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

Ovarian Serous Cystadenocarcinoma (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 OV-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1CN730X

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 OV-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: 192
Number of samples: 261
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 ] 102
pheno.type: 2 - 3 :[ clus2 ] 67
pheno.type: 3 - 3 :[ clus3 ] 92

For the expression subtypes of 18555 genes in 262 samples, GSEA found enriched gene sets in each cluster using 261 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA PYK2 PATHWAY

And common core enriched genes are FOS, MAPK11, TNF, CTSK, NFATC1, PPP3CC, VAV1, AKT3, PIK3CD, PIK3CG

clus2

Top enriched gene sets are BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA TOLL PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG FATTY ACID METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG GLUTATHIONE METABOLISM, KEGG SPHINGOLIPID METABOLISM, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

And common core enriched genes are IDH1, IDH2, CASP10, CASP8, TRADD, ABCD1, ACAA1, ACOX1, ACSL5, ACSL6

clus3

Top enriched gene sets are BIOCARTA ALK PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA WNT PATHWAY, KEGG RNA DEGRADATION, KEGG SPLICEOSOME, KEGG CARDIAC MUSCLE CONTRACTION, KEGG WNT SIGNALING PATHWAY

And common core enriched genes are MYH6, MYH7, GLI1, GLI2, LEF1, PTCH1, PTCH2, SHH, SMO, STK36

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 AT1R PATHWAY	32	genes.ES.table	0.37	1.5	0.097	0.15	0.91	0.41	0.28	0.29	0.11	0
BIOCARTA BCR PATHWAY	33	genes.ES.table	0.67	2.1	0	0.052	0.037	0.33	0.12	0.29	0	0.014
BIOCARTA EGF PATHWAY	30	genes.ES.table	0.49	1.7	0.026	0.067	0.55	0.5	0.25	0.38	0.032	0
BIOCARTA FAS PATHWAY	29	genes.ES.table	0.53	1.9	0.004	0.051	0.17	0.38	0.23	0.29	0	0.007
BIOCARTA FCER1 PATHWAY	37	genes.ES.table	0.58	1.8	0.0083	0.046	0.26	0.27	0.12	0.24	0	0.001
BIOCARTA HIVNEF PATHWAY	57	genes.ES.table	0.4	1.8	0.018	0.06	0.42	0.35	0.26	0.26	0	0.001
BIOCARTA IL2RB PATHWAY	37	genes.ES.table	0.61	1.8	0.013	0.053	0.39	0.27	0.13	0.24	0	0.001
BIOCARTA GSK3 PATHWAY	26	genes.ES.table	0.51	1.6	0.043	0.1	0.8	0.23	0.091	0.21	0.064	0
BIOCARTA KERATINOCYTE PATHWAY	45	genes.ES.table	0.52	1.8	0.0061	0.053	0.31	0.31	0.16	0.26	0	0.001
BIOCARTA PYK2 PATHWAY	27	genes.ES.table	0.39	1.6	0.042	0.084	0.72	0.37	0.27	0.27	0.048	0

genes ES table in pathway: BIOCARTA AT1R 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	CTSK	CTSK	CTSK	61	0.58	0.073	YES
2	CTSW	CTSW	CTSW	125	0.52	0.14	YES
3	CTSE	CTSE	CTSE	839	0.28	0.13	YES
4	LAPTM5	LAPTM5	LAPTM5	949	0.25	0.16	YES
5	CTSS	CTSS	CTSS	959	0.25	0.19	YES
6	CD68	CD68	CD68	1134	0.22	0.21	YES
7	SLC11A1	SLC11A1	SLC11A1	1505	0.18	0.22	YES
8	ATP6V0D2	ATP6V0D2	ATP6V0D2	1781	0.15	0.22	YES
9	CTSO	CTSO	CTSO	1954	0.14	0.23	YES
10	ARSB	ARSB	ARSB	2032	0.13	0.24	YES
11	LAMP3	LAMP3	LAMP3	2119	0.12	0.25	YES
12	ACP5	ACP5	ACP5	2164	0.12	0.27	YES
13	ARSA	ARSA	ARSA	2172	0.12	0.28	YES
14	TCIRG1	TCIRG1	TCIRG1	2185	0.12	0.3	YES
15	CTSL1	CTSL1	CTSL1	2484	0.1	0.29	YES
16	NPC1	NPC1	NPC1	2566	0.097	0.3	YES
17	AP4E1	AP4E1	AP4E1	2594	0.096	0.31	YES
18	CTSG	CTSG	CTSG	2682	0.092	0.32	YES
19	NAGA	NAGA	NAGA	2801	0.087	0.32	YES
20	CLTB	CLTB	CLTB	2808	0.087	0.34	YES
21	CTSZ	CTSZ	CTSZ	2823	0.086	0.35	YES
22	GM2A	GM2A	GM2A	2855	0.085	0.36	YES
23	AP1B1	AP1B1	AP1B1	2912	0.082	0.36	YES
24	CLTCL1	CLTCL1	CLTCL1	2934	0.082	0.37	YES
25	SMPD1	SMPD1	SMPD1	2965	0.081	0.38	YES
26	CTSA	CTSA	CTSA	2977	0.08	0.39	YES
27	TPP1	TPP1	TPP1	2988	0.08	0.4	YES
28	LAPTM4B	LAPTM4B	LAPTM4B	3021	0.078	0.41	YES
29	CTSB	CTSB	CTSB	3138	0.074	0.41	YES
30	CTSD	CTSD	CTSD	3175	0.073	0.42	YES
31	CTSC	CTSC	CTSC	3188	0.072	0.43	YES
32	CTSH	CTSH	CTSH	3223	0.072	0.44	YES
33	GALNS	GALNS	GALNS	3325	0.068	0.44	YES
34	ATP6AP1	ATP6AP1	ATP6AP1	3336	0.067	0.45	YES
35	GAA	GAA	GAA	3372	0.066	0.46	YES
36	MCOLN1	MCOLN1	MCOLN1	3391	0.066	0.46	YES
37	LIPA	LIPA	LIPA	3430	0.065	0.47	YES
38	LGMN	LGMN	LGMN	3833	0.054	0.45	YES
39	HEXB	HEXB	HEXB	3912	0.052	0.46	YES
40	NPC2	NPC2	NPC2	4024	0.05	0.46	YES
41	GNPTAB	GNPTAB	GNPTAB	4072	0.049	0.46	YES
42	ACP2	ACP2	ACP2	4104	0.048	0.46	YES
43	AP3S1	AP3S1	AP3S1	4105	0.048	0.47	YES
44	CLN3	CLN3	CLN3	4153	0.047	0.48	YES
45	ASAH1	ASAH1	ASAH1	4363	0.043	0.47	NO
46	ATP6V0B	ATP6V0B	ATP6V0B	4379	0.043	0.47	NO
47	PSAP	PSAP	PSAP	4569	0.039	0.47	NO
48	GGA3	GGA3	GGA3	4688	0.037	0.47	NO
49	GBA	GBA	GBA	4740	0.036	0.47	NO
50	HEXA	HEXA	HEXA	4841	0.035	0.47	NO
51	GLA	GLA	GLA	4970	0.033	0.47	NO
52	MANBA	MANBA	MANBA	5026	0.032	0.47	NO
53	GNPTG	GNPTG	GNPTG	5056	0.032	0.47	NO
54	DNASE2B	DNASE2B	DNASE2B	5215	0.029	0.46	NO
55	PLA2G15	PLA2G15	PLA2G15	5240	0.029	0.47	NO
56	IDS	IDS	IDS	5248	0.029	0.47	NO
57	SGSH	SGSH	SGSH	5321	0.028	0.47	NO
58	CLTC	CLTC	CLTC	5386	0.027	0.47	NO
59	AP1S2	AP1S2	AP1S2	5389	0.027	0.47	NO
60	NEU1	NEU1	NEU1	5512	0.026	0.47	NO
61	ENTPD4	ENTPD4	ENTPD4	5744	0.022	0.46	NO
62	HYAL1	HYAL1	HYAL1	5786	0.022	0.46	NO
63	SORT1	SORT1	SORT1	5881	0.02	0.46	NO
64	LAMP1	LAMP1	LAMP1	5972	0.019	0.46	NO
65	ATP6V0C	ATP6V0C	ATP6V0C	6000	0.019	0.46	NO
66	AGA	AGA	AGA	6045	0.018	0.46	NO
67	FUCA1	FUCA1	FUCA1	6115	0.017	0.46	NO
68	CLN5	CLN5	CLN5	6145	0.017	0.46	NO
69	ATP6V0D1	ATP6V0D1	ATP6V0D1	6298	0.015	0.45	NO
70	MFSD8	MFSD8	MFSD8	6406	0.014	0.45	NO
71	GGA1	GGA1	GGA1	6558	0.012	0.44	NO
72	AP1M2	AP1M2	AP1M2	6566	0.012	0.44	NO
73	CD63	CD63	CD63	6693	0.01	0.44	NO
74	AP3D1	AP3D1	AP3D1	6857	0.0084	0.43	NO
75	DNASE2	DNASE2	DNASE2	6927	0.0076	0.42	NO
76	GNS	GNS	GNS	6945	0.0075	0.42	NO
77	CTNS	CTNS	CTNS	6946	0.0075	0.42	NO
78	NAGPA	NAGPA	NAGPA	7035	0.0066	0.42	NO
79	ABCB9	ABCB9	ABCB9	7084	0.006	0.42	NO
80	SLC17A5	SLC17A5	SLC17A5	7118	0.0056	0.42	NO
81	LAMP2	LAMP2	LAMP2	7246	0.0042	0.41	NO
82	IGF2R	IGF2R	IGF2R	7446	0.0023	0.4	NO
83	GGA2	GGA2	GGA2	7506	0.0019	0.4	NO
84	MAN2B1	MAN2B1	MAN2B1	7577	0.0013	0.4	NO
85	AP3B1	AP3B1	AP3B1	7623	0.00079	0.39	NO
86	AP4B1	AP4B1	AP4B1	7691	0.000044	0.39	NO
87	SCARB2	SCARB2	SCARB2	7763	-0.00067	0.38	NO
88	CTSF	CTSF	CTSF	8017	-0.0029	0.37	NO
89	AP1G1	AP1G1	AP1G1	8373	-0.0063	0.35	NO
90	GUSB	GUSB	GUSB	8386	-0.0065	0.35	NO
91	NAGLU	NAGLU	NAGLU	8476	-0.0072	0.35	NO
92	CLTA	CLTA	CLTA	8574	-0.0084	0.35	NO
93	GALC	GALC	GALC	9029	-0.013	0.32	NO
94	AP3M1	AP3M1	AP3M1	9059	-0.013	0.32	NO
95	LAPTM4A	LAPTM4A	LAPTM4A	9678	-0.018	0.29	NO
96	M6PR	M6PR	M6PR	9807	-0.02	0.29	NO
97	CD164	CD164	CD164	9865	-0.021	0.29	NO
98	GLB1	GLB1	GLB1	9875	-0.021	0.29	NO
99	SLC11A2	SLC11A2	SLC11A2	9888	-0.021	0.29	NO
100	ATP6V0A2	ATP6V0A2	ATP6V0A2	9898	-0.021	0.29	NO
101	IDUA	IDUA	IDUA	9931	-0.021	0.29	NO
102	ATP6V1H	ATP6V1H	ATP6V1H	10236	-0.024	0.28	NO
103	PPT1	PPT1	PPT1	10334	-0.026	0.28	NO
104	NAPSA	NAPSA	NAPSA	10374	-0.026	0.28	NO
105	ATP6V0A1	ATP6V0A1	ATP6V0A1	10583	-0.028	0.27	NO
106	AP1S1	AP1S1	AP1S1	10662	-0.029	0.27	NO
107	AP1M1	AP1M1	AP1M1	10664	-0.029	0.28	NO
108	AP3S2	AP3S2	AP3S2	11031	-0.032	0.26	NO
109	AP4S1	AP4S1	AP4S1	11325	-0.036	0.25	NO
110	ABCA2	ABCA2	ABCA2	11565	-0.038	0.24	NO
111	SUMF1	SUMF1	SUMF1	11602	-0.039	0.24	NO
112	AP4M1	AP4M1	AP4M1	11608	-0.039	0.25	NO
113	PPT2	PPT2	PPT2	12925	-0.057	0.18	NO
114	PSAPL1	PSAPL1	PSAPL1	14192	-0.081	0.13	NO
115	ATP6V0A4	ATP6V0A4	ATP6V0A4	14917	-0.1	0.1	NO
116	AP1S3	AP1S3	AP1S3	14958	-0.1	0.11	NO
117	AP3M2	AP3M2	AP3M2	15148	-0.11	0.12	NO
118	ARSG	ARSG	ARSG	15230	-0.11	0.13	NO
119	CTSL2	CTSL2	CTSL2	16075	-0.15	0.099	NO
120	AP3B2	AP3B2	AP3B2	17580	-0.26	0.052	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 AT1R PATHWAY.

Figure S2. 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 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	BTK	BTK	BTK	265	0.44	0.11	YES
2	CD79A	CD79A	CD79A	382	0.4	0.22	YES
3	CD79B	CD79B	CD79B	404	0.39	0.33	YES
4	PRKCB	PRKCB	PRKCB	570	0.34	0.42	YES
5	VAV1	VAV1	VAV1	657	0.31	0.5	YES
6	NFATC1	NFATC1	NFATC1	1335	0.2	0.52	YES
7	BLNK	BLNK	BLNK	1713	0.16	0.55	YES
8	PPP3CC	PPP3CC	PPP3CC	1763	0.15	0.59	YES
9	FOS	FOS	FOS	1947	0.14	0.62	YES
10	PRKCA	PRKCA	PRKCA	2078	0.13	0.65	YES
11	LYN	LYN	LYN	2218	0.12	0.67	YES
12	GRB2	GRB2	GRB2	3635	0.059	0.61	NO
13	PPP3CA	PPP3CA	PPP3CA	4005	0.05	0.61	NO
14	SHC1	SHC1	SHC1	4213	0.046	0.61	NO
15	MAPK3	MAPK3	MAPK3	4466	0.041	0.61	NO
16	MAP2K1	MAP2K1	MAP2K1	4951	0.033	0.59	NO
17	CALM1	CALM1	CALM1	6900	0.0079	0.49	NO
18	JUN	JUN	JUN	6918	0.0077	0.49	NO
19	CALM3	CALM3	CALM3	7280	0.0038	0.47	NO
20	PPP3CB	PPP3CB	PPP3CB	7905	-0.0018	0.44	NO
21	RAC1	RAC1	RAC1	7911	-0.0019	0.44	NO
22	MAPK14	MAPK14	MAPK14	8248	-0.0052	0.42	NO
23	CALM2	CALM2	CALM2	8818	-0.011	0.39	NO
24	NFATC2	NFATC2	NFATC2	9968	-0.022	0.34	NO
25	MAP3K1	MAP3K1	MAP3K1	10162	-0.024	0.33	NO
26	SYK	SYK	SYK	10196	-0.024	0.34	NO
27	SOS1	SOS1	SOS1	10277	-0.025	0.34	NO
28	RAF1	RAF1	RAF1	10721	-0.029	0.33	NO
29	NFATC4	NFATC4	NFATC4	11424	-0.037	0.3	NO
30	ELK1	ELK1	ELK1	13064	-0.058	0.23	NO
31	MAPK8	MAPK8	MAPK8	13477	-0.066	0.22	NO
32	NFATC3	NFATC3	NFATC3	14097	-0.078	0.21	NO
33	PLCG1	PLCG1	PLCG1	14710	-0.095	0.21	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 BCR PATHWAY.

Figure S4. 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 EGF PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ITK	ITK	ITK	23	0.67	0.04	YES
2	CD3D	CD3D	CD3D	36	0.63	0.078	YES
3	CD247	CD247	CD247	37	0.63	0.12	YES
4	ICOS	ICOS	ICOS	50	0.6	0.15	YES
5	GRAP2	GRAP2	GRAP2	70	0.58	0.19	YES
6	CD3E	CD3E	CD3E	74	0.57	0.22	YES
7	CTLA4	CTLA4	CTLA4	95	0.55	0.26	YES
8	ZAP70	ZAP70	ZAP70	114	0.53	0.29	YES
9	CD40LG	CD40LG	CD40LG	133	0.52	0.32	YES
10	CD3G	CD3G	CD3G	159	0.5	0.35	YES
11	CD8A	CD8A	CD8A	176	0.49	0.38	YES
12	IFNG	IFNG	IFNG	276	0.44	0.4	YES
13	PTPRC	PTPRC	PTPRC	306	0.42	0.42	YES
14	LCK	LCK	LCK	379	0.4	0.44	YES
15	PIK3CG	PIK3CG	PIK3CG	383	0.39	0.47	YES
16	IL10	IL10	IL10	395	0.39	0.49	YES
17	LCP2	LCP2	LCP2	416	0.38	0.51	YES
18	PDCD1	PDCD1	PDCD1	441	0.38	0.54	YES
19	TNF	TNF	TNF	596	0.33	0.55	YES
20	VAV3	VAV3	VAV3	600	0.33	0.57	YES
21	VAV1	VAV1	VAV1	657	0.31	0.58	YES
22	PIK3R5	PIK3R5	PIK3R5	682	0.31	0.6	YES
23	CD8B	CD8B	CD8B	874	0.27	0.61	YES
24	CD28	CD28	CD28	892	0.26	0.62	YES
25	MAPK11	MAPK11	MAPK11	1035	0.24	0.63	YES
26	AKT3	AKT3	AKT3	1136	0.22	0.64	YES
27	CD4	CD4	CD4	1300	0.2	0.64	YES
28	CBLC	CBLC	CBLC	1302	0.2	0.66	YES
29	NFATC1	NFATC1	NFATC1	1335	0.2	0.66	YES
30	LAT	LAT	LAT	1451	0.18	0.67	YES
31	CSF2	CSF2	CSF2	1553	0.17	0.68	YES
32	PPP3CC	PPP3CC	PPP3CC	1763	0.15	0.67	YES
33	PIK3CD	PIK3CD	PIK3CD	1780	0.15	0.68	YES
34	RASGRP1	RASGRP1	RASGRP1	1853	0.14	0.69	YES
35	FOS	FOS	FOS	1947	0.14	0.69	YES
36	NFKBIE	NFKBIE	NFKBIE	2088	0.13	0.69	YES
37	CARD11	CARD11	CARD11	2109	0.12	0.7	YES
38	NFKB1	NFKB1	NFKB1	2487	0.1	0.68	NO
39	NFKBIA	NFKBIA	NFKBIA	2998	0.079	0.66	NO
40	NCK1	NCK1	NCK1	3000	0.079	0.66	NO
41	NFKBIB	NFKBIB	NFKBIB	3170	0.073	0.66	NO
42	MALT1	MALT1	MALT1	3295	0.069	0.66	NO
43	PAK3	PAK3	PAK3	3318	0.068	0.66	NO
44	CHP	CHP	CHP	3341	0.067	0.66	NO
45	MAPK9	MAPK9	MAPK9	3541	0.062	0.66	NO
46	MAPK12	MAPK12	MAPK12	3601	0.06	0.66	NO
47	GRB2	GRB2	GRB2	3635	0.059	0.66	NO
48	PPP3CA	PPP3CA	PPP3CA	4005	0.05	0.64	NO
49	PIK3CA	PIK3CA	PIK3CA	4051	0.049	0.64	NO
50	IKBKG	IKBKG	IKBKG	4278	0.044	0.63	NO
51	PIK3CB	PIK3CB	PIK3CB	4307	0.044	0.63	NO
52	MAPK3	MAPK3	MAPK3	4466	0.041	0.63	NO
53	BCL10	BCL10	BCL10	4710	0.037	0.62	NO
54	MAP3K14	MAP3K14	MAP3K14	4764	0.036	0.62	NO
55	MAPK1	MAPK1	MAPK1	4876	0.034	0.61	NO
56	VAV2	VAV2	VAV2	4886	0.034	0.62	NO
57	MAP2K1	MAP2K1	MAP2K1	4951	0.033	0.61	NO
58	CBLB	CBLB	CBLB	5005	0.032	0.61	NO
59	MAPK13	MAPK13	MAPK13	5260	0.029	0.6	NO
60	PTPN6	PTPN6	PTPN6	5289	0.028	0.6	NO
61	RHOA	RHOA	RHOA	5425	0.026	0.6	NO
62	RELA	RELA	RELA	5705	0.022	0.58	NO
63	PRKCQ	PRKCQ	PRKCQ	5889	0.02	0.57	NO
64	PIK3R3	PIK3R3	PIK3R3	5924	0.02	0.57	NO
65	MAP2K7	MAP2K7	MAP2K7	5948	0.019	0.57	NO
66	AKT1	AKT1	AKT1	6039	0.018	0.57	NO
67	MAP3K8	MAP3K8	MAP3K8	6062	0.018	0.57	NO
68	CDC42	CDC42	CDC42	6201	0.016	0.56	NO
69	PAK2	PAK2	PAK2	6512	0.012	0.55	NO
70	JUN	JUN	JUN	6918	0.0077	0.52	NO
71	SOS2	SOS2	SOS2	7129	0.0056	0.51	NO
72	MAP2K2	MAP2K2	MAP2K2	7220	0.0045	0.51	NO
73	PPP3CB	PPP3CB	PPP3CB	7905	-0.0018	0.47	NO
74	MAPK14	MAPK14	MAPK14	8248	-0.0052	0.45	NO
75	CBL	CBL	CBL	8800	-0.01	0.42	NO
76	AKT2	AKT2	AKT2	8822	-0.011	0.42	NO
77	NRAS	NRAS	NRAS	8946	-0.012	0.42	NO
78	PPP3R1	PPP3R1	PPP3R1	9052	-0.013	0.41	NO
79	PDK1	PDK1	PDK1	9191	-0.014	0.41	NO
80	DLG1	DLG1	DLG1	9401	-0.016	0.4	NO
81	PAK6	PAK6	PAK6	9633	-0.018	0.38	NO
82	NFATC2	NFATC2	NFATC2	9968	-0.022	0.37	NO
83	CHUK	CHUK	CHUK	10051	-0.023	0.36	NO
84	IKBKB	IKBKB	IKBKB	10068	-0.023	0.36	NO
85	SOS1	SOS1	SOS1	10277	-0.025	0.36	NO
86	NCK2	NCK2	NCK2	10525	-0.027	0.34	NO
87	RAF1	RAF1	RAF1	10721	-0.029	0.34	NO
88	MAP3K7	MAP3K7	MAP3K7	11038	-0.032	0.32	NO
89	NFAT5	NFAT5	NFAT5	11125	-0.033	0.32	NO
90	PAK4	PAK4	PAK4	11349	-0.036	0.31	NO
91	NFATC4	NFATC4	NFATC4	11424	-0.037	0.3	NO
92	KRAS	KRAS	KRAS	11827	-0.042	0.29	NO
93	PAK1	PAK1	PAK1	12201	-0.046	0.27	NO
94	GSK3B	GSK3B	GSK3B	12514	-0.05	0.26	NO
95	TEC	TEC	TEC	13119	-0.059	0.23	NO
96	CDK4	CDK4	CDK4	13516	-0.066	0.21	NO
97	PIK3R2	PIK3R2	PIK3R2	13983	-0.076	0.19	NO
98	NFATC3	NFATC3	NFATC3	14097	-0.078	0.19	NO
99	PIK3R1	PIK3R1	PIK3R1	14215	-0.082	0.18	NO
100	PLCG1	PLCG1	PLCG1	14710	-0.095	0.16	NO
101	IL5	IL5	IL5	15388	-0.12	0.14	NO
102	FYN	FYN	FYN	16201	-0.16	0.1	NO
103	CHP2	CHP2	CHP2	16955	-0.2	0.072	NO
104	PAK7	PAK7	PAK7	17208	-0.22	0.072	NO

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

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EGF 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 FAS PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CTSK	CTSK	CTSK	61	0.58	0.04	YES
2	CXCL9	CXCL9	CXCL9	77	0.56	0.08	YES
3	TLR8	TLR8	TLR8	152	0.51	0.11	YES
4	CCL5	CCL5	CCL5	182	0.49	0.15	YES
5	CD80	CD80	CD80	215	0.47	0.18	YES
6	CCL4	CCL4	CCL4	277	0.44	0.21	YES
7	CXCL11	CXCL11	CXCL11	307	0.42	0.24	YES
8	LY96	LY96	LY96	313	0.42	0.27	YES
9	TLR6	TLR6	TLR6	371	0.4	0.3	YES
10	PIK3CG	PIK3CG	PIK3CG	383	0.39	0.32	YES
11	TLR7	TLR7	TLR7	393	0.39	0.35	YES
12	CD86	CD86	CD86	396	0.39	0.38	YES
13	IL6	IL6	IL6	432	0.38	0.41	YES
14	CCL3	CCL3	CCL3	484	0.36	0.43	YES
15	CXCL10	CXCL10	CXCL10	492	0.36	0.46	YES
16	TNF	TNF	TNF	596	0.33	0.48	YES
17	PIK3R5	PIK3R5	PIK3R5	682	0.31	0.49	YES
18	IL1B	IL1B	IL1B	734	0.29	0.51	YES
19	TLR2	TLR2	TLR2	768	0.29	0.53	YES
20	TICAM2	TICAM2	TICAM2	814	0.28	0.55	YES
21	TLR4	TLR4	TLR4	835	0.28	0.57	YES
22	IL12B	IL12B	IL12B	921	0.26	0.58	YES
23	CD14	CD14	CD14	989	0.25	0.6	YES
24	IL12A	IL12A	IL12A	1019	0.24	0.61	YES
25	MAPK11	MAPK11	MAPK11	1035	0.24	0.63	YES
26	TLR1	TLR1	TLR1	1080	0.23	0.64	YES
27	AKT3	AKT3	AKT3	1136	0.22	0.66	YES
28	CD40	CD40	CD40	1247	0.21	0.67	YES
29	LBP	LBP	LBP	1313	0.2	0.68	YES
30	SPP1	SPP1	SPP1	1361	0.19	0.69	YES
31	IL8	IL8	IL8	1548	0.17	0.69	YES
32	PIK3CD	PIK3CD	PIK3CD	1780	0.15	0.69	YES
33	TICAM1	TICAM1	TICAM1	1854	0.14	0.7	YES
34	TLR3	TLR3	TLR3	1902	0.14	0.71	YES
35	FOS	FOS	FOS	1947	0.14	0.71	YES
36	IRF7	IRF7	IRF7	2025	0.13	0.72	YES
37	TLR5	TLR5	TLR5	2045	0.13	0.73	YES
38	IFNB1	IFNB1	IFNB1	2122	0.12	0.73	YES
39	IFNAR2	IFNAR2	IFNAR2	2478	0.1	0.72	NO
40	NFKB1	NFKB1	NFKB1	2487	0.1	0.73	NO
41	IKBKE	IKBKE	IKBKE	2538	0.099	0.73	NO
42	STAT1	STAT1	STAT1	2983	0.08	0.71	NO
43	NFKBIA	NFKBIA	NFKBIA	2998	0.079	0.72	NO
44	IRAK1	IRAK1	IRAK1	3252	0.07	0.71	NO
45	MAPK9	MAPK9	MAPK9	3541	0.062	0.7	NO
46	IRF5	IRF5	IRF5	3596	0.06	0.7	NO
47	MAPK12	MAPK12	MAPK12	3601	0.06	0.7	NO
48	MYD88	MYD88	MYD88	3631	0.059	0.71	NO
49	IRF3	IRF3	IRF3	3768	0.056	0.7	NO
50	TRAF3	TRAF3	TRAF3	3893	0.053	0.7	NO
51	PIK3CA	PIK3CA	PIK3CA	4051	0.049	0.7	NO
52	IKBKG	IKBKG	IKBKG	4278	0.044	0.69	NO
53	PIK3CB	PIK3CB	PIK3CB	4307	0.044	0.69	NO
54	IFNAR1	IFNAR1	IFNAR1	4430	0.042	0.69	NO
55	MAPK3	MAPK3	MAPK3	4466	0.041	0.69	NO
56	MAPK1	MAPK1	MAPK1	4876	0.034	0.67	NO
57	MAP2K1	MAP2K1	MAP2K1	4951	0.033	0.67	NO
58	MAPK13	MAPK13	MAPK13	5260	0.029	0.65	NO
59	RELA	RELA	RELA	5705	0.022	0.63	NO
60	RIPK1	RIPK1	RIPK1	5817	0.021	0.62	NO
61	PIK3R3	PIK3R3	PIK3R3	5924	0.02	0.62	NO
62	MAP2K7	MAP2K7	MAP2K7	5948	0.019	0.62	NO
63	MAP2K3	MAP2K3	MAP2K3	6021	0.018	0.62	NO
64	AKT1	AKT1	AKT1	6039	0.018	0.62	NO
65	MAP3K8	MAP3K8	MAP3K8	6062	0.018	0.62	NO
66	IRAK4	IRAK4	IRAK4	6363	0.014	0.6	NO
67	JUN	JUN	JUN	6918	0.0077	0.57	NO
68	TAB1	TAB1	TAB1	7114	0.0057	0.56	NO
69	MAP2K2	MAP2K2	MAP2K2	7220	0.0045	0.56	NO
70	TOLLIP	TOLLIP	TOLLIP	7230	0.0044	0.56	NO
71	TAB2	TAB2	TAB2	7473	0.0022	0.55	NO
72	FADD	FADD	FADD	7841	-0.0013	0.53	NO
73	RAC1	RAC1	RAC1	7911	-0.0019	0.52	NO
74	TRAF6	TRAF6	TRAF6	8046	-0.0032	0.52	NO
75	MAPK14	MAPK14	MAPK14	8248	-0.0052	0.5	NO
76	AKT2	AKT2	AKT2	8822	-0.011	0.47	NO
77	CASP8	CASP8	CASP8	8895	-0.012	0.47	NO
78	TIRAP	TIRAP	TIRAP	9387	-0.016	0.45	NO
79	CHUK	CHUK	CHUK	10051	-0.023	0.41	NO
80	IKBKB	IKBKB	IKBKB	10068	-0.023	0.41	NO
81	MAP3K7	MAP3K7	MAP3K7	11038	-0.032	0.36	NO
82	TLR9	TLR9	TLR9	12412	-0.049	0.29	NO
83	MAP2K4	MAP2K4	MAP2K4	12517	-0.051	0.29	NO
84	MAPK8	MAPK8	MAPK8	13477	-0.066	0.24	NO
85	PIK3R2	PIK3R2	PIK3R2	13983	-0.076	0.22	NO
86	PIK3R1	PIK3R1	PIK3R1	14215	-0.082	0.21	NO
87	MAP2K6	MAP2K6	MAP2K6	15756	-0.13	0.14	NO
88	MAPK10	MAPK10	MAPK10	15938	-0.14	0.14	NO

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

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FAS 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 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	CCL11	CCL11	CCL11	3	0.88	0.09	YES
2	CCL5	CCL5	CCL5	182	0.49	0.13	YES
3	NLRP3	NLRP3	NLRP3	384	0.39	0.16	YES
4	IL6	IL6	IL6	432	0.38	0.2	YES
5	PSTPIP1	PSTPIP1	PSTPIP1	449	0.37	0.23	YES
6	CASP5	CASP5	CASP5	485	0.36	0.27	YES
7	BIRC3	BIRC3	BIRC3	507	0.35	0.3	YES
8	MEFV	MEFV	MEFV	530	0.35	0.34	YES
9	CCL8	CCL8	CCL8	558	0.34	0.37	YES
10	CASP1	CASP1	CASP1	567	0.34	0.4	YES
11	TNF	TNF	TNF	596	0.33	0.44	YES
12	CXCL1	CXCL1	CXCL1	619	0.32	0.47	YES
13	IL1B	IL1B	IL1B	734	0.29	0.49	YES
14	CCL2	CCL2	CCL2	746	0.29	0.52	YES
15	IL18	IL18	IL18	779	0.28	0.55	YES
16	CCL7	CCL7	CCL7	793	0.28	0.58	YES
17	NLRC4	NLRC4	NLRC4	938	0.26	0.6	YES
18	CCL13	CCL13	CCL13	1006	0.24	0.62	YES
19	MAPK11	MAPK11	MAPK11	1035	0.24	0.64	YES
20	CXCL2	CXCL2	CXCL2	1124	0.22	0.66	YES
21	CARD9	CARD9	CARD9	1199	0.21	0.68	YES
22	TNFAIP3	TNFAIP3	TNFAIP3	1231	0.21	0.7	YES
23	NOD2	NOD2	NOD2	1289	0.2	0.71	YES
24	CARD6	CARD6	CARD6	1358	0.19	0.73	YES
25	NLRP1	NLRP1	NLRP1	1394	0.19	0.75	YES
26	PYCARD	PYCARD	PYCARD	1410	0.19	0.77	YES
27	IL8	IL8	IL8	1548	0.17	0.78	YES
28	RIPK2	RIPK2	RIPK2	1751	0.15	0.78	YES
29	NFKB1	NFKB1	NFKB1	2487	0.1	0.75	NO
30	NFKBIA	NFKBIA	NFKBIA	2998	0.079	0.73	NO
31	NFKBIB	NFKBIB	NFKBIB	3170	0.073	0.73	NO
32	NAIP	NAIP	NAIP	3272	0.07	0.73	NO
33	MAPK9	MAPK9	MAPK9	3541	0.062	0.72	NO
34	MAPK12	MAPK12	MAPK12	3601	0.06	0.73	NO
35	NOD1	NOD1	NOD1	3974	0.051	0.71	NO
36	CARD8	CARD8	CARD8	4116	0.048	0.71	NO
37	IKBKG	IKBKG	IKBKG	4278	0.044	0.71	NO
38	MAPK3	MAPK3	MAPK3	4466	0.041	0.7	NO
39	MAPK1	MAPK1	MAPK1	4876	0.034	0.68	NO
40	MAPK13	MAPK13	MAPK13	5260	0.029	0.66	NO
41	BIRC2	BIRC2	BIRC2	5551	0.025	0.65	NO
42	RELA	RELA	RELA	5705	0.022	0.64	NO
43	SUGT1	SUGT1	SUGT1	6331	0.014	0.61	NO
44	XIAP	XIAP	XIAP	6472	0.013	0.61	NO
45	HSP90AA1	HSP90AA1	HSP90AA1	6526	0.012	0.6	NO
46	TRIP6	TRIP6	TRIP6	6827	0.0086	0.59	NO
47	TAB1	TAB1	TAB1	7114	0.0057	0.57	NO
48	TAB3	TAB3	TAB3	7367	0.0031	0.56	NO
49	TAB2	TAB2	TAB2	7473	0.0022	0.56	NO
50	TRAF6	TRAF6	TRAF6	8046	-0.0032	0.52	NO
51	MAPK14	MAPK14	MAPK14	8248	-0.0052	0.51	NO
52	CASP8	CASP8	CASP8	8895	-0.012	0.48	NO
53	HSP90B1	HSP90B1	HSP90B1	9566	-0.018	0.45	NO
54	CHUK	CHUK	CHUK	10051	-0.023	0.42	NO
55	IKBKB	IKBKB	IKBKB	10068	-0.023	0.42	NO
56	ERBB2IP	ERBB2IP	ERBB2IP	11035	-0.032	0.37	NO
57	MAP3K7	MAP3K7	MAP3K7	11038	-0.032	0.38	NO
58	PYDC1	PYDC1	PYDC1	13464	-0.065	0.25	NO
59	MAPK8	MAPK8	MAPK8	13477	-0.066	0.26	NO
60	MAPK10	MAPK10	MAPK10	15938	-0.14	0.14	NO

Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S10. 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 HIVNEF PATHWAY

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	CXCL10	CXCL10	CXCL10	492	0.36	0.053	YES
2	TNF	TNF	TNF	596	0.33	0.12	YES
3	IL12B	IL12B	IL12B	921	0.26	0.16	YES
4	IL12A	IL12A	IL12A	1019	0.24	0.21	YES
5	MAPK11	MAPK11	MAPK11	1035	0.24	0.26	YES
6	IFNE	IFNE	IFNE	1441	0.18	0.28	YES
7	IL8	IL8	IL8	1548	0.17	0.31	YES
8	IRF7	IRF7	IRF7	2025	0.13	0.32	YES
9	IFIH1	IFIH1	IFIH1	2054	0.13	0.34	YES
10	IFNB1	IFNB1	IFNB1	2122	0.12	0.37	YES
11	NFKB1	NFKB1	NFKB1	2487	0.1	0.37	YES
12	CYLD	CYLD	CYLD	2530	0.099	0.39	YES
13	IKBKE	IKBKE	IKBKE	2538	0.099	0.41	YES
14	ISG15	ISG15	ISG15	2611	0.095	0.43	YES
15	DHX58	DHX58	DHX58	2629	0.094	0.45	YES
16	DDX58	DDX58	DDX58	2804	0.087	0.46	YES
17	NFKBIA	NFKBIA	NFKBIA	2998	0.079	0.46	YES
18	CASP10	CASP10	CASP10	3077	0.076	0.48	YES
19	NFKBIB	NFKBIB	NFKBIB	3170	0.073	0.49	YES
20	TMEM173	TMEM173	TMEM173	3204	0.072	0.5	YES
21	TRAF2	TRAF2	TRAF2	3220	0.072	0.52	YES
22	RNF125	RNF125	RNF125	3377	0.066	0.52	YES
23	MAPK9	MAPK9	MAPK9	3541	0.062	0.53	YES
24	TRADD	TRADD	TRADD	3574	0.061	0.54	YES
25	MAPK12	MAPK12	MAPK12	3601	0.06	0.55	YES
26	IRF3	IRF3	IRF3	3768	0.056	0.56	YES
27	TRAF3	TRAF3	TRAF3	3893	0.053	0.56	YES
28	IKBKG	IKBKG	IKBKG	4278	0.044	0.55	NO
29	ATG12	ATG12	ATG12	4333	0.043	0.56	NO
30	MAPK13	MAPK13	MAPK13	5260	0.029	0.51	NO
31	RELA	RELA	RELA	5705	0.022	0.49	NO
32	RIPK1	RIPK1	RIPK1	5817	0.021	0.49	NO
33	TBK1	TBK1	TBK1	6705	0.01	0.45	NO
34	TANK	TANK	TANK	6893	0.008	0.44	NO
35	NLRX1	NLRX1	NLRX1	7687	0.000072	0.4	NO
36	FADD	FADD	FADD	7841	-0.0013	0.39	NO
37	AZI2	AZI2	AZI2	8045	-0.0031	0.38	NO
38	TRAF6	TRAF6	TRAF6	8046	-0.0032	0.38	NO
39	MAPK14	MAPK14	MAPK14	8248	-0.0052	0.37	NO
40	CASP8	CASP8	CASP8	8895	-0.012	0.34	NO
41	DDX3X	DDX3X	DDX3X	8979	-0.012	0.33	NO
42	OTUD5	OTUD5	OTUD5	9747	-0.019	0.3	NO
43	CHUK	CHUK	CHUK	10051	-0.023	0.29	NO
44	PIN1	PIN1	PIN1	10065	-0.023	0.29	NO
45	IKBKB	IKBKB	IKBKB	10068	-0.023	0.3	NO
46	MAP3K1	MAP3K1	MAP3K1	10162	-0.024	0.3	NO
47	ATG5	ATG5	ATG5	10527	-0.028	0.28	NO
48	MAVS	MAVS	MAVS	10612	-0.028	0.28	NO
49	DAK	DAK	DAK	10984	-0.032	0.27	NO
50	MAP3K7	MAP3K7	MAP3K7	11038	-0.032	0.28	NO
51	TRIM25	TRIM25	TRIM25	11629	-0.039	0.25	NO
52	SIKE1	SIKE1	SIKE1	13465	-0.066	0.17	NO
53	MAPK8	MAPK8	MAPK8	13477	-0.066	0.18	NO
54	TBKBP1	TBKBP1	TBKBP1	15409	-0.12	0.1	NO
55	MAPK10	MAPK10	MAPK10	15938	-0.14	0.11	NO
56	IFNW1	IFNW1	IFNW1	16204	-0.16	0.13	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: BIOCARTA HIVNEF PATHWAY.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HIVNEF 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 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	CSF2RB	CSF2RB	CSF2RB	247	0.45	0.049	YES
2	PIK3CG	PIK3CG	PIK3CG	383	0.39	0.095	YES
3	BIRC3	BIRC3	BIRC3	507	0.35	0.14	YES
4	TNF	TNF	TNF	596	0.33	0.18	YES
5	IL3RA	IL3RA	IL3RA	660	0.31	0.22	YES
6	PIK3R5	PIK3R5	PIK3R5	682	0.31	0.26	YES
7	IL1B	IL1B	IL1B	734	0.29	0.3	YES
8	IRAK2	IRAK2	IRAK2	941	0.25	0.32	YES
9	AKT3	AKT3	AKT3	1136	0.22	0.34	YES
10	TNFSF10	TNFSF10	TNFSF10	1406	0.19	0.35	YES
11	FAS	FAS	FAS	1424	0.19	0.38	YES
12	TNFRSF10A	TNFRSF10A	TNFRSF10A	1471	0.18	0.4	YES
13	IRAK3	IRAK3	IRAK3	1599	0.17	0.41	YES
14	TNFRSF10C	TNFRSF10C	TNFRSF10C	1691	0.16	0.43	YES
15	PPP3CC	PPP3CC	PPP3CC	1763	0.15	0.45	YES
16	PIK3CD	PIK3CD	PIK3CD	1780	0.15	0.47	YES
17	NFKB1	NFKB1	NFKB1	2487	0.1	0.44	YES
18	IL1RAP	IL1RAP	IL1RAP	2628	0.094	0.45	YES
19	BID	BID	BID	2632	0.094	0.46	YES
20	NFKBIA	NFKBIA	NFKBIA	2998	0.079	0.45	YES
21	CASP10	CASP10	CASP10	3077	0.076	0.46	YES
22	IL1A	IL1A	IL1A	3095	0.075	0.47	YES
23	TRAF2	TRAF2	TRAF2	3220	0.072	0.47	YES
24	IRAK1	IRAK1	IRAK1	3252	0.07	0.48	YES
25	CHP	CHP	CHP	3341	0.067	0.48	YES
26	CAPN1	CAPN1	CAPN1	3452	0.064	0.48	YES
27	TRADD	TRADD	TRADD	3574	0.061	0.49	YES
28	ENDOD1	ENDOD1	ENDOD1	3606	0.06	0.49	YES
29	MYD88	MYD88	MYD88	3631	0.059	0.5	YES
30	BAX	BAX	BAX	3685	0.058	0.5	YES
31	CAPN2	CAPN2	CAPN2	3942	0.052	0.5	YES
32	TNFRSF10D	TNFRSF10D	TNFRSF10D	3969	0.051	0.5	YES
33	PPP3CA	PPP3CA	PPP3CA	4005	0.05	0.51	YES
34	PIK3CA	PIK3CA	PIK3CA	4051	0.049	0.51	YES
35	CASP7	CASP7	CASP7	4238	0.046	0.51	YES
36	BCL2L1	BCL2L1	BCL2L1	4264	0.045	0.51	YES
37	IKBKG	IKBKG	IKBKG	4278	0.044	0.52	YES
38	PRKX	PRKX	PRKX	4302	0.044	0.52	YES
39	PIK3CB	PIK3CB	PIK3CB	4307	0.044	0.53	YES
40	CFLAR	CFLAR	CFLAR	4316	0.044	0.54	YES
41	ENDOG	ENDOG	ENDOG	4463	0.041	0.53	NO
42	TNFRSF1A	TNFRSF1A	TNFRSF1A	4643	0.038	0.53	NO
43	MAP3K14	MAP3K14	MAP3K14	4764	0.036	0.53	NO
44	TNFRSF10B	TNFRSF10B	TNFRSF10B	5115	0.031	0.51	NO
45	CYCS	CYCS	CYCS	5539	0.025	0.49	NO
46	BIRC2	BIRC2	BIRC2	5551	0.025	0.5	NO
47	TP53	TP53	TP53	5561	0.025	0.5	NO
48	RELA	RELA	RELA	5705	0.022	0.49	NO
49	RIPK1	RIPK1	RIPK1	5817	0.021	0.49	NO
50	PRKACB	PRKACB	PRKACB	5888	0.02	0.49	NO
51	PIK3R3	PIK3R3	PIK3R3	5924	0.02	0.49	NO
52	AIFM1	AIFM1	AIFM1	5964	0.019	0.49	NO
53	AKT1	AKT1	AKT1	6039	0.018	0.49	NO
54	IRAK4	IRAK4	IRAK4	6363	0.014	0.47	NO
55	BAD	BAD	BAD	6382	0.014	0.48	NO
56	IL1R1	IL1R1	IL1R1	6404	0.014	0.48	NO
57	CASP3	CASP3	CASP3	6441	0.013	0.48	NO
58	XIAP	XIAP	XIAP	6472	0.013	0.48	NO
59	PRKAR1A	PRKAR1A	PRKAR1A	6546	0.012	0.47	NO
60	NTRK1	NTRK1	NTRK1	7739	-0.00044	0.41	NO
61	FADD	FADD	FADD	7841	-0.0013	0.4	NO
62	PPP3CB	PPP3CB	PPP3CB	7905	-0.0018	0.4	NO
63	ATM	ATM	ATM	8523	-0.0077	0.37	NO
64	AKT2	AKT2	AKT2	8822	-0.011	0.35	NO
65	CASP8	CASP8	CASP8	8895	-0.012	0.35	NO
66	PPP3R1	PPP3R1	PPP3R1	9052	-0.013	0.34	NO
67	EXOG	EXOG	EXOG	9956	-0.022	0.3	NO
68	CHUK	CHUK	CHUK	10051	-0.023	0.3	NO
69	IKBKB	IKBKB	IKBKB	10068	-0.023	0.3	NO
70	CASP6	CASP6	CASP6	10360	-0.026	0.29	NO
71	PRKAR2A	PRKAR2A	PRKAR2A	11213	-0.034	0.24	NO
72	DFFB	DFFB	DFFB	11718	-0.04	0.22	NO
73	PRKACA	PRKACA	PRKACA	12018	-0.044	0.21	NO
74	DFFA	DFFA	DFFA	12265	-0.047	0.21	NO
75	PRKAR1B	PRKAR1B	PRKAR1B	13350	-0.063	0.16	NO
76	PRKAR2B	PRKAR2B	PRKAR2B	13793	-0.072	0.14	NO
77	APAF1	APAF1	APAF1	13868	-0.073	0.15	NO
78	PIK3R2	PIK3R2	PIK3R2	13983	-0.076	0.15	NO
79	PIK3R1	PIK3R1	PIK3R1	14215	-0.082	0.15	NO
80	CASP9	CASP9	CASP9	14538	-0.09	0.14	NO
81	NGF	NGF	NGF	15943	-0.14	0.089	NO
82	BCL2	BCL2	BCL2	16498	-0.17	0.083	NO
83	CHP2	CHP2	CHP2	16955	-0.2	0.086	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: BIOCARTA IL2RB PATHWAY.

Figure S14. 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

genes ES table in pathway: BIOCARTA GSK3 PATHWAY

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	FASLG	FASLG	FASLG	91	0.55	0.25	YES
2	ARHGDIB	ARHGDIB	ARHGDIB	1186	0.21	0.29	YES
3	FAS	FAS	FAS	1424	0.19	0.36	YES
4	PTPN13	PTPN13	PTPN13	1499	0.18	0.44	YES
5	RIPK2	RIPK2	RIPK2	1751	0.15	0.5	YES
6	LMNA	LMNA	LMNA	2489	0.1	0.51	YES
7	CASP10	CASP10	CASP10	3077	0.076	0.51	YES
8	FAF1	FAF1	FAF1	4086	0.048	0.48	YES
9	RB1	RB1	RB1	4099	0.048	0.5	YES
10	CASP7	CASP7	CASP7	4238	0.046	0.51	YES
11	CFLAR	CFLAR	CFLAR	4316	0.044	0.53	YES
12	SPTAN1	SPTAN1	SPTAN1	6266	0.015	0.43	NO
13	CASP3	CASP3	CASP3	6441	0.013	0.43	NO
14	PAK2	PAK2	PAK2	6512	0.012	0.43	NO
15	JUN	JUN	JUN	6918	0.0077	0.41	NO
16	FADD	FADD	FADD	7841	-0.0013	0.36	NO
17	CASP8	CASP8	CASP8	8895	-0.012	0.31	NO
18	LMNB2	LMNB2	LMNB2	9173	-0.014	0.3	NO
19	DAXX	DAXX	DAXX	9600	-0.018	0.29	NO
20	MAP3K1	MAP3K1	MAP3K1	10162	-0.024	0.27	NO
21	CASP6	CASP6	CASP6	10360	-0.026	0.27	NO
22	PRKDC	PRKDC	PRKDC	10971	-0.032	0.25	NO
23	MAP3K7	MAP3K7	MAP3K7	11038	-0.032	0.26	NO
24	DFFB	DFFB	DFFB	11718	-0.04	0.24	NO
25	PAK1	PAK1	PAK1	12201	-0.046	0.24	NO
26	DFFA	DFFA	DFFA	12265	-0.047	0.26	NO
27	MAP2K4	MAP2K4	MAP2K4	12517	-0.051	0.27	NO
28	PARP1	PARP1	PARP1	12916	-0.056	0.27	NO
29	MAPK8	MAPK8	MAPK8	13477	-0.066	0.27	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: BIOCARTA GSK3 PATHWAY.

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GSK3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA KERATINOCYTE PATHWAY

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	AIM2	AIM2	AIM2	126	0.52	0.088	YES
2	CCL5	CCL5	CCL5	182	0.49	0.17	YES
3	CCL4	CCL4	CCL4	277	0.44	0.25	YES
4	IL6	IL6	IL6	432	0.38	0.31	YES
5	CXCL10	CXCL10	CXCL10	492	0.36	0.37	YES
6	CCL4L2	CCL4L2	CCL4L2	552	0.34	0.43	YES
7	CASP1	CASP1	CASP1	567	0.34	0.49	YES
8	IL1B	IL1B	IL1B	734	0.29	0.53	YES
9	ZBP1	ZBP1	ZBP1	749	0.29	0.58	YES
10	IL18	IL18	IL18	779	0.28	0.63	YES
11	PYCARD	PYCARD	PYCARD	1410	0.19	0.63	YES
12	RIPK3	RIPK3	RIPK3	1412	0.19	0.67	YES
13	IRF7	IRF7	IRF7	2025	0.13	0.66	YES
14	IFNB1	IFNB1	IFNB1	2122	0.12	0.67	YES
15	NFKB1	NFKB1	NFKB1	2487	0.1	0.67	YES
16	IKBKE	IKBKE	IKBKE	2538	0.099	0.69	YES
17	DDX58	DDX58	DDX58	2804	0.087	0.69	YES
18	NFKBIA	NFKBIA	NFKBIA	2998	0.079	0.69	YES
19	TREX1	TREX1	TREX1	3073	0.076	0.7	YES
20	NFKBIB	NFKBIB	NFKBIB	3170	0.073	0.71	YES
21	TMEM173	TMEM173	TMEM173	3204	0.072	0.72	YES
22	IRF3	IRF3	IRF3	3768	0.056	0.7	NO
23	IKBKG	IKBKG	IKBKG	4278	0.044	0.68	NO
24	POLR3GL	POLR3GL	POLR3GL	5441	0.026	0.62	NO
25	POLR3G	POLR3G	POLR3G	5575	0.024	0.62	NO
26	RELA	RELA	RELA	5705	0.022	0.62	NO
27	POLR3D	POLR3D	POLR3D	5727	0.022	0.62	NO
28	RIPK1	RIPK1	RIPK1	5817	0.021	0.62	NO
29	ADAR	ADAR	ADAR	6245	0.016	0.6	NO
30	POLR3H	POLR3H	POLR3H	6391	0.014	0.59	NO
31	TBK1	TBK1	TBK1	6705	0.01	0.58	NO
32	POLR3K	POLR3K	POLR3K	6727	0.0097	0.58	NO
33	IL33	IL33	IL33	7271	0.004	0.55	NO
34	POLR3C	POLR3C	POLR3C	7858	-0.0015	0.52	NO
35	POLR1D	POLR1D	POLR1D	8218	-0.0049	0.5	NO
36	POLR3A	POLR3A	POLR3A	8426	-0.0068	0.49	NO
37	CHUK	CHUK	CHUK	10051	-0.023	0.41	NO
38	IKBKB	IKBKB	IKBKB	10068	-0.023	0.41	NO
39	MAVS	MAVS	MAVS	10612	-0.028	0.39	NO
40	POLR1C	POLR1C	POLR1C	11815	-0.041	0.33	NO
41	POLR3F	POLR3F	POLR3F	13515	-0.066	0.25	NO
42	POLR3B	POLR3B	POLR3B	15487	-0.12	0.16	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: BIOCARTA KERATINOCYTE PATHWAY.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA KERATINOCYTE 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 PYK2 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CD247	CD247	CD247	37	0.63	0.026	YES
2	KLRK1	KLRK1	KLRK1	41	0.62	0.054	YES
3	SH2D1A	SH2D1A	SH2D1A	44	0.61	0.081	YES
4	PRF1	PRF1	PRF1	53	0.6	0.11	YES
5	GZMB	GZMB	GZMB	62	0.58	0.13	YES
6	FASLG	FASLG	FASLG	91	0.55	0.16	YES
7	ZAP70	ZAP70	ZAP70	114	0.53	0.18	YES
8	NCR3	NCR3	NCR3	135	0.52	0.2	YES
9	CD244	CD244	CD244	175	0.49	0.22	YES
10	KLRD1	KLRD1	KLRD1	184	0.48	0.24	YES
11	SH2D1B	SH2D1B	SH2D1B	203	0.47	0.26	YES
12	KLRC3	KLRC3	KLRC3	224	0.46	0.28	YES
13	KLRC1	KLRC1	KLRC1	233	0.46	0.3	YES
14	KIR2DL4	KIR2DL4	KIR2DL4	241	0.46	0.32	YES
15	CD48	CD48	CD48	270	0.44	0.34	YES
16	IFNG	IFNG	IFNG	276	0.44	0.36	YES
17	ITGAL	ITGAL	ITGAL	309	0.42	0.38	YES
18	LCK	LCK	LCK	379	0.4	0.39	YES
19	PIK3CG	PIK3CG	PIK3CG	383	0.39	0.41	YES
20	LCP2	LCP2	LCP2	416	0.38	0.42	YES
21	PRKCB	PRKCB	PRKCB	570	0.34	0.43	YES
22	KIR2DS4	KIR2DS4	KIR2DS4	594	0.33	0.44	YES
23	TNF	TNF	TNF	596	0.33	0.46	YES
24	NCR1	NCR1	NCR1	597	0.33	0.48	YES
25	VAV3	VAV3	VAV3	600	0.33	0.49	YES
26	KIR2DL1	KIR2DL1	KIR2DL1	606	0.32	0.5	YES
27	KIR3DL1	KIR3DL1	KIR3DL1	647	0.32	0.52	YES
28	VAV1	VAV1	VAV1	657	0.31	0.53	YES
29	FCGR3A	FCGR3A	FCGR3A	681	0.31	0.54	YES
30	PIK3R5	PIK3R5	PIK3R5	682	0.31	0.56	YES
31	HCST	HCST	HCST	721	0.3	0.57	YES
32	KIR3DL2	KIR3DL2	KIR3DL2	766	0.29	0.58	YES
33	RAC2	RAC2	RAC2	770	0.29	0.59	YES
34	ITGB2	ITGB2	ITGB2	772	0.29	0.6	YES
35	ICAM1	ICAM1	ICAM1	785	0.28	0.62	YES
36	FCER1G	FCER1G	FCER1G	787	0.28	0.63	YES
37	ULBP2	ULBP2	ULBP2	799	0.28	0.64	YES
38	KIR2DL3	KIR2DL3	KIR2DL3	806	0.28	0.65	YES
39	TYROBP	TYROBP	TYROBP	986	0.25	0.65	YES
40	KLRC2	KLRC2	KLRC2	1036	0.24	0.66	YES
41	NFATC1	NFATC1	NFATC1	1335	0.2	0.65	YES
42	TNFSF10	TNFSF10	TNFSF10	1406	0.19	0.66	YES
43	FAS	FAS	FAS	1424	0.19	0.67	YES
44	LAT	LAT	LAT	1451	0.18	0.67	YES
45	HLA-B	HLA-B	HLA-B	1467	0.18	0.68	YES
46	TNFRSF10A	TNFRSF10A	TNFRSF10A	1471	0.18	0.69	YES
47	HLA-G	HLA-G	HLA-G	1479	0.18	0.7	YES
48	CSF2	CSF2	CSF2	1553	0.17	0.7	YES
49	FCGR3B	FCGR3B	FCGR3B	1593	0.17	0.7	YES
50	TNFRSF10C	TNFRSF10C	TNFRSF10C	1691	0.16	0.71	YES
51	PPP3CC	PPP3CC	PPP3CC	1763	0.15	0.71	YES
52	PIK3CD	PIK3CD	PIK3CD	1780	0.15	0.72	YES
53	HLA-C	HLA-C	HLA-C	1880	0.14	0.72	YES
54	PRKCA	PRKCA	PRKCA	2078	0.13	0.71	YES
55	HLA-E	HLA-E	HLA-E	2095	0.12	0.72	YES
56	PTK2B	PTK2B	PTK2B	2103	0.12	0.72	YES
57	IFNB1	IFNB1	IFNB1	2122	0.12	0.73	YES
58	HLA-A	HLA-A	HLA-A	2138	0.12	0.73	YES
59	MICA	MICA	MICA	2139	0.12	0.74	YES
60	PLCG2	PLCG2	PLCG2	2457	0.1	0.72	NO
61	IFNAR2	IFNAR2	IFNAR2	2478	0.1	0.73	NO
62	BID	BID	BID	2632	0.094	0.72	NO
63	IFNGR1	IFNGR1	IFNGR1	2753	0.089	0.72	NO
64	ICAM2	ICAM2	ICAM2	3167	0.073	0.7	NO
65	CHP	CHP	CHP	3341	0.067	0.7	NO
66	GRB2	GRB2	GRB2	3635	0.059	0.68	NO
67	SH3BP2	SH3BP2	SH3BP2	3857	0.054	0.67	NO
68	TNFRSF10D	TNFRSF10D	TNFRSF10D	3969	0.051	0.67	NO
69	PPP3CA	PPP3CA	PPP3CA	4005	0.05	0.67	NO
70	PIK3CA	PIK3CA	PIK3CA	4051	0.049	0.67	NO
71	SHC1	SHC1	SHC1	4213	0.046	0.66	NO
72	PIK3CB	PIK3CB	PIK3CB	4307	0.044	0.66	NO
73	RAC3	RAC3	RAC3	4399	0.042	0.66	NO
74	ULBP1	ULBP1	ULBP1	4426	0.042	0.66	NO
75	IFNAR1	IFNAR1	IFNAR1	4430	0.042	0.66	NO
76	MAPK3	MAPK3	MAPK3	4466	0.041	0.66	NO
77	MAPK1	MAPK1	MAPK1	4876	0.034	0.64	NO
78	VAV2	VAV2	VAV2	4886	0.034	0.64	NO
79	MAP2K1	MAP2K1	MAP2K1	4951	0.033	0.64	NO
80	TNFRSF10B	TNFRSF10B	TNFRSF10B	5115	0.031	0.63	NO
81	HRAS	HRAS	HRAS	5172	0.03	0.63	NO
82	PTPN6	PTPN6	PTPN6	5289	0.028	0.62	NO
83	IFNGR2	IFNGR2	IFNGR2	5451	0.026	0.62	NO
84	PIK3R3	PIK3R3	PIK3R3	5924	0.02	0.59	NO
85	CASP3	CASP3	CASP3	6441	0.013	0.56	NO
86	SOS2	SOS2	SOS2	7129	0.0056	0.53	NO
87	MAP2K2	MAP2K2	MAP2K2	7220	0.0045	0.52	NO
88	ARAF	ARAF	ARAF	7303	0.0037	0.52	NO
89	BRAF	BRAF	BRAF	7550	0.0015	0.5	NO
90	PPP3CB	PPP3CB	PPP3CB	7905	-0.0018	0.48	NO
91	RAC1	RAC1	RAC1	7911	-0.0019	0.48	NO
92	NRAS	NRAS	NRAS	8946	-0.012	0.43	NO
93	PPP3R1	PPP3R1	PPP3R1	9052	-0.013	0.42	NO
94	NFATC2	NFATC2	NFATC2	9968	-0.022	0.38	NO
95	SYK	SYK	SYK	10196	-0.024	0.36	NO
96	SOS1	SOS1	SOS1	10277	-0.025	0.36	NO
97	RAF1	RAF1	RAF1	10721	-0.029	0.34	NO
98	NFAT5	NFAT5	NFAT5	11125	-0.033	0.32	NO
99	RAET1L	RAET1L	RAET1L	11366	-0.036	0.31	NO
100	NFATC4	NFATC4	NFATC4	11424	-0.037	0.3	NO
101	PTPN11	PTPN11	PTPN11	11477	-0.037	0.3	NO
102	KRAS	KRAS	KRAS	11827	-0.042	0.29	NO
103	NCR2	NCR2	NCR2	12186	-0.046	0.27	NO
104	PAK1	PAK1	PAK1	12201	-0.046	0.27	NO
105	SHC2	SHC2	SHC2	12879	-0.056	0.24	NO
106	SHC3	SHC3	SHC3	13861	-0.073	0.19	NO
107	PIK3R2	PIK3R2	PIK3R2	13983	-0.076	0.18	NO
108	NFATC3	NFATC3	NFATC3	14097	-0.078	0.18	NO
109	PIK3R1	PIK3R1	PIK3R1	14215	-0.082	0.18	NO
110	SHC4	SHC4	SHC4	14605	-0.092	0.16	NO
111	PLCG1	PLCG1	PLCG1	14710	-0.095	0.16	NO
112	RAET1E	RAET1E	RAET1E	14999	-0.1	0.15	NO
113	RAET1G	RAET1G	RAET1G	15139	-0.11	0.15	NO
114	FYN	FYN	FYN	16201	-0.16	0.095	NO
115	PRKCG	PRKCG	PRKCG	16676	-0.18	0.077	NO
116	CHP2	CHP2	CHP2	16955	-0.2	0.071	NO
117	ULBP3	ULBP3	ULBP3	17950	-0.32	0.032	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: BIOCARTA PYK2 PATHWAY.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA HIVNEF PATHWAY	57	genes.ES.table	0.31	1.3	0.17	1	0.99	0.42	0.3	0.3	0.91	0.45
BIOCARTA DEATH PATHWAY	32	genes.ES.table	0.43	1.5	0.084	0.83	0.92	0.5	0.28	0.36	0.62	0.3
BIOCARTA TOLL PATHWAY	36	genes.ES.table	0.43	1.3	0.26	1	1	0.53	0.28	0.38	1	0.59
KEGG CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.47	1.6	0.092	1	0.83	0.69	0.38	0.43	0.7	0.4
KEGG FATTY ACID METABOLISM	39	genes.ES.table	0.31	1.1	0.37	1	1	0.28	0.17	0.23	1	0.61
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	29	genes.ES.table	0.33	1	0.38	1	1	0.21	0.14	0.18	1	0.57
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	43	genes.ES.table	0.29	1.1	0.36	1	1	0.21	0.19	0.17	1	0.67
KEGG GLUTATHIONE METABOLISM	47	genes.ES.table	0.38	1.2	0.2	1	1	0.45	0.26	0.33	1	0.64
KEGG SPHINGOLIPID METABOLISM	38	genes.ES.table	0.36	1.2	0.21	1	1	0.24	0.15	0.2	1	0.67
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES	25	genes.ES.table	0.52	1.4	0.077	1	0.98	0.28	0.074	0.26	0.97	0.49

genes ES table in pathway: BIOCARTA HIVNEF 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	PIPOX	PIPOX	PIPOX	120	0.36	0.087	YES
2	DDO	DDO	DDO	393	0.26	0.14	YES
3	PEX11G	PEX11G	PEX11G	808	0.19	0.16	YES
4	ACSL5	ACSL5	ACSL5	814	0.19	0.21	YES
5	MPV17L	MPV17L	MPV17L	1126	0.15	0.24	YES
6	PEX11A	PEX11A	PEX11A	1712	0.12	0.23	YES
7	ACSL6	ACSL6	ACSL6	1806	0.11	0.26	YES
8	PEX6	PEX6	PEX6	2160	0.095	0.26	YES
9	CAT	CAT	CAT	2200	0.094	0.28	YES
10	EPHX2	EPHX2	EPHX2	2395	0.087	0.3	YES
11	MLYCD	MLYCD	MLYCD	2410	0.086	0.32	YES
12	GSTK1	GSTK1	GSTK1	2564	0.082	0.33	YES
13	PECR	PECR	PECR	2617	0.08	0.35	YES
14	IDH2	IDH2	IDH2	2961	0.072	0.35	YES
15	PAOX	PAOX	PAOX	3034	0.07	0.36	YES
16	DHRS4	DHRS4	DHRS4	3072	0.069	0.38	YES
17	ACAA1	ACAA1	ACAA1	3105	0.068	0.4	YES
18	PEX16	PEX16	PEX16	3152	0.067	0.41	YES
19	SCP2	SCP2	SCP2	3391	0.062	0.41	YES
20	CRAT	CRAT	CRAT	3424	0.061	0.43	YES
21	HAO2	HAO2	HAO2	3449	0.06	0.44	YES
22	NUDT12	NUDT12	NUDT12	3538	0.059	0.45	YES
23	PMVK	PMVK	PMVK	3817	0.054	0.45	YES
24	IDH1	IDH1	IDH1	3826	0.054	0.46	YES
25	SLC27A2	SLC27A2	SLC27A2	4252	0.046	0.45	YES
26	SOD1	SOD1	SOD1	4273	0.046	0.46	YES
27	ABCD1	ABCD1	ABCD1	4693	0.04	0.45	YES
28	PXMP4	PXMP4	PXMP4	4701	0.04	0.46	YES
29	PEX12	PEX12	PEX12	4803	0.038	0.46	YES
30	PEX2	PEX2	PEX2	4933	0.037	0.47	YES
31	PRDX5	PRDX5	PRDX5	4991	0.036	0.47	YES
32	PEX26	PEX26	PEX26	5029	0.036	0.48	YES
33	PEX11B	PEX11B	PEX11B	5276	0.032	0.48	YES
34	AMACR	AMACR	AMACR	5277	0.032	0.48	YES
35	ACOX1	ACOX1	ACOX1	5399	0.031	0.49	YES
36	HMGCL	HMGCL	HMGCL	5501	0.03	0.49	YES
37	PEX10	PEX10	PEX10	5593	0.029	0.49	YES
38	SOD2	SOD2	SOD2	6178	0.022	0.46	NO
39	ACOX3	ACOX3	ACOX3	6228	0.022	0.47	NO
40	PEX7	PEX7	PEX7	6437	0.02	0.46	NO
41	HACL1	HACL1	HACL1	6463	0.02	0.47	NO
42	NUDT19	NUDT19	NUDT19	7394	0.011	0.42	NO
43	AGPS	AGPS	AGPS	7453	0.01	0.42	NO
44	PRDX1	PRDX1	PRDX1	7574	0.0092	0.41	NO
45	PEX1	PEX1	PEX1	8093	0.0048	0.39	NO
46	MVK	MVK	MVK	8437	0.002	0.37	NO
47	CROT	CROT	CROT	8457	0.0018	0.37	NO
48	EHHADH	EHHADH	EHHADH	8654	0.0003	0.36	NO
49	HSD17B4	HSD17B4	HSD17B4	8878	-0.0016	0.35	NO
50	ACSL3	ACSL3	ACSL3	9015	-0.0026	0.34	NO
51	GNPAT	GNPAT	GNPAT	9068	-0.0032	0.34	NO
52	AGXT	AGXT	AGXT	9397	-0.006	0.32	NO
53	PEX13	PEX13	PEX13	9430	-0.0063	0.32	NO
54	SLC25A17	SLC25A17	SLC25A17	9601	-0.0078	0.31	NO
55	ACOT8	ACOT8	ACOT8	9627	-0.008	0.31	NO
56	PEX19	PEX19	PEX19	9768	-0.0093	0.31	NO
57	ABCD3	ABCD3	ABCD3	10025	-0.012	0.3	NO
58	PXMP2	PXMP2	PXMP2	10192	-0.013	0.29	NO
59	PEX5	PEX5	PEX5	10469	-0.016	0.28	NO
60	DECR2	DECR2	DECR2	10479	-0.016	0.28	NO
61	PEX14	PEX14	PEX14	10654	-0.017	0.28	NO
62	ACSL1	ACSL1	ACSL1	11086	-0.021	0.26	NO
63	FAR1	FAR1	FAR1	11372	-0.024	0.25	NO
64	ABCD4	ABCD4	ABCD4	11465	-0.025	0.26	NO
65	ACSL4	ACSL4	ACSL4	11547	-0.026	0.26	NO
66	MPV17	MPV17	MPV17	11614	-0.026	0.26	NO
67	XDH	XDH	XDH	11731	-0.027	0.26	NO
68	ABCD2	ABCD2	ABCD2	12136	-0.032	0.25	NO
69	PHYH	PHYH	PHYH	12392	-0.035	0.24	NO
70	NOS2	NOS2	NOS2	12465	-0.036	0.25	NO
71	PECI	PECI	PECI	12768	-0.039	0.24	NO
72	FAR2	FAR2	FAR2	13170	-0.045	0.23	NO
73	ECH1	ECH1	ECH1	13298	-0.047	0.24	NO
74	PEX3	PEX3	PEX3	14884	-0.078	0.17	NO
75	BAAT	BAAT	BAAT	15719	-0.1	0.15	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 HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA DEATH PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PCK1	PCK1	PCK1	1846	0.11	0.003	YES
2	IDH3A	IDH3A	IDH3A	1909	0.11	0.099	YES
3	SUCLG2	SUCLG2	SUCLG2	2898	0.073	0.12	YES
4	IDH2	IDH2	IDH2	2961	0.072	0.18	YES
5	SDHA	SDHA	SDHA	3309	0.063	0.22	YES
6	IDH3G	IDH3G	IDH3G	3606	0.058	0.26	YES
7	PDHA1	PDHA1	PDHA1	3701	0.056	0.3	YES
8	IDH1	IDH1	IDH1	3826	0.054	0.35	YES
9	MDH2	MDH2	MDH2	3913	0.052	0.39	YES
10	ACO2	ACO2	ACO2	4264	0.046	0.42	YES
11	SDHD	SDHD	SDHD	5294	0.032	0.39	YES
12	FH	FH	FH	5542	0.03	0.41	YES
13	DLD	DLD	DLD	6040	0.024	0.4	YES
14	OGDH	OGDH	OGDH	6108	0.024	0.42	YES
15	PDHB	PDHB	PDHB	6163	0.023	0.44	YES
16	SDHB	SDHB	SDHB	6273	0.022	0.45	YES
17	SUCLG1	SUCLG1	SUCLG1	6388	0.02	0.47	YES
18	PCK2	PCK2	PCK2	6790	0.016	0.46	YES
19	MDH1	MDH1	MDH1	7011	0.014	0.46	YES
20	PC	PC	PC	7092	0.014	0.47	YES
21	SDHC	SDHC	SDHC	7612	0.0088	0.45	NO
22	DLAT	DLAT	DLAT	7719	0.0079	0.45	NO
23	DLST	DLST	DLST	8756	-0.0006	0.4	NO
24	OGDHL	OGDHL	OGDHL	9130	-0.0037	0.38	NO
25	CS	CS	CS	9176	-0.0042	0.38	NO
26	IDH3B	IDH3B	IDH3B	10693	-0.018	0.32	NO
27	ACLY	ACLY	ACLY	11121	-0.022	0.31	NO
28	SUCLA2	SUCLA2	SUCLA2	12087	-0.031	0.29	NO
29	ACO1	ACO1	ACO1	14186	-0.063	0.24	NO

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

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

genes ES table in pathway: BIOCARTA TOLL 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	IL12A	IL12A	IL12A	300	0.28	0.058	YES
2	RNF125	RNF125	RNF125	727	0.2	0.088	YES
3	TMEM173	TMEM173	TMEM173	912	0.18	0.12	YES
4	IKBKE	IKBKE	IKBKE	1278	0.14	0.14	YES
5	CASP10	CASP10	CASP10	1373	0.13	0.17	YES
6	DHX58	DHX58	DHX58	1713	0.12	0.18	YES
7	IFIH1	IFIH1	IFIH1	1724	0.12	0.22	YES
8	CXCL10	CXCL10	CXCL10	1779	0.11	0.24	YES
9	IFNW1	IFNW1	IFNW1	1829	0.11	0.27	YES
10	TRADD	TRADD	TRADD	1838	0.11	0.3	YES
11	TNF	TNF	TNF	1863	0.11	0.32	YES
12	NLRX1	NLRX1	NLRX1	1998	0.1	0.34	YES
13	IRF7	IRF7	IRF7	2003	0.1	0.37	YES
14	IFNE	IFNE	IFNE	2058	0.099	0.4	YES
15	TANK	TANK	TANK	2071	0.099	0.42	YES
16	MAPK13	MAPK13	MAPK13	2602	0.08	0.41	YES
17	IFNB1	IFNB1	IFNB1	2635	0.08	0.43	YES
18	CASP8	CASP8	CASP8	2689	0.078	0.45	YES
19	IKBKB	IKBKB	IKBKB	3037	0.07	0.45	YES
20	ISG15	ISG15	ISG15	3181	0.066	0.46	YES
21	DDX58	DDX58	DDX58	3710	0.056	0.45	NO
22	TRAF6	TRAF6	TRAF6	4266	0.046	0.43	NO
23	IKBKG	IKBKG	IKBKG	4484	0.043	0.43	NO
24	IL8	IL8	IL8	4590	0.042	0.43	NO
25	NFKBIA	NFKBIA	NFKBIA	4633	0.041	0.44	NO
26	DAK	DAK	DAK	4643	0.041	0.45	NO
27	RELA	RELA	RELA	5018	0.036	0.44	NO
28	FADD	FADD	FADD	5095	0.035	0.45	NO
29	NFKB1	NFKB1	NFKB1	5198	0.033	0.45	NO
30	TRIM25	TRIM25	TRIM25	5216	0.033	0.46	NO
31	MAP3K1	MAP3K1	MAP3K1	6256	0.022	0.41	NO
32	MAVS	MAVS	MAVS	6561	0.019	0.4	NO
33	MAPK9	MAPK9	MAPK9	7059	0.014	0.37	NO
34	PIN1	PIN1	PIN1	7094	0.014	0.38	NO
35	TRAF2	TRAF2	TRAF2	7185	0.013	0.37	NO
36	CYLD	CYLD	CYLD	7579	0.0091	0.36	NO
37	RIPK1	RIPK1	RIPK1	7924	0.0062	0.34	NO
38	DDX3X	DDX3X	DDX3X	7935	0.0062	0.34	NO
39	TRAF3	TRAF3	TRAF3	8434	0.002	0.31	NO
40	MAPK14	MAPK14	MAPK14	8682	9e-05	0.3	NO
41	IL12B	IL12B	IL12B	8748	-0.00052	0.3	NO
42	TBK1	TBK1	TBK1	9045	-0.0028	0.28	NO
43	OTUD5	OTUD5	OTUD5	9187	-0.0043	0.28	NO
44	AZI2	AZI2	AZI2	10568	-0.016	0.2	NO
45	ATG12	ATG12	ATG12	11281	-0.023	0.17	NO
46	IRF3	IRF3	IRF3	11783	-0.028	0.15	NO
47	MAPK8	MAPK8	MAPK8	12039	-0.031	0.15	NO
48	MAPK11	MAPK11	MAPK11	12382	-0.035	0.14	NO
49	SIKE1	SIKE1	SIKE1	12783	-0.039	0.13	NO
50	CHUK	CHUK	CHUK	13238	-0.046	0.11	NO
51	ATG5	ATG5	ATG5	14025	-0.06	0.087	NO
52	MAP3K7	MAP3K7	MAP3K7	15526	-0.096	0.032	NO
53	MAPK12	MAPK12	MAPK12	15689	-0.1	0.05	NO
54	TBKBP1	TBKBP1	TBKBP1	15980	-0.11	0.064	NO
55	NFKBIB	NFKBIB	NFKBIB	16129	-0.12	0.088	NO
56	MAPK10	MAPK10	MAPK10	16928	-0.16	0.087	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 TOLL PATHWAY.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TOLL 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 CITRATE CYCLE TCA CYCLE

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	TNFRSF10A	TNFRSF10A	TNFRSF10A	959	0.17	0.045	YES
2	BIRC3	BIRC3	BIRC3	1237	0.14	0.11	YES
3	CASP10	CASP10	CASP10	1373	0.13	0.18	YES
4	TNFSF10	TNFSF10	TNFSF10	1645	0.12	0.24	YES
5	TRADD	TRADD	TRADD	1838	0.11	0.29	YES
6	TNFRSF25	TNFRSF25	TNFRSF25	2525	0.083	0.3	YES
7	CASP8	CASP8	CASP8	2689	0.078	0.34	YES
8	CASP7	CASP7	CASP7	3058	0.069	0.36	YES
9	CFLAR	CFLAR	CFLAR	3970	0.051	0.34	YES
10	LMNA	LMNA	LMNA	4018	0.05	0.36	YES
11	XIAP	XIAP	XIAP	4055	0.049	0.39	YES
12	MAP3K14	MAP3K14	MAP3K14	4543	0.042	0.39	YES
13	NFKBIA	NFKBIA	NFKBIA	4633	0.041	0.4	YES
14	RELA	RELA	RELA	5018	0.036	0.4	YES
15	FADD	FADD	FADD	5095	0.035	0.42	YES
16	NFKB1	NFKB1	NFKB1	5198	0.033	0.43	YES
17	DFFB	DFFB	DFFB	5566	0.029	0.43	NO
18	CYCS	CYCS	CYCS	6250	0.022	0.41	NO
19	BCL2	BCL2	BCL2	6937	0.015	0.38	NO
20	TRAF2	TRAF2	TRAF2	7185	0.013	0.37	NO
21	RIPK1	RIPK1	RIPK1	7924	0.0062	0.34	NO
22	TNFSF12	TNFSF12	TNFSF12	8552	0.001	0.3	NO
23	TNFRSF10B	TNFRSF10B	TNFRSF10B	8663	0.00025	0.3	NO
24	CASP6	CASP6	CASP6	9066	-0.0031	0.28	NO
25	CASP9	CASP9	CASP9	10415	-0.015	0.21	NO
26	BIRC2	BIRC2	BIRC2	11442	-0.025	0.17	NO
27	CASP3	CASP3	CASP3	11880	-0.029	0.16	NO
28	SPTAN1	SPTAN1	SPTAN1	12436	-0.035	0.15	NO
29	DFFA	DFFA	DFFA	12677	-0.038	0.16	NO
30	CHUK	CHUK	CHUK	13238	-0.046	0.16	NO
31	APAF1	APAF1	APAF1	14178	-0.062	0.14	NO
32	GAS2	GAS2	GAS2	16955	-0.16	0.085	NO

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

Figure S28. 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 FATTY ACID METABOLISM

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	B3GALT5	B3GALT5	B3GALT5	100	0.38	0.13	YES
2	FUT2	FUT2	FUT2	220	0.31	0.23	YES
3	FUT3	FUT3	FUT3	281	0.28	0.33	YES
4	ABO	ABO	ABO	669	0.21	0.38	YES
5	B3GNT3	B3GNT3	B3GNT3	832	0.18	0.44	YES
6	FUT6	FUT6	FUT6	1066	0.16	0.49	YES
7	FUT5	FUT5	FUT5	1377	0.13	0.52	YES
8	B4GALT1	B4GALT1	B4GALT1	2964	0.072	0.46	NO
9	ST3GAL6	ST3GAL6	ST3GAL6	3196	0.066	0.47	NO
10	ST3GAL4	ST3GAL4	ST3GAL4	3869	0.053	0.45	NO
11	B3GNT5	B3GNT5	B3GNT5	4523	0.042	0.43	NO
12	GCNT2	GCNT2	GCNT2	4617	0.041	0.44	NO
13	FUT7	FUT7	FUT7	4629	0.041	0.45	NO
14	B4GALT2	B4GALT2	B4GALT2	8410	0.0022	0.25	NO
15	B4GALT3	B4GALT3	B4GALT3	9212	-0.0044	0.21	NO
16	B3GNT2	B3GNT2	B3GNT2	9763	-0.0092	0.18	NO
17	B3GNT1	B3GNT1	B3GNT1	12262	-0.033	0.059	NO
18	FUT4	FUT4	FUT4	13619	-0.052	0.004	NO
19	B4GALT4	B4GALT4	B4GALT4	13778	-0.055	0.015	NO
20	FUT1	FUT1	FUT1	14093	-0.061	0.02	NO
21	B3GNT4	B3GNT4	B3GNT4	14648	-0.073	0.016	NO
22	ST3GAL3	ST3GAL3	ST3GAL3	15129	-0.084	0.02	NO
23	B3GALT2	B3GALT2	B3GALT2	15215	-0.086	0.046	NO
24	ST8SIA1	ST8SIA1	ST8SIA1	17126	-0.17	0.0048	NO
25	B3GALT1	B3GALT1	B3GALT1	17446	-0.2	0.059	NO

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

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	BIRC3	BIRC3	BIRC3	1237	0.14	-0.0038	YES
2	PRKCD	PRKCD	PRKCD	1647	0.12	0.026	YES
3	TRADD	TRADD	TRADD	1838	0.11	0.064	YES
4	TNF	TNF	TNF	1863	0.11	0.11	YES
5	CASP8	CASP8	CASP8	2689	0.078	0.099	YES
6	CASP7	CASP7	CASP7	3058	0.069	0.11	YES
7	CRADD	CRADD	CRADD	3076	0.069	0.14	YES
8	FAS	FAS	FAS	3197	0.066	0.16	YES
9	CFLAR	CFLAR	CFLAR	3970	0.051	0.14	YES
10	LMNA	LMNA	LMNA	4018	0.05	0.16	YES
11	XIAP	XIAP	XIAP	4055	0.049	0.18	YES
12	TRAF1	TRAF1	TRAF1	4102	0.049	0.2	YES
13	TNFRSF1B	TNFRSF1B	TNFRSF1B	4188	0.047	0.21	YES
14	MAP3K14	MAP3K14	MAP3K14	4543	0.042	0.21	YES
15	ARHGDIB	ARHGDIB	ARHGDIB	4614	0.041	0.23	YES
16	NFKBIA	NFKBIA	NFKBIA	4633	0.041	0.24	YES
17	PTK2	PTK2	PTK2	4961	0.036	0.24	YES
18	BID	BID	BID	5011	0.036	0.26	YES
19	RELA	RELA	RELA	5018	0.036	0.27	YES
20	FADD	FADD	FADD	5095	0.035	0.28	YES
21	NFKB1	NFKB1	NFKB1	5198	0.033	0.29	YES
22	GSN	GSN	GSN	5231	0.033	0.3	YES
23	TNFRSF1A	TNFRSF1A	TNFRSF1A	5482	0.03	0.3	YES
24	DFFB	DFFB	DFFB	5566	0.029	0.31	YES
25	CYCS	CYCS	CYCS	6250	0.022	0.28	NO
26	MAP3K1	MAP3K1	MAP3K1	6256	0.022	0.29	NO
27	PSEN2	PSEN2	PSEN2	6549	0.019	0.28	NO
28	BCL2	BCL2	BCL2	6937	0.015	0.27	NO
29	TRAF2	TRAF2	TRAF2	7185	0.013	0.26	NO
30	RIPK1	RIPK1	RIPK1	7924	0.0062	0.23	NO
31	CASP2	CASP2	CASP2	8123	0.0046	0.22	NO
32	NUMA1	NUMA1	NUMA1	8442	0.0019	0.2	NO
33	MDM2	MDM2	MDM2	8796	-0.00093	0.18	NO
34	CASP6	CASP6	CASP6	9066	-0.0031	0.17	NO
35	DAXX	DAXX	DAXX	9355	-0.0056	0.16	NO
36	BAG4	BAG4	BAG4	10036	-0.012	0.12	NO
37	CASP9	CASP9	CASP9	10415	-0.015	0.11	NO
38	PARP1	PARP1	PARP1	11241	-0.022	0.075	NO
39	ACTG1	ACTG1	ACTG1	11418	-0.024	0.076	NO
40	BIRC2	BIRC2	BIRC2	11442	-0.025	0.086	NO
41	PRKDC	PRKDC	PRKDC	11617	-0.026	0.088	NO
42	PSEN1	PSEN1	PSEN1	11635	-0.026	0.098	NO
43	CASP3	CASP3	CASP3	11880	-0.029	0.098	NO
44	MAPK8	MAPK8	MAPK8	12039	-0.031	0.1	NO
45	MAP2K7	MAP2K7	MAP2K7	12157	-0.032	0.11	NO
46	RASA1	RASA1	RASA1	12381	-0.035	0.11	NO
47	SPTAN1	SPTAN1	SPTAN1	12436	-0.035	0.13	NO
48	MAP3K5	MAP3K5	MAP3K5	12499	-0.036	0.14	NO
49	DFFA	DFFA	DFFA	12677	-0.038	0.14	NO
50	CDK11A	CDK11A	CDK11A	12730	-0.039	0.16	NO
51	PAK2	PAK2	PAK2	12906	-0.041	0.17	NO
52	CHUK	CHUK	CHUK	13238	-0.046	0.17	NO
53	CDK11B	CDK11B	CDK11B	13254	-0.046	0.19	NO
54	LMNB2	LMNB2	LMNB2	13567	-0.051	0.19	NO
55	LMNB1	LMNB1	LMNB1	13729	-0.054	0.21	NO
56	RB1	RB1	RB1	13742	-0.054	0.23	NO
57	APAF1	APAF1	APAF1	14178	-0.062	0.24	NO

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

Figure S32. 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 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	TLR3	TLR3	TLR3	821	0.18	0.056	YES
2	TLR7	TLR7	TLR7	1566	0.12	0.082	YES
3	TLR6	TLR6	TLR6	1642	0.12	0.14	YES
4	TLR10	TLR10	TLR10	1811	0.11	0.19	YES
5	TIRAP	TIRAP	TIRAP	2048	0.1	0.23	YES
6	MYD88	MYD88	MYD88	2792	0.075	0.24	YES
7	IRAK1	IRAK1	IRAK1	2968	0.072	0.26	YES
8	IKBKB	IKBKB	IKBKB	3037	0.07	0.3	YES
9	FOS	FOS	FOS	3920	0.052	0.28	YES
10	ELK1	ELK1	ELK1	3998	0.05	0.3	YES
11	TRAF6	TRAF6	TRAF6	4266	0.046	0.31	YES
12	MAP2K3	MAP2K3	MAP2K3	4435	0.044	0.33	YES
13	IKBKG	IKBKG	IKBKG	4484	0.043	0.35	YES
14	MAP3K14	MAP3K14	MAP3K14	4543	0.042	0.37	YES
15	NFKBIA	NFKBIA	NFKBIA	4633	0.041	0.38	YES
16	TLR4	TLR4	TLR4	4841	0.038	0.39	YES
17	RELA	RELA	RELA	5018	0.036	0.4	YES
18	TLR2	TLR2	TLR2	5143	0.034	0.41	YES
19	NFKB1	NFKB1	NFKB1	5198	0.033	0.43	YES
20	MAP3K1	MAP3K1	MAP3K1	6256	0.022	0.38	NO
21	CD14	CD14	CD14	7002	0.014	0.35	NO
22	ECSIT	ECSIT	ECSIT	7732	0.0077	0.32	NO
23	TOLLIP	TOLLIP	TOLLIP	8262	0.0033	0.29	NO
24	TAB1	TAB1	TAB1	8578	0.00077	0.27	NO
25	MAPK14	MAPK14	MAPK14	8682	9e-05	0.27	NO
26	EIF2AK2	EIF2AK2	EIF2AK2	9942	-0.011	0.2	NO
27	TLR9	TLR9	TLR9	10334	-0.014	0.19	NO
28	MAPK8	MAPK8	MAPK8	12039	-0.031	0.12	NO
29	JUN	JUN	JUN	12088	-0.031	0.13	NO
30	CHUK	CHUK	CHUK	13238	-0.046	0.093	NO
31	LY96	LY96	LY96	13466	-0.05	0.11	NO
32	PGLYRP1	PGLYRP1	PGLYRP1	13467	-0.05	0.13	NO
33	MAP2K6	MAP2K6	MAP2K6	13501	-0.05	0.16	NO
34	MAP2K4	MAP2K4	MAP2K4	13739	-0.054	0.18	NO
35	TAB2	TAB2	TAB2	13949	-0.058	0.2	NO
36	MAP3K7	MAP3K7	MAP3K7	15526	-0.096	0.16	NO

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

Figure S34. 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 GLUTATHIONE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GSTA3	GSTA3	GSTA3	160	0.34	0.096	YES
2	OPLAH	OPLAH	OPLAH	705	0.2	0.13	YES
3	GPX2	GPX2	GPX2	816	0.19	0.18	YES
4	GGT1	GGT1	GGT1	1076	0.16	0.22	YES
5	GSTM5	GSTM5	GSTM5	1132	0.15	0.26	YES
6	ANPEP	ANPEP	ANPEP	1812	0.11	0.26	YES
7	GGT6	GGT6	GGT6	2412	0.086	0.25	YES
8	MGST2	MGST2	MGST2	2502	0.084	0.27	YES
9	GSTK1	GSTK1	GSTK1	2564	0.082	0.3	YES
10	IDH2	IDH2	IDH2	2961	0.072	0.3	YES
11	GSTT1	GSTT1	GSTT1	3320	0.063	0.3	YES
12	GSR	GSR	GSR	3531	0.059	0.3	YES
13	GSTZ1	GSTZ1	GSTZ1	3615	0.057	0.32	YES
14	LAP3	LAP3	LAP3	3802	0.054	0.32	YES
15	IDH1	IDH1	IDH1	3826	0.054	0.34	YES
16	GGCT	GGCT	GGCT	3833	0.053	0.36	YES
17	GSTA1	GSTA1	GSTA1	4104	0.049	0.36	YES
18	RRM2B	RRM2B	RRM2B	4234	0.046	0.36	YES
19	GCLM	GCLM	GCLM	4340	0.045	0.37	YES
20	GSTA5	GSTA5	GSTA5	4568	0.042	0.37	YES
21	GSTP1	GSTP1	GSTP1	4740	0.039	0.38	YES
22	GPX1	GPX1	GPX1	5770	0.027	0.33	NO
23	GSTO2	GSTO2	GSTO2	5871	0.026	0.33	NO
24	SMS	SMS	SMS	6811	0.016	0.28	NO
25	MGST3	MGST3	MGST3	6940	0.015	0.28	NO
26	GSS	GSS	GSS	7489	0.0099	0.26	NO
27	GSTO1	GSTO1	GSTO1	7581	0.0091	0.25	NO
28	GSTM1	GSTM1	GSTM1	8151	0.0044	0.22	NO
29	GPX4	GPX4	GPX4	8458	0.0018	0.21	NO
30	TXNDC12	TXNDC12	TXNDC12	9316	-0.0053	0.16	NO
31	G6PD	G6PD	G6PD	10744	-0.018	0.092	NO
32	GSTM4	GSTM4	GSTM4	11258	-0.023	0.072	NO
33	GSTA4	GSTA4	GSTA4	11450	-0.025	0.069	NO
34	RRM1	RRM1	RRM1	11846	-0.029	0.057	NO
35	SRM	SRM	SRM	12281	-0.033	0.044	NO
36	GGT7	GGT7	GGT7	13001	-0.042	0.018	NO
37	GPX3	GPX3	GPX3	13536	-0.051	0.0048	NO
38	ODC1	ODC1	ODC1	14085	-0.061	-0.006	NO
39	GSTM2	GSTM2	GSTM2	14152	-0.062	0.0096	NO
40	GSTA2	GSTA2	GSTA2	14437	-0.068	0.015	NO
41	RRM2	RRM2	RRM2	14768	-0.075	0.021	NO
42	MGST1	MGST1	MGST1	14851	-0.077	0.04	NO
43	GCLC	GCLC	GCLC	14972	-0.08	0.059	NO
44	GGT5	GGT5	GGT5	15195	-0.086	0.073	NO
45	GPX7	GPX7	GPX7	15359	-0.09	0.093	NO
46	GSTM3	GSTM3	GSTM3	16077	-0.12	0.09	NO
47	GSTT2	GSTT2	GSTT2	16503	-0.14	0.11	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 GLUTATHIONE METABOLISM.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLUTATHIONE 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 SPHINGOLIPID METABOLISM

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	PPAP2C	PPAP2C	PPAP2C	304	0.28	0.088	YES
2	NEU4	NEU4	NEU4	376	0.26	0.18	YES
3	DEGS2	DEGS2	DEGS2	650	0.21	0.24	YES
4	SMPD3	SMPD3	SMPD3	1036	0.16	0.28	YES
5	ACER2	ACER2	ACER2	1390	0.13	0.32	YES
6	SGMS1	SGMS1	SGMS1	2033	0.1	0.32	YES
7	SGMS2	SGMS2	SGMS2	2453	0.085	0.33	YES
8	UGCG	UGCG	UGCG	2814	0.075	0.34	YES
9	ACER1	ACER1	ACER1	2825	0.075	0.36	YES
10	SMPD2	SMPD2	SMPD2	3897	0.052	0.32	NO
11	GLA	GLA	GLA	4526	0.042	0.31	NO
12	ARSA	ARSA	ARSA	5873	0.026	0.24	NO
13	GLB1	GLB1	GLB1	6122	0.023	0.24	NO
14	UGT8	UGT8	UGT8	6407	0.02	0.23	NO
15	SPTLC1	SPTLC1	SPTLC1	6840	0.016	0.22	NO
16	SPTLC2	SPTLC2	SPTLC2	7694	0.0081	0.17	NO
17	SGPP1	SGPP1	SGPP1	7754	0.0076	0.17	NO
18	KDSR	KDSR	KDSR	8061	0.0052	0.16	NO
19	ASAH1	ASAH1	ASAH1	8188	0.0039	0.15	NO
20	SGPP2	SGPP2	SGPP2	8422	0.0021	0.14	NO
21	NEU2	NEU2	NEU2	9209	-0.0044	0.098	NO
22	NEU3	NEU3	NEU3	10052	-0.012	0.057	NO
23	SMPD1	SMPD1	SMPD1	10306	-0.014	0.049	NO
24	ASAH2	ASAH2	ASAH2	10875	-0.019	0.026	NO
25	DEGS1	DEGS1	DEGS1	11196	-0.022	0.016	NO
26	SGPL1	SGPL1	SGPL1	11624	-0.026	0.0033	NO
27	NEU1	NEU1	NEU1	11979	-0.03	-0.0045	NO
28	ACER3	ACER3	ACER3	12097	-0.031	0.00092	NO
29	GBA	GBA	GBA	12983	-0.042	-0.031	NO
30	GALC	GALC	GALC	13033	-0.043	-0.018	NO
31	SMPD4	SMPD4	SMPD4	13110	-0.044	-0.005	NO
32	CERK	CERK	CERK	13361	-0.048	-0.00055	NO
33	PPAP2B	PPAP2B	PPAP2B	13876	-0.057	-0.0071	NO
34	GAL3ST1	GAL3ST1	GAL3ST1	14074	-0.06	0.0049	NO
35	PPAP2A	PPAP2A	PPAP2A	14793	-0.076	-0.0055	NO
36	SPHK2	SPHK2	SPHK2	15559	-0.097	-0.01	NO
37	B4GALT6	B4GALT6	B4GALT6	17208	-0.18	-0.032	NO
38	SPHK1	SPHK1	SPHK1	18051	-0.28	0.026	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 SPHINGOLIPID METABOLISM.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPHINGOLIPID 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

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	ABCA13	ABCA13	ABCA13	270	0.29	0.057	YES
2	ABCA10	ABCA10	ABCA10	545	0.22	0.097	YES
3	ABCG2	ABCG2	ABCG2	616	0.21	0.15	YES
4	ABCC2	ABCC2	ABCC2	624	0.21	0.2	YES
5	ABCG8	ABCG8	ABCG8	763	0.19	0.24	YES
6	ABCG5	ABCG5	ABCG5	791	0.19	0.28	YES
7	ABCA7	ABCA7	ABCA7	876	0.18	0.32	YES
8	ABCB11	ABCB11	ABCB11	961	0.17	0.36	YES
9	ABCA12	ABCA12	ABCA12	1058	0.16	0.39	YES
10	TAP2	TAP2	TAP2	1290	0.14	0.42	YES
11	TAP1	TAP1	TAP1	1848	0.11	0.41	NO
12	ABCC4	ABCC4	ABCC4	2566	0.082	0.39	NO
13	ABCB9	ABCB9	ABCB9	2662	0.079	0.41	NO
14	ABCA5	ABCA5	ABCA5	2886	0.074	0.41	NO
15	ABCB10	ABCB10	ABCB10	3506	0.059	0.4	NO
16	ABCG1	ABCG1	ABCG1	3929	0.052	0.38	NO
17	ABCA2	ABCA2	ABCA2	4293	0.046	0.38	NO
18	ABCD1	ABCD1	ABCD1	4693	0.04	0.36	NO
19	ABCB6	ABCB6	ABCB6	4836	0.038	0.37	NO
20	ABCC6	ABCC6	ABCC6	5036	0.036	0.36	NO
21	ABCA9	ABCA9	ABCA9	5699	0.028	0.34	NO
22	ABCG4	ABCG4	ABCG4	5734	0.027	0.34	NO
23	ABCB7	ABCB7	ABCB7	5942	0.025	0.34	NO
24	ABCB1	ABCB1	ABCB1	6075	0.024	0.33	NO
25	ABCC3	ABCC3	ABCC3	6175	0.022	0.33	NO
26	ABCC10	ABCC10	ABCC10	9754	-0.0091	0.14	NO
27	ABCD3	ABCD3	ABCD3	10025	-0.012	0.13	NO
28	ABCB8	ABCB8	ABCB8	10510	-0.016	0.11	NO
29	ABCD4	ABCD4	ABCD4	11465	-0.025	0.063	NO
30	ABCA1	ABCA1	ABCA1	11943	-0.03	0.045	NO
31	ABCD2	ABCD2	ABCD2	12136	-0.032	0.042	NO
32	ABCC12	ABCC12	ABCC12	12529	-0.036	0.03	NO
33	ABCC5	ABCC5	ABCC5	12687	-0.038	0.031	NO
34	ABCC11	ABCC11	ABCC11	12776	-0.039	0.036	NO
35	ABCA4	ABCA4	ABCA4	12777	-0.039	0.046	NO
36	ABCC1	ABCC1	ABCC1	13380	-0.048	0.025	NO
37	ABCA3	ABCA3	ABCA3	14261	-0.064	-0.0068	NO
38	CFTR	CFTR	CFTR	14858	-0.077	-0.02	NO
39	ABCB4	ABCB4	ABCB4	16097	-0.12	-0.058	NO
40	ABCA6	ABCA6	ABCA6	16910	-0.16	-0.063	NO
41	ABCC9	ABCC9	ABCC9	17022	-0.16	-0.029	NO
42	ABCB5	ABCB5	ABCB5	17650	-0.22	-0.0081	NO
43	ABCC8	ABCC8	ABCC8	17707	-0.23	0.045	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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, 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 ALK PATHWAY	33	genes.ES.table	0.49	1.4	0.11	0.89	0.98	0.36	0.24	0.28	0.71	0.32
BIOCARTA BIOPEPTIDES PATHWAY	40	genes.ES.table	0.37	1.3	0.16	0.89	1	0.2	0.12	0.18	0.76	0.32
BIOCARTA CARM ER PATHWAY	34	genes.ES.table	0.33	1.2	0.22	0.83	1	0.56	0.4	0.33	0.74	0.29
BIOCARTA MPR PATHWAY	32	genes.ES.table	0.4	1.4	0.12	1	0.97	0.25	0.22	0.2	0.96	0.48
BIOCARTA INTEGRIN PATHWAY	37	genes.ES.table	0.33	1.3	0.21	0.87	1	0.081	0.066	0.076	0.77	0.32
BIOCARTA WNT PATHWAY	25	genes.ES.table	0.42	1.4	0.14	1	0.97	0.44	0.33	0.29	0.84	0.4
KEGG RNA DEGRADATION	56	genes.ES.table	0.29	1.4	0.15	0.99	0.98	0.61	0.5	0.3	0.8	0.38
KEGG SPLICEOSOME	125	genes.ES.table	0.27	1.3	0.19	0.96	0.99	0.62	0.5	0.31	0.81	0.38
KEGG CARDIAC MUSCLE CONTRACTION	66	genes.ES.table	0.51	1.5	0.023	1	0.9	0.36	0.19	0.3	1	0.82
KEGG WNT SIGNALING PATHWAY	146	genes.ES.table	0.37	1.3	0.12	0.93	0.99	0.21	0.15	0.18	0.79	0.36

genes ES table in pathway: BIOCARTA ALK 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	CACNA2D2	CACNA2D2	CACNA2D2	28	0.63	0.061	YES
2	MYH6	MYH6	MYH6	41	0.6	0.12	YES
3	ATP1A2	ATP1A2	ATP1A2	98	0.54	0.17	YES
4	ATP1B2	ATP1B2	ATP1B2	149	0.5	0.22	YES
5	MYH7	MYH7	MYH7	245	0.45	0.26	YES
6	COX6A2	COX6A2	COX6A2	498	0.37	0.28	YES
7	ACTC1	ACTC1	ACTC1	717	0.33	0.3	YES
8	COX4I2	COX4I2	COX4I2	800	0.32	0.33	YES
9	CACNB4	CACNB4	CACNB4	807	0.32	0.36	YES
10	CACNA1D	CACNA1D	CACNA1D	931	0.3	0.38	YES
11	CACNA1S	CACNA1S	CACNA1S	941	0.3	0.41	YES
12	RYR2	RYR2	RYR2	947	0.3	0.44	YES
13	FXYD2	FXYD2	FXYD2	1186	0.27	0.45	YES
14	CACNG5	CACNG5	CACNG5	1437	0.25	0.46	YES
15	MYL3	MYL3	MYL3	1700	0.23	0.47	YES
16	COX6B2	COX6B2	COX6B2	1871	0.22	0.48	YES
17	ATP1A4	ATP1A4	ATP1A4	1920	0.21	0.5	YES
18	TNNT2	TNNT2	TNNT2	2399	0.18	0.49	YES
19	CACNA1C	CACNA1C	CACNA1C	3008	0.15	0.48	YES
20	CACNB3	CACNB3	CACNB3	3321	0.14	0.47	YES
21	CACNG6	CACNG6	CACNG6	3412	0.13	0.48	YES
22	COX8C	COX8C	COX8C	3428	0.13	0.49	YES
23	TNNC1	TNNC1	TNNC1	3483	0.13	0.5	YES
24	CACNB2	CACNB2	CACNB2	3519	0.13	0.51	YES
25	CACNA2D1	CACNA2D1	CACNA2D1	3862	0.12	0.51	NO
26	CACNG8	CACNG8	CACNG8	5502	0.076	0.42	NO
27	ATP1B1	ATP1B1	ATP1B1	5917	0.067	0.41	NO
28	COX7A2L	COX7A2L	COX7A2L	7154	0.047	0.35	NO
29	CACNB1	CACNB1	CACNB1	8456	0.03	0.28	NO
30	ATP1B3	ATP1B3	ATP1B3	10795	-0.00052	0.15	NO
31	SLC8A1	SLC8A1	SLC8A1	10873	-0.0016	0.15	NO
32	COX6B1	COX6B1	COX6B1	10943	-0.0027	0.15	NO
33	CACNA2D3	CACNA2D3	CACNA2D3	11355	-0.008	0.12	NO
34	COX7C	COX7C	COX7C	11485	-0.01	0.12	NO
35	TPM3	TPM3	TPM3	11922	-0.016	0.096	NO
36	ATP2A2	ATP2A2	ATP2A2	12052	-0.018	0.091	NO
37	COX7A2	COX7A2	COX7A2	12362	-0.023	0.076	NO
38	ATP1A1	ATP1A1	ATP1A1	12476	-0.024	0.073	NO
39	COX5B	COX5B	COX5B	12714	-0.028	0.063	NO
40	UQCRFS1	UQCRFS1	UQCRFS1	12831	-0.03	0.059	NO
41	TNNI3	TNNI3	TNNI3	12867	-0.03	0.06	NO
42	SLC9A1	SLC9A1	SLC9A1	12922	-0.032	0.061	NO
43	COX6A1	COX6A1	COX6A1	12994	-0.032	0.06	NO
44	TPM4	TPM4	TPM4	13098	-0.034	0.058	NO
45	UQCRC1	UQCRC1	UQCRC1	13149	-0.035	0.059	NO
46	COX4I1	COX4I1	COX4I1	13156	-0.035	0.062	NO
47	TPM1	TPM1	TPM1	13596	-0.044	0.042	NO
48	CACNG4	CACNG4	CACNG4	13606	-0.044	0.046	NO
49	CACNA1F	CACNA1F	CACNA1F	14320	-0.06	0.014	NO
50	SLC9A6	SLC9A6	SLC9A6	14595	-0.068	0.0054	NO
51	UQCR10	UQCR10	UQCR10	14848	-0.075	-0.00086	NO
52	UQCR11	UQCR11	UQCR11	14895	-0.077	0.0042	NO
53	TPM2	TPM2	TPM2	15024	-0.081	0.0053	NO
54	COX8A	COX8A	COX8A	15075	-0.083	0.011	NO
55	UQCRQ	UQCRQ	UQCRQ	15077	-0.083	0.019	NO
56	COX5A	COX5A	COX5A	15171	-0.086	0.022	NO
57	UQCRHL	UQCRHL	UQCRHL	15175	-0.086	0.031	NO
58	UQCRH	UQCRH	UQCRH	15419	-0.094	0.027	NO
59	COX7A1	COX7A1	COX7A1	15482	-0.097	0.033	NO
60	UQCRB	UQCRB	UQCRB	16107	-0.13	0.012	NO
61	COX7B	COX7B	COX7B	16279	-0.14	0.016	NO
62	CYC1	CYC1	CYC1	16620	-0.16	0.013	NO
63	COX6C	COX6C	COX6C	17060	-0.2	0.0091	NO
64	CACNG1	CACNG1	CACNG1	17087	-0.2	0.028	NO
65	CACNA2D4	CACNA2D4	CACNA2D4	17342	-0.23	0.037	NO
66	ATP1A3	ATP1A3	ATP1A3	17645	-0.28	0.048	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 ALK PATHWAY.

Figure S42. 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 BIOPEPTIDES 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	TCF7L1	TCF7L1	TCF7L1	115	0.52	0.054	YES
2	WNT2B	WNT2B	WNT2B	253	0.44	0.098	YES
3	PTCH2	PTCH2	PTCH2	337	0.41	0.14	YES
4	FZD2	FZD2	FZD2	388	0.4	0.18	YES
5	GLI1	GLI1	GLI1	412	0.39	0.23	YES
6	GLI2	GLI2	GLI2	460	0.38	0.27	YES
7	WNT11	WNT11	WNT11	687	0.34	0.3	YES
8	WNT8B	WNT8B	WNT8B	790	0.32	0.33	YES
9	WNT6	WNT6	WNT6	816	0.32	0.36	YES
10	WNT5B	WNT5B	WNT5B	876	0.31	0.4	YES
11	SMO	SMO	SMO	1091	0.28	0.42	YES
12	WNT10B	WNT10B	WNT10B	1238	0.27	0.44	YES
13	LEF1	LEF1	LEF1	1284	0.26	0.47	YES
14	WNT5A	WNT5A	WNT5A	1557	0.24	0.48	YES
15	FZD10	FZD10	FZD10	1993	0.21	0.48	YES
16	WNT3	WNT3	WNT3	2064	0.2	0.5	YES
17	FZD7	FZD7	FZD7	2276	0.19	0.51	YES
18	WNT4	WNT4	WNT4	2563	0.17	0.52	YES
19	FZD9	FZD9	FZD9	2716	0.16	0.53	YES
20	SHH	SHH	SHH	2905	0.16	0.54	YES
21	WNT8A	WNT8A	WNT8A	3066	0.15	0.55	YES
22	WNT16	WNT16	WNT16	3236	0.14	0.55	YES
23	PTCH1	PTCH1	PTCH1	3436	0.13	0.56	YES
24	APC2	APC2	APC2	3622	0.12	0.56	YES
25	STK36	STK36	STK36	3659	0.12	0.57	YES
26	FZD5	FZD5	FZD5	3693	0.12	0.59	YES
27	WNT1	WNT1	WNT1	4037	0.11	0.58	NO
28	DVL2	DVL2	DVL2	4165	0.11	0.59	NO
29	WNT9B	WNT9B	WNT9B	4994	0.086	0.55	NO
30	GLI3	GLI3	GLI3	5005	0.086	0.56	NO
31	SUFU	SUFU	SUFU	5165	0.083	0.56	NO
32	GSK3B	GSK3B	GSK3B	5265	0.081	0.57	NO
33	AXIN2	AXIN2	AXIN2	5648	0.073	0.55	NO
34	WNT10A	WNT10A	WNT10A	6173	0.062	0.53	NO
35	TCF7L2	TCF7L2	TCF7L2	6536	0.056	0.52	NO
36	CTNNB1	CTNNB1	CTNNB1	7349	0.044	0.48	NO
37	DVL3	DVL3	DVL3	7357	0.044	0.48	NO
38	TCF7	TCF7	TCF7	7359	0.044	0.49	NO
39	FZD3	FZD3	FZD3	8293	0.032	0.44	NO
40	WNT2	WNT2	WNT2	9222	0.02	0.4	NO
41	BMP4	BMP4	BMP4	9257	0.019	0.4	NO
42	DVL1	DVL1	DVL1	9331	0.018	0.39	NO
43	WNT9A	WNT9A	WNT9A	9746	0.013	0.37	NO
44	AXIN1	AXIN1	AXIN1	9811	0.012	0.37	NO
45	APC	APC	APC	10709	0.00083	0.32	NO
46	TP53	TP53	TP53	10964	-0.003	0.31	NO
47	BMP2	BMP2	BMP2	13314	-0.038	0.19	NO
48	HHIP	HHIP	HHIP	14032	-0.054	0.15	NO
49	FZD8	FZD8	FZD8	14661	-0.07	0.13	NO
50	FZD1	FZD1	FZD1	14699	-0.071	0.13	NO
51	FZD4	FZD4	FZD4	15163	-0.086	0.12	NO
52	WNT7A	WNT7A	WNT7A	15270	-0.089	0.12	NO
53	FZD6	FZD6	FZD6	16029	-0.12	0.097	NO
54	WNT7B	WNT7B	WNT7B	17923	-0.33	0.033	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 BIOPEPTIDES PATHWAY.

Figure S44. 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 CARM ER 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	WNT2B	WNT2B	WNT2B	253	0.44	0.041	YES
2	PTCH2	PTCH2	PTCH2	337	0.41	0.087	YES
3	GLI1	GLI1	GLI1	412	0.39	0.13	YES
4	GLI2	GLI2	GLI2	460	0.38	0.18	YES
5	BMP7	BMP7	BMP7	515	0.37	0.22	YES
6	WNT11	WNT11	WNT11	687	0.34	0.25	YES
7	BMP6	BMP6	BMP6	697	0.34	0.29	YES
8	WNT8B	WNT8B	WNT8B	790	0.32	0.33	YES
9	WNT6	WNT6	WNT6	816	0.32	0.36	YES
10	WNT5B	WNT5B	WNT5B	876	0.31	0.4	YES
11	SMO	SMO	SMO	1091	0.28	0.42	YES
12	WNT10B	WNT10B	WNT10B	1238	0.27	0.45	YES
13	ZIC2	ZIC2	ZIC2	1487	0.25	0.46	YES
14	WNT5A	WNT5A	WNT5A	1557	0.24	0.49	YES
15	WNT3	WNT3	WNT3	2064	0.2	0.49	YES
16	WNT4	WNT4	WNT4	2563	0.17	0.48	YES
17	SHH	SHH	SHH	2905	0.16	0.48	YES
18	WNT8A	WNT8A	WNT8A	3066	0.15	0.49	YES
19	IHH	IHH	IHH	3095	0.15	0.51	YES
20	WNT16	WNT16	WNT16	3236	0.14	0.52	YES
21	LRP2	LRP2	LRP2	3264	0.14	0.53	YES
22	CSNK1A1L	CSNK1A1L	CSNK1A1L	3380	0.13	0.54	YES
23	PTCH1	PTCH1	PTCH1	3436	0.13	0.56	YES
24	STK36	STK36	STK36	3659	0.12	0.56	YES
25	PRKACB	PRKACB	PRKACB	3998	0.11	0.56	YES
26	WNT1	WNT1	WNT1	4037	0.11	0.57	YES
27	RAB23	RAB23	RAB23	4389	0.1	0.56	YES
28	BTRC	BTRC	BTRC	4395	0.1	0.57	YES
29	WNT9B	WNT9B	WNT9B	4994	0.086	0.55	YES
30	GLI3	GLI3	GLI3	5005	0.086	0.56	YES
31	BMP8A	BMP8A	BMP8A	5007	0.086	0.57	YES
32	SUFU	SUFU	SUFU	5165	0.083	0.57	YES
33	GSK3B	GSK3B	GSK3B	5265	0.081	0.58	YES
34	WNT10A	WNT10A	WNT10A	6173	0.062	0.54	NO
35	CSNK1E	CSNK1E	CSNK1E	6524	0.056	0.52	NO
36	PRKACA	PRKACA	PRKACA	7798	0.038	0.46	NO
37	BMP8B	BMP8B	BMP8B	8626	0.027	0.42	NO
38	WNT2	WNT2	WNT2	9222	0.02	0.39	NO
39	BMP4	BMP4	BMP4	9257	0.019	0.39	NO
40	WNT9A	WNT9A	WNT9A	9746	0.013	0.37	NO
41	CSNK1G2	CSNK1G2	CSNK1G2	10042	0.0093	0.35	NO
42	FBXW11	FBXW11	FBXW11	10333	0.0057	0.34	NO
43	CSNK1G3	CSNK1G3	CSNK1G3	10354	0.0053	0.34	NO
44	CSNK1G1	CSNK1G1	CSNK1G1	10590	0.0023	0.32	NO
45	CSNK1D	CSNK1D	CSNK1D	12027	-0.018	0.25	NO
46	BMP2	BMP2	BMP2	13314	-0.038	0.18	NO
47	DHH	DHH	DHH	13794	-0.048	0.16	NO
48	HHIP	HHIP	HHIP	14032	-0.054	0.16	NO
49	CSNK1A1	CSNK1A1	CSNK1A1	14058	-0.054	0.16	NO
50	WNT7A	WNT7A	WNT7A	15270	-0.089	0.11	NO
51	GAS1	GAS1	GAS1	15615	-0.1	0.1	NO
52	PRKX	PRKX	PRKX	16080	-0.12	0.092	NO
53	WNT7B	WNT7B	WNT7B	17923	-0.33	0.033	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 CARM ER PATHWAY.

Figure S46. 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 MPR 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	CLDN19	CLDN19	CLDN19	33	0.62	0.041	YES
2	MYH6	MYH6	MYH6	41	0.6	0.082	YES
3	RAB3B	RAB3B	RAB3B	60	0.57	0.12	YES
4	CTNNA3	CTNNA3	CTNNA3	214	0.46	0.14	YES
5	MYH7	MYH7	MYH7	245	0.45	0.17	YES
6	CLDN6	CLDN6	CLDN6	364	0.4	0.19	YES
7	ACTN2	ACTN2	ACTN2	440	0.38	0.22	YES
8	MYL7	MYL7	MYL7	544	0.36	0.24	YES
9	MYH15	MYH15	MYH15	796	0.32	0.24	YES
10	CLDN9	CLDN9	CLDN9	799	0.32	0.26	YES
11	CLDN2	CLDN2	CLDN2	834	0.31	0.28	YES
12	ACTN3	ACTN3	ACTN3	1064	0.28	0.29	YES
13	IGSF5	IGSF5	IGSF5	1166	0.28	0.3	YES
14	CTNNA2	CTNNA2	CTNNA2	1370	0.26	0.31	YES
15	MYH7B	MYH7B	MYH7B	1524	0.24	0.32	YES
16	PRKCG	PRKCG	PRKCG	1550	0.24	0.34	YES
17	PARD6G	PARD6G	PARD6G	1649	0.23	0.35	YES
18	MPDZ	MPDZ	MPDZ	1687	0.23	0.36	YES
19	GNAI1	GNAI1	GNAI1	2126	0.2	0.35	NO
20	CLDN18	CLDN18	CLDN18	2196	0.19	0.36	NO
21	CLDN15	CLDN15	CLDN15	2810	0.16	0.34	NO
22	LLGL1	LLGL1	LLGL1	2857	0.16	0.34	NO
23	MAGI1	MAGI1	MAGI1	2990	0.15	0.35	NO
24	MYH10	MYH10	MYH10	3258	0.14	0.34	NO
25	AMOTL1	AMOTL1	AMOTL1	3291	0.14	0.35	NO
26	MYH3	MYH3	MYH3	3757	0.12	0.33	NO
27	SRC	SRC	SRC	3783	0.12	0.34	NO
28	MAGI2	MAGI2	MAGI2	3938	0.11	0.34	NO
29	EPB41	EPB41	EPB41	4146	0.11	0.34	NO
30	CDK4	CDK4	CDK4	4169	0.11	0.34	NO
31	KRAS	KRAS	KRAS	4250	0.1	0.34	NO
32	EPB41L2	EPB41L2	EPB41L2	4354	0.1	0.35	NO
33	JAM3	JAM3	JAM3	4850	0.09	0.33	NO
34	CLDN8	CLDN8	CLDN8	5493	0.076	0.3	NO
35	CSNK2A1	CSNK2A1	CSNK2A1	5589	0.074	0.3	NO
36	CLDN11	CLDN11	CLDN11	5739	0.071	0.29	NO
37	NRAS	NRAS	NRAS	6145	0.063	0.28	NO
38	PARD6A	PARD6A	PARD6A	6459	0.058	0.26	NO
39	MLLT4	MLLT4	MLLT4	6479	0.057	0.26	NO
40	CLDN5	CLDN5	CLDN5	6629	0.055	0.26	NO
41	TJP1	TJP1	TJP1	6660	0.054	0.26	NO
42	CSNK2A2	CSNK2A2	CSNK2A2	6671	0.054	0.27	NO
43	PRKCE	PRKCE	PRKCE	6756	0.053	0.26	NO
44	TJAP1	TJAP1	TJAP1	6792	0.052	0.27	NO
45	AKT2	AKT2	AKT2	6946	0.05	0.26	NO
46	PPP2R2D	PPP2R2D	PPP2R2D	7021	0.049	0.26	NO
47	CTNNB1	CTNNB1	CTNNB1	7349	0.044	0.25	NO
48	YES1	YES1	YES1	7418	0.043	0.24	NO
49	PRKCZ	PRKCZ	PRKCZ	7428	0.043	0.25	NO
50	ZAK	ZAK	ZAK	7568	0.041	0.24	NO
51	SYMPK	SYMPK	SYMPK	7954	0.036	0.22	NO
52	MPP5	MPP5	MPP5	8086	0.034	0.22	NO
53	PPP2R2C	PPP2R2C	PPP2R2C	8336	0.031	0.21	NO
54	PPP2CB	PPP2CB	PPP2CB	8360	0.031	0.21	NO
55	EXOC4	EXOC4	EXOC4	8499	0.029	0.2	NO
56	PPP2R1A	PPP2R1A	PPP2R1A	8608	0.027	0.2	NO
57	RRAS2	RRAS2	RRAS2	8673	0.027	0.2	NO
58	PPP2R2A	PPP2R2A	PPP2R2A	9565	0.016	0.15	NO
59	SPTAN1	SPTAN1	SPTAN1	9769	0.013	0.14	NO
60	PARD3	PARD3	PARD3	9877	0.012	0.14	NO
61	CASK	CASK	CASK	10054	0.0091	0.13	NO
62	PRKCQ	PRKCQ	PRKCQ	10226	0.007	0.12	NO
63	MAGI3	MAGI3	MAGI3	10319	0.0059	0.11	NO
64	CLDN20	CLDN20	CLDN20	10364	0.0052	0.11	NO
65	PARD6B	PARD6B	PARD6B	10603	0.0021	0.098	NO
66	ASH1L	ASH1L	ASH1L	10646	0.0015	0.096	NO
67	CSNK2B	CSNK2B	CSNK2B	10648	0.0015	0.096	NO
68	PTEN	PTEN	PTEN	10899	-0.002	0.083	NO
69	RAB13	RAB13	RAB13	11038	-0.0039	0.076	NO
70	CDC42	CDC42	CDC42	11199	-0.006	0.067	NO
71	MYLPF	MYLPF	MYLPF	11245	-0.0066	0.066	NO
72	GNAI3	GNAI3	GNAI3	11275	-0.007	0.064	NO
73	MRAS	MRAS	MRAS	11292	-0.0071	0.064	NO
74	PPP2R1B	PPP2R1B	PPP2R1B	11330	-0.0077	0.062	NO
75	CSDA	CSDA	CSDA	11394	-0.0086	0.06	NO
76	CLDN14	CLDN14	CLDN14	12152	-0.02	0.02	NO
77	ACTG1	ACTG1	ACTG1	12222	-0.02	0.018	NO
78	VAPA	VAPA	VAPA	12436	-0.024	0.0076	NO
79	ACTN4	ACTN4	ACTN4	12514	-0.025	0.0052	NO
80	CTNNA1	CTNNA1	CTNNA1	12559	-0.026	0.0045	NO
81	F11R	F11R	F11R	12706	-0.028	-0.0015	NO
82	PPP2CA	PPP2CA	PPP2CA	12713	-0.028	0.00015	NO
83	OCLN	OCLN	OCLN	12749	-0.029	0.00022	NO
84	CGN	CGN	CGN	12833	-0.03	-0.0022	NO
85	MYL9	MYL9	MYL9	13032	-0.033	-0.011	NO
86	ACTB	ACTB	ACTB	13084	-0.034	-0.011	NO
87	RHOA	RHOA	RHOA	13096	-0.034	-0.0094	NO
88	ACTN1	ACTN1	ACTN1	13126	-0.035	-0.0086	NO
89	MYL12B	MYL12B	MYL12B	13265	-0.038	-0.014	NO
90	JAM2	JAM2	JAM2	13605	-0.044	-0.029	NO
91	AKT1	AKT1	AKT1	13743	-0.047	-0.033	NO
92	EXOC3	EXOC3	EXOC3	13764	-0.048	-0.031	NO
93	GNAI2	GNAI2	GNAI2	13779	-0.048	-0.028	NO
94	EPB41L1	EPB41L1	EPB41L1	13952	-0.052	-0.034	NO
95	MYH13	MYH13	MYH13	14034	-0.054	-0.035	NO
96	AKT3	AKT3	AKT3	14171	-0.057	-0.038	NO
97	INADL	INADL	INADL	14252	-0.058	-0.039	NO
98	MYH11	MYH11	MYH11	14254	-0.059	-0.035	NO
99	MYH9	MYH9	MYH9	14358	-0.062	-0.036	NO
100	CLDN4	CLDN4	CLDN4	14664	-0.07	-0.048	NO
101	CLDN1	CLDN1	CLDN1	14863	-0.076	-0.053	NO
102	CTTN	CTTN	CTTN	15045	-0.082	-0.058	NO
103	LLGL2	LLGL2	LLGL2	15182	-0.087	-0.059	NO
104	MYL12A	MYL12A	MYL12A	15199	-0.087	-0.054	NO
105	MYL5	MYL5	MYL5	15368	-0.092	-0.057	NO
106	PRKCD	PRKCD	PRKCD	15502	-0.098	-0.057	NO
107	PRKCA	PRKCA	PRKCA	15680	-0.11	-0.06	NO
108	PRKCI	PRKCI	PRKCI	15696	-0.11	-0.053	NO
109	CLDN3	CLDN3	CLDN3	15742	-0.11	-0.048	NO
110	CLDN23	CLDN23	CLDN23	15990	-0.12	-0.053	NO
111	TJP2	TJP2	TJP2	16044	-0.12	-0.048	NO
112	MYH14	MYH14	MYH14	16070	-0.12	-0.041	NO
113	CRB3	CRB3	CRB3	16177	-0.13	-0.038	NO
114	PPP2R2B	PPP2R2B	PPP2R2B	16456	-0.15	-0.043	NO
115	RRAS	RRAS	RRAS	16512	-0.15	-0.035	NO
116	CLDN7	CLDN7	CLDN7	16527	-0.15	-0.026	NO
117	PRKCH	PRKCH	PRKCH	16773	-0.17	-0.027	NO
118	TJP3	TJP3	TJP3	17388	-0.24	-0.044	NO
119	HCLS1	HCLS1	HCLS1	17576	-0.27	-0.036	NO
120	CLDN16	CLDN16	CLDN16	17663	-0.28	-0.021	NO
121	PRKCB	PRKCB	PRKCB	17679	-0.29	-0.0021	NO
122	EPB41L3	EPB41L3	EPB41L3	17749	-0.3	0.015	NO
123	CLDN10	CLDN10	CLDN10	18188	-0.41	0.019	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 MPR PATHWAY.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MPR 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 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	TCF7L1	TCF7L1	TCF7L1	115	0.52	0.2	YES
2	RXRG	RXRG	RXRG	123	0.52	0.39	YES
3	LEF1	LEF1	LEF1	1284	0.26	0.43	YES
4	NTRK1	NTRK1	NTRK1	2888	0.16	0.41	NO
5	KRAS	KRAS	KRAS	4250	0.1	0.37	NO
6	NRAS	NRAS	NRAS	6145	0.063	0.3	NO
7	TPR	TPR	TPR	6160	0.063	0.32	NO
8	TCF7L2	TCF7L2	TCF7L2	6536	0.056	0.32	NO
9	CTNNB1	CTNNB1	CTNNB1	7349	0.044	0.29	NO
10	TCF7	TCF7	TCF7	7359	0.044	0.31	NO
11	TFG	TFG	TFG	7580	0.041	0.31	NO
12	RET	RET	RET	8363	0.031	0.28	NO
13	RXRB	RXRB	RXRB	9109	0.021	0.25	NO
14	CCND1	CCND1	CCND1	9337	0.018	0.24	NO
15	BRAF	BRAF	BRAF	9879	0.012	0.22	NO
16	TP53	TP53	TP53	10964	-0.003	0.16	NO
17	RXRA	RXRA	RXRA	11329	-0.0076	0.15	NO
18	MAP2K2	MAP2K2	MAP2K2	11541	-0.011	0.14	NO
19	TPM3	TPM3	TPM3	11922	-0.016	0.12	NO
20	MAP2K1	MAP2K1	MAP2K1	12234	-0.021	0.12	NO
21	NCOA4	NCOA4	NCOA4	12601	-0.026	0.11	NO
22	MAPK1	MAPK1	MAPK1	12606	-0.026	0.12	NO
23	CDH1	CDH1	CDH1	12797	-0.03	0.12	NO
24	PAX8	PAX8	PAX8	13766	-0.048	0.083	NO
25	CCDC6	CCDC6	CCDC6	14408	-0.063	0.073	NO
26	MAPK3	MAPK3	MAPK3	14995	-0.08	0.072	NO
27	MYC	MYC	MYC	15792	-0.11	0.072	NO
28	PPARG	PPARG	PPARG	17039	-0.2	0.081	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 INTEGRIN PATHWAY.

Figure S50. 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 WNT 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	MYT1	MYT1	MYT1	421	0.39	0.12	YES
2	GNGT1	GNGT1	GNGT1	555	0.36	0.23	YES
3	PAQR5	PAQR5	PAQR5	1406	0.25	0.28	YES
4	GNAI1	GNAI1	GNAI1	2126	0.2	0.31	YES
5	ACTA1	ACTA1	ACTA1	2606	0.17	0.34	YES
6	PGR	PGR	PGR	3043	0.15	0.37	YES
7	SRC	SRC	SRC	3783	0.12	0.38	YES
8	PRKACB	PRKACB	PRKACB	3998	0.11	0.4	YES
9	PRKAR1B	PRKAR1B	PRKAR1B	5246	0.081	0.36	NO
10	PAQR7	PAQR7	PAQR7	5615	0.073	0.37	NO
11	PRKAR2B	PRKAR2B	PRKAR2B	6384	0.059	0.35	NO
12	CCNB1	CCNB1	CCNB1	6416	0.058	0.37	NO
13	GNAS	GNAS	GNAS	7063	0.048	0.35	NO
14	CDC25C	CDC25C	CDC25C	7715	0.039	0.33	NO
15	GNB1	GNB1	GNB1	9240	0.019	0.26	NO
16	CDK1	CDK1	CDK1	9422	0.017	0.25	NO
17	PRKAR2A	PRKAR2A	PRKAR2A	9670	0.014	0.24	NO
18	PIN1	PIN1	PIN1	9815	0.012	0.24	NO
19	ACTR2	ACTR2	ACTR2	10399	0.0048	0.21	NO
20	PRKAR1A	PRKAR1A	PRKAR1A	11563	-0.011	0.15	NO
21	HRAS	HRAS	HRAS	11995	-0.017	0.13	NO
22	ARPC1A	ARPC1A	ARPC1A	12359	-0.023	0.12	NO
23	MAPK1	MAPK1	MAPK1	12606	-0.026	0.12	NO
24	ARPC2	ARPC2	ARPC2	12631	-0.027	0.13	NO
25	ARPC5	ARPC5	ARPC5	12834	-0.03	0.13	NO
26	ARPC3	ARPC3	ARPC3	13113	-0.034	0.12	NO
27	ARPC4	ARPC4	ARPC4	13344	-0.039	0.12	NO
28	CAP1	CAP1	CAP1	13568	-0.043	0.13	NO
29	ACTR3	ACTR3	ACTR3	13578	-0.044	0.14	NO
30	MAPK3	MAPK3	MAPK3	14995	-0.08	0.096	NO
31	RPS6KA1	RPS6KA1	RPS6KA1	15031	-0.081	0.12	NO
32	ARPC1B	ARPC1B	ARPC1B	16939	-0.19	0.086	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 WNT PATHWAY.

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

genes ES table in pathway: KEGG RNA DEGRADATION

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	WIF1	WIF1	WIF1	787	0.32	0.13	YES
2	LEF1	LEF1	LEF1	1284	0.26	0.25	YES
3	MAP3K7	MAP3K7	MAP3K7	3982	0.11	0.16	YES
4	WNT1	WNT1	WNT1	4037	0.11	0.22	YES
5	NLK	NLK	NLK	4237	0.1	0.27	YES
6	BTRC	BTRC	BTRC	4395	0.1	0.31	YES
7	GSK3B	GSK3B	GSK3B	5265	0.081	0.31	YES
8	FRAT1	FRAT1	FRAT1	5496	0.076	0.34	YES
9	CREBBP	CREBBP	CREBBP	5526	0.075	0.38	YES
10	CSNK2A1	CSNK2A1	CSNK2A1	5589	0.074	0.42	YES
11	CTBP1	CTBP1	CTBP1	6172	0.062	0.42	YES
12	CTNNB1	CTNNB1	CTNNB1	7349	0.044	0.38	NO
13	HDAC1	HDAC1	HDAC1	7379	0.043	0.4	NO
14	DVL1	DVL1	DVL1	9331	0.018	0.3	NO
15	CCND1	CCND1	CCND1	9337	0.018	0.31	NO
16	AXIN1	AXIN1	AXIN1	9811	0.012	0.3	NO
17	SMAD4	SMAD4	SMAD4	10160	0.0078	0.28	NO
18	APC	APC	APC	10709	0.00083	0.25	NO
19	TAB1	TAB1	TAB1	11246	-0.0066	0.22	NO
20	CSNK1D	CSNK1D	CSNK1D	12027	-0.018	0.19	NO
21	TLE1	TLE1	TLE1	12684	-0.028	0.17	NO
22	PPP2CA	PPP2CA	PPP2CA	12713	-0.028	0.19	NO
23	CSNK1A1	CSNK1A1	CSNK1A1	14058	-0.054	0.14	NO
24	FZD1	FZD1	FZD1	14699	-0.071	0.15	NO
25	MYC	MYC	MYC	15792	-0.11	0.15	NO

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

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA 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 SPLICEOSOME

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	ENO3	ENO3	ENO3	1515	0.24	0.014	YES
2	PAPOLB	PAPOLB	PAPOLB	2790	0.16	0.0071	YES
3	DCP1B	DCP1B	DCP1B	3051	0.15	0.051	YES
4	ENO2	ENO2	ENO2	3468	0.13	0.079	YES
5	PAPOLG	PAPOLG	PAPOLG	4489	0.098	0.063	YES
6	LSM5	LSM5	LSM5	4718	0.093	0.086	YES
7	CNOT2	CNOT2	CNOT2	5308	0.08	0.086	YES
8	XRN2	XRN2	XRN2	5350	0.08	0.12	YES
9	MPHOSPH6	MPHOSPH6	MPHOSPH6	5560	0.074	0.13	YES
10	RQCD1	RQCD1	RQCD1	5849	0.069	0.14	YES
11	DCP1A	DCP1A	DCP1A	5958	0.066	0.16	YES
12	CNOT7	CNOT7	CNOT7	6071	0.064	0.18	YES
13	EXOSC1	EXOSC1	EXOSC1	6120	0.063	0.2	YES
14	EXOSC9	EXOSC9	EXOSC9	6977	0.05	0.18	YES
15	EXOSC10	EXOSC10	EXOSC10	7024	0.049	0.2	YES
16	PNPT1	PNPT1	PNPT1	7040	0.048	0.21	YES
17	DIS3	DIS3	DIS3	7274	0.045	0.22	YES
18	EXOSC7	EXOSC7	EXOSC7	7532	0.041	0.22	YES
19	DCP2	DCP2	DCP2	7559	0.041	0.23	YES
20	EDC3	EDC3	EDC3	8136	0.034	0.22	YES
21	EDC4	EDC4	EDC4	8160	0.033	0.23	YES
22	LSM2	LSM2	LSM2	8235	0.032	0.24	YES
23	EXOSC6	EXOSC6	EXOSC6	8245	0.032	0.25	YES
24	LSM4	LSM4	LSM4	8254	0.032	0.26	YES
25	SKIV2L	SKIV2L	SKIV2L	8420	0.03	0.26	YES
26	DDX6	DDX6	DDX6	8483	0.029	0.27	YES
27	LSM1	LSM1	LSM1	8527	0.029	0.28	YES
28	EXOSC8	EXOSC8	EXOSC8	8796	0.025	0.28	YES
29	CNOT3	CNOT3	CNOT3	8801	0.025	0.29	YES
30	HSPD1	HSPD1	HSPD1	8941	0.023	0.29	YES
31	NAA38	NAA38	NAA38	9288	0.019	0.28	YES
32	PAPOLA	PAPOLA	PAPOLA	9300	0.019	0.28	YES
33	LSM6	LSM6	LSM6	9327	0.018	0.29	YES
34	WDR61	WDR61	WDR61	9340	0.018	0.3	YES
35	PARN	PARN	PARN	9585	0.016	0.29	NO
36	TTC37	TTC37	TTC37	9881	0.012	0.28	NO
37	CNOT10	CNOT10	CNOT10	9888	0.011	0.28	NO
38	C1D	C1D	C1D	10165	0.0077	0.27	NO
39	CNOT6	CNOT6	CNOT6	10194	0.0073	0.27	NO
40	LSM7	LSM7	LSM7	10289	0.0062	0.27	NO
41	SKIV2L2	SKIV2L2	SKIV2L2	10347	0.0054	0.27	NO
42	EXOSC2	EXOSC2	EXOSC2	10387	0.0048	0.27	NO
43	LSM3	LSM3	LSM3	10404	0.0047	0.27	NO
44	CNOT1	CNOT1	CNOT1	10505	0.0034	0.26	NO
45	EXOSC3	EXOSC3	EXOSC3	10674	0.0012	0.25	NO
46	ZCCHC7	ZCCHC7	ZCCHC7	10817	-0.0009	0.25	NO
47	PATL1	PATL1	PATL1	10970	-0.0031	0.24	NO
48	EXOSC5	EXOSC5	EXOSC5	12107	-0.019	0.19	NO
49	CNOT4	CNOT4	CNOT4	12128	-0.019	0.19	NO
50	DCPS	DCPS	DCPS	12648	-0.027	0.18	NO
51	ENO1	ENO1	ENO1	12733	-0.029	0.18	NO
52	PAPD7	PAPD7	PAPD7	13494	-0.042	0.16	NO
53	HSPA9	HSPA9	HSPA9	13897	-0.051	0.15	NO
54	XRN1	XRN1	XRN1	14159	-0.056	0.16	NO
55	CNOT6L	CNOT6L	CNOT6L	14569	-0.067	0.17	NO
56	EXOSC4	EXOSC4	EXOSC4	16066	-0.12	0.13	NO

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

Figure S56. 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 CARDIAC MUSCLE CONTRACTION

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	BMP7	BMP7	BMP7	515	0.37	0.087	YES
2	HNF1A	HNF1A	HNF1A	733	0.33	0.18	YES
3	NPPB	NPPB	NPPB	1020	0.29	0.25	YES
4	GATA4	GATA4	GATA4	1725	0.23	0.28	YES
5	TGFB2	TGFB2	TGFB2	1798	0.22	0.35	YES
6	NOG	NOG	NOG	2120	0.2	0.4	YES
7	NKX2-5	NKX2-5	NKX2-5	3094	0.15	0.39	YES
8	BMPR1A	BMPR1A	BMPR1A	3777	0.12	0.39	YES
9	TGFB3	TGFB3	TGFB3	3871	0.12	0.42	YES
10	MAP3K7	MAP3K7	MAP3K7	3982	0.11	0.45	YES
11	WNT1	WNT1	WNT1	4037	0.11	0.48	YES
12	NPPA	NPPA	NPPA	4416	0.1	0.49	YES
13	GSK3B	GSK3B	GSK3B	5265	0.081	0.47	NO
14	SMAD5	SMAD5	SMAD5	6634	0.055	0.41	NO
15	ATF2	ATF2	ATF2	7174	0.046	0.4	NO
16	RFC1	RFC1	RFC1	7328	0.044	0.4	NO
17	CTNNB1	CTNNB1	CTNNB1	7349	0.044	0.42	NO
18	TGFBR3	TGFBR3	TGFBR3	7515	0.041	0.42	NO
19	BMPR2	BMPR2	BMPR2	7593	0.04	0.43	NO
20	TGFBR1	TGFBR1	TGFBR1	8560	0.028	0.39	NO
21	BMP4	BMP4	BMP4	9257	0.019	0.35	NO
22	DVL1	DVL1	DVL1	9331	0.018	0.36	NO
23	AXIN1	AXIN1	AXIN1	9811	0.012	0.33	NO
24	SMAD4	SMAD4	SMAD4	10160	0.0078	0.32	NO
25	APC	APC	APC	10709	0.00083	0.29	NO
26	CHRD	CHRD	CHRD	11074	-0.0044	0.27	NO
27	SMAD6	SMAD6	SMAD6	11179	-0.0057	0.27	NO
28	ACVR1	ACVR1	ACVR1	12508	-0.025	0.2	NO
29	BMP2	BMP2	BMP2	13314	-0.038	0.17	NO
30	SMAD1	SMAD1	SMAD1	14268	-0.059	0.14	NO
31	FZD1	FZD1	FZD1	14699	-0.071	0.14	NO
32	TGFBR2	TGFBR2	TGFBR2	15611	-0.1	0.12	NO
33	TGFB1	TGFB1	TGFB1	16068	-0.12	0.13	NO

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

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

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

Table 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	PYGO1	PYGO1	PYGO1	63	0.57	0.048	YES
2	TCF7L1	TCF7L1	TCF7L1	115	0.52	0.092	YES
3	WNT2B	WNT2B	WNT2B	253	0.44	0.12	YES
4	CXXC4	CXXC4	CXXC4	366	0.4	0.15	YES
5	FZD2	FZD2	FZD2	388	0.4	0.19	YES
6	CCND2	CCND2	CCND2	595	0.35	0.21	YES
7	WNT11	WNT11	WNT11	687	0.34	0.23	YES
8	WIF1	WIF1	WIF1	787	0.32	0.26	YES
9	WNT6	WNT6	WNT6	816	0.32	0.28	YES
10	WNT5B	WNT5B	WNT5B	876	0.31	0.31	YES
11	FRZB	FRZB	FRZB	923	0.3	0.33	YES
12	LEF1	LEF1	LEF1	1284	0.26	0.34	YES
13	WNT5A	WNT5A	WNT5A	1557	0.24	0.34	YES
14	LRP6	LRP6	LRP6	1905	0.21	0.35	YES
15	WNT3	WNT3	WNT3	2064	0.2	0.36	YES
16	NKD1	NKD1	NKD1	2243	0.19	0.36	YES
17	FOXN1	FOXN1	FOXN1	2260	0.19	0.38	YES
18	FZD7	FZD7	FZD7	2276	0.19	0.4	YES
19	WNT4	WNT4	WNT4	2563	0.17	0.4	YES
20	SFRP1	SFRP1	SFRP1	2600	0.17	0.41	YES
21	KREMEN1	KREMEN1	KREMEN1	2865	0.16	0.41	YES
22	WNT8A	WNT8A	WNT8A	3066	0.15	0.41	YES
23	WNT16	WNT16	WNT16	3236	0.14	0.41	YES
24	DIXDC1	DIXDC1	DIXDC1	3358	0.14	0.42	YES
25	FZD5	FZD5	FZD5	3693	0.12	0.41	YES
26	RHOU	RHOU	RHOU	3958	0.11	0.41	YES
27	WNT1	WNT1	WNT1	4037	0.11	0.41	YES
28	DVL2	DVL2	DVL2	4165	0.11	0.42	YES
29	NLK	NLK	NLK	4237	0.1	0.42	YES
30	BTRC	BTRC	BTRC	4395	0.1	0.42	YES
31	BCL9	BCL9	BCL9	4400	0.1	0.43	YES
32	GSK3B	GSK3B	GSK3B	5265	0.081	0.39	NO
33	FRAT1	FRAT1	FRAT1	5496	0.076	0.39	NO
34	CSNK2A1	CSNK2A1	CSNK2A1	5589	0.074	0.39	NO
35	SENP2	SENP2	SENP2	5882	0.068	0.38	NO
36	CTBP1	CTBP1	CTBP1	6172	0.062	0.37	NO
37	WNT10A	WNT10A	WNT10A	6173	0.062	0.37	NO
38	CTNNB1	CTNNB1	CTNNB1	7349	0.044	0.32	NO
39	TCF7	TCF7	TCF7	7359	0.044	0.32	NO
40	GSK3A	GSK3A	GSK3A	7742	0.038	0.3	NO
41	DAAM1	DAAM1	DAAM1	7846	0.037	0.3	NO
42	CTNNBIP1	CTNNBIP1	CTNNBIP1	7861	0.037	0.3	NO
43	CTBP2	CTBP2	CTBP2	7985	0.036	0.3	NO
44	FZD3	FZD3	FZD3	8293	0.032	0.28	NO
45	SOX17	SOX17	SOX17	8590	0.028	0.27	NO
46	PPP2R1A	PPP2R1A	PPP2R1A	8608	0.027	0.27	NO
47	EP300	EP300	EP300	8888	0.024	0.26	NO
48	WNT2	WNT2	WNT2	9222	0.02	0.24	NO
49	DVL1	DVL1	DVL1	9331	0.018	0.24	NO
50	CCND1	CCND1	CCND1	9337	0.018	0.24	NO
51	JUN	JUN	JUN	9356	0.018	0.24	NO
52	GAPDH	GAPDH	GAPDH	9671	0.014	0.22	NO
53	WNT9A	WNT9A	WNT9A	9746	0.013	0.22	NO
54	AXIN1	AXIN1	AXIN1	9811	0.012	0.22	NO
55	LRP5	LRP5	LRP5	10005	0.0099	0.21	NO
56	FBXW2	FBXW2	FBXW2	10034	0.0094	0.21	NO
57	FBXW11	FBXW11	FBXW11	10333	0.0057	0.19	NO
58	FBXW4	FBXW4	FBXW4	10377	0.005	0.19	NO
59	CSNK1G1	CSNK1G1	CSNK1G1	10590	0.0023	0.18	NO
60	APC	APC	APC	10709	0.00083	0.17	NO
61	RPL13A	RPL13A	RPL13A	11581	-0.011	0.13	NO
62	CSNK1D	CSNK1D	CSNK1D	12027	-0.018	0.11	NO
63	TLE1	TLE1	TLE1	12684	-0.028	0.072	NO
64	PPP2CA	PPP2CA	PPP2CA	12713	-0.028	0.074	NO
65	ACTB	ACTB	ACTB	13084	-0.034	0.056	NO
66	TLE2	TLE2	TLE2	14035	-0.054	0.0098	NO
67	CSNK1A1	CSNK1A1	CSNK1A1	14058	-0.054	0.014	NO
68	HPRT1	HPRT1	HPRT1	14060	-0.054	0.018	NO
69	AES	AES	AES	14491	-0.066	0.00098	NO
70	SLC9A3R1	SLC9A3R1	SLC9A3R1	14529	-0.066	0.005	NO
71	FZD8	FZD8	FZD8	14661	-0.07	0.0041	NO
72	FZD1	FZD1	FZD1	14699	-0.071	0.0085	NO
73	CCND3	CCND3	CCND3	14744	-0.072	0.013	NO
74	PORCN	PORCN	PORCN	14838	-0.075	0.014	NO
75	FZD4	FZD4	FZD4	15163	-0.086	0.0045	NO
76	WNT7A	WNT7A	WNT7A	15270	-0.089	0.0068	NO
77	MYC	MYC	MYC	15792	-0.11	-0.012	NO
78	FZD6	FZD6	FZD6	16029	-0.12	-0.013	NO
79	DKK1	DKK1	DKK1	16385	-0.14	-0.02	NO
80	PITX2	PITX2	PITX2	16705	-0.17	-0.022	NO
81	B2M	B2M	B2M	16851	-0.18	-0.014	NO
82	SFRP4	SFRP4	SFRP4	17357	-0.24	-0.02	NO
83	WISP1	WISP1	WISP1	17728	-0.3	-0.014	NO
84	FOSL1	FOSL1	FOSL1	17759	-0.3	0.012	NO
85	WNT7B	WNT7B	WNT7B	17923	-0.33	0.033	NO

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

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

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