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

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (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 CESC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1CR5SJN

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 CESC-TP. This pipeline has the following features:

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

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 192
Number of samples: 304
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 ] 58
pheno.type: 2 - 4 :[ clus2 ] 105
pheno.type: 3 - 4 :[ clus3 ] 69
pheno.type: 4 - 4 :[ clus4 ] 72

For the expression subtypes of 18187 genes in 305 samples, GSEA found enriched gene sets in each cluster using 304 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are BIOCARTA NFAT PATHWAY, BIOCARTA WNT PATHWAY, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG SPLICEOSOME, KEGG OOCYTE MEIOSIS, KEGG CARDIAC MUSCLE CONTRACTION, KEGG VASCULAR SMOOTH MUSCLE CONTRACTION, KEGG WNT SIGNALING PATHWAY, KEGG HEDGEHOG SIGNALING PATHWAY, KEGG TGF BETA SIGNALING PATHWAY

And common core enriched genes are PRKACB, ADCY1, ADCY2, ADCY5, EGF, GUCY1A2, GUCY1A3, GUCY1B3, PDGFB, PDGFC

clus2

Top enriched gene sets are BIOCARTA EGF PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA MAPK PATHWAY, BIOCARTA TNFR1 PATHWAY, BIOCARTA TOLL PATHWAY

And common core enriched genes are CDKN1A, CHUK, IKBKB, IKBKG, NFKB1, NFKBIA, PIK3CA, PIK3R1, RB1, CASP3

clus3

Top enriched gene sets are BIOCARTA RHO PATHWAY, KEGG PURINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG N GLYCAN BIOSYNTHESIS, KEGG O GLYCAN BIOSYNTHESIS, KEGG INOSITOL PHOSPHATE METABOLISM

And common core enriched genes are ATP6V0A4, ATP6V0E2, ATP6V1B1, ATP6V1C2, ATP6V1G2, CFTR, KCNQ1, KDELR3, MUC2, PRKCA

clus4

Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA INFLAM PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA IL1R PATHWAY, KEGG PYRIMIDINE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG SPLICEOSOME, KEGG PROTEASOME

And common core enriched genes are IL1B, IL6, CASP1, CCL5, IL18, TNF, ACTN1, ACTN3, BCAR1, CAV1

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 NFAT PATHWAY	49	genes.ES.table	0.52	1.6	0.018	0.82	0.76	0.29	0.17	0.24	0.51	0.28
BIOCARTA WNT PATHWAY	25	genes.ES.table	0.42	1.5	0.087	0.49	0.94	0.08	0.008	0.08	0.38	0.12
KEGG CYSTEINE AND METHIONINE METABOLISM	32	genes.ES.table	0.48	1.5	0.035	0.63	0.91	0.25	0.15	0.21	0.46	0.19
KEGG SPLICEOSOME	125	genes.ES.table	0.35	1.5	0.12	0.52	0.94	0.78	0.54	0.36	0.39	0.13
KEGG OOCYTE MEIOSIS	105	genes.ES.table	0.32	1.4	0.078	0.49	0.95	0.14	0.19	0.12	0.38	0.12
KEGG CARDIAC MUSCLE CONTRACTION	64	genes.ES.table	0.53	1.6	0.01	0.69	0.77	0.28	0.17	0.24	0.44	0.22
KEGG VASCULAR SMOOTH MUSCLE CONTRACTION	106	genes.ES.table	0.55	1.6	0.027	1	0.75	0.4	0.18	0.32	0.65	0.36
KEGG WNT SIGNALING PATHWAY	144	genes.ES.table	0.4	1.4	0.047	0.5	0.96	0.24	0.18	0.2	0.4	0.11
KEGG HEDGEHOG SIGNALING PATHWAY	52	genes.ES.table	0.51	1.4	0.057	0.47	0.96	0.4	0.16	0.34	0.37	0.085
KEGG TGF BETA SIGNALING PATHWAY	83	genes.ES.table	0.47	1.5	0.028	0.56	0.91	0.42	0.26	0.32	0.41	0.16

genes ES table in pathway: BIOCARTA NFAT 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	TUBB2B	TUBB2B	TUBB2B	154	0.44	0.032	YES
2	PLCB4	PLCB4	PLCB4	189	0.42	0.07	YES
3	PDGFD	PDGFD	PDGFD	219	0.41	0.11	YES
4	GUCY1B3	GUCY1B3	GUCY1B3	290	0.39	0.14	YES
5	GUCY1A3	GUCY1A3	GUCY1A3	437	0.36	0.16	YES
6	GRM1	GRM1	GRM1	454	0.36	0.2	YES
7	ADCY5	ADCY5	ADCY5	668	0.32	0.22	YES
8	ADCY1	ADCY1	ADCY1	849	0.3	0.23	YES
9	ADCY2	ADCY2	ADCY2	894	0.29	0.26	YES
10	HTR2A	HTR2A	HTR2A	896	0.29	0.28	YES
11	PRKG1	PRKG1	PRKG1	920	0.29	0.31	YES
12	GUCY1A2	GUCY1A2	GUCY1A2	1036	0.28	0.33	YES
13	PDGFRA	PDGFRA	PDGFRA	1127	0.27	0.35	YES
14	TUBA1A	TUBA1A	TUBA1A	1208	0.26	0.37	YES
15	GJA1	GJA1	GJA1	1256	0.26	0.39	YES
16	TUBB1	TUBB1	TUBB1	1265	0.26	0.42	YES
17	HTR2B	HTR2B	HTR2B	1332	0.25	0.44	YES
18	PDGFC	PDGFC	PDGFC	1350	0.25	0.46	YES
19	EGF	EGF	EGF	1808	0.21	0.45	YES
20	TUBA3E	TUBA3E	TUBA3E	2102	0.19	0.45	YES
21	PDGFRB	PDGFRB	PDGFRB	2319	0.18	0.46	YES
22	PLCB1	PLCB1	PLCB1	2564	0.17	0.46	YES
23	PRKACB	PRKACB	PRKACB	2852	0.15	0.46	YES
24	PDGFB	PDGFB	PDGFB	2889	0.15	0.47	YES
25	PRKX	PRKX	PRKX	2977	0.14	0.48	YES
26	DRD2	DRD2	DRD2	3033	0.14	0.49	YES
27	DRD1	DRD1	DRD1	3137	0.14	0.5	YES
28	TUBA8	TUBA8	TUBA8	3194	0.13	0.51	YES
29	TUBA3D	TUBA3D	TUBA3D	3302	0.13	0.51	YES
30	TUBB4	TUBB4	TUBB4	3384	0.13	0.52	YES
31	HTR2C	HTR2C	HTR2C	3392	0.13	0.53	YES
32	TUBB3	TUBB3	TUBB3	3421	0.12	0.54	YES
33	TUBB8	TUBB8	TUBB8	3840	0.11	0.53	NO
34	PRKG2	PRKG2	PRKG2	4080	0.1	0.52	NO
35	TUBAL3	TUBAL3	TUBAL3	4104	0.1	0.53	NO
36	ADRB1	ADRB1	ADRB1	4601	0.086	0.51	NO
37	ADCY4	ADCY4	ADCY4	4702	0.084	0.52	NO
38	GNAS	GNAS	GNAS	5167	0.073	0.5	NO
39	TUBB	TUBB	TUBB	5685	0.062	0.47	NO
40	PRKCG	PRKCG	PRKCG	5897	0.059	0.47	NO
41	KRAS	KRAS	KRAS	6398	0.051	0.44	NO
42	TUBA3C	TUBA3C	TUBA3C	6464	0.05	0.45	NO
43	TUBB4Q	TUBB4Q	TUBB4Q	6561	0.049	0.44	NO
44	TUBA1B	TUBA1B	TUBA1B	7119	0.042	0.42	NO
45	TUBB2A	TUBB2A	TUBB2A	7186	0.041	0.42	NO
46	MAPK1	MAPK1	MAPK1	7627	0.036	0.4	NO
47	SOS1	SOS1	SOS1	8459	0.027	0.35	NO
48	GRM5	GRM5	GRM5	8739	0.024	0.34	NO
49	LPAR1	LPAR1	LPAR1	9132	0.02	0.32	NO
50	MAP2K5	MAP2K5	MAP2K5	9531	0.016	0.3	NO
51	RAF1	RAF1	RAF1	10070	0.01	0.27	NO
52	GRB2	GRB2	GRB2	10226	0.0085	0.26	NO
53	GNAI2	GNAI2	GNAI2	10280	0.0079	0.26	NO
54	CSNK1D	CSNK1D	CSNK1D	10541	0.005	0.25	NO
55	NRAS	NRAS	NRAS	10873	0.0016	0.23	NO
56	HRAS	HRAS	HRAS	11390	-0.0043	0.2	NO
57	MAP3K2	MAP3K2	MAP3K2	11485	-0.0056	0.2	NO
58	MAPK7	MAPK7	MAPK7	11671	-0.0078	0.19	NO
59	TUBB2C	TUBB2C	TUBB2C	11886	-0.01	0.18	NO
60	CDK1	CDK1	CDK1	11903	-0.01	0.18	NO
61	ITPR1	ITPR1	ITPR1	11942	-0.011	0.18	NO
62	MAP2K2	MAP2K2	MAP2K2	12197	-0.014	0.16	NO
63	GNA11	GNA11	GNA11	12252	-0.015	0.16	NO
64	GNAI3	GNAI3	GNAI3	12458	-0.018	0.15	NO
65	PRKCA	PRKCA	PRKCA	12571	-0.019	0.15	NO
66	PRKACA	PRKACA	PRKACA	12641	-0.02	0.14	NO
67	TUBA1C	TUBA1C	TUBA1C	13125	-0.028	0.12	NO
68	SRC	SRC	SRC	13153	-0.028	0.12	NO
69	ADCY6	ADCY6	ADCY6	13817	-0.041	0.09	NO
70	GNAQ	GNAQ	GNAQ	14074	-0.047	0.08	NO
71	SOS2	SOS2	SOS2	14218	-0.05	0.077	NO
72	PDGFA	PDGFA	PDGFA	14359	-0.053	0.074	NO
73	MAPK3	MAPK3	MAPK3	14457	-0.056	0.074	NO
74	MAP2K1	MAP2K1	MAP2K1	14637	-0.061	0.07	NO
75	ITPR3	ITPR3	ITPR3	14946	-0.07	0.059	NO
76	ITPR2	ITPR2	ITPR2	14986	-0.072	0.064	NO
77	PLCB3	PLCB3	PLCB3	15034	-0.073	0.068	NO
78	TUBB6	TUBB6	TUBB6	15283	-0.083	0.062	NO
79	PLCB2	PLCB2	PLCB2	15313	-0.084	0.068	NO
80	GNAI1	GNAI1	GNAI1	15615	-0.096	0.061	NO
81	TJP1	TJP1	TJP1	15681	-0.098	0.066	NO
82	PRKCB	PRKCB	PRKCB	15840	-0.11	0.067	NO
83	ADCY9	ADCY9	ADCY9	15904	-0.11	0.074	NO
84	ADCY7	ADCY7	ADCY7	16291	-0.13	0.065	NO
85	TUBA4A	TUBA4A	TUBA4A	17178	-0.19	0.034	NO
86	EGFR	EGFR	EGFR	17398	-0.22	0.043	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 NFAT PATHWAY.

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

genes ES table in pathway: BIOCARTA WNT PATHWAY

Table 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	FGF13	FGF13	FGF13	34	0.56	0.06	YES
2	FGFR1	FGFR1	FGFR1	125	0.45	0.11	YES
3	PDGFD	PDGFD	PDGFD	219	0.41	0.15	YES
4	FGF14	FGF14	FGF14	408	0.36	0.18	YES
5	FGF18	FGF18	FGF18	565	0.34	0.21	YES
6	FGF12	FGF12	FGF12	619	0.33	0.24	YES
7	IGF1	IGF1	IGF1	625	0.33	0.28	YES
8	AKT3	AKT3	AKT3	665	0.32	0.31	YES
9	FGF9	FGF9	FGF9	791	0.3	0.34	YES
10	HGF	HGF	HGF	870	0.3	0.36	YES
11	PDGFRA	PDGFRA	PDGFRA	1127	0.27	0.38	YES
12	FGF7	FGF7	FGF7	1244	0.26	0.4	YES
13	PDGFC	PDGFC	PDGFC	1350	0.25	0.42	YES
14	FGF2	FGF2	FGF2	1351	0.25	0.45	YES
15	EGF	EGF	EGF	1808	0.21	0.45	YES
16	PIK3R1	PIK3R1	PIK3R1	1834	0.21	0.47	YES
17	FGF17	FGF17	FGF17	1857	0.21	0.5	YES
18	FGF1	FGF1	FGF1	2021	0.2	0.51	YES
19	FGF19	FGF19	FGF19	2279	0.18	0.52	YES
20	PDGFRB	PDGFRB	PDGFRB	2319	0.18	0.53	YES
21	PDGFB	PDGFB	PDGFB	2889	0.15	0.52	YES
22	FGF10	FGF10	FGF10	2903	0.15	0.54	YES
23	BRAF	BRAF	BRAF	3088	0.14	0.54	YES
24	MITF	MITF	MITF	3298	0.13	0.54	YES
25	PIK3R3	PIK3R3	PIK3R3	3607	0.12	0.54	NO
26	FGF8	FGF8	FGF8	3876	0.11	0.54	NO
27	E2F3	E2F3	E2F3	4707	0.084	0.5	NO
28	CDK4	CDK4	CDK4	4799	0.081	0.5	NO
29	KRAS	KRAS	KRAS	6398	0.051	0.42	NO
30	TP53	TP53	TP53	7361	0.039	0.37	NO
31	MAPK1	MAPK1	MAPK1	7627	0.036	0.36	NO
32	PIK3R2	PIK3R2	PIK3R2	8069	0.031	0.34	NO
33	PIK3CA	PIK3CA	PIK3CA	8365	0.028	0.33	NO
34	AKT1	AKT1	AKT1	9331	0.018	0.28	NO
35	PIK3CB	PIK3CB	PIK3CB	9676	0.014	0.26	NO
36	BAD	BAD	BAD	9903	0.012	0.25	NO
37	RAF1	RAF1	RAF1	10070	0.01	0.24	NO
38	AKT2	AKT2	AKT2	10426	0.0061	0.22	NO
39	CDK6	CDK6	CDK6	10741	0.0031	0.2	NO
40	NRAS	NRAS	NRAS	10873	0.0016	0.2	NO
41	FGF22	FGF22	FGF22	10986	0.00039	0.19	NO
42	HRAS	HRAS	HRAS	11390	-0.0043	0.17	NO
43	CDH1	CDH1	CDH1	12062	-0.012	0.13	NO
44	MAP2K2	MAP2K2	MAP2K2	12197	-0.014	0.13	NO
45	MDM2	MDM2	MDM2	12628	-0.02	0.11	NO
46	ARAF	ARAF	ARAF	13681	-0.038	0.052	NO
47	CCND1	CCND1	CCND1	13720	-0.039	0.055	NO
48	IGF1R	IGF1R	IGF1R	13907	-0.043	0.049	NO
49	FGF5	FGF5	FGF5	14006	-0.045	0.049	NO
50	E2F2	E2F2	E2F2	14103	-0.048	0.049	NO
51	PDGFA	PDGFA	PDGFA	14359	-0.053	0.041	NO
52	MAPK3	MAPK3	MAPK3	14457	-0.056	0.042	NO
53	MAP2K1	MAP2K1	MAP2K1	14637	-0.061	0.039	NO
54	PIK3R5	PIK3R5	PIK3R5	14806	-0.066	0.037	NO
55	PTEN	PTEN	PTEN	14909	-0.069	0.039	NO
56	RB1	RB1	RB1	15252	-0.081	0.029	NO
57	CDKN1A	CDKN1A	CDKN1A	15794	-0.1	0.011	NO
58	PIK3CG	PIK3CG	PIK3CG	16589	-0.15	-0.017	NO
59	PIK3CD	PIK3CD	PIK3CD	16853	-0.16	-0.013	NO
60	MET	MET	MET	16896	-0.17	0.0039	NO
61	FGF11	FGF11	FGF11	16965	-0.18	0.02	NO
62	CDKN2A	CDKN2A	CDKN2A	17200	-0.2	0.029	NO
63	EGFR	EGFR	EGFR	17398	-0.22	0.043	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 WNT PATHWAY.

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

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE METABOLISM

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	PLCB4	PLCB4	PLCB4	189	0.42	0.019	YES
2	KCNMA1	KCNMA1	KCNMA1	241	0.4	0.044	YES
3	KCNMB2	KCNMB2	KCNMB2	281	0.39	0.069	YES
4	GUCY1B3	GUCY1B3	GUCY1B3	290	0.39	0.096	YES
5	MYH11	MYH11	MYH11	334	0.38	0.12	YES
6	ACTG2	ACTG2	ACTG2	373	0.37	0.14	YES
7	PLA2G5	PLA2G5	PLA2G5	376	0.37	0.17	YES
8	GUCY1A3	GUCY1A3	GUCY1A3	437	0.36	0.19	YES
9	NPR2	NPR2	NPR2	484	0.35	0.21	YES
10	KCNMB4	KCNMB4	KCNMB4	499	0.35	0.24	YES
11	ADCY5	ADCY5	ADCY5	668	0.32	0.25	YES
12	KCNMB1	KCNMB1	KCNMB1	723	0.31	0.27	YES
13	PPP1R14A	PPP1R14A	PPP1R14A	755	0.31	0.29	YES
14	ADCY1	ADCY1	ADCY1	849	0.3	0.3	YES
15	ADCY2	ADCY2	ADCY2	894	0.29	0.32	YES
16	PRKG1	PRKG1	PRKG1	920	0.29	0.34	YES
17	ACTA2	ACTA2	ACTA2	968	0.28	0.36	YES
18	EDNRA	EDNRA	EDNRA	988	0.28	0.37	YES
19	MYLK	MYLK	MYLK	1014	0.28	0.39	YES
20	AGTR1	AGTR1	AGTR1	1034	0.28	0.41	YES
21	GUCY1A2	GUCY1A2	GUCY1A2	1036	0.28	0.43	YES
22	CACNA1C	CACNA1C	CACNA1C	1456	0.24	0.42	YES
23	MRVI1	MRVI1	MRVI1	1662	0.22	0.43	YES
24	MYLK3	MYLK3	MYLK3	1793	0.21	0.44	YES
25	MYL9	MYL9	MYL9	1960	0.2	0.44	YES
26	RAMP2	RAMP2	RAMP2	1966	0.2	0.45	YES
27	CALCRL	CALCRL	CALCRL	2156	0.19	0.46	YES
28	CACNA1D	CACNA1D	CACNA1D	2266	0.18	0.46	YES
29	PTGIR	PTGIR	PTGIR	2431	0.17	0.47	YES
30	ADORA2A	ADORA2A	ADORA2A	2562	0.17	0.47	YES
31	PLCB1	PLCB1	PLCB1	2564	0.17	0.48	YES
32	ADRA1B	ADRA1B	ADRA1B	2579	0.16	0.49	YES
33	MYLK2	MYLK2	MYLK2	2764	0.15	0.49	YES
34	PRKACB	PRKACB	PRKACB	2852	0.15	0.5	YES
35	PLA2G6	PLA2G6	PLA2G6	2891	0.15	0.51	YES
36	AVPR1A	AVPR1A	AVPR1A	2966	0.14	0.51	YES
37	PRKX	PRKX	PRKX	2977	0.14	0.52	YES
38	CALD1	CALD1	CALD1	3076	0.14	0.53	YES
39	BRAF	BRAF	BRAF	3088	0.14	0.54	YES
40	RAMP3	RAMP3	RAMP3	3154	0.14	0.54	YES
41	CALML6	CALML6	CALML6	3290	0.13	0.54	YES
42	PLA2G2A	PLA2G2A	PLA2G2A	3364	0.13	0.55	YES
43	PLA2G1B	PLA2G1B	PLA2G1B	3661	0.12	0.54	NO
44	MYL6B	MYL6B	MYL6B	3844	0.11	0.54	NO
45	ADRA1D	ADRA1D	ADRA1D	4405	0.092	0.51	NO
46	ADCY4	ADCY4	ADCY4	4702	0.084	0.5	NO
47	GNAS	GNAS	GNAS	5167	0.073	0.48	NO
48	PRKCG	PRKCG	PRKCG	5897	0.059	0.44	NO
49	ROCK1	ROCK1	ROCK1	5962	0.058	0.44	NO
50	PLA2G4A	PLA2G4A	PLA2G4A	5977	0.058	0.45	NO
51	KCNMB3	KCNMB3	KCNMB3	6071	0.056	0.45	NO
52	PLA2G12A	PLA2G12A	PLA2G12A	6140	0.055	0.45	NO
53	GNA12	GNA12	GNA12	6338	0.052	0.44	NO
54	PLA2G3	PLA2G3	PLA2G3	6538	0.049	0.43	NO
55	RAMP1	RAMP1	RAMP1	7070	0.042	0.4	NO
56	GNA13	GNA13	GNA13	7305	0.04	0.4	NO
57	PPP1R12A	PPP1R12A	PPP1R12A	7336	0.039	0.4	NO
58	PPP1R12B	PPP1R12B	PPP1R12B	7488	0.038	0.39	NO
59	CALML5	CALML5	CALML5	7560	0.037	0.39	NO
60	MAPK1	MAPK1	MAPK1	7627	0.036	0.39	NO
61	PPP1CC	PPP1CC	PPP1CC	7710	0.035	0.39	NO
62	CALM2	CALM2	CALM2	8275	0.029	0.36	NO
63	NPR1	NPR1	NPR1	9161	0.02	0.31	NO
64	PPP1CB	PPP1CB	PPP1CB	10057	0.01	0.26	NO
65	RAF1	RAF1	RAF1	10070	0.01	0.26	NO
66	CYP4A22	CYP4A22	CYP4A22	10279	0.0079	0.25	NO
67	CALM1	CALM1	CALM1	10411	0.0063	0.24	NO
68	CALML3	CALML3	CALML3	10778	0.0025	0.22	NO
69	CALM3	CALM3	CALM3	10845	0.0019	0.22	NO
70	ARHGEF11	ARHGEF11	ARHGEF11	11326	-0.0036	0.19	NO
71	MYL6	MYL6	MYL6	11656	-0.0077	0.18	NO
72	ITPR1	ITPR1	ITPR1	11942	-0.011	0.16	NO
73	MAP2K2	MAP2K2	MAP2K2	12197	-0.014	0.15	NO
74	GNA11	GNA11	GNA11	12252	-0.015	0.14	NO
75	ARHGEF12	ARHGEF12	ARHGEF12	12511	-0.018	0.13	NO
76	PRKCA	PRKCA	PRKCA	12571	-0.019	0.13	NO
77	CACNA1F	CACNA1F	CACNA1F	12607	-0.02	0.13	NO
78	JMJD7-PLA2G4B	JMJD7-PLA2G4B	JMJD7-PLA2G4B	12620	-0.02	0.13	NO
79	PRKACA	PRKACA	PRKACA	12641	-0.02	0.13	NO
80	RHOA	RHOA	RHOA	12953	-0.025	0.12	NO
81	PPP1CA	PPP1CA	PPP1CA	12956	-0.025	0.12	NO
82	PRKCE	PRKCE	PRKCE	13298	-0.031	0.1	NO
83	ROCK2	ROCK2	ROCK2	13510	-0.035	0.09	NO
84	CYP4A11	CYP4A11	CYP4A11	13590	-0.036	0.089	NO
85	ARAF	ARAF	ARAF	13681	-0.038	0.086	NO
86	ADCY6	ADCY6	ADCY6	13817	-0.041	0.082	NO
87	PRKCQ	PRKCQ	PRKCQ	13986	-0.045	0.075	NO
88	GNAQ	GNAQ	GNAQ	14074	-0.047	0.074	NO
89	PLA2G10	PLA2G10	PLA2G10	14409	-0.055	0.059	NO
90	MAPK3	MAPK3	MAPK3	14457	-0.056	0.06	NO
91	ARHGEF1	ARHGEF1	ARHGEF1	14506	-0.057	0.062	NO
92	MAP2K1	MAP2K1	MAP2K1	14637	-0.061	0.059	NO
93	ITPR3	ITPR3	ITPR3	14946	-0.07	0.047	NO
94	ITPR2	ITPR2	ITPR2	14986	-0.072	0.049	NO
95	PLCB3	PLCB3	PLCB3	15034	-0.073	0.052	NO
96	PRKCD	PRKCD	PRKCD	15077	-0.075	0.055	NO
97	PLCB2	PLCB2	PLCB2	15313	-0.084	0.048	NO
98	PRKCH	PRKCH	PRKCH	15446	-0.089	0.046	NO
99	PLA2G2D	PLA2G2D	PLA2G2D	15617	-0.096	0.044	NO
100	AVPR1B	AVPR1B	AVPR1B	15731	-0.1	0.044	NO
101	PRKCB	PRKCB	PRKCB	15840	-0.11	0.046	NO
102	ADCY9	ADCY9	ADCY9	15904	-0.11	0.05	NO
103	ADCY7	ADCY7	ADCY7	16291	-0.13	0.038	NO
104	ADORA2B	ADORA2B	ADORA2B	17377	-0.22	-0.0073	NO
105	PLA2G2F	PLA2G2F	PLA2G2F	17883	-0.32	-0.013	NO
106	PLA2G4E	PLA2G4E	PLA2G4E	18061	-0.41	0.006	NO

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

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYSTEINE AND METHIONINE 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 SPLICEOSOME

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	IGF1	IGF1	IGF1	625	0.33	0.036	YES
2	NFATC4	NFATC4	NFATC4	833	0.3	0.09	YES
3	NKX2-5	NKX2-5	NKX2-5	1015	0.28	0.14	YES
4	PRKAR2B	PRKAR2B	PRKAR2B	1079	0.27	0.2	YES
5	HAND2	HAND2	HAND2	1174	0.26	0.25	YES
6	HAND1	HAND1	HAND1	1336	0.25	0.29	YES
7	FGF2	FGF2	FGF2	1351	0.25	0.35	YES
8	PIK3R1	PIK3R1	PIK3R1	1834	0.21	0.37	YES
9	CAMK4	CAMK4	CAMK4	1859	0.21	0.41	YES
10	GATA4	GATA4	GATA4	2016	0.2	0.44	YES
11	CAMK1G	CAMK1G	CAMK1G	2425	0.17	0.46	YES
12	AGT	AGT	AGT	2810	0.15	0.47	YES
13	PRKACB	PRKACB	PRKACB	2852	0.15	0.5	YES
14	ACTA1	ACTA1	ACTA1	3041	0.14	0.52	YES
15	CAMK1	CAMK1	CAMK1	5443	0.067	0.4	NO
16	NFATC1	NFATC1	NFATC1	6346	0.052	0.37	NO
17	FKBP1A	FKBP1A	FKBP1A	6660	0.048	0.36	NO
18	PRKAR1B	PRKAR1B	PRKAR1B	7158	0.041	0.34	NO
19	GSK3B	GSK3B	GSK3B	7254	0.04	0.34	NO
20	MAPK1	MAPK1	MAPK1	7627	0.036	0.33	NO
21	NFATC3	NFATC3	NFATC3	7717	0.035	0.33	NO
22	PPP3CB	PPP3CB	PPP3CB	7981	0.032	0.33	NO
23	CALM2	CALM2	CALM2	8275	0.029	0.32	NO
24	PIK3CA	PIK3CA	PIK3CA	8365	0.028	0.32	NO
25	CREBBP	CREBBP	CREBBP	8447	0.027	0.32	NO
26	LIF	LIF	LIF	8569	0.026	0.32	NO
27	NPPA	NPPA	NPPA	8604	0.026	0.32	NO
28	AKT1	AKT1	AKT1	9331	0.018	0.29	NO
29	RAF1	RAF1	RAF1	10070	0.01	0.25	NO
30	MAPK8	MAPK8	MAPK8	10373	0.0067	0.23	NO
31	CALM1	CALM1	CALM1	10411	0.0063	0.23	NO
32	PRKAR1A	PRKAR1A	PRKAR1A	10699	0.0034	0.22	NO
33	CALM3	CALM3	CALM3	10845	0.0019	0.21	NO
34	PPP3CA	PPP3CA	PPP3CA	10974	0.00049	0.2	NO
35	HRAS	HRAS	HRAS	11390	-0.0043	0.18	NO
36	CTF1	CTF1	CTF1	11452	-0.0052	0.18	NO
37	MAPK14	MAPK14	MAPK14	11462	-0.0054	0.18	NO
38	CALR	CALR	CALR	11725	-0.0084	0.16	NO
39	EDN1	EDN1	EDN1	12035	-0.012	0.15	NO
40	CSNK1A1	CSNK1A1	CSNK1A1	12756	-0.022	0.12	NO
41	RPS6KB1	RPS6KB1	RPS6KB1	12919	-0.024	0.11	NO
42	F2	F2	F2	13347	-0.032	0.096	NO
43	PPP3CC	PPP3CC	PPP3CC	13944	-0.044	0.072	NO
44	MAPK3	MAPK3	MAPK3	14457	-0.056	0.056	NO
45	MAP2K1	MAP2K1	MAP2K1	14637	-0.061	0.06	NO
46	PRKAR2A	PRKAR2A	PRKAR2A	15632	-0.096	0.026	NO
47	NFATC2	NFATC2	NFATC2	16039	-0.12	0.028	NO
48	PIK3CG	PIK3CG	PIK3CG	16589	-0.15	0.03	NO
49	HBEGF	HBEGF	HBEGF	17662	-0.26	0.028	NO

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

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

genes ES table in pathway: KEGG OOCYTE MEIOSIS

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	CACNB4	CACNB4	CACNB4	127	0.45	0.064	YES
2	CACNA2D2	CACNA2D2	CACNA2D2	320	0.38	0.11	YES
3	ATP1B2	ATP1B2	ATP1B2	496	0.35	0.16	YES
4	COX4I2	COX4I2	COX4I2	592	0.33	0.2	YES
5	COX7A1	COX7A1	COX7A1	1128	0.27	0.22	YES
6	CACNA2D3	CACNA2D3	CACNA2D3	1165	0.26	0.26	YES
7	CACNA2D1	CACNA2D1	CACNA2D1	1169	0.26	0.3	YES
8	ACTC1	ACTC1	ACTC1	1203	0.26	0.34	YES
9	CACNA1C	CACNA1C	CACNA1C	1456	0.24	0.36	YES
10	CACNB2	CACNB2	CACNB2	1763	0.22	0.38	YES
11	MYL3	MYL3	MYL3	1823	0.21	0.41	YES
12	RYR2	RYR2	RYR2	2107	0.19	0.42	YES
13	CACNA1D	CACNA1D	CACNA1D	2266	0.18	0.44	YES
14	SLC8A1	SLC8A1	SLC8A1	2286	0.18	0.47	YES
15	COX8C	COX8C	COX8C	2452	0.17	0.49	YES
16	ATP1A2	ATP1A2	ATP1A2	2681	0.16	0.5	YES
17	CACNG4	CACNG4	CACNG4	2760	0.16	0.52	YES
18	MYH6	MYH6	MYH6	3028	0.14	0.53	YES
19	TPM1	TPM1	TPM1	4595	0.086	0.46	NO
20	ATP1A3	ATP1A3	ATP1A3	5453	0.067	0.42	NO
21	CACNB3	CACNB3	CACNB3	5760	0.061	0.41	NO
22	TPM2	TPM2	TPM2	5891	0.059	0.41	NO
23	CACNG1	CACNG1	CACNG1	6162	0.054	0.41	NO
24	COX7A2L	COX7A2L	COX7A2L	6240	0.053	0.41	NO
25	CACNG6	CACNG6	CACNG6	6983	0.044	0.38	NO
26	ATP1A4	ATP1A4	ATP1A4	7218	0.041	0.37	NO
27	COX7A2	COX7A2	COX7A2	7536	0.037	0.36	NO
28	UQCR10	UQCR10	UQCR10	8003	0.032	0.34	NO
29	UQCRFS1	UQCRFS1	UQCRFS1	8376	0.028	0.32	NO
30	COX6A1	COX6A1	COX6A1	8677	0.025	0.31	NO
31	UQCRB	UQCRB	UQCRB	8932	0.022	0.3	NO
32	COX7C	COX7C	COX7C	9234	0.019	0.28	NO
33	COX6C	COX6C	COX6C	9284	0.018	0.28	NO
34	MYH7	MYH7	MYH7	9413	0.017	0.28	NO
35	COX6A2	COX6A2	COX6A2	9448	0.017	0.28	NO
36	CYC1	CYC1	CYC1	9800	0.013	0.26	NO
37	UQCR11	UQCR11	UQCR11	10071	0.01	0.25	NO
38	UQCRH	UQCRH	UQCRH	10078	0.01	0.25	NO
39	UQCRHL	UQCRHL	UQCRHL	10197	0.0088	0.25	NO
40	COX6B1	COX6B1	COX6B1	10264	0.0081	0.24	NO
41	ATP1A1	ATP1A1	ATP1A1	10742	0.0031	0.22	NO
42	FXYD2	FXYD2	FXYD2	10924	0.00094	0.21	NO
43	COX5B	COX5B	COX5B	10925	0.00093	0.21	NO
44	CACNB1	CACNB1	CACNB1	11037	-0.00013	0.2	NO
45	COX7B	COX7B	COX7B	11623	-0.0073	0.17	NO
46	COX8A	COX8A	COX8A	11855	-0.0099	0.16	NO
47	COX4I1	COX4I1	COX4I1	11916	-0.011	0.16	NO
48	SLC9A6	SLC9A6	SLC9A6	11975	-0.011	0.16	NO
49	UQCRQ	UQCRQ	UQCRQ	11991	-0.011	0.16	NO
50	ATP1B3	ATP1B3	ATP1B3	12345	-0.016	0.14	NO
51	COX5A	COX5A	COX5A	12349	-0.016	0.14	NO
52	UQCRC1	UQCRC1	UQCRC1	12417	-0.017	0.14	NO
53	CACNA1F	CACNA1F	CACNA1F	12607	-0.02	0.13	NO
54	TPM3	TPM3	TPM3	13381	-0.032	0.097	NO
55	ATP1B1	ATP1B1	ATP1B1	13394	-0.032	0.1	NO
56	MYL2	MYL2	MYL2	13756	-0.04	0.087	NO
57	ATP2A2	ATP2A2	ATP2A2	13940	-0.044	0.084	NO
58	TNNT2	TNNT2	TNNT2	14041	-0.046	0.086	NO
59	TPM4	TPM4	TPM4	15073	-0.075	0.041	NO
60	SLC9A1	SLC9A1	SLC9A1	15104	-0.076	0.051	NO
61	TNNI3	TNNI3	TNNI3	15423	-0.088	0.047	NO
62	TNNC1	TNNC1	TNNC1	16226	-0.13	0.022	NO
63	CACNA2D4	CACNA2D4	CACNA2D4	16891	-0.17	0.012	NO
64	COX6B2	COX6B2	COX6B2	17999	-0.37	0.0094	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 OOCYTE MEIOSIS.

Figure S10. 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

genes ES table in pathway: KEGG CARDIAC MUSCLE CONTRACTION

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	IGF1	IGF1	IGF1	625	0.33	0.019	YES
2	AKT3	AKT3	AKT3	665	0.32	0.068	YES
3	ADCY5	ADCY5	ADCY5	668	0.32	0.12	YES
4	CPEB1	CPEB1	CPEB1	796	0.3	0.16	YES
5	ADCY1	ADCY1	ADCY1	849	0.3	0.21	YES
6	ADCY2	ADCY2	ADCY2	894	0.29	0.25	YES
7	RPS6KA6	RPS6KA6	RPS6KA6	1365	0.25	0.27	YES
8	MAPK12	MAPK12	MAPK12	1707	0.22	0.28	YES
9	PIK3R1	PIK3R1	PIK3R1	1834	0.21	0.31	YES
10	SPDYA	SPDYA	SPDYA	2426	0.17	0.31	YES
11	PRKACB	PRKACB	PRKACB	2852	0.15	0.31	YES
12	PDE3A	PDE3A	PDE3A	2931	0.14	0.33	YES
13	PRKX	PRKX	PRKX	2977	0.14	0.35	YES
14	PGR	PGR	PGR	3020	0.14	0.37	YES
15	BRAF	BRAF	BRAF	3088	0.14	0.39	YES
16	PIK3R3	PIK3R3	PIK3R3	3607	0.12	0.38	NO
17	PDE3B	PDE3B	PDE3B	3970	0.11	0.38	NO
18	CCNB3	CCNB3	CCNB3	4607	0.086	0.36	NO
19	ADCY4	ADCY4	ADCY4	4702	0.084	0.36	NO
20	MAD2L2	MAD2L2	MAD2L2	5135	0.074	0.35	NO
21	CDC26	CDC26	CDC26	5975	0.058	0.32	NO
22	BUB1	BUB1	BUB1	6339	0.052	0.3	NO
23	KRAS	KRAS	KRAS	6398	0.051	0.31	NO
24	ANAPC1	ANAPC1	ANAPC1	6479	0.05	0.31	NO
25	ANAPC11	ANAPC11	ANAPC11	6653	0.048	0.31	NO
26	ANAPC13	ANAPC13	ANAPC13	6842	0.045	0.31	NO
27	HSP90AA1	HSP90AA1	HSP90AA1	6951	0.044	0.31	NO
28	MAPK1	MAPK1	MAPK1	7627	0.036	0.28	NO
29	MAD2L1	MAD2L1	MAD2L1	7631	0.036	0.28	NO
30	MAPK10	MAPK10	MAPK10	7702	0.035	0.28	NO
31	ANAPC5	ANAPC5	ANAPC5	7820	0.034	0.28	NO
32	PIK3R2	PIK3R2	PIK3R2	8069	0.031	0.28	NO
33	CCNA1	CCNA1	CCNA1	8252	0.029	0.27	NO
34	PIK3CA	PIK3CA	PIK3CA	8365	0.028	0.27	NO
35	ANAPC10	ANAPC10	ANAPC10	8620	0.025	0.26	NO
36	ANAPC7	ANAPC7	ANAPC7	8764	0.024	0.25	NO
37	ANAPC4	ANAPC4	ANAPC4	8879	0.022	0.25	NO
38	FZR1	FZR1	FZR1	8956	0.022	0.25	NO
39	CDC27	CDC27	CDC27	9059	0.021	0.25	NO
40	AKT1	AKT1	AKT1	9331	0.018	0.24	NO
41	CDC25A	CDC25A	CDC25A	9521	0.016	0.23	NO
42	PIK3CB	PIK3CB	PIK3CB	9676	0.014	0.22	NO
43	RAF1	RAF1	RAF1	10070	0.01	0.2	NO
44	CDC25C	CDC25C	CDC25C	10142	0.0094	0.2	NO
45	GNAI2	GNAI2	GNAI2	10280	0.0079	0.19	NO
46	MAPK9	MAPK9	MAPK9	10351	0.007	0.19	NO
47	MAPK8	MAPK8	MAPK8	10373	0.0067	0.19	NO
48	AKT2	AKT2	AKT2	10426	0.0061	0.19	NO
49	CCNB2	CCNB2	CCNB2	10996	0.00031	0.16	NO
50	ANAPC2	ANAPC2	ANAPC2	11203	-0.0021	0.15	NO
51	PLK1	PLK1	PLK1	11359	-0.004	0.14	NO
52	CDC23	CDC23	CDC23	11408	-0.0046	0.14	NO
53	MAPK14	MAPK14	MAPK14	11462	-0.0054	0.14	NO
54	CDK2	CDK2	CDK2	11553	-0.0064	0.13	NO
55	CCNB1	CCNB1	CCNB1	11756	-0.0088	0.12	NO
56	CDK1	CDK1	CDK1	11903	-0.01	0.12	NO
57	CDC16	CDC16	CDC16	12145	-0.013	0.1	NO
58	MAPK11	MAPK11	MAPK11	12161	-0.013	0.1	NO
59	GNAI3	GNAI3	GNAI3	12458	-0.018	0.092	NO
60	PRKACA	PRKACA	PRKACA	12641	-0.02	0.085	NO
61	CCNA2	CCNA2	CCNA2	13046	-0.026	0.067	NO
62	SPDYC	SPDYC	SPDYC	13061	-0.027	0.07	NO
63	ADCY3	ADCY3	ADCY3	13196	-0.029	0.068	NO
64	RPS6KA3	RPS6KA3	RPS6KA3	13535	-0.035	0.055	NO
65	ARAF	ARAF	ARAF	13681	-0.038	0.053	NO
66	CDC25B	CDC25B	CDC25B	13786	-0.04	0.054	NO
67	ADCY6	ADCY6	ADCY6	13817	-0.041	0.059	NO
68	IGF1R	IGF1R	IGF1R	13907	-0.043	0.061	NO
69	RPS6KA2	RPS6KA2	RPS6KA2	14161	-0.049	0.055	NO
70	PKMYT1	PKMYT1	PKMYT1	14392	-0.054	0.051	NO
71	MAPK3	MAPK3	MAPK3	14457	-0.056	0.056	NO
72	MAP2K1	MAP2K1	MAP2K1	14637	-0.061	0.057	NO
73	PIK3R5	PIK3R5	PIK3R5	14806	-0.066	0.058	NO
74	RPS6KA1	RPS6KA1	RPS6KA1	14874	-0.068	0.065	NO
75	MAPK13	MAPK13	MAPK13	14900	-0.068	0.075	NO
76	GNAI1	GNAI1	GNAI1	15615	-0.096	0.051	NO
77	ADCY9	ADCY9	ADCY9	15904	-0.11	0.053	NO
78	ADCY7	ADCY7	ADCY7	16291	-0.13	0.053	NO
79	PIK3CG	PIK3CG	PIK3CG	16589	-0.15	0.06	NO
80	PIK3CD	PIK3CD	PIK3CD	16853	-0.16	0.073	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 CARDIAC MUSCLE CONTRACTION.

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

genes ES table in pathway: KEGG VASCULAR SMOOTH MUSCLE CONTRACTION

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	FGFR1	FGFR1	FGFR1	125	0.45	0.048	YES
2	LEF1	LEF1	LEF1	146	0.44	0.1	YES
3	PDGFD	PDGFD	PDGFD	219	0.41	0.15	YES
4	IGF1	IGF1	IGF1	625	0.33	0.16	YES
5	AKT3	AKT3	AKT3	665	0.32	0.2	YES
6	BCL2	BCL2	BCL2	930	0.29	0.22	YES
7	PDGFRA	PDGFRA	PDGFRA	1127	0.27	0.24	YES
8	PDGFC	PDGFC	PDGFC	1350	0.25	0.26	YES
9	AR	AR	AR	1428	0.24	0.29	YES
10	TCF7L1	TCF7L1	TCF7L1	1610	0.23	0.31	YES
11	EGF	EGF	EGF	1808	0.21	0.32	YES
12	PIK3R1	PIK3R1	PIK3R1	1834	0.21	0.34	YES
13	CREB5	CREB5	CREB5	1986	0.2	0.36	YES
14	FGFR2	FGFR2	FGFR2	1990	0.2	0.39	YES
15	PDGFRB	PDGFRB	PDGFRB	2319	0.18	0.39	YES
16	PDGFB	PDGFB	PDGFB	2889	0.15	0.38	YES
17	BRAF	BRAF	BRAF	3088	0.14	0.38	YES
18	SRD5A2	SRD5A2	SRD5A2	3293	0.13	0.39	YES
19	INSRR	INSRR	INSRR	3316	0.13	0.4	YES
20	PIK3R3	PIK3R3	PIK3R3	3607	0.12	0.4	NO
21	TCF7	TCF7	TCF7	3833	0.11	0.4	NO
22	E2F3	E2F3	E2F3	4707	0.084	0.36	NO
23	CREB3L2	CREB3L2	CREB3L2	4915	0.079	0.36	NO
24	CDKN1B	CDKN1B	CDKN1B	5294	0.07	0.35	NO
25	CTNNB1	CTNNB1	CTNNB1	5757	0.061	0.33	NO
26	KRAS	KRAS	KRAS	6398	0.051	0.3	NO
27	HSP90AA1	HSP90AA1	HSP90AA1	6951	0.044	0.28	NO
28	CREB1	CREB1	CREB1	6997	0.043	0.28	NO
29	GSK3B	GSK3B	GSK3B	7254	0.04	0.27	NO
30	TP53	TP53	TP53	7361	0.039	0.27	NO
31	E2F1	E2F1	E2F1	7409	0.039	0.27	NO
32	CREB3L4	CREB3L4	CREB3L4	7517	0.037	0.27	NO
33	HSP90B1	HSP90B1	HSP90B1	7623	0.036	0.27	NO
34	MAPK1	MAPK1	MAPK1	7627	0.036	0.27	NO
35	EP300	EP300	EP300	7872	0.033	0.26	NO
36	PIK3R2	PIK3R2	PIK3R2	8069	0.031	0.26	NO
37	ATF4	ATF4	ATF4	8123	0.03	0.26	NO
38	CREB3L1	CREB3L1	CREB3L1	8149	0.03	0.26	NO
39	PIK3CA	PIK3CA	PIK3CA	8365	0.028	0.25	NO
40	CREBBP	CREBBP	CREBBP	8447	0.027	0.25	NO
41	SOS1	SOS1	SOS1	8459	0.027	0.25	NO
42	KLK3	KLK3	KLK3	8615	0.025	0.25	NO
43	CREB3	CREB3	CREB3	8831	0.023	0.24	NO
44	CCNE2	CCNE2	CCNE2	9142	0.02	0.22	NO
45	AKT1	AKT1	AKT1	9331	0.018	0.22	NO
46	PIK3CB	PIK3CB	PIK3CB	9676	0.014	0.2	NO
47	BAD	BAD	BAD	9903	0.012	0.19	NO
48	RAF1	RAF1	RAF1	10070	0.01	0.18	NO
49	MTOR	MTOR	MTOR	10214	0.0086	0.17	NO
50	GRB2	GRB2	GRB2	10226	0.0085	0.17	NO
51	TCF7L2	TCF7L2	TCF7L2	10258	0.0082	0.17	NO
52	AKT2	AKT2	AKT2	10426	0.0061	0.16	NO
53	CCNE1	CCNE1	CCNE1	10591	0.0046	0.16	NO
54	NRAS	NRAS	NRAS	10873	0.0016	0.14	NO
55	HRAS	HRAS	HRAS	11390	-0.0043	0.11	NO
56	CDK2	CDK2	CDK2	11553	-0.0064	0.1	NO
57	FOXO1	FOXO1	FOXO1	12067	-0.012	0.076	NO
58	MAP2K2	MAP2K2	MAP2K2	12197	-0.014	0.071	NO
59	CASP9	CASP9	CASP9	12264	-0.015	0.069	NO
60	IKBKB	IKBKB	IKBKB	12405	-0.017	0.064	NO
61	MDM2	MDM2	MDM2	12628	-0.02	0.054	NO
62	RELA	RELA	RELA	12674	-0.02	0.054	NO
63	PDPK1	PDPK1	PDPK1	13142	-0.028	0.031	NO
64	IKBKG	IKBKG	IKBKG	13396	-0.032	0.021	NO
65	ARAF	ARAF	ARAF	13681	-0.038	0.01	NO
66	CCND1	CCND1	CCND1	13720	-0.039	0.013	NO
67	CHUK	CHUK	CHUK	13893	-0.043	0.0086	NO
68	IGF1R	IGF1R	IGF1R	13907	-0.043	0.013	NO
69	E2F2	E2F2	E2F2	14103	-0.048	0.0082	NO
70	NKX3-1	NKX3-1	NKX3-1	14112	-0.048	0.014	NO
71	SOS2	SOS2	SOS2	14218	-0.05	0.014	NO
72	GSTP1	GSTP1	GSTP1	14278	-0.052	0.017	NO
73	PDGFA	PDGFA	PDGFA	14359	-0.053	0.019	NO
74	MAPK3	MAPK3	MAPK3	14457	-0.056	0.021	NO
75	NFKBIA	NFKBIA	NFKBIA	14606	-0.06	0.02	NO
76	MAP2K1	MAP2K1	MAP2K1	14637	-0.061	0.026	NO
77	PIK3R5	PIK3R5	PIK3R5	14806	-0.066	0.024	NO
78	PTEN	PTEN	PTEN	14909	-0.069	0.027	NO
79	ERBB2	ERBB2	ERBB2	15111	-0.076	0.025	NO
80	RB1	RB1	RB1	15252	-0.081	0.028	NO
81	NFKB1	NFKB1	NFKB1	15268	-0.082	0.037	NO
82	CREB3L3	CREB3L3	CREB3L3	15400	-0.087	0.04	NO
83	CDKN1A	CDKN1A	CDKN1A	15794	-0.1	0.031	NO
84	PIK3CG	PIK3CG	PIK3CG	16589	-0.15	0.0052	NO
85	PIK3CD	PIK3CD	PIK3CD	16853	-0.16	0.011	NO
86	EGFR	EGFR	EGFR	17398	-0.22	0.0079	NO
87	TGFA	TGFA	TGFA	17746	-0.28	0.023	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 VASCULAR SMOOTH MUSCLE CONTRACTION.

Figure S14. 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

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	POMC	POMC	POMC	17	0.58	0.05	YES
2	FZD3	FZD3	FZD3	84	0.48	0.088	YES
3	LEF1	LEF1	LEF1	146	0.44	0.12	YES
4	FZD7	FZD7	FZD7	168	0.43	0.16	YES
5	PLCB4	PLCB4	PLCB4	189	0.42	0.19	YES
6	KIT	KIT	KIT	233	0.4	0.23	YES
7	WNT6	WNT6	WNT6	493	0.35	0.24	YES
8	TYRP1	TYRP1	TYRP1	603	0.33	0.26	YES
9	ADCY5	ADCY5	ADCY5	668	0.32	0.29	YES
10	ADCY1	ADCY1	ADCY1	849	0.3	0.3	YES
11	ADCY2	ADCY2	ADCY2	894	0.29	0.33	YES
12	CAMK2B	CAMK2B	CAMK2B	1274	0.26	0.33	YES
13	WNT2	WNT2	WNT2	1305	0.25	0.35	YES
14	EDNRB	EDNRB	EDNRB	1321	0.25	0.37	YES
15	TCF7L1	TCF7L1	TCF7L1	1610	0.23	0.37	YES
16	WNT5B	WNT5B	WNT5B	1723	0.22	0.39	YES
17	GNAO1	GNAO1	GNAO1	1771	0.22	0.4	YES
18	FZD2	FZD2	FZD2	1785	0.22	0.42	YES
19	WNT5A	WNT5A	WNT5A	1819	0.21	0.44	YES
20	WNT11	WNT11	WNT11	2554	0.17	0.41	YES
21	PLCB1	PLCB1	PLCB1	2564	0.17	0.42	YES
22	WNT16	WNT16	WNT16	2685	0.16	0.43	YES
23	PRKACB	PRKACB	PRKACB	2852	0.15	0.44	YES
24	PRKX	PRKX	PRKX	2977	0.14	0.44	YES
25	FZD1	FZD1	FZD1	3057	0.14	0.45	YES
26	CALML6	CALML6	CALML6	3290	0.13	0.45	YES
27	FZD8	FZD8	FZD8	3297	0.13	0.46	YES
28	MITF	MITF	MITF	3298	0.13	0.47	YES
29	TCF7	TCF7	TCF7	3833	0.11	0.45	NO
30	WNT9B	WNT9B	WNT9B	3878	0.11	0.46	NO
31	DVL2	DVL2	DVL2	4025	0.1	0.46	NO
32	ADCY4	ADCY4	ADCY4	4702	0.084	0.43	NO
33	WNT10B	WNT10B	WNT10B	4859	0.08	0.43	NO
34	CREB3L2	CREB3L2	CREB3L2	4915	0.079	0.43	NO
35	GNAS	GNAS	GNAS	5167	0.073	0.42	NO
36	WNT2B	WNT2B	WNT2B	5263	0.071	0.42	NO
37	CTNNB1	CTNNB1	CTNNB1	5757	0.061	0.4	NO
38	PRKCG	PRKCG	PRKCG	5897	0.059	0.4	NO
39	KRAS	KRAS	KRAS	6398	0.051	0.38	NO
40	ASIP	ASIP	ASIP	6439	0.05	0.38	NO
41	WNT8B	WNT8B	WNT8B	6794	0.046	0.36	NO
42	CREB1	CREB1	CREB1	6997	0.043	0.35	NO
43	GSK3B	GSK3B	GSK3B	7254	0.04	0.34	NO
44	DVL3	DVL3	DVL3	7314	0.04	0.34	NO
45	CREB3L4	CREB3L4	CREB3L4	7517	0.037	0.34	NO
46	CALML5	CALML5	CALML5	7560	0.037	0.34	NO
47	MAPK1	MAPK1	MAPK1	7627	0.036	0.34	NO
48	EP300	EP300	EP300	7872	0.033	0.32	NO
49	CAMK2D	CAMK2D	CAMK2D	8111	0.031	0.32	NO
50	CREB3L1	CREB3L1	CREB3L1	8149	0.03	0.32	NO
51	CALM2	CALM2	CALM2	8275	0.029	0.31	NO
52	CREBBP	CREBBP	CREBBP	8447	0.027	0.3	NO
53	FZD10	FZD10	FZD10	8743	0.024	0.29	NO
54	CREB3	CREB3	CREB3	8831	0.023	0.29	NO
55	FZD6	FZD6	FZD6	9365	0.017	0.26	NO
56	FZD5	FZD5	FZD5	9595	0.015	0.25	NO
57	FZD4	FZD4	FZD4	9858	0.012	0.23	NO
58	KITLG	KITLG	KITLG	9899	0.012	0.23	NO
59	FZD9	FZD9	FZD9	9990	0.011	0.23	NO
60	RAF1	RAF1	RAF1	10070	0.01	0.22	NO
61	TCF7L2	TCF7L2	TCF7L2	10258	0.0082	0.22	NO
62	GNAI2	GNAI2	GNAI2	10280	0.0079	0.22	NO
63	CALM1	CALM1	CALM1	10411	0.0063	0.21	NO
64	CAMK2A	CAMK2A	CAMK2A	10679	0.0038	0.19	NO
65	CALML3	CALML3	CALML3	10778	0.0025	0.19	NO
66	CALM3	CALM3	CALM3	10845	0.0019	0.18	NO
67	NRAS	NRAS	NRAS	10873	0.0016	0.18	NO
68	HRAS	HRAS	HRAS	11390	-0.0043	0.16	NO
69	EDN1	EDN1	EDN1	12035	-0.012	0.12	NO
70	MAP2K2	MAP2K2	MAP2K2	12197	-0.014	0.11	NO
71	GNAI3	GNAI3	GNAI3	12458	-0.018	0.1	NO
72	PRKCA	PRKCA	PRKCA	12571	-0.019	0.096	NO
73	MC1R	MC1R	MC1R	12612	-0.02	0.096	NO
74	PRKACA	PRKACA	PRKACA	12641	-0.02	0.096	NO
75	ADCY6	ADCY6	ADCY6	13817	-0.041	0.034	NO
76	GNAQ	GNAQ	GNAQ	14074	-0.047	0.024	NO
77	MAPK3	MAPK3	MAPK3	14457	-0.056	0.008	NO
78	MAP2K1	MAP2K1	MAP2K1	14637	-0.061	0.0034	NO
79	DVL1	DVL1	DVL1	14717	-0.064	0.0046	NO
80	CAMK2G	CAMK2G	CAMK2G	14955	-0.07	-0.0025	NO
81	PLCB3	PLCB3	PLCB3	15034	-0.073	-0.00043	NO
82	PLCB2	PLCB2	PLCB2	15313	-0.084	-0.0086	NO
83	WNT3A	WNT3A	WNT3A	15328	-0.084	-0.002	NO
84	CREB3L3	CREB3L3	CREB3L3	15400	-0.087	0.0016	NO
85	WNT10A	WNT10A	WNT10A	15435	-0.088	0.0073	NO
86	GNAI1	GNAI1	GNAI1	15615	-0.096	0.0057	NO
87	PRKCB	PRKCB	PRKCB	15840	-0.11	0.0025	NO
88	WNT3	WNT3	WNT3	15842	-0.11	0.012	NO
89	ADCY9	ADCY9	ADCY9	15904	-0.11	0.018	NO
90	WNT1	WNT1	WNT1	16153	-0.12	0.015	NO
91	WNT4	WNT4	WNT4	16154	-0.12	0.025	NO
92	ADCY7	ADCY7	ADCY7	16291	-0.13	0.029	NO
93	WNT9A	WNT9A	WNT9A	16740	-0.16	0.018	NO
94	WNT7B	WNT7B	WNT7B	17705	-0.28	-0.012	NO
95	WNT7A	WNT7A	WNT7A	18086	-0.44	0.0046	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 WNT SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG HEDGEHOG 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	TRDMT1	TRDMT1	TRDMT1	238	0.4	0.1	YES
2	CDO1	CDO1	CDO1	358	0.38	0.2	YES
3	CBS	CBS	CBS	646	0.32	0.28	YES
4	BHMT	BHMT	BHMT	890	0.29	0.35	YES
5	CTH	CTH	CTH	1154	0.26	0.41	YES
6	LDHB	LDHB	LDHB	1661	0.22	0.45	YES
7	MAT1A	MAT1A	MAT1A	2434	0.17	0.46	YES
8	DNMT3B	DNMT3B	DNMT3B	2807	0.15	0.48	YES
9	DNMT3A	DNMT3A	DNMT3A	3499	0.12	0.48	NO
10	TAT	TAT	TAT	4364	0.093	0.46	NO
11	MTR	MTR	MTR	4451	0.09	0.48	NO
12	AHCY	AHCY	AHCY	4934	0.078	0.47	NO
13	APIP	APIP	APIP	5368	0.069	0.47	NO
14	LDHAL6A	LDHAL6A	LDHAL6A	8026	0.032	0.33	NO
15	ENOPH1	ENOPH1	ENOPH1	8583	0.026	0.31	NO
16	SMS	SMS	SMS	8784	0.024	0.3	NO
17	SRM	SRM	SRM	9730	0.014	0.26	NO
18	ADI1	ADI1	ADI1	9896	0.012	0.25	NO
19	AHCYL1	AHCYL1	AHCYL1	10043	0.01	0.24	NO
20	DNMT1	DNMT1	DNMT1	10453	0.0058	0.22	NO
21	SDS	SDS	SDS	10865	0.0018	0.2	NO
22	AHCYL2	AHCYL2	AHCYL2	11400	-0.0045	0.17	NO
23	AMD1	AMD1	AMD1	11568	-0.0066	0.17	NO
24	MAT2A	MAT2A	MAT2A	12239	-0.015	0.13	NO
25	MAT2B	MAT2B	MAT2B	12480	-0.018	0.12	NO
26	GOT2	GOT2	GOT2	12854	-0.023	0.11	NO
27	GOT1	GOT1	GOT1	12937	-0.025	0.11	NO
28	MPST	MPST	MPST	14379	-0.054	0.05	NO
29	MTAP	MTAP	MTAP	14405	-0.055	0.064	NO
30	LDHA	LDHA	LDHA	14887	-0.068	0.057	NO
31	IL4I1	IL4I1	IL4I1	15205	-0.079	0.062	NO
32	LDHAL6B	LDHAL6B	LDHAL6B	17954	-0.35	0.012	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 HEDGEHOG SIGNALING PATHWAY.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HEDGEHOG 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 TGF BETA SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	THBS4	THBS4	THBS4	16	0.6	0.059	YES
2	ID4	ID4	ID4	91	0.48	0.1	YES
3	LEFTY2	LEFTY2	LEFTY2	291	0.39	0.13	YES
4	COMP	COMP	COMP	455	0.36	0.16	YES
5	GDF5	GDF5	GDF5	463	0.35	0.19	YES
6	SMAD9	SMAD9	SMAD9	830	0.3	0.2	YES
7	THBS2	THBS2	THBS2	864	0.3	0.23	YES
8	E2F5	E2F5	E2F5	934	0.29	0.26	YES
9	BMP6	BMP6	BMP6	1001	0.28	0.28	YES
10	CHRD	CHRD	CHRD	1013	0.28	0.31	YES
11	INHBB	INHBB	INHBB	1064	0.27	0.33	YES
12	BMP8A	BMP8A	BMP8A	1167	0.26	0.35	YES
13	BMP4	BMP4	BMP4	1486	0.24	0.36	YES
14	NODAL	NODAL	NODAL	1520	0.23	0.38	YES
15	DCN	DCN	DCN	1686	0.22	0.39	YES
16	INHBE	INHBE	INHBE	1820	0.21	0.41	YES
17	TGFB3	TGFB3	TGFB3	2138	0.19	0.41	YES
18	BMP7	BMP7	BMP7	2719	0.16	0.39	YES
19	LEFTY1	LEFTY1	LEFTY1	2753	0.16	0.41	YES
20	GDF6	GDF6	GDF6	2928	0.14	0.41	YES
21	ACVR2B	ACVR2B	ACVR2B	3121	0.14	0.41	YES
22	INHBC	INHBC	INHBC	3495	0.12	0.4	YES
23	GDF7	GDF7	GDF7	3703	0.12	0.4	YES
24	SMAD6	SMAD6	SMAD6	3743	0.11	0.42	YES
25	LTBP1	LTBP1	LTBP1	3851	0.11	0.42	YES
26	ACVR2A	ACVR2A	ACVR2A	3889	0.11	0.43	YES
27	SMAD4	SMAD4	SMAD4	3940	0.11	0.44	YES
28	INHBA	INHBA	INHBA	4079	0.1	0.44	YES
29	THBS1	THBS1	THBS1	4241	0.096	0.44	YES
30	FST	FST	FST	4263	0.096	0.45	YES
31	ID3	ID3	ID3	4296	0.095	0.46	YES
32	ZFYVE9	ZFYVE9	ZFYVE9	4433	0.091	0.46	YES
33	ID2	ID2	ID2	4499	0.089	0.46	YES
34	ACVRL1	ACVRL1	ACVRL1	4663	0.085	0.46	YES
35	ACVR1	ACVR1	ACVR1	4677	0.084	0.47	YES
36	SMAD5	SMAD5	SMAD5	4970	0.078	0.46	NO
37	TGFB2	TGFB2	TGFB2	5531	0.065	0.44	NO
38	SMURF2	SMURF2	SMURF2	5559	0.065	0.44	NO
39	SMAD7	SMAD7	SMAD7	5584	0.064	0.45	NO
40	THBS3	THBS3	THBS3	5660	0.063	0.45	NO
41	SKP1	SKP1	SKP1	5879	0.059	0.44	NO
42	BMPR2	BMPR2	BMPR2	5887	0.059	0.45	NO
43	ROCK1	ROCK1	ROCK1	5962	0.058	0.45	NO
44	SMAD1	SMAD1	SMAD1	6064	0.056	0.45	NO
45	CUL1	CUL1	CUL1	6356	0.052	0.44	NO
46	BMPR1B	BMPR1B	BMPR1B	6960	0.044	0.41	NO
47	MAPK1	MAPK1	MAPK1	7627	0.036	0.38	NO
48	EP300	EP300	EP300	7872	0.033	0.37	NO
49	RBX1	RBX1	RBX1	7979	0.032	0.36	NO
50	CREBBP	CREBBP	CREBBP	8447	0.027	0.34	NO
51	PPP2R1A	PPP2R1A	PPP2R1A	8451	0.027	0.34	NO
52	SMAD2	SMAD2	SMAD2	9293	0.018	0.3	NO
53	ZFYVE16	ZFYVE16	ZFYVE16	10089	0.01	0.26	NO
54	BMPR1A	BMPR1A	BMPR1A	10451	0.0058	0.24	NO
55	AMHR2	AMHR2	AMHR2	11215	-0.0022	0.2	NO
56	PPP2CA	PPP2CA	PPP2CA	11652	-0.0077	0.17	NO
57	TFDP1	TFDP1	TFDP1	11728	-0.0085	0.17	NO
58	RBL2	RBL2	RBL2	11866	-0.0099	0.16	NO
59	PPP2CB	PPP2CB	PPP2CB	11982	-0.011	0.16	NO
60	RBL1	RBL1	RBL1	12392	-0.017	0.14	NO
61	TGFBR1	TGFBR1	TGFBR1	12872	-0.024	0.11	NO
62	RPS6KB1	RPS6KB1	RPS6KB1	12919	-0.024	0.11	NO
63	RHOA	RHOA	RHOA	12953	-0.025	0.11	NO
64	TGFB1	TGFB1	TGFB1	12962	-0.025	0.11	NO
65	E2F4	E2F4	E2F4	13250	-0.03	0.1	NO
66	PITX2	PITX2	PITX2	13480	-0.034	0.092	NO
67	ROCK2	ROCK2	ROCK2	13510	-0.035	0.094	NO
68	BMP8B	BMP8B	BMP8B	13674	-0.038	0.089	NO
69	PPP2R1B	PPP2R1B	PPP2R1B	13835	-0.041	0.084	NO
70	SP1	SP1	SP1	14060	-0.046	0.076	NO
71	TGFBR2	TGFBR2	TGFBR2	14431	-0.055	0.062	NO
72	MAPK3	MAPK3	MAPK3	14457	-0.056	0.066	NO
73	SMURF1	SMURF1	SMURF1	14499	-0.057	0.069	NO
74	RPS6KB2	RPS6KB2	RPS6KB2	14607	-0.06	0.069	NO
75	AMH	AMH	AMH	15155	-0.078	0.047	NO
76	MYC	MYC	MYC	15228	-0.08	0.051	NO
77	ACVR1C	ACVR1C	ACVR1C	15819	-0.1	0.029	NO
78	BMP2	BMP2	BMP2	16293	-0.13	0.016	NO
79	IFNG	IFNG	IFNG	16468	-0.14	0.02	NO
80	SMAD3	SMAD3	SMAD3	16822	-0.16	0.017	NO
81	CDKN2B	CDKN2B	CDKN2B	17061	-0.18	0.022	NO
82	ID1	ID1	ID1	17157	-0.19	0.036	NO
83	TNF	TNF	TNF	17237	-0.2	0.052	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 TGF BETA SIGNALING PATHWAY.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA EGF PATHWAY	30	genes.ES.table	0.51	1.6	0.034	0.6	0.72	0.6	0.31	0.42	0.38	0.18
BIOCARTA FAS PATHWAY	29	genes.ES.table	0.49	1.6	0.054	0.58	0.76	0.52	0.29	0.37	0.37	0.17
BIOCARTA FCER1 PATHWAY	37	genes.ES.table	0.52	1.6	0.05	0.55	0.78	0.49	0.28	0.35	0.36	0.15
BIOCARTA HIVNEF PATHWAY	57	genes.ES.table	0.36	1.5	0.12	0.53	0.93	0.68	0.39	0.42	0.4	0.13
BIOCARTA IL2RB PATHWAY	37	genes.ES.table	0.58	1.7	0.038	0.5	0.62	0.6	0.29	0.42	0.26	0.15
BIOCARTA GSK3 PATHWAY	26	genes.ES.table	0.51	1.5	0.057	0.57	0.91	0.54	0.23	0.42	0.41	0.15
BIOCARTA RACCYCD PATHWAY	25	genes.ES.table	0.5	1.9	0.012	0.53	0.2	0.48	0.29	0.34	0	0.16
BIOCARTA MAPK PATHWAY	86	genes.ES.table	0.35	1.6	0.073	0.6	0.84	0.44	0.29	0.31	0.4	0.18
BIOCARTA TNFR1 PATHWAY	28	genes.ES.table	0.51	1.8	0.0059	0.32	0.22	0.71	0.39	0.44	0	0.11
BIOCARTA TOLL PATHWAY	36	genes.ES.table	0.58	1.7	0.0077	0.45	0.5	0.61	0.28	0.44	0.21	0.14

genes ES table in pathway: BIOCARTA EGF 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	CDKN1A	CDKN1A	CDKN1A	2032	0.15	-0.001	YES
2	PIK3CA	PIK3CA	PIK3CA	2332	0.13	0.081	YES
3	PIK3R1	PIK3R1	PIK3R1	2798	0.11	0.14	YES
4	RAC1	RAC1	RAC1	3034	0.1	0.2	YES
5	NFKB1	NFKB1	NFKB1	3157	0.097	0.26	YES
6	RB1	RB1	RB1	3215	0.095	0.33	YES
7	NFKBIA	NFKBIA	NFKBIA	3299	0.091	0.4	YES
8	IKBKB	IKBKB	IKBKB	3819	0.075	0.42	YES
9	IKBKG	IKBKG	IKBKG	4329	0.062	0.44	YES
10	CHUK	CHUK	CHUK	4941	0.049	0.44	YES
11	CDK6	CDK6	CDK6	4961	0.049	0.48	YES
12	TFDP1	TFDP1	TFDP1	5219	0.044	0.5	YES
13	HRAS	HRAS	HRAS	5898	0.032	0.48	NO
14	RAF1	RAF1	RAF1	6475	0.024	0.47	NO
15	MAPK1	MAPK1	MAPK1	6533	0.023	0.48	NO
16	RELA	RELA	RELA	7514	0.01	0.44	NO
17	CDK2	CDK2	CDK2	8031	0.0036	0.41	NO
18	CCNE1	CCNE1	CCNE1	8422	-0.0012	0.39	NO
19	MAPK3	MAPK3	MAPK3	8658	-0.0045	0.38	NO
20	AKT1	AKT1	AKT1	9841	-0.019	0.33	NO
21	RHOA	RHOA	RHOA	10081	-0.022	0.33	NO
22	PAK1	PAK1	PAK1	10425	-0.027	0.34	NO
23	CDKN1B	CDKN1B	CDKN1B	11010	-0.035	0.33	NO
24	CDK4	CDK4	CDK4	11490	-0.042	0.33	NO
25	CCND1	CCND1	CCND1	11837	-0.047	0.35	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 EGF PATHWAY.

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

genes ES table in pathway: BIOCARTA FAS PATHWAY

Table 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	BAG4	BAG4	BAG4	2144	0.14	-0.0076	YES
2	MAP3K1	MAP3K1	MAP3K1	2185	0.14	0.099	YES
3	CRADD	CRADD	CRADD	2368	0.13	0.19	YES
4	RB1	RB1	RB1	3215	0.095	0.22	YES
5	JUN	JUN	JUN	3223	0.094	0.29	YES
6	CASP3	CASP3	CASP3	3867	0.074	0.31	YES
7	PAK2	PAK2	PAK2	4199	0.065	0.34	YES
8	MAP2K4	MAP2K4	MAP2K4	4445	0.06	0.38	YES
9	MAPK8	MAPK8	MAPK8	4862	0.05	0.39	YES
10	ARHGDIB	ARHGDIB	ARHGDIB	5088	0.046	0.42	YES
11	TRADD	TRADD	TRADD	5308	0.042	0.44	YES
12	TNF	TNF	TNF	5719	0.035	0.44	YES
13	CASP2	CASP2	CASP2	5732	0.035	0.47	YES
14	RIPK1	RIPK1	RIPK1	5947	0.031	0.48	YES
15	TNFRSF1A	TNFRSF1A	TNFRSF1A	6348	0.026	0.48	YES
16	LMNB2	LMNB2	LMNB2	6551	0.023	0.48	YES
17	DFFA	DFFA	DFFA	6707	0.021	0.49	YES
18	PRKDC	PRKDC	PRKDC	7060	0.016	0.48	YES
19	LMNA	LMNA	LMNA	7099	0.016	0.5	YES
20	LMNB1	LMNB1	LMNB1	7102	0.016	0.51	YES
21	CASP8	CASP8	CASP8	8153	0.002	0.45	NO
22	PARP1	PARP1	PARP1	8554	-0.003	0.43	NO
23	MAP3K7	MAP3K7	MAP3K7	9432	-0.014	0.39	NO
24	SPTAN1	SPTAN1	SPTAN1	9475	-0.015	0.4	NO
25	FADD	FADD	FADD	9640	-0.017	0.41	NO
26	MADD	MADD	MADD	10196	-0.024	0.4	NO
27	PAK1	PAK1	PAK1	10425	-0.027	0.4	NO
28	DFFB	DFFB	DFFB	10674	-0.03	0.41	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 FAS PATHWAY.

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

Table 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	TP53AIP1	TP53AIP1	TP53AIP1	104	0.54	0.096	YES
2	SERPINB5	SERPINB5	SERPINB5	269	0.42	0.16	YES
3	SFN	SFN	SFN	842	0.26	0.18	YES
4	PERP	PERP	PERP	899	0.26	0.23	YES
5	SESN3	SESN3	SESN3	917	0.25	0.27	YES
6	PMAIP1	PMAIP1	PMAIP1	1277	0.21	0.29	YES
7	TP73	TP73	TP73	1762	0.17	0.3	YES
8	CD82	CD82	CD82	1788	0.17	0.32	YES
9	ZMAT3	ZMAT3	ZMAT3	1826	0.16	0.35	YES
10	CCNE2	CCNE2	CCNE2	1940	0.16	0.38	YES
11	CDKN1A	CDKN1A	CDKN1A	2032	0.15	0.4	YES
12	CDKN2A	CDKN2A	CDKN2A	2450	0.13	0.4	YES
13	GADD45A	GADD45A	GADD45A	2704	0.11	0.41	YES
14	MDM2	MDM2	MDM2	3024	0.1	0.41	YES
15	ATR	ATR	ATR	3217	0.095	0.42	YES
16	IGF1	IGF1	IGF1	3275	0.092	0.43	YES
17	SHISA5	SHISA5	SHISA5	3309	0.091	0.44	YES
18	FAS	FAS	FAS	3696	0.078	0.44	YES
19	SESN2	SESN2	SESN2	3791	0.076	0.45	YES
20	CASP3	CASP3	CASP3	3867	0.074	0.46	YES
21	SESN1	SESN1	SESN1	4315	0.062	0.44	NO
22	CDK1	CDK1	CDK1	4431	0.06	0.45	NO
23	DDB2	DDB2	DDB2	4767	0.053	0.44	NO
24	CDK6	CDK6	CDK6	4961	0.049	0.44	NO
25	RFWD2	RFWD2	RFWD2	5024	0.047	0.44	NO
26	PPM1D	PPM1D	PPM1D	5194	0.044	0.44	NO
27	RRM2B	RRM2B	RRM2B	5314	0.042	0.44	NO
28	TP53	TP53	TP53	6063	0.03	0.41	NO
29	RRM2	RRM2	RRM2	6155	0.028	0.41	NO
30	BID	BID	BID	6309	0.026	0.4	NO
31	SIAH1	SIAH1	SIAH1	6371	0.026	0.41	NO
32	CASP9	CASP9	CASP9	6831	0.019	0.38	NO
33	MDM4	MDM4	MDM4	7046	0.016	0.38	NO
34	TP53I3	TP53I3	TP53I3	7130	0.015	0.37	NO
35	CYCS	CYCS	CYCS	7274	0.013	0.37	NO
36	CCNG2	CCNG2	CCNG2	7681	0.0081	0.35	NO
37	CDK2	CDK2	CDK2	8031	0.0036	0.33	NO
38	PTEN	PTEN	PTEN	8034	0.0036	0.33	NO
39	CASP8	CASP8	CASP8	8153	0.002	0.32	NO
40	LRDD	LRDD	LRDD	8184	0.0017	0.32	NO
41	CCNE1	CCNE1	CCNE1	8422	-0.0012	0.31	NO
42	CCNB2	CCNB2	CCNB2	8445	-0.0015	0.31	NO
43	APAF1	APAF1	APAF1	8619	-0.004	0.3	NO
44	CCNB1	CCNB1	CCNB1	8647	-0.0044	0.3	NO
45	CHEK2	CHEK2	CHEK2	8817	-0.0065	0.29	NO
46	TNFRSF10B	TNFRSF10B	TNFRSF10B	8894	-0.0075	0.29	NO
47	RCHY1	RCHY1	RCHY1	9188	-0.011	0.27	NO
48	BAI1	BAI1	BAI1	9918	-0.02	0.24	NO
49	EI24	EI24	EI24	10168	-0.024	0.23	NO
50	CCND3	CCND3	CCND3	10451	-0.027	0.22	NO
51	BAX	BAX	BAX	10639	-0.03	0.21	NO
52	TSC2	TSC2	TSC2	10782	-0.032	0.21	NO
53	ATM	ATM	ATM	10913	-0.034	0.21	NO
54	GTSE1	GTSE1	GTSE1	11006	-0.035	0.21	NO
55	CCNG1	CCNG1	CCNG1	11243	-0.038	0.2	NO
56	CCNB3	CCNB3	CCNB3	11410	-0.041	0.2	NO
57	CDK4	CDK4	CDK4	11490	-0.042	0.21	NO
58	CCND2	CCND2	CCND2	11768	-0.046	0.2	NO
59	RPRM	RPRM	RPRM	11835	-0.047	0.2	NO
60	CCND1	CCND1	CCND1	11837	-0.047	0.21	NO
61	CHEK1	CHEK1	CHEK1	12015	-0.05	0.21	NO
62	SERPINE1	SERPINE1	SERPINE1	12481	-0.057	0.2	NO
63	GADD45B	GADD45B	GADD45B	12625	-0.059	0.2	NO
64	BBC3	BBC3	BBC3	14939	-0.12	0.096	NO
65	IGFBP3	IGFBP3	IGFBP3	15341	-0.14	0.1	NO
66	GADD45G	GADD45G	GADD45G	15487	-0.14	0.12	NO
67	THBS1	THBS1	THBS1	15724	-0.16	0.14	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 FCER1 PATHWAY.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table 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	TLR10	TLR10	TLR10	146	0.5	0.14	YES
2	TLR7	TLR7	TLR7	684	0.29	0.2	YES
3	TLR6	TLR6	TLR6	1115	0.23	0.25	YES
4	TLR2	TLR2	TLR2	1388	0.2	0.29	YES
5	LY96	LY96	LY96	1586	0.18	0.34	YES
6	TLR3	TLR3	TLR3	1758	0.17	0.38	YES
7	TOLLIP	TOLLIP	TOLLIP	1839	0.16	0.42	YES
8	MAP3K1	MAP3K1	MAP3K1	2185	0.14	0.45	YES
9	NFKB1	NFKB1	NFKB1	3157	0.097	0.42	YES
10	JUN	JUN	JUN	3223	0.094	0.45	YES
11	NFKBIA	NFKBIA	NFKBIA	3299	0.091	0.47	YES
12	MYD88	MYD88	MYD88	3712	0.078	0.47	YES
13	IKBKB	IKBKB	IKBKB	3819	0.075	0.49	YES
14	TLR4	TLR4	TLR4	3928	0.072	0.5	YES
15	CD14	CD14	CD14	3995	0.07	0.52	YES
16	IKBKG	IKBKG	IKBKG	4329	0.062	0.52	YES
17	MAP2K4	MAP2K4	MAP2K4	4445	0.06	0.54	YES
18	FOS	FOS	FOS	4521	0.058	0.55	YES
19	TRAF6	TRAF6	TRAF6	4612	0.056	0.56	YES
20	MAPK8	MAPK8	MAPK8	4862	0.05	0.56	YES
21	CHUK	CHUK	CHUK	4941	0.049	0.57	YES
22	TLR9	TLR9	TLR9	5137	0.045	0.58	YES
23	EIF2AK2	EIF2AK2	EIF2AK2	5455	0.04	0.57	NO
24	IRAK1	IRAK1	IRAK1	6299	0.026	0.53	NO
25	TAB2	TAB2	TAB2	6572	0.023	0.52	NO
26	RELA	RELA	RELA	7514	0.01	0.48	NO
27	TAB1	TAB1	TAB1	7537	0.01	0.48	NO
28	ECSIT	ECSIT	ECSIT	7587	0.0094	0.48	NO
29	ELK1	ELK1	ELK1	7768	0.007	0.47	NO
30	MAPK14	MAPK14	MAPK14	8064	0.0033	0.46	NO
31	MAP3K14	MAP3K14	MAP3K14	8419	-0.0012	0.44	NO
32	MAP3K7	MAP3K7	MAP3K7	9432	-0.014	0.38	NO
33	TIRAP	TIRAP	TIRAP	10427	-0.027	0.34	NO
34	MAP2K3	MAP2K3	MAP2K3	12821	-0.063	0.22	NO
35	MAP2K6	MAP2K6	MAP2K6	14127	-0.093	0.18	NO
36	PGLYRP1	PGLYRP1	PGLYRP1	15294	-0.14	0.16	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 HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

Table 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	PIK3CG	PIK3CG	PIK3CG	924	0.25	0.033	YES
2	SYK	SYK	SYK	1243	0.21	0.086	YES
3	MYC	MYC	MYC	1293	0.21	0.15	YES
4	IL2RB	IL2RB	IL2RB	1479	0.19	0.21	YES
5	FASLG	FASLG	FASLG	1524	0.19	0.27	YES
6	IKZF3	IKZF3	IKZF3	1725	0.17	0.31	YES
7	STAT5A	STAT5A	STAT5A	1827	0.16	0.36	YES
8	IL2RA	IL2RA	IL2RA	1916	0.16	0.41	YES
9	IL2RG	IL2RG	IL2RG	2083	0.15	0.45	YES
10	PIK3CA	PIK3CA	PIK3CA	2332	0.13	0.48	YES
11	BCL2	BCL2	BCL2	2760	0.11	0.49	YES
12	PIK3R1	PIK3R1	PIK3R1	2798	0.11	0.52	YES
13	SOCS1	SOCS1	SOCS1	3372	0.089	0.52	YES
14	FAS	FAS	FAS	3696	0.078	0.53	YES
15	JAK3	JAK3	JAK3	4427	0.06	0.51	YES
16	FOS	FOS	FOS	4521	0.058	0.53	YES
17	RPS6KB1	RPS6KB1	RPS6KB1	4692	0.054	0.53	YES
18	CFLAR	CFLAR	CFLAR	4747	0.053	0.55	YES
19	CRKL	CRKL	CRKL	4748	0.053	0.57	YES
20	PTPN6	PTPN6	PTPN6	5052	0.047	0.56	YES
21	CBL	CBL	CBL	5150	0.045	0.57	YES
22	NMI	NMI	NMI	5351	0.042	0.58	YES
23	JAK1	JAK1	JAK1	5630	0.037	0.57	NO
24	HRAS	HRAS	HRAS	5898	0.032	0.57	NO
25	SOS1	SOS1	SOS1	6124	0.029	0.57	NO
26	RAF1	RAF1	RAF1	6475	0.024	0.56	NO
27	MAPK1	MAPK1	MAPK1	6533	0.023	0.56	NO
28	STAT5B	STAT5B	STAT5B	6703	0.021	0.56	NO
29	GRB2	GRB2	GRB2	7685	0.008	0.51	NO
30	PPIA	PPIA	PPIA	7749	0.0072	0.51	NO
31	MAPK3	MAPK3	MAPK3	8658	-0.0045	0.46	NO
32	IRS1	IRS1	IRS1	9054	-0.0094	0.44	NO
33	SHC1	SHC1	SHC1	9758	-0.018	0.41	NO
34	AKT1	AKT1	AKT1	9841	-0.019	0.41	NO
35	SOCS3	SOCS3	SOCS3	10874	-0.033	0.36	NO
36	BCL2L1	BCL2L1	BCL2L1	11701	-0.045	0.33	NO
37	BAD	BAD	BAD	13471	-0.076	0.26	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 IL2RB PATHWAY.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GSK3 PATHWAY

Table 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	EGFR	EGFR	EGFR	1174	0.22	0.039	YES
2	PRKCB	PRKCB	PRKCB	1182	0.22	0.14	YES
3	STAT5A	STAT5A	STAT5A	1827	0.16	0.18	YES
4	STAT4	STAT4	STAT4	2165	0.14	0.23	YES
5	MAP3K1	MAP3K1	MAP3K1	2185	0.14	0.3	YES
6	PIK3CA	PIK3CA	PIK3CA	2332	0.13	0.35	YES
7	PIK3R1	PIK3R1	PIK3R1	2798	0.11	0.38	YES
8	JUN	JUN	JUN	3223	0.094	0.4	YES
9	STAT6	STAT6	STAT6	3841	0.074	0.4	YES
10	STAT1	STAT1	STAT1	4265	0.064	0.4	YES
11	MAP2K4	MAP2K4	MAP2K4	4445	0.06	0.42	YES
12	FOS	FOS	FOS	4521	0.058	0.44	YES
13	STAT3	STAT3	STAT3	4711	0.054	0.46	YES
14	MAPK8	MAPK8	MAPK8	4862	0.05	0.48	YES
15	MAP2K1	MAP2K1	MAP2K1	4994	0.048	0.49	YES
16	STAT2	STAT2	STAT2	5174	0.045	0.5	YES
17	RASA1	RASA1	RASA1	5578	0.038	0.5	YES
18	JAK1	JAK1	JAK1	5630	0.037	0.51	YES
19	SOS1	SOS1	SOS1	6124	0.029	0.5	NO
20	CSNK2A1	CSNK2A1	CSNK2A1	6288	0.026	0.5	NO
21	RAF1	RAF1	RAF1	6475	0.024	0.5	NO
22	STAT5B	STAT5B	STAT5B	6703	0.021	0.5	NO
23	SRF	SRF	SRF	7432	0.011	0.46	NO
24	GRB2	GRB2	GRB2	7685	0.008	0.46	NO
25	ELK1	ELK1	ELK1	7768	0.007	0.45	NO
26	PLCG1	PLCG1	PLCG1	8590	-0.0036	0.41	NO
27	MAPK3	MAPK3	MAPK3	8658	-0.0045	0.41	NO
28	SHC1	SHC1	SHC1	9758	-0.018	0.36	NO
29	EGF	EGF	EGF	10442	-0.027	0.33	NO
30	PRKCA	PRKCA	PRKCA	16421	-0.2	0.096	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 GSK3 PATHWAY.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GSK3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PTPN13	PTPN13	PTPN13	530	0.32	0.14	YES
2	FASLG	FASLG	FASLG	1524	0.19	0.19	YES
3	MAP3K1	MAP3K1	MAP3K1	2185	0.14	0.23	YES
4	RB1	RB1	RB1	3215	0.095	0.22	YES
5	JUN	JUN	JUN	3223	0.094	0.28	YES
6	FAS	FAS	FAS	3696	0.078	0.29	YES
7	CASP3	CASP3	CASP3	3867	0.074	0.32	YES
8	CASP10	CASP10	CASP10	4072	0.068	0.35	YES
9	PAK2	PAK2	PAK2	4199	0.065	0.38	YES
10	CASP7	CASP7	CASP7	4307	0.063	0.4	YES
11	MAP2K4	MAP2K4	MAP2K4	4445	0.06	0.43	YES
12	CFLAR	CFLAR	CFLAR	4747	0.053	0.44	YES
13	MAPK8	MAPK8	MAPK8	4862	0.05	0.46	YES
14	ARHGDIB	ARHGDIB	ARHGDIB	5088	0.046	0.47	YES
15	FAF1	FAF1	FAF1	5255	0.043	0.49	YES
16	LMNB2	LMNB2	LMNB2	6551	0.023	0.43	NO
17	DFFA	DFFA	DFFA	6707	0.021	0.43	NO
18	PRKDC	PRKDC	PRKDC	7060	0.016	0.42	NO
19	LMNA	LMNA	LMNA	7099	0.016	0.43	NO
20	CASP8	CASP8	CASP8	8153	0.002	0.37	NO
21	PARP1	PARP1	PARP1	8554	-0.003	0.35	NO
22	MAP3K7	MAP3K7	MAP3K7	9432	-0.014	0.31	NO
23	SPTAN1	SPTAN1	SPTAN1	9475	-0.015	0.31	NO
24	FADD	FADD	FADD	9640	-0.017	0.31	NO
25	PAK1	PAK1	PAK1	10425	-0.027	0.28	NO
26	DFFB	DFFB	DFFB	10674	-0.03	0.29	NO
27	DAXX	DAXX	DAXX	11167	-0.037	0.28	NO
28	RIPK2	RIPK2	RIPK2	14274	-0.098	0.16	NO
29	CASP6	CASP6	CASP6	14291	-0.098	0.21	NO

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

Figure S34. 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 MAPK PATHWAY

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	FCER1A	FCER1A	FCER1A	524	0.32	0.075	YES
2	BTK	BTK	BTK	607	0.3	0.17	YES
3	PIK3CG	PIK3CG	PIK3CG	924	0.25	0.23	YES
4	PRKCB	PRKCB	PRKCB	1182	0.22	0.29	YES
5	SYK	SYK	SYK	1243	0.21	0.35	YES
6	FCER1G	FCER1G	FCER1G	1576	0.18	0.39	YES
7	MAP3K1	MAP3K1	MAP3K1	2185	0.14	0.4	YES
8	PIK3CA	PIK3CA	PIK3CA	2332	0.13	0.44	YES
9	PIK3R1	PIK3R1	PIK3R1	2798	0.11	0.45	YES
10	JUN	JUN	JUN	3223	0.094	0.46	YES
11	LYN	LYN	LYN	3454	0.086	0.47	YES
12	NFATC3	NFATC3	NFATC3	3595	0.082	0.49	YES
13	PAK2	PAK2	PAK2	4199	0.065	0.48	YES
14	PPP3CC	PPP3CC	PPP3CC	4430	0.06	0.48	YES
15	MAP2K4	MAP2K4	MAP2K4	4445	0.06	0.5	YES
16	FOS	FOS	FOS	4521	0.058	0.52	YES
17	MAPK8	MAPK8	MAPK8	4862	0.05	0.51	YES
18	MAP2K1	MAP2K1	MAP2K1	4994	0.048	0.52	YES
19	MAP2K7	MAP2K7	MAP2K7	6019	0.03	0.47	NO
20	SOS1	SOS1	SOS1	6124	0.029	0.48	NO
21	RAF1	RAF1	RAF1	6475	0.024	0.47	NO
22	MAPK1	MAPK1	MAPK1	6533	0.023	0.47	NO
23	CALM1	CALM1	CALM1	6786	0.02	0.46	NO
24	NFATC2	NFATC2	NFATC2	6990	0.017	0.46	NO
25	GRB2	GRB2	GRB2	7685	0.008	0.42	NO
26	ELK1	ELK1	ELK1	7768	0.007	0.42	NO
27	NFATC1	NFATC1	NFATC1	7847	0.006	0.42	NO
28	VAV1	VAV1	VAV1	8063	0.0033	0.41	NO
29	PPP3CA	PPP3CA	PPP3CA	8201	0.0015	0.4	NO
30	PLCG1	PLCG1	PLCG1	8590	-0.0036	0.38	NO
31	PPP3CB	PPP3CB	PPP3CB	8651	-0.0045	0.38	NO
32	MAPK3	MAPK3	MAPK3	8658	-0.0045	0.38	NO
33	SHC1	SHC1	SHC1	9758	-0.018	0.32	NO
34	PLA2G4A	PLA2G4A	PLA2G4A	10139	-0.023	0.31	NO
35	CALM2	CALM2	CALM2	12131	-0.051	0.22	NO
36	CALM3	CALM3	CALM3	13062	-0.067	0.19	NO
37	NFATC4	NFATC4	NFATC4	17386	-0.3	0.043	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: BIOCARTA MAPK PATHWAY.

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

genes ES table in pathway: BIOCARTA TNFR1 PATHWAY

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	MAPK10	MAPK10	MAPK10	437	0.35	0.03	YES
2	RPS6KA5	RPS6KA5	RPS6KA5	473	0.34	0.079	YES
3	CEBPA	CEBPA	CEBPA	1006	0.24	0.087	YES
4	MAP3K6	MAP3K6	MAP3K6	1093	0.23	0.12	YES
5	MAP4K1	MAP4K1	MAP4K1	1098	0.23	0.15	YES
6	MYC	MYC	MYC	1293	0.21	0.17	YES
7	MAP3K8	MAP3K8	MAP3K8	1334	0.2	0.2	YES
8	MAPK6	MAPK6	MAPK6	1800	0.16	0.2	YES
9	MAP3K9	MAP3K9	MAP3K9	2004	0.15	0.21	YES
10	MAP3K5	MAP3K5	MAP3K5	2184	0.14	0.22	YES
11	MAP3K1	MAP3K1	MAP3K1	2185	0.14	0.25	YES
12	MKNK2	MKNK2	MKNK2	2803	0.11	0.23	YES
13	RAC1	RAC1	RAC1	3034	0.1	0.23	YES
14	NFKB1	NFKB1	NFKB1	3157	0.097	0.24	YES
15	JUN	JUN	JUN	3223	0.094	0.25	YES
16	MEF2A	MEF2A	MEF2A	3292	0.091	0.26	YES
17	NFKBIA	NFKBIA	NFKBIA	3299	0.091	0.27	YES
18	TGFB1	TGFB1	TGFB1	3582	0.082	0.27	YES
19	MAX	MAX	MAX	3713	0.078	0.28	YES
20	IKBKB	IKBKB	IKBKB	3819	0.075	0.28	YES
21	MKNK1	MKNK1	MKNK1	3908	0.072	0.29	YES
22	MAP3K2	MAP3K2	MAP3K2	3996	0.07	0.29	YES
23	MAPK13	MAPK13	MAPK13	4097	0.068	0.3	YES
24	SP1	SP1	SP1	4118	0.067	0.31	YES
25	PAK2	PAK2	PAK2	4199	0.065	0.31	YES
26	STAT1	STAT1	STAT1	4265	0.064	0.32	YES
27	MAP4K5	MAP4K5	MAP4K5	4321	0.062	0.33	YES
28	MAP2K4	MAP2K4	MAP2K4	4445	0.06	0.33	YES
29	FOS	FOS	FOS	4521	0.058	0.33	YES
30	RPS6KB1	RPS6KB1	RPS6KB1	4692	0.054	0.33	YES
31	MAPK8	MAPK8	MAPK8	4862	0.05	0.33	YES
32	CHUK	CHUK	CHUK	4941	0.049	0.33	YES
33	MAP2K1	MAP2K1	MAP2K1	4994	0.048	0.34	YES
34	MAPK7	MAPK7	MAPK7	5013	0.048	0.34	YES
35	RPS6KA3	RPS6KA3	RPS6KA3	5099	0.046	0.35	YES
36	MAPKAPK2	MAPKAPK2	MAPKAPK2	5214	0.044	0.35	YES
37	TRADD	TRADD	TRADD	5308	0.042	0.35	YES
38	RPS6KA4	RPS6KA4	RPS6KA4	5328	0.042	0.35	YES
39	MAP3K10	MAP3K10	MAP3K10	5509	0.039	0.35	NO
40	HRAS	HRAS	HRAS	5898	0.032	0.33	NO
41	LOC729991-MEF2B	LOC729991-MEF2B	LOC729991-MEF2B	5914	0.032	0.34	NO
42	RIPK1	RIPK1	RIPK1	5947	0.031	0.34	NO
43	MAP2K7	MAP2K7	MAP2K7	6019	0.03	0.34	NO
44	BRAF	BRAF	BRAF	6244	0.027	0.33	NO
45	MAP3K4	MAP3K4	MAP3K4	6374	0.025	0.33	NO
46	RAF1	RAF1	RAF1	6475	0.024	0.33	NO
47	MAPK1	MAPK1	MAPK1	6533	0.023	0.33	NO
48	MAP3K3	MAP3K3	MAP3K3	6674	0.021	0.32	NO
49	MAPKAPK3	MAPKAPK3	MAPKAPK3	6919	0.018	0.31	NO
50	CREB1	CREB1	CREB1	7050	0.016	0.31	NO
51	RPS6KB2	RPS6KB2	RPS6KB2	7201	0.014	0.3	NO
52	MAP3K13	MAP3K13	MAP3K13	7230	0.014	0.3	NO
53	MAP2K5	MAP2K5	MAP2K5	7347	0.012	0.3	NO
54	MAP4K2	MAP4K2	MAP4K2	7450	0.011	0.29	NO
55	RELA	RELA	RELA	7514	0.01	0.29	NO
56	MAPK11	MAPK11	MAPK11	7577	0.0096	0.29	NO
57	GRB2	GRB2	GRB2	7685	0.008	0.29	NO
58	ELK1	ELK1	ELK1	7768	0.007	0.28	NO
59	MAPK14	MAPK14	MAPK14	8064	0.0033	0.27	NO
60	MAP2K2	MAP2K2	MAP2K2	8160	0.0019	0.26	NO
61	MAP3K11	MAP3K11	MAP3K11	8322	0.000025	0.25	NO
62	MAP3K14	MAP3K14	MAP3K14	8419	-0.0012	0.25	NO
63	MAPK3	MAPK3	MAPK3	8658	-0.0045	0.24	NO
64	RPS6KA1	RPS6KA1	RPS6KA1	8938	-0.008	0.22	NO
65	TRAF2	TRAF2	TRAF2	9010	-0.0089	0.22	NO
66	MAP3K7	MAP3K7	MAP3K7	9432	-0.014	0.2	NO
67	TGFBR1	TGFBR1	TGFBR1	9476	-0.015	0.2	NO
68	MEF2D	MEF2D	MEF2D	9490	-0.015	0.2	NO
69	SHC1	SHC1	SHC1	9758	-0.018	0.19	NO
70	TGFB3	TGFB3	TGFB3	9942	-0.021	0.18	NO
71	ARAF	ARAF	ARAF	9950	-0.021	0.18	NO
72	MAPKAPK5	MAPKAPK5	MAPKAPK5	10334	-0.026	0.16	NO
73	PAK1	PAK1	PAK1	10425	-0.027	0.16	NO
74	MAP4K3	MAP4K3	MAP4K3	10860	-0.033	0.14	NO
75	MAP4K4	MAP4K4	MAP4K4	10918	-0.034	0.15	NO
76	DAXX	DAXX	DAXX	11167	-0.037	0.14	NO
77	MAPK9	MAPK9	MAPK9	11445	-0.041	0.13	NO
78	ATF2	ATF2	ATF2	11476	-0.042	0.14	NO
79	RAPGEF2	RAPGEF2	RAPGEF2	12636	-0.06	0.08	NO
80	MAP2K3	MAP2K3	MAP2K3	12821	-0.063	0.079	NO
81	MAP2K6	MAP2K6	MAP2K6	14127	-0.093	0.022	NO
82	RPS6KA2	RPS6KA2	RPS6KA2	16009	-0.17	-0.056	NO
83	MAP3K12	MAP3K12	MAP3K12	16696	-0.22	-0.06	NO
84	MAPK4	MAPK4	MAPK4	16749	-0.23	-0.028	NO
85	MAPK12	MAPK12	MAPK12	17674	-0.34	-0.027	NO
86	TGFB2	TGFB2	TGFB2	17716	-0.36	0.025	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: BIOCARTA TNFR1 PATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 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 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	PLA2G4F	PLA2G4F	PLA2G4F	115	0.54	0.049	YES
2	PLA2G4E	PLA2G4E	PLA2G4E	230	0.44	0.088	YES
3	PLD1	PLD1	PLD1	613	0.3	0.097	YES
4	VAV3	VAV3	VAV3	687	0.29	0.12	YES
5	DNM1	DNM1	DNM1	719	0.28	0.15	YES
6	NCF1	NCF1	NCF1	820	0.26	0.17	YES
7	DOCK2	DOCK2	DOCK2	839	0.26	0.2	YES
8	PTPRC	PTPRC	PTPRC	874	0.26	0.22	YES
9	PIK3CG	PIK3CG	PIK3CG	924	0.25	0.25	YES
10	FCGR2C	FCGR2C	FCGR2C	1027	0.24	0.26	YES
11	PIK3R5	PIK3R5	PIK3R5	1091	0.23	0.28	YES
12	WAS	WAS	WAS	1167	0.22	0.3	YES
13	PRKCB	PRKCB	PRKCB	1182	0.22	0.33	YES
14	SYK	SYK	SYK	1243	0.21	0.34	YES
15	FCGR2B	FCGR2B	FCGR2B	1281	0.21	0.36	YES
16	HCK	HCK	HCK	1547	0.19	0.37	YES
17	WASF3	WASF3	WASF3	1903	0.16	0.36	YES
18	PLCG2	PLCG2	PLCG2	1990	0.15	0.38	YES
19	INPP5D	INPP5D	INPP5D	2040	0.15	0.39	YES
20	FCGR1A	FCGR1A	FCGR1A	2067	0.15	0.4	YES
21	PIK3CA	PIK3CA	PIK3CA	2332	0.13	0.4	YES
22	PLA2G4D	PLA2G4D	PLA2G4D	2466	0.12	0.41	YES
23	PLD2	PLD2	PLD2	2527	0.12	0.42	YES
24	PIK3CD	PIK3CD	PIK3CD	2743	0.11	0.42	YES
25	PIK3R1	PIK3R1	PIK3R1	2798	0.11	0.42	YES
26	FCGR3A	FCGR3A	FCGR3A	2838	0.11	0.43	YES
27	WASF2	WASF2	WASF2	2940	0.1	0.44	YES
28	RAC1	RAC1	RAC1	3034	0.1	0.44	YES
29	PPAP2A	PPAP2A	PPAP2A	3182	0.096	0.44	YES
30	FCGR2A	FCGR2A	FCGR2A	3414	0.088	0.44	YES
31	LYN	LYN	LYN	3454	0.086	0.45	YES
32	LAT	LAT	LAT	3605	0.081	0.45	YES
33	PIK3CB	PIK3CB	PIK3CB	3615	0.081	0.46	YES
34	ARF6	ARF6	ARF6	3753	0.076	0.46	YES
35	PRKCE	PRKCE	PRKCE	3972	0.071	0.45	NO
36	ARPC2	ARPC2	ARPC2	4238	0.064	0.44	NO
37	LIMK2	LIMK2	LIMK2	4274	0.063	0.45	NO
38	RPS6KB1	RPS6KB1	RPS6KB1	4692	0.054	0.43	NO
39	CDC42	CDC42	CDC42	4732	0.053	0.43	NO
40	CRKL	CRKL	CRKL	4748	0.053	0.44	NO
41	MAP2K1	MAP2K1	MAP2K1	4994	0.048	0.43	NO
42	ARPC5L	ARPC5L	ARPC5L	5075	0.046	0.43	NO
43	ARPC1A	ARPC1A	ARPC1A	5503	0.039	0.41	NO
44	PPAP2B	PPAP2B	PPAP2B	5627	0.037	0.41	NO
45	WASL	WASL	WASL	5643	0.037	0.41	NO
46	PRKCD	PRKCD	PRKCD	5700	0.036	0.41	NO
47	MARCKS	MARCKS	MARCKS	5843	0.033	0.41	NO
48	PIK3R2	PIK3R2	PIK3R2	5962	0.031	0.4	NO
49	ASAP3	ASAP3	ASAP3	6056	0.03	0.4	NO
50	ARPC5	ARPC5	ARPC5	6087	0.029	0.4	NO
51	LIMK1	LIMK1	LIMK1	6098	0.029	0.4	NO
52	ASAP1	ASAP1	ASAP1	6103	0.029	0.41	NO
53	RAC2	RAC2	RAC2	6105	0.029	0.41	NO
54	RAF1	RAF1	RAF1	6475	0.024	0.39	NO
55	MAPK1	MAPK1	MAPK1	6533	0.023	0.39	NO
56	GSN	GSN	GSN	6555	0.023	0.39	NO
57	PIP5K1C	PIP5K1C	PIP5K1C	6854	0.019	0.38	NO
58	ARPC3	ARPC3	ARPC3	6980	0.017	0.37	NO
59	DNM2	DNM2	DNM2	7142	0.015	0.37	NO
60	CRK	CRK	CRK	7208	0.014	0.36	NO
61	WASF1	WASF1	WASF1	7374	0.012	0.36	NO
62	DNM3	DNM3	DNM3	7485	0.011	0.35	NO
63	PIK3R3	PIK3R3	PIK3R3	7543	0.01	0.35	NO
64	SPHK1	SPHK1	SPHK1	7683	0.0081	0.34	NO
65	PIP5K1A	PIP5K1A	PIP5K1A	7737	0.0074	0.34	NO
66	PIKFYVE	PIKFYVE	PIKFYVE	7863	0.0058	0.33	NO
67	AKT2	AKT2	AKT2	8007	0.004	0.33	NO
68	VAV1	VAV1	VAV1	8063	0.0033	0.32	NO
69	PLCG1	PLCG1	PLCG1	8590	-0.0036	0.3	NO
70	MAPK3	MAPK3	MAPK3	8658	-0.0045	0.29	NO
71	DNM1L	DNM1L	DNM1L	8745	-0.0056	0.29	NO
72	AKT1	AKT1	AKT1	9841	-0.019	0.23	NO
73	ARPC4	ARPC4	ARPC4	9926	-0.02	0.23	NO
74	GAB2	GAB2	GAB2	9951	-0.021	0.23	NO
75	PPAP2C	PPAP2C	PPAP2C	9959	-0.021	0.23	NO
76	PLA2G4A	PLA2G4A	PLA2G4A	10139	-0.023	0.22	NO
77	PAK1	PAK1	PAK1	10425	-0.027	0.21	NO
78	CFL1	CFL1	CFL1	10449	-0.027	0.21	NO
79	SCIN	SCIN	SCIN	10888	-0.033	0.19	NO
80	MYO10	MYO10	MYO10	11366	-0.04	0.17	NO
81	PLA2G6	PLA2G6	PLA2G6	12099	-0.051	0.13	NO
82	SPHK2	SPHK2	SPHK2	12607	-0.059	0.11	NO
83	PIP4K2B	PIP4K2B	PIP4K2B	12795	-0.062	0.11	NO
84	AKT3	AKT3	AKT3	12998	-0.066	0.1	NO
85	VASP	VASP	VASP	13464	-0.076	0.084	NO
86	ARPC1B	ARPC1B	ARPC1B	13690	-0.081	0.08	NO
87	ASAP2	ASAP2	ASAP2	13929	-0.088	0.076	NO
88	AMPH	AMPH	AMPH	14582	-0.11	0.05	NO
89	MARCKSL1	MARCKSL1	MARCKSL1	14592	-0.11	0.061	NO
90	CFL2	CFL2	CFL2	16249	-0.19	-0.011	NO
91	PRKCA	PRKCA	PRKCA	16421	-0.2	0.00015	NO
92	VAV2	VAV2	VAV2	16538	-0.21	0.015	NO
93	PIP5K1B	PIP5K1B	PIP5K1B	17129	-0.26	0.01	NO
94	PRKCG	PRKCG	PRKCG	18041	-0.46	0.0071	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: BIOCARTA TOLL PATHWAY.

Figure S40. 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

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 RHO PATHWAY	31	genes.ES.table	0.4	1.5	0.066	0.37	0.85	0.032	0.0011	0.032	0.26	0.066
KEGG PURINE METABOLISM	150	genes.ES.table	0.38	1.5	0.019	0.47	0.85	0.22	0.18	0.18	0.34	0.11
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	30	genes.ES.table	0.5	1.5	0.042	0.4	0.94	0.33	0.16	0.28	0.31	0.069
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	43	genes.ES.table	0.41	1.5	0.068	0.41	0.85	0.54	0.36	0.34	0.3	0.083
KEGG HISTIDINE METABOLISM	28	genes.ES.table	0.51	1.4	0.088	0.51	0.99	0.39	0.19	0.32	0.42	0.1
KEGG TYROSINE METABOLISM	39	genes.ES.table	0.49	1.3	0.091	0.54	0.99	0.18	0.05	0.17	0.47	0.12
KEGG SELENOAMINO ACID METABOLISM	25	genes.ES.table	0.58	1.7	0.014	0.29	0.61	0.48	0.31	0.33	0.17	0.057
KEGG N GLYCAN BIOSYNTHESIS	45	genes.ES.table	0.53	1.8	0.0094	0.18	0.27	0.49	0.31	0.34	0	0.044
KEGG O GLYCAN BIOSYNTHESIS	28	genes.ES.table	0.6	1.5	0.044	0.45	0.92	0.57	0.18	0.47	0.35	0.085
KEGG INOSITOL PHOSPHATE METABOLISM	53	genes.ES.table	0.36	1.3	0.16	0.53	0.99	0.26	0.22	0.21	0.47	0.11

genes ES table in pathway: BIOCARTA RHO 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	CFTR	CFTR	CFTR	117	0.73	0.086	YES
2	KCNQ1	KCNQ1	KCNQ1	171	0.68	0.17	YES
3	ATP6V1B1	ATP6V1B1	ATP6V1B1	353	0.57	0.23	YES
4	ATP6V1C2	ATP6V1C2	ATP6V1C2	474	0.52	0.29	YES
5	MUC2	MUC2	MUC2	539	0.5	0.35	YES
6	PRKCG	PRKCG	PRKCG	743	0.43	0.39	YES
7	ATP6V0A4	ATP6V0A4	ATP6V0A4	912	0.39	0.43	YES
8	KDELR3	KDELR3	KDELR3	938	0.38	0.48	YES
9	SLC12A2	SLC12A2	SLC12A2	979	0.37	0.52	YES
10	ATP6V1G2	ATP6V1G2	ATP6V1G2	1311	0.31	0.55	YES
11	PRKCA	PRKCA	PRKCA	1701	0.26	0.56	YES
12	ATP6V0E2	ATP6V0E2	ATP6V0E2	1770	0.26	0.59	YES
13	TCIRG1	TCIRG1	TCIRG1	4020	0.11	0.48	NO
14	KDELR2	KDELR2	KDELR2	4338	0.095	0.47	NO
15	PDIA4	PDIA4	PDIA4	4653	0.085	0.46	NO
16	KDELR1	KDELR1	KDELR1	4930	0.078	0.46	NO
17	ADCY9	ADCY9	ADCY9	5598	0.059	0.43	NO
18	ARF1	ARF1	ARF1	7389	0.025	0.33	NO
19	SEC61B	SEC61B	SEC61B	7396	0.025	0.34	NO
20	ATP6AP1	ATP6AP1	ATP6AP1	7516	0.023	0.33	NO
21	GNAS	GNAS	GNAS	7687	0.02	0.32	NO
22	SEC61A1	SEC61A1	SEC61A1	7774	0.019	0.32	NO
23	SEC61A2	SEC61A2	SEC61A2	7880	0.017	0.32	NO
24	ATP6V0A1	ATP6V0A1	ATP6V0A1	8416	0.0093	0.29	NO
25	ATP6V0A2	ATP6V0A2	ATP6V0A2	8810	0.0038	0.27	NO
26	ATP6V0B	ATP6V0B	ATP6V0B	9089	0.00019	0.25	NO
27	ACTG1	ACTG1	ACTG1	9218	-0.0018	0.25	NO
28	TJP1	TJP1	TJP1	9361	-0.0038	0.24	NO
29	TJP2	TJP2	TJP2	9552	-0.0065	0.23	NO
30	SEC61G	SEC61G	SEC61G	10844	-0.026	0.16	NO
31	ATP6V0E1	ATP6V0E1	ATP6V0E1	11015	-0.028	0.16	NO
32	ATP6V0D1	ATP6V0D1	ATP6V0D1	11270	-0.031	0.15	NO
33	ATP6V0C	ATP6V0C	ATP6V0C	11356	-0.033	0.15	NO
34	ATP6V1C1	ATP6V1C1	ATP6V1C1	11467	-0.034	0.14	NO
35	PRKACB	PRKACB	PRKACB	11598	-0.036	0.14	NO
36	ACTB	ACTB	ACTB	11957	-0.042	0.13	NO
37	ATP6V1A	ATP6V1A	ATP6V1A	12247	-0.047	0.12	NO
38	PRKACA	PRKACA	PRKACA	12438	-0.05	0.11	NO
39	ATP6V1F	ATP6V1F	ATP6V1F	12781	-0.057	0.1	NO
40	ATP6V1H	ATP6V1H	ATP6V1H	12951	-0.06	0.1	NO
41	ATP6V1E1	ATP6V1E1	ATP6V1E1	13469	-0.072	0.08	NO
42	PLCG1	PLCG1	PLCG1	13891	-0.082	0.067	NO
43	ATP6V1G1	ATP6V1G1	ATP6V1G1	13910	-0.082	0.077	NO
44	ATP6V1B2	ATP6V1B2	ATP6V1B2	14134	-0.088	0.076	NO
45	PRKCB	PRKCB	PRKCB	14160	-0.089	0.085	NO
46	ATP6V1D	ATP6V1D	ATP6V1D	14195	-0.09	0.095	NO
47	ATP6V1E2	ATP6V1E2	ATP6V1E2	14782	-0.11	0.076	NO
48	ERO1L	ERO1L	ERO1L	15095	-0.12	0.075	NO
49	PRKX	PRKX	PRKX	16431	-0.2	0.027	NO
50	PLCG2	PLCG2	PLCG2	16900	-0.25	0.033	NO
51	ATP6V0D2	ATP6V0D2	ATP6V0D2	17170	-0.29	0.055	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 RHO PATHWAY.

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

genes ES table in pathway: KEGG PURINE METABOLISM

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	MGAT3	MGAT3	MGAT3	379	0.56	0.11	YES
2	ST6GAL1	ST6GAL1	ST6GAL1	407	0.55	0.23	YES
3	ALG11	ALG11	ALG11	1196	0.33	0.26	YES
4	MGAT4A	MGAT4A	MGAT4A	1493	0.28	0.31	YES
5	MAN1C1	MAN1C1	MAN1C1	1743	0.26	0.36	YES
6	DPM3	DPM3	DPM3	2716	0.17	0.34	YES
7	DPAGT1	DPAGT1	DPAGT1	3410	0.13	0.34	YES
8	ALG5	ALG5	ALG5	3484	0.13	0.36	YES
9	ALG10B	ALG10B	ALG10B	3542	0.13	0.39	YES
10	FUT8	FUT8	FUT8	3855	0.11	0.4	YES
11	ALG1	ALG1	ALG1	3922	0.11	0.42	YES
12	STT3A	STT3A	STT3A	4051	0.1	0.44	YES
13	ALG8	ALG8	ALG8	4081	0.1	0.46	YES
14	ALG14	ALG14	ALG14	4450	0.091	0.46	YES
15	MGAT5	MGAT5	MGAT5	4625	0.086	0.47	YES
16	ALG13	ALG13	ALG13	4678	0.085	0.48	YES
17	ALG9	ALG9	ALG9	4689	0.085	0.5	YES
18	MAN2A2	MAN2A2	MAN2A2	5112	0.072	0.5	YES
19	ALG12	ALG12	ALG12	5299	0.067	0.5	YES
20	ALG10	ALG10	ALG10	5313	0.067	0.52	YES
21	MGAT4B	MGAT4B	MGAT4B	5316	0.066	0.53	YES
22	ALG6	ALG6	ALG6	5563	0.06	0.53	YES
23	STT3B	STT3B	STT3B	6379	0.043	0.5	NO
24	MOGS	MOGS	MOGS	6398	0.043	0.5	NO
25	B4GALT1	B4GALT1	B4GALT1	6426	0.042	0.51	NO
26	RPN2	RPN2	RPN2	6614	0.039	0.51	NO
27	DAD1	DAD1	DAD1	6748	0.036	0.51	NO
28	RPN1	RPN1	RPN1	6958	0.033	0.51	NO
29	ALG2	ALG2	ALG2	6971	0.033	0.52	NO
30	MAN1A2	MAN1A2	MAN1A2	7671	0.02	0.48	NO
31	DDOST	DDOST	DDOST	8243	0.012	0.45	NO
32	MAN1B1	MAN1B1	MAN1B1	8517	0.0077	0.44	NO
33	GANAB	GANAB	GANAB	8849	0.0032	0.42	NO
34	MAN1A1	MAN1A1	MAN1A1	9561	-0.0066	0.38	NO
35	DPM2	DPM2	DPM2	10448	-0.02	0.34	NO
36	MGAT5B	MGAT5B	MGAT5B	10656	-0.023	0.33	NO
37	ALG3	ALG3	ALG3	10722	-0.024	0.34	NO
38	MGAT2	MGAT2	MGAT2	10745	-0.024	0.34	NO
39	MAN2A1	MAN2A1	MAN2A1	10876	-0.026	0.34	NO
40	DPM1	DPM1	DPM1	11263	-0.031	0.32	NO
41	B4GALT3	B4GALT3	B4GALT3	11277	-0.032	0.33	NO
42	MGAT1	MGAT1	MGAT1	11786	-0.039	0.31	NO
43	DOLPP1	DOLPP1	DOLPP1	12350	-0.049	0.29	NO
44	B4GALT2	B4GALT2	B4GALT2	12684	-0.055	0.29	NO
45	TUSC3	TUSC3	TUSC3	13511	-0.073	0.26	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: KEGG PURINE METABOLISM.

Figure S44. 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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	AQP2	AQP2	AQP2	46	0.88	0.17	YES
2	CREB3L1	CREB3L1	CREB3L1	110	0.74	0.3	YES
3	CREB3L4	CREB3L4	CREB3L4	1577	0.28	0.28	YES
4	ADCY6	ADCY6	ADCY6	1705	0.26	0.32	YES
5	AVPR2	AVPR2	AVPR2	1870	0.24	0.36	YES
6	CREB5	CREB5	CREB5	1905	0.24	0.4	YES
7	DYNC2LI1	DYNC2LI1	DYNC2LI1	2174	0.22	0.43	YES
8	AQP4	AQP4	AQP4	2190	0.22	0.47	YES
9	CREB3L2	CREB3L2	CREB3L2	2617	0.18	0.48	YES
10	CREB3L3	CREB3L3	CREB3L3	3249	0.14	0.47	NO
11	CREB3	CREB3	CREB3	4245	0.098	0.44	NO
12	NSF	NSF	NSF	4547	0.088	0.44	NO
13	ADCY9	ADCY9	ADCY9	5598	0.059	0.39	NO
14	VAMP2	VAMP2	VAMP2	5607	0.059	0.4	NO
15	RAB11B	RAB11B	RAB11B	6990	0.032	0.33	NO
16	RAB5A	RAB5A	RAB5A	7461	0.024	0.31	NO
17	GNAS	GNAS	GNAS	7687	0.02	0.3	NO
18	RAB5C	RAB5C	RAB5C	7876	0.018	0.29	NO
19	DCTN1	DCTN1	DCTN1	9499	-0.0059	0.21	NO
20	DYNC1LI2	DYNC1LI2	DYNC1LI2	9744	-0.0095	0.2	NO
21	ARHGDIA	ARHGDIA	ARHGDIA	9872	-0.011	0.19	NO
22	CREB1	CREB1	CREB1	10154	-0.016	0.18	NO
23	DYNLL2	DYNLL2	DYNLL2	10180	-0.016	0.18	NO
24	RAB11A	RAB11A	RAB11A	10389	-0.019	0.17	NO
25	DYNC1LI1	DYNC1LI1	DYNC1LI1	11079	-0.029	0.14	NO
26	DYNC1I2	DYNC1I2	DYNC1I2	11288	-0.032	0.13	NO
27	RAB5B	RAB5B	RAB5B	11311	-0.032	0.14	NO
28	DCTN5	DCTN5	DCTN5	11434	-0.034	0.14	NO
29	DYNC2H1	DYNC2H1	DYNC2H1	11493	-0.034	0.14	NO
30	PRKACB	PRKACB	PRKACB	11598	-0.036	0.14	NO
31	STX4	STX4	STX4	12011	-0.043	0.13	NO
32	PRKACA	PRKACA	PRKACA	12438	-0.05	0.11	NO
33	DCTN6	DCTN6	DCTN6	12725	-0.056	0.11	NO
34	DYNC1H1	DYNC1H1	DYNC1H1	12871	-0.059	0.11	NO
35	DCTN2	DCTN2	DCTN2	13010	-0.061	0.12	NO
36	DCTN4	DCTN4	DCTN4	13542	-0.073	0.1	NO
37	ARHGDIB	ARHGDIB	ARHGDIB	14181	-0.089	0.083	NO
38	DYNLL1	DYNLL1	DYNLL1	14201	-0.09	0.1	NO
39	PRKX	PRKX	PRKX	16431	-0.2	0.016	NO
40	DYNC1I1	DYNC1I1	DYNC1I1	16442	-0.2	0.054	NO
41	AQP3	AQP3	AQP3	16554	-0.22	0.089	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: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

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

Table 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	GGT1	GGT1	GGT1	852	0.4	0.11	YES
2	PAPSS2	PAPSS2	PAPSS2	855	0.4	0.26	YES
3	GGT6	GGT6	GGT6	1376	0.3	0.36	YES
4	GGT7	GGT7	GGT7	1963	0.24	0.41	YES
5	CTH	CTH	CTH	2001	0.23	0.5	YES
6	CBS	CBS	CBS	2564	0.18	0.54	YES
7	HEMK1	HEMK1	HEMK1	3229	0.14	0.56	YES
8	AHCYL2	AHCYL2	AHCYL2	4202	0.099	0.55	YES
9	SCLY	SCLY	SCLY	5032	0.075	0.53	YES
10	AHCYL1	AHCYL1	AHCYL1	5157	0.071	0.55	YES
11	WBSCR22	WBSCR22	WBSCR22	5528	0.061	0.56	YES
12	MAT2A	MAT2A	MAT2A	5614	0.059	0.57	YES
13	AHCY	AHCY	AHCY	6611	0.039	0.54	NO
14	SEPHS1	SEPHS1	SEPHS1	7326	0.026	0.51	NO
15	TRMT11	TRMT11	TRMT11	7592	0.022	0.5	NO
16	LCMT1	LCMT1	LCMT1	7886	0.017	0.49	NO
17	LCMT2	LCMT2	LCMT2	7939	0.016	0.5	NO
18	METTL2B	METTL2B	METTL2B	8106	0.014	0.49	NO
19	METTL6	METTL6	METTL6	9439	-0.005	0.42	NO
20	PAPSS1	PAPSS1	PAPSS1	9538	-0.0064	0.42	NO
21	MAT1A	MAT1A	MAT1A	9952	-0.012	0.4	NO
22	MAT2B	MAT2B	MAT2B	10316	-0.018	0.39	NO
23	MARS	MARS	MARS	10970	-0.028	0.36	NO
24	MARS2	MARS2	MARS2	12124	-0.045	0.32	NO
25	GGT5	GGT5	GGT5	12228	-0.047	0.33	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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG HISTIDINE 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	MPV17L	MPV17L	MPV17L	583	0.48	0.022	YES
2	SLC27A2	SLC27A2	SLC27A2	624	0.46	0.072	YES
3	PIPOX	PIPOX	PIPOX	887	0.39	0.1	YES
4	PECR	PECR	PECR	899	0.39	0.15	YES
5	PHYH	PHYH	PHYH	962	0.37	0.18	YES
6	DDO	DDO	DDO	1016	0.36	0.22	YES
7	ACSL5	ACSL5	ACSL5	1130	0.34	0.26	YES
8	AGXT	AGXT	AGXT	1504	0.28	0.27	YES
9	DECR2	DECR2	DECR2	1984	0.23	0.27	YES
10	PEX11G	PEX11G	PEX11G	2251	0.21	0.28	YES
11	CAT	CAT	CAT	2369	0.2	0.29	YES
12	FAR2	FAR2	FAR2	2414	0.19	0.31	YES
13	NUDT12	NUDT12	NUDT12	2687	0.18	0.32	YES
14	ABCD3	ABCD3	ABCD3	2706	0.17	0.34	YES
15	NOS2	NOS2	NOS2	2739	0.17	0.35	YES
16	PXMP2	PXMP2	PXMP2	2767	0.17	0.37	YES
17	PEX11A	PEX11A	PEX11A	3046	0.15	0.37	YES
18	CRAT	CRAT	CRAT	3217	0.14	0.38	YES
19	PXMP4	PXMP4	PXMP4	3317	0.14	0.39	YES
20	BAAT	BAAT	BAAT	3590	0.12	0.39	YES
21	PEX7	PEX7	PEX7	3808	0.11	0.39	YES
22	GSTK1	GSTK1	GSTK1	3943	0.11	0.4	YES
23	IDH1	IDH1	IDH1	4044	0.1	0.4	YES
24	HMGCL	HMGCL	HMGCL	4076	0.1	0.41	YES
25	ACSL4	ACSL4	ACSL4	4317	0.096	0.41	NO
26	PEX11B	PEX11B	PEX11B	4929	0.078	0.38	NO
27	HACL1	HACL1	HACL1	4969	0.077	0.39	NO
28	HAO2	HAO2	HAO2	5015	0.076	0.4	NO
29	MLYCD	MLYCD	MLYCD	5362	0.065	0.39	NO
30	PEX6	PEX6	PEX6	5416	0.064	0.39	NO
31	AMACR	AMACR	AMACR	5608	0.059	0.39	NO
32	ACOT8	ACOT8	ACOT8	5777	0.055	0.38	NO
33	PEX2	PEX2	PEX2	5946	0.052	0.38	NO
34	PEX1	PEX1	PEX1	6061	0.05	0.38	NO
35	SCP2	SCP2	SCP2	6113	0.049	0.38	NO
36	GNPAT	GNPAT	GNPAT	6127	0.048	0.39	NO
37	ABCD1	ABCD1	ABCD1	6263	0.046	0.38	NO
38	ABCD4	ABCD4	ABCD4	6395	0.043	0.38	NO
39	PRDX5	PRDX5	PRDX5	6730	0.037	0.37	NO
40	PEX16	PEX16	PEX16	6827	0.035	0.37	NO
41	ACOX1	ACOX1	ACOX1	6865	0.034	0.37	NO
42	PEX26	PEX26	PEX26	7227	0.028	0.35	NO
43	ACAA1	ACAA1	ACAA1	7320	0.026	0.35	NO
44	IDH2	IDH2	IDH2	7659	0.02	0.33	NO
45	HSD17B4	HSD17B4	HSD17B4	7660	0.02	0.34	NO
46	ECH1	ECH1	ECH1	7908	0.017	0.32	NO
47	ACSL3	ACSL3	ACSL3	8197	0.013	0.31	NO
48	PEX19	PEX19	PEX19	9291	-0.0029	0.25	NO
49	SOD1	SOD1	SOD1	9422	-0.0049	0.24	NO
50	EHHADH	EHHADH	EHHADH	9949	-0.012	0.22	NO
51	MPV17	MPV17	MPV17	10421	-0.019	0.19	NO
52	PMVK	PMVK	PMVK	10461	-0.02	0.19	NO
53	SLC25A17	SLC25A17	SLC25A17	10560	-0.021	0.19	NO
54	AGPS	AGPS	AGPS	10595	-0.022	0.19	NO
55	PEX10	PEX10	PEX10	11283	-0.032	0.16	NO
56	PEX13	PEX13	PEX13	11347	-0.032	0.16	NO
57	PRDX1	PRDX1	PRDX1	11394	-0.033	0.16	NO
58	PAOX	PAOX	PAOX	11963	-0.042	0.13	NO
59	PEX12	PEX12	PEX12	12077	-0.044	0.13	NO
60	DHRS4	DHRS4	DHRS4	12157	-0.045	0.13	NO
61	PEX3	PEX3	PEX3	12264	-0.047	0.13	NO
62	PEX5	PEX5	PEX5	12333	-0.049	0.13	NO
63	PEX14	PEX14	PEX14	12582	-0.053	0.12	NO
64	FAR1	FAR1	FAR1	13679	-0.077	0.071	NO
65	ACOX3	ACOX3	ACOX3	14035	-0.086	0.061	NO
66	ABCD2	ABCD2	ABCD2	14037	-0.086	0.071	NO
67	PECI	PECI	PECI	14272	-0.092	0.068	NO
68	SOD2	SOD2	SOD2	14305	-0.093	0.077	NO
69	NUDT19	NUDT19	NUDT19	14831	-0.11	0.061	NO
70	MVK	MVK	MVK	14980	-0.12	0.066	NO
71	ACSL1	ACSL1	ACSL1	15319	-0.13	0.063	NO
72	XDH	XDH	XDH	15618	-0.15	0.063	NO
73	ACSL6	ACSL6	ACSL6	16065	-0.18	0.058	NO
74	EPHX2	EPHX2	EPHX2	16901	-0.25	0.041	NO
75	CROT	CROT	CROT	16923	-0.26	0.069	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 HISTIDINE METABOLISM.

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

genes ES table in pathway: KEGG TYROSINE 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	ENTPD8	ENTPD8	ENTPD8	23	0.97	0.044	YES
2	PDE4C	PDE4C	PDE4C	156	0.7	0.07	YES
3	ENPP3	ENPP3	ENPP3	229	0.64	0.096	YES
4	FHIT	FHIT	FHIT	375	0.56	0.11	YES
5	NME5	NME5	NME5	397	0.55	0.14	YES
6	AK7	AK7	AK7	433	0.54	0.16	YES
7	GMPR	GMPR	GMPR	494	0.51	0.18	YES
8	PDE8B	PDE8B	PDE8B	502	0.51	0.21	YES
9	ENTPD2	ENTPD2	ENTPD2	508	0.5	0.23	YES
10	PDE11A	PDE11A	PDE11A	529	0.5	0.25	YES
11	ENPP1	ENPP1	ENPP1	585	0.48	0.27	YES
12	PDE9A	PDE9A	PDE9A	723	0.43	0.28	YES
13	GDA	GDA	GDA	731	0.43	0.3	YES
14	PAPSS2	PAPSS2	PAPSS2	855	0.4	0.32	YES
15	PDE3A	PDE3A	PDE3A	921	0.38	0.33	YES
16	ADCY2	ADCY2	ADCY2	994	0.37	0.34	YES
17	PDE4A	PDE4A	PDE4A	1563	0.28	0.32	YES
18	GUCY2C	GUCY2C	GUCY2C	1581	0.28	0.34	YES
19	PDE5A	PDE5A	PDE5A	1594	0.27	0.35	YES
20	NPR2	NPR2	NPR2	1611	0.27	0.36	YES
21	ADCY6	ADCY6	ADCY6	1705	0.26	0.37	YES
22	PDE6B	PDE6B	PDE6B	1778	0.26	0.38	YES
23	ADCY4	ADCY4	ADCY4	2327	0.2	0.36	YES
24	NT5E	NT5E	NT5E	2346	0.2	0.36	YES
25	ADCY5	ADCY5	ADCY5	2492	0.19	0.36	YES
26	ENTPD6	ENTPD6	ENTPD6	2693	0.18	0.36	YES
27	NT5M	NT5M	NT5M	2816	0.17	0.36	YES
28	AK1	AK1	AK1	2897	0.16	0.37	YES
29	PDE7B	PDE7B	PDE7B	2999	0.16	0.37	YES
30	NME4	NME4	NME4	3039	0.15	0.37	YES
31	PDE4D	PDE4D	PDE4D	3098	0.15	0.38	YES
32	PDE10A	PDE10A	PDE10A	3223	0.14	0.38	YES
33	NME3	NME3	NME3	3228	0.14	0.38	YES
34	PFAS	PFAS	PFAS	3369	0.14	0.38	NO
35	CANT1	CANT1	CANT1	3487	0.13	0.38	NO
36	NPR1	NPR1	NPR1	3634	0.12	0.38	NO
37	GUCY1B3	GUCY1B3	GUCY1B3	3713	0.12	0.38	NO
38	PDE1A	PDE1A	PDE1A	3944	0.11	0.37	NO
39	GUCY1A2	GUCY1A2	GUCY1A2	4404	0.093	0.35	NO
40	NME7	NME7	NME7	4582	0.087	0.34	NO
41	NUDT9	NUDT9	NUDT9	5004	0.076	0.32	NO
42	POLR3GL	POLR3GL	POLR3GL	5035	0.075	0.33	NO
43	AMPD1	AMPD1	AMPD1	5081	0.073	0.33	NO
44	PRPS2	PRPS2	PRPS2	5279	0.067	0.32	NO
45	ADCY9	ADCY9	ADCY9	5598	0.059	0.31	NO
46	POLD3	POLD3	POLD3	5704	0.057	0.3	NO
47	NT5C2	NT5C2	NT5C2	5790	0.055	0.3	NO
48	ATIC	ATIC	ATIC	5813	0.054	0.3	NO
49	POLR2H	POLR2H	POLR2H	5837	0.054	0.3	NO
50	POLD4	POLD4	POLD4	5869	0.053	0.3	NO
51	NT5C1B	NT5C1B	NT5C1B	5980	0.051	0.3	NO
52	GUCY1A3	GUCY1A3	GUCY1A3	6170	0.047	0.29	NO
53	POLA2	POLA2	POLA2	6202	0.047	0.29	NO
54	NME6	NME6	NME6	6846	0.035	0.26	NO
55	ENTPD5	ENTPD5	ENTPD5	6902	0.034	0.26	NO
56	ENTPD4	ENTPD4	ENTPD4	6964	0.033	0.26	NO
57	POLR2L	POLR2L	POLR2L	7081	0.031	0.25	NO
58	PDE6D	PDE6D	PDE6D	7140	0.03	0.25	NO
59	IMPDH2	IMPDH2	IMPDH2	7226	0.028	0.24	NO
60	PKLR	PKLR	PKLR	7235	0.028	0.25	NO
61	POLR2I	POLR2I	POLR2I	7263	0.028	0.24	NO
62	POLR3K	POLR3K	POLR3K	7264	0.028	0.25	NO
63	POLE	POLE	POLE	7358	0.026	0.24	NO
64	PDE8A	PDE8A	PDE8A	7417	0.025	0.24	NO
65	POLE4	POLE4	POLE4	7498	0.023	0.24	NO
66	POLR2J	POLR2J	POLR2J	7504	0.023	0.24	NO
67	POLR1C	POLR1C	POLR1C	7554	0.022	0.24	NO
68	PRIM2	PRIM2	PRIM2	8067	0.015	0.21	NO
69	NT5C	NT5C	NT5C	8249	0.012	0.2	NO
70	ZNRD1	ZNRD1	ZNRD1	8853	0.0032	0.17	NO
71	POLR3C	POLR3C	POLR3C	8900	0.0025	0.16	NO
72	PRIM1	PRIM1	PRIM1	9051	0.00064	0.16	NO
73	PRUNE	PRUNE	PRUNE	9118	-0.00024	0.15	NO
74	DCK	DCK	DCK	9120	-0.00028	0.15	NO
75	ADSL	ADSL	ADSL	9140	-0.00063	0.15	NO
76	POLA1	POLA1	POLA1	9261	-0.0025	0.14	NO
77	POLR2E	POLR2E	POLR2E	9399	-0.0045	0.14	NO
78	DGUOK	DGUOK	DGUOK	9406	-0.0046	0.14	NO
79	GUK1	GUK1	GUK1	9507	-0.006	0.13	NO
80	PAPSS1	PAPSS1	PAPSS1	9538	-0.0064	0.13	NO
81	ITPA	ITPA	ITPA	9682	-0.0085	0.12	NO
82	AK2	AK2	AK2	9695	-0.0087	0.12	NO
83	POLD2	POLD2	POLD2	9860	-0.011	0.11	NO
84	POLR2K	POLR2K	POLR2K	10084	-0.014	0.1	NO
85	GMPR2	GMPR2	GMPR2	10107	-0.015	0.1	NO
86	AMPD2	AMPD2	AMPD2	10196	-0.016	0.097	NO
87	NME2	NME2	NME2	10444	-0.02	0.084	NO
88	PPAT	PPAT	PPAT	10450	-0.02	0.085	NO
89	RRM2	RRM2	RRM2	10485	-0.02	0.084	NO
90	RRM2B	RRM2B	RRM2B	10626	-0.022	0.077	NO
91	NUDT5	NUDT5	NUDT5	10665	-0.023	0.076	NO
92	POLR2B	POLR2B	POLR2B	10739	-0.024	0.073	NO
93	NUDT2	NUDT2	NUDT2	10852	-0.026	0.068	NO
94	POLR2C	POLR2C	POLR2C	11280	-0.032	0.046	NO
95	POLR2G	POLR2G	POLR2G	11333	-0.032	0.045	NO
96	HPRT1	HPRT1	HPRT1	11443	-0.034	0.04	NO
97	NT5C3	NT5C3	NT5C3	11463	-0.034	0.041	NO
98	PAICS	PAICS	PAICS	11494	-0.034	0.041	NO
99	RRM1	RRM1	RRM1	11577	-0.036	0.038	NO
100	POLD1	POLD1	POLD1	11856	-0.041	0.024	NO
101	PNPT1	PNPT1	PNPT1	11896	-0.041	0.024	NO
102	POLR2D	POLR2D	POLR2D	11933	-0.042	0.024	NO
103	POLR3A	POLR3A	POLR3A	12080	-0.044	0.018	NO
104	ADSS	ADSS	ADSS	12102	-0.044	0.019	NO
105	ENTPD1	ENTPD1	ENTPD1	12256	-0.047	0.013	NO
106	POLE2	POLE2	POLE2	12343	-0.049	0.01	NO
107	POLR3H	POLR3H	POLR3H	12389	-0.05	0.01	NO
108	PDE7A	PDE7A	PDE7A	12532	-0.052	0.0047	NO
109	POLR2A	POLR2A	POLR2A	12546	-0.052	0.0065	NO
110	NME1	NME1	NME1	12778	-0.057	-0.0037	NO
111	GMPS	GMPS	GMPS	12795	-0.057	-0.0019	NO
112	PNP	PNP	PNP	13024	-0.062	-0.012	NO
113	POLR2F	POLR2F	POLR2F	13088	-0.063	-0.012	NO
114	PRPS1	PRPS1	PRPS1	13101	-0.063	-0.0099	NO
115	PKM2	PKM2	PKM2	13112	-0.063	-0.0075	NO
116	GART	GART	GART	13308	-0.068	-0.015	NO
117	POLR1B	POLR1B	POLR1B	13323	-0.068	-0.013	NO
118	POLE3	POLE3	POLE3	13374	-0.07	-0.012	NO
119	PDE4B	PDE4B	PDE4B	13496	-0.072	-0.016	NO
120	POLR1E	POLR1E	POLR1E	13712	-0.078	-0.024	NO
121	POLR3D	POLR3D	POLR3D	13721	-0.078	-0.021	NO
122	POLR3F	POLR3F	POLR3F	13762	-0.079	-0.019	NO
123	POLR2J2	POLR2J2	POLR2J2	13823	-0.08	-0.019	NO
124	APRT	APRT	APRT	13876	-0.081	-0.018	NO
125	IMPDH1	IMPDH1	IMPDH1	13963	-0.083	-0.019	NO
126	ADCY10	ADCY10	ADCY10	13980	-0.084	-0.016	NO
127	POLR1D	POLR1D	POLR1D	14049	-0.086	-0.015	NO
128	PDE1C	PDE1C	PDE1C	14089	-0.087	-0.013	NO
129	POLR1A	POLR1A	POLR1A	14370	-0.096	-0.024	NO
130	ENTPD3	ENTPD3	ENTPD3	15108	-0.12	-0.06	NO
131	XDH	XDH	XDH	15618	-0.15	-0.081	NO
132	PDE6A	PDE6A	PDE6A	15638	-0.15	-0.075	NO
133	PDE3B	PDE3B	PDE3B	15696	-0.15	-0.071	NO
134	AMPD3	AMPD3	AMPD3	15803	-0.16	-0.069	NO
135	POLR2J3	POLR2J3	POLR2J3	15812	-0.16	-0.062	NO
136	PRPS1L1	PRPS1L1	PRPS1L1	15847	-0.16	-0.056	NO
137	POLR3B	POLR3B	POLR3B	15961	-0.17	-0.055	NO
138	GUCY2D	GUCY2D	GUCY2D	16436	-0.2	-0.071	NO
139	ADK	ADK	ADK	16444	-0.2	-0.062	NO
140	PDE6G	PDE6G	PDE6G	16489	-0.21	-0.055	NO
141	NME1-NME2	NME1-NME2	NME1-NME2	16795	-0.24	-0.061	NO
142	AK3L1	AK3L1	AK3L1	16884	-0.25	-0.054	NO
143	AK5	AK5	AK5	16927	-0.26	-0.044	NO
144	ADSSL1	ADSSL1	ADSSL1	17014	-0.27	-0.036	NO
145	ADCY7	ADCY7	ADCY7	17248	-0.3	-0.035	NO
146	ADCY1	ADCY1	ADCY1	17322	-0.32	-0.024	NO
147	PDE1B	PDE1B	PDE1B	17484	-0.35	-0.016	NO
148	PDE2A	PDE2A	PDE2A	17492	-0.35	-0.00032	NO
149	ADA	ADA	ADA	17629	-0.39	0.01	NO
150	POLR3G	POLR3G	POLR3G	17726	-0.42	0.025	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 TYROSINE METABOLISM.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TYROSINE 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 SELENOAMINO ACID METABOLISM

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	HMGCS2	HMGCS2	HMGCS2	1363	0.3	0.015	YES
2	BCKDHB	BCKDHB	BCKDHB	1962	0.24	0.051	YES
3	IVD	IVD	IVD	2103	0.22	0.11	YES
4	ACAD8	ACAD8	ACAD8	2723	0.17	0.13	YES
5	PCCA	PCCA	PCCA	2798	0.17	0.17	YES
6	ALDH6A1	ALDH6A1	ALDH6A1	3135	0.15	0.2	YES
7	ALDH2	ALDH2	ALDH2	3282	0.14	0.23	YES
8	ALDH7A1	ALDH7A1	ALDH7A1	3436	0.13	0.26	YES
9	ACADS	ACADS	ACADS	3657	0.12	0.28	YES
10	ACAA2	ACAA2	ACAA2	4062	0.1	0.29	YES
11	HIBADH	HIBADH	HIBADH	4068	0.1	0.32	YES
12	HMGCL	HMGCL	HMGCL	4076	0.1	0.36	YES
13	AUH	AUH	AUH	4426	0.092	0.36	YES
14	ALDH1B1	ALDH1B1	ALDH1B1	4479	0.09	0.39	YES
15	ACADSB	ACADSB	ACADSB	4980	0.076	0.38	YES
16	ECHS1	ECHS1	ECHS1	5245	0.068	0.39	YES
17	MCCC2	MCCC2	MCCC2	5358	0.065	0.4	YES
18	ACADM	ACADM	ACADM	5732	0.056	0.4	YES
19	HADH	HADH	HADH	6060	0.05	0.39	YES
20	ALDH9A1	ALDH9A1	ALDH9A1	6235	0.046	0.4	YES
21	MCCC1	MCCC1	MCCC1	6428	0.042	0.4	YES
22	ACAT1	ACAT1	ACAT1	6429	0.042	0.41	YES
23	MCEE	MCEE	MCEE	6589	0.039	0.42	YES
24	ACAA1	ACAA1	ACAA1	7320	0.026	0.38	NO
25	AOX1	AOX1	AOX1	7488	0.024	0.38	NO
26	MUT	MUT	MUT	7547	0.022	0.38	NO
27	ALDH3A2	ALDH3A2	ALDH3A2	8275	0.012	0.35	NO
28	HADHB	HADHB	HADHB	8299	0.011	0.35	NO
29	PCCB	PCCB	PCCB	8690	0.0054	0.33	NO
30	BCAT2	BCAT2	BCAT2	8758	0.0046	0.33	NO
31	HSD17B10	HSD17B10	HSD17B10	8986	0.0013	0.31	NO
32	HADHA	HADHA	HADHA	8991	0.0013	0.32	NO
33	EHHADH	EHHADH	EHHADH	9949	-0.012	0.27	NO
34	DBT	DBT	DBT	10140	-0.015	0.26	NO
35	DLD	DLD	DLD	10225	-0.017	0.26	NO
36	HIBCH	HIBCH	HIBCH	10235	-0.017	0.26	NO
37	ACAT2	ACAT2	ACAT2	11631	-0.037	0.2	NO
38	IL4I1	IL4I1	IL4I1	11838	-0.04	0.2	NO
39	BCKDHA	BCKDHA	BCKDHA	11991	-0.043	0.2	NO
40	OXCT1	OXCT1	OXCT1	12709	-0.056	0.18	NO
41	HMGCS1	HMGCS1	HMGCS1	13011	-0.061	0.18	NO
42	ABAT	ABAT	ABAT	14889	-0.11	0.11	NO
43	OXCT2	OXCT2	OXCT2	16729	-0.23	0.08	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 SELENOAMINO ACID METABOLISM.

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

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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	PIP5K1B	PIP5K1B	PIP5K1B	20	0.99	0.4	YES
2	ARHGAP6	ARHGAP6	ARHGAP6	2673	0.18	0.32	NO
3	OPHN1	OPHN1	OPHN1	3849	0.11	0.3	NO
4	GSN	GSN	GSN	5597	0.059	0.23	NO
5	RHOA	RHOA	RHOA	7058	0.031	0.16	NO
6	BAIAP2	BAIAP2	BAIAP2	7484	0.024	0.15	NO
7	PFN1	PFN1	PFN1	8390	0.0096	0.1	NO
8	ARPC1B	ARPC1B	ARPC1B	8444	0.0089	0.1	NO
9	ARPC4	ARPC4	ARPC4	8477	0.0084	0.1	NO
10	ARHGAP4	ARHGAP4	ARHGAP4	9002	0.0012	0.074	NO
11	ARHGAP1	ARHGAP1	ARHGAP1	9274	-0.0027	0.06	NO
12	MYL2	MYL2	MYL2	9278	-0.0028	0.061	NO
13	ARHGEF11	ARHGEF11	ARHGEF11	9312	-0.0033	0.061	NO
14	ARHGAP5	ARHGAP5	ARHGAP5	9402	-0.0046	0.058	NO
15	DIAPH1	DIAPH1	DIAPH1	9630	-0.0077	0.048	NO
16	ARPC3	ARPC3	ARPC3	10012	-0.014	0.032	NO
17	ROCK1	ROCK1	ROCK1	10329	-0.018	0.022	NO
18	ARPC5	ARPC5	ARPC5	10639	-0.023	0.014	NO
19	CFL1	CFL1	CFL1	11246	-0.031	-0.0065	NO
20	ACTR2	ACTR2	ACTR2	11255	-0.031	0.0055	NO
21	VCL	VCL	VCL	11642	-0.037	-0.00096	NO
22	ARPC1A	ARPC1A	ARPC1A	11895	-0.041	0.0016	NO
23	ARHGEF1	ARHGEF1	ARHGEF1	12111	-0.044	0.0076	NO
24	PPP1R12B	PPP1R12B	PPP1R12B	12205	-0.046	0.021	NO
25	SRC	SRC	SRC	12402	-0.05	0.03	NO
26	PIP5K1A	PIP5K1A	PIP5K1A	13246	-0.066	0.01	NO
27	ACTR3	ACTR3	ACTR3	13631	-0.075	0.019	NO
28	LIMK1	LIMK1	LIMK1	13972	-0.084	0.034	NO
29	ARHGEF5	ARHGEF5	ARHGEF5	14456	-0.098	0.046	NO
30	ARPC2	ARPC2	ARPC2	15278	-0.13	0.054	NO
31	MYLK	MYLK	MYLK	16984	-0.26	0.065	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 N GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

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	ST6GALNAC1	ST6GALNAC1	ST6GALNAC1	167	0.69	0.083	YES
2	GCNT3	GCNT3	GCNT3	246	0.63	0.16	YES
3	GALNT12	GALNT12	GALNT12	460	0.53	0.22	YES
4	GALNTL6	GALNTL6	GALNTL6	515	0.5	0.29	YES
5	GALNT4	GALNT4	GALNT4	603	0.47	0.35	YES
6	GALNT9	GALNT9	GALNT9	705	0.44	0.4	YES
7	GALNT6	GALNT6	GALNT6	841	0.4	0.45	YES
8	B3GNT6	B3GNT6	B3GNT6	1047	0.36	0.48	YES
9	GALNTL1	GALNTL1	GALNTL1	1112	0.34	0.53	YES
10	GALNT7	GALNT7	GALNT7	1178	0.34	0.57	YES
11	GCNT1	GCNT1	GCNT1	1318	0.31	0.6	YES
12	GALNT5	GALNT5	GALNT5	2073	0.22	0.59	YES
13	GALNT10	GALNT10	GALNT10	2401	0.2	0.6	YES
14	GALNT8	GALNT8	GALNT8	2981	0.16	0.59	YES
15	C1GALT1	C1GALT1	C1GALT1	3155	0.14	0.6	YES
16	B4GALT5	B4GALT5	B4GALT5	3370	0.13	0.6	YES
17	C1GALT1C1	C1GALT1C1	C1GALT1C1	4388	0.094	0.56	NO
18	ST3GAL2	ST3GAL2	ST3GAL2	6906	0.034	0.43	NO
19	WBSCR17	WBSCR17	WBSCR17	10703	-0.024	0.22	NO
20	GALNT11	GALNT11	GALNT11	11379	-0.033	0.19	NO
21	GALNTL2	GALNTL2	GALNTL2	12494	-0.052	0.13	NO
22	GALNT13	GALNT13	GALNT13	12541	-0.052	0.14	NO
23	ST3GAL1	ST3GAL1	ST3GAL1	13681	-0.077	0.085	NO
24	GALNT2	GALNT2	GALNT2	14015	-0.085	0.078	NO
25	GALNT1	GALNT1	GALNT1	15181	-0.13	0.031	NO
26	GALNT14	GALNT14	GALNT14	16770	-0.24	-0.025	NO
27	GCNT4	GCNT4	GCNT4	17275	-0.31	-0.011	NO
28	GALNTL4	GALNTL4	GALNTL4	17822	-0.45	0.019	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 O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG INOSITOL PHOSPHATE METABOLISM

Table 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	SMPD3	SMPD3	SMPD3	128	0.72	0.1	YES
2	DEGS2	DEGS2	DEGS2	154	0.7	0.21	YES
3	NEU4	NEU4	NEU4	168	0.69	0.31	YES
4	GAL3ST1	GAL3ST1	GAL3ST1	177	0.68	0.42	YES
5	UGT8	UGT8	UGT8	595	0.47	0.47	YES
6	SGPP2	SGPP2	SGPP2	1780	0.25	0.44	YES
7	PPAP2C	PPAP2C	PPAP2C	1926	0.24	0.47	YES
8	GLB1	GLB1	GLB1	2758	0.17	0.45	YES
9	SGMS2	SGMS2	SGMS2	2888	0.16	0.47	YES
10	SMPD2	SMPD2	SMPD2	2914	0.16	0.49	YES
11	NEU1	NEU1	NEU1	3530	0.13	0.48	NO
12	PPAP2B	PPAP2B	PPAP2B	4380	0.094	0.44	NO
13	ASAH1	ASAH1	ASAH1	4539	0.088	0.45	NO
14	SMPD1	SMPD1	SMPD1	4543	0.088	0.46	NO
15	SPHK2	SPHK2	SPHK2	4753	0.083	0.46	NO
16	NEU3	NEU3	NEU3	4897	0.079	0.47	NO
17	SPTLC2	SPTLC2	SPTLC2	5571	0.06	0.44	NO
18	GALC	GALC	GALC	5665	0.058	0.44	NO
19	ARSA	ARSA	ARSA	6276	0.045	0.42	NO
20	CERK	CERK	CERK	6450	0.042	0.42	NO
21	SGPL1	SGPL1	SGPL1	7231	0.028	0.38	NO
22	GBA	GBA	GBA	8348	0.01	0.32	NO
23	SMPD4	SMPD4	SMPD4	9162	-0.00098	0.27	NO
24	ASAH2	ASAH2	ASAH2	10522	-0.021	0.2	NO
25	GLA	GLA	GLA	10573	-0.022	0.2	NO
26	SGMS1	SGMS1	SGMS1	11489	-0.034	0.16	NO
27	ACER3	ACER3	ACER3	12068	-0.044	0.13	NO
28	SPTLC1	SPTLC1	SPTLC1	13136	-0.064	0.081	NO
29	DEGS1	DEGS1	DEGS1	13724	-0.078	0.06	NO
30	UGCG	UGCG	UGCG	13867	-0.081	0.065	NO
31	PPAP2A	PPAP2A	PPAP2A	14003	-0.085	0.071	NO
32	B4GALT6	B4GALT6	B4GALT6	15112	-0.12	0.028	NO
33	SPHK1	SPHK1	SPHK1	15522	-0.14	0.028	NO
34	ACER2	ACER2	ACER2	15765	-0.16	0.038	NO
35	SGPP1	SGPP1	SGPP1	15805	-0.16	0.061	NO
36	KDSR	KDSR	KDSR	15818	-0.16	0.085	NO
37	ACER1	ACER1	ACER1	17165	-0.29	0.055	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 INOSITOL PHOSPHATE METABOLISM.

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

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 G1 PATHWAY	27	genes.ES.table	0.43	1.3	0.17	0.58	0.99	0.26	0.14	0.22	0.49	0.13
BIOCARTA INFLAM PATHWAY	26	genes.ES.table	0.68	1.4	0.081	0.56	0.96	0.5	0.094	0.45	0.46	0.14
BIOCARTA ERK PATHWAY	27	genes.ES.table	0.47	1.5	0.092	0.43	0.92	0.37	0.16	0.31	0.32	0.08
BIOCARTA INTEGRIN PATHWAY	37	genes.ES.table	0.57	2	0	0.13	0.077	0.3	0.13	0.26	0	0.052
BIOCARTA IL1R PATHWAY	32	genes.ES.table	0.62	1.7	0.012	0.23	0.52	0.28	0.08	0.26	0.12	0.05
KEGG PYRIMIDINE METABOLISM	96	genes.ES.table	0.32	1.5	0.065	0.43	0.9	0.31	0.22	0.24	0.31	0.086
KEGG AMINOACYL TRNA BIOSYNTHESIS	40	genes.ES.table	0.39	1.5	0.11	0.42	0.86	0.4	0.28	0.29	0.3	0.094
KEGG RIBOSOME	84	genes.ES.table	0.67	1.7	0.059	0.26	0.66	0.92	0.31	0.63	0.16	0.049
KEGG SPLICEOSOME	125	genes.ES.table	0.32	1.4	0.16	0.64	0.98	1	0.68	0.32	0.54	0.17
KEGG PROTEASOME	42	genes.ES.table	0.63	1.8	0.006	0.24	0.37	0.93	0.35	0.6	0	0.069

genes ES table in pathway: BIOCARTA G1 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	CAV1	CAV1	CAV1	71	0.5	0.16	YES
2	PXN	PXN	PXN	647	0.25	0.21	YES
3	ACTN1	ACTN1	ACTN1	824	0.22	0.27	YES
4	ITGA1	ITGA1	ITGA1	906	0.21	0.34	YES
5	BCAR1	BCAR1	BCAR1	1275	0.17	0.37	YES
6	SHC1	SHC1	SHC1	1378	0.16	0.42	YES
7	ITGB1	ITGB1	ITGB1	1496	0.16	0.46	YES
8	HRAS	HRAS	HRAS	1688	0.14	0.5	YES
9	ACTN3	ACTN3	ACTN3	1730	0.14	0.54	YES
10	ZYX	ZYX	ZYX	1986	0.12	0.56	YES
11	MAP2K1	MAP2K1	MAP2K1	2417	0.099	0.57	YES
12	FYN	FYN	FYN	3192	0.073	0.55	NO
13	VCL	VCL	VCL	3286	0.07	0.57	NO
14	BCR	BCR	BCR	4333	0.048	0.53	NO
15	CRKL	CRKL	CRKL	4710	0.041	0.52	NO
16	CAPNS1	CAPNS1	CAPNS1	5019	0.036	0.52	NO
17	CAPN1	CAPN1	CAPN1	5024	0.036	0.53	NO
18	PTK2	PTK2	PTK2	5047	0.035	0.54	NO
19	ACTN2	ACTN2	ACTN2	5269	0.032	0.54	NO
20	CAPNS2	CAPNS2	CAPNS2	5337	0.031	0.54	NO
21	RAPGEF1	RAPGEF1	RAPGEF1	5643	0.026	0.53	NO
22	RHOA	RHOA	RHOA	6111	0.019	0.51	NO
23	GRB2	GRB2	GRB2	6560	0.013	0.49	NO
24	RAP1A	RAP1A	RAP1A	7274	0.0033	0.46	NO
25	MAPK8	MAPK8	MAPK8	7474	0.00078	0.44	NO
26	MAPK3	MAPK3	MAPK3	7783	-0.0032	0.43	NO
27	MAPK1	MAPK1	MAPK1	8335	-0.011	0.4	NO
28	MAP2K2	MAP2K2	MAP2K2	8483	-0.013	0.4	NO
29	ROCK1	ROCK1	ROCK1	8496	-0.013	0.4	NO
30	CSK	CSK	CSK	8540	-0.014	0.4	NO
31	JUN	JUN	JUN	9413	-0.025	0.36	NO
32	SRC	SRC	SRC	10512	-0.041	0.32	NO
33	SOS1	SOS1	SOS1	10525	-0.042	0.33	NO
34	RAF1	RAF1	RAF1	10546	-0.042	0.34	NO
35	TNS1	TNS1	TNS1	11027	-0.05	0.33	NO
36	ACTA1	ACTA1	ACTA1	12510	-0.081	0.28	NO
37	PPP1R12B	PPP1R12B	PPP1R12B	13702	-0.11	0.25	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 G1 PATHWAY.

Figure S62. 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 INFLAM 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	IL1B	IL1B	IL1B	10	0.69	0.073	YES
2	IL6	IL6	IL6	58	0.52	0.13	YES
3	MEFV	MEFV	MEFV	61	0.51	0.18	YES
4	CXCL2	CXCL2	CXCL2	166	0.42	0.22	YES
5	IL8	IL8	IL8	172	0.41	0.26	YES
6	TNF	TNF	TNF	296	0.35	0.29	YES
7	CCL7	CCL7	CCL7	300	0.34	0.33	YES
8	CASP5	CASP5	CASP5	302	0.34	0.37	YES
9	CCL8	CCL8	CCL8	343	0.33	0.4	YES
10	BIRC3	BIRC3	BIRC3	377	0.32	0.43	YES
11	CASP1	CASP1	CASP1	539	0.27	0.45	YES
12	CXCL1	CXCL1	CXCL1	543	0.27	0.48	YES
13	MAPK12	MAPK12	MAPK12	545	0.27	0.51	YES
14	IL18	IL18	IL18	603	0.26	0.54	YES
15	BIRC2	BIRC2	BIRC2	610	0.26	0.56	YES
16	CCL13	CCL13	CCL13	685	0.24	0.58	YES
17	NLRP3	NLRP3	NLRP3	898	0.21	0.6	YES
18	MAPK11	MAPK11	MAPK11	1206	0.18	0.6	YES
19	CARD6	CARD6	CARD6	1207	0.18	0.62	YES
20	RIPK2	RIPK2	RIPK2	1240	0.18	0.63	YES
21	CCL2	CCL2	CCL2	1338	0.17	0.65	YES
22	CCL5	CCL5	CCL5	1444	0.16	0.66	YES
23	TNFAIP3	TNFAIP3	TNFAIP3	1472	0.16	0.67	YES
24	PYCARD	PYCARD	PYCARD	1936	0.12	0.66	NO
25	NLRC4	NLRC4	NLRC4	2264	0.11	0.65	NO
26	PSTPIP1	PSTPIP1	PSTPIP1	2489	0.096	0.65	NO
27	NOD1	NOD1	NOD1	2530	0.095	0.66	NO
28	NLRP1	NLRP1	NLRP1	2768	0.087	0.66	NO
29	TRIP6	TRIP6	TRIP6	3555	0.063	0.62	NO
30	MAPK14	MAPK14	MAPK14	3870	0.056	0.61	NO
31	MAPK13	MAPK13	MAPK13	4070	0.053	0.6	NO
32	HSP90B1	HSP90B1	HSP90B1	4408	0.047	0.59	NO
33	NFKBIA	NFKBIA	NFKBIA	4536	0.044	0.59	NO
34	SUGT1	SUGT1	SUGT1	5008	0.036	0.56	NO
35	IKBKG	IKBKG	IKBKG	5174	0.033	0.56	NO
36	NFKB1	NFKB1	NFKB1	5322	0.031	0.55	NO
37	MAPK9	MAPK9	MAPK9	5396	0.029	0.55	NO
38	TRAF6	TRAF6	TRAF6	5697	0.025	0.54	NO
39	NFKBIB	NFKBIB	NFKBIB	6322	0.016	0.51	NO
40	HSP90AA1	HSP90AA1	HSP90AA1	6765	0.01	0.48	NO
41	MAP3K7	MAP3K7	MAP3K7	6881	0.0085	0.48	NO
42	CASP8	CASP8	CASP8	6929	0.008	0.48	NO
43	MAPK8	MAPK8	MAPK8	7474	0.00078	0.44	NO
44	RELA	RELA	RELA	7740	-0.0026	0.43	NO
45	MAPK3	MAPK3	MAPK3	7783	-0.0032	0.43	NO
46	TAB2	TAB2	TAB2	8285	-0.01	0.4	NO
47	MAPK1	MAPK1	MAPK1	8335	-0.011	0.4	NO
48	CHUK	CHUK	CHUK	9118	-0.021	0.36	NO
49	CARD18	CARD18	CARD18	9208	-0.022	0.36	NO
50	PYDC1	PYDC1	PYDC1	9254	-0.023	0.36	NO
51	TAB3	TAB3	TAB3	10150	-0.036	0.31	NO
52	CARD8	CARD8	CARD8	10753	-0.046	0.28	NO
53	NOD2	NOD2	NOD2	11529	-0.06	0.25	NO
54	TAB1	TAB1	TAB1	11729	-0.064	0.24	NO
55	XIAP	XIAP	XIAP	11951	-0.069	0.24	NO
56	IKBKB	IKBKB	IKBKB	12625	-0.083	0.21	NO
57	ERBB2IP	ERBB2IP	ERBB2IP	13031	-0.094	0.2	NO
58	CCL11	CCL11	CCL11	13203	-0.098	0.2	NO
59	CARD9	CARD9	CARD9	15362	-0.18	0.099	NO
60	NAIP	NAIP	NAIP	15545	-0.2	0.11	NO
61	MAPK10	MAPK10	MAPK10	17214	-0.33	0.053	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 INFLAM PATHWAY.

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INFLAM PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA ERK 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	IFNG	IFNG	IFNG	604	0.26	0.081	YES
2	PSMB9	PSMB9	PSMB9	1401	0.16	0.11	YES
3	PSMB7	PSMB7	PSMB7	2243	0.11	0.11	YES
4	PSMD12	PSMD12	PSMD12	2269	0.1	0.16	YES
5	PSMA6	PSMA6	PSMA6	2693	0.089	0.17	YES
6	PSMB8	PSMB8	PSMB8	2722	0.088	0.21	YES
7	PSMC1	PSMC1	PSMC1	3084	0.076	0.22	YES
8	PSME2	PSME2	PSME2	3185	0.073	0.25	YES
9	PSMD14	PSMD14	PSMD14	3433	0.067	0.26	YES
10	PSMA2	PSMA2	PSMA2	3488	0.065	0.29	YES
11	PSMA4	PSMA4	PSMA4	3511	0.064	0.32	YES
12	PSMB5	PSMB5	PSMB5	3709	0.06	0.33	YES
13	PSMC6	PSMC6	PSMC6	3842	0.057	0.35	YES
14	PSMB2	PSMB2	PSMB2	3873	0.056	0.37	YES
15	PSMA3	PSMA3	PSMA3	3996	0.054	0.39	YES
16	PSMD8	PSMD8	PSMD8	3998	0.054	0.42	YES
17	PSMA7	PSMA7	PSMA7	4186	0.051	0.43	YES
18	POMP	POMP	POMP	4204	0.05	0.45	YES
19	PSMA1	PSMA1	PSMA1	4277	0.049	0.47	YES
20	PSMA5	PSMA5	PSMA5	4483	0.045	0.48	YES
21	PSMA8	PSMA8	PSMA8	4703	0.042	0.48	YES
22	PSMB3	PSMB3	PSMB3	4829	0.039	0.49	YES
23	PSMB4	PSMB4	PSMB4	4838	0.039	0.51	YES
24	PSMD6	PSMD6	PSMD6	4846	0.039	0.52	YES
25	PSMD3	PSMD3	PSMD3	4901	0.038	0.54	YES
26	PSMC4	PSMC4	PSMC4	4956	0.037	0.55	YES
27	PSME1	PSME1	PSME1	4957	0.037	0.57	YES
28	PSMD13	PSMD13	PSMD13	4980	0.036	0.58	YES
29	PSMB1	PSMB1	PSMB1	5005	0.036	0.6	YES
30	PSMD7	PSMD7	PSMD7	5093	0.034	0.61	YES
31	PSMD11	PSMD11	PSMD11	5348	0.03	0.61	YES
32	PSMD2	PSMD2	PSMD2	5546	0.027	0.61	YES
33	PSME3	PSME3	PSME3	5553	0.027	0.62	YES
34	PSMC3	PSMC3	PSMC3	5765	0.024	0.62	YES
35	PSMD4	PSMD4	PSMD4	5851	0.023	0.62	YES
36	PSMB6	PSMB6	PSMB6	5967	0.021	0.63	YES
37	PSMC5	PSMC5	PSMC5	6180	0.018	0.62	YES
38	PSMD1	PSMD1	PSMD1	6238	0.017	0.63	YES
39	PSMC2	PSMC2	PSMC2	6362	0.016	0.63	YES
40	SHFM1	SHFM1	SHFM1	6643	0.012	0.62	NO
41	PSMF1	PSMF1	PSMF1	6944	0.0078	0.6	NO
42	PSME4	PSME4	PSME4	9855	-0.031	0.46	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 ERK PATHWAY.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ERK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA INTEGRIN PATHWAY

Table 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	IL1B	IL1B	IL1B	10	0.69	0.13	YES
2	IL6	IL6	IL6	58	0.52	0.22	YES
3	AIM2	AIM2	AIM2	107	0.46	0.31	YES
4	CCL4	CCL4	CCL4	476	0.29	0.34	YES
5	CXCL10	CXCL10	CXCL10	528	0.28	0.39	YES
6	CASP1	CASP1	CASP1	539	0.27	0.44	YES
7	IL18	IL18	IL18	603	0.26	0.49	YES
8	CCL4L2	CCL4L2	CCL4L2	702	0.24	0.53	YES
9	POLR3G	POLR3G	POLR3G	888	0.22	0.56	YES
10	IL33	IL33	IL33	1408	0.16	0.56	YES
11	CCL5	CCL5	CCL5	1444	0.16	0.59	YES
12	IFNA13	IFNA13	IFNA13	1879	0.13	0.59	YES
13	DDX58	DDX58	DDX58	1883	0.13	0.62	YES
14	PYCARD	PYCARD	PYCARD	1936	0.12	0.64	YES
15	IFNB1	IFNB1	IFNB1	2312	0.1	0.63	YES
16	IRF7	IRF7	IRF7	2485	0.096	0.64	YES
17	ZBP1	ZBP1	ZBP1	2728	0.088	0.65	YES
18	POLR3A	POLR3A	POLR3A	3645	0.061	0.61	NO
19	IFNA1	IFNA1	IFNA1	3869	0.056	0.6	NO
20	IRF3	IRF3	IRF3	4071	0.053	0.6	NO
21	NFKBIA	NFKBIA	NFKBIA	4536	0.044	0.59	NO
22	IKBKG	IKBKG	IKBKG	5174	0.033	0.56	NO
23	POLR3D	POLR3D	POLR3D	5189	0.033	0.56	NO
24	NFKB1	NFKB1	NFKB1	5322	0.031	0.56	NO
25	POLR3H	POLR3H	POLR3H	5859	0.023	0.54	NO
26	POLR1C	POLR1C	POLR1C	6049	0.02	0.53	NO
27	RIPK1	RIPK1	RIPK1	6179	0.018	0.53	NO
28	TMEM173	TMEM173	TMEM173	6296	0.017	0.52	NO
29	NFKBIB	NFKBIB	NFKBIB	6322	0.016	0.52	NO
30	ADAR	ADAR	ADAR	6399	0.015	0.52	NO
31	POLR3K	POLR3K	POLR3K	6692	0.011	0.51	NO
32	RELA	RELA	RELA	7740	-0.0026	0.45	NO
33	POLR3B	POLR3B	POLR3B	7811	-0.0037	0.45	NO
34	TBK1	TBK1	TBK1	8481	-0.013	0.42	NO
35	POLR1D	POLR1D	POLR1D	8735	-0.016	0.4	NO
36	POLR3C	POLR3C	POLR3C	8747	-0.016	0.41	NO
37	CHUK	CHUK	CHUK	9118	-0.021	0.39	NO
38	MAVS	MAVS	MAVS	9157	-0.022	0.39	NO
39	POLR3F	POLR3F	POLR3F	10331	-0.039	0.33	NO
40	TREX1	TREX1	TREX1	11596	-0.061	0.28	NO
41	IKBKB	IKBKB	IKBKB	12625	-0.083	0.24	NO
42	IKBKE	IKBKE	IKBKE	12937	-0.092	0.24	NO
43	POLR3GL	POLR3GL	POLR3GL	14306	-0.14	0.18	NO
44	RIPK3	RIPK3	RIPK3	14612	-0.15	0.2	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 INTEGRIN PATHWAY.

Figure S68. 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 IL1R 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	IL1B	IL1B	IL1B	10	0.69	0.14	YES
2	IL1A	IL1A	IL1A	15	0.66	0.28	YES
3	IL6	IL6	IL6	58	0.52	0.38	YES
4	TGFB2	TGFB2	TGFB2	169	0.41	0.46	YES
5	TNF	TNF	TNF	296	0.35	0.52	YES
6	TGFB1	TGFB1	TGFB1	664	0.25	0.55	YES
7	IRAK2	IRAK2	IRAK2	1118	0.19	0.57	YES
8	IL1RAP	IL1RAP	IL1RAP	1311	0.17	0.59	YES
9	IL1RN	IL1RN	IL1RN	1462	0.16	0.62	YES
10	IFNB1	IFNB1	IFNB1	2312	0.1	0.59	NO
11	MAP2K3	MAP2K3	MAP2K3	2685	0.09	0.59	NO
12	IFNA1	IFNA1	IFNA1	3869	0.056	0.53	NO
13	MAPK14	MAPK14	MAPK14	3870	0.056	0.55	NO
14	NFKBIA	NFKBIA	NFKBIA	4536	0.044	0.52	NO
15	IRAK3	IRAK3	IRAK3	5265	0.032	0.48	NO
16	NFKB1	NFKB1	NFKB1	5322	0.031	0.49	NO
17	IRAK1	IRAK1	IRAK1	5503	0.028	0.48	NO
18	TRAF6	TRAF6	TRAF6	5697	0.025	0.48	NO
19	MYD88	MYD88	MYD88	6135	0.019	0.46	NO
20	MAP3K7	MAP3K7	MAP3K7	6881	0.0085	0.42	NO
21	MAPK8	MAPK8	MAPK8	7474	0.00078	0.38	NO
22	RELA	RELA	RELA	7740	-0.0026	0.37	NO
23	CHUK	CHUK	CHUK	9118	-0.021	0.3	NO
24	JUN	JUN	JUN	9413	-0.025	0.29	NO
25	TOLLIP	TOLLIP	TOLLIP	9570	-0.027	0.29	NO
26	MAP3K14	MAP3K14	MAP3K14	9706	-0.029	0.28	NO
27	ECSIT	ECSIT	ECSIT	11342	-0.056	0.2	NO
28	TAB1	TAB1	TAB1	11729	-0.064	0.2	NO
29	IKBKB	IKBKB	IKBKB	12625	-0.083	0.16	NO
30	TGFB3	TGFB3	TGFB3	14357	-0.14	0.097	NO
31	MAP3K1	MAP3K1	MAP3K1	14807	-0.16	0.1	NO
32	MAP2K6	MAP2K6	MAP2K6	17592	-0.4	0.032	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 IL1R PATHWAY.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

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	IFNK	IFNK	IFNK	8	0.7	0.12	YES
2	IL8	IL8	IL8	172	0.41	0.18	YES
3	TNF	TNF	TNF	296	0.35	0.23	YES
4	IFNE	IFNE	IFNE	342	0.33	0.28	YES
5	CXCL10	CXCL10	CXCL10	528	0.28	0.32	YES
6	MAPK12	MAPK12	MAPK12	545	0.27	0.37	YES
7	ISG15	ISG15	ISG15	871	0.22	0.38	YES
8	MAPK11	MAPK11	MAPK11	1206	0.18	0.4	YES
9	CASP10	CASP10	CASP10	1429	0.16	0.41	YES
10	IFNA13	IFNA13	IFNA13	1879	0.13	0.41	YES
11	DDX58	DDX58	DDX58	1883	0.13	0.43	YES
12	IFIH1	IFIH1	IFIH1	2039	0.12	0.44	YES
13	IFNB1	IFNB1	IFNB1	2312	0.1	0.44	YES
14	TBKBP1	TBKBP1	TBKBP1	2351	0.1	0.46	YES
15	FADD	FADD	FADD	2411	0.099	0.47	YES
16	IRF7	IRF7	IRF7	2485	0.096	0.48	YES
17	TRAF3	TRAF3	TRAF3	2511	0.095	0.5	YES
18	TRADD	TRADD	TRADD	2832	0.085	0.5	NO
19	ATG12	ATG12	ATG12	3691	0.06	0.46	NO
20	IFNA1	IFNA1	IFNA1	3869	0.056	0.46	NO
21	MAPK14	MAPK14	MAPK14	3870	0.056	0.47	NO
22	TRAF2	TRAF2	TRAF2	3883	0.056	0.48	NO
23	MAPK13	MAPK13	MAPK13	4070	0.053	0.48	NO
24	IRF3	IRF3	IRF3	4071	0.053	0.48	NO
25	NFKBIA	NFKBIA	NFKBIA	4536	0.044	0.47	NO
26	IKBKG	IKBKG	IKBKG	5174	0.033	0.44	NO
27	NFKB1	NFKB1	NFKB1	5322	0.031	0.43	NO
28	MAPK9	MAPK9	MAPK9	5396	0.029	0.43	NO
29	TRIM25	TRIM25	TRIM25	5597	0.027	0.43	NO
30	TRAF6	TRAF6	TRAF6	5697	0.025	0.43	NO
31	RIPK1	RIPK1	RIPK1	6179	0.018	0.4	NO
32	AZI2	AZI2	AZI2	6197	0.018	0.4	NO
33	TMEM173	TMEM173	TMEM173	6296	0.017	0.4	NO
34	NFKBIB	NFKBIB	NFKBIB	6322	0.016	0.4	NO
35	NLRX1	NLRX1	NLRX1	6640	0.012	0.39	NO
36	MAP3K7	MAP3K7	MAP3K7	6881	0.0085	0.38	NO
37	CASP8	CASP8	CASP8	6929	0.008	0.38	NO
38	MAPK8	MAPK8	MAPK8	7474	0.00078	0.34	NO
39	PIN1	PIN1	PIN1	7482	0.00071	0.34	NO
40	TANK	TANK	TANK	7626	-0.001	0.34	NO
41	RELA	RELA	RELA	7740	-0.0026	0.33	NO
42	OTUD5	OTUD5	OTUD5	8286	-0.01	0.3	NO
43	TBK1	TBK1	TBK1	8481	-0.013	0.3	NO
44	DHX58	DHX58	DHX58	8510	-0.013	0.3	NO
45	DAK	DAK	DAK	8579	-0.014	0.29	NO
46	CYLD	CYLD	CYLD	8606	-0.015	0.3	NO
47	ATG5	ATG5	ATG5	8842	-0.018	0.28	NO
48	CHUK	CHUK	CHUK	9118	-0.021	0.27	NO
49	MAVS	MAVS	MAVS	9157	-0.022	0.28	NO
50	DDX3X	DDX3X	DDX3X	9995	-0.033	0.23	NO
51	SIKE1	SIKE1	SIKE1	11971	-0.069	0.14	NO
52	IKBKB	IKBKB	IKBKB	12625	-0.083	0.12	NO
53	IKBKE	IKBKE	IKBKE	12937	-0.092	0.11	NO
54	RNF125	RNF125	RNF125	13016	-0.093	0.12	NO
55	MAP3K1	MAP3K1	MAP3K1	14807	-0.16	0.052	NO
56	IL12B	IL12B	IL12B	14955	-0.16	0.072	NO
57	IL12A	IL12A	IL12A	16841	-0.29	0.017	NO
58	MAPK10	MAPK10	MAPK10	17214	-0.33	0.053	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: KEGG PYRIMIDINE METABOLISM.

Figure S72. 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 AMINOACYL TRNA BIOSYNTHESIS

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	RPL3L	RPL3L	RPL3L	201	0.39	0.064	YES
2	RPL36A	RPL36A	RPL36A	834	0.22	0.073	YES
3	RPS26	RPS26	RPS26	2047	0.12	0.028	YES
4	RPL37	RPL37	RPL37	2297	0.1	0.034	YES
5	RPL26L1	RPL26L1	RPL26L1	2337	0.1	0.052	YES
6	RPS17	RPS17	RPS17	2401	0.1	0.068	YES
7	RPL39	RPL39	RPL39	2432	0.099	0.085	YES
8	RPL28	RPL28	RPL28	2438	0.098	0.1	YES
9	RPS2	RPS2	RPS2	2507	0.096	0.12	YES
10	RPL18A	RPL18A	RPL18A	2524	0.095	0.14	YES
11	RPL35	RPL35	RPL35	2564	0.094	0.15	YES
12	RPS16	RPS16	RPS16	2565	0.094	0.17	YES
13	RPL38	RPL38	RPL38	2577	0.093	0.19	YES
14	RPL13	RPL13	RPL13	2737	0.087	0.2	YES
15	RPL36AL	RPL36AL	RPL36AL	2751	0.087	0.21	YES
16	RPS10	RPS10	RPS10	2778	0.086	0.23	YES
17	RPS5	RPS5	RPS5	2801	0.086	0.24	YES
18	RPL27	RPL27	RPL27	2950	0.08	0.25	YES
19	RPL8	RPL8	RPL8	3001	0.078	0.26	YES
20	RPL12	RPL12	RPL12	3036	0.077	0.28	YES
21	RPS3	RPS3	RPS3	3121	0.075	0.28	YES
22	RPL4	RPL4	RPL4	3235	0.072	0.29	YES
23	RPL7A	RPL7A	RPL7A	3311	0.07	0.3	YES
24	RPS19	RPS19	RPS19	3363	0.068	0.31	YES
25	RPS18	RPS18	RPS18	3372	0.068	0.32	YES
26	RPL29	RPL29	RPL29	3401	0.068	0.34	YES
27	RPS28	RPS28	RPS28	3423	0.067	0.35	YES
28	RPS21	RPS21	RPS21	3457	0.066	0.36	YES
29	RPS24	RPS24	RPS24	3514	0.064	0.37	YES
30	RPS29	RPS29	RPS29	3517	0.064	0.38	YES
31	RPLP1	RPLP1	RPLP1	3532	0.064	0.39	YES
32	RPS27A	RPS27A	RPS27A	3622	0.062	0.4	YES
33	RPL23	RPL23	RPL23	3657	0.061	0.41	YES
34	RPL31	RPL31	RPL31	3678	0.06	0.42	YES
35	RPL6	RPL6	RPL6	3694	0.06	0.43	YES
36	RPS9	RPS9	RPS9	3708	0.06	0.44	YES
37	RPS25	RPS25	RPS25	3859	0.057	0.44	YES
38	RPL17	RPL17	RPL17	3880	0.056	0.45	YES
39	RPS7	RPS7	RPS7	3956	0.055	0.46	YES
40	RPS15A	RPS15A	RPS15A	3966	0.054	0.47	YES
41	RPL7	RPL7	RPL7	3978	0.054	0.48	YES
42	RPL14	RPL14	RPL14	3999	0.054	0.49	YES
43	RPL13A	RPL13A	RPL13A	4009	0.054	0.5	YES
44	RPL32	RPL32	RPL32	4024	0.054	0.51	YES
45	RPLP2	RPLP2	RPLP2	4039	0.053	0.52	YES
46	RPL30	RPL30	RPL30	4051	0.053	0.53	YES
47	RPSA	RPSA	RPSA	4082	0.052	0.54	YES
48	RPLP0	RPLP0	RPLP0	4089	0.052	0.55	YES
49	RPS12	RPS12	RPS12	4149	0.051	0.55	YES
50	RPS20	RPS20	RPS20	4211	0.05	0.56	YES
51	RPL11	RPL11	RPL11	4418	0.046	0.56	YES
52	RPL23A	RPL23A	RPL23A	4429	0.046	0.56	YES
53	RPS13	RPS13	RPS13	4611	0.043	0.56	YES
54	RPL26	RPL26	RPL26	4613	0.043	0.57	YES
55	RPS11	RPS11	RPS11	4665	0.042	0.58	YES
56	UBA52	UBA52	UBA52	4687	0.042	0.58	YES
57	RPL27A	RPL27A	RPL27A	4716	0.041	0.59	YES
58	RPS23	RPS23	RPS23	4762	0.04	0.6	YES
59	RPL37A	RPL37A	RPL37A	4785	0.04	0.6	YES
60	RPL34	RPL34	RPL34	4849	0.039	0.6	YES
61	RSL24D1	RSL24D1	RSL24D1	4851	0.039	0.61	YES
62	RPL10A	RPL10A	RPL10A	4866	0.039	0.62	YES
63	RPL10	RPL10	RPL10	4952	0.037	0.62	YES
64	RPS8	RPS8	RPS8	4991	0.036	0.63	YES
65	RPS6	RPS6	RPS6	5017	0.036	0.63	YES
66	RPL19	RPL19	RPL19	5063	0.035	0.64	YES
67	RPL21	RPL21	RPL21	5072	0.035	0.64	YES
68	RPL41	RPL41	RPL41	5078	0.034	0.65	YES
69	RPS3A	RPS3A	RPS3A	5101	0.034	0.65	YES
70	RPL36	RPL36	RPL36	5165	0.033	0.66	YES
71	RPL24	RPL24	RPL24	5279	0.032	0.66	YES
72	RPL5	RPL5	RPL5	5355	0.03	0.66	YES
73	FAU	FAU	FAU	5386	0.03	0.66	YES
74	RPS4X	RPS4X	RPS4X	5560	0.027	0.66	YES
75	MRPL13	MRPL13	MRPL13	5642	0.026	0.66	YES
76	RPS27	RPS27	RPS27	5653	0.026	0.66	YES
77	RPL3	RPL3	RPL3	5676	0.026	0.67	YES
78	RPS15	RPS15	RPS15	5915	0.022	0.66	NO
79	RPS27L	RPS27L	RPS27L	6028	0.02	0.66	NO
80	RPL22L1	RPL22L1	RPL22L1	6196	0.018	0.65	NO
81	RPL22	RPL22	RPL22	6480	0.014	0.64	NO
82	RPL35A	RPL35A	RPL35A	7186	0.0045	0.6	NO
83	RPL15	RPL15	RPL15	7370	0.0021	0.59	NO
84	RPL9	RPL9	RPL9	10477	-0.041	0.42	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: KEGG AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RIBOSOME

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	MMP1	MMP1	MMP1	53	0.53	0.086	YES
2	VEGFC	VEGFC	VEGFC	92	0.47	0.16	YES
3	IL8	IL8	IL8	172	0.41	0.23	YES
4	MMP9	MMP9	MMP9	335	0.33	0.27	YES
5	EGFR	EGFR	EGFR	405	0.31	0.32	YES
6	THBS1	THBS1	THBS1	609	0.26	0.35	YES
7	MYC	MYC	MYC	662	0.25	0.39	YES
8	CCND1	CCND1	CCND1	681	0.25	0.43	YES
9	TYMP	TYMP	TYMP	1167	0.18	0.44	YES
10	PGF	PGF	PGF	1191	0.18	0.46	YES
11	HRAS	HRAS	HRAS	1688	0.14	0.46	YES
12	DAPK1	DAPK1	DAPK1	1807	0.13	0.47	YES
13	CDKN2A	CDKN2A	CDKN2A	2194	0.11	0.47	YES
14	VEGFA	VEGFA	VEGFA	2374	0.1	0.48	YES
15	MAP2K1	MAP2K1	MAP2K1	2417	0.099	0.49	YES
16	DAPK3	DAPK3	DAPK3	3048	0.077	0.47	NO
17	CDKN1A	CDKN1A	CDKN1A	3501	0.065	0.46	NO
18	E2F3	E2F3	E2F3	3763	0.058	0.45	NO
19	CDK4	CDK4	CDK4	6309	0.016	0.31	NO
20	RASSF1	RASSF1	RASSF1	7182	0.0046	0.27	NO
21	NRAS	NRAS	NRAS	7192	0.0044	0.27	NO
22	VEGFB	VEGFB	VEGFB	7756	-0.0028	0.24	NO
23	MAPK3	MAPK3	MAPK3	7783	-0.0032	0.24	NO
24	MAPK1	MAPK1	MAPK1	8335	-0.011	0.21	NO
25	MAP2K2	MAP2K2	MAP2K2	8483	-0.013	0.2	NO
26	ARAF	ARAF	ARAF	8706	-0.016	0.19	NO
27	CDH1	CDH1	CDH1	9109	-0.021	0.17	NO
28	RAF1	RAF1	RAF1	10546	-0.042	0.1	NO
29	KRAS	KRAS	KRAS	11262	-0.054	0.07	NO
30	MDM2	MDM2	MDM2	11281	-0.055	0.078	NO
31	MMP2	MMP2	MMP2	11737	-0.064	0.063	NO
32	RB1	RB1	RB1	11903	-0.067	0.066	NO
33	TP53	TP53	TP53	12738	-0.086	0.034	NO
34	DAPK2	DAPK2	DAPK2	13942	-0.12	-0.012	NO
35	ERBB2	ERBB2	ERBB2	14059	-0.12	0.0018	NO
36	BRAF	BRAF	BRAF	14221	-0.13	0.015	NO
37	E2F2	E2F2	E2F2	14451	-0.14	0.026	NO
38	FGFR3	FGFR3	FGFR3	14896	-0.16	0.028	NO
39	RPS6KA5	RPS6KA5	RPS6KA5	16748	-0.28	-0.027	NO
40	EGF	EGF	EGF	17017	-0.31	0.0092	NO
41	FIGF	FIGF	FIGF	17168	-0.33	0.055	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: KEGG RIBOSOME.

Figure S76. 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 SPLICEOSOME

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	WARS	WARS	WARS	630	0.26	0.094	YES
2	TARSL2	TARSL2	TARSL2	890	0.22	0.19	YES
3	RARS	RARS	RARS	2440	0.098	0.15	YES
4	TARS	TARS	TARS	2777	0.086	0.18	YES
5	VARS	VARS	VARS	2856	0.084	0.22	YES
6	CARS2	CARS2	CARS2	3303	0.07	0.23	YES
7	KARS	KARS	KARS	3358	0.068	0.26	YES
8	YARS	YARS	YARS	3359	0.068	0.29	YES
9	FARS2	FARS2	FARS2	3441	0.066	0.32	YES
10	GARS	GARS	GARS	3568	0.063	0.34	YES
11	YARS2	YARS2	YARS2	3955	0.055	0.35	YES
12	HARS2	HARS2	HARS2	4380	0.047	0.35	YES
13	DARS	DARS	DARS	4500	0.045	0.37	YES
14	SARS2	SARS2	SARS2	4904	0.038	0.36	YES
15	FARSA	FARSA	FARSA	4976	0.037	0.38	YES
16	HARS	HARS	HARS	5084	0.034	0.39	YES
17	CARS	CARS	CARS	5672	0.026	0.37	NO
18	IARS	IARS	IARS	5700	0.025	0.38	NO
19	MTFMT	MTFMT	MTFMT	6306	0.016	0.36	NO
20	MARS	MARS	MARS	6942	0.0078	0.33	NO
21	IARS2	IARS2	IARS2	6981	0.0073	0.33	NO
22	AARS	AARS	AARS	6993	0.007	0.33	NO
23	NARS2	NARS2	NARS2	7160	0.0049	0.32	NO
24	RARS2	RARS2	RARS2	7355	0.0022	0.32	NO
25	FARSB	FARSB	FARSB	7432	0.0012	0.31	NO
26	QARS	QARS	QARS	7787	-0.0033	0.29	NO
27	VARS2	VARS2	VARS2	7935	-0.0053	0.29	NO
28	SARS	SARS	SARS	8159	-0.0084	0.28	NO
29	DARS2	DARS2	DARS2	8575	-0.014	0.26	NO
30	MARS2	MARS2	MARS2	8671	-0.015	0.27	NO
31	AARS2	AARS2	AARS2	8871	-0.018	0.26	NO
32	LARS2	LARS2	LARS2	9204	-0.022	0.26	NO
33	EPRS	EPRS	EPRS	9433	-0.025	0.26	NO
34	LARS	LARS	LARS	9669	-0.028	0.26	NO
35	PSTK	PSTK	PSTK	10037	-0.034	0.26	NO
36	EARS2	EARS2	EARS2	10409	-0.04	0.26	NO
37	NARS	NARS	NARS	10540	-0.042	0.27	NO
38	PARS2	PARS2	PARS2	12542	-0.081	0.2	NO
39	WARS2	WARS2	WARS2	13009	-0.093	0.22	NO
40	SEPSECS	SEPSECS	SEPSECS	14088	-0.13	0.22	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: KEGG SPLICEOSOME.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPLICEOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PROTEASOME

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	FBXO2	FBXO2	FBXO2	20	0.62	0.075	YES
2	BIRC3	BIRC3	BIRC3	377	0.32	0.094	YES
3	BIRC2	BIRC2	BIRC2	610	0.26	0.11	YES
4	NEDD4	NEDD4	NEDD4	621	0.26	0.14	YES
5	RHOBTB2	RHOBTB2	RHOBTB2	734	0.24	0.17	YES
6	SOCS3	SOCS3	SOCS3	1369	0.16	0.15	YES
7	UBE2S	UBE2S	UBE2S	1665	0.14	0.15	YES
8	PML	PML	PML	1802	0.13	0.16	YES
9	CBLC	CBLC	CBLC	1825	0.13	0.18	YES
10	UBE2L6	UBE2L6	UBE2L6	1903	0.12	0.19	YES
11	UBE2F	UBE2F	UBE2F	1967	0.12	0.2	YES
12	HERC4	HERC4	HERC4	2038	0.12	0.21	YES
13	UBE2Q2	UBE2Q2	UBE2Q2	2538	0.095	0.19	YES
14	UBA6	UBA6	UBA6	2571	0.094	0.2	YES
15	SKP2	SKP2	SKP2	2584	0.093	0.21	YES
16	NEDD4L	NEDD4L	NEDD4L	2596	0.093	0.22	YES
17	CDC20	CDC20	CDC20	2640	0.091	0.23	YES
18	SMURF2	SMURF2	SMURF2	2677	0.09	0.24	YES
19	UBE2D1	UBE2D1	UBE2D1	2959	0.08	0.24	YES
20	UBE2M	UBE2M	UBE2M	2988	0.079	0.24	YES
21	TCEB1	TCEB1	TCEB1	3284	0.07	0.24	NO
22	TRIM32	TRIM32	TRIM32	3420	0.067	0.24	NO
23	STUB1	STUB1	STUB1	3600	0.062	0.24	NO
24	UBE2L3	UBE2L3	UBE2L3	4259	0.049	0.2	NO
25	CDC27	CDC27	CDC27	4339	0.048	0.21	NO
26	UBE2C	UBE2C	UBE2C	4372	0.047	0.21	NO
27	CDC16	CDC16	CDC16	4694	0.042	0.2	NO
28	UBE2I	UBE2I	UBE2I	4702	0.042	0.2	NO
29	CBL	CBL	CBL	4923	0.038	0.2	NO
30	UBE2R2	UBE2R2	UBE2R2	5260	0.032	0.18	NO
31	TCEB2	TCEB2	TCEB2	5379	0.03	0.18	NO
32	UBE2E2	UBE2E2	UBE2E2	5496	0.028	0.18	NO
33	UBE2Z	UBE2Z	UBE2Z	5694	0.025	0.17	NO
34	TRAF6	TRAF6	TRAF6	5697	0.025	0.17	NO
35	UBA2	UBA2	UBA2	5747	0.024	0.17	NO
36	HERC3	HERC3	HERC3	5804	0.024	0.17	NO
37	PRPF19	PRPF19	PRPF19	5890	0.022	0.17	NO
38	CUL1	CUL1	CUL1	5918	0.022	0.17	NO
39	UBE2H	UBE2H	UBE2H	5933	0.022	0.17	NO
40	PIAS1	PIAS1	PIAS1	6060	0.02	0.17	NO
41	UBE2B	UBE2B	UBE2B	6072	0.02	0.17	NO
42	SAE1	SAE1	SAE1	6115	0.019	0.17	NO
43	CDC34	CDC34	CDC34	6169	0.018	0.17	NO
44	SYVN1	SYVN1	SYVN1	6304	0.016	0.16	NO
45	UBE2J2	UBE2J2	UBE2J2	6360	0.016	0.16	NO
46	RBX1	RBX1	RBX1	6499	0.014	0.16	NO
47	UBE2D3	UBE2D3	UBE2D3	6634	0.012	0.15	NO
48	CUL7	CUL7	CUL7	6649	0.012	0.15	NO
49	ANAPC1	ANAPC1	ANAPC1	6688	0.011	0.15	NO
50	ANAPC10	ANAPC10	ANAPC10	6721	0.011	0.15	NO
51	UBE2N	UBE2N	UBE2N	6781	0.0099	0.15	NO
52	UBE2NL	UBE2NL	UBE2NL	6990	0.0071	0.14	NO
53	SOCS1	SOCS1	SOCS1	7047	0.0065	0.13	NO
54	UBE3C	UBE3C	UBE3C	7066	0.0062	0.13	NO
55	SIAH1	SIAH1	SIAH1	7078	0.0059	0.13	NO
56	UBE2O	UBE2O	UBE2O	7261	0.0035	0.12	NO
57	UBE2A	UBE2A	UBE2A	7288	0.0032	0.12	NO
58	CDC26	CDC26	CDC26	7344	0.0024	0.12	NO
59	UBE3B	UBE3B	UBE3B	7386	0.0018	0.12	NO
60	DDB1	DDB1	DDB1	7449	0.0011	0.12	NO
61	CUL4A	CUL4A	CUL4A	7476	0.00077	0.11	NO
62	UBR5	UBR5	UBR5	7534	0.00014	0.11	NO
63	DDB2	DDB2	DDB2	7659	-0.0014	0.1	NO
64	CUL2	CUL2	CUL2	7712	-0.0021	0.1	NO
65	CDC23	CDC23	CDC23	7714	-0.0021	0.1	NO
66	UBE2G1	UBE2G1	UBE2G1	7718	-0.0022	0.1	NO
67	ANAPC11	ANAPC11	ANAPC11	7785	-0.0033	0.098	NO
68	UBA1	UBA1	UBA1	7821	-0.0038	0.096	NO
69	UBE2Q1	UBE2Q1	UBE2Q1	7870	-0.0044	0.094	NO
70	ANAPC13	ANAPC13	ANAPC13	8089	-0.0072	0.083	NO
71	UBE2K	UBE2K	UBE2K	8092	-0.0073	0.084	NO
72	CUL5	CUL5	CUL5	8120	-0.0077	0.083	NO
73	CUL4B	CUL4B	CUL4B	8222	-0.0092	0.079	NO
74	UBE2D2	UBE2D2	UBE2D2	8234	-0.0094	0.08	NO
75	UBE2E3	UBE2E3	UBE2E3	8249	-0.0095	0.08	NO
76	ANAPC5	ANAPC5	ANAPC5	8353	-0.011	0.076	NO
77	UBE2G2	UBE2G2	UBE2G2	8377	-0.011	0.076	NO
78	ITCH	ITCH	ITCH	8390	-0.012	0.076	NO
79	FBXO4	FBXO4	FBXO4	8505	-0.013	0.072	NO
80	FBXW7	FBXW7	FBXW7	8518	-0.013	0.073	NO
81	ANAPC2	ANAPC2	ANAPC2	8550	-0.014	0.073	NO
82	WWP1	WWP1	WWP1	8582	-0.014	0.073	NO
83	SKP1	SKP1	SKP1	8608	-0.015	0.073	NO
84	TRIP12	TRIP12	TRIP12	8649	-0.015	0.073	NO
85	UBA3	UBA3	UBA3	8673	-0.015	0.073	NO
86	SMURF1	SMURF1	SMURF1	8752	-0.016	0.071	NO
87	ERCC8	ERCC8	ERCC8	8991	-0.02	0.06	NO
88	NHLRC1	NHLRC1	NHLRC1	9037	-0.02	0.06	NO
89	FBXW8	FBXW8	FBXW8	9067	-0.021	0.061	NO
90	BIRC6	BIRC6	BIRC6	9342	-0.024	0.049	NO
91	UBE4A	UBE4A	UBE4A	9348	-0.024	0.052	NO
92	WWP2	WWP2	WWP2	9485	-0.026	0.047	NO
93	UBA7	UBA7	UBA7	9523	-0.027	0.049	NO
94	MGRN1	MGRN1	MGRN1	9583	-0.027	0.049	NO
95	HUWE1	HUWE1	HUWE1	9615	-0.028	0.05	NO
96	FBXW11	FBXW11	FBXW11	9635	-0.028	0.053	NO
97	UBE2D4	UBE2D4	UBE2D4	9638	-0.028	0.056	NO
98	KEAP1	KEAP1	KEAP1	9690	-0.029	0.057	NO
99	BRCA1	BRCA1	BRCA1	9835	-0.031	0.052	NO
100	UBE2E1	UBE2E1	UBE2E1	9909	-0.032	0.052	NO
101	UBE2W	UBE2W	UBE2W	10083	-0.035	0.047	NO
102	ANAPC4	ANAPC4	ANAPC4	10115	-0.035	0.05	NO
103	HERC1	HERC1	HERC1	10207	-0.037	0.049	NO
104	RNF7	RNF7	RNF7	10509	-0.041	0.038	NO
105	PPIL2	PPIL2	PPIL2	10557	-0.042	0.04	NO
106	UBE3A	UBE3A	UBE3A	10687	-0.044	0.038	NO
107	RCHY1	RCHY1	RCHY1	11041	-0.051	0.025	NO
108	UBOX5	UBOX5	UBOX5	11049	-0.051	0.031	NO
109	MDM2	MDM2	MDM2	11281	-0.055	0.025	NO
110	HERC2	HERC2	HERC2	11313	-0.056	0.03	NO
111	FZR1	FZR1	FZR1	11388	-0.057	0.033	NO
112	TRIM37	TRIM37	TRIM37	11691	-0.063	0.024	NO
113	MID1	MID1	MID1	11892	-0.067	0.021	NO
114	XIAP	XIAP	XIAP	11951	-0.069	0.026	NO
115	UBE2J1	UBE2J1	UBE2J1	12010	-0.07	0.032	NO
116	KLHL9	KLHL9	KLHL9	12086	-0.071	0.036	NO
117	ANAPC7	ANAPC7	ANAPC7	12276	-0.075	0.035	NO
118	PIAS4	PIAS4	PIAS4	12358	-0.077	0.04	NO
119	VHL	VHL	VHL	12522	-0.081	0.041	NO
120	UBE4B	UBE4B	UBE4B	12688	-0.085	0.042	NO
121	FANCL	FANCL	FANCL	12699	-0.085	0.052	NO
122	UBE2QL1	UBE2QL1	UBE2QL1	12787	-0.087	0.058	NO
123	CUL3	CUL3	CUL3	13155	-0.097	0.05	NO
124	CBLB	CBLB	CBLB	13216	-0.098	0.058	NO
125	RFWD2	RFWD2	RFWD2	13291	-0.1	0.066	NO
126	KLHL13	KLHL13	KLHL13	13792	-0.12	0.053	NO
127	PIAS3	PIAS3	PIAS3	14746	-0.15	0.019	NO
128	MAP3K1	MAP3K1	MAP3K1	14807	-0.16	0.035	NO
129	DET1	DET1	DET1	15329	-0.18	0.028	NO
130	PIAS2	PIAS2	PIAS2	15693	-0.2	0.033	NO
131	AIRE	AIRE	AIRE	16646	-0.27	0.014	NO
132	PARK2	PARK2	PARK2	18082	-0.57	0.0049	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: KEGG PROTEASOME.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROTEASOME, 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 = CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = CESC-TP.mergedcluster.txt

GSEA analysis

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

Download Results

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

References

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

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