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

Pheochromocytoma and Paraganglioma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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 PCPG-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1G1603C

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 PCPG-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: 187
Number of samples: 179
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 39
pheno.type: 2 - 4 :[ clus2 ] 69
pheno.type: 3 - 4 :[ clus3 ] 50
pheno.type: 4 - 4 :[ clus4 ] 21

For the expression subtypes of 17994 genes in 180 samples, GSEA found enriched gene sets in each cluster using 179 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA MYOSIN PATHWAY, BIOCARTA CHREBP2 PATHWAY, KEGG SPHINGOLIPID METABOLISM, KEGG RIBOSOME, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG ERBB SIGNALING PATHWAY, KEGG OOCYTE MEIOSIS

And common core enriched genes are PRKCA, PRKCB, PRKCG, MYH7, PRKACG, CACNA1C, CERK, DEGS2, GAL3ST1, SGPP2

clus2

Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA PDGF PATHWAY, BIOCARTA TOLL PATHWAY, KEGG ABC TRANSPORTERS, KEGG PEROXISOME, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY

And common core enriched genes are MAPK8, MAP3K1, PRKCB, SHC1, CALM1, CALM2, PTK2B, STAT1, STAT4, STAT5A

clus3

Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA VEGF PATHWAY, KEGG PURINE METABOLISM, KEGG PYRIMIDINE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG RIBOSOME, KEGG CALCIUM SIGNALING PATHWAY, KEGG VASCULAR SMOOTH MUSCLE CONTRACTION

And common core enriched genes are VEGFA, FLT1, FLT4, KDR, NOS3, DLL1, DLL4, DTX2, DVL1, HDAC1

clus4

Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA IL2RB PATHWAY

And common core enriched genes are ACAT1, ACAT2, ALDH1B1, ALDH2, ALDH3A2, ALDH7A1, AOX1, IL4I1, GSTZ1, ACAA1

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 G1 PATHWAY	27	genes.ES.table	0.44	1.3	0.15	0.95	0.94	0.3	0.15	0.25	0.72	0.36
BIOCARTA RACCYCD PATHWAY	25	genes.ES.table	0.26	1.1	0.34	1	1	0.04	0.018	0.039	1	0.54
BIOCARTA MYOSIN PATHWAY	27	genes.ES.table	0.4	1.2	0.22	0.82	0.98	0.22	0.12	0.2	0.67	0.29
BIOCARTA CHREBP2 PATHWAY	41	genes.ES.table	0.34	1.3	0.14	0.76	0.95	0.34	0.27	0.25	0.58	0.25
KEGG SPHINGOLIPID METABOLISM	36	genes.ES.table	0.49	1.4	0.09	1	0.88	0.14	0.078	0.13	1	0.8
KEGG RIBOSOME	84	genes.ES.table	0.39	1	0.5	1	1	0.57	0.41	0.34	0.95	0.45
KEGG NUCLEOTIDE EXCISION REPAIR	43	genes.ES.table	0.3	1.3	0.15	0.85	0.95	0.58	0.39	0.36	0.65	0.3
KEGG HOMOLOGOUS RECOMBINATION	27	genes.ES.table	0.42	1.1	0.35	1	0.99	0.41	0.24	0.31	0.98	0.49
KEGG ERBB SIGNALING PATHWAY	85	genes.ES.table	0.29	1	0.42	0.98	1	0.11	0.074	0.099	0.91	0.41
KEGG OOCYTE MEIOSIS	106	genes.ES.table	0.31	1.1	0.36	1	1	0.35	0.27	0.26	0.99	0.49

genes ES table in pathway: BIOCARTA G1 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	GAL3ST1	GAL3ST1	GAL3ST1	146	0.49	0.15	YES
2	UGT8	UGT8	UGT8	341	0.38	0.26	YES
3	DEGS2	DEGS2	DEGS2	418	0.35	0.38	YES
4	SGPP2	SGPP2	SGPP2	467	0.34	0.48	YES
5	CERK	CERK	CERK	1412	0.18	0.49	YES
6	ACER3	ACER3	ACER3	2170	0.13	0.49	NO
7	ASAH2	ASAH2	ASAH2	3172	0.087	0.46	NO
8	PPAP2C	PPAP2C	PPAP2C	4402	0.059	0.41	NO
9	SGPL1	SGPL1	SGPL1	4915	0.05	0.4	NO
10	SMPD3	SMPD3	SMPD3	5818	0.037	0.36	NO
11	SMPD4	SMPD4	SMPD4	5888	0.036	0.37	NO
12	SGPP1	SGPP1	SGPP1	7333	0.018	0.29	NO
13	PPAP2A	PPAP2A	PPAP2A	7391	0.018	0.3	NO
14	ASAH1	ASAH1	ASAH1	7485	0.016	0.3	NO
15	SPHK2	SPHK2	SPHK2	7737	0.014	0.29	NO
16	KDSR	KDSR	KDSR	8190	0.0089	0.26	NO
17	DEGS1	DEGS1	DEGS1	8204	0.0087	0.27	NO
18	UGCG	UGCG	UGCG	8302	0.0076	0.26	NO
19	SPTLC2	SPTLC2	SPTLC2	9422	-0.0048	0.2	NO
20	NEU4	NEU4	NEU4	9538	-0.0062	0.2	NO
21	SMPD1	SMPD1	SMPD1	9890	-0.01	0.18	NO
22	GLB1	GLB1	GLB1	10049	-0.012	0.18	NO
23	NEU1	NEU1	NEU1	10225	-0.014	0.17	NO
24	SPTLC1	SPTLC1	SPTLC1	10251	-0.014	0.18	NO
25	NEU3	NEU3	NEU3	10543	-0.018	0.16	NO
26	SGMS1	SGMS1	SGMS1	10975	-0.023	0.15	NO
27	PPAP2B	PPAP2B	PPAP2B	11038	-0.024	0.15	NO
28	ACER2	ACER2	ACER2	11112	-0.025	0.16	NO
29	SPHK1	SPHK1	SPHK1	11482	-0.031	0.15	NO
30	SMPD2	SMPD2	SMPD2	11547	-0.032	0.15	NO
31	GBA	GBA	GBA	12725	-0.055	0.11	NO
32	ARSA	ARSA	ARSA	12925	-0.06	0.11	NO
33	B4GALT6	B4GALT6	B4GALT6	13219	-0.067	0.12	NO
34	SGMS2	SGMS2	SGMS2	15027	-0.14	0.065	NO
35	GALC	GALC	GALC	15094	-0.15	0.11	NO
36	GLA	GLA	GLA	15278	-0.16	0.15	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 G1 PATHWAY.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RACCYCD 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	TJP3	TJP3	TJP3	32	0.68	0.046	YES
2	PRKCG	PRKCG	PRKCG	48	0.63	0.089	YES
3	MYH14	MYH14	MYH14	66	0.6	0.13	YES
4	CLDN6	CLDN6	CLDN6	243	0.43	0.15	YES
5	MYH7	MYH7	MYH7	447	0.34	0.16	YES
6	PARD6B	PARD6B	PARD6B	517	0.32	0.18	YES
7	CTNNA3	CTNNA3	CTNNA3	544	0.32	0.2	YES
8	CTNNA2	CTNNA2	CTNNA2	618	0.3	0.22	YES
9	CLDN3	CLDN3	CLDN3	637	0.3	0.24	YES
10	CLDN11	CLDN11	CLDN11	701	0.28	0.25	YES
11	RAB3B	RAB3B	RAB3B	799	0.26	0.27	YES
12	MYH7B	MYH7B	MYH7B	870	0.25	0.28	YES
13	OCLN	OCLN	OCLN	879	0.25	0.3	YES
14	CLDN15	CLDN15	CLDN15	886	0.25	0.31	YES
15	LLGL2	LLGL2	LLGL2	953	0.24	0.33	YES
16	CLDN4	CLDN4	CLDN4	1031	0.23	0.34	YES
17	MYH3	MYH3	MYH3	1093	0.22	0.35	YES
18	PRKCA	PRKCA	PRKCA	1247	0.2	0.36	YES
19	CRB3	CRB3	CRB3	1306	0.2	0.36	YES
20	PRKCQ	PRKCQ	PRKCQ	1351	0.19	0.38	YES
21	MYL5	MYL5	MYL5	1619	0.17	0.37	YES
22	CLDN10	CLDN10	CLDN10	1652	0.16	0.38	YES
23	PRKCB	PRKCB	PRKCB	2078	0.13	0.37	YES
24	PARD6G	PARD6G	PARD6G	2325	0.12	0.36	YES
25	CGN	CGN	CGN	2359	0.12	0.37	YES
26	PARD3	PARD3	PARD3	2458	0.11	0.37	YES
27	EPB41	EPB41	EPB41	2545	0.11	0.37	YES
28	CLDN23	CLDN23	CLDN23	2588	0.11	0.38	YES
29	CLDN9	CLDN9	CLDN9	2615	0.11	0.38	YES
30	PRKCZ	PRKCZ	PRKCZ	2653	0.11	0.39	YES
31	INADL	INADL	INADL	2773	0.1	0.39	YES
32	SYMPK	SYMPK	SYMPK	2941	0.095	0.39	NO
33	ZAK	ZAK	ZAK	3014	0.092	0.39	NO
34	PPP2R2C	PPP2R2C	PPP2R2C	3150	0.088	0.39	NO
35	PPP2R2A	PPP2R2A	PPP2R2A	3290	0.084	0.39	NO
36	LLGL1	LLGL1	LLGL1	3598	0.076	0.38	NO
37	CASK	CASK	CASK	3599	0.076	0.38	NO
38	AKT3	AKT3	AKT3	3745	0.073	0.38	NO
39	MPP5	MPP5	MPP5	3977	0.068	0.37	NO
40	PPP2R2D	PPP2R2D	PPP2R2D	4052	0.066	0.37	NO
41	PPP2CB	PPP2CB	PPP2CB	4629	0.055	0.34	NO
42	ASH1L	ASH1L	ASH1L	4759	0.052	0.34	NO
43	CLDN18	CLDN18	CLDN18	4933	0.049	0.33	NO
44	PRKCI	PRKCI	PRKCI	5096	0.047	0.32	NO
45	CSNK2A1	CSNK2A1	CSNK2A1	5298	0.044	0.32	NO
46	EPB41L3	EPB41L3	EPB41L3	5411	0.042	0.31	NO
47	CDK4	CDK4	CDK4	5588	0.04	0.31	NO
48	GNAI3	GNAI3	GNAI3	5733	0.038	0.3	NO
49	NRAS	NRAS	NRAS	5809	0.037	0.3	NO
50	MAGI3	MAGI3	MAGI3	5822	0.037	0.3	NO
51	SRC	SRC	SRC	5861	0.036	0.3	NO
52	MAGI2	MAGI2	MAGI2	5957	0.035	0.3	NO
53	ACTN2	ACTN2	ACTN2	5977	0.035	0.3	NO
54	VAPA	VAPA	VAPA	6104	0.033	0.3	NO
55	CSNK2A2	CSNK2A2	CSNK2A2	6316	0.03	0.29	NO
56	TJAP1	TJAP1	TJAP1	6328	0.03	0.29	NO
57	SPTAN1	SPTAN1	SPTAN1	6403	0.029	0.28	NO
58	CDC42	CDC42	CDC42	7014	0.022	0.25	NO
59	EXOC3	EXOC3	EXOC3	7018	0.022	0.25	NO
60	MLLT4	MLLT4	MLLT4	7049	0.021	0.25	NO
61	KRAS	KRAS	KRAS	7270	0.019	0.24	NO
62	CTNNB1	CTNNB1	CTNNB1	7468	0.017	0.23	NO
63	PPP2R1A	PPP2R1A	PPP2R1A	7495	0.016	0.23	NO
64	GNAI2	GNAI2	GNAI2	7795	0.013	0.22	NO
65	AKT2	AKT2	AKT2	8138	0.0096	0.2	NO
66	EPB41L2	EPB41L2	EPB41L2	8217	0.0086	0.19	NO
67	TJP2	TJP2	TJP2	8577	0.0049	0.18	NO
68	JAM3	JAM3	JAM3	8905	0.0011	0.16	NO
69	MPDZ	MPDZ	MPDZ	8929	0.00079	0.16	NO
70	GNAI1	GNAI1	GNAI1	9099	-0.0012	0.15	NO
71	CSNK2B	CSNK2B	CSNK2B	9177	-0.0021	0.14	NO
72	PTEN	PTEN	PTEN	9642	-0.0072	0.12	NO
73	RHOA	RHOA	RHOA	9931	-0.01	0.1	NO
74	PRKCE	PRKCE	PRKCE	9964	-0.011	0.1	NO
75	EPB41L1	EPB41L1	EPB41L1	10282	-0.015	0.083	NO
76	PRKCH	PRKCH	PRKCH	10348	-0.016	0.08	NO
77	CSDA	CSDA	CSDA	10406	-0.016	0.078	NO
78	TJP1	TJP1	TJP1	10526	-0.018	0.073	NO
79	YES1	YES1	YES1	10652	-0.019	0.067	NO
80	EXOC4	EXOC4	EXOC4	10863	-0.022	0.057	NO
81	PPP2CA	PPP2CA	PPP2CA	10947	-0.023	0.054	NO
82	CTNNA1	CTNNA1	CTNNA1	11214	-0.027	0.041	NO
83	PARD6A	PARD6A	PARD6A	11335	-0.029	0.036	NO
84	CTTN	CTTN	CTTN	11594	-0.033	0.024	NO
85	MYH10	MYH10	MYH10	11618	-0.033	0.025	NO
86	MAGI1	MAGI1	MAGI1	12012	-0.04	0.0058	NO
87	MYL12B	MYL12B	MYL12B	12302	-0.046	-0.0072	NO
88	MYH9	MYH9	MYH9	12456	-0.049	-0.012	NO
89	RRAS	RRAS	RRAS	12563	-0.052	-0.015	NO
90	ACTB	ACTB	ACTB	12610	-0.053	-0.014	NO
91	ACTN4	ACTN4	ACTN4	12664	-0.054	-0.013	NO
92	RAB13	RAB13	RAB13	12835	-0.058	-0.018	NO
93	AKT1	AKT1	AKT1	12998	-0.061	-0.023	NO
94	RRAS2	RRAS2	RRAS2	13104	-0.064	-0.025	NO
95	ACTG1	ACTG1	ACTG1	13265	-0.068	-0.029	NO
96	F11R	F11R	F11R	13309	-0.07	-0.026	NO
97	AMOTL1	AMOTL1	AMOTL1	13343	-0.071	-0.023	NO
98	CLDN5	CLDN5	CLDN5	13430	-0.073	-0.023	NO
99	JAM2	JAM2	JAM2	13640	-0.079	-0.029	NO
100	MYL12A	MYL12A	MYL12A	13886	-0.088	-0.037	NO
101	ACTN3	ACTN3	ACTN3	14366	-0.11	-0.056	NO
102	PPP2R1B	PPP2R1B	PPP2R1B	14567	-0.12	-0.059	NO
103	MRAS	MRAS	MRAS	14579	-0.12	-0.052	NO
104	ACTN1	ACTN1	ACTN1	14688	-0.12	-0.049	NO
105	PPP2R2B	PPP2R2B	PPP2R2B	14981	-0.14	-0.056	NO
106	MYL9	MYL9	MYL9	15119	-0.15	-0.053	NO
107	MYH11	MYH11	MYH11	15272	-0.16	-0.051	NO
108	MYH6	MYH6	MYH6	15276	-0.16	-0.04	NO
109	CLDN7	CLDN7	CLDN7	15341	-0.16	-0.032	NO
110	CLDN2	CLDN2	CLDN2	15470	-0.17	-0.028	NO
111	CLDN14	CLDN14	CLDN14	15774	-0.19	-0.031	NO
112	HCLS1	HCLS1	HCLS1	15795	-0.2	-0.019	NO
113	CLDN1	CLDN1	CLDN1	16168	-0.23	-0.024	NO
114	MYH15	MYH15	MYH15	16667	-0.28	-0.032	NO
115	PRKCD	PRKCD	PRKCD	16702	-0.28	-0.014	NO
116	MYLPF	MYLPF	MYLPF	17016	-0.33	-0.0085	NO
117	CLDN20	CLDN20	CLDN20	17217	-0.36	0.0055	NO
118	IGSF5	IGSF5	IGSF5	17843	-0.53	0.0074	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 RACCYCD PATHWAY.

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

genes ES table in pathway: BIOCARTA MYOSIN PATHWAY

Table 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	PRKCG	PRKCG	PRKCG	48	0.63	0.16	YES
2	ATP6V0A4	ATP6V0A4	ATP6V0A4	75	0.58	0.32	YES
3	PRKCA	PRKCA	PRKCA	1247	0.2	0.31	YES
4	PRKACG	PRKACG	PRKACG	2059	0.13	0.3	YES
5	PRKCB	PRKCB	PRKCB	2078	0.13	0.33	YES
6	SEC61A2	SEC61A2	SEC61A2	2233	0.12	0.36	YES
7	ADCY9	ADCY9	ADCY9	3543	0.078	0.3	NO
8	PLCG1	PLCG1	PLCG1	3755	0.073	0.31	NO
9	ATP6V1B2	ATP6V1B2	ATP6V1B2	3921	0.069	0.32	NO
10	PRKX	PRKX	PRKX	4074	0.066	0.33	NO
11	ATP6V1G2	ATP6V1G2	ATP6V1G2	4804	0.052	0.3	NO
12	ATP6V1E2	ATP6V1E2	ATP6V1E2	5395	0.043	0.28	NO
13	SLC12A2	SLC12A2	SLC12A2	5585	0.04	0.28	NO
14	ATP6V1F	ATP6V1F	ATP6V1F	5796	0.037	0.28	NO
15	ATP6V1C1	ATP6V1C1	ATP6V1C1	6234	0.031	0.26	NO
16	ATP6V1A	ATP6V1A	ATP6V1A	6689	0.026	0.25	NO
17	ATP6V1H	ATP6V1H	ATP6V1H	6774	0.025	0.25	NO
18	GNAS	GNAS	GNAS	6861	0.024	0.25	NO
19	KDELR1	KDELR1	KDELR1	6921	0.023	0.25	NO
20	KDELR2	KDELR2	KDELR2	7609	0.015	0.22	NO
21	ATP6V1E1	ATP6V1E1	ATP6V1E1	8296	0.0077	0.18	NO
22	ATP6V0A1	ATP6V0A1	ATP6V0A1	8381	0.0069	0.18	NO
23	TJP2	TJP2	TJP2	8577	0.0049	0.17	NO
24	ATP6V1D	ATP6V1D	ATP6V1D	8693	0.0033	0.16	NO
25	PDIA4	PDIA4	PDIA4	8849	0.0017	0.16	NO
26	ERO1L	ERO1L	ERO1L	8947	0.00061	0.15	NO
27	ATP6V1G1	ATP6V1G1	ATP6V1G1	9011	-0.00017	0.15	NO
28	ATP6V0E1	ATP6V0E1	ATP6V0E1	9594	-0.0067	0.12	NO
29	ATP6V0C	ATP6V0C	ATP6V0C	9970	-0.011	0.098	NO
30	ATP6V0D2	ATP6V0D2	ATP6V0D2	9988	-0.011	0.1	NO
31	ATP6AP1	ATP6AP1	ATP6AP1	10081	-0.012	0.098	NO
32	SEC61A1	SEC61A1	SEC61A1	10273	-0.014	0.091	NO
33	TJP1	TJP1	TJP1	10526	-0.018	0.082	NO
34	ATP6V0A2	ATP6V0A2	ATP6V0A2	10653	-0.019	0.08	NO
35	ATP6V0B	ATP6V0B	ATP6V0B	11097	-0.025	0.062	NO
36	ATP6V0E2	ATP6V0E2	ATP6V0E2	11255	-0.028	0.061	NO
37	ARF1	ARF1	ARF1	11288	-0.028	0.066	NO
38	ATP6V0D1	ATP6V0D1	ATP6V0D1	11311	-0.028	0.073	NO
39	ATP6V1C2	ATP6V1C2	ATP6V1C2	11538	-0.032	0.069	NO
40	SEC61B	SEC61B	SEC61B	11637	-0.034	0.072	NO
41	PRKACA	PRKACA	PRKACA	11704	-0.035	0.078	NO
42	ACTB	ACTB	ACTB	12610	-0.053	0.041	NO
43	SEC61G	SEC61G	SEC61G	12974	-0.061	0.037	NO
44	ACTG1	ACTG1	ACTG1	13265	-0.068	0.039	NO
45	KDELR3	KDELR3	KDELR3	13703	-0.081	0.036	NO
46	PRKACB	PRKACB	PRKACB	13807	-0.085	0.053	NO
47	PLCG2	PLCG2	PLCG2	14222	-0.1	0.057	NO
48	ATP6V1B1	ATP6V1B1	ATP6V1B1	14368	-0.11	0.077	NO
49	TCIRG1	TCIRG1	TCIRG1	14535	-0.12	0.099	NO
50	KCNQ1	KCNQ1	KCNQ1	17146	-0.35	0.046	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 MYOSIN PATHWAY.

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

genes ES table in pathway: BIOCARTA CHREBP2 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	CACNG7	CACNG7	CACNG7	1	1.1	0.12	YES
2	CACNG6	CACNG6	CACNG6	232	0.43	0.15	YES
3	CACNA2D2	CACNA2D2	CACNA2D2	392	0.36	0.18	YES
4	ATP1A2	ATP1A2	ATP1A2	394	0.36	0.21	YES
5	MYH7	MYH7	MYH7	447	0.34	0.24	YES
6	COX6B2	COX6B2	COX6B2	509	0.32	0.27	YES
7	TNNI3	TNNI3	TNNI3	617	0.3	0.3	YES
8	COX4I2	COX4I2	COX4I2	663	0.29	0.32	YES
9	CACNG8	CACNG8	CACNG8	805	0.26	0.34	YES
10	CACNB1	CACNB1	CACNB1	1203	0.21	0.34	YES
11	COX8C	COX8C	COX8C	1255	0.2	0.36	YES
12	ATP1B2	ATP1B2	ATP1B2	1314	0.2	0.38	YES
13	RYR2	RYR2	RYR2	1585	0.17	0.38	YES
14	CACNG2	CACNG2	CACNG2	1740	0.16	0.39	YES
15	CACNB4	CACNB4	CACNB4	1833	0.15	0.4	YES
16	CACNA1C	CACNA1C	CACNA1C	1871	0.15	0.41	YES
17	CACNB2	CACNB2	CACNB2	1959	0.14	0.42	YES
18	FXYD2	FXYD2	FXYD2	2060	0.13	0.43	YES
19	CACNB3	CACNB3	CACNB3	2182	0.13	0.43	YES
20	UQCRHL	UQCRHL	UQCRHL	2455	0.11	0.43	NO
21	UQCRH	UQCRH	UQCRH	3243	0.085	0.39	NO
22	COX7C	COX7C	COX7C	4625	0.055	0.32	NO
23	COX7A2L	COX7A2L	COX7A2L	4626	0.055	0.33	NO
24	CACNG3	CACNG3	CACNG3	5008	0.048	0.31	NO
25	ATP1A3	ATP1A3	ATP1A3	6227	0.031	0.25	NO
26	SLC9A6	SLC9A6	SLC9A6	6229	0.031	0.25	NO
27	UQCRB	UQCRB	UQCRB	6240	0.031	0.25	NO
28	COX7A2	COX7A2	COX7A2	6371	0.03	0.25	NO
29	UQCRFS1	UQCRFS1	UQCRFS1	6439	0.029	0.25	NO
30	ATP2A2	ATP2A2	ATP2A2	6613	0.026	0.24	NO
31	COX4I1	COX4I1	COX4I1	7558	0.016	0.19	NO
32	ATP1A4	ATP1A4	ATP1A4	7637	0.015	0.19	NO
33	UQCR11	UQCR11	UQCR11	8747	0.0029	0.12	NO
34	COX8A	COX8A	COX8A	8854	0.0017	0.12	NO
35	COX6B1	COX6B1	COX6B1	9283	-0.0034	0.096	NO
36	ATP1B1	ATP1B1	ATP1B1	9593	-0.0067	0.079	NO
37	CYC1	CYC1	CYC1	9705	-0.008	0.074	NO
38	CACNA2D1	CACNA2D1	CACNA2D1	9919	-0.01	0.063	NO
39	COX6A1	COX6A1	COX6A1	9977	-0.011	0.061	NO
40	COX6C	COX6C	COX6C	9999	-0.011	0.061	NO
41	UQCR10	UQCR10	UQCR10	10100	-0.013	0.056	NO
42	SLC8A1	SLC8A1	SLC8A1	10397	-0.016	0.042	NO
43	COX5A	COX5A	COX5A	10522	-0.018	0.036	NO
44	COX7B	COX7B	COX7B	10735	-0.02	0.027	NO
45	COX5B	COX5B	COX5B	11051	-0.024	0.012	NO
46	CACNA1D	CACNA1D	CACNA1D	11201	-0.027	0.006	NO
47	UQCRC1	UQCRC1	UQCRC1	11607	-0.033	-0.013	NO
48	UQCRQ	UQCRQ	UQCRQ	11980	-0.04	-0.03	NO
49	TPM3	TPM3	TPM3	12063	-0.041	-0.03	NO
50	CACNG4	CACNG4	CACNG4	12619	-0.053	-0.056	NO
51	SLC9A1	SLC9A1	SLC9A1	13114	-0.064	-0.077	NO
52	COX7A1	COX7A1	COX7A1	13304	-0.069	-0.081	NO
53	ATP1A1	ATP1A1	ATP1A1	13324	-0.07	-0.074	NO
54	TPM1	TPM1	TPM1	13649	-0.079	-0.085	NO
55	TNNC1	TNNC1	TNNC1	14064	-0.095	-0.098	NO
56	TPM4	TPM4	TPM4	14083	-0.095	-0.089	NO
57	ATP1B3	ATP1B3	ATP1B3	14605	-0.12	-0.11	NO
58	CACNG1	CACNG1	CACNG1	14674	-0.12	-0.098	NO
59	MYH6	MYH6	MYH6	15276	-0.16	-0.12	NO
60	ACTC1	ACTC1	ACTC1	15289	-0.16	-0.1	NO
61	TPM2	TPM2	TPM2	15473	-0.17	-0.093	NO
62	CACNG5	CACNG5	CACNG5	15784	-0.2	-0.09	NO
63	CACNA1S	CACNA1S	CACNA1S	15865	-0.2	-0.074	NO
64	MYL3	MYL3	MYL3	15884	-0.2	-0.055	NO
65	CACNA2D4	CACNA2D4	CACNA2D4	16073	-0.22	-0.043	NO
66	TNNT2	TNNT2	TNNT2	16639	-0.28	-0.046	NO
67	COX6A2	COX6A2	COX6A2	17085	-0.34	-0.036	NO
68	CACNA1F	CACNA1F	CACNA1F	17283	-0.37	-0.0092	NO
69	CACNA2D3	CACNA2D3	CACNA2D3	17710	-0.47	0.015	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 CHREBP2 PATHWAY.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 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 SPHINGOLIPID METABOLISM

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	PRKCG	PRKCG	PRKCG	48	0.63	0.1	YES
2	GRIN1	GRIN1	GRIN1	64	0.6	0.21	YES
3	GRM5	GRM5	GRM5	390	0.36	0.25	YES
4	PRKCA	PRKCA	PRKCA	1247	0.2	0.24	YES
5	PPP1R1A	PPP1R1A	PPP1R1A	1253	0.2	0.27	YES
6	GRIN2B	GRIN2B	GRIN2B	1413	0.18	0.29	YES
7	CACNA1C	CACNA1C	CACNA1C	1871	0.15	0.29	YES
8	CHP2	CHP2	CHP2	1926	0.14	0.32	YES
9	PRKACG	PRKACG	PRKACG	2059	0.13	0.33	YES
10	PRKCB	PRKCB	PRKCB	2078	0.13	0.35	YES
11	MAP2K1	MAP2K1	MAP2K1	2281	0.12	0.36	YES
12	RPS6KA6	RPS6KA6	RPS6KA6	2860	0.097	0.35	YES
13	PPP3R1	PPP3R1	PPP3R1	3038	0.092	0.35	YES
14	CAMK2D	CAMK2D	CAMK2D	3205	0.086	0.36	YES
15	GRM1	GRM1	GRM1	3382	0.081	0.36	YES
16	GRIN2A	GRIN2A	GRIN2A	3429	0.08	0.37	YES
17	CAMK4	CAMK4	CAMK4	3828	0.071	0.36	YES
18	CREBBP	CREBBP	CREBBP	3837	0.071	0.37	YES
19	RPS6KA2	RPS6KA2	RPS6KA2	3946	0.069	0.38	YES
20	PPP1R12A	PPP1R12A	PPP1R12A	4014	0.067	0.39	YES
21	PRKX	PRKX	PRKX	4074	0.066	0.4	YES
22	PLCB1	PLCB1	PLCB1	4449	0.058	0.38	YES
23	MAPK1	MAPK1	MAPK1	4549	0.056	0.39	YES
24	CALM3	CALM3	CALM3	4571	0.056	0.4	YES
25	EP300	EP300	EP300	4747	0.053	0.4	NO
26	GNAQ	GNAQ	GNAQ	5698	0.038	0.35	NO
27	NRAS	NRAS	NRAS	5809	0.037	0.35	NO
28	PPP3CA	PPP3CA	PPP3CA	6195	0.031	0.33	NO
29	ITPR1	ITPR1	ITPR1	6210	0.031	0.34	NO
30	PLCB4	PLCB4	PLCB4	6285	0.03	0.34	NO
31	PPP3CB	PPP3CB	PPP3CB	6583	0.027	0.33	NO
32	PPP1CC	PPP1CC	PPP1CC	6865	0.024	0.32	NO
33	MAP2K2	MAP2K2	MAP2K2	7019	0.022	0.31	NO
34	ARAF	ARAF	ARAF	7164	0.02	0.31	NO
35	KRAS	KRAS	KRAS	7270	0.019	0.3	NO
36	PLCB3	PLCB3	PLCB3	7669	0.014	0.28	NO
37	BRAF	BRAF	BRAF	7985	0.011	0.27	NO
38	MAPK3	MAPK3	MAPK3	8088	0.01	0.26	NO
39	PPP3CC	PPP3CC	PPP3CC	8573	0.0049	0.24	NO
40	ADCY8	ADCY8	ADCY8	8879	0.0015	0.22	NO
41	RAF1	RAF1	RAF1	9989	-0.011	0.16	NO
42	PPP1CB	PPP1CB	PPP1CB	10047	-0.012	0.16	NO
43	RPS6KA1	RPS6KA1	RPS6KA1	10121	-0.013	0.16	NO
44	ATF4	ATF4	ATF4	10413	-0.016	0.14	NO
45	ITPR2	ITPR2	ITPR2	10432	-0.016	0.15	NO
46	ITPR3	ITPR3	ITPR3	10996	-0.024	0.12	NO
47	CHP	CHP	CHP	11012	-0.024	0.12	NO
48	RPS6KA3	RPS6KA3	RPS6KA3	11056	-0.024	0.12	NO
49	GRIA1	GRIA1	GRIA1	11703	-0.035	0.094	NO
50	PRKACA	PRKACA	PRKACA	11704	-0.035	0.1	NO
51	RAP1A	RAP1A	RAP1A	11948	-0.039	0.093	NO
52	CAMK2G	CAMK2G	CAMK2G	11965	-0.039	0.098	NO
53	GRIA2	GRIA2	GRIA2	12376	-0.048	0.084	NO
54	RAP1B	RAP1B	RAP1B	12377	-0.048	0.092	NO
55	HRAS	HRAS	HRAS	12643	-0.053	0.086	NO
56	PPP3R2	PPP3R2	PPP3R2	12648	-0.053	0.095	NO
57	GRIN2D	GRIN2D	GRIN2D	12812	-0.057	0.096	NO
58	CALM1	CALM1	CALM1	13195	-0.066	0.086	NO
59	PPP1CA	PPP1CA	PPP1CA	13390	-0.072	0.087	NO
60	GRIN2C	GRIN2C	GRIN2C	13534	-0.075	0.092	NO
61	CALML6	CALML6	CALML6	13636	-0.079	0.1	NO
62	RAPGEF3	RAPGEF3	RAPGEF3	13687	-0.08	0.11	NO
63	CAMK2B	CAMK2B	CAMK2B	13692	-0.081	0.12	NO
64	PRKACB	PRKACB	PRKACB	13807	-0.085	0.13	NO
65	CALM2	CALM2	CALM2	14002	-0.093	0.14	NO
66	CAMK2A	CAMK2A	CAMK2A	15882	-0.2	0.067	NO
67	PLCB2	PLCB2	PLCB2	16756	-0.29	0.068	NO

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

Figure S10. 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 RIBOSOME

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	CCNE1	CCNE1	CCNE1	333	0.39	0.12	YES
2	CCNA1	CCNA1	CCNA1	342	0.38	0.26	YES
3	CDC25A	CDC25A	CDC25A	1257	0.2	0.28	YES
4	TGFB2	TGFB2	TGFB2	1376	0.19	0.34	YES
5	CDK1	CDK1	CDK1	1732	0.16	0.38	YES
6	CDK6	CDK6	CDK6	2296	0.12	0.39	YES
7	HDAC1	HDAC1	HDAC1	2415	0.12	0.42	YES
8	DHFR	DHFR	DHFR	2703	0.1	0.44	YES
9	CDKN2A	CDKN2A	CDKN2A	3631	0.075	0.42	NO
10	RB1	RB1	RB1	4073	0.066	0.42	NO
11	SMAD3	SMAD3	SMAD3	5128	0.046	0.38	NO
12	SMAD4	SMAD4	SMAD4	5219	0.045	0.39	NO
13	TFDP1	TFDP1	TFDP1	5232	0.045	0.4	NO
14	CDK4	CDK4	CDK4	5588	0.04	0.4	NO
15	GSK3B	GSK3B	GSK3B	6435	0.029	0.36	NO
16	TGFB1	TGFB1	TGFB1	6818	0.024	0.35	NO
17	CDKN1B	CDKN1B	CDKN1B	7597	0.015	0.31	NO
18	CDK2	CDK2	CDK2	9664	-0.0075	0.2	NO
19	ATM	ATM	ATM	10727	-0.02	0.14	NO
20	TP53	TP53	TP53	10886	-0.022	0.14	NO
21	CCND1	CCND1	CCND1	11072	-0.025	0.14	NO
22	ABL1	ABL1	ABL1	11285	-0.028	0.14	NO
23	SKP2	SKP2	SKP2	13046	-0.062	0.065	NO
24	CDKN1A	CDKN1A	CDKN1A	13278	-0.069	0.077	NO
25	ATR	ATR	ATR	13691	-0.081	0.083	NO
26	CDKN2B	CDKN2B	CDKN2B	14565	-0.12	0.076	NO
27	TGFB3	TGFB3	TGFB3	16944	-0.32	0.058	NO

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

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

genes ES table in pathway: KEGG NUCLEOTIDE EXCISION REPAIR

Table 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	POLE	POLE	POLE	1518	0.17	0.0073	YES
2	POLD1	POLD1	POLD1	2741	0.1	-0.0072	YES
3	POLE2	POLE2	POLE2	3010	0.093	0.027	YES
4	LIG1	LIG1	LIG1	3047	0.091	0.073	YES
5	ERCC2	ERCC2	ERCC2	3318	0.083	0.1	YES
6	RPA1	RPA1	RPA1	3810	0.072	0.11	YES
7	RPA4	RPA4	RPA4	4130	0.065	0.13	YES
8	RPA2	RPA2	RPA2	4801	0.052	0.12	YES
9	RFC1	RFC1	RFC1	5154	0.046	0.12	YES
10	MNAT1	MNAT1	MNAT1	5218	0.045	0.14	YES
11	CUL4A	CUL4A	CUL4A	5355	0.043	0.16	YES
12	ERCC6	ERCC6	ERCC6	5415	0.042	0.18	YES
13	CUL4B	CUL4B	CUL4B	5490	0.041	0.2	YES
14	POLD3	POLD3	POLD3	5661	0.039	0.21	YES
15	GTF2H1	GTF2H1	GTF2H1	5749	0.038	0.22	YES
16	RFC4	RFC4	RFC4	5800	0.037	0.24	YES
17	DDB2	DDB2	DDB2	5894	0.036	0.25	YES
18	PCNA	PCNA	PCNA	6016	0.034	0.26	YES
19	GTF2H4	GTF2H4	GTF2H4	6376	0.029	0.26	YES
20	GTF2H3	GTF2H3	GTF2H3	6482	0.028	0.27	YES
21	ERCC4	ERCC4	ERCC4	6602	0.027	0.28	YES
22	RFC5	RFC5	RFC5	6709	0.025	0.28	YES
23	GTF2H2	GTF2H2	GTF2H2	6822	0.024	0.29	YES
24	XPC	XPC	XPC	6927	0.023	0.3	YES
25	GTF2H5	GTF2H5	GTF2H5	7041	0.021	0.3	YES
26	XPA	XPA	XPA	7778	0.013	0.27	NO
27	POLD2	POLD2	POLD2	7897	0.012	0.27	NO
28	RFC2	RFC2	RFC2	8924	0.00082	0.21	NO
29	ERCC1	ERCC1	ERCC1	8966	0.00038	0.21	NO
30	RBX1	RBX1	RBX1	9207	-0.0025	0.2	NO
31	ERCC3	ERCC3	ERCC3	9754	-0.0084	0.17	NO
32	DDB1	DDB1	DDB1	9759	-0.0085	0.17	NO
33	RAD23A	RAD23A	RAD23A	10697	-0.02	0.13	NO
34	POLE3	POLE3	POLE3	10751	-0.02	0.14	NO
35	ERCC5	ERCC5	ERCC5	10824	-0.021	0.15	NO
36	ERCC8	ERCC8	ERCC8	10986	-0.024	0.15	NO
37	CETN2	CETN2	CETN2	11340	-0.029	0.15	NO
38	RFC3	RFC3	RFC3	11485	-0.031	0.16	NO
39	RPA3	RPA3	RPA3	12300	-0.046	0.13	NO
40	CCNH	CCNH	CCNH	12580	-0.052	0.15	NO
41	CDK7	CDK7	CDK7	12865	-0.058	0.16	NO
42	POLD4	POLD4	POLD4	13781	-0.084	0.15	NO
43	POLE4	POLE4	POLE4	15155	-0.15	0.16	NO

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

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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	MLXIPL	MLXIPL	MLXIPL	199	0.45	0.16	YES
2	PKLR	PKLR	PKLR	1494	0.18	0.15	YES
3	PRKACG	PRKACG	PRKACG	2059	0.13	0.17	YES
4	PRKAA2	PRKAA2	PRKAA2	2083	0.13	0.22	YES
5	PRKAR1B	PRKAR1B	PRKAR1B	2351	0.12	0.24	YES
6	PPP2R3B	PPP2R3B	PPP2R3B	2578	0.11	0.27	YES
7	PPP2R2C	PPP2R2C	PPP2R2C	3150	0.088	0.27	YES
8	PPP2R2A	PPP2R2A	PPP2R2A	3290	0.084	0.3	YES
9	PRKAB1	PRKAB1	PRKAB1	3902	0.069	0.29	YES
10	PPP2R2D	PPP2R2D	PPP2R2D	4052	0.066	0.3	YES
11	PPP2CB	PPP2CB	PPP2CB	4629	0.055	0.29	YES
12	PRKAB2	PRKAB2	PRKAB2	4682	0.054	0.31	YES
13	PPP2R5E	PPP2R5E	PPP2R5E	4797	0.052	0.32	YES
14	PRKAG1	PRKAG1	PRKAG1	4873	0.05	0.34	YES
15	YWHAH	YWHAH	YWHAH	5920	0.035	0.29	NO
16	PRKAR2A	PRKAR2A	PRKAR2A	6560	0.027	0.27	NO
17	PPP2R5D	PPP2R5D	PPP2R5D	6693	0.026	0.27	NO
18	YWHAE	YWHAE	YWHAE	7361	0.018	0.24	NO
19	PPP2R1A	PPP2R1A	PPP2R1A	7495	0.016	0.24	NO
20	YWHAQ	YWHAQ	YWHAQ	7587	0.015	0.24	NO
21	PPP2R5C	PPP2R5C	PPP2R5C	8652	0.0038	0.18	NO
22	ACACA	ACACA	ACACA	8809	0.0022	0.17	NO
23	YWHAG	YWHAG	YWHAG	8971	0.00035	0.16	NO
24	PRKAR1A	PRKAR1A	PRKAR1A	10058	-0.012	0.11	NO
25	PRKAA1	PRKAA1	PRKAA1	10681	-0.02	0.079	NO
26	PPP2CA	PPP2CA	PPP2CA	10947	-0.023	0.072	NO
27	PPP2R4	PPP2R4	PPP2R4	11029	-0.024	0.077	NO
28	YWHAZ	YWHAZ	YWHAZ	11032	-0.024	0.086	NO
29	YWHAB	YWHAB	YWHAB	11338	-0.029	0.08	NO
30	GCK	GCK	GCK	11377	-0.03	0.088	NO
31	PPP2R5A	PPP2R5A	PPP2R5A	11555	-0.032	0.09	NO
32	PRKACA	PRKACA	PRKACA	11704	-0.035	0.095	NO
33	FASN	FASN	FASN	11890	-0.038	0.099	NO
34	MLX	MLX	MLX	12002	-0.04	0.11	NO
35	PPP2R5B	PPP2R5B	PPP2R5B	12310	-0.046	0.11	NO
36	PPP2R3A	PPP2R3A	PPP2R3A	12413	-0.048	0.12	NO
37	PRKAG2	PRKAG2	PRKAG2	13487	-0.074	0.087	NO
38	PRKACB	PRKACB	PRKACB	13807	-0.085	0.1	NO
39	PRKAR2B	PRKAR2B	PRKAR2B	14182	-0.099	0.12	NO
40	PPP2R1B	PPP2R1B	PPP2R1B	14567	-0.12	0.14	NO
41	PPP2R2B	PPP2R2B	PPP2R2B	14981	-0.14	0.17	NO

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

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

genes ES table in pathway: KEGG ERBB SIGNALING 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	GNG13	GNG13	GNG13	16	0.76	0.11	YES
2	GNG3	GNG3	GNG3	87	0.56	0.19	YES
3	TAS2R4	TAS2R4	TAS2R4	105	0.54	0.28	YES
4	TAS2R5	TAS2R5	TAS2R5	493	0.33	0.3	YES
5	TAS2R19	TAS2R19	TAS2R19	683	0.28	0.34	YES
6	TAS2R20	TAS2R20	TAS2R20	835	0.26	0.36	YES
7	TAS2R3	TAS2R3	TAS2R3	1086	0.22	0.38	YES
8	TAS2R50	TAS2R50	TAS2R50	1128	0.22	0.42	YES
9	TAS1R3	TAS1R3	TAS1R3	1310	0.2	0.43	YES
10	KCNB1	KCNB1	KCNB1	1502	0.18	0.45	YES
11	TAS2R14	TAS2R14	TAS2R14	1683	0.16	0.46	YES
12	TAS2R10	TAS2R10	TAS2R10	1979	0.14	0.47	YES
13	PRKACG	PRKACG	PRKACG	2059	0.13	0.48	YES
14	TAS2R31	TAS2R31	TAS2R31	2181	0.13	0.5	YES
15	SCNN1B	SCNN1B	SCNN1B	2280	0.12	0.51	YES
16	TAS2R8	TAS2R8	TAS2R8	2283	0.12	0.53	YES
17	SCNN1G	SCNN1G	SCNN1G	2770	0.1	0.52	NO
18	TAS2R43	TAS2R43	TAS2R43	2952	0.094	0.52	NO
19	TAS2R13	TAS2R13	TAS2R13	3140	0.088	0.52	NO
20	ADCY6	ADCY6	ADCY6	3642	0.075	0.51	NO
21	TAS2R42	TAS2R42	TAS2R42	3976	0.068	0.5	NO
22	PRKX	PRKX	PRKX	4074	0.066	0.5	NO
23	GNB1	GNB1	GNB1	6300	0.03	0.38	NO
24	GNAS	GNAS	GNAS	6861	0.024	0.36	NO
25	ADCY8	ADCY8	ADCY8	8879	0.0015	0.24	NO
26	ADCY4	ADCY4	ADCY4	10995	-0.024	0.13	NO
27	ITPR3	ITPR3	ITPR3	10996	-0.024	0.13	NO
28	PRKACA	PRKACA	PRKACA	11704	-0.035	0.098	NO
29	GRM4	GRM4	GRM4	12240	-0.045	0.075	NO
30	TRPM5	TRPM5	TRPM5	13727	-0.082	0.0047	NO
31	PRKACB	PRKACB	PRKACB	13807	-0.085	0.013	NO
32	CACNA1B	CACNA1B	CACNA1B	14305	-0.1	0.0011	NO
33	PDE1A	PDE1A	PDE1A	14342	-0.11	0.015	NO
34	SCNN1A	SCNN1A	SCNN1A	15411	-0.17	-0.02	NO
35	GNB3	GNB3	GNB3	15637	-0.18	-0.0047	NO
36	CACNA1A	CACNA1A	CACNA1A	15660	-0.18	0.022	NO
37	ACCN1	ACCN1	ACCN1	15791	-0.2	0.044	NO
38	TAS1R1	TAS1R1	TAS1R1	16093	-0.22	0.061	NO
39	PLCB2	PLCB2	PLCB2	16756	-0.29	0.068	NO

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

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

genes ES table in pathway: KEGG OOCYTE MEIOSIS

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	GRIN1	GRIN1	GRIN1	64	0.6	0.051	YES
2	GRM5	GRM5	GRM5	390	0.36	0.066	YES
3	NDUFA4L2	NDUFA4L2	NDUFA4L2	480	0.33	0.091	YES
4	DNAI1	DNAI1	DNAI1	481	0.33	0.12	YES
5	COX6B2	COX6B2	COX6B2	509	0.32	0.15	YES
6	DNAH2	DNAH2	DNAH2	528	0.32	0.18	YES
7	HAP1	HAP1	HAP1	570	0.31	0.2	YES
8	COX4I2	COX4I2	COX4I2	663	0.29	0.22	YES
9	COX8C	COX8C	COX8C	1255	0.2	0.21	YES
10	GRIN2B	GRIN2B	GRIN2B	1413	0.18	0.22	YES
11	BBC3	BBC3	BBC3	1645	0.16	0.22	YES
12	CREB3L4	CREB3L4	CREB3L4	2241	0.12	0.2	YES
13	RCOR1	RCOR1	RCOR1	2259	0.12	0.21	YES
14	POLR2J3	POLR2J3	POLR2J3	2327	0.12	0.21	YES
15	PPARGC1A	PPARGC1A	PPARGC1A	2370	0.12	0.22	YES
16	HDAC1	HDAC1	HDAC1	2415	0.12	0.23	YES
17	DLG4	DLG4	DLG4	2423	0.12	0.24	YES
18	UQCRHL	UQCRHL	UQCRHL	2455	0.11	0.25	YES
19	DNAH3	DNAH3	DNAH3	3185	0.087	0.22	NO
20	UQCRH	UQCRH	UQCRH	3243	0.085	0.22	NO
21	TBPL1	TBPL1	TBPL1	3813	0.072	0.19	NO
22	CREBBP	CREBBP	CREBBP	3837	0.071	0.2	NO
23	SLC25A31	SLC25A31	SLC25A31	3856	0.07	0.2	NO
24	HDAC2	HDAC2	HDAC2	3881	0.07	0.21	NO
25	BAX	BAX	BAX	4314	0.061	0.19	NO
26	TBP	TBP	TBP	4351	0.06	0.2	NO
27	PLCB1	PLCB1	PLCB1	4449	0.058	0.19	NO
28	COX7C	COX7C	COX7C	4625	0.055	0.19	NO
29	COX7A2L	COX7A2L	COX7A2L	4626	0.055	0.2	NO
30	NDUFS4	NDUFS4	NDUFS4	4695	0.054	0.2	NO
31	NRF1	NRF1	NRF1	4698	0.054	0.2	NO
32	POLR2J2	POLR2J2	POLR2J2	4725	0.053	0.2	NO
33	EP300	EP300	EP300	4747	0.053	0.21	NO
34	VDAC2	VDAC2	VDAC2	4756	0.052	0.21	NO
35	CASP9	CASP9	CASP9	4878	0.05	0.21	NO
36	DCTN4	DCTN4	DCTN4	5192	0.046	0.2	NO
37	DNAL4	DNAL4	DNAL4	5304	0.044	0.19	NO
38	CLTA	CLTA	CLTA	5680	0.038	0.18	NO
39	GNAQ	GNAQ	GNAQ	5698	0.038	0.18	NO
40	ATP5F1	ATP5F1	ATP5F1	5795	0.037	0.18	NO
41	CREB1	CREB1	CREB1	5918	0.035	0.17	NO
42	TAF4	TAF4	TAF4	5940	0.035	0.18	NO
43	UQCRC2	UQCRC2	UQCRC2	5991	0.034	0.18	NO
44	SIN3A	SIN3A	SIN3A	6079	0.033	0.17	NO
45	NDUFV3	NDUFV3	NDUFV3	6131	0.032	0.17	NO
46	TFAM	TFAM	TFAM	6172	0.032	0.17	NO
47	ITPR1	ITPR1	ITPR1	6210	0.031	0.18	NO
48	SP1	SP1	SP1	6218	0.031	0.18	NO
49	UQCRB	UQCRB	UQCRB	6240	0.031	0.18	NO
50	HTT	HTT	HTT	6265	0.031	0.18	NO
51	PLCB4	PLCB4	PLCB4	6285	0.03	0.18	NO
52	COX7A2	COX7A2	COX7A2	6371	0.03	0.18	NO
53	UQCRFS1	UQCRFS1	UQCRFS1	6439	0.029	0.18	NO
54	DCTN2	DCTN2	DCTN2	6449	0.029	0.18	NO
55	DCTN1	DCTN1	DCTN1	6488	0.028	0.18	NO
56	POLR2G	POLR2G	POLR2G	6507	0.028	0.18	NO
57	VDAC3	VDAC3	VDAC3	6534	0.027	0.18	NO
58	POLR2H	POLR2H	POLR2H	6683	0.026	0.18	NO
59	NDUFS7	NDUFS7	NDUFS7	6684	0.026	0.18	NO
60	NDUFA9	NDUFA9	NDUFA9	6685	0.026	0.18	NO
61	ATP5G3	ATP5G3	ATP5G3	6828	0.024	0.18	NO
62	HIP1	HIP1	HIP1	6915	0.023	0.17	NO
63	ATP5B	ATP5B	ATP5B	6934	0.023	0.18	NO
64	SLC25A5	SLC25A5	SLC25A5	6951	0.022	0.18	NO
65	ATP5O	ATP5O	ATP5O	7150	0.02	0.17	NO
66	CLTCL1	CLTCL1	CLTCL1	7183	0.02	0.17	NO
67	NDUFC2	NDUFC2	NDUFC2	7197	0.02	0.17	NO
68	ATP5A1	ATP5A1	ATP5A1	7218	0.02	0.17	NO
69	CREB3L2	CREB3L2	CREB3L2	7520	0.016	0.15	NO
70	COX4I1	COX4I1	COX4I1	7558	0.016	0.15	NO
71	NDUFV1	NDUFV1	NDUFV1	7629	0.015	0.15	NO
72	PLCB3	PLCB3	PLCB3	7669	0.014	0.15	NO
73	POLR2B	POLR2B	POLR2B	7743	0.014	0.15	NO
74	ATP5G2	ATP5G2	ATP5G2	7914	0.012	0.14	NO
75	NDUFB9	NDUFB9	NDUFB9	7956	0.011	0.14	NO
76	POLR2E	POLR2E	POLR2E	7997	0.011	0.14	NO
77	CYCS	CYCS	CYCS	8083	0.01	0.13	NO
78	ATP5J	ATP5J	ATP5J	8113	0.0098	0.13	NO
79	AP2B1	AP2B1	AP2B1	8584	0.0048	0.1	NO
80	NDUFS6	NDUFS6	NDUFS6	8700	0.0032	0.098	NO
81	NDUFS5	NDUFS5	NDUFS5	8703	0.0032	0.099	NO
82	UQCR11	UQCR11	UQCR11	8747	0.0029	0.096	NO
83	SLC25A4	SLC25A4	SLC25A4	8812	0.0021	0.093	NO
84	ATP5C1	ATP5C1	ATP5C1	8819	0.002	0.093	NO
85	COX8A	COX8A	COX8A	8854	0.0017	0.091	NO
86	DNAL1	DNAL1	DNAL1	8866	0.0015	0.091	NO
87	CLTC	CLTC	CLTC	8872	0.0015	0.09	NO
88	NDUFB10	NDUFB10	NDUFB10	8880	0.0014	0.09	NO
89	SOD2	SOD2	SOD2	8948	0.00059	0.086	NO
90	NDUFA8	NDUFA8	NDUFA8	8962	0.00041	0.086	NO
91	NDUFA6	NDUFA6	NDUFA6	8969	0.00035	0.086	NO
92	PPID	PPID	PPID	9071	-0.00086	0.08	NO
93	NDUFB6	NDUFB6	NDUFB6	9260	-0.0031	0.07	NO
94	COX6B1	COX6B1	COX6B1	9283	-0.0034	0.069	NO
95	POLR2C	POLR2C	POLR2C	9333	-0.004	0.066	NO
96	POLR2D	POLR2D	POLR2D	9415	-0.0047	0.062	NO
97	SDHD	SDHD	SDHD	9499	-0.0057	0.058	NO
98	NDUFA10	NDUFA10	NDUFA10	9557	-0.0064	0.055	NO
99	POLR2A	POLR2A	POLR2A	9645	-0.0073	0.051	NO
100	POLR2I	POLR2I	POLR2I	9700	-0.0079	0.049	NO
101	CYC1	CYC1	CYC1	9705	-0.008	0.049	NO
102	SOD1	SOD1	SOD1	9727	-0.0081	0.049	NO
103	ATP5G1	ATP5G1	ATP5G1	9794	-0.0089	0.046	NO
104	NDUFAB1	NDUFAB1	NDUFAB1	9850	-0.0094	0.044	NO
105	NDUFA7	NDUFA7	NDUFA7	9969	-0.011	0.038	NO
106	COX6A1	COX6A1	COX6A1	9977	-0.011	0.039	NO
107	COX6C	COX6C	COX6C	9999	-0.011	0.039	NO
108	UQCR10	UQCR10	UQCR10	10100	-0.013	0.034	NO
109	NDUFB8	NDUFB8	NDUFB8	10197	-0.014	0.03	NO
110	NDUFB2	NDUFB2	NDUFB2	10240	-0.014	0.029	NO
111	APAF1	APAF1	APAF1	10277	-0.014	0.028	NO
112	SDHA	SDHA	SDHA	10329	-0.015	0.027	NO
113	NDUFS8	NDUFS8	NDUFS8	10330	-0.015	0.028	NO
114	AP2A1	AP2A1	AP2A1	10363	-0.016	0.028	NO
115	IFT57	IFT57	IFT57	10429	-0.016	0.026	NO
116	COX5A	COX5A	COX5A	10522	-0.018	0.022	NO
117	NDUFB7	NDUFB7	NDUFB7	10597	-0.018	0.02	NO
118	NDUFB5	NDUFB5	NDUFB5	10619	-0.019	0.02	NO
119	AP2S1	AP2S1	AP2S1	10663	-0.019	0.019	NO
120	NDUFS2	NDUFS2	NDUFS2	10674	-0.02	0.021	NO
121	CLTB	CLTB	CLTB	10684	-0.02	0.022	NO
122	COX7B	COX7B	COX7B	10735	-0.02	0.021	NO
123	NDUFA5	NDUFA5	NDUFA5	10797	-0.021	0.019	NO
124	NDUFA1	NDUFA1	NDUFA1	10798	-0.021	0.021	NO
125	AP2A2	AP2A2	AP2A2	10855	-0.022	0.02	NO
126	TP53	TP53	TP53	10886	-0.022	0.02	NO
127	COX5B	COX5B	COX5B	11051	-0.024	0.014	NO
128	POLR2F	POLR2F	POLR2F	11331	-0.029	0.0004	NO
129	NDUFS3	NDUFS3	NDUFS3	11356	-0.029	0.0017	NO
130	NDUFA2	NDUFA2	NDUFA2	11395	-0.03	0.0023	NO
131	ATP5E	ATP5E	ATP5E	11451	-0.031	0.002	NO
132	UQCRC1	UQCRC1	UQCRC1	11607	-0.033	-0.0038	NO
133	UQCRQ	UQCRQ	UQCRQ	11980	-0.04	-0.021	NO
134	AP2M1	AP2M1	AP2M1	12021	-0.04	-0.02	NO
135	ATP5D	ATP5D	ATP5D	12025	-0.04	-0.016	NO
136	POLR2J	POLR2J	POLR2J	12093	-0.042	-0.016	NO
137	ATP5H	ATP5H	ATP5H	12138	-0.042	-0.015	NO
138	SDHB	SDHB	SDHB	12281	-0.046	-0.019	NO
139	SLC25A6	SLC25A6	SLC25A6	12322	-0.046	-0.017	NO
140	NDUFV2	NDUFV2	NDUFV2	12365	-0.047	-0.015	NO
141	NDUFB1	NDUFB1	NDUFB1	12369	-0.047	-0.011	NO
142	POLR2K	POLR2K	POLR2K	12587	-0.052	-0.018	NO
143	NDUFS1	NDUFS1	NDUFS1	12606	-0.053	-0.014	NO
144	CREB3L3	CREB3L3	CREB3L3	12649	-0.053	-0.012	NO
145	SDHC	SDHC	SDHC	12730	-0.055	-0.011	NO
146	VDAC1	VDAC1	VDAC1	12915	-0.06	-0.016	NO
147	CREB3	CREB3	CREB3	12989	-0.061	-0.015	NO
148	NDUFA3	NDUFA3	NDUFA3	13068	-0.063	-0.014	NO
149	DNAH1	DNAH1	DNAH1	13158	-0.065	-0.013	NO
150	NDUFB3	NDUFB3	NDUFB3	13181	-0.066	-0.0079	NO
151	COX7A1	COX7A1	COX7A1	13304	-0.069	-0.0085	NO
152	NDUFB4	NDUFB4	NDUFB4	13327	-0.07	-0.0034	NO
153	REST	REST	REST	13349	-0.071	0.0019	NO
154	DNALI1	DNALI1	DNALI1	13367	-0.071	0.0074	NO
155	NDUFC1	NDUFC1	NDUFC1	13409	-0.072	0.012	NO
156	PPARG	PPARG	PPARG	13549	-0.076	0.011	NO
157	NDUFA4	NDUFA4	NDUFA4	13878	-0.088	0.00023	NO
158	CASP3	CASP3	CASP3	14058	-0.094	-0.0013	NO
159	POLR2L	POLR2L	POLR2L	14114	-0.096	0.0044	NO
160	TAF4B	TAF4B	TAF4B	14458	-0.11	-0.0048	NO
161	GPX1	GPX1	GPX1	14651	-0.12	-0.0046	NO
162	CASP8	CASP8	CASP8	15079	-0.14	-0.015	NO
163	BDNF	BDNF	BDNF	15832	-0.2	-0.04	NO
164	TGM2	TGM2	TGM2	16015	-0.22	-0.03	NO
165	PLCB2	PLCB2	PLCB2	16756	-0.29	-0.045	NO
166	COX6A2	COX6A2	COX6A2	17085	-0.34	-0.033	NO
167	CREB5	CREB5	CREB5	17408	-0.4	-0.015	NO
168	CREB3L1	CREB3L1	CREB3L1	17826	-0.52	0.0084	NO

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

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA AT1R PATHWAY	32	genes.ES.table	0.3	1.1	0.37	1	1	0.28	0.14	0.24	1	0.56
BIOCARTA BIOPEPTIDES PATHWAY	37	genes.ES.table	0.43	1.6	0.04	1	0.72	0.35	0.2	0.28	0.61	0.34
BIOCARTA EGF PATHWAY	30	genes.ES.table	0.39	1.2	0.25	1	0.99	0.3	0.17	0.25	1	0.54
BIOCARTA PYK2 PATHWAY	27	genes.ES.table	0.44	1.7	0.036	0.9	0.49	0.3	0.14	0.26	0	0.31
BIOCARTA PDGF PATHWAY	31	genes.ES.table	0.49	1.5	0.089	0.7	0.84	0.32	0.17	0.27	0.48	0.24
BIOCARTA TOLL PATHWAY	36	genes.ES.table	0.57	1.5	0.057	0.78	0.75	0.44	0.17	0.37	0.5	0.26
KEGG ABC TRANSPORTERS	39	genes.ES.table	0.39	1.1	0.32	1	1	0.13	0.062	0.12	1	0.63
KEGG PEROXISOME	75	genes.ES.table	0.3	1.1	0.3	1	0.99	0.29	0.23	0.23	1	0.58
KEGG ANTIGEN PROCESSING AND PRESENTATION	68	genes.ES.table	0.48	1.2	0.29	1	0.99	0.53	0.29	0.38	1	0.5
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY	88	genes.ES.table	0.5	1.3	0.19	1	0.96	0.38	0.17	0.31	1	0.58

genes ES table in pathway: BIOCARTA AT1R PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PTK2B	PTK2B	PTK2B	1246	0.22	0.033	YES
2	SHC1	SHC1	SHC1	2007	0.16	0.065	YES
3	MAPK8	MAPK8	MAPK8	2241	0.14	0.12	YES
4	MAP3K1	MAP3K1	MAP3K1	2259	0.14	0.19	YES
5	CALM1	CALM1	CALM1	2289	0.14	0.25	YES
6	PAK1	PAK1	PAK1	2324	0.14	0.32	YES
7	CALM2	CALM2	CALM2	2330	0.14	0.38	YES
8	PRKCB	PRKCB	PRKCB	2465	0.13	0.44	YES
9	MAPK3	MAPK3	MAPK3	4685	0.067	0.34	NO
10	GNAQ	GNAQ	GNAQ	5168	0.057	0.34	NO
11	MAPK14	MAPK14	MAPK14	6173	0.04	0.31	NO
12	SOS1	SOS1	SOS1	6339	0.038	0.32	NO
13	GRB2	GRB2	GRB2	7081	0.027	0.29	NO
14	SRC	SRC	SRC	9312	-0.0031	0.16	NO
15	CALM3	CALM3	CALM3	9409	-0.0043	0.16	NO
16	MAP2K4	MAP2K4	MAP2K4	10746	-0.025	0.098	NO
17	CRKL	CRKL	CRKL	10748	-0.025	0.11	NO
18	MAPK1	MAPK1	MAPK1	10750	-0.025	0.12	NO
19	BCAR1	BCAR1	BCAR1	11110	-0.031	0.12	NO
20	RAC1	RAC1	RAC1	11563	-0.039	0.11	NO
21	MAP2K2	MAP2K2	MAP2K2	11890	-0.046	0.11	NO
22	PLCG1	PLCG1	PLCG1	11996	-0.048	0.13	NO
23	JUN	JUN	JUN	12397	-0.056	0.13	NO
24	MAP2K1	MAP2K1	MAP2K1	12783	-0.064	0.14	NO
25	RAF1	RAF1	RAF1	13027	-0.07	0.16	NO
26	MAP2K3	MAP2K3	MAP2K3	14186	-0.11	0.15	NO
27	PRKCA	PRKCA	PRKCA	14826	-0.14	0.18	NO

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

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES 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	STAT4	STAT4	STAT4	39	0.63	0.16	YES
2	PTK2B	PTK2B	PTK2B	1246	0.22	0.15	YES
3	STAT5A	STAT5A	STAT5A	1254	0.22	0.21	YES
4	STAT1	STAT1	STAT1	1500	0.19	0.24	YES
5	SHC1	SHC1	SHC1	2007	0.16	0.26	YES
6	CAMK2G	CAMK2G	CAMK2G	2192	0.15	0.29	YES
7	MAPK8	MAPK8	MAPK8	2241	0.14	0.32	YES
8	CALM1	CALM1	CALM1	2289	0.14	0.36	YES
9	CALM2	CALM2	CALM2	2330	0.14	0.39	YES
10	PRKCB	PRKCB	PRKCB	2465	0.13	0.42	YES
11	MAPT	MAPT	MAPT	2768	0.12	0.43	YES
12	CAMK2B	CAMK2B	CAMK2B	3472	0.098	0.42	YES
13	JAK2	JAK2	JAK2	3611	0.094	0.44	YES
14	GNA11	GNA11	GNA11	4142	0.079	0.43	NO
15	STAT6	STAT6	STAT6	4682	0.067	0.41	NO
16	MAPK3	MAPK3	MAPK3	4685	0.067	0.43	NO
17	STAT5B	STAT5B	STAT5B	5482	0.052	0.4	NO
18	MAPK14	MAPK14	MAPK14	6173	0.04	0.37	NO
19	SOS1	SOS1	SOS1	6339	0.038	0.37	NO
20	GNAI1	GNAI1	GNAI1	6480	0.036	0.37	NO
21	STAT2	STAT2	STAT2	6570	0.034	0.38	NO
22	GRB2	GRB2	GRB2	7081	0.027	0.36	NO
23	CALM3	CALM3	CALM3	9409	-0.0043	0.23	NO
24	CDK5	CDK5	CDK5	9470	-0.0052	0.23	NO
25	CAMK2D	CAMK2D	CAMK2D	9824	-0.0097	0.21	NO
26	STAT3	STAT3	STAT3	10477	-0.02	0.18	NO
27	MAPK1	MAPK1	MAPK1	10750	-0.025	0.17	NO
28	MAP2K2	MAP2K2	MAP2K2	11890	-0.046	0.12	NO
29	PLCG1	PLCG1	PLCG1	11996	-0.048	0.12	NO
30	MAP2K1	MAP2K1	MAP2K1	12783	-0.064	0.097	NO
31	RAF1	RAF1	RAF1	13027	-0.07	0.1	NO
32	GNB1	GNB1	GNB1	13058	-0.071	0.12	NO
33	AGT	AGT	AGT	13805	-0.094	0.1	NO
34	FYN	FYN	FYN	13989	-0.1	0.12	NO
35	MYLK	MYLK	MYLK	14772	-0.13	0.11	NO
36	CAMK2A	CAMK2A	CAMK2A	14809	-0.14	0.14	NO
37	PRKCA	PRKCA	PRKCA	14826	-0.14	0.18	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 BIOPEPTIDES PATHWAY.

Figure S24. 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 EGF 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	TLR9	TLR9	TLR9	679	0.3	0.036	YES
2	TLR3	TLR3	TLR3	934	0.26	0.084	YES
3	MAP2K6	MAP2K6	MAP2K6	980	0.25	0.14	YES
4	TLR10	TLR10	TLR10	1009	0.25	0.2	YES
5	EIF2AK2	EIF2AK2	EIF2AK2	1021	0.24	0.26	YES
6	PGLYRP1	PGLYRP1	PGLYRP1	1159	0.23	0.31	YES
7	TLR6	TLR6	TLR6	1399	0.2	0.35	YES
8	TLR7	TLR7	TLR7	1479	0.19	0.39	YES
9	MYD88	MYD88	MYD88	1737	0.18	0.42	YES
10	MAPK8	MAPK8	MAPK8	2241	0.14	0.43	YES
11	MAP3K1	MAP3K1	MAP3K1	2259	0.14	0.46	YES
12	TLR4	TLR4	TLR4	2420	0.14	0.49	YES
13	TRAF6	TRAF6	TRAF6	2492	0.13	0.52	YES
14	TLR2	TLR2	TLR2	2514	0.13	0.55	YES
15	FOS	FOS	FOS	3012	0.11	0.55	YES
16	TIRAP	TIRAP	TIRAP	3067	0.11	0.57	YES
17	TOLLIP	TOLLIP	TOLLIP	3806	0.088	0.55	NO
18	CHUK	CHUK	CHUK	4466	0.071	0.53	NO
19	MAP3K14	MAP3K14	MAP3K14	5242	0.056	0.5	NO
20	CD14	CD14	CD14	5885	0.045	0.48	NO
21	MAPK14	MAPK14	MAPK14	6173	0.04	0.47	NO
22	MAP3K7	MAP3K7	MAP3K7	6886	0.03	0.44	NO
23	NFKB1	NFKB1	NFKB1	8668	0.0054	0.34	NO
24	TAB2	TAB2	TAB2	9528	-0.0059	0.3	NO
25	IRAK1	IRAK1	IRAK1	9777	-0.0091	0.28	NO
26	IKBKG	IKBKG	IKBKG	9993	-0.012	0.27	NO
27	IKBKB	IKBKB	IKBKB	10587	-0.022	0.25	NO
28	MAP2K4	MAP2K4	MAP2K4	10746	-0.025	0.24	NO
29	ELK1	ELK1	ELK1	11151	-0.032	0.23	NO
30	NFKBIA	NFKBIA	NFKBIA	11993	-0.048	0.19	NO
31	JUN	JUN	JUN	12397	-0.056	0.19	NO
32	RELA	RELA	RELA	12894	-0.067	0.17	NO
33	ECSIT	ECSIT	ECSIT	13080	-0.072	0.18	NO
34	MAP2K3	MAP2K3	MAP2K3	14186	-0.11	0.15	NO
35	LY96	LY96	LY96	14600	-0.12	0.15	NO
36	TAB1	TAB1	TAB1	14860	-0.14	0.17	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 EGF PATHWAY.

Figure S26. 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 PYK2 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MAPK13	MAPK13	MAPK13	517	0.34	0.035	YES
2	IFIH1	IFIH1	IFIH1	741	0.28	0.076	YES
3	IKBKE	IKBKE	IKBKE	808	0.27	0.12	YES
4	CXCL10	CXCL10	CXCL10	920	0.26	0.17	YES
5	DDX58	DDX58	DDX58	925	0.26	0.22	YES
6	IFNW1	IFNW1	IFNW1	1312	0.21	0.23	YES
7	IL8	IL8	IL8	1387	0.2	0.27	YES
8	TRAF3	TRAF3	TRAF3	1608	0.18	0.29	YES
9	TNF	TNF	TNF	1909	0.16	0.3	YES
10	ISG15	ISG15	ISG15	1926	0.16	0.33	YES
11	MAPK8	MAPK8	MAPK8	2241	0.14	0.34	YES
12	MAP3K1	MAP3K1	MAP3K1	2259	0.14	0.37	YES
13	IRF7	IRF7	IRF7	2315	0.14	0.39	YES
14	IL12B	IL12B	IL12B	2432	0.14	0.41	YES
15	TRAF6	TRAF6	TRAF6	2492	0.13	0.44	YES
16	CYLD	CYLD	CYLD	2627	0.13	0.45	YES
17	DDX3Y	DDX3Y	DDX3Y	3039	0.11	0.45	YES
18	MAPK9	MAPK9	MAPK9	3612	0.094	0.44	YES
19	AZI2	AZI2	AZI2	3737	0.09	0.44	YES
20	TRIM25	TRIM25	TRIM25	3880	0.086	0.45	YES
21	CHUK	CHUK	CHUK	4466	0.071	0.43	NO
22	MAPK11	MAPK11	MAPK11	4751	0.066	0.43	NO
23	MAPK10	MAPK10	MAPK10	4808	0.064	0.44	NO
24	DHX58	DHX58	DHX58	4863	0.063	0.45	NO
25	ATG12	ATG12	ATG12	5048	0.059	0.45	NO
26	MAPK12	MAPK12	MAPK12	5458	0.052	0.44	NO
27	TBK1	TBK1	TBK1	5651	0.048	0.44	NO
28	RIPK1	RIPK1	RIPK1	6136	0.041	0.42	NO
29	MAPK14	MAPK14	MAPK14	6173	0.04	0.42	NO
30	DAK	DAK	DAK	6284	0.039	0.42	NO
31	TANK	TANK	TANK	6711	0.032	0.4	NO
32	MAP3K7	MAP3K7	MAP3K7	6886	0.03	0.4	NO
33	DDX3X	DDX3X	DDX3X	8113	0.013	0.34	NO
34	OTUD5	OTUD5	OTUD5	8222	0.011	0.33	NO
35	NFKB1	NFKB1	NFKB1	8668	0.0054	0.31	NO
36	PIN1	PIN1	PIN1	9276	-0.0024	0.27	NO
37	TRADD	TRADD	TRADD	9352	-0.0037	0.27	NO
38	RNF125	RNF125	RNF125	9892	-0.011	0.24	NO
39	IKBKG	IKBKG	IKBKG	9993	-0.012	0.24	NO
40	TRAF2	TRAF2	TRAF2	10307	-0.018	0.22	NO
41	IKBKB	IKBKB	IKBKB	10587	-0.022	0.21	NO
42	FADD	FADD	FADD	10593	-0.022	0.22	NO
43	IFNA5	IFNA5	IFNA5	10932	-0.028	0.2	NO
44	MAVS	MAVS	MAVS	11062	-0.03	0.2	NO
45	ATG5	ATG5	ATG5	11347	-0.035	0.19	NO
46	CASP8	CASP8	CASP8	11386	-0.036	0.2	NO
47	NFKBIA	NFKBIA	NFKBIA	11993	-0.048	0.17	NO
48	TBKBP1	TBKBP1	TBKBP1	12014	-0.048	0.18	NO
49	NLRX1	NLRX1	NLRX1	12089	-0.05	0.19	NO
50	NFKBIB	NFKBIB	NFKBIB	12708	-0.063	0.16	NO
51	IL12A	IL12A	IL12A	12876	-0.066	0.17	NO
52	RELA	RELA	RELA	12894	-0.067	0.18	NO
53	IRF3	IRF3	IRF3	13480	-0.083	0.16	NO
54	SIKE1	SIKE1	SIKE1	13907	-0.098	0.16	NO
55	CASP10	CASP10	CASP10	15495	-0.18	0.1	NO
56	TMEM173	TMEM173	TMEM173	15805	-0.2	0.12	NO

Figure S27. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PYK2 PATHWAY.

Figure S28. 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

genes ES table in pathway: BIOCARTA PDGF PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	STAT4	STAT4	STAT4	39	0.63	0.2	YES
2	STAT5A	STAT5A	STAT5A	1254	0.22	0.2	YES
3	STAT1	STAT1	STAT1	1500	0.19	0.25	YES
4	PIK3R1	PIK3R1	PIK3R1	1846	0.17	0.28	YES
5	SHC1	SHC1	SHC1	2007	0.16	0.33	YES
6	PIK3CG	PIK3CG	PIK3CG	2134	0.15	0.37	YES
7	MAPK8	MAPK8	MAPK8	2241	0.14	0.41	YES
8	MAP3K1	MAP3K1	MAP3K1	2259	0.14	0.45	YES
9	PRKCB	PRKCB	PRKCB	2465	0.13	0.48	YES
10	FOS	FOS	FOS	3012	0.11	0.49	YES
11	STAT6	STAT6	STAT6	4682	0.067	0.42	NO
12	MAPK3	MAPK3	MAPK3	4685	0.067	0.44	NO
13	STAT5B	STAT5B	STAT5B	5482	0.052	0.41	NO
14	RASA1	RASA1	RASA1	6308	0.038	0.38	NO
15	SOS1	SOS1	SOS1	6339	0.038	0.39	NO
16	STAT2	STAT2	STAT2	6570	0.034	0.39	NO
17	CSNK2A1	CSNK2A1	CSNK2A1	7064	0.027	0.37	NO
18	GRB2	GRB2	GRB2	7081	0.027	0.38	NO
19	PDGFRA	PDGFRA	PDGFRA	7974	0.014	0.33	NO
20	SRF	SRF	SRF	9347	-0.0037	0.26	NO
21	STAT3	STAT3	STAT3	10477	-0.02	0.2	NO
22	MAP2K4	MAP2K4	MAP2K4	10746	-0.025	0.19	NO
23	ELK1	ELK1	ELK1	11151	-0.032	0.18	NO
24	PIK3CA	PIK3CA	PIK3CA	11547	-0.039	0.17	NO
25	PLCG1	PLCG1	PLCG1	11996	-0.048	0.16	NO
26	JUN	JUN	JUN	12397	-0.056	0.16	NO
27	JAK1	JAK1	JAK1	12745	-0.063	0.16	NO
28	MAP2K1	MAP2K1	MAP2K1	12783	-0.064	0.18	NO
29	RAF1	RAF1	RAF1	13027	-0.07	0.18	NO
30	PRKCA	PRKCA	PRKCA	14826	-0.14	0.13	NO
31	PDGFA	PDGFA	PDGFA	15046	-0.15	0.16	NO

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

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PDGF 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 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	MAPK13	MAPK13	MAPK13	517	0.34	0.008	YES
2	TLR9	TLR9	TLR9	679	0.3	0.032	YES
3	TLR1	TLR1	TLR1	690	0.3	0.064	YES
4	IKBKE	IKBKE	IKBKE	808	0.27	0.087	YES
5	CXCL10	CXCL10	CXCL10	920	0.26	0.11	YES
6	TLR3	TLR3	TLR3	934	0.26	0.14	YES
7	MAP2K6	MAP2K6	MAP2K6	980	0.25	0.16	YES
8	IFNA21	IFNA21	IFNA21	1355	0.2	0.16	YES
9	IL8	IL8	IL8	1387	0.2	0.18	YES
10	TLR6	TLR6	TLR6	1399	0.2	0.2	YES
11	TLR7	TLR7	TLR7	1479	0.19	0.22	YES
12	STAT1	STAT1	STAT1	1500	0.19	0.24	YES
13	TRAF3	TRAF3	TRAF3	1608	0.18	0.26	YES
14	CD80	CD80	CD80	1631	0.18	0.28	YES
15	CXCL11	CXCL11	CXCL11	1703	0.18	0.29	YES
16	MYD88	MYD88	MYD88	1737	0.18	0.31	YES
17	PIK3R1	PIK3R1	PIK3R1	1846	0.17	0.32	YES
18	TNF	TNF	TNF	1909	0.16	0.34	YES
19	CXCL9	CXCL9	CXCL9	1946	0.16	0.35	YES
20	PIK3CG	PIK3CG	PIK3CG	2134	0.15	0.36	YES
21	CD86	CD86	CD86	2209	0.15	0.37	YES
22	MAPK8	MAPK8	MAPK8	2241	0.14	0.38	YES
23	CCL3	CCL3	CCL3	2284	0.14	0.4	YES
24	IRF7	IRF7	IRF7	2315	0.14	0.41	YES
25	CCL4	CCL4	CCL4	2351	0.14	0.42	YES
26	TLR4	TLR4	TLR4	2420	0.14	0.44	YES
27	IL12B	IL12B	IL12B	2432	0.14	0.45	YES
28	CCL5	CCL5	CCL5	2475	0.13	0.46	YES
29	TRAF6	TRAF6	TRAF6	2492	0.13	0.48	YES
30	TLR2	TLR2	TLR2	2514	0.13	0.49	YES
31	TLR8	TLR8	TLR8	2797	0.12	0.49	YES
32	FOS	FOS	FOS	3012	0.11	0.49	YES
33	TIRAP	TIRAP	TIRAP	3067	0.11	0.5	YES
34	MAPK9	MAPK9	MAPK9	3612	0.094	0.48	NO
35	TOLLIP	TOLLIP	TOLLIP	3806	0.088	0.48	NO
36	IL1B	IL1B	IL1B	3913	0.085	0.48	NO
37	CHUK	CHUK	CHUK	4466	0.071	0.46	NO
38	TLR5	TLR5	TLR5	4663	0.067	0.45	NO
39	AKT3	AKT3	AKT3	4679	0.067	0.46	NO
40	MAPK3	MAPK3	MAPK3	4685	0.067	0.46	NO
41	MAPK11	MAPK11	MAPK11	4751	0.066	0.47	NO
42	MAPK10	MAPK10	MAPK10	4808	0.064	0.47	NO
43	CD40	CD40	CD40	4928	0.062	0.47	NO
44	MAPK12	MAPK12	MAPK12	5458	0.052	0.45	NO
45	CD14	CD14	CD14	5885	0.045	0.43	NO
46	PIK3R5	PIK3R5	PIK3R5	6011	0.043	0.43	NO
47	RIPK1	RIPK1	RIPK1	6136	0.041	0.42	NO
48	MAPK14	MAPK14	MAPK14	6173	0.04	0.43	NO
49	AKT1	AKT1	AKT1	6793	0.031	0.4	NO
50	MAP3K7	MAP3K7	MAP3K7	6886	0.03	0.39	NO
51	TICAM1	TICAM1	TICAM1	7922	0.015	0.34	NO
52	SPP1	SPP1	SPP1	8095	0.013	0.33	NO
53	IFNAR2	IFNAR2	IFNAR2	8168	0.012	0.33	NO
54	NFKB1	NFKB1	NFKB1	8668	0.0054	0.3	NO
55	IRAK4	IRAK4	IRAK4	9396	-0.0042	0.26	NO
56	TAB2	TAB2	TAB2	9528	-0.0059	0.25	NO
57	MAP2K7	MAP2K7	MAP2K7	9618	-0.007	0.25	NO
58	IRAK1	IRAK1	IRAK1	9777	-0.0091	0.24	NO
59	IKBKG	IKBKG	IKBKG	9993	-0.012	0.23	NO
60	PIK3CB	PIK3CB	PIK3CB	10564	-0.022	0.2	NO
61	IKBKB	IKBKB	IKBKB	10587	-0.022	0.2	NO
62	FADD	FADD	FADD	10593	-0.022	0.2	NO
63	IFNAR1	IFNAR1	IFNAR1	10735	-0.025	0.2	NO
64	MAP2K4	MAP2K4	MAP2K4	10746	-0.025	0.2	NO
65	MAPK1	MAPK1	MAPK1	10750	-0.025	0.2	NO
66	IFNA5	IFNA5	IFNA5	10932	-0.028	0.2	NO
67	PIK3R2	PIK3R2	PIK3R2	10950	-0.028	0.2	NO
68	CASP8	CASP8	CASP8	11386	-0.036	0.18	NO
69	PIK3CA	PIK3CA	PIK3CA	11547	-0.039	0.17	NO
70	RAC1	RAC1	RAC1	11563	-0.039	0.18	NO
71	MAP2K2	MAP2K2	MAP2K2	11890	-0.046	0.16	NO
72	NFKBIA	NFKBIA	NFKBIA	11993	-0.048	0.16	NO
73	AKT2	AKT2	AKT2	12378	-0.056	0.15	NO
74	JUN	JUN	JUN	12397	-0.056	0.15	NO
75	MAP2K1	MAP2K1	MAP2K1	12783	-0.064	0.14	NO
76	IL12A	IL12A	IL12A	12876	-0.066	0.14	NO
77	RELA	RELA	RELA	12894	-0.067	0.15	NO
78	PIK3CD	PIK3CD	PIK3CD	12942	-0.068	0.15	NO
79	IL6	IL6	IL6	13015	-0.07	0.16	NO
80	IRF5	IRF5	IRF5	13469	-0.083	0.14	NO
81	IRF3	IRF3	IRF3	13480	-0.083	0.15	NO
82	TICAM2	TICAM2	TICAM2	13718	-0.091	0.14	NO
83	MAP2K3	MAP2K3	MAP2K3	14186	-0.11	0.13	NO
84	PIK3R3	PIK3R3	PIK3R3	14539	-0.12	0.12	NO
85	LY96	LY96	LY96	14600	-0.12	0.14	NO
86	TAB1	TAB1	TAB1	14860	-0.14	0.14	NO
87	MAP3K8	MAP3K8	MAP3K8	15100	-0.15	0.14	NO
88	CTSK	CTSK	CTSK	15845	-0.2	0.12	NO

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

Figure S32. 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 ABC TRANSPORTERS

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	NCAM2	NCAM2	NCAM2	238	0.43	0.12	YES
2	IL1A	IL1A	IL1A	341	0.39	0.24	YES
3	C6	C6	C6	608	0.31	0.33	YES
4	EGR1	EGR1	EGR1	1172	0.23	0.37	YES
5	C5	C5	C5	1453	0.2	0.41	YES
6	CCL5	CCL5	CCL5	2475	0.13	0.4	YES
7	PRNP	PRNP	PRNP	2533	0.13	0.44	YES
8	NCAM1	NCAM1	NCAM1	3056	0.11	0.44	YES
9	PRKACB	PRKACB	PRKACB	3116	0.11	0.47	YES
10	IL1B	IL1B	IL1B	3913	0.085	0.46	NO
11	MAPK3	MAPK3	MAPK3	4685	0.067	0.44	NO
12	STIP1	STIP1	STIP1	6019	0.043	0.37	NO
13	HSPA5	HSPA5	HSPA5	6406	0.037	0.36	NO
14	PRKACA	PRKACA	PRKACA	7007	0.028	0.34	NO
15	HSPA1A	HSPA1A	HSPA1A	7616	0.019	0.31	NO
16	C1QC	C1QC	C1QC	8179	0.012	0.28	NO
17	C1QB	C1QB	C1QB	8256	0.01	0.28	NO
18	SOD1	SOD1	SOD1	8579	0.0066	0.27	NO
19	PRKX	PRKX	PRKX	10105	-0.014	0.19	NO
20	MAPK1	MAPK1	MAPK1	10750	-0.025	0.16	NO
21	ELK1	ELK1	ELK1	11151	-0.032	0.15	NO
22	PRKACG	PRKACG	PRKACG	11313	-0.034	0.15	NO
23	C1QA	C1QA	C1QA	11573	-0.039	0.15	NO
24	C8G	C8G	C8G	11635	-0.04	0.16	NO
25	MAP2K2	MAP2K2	MAP2K2	11890	-0.046	0.16	NO
26	MAP2K1	MAP2K1	MAP2K1	12783	-0.064	0.13	NO
27	IL6	IL6	IL6	13015	-0.07	0.14	NO
28	LAMC1	LAMC1	LAMC1	13018	-0.07	0.16	NO
29	FYN	FYN	FYN	13989	-0.1	0.14	NO
30	BAX	BAX	BAX	14169	-0.11	0.16	NO
31	NOTCH1	NOTCH1	NOTCH1	15342	-0.16	0.15	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 ABC TRANSPORTERS.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ABC TRANSPORTERS, 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 PEROXISOME

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	IL1A	IL1A	IL1A	341	0.39	0.1	YES
2	KLRC1	KLRC1	KLRC1	971	0.25	0.14	YES
3	FASLG	FASLG	FASLG	1253	0.22	0.19	YES
4	CD80	CD80	CD80	1631	0.18	0.22	YES
5	TNF	TNF	TNF	1909	0.16	0.26	YES
6	CD86	CD86	CD86	2209	0.15	0.29	YES
7	KIR2DL1	KIR2DL1	KIR2DL1	2429	0.14	0.32	YES
8	HLA-DOA	HLA-DOA	HLA-DOA	2680	0.12	0.34	YES
9	HLA-DQA2	HLA-DQA2	HLA-DQA2	2802	0.12	0.37	YES
10	HLA-DOB	HLA-DOB	HLA-DOB	3332	0.1	0.37	YES
11	HLA-DPA1	HLA-DPA1	HLA-DPA1	3381	0.1	0.4	YES
12	PRF1	PRF1	PRF1	3478	0.098	0.42	YES
13	HLA-G	HLA-G	HLA-G	3814	0.088	0.43	YES
14	HLA-DQA1	HLA-DQA1	HLA-DQA1	3820	0.088	0.46	YES
15	IL1B	IL1B	IL1B	3913	0.085	0.48	YES
16	KIR3DL1	KIR3DL1	KIR3DL1	4054	0.081	0.5	YES
17	KIR2DL3	KIR2DL3	KIR2DL3	4055	0.081	0.52	YES
18	HLA-DRB5	HLA-DRB5	HLA-DRB5	4320	0.074	0.53	YES
19	IFNG	IFNG	IFNG	4866	0.063	0.52	YES
20	KLRD1	KLRD1	KLRD1	4907	0.062	0.53	YES
21	HLA-DMB	HLA-DMB	HLA-DMB	4977	0.061	0.55	YES
22	HLA-B	HLA-B	HLA-B	5034	0.06	0.56	YES
23	CD28	CD28	CD28	5084	0.059	0.58	YES
24	HLA-C	HLA-C	HLA-C	5114	0.058	0.59	YES
25	HLA-DPB1	HLA-DPB1	HLA-DPB1	5136	0.058	0.61	YES
26	HLA-A	HLA-A	HLA-A	5231	0.056	0.62	YES
27	HLA-DRA	HLA-DRA	HLA-DRA	6718	0.032	0.55	NO
28	GZMB	GZMB	GZMB	6748	0.032	0.56	NO
29	FAS	FAS	FAS	7018	0.028	0.55	NO
30	KIR3DL2	KIR3DL2	KIR3DL2	8629	0.0059	0.46	NO
31	HLA-DRB1	HLA-DRB1	HLA-DRB1	9077	0.00012	0.44	NO
32	HLA-DMA	HLA-DMA	HLA-DMA	10002	-0.012	0.39	NO
33	HLA-F	HLA-F	HLA-F	10628	-0.023	0.36	NO
34	IL6	IL6	IL6	13015	-0.07	0.25	NO
35	HLA-E	HLA-E	HLA-E	13566	-0.086	0.25	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 PEROXISOME.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PEROXISOME, 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 ANTIGEN PROCESSING AND PRESENTATION

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	HIST1H3H	HIST1H3H	HIST1H3H	232	0.44	0.02	YES
2	HIST3H2BB	HIST3H2BB	HIST3H2BB	309	0.4	0.046	YES
3	C7	C7	C7	450	0.36	0.065	YES
4	HIST1H4I	HIST1H4I	HIST1H4I	530	0.33	0.086	YES
5	HIST2H2BF	HIST2H2BF	HIST2H2BF	551	0.33	0.11	YES
6	HIST1H2BG	HIST1H2BG	HIST1H2BG	589	0.32	0.13	YES
7	HIST1H2AG	HIST1H2AG	HIST1H2AG	593	0.32	0.16	YES
8	HIST1H4H	HIST1H4H	HIST1H4H	597	0.31	0.18	YES
9	C6	C6	C6	608	0.31	0.2	YES
10	HIST1H2BN	HIST1H2BN	HIST1H2BN	642	0.3	0.22	YES
11	HIST1H2BL	HIST1H2BL	HIST1H2BL	940	0.26	0.22	YES
12	HIST1H2AM	HIST1H2AM	HIST1H2AM	1041	0.24	0.24	YES
13	TRIM21	TRIM21	TRIM21	1165	0.23	0.25	YES
14	HIST1H3E	HIST1H3E	HIST1H3E	1185	0.22	0.26	YES
15	FCGR3B	FCGR3B	FCGR3B	1294	0.21	0.27	YES
16	CD40LG	CD40LG	CD40LG	1386	0.2	0.28	YES
17	C5	C5	C5	1453	0.2	0.3	YES
18	HIST1H2BC	HIST1H2BC	HIST1H2BC	1563	0.19	0.3	YES
19	CD80	CD80	CD80	1631	0.18	0.31	YES
20	HIST1H2BO	HIST1H2BO	HIST1H2BO	1648	0.18	0.33	YES
21	HIST1H2AL	HIST1H2AL	HIST1H2AL	1663	0.18	0.34	YES
22	HIST1H2AK	HIST1H2AK	HIST1H2AK	1740	0.18	0.35	YES
23	HIST1H2AD	HIST1H2AD	HIST1H2AD	1827	0.17	0.36	YES
24	HIST1H3A	HIST1H3A	HIST1H3A	1850	0.17	0.37	YES
25	FCGR2B	FCGR2B	FCGR2B	1861	0.17	0.38	YES
26	HIST2H3D	HIST2H3D	HIST2H3D	1902	0.16	0.39	YES
27	TNF	TNF	TNF	1909	0.16	0.4	YES
28	HIST1H2AB	HIST1H2AB	HIST1H2AB	1933	0.16	0.41	YES
29	FCGR2C	FCGR2C	FCGR2C	1939	0.16	0.42	YES
30	HIST1H2AE	HIST1H2AE	HIST1H2AE	2095	0.15	0.43	YES
31	CD86	CD86	CD86	2209	0.15	0.43	YES
32	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	2273	0.14	0.44	YES
33	ACTN1	ACTN1	ACTN1	2345	0.14	0.45	YES
34	HIST1H3J	HIST1H3J	HIST1H3J	2385	0.14	0.45	YES
35	H2AFY2	H2AFY2	H2AFY2	2529	0.13	0.46	YES
36	FCGR3A	FCGR3A	FCGR3A	2600	0.13	0.46	YES
37	IL10	IL10	IL10	2622	0.13	0.47	YES
38	HIST1H2AH	HIST1H2AH	HIST1H2AH	2673	0.12	0.48	YES
39	HLA-DOA	HLA-DOA	HLA-DOA	2680	0.12	0.49	YES
40	HIST1H3G	HIST1H3G	HIST1H3G	2687	0.12	0.5	YES
41	HIST2H2BE	HIST2H2BE	HIST2H2BE	2717	0.12	0.5	YES
42	HIST1H2BM	HIST1H2BM	HIST1H2BM	2771	0.12	0.51	YES
43	HLA-DQA2	HLA-DQA2	HLA-DQA2	2802	0.12	0.52	YES
44	HIST1H2BF	HIST1H2BF	HIST1H2BF	2838	0.12	0.52	YES
45	HIST1H2BE	HIST1H2BE	HIST1H2BE	3138	0.11	0.52	NO
46	HLA-DOB	HLA-DOB	HLA-DOB	3332	0.1	0.51	NO
47	HLA-DPA1	HLA-DPA1	HLA-DPA1	3381	0.1	0.52	NO
48	HLA-DQA1	HLA-DQA1	HLA-DQA1	3820	0.088	0.5	NO
49	HIST1H2AC	HIST1H2AC	HIST1H2AC	3947	0.084	0.5	NO
50	HIST1H3D	HIST1H3D	HIST1H3D	3979	0.083	0.5	NO
51	HLA-DRB5	HLA-DRB5	HLA-DRB5	4320	0.074	0.49	NO
52	HIST1H2BK	HIST1H2BK	HIST1H2BK	4662	0.067	0.48	NO
53	HIST1H4E	HIST1H4E	HIST1H4E	4708	0.066	0.48	NO
54	HIST3H2A	HIST3H2A	HIST3H2A	4849	0.063	0.48	NO
55	IFNG	IFNG	IFNG	4866	0.063	0.48	NO
56	CD40	CD40	CD40	4928	0.062	0.48	NO
57	HLA-DMB	HLA-DMB	HLA-DMB	4977	0.061	0.48	NO
58	CD28	CD28	CD28	5084	0.059	0.48	NO
59	HLA-DPB1	HLA-DPB1	HLA-DPB1	5136	0.058	0.48	NO
60	HIST2H4A	HIST2H4A	HIST2H4A	5994	0.043	0.44	NO
61	HIST1H4K	HIST1H4K	HIST1H4K	6197	0.04	0.43	NO
62	HIST1H4D	HIST1H4D	HIST1H4D	6527	0.035	0.41	NO
63	SNRPD1	SNRPD1	SNRPD1	6565	0.034	0.41	NO
64	C3	C3	C3	6652	0.033	0.41	NO
65	HLA-DRA	HLA-DRA	HLA-DRA	6718	0.032	0.41	NO
66	TROVE2	TROVE2	TROVE2	6760	0.032	0.41	NO
67	H2AFZ	H2AFZ	H2AFZ	6866	0.03	0.41	NO
68	SSB	SSB	SSB	7587	0.02	0.37	NO
69	FCGR1A	FCGR1A	FCGR1A	7916	0.015	0.35	NO
70	C1QC	C1QC	C1QC	8179	0.012	0.34	NO
71	ACTN3	ACTN3	ACTN3	8203	0.011	0.34	NO
72	C1QB	C1QB	C1QB	8256	0.01	0.33	NO
73	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	8446	0.008	0.32	NO
74	C1S	C1S	C1S	8558	0.0068	0.32	NO
75	GRIN2A	GRIN2A	GRIN2A	8692	0.0053	0.31	NO
76	FCGR2A	FCGR2A	FCGR2A	9003	0.00096	0.29	NO
77	HLA-DRB1	HLA-DRB1	HLA-DRB1	9077	0.00012	0.29	NO
78	C2	C2	C2	9202	-0.0014	0.28	NO
79	HIST1H2BD	HIST1H2BD	HIST1H2BD	9360	-0.0038	0.28	NO
80	HIST1H4A	HIST1H4A	HIST1H4A	9433	-0.0045	0.27	NO
81	H2AFX	H2AFX	H2AFX	9449	-0.0048	0.27	NO
82	H3F3C	H3F3C	H3F3C	9853	-0.01	0.25	NO
83	HLA-DMA	HLA-DMA	HLA-DMA	10002	-0.012	0.24	NO
84	H2AFY	H2AFY	H2AFY	10256	-0.017	0.23	NO
85	ELANE	ELANE	ELANE	10330	-0.018	0.23	NO
86	H3F3B	H3F3B	H3F3B	10705	-0.024	0.21	NO
87	HLA-DQB1	HLA-DQB1	HLA-DQB1	10804	-0.026	0.2	NO
88	H2AFV	H2AFV	H2AFV	11393	-0.036	0.17	NO
89	C1QA	C1QA	C1QA	11573	-0.039	0.17	NO
90	C8G	C8G	C8G	11635	-0.04	0.17	NO
91	SNRPB	SNRPB	SNRPB	11652	-0.041	0.17	NO
92	SNRPD3	SNRPD3	SNRPD3	12353	-0.055	0.13	NO
93	ACTN4	ACTN4	ACTN4	12476	-0.058	0.13	NO
94	HIST1H3B	HIST1H3B	HIST1H3B	12583	-0.06	0.13	NO
95	H2AFB1	H2AFB1	H2AFB1	12669	-0.062	0.13	NO
96	H3F3A	H3F3A	H3F3A	12767	-0.064	0.13	NO
97	C1R	C1R	C1R	13079	-0.072	0.12	NO
98	H2AFJ	H2AFJ	H2AFJ	13082	-0.072	0.12	NO
99	GRIN2B	GRIN2B	GRIN2B	13125	-0.073	0.12	NO
100	HIST2H3C	HIST2H3C	HIST2H3C	13440	-0.082	0.11	NO
101	ACTN2	ACTN2	ACTN2	13574	-0.086	0.11	NO
102	HIST2H2AB	HIST2H2AB	HIST2H2AB	14037	-0.1	0.094	NO
103	HIST1H4B	HIST1H4B	HIST1H4B	14327	-0.11	0.087	NO
104	C4A	C4A	C4A	14480	-0.12	0.087	NO
105	HIST1H2BH	HIST1H2BH	HIST1H2BH	14837	-0.14	0.077	NO
106	HIST4H4	HIST4H4	HIST4H4	14865	-0.14	0.086	NO
107	HIST1H4C	HIST1H4C	HIST1H4C	15443	-0.17	0.067	NO
108	HIST1H3C	HIST1H3C	HIST1H3C	15998	-0.21	0.052	NO
109	CTSG	CTSG	CTSG	16321	-0.24	0.052	NO
110	HIST1H4J	HIST1H4J	HIST1H4J	16585	-0.26	0.056	NO
111	HIST2H2AC	HIST2H2AC	HIST2H2AC	16833	-0.28	0.064	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 ANTIGEN PROCESSING AND PRESENTATION.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION, 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 TOLL LIKE RECEPTOR SIGNALING PATHWAY

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	STAT4	STAT4	STAT4	39	0.63	0.18	YES
2	STAT5A	STAT5A	STAT5A	1254	0.22	0.18	YES
3	STAT1	STAT1	STAT1	1500	0.19	0.22	YES
4	PIK3R1	PIK3R1	PIK3R1	1846	0.17	0.26	YES
5	SHC1	SHC1	SHC1	2007	0.16	0.29	YES
6	MAPK8	MAPK8	MAPK8	2241	0.14	0.32	YES
7	MAP3K1	MAP3K1	MAP3K1	2259	0.14	0.36	YES
8	PRKCB	PRKCB	PRKCB	2465	0.13	0.39	YES
9	FOS	FOS	FOS	3012	0.11	0.39	YES
10	STAT6	STAT6	STAT6	4682	0.067	0.32	NO
11	MAPK3	MAPK3	MAPK3	4685	0.067	0.34	NO
12	STAT5B	STAT5B	STAT5B	5482	0.052	0.31	NO
13	RASA1	RASA1	RASA1	6308	0.038	0.28	NO
14	SOS1	SOS1	SOS1	6339	0.038	0.29	NO
15	STAT2	STAT2	STAT2	6570	0.034	0.28	NO
16	CSNK2A1	CSNK2A1	CSNK2A1	7064	0.027	0.26	NO
17	GRB2	GRB2	GRB2	7081	0.027	0.27	NO
18	SRF	SRF	SRF	9347	-0.0037	0.15	NO
19	STAT3	STAT3	STAT3	10477	-0.02	0.089	NO
20	MAP2K4	MAP2K4	MAP2K4	10746	-0.025	0.082	NO
21	ELK1	ELK1	ELK1	11151	-0.032	0.068	NO
22	PIK3CA	PIK3CA	PIK3CA	11547	-0.039	0.058	NO
23	PLCG1	PLCG1	PLCG1	11996	-0.048	0.047	NO
24	JUN	JUN	JUN	12397	-0.056	0.041	NO
25	JAK1	JAK1	JAK1	12745	-0.063	0.04	NO
26	MAP2K1	MAP2K1	MAP2K1	12783	-0.064	0.057	NO
27	RAF1	RAF1	RAF1	13027	-0.07	0.065	NO
28	PRKCA	PRKCA	PRKCA	14826	-0.14	0.0043	NO
29	EGF	EGF	EGF	15045	-0.15	0.036	NO
30	EGFR	EGFR	EGFR	17658	-0.43	0.018	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 TOLL LIKE RECEPTOR SIGNALING PATHWAY.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus3 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA NO1 PATHWAY	28	genes.ES.table	0.6	1.5	0.044	1	0.82	0.46	0.15	0.39	1	0.71
BIOCARTA INTEGRIN PATHWAY	37	genes.ES.table	0.39	1.4	0.12	1	0.89	0.6	0.35	0.39	0.99	0.5
BIOCARTA VEGF PATHWAY	28	genes.ES.table	0.47	1.5	0.11	1	0.86	0.18	0.078	0.16	1	0.59
KEGG PURINE METABOLISM	154	genes.ES.table	0.32	1.3	0.11	1	0.97	0.18	0.14	0.16	1	0.6
KEGG PYRIMIDINE METABOLISM	97	genes.ES.table	0.25	1.2	0.21	1	0.99	0.18	0.18	0.14	1	0.56
KEGG STARCH AND SUCROSE METABOLISM	27	genes.ES.table	0.53	1.4	0.12	1	0.94	0.41	0.18	0.33	1	0.55
KEGG DRUG METABOLISM OTHER ENZYMES	31	genes.ES.table	0.52	1.4	0.1	1	0.94	0.32	0.18	0.26	1	0.52
KEGG RIBOSOME	84	genes.ES.table	0.52	1.4	0.21	1	0.88	0.74	0.37	0.47	1	0.55
KEGG CALCIUM SIGNALING PATHWAY	168	genes.ES.table	0.42	1.2	0.14	1	0.98	0.29	0.13	0.26	1	0.57
KEGG VASCULAR SMOOTH MUSCLE CONTRACTION	103	genes.ES.table	0.48	1.4	0.054	1	0.89	0.29	0.14	0.25	0.88	0.44

genes ES table in pathway: BIOCARTA NO1 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	LFNG	LFNG	LFNG	170	0.42	0.077	YES
2	DLL4	DLL4	DLL4	378	0.35	0.14	YES
3	DLL1	DLL1	DLL1	567	0.3	0.19	YES
4	NOTCH3	NOTCH3	NOTCH3	652	0.29	0.24	YES
5	JAG2	JAG2	JAG2	876	0.25	0.28	YES
6	NOTCH4	NOTCH4	NOTCH4	1103	0.23	0.32	YES
7	NOTCH1	NOTCH1	NOTCH1	1106	0.22	0.36	YES
8	JAG1	JAG1	JAG1	1206	0.22	0.4	YES
9	PTCRA	PTCRA	PTCRA	1712	0.17	0.41	YES
10	HES1	HES1	HES1	2176	0.14	0.41	YES
11	MAML3	MAML3	MAML3	2229	0.14	0.44	YES
12	HDAC1	HDAC1	HDAC1	2682	0.11	0.43	YES
13	DTX2	DTX2	DTX2	2753	0.11	0.45	YES
14	HES5	HES5	HES5	3061	0.096	0.45	YES
15	DVL1	DVL1	DVL1	3312	0.088	0.46	YES
16	RBPJ	RBPJ	RBPJ	4002	0.067	0.43	NO
17	PSENEN	PSENEN	PSENEN	4286	0.06	0.43	NO
18	NOTCH2	NOTCH2	NOTCH2	4366	0.058	0.44	NO
19	DVL3	DVL3	DVL3	4573	0.053	0.44	NO
20	CTBP2	CTBP2	CTBP2	5952	0.027	0.37	NO
21	HDAC2	HDAC2	HDAC2	6096	0.025	0.36	NO
22	MAML1	MAML1	MAML1	6323	0.022	0.36	NO
23	EP300	EP300	EP300	6568	0.018	0.34	NO
24	NCSTN	NCSTN	NCSTN	6646	0.017	0.34	NO
25	DVL2	DVL2	DVL2	7061	0.012	0.32	NO
26	DTX3	DTX3	DTX3	7556	0.0055	0.3	NO
27	PSEN1	PSEN1	PSEN1	8757	-0.0094	0.23	NO
28	CTBP1	CTBP1	CTBP1	8899	-0.011	0.23	NO
29	PSEN2	PSEN2	PSEN2	9459	-0.018	0.2	NO
30	CREBBP	CREBBP	CREBBP	9542	-0.018	0.2	NO
31	APH1A	APH1A	APH1A	9763	-0.021	0.19	NO
32	RFNG	RFNG	RFNG	9864	-0.022	0.19	NO
33	SNW1	SNW1	SNW1	10176	-0.026	0.18	NO
34	NCOR2	NCOR2	NCOR2	10426	-0.029	0.17	NO
35	ADAM17	ADAM17	ADAM17	10586	-0.031	0.17	NO
36	DTX4	DTX4	DTX4	10882	-0.035	0.16	NO
37	DTX3L	DTX3L	DTX3L	11008	-0.037	0.16	NO
38	NUMB	NUMB	NUMB	11039	-0.037	0.16	NO
39	CIR1	CIR1	CIR1	11184	-0.039	0.16	NO
40	KAT2A	KAT2A	KAT2A	11808	-0.048	0.14	NO
41	NUMBL	NUMBL	NUMBL	12622	-0.059	0.11	NO
42	KAT2B	KAT2B	KAT2B	14822	-0.11	0.0052	NO
43	MAML2	MAML2	MAML2	16541	-0.19	-0.051	NO
44	DTX1	DTX1	DTX1	17395	-0.29	-0.04	NO
45	DLL3	DLL3	DLL3	17671	-0.35	0.017	NO

Figure S41. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA INTEGRIN 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	RYR2	RYR2	RYR2	128	0.44	0.1	YES
2	BDKRB2	BDKRB2	BDKRB2	202	0.41	0.2	YES
3	FLT4	FLT4	FLT4	593	0.3	0.25	YES
4	FLT1	FLT1	FLT1	844	0.26	0.3	YES
5	PDE2A	PDE2A	PDE2A	852	0.26	0.36	YES
6	KDR	KDR	KDR	980	0.24	0.41	YES
7	PDE3A	PDE3A	PDE3A	1128	0.22	0.46	YES
8	VEGFA	VEGFA	VEGFA	1339	0.2	0.5	YES
9	NOS3	NOS3	NOS3	1394	0.2	0.54	YES
10	PRKG1	PRKG1	PRKG1	1975	0.15	0.55	YES
11	CHRNA1	CHRNA1	CHRNA1	2072	0.15	0.58	YES
12	ACTA1	ACTA1	ACTA1	2398	0.13	0.59	YES
13	TNNI1	TNNI1	TNNI1	2749	0.11	0.6	YES
14	CHRM1	CHRM1	CHRM1	6904	0.014	0.37	NO
15	AKT1	AKT1	AKT1	8168	-0.0023	0.3	NO
16	PRKACB	PRKACB	PRKACB	9582	-0.019	0.22	NO
17	CALM3	CALM3	CALM3	10350	-0.028	0.19	NO
18	PDE3B	PDE3B	PDE3B	10736	-0.033	0.18	NO
19	PRKAR1A	PRKAR1A	PRKAR1A	10887	-0.035	0.18	NO
20	HSP90AA1	HSP90AA1	HSP90AA1	11302	-0.04	0.16	NO
21	CALM2	CALM2	CALM2	12676	-0.06	0.1	NO
22	PRKG2	PRKG2	PRKG2	12998	-0.066	0.099	NO
23	CALM1	CALM1	CALM1	13871	-0.083	0.071	NO
24	SLC7A1	SLC7A1	SLC7A1	13878	-0.083	0.091	NO
25	PRKAR1B	PRKAR1B	PRKAR1B	14570	-0.1	0.077	NO
26	PRKACG	PRKACG	PRKACG	14594	-0.1	0.1	NO
27	PRKAR2A	PRKAR2A	PRKAR2A	16189	-0.17	0.052	NO
28	PRKAR2B	PRKAR2B	PRKAR2B	16555	-0.19	0.079	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 INTEGRIN PATHWAY.

Figure S44. 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 VEGF 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	PGF	PGF	PGF	76	0.49	0.1	YES
2	EGFR	EGFR	EGFR	167	0.42	0.18	YES
3	MMP9	MMP9	MMP9	937	0.24	0.19	YES
4	MMP2	MMP2	MMP2	1078	0.23	0.23	YES
5	E2F2	E2F2	E2F2	1086	0.23	0.28	YES
6	MMP1	MMP1	MMP1	1088	0.23	0.33	YES
7	DAPK2	DAPK2	DAPK2	1219	0.21	0.37	YES
8	VEGFA	VEGFA	VEGFA	1339	0.2	0.4	YES
9	VEGFC	VEGFC	VEGFC	1576	0.18	0.43	YES
10	MYC	MYC	MYC	1680	0.17	0.46	YES
11	THBS1	THBS1	THBS1	1849	0.16	0.48	YES
12	NRAS	NRAS	NRAS	2307	0.13	0.49	YES
13	DAPK1	DAPK1	DAPK1	2465	0.12	0.5	YES
14	TYMP	TYMP	TYMP	2735	0.11	0.51	YES
15	FGFR3	FGFR3	FGFR3	2969	0.1	0.52	YES
16	TP53	TP53	TP53	3054	0.096	0.54	YES
17	DAPK3	DAPK3	DAPK3	3980	0.068	0.5	NO
18	RASSF1	RASSF1	RASSF1	4261	0.061	0.5	NO
19	ARAF	ARAF	ARAF	4329	0.059	0.5	NO
20	RAF1	RAF1	RAF1	4794	0.048	0.49	NO
21	ERBB2	ERBB2	ERBB2	5090	0.042	0.48	NO
22	MAP2K2	MAP2K2	MAP2K2	5991	0.027	0.44	NO
23	CDKN1A	CDKN1A	CDKN1A	6229	0.023	0.43	NO
24	RB1	RB1	RB1	6880	0.014	0.4	NO
25	EGF	EGF	EGF	7030	0.012	0.39	NO
26	MAP2K1	MAP2K1	MAP2K1	7073	0.012	0.39	NO
27	MDM2	MDM2	MDM2	7442	0.0069	0.37	NO
28	CDK4	CDK4	CDK4	8437	-0.0054	0.32	NO
29	MAPK1	MAPK1	MAPK1	8606	-0.0075	0.31	NO
30	KRAS	KRAS	KRAS	9144	-0.014	0.28	NO
31	CDH1	CDH1	CDH1	9433	-0.017	0.27	NO
32	CCND1	CCND1	CCND1	10291	-0.027	0.23	NO
33	CDKN2A	CDKN2A	CDKN2A	10592	-0.032	0.22	NO
34	IL8	IL8	IL8	10639	-0.032	0.22	NO
35	VEGFB	VEGFB	VEGFB	11708	-0.046	0.17	NO
36	HRAS	HRAS	HRAS	12816	-0.062	0.12	NO
37	MAPK3	MAPK3	MAPK3	13077	-0.067	0.12	NO
38	RPS6KA5	RPS6KA5	RPS6KA5	14326	-0.093	0.073	NO
39	BRAF	BRAF	BRAF	14987	-0.11	0.06	NO
40	E2F3	E2F3	E2F3	16284	-0.17	0.024	NO
41	FIGF	FIGF	FIGF	17608	-0.33	0.02	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 VEGF PATHWAY.

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

genes ES table in pathway: KEGG PURINE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FLT4	FLT4	FLT4	593	0.3	0.1	YES
2	FLT1	FLT1	FLT1	844	0.26	0.21	YES
3	KDR	KDR	KDR	980	0.24	0.31	YES
4	VEGFA	VEGFA	VEGFA	1339	0.2	0.38	YES
5	NOS3	NOS3	NOS3	1394	0.2	0.47	YES
6	PTK2	PTK2	PTK2	3996	0.067	0.36	NO
7	EIF2B5	EIF2B5	EIF2B5	5657	0.032	0.28	NO
8	EIF1	EIF1	EIF1	6111	0.025	0.27	NO
9	PXN	PXN	PXN	6181	0.024	0.27	NO
10	PLCG1	PLCG1	PLCG1	6730	0.016	0.25	NO
11	ARNT	ARNT	ARNT	7201	0.01	0.23	NO
12	EIF2B3	EIF2B3	EIF2B3	7511	0.0061	0.22	NO
13	PIK3CG	PIK3CG	PIK3CG	7568	0.0054	0.21	NO
14	PIK3CA	PIK3CA	PIK3CA	7683	0.0038	0.21	NO
15	ELAVL1	ELAVL1	ELAVL1	7727	0.0032	0.21	NO
16	HIF1A	HIF1A	HIF1A	8428	-0.0054	0.17	NO
17	EIF2S3	EIF2S3	EIF2S3	8665	-0.0083	0.16	NO
18	EIF2B1	EIF2B1	EIF2B1	8788	-0.0098	0.16	NO
19	EIF2S2	EIF2S2	EIF2S2	9101	-0.013	0.15	NO
20	EIF1AX	EIF1AX	EIF1AX	9627	-0.02	0.13	NO
21	EIF2S1	EIF2S1	EIF2S1	9800	-0.022	0.13	NO
22	EIF2B4	EIF2B4	EIF2B4	9890	-0.022	0.13	NO
23	SHC1	SHC1	SHC1	11576	-0.044	0.061	NO
24	EIF2B2	EIF2B2	EIF2B2	12126	-0.052	0.054	NO
25	PRKCA	PRKCA	PRKCA	12730	-0.061	0.049	NO
26	PIK3R1	PIK3R1	PIK3R1	13332	-0.072	0.048	NO
27	VHL	VHL	VHL	15027	-0.11	0.0066	NO
28	PRKCB	PRKCB	PRKCB	17634	-0.34	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: KEGG PURINE METABOLISM.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE 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 PYRIMIDINE METABOLISM

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	RPLP0	RPLP0	RPLP0	2939	0.1	-0.13	YES
2	RPS8	RPS8	RPS8	3270	0.089	-0.12	YES
3	RPL21	RPL21	RPL21	3289	0.089	-0.09	YES
4	RPS19	RPS19	RPS19	3340	0.087	-0.063	YES
5	RPL11	RPL11	RPL11	3359	0.086	-0.035	YES
6	RPL39	RPL39	RPL39	3415	0.084	-0.0097	YES
7	RPL5	RPL5	RPL5	3420	0.084	0.018	YES
8	RPS2	RPS2	RPS2	3651	0.077	0.032	YES
9	RPL35A	RPL35A	RPL35A	3872	0.071	0.043	YES
10	RPL12	RPL12	RPL12	3989	0.068	0.06	YES
11	RPL22L1	RPL22L1	RPL22L1	4067	0.065	0.077	YES
12	RPL24	RPL24	RPL24	4136	0.064	0.095	YES
13	RPS9	RPS9	RPS9	4220	0.062	0.11	YES
14	RPL10	RPL10	RPL10	4446	0.056	0.12	YES
15	RPL22	RPL22	RPL22	4603	0.052	0.13	YES
16	RPS5	RPS5	RPS5	4633	0.052	0.14	YES
17	RPL8	RPL8	RPL8	4651	0.051	0.16	YES
18	RPL3	RPL3	RPL3	4652	0.051	0.18	YES
19	RPL17	RPL17	RPL17	4728	0.05	0.19	YES
20	RPL9	RPL9	RPL9	4815	0.048	0.2	YES
21	RPLP1	RPLP1	RPLP1	4909	0.046	0.21	YES
22	RPL18A	RPL18A	RPL18A	4924	0.046	0.22	YES
23	RPL23A	RPL23A	RPL23A	5187	0.04	0.22	YES
24	RPS16	RPS16	RPS16	5189	0.04	0.24	YES
25	RPL19	RPL19	RPL19	5201	0.04	0.25	YES
26	RPL26	RPL26	RPL26	5228	0.04	0.26	YES
27	RPS4Y1	RPS4Y1	RPS4Y1	5259	0.039	0.27	YES
28	RPL13A	RPL13A	RPL13A	5315	0.038	0.28	YES
29	RPL4	RPL4	RPL4	5349	0.038	0.3	YES
30	RPL30	RPL30	RPL30	5353	0.038	0.31	YES
31	RPL28	RPL28	RPL28	5356	0.038	0.32	YES
32	RPS20	RPS20	RPS20	5402	0.037	0.33	YES
33	RPS7	RPS7	RPS7	5418	0.036	0.34	YES
34	RPS6	RPS6	RPS6	5489	0.035	0.35	YES
35	RPL13	RPL13	RPL13	5502	0.035	0.36	YES
36	RPS12	RPS12	RPS12	5518	0.035	0.37	YES
37	RPS27	RPS27	RPS27	5527	0.035	0.38	YES
38	RPS11	RPS11	RPS11	5634	0.033	0.39	YES
39	RPL7A	RPL7A	RPL7A	5663	0.032	0.4	YES
40	RPL6	RPL6	RPL6	5691	0.032	0.41	YES
41	RPL37A	RPL37A	RPL37A	5724	0.031	0.42	YES
42	RPL23	RPL23	RPL23	5743	0.03	0.42	YES
43	RPL37	RPL37	RPL37	5746	0.03	0.43	YES
44	RPS17	RPS17	RPS17	5771	0.03	0.44	YES
45	UBA52	UBA52	UBA52	5813	0.029	0.45	YES
46	RPL35	RPL35	RPL35	5867	0.029	0.46	YES
47	RPL31	RPL31	RPL31	6091	0.025	0.45	YES
48	RPS10	RPS10	RPS10	6123	0.025	0.46	YES
49	RPS15	RPS15	RPS15	6218	0.023	0.46	YES
50	RPS15A	RPS15A	RPS15A	6286	0.022	0.47	YES
51	RPL27	RPL27	RPL27	6317	0.022	0.47	YES
52	RPL36	RPL36	RPL36	6326	0.022	0.48	YES
53	FAU	FAU	FAU	6352	0.021	0.48	YES
54	RPS21	RPS21	RPS21	6474	0.019	0.48	YES
55	RPL27A	RPL27A	RPL27A	6503	0.019	0.49	YES
56	RPL10A	RPL10A	RPL10A	6520	0.018	0.49	YES
57	RPS18	RPS18	RPS18	6522	0.018	0.5	YES
58	RPL38	RPL38	RPL38	6551	0.018	0.5	YES
59	RPL41	RPL41	RPL41	6563	0.018	0.51	YES
60	RPS4X	RPS4X	RPS4X	6570	0.018	0.52	YES
61	RPS27L	RPS27L	RPS27L	6609	0.017	0.52	YES
62	RPL29	RPL29	RPL29	6657	0.017	0.52	YES
63	RPS27A	RPS27A	RPS27A	6768	0.015	0.52	NO
64	RPL14	RPL14	RPL14	7022	0.012	0.51	NO
65	RPS23	RPS23	RPS23	7116	0.011	0.51	NO
66	RPL34	RPL34	RPL34	7130	0.011	0.51	NO
67	RPS3	RPS3	RPS3	7288	0.009	0.51	NO
68	RPLP2	RPLP2	RPLP2	7328	0.0085	0.51	NO
69	RPS3A	RPS3A	RPS3A	7366	0.0079	0.51	NO
70	RPS24	RPS24	RPS24	7424	0.0071	0.51	NO
71	RPS28	RPS28	RPS28	7654	0.0042	0.5	NO
72	RPL32	RPL32	RPL32	8051	-0.00091	0.48	NO
73	RPL7	RPL7	RPL7	8104	-0.0016	0.47	NO
74	MRPL13	MRPL13	MRPL13	8283	-0.0037	0.46	NO
75	RPL15	RPL15	RPL15	8303	-0.0039	0.46	NO
76	RPS29	RPS29	RPS29	8432	-0.0054	0.46	NO
77	RPSA	RPSA	RPSA	8924	-0.011	0.44	NO
78	RSL24D1	RSL24D1	RSL24D1	9127	-0.014	0.43	NO
79	RPS26	RPS26	RPS26	9590	-0.019	0.41	NO
80	RPS25	RPS25	RPS25	9624	-0.019	0.41	NO
81	RPL36AL	RPL36AL	RPL36AL	11019	-0.037	0.35	NO
82	RPS13	RPS13	RPS13	11203	-0.039	0.35	NO
83	RPL36A	RPL36A	RPL36A	11259	-0.04	0.36	NO
84	RPL26L1	RPL26L1	RPL26L1	11366	-0.041	0.37	NO

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

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRIMIDINE 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 STARCH AND SUCROSE METABOLISM

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	CAV1	CAV1	CAV1	700	0.28	0.087	YES
2	ZYX	ZYX	ZYX	1761	0.16	0.1	YES
3	FYN	FYN	FYN	1906	0.16	0.16	YES
4	ACTA1	ACTA1	ACTA1	2398	0.13	0.2	YES
5	TNS1	TNS1	TNS1	2991	0.099	0.21	YES
6	ACTN2	ACTN2	ACTN2	3159	0.093	0.24	YES
7	RAP1A	RAP1A	RAP1A	3206	0.091	0.28	YES
8	ACTN3	ACTN3	ACTN3	3579	0.079	0.29	YES
9	PTK2	PTK2	PTK2	3996	0.067	0.3	YES
10	RAPGEF1	RAPGEF1	RAPGEF1	4069	0.065	0.33	YES
11	ITGA1	ITGA1	ITGA1	4581	0.053	0.32	YES
12	RAF1	RAF1	RAF1	4794	0.048	0.33	YES
13	BCAR1	BCAR1	BCAR1	5198	0.04	0.33	YES
14	VCL	VCL	VCL	5267	0.039	0.34	YES
15	CSK	CSK	CSK	5304	0.038	0.36	YES
16	JUN	JUN	JUN	5461	0.036	0.36	YES
17	ITGB1	ITGB1	ITGB1	5879	0.028	0.35	YES
18	MAP2K2	MAP2K2	MAP2K2	5991	0.027	0.36	YES
19	CRKL	CRKL	CRKL	6018	0.026	0.37	YES
20	PXN	PXN	PXN	6181	0.024	0.37	YES
21	RHOA	RHOA	RHOA	6209	0.023	0.38	YES
22	BCR	BCR	BCR	6292	0.022	0.39	YES
23	CAPNS1	CAPNS1	CAPNS1	6788	0.015	0.37	NO
24	MAP2K1	MAP2K1	MAP2K1	7073	0.012	0.36	NO
25	PPP1R12B	PPP1R12B	PPP1R12B	7763	0.0028	0.32	NO
26	CAPN1	CAPN1	CAPN1	8159	-0.0022	0.3	NO
27	MAPK1	MAPK1	MAPK1	8606	-0.0075	0.28	NO
28	ROCK1	ROCK1	ROCK1	8923	-0.011	0.26	NO
29	SOS1	SOS1	SOS1	9606	-0.019	0.23	NO
30	GRB2	GRB2	GRB2	10496	-0.03	0.2	NO
31	ACTN1	ACTN1	ACTN1	10809	-0.034	0.2	NO
32	SHC1	SHC1	SHC1	11576	-0.044	0.17	NO
33	HRAS	HRAS	HRAS	12816	-0.062	0.13	NO
34	MAPK3	MAPK3	MAPK3	13077	-0.067	0.15	NO
35	SRC	SRC	SRC	13394	-0.073	0.16	NO
36	CAPNS2	CAPNS2	CAPNS2	13840	-0.082	0.18	NO
37	MAPK8	MAPK8	MAPK8	15250	-0.12	0.15	NO

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

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STARCH AND SUCROSE 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 DRUG METABOLISM OTHER ENZYMES

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	MYLK3	MYLK3	MYLK3	2	0.71	0.054	YES
2	ADRA1B	ADRA1B	ADRA1B	38	0.55	0.093	YES
3	ADORA2A	ADORA2A	ADORA2A	111	0.46	0.12	YES
4	KCNMB1	KCNMB1	KCNMB1	162	0.42	0.15	YES
5	NPR1	NPR1	NPR1	344	0.36	0.17	YES
6	MYLK2	MYLK2	MYLK2	400	0.34	0.19	YES
7	EDNRA	EDNRA	EDNRA	415	0.34	0.22	YES
8	PRKCH	PRKCH	PRKCH	473	0.32	0.24	YES
9	MRVI1	MRVI1	MRVI1	481	0.32	0.26	YES
10	GUCY1A2	GUCY1A2	GUCY1A2	496	0.32	0.29	YES
11	CYP4A11	CYP4A11	CYP4A11	560	0.3	0.31	YES
12	RAMP2	RAMP2	RAMP2	568	0.3	0.33	YES
13	ADCY4	ADCY4	ADCY4	651	0.29	0.34	YES
14	PPP1R14A	PPP1R14A	PPP1R14A	705	0.28	0.36	YES
15	CALCRL	CALCRL	CALCRL	711	0.28	0.38	YES
16	RAMP3	RAMP3	RAMP3	858	0.25	0.4	YES
17	ADORA2B	ADORA2B	ADORA2B	1085	0.23	0.4	YES
18	ACTG2	ACTG2	ACTG2	1134	0.22	0.41	YES
19	ADCY1	ADCY1	ADCY1	1179	0.22	0.43	YES
20	MYH11	MYH11	MYH11	1265	0.21	0.44	YES
21	ACTA2	ACTA2	ACTA2	1582	0.18	0.43	YES
22	MYL9	MYL9	MYL9	1611	0.18	0.45	YES
23	MYLK	MYLK	MYLK	1791	0.16	0.45	YES
24	CALML6	CALML6	CALML6	1829	0.16	0.46	YES
25	PRKG1	PRKG1	PRKG1	1975	0.15	0.46	YES
26	CACNA1C	CACNA1C	CACNA1C	2050	0.15	0.47	YES
27	ADCY5	ADCY5	ADCY5	2097	0.14	0.48	YES
28	GNAS	GNAS	GNAS	2279	0.13	0.48	YES
29	KCNMB3	KCNMB3	KCNMB3	2520	0.12	0.47	YES
30	PLA2G4A	PLA2G4A	PLA2G4A	2527	0.12	0.48	YES
31	PLA2G6	PLA2G6	PLA2G6	3155	0.093	0.45	NO
32	MYL6	MYL6	MYL6	3800	0.073	0.42	NO
33	PLA2G5	PLA2G5	PLA2G5	3858	0.071	0.42	NO
34	ADRA1D	ADRA1D	ADRA1D	3947	0.069	0.43	NO
35	AVPR1A	AVPR1A	AVPR1A	3990	0.068	0.43	NO
36	ADCY2	ADCY2	ADCY2	4011	0.067	0.43	NO
37	GUCY1A3	GUCY1A3	GUCY1A3	4065	0.065	0.43	NO
38	ARAF	ARAF	ARAF	4329	0.059	0.42	NO
39	ARHGEF1	ARHGEF1	ARHGEF1	4359	0.058	0.43	NO
40	PLA2G10	PLA2G10	PLA2G10	4667	0.051	0.41	NO
41	RAF1	RAF1	RAF1	4794	0.048	0.41	NO
42	CALD1	CALD1	CALD1	4877	0.047	0.41	NO
43	CACNA1F	CACNA1F	CACNA1F	4903	0.046	0.41	NO
44	PLCB2	PLCB2	PLCB2	5185	0.04	0.4	NO
45	ADCY8	ADCY8	ADCY8	5681	0.032	0.37	NO
46	ADCY7	ADCY7	ADCY7	5721	0.031	0.37	NO
47	MAP2K2	MAP2K2	MAP2K2	5991	0.027	0.36	NO
48	PPP1CA	PPP1CA	PPP1CA	6088	0.025	0.36	NO
49	ADRA1A	ADRA1A	ADRA1A	6179	0.024	0.35	NO
50	RHOA	RHOA	RHOA	6209	0.023	0.35	NO
51	JMJD7-PLA2G4B	JMJD7-PLA2G4B	JMJD7-PLA2G4B	6211	0.023	0.36	NO
52	KCNMA1	KCNMA1	KCNMA1	6347	0.022	0.35	NO
53	GUCY1B3	GUCY1B3	GUCY1B3	6744	0.016	0.33	NO
54	RAMP1	RAMP1	RAMP1	6886	0.014	0.32	NO
55	MAP2K1	MAP2K1	MAP2K1	7073	0.012	0.31	NO
56	PPP1R12B	PPP1R12B	PPP1R12B	7763	0.0028	0.27	NO
57	AGTR1	AGTR1	AGTR1	7865	0.0014	0.27	NO
58	ARHGEF12	ARHGEF12	ARHGEF12	8152	-0.0021	0.25	NO
59	PPP1CC	PPP1CC	PPP1CC	8231	-0.0031	0.25	NO
60	PPP1R12A	PPP1R12A	PPP1R12A	8450	-0.0055	0.24	NO
61	MAPK1	MAPK1	MAPK1	8606	-0.0075	0.23	NO
62	PLA2G2A	PLA2G2A	PLA2G2A	8624	-0.0078	0.23	NO
63	GNA12	GNA12	GNA12	8902	-0.011	0.21	NO
64	ROCK1	ROCK1	ROCK1	8923	-0.011	0.21	NO
65	PRKACA	PRKACA	PRKACA	9045	-0.013	0.21	NO
66	PPP1CB	PPP1CB	PPP1CB	9084	-0.013	0.21	NO
67	PRKACB	PRKACB	PRKACB	9582	-0.019	0.18	NO
68	ITPR1	ITPR1	ITPR1	9621	-0.019	0.18	NO
69	CALM3	CALM3	CALM3	10350	-0.028	0.14	NO
70	ADCY6	ADCY6	ADCY6	10728	-0.033	0.12	NO
71	MYL6B	MYL6B	MYL6B	11153	-0.039	0.1	NO
72	ROCK2	ROCK2	ROCK2	11660	-0.045	0.076	NO
73	ARHGEF11	ARHGEF11	ARHGEF11	12027	-0.05	0.06	NO
74	PLCB4	PLCB4	PLCB4	12031	-0.05	0.063	NO
75	PLCB3	PLCB3	PLCB3	12165	-0.053	0.06	NO
76	CALM2	CALM2	CALM2	12676	-0.06	0.036	NO
77	PRKCA	PRKCA	PRKCA	12730	-0.061	0.037	NO
78	NPR2	NPR2	NPR2	12747	-0.061	0.041	NO
79	GNA11	GNA11	GNA11	12759	-0.061	0.045	NO
80	GNA13	GNA13	GNA13	12809	-0.062	0.047	NO
81	PRKX	PRKX	PRKX	12994	-0.065	0.042	NO
82	MAPK3	MAPK3	MAPK3	13077	-0.067	0.042	NO
83	GNAQ	GNAQ	GNAQ	13417	-0.074	0.029	NO
84	CACNA1D	CACNA1D	CACNA1D	13727	-0.08	0.018	NO
85	CALM1	CALM1	CALM1	13871	-0.083	0.016	NO
86	CACNA1S	CACNA1S	CACNA1S	14197	-0.09	0.0044	NO
87	PTGIR	PTGIR	PTGIR	14465	-0.097	-0.0033	NO
88	PLA2G12A	PLA2G12A	PLA2G12A	14487	-0.097	0.0029	NO
89	PRKACG	PRKACG	PRKACG	14594	-0.1	0.0045	NO
90	ADCY9	ADCY9	ADCY9	14620	-0.1	0.011	NO
91	PRKCD	PRKCD	PRKCD	14756	-0.1	0.011	NO
92	ITPR3	ITPR3	ITPR3	14769	-0.11	0.018	NO
93	BRAF	BRAF	BRAF	14987	-0.11	0.015	NO
94	KCNMB2	KCNMB2	KCNMB2	15557	-0.13	-0.007	NO
95	PRKCG	PRKCG	PRKCG	15632	-0.14	-0.00085	NO
96	ITPR2	ITPR2	ITPR2	15833	-0.15	-0.00097	NO
97	KCNMB4	KCNMB4	KCNMB4	15930	-0.15	0.0051	NO
98	PLA2G1B	PLA2G1B	PLA2G1B	16445	-0.18	-0.0097	NO
99	PRKCE	PRKCE	PRKCE	16575	-0.19	-0.0023	NO
100	PLCB1	PLCB1	PLCB1	16768	-0.21	0.0029	NO
101	PLA2G2D	PLA2G2D	PLA2G2D	16845	-0.22	0.015	NO
102	PRKCQ	PRKCQ	PRKCQ	17448	-0.3	0.0037	NO
103	PRKCB	PRKCB	PRKCB	17634	-0.34	0.019	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 DRUG METABOLISM OTHER ENZYMES.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM OTHER ENZYMES, 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 RIBOSOME

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	HK2	HK2	HK2	14	0.64	0.21	YES
2	GCK	GCK	GCK	420	0.34	0.3	YES
3	PYGM	PYGM	PYGM	1386	0.2	0.31	YES
4	HK3	HK3	HK3	1506	0.19	0.36	YES
5	G6PC2	G6PC2	G6PC2	1837	0.16	0.4	YES
6	AMY2B	AMY2B	AMY2B	2409	0.13	0.41	YES
7	AMY1A	AMY1A	AMY1A	2423	0.13	0.45	YES
8	PGM2L1	PGM2L1	PGM2L1	2558	0.12	0.48	YES
9	GYS1	GYS1	GYS1	2926	0.1	0.49	YES
10	PGM2	PGM2	PGM2	3202	0.091	0.51	YES
11	GUSB	GUSB	GUSB	3298	0.088	0.53	YES
12	MGAM	MGAM	MGAM	4498	0.055	0.48	NO
13	AGL	AGL	AGL	4895	0.046	0.47	NO
14	UGDH	UGDH	UGDH	5590	0.034	0.45	NO
15	PGM1	PGM1	PGM1	6152	0.024	0.42	NO
16	GPI	GPI	GPI	6207	0.023	0.43	NO
17	GAA	GAA	GAA	7315	0.0087	0.37	NO
18	HK1	HK1	HK1	7496	0.0063	0.36	NO
19	PYGL	PYGL	PYGL	7846	0.0016	0.34	NO
20	PYGB	PYGB	PYGB	8912	-0.011	0.29	NO
21	AMY2A	AMY2A	AMY2A	8972	-0.012	0.29	NO
22	GBE1	GBE1	GBE1	10800	-0.034	0.2	NO
23	UGP2	UGP2	UGP2	10825	-0.034	0.21	NO
24	GYS2	GYS2	GYS2	14705	-0.1	0.024	NO
25	ENPP1	ENPP1	ENPP1	14757	-0.1	0.056	NO
26	GANC	GANC	GANC	15301	-0.12	0.066	NO
27	ENPP3	ENPP3	ENPP3	17176	-0.25	0.045	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 RIBOSOME.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIBOSOME, 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 CALCIUM SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CDA	CDA	CDA	52	0.52	0.15	YES
2	UPB1	UPB1	UPB1	61	0.51	0.3	YES
3	UPP2	UPP2	UPP2	549	0.31	0.36	YES
4	TK1	TK1	TK1	569	0.3	0.44	YES
5	NAT1	NAT1	NAT1	1204	0.22	0.47	YES
6	NAT2	NAT2	NAT2	1707	0.17	0.49	YES
7	TYMP	TYMP	TYMP	2735	0.11	0.47	YES
8	IMPDH1	IMPDH1	IMPDH1	2827	0.11	0.49	YES
9	DPYD	DPYD	DPYD	3283	0.089	0.49	YES
10	GUSB	GUSB	GUSB	3298	0.088	0.52	YES
11	CYP3A43	CYP3A43	CYP3A43	4386	0.058	0.47	NO
12	UCK2	UCK2	UCK2	4631	0.052	0.48	NO
13	UMPS	UMPS	UMPS	5759	0.03	0.42	NO
14	CYP2A7	CYP2A7	CYP2A7	6001	0.026	0.42	NO
15	CYP3A5	CYP3A5	CYP3A5	6159	0.024	0.41	NO
16	ITPA	ITPA	ITPA	6840	0.014	0.38	NO
17	CYP3A7	CYP3A7	CYP3A7	7117	0.011	0.37	NO
18	UCK1	UCK1	UCK1	7448	0.0068	0.35	NO
19	UCKL1	UCKL1	UCKL1	7798	0.0024	0.33	NO
20	CYP2A6	CYP2A6	CYP2A6	8759	-0.0094	0.28	NO
21	IMPDH2	IMPDH2	IMPDH2	8876	-0.011	0.28	NO
22	GMPS	GMPS	GMPS	9476	-0.018	0.25	NO
23	UPP1	UPP1	UPP1	9587	-0.019	0.25	NO
24	HPRT1	HPRT1	HPRT1	10587	-0.031	0.2	NO
25	CES7	CES7	CES7	11900	-0.049	0.14	NO
26	CES2	CES2	CES2	12803	-0.062	0.11	NO
27	TK2	TK2	TK2	12895	-0.064	0.13	NO
28	DPYS	DPYS	DPYS	12926	-0.064	0.14	NO
29	TPMT	TPMT	TPMT	14825	-0.11	0.068	NO
30	CES1	CES1	CES1	15535	-0.13	0.067	NO
31	XDH	XDH	XDH	17040	-0.24	0.052	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 CALCIUM SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG VASCULAR SMOOTH MUSCLE CONTRACTION

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	PGF	PGF	PGF	76	0.49	0.073	YES
2	SLC2A1	SLC2A1	SLC2A1	341	0.36	0.12	YES
3	EGLN3	EGLN3	EGLN3	383	0.35	0.17	YES
4	PDGFB	PDGFB	PDGFB	866	0.25	0.18	YES
5	TGFB2	TGFB2	TGFB2	1015	0.23	0.21	YES
6	ETS1	ETS1	ETS1	1272	0.21	0.23	YES
7	EPAS1	EPAS1	EPAS1	1319	0.2	0.26	YES
8	VEGFA	VEGFA	VEGFA	1339	0.2	0.29	YES
9	VEGFC	VEGFC	VEGFC	1576	0.18	0.3	YES
10	MET	MET	MET	2040	0.15	0.3	YES
11	PIK3R3	PIK3R3	PIK3R3	2210	0.14	0.31	YES
12	NRAS	NRAS	NRAS	2307	0.13	0.33	YES
13	HGF	HGF	HGF	2348	0.13	0.35	YES
14	CRK	CRK	CRK	2402	0.13	0.36	YES
15	CDC42	CDC42	CDC42	3142	0.093	0.34	NO
16	RAP1A	RAP1A	RAP1A	3206	0.091	0.35	NO
17	TGFB3	TGFB3	TGFB3	3250	0.09	0.36	NO
18	PIK3CD	PIK3CD	PIK3CD	3657	0.076	0.35	NO
19	TGFB1	TGFB1	TGFB1	3823	0.072	0.35	NO
20	RAPGEF1	RAPGEF1	RAPGEF1	4069	0.065	0.35	NO
21	ARAF	ARAF	ARAF	4329	0.059	0.34	NO
22	RBX1	RBX1	RBX1	4528	0.054	0.34	NO
23	RAF1	RAF1	RAF1	4794	0.048	0.34	NO
24	PIK3R5	PIK3R5	PIK3R5	5034	0.044	0.33	NO
25	RAP1B	RAP1B	RAP1B	5227	0.04	0.32	NO
26	JUN	JUN	JUN	5461	0.036	0.32	NO
27	PAK2	PAK2	PAK2	5545	0.034	0.32	NO
28	RAC1	RAC1	RAC1	5635	0.033	0.32	NO
29	EGLN2	EGLN2	EGLN2	5741	0.031	0.32	NO
30	MAP2K2	MAP2K2	MAP2K2	5991	0.027	0.31	NO
31	CRKL	CRKL	CRKL	6018	0.026	0.31	NO
32	EP300	EP300	EP300	6568	0.018	0.28	NO
33	TGFA	TGFA	TGFA	6794	0.015	0.27	NO
34	AKT2	AKT2	AKT2	6822	0.015	0.27	NO
35	MAP2K1	MAP2K1	MAP2K1	7073	0.012	0.26	NO
36	TCEB2	TCEB2	TCEB2	7094	0.011	0.26	NO
37	ARNT	ARNT	ARNT	7201	0.01	0.26	NO
38	PIK3CG	PIK3CG	PIK3CG	7568	0.0054	0.24	NO
39	GAB1	GAB1	GAB1	7602	0.0048	0.24	NO
40	PIK3CA	PIK3CA	PIK3CA	7683	0.0038	0.23	NO
41	PAK4	PAK4	PAK4	7934	0.00052	0.22	NO
42	TCEB1	TCEB1	TCEB1	8134	-0.0019	0.21	NO
43	AKT1	AKT1	AKT1	8168	-0.0023	0.21	NO
44	HIF1A	HIF1A	HIF1A	8428	-0.0054	0.19	NO
45	PIK3R2	PIK3R2	PIK3R2	8511	-0.0062	0.19	NO
46	MAPK1	MAPK1	MAPK1	8606	-0.0075	0.18	NO
47	EGLN1	EGLN1	EGLN1	8644	-0.0079	0.18	NO
48	KRAS	KRAS	KRAS	9144	-0.014	0.16	NO
49	CREBBP	CREBBP	CREBBP	9542	-0.018	0.14	NO
50	SOS1	SOS1	SOS1	9606	-0.019	0.14	NO
51	GRB2	GRB2	GRB2	10496	-0.03	0.093	NO
52	PIK3CB	PIK3CB	PIK3CB	10570	-0.031	0.094	NO
53	FLCN	FLCN	FLCN	10842	-0.035	0.084	NO
54	SOS2	SOS2	SOS2	11591	-0.044	0.05	NO
55	VEGFB	VEGFB	VEGFB	11708	-0.046	0.05	NO
56	PTPN11	PTPN11	PTPN11	12818	-0.062	-0.0017	NO
57	FH	FH	FH	12930	-0.064	0.0023	NO
58	CUL2	CUL2	CUL2	12982	-0.065	0.0097	NO
59	AKT3	AKT3	AKT3	13025	-0.066	0.018	NO
60	MAPK3	MAPK3	MAPK3	13077	-0.067	0.026	NO
61	PIK3R1	PIK3R1	PIK3R1	13332	-0.072	0.023	NO
62	PAK6	PAK6	PAK6	13891	-0.083	0.0047	NO
63	PAK1	PAK1	PAK1	14573	-0.1	-0.018	NO
64	BRAF	BRAF	BRAF	14987	-0.11	-0.023	NO
65	VHL	VHL	VHL	15027	-0.11	-0.007	NO
66	PAK3	PAK3	PAK3	15870	-0.15	-0.031	NO
67	ARNT2	ARNT2	ARNT2	16616	-0.2	-0.041	NO
68	FIGF	FIGF	FIGF	17608	-0.33	-0.044	NO
69	PAK7	PAK7	PAK7	17806	-0.41	0.0095	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 VASCULAR SMOOTH MUSCLE CONTRACTION.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VASCULAR SMOOTH MUSCLE CONTRACTION, 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 clus4 enriched pathways

Table 6. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus4. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA NO1 PATHWAY	28	genes.ES.table	0.21	0.52	1	0.98	1	0.11	0.13	0.093	0.98	0.25
BIOCARTA ALK PATHWAY	34	genes.ES.table	0.51	1.3	0.13	0.21	0.95	0.35	0.19	0.28	0.16	0.006
BIOCARTA BCR PATHWAY	33	genes.ES.table	0.5	1.3	0.18	0.22	0.95	0.36	0.28	0.26	0.17	0.005
BIOCARTA ERK PATHWAY	26	genes.ES.table	0.59	1.7	0.016	0.091	0.42	0.23	0.12	0.2	0	0.003
BIOCARTA FCER1 PATHWAY	37	genes.ES.table	0.49	1.3	0.2	0.22	0.96	0.32	0.24	0.24	0.17	0.003
BIOCARTA FMLP PATHWAY	34	genes.ES.table	0.52	1.5	0.049	0.13	0.77	0.24	0.16	0.2	0.08	0.002
BIOCARTA GH PATHWAY	26	genes.ES.table	0.54	1.5	0.025	0.13	0.79	0.19	0.081	0.18	0.086	0.003
BIOCARTA HIVNEF PATHWAY	57	genes.ES.table	0.34	1.3	0.18	0.21	0.94	0.28	0.26	0.21	0.15	0.006
BIOCARTA MPR PATHWAY	32	genes.ES.table	0.58	1.9	0.002	0.096	0.083	0.16	0.097	0.14	0	0.031
BIOCARTA IL2RB PATHWAY	37	genes.ES.table	0.61	1.5	0.083	0.13	0.8	0.49	0.23	0.38	0.082	0.003

genes ES table in pathway: BIOCARTA NO1 PATHWAY

Table S31. 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	AOX1	AOX1	AOX1	55	1.4	0.17	YES
2	ACADS	ACADS	ACADS	1101	0.41	0.17	YES
3	ALDH3A2	ALDH3A2	ALDH3A2	1115	0.41	0.22	YES
4	ACAT2	ACAT2	ACAT2	1167	0.4	0.27	YES
5	HIBCH	HIBCH	HIBCH	1414	0.35	0.3	YES
6	HMGCS1	HMGCS1	HMGCS1	1806	0.3	0.31	YES
7	MCCC1	MCCC1	MCCC1	2038	0.27	0.34	YES
8	PCCA	PCCA	PCCA	2146	0.25	0.36	YES
9	ALDH2	ALDH2	ALDH2	2210	0.25	0.39	YES
10	ALDH1B1	ALDH1B1	ALDH1B1	2356	0.23	0.41	YES
11	BCAT2	BCAT2	BCAT2	2525	0.21	0.43	YES
12	OXCT2	OXCT2	OXCT2	2537	0.21	0.46	YES
13	ACAA1	ACAA1	ACAA1	2594	0.21	0.48	YES
14	IL4I1	IL4I1	IL4I1	2670	0.2	0.5	YES
15	HIBADH	HIBADH	HIBADH	2690	0.2	0.53	YES
16	PCCB	PCCB	PCCB	2717	0.2	0.55	YES
17	ACADM	ACADM	ACADM	2745	0.19	0.57	YES
18	DBT	DBT	DBT	2786	0.19	0.6	YES
19	ALDH6A1	ALDH6A1	ALDH6A1	2809	0.19	0.62	YES
20	HMGCL	HMGCL	HMGCL	3078	0.17	0.62	YES
21	ACAT1	ACAT1	ACAT1	3139	0.16	0.64	YES
22	HADHB	HADHB	HADHB	3169	0.16	0.66	YES
23	MCEE	MCEE	MCEE	3245	0.16	0.68	YES
24	MCCC2	MCCC2	MCCC2	3553	0.14	0.68	YES
25	AUH	AUH	AUH	3736	0.13	0.68	YES
26	ALDH7A1	ALDH7A1	ALDH7A1	3982	0.12	0.69	YES
27	DLD	DLD	DLD	4839	0.086	0.65	NO
28	ECHS1	ECHS1	ECHS1	5231	0.076	0.64	NO
29	ALDH9A1	ALDH9A1	ALDH9A1	5310	0.074	0.64	NO
30	HSD17B10	HSD17B10	HSD17B10	5374	0.072	0.65	NO
31	BCKDHA	BCKDHA	BCKDHA	5513	0.068	0.65	NO
32	ACAA2	ACAA2	ACAA2	5674	0.063	0.65	NO
33	ACAD8	ACAD8	ACAD8	6183	0.052	0.63	NO
34	IVD	IVD	IVD	6625	0.043	0.61	NO
35	EHHADH	EHHADH	EHHADH	6798	0.04	0.6	NO
36	HADHA	HADHA	HADHA	7303	0.03	0.58	NO
37	HADH	HADH	HADH	7660	0.024	0.56	NO
38	BCKDHB	BCKDHB	BCKDHB	9066	0.0021	0.48	NO
39	ACADSB	ACADSB	ACADSB	9178	0.00045	0.48	NO
40	OXCT1	OXCT1	OXCT1	9407	-0.0029	0.46	NO
41	MUT	MUT	MUT	9629	-0.006	0.45	NO
42	ABAT	ABAT	ABAT	14428	-0.088	0.2	NO

Figure S61. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S62. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA ALK PATHWAY

Table S32. 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	AKR1B1	AKR1B1	AKR1B1	933	0.44	0.03	YES
2	ALDH3A2	ALDH3A2	ALDH3A2	1115	0.41	0.095	YES
3	ACAT2	ACAT2	ACAT2	1167	0.4	0.17	YES
4	PCK1	PCK1	PCK1	1400	0.35	0.22	YES
5	ACSS2	ACSS2	ACSS2	1632	0.32	0.26	YES
6	ACSS1	ACSS1	ACSS1	1691	0.31	0.32	YES
7	ALDH2	ALDH2	ALDH2	2210	0.25	0.34	YES
8	ALDH1B1	ALDH1B1	ALDH1B1	2356	0.23	0.37	YES
9	ACOT12	ACOT12	ACOT12	2357	0.23	0.41	YES
10	ACYP1	ACYP1	ACYP1	2510	0.21	0.44	YES
11	LDHD	LDHD	LDHD	2792	0.19	0.46	YES
12	GRHPR	GRHPR	GRHPR	3070	0.17	0.48	YES
13	ACAT1	ACAT1	ACAT1	3139	0.16	0.5	YES
14	ME1	ME1	ME1	3299	0.15	0.52	YES
15	PC	PC	PC	3640	0.13	0.53	YES
16	ALDH7A1	ALDH7A1	ALDH7A1	3982	0.12	0.53	YES
17	LDHB	LDHB	LDHB	4088	0.11	0.54	YES
18	ACACB	ACACB	ACACB	4224	0.11	0.56	YES
19	PDHB	PDHB	PDHB	4295	0.1	0.57	YES
20	DLD	DLD	DLD	4839	0.086	0.56	NO
21	ALDH9A1	ALDH9A1	ALDH9A1	5310	0.074	0.54	NO
22	ACYP2	ACYP2	ACYP2	6185	0.052	0.5	NO
23	PDHA1	PDHA1	PDHA1	6186	0.052	0.51	NO
24	MDH2	MDH2	MDH2	6204	0.051	0.52	NO
25	ACACA	ACACA	ACACA	6305	0.049	0.53	NO
26	HAGH	HAGH	HAGH	7140	0.034	0.49	NO
27	MDH1	MDH1	MDH1	7561	0.026	0.47	NO
28	LDHA	LDHA	LDHA	7658	0.024	0.47	NO
29	LDHAL6A	LDHAL6A	LDHAL6A	8445	0.011	0.42	NO
30	GLO1	GLO1	GLO1	8720	0.0072	0.41	NO
31	ME3	ME3	ME3	8947	0.0038	0.4	NO
32	DLAT	DLAT	DLAT	10714	-0.022	0.3	NO
33	PKM2	PKM2	PKM2	11420	-0.032	0.27	NO
34	PCK2	PCK2	PCK2	11910	-0.04	0.25	NO
35	ME2	ME2	ME2	12031	-0.042	0.25	NO
36	PKLR	PKLR	PKLR	14572	-0.093	0.13	NO
37	HAGHL	HAGHL	HAGHL	15797	-0.13	0.084	NO
38	LDHAL6B	LDHAL6B	LDHAL6B	16963	-0.2	0.056	NO

Figure S63. 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 S64. 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 BCR PATHWAY

Table S33. 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	PAQR5	PAQR5	PAQR5	27	1.6	0.31	YES
2	PGR	PGR	PGR	273	0.78	0.45	YES
3	RPS6KA1	RPS6KA1	RPS6KA1	1093	0.41	0.49	YES
4	PRKAR2B	PRKAR2B	PRKAR2B	1255	0.38	0.55	YES
5	PAQR7	PAQR7	PAQR7	1741	0.3	0.58	YES
6	SRC	SRC	SRC	4778	0.088	0.43	NO
7	ARPC4	ARPC4	ARPC4	4861	0.085	0.44	NO
8	ARPC1B	ARPC1B	ARPC1B	4994	0.081	0.45	NO
9	ACTR3	ACTR3	ACTR3	5442	0.07	0.44	NO
10	GNAI1	GNAI1	GNAI1	5821	0.06	0.43	NO
11	ARPC3	ARPC3	ARPC3	6679	0.042	0.39	NO
12	ARPC1A	ARPC1A	ARPC1A	7266	0.031	0.37	NO
13	PRKACG	PRKACG	PRKACG	7458	0.028	0.36	NO
14	CAP1	CAP1	CAP1	8749	0.0068	0.29	NO
15	ARPC2	ARPC2	ARPC2	8912	0.0042	0.28	NO
16	PRKAR1A	PRKAR1A	PRKAR1A	10274	-0.016	0.21	NO
17	ARPC5	ARPC5	ARPC5	10275	-0.016	0.21	NO
18	MAPK1	MAPK1	MAPK1	10732	-0.022	0.19	NO
19	CCNB1	CCNB1	CCNB1	10951	-0.026	0.18	NO
20	ACTA1	ACTA1	ACTA1	11338	-0.031	0.17	NO
21	HRAS	HRAS	HRAS	11443	-0.032	0.17	NO
22	PIN1	PIN1	PIN1	11444	-0.032	0.18	NO
23	ACTR2	ACTR2	ACTR2	11556	-0.034	0.18	NO
24	GNB1	GNB1	GNB1	11781	-0.038	0.17	NO
25	MAPK3	MAPK3	MAPK3	11917	-0.04	0.17	NO
26	PRKAR2A	PRKAR2A	PRKAR2A	13029	-0.058	0.12	NO
27	GNAS	GNAS	GNAS	13546	-0.068	0.1	NO
28	PRKACB	PRKACB	PRKACB	13913	-0.076	0.099	NO
29	CDC25C	CDC25C	CDC25C	15756	-0.13	0.022	NO
30	MYT1	MYT1	MYT1	16012	-0.14	0.036	NO
31	PRKAR1B	PRKAR1B	PRKAR1B	16610	-0.18	0.037	NO
32	CDK1	CDK1	CDK1	16939	-0.2	0.058	NO

Figure S65. 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 S66. 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 ERK PATHWAY

Table S34. 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	AOX1	AOX1	AOX1	55	1.4	0.11	YES
2	ADH1A	ADH1A	ADH1A	61	1.3	0.23	YES
3	HPD	HPD	HPD	87	1.2	0.33	YES
4	ADH1B	ADH1B	ADH1B	116	1.1	0.42	YES
5	ALDH3B1	ALDH3B1	ALDH3B1	227	0.85	0.49	YES
6	ALDH3B2	ALDH3B2	ALDH3B2	415	0.65	0.54	YES
7	ADH1C	ADH1C	ADH1C	476	0.61	0.59	YES
8	FAH	FAH	FAH	757	0.49	0.61	YES
9	MAOB	MAOB	MAOB	964	0.44	0.64	YES
10	AOC3	AOC3	AOC3	1006	0.43	0.67	YES
11	ALDH3A1	ALDH3A1	ALDH3A1	1119	0.41	0.7	YES
12	HGD	HGD	HGD	1504	0.34	0.71	YES
13	PNMT	PNMT	PNMT	2468	0.22	0.68	YES
14	GSTZ1	GSTZ1	GSTZ1	2617	0.2	0.69	YES
15	IL4I1	IL4I1	IL4I1	2670	0.2	0.7	YES
16	TAT	TAT	TAT	2695	0.2	0.72	YES
17	MAOA	MAOA	MAOA	2754	0.19	0.73	YES
18	COMT	COMT	COMT	3142	0.16	0.72	YES
19	ALDH1A3	ALDH1A3	ALDH1A3	3234	0.16	0.73	YES
20	HEMK1	HEMK1	HEMK1	4448	0.098	0.67	NO
21	GOT1	GOT1	GOT1	5706	0.062	0.61	NO
22	ADH5	ADH5	ADH5	6424	0.047	0.57	NO
23	WBSCR22	WBSCR22	WBSCR22	6530	0.045	0.57	NO
24	NAT6	NAT6	NAT6	7227	0.032	0.53	NO
25	MIF	MIF	MIF	8091	0.017	0.49	NO
26	LCMT1	LCMT1	LCMT1	8530	0.0099	0.46	NO
27	METTL6	METTL6	METTL6	9398	-0.0028	0.42	NO
28	GOT2	GOT2	GOT2	9455	-0.0037	0.41	NO
29	AOC2	AOC2	AOC2	9791	-0.0084	0.39	NO
30	TRMT11	TRMT11	TRMT11	10179	-0.014	0.37	NO
31	DBH	DBH	DBH	10515	-0.019	0.36	NO
32	DCT	DCT	DCT	12566	-0.05	0.25	NO
33	LCMT2	LCMT2	LCMT2	12585	-0.051	0.25	NO
34	METTL2B	METTL2B	METTL2B	12916	-0.056	0.24	NO
35	TH	TH	TH	14621	-0.094	0.15	NO
36	DDC	DDC	DDC	16945	-0.2	0.038	NO
37	TPO	TPO	TPO	17208	-0.23	0.043	NO

Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA ERK PATHWAY.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ERK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

Table S35. 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	GSTA1	GSTA1	GSTA1	7	2	0.19	YES
2	MGST1	MGST1	MGST1	11	1.9	0.38	YES
3	OPLAH	OPLAH	OPLAH	328	0.73	0.44	YES
4	GSTM5	GSTM5	GSTM5	401	0.66	0.5	YES
5	GGT5	GGT5	GGT5	1022	0.43	0.5	YES
6	IDH1	IDH1	IDH1	1247	0.38	0.53	YES
7	GSTA4	GSTA4	GSTA4	1749	0.3	0.53	YES
8	ANPEP	ANPEP	ANPEP	1803	0.3	0.56	YES
9	GSTT2	GSTT2	GSTT2	1855	0.29	0.58	YES
10	GSTM1	GSTM1	GSTM1	2450	0.22	0.57	YES
11	GSTZ1	GSTZ1	GSTZ1	2617	0.2	0.58	YES
12	GPX1	GPX1	GPX1	2978	0.17	0.58	YES
13	GCLM	GCLM	GCLM	3052	0.17	0.59	YES
14	SMS	SMS	SMS	3132	0.16	0.6	YES
15	GPX3	GPX3	GPX3	3151	0.16	0.62	YES
16	GSTT1	GSTT1	GSTT1	3335	0.15	0.62	YES
17	GSTK1	GSTK1	GSTK1	3804	0.12	0.61	NO
18	GSTM2	GSTM2	GSTM2	3949	0.12	0.61	NO
19	LAP3	LAP3	LAP3	4692	0.09	0.58	NO
20	GSS	GSS	GSS	4771	0.088	0.58	NO
21	MGST2	MGST2	MGST2	4884	0.084	0.58	NO
22	GGT1	GGT1	GGT1	5044	0.08	0.58	NO
23	G6PD	G6PD	G6PD	5187	0.077	0.58	NO
24	GSTO1	GSTO1	GSTO1	5235	0.076	0.59	NO
25	SRM	SRM	SRM	5238	0.075	0.59	NO
26	GSTP1	GSTP1	GSTP1	5335	0.073	0.6	NO
27	MGST3	MGST3	MGST3	5533	0.067	0.59	NO
28	GPX4	GPX4	GPX4	5661	0.064	0.59	NO
29	GPX7	GPX7	GPX7	6046	0.054	0.57	NO
30	GSTM4	GSTM4	GSTM4	6236	0.051	0.57	NO
31	TXNDC12	TXNDC12	TXNDC12	6407	0.047	0.56	NO
32	RRM1	RRM1	RRM1	6708	0.042	0.55	NO
33	GSTM3	GSTM3	GSTM3	7136	0.034	0.53	NO
34	RRM2B	RRM2B	RRM2B	8527	0.01	0.45	NO
35	GCLC	GCLC	GCLC	9957	-0.011	0.38	NO
36	GGCT	GGCT	GGCT	10474	-0.018	0.35	NO
37	ODC1	ODC1	ODC1	10573	-0.02	0.34	NO
38	GSR	GSR	GSR	10699	-0.022	0.34	NO
39	IDH2	IDH2	IDH2	11092	-0.028	0.32	NO
40	GGT7	GGT7	GGT7	14142	-0.082	0.16	NO
41	GSTO2	GSTO2	GSTO2	14369	-0.087	0.16	NO
42	RRM2	RRM2	RRM2	14447	-0.089	0.16	NO
43	GPX2	GPX2	GPX2	17894	-0.38	0.0046	NO

Figure S69. 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 S70. 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 FMLP PATHWAY

Table S36. 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	ADH1A	ADH1A	ADH1A	61	1.3	0.15	YES
2	ADH1B	ADH1B	ADH1B	116	1.1	0.28	YES
3	ADH1C	ADH1C	ADH1C	476	0.61	0.33	YES
4	ACADL	ACADL	ACADL	582	0.55	0.39	YES
5	ACADS	ACADS	ACADS	1101	0.41	0.41	YES
6	ALDH3A2	ALDH3A2	ALDH3A2	1115	0.41	0.46	YES
7	ACAT2	ACAT2	ACAT2	1167	0.4	0.5	YES
8	ALDH2	ALDH2	ALDH2	2210	0.25	0.47	YES
9	ALDH1B1	ALDH1B1	ALDH1B1	2356	0.23	0.49	YES
10	ACADVL	ACADVL	ACADVL	2445	0.22	0.51	YES
11	ACSL5	ACSL5	ACSL5	2568	0.21	0.53	YES
12	ACAA1	ACAA1	ACAA1	2594	0.21	0.55	YES
13	CPT2	CPT2	CPT2	2649	0.2	0.57	YES
14	ACADM	ACADM	ACADM	2745	0.19	0.59	YES
15	ACAT1	ACAT1	ACAT1	3139	0.16	0.59	YES
16	HADHB	HADHB	HADHB	3169	0.16	0.6	YES
17	GCDH	GCDH	GCDH	3504	0.14	0.6	YES
18	CPT1B	CPT1B	CPT1B	3788	0.12	0.6	YES
19	CPT1A	CPT1A	CPT1A	3792	0.12	0.62	YES
20	ALDH7A1	ALDH7A1	ALDH7A1	3982	0.12	0.62	YES
21	PECI	PECI	PECI	4068	0.11	0.63	YES
22	ACSL1	ACSL1	ACSL1	4427	0.099	0.62	NO
23	ACOX3	ACOX3	ACOX3	4797	0.087	0.61	NO
24	ECHS1	ECHS1	ECHS1	5231	0.076	0.59	NO
25	ALDH9A1	ALDH9A1	ALDH9A1	5310	0.074	0.6	NO
26	DCI	DCI	DCI	5383	0.072	0.6	NO
27	ACSL4	ACSL4	ACSL4	5655	0.064	0.6	NO
28	ACAA2	ACAA2	ACAA2	5674	0.063	0.6	NO
29	ADH5	ADH5	ADH5	6424	0.047	0.57	NO
30	EHHADH	EHHADH	EHHADH	6798	0.04	0.55	NO
31	HADHA	HADHA	HADHA	7303	0.03	0.52	NO
32	HADH	HADH	HADH	7660	0.024	0.51	NO
33	ACSL3	ACSL3	ACSL3	7820	0.021	0.5	NO
34	ACADSB	ACADSB	ACADSB	9178	0.00045	0.43	NO
35	ACSL6	ACSL6	ACSL6	16119	-0.15	0.057	NO
36	CYP4A11	CYP4A11	CYP4A11	16704	-0.18	0.046	NO
37	CPT1C	CPT1C	CPT1C	16981	-0.21	0.056	NO

Figure S71. 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 FMLP PATHWAY.

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FMLP PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GH PATHWAY

Table S37. 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	ADH1A	ADH1A	ADH1A	61	1.3	0.1	YES
2	GALM	GALM	GALM	97	1.1	0.19	YES
3	ADH1B	ADH1B	ADH1B	116	1.1	0.28	YES
4	ALDH3B1	ALDH3B1	ALDH3B1	227	0.85	0.34	YES
5	FBP1	FBP1	FBP1	297	0.76	0.4	YES
6	ALDH3B2	ALDH3B2	ALDH3B2	415	0.65	0.44	YES
7	ALDOB	ALDOB	ALDOB	428	0.65	0.49	YES
8	ADH1C	ADH1C	ADH1C	476	0.61	0.54	YES
9	ALDH3A2	ALDH3A2	ALDH3A2	1115	0.41	0.54	YES
10	ALDH3A1	ALDH3A1	ALDH3A1	1119	0.41	0.57	YES
11	HK3	HK3	HK3	1335	0.37	0.59	YES
12	PCK1	PCK1	PCK1	1400	0.35	0.61	YES
13	ACSS2	ACSS2	ACSS2	1632	0.32	0.62	YES
14	ACSS1	ACSS1	ACSS1	1691	0.31	0.64	YES
15	ALDH2	ALDH2	ALDH2	2210	0.25	0.64	YES
16	ALDH1B1	ALDH1B1	ALDH1B1	2356	0.23	0.65	YES
17	PGM1	PGM1	PGM1	2897	0.18	0.63	NO
18	PGM2	PGM2	PGM2	3122	0.16	0.63	NO
19	ALDH1A3	ALDH1A3	ALDH1A3	3234	0.16	0.64	NO
20	ALDH7A1	ALDH7A1	ALDH7A1	3982	0.12	0.6	NO
21	LDHB	LDHB	LDHB	4088	0.11	0.61	NO
22	AKR1A1	AKR1A1	AKR1A1	4219	0.11	0.61	NO
23	ENO3	ENO3	ENO3	4263	0.1	0.62	NO
24	PDHB	PDHB	PDHB	4295	0.1	0.62	NO
25	DLD	DLD	DLD	4839	0.086	0.6	NO
26	ALDH9A1	ALDH9A1	ALDH9A1	5310	0.074	0.58	NO
27	PDHA1	PDHA1	PDHA1	6186	0.052	0.53	NO
28	ADH5	ADH5	ADH5	6424	0.047	0.52	NO
29	PGAM2	PGAM2	PGAM2	7316	0.03	0.48	NO
30	GCK	GCK	GCK	7542	0.026	0.47	NO
31	LDHA	LDHA	LDHA	7658	0.024	0.46	NO
32	LDHAL6A	LDHAL6A	LDHAL6A	8445	0.011	0.42	NO
33	ENO1	ENO1	ENO1	8686	0.0077	0.41	NO
34	HK2	HK2	HK2	8875	0.005	0.4	NO
35	PGAM1	PGAM1	PGAM1	9165	0.00068	0.38	NO
36	G6PC2	G6PC2	G6PC2	10178	-0.014	0.32	NO
37	PFKM	PFKM	PFKM	10564	-0.02	0.3	NO
38	BPGM	BPGM	BPGM	10596	-0.02	0.3	NO
39	GPI	GPI	GPI	10613	-0.02	0.3	NO
40	DLAT	DLAT	DLAT	10714	-0.022	0.3	NO
41	PKM2	PKM2	PKM2	11420	-0.032	0.26	NO
42	TPI1	TPI1	TPI1	11746	-0.037	0.25	NO
43	GAPDH	GAPDH	GAPDH	11829	-0.038	0.25	NO
44	PCK2	PCK2	PCK2	11910	-0.04	0.25	NO
45	ALDOA	ALDOA	ALDOA	12298	-0.046	0.23	NO
46	PGK1	PGK1	PGK1	12358	-0.047	0.23	NO
47	ALDOC	ALDOC	ALDOC	12491	-0.049	0.23	NO
48	PGAM4	PGAM4	PGAM4	12849	-0.055	0.21	NO
49	PFKL	PFKL	PFKL	12917	-0.056	0.21	NO
50	PKLR	PKLR	PKLR	14572	-0.093	0.13	NO
51	HK1	HK1	HK1	15231	-0.11	0.098	NO
52	ENO2	ENO2	ENO2	16799	-0.19	0.026	NO
53	LDHAL6B	LDHAL6B	LDHAL6B	16963	-0.2	0.034	NO
54	PFKP	PFKP	PFKP	17600	-0.29	0.021	NO

Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GH PATHWAY.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GH PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table S38. 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	GSTA1	GSTA1	GSTA1	7	2	0.1	YES
2	MGST1	MGST1	MGST1	11	1.9	0.2	YES
3	AOX1	AOX1	AOX1	55	1.4	0.27	YES
4	ADH1A	ADH1A	ADH1A	61	1.3	0.34	YES
5	FMO1	FMO1	FMO1	88	1.2	0.4	YES
6	ADH1B	ADH1B	ADH1B	116	1.1	0.45	YES
7	FMO2	FMO2	FMO2	164	0.96	0.5	YES
8	ALDH3B1	ALDH3B1	ALDH3B1	227	0.85	0.54	YES
9	FMO5	FMO5	FMO5	306	0.75	0.57	YES
10	CYP3A5	CYP3A5	CYP3A5	345	0.71	0.6	YES
11	GSTM5	GSTM5	GSTM5	401	0.66	0.64	YES
12	FMO4	FMO4	FMO4	402	0.66	0.67	YES
13	ALDH3B2	ALDH3B2	ALDH3B2	415	0.65	0.7	YES
14	ADH1C	ADH1C	ADH1C	476	0.61	0.73	YES
15	FMO3	FMO3	FMO3	573	0.56	0.75	YES
16	CYP3A7	CYP3A7	CYP3A7	819	0.47	0.76	YES
17	MAOB	MAOB	MAOB	964	0.44	0.78	YES
18	ALDH3A1	ALDH3A1	ALDH3A1	1119	0.41	0.79	YES
19	GSTA4	GSTA4	GSTA4	1749	0.3	0.77	NO
20	GSTT2	GSTT2	GSTT2	1855	0.29	0.78	NO
21	GSTM1	GSTM1	GSTM1	2450	0.22	0.76	NO
22	GSTZ1	GSTZ1	GSTZ1	2617	0.2	0.76	NO
23	MAOA	MAOA	MAOA	2754	0.19	0.76	NO
24	ALDH1A3	ALDH1A3	ALDH1A3	3234	0.16	0.74	NO
25	GSTT1	GSTT1	GSTT1	3335	0.15	0.75	NO
26	CYP2A6	CYP2A6	CYP2A6	3350	0.15	0.75	NO
27	CYP2C8	CYP2C8	CYP2C8	3598	0.14	0.75	NO
28	GSTK1	GSTK1	GSTK1	3804	0.12	0.74	NO
29	GSTM2	GSTM2	GSTM2	3949	0.12	0.74	NO
30	MGST2	MGST2	MGST2	4884	0.084	0.69	NO
31	GSTO1	GSTO1	GSTO1	5235	0.076	0.68	NO
32	GSTP1	GSTP1	GSTP1	5335	0.073	0.68	NO
33	CYP2E1	CYP2E1	CYP2E1	5466	0.069	0.67	NO
34	MGST3	MGST3	MGST3	5533	0.067	0.67	NO
35	GSTM4	GSTM4	GSTM4	6236	0.051	0.63	NO
36	ADH5	ADH5	ADH5	6424	0.047	0.63	NO
37	GSTM3	GSTM3	GSTM3	7136	0.034	0.59	NO
38	CYP3A43	CYP3A43	CYP3A43	7409	0.029	0.57	NO
39	CYP2C18	CYP2C18	CYP2C18	11459	-0.033	0.35	NO
40	CYP2A7	CYP2A7	CYP2A7	11866	-0.039	0.33	NO
41	GSTO2	GSTO2	GSTO2	14369	-0.087	0.2	NO
42	CYP2D6	CYP2D6	CYP2D6	15515	-0.12	0.14	NO

Figure S75. 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 S76. 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 MPR PATHWAY

Table S39. 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	ACSM3	ACSM3	ACSM3	129	1	0.16	YES
2	ACSM1	ACSM1	ACSM1	512	0.58	0.23	YES
3	ACSM5	ACSM5	ACSM5	985	0.43	0.27	YES
4	ACADS	ACADS	ACADS	1101	0.41	0.33	YES
5	ALDH3A2	ALDH3A2	ALDH3A2	1115	0.41	0.4	YES
6	ACAT2	ACAT2	ACAT2	1167	0.4	0.46	YES
7	AKR1B10	AKR1B10	AKR1B10	1197	0.39	0.52	YES
8	BDH2	BDH2	BDH2	1711	0.31	0.54	YES
9	HMGCS1	HMGCS1	HMGCS1	1806	0.3	0.58	YES
10	ALDH2	ALDH2	ALDH2	2210	0.25	0.6	YES
11	ALDH1B1	ALDH1B1	ALDH1B1	2356	0.23	0.63	YES
12	OXCT2	OXCT2	OXCT2	2537	0.21	0.65	YES
13	HMGCL	HMGCL	HMGCL	3078	0.17	0.65	YES
14	ACAT1	ACAT1	ACAT1	3139	0.16	0.67	YES
15	ALDH7A1	ALDH7A1	ALDH7A1	3982	0.12	0.64	NO
16	GAD1	GAD1	GAD1	4110	0.11	0.65	NO
17	PDHB	PDHB	PDHB	4295	0.1	0.66	NO
18	ECHS1	ECHS1	ECHS1	5231	0.076	0.62	NO
19	ALDH9A1	ALDH9A1	ALDH9A1	5310	0.074	0.63	NO
20	AACS	AACS	AACS	5685	0.063	0.62	NO
21	BDH1	BDH1	BDH1	5805	0.06	0.62	NO
22	PDHA1	PDHA1	PDHA1	6186	0.052	0.61	NO
23	HADHA	HADHA	HADHA	7303	0.03	0.55	NO
24	ALDH5A1	ALDH5A1	ALDH5A1	7536	0.026	0.54	NO
25	HADH	HADH	HADH	7660	0.024	0.54	NO
26	OXCT1	OXCT1	OXCT1	9407	-0.0029	0.44	NO
27	ABAT	ABAT	ABAT	14428	-0.088	0.18	NO
28	L2HGDH	L2HGDH	L2HGDH	15983	-0.14	0.11	NO

Figure S77. 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 S78. 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 IL2RB PATHWAY

Table S40. 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	ALDH3A2	ALDH3A2	ALDH3A2	1115	0.41	0.018	YES
2	ACSS3	ACSS3	ACSS3	1143	0.4	0.095	YES
3	ACAT2	ACAT2	ACAT2	1167	0.4	0.17	YES
4	HIBCH	HIBCH	HIBCH	1414	0.35	0.23	YES
5	ACSS2	ACSS2	ACSS2	1632	0.32	0.28	YES
6	ACSS1	ACSS1	ACSS1	1691	0.31	0.33	YES
7	PCCA	PCCA	PCCA	2146	0.25	0.36	YES
8	ALDH2	ALDH2	ALDH2	2210	0.25	0.4	YES
9	ALDH1B1	ALDH1B1	ALDH1B1	2356	0.23	0.44	YES
10	SUCLG2	SUCLG2	SUCLG2	2359	0.23	0.48	YES
11	PCCB	PCCB	PCCB	2717	0.2	0.5	YES
12	ACADM	ACADM	ACADM	2745	0.19	0.54	YES
13	ALDH6A1	ALDH6A1	ALDH6A1	2809	0.19	0.57	YES
14	ACAT1	ACAT1	ACAT1	3139	0.16	0.58	YES
15	MCEE	MCEE	MCEE	3245	0.16	0.61	YES
16	MLYCD	MLYCD	MLYCD	3625	0.13	0.61	YES
17	ALDH7A1	ALDH7A1	ALDH7A1	3982	0.12	0.62	YES
18	LDHB	LDHB	LDHB	4088	0.11	0.63	YES
19	ACACB	ACACB	ACACB	4224	0.11	0.64	YES
20	ECHS1	ECHS1	ECHS1	5231	0.076	0.6	NO
21	ALDH9A1	ALDH9A1	ALDH9A1	5310	0.074	0.61	NO
22	ACACA	ACACA	ACACA	6305	0.049	0.57	NO
23	EHHADH	EHHADH	EHHADH	6798	0.04	0.55	NO
24	HADHA	HADHA	HADHA	7303	0.03	0.53	NO
25	LDHA	LDHA	LDHA	7658	0.024	0.51	NO
26	SUCLG1	SUCLG1	SUCLG1	8324	0.013	0.48	NO
27	LDHAL6A	LDHAL6A	LDHAL6A	8445	0.011	0.47	NO
28	SUCLA2	SUCLA2	SUCLA2	9493	-0.0041	0.41	NO
29	MUT	MUT	MUT	9629	-0.006	0.41	NO
30	ABAT	ABAT	ABAT	14428	-0.088	0.16	NO
31	LDHAL6B	LDHAL6B	LDHAL6B	16963	-0.2	0.056	NO

Figure S79. 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 S80. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

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

Made with Nozzle