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

Adrenocortical Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in ACC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1J965QW

Overview

Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "ACC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

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

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 703
Number of samples: 79
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 24
pheno.type: 2 - 4 :[ clus2 ] 15
pheno.type: 3 - 4 :[ clus3 ] 17
pheno.type: 4 - 4 :[ clus4 ] 23

For the expression subtypes of 17733 genes in 80 samples, GSEA found enriched gene sets in each cluster using 79 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG RIBOSOME, KEGG SPLICEOSOME, KEGG PROTEASOME, KEGG BASE EXCISION REPAIR, KEGG CELL CYCLE, PID MYC ACTIVPATHWAY, PID ILK PATHWAY, PID ATM PATHWAY, PID MYC PATHWAY, PID FOXM1PATHWAY

And common core enriched genes are PSMA1, PSMA4, PSMA5, PSMA8, PSMB3, PSMB4, PSMB5, PSMB9, PSMC1, PSMC3

clus2

Top enriched gene sets are KEGG WNT SIGNALING PATHWAY, KEGG HEDGEHOG SIGNALING PATHWAY, KEGG TASTE TRANSDUCTION, KEGG BASAL CELL CARCINOMA, BIOCARTA NO1 PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA WNT PATHWAY, ST WNT BETA CATENIN PATHWAY, PID REELINPATHWAY, PID NECTIN PATHWAY

And common core enriched genes are MYC, CTNNB1, FRAT1, WIF1, CREBBP, CSNK1A1, GLI1, GLI2, GLI3, GNAO1

clus3

Top enriched gene sets are KEGG PENTOSE PHOSPHATE PATHWAY, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG BUTANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG BASAL TRANSCRIPTION FACTORS, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG UBIQUITIN MEDIATED PROTEOLYSIS, BIOCARTA GH PATHWAY, BIOCARTA CREB PATHWAY, ST ERK1 ERK2 MAPK PATHWAY

And common core enriched genes are CCNH, CDK7, CUL4A, CUL4B, ERCC2, ERCC8, GTF2H2, GTF2H3, MNAT1, BRAF

clus4

Top enriched gene sets are KEGG STARCH AND SUCROSE METABOLISM, BIOCARTA HDAC PATHWAY, BIOCARTA IL2RB PATHWAY, SIG BCR SIGNALING PATHWAY, PID FCER1PATHWAY, PID BCR 5PATHWAY, PID GMCSF PATHWAY, PID TCR PATHWAY, PID CD8TCRPATHWAY, PID TCPTP PATHWAY

And common core enriched genes are PIK3R1, SYK, FAS, FASLG, PIK3CG, MAP2K6, MEF2C, BCL2, IKZF3, IL2RA

Results

Subtype clus1 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG RIBOSOME	85	genes.ES.table	0.57	1.6	0.077	0.17	0.9	0.8	0.33	0.54	0.098	0.014
KEGG SPLICEOSOME	114	genes.ES.table	0.35	1.5	0.12	0.22	0.96	0.54	0.34	0.36	0.14	0.016
KEGG PROTEASOME	44	genes.ES.table	0.56	1.9	0.0083	0.18	0.26	0.77	0.36	0.5	0	0.041
KEGG BASE EXCISION REPAIR	33	genes.ES.table	0.47	1.7	0.047	0.13	0.84	0.55	0.3	0.38	0.072	0.01
KEGG CELL CYCLE	118	genes.ES.table	0.53	1.6	0.078	0.17	0.92	0.42	0.19	0.34	0.1	0.011
PID MYC ACTIVPATHWAY	78	genes.ES.table	0.45	1.7	0.027	0.1	0.73	0.45	0.22	0.35	0.047	0.008
PID ILK PATHWAY	45	genes.ES.table	0.37	1.5	0.096	0.23	0.97	0.24	0.18	0.2	0.15	0.015
PID ATM PATHWAY	34	genes.ES.table	0.51	1.6	0.081	0.17	0.92	0.41	0.2	0.33	0.1	0.01
PID MYC PATHWAY	25	genes.ES.table	0.42	1.6	0.059	0.18	0.92	0.52	0.31	0.36	0.11	0.015
PID FOXM1PATHWAY	38	genes.ES.table	0.73	1.6	0.008	0.14	0.87	0.47	0.088	0.43	0.077	0.012

genes ES table in pathway: KEGG RIBOSOME

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	CCNE2	CCNE2	CCNE2	779	0.3	0.027	YES
2	PSME4	PSME4	PSME4	1376	0.22	0.045	YES
3	RPS27A	RPS27A	RPS27A	1532	0.21	0.085	YES
4	PSMD4	PSMD4	PSMD4	1650	0.2	0.12	YES
5	PSMB9	PSMB9	PSMB9	1983	0.18	0.15	YES
6	PSMD13	PSMD13	PSMD13	2328	0.16	0.16	YES
7	PSMC3	PSMC3	PSMC3	2489	0.15	0.19	YES
8	PSMD1	PSMD1	PSMD1	2660	0.14	0.21	YES
9	PSMA8	PSMA8	PSMA8	2734	0.14	0.24	YES
10	PSMB4	PSMB4	PSMB4	2757	0.13	0.27	YES
11	PSMD14	PSMD14	PSMD14	2916	0.13	0.29	YES
12	RFWD2	RFWD2	RFWD2	3192	0.12	0.3	YES
13	PSMC1	PSMC1	PSMC1	3248	0.12	0.32	YES
14	PSMC5	PSMC5	PSMC5	3270	0.11	0.35	YES
15	PSMA4	PSMA4	PSMA4	3457	0.11	0.36	YES
16	PSME2	PSME2	PSME2	3463	0.11	0.39	YES
17	PSMD11	PSMD11	PSMD11	3532	0.1	0.41	YES
18	PSMA1	PSMA1	PSMA1	3842	0.095	0.42	YES
19	PSMB5	PSMB5	PSMB5	3913	0.092	0.43	YES
20	PSMB3	PSMB3	PSMB3	4061	0.088	0.44	YES
21	PSMA5	PSMA5	PSMA5	4206	0.084	0.46	YES
22	PSMD2	PSMD2	PSMD2	4300	0.081	0.47	YES
23	UBA52	UBA52	UBA52	4612	0.072	0.47	YES
24	PSMD12	PSMD12	PSMD12	4875	0.065	0.47	YES
25	PSMB7	PSMB7	PSMB7	5071	0.06	0.47	YES
26	CDK2	CDK2	CDK2	5385	0.053	0.47	YES
27	PSMA6	PSMA6	PSMA6	5425	0.052	0.48	YES
28	PSMC6	PSMC6	PSMC6	5427	0.052	0.49	YES
29	PSMB1	PSMB1	PSMB1	5759	0.043	0.48	YES
30	PSMA3	PSMA3	PSMA3	5824	0.041	0.49	YES
31	PSMD3	PSMD3	PSMD3	6039	0.036	0.48	YES
32	PSMC4	PSMC4	PSMC4	6156	0.034	0.48	YES
33	PSMD6	PSMD6	PSMD6	6170	0.033	0.49	YES
34	CCNE1	CCNE1	CCNE1	6213	0.032	0.5	YES
35	PSME1	PSME1	PSME1	6256	0.031	0.5	YES
36	CDKN1A	CDKN1A	CDKN1A	6292	0.03	0.51	YES
37	PSMB6	PSMB6	PSMB6	6329	0.029	0.51	YES
38	MDM2	MDM2	MDM2	6349	0.029	0.52	YES
39	PSMB2	PSMB2	PSMB2	6872	0.017	0.49	NO
40	TP53	TP53	TP53	7338	0.0068	0.47	NO
41	PSMA7	PSMA7	PSMA7	7461	0.0041	0.46	NO
42	PSMA2	PSMA2	PSMA2	7554	0.0021	0.46	NO
43	PSMD9	PSMD9	PSMD9	7828	-0.0041	0.44	NO
44	PSMF1	PSMF1	PSMF1	8465	-0.018	0.41	NO
45	ATM	ATM	ATM	8503	-0.019	0.41	NO
46	PSMB8	PSMB8	PSMB8	8609	-0.021	0.41	NO
47	PSMD7	PSMD7	PSMD7	8689	-0.023	0.41	NO
48	PSMD8	PSMD8	PSMD8	8968	-0.029	0.4	NO
49	PSMB10	PSMB10	PSMB10	9282	-0.037	0.39	NO
50	PSMC2	PSMC2	PSMC2	9757	-0.049	0.38	NO
51	PSMD5	PSMD5	PSMD5	10267	-0.062	0.36	NO
52	CDKN1B	CDKN1B	CDKN1B	10878	-0.077	0.35	NO
53	PSMD10	PSMD10	PSMD10	13784	-0.17	0.22	NO

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

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

genes ES table in pathway: KEGG SPLICEOSOME

Table 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	CDC20	CDC20	CDC20	83	0.57	0.073	YES
2	AURKB	AURKB	AURKB	84	0.57	0.15	YES
3	UBE2C	UBE2C	UBE2C	247	0.45	0.2	YES
4	PLK1	PLK1	PLK1	285	0.43	0.26	YES
5	PTTG1	PTTG1	PTTG1	470	0.37	0.3	YES
6	AURKA	AURKA	AURKA	598	0.34	0.34	YES
7	PSME4	PSME4	PSME4	1376	0.22	0.32	YES
8	SKP2	SKP2	SKP2	1495	0.21	0.35	YES
9	RPS27A	RPS27A	RPS27A	1532	0.21	0.37	YES
10	PSMD4	PSMD4	PSMD4	1650	0.2	0.39	YES
11	PSMB9	PSMB9	PSMB9	1983	0.18	0.4	YES
12	PSMD13	PSMD13	PSMD13	2328	0.16	0.4	YES
13	PSMC3	PSMC3	PSMC3	2489	0.15	0.41	YES
14	PSMD1	PSMD1	PSMD1	2660	0.14	0.42	YES
15	PSMA8	PSMA8	PSMA8	2734	0.14	0.44	YES
16	PSMB4	PSMB4	PSMB4	2757	0.13	0.45	YES
17	PSMD14	PSMD14	PSMD14	2916	0.13	0.46	YES
18	ANAPC1	ANAPC1	ANAPC1	3099	0.12	0.47	YES
19	PSMC1	PSMC1	PSMC1	3248	0.12	0.47	YES
20	PSMC5	PSMC5	PSMC5	3270	0.11	0.49	YES
21	ANAPC11	ANAPC11	ANAPC11	3430	0.11	0.49	YES
22	PSMA4	PSMA4	PSMA4	3457	0.11	0.51	YES
23	PSME2	PSME2	PSME2	3463	0.11	0.52	YES
24	PSMD11	PSMD11	PSMD11	3532	0.1	0.53	YES
25	CDC26	CDC26	CDC26	3732	0.099	0.53	YES
26	PSMA1	PSMA1	PSMA1	3842	0.095	0.54	YES
27	PSMB5	PSMB5	PSMB5	3913	0.092	0.55	YES
28	PSMB3	PSMB3	PSMB3	4061	0.088	0.55	YES
29	PSMA5	PSMA5	PSMA5	4206	0.084	0.56	YES
30	PSMD2	PSMD2	PSMD2	4300	0.081	0.56	YES
31	UBA52	UBA52	UBA52	4612	0.072	0.55	NO
32	PSMD12	PSMD12	PSMD12	4875	0.065	0.55	NO
33	PSMB7	PSMB7	PSMB7	5071	0.06	0.55	NO
34	PSMA6	PSMA6	PSMA6	5425	0.052	0.53	NO
35	PSMC6	PSMC6	PSMC6	5427	0.052	0.54	NO
36	PSMB1	PSMB1	PSMB1	5759	0.043	0.53	NO
37	PSMA3	PSMA3	PSMA3	5824	0.041	0.53	NO
38	PSMD3	PSMD3	PSMD3	6039	0.036	0.52	NO
39	PSMC4	PSMC4	PSMC4	6156	0.034	0.52	NO
40	PSMD6	PSMD6	PSMD6	6170	0.033	0.52	NO
41	UBE2E1	UBE2E1	UBE2E1	6224	0.032	0.52	NO
42	PSME1	PSME1	PSME1	6256	0.031	0.53	NO
43	PSMB6	PSMB6	PSMB6	6329	0.029	0.53	NO
44	CDC16	CDC16	CDC16	6455	0.026	0.52	NO
45	ANAPC7	ANAPC7	ANAPC7	6541	0.024	0.52	NO
46	PSMB2	PSMB2	PSMB2	6872	0.017	0.5	NO
47	PSMA7	PSMA7	PSMA7	7461	0.0041	0.47	NO
48	CDC27	CDC27	CDC27	7522	0.0029	0.47	NO
49	PSMA2	PSMA2	PSMA2	7554	0.0021	0.47	NO
50	PSMD9	PSMD9	PSMD9	7828	-0.0041	0.45	NO
51	ANAPC2	ANAPC2	ANAPC2	8293	-0.014	0.43	NO
52	PSMF1	PSMF1	PSMF1	8465	-0.018	0.42	NO
53	ANAPC5	ANAPC5	ANAPC5	8543	-0.02	0.42	NO
54	PSMB8	PSMB8	PSMB8	8609	-0.021	0.42	NO
55	PSMD7	PSMD7	PSMD7	8689	-0.023	0.42	NO
56	ANAPC10	ANAPC10	ANAPC10	8944	-0.028	0.41	NO
57	PSMD8	PSMD8	PSMD8	8968	-0.029	0.41	NO
58	PSMB10	PSMB10	PSMB10	9282	-0.037	0.4	NO
59	PSMC2	PSMC2	PSMC2	9757	-0.049	0.38	NO
60	PSMD5	PSMD5	PSMD5	10267	-0.062	0.36	NO
61	UBE2D1	UBE2D1	UBE2D1	11121	-0.083	0.32	NO
62	CDC23	CDC23	CDC23	11409	-0.091	0.32	NO
63	ANAPC4	ANAPC4	ANAPC4	12869	-0.14	0.25	NO
64	PSMD10	PSMD10	PSMD10	13784	-0.17	0.22	NO

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

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

genes ES table in pathway: KEGG PROTEASOME

Table 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	PSME4	PSME4	PSME4	1376	0.22	-0.011	YES
2	PSMD4	PSMD4	PSMD4	1650	0.2	0.033	YES
3	PSMB9	PSMB9	PSMB9	1983	0.18	0.066	YES
4	PSMD13	PSMD13	PSMD13	2328	0.16	0.093	YES
5	PSMC3	PSMC3	PSMC3	2489	0.15	0.13	YES
6	PSMD1	PSMD1	PSMD1	2660	0.14	0.16	YES
7	PSMA8	PSMA8	PSMA8	2734	0.14	0.2	YES
8	PSMB4	PSMB4	PSMB4	2757	0.13	0.23	YES
9	PSMD14	PSMD14	PSMD14	2916	0.13	0.26	YES
10	PSMC1	PSMC1	PSMC1	3248	0.12	0.28	YES
11	PSMC5	PSMC5	PSMC5	3270	0.11	0.31	YES
12	PSMA4	PSMA4	PSMA4	3457	0.11	0.33	YES
13	PSME2	PSME2	PSME2	3463	0.11	0.36	YES
14	PSMD11	PSMD11	PSMD11	3532	0.1	0.39	YES
15	PSMA1	PSMA1	PSMA1	3842	0.095	0.4	YES
16	PSMB5	PSMB5	PSMB5	3913	0.092	0.42	YES
17	PSMB3	PSMB3	PSMB3	4061	0.088	0.44	YES
18	PSMA5	PSMA5	PSMA5	4206	0.084	0.46	YES
19	PSMD2	PSMD2	PSMD2	4300	0.081	0.48	YES
20	PSMB11	PSMB11	PSMB11	4623	0.072	0.48	YES
21	PSMD12	PSMD12	PSMD12	4875	0.065	0.49	YES
22	PSMB7	PSMB7	PSMB7	5071	0.06	0.49	YES
23	POMP	POMP	POMP	5259	0.056	0.5	YES
24	PSMA6	PSMA6	PSMA6	5425	0.052	0.51	YES
25	PSMC6	PSMC6	PSMC6	5427	0.052	0.52	YES
26	PSMB1	PSMB1	PSMB1	5759	0.043	0.52	YES
27	PSMA3	PSMA3	PSMA3	5824	0.041	0.52	YES
28	PSME3	PSME3	PSME3	6028	0.036	0.52	YES
29	PSMD3	PSMD3	PSMD3	6039	0.036	0.53	YES
30	PSMC4	PSMC4	PSMC4	6156	0.034	0.54	YES
31	PSMD6	PSMD6	PSMD6	6170	0.033	0.55	YES
32	PSME1	PSME1	PSME1	6256	0.031	0.55	YES
33	IFNG	IFNG	IFNG	6322	0.029	0.56	YES
34	PSMB6	PSMB6	PSMB6	6329	0.029	0.56	YES
35	PSMB2	PSMB2	PSMB2	6872	0.017	0.54	NO
36	PSMA7	PSMA7	PSMA7	7461	0.0041	0.51	NO
37	PSMA2	PSMA2	PSMA2	7554	0.0021	0.5	NO
38	PSMF1	PSMF1	PSMF1	8465	-0.018	0.46	NO
39	PSMB8	PSMB8	PSMB8	8609	-0.021	0.45	NO
40	PSMD7	PSMD7	PSMD7	8689	-0.023	0.46	NO
41	PSMD8	PSMD8	PSMD8	8968	-0.029	0.45	NO
42	PSMB10	PSMB10	PSMB10	9282	-0.037	0.44	NO
43	PSMC2	PSMC2	PSMC2	9757	-0.049	0.43	NO
44	SHFM1	SHFM1	SHFM1	10522	-0.068	0.41	NO

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

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

genes ES table in pathway: KEGG BASE EXCISION REPAIR

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	E2F2	E2F2	E2F2	135	0.52	0.072	YES
2	CDT1	CDT1	CDT1	150	0.51	0.15	YES
3	CDC6	CDC6	CDC6	1019	0.27	0.14	YES
4	MCM6	MCM6	MCM6	1046	0.26	0.18	YES
5	MCM2	MCM2	MCM2	1182	0.25	0.21	YES
6	MCM5	MCM5	MCM5	1270	0.24	0.24	YES
7	PSME4	PSME4	PSME4	1376	0.22	0.27	YES
8	RPS27A	RPS27A	RPS27A	1532	0.21	0.29	YES
9	MCM7	MCM7	MCM7	1634	0.2	0.32	YES
10	PSMD4	PSMD4	PSMD4	1650	0.2	0.34	YES
11	GMNN	GMNN	GMNN	1794	0.19	0.36	YES
12	PSMB9	PSMB9	PSMB9	1983	0.18	0.38	YES
13	PSMD13	PSMD13	PSMD13	2328	0.16	0.38	YES
14	PSMC3	PSMC3	PSMC3	2489	0.15	0.4	YES
15	PSMD1	PSMD1	PSMD1	2660	0.14	0.41	YES
16	MCM4	MCM4	MCM4	2694	0.14	0.43	YES
17	PSMA8	PSMA8	PSMA8	2734	0.14	0.45	YES
18	PSMB4	PSMB4	PSMB4	2757	0.13	0.47	YES
19	PSMD14	PSMD14	PSMD14	2916	0.13	0.48	YES
20	MCM3	MCM3	MCM3	3110	0.12	0.48	YES
21	PSMC1	PSMC1	PSMC1	3248	0.12	0.49	YES
22	PSMC5	PSMC5	PSMC5	3270	0.11	0.51	YES
23	E2F1	E2F1	E2F1	3398	0.11	0.52	YES
24	PSMA4	PSMA4	PSMA4	3457	0.11	0.53	YES
25	PSME2	PSME2	PSME2	3463	0.11	0.55	YES
26	PSMD11	PSMD11	PSMD11	3532	0.1	0.56	YES
27	PSMA1	PSMA1	PSMA1	3842	0.095	0.56	YES
28	PSMB5	PSMB5	PSMB5	3913	0.092	0.57	YES
29	PSMB3	PSMB3	PSMB3	4061	0.088	0.57	YES
30	MCM8	MCM8	MCM8	4123	0.087	0.58	YES
31	PSMA5	PSMA5	PSMA5	4206	0.084	0.59	YES
32	PSMD2	PSMD2	PSMD2	4300	0.081	0.6	YES
33	UBA52	UBA52	UBA52	4612	0.072	0.59	NO
34	PSMD12	PSMD12	PSMD12	4875	0.065	0.59	NO
35	PSMB7	PSMB7	PSMB7	5071	0.06	0.58	NO
36	PSMA6	PSMA6	PSMA6	5425	0.052	0.57	NO
37	PSMC6	PSMC6	PSMC6	5427	0.052	0.58	NO
38	PSMB1	PSMB1	PSMB1	5759	0.043	0.57	NO
39	PSMA3	PSMA3	PSMA3	5824	0.041	0.57	NO
40	PSMD3	PSMD3	PSMD3	6039	0.036	0.56	NO
41	PSMC4	PSMC4	PSMC4	6156	0.034	0.56	NO
42	PSMD6	PSMD6	PSMD6	6170	0.033	0.57	NO
43	PSME1	PSME1	PSME1	6256	0.031	0.57	NO
44	PSMB6	PSMB6	PSMB6	6329	0.029	0.57	NO
45	PSMB2	PSMB2	PSMB2	6872	0.017	0.54	NO
46	PSMA7	PSMA7	PSMA7	7461	0.0041	0.51	NO
47	PSMA2	PSMA2	PSMA2	7554	0.0021	0.5	NO
48	PSMD9	PSMD9	PSMD9	7828	-0.0041	0.49	NO
49	PSMF1	PSMF1	PSMF1	8465	-0.018	0.45	NO
50	PSMB8	PSMB8	PSMB8	8609	-0.021	0.45	NO
51	PSMD7	PSMD7	PSMD7	8689	-0.023	0.45	NO
52	PSMD8	PSMD8	PSMD8	8968	-0.029	0.44	NO
53	PSMB10	PSMB10	PSMB10	9282	-0.037	0.42	NO
54	PSMC2	PSMC2	PSMC2	9757	-0.049	0.4	NO
55	PSMD5	PSMD5	PSMD5	10267	-0.062	0.38	NO
56	E2F3	E2F3	E2F3	10696	-0.072	0.37	NO
57	PSMD10	PSMD10	PSMD10	13784	-0.17	0.22	NO

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

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

genes ES table in pathway: KEGG CELL CYCLE

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	CDT1	CDT1	CDT1	150	0.51	0.071	YES
2	CCNA2	CCNA2	CCNA2	505	0.36	0.11	YES
3	CDC6	CDC6	CDC6	1019	0.27	0.12	YES
4	MCM6	MCM6	MCM6	1046	0.26	0.16	YES
5	MCM2	MCM2	MCM2	1182	0.25	0.19	YES
6	MCM5	MCM5	MCM5	1270	0.24	0.22	YES
7	PSME4	PSME4	PSME4	1376	0.22	0.25	YES
8	RPS27A	RPS27A	RPS27A	1532	0.21	0.28	YES
9	MCM7	MCM7	MCM7	1634	0.2	0.3	YES
10	PSMD4	PSMD4	PSMD4	1650	0.2	0.33	YES
11	PSMB9	PSMB9	PSMB9	1983	0.18	0.34	YES
12	PSMD13	PSMD13	PSMD13	2328	0.16	0.35	YES
13	PSMC3	PSMC3	PSMC3	2489	0.15	0.36	YES
14	PSMD1	PSMD1	PSMD1	2660	0.14	0.37	YES
15	MCM4	MCM4	MCM4	2694	0.14	0.39	YES
16	PSMA8	PSMA8	PSMA8	2734	0.14	0.41	YES
17	PSMB4	PSMB4	PSMB4	2757	0.13	0.43	YES
18	PSMD14	PSMD14	PSMD14	2916	0.13	0.44	YES
19	MCM3	MCM3	MCM3	3110	0.12	0.45	YES
20	PSMC1	PSMC1	PSMC1	3248	0.12	0.46	YES
21	PSMC5	PSMC5	PSMC5	3270	0.11	0.48	YES
22	PSMA4	PSMA4	PSMA4	3457	0.11	0.48	YES
23	PSME2	PSME2	PSME2	3463	0.11	0.5	YES
24	PSMD11	PSMD11	PSMD11	3532	0.1	0.51	YES
25	PSMA1	PSMA1	PSMA1	3842	0.095	0.51	YES
26	PSMB5	PSMB5	PSMB5	3913	0.092	0.52	YES
27	PSMB3	PSMB3	PSMB3	4061	0.088	0.53	YES
28	MCM8	MCM8	MCM8	4123	0.087	0.54	YES
29	PSMA5	PSMA5	PSMA5	4206	0.084	0.55	YES
30	PSMD2	PSMD2	PSMD2	4300	0.081	0.55	YES
31	UBA52	UBA52	UBA52	4612	0.072	0.55	NO
32	PSMD12	PSMD12	PSMD12	4875	0.065	0.54	NO
33	PSMB7	PSMB7	PSMB7	5071	0.06	0.54	NO
34	CDK2	CDK2	CDK2	5385	0.053	0.53	NO
35	PSMA6	PSMA6	PSMA6	5425	0.052	0.54	NO
36	PSMC6	PSMC6	PSMC6	5427	0.052	0.55	NO
37	PSMB1	PSMB1	PSMB1	5759	0.043	0.53	NO
38	PSMA3	PSMA3	PSMA3	5824	0.041	0.54	NO
39	PSMD3	PSMD3	PSMD3	6039	0.036	0.53	NO
40	PSMC4	PSMC4	PSMC4	6156	0.034	0.53	NO
41	PSMD6	PSMD6	PSMD6	6170	0.033	0.53	NO
42	PSME1	PSME1	PSME1	6256	0.031	0.53	NO
43	CDKN1A	CDKN1A	CDKN1A	6292	0.03	0.54	NO
44	PSMB6	PSMB6	PSMB6	6329	0.029	0.54	NO
45	PSMB2	PSMB2	PSMB2	6872	0.017	0.51	NO
46	PSMA7	PSMA7	PSMA7	7461	0.0041	0.48	NO
47	PSMA2	PSMA2	PSMA2	7554	0.0021	0.47	NO
48	PSMD9	PSMD9	PSMD9	7828	-0.0041	0.46	NO
49	PSMF1	PSMF1	PSMF1	8465	-0.018	0.42	NO
50	PSMB8	PSMB8	PSMB8	8609	-0.021	0.42	NO
51	PSMD7	PSMD7	PSMD7	8689	-0.023	0.42	NO
52	PSMD8	PSMD8	PSMD8	8968	-0.029	0.41	NO
53	PSMB10	PSMB10	PSMB10	9282	-0.037	0.4	NO
54	CCNA1	CCNA1	CCNA1	9427	-0.041	0.4	NO
55	PSMC2	PSMC2	PSMC2	9757	-0.049	0.38	NO
56	PSMD5	PSMD5	PSMD5	10267	-0.062	0.36	NO
57	CDKN1B	CDKN1B	CDKN1B	10878	-0.077	0.34	NO
58	RB1	RB1	RB1	12214	-0.11	0.28	NO
59	PSMD10	PSMD10	PSMD10	13784	-0.17	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: KEGG CELL CYCLE.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL 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: PID MYC ACTIVPATHWAY

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	CDC20	CDC20	CDC20	83	0.57	0.077	YES
2	UBE2C	UBE2C	UBE2C	247	0.45	0.13	YES
3	BUB1B	BUB1B	BUB1B	351	0.4	0.18	YES
4	CDK1	CDK1	CDK1	365	0.4	0.24	YES
5	PTTG1	PTTG1	PTTG1	470	0.37	0.29	YES
6	PSME4	PSME4	PSME4	1376	0.22	0.27	YES
7	RPS27A	RPS27A	RPS27A	1532	0.21	0.29	YES
8	CCNB1	CCNB1	CCNB1	1566	0.21	0.32	YES
9	PSMD4	PSMD4	PSMD4	1650	0.2	0.34	YES
10	PSMB9	PSMB9	PSMB9	1983	0.18	0.35	YES
11	PSMD13	PSMD13	PSMD13	2328	0.16	0.35	YES
12	PSMC3	PSMC3	PSMC3	2489	0.15	0.36	YES
13	PSMD1	PSMD1	PSMD1	2660	0.14	0.37	YES
14	PSMA8	PSMA8	PSMA8	2734	0.14	0.39	YES
15	PSMB4	PSMB4	PSMB4	2757	0.13	0.4	YES
16	PSMD14	PSMD14	PSMD14	2916	0.13	0.41	YES
17	ANAPC1	ANAPC1	ANAPC1	3099	0.12	0.42	YES
18	PSMC1	PSMC1	PSMC1	3248	0.12	0.43	YES
19	PSMC5	PSMC5	PSMC5	3270	0.11	0.44	YES
20	BUB3	BUB3	BUB3	3379	0.11	0.45	YES
21	ANAPC11	ANAPC11	ANAPC11	3430	0.11	0.47	YES
22	PSMA4	PSMA4	PSMA4	3457	0.11	0.48	YES
23	PSME2	PSME2	PSME2	3463	0.11	0.5	YES
24	PSMD11	PSMD11	PSMD11	3532	0.1	0.51	YES
25	CDC26	CDC26	CDC26	3732	0.099	0.51	YES
26	PSMA1	PSMA1	PSMA1	3842	0.095	0.52	YES
27	PSMB5	PSMB5	PSMB5	3913	0.092	0.52	YES
28	PSMB3	PSMB3	PSMB3	4061	0.088	0.53	YES
29	MAD2L1	MAD2L1	MAD2L1	4086	0.088	0.54	YES
30	PSMA5	PSMA5	PSMA5	4206	0.084	0.55	YES
31	PSMD2	PSMD2	PSMD2	4300	0.081	0.55	YES
32	UBA52	UBA52	UBA52	4612	0.072	0.55	NO
33	PSMD12	PSMD12	PSMD12	4875	0.065	0.54	NO
34	PSMB7	PSMB7	PSMB7	5071	0.06	0.54	NO
35	PSMA6	PSMA6	PSMA6	5425	0.052	0.52	NO
36	PSMC6	PSMC6	PSMC6	5427	0.052	0.53	NO
37	PSMB1	PSMB1	PSMB1	5759	0.043	0.52	NO
38	PSMA3	PSMA3	PSMA3	5824	0.041	0.52	NO
39	PSMD3	PSMD3	PSMD3	6039	0.036	0.51	NO
40	PSMC4	PSMC4	PSMC4	6156	0.034	0.51	NO
41	PSMD6	PSMD6	PSMD6	6170	0.033	0.52	NO
42	UBE2E1	UBE2E1	UBE2E1	6224	0.032	0.52	NO
43	PSME1	PSME1	PSME1	6256	0.031	0.52	NO
44	PSMB6	PSMB6	PSMB6	6329	0.029	0.52	NO
45	CDC16	CDC16	CDC16	6455	0.026	0.52	NO
46	ANAPC7	ANAPC7	ANAPC7	6541	0.024	0.52	NO
47	PSMB2	PSMB2	PSMB2	6872	0.017	0.5	NO
48	PSMA7	PSMA7	PSMA7	7461	0.0041	0.47	NO
49	CDC27	CDC27	CDC27	7522	0.0029	0.46	NO
50	PSMA2	PSMA2	PSMA2	7554	0.0021	0.46	NO
51	PSMD9	PSMD9	PSMD9	7828	-0.0041	0.45	NO
52	ANAPC2	ANAPC2	ANAPC2	8293	-0.014	0.42	NO
53	PSMF1	PSMF1	PSMF1	8465	-0.018	0.42	NO
54	ANAPC5	ANAPC5	ANAPC5	8543	-0.02	0.42	NO
55	PSMB8	PSMB8	PSMB8	8609	-0.021	0.41	NO
56	PSMD7	PSMD7	PSMD7	8689	-0.023	0.41	NO
57	ANAPC10	ANAPC10	ANAPC10	8944	-0.028	0.4	NO
58	PSMD8	PSMD8	PSMD8	8968	-0.029	0.41	NO
59	PSMB10	PSMB10	PSMB10	9282	-0.037	0.39	NO
60	PSMC2	PSMC2	PSMC2	9757	-0.049	0.37	NO
61	PSMD5	PSMD5	PSMD5	10267	-0.062	0.35	NO
62	UBE2D1	UBE2D1	UBE2D1	11121	-0.083	0.32	NO
63	CDC23	CDC23	CDC23	11409	-0.091	0.31	NO
64	ANAPC4	ANAPC4	ANAPC4	12869	-0.14	0.25	NO
65	PSMD10	PSMD10	PSMD10	13784	-0.17	0.22	NO

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

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

genes ES table in pathway: PID ILK 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	CDC20	CDC20	CDC20	83	0.57	0.038	YES
2	CDC25A	CDC25A	CDC25A	109	0.54	0.077	YES
3	CDC45	CDC45	CDC45	130	0.52	0.12	YES
4	UBE2C	UBE2C	UBE2C	247	0.45	0.14	YES
5	CCNB2	CCNB2	CCNB2	298	0.42	0.17	YES
6	MCM10	MCM10	MCM10	327	0.41	0.2	YES
7	BUB1B	BUB1B	BUB1B	351	0.4	0.23	YES
8	CDK1	CDK1	CDK1	365	0.4	0.26	YES
9	CDC7	CDC7	CDC7	469	0.37	0.28	YES
10	CDC25C	CDC25C	CDC25C	751	0.31	0.29	YES
11	CCNE2	CCNE2	CCNE2	779	0.3	0.31	YES
12	CHEK2	CHEK2	CHEK2	920	0.28	0.32	YES
13	CHEK1	CHEK1	CHEK1	959	0.28	0.34	YES
14	CDC6	CDC6	CDC6	1019	0.27	0.36	YES
15	MCM6	MCM6	MCM6	1046	0.26	0.37	YES
16	MCM2	MCM2	MCM2	1182	0.25	0.38	YES
17	MCM5	MCM5	MCM5	1270	0.24	0.4	YES
18	DBF4	DBF4	DBF4	1326	0.23	0.41	YES
19	PSME4	PSME4	PSME4	1376	0.22	0.42	YES
20	RPS27A	RPS27A	RPS27A	1532	0.21	0.43	YES
21	CCNB1	CCNB1	CCNB1	1566	0.21	0.44	YES
22	MCM7	MCM7	MCM7	1634	0.2	0.46	YES
23	PSMD4	PSMD4	PSMD4	1650	0.2	0.47	YES
24	PSMB9	PSMB9	PSMB9	1983	0.18	0.46	YES
25	RAD9A	RAD9A	RAD9A	2242	0.16	0.46	YES
26	PSMD13	PSMD13	PSMD13	2328	0.16	0.47	YES
27	PSMC3	PSMC3	PSMC3	2489	0.15	0.47	YES
28	PSMD1	PSMD1	PSMD1	2660	0.14	0.47	YES
29	MCM4	MCM4	MCM4	2694	0.14	0.48	YES
30	PSMA8	PSMA8	PSMA8	2734	0.14	0.49	YES
31	PSMB4	PSMB4	PSMB4	2757	0.13	0.5	YES
32	RFC4	RFC4	RFC4	2777	0.13	0.5	YES
33	PSMD14	PSMD14	PSMD14	2916	0.13	0.51	YES
34	ANAPC1	ANAPC1	ANAPC1	3099	0.12	0.5	YES
35	MCM3	MCM3	MCM3	3110	0.12	0.51	YES
36	MAD1L1	MAD1L1	MAD1L1	3189	0.12	0.52	YES
37	RFWD2	RFWD2	RFWD2	3192	0.12	0.53	YES
38	WEE1	WEE1	WEE1	3241	0.12	0.53	YES
39	PSMC1	PSMC1	PSMC1	3248	0.12	0.54	YES
40	PSMC5	PSMC5	PSMC5	3270	0.11	0.55	YES
41	RFC2	RFC2	RFC2	3302	0.11	0.56	YES
42	BUB3	BUB3	BUB3	3379	0.11	0.56	YES
43	ANAPC11	ANAPC11	ANAPC11	3430	0.11	0.56	YES
44	PSMA4	PSMA4	PSMA4	3457	0.11	0.57	YES
45	PSME2	PSME2	PSME2	3463	0.11	0.58	YES
46	PSMD11	PSMD11	PSMD11	3532	0.1	0.58	YES
47	CDC26	CDC26	CDC26	3732	0.099	0.58	YES
48	PSMA1	PSMA1	PSMA1	3842	0.095	0.58	YES
49	RAD1	RAD1	RAD1	3901	0.093	0.58	YES
50	PSMB5	PSMB5	PSMB5	3913	0.092	0.59	YES
51	PSMB3	PSMB3	PSMB3	4061	0.088	0.59	YES
52	MAD2L1	MAD2L1	MAD2L1	4086	0.088	0.59	YES
53	MCM8	MCM8	MCM8	4123	0.087	0.6	YES
54	PSMA5	PSMA5	PSMA5	4206	0.084	0.6	YES
55	PSMD2	PSMD2	PSMD2	4300	0.081	0.6	YES
56	UBA52	UBA52	UBA52	4612	0.072	0.59	NO
57	RFC3	RFC3	RFC3	4738	0.069	0.58	NO
58	PSMD12	PSMD12	PSMD12	4875	0.065	0.58	NO
59	PSMB7	PSMB7	PSMB7	5071	0.06	0.57	NO
60	CDK2	CDK2	CDK2	5385	0.053	0.56	NO
61	PSMA6	PSMA6	PSMA6	5425	0.052	0.56	NO
62	PSMC6	PSMC6	PSMC6	5427	0.052	0.57	NO
63	ATRIP	ATRIP	ATRIP	5715	0.044	0.55	NO
64	PSMB1	PSMB1	PSMB1	5759	0.043	0.55	NO
65	PSMA3	PSMA3	PSMA3	5824	0.041	0.55	NO
66	PSMD3	PSMD3	PSMD3	6039	0.036	0.54	NO
67	PSMC4	PSMC4	PSMC4	6156	0.034	0.54	NO
68	PSMD6	PSMD6	PSMD6	6170	0.033	0.54	NO
69	CCNE1	CCNE1	CCNE1	6213	0.032	0.54	NO
70	UBE2E1	UBE2E1	UBE2E1	6224	0.032	0.54	NO
71	PSME1	PSME1	PSME1	6256	0.031	0.55	NO
72	CDKN1A	CDKN1A	CDKN1A	6292	0.03	0.55	NO
73	PSMB6	PSMB6	PSMB6	6329	0.029	0.55	NO
74	MDM2	MDM2	MDM2	6349	0.029	0.55	NO
75	CDC16	CDC16	CDC16	6455	0.026	0.54	NO
76	ANAPC7	ANAPC7	ANAPC7	6541	0.024	0.54	NO
77	RFC5	RFC5	RFC5	6738	0.02	0.53	NO
78	PSMB2	PSMB2	PSMB2	6872	0.017	0.52	NO
79	TP53	TP53	TP53	7338	0.0068	0.5	NO
80	PSMA7	PSMA7	PSMA7	7461	0.0041	0.49	NO
81	CDC27	CDC27	CDC27	7522	0.0029	0.49	NO
82	PSMA2	PSMA2	PSMA2	7554	0.0021	0.49	NO
83	PSMD9	PSMD9	PSMD9	7828	-0.0041	0.47	NO
84	RPA3	RPA3	RPA3	8119	-0.011	0.46	NO
85	ANAPC2	ANAPC2	ANAPC2	8293	-0.014	0.45	NO
86	RPA1	RPA1	RPA1	8295	-0.014	0.45	NO
87	PSMF1	PSMF1	PSMF1	8465	-0.018	0.44	NO
88	ATM	ATM	ATM	8503	-0.019	0.44	NO
89	ANAPC5	ANAPC5	ANAPC5	8543	-0.02	0.44	NO
90	PSMB8	PSMB8	PSMB8	8609	-0.021	0.44	NO
91	PSMD7	PSMD7	PSMD7	8689	-0.023	0.43	NO
92	RPA2	RPA2	RPA2	8717	-0.023	0.43	NO
93	ANAPC10	ANAPC10	ANAPC10	8944	-0.028	0.42	NO
94	PSMD8	PSMD8	PSMD8	8968	-0.029	0.42	NO
95	PSMB10	PSMB10	PSMB10	9282	-0.037	0.41	NO
96	ATR	ATR	ATR	9603	-0.045	0.39	NO
97	PSMC2	PSMC2	PSMC2	9757	-0.049	0.39	NO
98	PSMD5	PSMD5	PSMD5	10267	-0.062	0.36	NO
99	HUS1	HUS1	HUS1	10675	-0.072	0.35	NO
100	CDKN1B	CDKN1B	CDKN1B	10878	-0.077	0.34	NO
101	UBE2D1	UBE2D1	UBE2D1	11121	-0.083	0.33	NO
102	CDC23	CDC23	CDC23	11409	-0.091	0.32	NO
103	ANAPC4	ANAPC4	ANAPC4	12869	-0.14	0.25	NO
104	RAD17	RAD17	RAD17	13568	-0.16	0.22	NO
105	PSMD10	PSMD10	PSMD10	13784	-0.17	0.22	NO

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

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

genes ES table in pathway: PID ATM 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	CDC25A	CDC25A	CDC25A	109	0.54	0.11	YES
2	CHEK2	CHEK2	CHEK2	920	0.28	0.12	YES
3	CHEK1	CHEK1	CHEK1	959	0.28	0.18	YES
4	PSME4	PSME4	PSME4	1376	0.22	0.2	YES
5	RPS27A	RPS27A	RPS27A	1532	0.21	0.24	YES
6	PSMD4	PSMD4	PSMD4	1650	0.2	0.27	YES
7	PSMB9	PSMB9	PSMB9	1983	0.18	0.29	YES
8	PSMD13	PSMD13	PSMD13	2328	0.16	0.3	YES
9	PSMC3	PSMC3	PSMC3	2489	0.15	0.33	YES
10	PSMD1	PSMD1	PSMD1	2660	0.14	0.35	YES
11	PSMA8	PSMA8	PSMA8	2734	0.14	0.37	YES
12	PSMB4	PSMB4	PSMB4	2757	0.13	0.4	YES
13	PSMD14	PSMD14	PSMD14	2916	0.13	0.42	YES
14	PSMC1	PSMC1	PSMC1	3248	0.12	0.42	YES
15	PSMC5	PSMC5	PSMC5	3270	0.11	0.44	YES
16	PSMA4	PSMA4	PSMA4	3457	0.11	0.46	YES
17	PSME2	PSME2	PSME2	3463	0.11	0.48	YES
18	PSMD11	PSMD11	PSMD11	3532	0.1	0.5	YES
19	PSMA1	PSMA1	PSMA1	3842	0.095	0.5	YES
20	PSMB5	PSMB5	PSMB5	3913	0.092	0.51	YES
21	PSMB3	PSMB3	PSMB3	4061	0.088	0.52	YES
22	PSMA5	PSMA5	PSMA5	4206	0.084	0.53	YES
23	PSMD2	PSMD2	PSMD2	4300	0.081	0.55	YES
24	UBA52	UBA52	UBA52	4612	0.072	0.54	YES
25	PSMD12	PSMD12	PSMD12	4875	0.065	0.54	YES
26	PSMB7	PSMB7	PSMB7	5071	0.06	0.54	YES
27	PSMA6	PSMA6	PSMA6	5425	0.052	0.54	YES
28	PSMC6	PSMC6	PSMC6	5427	0.052	0.55	YES
29	PSMB1	PSMB1	PSMB1	5759	0.043	0.54	YES
30	PSMA3	PSMA3	PSMA3	5824	0.041	0.54	YES
31	PSMD3	PSMD3	PSMD3	6039	0.036	0.54	YES
32	PSMC4	PSMC4	PSMC4	6156	0.034	0.54	YES
33	PSMD6	PSMD6	PSMD6	6170	0.033	0.54	YES
34	PSME1	PSME1	PSME1	6256	0.031	0.55	YES
35	PSMB6	PSMB6	PSMB6	6329	0.029	0.55	YES
36	PSMB2	PSMB2	PSMB2	6872	0.017	0.52	NO
37	PSMA7	PSMA7	PSMA7	7461	0.0041	0.49	NO
38	PSMA2	PSMA2	PSMA2	7554	0.0021	0.48	NO
39	PSMD9	PSMD9	PSMD9	7828	-0.0041	0.47	NO
40	PSMF1	PSMF1	PSMF1	8465	-0.018	0.44	NO
41	ATM	ATM	ATM	8503	-0.019	0.44	NO
42	PSMB8	PSMB8	PSMB8	8609	-0.021	0.44	NO
43	PSMD7	PSMD7	PSMD7	8689	-0.023	0.44	NO
44	PSMD8	PSMD8	PSMD8	8968	-0.029	0.43	NO
45	PSMB10	PSMB10	PSMB10	9282	-0.037	0.42	NO
46	PSMC2	PSMC2	PSMC2	9757	-0.049	0.4	NO
47	PSMD5	PSMD5	PSMD5	10267	-0.062	0.39	NO
48	PSMD10	PSMD10	PSMD10	13784	-0.17	0.22	NO

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

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

genes ES table in pathway: PID MYC 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	RPL21	RPL21	RPL21	446	0.38	-0.0087	YES
2	MAPK11	MAPK11	MAPK11	1025	0.27	-0.03	YES
3	EXOSC8	EXOSC8	EXOSC8	1030	0.27	-0.018	YES
4	WDR77	WDR77	WDR77	1232	0.24	-0.019	YES
5	PSME4	PSME4	PSME4	1376	0.22	-0.018	YES
6	RQCD1	RQCD1	RQCD1	1468	0.21	-0.013	YES
7	RPSAP9	RPSAP9	RPSAP9	1471	0.21	-0.0037	YES
8	RPS27A	RPS27A	RPS27A	1532	0.21	0.0021	YES
9	SNRPG	SNRPG	SNRPG	1608	0.2	0.0068	YES
10	EIF4A3	EIF4A3	EIF4A3	1627	0.2	0.015	YES
11	PSMD4	PSMD4	PSMD4	1650	0.2	0.022	YES
12	RPS7	RPS7	RPS7	1694	0.2	0.029	YES
13	RPL37A	RPL37A	RPL37A	1726	0.19	0.035	YES
14	RPL27A	RPL27A	RPL27A	1760	0.19	0.042	YES
15	SNRPD1	SNRPD1	SNRPD1	1835	0.18	0.046	YES
16	RPL27	RPL27	RPL27	1891	0.18	0.051	YES
17	DCPS	DCPS	DCPS	1964	0.18	0.054	YES
18	PSMB9	PSMB9	PSMB9	1983	0.18	0.061	YES
19	ANP32A	ANP32A	ANP32A	2040	0.17	0.066	YES
20	RPL23A	RPL23A	RPL23A	2104	0.17	0.07	YES
21	RPS3	RPS3	RPS3	2214	0.16	0.071	YES
22	RPL31	RPL31	RPL31	2312	0.16	0.072	YES
23	PSMD13	PSMD13	PSMD13	2328	0.16	0.078	YES
24	RPS25	RPS25	RPS25	2368	0.15	0.082	YES
25	RPS18	RPS18	RPS18	2411	0.15	0.087	YES
26	GEMIN6	GEMIN6	GEMIN6	2415	0.15	0.093	YES
27	RPL17	RPL17	RPL17	2456	0.15	0.098	YES
28	PSMC3	PSMC3	PSMC3	2489	0.15	0.1	YES
29	SNRPE	SNRPE	SNRPE	2531	0.14	0.11	YES
30	RPLP2	RPLP2	RPLP2	2540	0.14	0.11	YES
31	EXOSC4	EXOSC4	EXOSC4	2570	0.14	0.12	YES
32	RBM8A	RBM8A	RBM8A	2650	0.14	0.12	YES
33	PSMD1	PSMD1	PSMD1	2660	0.14	0.12	YES
34	NUP35	NUP35	NUP35	2697	0.14	0.13	YES
35	RPS29	RPS29	RPS29	2715	0.14	0.13	YES
36	PSMA8	PSMA8	PSMA8	2734	0.14	0.14	YES
37	PSMB4	PSMB4	PSMB4	2757	0.13	0.14	YES
38	EXOSC1	EXOSC1	EXOSC1	2798	0.13	0.15	YES
39	PRMT5	PRMT5	PRMT5	2825	0.13	0.15	YES
40	RPSA	RPSA	RPSA	2849	0.13	0.16	YES
41	RPS13	RPS13	RPS13	2859	0.13	0.16	YES
42	RPS19	RPS19	RPS19	2868	0.13	0.17	YES
43	PSMD14	PSMD14	PSMD14	2916	0.13	0.17	YES
44	HSPA1B	HSPA1B	HSPA1B	2922	0.13	0.17	YES
45	RPS12	RPS12	RPS12	2925	0.13	0.18	YES
46	RPS24	RPS24	RPS24	2954	0.13	0.18	YES
47	C2orf29	C2orf29	C2orf29	2969	0.12	0.19	YES
48	RPL36	RPL36	RPL36	2974	0.12	0.19	YES
49	RPLP1	RPLP1	RPLP1	2990	0.12	0.2	YES
50	RPS17	RPS17	RPS17	3027	0.12	0.2	YES
51	EXOSC2	EXOSC2	EXOSC2	3037	0.12	0.21	YES
52	NUP88	NUP88	NUP88	3051	0.12	0.21	YES
53	SNRPD3	SNRPD3	SNRPD3	3125	0.12	0.21	YES
54	PATL1	PATL1	PATL1	3147	0.12	0.22	YES
55	SMG5	SMG5	SMG5	3178	0.12	0.22	YES
56	FAU	FAU	FAU	3183	0.12	0.22	YES
57	EDC3	EDC3	EDC3	3229	0.12	0.23	YES
58	NUP85	NUP85	NUP85	3242	0.12	0.23	YES
59	RPL29	RPL29	RPL29	3247	0.12	0.24	YES
60	PSMC1	PSMC1	PSMC1	3248	0.12	0.24	YES
61	PSMC5	PSMC5	PSMC5	3270	0.11	0.25	YES
62	RPL22	RPL22	RPL22	3374	0.11	0.24	YES
63	NUP188	NUP188	NUP188	3380	0.11	0.25	YES
64	RPS8	RPS8	RPS8	3415	0.11	0.25	YES
65	RPL18A	RPL18A	RPL18A	3454	0.11	0.26	YES
66	PSMA4	PSMA4	PSMA4	3457	0.11	0.26	YES
67	RPL4	RPL4	RPL4	3459	0.11	0.26	YES
68	PSME2	PSME2	PSME2	3463	0.11	0.27	YES
69	SNUPN	SNUPN	SNUPN	3476	0.11	0.27	YES
70	PSMD11	PSMD11	PSMD11	3532	0.1	0.27	YES
71	RPL35	RPL35	RPL35	3533	0.1	0.28	YES
72	RPS10	RPS10	RPS10	3548	0.1	0.28	YES
73	RPL32	RPL32	RPL32	3653	0.1	0.28	YES
74	RPS9	RPS9	RPS9	3655	0.1	0.29	YES
75	EXOSC6	EXOSC6	EXOSC6	3683	0.1	0.29	YES
76	RPLP0	RPLP0	RPLP0	3724	0.099	0.29	YES
77	LSM2	LSM2	LSM2	3773	0.097	0.29	YES
78	EIF4A1	EIF4A1	EIF4A1	3792	0.097	0.3	YES
79	RPL11	RPL11	RPL11	3795	0.096	0.3	YES
80	PSMA1	PSMA1	PSMA1	3842	0.095	0.3	YES
81	RPS2	RPS2	RPS2	3875	0.094	0.3	YES
82	PSMB5	PSMB5	PSMB5	3913	0.092	0.31	YES
83	LSM4	LSM4	LSM4	3964	0.091	0.31	YES
84	LSM3	LSM3	LSM3	3968	0.091	0.31	YES
85	NUP50	NUP50	NUP50	3982	0.091	0.31	YES
86	RPL14	RPL14	RPL14	3983	0.091	0.32	YES
87	RPL35A	RPL35A	RPL35A	3987	0.091	0.32	YES
88	PSMB3	PSMB3	PSMB3	4061	0.088	0.32	YES
89	LSM1	LSM1	LSM1	4077	0.088	0.32	YES
90	RPL13A	RPL13A	RPL13A	4140	0.086	0.32	YES
91	EXOSC7	EXOSC7	EXOSC7	4167	0.085	0.33	YES
92	RPS27	RPS27	RPS27	4182	0.085	0.33	YES
93	CLNS1A	CLNS1A	CLNS1A	4204	0.084	0.33	YES
94	PSMA5	PSMA5	PSMA5	4206	0.084	0.34	YES
95	RPL23	RPL23	RPL23	4220	0.084	0.34	YES
96	RPL8	RPL8	RPL8	4290	0.082	0.34	YES
97	RPL30	RPL30	RPL30	4293	0.082	0.34	YES
98	PSMD2	PSMD2	PSMD2	4300	0.081	0.35	YES
99	RPS20	RPS20	RPS20	4315	0.081	0.35	YES
100	RPS16	RPS16	RPS16	4332	0.08	0.35	YES
101	RPL12	RPL12	RPL12	4379	0.079	0.35	YES
102	CNOT3	CNOT3	CNOT3	4406	0.078	0.35	YES
103	RPL26	RPL26	RPL26	4544	0.074	0.35	YES
104	RPL19	RPL19	RPL19	4565	0.073	0.35	YES
105	NUP210	NUP210	NUP210	4583	0.073	0.35	YES
106	RPS11	RPS11	RPS11	4597	0.072	0.36	YES
107	UBA52	UBA52	UBA52	4612	0.072	0.36	YES
108	RPL5	RPL5	RPL5	4634	0.072	0.36	YES
109	RPL24	RPL24	RPL24	4668	0.071	0.36	YES
110	MAPK14	MAPK14	MAPK14	4723	0.069	0.36	YES
111	CASC3	CASC3	CASC3	4730	0.069	0.36	YES
112	RPS26	RPS26	RPS26	4736	0.069	0.37	YES
113	TPR	TPR	TPR	4802	0.067	0.37	YES
114	RPL3	RPL3	RPL3	4831	0.066	0.37	YES
115	RPS15	RPS15	RPS15	4845	0.066	0.37	YES
116	RPL28	RPL28	RPL28	4862	0.066	0.37	YES
117	PSMD12	PSMD12	PSMD12	4875	0.065	0.37	YES
118	DCP2	DCP2	DCP2	4889	0.065	0.38	YES
119	NUP62	NUP62	NUP62	4891	0.065	0.38	YES
120	RPL10A	RPL10A	RPL10A	4930	0.064	0.38	YES
121	RAE1	RAE1	RAE1	4957	0.063	0.38	YES
122	RPL38	RPL38	RPL38	4979	0.062	0.38	YES
123	RPL7	RPL7	RPL7	5008	0.062	0.38	YES
124	PSMB7	PSMB7	PSMB7	5071	0.06	0.38	YES
125	NCBP1	NCBP1	NCBP1	5107	0.06	0.38	YES
126	RPL7A	RPL7A	RPL7A	5145	0.059	0.38	YES
127	RPL18	RPL18	RPL18	5360	0.054	0.37	NO
128	PSMA6	PSMA6	PSMA6	5425	0.052	0.37	NO
129	PSMC6	PSMC6	PSMC6	5427	0.052	0.38	NO
130	SEH1L	SEH1L	SEH1L	5433	0.052	0.38	NO
131	RPS3A	RPS3A	RPS3A	5454	0.051	0.38	NO
132	RPS15A	RPS15A	RPS15A	5465	0.051	0.38	NO
133	NUP133	NUP133	NUP133	5515	0.05	0.38	NO
134	EXOSC3	EXOSC3	EXOSC3	5588	0.047	0.38	NO
135	RPL13	RPL13	RPL13	5603	0.047	0.38	NO
136	RPL15	RPL15	RPL15	5625	0.046	0.38	NO
137	NCBP2	NCBP2	NCBP2	5683	0.045	0.38	NO
138	RPS5	RPS5	RPS5	5701	0.044	0.38	NO
139	PSMB1	PSMB1	PSMB1	5759	0.043	0.38	NO
140	RPL41	RPL41	RPL41	5783	0.042	0.38	NO
141	HNRNPD	HNRNPD	HNRNPD	5795	0.042	0.38	NO
142	GEMIN7	GEMIN7	GEMIN7	5803	0.042	0.38	NO
143	RANBP2	RANBP2	RANBP2	5811	0.041	0.38	NO
144	PSMA3	PSMA3	PSMA3	5824	0.041	0.38	NO
145	CNOT10	CNOT10	CNOT10	5886	0.039	0.38	NO
146	KHSRP	KHSRP	KHSRP	5895	0.039	0.38	NO
147	XPO1	XPO1	XPO1	5922	0.039	0.38	NO
148	NUPL1	NUPL1	NUPL1	5964	0.038	0.38	NO
149	PSMD3	PSMD3	PSMD3	6039	0.036	0.38	NO
150	ZFP36	ZFP36	ZFP36	6057	0.036	0.38	NO
151	PSMC4	PSMC4	PSMC4	6156	0.034	0.38	NO
152	PSMD6	PSMD6	PSMD6	6170	0.033	0.38	NO
153	PSME1	PSME1	PSME1	6256	0.031	0.37	NO
154	PSMB6	PSMB6	PSMB6	6329	0.029	0.37	NO
155	EDC4	EDC4	EDC4	6352	0.029	0.37	NO
156	RPS21	RPS21	RPS21	6403	0.027	0.37	NO
157	SNRPD2	SNRPD2	SNRPD2	6436	0.026	0.37	NO
158	CNOT2	CNOT2	CNOT2	6457	0.026	0.37	NO
159	PABPC1	PABPC1	PABPC1	6532	0.024	0.37	NO
160	NUP93	NUP93	NUP93	6574	0.024	0.36	NO
161	RPS6	RPS6	RPS6	6663	0.022	0.36	NO
162	MAGOH	MAGOH	MAGOH	6730	0.02	0.36	NO
163	SNRPB	SNRPB	SNRPB	6803	0.018	0.35	NO
164	RPL37	RPL37	RPL37	6817	0.018	0.35	NO
165	SNRPF	SNRPF	SNRPF	6855	0.017	0.35	NO
166	PSMB2	PSMB2	PSMB2	6872	0.017	0.35	NO
167	PPP2R2A	PPP2R2A	PPP2R2A	6902	0.016	0.35	NO
168	GEMIN4	GEMIN4	GEMIN4	7042	0.013	0.34	NO
169	RPL39	RPL39	RPL39	7139	0.011	0.34	NO
170	RPL6	RPL6	RPL6	7234	0.0091	0.34	NO
171	LSM6	LSM6	LSM6	7273	0.0082	0.33	NO
172	SMG7	SMG7	SMG7	7347	0.0066	0.33	NO
173	HSPA8	HSPA8	HSPA8	7364	0.0062	0.33	NO
174	YWHAZ	YWHAZ	YWHAZ	7370	0.0061	0.33	NO
175	DDX20	DDX20	DDX20	7397	0.0055	0.33	NO
176	LSM5	LSM5	LSM5	7406	0.0051	0.33	NO
177	PSMA7	PSMA7	PSMA7	7461	0.0041	0.32	NO
178	PPP2R1A	PPP2R1A	PPP2R1A	7485	0.0035	0.32	NO
179	UPF2	UPF2	UPF2	7545	0.0024	0.32	NO
180	PSMA2	PSMA2	PSMA2	7554	0.0021	0.32	NO
181	EXOSC9	EXOSC9	EXOSC9	7576	0.0017	0.32	NO
182	NUP214	NUP214	NUP214	7608	0.001	0.32	NO
183	RPS4X	RPS4X	RPS4X	7716	-0.0016	0.31	NO
184	PSMD9	PSMD9	PSMD9	7828	-0.0041	0.3	NO
185	DCP1A	DCP1A	DCP1A	7847	-0.0045	0.3	NO
186	CNOT7	CNOT7	CNOT7	7882	-0.0053	0.3	NO
187	NUP43	NUP43	NUP43	7925	-0.0061	0.3	NO
188	EXOSC5	EXOSC5	EXOSC5	7999	-0.0077	0.3	NO
189	ELAVL1	ELAVL1	ELAVL1	8034	-0.0084	0.29	NO
190	NUP107	NUP107	NUP107	8036	-0.0084	0.29	NO
191	RPL34	RPL34	RPL34	8102	-0.01	0.29	NO
192	MAPKAPK2	MAPKAPK2	MAPKAPK2	8202	-0.012	0.29	NO
193	RPL10	RPL10	RPL10	8258	-0.014	0.28	NO
194	EIF4G1	EIF4G1	EIF4G1	8332	-0.015	0.28	NO
195	AAAS	AAAS	AAAS	8379	-0.016	0.28	NO
196	AKT1	AKT1	AKT1	8423	-0.017	0.28	NO
197	PSMF1	PSMF1	PSMF1	8465	-0.018	0.28	NO
198	RPS14	RPS14	RPS14	8594	-0.021	0.27	NO
199	PSMB8	PSMB8	PSMB8	8609	-0.021	0.27	NO
200	SMN2	SMN2	SMN2	8679	-0.022	0.26	NO
201	PSMD7	PSMD7	PSMD7	8689	-0.023	0.27	NO
202	RPS23	RPS23	RPS23	8692	-0.023	0.27	NO
203	DIS3	DIS3	DIS3	8726	-0.024	0.27	NO
204	EIF4B	EIF4B	EIF4B	8811	-0.025	0.26	NO
205	SMG6	SMG6	SMG6	8919	-0.028	0.26	NO
206	RNPS1	RNPS1	RNPS1	8958	-0.029	0.26	NO
207	PSMD8	PSMD8	PSMD8	8968	-0.029	0.26	NO
208	PSMB10	PSMB10	PSMB10	9282	-0.037	0.24	NO
209	DDX6	DDX6	DDX6	9368	-0.039	0.24	NO
210	EIF4A2	EIF4A2	EIF4A2	9543	-0.044	0.23	NO
211	PRKCD	PRKCD	PRKCD	9550	-0.044	0.23	NO
212	PSMC2	PSMC2	PSMC2	9757	-0.049	0.22	NO
213	YWHAB	YWHAB	YWHAB	9778	-0.05	0.22	NO
214	NUP54	NUP54	NUP54	9811	-0.05	0.22	NO
215	CNOT6	CNOT6	CNOT6	10018	-0.055	0.21	NO
216	TNKS1BP1	TNKS1BP1	TNKS1BP1	10172	-0.059	0.21	NO
217	PSMD5	PSMD5	PSMD5	10267	-0.062	0.2	NO
218	UPF3A	UPF3A	UPF3A	10334	-0.063	0.2	NO
219	XRN1	XRN1	XRN1	10457	-0.066	0.2	NO
220	POM121	POM121	POM121	10639	-0.071	0.19	NO
221	RPS28	RPS28	RPS28	10647	-0.071	0.2	NO
222	RPL26L1	RPL26L1	RPL26L1	10697	-0.072	0.2	NO
223	NUP153	NUP153	NUP153	10758	-0.074	0.2	NO
224	TGS1	TGS1	TGS1	10781	-0.074	0.2	NO
225	ETF1	ETF1	ETF1	10817	-0.075	0.2	NO
226	PPP2CA	PPP2CA	PPP2CA	10835	-0.076	0.2	NO
227	NUP37	NUP37	NUP37	10866	-0.077	0.2	NO
228	PAIP1	PAIP1	PAIP1	10885	-0.077	0.21	NO
229	PARN	PARN	PARN	11123	-0.083	0.2	NO
230	TNFSF13	TNFSF13	TNFSF13	11141	-0.084	0.2	NO
231	CNOT8	CNOT8	CNOT8	11152	-0.084	0.2	NO
232	NUP155	NUP155	NUP155	11198	-0.085	0.2	NO
233	NUP205	NUP205	NUP205	11211	-0.085	0.21	NO
234	RPS4Y1	RPS4Y1	RPS4Y1	11213	-0.085	0.21	NO
235	NUPL2	NUPL2	NUPL2	11340	-0.089	0.21	NO
236	SMN1	SMN1	SMN1	11361	-0.089	0.21	NO
237	ZFP36L1	ZFP36L1	ZFP36L1	11494	-0.093	0.21	NO
238	SMG1	SMG1	SMG1	11622	-0.097	0.2	NO
239	UPF3B	UPF3B	UPF3B	12251	-0.12	0.17	NO
240	EIF4E	EIF4E	EIF4E	12357	-0.12	0.17	NO
241	TNPO1	TNPO1	TNPO1	13032	-0.14	0.14	NO
242	GEMIN5	GEMIN5	GEMIN5	13105	-0.14	0.14	NO
243	PSMD10	PSMD10	PSMD10	13784	-0.17	0.11	NO
244	DCP1B	DCP1B	DCP1B	13910	-0.18	0.11	NO
245	RPL9	RPL9	RPL9	13932	-0.18	0.12	NO
246	CNOT4	CNOT4	CNOT4	14389	-0.2	0.1	NO
247	HSPB1	HSPB1	HSPB1	14686	-0.21	0.092	NO
248	PHAX	PHAX	PHAX	15156	-0.24	0.076	NO
249	RPL36A	RPL36A	RPL36A	15622	-0.28	0.062	NO
250	GSPT2	GSPT2	GSPT2	15678	-0.28	0.071	NO
251	PRKCA	PRKCA	PRKCA	16794	-0.42	0.026	NO
252	FAM153A	FAM153A	FAM153A	17452	-0.6	0.015	NO

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

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

genes ES table in pathway: PID FOXM1PATHWAY

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	POLR2D	POLR2D	POLR2D	1127	0.25	0.013	YES
2	SF3B4	SF3B4	SF3B4	1350	0.23	0.07	YES
3	POLR2G	POLR2G	POLR2G	1368	0.22	0.14	YES
4	SNRPG	SNRPG	SNRPG	1608	0.2	0.19	YES
5	SNRPD1	SNRPD1	SNRPD1	1835	0.18	0.23	YES
6	POLR2L	POLR2L	POLR2L	1914	0.18	0.28	YES
7	POLR2H	POLR2H	POLR2H	2527	0.14	0.29	YES
8	SNRPE	SNRPE	SNRPE	2531	0.14	0.33	YES
9	SF3B14	SF3B14	SF3B14	2551	0.14	0.38	YES
10	GTF2F2	GTF2F2	GTF2F2	3003	0.12	0.39	YES
11	SNRPD3	SNRPD3	SNRPD3	3125	0.12	0.42	YES
12	SNRNP40	SNRNP40	SNRNP40	3196	0.12	0.45	YES
13	SF3B2	SF3B2	SF3B2	3549	0.1	0.46	YES
14	LSM2	LSM2	LSM2	3773	0.097	0.48	YES
15	NHP2L1	NHP2L1	NHP2L1	4024	0.089	0.49	YES
16	TXNL4A	TXNL4A	TXNL4A	4466	0.076	0.49	YES
17	POLR2F	POLR2F	POLR2F	4520	0.074	0.51	YES
18	SF3B5	SF3B5	SF3B5	4834	0.066	0.51	YES
19	SF3B1	SF3B1	SF3B1	4906	0.064	0.53	YES
20	NCBP1	NCBP1	NCBP1	5107	0.06	0.53	YES
21	NCBP2	NCBP2	NCBP2	5683	0.045	0.51	NO
22	EFTUD2	EFTUD2	EFTUD2	5693	0.044	0.53	NO
23	SNRNP200	SNRNP200	SNRNP200	6090	0.035	0.52	NO
24	SNRPD2	SNRPD2	SNRPD2	6436	0.026	0.5	NO
25	POLR2E	POLR2E	POLR2E	6494	0.025	0.51	NO
26	SNRPB	SNRPB	SNRPB	6803	0.018	0.5	NO
27	SNRPF	SNRPF	SNRPF	6855	0.017	0.5	NO
28	POLR2A	POLR2A	POLR2A	7066	0.013	0.49	NO
29	GTF2F1	GTF2F1	GTF2F1	8299	-0.014	0.43	NO
30	POLR2K	POLR2K	POLR2K	8522	-0.019	0.42	NO
31	SF3B3	SF3B3	SF3B3	8548	-0.02	0.42	NO
32	PRPF8	PRPF8	PRPF8	8649	-0.022	0.42	NO
33	POLR2J	POLR2J	POLR2J	8809	-0.025	0.42	NO
34	POLR2I	POLR2I	POLR2I	8916	-0.028	0.43	NO
35	PRPF6	PRPF6	PRPF6	8984	-0.029	0.43	NO
36	DDX23	DDX23	DDX23	9246	-0.036	0.43	NO
37	POLR2B	POLR2B	POLR2B	10993	-0.08	0.35	NO
38	POLR2C	POLR2C	POLR2C	11422	-0.091	0.36	NO

Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FOXM1PATHWAY.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: PID FOXM1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG WNT SIGNALING PATHWAY	145	genes.ES.table	0.4	1.5	0.031	0.95	0.99	0.37	0.27	0.28	0.69	0.32
KEGG HEDGEHOG SIGNALING PATHWAY	54	genes.ES.table	0.56	1.5	0.013	1	0.96	0.44	0.17	0.37	0.73	0.38
KEGG TASTE TRANSDUCTION	38	genes.ES.table	0.57	1.5	0.013	1	0.98	0.4	0.099	0.36	0.77	0.4
KEGG BASAL CELL CARCINOMA	54	genes.ES.table	0.6	1.6	0.01	0.93	0.91	0.46	0.17	0.39	0.54	0.29
BIOCARTA NO1 PATHWAY	28	genes.ES.table	0.53	1.5	0.056	1	0.99	0.29	0.15	0.24	0.83	0.42
BIOCARTA CHREBP2 PATHWAY	41	genes.ES.table	0.4	1.5	0.091	1	0.99	0.12	0.1	0.11	0.73	0.35
BIOCARTA WNT PATHWAY	26	genes.ES.table	0.48	1.7	0.036	1	0.84	0.58	0.38	0.36	0.52	0.3
ST WNT BETA CATENIN PATHWAY	31	genes.ES.table	0.58	1.7	0.028	1	0.84	0.42	0.24	0.32	0.64	0.36
PID REELINPATHWAY	28	genes.ES.table	0.48	1.6	0.029	1	0.94	0.21	0.12	0.19	0.7	0.37
PID NECTIN PATHWAY	30	genes.ES.table	0.42	1.5	0.07	1	0.99	0.3	0.23	0.23	0.75	0.37

genes ES table in pathway: KEGG WNT SIGNALING 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	SSPO	SSPO	SSPO	41	0.79	0.12	YES
2	GLI1	GLI1	GLI1	235	0.57	0.2	YES
3	SHH	SHH	SHH	352	0.52	0.28	YES
4	SMO	SMO	SMO	505	0.46	0.34	YES
5	GNAO1	GNAO1	GNAO1	927	0.38	0.38	YES
6	GNAZ	GNAZ	GNAZ	1027	0.36	0.43	YES
7	PTCH1	PTCH1	PTCH1	1572	0.29	0.44	YES
8	GLI3	GLI3	GLI3	1726	0.28	0.48	YES
9	KIF3A	KIF3A	KIF3A	2413	0.22	0.48	YES
10	GLI2	GLI2	GLI2	2584	0.21	0.5	YES
11	FBXW11	FBXW11	FBXW11	4698	0.11	0.4	NO
12	CSNK1G3	CSNK1G3	CSNK1G3	4724	0.11	0.41	NO
13	SIN3B	SIN3B	SIN3B	5523	0.089	0.38	NO
14	SUFU	SUFU	SUFU	5603	0.087	0.39	NO
15	GNAI1	GNAI1	GNAI1	5614	0.086	0.4	NO
16	CSNK1A1	CSNK1A1	CSNK1A1	6021	0.076	0.39	NO
17	MTSS1	MTSS1	MTSS1	6065	0.076	0.4	NO
18	CREBBP	CREBBP	CREBBP	6359	0.069	0.4	NO
19	CSNK1E	CSNK1E	CSNK1E	6413	0.068	0.41	NO
20	GSK3B	GSK3B	GSK3B	6428	0.068	0.42	NO
21	PRKACA	PRKACA	PRKACA	6541	0.065	0.42	NO
22	LGALS3	LGALS3	LGALS3	7181	0.052	0.39	NO
23	IFT88	IFT88	IFT88	7667	0.042	0.37	NO
24	CSNK1G2	CSNK1G2	CSNK1G2	8115	0.033	0.35	NO
25	AKT1	AKT1	AKT1	8174	0.032	0.35	NO
26	GNAI3	GNAI3	GNAI3	8750	0.022	0.32	NO
27	CSNK1G1	CSNK1G1	CSNK1G1	9052	0.016	0.31	NO
28	CSNK1D	CSNK1D	CSNK1D	9298	0.011	0.3	NO
29	XPO1	XPO1	XPO1	9360	0.0095	0.3	NO
30	GNAI2	GNAI2	GNAI2	9433	0.0083	0.29	NO
31	PIAS1	PIAS1	PIAS1	9486	0.0074	0.29	NO
32	SAP30	SAP30	SAP30	9673	0.0037	0.28	NO
33	SIN3A	SIN3A	SIN3A	9878	0.00029	0.27	NO
34	RBBP4	RBBP4	RBBP4	9926	-0.00053	0.27	NO
35	MAP2K1	MAP2K1	MAP2K1	9967	-0.0014	0.26	NO
36	SPOP	SPOP	SPOP	11179	-0.024	0.2	NO
37	STK36	STK36	STK36	11558	-0.032	0.18	NO
38	HDAC2	HDAC2	HDAC2	11626	-0.033	0.18	NO
39	GNG2	GNG2	GNG2	11840	-0.038	0.18	NO
40	SAP18	SAP18	SAP18	11974	-0.04	0.18	NO
41	RBBP7	RBBP7	RBBP7	13133	-0.067	0.12	NO
42	PRKCD	PRKCD	PRKCD	13362	-0.073	0.12	NO
43	GNB1	GNB1	GNB1	13491	-0.077	0.13	NO
44	IFT172	IFT172	IFT172	13504	-0.077	0.14	NO
45	HDAC1	HDAC1	HDAC1	14125	-0.096	0.12	NO
46	RAB23	RAB23	RAB23	14821	-0.12	0.098	NO
47	FOXA2	FOXA2	FOXA2	15085	-0.14	0.1	NO
48	ARRB2	ARRB2	ARRB2	16737	-0.28	0.056	NO

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

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

genes ES table in pathway: KEGG HEDGEHOG SIGNALING PATHWAY

Table 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	RORB	RORB	RORB	10	0.97	0.018	YES
2	ZNF114	ZNF114	ZNF114	37	0.82	0.032	YES
3	TBX5	TBX5	TBX5	278	0.55	0.029	YES
4	ZFP37	ZFP37	ZFP37	476	0.48	0.027	YES
5	ZNF483	ZNF483	ZNF483	572	0.45	0.03	YES
6	ZNF215	ZNF215	ZNF215	582	0.44	0.038	YES
7	ZNF426	ZNF426	ZNF426	640	0.43	0.043	YES
8	CCNT1	CCNT1	CCNT1	847	0.39	0.038	YES
9	ZNF418	ZNF418	ZNF418	941	0.37	0.04	YES
10	ZNF485	ZNF485	ZNF485	953	0.37	0.046	YES
11	AR	AR	AR	972	0.37	0.052	YES
12	ZNF354C	ZNF354C	ZNF354C	973	0.37	0.06	YES
13	ZNF442	ZNF442	ZNF442	1054	0.36	0.062	YES
14	ZNF540	ZNF540	ZNF540	1096	0.35	0.066	YES
15	ZNF582	ZNF582	ZNF582	1110	0.35	0.072	YES
16	ZNF221	ZNF221	ZNF221	1118	0.35	0.078	YES
17	MAML3	MAML3	MAML3	1165	0.34	0.082	YES
18	NR3C2	NR3C2	NR3C2	1200	0.34	0.087	YES
19	ZIK1	ZIK1	ZIK1	1219	0.33	0.092	YES
20	ZNF454	ZNF454	ZNF454	1229	0.33	0.098	YES
21	ZNF382	ZNF382	ZNF382	1254	0.33	0.1	YES
22	ZNF441	ZNF441	ZNF441	1275	0.33	0.11	YES
23	ZNF658	ZNF658	ZNF658	1298	0.32	0.11	YES
24	NR2E1	NR2E1	NR2E1	1368	0.32	0.12	YES
25	PGR	PGR	PGR	1370	0.32	0.12	YES
26	ZNF30	ZNF30	ZNF30	1406	0.31	0.12	YES
27	ZIM2	ZIM2	ZIM2	1425	0.31	0.13	YES
28	ZFP2	ZFP2	ZFP2	1438	0.31	0.14	YES
29	NR4A3	NR4A3	NR4A3	1523	0.3	0.14	YES
30	ZNF596	ZNF596	ZNF596	1551	0.29	0.14	YES
31	ZNF551	ZNF551	ZNF551	1557	0.29	0.14	YES
32	ZNF417	ZNF417	ZNF417	1576	0.29	0.15	YES
33	ZNF625	ZNF625	ZNF625	1613	0.28	0.15	YES
34	ZNF324	ZNF324	ZNF324	1630	0.28	0.16	YES
35	ZNF273	ZNF273	ZNF273	1675	0.28	0.16	YES
36	ZNF157	ZNF157	ZNF157	1701	0.28	0.16	YES
37	TEAD2	TEAD2	TEAD2	1711	0.28	0.17	YES
38	ZNF17	ZNF17	ZNF17	1801	0.27	0.17	YES
39	ZNF565	ZNF565	ZNF565	1815	0.26	0.17	YES
40	ZNF471	ZNF471	ZNF471	1822	0.26	0.18	YES
41	ZNF333	ZNF333	ZNF333	1830	0.26	0.18	YES
42	RORA	RORA	RORA	1851	0.26	0.19	YES
43	ZNF585B	ZNF585B	ZNF585B	1856	0.26	0.19	YES
44	ZNF443	ZNF443	ZNF443	1866	0.26	0.2	YES
45	RARG	RARG	RARG	1868	0.26	0.2	YES
46	ZNF560	ZNF560	ZNF560	1884	0.26	0.2	YES
47	ZNF530	ZNF530	ZNF530	1905	0.26	0.21	YES
48	ZNF14	ZNF14	ZNF14	1915	0.26	0.21	YES
49	ZNF354B	ZNF354B	ZNF354B	1924	0.26	0.22	YES
50	ZNF25	ZNF25	ZNF25	1934	0.26	0.22	YES
51	ZNF222	ZNF222	ZNF222	1974	0.25	0.22	YES
52	ZNF595	ZNF595	ZNF595	1999	0.25	0.23	YES
53	ZNF33B	ZNF33B	ZNF33B	2015	0.25	0.23	YES
54	ZNF627	ZNF627	ZNF627	2023	0.25	0.24	YES
55	ZNF432	ZNF432	ZNF432	2039	0.25	0.24	YES
56	ZNF37A	ZNF37A	ZNF37A	2043	0.25	0.24	YES
57	ZNF547	ZNF547	ZNF547	2057	0.25	0.25	YES
58	TBL1X	TBL1X	TBL1X	2065	0.25	0.25	YES
59	ZNF230	ZNF230	ZNF230	2080	0.24	0.26	YES
60	ZFP28	ZFP28	ZFP28	2086	0.24	0.26	YES
61	ZNF425	ZNF425	ZNF425	2114	0.24	0.26	YES
62	ZNF566	ZNF566	ZNF566	2121	0.24	0.27	YES
63	NCOA2	NCOA2	NCOA2	2136	0.24	0.27	YES
64	ZNF510	ZNF510	ZNF510	2154	0.24	0.28	YES
65	ZNF570	ZNF570	ZNF570	2177	0.24	0.28	YES
66	ZNF616	ZNF616	ZNF616	2184	0.24	0.28	YES
67	ZNF420	ZNF420	ZNF420	2213	0.24	0.29	YES
68	ZNF556	ZNF556	ZNF556	2247	0.23	0.29	YES
69	ZNF304	ZNF304	ZNF304	2254	0.23	0.29	YES
70	ZNF331	ZNF331	ZNF331	2257	0.23	0.3	YES
71	ZNF416	ZNF416	ZNF416	2262	0.23	0.3	YES
72	ZNF211	ZNF211	ZNF211	2265	0.23	0.31	YES
73	ZNF354A	ZNF354A	ZNF354A	2297	0.23	0.31	YES
74	ZNF440	ZNF440	ZNF440	2349	0.22	0.31	YES
75	ZNF419	ZNF419	ZNF419	2377	0.22	0.31	YES
76	ZNF460	ZNF460	ZNF460	2386	0.22	0.32	YES
77	ZNF192	ZNF192	ZNF192	2402	0.22	0.32	YES
78	ZNF773	ZNF773	ZNF773	2441	0.22	0.32	YES
79	ZNF383	ZNF383	ZNF383	2444	0.22	0.33	YES
80	TEAD3	TEAD3	TEAD3	2448	0.22	0.33	YES
81	THRB	THRB	THRB	2483	0.21	0.33	YES
82	ZNF189	ZNF189	ZNF189	2508	0.21	0.33	YES
83	ZNF558	ZNF558	ZNF558	2515	0.21	0.34	YES
84	ZNF180	ZNF180	ZNF180	2523	0.21	0.34	YES
85	ZKSCAN1	ZKSCAN1	ZKSCAN1	2526	0.21	0.35	YES
86	NR1D2	NR1D2	NR1D2	2545	0.21	0.35	YES
87	ZNF138	ZNF138	ZNF138	2557	0.21	0.35	YES
88	ZNF587	ZNF587	ZNF587	2572	0.21	0.36	YES
89	ZNF234	ZNF234	ZNF234	2588	0.21	0.36	YES
90	ZNF225	ZNF225	ZNF225	2622	0.2	0.36	YES
91	ZNF175	ZNF175	ZNF175	2628	0.2	0.36	YES
92	ESRRB	ESRRB	ESRRB	2655	0.2	0.37	YES
93	ZNF169	ZNF169	ZNF169	2665	0.2	0.37	YES
94	ZNF473	ZNF473	ZNF473	2666	0.2	0.37	YES
95	ZNF274	ZNF274	ZNF274	2676	0.2	0.38	YES
96	ZNF254	ZNF254	ZNF254	2721	0.2	0.38	YES
97	ZNF583	ZNF583	ZNF583	2745	0.2	0.38	YES
98	ZNF484	ZNF484	ZNF484	2782	0.19	0.38	YES
99	ZNF248	ZNF248	ZNF248	2803	0.19	0.38	YES
100	ZNF557	ZNF557	ZNF557	2844	0.19	0.39	YES
101	ZNF223	ZNF223	ZNF223	2847	0.19	0.39	YES
102	ZNF256	ZNF256	ZNF256	2853	0.19	0.39	YES
103	ZNF45	ZNF45	ZNF45	2861	0.19	0.4	YES
104	ESRRG	ESRRG	ESRRG	2868	0.19	0.4	YES
105	ZNF92	ZNF92	ZNF92	2906	0.19	0.4	YES
106	ZFP112	ZFP112	ZFP112	2920	0.19	0.4	YES
107	ZNF33A	ZNF33A	ZNF33A	2921	0.19	0.41	YES
108	ZNF264	ZNF264	ZNF264	2930	0.18	0.41	YES
109	ZNF334	ZNF334	ZNF334	2958	0.18	0.41	YES
110	ZNF430	ZNF430	ZNF430	2977	0.18	0.42	YES
111	ZNF607	ZNF607	ZNF607	2997	0.18	0.42	YES
112	ZNF10	ZNF10	ZNF10	3002	0.18	0.42	YES
113	ZNF544	ZNF544	ZNF544	3013	0.18	0.42	YES
114	HNF4G	HNF4G	HNF4G	3033	0.18	0.43	YES
115	ZNF496	ZNF496	ZNF496	3063	0.18	0.43	YES
116	ZNF615	ZNF615	ZNF615	3083	0.18	0.43	YES
117	ZFP1	ZFP1	ZFP1	3084	0.18	0.43	YES
118	ZNF606	ZNF606	ZNF606	3097	0.18	0.44	YES
119	ZNF235	ZNF235	ZNF235	3113	0.18	0.44	YES
120	ZNF569	ZNF569	ZNF569	3133	0.17	0.44	YES
121	ZNF614	ZNF614	ZNF614	3140	0.17	0.44	YES
122	MED27	MED27	MED27	3148	0.17	0.45	YES
123	ZNF584	ZNF584	ZNF584	3185	0.17	0.45	YES
124	ZNF227	ZNF227	ZNF227	3192	0.17	0.45	YES
125	ZNF155	ZNF155	ZNF155	3194	0.17	0.45	YES
126	ZNF214	ZNF214	ZNF214	3201	0.17	0.46	YES
127	ZNF224	ZNF224	ZNF224	3284	0.17	0.46	YES
128	ZNF564	ZNF564	ZNF564	3290	0.17	0.46	YES
129	ZNF561	ZNF561	ZNF561	3292	0.17	0.46	YES
130	ZNF559	ZNF559	ZNF559	3317	0.16	0.46	YES
131	ZNF567	ZNF567	ZNF567	3329	0.16	0.46	YES
132	ZNF20	ZNF20	ZNF20	3334	0.16	0.47	YES
133	ZNF546	ZNF546	ZNF546	3341	0.16	0.47	YES
134	ZNF226	ZNF226	ZNF226	3346	0.16	0.47	YES
135	MYC	MYC	MYC	3359	0.16	0.48	YES
136	RXRA	RXRA	RXRA	3387	0.16	0.48	YES
137	ZNF543	ZNF543	ZNF543	3451	0.16	0.48	YES
138	ZNF611	ZNF611	ZNF611	3504	0.16	0.48	YES
139	WWTR1	WWTR1	WWTR1	3507	0.16	0.48	YES
140	ZNF141	ZNF141	ZNF141	3526	0.16	0.48	YES
141	SKIL	SKIL	SKIL	3637	0.15	0.48	YES
142	ZNF599	ZNF599	ZNF599	3651	0.15	0.48	YES
143	ZNF287	ZNF287	ZNF287	3715	0.15	0.48	YES
144	ZNF498	ZNF498	ZNF498	3761	0.15	0.48	YES
145	PPM1A	PPM1A	PPM1A	3805	0.14	0.48	YES
146	ZNF613	ZNF613	ZNF613	3815	0.14	0.48	YES
147	ZNF43	ZNF43	ZNF43	3845	0.14	0.48	YES
148	ZNF320	ZNF320	ZNF320	3865	0.14	0.48	YES
149	SMAD7	SMAD7	SMAD7	3873	0.14	0.49	YES
150	MAML1	MAML1	MAML1	3897	0.14	0.49	YES
151	ZNF136	ZNF136	ZNF136	3916	0.14	0.49	YES
152	ZNF655	ZNF655	ZNF655	3924	0.14	0.49	YES
153	ZNF285	ZNF285	ZNF285	3933	0.14	0.5	YES
154	ZNF548	ZNF548	ZNF548	3934	0.14	0.5	YES
155	ZNF446	ZNF446	ZNF446	3979	0.14	0.5	YES
156	ZNF250	ZNF250	ZNF250	4071	0.13	0.5	YES
157	ZNF490	ZNF490	ZNF490	4085	0.13	0.5	YES
158	ZNF641	ZNF641	ZNF641	4090	0.13	0.5	YES
159	ZNF708	ZNF708	ZNF708	4114	0.13	0.5	YES
160	ZNF154	ZNF154	ZNF154	4124	0.13	0.5	YES
161	SMAD3	SMAD3	SMAD3	4130	0.13	0.5	YES
162	ZNF350	ZNF350	ZNF350	4162	0.13	0.5	YES
163	ZNF266	ZNF266	ZNF266	4168	0.13	0.51	YES
164	ZNF514	ZNF514	ZNF514	4182	0.13	0.51	YES
165	ZNF577	ZNF577	ZNF577	4279	0.13	0.51	YES
166	ZNF212	ZNF212	ZNF212	4281	0.12	0.51	YES
167	CDKN2B	CDKN2B	CDKN2B	4302	0.12	0.51	YES
168	TFDP1	TFDP1	TFDP1	4332	0.12	0.51	YES
169	SMURF2	SMURF2	SMURF2	4422	0.12	0.51	YES
170	NR1D1	NR1D1	NR1D1	4527	0.12	0.5	YES
171	NR1H2	NR1H2	NR1H2	4572	0.12	0.5	YES
172	MED26	MED26	MED26	4576	0.12	0.51	YES
173	ZNF610	ZNF610	ZNF610	4582	0.12	0.51	YES
174	ZNF317	ZNF317	ZNF317	4590	0.12	0.51	YES
175	ZNF140	ZNF140	ZNF140	4649	0.11	0.51	YES
176	ZNF529	ZNF529	ZNF529	4654	0.11	0.51	YES
177	ZNF347	ZNF347	ZNF347	4664	0.11	0.51	YES
178	NOTCH2	NOTCH2	NOTCH2	4746	0.11	0.51	YES
179	ZFP90	ZFP90	ZFP90	4767	0.11	0.51	YES
180	ZNF506	ZNF506	ZNF506	4805	0.11	0.51	YES
181	ZNF585A	ZNF585A	ZNF585A	4832	0.11	0.51	YES
182	ZNF12	ZNF12	ZNF12	4879	0.11	0.51	YES
183	ZKSCAN5	ZKSCAN5	ZKSCAN5	4905	0.1	0.51	YES
184	CDK9	CDK9	CDK9	4924	0.1	0.51	YES
185	ZNF600	ZNF600	ZNF600	4944	0.1	0.51	YES
186	NR2F1	NR2F1	NR2F1	4986	0.1	0.51	NO
187	SMARCD3	SMARCD3	SMARCD3	5031	0.1	0.51	NO
188	ZNF282	ZNF282	ZNF282	5144	0.1	0.51	NO
189	PPARA	PPARA	PPARA	5166	0.099	0.51	NO
190	THRA	THRA	THRA	5189	0.098	0.51	NO
191	VDR	VDR	VDR	5228	0.097	0.51	NO
192	ZNF167	ZNF167	ZNF167	5306	0.095	0.5	NO
193	ZNF563	ZNF563	ZNF563	5308	0.095	0.51	NO
194	NR5A1	NR5A1	NR5A1	5385	0.093	0.5	NO
195	ZNF398	ZNF398	ZNF398	5410	0.092	0.5	NO
196	ZNF23	ZNF23	ZNF23	5503	0.09	0.5	NO
197	ZNF434	ZNF434	ZNF434	5589	0.087	0.5	NO
198	ZNF343	ZNF343	ZNF343	5619	0.086	0.5	NO
199	E2F5	E2F5	E2F5	5635	0.086	0.5	NO
200	ZNF3	ZNF3	ZNF3	5682	0.084	0.5	NO
201	TGIF2	TGIF2	TGIF2	5734	0.083	0.5	NO
202	MED6	MED6	MED6	5775	0.082	0.5	NO
203	MED12	MED12	MED12	5779	0.082	0.5	NO
204	TRIM28	TRIM28	TRIM28	5812	0.082	0.5	NO
205	NR1I2	NR1I2	NR1I2	5817	0.082	0.5	NO
206	ZNF500	ZNF500	ZNF500	5845	0.081	0.5	NO
207	ZNF620	ZNF620	ZNF620	5924	0.079	0.5	NO
208	NR2C2AP	NR2C2AP	NR2C2AP	5935	0.079	0.5	NO
209	ZNF101	ZNF101	ZNF101	5939	0.079	0.5	NO
210	ZNF571	ZNF571	ZNF571	5973	0.078	0.5	NO
211	ZNF197	ZNF197	ZNF197	6003	0.077	0.5	NO
212	ZNF619	ZNF619	ZNF619	6005	0.077	0.5	NO
213	ZNF519	ZNF519	ZNF519	6022	0.076	0.5	NO
214	ZNF433	ZNF433	ZNF433	6034	0.076	0.5	NO
215	UBE2D1	UBE2D1	UBE2D1	6158	0.073	0.49	NO
216	ZNF263	ZNF263	ZNF263	6226	0.072	0.49	NO
217	CREBBP	CREBBP	CREBBP	6359	0.069	0.48	NO
218	ZNF394	ZNF394	ZNF394	6397	0.068	0.48	NO
219	MED10	MED10	MED10	6418	0.068	0.48	NO
220	ZNF480	ZNF480	ZNF480	6431	0.068	0.48	NO
221	ZNF597	ZNF597	ZNF597	6515	0.066	0.48	NO
222	ZNF337	ZNF337	ZNF337	6600	0.064	0.48	NO
223	TBL1XR1	TBL1XR1	TBL1XR1	6607	0.064	0.48	NO
224	ZNF200	ZNF200	ZNF200	6639	0.063	0.48	NO
225	ZNF286A	ZNF286A	ZNF286A	6658	0.063	0.48	NO
226	ZNF19	ZNF19	ZNF19	6686	0.062	0.48	NO
227	ZNF621	ZNF621	ZNF621	6707	0.062	0.48	NO
228	ZNF589	ZNF589	ZNF589	6723	0.061	0.48	NO
229	ZNF555	ZNF555	ZNF555	6859	0.058	0.47	NO
230	TRIM33	TRIM33	TRIM33	6875	0.058	0.47	NO
231	NR4A1	NR4A1	NR4A1	7104	0.054	0.46	NO
232	ZNF205	ZNF205	ZNF205	7169	0.052	0.46	NO
233	NR3C1	NR3C1	NR3C1	7182	0.052	0.46	NO
234	SP1	SP1	SP1	7467	0.046	0.44	NO
235	ZNF493	ZNF493	ZNF493	7512	0.045	0.44	NO
236	CCNT2	CCNT2	CCNT2	7569	0.044	0.44	NO
237	CDK8	CDK8	CDK8	7595	0.043	0.44	NO
238	SMAD2	SMAD2	SMAD2	7626	0.043	0.44	NO
239	NR5A2	NR5A2	NR5A2	7677	0.042	0.43	NO
240	ZNF202	ZNF202	ZNF202	7767	0.04	0.43	NO
241	NCOR2	NCOR2	NCOR2	7975	0.036	0.42	NO
242	YAP1	YAP1	YAP1	8051	0.034	0.42	NO
243	SNW1	SNW1	SNW1	8065	0.034	0.42	NO
244	TEAD1	TEAD1	TEAD1	8082	0.034	0.42	NO
245	ZNF605	ZNF605	ZNF605	8087	0.034	0.42	NO
246	ESR2	ESR2	ESR2	8119	0.033	0.41	NO
247	UBE2D3	UBE2D3	UBE2D3	8177	0.032	0.41	NO
248	ZNF184	ZNF184	ZNF184	8191	0.032	0.41	NO
249	ZNF28	ZNF28	ZNF28	8276	0.03	0.41	NO
250	RXRG	RXRG	RXRG	8365	0.029	0.4	NO
251	ZNF468	ZNF468	ZNF468	8681	0.023	0.38	NO
252	ZNF311	ZNF311	ZNF311	8722	0.022	0.38	NO
253	UBA52	UBA52	UBA52	8799	0.021	0.38	NO
254	ZNF100	ZNF100	ZNF100	8839	0.02	0.38	NO
255	ZNF160	ZNF160	ZNF160	8876	0.019	0.38	NO
256	NCOA6	NCOA6	NCOA6	9113	0.014	0.36	NO
257	ZNF208	ZNF208	ZNF208	9136	0.014	0.36	NO
258	ZNF528	ZNF528	ZNF528	9189	0.013	0.36	NO
259	ZNF439	ZNF439	ZNF439	9190	0.013	0.36	NO
260	NCOR1	NCOR1	NCOR1	9278	0.011	0.35	NO
261	ZNF552	ZNF552	ZNF552	9320	0.01	0.35	NO
262	MED31	MED31	MED31	9354	0.0097	0.35	NO
263	PRIC285	PRIC285	PRIC285	9390	0.0089	0.35	NO
264	ZNF445	ZNF445	ZNF445	9441	0.008	0.34	NO
265	NOTCH4	NOTCH4	NOTCH4	9453	0.0079	0.34	NO
266	MED7	MED7	MED7	9608	0.0048	0.34	NO
267	MED25	MED25	MED25	9642	0.0043	0.33	NO
268	NRBF2	NRBF2	NRBF2	9655	0.004	0.33	NO
269	ZNF2	ZNF2	ZNF2	9657	0.004	0.33	NO
270	ZNF436	ZNF436	ZNF436	9687	0.0035	0.33	NO
271	MEN1	MEN1	MEN1	9752	0.0026	0.33	NO
272	ZNF26	ZNF26	ZNF26	9905	-0.000059	0.32	NO
273	ZNF213	ZNF213	ZNF213	9911	-0.00018	0.32	NO
274	TGS1	TGS1	TGS1	10010	-0.0022	0.31	NO
275	ZNF431	ZNF431	ZNF431	10072	-0.0032	0.31	NO
276	SKI	SKI	SKI	10111	-0.0041	0.31	NO
277	MED14	MED14	MED14	10255	-0.0069	0.3	NO
278	ZNF18	ZNF18	ZNF18	10462	-0.011	0.29	NO
279	E2F4	E2F4	E2F4	10515	-0.012	0.29	NO
280	USP9X	USP9X	USP9X	10561	-0.012	0.28	NO
281	MED23	MED23	MED23	10635	-0.014	0.28	NO
282	NCOA1	NCOA1	NCOA1	10657	-0.014	0.28	NO
283	MED8	MED8	MED8	10682	-0.014	0.28	NO
284	MED15	MED15	MED15	11008	-0.021	0.26	NO
285	SMAD4	SMAD4	SMAD4	11033	-0.021	0.26	NO
286	ZNF517	ZNF517	ZNF517	11093	-0.022	0.26	NO
287	JUNB	JUNB	JUNB	11167	-0.024	0.25	NO
288	KAT2A	KAT2A	KAT2A	11248	-0.026	0.25	NO
289	NR6A1	NR6A1	NR6A1	11315	-0.027	0.24	NO
290	MED17	MED17	MED17	11366	-0.028	0.24	NO
291	ZNF649	ZNF649	ZNF649	11393	-0.028	0.24	NO
292	RBL1	RBL1	RBL1	11525	-0.031	0.23	NO
293	NR2F6	NR2F6	NR2F6	11621	-0.033	0.23	NO
294	MED16	MED16	MED16	11742	-0.035	0.22	NO
295	NR4A2	NR4A2	NR4A2	11996	-0.041	0.21	NO
296	RBPJ	RBPJ	RBPJ	12062	-0.042	0.21	NO
297	NCOA3	NCOA3	NCOA3	12365	-0.049	0.19	NO
298	MED4	MED4	MED4	12378	-0.049	0.19	NO
299	ZNF643	ZNF643	ZNF643	12457	-0.051	0.19	NO
300	HNF4A	HNF4A	HNF4A	12815	-0.059	0.17	NO
301	MED30	MED30	MED30	12840	-0.06	0.17	NO
302	ZNF98	ZNF98	ZNF98	12983	-0.063	0.16	NO
303	CTGF	CTGF	CTGF	13038	-0.065	0.16	NO
304	ZNF300	ZNF300	ZNF300	13055	-0.065	0.16	NO
305	MED1	MED1	MED1	13078	-0.066	0.16	NO
306	NR2E3	NR2E3	NR2E3	13138	-0.068	0.16	NO
307	RXRB	RXRB	RXRB	13278	-0.071	0.15	NO
308	MAMLD1	MAMLD1	MAMLD1	13358	-0.073	0.15	NO
309	ZKSCAN4	ZKSCAN4	ZKSCAN4	13416	-0.075	0.14	NO
310	ZKSCAN3	ZKSCAN3	ZKSCAN3	13815	-0.086	0.12	NO
311	CCNC	CCNC	CCNC	13829	-0.086	0.12	NO
312	NOTCH3	NOTCH3	NOTCH3	14004	-0.092	0.12	NO
313	HDAC1	HDAC1	HDAC1	14125	-0.096	0.11	NO
314	NRBP1	NRBP1	NRBP1	14201	-0.098	0.11	NO
315	NR1I3	NR1I3	NR1I3	14245	-0.1	0.11	NO
316	RARA	RARA	RARA	14526	-0.11	0.094	NO
317	RPS27A	RPS27A	RPS27A	14536	-0.11	0.095	NO
318	PARP1	PARP1	PARP1	14731	-0.12	0.086	NO
319	ZNF267	ZNF267	ZNF267	14774	-0.12	0.086	NO
320	ESRRA	ESRRA	ESRRA	14797	-0.12	0.087	NO
321	ESR1	ESR1	ESR1	14836	-0.12	0.087	NO
322	ZNF492	ZNF492	ZNF492	14916	-0.13	0.085	NO
323	NR0B1	NR0B1	NR0B1	15174	-0.14	0.073	NO
324	MED24	MED24	MED24	15240	-0.14	0.072	NO
325	NPPA	NPPA	NPPA	15278	-0.15	0.073	NO
326	KAT2B	KAT2B	KAT2B	15316	-0.15	0.074	NO
327	NR1H3	NR1H3	NR1H3	15401	-0.15	0.072	NO
328	ZNF415	ZNF415	ZNF415	15434	-0.16	0.073	NO
329	RUNX2	RUNX2	RUNX2	15493	-0.16	0.073	NO
330	ZNF624	ZNF624	ZNF624	15506	-0.16	0.075	NO
331	TGIF1	TGIF1	TGIF1	15560	-0.16	0.075	NO
332	PPARG	PPARG	PPARG	15567	-0.16	0.078	NO
333	SERPINE1	SERPINE1	SERPINE1	15671	-0.17	0.075	NO
334	MAML2	MAML2	MAML2	15685	-0.17	0.078	NO
335	TEAD4	TEAD4	TEAD4	15736	-0.18	0.078	NO
336	PPARD	PPARD	PPARD	16122	-0.21	0.06	NO
337	MED20	MED20	MED20	16234	-0.22	0.058	NO
338	ZNF642	ZNF642	ZNF642	17021	-0.32	0.019	NO
339	RORC	RORC	RORC	17443	-0.42	0.0026	NO
340	NR0B2	NR0B2	NR0B2	17701	-0.68	0.00092	NO

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

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

genes ES table in pathway: KEGG TASTE TRANSDUCTION

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	FGF9	FGF9	FGF9	556	0.45	0.071	YES
2	FGF2	FGF2	FGF2	905	0.38	0.14	YES
3	FGF8	FGF8	FGF8	1036	0.36	0.21	YES
4	FGF22	FGF22	FGF22	1131	0.35	0.29	YES
5	FGF18	FGF18	FGF18	1157	0.34	0.36	YES
6	GAB2	GAB2	GAB2	2654	0.2	0.32	YES
7	FGFR3	FGFR3	FGFR3	2757	0.2	0.36	YES
8	ZMYM2	ZMYM2	ZMYM2	3307	0.16	0.37	YES
9	KRAS	KRAS	KRAS	3807	0.14	0.37	YES
10	FGF20	FGF20	FGF20	3828	0.14	0.41	YES
11	FGFR1	FGFR1	FGFR1	3904	0.14	0.43	YES
12	FRS2	FRS2	FRS2	3948	0.14	0.46	YES
13	FGFR2	FGFR2	FGFR2	4135	0.13	0.48	YES
14	TRIM24	TRIM24	TRIM24	4211	0.13	0.51	YES
15	PLCG1	PLCG1	PLCG1	4888	0.11	0.49	NO
16	CUX1	CUX1	CUX1	6576	0.064	0.41	NO
17	FGFR1OP2	FGFR1OP2	FGFR1OP2	6742	0.061	0.42	NO
18	PIK3CA	PIK3CA	PIK3CA	6863	0.058	0.42	NO
19	CPSF6	CPSF6	CPSF6	6894	0.057	0.43	NO
20	FGFR1OP	FGFR1OP	FGFR1OP	7599	0.043	0.4	NO
21	BCR	BCR	BCR	7895	0.038	0.4	NO
22	SOS1	SOS1	SOS1	8256	0.03	0.38	NO
23	PIK3R1	PIK3R1	PIK3R1	8934	0.018	0.35	NO
24	GAB1	GAB1	GAB1	8968	0.017	0.35	NO
25	FGF1	FGF1	FGF1	9002	0.016	0.35	NO
26	MYO18A	MYO18A	MYO18A	9344	0.0099	0.34	NO
27	FGFR4	FGFR4	FGFR4	10404	-0.0094	0.28	NO
28	FGF17	FGF17	FGF17	10770	-0.016	0.26	NO
29	STAT1	STAT1	STAT1	11096	-0.022	0.25	NO
30	FGF7	FGF7	FGF7	12314	-0.048	0.19	NO
31	GRB2	GRB2	GRB2	12320	-0.048	0.2	NO
32	HRAS	HRAS	HRAS	13072	-0.066	0.17	NO
33	STAT3	STAT3	STAT3	13177	-0.068	0.18	NO
34	STAT5B	STAT5B	STAT5B	13552	-0.079	0.18	NO
35	STAT5A	STAT5A	STAT5A	14755	-0.12	0.14	NO
36	NRAS	NRAS	NRAS	14911	-0.13	0.16	NO

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

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TASTE TRANSDUCTION, 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 BASAL CELL CARCINOMA

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	NKD1	NKD1	NKD1	50	0.76	0.14	YES
2	WIF1	WIF1	WIF1	141	0.64	0.26	YES
3	DACT1	DACT1	DACT1	181	0.6	0.37	YES
4	AXIN2	AXIN2	AXIN2	451	0.48	0.45	YES
5	DKK3	DKK3	DKK3	934	0.38	0.5	YES
6	AKT3	AKT3	AKT3	2072	0.25	0.48	YES
7	SFRP1	SFRP1	SFRP1	2599	0.21	0.49	YES
8	NKD2	NKD2	NKD2	2726	0.2	0.52	YES
9	ANKRD6	ANKRD6	ANKRD6	2742	0.2	0.56	YES
10	CXXC4	CXXC4	CXXC4	3499	0.16	0.54	YES
11	AKT2	AKT2	AKT2	3774	0.14	0.56	YES
12	CTNNB1	CTNNB1	CTNNB1	3968	0.14	0.57	YES
13	FRAT1	FRAT1	FRAT1	4293	0.12	0.58	YES
14	APC	APC	APC	4952	0.1	0.56	NO
15	DKK1	DKK1	DKK1	5883	0.08	0.52	NO
16	CSNK1A1	CSNK1A1	CSNK1A1	6021	0.076	0.53	NO
17	GSK3A	GSK3A	GSK3A	6082	0.075	0.54	NO
18	GSK3B	GSK3B	GSK3B	6428	0.068	0.54	NO
19	PIN1	PIN1	PIN1	7351	0.048	0.49	NO
20	PTPRA	PTPRA	PTPRA	7648	0.042	0.48	NO
21	SENP2	SENP2	SENP2	7916	0.037	0.48	NO
22	AXIN1	AXIN1	AXIN1	7987	0.036	0.48	NO
23	AKT1	AKT1	AKT1	8174	0.032	0.47	NO
24	CBY1	CBY1	CBY1	9077	0.015	0.43	NO
25	PSEN1	PSEN1	PSEN1	9505	0.007	0.4	NO
26	LRP1	LRP1	LRP1	10065	-0.0031	0.37	NO
27	DVL1	DVL1	DVL1	10092	-0.0037	0.37	NO
28	FSTL1	FSTL1	FSTL1	10709	-0.015	0.34	NO
29	MVP	MVP	MVP	11240	-0.025	0.31	NO
30	RPSA	RPSA	RPSA	11705	-0.035	0.29	NO
31	DKK2	DKK2	DKK2	16361	-0.24	0.077	NO

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

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASAL CELL CARCINOMA, 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 NO1 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	WIF1	WIF1	WIF1	141	0.64	0.2	YES
2	LEF1	LEF1	LEF1	228	0.57	0.38	YES
3	TLE1	TLE1	TLE1	2318	0.23	0.34	YES
4	MYC	MYC	MYC	3359	0.16	0.33	YES
5	CTNNB1	CTNNB1	CTNNB1	3968	0.14	0.34	YES
6	CCND1	CCND1	CCND1	4244	0.13	0.37	YES
7	FRAT1	FRAT1	FRAT1	4293	0.12	0.4	YES
8	BTRC	BTRC	BTRC	4606	0.11	0.42	YES
9	APC	APC	APC	4952	0.1	0.44	YES
10	FZD1	FZD1	FZD1	5136	0.1	0.46	YES
11	CSNK1A1	CSNK1A1	CSNK1A1	6021	0.076	0.44	YES
12	CREBBP	CREBBP	CREBBP	6359	0.069	0.44	YES
13	GSK3B	GSK3B	GSK3B	6428	0.068	0.46	YES
14	NLK	NLK	NLK	6460	0.067	0.48	YES
15	WNT1	WNT1	WNT1	6759	0.061	0.48	YES
16	AXIN1	AXIN1	AXIN1	7987	0.036	0.42	NO
17	MAP3K7	MAP3K7	MAP3K7	9207	0.012	0.36	NO
18	PPP2CA	PPP2CA	PPP2CA	9266	0.011	0.36	NO
19	CSNK1D	CSNK1D	CSNK1D	9298	0.011	0.36	NO
20	CTBP1	CTBP1	CTBP1	9559	0.0058	0.35	NO
21	CSNK2A1	CSNK2A1	CSNK2A1	9690	0.0035	0.34	NO
22	DVL1	DVL1	DVL1	10092	-0.0037	0.32	NO
23	TAB1	TAB1	TAB1	10752	-0.016	0.29	NO
24	SMAD4	SMAD4	SMAD4	11033	-0.021	0.28	NO
25	HDAC1	HDAC1	HDAC1	14125	-0.096	0.14	NO
26	PPARD	PPARD	PPARD	16122	-0.21	0.09	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 NO1 PATHWAY.

Figure S30. 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 CHREBP2 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	ETV4	ETV4	ETV4	46	0.78	0.16	YES
2	BRSK2	BRSK2	BRSK2	565	0.45	0.22	YES
3	BRSK1	BRSK1	BRSK1	600	0.44	0.31	YES
4	MAPT	MAPT	MAPT	760	0.41	0.39	YES
5	MYC	MYC	MYC	3359	0.16	0.28	NO
6	MST4	MST4	MST4	3503	0.16	0.3	NO
7	MARK4	MARK4	MARK4	4592	0.12	0.26	NO
8	SMARCD3	SMARCD3	SMARCD3	5031	0.1	0.26	NO
9	TP53	TP53	TP53	5328	0.094	0.26	NO
10	TSC1	TSC1	TSC1	5857	0.08	0.25	NO
11	GSK3B	GSK3B	GSK3B	6428	0.068	0.23	NO
12	PRKACA	PRKACA	PRKACA	6541	0.065	0.24	NO
13	CDC37	CDC37	CDC37	6562	0.065	0.25	NO
14	PRKAG1	PRKAG1	PRKAG1	6771	0.06	0.25	NO
15	PRKAB1	PRKAB1	PRKAB1	6800	0.06	0.26	NO
16	AKT1S1	AKT1S1	AKT1S1	7054	0.054	0.26	NO
17	SIK1	SIK1	SIK1	7065	0.054	0.27	NO
18	STK11IP	STK11IP	STK11IP	7275	0.05	0.27	NO
19	MTOR	MTOR	MTOR	7668	0.042	0.25	NO
20	STK11	STK11	STK11	8302	0.03	0.22	NO
21	YWHAG	YWHAG	YWHAG	8349	0.029	0.23	NO
22	TSC2	TSC2	TSC2	8865	0.019	0.2	NO
23	SIK3	SIK3	SIK3	9237	0.012	0.18	NO
24	YWHAB	YWHAB	YWHAB	9651	0.004	0.16	NO
25	SIK2	SIK2	SIK2	10562	-0.012	0.11	NO
26	RPTOR	RPTOR	RPTOR	10582	-0.013	0.11	NO
27	MARK2	MARK2	MARK2	10827	-0.018	0.1	NO
28	YWHAE	YWHAE	YWHAE	10875	-0.018	0.1	NO
29	HSP90AA1	HSP90AA1	HSP90AA1	10908	-0.019	0.11	NO
30	YWHAZ	YWHAZ	YWHAZ	10951	-0.02	0.11	NO
31	PRKAA1	PRKAA1	PRKAA1	10984	-0.02	0.11	NO
32	SMAD4	SMAD4	SMAD4	11033	-0.021	0.11	NO
33	MAP2	MAP2	MAP2	11502	-0.03	0.093	NO
34	YWHAQ	YWHAQ	YWHAQ	11688	-0.034	0.09	NO
35	CRTC2	CRTC2	CRTC2	11800	-0.037	0.091	NO
36	CAB39	CAB39	CAB39	11882	-0.038	0.094	NO
37	PSEN2	PSEN2	PSEN2	13057	-0.066	0.042	NO
38	MLST8	MLST8	MLST8	13289	-0.071	0.043	NO
39	YWHAH	YWHAH	YWHAH	13419	-0.075	0.052	NO
40	CREB1	CREB1	CREB1	13547	-0.078	0.061	NO
41	SFN	SFN	SFN	13700	-0.083	0.069	NO
42	EZR	EZR	EZR	13755	-0.084	0.084	NO
43	STRADA	STRADA	STRADA	13957	-0.09	0.091	NO
44	PRKAA2	PRKAA2	PRKAA2	14706	-0.12	0.074	NO
45	ESR1	ESR1	ESR1	14836	-0.12	0.092	NO
46	CTSD	CTSD	CTSD	15256	-0.14	0.099	NO
47	STRADB	STRADB	STRADB	15975	-0.2	0.099	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 CHREBP2 PATHWAY.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA WNT 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	FGF9	FGF9	FGF9	556	0.45	0.095	YES
2	FGF2	FGF2	FGF2	905	0.38	0.18	YES
3	FGF8	FGF8	FGF8	1036	0.36	0.28	YES
4	FGF22	FGF22	FGF22	1131	0.35	0.37	YES
5	FGF18	FGF18	FGF18	1157	0.34	0.46	YES
6	FGFR3	FGFR3	FGFR3	2757	0.2	0.43	YES
7	KRAS	KRAS	KRAS	3807	0.14	0.41	YES
8	FGF20	FGF20	FGF20	3828	0.14	0.45	YES
9	FGFR1	FGFR1	FGFR1	3904	0.14	0.48	YES
10	FRS2	FRS2	FRS2	3948	0.14	0.52	YES
11	FGFR2	FGFR2	FGFR2	4135	0.13	0.55	YES
12	SOS1	SOS1	SOS1	8256	0.03	0.32	NO
13	MAPK1	MAPK1	MAPK1	8430	0.027	0.32	NO
14	FGF1	FGF1	FGF1	9002	0.016	0.29	NO
15	YWHAB	YWHAB	YWHAB	9651	0.004	0.26	NO
16	KL	KL	KL	9677	0.0037	0.26	NO
17	MAP2K2	MAP2K2	MAP2K2	9851	0.0009	0.25	NO
18	RAF1	RAF1	RAF1	9938	-0.0008	0.24	NO
19	MAP2K1	MAP2K1	MAP2K1	9967	-0.0014	0.24	NO
20	CDK1	CDK1	CDK1	10143	-0.0046	0.23	NO
21	FGFR4	FGFR4	FGFR4	10404	-0.0094	0.22	NO
22	FGF17	FGF17	FGF17	10770	-0.016	0.2	NO
23	FGF7	FGF7	FGF7	12314	-0.048	0.13	NO
24	GRB2	GRB2	GRB2	12320	-0.048	0.14	NO
25	MAPK3	MAPK3	MAPK3	12350	-0.048	0.16	NO
26	HRAS	HRAS	HRAS	13072	-0.066	0.13	NO
27	FRS3	FRS3	FRS3	14456	-0.11	0.086	NO
28	NRAS	NRAS	NRAS	14911	-0.13	0.096	NO
29	KLB	KLB	KLB	16228	-0.22	0.084	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 WNT PATHWAY.

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

genes ES table in pathway: ST WNT BETA CATENIN 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	WNT4	WNT4	WNT4	158	0.62	0.048	YES
2	LEF1	LEF1	LEF1	228	0.57	0.096	YES
3	GLI1	GLI1	GLI1	235	0.57	0.15	YES
4	SHH	SHH	SHH	352	0.52	0.19	YES
5	AXIN2	AXIN2	AXIN2	451	0.48	0.23	YES
6	SMO	SMO	SMO	505	0.46	0.27	YES
7	BMP4	BMP4	BMP4	748	0.41	0.29	YES
8	FZD10	FZD10	FZD10	858	0.39	0.32	YES
9	PTCH2	PTCH2	PTCH2	937	0.38	0.35	YES
10	TCF7	TCF7	TCF7	1326	0.32	0.36	YES
11	FZD9	FZD9	FZD9	1344	0.32	0.38	YES
12	WNT10B	WNT10B	WNT10B	1420	0.31	0.41	YES
13	APC2	APC2	APC2	1448	0.3	0.43	YES
14	PTCH1	PTCH1	PTCH1	1572	0.29	0.45	YES
15	WNT9A	WNT9A	WNT9A	1586	0.29	0.48	YES
16	FZD7	FZD7	FZD7	1713	0.28	0.5	YES
17	GLI3	GLI3	GLI3	1726	0.28	0.52	YES
18	FZD6	FZD6	FZD6	1740	0.27	0.55	YES
19	GLI2	GLI2	GLI2	2584	0.21	0.52	YES
20	WNT5A	WNT5A	WNT5A	2650	0.2	0.53	YES
21	WNT3	WNT3	WNT3	2669	0.2	0.55	YES
22	FZD8	FZD8	FZD8	2696	0.2	0.56	YES
23	HHIP	HHIP	HHIP	2902	0.19	0.57	YES
24	TCF7L2	TCF7L2	TCF7L2	2961	0.18	0.58	YES
25	WNT16	WNT16	WNT16	2964	0.18	0.6	YES
26	TCF7L1	TCF7L1	TCF7L1	3474	0.16	0.59	NO
27	CTNNB1	CTNNB1	CTNNB1	3968	0.14	0.57	NO
28	WNT2	WNT2	WNT2	4289	0.12	0.56	NO
29	WNT6	WNT6	WNT6	4568	0.12	0.56	NO
30	APC	APC	APC	4952	0.1	0.55	NO
31	FZD1	FZD1	FZD1	5136	0.1	0.55	NO
32	TP53	TP53	TP53	5328	0.094	0.54	NO
33	DVL3	DVL3	DVL3	5579	0.087	0.54	NO
34	SUFU	SUFU	SUFU	5603	0.087	0.54	NO
35	WNT3A	WNT3A	WNT3A	5652	0.085	0.55	NO
36	WNT11	WNT11	WNT11	5767	0.083	0.55	NO
37	WNT7B	WNT7B	WNT7B	5999	0.077	0.54	NO
38	FZD3	FZD3	FZD3	6198	0.072	0.54	NO
39	GSK3B	GSK3B	GSK3B	6428	0.068	0.53	NO
40	WNT1	WNT1	WNT1	6759	0.061	0.52	NO
41	AXIN1	AXIN1	AXIN1	7987	0.036	0.45	NO
42	FZD5	FZD5	FZD5	8214	0.031	0.44	NO
43	BMP2	BMP2	BMP2	9587	0.0051	0.36	NO
44	DVL1	DVL1	DVL1	10092	-0.0037	0.34	NO
45	WNT8B	WNT8B	WNT8B	10660	-0.014	0.31	NO
46	FZD2	FZD2	FZD2	10815	-0.017	0.3	NO
47	STK36	STK36	STK36	11558	-0.032	0.26	NO
48	WNT10A	WNT10A	WNT10A	11773	-0.036	0.25	NO
49	DVL2	DVL2	DVL2	11799	-0.037	0.25	NO
50	WNT2B	WNT2B	WNT2B	13273	-0.071	0.18	NO
51	FZD4	FZD4	FZD4	14102	-0.095	0.14	NO
52	WNT7A	WNT7A	WNT7A	14968	-0.13	0.1	NO
53	WNT9B	WNT9B	WNT9B	15913	-0.19	0.065	NO
54	WNT5B	WNT5B	WNT5B	17411	-0.41	0.017	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: ST WNT BETA CATENIN PATHWAY.

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

genes ES table in pathway: PID REELINPATHWAY

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	RELN	RELN	RELN	291	0.54	0.14	YES
2	MAPT	MAPT	MAPT	760	0.41	0.23	YES
3	VLDLR	VLDLR	VLDLR	1129	0.35	0.31	YES
4	MAPK8	MAPK8	MAPK8	1690	0.28	0.35	YES
5	MAP1B	MAP1B	MAP1B	1859	0.26	0.42	YES
6	LRP8	LRP8	LRP8	2078	0.24	0.48	YES
7	RAPGEF1	RAPGEF1	RAPGEF1	4103	0.13	0.4	NO
8	MAPK8IP1	MAPK8IP1	MAPK8IP1	4625	0.11	0.4	NO
9	MAP2K7	MAP2K7	MAP2K7	5273	0.096	0.39	NO
10	CBL	CBL	CBL	6312	0.07	0.36	NO
11	GSK3B	GSK3B	GSK3B	6428	0.068	0.37	NO
12	PIK3CA	PIK3CA	PIK3CA	6863	0.058	0.36	NO
13	PAFAH1B1	PAFAH1B1	PAFAH1B1	7305	0.049	0.35	NO
14	CRKL	CRKL	CRKL	7678	0.041	0.34	NO
15	ITGB1	ITGB1	ITGB1	8136	0.032	0.32	NO
16	AKT1	AKT1	AKT1	8174	0.032	0.33	NO
17	CDK5	CDK5	CDK5	8761	0.021	0.3	NO
18	PIK3R1	PIK3R1	PIK3R1	8934	0.018	0.3	NO
19	CDK5R1	CDK5R1	CDK5R1	9893	0.0001	0.24	NO
20	RAP1A	RAP1A	RAP1A	11031	-0.021	0.19	NO
21	NCK2	NCK2	NCK2	11036	-0.021	0.19	NO
22	FYN	FYN	FYN	11960	-0.04	0.15	NO
23	LRPAP1	LRPAP1	LRPAP1	11988	-0.04	0.16	NO
24	DAB1	DAB1	DAB1	12843	-0.06	0.13	NO
25	MAP3K11	MAP3K11	MAP3K11	13095	-0.066	0.14	NO
26	GRIN2A	GRIN2A	GRIN2A	15178	-0.14	0.058	NO
27	ARHGEF2	ARHGEF2	ARHGEF2	15265	-0.15	0.094	NO
28	ITGA3	ITGA3	ITGA3	15438	-0.16	0.13	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: PID REELINPATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: PID REELINPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID NECTIN PATHWAY

Table 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	FGF9	FGF9	FGF9	556	0.45	0.08	YES
2	FGF2	FGF2	FGF2	905	0.38	0.16	YES
3	FGF8	FGF8	FGF8	1036	0.36	0.24	YES
4	FGF22	FGF22	FGF22	1131	0.35	0.32	YES
5	FGF18	FGF18	FGF18	1157	0.34	0.4	YES
6	BRAF	BRAF	BRAF	2132	0.24	0.41	YES
7	SRC	SRC	SRC	2529	0.21	0.44	YES
8	FGFR3	FGFR3	FGFR3	2757	0.2	0.47	YES
9	FGF20	FGF20	FGF20	3828	0.14	0.45	YES
10	FGFR1	FGFR1	FGFR1	3904	0.14	0.48	YES
11	FRS2	FRS2	FRS2	3948	0.14	0.51	YES
12	FGFR2	FGFR2	FGFR2	4135	0.13	0.53	YES
13	SPRY2	SPRY2	SPRY2	6147	0.074	0.44	NO
14	CBL	CBL	CBL	6312	0.07	0.44	NO
15	PPP2R1A	PPP2R1A	PPP2R1A	7309	0.049	0.4	NO
16	MAPK1	MAPK1	MAPK1	8430	0.027	0.34	NO
17	UBA52	UBA52	UBA52	8799	0.021	0.33	NO
18	FGF1	FGF1	FGF1	9002	0.016	0.32	NO
19	PPP2CA	PPP2CA	PPP2CA	9266	0.011	0.31	NO
20	KL	KL	KL	9677	0.0037	0.28	NO
21	FGFR4	FGFR4	FGFR4	10404	-0.0094	0.25	NO
22	FGF17	FGF17	FGF17	10770	-0.016	0.23	NO
23	PPP2CB	PPP2CB	PPP2CB	12152	-0.044	0.16	NO
24	FGF7	FGF7	FGF7	12314	-0.048	0.17	NO
25	GRB2	GRB2	GRB2	12320	-0.048	0.18	NO
26	MAPK3	MAPK3	MAPK3	12350	-0.048	0.19	NO
27	RPS27A	RPS27A	RPS27A	14536	-0.11	0.092	NO
28	MKNK1	MKNK1	MKNK1	15028	-0.13	0.097	NO
29	KLB	KLB	KLB	16228	-0.22	0.084	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: PID NECTIN PATHWAY.

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

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 PENTOSE PHOSPHATE PATHWAY	26	genes.ES.table	0.51	1.6	0.034	1	0.94	0.35	0.18	0.28	0.77	0.42
KEGG STEROID HORMONE BIOSYNTHESIS	42	genes.ES.table	0.59	1.5	0.044	1	0.98	0.55	0.15	0.47	0.91	0.45
KEGG BUTANOATE METABOLISM	31	genes.ES.table	0.57	1.6	0.033	1	0.94	0.45	0.19	0.37	0.85	0.44
KEGG AMINOACYL TRNA BIOSYNTHESIS	41	genes.ES.table	0.44	1.6	0.078	1	0.91	0.58	0.41	0.35	0.86	0.45
KEGG BASAL TRANSCRIPTION FACTORS	34	genes.ES.table	0.42	1.5	0.094	1	0.97	0.5	0.36	0.32	0.83	0.42
KEGG NUCLEOTIDE EXCISION REPAIR	44	genes.ES.table	0.43	1.7	0.057	1	0.85	0.46	0.34	0.3	1	0.81
KEGG UBIQUITIN MEDIATED PROTEOLYSIS	132	genes.ES.table	0.26	1.6	0.04	1	0.9	0.38	0.34	0.25	1	0.5
BIOCARTA GH PATHWAY	27	genes.ES.table	0.42	1.4	0.053	1	0.99	0.22	0.14	0.19	1	0.58
BIOCARTA CREB PATHWAY	27	genes.ES.table	0.51	1.6	0.028	1	0.94	0.22	0.12	0.2	0.89	0.46
ST ERK1 ERK2 MAPK PATHWAY	31	genes.ES.table	0.43	1.6	0.037	1	0.9	0.29	0.23	0.22	1	0.57

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	RPA4	RPA4	RPA4	152	0.45	0.13	YES
2	ERCC4	ERCC4	ERCC4	1050	0.25	0.16	YES
3	GTF2H3	GTF2H3	GTF2H3	1867	0.18	0.17	YES
4	ERCC8	ERCC8	ERCC8	2105	0.16	0.2	YES
5	GTF2H2	GTF2H2	GTF2H2	2874	0.13	0.2	YES
6	RPA3	RPA3	RPA3	3019	0.13	0.23	YES
7	ERCC2	ERCC2	ERCC2	3079	0.12	0.27	YES
8	CDK7	CDK7	CDK7	3173	0.12	0.3	YES
9	RPA2	RPA2	RPA2	3337	0.12	0.32	YES
10	LIG1	LIG1	LIG1	3916	0.1	0.32	YES
11	CUL4B	CUL4B	CUL4B	3933	0.1	0.35	YES
12	CCNH	CCNH	CCNH	4055	0.097	0.38	YES
13	ERCC5	ERCC5	ERCC5	4492	0.086	0.38	YES
14	GTF2H5	GTF2H5	GTF2H5	4771	0.08	0.39	YES
15	CUL4A	CUL4A	CUL4A	5069	0.074	0.39	YES
16	RFC2	RFC2	RFC2	5509	0.066	0.39	YES
17	POLE2	POLE2	POLE2	5590	0.064	0.4	YES
18	CETN2	CETN2	CETN2	5768	0.06	0.41	YES
19	RFC1	RFC1	RFC1	6049	0.055	0.42	YES
20	MNAT1	MNAT1	MNAT1	6114	0.054	0.43	YES
21	RFC3	RFC3	RFC3	6608	0.046	0.41	NO
22	POLD2	POLD2	POLD2	6911	0.04	0.41	NO
23	POLE4	POLE4	POLE4	6970	0.039	0.42	NO
24	PCNA	PCNA	PCNA	7536	0.029	0.4	NO
25	RFC5	RFC5	RFC5	7665	0.027	0.4	NO
26	POLD3	POLD3	POLD3	7790	0.024	0.4	NO
27	GTF2H4	GTF2H4	GTF2H4	8105	0.019	0.38	NO
28	POLE3	POLE3	POLE3	8203	0.017	0.38	NO
29	POLD1	POLD1	POLD1	8355	0.015	0.38	NO
30	DDB1	DDB1	DDB1	8929	0.0054	0.35	NO
31	RAD23B	RAD23B	RAD23B	9006	0.0041	0.35	NO
32	GTF2H1	GTF2H1	GTF2H1	9481	-0.0032	0.32	NO
33	RAD23A	RAD23A	RAD23A	9878	-0.0099	0.3	NO
34	XPC	XPC	XPC	9917	-0.01	0.3	NO
35	POLE	POLE	POLE	9999	-0.012	0.3	NO
36	ERCC1	ERCC1	ERCC1	10554	-0.021	0.28	NO
37	ERCC3	ERCC3	ERCC3	10612	-0.022	0.28	NO
38	ERCC6	ERCC6	ERCC6	11432	-0.038	0.25	NO
39	POLD4	POLD4	POLD4	11951	-0.048	0.23	NO
40	RPA1	RPA1	RPA1	12059	-0.051	0.24	NO
41	DDB2	DDB2	DDB2	12122	-0.052	0.25	NO
42	RBX1	RBX1	RBX1	12435	-0.059	0.26	NO
43	RFC4	RFC4	RFC4	12603	-0.063	0.26	NO
44	XPA	XPA	XPA	13291	-0.08	0.25	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 PENTOSE PHOSPHATE PATHWAY.

Figure S42. 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 STEROID HORMONE BIOSYNTHESIS

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	BRAF	BRAF	BRAF	695	0.3	0.018	YES
2	SGK1	SGK1	SGK1	1089	0.24	0.042	YES
3	PXN	PXN	PXN	2038	0.17	0.02	YES
4	PRKCA	PRKCA	PRKCA	2051	0.17	0.051	YES
5	EEF2K	EEF2K	EEF2K	2094	0.16	0.081	YES
6	CCNE1	CCNE1	CCNE1	2298	0.16	0.099	YES
7	EIF4E	EIF4E	EIF4E	2681	0.14	0.1	YES
8	RRAGC	RRAGC	RRAGC	2757	0.14	0.12	YES
9	PDPK1	PDPK1	PDPK1	3024	0.13	0.13	YES
10	RRAGB	RRAGB	RRAGB	3165	0.12	0.15	YES
11	BNIP3	BNIP3	BNIP3	3306	0.12	0.16	YES
12	CYCS	CYCS	CYCS	3362	0.12	0.18	YES
13	CLIP1	CLIP1	CLIP1	3367	0.12	0.2	YES
14	SFN	SFN	SFN	3657	0.11	0.21	YES
15	RRN3	RRN3	RRN3	3902	0.1	0.22	YES
16	PDCD4	PDCD4	PDCD4	3904	0.1	0.23	YES
17	MAP2K1	MAP2K1	MAP2K1	3952	0.099	0.25	YES
18	PPARGC1A	PPARGC1A	PPARGC1A	3977	0.099	0.27	YES
19	DDIT4	DDIT4	DDIT4	4350	0.09	0.26	YES
20	FBXW11	FBXW11	FBXW11	4621	0.084	0.26	YES
21	YWHAG	YWHAG	YWHAG	4641	0.083	0.28	YES
22	YY1	YY1	YY1	4678	0.082	0.29	YES
23	RHEB	RHEB	RHEB	4707	0.082	0.31	YES
24	ULK1	ULK1	ULK1	5078	0.074	0.3	NO
25	RRAGA	RRAGA	RRAGA	5458	0.067	0.29	NO
26	RRAGD	RRAGD	RRAGD	5517	0.066	0.3	NO
27	MLST8	MLST8	MLST8	5693	0.062	0.3	NO
28	TSC2	TSC2	TSC2	6452	0.048	0.27	NO
29	RICTOR	RICTOR	RICTOR	6819	0.042	0.26	NO
30	EEF2	EEF2	EEF2	6985	0.039	0.25	NO
31	YWHAB	YWHAB	YWHAB	8259	0.016	0.18	NO
32	NRAS	NRAS	NRAS	8471	0.013	0.18	NO
33	MTOR	MTOR	MTOR	8579	0.011	0.17	NO
34	RAC1	RAC1	RAC1	8704	0.009	0.17	NO
35	EIF4B	EIF4B	EIF4B	9117	0.0024	0.14	NO
36	MAP2K2	MAP2K2	MAP2K2	9266	-0.000032	0.14	NO
37	YWHAQ	YWHAQ	YWHAQ	9393	-0.0018	0.13	NO
38	AKT1	AKT1	AKT1	9408	-0.0022	0.13	NO
39	YWHAZ	YWHAZ	YWHAZ	9455	-0.0029	0.13	NO
40	MAPK3	MAPK3	MAPK3	9483	-0.0032	0.12	NO
41	IRS1	IRS1	IRS1	9609	-0.0053	0.12	NO
42	CDK2	CDK2	CDK2	9716	-0.0069	0.11	NO
43	RB1CC1	RB1CC1	RB1CC1	9900	-0.01	0.11	NO
44	AKT1S1	AKT1S1	AKT1S1	9987	-0.012	0.1	NO
45	MAPK1	MAPK1	MAPK1	10010	-0.012	0.1	NO
46	POLDIP3	POLDIP3	POLDIP3	10173	-0.015	0.098	NO
47	YWHAH	YWHAH	YWHAH	10503	-0.02	0.083	NO
48	YWHAE	YWHAE	YWHAE	10698	-0.024	0.077	NO
49	RPS6KB1	RPS6KB1	RPS6KB1	10708	-0.024	0.081	NO
50	KRAS	KRAS	KRAS	10924	-0.028	0.074	NO
51	PML	PML	PML	11230	-0.034	0.063	NO
52	RAF1	RAF1	RAF1	11242	-0.034	0.069	NO
53	EIF4A1	EIF4A1	EIF4A1	11297	-0.035	0.073	NO
54	RHOA	RHOA	RHOA	11562	-0.04	0.066	NO
55	TSC1	TSC1	TSC1	11624	-0.042	0.07	NO
56	RPS6KA1	RPS6KA1	RPS6KA1	11946	-0.048	0.061	NO
57	IKBKB	IKBKB	IKBKB	11974	-0.049	0.069	NO
58	MAPKAP1	MAPKAP1	MAPKAP1	12559	-0.062	0.048	NO
59	SREBF1	SREBF1	SREBF1	12817	-0.068	0.046	NO
60	PLD1	PLD1	PLD1	12820	-0.068	0.059	NO
61	PLD2	PLD2	PLD2	13364	-0.082	0.044	NO
62	RPTOR	RPTOR	RPTOR	13628	-0.089	0.046	NO
63	ULK2	ULK2	ULK2	14420	-0.12	0.024	NO
64	EIF4EBP1	EIF4EBP1	EIF4EBP1	14475	-0.12	0.043	NO
65	HRAS	HRAS	HRAS	14854	-0.13	0.047	NO
66	SSPO	SSPO	SSPO	16447	-0.24	0.0029	NO
67	PRR5	PRR5	PRR5	17269	-0.36	0.025	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 STEROID HORMONE BIOSYNTHESIS.

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

genes ES table in pathway: KEGG BUTANOATE 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	GTF2A1	GTF2A1	GTF2A1	580	0.32	0.026	YES
2	TAF13	TAF13	TAF13	613	0.31	0.081	YES
3	CCNT1	CCNT1	CCNT1	1210	0.23	0.09	YES
4	GTF2H3	GTF2H3	GTF2H3	1867	0.18	0.085	YES
5	LSM11	LSM11	LSM11	2269	0.16	0.091	YES
6	ZNF473	ZNF473	ZNF473	2492	0.15	0.11	YES
7	RNGTT	RNGTT	RNGTT	2591	0.14	0.13	YES
8	GTF2H2	GTF2H2	GTF2H2	2874	0.13	0.14	YES
9	UPF3B	UPF3B	UPF3B	3073	0.12	0.15	YES
10	ERCC2	ERCC2	ERCC2	3079	0.12	0.17	YES
11	TAF1	TAF1	TAF1	3167	0.12	0.19	YES
12	CDK7	CDK7	CDK7	3173	0.12	0.21	YES
13	TBP	TBP	TBP	3789	0.1	0.19	YES
14	CDC40	CDC40	CDC40	3896	0.1	0.2	YES
15	CCNH	CCNH	CCNH	4055	0.097	0.21	YES
16	PAPOLA	PAPOLA	PAPOLA	4240	0.093	0.22	YES
17	TAF9	TAF9	TAF9	4344	0.09	0.23	YES
18	CSTF2	CSTF2	CSTF2	4564	0.085	0.24	YES
19	POLR2B	POLR2B	POLR2B	4582	0.084	0.25	YES
20	GTF2A2	GTF2A2	GTF2A2	5337	0.069	0.22	YES
21	LSM10	LSM10	LSM10	5344	0.069	0.23	YES
22	RNMT	RNMT	RNMT	5546	0.065	0.23	YES
23	RNPS1	RNPS1	RNPS1	5580	0.064	0.24	YES
24	SLBP	SLBP	SLBP	5604	0.064	0.25	YES
25	TAF12	TAF12	TAF12	5628	0.063	0.26	YES
26	SUPT16H	SUPT16H	SUPT16H	5663	0.062	0.27	YES
27	POLR2C	POLR2C	POLR2C	5865	0.059	0.27	YES
28	DHX38	DHX38	DHX38	5942	0.057	0.28	YES
29	WHSC2	WHSC2	WHSC2	5983	0.056	0.29	YES
30	MNAT1	MNAT1	MNAT1	6114	0.054	0.29	YES
31	GTF2F1	GTF2F1	GTF2F1	6201	0.052	0.29	YES
32	U2AF2	U2AF2	U2AF2	6225	0.052	0.3	YES
33	SNRPF	SNRPF	SNRPF	6284	0.051	0.31	YES
34	MAGOH	MAGOH	MAGOH	6353	0.05	0.31	YES
35	CPSF2	CPSF2	CPSF2	6391	0.049	0.32	YES
36	NFX1	NFX1	NFX1	6466	0.048	0.32	YES
37	POLR2J	POLR2J	POLR2J	6488	0.047	0.33	YES
38	NCBP1	NCBP1	NCBP1	6564	0.046	0.34	YES
39	TAF5	TAF5	TAF5	6792	0.042	0.33	NO
40	TCEB2	TCEB2	TCEB2	7002	0.038	0.33	NO
41	NUDT21	NUDT21	NUDT21	7019	0.038	0.33	NO
42	CTDP1	CTDP1	CTDP1	7266	0.034	0.32	NO
43	SUPT5H	SUPT5H	SUPT5H	7464	0.03	0.32	NO
44	POLR2I	POLR2I	POLR2I	7565	0.028	0.32	NO
45	POLR2F	POLR2F	POLR2F	7618	0.027	0.32	NO
46	TAF11	TAF11	TAF11	7856	0.023	0.31	NO
47	GTF2B	GTF2B	GTF2B	8001	0.021	0.31	NO
48	GTF2H4	GTF2H4	GTF2H4	8105	0.019	0.3	NO
49	SRRM1	SRRM1	SRRM1	8230	0.017	0.3	NO
50	ELL	ELL	ELL	8338	0.015	0.3	NO
51	SNRPB	SNRPB	SNRPB	8430	0.014	0.3	NO
52	POLR2D	POLR2D	POLR2D	8562	0.011	0.29	NO
53	TAF4	TAF4	TAF4	8629	0.01	0.29	NO
54	GTF2H2B	GTF2H2B	GTF2H2B	8875	0.0062	0.28	NO
55	POLR2E	POLR2E	POLR2E	8925	0.0055	0.27	NO
56	TCEB1	TCEB1	TCEB1	9038	0.0036	0.27	NO
57	POLR2A	POLR2A	POLR2A	9187	0.0013	0.26	NO
58	POLR2K	POLR2K	POLR2K	9436	-0.0026	0.25	NO
59	GTF2H1	GTF2H1	GTF2H1	9481	-0.0032	0.24	NO
60	CCNT2	CCNT2	CCNT2	9539	-0.0041	0.24	NO
61	RDBP	RDBP	RDBP	9655	-0.006	0.24	NO
62	CPSF3	CPSF3	CPSF3	9712	-0.0069	0.23	NO
63	CDK9	CDK9	CDK9	9797	-0.0084	0.23	NO
64	SNRPG	SNRPG	SNRPG	9845	-0.0092	0.23	NO
65	TCEB3	TCEB3	TCEB3	9850	-0.0093	0.23	NO
66	TAF6	TAF6	TAF6	9933	-0.011	0.23	NO
67	COBRA1	COBRA1	COBRA1	9983	-0.012	0.23	NO
68	CLP1	CLP1	CLP1	10085	-0.014	0.22	NO
69	RBM8A	RBM8A	RBM8A	10214	-0.016	0.22	NO
70	GTF2F2	GTF2F2	GTF2F2	10282	-0.017	0.22	NO
71	CSTF1	CSTF1	CSTF1	10323	-0.017	0.22	NO
72	U2AF1	U2AF1	U2AF1	10357	-0.018	0.22	NO
73	PABPN1	PABPN1	PABPN1	10501	-0.02	0.22	NO
74	ERCC3	ERCC3	ERCC3	10612	-0.022	0.22	NO
75	SNRPE	SNRPE	SNRPE	10648	-0.022	0.22	NO
76	POLR2L	POLR2L	POLR2L	10778	-0.025	0.22	NO
77	CPSF1	CPSF1	CPSF1	10789	-0.026	0.22	NO
78	GTF2E1	GTF2E1	GTF2E1	11211	-0.033	0.2	NO
79	CSTF3	CSTF3	CSTF3	11302	-0.035	0.2	NO
80	SUPT4H1	SUPT4H1	SUPT4H1	11421	-0.038	0.2	NO
81	TCEA1	TCEA1	TCEA1	11448	-0.038	0.21	NO
82	SSRP1	SSRP1	SSRP1	11457	-0.038	0.22	NO
83	GTF2E2	GTF2E2	GTF2E2	11459	-0.038	0.22	NO
84	TAF4B	TAF4B	TAF4B	11586	-0.041	0.22	NO
85	SNRPD3	SNRPD3	SNRPD3	11746	-0.044	0.22	NO
86	PCF11	PCF11	PCF11	12113	-0.052	0.21	NO
87	CPSF7	CPSF7	CPSF7	12210	-0.054	0.22	NO
88	TH1L	TH1L	TH1L	12746	-0.066	0.2	NO
89	NCBP2	NCBP2	NCBP2	12870	-0.069	0.2	NO
90	POLR2G	POLR2G	POLR2G	13040	-0.073	0.21	NO
91	THOC4	THOC4	THOC4	13639	-0.09	0.19	NO
92	TAF10	TAF10	TAF10	14210	-0.11	0.18	NO
93	POLR2H	POLR2H	POLR2H	14479	-0.12	0.18	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 BUTANOATE METABOLISM.

Figure S46. 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 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	CREB5	CREB5	CREB5	446	0.35	0.11	YES
2	BRAF	BRAF	BRAF	695	0.3	0.2	YES
3	DUSP9	DUSP9	DUSP9	763	0.29	0.31	YES
4	RPS6KA2	RPS6KA2	RPS6KA2	1572	0.2	0.34	YES
5	EEF2K	EEF2K	EEF2K	2094	0.16	0.37	YES
6	EIF4E	EIF4E	EIF4E	2681	0.14	0.39	YES
7	RAP1A	RAP1A	RAP1A	3356	0.12	0.4	YES
8	MAP2K1	MAP2K1	MAP2K1	3952	0.099	0.4	YES
9	SOS2	SOS2	SOS2	4101	0.096	0.43	YES
10	ARAF	ARAF	ARAF	5270	0.07	0.39	NO
11	ATF1	ATF1	ATF1	5842	0.059	0.38	NO
12	CREB3	CREB3	CREB3	6270	0.051	0.37	NO
13	NFKB1	NFKB1	NFKB1	8556	0.012	0.25	NO
14	KLF6	KLF6	KLF6	8776	0.0076	0.24	NO
15	MKNK2	MKNK2	MKNK2	8872	0.0062	0.24	NO
16	MAP2K2	MAP2K2	MAP2K2	9266	-0.000032	0.21	NO
17	MAPK3	MAPK3	MAPK3	9483	-0.0032	0.2	NO
18	DUSP4	DUSP4	DUSP4	9618	-0.0054	0.2	NO
19	GRB2	GRB2	GRB2	9634	-0.0055	0.2	NO
20	SOS1	SOS1	SOS1	9679	-0.0063	0.2	NO
21	MAPK1	MAPK1	MAPK1	10010	-0.012	0.18	NO
22	MKNK1	MKNK1	MKNK1	10877	-0.027	0.14	NO
23	CREB1	CREB1	CREB1	11489	-0.039	0.13	NO
24	RPS6KA1	RPS6KA1	RPS6KA1	11946	-0.048	0.12	NO
25	KAT5	KAT5	KAT5	12085	-0.051	0.13	NO
26	SHC1	SHC1	SHC1	12156	-0.053	0.15	NO
27	RPS6KA3	RPS6KA3	RPS6KA3	12590	-0.062	0.14	NO
28	TRAF3	TRAF3	TRAF3	12794	-0.068	0.16	NO
29	BAD	BAD	BAD	13029	-0.073	0.17	NO
30	DUSP6	DUSP6	DUSP6	13055	-0.074	0.2	NO
31	MAP3K8	MAP3K8	MAP3K8	15535	-0.17	0.12	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 AMINOACYL TRNA BIOSYNTHESIS.

Figure S48. 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 BASAL TRANSCRIPTION FACTORS

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	SOCS1	SOCS1	SOCS1	244	0.41	0.03	YES
2	PARK2	PARK2	PARK2	371	0.37	0.062	YES
3	NHLRC1	NHLRC1	NHLRC1	551	0.32	0.086	YES
4	UBE2NL	UBE2NL	UBE2NL	648	0.3	0.11	YES
5	HERC3	HERC3	HERC3	808	0.28	0.13	YES
6	UBE2QL1	UBE2QL1	UBE2QL1	1532	0.2	0.11	YES
7	UBE2D4	UBE2D4	UBE2D4	2070	0.17	0.1	YES
8	ERCC8	ERCC8	ERCC8	2105	0.16	0.12	YES
9	NEDD4	NEDD4	NEDD4	2762	0.14	0.094	YES
10	XIAP	XIAP	XIAP	2945	0.13	0.097	YES
11	FBXO4	FBXO4	FBXO4	3168	0.12	0.097	YES
12	CDC23	CDC23	CDC23	3183	0.12	0.11	YES
13	NEDD4L	NEDD4L	NEDD4L	3388	0.12	0.11	YES
14	SAE1	SAE1	SAE1	3420	0.11	0.12	YES
15	ANAPC10	ANAPC10	ANAPC10	3729	0.1	0.11	YES
16	UBE2B	UBE2B	UBE2B	3791	0.1	0.12	YES
17	UBE3C	UBE3C	UBE3C	3899	0.1	0.13	YES
18	UBE2A	UBE2A	UBE2A	3918	0.1	0.14	YES
19	CUL4B	CUL4B	CUL4B	3933	0.1	0.14	YES
20	RCHY1	RCHY1	RCHY1	4056	0.097	0.15	YES
21	KLHL9	KLHL9	KLHL9	4165	0.094	0.15	YES
22	UBE2H	UBE2H	UBE2H	4352	0.09	0.15	YES
23	UBA6	UBA6	UBA6	4436	0.088	0.16	YES
24	UBE2K	UBE2K	UBE2K	4454	0.087	0.16	YES
25	BIRC3	BIRC3	BIRC3	4487	0.086	0.17	YES
26	FBXW11	FBXW11	FBXW11	4621	0.084	0.17	YES
27	SKP1	SKP1	SKP1	4658	0.083	0.18	YES
28	UBE2D2	UBE2D2	UBE2D2	4663	0.083	0.19	YES
29	UBOX5	UBOX5	UBOX5	4694	0.082	0.2	YES
30	HUWE1	HUWE1	HUWE1	4865	0.079	0.19	YES
31	UBE2C	UBE2C	UBE2C	4890	0.078	0.2	YES
32	UBE2D3	UBE2D3	UBE2D3	4956	0.077	0.21	YES
33	MGRN1	MGRN1	MGRN1	5044	0.074	0.21	YES
34	CUL4A	CUL4A	CUL4A	5069	0.074	0.22	YES
35	SMURF1	SMURF1	SMURF1	5082	0.074	0.22	YES
36	SKP2	SKP2	SKP2	5219	0.071	0.22	YES
37	FZR1	FZR1	FZR1	5232	0.071	0.23	YES
38	FBXW8	FBXW8	FBXW8	5390	0.068	0.23	YES
39	UBE2E2	UBE2E2	UBE2E2	5611	0.064	0.22	YES
40	UBE2I	UBE2I	UBE2I	5648	0.063	0.23	YES
41	BTRC	BTRC	BTRC	5706	0.062	0.23	YES
42	RHOBTB2	RHOBTB2	RHOBTB2	5729	0.061	0.24	YES
43	ANAPC4	ANAPC4	ANAPC4	5741	0.061	0.24	YES
44	UBA1	UBA1	UBA1	5810	0.06	0.24	YES
45	UBE3B	UBE3B	UBE3B	5853	0.059	0.25	YES
46	FANCL	FANCL	FANCL	5917	0.057	0.25	YES
47	UBE2N	UBE2N	UBE2N	5951	0.056	0.25	YES
48	CUL1	CUL1	CUL1	6028	0.055	0.26	YES
49	UBE3A	UBE3A	UBE3A	6039	0.055	0.26	YES
50	ANAPC5	ANAPC5	ANAPC5	6113	0.054	0.26	YES
51	UBE2M	UBE2M	UBE2M	6359	0.049	0.25	NO
52	PIAS4	PIAS4	PIAS4	6390	0.049	0.26	NO
53	SIAH1	SIAH1	SIAH1	6615	0.046	0.25	NO
54	CDC20	CDC20	CDC20	6856	0.041	0.24	NO
55	WWP2	WWP2	WWP2	6917	0.04	0.24	NO
56	TCEB2	TCEB2	TCEB2	7002	0.038	0.24	NO
57	SYVN1	SYVN1	SYVN1	7048	0.038	0.24	NO
58	KEAP1	KEAP1	KEAP1	7169	0.035	0.24	NO
59	ANAPC13	ANAPC13	ANAPC13	7175	0.035	0.24	NO
60	MID1	MID1	MID1	7244	0.034	0.24	NO
61	UBE2G2	UBE2G2	UBE2G2	7296	0.033	0.24	NO
62	BIRC6	BIRC6	BIRC6	7552	0.029	0.23	NO
63	CUL3	CUL3	CUL3	7593	0.028	0.23	NO
64	UBA2	UBA2	UBA2	7631	0.027	0.23	NO
65	UBE2J1	UBE2J1	UBE2J1	7656	0.027	0.23	NO
66	ANAPC7	ANAPC7	ANAPC7	7736	0.025	0.23	NO
67	HERC2	HERC2	HERC2	7850	0.024	0.23	NO
68	STUB1	STUB1	STUB1	7866	0.023	0.23	NO
69	UBE4A	UBE4A	UBE4A	7911	0.022	0.23	NO
70	MAP3K1	MAP3K1	MAP3K1	7941	0.022	0.23	NO
71	PPIL2	PPIL2	PPIL2	7973	0.021	0.23	NO
72	UBE2S	UBE2S	UBE2S	8103	0.019	0.22	NO
73	CUL7	CUL7	CUL7	8180	0.018	0.22	NO
74	KLHL13	KLHL13	KLHL13	8205	0.017	0.22	NO
75	HERC1	HERC1	HERC1	8268	0.016	0.22	NO
76	DET1	DET1	DET1	8462	0.013	0.21	NO
77	CDC16	CDC16	CDC16	8469	0.013	0.21	NO
78	CDC26	CDC26	CDC26	8520	0.012	0.21	NO
79	CUL2	CUL2	CUL2	8581	0.011	0.21	NO
80	UBE2R2	UBE2R2	UBE2R2	8659	0.0097	0.2	NO
81	DDB1	DDB1	DDB1	8929	0.0054	0.19	NO
82	UBE2W	UBE2W	UBE2W	9000	0.0042	0.19	NO
83	TCEB1	TCEB1	TCEB1	9038	0.0036	0.18	NO
84	FBXW7	FBXW7	FBXW7	9337	-0.0011	0.17	NO
85	SOCS3	SOCS3	SOCS3	9463	-0.003	0.16	NO
86	TRIP12	TRIP12	TRIP12	9816	-0.0087	0.14	NO
87	PIAS2	PIAS2	PIAS2	9890	-0.01	0.14	NO
88	BRCA1	BRCA1	BRCA1	9914	-0.01	0.14	NO
89	RNF7	RNF7	RNF7	9978	-0.012	0.14	NO
90	ANAPC2	ANAPC2	ANAPC2	10106	-0.014	0.13	NO
91	PIAS1	PIAS1	PIAS1	10178	-0.015	0.13	NO
92	CDC34	CDC34	CDC34	10260	-0.016	0.13	NO
93	ITCH	ITCH	ITCH	10291	-0.017	0.13	NO
94	CUL5	CUL5	CUL5	10383	-0.018	0.12	NO
95	UBE2F	UBE2F	UBE2F	10391	-0.018	0.12	NO
96	UBE2O	UBE2O	UBE2O	10502	-0.02	0.12	NO
97	UBE2Z	UBE2Z	UBE2Z	10791	-0.026	0.11	NO
98	UBE2G1	UBE2G1	UBE2G1	10894	-0.027	0.1	NO
99	CDC27	CDC27	CDC27	10911	-0.028	0.11	NO
100	UBE2Q2	UBE2Q2	UBE2Q2	11207	-0.033	0.092	NO
101	PML	PML	PML	11230	-0.034	0.095	NO
102	UBA3	UBA3	UBA3	11273	-0.035	0.096	NO
103	ANAPC11	ANAPC11	ANAPC11	11348	-0.036	0.096	NO
104	UBE2J2	UBE2J2	UBE2J2	11393	-0.037	0.097	NO
105	UBE2L3	UBE2L3	UBE2L3	11504	-0.039	0.095	NO
106	TRIM37	TRIM37	TRIM37	11615	-0.042	0.093	NO
107	UBE2Q1	UBE2Q1	UBE2Q1	11679	-0.043	0.094	NO
108	ANAPC1	ANAPC1	ANAPC1	11794	-0.045	0.092	NO
109	UBE2L6	UBE2L6	UBE2L6	12016	-0.05	0.085	NO
110	DDB2	DDB2	DDB2	12122	-0.052	0.085	NO
111	TRAF6	TRAF6	TRAF6	12131	-0.052	0.09	NO
112	CBL	CBL	CBL	12163	-0.053	0.094	NO
113	RFWD2	RFWD2	RFWD2	12278	-0.056	0.093	NO
114	UBR5	UBR5	UBR5	12392	-0.058	0.093	NO
115	RBX1	RBX1	RBX1	12435	-0.059	0.097	NO
116	WWP1	WWP1	WWP1	12469	-0.06	0.1	NO
117	UBE4B	UBE4B	UBE4B	12491	-0.06	0.11	NO
118	UBE2D1	UBE2D1	UBE2D1	12698	-0.065	0.1	NO
119	TRIM32	TRIM32	TRIM32	12821	-0.068	0.1	NO
120	HERC4	HERC4	HERC4	12891	-0.07	0.11	NO
121	PRPF19	PRPF19	PRPF19	12920	-0.07	0.11	NO
122	UBE2E3	UBE2E3	UBE2E3	13307	-0.08	0.098	NO
123	BIRC2	BIRC2	BIRC2	13409	-0.083	0.1	NO
124	PIAS3	PIAS3	PIAS3	13779	-0.093	0.09	NO
125	UBE2E1	UBE2E1	UBE2E1	13784	-0.093	0.1	NO
126	VHL	VHL	VHL	13910	-0.097	0.1	NO
127	MDM2	MDM2	MDM2	14121	-0.1	0.1	NO
128	UBA7	UBA7	UBA7	14502	-0.12	0.093	NO
129	CBLB	CBLB	CBLB	14563	-0.12	0.1	NO
130	FBXO2	FBXO2	FBXO2	16100	-0.21	0.038	NO
131	SMURF2	SMURF2	SMURF2	16492	-0.24	0.042	NO
132	AIRE	AIRE	AIRE	16682	-0.26	0.059	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 BASAL TRANSCRIPTION FACTORS.

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

genes ES table in pathway: KEGG NUCLEOTIDE EXCISION REPAIR

Table 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	MARS2	MARS2	MARS2	1354	0.22	0.017	YES
2	TARSL2	TARSL2	TARSL2	2227	0.16	0.036	YES
3	RARS	RARS	RARS	3344	0.12	0.023	YES
4	HARS2	HARS2	HARS2	3467	0.11	0.064	YES
5	MTFMT	MTFMT	MTFMT	3596	0.11	0.1	YES
6	HARS	HARS	HARS	3751	0.1	0.14	YES
7	GARS	GARS	GARS	3877	0.1	0.18	YES
8	FARS2	FARS2	FARS2	4121	0.096	0.2	YES
9	LARS	LARS	LARS	4157	0.095	0.24	YES
10	EARS2	EARS2	EARS2	4283	0.092	0.28	YES
11	VARS2	VARS2	VARS2	4616	0.084	0.29	YES
12	PSTK	PSTK	PSTK	5187	0.072	0.29	YES
13	YARS2	YARS2	YARS2	5366	0.068	0.31	YES
14	VARS	VARS	VARS	5705	0.062	0.32	YES
15	AARS2	AARS2	AARS2	5795	0.06	0.34	YES
16	MARS	MARS	MARS	5888	0.058	0.36	YES
17	SEPSECS	SEPSECS	SEPSECS	5991	0.056	0.38	YES
18	SARS	SARS	SARS	6063	0.055	0.4	YES
19	SARS2	SARS2	SARS2	6133	0.053	0.42	YES
20	TARS2	TARS2	TARS2	6575	0.046	0.41	YES
21	IARS2	IARS2	IARS2	7032	0.038	0.4	YES
22	FARSA	FARSA	FARSA	7061	0.037	0.41	YES
23	LARS2	LARS2	LARS2	7201	0.035	0.42	YES
24	KARS	KARS	KARS	7212	0.035	0.44	YES
25	PARS2	PARS2	PARS2	7455	0.031	0.44	NO
26	TARS	TARS	TARS	7870	0.023	0.42	NO
27	IARS	IARS	IARS	8024	0.02	0.42	NO
28	FARSB	FARSB	FARSB	8067	0.019	0.43	NO
29	WARS	WARS	WARS	8172	0.018	0.43	NO
30	NARS	NARS	NARS	8458	0.013	0.42	NO
31	EPRS	EPRS	EPRS	8645	0.01	0.41	NO
32	NARS2	NARS2	NARS2	8810	0.0072	0.41	NO
33	WARS2	WARS2	WARS2	9126	0.0022	0.39	NO
34	DARS2	DARS2	DARS2	9708	-0.0068	0.36	NO
35	DARS	DARS	DARS	9897	-0.01	0.35	NO
36	YARS	YARS	YARS	10125	-0.014	0.35	NO
37	RARS2	RARS2	RARS2	10336	-0.017	0.34	NO
38	CARS2	CARS2	CARS2	11084	-0.031	0.31	NO
39	AARS	AARS	AARS	11128	-0.032	0.32	NO
40	CARS	CARS	CARS	11594	-0.041	0.32	NO
41	QARS	QARS	QARS	12900	-0.07	0.27	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 NUCLEOTIDE EXCISION REPAIR.

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

genes ES table in pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS

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	ERCC4	ERCC4	ERCC4	1050	0.25	0.072	YES
2	GTF2H3	GTF2H3	GTF2H3	1867	0.18	0.12	YES
3	ERCC8	ERCC8	ERCC8	2105	0.16	0.19	YES
4	GTF2H2	GTF2H2	GTF2H2	2874	0.13	0.22	YES
5	ERCC2	ERCC2	ERCC2	3079	0.12	0.28	YES
6	CDK7	CDK7	CDK7	3173	0.12	0.34	YES
7	CCNH	CCNH	CCNH	4055	0.097	0.34	YES
8	ERCC5	ERCC5	ERCC5	4492	0.086	0.36	YES
9	POLR2B	POLR2B	POLR2B	4582	0.084	0.4	YES
10	POLR2C	POLR2C	POLR2C	5865	0.059	0.36	NO
11	MNAT1	MNAT1	MNAT1	6114	0.054	0.37	NO
12	POLR2J	POLR2J	POLR2J	6488	0.047	0.38	NO
13	XAB2	XAB2	XAB2	6666	0.044	0.39	NO
14	POLR2I	POLR2I	POLR2I	7565	0.028	0.35	NO
15	POLR2F	POLR2F	POLR2F	7618	0.027	0.36	NO
16	GTF2H4	GTF2H4	GTF2H4	8105	0.019	0.35	NO
17	POLR2D	POLR2D	POLR2D	8562	0.011	0.33	NO
18	GTF2H2B	GTF2H2B	GTF2H2B	8875	0.0062	0.31	NO
19	POLR2E	POLR2E	POLR2E	8925	0.0055	0.31	NO
20	POLR2A	POLR2A	POLR2A	9187	0.0013	0.3	NO
21	POLR2K	POLR2K	POLR2K	9436	-0.0026	0.29	NO
22	GTF2H1	GTF2H1	GTF2H1	9481	-0.0032	0.29	NO
23	ERCC1	ERCC1	ERCC1	10554	-0.021	0.24	NO
24	ERCC3	ERCC3	ERCC3	10612	-0.022	0.24	NO
25	POLR2L	POLR2L	POLR2L	10778	-0.025	0.25	NO
26	ERCC6	ERCC6	ERCC6	11432	-0.038	0.23	NO
27	TCEA1	TCEA1	TCEA1	11448	-0.038	0.25	NO
28	POLR2G	POLR2G	POLR2G	13040	-0.073	0.2	NO
29	POLR2H	POLR2H	POLR2H	14479	-0.12	0.18	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 UBIQUITIN MEDIATED PROTEOLYSIS.

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

genes ES table in pathway: BIOCARTA GH PATHWAY

Table S28. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PRKCB	PRKCB	PRKCB	117	0.48	0.18	YES
2	PIK3R1	PIK3R1	PIK3R1	796	0.28	0.26	YES
3	CAMK2B	CAMK2B	CAMK2B	1070	0.24	0.34	YES
4	PRKAR2B	PRKAR2B	PRKAR2B	1204	0.23	0.43	YES
5	RPS6KA5	RPS6KA5	RPS6KA5	1957	0.17	0.45	YES
6	PRKCA	PRKCA	PRKCA	2051	0.17	0.51	YES
7	CAMK2D	CAMK2D	CAMK2D	4239	0.093	0.43	NO
8	PRKACG	PRKACG	PRKACG	4386	0.089	0.46	NO
9	PRKAR2A	PRKAR2A	PRKAR2A	4473	0.087	0.48	NO
10	PRKAR1B	PRKAR1B	PRKAR1B	5667	0.062	0.44	NO
11	PRKACB	PRKACB	PRKACB	8136	0.018	0.31	NO
12	GNAS	GNAS	GNAS	8439	0.014	0.3	NO
13	RAC1	RAC1	RAC1	8704	0.009	0.29	NO
14	MAPK14	MAPK14	MAPK14	8841	0.0067	0.28	NO
15	AKT1	AKT1	AKT1	9408	-0.0022	0.25	NO
16	MAPK3	MAPK3	MAPK3	9483	-0.0032	0.25	NO
17	GRB2	GRB2	GRB2	9634	-0.0055	0.24	NO
18	SOS1	SOS1	SOS1	9679	-0.0063	0.24	NO
19	MAPK1	MAPK1	MAPK1	10010	-0.012	0.23	NO
20	ADCY1	ADCY1	ADCY1	10564	-0.021	0.21	NO
21	CAMK2G	CAMK2G	CAMK2G	10983	-0.029	0.19	NO
22	CREB1	CREB1	CREB1	11489	-0.039	0.18	NO
23	RPS6KA1	RPS6KA1	RPS6KA1	11946	-0.048	0.18	NO
24	PRKAR1A	PRKAR1A	PRKAR1A	12311	-0.056	0.18	NO
25	PIK3CA	PIK3CA	PIK3CA	13093	-0.074	0.16	NO
26	CAMK2A	CAMK2A	CAMK2A	14344	-0.11	0.14	NO
27	HRAS	HRAS	HRAS	14854	-0.13	0.16	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: BIOCARTA GH PATHWAY.

Figure S56. 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 CREB PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ACSM1	ACSM1	ACSM1	14	0.67	0.14	YES
2	ACSM3	ACSM3	ACSM3	84	0.51	0.24	YES
3	GAD1	GAD1	GAD1	308	0.39	0.3	YES
4	ABAT	ABAT	ABAT	434	0.35	0.37	YES
5	L2HGDH	L2HGDH	L2HGDH	976	0.26	0.39	YES
6	HMGCS1	HMGCS1	HMGCS1	977	0.26	0.44	YES
7	ACSM2A	ACSM2A	ACSM2A	1232	0.23	0.47	YES
8	ACSM5	ACSM5	ACSM5	1235	0.23	0.52	YES
9	ALDH5A1	ALDH5A1	ALDH5A1	2130	0.16	0.5	YES
10	ACAT2	ACAT2	ACAT2	2263	0.16	0.52	YES
11	HMGCS2	HMGCS2	HMGCS2	2626	0.14	0.53	YES
12	AACS	AACS	AACS	2862	0.13	0.55	YES
13	OXCT1	OXCT1	OXCT1	3107	0.12	0.56	YES
14	HADH	HADH	HADH	3313	0.12	0.57	YES
15	AKR1B10	AKR1B10	AKR1B10	3762	0.1	0.56	NO
16	ALDH1B1	ALDH1B1	ALDH1B1	4294	0.091	0.55	NO
17	ACADS	ACADS	ACADS	4819	0.079	0.54	NO
18	PDHA1	PDHA1	PDHA1	5063	0.074	0.54	NO
19	BDH2	BDH2	BDH2	5518	0.065	0.53	NO
20	ALDH3A2	ALDH3A2	ALDH3A2	5552	0.065	0.54	NO
21	ALDH9A1	ALDH9A1	ALDH9A1	6002	0.056	0.53	NO
22	HMGCL	HMGCL	HMGCL	6975	0.039	0.48	NO
23	ALDH7A1	ALDH7A1	ALDH7A1	8293	0.016	0.41	NO
24	ALDH2	ALDH2	ALDH2	8397	0.014	0.4	NO
25	ECHS1	ECHS1	ECHS1	8543	0.012	0.4	NO
26	HADHA	HADHA	HADHA	10064	-0.013	0.32	NO
27	ACAT1	ACAT1	ACAT1	11704	-0.043	0.23	NO
28	OXCT2	OXCT2	OXCT2	12743	-0.066	0.19	NO
29	PDHB	PDHB	PDHB	13552	-0.087	0.16	NO
30	BDH1	BDH1	BDH1	15577	-0.17	0.078	NO
31	EHHADH	EHHADH	EHHADH	16105	-0.21	0.091	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: BIOCARTA CREB PATHWAY.

Figure S58. 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: ST ERK1 ERK2 MAPK PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PRPS2	PRPS2	PRPS2	38	0.6	0.22	YES
2	ALDOB	ALDOB	ALDOB	443	0.35	0.32	YES
3	TKTL1	TKTL1	TKTL1	2302	0.16	0.27	YES
4	PRPS1	PRPS1	PRPS1	2651	0.14	0.3	YES
5	LOC729020	LOC729020	LOC729020	2659	0.14	0.35	YES
6	GPI	GPI	GPI	2869	0.13	0.39	YES
7	PGM2	PGM2	PGM2	2968	0.13	0.43	YES
8	PGM1	PGM1	PGM1	2988	0.13	0.47	YES
9	ALDOC	ALDOC	ALDOC	3142	0.12	0.51	YES
10	FBP2	FBP2	FBP2	4257	0.092	0.48	NO
11	PFKM	PFKM	PFKM	5051	0.074	0.46	NO
12	ALDOA	ALDOA	ALDOA	5188	0.072	0.48	NO
13	PFKL	PFKL	PFKL	5901	0.057	0.46	NO
14	PGLS	PGLS	PGLS	5925	0.057	0.48	NO
15	DERA	DERA	DERA	6961	0.039	0.44	NO
16	RPE	RPE	RPE	7178	0.035	0.44	NO
17	PGD	PGD	PGD	8916	0.0056	0.34	NO
18	RBKS	RBKS	RBKS	9659	-0.006	0.3	NO
19	PFKP	PFKP	PFKP	9879	-0.0099	0.29	NO
20	G6PD	G6PD	G6PD	10188	-0.015	0.28	NO
21	H6PD	H6PD	H6PD	10426	-0.019	0.27	NO
22	TALDO1	TALDO1	TALDO1	12267	-0.055	0.19	NO
23	RPIA	RPIA	RPIA	12494	-0.06	0.2	NO
24	TKT	TKT	TKT	12647	-0.064	0.21	NO
25	PRPS1L1	PRPS1L1	PRPS1L1	12996	-0.072	0.22	NO
26	FBP1	FBP1	FBP1	14708	-0.13	0.17	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: ST ERK1 ERK2 MAPK PATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: ST ERK1 ERK2 MAPK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus4 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG STARCH AND SUCROSE METABOLISM	35	genes.ES.table	0.65	1.7	0.0042	0.39	0.75	0.29	0.061	0.27	0.18	0.1
BIOCARTA HDAC PATHWAY	26	genes.ES.table	0.59	1.8	0	1	0.52	0.31	0.18	0.25	0.42	0.3
BIOCARTA IL2RB PATHWAY	38	genes.ES.table	0.71	1.9	0.002	0.95	0.28	0.34	0.097	0.31	0	0.24
SIG BCR SIGNALING PATHWAY	46	genes.ES.table	0.6	1.7	0.014	0.52	0.73	0.3	0.12	0.27	0.24	0.14
PID FCER1PATHWAY	61	genes.ES.table	0.63	1.7	0.006	0.63	0.69	0.3	0.095	0.27	0.28	0.18
PID BCR 5PATHWAY	65	genes.ES.table	0.56	1.7	0.04	0.38	0.81	0.31	0.16	0.26	0.19	0.095
PID GMCSF PATHWAY	37	genes.ES.table	0.64	1.7	0.01	0.41	0.75	0.35	0.16	0.3	0.19	0.11
PID TCR PATHWAY	66	genes.ES.table	0.73	1.7	0.012	0.49	0.73	0.44	0.12	0.39	0.23	0.13
PID CD8TCRPATHWAY	53	genes.ES.table	0.73	1.7	0.0081	0.39	0.77	0.47	0.15	0.4	0.18	0.099
PID TCPTP PATHWAY	42	genes.ES.table	0.53	1.7	0.018	0.38	0.8	0.36	0.2	0.28	0.19	0.097

genes ES table in pathway: KEGG STARCH AND SUCROSE METABOLISM

Table S31. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IL2RB	IL2RB	IL2RB	31	0.88	0.11	YES
2	FASLG	FASLG	FASLG	138	0.68	0.18	YES
3	PIK3CG	PIK3CG	PIK3CG	163	0.66	0.27	YES
4	IL2RG	IL2RG	IL2RG	202	0.64	0.34	YES
5	IL2RA	IL2RA	IL2RA	336	0.58	0.41	YES
6	IKZF3	IKZF3	IKZF3	395	0.55	0.47	YES
7	SYK	SYK	SYK	545	0.5	0.53	YES
8	JAK3	JAK3	JAK3	794	0.44	0.57	YES
9	BCL2	BCL2	BCL2	1394	0.33	0.57	YES
10	PTPN6	PTPN6	PTPN6	1559	0.31	0.6	YES
11	STAT5A	STAT5A	STAT5A	1627	0.3	0.64	YES
12	PIK3R1	PIK3R1	PIK3R1	1657	0.3	0.67	YES
13	FAS	FAS	FAS	1721	0.29	0.71	YES
14	STAT5B	STAT5B	STAT5B	2744	0.2	0.67	NO
15	MAPK3	MAPK3	MAPK3	4472	0.11	0.59	NO
16	JAK1	JAK1	JAK1	4779	0.097	0.58	NO
17	FOS	FOS	FOS	6045	0.06	0.52	NO
18	CFLAR	CFLAR	CFLAR	6344	0.052	0.51	NO
19	SOS1	SOS1	SOS1	6990	0.037	0.48	NO
20	BAD	BAD	BAD	7089	0.034	0.48	NO
21	RPS6KB1	RPS6KB1	RPS6KB1	7186	0.032	0.48	NO
22	BCL2L1	BCL2L1	BCL2L1	7288	0.03	0.47	NO
23	SOCS3	SOCS3	SOCS3	7444	0.027	0.47	NO
24	GRB2	GRB2	GRB2	8173	0.012	0.43	NO
25	RAF1	RAF1	RAF1	8205	0.012	0.43	NO
26	PIK3CA	PIK3CA	PIK3CA	8369	0.0084	0.42	NO
27	SHC1	SHC1	SHC1	8921	-0.0026	0.39	NO
28	NMI	NMI	NMI	8928	-0.0029	0.39	NO
29	AKT1	AKT1	AKT1	9017	-0.0045	0.38	NO
30	IRS1	IRS1	IRS1	10772	-0.038	0.29	NO
31	CBL	CBL	CBL	11295	-0.049	0.27	NO
32	MAPK1	MAPK1	MAPK1	11645	-0.056	0.25	NO
33	CRKL	CRKL	CRKL	11706	-0.058	0.26	NO
34	SOCS1	SOCS1	SOCS1	12933	-0.088	0.2	NO
35	E2F1	E2F1	E2F1	13396	-0.1	0.18	NO
36	PPIA	PPIA	PPIA	13454	-0.1	0.2	NO
37	HRAS	HRAS	HRAS	13470	-0.1	0.21	NO
38	MYC	MYC	MYC	16006	-0.27	0.097	NO

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

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

genes ES table in pathway: BIOCARTA HDAC PATHWAY

Table S32. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IGF1	IGF1	IGF1	95	0.72	0.18	YES
2	PIK3CG	PIK3CG	PIK3CG	163	0.66	0.35	YES
3	MAP2K6	MAP2K6	MAP2K6	1006	0.4	0.41	YES
4	PIK3R1	PIK3R1	PIK3R1	1657	0.3	0.45	YES
5	MEF2C	MEF2C	MEF2C	2003	0.26	0.5	YES
6	NFATC2	NFATC2	NFATC2	2108	0.25	0.56	YES
7	HDAC5	HDAC5	HDAC5	2984	0.18	0.56	YES
8	CAMK1G	CAMK1G	CAMK1G	3168	0.17	0.59	YES
9	NFATC1	NFATC1	NFATC1	4772	0.097	0.53	NO
10	IGF1R	IGF1R	IGF1R	6025	0.06	0.47	NO
11	PPP3CA	PPP3CA	PPP3CA	6175	0.056	0.48	NO
12	PPP3CC	PPP3CC	PPP3CC	7429	0.027	0.41	NO
13	MEF2A	MEF2A	MEF2A	7868	0.018	0.39	NO
14	PIK3CA	PIK3CA	PIK3CA	8369	0.0084	0.37	NO
15	MAPK7	MAPK7	MAPK7	8375	0.0082	0.37	NO
16	AKT1	AKT1	AKT1	9017	-0.0045	0.33	NO
17	CABIN1	CABIN1	CABIN1	9655	-0.016	0.3	NO
18	PPP3CB	PPP3CB	PPP3CB	10164	-0.026	0.28	NO
19	CALM1	CALM1	CALM1	10276	-0.029	0.28	NO
20	MEF2D	MEF2D	MEF2D	10534	-0.034	0.28	NO
21	CAMK1	CAMK1	CAMK1	11781	-0.06	0.22	NO
22	INSR	INSR	INSR	12175	-0.069	0.22	NO
23	YWHAH	YWHAH	YWHAH	12597	-0.079	0.21	NO
24	CALM3	CALM3	CALM3	12638	-0.08	0.23	NO
25	CALM2	CALM2	CALM2	12956	-0.089	0.24	NO
26	MAPK14	MAPK14	MAPK14	13897	-0.12	0.22	NO

Figure S63. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA HDAC PATHWAY.

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

Table S33. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FASLG	FASLG	FASLG	138	0.68	0.1	YES
2	PIK3CD	PIK3CD	PIK3CD	513	0.51	0.16	YES
3	SYK	SYK	SYK	545	0.5	0.24	YES
4	BTK	BTK	BTK	610	0.48	0.32	YES
5	MAP2K6	MAP2K6	MAP2K6	1006	0.4	0.36	YES
6	FAIM2	FAIM2	FAIM2	1308	0.35	0.4	YES
7	BIRC3	BIRC3	BIRC3	1313	0.35	0.45	YES
8	PIK3R1	PIK3R1	PIK3R1	1657	0.3	0.48	YES
9	FAS	FAS	FAS	1721	0.29	0.53	YES
10	CASP10	CASP10	CASP10	2105	0.25	0.55	YES
11	SMPD1	SMPD1	SMPD1	2437	0.22	0.56	YES
12	IKBKB	IKBKB	IKBKB	2693	0.21	0.58	YES
13	PIK3CB	PIK3CB	PIK3CB	3429	0.16	0.57	NO
14	PIK3R2	PIK3R2	PIK3R2	4715	0.099	0.51	NO
15	MAP3K1	MAP3K1	MAP3K1	4767	0.097	0.52	NO
16	MAPK9	MAPK9	MAPK9	5210	0.083	0.51	NO
17	SRC	SRC	SRC	5993	0.061	0.48	NO
18	MAPK10	MAPK10	MAPK10	6087	0.058	0.48	NO
19	CASP8	CASP8	CASP8	6103	0.058	0.49	NO
20	FADD	FADD	FADD	6136	0.057	0.5	NO
21	CFLAR	CFLAR	CFLAR	6344	0.052	0.49	NO
22	PDPK1	PDPK1	PDPK1	7074	0.035	0.46	NO
23	IKBKG	IKBKG	IKBKG	7452	0.026	0.44	NO
24	EZR	EZR	EZR	7760	0.02	0.43	NO
25	RIPK1	RIPK1	RIPK1	7939	0.017	0.42	NO
26	CLTC	CLTC	CLTC	8069	0.014	0.41	NO
27	PIK3R3	PIK3R3	PIK3R3	8181	0.012	0.41	NO
28	PIK3CA	PIK3CA	PIK3CA	8369	0.0084	0.4	NO
29	AKT1	AKT1	AKT1	9017	-0.0045	0.36	NO
30	BID	BID	BID	9843	-0.021	0.32	NO
31	MAP2K7	MAP2K7	MAP2K7	11117	-0.045	0.26	NO
32	RFC1	RFC1	RFC1	11608	-0.056	0.24	NO
33	CHUK	CHUK	CHUK	12387	-0.074	0.2	NO
34	MAPK11	MAPK11	MAPK11	13383	-0.1	0.17	NO
35	BIRC2	BIRC2	BIRC2	13518	-0.11	0.18	NO
36	MAPK14	MAPK14	MAPK14	13897	-0.12	0.17	NO
37	CASP3	CASP3	CASP3	13926	-0.12	0.19	NO
38	MAPK8	MAPK8	MAPK8	14381	-0.14	0.19	NO

Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL2RB PATHWAY.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: SIG BCR SIGNALING PATHWAY

Table S34. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PPARGC1A	PPARGC1A	PPARGC1A	68	0.77	0.13	YES
2	KRT8	KRT8	KRT8	73	0.77	0.26	YES
3	MITF	MITF	MITF	373	0.56	0.34	YES
4	KRT19	KRT19	KRT19	541	0.5	0.41	YES
5	PLA2G4A	PLA2G4A	PLA2G4A	936	0.41	0.46	YES
6	NOS2	NOS2	NOS2	1786	0.28	0.46	YES
7	MEF2C	MEF2C	MEF2C	2003	0.26	0.49	YES
8	MAPKAPK3	MAPKAPK3	MAPKAPK3	2024	0.26	0.53	YES
9	HSPB1	HSPB1	HSPB1	2238	0.24	0.56	YES
10	ESR1	ESR1	ESR1	4290	0.12	0.47	NO
11	MAPKAPK5	MAPKAPK5	MAPKAPK5	4733	0.098	0.46	NO
12	JUN	JUN	JUN	4911	0.093	0.46	NO
13	CEBPB	CEBPB	CEBPB	4972	0.09	0.48	NO
14	CSNK2A2	CSNK2A2	CSNK2A2	5400	0.077	0.46	NO
15	RPS6KA5	RPS6KA5	RPS6KA5	5544	0.072	0.47	NO
16	DDIT3	DDIT3	DDIT3	5609	0.071	0.48	NO
17	CSNK2A1	CSNK2A1	CSNK2A1	5932	0.062	0.47	NO
18	CREB1	CREB1	CREB1	6212	0.055	0.46	NO
19	PTGS2	PTGS2	PTGS2	6302	0.053	0.47	NO
20	MKNK1	MKNK1	MKNK1	6472	0.049	0.47	NO
21	MAPKAPK2	MAPKAPK2	MAPKAPK2	6764	0.042	0.46	NO
22	SLC9A1	SLC9A1	SLC9A1	6831	0.041	0.46	NO
23	MEF2A	MEF2A	MEF2A	7868	0.018	0.4	NO
24	RAB5A	RAB5A	RAB5A	7912	0.017	0.4	NO
25	GDI1	GDI1	GDI1	8188	0.012	0.39	NO
26	ATF6	ATF6	ATF6	8691	0.0019	0.36	NO
27	USF1	USF1	USF1	9539	-0.014	0.32	NO
28	EIF4E	EIF4E	EIF4E	9856	-0.021	0.3	NO
29	TP53	TP53	TP53	9995	-0.023	0.3	NO
30	EIF4EBP1	EIF4EBP1	EIF4EBP1	10341	-0.03	0.29	NO
31	RPS6KA4	RPS6KA4	RPS6KA4	11563	-0.054	0.23	NO
32	HBP1	HBP1	HBP1	11612	-0.056	0.23	NO
33	CSNK2B	CSNK2B	CSNK2B	12182	-0.069	0.21	NO
34	ATF2	ATF2	ATF2	12189	-0.069	0.22	NO
35	ATF1	ATF1	ATF1	12200	-0.07	0.24	NO
36	MAPK11	MAPK11	MAPK11	13383	-0.1	0.18	NO
37	MAPK14	MAPK14	MAPK14	13897	-0.12	0.18	NO
38	ELK4	ELK4	ELK4	15666	-0.23	0.12	NO

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

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

genes ES table in pathway: PID FCER1PATHWAY

Table S35. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SNCAIP	SNCAIP	SNCAIP	126	0.7	0.11	YES
2	LCK	LCK	LCK	342	0.57	0.19	YES
3	SNCA	SNCA	SNCA	519	0.51	0.26	YES
4	SYK	SYK	SYK	545	0.5	0.34	YES
5	PLCB2	PLCB2	PLCB2	553	0.5	0.42	YES
6	HCK	HCK	HCK	977	0.41	0.47	YES
7	MAOB	MAOB	MAOB	1184	0.37	0.51	YES
8	LYN	LYN	LYN	1350	0.34	0.56	YES
9	SLC6A3	SLC6A3	SLC6A3	1518	0.32	0.6	YES
10	BLK	BLK	BLK	2486	0.22	0.58	YES
11	FGR	FGR	FGR	2503	0.22	0.62	YES
12	PARK2	PARK2	PARK2	2751	0.2	0.64	YES
13	PTK2B	PTK2B	PTK2B	2950	0.19	0.66	YES
14	FYN	FYN	FYN	4175	0.12	0.61	NO
15	MAPK3	MAPK3	MAPK3	4472	0.11	0.61	NO
16	PLD1	PLD1	PLD1	5100	0.086	0.59	NO
17	PLD2	PLD2	PLD2	5115	0.086	0.6	NO
18	CSNK2A1	CSNK2A1	CSNK2A1	5932	0.062	0.56	NO
19	SRC	SRC	SRC	5993	0.061	0.57	NO
20	PRKCD	PRKCD	PRKCD	6400	0.05	0.56	NO
21	BAD	BAD	BAD	7089	0.034	0.52	NO
22	STUB1	STUB1	STUB1	7516	0.025	0.5	NO
23	YES1	YES1	YES1	7984	0.016	0.48	NO
24	PARK7	PARK7	PARK7	8295	0.0099	0.46	NO
25	GRK5	GRK5	GRK5	8613	0.0037	0.45	NO
26	FKBP1A	FKBP1A	FKBP1A	10031	-0.024	0.37	NO
27	PPP2R5D	PPP2R5D	PPP2R5D	10807	-0.039	0.33	NO
28	UBE2L3	UBE2L3	UBE2L3	11144	-0.046	0.32	NO
29	MAPK1	MAPK1	MAPK1	11645	-0.056	0.3	NO
30	UCHL1	UCHL1	UCHL1	11842	-0.061	0.3	NO
31	TOR1A	TOR1A	TOR1A	12674	-0.081	0.27	NO
32	TH	TH	TH	13575	-0.11	0.23	NO

Figure S69. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FCER1PATHWAY.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: PID FCER1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID BCR 5PATHWAY

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ITK	ITK	ITK	27	0.89	0.057	YES
2	CD247	CD247	CD247	62	0.78	0.1	YES
3	CD3E	CD3E	CD3E	64	0.78	0.16	YES
4	PTPRC	PTPRC	PTPRC	116	0.7	0.2	YES
5	GRAP2	GRAP2	GRAP2	158	0.67	0.24	YES
6	HLA-DRB5	HLA-DRB5	HLA-DRB5	174	0.66	0.28	YES
7	HLA-DQA1	HLA-DQA1	HLA-DQA1	206	0.64	0.32	YES
8	CD3G	CD3G	CD3G	213	0.64	0.36	YES
9	TRAT1	TRAT1	TRAT1	225	0.63	0.4	YES
10	CD3D	CD3D	CD3D	265	0.6	0.44	YES
11	HLA-DQA2	HLA-DQA2	HLA-DQA2	284	0.6	0.48	YES
12	ZAP70	ZAP70	ZAP70	308	0.59	0.52	YES
13	FYB	FYB	FYB	317	0.58	0.56	YES
14	CD4	CD4	CD4	328	0.58	0.59	YES
15	LCK	LCK	LCK	342	0.57	0.63	YES
16	LCP2	LCP2	LCP2	360	0.56	0.66	YES
17	HLA-DRB1	HLA-DRB1	HLA-DRB1	584	0.49	0.68	YES
18	HLA-DPA1	HLA-DPA1	HLA-DPA1	666	0.47	0.71	YES
19	WAS	WAS	WAS	702	0.46	0.74	YES
20	PAG1	PAG1	PAG1	744	0.45	0.77	YES
21	HLA-DPB1	HLA-DPB1	HLA-DPB1	865	0.43	0.79	YES
22	LAT	LAT	LAT	1652	0.3	0.76	NO
23	PIK3R1	PIK3R1	PIK3R1	1657	0.3	0.78	NO
24	CARD11	CARD11	CARD11	2060	0.25	0.78	NO
25	IKBKB	IKBKB	IKBKB	2693	0.21	0.75	NO
26	PIK3CB	PIK3CB	PIK3CB	3429	0.16	0.72	NO
27	RIPK2	RIPK2	RIPK2	4431	0.11	0.67	NO
28	PIK3R2	PIK3R2	PIK3R2	4715	0.099	0.66	NO
29	NFKBIA	NFKBIA	NFKBIA	4886	0.094	0.66	NO
30	NCK1	NCK1	NCK1	5107	0.086	0.65	NO
31	MALT1	MALT1	MALT1	5924	0.062	0.61	NO
32	PAK1	PAK1	PAK1	6317	0.053	0.59	NO
33	TRAF6	TRAF6	TRAF6	6412	0.05	0.59	NO
34	TAB2	TAB2	TAB2	7068	0.035	0.56	NO
35	PDPK1	PDPK1	PDPK1	7074	0.035	0.56	NO
36	IKBKG	IKBKG	IKBKG	7452	0.026	0.54	NO
37	PAK2	PAK2	PAK2	7769	0.02	0.52	NO
38	PLCG1	PLCG1	PLCG1	8085	0.014	0.5	NO
39	PIK3CA	PIK3CA	PIK3CA	8369	0.0084	0.49	NO
40	RELA	RELA	RELA	8802	-0.00044	0.46	NO
41	VASP	VASP	VASP	9469	-0.013	0.43	NO
42	UBE2N	UBE2N	UBE2N	9511	-0.014	0.42	NO
43	CSK	CSK	CSK	9698	-0.018	0.42	NO
44	MAP3K7	MAP3K7	MAP3K7	9753	-0.019	0.41	NO
45	ENAH	ENAH	ENAH	9897	-0.022	0.41	NO
46	PTEN	PTEN	PTEN	9998	-0.023	0.4	NO
47	BCL10	BCL10	BCL10	10492	-0.033	0.38	NO
48	PRKCQ	PRKCQ	PRKCQ	10545	-0.034	0.38	NO
49	EVL	EVL	EVL	11459	-0.052	0.33	NO
50	CHUK	CHUK	CHUK	12387	-0.074	0.28	NO
51	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	16414	-0.32	0.074	NO

Figure S71. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID BCR 5PATHWAY.

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

genes ES table in pathway: PID GMCSF PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PIK3CG	PIK3CG	PIK3CG	163	0.66	0.15	YES
2	PIK3CD	PIK3CD	PIK3CD	513	0.51	0.25	YES
3	PIK3R6	PIK3R6	PIK3R6	1148	0.37	0.3	YES
4	PIK3C2B	PIK3C2B	PIK3C2B	1630	0.3	0.34	YES
5	PIK3R1	PIK3R1	PIK3R1	1657	0.3	0.41	YES
6	PIP4K2A	PIP4K2A	PIP4K2A	1915	0.27	0.46	YES
7	INPP4B	INPP4B	INPP4B	1943	0.26	0.52	YES
8	PIK3R5	PIK3R5	PIK3R5	1998	0.26	0.58	YES
9	MTM1	MTM1	MTM1	2655	0.21	0.59	YES
10	PIK3CB	PIK3CB	PIK3CB	3429	0.16	0.58	NO
11	MTMR1	MTMR1	MTMR1	4208	0.12	0.57	NO
12	PIK3C2G	PIK3C2G	PIK3C2G	4380	0.11	0.58	NO
13	PIK3R2	PIK3R2	PIK3R2	4715	0.099	0.59	NO
14	PIP5K1B	PIP5K1B	PIP5K1B	5112	0.086	0.59	NO
15	INPP5K	INPP5K	INPP5K	6220	0.055	0.54	NO
16	MTMR14	MTMR14	MTMR14	6748	0.043	0.52	NO
17	INPP5J	INPP5J	INPP5J	7067	0.035	0.51	NO
18	PIK3R3	PIK3R3	PIK3R3	8181	0.012	0.45	NO
19	PIP4K2B	PIP4K2B	PIP4K2B	8210	0.012	0.45	NO
20	PIK3CA	PIK3CA	PIK3CA	8369	0.0084	0.44	NO
21	PIK3C2A	PIK3C2A	PIK3C2A	8590	0.0042	0.43	NO
22	SYNJ2	SYNJ2	SYNJ2	8833	-0.0011	0.42	NO
23	PI4K2B	PI4K2B	PI4K2B	9891	-0.022	0.36	NO
24	PIP5K1C	PIP5K1C	PIP5K1C	9909	-0.022	0.37	NO
25	PTEN	PTEN	PTEN	9998	-0.023	0.37	NO
26	MTMR6	MTMR6	MTMR6	10226	-0.028	0.36	NO
27	PI4K2A	PI4K2A	PI4K2A	10347	-0.03	0.36	NO
28	INPPL1	INPPL1	INPPL1	11723	-0.058	0.3	NO
29	SYNJ1	SYNJ1	SYNJ1	12527	-0.077	0.27	NO
30	MTMR3	MTMR3	MTMR3	13409	-0.1	0.24	NO

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

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

genes ES table in pathway: PID TCR PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MS4A2	MS4A2	MS4A2	24	0.9	0.076	YES
2	ITK	ITK	ITK	27	0.89	0.15	YES
3	FCER1A	FCER1A	FCER1A	358	0.56	0.18	YES
4	LCP2	LCP2	LCP2	360	0.56	0.23	YES
5	SYK	SYK	SYK	545	0.5	0.26	YES
6	BTK	BTK	BTK	610	0.48	0.3	YES
7	INPP5D	INPP5D	INPP5D	643	0.48	0.34	YES
8	KLRG1	KLRG1	KLRG1	737	0.46	0.38	YES
9	FCGR2B	FCGR2B	FCGR2B	754	0.45	0.41	YES
10	VAV1	VAV1	VAV1	889	0.42	0.44	YES
11	FCER1G	FCER1G	FCER1G	935	0.41	0.48	YES
12	PLA2G4A	PLA2G4A	PLA2G4A	936	0.41	0.51	YES
13	LAT2	LAT2	LAT2	1176	0.37	0.53	YES
14	LYN	LYN	LYN	1350	0.34	0.55	YES
15	LAT	LAT	LAT	1652	0.3	0.56	YES
16	PIK3R1	PIK3R1	PIK3R1	1657	0.3	0.58	YES
17	HCLS1	HCLS1	HCLS1	1673	0.3	0.61	YES
18	DOK1	DOK1	DOK1	1686	0.3	0.63	YES
19	NFATC2	NFATC2	NFATC2	2108	0.25	0.63	NO
20	IKBKB	IKBKB	IKBKB	2693	0.21	0.61	NO
21	WIPF1	WIPF1	WIPF1	2858	0.2	0.62	NO
22	PXN	PXN	PXN	3957	0.13	0.57	NO
23	FYN	FYN	FYN	4175	0.12	0.57	NO
24	MAPK3	MAPK3	MAPK3	4472	0.11	0.56	NO
25	DUSP1	DUSP1	DUSP1	4637	0.1	0.56	NO
26	MAP3K1	MAP3K1	MAP3K1	4767	0.097	0.56	NO
27	MAP2K4	MAP2K4	MAP2K4	4774	0.097	0.57	NO
28	JUN	JUN	JUN	4911	0.093	0.57	NO
29	NFKB1	NFKB1	NFKB1	4945	0.091	0.58	NO
30	PLD2	PLD2	PLD2	5115	0.086	0.57	NO
31	FER	FER	FER	5432	0.076	0.56	NO
32	RASA1	RASA1	RASA1	5938	0.062	0.54	NO
33	FOS	FOS	FOS	6045	0.06	0.54	NO
34	S1PR1	S1PR1	S1PR1	6083	0.058	0.54	NO
35	PTPN13	PTPN13	PTPN13	6392	0.051	0.53	NO
36	PTPN11	PTPN11	PTPN11	6523	0.048	0.52	NO
37	CBLB	CBLB	CBLB	6956	0.038	0.5	NO
38	PRKCB	PRKCB	PRKCB	6978	0.037	0.51	NO
39	SOS1	SOS1	SOS1	6990	0.037	0.51	NO
40	PTK2	PTK2	PTK2	7287	0.03	0.5	NO
41	IKBKG	IKBKG	IKBKG	7452	0.026	0.49	NO
42	PAK2	PAK2	PAK2	7769	0.02	0.47	NO
43	PLCG1	PLCG1	PLCG1	8085	0.014	0.46	NO
44	GRB2	GRB2	GRB2	8173	0.012	0.45	NO
45	RAF1	RAF1	RAF1	8205	0.012	0.45	NO
46	PIK3CA	PIK3CA	PIK3CA	8369	0.0084	0.44	NO
47	PPAP2A	PPAP2A	PPAP2A	8660	0.0027	0.43	NO
48	RELA	RELA	RELA	8802	-0.00044	0.42	NO
49	SHC1	SHC1	SHC1	8921	-0.0026	0.41	NO
50	AKT1	AKT1	AKT1	9017	-0.0045	0.41	NO
51	MAP2K2	MAP2K2	MAP2K2	10117	-0.026	0.35	NO
52	MAP2K7	MAP2K7	MAP2K7	11117	-0.045	0.29	NO
53	CBL	CBL	CBL	11295	-0.049	0.29	NO
54	MAPK1	MAPK1	MAPK1	11645	-0.056	0.27	NO
55	CHUK	CHUK	CHUK	12387	-0.074	0.24	NO
56	MAP2K1	MAP2K1	MAP2K1	12405	-0.074	0.24	NO
57	GAB2	GAB2	GAB2	13183	-0.095	0.21	NO
58	HRAS	HRAS	HRAS	13470	-0.1	0.2	NO
59	PLA2G1B	PLA2G1B	PLA2G1B	13562	-0.11	0.2	NO
60	MAPK8	MAPK8	MAPK8	14381	-0.14	0.17	NO
61	SPHK1	SPHK1	SPHK1	15596	-0.22	0.12	NO

Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TCR PATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: PID TCR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID CD8TCRPATHWAY

Table S39. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CISH	CISH	CISH	10	0.98	0.022	YES
2	IL2RB	IL2RB	IL2RB	31	0.88	0.041	YES
3	CASP1	CASP1	CASP1	152	0.67	0.049	YES
4	IRF6	IRF6	IRF6	164	0.66	0.064	YES
5	GBP7	GBP7	GBP7	166	0.66	0.078	YES
6	GBP5	GBP5	GBP5	172	0.66	0.093	YES
7	HLA-DRB5	HLA-DRB5	HLA-DRB5	174	0.66	0.11	YES
8	CSF2RB	CSF2RB	CSF2RB	175	0.66	0.12	YES
9	GBP2	GBP2	GBP2	186	0.65	0.14	YES
10	IL2RG	IL2RG	IL2RG	202	0.64	0.15	YES
11	HLA-DQA1	HLA-DQA1	HLA-DQA1	206	0.64	0.17	YES
12	PRLR	PRLR	PRLR	218	0.63	0.18	YES
13	PTAFR	PTAFR	PTAFR	241	0.62	0.19	YES
14	HLA-DQA2	HLA-DQA2	HLA-DQA2	284	0.6	0.2	YES
15	HGF	HGF	HGF	295	0.59	0.22	YES
16	IL2RA	IL2RA	IL2RA	336	0.58	0.23	YES
17	LCK	LCK	LCK	342	0.57	0.24	YES
18	CAMK2A	CAMK2A	CAMK2A	349	0.57	0.25	YES
19	IL7	IL7	IL7	370	0.56	0.26	YES
20	IRF5	IRF5	IRF5	496	0.52	0.27	YES
21	PIK3CD	PIK3CD	PIK3CD	513	0.51	0.28	YES
22	PELI2	PELI2	PELI2	532	0.51	0.29	YES
23	SYK	SYK	SYK	545	0.5	0.3	YES
24	HLA-DRB1	HLA-DRB1	HLA-DRB1	584	0.49	0.31	YES
25	CIITA	CIITA	CIITA	598	0.49	0.32	YES
26	CSF2RA	CSF2RA	CSF2RA	647	0.47	0.33	YES
27	HLA-DPA1	HLA-DPA1	HLA-DPA1	666	0.47	0.34	YES
28	JAK3	JAK3	JAK3	794	0.44	0.34	YES
29	IRF4	IRF4	IRF4	803	0.44	0.35	YES
30	HLA-DPB1	HLA-DPB1	HLA-DPB1	865	0.43	0.36	YES
31	VAV1	VAV1	VAV1	889	0.42	0.36	YES
32	CD44	CD44	CD44	894	0.42	0.37	YES
33	IRF8	IRF8	IRF8	913	0.42	0.38	YES
34	HCK	HCK	HCK	977	0.41	0.39	YES
35	MX2	MX2	MX2	986	0.4	0.4	YES
36	MAP2K6	MAP2K6	MAP2K6	1006	0.4	0.4	YES
37	IRAK2	IRAK2	IRAK2	1029	0.4	0.41	YES
38	GBP4	GBP4	GBP4	1160	0.37	0.41	YES
39	HLA-F	HLA-F	HLA-F	1179	0.37	0.42	YES
40	IRF1	IRF1	IRF1	1271	0.35	0.42	YES
41	LYN	LYN	LYN	1350	0.34	0.43	YES
42	MAP3K8	MAP3K8	MAP3K8	1551	0.31	0.42	YES
43	PTPN6	PTPN6	PTPN6	1559	0.31	0.43	YES
44	FCGR1A	FCGR1A	FCGR1A	1591	0.3	0.44	YES
45	IL6R	IL6R	IL6R	1597	0.3	0.44	YES
46	STAT5A	STAT5A	STAT5A	1627	0.3	0.45	YES
47	PIK3R1	PIK3R1	PIK3R1	1657	0.3	0.45	YES
48	EIF4E3	EIF4E3	EIF4E3	1682	0.3	0.46	YES
49	IL18	IL18	IL18	1807	0.28	0.46	YES
50	FCGR1B	FCGR1B	FCGR1B	1921	0.27	0.46	YES
51	IFI35	IFI35	IFI35	1931	0.27	0.46	YES
52	SOCS2	SOCS2	SOCS2	2089	0.25	0.46	YES
53	PELI3	PELI3	PELI3	2284	0.24	0.45	YES
54	HLA-B	HLA-B	HLA-B	2307	0.24	0.46	YES
55	OAS2	OAS2	OAS2	2313	0.24	0.46	YES
56	HLA-A	HLA-A	HLA-A	2371	0.23	0.46	YES
57	IL1B	IL1B	IL1B	2463	0.22	0.46	YES
58	GBP1	GBP1	GBP1	2519	0.22	0.47	YES
59	CSF2	CSF2	CSF2	2535	0.22	0.47	YES
60	IL6ST	IL6ST	IL6ST	2563	0.22	0.47	YES
61	SQSTM1	SQSTM1	SQSTM1	2620	0.21	0.48	YES
62	IRF7	IRF7	IRF7	2641	0.21	0.48	YES
63	BLNK	BLNK	BLNK	2674	0.21	0.48	YES
64	IRAK3	IRAK3	IRAK3	2687	0.21	0.48	YES
65	IKBKB	IKBKB	IKBKB	2693	0.21	0.49	YES
66	STAT5B	STAT5B	STAT5B	2744	0.2	0.49	YES
67	PSMB8	PSMB8	PSMB8	2748	0.2	0.5	YES
68	UBA7	UBA7	UBA7	2764	0.2	0.5	YES
69	IL1RN	IL1RN	IL1RN	2876	0.19	0.5	YES
70	PELI1	PELI1	PELI1	2941	0.19	0.5	YES
71	PTK2B	PTK2B	PTK2B	2950	0.19	0.5	YES
72	HERC5	HERC5	HERC5	3004	0.18	0.5	YES
73	HLA-C	HLA-C	HLA-C	3011	0.18	0.51	YES
74	IL1A	IL1A	IL1A	3025	0.18	0.51	YES
75	NOD1	NOD1	NOD1	3061	0.18	0.51	YES
76	B2M	B2M	B2M	3070	0.18	0.52	YES
77	IL7R	IL7R	IL7R	3411	0.16	0.5	NO
78	HLA-G	HLA-G	HLA-G	3427	0.16	0.5	NO
79	PIK3CB	PIK3CB	PIK3CB	3429	0.16	0.51	NO
80	IFITM1	IFITM1	IFITM1	3436	0.16	0.51	NO
81	IFIT3	IFIT3	IFIT3	3487	0.15	0.51	NO
82	IFNG	IFNG	IFNG	3532	0.15	0.51	NO
83	IRAK4	IRAK4	IRAK4	3672	0.14	0.51	NO
84	GBP6	GBP6	GBP6	3930	0.13	0.5	NO
85	IFIT2	IFIT2	IFIT2	3982	0.13	0.5	NO
86	MYD88	MYD88	MYD88	4115	0.12	0.49	NO
87	FYN	FYN	FYN	4175	0.12	0.49	NO
88	DDX58	DDX58	DDX58	4224	0.12	0.49	NO
89	PML	PML	PML	4244	0.12	0.49	NO
90	RIPK2	RIPK2	RIPK2	4431	0.11	0.48	NO
91	MAPK3	MAPK3	MAPK3	4472	0.11	0.48	NO
92	ICAM1	ICAM1	ICAM1	4597	0.1	0.48	NO
93	IL3RA	IL3RA	IL3RA	4638	0.1	0.48	NO
94	NOD2	NOD2	NOD2	4699	0.1	0.48	NO
95	PIK3R2	PIK3R2	PIK3R2	4715	0.099	0.48	NO
96	SP100	SP100	SP100	4743	0.098	0.48	NO
97	IFITM2	IFITM2	IFITM2	4766	0.097	0.48	NO
98	MAP2K4	MAP2K4	MAP2K4	4774	0.097	0.48	NO
99	JAK1	JAK1	JAK1	4779	0.097	0.48	NO
100	CAMK2D	CAMK2D	CAMK2D	4842	0.095	0.48	NO
101	MAP3K3	MAP3K3	MAP3K3	4931	0.092	0.48	NO
102	STAT2	STAT2	STAT2	4938	0.091	0.48	NO
103	RNASEL	RNASEL	RNASEL	5012	0.088	0.48	NO
104	IRS2	IRS2	IRS2	5066	0.087	0.48	NO
105	STAT3	STAT3	STAT3	5143	0.085	0.48	NO
106	XAF1	XAF1	XAF1	5156	0.084	0.48	NO
107	IFNAR2	IFNAR2	IFNAR2	5191	0.084	0.48	NO
108	GHR	GHR	GHR	5268	0.081	0.48	NO
109	UBE2L6	UBE2L6	UBE2L6	5281	0.081	0.48	NO
110	PRKACB	PRKACB	PRKACB	5535	0.073	0.46	NO
111	TAB3	TAB3	TAB3	5554	0.072	0.46	NO
112	JAK2	JAK2	JAK2	5762	0.067	0.45	NO
113	IL6	IL6	IL6	5982	0.061	0.44	NO
114	TNIP2	TNIP2	TNIP2	6173	0.056	0.43	NO
115	PTPN1	PTPN1	PTPN1	6347	0.052	0.42	NO
116	PRKCD	PRKCD	PRKCD	6400	0.05	0.42	NO
117	TRAF6	TRAF6	TRAF6	6412	0.05	0.42	NO
118	KPNA4	KPNA4	KPNA4	6536	0.047	0.42	NO
119	UBE2E1	UBE2E1	UBE2E1	6562	0.047	0.42	NO
120	FLNB	FLNB	FLNB	6669	0.044	0.41	NO
121	TOLLIP	TOLLIP	TOLLIP	6772	0.042	0.41	NO
122	KPNA1	KPNA1	KPNA1	6819	0.041	0.4	NO
123	SOS1	SOS1	SOS1	6990	0.037	0.4	NO
124	NCAM1	NCAM1	NCAM1	7061	0.035	0.39	NO
125	TAB2	TAB2	TAB2	7068	0.035	0.39	NO
126	NFKB2	NFKB2	NFKB2	7094	0.034	0.39	NO
127	YWHAB	YWHAB	YWHAB	7106	0.034	0.39	NO
128	PPM1B	PPM1B	PPM1B	7167	0.033	0.39	NO
129	IFITM3	IFITM3	IFITM3	7402	0.028	0.38	NO
130	SOCS3	SOCS3	SOCS3	7444	0.027	0.38	NO
131	IKBKG	IKBKG	IKBKG	7452	0.026	0.38	NO
132	NUP43	NUP43	NUP43	7527	0.025	0.37	NO
133	TEC	TEC	TEC	7695	0.022	0.36	NO
134	OASL	OASL	OASL	7765	0.02	0.36	NO
135	EIF4G2	EIF4G2	EIF4G2	7850	0.018	0.36	NO
136	IFIT1	IFIT1	IFIT1	7852	0.018	0.36	NO
137	YES1	YES1	YES1	7984	0.016	0.35	NO
138	IP6K2	IP6K2	IP6K2	7993	0.016	0.35	NO
139	OAS1	OAS1	OAS1	8004	0.015	0.35	NO
140	IRF3	IRF3	IRF3	8027	0.015	0.35	NO
141	PLCG1	PLCG1	PLCG1	8085	0.014	0.34	NO
142	EIF4G1	EIF4G1	EIF4G1	8155	0.013	0.34	NO
143	GRB2	GRB2	GRB2	8173	0.012	0.34	NO
144	PIK3R3	PIK3R3	PIK3R3	8181	0.012	0.34	NO
145	RAF1	RAF1	RAF1	8205	0.012	0.34	NO
146	YWHAZ	YWHAZ	YWHAZ	8261	0.011	0.34	NO
147	CRK	CRK	CRK	8267	0.01	0.34	NO
148	NUP88	NUP88	NUP88	8269	0.01	0.34	NO
149	PIK3CA	PIK3CA	PIK3CA	8369	0.0084	0.33	NO
150	EIF4G3	EIF4G3	EIF4G3	8412	0.0075	0.33	NO
151	AAAS	AAAS	AAAS	8454	0.0066	0.33	NO
152	PIAS1	PIAS1	PIAS1	8469	0.0063	0.32	NO
153	SH2B1	SH2B1	SH2B1	8756	0.0007	0.31	NO
154	RELA	RELA	RELA	8802	-0.00044	0.31	NO
155	EIF4A2	EIF4A2	EIF4A2	8826	-0.001	0.3	NO
156	ISG15	ISG15	ISG15	8828	-0.001	0.3	NO
157	SHC1	SHC1	SHC1	8921	-0.0026	0.3	NO
158	SKP1	SKP1	SKP1	8931	-0.0029	0.3	NO
159	ADAR	ADAR	ADAR	8997	-0.0042	0.3	NO
160	NUP153	NUP153	NUP153	9061	-0.0052	0.29	NO
161	SEH1L	SEH1L	SEH1L	9238	-0.0083	0.28	NO
162	IFNGR1	IFNGR1	IFNGR1	9400	-0.012	0.27	NO
163	RANBP2	RANBP2	RANBP2	9411	-0.012	0.27	NO
164	POM121	POM121	POM121	9416	-0.012	0.27	NO
165	IL1R1	IL1R1	IL1R1	9422	-0.012	0.27	NO
166	UBE2N	UBE2N	UBE2N	9511	-0.014	0.27	NO
167	IRF2	IRF2	IRF2	9569	-0.015	0.26	NO
168	TAB1	TAB1	TAB1	9712	-0.018	0.26	NO
169	MAP3K7	MAP3K7	MAP3K7	9753	-0.019	0.26	NO
170	EIF4E	EIF4E	EIF4E	9856	-0.021	0.25	NO
171	STAT1	STAT1	STAT1	9907	-0.022	0.25	NO
172	NUP85	NUP85	NUP85	9932	-0.022	0.25	NO
173	EGR1	EGR1	EGR1	10042	-0.024	0.24	NO
174	ARIH1	ARIH1	ARIH1	10047	-0.024	0.24	NO
175	CUL1	CUL1	CUL1	10077	-0.025	0.24	NO
176	MAP2K2	MAP2K2	MAP2K2	10117	-0.026	0.24	NO
177	NUP37	NUP37	NUP37	10476	-0.033	0.22	NO
178	NUP50	NUP50	NUP50	10517	-0.033	0.22	NO
179	IL1RAP	IL1RAP	IL1RAP	10551	-0.034	0.22	NO
180	IRS1	IRS1	IRS1	10772	-0.038	0.2	NO
181	NUP107	NUP107	NUP107	11063	-0.044	0.19	NO
182	CBL	CBL	CBL	11295	-0.049	0.18	NO
183	NUP214	NUP214	NUP214	11303	-0.049	0.18	NO
184	NEDD4	NEDD4	NEDD4	11353	-0.05	0.18	NO
185	NUP54	NUP54	NUP54	11372	-0.05	0.18	NO
186	RAE1	RAE1	RAE1	11381	-0.05	0.18	NO
187	NUP93	NUP93	NUP93	11412	-0.051	0.18	NO
188	NUP155	NUP155	NUP155	11456	-0.052	0.18	NO
189	NUP133	NUP133	NUP133	11519	-0.053	0.17	NO
190	KPNA3	KPNA3	KPNA3	11548	-0.054	0.17	NO
191	TPR	TPR	TPR	11598	-0.055	0.17	NO
192	NUPL2	NUPL2	NUPL2	11605	-0.055	0.17	NO
193	MAPK1	MAPK1	MAPK1	11645	-0.056	0.17	NO
194	CRKL	CRKL	CRKL	11706	-0.058	0.17	NO
195	PTPN2	PTPN2	PTPN2	11708	-0.058	0.17	NO
196	INPPL1	INPPL1	INPPL1	11723	-0.058	0.17	NO
197	IFNGR2	IFNGR2	IFNGR2	11808	-0.06	0.17	NO
198	MT2A	MT2A	MT2A	11944	-0.064	0.16	NO
199	BTRC	BTRC	BTRC	11984	-0.064	0.16	NO
200	MX1	MX1	MX1	12070	-0.066	0.16	NO
201	IRAK1	IRAK1	IRAK1	12302	-0.072	0.14	NO
202	CHUK	CHUK	CHUK	12387	-0.074	0.14	NO
203	MAP2K1	MAP2K1	MAP2K1	12405	-0.074	0.14	NO
204	KPNB1	KPNB1	KPNB1	12412	-0.074	0.14	NO
205	IFI6	IFI6	IFI6	12464	-0.076	0.14	NO
206	NRAS	NRAS	NRAS	12488	-0.076	0.14	NO
207	TYK2	TYK2	TYK2	12507	-0.077	0.14	NO
208	SUMO1	SUMO1	SUMO1	12639	-0.08	0.14	NO
209	IFNAR1	IFNAR1	IFNAR1	12668	-0.081	0.14	NO
210	NUP205	NUP205	NUP205	12725	-0.082	0.14	NO
211	OAS3	OAS3	OAS3	12773	-0.084	0.14	NO
212	UBA52	UBA52	UBA52	12879	-0.087	0.13	NO
213	SOCS1	SOCS1	SOCS1	12933	-0.088	0.13	NO
214	RBX1	RBX1	RBX1	12962	-0.089	0.13	NO
215	EIF4A1	EIF4A1	EIF4A1	13026	-0.091	0.13	NO
216	KRAS	KRAS	KRAS	13044	-0.091	0.13	NO
217	RPS27A	RPS27A	RPS27A	13117	-0.093	0.13	NO
218	GAB2	GAB2	GAB2	13183	-0.095	0.13	NO
219	EIF2AK2	EIF2AK2	EIF2AK2	13215	-0.096	0.13	NO
220	NUPL1	NUPL1	NUPL1	13317	-0.1	0.12	NO
221	HRAS	HRAS	HRAS	13470	-0.1	0.12	NO
222	EIF4E2	EIF4E2	EIF4E2	13658	-0.11	0.11	NO
223	TRIM25	TRIM25	TRIM25	13740	-0.12	0.11	NO
224	EIF4A3	EIF4A3	EIF4A3	13990	-0.12	0.097	NO
225	PIN1	PIN1	PIN1	14053	-0.13	0.096	NO
226	NUP62	NUP62	NUP62	14096	-0.13	0.097	NO
227	KPNA5	KPNA5	KPNA5	14125	-0.13	0.098	NO
228	USP18	USP18	USP18	14157	-0.13	0.099	NO
229	RAPGEF1	RAPGEF1	RAPGEF1	14367	-0.14	0.091	NO
230	NUP188	NUP188	NUP188	14616	-0.16	0.08	NO
231	VCAM1	VCAM1	VCAM1	14723	-0.16	0.078	NO
232	NUP35	NUP35	NUP35	14755	-0.16	0.08	NO
233	ADAM17	ADAM17	ADAM17	14780	-0.16	0.082	NO
234	NUP210	NUP210	NUP210	14896	-0.17	0.079	NO
235	IRF9	IRF9	IRF9	15081	-0.18	0.073	NO
236	CAMK2B	CAMK2B	CAMK2B	15516	-0.22	0.053	NO
237	GH1	GH1	GH1	15775	-0.24	0.044	NO
238	KPNA2	KPNA2	KPNA2	15901	-0.26	0.042	NO
239	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	16414	-0.32	0.02	NO
240	IFI27	IFI27	IFI27	16685	-0.36	0.013	NO
241	ISG20	ISG20	ISG20	17112	-0.46	-0.00083	NO
242	PRL	PRL	PRL	17254	-0.5	0.0025	NO
243	IL1R2	IL1R2	IL1R2	17301	-0.52	0.012	NO
244	CDK1	CDK1	CDK1	17336	-0.53	0.022	NO

Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID CD8TCRPATHWAY.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: PID CD8TCRPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID TCPTP PATHWAY

Table S40. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CD247	CD247	CD247	62	0.78	0.044	YES
2	CD3E	CD3E	CD3E	64	0.78	0.092	YES
3	PDCD1LG2	PDCD1LG2	PDCD1LG2	153	0.67	0.13	YES
4	GRAP2	GRAP2	GRAP2	158	0.67	0.17	YES
5	HLA-DRB5	HLA-DRB5	HLA-DRB5	174	0.66	0.21	YES
6	CD28	CD28	CD28	183	0.65	0.25	YES
7	HLA-DQA1	HLA-DQA1	HLA-DQA1	206	0.64	0.28	YES
8	CD3G	CD3G	CD3G	213	0.64	0.32	YES
9	CD3D	CD3D	CD3D	265	0.6	0.36	YES
10	HLA-DQA2	HLA-DQA2	HLA-DQA2	284	0.6	0.39	YES
11	ICOS	ICOS	ICOS	306	0.59	0.43	YES
12	CD4	CD4	CD4	328	0.58	0.46	YES
13	LCK	LCK	LCK	342	0.57	0.5	YES
14	HLA-DRB1	HLA-DRB1	HLA-DRB1	584	0.49	0.51	YES
15	ICOSLG	ICOSLG	ICOSLG	629	0.48	0.54	YES
16	HLA-DPA1	HLA-DPA1	HLA-DPA1	666	0.47	0.57	YES
17	HLA-DPB1	HLA-DPB1	HLA-DPB1	865	0.43	0.58	YES
18	VAV1	VAV1	VAV1	889	0.42	0.61	YES
19	CTLA4	CTLA4	CTLA4	961	0.41	0.63	YES
20	CD274	CD274	CD274	964	0.41	0.65	YES
21	PDCD1	PDCD1	PDCD1	1042	0.39	0.67	YES
22	CD86	CD86	CD86	1348	0.34	0.68	YES
23	LYN	LYN	LYN	1350	0.34	0.7	YES
24	MAP3K8	MAP3K8	MAP3K8	1551	0.31	0.7	YES
25	PTPN6	PTPN6	PTPN6	1559	0.31	0.72	YES
26	PIK3R1	PIK3R1	PIK3R1	1657	0.3	0.74	YES
27	CD80	CD80	CD80	2487	0.22	0.7	NO
28	AKT3	AKT3	AKT3	3103	0.18	0.68	NO
29	BTLA	BTLA	BTLA	3281	0.17	0.68	NO
30	TNFRSF14	TNFRSF14	TNFRSF14	3750	0.14	0.66	NO
31	MAP3K14	MAP3K14	MAP3K14	3921	0.13	0.66	NO
32	FYN	FYN	FYN	4175	0.12	0.65	NO
33	RICTOR	RICTOR	RICTOR	4606	0.1	0.63	NO
34	PIK3R2	PIK3R2	PIK3R2	4715	0.099	0.63	NO
35	MLST8	MLST8	MLST8	5744	0.067	0.58	NO
36	PPP2CB	PPP2CB	PPP2CB	5913	0.063	0.57	NO
37	SRC	SRC	SRC	5993	0.061	0.57	NO
38	PAK1	PAK1	PAK1	6317	0.053	0.56	NO
39	PDPK1	PDPK1	PDPK1	7074	0.035	0.52	NO
40	THEM4	THEM4	THEM4	7159	0.033	0.52	NO
41	PAK2	PAK2	PAK2	7769	0.02	0.48	NO
42	YES1	YES1	YES1	7984	0.016	0.47	NO
43	GRB2	GRB2	GRB2	8173	0.012	0.46	NO
44	PIK3R3	PIK3R3	PIK3R3	8181	0.012	0.46	NO
45	PIK3CA	PIK3CA	PIK3CA	8369	0.0084	0.45	NO
46	PPP2CA	PPP2CA	PPP2CA	8919	-0.0026	0.42	NO
47	AKT1	AKT1	AKT1	9017	-0.0045	0.42	NO
48	RAC1	RAC1	RAC1	9616	-0.016	0.38	NO
49	CSK	CSK	CSK	9698	-0.018	0.38	NO
50	TRIB3	TRIB3	TRIB3	9871	-0.021	0.37	NO
51	MAPKAP1	MAPKAP1	MAPKAP1	10184	-0.027	0.35	NO
52	CDC42	CDC42	CDC42	10489	-0.033	0.34	NO
53	PPP2R5D	PPP2R5D	PPP2R5D	10807	-0.039	0.32	NO
54	PPP2R1B	PPP2R1B	PPP2R1B	11547	-0.054	0.28	NO
55	PPP2R5A	PPP2R5A	PPP2R5A	12314	-0.072	0.24	NO
56	MTOR	MTOR	MTOR	13637	-0.11	0.18	NO
57	PPP2R1A	PPP2R1A	PPP2R1A	14403	-0.14	0.14	NO
58	AKT2	AKT2	AKT2	14564	-0.15	0.14	NO
59	PPP2R5C	PPP2R5C	PPP2R5C	15083	-0.18	0.12	NO
60	PPP2R5E	PPP2R5E	PPP2R5E	15272	-0.2	0.13	NO
61	PPP2R5B	PPP2R5B	PPP2R5B	15306	-0.2	0.14	NO

Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TCPTP PATHWAY.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

Gene set database = c2.cp.v4.0.symbols.gmt
Expression data file = ACC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = ACC-TP.mergedcluster.txt

GSEA analysis

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

Download Results

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

References

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

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