GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LAML-TB

Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LAML-TB. Broad Institute of MIT and Harvard. doi:10.7908/C1PC31FF

Overview

Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes in LAML-TB. This pipeline has the following features:

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

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 187
Number of samples: 173
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 74
pheno.type: 2 - 3 :[ clus2 ] 54
pheno.type: 3 - 3 :[ clus3 ] 45

For the expression subtypes of 17276 genes in 174 samples, GSEA found enriched gene sets in each cluster using 173 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA MYOSIN PATHWAY

And common core enriched genes are EGFR, AKT3, CCND1, EGF, ERBB2, LEF1, PIK3R3, TCF7, IGF1R, PDGFRA

clus2

Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA RHO PATHWAY, BIOCARTA TOLL PATHWAY, BIOCARTA CREB PATHWAY, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

And common core enriched genes are NFKB1, NFKBIA, CHUK, GSN, MAP3K14, PRKCD, MAP2K1, MAP2K3, MAP2K6, PAK1

clus3

Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG BUTANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA DEGRADATION

And common core enriched genes are MARS2, POLR1A, POLR1B, POLR1C, POLR1D, POLR1E, POLR2A, POLR2D, POLR2F, POLR2I

Results

Subtype clus1 enriched pathways

Table 3. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA NO1 PATHWAY	25	genes.ES.table	0.64	1.6	0.027	0.21	0.72	0.52	0.2	0.42	0.13	0.019
BIOCARTA AGR PATHWAY	31	genes.ES.table	0.54	1.4	0.074	0.23	0.9	0.23	0.15	0.19	0.18	0.01
BIOCARTA ALK PATHWAY	32	genes.ES.table	0.53	1.4	0.054	0.23	0.88	0.31	0.17	0.26	0.18	0.011
BIOCARTA AT1R PATHWAY	32	genes.ES.table	0.52	1.6	0.034	0.21	0.56	0.094	0.028	0.091	0.1	0.032
BIOCARTA EGF PATHWAY	30	genes.ES.table	0.47	1.5	0.06	0.2	0.76	0.13	0.11	0.12	0.14	0.012
BIOCARTA ERK PATHWAY	25	genes.ES.table	0.59	1.8	0.02	0.19	0.26	0.2	0.13	0.18	0	0.057
BIOCARTA GH PATHWAY	26	genes.ES.table	0.49	1.5	0.087	0.24	0.85	0.15	0.11	0.14	0.17	0.021
BIOCARTA GSK3 PATHWAY	26	genes.ES.table	0.55	1.5	0.069	0.23	0.85	0.19	0.046	0.18	0.16	0.012
BIOCARTA INTEGRIN PATHWAY	37	genes.ES.table	0.46	1.5	0.053	0.23	0.85	0.14	0.11	0.12	0.17	0.016
BIOCARTA MYOSIN PATHWAY	27	genes.ES.table	0.61	1.6	0.013	0.22	0.56	0.33	0.17	0.28	0.1	0.037

genes ES table in pathway: BIOCARTA NO1 PATHWAY

Table S1. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCND1	CCND1	CCND1	38	0.65	0.12	YES
2	CDH1	CDH1	CDH1	143	0.56	0.21	YES
3	EGFR	EGFR	EGFR	152	0.56	0.31	YES
4	EGF	EGF	EGF	271	0.51	0.39	YES
5	LEF1	LEF1	LEF1	798	0.39	0.43	YES
6	TCF7	TCF7	TCF7	1776	0.28	0.42	YES
7	AXIN2	AXIN2	AXIN2	2170	0.25	0.45	YES
8	PIK3R3	PIK3R3	PIK3R3	2444	0.23	0.47	YES
9	ERBB2	ERBB2	ERBB2	2518	0.22	0.51	YES
10	AKT3	AKT3	AKT3	2541	0.22	0.55	YES
11	CTNNA3	CTNNA3	CTNNA3	3860	0.15	0.5	NO
12	MYC	MYC	MYC	5337	0.095	0.43	NO
13	PIK3CA	PIK3CA	PIK3CA	5484	0.091	0.44	NO
14	TCF7L2	TCF7L2	TCF7L2	5604	0.088	0.44	NO
15	FOXO3	FOXO3	FOXO3	5618	0.088	0.46	NO
16	SOS1	SOS1	SOS1	5807	0.082	0.46	NO
17	BRAF	BRAF	BRAF	6148	0.074	0.46	NO
18	PIK3R1	PIK3R1	PIK3R1	6906	0.058	0.42	NO
19	APC	APC	APC	8323	0.037	0.35	NO
20	NRAS	NRAS	NRAS	8929	0.029	0.32	NO
21	AXIN1	AXIN1	AXIN1	9014	0.028	0.32	NO
22	PTEN	PTEN	PTEN	9249	0.025	0.31	NO
23	PIK3CG	PIK3CG	PIK3CG	10020	0.016	0.27	NO
24	GSK3B	GSK3B	GSK3B	10415	0.01	0.25	NO
25	MAPK1	MAPK1	MAPK1	10485	0.0096	0.24	NO
26	MAP2K2	MAP2K2	MAP2K2	10631	0.0077	0.24	NO
27	AKT2	AKT2	AKT2	11025	0.003	0.21	NO
28	RAF1	RAF1	RAF1	11386	-0.0016	0.19	NO
29	MLH1	MLH1	MLH1	11391	-0.0017	0.19	NO
30	PIK3CD	PIK3CD	PIK3CD	11442	-0.0024	0.19	NO
31	APC2	APC2	APC2	11492	-0.0031	0.19	NO
32	PDPK1	PDPK1	PDPK1	11509	-0.0033	0.19	NO
33	ELK1	ELK1	ELK1	11607	-0.0049	0.18	NO
34	KRAS	KRAS	KRAS	11860	-0.0084	0.17	NO
35	TP53	TP53	TP53	11922	-0.0094	0.17	NO
36	TCF7L1	TCF7L1	TCF7L1	12137	-0.013	0.16	NO
37	CTNNB1	CTNNB1	CTNNB1	12519	-0.019	0.14	NO
38	MAPK3	MAPK3	MAPK3	12587	-0.02	0.14	NO
39	SOS2	SOS2	SOS2	12601	-0.02	0.14	NO
40	PIK3R2	PIK3R2	PIK3R2	12846	-0.024	0.13	NO
41	ARAF	ARAF	ARAF	12876	-0.025	0.14	NO
42	BAD	BAD	BAD	14324	-0.055	0.061	NO
43	PIK3CB	PIK3CB	PIK3CB	14800	-0.069	0.045	NO
44	AKT1	AKT1	AKT1	14813	-0.069	0.057	NO
45	CASP9	CASP9	CASP9	14840	-0.07	0.068	NO
46	PIK3R5	PIK3R5	PIK3R5	14867	-0.071	0.079	NO
47	ILK	ILK	ILK	14889	-0.072	0.091	NO
48	GRB2	GRB2	GRB2	14895	-0.072	0.1	NO
49	MAP2K1	MAP2K1	MAP2K1	14920	-0.073	0.12	NO
50	CTNNA1	CTNNA1	CTNNA1	15809	-0.12	0.084	NO

Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA AGR PATHWAY

Table 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	CCND1	CCND1	CCND1	38	0.65	0.061	YES
2	EGFR	EGFR	EGFR	152	0.56	0.11	YES
3	EGF	EGF	EGF	271	0.51	0.15	YES
4	IGF1	IGF1	IGF1	346	0.49	0.19	YES
5	FGFR2	FGFR2	FGFR2	549	0.44	0.22	YES
6	FGFR1	FGFR1	FGFR1	628	0.42	0.26	YES
7	PDGFRA	PDGFRA	PDGFRA	658	0.42	0.3	YES
8	LEF1	LEF1	LEF1	798	0.39	0.33	YES
9	IGF1R	IGF1R	IGF1R	1308	0.33	0.33	YES
10	PDGFB	PDGFB	PDGFB	1432	0.32	0.35	YES
11	PDGFRB	PDGFRB	PDGFRB	1462	0.32	0.38	YES
12	FOXO1	FOXO1	FOXO1	1665	0.29	0.4	YES
13	TCF7	TCF7	TCF7	1776	0.28	0.42	YES
14	CREB3L3	CREB3L3	CREB3L3	1845	0.28	0.44	YES
15	AR	AR	AR	2174	0.25	0.44	YES
16	PIK3R3	PIK3R3	PIK3R3	2444	0.23	0.45	YES
17	ERBB2	ERBB2	ERBB2	2518	0.22	0.47	YES
18	AKT3	AKT3	AKT3	2541	0.22	0.49	YES
19	PDGFC	PDGFC	PDGFC	2723	0.21	0.5	YES
20	PDGFA	PDGFA	PDGFA	3048	0.19	0.5	YES
21	CREB3L1	CREB3L1	CREB3L1	3055	0.19	0.52	YES
22	BCL2	BCL2	BCL2	4205	0.13	0.46	NO
23	CREB3L4	CREB3L4	CREB3L4	4214	0.13	0.48	NO
24	SRD5A2	SRD5A2	SRD5A2	5343	0.095	0.42	NO
25	E2F2	E2F2	E2F2	5372	0.094	0.43	NO
26	PIK3CA	PIK3CA	PIK3CA	5484	0.091	0.43	NO
27	TCF7L2	TCF7L2	TCF7L2	5604	0.088	0.43	NO
28	SOS1	SOS1	SOS1	5807	0.082	0.43	NO
29	CCNE1	CCNE1	CCNE1	5844	0.081	0.43	NO
30	BRAF	BRAF	BRAF	6148	0.074	0.42	NO
31	CCNE2	CCNE2	CCNE2	6174	0.074	0.43	NO
32	PIK3R1	PIK3R1	PIK3R1	6906	0.058	0.39	NO
33	RB1	RB1	RB1	7691	0.046	0.35	NO
34	CREB1	CREB1	CREB1	7788	0.044	0.35	NO
35	E2F1	E2F1	E2F1	8321	0.037	0.32	NO
36	CREBBP	CREBBP	CREBBP	8375	0.037	0.32	NO
37	CREB3L2	CREB3L2	CREB3L2	8793	0.031	0.3	NO
38	NRAS	NRAS	NRAS	8929	0.029	0.29	NO
39	CDK2	CDK2	CDK2	9190	0.026	0.28	NO
40	PTEN	PTEN	PTEN	9249	0.025	0.28	NO
41	MTOR	MTOR	MTOR	9422	0.023	0.27	NO
42	IKBKB	IKBKB	IKBKB	9615	0.021	0.26	NO
43	EP300	EP300	EP300	9626	0.021	0.26	NO
44	INSRR	INSRR	INSRR	9749	0.019	0.26	NO
45	E2F3	E2F3	E2F3	9996	0.016	0.25	NO
46	PIK3CG	PIK3CG	PIK3CG	10020	0.016	0.25	NO
47	ATF4	ATF4	ATF4	10066	0.015	0.25	NO
48	GSK3B	GSK3B	GSK3B	10415	0.01	0.23	NO
49	HSP90B1	HSP90B1	HSP90B1	10471	0.0098	0.22	NO
50	MAPK1	MAPK1	MAPK1	10485	0.0096	0.22	NO
51	MAP2K2	MAP2K2	MAP2K2	10631	0.0077	0.22	NO
52	NKX3-1	NKX3-1	NKX3-1	10797	0.0057	0.21	NO
53	HSP90AA1	HSP90AA1	HSP90AA1	10960	0.0038	0.2	NO
54	AKT2	AKT2	AKT2	11025	0.003	0.2	NO
55	CDKN1B	CDKN1B	CDKN1B	11196	0.0009	0.18	NO
56	RAF1	RAF1	RAF1	11386	-0.0016	0.18	NO
57	PIK3CD	PIK3CD	PIK3CD	11442	-0.0024	0.17	NO
58	PDPK1	PDPK1	PDPK1	11509	-0.0033	0.17	NO
59	KRAS	KRAS	KRAS	11860	-0.0084	0.15	NO
60	TP53	TP53	TP53	11922	-0.0094	0.15	NO
61	CHUK	CHUK	CHUK	11937	-0.0096	0.15	NO
62	TCF7L1	TCF7L1	TCF7L1	12137	-0.013	0.14	NO
63	RELA	RELA	RELA	12401	-0.017	0.12	NO
64	CTNNB1	CTNNB1	CTNNB1	12519	-0.019	0.12	NO
65	MAPK3	MAPK3	MAPK3	12587	-0.02	0.12	NO
66	SOS2	SOS2	SOS2	12601	-0.02	0.12	NO
67	PIK3R2	PIK3R2	PIK3R2	12846	-0.024	0.1	NO
68	ARAF	ARAF	ARAF	12876	-0.025	0.1	NO
69	CREB3	CREB3	CREB3	13146	-0.029	0.092	NO
70	NFKB1	NFKB1	NFKB1	13421	-0.034	0.079	NO
71	GSTP1	GSTP1	GSTP1	13471	-0.035	0.08	NO
72	IKBKG	IKBKG	IKBKG	13491	-0.036	0.082	NO
73	TGFA	TGFA	TGFA	13739	-0.041	0.072	NO
74	HRAS	HRAS	HRAS	14315	-0.055	0.044	NO
75	BAD	BAD	BAD	14324	-0.055	0.048	NO
76	NFKBIA	NFKBIA	NFKBIA	14477	-0.059	0.045	NO
77	PIK3CB	PIK3CB	PIK3CB	14800	-0.069	0.033	NO
78	AKT1	AKT1	AKT1	14813	-0.069	0.039	NO
79	CASP9	CASP9	CASP9	14840	-0.07	0.044	NO
80	PIK3R5	PIK3R5	PIK3R5	14867	-0.071	0.05	NO
81	GRB2	GRB2	GRB2	14895	-0.072	0.055	NO
82	MAP2K1	MAP2K1	MAP2K1	14920	-0.073	0.06	NO
83	MDM2	MDM2	MDM2	15279	-0.087	0.048	NO
84	PDGFD	PDGFD	PDGFD	16594	-0.2	-0.0092	NO
85	CDKN1A	CDKN1A	CDKN1A	16818	-0.25	0.0016	NO
86	CREB5	CREB5	CREB5	16830	-0.25	0.025	NO

Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AGR PATHWAY.

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

genes ES table in pathway: BIOCARTA ALK PATHWAY

Table 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	MGAT5B	MGAT5B	MGAT5B	380	0.48	0.098	YES
2	TUSC3	TUSC3	TUSC3	647	0.42	0.19	YES
3	MAN1A1	MAN1A1	MAN1A1	729	0.4	0.28	YES
4	MGAT3	MGAT3	MGAT3	838	0.38	0.37	YES
5	MAN1C1	MAN1C1	MAN1C1	2630	0.22	0.32	YES
6	ALG11	ALG11	ALG11	2651	0.22	0.38	YES
7	MGAT4A	MGAT4A	MGAT4A	2781	0.21	0.42	YES
8	FUT8	FUT8	FUT8	3992	0.14	0.39	YES
9	ALG10B	ALG10B	ALG10B	4423	0.12	0.39	YES
10	MGAT5	MGAT5	MGAT5	4810	0.11	0.4	YES
11	ALG10	ALG10	ALG10	4892	0.11	0.42	YES
12	ST6GAL1	ST6GAL1	ST6GAL1	4936	0.11	0.44	YES
13	STT3B	STT3B	STT3B	4978	0.11	0.47	YES
14	ALG14	ALG14	ALG14	5860	0.081	0.44	NO
15	ALG9	ALG9	ALG9	6003	0.078	0.45	NO
16	MAN1A2	MAN1A2	MAN1A2	6649	0.064	0.43	NO
17	ALG13	ALG13	ALG13	7609	0.047	0.38	NO
18	MAN2A2	MAN2A2	MAN2A2	8810	0.031	0.32	NO
19	B4GALT3	B4GALT3	B4GALT3	8840	0.03	0.33	NO
20	ALG12	ALG12	ALG12	8977	0.029	0.33	NO
21	GANAB	GANAB	GANAB	9235	0.025	0.32	NO
22	STT3A	STT3A	STT3A	9403	0.023	0.31	NO
23	B4GALT2	B4GALT2	B4GALT2	9843	0.018	0.29	NO
24	ALG6	ALG6	ALG6	9849	0.018	0.3	NO
25	MAN1B1	MAN1B1	MAN1B1	10336	0.012	0.27	NO
26	DOLPP1	DOLPP1	DOLPP1	10570	0.0085	0.26	NO
27	DPM3	DPM3	DPM3	10588	0.0083	0.26	NO
28	ALG3	ALG3	ALG3	10955	0.0039	0.24	NO
29	DPAGT1	DPAGT1	DPAGT1	11203	0.00082	0.23	NO
30	ALG2	ALG2	ALG2	11508	-0.0033	0.21	NO
31	RPN1	RPN1	RPN1	11722	-0.0065	0.2	NO
32	DDOST	DDOST	DDOST	11769	-0.0072	0.2	NO
33	RPN2	RPN2	RPN2	11803	-0.0078	0.2	NO
34	DPM1	DPM1	DPM1	11845	-0.0083	0.2	NO
35	DPM2	DPM2	DPM2	11889	-0.0089	0.2	NO
36	ALG5	ALG5	ALG5	12077	-0.012	0.19	NO
37	MAN2A1	MAN2A1	MAN2A1	12582	-0.02	0.17	NO
38	MOGS	MOGS	MOGS	13285	-0.032	0.13	NO
39	ALG8	ALG8	ALG8	13358	-0.033	0.14	NO
40	MGAT2	MGAT2	MGAT2	13623	-0.038	0.13	NO
41	ALG1	ALG1	ALG1	14005	-0.047	0.12	NO
42	DAD1	DAD1	DAD1	14563	-0.062	0.1	NO
43	MGAT1	MGAT1	MGAT1	14793	-0.069	0.11	NO
44	B4GALT1	B4GALT1	B4GALT1	14844	-0.07	0.12	NO
45	MGAT4B	MGAT4B	MGAT4B	14877	-0.071	0.14	NO

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

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

genes ES table in pathway: BIOCARTA AT1R PATHWAY

Table 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	EGFR	EGFR	EGFR	152	0.56	0.2	YES
2	PDGFRA	PDGFRA	PDGFRA	658	0.42	0.34	YES
3	IGF1R	IGF1R	IGF1R	1308	0.33	0.43	YES
4	NGFR	NGFR	NGFR	1627	0.3	0.52	YES
5	PTPRR	PTPRR	PTPRR	2197	0.25	0.59	YES
6	MYC	MYC	MYC	5337	0.095	0.44	NO
7	SOS1	SOS1	SOS1	5807	0.082	0.45	NO
8	MKNK2	MKNK2	MKNK2	7127	0.055	0.39	NO
9	ITGB1	ITGB1	ITGB1	7805	0.044	0.37	NO
10	STAT3	STAT3	STAT3	10112	0.014	0.24	NO
11	MAPK1	MAPK1	MAPK1	10485	0.0096	0.22	NO
12	GNB1	GNB1	GNB1	10617	0.0078	0.22	NO
13	MAP2K2	MAP2K2	MAP2K2	10631	0.0077	0.22	NO
14	SHC1	SHC1	SHC1	10888	0.0046	0.21	NO
15	RAF1	RAF1	RAF1	11386	-0.0016	0.18	NO
16	GNAS	GNAS	GNAS	11413	-0.0021	0.18	NO
17	ELK1	ELK1	ELK1	11607	-0.0049	0.17	NO
18	RPS6KA5	RPS6KA5	RPS6KA5	11669	-0.0057	0.17	NO
19	MAPK3	MAPK3	MAPK3	12587	-0.02	0.12	NO
20	MKNK1	MKNK1	MKNK1	14060	-0.048	0.055	NO
21	PPP2CA	PPP2CA	PPP2CA	14139	-0.05	0.07	NO
22	RPS6KA1	RPS6KA1	RPS6KA1	14430	-0.058	0.075	NO
23	GRB2	GRB2	GRB2	14895	-0.072	0.076	NO
24	MAP2K1	MAP2K1	MAP2K1	14920	-0.073	0.1	NO
25	SRC	SRC	SRC	15236	-0.085	0.12	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 AT1R PATHWAY.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA EGF 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	FLT4	FLT4	FLT4	101	0.59	0.17	YES
2	KDR	KDR	KDR	377	0.48	0.3	YES
3	PTK2	PTK2	PTK2	476	0.46	0.43	YES
4	FLT1	FLT1	FLT1	649	0.42	0.55	YES
5	PLCG1	PLCG1	PLCG1	712	0.41	0.67	YES
6	VEGFA	VEGFA	VEGFA	1844	0.28	0.68	YES
7	NOS3	NOS3	NOS3	3419	0.17	0.64	NO
8	PIK3CA	PIK3CA	PIK3CA	5484	0.091	0.55	NO
9	HIF1A	HIF1A	HIF1A	6375	0.069	0.52	NO
10	PIK3R1	PIK3R1	PIK3R1	6906	0.058	0.51	NO
11	PRKCB	PRKCB	PRKCB	7567	0.048	0.48	NO
12	EIF1AX	EIF1AX	EIF1AX	8733	0.032	0.43	NO
13	EIF2S1	EIF2S1	EIF2S1	8770	0.031	0.43	NO
14	ELAVL1	ELAVL1	ELAVL1	9112	0.027	0.42	NO
15	PIK3CG	PIK3CG	PIK3CG	10020	0.016	0.37	NO
16	PXN	PXN	PXN	10151	0.014	0.37	NO
17	EIF2B5	EIF2B5	EIF2B5	10754	0.0063	0.34	NO
18	SHC1	SHC1	SHC1	10888	0.0046	0.33	NO
19	EIF2B3	EIF2B3	EIF2B3	10928	0.0042	0.33	NO
20	VHL	VHL	VHL	11317	-0.00064	0.31	NO
21	EIF2S3	EIF2S3	EIF2S3	11590	-0.0046	0.29	NO
22	EIF2B4	EIF2B4	EIF2B4	11623	-0.0051	0.29	NO
23	EIF2S2	EIF2S2	EIF2S2	11866	-0.0086	0.28	NO
24	PRKCA	PRKCA	PRKCA	11977	-0.01	0.28	NO
25	EIF2B2	EIF2B2	EIF2B2	12303	-0.015	0.26	NO
26	EIF2B1	EIF2B1	EIF2B1	12340	-0.016	0.27	NO
27	ARNT	ARNT	ARNT	12857	-0.024	0.24	NO
28	EIF1	EIF1	EIF1	13500	-0.036	0.22	NO

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

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EGF PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA ERK 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	CCND1	CCND1	CCND1	38	0.65	0.09	YES
2	EGFR	EGFR	EGFR	152	0.56	0.16	YES
3	EGF	EGF	EGF	271	0.51	0.23	YES
4	PGF	PGF	PGF	831	0.39	0.25	YES
5	TGFB2	TGFB2	TGFB2	1668	0.29	0.24	YES
6	VEGFA	VEGFA	VEGFA	1844	0.28	0.27	YES
7	VEGFC	VEGFC	VEGFC	2042	0.26	0.3	YES
8	FIGF	FIGF	FIGF	2109	0.26	0.33	YES
9	RAC3	RAC3	RAC3	2225	0.25	0.36	YES
10	PIK3R3	PIK3R3	PIK3R3	2444	0.23	0.38	YES
11	ERBB2	ERBB2	ERBB2	2518	0.22	0.4	YES
12	AKT3	AKT3	AKT3	2541	0.22	0.43	YES
13	TGFB3	TGFB3	TGFB3	2947	0.2	0.44	YES
14	BCL2L1	BCL2L1	BCL2L1	3685	0.16	0.42	NO
15	CDK6	CDK6	CDK6	3962	0.15	0.42	NO
16	MAPK8	MAPK8	MAPK8	5072	0.1	0.37	NO
17	STAT1	STAT1	STAT1	5277	0.097	0.37	NO
18	E2F2	E2F2	E2F2	5372	0.094	0.38	NO
19	PIK3CA	PIK3CA	PIK3CA	5484	0.091	0.39	NO
20	MAPK10	MAPK10	MAPK10	5507	0.09	0.4	NO
21	JAK1	JAK1	JAK1	5697	0.085	0.4	NO
22	BRAF	BRAF	BRAF	6148	0.074	0.38	NO
23	ARHGEF6	ARHGEF6	ARHGEF6	6346	0.07	0.38	NO
24	PIK3R1	PIK3R1	PIK3R1	6906	0.058	0.36	NO
25	SMAD4	SMAD4	SMAD4	7348	0.051	0.34	NO
26	SMAD3	SMAD3	SMAD3	7475	0.049	0.34	NO
27	RB1	RB1	RB1	7691	0.046	0.33	NO
28	TGFBR1	TGFBR1	TGFBR1	7851	0.043	0.33	NO
29	CDK4	CDK4	CDK4	7888	0.043	0.33	NO
30	BRCA2	BRCA2	BRCA2	7944	0.042	0.34	NO
31	VEGFB	VEGFB	VEGFB	8370	0.037	0.32	NO
32	RALGDS	RALGDS	RALGDS	8456	0.036	0.32	NO
33	RALBP1	RALBP1	RALBP1	8609	0.034	0.31	NO
34	RALA	RALA	RALA	8730	0.032	0.31	NO
35	SMAD2	SMAD2	SMAD2	8971	0.029	0.3	NO
36	IKBKB	IKBKB	IKBKB	9615	0.021	0.27	NO
37	TGFBR2	TGFBR2	TGFBR2	9736	0.019	0.26	NO
38	E2F3	E2F3	E2F3	9996	0.016	0.25	NO
39	PIK3CG	PIK3CG	PIK3CG	10020	0.016	0.25	NO
40	STAT3	STAT3	STAT3	10112	0.014	0.25	NO
41	MAPK1	MAPK1	MAPK1	10485	0.0096	0.23	NO
42	AKT2	AKT2	AKT2	11025	0.003	0.2	NO
43	RAF1	RAF1	RAF1	11386	-0.0016	0.18	NO
44	PIK3CD	PIK3CD	PIK3CD	11442	-0.0024	0.17	NO
45	KRAS	KRAS	KRAS	11860	-0.0084	0.15	NO
46	TP53	TP53	TP53	11922	-0.0094	0.15	NO
47	CHUK	CHUK	CHUK	11937	-0.0096	0.15	NO
48	RAD51	RAD51	RAD51	12177	-0.013	0.14	NO
49	RELA	RELA	RELA	12401	-0.017	0.12	NO
50	MAPK3	MAPK3	MAPK3	12587	-0.02	0.12	NO
51	PIK3R2	PIK3R2	PIK3R2	12846	-0.024	0.1	NO
52	ARAF	ARAF	ARAF	12876	-0.025	0.11	NO
53	MAPK9	MAPK9	MAPK9	12894	-0.025	0.11	NO
54	NFKB1	NFKB1	NFKB1	13421	-0.034	0.083	NO
55	IKBKG	IKBKG	IKBKG	13491	-0.036	0.084	NO
56	RAC2	RAC2	RAC2	13533	-0.036	0.087	NO
57	TGFA	TGFA	TGFA	13739	-0.041	0.081	NO
58	CDC42	CDC42	CDC42	14232	-0.052	0.06	NO
59	BAD	BAD	BAD	14324	-0.055	0.062	NO
60	PLD1	PLD1	PLD1	14492	-0.06	0.061	NO
61	RAC1	RAC1	RAC1	14605	-0.063	0.063	NO
62	TGFB1	TGFB1	TGFB1	14701	-0.066	0.067	NO
63	PIK3CB	PIK3CB	PIK3CB	14800	-0.069	0.071	NO
64	AKT1	AKT1	AKT1	14813	-0.069	0.08	NO
65	CASP9	CASP9	CASP9	14840	-0.07	0.088	NO
66	PIK3R5	PIK3R5	PIK3R5	14867	-0.071	0.097	NO
67	MAP2K1	MAP2K1	MAP2K1	14920	-0.073	0.1	NO
68	RALB	RALB	RALB	15755	-0.11	0.072	NO
69	CDKN2A	CDKN2A	CDKN2A	15774	-0.11	0.086	NO

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

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

genes ES table in pathway: BIOCARTA GH 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	CCND1	CCND1	CCND1	38	0.65	0.22	YES
2	CDH1	CDH1	CDH1	143	0.56	0.4	YES
3	LEF1	LEF1	LEF1	798	0.39	0.5	YES
4	TCF7	TCF7	TCF7	1776	0.28	0.54	YES
5	NTRK1	NTRK1	NTRK1	2311	0.24	0.59	YES
6	MYC	MYC	MYC	5337	0.095	0.45	NO
7	TCF7L2	TCF7L2	TCF7L2	5604	0.088	0.46	NO
8	BRAF	BRAF	BRAF	6148	0.074	0.46	NO
9	TPR	TPR	TPR	8048	0.041	0.36	NO
10	NRAS	NRAS	NRAS	8929	0.029	0.32	NO
11	PAX8	PAX8	PAX8	9337	0.024	0.3	NO
12	TFG	TFG	TFG	9636	0.02	0.29	NO
13	RXRB	RXRB	RXRB	10363	0.011	0.25	NO
14	MAPK1	MAPK1	MAPK1	10485	0.0096	0.25	NO
15	MAP2K2	MAP2K2	MAP2K2	10631	0.0077	0.24	NO
16	PPARG	PPARG	PPARG	11291	-0.00027	0.21	NO
17	KRAS	KRAS	KRAS	11860	-0.0084	0.18	NO
18	TP53	TP53	TP53	11922	-0.0094	0.18	NO
19	TCF7L1	TCF7L1	TCF7L1	12137	-0.013	0.17	NO
20	CCDC6	CCDC6	CCDC6	12378	-0.016	0.16	NO
21	CTNNB1	CTNNB1	CTNNB1	12519	-0.019	0.16	NO
22	MAPK3	MAPK3	MAPK3	12587	-0.02	0.16	NO
23	RET	RET	RET	12665	-0.021	0.16	NO
24	TPM3	TPM3	TPM3	12906	-0.025	0.16	NO
25	NCOA4	NCOA4	NCOA4	14409	-0.057	0.09	NO
26	MAP2K1	MAP2K1	MAP2K1	14920	-0.073	0.086	NO
27	RXRA	RXRA	RXRA	16190	-0.15	0.062	NO

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

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

genes ES table in pathway: BIOCARTA GSK3 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCND1	CCND1	CCND1	38	0.65	0.13	YES
2	EGFR	EGFR	EGFR	152	0.56	0.23	YES
3	EGF	EGF	EGF	271	0.51	0.33	YES
4	PLCG1	PLCG1	PLCG1	712	0.41	0.38	YES
5	PIK3R3	PIK3R3	PIK3R3	2444	0.23	0.33	YES
6	ERBB2	ERBB2	ERBB2	2518	0.22	0.37	YES
7	FHIT	FHIT	FHIT	2526	0.22	0.42	YES
8	AKT3	AKT3	AKT3	2541	0.22	0.46	YES
9	CDK6	CDK6	CDK6	3962	0.15	0.4	NO
10	E2F2	E2F2	E2F2	5372	0.094	0.34	NO
11	PIK3CA	PIK3CA	PIK3CA	5484	0.091	0.35	NO
12	FOXO3	FOXO3	FOXO3	5618	0.088	0.36	NO
13	SOS1	SOS1	SOS1	5807	0.082	0.37	NO
14	BRAF	BRAF	BRAF	6148	0.074	0.36	NO
15	PIK3R1	PIK3R1	PIK3R1	6906	0.058	0.33	NO
16	RARB	RARB	RARB	7490	0.049	0.31	NO
17	PRKCB	PRKCB	PRKCB	7567	0.048	0.31	NO
18	RB1	RB1	RB1	7691	0.046	0.32	NO
19	CDK4	CDK4	CDK4	7888	0.043	0.31	NO
20	PLCG2	PLCG2	PLCG2	8818	0.031	0.26	NO
21	NRAS	NRAS	NRAS	8929	0.029	0.26	NO
22	E2F3	E2F3	E2F3	9996	0.016	0.21	NO
23	PIK3CG	PIK3CG	PIK3CG	10020	0.016	0.21	NO
24	RXRB	RXRB	RXRB	10363	0.011	0.19	NO
25	MAPK1	MAPK1	MAPK1	10485	0.0096	0.18	NO
26	MAP2K2	MAP2K2	MAP2K2	10631	0.0077	0.18	NO
27	AKT2	AKT2	AKT2	11025	0.003	0.16	NO
28	RASSF1	RASSF1	RASSF1	11088	0.0022	0.15	NO
29	RAF1	RAF1	RAF1	11386	-0.0016	0.14	NO
30	PIK3CD	PIK3CD	PIK3CD	11442	-0.0024	0.13	NO
31	PDPK1	PDPK1	PDPK1	11509	-0.0033	0.13	NO
32	PRKCG	PRKCG	PRKCG	11775	-0.0073	0.12	NO
33	KRAS	KRAS	KRAS	11860	-0.0084	0.11	NO
34	TP53	TP53	TP53	11922	-0.0094	0.11	NO
35	PRKCA	PRKCA	PRKCA	11977	-0.01	0.11	NO
36	MAPK3	MAPK3	MAPK3	12587	-0.02	0.078	NO
37	SOS2	SOS2	SOS2	12601	-0.02	0.082	NO
38	STK4	STK4	STK4	12644	-0.021	0.083	NO
39	PIK3R2	PIK3R2	PIK3R2	12846	-0.024	0.076	NO
40	ARAF	ARAF	ARAF	12876	-0.025	0.08	NO
41	RASSF5	RASSF5	RASSF5	13462	-0.035	0.053	NO
42	TGFA	TGFA	TGFA	13739	-0.041	0.045	NO
43	HRAS	HRAS	HRAS	14315	-0.055	0.022	NO
44	BAD	BAD	BAD	14324	-0.055	0.033	NO
45	PIK3CB	PIK3CB	PIK3CB	14800	-0.069	0.019	NO
46	AKT1	AKT1	AKT1	14813	-0.069	0.032	NO
47	CASP9	CASP9	CASP9	14840	-0.07	0.045	NO
48	PIK3R5	PIK3R5	PIK3R5	14867	-0.071	0.058	NO
49	GRB2	GRB2	GRB2	14895	-0.072	0.07	NO
50	MAP2K1	MAP2K1	MAP2K1	14920	-0.073	0.084	NO
51	CDKN2A	CDKN2A	CDKN2A	15774	-0.11	0.057	NO
52	RXRA	RXRA	RXRA	16190	-0.15	0.062	NO

Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GSK3 PATHWAY.

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

genes ES table in pathway: BIOCARTA INTEGRIN PATHWAY

Table S9. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SORBS1	SORBS1	SORBS1	57	0.63	0.057	YES
2	CDH1	CDH1	CDH1	143	0.56	0.1	YES
3	EGFR	EGFR	EGFR	152	0.56	0.16	YES
4	SNAI2	SNAI2	SNAI2	358	0.48	0.19	YES
5	TJP1	TJP1	TJP1	399	0.47	0.24	YES
6	FGFR1	FGFR1	FGFR1	628	0.42	0.26	YES
7	MET	MET	MET	758	0.4	0.29	YES
8	LEF1	LEF1	LEF1	798	0.39	0.33	YES
9	PTPRB	PTPRB	PTPRB	909	0.38	0.36	YES
10	WASF1	WASF1	WASF1	910	0.38	0.39	YES
11	WASF3	WASF3	WASF3	1058	0.36	0.42	YES
12	PARD3	PARD3	PARD3	1223	0.34	0.44	YES
13	IGF1R	IGF1R	IGF1R	1308	0.33	0.47	YES
14	PTPRM	PTPRM	PTPRM	1311	0.33	0.5	YES
15	PVRL3	PVRL3	PVRL3	1424	0.32	0.52	YES
16	MLLT4	MLLT4	MLLT4	1555	0.31	0.55	YES
17	TCF7	TCF7	TCF7	1776	0.28	0.56	YES
18	RAC3	RAC3	RAC3	2225	0.25	0.56	YES
19	ERBB2	ERBB2	ERBB2	2518	0.22	0.56	YES
20	LMO7	LMO7	LMO7	3473	0.17	0.52	NO
21	SNAI1	SNAI1	SNAI1	3797	0.16	0.52	NO
22	CTNNA3	CTNNA3	CTNNA3	3860	0.15	0.53	NO
23	YES1	YES1	YES1	4293	0.13	0.52	NO
24	PVRL2	PVRL2	PVRL2	5540	0.089	0.45	NO
25	TCF7L2	TCF7L2	TCF7L2	5604	0.088	0.46	NO
26	CSNK2A2	CSNK2A2	CSNK2A2	7054	0.056	0.38	NO
27	CSNK2A1	CSNK2A1	CSNK2A1	7096	0.056	0.38	NO
28	ACP1	ACP1	ACP1	7217	0.054	0.38	NO
29	SMAD4	SMAD4	SMAD4	7348	0.051	0.38	NO
30	MAP3K7	MAP3K7	MAP3K7	7398	0.051	0.38	NO
31	SMAD3	SMAD3	SMAD3	7475	0.049	0.38	NO
32	TGFBR1	TGFBR1	TGFBR1	7851	0.043	0.36	NO
33	FARP2	FARP2	FARP2	7940	0.042	0.36	NO
34	PVRL1	PVRL1	PVRL1	7976	0.042	0.36	NO
35	VCL	VCL	VCL	8178	0.039	0.36	NO
36	CREBBP	CREBBP	CREBBP	8375	0.037	0.35	NO
37	NLK	NLK	NLK	8469	0.036	0.34	NO
38	BAIAP2	BAIAP2	BAIAP2	8543	0.034	0.34	NO
39	FYN	FYN	FYN	8927	0.029	0.32	NO
40	SMAD2	SMAD2	SMAD2	8971	0.029	0.32	NO
41	WASL	WASL	WASL	9263	0.025	0.31	NO
42	PTPRF	PTPRF	PTPRF	9405	0.023	0.3	NO
43	WASF2	WASF2	WASF2	9431	0.023	0.3	NO
44	EP300	EP300	EP300	9626	0.021	0.3	NO
45	TGFBR2	TGFBR2	TGFBR2	9736	0.019	0.29	NO
46	MAPK1	MAPK1	MAPK1	10485	0.0096	0.25	NO
47	ACTN2	ACTN2	ACTN2	11083	0.0023	0.21	NO
48	CTNND1	CTNND1	CTNND1	11385	-0.0016	0.2	NO
49	ACTN3	ACTN3	ACTN3	11410	-0.0021	0.2	NO
50	FER	FER	FER	11924	-0.0094	0.17	NO
51	TCF7L1	TCF7L1	TCF7L1	12137	-0.013	0.16	NO
52	ACTN1	ACTN1	ACTN1	12355	-0.016	0.14	NO
53	PTPN1	PTPN1	PTPN1	12502	-0.018	0.14	NO
54	CSNK2B	CSNK2B	CSNK2B	12514	-0.018	0.14	NO
55	CTNNB1	CTNNB1	CTNNB1	12519	-0.019	0.14	NO
56	MAPK3	MAPK3	MAPK3	12587	-0.02	0.14	NO
57	RAC2	RAC2	RAC2	13533	-0.036	0.087	NO
58	ACTG1	ACTG1	ACTG1	13683	-0.04	0.082	NO
59	ACTB	ACTB	ACTB	13724	-0.04	0.083	NO
60	ACTN4	ACTN4	ACTN4	13734	-0.041	0.087	NO
61	INSR	INSR	INSR	14125	-0.05	0.069	NO
62	CDC42	CDC42	CDC42	14232	-0.052	0.068	NO
63	RHOA	RHOA	RHOA	14261	-0.053	0.071	NO
64	SSX2IP	SSX2IP	SSX2IP	14290	-0.054	0.074	NO
65	IQGAP1	IQGAP1	IQGAP1	14308	-0.054	0.079	NO
66	RAC1	RAC1	RAC1	14605	-0.063	0.068	NO
67	SRC	SRC	SRC	15236	-0.085	0.039	NO
68	WAS	WAS	WAS	15504	-0.097	0.033	NO
69	CTNNA1	CTNNA1	CTNNA1	15809	-0.12	0.026	NO
70	PTPRJ	PTPRJ	PTPRJ	15865	-0.12	0.034	NO
71	PTPN6	PTPN6	PTPN6	16162	-0.14	0.031	NO
72	PVRL4	PVRL4	PVRL4	17082	-0.34	0.01	NO

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

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

genes ES table in pathway: BIOCARTA MYOSIN 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	CCND1	CCND1	CCND1	38	0.65	0.018	YES
2	TNXB	TNXB	TNXB	58	0.63	0.037	YES
3	FLT4	FLT4	FLT4	101	0.59	0.052	YES
4	ITGA9	ITGA9	ITGA9	117	0.58	0.07	YES
5	COL6A3	COL6A3	COL6A3	151	0.56	0.085	YES
6	EGFR	EGFR	EGFR	152	0.56	0.1	YES
7	COL6A2	COL6A2	COL6A2	173	0.54	0.12	YES
8	COL5A2	COL5A2	COL5A2	184	0.54	0.13	YES
9	ITGA8	ITGA8	ITGA8	226	0.52	0.15	YES
10	COL1A2	COL1A2	COL1A2	229	0.52	0.16	YES
11	PARVA	PARVA	PARVA	243	0.51	0.18	YES
12	LAMA4	LAMA4	LAMA4	256	0.51	0.2	YES
13	EGF	EGF	EGF	271	0.51	0.21	YES
14	BCAR1	BCAR1	BCAR1	329	0.49	0.22	YES
15	IGF1	IGF1	IGF1	346	0.49	0.24	YES
16	KDR	KDR	KDR	377	0.48	0.25	YES
17	COL3A1	COL3A1	COL3A1	426	0.47	0.26	YES
18	TNC	TNC	TNC	456	0.46	0.27	YES
19	PTK2	PTK2	PTK2	476	0.46	0.29	YES
20	ITGB4	ITGB4	ITGB4	520	0.45	0.3	YES
21	COL6A1	COL6A1	COL6A1	570	0.43	0.31	YES
22	MYLK	MYLK	MYLK	578	0.43	0.32	YES
23	FLT1	FLT1	FLT1	649	0.42	0.33	YES
24	PDGFRA	PDGFRA	PDGFRA	658	0.42	0.34	YES
25	COL5A3	COL5A3	COL5A3	717	0.41	0.35	YES
26	MET	MET	MET	758	0.4	0.36	YES
27	LAMB1	LAMB1	LAMB1	797	0.39	0.37	YES
28	COL1A1	COL1A1	COL1A1	828	0.39	0.38	YES
29	PGF	PGF	PGF	831	0.39	0.4	YES
30	SHC2	SHC2	SHC2	893	0.38	0.4	YES
31	ARHGAP5	ARHGAP5	ARHGAP5	1069	0.36	0.4	YES
32	RELN	RELN	RELN	1070	0.36	0.42	YES
33	COL5A1	COL5A1	COL5A1	1078	0.35	0.42	YES
34	SHC4	SHC4	SHC4	1209	0.34	0.43	YES
35	LAMC1	LAMC1	LAMC1	1264	0.33	0.44	YES
36	IGF1R	IGF1R	IGF1R	1308	0.33	0.44	YES
37	CAV1	CAV1	CAV1	1412	0.32	0.45	YES
38	PDGFB	PDGFB	PDGFB	1432	0.32	0.46	YES
39	PDGFRB	PDGFRB	PDGFRB	1462	0.32	0.46	YES
40	SPP1	SPP1	SPP1	1490	0.31	0.47	YES
41	ITGA6	ITGA6	ITGA6	1492	0.31	0.48	YES
42	COL4A1	COL4A1	COL4A1	1604	0.3	0.48	YES
43	ITGA1	ITGA1	ITGA1	1661	0.29	0.49	YES
44	VEGFA	VEGFA	VEGFA	1844	0.28	0.49	YES
45	COL4A2	COL4A2	COL4A2	1905	0.27	0.49	YES
46	MYLK2	MYLK2	MYLK2	1928	0.27	0.5	YES
47	COL11A2	COL11A2	COL11A2	2011	0.26	0.5	YES
48	VEGFC	VEGFC	VEGFC	2042	0.26	0.51	YES
49	HGF	HGF	HGF	2055	0.26	0.52	YES
50	FIGF	FIGF	FIGF	2109	0.26	0.52	YES
51	ITGB3	ITGB3	ITGB3	2125	0.25	0.53	YES
52	RAC3	RAC3	RAC3	2225	0.25	0.53	YES
53	CCND2	CCND2	CCND2	2244	0.24	0.54	YES
54	LAMA5	LAMA5	LAMA5	2246	0.24	0.55	YES
55	MYL9	MYL9	MYL9	2355	0.24	0.55	YES
56	PIK3R3	PIK3R3	PIK3R3	2444	0.23	0.55	YES
57	COL11A1	COL11A1	COL11A1	2471	0.23	0.55	YES
58	ERBB2	ERBB2	ERBB2	2518	0.22	0.56	YES
59	LAMA3	LAMA3	LAMA3	2535	0.22	0.56	YES
60	AKT3	AKT3	AKT3	2541	0.22	0.57	YES
61	ITGA3	ITGA3	ITGA3	2603	0.22	0.57	YES
62	PDGFC	PDGFC	PDGFC	2723	0.21	0.57	YES
63	COL6A6	COL6A6	COL6A6	2779	0.21	0.58	YES
64	PDGFA	PDGFA	PDGFA	3048	0.19	0.57	NO
65	FLNB	FLNB	FLNB	3184	0.18	0.57	NO
66	CAV2	CAV2	CAV2	3435	0.17	0.56	NO
67	COL2A1	COL2A1	COL2A1	3484	0.17	0.56	NO
68	CHAD	CHAD	CHAD	3542	0.17	0.56	NO
69	ITGA2B	ITGA2B	ITGA2B	3552	0.16	0.57	NO
70	TLN2	TLN2	TLN2	4030	0.14	0.54	NO
71	LAMC3	LAMC3	LAMC3	4067	0.14	0.54	NO
72	TNR	TNR	TNR	4188	0.14	0.54	NO
73	BCL2	BCL2	BCL2	4205	0.13	0.55	NO
74	ITGB5	ITGB5	ITGB5	4436	0.12	0.54	NO
75	ITGAV	ITGAV	ITGAV	4504	0.12	0.54	NO
76	CAV3	CAV3	CAV3	4568	0.12	0.54	NO
77	PAK3	PAK3	PAK3	4693	0.12	0.53	NO
78	ITGA2	ITGA2	ITGA2	4709	0.11	0.53	NO
79	FLNC	FLNC	FLNC	4828	0.11	0.53	NO
80	MAPK8	MAPK8	MAPK8	5072	0.1	0.52	NO
81	COL4A4	COL4A4	COL4A4	5349	0.095	0.51	NO
82	ITGA4	ITGA4	ITGA4	5463	0.092	0.5	NO
83	PIK3CA	PIK3CA	PIK3CA	5484	0.091	0.5	NO
84	MAPK10	MAPK10	MAPK10	5507	0.09	0.51	NO
85	PAK6	PAK6	PAK6	5571	0.089	0.5	NO
86	SOS1	SOS1	SOS1	5807	0.082	0.49	NO
87	GRLF1	GRLF1	GRLF1	6120	0.075	0.48	NO
88	VWF	VWF	VWF	6126	0.075	0.48	NO
89	BRAF	BRAF	BRAF	6148	0.074	0.48	NO
90	VAV3	VAV3	VAV3	6216	0.072	0.48	NO
91	FN1	FN1	FN1	6276	0.071	0.48	NO
92	COL4A6	COL4A6	COL4A6	6417	0.068	0.47	NO
93	PIK3R1	PIK3R1	PIK3R1	6906	0.058	0.44	NO
94	BIRC3	BIRC3	BIRC3	7213	0.054	0.43	NO
95	ITGB8	ITGB8	ITGB8	7242	0.053	0.43	NO
96	PRKCB	PRKCB	PRKCB	7567	0.048	0.41	NO
97	ITGB1	ITGB1	ITGB1	7805	0.044	0.4	NO
98	XIAP	XIAP	XIAP	7969	0.042	0.39	NO
99	ROCK2	ROCK2	ROCK2	8173	0.039	0.38	NO
100	VCL	VCL	VCL	8178	0.039	0.38	NO
101	LAMB2	LAMB2	LAMB2	8211	0.039	0.38	NO
102	VEGFB	VEGFB	VEGFB	8370	0.037	0.37	NO
103	DOCK1	DOCK1	DOCK1	8499	0.035	0.37	NO
104	FYN	FYN	FYN	8927	0.029	0.34	NO
105	CRKL	CRKL	CRKL	8969	0.029	0.34	NO
106	PTEN	PTEN	PTEN	9249	0.025	0.32	NO
107	PIK3CG	PIK3CG	PIK3CG	10020	0.016	0.28	NO
108	RAPGEF1	RAPGEF1	RAPGEF1	10049	0.015	0.28	NO
109	PXN	PXN	PXN	10151	0.014	0.27	NO
110	PPP1R12A	PPP1R12A	PPP1R12A	10228	0.013	0.27	NO
111	PPP1CB	PPP1CB	PPP1CB	10391	0.011	0.26	NO
112	GSK3B	GSK3B	GSK3B	10415	0.01	0.26	NO
113	PAK4	PAK4	PAK4	10476	0.0097	0.26	NO
114	MAPK1	MAPK1	MAPK1	10485	0.0096	0.26	NO
115	TNN	TNN	TNN	10611	0.008	0.25	NO
116	ROCK1	ROCK1	ROCK1	10661	0.0072	0.25	NO
117	SHC1	SHC1	SHC1	10888	0.0046	0.23	NO
118	AKT2	AKT2	AKT2	11025	0.003	0.22	NO
119	ITGA10	ITGA10	ITGA10	11068	0.0024	0.22	NO
120	ACTN2	ACTN2	ACTN2	11083	0.0023	0.22	NO
121	RAF1	RAF1	RAF1	11386	-0.0016	0.2	NO
122	ACTN3	ACTN3	ACTN3	11410	-0.0021	0.2	NO
123	PIK3CD	PIK3CD	PIK3CD	11442	-0.0024	0.2	NO
124	THBS4	THBS4	THBS4	11480	-0.003	0.2	NO
125	PDPK1	PDPK1	PDPK1	11509	-0.0033	0.2	NO
126	ELK1	ELK1	ELK1	11607	-0.0049	0.19	NO
127	BIRC2	BIRC2	BIRC2	11620	-0.0051	0.19	NO
128	VAV1	VAV1	VAV1	11721	-0.0065	0.19	NO
129	PRKCG	PRKCG	PRKCG	11775	-0.0073	0.18	NO
130	DIAPH1	DIAPH1	DIAPH1	11940	-0.0096	0.17	NO
131	PRKCA	PRKCA	PRKCA	11977	-0.01	0.17	NO
132	TLN1	TLN1	TLN1	12051	-0.012	0.17	NO
133	ACTN1	ACTN1	ACTN1	12355	-0.016	0.15	NO
134	MYL12B	MYL12B	MYL12B	12420	-0.017	0.15	NO
135	PPP1CC	PPP1CC	PPP1CC	12499	-0.018	0.14	NO
136	LAMA2	LAMA2	LAMA2	12506	-0.018	0.14	NO
137	CTNNB1	CTNNB1	CTNNB1	12519	-0.019	0.14	NO
138	THBS1	THBS1	THBS1	12529	-0.019	0.14	NO
139	MAPK3	MAPK3	MAPK3	12587	-0.02	0.14	NO
140	SOS2	SOS2	SOS2	12601	-0.02	0.14	NO
141	PARVB	PARVB	PARVB	12741	-0.022	0.13	NO
142	PIK3R2	PIK3R2	PIK3R2	12846	-0.024	0.13	NO
143	MAPK9	MAPK9	MAPK9	12894	-0.025	0.13	NO
144	PPP1CA	PPP1CA	PPP1CA	12936	-0.026	0.12	NO
145	RAP1B	RAP1B	RAP1B	12988	-0.027	0.12	NO
146	PAK2	PAK2	PAK2	13191	-0.03	0.11	NO
147	PIP5K1C	PIP5K1C	PIP5K1C	13331	-0.032	0.1	NO
148	THBS2	THBS2	THBS2	13436	-0.034	0.099	NO
149	RAC2	RAC2	RAC2	13533	-0.036	0.095	NO
150	ACTG1	ACTG1	ACTG1	13683	-0.04	0.087	NO
151	ACTB	ACTB	ACTB	13724	-0.04	0.086	NO
152	ACTN4	ACTN4	ACTN4	13734	-0.041	0.087	NO
153	THBS3	THBS3	THBS3	13864	-0.044	0.081	NO
154	RAP1A	RAP1A	RAP1A	13867	-0.044	0.082	NO
155	ITGA5	ITGA5	ITGA5	13965	-0.046	0.078	NO
156	PAK1	PAK1	PAK1	14064	-0.048	0.073	NO
157	MYL5	MYL5	MYL5	14077	-0.048	0.074	NO
158	VTN	VTN	VTN	14146	-0.05	0.072	NO
159	CDC42	CDC42	CDC42	14232	-0.052	0.068	NO
160	RHOA	RHOA	RHOA	14261	-0.053	0.068	NO
161	BAD	BAD	BAD	14324	-0.055	0.066	NO
162	PARVG	PARVG	PARVG	14442	-0.058	0.062	NO
163	CRK	CRK	CRK	14443	-0.058	0.063	NO
164	ITGB6	ITGB6	ITGB6	14444	-0.058	0.065	NO
165	FLNA	FLNA	FLNA	14597	-0.062	0.058	NO
166	RAC1	RAC1	RAC1	14605	-0.063	0.06	NO
167	MYLK3	MYLK3	MYLK3	14663	-0.064	0.058	NO
168	VASP	VASP	VASP	14776	-0.068	0.054	NO
169	PIK3CB	PIK3CB	PIK3CB	14800	-0.069	0.055	NO
170	AKT1	AKT1	AKT1	14813	-0.069	0.056	NO
171	JUN	JUN	JUN	14856	-0.071	0.056	NO
172	PIK3R5	PIK3R5	PIK3R5	14867	-0.071	0.058	NO
173	ILK	ILK	ILK	14889	-0.072	0.059	NO
174	GRB2	GRB2	GRB2	14895	-0.072	0.06	NO
175	MAP2K1	MAP2K1	MAP2K1	14920	-0.073	0.061	NO
176	MYL12A	MYL12A	MYL12A	14977	-0.075	0.06	NO
177	COMP	COMP	COMP	15221	-0.084	0.049	NO
178	SRC	SRC	SRC	15236	-0.085	0.051	NO
179	CCND3	CCND3	CCND3	15512	-0.098	0.038	NO
180	ZYX	ZYX	ZYX	15534	-0.099	0.039	NO
181	MYLPF	MYLPF	MYLPF	15664	-0.11	0.035	NO
182	RASGRF1	RASGRF1	RASGRF1	15904	-0.12	0.025	NO
183	ITGA11	ITGA11	ITGA11	16231	-0.15	0.011	NO
184	CAPN2	CAPN2	CAPN2	16520	-0.19	-0.00031	NO
185	ITGB7	ITGB7	ITGB7	16523	-0.19	0.0055	NO
186	VAV2	VAV2	VAV2	16539	-0.19	0.011	NO
187	PDGFD	PDGFD	PDGFD	16594	-0.2	0.014	NO
188	LAMB3	LAMB3	LAMB3	17054	-0.33	-0.003	NO
189	ITGA7	ITGA7	ITGA7	17224	-0.48	0.002	NO

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

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA AT1R PATHWAY	32	genes.ES.table	0.46	1.4	0.12	0.54	0.92	0.56	0.22	0.44	0.43	0.13
BIOCARTA FCER1 PATHWAY	37	genes.ES.table	0.41	1.4	0.11	0.5	0.89	0.49	0.22	0.38	0.39	0.13
BIOCARTA FMLP PATHWAY	32	genes.ES.table	0.61	1.8	0.004	0.23	0.3	0.38	0.14	0.32	0	0.071
BIOCARTA HIVNEF PATHWAY	57	genes.ES.table	0.43	1.9	0.0078	0.17	0.082	0.46	0.21	0.36	0	0.051
BIOCARTA PYK2 PATHWAY	27	genes.ES.table	0.53	1.6	0.028	0.26	0.66	0.63	0.22	0.49	0.15	0.046
BIOCARTA RHO PATHWAY	30	genes.ES.table	0.53	1.5	0.053	0.39	0.81	0.67	0.17	0.56	0.27	0.088
BIOCARTA TOLL PATHWAY	36	genes.ES.table	0.62	1.7	0.018	0.2	0.39	0.56	0.2	0.45	0	0.045
BIOCARTA CREB PATHWAY	26	genes.ES.table	0.47	1.4	0.081	0.45	0.88	0.42	0.17	0.35	0.35	0.1
KEGG PENTOSE PHOSPHATE PATHWAY	25	genes.ES.table	0.51	1.5	0.059	0.42	0.85	0.4	0.16	0.34	0.32	0.089
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	41	genes.ES.table	0.5	1.6	0.05	0.27	0.7	0.22	0.12	0.19	0.17	0.049

genes ES table in pathway: BIOCARTA AT1R PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TNFRSF1B	TNFRSF1B	TNFRSF1B	271	0.52	0.083	YES
2	LMNA	LMNA	LMNA	772	0.3	0.11	YES
3	PRKCD	PRKCD	PRKCD	873	0.27	0.16	YES
4	TNF	TNF	TNF	924	0.26	0.2	YES
5	APAF1	APAF1	APAF1	1587	0.16	0.19	YES
6	GSN	GSN	GSN	1718	0.15	0.22	YES
7	PTK2	PTK2	PTK2	1733	0.15	0.24	YES
8	FAS	FAS	FAS	1967	0.13	0.25	YES
9	MDM2	MDM2	MDM2	2139	0.12	0.26	YES
10	NFKBIA	NFKBIA	NFKBIA	2171	0.11	0.28	YES
11	BID	BID	BID	2239	0.11	0.3	YES
12	PSEN2	PSEN2	PSEN2	2328	0.1	0.32	YES
13	BIRC3	BIRC3	BIRC3	2372	0.1	0.33	YES
14	NFKB1	NFKB1	NFKB1	2376	0.1	0.35	YES
15	PSEN1	PSEN1	PSEN1	2490	0.095	0.36	YES
16	LMNB1	LMNB1	LMNB1	2597	0.09	0.37	YES
17	MAP3K14	MAP3K14	MAP3K14	2751	0.082	0.38	YES
18	ARHGDIB	ARHGDIB	ARHGDIB	2813	0.078	0.39	YES
19	CFLAR	CFLAR	CFLAR	2902	0.074	0.4	YES
20	CHUK	CHUK	CHUK	2962	0.072	0.41	YES
21	CYCS	CYCS	CYCS	3258	0.06	0.4	YES
22	PAK2	PAK2	PAK2	3373	0.056	0.41	YES
23	FADD	FADD	FADD	3395	0.056	0.42	YES
24	BAG4	BAG4	BAG4	3492	0.053	0.42	YES
25	RB1	RB1	RB1	3549	0.051	0.43	YES
26	MAP3K1	MAP3K1	MAP3K1	3582	0.05	0.43	YES
27	ACTG1	ACTG1	ACTG1	4237	0.032	0.4	NO
28	CDK11B	CDK11B	CDK11B	4260	0.032	0.41	NO
29	CDK11A	CDK11A	CDK11A	4546	0.025	0.4	NO
30	TRADD	TRADD	TRADD	4592	0.024	0.4	NO
31	BIRC2	BIRC2	BIRC2	4778	0.019	0.39	NO
32	TNFRSF1A	TNFRSF1A	TNFRSF1A	4923	0.016	0.38	NO
33	CASP7	CASP7	CASP7	4995	0.015	0.38	NO
34	MAP3K5	MAP3K5	MAP3K5	5006	0.014	0.38	NO
35	CASP9	CASP9	CASP9	5012	0.014	0.39	NO
36	XIAP	XIAP	XIAP	5413	0.007	0.36	NO
37	TRAF1	TRAF1	TRAF1	5456	0.0062	0.36	NO
38	RELA	RELA	RELA	5607	0.0036	0.36	NO
39	RASA1	RASA1	RASA1	5702	0.0015	0.35	NO
40	CASP8	CASP8	CASP8	6638	-0.017	0.3	NO
41	RIPK1	RIPK1	RIPK1	6810	-0.02	0.29	NO
42	DAXX	DAXX	DAXX	7091	-0.024	0.28	NO
43	MAP2K7	MAP2K7	MAP2K7	7219	-0.026	0.28	NO
44	CASP2	CASP2	CASP2	7576	-0.032	0.26	NO
45	SPTAN1	SPTAN1	SPTAN1	8868	-0.056	0.2	NO
46	LMNB2	LMNB2	LMNB2	8899	-0.056	0.21	NO
47	PRKDC	PRKDC	PRKDC	8969	-0.058	0.22	NO
48	NUMA1	NUMA1	NUMA1	9508	-0.067	0.2	NO
49	PARP1	PARP1	PARP1	10343	-0.084	0.16	NO
50	DFFA	DFFA	DFFA	10846	-0.095	0.15	NO
51	TRAF2	TRAF2	TRAF2	11562	-0.11	0.13	NO
52	CRADD	CRADD	CRADD	12278	-0.14	0.12	NO
53	CASP3	CASP3	CASP3	12351	-0.14	0.14	NO
54	DFFB	DFFB	DFFB	12531	-0.14	0.15	NO
55	MAPK8	MAPK8	MAPK8	12995	-0.16	0.16	NO
56	BCL2	BCL2	BCL2	14631	-0.24	0.11	NO
57	CASP6	CASP6	CASP6	14767	-0.24	0.14	NO

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

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SLC11A1	SLC11A1	SLC11A1	25	0.86	0.042	YES
2	SORT1	SORT1	SORT1	133	0.66	0.07	YES
3	CTSH	CTSH	CTSH	192	0.6	0.097	YES
4	SGSH	SGSH	SGSH	201	0.59	0.13	YES
5	CTSL1	CTSL1	CTSL1	235	0.56	0.15	YES
6	CD68	CD68	CD68	306	0.5	0.17	YES
7	CTSL2	CTSL2	CTSL2	327	0.49	0.2	YES
8	AP1S2	AP1S2	AP1S2	463	0.41	0.21	YES
9	CTSS	CTSS	CTSS	500	0.39	0.23	YES
10	IGF2R	IGF2R	IGF2R	521	0.38	0.25	YES
11	AP1S3	AP1S3	AP1S3	556	0.37	0.26	YES
12	CTSZ	CTSZ	CTSZ	564	0.37	0.28	YES
13	GAA	GAA	GAA	707	0.32	0.29	YES
14	ARSG	ARSG	ARSG	710	0.32	0.31	YES
15	NAGA	NAGA	NAGA	714	0.32	0.32	YES
16	HEXB	HEXB	HEXB	725	0.32	0.34	YES
17	CLTCL1	CLTCL1	CLTCL1	846	0.28	0.35	YES
18	PSAP	PSAP	PSAP	870	0.28	0.36	YES
19	CTSB	CTSB	CTSB	898	0.27	0.37	YES
20	GNS	GNS	GNS	953	0.26	0.38	YES
21	ATP6V0D1	ATP6V0D1	ATP6V0D1	984	0.25	0.39	YES
22	FUCA1	FUCA1	FUCA1	1013	0.24	0.4	YES
23	TCIRG1	TCIRG1	TCIRG1	1065	0.23	0.41	YES
24	CTSD	CTSD	CTSD	1066	0.23	0.42	YES
25	NPC2	NPC2	NPC2	1111	0.23	0.43	YES
26	GM2A	GM2A	GM2A	1160	0.22	0.44	YES
27	ATP6V0A1	ATP6V0A1	ATP6V0A1	1241	0.2	0.45	YES
28	MCOLN1	MCOLN1	MCOLN1	1303	0.2	0.45	YES
29	LIPA	LIPA	LIPA	1516	0.17	0.45	YES
30	PPT1	PPT1	PPT1	1589	0.16	0.45	YES
31	LAPTM5	LAPTM5	LAPTM5	1615	0.16	0.46	YES
32	PLA2G15	PLA2G15	PLA2G15	1632	0.16	0.47	YES
33	MAN2B1	MAN2B1	MAN2B1	1731	0.15	0.47	YES
34	GBA	GBA	GBA	1817	0.14	0.47	YES
35	AP1S1	AP1S1	AP1S1	1821	0.14	0.48	YES
36	ASAH1	ASAH1	ASAH1	1840	0.14	0.48	YES
37	GUSB	GUSB	GUSB	1849	0.14	0.49	YES
38	CD63	CD63	CD63	1885	0.13	0.5	YES
39	SLC17A5	SLC17A5	SLC17A5	1906	0.13	0.5	YES
40	TPP1	TPP1	TPP1	1925	0.13	0.51	YES
41	ATP6V0C	ATP6V0C	ATP6V0C	1941	0.13	0.51	YES
42	ATP6V0B	ATP6V0B	ATP6V0B	1974	0.13	0.52	YES
43	ARSB	ARSB	ARSB	1990	0.13	0.52	YES
44	GGA2	GGA2	GGA2	1998	0.12	0.53	YES
45	CTSA	CTSA	CTSA	2028	0.12	0.53	YES
46	SMPD1	SMPD1	SMPD1	2039	0.12	0.54	YES
47	CLTB	CLTB	CLTB	2043	0.12	0.54	YES
48	NAGPA	NAGPA	NAGPA	2088	0.12	0.55	YES
49	ACP2	ACP2	ACP2	2096	0.12	0.55	YES
50	GLB1	GLB1	GLB1	2178	0.11	0.56	YES
51	NEU1	NEU1	NEU1	2210	0.11	0.56	YES
52	CTSK	CTSK	CTSK	2250	0.11	0.56	YES
53	CTSO	CTSO	CTSO	2373	0.1	0.56	NO
54	ARSA	ARSA	ARSA	2522	0.094	0.56	NO
55	GLA	GLA	GLA	2620	0.088	0.56	NO
56	SUMF1	SUMF1	SUMF1	2712	0.084	0.55	NO
57	CLTA	CLTA	CLTA	2797	0.079	0.55	NO
58	GALC	GALC	GALC	2961	0.072	0.55	NO
59	LAMP1	LAMP1	LAMP1	3078	0.067	0.54	NO
60	AGA	AGA	AGA	3100	0.066	0.55	NO
61	AP3S1	AP3S1	AP3S1	3106	0.066	0.55	NO
62	AP1M1	AP1M1	AP1M1	3150	0.065	0.55	NO
63	CLN3	CLN3	CLN3	3154	0.064	0.55	NO
64	AP3B1	AP3B1	AP3B1	3269	0.06	0.55	NO
65	M6PR	M6PR	M6PR	3324	0.058	0.55	NO
66	CTSG	CTSG	CTSG	3365	0.057	0.55	NO
67	HYAL1	HYAL1	HYAL1	3393	0.056	0.55	NO
68	ACP5	ACP5	ACP5	3465	0.054	0.55	NO
69	HEXA	HEXA	HEXA	3511	0.052	0.55	NO
70	SCARB2	SCARB2	SCARB2	3680	0.047	0.54	NO
71	GALNS	GALNS	GALNS	3691	0.047	0.54	NO
72	CLTC	CLTC	CLTC	3712	0.046	0.55	NO
73	MANBA	MANBA	MANBA	3847	0.042	0.54	NO
74	ATP6AP1	ATP6AP1	ATP6AP1	3875	0.041	0.54	NO
75	AP3S2	AP3S2	AP3S2	3974	0.039	0.54	NO
76	GNPTG	GNPTG	GNPTG	4015	0.038	0.54	NO
77	CLN5	CLN5	CLN5	4363	0.029	0.52	NO
78	AP3D1	AP3D1	AP3D1	4448	0.027	0.51	NO
79	NPC1	NPC1	NPC1	4466	0.027	0.51	NO
80	LAMP2	LAMP2	LAMP2	4651	0.022	0.5	NO
81	ATP6V1H	ATP6V1H	ATP6V1H	4743	0.02	0.5	NO
82	AP3M1	AP3M1	AP3M1	5109	0.012	0.48	NO
83	ENTPD4	ENTPD4	ENTPD4	5224	0.01	0.47	NO
84	AP1B1	AP1B1	AP1B1	5279	0.0092	0.47	NO
85	NAGLU	NAGLU	NAGLU	5294	0.009	0.47	NO
86	AP4E1	AP4E1	AP4E1	5419	0.0069	0.46	NO
87	AP1G1	AP1G1	AP1G1	5520	0.0052	0.46	NO
88	LAPTM4A	LAPTM4A	LAPTM4A	5633	0.003	0.45	NO
89	CTSC	CTSC	CTSC	5713	0.0011	0.45	NO
90	GGA3	GGA3	GGA3	5954	-0.0034	0.43	NO
91	GGA1	GGA1	GGA1	5999	-0.0044	0.43	NO
92	CTNS	CTNS	CTNS	6273	-0.01	0.42	NO
93	AP4M1	AP4M1	AP4M1	7553	-0.032	0.34	NO
94	SLC11A2	SLC11A2	SLC11A2	7624	-0.033	0.34	NO
95	ATP6V0D2	ATP6V0D2	ATP6V0D2	7680	-0.034	0.34	NO
96	AP4B1	AP4B1	AP4B1	7844	-0.037	0.33	NO
97	GNPTAB	GNPTAB	GNPTAB	8716	-0.053	0.28	NO
98	DNASE2	DNASE2	DNASE2	9217	-0.062	0.26	NO
99	IDS	IDS	IDS	9281	-0.063	0.26	NO
100	CD164	CD164	CD164	9806	-0.073	0.23	NO
101	AP3B2	AP3B2	AP3B2	10159	-0.08	0.21	NO
102	LGMN	LGMN	LGMN	10418	-0.086	0.2	NO
103	IDUA	IDUA	IDUA	10576	-0.089	0.2	NO
104	ATP6V0A2	ATP6V0A2	ATP6V0A2	11995	-0.13	0.12	NO
105	AP1M2	AP1M2	AP1M2	12523	-0.14	0.098	NO
106	MFSD8	MFSD8	MFSD8	12605	-0.15	0.1	NO
107	AP3M2	AP3M2	AP3M2	13578	-0.19	0.053	NO
108	AP4S1	AP4S1	AP4S1	13764	-0.2	0.052	NO
109	LAMP3	LAMP3	LAMP3	14480	-0.23	0.022	NO
110	NAPSA	NAPSA	NAPSA	14827	-0.25	0.015	NO
111	CTSW	CTSW	CTSW	14860	-0.25	0.025	NO
112	ABCA2	ABCA2	ABCA2	15267	-0.28	0.016	NO
113	ABCB9	ABCB9	ABCB9	15696	-0.31	0.0064	NO
114	PPT2	PPT2	PPT2	16007	-0.33	0.0053	NO
115	CTSE	CTSE	CTSE	16396	-0.38	0.0019	NO
116	CTSF	CTSF	CTSF	16921	-0.48	-0.0045	NO
117	LAPTM4B	LAPTM4B	LAPTM4B	16924	-0.48	0.02	NO

Figure S23. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA FMLP PATHWAY

Table 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	NCF1C	NCF1C	NCF1C	12	0.92	0.16	YES
2	FPR1	FPR1	FPR1	64	0.77	0.3	YES
3	NCF2	NCF2	NCF2	125	0.67	0.42	YES
4	CAMK1	CAMK1	CAMK1	275	0.52	0.5	YES
5	PAK1	PAK1	PAK1	952	0.26	0.51	YES
6	MAP2K6	MAP2K6	MAP2K6	1095	0.23	0.55	YES
7	MAP2K1	MAP2K1	MAP2K1	1186	0.21	0.58	YES
8	RAC1	RAC1	RAC1	1954	0.13	0.56	YES
9	MAP2K3	MAP2K3	MAP2K3	2138	0.12	0.57	YES
10	NFKBIA	NFKBIA	NFKBIA	2171	0.11	0.59	YES
11	CALM1	CALM1	CALM1	2196	0.11	0.6	YES
12	NFKB1	NFKB1	NFKB1	2376	0.1	0.61	YES
13	MAPK3	MAPK3	MAPK3	2766	0.081	0.6	NO
14	CALM2	CALM2	CALM2	3225	0.062	0.59	NO
15	MAP3K1	MAP3K1	MAP3K1	3582	0.05	0.58	NO
16	CALM3	CALM3	CALM3	3786	0.044	0.57	NO
17	MAPK14	MAPK14	MAPK14	3843	0.042	0.58	NO
18	MAPK1	MAPK1	MAPK1	4183	0.034	0.56	NO
19	GNB1	GNB1	GNB1	4273	0.031	0.56	NO
20	RAF1	RAF1	RAF1	4339	0.03	0.57	NO
21	PPP3CB	PPP3CB	PPP3CB	5139	0.012	0.52	NO
22	MAP2K2	MAP2K2	MAP2K2	5267	0.0094	0.52	NO
23	RELA	RELA	RELA	5607	0.0036	0.5	NO
24	PPP3CA	PPP3CA	PPP3CA	6389	-0.012	0.45	NO
25	HRAS	HRAS	HRAS	7113	-0.025	0.42	NO
26	NFATC3	NFATC3	NFATC3	7427	-0.03	0.4	NO
27	NFATC1	NFATC1	NFATC1	7545	-0.032	0.4	NO
28	ELK1	ELK1	ELK1	7603	-0.033	0.41	NO
29	PPP3CC	PPP3CC	PPP3CC	10083	-0.078	0.28	NO
30	PLCB1	PLCB1	PLCB1	12967	-0.16	0.14	NO
31	NFATC4	NFATC4	NFATC4	14834	-0.25	0.074	NO
32	NFATC2	NFATC2	NFATC2	16343	-0.37	0.053	NO

Figure S25. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FMLP PATHWAY.

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NCF1	NCF1	NCF1	19	0.88	0.059	YES
2	FCGR2C	FCGR2C	FCGR2C	120	0.68	0.1	YES
3	PLD2	PLD2	PLD2	144	0.65	0.14	YES
4	FCGR1A	FCGR1A	FCGR1A	223	0.56	0.18	YES
5	FCGR2A	FCGR2A	FCGR2A	233	0.56	0.22	YES
6	FCGR2B	FCGR2B	FCGR2B	237	0.55	0.25	YES
7	HCK	HCK	HCK	305	0.5	0.28	YES
8	FCGR3A	FCGR3A	FCGR3A	379	0.46	0.31	YES
9	VAV2	VAV2	VAV2	555	0.37	0.33	YES
10	MARCKS	MARCKS	MARCKS	656	0.34	0.34	YES
11	PRKCA	PRKCA	PRKCA	702	0.32	0.36	YES
12	PLA2G4A	PLA2G4A	PLA2G4A	849	0.28	0.37	YES
13	PRKCD	PRKCD	PRKCD	873	0.27	0.39	YES
14	PAK1	PAK1	PAK1	952	0.26	0.4	YES
15	ARPC1B	ARPC1B	ARPC1B	1001	0.24	0.42	YES
16	PIK3R5	PIK3R5	PIK3R5	1109	0.23	0.43	YES
17	MAP2K1	MAP2K1	MAP2K1	1186	0.21	0.44	YES
18	VASP	VASP	VASP	1270	0.2	0.45	YES
19	LYN	LYN	LYN	1377	0.19	0.45	YES
20	ARPC5	ARPC5	ARPC5	1467	0.17	0.46	YES
21	ASAP1	ASAP1	ASAP1	1581	0.16	0.46	YES
22	SYK	SYK	SYK	1660	0.16	0.47	YES
23	ARPC4	ARPC4	ARPC4	1692	0.15	0.48	YES
24	GSN	GSN	GSN	1718	0.15	0.49	YES
25	WAS	WAS	WAS	1864	0.14	0.49	YES
26	ARPC3	ARPC3	ARPC3	1867	0.14	0.5	YES
27	RAC1	RAC1	RAC1	1954	0.13	0.5	YES
28	LIMK1	LIMK1	LIMK1	1962	0.13	0.51	YES
29	PTPRC	PTPRC	PTPRC	2137	0.12	0.51	YES
30	ARPC2	ARPC2	ARPC2	2319	0.1	0.5	YES
31	ARF6	ARF6	ARF6	2343	0.1	0.51	YES
32	CRK	CRK	CRK	2435	0.099	0.51	YES
33	AMPH	AMPH	AMPH	2485	0.096	0.52	YES
34	PRKCB	PRKCB	PRKCB	2532	0.093	0.52	YES
35	CFL1	CFL1	CFL1	2556	0.092	0.52	YES
36	CDC42	CDC42	CDC42	2558	0.092	0.53	YES
37	PIK3CD	PIK3CD	PIK3CD	2579	0.091	0.54	YES
38	AKT3	AKT3	AKT3	2704	0.084	0.54	YES
39	PIK3CG	PIK3CG	PIK3CG	2707	0.084	0.54	YES
40	MAPK3	MAPK3	MAPK3	2766	0.081	0.54	YES
41	ARPC1A	ARPC1A	ARPC1A	2871	0.076	0.54	NO
42	DOCK2	DOCK2	DOCK2	3080	0.067	0.53	NO
43	SPHK1	SPHK1	SPHK1	3298	0.059	0.53	NO
44	RAC2	RAC2	RAC2	3318	0.058	0.53	NO
45	VAV1	VAV1	VAV1	3459	0.054	0.52	NO
46	PIP5K1C	PIP5K1C	PIP5K1C	3722	0.046	0.51	NO
47	AKT1	AKT1	AKT1	3922	0.04	0.5	NO
48	MAPK1	MAPK1	MAPK1	4183	0.034	0.49	NO
49	RAF1	RAF1	RAF1	4339	0.03	0.48	NO
50	WASF2	WASF2	WASF2	4556	0.024	0.47	NO
51	DNM2	DNM2	DNM2	4876	0.018	0.46	NO
52	PRKCE	PRKCE	PRKCE	5410	0.0071	0.42	NO
53	ARPC5L	ARPC5L	ARPC5L	5436	0.0065	0.42	NO
54	GAB2	GAB2	GAB2	5754	0.00043	0.4	NO
55	INPP5D	INPP5D	INPP5D	5852	-0.0017	0.4	NO
56	PIK3CB	PIK3CB	PIK3CB	5887	-0.0022	0.4	NO
57	WASL	WASL	WASL	5941	-0.0032	0.4	NO
58	SPHK2	SPHK2	SPHK2	6048	-0.0053	0.39	NO
59	PLCG2	PLCG2	PLCG2	6099	-0.0064	0.39	NO
60	PIP5K1A	PIP5K1A	PIP5K1A	6282	-0.01	0.38	NO
61	LIMK2	LIMK2	LIMK2	6408	-0.013	0.37	NO
62	DNM1L	DNM1L	DNM1L	6933	-0.022	0.34	NO
63	CRKL	CRKL	CRKL	7124	-0.025	0.33	NO
64	MYO10	MYO10	MYO10	7343	-0.028	0.32	NO
65	RPS6KB1	RPS6KB1	RPS6KB1	7569	-0.032	0.31	NO
66	PIK3R2	PIK3R2	PIK3R2	8013	-0.04	0.29	NO
67	PLD1	PLD1	PLD1	8112	-0.042	0.28	NO
68	PIK3CA	PIK3CA	PIK3CA	8178	-0.043	0.28	NO
69	PPAP2B	PPAP2B	PPAP2B	8253	-0.045	0.28	NO
70	AKT2	AKT2	AKT2	9173	-0.061	0.23	NO
71	PIKFYVE	PIKFYVE	PIKFYVE	9187	-0.061	0.24	NO
72	VAV3	VAV3	VAV3	9293	-0.063	0.23	NO
73	ASAP3	ASAP3	ASAP3	9474	-0.066	0.23	NO
74	PIK3R1	PIK3R1	PIK3R1	9638	-0.069	0.22	NO
75	CFL2	CFL2	CFL2	9665	-0.07	0.23	NO
76	LAT	LAT	LAT	10146	-0.08	0.2	NO
77	PRKCG	PRKCG	PRKCG	10391	-0.085	0.2	NO
78	PIP4K2B	PIP4K2B	PIP4K2B	10398	-0.085	0.2	NO
79	WASF3	WASF3	WASF3	10533	-0.088	0.2	NO
80	ASAP2	ASAP2	ASAP2	10600	-0.09	0.2	NO
81	PPAP2A	PPAP2A	PPAP2A	11822	-0.12	0.14	NO
82	PLCG1	PLCG1	PLCG1	11906	-0.12	0.14	NO
83	SCIN	SCIN	SCIN	12989	-0.16	0.091	NO
84	PIK3R3	PIK3R3	PIK3R3	13183	-0.17	0.092	NO
85	PPAP2C	PPAP2C	PPAP2C	13276	-0.18	0.098	NO
86	PIP5K1B	PIP5K1B	PIP5K1B	13607	-0.19	0.092	NO
87	MARCKSL1	MARCKSL1	MARCKSL1	13953	-0.2	0.086	NO
88	PLA2G6	PLA2G6	PLA2G6	15784	-0.31	0.00095	NO
89	DNM3	DNM3	DNM3	16162	-0.35	0.0029	NO
90	DNM1	DNM1	DNM1	16373	-0.37	0.016	NO
91	WASF1	WASF1	WASF1	17042	-0.51	0.013	NO

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

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CD14	CD14	CD14	33	0.84	0.13	YES
2	TLR7	TLR7	TLR7	67	0.76	0.26	YES
3	LY96	LY96	LY96	118	0.68	0.36	YES
4	TLR4	TLR4	TLR4	287	0.52	0.44	YES
5	TLR6	TLR6	TLR6	588	0.36	0.48	YES
6	TLR2	TLR2	TLR2	657	0.34	0.53	YES
7	MAP2K6	MAP2K6	MAP2K6	1095	0.23	0.54	YES
8	MYD88	MYD88	MYD88	1311	0.19	0.56	YES
9	FOS	FOS	FOS	1707	0.15	0.56	YES
10	TOLLIP	TOLLIP	TOLLIP	2020	0.12	0.56	YES
11	MAP2K3	MAP2K3	MAP2K3	2138	0.12	0.57	YES
12	TIRAP	TIRAP	TIRAP	2167	0.12	0.59	YES
13	NFKBIA	NFKBIA	NFKBIA	2171	0.11	0.61	YES
14	NFKB1	NFKB1	NFKB1	2376	0.1	0.62	YES
15	MAP3K14	MAP3K14	MAP3K14	2751	0.082	0.61	YES
16	IKBKG	IKBKG	IKBKG	2812	0.078	0.62	YES
17	CHUK	CHUK	CHUK	2962	0.072	0.62	YES
18	TLR10	TLR10	TLR10	3199	0.063	0.62	YES
19	JUN	JUN	JUN	3416	0.055	0.61	YES
20	IRAK1	IRAK1	IRAK1	3431	0.055	0.62	YES
21	MAP3K1	MAP3K1	MAP3K1	3582	0.05	0.62	NO
22	MAPK14	MAPK14	MAPK14	3843	0.042	0.61	NO
23	PGLYRP1	PGLYRP1	PGLYRP1	4898	0.017	0.55	NO
24	MAP2K4	MAP2K4	MAP2K4	5179	0.011	0.54	NO
25	RELA	RELA	RELA	5607	0.0036	0.51	NO
26	ECSIT	ECSIT	ECSIT	6619	-0.017	0.46	NO
27	TAB2	TAB2	TAB2	7212	-0.026	0.43	NO
28	ELK1	ELK1	ELK1	7603	-0.033	0.41	NO
29	MAP3K7	MAP3K7	MAP3K7	7614	-0.033	0.42	NO
30	IKBKB	IKBKB	IKBKB	7706	-0.035	0.42	NO
31	TRAF6	TRAF6	TRAF6	8348	-0.046	0.39	NO
32	TAB1	TAB1	TAB1	8462	-0.048	0.39	NO
33	EIF2AK2	EIF2AK2	EIF2AK2	11025	-0.1	0.25	NO
34	TLR9	TLR9	TLR9	11982	-0.13	0.22	NO
35	MAPK8	MAPK8	MAPK8	12995	-0.16	0.19	NO
36	TLR3	TLR3	TLR3	16379	-0.37	0.051	NO

Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PYK2 PATHWAY.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RHO PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NCF1	NCF1	NCF1	19	0.88	0.056	YES
2	FCGR2C	FCGR2C	FCGR2C	120	0.68	0.094	YES
3	NCF2	NCF2	NCF2	125	0.67	0.14	YES
4	FCGR1A	FCGR1A	FCGR1A	223	0.56	0.17	YES
5	FCGR2A	FCGR2A	FCGR2A	233	0.56	0.2	YES
6	CR1	CR1	CR1	243	0.55	0.24	YES
7	C3	C3	C3	246	0.54	0.27	YES
8	ITGAM	ITGAM	ITGAM	276	0.52	0.3	YES
9	TLR4	TLR4	TLR4	287	0.52	0.34	YES
10	FCGR3A	FCGR3A	FCGR3A	379	0.46	0.36	YES
11	HLA-DQB1	HLA-DQB1	HLA-DQB1	471	0.41	0.38	YES
12	HLA-DRB5	HLA-DRB5	HLA-DRB5	561	0.37	0.4	YES
13	HLA-DRB1	HLA-DRB1	HLA-DRB1	582	0.36	0.42	YES
14	IL10	IL10	IL10	596	0.36	0.45	YES
15	ITGB2	ITGB2	ITGB2	609	0.35	0.47	YES
16	HLA-DMB	HLA-DMB	HLA-DMB	626	0.35	0.49	YES
17	TLR2	TLR2	TLR2	657	0.34	0.51	YES
18	HLA-DQA1	HLA-DQA1	HLA-DQA1	815	0.29	0.52	YES
19	IFNGR1	IFNGR1	IFNGR1	816	0.29	0.54	YES
20	IFNGR2	IFNGR2	IFNGR2	818	0.29	0.56	YES
21	HLA-DRA	HLA-DRA	HLA-DRA	910	0.27	0.57	YES
22	HLA-DPA1	HLA-DPA1	HLA-DPA1	913	0.26	0.59	YES
23	TNF	TNF	TNF	924	0.26	0.6	YES
24	HLA-DPB1	HLA-DPB1	HLA-DPB1	1070	0.23	0.61	YES
25	FCGR3B	FCGR3B	FCGR3B	1121	0.23	0.62	YES
26	MYD88	MYD88	MYD88	1311	0.19	0.62	YES
27	JAK2	JAK2	JAK2	1432	0.18	0.63	YES
28	HLA-DMA	HLA-DMA	HLA-DMA	1464	0.17	0.64	YES
29	PTPN6	PTPN6	PTPN6	1557	0.16	0.64	YES
30	FOS	FOS	FOS	1707	0.15	0.64	YES
31	HLA-DQA2	HLA-DQA2	HLA-DQA2	1787	0.14	0.65	YES
32	CYBA	CYBA	CYBA	2059	0.12	0.64	YES
33	NFKBIA	NFKBIA	NFKBIA	2171	0.11	0.64	YES
34	TGFB1	TGFB1	TGFB1	2255	0.11	0.64	YES
35	MAPK13	MAPK13	MAPK13	2272	0.11	0.65	YES
36	NFKB1	NFKB1	NFKB1	2376	0.1	0.65	YES
37	PRKCB	PRKCB	PRKCB	2532	0.093	0.65	NO
38	MAPK3	MAPK3	MAPK3	2766	0.081	0.64	NO
39	NCF4	NCF4	NCF4	3155	0.064	0.62	NO
40	IL1A	IL1A	IL1A	3389	0.056	0.61	NO
41	JUN	JUN	JUN	3416	0.055	0.61	NO
42	IRAK1	IRAK1	IRAK1	3431	0.055	0.61	NO
43	IRAK4	IRAK4	IRAK4	3481	0.053	0.61	NO
44	MAPK14	MAPK14	MAPK14	3843	0.042	0.6	NO
45	NFKBIB	NFKBIB	NFKBIB	3849	0.042	0.6	NO
46	MAPK1	MAPK1	MAPK1	4183	0.034	0.58	NO
47	ITGB1	ITGB1	ITGB1	5035	0.014	0.53	NO
48	HLA-DOA	HLA-DOA	HLA-DOA	5305	0.0088	0.52	NO
49	RELA	RELA	RELA	5607	0.0036	0.5	NO
50	STAT1	STAT1	STAT1	5608	0.0036	0.5	NO
51	JAK1	JAK1	JAK1	6499	-0.014	0.45	NO
52	IFNG	IFNG	IFNG	6880	-0.021	0.43	NO
53	TAB2	TAB2	TAB2	7212	-0.026	0.41	NO
54	ELK1	ELK1	ELK1	7603	-0.033	0.39	NO
55	MAP3K7	MAP3K7	MAP3K7	7614	-0.033	0.39	NO
56	HLA-DOB	HLA-DOB	HLA-DOB	7779	-0.036	0.38	NO
57	TRAF6	TRAF6	TRAF6	8348	-0.046	0.36	NO
58	TAB1	TAB1	TAB1	8462	-0.048	0.35	NO
59	ITGA4	ITGA4	ITGA4	10381	-0.085	0.25	NO
60	IL12B	IL12B	IL12B	10804	-0.094	0.23	NO
61	IL1B	IL1B	IL1B	12833	-0.16	0.12	NO
62	NOS2	NOS2	NOS2	13715	-0.19	0.08	NO
63	MARCKSL1	MARCKSL1	MARCKSL1	13953	-0.2	0.08	NO
64	TGFB3	TGFB3	TGFB3	15081	-0.26	0.031	NO
65	MAPK12	MAPK12	MAPK12	15139	-0.27	0.045	NO
66	IL12A	IL12A	IL12A	15420	-0.29	0.047	NO
67	TGFB2	TGFB2	TGFB2	16434	-0.38	0.013	NO
68	MAPK11	MAPK11	MAPK11	17106	-0.54	0.0089	NO

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

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

genes ES table in pathway: BIOCARTA TOLL 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	PSME2	PSME2	PSME2	2433	0.099	-0.078	YES
2	PSMB3	PSMB3	PSMB3	2465	0.097	-0.018	YES
3	PSMB9	PSMB9	PSMB9	2840	0.077	0.0094	YES
4	POMP	POMP	POMP	3094	0.066	0.037	YES
5	PSMA7	PSMA7	PSMA7	3171	0.064	0.073	YES
6	PSMC4	PSMC4	PSMC4	3198	0.063	0.11	YES
7	PSMB8	PSMB8	PSMB8	3207	0.062	0.15	YES
8	PSMD4	PSMD4	PSMD4	3239	0.061	0.19	YES
9	PSME3	PSME3	PSME3	3383	0.056	0.22	YES
10	PSMB6	PSMB6	PSMB6	3620	0.049	0.23	YES
11	SHFM1	SHFM1	SHFM1	3647	0.048	0.26	YES
12	PSMC2	PSMC2	PSMC2	3650	0.048	0.29	YES
13	PSMA4	PSMA4	PSMA4	3679	0.047	0.32	YES
14	PSMD12	PSMD12	PSMD12	3780	0.044	0.34	YES
15	PSMD7	PSMD7	PSMD7	3831	0.042	0.37	YES
16	PSMD1	PSMD1	PSMD1	3963	0.039	0.39	YES
17	PSMA5	PSMA5	PSMA5	4087	0.036	0.4	YES
18	PSMD8	PSMD8	PSMD8	4129	0.035	0.42	YES
19	PSMC1	PSMC1	PSMC1	4193	0.033	0.44	YES
20	PSMD13	PSMD13	PSMD13	4199	0.033	0.46	YES
21	PSMD2	PSMD2	PSMD2	4200	0.033	0.48	YES
22	PSMA2	PSMA2	PSMA2	4306	0.03	0.49	YES
23	PSMB1	PSMB1	PSMB1	4458	0.027	0.5	YES
24	PSME1	PSME1	PSME1	4473	0.026	0.52	YES
25	PSMD6	PSMD6	PSMD6	4479	0.026	0.54	YES
26	PSMC3	PSMC3	PSMC3	4506	0.026	0.55	YES
27	PSMA6	PSMA6	PSMA6	5287	0.0091	0.51	NO
28	PSMA3	PSMA3	PSMA3	5355	0.0079	0.51	NO
29	PSMA1	PSMA1	PSMA1	5365	0.0078	0.52	NO
30	PSMB4	PSMB4	PSMB4	5443	0.0064	0.52	NO
31	PSMF1	PSMF1	PSMF1	5466	0.0061	0.52	NO
32	PSMD11	PSMD11	PSMD11	5486	0.0057	0.52	NO
33	PSMC5	PSMC5	PSMC5	5487	0.0056	0.52	NO
34	PSMD3	PSMD3	PSMD3	5728	0.00085	0.51	NO
35	PSMB5	PSMB5	PSMB5	6056	-0.0055	0.5	NO
36	PSMD14	PSMD14	PSMD14	6447	-0.013	0.48	NO
37	PSMB7	PSMB7	PSMB7	6705	-0.018	0.48	NO
38	IFNG	IFNG	IFNG	6880	-0.021	0.48	NO
39	PSMC6	PSMC6	PSMC6	6894	-0.021	0.49	NO
40	PSMB2	PSMB2	PSMB2	7399	-0.029	0.48	NO
41	PSME4	PSME4	PSME4	8847	-0.055	0.44	NO
42	PSMA8	PSMA8	PSMA8	10312	-0.083	0.4	NO

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

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TOLL PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CREB PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MEFV	MEFV	MEFV	14	0.9	0.1	YES
2	NLRC4	NLRC4	NLRC4	73	0.75	0.18	YES
3	NOD2	NOD2	NOD2	159	0.63	0.25	YES
4	CASP5	CASP5	CASP5	250	0.54	0.3	YES
5	NLRP3	NLRP3	NLRP3	565	0.37	0.33	YES
6	CASP1	CASP1	CASP1	585	0.36	0.37	YES
7	NAIP	NAIP	NAIP	619	0.35	0.4	YES
8	CARD9	CARD9	CARD9	715	0.32	0.43	YES
9	NLRP1	NLRP1	NLRP1	802	0.3	0.46	YES
10	PSTPIP1	PSTPIP1	PSTPIP1	879	0.27	0.49	YES
11	TNF	TNF	TNF	924	0.26	0.52	YES
12	PYCARD	PYCARD	PYCARD	1103	0.23	0.53	YES
13	CCL5	CCL5	CCL5	1545	0.17	0.52	YES
14	TRIP6	TRIP6	TRIP6	1833	0.14	0.52	YES
15	CXCL1	CXCL1	CXCL1	2103	0.12	0.52	YES
16	NFKBIA	NFKBIA	NFKBIA	2171	0.11	0.53	YES
17	MAPK13	MAPK13	MAPK13	2272	0.11	0.54	YES
18	BIRC3	BIRC3	BIRC3	2372	0.1	0.54	YES
19	NFKB1	NFKB1	NFKB1	2376	0.1	0.55	YES
20	TNFAIP3	TNFAIP3	TNFAIP3	2658	0.086	0.55	YES
21	CARD6	CARD6	CARD6	2746	0.082	0.55	YES
22	MAPK3	MAPK3	MAPK3	2766	0.081	0.56	YES
23	IKBKG	IKBKG	IKBKG	2812	0.078	0.56	YES
24	CHUK	CHUK	CHUK	2962	0.072	0.56	NO
25	MAPK14	MAPK14	MAPK14	3843	0.042	0.52	NO
26	NFKBIB	NFKBIB	NFKBIB	3849	0.042	0.52	NO
27	RIPK2	RIPK2	RIPK2	3939	0.04	0.52	NO
28	MAPK1	MAPK1	MAPK1	4183	0.034	0.51	NO
29	ERBB2IP	ERBB2IP	ERBB2IP	4269	0.031	0.51	NO
30	IL18	IL18	IL18	4492	0.026	0.5	NO
31	IL8	IL8	IL8	4669	0.022	0.49	NO
32	BIRC2	BIRC2	BIRC2	4778	0.019	0.49	NO
33	MAPK9	MAPK9	MAPK9	4943	0.016	0.48	NO
34	HSP90B1	HSP90B1	HSP90B1	5188	0.011	0.47	NO
35	XIAP	XIAP	XIAP	5413	0.007	0.46	NO
36	RELA	RELA	RELA	5607	0.0036	0.44	NO
37	SUGT1	SUGT1	SUGT1	5756	0.00038	0.44	NO
38	CASP8	CASP8	CASP8	6638	-0.017	0.39	NO
39	CCL2	CCL2	CCL2	6889	-0.021	0.37	NO
40	IL6	IL6	IL6	7039	-0.024	0.37	NO
41	CARD8	CARD8	CARD8	7128	-0.025	0.37	NO
42	HSP90AA1	HSP90AA1	HSP90AA1	7204	-0.026	0.36	NO
43	TAB2	TAB2	TAB2	7212	-0.026	0.37	NO
44	MAP3K7	MAP3K7	MAP3K7	7614	-0.033	0.35	NO
45	MAPK10	MAPK10	MAPK10	7686	-0.034	0.35	NO
46	IKBKB	IKBKB	IKBKB	7706	-0.035	0.35	NO
47	TRAF6	TRAF6	TRAF6	8348	-0.046	0.32	NO
48	TAB1	TAB1	TAB1	8462	-0.048	0.32	NO
49	NOD1	NOD1	NOD1	8784	-0.054	0.3	NO
50	TAB3	TAB3	TAB3	8994	-0.058	0.3	NO
51	CCL13	CCL13	CCL13	11210	-0.1	0.18	NO
52	CCL8	CCL8	CCL8	12820	-0.16	0.1	NO
53	IL1B	IL1B	IL1B	12833	-0.16	0.12	NO
54	MAPK8	MAPK8	MAPK8	12995	-0.16	0.13	NO
55	CXCL2	CXCL2	CXCL2	14448	-0.23	0.072	NO
56	MAPK12	MAPK12	MAPK12	15139	-0.27	0.062	NO
57	MAPK11	MAPK11	MAPK11	17106	-0.54	0.0089	NO

Figure S35. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CREB PATHWAY.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CREB 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 PHOSPHATE PATHWAY

Table S19. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TNFSF10	TNFSF10	TNFSF10	374	0.46	0.035	YES
2	CAPN2	CAPN2	CAPN2	618	0.35	0.064	YES
3	PRKAR2B	PRKAR2B	PRKAR2B	805	0.3	0.089	YES
4	TNF	TNF	TNF	924	0.26	0.12	YES
5	PRKACA	PRKACA	PRKACA	1096	0.23	0.13	YES
6	PIK3R5	PIK3R5	PIK3R5	1109	0.23	0.16	YES
7	MYD88	MYD88	MYD88	1311	0.19	0.17	YES
8	TNFRSF10C	TNFRSF10C	TNFRSF10C	1531	0.17	0.18	YES
9	CHP	CHP	CHP	1553	0.17	0.2	YES
10	TNFRSF10B	TNFRSF10B	TNFRSF10B	1558	0.16	0.22	YES
11	APAF1	APAF1	APAF1	1587	0.16	0.24	YES
12	FAS	FAS	FAS	1967	0.13	0.23	YES
13	PRKAR2A	PRKAR2A	PRKAR2A	2076	0.12	0.24	YES
14	IRAK3	IRAK3	IRAK3	2080	0.12	0.26	YES
15	NFKBIA	NFKBIA	NFKBIA	2171	0.11	0.26	YES
16	BID	BID	BID	2239	0.11	0.27	YES
17	BIRC3	BIRC3	BIRC3	2372	0.1	0.28	YES
18	NFKB1	NFKB1	NFKB1	2376	0.1	0.29	YES
19	PIK3CD	PIK3CD	PIK3CD	2579	0.091	0.29	YES
20	ENDOG	ENDOG	ENDOG	2619	0.088	0.3	YES
21	AKT3	AKT3	AKT3	2704	0.084	0.3	YES
22	PIK3CG	PIK3CG	PIK3CG	2707	0.084	0.32	YES
23	MAP3K14	MAP3K14	MAP3K14	2751	0.082	0.32	YES
24	IKBKG	IKBKG	IKBKG	2812	0.078	0.33	YES
25	CFLAR	CFLAR	CFLAR	2902	0.074	0.33	YES
26	PRKAR1A	PRKAR1A	PRKAR1A	2928	0.073	0.34	YES
27	BAX	BAX	BAX	2954	0.072	0.35	YES
28	CHUK	CHUK	CHUK	2962	0.072	0.36	YES
29	PPP3R2	PPP3R2	PPP3R2	3073	0.067	0.36	YES
30	CAPN1	CAPN1	CAPN1	3159	0.064	0.36	YES
31	CYCS	CYCS	CYCS	3258	0.06	0.36	YES
32	TNFRSF10D	TNFRSF10D	TNFRSF10D	3374	0.056	0.36	YES
33	IL1A	IL1A	IL1A	3389	0.056	0.37	YES
34	FADD	FADD	FADD	3395	0.056	0.38	YES
35	IRAK1	IRAK1	IRAK1	3431	0.055	0.38	YES
36	IRAK4	IRAK4	IRAK4	3481	0.053	0.38	YES
37	TNFRSF10A	TNFRSF10A	TNFRSF10A	3584	0.05	0.38	YES
38	AKT1	AKT1	AKT1	3922	0.04	0.37	NO
39	AIFM1	AIFM1	AIFM1	3959	0.039	0.37	NO
40	TRADD	TRADD	TRADD	4592	0.024	0.34	NO
41	PRKX	PRKX	PRKX	4653	0.022	0.34	NO
42	ATM	ATM	ATM	4678	0.022	0.34	NO
43	PPP3R1	PPP3R1	PPP3R1	4691	0.021	0.34	NO
44	BIRC2	BIRC2	BIRC2	4778	0.019	0.34	NO
45	CASP10	CASP10	CASP10	4873	0.018	0.34	NO
46	PRKACG	PRKACG	PRKACG	4909	0.017	0.34	NO
47	TNFRSF1A	TNFRSF1A	TNFRSF1A	4923	0.016	0.34	NO
48	CASP7	CASP7	CASP7	4995	0.015	0.33	NO
49	CASP9	CASP9	CASP9	5012	0.014	0.33	NO
50	CSF2RB	CSF2RB	CSF2RB	5115	0.012	0.33	NO
51	PPP3CB	PPP3CB	PPP3CB	5139	0.012	0.33	NO
52	XIAP	XIAP	XIAP	5413	0.007	0.32	NO
53	RELA	RELA	RELA	5607	0.0036	0.3	NO
54	PIK3CB	PIK3CB	PIK3CB	5887	-0.0022	0.29	NO
55	IL1RAP	IL1RAP	IL1RAP	6037	-0.0051	0.28	NO
56	PPP3CA	PPP3CA	PPP3CA	6389	-0.012	0.26	NO
57	CASP8	CASP8	CASP8	6638	-0.017	0.25	NO
58	TP53	TP53	TP53	6748	-0.019	0.24	NO
59	RIPK1	RIPK1	RIPK1	6810	-0.02	0.24	NO
60	BAD	BAD	BAD	7064	-0.024	0.23	NO
61	ENDOD1	ENDOD1	ENDOD1	7180	-0.025	0.23	NO
62	IKBKB	IKBKB	IKBKB	7706	-0.035	0.2	NO
63	PIK3R2	PIK3R2	PIK3R2	8013	-0.04	0.19	NO
64	IL3RA	IL3RA	IL3RA	8097	-0.042	0.19	NO
65	PIK3CA	PIK3CA	PIK3CA	8178	-0.043	0.19	NO
66	EXOG	EXOG	EXOG	8849	-0.055	0.16	NO
67	AKT2	AKT2	AKT2	9173	-0.061	0.15	NO
68	PIK3R1	PIK3R1	PIK3R1	9638	-0.069	0.13	NO
69	PPP3CC	PPP3CC	PPP3CC	10083	-0.078	0.11	NO
70	DFFA	DFFA	DFFA	10846	-0.095	0.08	NO
71	IRAK2	IRAK2	IRAK2	11006	-0.099	0.083	NO
72	IL1R1	IL1R1	IL1R1	11416	-0.11	0.072	NO
73	TRAF2	TRAF2	TRAF2	11562	-0.11	0.078	NO
74	CASP3	CASP3	CASP3	12351	-0.14	0.049	NO
75	PRKACB	PRKACB	PRKACB	12527	-0.14	0.057	NO
76	DFFB	DFFB	DFFB	12531	-0.14	0.074	NO
77	IL1B	IL1B	IL1B	12833	-0.16	0.076	NO
78	PIK3R3	PIK3R3	PIK3R3	13183	-0.17	0.077	NO
79	BCL2L1	BCL2L1	BCL2L1	13727	-0.19	0.069	NO
80	BCL2	BCL2	BCL2	14631	-0.24	0.045	NO
81	CASP6	CASP6	CASP6	14767	-0.24	0.067	NO
82	NTRK1	NTRK1	NTRK1	14922	-0.25	0.09	NO
83	PRKAR1B	PRKAR1B	PRKAR1B	16392	-0.38	0.05	NO

Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY.

Figure S38. 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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	PRKCA	PRKCA	PRKCA	702	0.32	0.078	YES
2	PAK1	PAK1	PAK1	952	0.26	0.16	YES
3	SRC	SRC	SRC	999	0.24	0.24	YES
4	MAP2K1	MAP2K1	MAP2K1	1186	0.21	0.31	YES
5	GRB2	GRB2	GRB2	1945	0.13	0.31	YES
6	RAC1	RAC1	RAC1	1954	0.13	0.36	YES
7	MAP2K3	MAP2K3	MAP2K3	2138	0.12	0.39	YES
8	CALM1	CALM1	CALM1	2196	0.11	0.43	YES
9	PRKCB	PRKCB	PRKCB	2532	0.093	0.45	YES
10	MAPK3	MAPK3	MAPK3	2766	0.081	0.46	YES
11	PTK2B	PTK2B	PTK2B	3040	0.069	0.47	YES
12	CALM2	CALM2	CALM2	3225	0.062	0.48	YES
13	JUN	JUN	JUN	3416	0.055	0.49	YES
14	MAP3K1	MAP3K1	MAP3K1	3582	0.05	0.5	YES
15	SHC1	SHC1	SHC1	3707	0.046	0.51	YES
16	CALM3	CALM3	CALM3	3786	0.044	0.52	YES
17	MAPK14	MAPK14	MAPK14	3843	0.042	0.53	YES
18	MAPK1	MAPK1	MAPK1	4183	0.034	0.53	NO
19	RAF1	RAF1	RAF1	4339	0.03	0.53	NO
20	MAP2K4	MAP2K4	MAP2K4	5179	0.011	0.48	NO
21	MAP2K2	MAP2K2	MAP2K2	5267	0.0094	0.48	NO
22	GNAQ	GNAQ	GNAQ	6554	-0.016	0.41	NO
23	CRKL	CRKL	CRKL	7124	-0.025	0.39	NO
24	SOS1	SOS1	SOS1	11058	-0.1	0.2	NO
25	PLCG1	PLCG1	PLCG1	11906	-0.12	0.19	NO
26	BCAR1	BCAR1	BCAR1	12850	-0.16	0.2	NO
27	MAPK8	MAPK8	MAPK8	12995	-0.16	0.25	NO

Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR 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 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 CITRATE CYCLE TCA CYCLE	28	genes.ES.table	0.26	0.81	0.66	1	1	0.036	0.019	0.035	1	0.69
KEGG OXIDATIVE PHOSPHORYLATION	111	genes.ES.table	0.17	0.6	0.82	0.98	1	0.4	0.41	0.24	1	0.46
KEGG PYRIMIDINE METABOLISM	95	genes.ES.table	0.2	0.88	0.6	1	1	0.32	0.26	0.23	1	0.59
KEGG GLYCINE SERINE AND THREONINE METABOLISM	28	genes.ES.table	0.4	0.95	0.54	1	1	0.43	0.14	0.37	1	0.82
KEGG CYSTEINE AND METHIONINE METABOLISM	32	genes.ES.table	0.27	0.84	0.7	1	1	0.22	0.14	0.19	1	0.69
KEGG SELENOAMINO ACID METABOLISM	25	genes.ES.table	0.35	1.1	0.42	1	1	0.48	0.25	0.36	1	0.73
KEGG BUTANOATE METABOLISM	27	genes.ES.table	0.33	0.95	0.54	1	1	0.3	0.15	0.25	1	0.71
KEGG AMINOACYL TRNA BIOSYNTHESIS	40	genes.ES.table	0.41	1.4	0.17	0.97	0.93	0.5	0.35	0.33	0.75	0.36
KEGG RIBOSOME	84	genes.ES.table	0.48	1.3	0.25	0.89	0.96	0.86	0.42	0.5	0.71	0.33
KEGG RNA DEGRADATION	56	genes.ES.table	0.2	0.93	0.52	1	1	0.43	0.4	0.26	1	0.52

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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	POLR3G	POLR3G	POLR3G	1831	0.14	0.011	YES
2	POLR1C	POLR1C	POLR1C	1979	0.14	0.11	YES
3	ZNRD1	ZNRD1	ZNRD1	2422	0.12	0.18	YES
4	POLR2I	POLR2I	POLR2I	2591	0.11	0.26	YES
5	POLR2F	POLR2F	POLR2F	3816	0.072	0.25	YES
6	POLR2J3	POLR2J3	POLR2J3	3924	0.07	0.3	YES
7	POLR2J2	POLR2J2	POLR2J2	4276	0.062	0.33	YES
8	POLR3H	POLR3H	POLR3H	4468	0.059	0.36	YES
9	POLR3B	POLR3B	POLR3B	4556	0.057	0.4	YES
10	POLR3D	POLR3D	POLR3D	4754	0.053	0.44	YES
11	POLR3K	POLR3K	POLR3K	5534	0.041	0.42	YES
12	POLR1B	POLR1B	POLR1B	5965	0.035	0.43	YES
13	POLR1D	POLR1D	POLR1D	6291	0.031	0.44	YES
14	POLR2A	POLR2A	POLR2A	6354	0.03	0.46	YES
15	POLR2L	POLR2L	POLR2L	6706	0.026	0.46	YES
16	POLR2D	POLR2D	POLR2D	6719	0.026	0.48	YES
17	POLR3F	POLR3F	POLR3F	6871	0.024	0.49	YES
18	POLR1A	POLR1A	POLR1A	7096	0.021	0.49	YES
19	POLR1E	POLR1E	POLR1E	7330	0.018	0.49	YES
20	POLR2C	POLR2C	POLR2C	8099	0.0086	0.45	NO
21	POLR2J	POLR2J	POLR2J	8105	0.0085	0.46	NO
22	POLR2G	POLR2G	POLR2G	8366	0.0057	0.45	NO
23	POLR3GL	POLR3GL	POLR3GL	8482	0.0043	0.45	NO
24	POLR3A	POLR3A	POLR3A	9179	-0.0037	0.41	NO
25	POLR3C	POLR3C	POLR3C	10112	-0.016	0.37	NO
26	POLR2E	POLR2E	POLR2E	10183	-0.017	0.38	NO
27	POLR2K	POLR2K	POLR2K	10288	-0.018	0.39	NO
28	POLR2B	POLR2B	POLR2B	10575	-0.022	0.39	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 CITRATE CYCLE TCA CYCLE.

Figure S42. 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 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	PSTK	PSTK	PSTK	2317	0.12	-0.067	YES
2	FARSA	FARSA	FARSA	2425	0.12	-0.0084	YES
3	PARS2	PARS2	PARS2	2488	0.11	0.052	YES
4	MARS2	MARS2	MARS2	2561	0.11	0.11	YES
5	TARSL2	TARSL2	TARSL2	2982	0.094	0.14	YES
6	SARS2	SARS2	SARS2	3021	0.093	0.19	YES
7	YARS2	YARS2	YARS2	3326	0.084	0.22	YES
8	FARS2	FARS2	FARS2	3706	0.075	0.24	YES
9	NARS2	NARS2	NARS2	3808	0.072	0.27	YES
10	MTFMT	MTFMT	MTFMT	4795	0.053	0.24	YES
11	AARS2	AARS2	AARS2	4841	0.052	0.27	YES
12	VARS2	VARS2	VARS2	5093	0.047	0.28	YES
13	DARS	DARS	DARS	5109	0.047	0.31	YES
14	HARS	HARS	HARS	5275	0.045	0.32	YES
15	LARS	LARS	LARS	5437	0.042	0.34	YES
16	EARS2	EARS2	EARS2	5476	0.042	0.36	YES
17	SEPSECS	SEPSECS	SEPSECS	5782	0.038	0.36	YES
18	HARS2	HARS2	HARS2	5795	0.037	0.38	YES
19	WARS2	WARS2	WARS2	5824	0.037	0.4	YES
20	FARSB	FARSB	FARSB	6047	0.034	0.41	YES
21	LARS2	LARS2	LARS2	6531	0.028	0.4	NO
22	CARS2	CARS2	CARS2	7334	0.018	0.36	NO
23	YARS	YARS	YARS	7960	0.011	0.33	NO
24	IARS	IARS	IARS	8232	0.0071	0.32	NO
25	MARS	MARS	MARS	8294	0.0065	0.32	NO
26	TARS	TARS	TARS	8364	0.0057	0.32	NO
27	VARS	VARS	VARS	8380	0.0056	0.32	NO
28	AARS	AARS	AARS	8735	0.0012	0.3	NO
29	QARS	QARS	QARS	9395	-0.0062	0.26	NO
30	RARS	RARS	RARS	9538	-0.0079	0.26	NO
31	KARS	KARS	KARS	9626	-0.0092	0.26	NO
32	EPRS	EPRS	EPRS	10194	-0.017	0.24	NO
33	CARS	CARS	CARS	10556	-0.022	0.23	NO
34	DARS2	DARS2	DARS2	10590	-0.022	0.24	NO
35	RARS2	RARS2	RARS2	10704	-0.024	0.24	NO
36	NARS	NARS	NARS	10857	-0.027	0.25	NO
37	GARS	GARS	GARS	11277	-0.034	0.25	NO
38	SARS	SARS	SARS	11530	-0.039	0.25	NO
39	IARS2	IARS2	IARS2	11635	-0.041	0.27	NO
40	WARS	WARS	WARS	13437	-0.1	0.22	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 OXIDATIVE PHOSPHORYLATION.

Figure S44. 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 PYRIMIDINE METABOLISM

Table S23. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	RPL9	RPL9	RPL9	1845	0.14	-0.067	YES
2	RPS26	RPS26	RPS26	1982	0.14	-0.036	YES
3	RPL36A	RPL36A	RPL36A	2460	0.11	-0.031	YES
4	RPL22L1	RPL22L1	RPL22L1	2920	0.096	-0.03	YES
5	RPL37	RPL37	RPL37	3491	0.079	-0.041	YES
6	RPL21	RPL21	RPL21	3661	0.076	-0.029	YES
7	RPL12	RPL12	RPL12	3791	0.073	-0.016	YES
8	RPL35A	RPL35A	RPL35A	3813	0.072	0.0031	YES
9	RPL36	RPL36	RPL36	4036	0.067	0.0093	YES
10	RPL31	RPL31	RPL31	4237	0.063	0.016	YES
11	RPL39	RPL39	RPL39	4250	0.063	0.033	YES
12	RPL10A	RPL10A	RPL10A	4364	0.061	0.044	YES
13	RPL29	RPL29	RPL29	4418	0.06	0.058	YES
14	RPL23	RPL23	RPL23	4446	0.059	0.073	YES
15	RPS15	RPS15	RPS15	4465	0.059	0.088	YES
16	RPL26	RPL26	RPL26	4600	0.056	0.097	YES
17	RPS4X	RPS4X	RPS4X	4676	0.055	0.11	YES
18	RPS17	RPS17	RPS17	4680	0.055	0.12	YES
19	RPL17	RPL17	RPL17	4719	0.054	0.14	YES
20	RPL22	RPL22	RPL22	4910	0.051	0.14	YES
21	RPS15A	RPS15A	RPS15A	4993	0.049	0.15	YES
22	RPL13	RPL13	RPL13	5056	0.048	0.16	YES
23	RPL28	RPL28	RPL28	5214	0.046	0.16	YES
24	RPS10	RPS10	RPS10	5233	0.046	0.18	YES
25	RPS24	RPS24	RPS24	5237	0.045	0.19	YES
26	RPL32	RPL32	RPL32	5248	0.045	0.2	YES
27	RPL34	RPL34	RPL34	5262	0.045	0.21	YES
28	RPL37A	RPL37A	RPL37A	5305	0.044	0.22	YES
29	RPL41	RPL41	RPL41	5377	0.043	0.23	YES
30	RPL38	RPL38	RPL38	5394	0.043	0.24	YES
31	RPSA	RPSA	RPSA	5483	0.042	0.25	YES
32	RPS23	RPS23	RPS23	5574	0.04	0.25	YES
33	RPS20	RPS20	RPS20	5586	0.04	0.26	YES
34	RPL27	RPL27	RPL27	5619	0.04	0.28	YES
35	RPS18	RPS18	RPS18	5758	0.038	0.28	YES
36	RPL23A	RPL23A	RPL23A	5835	0.037	0.28	YES
37	RPL35	RPL35	RPL35	5847	0.037	0.29	YES
38	RPS2	RPS2	RPS2	5853	0.036	0.3	YES
39	RPS7	RPS7	RPS7	5868	0.036	0.31	YES
40	RPS5	RPS5	RPS5	5925	0.036	0.32	YES
41	RPL18A	RPL18A	RPL18A	5993	0.034	0.33	YES
42	RPL24	RPL24	RPL24	6058	0.034	0.33	YES
43	RPL14	RPL14	RPL14	6113	0.033	0.34	YES
44	RPS13	RPS13	RPS13	6140	0.033	0.34	YES
45	RPS28	RPS28	RPS28	6146	0.033	0.35	YES
46	RPLP2	RPLP2	RPLP2	6154	0.032	0.36	YES
47	RPLP1	RPLP1	RPLP1	6278	0.031	0.36	YES
48	RPL10	RPL10	RPL10	6286	0.031	0.37	YES
49	RPS27L	RPS27L	RPS27L	6355	0.03	0.38	YES
50	RPL15	RPL15	RPL15	6391	0.03	0.38	YES
51	RPS9	RPS9	RPS9	6439	0.029	0.39	YES
52	RPS3	RPS3	RPS3	6468	0.028	0.4	YES
53	RPL11	RPL11	RPL11	6479	0.028	0.4	YES
54	RPS27A	RPS27A	RPS27A	6511	0.028	0.41	YES
55	RPS19	RPS19	RPS19	6532	0.028	0.42	YES
56	RPS6	RPS6	RPS6	6541	0.028	0.42	YES
57	RPL30	RPL30	RPL30	6596	0.027	0.43	YES
58	RPLP0	RPLP0	RPLP0	6712	0.026	0.43	YES
59	RPS11	RPS11	RPS11	6743	0.025	0.43	YES
60	RPL27A	RPL27A	RPL27A	6765	0.025	0.44	YES
61	RPS21	RPS21	RPS21	6848	0.024	0.44	YES
62	RPS29	RPS29	RPS29	6899	0.024	0.45	YES
63	RPS16	RPS16	RPS16	6904	0.023	0.45	YES
64	RPL3	RPL3	RPL3	6913	0.023	0.46	YES
65	RPS3A	RPS3A	RPS3A	6972	0.022	0.46	YES
66	RPL6	RPL6	RPL6	6992	0.022	0.47	YES
67	RPS8	RPS8	RPS8	7085	0.021	0.47	YES
68	RPS12	RPS12	RPS12	7146	0.02	0.47	YES
69	RSL24D1	RSL24D1	RSL24D1	7189	0.02	0.47	YES
70	RPL36AL	RPL36AL	RPL36AL	7237	0.019	0.48	YES
71	RPL5	RPL5	RPL5	7241	0.019	0.48	YES
72	FAU	FAU	FAU	7290	0.019	0.48	YES
73	RPL13A	RPL13A	RPL13A	7400	0.017	0.48	NO
74	RPL8	RPL8	RPL8	7615	0.015	0.47	NO
75	UBA52	UBA52	UBA52	7932	0.011	0.46	NO
76	RPL7A	RPL7A	RPL7A	8044	0.0094	0.46	NO
77	RPL26L1	RPL26L1	RPL26L1	8344	0.0059	0.44	NO
78	RPL7	RPL7	RPL7	8361	0.0058	0.44	NO
79	RPS25	RPS25	RPS25	8430	0.0051	0.44	NO
80	MRPL13	MRPL13	MRPL13	8557	0.0033	0.43	NO
81	RPL4	RPL4	RPL4	8676	0.002	0.42	NO
82	RPL19	RPL19	RPL19	9019	-0.0019	0.4	NO
83	RPS27	RPS27	RPS27	13044	-0.082	0.19	NO
84	RPS4Y1	RPS4Y1	RPS4Y1	14774	-0.18	0.14	NO

Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PYRIMIDINE METABOLISM.

Figure S46. 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 GLYCINE SERINE AND THREONINE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NEIL3	NEIL3	NEIL3	752	0.24	0.1	YES
2	NEIL2	NEIL2	NEIL2	2471	0.11	0.077	YES
3	POLD2	POLD2	POLD2	2836	0.099	0.12	YES
4	NTHL1	NTHL1	NTHL1	3177	0.089	0.15	YES
5	MPG	MPG	MPG	3352	0.083	0.19	YES
6	LIG3	LIG3	LIG3	3375	0.083	0.24	YES
7	MUTYH	MUTYH	MUTYH	3909	0.07	0.26	YES
8	UNG	UNG	UNG	3956	0.069	0.3	YES
9	APEX1	APEX1	APEX1	4822	0.052	0.28	YES
10	XRCC1	XRCC1	XRCC1	5203	0.046	0.28	YES
11	SMUG1	SMUG1	SMUG1	5817	0.037	0.27	YES
12	LIG1	LIG1	LIG1	6099	0.033	0.28	YES
13	POLL	POLL	POLL	6160	0.032	0.29	YES
14	POLE3	POLE3	POLE3	6217	0.032	0.31	YES
15	POLD1	POLD1	POLD1	6387	0.03	0.32	YES
16	MBD4	MBD4	MBD4	6455	0.029	0.33	YES
17	PARP1	PARP1	PARP1	6528	0.028	0.34	YES
18	POLE2	POLE2	POLE2	7081	0.021	0.33	NO
19	NEIL1	NEIL1	NEIL1	8107	0.0085	0.27	NO
20	PARP2	PARP2	PARP2	8173	0.0078	0.27	NO
21	APEX2	APEX2	APEX2	8339	0.006	0.27	NO
22	FEN1	FEN1	FEN1	8345	0.0059	0.27	NO
23	PCNA	PCNA	PCNA	8402	0.0054	0.27	NO
24	PARP4	PARP4	PARP4	8546	0.0035	0.26	NO
25	POLB	POLB	POLB	9759	-0.011	0.2	NO
26	TDG	TDG	TDG	10908	-0.027	0.15	NO
27	POLD3	POLD3	POLD3	11460	-0.038	0.14	NO
28	POLE4	POLE4	POLE4	11695	-0.043	0.16	NO
29	POLE	POLE	POLE	12281	-0.056	0.16	NO
30	POLD4	POLD4	POLD4	12443	-0.062	0.18	NO
31	OGG1	OGG1	OGG1	12798	-0.073	0.21	NO
32	PARP3	PARP3	PARP3	12953	-0.078	0.25	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 GLYCINE SERINE AND THREONINE METABOLISM.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCINE SERINE AND THREONINE 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 CYSTEINE AND METHIONINE METABOLISM

Table S25. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CBS	CBS	CBS	803	0.24	0.05	YES
2	GGT6	GGT6	GGT6	967	0.22	0.13	YES
3	GGT5	GGT5	GGT5	1345	0.18	0.18	YES
4	CTH	CTH	CTH	1948	0.14	0.2	YES
5	HEMK1	HEMK1	HEMK1	2024	0.13	0.25	YES
6	MARS2	MARS2	MARS2	2561	0.11	0.27	YES
7	LCMT2	LCMT2	LCMT2	2688	0.1	0.3	YES
8	SCLY	SCLY	SCLY	3454	0.081	0.29	YES
9	AHCY	AHCY	AHCY	3631	0.076	0.31	YES
10	WBSCR22	WBSCR22	WBSCR22	3866	0.071	0.33	YES
11	TRMT11	TRMT11	TRMT11	4094	0.066	0.34	YES
12	MAT2A	MAT2A	MAT2A	4375	0.061	0.35	YES
13	LCMT1	LCMT1	LCMT1	5813	0.037	0.28	NO
14	PAPSS1	PAPSS1	PAPSS1	6280	0.031	0.27	NO
15	SEPHS1	SEPHS1	SEPHS1	6689	0.026	0.25	NO
16	METTL6	METTL6	METTL6	7284	0.019	0.23	NO
17	METTL2B	METTL2B	METTL2B	8203	0.0075	0.18	NO
18	MARS	MARS	MARS	8294	0.0065	0.17	NO
19	MAT2B	MAT2B	MAT2B	9833	-0.012	0.089	NO
20	AHCYL1	AHCYL1	AHCYL1	10517	-0.022	0.058	NO
21	AHCYL2	AHCYL2	AHCYL2	10651	-0.023	0.06	NO
22	GGT7	GGT7	GGT7	11891	-0.047	0.0071	NO
23	MAT1A	MAT1A	MAT1A	13122	-0.085	-0.029	NO
24	GGT1	GGT1	GGT1	15485	-0.25	-0.065	NO
25	PAPSS2	PAPSS2	PAPSS2	16626	-0.41	0.037	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 CYSTEINE AND METHIONINE METABOLISM.

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

genes ES table in pathway: KEGG SELENOAMINO ACID METABOLISM

Table S26. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	DYNC2H1	DYNC2H1	DYNC2H1	219	0.37	0.09	YES
2	AQP3	AQP3	AQP3	254	0.36	0.19	YES
3	DYNC2LI1	DYNC2LI1	DYNC2LI1	323	0.32	0.27	YES
4	AQP4	AQP4	AQP4	1120	0.2	0.28	YES
5	CREB3L4	CREB3L4	CREB3L4	1906	0.14	0.28	NO
6	ADCY6	ADCY6	ADCY6	3295	0.085	0.22	NO
7	DYNLL1	DYNLL1	DYNLL1	3549	0.078	0.22	NO
8	VAMP2	VAMP2	VAMP2	5783	0.038	0.11	NO
9	RAB5B	RAB5B	RAB5B	5806	0.037	0.12	NO
10	STX4	STX4	STX4	6604	0.027	0.076	NO
11	RAB11B	RAB11B	RAB11B	6660	0.026	0.08	NO
12	PRKACB	PRKACB	PRKACB	6832	0.024	0.077	NO
13	CREB3L2	CREB3L2	CREB3L2	7163	0.02	0.064	NO
14	ARHGDIA	ARHGDIA	ARHGDIA	7250	0.019	0.064	NO
15	GNAS	GNAS	GNAS	7380	0.017	0.061	NO
16	DCTN1	DCTN1	DCTN1	8277	0.0067	0.011	NO
17	CREB3	CREB3	CREB3	8503	0.0041	-0.00093	NO
18	DYNC1LI2	DYNC1LI2	DYNC1LI2	8566	0.0032	-0.0036	NO
19	DYNC1I2	DYNC1I2	DYNC1I2	8717	0.0015	-0.012	NO
20	DCTN4	DCTN4	DCTN4	9006	-0.0017	-0.028	NO
21	CREB3L3	CREB3L3	CREB3L3	9188	-0.0038	-0.038	NO
22	DCTN5	DCTN5	DCTN5	9310	-0.0051	-0.043	NO
23	DYNLL2	DYNLL2	DYNLL2	9448	-0.007	-0.049	NO
24	PRKX	PRKX	PRKX	9482	-0.0073	-0.049	NO
25	CREB1	CREB1	CREB1	9581	-0.0086	-0.052	NO
26	DYNC1LI1	DYNC1LI1	DYNC1LI1	10295	-0.018	-0.089	NO
27	DCTN2	DCTN2	DCTN2	10322	-0.019	-0.085	NO
28	DCTN6	DCTN6	DCTN6	11356	-0.035	-0.14	NO
29	DYNC1H1	DYNC1H1	DYNC1H1	11647	-0.042	-0.14	NO
30	RAB5A	RAB5A	RAB5A	11799	-0.045	-0.14	NO
31	RAB5C	RAB5C	RAB5C	11923	-0.047	-0.13	NO
32	NSF	NSF	NSF	12055	-0.05	-0.12	NO
33	RAB11A	RAB11A	RAB11A	12086	-0.051	-0.11	NO
34	ARHGDIB	ARHGDIB	ARHGDIB	12906	-0.077	-0.14	NO
35	AVPR2	AVPR2	AVPR2	12984	-0.08	-0.12	NO
36	PRKACA	PRKACA	PRKACA	13558	-0.1	-0.12	NO
37	ADCY9	ADCY9	ADCY9	14935	-0.19	-0.15	NO
38	CREB3L1	CREB3L1	CREB3L1	15149	-0.21	-0.1	NO
39	CREB5	CREB5	CREB5	15422	-0.24	-0.054	NO
40	DYNC1I1	DYNC1I1	DYNC1I1	15766	-0.28	0.003	NO
41	PRKACG	PRKACG	PRKACG	15952	-0.3	0.076	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 SELENOAMINO ACID METABOLISM.

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table S27. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SARDH	SARDH	SARDH	359	0.31	0.049	YES
2	PHGDH	PHGDH	PHGDH	586	0.27	0.095	YES
3	AGXT	AGXT	AGXT	661	0.26	0.15	YES
4	CBS	CBS	CBS	803	0.24	0.19	YES
5	GCAT	GCAT	GCAT	843	0.23	0.24	YES
6	GAMT	GAMT	GAMT	1117	0.2	0.27	YES
7	BHMT	BHMT	BHMT	1206	0.19	0.3	YES
8	MAOA	MAOA	MAOA	1301	0.18	0.34	YES
9	DMGDH	DMGDH	DMGDH	1329	0.18	0.38	YES
10	CTH	CTH	CTH	1948	0.14	0.37	YES
11	PSPH	PSPH	PSPH	2112	0.13	0.39	YES
12	SDS	SDS	SDS	2392	0.12	0.4	YES
13	GNMT	GNMT	GNMT	3187	0.088	0.37	NO
14	GLDC	GLDC	GLDC	3472	0.08	0.38	NO
15	SRR	SRR	SRR	4176	0.064	0.35	NO
16	ALAS1	ALAS1	ALAS1	4400	0.06	0.35	NO
17	PIPOX	PIPOX	PIPOX	5974	0.035	0.26	NO
18	SHMT1	SHMT1	SHMT1	6557	0.028	0.24	NO
19	GLYCTK	GLYCTK	GLYCTK	7709	0.014	0.17	NO
20	DLD	DLD	DLD	9637	-0.0093	0.064	NO
21	SHMT2	SHMT2	SHMT2	12149	-0.053	-0.07	NO
22	AOC2	AOC2	AOC2	12823	-0.074	-0.093	NO
23	GATM	GATM	GATM	13514	-0.1	-0.11	NO
24	PSAT1	PSAT1	PSAT1	14834	-0.19	-0.15	NO
25	CHDH	CHDH	CHDH	14999	-0.2	-0.11	NO
26	ALAS2	ALAS2	ALAS2	15546	-0.26	-0.086	NO
27	AOC3	AOC3	AOC3	16340	-0.36	-0.054	NO
28	MAOB	MAOB	MAOB	16907	-0.48	0.02	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 BUTANOATE METABOLISM.

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

Table 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	ACSM1	ACSM1	ACSM1	148	0.4	0.11	YES
2	ACSM3	ACSM3	ACSM3	248	0.36	0.21	YES
3	ALDH7A1	ALDH7A1	ALDH7A1	871	0.23	0.24	YES
4	BDH1	BDH1	BDH1	1313	0.18	0.27	YES
5	ALDH1B1	ALDH1B1	ALDH1B1	2285	0.12	0.25	YES
6	ALDH5A1	ALDH5A1	ALDH5A1	2329	0.12	0.28	YES
7	L2HGDH	L2HGDH	L2HGDH	2540	0.11	0.3	YES
8	AACS	AACS	AACS	2572	0.11	0.33	YES
9	BDH2	BDH2	BDH2	3427	0.082	0.31	NO
10	ACAT2	ACAT2	ACAT2	5540	0.041	0.2	NO
11	PDHA1	PDHA1	PDHA1	6753	0.025	0.14	NO
12	ECHS1	ECHS1	ECHS1	7079	0.021	0.12	NO
13	ACADS	ACADS	ACADS	7082	0.021	0.13	NO
14	PDHB	PDHB	PDHB	9034	-0.0022	0.016	NO
15	HADH	HADH	HADH	9193	-0.0038	0.0082	NO
16	OXCT1	OXCT1	OXCT1	9429	-0.0067	-0.0035	NO
17	HADHA	HADHA	HADHA	10416	-0.02	-0.055	NO
18	HMGCS1	HMGCS1	HMGCS1	10588	-0.022	-0.058	NO
19	HMGCL	HMGCL	HMGCL	10896	-0.027	-0.068	NO
20	ALDH2	ALDH2	ALDH2	12155	-0.053	-0.12	NO
21	ALDH9A1	ALDH9A1	ALDH9A1	12780	-0.073	-0.14	NO
22	ABAT	ABAT	ABAT	13524	-0.1	-0.15	NO
23	ACAT1	ACAT1	ACAT1	14067	-0.13	-0.14	NO
24	ALDH3A2	ALDH3A2	ALDH3A2	14827	-0.19	-0.13	NO
25	OXCT2	OXCT2	OXCT2	14917	-0.19	-0.083	NO
26	GAD1	GAD1	GAD1	15537	-0.25	-0.044	NO
27	ACSM5	ACSM5	ACSM5	16918	-0.49	0.02	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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RIBOSOME

Table 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	RPA4	RPA4	RPA4	1077	0.2	0.13	YES
2	POLD2	POLD2	POLD2	2836	0.099	0.12	YES
3	EME1	EME1	EME1	3619	0.077	0.15	YES
4	XRCC3	XRCC3	XRCC3	4433	0.06	0.16	YES
5	RPA3	RPA3	RPA3	4657	0.055	0.2	YES
6	RAD51L3	RAD51L3	RAD51L3	5017	0.049	0.22	YES
7	XRCC2	XRCC2	XRCC2	5175	0.046	0.26	YES
8	SSBP1	SSBP1	SSBP1	5480	0.042	0.28	YES
9	RAD52	RAD52	RAD52	5496	0.042	0.32	YES
10	TOP3B	TOP3B	TOP3B	6122	0.033	0.31	YES
11	POLD1	POLD1	POLD1	6387	0.03	0.33	YES
12	RAD51L1	RAD51L1	RAD51L1	7248	0.019	0.29	NO
13	SHFM1	SHFM1	SHFM1	7354	0.018	0.3	NO
14	RAD50	RAD50	RAD50	7536	0.016	0.31	NO
15	MUS81	MUS81	MUS81	7854	0.012	0.3	NO
16	MRE11A	MRE11A	MRE11A	7996	0.01	0.3	NO
17	BLM	BLM	BLM	8512	0.004	0.28	NO
18	RAD54B	RAD54B	RAD54B	8633	0.0025	0.27	NO
19	RAD54L	RAD54L	RAD54L	9124	-0.0031	0.25	NO
20	RPA2	RPA2	RPA2	9235	-0.0042	0.24	NO
21	RPA1	RPA1	RPA1	10015	-0.014	0.21	NO
22	RAD51	RAD51	RAD51	10086	-0.016	0.22	NO
23	TOP3A	TOP3A	TOP3A	10098	-0.016	0.24	NO
24	NBN	NBN	NBN	10144	-0.016	0.25	NO
25	POLD3	POLD3	POLD3	11460	-0.038	0.21	NO
26	POLD4	POLD4	POLD4	12443	-0.062	0.21	NO
27	BRCA2	BRCA2	BRCA2	12748	-0.071	0.26	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 RIBOSOME.

Figure S58. 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 RNA DEGRADATION

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	ENO3	ENO3	ENO3	1289	0.18	-0.0034	YES
2	EXOSC4	EXOSC4	EXOSC4	1761	0.15	0.028	YES
3	ENO2	ENO2	ENO2	1777	0.15	0.085	YES
4	LSM7	LSM7	LSM7	2627	0.11	0.078	YES
5	EXOSC5	EXOSC5	EXOSC5	2921	0.096	0.098	YES
6	EXOSC6	EXOSC6	EXOSC6	2954	0.095	0.13	YES
7	DCP1B	DCP1B	DCP1B	3702	0.075	0.12	YES
8	EXOSC2	EXOSC2	EXOSC2	3989	0.068	0.13	YES
9	LSM2	LSM2	LSM2	4063	0.067	0.15	YES
10	EXOSC7	EXOSC7	EXOSC7	4212	0.064	0.17	YES
11	WDR61	WDR61	WDR61	4576	0.057	0.17	YES
12	LSM5	LSM5	LSM5	4908	0.051	0.17	YES
13	EDC3	EDC3	EDC3	5018	0.048	0.18	YES
14	DCPS	DCPS	DCPS	5815	0.037	0.15	YES
15	HSPD1	HSPD1	HSPD1	6107	0.033	0.15	YES
16	MPHOSPH6	MPHOSPH6	MPHOSPH6	6125	0.033	0.16	YES
17	SKIV2L	SKIV2L	SKIV2L	6166	0.032	0.17	YES
18	PNPT1	PNPT1	PNPT1	6363	0.03	0.17	YES
19	EXOSC8	EXOSC8	EXOSC8	6445	0.029	0.18	YES
20	EXOSC3	EXOSC3	EXOSC3	6454	0.029	0.19	YES
21	CNOT10	CNOT10	CNOT10	6565	0.027	0.19	YES
22	PARN	PARN	PARN	6573	0.027	0.2	YES
23	LSM4	LSM4	LSM4	6790	0.025	0.2	YES
24	CNOT3	CNOT3	CNOT3	6849	0.024	0.2	YES
25	DCP1A	DCP1A	DCP1A	7194	0.02	0.19	NO
26	ENO1	ENO1	ENO1	7255	0.019	0.2	NO
27	CNOT4	CNOT4	CNOT4	7366	0.018	0.2	NO
28	EXOSC1	EXOSC1	EXOSC1	7481	0.016	0.2	NO
29	EDC4	EDC4	EDC4	7513	0.016	0.2	NO
30	EXOSC10	EXOSC10	EXOSC10	7689	0.014	0.2	NO
31	NAA38	NAA38	NAA38	7867	0.012	0.19	NO
32	LSM3	LSM3	LSM3	7913	0.011	0.19	NO
33	HSPA9	HSPA9	HSPA9	7914	0.011	0.2	NO
34	TTC37	TTC37	TTC37	8241	0.007	0.18	NO
35	LSM1	LSM1	LSM1	8259	0.0068	0.18	NO
36	CNOT2	CNOT2	CNOT2	8381	0.0056	0.18	NO
37	CNOT6	CNOT6	CNOT6	8579	0.0031	0.17	NO
38	RQCD1	RQCD1	RQCD1	8739	0.0012	0.16	NO
39	DIS3	DIS3	DIS3	9016	-0.0019	0.14	NO
40	EXOSC9	EXOSC9	EXOSC9	9525	-0.0078	0.12	NO
41	CNOT7	CNOT7	CNOT7	9689	-0.01	0.11	NO
42	SKIV2L2	SKIV2L2	SKIV2L2	10391	-0.02	0.078	NO
43	PAPOLA	PAPOLA	PAPOLA	10663	-0.024	0.072	NO
44	CNOT1	CNOT1	CNOT1	10799	-0.026	0.074	NO
45	LSM6	LSM6	LSM6	11027	-0.03	0.072	NO
46	PAPOLG	PAPOLG	PAPOLG	11270	-0.034	0.071	NO
47	XRN2	XRN2	XRN2	11416	-0.037	0.077	NO
48	ZCCHC7	ZCCHC7	ZCCHC7	11524	-0.039	0.086	NO
49	DDX6	DDX6	DDX6	11711	-0.043	0.093	NO
50	C1D	C1D	C1D	11876	-0.046	0.1	NO
51	XRN1	XRN1	XRN1	12084	-0.051	0.11	NO
52	PATL1	PATL1	PATL1	12406	-0.06	0.11	NO
53	CNOT6L	CNOT6L	CNOT6L	12439	-0.061	0.14	NO
54	DCP2	DCP2	DCP2	12691	-0.07	0.15	NO
55	PAPD7	PAPD7	PAPD7	12722	-0.071	0.18	NO
56	PAPOLB	PAPOLB	PAPOLB	15266	-0.22	0.12	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 RNA DEGRADATION.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

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