.4	NO
36	FOS	FOS	FOS	11836	-0.025	0.4	NO
37	NFKB1	NFKB1	NFKB1	12213	-0.029	0.39	NO
38	RELA	RELA	RELA	12279	-0.03	0.4	NO
39	SHC1	SHC1	SHC1	12436	-0.032	0.4	NO
40	MAPK3	MAPK3	MAPK3	12775	-0.035	0.39	NO
41	MAPK8	MAPK8	MAPK8	14881	-0.057	0.31	NO
42	MAP2K4	MAP2K4	MAP2K4	15503	-0.064	0.29	NO
43	MAP2K1	MAP2K1	MAP2K1	15891	-0.069	0.29	NO
44	RAC1	RAC1	RAC1	16487	-0.076	0.28	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: BIOCARTA IL2RB PATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB 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

Methods & Data

Input

Gene set database = c2.cp.v3.0-2.symbols.gmt
Expression data file = STES-TP.mRNAseq_RPKM_log2.txt
Phenotype data file = STES-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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