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

Cholangiocarcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in CHOL-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1XK8DXD

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 having more than three samples and the input expression file "CHOL-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. 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: 719
Number of samples: 36
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 6 :[ clus1 ] 6
pheno.type: 2 - 6 :[ clus2 ] 4
pheno.type: 3 - 6 :[ clus3 ] 5
pheno.type: 4 - 6 :[ clus4 ] 6
pheno.type: 5 - 6 :[ clus5 ] 9
pheno.type: 6 - 6 :[ clus6 ] 6

For the expression subtypes of 18131 genes in 37 samples, GSEA found enriched gene sets in each cluster using 36 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG UBIQUITIN MEDIATED PROTEOLYSIS, KEGG THYROID CANCER, BIOCARTA GPCR PATHWAY, PID ER NONGENOMIC PATHWAY, PID MET PATHWAY, PID CDC42 PATHWAY, PID RETINOIC ACID PATHWAY, PID DELTANP63PATHWAY, PID A6B1 A6B4 INTEGRIN PATHWAY

And common core enriched genes are MAPK3, RXRG, PRKCG, CTNNB1, LEF1, NTRK1, PPARG, RET, TCF7, TCF7L2

clus2

Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG OXIDATIVE PHOSPHORYLATION, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG ALZHEIMERS DISEASE, KEGG PARKINSONS DISEASE, KEGG HUNTINGTONS DISEASE, ST GAQ PATHWAY, PID MTOR 4PATHWAY, REACTOME TRANSLATION, REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE

And common core enriched genes are ACO2, ATP5A1, ATP5B, ATP5G1, CS, CYC1, C18orf55, CHCHD4, COQ2, DNAJC19

clus3

Top enriched gene sets are KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG ENDOCYTOSIS, KEGG MTOR SIGNALING PATHWAY, KEGG APOPTOSIS, KEGG CELL ADHESION MOLECULES CAMS, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY

And common core enriched genes are FYN, IKBKB, PIK3CD, PRKCB, SYK, CASP8, CXCL10, CYLD, DDX58, DHX58

clus4

Top enriched gene sets are KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG GLUTATHIONE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG RIBOSOME, KEGG SPLICEOSOME, KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, BIOCARTA PROTEASOME PATHWAY, REACTOME ER PHAGOSOME PATHWAY, REACTOME MEMBRANE TRAFFICKING, REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT

And common core enriched genes are NQO1, OAZ1, OAZ3, ODC1, PSMA4, PSMA5, PSMA6, PSMB10, PSMB2, PSMB3

clus5

Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PURINE METABOLISM, KEGG PYRIMIDINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

And common core enriched genes are ABCA1, ABCB4, ACADM, ACOX1, ACSL1, AGT, ALAS1, ANGPTL4, ANKRD1, APOA1

clus6

Top enriched gene sets are KEGG NOTCH SIGNALING PATHWAY, ST ERK1 ERK2 MAPK PATHWAY, PID INTEGRIN3 PATHWAY, PID RHOA REG PATHWAY, PID NECTIN PATHWAY, PID TGFBRPATHWAY, REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION, REACTOME PRE NOTCH EXPRESSION AND PROCESSING, REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION

And common core enriched genes are SKIL, SMAD7, SMURF2, NCOR2, MAML2, MAML3, MAMLD1, CTGF, SMAD4, ZFYVE9

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
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM	74	genes.ES.table	0.49	1.7	0.002	1	0.87	0.43	0.29	0.31	1	0.72
KEGG UBIQUITIN MEDIATED PROTEOLYSIS	134	genes.ES.table	0.26	1.6	0.031	1	0.93	0.44	0.41	0.26	1	0.74
KEGG THYROID CANCER	29	genes.ES.table	0.54	1.8	0.0044	1	0.61	0.31	0.2	0.25	1	0.6
BIOCARTA GPCR PATHWAY	32	genes.ES.table	0.46	1.5	0.047	1	0.98	0.62	0.39	0.38	1	0.77
PID ER NONGENOMIC PATHWAY	41	genes.ES.table	0.53	1.5	0.042	1	0.99	0.63	0.33	0.42	1	0.8
PID MET PATHWAY	79	genes.ES.table	0.34	1.6	0.042	1	0.95	0.46	0.39	0.28	1	0.74
PID CDC42 PATHWAY	70	genes.ES.table	0.32	1.4	0.093	1	0.99	0.49	0.39	0.3	1	0.78
PID RETINOIC ACID PATHWAY	30	genes.ES.table	0.54	1.7	0.0076	1	0.84	0.5	0.26	0.37	1	0.75
PID DELTANP63PATHWAY	46	genes.ES.table	0.52	1.4	0.065	1	0.99	0.46	0.28	0.33	1	0.79
PID A6B1 A6B4 INTEGRIN PATHWAY	46	genes.ES.table	0.45	1.4	0.083	1	1	0.2	0.15	0.17	1	0.77

genes ES table in pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

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	PPARG	PPARG	PPARG	469	0.57	0.12	YES
2	NTRK1	NTRK1	NTRK1	1055	0.42	0.19	YES
3	RXRG	RXRG	RXRG	1126	0.4	0.29	YES
4	TCF7	TCF7	TCF7	1267	0.38	0.38	YES
5	LEF1	LEF1	LEF1	2057	0.28	0.4	YES
6	CTNNB1	CTNNB1	CTNNB1	2340	0.26	0.45	YES
7	TCF7L2	TCF7L2	TCF7L2	2751	0.23	0.49	YES
8	MAPK3	MAPK3	MAPK3	3551	0.18	0.49	YES
9	RET	RET	RET	3581	0.18	0.54	YES
10	KRAS	KRAS	KRAS	5151	0.12	0.48	NO
11	MAPK1	MAPK1	MAPK1	6964	0.068	0.4	NO
12	BRAF	BRAF	BRAF	7026	0.066	0.41	NO
13	RXRA	RXRA	RXRA	7543	0.053	0.39	NO
14	TFG	TFG	TFG	7554	0.053	0.41	NO
15	HRAS	HRAS	HRAS	8060	0.04	0.39	NO
16	MAP2K1	MAP2K1	MAP2K1	9340	0.013	0.32	NO
17	TPM3	TPM3	TPM3	9649	0.0061	0.3	NO
18	CCDC6	CCDC6	CCDC6	10656	-0.016	0.25	NO
19	PAX8	PAX8	PAX8	10829	-0.02	0.25	NO
20	NCOA4	NCOA4	NCOA4	11044	-0.024	0.24	NO
21	TCF7L1	TCF7L1	TCF7L1	11143	-0.026	0.24	NO
22	CCND1	CCND1	CCND1	11245	-0.028	0.25	NO
23	NRAS	NRAS	NRAS	11600	-0.036	0.24	NO
24	CDH1	CDH1	CDH1	12179	-0.049	0.22	NO
25	MAP2K2	MAP2K2	MAP2K2	12248	-0.05	0.22	NO
26	TPR	TPR	TPR	13130	-0.071	0.19	NO
27	RXRB	RXRB	RXRB	13142	-0.072	0.21	NO
28	MYC	MYC	MYC	14445	-0.11	0.17	NO
29	TP53	TP53	TP53	15113	-0.14	0.17	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: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, 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 UBIQUITIN MEDIATED PROTEOLYSIS

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	VDR	VDR	VDR	496	0.56	0.083	YES
2	RARB	RARB	RARB	890	0.45	0.15	YES
3	RBP1	RBP1	RBP1	1025	0.43	0.23	YES
4	PRKCG	PRKCG	PRKCG	1032	0.42	0.31	YES
5	RXRG	RXRG	RXRG	1126	0.4	0.39	YES
6	MAPK8	MAPK8	MAPK8	2291	0.27	0.38	YES
7	MNAT1	MNAT1	MNAT1	2587	0.24	0.41	YES
8	NRIP1	NRIP1	NRIP1	3534	0.18	0.39	YES
9	MAPK3	MAPK3	MAPK3	3551	0.18	0.43	YES
10	NCOA2	NCOA2	NCOA2	3637	0.18	0.46	YES
11	CDK1	CDK1	CDK1	3882	0.17	0.48	YES
12	KAT2B	KAT2B	KAT2B	4309	0.15	0.48	YES
13	HDAC1	HDAC1	HDAC1	4422	0.15	0.51	YES
14	AKT1	AKT1	AKT1	4692	0.14	0.52	YES
15	RARG	RARG	RARG	4732	0.14	0.54	YES
16	NCOA1	NCOA1	NCOA1	5920	0.096	0.5	NO
17	PRKCA	PRKCA	PRKCA	6132	0.09	0.5	NO
18	NCOA3	NCOA3	NCOA3	6637	0.076	0.49	NO
19	MAPK1	MAPK1	MAPK1	6964	0.068	0.48	NO
20	RXRA	RXRA	RXRA	7543	0.053	0.46	NO
21	CREBBP	CREBBP	CREBBP	7829	0.046	0.46	NO
22	EP300	EP300	EP300	8470	0.031	0.43	NO
23	PRKACA	PRKACA	PRKACA	10370	-0.0095	0.32	NO
24	MAPK14	MAPK14	MAPK14	11262	-0.029	0.28	NO
25	NCOR2	NCOR2	NCOR2	11622	-0.037	0.27	NO
26	CCNH	CCNH	CCNH	12854	-0.064	0.21	NO
27	RXRB	RXRB	RXRB	13142	-0.072	0.21	NO
28	HDAC3	HDAC3	HDAC3	13206	-0.073	0.22	NO
29	RARA	RARA	RARA	13304	-0.076	0.23	NO
30	CDK7	CDK7	CDK7	15654	-0.17	0.14	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: KEGG UBIQUITIN MEDIATED PROTEOLYSIS.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS, 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 THYROID CANCER

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	PIP5K1B	PIP5K1B	PIP5K1B	302	0.65	0.041	YES
2	CALML3	CALML3	CALML3	381	0.6	0.09	YES
3	ITPR1	ITPR1	ITPR1	417	0.58	0.14	YES
4	DGKB	DGKB	DGKB	486	0.56	0.18	YES
5	INPP4B	INPP4B	INPP4B	522	0.55	0.23	YES
6	DGKI	DGKI	DGKI	678	0.5	0.27	YES
7	PRKCG	PRKCG	PRKCG	1032	0.42	0.28	YES
8	PLCB4	PLCB4	PLCB4	1341	0.37	0.3	YES
9	PIK3C2G	PIK3C2G	PIK3C2G	1750	0.32	0.31	YES
10	DGKG	DGKG	DGKG	2021	0.29	0.32	YES
11	CALM1	CALM1	CALM1	2342	0.26	0.32	YES
12	ITPKA	ITPKA	ITPKA	2431	0.26	0.34	YES
13	PIK3CG	PIK3CG	PIK3CG	2550	0.24	0.36	YES
14	ITPKB	ITPKB	ITPKB	2606	0.24	0.37	YES
15	PLCE1	PLCE1	PLCE1	2730	0.23	0.39	YES
16	PIK3R3	PIK3R3	PIK3R3	2846	0.22	0.4	YES
17	DGKE	DGKE	DGKE	2930	0.22	0.42	YES
18	DGKH	DGKH	DGKH	2972	0.22	0.43	YES
19	CDS1	CDS1	CDS1	3452	0.19	0.42	YES
20	ITPK1	ITPK1	ITPK1	3634	0.18	0.43	YES
21	IPPK	IPPK	IPPK	3871	0.17	0.43	YES
22	PIK3CD	PIK3CD	PIK3CD	3972	0.16	0.44	YES
23	PIK3CA	PIK3CA	PIK3CA	4081	0.16	0.45	YES
24	ITPR2	ITPR2	ITPR2	4187	0.16	0.46	YES
25	INPP1	INPP1	INPP1	4223	0.15	0.47	YES
26	PIP4K2A	PIP4K2A	PIP4K2A	4362	0.15	0.47	YES
27	DGKA	DGKA	DGKA	4436	0.15	0.48	YES
28	PLCB2	PLCB2	PLCB2	4775	0.13	0.48	YES
29	DGKQ	DGKQ	DGKQ	4929	0.13	0.48	YES
30	PIK3R5	PIK3R5	PIK3R5	5119	0.12	0.48	YES
31	DGKZ	DGKZ	DGKZ	5129	0.12	0.49	YES
32	PLCB1	PLCB1	PLCB1	5282	0.12	0.49	YES
33	PIK3C2A	PIK3C2A	PIK3C2A	5587	0.11	0.48	NO
34	PLCG1	PLCG1	PLCG1	5675	0.1	0.49	NO
35	PLCB3	PLCB3	PLCB3	5958	0.095	0.48	NO
36	PRKCA	PRKCA	PRKCA	6132	0.09	0.48	NO
37	ITPR3	ITPR3	ITPR3	6252	0.086	0.48	NO
38	INPP5D	INPP5D	INPP5D	7007	0.067	0.44	NO
39	IMPA2	IMPA2	IMPA2	7385	0.057	0.43	NO
40	PIK3CB	PIK3CB	PIK3CB	7508	0.054	0.43	NO
41	PTEN	PTEN	PTEN	7787	0.047	0.42	NO
42	INPP5A	INPP5A	INPP5A	7819	0.046	0.42	NO
43	PIP5K1C	PIP5K1C	PIP5K1C	7928	0.043	0.42	NO
44	IMPA1	IMPA1	IMPA1	8008	0.041	0.41	NO
45	CALM3	CALM3	CALM3	8202	0.037	0.41	NO
46	PLCD1	PLCD1	PLCD1	8229	0.036	0.41	NO
47	INPPL1	INPPL1	INPPL1	8273	0.035	0.41	NO
48	SYNJ2	SYNJ2	SYNJ2	8422	0.032	0.4	NO
49	DGKD	DGKD	DGKD	8587	0.028	0.4	NO
50	PIKFYVE	PIKFYVE	PIKFYVE	8822	0.023	0.39	NO
51	INPP4A	INPP4A	INPP4A	8933	0.021	0.38	NO
52	PIK3C2B	PIK3C2B	PIK3C2B	9468	0.01	0.35	NO
53	OCRL	OCRL	OCRL	9589	0.0073	0.35	NO
54	PLCG2	PLCG2	PLCG2	9669	0.0055	0.34	NO
55	INPP5E	INPP5E	INPP5E	9683	0.0052	0.34	NO
56	PI4KA	PI4KA	PI4KA	9786	0.0027	0.34	NO
57	CDIPT	CDIPT	CDIPT	9907	0.0003	0.33	NO
58	PIP4K2B	PIP4K2B	PIP4K2B	9959	-0.0007	0.33	NO
59	CALM2	CALM2	CALM2	10480	-0.012	0.3	NO
60	INPP5K	INPP5K	INPP5K	10573	-0.014	0.3	NO
61	PIK3R1	PIK3R1	PIK3R1	11051	-0.024	0.27	NO
62	PIK3C3	PIK3C3	PIK3C3	11229	-0.028	0.26	NO
63	PRKCB	PRKCB	PRKCB	11448	-0.033	0.26	NO
64	PIP5K1A	PIP5K1A	PIP5K1A	11961	-0.044	0.23	NO
65	PIP4K2C	PIP4K2C	PIP4K2C	12546	-0.057	0.2	NO
66	INPP5B	INPP5B	INPP5B	12959	-0.067	0.19	NO
67	PIK3R2	PIK3R2	PIK3R2	13077	-0.07	0.19	NO
68	SYNJ1	SYNJ1	SYNJ1	13362	-0.078	0.18	NO
69	PI4KB	PI4KB	PI4KB	13690	-0.087	0.17	NO
70	CALML6	CALML6	CALML6	13880	-0.093	0.16	NO
71	CDS2	CDS2	CDS2	14102	-0.1	0.16	NO
72	INPP5J	INPP5J	INPP5J	15427	-0.16	0.1	NO
73	PLCD3	PLCD3	PLCD3	15446	-0.16	0.12	NO
74	PLCD4	PLCD4	PLCD4	17249	-0.36	0.048	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 THYROID CANCER.

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

genes ES table in pathway: BIOCARTA GPCR PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GJB6	GJB6	GJB6	136	0.77	0.049	YES
2	GJB2	GJB2	GJB2	304	0.65	0.088	YES
3	GJA1	GJA1	GJA1	434	0.58	0.12	YES
4	TPD52L1	TPD52L1	TPD52L1	630	0.52	0.15	YES
5	VPS37D	VPS37D	VPS37D	1127	0.4	0.15	YES
6	GJA3	GJA3	GJA3	1662	0.33	0.15	YES
7	GJB7	GJB7	GJB7	1723	0.32	0.17	YES
8	AP1S2	AP1S2	AP1S2	1786	0.31	0.19	YES
9	AP1M2	AP1M2	AP1M2	1799	0.31	0.21	YES
10	GJB3	GJB3	GJB3	1971	0.29	0.22	YES
11	SEC24D	SEC24D	SEC24D	2368	0.26	0.22	YES
12	SNX9	SNX9	SNX9	2663	0.24	0.22	YES
13	CHMP2B	CHMP2B	CHMP2B	2717	0.23	0.24	YES
14	SEC23A	SEC23A	SEC23A	3447	0.19	0.21	YES
15	VTA1	VTA1	VTA1	3459	0.19	0.22	YES
16	CLTCL1	CLTCL1	CLTCL1	3492	0.19	0.23	YES
17	TBC1D8B	TBC1D8B	TBC1D8B	3556	0.18	0.24	YES
18	GJA9	GJA9	GJA9	3736	0.18	0.25	YES
19	SH3GL2	SH3GL2	SH3GL2	3869	0.17	0.25	YES
20	GJB4	GJB4	GJB4	4105	0.16	0.25	YES
21	SH3D19	SH3D19	SH3D19	4281	0.15	0.25	YES
22	CPD	CPD	CPD	4322	0.15	0.26	YES
23	AP4B1	AP4B1	AP4B1	4360	0.15	0.27	YES
24	AP1S1	AP1S1	AP1S1	4398	0.15	0.28	YES
25	GJC2	GJC2	GJC2	4427	0.15	0.29	YES
26	VPS36	VPS36	VPS36	4452	0.14	0.3	YES
27	GJA5	GJA5	GJA5	4547	0.14	0.3	YES
28	SEC13	SEC13	SEC13	4791	0.13	0.3	YES
29	GJD4	GJD4	GJD4	4900	0.13	0.3	YES
30	PUM1	PUM1	PUM1	5055	0.12	0.3	YES
31	COPB2	COPB2	COPB2	5065	0.12	0.31	YES
32	ARRB1	ARRB1	ARRB1	5127	0.12	0.32	YES
33	YIPF6	YIPF6	YIPF6	5199	0.12	0.32	YES
34	NECAP1	NECAP1	NECAP1	5357	0.11	0.32	YES
35	AP3S1	AP3S1	AP3S1	5459	0.11	0.32	YES
36	GJB5	GJB5	GJB5	5556	0.11	0.33	YES
37	PIK3C2A	PIK3C2A	PIK3C2A	5587	0.11	0.33	YES
38	GJA4	GJA4	GJA4	5636	0.1	0.34	YES
39	MYO6	MYO6	MYO6	5772	0.1	0.34	YES
40	ARCN1	ARCN1	ARCN1	6164	0.089	0.32	YES
41	CHMP5	CHMP5	CHMP5	6241	0.087	0.33	YES
42	AP1B1	AP1B1	AP1B1	6350	0.084	0.33	YES
43	FTL	FTL	FTL	6429	0.082	0.33	YES
44	SNAP23	SNAP23	SNAP23	6523	0.079	0.33	YES
45	VPS4A	VPS4A	VPS4A	6568	0.078	0.33	YES
46	SAR1B	SAR1B	SAR1B	6593	0.078	0.34	YES
47	IGF2R	IGF2R	IGF2R	6649	0.076	0.34	YES
48	SRC	SRC	SRC	6743	0.073	0.34	YES
49	GJC1	GJC1	GJC1	6838	0.07	0.34	YES
50	COPB1	COPB1	COPB1	6894	0.069	0.34	YES
51	GAK	GAK	GAK	6907	0.069	0.35	YES
52	CTSZ	CTSZ	CTSZ	7088	0.065	0.34	NO
53	STAM2	STAM2	STAM2	7222	0.061	0.34	NO
54	COPG	COPG	COPG	7587	0.052	0.32	NO
55	TFRC	TFRC	TFRC	7835	0.045	0.31	NO
56	DNM2	DNM2	DNM2	7851	0.045	0.31	NO
57	SEC24B	SEC24B	SEC24B	7927	0.043	0.31	NO
58	GNS	GNS	GNS	8090	0.039	0.31	NO
59	VPS37B	VPS37B	VPS37B	8182	0.037	0.3	NO
60	AP1G1	AP1G1	AP1G1	8189	0.037	0.31	NO
61	RAB5C	RAB5C	RAB5C	8212	0.037	0.31	NO
62	VPS25	VPS25	VPS25	8266	0.035	0.31	NO
63	CHMP4B	CHMP4B	CHMP4B	8547	0.029	0.29	NO
64	VAMP2	VAMP2	VAMP2	8669	0.026	0.29	NO
65	SORT1	SORT1	SORT1	8737	0.025	0.29	NO
66	VPS37A	VPS37A	VPS37A	8764	0.024	0.29	NO
67	TSG101	TSG101	TSG101	8768	0.024	0.29	NO
68	GBF1	GBF1	GBF1	8789	0.024	0.29	NO
69	HSPA8	HSPA8	HSPA8	8898	0.022	0.29	NO
70	CHMP4C	CHMP4C	CHMP4C	8941	0.021	0.28	NO
71	CNO	CNO	CNO	8946	0.021	0.29	NO
72	AP2M1	AP2M1	AP2M1	8961	0.02	0.29	NO
73	PICALM	PICALM	PICALM	9051	0.019	0.28	NO
74	TPD52	TPD52	TPD52	9143	0.017	0.28	NO
75	SEC31A	SEC31A	SEC31A	9366	0.012	0.27	NO
76	PREB	PREB	PREB	9369	0.012	0.27	NO
77	OCRL	OCRL	OCRL	9589	0.0073	0.26	NO
78	M6PR	M6PR	M6PR	9904	0.00036	0.24	NO
79	VPS4B	VPS4B	VPS4B	9913	0.00023	0.24	NO
80	CLTC	CLTC	CLTC	9965	-0.0008	0.24	NO
81	AP4E1	AP4E1	AP4E1	10045	-0.0026	0.23	NO
82	FTH1	FTH1	FTH1	10107	-0.004	0.23	NO
83	ARFGAP1	ARFGAP1	ARFGAP1	10167	-0.0055	0.23	NO
84	TJP1	TJP1	TJP1	10351	-0.0092	0.22	NO
85	VAMP7	VAMP7	VAMP7	10754	-0.018	0.2	NO
86	VPS37C	VPS37C	VPS37C	10872	-0.021	0.19	NO
87	ARF1	ARF1	ARF1	10874	-0.021	0.19	NO
88	PLDN	PLDN	PLDN	10880	-0.021	0.19	NO
89	VAMP8	VAMP8	VAMP8	11233	-0.028	0.18	NO
90	CHMP6	CHMP6	CHMP6	11301	-0.03	0.18	NO
91	SNX2	SNX2	SNX2	11457	-0.033	0.17	NO
92	DNAJC6	DNAJC6	DNAJC6	11578	-0.036	0.16	NO
93	HGS	HGS	HGS	11588	-0.036	0.17	NO
94	SNF8	SNF8	SNF8	11619	-0.037	0.17	NO
95	TXNDC5	TXNDC5	TXNDC5	11670	-0.038	0.17	NO
96	NAPA	NAPA	NAPA	11733	-0.039	0.17	NO
97	CHMP4A	CHMP4A	CHMP4A	11751	-0.04	0.17	NO
98	COPA	COPA	COPA	11759	-0.04	0.17	NO
99	CLTB	CLTB	CLTB	11785	-0.041	0.17	NO
100	TGOLN2	TGOLN2	TGOLN2	11814	-0.041	0.18	NO
101	COPE	COPE	COPE	12019	-0.045	0.17	NO
102	CHMP2A	CHMP2A	CHMP2A	12049	-0.046	0.17	NO
103	SNX5	SNX5	SNX5	12244	-0.05	0.16	NO
104	STX4	STX4	STX4	12338	-0.052	0.16	NO
105	DTNBP1	DTNBP1	DTNBP1	12401	-0.054	0.16	NO
106	BLOC1S1	BLOC1S1	BLOC1S1	12441	-0.054	0.16	NO
107	SEC24C	SEC24C	SEC24C	12549	-0.057	0.16	NO
108	CLTA	CLTA	CLTA	12652	-0.06	0.16	NO
109	STAM	STAM	STAM	12672	-0.06	0.16	NO
110	AP3B1	AP3B1	AP3B1	12891	-0.065	0.16	NO
111	CHMP7	CHMP7	CHMP7	13641	-0.086	0.12	NO
112	BLOC1S3	BLOC1S3	BLOC1S3	13876	-0.093	0.11	NO
113	RPS27A	RPS27A	RPS27A	13992	-0.096	0.12	NO
114	DNASE2	DNASE2	DNASE2	14110	-0.1	0.12	NO
115	COPZ1	COPZ1	COPZ1	14274	-0.11	0.12	NO
116	VPS28	VPS28	VPS28	14277	-0.11	0.12	NO
117	UBA52	UBA52	UBA52	14355	-0.11	0.13	NO
118	DAB2	DAB2	DAB2	14480	-0.11	0.13	NO
119	SNAPIN	SNAPIN	SNAPIN	14555	-0.12	0.13	NO
120	AP1M1	AP1M1	AP1M1	15500	-0.16	0.092	NO
121	GJB1	GJB1	GJB1	15832	-0.18	0.087	NO
122	DNM1	DNM1	DNM1	16472	-0.24	0.069	NO
123	HIP1R	HIP1R	HIP1R	16896	-0.3	0.068	NO

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

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

genes ES table in pathway: PID ER NONGENOMIC PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HERC3	HERC3	HERC3	575	0.53	0.011	YES
2	FBXO2	FBXO2	FBXO2	1042	0.42	0.019	YES
3	MID1	MID1	MID1	1306	0.37	0.035	YES
4	PARK2	PARK2	PARK2	1807	0.31	0.032	YES
5	DET1	DET1	DET1	2147	0.28	0.036	YES
6	SOCS3	SOCS3	SOCS3	2370	0.26	0.044	YES
7	UBE2E2	UBE2E2	UBE2E2	2670	0.24	0.047	YES
8	SKP2	SKP2	SKP2	2939	0.22	0.049	YES
9	UBE2C	UBE2C	UBE2C	3012	0.21	0.063	YES
10	UBE4B	UBE4B	UBE4B	3187	0.2	0.069	YES
11	CDC26	CDC26	CDC26	3254	0.2	0.082	YES
12	TRAF6	TRAF6	TRAF6	3322	0.2	0.094	YES
13	UBE2S	UBE2S	UBE2S	3427	0.19	0.1	YES
14	CDC20	CDC20	CDC20	3555	0.18	0.11	YES
15	ANAPC10	ANAPC10	ANAPC10	3586	0.18	0.12	YES
16	SOCS1	SOCS1	SOCS1	3636	0.18	0.14	YES
17	UBE2E1	UBE2E1	UBE2E1	3783	0.17	0.14	YES
18	VHL	VHL	VHL	4131	0.16	0.14	YES
19	SMURF2	SMURF2	SMURF2	4140	0.16	0.15	YES
20	FBXW7	FBXW7	FBXW7	4392	0.15	0.15	YES
21	UBE2O	UBE2O	UBE2O	4484	0.14	0.15	YES
22	UBE2J1	UBE2J1	UBE2J1	4625	0.14	0.16	YES
23	BRCA1	BRCA1	BRCA1	4744	0.13	0.16	YES
24	FANCL	FANCL	FANCL	4752	0.13	0.17	YES
25	SIAH1	SIAH1	SIAH1	4761	0.13	0.18	YES
26	CBLB	CBLB	CBLB	4810	0.13	0.19	YES
27	KLHL13	KLHL13	KLHL13	4834	0.13	0.2	YES
28	CUL4A	CUL4A	CUL4A	4916	0.13	0.2	YES
29	CDC27	CDC27	CDC27	4934	0.13	0.21	YES
30	UBE2H	UBE2H	UBE2H	5193	0.12	0.21	YES
31	UBA3	UBA3	UBA3	5260	0.12	0.21	YES
32	BTRC	BTRC	BTRC	5631	0.1	0.2	YES
33	CUL1	CUL1	CUL1	5849	0.099	0.2	YES
34	UBE2D4	UBE2D4	UBE2D4	6129	0.09	0.19	YES
35	UBE2F	UBE2F	UBE2F	6206	0.088	0.19	YES
36	CDC16	CDC16	CDC16	6223	0.087	0.2	YES
37	PIAS3	PIAS3	PIAS3	6227	0.087	0.21	YES
38	UBE2D1	UBE2D1	UBE2D1	6243	0.087	0.21	YES
39	UBE2K	UBE2K	UBE2K	6638	0.076	0.2	YES
40	ITCH	ITCH	ITCH	6868	0.07	0.19	YES
41	ANAPC13	ANAPC13	ANAPC13	6875	0.07	0.19	YES
42	UBE3C	UBE3C	UBE3C	6890	0.069	0.2	YES
43	XIAP	XIAP	XIAP	6930	0.068	0.2	YES
44	PML	PML	PML	6950	0.068	0.21	YES
45	TRIM32	TRIM32	TRIM32	7010	0.066	0.21	YES
46	UBE2D3	UBE2D3	UBE2D3	7063	0.065	0.21	YES
47	ANAPC11	ANAPC11	ANAPC11	7092	0.064	0.22	YES
48	HERC2	HERC2	HERC2	7093	0.064	0.22	YES
49	UBR5	UBR5	UBR5	7136	0.063	0.22	YES
50	UBA1	UBA1	UBA1	7175	0.062	0.23	YES
51	UBE2N	UBE2N	UBE2N	7184	0.062	0.23	YES
52	UBA7	UBA7	UBA7	7221	0.061	0.23	YES
53	BIRC2	BIRC2	BIRC2	7240	0.06	0.24	YES
54	MDM2	MDM2	MDM2	7301	0.059	0.24	YES
55	UBE2J2	UBE2J2	UBE2J2	7336	0.058	0.24	YES
56	BIRC6	BIRC6	BIRC6	7370	0.057	0.24	YES
57	RHOBTB2	RHOBTB2	RHOBTB2	7376	0.057	0.25	YES
58	UBE2E3	UBE2E3	UBE2E3	7388	0.057	0.25	YES
59	RNF7	RNF7	RNF7	7398	0.057	0.26	YES
60	TRIM37	TRIM37	TRIM37	7816	0.046	0.24	NO
61	UBE4A	UBE4A	UBE4A	7908	0.044	0.24	NO
62	UBA6	UBA6	UBA6	8066	0.04	0.23	NO
63	CBL	CBL	CBL	8184	0.037	0.23	NO
64	TCEB1	TCEB1	TCEB1	8260	0.035	0.22	NO
65	KEAP1	KEAP1	KEAP1	8267	0.035	0.23	NO
66	PIAS1	PIAS1	PIAS1	8334	0.034	0.23	NO
67	STUB1	STUB1	STUB1	8353	0.033	0.23	NO
68	SMURF1	SMURF1	SMURF1	8459	0.031	0.22	NO
69	UBE2G1	UBE2G1	UBE2G1	8555	0.029	0.22	NO
70	UBE2A	UBE2A	UBE2A	8653	0.027	0.22	NO
71	TRIP12	TRIP12	TRIP12	8739	0.025	0.22	NO
72	UBE2W	UBE2W	UBE2W	9001	0.02	0.2	NO
73	TCEB2	TCEB2	TCEB2	9005	0.02	0.2	NO
74	WWP2	WWP2	WWP2	9118	0.017	0.2	NO
75	CUL3	CUL3	CUL3	9225	0.015	0.2	NO
76	UBA2	UBA2	UBA2	9238	0.015	0.2	NO
77	CUL4B	CUL4B	CUL4B	9384	0.012	0.19	NO
78	RBX1	RBX1	RBX1	9388	0.012	0.19	NO
79	UBE2R2	UBE2R2	UBE2R2	9407	0.011	0.19	NO
80	SAE1	SAE1	SAE1	9438	0.01	0.19	NO
81	HERC4	HERC4	HERC4	9488	0.0095	0.19	NO
82	UBE2NL	UBE2NL	UBE2NL	9511	0.009	0.19	NO
83	HUWE1	HUWE1	HUWE1	9517	0.0089	0.19	NO
84	KLHL9	KLHL9	KLHL9	9574	0.0077	0.18	NO
85	FZR1	FZR1	FZR1	9579	0.0076	0.18	NO
86	UBE2I	UBE2I	UBE2I	9590	0.0073	0.18	NO
87	PRPF19	PRPF19	PRPF19	9618	0.0067	0.18	NO
88	UBE2L3	UBE2L3	UBE2L3	9654	0.0059	0.18	NO
89	FBXO4	FBXO4	FBXO4	9793	0.0026	0.18	NO
90	CUL2	CUL2	CUL2	9879	0.00083	0.17	NO
91	HERC1	HERC1	HERC1	10056	-0.0028	0.16	NO
92	MGRN1	MGRN1	MGRN1	10136	-0.0047	0.16	NO
93	RCHY1	RCHY1	RCHY1	10240	-0.0071	0.15	NO
94	ANAPC7	ANAPC7	ANAPC7	10264	-0.0078	0.15	NO
95	CUL5	CUL5	CUL5	10285	-0.0081	0.15	NO
96	ANAPC1	ANAPC1	ANAPC1	10350	-0.0092	0.15	NO
97	CBLC	CBLC	CBLC	10396	-0.01	0.15	NO
98	UBOX5	UBOX5	UBOX5	10450	-0.011	0.14	NO
99	UBE2QL1	UBE2QL1	UBE2QL1	10749	-0.018	0.13	NO
100	UBE3A	UBE3A	UBE3A	10801	-0.019	0.13	NO
101	ANAPC2	ANAPC2	ANAPC2	10952	-0.022	0.12	NO
102	SKP1	SKP1	SKP1	11022	-0.024	0.12	NO
103	UBE2D2	UBE2D2	UBE2D2	11058	-0.024	0.12	NO
104	PIAS2	PIAS2	PIAS2	11156	-0.026	0.12	NO
105	CDC34	CDC34	CDC34	11184	-0.027	0.12	NO
106	ANAPC5	ANAPC5	ANAPC5	11374	-0.031	0.11	NO
107	UBE2G2	UBE2G2	UBE2G2	11434	-0.033	0.11	NO
108	NHLRC1	NHLRC1	NHLRC1	11562	-0.036	0.1	NO
109	PPIL2	PPIL2	PPIL2	11596	-0.036	0.1	NO
110	UBE3B	UBE3B	UBE3B	11646	-0.038	0.1	NO
111	DDB1	DDB1	DDB1	11743	-0.04	0.1	NO
112	NEDD4L	NEDD4L	NEDD4L	11767	-0.04	0.1	NO
113	FBXW8	FBXW8	FBXW8	11833	-0.042	0.1	NO
114	UBE2Q2	UBE2Q2	UBE2Q2	12145	-0.048	0.091	NO
115	UBE2Z	UBE2Z	UBE2Z	12714	-0.061	0.064	NO
116	UBE2B	UBE2B	UBE2B	12735	-0.062	0.068	NO
117	CDC23	CDC23	CDC23	12750	-0.062	0.072	NO
118	UBE2M	UBE2M	UBE2M	13236	-0.074	0.051	NO
119	ANAPC4	ANAPC4	ANAPC4	13384	-0.078	0.05	NO
120	SYVN1	SYVN1	SYVN1	13555	-0.083	0.047	NO
121	WWP1	WWP1	WWP1	13620	-0.085	0.05	NO
122	CUL7	CUL7	CUL7	13911	-0.094	0.042	NO
123	UBE2Q1	UBE2Q1	UBE2Q1	14381	-0.11	0.024	NO
124	PIAS4	PIAS4	PIAS4	14444	-0.11	0.03	NO
125	RFWD2	RFWD2	RFWD2	14858	-0.13	0.017	NO
126	AIRE	AIRE	AIRE	15167	-0.14	0.012	NO
127	UBE2L6	UBE2L6	UBE2L6	15244	-0.15	0.019	NO
128	BIRC3	BIRC3	BIRC3	15833	-0.18	0.0013	NO
129	FBXW11	FBXW11	FBXW11	15944	-0.19	0.011	NO
130	NEDD4	NEDD4	NEDD4	15986	-0.2	0.024	NO
131	ERCC8	ERCC8	ERCC8	16006	-0.2	0.039	NO
132	DDB2	DDB2	DDB2	16305	-0.22	0.041	NO
133	MAP3K1	MAP3K1	MAP3K1	16464	-0.24	0.051	NO
134	UBE2U	UBE2U	UBE2U	17718	-0.5	0.022	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: PID ER NONGENOMIC PATHWAY.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: PID ER NONGENOMIC 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: PID MET PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	F2RL2	F2RL2	F2RL2	321	0.64	0.061	YES
2	ARHGEF4	ARHGEF4	ARHGEF4	741	0.48	0.097	YES
3	RIN2	RIN2	RIN2	1738	0.32	0.082	YES
4	MAPK8	MAPK8	MAPK8	2291	0.27	0.084	YES
5	CTNNB1	CTNNB1	CTNNB1	2340	0.26	0.11	YES
6	SH3KBP1	SH3KBP1	SH3KBP1	2909	0.22	0.11	YES
7	PARD6A	PARD6A	PARD6A	2970	0.22	0.13	YES
8	PRKCI	PRKCI	PRKCI	3304	0.2	0.14	YES
9	MAPK3	MAPK3	MAPK3	3551	0.18	0.15	YES
10	EIF4E	EIF4E	EIF4E	3865	0.17	0.15	YES
11	SH3GL2	SH3GL2	SH3GL2	3869	0.17	0.17	YES
12	SNAI1	SNAI1	SNAI1	3928	0.17	0.19	YES
13	ETS1	ETS1	ETS1	3935	0.17	0.21	YES
14	RAB5A	RAB5A	RAB5A	3947	0.17	0.23	YES
15	PIK3CA	PIK3CA	PIK3CA	4081	0.16	0.24	YES
16	RAP1B	RAP1B	RAP1B	4207	0.16	0.25	YES
17	CDC42	CDC42	CDC42	4354	0.15	0.26	YES
18	RAF1	RAF1	RAF1	4565	0.14	0.27	YES
19	MTOR	MTOR	MTOR	4573	0.14	0.29	YES
20	AKT1	AKT1	AKT1	4692	0.14	0.3	YES
21	RAP1A	RAP1A	RAP1A	4786	0.13	0.31	YES
22	PAK1	PAK1	PAK1	4897	0.13	0.32	YES
23	NUMB	NUMB	NUMB	4945	0.13	0.33	YES
24	PLCG1	PLCG1	PLCG1	5675	0.1	0.3	YES
25	RHOA	RHOA	RHOA	5729	0.1	0.31	YES
26	MET	MET	MET	6214	0.087	0.3	YES
27	PTPN1	PTPN1	PTPN1	6490	0.08	0.29	YES
28	PTK2	PTK2	PTK2	6541	0.079	0.3	YES
29	RANBP9	RANBP9	RANBP9	6575	0.078	0.31	YES
30	PRKCZ	PRKCZ	PRKCZ	6582	0.078	0.32	YES
31	PAK2	PAK2	PAK2	6598	0.077	0.32	YES
32	SRC	SRC	SRC	6743	0.073	0.32	YES
33	HGF	HGF	HGF	6781	0.072	0.33	YES
34	MAPK1	MAPK1	MAPK1	6964	0.068	0.33	YES
35	INPP5D	INPP5D	INPP5D	7007	0.067	0.34	YES
36	JUN	JUN	JUN	7076	0.065	0.34	YES
37	PXN	PXN	PXN	7374	0.057	0.33	NO
38	RAPGEF1	RAPGEF1	RAPGEF1	7452	0.055	0.33	NO
39	NCK1	NCK1	NCK1	7511	0.054	0.34	NO
40	SOS1	SOS1	SOS1	7686	0.049	0.33	NO
41	CRK	CRK	CRK	7731	0.048	0.34	NO
42	HRAS	HRAS	HRAS	8060	0.04	0.32	NO
43	CBL	CBL	CBL	8184	0.037	0.32	NO
44	ARF6	ARF6	ARF6	8218	0.036	0.32	NO
45	INPPL1	INPPL1	INPPL1	8273	0.035	0.32	NO
46	CRKL	CRKL	CRKL	8488	0.03	0.32	NO
47	RAC1	RAC1	RAC1	8686	0.026	0.31	NO
48	EPS15	EPS15	EPS15	8945	0.021	0.3	NO
49	WASL	WASL	WASL	9008	0.02	0.3	NO
50	BCAR1	BCAR1	BCAR1	9065	0.018	0.3	NO
51	MAP2K4	MAP2K4	MAP2K4	9204	0.015	0.29	NO
52	KPNB1	KPNB1	KPNB1	9214	0.015	0.29	NO
53	EIF4EBP1	EIF4EBP1	EIF4EBP1	9220	0.015	0.29	NO
54	MAP2K1	MAP2K1	MAP2K1	9340	0.013	0.29	NO
55	PDPK1	PDPK1	PDPK1	9529	0.0087	0.28	NO
56	GRB2	GRB2	GRB2	9753	0.0037	0.27	NO
57	PTPRJ	PTPRJ	PTPRJ	10087	-0.0035	0.25	NO
58	CTNNA1	CTNNA1	CTNNA1	10508	-0.012	0.23	NO
59	PIK3R1	PIK3R1	PIK3R1	11051	-0.024	0.2	NO
60	MLST8	MLST8	MLST8	11075	-0.025	0.2	NO
61	GAB1	GAB1	GAB1	11391	-0.032	0.19	NO
62	HGS	HGS	HGS	11588	-0.036	0.18	NO
63	RPTOR	RPTOR	RPTOR	11636	-0.037	0.18	NO
64	PTPN11	PTPN11	PTPN11	11821	-0.041	0.18	NO
65	RANBP10	RANBP10	RANBP10	11927	-0.043	0.18	NO
66	CDH1	CDH1	CDH1	12179	-0.049	0.17	NO
67	MAP2K2	MAP2K2	MAP2K2	12248	-0.05	0.17	NO
68	MUC20	MUC20	MUC20	12277	-0.051	0.18	NO
69	BAD	BAD	BAD	12816	-0.063	0.16	NO
70	EGR1	EGR1	EGR1	12915	-0.066	0.16	NO
71	PAK4	PAK4	PAK4	13036	-0.068	0.16	NO
72	SHC1	SHC1	SHC1	13047	-0.069	0.17	NO
73	NCK2	NCK2	NCK2	13186	-0.072	0.17	NO
74	GAB2	GAB2	GAB2	13627	-0.085	0.16	NO
75	APC	APC	APC	13927	-0.094	0.15	NO
76	AKT1S1	AKT1S1	AKT1S1	14362	-0.11	0.14	NO
77	AKT2	AKT2	AKT2	14805	-0.13	0.13	NO
78	PTPN2	PTPN2	PTPN2	15901	-0.19	0.093	NO
79	MAP3K1	MAP3K1	MAP3K1	16464	-0.24	0.091	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: PID MET PATHWAY.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: PID MET 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: PID CDC42 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	AGPAT9	AGPAT9	AGPAT9	25	0.98	0.16	YES
2	PLA2G10	PLA2G10	PLA2G10	170	0.73	0.26	YES
3	PLA2G4A	PLA2G4A	PLA2G4A	450	0.57	0.34	YES
4	PLA2G2F	PLA2G2F	PLA2G2F	637	0.51	0.41	YES
5	PLA2G1B	PLA2G1B	PLA2G1B	1136	0.4	0.45	YES
6	GPD1L	GPD1L	GPD1L	1151	0.4	0.51	YES
7	GPAT2	GPAT2	GPAT2	1432	0.36	0.55	YES
8	AGPAT4	AGPAT4	AGPAT4	1956	0.3	0.57	YES
9	PLA2G4D	PLA2G4D	PLA2G4D	2823	0.22	0.56	NO
10	LCLAT1	LCLAT1	LCLAT1	3490	0.19	0.55	NO
11	PLA2G5	PLA2G5	PLA2G5	5174	0.12	0.48	NO
12	LPCAT4	LPCAT4	LPCAT4	7478	0.055	0.36	NO
13	AGPAT5	AGPAT5	AGPAT5	8168	0.038	0.32	NO
14	LPCAT1	LPCAT1	LPCAT1	9466	0.01	0.25	NO
15	PLA2G12A	PLA2G12A	PLA2G12A	10739	-0.017	0.19	NO
16	AGPAT2	AGPAT2	AGPAT2	11792	-0.041	0.14	NO
17	GPAM	GPAM	GPAM	11926	-0.043	0.13	NO
18	PLD2	PLD2	PLD2	12108	-0.047	0.13	NO
19	PLA2G2D	PLA2G2D	PLA2G2D	12835	-0.064	0.1	NO
20	AGPAT1	AGPAT1	AGPAT1	12863	-0.064	0.11	NO
21	AGPAT3	AGPAT3	AGPAT3	13246	-0.075	0.1	NO
22	GPD1	GPD1	GPD1	13494	-0.081	0.1	NO
23	GNPAT	GNPAT	GNPAT	14267	-0.11	0.075	NO
24	AGPAT6	AGPAT6	AGPAT6	15414	-0.16	0.036	NO
25	PLD1	PLD1	PLD1	16792	-0.28	0.0048	NO
26	PLA2G2A	PLA2G2A	PLA2G2A	17504	-0.43	0.034	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: PID CDC42 PATHWAY.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: PID CDC42 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: PID RETINOIC ACID 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	MAP3K5	MAP3K5	MAP3K5	1077	0.41	0.042	YES
2	FOXO1	FOXO1	FOXO1	2499	0.25	0.024	YES
3	SFN	SFN	SFN	2657	0.24	0.073	YES
4	TBC1D4	TBC1D4	TBC1D4	2804	0.23	0.12	YES
5	CASP9	CASP9	CASP9	2816	0.22	0.18	YES
6	FOXO3	FOXO3	FOXO3	2952	0.22	0.22	YES
7	SLC2A4	SLC2A4	SLC2A4	4383	0.15	0.18	YES
8	RAF1	RAF1	RAF1	4565	0.14	0.2	YES
9	MTOR	MTOR	MTOR	4573	0.14	0.24	YES
10	HSP90AA1	HSP90AA1	HSP90AA1	4605	0.14	0.27	YES
11	AKT1	AKT1	AKT1	4692	0.14	0.3	YES
12	CDKN1B	CDKN1B	CDKN1B	4893	0.13	0.32	YES
13	KPNA1	KPNA1	KPNA1	5536	0.11	0.31	YES
14	FOXO4	FOXO4	FOXO4	5799	0.1	0.32	YES
15	MAPKAP1	MAPKAP1	MAPKAP1	6285	0.086	0.31	YES
16	YWHAZ	YWHAZ	YWHAZ	6493	0.08	0.32	YES
17	SRC	SRC	SRC	6743	0.073	0.32	YES
18	CHUK	CHUK	CHUK	6773	0.072	0.34	YES
19	PRKDC	PRKDC	PRKDC	6817	0.071	0.36	YES
20	GSK3B	GSK3B	GSK3B	6992	0.067	0.36	YES
21	YWHAB	YWHAB	YWHAB	7116	0.064	0.37	YES
22	YWHAG	YWHAG	YWHAG	7697	0.049	0.35	NO
23	YWHAE	YWHAE	YWHAE	8321	0.034	0.32	NO
24	PDPK1	PDPK1	PDPK1	9529	0.0087	0.26	NO
25	PRKACA	PRKACA	PRKACA	10370	-0.0095	0.22	NO
26	CDKN1A	CDKN1A	CDKN1A	10916	-0.022	0.19	NO
27	MLST8	MLST8	MLST8	11075	-0.025	0.19	NO
28	YWHAQ	YWHAQ	YWHAQ	11610	-0.037	0.17	NO
29	YWHAH	YWHAH	YWHAH	12075	-0.046	0.15	NO
30	GSK3A	GSK3A	GSK3A	12182	-0.049	0.16	NO
31	BAD	BAD	BAD	12816	-0.063	0.14	NO
32	RICTOR	RICTOR	RICTOR	13242	-0.075	0.14	NO
33	AKT2	AKT2	AKT2	14805	-0.13	0.08	NO
34	AKT3	AKT3	AKT3	16090	-0.21	0.059	NO
35	BCL2L1	BCL2L1	BCL2L1	16219	-0.22	0.1	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: PID RETINOIC ACID PATHWAY.

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: PID RETINOIC ACID 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: PID DELTANP63PATHWAY

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	GRIA1	GRIA1	GRIA1	709	0.49	0.096	YES
2	GRIA2	GRIA2	GRIA2	713	0.49	0.23	YES
3	GRIA3	GRIA3	GRIA3	938	0.44	0.34	YES
4	PRKCG	PRKCG	PRKCG	1032	0.42	0.45	YES
5	CACNG4	CACNG4	CACNG4	1159	0.4	0.56	YES
6	AKAP5	AKAP5	AKAP5	3390	0.19	0.49	NO
7	NSF	NSF	NSF	5704	0.1	0.39	NO
8	MYO6	MYO6	MYO6	5772	0.1	0.41	NO
9	CAMK2D	CAMK2D	CAMK2D	5931	0.096	0.43	NO
10	DLG1	DLG1	DLG1	5993	0.094	0.45	NO
11	PRKCA	PRKCA	PRKCA	6132	0.09	0.47	NO
12	CACNG3	CACNG3	CACNG3	6966	0.068	0.44	NO
13	MDM2	MDM2	MDM2	7301	0.059	0.44	NO
14	AP2S1	AP2S1	AP2S1	8027	0.041	0.41	NO
15	AP2A1	AP2A1	AP2A1	8604	0.028	0.39	NO
16	AP2M1	AP2M1	AP2M1	8961	0.02	0.37	NO
17	CAMK2B	CAMK2B	CAMK2B	10717	-0.017	0.28	NO
18	PRKCB	PRKCB	PRKCB	11448	-0.033	0.25	NO
19	AP2B1	AP2B1	AP2B1	11663	-0.038	0.25	NO
20	EPB41L1	EPB41L1	EPB41L1	12028	-0.045	0.24	NO
21	AP2A2	AP2A2	AP2A2	12043	-0.046	0.25	NO
22	GRIA4	GRIA4	GRIA4	12135	-0.048	0.26	NO
23	CAMK2A	CAMK2A	CAMK2A	13009	-0.068	0.23	NO
24	PICK1	PICK1	PICK1	13865	-0.092	0.21	NO
25	GRIP2	GRIP2	GRIP2	13935	-0.094	0.23	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: PID DELTANP63PATHWAY.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: PID DELTANP63PATHWAY, 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: PID A6B1 A6B4 INTEGRIN 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	PIP5K1B	PIP5K1B	PIP5K1B	302	0.65	0.1	YES
2	INPP4B	INPP4B	INPP4B	522	0.55	0.19	YES
3	TPTE2	TPTE2	TPTE2	1314	0.37	0.22	YES
4	PIK3C2G	PIK3C2G	PIK3C2G	1750	0.32	0.25	YES
5	PIK3CG	PIK3CG	PIK3CG	2550	0.24	0.26	YES
6	PIK3R3	PIK3R3	PIK3R3	2846	0.22	0.28	YES
7	FIG4	FIG4	FIG4	2964	0.22	0.31	YES
8	SACM1L	SACM1L	SACM1L	3377	0.19	0.33	YES
9	MTM1	MTM1	MTM1	3788	0.17	0.34	YES
10	PIK3CD	PIK3CD	PIK3CD	3972	0.16	0.36	YES
11	PIK3CA	PIK3CA	PIK3CA	4081	0.16	0.38	YES
12	PIP4K2A	PIP4K2A	PIP4K2A	4362	0.15	0.39	YES
13	PIK3R5	PIK3R5	PIK3R5	5119	0.12	0.37	YES
14	MTMR6	MTMR6	MTMR6	5137	0.12	0.4	YES
15	PIK3R4	PIK3R4	PIK3R4	5444	0.11	0.4	YES
16	PIK3C2A	PIK3C2A	PIK3C2A	5587	0.11	0.41	YES
17	MTMR2	MTMR2	MTMR2	6040	0.093	0.4	YES
18	PI4K2B	PI4K2B	PI4K2B	6108	0.091	0.42	YES
19	PI4K2A	PI4K2A	PI4K2A	6137	0.09	0.43	YES
20	PITPNB	PITPNB	PITPNB	6587	0.078	0.42	NO
21	PIK3CB	PIK3CB	PIK3CB	7508	0.054	0.38	NO
22	PTEN	PTEN	PTEN	7787	0.047	0.37	NO
23	PIP5K1C	PIP5K1C	PIP5K1C	7928	0.043	0.37	NO
24	VAC14	VAC14	VAC14	8039	0.041	0.38	NO
25	MTMR3	MTMR3	MTMR3	8115	0.039	0.38	NO
26	INPPL1	INPPL1	INPPL1	8273	0.035	0.38	NO
27	SYNJ2	SYNJ2	SYNJ2	8422	0.032	0.37	NO
28	PIKFYVE	PIKFYVE	PIKFYVE	8822	0.023	0.36	NO
29	PIK3C2B	PIK3C2B	PIK3C2B	9468	0.01	0.32	NO
30	OCRL	OCRL	OCRL	9589	0.0073	0.32	NO
31	INPP5E	INPP5E	INPP5E	9683	0.0052	0.31	NO
32	PI4KA	PI4KA	PI4KA	9786	0.0027	0.31	NO
33	PIP4K2B	PIP4K2B	PIP4K2B	9959	-0.0007	0.3	NO
34	MTMR4	MTMR4	MTMR4	10183	-0.006	0.29	NO
35	INPP5K	INPP5K	INPP5K	10573	-0.014	0.27	NO
36	ARF1	ARF1	ARF1	10874	-0.021	0.26	NO
37	PIK3R1	PIK3R1	PIK3R1	11051	-0.024	0.25	NO
38	PIK3C3	PIK3C3	PIK3C3	11229	-0.028	0.25	NO
39	ARF3	ARF3	ARF3	11871	-0.042	0.22	NO
40	MTMR1	MTMR1	MTMR1	12054	-0.046	0.22	NO
41	MTMR14	MTMR14	MTMR14	12148	-0.048	0.22	NO
42	PIK3R2	PIK3R2	PIK3R2	13077	-0.07	0.18	NO
43	SYNJ1	SYNJ1	SYNJ1	13362	-0.078	0.18	NO
44	PI4KB	PI4KB	PI4KB	13690	-0.087	0.18	NO
45	PIK3R6	PIK3R6	PIK3R6	13948	-0.095	0.18	NO
46	MTMR7	MTMR7	MTMR7	14201	-0.1	0.19	NO
47	INPP5J	INPP5J	INPP5J	15427	-0.16	0.15	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: PID A6B1 A6B4 INTEGRIN PATHWAY.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: PID A6B1 A6B4 INTEGRIN 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
KEGG CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.64	1.6	0.067	0.67	0.91	0.59	0.12	0.52	0.38	0.22
KEGG OXIDATIVE PHOSPHORYLATION	111	genes.ES.table	0.51	1.5	0.13	0.94	0.97	0.59	0.2	0.47	0.67	0.35
KEGG AMINOACYL TRNA BIOSYNTHESIS	41	genes.ES.table	0.44	1.8	0.037	0.63	0.6	0.51	0.29	0.36	0.2	0.17
KEGG ALZHEIMERS DISEASE	152	genes.ES.table	0.33	1.4	0.084	1	0.99	0.44	0.19	0.36	0.99	0.5
KEGG PARKINSONS DISEASE	110	genes.ES.table	0.45	1.4	0.18	1	0.99	0.55	0.19	0.45	0.92	0.46
KEGG HUNTINGTONS DISEASE	166	genes.ES.table	0.36	1.6	0.056	0.68	0.94	0.48	0.22	0.38	0.42	0.23
ST GAQ PATHWAY	27	genes.ES.table	0.48	1.7	0.027	0.75	0.75	0.41	0.21	0.32	0.3	0.22
PID MTOR 4PATHWAY	67	genes.ES.table	0.25	1.3	0.16	1	1	0.15	0.13	0.13	1	0.74
REACTOME TRANSLATION	146	genes.ES.table	0.39	1.3	0.28	1	1	0.62	0.37	0.4	1	0.77
REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE	40	genes.ES.table	0.5	1.6	0.057	0.66	0.89	0.45	0.12	0.4	0.35	0.21

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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	SLC25A4	SLC25A4	SLC25A4	655	0.29	0.013	YES
2	ATP5G1	ATP5G1	ATP5G1	752	0.27	0.054	YES
3	FXN	FXN	FXN	760	0.27	0.1	YES
4	TOMM40	TOMM40	TOMM40	868	0.25	0.14	YES
5	CS	CS	CS	996	0.24	0.17	YES
6	ATP5B	ATP5B	ATP5B	1122	0.22	0.2	YES
7	LDHD	LDHD	LDHD	1128	0.22	0.24	YES
8	ACO2	ACO2	ACO2	1149	0.22	0.28	YES
9	DNAJC19	DNAJC19	DNAJC19	1305	0.2	0.3	YES
10	TIMM50	TIMM50	TIMM50	1363	0.2	0.33	YES
11	GRPEL1	GRPEL1	GRPEL1	1464	0.19	0.36	YES
12	CHCHD4	CHCHD4	CHCHD4	1498	0.19	0.39	YES
13	ATP5A1	ATP5A1	ATP5A1	1551	0.18	0.42	YES
14	C18orf55	C18orf55	C18orf55	1884	0.16	0.43	YES
15	TIMM22	TIMM22	TIMM22	1944	0.16	0.45	YES
16	CYC1	CYC1	CYC1	2004	0.16	0.48	YES
17	TIMM17A	TIMM17A	TIMM17A	2032	0.16	0.5	YES
18	TOMM5	TOMM5	TOMM5	2040	0.15	0.53	YES
19	TIMM10	TIMM10	TIMM10	2209	0.14	0.54	YES
20	TIMM44	TIMM44	TIMM44	2354	0.14	0.56	YES
21	MTX1	MTX1	MTX1	2729	0.12	0.56	YES
22	SAMM50	SAMM50	SAMM50	2779	0.12	0.58	YES
23	PMPCA	PMPCA	PMPCA	2834	0.12	0.59	YES
24	MTX2	MTX2	MTX2	3082	0.11	0.6	YES
25	TIMM13	TIMM13	TIMM13	3228	0.1	0.61	YES
26	SLC25A6	SLC25A6	SLC25A6	3483	0.095	0.61	YES
27	TAZ	TAZ	TAZ	3586	0.092	0.62	YES
28	TOMM20	TOMM20	TOMM20	3700	0.089	0.63	YES
29	VDAC1	VDAC1	VDAC1	3725	0.088	0.64	YES
30	TIMM8B	TIMM8B	TIMM8B	3967	0.082	0.64	YES
31	FXC1	FXC1	FXC1	4005	0.08	0.65	YES
32	COQ2	COQ2	COQ2	4012	0.08	0.67	YES
33	HSPA9	HSPA9	HSPA9	4037	0.079	0.68	YES
34	HSPD1	HSPD1	HSPD1	4411	0.07	0.67	NO
35	GFER	GFER	GFER	4625	0.064	0.67	NO
36	IDH3G	IDH3G	IDH3G	5192	0.053	0.65	NO
37	TOMM22	TOMM22	TOMM22	5462	0.047	0.64	NO
38	SLC25A12	SLC25A12	SLC25A12	5751	0.041	0.63	NO
39	TIMM17B	TIMM17B	TIMM17B	5843	0.039	0.63	NO
40	COX17	COX17	COX17	5987	0.037	0.63	NO
41	BCS1L	BCS1L	BCS1L	6350	0.03	0.62	NO
42	PMPCB	PMPCB	PMPCB	6541	0.026	0.61	NO
43	TOMM70A	TOMM70A	TOMM70A	7019	0.016	0.59	NO
44	TOMM7	TOMM7	TOMM7	7394	0.0091	0.57	NO
45	HSCB	HSCB	HSCB	7606	0.0049	0.56	NO
46	GRPEL2	GRPEL2	GRPEL2	9098	-0.024	0.48	NO
47	TIMM9	TIMM9	TIMM9	9696	-0.037	0.45	NO
48	SLC25A13	SLC25A13	SLC25A13	9822	-0.04	0.45	NO
49	TIMM8A	TIMM8A	TIMM8A	9878	-0.041	0.46	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: KEGG CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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	ADHFE1	ADHFE1	ADHFE1	176	0.46	0.016	YES
2	NDUFA8	NDUFA8	NDUFA8	412	0.35	0.022	YES
3	IDH3A	IDH3A	IDH3A	415	0.35	0.041	YES
4	NNT	NNT	NNT	482	0.33	0.056	YES
5	UQCRFS1	UQCRFS1	UQCRFS1	504	0.32	0.073	YES
6	NDUFB5	NDUFB5	NDUFB5	634	0.29	0.082	YES
7	COX5A	COX5A	COX5A	713	0.28	0.093	YES
8	COX7B	COX7B	COX7B	746	0.27	0.11	YES
9	ATP5G1	ATP5G1	ATP5G1	752	0.27	0.12	YES
10	COX6B1	COX6B1	COX6B1	875	0.25	0.13	YES
11	CYCS	CYCS	CYCS	879	0.25	0.14	YES
12	NDUFA12	NDUFA12	NDUFA12	926	0.25	0.15	YES
13	ATP5D	ATP5D	ATP5D	972	0.24	0.16	YES
14	SDHA	SDHA	SDHA	992	0.24	0.18	YES
15	CS	CS	CS	996	0.24	0.19	YES
16	PDHA1	PDHA1	PDHA1	1024	0.24	0.2	YES
17	SUCLG1	SUCLG1	SUCLG1	1033	0.23	0.21	YES
18	NDUFS4	NDUFS4	NDUFS4	1091	0.23	0.22	YES
19	NDUFS3	NDUFS3	NDUFS3	1092	0.23	0.24	YES
20	ATP5B	ATP5B	ATP5B	1122	0.22	0.25	YES
21	ACO2	ACO2	ACO2	1149	0.22	0.26	YES
22	COX5B	COX5B	COX5B	1157	0.22	0.27	YES
23	SUCLA2	SUCLA2	SUCLA2	1183	0.22	0.28	YES
24	NDUFB6	NDUFB6	NDUFB6	1217	0.22	0.29	YES
25	ATP5O	ATP5O	ATP5O	1233	0.21	0.3	YES
26	SDHD	SDHD	SDHD	1319	0.2	0.31	YES
27	NDUFV3	NDUFV3	NDUFV3	1337	0.2	0.32	YES
28	OGDH	OGDH	OGDH	1359	0.2	0.33	YES
29	ATP5J	ATP5J	ATP5J	1393	0.2	0.34	YES
30	ATP5C1	ATP5C1	ATP5C1	1394	0.2	0.35	YES
31	UQCRB	UQCRB	UQCRB	1438	0.19	0.36	YES
32	COX8A	COX8A	COX8A	1447	0.19	0.37	YES
33	NDUFA6	NDUFA6	NDUFA6	1523	0.19	0.37	YES
34	ATP5A1	ATP5A1	ATP5A1	1551	0.18	0.38	YES
35	UQCR11	UQCR11	UQCR11	1570	0.18	0.39	YES
36	DLAT	DLAT	DLAT	1579	0.18	0.4	YES
37	IDH2	IDH2	IDH2	1631	0.18	0.41	YES
38	ATP5L	ATP5L	ATP5L	1751	0.17	0.41	YES
39	COX7C	COX7C	COX7C	1780	0.17	0.42	YES
40	FH	FH	FH	1795	0.17	0.43	YES
41	UQCRC2	UQCRC2	UQCRC2	1798	0.17	0.44	YES
42	LDHA	LDHA	LDHA	1839	0.17	0.44	YES
43	COX4I1	COX4I1	COX4I1	1865	0.16	0.45	YES
44	COX6A1	COX6A1	COX6A1	1921	0.16	0.46	YES
45	DLD	DLD	DLD	1922	0.16	0.47	YES
46	NDUFA1	NDUFA1	NDUFA1	1988	0.16	0.47	YES
47	NDUFA4	NDUFA4	NDUFA4	1991	0.16	0.48	YES
48	CYC1	CYC1	CYC1	2004	0.16	0.49	YES
49	NDUFA3	NDUFA3	NDUFA3	2052	0.15	0.49	YES
50	ATP5J2	ATP5J2	ATP5J2	2083	0.15	0.5	YES
51	NDUFS7	NDUFS7	NDUFS7	2100	0.15	0.51	YES
52	NDUFB2	NDUFB2	NDUFB2	2130	0.15	0.51	YES
53	UQCRC1	UQCRC1	UQCRC1	2162	0.15	0.52	YES
54	ATP5H	ATP5H	ATP5H	2171	0.15	0.53	YES
55	MDH2	MDH2	MDH2	2178	0.15	0.54	YES
56	NDUFA10	NDUFA10	NDUFA10	2182	0.15	0.54	YES
57	NDUFB3	NDUFB3	NDUFB3	2202	0.15	0.55	YES
58	ATP5I	ATP5I	ATP5I	2217	0.14	0.56	YES
59	NDUFB9	NDUFB9	NDUFB9	2222	0.14	0.57	YES
60	PDHX	PDHX	PDHX	2247	0.14	0.57	YES
61	NDUFA13	NDUFA13	NDUFA13	2362	0.14	0.57	YES
62	UQCRQ	UQCRQ	UQCRQ	2398	0.14	0.58	YES
63	NDUFB7	NDUFB7	NDUFB7	2479	0.13	0.58	YES
64	SDHC	SDHC	SDHC	2757	0.12	0.57	YES
65	NDUFB10	NDUFB10	NDUFB10	2825	0.12	0.58	YES
66	NDUFS8	NDUFS8	NDUFS8	2826	0.12	0.58	YES
67	NDUFS2	NDUFS2	NDUFS2	2829	0.12	0.59	YES
68	NDUFS1	NDUFS1	NDUFS1	2863	0.12	0.59	YES
69	NDUFV2	NDUFV2	NDUFV2	2974	0.11	0.59	YES
70	COX6C	COX6C	COX6C	3073	0.11	0.6	YES
71	NDUFAB1	NDUFAB1	NDUFAB1	3132	0.11	0.6	YES
72	PDPR	PDPR	PDPR	3273	0.1	0.6	YES
73	SDHB	SDHB	SDHB	3291	0.1	0.6	YES
74	NDUFA7	NDUFA7	NDUFA7	3304	0.1	0.6	YES
75	NDUFA9	NDUFA9	NDUFA9	3360	0.1	0.61	YES
76	DLST	DLST	DLST	3612	0.092	0.6	NO
77	NDUFV1	NDUFV1	NDUFV1	3632	0.091	0.6	NO
78	D2HGDH	D2HGDH	D2HGDH	3688	0.089	0.6	NO
79	ATP5E	ATP5E	ATP5E	3790	0.086	0.6	NO
80	NDUFC1	NDUFC1	NDUFC1	3839	0.085	0.61	NO
81	NDUFS6	NDUFS6	NDUFS6	4088	0.078	0.6	NO
82	ATP5F1	ATP5F1	ATP5F1	4255	0.074	0.59	NO
83	NDUFA2	NDUFA2	NDUFA2	4258	0.074	0.6	NO
84	NDUFA11	NDUFA11	NDUFA11	4271	0.074	0.6	NO
85	NDUFB4	NDUFB4	NDUFB4	4371	0.071	0.6	NO
86	ETFA	ETFA	ETFA	4372	0.071	0.6	NO
87	NDUFB1	NDUFB1	NDUFB1	4788	0.061	0.58	NO
88	IDH3G	IDH3G	IDH3G	5192	0.053	0.56	NO
89	ETFB	ETFB	ETFB	5219	0.052	0.56	NO
90	NDUFB8	NDUFB8	NDUFB8	5220	0.052	0.57	NO
91	BSG	BSG	BSG	5277	0.051	0.57	NO
92	IDH3B	IDH3B	IDH3B	5416	0.048	0.56	NO
93	NDUFA5	NDUFA5	NDUFA5	5714	0.042	0.55	NO
94	COX7A2L	COX7A2L	COX7A2L	5827	0.04	0.54	NO
95	NDUFS5	NDUFS5	NDUFS5	6167	0.033	0.53	NO
96	NDUFC2	NDUFC2	NDUFC2	6181	0.033	0.53	NO
97	PDK2	PDK2	PDK2	6286	0.03	0.52	NO
98	PDK1	PDK1	PDK1	6660	0.023	0.5	NO
99	PDHB	PDHB	PDHB	6768	0.021	0.5	NO
100	UQCRHL	UQCRHL	UQCRHL	7431	0.0084	0.46	NO
101	SLC16A3	SLC16A3	SLC16A3	7910	-0.00084	0.44	NO
102	SUCLG2	SUCLG2	SUCLG2	8054	-0.0034	0.43	NO
103	PDP2	PDP2	PDP2	8117	-0.0046	0.42	NO
104	UQCRH	UQCRH	UQCRH	8307	-0.0079	0.42	NO
105	LDHB	LDHB	LDHB	9208	-0.026	0.37	NO
106	IDH1	IDH1	IDH1	11738	-0.086	0.23	NO
107	ETFDH	ETFDH	ETFDH	12287	-0.1	0.21	NO
108	UCP2	UCP2	UCP2	12461	-0.11	0.2	NO
109	SLC16A8	SLC16A8	SLC16A8	13050	-0.13	0.18	NO
110	L2HGDH	L2HGDH	L2HGDH	14268	-0.19	0.12	NO
111	PDP1	PDP1	PDP1	15683	-0.29	0.057	NO
112	SLC16A1	SLC16A1	SLC16A1	15872	-0.31	0.064	NO
113	PDK4	PDK4	PDK4	16057	-0.33	0.072	NO
114	UCP3	UCP3	UCP3	16269	-0.35	0.08	NO
115	PDK3	PDK3	PDK3	16712	-0.41	0.078	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: KEGG OXIDATIVE PHOSPHORYLATION.

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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	MTFMT	MTFMT	MTFMT	784	0.27	0.035	YES
2	TARSL2	TARSL2	TARSL2	1034	0.23	0.09	YES
3	IARS	IARS	IARS	1345	0.2	0.13	YES
4	CARS2	CARS2	CARS2	1516	0.19	0.18	YES
5	WARS2	WARS2	WARS2	1641	0.18	0.22	YES
6	SARS2	SARS2	SARS2	2018	0.16	0.25	YES
7	AARS	AARS	AARS	2524	0.13	0.26	YES
8	MARS2	MARS2	MARS2	2878	0.12	0.27	YES
9	LARS	LARS	LARS	2902	0.12	0.31	YES
10	DARS2	DARS2	DARS2	2908	0.11	0.34	YES
11	KARS	KARS	KARS	3196	0.1	0.36	YES
12	FARS2	FARS2	FARS2	3263	0.1	0.38	YES
13	EARS2	EARS2	EARS2	3503	0.095	0.4	YES
14	IARS2	IARS2	IARS2	4148	0.077	0.38	YES
15	GARS	GARS	GARS	4460	0.069	0.39	YES
16	CARS	CARS	CARS	4521	0.067	0.4	YES
17	EPRS	EPRS	EPRS	4781	0.062	0.41	YES
18	NARS	NARS	NARS	4961	0.058	0.41	YES
19	RARS	RARS	RARS	5188	0.053	0.42	YES
20	QARS	QARS	QARS	5300	0.05	0.43	YES
21	FARSA	FARSA	FARSA	5327	0.05	0.44	YES
22	TARS	TARS	TARS	5659	0.043	0.43	NO
23	DARS	DARS	DARS	5901	0.038	0.43	NO
24	VARS2	VARS2	VARS2	6335	0.03	0.42	NO
25	AARS2	AARS2	AARS2	6344	0.03	0.42	NO
26	VARS	VARS	VARS	7256	0.012	0.38	NO
27	HARS2	HARS2	HARS2	7301	0.011	0.38	NO
28	TARS2	TARS2	TARS2	7803	0.0011	0.35	NO
29	YARS2	YARS2	YARS2	7960	-0.0017	0.34	NO
30	MARS	MARS	MARS	8140	-0.0051	0.33	NO
31	SARS	SARS	SARS	8586	-0.013	0.31	NO
32	YARS	YARS	YARS	8623	-0.014	0.32	NO
33	FARSB	FARSB	FARSB	8683	-0.015	0.32	NO
34	LARS2	LARS2	LARS2	8917	-0.02	0.31	NO
35	SEPSECS	SEPSECS	SEPSECS	9605	-0.035	0.28	NO
36	PSTK	PSTK	PSTK	9764	-0.038	0.28	NO
37	RARS2	RARS2	RARS2	10182	-0.048	0.28	NO
38	HARS	HARS	HARS	10212	-0.048	0.29	NO
39	WARS	WARS	WARS	12356	-0.11	0.2	NO
40	NARS2	NARS2	NARS2	13364	-0.14	0.19	NO
41	PARS2	PARS2	PARS2	15242	-0.26	0.16	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: KEGG AMINOACYL TRNA BIOSYNTHESIS.

Figure S26. 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 ALZHEIMERS DISEASE

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	ITPKA	ITPKA	ITPKA	46	0.64	0.19	YES
2	VN1R1	VN1R1	VN1R1	398	0.35	0.28	YES
3	AKT3	AKT3	AKT3	579	0.31	0.36	YES
4	CFB	CFB	CFB	1427	0.2	0.38	YES
5	PLD1	PLD1	PLD1	2339	0.14	0.37	YES
6	NFKBIL1	NFKBIL1	NFKBIL1	2485	0.13	0.4	YES
7	PITX2	PITX2	PITX2	2513	0.13	0.44	YES
8	NFKBIB	NFKBIB	NFKBIB	2808	0.12	0.46	YES
9	AKT2	AKT2	AKT2	3542	0.094	0.44	YES
10	ITPKB	ITPKB	ITPKB	3660	0.09	0.47	YES
11	NFKB1	NFKB1	NFKB1	3846	0.085	0.48	YES
12	NFKBIE	NFKBIE	NFKBIE	4256	0.074	0.48	NO
13	GNAQ	GNAQ	GNAQ	4779	0.062	0.47	NO
14	PIK3CB	PIK3CB	PIK3CB	6304	0.03	0.4	NO
15	PHKA2	PHKA2	PHKA2	6555	0.026	0.39	NO
16	PDK1	PDK1	PDK1	6660	0.023	0.39	NO
17	ITPR2	ITPR2	ITPR2	6882	0.019	0.38	NO
18	PLD3	PLD3	PLD3	6941	0.018	0.39	NO
19	AKT1	AKT1	AKT1	8860	-0.019	0.29	NO
20	ITPR3	ITPR3	ITPR3	9732	-0.038	0.25	NO
21	PLD2	PLD2	PLD2	9926	-0.042	0.25	NO
22	NFKB2	NFKB2	NFKB2	10580	-0.057	0.23	NO
23	IKBKG	IKBKG	IKBKG	10600	-0.057	0.25	NO
24	DAG1	DAG1	DAG1	10945	-0.065	0.25	NO
25	ADRBK1	ADRBK1	ADRBK1	11855	-0.089	0.23	NO
26	NFKBIA	NFKBIA	NFKBIA	13094	-0.13	0.2	NO
27	ITPR1	ITPR1	ITPR1	15272	-0.26	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: KEGG ALZHEIMERS DISEASE.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ALZHEIMERS DISEASE, 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 PARKINSONS DISEASE

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	IGFBP1	IGFBP1	IGFBP1	185	0.46	0.16	YES
2	EXOSC5	EXOSC5	EXOSC5	924	0.25	0.22	YES
3	DDIT3	DDIT3	DDIT3	1327	0.2	0.27	YES
4	ATF3	ATF3	ATF3	1500	0.19	0.33	YES
5	EXOSC8	EXOSC8	EXOSC8	1651	0.18	0.39	YES
6	CCL2	CCL2	CCL2	2600	0.13	0.39	YES
7	HSPA5	HSPA5	HSPA5	2844	0.12	0.42	YES
8	DIS3	DIS3	DIS3	3103	0.11	0.44	YES
9	HERPUD1	HERPUD1	HERPUD1	3710	0.088	0.44	YES
10	EXOSC2	EXOSC2	EXOSC2	3794	0.086	0.47	YES
11	EXOSC3	EXOSC3	EXOSC3	4579	0.066	0.45	YES
12	ASNS	ASNS	ASNS	4647	0.064	0.47	YES
13	EXOSC6	EXOSC6	EXOSC6	4793	0.061	0.49	YES
14	PARN	PARN	PARN	5607	0.044	0.46	NO
15	ATF6	ATF6	ATF6	6241	0.031	0.44	NO
16	EIF2S1	EIF2S1	EIF2S1	6604	0.024	0.43	NO
17	IL8	IL8	IL8	7769	0.0017	0.36	NO
18	NFYA	NFYA	NFYA	7853	0.00012	0.36	NO
19	EXOSC9	EXOSC9	EXOSC9	8162	-0.0054	0.34	NO
20	KHSRP	KHSRP	KHSRP	8790	-0.017	0.32	NO
21	NFYB	NFYB	NFYB	8802	-0.017	0.32	NO
22	ATF4	ATF4	ATF4	10617	-0.058	0.24	NO
23	DCP2	DCP2	DCP2	11000	-0.066	0.25	NO
24	EXOSC1	EXOSC1	EXOSC1	11255	-0.072	0.26	NO
25	EIF2AK3	EIF2AK3	EIF2AK3	11525	-0.08	0.28	NO
26	EXOSC7	EXOSC7	EXOSC7	11853	-0.089	0.29	NO
27	EXOSC4	EXOSC4	EXOSC4	13294	-0.14	0.27	NO

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

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PARKINSONS DISEASE, 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 HUNTINGTONS DISEASE

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	NDUFA8	NDUFA8	NDUFA8	412	0.35	0.006	YES
2	UQCRFS1	UQCRFS1	UQCRFS1	504	0.32	0.028	YES
3	NDUFB5	NDUFB5	NDUFB5	634	0.29	0.045	YES
4	COX5A	COX5A	COX5A	713	0.28	0.064	YES
5	COX7B	COX7B	COX7B	746	0.27	0.084	YES
6	ATP5G1	ATP5G1	ATP5G1	752	0.27	0.11	YES
7	COX6B1	COX6B1	COX6B1	875	0.25	0.12	YES
8	CYCS	CYCS	CYCS	879	0.25	0.14	YES
9	NDUFA12	NDUFA12	NDUFA12	926	0.25	0.16	YES
10	ATP5D	ATP5D	ATP5D	972	0.24	0.18	YES
11	SDHA	SDHA	SDHA	992	0.24	0.2	YES
12	NDUFS4	NDUFS4	NDUFS4	1091	0.23	0.21	YES
13	NDUFS3	NDUFS3	NDUFS3	1092	0.23	0.23	YES
14	ATP5B	ATP5B	ATP5B	1122	0.22	0.24	YES
15	COX5B	COX5B	COX5B	1157	0.22	0.26	YES
16	NDUFB6	NDUFB6	NDUFB6	1217	0.22	0.28	YES
17	ATP5O	ATP5O	ATP5O	1233	0.21	0.29	YES
18	SDHD	SDHD	SDHD	1319	0.2	0.3	YES
19	NDUFV3	NDUFV3	NDUFV3	1337	0.2	0.32	YES
20	ATP5J	ATP5J	ATP5J	1393	0.2	0.33	YES
21	ATP5C1	ATP5C1	ATP5C1	1394	0.2	0.35	YES
22	UQCRB	UQCRB	UQCRB	1438	0.19	0.36	YES
23	COX8A	COX8A	COX8A	1447	0.19	0.38	YES
24	NDUFA6	NDUFA6	NDUFA6	1523	0.19	0.39	YES
25	ATP5A1	ATP5A1	ATP5A1	1551	0.18	0.4	YES
26	UQCR11	UQCR11	UQCR11	1570	0.18	0.42	YES
27	ATP5L	ATP5L	ATP5L	1751	0.17	0.42	YES
28	COX7C	COX7C	COX7C	1780	0.17	0.44	YES
29	UQCRC2	UQCRC2	UQCRC2	1798	0.17	0.45	YES
30	COX4I1	COX4I1	COX4I1	1865	0.16	0.46	YES
31	COX6A1	COX6A1	COX6A1	1921	0.16	0.47	YES
32	NDUFA1	NDUFA1	NDUFA1	1988	0.16	0.48	YES
33	NDUFA4	NDUFA4	NDUFA4	1991	0.16	0.49	YES
34	CYC1	CYC1	CYC1	2004	0.16	0.5	YES
35	NDUFA3	NDUFA3	NDUFA3	2052	0.15	0.51	YES
36	ATP5J2	ATP5J2	ATP5J2	2083	0.15	0.52	YES
37	NDUFS7	NDUFS7	NDUFS7	2100	0.15	0.54	YES
38	NDUFB2	NDUFB2	NDUFB2	2130	0.15	0.55	YES
39	UQCRC1	UQCRC1	UQCRC1	2162	0.15	0.56	YES
40	ATP5H	ATP5H	ATP5H	2171	0.15	0.57	YES
41	NDUFA10	NDUFA10	NDUFA10	2182	0.15	0.58	YES
42	NDUFB3	NDUFB3	NDUFB3	2202	0.15	0.59	YES
43	ATP5I	ATP5I	ATP5I	2217	0.14	0.6	YES
44	NDUFB9	NDUFB9	NDUFB9	2222	0.14	0.61	YES
45	NDUFA13	NDUFA13	NDUFA13	2362	0.14	0.62	YES
46	UQCRQ	UQCRQ	UQCRQ	2398	0.14	0.63	YES
47	NDUFB7	NDUFB7	NDUFB7	2479	0.13	0.63	YES
48	SDHC	SDHC	SDHC	2757	0.12	0.63	YES
49	NDUFB10	NDUFB10	NDUFB10	2825	0.12	0.63	YES
50	NDUFS8	NDUFS8	NDUFS8	2826	0.12	0.64	YES
51	NDUFS2	NDUFS2	NDUFS2	2829	0.12	0.65	YES
52	NDUFS1	NDUFS1	NDUFS1	2863	0.12	0.66	YES
53	NDUFV2	NDUFV2	NDUFV2	2974	0.11	0.66	YES
54	COX6C	COX6C	COX6C	3073	0.11	0.67	YES
55	NDUFAB1	NDUFAB1	NDUFAB1	3132	0.11	0.67	YES
56	SDHB	SDHB	SDHB	3291	0.1	0.67	YES
57	NDUFA7	NDUFA7	NDUFA7	3304	0.1	0.68	YES
58	NDUFA9	NDUFA9	NDUFA9	3360	0.1	0.68	YES
59	NDUFV1	NDUFV1	NDUFV1	3632	0.091	0.68	YES
60	ATP5E	ATP5E	ATP5E	3790	0.086	0.68	YES
61	NDUFC1	NDUFC1	NDUFC1	3839	0.085	0.68	YES
62	NDUFS6	NDUFS6	NDUFS6	4088	0.078	0.67	YES
63	ATP5F1	ATP5F1	ATP5F1	4255	0.074	0.67	YES
64	NDUFA2	NDUFA2	NDUFA2	4258	0.074	0.68	YES
65	NDUFA11	NDUFA11	NDUFA11	4271	0.074	0.68	YES
66	NDUFB4	NDUFB4	NDUFB4	4371	0.071	0.68	YES
67	ETFA	ETFA	ETFA	4372	0.071	0.69	YES
68	NDUFB1	NDUFB1	NDUFB1	4788	0.061	0.67	NO
69	ETFB	ETFB	ETFB	5219	0.052	0.65	NO
70	NDUFB8	NDUFB8	NDUFB8	5220	0.052	0.65	NO
71	NDUFA5	NDUFA5	NDUFA5	5714	0.042	0.63	NO
72	COX7A2L	COX7A2L	COX7A2L	5827	0.04	0.63	NO
73	NDUFS5	NDUFS5	NDUFS5	6167	0.033	0.61	NO
74	NDUFC2	NDUFC2	NDUFC2	6181	0.033	0.61	NO
75	UQCRHL	UQCRHL	UQCRHL	7431	0.0084	0.55	NO
76	UQCRH	UQCRH	UQCRH	8307	-0.0079	0.5	NO
77	ETFDH	ETFDH	ETFDH	12287	-0.1	0.28	NO
78	UCP2	UCP2	UCP2	12461	-0.11	0.28	NO
79	UCP3	UCP3	UCP3	16269	-0.35	0.1	NO

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

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HUNTINGTONS DISEASE, 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: ST GAQ 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	IARS	IARS	IARS	1345	0.2	-0.012	YES
2	CARS2	CARS2	CARS2	1516	0.19	0.037	YES
3	WARS2	WARS2	WARS2	1641	0.18	0.085	YES
4	PPA2	PPA2	PPA2	1747	0.17	0.13	YES
5	AIMP2	AIMP2	AIMP2	1857	0.16	0.18	YES
6	SARS2	SARS2	SARS2	2018	0.16	0.22	YES
7	AARS	AARS	AARS	2524	0.13	0.23	YES
8	MARS2	MARS2	MARS2	2878	0.12	0.25	YES
9	LARS	LARS	LARS	2902	0.12	0.28	YES
10	DARS2	DARS2	DARS2	2908	0.11	0.32	YES
11	KARS	KARS	KARS	3196	0.1	0.33	YES
12	FARS2	FARS2	FARS2	3263	0.1	0.36	YES
13	EARS2	EARS2	EARS2	3503	0.095	0.38	YES
14	IARS2	IARS2	IARS2	4148	0.077	0.36	YES
15	GARS	GARS	GARS	4460	0.069	0.37	YES
16	CARS	CARS	CARS	4521	0.067	0.39	YES
17	EPRS	EPRS	EPRS	4781	0.062	0.39	YES
18	NARS	NARS	NARS	4961	0.058	0.4	YES
19	RARS	RARS	RARS	5188	0.053	0.4	YES
20	QARS	QARS	QARS	5300	0.05	0.41	YES
21	FARSA	FARSA	FARSA	5327	0.05	0.43	YES
22	TARS	TARS	TARS	5659	0.043	0.42	NO
23	DARS	DARS	DARS	5901	0.038	0.42	NO
24	VARS2	VARS2	VARS2	6335	0.03	0.4	NO
25	AARS2	AARS2	AARS2	6344	0.03	0.41	NO
26	AIMP1	AIMP1	AIMP1	6955	0.018	0.39	NO
27	VARS	VARS	VARS	7256	0.012	0.37	NO
28	HARS2	HARS2	HARS2	7301	0.011	0.37	NO
29	TARS2	TARS2	TARS2	7803	0.0011	0.35	NO
30	EEF1E1	EEF1E1	EEF1E1	7877	-0.00032	0.34	NO
31	YARS2	YARS2	YARS2	7960	-0.0017	0.34	NO
32	MARS	MARS	MARS	8140	-0.0051	0.33	NO
33	SARS	SARS	SARS	8586	-0.013	0.31	NO
34	YARS	YARS	YARS	8623	-0.014	0.31	NO
35	FARSB	FARSB	FARSB	8683	-0.015	0.31	NO
36	LARS2	LARS2	LARS2	8917	-0.02	0.31	NO
37	RARS2	RARS2	RARS2	10182	-0.048	0.25	NO
38	HARS	HARS	HARS	10212	-0.048	0.26	NO
39	PPA1	PPA1	PPA1	10307	-0.05	0.28	NO
40	WARS	WARS	WARS	12356	-0.11	0.19	NO
41	NARS2	NARS2	NARS2	13364	-0.14	0.18	NO
42	PARS2	PARS2	PARS2	15242	-0.26	0.16	NO

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

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: ST GAQ 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: PID MTOR 4PATHWAY

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	ADHFE1	ADHFE1	ADHFE1	176	0.46	0.06	YES
2	IDH3A	IDH3A	IDH3A	415	0.35	0.1	YES
3	NNT	NNT	NNT	482	0.33	0.15	YES
4	SDHA	SDHA	SDHA	992	0.24	0.16	YES
5	CS	CS	CS	996	0.24	0.19	YES
6	PDHA1	PDHA1	PDHA1	1024	0.24	0.22	YES
7	SUCLG1	SUCLG1	SUCLG1	1033	0.23	0.26	YES
8	ACO2	ACO2	ACO2	1149	0.22	0.29	YES
9	SUCLA2	SUCLA2	SUCLA2	1183	0.22	0.32	YES
10	SDHD	SDHD	SDHD	1319	0.2	0.34	YES
11	OGDH	OGDH	OGDH	1359	0.2	0.37	YES
12	DLAT	DLAT	DLAT	1579	0.18	0.39	YES
13	IDH2	IDH2	IDH2	1631	0.18	0.41	YES
14	FH	FH	FH	1795	0.17	0.43	YES
15	LDHA	LDHA	LDHA	1839	0.17	0.45	YES
16	DLD	DLD	DLD	1922	0.16	0.47	YES
17	MDH2	MDH2	MDH2	2178	0.15	0.48	YES
18	PDHX	PDHX	PDHX	2247	0.14	0.5	YES
19	SDHC	SDHC	SDHC	2757	0.12	0.49	NO
20	PDPR	PDPR	PDPR	3273	0.1	0.47	NO
21	SDHB	SDHB	SDHB	3291	0.1	0.49	NO
22	DLST	DLST	DLST	3612	0.092	0.48	NO
23	D2HGDH	D2HGDH	D2HGDH	3688	0.089	0.49	NO
24	IDH3G	IDH3G	IDH3G	5192	0.053	0.42	NO
25	BSG	BSG	BSG	5277	0.051	0.42	NO
26	IDH3B	IDH3B	IDH3B	5416	0.048	0.42	NO
27	PDK2	PDK2	PDK2	6286	0.03	0.38	NO
28	PDK1	PDK1	PDK1	6660	0.023	0.36	NO
29	PDHB	PDHB	PDHB	6768	0.021	0.36	NO
30	SLC16A3	SLC16A3	SLC16A3	7910	-0.00084	0.29	NO
31	SUCLG2	SUCLG2	SUCLG2	8054	-0.0034	0.29	NO
32	PDP2	PDP2	PDP2	8117	-0.0046	0.28	NO
33	LDHB	LDHB	LDHB	9208	-0.026	0.23	NO
34	IDH1	IDH1	IDH1	11738	-0.086	0.1	NO
35	SLC16A8	SLC16A8	SLC16A8	13050	-0.13	0.048	NO
36	L2HGDH	L2HGDH	L2HGDH	14268	-0.19	0.0094	NO
37	PDP1	PDP1	PDP1	15683	-0.29	-0.025	NO
38	SLC16A1	SLC16A1	SLC16A1	15872	-0.31	0.012	NO
39	PDK4	PDK4	PDK4	16057	-0.33	0.051	NO
40	PDK3	PDK3	PDK3	16712	-0.41	0.078	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: PID MTOR 4PATHWAY.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: PID MTOR 4PATHWAY, 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: REACTOME TRANSLATION

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	OGDHL	OGDHL	OGDHL	110	0.53	0.094	YES
2	IDH3A	IDH3A	IDH3A	415	0.35	0.14	YES
3	ACO1	ACO1	ACO1	418	0.35	0.21	YES
4	SDHA	SDHA	SDHA	992	0.24	0.22	YES
5	CS	CS	CS	996	0.24	0.27	YES
6	PDHA1	PDHA1	PDHA1	1024	0.24	0.31	YES
7	SUCLG1	SUCLG1	SUCLG1	1033	0.23	0.35	YES
8	ACO2	ACO2	ACO2	1149	0.22	0.39	YES
9	SUCLA2	SUCLA2	SUCLA2	1183	0.22	0.43	YES
10	SDHD	SDHD	SDHD	1319	0.2	0.46	YES
11	OGDH	OGDH	OGDH	1359	0.2	0.5	YES
12	DLAT	DLAT	DLAT	1579	0.18	0.52	YES
13	IDH2	IDH2	IDH2	1631	0.18	0.55	YES
14	FH	FH	FH	1795	0.17	0.57	YES
15	DLD	DLD	DLD	1922	0.16	0.6	YES
16	MDH1	MDH1	MDH1	2176	0.15	0.61	YES
17	MDH2	MDH2	MDH2	2178	0.15	0.64	YES
18	SDHC	SDHC	SDHC	2757	0.12	0.63	NO
19	SDHB	SDHB	SDHB	3291	0.1	0.62	NO
20	DLST	DLST	DLST	3612	0.092	0.62	NO
21	ACLY	ACLY	ACLY	4527	0.067	0.58	NO
22	IDH3G	IDH3G	IDH3G	5192	0.053	0.55	NO
23	IDH3B	IDH3B	IDH3B	5416	0.048	0.55	NO
24	PDHB	PDHB	PDHB	6768	0.021	0.48	NO
25	SUCLG2	SUCLG2	SUCLG2	8054	-0.0034	0.41	NO
26	IDH1	IDH1	IDH1	11738	-0.086	0.22	NO
27	PCK2	PCK2	PCK2	13641	-0.16	0.15	NO
28	PCK1	PCK1	PCK1	15217	-0.25	0.11	NO
29	PC	PC	PC	15610	-0.28	0.14	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: REACTOME TRANSLATION.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSLATION, 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: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NDUFA8	NDUFA8	NDUFA8	412	0.35	0.014	YES
2	UQCRFS1	UQCRFS1	UQCRFS1	504	0.32	0.044	YES
3	NDUFB5	NDUFB5	NDUFB5	634	0.29	0.069	YES
4	COX5A	COX5A	COX5A	713	0.28	0.094	YES
5	COX7B	COX7B	COX7B	746	0.27	0.12	YES
6	COX6B1	COX6B1	COX6B1	875	0.25	0.14	YES
7	CYCS	CYCS	CYCS	879	0.25	0.17	YES
8	NDUFA12	NDUFA12	NDUFA12	926	0.25	0.19	YES
9	SDHA	SDHA	SDHA	992	0.24	0.21	YES
10	NDUFS4	NDUFS4	NDUFS4	1091	0.23	0.23	YES
11	NDUFS3	NDUFS3	NDUFS3	1092	0.23	0.26	YES
12	COX5B	COX5B	COX5B	1157	0.22	0.28	YES
13	NDUFB6	NDUFB6	NDUFB6	1217	0.22	0.3	YES
14	SDHD	SDHD	SDHD	1319	0.2	0.31	YES
15	NDUFV3	NDUFV3	NDUFV3	1337	0.2	0.33	YES
16	UQCRB	UQCRB	UQCRB	1438	0.19	0.35	YES
17	COX8A	COX8A	COX8A	1447	0.19	0.37	YES
18	NDUFA6	NDUFA6	NDUFA6	1523	0.19	0.39	YES
19	UQCR11	UQCR11	UQCR11	1570	0.18	0.4	YES
20	COX7C	COX7C	COX7C	1780	0.17	0.41	YES
21	UQCRC2	UQCRC2	UQCRC2	1798	0.17	0.43	YES
22	COX4I1	COX4I1	COX4I1	1865	0.16	0.44	YES
23	COX6A1	COX6A1	COX6A1	1921	0.16	0.46	YES
24	NDUFA1	NDUFA1	NDUFA1	1988	0.16	0.47	YES
25	NDUFA4	NDUFA4	NDUFA4	1991	0.16	0.48	YES
26	CYC1	CYC1	CYC1	2004	0.16	0.5	YES
27	NDUFA3	NDUFA3	NDUFA3	2052	0.15	0.51	YES
28	NDUFS7	NDUFS7	NDUFS7	2100	0.15	0.53	YES
29	NDUFB2	NDUFB2	NDUFB2	2130	0.15	0.54	YES
30	UQCRC1	UQCRC1	UQCRC1	2162	0.15	0.56	YES
31	NDUFA10	NDUFA10	NDUFA10	2182	0.15	0.57	YES
32	NDUFB3	NDUFB3	NDUFB3	2202	0.15	0.59	YES
33	NDUFB9	NDUFB9	NDUFB9	2222	0.14	0.6	YES
34	NDUFA13	NDUFA13	NDUFA13	2362	0.14	0.61	YES
35	UQCRQ	UQCRQ	UQCRQ	2398	0.14	0.62	YES
36	NDUFB7	NDUFB7	NDUFB7	2479	0.13	0.63	YES
37	SDHC	SDHC	SDHC	2757	0.12	0.63	YES
38	NDUFB10	NDUFB10	NDUFB10	2825	0.12	0.64	YES
39	NDUFS8	NDUFS8	NDUFS8	2826	0.12	0.65	YES
40	NDUFS2	NDUFS2	NDUFS2	2829	0.12	0.66	YES
41	NDUFS1	NDUFS1	NDUFS1	2863	0.12	0.67	YES
42	NDUFV2	NDUFV2	NDUFV2	2974	0.11	0.68	YES
43	COX6C	COX6C	COX6C	3073	0.11	0.68	YES
44	NDUFAB1	NDUFAB1	NDUFAB1	3132	0.11	0.69	YES
45	SDHB	SDHB	SDHB	3291	0.1	0.69	YES
46	NDUFA7	NDUFA7	NDUFA7	3304	0.1	0.7	YES
47	NDUFA9	NDUFA9	NDUFA9	3360	0.1	0.71	YES
48	NDUFV1	NDUFV1	NDUFV1	3632	0.091	0.71	YES
49	NDUFC1	NDUFC1	NDUFC1	3839	0.085	0.7	YES
50	NDUFS6	NDUFS6	NDUFS6	4088	0.078	0.7	YES
51	NDUFA2	NDUFA2	NDUFA2	4258	0.074	0.7	YES
52	NDUFA11	NDUFA11	NDUFA11	4271	0.074	0.7	YES
53	NDUFB4	NDUFB4	NDUFB4	4371	0.071	0.71	YES
54	ETFA	ETFA	ETFA	4372	0.071	0.71	YES
55	NDUFB1	NDUFB1	NDUFB1	4788	0.061	0.7	NO
56	ETFB	ETFB	ETFB	5219	0.052	0.68	NO
57	NDUFB8	NDUFB8	NDUFB8	5220	0.052	0.68	NO
58	NDUFA5	NDUFA5	NDUFA5	5714	0.042	0.66	NO
59	COX7A2L	COX7A2L	COX7A2L	5827	0.04	0.66	NO
60	NDUFS5	NDUFS5	NDUFS5	6167	0.033	0.64	NO
61	NDUFC2	NDUFC2	NDUFC2	6181	0.033	0.65	NO
62	UQCRHL	UQCRHL	UQCRHL	7431	0.0084	0.58	NO
63	UQCRH	UQCRH	UQCRH	8307	-0.0079	0.53	NO
64	ETFDH	ETFDH	ETFDH	12287	-0.1	0.32	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: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus3 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION	234	genes.ES.table	0.64	1.6	0.011	0.2	0.92	0.48	0.16	0.41	0.12	0.022
KEGG CHEMOKINE SIGNALING PATHWAY	183	genes.ES.table	0.66	1.8	0.002	0.21	0.56	0.42	0.16	0.35	0.059	0.06
KEGG ENDOCYTOSIS	179	genes.ES.table	0.36	1.6	0.036	0.21	0.95	0.27	0.26	0.2	0.14	0.016
KEGG MTOR SIGNALING PATHWAY	51	genes.ES.table	0.39	1.5	0.043	0.24	0.97	0.14	0.13	0.12	0.17	0.013
KEGG APOPTOSIS	84	genes.ES.table	0.48	1.7	0.022	0.18	0.83	0.31	0.21	0.24	0.087	0.021
KEGG CELL ADHESION MOLECULES CAMS	129	genes.ES.table	0.6	1.6	0.024	0.22	0.96	0.5	0.17	0.42	0.15	0.015
KEGG ANTIGEN PROCESSING AND PRESENTATION	67	genes.ES.table	0.66	1.6	0.03	0.18	0.88	0.46	0.15	0.39	0.1	0.021
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY	89	genes.ES.table	0.67	1.8	0	0.24	0.45	0.34	0.13	0.29	0	0.065
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY	61	genes.ES.table	0.57	1.5	0.065	0.23	0.96	0.46	0.27	0.34	0.16	0.015
KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY	56	genes.ES.table	0.56	2	0	0.33	0.16	0.38	0.25	0.28	0	0.081

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

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	CD79A	CD79A	CD79A	30	0.95	0.06	YES
2	CD79B	CD79B	CD79B	51	0.89	0.12	YES
3	CD19	CD19	CD19	93	0.82	0.17	YES
4	PRKCB	PRKCB	PRKCB	140	0.77	0.22	YES
5	RASGRP1	RASGRP1	RASGRP1	366	0.63	0.24	YES
6	BLK	BLK	BLK	387	0.62	0.28	YES
7	BTK	BTK	BTK	405	0.62	0.32	YES
8	PIK3CD	PIK3CD	PIK3CD	604	0.54	0.35	YES
9	VAV1	VAV1	VAV1	622	0.54	0.38	YES
10	REL	REL	REL	802	0.49	0.4	YES
11	CARD11	CARD11	CARD11	991	0.44	0.42	YES
12	RASGRP3	RASGRP3	RASGRP3	1147	0.42	0.44	YES
13	BLNK	BLNK	BLNK	1587	0.35	0.44	YES
14	PSMB9	PSMB9	PSMB9	1841	0.32	0.45	YES
15	SYK	SYK	SYK	2066	0.29	0.45	YES
16	FYN	FYN	FYN	2329	0.26	0.46	YES
17	THEM4	THEM4	THEM4	2699	0.23	0.45	YES
18	PLCG2	PLCG2	PLCG2	2854	0.22	0.46	YES
19	PSMB10	PSMB10	PSMB10	2983	0.21	0.46	YES
20	LYN	LYN	LYN	3058	0.2	0.47	YES
21	ITPR2	ITPR2	ITPR2	3079	0.2	0.48	YES
22	PSMB8	PSMB8	PSMB8	4018	0.15	0.44	NO
23	IKBKB	IKBKB	IKBKB	4144	0.14	0.44	NO
24	SH3KBP1	SH3KBP1	SH3KBP1	4527	0.13	0.43	NO
25	AKT3	AKT3	AKT3	4602	0.13	0.44	NO
26	SOS1	SOS1	SOS1	4921	0.12	0.43	NO
27	PLCG1	PLCG1	PLCG1	5006	0.11	0.43	NO
28	NCK1	NCK1	NCK1	5080	0.11	0.43	NO
29	BCL10	BCL10	BCL10	5448	0.097	0.42	NO
30	MAP3K7	MAP3K7	MAP3K7	5552	0.094	0.42	NO
31	RPS6KB2	RPS6KB2	RPS6KB2	5699	0.09	0.42	NO
32	ITPR3	ITPR3	ITPR3	5724	0.09	0.42	NO
33	CDKN1B	CDKN1B	CDKN1B	5730	0.09	0.43	NO
34	CBLB	CBLB	CBLB	5911	0.085	0.42	NO
35	NFKBIA	NFKBIA	NFKBIA	6092	0.081	0.42	NO
36	CBL	CBL	CBL	6102	0.081	0.42	NO
37	PSME4	PSME4	PSME4	6211	0.078	0.42	NO
38	MALT1	MALT1	MALT1	6423	0.073	0.41	NO
39	RICTOR	RICTOR	RICTOR	6462	0.072	0.42	NO
40	PSMB2	PSMB2	PSMB2	6564	0.07	0.42	NO
41	NFKBIE	NFKBIE	NFKBIE	6622	0.068	0.42	NO
42	RPS27A	RPS27A	RPS27A	6857	0.063	0.41	NO
43	PDPK1	PDPK1	PDPK1	7024	0.06	0.4	NO
44	PSME2	PSME2	PSME2	7053	0.06	0.4	NO
45	AKT2	AKT2	AKT2	7055	0.06	0.41	NO
46	FOXO4	FOXO4	FOXO4	7208	0.056	0.4	NO
47	IKBKG	IKBKG	IKBKG	7261	0.055	0.4	NO
48	FBXW11	FBXW11	FBXW11	7384	0.052	0.4	NO
49	STIM1	STIM1	STIM1	7413	0.052	0.4	NO
50	PSME1	PSME1	PSME1	7515	0.05	0.4	NO
51	UBA52	UBA52	UBA52	7532	0.05	0.4	NO
52	MTOR	MTOR	MTOR	7612	0.048	0.4	NO
53	FOXO1	FOXO1	FOXO1	7694	0.047	0.4	NO
54	GRB2	GRB2	GRB2	7701	0.046	0.4	NO
55	ORAI1	ORAI1	ORAI1	7802	0.044	0.4	NO
56	TSC2	TSC2	TSC2	7902	0.042	0.4	NO
57	CUL1	CUL1	CUL1	7996	0.04	0.4	NO
58	PSMA4	PSMA4	PSMA4	8048	0.04	0.4	NO
59	FOXO3	FOXO3	FOXO3	8232	0.037	0.39	NO
60	PTEN	PTEN	PTEN	8353	0.034	0.38	NO
61	CHUK	CHUK	CHUK	8406	0.033	0.38	NO
62	CREB1	CREB1	CREB1	8753	0.028	0.36	NO
63	PSMD13	PSMD13	PSMD13	8761	0.028	0.37	NO
64	PSMD5	PSMD5	PSMD5	9301	0.019	0.34	NO
65	NFKBIB	NFKBIB	NFKBIB	9396	0.017	0.33	NO
66	PSMA5	PSMA5	PSMA5	9401	0.017	0.33	NO
67	MAPKAP1	MAPKAP1	MAPKAP1	9409	0.017	0.34	NO
68	PSMD10	PSMD10	PSMD10	9739	0.011	0.32	NO
69	PSMB1	PSMB1	PSMB1	9886	0.0087	0.31	NO
70	MDM2	MDM2	MDM2	9954	0.0077	0.31	NO
71	PSMC2	PSMC2	PSMC2	10114	0.0049	0.3	NO
72	RELA	RELA	RELA	10186	0.0039	0.29	NO
73	NR4A1	NR4A1	NR4A1	10197	0.0036	0.29	NO
74	PSMD11	PSMD11	PSMD11	10232	0.003	0.29	NO
75	PSMB3	PSMB3	PSMB3	10329	0.0011	0.29	NO
76	PSMA2	PSMA2	PSMA2	10460	-0.0012	0.28	NO
77	PSMA7	PSMA7	PSMA7	10541	-0.0025	0.28	NO
78	PSMD12	PSMD12	PSMD12	10663	-0.0049	0.27	NO
79	PSMD3	PSMD3	PSMD3	10703	-0.0055	0.27	NO
80	PSMA1	PSMA1	PSMA1	10839	-0.0078	0.26	NO
81	PSMD4	PSMD4	PSMD4	10862	-0.0082	0.26	NO
82	SKP1	SKP1	SKP1	11050	-0.011	0.25	NO
83	PSMF1	PSMF1	PSMF1	11208	-0.014	0.24	NO
84	BTRC	BTRC	BTRC	11320	-0.016	0.24	NO
85	PSMC5	PSMC5	PSMC5	11348	-0.017	0.24	NO
86	MLST8	MLST8	MLST8	11392	-0.018	0.24	NO
87	PSMD1	PSMD1	PSMD1	11449	-0.019	0.23	NO
88	GSK3A	GSK3A	GSK3A	11493	-0.02	0.23	NO
89	PSMC4	PSMC4	PSMC4	11567	-0.021	0.23	NO
90	KRAS	KRAS	KRAS	11599	-0.021	0.23	NO
91	CASP9	CASP9	CASP9	11704	-0.023	0.22	NO
92	PSMD6	PSMD6	PSMD6	11710	-0.023	0.23	NO
93	PSMB4	PSMB4	PSMB4	11839	-0.026	0.22	NO
94	HRAS	HRAS	HRAS	11910	-0.028	0.22	NO
95	PSMD7	PSMD7	PSMD7	12043	-0.03	0.21	NO
96	PSMD2	PSMD2	PSMD2	12188	-0.033	0.21	NO
97	CALM3	CALM3	CALM3	12242	-0.035	0.21	NO
98	NRAS	NRAS	NRAS	12308	-0.036	0.21	NO
99	PSMC3	PSMC3	PSMC3	12313	-0.036	0.21	NO
100	CALM1	CALM1	CALM1	12485	-0.039	0.2	NO
101	CALM2	CALM2	CALM2	12515	-0.04	0.2	NO
102	PSMA6	PSMA6	PSMA6	12613	-0.042	0.2	NO
103	PSMB6	PSMB6	PSMB6	12816	-0.046	0.19	NO
104	PIK3AP1	PIK3AP1	PIK3AP1	13039	-0.051	0.18	NO
105	PSMD9	PSMD9	PSMD9	13156	-0.053	0.18	NO
106	BAD	BAD	BAD	13477	-0.062	0.16	NO
107	PIK3R1	PIK3R1	PIK3R1	13802	-0.071	0.15	NO
108	PSMA3	PSMA3	PSMA3	13963	-0.075	0.15	NO
109	AKT1S1	AKT1S1	AKT1S1	14047	-0.078	0.15	NO
110	PSMD8	PSMD8	PSMD8	14124	-0.08	0.15	NO
111	PSMC6	PSMC6	PSMC6	14197	-0.082	0.15	NO
112	PSMD14	PSMD14	PSMD14	14305	-0.085	0.15	NO
113	PSMB7	PSMB7	PSMB7	14330	-0.086	0.16	NO
114	PSMC1	PSMC1	PSMC1	14562	-0.093	0.15	NO
115	AKT1	AKT1	AKT1	14849	-0.1	0.14	NO
116	PSMB5	PSMB5	PSMB5	14932	-0.11	0.14	NO
117	SHC1	SHC1	SHC1	15281	-0.12	0.13	NO
118	PHLPP1	PHLPP1	PHLPP1	15374	-0.13	0.13	NO
119	TRIB3	TRIB3	TRIB3	15553	-0.14	0.13	NO
120	CDKN1A	CDKN1A	CDKN1A	15853	-0.16	0.13	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: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table 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	IL12B	IL12B	IL12B	5	1.1	0.12	YES
2	IFNB1	IFNB1	IFNB1	9	1	0.23	YES
3	TNF	TNF	TNF	196	0.72	0.3	YES
4	CXCL10	CXCL10	CXCL10	289	0.67	0.36	YES
5	IL12A	IL12A	IL12A	608	0.54	0.4	YES
6	MAPK10	MAPK10	MAPK10	919	0.46	0.44	YES
7	TMEM173	TMEM173	TMEM173	1927	0.31	0.42	YES
8	RNF125	RNF125	RNF125	1985	0.3	0.44	YES
9	IKBKE	IKBKE	IKBKE	2153	0.28	0.47	YES
10	TBKBP1	TBKBP1	TBKBP1	2338	0.26	0.48	YES
11	CYLD	CYLD	CYLD	2513	0.25	0.5	YES
12	TRAF3	TRAF3	TRAF3	3134	0.2	0.49	YES
13	DHX58	DHX58	DHX58	3403	0.18	0.49	YES
14	CASP8	CASP8	CASP8	3526	0.18	0.51	YES
15	IFNE	IFNE	IFNE	3809	0.16	0.51	YES
16	TRIM25	TRIM25	TRIM25	3886	0.16	0.52	YES
17	IKBKB	IKBKB	IKBKB	4144	0.14	0.52	YES
18	IFIH1	IFIH1	IFIH1	4297	0.14	0.53	YES
19	MAP3K1	MAP3K1	MAP3K1	4349	0.14	0.54	YES
20	TRAF6	TRAF6	TRAF6	4472	0.13	0.55	YES
21	DDX58	DDX58	DDX58	4480	0.13	0.56	YES
22	CASP10	CASP10	CASP10	5038	0.11	0.54	NO
23	TRAF2	TRAF2	TRAF2	5475	0.096	0.53	NO
24	MAP3K7	MAP3K7	MAP3K7	5552	0.094	0.54	NO
25	NFKBIA	NFKBIA	NFKBIA	6092	0.081	0.52	NO
26	ATG12	ATG12	ATG12	6616	0.068	0.49	NO
27	NFKB1	NFKB1	NFKB1	6992	0.061	0.48	NO
28	MAVS	MAVS	MAVS	7031	0.06	0.48	NO
29	MAPK9	MAPK9	MAPK9	7132	0.058	0.48	NO
30	OTUD5	OTUD5	OTUD5	7216	0.056	0.49	NO
31	IKBKG	IKBKG	IKBKG	7261	0.055	0.49	NO
32	ISG15	ISG15	ISG15	7671	0.047	0.47	NO
33	DDX3X	DDX3X	DDX3X	7937	0.042	0.46	NO
34	TRADD	TRADD	TRADD	8046	0.04	0.46	NO
35	TBK1	TBK1	TBK1	8301	0.035	0.45	NO
36	CHUK	CHUK	CHUK	8406	0.033	0.45	NO
37	MAPK11	MAPK11	MAPK11	8426	0.033	0.45	NO
38	MAPK13	MAPK13	MAPK13	9063	0.023	0.42	NO
39	NFKBIB	NFKBIB	NFKBIB	9396	0.017	0.4	NO
40	ATG5	ATG5	ATG5	9593	0.014	0.39	NO
41	IRF3	IRF3	IRF3	9795	0.01	0.38	NO
42	IRF7	IRF7	IRF7	9887	0.0087	0.38	NO
43	RELA	RELA	RELA	10186	0.0039	0.36	NO
44	MAPK14	MAPK14	MAPK14	10199	0.0035	0.36	NO
45	SIKE1	SIKE1	SIKE1	10636	-0.0044	0.34	NO
46	TANK	TANK	TANK	10700	-0.0054	0.33	NO
47	AZI2	AZI2	AZI2	11235	-0.015	0.31	NO
48	PIN1	PIN1	PIN1	11435	-0.019	0.3	NO
49	FADD	FADD	FADD	11691	-0.023	0.29	NO
50	RIPK1	RIPK1	RIPK1	12224	-0.034	0.26	NO
51	DDX3Y	DDX3Y	DDX3Y	12425	-0.038	0.25	NO
52	MAPK8	MAPK8	MAPK8	13671	-0.067	0.19	NO
53	NLRX1	NLRX1	NLRX1	14513	-0.092	0.16	NO
54	DAK	DAK	DAK	14642	-0.096	0.16	NO
55	IL8	IL8	IL8	15598	-0.14	0.12	NO
56	MAPK12	MAPK12	MAPK12	16090	-0.17	0.11	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 CHEMOKINE SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG ENDOCYTOSIS

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	IKZF3	IKZF3	IKZF3	3	1.1	0.093	YES
2	IFNG	IFNG	IFNG	46	0.9	0.17	YES
3	PRKCB	PRKCB	PRKCB	140	0.77	0.23	YES
4	LCK	LCK	LCK	216	0.7	0.28	YES
5	IL2	IL2	IL2	228	0.7	0.34	YES
6	IL2RB	IL2RB	IL2RB	252	0.68	0.4	YES
7	DOK2	DOK2	DOK2	512	0.57	0.44	YES
8	IL2RA	IL2RA	IL2RA	614	0.54	0.48	YES
9	BCL2	BCL2	BCL2	668	0.52	0.52	YES
10	SOCS1	SOCS1	SOCS1	986	0.45	0.54	YES
11	IL2RG	IL2RG	IL2RG	1076	0.43	0.57	YES
12	JAK3	JAK3	JAK3	1122	0.42	0.6	YES
13	STAT5A	STAT5A	STAT5A	1660	0.34	0.6	YES
14	PTK2B	PTK2B	PTK2B	1726	0.33	0.63	YES
15	MYC	MYC	MYC	1917	0.31	0.64	YES
16	SYK	SYK	SYK	2066	0.29	0.66	YES
17	FYN	FYN	FYN	2329	0.26	0.67	YES
18	SOCS2	SOCS2	SOCS2	2981	0.21	0.65	NO
19	GAB2	GAB2	GAB2	3423	0.18	0.64	NO
20	PRKCE	PRKCE	PRKCE	4848	0.12	0.57	NO
21	SOCS3	SOCS3	SOCS3	4920	0.12	0.58	NO
22	SOS1	SOS1	SOS1	4921	0.12	0.59	NO
23	STAT5B	STAT5B	STAT5B	5007	0.11	0.6	NO
24	JAK1	JAK1	JAK1	5307	0.1	0.59	NO
25	STAT1	STAT1	STAT1	6262	0.077	0.54	NO
26	MAP2K1	MAP2K1	MAP2K1	7117	0.058	0.5	NO
27	MAPK9	MAPK9	MAPK9	7132	0.058	0.5	NO
28	GRB2	GRB2	GRB2	7701	0.046	0.48	NO
29	STAT3	STAT3	STAT3	7934	0.042	0.47	NO
30	PIK3CA	PIK3CA	PIK3CA	8332	0.035	0.45	NO
31	MAPK11	MAPK11	MAPK11	8426	0.033	0.44	NO
32	CISH	CISH	CISH	8733	0.028	0.43	NO
33	RAF1	RAF1	RAF1	8847	0.026	0.43	NO
34	MAPK1	MAPK1	MAPK1	9247	0.02	0.41	NO
35	PPP2R5D	PPP2R5D	PPP2R5D	9335	0.018	0.4	NO
36	RHOA	RHOA	RHOA	9637	0.013	0.39	NO
37	MAP2K2	MAP2K2	MAP2K2	9685	0.012	0.39	NO
38	STAM	STAM	STAM	9922	0.0082	0.37	NO
39	MAPK14	MAPK14	MAPK14	10199	0.0035	0.36	NO
40	CDK2	CDK2	CDK2	10470	-0.0013	0.34	NO
41	MAPK3	MAPK3	MAPK3	11313	-0.016	0.3	NO
42	STAM2	STAM2	STAM2	11317	-0.016	0.3	NO
43	KRAS	KRAS	KRAS	11599	-0.021	0.29	NO
44	HRAS	HRAS	HRAS	11910	-0.028	0.27	NO
45	RASA1	RASA1	RASA1	12005	-0.03	0.27	NO
46	MAPKAPK2	MAPKAPK2	MAPKAPK2	12071	-0.031	0.27	NO
47	NRAS	NRAS	NRAS	12308	-0.036	0.26	NO
48	PTPN11	PTPN11	PTPN11	13114	-0.052	0.22	NO
49	JUN	JUN	JUN	13526	-0.063	0.2	NO
50	MAPK8	MAPK8	MAPK8	13671	-0.067	0.2	NO
51	PIK3R1	PIK3R1	PIK3R1	13802	-0.071	0.2	NO
52	FOS	FOS	FOS	15246	-0.12	0.13	NO
53	IRS2	IRS2	IRS2	15254	-0.12	0.14	NO
54	SHC1	SHC1	SHC1	15281	-0.12	0.15	NO
55	IRS1	IRS1	IRS1	15338	-0.12	0.15	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 ENDOCYTOSIS.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ENDOCYTOSIS, 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 MTOR SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IFNB1	IFNB1	IFNB1	9	1	0.13	YES
2	HERC5	HERC5	HERC5	933	0.46	0.13	YES
3	NLRC5	NLRC5	NLRC5	1053	0.43	0.18	YES
4	TNFAIP3	TNFAIP3	TNFAIP3	1676	0.34	0.19	YES
5	S100B	S100B	S100B	1944	0.31	0.21	YES
6	RNF125	RNF125	RNF125	1985	0.3	0.25	YES
7	IKBKE	IKBKE	IKBKE	2153	0.28	0.27	YES
8	IRF1	IRF1	IRF1	2315	0.26	0.3	YES
9	CYLD	CYLD	CYLD	2513	0.25	0.32	YES
10	RNF135	RNF135	RNF135	2675	0.23	0.34	YES
11	UBA7	UBA7	UBA7	2704	0.23	0.36	YES
12	TRAF3	TRAF3	TRAF3	3134	0.2	0.36	YES
13	NFKB2	NFKB2	NFKB2	3315	0.19	0.38	YES
14	DHX58	DHX58	DHX58	3403	0.18	0.4	YES
15	CASP8	CASP8	CASP8	3526	0.18	0.41	YES
16	TRIM25	TRIM25	TRIM25	3886	0.16	0.41	YES
17	AGER	AGER	AGER	3975	0.15	0.42	YES
18	UBE2L6	UBE2L6	UBE2L6	4017	0.15	0.44	YES
19	IKBKB	IKBKB	IKBKB	4144	0.14	0.45	YES
20	IFIH1	IFIH1	IFIH1	4297	0.14	0.46	YES
21	MAP3K1	MAP3K1	MAP3K1	4349	0.14	0.48	YES
22	TRAF6	TRAF6	TRAF6	4472	0.13	0.48	YES
23	DDX58	DDX58	DDX58	4480	0.13	0.5	YES
24	IRF2	IRF2	IRF2	4799	0.12	0.5	NO
25	CASP10	CASP10	CASP10	5038	0.11	0.5	NO
26	TRAF2	TRAF2	TRAF2	5475	0.096	0.49	NO
27	NFKBIA	NFKBIA	NFKBIA	6092	0.081	0.46	NO
28	ATG12	ATG12	ATG12	6616	0.068	0.44	NO
29	RPS27A	RPS27A	RPS27A	6857	0.063	0.44	NO
30	MAVS	MAVS	MAVS	7031	0.06	0.43	NO
31	OTUD5	OTUD5	OTUD5	7216	0.056	0.43	NO
32	IKBKG	IKBKG	IKBKG	7261	0.055	0.44	NO
33	UBA52	UBA52	UBA52	7532	0.05	0.43	NO
34	ISG15	ISG15	ISG15	7671	0.047	0.42	NO
35	TBK1	TBK1	TBK1	8301	0.035	0.39	NO
36	CREBBP	CREBBP	CREBBP	8388	0.034	0.39	NO
37	CHUK	CHUK	CHUK	8406	0.033	0.4	NO
38	UBE2D2	UBE2D2	UBE2D2	9001	0.024	0.37	NO
39	TAX1BP1	TAX1BP1	TAX1BP1	9064	0.023	0.37	NO
40	UBE2D3	UBE2D3	UBE2D3	9300	0.019	0.36	NO
41	NFKBIB	NFKBIB	NFKBIB	9396	0.017	0.35	NO
42	ATG5	ATG5	ATG5	9593	0.014	0.34	NO
43	IRF3	IRF3	IRF3	9795	0.01	0.33	NO
44	IRF7	IRF7	IRF7	9887	0.0087	0.33	NO
45	EP300	EP300	EP300	10098	0.0051	0.32	NO
46	RELA	RELA	RELA	10186	0.0039	0.31	NO
47	PCBP2	PCBP2	PCBP2	10213	0.0033	0.31	NO
48	SIKE1	SIKE1	SIKE1	10636	-0.0044	0.29	NO
49	TANK	TANK	TANK	10700	-0.0054	0.29	NO
50	HMGB1	HMGB1	HMGB1	10992	-0.01	0.27	NO
51	PIN1	PIN1	PIN1	11435	-0.019	0.25	NO
52	FADD	FADD	FADD	11691	-0.023	0.24	NO
53	UBE2K	UBE2K	UBE2K	12073	-0.031	0.22	NO
54	RIPK1	RIPK1	RIPK1	12224	-0.034	0.22	NO
55	UBE2D1	UBE2D1	UBE2D1	13124	-0.052	0.18	NO
56	NLRX1	NLRX1	NLRX1	14513	-0.092	0.11	NO
57	DAK	DAK	DAK	14642	-0.096	0.11	NO
58	APP	APP	APP	16221	-0.18	0.05	NO
59	S100A12	S100A12	S100A12	16515	-0.21	0.059	NO
60	SAA1	SAA1	SAA1	16759	-0.23	0.075	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 MTOR SIGNALING PATHWAY.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MTOR 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 APOPTOSIS

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	CXCL13	CXCL13	CXCL13	58	0.88	0.098	YES
2	CXCL11	CXCL11	CXCL11	137	0.77	0.18	YES
3	CXCL9	CXCL9	CXCL9	145	0.76	0.27	YES
4	CXCR3	CXCR3	CXCR3	160	0.75	0.36	YES
5	CXCL10	CXCL10	CXCL10	289	0.67	0.43	YES
6	ITGAL	ITGAL	ITGAL	294	0.67	0.5	YES
7	PIK3CD	PIK3CD	PIK3CD	604	0.54	0.55	YES
8	PF4	PF4	PF4	977	0.45	0.58	YES
9	ITGB2	ITGB2	ITGB2	1367	0.38	0.6	YES
10	GNG2	GNG2	GNG2	1388	0.38	0.65	YES
11	PIK3R3	PIK3R3	PIK3R3	2404	0.26	0.62	NO
12	ARRB1	ARRB1	ARRB1	2779	0.22	0.62	NO
13	CCL11	CCL11	CCL11	3025	0.21	0.64	NO
14	GNAO1	GNAO1	GNAO1	3326	0.19	0.64	NO
15	GNAZ	GNAZ	GNAZ	5870	0.086	0.51	NO
16	RICTOR	RICTOR	RICTOR	6462	0.072	0.48	NO
17	PDPK1	PDPK1	PDPK1	7024	0.06	0.46	NO
18	MAP2K1	MAP2K1	MAP2K1	7117	0.058	0.46	NO
19	MTOR	MTOR	MTOR	7612	0.048	0.44	NO
20	GNAI2	GNAI2	GNAI2	7880	0.043	0.43	NO
21	PIK3CA	PIK3CA	PIK3CA	8332	0.035	0.41	NO
22	MAPK11	MAPK11	MAPK11	8426	0.033	0.41	NO
23	PIK3CB	PIK3CB	PIK3CB	8488	0.032	0.41	NO
24	RAF1	RAF1	RAF1	8847	0.026	0.39	NO
25	MAPK1	MAPK1	MAPK1	9247	0.02	0.37	NO
26	MAPKAP1	MAPKAP1	MAPKAP1	9409	0.017	0.37	NO
27	MAP2K2	MAP2K2	MAP2K2	9685	0.012	0.35	NO
28	MAPK14	MAPK14	MAPK14	10199	0.0035	0.32	NO
29	GNB1	GNB1	GNB1	10660	-0.0049	0.3	NO
30	MAPK3	MAPK3	MAPK3	11313	-0.016	0.26	NO
31	MLST8	MLST8	MLST8	11392	-0.018	0.26	NO
32	KRAS	KRAS	KRAS	11599	-0.021	0.25	NO
33	PIK3R2	PIK3R2	PIK3R2	11896	-0.027	0.24	NO
34	HRAS	HRAS	HRAS	11910	-0.028	0.24	NO
35	NRAS	NRAS	NRAS	12308	-0.036	0.22	NO
36	GNAI3	GNAI3	GNAI3	12736	-0.044	0.21	NO
37	SRC	SRC	SRC	13184	-0.054	0.19	NO
38	PIK3R1	PIK3R1	PIK3R1	13802	-0.071	0.16	NO
39	MAP2K6	MAP2K6	MAP2K6	14134	-0.08	0.15	NO
40	AKT1	AKT1	AKT1	14849	-0.1	0.13	NO
41	DNM1	DNM1	DNM1	14963	-0.11	0.13	NO
42	MAP2K3	MAP2K3	MAP2K3	15642	-0.14	0.11	NO
43	GNAI1	GNAI1	GNAI1	16616	-0.22	0.083	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 APOPTOSIS.

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

genes ES table in pathway: KEGG CELL ADHESION MOLECULES CAMS

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	TNF	TNF	TNF	196	0.72	0.13	YES
2	BCL2	BCL2	BCL2	668	0.52	0.2	YES
3	BIRC3	BIRC3	BIRC3	1254	0.4	0.24	YES
4	EGF	EGF	EGF	1530	0.36	0.3	YES
5	IGF1	IGF1	IGF1	1615	0.35	0.36	YES
6	MYC	MYC	MYC	1917	0.31	0.4	YES
7	KSR1	KSR1	KSR1	2387	0.26	0.42	YES
8	SMPD3	SMPD3	SMPD3	2910	0.21	0.43	YES
9	CASP8	CASP8	CASP8	3526	0.18	0.43	NO
10	MAP3K1	MAP3K1	MAP3K1	4349	0.14	0.41	NO
11	PRKCD	PRKCD	PRKCD	4661	0.12	0.42	NO
12	NSMAF	NSMAF	NSMAF	5293	0.1	0.4	NO
13	TRAF2	TRAF2	TRAF2	5475	0.096	0.41	NO
14	NFKBIA	NFKBIA	NFKBIA	6092	0.081	0.39	NO
15	BID	BID	BID	6970	0.061	0.36	NO
16	NFKB1	NFKB1	NFKB1	6992	0.061	0.37	NO
17	MAP2K1	MAP2K1	MAP2K1	7117	0.058	0.37	NO
18	PAWR	PAWR	PAWR	7979	0.041	0.33	NO
19	EIF2A	EIF2A	EIF2A	8032	0.04	0.33	NO
20	TRADD	TRADD	TRADD	8046	0.04	0.34	NO
21	EIF2AK2	EIF2AK2	EIF2AK2	8257	0.036	0.34	NO
22	RAF1	RAF1	RAF1	8847	0.026	0.31	NO
23	ASAH1	ASAH1	ASAH1	9150	0.022	0.3	NO
24	MAPK1	MAPK1	MAPK1	9247	0.02	0.3	NO
25	MAP2K2	MAP2K2	MAP2K2	9685	0.012	0.27	NO
26	BAG4	BAG4	BAG4	9888	0.0086	0.26	NO
27	RELA	RELA	RELA	10186	0.0039	0.25	NO
28	MADD	MADD	MADD	10305	0.0016	0.24	NO
29	SMPD1	SMPD1	SMPD1	10315	0.0014	0.24	NO
30	PRKCZ	PRKCZ	PRKCZ	10771	-0.0067	0.22	NO
31	RB1	RB1	RB1	11082	-0.012	0.2	NO
32	PRKRA	PRKRA	PRKRA	11155	-0.013	0.2	NO
33	MAPK3	MAPK3	MAPK3	11313	-0.016	0.2	NO
34	FADD	FADD	FADD	11691	-0.023	0.18	NO
35	MAP2K4	MAP2K4	MAP2K4	11883	-0.027	0.17	NO
36	RIPK1	RIPK1	RIPK1	12224	-0.034	0.16	NO
37	MAP4K4	MAP4K4	MAP4K4	12410	-0.038	0.16	NO
38	SPHK2	SPHK2	SPHK2	12837	-0.046	0.14	NO
39	AIFM1	AIFM1	AIFM1	13159	-0.054	0.14	NO
40	CYCS	CYCS	CYCS	13458	-0.061	0.13	NO
41	BAD	BAD	BAD	13477	-0.062	0.14	NO
42	CTSD	CTSD	CTSD	13493	-0.062	0.15	NO
43	MAPK8	MAPK8	MAPK8	13671	-0.067	0.16	NO
44	BAX	BAX	BAX	13721	-0.068	0.16	NO
45	TNFRSF1A	TNFRSF1A	TNFRSF1A	14364	-0.087	0.15	NO
46	AKT1	AKT1	AKT1	14849	-0.1	0.14	NO
47	PDGFA	PDGFA	PDGFA	14859	-0.1	0.16	NO
48	CRADD	CRADD	CRADD	15157	-0.12	0.16	NO

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

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

genes ES table in pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION

Table 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	FASLG	FASLG	FASLG	120	0.79	0.13	YES
2	TNF	TNF	TNF	196	0.72	0.25	YES
3	CD247	CD247	CD247	269	0.68	0.36	YES
4	BCL2	BCL2	BCL2	668	0.52	0.42	YES
5	BIRC3	BIRC3	BIRC3	1254	0.4	0.46	YES
6	TRAF1	TRAF1	TRAF1	1648	0.34	0.5	YES
7	MAP3K14	MAP3K14	MAP3K14	2220	0.27	0.51	YES
8	DFFB	DFFB	DFFB	2484	0.25	0.54	YES
9	FAS	FAS	FAS	2573	0.24	0.57	YES
10	MAP3K5	MAP3K5	MAP3K5	3126	0.2	0.58	YES
11	CASP8	CASP8	CASP8	3526	0.18	0.58	YES
12	CFLAR	CFLAR	CFLAR	3841	0.16	0.6	YES
13	TRAF2	TRAF2	TRAF2	5475	0.096	0.52	NO
14	NFKBIA	NFKBIA	NFKBIA	6092	0.081	0.5	NO
15	CASP2	CASP2	CASP2	6208	0.078	0.51	NO
16	BID	BID	BID	6970	0.061	0.48	NO
17	NFKB1	NFKB1	NFKB1	6992	0.061	0.48	NO
18	DAXX	DAXX	DAXX	7097	0.058	0.49	NO
19	DFFA	DFFA	DFFA	7689	0.047	0.46	NO
20	CASP6	CASP6	CASP6	7693	0.047	0.47	NO
21	MAP2K7	MAP2K7	MAP2K7	7959	0.041	0.46	NO
22	CASP3	CASP3	CASP3	7967	0.041	0.47	NO
23	TRADD	TRADD	TRADD	8046	0.04	0.47	NO
24	CHUK	CHUK	CHUK	8406	0.033	0.46	NO
25	BAG4	BAG4	BAG4	9888	0.0086	0.38	NO
26	RELA	RELA	RELA	10186	0.0039	0.36	NO
27	APAF1	APAF1	APAF1	11040	-0.011	0.32	NO
28	CASP7	CASP7	CASP7	11589	-0.021	0.29	NO
29	FADD	FADD	FADD	11691	-0.023	0.29	NO
30	CASP9	CASP9	CASP9	11704	-0.023	0.29	NO
31	RIPK1	RIPK1	RIPK1	12224	-0.034	0.27	NO
32	CYCS	CYCS	CYCS	13458	-0.061	0.21	NO
33	MAPK8	MAPK8	MAPK8	13671	-0.067	0.21	NO
34	TNFRSF1A	TNFRSF1A	TNFRSF1A	14364	-0.087	0.19	NO
35	CRADD	CRADD	CRADD	15157	-0.12	0.16	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 ANTIGEN PROCESSING AND PRESENTATION.

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

genes ES table in pathway: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY

Table 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	IFNG	IFNG	IFNG	46	0.9	0.031	YES
2	ICOS	ICOS	ICOS	56	0.88	0.063	YES
3	CD40LG	CD40LG	CD40LG	81	0.84	0.093	YES
4	CTLA4	CTLA4	CTLA4	89	0.83	0.12	YES
5	ITK	ITK	ITK	98	0.82	0.15	YES
6	ZAP70	ZAP70	ZAP70	153	0.76	0.18	YES
7	CD3E	CD3E	CD3E	155	0.75	0.21	YES
8	PDCD1	PDCD1	PDCD1	171	0.74	0.23	YES
9	PIK3CG	PIK3CG	PIK3CG	174	0.74	0.26	YES
10	CD28	CD28	CD28	190	0.73	0.29	YES
11	TNF	TNF	TNF	196	0.72	0.32	YES
12	CD8A	CD8A	CD8A	215	0.7	0.34	YES
13	LCK	LCK	LCK	216	0.7	0.37	YES
14	IL2	IL2	IL2	228	0.7	0.39	YES
15	CD247	CD247	CD247	269	0.68	0.42	YES
16	PTPRC	PTPRC	PTPRC	311	0.66	0.44	YES
17	CD8B	CD8B	CD8B	328	0.65	0.46	YES
18	GRAP2	GRAP2	GRAP2	338	0.65	0.48	YES
19	IL10	IL10	IL10	353	0.64	0.51	YES
20	CD3G	CD3G	CD3G	360	0.64	0.53	YES
21	RASGRP1	RASGRP1	RASGRP1	366	0.63	0.56	YES
22	CD3D	CD3D	CD3D	504	0.57	0.57	YES
23	PIK3R5	PIK3R5	PIK3R5	568	0.55	0.59	YES
24	PIK3CD	PIK3CD	PIK3CD	604	0.54	0.6	YES
25	VAV1	VAV1	VAV1	622	0.54	0.62	YES
26	PRKCQ	PRKCQ	PRKCQ	807	0.48	0.63	YES
27	CARD11	CARD11	CARD11	991	0.44	0.64	YES
28	LCP2	LCP2	LCP2	1063	0.43	0.65	YES
29	LAT	LAT	LAT	1293	0.4	0.65	YES
30	CD4	CD4	CD4	1566	0.35	0.65	YES
31	MAP3K8	MAP3K8	MAP3K8	1868	0.32	0.64	YES
32	TEC	TEC	TEC	1938	0.31	0.65	YES
33	MAP3K14	MAP3K14	MAP3K14	2220	0.27	0.65	YES
34	NFATC2	NFATC2	NFATC2	2233	0.27	0.66	YES
35	FYN	FYN	FYN	2329	0.26	0.66	YES
36	PIK3R3	PIK3R3	PIK3R3	2404	0.26	0.67	YES
37	NFATC1	NFATC1	NFATC1	2925	0.21	0.64	NO
38	PTPN6	PTPN6	PTPN6	3411	0.18	0.62	NO
39	PPP3CC	PPP3CC	PPP3CC	3686	0.17	0.62	NO
40	IKBKB	IKBKB	IKBKB	4144	0.14	0.6	NO
41	PDK1	PDK1	PDK1	4328	0.14	0.59	NO
42	AKT3	AKT3	AKT3	4602	0.13	0.58	NO
43	SOS1	SOS1	SOS1	4921	0.12	0.57	NO
44	PLCG1	PLCG1	PLCG1	5006	0.11	0.57	NO
45	NCK1	NCK1	NCK1	5080	0.11	0.57	NO
46	BCL10	BCL10	BCL10	5448	0.097	0.55	NO
47	MAP3K7	MAP3K7	MAP3K7	5552	0.094	0.55	NO
48	VAV3	VAV3	VAV3	5867	0.086	0.53	NO
49	CBLB	CBLB	CBLB	5911	0.085	0.54	NO
50	NFKBIA	NFKBIA	NFKBIA	6092	0.081	0.53	NO
51	CBL	CBL	CBL	6102	0.081	0.53	NO
52	MALT1	MALT1	MALT1	6423	0.073	0.52	NO
53	NFKBIE	NFKBIE	NFKBIE	6622	0.068	0.51	NO
54	NFATC4	NFATC4	NFATC4	6734	0.066	0.5	NO
55	NFKB1	NFKB1	NFKB1	6992	0.061	0.49	NO
56	AKT2	AKT2	AKT2	7055	0.06	0.49	NO
57	MAP2K1	MAP2K1	MAP2K1	7117	0.058	0.49	NO
58	MAPK9	MAPK9	MAPK9	7132	0.058	0.49	NO
59	IKBKG	IKBKG	IKBKG	7261	0.055	0.48	NO
60	VAV2	VAV2	VAV2	7674	0.047	0.46	NO
61	GRB2	GRB2	GRB2	7701	0.046	0.46	NO
62	MAP2K7	MAP2K7	MAP2K7	7959	0.041	0.45	NO
63	NFATC3	NFATC3	NFATC3	7964	0.041	0.45	NO
64	GSK3B	GSK3B	GSK3B	8088	0.039	0.45	NO
65	PIK3CA	PIK3CA	PIK3CA	8332	0.035	0.44	NO
66	CHUK	CHUK	CHUK	8406	0.033	0.43	NO
67	MAPK11	MAPK11	MAPK11	8426	0.033	0.43	NO
68	PIK3CB	PIK3CB	PIK3CB	8488	0.032	0.43	NO
69	PAK2	PAK2	PAK2	8657	0.03	0.42	NO
70	RAF1	RAF1	RAF1	8847	0.026	0.41	NO
71	NFAT5	NFAT5	NFAT5	9038	0.023	0.4	NO
72	MAPK13	MAPK13	MAPK13	9063	0.023	0.4	NO
73	PAK7	PAK7	PAK7	9232	0.02	0.39	NO
74	MAPK1	MAPK1	MAPK1	9247	0.02	0.39	NO
75	NFKBIB	NFKBIB	NFKBIB	9396	0.017	0.39	NO
76	RHOA	RHOA	RHOA	9637	0.013	0.37	NO
77	MAP2K2	MAP2K2	MAP2K2	9685	0.012	0.37	NO
78	RELA	RELA	RELA	10186	0.0039	0.34	NO
79	MAPK14	MAPK14	MAPK14	10199	0.0035	0.34	NO
80	PPP3R1	PPP3R1	PPP3R1	10704	-0.0055	0.32	NO
81	PAK1	PAK1	PAK1	11171	-0.013	0.29	NO
82	MAPK3	MAPK3	MAPK3	11313	-0.016	0.28	NO
83	KRAS	KRAS	KRAS	11599	-0.021	0.27	NO
84	PIK3R2	PIK3R2	PIK3R2	11896	-0.027	0.25	NO
85	HRAS	HRAS	HRAS	11910	-0.028	0.25	NO
86	NRAS	NRAS	NRAS	12308	-0.036	0.23	NO
87	PPP3CB	PPP3CB	PPP3CB	12472	-0.039	0.22	NO
88	PPP3CA	PPP3CA	PPP3CA	12820	-0.046	0.21	NO
89	SOS2	SOS2	SOS2	12947	-0.049	0.2	NO
90	CHP	CHP	CHP	12995	-0.05	0.2	NO
91	JUN	JUN	JUN	13526	-0.063	0.17	NO
92	CDC42	CDC42	CDC42	13563	-0.064	0.17	NO
93	DLG1	DLG1	DLG1	13651	-0.066	0.17	NO
94	PIK3R1	PIK3R1	PIK3R1	13802	-0.071	0.17	NO
95	PAK3	PAK3	PAK3	13820	-0.072	0.17	NO
96	CDK4	CDK4	CDK4	14110	-0.08	0.16	NO
97	NCK2	NCK2	NCK2	14177	-0.081	0.15	NO
98	PAK6	PAK6	PAK6	14406	-0.088	0.14	NO
99	AKT1	AKT1	AKT1	14849	-0.1	0.12	NO
100	FOS	FOS	FOS	15246	-0.12	0.11	NO
101	PAK4	PAK4	PAK4	15716	-0.15	0.086	NO
102	MAPK12	MAPK12	MAPK12	16090	-0.17	0.072	NO
103	CSF2	CSF2	CSF2	17406	-0.33	0.011	NO
104	CBLC	CBLC	CBLC	17455	-0.34	0.021	NO
105	CHP2	CHP2	CHP2	17725	-0.42	0.022	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 TOLL LIKE RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HERC5	HERC5	HERC5	933	0.46	0.064	YES
2	NLRC5	NLRC5	NLRC5	1053	0.43	0.17	YES
3	TNFAIP3	TNFAIP3	TNFAIP3	1676	0.34	0.22	YES
4	RNF125	RNF125	RNF125	1985	0.3	0.28	YES
5	IKBKE	IKBKE	IKBKE	2153	0.28	0.34	YES
6	CYLD	CYLD	CYLD	2513	0.25	0.38	YES
7	RNF135	RNF135	RNF135	2675	0.23	0.43	YES
8	UBA7	UBA7	UBA7	2704	0.23	0.49	YES
9	TRAF3	TRAF3	TRAF3	3134	0.2	0.51	YES
10	TRIM25	TRIM25	TRIM25	3886	0.16	0.51	YES
11	UBE2L6	UBE2L6	UBE2L6	4017	0.15	0.54	YES
12	IFIH1	IFIH1	IFIH1	4297	0.14	0.56	YES
13	DDX58	DDX58	DDX58	4480	0.13	0.58	YES
14	ATG12	ATG12	ATG12	6616	0.068	0.48	NO
15	RPS27A	RPS27A	RPS27A	6857	0.063	0.49	NO
16	MAVS	MAVS	MAVS	7031	0.06	0.49	NO
17	OTUD5	OTUD5	OTUD5	7216	0.056	0.5	NO
18	UBA52	UBA52	UBA52	7532	0.05	0.49	NO
19	ISG15	ISG15	ISG15	7671	0.047	0.5	NO
20	TBK1	TBK1	TBK1	8301	0.035	0.47	NO
21	UBE2D2	UBE2D2	UBE2D2	9001	0.024	0.44	NO
22	TAX1BP1	TAX1BP1	TAX1BP1	9064	0.023	0.44	NO
23	UBE2D3	UBE2D3	UBE2D3	9300	0.019	0.43	NO
24	ATG5	ATG5	ATG5	9593	0.014	0.42	NO
25	IRF3	IRF3	IRF3	9795	0.01	0.41	NO
26	PCBP2	PCBP2	PCBP2	10213	0.0033	0.39	NO
27	PIN1	PIN1	PIN1	11435	-0.019	0.32	NO
28	UBE2K	UBE2K	UBE2K	12073	-0.031	0.3	NO
29	UBE2D1	UBE2D1	UBE2D1	13124	-0.052	0.25	NO
30	NLRX1	NLRX1	NLRX1	14513	-0.092	0.2	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 NOD LIKE RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FASLG	FASLG	FASLG	120	0.79	0.12	YES
2	FAIM2	FAIM2	FAIM2	271	0.68	0.22	YES
3	BTK	BTK	BTK	405	0.62	0.32	YES
4	PIK3CD	PIK3CD	PIK3CD	604	0.54	0.4	YES
5	MAPK10	MAPK10	MAPK10	919	0.46	0.45	YES
6	BIRC3	BIRC3	BIRC3	1254	0.4	0.5	YES
7	SYK	SYK	SYK	2066	0.29	0.5	YES
8	PIK3R3	PIK3R3	PIK3R3	2404	0.26	0.53	YES
9	FAS	FAS	FAS	2573	0.24	0.56	YES
10	CASP8	CASP8	CASP8	3526	0.18	0.53	YES
11	CFLAR	CFLAR	CFLAR	3841	0.16	0.54	YES
12	IKBKB	IKBKB	IKBKB	4144	0.14	0.55	YES
13	MAP3K1	MAP3K1	MAP3K1	4349	0.14	0.56	YES
14	CASP10	CASP10	CASP10	5038	0.11	0.54	NO
15	RFC1	RFC1	RFC1	6816	0.064	0.45	NO
16	BID	BID	BID	6970	0.061	0.45	NO
17	EZR	EZR	EZR	7012	0.06	0.46	NO
18	PDPK1	PDPK1	PDPK1	7024	0.06	0.47	NO
19	MAPK9	MAPK9	MAPK9	7132	0.058	0.48	NO
20	IKBKG	IKBKG	IKBKG	7261	0.055	0.48	NO
21	MAP2K7	MAP2K7	MAP2K7	7959	0.041	0.44	NO
22	CASP3	CASP3	CASP3	7967	0.041	0.45	NO
23	PIK3CA	PIK3CA	PIK3CA	8332	0.035	0.44	NO
24	CHUK	CHUK	CHUK	8406	0.033	0.44	NO
25	MAPK11	MAPK11	MAPK11	8426	0.033	0.44	NO
26	PIK3CB	PIK3CB	PIK3CB	8488	0.032	0.44	NO
27	MAPK14	MAPK14	MAPK14	10199	0.0035	0.35	NO
28	SMPD1	SMPD1	SMPD1	10315	0.0014	0.34	NO
29	FADD	FADD	FADD	11691	-0.023	0.27	NO
30	BIRC2	BIRC2	BIRC2	11823	-0.026	0.27	NO
31	PIK3R2	PIK3R2	PIK3R2	11896	-0.027	0.27	NO
32	RIPK1	RIPK1	RIPK1	12224	-0.034	0.26	NO
33	CLTC	CLTC	CLTC	12647	-0.042	0.24	NO
34	SRC	SRC	SRC	13184	-0.054	0.22	NO
35	MAPK8	MAPK8	MAPK8	13671	-0.067	0.2	NO
36	PIK3R1	PIK3R1	PIK3R1	13802	-0.071	0.21	NO
37	MAP2K6	MAP2K6	MAP2K6	14134	-0.08	0.2	NO
38	AKT1	AKT1	AKT1	14849	-0.1	0.18	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 RIG I LIKE RECEPTOR SIGNALING PATHWAY.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype 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
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS	27	genes.ES.table	0.68	1.4	0.14	1	1	0.33	0.026	0.32	1	0.95
KEGG GLUTATHIONE METABOLISM	46	genes.ES.table	0.44	1.3	0.16	1	1	0.22	0.077	0.2	1	0.88
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM	39	genes.ES.table	0.57	1.3	0.21	1	1	0.23	0.026	0.22	1	0.86
KEGG RIBOSOME	85	genes.ES.table	0.49	1.2	0.36	1	1	0.68	0.34	0.45	1	0.86
KEGG SPLICEOSOME	114	genes.ES.table	0.26	1.2	0.24	1	1	0.37	0.26	0.27	1	0.91
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT	38	genes.ES.table	0.3	1.3	0.16	1	1	0.26	0.16	0.22	1	0.94
BIOCARTA PROTEASOME PATHWAY	28	genes.ES.table	0.44	1.2	0.25	1	1	1	0.56	0.44	1	0.88
REACTOME ER PHAGOSOME PATHWAY	57	genes.ES.table	0.4	1.1	0.37	1	1	0.51	0.31	0.35	1	0.85
REACTOME MEMBRANE TRAFFICKING	123	genes.ES.table	0.25	1.2	0.28	1	1	0.21	0.17	0.18	1	0.9
REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT	47	genes.ES.table	0.37	1.2	0.36	1	1	0.38	0.22	0.3	1	0.85

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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	NQO1	NQO1	NQO1	408	0.37	0.091	YES
2	ODC1	ODC1	ODC1	1387	0.2	0.097	YES
3	PSMB2	PSMB2	PSMB2	2455	0.13	0.077	YES
4	OAZ3	OAZ3	OAZ3	2576	0.12	0.11	YES
5	PSMB6	PSMB6	PSMB6	2650	0.12	0.14	YES
6	PSMB9	PSMB9	PSMB9	2690	0.12	0.17	YES
7	PSMA5	PSMA5	PSMA5	2955	0.1	0.19	YES
8	PSMB3	PSMB3	PSMB3	3017	0.1	0.22	YES
9	PSMC4	PSMC4	PSMC4	3032	0.1	0.25	YES
10	PSMD9	PSMD9	PSMD9	3077	0.1	0.28	YES
11	PSMB8	PSMB8	PSMB8	3462	0.088	0.28	YES
12	PSMC5	PSMC5	PSMC5	3504	0.086	0.3	YES
13	PSMC3	PSMC3	PSMC3	3582	0.084	0.33	YES
14	PSMB10	PSMB10	PSMB10	3616	0.083	0.35	YES
15	PSMD4	PSMD4	PSMD4	3651	0.082	0.37	YES
16	PSMD13	PSMD13	PSMD13	3753	0.078	0.39	YES
17	PSME2	PSME2	PSME2	3912	0.074	0.4	YES
18	PSMF1	PSMF1	PSMF1	4032	0.07	0.42	YES
19	PSMA4	PSMA4	PSMA4	4525	0.057	0.41	YES
20	PSMB5	PSMB5	PSMB5	4836	0.049	0.41	YES
21	OAZ1	OAZ1	OAZ1	5045	0.044	0.41	YES
22	PSMB4	PSMB4	PSMB4	5068	0.044	0.42	YES
23	PSMA6	PSMA6	PSMA6	5242	0.04	0.42	YES
24	PSMC1	PSMC1	PSMC1	5341	0.037	0.43	YES
25	OAZ2	OAZ2	OAZ2	5997	0.022	0.4	NO
26	PSMD8	PSMD8	PSMD8	6256	0.017	0.39	NO
27	PSMB7	PSMB7	PSMB7	6305	0.016	0.39	NO
28	PSME1	PSME1	PSME1	6498	0.011	0.39	NO
29	PSMA3	PSMA3	PSMA3	6620	0.0083	0.38	NO
30	PSMA7	PSMA7	PSMA7	6781	0.0049	0.38	NO
31	PSMD14	PSMD14	PSMD14	6898	0.0023	0.37	NO
32	PSMD7	PSMD7	PSMD7	7134	-0.0025	0.36	NO
33	PSMA2	PSMA2	PSMA2	7567	-0.012	0.34	NO
34	PSMC6	PSMC6	PSMC6	7607	-0.012	0.34	NO
35	PSMA1	PSMA1	PSMA1	7708	-0.015	0.34	NO
36	PSMB1	PSMB1	PSMB1	8066	-0.023	0.32	NO
37	PSMD1	PSMD1	PSMD1	8110	-0.024	0.33	NO
38	PSMC2	PSMC2	PSMC2	8243	-0.027	0.33	NO
39	PSMD11	PSMD11	PSMD11	8256	-0.027	0.34	NO
40	PSMD12	PSMD12	PSMD12	8298	-0.028	0.34	NO
41	PSMD3	PSMD3	PSMD3	8649	-0.036	0.34	NO
42	PSMD10	PSMD10	PSMD10	10070	-0.069	0.28	NO
43	PSMD6	PSMD6	PSMD6	10163	-0.072	0.3	NO
44	PSME4	PSME4	PSME4	10314	-0.075	0.31	NO
45	PSMD2	PSMD2	PSMD2	10396	-0.078	0.33	NO
46	AZIN1	AZIN1	AZIN1	12591	-0.14	0.25	NO
47	PSMD5	PSMD5	PSMD5	13390	-0.18	0.26	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: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS.

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

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

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	GTF2H2	GTF2H2	GTF2H2	1005	0.24	0.033	YES
2	GTF2H2B	GTF2H2B	GTF2H2B	1209	0.22	0.1	YES
3	POLR2I	POLR2I	POLR2I	1859	0.16	0.12	YES
4	GTF2H4	GTF2H4	GTF2H4	2422	0.13	0.14	YES
5	RDBP	RDBP	RDBP	2529	0.12	0.18	YES
6	POLR2E	POLR2E	POLR2E	2582	0.12	0.22	YES
7	POLR2C	POLR2C	POLR2C	3033	0.1	0.23	YES
8	POLR2L	POLR2L	POLR2L	3344	0.091	0.25	YES
9	CTDP1	CTDP1	CTDP1	3679	0.081	0.26	YES
10	GTF2F1	GTF2F1	GTF2F1	3726	0.08	0.29	YES
11	POLR2J	POLR2J	POLR2J	3782	0.078	0.31	YES
12	SUPT4H1	SUPT4H1	SUPT4H1	3812	0.077	0.34	YES
13	POLR2G	POLR2G	POLR2G	3815	0.077	0.36	YES
14	POLR2F	POLR2F	POLR2F	4817	0.05	0.33	NO
15	SUPT5H	SUPT5H	SUPT5H	5471	0.034	0.3	NO
16	POLR2K	POLR2K	POLR2K	5819	0.026	0.3	NO
17	GTF2H1	GTF2H1	GTF2H1	6037	0.021	0.29	NO
18	TH1L	TH1L	TH1L	6063	0.021	0.3	NO
19	POLR2H	POLR2H	POLR2H	6091	0.02	0.3	NO
20	CDK7	CDK7	CDK7	6603	0.0086	0.28	NO
21	ERCC2	ERCC2	ERCC2	6696	0.0067	0.28	NO
22	ERCC3	ERCC3	ERCC3	7282	-0.0054	0.24	NO
23	WHSC2	WHSC2	WHSC2	7499	-0.01	0.24	NO
24	GTF2F2	GTF2F2	GTF2F2	8288	-0.028	0.2	NO
25	COBRA1	COBRA1	COBRA1	8659	-0.036	0.2	NO
26	POLR2A	POLR2A	POLR2A	8701	-0.037	0.21	NO
27	NCBP2	NCBP2	NCBP2	8840	-0.041	0.22	NO
28	CCNH	CCNH	CCNH	9146	-0.048	0.22	NO
29	POLR2D	POLR2D	POLR2D	10029	-0.068	0.19	NO
30	POLR2B	POLR2B	POLR2B	11370	-0.1	0.16	NO
31	NCBP1	NCBP1	NCBP1	12851	-0.15	0.13	NO
32	MNAT1	MNAT1	MNAT1	13964	-0.21	0.14	NO
33	GTF2H3	GTF2H3	GTF2H3	14445	-0.23	0.2	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: KEGG GLUTATHIONE METABOLISM.

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

genes ES table in pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

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	UGT1A9	UGT1A9	UGT1A9	84	0.59	0.092	YES
2	UGT2B11	UGT2B11	UGT2B11	133	0.52	0.18	YES
3	UGT1A8	UGT1A8	UGT1A8	136	0.52	0.26	YES
4	UGT1A6	UGT1A6	UGT1A6	139	0.52	0.35	YES
5	UGT1A10	UGT1A10	UGT1A10	175	0.49	0.42	YES
6	UGT1A7	UGT1A7	UGT1A7	197	0.48	0.5	YES
7	UGT2B28	UGT2B28	UGT2B28	266	0.44	0.57	YES
8	UGT1A5	UGT1A5	UGT1A5	308	0.41	0.64	YES
9	UGT2B4	UGT2B4	UGT2B4	476	0.35	0.68	YES
10	UGT2A1	UGT2A1	UGT2A1	2875	0.11	0.57	NO
11	UGT2B15	UGT2B15	UGT2B15	2928	0.1	0.58	NO
12	UGDH	UGDH	UGDH	6107	0.02	0.41	NO
13	GUSB	GUSB	GUSB	6524	0.01	0.39	NO
14	XYLB	XYLB	XYLB	6672	0.0072	0.38	NO
15	DCXR	DCXR	DCXR	10586	-0.082	0.18	NO
16	RPE	RPE	RPE	10728	-0.086	0.18	NO
17	AKR1B1	AKR1B1	AKR1B1	10818	-0.089	0.2	NO
18	UGT2B7	UGT2B7	UGT2B7	10886	-0.09	0.21	NO
19	UGT1A3	UGT1A3	UGT1A3	11432	-0.11	0.19	NO
20	DHDH	DHDH	DHDH	11547	-0.11	0.2	NO
21	UGP2	UGP2	UGP2	11576	-0.11	0.22	NO
22	UGT1A1	UGT1A1	UGT1A1	11652	-0.11	0.24	NO
23	UGT2A3	UGT2A3	UGT2A3	11820	-0.12	0.24	NO
24	LOC729020	LOC729020	LOC729020	12479	-0.14	0.23	NO
25	UGT2B10	UGT2B10	UGT2B10	12717	-0.15	0.24	NO
26	UGT1A4	UGT1A4	UGT1A4	12816	-0.15	0.26	NO
27	CRYL1	CRYL1	CRYL1	13497	-0.18	0.26	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: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM.

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

genes ES table in pathway: KEGG RIBOSOME

Table 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	VPS37D	VPS37D	VPS37D	403	0.37	0.15	YES
2	SNF8	SNF8	SNF8	1756	0.17	0.15	YES
3	CHMP6	CHMP6	CHMP6	2018	0.15	0.21	YES
4	CHMP2A	CHMP2A	CHMP2A	2366	0.13	0.25	YES
5	CHMP4A	CHMP4A	CHMP4A	3120	0.098	0.25	YES
6	UBA52	UBA52	UBA52	3125	0.098	0.3	YES
7	CHMP4B	CHMP4B	CHMP4B	4016	0.071	0.28	YES
8	VPS25	VPS25	VPS25	4079	0.069	0.31	YES
9	VPS37C	VPS37C	VPS37C	4663	0.054	0.3	YES
10	TSG101	TSG101	TSG101	4673	0.054	0.33	YES
11	VPS28	VPS28	VPS28	4717	0.052	0.35	YES
12	HGS	HGS	HGS	4908	0.048	0.36	YES
13	RPS27A	RPS27A	RPS27A	5515	0.033	0.34	NO
14	VPS4A	VPS4A	VPS4A	5845	0.026	0.34	NO
15	CHMP7	CHMP7	CHMP7	6103	0.02	0.33	NO
16	CHMP4C	CHMP4C	CHMP4C	7692	-0.014	0.25	NO
17	VPS37B	VPS37B	VPS37B	8244	-0.027	0.23	NO
18	VPS4B	VPS4B	VPS4B	8349	-0.029	0.24	NO
19	VPS36	VPS36	VPS36	8801	-0.04	0.23	NO
20	STAM2	STAM2	STAM2	10098	-0.07	0.19	NO
21	VPS37A	VPS37A	VPS37A	10585	-0.082	0.2	NO
22	STAM	STAM	STAM	10835	-0.089	0.23	NO
23	CHMP5	CHMP5	CHMP5	11785	-0.12	0.23	NO
24	VTA1	VTA1	VTA1	12041	-0.12	0.28	NO
25	CHMP2B	CHMP2B	CHMP2B	12235	-0.13	0.32	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: KEGG RIBOSOME.

Figure S68. 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 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	SNAP25	SNAP25	SNAP25	712	0.29	0.036	YES
2	USE1	USE1	USE1	1070	0.23	0.076	YES
3	VAMP5	VAMP5	VAMP5	1229	0.22	0.12	YES
4	STX1A	STX1A	STX1A	1379	0.2	0.17	YES
5	STX3	STX3	STX3	1568	0.18	0.2	YES
6	STX1B	STX1B	STX1B	1902	0.16	0.22	YES
7	BNIP1	BNIP1	BNIP1	2120	0.14	0.25	YES
8	VAMP8	VAMP8	VAMP8	2320	0.13	0.27	YES
9	STX8	STX8	STX8	2569	0.12	0.29	YES
10	STX10	STX10	STX10	2870	0.11	0.3	YES
11	STX4	STX4	STX4	3603	0.084	0.28	NO
12	VTI1B	VTI1B	VTI1B	4154	0.067	0.27	NO
13	STX5	STX5	STX5	4560	0.056	0.26	NO
14	BET1L	BET1L	BET1L	5564	0.032	0.22	NO
15	YKT6	YKT6	YKT6	5637	0.03	0.22	NO
16	SEC22B	SEC22B	SEC22B	6420	0.013	0.18	NO
17	SNAP29	SNAP29	SNAP29	6526	0.01	0.18	NO
18	STX18	STX18	STX18	7096	-0.0018	0.14	NO
19	STX2	STX2	STX2	8418	-0.031	0.08	NO
20	VAMP3	VAMP3	VAMP3	8466	-0.032	0.086	NO
21	STX7	STX7	STX7	8581	-0.035	0.088	NO
22	VTI1A	VTI1A	VTI1A	8695	-0.037	0.092	NO
23	STX16	STX16	STX16	8962	-0.043	0.088	NO
24	GOSR2	GOSR2	GOSR2	9305	-0.051	0.083	NO
25	VAMP4	VAMP4	VAMP4	9702	-0.06	0.076	NO
26	TSNARE1	TSNARE1	TSNARE1	9748	-0.062	0.09	NO
27	GOSR1	GOSR1	GOSR1	9997	-0.068	0.094	NO
28	SNAP47	SNAP47	SNAP47	10319	-0.075	0.095	NO
29	STX12	STX12	STX12	10513	-0.08	0.1	NO
30	SNAP23	SNAP23	SNAP23	10515	-0.08	0.13	NO
31	BET1	BET1	BET1	10712	-0.086	0.14	NO
32	VAMP2	VAMP2	VAMP2	10779	-0.088	0.16	NO
33	STX6	STX6	STX6	10848	-0.089	0.18	NO
34	VAMP7	VAMP7	VAMP7	10894	-0.091	0.2	NO
35	STX17	STX17	STX17	11310	-0.1	0.2	NO
36	STX19	STX19	STX19	12501	-0.14	0.17	NO
37	VAMP1	VAMP1	VAMP1	13743	-0.19	0.15	NO
38	STX11	STX11	STX11	16029	-0.35	0.12	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: KEGG SPLICEOSOME.

Figure S70. 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 SNARE INTERACTIONS IN VESICULAR TRANSPORT

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	LSM2	LSM2	LSM2	1735	0.17	-0.03	YES
2	POLR2I	POLR2I	POLR2I	1859	0.16	0.025	YES
3	TXNL4A	TXNL4A	TXNL4A	2332	0.13	0.05	YES
4	POLR2E	POLR2E	POLR2E	2582	0.12	0.083	YES
5	POLR2C	POLR2C	POLR2C	3033	0.1	0.098	YES
6	SF3B4	SF3B4	SF3B4	3139	0.098	0.13	YES
7	SNRPB	SNRPB	SNRPB	3160	0.097	0.17	YES
8	SNRPD2	SNRPD2	SNRPD2	3334	0.092	0.19	YES
9	POLR2L	POLR2L	POLR2L	3344	0.091	0.23	YES
10	GTF2F1	GTF2F1	GTF2F1	3726	0.08	0.24	YES
11	POLR2J	POLR2J	POLR2J	3782	0.078	0.26	YES
12	SNRPD1	SNRPD1	SNRPD1	3807	0.077	0.29	YES
13	POLR2G	POLR2G	POLR2G	3815	0.077	0.32	YES
14	SNRPG	SNRPG	SNRPG	3832	0.076	0.35	YES
15	SNRPF	SNRPF	SNRPF	3911	0.074	0.38	YES
16	PRPF6	PRPF6	PRPF6	3969	0.072	0.4	YES
17	SNRPE	SNRPE	SNRPE	4708	0.053	0.38	YES
18	SNRPD3	SNRPD3	SNRPD3	4741	0.052	0.4	YES
19	POLR2F	POLR2F	POLR2F	4817	0.05	0.41	YES
20	DDX23	DDX23	DDX23	5296	0.038	0.4	NO
21	SF3B5	SF3B5	SF3B5	5712	0.029	0.39	NO
22	POLR2K	POLR2K	POLR2K	5819	0.026	0.39	NO
23	SF3B2	SF3B2	SF3B2	5981	0.023	0.39	NO
24	POLR2H	POLR2H	POLR2H	6091	0.02	0.4	NO
25	NHP2L1	NHP2L1	NHP2L1	6191	0.018	0.4	NO
26	SNRNP40	SNRNP40	SNRNP40	6330	0.015	0.4	NO
27	SF3B14	SF3B14	SF3B14	6519	0.01	0.39	NO
28	SF3B3	SF3B3	SF3B3	7043	-0.0007	0.36	NO
29	EFTUD2	EFTUD2	EFTUD2	8275	-0.028	0.3	NO
30	GTF2F2	GTF2F2	GTF2F2	8288	-0.028	0.31	NO
31	POLR2A	POLR2A	POLR2A	8701	-0.037	0.3	NO
32	SNRNP200	SNRNP200	SNRNP200	8741	-0.038	0.32	NO
33	NCBP2	NCBP2	NCBP2	8840	-0.041	0.33	NO
34	POLR2D	POLR2D	POLR2D	10029	-0.068	0.29	NO
35	PRPF8	PRPF8	PRPF8	10034	-0.068	0.32	NO
36	SF3B1	SF3B1	SF3B1	10509	-0.08	0.32	NO
37	POLR2B	POLR2B	POLR2B	11370	-0.1	0.31	NO
38	NCBP1	NCBP1	NCBP1	12851	-0.15	0.29	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 SNARE INTERACTIONS IN VESICULAR TRANSPORT.

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, 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 PROTEASOME PATHWAY

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GMNN	GMNN	GMNN	1854	0.16	-0.046	YES
2	PSMB2	PSMB2	PSMB2	2455	0.13	-0.035	YES
3	PSMB6	PSMB6	PSMB6	2650	0.12	-0.005	YES
4	PSMB9	PSMB9	PSMB9	2690	0.12	0.033	YES
5	PSMA5	PSMA5	PSMA5	2955	0.1	0.055	YES
6	PSMB3	PSMB3	PSMB3	3017	0.1	0.088	YES
7	PSMC4	PSMC4	PSMC4	3032	0.1	0.12	YES
8	PSMD9	PSMD9	PSMD9	3077	0.1	0.16	YES
9	UBA52	UBA52	UBA52	3125	0.098	0.19	YES
10	CDT1	CDT1	CDT1	3379	0.09	0.2	YES
11	PSMB8	PSMB8	PSMB8	3462	0.088	0.23	YES
12	PSMC5	PSMC5	PSMC5	3504	0.086	0.26	YES
13	PSMC3	PSMC3	PSMC3	3582	0.084	0.28	YES
14	PSMB10	PSMB10	PSMB10	3616	0.083	0.31	YES
15	PSMD4	PSMD4	PSMD4	3651	0.082	0.34	YES
16	PSMD13	PSMD13	PSMD13	3753	0.078	0.36	YES
17	PSME2	PSME2	PSME2	3912	0.074	0.38	YES
18	PSMF1	PSMF1	PSMF1	4032	0.07	0.4	YES
19	MCM8	MCM8	MCM8	4086	0.069	0.42	YES
20	PSMA4	PSMA4	PSMA4	4525	0.057	0.41	YES
21	PSMB5	PSMB5	PSMB5	4836	0.049	0.41	YES
22	PSMB4	PSMB4	PSMB4	5068	0.044	0.41	YES
23	PSMA6	PSMA6	PSMA6	5242	0.04	0.42	YES
24	PSMC1	PSMC1	PSMC1	5341	0.037	0.43	YES
25	RPS27A	RPS27A	RPS27A	5515	0.033	0.43	YES
26	CDC6	CDC6	CDC6	5772	0.027	0.42	NO
27	PSMD8	PSMD8	PSMD8	6256	0.017	0.4	NO
28	PSMB7	PSMB7	PSMB7	6305	0.016	0.4	NO
29	PSME1	PSME1	PSME1	6498	0.011	0.4	NO
30	PSMA3	PSMA3	PSMA3	6620	0.0083	0.4	NO
31	PSMA7	PSMA7	PSMA7	6781	0.0049	0.39	NO
32	PSMD14	PSMD14	PSMD14	6898	0.0023	0.38	NO
33	PSMD7	PSMD7	PSMD7	7134	-0.0025	0.37	NO
34	PSMA2	PSMA2	PSMA2	7567	-0.012	0.35	NO
35	PSMC6	PSMC6	PSMC6	7607	-0.012	0.35	NO
36	PSMA1	PSMA1	PSMA1	7708	-0.015	0.35	NO
37	PSMB1	PSMB1	PSMB1	8066	-0.023	0.34	NO
38	PSMD1	PSMD1	PSMD1	8110	-0.024	0.35	NO
39	PSMC2	PSMC2	PSMC2	8243	-0.027	0.35	NO
40	PSMD11	PSMD11	PSMD11	8256	-0.027	0.36	NO
41	PSMD12	PSMD12	PSMD12	8298	-0.028	0.36	NO
42	PSMD3	PSMD3	PSMD3	8649	-0.036	0.36	NO
43	PSMD10	PSMD10	PSMD10	10070	-0.069	0.3	NO
44	PSMD6	PSMD6	PSMD6	10163	-0.072	0.32	NO
45	PSME4	PSME4	PSME4	10314	-0.075	0.34	NO
46	PSMD2	PSMD2	PSMD2	10396	-0.078	0.36	NO
47	PSMD5	PSMD5	PSMD5	13390	-0.18	0.26	NO

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

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PROTEASOME 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: REACTOME ER PHAGOSOME PATHWAY

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GGT1	GGT1	GGT1	259	0.44	0.064	YES
2	GPX2	GPX2	GPX2	393	0.38	0.12	YES
3	GSTO2	GSTO2	GSTO2	451	0.36	0.18	YES
4	ANPEP	ANPEP	ANPEP	570	0.32	0.23	YES
5	GSTM2	GSTM2	GSTM2	865	0.26	0.26	YES
6	GSTP1	GSTP1	GSTP1	875	0.26	0.31	YES
7	GSTT1	GSTT1	GSTT1	918	0.26	0.35	YES
8	G6PD	G6PD	G6PD	1095	0.23	0.38	YES
9	GPX4	GPX4	GPX4	1291	0.21	0.41	YES
10	ODC1	ODC1	ODC1	1387	0.2	0.44	YES
11	GSTM4	GSTM4	GSTM4	2166	0.14	0.42	NO
12	GSTZ1	GSTZ1	GSTZ1	2658	0.12	0.41	NO
13	GSTM1	GSTM1	GSTM1	2846	0.11	0.42	NO
14	GSTO1	GSTO1	GSTO1	3106	0.099	0.42	NO
15	GSTA1	GSTA1	GSTA1	3721	0.08	0.4	NO
16	GCLM	GCLM	GCLM	4254	0.065	0.39	NO
17	TXNDC12	TXNDC12	TXNDC12	4736	0.052	0.37	NO
18	GPX1	GPX1	GPX1	4865	0.049	0.37	NO
19	OPLAH	OPLAH	OPLAH	5012	0.045	0.37	NO
20	MGST3	MGST3	MGST3	5393	0.036	0.36	NO
21	GSS	GSS	GSS	5520	0.033	0.35	NO
22	PGD	PGD	PGD	5657	0.03	0.35	NO
23	GSTM3	GSTM3	GSTM3	5879	0.025	0.34	NO
24	GPX7	GPX7	GPX7	6261	0.016	0.33	NO
25	SRM	SRM	SRM	6435	0.012	0.32	NO
26	GSTA2	GSTA2	GSTA2	6785	0.0048	0.3	NO
27	IDH1	IDH1	IDH1	6832	0.0038	0.3	NO
28	MGST2	MGST2	MGST2	6891	0.0024	0.3	NO
29	IDH2	IDH2	IDH2	7165	-0.0034	0.28	NO
30	GSR	GSR	GSR	7408	-0.0082	0.27	NO
31	GSTK1	GSTK1	GSTK1	7483	-0.0099	0.27	NO
32	GCLC	GCLC	GCLC	7970	-0.021	0.24	NO
33	RRM2	RRM2	RRM2	8531	-0.034	0.22	NO
34	MGST1	MGST1	MGST1	8858	-0.041	0.21	NO
35	GSTA4	GSTA4	GSTA4	8970	-0.044	0.21	NO
36	GGCT	GGCT	GGCT	9248	-0.05	0.2	NO
37	RRM1	RRM1	RRM1	9366	-0.052	0.2	NO
38	RRM2B	RRM2B	RRM2B	9557	-0.057	0.2	NO
39	SMS	SMS	SMS	9841	-0.064	0.2	NO
40	GPX3	GPX3	GPX3	9983	-0.067	0.2	NO
41	LAP3	LAP3	LAP3	11427	-0.11	0.14	NO
42	GGT5	GGT5	GGT5	13055	-0.16	0.082	NO
43	GGT7	GGT7	GGT7	13077	-0.16	0.11	NO
44	GSTM5	GSTM5	GSTM5	14091	-0.22	0.091	NO
45	GSTT2	GSTT2	GSTT2	16070	-0.35	0.043	NO
46	GGT6	GGT6	GGT6	16529	-0.4	0.088	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: REACTOME ER PHAGOSOME PATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ER PHAGOSOME 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: REACTOME MEMBRANE TRAFFICKING

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	UGT1A9	UGT1A9	UGT1A9	84	0.59	0.076	YES
2	UGT2B11	UGT2B11	UGT2B11	133	0.52	0.15	YES
3	UGT1A8	UGT1A8	UGT1A8	136	0.52	0.22	YES
4	UGT1A6	UGT1A6	UGT1A6	139	0.52	0.29	YES
5	UGT1A10	UGT1A10	UGT1A10	175	0.49	0.36	YES
6	UGT1A7	UGT1A7	UGT1A7	197	0.48	0.42	YES
7	UGT2B28	UGT2B28	UGT2B28	266	0.44	0.48	YES
8	UGT1A5	UGT1A5	UGT1A5	308	0.41	0.53	YES
9	UGT2B4	UGT2B4	UGT2B4	476	0.35	0.57	YES
10	FTH1	FTH1	FTH1	2132	0.14	0.5	NO
11	UROD	UROD	UROD	2852	0.11	0.47	NO
12	UGT2A1	UGT2A1	UGT2A1	2875	0.11	0.49	NO
13	UGT2B15	UGT2B15	UGT2B15	2928	0.1	0.5	NO
14	PPOX	PPOX	PPOX	2997	0.1	0.51	NO
15	ALAS2	ALAS2	ALAS2	3187	0.096	0.51	NO
16	HMOX1	HMOX1	HMOX1	3417	0.089	0.51	NO
17	HMBS	HMBS	HMBS	3746	0.079	0.5	NO
18	BLVRB	BLVRB	BLVRB	4180	0.066	0.49	NO
19	MMAB	MMAB	MMAB	5364	0.037	0.43	NO
20	COX10	COX10	COX10	5830	0.026	0.41	NO
21	FECH	FECH	FECH	6126	0.02	0.39	NO
22	COX15	COX15	COX15	6463	0.012	0.38	NO
23	GUSB	GUSB	GUSB	6524	0.01	0.37	NO
24	EARS2	EARS2	EARS2	6814	0.0041	0.36	NO
25	HMOX2	HMOX2	HMOX2	7399	-0.008	0.33	NO
26	UROS	UROS	UROS	7495	-0.01	0.32	NO
27	HCCS	HCCS	HCCS	9825	-0.064	0.2	NO
28	BLVRA	BLVRA	BLVRA	10198	-0.073	0.19	NO
29	ALAS1	ALAS1	ALAS1	10313	-0.075	0.2	NO
30	UGT2B7	UGT2B7	UGT2B7	10886	-0.09	0.18	NO
31	ALAD	ALAD	ALAD	11032	-0.094	0.18	NO
32	EPRS	EPRS	EPRS	11413	-0.1	0.18	NO
33	UGT1A3	UGT1A3	UGT1A3	11432	-0.11	0.19	NO
34	UGT1A1	UGT1A1	UGT1A1	11652	-0.11	0.19	NO
35	UGT2A3	UGT2A3	UGT2A3	11820	-0.12	0.2	NO
36	UGT2B10	UGT2B10	UGT2B10	12717	-0.15	0.17	NO
37	UGT1A4	UGT1A4	UGT1A4	12816	-0.15	0.19	NO
38	CPOX	CPOX	CPOX	14566	-0.24	0.12	NO
39	CP	CP	CP	17409	-0.53	0.039	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: REACTOME MEMBRANE TRAFFICKING.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MEMBRANE TRAFFICKING, 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: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT

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	APOBEC3G	APOBEC3G	APOBEC3G	1622	0.18	-0.029	YES
2	PSMB2	PSMB2	PSMB2	2455	0.13	-0.031	YES
3	PSMB6	PSMB6	PSMB6	2650	0.12	-0.0015	YES
4	PSMB9	PSMB9	PSMB9	2690	0.12	0.036	YES
5	PSMA5	PSMA5	PSMA5	2955	0.1	0.058	YES
6	PSMB3	PSMB3	PSMB3	3017	0.1	0.089	YES
7	PSMC4	PSMC4	PSMC4	3032	0.1	0.12	YES
8	PSMD9	PSMD9	PSMD9	3077	0.1	0.16	YES
9	UBA52	UBA52	UBA52	3125	0.098	0.19	YES
10	TCEB2	TCEB2	TCEB2	3316	0.092	0.21	YES
11	PSMB8	PSMB8	PSMB8	3462	0.088	0.23	YES
12	PSMC5	PSMC5	PSMC5	3504	0.086	0.26	YES
13	PSMC3	PSMC3	PSMC3	3582	0.084	0.28	YES
14	PSMB10	PSMB10	PSMB10	3616	0.083	0.31	YES
15	PSMD4	PSMD4	PSMD4	3651	0.082	0.34	YES
16	PSMD13	PSMD13	PSMD13	3753	0.078	0.36	YES
17	PSME2	PSME2	PSME2	3912	0.074	0.37	YES
18	PSMF1	PSMF1	PSMF1	4032	0.07	0.39	YES
19	RBX1	RBX1	RBX1	4482	0.059	0.39	YES
20	PSMA4	PSMA4	PSMA4	4525	0.057	0.4	YES
21	PSMB5	PSMB5	PSMB5	4836	0.049	0.4	YES
22	PSMB4	PSMB4	PSMB4	5068	0.044	0.41	YES
23	PSMA6	PSMA6	PSMA6	5242	0.04	0.41	YES
24	PSMC1	PSMC1	PSMC1	5341	0.037	0.42	YES
25	RPS27A	RPS27A	RPS27A	5515	0.033	0.42	YES
26	TCEB1	TCEB1	TCEB1	6163	0.019	0.39	NO
27	PSMD8	PSMD8	PSMD8	6256	0.017	0.39	NO
28	PSMB7	PSMB7	PSMB7	6305	0.016	0.39	NO
29	PSME1	PSME1	PSME1	6498	0.011	0.39	NO
30	PSMA3	PSMA3	PSMA3	6620	0.0083	0.38	NO
31	PSMA7	PSMA7	PSMA7	6781	0.0049	0.38	NO
32	PSMD14	PSMD14	PSMD14	6898	0.0023	0.37	NO
33	PSMD7	PSMD7	PSMD7	7134	-0.0025	0.36	NO
34	PSMA2	PSMA2	PSMA2	7567	-0.012	0.34	NO
35	PSMC6	PSMC6	PSMC6	7607	-0.012	0.34	NO
36	PSMA1	PSMA1	PSMA1	7708	-0.015	0.34	NO
37	PSMB1	PSMB1	PSMB1	8066	-0.023	0.33	NO
38	PSMD1	PSMD1	PSMD1	8110	-0.024	0.33	NO
39	PSMC2	PSMC2	PSMC2	8243	-0.027	0.34	NO
40	PSMD11	PSMD11	PSMD11	8256	-0.027	0.34	NO
41	PSMD12	PSMD12	PSMD12	8298	-0.028	0.35	NO
42	PSMD3	PSMD3	PSMD3	8649	-0.036	0.35	NO
43	CUL5	CUL5	CUL5	9018	-0.045	0.34	NO
44	PSMD10	PSMD10	PSMD10	10070	-0.069	0.31	NO
45	PSMD6	PSMD6	PSMD6	10163	-0.072	0.33	NO
46	PSME4	PSME4	PSME4	10314	-0.075	0.34	NO
47	PSMD2	PSMD2	PSMD2	10396	-0.078	0.37	NO
48	PSMD5	PSMD5	PSMD5	13390	-0.18	0.26	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: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT, 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 clus5 enriched pathways

Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. 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
KEGG GLYCOLYSIS GLUCONEOGENESIS	58	genes.ES.table	0.7	2.1	0	0.014	0.042	0.31	0.094	0.28	0	0.002
KEGG CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.6	1.6	0.12	0.21	0.95	0.48	0.28	0.35	0.14	0.014
KEGG PENTOSE PHOSPHATE PATHWAY	25	genes.ES.table	0.54	1.6	0.036	0.18	0.94	0.2	0.12	0.18	0.12	0.011
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS	27	genes.ES.table	0.78	1.5	0.042	0.24	0.97	0.52	0.061	0.49	0.17	0.018
KEGG FRUCTOSE AND MANNOSE METABOLISM	33	genes.ES.table	0.68	2.1	0	0.011	0.05	0.15	0.034	0.15	0	0
KEGG FATTY ACID METABOLISM	39	genes.ES.table	0.8	1.9	0	0.033	0.24	0.62	0.14	0.53	0	0.001
KEGG STEROID HORMONE BIOSYNTHESIS	51	genes.ES.table	0.81	1.8	0	0.066	0.64	0.49	0.061	0.46	0.024	0.001
KEGG PURINE METABOLISM	153	genes.ES.table	0.41	1.8	0.002	0.067	0.64	0.2	0.15	0.17	0.024	0.001
KEGG PYRIMIDINE METABOLISM	97	genes.ES.table	0.49	2.2	0	0.011	0.03	0.093	0.068	0.087	0	0.002
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	32	genes.ES.table	0.78	2	0	0.028	0.18	0.53	0.12	0.47	0	0.003

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

Table S41. 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	SULT2A1	SULT2A1	SULT2A1	26	2	0.087	YES
2	APOA5	APOA5	APOA5	29	1.9	0.17	YES
3	APOA1	APOA1	APOA1	83	1.5	0.24	YES
4	FABP1	FABP1	FABP1	121	1.3	0.3	YES
5	ABCB4	ABCB4	ABCB4	142	1.2	0.35	YES
6	CYP7A1	CYP7A1	CYP7A1	144	1.2	0.4	YES
7	CYP1A1	CYP1A1	CYP1A1	154	1.1	0.46	YES
8	APOA2	APOA2	APOA2	155	1.1	0.51	YES
9	HMGCS2	HMGCS2	HMGCS2	175	1	0.55	YES
10	CYP4A11	CYP4A11	CYP4A11	239	0.83	0.59	YES
11	G0S2	G0S2	G0S2	435	0.52	0.6	YES
12	ACSL1	ACSL1	ACSL1	473	0.49	0.62	YES
13	UGT1A9	UGT1A9	UGT1A9	562	0.43	0.64	YES
14	CD36	CD36	CD36	651	0.38	0.65	YES
15	PLIN2	PLIN2	PLIN2	655	0.38	0.66	YES
16	ANGPTL4	ANGPTL4	ANGPTL4	805	0.33	0.67	YES
17	ANKRD1	ANKRD1	ANKRD1	1135	0.26	0.66	YES
18	AGT	AGT	AGT	1136	0.26	0.68	YES
19	ALAS1	ALAS1	ALAS1	1388	0.22	0.67	YES
20	HMGCS1	HMGCS1	HMGCS1	1538	0.2	0.67	YES
21	ABCA1	ABCA1	ABCA1	1641	0.19	0.68	YES
22	ACADM	ACADM	ACADM	1865	0.17	0.67	YES
23	CPT2	CPT2	CPT2	1964	0.16	0.67	YES
24	PPARA	PPARA	PPARA	1990	0.16	0.68	YES
25	ACOX1	ACOX1	ACOX1	2024	0.16	0.68	YES
26	ARNTL	ARNTL	ARNTL	2245	0.15	0.68	NO
27	GRHL1	GRHL1	GRHL1	2312	0.14	0.68	NO
28	TRIB3	TRIB3	TRIB3	2442	0.14	0.68	NO
29	MED8	MED8	MED8	3004	0.11	0.65	NO
30	HMGCR	HMGCR	HMGCR	3112	0.1	0.65	NO
31	FADS1	FADS1	FADS1	3220	0.099	0.65	NO
32	NPAS2	NPAS2	NPAS2	3223	0.099	0.66	NO
33	MED31	MED31	MED31	3416	0.094	0.65	NO
34	CCNC	CCNC	CCNC	3705	0.085	0.64	NO
35	NCOA2	NCOA2	NCOA2	3791	0.083	0.64	NO
36	SREBF2	SREBF2	SREBF2	4155	0.073	0.62	NO
37	PPARGC1B	PPARGC1B	PPARGC1B	4367	0.068	0.61	NO
38	PPARGC1A	PPARGC1A	PPARGC1A	4518	0.064	0.61	NO
39	EP300	EP300	EP300	4615	0.062	0.6	NO
40	PEX11A	PEX11A	PEX11A	4914	0.055	0.59	NO
41	TIAM2	TIAM2	TIAM2	5094	0.052	0.58	NO
42	CPT1A	CPT1A	CPT1A	5540	0.043	0.56	NO
43	SREBF1	SREBF1	SREBF1	5824	0.038	0.55	NO
44	MED23	MED23	MED23	5963	0.036	0.54	NO
45	CDK8	CDK8	CDK8	6256	0.032	0.52	NO
46	ESRRA	ESRRA	ESRRA	6409	0.03	0.52	NO
47	MED29	MED29	MED29	6459	0.029	0.52	NO
48	MED10	MED10	MED10	6523	0.028	0.51	NO
49	ME1	ME1	ME1	6698	0.026	0.5	NO
50	TEAD1	TEAD1	TEAD1	6893	0.024	0.5	NO
51	CDK19	CDK19	CDK19	6987	0.022	0.49	NO
52	RXRA	RXRA	RXRA	7058	0.021	0.49	NO
53	NFYB	NFYB	NFYB	7150	0.02	0.48	NO
54	NCOA3	NCOA3	NCOA3	7449	0.016	0.47	NO
55	MED11	MED11	MED11	7594	0.014	0.46	NO
56	TBL1X	TBL1X	TBL1X	7812	0.012	0.45	NO
57	PPARG	PPARG	PPARG	8013	0.0092	0.44	NO
58	HDAC3	HDAC3	HDAC3	8129	0.008	0.43	NO
59	RORA	RORA	RORA	8204	0.007	0.43	NO
60	MED9	MED9	MED9	8990	-0.0021	0.38	NO
61	GLIPR1	GLIPR1	GLIPR1	9568	-0.0085	0.35	NO
62	FHL2	FHL2	FHL2	9647	-0.0095	0.35	NO
63	MED1	MED1	MED1	9875	-0.012	0.34	NO
64	MED25	MED25	MED25	9885	-0.012	0.34	NO
65	MED6	MED6	MED6	9947	-0.013	0.34	NO
66	YAP1	YAP1	YAP1	10003	-0.013	0.33	NO
67	MED13L	MED13L	MED13L	10117	-0.015	0.33	NO
68	MED26	MED26	MED26	10151	-0.015	0.33	NO
69	NCOR1	NCOR1	NCOR1	10218	-0.016	0.32	NO
70	MED14	MED14	MED14	10229	-0.016	0.32	NO
71	MED4	MED4	MED4	10281	-0.017	0.32	NO
72	MED18	MED18	MED18	10438	-0.019	0.31	NO
73	NCOA6	NCOA6	NCOA6	10527	-0.02	0.31	NO
74	MED15	MED15	MED15	10546	-0.02	0.31	NO
75	CLOCK	CLOCK	CLOCK	10649	-0.021	0.3	NO
76	NFYA	NFYA	NFYA	11046	-0.026	0.28	NO
77	TXNRD1	TXNRD1	TXNRD1	11066	-0.026	0.28	NO
78	MED7	MED7	MED7	11226	-0.029	0.28	NO
79	MED12	MED12	MED12	11230	-0.029	0.28	NO
80	CREBBP	CREBBP	CREBBP	11359	-0.03	0.27	NO
81	MED16	MED16	MED16	12225	-0.042	0.22	NO
82	SLC27A1	SLC27A1	SLC27A1	12327	-0.044	0.22	NO
83	TBL1XR1	TBL1XR1	TBL1XR1	12414	-0.045	0.22	NO
84	MED24	MED24	MED24	12650	-0.049	0.21	NO
85	PRIC285	PRIC285	PRIC285	12882	-0.053	0.2	NO
86	MED19	MED19	MED19	12960	-0.054	0.2	NO
87	CTGF	CTGF	CTGF	12990	-0.054	0.2	NO
88	NCOA1	NCOA1	NCOA1	13130	-0.056	0.19	NO
89	NRF1	NRF1	NRF1	13517	-0.063	0.17	NO
90	WWTR1	WWTR1	WWTR1	13856	-0.07	0.16	NO
91	TEAD2	TEAD2	TEAD2	13980	-0.072	0.15	NO
92	TGS1	TGS1	TGS1	14177	-0.076	0.15	NO
93	TEAD3	TEAD3	TEAD3	14408	-0.082	0.14	NO
94	TEAD4	TEAD4	TEAD4	14578	-0.086	0.13	NO
95	FDFT1	FDFT1	FDFT1	14693	-0.089	0.13	NO
96	MED21	MED21	MED21	15304	-0.11	0.1	NO
97	MED27	MED27	MED27	15307	-0.11	0.1	NO
98	MED30	MED30	MED30	15546	-0.12	0.097	NO
99	MED17	MED17	MED17	15610	-0.12	0.099	NO
100	MED22	MED22	MED22	15655	-0.12	0.1	NO
101	TNFRSF21	TNFRSF21	TNFRSF21	15828	-0.13	0.098	NO
102	MED20	MED20	MED20	16432	-0.16	0.072	NO
103	NR1D1	NR1D1	NR1D1	17067	-0.22	0.047	NO
104	SMARCD3	SMARCD3	SMARCD3	17338	-0.24	0.043	NO

Figure S81. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS.

Figure S82. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table S42. 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	AKR1D1	AKR1D1	AKR1D1	14	2.1	0.023	YES
2	SLC10A1	SLC10A1	SLC10A1	20	2	0.046	YES
3	SULT2A1	SULT2A1	SULT2A1	26	2	0.068	YES
4	CYP8B1	CYP8B1	CYP8B1	28	1.9	0.09	YES
5	APOA5	APOA5	APOA5	29	1.9	0.11	YES
6	MTTP	MTTP	MTTP	47	1.8	0.13	YES
7	ABCB11	ABCB11	ABCB11	48	1.8	0.15	YES
8	SRD5A2	SRD5A2	SRD5A2	57	1.7	0.17	YES
9	APOC3	APOC3	APOC3	61	1.7	0.19	YES
10	APOA1	APOA1	APOA1	83	1.5	0.2	YES
11	LPA	LPA	LPA	100	1.4	0.22	YES
12	FABP1	FABP1	FABP1	121	1.3	0.23	YES
13	APOC2	APOC2	APOC2	123	1.3	0.25	YES
14	ENPP7	ENPP7	ENPP7	126	1.3	0.26	YES
15	ABCG8	ABCG8	ABCG8	134	1.2	0.28	YES
16	PLA2G2A	PLA2G2A	PLA2G2A	135	1.2	0.29	YES
17	ABCB4	ABCB4	ABCB4	142	1.2	0.3	YES
18	CYP7A1	CYP7A1	CYP7A1	144	1.2	0.32	YES
19	ABCG5	ABCG5	ABCG5	146	1.2	0.33	YES
20	CYP1A1	CYP1A1	CYP1A1	154	1.1	0.34	YES
21	APOA2	APOA2	APOA2	155	1.1	0.36	YES
22	SLC27A5	SLC27A5	SLC27A5	156	1.1	0.37	YES
23	SLCO1B1	SLCO1B1	SLCO1B1	174	1	0.38	YES
24	HMGCS2	HMGCS2	HMGCS2	175	1	0.39	YES
25	AKR1C4	AKR1C4	AKR1C4	178	1	0.4	YES
26	CYP39A1	CYP39A1	CYP39A1	188	1	0.42	YES
27	GBA3	GBA3	GBA3	215	0.92	0.42	YES
28	ACOX2	ACOX2	ACOX2	226	0.87	0.43	YES
29	CYP4A11	CYP4A11	CYP4A11	239	0.83	0.44	YES
30	NEU4	NEU4	NEU4	241	0.83	0.45	YES
31	PLIN1	PLIN1	PLIN1	242	0.83	0.46	YES
32	GPD1	GPD1	GPD1	273	0.77	0.47	YES
33	PIK3C2G	PIK3C2G	PIK3C2G	283	0.74	0.48	YES
34	ACADL	ACADL	ACADL	288	0.72	0.48	YES
35	BDH1	BDH1	BDH1	330	0.66	0.49	YES
36	SLCO1B3	SLCO1B3	SLCO1B3	335	0.64	0.5	YES
37	GPAM	GPAM	GPAM	356	0.61	0.5	YES
38	CYP17A1	CYP17A1	CYP17A1	360	0.61	0.51	YES
39	DGAT2	DGAT2	DGAT2	386	0.57	0.52	YES
40	ALB	ALB	ALB	388	0.57	0.52	YES
41	APOB	APOB	APOB	410	0.54	0.53	YES
42	G0S2	G0S2	G0S2	435	0.52	0.53	YES
43	PLA2G5	PLA2G5	PLA2G5	454	0.5	0.54	YES
44	ACSL1	ACSL1	ACSL1	473	0.49	0.54	YES
45	HSD11B1	HSD11B1	HSD11B1	485	0.48	0.55	YES
46	APOE	APOE	APOE	501	0.47	0.55	YES
47	ELOVL2	ELOVL2	ELOVL2	502	0.47	0.56	YES
48	SLC27A2	SLC27A2	SLC27A2	507	0.46	0.56	YES
49	CYP11A1	CYP11A1	CYP11A1	536	0.45	0.56	YES
50	UGT1A9	UGT1A9	UGT1A9	562	0.43	0.57	YES
51	BAAT	BAAT	BAAT	568	0.42	0.57	YES
52	CYP27A1	CYP27A1	CYP27A1	581	0.42	0.58	YES
53	SLCO1A2	SLCO1A2	SLCO1A2	635	0.39	0.58	YES
54	CD36	CD36	CD36	651	0.38	0.58	YES
55	PLIN2	PLIN2	PLIN2	655	0.38	0.58	YES
56	LCAT	LCAT	LCAT	681	0.37	0.59	YES
57	ANGPTL4	ANGPTL4	ANGPTL4	805	0.33	0.58	YES
58	CETP	CETP	CETP	833	0.32	0.59	YES
59	ACSL6	ACSL6	ACSL6	864	0.31	0.59	YES
60	GC	GC	GC	867	0.31	0.59	YES
61	ARSF	ARSF	ARSF	940	0.29	0.59	YES
62	ELOVL6	ELOVL6	ELOVL6	972	0.28	0.59	YES
63	CHPT1	CHPT1	CHPT1	1003	0.28	0.59	YES
64	LIPC	LIPC	LIPC	1012	0.28	0.6	YES
65	SLC25A20	SLC25A20	SLC25A20	1026	0.27	0.6	YES
66	ANKRD1	ANKRD1	ANKRD1	1135	0.26	0.6	YES
67	AGT	AGT	AGT	1136	0.26	0.6	YES
68	MCEE	MCEE	MCEE	1162	0.25	0.6	YES
69	ACAT1	ACAT1	ACAT1	1163	0.25	0.6	YES
70	BCMO1	BCMO1	BCMO1	1193	0.25	0.6	YES
71	A2M	A2M	A2M	1205	0.24	0.61	YES
72	ETNK2	ETNK2	ETNK2	1230	0.24	0.61	YES
73	PHYH	PHYH	PHYH	1233	0.24	0.61	YES
74	ACSL5	ACSL5	ACSL5	1246	0.24	0.61	YES
75	SCARB1	SCARB1	SCARB1	1368	0.22	0.61	YES
76	ELOVL7	ELOVL7	ELOVL7	1369	0.22	0.61	YES
77	ALAS1	ALAS1	ALAS1	1388	0.22	0.61	YES
78	STARD5	STARD5	STARD5	1410	0.22	0.61	YES
79	FABP4	FABP4	FABP4	1465	0.21	0.61	YES
80	ARSJ	ARSJ	ARSJ	1517	0.2	0.61	YES
81	HMGCS1	HMGCS1	HMGCS1	1538	0.2	0.61	YES
82	SC5DL	SC5DL	SC5DL	1603	0.19	0.61	YES
83	FASN	FASN	FASN	1623	0.19	0.61	YES
84	ABCA1	ABCA1	ABCA1	1641	0.19	0.61	YES
85	TM7SF2	TM7SF2	TM7SF2	1671	0.19	0.62	YES
86	ACAA1	ACAA1	ACAA1	1754	0.18	0.61	YES
87	HMGCL	HMGCL	HMGCL	1756	0.18	0.61	YES
88	PEMT	PEMT	PEMT	1764	0.18	0.62	YES
89	DHCR24	DHCR24	DHCR24	1774	0.18	0.62	YES
90	ACACB	ACACB	ACACB	1791	0.18	0.62	YES
91	SCP2	SCP2	SCP2	1818	0.18	0.62	YES
92	STARD4	STARD4	STARD4	1858	0.17	0.62	YES
93	ACADM	ACADM	ACADM	1865	0.17	0.62	YES
94	ARSE	ARSE	ARSE	1902	0.17	0.62	YES
95	PIK3R1	PIK3R1	PIK3R1	1936	0.17	0.62	YES
96	CPT2	CPT2	CPT2	1964	0.16	0.62	YES
97	PPARA	PPARA	PPARA	1990	0.16	0.62	YES
98	HSD17B3	HSD17B3	HSD17B3	2004	0.16	0.62	YES
99	ACOX1	ACOX1	ACOX1	2024	0.16	0.62	YES
100	PLD1	PLD1	PLD1	2026	0.16	0.62	YES
101	SAR1B	SAR1B	SAR1B	2045	0.16	0.62	YES
102	PRKAA2	PRKAA2	PRKAA2	2091	0.16	0.62	NO
103	ECHS1	ECHS1	ECHS1	2114	0.15	0.62	NO
104	ELOVL3	ELOVL3	ELOVL3	2155	0.15	0.62	NO
105	ARNTL	ARNTL	ARNTL	2245	0.15	0.62	NO
106	PPAP2B	PPAP2B	PPAP2B	2254	0.14	0.62	NO
107	SDC1	SDC1	SDC1	2294	0.14	0.62	NO
108	P4HB	P4HB	P4HB	2306	0.14	0.62	NO
109	GRHL1	GRHL1	GRHL1	2312	0.14	0.62	NO
110	PHOSPHO1	PHOSPHO1	PHOSPHO1	2365	0.14	0.62	NO
111	ASAH2	ASAH2	ASAH2	2389	0.14	0.62	NO
112	TRIB3	TRIB3	TRIB3	2442	0.14	0.62	NO
113	MUT	MUT	MUT	2466	0.13	0.62	NO
114	HSD17B4	HSD17B4	HSD17B4	2509	0.13	0.62	NO
115	ACADS	ACADS	ACADS	2519	0.13	0.62	NO
116	SRD5A1	SRD5A1	SRD5A1	2538	0.13	0.62	NO
117	AMACR	AMACR	AMACR	2687	0.12	0.62	NO
118	GAL3ST1	GAL3ST1	GAL3ST1	2752	0.12	0.61	NO
119	PIK3R5	PIK3R5	PIK3R5	2819	0.12	0.61	NO
120	ELOVL5	ELOVL5	ELOVL5	2884	0.11	0.61	NO
121	EBP	EBP	EBP	2958	0.11	0.61	NO
122	COL4A3BP	COL4A3BP	COL4A3BP	2984	0.11	0.6	NO
123	PLA2G2D	PLA2G2D	PLA2G2D	2997	0.11	0.61	NO
124	MED8	MED8	MED8	3004	0.11	0.61	NO
125	HMGCR	HMGCR	HMGCR	3112	0.1	0.6	NO
126	IDI1	IDI1	IDI1	3124	0.1	0.6	NO
127	HEXB	HEXB	HEXB	3184	0.1	0.6	NO
128	HSD17B1	HSD17B1	HSD17B1	3185	0.1	0.6	NO
129	SYNJ1	SYNJ1	SYNJ1	3186	0.1	0.6	NO
130	DHCR7	DHCR7	DHCR7	3197	0.1	0.6	NO
131	FADS1	FADS1	FADS1	3220	0.099	0.6	NO
132	NPAS2	NPAS2	NPAS2	3223	0.099	0.6	NO
133	IDH1	IDH1	IDH1	3226	0.099	0.6	NO
134	PRKACB	PRKACB	PRKACB	3272	0.097	0.6	NO
135	ARSK	ARSK	ARSK	3278	0.097	0.6	NO
136	CYP27B1	CYP27B1	CYP27B1	3328	0.096	0.6	NO
137	MED31	MED31	MED31	3416	0.094	0.6	NO
138	ACADVL	ACADVL	ACADVL	3459	0.092	0.6	NO
139	MTMR4	MTMR4	MTMR4	3469	0.092	0.6	NO
140	PI4K2B	PI4K2B	PI4K2B	3480	0.092	0.6	NO
141	LBR	LBR	LBR	3501	0.091	0.6	NO
142	ARSB	ARSB	ARSB	3555	0.09	0.6	NO
143	CROT	CROT	CROT	3645	0.087	0.59	NO
144	PPAP2A	PPAP2A	PPAP2A	3676	0.086	0.59	NO
145	CRLS1	CRLS1	CRLS1	3683	0.086	0.59	NO
146	CCNC	CCNC	CCNC	3705	0.085	0.59	NO
147	ELOVL1	ELOVL1	ELOVL1	3744	0.084	0.59	NO
148	NCOA2	NCOA2	NCOA2	3791	0.083	0.59	NO
149	PCYT2	PCYT2	PCYT2	3898	0.079	0.58	NO
150	PCYT1A	PCYT1A	PCYT1A	3958	0.078	0.58	NO
151	ACSL3	ACSL3	ACSL3	4014	0.076	0.58	NO
152	HADHB	HADHB	HADHB	4022	0.076	0.58	NO
153	FAR2	FAR2	FAR2	4025	0.076	0.58	NO
154	SLC25A17	SLC25A17	SLC25A17	4076	0.075	0.58	NO
155	EPT1	EPT1	EPT1	4092	0.074	0.58	NO
156	SYNJ2	SYNJ2	SYNJ2	4142	0.073	0.58	NO
157	SREBF2	SREBF2	SREBF2	4155	0.073	0.58	NO
158	CYP2R1	CYP2R1	CYP2R1	4173	0.072	0.58	NO
159	OSBP	OSBP	OSBP	4176	0.072	0.58	NO
160	ARSG	ARSG	ARSG	4262	0.07	0.57	NO
161	SMPD1	SMPD1	SMPD1	4297	0.069	0.57	NO
162	GALC	GALC	GALC	4313	0.069	0.57	NO
163	CRAT	CRAT	CRAT	4335	0.068	0.57	NO
164	PPARGC1B	PPARGC1B	PPARGC1B	4367	0.068	0.57	NO
165	MVK	MVK	MVK	4379	0.067	0.57	NO
166	PI4K2A	PI4K2A	PI4K2A	4405	0.067	0.57	NO
167	AGPAT3	AGPAT3	AGPAT3	4456	0.065	0.57	NO
168	LSS	LSS	LSS	4469	0.065	0.57	NO
169	PPARGC1A	PPARGC1A	PPARGC1A	4518	0.064	0.57	NO
170	AGPS	AGPS	AGPS	4524	0.064	0.57	NO
171	MBOAT7	MBOAT7	MBOAT7	4529	0.064	0.57	NO
172	LPIN2	LPIN2	LPIN2	4590	0.062	0.56	NO
173	EP300	EP300	EP300	4615	0.062	0.56	NO
174	LDLR	LDLR	LDLR	4649	0.061	0.56	NO
175	PPM1L	PPM1L	PPM1L	4653	0.061	0.56	NO
176	LPCAT3	LPCAT3	LPCAT3	4672	0.06	0.56	NO
177	CYP51A1	CYP51A1	CYP51A1	4674	0.06	0.56	NO
178	UGCG	UGCG	UGCG	4790	0.058	0.56	NO
179	SPTLC2	SPTLC2	SPTLC2	4893	0.056	0.55	NO
180	HADH	HADH	HADH	4896	0.056	0.55	NO
181	PEX11A	PEX11A	PEX11A	4914	0.055	0.55	NO
182	PLD3	PLD3	PLD3	4944	0.055	0.55	NO
183	PRKAG2	PRKAG2	PRKAG2	5014	0.053	0.55	NO
184	SPHK2	SPHK2	SPHK2	5020	0.053	0.55	NO
185	PIK3C2B	PIK3C2B	PIK3C2B	5083	0.052	0.55	NO
186	TIAM2	TIAM2	TIAM2	5094	0.052	0.55	NO
187	ARSI	ARSI	ARSI	5102	0.052	0.55	NO
188	GK	GK	GK	5111	0.052	0.55	NO
189	HSD17B12	HSD17B12	HSD17B12	5120	0.051	0.55	NO
190	HADHA	HADHA	HADHA	5144	0.051	0.55	NO
191	PITPNB	PITPNB	PITPNB	5160	0.05	0.55	NO
192	GPD1L	GPD1L	GPD1L	5179	0.05	0.55	NO
193	SGPP1	SGPP1	SGPP1	5237	0.049	0.54	NO
194	HSPG2	HSPG2	HSPG2	5272	0.048	0.54	NO
195	PCCB	PCCB	PCCB	5362	0.047	0.54	NO
196	LPGAT1	LPGAT1	LPGAT1	5396	0.046	0.54	NO
197	PIK3R3	PIK3R3	PIK3R3	5445	0.045	0.53	NO
198	PRKACA	PRKACA	PRKACA	5473	0.044	0.53	NO
199	HSD3B7	HSD3B7	HSD3B7	5482	0.044	0.53	NO
200	CPT1A	CPT1A	CPT1A	5540	0.043	0.53	NO
201	AGPAT9	AGPAT9	AGPAT9	5549	0.043	0.53	NO
202	SGMS2	SGMS2	SGMS2	5559	0.043	0.53	NO
203	PI4KA	PI4KA	PI4KA	5601	0.042	0.53	NO
204	PRKAB2	PRKAB2	PRKAB2	5699	0.04	0.52	NO
205	CEPT1	CEPT1	CEPT1	5743	0.04	0.52	NO
206	ARSA	ARSA	ARSA	5814	0.038	0.52	NO
207	PSAP	PSAP	PSAP	5822	0.038	0.52	NO
208	SREBF1	SREBF1	SREBF1	5824	0.038	0.52	NO
209	RDH11	RDH11	RDH11	5839	0.038	0.52	NO
210	GM2A	GM2A	GM2A	5894	0.037	0.51	NO
211	GLA	GLA	GLA	5908	0.037	0.51	NO
212	MED23	MED23	MED23	5963	0.036	0.51	NO
213	ACER3	ACER3	ACER3	5964	0.036	0.51	NO
214	PNPLA8	PNPLA8	PNPLA8	6009	0.036	0.51	NO
215	LCLAT1	LCLAT1	LCLAT1	6052	0.035	0.51	NO
216	HACL1	HACL1	HACL1	6076	0.035	0.51	NO
217	SQLE	SQLE	SQLE	6096	0.034	0.51	NO
218	PIK3CB	PIK3CB	PIK3CB	6219	0.033	0.5	NO
219	PIK3CA	PIK3CA	PIK3CA	6229	0.033	0.5	NO
220	CDK8	CDK8	CDK8	6256	0.032	0.5	NO
221	SLC44A2	SLC44A2	SLC44A2	6320	0.031	0.5	NO
222	PRKD1	PRKD1	PRKD1	6391	0.03	0.49	NO
223	ESRRA	ESRRA	ESRRA	6409	0.03	0.49	NO
224	MED29	MED29	MED29	6459	0.029	0.49	NO
225	PIK3R2	PIK3R2	PIK3R2	6497	0.029	0.49	NO
226	MED10	MED10	MED10	6523	0.028	0.49	NO
227	SUMF2	SUMF2	SUMF2	6630	0.027	0.48	NO
228	PLA2G16	PLA2G16	PLA2G16	6632	0.027	0.48	NO
229	ME1	ME1	ME1	6698	0.026	0.48	NO
230	MGLL	MGLL	MGLL	6699	0.026	0.48	NO
231	PCCA	PCCA	PCCA	6736	0.026	0.48	NO
232	TEAD1	TEAD1	TEAD1	6893	0.024	0.47	NO
233	LPCAT1	LPCAT1	LPCAT1	6930	0.023	0.46	NO
234	OCRL	OCRL	OCRL	6936	0.023	0.46	NO
235	MTM1	MTM1	MTM1	6942	0.023	0.46	NO
236	CDK19	CDK19	CDK19	6987	0.022	0.46	NO
237	PIK3C2A	PIK3C2A	PIK3C2A	7002	0.022	0.46	NO
238	MTMR7	MTMR7	MTMR7	7005	0.022	0.46	NO
239	AKR1B1	AKR1B1	AKR1B1	7026	0.022	0.46	NO
240	GLB1	GLB1	GLB1	7049	0.022	0.46	NO
241	RXRA	RXRA	RXRA	7058	0.021	0.46	NO
242	ARF1	ARF1	ARF1	7072	0.021	0.46	NO
243	CH25H	CH25H	CH25H	7086	0.021	0.46	NO
244	NEU1	NEU1	NEU1	7130	0.02	0.46	NO
245	NFYB	NFYB	NFYB	7150	0.02	0.46	NO
246	ACLY	ACLY	ACLY	7156	0.02	0.46	NO
247	ACACA	ACACA	ACACA	7181	0.02	0.46	NO
248	SLC44A3	SLC44A3	SLC44A3	7214	0.019	0.45	NO
249	PPP1CA	PPP1CA	PPP1CA	7221	0.019	0.45	NO
250	PIK3CG	PIK3CG	PIK3CG	7376	0.017	0.44	NO
251	LPIN1	LPIN1	LPIN1	7412	0.017	0.44	NO
252	IDI2	IDI2	IDI2	7425	0.016	0.44	NO
253	ABCC3	ABCC3	ABCC3	7426	0.016	0.44	NO
254	SGMS1	SGMS1	SGMS1	7440	0.016	0.44	NO
255	NCOA3	NCOA3	NCOA3	7449	0.016	0.44	NO
256	VAPB	VAPB	VAPB	7562	0.014	0.44	NO
257	MED11	MED11	MED11	7594	0.014	0.43	NO
258	SLC25A1	SLC25A1	SLC25A1	7615	0.014	0.43	NO
259	VAC14	VAC14	VAC14	7649	0.013	0.43	NO
260	ACER2	ACER2	ACER2	7718	0.012	0.43	NO
261	GBA	GBA	GBA	7721	0.012	0.43	NO
262	NSDHL	NSDHL	NSDHL	7741	0.012	0.43	NO
263	PLTP	PLTP	PLTP	7779	0.012	0.42	NO
264	TBL1X	TBL1X	TBL1X	7812	0.012	0.42	NO
265	ACOX3	ACOX3	ACOX3	7887	0.011	0.42	NO
266	ETNK1	ETNK1	ETNK1	7943	0.01	0.42	NO
267	PPARG	PPARG	PPARG	8013	0.0092	0.41	NO
268	PLA2G4C	PLA2G4C	PLA2G4C	8042	0.0089	0.41	NO
269	HEXA	HEXA	HEXA	8064	0.0087	0.41	NO
270	CPT1B	CPT1B	CPT1B	8122	0.0081	0.41	NO
271	HDAC3	HDAC3	HDAC3	8129	0.008	0.41	NO
272	CYP46A1	CYP46A1	CYP46A1	8142	0.0079	0.41	NO
273	LGMN	LGMN	LGMN	8182	0.0073	0.4	NO
274	MTMR6	MTMR6	MTMR6	8202	0.007	0.4	NO
275	RORA	RORA	RORA	8204	0.007	0.4	NO
276	PPP1CC	PPP1CC	PPP1CC	8253	0.0064	0.4	NO
277	PIKFYVE	PIKFYVE	PIKFYVE	8281	0.0061	0.4	NO
278	GNPAT	GNPAT	GNPAT	8305	0.0058	0.4	NO
279	CDS1	CDS1	CDS1	8313	0.0056	0.4	NO
280	SACM1L	SACM1L	SACM1L	8343	0.0052	0.4	NO
281	HSD17B7	HSD17B7	HSD17B7	8366	0.005	0.39	NO
282	CTSA	CTSA	CTSA	8440	0.0041	0.39	NO
283	FAR1	FAR1	FAR1	8459	0.0039	0.39	NO
284	CYP7B1	CYP7B1	CYP7B1	8523	0.0032	0.39	NO
285	ABHD5	ABHD5	ABHD5	8569	0.0026	0.38	NO
286	AGPAT5	AGPAT5	AGPAT5	8739	0.00072	0.37	NO
287	PMVK	PMVK	PMVK	8755	0.00058	0.37	NO
288	NCOR2	NCOR2	NCOR2	8825	-0.00015	0.37	NO
289	SGPL1	SGPL1	SGPL1	8917	-0.0012	0.36	NO
290	MED9	MED9	MED9	8990	-0.0021	0.36	NO
291	KDSR	KDSR	KDSR	9005	-0.0022	0.36	NO
292	PTEN	PTEN	PTEN	9083	-0.003	0.36	NO
293	CGA	CGA	CGA	9155	-0.0039	0.35	NO
294	DEGS1	DEGS1	DEGS1	9169	-0.0041	0.35	NO
295	FDPS	FDPS	FDPS	9234	-0.0049	0.35	NO
296	MVD	MVD	MVD	9285	-0.0053	0.34	NO
297	CDS2	CDS2	CDS2	9343	-0.006	0.34	NO
298	CERK	CERK	CERK	9352	-0.0061	0.34	NO
299	SUMF1	SUMF1	SUMF1	9386	-0.0064	0.34	NO
300	GLIPR1	GLIPR1	GLIPR1	9568	-0.0085	0.33	NO
301	MTMR1	MTMR1	MTMR1	9600	-0.009	0.33	NO
302	ARF3	ARF3	ARF3	9639	-0.0095	0.32	NO
303	FHL2	FHL2	FHL2	9647	-0.0095	0.32	NO
304	MED1	MED1	MED1	9875	-0.012	0.31	NO
305	MED25	MED25	MED25	9885	-0.012	0.31	NO
306	GGPS1	GGPS1	GGPS1	9902	-0.012	0.31	NO
307	MED6	MED6	MED6	9947	-0.013	0.31	NO
308	PIK3C3	PIK3C3	PIK3C3	9997	-0.013	0.3	NO
309	YAP1	YAP1	YAP1	10003	-0.013	0.3	NO
310	PNPLA3	PNPLA3	PNPLA3	10019	-0.014	0.3	NO
311	SMPD4	SMPD4	SMPD4	10046	-0.014	0.3	NO
312	AGPAT2	AGPAT2	AGPAT2	10079	-0.014	0.3	NO
313	MED13L	MED13L	MED13L	10117	-0.015	0.3	NO
314	MED26	MED26	MED26	10151	-0.015	0.3	NO
315	NCOR1	NCOR1	NCOR1	10218	-0.016	0.29	NO
316	MED14	MED14	MED14	10229	-0.016	0.29	NO
317	MED4	MED4	MED4	10281	-0.017	0.29	NO
318	MTMR3	MTMR3	MTMR3	10350	-0.018	0.29	NO
319	CYP21A2	CYP21A2	CYP21A2	10362	-0.018	0.29	NO
320	MED18	MED18	MED18	10438	-0.019	0.28	NO
321	NCOA6	NCOA6	NCOA6	10527	-0.02	0.28	NO
322	DECR1	DECR1	DECR1	10540	-0.02	0.28	NO
323	MED15	MED15	MED15	10546	-0.02	0.28	NO
324	PLA2G12A	PLA2G12A	PLA2G12A	10633	-0.021	0.27	NO
325	CLOCK	CLOCK	CLOCK	10649	-0.021	0.27	NO
326	MBOAT2	MBOAT2	MBOAT2	10682	-0.022	0.27	NO
327	MTMR14	MTMR14	MTMR14	10767	-0.023	0.27	NO
328	PPP1CB	PPP1CB	PPP1CB	10797	-0.023	0.26	NO
329	AMN	AMN	AMN	10830	-0.023	0.26	NO
330	LDLRAP1	LDLRAP1	LDLRAP1	10895	-0.024	0.26	NO
331	PIK3R4	PIK3R4	PIK3R4	10926	-0.025	0.26	NO
332	AGPAT1	AGPAT1	AGPAT1	10928	-0.025	0.26	NO
333	FADS2	FADS2	FADS2	10935	-0.025	0.26	NO
334	PIP4K2B	PIP4K2B	PIP4K2B	11012	-0.026	0.26	NO
335	NFYA	NFYA	NFYA	11046	-0.026	0.25	NO
336	TXNRD1	TXNRD1	TXNRD1	11066	-0.026	0.25	NO
337	LPIN3	LPIN3	LPIN3	11196	-0.028	0.25	NO
338	PGS1	PGS1	PGS1	11202	-0.028	0.25	NO
339	MED7	MED7	MED7	11226	-0.029	0.24	NO
340	MED12	MED12	MED12	11230	-0.029	0.24	NO
341	FABP6	FABP6	FABP6	11291	-0.03	0.24	NO
342	CDIPT	CDIPT	CDIPT	11308	-0.03	0.24	NO
343	CREBBP	CREBBP	CREBBP	11359	-0.03	0.24	NO
344	GBA2	GBA2	GBA2	11442	-0.032	0.24	NO
345	CHKA	CHKA	CHKA	11654	-0.034	0.22	NO
346	SLC44A1	SLC44A1	SLC44A1	11674	-0.034	0.22	NO
347	VAPA	VAPA	VAPA	11697	-0.035	0.22	NO
348	ABCD1	ABCD1	ABCD1	11742	-0.035	0.22	NO
349	PTDSS1	PTDSS1	PTDSS1	11751	-0.036	0.22	NO
350	PLA2G3	PLA2G3	PLA2G3	11892	-0.037	0.21	NO
351	SIN3B	SIN3B	SIN3B	11945	-0.038	0.21	NO
352	ACOT8	ACOT8	ACOT8	11979	-0.039	0.21	NO
353	PLA2G6	PLA2G6	PLA2G6	12065	-0.04	0.2	NO
354	AGPAT6	AGPAT6	AGPAT6	12072	-0.04	0.2	NO
355	LRP2	LRP2	LRP2	12213	-0.042	0.2	NO
356	MED16	MED16	MED16	12225	-0.042	0.2	NO
357	NEU3	NEU3	NEU3	12235	-0.042	0.2	NO
358	SLC27A1	SLC27A1	SLC27A1	12327	-0.044	0.19	NO
359	TBL1XR1	TBL1XR1	TBL1XR1	12414	-0.045	0.19	NO
360	TECR	TECR	TECR	12488	-0.046	0.18	NO
361	GPAT2	GPAT2	GPAT2	12564	-0.047	0.18	NO
362	FIG4	FIG4	FIG4	12570	-0.047	0.18	NO
363	MED24	MED24	MED24	12650	-0.049	0.18	NO
364	BMP1	BMP1	BMP1	12703	-0.05	0.17	NO
365	INPPL1	INPPL1	INPPL1	12829	-0.052	0.17	NO
366	SLC44A5	SLC44A5	SLC44A5	12850	-0.052	0.17	NO
367	PLA2G4A	PLA2G4A	PLA2G4A	12853	-0.052	0.17	NO
368	PRIC285	PRIC285	PRIC285	12882	-0.053	0.17	NO
369	PLD2	PLD2	PLD2	12907	-0.053	0.16	NO
370	MED19	MED19	MED19	12960	-0.054	0.16	NO
371	CTGF	CTGF	CTGF	12990	-0.054	0.16	NO
372	NCOA1	NCOA1	NCOA1	13130	-0.056	0.16	NO
373	SMPD3	SMPD3	SMPD3	13138	-0.056	0.16	NO
374	POMC	POMC	POMC	13158	-0.057	0.16	NO
375	MBOAT1	MBOAT1	MBOAT1	13173	-0.057	0.16	NO
376	SPTLC1	SPTLC1	SPTLC1	13317	-0.059	0.15	NO
377	ACSL4	ACSL4	ACSL4	13367	-0.06	0.14	NO
378	PLA2G2F	PLA2G2F	PLA2G2F	13499	-0.063	0.14	NO
379	NRF1	NRF1	NRF1	13517	-0.063	0.14	NO
380	DGAT1	DGAT1	DGAT1	13525	-0.063	0.14	NO
381	SIN3A	SIN3A	SIN3A	13572	-0.064	0.14	NO
382	CYP19A1	CYP19A1	CYP19A1	13584	-0.064	0.14	NO
383	PLA2G1B	PLA2G1B	PLA2G1B	13703	-0.066	0.13	NO
384	PPAP2C	PPAP2C	PPAP2C	13738	-0.067	0.13	NO
385	INPP4B	INPP4B	INPP4B	13827	-0.069	0.12	NO
386	CSNK1G2	CSNK1G2	CSNK1G2	13842	-0.07	0.12	NO
387	SMPD2	SMPD2	SMPD2	13843	-0.07	0.13	NO
388	WWTR1	WWTR1	WWTR1	13856	-0.07	0.13	NO
389	AGPAT4	AGPAT4	AGPAT4	13864	-0.07	0.13	NO
390	TEAD2	TEAD2	TEAD2	13980	-0.072	0.12	NO
391	INPP5J	INPP5J	INPP5J	13987	-0.072	0.12	NO
392	PIP4K2A	PIP4K2A	PIP4K2A	14116	-0.075	0.12	NO
393	TGS1	TGS1	TGS1	14177	-0.076	0.11	NO
394	LPCAT2	LPCAT2	LPCAT2	14205	-0.077	0.11	NO
395	PIP5K1C	PIP5K1C	PIP5K1C	14248	-0.078	0.11	NO
396	PLD6	PLD6	PLD6	14272	-0.078	0.11	NO
397	PCYT1B	PCYT1B	PCYT1B	14331	-0.08	0.11	NO
398	INPP5K	INPP5K	INPP5K	14367	-0.081	0.11	NO
399	LRAT	LRAT	LRAT	14393	-0.081	0.11	NO
400	TEAD3	TEAD3	TEAD3	14408	-0.082	0.11	NO
401	TAZ	TAZ	TAZ	14455	-0.083	0.1	NO
402	PI4KB	PI4KB	PI4KB	14458	-0.083	0.1	NO
403	INPP5E	INPP5E	INPP5E	14557	-0.085	0.1	NO
404	TEAD4	TEAD4	TEAD4	14578	-0.086	0.1	NO
405	FDFT1	FDFT1	FDFT1	14693	-0.089	0.095	NO
406	ASAH1	ASAH1	ASAH1	14714	-0.09	0.095	NO
407	STS	STS	STS	14733	-0.09	0.095	NO
408	PIK3CD	PIK3CD	PIK3CD	14903	-0.095	0.087	NO
409	GPD2	GPD2	GPD2	14977	-0.097	0.084	NO
410	CHKB	CHKB	CHKB	15028	-0.098	0.082	NO
411	LHB	LHB	LHB	15223	-0.1	0.072	NO
412	MED21	MED21	MED21	15304	-0.11	0.069	NO
413	MED27	MED27	MED27	15307	-0.11	0.07	NO
414	PNPLA2	PNPLA2	PNPLA2	15336	-0.11	0.07	NO
415	ACHE	ACHE	ACHE	15521	-0.12	0.061	NO
416	MED30	MED30	MED30	15546	-0.12	0.06	NO
417	SRD5A3	SRD5A3	SRD5A3	15576	-0.12	0.06	NO
418	MED17	MED17	MED17	15610	-0.12	0.06	NO
419	MED22	MED22	MED22	15655	-0.12	0.059	NO
420	PLD4	PLD4	PLD4	15678	-0.12	0.059	NO
421	PTDSS2	PTDSS2	PTDSS2	15687	-0.12	0.06	NO
422	TNFRSF21	TNFRSF21	TNFRSF21	15828	-0.13	0.053	NO
423	LPL	LPL	LPL	15982	-0.13	0.046	NO
424	GPCPD1	GPCPD1	GPCPD1	16178	-0.14	0.037	NO
425	PLBD1	PLBD1	PLBD1	16197	-0.15	0.037	NO
426	CYP24A1	CYP24A1	CYP24A1	16240	-0.15	0.037	NO
427	LPCAT4	LPCAT4	LPCAT4	16247	-0.15	0.038	NO
428	MTMR2	MTMR2	MTMR2	16253	-0.15	0.04	NO
429	MED20	MED20	MED20	16432	-0.16	0.031	NO
430	PLA2G4F	PLA2G4F	PLA2G4F	16488	-0.16	0.03	NO
431	SPHK1	SPHK1	SPHK1	16527	-0.17	0.03	NO
432	CAV1	CAV1	CAV1	16666	-0.18	0.024	NO
433	ABCG1	ABCG1	ABCG1	16790	-0.19	0.019	NO
434	CUBN	CUBN	CUBN	16807	-0.19	0.02	NO
435	HSD3B2	HSD3B2	HSD3B2	16823	-0.19	0.022	NO
436	PIP5K1B	PIP5K1B	PIP5K1B	16860	-0.19	0.022	NO
437	PLA2G10	PLA2G10	PLA2G10	16940	-0.2	0.02	NO
438	STAR	STAR	STAR	16974	-0.21	0.02	NO
439	NR1D1	NR1D1	NR1D1	17067	-0.22	0.018	NO
440	ELOVL4	ELOVL4	ELOVL4	17172	-0.23	0.014	NO
441	SGPP2	SGPP2	SGPP2	17209	-0.23	0.015	NO
442	OXCT1	OXCT1	OXCT1	17213	-0.23	0.017	NO
443	RBP2	RBP2	RBP2	17263	-0.24	0.017	NO
444	SMARCD3	SMARCD3	SMARCD3	17338	-0.24	0.016	NO
445	PLA2G4D	PLA2G4D	PLA2G4D	17437	-0.26	0.013	NO
446	SLC10A2	SLC10A2	SLC10A2	17447	-0.26	0.016	NO
447	DEGS2	DEGS2	DEGS2	17527	-0.28	0.014	NO
448	PIK3R6	PIK3R6	PIK3R6	17568	-0.28	0.016	NO
449	TPTE2	TPTE2	TPTE2	17683	-0.31	0.013	NO
450	ARSH	ARSH	ARSH	17758	-0.33	0.012	NO
451	LIPE	LIPE	LIPE	17826	-0.34	0.012	NO
452	SLC44A4	SLC44A4	SLC44A4	17831	-0.35	0.016	NO

Figure S83. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE.

Figure S84. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

Table S43. 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	SULT2A1	SULT2A1	SULT2A1	26	2	0.061	YES
2	APOA5	APOA5	APOA5	29	1.9	0.12	YES
3	APOA1	APOA1	APOA1	83	1.5	0.17	YES
4	FABP1	FABP1	FABP1	121	1.3	0.21	YES
5	ABCB4	ABCB4	ABCB4	142	1.2	0.24	YES
6	CYP7A1	CYP7A1	CYP7A1	144	1.2	0.28	YES
7	CYP1A1	CYP1A1	CYP1A1	154	1.1	0.32	YES
8	APOA2	APOA2	APOA2	155	1.1	0.35	YES
9	HMGCS2	HMGCS2	HMGCS2	175	1	0.39	YES
10	CYP4A11	CYP4A11	CYP4A11	239	0.83	0.41	YES
11	GPD1	GPD1	GPD1	273	0.77	0.43	YES
12	ACADL	ACADL	ACADL	288	0.72	0.46	YES
13	BDH1	BDH1	BDH1	330	0.66	0.47	YES
14	GPAM	GPAM	GPAM	356	0.61	0.49	YES
15	DGAT2	DGAT2	DGAT2	386	0.57	0.51	YES
16	G0S2	G0S2	G0S2	435	0.52	0.52	YES
17	ACSL1	ACSL1	ACSL1	473	0.49	0.54	YES
18	ELOVL2	ELOVL2	ELOVL2	502	0.47	0.55	YES
19	UGT1A9	UGT1A9	UGT1A9	562	0.43	0.56	YES
20	CD36	CD36	CD36	651	0.38	0.57	YES
21	PLIN2	PLIN2	PLIN2	655	0.38	0.58	YES
22	ANGPTL4	ANGPTL4	ANGPTL4	805	0.33	0.58	YES
23	ACSL6	ACSL6	ACSL6	864	0.31	0.59	YES
24	ELOVL6	ELOVL6	ELOVL6	972	0.28	0.59	YES
25	SLC25A20	SLC25A20	SLC25A20	1026	0.27	0.6	YES
26	ANKRD1	ANKRD1	ANKRD1	1135	0.26	0.6	YES
27	AGT	AGT	AGT	1136	0.26	0.61	YES
28	MCEE	MCEE	MCEE	1162	0.25	0.61	YES
29	ACAT1	ACAT1	ACAT1	1163	0.25	0.62	YES
30	ACSL5	ACSL5	ACSL5	1246	0.24	0.62	YES
31	ELOVL7	ELOVL7	ELOVL7	1369	0.22	0.62	YES
32	ALAS1	ALAS1	ALAS1	1388	0.22	0.63	YES
33	HMGCS1	HMGCS1	HMGCS1	1538	0.2	0.63	YES
34	FASN	FASN	FASN	1623	0.19	0.63	YES
35	ABCA1	ABCA1	ABCA1	1641	0.19	0.64	YES
36	HMGCL	HMGCL	HMGCL	1756	0.18	0.63	YES
37	ACACB	ACACB	ACACB	1791	0.18	0.64	YES
38	ACADM	ACADM	ACADM	1865	0.17	0.64	YES
39	CPT2	CPT2	CPT2	1964	0.16	0.64	YES
40	PPARA	PPARA	PPARA	1990	0.16	0.64	YES
41	ACOX1	ACOX1	ACOX1	2024	0.16	0.65	YES
42	PRKAA2	PRKAA2	PRKAA2	2091	0.16	0.65	YES
43	ECHS1	ECHS1	ECHS1	2114	0.15	0.65	YES
44	ELOVL3	ELOVL3	ELOVL3	2155	0.15	0.65	YES
45	ARNTL	ARNTL	ARNTL	2245	0.15	0.65	YES
46	GRHL1	GRHL1	GRHL1	2312	0.14	0.65	YES
47	TRIB3	TRIB3	TRIB3	2442	0.14	0.65	YES
48	MUT	MUT	MUT	2466	0.13	0.65	YES
49	ACADS	ACADS	ACADS	2519	0.13	0.66	YES
50	ELOVL5	ELOVL5	ELOVL5	2884	0.11	0.64	NO
51	MED8	MED8	MED8	3004	0.11	0.64	NO
52	HMGCR	HMGCR	HMGCR	3112	0.1	0.63	NO
53	FADS1	FADS1	FADS1	3220	0.099	0.63	NO
54	NPAS2	NPAS2	NPAS2	3223	0.099	0.63	NO
55	MED31	MED31	MED31	3416	0.094	0.63	NO
56	ACADVL	ACADVL	ACADVL	3459	0.092	0.63	NO
57	CCNC	CCNC	CCNC	3705	0.085	0.62	NO
58	ELOVL1	ELOVL1	ELOVL1	3744	0.084	0.62	NO
59	NCOA2	NCOA2	NCOA2	3791	0.083	0.62	NO
60	ACSL3	ACSL3	ACSL3	4014	0.076	0.61	NO
61	HADHB	HADHB	HADHB	4022	0.076	0.61	NO
62	SREBF2	SREBF2	SREBF2	4155	0.073	0.6	NO
63	PPARGC1B	PPARGC1B	PPARGC1B	4367	0.068	0.59	NO
64	AGPAT3	AGPAT3	AGPAT3	4456	0.065	0.59	NO
65	PPARGC1A	PPARGC1A	PPARGC1A	4518	0.064	0.59	NO
66	LPIN2	LPIN2	LPIN2	4590	0.062	0.59	NO
67	EP300	EP300	EP300	4615	0.062	0.59	NO
68	HADH	HADH	HADH	4896	0.056	0.57	NO
69	PEX11A	PEX11A	PEX11A	4914	0.055	0.57	NO
70	PRKAG2	PRKAG2	PRKAG2	5014	0.053	0.57	NO
71	TIAM2	TIAM2	TIAM2	5094	0.052	0.57	NO
72	GK	GK	GK	5111	0.052	0.57	NO
73	HSD17B12	HSD17B12	HSD17B12	5120	0.051	0.57	NO
74	HADHA	HADHA	HADHA	5144	0.051	0.57	NO
75	GPD1L	GPD1L	GPD1L	5179	0.05	0.57	NO
76	PCCB	PCCB	PCCB	5362	0.047	0.56	NO
77	CPT1A	CPT1A	CPT1A	5540	0.043	0.55	NO
78	AGPAT9	AGPAT9	AGPAT9	5549	0.043	0.55	NO
79	PRKAB2	PRKAB2	PRKAB2	5699	0.04	0.55	NO
80	SREBF1	SREBF1	SREBF1	5824	0.038	0.54	NO
81	MED23	MED23	MED23	5963	0.036	0.54	NO
82	LCLAT1	LCLAT1	LCLAT1	6052	0.035	0.53	NO
83	CDK8	CDK8	CDK8	6256	0.032	0.52	NO
84	ESRRA	ESRRA	ESRRA	6409	0.03	0.51	NO
85	MED29	MED29	MED29	6459	0.029	0.51	NO
86	MED10	MED10	MED10	6523	0.028	0.51	NO
87	ME1	ME1	ME1	6698	0.026	0.5	NO
88	PCCA	PCCA	PCCA	6736	0.026	0.5	NO
89	TEAD1	TEAD1	TEAD1	6893	0.024	0.49	NO
90	LPCAT1	LPCAT1	LPCAT1	6930	0.023	0.49	NO
91	CDK19	CDK19	CDK19	6987	0.022	0.49	NO
92	RXRA	RXRA	RXRA	7058	0.021	0.48	NO
93	NFYB	NFYB	NFYB	7150	0.02	0.48	NO
94	ACLY	ACLY	ACLY	7156	0.02	0.48	NO
95	ACACA	ACACA	ACACA	7181	0.02	0.48	NO
96	LPIN1	LPIN1	LPIN1	7412	0.017	0.47	NO
97	NCOA3	NCOA3	NCOA3	7449	0.016	0.46	NO
98	MED11	MED11	MED11	7594	0.014	0.46	NO
99	SLC25A1	SLC25A1	SLC25A1	7615	0.014	0.46	NO
100	TBL1X	TBL1X	TBL1X	7812	0.012	0.45	NO
101	PPARG	PPARG	PPARG	8013	0.0092	0.44	NO
102	CPT1B	CPT1B	CPT1B	8122	0.0081	0.43	NO
103	HDAC3	HDAC3	HDAC3	8129	0.008	0.43	NO
104	RORA	RORA	RORA	8204	0.007	0.43	NO
105	AGPAT5	AGPAT5	AGPAT5	8739	0.00072	0.4	NO
106	NCOR2	NCOR2	NCOR2	8825	-0.00015	0.39	NO
107	MED9	MED9	MED9	8990	-0.0021	0.38	NO
108	GLIPR1	GLIPR1	GLIPR1	9568	-0.0085	0.35	NO
109	FHL2	FHL2	FHL2	9647	-0.0095	0.35	NO
110	MED1	MED1	MED1	9875	-0.012	0.33	NO
111	MED25	MED25	MED25	9885	-0.012	0.33	NO
112	MED6	MED6	MED6	9947	-0.013	0.33	NO
113	YAP1	YAP1	YAP1	10003	-0.013	0.33	NO
114	AGPAT2	AGPAT2	AGPAT2	10079	-0.014	0.32	NO
115	MED13L	MED13L	MED13L	10117	-0.015	0.32	NO
116	MED26	MED26	MED26	10151	-0.015	0.32	NO
117	NCOR1	NCOR1	NCOR1	10218	-0.016	0.32	NO
118	MED14	MED14	MED14	10229	-0.016	0.32	NO
119	MED4	MED4	MED4	10281	-0.017	0.32	NO
120	MED18	MED18	MED18	10438	-0.019	0.31	NO
121	NCOA6	NCOA6	NCOA6	10527	-0.02	0.3	NO
122	DECR1	DECR1	DECR1	10540	-0.02	0.3	NO
123	MED15	MED15	MED15	10546	-0.02	0.3	NO
124	CLOCK	CLOCK	CLOCK	10649	-0.021	0.3	NO
125	AGPAT1	AGPAT1	AGPAT1	10928	-0.025	0.28	NO
126	NFYA	NFYA	NFYA	11046	-0.026	0.28	NO
127	TXNRD1	TXNRD1	TXNRD1	11066	-0.026	0.28	NO
128	LPIN3	LPIN3	LPIN3	11196	-0.028	0.27	NO
129	MED7	MED7	MED7	11226	-0.029	0.27	NO
130	MED12	MED12	MED12	11230	-0.029	0.27	NO
131	CREBBP	CREBBP	CREBBP	11359	-0.03	0.27	NO
132	SIN3B	SIN3B	SIN3B	11945	-0.038	0.24	NO
133	AGPAT6	AGPAT6	AGPAT6	12072	-0.04	0.23	NO
134	MED16	MED16	MED16	12225	-0.042	0.22	NO
135	SLC27A1	SLC27A1	SLC27A1	12327	-0.044	0.22	NO
136	TBL1XR1	TBL1XR1	TBL1XR1	12414	-0.045	0.21	NO
137	TECR	TECR	TECR	12488	-0.046	0.21	NO
138	GPAT2	GPAT2	GPAT2	12564	-0.047	0.21	NO
139	MED24	MED24	MED24	12650	-0.049	0.21	NO
140	PRIC285	PRIC285	PRIC285	12882	-0.053	0.2	NO
141	MED19	MED19	MED19	12960	-0.054	0.19	NO
142	CTGF	CTGF	CTGF	12990	-0.054	0.19	NO
143	NCOA1	NCOA1	NCOA1	13130	-0.056	0.19	NO
144	ACSL4	ACSL4	ACSL4	13367	-0.06	0.18	NO
145	NRF1	NRF1	NRF1	13517	-0.063	0.17	NO
146	DGAT1	DGAT1	DGAT1	13525	-0.063	0.17	NO
147	SIN3A	SIN3A	SIN3A	13572	-0.064	0.17	NO
148	WWTR1	WWTR1	WWTR1	13856	-0.07	0.16	NO
149	AGPAT4	AGPAT4	AGPAT4	13864	-0.07	0.16	NO
150	TEAD2	TEAD2	TEAD2	13980	-0.072	0.15	NO
151	TGS1	TGS1	TGS1	14177	-0.076	0.15	NO
152	TEAD3	TEAD3	TEAD3	14408	-0.082	0.14	NO
153	TEAD4	TEAD4	TEAD4	14578	-0.086	0.13	NO
154	FDFT1	FDFT1	FDFT1	14693	-0.089	0.12	NO
155	GPD2	GPD2	GPD2	14977	-0.097	0.11	NO
156	MED21	MED21	MED21	15304	-0.11	0.098	NO
157	MED27	MED27	MED27	15307	-0.11	0.1	NO
158	MED30	MED30	MED30	15546	-0.12	0.092	NO
159	MED17	MED17	MED17	15610	-0.12	0.092	NO
160	MED22	MED22	MED22	15655	-0.12	0.093	NO
161	TNFRSF21	TNFRSF21	TNFRSF21	15828	-0.13	0.088	NO
162	LPCAT4	LPCAT4	LPCAT4	16247	-0.15	0.069	NO
163	MED20	MED20	MED20	16432	-0.16	0.064	NO
164	NR1D1	NR1D1	NR1D1	17067	-0.22	0.036	NO
165	ELOVL4	ELOVL4	ELOVL4	17172	-0.23	0.037	NO
166	OXCT1	OXCT1	OXCT1	17213	-0.23	0.042	NO
167	SMARCD3	SMARCD3	SMARCD3	17338	-0.24	0.043	NO

Figure S85. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY.

Figure S86. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

Table S44. 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	HAO1	HAO1	HAO1	5	2.3	0.044	YES
2	ARG1	ARG1	ARG1	12	2.1	0.085	YES
3	UROC1	UROC1	UROC1	16	2.1	0.12	YES
4	TAT	TAT	TAT	27	1.9	0.16	YES
5	CPS1	CPS1	CPS1	38	1.8	0.2	YES
6	OTC	OTC	OTC	46	1.8	0.23	YES
7	DAO	DAO	DAO	58	1.7	0.26	YES
8	AGXT	AGXT	AGXT	59	1.7	0.3	YES
9	BHMT	BHMT	BHMT	60	1.7	0.33	YES
10	CDO1	CDO1	CDO1	67	1.6	0.36	YES
11	INHBC	INHBC	INHBC	137	1.2	0.38	YES
12	TDO2	TDO2	TDO2	138	1.2	0.4	YES
13	HPD	HPD	HPD	157	1.1	0.42	YES
14	AGXT2	AGXT2	AGXT2	170	1.1	0.44	YES
15	MAT1A	MAT1A	MAT1A	190	1	0.46	YES
16	AMDHD1	AMDHD1	AMDHD1	193	0.99	0.48	YES
17	HAL	HAL	HAL	197	0.99	0.5	YES
18	DIO1	DIO1	DIO1	213	0.93	0.52	YES
19	DBH	DBH	DBH	214	0.92	0.53	YES
20	KMO	KMO	KMO	228	0.87	0.55	YES
21	GLS2	GLS2	GLS2	263	0.8	0.56	YES
22	FTCD	FTCD	FTCD	286	0.73	0.58	YES
23	CTH	CTH	CTH	318	0.67	0.59	YES
24	DDC	DDC	DDC	375	0.58	0.6	YES
25	INHBE	INHBE	INHBE	391	0.56	0.61	YES
26	PSAT1	PSAT1	PSAT1	397	0.56	0.62	YES
27	IDO2	IDO2	IDO2	414	0.54	0.63	YES
28	GPT2	GPT2	GPT2	448	0.51	0.64	YES
29	KYNU	KYNU	KYNU	462	0.5	0.64	YES
30	ALDH6A1	ALDH6A1	ALDH6A1	477	0.48	0.65	YES
31	AGMAT	AGMAT	AGMAT	516	0.46	0.66	YES
32	NAGS	NAGS	NAGS	531	0.45	0.67	YES
33	PAH	PAH	PAH	532	0.45	0.68	YES
34	HAAO	HAAO	HAAO	555	0.43	0.68	YES
35	ACADSB	ACADSB	ACADSB	612	0.4	0.69	YES
36	IYD	IYD	IYD	705	0.36	0.69	YES
37	GAMT	GAMT	GAMT	720	0.35	0.7	YES
38	GATM	GATM	GATM	731	0.35	0.7	YES
39	CBS	CBS	CBS	739	0.34	0.71	YES
40	SLC25A15	SLC25A15	SLC25A15	787	0.33	0.71	YES
41	GPT	GPT	GPT	810	0.32	0.72	YES
42	ALDH4A1	ALDH4A1	ALDH4A1	902	0.3	0.72	YES
43	BCKDHB	BCKDHB	BCKDHB	915	0.3	0.72	YES
44	AADAT	AADAT	AADAT	927	0.3	0.73	YES
45	ACMSD	ACMSD	ACMSD	939	0.29	0.73	YES
46	FAH	FAH	FAH	955	0.29	0.74	YES
47	SHMT1	SHMT1	SHMT1	1093	0.26	0.74	YES
48	ACAT1	ACAT1	ACAT1	1163	0.25	0.74	YES
49	PRODH	PRODH	PRODH	1258	0.24	0.74	YES
50	HGD	HGD	HGD	1261	0.24	0.74	YES
51	TST	TST	TST	1287	0.23	0.74	YES
52	AANAT	AANAT	AANAT	1443	0.21	0.74	YES
53	AASS	AASS	AASS	1471	0.21	0.74	YES
54	PYCR1	PYCR1	PYCR1	1510	0.2	0.74	YES
55	GOT1	GOT1	GOT1	1532	0.2	0.75	YES
56	PSPH	PSPH	PSPH	1633	0.19	0.74	NO
57	GSTZ1	GSTZ1	GSTZ1	1752	0.18	0.74	NO
58	CKMT2	CKMT2	CKMT2	1798	0.18	0.74	NO
59	SLC25A10	SLC25A10	SLC25A10	1832	0.17	0.74	NO
60	GOT2	GOT2	GOT2	1968	0.16	0.74	NO
61	ASL	ASL	ASL	2040	0.16	0.74	NO
62	PHGDH	PHGDH	PHGDH	2050	0.16	0.74	NO
63	QDPR	QDPR	QDPR	2071	0.16	0.74	NO
64	AFMID	AFMID	AFMID	2437	0.14	0.72	NO
65	GRHPR	GRHPR	GRHPR	2469	0.13	0.73	NO
66	ALDH7A1	ALDH7A1	ALDH7A1	2555	0.13	0.72	NO
67	HIBADH	HIBADH	HIBADH	2789	0.12	0.71	NO
68	CKB	CKB	CKB	3022	0.11	0.7	NO
69	CSAD	CSAD	CSAD	3071	0.1	0.7	NO
70	ASS1	ASS1	ASS1	3145	0.1	0.7	NO
71	PAOX	PAOX	PAOX	3189	0.1	0.7	NO
72	ADI1	ADI1	ADI1	3269	0.098	0.7	NO
73	PCBD1	PCBD1	PCBD1	3296	0.096	0.7	NO
74	HIBCH	HIBCH	HIBCH	3632	0.087	0.68	NO
75	GLUD1	GLUD1	GLUD1	3722	0.085	0.68	NO
76	PSMD12	PSMD12	PSMD12	3730	0.084	0.68	NO
77	OAT	OAT	OAT	3863	0.08	0.67	NO
78	HDC	HDC	HDC	3961	0.078	0.67	NO
79	MCCC2	MCCC2	MCCC2	3962	0.078	0.67	NO
80	IVD	IVD	IVD	3974	0.077	0.67	NO
81	CNDP2	CNDP2	CNDP2	4032	0.076	0.67	NO
82	CKM	CKM	CKM	4130	0.074	0.66	NO
83	PSMD11	PSMD11	PSMD11	4256	0.07	0.66	NO
84	GCLC	GCLC	GCLC	4371	0.068	0.65	NO
85	PSMC4	PSMC4	PSMC4	4427	0.066	0.65	NO
86	SUOX	SUOX	SUOX	4440	0.066	0.65	NO
87	BCKDHA	BCKDHA	BCKDHA	4442	0.066	0.65	NO
88	PSMC2	PSMC2	PSMC2	4473	0.065	0.65	NO
89	AHCY	AHCY	AHCY	4629	0.062	0.65	NO
90	ODC1	ODC1	ODC1	4655	0.061	0.65	NO
91	SLC25A21	SLC25A21	SLC25A21	4691	0.06	0.64	NO
92	ALDH18A1	ALDH18A1	ALDH18A1	4798	0.058	0.64	NO
93	DLD	DLD	DLD	4899	0.056	0.64	NO
94	MAT2A	MAT2A	MAT2A	5257	0.049	0.62	NO
95	SLC25A2	SLC25A2	SLC25A2	5335	0.047	0.61	NO
96	PSMC6	PSMC6	PSMC6	5448	0.045	0.61	NO
97	SLC5A5	SLC5A5	SLC5A5	5464	0.044	0.61	NO
98	GCDH	GCDH	GCDH	5503	0.044	0.61	NO
99	ARG2	ARG2	ARG2	5534	0.043	0.61	NO
100	PSMA2	PSMA2	PSMA2	5536	0.043	0.61	NO
101	DBT	DBT	DBT	5547	0.043	0.61	NO
102	PSMD6	PSMD6	PSMD6	5548	0.043	0.61	NO
103	PSMB5	PSMB5	PSMB5	5673	0.041	0.6	NO
104	DIO3	DIO3	DIO3	5685	0.04	0.6	NO
105	MTAP	MTAP	MTAP	5801	0.038	0.6	NO
106	PSMC5	PSMC5	PSMC5	5811	0.038	0.6	NO
107	PSME4	PSME4	PSME4	5845	0.038	0.6	NO
108	DLST	DLST	DLST	5883	0.037	0.59	NO
109	PSMA3	PSMA3	PSMA3	5942	0.036	0.59	NO
110	INHBB	INHBB	INHBB	6054	0.035	0.59	NO
111	PSMD8	PSMD8	PSMD8	6278	0.032	0.57	NO
112	PSMD10	PSMD10	PSMD10	6337	0.031	0.57	NO
113	PSMA5	PSMA5	PSMA5	6445	0.03	0.57	NO
114	PSMD2	PSMD2	PSMD2	6532	0.028	0.56	NO
115	PSMA6	PSMA6	PSMA6	6553	0.028	0.56	NO
116	ASNS	ASNS	ASNS	6829	0.025	0.55	NO
117	PSMD14	PSMD14	PSMD14	6914	0.023	0.54	NO
118	PSMD1	PSMD1	PSMD1	6960	0.023	0.54	NO
119	PSMF1	PSMF1	PSMF1	7131	0.02	0.53	NO
120	OAZ2	OAZ2	OAZ2	7151	0.02	0.53	NO
121	HSD17B10	HSD17B10	HSD17B10	7193	0.019	0.53	NO
122	PSMD3	PSMD3	PSMD3	7324	0.018	0.52	NO
123	OGDH	OGDH	OGDH	7415	0.016	0.52	NO
124	ETHE1	ETHE1	ETHE1	7503	0.015	0.51	NO
125	MTR	MTR	MTR	7532	0.015	0.51	NO
126	PSME2	PSME2	PSME2	7543	0.015	0.51	NO
127	MAT2B	MAT2B	MAT2B	7683	0.013	0.5	NO
128	PSMD7	PSMD7	PSMD7	7928	0.01	0.49	NO
129	PSMD9	PSMD9	PSMD9	7959	0.0099	0.49	NO
130	TMLHE	TMLHE	TMLHE	8132	0.008	0.48	NO
131	PSMB3	PSMB3	PSMB3	8190	0.0072	0.48	NO
132	ALDH9A1	ALDH9A1	ALDH9A1	8254	0.0064	0.47	NO
133	BBOX1	BBOX1	BBOX1	8353	0.0051	0.47	NO
134	PSME1	PSME1	PSME1	8385	0.0048	0.47	NO
135	SRM	SRM	SRM	8631	0.0018	0.45	NO
136	AUH	AUH	AUH	8738	0.00072	0.45	NO
137	NQO1	NQO1	NQO1	9047	-0.0027	0.43	NO
138	PSMB6	PSMB6	PSMB6	9089	-0.0031	0.43	NO
139	CGA	CGA	CGA	9155	-0.0039	0.42	NO
140	MCCC1	MCCC1	MCCC1	9161	-0.004	0.42	NO
141	SQRDL	SQRDL	SQRDL	9197	-0.0044	0.42	NO
142	AMD1	AMD1	AMD1	9570	-0.0085	0.4	NO
143	GLS	GLS	GLS	9778	-0.011	0.39	NO
144	GLUL	GLUL	GLUL	9813	-0.011	0.39	NO
145	AZIN1	AZIN1	AZIN1	9835	-0.012	0.39	NO
146	GCLM	GCLM	GCLM	9985	-0.013	0.38	NO
147	TH	TH	TH	10134	-0.015	0.37	NO
148	PSMA1	PSMA1	PSMA1	10179	-0.016	0.37	NO
149	TPH1	TPH1	TPH1	10293	-0.017	0.36	NO
150	PSMB4	PSMB4	PSMB4	10693	-0.022	0.34	NO
151	PSMB7	PSMB7	PSMB7	10877	-0.024	0.33	NO
152	PSMB2	PSMB2	PSMB2	10893	-0.024	0.33	NO
153	PSMA7	PSMA7	PSMA7	11015	-0.026	0.32	NO
154	SMS	SMS	SMS	11054	-0.026	0.32	NO
155	OAZ1	OAZ1	OAZ1	11068	-0.026	0.32	NO
156	PSMB1	PSMB1	PSMB1	11076	-0.027	0.32	NO
157	INHBA	INHBA	INHBA	11329	-0.03	0.31	NO
158	PSMD5	PSMD5	PSMD5	11587	-0.033	0.3	NO
159	PSMD4	PSMD4	PSMD4	11635	-0.034	0.29	NO
160	OAZ3	OAZ3	OAZ3	11637	-0.034	0.29	NO
161	ACAD8	ACAD8	ACAD8	11741	-0.035	0.29	NO
162	PSMA4	PSMA4	PSMA4	11850	-0.037	0.28	NO
163	PSMC1	PSMC1	PSMC1	11902	-0.038	0.28	NO
164	DIO2	DIO2	DIO2	12446	-0.046	0.25	NO
165	PSMC3	PSMC3	PSMC3	12563	-0.047	0.25	NO
166	PSMB8	PSMB8	PSMB8	12814	-0.051	0.23	NO
167	CCBL1	CCBL1	CCBL1	12832	-0.052	0.23	NO
168	PSMB9	PSMB9	PSMB9	12886	-0.053	0.23	NO
169	POMC	POMC	POMC	13158	-0.057	0.22	NO
170	SAT1	SAT1	SAT1	13228	-0.058	0.22	NO
171	INHA	INHA	INHA	13232	-0.058	0.22	NO
172	ENOPH1	ENOPH1	ENOPH1	13723	-0.067	0.19	NO
173	PNMT	PNMT	PNMT	13776	-0.068	0.19	NO
174	PSMD13	PSMD13	PSMD13	14082	-0.074	0.17	NO
175	PSMB10	PSMB10	PSMB10	14346	-0.08	0.16	NO
176	SLC6A8	SLC6A8	SLC6A8	14428	-0.082	0.16	NO
177	SMOX	SMOX	SMOX	14687	-0.089	0.14	NO
178	APIP	APIP	APIP	14703	-0.089	0.14	NO
179	PCSK1	PCSK1	PCSK1	14802	-0.092	0.14	NO
180	LHB	LHB	LHB	15223	-0.1	0.12	NO
181	BCAT2	BCAT2	BCAT2	15459	-0.11	0.11	NO
182	IDO1	IDO1	IDO1	15577	-0.12	0.1	NO
183	MRI1	MRI1	MRI1	15757	-0.12	0.097	NO
184	BCAT1	BCAT1	BCAT1	15968	-0.13	0.088	NO
185	CCBL2	CCBL2	CCBL2	16060	-0.14	0.085	NO
186	CGB8	CGB8	CGB8	16406	-0.16	0.069	NO
187	CKMT1A	CKMT1A	CKMT1A	16620	-0.17	0.061	NO
188	CKMT1B	CKMT1B	CKMT1B	16739	-0.18	0.058	NO
189	CGB	CGB	CGB	16864	-0.19	0.055	NO
190	CGB5	CGB5	CGB5	16933	-0.2	0.055	NO
191	ADC	ADC	ADC	17351	-0.25	0.036	NO
192	TPO	TPO	TPO	17742	-0.32	0.021	NO

Figure S87. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table S45. 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	GYS2	GYS2	GYS2	4	2.8	0.21	YES
2	PFKFB1	PFKFB1	PFKFB1	89	1.5	0.32	YES
3	ALDOB	ALDOB	ALDOB	129	1.2	0.41	YES
4	PCK1	PCK1	PCK1	140	1.2	0.5	YES
5	PKLR	PKLR	PKLR	279	0.74	0.55	YES
6	PC	PC	PC	465	0.5	0.57	YES
7	FBP1	FBP1	FBP1	490	0.48	0.61	YES
8	PYGL	PYGL	PYGL	618	0.4	0.63	YES
9	PCK2	PCK2	PCK2	791	0.33	0.65	YES
10	PGAM2	PGAM2	PGAM2	1378	0.22	0.63	YES
11	PPP2R1B	PPP2R1B	PPP2R1B	1464	0.21	0.64	YES
12	GOT1	GOT1	GOT1	1532	0.2	0.65	YES
13	SLC25A13	SLC25A13	SLC25A13	1706	0.18	0.66	YES
14	SLC25A10	SLC25A10	SLC25A10	1832	0.17	0.66	YES
15	GOT2	GOT2	GOT2	1968	0.16	0.67	YES
16	PGM1	PGM1	PGM1	2116	0.15	0.67	YES
17	UGP2	UGP2	UGP2	2161	0.15	0.68	YES
18	ENO3	ENO3	ENO3	2164	0.15	0.69	YES
19	SLC25A12	SLC25A12	SLC25A12	2866	0.11	0.66	NO
20	AGL	AGL	AGL	2966	0.11	0.66	NO
21	GBE1	GBE1	GBE1	3212	0.1	0.66	NO
22	PRKACB	PRKACB	PRKACB	3272	0.097	0.66	NO
23	ALDOC	ALDOC	ALDOC	3400	0.094	0.66	NO
24	MDH1	MDH1	MDH1	3617	0.088	0.66	NO
25	PHKA2	PHKA2	PHKA2	4059	0.075	0.64	NO
26	GAPDHS	GAPDHS	GAPDHS	4161	0.073	0.64	NO
27	PFKFB3	PFKFB3	PFKFB3	4816	0.057	0.61	NO
28	PRKACA	PRKACA	PRKACA	5473	0.044	0.57	NO
29	MDH2	MDH2	MDH2	5897	0.037	0.55	NO
30	PGM2	PGM2	PGM2	6058	0.035	0.55	NO
31	PGAM1	PGAM1	PGAM1	6294	0.032	0.54	NO
32	PHKA1	PHKA1	PHKA1	6446	0.03	0.53	NO
33	PPP2CA	PPP2CA	PPP2CA	6548	0.028	0.53	NO
34	PHKB	PHKB	PHKB	6926	0.023	0.51	NO
35	GYG1	GYG1	GYG1	7237	0.019	0.49	NO
36	SLC25A1	SLC25A1	SLC25A1	7615	0.014	0.47	NO
37	PFKM	PFKM	PFKM	7898	0.011	0.46	NO
38	GPI	GPI	GPI	8060	0.0088	0.45	NO
39	PFKFB2	PFKFB2	PFKFB2	8089	0.0084	0.45	NO
40	PPP2R1A	PPP2R1A	PPP2R1A	8321	0.0054	0.44	NO
41	SLC25A11	SLC25A11	SLC25A11	8355	0.0051	0.43	NO
42	PGK1	PGK1	PGK1	9470	-0.0074	0.37	NO
43	ENO1	ENO1	ENO1	9872	-0.012	0.35	NO
44	PFKL	PFKL	PFKL	9990	-0.013	0.35	NO
45	CALM2	CALM2	CALM2	10082	-0.014	0.34	NO
46	PPP2CB	PPP2CB	PPP2CB	10091	-0.014	0.34	NO
47	GAPDH	GAPDH	GAPDH	10701	-0.022	0.31	NO
48	PPP2R5D	PPP2R5D	PPP2R5D	10729	-0.022	0.31	NO
49	TPI1	TPI1	TPI1	11099	-0.027	0.29	NO
50	PYGM	PYGM	PYGM	11536	-0.033	0.27	NO
51	PHKG2	PHKG2	PHKG2	11783	-0.036	0.26	NO
52	CALM3	CALM3	CALM3	11933	-0.038	0.25	NO
53	CALM1	CALM1	CALM1	12264	-0.043	0.24	NO
54	PYGB	PYGB	PYGB	12513	-0.046	0.23	NO
55	ALDOA	ALDOA	ALDOA	13590	-0.064	0.17	NO
56	GYG2	GYG2	GYG2	13961	-0.072	0.16	NO
57	PKM2	PKM2	PKM2	15166	-0.1	0.1	NO
58	GYS1	GYS1	GYS1	15308	-0.11	0.1	NO
59	PFKP	PFKP	PFKP	15414	-0.11	0.1	NO
60	PHKG1	PHKG1	PHKG1	16735	-0.18	0.044	NO
61	ENO2	ENO2	ENO2	16948	-0.2	0.048	NO
62	PFKFB4	PFKFB4	PFKFB4	17143	-0.22	0.054	NO

Figure S89. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM.

Figure S90. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table S46. 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	TAT	TAT	TAT	27	1.9	0.17	YES
2	BHMT	BHMT	BHMT	60	1.7	0.31	YES
3	CDO1	CDO1	CDO1	67	1.6	0.45	YES
4	DNMT3L	DNMT3L	DNMT3L	131	1.2	0.56	YES
5	MAT1A	MAT1A	MAT1A	190	1	0.64	YES
6	SDS	SDS	SDS	284	0.73	0.7	YES
7	CTH	CTH	CTH	318	0.67	0.76	YES
8	CBS	CBS	CBS	739	0.34	0.76	YES
9	LDHAL6B	LDHAL6B	LDHAL6B	795	0.33	0.79	YES
10	LDHC	LDHC	LDHC	1468	0.21	0.77	NO
11	GOT1	GOT1	GOT1	1532	0.2	0.78	NO
12	GOT2	GOT2	GOT2	1968	0.16	0.77	NO
13	LDHAL6A	LDHAL6A	LDHAL6A	2287	0.14	0.77	NO
14	MPST	MPST	MPST	3093	0.1	0.73	NO
15	ADI1	ADI1	ADI1	3269	0.098	0.73	NO
16	AHCY	AHCY	AHCY	4629	0.062	0.66	NO
17	MAT2A	MAT2A	MAT2A	5257	0.049	0.63	NO
18	MTAP	MTAP	MTAP	5801	0.038	0.61	NO
19	AHCYL1	AHCYL1	AHCYL1	5893	0.037	0.6	NO
20	MTR	MTR	MTR	7532	0.015	0.52	NO
21	MAT2B	MAT2B	MAT2B	7683	0.013	0.51	NO
22	DNMT1	DNMT1	DNMT1	8359	0.005	0.47	NO
23	AHCYL2	AHCYL2	AHCYL2	8476	0.0037	0.46	NO
24	SRM	SRM	SRM	8631	0.0018	0.46	NO
25	LDHA	LDHA	LDHA	9002	-0.0022	0.44	NO
26	AMD1	AMD1	AMD1	9570	-0.0085	0.4	NO
27	SMS	SMS	SMS	11054	-0.026	0.32	NO
28	LDHB	LDHB	LDHB	13454	-0.062	0.2	NO
29	ENOPH1	ENOPH1	ENOPH1	13723	-0.067	0.19	NO
30	DNMT3B	DNMT3B	DNMT3B	14566	-0.086	0.15	NO
31	APIP	APIP	APIP	14703	-0.089	0.15	NO
32	TRDMT1	TRDMT1	TRDMT1	14721	-0.09	0.16	NO
33	DNMT3A	DNMT3A	DNMT3A	14886	-0.094	0.16	NO
34	IL4I1	IL4I1	IL4I1	17380	-0.25	0.04	NO

Figure S91. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FATTY ACID METABOLISM.

Figure S92. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FATTY ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

Table S47. 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	DPYS	DPYS	DPYS	44	1.8	0.17	YES
2	UPB1	UPB1	UPB1	72	1.6	0.32	YES
3	UPP2	UPP2	UPP2	270	0.78	0.38	YES
4	DPYD	DPYD	DPYD	844	0.32	0.38	YES
5	DHODH	DHODH	DHODH	866	0.31	0.41	YES
6	POLR3G	POLR3G	POLR3G	900	0.3	0.43	YES
7	CDA	CDA	CDA	918	0.3	0.46	YES
8	ENTPD5	ENTPD5	ENTPD5	968	0.29	0.48	YES
9	POLE2	POLE2	POLE2	1239	0.24	0.49	YES
10	RRM2	RRM2	RRM2	1650	0.19	0.49	NO
11	NT5C1B	NT5C1B	NT5C1B	2090	0.16	0.48	NO
12	ENTPD8	ENTPD8	ENTPD8	2433	0.14	0.47	NO
13	NT5E	NT5E	NT5E	2540	0.13	0.48	NO
14	TK1	TK1	TK1	3001	0.11	0.46	NO
15	NME1-NME2	NME1-NME2	NME1-NME2	3845	0.081	0.42	NO
16	TYMS	TYMS	TYMS	4068	0.075	0.42	NO
17	CMPK1	CMPK1	CMPK1	4399	0.067	0.41	NO
18	PNP	PNP	PNP	4901	0.055	0.38	NO
19	POLR3A	POLR3A	POLR3A	4978	0.054	0.38	NO
20	POLR2C	POLR2C	POLR2C	5361	0.047	0.37	NO
21	NME1	NME1	NME1	5373	0.046	0.37	NO
22	NT5M	NT5M	NT5M	5380	0.046	0.38	NO
23	TXNRD2	TXNRD2	TXNRD2	5436	0.045	0.38	NO
24	AK3	AK3	AK3	5598	0.042	0.37	NO
25	POLD4	POLD4	POLD4	5683	0.04	0.37	NO
26	UPRT	UPRT	UPRT	5916	0.037	0.36	NO
27	POLR2F	POLR2F	POLR2F	5941	0.036	0.36	NO
28	POLD2	POLD2	POLD2	5954	0.036	0.37	NO
29	NME4	NME4	NME4	6064	0.035	0.36	NO
30	NUDT2	NUDT2	NUDT2	6556	0.028	0.34	NO
31	POLR1B	POLR1B	POLR1B	6709	0.026	0.33	NO
32	NT5C2	NT5C2	NT5C2	6956	0.023	0.32	NO
33	CAD	CAD	CAD	7404	0.017	0.3	NO
34	PNPT1	PNPT1	PNPT1	7547	0.015	0.29	NO
35	POLE	POLE	POLE	7602	0.014	0.29	NO
36	POLR1A	POLR1A	POLR1A	7830	0.011	0.28	NO
37	NME2	NME2	NME2	7935	0.01	0.28	NO
38	POLR3H	POLR3H	POLR3H	7955	0.01	0.28	NO
39	POLR2E	POLR2E	POLR2E	8034	0.009	0.27	NO
40	TYMP	TYMP	TYMP	8112	0.0082	0.27	NO
41	POLE4	POLE4	POLE4	8495	0.0035	0.25	NO
42	POLR3B	POLR3B	POLR3B	8543	0.0029	0.24	NO
43	CANT1	CANT1	CANT1	8554	0.0028	0.24	NO
44	UPP1	UPP1	UPP1	8705	0.0011	0.24	NO
45	RRM2B	RRM2B	RRM2B	8994	-0.0021	0.22	NO
46	POLR2G	POLR2G	POLR2G	9127	-0.0035	0.21	NO
47	TK2	TK2	TK2	9179	-0.0042	0.21	NO
48	POLR2D	POLR2D	POLR2D	9584	-0.0087	0.19	NO
49	POLR1E	POLR1E	POLR1E	9690	-0.01	0.18	NO
50	POLD1	POLD1	POLD1	9777	-0.011	0.18	NO
51	POLE3	POLE3	POLE3	9811	-0.011	0.18	NO
52	UCK1	UCK1	UCK1	10073	-0.014	0.17	NO
53	UMPS	UMPS	UMPS	10236	-0.016	0.16	NO
54	POLR2J	POLR2J	POLR2J	10264	-0.017	0.16	NO
55	POLR3GL	POLR3GL	POLR3GL	10516	-0.02	0.15	NO
56	POLR2H	POLR2H	POLR2H	10531	-0.02	0.15	NO
57	POLR3F	POLR3F	POLR3F	10582	-0.02	0.15	NO
58	DTYMK	DTYMK	DTYMK	10618	-0.021	0.15	NO
59	POLR2I	POLR2I	POLR2I	10880	-0.024	0.14	NO
60	POLR2K	POLR2K	POLR2K	11010	-0.026	0.13	NO
61	NME5	NME5	NME5	11013	-0.026	0.13	NO
62	TXNRD1	TXNRD1	TXNRD1	11066	-0.026	0.13	NO
63	ENTPD6	ENTPD6	ENTPD6	11513	-0.032	0.11	NO
64	RRM1	RRM1	RRM1	11628	-0.034	0.11	NO
65	CMPK2	CMPK2	CMPK2	11748	-0.036	0.1	NO
66	POLR3K	POLR3K	POLR3K	12141	-0.041	0.087	NO
67	POLD3	POLD3	POLD3	12143	-0.041	0.091	NO
68	POLA2	POLA2	POLA2	12452	-0.046	0.078	NO
69	NT5C3	NT5C3	NT5C3	12592	-0.048	0.075	NO
70	ENTPD3	ENTPD3	ENTPD3	12887	-0.053	0.064	NO
71	PRIM1	PRIM1	PRIM1	13176	-0.057	0.053	NO
72	POLR2A	POLR2A	POLR2A	13308	-0.059	0.052	NO
73	NME6	NME6	NME6	13412	-0.061	0.052	NO
74	CTPS	CTPS	CTPS	13600	-0.064	0.047	NO
75	POLR3C	POLR3C	POLR3C	13655	-0.065	0.051	NO
76	DUT	DUT	DUT	13700	-0.066	0.054	NO
77	POLR2J3	POLR2J3	POLR2J3	13780	-0.068	0.057	NO
78	POLR2L	POLR2L	POLR2L	14034	-0.073	0.05	NO
79	ENTPD1	ENTPD1	ENTPD1	14134	-0.075	0.051	NO
80	ITPA	ITPA	ITPA	14266	-0.078	0.051	NO
81	POLR2B	POLR2B	POLR2B	14339	-0.08	0.055	NO
82	ENTPD4	ENTPD4	ENTPD4	14385	-0.081	0.06	NO
83	DCTD	DCTD	DCTD	14520	-0.084	0.061	NO
84	PRIM2	PRIM2	PRIM2	14579	-0.086	0.066	NO
85	POLA1	POLA1	POLA1	14582	-0.086	0.074	NO
86	POLR1C	POLR1C	POLR1C	14605	-0.087	0.081	NO
87	CTPS2	CTPS2	CTPS2	14695	-0.089	0.084	NO
88	NT5C	NT5C	NT5C	14741	-0.09	0.091	NO
89	NME3	NME3	NME3	14925	-0.096	0.09	NO
90	UCK2	UCK2	UCK2	15022	-0.098	0.094	NO
91	NME7	NME7	NME7	15079	-0.1	0.1	NO
92	POLR1D	POLR1D	POLR1D	15115	-0.1	0.11	NO
93	POLR3D	POLR3D	POLR3D	15209	-0.1	0.11	NO
94	ZNRD1	ZNRD1	ZNRD1	15264	-0.11	0.12	NO
95	DCK	DCK	DCK	15419	-0.11	0.12	NO
96	UCKL1	UCKL1	UCKL1	15746	-0.12	0.12	NO
97	POLR2J2	POLR2J2	POLR2J2	16583	-0.17	0.085	NO

Figure S93. 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 STEROID HORMONE BIOSYNTHESIS.

Figure S94. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STEROID HORMONE 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 PURINE METABOLISM

Table S48. 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	DPYS	DPYS	DPYS	44	1.8	0.16	YES
2	UPB1	UPB1	UPB1	72	1.6	0.3	YES
3	AGXT2	AGXT2	AGXT2	170	1.1	0.4	YES
4	UPP2	UPP2	UPP2	270	0.78	0.46	YES
5	XDH	XDH	XDH	630	0.39	0.48	YES
6	DPYD	DPYD	DPYD	844	0.32	0.5	YES
7	DHODH	DHODH	DHODH	866	0.31	0.52	YES
8	CDA	CDA	CDA	918	0.3	0.55	YES
9	GLRX	GLRX	GLRX	976	0.28	0.57	YES
10	GDA	GDA	GDA	1208	0.24	0.58	YES
11	AK5	AK5	AK5	1551	0.2	0.58	YES
12	ADSSL1	ADSSL1	ADSSL1	1639	0.19	0.6	YES
13	RRM2	RRM2	RRM2	1650	0.19	0.61	YES
14	GMPR	GMPR	GMPR	1739	0.18	0.62	YES
15	CAT	CAT	CAT	1814	0.18	0.64	YES
16	ADK	ADK	ADK	2085	0.16	0.64	YES
17	NT5C1B	NT5C1B	NT5C1B	2090	0.16	0.65	YES
18	NT5E	NT5E	NT5E	2540	0.13	0.64	NO
19	ADA	ADA	ADA	2583	0.13	0.64	NO
20	TK1	TK1	TK1	3001	0.11	0.63	NO
21	NME1-NME2	NME1-NME2	NME1-NME2	3845	0.081	0.59	NO
22	TYMS	TYMS	TYMS	4068	0.075	0.59	NO
23	ADAL	ADAL	ADAL	4116	0.074	0.59	NO
24	CMPK1	CMPK1	CMPK1	4399	0.067	0.58	NO
25	ADSS	ADSS	ADSS	4791	0.058	0.57	NO
26	PNP	PNP	PNP	4901	0.055	0.56	NO
27	GMPS	GMPS	GMPS	5266	0.049	0.55	NO
28	NME1	NME1	NME1	5373	0.046	0.55	NO
29	NT5M	NT5M	NT5M	5380	0.046	0.55	NO
30	APRT	APRT	APRT	5411	0.046	0.55	NO
31	GMPR2	GMPR2	GMPR2	5625	0.042	0.55	NO
32	ADSL	ADSL	ADSL	5753	0.039	0.54	NO
33	GUK1	GUK1	GUK1	5803	0.038	0.54	NO
34	NME4	NME4	NME4	6064	0.035	0.53	NO
35	GART	GART	GART	6134	0.034	0.53	NO
36	NT5C2	NT5C2	NT5C2	6956	0.023	0.49	NO
37	HPRT1	HPRT1	HPRT1	7109	0.021	0.48	NO
38	CAD	CAD	CAD	7404	0.017	0.47	NO
39	AMPD2	AMPD2	AMPD2	7745	0.012	0.45	NO
40	NME2	NME2	NME2	7935	0.01	0.44	NO
41	TYMP	TYMP	TYMP	8112	0.0082	0.43	NO
42	ATIC	ATIC	ATIC	8201	0.007	0.43	NO
43	AK2	AK2	AK2	8288	0.006	0.42	NO
44	IMPDH1	IMPDH1	IMPDH1	8315	0.0055	0.42	NO
45	PAICS	PAICS	PAICS	8357	0.005	0.42	NO
46	UPP1	UPP1	UPP1	8705	0.0011	0.4	NO
47	RRM2B	RRM2B	RRM2B	8994	-0.0021	0.38	NO
48	TK2	TK2	TK2	9179	-0.0042	0.38	NO
49	GPX1	GPX1	GPX1	9226	-0.0048	0.37	NO
50	UCK1	UCK1	UCK1	10073	-0.014	0.33	NO
51	GSR	GSR	GSR	10199	-0.016	0.32	NO
52	UMPS	UMPS	UMPS	10236	-0.016	0.32	NO
53	DTYMK	DTYMK	DTYMK	10618	-0.021	0.3	NO
54	PFAS	PFAS	PFAS	10920	-0.024	0.29	NO
55	TXNRD1	TXNRD1	TXNRD1	11066	-0.026	0.28	NO
56	RRM1	RRM1	RRM1	11628	-0.034	0.25	NO
57	PPAT	PPAT	PPAT	11887	-0.037	0.24	NO
58	DGUOK	DGUOK	DGUOK	12084	-0.04	0.24	NO
59	TXN	TXN	TXN	12326	-0.044	0.23	NO
60	NT5C3	NT5C3	NT5C3	12592	-0.048	0.22	NO
61	AK1	AK1	AK1	13107	-0.056	0.19	NO
62	CTPS	CTPS	CTPS	13600	-0.064	0.17	NO
63	DUT	DUT	DUT	13700	-0.066	0.17	NO
64	IMPDH2	IMPDH2	IMPDH2	14060	-0.074	0.16	NO
65	AMPD3	AMPD3	AMPD3	14292	-0.079	0.15	NO
66	DCTD	DCTD	DCTD	14520	-0.084	0.15	NO
67	CTPS2	CTPS2	CTPS2	14695	-0.089	0.15	NO
68	NT5C	NT5C	NT5C	14741	-0.09	0.15	NO
69	UCK2	UCK2	UCK2	15022	-0.098	0.15	NO
70	DCK	DCK	DCK	15419	-0.11	0.14	NO
71	AMPD1	AMPD1	AMPD1	16373	-0.16	0.096	NO

Figure S95. 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 S96. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

Table S49. 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	ADH4	ADH4	ADH4	43	1.8	0.12	YES
2	ALDOB	ALDOB	ALDOB	129	1.2	0.2	YES
3	PCK1	PCK1	PCK1	140	1.2	0.28	YES
4	ADH1A	ADH1A	ADH1A	147	1.2	0.36	YES
5	ADH1B	ADH1B	ADH1B	196	0.99	0.43	YES
6	PKLR	PKLR	PKLR	279	0.74	0.47	YES
7	G6PC	G6PC	G6PC	297	0.69	0.52	YES
8	ADH1C	ADH1C	ADH1C	302	0.69	0.57	YES
9	ADH6	ADH6	ADH6	329	0.66	0.61	YES
10	FBP1	FBP1	FBP1	490	0.48	0.63	YES
11	PCK2	PCK2	PCK2	791	0.33	0.64	YES
12	LDHAL6B	LDHAL6B	LDHAL6B	795	0.33	0.66	YES
13	ALDH2	ALDH2	ALDH2	1082	0.26	0.66	YES
14	ALDH1B1	ALDH1B1	ALDH1B1	1370	0.22	0.66	YES
15	PGAM2	PGAM2	PGAM2	1378	0.22	0.68	YES
16	LDHC	LDHC	LDHC	1468	0.21	0.69	YES
17	HK3	HK3	HK3	1599	0.19	0.69	YES
18	ALDH1A3	ALDH1A3	ALDH1A3	1708	0.18	0.7	YES
19	PGM1	PGM1	PGM1	2116	0.15	0.69	NO
20	ENO3	ENO3	ENO3	2164	0.15	0.7	NO
21	LDHAL6A	LDHAL6A	LDHAL6A	2287	0.14	0.7	NO
22	ALDH7A1	ALDH7A1	ALDH7A1	2555	0.13	0.69	NO
23	PGAM4	PGAM4	PGAM4	2702	0.12	0.69	NO
24	ALDH3A1	ALDH3A1	ALDH3A1	2979	0.11	0.68	NO
25	GALM	GALM	GALM	3147	0.1	0.68	NO
26	ALDOC	ALDOC	ALDOC	3400	0.094	0.68	NO
27	PDHB	PDHB	PDHB	4464	0.065	0.62	NO
28	AKR1A1	AKR1A1	AKR1A1	4495	0.064	0.62	NO
29	DLD	DLD	DLD	4899	0.056	0.6	NO
30	PGM2	PGM2	PGM2	6058	0.035	0.54	NO
31	ALDH3A2	ALDH3A2	ALDH3A2	6217	0.033	0.54	NO
32	PGAM1	PGAM1	PGAM1	6294	0.032	0.54	NO
33	PDHA1	PDHA1	PDHA1	6509	0.029	0.52	NO
34	ACSS2	ACSS2	ACSS2	7075	0.021	0.5	NO
35	PFKM	PFKM	PFKM	7898	0.011	0.45	NO
36	GPI	GPI	GPI	8060	0.0088	0.44	NO
37	ALDH9A1	ALDH9A1	ALDH9A1	8254	0.0064	0.43	NO
38	LDHA	LDHA	LDHA	9002	-0.0022	0.39	NO
39	ALDH3B1	ALDH3B1	ALDH3B1	9412	-0.0067	0.37	NO
40	PGK1	PGK1	PGK1	9470	-0.0074	0.37	NO
41	ENO1	ENO1	ENO1	9872	-0.012	0.34	NO
42	PFKL	PFKL	PFKL	9990	-0.013	0.34	NO
43	ADH5	ADH5	ADH5	10368	-0.018	0.32	NO
44	BPGM	BPGM	BPGM	10665	-0.021	0.3	NO
45	GAPDH	GAPDH	GAPDH	10701	-0.022	0.3	NO
46	ACSS1	ACSS1	ACSS1	11074	-0.027	0.28	NO
47	TPI1	TPI1	TPI1	11099	-0.027	0.28	NO
48	DLAT	DLAT	DLAT	12129	-0.041	0.23	NO
49	HK2	HK2	HK2	12234	-0.042	0.23	NO
50	HK1	HK1	HK1	13126	-0.056	0.18	NO
51	LDHB	LDHB	LDHB	13454	-0.062	0.17	NO
52	ALDOA	ALDOA	ALDOA	13590	-0.064	0.17	NO
53	PKM2	PKM2	PKM2	15166	-0.1	0.086	NO
54	PFKP	PFKP	PFKP	15414	-0.11	0.08	NO
55	GCK	GCK	GCK	16688	-0.18	0.022	NO
56	ENO2	ENO2	ENO2	16948	-0.2	0.021	NO
57	ALDH3B2	ALDH3B2	ALDH3B2	17479	-0.27	0.01	NO
58	G6PC2	G6PC2	G6PC2	17869	-0.36	0.014	NO

Figure S97. 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 S98. 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

Table S50. 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	CYP8B1	CYP8B1	CYP8B1	28	1.9	0.071	YES
2	APOA5	APOA5	APOA5	29	1.9	0.14	YES
3	CYP4A22	CYP4A22	CYP4A22	31	1.9	0.22	YES
4	APOC3	APOC3	APOC3	61	1.7	0.28	YES
5	APOA1	APOA1	APOA1	83	1.5	0.33	YES
6	FABP1	FABP1	FABP1	121	1.3	0.38	YES
7	PCK1	PCK1	PCK1	140	1.2	0.42	YES
8	CYP7A1	CYP7A1	CYP7A1	144	1.2	0.47	YES
9	APOA2	APOA2	APOA2	155	1.1	0.51	YES
10	SLC27A5	SLC27A5	SLC27A5	156	1.1	0.55	YES
11	HMGCS2	HMGCS2	HMGCS2	175	1	0.59	YES
12	ACOX2	ACOX2	ACOX2	226	0.87	0.62	YES
13	CYP4A11	CYP4A11	CYP4A11	239	0.83	0.65	YES
14	PLIN1	PLIN1	PLIN1	242	0.83	0.68	YES
15	ACADL	ACADL	ACADL	288	0.72	0.71	YES
16	EHHADH	EHHADH	EHHADH	333	0.65	0.73	YES
17	ACSL1	ACSL1	ACSL1	473	0.49	0.74	YES
18	SLC27A2	SLC27A2	SLC27A2	507	0.46	0.76	YES
19	CYP27A1	CYP27A1	CYP27A1	581	0.42	0.77	YES
20	CD36	CD36	CD36	651	0.38	0.78	YES
21	PCK2	PCK2	PCK2	791	0.33	0.78	YES
22	ANGPTL4	ANGPTL4	ANGPTL4	805	0.33	0.79	YES
23	ACSL6	ACSL6	ACSL6	864	0.31	0.8	YES
24	FABP3	FABP3	FABP3	1179	0.25	0.79	YES
25	ACSL5	ACSL5	ACSL5	1246	0.24	0.8	YES
26	SCD	SCD	SCD	1387	0.22	0.8	YES
27	FABP4	FABP4	FABP4	1465	0.21	0.8	YES
28	ACAA1	ACAA1	ACAA1	1754	0.18	0.8	YES
29	SCP2	SCP2	SCP2	1818	0.18	0.8	YES
30	ACADM	ACADM	ACADM	1865	0.17	0.8	YES
31	RXRG	RXRG	RXRG	1917	0.17	0.8	YES
32	CPT2	CPT2	CPT2	1964	0.16	0.81	YES
33	PPARA	PPARA	PPARA	1990	0.16	0.81	YES
34	ACOX1	ACOX1	ACOX1	2024	0.16	0.82	YES
35	SORBS1	SORBS1	SORBS1	2470	0.13	0.8	NO
36	CPT1C	CPT1C	CPT1C	2480	0.13	0.8	NO
37	AQP7	AQP7	AQP7	3697	0.085	0.74	NO
38	ACSL3	ACSL3	ACSL3	4014	0.076	0.72	NO
39	GK	GK	GK	5111	0.052	0.66	NO
40	CPT1A	CPT1A	CPT1A	5540	0.043	0.64	NO
41	ME1	ME1	ME1	6698	0.026	0.58	NO
42	RXRA	RXRA	RXRA	7058	0.021	0.56	NO
43	FABP5	FABP5	FABP5	7106	0.021	0.56	NO
44	PDPK1	PDPK1	PDPK1	7420	0.016	0.54	NO
45	PLTP	PLTP	PLTP	7779	0.012	0.52	NO
46	ACOX3	ACOX3	ACOX3	7887	0.011	0.52	NO
47	PPARG	PPARG	PPARG	8013	0.0092	0.51	NO
48	CPT1B	CPT1B	CPT1B	8122	0.0081	0.5	NO
49	SLC27A4	SLC27A4	SLC27A4	9019	-0.0025	0.46	NO
50	PPARD	PPARD	PPARD	9334	-0.0059	0.44	NO
51	UBC	UBC	UBC	9593	-0.0088	0.42	NO
52	DBI	DBI	DBI	10492	-0.019	0.38	NO
53	RXRB	RXRB	RXRB	10934	-0.025	0.35	NO
54	FADS2	FADS2	FADS2	10935	-0.025	0.35	NO
55	FABP6	FABP6	FABP6	11291	-0.03	0.33	NO
56	SLC27A1	SLC27A1	SLC27A1	12327	-0.044	0.28	NO
57	ILK	ILK	ILK	12767	-0.051	0.26	NO
58	NR1H3	NR1H3	NR1H3	13296	-0.059	0.23	NO
59	ACSL4	ACSL4	ACSL4	13367	-0.06	0.23	NO
60	SCD5	SCD5	SCD5	14093	-0.074	0.19	NO
61	OLR1	OLR1	OLR1	15569	-0.12	0.11	NO
62	LPL	LPL	LPL	15982	-0.13	0.095	NO
63	MMP1	MMP1	MMP1	17642	-0.3	0.014	NO
64	SLC27A6	SLC27A6	SLC27A6	17735	-0.32	0.021	NO

Figure S99. 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 S100. 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

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 clus6 enriched pathways

Table 8. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus6. 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
KEGG NOTCH SIGNALING PATHWAY	47	genes.ES.table	0.35	1.3	0.15	1	1	0.3	0.2	0.24	1	0.86
ST ERK1 ERK2 MAPK PATHWAY	31	genes.ES.table	0.3	1.2	0.23	1	1	0.48	0.32	0.33	1	0.8
PID INTEGRIN3 PATHWAY	43	genes.ES.table	0.48	1.2	0.25	1	1	0.42	0.22	0.33	1	0.78
PID RHOA REG PATHWAY	44	genes.ES.table	0.39	1.3	0.13	1	1	0.46	0.26	0.34	1	0.88
PID NECTIN PATHWAY	30	genes.ES.table	0.39	1.2	0.28	1	1	0.3	0.24	0.23	1	0.83
PID TGFBRPATHWAY	55	genes.ES.table	0.43	1.7	0.032	1	0.84	0.27	0.23	0.21	1	0.64
REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS	38	genes.ES.table	0.38	1.3	0.12	1	1	0.37	0.27	0.27	1	0.87
REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION	27	genes.ES.table	0.47	1.5	0.098	1	0.98	0.74	0.38	0.46	1	0.72
REACTOME PRE NOTCH EXPRESSION AND PROCESSING	41	genes.ES.table	0.31	1.2	0.21	1	1	0.42	0.33	0.28	1	0.81
REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION	44	genes.ES.table	0.43	1.6	0.061	1	0.96	0.43	0.33	0.29	1	0.63

genes ES table in pathway: KEGG NOTCH SIGNALING PATHWAY

Table S51. 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	DACT2	DACT2	DACT2	99	0.64	0.11	YES
2	CTGF	CTGF	CTGF	548	0.39	0.15	YES
3	BAMBI	BAMBI	BAMBI	558	0.39	0.22	YES
4	TGFB2	TGFB2	TGFB2	625	0.37	0.28	YES
5	SMAD7	SMAD7	SMAD7	1537	0.25	0.28	YES
6	OCLN	OCLN	OCLN	1660	0.24	0.31	YES
7	TGFBRAP1	TGFBRAP1	TGFBRAP1	1697	0.23	0.35	YES
8	TGFBR3	TGFBR3	TGFBR3	2037	0.21	0.37	YES
9	ZFYVE9	ZFYVE9	ZFYVE9	2200	0.2	0.4	YES
10	SMURF2	SMURF2	SMURF2	2784	0.16	0.39	YES
11	SKIL	SKIL	SKIL	3199	0.14	0.39	YES
12	PPP2R2A	PPP2R2A	PPP2R2A	3495	0.13	0.4	YES
13	SHC1	SHC1	SHC1	3529	0.13	0.42	YES
14	PPP2CB	PPP2CB	PPP2CB	3854	0.12	0.42	YES
15	WWP1	WWP1	WWP1	4134	0.11	0.43	YES
16	ZFYVE16	ZFYVE16	ZFYVE16	4610	0.091	0.42	NO
17	SMAD4	SMAD4	SMAD4	4853	0.084	0.42	NO
18	PDPK1	PDPK1	PDPK1	5007	0.08	0.42	NO
19	TAB1	TAB1	TAB1	5374	0.07	0.42	NO
20	XIAP	XIAP	XIAP	6021	0.054	0.39	NO
21	PPP1R15A	PPP1R15A	PPP1R15A	6264	0.048	0.38	NO
22	YWHAE	YWHAE	YWHAE	6529	0.043	0.38	NO
23	CTNNB1	CTNNB1	CTNNB1	6607	0.041	0.38	NO
24	YAP1	YAP1	YAP1	6796	0.037	0.38	NO
25	SMAD2	SMAD2	SMAD2	7026	0.032	0.37	NO
26	TGFB1	TGFB1	TGFB1	7051	0.032	0.38	NO
27	DAXX	DAXX	DAXX	7410	0.025	0.36	NO
28	TGFB3	TGFB3	TGFB3	7775	0.018	0.34	NO
29	AXIN1	AXIN1	AXIN1	7933	0.015	0.34	NO
30	FKBP1A	FKBP1A	FKBP1A	8525	0.0037	0.3	NO
31	RHOA	RHOA	RHOA	8539	0.0034	0.3	NO
32	RNF111	RNF111	RNF111	8583	0.0028	0.3	NO
33	ITCH	ITCH	ITCH	8640	0.0019	0.3	NO
34	SMAD3	SMAD3	SMAD3	8685	0.0011	0.3	NO
35	STRAP	STRAP	STRAP	8850	-0.0018	0.29	NO
36	SMURF1	SMURF1	SMURF1	8971	-0.004	0.28	NO
37	NEDD4L	NEDD4L	NEDD4L	9041	-0.0053	0.28	NO
38	TGFBR1	TGFBR1	TGFBR1	9571	-0.014	0.25	NO
39	SPTBN1	SPTBN1	SPTBN1	9608	-0.015	0.25	NO
40	DYNLRB1	DYNLRB1	DYNLRB1	10063	-0.023	0.23	NO
41	MAP3K7	MAP3K7	MAP3K7	10225	-0.026	0.23	NO
42	EIF2A	EIF2A	EIF2A	10303	-0.027	0.23	NO
43	PML	PML	PML	11238	-0.046	0.18	NO
44	RPS6KB1	RPS6KB1	RPS6KB1	11443	-0.05	0.18	NO
45	PPP2CA	PPP2CA	PPP2CA	11653	-0.055	0.18	NO
46	TAB2	TAB2	TAB2	11972	-0.062	0.18	NO
47	CAV1	CAV1	CAV1	11982	-0.062	0.18	NO
48	PPP1CA	PPP1CA	PPP1CA	12093	-0.065	0.19	NO
49	GRB2	GRB2	GRB2	12474	-0.074	0.18	NO
50	TGFBR2	TGFBR2	TGFBR2	12522	-0.076	0.19	NO
51	SOS1	SOS1	SOS1	12817	-0.085	0.19	NO
52	DAB2	DAB2	DAB2	12986	-0.09	0.2	NO
53	ARRB2	ARRB2	ARRB2	13205	-0.097	0.2	NO
54	PARD6A	PARD6A	PARD6A	13705	-0.11	0.2	NO
55	CAMK2A	CAMK2A	CAMK2A	15984	-0.27	0.12	NO

Figure S101. 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 NOTCH SIGNALING PATHWAY.

Figure S102. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH 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: ST ERK1 ERK2 MAPK PATHWAY

Table S52. 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	WWTR1	WWTR1	WWTR1	778	0.34	0.018	YES
2	E2F5	E2F5	E2F5	896	0.32	0.069	YES
3	SERPINE1	SERPINE1	SERPINE1	997	0.3	0.12	YES
4	PMEPA1	PMEPA1	PMEPA1	1083	0.3	0.17	YES
5	SMAD7	SMAD7	SMAD7	1537	0.25	0.19	YES
6	FURIN	FURIN	FURIN	2148	0.2	0.19	YES
7	ZFYVE9	ZFYVE9	ZFYVE9	2200	0.2	0.22	YES
8	TGIF2	TGIF2	TGIF2	2482	0.18	0.24	YES
9	CGN	CGN	CGN	2566	0.17	0.26	YES
10	SMURF2	SMURF2	SMURF2	2784	0.16	0.28	YES
11	SKIL	SKIL	SKIL	3199	0.14	0.28	YES
12	F11R	F11R	F11R	3265	0.14	0.3	YES
13	RBL1	RBL1	RBL1	3296	0.14	0.33	YES
14	SKI	SKI	SKI	3341	0.14	0.35	YES
15	JUNB	JUNB	JUNB	3534	0.13	0.36	YES
16	ARHGEF18	ARHGEF18	ARHGEF18	3758	0.12	0.37	YES
17	PARP1	PARP1	PARP1	3793	0.12	0.39	YES
18	CDK9	CDK9	CDK9	4209	0.1	0.39	YES
19	CDKN2B	CDKN2B	CDKN2B	4391	0.098	0.39	YES
20	NCOR2	NCOR2	NCOR2	4640	0.09	0.4	YES
21	SMAD4	SMAD4	SMAD4	4853	0.084	0.4	YES
22	UCHL5	UCHL5	UCHL5	5062	0.078	0.4	YES
23	PARD3	PARD3	PARD3	5383	0.07	0.4	YES
24	NCOR1	NCOR1	NCOR1	5489	0.067	0.4	YES
25	CCNT1	CCNT1	CCNT1	5577	0.064	0.41	YES
26	SP1	SP1	SP1	5641	0.062	0.42	YES
27	PPP1R15A	PPP1R15A	PPP1R15A	6264	0.048	0.39	NO
28	PPM1A	PPM1A	PPM1A	6327	0.047	0.4	NO
29	TRIM33	TRIM33	TRIM33	6960	0.034	0.37	NO
30	SMAD2	SMAD2	SMAD2	7026	0.032	0.37	NO
31	TGFB1	TGFB1	TGFB1	7051	0.032	0.38	NO
32	UBE2D3	UBE2D3	UBE2D3	7577	0.022	0.35	NO
33	CCNT2	CCNT2	CCNT2	7584	0.022	0.35	NO
34	TGIF1	TGIF1	TGIF1	7809	0.017	0.34	NO
35	FKBP1A	FKBP1A	FKBP1A	8525	0.0037	0.3	NO
36	RHOA	RHOA	RHOA	8539	0.0034	0.3	NO
37	PPP1CC	PPP1CC	PPP1CC	8560	0.0032	0.3	NO
38	USP9X	USP9X	USP9X	8612	0.0025	0.3	NO
39	SMAD3	SMAD3	SMAD3	8685	0.0011	0.3	NO
40	STRAP	STRAP	STRAP	8850	-0.0018	0.29	NO
41	SMURF1	SMURF1	SMURF1	8971	-0.004	0.28	NO
42	RPS27A	RPS27A	RPS27A	9002	-0.0045	0.28	NO
43	TGFBR1	TGFBR1	TGFBR1	9571	-0.014	0.25	NO
44	UBE2D1	UBE2D1	UBE2D1	9908	-0.02	0.24	NO
45	UBA52	UBA52	UBA52	10586	-0.033	0.21	NO
46	MEN1	MEN1	MEN1	10711	-0.036	0.21	NO
47	MTMR4	MTMR4	MTMR4	10901	-0.039	0.2	NO
48	CCNC	CCNC	CCNC	11183	-0.045	0.2	NO
49	XPO1	XPO1	XPO1	11253	-0.046	0.2	NO
50	STUB1	STUB1	STUB1	11656	-0.055	0.19	NO
51	HDAC1	HDAC1	HDAC1	11744	-0.057	0.19	NO
52	PPP1CB	PPP1CB	PPP1CB	11770	-0.057	0.2	NO
53	PRKCZ	PRKCZ	PRKCZ	11991	-0.062	0.2	NO
54	PPP1CA	PPP1CA	PPP1CA	12093	-0.065	0.21	NO
55	TGFBR2	TGFBR2	TGFBR2	12522	-0.076	0.2	NO
56	TFDP1	TFDP1	TFDP1	12753	-0.083	0.2	NO
57	MYC	MYC	MYC	13449	-0.1	0.18	NO
58	PARD6A	PARD6A	PARD6A	13705	-0.11	0.19	NO
59	CDK8	CDK8	CDK8	14027	-0.13	0.19	NO
60	E2F4	E2F4	E2F4	15123	-0.19	0.17	NO

Figure S103. 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: ST ERK1 ERK2 MAPK PATHWAY.

Figure S104. Get High-res Image For the top 5 core enriched genes in the pathway: ST ERK1 ERK2 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: PID INTEGRIN3 PATHWAY

Table S53. 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	TLE2	TLE2	TLE2	454	0.41	0.074	YES
2	HEY1	HEY1	HEY1	730	0.34	0.14	YES
3	MAML3	MAML3	MAML3	735	0.34	0.22	YES
4	MAMLD1	MAMLD1	MAMLD1	1011	0.3	0.28	YES
5	MAML2	MAML2	MAML2	1501	0.25	0.32	YES
6	HES1	HES1	HES1	1886	0.22	0.35	YES
7	HDAC11	HDAC11	HDAC11	2444	0.18	0.36	YES
8	TLE4	TLE4	TLE4	2668	0.17	0.39	YES
9	HDAC5	HDAC5	HDAC5	2840	0.16	0.42	YES
10	HDAC7	HDAC7	HDAC7	3984	0.11	0.38	YES
11	TLE1	TLE1	TLE1	4408	0.097	0.38	YES
12	NCOR2	NCOR2	NCOR2	4640	0.09	0.39	YES
13	MAML1	MAML1	MAML1	5273	0.073	0.37	YES
14	HDAC4	HDAC4	HDAC4	5359	0.07	0.38	YES
15	KAT2A	KAT2A	KAT2A	5366	0.07	0.4	YES
16	NCOR1	NCOR1	NCOR1	5489	0.067	0.41	YES
17	CREBBP	CREBBP	CREBBP	5599	0.064	0.42	YES
18	KAT2B	KAT2B	KAT2B	5825	0.059	0.42	YES
19	EP300	EP300	EP300	5906	0.057	0.43	YES
20	HEYL	HEYL	HEYL	6272	0.048	0.42	NO
21	FBXW7	FBXW7	FBXW7	6548	0.042	0.42	NO
22	RBPJ	RBPJ	RBPJ	6818	0.037	0.41	NO
23	HDAC10	HDAC10	HDAC10	6931	0.035	0.41	NO
24	HDAC2	HDAC2	HDAC2	7338	0.026	0.4	NO
25	HIF1A	HIF1A	HIF1A	7342	0.026	0.4	NO
26	SKP1	SKP1	SKP1	7525	0.023	0.4	NO
27	HES5	HES5	HES5	7826	0.017	0.38	NO
28	HDAC8	HDAC8	HDAC8	7924	0.015	0.38	NO
29	HEY2	HEY2	HEY2	8335	0.0074	0.36	NO
30	RPS27A	RPS27A	RPS27A	9002	-0.0045	0.33	NO
31	TBL1X	TBL1X	TBL1X	9567	-0.014	0.3	NO
32	HDAC6	HDAC6	HDAC6	9927	-0.021	0.28	NO
33	CUL1	CUL1	CUL1	10217	-0.026	0.27	NO
34	HDAC9	HDAC9	HDAC9	10351	-0.028	0.27	NO
35	UBA52	UBA52	UBA52	10586	-0.033	0.27	NO
36	SNW1	SNW1	SNW1	10685	-0.035	0.27	NO
37	HDAC3	HDAC3	HDAC3	11172	-0.045	0.26	NO
38	CCNC	CCNC	CCNC	11183	-0.045	0.27	NO
39	HDAC1	HDAC1	HDAC1	11744	-0.057	0.25	NO
40	RBX1	RBX1	RBX1	11908	-0.06	0.25	NO
41	TBL1XR1	TBL1XR1	TBL1XR1	12105	-0.065	0.26	NO
42	TLE3	TLE3	TLE3	12478	-0.074	0.26	NO
43	MYC	MYC	MYC	13449	-0.1	0.23	NO
44	CDK8	CDK8	CDK8	14027	-0.13	0.23	NO

Figure S105. 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: PID INTEGRIN3 PATHWAY.

Figure S106. Get High-res Image For the top 5 core enriched genes in the pathway: PID INTEGRIN3 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: PID RHOA REG PATHWAY

Table S54. 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	MAML3	MAML3	MAML3	735	0.34	0.076	YES
2	MAMLD1	MAMLD1	MAMLD1	1011	0.3	0.16	YES
3	MAML2	MAML2	MAML2	1501	0.25	0.22	YES
4	NOTCH3	NOTCH3	NOTCH3	1554	0.25	0.3	YES
5	CCND1	CCND1	CCND1	1727	0.23	0.37	YES
6	TP53	TP53	TP53	3221	0.14	0.34	YES
7	EIF2C2	EIF2C2	EIF2C2	3291	0.14	0.38	YES
8	NOTCH2	NOTCH2	NOTCH2	3650	0.12	0.4	YES
9	TNRC6C	TNRC6C	TNRC6C	4910	0.082	0.36	YES
10	E2F3	E2F3	E2F3	5132	0.076	0.38	YES
11	MAML1	MAML1	MAML1	5273	0.073	0.39	YES
12	KAT2A	KAT2A	KAT2A	5366	0.07	0.41	YES
13	CREBBP	CREBBP	CREBBP	5599	0.064	0.42	YES
14	EIF2C4	EIF2C4	EIF2C4	5799	0.059	0.43	YES
15	KAT2B	KAT2B	KAT2B	5825	0.059	0.45	YES
16	EP300	EP300	EP300	5906	0.057	0.46	YES
17	TNRC6A	TNRC6A	TNRC6A	6407	0.045	0.45	YES
18	E2F1	E2F1	E2F1	6555	0.042	0.46	YES
19	JUN	JUN	JUN	6765	0.038	0.46	YES
20	RBPJ	RBPJ	RBPJ	6818	0.037	0.47	YES
21	TNRC6B	TNRC6B	TNRC6B	8817	-0.0011	0.36	NO
22	SNW1	SNW1	SNW1	10685	-0.035	0.26	NO
23	EIF2C1	EIF2C1	EIF2C1	10809	-0.037	0.27	NO
24	MOV10	MOV10	MOV10	12298	-0.069	0.21	NO
25	NOTCH4	NOTCH4	NOTCH4	12559	-0.077	0.22	NO
26	TFDP1	TFDP1	TFDP1	12753	-0.083	0.24	NO
27	EIF2C3	EIF2C3	EIF2C3	14690	-0.16	0.19	NO

Figure S107. 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: PID RHOA REG PATHWAY.

Figure S108. Get High-res Image For the top 5 core enriched genes in the pathway: PID RHOA REG 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: PID NECTIN PATHWAY

Table S55. 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	ZFP37	ZFP37	ZFP37	61	0.7	0.01	YES
2	ZNF439	ZNF439	ZNF439	85	0.66	0.022	YES
3	ZNF433	ZNF433	ZNF433	110	0.62	0.032	YES
4	ZNF415	ZNF415	ZNF415	147	0.58	0.041	YES
5	NR3C2	NR3C2	NR3C2	171	0.55	0.05	YES
6	ZFP2	ZFP2	ZFP2	195	0.53	0.06	YES
7	ESRRG	ESRRG	ESRRG	226	0.51	0.068	YES
8	ZNF577	ZNF577	ZNF577	229	0.51	0.077	YES
9	NR5A2	NR5A2	NR5A2	242	0.5	0.086	YES
10	ZNF382	ZNF382	ZNF382	288	0.48	0.093	YES
11	ZNF582	ZNF582	ZNF582	302	0.47	0.1	YES
12	ZNF454	ZNF454	ZNF454	357	0.45	0.11	YES
13	ZNF649	ZNF649	ZNF649	459	0.41	0.11	YES
14	ZNF30	ZNF30	ZNF30	476	0.41	0.12	YES
15	ZNF347	ZNF347	ZNF347	487	0.4	0.12	YES
16	ZNF10	ZNF10	ZNF10	546	0.39	0.13	YES
17	CTGF	CTGF	CTGF	548	0.39	0.14	YES
18	ZNF625	ZNF625	ZNF625	549	0.39	0.14	YES
19	ZNF214	ZNF214	ZNF214	551	0.39	0.15	YES
20	ZNF287	ZNF287	ZNF287	600	0.38	0.15	YES
21	ZNF418	ZNF418	ZNF418	653	0.36	0.16	YES
22	ZNF641	ZNF641	ZNF641	656	0.36	0.16	YES
23	ZNF540	ZNF540	ZNF540	684	0.35	0.17	YES
24	ZNF620	ZNF620	ZNF620	702	0.35	0.18	YES
25	ZNF528	ZNF528	ZNF528	715	0.35	0.18	YES
26	MAML3	MAML3	MAML3	735	0.34	0.19	YES
27	WWTR1	WWTR1	WWTR1	778	0.34	0.19	YES
28	ZNF425	ZNF425	ZNF425	796	0.34	0.2	YES
29	ZIK1	ZIK1	ZIK1	800	0.34	0.2	YES
30	ZNF615	ZNF615	ZNF615	824	0.33	0.21	YES
31	ZNF354C	ZNF354C	ZNF354C	857	0.32	0.21	YES
32	E2F5	E2F5	E2F5	896	0.32	0.22	YES
33	ZNF485	ZNF485	ZNF485	961	0.31	0.22	YES
34	SERPINE1	SERPINE1	SERPINE1	997	0.3	0.22	YES
35	ZNF619	ZNF619	ZNF619	998	0.3	0.23	YES
36	MAMLD1	MAMLD1	MAMLD1	1011	0.3	0.23	YES
37	RARG	RARG	RARG	1051	0.3	0.24	YES
38	ZNF583	ZNF583	ZNF583	1152	0.29	0.24	YES
39	ZNF141	ZNF141	ZNF141	1169	0.29	0.24	YES
40	ZNF426	ZNF426	ZNF426	1253	0.28	0.24	YES
41	ZNF643	ZNF643	ZNF643	1333	0.27	0.24	YES
42	ZNF442	ZNF442	ZNF442	1363	0.27	0.25	YES
43	ZNF154	ZNF154	ZNF154	1380	0.26	0.25	YES
44	ZNF596	ZNF596	ZNF596	1414	0.26	0.25	YES
45	ZNF192	ZNF192	ZNF192	1455	0.26	0.26	YES
46	MAML2	MAML2	MAML2	1501	0.25	0.26	YES
47	ZNF157	ZNF157	ZNF157	1523	0.25	0.26	YES
48	ZNF642	ZNF642	ZNF642	1535	0.25	0.27	YES
49	SMAD7	SMAD7	SMAD7	1537	0.25	0.27	YES
50	ZNF285	ZNF285	ZNF285	1546	0.25	0.28	YES
51	ZNF250	ZNF250	ZNF250	1551	0.25	0.28	YES
52	NOTCH3	NOTCH3	NOTCH3	1554	0.25	0.28	YES
53	ZNF585B	ZNF585B	ZNF585B	1595	0.24	0.29	YES
54	ZNF286A	ZNF286A	ZNF286A	1607	0.24	0.29	YES
55	ZNF519	ZNF519	ZNF519	1641	0.24	0.29	YES
56	ZNF215	ZNF215	ZNF215	1670	0.24	0.3	YES
57	TEAD2	TEAD2	TEAD2	1680	0.24	0.3	YES
58	ZNF563	ZNF563	ZNF563	1689	0.23	0.3	YES
59	ZKSCAN4	ZKSCAN4	ZKSCAN4	1702	0.23	0.31	YES
60	ZNF614	ZNF614	ZNF614	1717	0.23	0.31	YES
61	ZNF483	ZNF483	ZNF483	1734	0.23	0.32	YES
62	ZNF514	ZNF514	ZNF514	1791	0.22	0.32	YES
63	ZNF266	ZNF266	ZNF266	1802	0.22	0.32	YES
64	ZKSCAN3	ZKSCAN3	ZKSCAN3	1838	0.22	0.32	YES
65	ZKSCAN1	ZKSCAN1	ZKSCAN1	1935	0.21	0.32	YES
66	ZNF569	ZNF569	ZNF569	1963	0.21	0.32	YES
67	ZNF613	ZNF613	ZNF613	1967	0.21	0.33	YES
68	NR2E3	NR2E3	NR2E3	2001	0.21	0.33	YES
69	ZNF571	ZNF571	ZNF571	2032	0.21	0.33	YES
70	ZNF599	ZNF599	ZNF599	2034	0.21	0.34	YES
71	TEAD3	TEAD3	TEAD3	2156	0.2	0.33	YES
72	ZNF773	ZNF773	ZNF773	2157	0.2	0.34	YES
73	ZNF221	ZNF221	ZNF221	2171	0.2	0.34	YES
74	ZNF169	ZNF169	ZNF169	2175	0.2	0.34	YES
75	ZNF610	ZNF610	ZNF610	2176	0.2	0.35	YES
76	ZNF419	ZNF419	ZNF419	2180	0.2	0.35	YES
77	ZNF585A	ZNF585A	ZNF585A	2195	0.2	0.36	YES
78	ZNF559	ZNF559	ZNF559	2254	0.19	0.36	YES
79	TBX5	TBX5	TBX5	2356	0.19	0.35	YES
80	ZNF607	ZNF607	ZNF607	2368	0.19	0.36	YES
81	ZNF432	ZNF432	ZNF432	2407	0.18	0.36	YES
82	ZNF175	ZNF175	ZNF175	2417	0.18	0.36	YES
83	ZNF517	ZNF517	ZNF517	2430	0.18	0.36	YES
84	ZNF167	ZNF167	ZNF167	2440	0.18	0.37	YES
85	ZNF560	ZNF560	ZNF560	2465	0.18	0.37	YES
86	ZNF611	ZNF611	ZNF611	2474	0.18	0.37	YES
87	TGIF2	TGIF2	TGIF2	2482	0.18	0.37	YES
88	ZNF600	ZNF600	ZNF600	2516	0.18	0.38	YES
89	NR1D1	NR1D1	NR1D1	2527	0.18	0.38	YES
90	ZNF223	ZNF223	ZNF223	2541	0.18	0.38	YES
91	ZNF496	ZNF496	ZNF496	2563	0.17	0.38	YES
92	ZNF546	ZNF546	ZNF546	2569	0.17	0.39	YES
93	ZFP28	ZFP28	ZFP28	2708	0.16	0.38	YES
94	NR1D2	NR1D2	NR1D2	2749	0.16	0.38	YES
95	ZNF471	ZNF471	ZNF471	2779	0.16	0.38	YES
96	SMURF2	SMURF2	SMURF2	2784	0.16	0.39	YES
97	ZNF211	ZNF211	ZNF211	2839	0.16	0.39	YES
98	ZNF25	ZNF25	ZNF25	2849	0.16	0.39	YES
99	ZNF20	ZNF20	ZNF20	2851	0.16	0.39	YES
100	ZNF33B	ZNF33B	ZNF33B	2864	0.16	0.4	YES
101	NCOA2	NCOA2	NCOA2	2874	0.16	0.4	YES
102	ZNF493	ZNF493	ZNF493	2878	0.16	0.4	YES
103	ZNF256	ZNF256	ZNF256	2879	0.16	0.4	YES
104	ZNF225	ZNF225	ZNF225	2880	0.16	0.41	YES
105	ZNF443	ZNF443	ZNF443	2882	0.16	0.41	YES
106	ZNF222	ZNF222	ZNF222	2889	0.16	0.41	YES
107	ZNF551	ZNF551	ZNF551	2915	0.16	0.41	YES
108	ZNF337	ZNF337	ZNF337	2974	0.15	0.41	YES
109	ZNF627	ZNF627	ZNF627	2982	0.15	0.42	YES
110	ZNF565	ZNF565	ZNF565	3002	0.15	0.42	YES
111	ZNF343	ZNF343	ZNF343	3022	0.15	0.42	YES
112	ZNF300	ZNF300	ZNF300	3064	0.15	0.42	YES
113	MED30	MED30	MED30	3083	0.14	0.42	YES
114	ZFP112	ZFP112	ZFP112	3086	0.14	0.42	YES
115	ZNF605	ZNF605	ZNF605	3102	0.14	0.43	YES
116	ZNF606	ZNF606	ZNF606	3139	0.14	0.43	YES
117	NR0B2	NR0B2	NR0B2	3144	0.14	0.43	YES
118	ZNF566	ZNF566	ZNF566	3165	0.14	0.43	YES
119	SKIL	SKIL	SKIL	3199	0.14	0.43	YES
120	RORA	RORA	RORA	3204	0.14	0.43	YES
121	PGR	PGR	PGR	3227	0.14	0.44	YES
122	ZNF416	ZNF416	ZNF416	3247	0.14	0.44	YES
123	ZNF441	ZNF441	ZNF441	3259	0.14	0.44	YES
124	MED12	MED12	MED12	3261	0.14	0.44	YES
125	ZNF570	ZNF570	ZNF570	3274	0.14	0.44	YES
126	RBL1	RBL1	RBL1	3296	0.14	0.44	YES
127	ZNF595	ZNF595	ZNF595	3301	0.14	0.45	YES
128	SKI	SKI	SKI	3341	0.14	0.45	YES
129	ZNF500	ZNF500	ZNF500	3502	0.13	0.44	YES
130	ZNF320	ZNF320	ZNF320	3512	0.13	0.44	YES
131	JUNB	JUNB	JUNB	3534	0.13	0.44	YES
132	ZNF708	ZNF708	ZNF708	3561	0.13	0.44	YES
133	ZNF274	ZNF274	ZNF274	3602	0.12	0.44	YES
134	NOTCH2	NOTCH2	NOTCH2	3650	0.12	0.44	YES
135	ZNF184	ZNF184	ZNF184	3676	0.12	0.45	YES
136	ZNF420	ZNF420	ZNF420	3681	0.12	0.45	YES
137	ZNF235	ZNF235	ZNF235	3715	0.12	0.45	YES
138	TEAD1	TEAD1	TEAD1	3761	0.12	0.45	YES
139	ZNF33A	ZNF33A	ZNF33A	3762	0.12	0.45	YES
140	PARP1	PARP1	PARP1	3793	0.12	0.45	YES
141	ZNF529	ZNF529	ZNF529	3848	0.12	0.45	YES
142	ZNF140	ZNF140	ZNF140	3853	0.12	0.45	YES
143	ZNF331	ZNF331	ZNF331	3894	0.11	0.45	YES
144	SMARCD3	SMARCD3	SMARCD3	3993	0.11	0.45	YES
145	ZNF589	ZNF589	ZNF589	3999	0.11	0.45	YES
146	ZNF37A	ZNF37A	ZNF37A	4033	0.11	0.45	YES
147	ZNF543	ZNF543	ZNF543	4048	0.11	0.45	YES
148	ZNF354B	ZNF354B	ZNF354B	4054	0.11	0.45	YES
149	PRIC285	PRIC285	PRIC285	4099	0.11	0.45	YES
150	ZNF45	ZNF45	ZNF45	4105	0.11	0.46	YES
151	HNF4A	HNF4A	HNF4A	4139	0.11	0.46	YES
152	ZNF621	ZNF621	ZNF621	4144	0.1	0.46	YES
153	CDK9	CDK9	CDK9	4209	0.1	0.46	YES
154	ZNF43	ZNF43	ZNF43	4239	0.1	0.46	YES
155	ZNF398	ZNF398	ZNF398	4292	0.1	0.46	YES
156	ZNF552	ZNF552	ZNF552	4302	0.1	0.46	YES
157	THRB	THRB	THRB	4311	0.1	0.46	YES
158	ZNF510	ZNF510	ZNF510	4333	0.1	0.46	YES
159	CDKN2B	CDKN2B	CDKN2B	4391	0.098	0.46	YES
160	HNF4G	HNF4G	HNF4G	4398	0.097	0.46	YES
161	NR6A1	NR6A1	NR6A1	4514	0.094	0.45	YES
162	MED20	MED20	MED20	4526	0.093	0.46	YES
163	ZNF28	ZNF28	ZNF28	4552	0.092	0.46	YES
164	ZNF417	ZNF417	ZNF417	4614	0.091	0.45	YES
165	ZNF350	ZNF350	ZNF350	4628	0.09	0.46	YES
166	NCOR2	NCOR2	NCOR2	4640	0.09	0.46	YES
167	ZNF624	ZNF624	ZNF624	4653	0.09	0.46	YES
168	ZNF383	ZNF383	ZNF383	4680	0.089	0.46	YES
169	ZNF548	ZNF548	ZNF548	4697	0.088	0.46	YES
170	ZNF234	ZNF234	ZNF234	4709	0.088	0.46	YES
171	ZNF440	ZNF440	ZNF440	4714	0.088	0.46	YES
172	ZNF160	ZNF160	ZNF160	4732	0.087	0.46	YES
173	NR4A2	NR4A2	NR4A2	4740	0.087	0.46	YES
174	ZNF205	ZNF205	ZNF205	4757	0.087	0.46	YES
175	ZNF2	ZNF2	ZNF2	4798	0.085	0.46	YES
176	SMAD4	SMAD4	SMAD4	4853	0.084	0.46	YES
177	ZNF468	ZNF468	ZNF468	4878	0.083	0.46	YES
178	ZNF304	ZNF304	ZNF304	4882	0.083	0.46	YES
179	ZNF561	ZNF561	ZNF561	4913	0.082	0.46	YES
180	ZNF558	ZNF558	ZNF558	4924	0.082	0.46	YES
181	ZNF197	ZNF197	ZNF197	4931	0.082	0.47	YES
182	ZNF334	ZNF334	ZNF334	4960	0.081	0.46	YES
183	ZNF100	ZNF100	ZNF100	4985	0.08	0.47	YES
184	ZNF555	ZNF555	ZNF555	5004	0.08	0.47	YES
185	ZNF248	ZNF248	ZNF248	5068	0.078	0.46	NO
186	ZNF333	ZNF333	ZNF333	5084	0.078	0.46	NO
187	MAML1	MAML1	MAML1	5273	0.073	0.46	NO
188	NCOA3	NCOA3	NCOA3	5317	0.072	0.46	NO
189	ZNF311	ZNF311	ZNF311	5360	0.07	0.45	NO
190	KAT2A	KAT2A	KAT2A	5366	0.07	0.46	NO
191	NCOR1	NCOR1	NCOR1	5489	0.067	0.45	NO
192	RARA	RARA	RARA	5571	0.064	0.45	NO
193	CCNT1	CCNT1	CCNT1	5577	0.064	0.45	NO
194	CREBBP	CREBBP	CREBBP	5599	0.064	0.45	NO
195	ZNF213	ZNF213	ZNF213	5628	0.063	0.45	NO
196	SP1	SP1	SP1	5641	0.062	0.45	NO
197	TGS1	TGS1	TGS1	5823	0.059	0.44	NO
198	KAT2B	KAT2B	KAT2B	5825	0.059	0.44	NO
199	ZNF254	ZNF254	ZNF254	5944	0.056	0.43	NO
200	NCOA6	NCOA6	NCOA6	5966	0.055	0.43	NO
201	ZNF557	ZNF557	ZNF557	6025	0.054	0.43	NO
202	ZNF230	ZNF230	ZNF230	6051	0.053	0.43	NO
203	ZNF658	ZNF658	ZNF658	6056	0.053	0.43	NO
204	ZNF212	ZNF212	ZNF212	6100	0.052	0.43	NO
205	ZNF26	ZNF26	ZNF26	6123	0.052	0.43	NO
206	ZNF224	ZNF224	ZNF224	6182	0.05	0.43	NO
207	ZNF564	ZNF564	ZNF564	6313	0.047	0.42	NO
208	PPM1A	PPM1A	PPM1A	6327	0.047	0.42	NO
209	ZNF264	ZNF264	ZNF264	6432	0.044	0.42	NO
210	ZNF597	ZNF597	ZNF597	6446	0.044	0.42	NO
211	RXRB	RXRB	RXRB	6480	0.044	0.42	NO
212	TEAD4	TEAD4	TEAD4	6584	0.042	0.41	NO
213	ZNF484	ZNF484	ZNF484	6641	0.04	0.41	NO
214	MED17	MED17	MED17	6645	0.04	0.41	NO
215	ZNF282	ZNF282	ZNF282	6663	0.04	0.41	NO
216	ZNF354A	ZNF354A	ZNF354A	6769	0.038	0.4	NO
217	YAP1	YAP1	YAP1	6796	0.037	0.4	NO
218	RBPJ	RBPJ	RBPJ	6818	0.037	0.4	NO
219	NR1H3	NR1H3	NR1H3	6854	0.036	0.4	NO
220	ZNF227	ZNF227	ZNF227	6915	0.035	0.4	NO
221	ZNF14	ZNF14	ZNF14	6917	0.035	0.4	NO
222	TRIM33	TRIM33	TRIM33	6960	0.034	0.4	NO
223	ZNF530	ZNF530	ZNF530	6995	0.033	0.4	NO
224	SMAD2	SMAD2	SMAD2	7026	0.032	0.39	NO
225	ZNF17	ZNF17	ZNF17	7094	0.031	0.39	NO
226	ZNF434	ZNF434	ZNF434	7116	0.03	0.39	NO
227	ZNF584	ZNF584	ZNF584	7145	0.03	0.39	NO
228	MED31	MED31	MED31	7167	0.03	0.39	NO
229	PPARD	PPARD	PPARD	7397	0.025	0.38	NO
230	MED14	MED14	MED14	7448	0.024	0.37	NO
231	ZNF567	ZNF567	ZNF567	7488	0.023	0.37	NO
232	ZNF202	ZNF202	ZNF202	7503	0.023	0.37	NO
233	ZNF445	ZNF445	ZNF445	7559	0.022	0.37	NO
234	UBE2D3	UBE2D3	UBE2D3	7577	0.022	0.37	NO
235	CCNT2	CCNT2	CCNT2	7584	0.022	0.37	NO
236	ZNF490	ZNF490	ZNF490	7707	0.019	0.36	NO
237	NR4A1	NR4A1	NR4A1	7727	0.019	0.36	NO
238	ZNF446	ZNF446	ZNF446	7757	0.018	0.36	NO
239	TGIF1	TGIF1	TGIF1	7809	0.017	0.36	NO
240	ZNF587	ZNF587	ZNF587	7836	0.017	0.36	NO
241	ZNF430	ZNF430	ZNF430	7890	0.016	0.35	NO
242	ZNF473	ZNF473	ZNF473	7893	0.016	0.35	NO
243	ZNF3	ZNF3	ZNF3	7970	0.014	0.35	NO
244	ZNF136	ZNF136	ZNF136	8049	0.013	0.35	NO
245	NR2F6	NR2F6	NR2F6	8181	0.01	0.34	NO
246	MED23	MED23	MED23	8240	0.0091	0.34	NO
247	ZNF208	ZNF208	ZNF208	8420	0.0057	0.33	NO
248	ZNF180	ZNF180	ZNF180	8538	0.0034	0.32	NO
249	RXRA	RXRA	RXRA	8545	0.0033	0.32	NO
250	MED1	MED1	MED1	8591	0.0027	0.32	NO
251	USP9X	USP9X	USP9X	8612	0.0025	0.32	NO
252	ZNF18	ZNF18	ZNF18	8650	0.0018	0.31	NO
253	SMAD3	SMAD3	SMAD3	8685	0.0011	0.31	NO
254	ZNF498	ZNF498	ZNF498	8761	-0.00015	0.31	NO
255	TRIM28	TRIM28	TRIM28	8979	-0.0041	0.3	NO
256	NR2C2AP	NR2C2AP	NR2C2AP	8982	-0.0042	0.3	NO
257	RPS27A	RPS27A	RPS27A	9002	-0.0045	0.29	NO
258	ZNF155	ZNF155	ZNF155	9033	-0.0051	0.29	NO
259	ZNF317	ZNF317	ZNF317	9071	-0.0059	0.29	NO
260	NCOA1	NCOA1	NCOA1	9212	-0.0085	0.28	NO
261	ZNF263	ZNF263	ZNF263	9272	-0.0095	0.28	NO
262	MED25	MED25	MED25	9295	-0.0098	0.28	NO
263	MED24	MED24	MED24	9317	-0.01	0.28	NO
264	ZNF616	ZNF616	ZNF616	9400	-0.012	0.27	NO
265	ZNF547	ZNF547	ZNF547	9481	-0.013	0.27	NO
266	MED16	MED16	MED16	9509	-0.014	0.27	NO
267	TBL1X	TBL1X	TBL1X	9567	-0.014	0.26	NO
268	ZNF655	ZNF655	ZNF655	9899	-0.02	0.25	NO
269	UBE2D1	UBE2D1	UBE2D1	9908	-0.02	0.25	NO
270	MED15	MED15	MED15	9977	-0.022	0.24	NO
271	ZNF19	ZNF19	ZNF19	9991	-0.022	0.24	NO
272	ZNF226	ZNF226	ZNF226	10055	-0.023	0.24	NO
273	ZNF324	ZNF324	ZNF324	10146	-0.024	0.24	NO
274	NR2F1	NR2F1	NR2F1	10270	-0.027	0.23	NO
275	UBA52	UBA52	UBA52	10586	-0.033	0.21	NO
276	MED27	MED27	MED27	10646	-0.034	0.21	NO
277	SNW1	SNW1	SNW1	10685	-0.035	0.21	NO
278	MEN1	MEN1	MEN1	10711	-0.036	0.21	NO
279	MED26	MED26	MED26	10822	-0.038	0.2	NO
280	ZNF436	ZNF436	ZNF436	10860	-0.038	0.2	NO
281	NRBF2	NRBF2	NRBF2	10908	-0.039	0.2	NO
282	NRBP1	NRBP1	NRBP1	11098	-0.043	0.19	NO
283	NR1H2	NR1H2	NR1H2	11101	-0.043	0.19	NO
284	ZNF394	ZNF394	ZNF394	11174	-0.045	0.19	NO
285	CCNC	CCNC	CCNC	11183	-0.045	0.19	NO
286	ZNF480	ZNF480	ZNF480	11197	-0.045	0.19	NO
287	VDR	VDR	VDR	11482	-0.051	0.17	NO
288	NR3C1	NR3C1	NR3C1	11553	-0.052	0.17	NO
289	ZNF460	ZNF460	ZNF460	11729	-0.056	0.16	NO
290	HDAC1	HDAC1	HDAC1	11744	-0.057	0.16	NO
291	ZNF431	ZNF431	ZNF431	11810	-0.058	0.16	NO
292	ZFP90	ZFP90	ZFP90	12077	-0.064	0.14	NO
293	TBL1XR1	TBL1XR1	TBL1XR1	12105	-0.065	0.14	NO
294	MED8	MED8	MED8	12144	-0.066	0.14	NO
295	ZNF544	ZNF544	ZNF544	12228	-0.068	0.14	NO
296	ZNF12	ZNF12	ZNF12	12246	-0.068	0.14	NO
297	ZKSCAN5	ZKSCAN5	ZKSCAN5	12371	-0.072	0.13	NO
298	THRA	THRA	THRA	12482	-0.075	0.13	NO
299	NOTCH4	NOTCH4	NOTCH4	12559	-0.077	0.13	NO
300	ZNF23	ZNF23	ZNF23	12660	-0.08	0.12	NO
301	TFDP1	TFDP1	TFDP1	12753	-0.083	0.12	NO
302	ZNF200	ZNF200	ZNF200	12857	-0.086	0.12	NO
303	MED7	MED7	MED7	12973	-0.089	0.11	NO
304	ZNF506	ZNF506	ZNF506	13028	-0.091	0.11	NO
305	ZNF189	ZNF189	ZNF189	13263	-0.099	0.098	NO
306	NR0B1	NR0B1	NR0B1	13339	-0.1	0.095	NO
307	NR4A3	NR4A3	NR4A3	13365	-0.1	0.096	NO
308	MYC	MYC	MYC	13449	-0.1	0.093	NO
309	MED10	MED10	MED10	13505	-0.11	0.092	NO
310	ESRRA	ESRRA	ESRRA	13529	-0.11	0.093	NO
311	MED4	MED4	MED4	13739	-0.12	0.083	NO
312	ZNF267	ZNF267	ZNF267	13752	-0.12	0.085	NO
313	ZNF138	ZNF138	ZNF138	13825	-0.12	0.083	NO
314	RORC	RORC	RORC	14025	-0.13	0.074	NO
315	CDK8	CDK8	CDK8	14027	-0.13	0.077	NO
316	MED6	MED6	MED6	14172	-0.13	0.071	NO
317	NR5A1	NR5A1	NR5A1	14201	-0.13	0.072	NO
318	NR2E1	NR2E1	NR2E1	14204	-0.13	0.075	NO
319	ZFP1	ZFP1	ZFP1	14270	-0.14	0.074	NO
320	PPARA	PPARA	PPARA	14351	-0.14	0.072	NO
321	ZNF273	ZNF273	ZNF273	14471	-0.15	0.068	NO
322	ZNF101	ZNF101	ZNF101	14598	-0.16	0.064	NO
323	E2F4	E2F4	E2F4	15123	-0.19	0.038	NO
324	ZNF92	ZNF92	ZNF92	15276	-0.2	0.033	NO
325	NR1I3	NR1I3	NR1I3	15496	-0.22	0.025	NO
326	RUNX2	RUNX2	RUNX2	15809	-0.25	0.012	NO
327	RORB	RORB	RORB	16293	-0.3	-0.0092	NO
328	ESR2	ESR2	ESR2	16407	-0.32	-0.0095	NO
329	PPARG	PPARG	PPARG	16731	-0.36	-0.021	NO
330	ZNF98	ZNF98	ZNF98	16861	-0.39	-0.02	NO
331	ESRRB	ESRRB	ESRRB	17142	-0.44	-0.028	NO
332	RXRG	RXRG	RXRG	17163	-0.44	-0.02	NO
333	AR	AR	AR	17480	-0.51	-0.028	NO
334	ZNF492	ZNF492	ZNF492	17540	-0.53	-0.021	NO
335	NPPA	NPPA	NPPA	17698	-0.58	-0.019	NO
336	ZNF114	ZNF114	ZNF114	17811	-0.64	-0.013	NO
337	ESR1	ESR1	ESR1	17962	-0.72	-0.0078	NO
338	NR1I2	NR1I2	NR1I2	18062	-0.84	0.0029	NO

Figure S109. 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: PID NECTIN PATHWAY.

Figure S110. Get High-res Image For the top 5 core enriched genes in the pathway: PID NECTIN 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: PID TGFBRPATHWAY

Table S56. 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	WWTR1	WWTR1	WWTR1	778	0.34	0.05	YES
2	E2F5	E2F5	E2F5	896	0.32	0.13	YES
3	SERPINE1	SERPINE1	SERPINE1	997	0.3	0.21	YES
4	SMAD7	SMAD7	SMAD7	1537	0.25	0.25	YES
5	TGIF2	TGIF2	TGIF2	2482	0.18	0.24	YES
6	SMURF2	SMURF2	SMURF2	2784	0.16	0.27	YES
7	SKIL	SKIL	SKIL	3199	0.14	0.29	YES
8	RBL1	RBL1	RBL1	3296	0.14	0.32	YES
9	SKI	SKI	SKI	3341	0.14	0.35	YES
10	JUNB	JUNB	JUNB	3534	0.13	0.38	YES
11	PARP1	PARP1	PARP1	3793	0.12	0.4	YES
12	CDK9	CDK9	CDK9	4209	0.1	0.4	YES
13	CDKN2B	CDKN2B	CDKN2B	4391	0.098	0.42	YES
14	NCOR2	NCOR2	NCOR2	4640	0.09	0.43	YES
15	SMAD4	SMAD4	SMAD4	4853	0.084	0.44	YES
16	NCOR1	NCOR1	NCOR1	5489	0.067	0.42	YES
17	CCNT1	CCNT1	CCNT1	5577	0.064	0.44	YES
18	SP1	SP1	SP1	5641	0.062	0.45	YES
19	PPM1A	PPM1A	PPM1A	6327	0.047	0.42	NO
20	TRIM33	TRIM33	TRIM33	6960	0.034	0.4	NO
21	SMAD2	SMAD2	SMAD2	7026	0.032	0.4	NO
22	UBE2D3	UBE2D3	UBE2D3	7577	0.022	0.38	NO
23	CCNT2	CCNT2	CCNT2	7584	0.022	0.38	NO
24	TGIF1	TGIF1	TGIF1	7809	0.017	0.38	NO
25	USP9X	USP9X	USP9X	8612	0.0025	0.33	NO
26	SMAD3	SMAD3	SMAD3	8685	0.0011	0.33	NO
27	RPS27A	RPS27A	RPS27A	9002	-0.0045	0.31	NO
28	UBE2D1	UBE2D1	UBE2D1	9908	-0.02	0.27	NO
29	UBA52	UBA52	UBA52	10586	-0.033	0.24	NO
30	MEN1	MEN1	MEN1	10711	-0.036	0.24	NO
31	CCNC	CCNC	CCNC	11183	-0.045	0.23	NO
32	HDAC1	HDAC1	HDAC1	11744	-0.057	0.22	NO
33	TFDP1	TFDP1	TFDP1	12753	-0.083	0.18	NO
34	MYC	MYC	MYC	13449	-0.1	0.17	NO
35	CDK8	CDK8	CDK8	14027	-0.13	0.18	NO
36	E2F4	E2F4	E2F4	15123	-0.19	0.16	NO

Figure S111. 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: PID TGFBRPATHWAY.

Figure S112. Get High-res Image For the top 5 core enriched genes in the pathway: PID TGFBRPATHWAY, 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: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS

Table S57. 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	PLEKHG6	PLEKHG6	PLEKHG6	329	0.46	0.056	YES
2	ARHGAP6	ARHGAP6	ARHGAP6	638	0.36	0.098	YES
3	OBSCN	OBSCN	OBSCN	752	0.34	0.15	YES
4	VAV3	VAV3	VAV3	880	0.32	0.19	YES
5	ARHGAP8	ARHGAP8	ARHGAP8	907	0.32	0.24	YES
6	ARHGDIG	ARHGDIG	ARHGDIG	1301	0.27	0.26	YES
7	ARHGEF2	ARHGEF2	ARHGEF2	1356	0.27	0.3	YES
8	ARAP3	ARAP3	ARAP3	1649	0.24	0.33	YES
9	NGEF	NGEF	NGEF	2673	0.17	0.3	YES
10	ARHGEF11	ARHGEF11	ARHGEF11	2766	0.16	0.32	YES
11	RGNEF	RGNEF	RGNEF	2860	0.16	0.34	YES
12	DLC1	DLC1	DLC1	3104	0.14	0.35	YES
13	NET1	NET1	NET1	3196	0.14	0.37	YES
14	ARHGEF5	ARHGEF5	ARHGEF5	3591	0.12	0.36	YES
15	ARHGEF18	ARHGEF18	ARHGEF18	3758	0.12	0.38	YES
16	ARHGEF17	ARHGEF17	ARHGEF17	4358	0.098	0.36	YES
17	ARHGAP4	ARHGAP4	ARHGAP4	4479	0.095	0.37	YES
18	FARP1	FARP1	FARP1	4629	0.09	0.37	YES
19	ABR	ABR	ABR	4718	0.088	0.38	YES
20	SRGAP1	SRGAP1	SRGAP1	4765	0.086	0.39	YES
21	ARHGEF1	ARHGEF1	ARHGEF1	5169	0.075	0.38	NO
22	CDKN1B	CDKN1B	CDKN1B	5325	0.072	0.39	NO
23	BCR	BCR	BCR	5688	0.062	0.38	NO
24	ARHGEF10	ARHGEF10	ARHGEF10	6023	0.054	0.37	NO
25	ARHGAP5	ARHGAP5	ARHGAP5	7437	0.024	0.29	NO
26	ARHGEF12	ARHGEF12	ARHGEF12	7452	0.024	0.3	NO
27	MCF2L	MCF2L	MCF2L	7720	0.019	0.28	NO
28	MYO9B	MYO9B	MYO9B	8045	0.013	0.27	NO
29	RHOA	RHOA	RHOA	8539	0.0034	0.24	NO
30	AKAP13	AKAP13	AKAP13	9028	-0.0051	0.22	NO
31	ECT2	ECT2	ECT2	9139	-0.0073	0.21	NO
32	VAV2	VAV2	VAV2	9149	-0.0075	0.21	NO
33	ARHGEF10L	ARHGEF10L	ARHGEF10L	9221	-0.0086	0.21	NO
34	TRIO	TRIO	TRIO	9344	-0.011	0.2	NO
35	MCF2	MCF2	MCF2	10975	-0.04	0.12	NO
36	ARAP1	ARAP1	ARAP1	11349	-0.048	0.11	NO
37	ARHGDIA	ARHGDIA	ARHGDIA	11519	-0.052	0.11	NO
38	ARHGDIB	ARHGDIB	ARHGDIB	14593	-0.15	-0.039	NO
39	ARHGEF3	ARHGEF3	ARHGEF3	14857	-0.17	-0.026	NO
40	OPHN1	OPHN1	OPHN1	14889	-0.17	-0.00016	NO
41	DEF6	DEF6	DEF6	15470	-0.21	0.0025	NO
42	ARHGEF15	ARHGEF15	ARHGEF15	15491	-0.22	0.036	NO
43	VAV1	VAV1	VAV1	15621	-0.23	0.066	NO
44	ARHGAP9	ARHGAP9	ARHGAP9	17158	-0.44	0.053	NO

Figure S113. 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: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS.

Figure S114. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, 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: REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION

Table S58. 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	PKP1	PKP1	PKP1	52	0.73	0.16	YES
2	GAS2	GAS2	GAS2	203	0.53	0.27	YES
3	MAPT	MAPT	MAPT	1039	0.3	0.29	YES
4	OCLN	OCLN	OCLN	1660	0.24	0.31	YES
5	DSP	DSP	DSP	2554	0.17	0.3	YES
6	PTK2	PTK2	PTK2	3482	0.13	0.28	YES
7	PRKCQ	PRKCQ	PRKCQ	3535	0.13	0.3	YES
8	CASP7	CASP7	CASP7	3747	0.12	0.32	YES
9	LMNA	LMNA	LMNA	4167	0.1	0.32	YES
10	CASP6	CASP6	CASP6	4345	0.099	0.33	YES
11	DSG3	DSG3	DSG3	4557	0.092	0.34	YES
12	FNTA	FNTA	FNTA	4670	0.089	0.35	YES
13	APC	APC	APC	4782	0.086	0.36	YES
14	PLEC	PLEC	PLEC	4826	0.085	0.38	YES
15	DSG2	DSG2	DSG2	5150	0.076	0.38	NO
16	TJP1	TJP1	TJP1	5585	0.064	0.37	NO
17	VIM	VIM	VIM	5689	0.062	0.38	NO
18	TJP2	TJP2	TJP2	6133	0.052	0.37	NO
19	CTNNB1	CTNNB1	CTNNB1	6607	0.041	0.35	NO
20	SPTAN1	SPTAN1	SPTAN1	6978	0.034	0.34	NO
21	ROCK1	ROCK1	ROCK1	7401	0.025	0.32	NO
22	GSN	GSN	GSN	7612	0.021	0.31	NO
23	ADD1	ADD1	ADD1	7751	0.018	0.31	NO
24	BCAP31	BCAP31	BCAP31	7765	0.018	0.31	NO
25	ACIN1	ACIN1	ACIN1	7816	0.017	0.31	NO
26	LOC647859	LOC647859	LOC647859	8390	0.0062	0.28	NO
27	PRKCD	PRKCD	PRKCD	8643	0.0018	0.27	NO
28	BIRC2	BIRC2	BIRC2	9007	-0.0047	0.25	NO
29	STK24	STK24	STK24	10334	-0.028	0.18	NO
30	LMNB1	LMNB1	LMNB1	10977	-0.04	0.16	NO
31	CASP3	CASP3	CASP3	11678	-0.055	0.13	NO
32	SATB1	SATB1	SATB1	11813	-0.058	0.14	NO
33	CDH1	CDH1	CDH1	11840	-0.059	0.15	NO
34	DSG1	DSG1	DSG1	12436	-0.073	0.13	NO
35	DBNL	DBNL	DBNL	12513	-0.076	0.14	NO
36	CASP8	CASP8	CASP8	12916	-0.087	0.14	NO
37	MST4	MST4	MST4	14141	-0.13	0.1	NO
38	BMX	BMX	BMX	17539	-0.53	0.032	NO

Figure S115. 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: REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION.

Figure S116. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION, 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: REACTOME PRE NOTCH EXPRESSION AND PROCESSING

Table S59. 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	DTX1	DTX1	DTX1	450	0.41	0.052	YES
2	MAML3	MAML3	MAML3	735	0.34	0.1	YES
3	MAML2	MAML2	MAML2	1501	0.25	0.11	YES
4	NOTCH3	NOTCH3	NOTCH3	1554	0.25	0.15	YES
5	HES1	HES1	HES1	1886	0.22	0.17	YES
6	JAG1	JAG1	JAG1	2003	0.21	0.2	YES
7	NOTCH1	NOTCH1	NOTCH1	2047	0.2	0.24	YES
8	PSEN2	PSEN2	PSEN2	2204	0.2	0.27	YES
9	DTX3	DTX3	DTX3	2687	0.17	0.27	YES
10	DTX4	DTX4	DTX4	3050	0.15	0.28	YES
11	CTBP2	CTBP2	CTBP2	3206	0.14	0.3	YES
12	NCSTN	NCSTN	NCSTN	3242	0.14	0.32	YES
13	APH1A	APH1A	APH1A	3648	0.12	0.32	YES
14	NOTCH2	NOTCH2	NOTCH2	3650	0.12	0.35	YES
15	DLL3	DLL3	DLL3	4612	0.091	0.31	NO
16	NCOR2	NCOR2	NCOR2	4640	0.09	0.32	NO
17	MAML1	MAML1	MAML1	5273	0.073	0.3	NO
18	KAT2A	KAT2A	KAT2A	5366	0.07	0.31	NO
19	CREBBP	CREBBP	CREBBP	5599	0.064	0.31	NO
20	KAT2B	KAT2B	KAT2B	5825	0.059	0.31	NO
21	DVL2	DVL2	DVL2	5860	0.058	0.32	NO
22	EP300	EP300	EP300	5906	0.057	0.33	NO
23	JAG2	JAG2	JAG2	6124	0.052	0.32	NO
24	RBPJ	RBPJ	RBPJ	6818	0.037	0.29	NO
25	CIR1	CIR1	CIR1	6997	0.033	0.29	NO
26	HDAC2	HDAC2	HDAC2	7338	0.026	0.28	NO
27	DTX3L	DTX3L	DTX3L	7400	0.025	0.28	NO
28	HES5	HES5	HES5	7826	0.017	0.26	NO
29	MFNG	MFNG	MFNG	7935	0.015	0.25	NO
30	DVL1	DVL1	DVL1	8145	0.011	0.24	NO
31	CTBP1	CTBP1	CTBP1	8727	0.00026	0.21	NO
32	RFNG	RFNG	RFNG	9841	-0.02	0.15	NO
33	PSEN1	PSEN1	PSEN1	10502	-0.031	0.12	NO
34	DLL4	DLL4	DLL4	10597	-0.033	0.12	NO
35	SNW1	SNW1	SNW1	10685	-0.035	0.13	NO
36	DVL3	DVL3	DVL3	10964	-0.04	0.12	NO
37	PSENEN	PSENEN	PSENEN	11549	-0.052	0.096	NO
38	LFNG	LFNG	LFNG	11726	-0.056	0.096	NO
39	HDAC1	HDAC1	HDAC1	11744	-0.057	0.11	NO
40	ADAM17	ADAM17	ADAM17	12060	-0.064	0.1	NO
41	NOTCH4	NOTCH4	NOTCH4	12559	-0.077	0.087	NO
42	NUMB	NUMB	NUMB	12827	-0.085	0.089	NO
43	DTX2	DTX2	DTX2	13086	-0.093	0.092	NO
44	NUMBL	NUMBL	NUMBL	14356	-0.14	0.048	NO
45	RBPJL	RBPJL	RBPJL	14602	-0.16	0.063	NO
46	PTCRA	PTCRA	PTCRA	16455	-0.32	0.022	NO
47	DLL1	DLL1	DLL1	16779	-0.37	0.074	NO

Figure S117. 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: REACTOME PRE NOTCH EXPRESSION AND PROCESSING.

Figure S118. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PRE NOTCH EXPRESSION AND PROCESSING, 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: REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION

Table S60. 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	DTX1	DTX1	DTX1	450	0.41	0.015	YES
2	TLE2	TLE2	TLE2	454	0.41	0.055	YES
3	HEY1	HEY1	HEY1	730	0.34	0.073	YES
4	MAML3	MAML3	MAML3	735	0.34	0.11	YES
5	MAMLD1	MAMLD1	MAMLD1	1011	0.3	0.12	YES
6	APH1B	APH1B	APH1B	1235	0.28	0.14	YES
7	MAML2	MAML2	MAML2	1501	0.25	0.14	YES
8	NOTCH3	NOTCH3	NOTCH3	1554	0.25	0.17	YES
9	CCND1	CCND1	CCND1	1727	0.23	0.18	YES
10	HES1	HES1	HES1	1886	0.22	0.19	YES
11	JAG1	JAG1	JAG1	2003	0.21	0.2	YES
12	FURIN	FURIN	FURIN	2148	0.2	0.22	YES
13	PSEN2	PSEN2	PSEN2	2204	0.2	0.23	YES
14	HDAC11	HDAC11	HDAC11	2444	0.18	0.24	YES
15	TLE4	TLE4	TLE4	2668	0.17	0.24	YES
16	HDAC5	HDAC5	HDAC5	2840	0.16	0.25	YES
17	NEURL	NEURL	NEURL	2903	0.16	0.26	YES
18	DTX4	DTX4	DTX4	3050	0.15	0.26	YES
19	TP53	TP53	TP53	3221	0.14	0.27	YES
20	NCSTN	NCSTN	NCSTN	3242	0.14	0.28	YES
21	EIF2C2	EIF2C2	EIF2C2	3291	0.14	0.29	YES
22	APH1A	APH1A	APH1A	3648	0.12	0.28	YES
23	NOTCH2	NOTCH2	NOTCH2	3650	0.12	0.3	YES
24	HDAC7	HDAC7	HDAC7	3984	0.11	0.29	NO
25	TLE1	TLE1	TLE1	4408	0.097	0.27	NO
26	NCOR2	NCOR2	NCOR2	4640	0.09	0.27	NO
27	TNRC6C	TNRC6C	TNRC6C	4910	0.082	0.26	NO
28	E2F3	E2F3	E2F3	5132	0.076	0.26	NO
29	MAML1	MAML1	MAML1	5273	0.073	0.26	NO
30	HDAC4	HDAC4	HDAC4	5359	0.07	0.26	NO
31	KAT2A	KAT2A	KAT2A	5366	0.07	0.26	NO
32	CNTN1	CNTN1	CNTN1	5471	0.067	0.27	NO
33	NCOR1	NCOR1	NCOR1	5489	0.067	0.27	NO
34	CREBBP	CREBBP	CREBBP	5599	0.064	0.27	NO
35	EIF2C4	EIF2C4	EIF2C4	5799	0.059	0.27	NO
36	KAT2B	KAT2B	KAT2B	5825	0.059	0.27	NO
37	EP300	EP300	EP300	5906	0.057	0.27	NO
38	JAG2	JAG2	JAG2	6124	0.052	0.26	NO
39	ADAM10	ADAM10	ADAM10	6200	0.05	0.26	NO
40	HEYL	HEYL	HEYL	6272	0.048	0.27	NO
41	TNRC6A	TNRC6A	TNRC6A	6407	0.045	0.26	NO
42	FBXW7	FBXW7	FBXW7	6548	0.042	0.26	NO
43	E2F1	E2F1	E2F1	6555	0.042	0.26	NO
44	JUN	JUN	JUN	6765	0.038	0.26	NO
45	RBPJ	RBPJ	RBPJ	6818	0.037	0.26	NO
46	HDAC10	HDAC10	HDAC10	6931	0.035	0.25	NO
47	B4GALT1	B4GALT1	B4GALT1	7137	0.03	0.24	NO
48	MIB1	MIB1	MIB1	7331	0.026	0.24	NO
49	HDAC2	HDAC2	HDAC2	7338	0.026	0.24	NO
50	HIF1A	HIF1A	HIF1A	7342	0.026	0.24	NO
51	SKP1	SKP1	SKP1	7525	0.023	0.23	NO
52	HES5	HES5	HES5	7826	0.017	0.22	NO
53	HDAC8	HDAC8	HDAC8	7924	0.015	0.21	NO
54	MFNG	MFNG	MFNG	7935	0.015	0.21	NO
55	HEY2	HEY2	HEY2	8335	0.0074	0.19	NO
56	POFUT1	POFUT1	POFUT1	8600	0.0026	0.18	NO
57	ATP2A2	ATP2A2	ATP2A2	8680	0.0012	0.17	NO
58	TNRC6B	TNRC6B	TNRC6B	8817	-0.0011	0.17	NO
59	RPS27A	RPS27A	RPS27A	9002	-0.0045	0.16	NO
60	TBL1X	TBL1X	TBL1X	9567	-0.014	0.13	NO
61	TMED2	TMED2	TMED2	9761	-0.018	0.12	NO
62	RFNG	RFNG	RFNG	9841	-0.02	0.12	NO
63	ARRB1	ARRB1	ARRB1	9925	-0.021	0.11	NO
64	HDAC6	HDAC6	HDAC6	9927	-0.021	0.12	NO
65	CUL1	CUL1	CUL1	10217	-0.026	0.1	NO
66	RAB6A	RAB6A	RAB6A	10279	-0.027	0.1	NO
67	HDAC9	HDAC9	HDAC9	10351	-0.028	0.1	NO
68	PSEN1	PSEN1	PSEN1	10502	-0.031	0.094	NO
69	UBA52	UBA52	UBA52	10586	-0.033	0.093	NO
70	DLL4	DLL4	DLL4	10597	-0.033	0.096	NO
71	SNW1	SNW1	SNW1	10685	-0.035	0.094	NO
72	EIF2C1	EIF2C1	EIF2C1	10809	-0.037	0.091	NO
73	DLK1	DLK1	DLK1	10867	-0.038	0.092	NO
74	HDAC3	HDAC3	HDAC3	11172	-0.045	0.079	NO
75	CCNC	CCNC	CCNC	11183	-0.045	0.083	NO
76	PSENEN	PSENEN	PSENEN	11549	-0.052	0.068	NO
77	LFNG	LFNG	LFNG	11726	-0.056	0.063	NO
78	HDAC1	HDAC1	HDAC1	11744	-0.057	0.068	NO
79	RBX1	RBX1	RBX1	11908	-0.06	0.065	NO
80	ADAM17	ADAM17	ADAM17	12060	-0.064	0.062	NO
81	TBL1XR1	TBL1XR1	TBL1XR1	12105	-0.065	0.066	NO
82	SEL1L	SEL1L	SEL1L	12294	-0.069	0.063	NO
83	MOV10	MOV10	MOV10	12298	-0.069	0.069	NO
84	TLE3	TLE3	TLE3	12478	-0.074	0.066	NO
85	NOTCH4	NOTCH4	NOTCH4	12559	-0.077	0.069	NO
86	TFDP1	TFDP1	TFDP1	12753	-0.083	0.067	NO
87	NUMB	NUMB	NUMB	12827	-0.085	0.071	NO
88	DTX2	DTX2	DTX2	13086	-0.093	0.066	NO
89	ARRB2	ARRB2	ARRB2	13205	-0.097	0.068	NO
90	MIB2	MIB2	MIB2	13221	-0.097	0.077	NO
91	ST3GAL6	ST3GAL6	ST3GAL6	13407	-0.1	0.077	NO
92	MYC	MYC	MYC	13449	-0.1	0.085	NO
93	ATP2A1	ATP2A1	ATP2A1	13865	-0.12	0.073	NO
94	CDK8	CDK8	CDK8	14027	-0.13	0.077	NO
95	ST3GAL3	ST3GAL3	ST3GAL3	14110	-0.13	0.085	NO
96	EIF2C3	EIF2C3	EIF2C3	14690	-0.16	0.068	NO
97	ATP2A3	ATP2A3	ATP2A3	15571	-0.22	0.041	NO
98	DLL1	DLL1	DLL1	16779	-0.37	0.01	NO
99	DNER	DNER	DNER	17860	-0.66	0.014	NO

Figure S119. 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: REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION.

Figure S120. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION, 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.v4.0.symbols.gmt
Expression data file = CHOL-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = CHOL-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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