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

Esophageal 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 ESCA-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1Q52P1S

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 "ESCA-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: 724
Number of samples: 184
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 6 :[ clus1 ] 74
pheno.type: 2 - 6 :[ clus2 ] 14
pheno.type: 3 - 6 :[ clus3 ] 42
pheno.type: 4 - 6 :[ clus4 ] 29
pheno.type: 5 - 6 :[ clus5 ] 9
pheno.type: 6 - 6 :[ clus6 ] 16

For the expression subtypes of 18768 genes in 185 samples, GSEA found enriched gene sets in each cluster using 184 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG HISTIDINE METABOLISM, KEGG SPHINGOLIPID METABOLISM, KEGG PROPANOATE METABOLISM, KEGG PEROXISOME, KEGG VASOPRESSIN REGULATED WATER REABSORPTION, KEGG VIBRIO CHOLERAE INFECTION, BIOCARTA DEATH PATHWAY, BIOCARTA PPARA PATHWAY, BIOCARTA RHO PATHWAY, ST INTERLEUKIN 4 PATHWAY

And common core enriched genes are MUC2, ABCD1, ABCD3, ABCD4, ACAA1, ACOT8, ACOX1, ACOX2, ACSL5, AGXT

clus2

Top enriched gene sets are KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG RNA DEGRADATION, KEGG BASAL TRANSCRIPTION FACTORS, KEGG SPLICEOSOME, PID FANCONI PATHWAY, PID AURORA B PATHWAY, PID ATR PATHWAY, PID ATM PATHWAY, PID PLK1 PATHWAY, PID FOXM1PATHWAY

And common core enriched genes are E2F5, RBL1, BRCA1, CDC25A, CDC25C, CHEK2, H2AFX, NUP107, NUP133, NUP43

clus3

Top enriched gene sets are KEGG BLADDER CANCER, BIOCARTA ERK PATHWAY, PID P73PATHWAY, PID AVB3 OPN PATHWAY, PID MTOR 4PATHWAY, PID ERBB1 RECEPTOR PROXIMAL PATHWAY, PID MYC PATHWAY, PID ECADHERIN NASCENTAJ PATHWAY, PID DELTANP63PATHWAY, PID A6B1 A6B4 INTEGRIN PATHWAY

And common core enriched genes are ADA, SFN, TP63, CDKN1A, MYC, CCT2, CCT4, CCT5, CCT6A, CCT7

clus4

Top enriched gene sets are KEGG GLUTATHIONE METABOLISM, KEGG NEUROTROPHIN SIGNALING PATHWAY, KEGG BASAL CELL CARCINOMA, BIOCARTA CHREBP2 PATHWAY, ST P38 MAPK PATHWAY, WNT SIGNALING, SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES, PID P75NTRPATHWAY, PID TRKRPATHWAY, PID HEDGEHOG GLIPATHWAY

And common core enriched genes are GPC1, BDNF, NGF, NGFR, NTF3, NTF4, NTRK2, PIK3CA, GPC2, GPC3

clus5

Top enriched gene sets are KEGG PURINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG ABC TRANSPORTERS, KEGG MAPK SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, KEGG LYSOSOME

And common core enriched genes are AKT3, PIK3CD, PIK3R1, PIK3CG, PIK3R5, BTK, INPP5D, NFATC2, VAV1, CAB39L

clus6

Top enriched gene sets are KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG NOTCH SIGNALING PATHWAY, KEGG THYROID CANCER, PID FOXOPATHWAY, PID ECADHERIN NASCENTAJ PATHWAY, PID RETINOIC ACID PATHWAY, PID TAP63PATHWAY, PID MAPKTRKPATHWAY, REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, REACTOME TRIF MEDIATED TLR3 SIGNALING

And common core enriched genes are MAP2K1, MAPK3, CDH1, AGER, DUSP4, DUSP7, FOS, IKBKB, IRAK2, MAP2K3

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 HISTIDINE METABOLISM	29	genes.ES.table	0.61	1.6	0.01	0.65	0.95	0.21	0.035	0.2	0.32	0.18
KEGG SPHINGOLIPID METABOLISM	39	genes.ES.table	0.55	1.6	0.0062	0.69	0.92	0.41	0.17	0.34	0.32	0.18
KEGG PROPANOATE METABOLISM	32	genes.ES.table	0.51	1.7	0.03	0.74	0.9	0.53	0.26	0.39	0.32	0.19
KEGG PEROXISOME	75	genes.ES.table	0.54	1.9	0.0062	1	0.44	0.48	0.24	0.37	0	0.33
KEGG VASOPRESSIN REGULATED WATER REABSORPTION	43	genes.ES.table	0.42	1.7	0.018	0.81	0.87	0.12	0.057	0.11	0.34	0.21
KEGG VIBRIO CHOLERAE INFECTION	53	genes.ES.table	0.48	1.9	0.0039	1	0.51	0.15	0.071	0.14	0.32	0.25
BIOCARTA DEATH PATHWAY	33	genes.ES.table	0.49	1.7	0.032	0.69	0.9	0.52	0.26	0.38	0.29	0.18
BIOCARTA PPARA PATHWAY	56	genes.ES.table	0.46	1.6	0.028	0.71	0.95	0.29	0.2	0.23	0.34	0.19
BIOCARTA RHO PATHWAY	32	genes.ES.table	0.44	1.8	0.01	1	0.67	0.062	0.03	0.061	0.4	0.27
ST INTERLEUKIN 4 PATHWAY	25	genes.ES.table	0.55	1.7	0.016	0.96	0.83	0.16	0.073	0.15	0.36	0.22

genes ES table in pathway: KEGG HISTIDINE METABOLISM

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	ACSL5	ACSL5	ACSL5	244	0.86	0.06	YES
2	FAR2	FAR2	FAR2	354	0.75	0.12	YES
3	NOS2	NOS2	NOS2	414	0.7	0.18	YES
4	SLC27A2	SLC27A2	SLC27A2	532	0.63	0.22	YES
5	AGXT	AGXT	AGXT	636	0.57	0.27	YES
6	BAAT	BAAT	BAAT	698	0.55	0.31	YES
7	PHYH	PHYH	PHYH	1516	0.32	0.29	YES
8	HAO2	HAO2	HAO2	1693	0.3	0.31	YES
9	PECR	PECR	PECR	1786	0.28	0.33	YES
10	PEX11A	PEX11A	PEX11A	1920	0.26	0.34	YES
11	EPHX2	EPHX2	EPHX2	2240	0.23	0.35	YES
12	PEX11G	PEX11G	PEX11G	2310	0.22	0.36	YES
13	DECR2	DECR2	DECR2	2496	0.21	0.37	YES
14	DDO	DDO	DDO	2532	0.21	0.39	YES
15	ABCD1	ABCD1	ABCD1	2811	0.18	0.39	YES
16	ABCD3	ABCD3	ABCD3	2862	0.18	0.4	YES
17	PEX7	PEX7	PEX7	2938	0.18	0.41	YES
18	CAT	CAT	CAT	3005	0.17	0.42	YES
19	PIPOX	PIPOX	PIPOX	3202	0.16	0.42	YES
20	AMACR	AMACR	AMACR	3203	0.16	0.44	YES
21	HACL1	HACL1	HACL1	3278	0.15	0.45	YES
22	CRAT	CRAT	CRAT	3358	0.15	0.46	YES
23	ACOX1	ACOX1	ACOX1	3419	0.14	0.46	YES
24	MLYCD	MLYCD	MLYCD	3453	0.14	0.47	YES
25	HMGCL	HMGCL	HMGCL	3502	0.14	0.48	YES
26	ACAA1	ACAA1	ACAA1	3521	0.14	0.49	YES
27	NUDT12	NUDT12	NUDT12	3611	0.13	0.5	YES
28	IDH1	IDH1	IDH1	3708	0.13	0.51	YES
29	PXMP2	PXMP2	PXMP2	3793	0.12	0.51	YES
30	PEX1	PEX1	PEX1	3912	0.12	0.52	YES
31	GSTK1	GSTK1	GSTK1	3954	0.12	0.52	YES
32	SCP2	SCP2	SCP2	4107	0.11	0.53	YES
33	ACOT8	ACOT8	ACOT8	4126	0.11	0.53	YES
34	PXMP4	PXMP4	PXMP4	4269	0.1	0.54	YES
35	ABCD4	ABCD4	ABCD4	4370	0.1	0.54	YES
36	ACOX2	ACOX2	ACOX2	4464	0.097	0.54	YES
37	IDH2	IDH2	IDH2	4732	0.088	0.54	NO
38	PEX6	PEX6	PEX6	5313	0.07	0.51	NO
39	GNPAT	GNPAT	GNPAT	5705	0.06	0.49	NO
40	ECH1	ECH1	ECH1	5804	0.057	0.49	NO
41	PEX2	PEX2	PEX2	6241	0.047	0.48	NO
42	HSD17B4	HSD17B4	HSD17B4	6282	0.046	0.48	NO
43	ACSL4	ACSL4	ACSL4	6343	0.044	0.48	NO
44	PEX16	PEX16	PEX16	6423	0.043	0.48	NO
45	ABCD2	ABCD2	ABCD2	6490	0.041	0.48	NO
46	ACSL3	ACSL3	ACSL3	6551	0.04	0.48	NO
47	PEX11B	PEX11B	PEX11B	6991	0.031	0.46	NO
48	AGPS	AGPS	AGPS	7660	0.017	0.42	NO
49	FAR1	FAR1	FAR1	8127	0.0081	0.4	NO
50	PEX26	PEX26	PEX26	8278	0.0055	0.39	NO
51	ACOX3	ACOX3	ACOX3	8779	-0.0031	0.36	NO
52	XDH	XDH	XDH	8849	-0.0043	0.36	NO
53	SOD1	SOD1	SOD1	9585	-0.017	0.32	NO
54	PEX19	PEX19	PEX19	10076	-0.025	0.3	NO
55	ACSL6	ACSL6	ACSL6	10080	-0.025	0.3	NO
56	PMVK	PMVK	PMVK	10281	-0.029	0.29	NO
57	EHHADH	EHHADH	EHHADH	10318	-0.03	0.29	NO
58	PEX14	PEX14	PEX14	10900	-0.04	0.26	NO
59	PEX13	PEX13	PEX13	10959	-0.041	0.26	NO
60	PRDX5	PRDX5	PRDX5	11154	-0.045	0.26	NO
61	PEX3	PEX3	PEX3	11169	-0.046	0.26	NO
62	SOD2	SOD2	SOD2	11739	-0.058	0.24	NO
63	PEX12	PEX12	PEX12	11743	-0.058	0.24	NO
64	PEX5	PEX5	PEX5	11799	-0.059	0.24	NO
65	PEX10	PEX10	PEX10	12210	-0.068	0.23	NO
66	NUDT19	NUDT19	NUDT19	12999	-0.089	0.19	NO
67	PRDX1	PRDX1	PRDX1	13119	-0.093	0.19	NO
68	MPV17	MPV17	MPV17	13581	-0.11	0.18	NO
69	SLC25A17	SLC25A17	SLC25A17	14089	-0.12	0.16	NO
70	DHRS4	DHRS4	DHRS4	14586	-0.14	0.15	NO
71	PAOX	PAOX	PAOX	14841	-0.16	0.15	NO
72	ACSL1	ACSL1	ACSL1	14894	-0.16	0.16	NO
73	MPV17L	MPV17L	MPV17L	14937	-0.16	0.17	NO
74	MVK	MVK	MVK	15154	-0.17	0.17	NO
75	CROT	CROT	CROT	15994	-0.23	0.15	NO

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

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

genes ES table in pathway: KEGG SPHINGOLIPID METABOLISM

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	CFTR	CFTR	CFTR	97	1.1	0.11	YES
2	KCNQ1	KCNQ1	KCNQ1	284	0.81	0.19	YES
3	PRKACG	PRKACG	PRKACG	330	0.77	0.27	YES
4	MUC2	MUC2	MUC2	421	0.7	0.34	YES
5	PRKCG	PRKCG	PRKCG	617	0.58	0.39	YES
6	SLC12A2	SLC12A2	SLC12A2	842	0.5	0.43	YES
7	KDELR3	KDELR3	KDELR3	1259	0.37	0.44	YES
8	PRKCA	PRKCA	PRKCA	1339	0.35	0.48	YES
9	TJP2	TJP2	TJP2	2460	0.21	0.44	NO
10	ATP6V1C2	ATP6V1C2	ATP6V1C2	2772	0.19	0.44	NO
11	TCIRG1	TCIRG1	TCIRG1	3399	0.14	0.42	NO
12	KDELR2	KDELR2	KDELR2	3490	0.14	0.44	NO
13	KDELR1	KDELR1	KDELR1	4615	0.092	0.38	NO
14	ATP6V0A2	ATP6V0A2	ATP6V0A2	4637	0.091	0.39	NO
15	PDIA4	PDIA4	PDIA4	5193	0.074	0.37	NO
16	ATP6V0B	ATP6V0B	ATP6V0B	5589	0.063	0.36	NO
17	ATP6V0A1	ATP6V0A1	ATP6V0A1	5749	0.058	0.36	NO
18	PRKCB	PRKCB	PRKCB	5846	0.056	0.36	NO
19	SEC61A2	SEC61A2	SEC61A2	6436	0.042	0.33	NO
20	ATP6V0E2	ATP6V0E2	ATP6V0E2	6619	0.038	0.32	NO
21	ARF1	ARF1	ARF1	6635	0.038	0.33	NO
22	TJP1	TJP1	TJP1	7082	0.029	0.3	NO
23	ATP6V1C1	ATP6V1C1	ATP6V1C1	7622	0.017	0.28	NO
24	ATP6AP1	ATP6AP1	ATP6AP1	7813	0.014	0.27	NO
25	SEC61A1	SEC61A1	SEC61A1	8614	-0.00027	0.23	NO
26	SEC61B	SEC61B	SEC61B	8791	-0.0032	0.22	NO
27	SEC61G	SEC61G	SEC61G	9424	-0.014	0.18	NO
28	ACTG1	ACTG1	ACTG1	9649	-0.018	0.18	NO
29	ACTB	ACTB	ACTB	9675	-0.019	0.18	NO
30	ATP6V0D1	ATP6V0D1	ATP6V0D1	10567	-0.034	0.13	NO
31	ATP6V0E1	ATP6V0E1	ATP6V0E1	10583	-0.034	0.14	NO
32	ATP6V1B2	ATP6V1B2	ATP6V1B2	10867	-0.04	0.12	NO
33	GNAS	GNAS	GNAS	11553	-0.054	0.093	NO
34	ERO1L	ERO1L	ERO1L	11692	-0.057	0.091	NO
35	ADCY9	ADCY9	ADCY9	11954	-0.062	0.084	NO
36	ATP6V0C	ATP6V0C	ATP6V0C	12065	-0.064	0.085	NO
37	ATP6V1G1	ATP6V1G1	ATP6V1G1	12167	-0.067	0.087	NO
38	ATP6V1A	ATP6V1A	ATP6V1A	12390	-0.072	0.082	NO
39	ATP6V1H	ATP6V1H	ATP6V1H	12408	-0.073	0.089	NO
40	ATP6V1D	ATP6V1D	ATP6V1D	12600	-0.078	0.087	NO
41	PRKACB	PRKACB	PRKACB	12868	-0.085	0.082	NO
42	PRKACA	PRKACA	PRKACA	13025	-0.09	0.083	NO
43	PLCG1	PLCG1	PLCG1	13245	-0.096	0.082	NO
44	ATP6V1F	ATP6V1F	ATP6V1F	13361	-0.099	0.086	NO
45	ATP6V1G2	ATP6V1G2	ATP6V1G2	13652	-0.11	0.082	NO
46	PLCG2	PLCG2	PLCG2	13748	-0.11	0.088	NO
47	ATP6V1E1	ATP6V1E1	ATP6V1E1	13946	-0.12	0.09	NO
48	ADCY3	ADCY3	ADCY3	14503	-0.14	0.076	NO
49	ATP6V0D2	ATP6V0D2	ATP6V0D2	14622	-0.15	0.085	NO
50	PRKX	PRKX	PRKX	15967	-0.23	0.037	NO
51	ATP6V0A4	ATP6V0A4	ATP6V0A4	16910	-0.33	0.022	NO
52	ATP6V1E2	ATP6V1E2	ATP6V1E2	16995	-0.35	0.054	NO
53	ATP6V1B1	ATP6V1B1	ATP6V1B1	17180	-0.37	0.084	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 SPHINGOLIPID METABOLISM.

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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PIP5K1B	PIP5K1B	PIP5K1B	67	1.2	0.31	YES
2	ARHGAP6	ARHGAP6	ARHGAP6	554	0.62	0.44	YES
3	ARHGAP4	ARHGAP4	ARHGAP4	2875	0.18	0.36	NO
4	SRC	SRC	SRC	3144	0.16	0.39	NO
5	ARPC1B	ARPC1B	ARPC1B	5049	0.078	0.31	NO
6	ARPC4	ARPC4	ARPC4	5758	0.058	0.28	NO
7	RHOA	RHOA	RHOA	5932	0.054	0.29	NO
8	ARHGEF11	ARHGEF11	ARHGEF11	6035	0.051	0.3	NO
9	PPP1R12B	PPP1R12B	PPP1R12B	6312	0.045	0.29	NO
10	ARHGEF1	ARHGEF1	ARHGEF1	6919	0.032	0.27	NO
11	DIAPH1	DIAPH1	DIAPH1	7025	0.03	0.27	NO
12	OPHN1	OPHN1	OPHN1	7434	0.021	0.26	NO
13	ROCK1	ROCK1	ROCK1	7484	0.02	0.26	NO
14	CFL1	CFL1	CFL1	7883	0.013	0.24	NO
15	ARHGAP5	ARHGAP5	ARHGAP5	8425	0.0028	0.21	NO
16	ACTR2	ACTR2	ACTR2	8596	0.000041	0.2	NO
17	ARPC5	ARPC5	ARPC5	8676	-0.0014	0.2	NO
18	ARPC1A	ARPC1A	ARPC1A	8786	-0.0032	0.19	NO
19	TLN1	TLN1	TLN1	8913	-0.0055	0.19	NO
20	PFN1	PFN1	PFN1	10062	-0.025	0.13	NO
21	PIP5K1A	PIP5K1A	PIP5K1A	10540	-0.033	0.12	NO
22	ARPC3	ARPC3	ARPC3	10658	-0.035	0.12	NO
23	VCL	VCL	VCL	10883	-0.04	0.12	NO
24	GSN	GSN	GSN	11855	-0.06	0.081	NO
25	ARHGAP1	ARHGAP1	ARHGAP1	11926	-0.062	0.093	NO
26	MYL2	MYL2	MYL2	12129	-0.066	0.099	NO
27	ACTR3	ACTR3	ACTR3	12166	-0.067	0.11	NO
28	ARPC2	ARPC2	ARPC2	12473	-0.074	0.12	NO
29	LIMK1	LIMK1	LIMK1	14829	-0.16	0.032	NO
30	ARHGEF5	ARHGEF5	ARHGEF5	14905	-0.16	0.069	NO
31	MYLK	MYLK	MYLK	16127	-0.24	0.067	NO
32	BAIAP2	BAIAP2	BAIAP2	16503	-0.28	0.12	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 PROPANOATE METABOLISM.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROPANOATE 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 PEROXISOME

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	MUC13	MUC13	MUC13	17	1.4	0.034	YES
2	MUC17	MUC17	MUC17	53	1.3	0.064	YES
3	ARSE	ARSE	ARSE	108	1.1	0.087	YES
4	GCNT3	GCNT3	GCNT3	109	1.1	0.11	YES
5	MUC6	MUC6	MUC6	255	0.84	0.13	YES
6	B3GNT3	B3GNT3	B3GNT3	263	0.83	0.15	YES
7	MUC5B	MUC5B	MUC5B	280	0.81	0.16	YES
8	B3GNT7	B3GNT7	B3GNT7	285	0.8	0.18	YES
9	MGAT3	MGAT3	MGAT3	316	0.78	0.2	YES
10	GCNT1	GCNT1	GCNT1	327	0.78	0.22	YES
11	MUC12	MUC12	MUC12	332	0.77	0.24	YES
12	MUC2	MUC2	MUC2	421	0.7	0.25	YES
13	GALNT5	GALNT5	GALNT5	535	0.63	0.26	YES
14	MGAT4A	MGAT4A	MGAT4A	589	0.6	0.27	YES
15	MUC4	MUC4	MUC4	826	0.5	0.27	YES
16	GALNT12	GALNT12	GALNT12	898	0.47	0.28	YES
17	GALNT8	GALNT8	GALNT8	905	0.47	0.29	YES
18	ALG11	ALG11	ALG11	928	0.46	0.3	YES
19	F10	F10	F10	982	0.45	0.31	YES
20	STS	STS	STS	1074	0.41	0.31	YES
21	ST6GALNAC3	ST6GALNAC3	ST6GALNAC3	1075	0.41	0.32	YES
22	GALNTL6	GALNTL6	GALNTL6	1098	0.41	0.33	YES
23	ST6GAL1	ST6GAL1	ST6GAL1	1183	0.39	0.34	YES
24	ST8SIA3	ST8SIA3	ST8SIA3	1227	0.38	0.34	YES
25	F7	F7	F7	1254	0.37	0.35	YES
26	C1GALT1	C1GALT1	C1GALT1	1295	0.36	0.36	YES
27	PROZ	PROZ	PROZ	1344	0.35	0.36	YES
28	FUT8	FUT8	FUT8	1351	0.35	0.37	YES
29	PROC	PROC	PROC	1490	0.32	0.37	YES
30	B3GNT6	B3GNT6	B3GNT6	1569	0.31	0.38	YES
31	ARSH	ARSH	ARSH	1762	0.29	0.37	YES
32	MGAT5	MGAT5	MGAT5	1811	0.28	0.38	YES
33	GALNT9	GALNT9	GALNT9	1915	0.27	0.38	YES
34	GALNT7	GALNT7	GALNT7	1951	0.26	0.38	YES
35	GALNT3	GALNT3	GALNT3	2013	0.26	0.39	YES
36	MAN1A1	MAN1A1	MAN1A1	2070	0.25	0.39	YES
37	MGAT4B	MGAT4B	MGAT4B	2132	0.24	0.39	YES
38	GALNT6	GALNT6	GALNT6	2150	0.24	0.4	YES
39	ALG5	ALG5	ALG5	2280	0.23	0.4	YES
40	F2	F2	F2	2306	0.23	0.4	YES
41	B3GNTL1	B3GNTL1	B3GNTL1	2375	0.22	0.4	YES
42	MLEC	MLEC	MLEC	2383	0.22	0.41	YES
43	PLAUR	PLAUR	PLAUR	2415	0.22	0.41	YES
44	GMPPB	GMPPB	GMPPB	2500	0.21	0.41	YES
45	UGGT2	UGGT2	UGGT2	2661	0.2	0.41	YES
46	EDEM3	EDEM3	EDEM3	2663	0.2	0.41	YES
47	ALG14	ALG14	ALG14	2713	0.19	0.41	YES
48	ST6GALNAC4	ST6GALNAC4	ST6GALNAC4	2731	0.19	0.42	YES
49	GALNT10	GALNT10	GALNT10	2737	0.19	0.42	YES
50	C1GALT1C1	C1GALT1C1	C1GALT1C1	2925	0.18	0.42	NO
51	DPAGT1	DPAGT1	DPAGT1	2948	0.18	0.42	NO
52	PGM3	PGM3	PGM3	3096	0.16	0.42	NO
53	GMPPA	GMPPA	GMPPA	3125	0.16	0.42	NO
54	SEC24D	SEC24D	SEC24D	3169	0.16	0.42	NO
55	ALG1	ALG1	ALG1	3229	0.16	0.42	NO
56	PIGG	PIGG	PIGG	3306	0.15	0.42	NO
57	ST3GAL2	ST3GAL2	ST3GAL2	3346	0.15	0.42	NO
58	GNPNAT1	GNPNAT1	GNPNAT1	3431	0.14	0.42	NO
59	PIGT	PIGT	PIGT	3663	0.13	0.41	NO
60	MAN1C1	MAN1C1	MAN1C1	3673	0.13	0.41	NO
61	PIGM	PIGM	PIGM	3776	0.12	0.41	NO
62	B4GALT6	B4GALT6	B4GALT6	3799	0.12	0.41	NO
63	B4GALT5	B4GALT5	B4GALT5	4048	0.11	0.4	NO
64	STT3A	STT3A	STT3A	4158	0.11	0.4	NO
65	SUMF2	SUMF2	SUMF2	4459	0.097	0.38	NO
66	SEC13	SEC13	SEC13	4475	0.097	0.39	NO
67	MAN2A1	MAN2A1	MAN2A1	4480	0.097	0.39	NO
68	PMM2	PMM2	PMM2	4504	0.096	0.39	NO
69	EDEM2	EDEM2	EDEM2	4538	0.095	0.39	NO
70	PIGO	PIGO	PIGO	4573	0.094	0.39	NO
71	ALG8	ALG8	ALG8	4950	0.082	0.37	NO
72	RPN2	RPN2	RPN2	5032	0.079	0.37	NO
73	SUMF1	SUMF1	SUMF1	5070	0.078	0.37	NO
74	PDIA3	PDIA3	PDIA3	5114	0.076	0.37	NO
75	B3GNT2	B3GNT2	B3GNT2	5180	0.074	0.37	NO
76	ALG2	ALG2	ALG2	5231	0.072	0.37	NO
77	PROS1	PROS1	PROS1	5253	0.072	0.37	NO
78	RFT1	RFT1	RFT1	5308	0.07	0.37	NO
79	ALG13	ALG13	ALG13	5505	0.065	0.36	NO
80	CANX	CANX	CANX	5701	0.06	0.35	NO
81	DPM3	DPM3	DPM3	5730	0.059	0.35	NO
82	PIGB	PIGB	PIGB	5773	0.058	0.35	NO
83	SAR1B	SAR1B	SAR1B	5856	0.056	0.34	NO
84	DDOST	DDOST	DDOST	5938	0.054	0.34	NO
85	PIGK	PIGK	PIGK	5990	0.052	0.34	NO
86	UGGT1	UGGT1	UGGT1	6208	0.047	0.33	NO
87	PIGH	PIGH	PIGH	6285	0.046	0.33	NO
88	PIGU	PIGU	PIGU	6289	0.046	0.33	NO
89	B4GALT3	B4GALT3	B4GALT3	6421	0.043	0.32	NO
90	ALG9	ALG9	ALG9	6443	0.042	0.32	NO
91	PIGF	PIGF	PIGF	6485	0.042	0.32	NO
92	PREB	PREB	PREB	6660	0.037	0.31	NO
93	DOLPP1	DOLPP1	DOLPP1	6821	0.034	0.3	NO
94	PIGS	PIGS	PIGS	7201	0.026	0.28	NO
95	B4GALT4	B4GALT4	B4GALT4	7222	0.025	0.28	NO
96	PIGL	PIGL	PIGL	7247	0.025	0.28	NO
97	MCFD2	MCFD2	MCFD2	7432	0.021	0.27	NO
98	CALR	CALR	CALR	7663	0.017	0.26	NO
99	EDEM1	EDEM1	EDEM1	7671	0.016	0.26	NO
100	GPAA1	GPAA1	GPAA1	7710	0.016	0.26	NO
101	FURIN	FURIN	FURIN	7740	0.015	0.26	NO
102	RPN1	RPN1	RPN1	7892	0.012	0.25	NO
103	PIGC	PIGC	PIGC	7913	0.012	0.25	NO
104	GALNTL2	GALNTL2	GALNTL2	7917	0.012	0.25	NO
105	MAN1A2	MAN1A2	MAN1A2	7987	0.011	0.25	NO
106	DAD1	DAD1	DAD1	8078	0.0093	0.24	NO
107	DPM2	DPM2	DPM2	8128	0.0081	0.24	NO
108	SEC24C	SEC24C	SEC24C	8175	0.0073	0.24	NO
109	MOGS	MOGS	MOGS	8197	0.007	0.24	NO
110	DOLK	DOLK	DOLK	8303	0.0051	0.23	NO
111	B4GALT1	B4GALT1	B4GALT1	8311	0.005	0.23	NO
112	MPI	MPI	MPI	8349	0.0044	0.23	NO
113	ALG6	ALG6	ALG6	8563	0.00061	0.22	NO
114	MGAT2	MGAT2	MGAT2	8672	-0.0013	0.21	NO
115	PIGQ	PIGQ	PIGQ	9004	-0.007	0.19	NO
116	GANAB	GANAB	GANAB	9048	-0.0078	0.19	NO
117	PRKCSH	PRKCSH	PRKCSH	9369	-0.013	0.17	NO
118	PIGP	PIGP	PIGP	9571	-0.017	0.16	NO
119	SEC31A	SEC31A	SEC31A	9722	-0.019	0.16	NO
120	PIGA	PIGA	PIGA	9824	-0.021	0.15	NO
121	MAN1B1	MAN1B1	MAN1B1	9942	-0.023	0.15	NO
122	DPM1	DPM1	DPM1	10037	-0.025	0.14	NO
123	SEC23A	SEC23A	SEC23A	10077	-0.025	0.14	NO
124	MANEA	MANEA	MANEA	10282	-0.029	0.13	NO
125	ALG12	ALG12	ALG12	10408	-0.031	0.12	NO
126	GALNTL1	GALNTL1	GALNTL1	10501	-0.033	0.12	NO
127	DOHH	DOHH	DOHH	10535	-0.033	0.12	NO
128	SEC24B	SEC24B	SEC24B	10580	-0.034	0.12	NO
129	MGAT1	MGAT1	MGAT1	10700	-0.036	0.11	NO
130	ARSA	ARSA	ARSA	11234	-0.047	0.084	NO
131	ALG3	ALG3	ALG3	11328	-0.049	0.08	NO
132	GALNT2	GALNT2	GALNT2	11342	-0.049	0.08	NO
133	GGCX	GGCX	GGCX	11418	-0.051	0.078	NO
134	LMAN1	LMAN1	LMAN1	11500	-0.053	0.074	NO
135	ARSG	ARSG	ARSG	11707	-0.057	0.065	NO
136	DHPS	DHPS	DHPS	11726	-0.058	0.065	NO
137	ALG10	ALG10	ALG10	11924	-0.062	0.056	NO
138	ST3GAL1	ST3GAL1	ST3GAL1	11952	-0.062	0.056	NO
139	PIGW	PIGW	PIGW	12169	-0.067	0.046	NO
140	WBSCR17	WBSCR17	WBSCR17	12747	-0.082	0.017	NO
141	PIGV	PIGV	PIGV	12848	-0.084	0.014	NO
142	PIGN	PIGN	PIGN	12864	-0.085	0.015	NO
143	VKORC1	VKORC1	VKORC1	12884	-0.085	0.016	NO
144	EIF5A	EIF5A	EIF5A	12934	-0.087	0.016	NO
145	MUC21	MUC21	MUC21	12972	-0.088	0.016	NO
146	EIF5A2	EIF5A2	EIF5A2	13105	-0.092	0.011	NO
147	ALG10B	ALG10B	ALG10B	13406	-0.1	-0.0029	NO
148	GCNT4	GCNT4	GCNT4	13460	-0.1	-0.0032	NO
149	ARSB	ARSB	ARSB	13674	-0.11	-0.012	NO
150	GALNT1	GALNT1	GALNT1	14031	-0.12	-0.028	NO
151	GALNT11	GALNT11	GALNT11	14056	-0.12	-0.027	NO
152	B3GNT8	B3GNT8	B3GNT8	14435	-0.14	-0.044	NO
153	ARSK	ARSK	ARSK	14789	-0.15	-0.059	NO
154	B4GALT2	B4GALT2	B4GALT2	14863	-0.16	-0.059	NO
155	PMM1	PMM1	PMM1	15171	-0.18	-0.071	NO
156	MUC16	MUC16	MUC16	15183	-0.18	-0.068	NO
157	ARSF	ARSF	ARSF	15230	-0.18	-0.066	NO
158	PGAP1	PGAP1	PGAP1	15690	-0.21	-0.085	NO
159	B3GNT9	B3GNT9	B3GNT9	15926	-0.23	-0.092	NO
160	B3GNT5	B3GNT5	B3GNT5	15978	-0.23	-0.09	NO
161	SEMA6D	SEMA6D	SEMA6D	16198	-0.25	-0.095	NO
162	PIGX	PIGX	PIGX	16306	-0.26	-0.094	NO
163	ARSJ	ARSJ	ARSJ	16375	-0.27	-0.092	NO
164	MGAT4C	MGAT4C	MGAT4C	17225	-0.38	-0.13	NO
165	ST8SIA6	ST8SIA6	ST8SIA6	17274	-0.39	-0.12	NO
166	ST3GAL3	ST3GAL3	ST3GAL3	17775	-0.49	-0.14	NO
167	MUCL1	MUCL1	MUCL1	17797	-0.5	-0.12	NO
168	GFPT2	GFPT2	GFPT2	17931	-0.54	-0.12	NO
169	ST8SIA2	ST8SIA2	ST8SIA2	17971	-0.55	-0.11	NO
170	GALNTL4	GALNTL4	GALNTL4	17980	-0.55	-0.095	NO
171	MUC15	MUC15	MUC15	18100	-0.59	-0.087	NO
172	GALNT13	GALNT13	GALNT13	18116	-0.6	-0.073	NO
173	ST6GALNAC2	ST6GALNAC2	ST6GALNAC2	18457	-0.76	-0.073	NO
174	B3GNT4	B3GNT4	B3GNT4	18479	-0.78	-0.055	NO
175	ARSI	ARSI	ARSI	18577	-0.85	-0.04	NO
176	TUSC3	TUSC3	TUSC3	18643	-0.93	-0.021	NO
177	GALNT14	GALNT14	GALNT14	18702	-1.1	0.0025	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 PEROXISOME.

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

genes ES table in pathway: KEGG VASOPRESSIN REGULATED WATER REABSORPTION

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	TPK1	TPK1	TPK1	454	0.67	0.07	YES
2	SLC19A3	SLC19A3	SLC19A3	572	0.61	0.15	YES
3	ENPP1	ENPP1	ENPP1	831	0.5	0.2	YES
4	GSTO2	GSTO2	GSTO2	1125	0.4	0.24	YES
5	QPRT	QPRT	QPRT	1292	0.36	0.29	YES
6	RFK	RFK	RFK	1296	0.36	0.34	YES
7	PANK1	PANK1	PANK1	1500	0.32	0.37	YES
8	NMNAT2	NMNAT2	NMNAT2	1716	0.29	0.4	YES
9	SLC23A1	SLC23A1	SLC23A1	2444	0.21	0.39	YES
10	NMNAT1	NMNAT1	NMNAT1	2664	0.2	0.41	YES
11	MTHFR	MTHFR	MTHFR	2714	0.19	0.43	YES
12	CYB5A	CYB5A	CYB5A	3257	0.15	0.42	YES
13	SLC19A2	SLC19A2	SLC19A2	3390	0.14	0.44	YES
14	SLC46A1	SLC46A1	SLC46A1	3412	0.14	0.46	YES
15	NADK	NADK	NADK	3878	0.12	0.45	YES
16	SLC19A1	SLC19A1	SLC19A1	3929	0.12	0.46	YES
17	MOCOS	MOCOS	MOCOS	4356	0.1	0.45	YES
18	PDXK	PDXK	PDXK	4372	0.1	0.47	YES
19	SLC5A6	SLC5A6	SLC5A6	4651	0.091	0.46	YES
20	PPCDC	PPCDC	PPCDC	4828	0.085	0.47	YES
21	PANK3	PANK3	PANK3	5037	0.079	0.47	YES
22	GPHN	GPHN	GPHN	5051	0.078	0.48	YES
23	PPCS	PPCS	PPCS	5542	0.064	0.46	NO
24	SLC25A16	SLC25A16	SLC25A16	5703	0.06	0.46	NO
25	FPGS	FPGS	FPGS	5803	0.057	0.46	NO
26	DHFR	DHFR	DHFR	6301	0.045	0.44	NO
27	SLC25A32	SLC25A32	SLC25A32	6557	0.04	0.43	NO
28	SLC2A3	SLC2A3	SLC2A3	6672	0.037	0.43	NO
29	MOCS3	MOCS3	MOCS3	7036	0.029	0.42	NO
30	PNPO	PNPO	PNPO	7064	0.029	0.42	NO
31	NFS1	NFS1	NFS1	8137	0.008	0.36	NO
32	COASY	COASY	COASY	8474	0.002	0.35	NO
33	THTPA	THTPA	THTPA	8883	-0.0049	0.32	NO
34	SHMT1	SHMT1	SHMT1	9502	-0.016	0.3	NO
35	PANK4	PANK4	PANK4	9781	-0.02	0.28	NO
36	FASN	FASN	FASN	9936	-0.023	0.28	NO
37	MTHFD1	MTHFD1	MTHFD1	10362	-0.03	0.26	NO
38	MOCS2	MOCS2	MOCS2	10912	-0.04	0.24	NO
39	PANK2	PANK2	PANK2	11190	-0.046	0.23	NO
40	FLAD1	FLAD1	FLAD1	11586	-0.054	0.21	NO
41	GSTO1	GSTO1	GSTO1	11988	-0.063	0.2	NO
42	AASDHPPT	AASDHPPT	AASDHPPT	12386	-0.072	0.19	NO
43	NADSYN1	NADSYN1	NADSYN1	12392	-0.072	0.2	NO
44	CYB5R3	CYB5R3	CYB5R3	12584	-0.077	0.2	NO
45	SLC23A2	SLC23A2	SLC23A2	12610	-0.078	0.21	NO
46	MOCS1	MOCS1	MOCS1	13437	-0.1	0.18	NO
47	NMNAT3	NMNAT3	NMNAT3	13801	-0.11	0.18	NO
48	NAMPT	NAMPT	NAMPT	14039	-0.12	0.18	NO
49	ACP5	ACP5	ACP5	14955	-0.16	0.15	NO
50	SLC2A1	SLC2A1	SLC2A1	17006	-0.35	0.093	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 VASOPRESSIN REGULATED WATER REABSORPTION.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VASOPRESSIN REGULATED WATER REABSORPTION, 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 VIBRIO CHOLERAE INFECTION

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	ARRB1	ARRB1	ARRB1	544	0.62	0.072	YES
2	DNAJC6	DNAJC6	DNAJC6	1735	0.29	0.056	YES
3	TBC1D8B	TBC1D8B	TBC1D8B	1752	0.29	0.1	YES
4	AP1M2	AP1M2	AP1M2	2257	0.23	0.11	YES
5	AP4B1	AP4B1	AP4B1	2399	0.22	0.14	YES
6	TPD52	TPD52	TPD52	2587	0.2	0.16	YES
7	TGOLN2	TGOLN2	TGOLN2	2779	0.19	0.18	YES
8	GAK	GAK	GAK	2956	0.18	0.2	YES
9	SORT1	SORT1	SORT1	3213	0.16	0.22	YES
10	CPD	CPD	CPD	3223	0.16	0.24	YES
11	HIP1R	HIP1R	HIP1R	3547	0.14	0.24	YES
12	SNX9	SNX9	SNX9	3584	0.14	0.26	YES
13	DTNBP1	DTNBP1	DTNBP1	3792	0.12	0.27	YES
14	CTSZ	CTSZ	CTSZ	3883	0.12	0.29	YES
15	DNM2	DNM2	DNM2	4041	0.11	0.3	YES
16	YIPF6	YIPF6	YIPF6	4357	0.1	0.3	YES
17	PIK3C2A	PIK3C2A	PIK3C2A	4398	0.1	0.31	YES
18	GNS	GNS	GNS	4654	0.091	0.31	YES
19	SNAP23	SNAP23	SNAP23	4703	0.089	0.33	YES
20	AP1S1	AP1S1	AP1S1	4928	0.082	0.33	YES
21	TXNDC5	TXNDC5	TXNDC5	4962	0.081	0.34	YES
22	SH3D19	SH3D19	SH3D19	5031	0.079	0.35	YES
23	CNO	CNO	CNO	5507	0.065	0.33	NO
24	BLOC1S1	BLOC1S1	BLOC1S1	6094	0.05	0.31	NO
25	NECAP1	NECAP1	NECAP1	6297	0.045	0.31	NO
26	SNX5	SNX5	SNX5	6310	0.045	0.31	NO
27	RAB5C	RAB5C	RAB5C	6353	0.044	0.32	NO
28	CLTC	CLTC	CLTC	6607	0.039	0.31	NO
29	ARF1	ARF1	ARF1	6635	0.038	0.32	NO
30	OCRL	OCRL	OCRL	6763	0.035	0.32	NO
31	HSPA8	HSPA8	HSPA8	6855	0.034	0.32	NO
32	GBF1	GBF1	GBF1	7375	0.022	0.29	NO
33	FTL	FTL	FTL	7541	0.019	0.29	NO
34	CLTA	CLTA	CLTA	7588	0.018	0.29	NO
35	PICALM	PICALM	PICALM	7720	0.016	0.28	NO
36	VAMP8	VAMP8	VAMP8	8233	0.0064	0.26	NO
37	AP1G1	AP1G1	AP1G1	8235	0.0063	0.26	NO
38	VAMP7	VAMP7	VAMP7	8488	0.0018	0.24	NO
39	SNX2	SNX2	SNX2	8580	0.00037	0.24	NO
40	STX4	STX4	STX4	8695	-0.0016	0.23	NO
41	PUM1	PUM1	PUM1	8727	-0.0023	0.23	NO
42	FTH1	FTH1	FTH1	8731	-0.0024	0.23	NO
43	AP3B1	AP3B1	AP3B1	9016	-0.0072	0.22	NO
44	IGF2R	IGF2R	IGF2R	9176	-0.01	0.21	NO
45	NAPA	NAPA	NAPA	9773	-0.02	0.18	NO
46	DNASE2	DNASE2	DNASE2	9995	-0.024	0.17	NO
47	PLDN	PLDN	PLDN	10222	-0.028	0.17	NO
48	BLOC1S3	BLOC1S3	BLOC1S3	10258	-0.029	0.17	NO
49	M6PR	M6PR	M6PR	11830	-0.06	0.095	NO
50	TFRC	TFRC	TFRC	12023	-0.064	0.095	NO
51	AP1B1	AP1B1	AP1B1	12156	-0.067	0.099	NO
52	VAMP2	VAMP2	VAMP2	12979	-0.088	0.069	NO
53	AP3S1	AP3S1	AP3S1	13353	-0.099	0.066	NO
54	AP4E1	AP4E1	AP4E1	13744	-0.11	0.063	NO
55	SNAPIN	SNAPIN	SNAPIN	13909	-0.12	0.073	NO
56	AP1M1	AP1M1	AP1M1	14183	-0.13	0.08	NO
57	SH3GL2	SH3GL2	SH3GL2	15397	-0.19	0.045	NO
58	AP1S2	AP1S2	AP1S2	15505	-0.2	0.071	NO
59	TPD52L1	TPD52L1	TPD52L1	18193	-0.62	0.03	NO

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

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VIBRIO CHOLERAE INFECTION, 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 DEATH 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	HNF1B	HNF1B	HNF1B	8	1.5	0.1	YES
2	HNF4A	HNF4A	HNF4A	15	1.5	0.2	YES
3	PDX1	PDX1	PDX1	33	1.4	0.3	YES
4	FOXA3	FOXA3	FOXA3	38	1.4	0.39	YES
5	HNF1A	HNF1A	HNF1A	60	1.2	0.47	YES
6	FOXA2	FOXA2	FOXA2	82	1.2	0.55	YES
7	HNF4G	HNF4G	HNF4G	92	1.1	0.63	YES
8	NR5A2	NR5A2	NR5A2	249	0.85	0.68	YES
9	NEUROG3	NEUROG3	NEUROG3	386	0.72	0.72	YES
10	ONECUT3	ONECUT3	ONECUT3	420	0.7	0.76	YES
11	INSM1	INSM1	INSM1	1683	0.3	0.72	NO
12	SLC2A2	SLC2A2	SLC2A2	1943	0.26	0.72	NO
13	NEUROD1	NEUROD1	NEUROD1	2429	0.22	0.71	NO
14	FGF10	FGF10	FGF10	2513	0.21	0.72	NO
15	ONECUT1	ONECUT1	ONECUT1	6484	0.042	0.51	NO
16	AKT1	AKT1	AKT1	8693	-0.0016	0.39	NO
17	RBPJ	RBPJ	RBPJ	9731	-0.02	0.34	NO
18	PAX6	PAX6	PAX6	10416	-0.031	0.3	NO
19	HES1	HES1	HES1	10807	-0.038	0.29	NO
20	NKX2-2	NKX2-2	NKX2-2	11751	-0.058	0.24	NO
21	FOXO1	FOXO1	FOXO1	12118	-0.066	0.22	NO
22	AKT2	AKT2	AKT2	12528	-0.076	0.21	NO
23	PKLR	PKLR	PKLR	13172	-0.094	0.18	NO
24	GCK	GCK	GCK	13345	-0.099	0.18	NO
25	AKT3	AKT3	AKT3	16341	-0.26	0.036	NO
26	MAFA	MAFA	MAFA	17415	-0.42	0.0066	NO
27	NKX6-1	NKX6-1	NKX6-1	17455	-0.43	0.034	NO
28	IAPP	IAPP	IAPP	17884	-0.52	0.046	NO

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

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA DEATH 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 PPARA 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	NR0B2	NR0B2	NR0B2	75	1.2	0.24	YES
2	SERPINA4	SERPINA4	SERPINA4	141	1	0.44	YES
3	IL2RG	IL2RG	IL2RG	790	0.51	0.51	YES
4	INPP5D	INPP5D	INPP5D	1370	0.35	0.55	YES
5	JAK2	JAK2	JAK2	2402	0.22	0.54	NO
6	SRC	SRC	SRC	3144	0.16	0.54	NO
7	JAK3	JAK3	JAK3	4094	0.11	0.51	NO
8	IL13RA1	IL13RA1	IL13RA1	4281	0.1	0.52	NO
9	JAK1	JAK1	JAK1	4973	0.081	0.5	NO
10	CISH	CISH	CISH	4981	0.08	0.52	NO
11	STAT6	STAT6	STAT6	6002	0.052	0.47	NO
12	IARS	IARS	IARS	7223	0.025	0.41	NO
13	TYK2	TYK2	TYK2	7257	0.024	0.42	NO
14	GRB2	GRB2	GRB2	7394	0.021	0.41	NO
15	IL4R	IL4R	IL4R	8495	0.0017	0.35	NO
16	AKT1	AKT1	AKT1	8693	-0.0016	0.34	NO
17	PPP1R13B	PPP1R13B	PPP1R13B	10459	-0.032	0.26	NO
18	SOS1	SOS1	SOS1	10685	-0.036	0.25	NO
19	RPS6KB1	RPS6KB1	RPS6KB1	10896	-0.04	0.25	NO
20	SOS2	SOS2	SOS2	11949	-0.062	0.2	NO
21	AKT2	AKT2	AKT2	12528	-0.076	0.19	NO
22	SHC1	SHC1	SHC1	13302	-0.098	0.17	NO
23	PI3	PI3	PI3	14458	-0.14	0.14	NO
24	PIK3CA	PIK3CA	PIK3CA	15423	-0.19	0.12	NO
25	AKT3	AKT3	AKT3	16341	-0.26	0.13	NO

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

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

genes ES table in pathway: BIOCARTA RHO PATHWAY

Table 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	SLC44A4	SLC44A4	SLC44A4	46	1.3	0.031	YES
2	GAL3ST1	GAL3ST1	GAL3ST1	61	1.2	0.062	YES
3	PIP5K1B	PIP5K1B	PIP5K1B	67	1.2	0.092	YES
4	PLA2G10	PLA2G10	PLA2G10	96	1.1	0.12	YES
5	ARSE	ARSE	ARSE	108	1.1	0.15	YES
6	GPD1	GPD1	GPD1	142	1	0.17	YES
7	SMPD3	SMPD3	SMPD3	145	0.99	0.2	YES
8	SLC44A3	SLC44A3	SLC44A3	310	0.79	0.21	YES
9	ACHE	ACHE	ACHE	337	0.77	0.22	YES
10	PLA2G16	PLA2G16	PLA2G16	344	0.76	0.24	YES
11	NEU4	NEU4	NEU4	398	0.72	0.26	YES
12	DEGS2	DEGS2	DEGS2	490	0.66	0.27	YES
13	PLA2G2A	PLA2G2A	PLA2G2A	704	0.55	0.27	YES
14	LPIN2	LPIN2	LPIN2	788	0.52	0.28	YES
15	CHKA	CHKA	CHKA	876	0.48	0.29	YES
16	GBA3	GBA3	GBA3	945	0.46	0.3	YES
17	INPP5J	INPP5J	INPP5J	980	0.45	0.31	YES
18	ACER2	ACER2	ACER2	1055	0.42	0.31	YES
19	STS	STS	STS	1074	0.41	0.32	YES
20	DGAT2	DGAT2	DGAT2	1077	0.41	0.33	YES
21	GALC	GALC	GALC	1182	0.39	0.34	YES
22	CHPT1	CHPT1	CHPT1	1382	0.35	0.34	YES
23	PLBD1	PLBD1	PLBD1	1537	0.32	0.34	YES
24	MGLL	MGLL	MGLL	1582	0.31	0.34	YES
25	PIK3C2B	PIK3C2B	PIK3C2B	1654	0.3	0.35	YES
26	AGPAT2	AGPAT2	AGPAT2	1744	0.29	0.35	YES
27	ENPP7	ENPP7	ENPP7	1750	0.29	0.36	YES
28	ARSH	ARSH	ARSH	1762	0.29	0.36	YES
29	DGAT1	DGAT1	DGAT1	1837	0.28	0.36	YES
30	GPD1L	GPD1L	GPD1L	2037	0.25	0.36	YES
31	MBOAT1	MBOAT1	MBOAT1	2136	0.24	0.36	YES
32	ETNK1	ETNK1	ETNK1	2172	0.24	0.37	YES
33	INPP4B	INPP4B	INPP4B	2174	0.24	0.37	YES
34	GBA2	GBA2	GBA2	2191	0.24	0.38	YES
35	PIK3CG	PIK3CG	PIK3CG	2208	0.24	0.38	YES
36	AGPAT9	AGPAT9	AGPAT9	2293	0.23	0.38	YES
37	LPCAT4	LPCAT4	LPCAT4	2328	0.22	0.39	YES
38	GLB1	GLB1	GLB1	2331	0.22	0.39	YES
39	SMPD2	SMPD2	SMPD2	2391	0.22	0.4	YES
40	SYNJ2	SYNJ2	SYNJ2	2394	0.22	0.4	YES
41	PNPLA2	PNPLA2	PNPLA2	2405	0.22	0.41	YES
42	NEU3	NEU3	NEU3	2409	0.22	0.41	YES
43	SGPP2	SGPP2	SGPP2	2503	0.21	0.41	YES
44	SGMS2	SGMS2	SGMS2	2540	0.21	0.42	YES
45	PCYT2	PCYT2	PCYT2	2560	0.2	0.42	YES
46	PLA2G4F	PLA2G4F	PLA2G4F	2937	0.18	0.4	NO
47	CRLS1	CRLS1	CRLS1	3000	0.17	0.4	NO
48	PLA2G4A	PLA2G4A	PLA2G4A	3029	0.17	0.41	NO
49	SPHK2	SPHK2	SPHK2	3059	0.17	0.41	NO
50	ASAH2	ASAH2	ASAH2	3100	0.16	0.41	NO
51	PPAP2C	PPAP2C	PPAP2C	3182	0.16	0.41	NO
52	PIK3R3	PIK3R3	PIK3R3	3297	0.15	0.41	NO
53	LPIN1	LPIN1	LPIN1	3382	0.14	0.41	NO
54	AGPAT5	AGPAT5	AGPAT5	3458	0.14	0.41	NO
55	CDS1	CDS1	CDS1	3542	0.14	0.41	NO
56	CTSA	CTSA	CTSA	3787	0.12	0.4	NO
57	MTMR14	MTMR14	MTMR14	3812	0.12	0.4	NO
58	HEXB	HEXB	HEXB	3849	0.12	0.4	NO
59	SPTLC2	SPTLC2	SPTLC2	3910	0.12	0.4	NO
60	ASAH1	ASAH1	ASAH1	3928	0.12	0.4	NO
61	PIK3C2G	PIK3C2G	PIK3C2G	3956	0.12	0.4	NO
62	GPAM	GPAM	GPAM	4127	0.11	0.4	NO
63	MTMR6	MTMR6	MTMR6	4172	0.11	0.4	NO
64	AGPAT6	AGPAT6	AGPAT6	4222	0.11	0.4	NO
65	GPAT2	GPAT2	GPAT2	4312	0.1	0.4	NO
66	PIK3C2A	PIK3C2A	PIK3C2A	4398	0.1	0.39	NO
67	PLA2G1B	PLA2G1B	PLA2G1B	4430	0.099	0.39	NO
68	AGPAT1	AGPAT1	AGPAT1	4453	0.098	0.4	NO
69	SUMF2	SUMF2	SUMF2	4459	0.097	0.4	NO
70	PIP4K2A	PIP4K2A	PIP4K2A	4562	0.094	0.4	NO
71	FIG4	FIG4	FIG4	4665	0.09	0.39	NO
72	PIK3CB	PIK3CB	PIK3CB	4789	0.087	0.39	NO
73	NEU1	NEU1	NEU1	4819	0.086	0.39	NO
74	PIK3R5	PIK3R5	PIK3R5	4885	0.084	0.39	NO
75	SACM1L	SACM1L	SACM1L	4917	0.083	0.39	NO
76	PLA2G2F	PLA2G2F	PLA2G2F	4957	0.081	0.39	NO
77	OSBP	OSBP	OSBP	4968	0.081	0.39	NO
78	SUMF1	SUMF1	SUMF1	5070	0.078	0.38	NO
79	CERK	CERK	CERK	5199	0.073	0.38	NO
80	PHOSPHO1	PHOSPHO1	PHOSPHO1	5227	0.072	0.38	NO
81	PLA2G12A	PLA2G12A	PLA2G12A	5449	0.066	0.37	NO
82	PTDSS2	PTDSS2	PTDSS2	5487	0.066	0.37	NO
83	GBA	GBA	GBA	5525	0.064	0.37	NO
84	LPGAT1	LPGAT1	LPGAT1	5545	0.064	0.37	NO
85	TPTE2	TPTE2	TPTE2	5602	0.062	0.37	NO
86	GNPAT	GNPAT	GNPAT	5705	0.06	0.36	NO
87	INPPL1	INPPL1	INPPL1	5839	0.056	0.36	NO
88	LPIN3	LPIN3	LPIN3	5858	0.056	0.36	NO
89	PPAP2A	PPAP2A	PPAP2A	6019	0.052	0.35	NO
90	VAPB	VAPB	VAPB	6044	0.051	0.35	NO
91	LPCAT1	LPCAT1	LPCAT1	6104	0.05	0.35	NO
92	MBOAT7	MBOAT7	MBOAT7	6160	0.048	0.35	NO
93	SLC44A2	SLC44A2	SLC44A2	6242	0.047	0.34	NO
94	HEXA	HEXA	HEXA	6349	0.044	0.34	NO
95	MTM1	MTM1	MTM1	6497	0.041	0.33	NO
96	SYNJ1	SYNJ1	SYNJ1	6552	0.04	0.33	NO
97	ARF1	ARF1	ARF1	6635	0.038	0.33	NO
98	LPCAT3	LPCAT3	LPCAT3	6711	0.036	0.32	NO
99	PLA2G2D	PLA2G2D	PLA2G2D	6726	0.036	0.33	NO
100	OCRL	OCRL	OCRL	6763	0.035	0.32	NO
101	MTMR7	MTMR7	MTMR7	7059	0.029	0.31	NO
102	PPM1L	PPM1L	PPM1L	7060	0.029	0.31	NO
103	CEPT1	CEPT1	CEPT1	7063	0.029	0.31	NO
104	PPAP2B	PPAP2B	PPAP2B	7186	0.026	0.3	NO
105	PIKFYVE	PIKFYVE	PIKFYVE	7195	0.026	0.3	NO
106	HADHA	HADHA	HADHA	7895	0.012	0.27	NO
107	MTMR4	MTMR4	MTMR4	7944	0.012	0.26	NO
108	SGMS1	SGMS1	SGMS1	7963	0.011	0.26	NO
109	LCLAT1	LCLAT1	LCLAT1	8336	0.0046	0.24	NO
110	PI4K2B	PI4K2B	PI4K2B	8343	0.0045	0.24	NO
111	CDS2	CDS2	CDS2	8354	0.0042	0.24	NO
112	ACER3	ACER3	ACER3	8477	0.002	0.24	NO
113	TAZ	TAZ	TAZ	8507	0.0016	0.24	NO
114	PSAP	PSAP	PSAP	8523	0.0013	0.24	NO
115	COL4A3BP	COL4A3BP	COL4A3BP	8583	0.0003	0.23	NO
116	AGPAT3	AGPAT3	AGPAT3	8628	-0.00053	0.23	NO
117	PIK3R1	PIK3R1	PIK3R1	9030	-0.0074	0.21	NO
118	PI4KB	PI4KB	PI4KB	9249	-0.011	0.2	NO
119	SMPD4	SMPD4	SMPD4	9266	-0.012	0.2	NO
120	SLC44A1	SLC44A1	SLC44A1	9591	-0.017	0.18	NO
121	PTEN	PTEN	PTEN	9633	-0.018	0.18	NO
122	SMPD1	SMPD1	SMPD1	9648	-0.018	0.18	NO
123	GPCPD1	GPCPD1	GPCPD1	9721	-0.019	0.17	NO
124	PI4KA	PI4KA	PI4KA	9726	-0.019	0.17	NO
125	SPTLC1	SPTLC1	SPTLC1	10073	-0.025	0.16	NO
126	UGCG	UGCG	UGCG	10219	-0.028	0.15	NO
127	VAPA	VAPA	VAPA	10339	-0.03	0.14	NO
128	SGPL1	SGPL1	SGPL1	10364	-0.03	0.14	NO
129	MTMR2	MTMR2	MTMR2	10385	-0.031	0.14	NO
130	CDIPT	CDIPT	CDIPT	10589	-0.034	0.13	NO
131	GLA	GLA	GLA	10591	-0.034	0.13	NO
132	PGS1	PGS1	PGS1	10645	-0.035	0.13	NO
133	PIP4K2B	PIP4K2B	PIP4K2B	10698	-0.036	0.13	NO
134	ARF3	ARF3	ARF3	10745	-0.037	0.13	NO
135	ARSA	ARSA	ARSA	11234	-0.047	0.1	NO
136	PIP5K1C	PIP5K1C	PIP5K1C	11441	-0.051	0.093	NO
137	PLA2G6	PLA2G6	PLA2G6	11451	-0.052	0.094	NO
138	CHKB	CHKB	CHKB	11495	-0.053	0.093	NO
139	PNPLA8	PNPLA8	PNPLA8	11499	-0.053	0.094	NO
140	EPT1	EPT1	EPT1	11620	-0.055	0.089	NO
141	ARSG	ARSG	ARSG	11707	-0.057	0.086	NO
142	SGPP1	SGPP1	SGPP1	11810	-0.059	0.082	NO
143	VAC14	VAC14	VAC14	12121	-0.066	0.067	NO
144	HADHB	HADHB	HADHB	12125	-0.066	0.069	NO
145	CSNK1G2	CSNK1G2	CSNK1G2	12273	-0.069	0.062	NO
146	MTMR3	MTMR3	MTMR3	12801	-0.083	0.036	NO
147	INPP5K	INPP5K	INPP5K	12863	-0.085	0.035	NO
148	PIK3R2	PIK3R2	PIK3R2	12960	-0.088	0.032	NO
149	PTDSS1	PTDSS1	PTDSS1	13018	-0.09	0.031	NO
150	PLD3	PLD3	PLD3	13129	-0.093	0.028	NO
151	PLD6	PLD6	PLD6	13354	-0.099	0.018	NO
152	INPP5E	INPP5E	INPP5E	13428	-0.1	0.017	NO
153	ARSB	ARSB	ARSB	13674	-0.11	0.0064	NO
154	PIK3R4	PIK3R4	PIK3R4	13727	-0.11	0.0065	NO
155	PIK3C3	PIK3C3	PIK3C3	13832	-0.11	0.0038	NO
156	KDSR	KDSR	KDSR	13891	-0.12	0.0036	NO
157	PEMT	PEMT	PEMT	13952	-0.12	0.0034	NO
158	PITPNB	PITPNB	PITPNB	14108	-0.12	-0.0017	NO
159	PIK3R6	PIK3R6	PIK3R6	14478	-0.14	-0.018	NO
160	PI4K2A	PI4K2A	PI4K2A	14779	-0.15	-0.03	NO
161	ARSK	ARSK	ARSK	14789	-0.15	-0.027	NO
162	PLA2G4C	PLA2G4C	PLA2G4C	14847	-0.16	-0.026	NO
163	PLD4	PLD4	PLD4	14992	-0.17	-0.029	NO
164	MTMR1	MTMR1	MTMR1	15022	-0.17	-0.027	NO
165	LPCAT2	LPCAT2	LPCAT2	15087	-0.17	-0.026	NO
166	MBOAT2	MBOAT2	MBOAT2	15155	-0.17	-0.025	NO
167	ARSF	ARSF	ARSF	15230	-0.18	-0.024	NO
168	PLD1	PLD1	PLD1	15375	-0.19	-0.027	NO
169	PIK3CA	PIK3CA	PIK3CA	15423	-0.19	-0.025	NO
170	DEGS1	DEGS1	DEGS1	15474	-0.19	-0.023	NO
171	AGPAT4	AGPAT4	AGPAT4	15711	-0.21	-0.03	NO
172	PLD2	PLD2	PLD2	15758	-0.21	-0.027	NO
173	PCYT1A	PCYT1A	PCYT1A	15789	-0.22	-0.023	NO
174	PLA2G4D	PLA2G4D	PLA2G4D	16148	-0.25	-0.036	NO
175	ARSJ	ARSJ	ARSJ	16375	-0.27	-0.042	NO
176	SLC44A5	SLC44A5	SLC44A5	16972	-0.34	-0.065	NO
177	PNPLA3	PNPLA3	PNPLA3	16978	-0.34	-0.056	NO
178	PIK3CD	PIK3CD	PIK3CD	17055	-0.35	-0.052	NO
179	PLA2G5	PLA2G5	PLA2G5	17194	-0.37	-0.049	NO
180	PLA2G3	PLA2G3	PLA2G3	17258	-0.39	-0.043	NO
181	GM2A	GM2A	GM2A	17286	-0.39	-0.034	NO
182	ACER1	ACER1	ACER1	17517	-0.44	-0.036	NO
183	PRKD1	PRKD1	PRKD1	17522	-0.44	-0.024	NO
184	NEU2	NEU2	NEU2	17607	-0.46	-0.017	NO
185	SPHK1	SPHK1	SPHK1	17947	-0.54	-0.022	NO
186	PCYT1B	PCYT1B	PCYT1B	18547	-0.83	-0.033	NO
187	ETNK2	ETNK2	ETNK2	18576	-0.85	-0.013	NO
188	ARSI	ARSI	ARSI	18577	-0.85	0.0092	NO

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

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

genes ES table in pathway: ST INTERLEUKIN 4 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	C4BPB	C4BPB	C4BPB	31	1.4	0.11	YES
2	FOXA3	FOXA3	FOXA3	38	1.4	0.21	YES
3	TFF1	TFF1	TFF1	68	1.2	0.3	YES
4	FOXA2	FOXA2	FOXA2	82	1.2	0.39	YES
5	SHH	SHH	SHH	180	0.93	0.46	YES
6	SERPINA1	SERPINA1	SERPINA1	349	0.75	0.51	YES
7	SFTPA2	SFTPA2	SFTPA2	760	0.53	0.52	YES
8	FOXA1	FOXA1	FOXA1	1063	0.42	0.54	YES
9	VTN	VTN	VTN	1447	0.33	0.55	YES
10	CYP2C18	CYP2C18	CYP2C18	1622	0.3	0.56	YES
11	KLK3	KLK3	KLK3	1796	0.28	0.57	YES
12	NR2F2	NR2F2	NR2F2	2164	0.24	0.57	NO
13	XBP1	XBP1	XBP1	2674	0.2	0.56	NO
14	APOB	APOB	APOB	3028	0.17	0.56	NO
15	NFIB	NFIB	NFIB	4918	0.083	0.46	NO
16	POU2F1	POU2F1	POU2F1	6400	0.043	0.38	NO
17	PISD	PISD	PISD	8160	0.0076	0.29	NO
18	FOS	FOS	FOS	8164	0.0075	0.29	NO
19	SP1	SP1	SP1	8353	0.0042	0.28	NO
20	CDKN1B	CDKN1B	CDKN1B	9503	-0.016	0.22	NO
21	NFIA	NFIA	NFIA	9534	-0.016	0.22	NO
22	SOD1	SOD1	SOD1	9585	-0.017	0.22	NO
23	BRCA1	BRCA1	BRCA1	9960	-0.023	0.2	NO
24	EP300	EP300	EP300	10581	-0.034	0.17	NO
25	COL18A1	COL18A1	COL18A1	10879	-0.04	0.16	NO
26	CREBBP	CREBBP	CREBBP	11638	-0.056	0.12	NO
27	NDUFV3	NDUFV3	NDUFV3	11887	-0.061	0.11	NO
28	ATP5J	ATP5J	ATP5J	12106	-0.065	0.11	NO
29	AP1B1	AP1B1	AP1B1	12156	-0.067	0.11	NO
30	PRDM15	PRDM15	PRDM15	12503	-0.075	0.097	NO
31	JUN	JUN	JUN	13371	-0.1	0.058	NO
32	NFIC	NFIC	NFIC	13890	-0.12	0.039	NO
33	NRIP1	NRIP1	NRIP1	13955	-0.12	0.045	NO
34	NCOA3	NCOA3	NCOA3	13997	-0.12	0.052	NO
35	AR	AR	AR	14291	-0.13	0.047	NO
36	SCGB1A1	SCGB1A1	SCGB1A1	14511	-0.14	0.046	NO
37	CEBPB	CEBPB	CEBPB	15126	-0.17	0.026	NO
38	SFTPA1	SFTPA1	SFTPA1	15868	-0.22	0.0041	NO
39	NKX3-1	NKX3-1	NKX3-1	17450	-0.43	-0.047	NO
40	DSCAM	DSCAM	DSCAM	17547	-0.45	-0.018	NO
41	ESR1	ESR1	ESR1	17810	-0.5	0.0068	NO
42	SFTPD	SFTPD	SFTPD	18014	-0.56	0.039	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: ST INTERLEUKIN 4 PATHWAY.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: ST INTERLEUKIN 4 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG CYSTEINE AND METHIONINE METABOLISM	34	genes.ES.table	0.52	1.6	0.028	1	0.96	0.35	0.18	0.29	0.7	0.37
KEGG RNA DEGRADATION	57	genes.ES.table	0.4	1.8	0.024	1	0.67	0.72	0.54	0.34	1	0.59
KEGG BASAL TRANSCRIPTION FACTORS	34	genes.ES.table	0.41	1.6	0.069	1	0.96	0.5	0.46	0.27	0.78	0.41
KEGG SPLICEOSOME	114	genes.ES.table	0.4	1.6	0.097	1	0.95	0.74	0.52	0.35	0.8	0.43
PID FANCONI PATHWAY	46	genes.ES.table	0.52	1.6	0.093	1	0.93	0.85	0.44	0.48	0.93	0.48
PID AURORA B PATHWAY	39	genes.ES.table	0.51	1.6	0.043	1	0.92	0.51	0.32	0.35	0.92	0.48
PID ATR PATHWAY	39	genes.ES.table	0.51	1.6	0.11	1	0.97	0.59	0.33	0.4	0.7	0.38
PID ATM PATHWAY	34	genes.ES.table	0.48	1.6	0.059	1	0.91	0.71	0.48	0.37	1	0.53
PID PLK1 PATHWAY	45	genes.ES.table	0.49	1.5	0.12	1	0.99	0.44	0.29	0.32	0.78	0.42
PID FOXM1PATHWAY	39	genes.ES.table	0.51	1.6	0.053	1	0.94	0.54	0.29	0.38	0.95	0.48

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE METABOLISM

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	ENO3	ENO3	ENO3	201	0.6	0.12	YES
2	PAPOLB	PAPOLB	PAPOLB	539	0.49	0.2	YES
3	DCP2	DCP2	DCP2	3641	0.2	0.075	YES
4	LSM6	LSM6	LSM6	3827	0.2	0.11	YES
5	DCP1B	DCP1B	DCP1B	4253	0.18	0.12	YES
6	EXOSC9	EXOSC9	EXOSC9	4868	0.16	0.12	YES
7	PAPOLG	PAPOLG	PAPOLG	5292	0.14	0.13	YES
8	LSM2	LSM2	LSM2	5661	0.13	0.14	YES
9	PNPT1	PNPT1	PNPT1	5838	0.12	0.15	YES
10	CNOT3	CNOT3	CNOT3	6272	0.11	0.15	YES
11	CNOT10	CNOT10	CNOT10	6322	0.11	0.17	YES
12	EDC3	EDC3	EDC3	6441	0.11	0.19	YES
13	CNOT7	CNOT7	CNOT7	6673	0.1	0.2	YES
14	EXOSC5	EXOSC5	EXOSC5	6755	0.1	0.22	YES
15	EXOSC3	EXOSC3	EXOSC3	7533	0.086	0.19	YES
16	EXOSC8	EXOSC8	EXOSC8	7550	0.086	0.21	YES
17	HSPD1	HSPD1	HSPD1	7575	0.085	0.23	YES
18	C1D	C1D	C1D	7649	0.084	0.24	YES
19	CNOT6	CNOT6	CNOT6	7774	0.082	0.25	YES
20	PARN	PARN	PARN	7786	0.081	0.27	YES
21	ZCCHC7	ZCCHC7	ZCCHC7	8014	0.077	0.27	YES
22	RQCD1	RQCD1	RQCD1	8185	0.074	0.28	YES
23	XRN2	XRN2	XRN2	8193	0.074	0.29	YES
24	DCPS	DCPS	DCPS	8227	0.073	0.3	YES
25	EXOSC10	EXOSC10	EXOSC10	8307	0.072	0.32	YES
26	LSM1	LSM1	LSM1	8415	0.07	0.32	YES
27	DCP1A	DCP1A	DCP1A	8441	0.07	0.34	YES
28	LSM4	LSM4	LSM4	8581	0.067	0.34	YES
29	EDC4	EDC4	EDC4	8967	0.06	0.34	YES
30	CNOT6L	CNOT6L	CNOT6L	9078	0.058	0.34	YES
31	SKIV2L2	SKIV2L2	SKIV2L2	9082	0.058	0.36	YES
32	CNOT2	CNOT2	CNOT2	9146	0.057	0.36	YES
33	LSM5	LSM5	LSM5	9434	0.052	0.36	YES
34	EXOSC2	EXOSC2	EXOSC2	9522	0.05	0.36	YES
35	NAA38	NAA38	NAA38	9576	0.049	0.37	YES
36	PAPOLA	PAPOLA	PAPOLA	9792	0.045	0.37	YES
37	LSM3	LSM3	LSM3	9802	0.045	0.38	YES
38	PATL1	PATL1	PATL1	9830	0.044	0.39	YES
39	EXOSC4	EXOSC4	EXOSC4	9879	0.043	0.39	YES
40	SKIV2L	SKIV2L	SKIV2L	10017	0.041	0.39	YES
41	EXOSC6	EXOSC6	EXOSC6	10045	0.041	0.4	YES
42	WDR61	WDR61	WDR61	10223	0.038	0.4	NO
43	PAPD7	PAPD7	PAPD7	10713	0.029	0.38	NO
44	CNOT4	CNOT4	CNOT4	11075	0.022	0.36	NO
45	DDX6	DDX6	DDX6	11189	0.021	0.36	NO
46	CNOT8	CNOT8	CNOT8	11650	0.013	0.34	NO
47	HSPA9	HSPA9	HSPA9	11651	0.013	0.34	NO
48	MPHOSPH6	MPHOSPH6	MPHOSPH6	12006	0.0066	0.33	NO
49	EXOSC1	EXOSC1	EXOSC1	12075	0.0054	0.32	NO
50	TTC37	TTC37	TTC37	12185	0.0032	0.32	NO
51	ENO2	ENO2	ENO2	12280	0.0014	0.31	NO
52	ENO1	ENO1	ENO1	12965	-0.012	0.28	NO
53	LSM7	LSM7	LSM7	13155	-0.015	0.27	NO
54	EXOSC7	EXOSC7	EXOSC7	13169	-0.016	0.28	NO
55	XRN1	XRN1	XRN1	13287	-0.018	0.27	NO
56	CNOT1	CNOT1	CNOT1	13778	-0.028	0.25	NO
57	DIS3	DIS3	DIS3	15159	-0.063	0.19	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 CYSTEINE AND METHIONINE METABOLISM.

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

genes ES table in pathway: KEGG RNA DEGRADATION

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	ZNF569	ZNF569	ZNF569	110	0.65	0.005	YES
2	ZNF418	ZNF418	ZNF418	144	0.62	0.014	YES
3	ZNF331	ZNF331	ZNF331	173	0.61	0.022	YES
4	ZNF221	ZNF221	ZNF221	195	0.6	0.031	YES
5	ZNF157	ZNF157	ZNF157	207	0.6	0.041	YES
6	ZNF606	ZNF606	ZNF606	212	0.6	0.05	YES
7	ZNF256	ZNF256	ZNF256	247	0.58	0.058	YES
8	ZNF420	ZNF420	ZNF420	258	0.57	0.067	YES
9	ZNF98	ZNF98	ZNF98	281	0.56	0.076	YES
10	ZNF570	ZNF570	ZNF570	308	0.55	0.083	YES
11	ZNF571	ZNF571	ZNF571	350	0.54	0.09	YES
12	ZNF607	ZNF607	ZNF607	386	0.53	0.097	YES
13	ZNF492	ZNF492	ZNF492	409	0.52	0.1	YES
14	ZNF334	ZNF334	ZNF334	424	0.51	0.11	YES
15	ZNF439	ZNF439	ZNF439	443	0.51	0.12	YES
16	ZNF285	ZNF285	ZNF285	455	0.51	0.13	YES
17	ZNF433	ZNF433	ZNF433	589	0.48	0.13	YES
18	ZIK1	ZIK1	ZIK1	624	0.47	0.14	YES
19	ZNF347	ZNF347	ZNF347	633	0.47	0.14	YES
20	ZNF442	ZNF442	ZNF442	703	0.46	0.15	YES
21	ZNF43	ZNF43	ZNF43	735	0.45	0.15	YES
22	ZNF599	ZNF599	ZNF599	738	0.45	0.16	YES
23	ZNF620	ZNF620	ZNF620	747	0.45	0.17	YES
24	TBX5	TBX5	TBX5	755	0.45	0.17	YES
25	ZIM2	ZIM2	ZIM2	762	0.45	0.18	YES
26	ZNF519	ZNF519	ZNF519	778	0.44	0.19	YES
27	ZNF311	ZNF311	ZNF311	806	0.44	0.19	YES
28	ZNF540	ZNF540	ZNF540	813	0.44	0.2	YES
29	ZNF454	ZNF454	ZNF454	887	0.43	0.2	YES
30	ZNF354C	ZNF354C	ZNF354C	922	0.42	0.21	YES
31	ZNF577	ZNF577	ZNF577	945	0.42	0.21	YES
32	ZNF613	ZNF613	ZNF613	962	0.42	0.22	YES
33	ZNF773	ZNF773	ZNF773	990	0.41	0.22	YES
34	ZNF605	ZNF605	ZNF605	1062	0.4	0.23	YES
35	ZNF254	ZNF254	ZNF254	1086	0.4	0.23	YES
36	ZNF10	ZNF10	ZNF10	1134	0.39	0.24	YES
37	ZNF595	ZNF595	ZNF595	1141	0.39	0.24	YES
38	ZNF649	ZNF649	ZNF649	1145	0.39	0.25	YES
39	TEAD2	TEAD2	TEAD2	1193	0.39	0.25	YES
40	ZNF547	ZNF547	ZNF547	1241	0.38	0.26	YES
41	ZNF566	ZNF566	ZNF566	1249	0.38	0.26	YES
42	ZNF167	ZNF167	ZNF167	1295	0.37	0.27	YES
43	E2F5	E2F5	E2F5	1297	0.37	0.27	YES
44	ZNF596	ZNF596	ZNF596	1327	0.37	0.28	YES
45	ZNF563	ZNF563	ZNF563	1385	0.36	0.28	YES
46	ZNF567	ZNF567	ZNF567	1397	0.36	0.29	YES
47	NR1I3	NR1I3	NR1I3	1407	0.36	0.29	YES
48	ZNF214	ZNF214	ZNF214	1473	0.35	0.3	YES
49	ZNF30	ZNF30	ZNF30	1524	0.35	0.3	YES
50	ZNF614	ZNF614	ZNF614	1528	0.35	0.3	YES
51	ZNF583	ZNF583	ZNF583	1554	0.35	0.31	YES
52	TGIF2	TGIF2	TGIF2	1562	0.34	0.31	YES
53	ZNF529	ZNF529	ZNF529	1597	0.34	0.32	YES
54	ESRRG	ESRRG	ESRRG	1604	0.34	0.32	YES
55	ZNF615	ZNF615	ZNF615	1618	0.34	0.33	YES
56	ZNF643	ZNF643	ZNF643	1702	0.33	0.33	YES
57	ZNF415	ZNF415	ZNF415	1706	0.33	0.33	YES
58	ZNF559	ZNF559	ZNF559	1724	0.33	0.34	YES
59	ZNF546	ZNF546	ZNF546	1750	0.33	0.34	YES
60	ZNF350	ZNF350	ZNF350	1799	0.32	0.35	YES
61	ZNF560	ZNF560	ZNF560	1812	0.32	0.35	YES
62	ZFP28	ZFP28	ZFP28	1834	0.32	0.36	YES
63	ZNF530	ZNF530	ZNF530	1835	0.32	0.36	YES
64	ZNF483	ZNF483	ZNF483	1837	0.32	0.36	YES
65	ZNF585A	ZNF585A	ZNF585A	1934	0.31	0.36	YES
66	ZNF155	ZNF155	ZNF155	2025	0.3	0.36	YES
67	SMARCD3	SMARCD3	SMARCD3	2076	0.3	0.37	YES
68	ZFP37	ZFP37	ZFP37	2127	0.29	0.37	YES
69	NR2E3	NR2E3	NR2E3	2132	0.29	0.37	YES
70	ZNF382	ZNF382	ZNF382	2174	0.29	0.38	YES
71	ZNF658	ZNF658	ZNF658	2203	0.29	0.38	YES
72	ZNF443	ZNF443	ZNF443	2223	0.29	0.38	YES
73	ZNF419	ZNF419	ZNF419	2230	0.29	0.39	YES
74	ZNF286A	ZNF286A	ZNF286A	2271	0.28	0.39	YES
75	ESRRB	ESRRB	ESRRB	2278	0.28	0.4	YES
76	ZNF26	ZNF26	ZNF26	2358	0.28	0.4	YES
77	ZNF273	ZNF273	ZNF273	2365	0.28	0.4	YES
78	ZNF140	ZNF140	ZNF140	2378	0.28	0.4	YES
79	ZNF528	ZNF528	ZNF528	2401	0.28	0.41	YES
80	ZFP2	ZFP2	ZFP2	2437	0.27	0.41	YES
81	NR2E1	NR2E1	NR2E1	2439	0.27	0.42	YES
82	ZNF14	ZNF14	ZNF14	2440	0.27	0.42	YES
83	ZNF235	ZNF235	ZNF235	2453	0.27	0.42	YES
84	ZNF92	ZNF92	ZNF92	2567	0.26	0.42	YES
85	ZNF222	ZNF222	ZNF222	2608	0.26	0.42	YES
86	ZNF230	ZNF230	ZNF230	2644	0.26	0.43	YES
87	ZNF287	ZNF287	ZNF287	2695	0.26	0.43	YES
88	ZNF184	ZNF184	ZNF184	2752	0.25	0.43	YES
89	ZFP112	ZFP112	ZFP112	2756	0.25	0.43	YES
90	ZNF610	ZNF610	ZNF610	2766	0.25	0.44	YES
91	ZNF300	ZNF300	ZNF300	2788	0.25	0.44	YES
92	ZNF642	ZNF642	ZNF642	2798	0.25	0.44	YES
93	ZNF100	ZNF100	ZNF100	2863	0.24	0.44	YES
94	ZNF585B	ZNF585B	ZNF585B	2874	0.24	0.45	YES
95	ZNF225	ZNF225	ZNF225	2961	0.24	0.45	YES
96	ZNF354A	ZNF354A	ZNF354A	2970	0.24	0.45	YES
97	ZNF227	ZNF227	ZNF227	3037	0.23	0.45	YES
98	ZNF208	ZNF208	ZNF208	3071	0.23	0.45	YES
99	ZNF160	ZNF160	ZNF160	3195	0.23	0.45	YES
100	ZNF154	ZNF154	ZNF154	3216	0.22	0.45	YES
101	ZKSCAN4	ZKSCAN4	ZKSCAN4	3237	0.22	0.46	YES
102	ZNF558	ZNF558	ZNF558	3241	0.22	0.46	YES
103	ESR2	ESR2	ESR2	3246	0.22	0.46	YES
104	ZNF551	ZNF551	ZNF551	3265	0.22	0.46	YES
105	ZNF138	ZNF138	ZNF138	3279	0.22	0.47	YES
106	ZNF320	ZNF320	ZNF320	3482	0.21	0.46	YES
107	ESR1	ESR1	ESR1	3484	0.21	0.46	YES
108	ZNF2	ZNF2	ZNF2	3522	0.21	0.47	YES
109	NR5A1	NR5A1	NR5A1	3586	0.21	0.47	YES
110	ZNF493	ZNF493	ZNF493	3613	0.2	0.47	YES
111	ZNF136	ZNF136	ZNF136	3635	0.2	0.47	YES
112	ZNF114	ZNF114	ZNF114	3646	0.2	0.47	YES
113	ZNF471	ZNF471	ZNF471	3698	0.2	0.47	YES
114	ZNF383	ZNF383	ZNF383	3711	0.2	0.48	YES
115	ZNF548	ZNF548	ZNF548	3736	0.2	0.48	YES
116	ZNF544	ZNF544	ZNF544	3785	0.2	0.48	YES
117	ZNF223	ZNF223	ZNF223	3800	0.2	0.48	YES
118	ZNF234	ZNF234	ZNF234	3805	0.2	0.48	YES
119	ZNF417	ZNF417	ZNF417	3833	0.2	0.49	YES
120	ZNF496	ZNF496	ZNF496	3918	0.19	0.48	YES
121	ZNF180	ZNF180	ZNF180	3922	0.19	0.49	YES
122	ZNF517	ZNF517	ZNF517	3923	0.19	0.49	YES
123	ZNF304	ZNF304	ZNF304	3954	0.19	0.49	YES
124	ZNF192	ZNF192	ZNF192	3988	0.19	0.49	YES
125	ZNF485	ZNF485	ZNF485	3999	0.19	0.5	YES
126	ZNF354B	ZNF354B	ZNF354B	4036	0.19	0.5	YES
127	ZNF45	ZNF45	ZNF45	4055	0.19	0.5	YES
128	RBL1	RBL1	RBL1	4106	0.18	0.5	YES
129	ZNF248	ZNF248	ZNF248	4107	0.18	0.5	YES
130	ZKSCAN5	ZKSCAN5	ZKSCAN5	4127	0.18	0.51	YES
131	ZNF582	ZNF582	ZNF582	4351	0.17	0.5	YES
132	ZNF625	ZNF625	ZNF625	4364	0.17	0.5	YES
133	ZNF215	ZNF215	ZNF215	4455	0.17	0.5	YES
134	ZNF212	ZNF212	ZNF212	4544	0.17	0.5	YES
135	ZNF473	ZNF473	ZNF473	4585	0.16	0.5	YES
136	ZFP1	ZFP1	ZFP1	4595	0.16	0.5	YES
137	ZNF627	ZNF627	ZNF627	4605	0.16	0.5	YES
138	ZNF23	ZNF23	ZNF23	4643	0.16	0.5	YES
139	ZNF498	ZNF498	ZNF498	4645	0.16	0.5	YES
140	ZNF17	ZNF17	ZNF17	4724	0.16	0.5	YES
141	AR	AR	AR	4765	0.16	0.5	YES
142	ZNF624	ZNF624	ZNF624	4842	0.16	0.5	YES
143	ZNF274	ZNF274	ZNF274	4897	0.15	0.5	YES
144	ZNF555	ZNF555	ZNF555	4912	0.15	0.5	YES
145	ZKSCAN3	ZKSCAN3	ZKSCAN3	4922	0.15	0.5	YES
146	RORB	RORB	RORB	4924	0.15	0.51	YES
147	ZNF226	ZNF226	ZNF226	4990	0.15	0.51	YES
148	ZNF416	ZNF416	ZNF416	5074	0.15	0.5	YES
149	ZNF446	ZNF446	ZNF446	5080	0.15	0.51	YES
150	SMAD4	SMAD4	SMAD4	5142	0.15	0.5	YES
151	ZNF200	ZNF200	ZNF200	5293	0.14	0.5	YES
152	ZNF655	ZNF655	ZNF655	5297	0.14	0.5	YES
153	ZNF436	ZNF436	ZNF436	5311	0.14	0.5	YES
154	ZNF141	ZNF141	ZNF141	5360	0.14	0.5	YES
155	ZNF616	ZNF616	ZNF616	5418	0.14	0.5	YES
156	PGR	PGR	PGR	5433	0.14	0.5	YES
157	ZNF708	ZNF708	ZNF708	5451	0.14	0.5	YES
158	ZNF641	ZNF641	ZNF641	5485	0.14	0.5	YES
159	ZNF33B	ZNF33B	ZNF33B	5499	0.13	0.51	YES
160	ZNF333	ZNF333	ZNF333	5626	0.13	0.5	NO
161	ZNF175	ZNF175	ZNF175	5644	0.13	0.5	NO
162	ZNF202	ZNF202	ZNF202	5697	0.13	0.5	NO
163	ZNF3	ZNF3	ZNF3	5815	0.12	0.5	NO
164	MED12	MED12	MED12	5831	0.12	0.5	NO
165	ZNF543	ZNF543	ZNF543	5847	0.12	0.5	NO
166	ZNF445	ZNF445	ZNF445	5935	0.12	0.5	NO
167	ZNF33A	ZNF33A	ZNF33A	5948	0.12	0.5	NO
168	SMAD2	SMAD2	SMAD2	5952	0.12	0.5	NO
169	TGS1	TGS1	TGS1	6013	0.12	0.5	NO
170	NR2F1	NR2F1	NR2F1	6058	0.12	0.5	NO
171	KAT2A	KAT2A	KAT2A	6061	0.12	0.5	NO
172	ZNF584	ZNF584	ZNF584	6266	0.11	0.49	NO
173	TRIM33	TRIM33	TRIM33	6277	0.11	0.49	NO
174	ZNF28	ZNF28	ZNF28	6370	0.11	0.49	NO
175	TRIM28	TRIM28	TRIM28	6380	0.11	0.49	NO
176	ZNF514	ZNF514	ZNF514	6392	0.11	0.49	NO
177	PARP1	PARP1	PARP1	6537	0.11	0.49	NO
178	ZNF432	ZNF432	ZNF432	6590	0.11	0.49	NO
179	ZNF441	ZNF441	ZNF441	6653	0.1	0.48	NO
180	ZNF611	ZNF611	ZNF611	6837	0.1	0.48	NO
181	TEAD4	TEAD4	TEAD4	6886	0.1	0.48	NO
182	ZFP90	ZFP90	ZFP90	6967	0.098	0.47	NO
183	MEN1	MEN1	MEN1	7096	0.095	0.47	NO
184	NR5A2	NR5A2	NR5A2	7116	0.095	0.47	NO
185	ZNF510	ZNF510	ZNF510	7117	0.095	0.47	NO
186	RBPJ	RBPJ	RBPJ	7152	0.094	0.47	NO
187	NR1H3	NR1H3	NR1H3	7238	0.092	0.47	NO
188	SMURF2	SMURF2	SMURF2	7240	0.092	0.47	NO
189	NR2C2AP	NR2C2AP	NR2C2AP	7316	0.091	0.46	NO
190	ZNF490	ZNF490	ZNF490	7358	0.09	0.46	NO
191	MED17	MED17	MED17	7374	0.089	0.46	NO
192	ZNF250	ZNF250	ZNF250	7433	0.088	0.46	NO
193	ZNF552	ZNF552	ZNF552	7448	0.088	0.46	NO
194	ZNF565	ZNF565	ZNF565	7528	0.086	0.46	NO
195	SMAD7	SMAD7	SMAD7	7535	0.086	0.46	NO
196	ZNF468	ZNF468	ZNF468	7623	0.085	0.46	NO
197	ZNF25	ZNF25	ZNF25	7670	0.084	0.46	NO
198	MED30	MED30	MED30	7700	0.083	0.46	NO
199	NOTCH2	NOTCH2	NOTCH2	7756	0.082	0.46	NO
200	SKI	SKI	SKI	7796	0.081	0.46	NO
201	ZNF266	ZNF266	ZNF266	7827	0.081	0.46	NO
202	ZNF224	ZNF224	ZNF224	7852	0.08	0.46	NO
203	ZNF394	ZNF394	ZNF394	7963	0.078	0.45	NO
204	ZNF12	ZNF12	ZNF12	8088	0.076	0.44	NO
205	ZNF169	ZNF169	ZNF169	8156	0.075	0.44	NO
206	TEAD3	TEAD3	TEAD3	8173	0.074	0.44	NO
207	MAMLD1	MAMLD1	MAMLD1	8211	0.074	0.44	NO
208	CCNT2	CCNT2	CCNT2	8336	0.071	0.44	NO
209	RXRB	RXRB	RXRB	8360	0.071	0.44	NO
210	NR6A1	NR6A1	NR6A1	8473	0.069	0.43	NO
211	NCOR2	NCOR2	NCOR2	8530	0.068	0.43	NO
212	ZNF589	ZNF589	ZNF589	8535	0.068	0.43	NO
213	NPPA	NPPA	NPPA	8683	0.065	0.42	NO
214	ZNF500	ZNF500	ZNF500	8685	0.065	0.42	NO
215	CCNC	CCNC	CCNC	8715	0.065	0.42	NO
216	ZNF189	ZNF189	ZNF189	8726	0.064	0.42	NO
217	RARA	RARA	RARA	8737	0.064	0.42	NO
218	ZNF587	ZNF587	ZNF587	8757	0.064	0.42	NO
219	MED31	MED31	MED31	8764	0.064	0.43	NO
220	ZNF621	ZNF621	ZNF621	8831	0.062	0.42	NO
221	MED1	MED1	MED1	8840	0.062	0.42	NO
222	MED7	MED7	MED7	8897	0.061	0.42	NO
223	ZNF480	ZNF480	ZNF480	9056	0.058	0.42	NO
224	ZNF20	ZNF20	ZNF20	9061	0.058	0.42	NO
225	MED20	MED20	MED20	9073	0.058	0.42	NO
226	ZNF101	ZNF101	ZNF101	9136	0.057	0.41	NO
227	ZNF434	ZNF434	ZNF434	9173	0.056	0.41	NO
228	ZNF37A	ZNF37A	ZNF37A	9372	0.052	0.4	NO
229	MED26	MED26	MED26	9390	0.052	0.4	NO
230	TEAD1	TEAD1	TEAD1	9485	0.05	0.4	NO
231	UBE2D1	UBE2D1	UBE2D1	9550	0.049	0.4	NO
232	MED24	MED24	MED24	9679	0.047	0.39	NO
233	WWTR1	WWTR1	WWTR1	9694	0.047	0.39	NO
234	SP1	SP1	SP1	9723	0.046	0.39	NO
235	NR3C1	NR3C1	NR3C1	9803	0.045	0.38	NO
236	ZNF506	ZNF506	ZNF506	9826	0.044	0.38	NO
237	TBL1XR1	TBL1XR1	TBL1XR1	9870	0.044	0.38	NO
238	NCOA6	NCOA6	NCOA6	9929	0.042	0.38	NO
239	MAML1	MAML1	MAML1	9940	0.042	0.38	NO
240	NR4A3	NR4A3	NR4A3	10000	0.041	0.38	NO
241	MED6	MED6	MED6	10093	0.04	0.37	NO
242	ZNF564	ZNF564	ZNF564	10159	0.039	0.37	NO
243	TGIF1	TGIF1	TGIF1	10260	0.037	0.37	NO
244	CCNT1	CCNT1	CCNT1	10306	0.036	0.36	NO
245	ZNF425	ZNF425	ZNF425	10308	0.036	0.36	NO
246	ZNF557	ZNF557	ZNF557	10356	0.035	0.36	NO
247	ZNF282	ZNF282	ZNF282	10382	0.035	0.36	NO
248	ZNF211	ZNF211	ZNF211	10456	0.033	0.36	NO
249	SNW1	SNW1	SNW1	10516	0.032	0.36	NO
250	ZNF267	ZNF267	ZNF267	10676	0.03	0.35	NO
251	MED23	MED23	MED23	10678	0.03	0.35	NO
252	ZNF263	ZNF263	ZNF263	10747	0.028	0.34	NO
253	RPS27A	RPS27A	RPS27A	10751	0.028	0.34	NO
254	MED25	MED25	MED25	10971	0.024	0.33	NO
255	YAP1	YAP1	YAP1	11077	0.022	0.33	NO
256	E2F4	E2F4	E2F4	11146	0.021	0.32	NO
257	NRBP1	NRBP1	NRBP1	11204	0.02	0.32	NO
258	TBL1X	TBL1X	TBL1X	11366	0.018	0.31	NO
259	NR2F6	NR2F6	NR2F6	11403	0.017	0.31	NO
260	RXRG	RXRG	RXRG	11443	0.016	0.31	NO
261	TFDP1	TFDP1	TFDP1	11496	0.015	0.31	NO
262	MAML3	MAML3	MAML3	11512	0.015	0.31	NO
263	ZNF398	ZNF398	ZNF398	11541	0.015	0.31	NO
264	NR4A1	NR4A1	NR4A1	11599	0.014	0.3	NO
265	NOTCH3	NOTCH3	NOTCH3	11600	0.014	0.3	NO
266	MED4	MED4	MED4	11676	0.013	0.3	NO
267	NCOR1	NCOR1	NCOR1	11678	0.013	0.3	NO
268	USP9X	USP9X	USP9X	11705	0.012	0.3	NO
269	CREBBP	CREBBP	CREBBP	11727	0.012	0.3	NO
270	UBE2D3	UBE2D3	UBE2D3	11817	0.01	0.29	NO
271	ZNF205	ZNF205	ZNF205	11830	0.01	0.29	NO
272	NCOA2	NCOA2	NCOA2	11834	0.01	0.29	NO
273	ZNF343	ZNF343	ZNF343	11847	0.0098	0.29	NO
274	PPM1A	PPM1A	PPM1A	11886	0.009	0.29	NO
275	ZNF317	ZNF317	ZNF317	12104	0.0048	0.28	NO
276	ZNF460	ZNF460	ZNF460	12115	0.0046	0.28	NO
277	ZNF18	ZNF18	ZNF18	12138	0.0041	0.28	NO
278	NCOA1	NCOA1	NCOA1	12307	0.00092	0.27	NO
279	ZNF324	ZNF324	ZNF324	12341	0.00035	0.27	NO
280	ZNF19	ZNF19	ZNF19	12390	-0.00073	0.26	NO
281	ZNF597	ZNF597	ZNF597	12409	-0.0011	0.26	NO
282	HDAC1	HDAC1	HDAC1	12427	-0.0015	0.26	NO
283	MAML2	MAML2	MAML2	12497	-0.0026	0.26	NO
284	NR1D2	NR1D2	NR1D2	12584	-0.0042	0.25	NO
285	MED14	MED14	MED14	12613	-0.0046	0.25	NO
286	NCOA3	NCOA3	NCOA3	12623	-0.0048	0.25	NO
287	UBA52	UBA52	UBA52	12729	-0.0067	0.25	NO
288	CTGF	CTGF	CTGF	12791	-0.0079	0.24	NO
289	SKIL	SKIL	SKIL	12861	-0.0092	0.24	NO
290	ZKSCAN1	ZKSCAN1	ZKSCAN1	12863	-0.0092	0.24	NO
291	RARG	RARG	RARG	13044	-0.013	0.23	NO
292	ZNF440	ZNF440	ZNF440	13156	-0.015	0.22	NO
293	ZNF556	ZNF556	ZNF556	13197	-0.016	0.22	NO
294	CDK9	CDK9	CDK9	13288	-0.018	0.22	NO
295	ZNF431	ZNF431	ZNF431	13307	-0.018	0.22	NO
296	NOTCH4	NOTCH4	NOTCH4	13330	-0.019	0.22	NO
297	ZNF264	ZNF264	ZNF264	13350	-0.02	0.22	NO
298	ZNF619	ZNF619	ZNF619	13535	-0.023	0.2	NO
299	NRBF2	NRBF2	NRBF2	13782	-0.029	0.19	NO
300	CDK8	CDK8	CDK8	13801	-0.029	0.19	NO
301	MED8	MED8	MED8	13829	-0.03	0.19	NO
302	ZNF561	ZNF561	ZNF561	13931	-0.032	0.19	NO
303	MED27	MED27	MED27	14067	-0.035	0.18	NO
304	MED15	MED15	MED15	14209	-0.038	0.17	NO
305	MED16	MED16	MED16	14501	-0.045	0.16	NO
306	ZNF197	ZNF197	ZNF197	14616	-0.048	0.15	NO
307	MED10	MED10	MED10	14642	-0.049	0.15	NO
308	ZNF426	ZNF426	ZNF426	14658	-0.049	0.15	NO
309	ZNF337	ZNF337	ZNF337	15046	-0.059	0.13	NO
310	ZNF600	ZNF600	ZNF600	15080	-0.06	0.13	NO
311	ZNF213	ZNF213	ZNF213	15135	-0.062	0.13	NO
312	ZNF484	ZNF484	ZNF484	15219	-0.065	0.12	NO
313	KAT2B	KAT2B	KAT2B	15245	-0.066	0.12	NO
314	NR1H2	NR1H2	NR1H2	15700	-0.08	0.1	NO
315	RUNX2	RUNX2	RUNX2	15749	-0.082	0.1	NO
316	THRA	THRA	THRA	15905	-0.088	0.093	NO
317	NR4A2	NR4A2	NR4A2	15933	-0.089	0.094	NO
318	PRIC285	PRIC285	PRIC285	16130	-0.096	0.084	NO
319	NR3C2	NR3C2	NR3C2	16234	-0.1	0.08	NO
320	PPARD	PPARD	PPARD	16440	-0.11	0.071	NO
321	JUNB	JUNB	JUNB	16578	-0.12	0.066	NO
322	PPARA	PPARA	PPARA	16608	-0.12	0.066	NO
323	RXRA	RXRA	RXRA	16647	-0.12	0.066	NO
324	RORA	RORA	RORA	16652	-0.12	0.068	NO
325	RORC	RORC	RORC	16738	-0.13	0.066	NO
326	THRB	THRB	THRB	16811	-0.13	0.064	NO
327	NR0B2	NR0B2	NR0B2	16819	-0.13	0.066	NO
328	MYC	MYC	MYC	16826	-0.13	0.068	NO
329	SMAD3	SMAD3	SMAD3	16883	-0.14	0.067	NO
330	HNF4G	HNF4G	HNF4G	16914	-0.14	0.067	NO
331	ZNF430	ZNF430	ZNF430	17032	-0.14	0.064	NO
332	PPARG	PPARG	PPARG	17062	-0.15	0.064	NO
333	NR1I2	NR1I2	NR1I2	17105	-0.15	0.065	NO
334	ESRRA	ESRRA	ESRRA	17305	-0.17	0.057	NO
335	HNF4A	HNF4A	HNF4A	17427	-0.18	0.053	NO
336	CDKN2B	CDKN2B	CDKN2B	17527	-0.19	0.051	NO
337	VDR	VDR	VDR	17774	-0.22	0.041	NO
338	SERPINE1	SERPINE1	SERPINE1	17827	-0.22	0.042	NO
339	NR1D1	NR1D1	NR1D1	17898	-0.24	0.042	NO
340	NR0B1	NR0B1	NR0B1	17926	-0.24	0.045	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 RNA DEGRADATION.

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

genes ES table in pathway: KEGG BASAL TRANSCRIPTION FACTORS

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	SMC1B	SMC1B	SMC1B	11	0.85	0.016	YES
2	HIST1H2BN	HIST1H2BN	HIST1H2BN	353	0.54	0.0079	YES
3	HIST3H2BB	HIST3H2BB	HIST3H2BB	507	0.5	0.0093	YES
4	HIST1H4I	HIST1H4I	HIST1H4I	550	0.49	0.016	YES
5	HIST1H4E	HIST1H4E	HIST1H4E	608	0.47	0.023	YES
6	PSMA8	PSMA8	PSMA8	619	0.47	0.031	YES
7	SYCP2	SYCP2	SYCP2	664	0.46	0.038	YES
8	HIST1H2BF	HIST1H2BF	HIST1H2BF	685	0.46	0.046	YES
9	HIST1H4D	HIST1H4D	HIST1H4D	772	0.44	0.05	YES
10	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	856	0.43	0.054	YES
11	HIST1H2BO	HIST1H2BO	HIST1H2BO	961	0.42	0.056	YES
12	TERT	TERT	TERT	1147	0.39	0.054	YES
13	HIST2H4A	HIST2H4A	HIST2H4A	1189	0.39	0.059	YES
14	HIST1H2BE	HIST1H2BE	HIST1H2BE	1201	0.38	0.066	YES
15	E2F5	E2F5	E2F5	1297	0.37	0.068	YES
16	CDC7	CDC7	CDC7	1300	0.37	0.075	YES
17	SKA1	SKA1	SKA1	1475	0.35	0.073	YES
18	GINS4	GINS4	GINS4	1632	0.34	0.071	YES
19	DNA2	DNA2	DNA2	1771	0.32	0.07	YES
20	HIST1H2AE	HIST1H2AE	HIST1H2AE	1849	0.32	0.072	YES
21	STAG3	STAG3	STAG3	1905	0.31	0.075	YES
22	HIST1H2BB	HIST1H2BB	HIST1H2BB	1926	0.31	0.08	YES
23	PRIM1	PRIM1	PRIM1	1946	0.31	0.085	YES
24	SGOL1	SGOL1	SGOL1	2018	0.3	0.087	YES
25	NUF2	NUF2	NUF2	2020	0.3	0.092	YES
26	TYMS	TYMS	TYMS	2072	0.3	0.096	YES
27	HIST1H2BL	HIST1H2BL	HIST1H2BL	2118	0.3	0.099	YES
28	HIST1H4K	HIST1H4K	HIST1H4K	2125	0.29	0.1	YES
29	FBXO5	FBXO5	FBXO5	2129	0.29	0.11	YES
30	HIST1H4C	HIST1H4C	HIST1H4C	2144	0.29	0.12	YES
31	NDC80	NDC80	NDC80	2159	0.29	0.12	YES
32	HIST1H2AD	HIST1H2AD	HIST1H2AD	2214	0.29	0.12	YES
33	MLF1IP	MLF1IP	MLF1IP	2249	0.29	0.13	YES
34	PLK4	PLK4	PLK4	2297	0.28	0.13	YES
35	OIP5	OIP5	OIP5	2299	0.28	0.14	YES
36	HIST1H4L	HIST1H4L	HIST1H4L	2318	0.28	0.14	YES
37	HIST1H4B	HIST1H4B	HIST1H4B	2349	0.28	0.14	YES
38	CDC25A	CDC25A	CDC25A	2369	0.28	0.15	YES
39	E2F3	E2F3	E2F3	2420	0.27	0.15	YES
40	HIST1H2BG	HIST1H2BG	HIST1H2BG	2460	0.27	0.15	YES
41	MCM10	MCM10	MCM10	2535	0.27	0.15	YES
42	GMNN	GMNN	GMNN	2609	0.26	0.16	YES
43	HIST1H2BI	HIST1H2BI	HIST1H2BI	2713	0.25	0.16	YES
44	POLE2	POLE2	POLE2	2715	0.25	0.16	YES
45	NEK2	NEK2	NEK2	2725	0.25	0.16	YES
46	BIRC5	BIRC5	BIRC5	2742	0.25	0.17	YES
47	HIST1H4H	HIST1H4H	HIST1H4H	2753	0.25	0.17	YES
48	HIST1H2BH	HIST1H2BH	HIST1H2BH	2758	0.25	0.18	YES
49	SPC24	SPC24	SPC24	2787	0.25	0.18	YES
50	HIST1H4A	HIST1H4A	HIST1H4A	2801	0.25	0.18	YES
51	CENPA	CENPA	CENPA	2883	0.24	0.18	YES
52	PRKAR2B	PRKAR2B	PRKAR2B	2891	0.24	0.19	YES
53	LIN9	LIN9	LIN9	2915	0.24	0.19	YES
54	CENPH	CENPH	CENPH	2953	0.24	0.2	YES
55	CHEK2	CHEK2	CHEK2	2965	0.24	0.2	YES
56	CDK2	CDK2	CDK2	2966	0.24	0.2	YES
57	CEP135	CEP135	CEP135	2981	0.24	0.21	YES
58	CEP290	CEP290	CEP290	2984	0.24	0.21	YES
59	CCNE2	CCNE2	CCNE2	2994	0.24	0.22	YES
60	KIF20A	KIF20A	KIF20A	3020	0.24	0.22	YES
61	MAD2L1	MAD2L1	MAD2L1	3033	0.24	0.22	YES
62	HIST1H2AB	HIST1H2AB	HIST1H2AB	3038	0.23	0.23	YES
63	KNTC1	KNTC1	KNTC1	3076	0.23	0.23	YES
64	CDC25C	CDC25C	CDC25C	3137	0.23	0.23	YES
65	HIST1H2BM	HIST1H2BM	HIST1H2BM	3161	0.23	0.24	YES
66	AURKB	AURKB	AURKB	3165	0.23	0.24	YES
67	CHEK1	CHEK1	CHEK1	3175	0.23	0.24	YES
68	HIST1H2BD	HIST1H2BD	HIST1H2BD	3211	0.22	0.25	YES
69	CDC14A	CDC14A	CDC14A	3224	0.22	0.25	YES
70	ERCC6L	ERCC6L	ERCC6L	3300	0.22	0.25	YES
71	KIF2C	KIF2C	KIF2C	3305	0.22	0.25	YES
72	UBE2C	UBE2C	UBE2C	3372	0.22	0.26	YES
73	ZWINT	ZWINT	ZWINT	3380	0.22	0.26	YES
74	E2F1	E2F1	E2F1	3390	0.22	0.26	YES
75	CENPQ	CENPQ	CENPQ	3437	0.21	0.26	YES
76	HIST1H4J	HIST1H4J	HIST1H4J	3439	0.21	0.27	YES
77	SGOL2	SGOL2	SGOL2	3444	0.21	0.27	YES
78	KIF18A	KIF18A	KIF18A	3476	0.21	0.27	YES
79	KIF23	KIF23	KIF23	3496	0.21	0.28	YES
80	ITGB3BP	ITGB3BP	ITGB3BP	3556	0.21	0.28	YES
81	ALMS1	ALMS1	ALMS1	3567	0.21	0.28	YES
82	NUP107	NUP107	NUP107	3597	0.21	0.28	YES
83	CENPL	CENPL	CENPL	3611	0.2	0.29	YES
84	NSL1	NSL1	NSL1	3648	0.2	0.29	YES
85	CENPO	CENPO	CENPO	3654	0.2	0.29	YES
86	BUB1B	BUB1B	BUB1B	3694	0.2	0.3	YES
87	LMNB1	LMNB1	LMNB1	3704	0.2	0.3	YES
88	HJURP	HJURP	HJURP	3722	0.2	0.3	YES
89	DBF4	DBF4	DBF4	3729	0.2	0.3	YES
90	HIST1H2BC	HIST1H2BC	HIST1H2BC	3741	0.2	0.31	YES
91	RFC4	RFC4	RFC4	3743	0.2	0.31	YES
92	CDC6	CDC6	CDC6	3821	0.2	0.31	YES
93	CDKN1B	CDKN1B	CDKN1B	3846	0.2	0.31	YES
94	HIST1H2BK	HIST1H2BK	HIST1H2BK	3849	0.2	0.32	YES
95	HIST1H4F	HIST1H4F	HIST1H4F	3856	0.2	0.32	YES
96	CCNE1	CCNE1	CCNE1	3871	0.19	0.32	YES
97	CENPI	CENPI	CENPI	3940	0.19	0.32	YES
98	TEX12	TEX12	TEX12	3942	0.19	0.33	YES
99	PRIM2	PRIM2	PRIM2	3943	0.19	0.33	YES
100	CCDC99	CCDC99	CCDC99	3986	0.19	0.33	YES
101	RFC5	RFC5	RFC5	4058	0.19	0.33	YES
102	SPC25	SPC25	SPC25	4102	0.18	0.34	YES
103	FKBP6	FKBP6	FKBP6	4105	0.18	0.34	YES
104	RBL1	RBL1	RBL1	4106	0.18	0.34	YES
105	POLE	POLE	POLE	4145	0.18	0.34	YES
106	CDC45	CDC45	CDC45	4182	0.18	0.34	YES
107	CENPK	CENPK	CENPK	4193	0.18	0.35	YES
108	GINS1	GINS1	GINS1	4198	0.18	0.35	YES
109	CKS1B	CKS1B	CKS1B	4201	0.18	0.35	YES
110	APITD1	APITD1	APITD1	4251	0.18	0.36	YES
111	CEP70	CEP70	CEP70	4266	0.18	0.36	YES
112	SKP2	SKP2	SKP2	4280	0.18	0.36	YES
113	CEP250	CEP250	CEP250	4286	0.18	0.36	YES
114	HIST4H4	HIST4H4	HIST4H4	4288	0.18	0.37	YES
115	CDK4	CDK4	CDK4	4328	0.18	0.37	YES
116	RFC3	RFC3	RFC3	4422	0.17	0.37	YES
117	MYBL2	MYBL2	MYBL2	4434	0.17	0.37	YES
118	RBBP4	RBBP4	RBBP4	4461	0.17	0.37	YES
119	MCM6	MCM6	MCM6	4464	0.17	0.38	YES
120	HIST2H2AC	HIST2H2AC	HIST2H2AC	4484	0.17	0.38	YES
121	HIST2H2BE	HIST2H2BE	HIST2H2BE	4543	0.17	0.38	YES
122	POLD1	POLD1	POLD1	4561	0.17	0.38	YES
123	RFC2	RFC2	RFC2	4613	0.16	0.38	YES
124	CCNA2	CCNA2	CCNA2	4616	0.16	0.38	YES
125	DHFR	DHFR	DHFR	4626	0.16	0.38	YES
126	CCNB2	CCNB2	CCNB2	4658	0.16	0.39	YES
127	RPA2	RPA2	RPA2	4846	0.16	0.38	YES
128	POT1	POT1	POT1	4850	0.16	0.38	YES
129	CENPM	CENPM	CENPM	4902	0.15	0.38	YES
130	DSN1	DSN1	DSN1	4936	0.15	0.38	YES
131	CDKN2C	CDKN2C	CDKN2C	4974	0.15	0.38	YES
132	LIN52	LIN52	LIN52	5021	0.15	0.38	YES
133	MIS12	MIS12	MIS12	5024	0.15	0.39	YES
134	PPP2R3B	PPP2R3B	PPP2R3B	5090	0.15	0.39	YES
135	CDK1	CDK1	CDK1	5112	0.15	0.39	YES
136	AKAP9	AKAP9	AKAP9	5147	0.15	0.39	YES
137	MCM2	MCM2	MCM2	5157	0.15	0.39	YES
138	FGFR1OP	FGFR1OP	FGFR1OP	5160	0.15	0.4	YES
139	AURKA	AURKA	AURKA	5164	0.14	0.4	YES
140	CDCA8	CDCA8	CDCA8	5191	0.14	0.4	YES
141	LIG1	LIG1	LIG1	5289	0.14	0.4	YES
142	CEP76	CEP76	CEP76	5290	0.14	0.4	YES
143	ZWILCH	ZWILCH	ZWILCH	5302	0.14	0.4	YES
144	BRCA1	BRCA1	BRCA1	5328	0.14	0.4	YES
145	NEDD1	NEDD1	NEDD1	5336	0.14	0.41	YES
146	AZI1	AZI1	AZI1	5369	0.14	0.41	YES
147	CCNB1	CCNB1	CCNB1	5404	0.14	0.41	YES
148	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	5413	0.14	0.41	YES
149	CDC20	CDC20	CDC20	5428	0.14	0.41	YES
150	NINL	NINL	NINL	5429	0.14	0.41	YES
151	CDT1	CDT1	CDT1	5458	0.14	0.42	YES
152	MCM8	MCM8	MCM8	5468	0.14	0.42	YES
153	WEE1	WEE1	WEE1	5489	0.14	0.42	YES
154	GINS2	GINS2	GINS2	5494	0.14	0.42	YES
155	BUB1	BUB1	BUB1	5498	0.13	0.42	YES
156	ANAPC10	ANAPC10	ANAPC10	5528	0.13	0.42	YES
157	TUBG2	TUBG2	TUBG2	5583	0.13	0.42	YES
158	MCM4	MCM4	MCM4	5587	0.13	0.43	YES
159	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	5588	0.13	0.43	YES
160	H2AFX	H2AFX	H2AFX	5591	0.13	0.43	YES
161	ANAPC4	ANAPC4	ANAPC4	5606	0.13	0.43	YES
162	POLA1	POLA1	POLA1	5620	0.13	0.44	YES
163	SMC3	SMC3	SMC3	5757	0.13	0.43	YES
164	XPO1	XPO1	XPO1	5786	0.13	0.43	YES
165	CENPJ	CENPJ	CENPJ	5798	0.13	0.43	YES
166	TUBA1A	TUBA1A	TUBA1A	5863	0.12	0.43	YES
167	RCC2	RCC2	RCC2	5915	0.12	0.43	YES
168	CASC5	CASC5	CASC5	5969	0.12	0.43	YES
169	RPA1	RPA1	RPA1	5974	0.12	0.43	YES
170	NUP43	NUP43	NUP43	6040	0.12	0.43	YES
171	AHCTF1	AHCTF1	AHCTF1	6050	0.12	0.43	YES
172	NUP133	NUP133	NUP133	6083	0.12	0.44	YES
173	RAD9A	RAD9A	RAD9A	6109	0.12	0.44	YES
174	MCM7	MCM7	MCM7	6121	0.12	0.44	YES
175	WRAP53	WRAP53	WRAP53	6246	0.11	0.43	YES
176	E2F2	E2F2	E2F2	6261	0.11	0.44	YES
177	CDC23	CDC23	CDC23	6263	0.11	0.44	YES
178	PCNT	PCNT	PCNT	6312	0.11	0.44	YES
179	MCM3	MCM3	MCM3	6318	0.11	0.44	YES
180	DYRK1A	DYRK1A	DYRK1A	6427	0.11	0.44	NO
181	PSMB4	PSMB4	PSMB4	6469	0.11	0.43	NO
182	TUBB	TUBB	TUBB	6557	0.11	0.43	NO
183	SKA2	SKA2	SKA2	6572	0.11	0.43	NO
184	PTTG1	PTTG1	PTTG1	6650	0.1	0.43	NO
185	NUP37	NUP37	NUP37	6701	0.1	0.43	NO
186	MDM2	MDM2	MDM2	6712	0.1	0.43	NO
187	POLA2	POLA2	POLA2	6754	0.1	0.43	NO
188	PCM1	PCM1	PCM1	6762	0.1	0.43	NO
189	MCM5	MCM5	MCM5	6776	0.1	0.43	NO
190	FEN1	FEN1	FEN1	6801	0.1	0.44	NO
191	RAD21	RAD21	RAD21	6846	0.1	0.44	NO
192	SEH1L	SEH1L	SEH1L	6870	0.1	0.44	NO
193	HIST1H2AC	HIST1H2AC	HIST1H2AC	6949	0.098	0.43	NO
194	H2AFZ	H2AFZ	H2AFZ	6960	0.098	0.43	NO
195	HSPA2	HSPA2	HSPA2	6992	0.097	0.44	NO
196	CEP57	CEP57	CEP57	7069	0.096	0.43	NO
197	ANAPC5	ANAPC5	ANAPC5	7211	0.093	0.43	NO
198	ANAPC7	ANAPC7	ANAPC7	7234	0.092	0.43	NO
199	RAD1	RAD1	RAD1	7246	0.092	0.43	NO
200	PMF1	PMF1	PMF1	7251	0.092	0.43	NO
201	ATM	ATM	ATM	7338	0.09	0.43	NO
202	STAG2	STAG2	STAG2	7416	0.088	0.42	NO
203	CENPC1	CENPC1	CENPC1	7472	0.087	0.42	NO
204	RRM2	RRM2	RRM2	7557	0.086	0.42	NO
205	CEP192	CEP192	CEP192	7561	0.086	0.42	NO
206	PSMD4	PSMD4	PSMD4	7581	0.085	0.42	NO
207	CUL1	CUL1	CUL1	7594	0.085	0.42	NO
208	YWHAE	YWHAE	YWHAE	7630	0.084	0.42	NO
209	UBE2E1	UBE2E1	UBE2E1	7638	0.084	0.42	NO
210	LIN37	LIN37	LIN37	7683	0.083	0.42	NO
211	SMARCA5	SMARCA5	SMARCA5	7695	0.083	0.42	NO
212	CKAP5	CKAP5	CKAP5	7765	0.082	0.42	NO
213	DKC1	DKC1	DKC1	7771	0.082	0.42	NO
214	RUVBL1	RUVBL1	RUVBL1	7877	0.08	0.42	NO
215	BUB3	BUB3	BUB3	7927	0.079	0.42	NO
216	OFD1	OFD1	OFD1	7965	0.078	0.42	NO
217	RAD17	RAD17	RAD17	8001	0.077	0.42	NO
218	PPP1CC	PPP1CC	PPP1CC	8049	0.076	0.42	NO
219	TERF1	TERF1	TERF1	8062	0.076	0.42	NO
220	SYNE1	SYNE1	SYNE1	8078	0.076	0.42	NO
221	SYCP3	SYCP3	SYCP3	8118	0.075	0.42	NO
222	LIN54	LIN54	LIN54	8129	0.075	0.42	NO
223	PSMD10	PSMD10	PSMD10	8313	0.072	0.41	NO
224	TP53	TP53	TP53	8356	0.071	0.41	NO
225	NUP85	NUP85	NUP85	8454	0.07	0.4	NO
226	TUBG1	TUBG1	TUBG1	8478	0.069	0.4	NO
227	SMC1A	SMC1A	SMC1A	8495	0.069	0.41	NO
228	CEP63	CEP63	CEP63	8533	0.068	0.4	NO
229	CENPT	CENPT	CENPT	8534	0.068	0.41	NO
230	MAPRE1	MAPRE1	MAPRE1	8607	0.067	0.4	NO
231	CENPN	CENPN	CENPN	8711	0.065	0.4	NO
232	NPM1	NPM1	NPM1	8743	0.064	0.4	NO
233	PSMC4	PSMC4	PSMC4	8744	0.064	0.4	NO
234	SDCCAG8	SDCCAG8	SDCCAG8	8907	0.061	0.39	NO
235	ATRIP	ATRIP	ATRIP	8916	0.061	0.39	NO
236	ACD	ACD	ACD	8922	0.061	0.39	NO
237	RUVBL2	RUVBL2	RUVBL2	8923	0.061	0.4	NO
238	PSMA4	PSMA4	PSMA4	8951	0.06	0.4	NO
239	RFWD2	RFWD2	RFWD2	8971	0.06	0.4	NO
240	PKMYT1	PKMYT1	PKMYT1	8979	0.06	0.4	NO
241	PSMD9	PSMD9	PSMD9	9150	0.057	0.39	NO
242	RPA3	RPA3	RPA3	9154	0.057	0.39	NO
243	PSMD12	PSMD12	PSMD12	9224	0.055	0.39	NO
244	PLK1	PLK1	PLK1	9263	0.055	0.38	NO
245	RPA4	RPA4	RPA4	9300	0.054	0.38	NO
246	MNAT1	MNAT1	MNAT1	9314	0.054	0.38	NO
247	PSMC6	PSMC6	PSMC6	9339	0.053	0.38	NO
248	PSMB6	PSMB6	PSMB6	9365	0.053	0.38	NO
249	ZW10	ZW10	ZW10	9543	0.049	0.38	NO
250	UBE2D1	UBE2D1	UBE2D1	9550	0.049	0.38	NO
251	PCNA	PCNA	PCNA	9562	0.049	0.38	NO
252	STAG1	STAG1	STAG1	9606	0.048	0.38	NO
253	DIDO1	DIDO1	DIDO1	9644	0.047	0.37	NO
254	CEP164	CEP164	CEP164	9831	0.044	0.36	NO
255	PRKACA	PRKACA	PRKACA	9845	0.044	0.36	NO
256	ANAPC1	ANAPC1	ANAPC1	9976	0.042	0.36	NO
257	PSMB2	PSMB2	PSMB2	10086	0.04	0.35	NO
258	CETN2	CETN2	CETN2	10189	0.038	0.35	NO
259	PSME4	PSME4	PSME4	10274	0.037	0.34	NO
260	PSMC2	PSMC2	PSMC2	10331	0.036	0.34	NO
261	RBBP7	RBBP7	RBBP7	10358	0.035	0.34	NO
262	ATR	ATR	ATR	10374	0.035	0.34	NO
263	PSMA5	PSMA5	PSMA5	10483	0.033	0.34	NO
264	HIST3H3	HIST3H3	HIST3H3	10519	0.032	0.34	NO
265	TUBGCP5	TUBGCP5	TUBGCP5	10584	0.031	0.33	NO
266	HSP90AA1	HSP90AA1	HSP90AA1	10596	0.031	0.33	NO
267	PSMC3	PSMC3	PSMC3	10608	0.031	0.33	NO
268	PSMD13	PSMD13	PSMD13	10627	0.03	0.33	NO
269	NUMA1	NUMA1	NUMA1	10715	0.029	0.33	NO
270	NUDC	NUDC	NUDC	10726	0.029	0.33	NO
271	RPS27A	RPS27A	RPS27A	10751	0.028	0.33	NO
272	PSMD3	PSMD3	PSMD3	10753	0.028	0.33	NO
273	PSMD2	PSMD2	PSMD2	10772	0.028	0.33	NO
274	TERF2IP	TERF2IP	TERF2IP	10788	0.028	0.33	NO
275	POLD2	POLD2	POLD2	10805	0.027	0.33	NO
276	CSNK1E	CSNK1E	CSNK1E	10881	0.026	0.32	NO
277	PSMA7	PSMA7	PSMA7	10927	0.025	0.32	NO
278	CDC27	CDC27	CDC27	10956	0.025	0.32	NO
279	PSMD11	PSMD11	PSMD11	10968	0.024	0.32	NO
280	HAUS2	HAUS2	HAUS2	10976	0.024	0.32	NO
281	TUBGCP2	TUBGCP2	TUBGCP2	10983	0.024	0.32	NO
282	PSMA3	PSMA3	PSMA3	11053	0.023	0.32	NO
283	CDK5RAP2	CDK5RAP2	CDK5RAP2	11057	0.023	0.32	NO
284	PSMD14	PSMD14	PSMD14	11094	0.022	0.32	NO
285	E2F4	E2F4	E2F4	11146	0.021	0.31	NO
286	DCTN1	DCTN1	DCTN1	11149	0.021	0.31	NO
287	DYNLL1	DYNLL1	DYNLL1	11220	0.02	0.31	NO
288	PSMA1	PSMA1	PSMA1	11259	0.019	0.31	NO
289	NHP2	NHP2	NHP2	11262	0.019	0.31	NO
290	CCND1	CCND1	CCND1	11265	0.019	0.31	NO
291	PPP2R1B	PPP2R1B	PPP2R1B	11326	0.018	0.3	NO
292	PSMD5	PSMD5	PSMD5	11365	0.018	0.3	NO
293	RANGAP1	RANGAP1	RANGAP1	11372	0.017	0.3	NO
294	KIF2A	KIF2A	KIF2A	11373	0.017	0.3	NO
295	TFDP1	TFDP1	TFDP1	11496	0.015	0.3	NO
296	MAD1L1	MAD1L1	MAD1L1	11597	0.014	0.29	NO
297	PSMB1	PSMB1	PSMB1	11681	0.013	0.29	NO
298	TUBGCP6	TUBGCP6	TUBGCP6	11683	0.012	0.29	NO
299	PSMB3	PSMB3	PSMB3	11685	0.012	0.29	NO
300	TUBGCP3	TUBGCP3	TUBGCP3	11695	0.012	0.29	NO
301	TERF2	TERF2	TERF2	11772	0.011	0.28	NO
302	CLASP1	CLASP1	CLASP1	11785	0.011	0.28	NO
303	PSMA6	PSMA6	PSMA6	11858	0.0097	0.28	NO
304	RSF1	RSF1	RSF1	11991	0.0069	0.27	NO
305	CEP72	CEP72	CEP72	12002	0.0066	0.27	NO
306	PPP2R1A	PPP2R1A	PPP2R1A	12010	0.0065	0.27	NO
307	CDK6	CDK6	CDK6	12048	0.0058	0.27	NO
308	PSMB5	PSMB5	PSMB5	12081	0.0053	0.27	NO
309	PSMC1	PSMC1	PSMC1	12239	0.002	0.26	NO
310	INCENP	INCENP	INCENP	12252	0.0018	0.26	NO
311	UBE2I	UBE2I	UBE2I	12306	0.00092	0.26	NO
312	CDC16	CDC16	CDC16	12335	0.0005	0.26	NO
313	CDC26	CDC26	CDC26	12339	0.0004	0.26	NO
314	PPP2CB	PPP2CB	PPP2CB	12401	-0.00094	0.25	NO
315	RANBP2	RANBP2	RANBP2	12406	-0.001	0.25	NO
316	HDAC1	HDAC1	HDAC1	12427	-0.0015	0.25	NO
317	DCTN2	DCTN2	DCTN2	12450	-0.002	0.25	NO
318	YWHAG	YWHAG	YWHAG	12610	-0.0045	0.24	NO
319	PSMD1	PSMD1	PSMD1	12616	-0.0047	0.24	NO
320	RPS27	RPS27	RPS27	12635	-0.0049	0.24	NO
321	SKP1	SKP1	SKP1	12674	-0.0056	0.24	NO
322	UBA52	UBA52	UBA52	12729	-0.0067	0.24	NO
323	PSMD6	PSMD6	PSMD6	12782	-0.0077	0.23	NO
324	CCNH	CCNH	CCNH	12810	-0.0082	0.23	NO
325	PSMC5	PSMC5	PSMC5	12833	-0.0086	0.23	NO
326	PSMA2	PSMA2	PSMA2	12903	-0.01	0.23	NO
327	PSMD7	PSMD7	PSMD7	12970	-0.012	0.22	NO
328	PPP2R5D	PPP2R5D	PPP2R5D	12977	-0.012	0.22	NO
329	PSME2	PSME2	PSME2	12986	-0.012	0.22	NO
330	PSMD8	PSMD8	PSMD8	12993	-0.012	0.22	NO
331	PSMB7	PSMB7	PSMB7	13001	-0.012	0.22	NO
332	PAFAH1B1	PAFAH1B1	PAFAH1B1	13122	-0.015	0.22	NO
333	PPP2R5E	PPP2R5E	PPP2R5E	13265	-0.018	0.21	NO
334	PPP2CA	PPP2CA	PPP2CA	13332	-0.019	0.21	NO
335	TAOK1	TAOK1	TAOK1	13423	-0.021	0.2	NO
336	MAX	MAX	MAX	13436	-0.021	0.2	NO
337	ANAPC11	ANAPC11	ANAPC11	13464	-0.022	0.2	NO
338	CSNK1D	CSNK1D	CSNK1D	13556	-0.024	0.2	NO
339	RBL2	RBL2	RBL2	13757	-0.028	0.18	NO
340	TK2	TK2	TK2	13772	-0.028	0.18	NO
341	CDKN2A	CDKN2A	CDKN2A	13834	-0.03	0.18	NO
342	B9D2	B9D2	B9D2	13858	-0.03	0.18	NO
343	BTRC	BTRC	BTRC	13865	-0.03	0.18	NO
344	SSNA1	SSNA1	SSNA1	13924	-0.032	0.18	NO
345	POLD3	POLD3	POLD3	14001	-0.033	0.18	NO
346	CLIP1	CLIP1	CLIP1	14227	-0.039	0.16	NO
347	ANAPC2	ANAPC2	ANAPC2	14242	-0.039	0.16	NO
348	PSME1	PSME1	PSME1	14245	-0.039	0.16	NO
349	PPP2R2A	PPP2R2A	PPP2R2A	14249	-0.039	0.17	NO
350	SYNE2	SYNE2	SYNE2	14371	-0.042	0.16	NO
351	CDK7	CDK7	CDK7	14513	-0.045	0.15	NO
352	DYNC1I2	DYNC1I2	DYNC1I2	14558	-0.046	0.15	NO
353	SUN2	SUN2	SUN2	14578	-0.047	0.15	NO
354	SEC13	SEC13	SEC13	14619	-0.048	0.15	NO
355	DYNC1H1	DYNC1H1	DYNC1H1	14622	-0.048	0.15	NO
356	GORASP1	GORASP1	GORASP1	15022	-0.058	0.13	NO
357	HUS1	HUS1	HUS1	15052	-0.059	0.13	NO
358	ACTR1A	ACTR1A	ACTR1A	15096	-0.061	0.13	NO
359	CDC25B	CDC25B	CDC25B	15113	-0.061	0.13	NO
360	DCTN3	DCTN3	DCTN3	15224	-0.065	0.12	NO
361	TINF2	TINF2	TINF2	15334	-0.068	0.12	NO
362	PSMF1	PSMF1	PSMF1	15381	-0.07	0.12	NO
363	PSMB9	PSMB9	PSMB9	15382	-0.07	0.12	NO
364	PPP2R5C	PPP2R5C	PPP2R5C	15662	-0.079	0.11	NO
365	PSMB8	PSMB8	PSMB8	15680	-0.079	0.11	NO
366	CENPP	CENPP	CENPP	16191	-0.098	0.081	NO
367	CCND3	CCND3	CCND3	16425	-0.11	0.071	NO
368	CDKN2D	CDKN2D	CDKN2D	16455	-0.11	0.071	NO
369	NDEL1	NDEL1	NDEL1	16510	-0.12	0.071	NO
370	RB1	RB1	RB1	16623	-0.12	0.067	NO
371	REC8	REC8	REC8	16722	-0.13	0.064	NO
372	LMNA	LMNA	LMNA	16755	-0.13	0.065	NO
373	MYC	MYC	MYC	16826	-0.13	0.064	NO
374	PSMB10	PSMB10	PSMB10	16983	-0.14	0.058	NO
375	CCND2	CCND2	CCND2	17107	-0.15	0.054	NO
376	PPP2R5A	PPP2R5A	PPP2R5A	17206	-0.16	0.052	NO
377	CDKN2B	CDKN2B	CDKN2B	17527	-0.19	0.038	NO
378	CCNA1	CCNA1	CCNA1	17549	-0.19	0.041	NO
379	PPP2R5B	PPP2R5B	PPP2R5B	17974	-0.24	0.022	NO
380	POLD4	POLD4	POLD4	18162	-0.28	0.018	NO
381	CDKN1A	CDKN1A	CDKN1A	18175	-0.28	0.023	NO
382	TUBA4A	TUBA4A	TUBA4A	18575	-0.43	0.0094	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 BASAL TRANSCRIPTION FACTORS.

Figure S26. 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 SPLICEOSOME

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	NUP210	NUP210	NUP210	2650	0.26	-0.044	YES
2	NUP107	NUP107	NUP107	3597	0.21	-0.018	YES
3	GCK	GCK	GCK	3804	0.2	0.045	YES
4	NUP153	NUP153	NUP153	4692	0.16	0.058	YES
5	AAAS	AAAS	AAAS	4885	0.16	0.1	YES
6	NUP35	NUP35	NUP35	5118	0.15	0.15	YES
7	RAE1	RAE1	RAE1	5265	0.14	0.19	YES
8	NUP43	NUP43	NUP43	6040	0.12	0.2	YES
9	NUP133	NUP133	NUP133	6083	0.12	0.24	YES
10	TPR	TPR	TPR	6157	0.12	0.28	YES
11	NUP54	NUP54	NUP54	6363	0.11	0.31	YES
12	NUP93	NUP93	NUP93	6478	0.11	0.34	YES
13	NUP37	NUP37	NUP37	6701	0.1	0.37	YES
14	NUP155	NUP155	NUP155	6807	0.1	0.4	YES
15	SEH1L	SEH1L	SEH1L	6870	0.1	0.44	YES
16	NUP205	NUP205	NUP205	7362	0.09	0.44	YES
17	NUP88	NUP88	NUP88	7828	0.081	0.45	YES
18	NUP85	NUP85	NUP85	8454	0.07	0.44	YES
19	NUP62	NUP62	NUP62	8562	0.067	0.46	YES
20	NUPL2	NUPL2	NUPL2	9205	0.056	0.45	NO
21	NUPL1	NUPL1	NUPL1	9641	0.047	0.44	NO
22	POM121	POM121	POM121	10514	0.032	0.41	NO
23	NUP188	NUP188	NUP188	11115	0.022	0.38	NO
24	NUP214	NUP214	NUP214	11663	0.013	0.36	NO
25	NUP50	NUP50	NUP50	12151	0.0038	0.34	NO
26	RANBP2	RANBP2	RANBP2	12406	-0.001	0.32	NO
27	GCKR	GCKR	GCKR	14377	-0.042	0.23	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 SPLICEOSOME.

Figure S28. 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: PID FANCONI 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	CDC25A	CDC25A	CDC25A	2369	0.28	-0.04	YES
2	CHEK2	CHEK2	CHEK2	2965	0.24	0.0032	YES
3	CDC25C	CDC25C	CDC25C	3137	0.23	0.066	YES
4	BLM	BLM	BLM	4447	0.17	0.049	YES
5	FANCD2	FANCD2	FANCD2	5135	0.15	0.058	YES
6	FAM175A	FAM175A	FAM175A	5205	0.14	0.1	YES
7	BRCA1	BRCA1	BRCA1	5328	0.14	0.14	YES
8	H2AFX	H2AFX	H2AFX	5591	0.13	0.16	YES
9	MDC1	MDC1	MDC1	5652	0.13	0.2	YES
10	SMC3	SMC3	SMC3	5757	0.13	0.24	YES
11	RBBP8	RBBP8	RBBP8	5841	0.12	0.27	YES
12	RAD9A	RAD9A	RAD9A	6109	0.12	0.29	YES
13	NBN	NBN	NBN	6130	0.12	0.33	YES
14	TP53BP1	TP53BP1	TP53BP1	6282	0.11	0.36	YES
15	TRIM28	TRIM28	TRIM28	6380	0.11	0.39	YES
16	MDM2	MDM2	MDM2	6712	0.1	0.4	YES
17	TOP3A	TOP3A	TOP3A	7108	0.095	0.41	YES
18	MRE11A	MRE11A	MRE11A	7248	0.092	0.43	YES
19	ATM	ATM	ATM	7338	0.09	0.46	YES
20	UBE2N	UBE2N	UBE2N	7967	0.078	0.45	YES
21	RAD17	RAD17	RAD17	8001	0.077	0.47	YES
22	SMC1A	SMC1A	SMC1A	8495	0.069	0.46	YES
23	RFWD2	RFWD2	RFWD2	8971	0.06	0.46	YES
24	DCLRE1C	DCLRE1C	DCLRE1C	8978	0.06	0.48	YES
25	RAD50	RAD50	RAD50	11221	0.02	0.36	NO
26	CTBP1	CTBP1	CTBP1	11760	0.011	0.34	NO
27	TERF2	TERF2	TERF2	11772	0.011	0.34	NO
28	XRCC4	XRCC4	XRCC4	11949	0.0075	0.33	NO
29	KAT5	KAT5	KAT5	12272	0.0015	0.32	NO
30	YWHAB	YWHAB	YWHAB	13079	-0.014	0.28	NO
31	RNF8	RNF8	RNF8	13238	-0.017	0.27	NO
32	ABL1	ABL1	ABL1	13329	-0.019	0.28	NO
33	BID	BID	BID	13440	-0.021	0.28	NO
34	UIMC1	UIMC1	UIMC1	13650	-0.026	0.27	NO

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

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: PID FANCONI 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 AURORA B 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	SGOL1	SGOL1	SGOL1	2018	0.3	-0.044	YES
2	NDC80	NDC80	NDC80	2159	0.29	0.011	YES
3	STMN1	STMN1	STMN1	2444	0.27	0.054	YES
4	BIRC5	BIRC5	BIRC5	2742	0.25	0.092	YES
5	CENPA	CENPA	CENPA	2883	0.24	0.14	YES
6	KIF20A	KIF20A	KIF20A	3020	0.24	0.18	YES
7	AURKB	AURKB	AURKB	3165	0.23	0.22	YES
8	KIF2C	KIF2C	KIF2C	3305	0.22	0.26	YES
9	KIF23	KIF23	KIF23	3496	0.21	0.29	YES
10	NCAPG	NCAPG	NCAPG	3633	0.2	0.33	YES
11	NCAPH	NCAPH	NCAPH	3916	0.19	0.36	YES
12	NCAPD2	NCAPD2	NCAPD2	5029	0.15	0.33	YES
13	KLHL13	KLHL13	KLHL13	5107	0.15	0.35	YES
14	AURKA	AURKA	AURKA	5164	0.14	0.38	YES
15	CDCA8	CDCA8	CDCA8	5191	0.14	0.41	YES
16	SMC4	SMC4	SMC4	5246	0.14	0.44	YES
17	CBX5	CBX5	CBX5	5325	0.14	0.46	YES
18	BUB1	BUB1	BUB1	5498	0.13	0.48	YES
19	PEBP1	PEBP1	PEBP1	5564	0.13	0.51	YES
20	RACGAP1	RACGAP1	RACGAP1	5973	0.12	0.51	YES
21	SMC2	SMC2	SMC2	6892	0.1	0.48	NO
22	AURKC	AURKC	AURKC	7650	0.084	0.46	NO
23	PPP1CC	PPP1CC	PPP1CC	8049	0.076	0.46	NO
24	NCL	NCL	NCL	8221	0.073	0.46	NO
25	KLHL9	KLHL9	KLHL9	8482	0.069	0.46	NO
26	NPM1	NPM1	NPM1	8743	0.064	0.46	NO
27	SEPT1	SEPT1	SEPT1	9523	0.05	0.43	NO
28	VIM	VIM	VIM	10517	0.032	0.39	NO
29	CUL3	CUL3	CUL3	10827	0.027	0.38	NO
30	PSMA3	PSMA3	PSMA3	11053	0.023	0.37	NO
31	NSUN2	NSUN2	NSUN2	12187	0.0032	0.31	NO
32	INCENP	INCENP	INCENP	12252	0.0018	0.3	NO
33	TACC1	TACC1	TACC1	12353	0.00017	0.3	NO
34	RASA1	RASA1	RASA1	12480	-0.0024	0.29	NO
35	PPP2R5D	PPP2R5D	PPP2R5D	12977	-0.012	0.27	NO
36	MYLK	MYLK	MYLK	12991	-0.012	0.27	NO
37	EVI5	EVI5	EVI5	13027	-0.013	0.27	NO
38	RHOA	RHOA	RHOA	13606	-0.025	0.25	NO
39	DES	DES	DES	16817	-0.13	0.1	NO

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

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: PID AURORA B 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 ATR 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	SSPO	SSPO	SSPO	1016	0.41	0.011	YES
2	C19orf40	C19orf40	C19orf40	1088	0.4	0.072	YES
3	FANCL	FANCL	FANCL	2569	0.26	0.035	YES
4	BRIP1	BRIP1	BRIP1	2867	0.24	0.059	YES
5	CHEK1	CHEK1	CHEK1	3175	0.23	0.079	YES
6	RFC4	RFC4	RFC4	3743	0.2	0.081	YES
7	FANCB	FANCB	FANCB	3811	0.2	0.11	YES
8	RFC5	RFC5	RFC5	4058	0.19	0.13	YES
9	USP1	USP1	USP1	4089	0.18	0.15	YES
10	APITD1	APITD1	APITD1	4251	0.18	0.17	YES
11	RFC3	RFC3	RFC3	4422	0.17	0.19	YES
12	BLM	BLM	BLM	4447	0.17	0.22	YES
13	RFC2	RFC2	RFC2	4613	0.16	0.24	YES
14	FANCC	FANCC	FANCC	4639	0.16	0.26	YES
15	UBE2T	UBE2T	UBE2T	4644	0.16	0.29	YES
16	RPA2	RPA2	RPA2	4846	0.16	0.3	YES
17	FANCD2	FANCD2	FANCD2	5135	0.15	0.31	YES
18	BRCA1	BRCA1	BRCA1	5328	0.14	0.32	YES
19	FANCI	FANCI	FANCI	5406	0.14	0.34	YES
20	BRCA2	BRCA2	BRCA2	5474	0.14	0.36	YES
21	FANCG	FANCG	FANCG	5572	0.13	0.37	YES
22	H2AFX	H2AFX	H2AFX	5591	0.13	0.4	YES
23	RPA1	RPA1	RPA1	5974	0.12	0.39	YES
24	FANCA	FANCA	FANCA	6065	0.12	0.41	YES
25	RAD9A	RAD9A	RAD9A	6109	0.12	0.42	YES
26	NBN	NBN	NBN	6130	0.12	0.44	YES
27	RMI1	RMI1	RMI1	6497	0.11	0.44	YES
28	FANCM	FANCM	FANCM	6779	0.1	0.44	YES
29	TOP3A	TOP3A	TOP3A	7108	0.095	0.44	YES
30	RAD1	RAD1	RAD1	7246	0.092	0.45	YES
31	MRE11A	MRE11A	MRE11A	7248	0.092	0.46	YES
32	ATM	ATM	ATM	7338	0.09	0.47	YES
33	TOPBP1	TOPBP1	TOPBP1	7354	0.09	0.48	YES
34	PALB2	PALB2	PALB2	7495	0.087	0.49	YES
35	FANCE	FANCE	FANCE	7519	0.086	0.5	YES
36	WDR48	WDR48	WDR48	7673	0.083	0.51	YES
37	FANCF	FANCF	FANCF	7939	0.078	0.51	YES
38	RAD17	RAD17	RAD17	8001	0.077	0.52	YES
39	XRCC3	XRCC3	XRCC3	8164	0.074	0.52	YES
40	ATRIP	ATRIP	ATRIP	8916	0.061	0.49	NO
41	HES1	HES1	HES1	9298	0.054	0.48	NO
42	ATR	ATR	ATR	10374	0.035	0.43	NO
43	RAD50	RAD50	RAD50	11221	0.02	0.38	NO
44	C17orf70	C17orf70	C17orf70	11316	0.018	0.38	NO
45	FBXW11	FBXW11	FBXW11	13833	-0.03	0.25	NO
46	HUS1	HUS1	HUS1	15052	-0.059	0.2	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: PID ATR PATHWAY.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: PID ATR 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 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	NEK2	NEK2	NEK2	2725	0.25	-0.096	YES
2	BIRC5	BIRC5	BIRC5	2742	0.25	-0.048	YES
3	CENPA	CENPA	CENPA	2883	0.24	-0.008	YES
4	CHEK2	CHEK2	CHEK2	2965	0.24	0.034	YES
5	CDK2	CDK2	CDK2	2966	0.24	0.081	YES
6	GAS1	GAS1	GAS1	3009	0.24	0.12	YES
7	ONECUT1	ONECUT1	ONECUT1	3026	0.24	0.17	YES
8	AURKB	AURKB	AURKB	3165	0.23	0.21	YES
9	ESR1	ESR1	ESR1	3484	0.21	0.23	YES
10	CCNE1	CCNE1	CCNE1	3871	0.19	0.25	YES
11	CKS1B	CKS1B	CKS1B	4201	0.18	0.26	YES
12	CENPF	CENPF	CENPF	4227	0.18	0.3	YES
13	SKP2	SKP2	SKP2	4280	0.18	0.33	YES
14	CDK4	CDK4	CDK4	4328	0.18	0.36	YES
15	FOXM1	FOXM1	FOXM1	4379	0.17	0.39	YES
16	CCNA2	CCNA2	CCNA2	4616	0.16	0.41	YES
17	CCNB2	CCNB2	CCNB2	4658	0.16	0.44	YES
18	CDK1	CDK1	CDK1	5112	0.15	0.45	YES
19	ETV5	ETV5	ETV5	5357	0.14	0.46	YES
20	CCNB1	CCNB1	CCNB1	5404	0.14	0.48	YES
21	BRCA2	BRCA2	BRCA2	5474	0.14	0.51	YES
22	NFATC3	NFATC3	NFATC3	6419	0.11	0.48	NO
23	XRCC1	XRCC1	XRCC1	9261	0.055	0.34	NO
24	PLK1	PLK1	PLK1	9263	0.055	0.35	NO
25	MMP2	MMP2	MMP2	9718	0.046	0.33	NO
26	SP1	SP1	SP1	9723	0.046	0.34	NO
27	EP300	EP300	EP300	11000	0.024	0.28	NO
28	CCND1	CCND1	CCND1	11265	0.019	0.27	NO
29	GSK3A	GSK3A	GSK3A	11338	0.018	0.27	NO
30	CREBBP	CREBBP	CREBBP	11727	0.012	0.25	NO
31	LAMA4	LAMA4	LAMA4	11902	0.0084	0.24	NO
32	CENPB	CENPB	CENPB	13783	-0.029	0.15	NO
33	CDKN2A	CDKN2A	CDKN2A	13834	-0.03	0.15	NO
34	CDC25B	CDC25B	CDC25B	15113	-0.061	0.092	NO
35	MAP2K1	MAP2K1	MAP2K1	15166	-0.063	0.1	NO
36	TGFA	TGFA	TGFA	15367	-0.069	0.1	NO
37	RB1	RB1	RB1	16623	-0.12	0.061	NO
38	MYC	MYC	MYC	16826	-0.13	0.076	NO
39	FOS	FOS	FOS	16903	-0.14	0.099	NO

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

Figure S36. 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 PLK1 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NUP210	NUP210	NUP210	2650	0.26	-0.085	YES
2	DDX20	DDX20	DDX20	3282	0.22	-0.07	YES
3	NUP107	NUP107	NUP107	3597	0.21	-0.041	YES
4	GEMIN6	GEMIN6	GEMIN6	3854	0.2	-0.012	YES
5	NUP153	NUP153	NUP153	4692	0.16	-0.021	YES
6	SMN2	SMN2	SMN2	4694	0.16	0.014	YES
7	AAAS	AAAS	AAAS	4885	0.16	0.038	YES
8	NUP35	NUP35	NUP35	5118	0.15	0.058	YES
9	SNRPG	SNRPG	SNRPG	5236	0.14	0.083	YES
10	RAE1	RAE1	RAE1	5265	0.14	0.11	YES
11	SNRPE	SNRPE	SNRPE	5630	0.13	0.12	YES
12	SNRPF	SNRPF	SNRPF	5855	0.12	0.14	YES
13	TGS1	TGS1	TGS1	6013	0.12	0.16	YES
14	NUP43	NUP43	NUP43	6040	0.12	0.18	YES
15	NUP133	NUP133	NUP133	6083	0.12	0.2	YES
16	TPR	TPR	TPR	6157	0.12	0.23	YES
17	NUP54	NUP54	NUP54	6363	0.11	0.24	YES
18	NUP93	NUP93	NUP93	6478	0.11	0.26	YES
19	WDR77	WDR77	WDR77	6576	0.11	0.28	YES
20	SNUPN	SNUPN	SNUPN	6578	0.11	0.3	YES
21	NUP37	NUP37	NUP37	6701	0.1	0.32	YES
22	NUP155	NUP155	NUP155	6807	0.1	0.33	YES
23	SEH1L	SEH1L	SEH1L	6870	0.1	0.35	YES
24	GEMIN5	GEMIN5	GEMIN5	6882	0.1	0.37	YES
25	SNRPD1	SNRPD1	SNRPD1	7101	0.095	0.38	YES
26	SNRPD3	SNRPD3	SNRPD3	7126	0.095	0.4	YES
27	PHAX	PHAX	PHAX	7309	0.091	0.41	YES
28	NUP205	NUP205	NUP205	7362	0.09	0.43	YES
29	NCBP2	NCBP2	NCBP2	7458	0.088	0.44	YES
30	SMN1	SMN1	SMN1	7749	0.082	0.44	YES
31	NUP88	NUP88	NUP88	7828	0.081	0.46	YES
32	NUP85	NUP85	NUP85	8454	0.07	0.44	NO
33	NUP62	NUP62	NUP62	8562	0.067	0.45	NO
34	GEMIN4	GEMIN4	GEMIN4	9134	0.057	0.43	NO
35	NUPL2	NUPL2	NUPL2	9205	0.056	0.44	NO
36	PRMT5	PRMT5	PRMT5	9360	0.053	0.44	NO
37	NUPL1	NUPL1	NUPL1	9641	0.047	0.44	NO
38	SNRPD2	SNRPD2	SNRPD2	9745	0.046	0.44	NO
39	CLNS1A	CLNS1A	CLNS1A	10257	0.037	0.42	NO
40	POM121	POM121	POM121	10514	0.032	0.42	NO
41	GEMIN7	GEMIN7	GEMIN7	10937	0.025	0.4	NO
42	NUP188	NUP188	NUP188	11115	0.022	0.4	NO
43	NCBP1	NCBP1	NCBP1	11289	0.019	0.39	NO
44	SNRPB	SNRPB	SNRPB	11404	0.017	0.39	NO
45	NUP214	NUP214	NUP214	11663	0.013	0.38	NO
46	NUP50	NUP50	NUP50	12151	0.0038	0.35	NO
47	RANBP2	RANBP2	RANBP2	12406	-0.001	0.34	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 PLK1 PATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: PID PLK1 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 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	LZTS1	LZTS1	LZTS1	2229	0.29	-0.0034	YES
2	POLR3B	POLR3B	POLR3B	3772	0.2	-0.006	YES
3	NFIB	NFIB	NFIB	4754	0.16	0.0059	YES
4	SSB	SSB	SSB	5784	0.13	0.0017	YES
5	TBP	TBP	TBP	6317	0.11	0.019	YES
6	BRF2	BRF2	BRF2	6644	0.1	0.044	YES
7	SNAPC4	SNAPC4	SNAPC4	6940	0.098	0.067	YES
8	SNAPC5	SNAPC5	SNAPC5	7020	0.097	0.1	YES
9	POLR3F	POLR3F	POLR3F	7059	0.096	0.14	YES
10	POLR2K	POLR2K	POLR2K	7073	0.096	0.18	YES
11	GTF3C2	GTF3C2	GTF3C2	7600	0.085	0.18	YES
12	POLR3C	POLR3C	POLR3C	7784	0.081	0.21	YES
13	ZNF143	ZNF143	ZNF143	7791	0.081	0.24	YES
14	POLR2F	POLR2F	POLR2F	7874	0.08	0.27	YES
15	POU2F1	POU2F1	POU2F1	8309	0.072	0.27	YES
16	GTF3C3	GTF3C3	GTF3C3	8429	0.07	0.29	YES
17	POLR3A	POLR3A	POLR3A	8459	0.069	0.32	YES
18	POLR2H	POLR2H	POLR2H	8522	0.068	0.34	YES
19	POLR3E	POLR3E	POLR3E	8945	0.06	0.35	YES
20	POLR1C	POLR1C	POLR1C	9447	0.051	0.34	YES
21	POLR3D	POLR3D	POLR3D	9742	0.046	0.34	YES
22	SNAPC1	SNAPC1	SNAPC1	9896	0.043	0.35	YES
23	BRF1	BRF1	BRF1	9927	0.042	0.37	YES
24	POLR3H	POLR3H	POLR3H	9985	0.042	0.38	YES
25	GTF3C4	GTF3C4	GTF3C4	10158	0.039	0.39	YES
26	POLR2L	POLR2L	POLR2L	10169	0.039	0.4	YES
27	POLR3K	POLR3K	POLR3K	11504	0.015	0.34	NO
28	POLR3GL	POLR3GL	POLR3GL	11752	0.011	0.33	NO
29	POLR2E	POLR2E	POLR2E	12793	-0.0079	0.28	NO
30	SNAPC2	SNAPC2	SNAPC2	12959	-0.011	0.27	NO
31	POLR1D	POLR1D	POLR1D	13689	-0.026	0.24	NO
32	SNAPC3	SNAPC3	SNAPC3	13897	-0.031	0.24	NO
33	GTF3C5	GTF3C5	GTF3C5	14087	-0.035	0.25	NO

Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FOXM1PATHWAY.

Figure S40. 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 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 BLADDER CANCER	42	genes.ES.table	0.48	1.6	0.014	0.67	0.92	0.43	0.18	0.35	0.33	0.18
BIOCARTA ERK PATHWAY	28	genes.ES.table	0.5	1.7	0.022	0.66	0.91	0.29	0.13	0.25	0.32	0.17
PID P73PATHWAY	79	genes.ES.table	0.48	1.8	0	0.67	0.56	0.28	0.14	0.24	0.16	0.14
PID AVB3 OPN PATHWAY	31	genes.ES.table	0.51	1.6	0.033	0.64	0.93	0.36	0.22	0.28	0.32	0.16
PID MTOR 4PATHWAY	67	genes.ES.table	0.39	1.8	0.023	0.57	0.62	0.43	0.28	0.32	0.14	0.13
PID ERBB1 RECEPTOR PROXIMAL PATHWAY	35	genes.ES.table	0.48	1.8	0.014	0.81	0.54	0.4	0.22	0.31	0.19	0.16
PID MYC PATHWAY	25	genes.ES.table	0.47	1.7	0.023	0.68	0.79	0.52	0.24	0.4	0.25	0.17
PID ECADHERIN NASCENTAJ PATHWAY	39	genes.ES.table	0.37	1.6	0.072	0.62	0.94	0.64	0.35	0.42	0.32	0.16
PID DELTANP63PATHWAY	47	genes.ES.table	0.69	1.9	0	0.87	0.33	0.32	0.084	0.29	0	0.15
PID A6B1 A6B4 INTEGRIN PATHWAY	46	genes.ES.table	0.52	1.7	0.027	0.6	0.81	0.35	0.16	0.29	0.23	0.15

genes ES table in pathway: KEGG BLADDER CANCER

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	SPHK1	SPHK1	SPHK1	494	0.43	0.2	YES
2	KIFC3	KIFC3	KIFC3	1359	0.24	0.28	YES
3	KIF13A	KIF13A	KIF13A	2250	0.16	0.31	YES
4	FBXO6	FBXO6	FBXO6	2294	0.16	0.39	YES
5	FKBP9	FKBP9	FKBP9	2768	0.12	0.43	YES
6	CCT5	CCT5	CCT5	2871	0.12	0.48	YES
7	FBXO4	FBXO4	FBXO4	4617	0.062	0.42	YES
8	CCT4	CCT4	CCT4	4638	0.061	0.45	YES
9	CCT8	CCT8	CCT8	4730	0.059	0.48	YES
10	CCT6A	CCT6A	CCT6A	4779	0.057	0.5	YES
11	CCT7	CCT7	CCT7	5308	0.046	0.5	YES
12	TCP1	TCP1	TCP1	5549	0.041	0.51	YES
13	CCT2	CCT2	CCT2	5781	0.036	0.52	YES
14	FBXW4	FBXW4	FBXW4	5922	0.033	0.52	YES
15	CCT3	CCT3	CCT3	6214	0.028	0.52	NO
16	XRN2	XRN2	XRN2	6633	0.021	0.51	NO
17	NOP56	NOP56	NOP56	6711	0.02	0.52	NO
18	LONP2	LONP2	LONP2	6832	0.018	0.52	NO
19	FBXW7	FBXW7	FBXW7	7151	0.012	0.51	NO
20	FBXW2	FBXW2	FBXW2	7245	0.011	0.51	NO
21	FBXL5	FBXL5	FBXL5	7736	0.0023	0.49	NO
22	FBXL3	FBXL3	FBXL3	7820	0.0012	0.48	NO
23	USP11	USP11	USP11	8760	-0.014	0.44	NO
24	FBXW5	FBXW5	FBXW5	9651	-0.029	0.41	NO
25	AP3M1	AP3M1	AP3M1	11080	-0.057	0.36	NO
26	ARFGEF2	ARFGEF2	ARFGEF2	12581	-0.095	0.33	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 BLADDER CANCER.

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

genes ES table in pathway: BIOCARTA ERK PATHWAY

Table S22. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	KRT14	KRT14	KRT14	14	0.9	0.091	YES
2	IL1A	IL1A	IL1A	17	0.88	0.18	YES
3	RAB38	RAB38	RAB38	77	0.71	0.25	YES
4	TP63	TP63	TP63	80	0.7	0.32	YES
5	KRT5	KRT5	KRT5	85	0.7	0.39	YES
6	NRG1	NRG1	NRG1	86	0.7	0.46	YES
7	DLX5	DLX5	DLX5	275	0.52	0.5	YES
8	SFN	SFN	SFN	341	0.49	0.55	YES
9	ADA	ADA	ADA	752	0.35	0.57	YES
10	TCF7L1	TCF7L1	TCF7L1	949	0.31	0.59	YES
11	PERP	PERP	PERP	1025	0.3	0.61	YES
12	ITGA3	ITGA3	ITGA3	1060	0.29	0.64	YES
13	SEC14L2	SEC14L2	SEC14L2	1170	0.27	0.66	YES
14	COL5A1	COL5A1	COL5A1	1364	0.24	0.68	YES
15	DLX6	DLX6	DLX6	1576	0.22	0.69	YES
16	BDKRB2	BDKRB2	BDKRB2	2102	0.17	0.68	NO
17	VDR	VDR	VDR	2601	0.13	0.66	NO
18	T	T	T	3537	0.091	0.62	NO
19	CEBPD	CEBPD	CEBPD	3554	0.091	0.63	NO
20	NOTCH1	NOTCH1	NOTCH1	3791	0.083	0.63	NO
21	GSK3B	GSK3B	GSK3B	4023	0.077	0.62	NO
22	RUNX1	RUNX1	RUNX1	4260	0.07	0.62	NO
23	AXL	AXL	AXL	5035	0.052	0.58	NO
24	CCNB2	CCNB2	CCNB2	5487	0.042	0.56	NO
25	RRAD	RRAD	RRAD	5507	0.042	0.56	NO
26	FOSL2	FOSL2	FOSL2	5533	0.041	0.57	NO
27	ADRM1	ADRM1	ADRM1	5856	0.035	0.55	NO
28	YAP1	YAP1	YAP1	6461	0.024	0.52	NO
29	GNB2L1	GNB2L1	GNB2L1	6547	0.022	0.52	NO
30	FASN	FASN	FASN	6927	0.016	0.5	NO
31	FBXW7	FBXW7	FBXW7	7151	0.012	0.49	NO
32	HBP1	HBP1	HBP1	8259	-0.006	0.43	NO
33	ITCH	ITCH	ITCH	8266	-0.0061	0.43	NO
34	POU2F2	POU2F2	POU2F2	8385	-0.0083	0.43	NO
35	STXBP4	STXBP4	STXBP4	8788	-0.014	0.41	NO
36	HELLS	HELLS	HELLS	8999	-0.018	0.4	NO
37	WWP1	WWP1	WWP1	9684	-0.03	0.36	NO
38	HES1	HES1	HES1	10219	-0.039	0.34	NO
39	MDM2	MDM2	MDM2	10508	-0.045	0.33	NO
40	IGFBP3	IGFBP3	IGFBP3	10797	-0.051	0.32	NO
41	PPP2R5A	PPP2R5A	PPP2R5A	11360	-0.063	0.3	NO
42	TOP2A	TOP2A	TOP2A	11742	-0.072	0.28	NO
43	BRCA2	BRCA2	BRCA2	11805	-0.074	0.29	NO
44	MRE11A	MRE11A	MRE11A	11855	-0.075	0.29	NO
45	ATM	ATM	ATM	12577	-0.095	0.26	NO
46	CDKN2A	CDKN2A	CDKN2A	15767	-0.24	0.12	NO
47	GPX2	GPX2	GPX2	17435	-0.42	0.07	NO

Figure S43. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA ERK PATHWAY.

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

genes ES table in pathway: PID P73PATHWAY

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	CCNA1	CCNA1	CCNA1	92	0.69	0.16	YES
2	PKMYT1	PKMYT1	PKMYT1	1509	0.22	0.14	YES
3	CDKN1A	CDKN1A	CDKN1A	1685	0.21	0.18	YES
4	MNAT1	MNAT1	MNAT1	2070	0.17	0.2	YES
5	MYC	MYC	MYC	2458	0.14	0.21	YES
6	PSMD9	PSMD9	PSMD9	2880	0.12	0.22	YES
7	CDK7	CDK7	CDK7	3002	0.11	0.24	YES
8	PSMC1	PSMC1	PSMC1	3013	0.11	0.26	YES
9	PSMD2	PSMD2	PSMD2	3071	0.11	0.28	YES
10	PSMB7	PSMB7	PSMB7	3404	0.096	0.29	YES
11	PSMB6	PSMB6	PSMB6	3480	0.093	0.31	YES
12	PSMA6	PSMA6	PSMA6	3633	0.088	0.32	YES
13	CCNE2	CCNE2	CCNE2	3871	0.081	0.33	YES
14	PSMC2	PSMC2	PSMC2	3970	0.078	0.34	YES
15	SKP2	SKP2	SKP2	3971	0.078	0.36	YES
16	PSMB2	PSMB2	PSMB2	4134	0.074	0.37	YES
17	CKS1B	CKS1B	CKS1B	4232	0.071	0.38	YES
18	PSMC3	PSMC3	PSMC3	4274	0.07	0.39	YES
19	PSMD12	PSMD12	PSMD12	4475	0.064	0.4	YES
20	CCNA2	CCNA2	CCNA2	4498	0.064	0.41	YES
21	PSMD10	PSMD10	PSMD10	4572	0.062	0.42	YES
22	PSMC6	PSMC6	PSMC6	4636	0.061	0.43	YES
23	PSMD7	PSMD7	PSMD7	4828	0.056	0.44	YES
24	PSMD5	PSMD5	PSMD5	4859	0.055	0.45	YES
25	PSMB5	PSMB5	PSMB5	4911	0.054	0.46	YES
26	PSMD14	PSMD14	PSMD14	4922	0.054	0.47	YES
27	PSMA3	PSMA3	PSMA3	5221	0.048	0.47	YES
28	PSMC5	PSMC5	PSMC5	5421	0.043	0.47	YES
29	PSMB1	PSMB1	PSMB1	5541	0.041	0.47	YES
30	RB1	RB1	RB1	5545	0.041	0.48	YES
31	PSMA1	PSMA1	PSMA1	5623	0.039	0.48	YES
32	SKP1	SKP1	SKP1	5666	0.038	0.49	YES
33	PSMD11	PSMD11	PSMD11	5753	0.037	0.5	YES
34	PSMA7	PSMA7	PSMA7	5805	0.036	0.5	YES
35	PSMD6	PSMD6	PSMD6	5806	0.036	0.51	YES
36	PSMA4	PSMA4	PSMA4	5914	0.033	0.51	YES
37	PSMA2	PSMA2	PSMA2	5923	0.033	0.52	YES
38	CDK2	CDK2	CDK2	5986	0.032	0.52	YES
39	PSMD8	PSMD8	PSMD8	6131	0.03	0.52	YES
40	PSMA5	PSMA5	PSMA5	6198	0.028	0.53	YES
41	PSMF1	PSMF1	PSMF1	6337	0.026	0.52	YES
42	PSMD13	PSMD13	PSMD13	6378	0.025	0.53	YES
43	WEE1	WEE1	WEE1	6658	0.021	0.52	NO
44	PSMD4	PSMD4	PSMD4	6735	0.02	0.52	NO
45	CUL1	CUL1	CUL1	7044	0.014	0.51	NO
46	PSMD1	PSMD1	PSMD1	7082	0.014	0.51	NO
47	UBA52	UBA52	UBA52	7138	0.013	0.51	NO
48	PSMB9	PSMB9	PSMB9	7334	0.0092	0.5	NO
49	MAX	MAX	MAX	8106	-0.0033	0.46	NO
50	PSME2	PSME2	PSME2	8120	-0.0035	0.46	NO
51	PSMB3	PSMB3	PSMB3	8191	-0.0048	0.46	NO
52	CCNE1	CCNE1	CCNE1	8196	-0.0048	0.46	NO
53	PSMD3	PSMD3	PSMD3	8356	-0.0077	0.45	NO
54	PSMB4	PSMB4	PSMB4	8445	-0.0093	0.45	NO
55	PSME1	PSME1	PSME1	8636	-0.012	0.44	NO
56	CCNH	CCNH	CCNH	9016	-0.018	0.42	NO
57	RPS27A	RPS27A	RPS27A	9423	-0.025	0.41	NO
58	PSMC4	PSMC4	PSMC4	9597	-0.028	0.41	NO
59	PSMB8	PSMB8	PSMB8	11168	-0.059	0.34	NO
60	PSMB10	PSMB10	PSMB10	12074	-0.081	0.31	NO
61	CDKN1B	CDKN1B	CDKN1B	12766	-0.1	0.29	NO
62	CDC25A	CDC25A	CDC25A	13086	-0.11	0.3	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: PID P73PATHWAY.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: PID P73PATHWAY, 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 AVB3 OPN PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GNAI1	GNAI1	GNAI1	352	0.48	0.12	YES
2	EGFR	EGFR	EGFR	718	0.36	0.21	YES
3	PIK3CD	PIK3CD	PIK3CD	961	0.3	0.28	YES
4	HRAS	HRAS	HRAS	1167	0.27	0.35	YES
5	SHC1	SHC1	SHC1	2384	0.15	0.33	YES
6	EGF	EGF	EGF	2792	0.12	0.34	YES
7	GNAI3	GNAI3	GNAI3	2964	0.11	0.37	YES
8	PTPN1	PTPN1	PTPN1	3096	0.11	0.39	YES
9	PLCG1	PLCG1	PLCG1	3677	0.086	0.39	YES
10	PIK3CA	PIK3CA	PIK3CA	3684	0.086	0.41	YES
11	NCK1	NCK1	NCK1	3749	0.085	0.43	YES
12	STAT1	STAT1	STAT1	3899	0.08	0.45	YES
13	NRAS	NRAS	NRAS	4053	0.076	0.46	YES
14	RASA1	RASA1	RASA1	4086	0.075	0.48	YES
15	MAPK1	MAPK1	MAPK1	4698	0.06	0.47	NO
16	PIP5K1C	PIP5K1C	PIP5K1C	5146	0.049	0.46	NO
17	PTK2	PTK2	PTK2	5685	0.038	0.44	NO
18	NCK2	NCK2	NCK2	7154	0.012	0.36	NO
19	STAT3	STAT3	STAT3	7542	0.0057	0.34	NO
20	PIK3R2	PIK3R2	PIK3R2	7590	0.0048	0.34	NO
21	PTPN11	PTPN11	PTPN11	7961	-0.00098	0.32	NO
22	SOS1	SOS1	SOS1	8043	-0.0023	0.32	NO
23	GSN	GSN	GSN	8616	-0.012	0.29	NO
24	TLN1	TLN1	TLN1	8932	-0.017	0.28	NO
25	GRB2	GRB2	GRB2	8985	-0.018	0.28	NO
26	PAK1	PAK1	PAK1	9180	-0.021	0.28	NO
27	WASL	WASL	WASL	10038	-0.036	0.24	NO
28	PIK3R1	PIK3R1	PIK3R1	10668	-0.048	0.22	NO
29	PTPN6	PTPN6	PTPN6	10781	-0.05	0.23	NO
30	GAB1	GAB1	GAB1	10935	-0.054	0.24	NO
31	MAPK3	MAPK3	MAPK3	11470	-0.066	0.23	NO
32	SRC	SRC	SRC	12821	-0.1	0.19	NO
33	KRAS	KRAS	KRAS	12846	-0.1	0.22	NO
34	PIK3CB	PIK3CB	PIK3CB	13249	-0.12	0.23	NO
35	PIK3R3	PIK3R3	PIK3R3	15426	-0.22	0.18	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: PID AVB3 OPN PATHWAY.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: PID AVB3 OPN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID MTOR 4PATHWAY

Table 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	CLCA2	CLCA2	CLCA2	42	0.77	0.058	YES
2	S100A2	S100A2	S100A2	59	0.73	0.11	YES
3	TP63	TP63	TP63	80	0.7	0.17	YES
4	TP53AIP1	TP53AIP1	TP53AIP1	93	0.69	0.22	YES
5	SERPINE1	SERPINE1	SERPINE1	325	0.5	0.25	YES
6	SFN	SFN	SFN	341	0.49	0.28	YES
7	IL1RAP	IL1RAP	IL1RAP	402	0.46	0.32	YES
8	TP73	TP73	TP73	407	0.46	0.35	YES
9	MAPK11	MAPK11	MAPK11	484	0.43	0.38	YES
10	D4S234E	D4S234E	D4S234E	702	0.37	0.4	YES
11	ADA	ADA	ADA	752	0.35	0.42	YES
12	JAG2	JAG2	JAG2	932	0.31	0.44	YES
13	CDK6	CDK6	CDK6	1662	0.21	0.42	YES
14	CDKN1A	CDKN1A	CDKN1A	1685	0.21	0.43	YES
15	WT1	WT1	WT1	1735	0.2	0.44	YES
16	FBXO45	FBXO45	FBXO45	1938	0.18	0.45	YES
17	HEY2	HEY2	HEY2	2115	0.17	0.45	YES
18	PML	PML	PML	2189	0.16	0.46	YES
19	MYC	MYC	MYC	2458	0.14	0.46	YES
20	IL4R	IL4R	IL4R	2550	0.14	0.46	YES
21	CCNB1	CCNB1	CCNB1	2567	0.14	0.47	YES
22	HSF1	HSF1	HSF1	2585	0.14	0.48	YES
23	TUBA1A	TUBA1A	TUBA1A	3259	0.1	0.46	NO
24	PLK1	PLK1	PLK1	3487	0.093	0.45	NO
25	BAK1	BAK1	BAK1	3803	0.083	0.44	NO
26	PLK3	PLK3	PLK3	3827	0.082	0.44	NO
27	CCNE2	CCNE2	CCNE2	3871	0.081	0.45	NO
28	PIN1	PIN1	PIN1	3993	0.078	0.45	NO
29	FAS	FAS	FAS	4163	0.073	0.44	NO
30	CCNA2	CCNA2	CCNA2	4498	0.064	0.43	NO
31	CHEK1	CHEK1	CHEK1	4594	0.062	0.43	NO
32	RAD51	RAD51	RAD51	4627	0.061	0.43	NO
33	NTRK1	NTRK1	NTRK1	4693	0.06	0.44	NO
34	RELA	RELA	RELA	5179	0.049	0.41	NO
35	RB1	RB1	RB1	5545	0.041	0.4	NO
36	PEA15	PEA15	PEA15	5622	0.039	0.4	NO
37	KAT5	KAT5	KAT5	5885	0.034	0.38	NO
38	CDK2	CDK2	CDK2	5986	0.032	0.38	NO
39	FLOT2	FLOT2	FLOT2	6455	0.024	0.36	NO
40	YAP1	YAP1	YAP1	6461	0.024	0.36	NO
41	GNB2L1	GNB2L1	GNB2L1	6547	0.022	0.36	NO
42	CDK1	CDK1	CDK1	6578	0.022	0.36	NO
43	MAPK14	MAPK14	MAPK14	6675	0.02	0.35	NO
44	FASN	FASN	FASN	6927	0.016	0.34	NO
45	ABL1	ABL1	ABL1	6983	0.015	0.34	NO
46	UBE4B	UBE4B	UBE4B	7161	0.012	0.33	NO
47	EP300	EP300	EP300	7243	0.011	0.33	NO
48	BUB1	BUB1	BUB1	7490	0.0066	0.32	NO
49	GRAMD4	GRAMD4	GRAMD4	7959	-0.00097	0.29	NO
50	DEDD	DEDD	DEDD	8039	-0.0022	0.29	NO
51	CASP2	CASP2	CASP2	8230	-0.0056	0.28	NO
52	ITCH	ITCH	ITCH	8266	-0.0061	0.28	NO
53	BUB3	BUB3	BUB3	8282	-0.0064	0.28	NO
54	PFDN5	PFDN5	PFDN5	8611	-0.012	0.26	NO
55	HAGH	HAGH	HAGH	8984	-0.018	0.24	NO
56	AEN	AEN	AEN	9319	-0.024	0.22	NO
57	PRKACB	PRKACB	PRKACB	9570	-0.028	0.21	NO
58	JAK1	JAK1	JAK1	9733	-0.03	0.21	NO
59	MDM2	MDM2	MDM2	10508	-0.045	0.17	NO
60	SP1	SP1	SP1	10608	-0.047	0.17	NO
61	BCL2L11	BCL2L11	BCL2L11	10624	-0.047	0.17	NO
62	FOXO3	FOXO3	FOXO3	11766	-0.073	0.11	NO
63	BRCA2	BRCA2	BRCA2	11805	-0.074	0.12	NO
64	BAX	BAX	BAX	11911	-0.077	0.12	NO
65	NDUFS2	NDUFS2	NDUFS2	11989	-0.079	0.12	NO
66	PPAP2A	PPAP2A	PPAP2A	12724	-0.1	0.089	NO
67	WWOX	WWOX	WWOX	12881	-0.1	0.088	NO
68	NEDD4L	NEDD4L	NEDD4L	13369	-0.12	0.072	NO
69	SIRT1	SIRT1	SIRT1	13511	-0.12	0.074	NO
70	AFP	AFP	AFP	13533	-0.13	0.082	NO
71	BIN1	BIN1	BIN1	13575	-0.13	0.09	NO
72	RCHY1	RCHY1	RCHY1	13604	-0.13	0.099	NO
73	TP53I3	TP53I3	TP53I3	14009	-0.14	0.088	NO
74	RNF43	RNF43	RNF43	14112	-0.15	0.095	NO
75	DCP1B	DCP1B	DCP1B	15005	-0.19	0.062	NO
76	BBC3	BBC3	BBC3	16230	-0.28	0.018	NO
77	GATA1	GATA1	GATA1	16576	-0.31	0.023	NO
78	SERPINA1	SERPINA1	SERPINA1	17804	-0.49	-0.0044	NO
79	GDF15	GDF15	GDF15	18425	-0.7	0.017	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: PID MTOR 4PATHWAY.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: PID MTOR 4PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID ERBB1 RECEPTOR PROXIMAL PATHWAY

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	CCNA1	CCNA1	CCNA1	92	0.69	0.2	YES
2	CDKN1A	CDKN1A	CDKN1A	1685	0.21	0.18	YES
3	PSMD9	PSMD9	PSMD9	2880	0.12	0.15	YES
4	PSMC1	PSMC1	PSMC1	3013	0.11	0.17	YES
5	PSMD2	PSMD2	PSMD2	3071	0.11	0.2	YES
6	PSMB7	PSMB7	PSMB7	3404	0.096	0.21	YES
7	PSMB6	PSMB6	PSMB6	3480	0.093	0.24	YES
8	PSMA6	PSMA6	PSMA6	3633	0.088	0.26	YES
9	CCNE2	CCNE2	CCNE2	3871	0.081	0.27	YES
10	PSMC2	PSMC2	PSMC2	3970	0.078	0.28	YES
11	SKP2	SKP2	SKP2	3971	0.078	0.31	YES
12	PSMB2	PSMB2	PSMB2	4134	0.074	0.32	YES
13	CKS1B	CKS1B	CKS1B	4232	0.071	0.34	YES
14	PSMC3	PSMC3	PSMC3	4274	0.07	0.36	YES
15	PSMD12	PSMD12	PSMD12	4475	0.064	0.36	YES
16	CCNA2	CCNA2	CCNA2	4498	0.064	0.38	YES
17	PSMD10	PSMD10	PSMD10	4572	0.062	0.4	YES
18	PSMC6	PSMC6	PSMC6	4636	0.061	0.41	YES
19	PSMD7	PSMD7	PSMD7	4828	0.056	0.42	YES
20	PSMD5	PSMD5	PSMD5	4859	0.055	0.43	YES
21	PSMB5	PSMB5	PSMB5	4911	0.054	0.45	YES
22	PSMD14	PSMD14	PSMD14	4922	0.054	0.46	YES
23	PSMA3	PSMA3	PSMA3	5221	0.048	0.46	YES
24	PSMC5	PSMC5	PSMC5	5421	0.043	0.46	YES
25	PSMB1	PSMB1	PSMB1	5541	0.041	0.47	YES
26	PSMA1	PSMA1	PSMA1	5623	0.039	0.48	YES
27	SKP1	SKP1	SKP1	5666	0.038	0.48	YES
28	PSMD11	PSMD11	PSMD11	5753	0.037	0.49	YES
29	PSMA7	PSMA7	PSMA7	5805	0.036	0.5	YES
30	PSMD6	PSMD6	PSMD6	5806	0.036	0.51	YES
31	PSMA4	PSMA4	PSMA4	5914	0.033	0.51	YES
32	PSMA2	PSMA2	PSMA2	5923	0.033	0.52	YES
33	CDK2	CDK2	CDK2	5986	0.032	0.53	YES
34	PSMD8	PSMD8	PSMD8	6131	0.03	0.53	YES
35	PSMA5	PSMA5	PSMA5	6198	0.028	0.54	YES
36	PSMF1	PSMF1	PSMF1	6337	0.026	0.54	YES
37	PSMD13	PSMD13	PSMD13	6378	0.025	0.54	YES
38	PSMD4	PSMD4	PSMD4	6735	0.02	0.53	NO
39	CUL1	CUL1	CUL1	7044	0.014	0.52	NO
40	PSMD1	PSMD1	PSMD1	7082	0.014	0.52	NO
41	UBA52	UBA52	UBA52	7138	0.013	0.52	NO
42	PSMB9	PSMB9	PSMB9	7334	0.0092	0.51	NO
43	PSME2	PSME2	PSME2	8120	-0.0035	0.47	NO
44	PSMB3	PSMB3	PSMB3	8191	-0.0048	0.47	NO
45	CCNE1	CCNE1	CCNE1	8196	-0.0048	0.47	NO
46	PSMD3	PSMD3	PSMD3	8356	-0.0077	0.46	NO
47	PSMB4	PSMB4	PSMB4	8445	-0.0093	0.46	NO
48	PSME1	PSME1	PSME1	8636	-0.012	0.45	NO
49	RPS27A	RPS27A	RPS27A	9423	-0.025	0.42	NO
50	PSMC4	PSMC4	PSMC4	9597	-0.028	0.42	NO
51	PSMB8	PSMB8	PSMB8	11168	-0.059	0.35	NO
52	PSMB10	PSMB10	PSMB10	12074	-0.081	0.33	NO
53	CDKN1B	CDKN1B	CDKN1B	12766	-0.1	0.32	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: PID ERBB1 RECEPTOR PROXIMAL PATHWAY.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: PID ERBB1 RECEPTOR PROXIMAL 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 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	BNIP3	BNIP3	BNIP3	152	0.62	0.086	YES
2	SFN	SFN	SFN	341	0.49	0.15	YES
3	HRAS	HRAS	HRAS	1167	0.27	0.15	YES
4	EIF4EBP1	EIF4EBP1	EIF4EBP1	1711	0.2	0.15	YES
5	DDIT4	DDIT4	DDIT4	1870	0.19	0.17	YES
6	IRS1	IRS1	IRS1	1884	0.19	0.2	YES
7	ULK2	ULK2	ULK2	2059	0.17	0.21	YES
8	PLD2	PLD2	PLD2	2072	0.17	0.24	YES
9	RRAGC	RRAGC	RRAGC	2082	0.17	0.26	YES
10	SGK1	SGK1	SGK1	2109	0.17	0.29	YES
11	PML	PML	PML	2189	0.16	0.31	YES
12	CLIP1	CLIP1	CLIP1	2248	0.16	0.33	YES
13	ULK1	ULK1	ULK1	2325	0.15	0.35	YES
14	PXN	PXN	PXN	2575	0.14	0.36	YES
15	YWHAQ	YWHAQ	YWHAQ	2588	0.14	0.38	YES
16	YWHAG	YWHAG	YWHAG	2940	0.12	0.37	YES
17	PLD1	PLD1	PLD1	3114	0.11	0.38	YES
18	MAP2K1	MAP2K1	MAP2K1	3329	0.099	0.38	YES
19	YWHAZ	YWHAZ	YWHAZ	3654	0.087	0.38	YES
20	NRAS	NRAS	NRAS	4053	0.076	0.37	YES
21	EIF4A1	EIF4A1	EIF4A1	4138	0.073	0.38	YES
22	RICTOR	RICTOR	RICTOR	4381	0.067	0.37	YES
23	MAPK1	MAPK1	MAPK1	4698	0.06	0.37	YES
24	RPTOR	RPTOR	RPTOR	4742	0.059	0.37	YES
25	YWHAE	YWHAE	YWHAE	4879	0.055	0.37	YES
26	YY1	YY1	YY1	4971	0.053	0.38	YES
27	SREBF1	SREBF1	SREBF1	5081	0.051	0.38	YES
28	MAPKAP1	MAPKAP1	MAPKAP1	5147	0.049	0.38	YES
29	YWHAH	YWHAH	YWHAH	5166	0.049	0.39	YES
30	TSC2	TSC2	TSC2	5512	0.042	0.38	NO
31	MLST8	MLST8	MLST8	5556	0.041	0.38	NO
32	RRAGA	RRAGA	RRAGA	5671	0.038	0.38	NO
33	AKT1	AKT1	AKT1	5951	0.033	0.37	NO
34	CDK2	CDK2	CDK2	5986	0.032	0.37	NO
35	MAP2K2	MAP2K2	MAP2K2	6205	0.028	0.37	NO
36	RAC1	RAC1	RAC1	6388	0.025	0.36	NO
37	POLDIP3	POLDIP3	POLDIP3	6496	0.023	0.36	NO
38	RPS6KB1	RPS6KB1	RPS6KB1	6527	0.023	0.36	NO
39	EEF2K	EEF2K	EEF2K	6642	0.021	0.36	NO
40	RRN3	RRN3	RRN3	6659	0.021	0.36	NO
41	EEF2	EEF2	EEF2	6841	0.018	0.35	NO
42	EIF4E	EIF4E	EIF4E	7041	0.014	0.34	NO
43	AKT1S1	AKT1S1	AKT1S1	7271	0.01	0.33	NO
44	RHEB	RHEB	RHEB	7445	0.0074	0.32	NO
45	FBXW11	FBXW11	FBXW11	7645	0.0039	0.32	NO
46	RB1CC1	RB1CC1	RB1CC1	7666	0.0035	0.32	NO
47	MTOR	MTOR	MTOR	7694	0.0032	0.31	NO
48	RPS6KA1	RPS6KA1	RPS6KA1	8136	-0.0038	0.29	NO
49	CCNE1	CCNE1	CCNE1	8196	-0.0048	0.29	NO
50	PDPK1	PDPK1	PDPK1	8229	-0.0055	0.29	NO
51	YWHAB	YWHAB	YWHAB	9276	-0.023	0.24	NO
52	TSC1	TSC1	TSC1	9393	-0.025	0.23	NO
53	BRAF	BRAF	BRAF	9500	-0.027	0.23	NO
54	EIF4B	EIF4B	EIF4B	9548	-0.027	0.23	NO
55	PRR5	PRR5	PRR5	9568	-0.028	0.24	NO
56	CYCS	CYCS	CYCS	9916	-0.034	0.22	NO
57	RHOA	RHOA	RHOA	10119	-0.037	0.22	NO
58	RAF1	RAF1	RAF1	10294	-0.041	0.21	NO
59	PDCD4	PDCD4	PDCD4	11433	-0.065	0.16	NO
60	MAPK3	MAPK3	MAPK3	11470	-0.066	0.17	NO
61	RRAGD	RRAGD	RRAGD	11747	-0.073	0.17	NO
62	RRAGB	RRAGB	RRAGB	12732	-0.1	0.13	NO
63	KRAS	KRAS	KRAS	12846	-0.1	0.14	NO
64	PRKCA	PRKCA	PRKCA	13401	-0.12	0.13	NO
65	IKBKB	IKBKB	IKBKB	13422	-0.12	0.15	NO
66	SSPO	SSPO	SSPO	17576	-0.44	-0.0097	NO
67	PPARGC1A	PPARGC1A	PPARGC1A	17734	-0.48	0.054	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: PID MYC PATHWAY.

Figure S54. 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 ECADHERIN NASCENTAJ 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	JUB	JUB	JUB	1282	0.25	0.043	YES
2	GADD45A	GADD45A	GADD45A	1828	0.19	0.098	YES
3	NDEL1	NDEL1	NDEL1	2181	0.16	0.15	YES
4	BIRC5	BIRC5	BIRC5	2432	0.14	0.2	YES
5	DLGAP5	DLGAP5	DLGAP5	2703	0.13	0.24	YES
6	CENPA	CENPA	CENPA	2749	0.13	0.29	YES
7	AURKB	AURKB	AURKB	3363	0.098	0.3	YES
8	FZR1	FZR1	FZR1	3493	0.093	0.34	YES
9	RAN	RAN	RAN	3645	0.087	0.37	YES
10	CDC25B	CDC25B	CDC25B	3836	0.082	0.39	YES
11	NFKBIA	NFKBIA	NFKBIA	3923	0.08	0.42	YES
12	GSK3B	GSK3B	GSK3B	4023	0.077	0.45	YES
13	CPEB1	CPEB1	CPEB1	4055	0.076	0.48	YES
14	RASA1	RASA1	RASA1	4086	0.075	0.52	YES
15	CKAP5	CKAP5	CKAP5	5348	0.045	0.47	NO
16	TPX2	TPX2	TPX2	5406	0.044	0.48	NO
17	PRKACA	PRKACA	PRKACA	5698	0.038	0.49	NO
18	OAZ1	OAZ1	OAZ1	5903	0.033	0.49	NO
19	AKT1	AKT1	AKT1	5951	0.033	0.5	NO
20	AURKAIP1	AURKAIP1	AURKAIP1	6953	0.016	0.46	NO
21	TP53	TP53	TP53	7029	0.014	0.46	NO
22	PPP2R5D	PPP2R5D	PPP2R5D	7839	0.0009	0.41	NO
23	TACC3	TACC3	TACC3	7884	0.00021	0.41	NO
24	TDRD7	TDRD7	TDRD7	8257	-0.006	0.4	NO
25	GIT1	GIT1	GIT1	8355	-0.0077	0.39	NO
26	BRCA1	BRCA1	BRCA1	9017	-0.018	0.36	NO
27	PAK1	PAK1	PAK1	9180	-0.021	0.37	NO
28	ARHGEF7	ARHGEF7	ARHGEF7	9895	-0.033	0.34	NO
29	AURKA	AURKA	AURKA	9900	-0.033	0.36	NO
30	MDM2	MDM2	MDM2	10508	-0.045	0.34	NO
31	TACC1	TACC1	TACC1	15443	-0.22	0.18	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: PID ECADHERIN NASCENTAJ PATHWAY.

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

genes ES table in pathway: PID DELTANP63PATHWAY

Table 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	MRC2	MRC2	MRC2	1228	0.26	0.017	YES
2	MRC1	MRC1	MRC1	1309	0.25	0.093	YES
3	FCGR1A	FCGR1A	FCGR1A	1889	0.18	0.12	YES
4	CD207	CD207	CD207	2530	0.14	0.13	YES
5	FCGR1B	FCGR1B	FCGR1B	2836	0.12	0.15	YES
6	PSMD9	PSMD9	PSMD9	2880	0.12	0.19	YES
7	PSMC1	PSMC1	PSMC1	3013	0.11	0.22	YES
8	PSMD2	PSMD2	PSMD2	3071	0.11	0.25	YES
9	PSMB7	PSMB7	PSMB7	3404	0.096	0.26	YES
10	PSMB6	PSMB6	PSMB6	3480	0.093	0.29	YES
11	PSMA6	PSMA6	PSMA6	3633	0.088	0.31	YES
12	PSMC2	PSMC2	PSMC2	3970	0.078	0.31	YES
13	PSMB2	PSMB2	PSMB2	4134	0.074	0.33	YES
14	PSMC3	PSMC3	PSMC3	4274	0.07	0.34	YES
15	PSMD12	PSMD12	PSMD12	4475	0.064	0.35	YES
16	PSMD10	PSMD10	PSMD10	4572	0.062	0.37	YES
17	PSMC6	PSMC6	PSMC6	4636	0.061	0.38	YES
18	PSMD7	PSMD7	PSMD7	4828	0.056	0.39	YES
19	PSMD5	PSMD5	PSMD5	4859	0.055	0.41	YES
20	PSMB5	PSMB5	PSMB5	4911	0.054	0.42	YES
21	PSMD14	PSMD14	PSMD14	4922	0.054	0.44	YES
22	PSMA3	PSMA3	PSMA3	5221	0.048	0.44	YES
23	PSME4	PSME4	PSME4	5363	0.044	0.44	YES
24	PSMC5	PSMC5	PSMC5	5421	0.043	0.46	YES
25	PSMB1	PSMB1	PSMB1	5541	0.041	0.46	YES
26	PSMA1	PSMA1	PSMA1	5623	0.039	0.47	YES
27	PSMD11	PSMD11	PSMD11	5753	0.037	0.47	YES
28	PSMA7	PSMA7	PSMA7	5805	0.036	0.48	YES
29	PSMD6	PSMD6	PSMD6	5806	0.036	0.49	YES
30	PSMA4	PSMA4	PSMA4	5914	0.033	0.5	YES
31	PSMA2	PSMA2	PSMA2	5923	0.033	0.51	YES
32	PSMD8	PSMD8	PSMD8	6131	0.03	0.51	YES
33	PSMA5	PSMA5	PSMA5	6198	0.028	0.51	YES
34	PSMF1	PSMF1	PSMF1	6337	0.026	0.51	YES
35	PSMD13	PSMD13	PSMD13	6378	0.025	0.52	YES
36	PSMD4	PSMD4	PSMD4	6735	0.02	0.51	NO
37	PSMD1	PSMD1	PSMD1	7082	0.014	0.49	NO
38	PSMB9	PSMB9	PSMB9	7334	0.0092	0.48	NO
39	PSME2	PSME2	PSME2	8120	-0.0035	0.44	NO
40	PSMB3	PSMB3	PSMB3	8191	-0.0048	0.44	NO
41	PSMD3	PSMD3	PSMD3	8356	-0.0077	0.43	NO
42	PSMB4	PSMB4	PSMB4	8445	-0.0093	0.43	NO
43	PSME1	PSME1	PSME1	8636	-0.012	0.42	NO
44	PSMC4	PSMC4	PSMC4	9597	-0.028	0.38	NO
45	PSMB8	PSMB8	PSMB8	11168	-0.059	0.32	NO
46	PSMB10	PSMB10	PSMB10	12074	-0.081	0.3	NO
47	PSMA8	PSMA8	PSMA8	15037	-0.2	0.2	NO

Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID DELTANP63PATHWAY.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: PID DELTANP63PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID A6B1 A6B4 INTEGRIN PATHWAY

Table 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	PML	PML	PML	2189	0.16	-0.025	YES
2	MYC	MYC	MYC	2458	0.14	0.043	YES
3	TAF12	TAF12	TAF12	2706	0.13	0.1	YES
4	ZBTB17	ZBTB17	ZBTB17	2972	0.11	0.15	YES
5	RUVBL1	RUVBL1	RUVBL1	3620	0.088	0.17	YES
6	PAK2	PAK2	PAK2	3777	0.084	0.21	YES
7	SUPT3H	SUPT3H	SUPT3H	3885	0.08	0.25	YES
8	SKP2	SKP2	SKP2	3971	0.078	0.29	YES
9	PIN1	PIN1	PIN1	3993	0.078	0.33	YES
10	GSK3B	GSK3B	GSK3B	4023	0.077	0.38	YES
11	PPP2CA	PPP2CA	PPP2CA	4083	0.075	0.42	YES
12	ACTL6A	ACTL6A	ACTL6A	4171	0.073	0.45	YES
13	AXIN1	AXIN1	AXIN1	4479	0.064	0.47	YES
14	TAF9	TAF9	TAF9	5181	0.048	0.46	NO
15	KAT5	KAT5	KAT5	5885	0.034	0.44	NO
16	FBXW7	FBXW7	FBXW7	7151	0.012	0.38	NO
17	RUVBL2	RUVBL2	RUVBL2	7396	0.0083	0.38	NO
18	SUPT7L	SUPT7L	SUPT7L	7711	0.0028	0.36	NO
19	MAX	MAX	MAX	8106	-0.0033	0.34	NO
20	HBP1	HBP1	HBP1	8259	-0.006	0.34	NO
21	TAF10	TAF10	TAF10	8766	-0.014	0.32	NO
22	KAT2A	KAT2A	KAT2A	8839	-0.015	0.32	NO
23	TRRAP	TRRAP	TRRAP	11144	-0.058	0.23	NO
24	PPP2R5A	PPP2R5A	PPP2R5A	11360	-0.063	0.26	NO
25	CDKN2A	CDKN2A	CDKN2A	15767	-0.24	0.16	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: PID A6B1 A6B4 INTEGRIN PATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: PID A6B1 A6B4 INTEGRIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype 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 GLUTATHIONE METABOLISM	46	genes.ES.table	0.54	1.6	0.042	1	0.97	0.28	0.071	0.26	0.59	0.31
KEGG NEUROTROPHIN SIGNALING PATHWAY	126	genes.ES.table	0.44	1.7	0.0062	1	0.79	0.18	0.15	0.16	0.86	0.46
KEGG BASAL CELL CARCINOMA	54	genes.ES.table	0.61	1.6	0.014	1	0.97	0.54	0.16	0.45	0.62	0.33
BIOCARTA CHREBP2 PATHWAY	42	genes.ES.table	0.42	1.6	0.032	1	0.94	0.12	0.089	0.11	0.68	0.36
ST P38 MAPK PATHWAY	37	genes.ES.table	0.41	1.6	0.045	1	0.97	0.14	0.12	0.12	0.61	0.32
WNT SIGNALING	87	genes.ES.table	0.51	1.6	0.014	1	0.96	0.34	0.16	0.29	0.6	0.32
SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES	34	genes.ES.table	0.48	1.6	0.044	0.98	0.98	0.26	0.17	0.22	0.61	0.32
PID P75NTRPATHWAY	68	genes.ES.table	0.39	1.6	0.029	0.95	0.97	0.19	0.15	0.16	0.56	0.3
PID TRKRPATHWAY	61	genes.ES.table	0.46	1.7	0.01	1	0.82	0.23	0.19	0.19	0.62	0.35
PID HEDGEHOG GLIPATHWAY	48	genes.ES.table	0.47	1.8	0.0063	1	0.73	0.17	0.1	0.15	0.99	0.5

genes ES table in pathway: KEGG GLUTATHIONE 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	HS6ST2	HS6ST2	HS6ST2	99	0.77	0.11	YES
2	HS3ST6	HS3ST6	HS3ST6	243	0.63	0.2	YES
3	GPC3	GPC3	GPC3	337	0.57	0.28	YES
4	HS3ST3A1	HS3ST3A1	HS3ST3A1	479	0.5	0.35	YES
5	GPC1	GPC1	GPC1	704	0.43	0.41	YES
6	HS3ST4	HS3ST4	HS3ST4	846	0.39	0.46	YES
7	HS3ST5	HS3ST5	HS3ST5	938	0.38	0.51	YES
8	GPC2	GPC2	GPC2	1046	0.35	0.56	YES
9	GPC5	GPC5	GPC5	1050	0.35	0.61	YES
10	HS6ST3	HS6ST3	HS6ST3	1420	0.29	0.64	YES
11	HS3ST3B1	HS3ST3B1	HS3ST3B1	1592	0.27	0.67	YES
12	HS6ST1	HS6ST1	HS6ST1	1713	0.26	0.7	YES
13	SDC1	SDC1	SDC1	2356	0.2	0.7	NO
14	SDC2	SDC2	SDC2	5423	0.07	0.55	NO
15	EXT1	EXT1	EXT1	5814	0.061	0.54	NO
16	NDST3	NDST3	NDST3	7649	0.028	0.44	NO
17	EXT2	EXT2	EXT2	9178	0.0035	0.36	NO
18	AGRN	AGRN	AGRN	9400	0.000091	0.35	NO
19	NDST2	NDST2	NDST2	10237	-0.014	0.31	NO
20	GPC6	GPC6	GPC6	10619	-0.021	0.29	NO
21	GPC4	GPC4	GPC4	10790	-0.024	0.28	NO
22	NDST1	NDST1	NDST1	11215	-0.032	0.27	NO
23	GLCE	GLCE	GLCE	12489	-0.059	0.21	NO
24	HS3ST2	HS3ST2	HS3ST2	12538	-0.06	0.21	NO
25	SDC3	SDC3	SDC3	13083	-0.073	0.2	NO
26	HSPG2	HSPG2	HSPG2	13787	-0.093	0.17	NO
27	NDST4	NDST4	NDST4	13966	-0.099	0.18	NO
28	HS2ST1	HS2ST1	HS2ST1	14166	-0.11	0.18	NO
29	SDC4	SDC4	SDC4	15521	-0.16	0.14	NO
30	HS3ST1	HS3ST1	HS3ST1	16640	-0.24	0.11	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 GLUTATHIONE METABOLISM.

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

genes ES table in pathway: KEGG NEUROTROPHIN SIGNALING 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	GLI2	GLI2	GLI2	75	0.81	0.13	YES
2	GLI1	GLI1	GLI1	180	0.68	0.24	YES
3	SMO	SMO	SMO	281	0.6	0.34	YES
4	MTSS1	MTSS1	MTSS1	1348	0.3	0.33	YES
5	GNAI1	GNAI1	GNAI1	1483	0.29	0.37	YES
6	GLI3	GLI3	GLI3	1567	0.28	0.41	YES
7	PTCH1	PTCH1	PTCH1	1869	0.24	0.44	YES
8	GNAZ	GNAZ	GNAZ	1958	0.23	0.47	YES
9	GNAO1	GNAO1	GNAO1	4947	0.081	0.32	NO
10	SIN3A	SIN3A	SIN3A	5809	0.062	0.29	NO
11	GSK3B	GSK3B	GSK3B	6462	0.049	0.26	NO
12	CSNK1G2	CSNK1G2	CSNK1G2	6537	0.047	0.26	NO
13	SAP18	SAP18	SAP18	6686	0.044	0.26	NO
14	CSNK1A1	CSNK1A1	CSNK1A1	7124	0.036	0.25	NO
15	PRKACA	PRKACA	PRKACA	7334	0.033	0.24	NO
16	AKT1	AKT1	AKT1	7784	0.025	0.22	NO
17	XPO1	XPO1	XPO1	7840	0.024	0.22	NO
18	RBBP4	RBBP4	RBBP4	7992	0.022	0.22	NO
19	SPOP	SPOP	SPOP	8084	0.02	0.22	NO
20	CREBBP	CREBBP	CREBBP	8234	0.018	0.21	NO
21	SIN3B	SIN3B	SIN3B	8259	0.018	0.21	NO
22	CSNK1G1	CSNK1G1	CSNK1G1	8477	0.015	0.2	NO
23	CSNK1E	CSNK1E	CSNK1E	8782	0.01	0.19	NO
24	SUFU	SUFU	SUFU	9069	0.0056	0.18	NO
25	HDAC2	HDAC2	HDAC2	9285	0.0018	0.16	NO
26	IFT172	IFT172	IFT172	9388	0.00026	0.16	NO
27	RAB23	RAB23	RAB23	9488	-0.0012	0.15	NO
28	HDAC1	HDAC1	HDAC1	9910	-0.0086	0.13	NO
29	MAP2K1	MAP2K1	MAP2K1	9916	-0.0086	0.14	NO
30	CSNK1D	CSNK1D	CSNK1D	10911	-0.026	0.086	NO
31	SSPO	SSPO	SSPO	11291	-0.034	0.071	NO
32	GNB1	GNB1	GNB1	11297	-0.034	0.076	NO
33	GNAI2	GNAI2	GNAI2	11312	-0.034	0.082	NO
34	RBBP7	RBBP7	RBBP7	11367	-0.035	0.084	NO
35	IFT88	IFT88	IFT88	11368	-0.035	0.09	NO
36	GNAI3	GNAI3	GNAI3	11477	-0.038	0.091	NO
37	FBXW11	FBXW11	FBXW11	11991	-0.048	0.071	NO
38	CSNK1G3	CSNK1G3	CSNK1G3	12462	-0.058	0.056	NO
39	KIF3A	KIF3A	KIF3A	12650	-0.062	0.056	NO
40	SAP30	SAP30	SAP30	12855	-0.067	0.057	NO
41	PIAS1	PIAS1	PIAS1	13133	-0.074	0.054	NO
42	PRKCD	PRKCD	PRKCD	13355	-0.08	0.056	NO
43	STK36	STK36	STK36	13525	-0.085	0.061	NO
44	SHH	SHH	SHH	13830	-0.095	0.061	NO
45	ARRB2	ARRB2	ARRB2	14235	-0.11	0.057	NO
46	GNG2	GNG2	GNG2	16378	-0.22	-0.021	NO
47	LGALS3	LGALS3	LGALS3	16506	-0.22	0.0094	NO
48	FOXA2	FOXA2	FOXA2	18579	-0.66	0.009	NO

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

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NEUROTROPHIN 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 BASAL CELL CARCINOMA

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	NTRK2	NTRK2	NTRK2	30	0.95	0.055	YES
2	MAPK10	MAPK10	MAPK10	67	0.83	0.1	YES
3	BDNF	BDNF	BDNF	69	0.82	0.15	YES
4	NTF4	NTF4	NTF4	94	0.77	0.19	YES
5	IRS4	IRS4	IRS4	106	0.76	0.24	YES
6	CALML3	CALML3	CALML3	150	0.71	0.28	YES
7	NGFR	NGFR	NGFR	498	0.5	0.29	YES
8	NGFRAP1	NGFRAP1	NGFRAP1	547	0.48	0.32	YES
9	MAPK12	MAPK12	MAPK12	607	0.46	0.34	YES
10	TP73	TP73	TP73	735	0.43	0.36	YES
11	RPS6KA6	RPS6KA6	RPS6KA6	879	0.39	0.37	YES
12	CALML5	CALML5	CALML5	1078	0.35	0.38	YES
13	CAMK2B	CAMK2B	CAMK2B	1268	0.32	0.39	YES
14	IRS2	IRS2	IRS2	1620	0.27	0.39	YES
15	BCL2	BCL2	BCL2	1698	0.26	0.4	YES
16	NGF	NGF	NGF	1783	0.25	0.41	YES
17	AKT3	AKT3	AKT3	1898	0.24	0.42	YES
18	NTF3	NTF3	NTF3	2287	0.2	0.41	YES
19	MAPK11	MAPK11	MAPK11	2323	0.2	0.42	YES
20	CALML6	CALML6	CALML6	2363	0.2	0.43	YES
21	PIK3CA	PIK3CA	PIK3CA	2620	0.18	0.43	YES
22	RPS6KA5	RPS6KA5	RPS6KA5	2720	0.17	0.43	YES
23	CAMK4	CAMK4	CAMK4	2733	0.17	0.44	YES
24	NFKBIA	NFKBIA	NFKBIA	3378	0.14	0.41	NO
25	HRAS	HRAS	HRAS	3585	0.13	0.41	NO
26	PIK3R2	PIK3R2	PIK3R2	3630	0.12	0.42	NO
27	CRKL	CRKL	CRKL	3954	0.11	0.4	NO
28	PDK1	PDK1	PDK1	4115	0.11	0.4	NO
29	BRAF	BRAF	BRAF	4432	0.096	0.39	NO
30	IKBKB	IKBKB	IKBKB	4558	0.093	0.39	NO
31	YWHAG	YWHAG	YWHAG	4750	0.087	0.38	NO
32	YWHAQ	YWHAQ	YWHAQ	4932	0.082	0.38	NO
33	KIDINS220	KIDINS220	KIDINS220	5095	0.077	0.38	NO
34	SHC4	SHC4	SHC4	5204	0.075	0.37	NO
35	BAD	BAD	BAD	5369	0.071	0.37	NO
36	YWHAE	YWHAE	YWHAE	5431	0.069	0.37	NO
37	BAX	BAX	BAX	6179	0.054	0.33	NO
38	AKT2	AKT2	AKT2	6189	0.053	0.34	NO
39	PIK3CD	PIK3CD	PIK3CD	6219	0.053	0.34	NO
40	ATF4	ATF4	ATF4	6318	0.051	0.34	NO
41	GSK3B	GSK3B	GSK3B	6462	0.049	0.33	NO
42	MAPK7	MAPK7	MAPK7	6692	0.044	0.32	NO
43	MAP2K5	MAP2K5	MAP2K5	6804	0.042	0.32	NO
44	MAP2K7	MAP2K7	MAP2K7	6808	0.042	0.32	NO
45	MAP2K2	MAP2K2	MAP2K2	7036	0.038	0.31	NO
46	SHC1	SHC1	SHC1	7367	0.033	0.29	NO
47	YWHAZ	YWHAZ	YWHAZ	7375	0.032	0.3	NO
48	GAB1	GAB1	GAB1	7534	0.03	0.29	NO
49	CALM1	CALM1	CALM1	7552	0.03	0.29	NO
50	CAMK2A	CAMK2A	CAMK2A	7668	0.027	0.28	NO
51	AKT1	AKT1	AKT1	7784	0.025	0.28	NO
52	SHC3	SHC3	SHC3	7817	0.024	0.28	NO
53	RAPGEF1	RAPGEF1	RAPGEF1	7863	0.024	0.28	NO
54	IRAK4	IRAK4	IRAK4	7933	0.022	0.28	NO
55	SH2B2	SH2B2	SH2B2	7949	0.022	0.28	NO
56	TRAF6	TRAF6	TRAF6	8093	0.02	0.27	NO
57	ABL1	ABL1	ABL1	8133	0.02	0.27	NO
58	CRK	CRK	CRK	8239	0.018	0.26	NO
59	PLCG2	PLCG2	PLCG2	8254	0.018	0.26	NO
60	MAPK1	MAPK1	MAPK1	8337	0.017	0.26	NO
61	NTRK3	NTRK3	NTRK3	8345	0.016	0.26	NO
62	SH2B1	SH2B1	SH2B1	8479	0.014	0.26	NO
63	MAPK13	MAPK13	MAPK13	8700	0.012	0.24	NO
64	IRAK1	IRAK1	IRAK1	8788	0.01	0.24	NO
65	TP53	TP53	TP53	9175	0.0035	0.22	NO
66	ZNF274	ZNF274	ZNF274	9210	0.003	0.22	NO
67	RAC1	RAC1	RAC1	9414	-0.0002	0.21	NO
68	MAP3K1	MAP3K1	MAP3K1	9498	-0.0015	0.2	NO
69	FRS2	FRS2	FRS2	9515	-0.0018	0.2	NO
70	CAMK2G	CAMK2G	CAMK2G	9530	-0.002	0.2	NO
71	SOS1	SOS1	SOS1	9615	-0.0034	0.2	NO
72	GRB2	GRB2	GRB2	9721	-0.005	0.19	NO
73	ARHGDIA	ARHGDIA	ARHGDIA	9883	-0.0082	0.18	NO
74	MAGED1	MAGED1	MAGED1	9912	-0.0086	0.18	NO
75	MAP2K1	MAP2K1	MAP2K1	9916	-0.0086	0.18	NO
76	PIK3R1	PIK3R1	PIK3R1	10011	-0.01	0.18	NO
77	MAPKAPK2	MAPKAPK2	MAPKAPK2	10016	-0.01	0.18	NO
78	CSK	CSK	CSK	10179	-0.013	0.17	NO
79	JUN	JUN	JUN	10308	-0.015	0.17	NO
80	PTPN11	PTPN11	PTPN11	10355	-0.016	0.16	NO
81	RELA	RELA	RELA	10408	-0.017	0.16	NO
82	RAF1	RAF1	RAF1	10491	-0.018	0.16	NO
83	PIK3CB	PIK3CB	PIK3CB	10498	-0.018	0.16	NO
84	KRAS	KRAS	KRAS	10549	-0.019	0.16	NO
85	MAP3K3	MAP3K3	MAP3K3	10589	-0.02	0.16	NO
86	CALM2	CALM2	CALM2	10641	-0.021	0.16	NO
87	RAP1B	RAP1B	RAP1B	10691	-0.022	0.16	NO
88	YWHAH	YWHAH	YWHAH	10769	-0.024	0.15	NO
89	PLCG1	PLCG1	PLCG1	10903	-0.026	0.15	NO
90	NFKBIB	NFKBIB	NFKBIB	11058	-0.029	0.14	NO
91	NFKB1	NFKB1	NFKB1	11303	-0.034	0.13	NO
92	SHC2	SHC2	SHC2	11604	-0.04	0.12	NO
93	PRDM4	PRDM4	PRDM4	11855	-0.045	0.1	NO
94	YWHAB	YWHAB	YWHAB	12111	-0.05	0.093	NO
95	SOS2	SOS2	SOS2	12220	-0.052	0.091	NO
96	CDC42	CDC42	CDC42	12250	-0.053	0.092	NO
97	CAMK2D	CAMK2D	CAMK2D	12306	-0.054	0.092	NO
98	MAPK9	MAPK9	MAPK9	12344	-0.055	0.094	NO
99	FOXO3	FOXO3	FOXO3	12524	-0.06	0.088	NO
100	MAPK14	MAPK14	MAPK14	12584	-0.061	0.088	NO
101	RPS6KA4	RPS6KA4	RPS6KA4	12601	-0.061	0.091	NO
102	PSEN1	PSEN1	PSEN1	12648	-0.062	0.092	NO
103	MAP3K5	MAP3K5	MAP3K5	12686	-0.063	0.094	NO
104	RHOA	RHOA	RHOA	13111	-0.074	0.075	NO
105	IRS1	IRS1	IRS1	13332	-0.079	0.068	NO
106	PRKCD	PRKCD	PRKCD	13355	-0.08	0.072	NO
107	ARHGDIB	ARHGDIB	ARHGDIB	13732	-0.091	0.057	NO
108	NRAS	NRAS	NRAS	13763	-0.092	0.061	NO
109	RPS6KA1	RPS6KA1	RPS6KA1	13768	-0.092	0.066	NO
110	RPS6KA3	RPS6KA3	RPS6KA3	13816	-0.094	0.069	NO
111	NTRK1	NTRK1	NTRK1	14230	-0.11	0.053	NO
112	CALM3	CALM3	CALM3	14277	-0.11	0.057	NO
113	RAP1A	RAP1A	RAP1A	14410	-0.11	0.057	NO
114	RPS6KA2	RPS6KA2	RPS6KA2	14697	-0.12	0.049	NO
115	MAPK3	MAPK3	MAPK3	14864	-0.13	0.048	NO
116	MAPK8	MAPK8	MAPK8	14983	-0.14	0.05	NO
117	PIK3R3	PIK3R3	PIK3R3	15679	-0.17	0.022	NO
118	RIPK2	RIPK2	RIPK2	15752	-0.18	0.029	NO
119	SORT1	SORT1	SORT1	16020	-0.19	0.026	NO
120	FASLG	FASLG	FASLG	16140	-0.2	0.032	NO
121	NFKBIE	NFKBIE	NFKBIE	16368	-0.21	0.032	NO
122	SH2B3	SH2B3	SH2B3	16655	-0.24	0.03	NO
123	IRAK3	IRAK3	IRAK3	17232	-0.29	0.017	NO
124	PIK3R5	PIK3R5	PIK3R5	17337	-0.3	0.029	NO
125	IRAK2	IRAK2	IRAK2	17649	-0.35	0.033	NO
126	PIK3CG	PIK3CG	PIK3CG	18123	-0.45	0.034	NO

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

Figure S66. 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 CHREBP2 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	PAK7	PAK7	PAK7	49	0.88	0.19	YES
2	SRGAP3	SRGAP3	SRGAP3	604	0.46	0.27	YES
3	PFN2	PFN2	PFN2	622	0.46	0.37	YES
4	GPC1	GPC1	GPC1	704	0.43	0.46	YES
5	ROBO2	ROBO2	ROBO2	1687	0.26	0.46	YES
6	PAK6	PAK6	PAK6	1776	0.25	0.52	YES
7	SLIT2	SLIT2	SLIT2	1825	0.25	0.57	YES
8	NCK1	NCK1	NCK1	2543	0.18	0.57	YES
9	EVL	EVL	EVL	2687	0.17	0.6	YES
10	CLASP1	CLASP1	CLASP1	4199	0.1	0.55	NO
11	PAK1	PAK1	PAK1	4224	0.1	0.57	NO
12	PAK2	PAK2	PAK2	4698	0.089	0.56	NO
13	ENAH	ENAH	ENAH	4836	0.084	0.57	NO
14	SRGAP2	SRGAP2	SRGAP2	6031	0.057	0.52	NO
15	ABL2	ABL2	ABL2	7172	0.036	0.47	NO
16	PAK4	PAK4	PAK4	7442	0.031	0.46	NO
17	ABL1	ABL1	ABL1	8133	0.02	0.43	NO
18	ROBO1	ROBO1	ROBO1	8936	0.0077	0.39	NO
19	RAC1	RAC1	RAC1	9414	-0.0002	0.36	NO
20	CAP2	CAP2	CAP2	9532	-0.002	0.36	NO
21	SOS1	SOS1	SOS1	9615	-0.0034	0.35	NO
22	PFN1	PFN1	PFN1	10228	-0.014	0.32	NO
23	NCK2	NCK2	NCK2	12216	-0.052	0.23	NO
24	SOS2	SOS2	SOS2	12220	-0.052	0.24	NO
25	CDC42	CDC42	CDC42	12250	-0.053	0.25	NO
26	CAP1	CAP1	CAP1	12293	-0.054	0.26	NO
27	ROBO3	ROBO3	ROBO3	13659	-0.089	0.21	NO
28	VASP	VASP	VASP	14121	-0.1	0.2	NO
29	SRGAP1	SRGAP1	SRGAP1	15962	-0.19	0.15	NO

Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CHREBP2 PATHWAY.

Figure S68. 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: ST P38 MAPK PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NTRK2	NTRK2	NTRK2	30	0.95	0.12	YES
2	BDNF	BDNF	BDNF	69	0.82	0.22	YES
3	NTF4	NTF4	NTF4	94	0.77	0.31	YES
4	NGFR	NGFR	NGFR	498	0.5	0.35	YES
5	RIT1	RIT1	RIT1	965	0.37	0.37	YES
6	DNM1	DNM1	DNM1	1663	0.26	0.37	YES
7	ELMO1	ELMO1	ELMO1	1773	0.25	0.39	YES
8	NGF	NGF	NGF	1783	0.25	0.42	YES
9	TIAM1	TIAM1	TIAM1	1794	0.25	0.46	YES
10	NTF3	NTF3	NTF3	2287	0.2	0.45	YES
11	PIK3CA	PIK3CA	PIK3CA	2620	0.18	0.46	YES
12	FAIM	FAIM	FAIM	3062	0.15	0.45	YES
13	MATK	MATK	MATK	3375	0.14	0.45	YES
14	HRAS	HRAS	HRAS	3585	0.13	0.46	YES
15	CRKL	CRKL	CRKL	3954	0.11	0.45	NO
16	NEDD4L	NEDD4L	NEDD4L	4414	0.097	0.44	NO
17	CCND1	CCND1	CCND1	5267	0.073	0.4	NO
18	SQSTM1	SQSTM1	SQSTM1	5645	0.065	0.39	NO
19	MCF2L	MCF2L	MCF2L	5783	0.062	0.39	NO
20	PRKCI	PRKCI	PRKCI	5833	0.061	0.4	NO
21	DNAJA3	DNAJA3	DNAJA3	6101	0.055	0.39	NO
22	RGS19	RGS19	RGS19	7086	0.037	0.34	NO
23	SHC1	SHC1	SHC1	7367	0.033	0.33	NO
24	GAB1	GAB1	GAB1	7534	0.03	0.32	NO
25	GIPC1	GIPC1	GIPC1	7694	0.027	0.32	NO
26	SHC3	SHC3	SHC3	7817	0.024	0.32	NO
27	RAPGEF1	RAPGEF1	RAPGEF1	7863	0.024	0.32	NO
28	ABL1	ABL1	ABL1	8133	0.02	0.3	NO
29	CRK	CRK	CRK	8239	0.018	0.3	NO
30	MAPK1	MAPK1	MAPK1	8337	0.017	0.3	NO
31	NTRK3	NTRK3	NTRK3	8345	0.016	0.3	NO
32	SH2B1	SH2B1	SH2B1	8479	0.014	0.3	NO
33	RAC1	RAC1	RAC1	9414	-0.0002	0.24	NO
34	FRS2	FRS2	FRS2	9515	-0.0018	0.24	NO
35	SOS1	SOS1	SOS1	9615	-0.0034	0.24	NO
36	GRB2	GRB2	GRB2	9721	-0.005	0.23	NO
37	MAGED1	MAGED1	MAGED1	9912	-0.0086	0.22	NO
38	MAP2K1	MAP2K1	MAP2K1	9916	-0.0086	0.22	NO
39	PIK3R1	PIK3R1	PIK3R1	10011	-0.01	0.22	NO
40	DOCK1	DOCK1	DOCK1	10157	-0.013	0.21	NO
41	PTPN11	PTPN11	PTPN11	10355	-0.016	0.2	NO
42	KRAS	KRAS	KRAS	10549	-0.019	0.2	NO
43	RAP1B	RAP1B	RAP1B	10691	-0.022	0.19	NO
44	PLCG1	PLCG1	PLCG1	10903	-0.026	0.18	NO
45	DYNLT1	DYNLT1	DYNLT1	11013	-0.028	0.18	NO
46	STAT3	STAT3	STAT3	11258	-0.033	0.17	NO
47	SHC2	SHC2	SHC2	11604	-0.04	0.16	NO
48	CDC42	CDC42	CDC42	12250	-0.053	0.13	NO
49	RHOG	RHOG	RHOG	12523	-0.06	0.12	NO
50	FRS3	FRS3	FRS3	12633	-0.062	0.12	NO
51	RHOA	RHOA	RHOA	13111	-0.074	0.11	NO
52	ARHGAP32	ARHGAP32	ARHGAP32	13240	-0.077	0.11	NO
53	RASA1	RASA1	RASA1	13242	-0.077	0.12	NO
54	EHD4	EHD4	EHD4	13556	-0.086	0.11	NO
55	NRAS	NRAS	NRAS	13763	-0.092	0.12	NO
56	PRKCZ	PRKCZ	PRKCZ	13955	-0.098	0.12	NO
57	NTRK1	NTRK1	NTRK1	14230	-0.11	0.12	NO
58	RAP1A	RAP1A	RAP1A	14410	-0.11	0.12	NO
59	MAPK3	MAPK3	MAPK3	14864	-0.13	0.11	NO
60	GAB2	GAB2	GAB2	16980	-0.26	0.031	NO
61	RASGRF1	RASGRF1	RASGRF1	18334	-0.51	0.022	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: ST P38 MAPK PATHWAY.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: ST P38 MAPK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: WNT SIGNALING

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	SNAPC1	SNAPC1	SNAPC1	1659	0.26	0.074	YES
2	SNAPC5	SNAPC5	SNAPC5	3871	0.12	0.026	YES
3	POLR2H	POLR2H	POLR2H	3962	0.11	0.09	YES
4	GTF3C5	GTF3C5	GTF3C5	4227	0.1	0.14	YES
5	BRF2	BRF2	BRF2	4460	0.096	0.18	YES
6	SNAPC2	SNAPC2	SNAPC2	4495	0.095	0.24	YES
7	POLR1D	POLR1D	POLR1D	4838	0.084	0.28	YES
8	POLR2F	POLR2F	POLR2F	4843	0.084	0.33	YES
9	POLR2E	POLR2E	POLR2E	4957	0.081	0.37	YES
10	GTF3C2	GTF3C2	GTF3C2	5671	0.064	0.37	YES
11	POLR3H	POLR3H	POLR3H	5815	0.061	0.4	YES
12	GTF3C3	GTF3C3	GTF3C3	5983	0.058	0.43	YES
13	POLR3D	POLR3D	POLR3D	7189	0.036	0.38	NO
14	SSB	SSB	SSB	7666	0.027	0.38	NO
15	LZTS1	LZTS1	LZTS1	7739	0.026	0.39	NO
16	POLR3K	POLR3K	POLR3K	7833	0.024	0.4	NO
17	GTF3C4	GTF3C4	GTF3C4	7887	0.023	0.41	NO
18	POLR3C	POLR3C	POLR3C	8336	0.017	0.4	NO
19	BRF1	BRF1	BRF1	8361	0.016	0.4	NO
20	SNAPC4	SNAPC4	SNAPC4	9131	0.0043	0.37	NO
21	POLR2K	POLR2K	POLR2K	9300	0.0016	0.36	NO
22	POU2F1	POU2F1	POU2F1	9333	0.0011	0.36	NO
23	POLR3E	POLR3E	POLR3E	9526	-0.002	0.35	NO
24	POLR3F	POLR3F	POLR3F	9634	-0.0036	0.34	NO
25	POLR3B	POLR3B	POLR3B	9646	-0.0038	0.35	NO
26	SNAPC3	SNAPC3	SNAPC3	9650	-0.0038	0.35	NO
27	POLR1C	POLR1C	POLR1C	10010	-0.01	0.34	NO
28	POLR2L	POLR2L	POLR2L	10611	-0.02	0.32	NO
29	ZNF143	ZNF143	ZNF143	10650	-0.021	0.33	NO
30	NFIB	NFIB	NFIB	10704	-0.022	0.34	NO
31	POLR3GL	POLR3GL	POLR3GL	10729	-0.023	0.35	NO
32	TBP	TBP	TBP	11878	-0.045	0.32	NO
33	POLR3A	POLR3A	POLR3A	13398	-0.082	0.29	NO

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

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: WNT SIGNALING, 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 REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES

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	NUP210	NUP210	NUP210	1769	0.25	0.053	YES
2	SLC25A4	SLC25A4	SLC25A4	3294	0.14	0.053	YES
3	NUP205	NUP205	NUP205	4504	0.095	0.044	YES
4	NUP93	NUP93	NUP93	4507	0.095	0.099	YES
5	NUP37	NUP37	NUP37	4582	0.092	0.15	YES
6	KPNA1	KPNA1	KPNA1	4768	0.086	0.19	YES
7	SLC25A5	SLC25A5	SLC25A5	5456	0.069	0.19	YES
8	NUP35	NUP35	NUP35	5943	0.059	0.2	YES
9	NUP155	NUP155	NUP155	5967	0.058	0.23	YES
10	PSIP1	PSIP1	PSIP1	6057	0.056	0.26	YES
11	BANF1	BANF1	BANF1	6073	0.056	0.29	YES
12	NUP133	NUP133	NUP133	6185	0.054	0.32	YES
13	AAAS	AAAS	AAAS	6252	0.052	0.34	YES
14	NUPL2	NUPL2	NUPL2	6275	0.052	0.37	YES
15	NUP188	NUP188	NUP188	6310	0.051	0.4	YES
16	NUP88	NUP88	NUP88	6716	0.044	0.4	YES
17	NUP62	NUP62	NUP62	7161	0.036	0.4	YES
18	NUP214	NUP214	NUP214	7292	0.034	0.42	YES
19	NUP153	NUP153	NUP153	7446	0.031	0.42	YES
20	NUP50	NUP50	NUP50	7608	0.028	0.43	YES
21	RAE1	RAE1	RAE1	7702	0.026	0.44	YES
22	POM121	POM121	POM121	7880	0.023	0.45	YES
23	NUP107	NUP107	NUP107	8000	0.022	0.45	YES
24	NUP54	NUP54	NUP54	8046	0.021	0.46	YES
25	SEH1L	SEH1L	SEH1L	8476	0.015	0.45	NO
26	HMGA1	HMGA1	HMGA1	9267	0.0021	0.41	NO
27	NUP85	NUP85	NUP85	10072	-0.011	0.37	NO
28	TPR	TPR	TPR	10224	-0.014	0.37	NO
29	SLC25A6	SLC25A6	SLC25A6	10521	-0.019	0.37	NO
30	NUPL1	NUPL1	NUPL1	10660	-0.022	0.37	NO
31	RANBP2	RANBP2	RANBP2	12092	-0.05	0.32	NO
32	NUP43	NUP43	NUP43	12285	-0.054	0.34	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: SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES, 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 P75NTRPATHWAY

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	SNAPC1	SNAPC1	SNAPC1	1659	0.26	0.11	YES
2	SNAPC5	SNAPC5	SNAPC5	3871	0.12	0.082	YES
3	POLR2H	POLR2H	POLR2H	3962	0.11	0.16	YES
4	BRF2	BRF2	BRF2	4460	0.096	0.21	YES
5	SNAPC2	SNAPC2	SNAPC2	4495	0.095	0.28	YES
6	POLR1D	POLR1D	POLR1D	4838	0.084	0.32	YES
7	POLR2F	POLR2F	POLR2F	4843	0.084	0.39	YES
8	POLR2E	POLR2E	POLR2E	4957	0.081	0.44	YES
9	POLR3H	POLR3H	POLR3H	5815	0.061	0.44	YES
10	POLR3D	POLR3D	POLR3D	7189	0.036	0.4	NO
11	LZTS1	LZTS1	LZTS1	7739	0.026	0.39	NO
12	POLR3K	POLR3K	POLR3K	7833	0.024	0.4	NO
13	POLR3C	POLR3C	POLR3C	8336	0.017	0.39	NO
14	SNAPC4	SNAPC4	SNAPC4	9131	0.0043	0.35	NO
15	POLR2K	POLR2K	POLR2K	9300	0.0016	0.34	NO
16	POU2F1	POU2F1	POU2F1	9333	0.0011	0.34	NO
17	POLR3E	POLR3E	POLR3E	9526	-0.002	0.33	NO
18	POLR3F	POLR3F	POLR3F	9634	-0.0036	0.33	NO
19	POLR3B	POLR3B	POLR3B	9646	-0.0038	0.33	NO
20	SNAPC3	SNAPC3	SNAPC3	9650	-0.0038	0.33	NO
21	POLR1C	POLR1C	POLR1C	10010	-0.01	0.32	NO
22	POLR2L	POLR2L	POLR2L	10611	-0.02	0.3	NO
23	ZNF143	ZNF143	ZNF143	10650	-0.021	0.32	NO
24	POLR3GL	POLR3GL	POLR3GL	10729	-0.023	0.33	NO
25	TBP	TBP	TBP	11878	-0.045	0.3	NO
26	POLR3A	POLR3A	POLR3A	13398	-0.082	0.29	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 P75NTRPATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: PID P75NTRPATHWAY, 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 TRKRPATHWAY

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	TP63	TP63	TP63	136	0.73	0.079	YES
2	CLCA2	CLCA2	CLCA2	287	0.6	0.14	YES
3	SMARCD3	SMARCD3	SMARCD3	562	0.48	0.18	YES
4	TFAP2C	TFAP2C	TFAP2C	570	0.47	0.24	YES
5	S100A2	S100A2	S100A2	638	0.45	0.29	YES
6	GPX2	GPX2	GPX2	821	0.4	0.33	YES
7	IGFBP3	IGFBP3	IGFBP3	1208	0.33	0.35	YES
8	NQO1	NQO1	NQO1	1500	0.28	0.36	YES
9	EGR2	EGR2	EGR2	1517	0.28	0.4	YES
10	SERPINB5	SERPINB5	SERPINB5	1708	0.26	0.42	YES
11	PERP	PERP	PERP	1957	0.23	0.43	YES
12	PMAIP1	PMAIP1	PMAIP1	2085	0.22	0.45	YES
13	FDXR	FDXR	FDXR	2177	0.21	0.47	YES
14	DST	DST	DST	3652	0.12	0.41	NO
15	FLOT2	FLOT2	FLOT2	3866	0.12	0.41	NO
16	EVPL	EVPL	EVPL	3875	0.12	0.42	NO
17	DHRS3	DHRS3	DHRS3	4290	0.1	0.41	NO
18	IKBKB	IKBKB	IKBKB	4558	0.093	0.41	NO
19	YWHAQ	YWHAQ	YWHAQ	4932	0.082	0.4	NO
20	HBP1	HBP1	HBP1	5710	0.063	0.36	NO
21	JAG1	JAG1	JAG1	6127	0.055	0.35	NO
22	BAX	BAX	BAX	6179	0.054	0.35	NO
23	ADA	ADA	ADA	6778	0.043	0.33	NO
24	MDM2	MDM2	MDM2	7197	0.036	0.31	NO
25	SSRP1	SSRP1	SSRP1	7900	0.023	0.27	NO
26	ABL1	ABL1	ABL1	8133	0.02	0.26	NO
27	GADD45A	GADD45A	GADD45A	8776	0.01	0.23	NO
28	EP300	EP300	EP300	9002	0.0066	0.22	NO
29	MFGE8	MFGE8	MFGE8	9185	0.0034	0.21	NO
30	CDKN1A	CDKN1A	CDKN1A	9289	0.0018	0.2	NO
31	BBC3	BBC3	BBC3	9291	0.0018	0.2	NO
32	DICER1	DICER1	DICER1	9545	-0.0023	0.19	NO
33	WWP1	WWP1	WWP1	9632	-0.0036	0.19	NO
34	PLK1	PLK1	PLK1	9686	-0.0044	0.18	NO
35	SP1	SP1	SP1	9939	-0.0091	0.17	NO
36	PML	PML	PML	10235	-0.014	0.16	NO
37	ITGB4	ITGB4	ITGB4	10376	-0.016	0.15	NO
38	FAS	FAS	FAS	11276	-0.033	0.11	NO
39	SSPO	SSPO	SSPO	11291	-0.034	0.11	NO
40	TRAF4	TRAF4	TRAF4	11799	-0.043	0.089	NO
41	ITCH	ITCH	ITCH	12701	-0.064	0.049	NO
42	OGG1	OGG1	OGG1	12998	-0.071	0.041	NO
43	NOC2L	NOC2L	NOC2L	13068	-0.073	0.046	NO
44	PRKCD	PRKCD	PRKCD	13355	-0.08	0.04	NO
45	CHUK	CHUK	CHUK	13605	-0.088	0.037	NO
46	AEN	AEN	AEN	13779	-0.093	0.039	NO
47	SHH	SHH	SHH	13830	-0.095	0.048	NO
48	ITGA3	ITGA3	ITGA3	15114	-0.14	-0.0039	NO
49	SPATA18	SPATA18	SPATA18	15204	-0.15	0.0088	NO
50	TP53I3	TP53I3	TP53I3	15285	-0.15	0.023	NO
51	VDR	VDR	VDR	15709	-0.18	0.021	NO
52	GDF15	GDF15	GDF15	17590	-0.34	-0.04	NO
53	CDKN2A	CDKN2A	CDKN2A	17826	-0.38	-0.0072	NO
54	CABLES1	CABLES1	CABLES1	18224	-0.48	0.028	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 TRKRPATHWAY.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: PID TRKRPATHWAY, 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 HEDGEHOG GLIPATHWAY

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	PPP2R2B	PPP2R2B	PPP2R2B	128	0.74	0.15	YES
2	PPP2R2C	PPP2R2C	PPP2R2C	377	0.55	0.26	YES
3	PRKAA2	PRKAA2	PRKAA2	580	0.47	0.35	YES
4	PPP2R3A	PPP2R3A	PPP2R3A	1058	0.35	0.4	YES
5	PRKAR2B	PRKAR2B	PRKAR2B	1667	0.26	0.42	YES
6	PPP2R3B	PPP2R3B	PPP2R3B	2634	0.18	0.41	NO
7	PRKAG3	PRKAG3	PRKAG3	3530	0.13	0.39	NO
8	PPP2R5A	PPP2R5A	PPP2R5A	3861	0.12	0.4	NO
9	YWHAG	YWHAG	YWHAG	4750	0.087	0.37	NO
10	YWHAQ	YWHAQ	YWHAQ	4932	0.082	0.38	NO
11	YWHAE	YWHAE	YWHAE	5431	0.069	0.36	NO
12	PPP2R4	PPP2R4	PPP2R4	5547	0.067	0.37	NO
13	ACACA	ACACA	ACACA	5682	0.064	0.38	NO
14	PPP2R2D	PPP2R2D	PPP2R2D	6725	0.044	0.33	NO
15	FASN	FASN	FASN	7238	0.035	0.31	NO
16	PRKAG1	PRKAG1	PRKAG1	7241	0.035	0.32	NO
17	PRKACA	PRKACA	PRKACA	7334	0.033	0.32	NO
18	YWHAZ	YWHAZ	YWHAZ	7375	0.032	0.33	NO
19	PPP2CA	PPP2CA	PPP2CA	8471	0.015	0.27	NO
20	PRKACB	PRKACB	PRKACB	8801	0.01	0.26	NO
21	PPP2R5C	PPP2R5C	PPP2R5C	8856	0.0091	0.26	NO
22	PPP2R5D	PPP2R5D	PPP2R5D	9108	0.0048	0.24	NO
23	PPP2CB	PPP2CB	PPP2CB	9233	0.0026	0.24	NO
24	PPP2R5B	PPP2R5B	PPP2R5B	9483	-0.0012	0.22	NO
25	PPP2R2A	PPP2R2A	PPP2R2A	9628	-0.0036	0.22	NO
26	PRKAR1B	PRKAR1B	PRKAR1B	9887	-0.0082	0.2	NO
27	MLX	MLX	MLX	10092	-0.012	0.2	NO
28	PRKAR1A	PRKAR1A	PRKAR1A	10118	-0.012	0.2	NO
29	PRKAB2	PRKAB2	PRKAB2	10231	-0.014	0.19	NO
30	PRKAA1	PRKAA1	PRKAA1	10306	-0.015	0.19	NO
31	PPP2R1A	PPP2R1A	PPP2R1A	10448	-0.018	0.19	NO
32	PPP2R5E	PPP2R5E	PPP2R5E	10558	-0.02	0.19	NO
33	YWHAH	YWHAH	YWHAH	10769	-0.024	0.18	NO
34	PRKAB1	PRKAB1	PRKAB1	11409	-0.036	0.16	NO
35	PRKAG2	PRKAG2	PRKAG2	11440	-0.037	0.16	NO
36	GCK	GCK	GCK	11448	-0.037	0.17	NO
37	YWHAB	YWHAB	YWHAB	12111	-0.05	0.14	NO
38	PPP2R1B	PPP2R1B	PPP2R1B	13397	-0.082	0.094	NO
39	MLXIPL	MLXIPL	MLXIPL	13560	-0.086	0.1	NO
40	PKLR	PKLR	PKLR	14695	-0.12	0.07	NO
41	PRKAR2A	PRKAR2A	PRKAR2A	15619	-0.17	0.057	NO
42	PRKACG	PRKACG	PRKACG	18339	-0.51	0.022	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 HEDGEHOG GLIPATHWAY.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus5 enriched pathways

Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG PURINE METABOLISM	154	genes.ES.table	0.4	1.7	0.0063	0.19	0.91	0.21	0.16	0.18	0.094	0.024
KEGG TRYPTOPHAN METABOLISM	39	genes.ES.table	0.52	1.5	0.044	0.19	1	0.28	0.15	0.24	0.14	0.003
KEGG ABC TRANSPORTERS	43	genes.ES.table	0.55	1.5	0.035	0.18	1	0.21	0.083	0.19	0.13	0.004
KEGG MAPK SIGNALING PATHWAY	256	genes.ES.table	0.4	1.5	0.0096	0.18	0.99	0.32	0.26	0.24	0.12	0.004
KEGG CALCIUM SIGNALING PATHWAY	175	genes.ES.table	0.56	1.6	0.0023	0.19	0.93	0.46	0.22	0.36	0.094	0.023
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION	244	genes.ES.table	0.58	1.5	0.032	0.19	1	0.42	0.16	0.36	0.13	0.005
KEGG CHEMOKINE SIGNALING PATHWAY	186	genes.ES.table	0.61	1.7	0.0081	0.24	0.78	0.38	0.18	0.31	0.086	0.06
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM	76	genes.ES.table	0.4	1.5	0.051	0.18	1	0.33	0.25	0.25	0.13	0.004
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION	242	genes.ES.table	0.55	1.5	0.0074	0.18	0.99	0.43	0.18	0.35	0.12	0.004
KEGG LYSOSOME	121	genes.ES.table	0.34	1.6	0.052	0.17	0.96	0.5	0.4	0.3	0.099	0.011

genes ES table in pathway: KEGG PURINE METABOLISM

Table S41. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IGF1	IGF1	IGF1	151	0.94	0.1	YES
2	PIK3CG	PIK3CG	PIK3CG	466	0.77	0.18	YES
3	PIK3R5	PIK3R5	PIK3R5	589	0.72	0.26	YES
4	FIGF	FIGF	FIGF	784	0.67	0.32	YES
5	RPS6KA6	RPS6KA6	RPS6KA6	1637	0.49	0.34	YES
6	AKT3	AKT3	AKT3	1994	0.43	0.37	YES
7	PRKAA2	PRKAA2	PRKAA2	2160	0.41	0.41	YES
8	VEGFC	VEGFC	VEGFC	2187	0.4	0.46	YES
9	CAB39L	CAB39L	CAB39L	2477	0.36	0.48	YES
10	PIK3CD	PIK3CD	PIK3CD	2845	0.32	0.5	YES
11	PIK3R1	PIK3R1	PIK3R1	3194	0.28	0.52	YES
12	RPS6KA2	RPS6KA2	RPS6KA2	3868	0.22	0.51	NO
13	PIK3R3	PIK3R3	PIK3R3	4641	0.17	0.48	NO
14	VEGFB	VEGFB	VEGFB	4843	0.16	0.49	NO
15	ULK2	ULK2	ULK2	4881	0.15	0.51	NO
16	PIK3CA	PIK3CA	PIK3CA	6306	0.09	0.44	NO
17	RPS6KA3	RPS6KA3	RPS6KA3	6506	0.083	0.44	NO
18	RICTOR	RICTOR	RICTOR	6724	0.076	0.44	NO
19	STRADA	STRADA	STRADA	7121	0.064	0.43	NO
20	ULK1	ULK1	ULK1	7455	0.054	0.41	NO
21	BRAF	BRAF	BRAF	7839	0.044	0.4	NO
22	EIF4B	EIF4B	EIF4B	7910	0.042	0.4	NO
23	MTOR	MTOR	MTOR	8400	0.03	0.38	NO
24	RPS6	RPS6	RPS6	8645	0.024	0.37	NO
25	RPTOR	RPTOR	RPTOR	8668	0.023	0.37	NO
26	AKT2	AKT2	AKT2	8672	0.023	0.37	NO
27	TSC2	TSC2	TSC2	8705	0.022	0.37	NO
28	TSC1	TSC1	TSC1	8783	0.02	0.37	NO
29	HIF1A	HIF1A	HIF1A	8959	0.016	0.36	NO
30	RPS6KB1	RPS6KB1	RPS6KB1	9041	0.014	0.36	NO
31	PIK3CB	PIK3CB	PIK3CB	9191	0.011	0.35	NO
32	PRKAA1	PRKAA1	PRKAA1	9320	0.0086	0.35	NO
33	PGF	PGF	PGF	9343	0.0082	0.35	NO
34	STK11	STK11	STK11	9962	-0.0042	0.32	NO
35	MAPK1	MAPK1	MAPK1	10237	-0.01	0.3	NO
36	PDPK1	PDPK1	PDPK1	10781	-0.021	0.28	NO
37	AKT1	AKT1	AKT1	10842	-0.022	0.27	NO
38	MAPK3	MAPK3	MAPK3	11157	-0.028	0.26	NO
39	CAB39	CAB39	CAB39	11217	-0.029	0.26	NO
40	RHEB	RHEB	RHEB	11505	-0.035	0.25	NO
41	EIF4E	EIF4E	EIF4E	11636	-0.038	0.25	NO
42	RPS6KA1	RPS6KA1	RPS6KA1	12422	-0.054	0.21	NO
43	PIK3R2	PIK3R2	PIK3R2	13461	-0.078	0.17	NO
44	DDIT4	DDIT4	DDIT4	14043	-0.092	0.14	NO
45	ULK3	ULK3	ULK3	14177	-0.096	0.15	NO
46	EIF4E2	EIF4E2	EIF4E2	14300	-0.099	0.16	NO
47	RPS6KB2	RPS6KB2	RPS6KB2	14652	-0.11	0.15	NO
48	MLST8	MLST8	MLST8	15033	-0.12	0.14	NO
49	EIF4EBP1	EIF4EBP1	EIF4EBP1	17055	-0.23	0.062	NO
50	VEGFA	VEGFA	VEGFA	17128	-0.24	0.087	NO

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

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

genes ES table in pathway: KEGG TRYPTOPHAN METABOLISM

Table S42. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ITGA8	ITGA8	ITGA8	135	0.95	0.069	YES
2	SLC2A4	SLC2A4	SLC2A4	276	0.86	0.13	YES
3	AVPR2	AVPR2	AVPR2	277	0.86	0.2	YES
4	AGTR1	AGTR1	AGTR1	291	0.85	0.27	YES
5	ITGA9	ITGA9	ITGA9	425	0.78	0.32	YES
6	ITGA7	ITGA7	ITGA7	628	0.71	0.37	YES
7	ITGA10	ITGA10	ITGA10	798	0.66	0.41	YES
8	ACAP1	ACAP1	ACAP1	854	0.65	0.46	YES
9	IL2RA	IL2RA	IL2RA	1095	0.6	0.5	YES
10	EDNRB	EDNRB	EDNRB	1130	0.59	0.54	YES
11	ITGA4	ITGA4	ITGA4	1354	0.55	0.57	YES
12	TSHR	TSHR	TSHR	1428	0.54	0.61	YES
13	CPE	CPE	CPE	1566	0.5	0.64	YES
14	ITGA11	ITGA11	ITGA11	2127	0.41	0.65	YES
15	ITGA1	ITGA1	ITGA1	2517	0.36	0.66	YES
16	PIP5K1C	PIP5K1C	PIP5K1C	4243	0.19	0.58	NO
17	ITGAV	ITGAV	ITGAV	5316	0.13	0.53	NO
18	ADRB2	ADRB2	ADRB2	5625	0.12	0.52	NO
19	ITGA5	ITGA5	ITGA5	6119	0.096	0.51	NO
20	MAPK8IP3	MAPK8IP3	MAPK8IP3	6228	0.092	0.51	NO
21	ITGB1	ITGB1	ITGB1	6891	0.07	0.48	NO
22	EXOC2	EXOC2	EXOC2	7343	0.058	0.46	NO
23	KLC1	KLC1	KLC1	7388	0.057	0.46	NO
24	EXOC6	EXOC6	EXOC6	7532	0.052	0.46	NO
25	EXOC5	EXOC5	EXOC5	8236	0.034	0.42	NO
26	EXOC4	EXOC4	EXOC4	8273	0.033	0.42	NO
27	EXOC7	EXOC7	EXOC7	8455	0.029	0.42	NO
28	VAMP3	VAMP3	VAMP3	8918	0.016	0.39	NO
29	SPAG9	SPAG9	SPAG9	8961	0.016	0.39	NO
30	EXOC1	EXOC1	EXOC1	10325	-0.012	0.32	NO
31	CTNNB1	CTNNB1	CTNNB1	10472	-0.015	0.31	NO
32	EXOC3	EXOC3	EXOC3	10676	-0.019	0.3	NO
33	DNM2	DNM2	DNM2	11520	-0.036	0.26	NO
34	ARF6	ARF6	ARF6	11790	-0.041	0.25	NO
35	BIN1	BIN1	BIN1	11889	-0.043	0.25	NO
36	PLD2	PLD2	PLD2	12358	-0.053	0.23	NO
37	CLTC	CLTC	CLTC	12426	-0.054	0.23	NO
38	PLD1	PLD1	PLD1	12660	-0.06	0.22	NO
39	ITGA2	ITGA2	ITGA2	13103	-0.07	0.2	NO
40	CTNNA1	CTNNA1	CTNNA1	13342	-0.075	0.2	NO
41	SCAMP2	SCAMP2	SCAMP2	13978	-0.09	0.17	NO
42	CTNND1	CTNND1	CTNND1	14297	-0.099	0.16	NO
43	RALA	RALA	RALA	15018	-0.12	0.13	NO
44	ASAP2	ASAP2	ASAP2	15063	-0.12	0.14	NO
45	ITGA3	ITGA3	ITGA3	15736	-0.15	0.12	NO
46	NME1	NME1	NME1	16288	-0.18	0.1	NO
47	ITGA6	ITGA6	ITGA6	16344	-0.18	0.11	NO
48	CDH1	CDH1	CDH1	16729	-0.21	0.11	NO

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

Figure S84. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TRYPTOPHAN 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 ABC TRANSPORTERS

Table S43. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FLT3	FLT3	FLT3	60	1.1	0.092	YES
2	ZBTB16	ZBTB16	ZBTB16	77	1	0.18	YES
3	RUNX1T1	RUNX1T1	RUNX1T1	136	0.95	0.26	YES
4	PIK3CG	PIK3CG	PIK3CG	466	0.77	0.31	YES
5	PIK3R5	PIK3R5	PIK3R5	589	0.72	0.37	YES
6	KIT	KIT	KIT	630	0.71	0.43	YES
7	SPI1	SPI1	SPI1	1466	0.53	0.43	YES
8	AKT3	AKT3	AKT3	1994	0.43	0.44	YES
9	LEF1	LEF1	LEF1	2441	0.37	0.45	YES
10	PIM2	PIM2	PIM2	2475	0.36	0.48	YES
11	PIK3CD	PIK3CD	PIK3CD	2845	0.32	0.49	YES
12	PIK3R1	PIK3R1	PIK3R1	3194	0.28	0.5	YES
13	STAT5A	STAT5A	STAT5A	3423	0.26	0.51	YES
14	TCF7L1	TCF7L1	TCF7L1	3629	0.24	0.52	YES
15	TCF7	TCF7	TCF7	3882	0.22	0.52	YES
16	STAT5B	STAT5B	STAT5B	4489	0.18	0.51	NO
17	PIK3R3	PIK3R3	PIK3R3	4641	0.17	0.51	NO
18	SOS2	SOS2	SOS2	5457	0.12	0.48	NO
19	RUNX1	RUNX1	RUNX1	5644	0.12	0.48	NO
20	RARA	RARA	RARA	5928	0.1	0.47	NO
21	PIK3CA	PIK3CA	PIK3CA	6306	0.09	0.46	NO
22	NFKB1	NFKB1	NFKB1	6664	0.078	0.45	NO
23	IKBKB	IKBKB	IKBKB	6765	0.074	0.45	NO
24	PIM1	PIM1	PIM1	7160	0.063	0.44	NO
25	BRAF	BRAF	BRAF	7839	0.044	0.4	NO
26	PML	PML	PML	7973	0.041	0.4	NO
27	MTOR	MTOR	MTOR	8400	0.03	0.38	NO
28	SOS1	SOS1	SOS1	8517	0.027	0.38	NO
29	STAT3	STAT3	STAT3	8641	0.024	0.37	NO
30	AKT2	AKT2	AKT2	8672	0.023	0.37	NO
31	RAF1	RAF1	RAF1	8957	0.016	0.36	NO
32	RPS6KB1	RPS6KB1	RPS6KB1	9041	0.014	0.35	NO
33	ARAF	ARAF	ARAF	9066	0.013	0.35	NO
34	GRB2	GRB2	GRB2	9071	0.013	0.36	NO
35	PIK3CB	PIK3CB	PIK3CB	9191	0.011	0.35	NO
36	BAD	BAD	BAD	9780	-0.00056	0.32	NO
37	RELA	RELA	RELA	9850	-0.0018	0.32	NO
38	MAP2K2	MAP2K2	MAP2K2	10161	-0.0085	0.3	NO
39	MAPK1	MAPK1	MAPK1	10237	-0.01	0.3	NO
40	AKT1	AKT1	AKT1	10842	-0.022	0.26	NO
41	KRAS	KRAS	KRAS	10908	-0.023	0.26	NO
42	TCF7L2	TCF7L2	TCF7L2	11051	-0.026	0.26	NO
43	MAPK3	MAPK3	MAPK3	11157	-0.028	0.26	NO
44	IKBKG	IKBKG	IKBKG	11455	-0.034	0.24	NO
45	CHUK	CHUK	CHUK	11542	-0.036	0.24	NO
46	PPARD	PPARD	PPARD	12456	-0.055	0.2	NO
47	CCND1	CCND1	CCND1	12647	-0.059	0.19	NO
48	PIK3R2	PIK3R2	PIK3R2	13461	-0.078	0.16	NO
49	MYC	MYC	MYC	13915	-0.089	0.14	NO
50	MAP2K1	MAP2K1	MAP2K1	13954	-0.09	0.14	NO
51	NRAS	NRAS	NRAS	14139	-0.095	0.14	NO
52	RPS6KB2	RPS6KB2	RPS6KB2	14652	-0.11	0.12	NO
53	CEBPA	CEBPA	CEBPA	15385	-0.14	0.098	NO
54	CCNA1	CCNA1	CCNA1	16147	-0.17	0.073	NO
55	HRAS	HRAS	HRAS	17024	-0.23	0.046	NO
56	EIF4EBP1	EIF4EBP1	EIF4EBP1	17055	-0.23	0.065	NO
57	JUP	JUP	JUP	17683	-0.29	0.057	NO

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

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

genes ES table in pathway: KEGG MAPK SIGNALING PATHWAY

Table S44. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	BTK	BTK	BTK	280	0.86	0.069	YES
2	CD22	CD22	CD22	541	0.74	0.13	YES
3	VAV1	VAV1	VAV1	625	0.71	0.19	YES
4	MAP4K1	MAP4K1	MAP4K1	633	0.71	0.26	YES
5	ITPR1	ITPR1	ITPR1	905	0.64	0.31	YES
6	PTPRC	PTPRC	PTPRC	1016	0.62	0.36	YES
7	BCL2	BCL2	BCL2	1151	0.59	0.41	YES
8	CD19	CD19	CD19	1393	0.54	0.45	YES
9	PLCG2	PLCG2	PLCG2	1818	0.46	0.48	YES
10	NFATC2	NFATC2	NFATC2	1823	0.46	0.52	YES
11	INPP5D	INPP5D	INPP5D	1889	0.45	0.56	YES
12	AKT3	AKT3	AKT3	1994	0.43	0.6	YES
13	CR2	CR2	CR2	2066	0.42	0.64	YES
14	PIK3CD	PIK3CD	PIK3CD	2845	0.32	0.62	YES
15	PIK3R1	PIK3R1	PIK3R1	3194	0.28	0.63	YES
16	NFATC1	NFATC1	NFATC1	3954	0.21	0.62	YES
17	ITPR2	ITPR2	ITPR2	4094	0.2	0.63	YES
18	PPP3CC	PPP3CC	PPP3CC	4150	0.2	0.64	YES
19	CD81	CD81	CD81	4806	0.16	0.62	NO
20	SOS2	SOS2	SOS2	5457	0.12	0.6	NO
21	BLNK	BLNK	BLNK	5711	0.11	0.6	NO
22	PPP3CB	PPP3CB	PPP3CB	5754	0.11	0.61	NO
23	PIK3CA	PIK3CA	PIK3CA	6306	0.09	0.59	NO
24	LYN	LYN	LYN	7450	0.055	0.53	NO
25	PDK1	PDK1	PDK1	7930	0.042	0.51	NO
26	SYK	SYK	SYK	7935	0.042	0.51	NO
27	FLOT1	FLOT1	FLOT1	8001	0.04	0.51	NO
28	SOS1	SOS1	SOS1	8517	0.027	0.49	NO
29	AKT2	AKT2	AKT2	8672	0.023	0.48	NO
30	PPP3CA	PPP3CA	PPP3CA	8872	0.018	0.47	NO
31	DAG1	DAG1	DAG1	8885	0.018	0.48	NO
32	RAF1	RAF1	RAF1	8957	0.016	0.47	NO
33	GRB2	GRB2	GRB2	9071	0.013	0.47	NO
34	FLOT2	FLOT2	FLOT2	9335	0.0083	0.45	NO
35	BAD	BAD	BAD	9780	-0.00056	0.43	NO
36	MAPK1	MAPK1	MAPK1	10237	-0.01	0.41	NO
37	CSK	CSK	CSK	10735	-0.02	0.38	NO
38	AKT1	AKT1	AKT1	10842	-0.022	0.38	NO
39	SHC1	SHC1	SHC1	11142	-0.028	0.37	NO
40	MAPK3	MAPK3	MAPK3	11157	-0.028	0.37	NO
41	GSK3B	GSK3B	GSK3B	11562	-0.036	0.35	NO
42	GSK3A	GSK3A	GSK3A	11893	-0.043	0.34	NO
43	PPP1R13B	PPP1R13B	PPP1R13B	12120	-0.047	0.33	NO
44	BCR	BCR	BCR	12502	-0.056	0.31	NO
45	NR0B2	NR0B2	NR0B2	13976	-0.09	0.24	NO
46	ITPR3	ITPR3	ITPR3	14717	-0.11	0.22	NO

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

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MAPK 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 CALCIUM SIGNALING PATHWAY

Table S45. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FCER1A	FCER1A	FCER1A	260	0.86	0.044	YES
2	ITK	ITK	ITK	278	0.86	0.1	YES
3	BTK	BTK	BTK	280	0.86	0.16	YES
4	KLRG1	KLRG1	KLRG1	302	0.84	0.22	YES
5	PRKCB	PRKCB	PRKCB	319	0.83	0.27	YES
6	FCGR2B	FCGR2B	FCGR2B	342	0.82	0.32	YES
7	VAV1	VAV1	VAV1	625	0.71	0.36	YES
8	MS4A2	MS4A2	MS4A2	914	0.64	0.38	YES
9	S1PR1	S1PR1	S1PR1	975	0.63	0.42	YES
10	LAT	LAT	LAT	1224	0.57	0.45	YES
11	LAT2	LAT2	LAT2	1418	0.54	0.48	YES
12	HCLS1	HCLS1	HCLS1	1471	0.52	0.51	YES
13	LCP2	LCP2	LCP2	1731	0.48	0.53	YES
14	NFATC2	NFATC2	NFATC2	1823	0.46	0.55	YES
15	INPP5D	INPP5D	INPP5D	1889	0.45	0.58	YES
16	WIPF1	WIPF1	WIPF1	1931	0.44	0.61	YES
17	FCER1G	FCER1G	FCER1G	2602	0.35	0.6	YES
18	PPAP2A	PPAP2A	PPAP2A	2686	0.34	0.61	YES
19	FYN	FYN	FYN	2797	0.33	0.63	YES
20	PIK3R1	PIK3R1	PIK3R1	3194	0.28	0.63	NO
21	GAB2	GAB2	GAB2	3939	0.22	0.6	NO
22	DUSP1	DUSP1	DUSP1	3977	0.21	0.62	NO
23	DOK1	DOK1	DOK1	4131	0.2	0.62	NO
24	PLA2G1B	PLA2G1B	PLA2G1B	4456	0.18	0.62	NO
25	PLCG1	PLCG1	PLCG1	5718	0.11	0.56	NO
26	MAP3K1	MAP3K1	MAP3K1	5776	0.11	0.56	NO
27	CBLB	CBLB	CBLB	5823	0.11	0.56	NO
28	FOS	FOS	FOS	6241	0.092	0.55	NO
29	PIK3CA	PIK3CA	PIK3CA	6306	0.09	0.55	NO
30	NFKB1	NFKB1	NFKB1	6664	0.078	0.54	NO
31	IKBKB	IKBKB	IKBKB	6765	0.074	0.54	NO
32	CBL	CBL	CBL	6956	0.068	0.53	NO
33	LYN	LYN	LYN	7450	0.055	0.51	NO
34	MAP2K7	MAP2K7	MAP2K7	7493	0.053	0.51	NO
35	RASA1	RASA1	RASA1	7517	0.053	0.51	NO
36	FER	FER	FER	7770	0.045	0.5	NO
37	SYK	SYK	SYK	7935	0.042	0.5	NO
38	PTPN13	PTPN13	PTPN13	8049	0.039	0.49	NO
39	SPHK1	SPHK1	SPHK1	8215	0.034	0.48	NO
40	JUN	JUN	JUN	8357	0.031	0.48	NO
41	SOS1	SOS1	SOS1	8517	0.027	0.47	NO
42	RAF1	RAF1	RAF1	8957	0.016	0.45	NO
43	GRB2	GRB2	GRB2	9071	0.013	0.45	NO
44	PTPN11	PTPN11	PTPN11	9307	0.0089	0.43	NO
45	RELA	RELA	RELA	9850	-0.0018	0.4	NO
46	MAP2K2	MAP2K2	MAP2K2	10161	-0.0085	0.39	NO
47	PAK2	PAK2	PAK2	10232	-0.01	0.39	NO
48	MAPK1	MAPK1	MAPK1	10237	-0.01	0.39	NO
49	AKT1	AKT1	AKT1	10842	-0.022	0.36	NO
50	SHC1	SHC1	SHC1	11142	-0.028	0.34	NO
51	MAPK3	MAPK3	MAPK3	11157	-0.028	0.34	NO
52	IKBKG	IKBKG	IKBKG	11455	-0.034	0.33	NO
53	MAP2K4	MAP2K4	MAP2K4	11499	-0.035	0.33	NO
54	CHUK	CHUK	CHUK	11542	-0.036	0.33	NO
55	PXN	PXN	PXN	11794	-0.041	0.32	NO
56	PLD2	PLD2	PLD2	12358	-0.053	0.29	NO
57	PTK2	PTK2	PTK2	12846	-0.064	0.27	NO
58	MAP2K1	MAP2K1	MAP2K1	13954	-0.09	0.22	NO
59	MAPK8	MAPK8	MAPK8	14059	-0.093	0.22	NO
60	HRAS	HRAS	HRAS	17024	-0.23	0.075	NO
61	PLA2G4A	PLA2G4A	PLA2G4A	17372	-0.26	0.074	NO

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

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

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

Table S46. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	VAV1	VAV1	VAV1	625	0.71	0.04	YES
2	KIT	KIT	KIT	630	0.71	0.11	YES
3	MAP4K1	MAP4K1	MAP4K1	633	0.71	0.18	YES
4	STAP1	STAP1	STAP1	659	0.7	0.26	YES
5	GRAP2	GRAP2	GRAP2	746	0.68	0.32	YES
6	BCL2	BCL2	BCL2	1151	0.59	0.36	YES
7	MITF	MITF	MITF	1182	0.58	0.42	YES
8	MATK	MATK	MATK	1664	0.49	0.44	YES
9	PTPRO	PTPRO	PTPRO	2244	0.4	0.45	YES
10	PIK3R1	PIK3R1	PIK3R1	3194	0.28	0.43	YES
11	SH2B2	SH2B2	SH2B2	3286	0.27	0.45	YES
12	STAT5A	STAT5A	STAT5A	3423	0.26	0.47	YES
13	JAK2	JAK2	JAK2	3425	0.26	0.5	YES
14	SH2B3	SH2B3	SH2B3	3668	0.24	0.51	YES
15	GAB1	GAB1	GAB1	3792	0.23	0.53	YES
16	EPOR	EPOR	EPOR	4130	0.2	0.53	YES
17	DOK1	DOK1	DOK1	4131	0.2	0.55	YES
18	SOCS1	SOCS1	SOCS1	4271	0.19	0.56	YES
19	TEC	TEC	TEC	4579	0.17	0.56	YES
20	PTPN6	PTPN6	PTPN6	4889	0.15	0.56	NO
21	KITLG	KITLG	KITLG	6150	0.095	0.5	NO
22	PIK3CA	PIK3CA	PIK3CA	6306	0.09	0.51	NO
23	PIK3C2B	PIK3C2B	PIK3C2B	6778	0.074	0.49	NO
24	CBL	CBL	CBL	6956	0.068	0.49	NO
25	PTEN	PTEN	PTEN	6974	0.068	0.49	NO
26	STAT1	STAT1	STAT1	7136	0.063	0.49	NO
27	FOXO3	FOXO3	FOXO3	7341	0.058	0.48	NO
28	LYN	LYN	LYN	7450	0.055	0.48	NO
29	FER	FER	FER	7770	0.045	0.47	NO
30	CREBBP	CREBBP	CREBBP	7811	0.044	0.48	NO
31	SPRED1	SPRED1	SPRED1	8374	0.031	0.45	NO
32	SOS1	SOS1	SOS1	8517	0.027	0.44	NO
33	STAT3	STAT3	STAT3	8641	0.024	0.44	NO
34	RAF1	RAF1	RAF1	8957	0.016	0.42	NO
35	RPS6KB1	RPS6KB1	RPS6KB1	9041	0.014	0.42	NO
36	GRB2	GRB2	GRB2	9071	0.013	0.42	NO
37	PTPN11	PTPN11	PTPN11	9307	0.0089	0.41	NO
38	SNAI2	SNAI2	SNAI2	9627	0.0026	0.39	NO
39	BAD	BAD	BAD	9780	-0.00056	0.38	NO
40	MAP2K2	MAP2K2	MAP2K2	10161	-0.0085	0.36	NO
41	PDPK1	PDPK1	PDPK1	10781	-0.021	0.33	NO
42	AKT1	AKT1	AKT1	10842	-0.022	0.33	NO
43	SHC1	SHC1	SHC1	11142	-0.028	0.32	NO
44	MAPK3	MAPK3	MAPK3	11157	-0.028	0.32	NO
45	SPRED2	SPRED2	SPRED2	11268	-0.03	0.32	NO
46	GSK3B	GSK3B	GSK3B	11562	-0.036	0.31	NO
47	CRKL	CRKL	CRKL	12903	-0.065	0.24	NO
48	GRB10	GRB10	GRB10	12933	-0.066	0.25	NO
49	MAP2K1	MAP2K1	MAP2K1	13954	-0.09	0.2	NO
50	MAPK8	MAPK8	MAPK8	14059	-0.093	0.21	NO
51	EPO	EPO	EPO	16688	-0.2	0.086	NO
52	HRAS	HRAS	HRAS	17024	-0.23	0.092	NO

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

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table S47. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	BTK	BTK	BTK	280	0.86	0.091	YES
2	PIK3R5	PIK3R5	PIK3R5	589	0.72	0.16	YES
3	VAV1	VAV1	VAV1	625	0.71	0.25	YES
4	ITPR1	ITPR1	ITPR1	905	0.64	0.32	YES
5	PTPRC	PTPRC	PTPRC	1016	0.62	0.39	YES
6	CD19	CD19	CD19	1393	0.54	0.43	YES
7	NR4A3	NR4A3	NR4A3	1530	0.51	0.49	YES
8	PLCG2	PLCG2	PLCG2	1818	0.46	0.53	YES
9	PREX1	PREX1	PREX1	1883	0.45	0.58	YES
10	AKT3	AKT3	AKT3	1994	0.43	0.63	YES
11	GAB1	GAB1	GAB1	3792	0.23	0.56	NO
12	RPS6KA2	RPS6KA2	RPS6KA2	3868	0.22	0.59	NO
13	ITPR2	ITPR2	ITPR2	4094	0.2	0.6	NO
14	DAPP1	DAPP1	DAPP1	4273	0.19	0.61	NO
15	CYTH3	CYTH3	CYTH3	5922	0.1	0.54	NO
16	PIK3CA	PIK3CA	PIK3CA	6306	0.09	0.53	NO
17	RPS6KA3	RPS6KA3	RPS6KA3	6506	0.083	0.53	NO
18	PHF11	PHF11	PHF11	6524	0.082	0.54	NO
19	PTEN	PTEN	PTEN	6974	0.068	0.52	NO
20	FOXO3	FOXO3	FOXO3	7341	0.058	0.51	NO
21	LYN	LYN	LYN	7450	0.055	0.51	NO
22	PDK1	PDK1	PDK1	7930	0.042	0.49	NO
23	SYK	SYK	SYK	7935	0.042	0.5	NO
24	FLOT1	FLOT1	FLOT1	8001	0.04	0.5	NO
25	AKT2	AKT2	AKT2	8672	0.023	0.46	NO
26	RPS6KB1	RPS6KB1	RPS6KB1	9041	0.014	0.45	NO
27	PITX2	PITX2	PITX2	9210	0.011	0.44	NO
28	FLOT2	FLOT2	FLOT2	9335	0.0083	0.43	NO
29	AKT1	AKT1	AKT1	10842	-0.022	0.36	NO
30	PPP1R13B	PPP1R13B	PPP1R13B	12120	-0.047	0.29	NO
31	RPS6KA1	RPS6KA1	RPS6KA1	12422	-0.054	0.28	NO
32	BCR	BCR	BCR	12502	-0.056	0.29	NO
33	NR0B2	NR0B2	NR0B2	13976	-0.09	0.22	NO
34	ITPR3	ITPR3	ITPR3	14717	-0.11	0.19	NO
35	CDKN2A	CDKN2A	CDKN2A	16228	-0.18	0.14	NO

Figure S93. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

Figure S94. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

Table S48. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TLR10	TLR10	TLR10	54	1.1	0.16	YES
2	TLR7	TLR7	TLR7	186	0.91	0.29	YES
3	TLR9	TLR9	TLR9	889	0.64	0.34	YES
4	TLR4	TLR4	TLR4	939	0.63	0.44	YES
5	LY96	LY96	LY96	1135	0.59	0.51	YES
6	TLR6	TLR6	TLR6	1630	0.49	0.56	YES
7	MAP3K14	MAP3K14	MAP3K14	2960	0.31	0.53	YES
8	CD14	CD14	CD14	2986	0.3	0.58	YES
9	TLR3	TLR3	TLR3	4061	0.2	0.55	NO
10	PGLYRP1	PGLYRP1	PGLYRP1	4415	0.18	0.56	NO
11	TIRAP	TIRAP	TIRAP	5643	0.12	0.51	NO
12	MAP3K1	MAP3K1	MAP3K1	5776	0.11	0.52	NO
13	FOS	FOS	FOS	6241	0.092	0.51	NO
14	NFKB1	NFKB1	NFKB1	6664	0.078	0.5	NO
15	IKBKB	IKBKB	IKBKB	6765	0.074	0.5	NO
16	TAB1	TAB1	TAB1	7231	0.061	0.49	NO
17	TLR2	TLR2	TLR2	7321	0.059	0.49	NO
18	TAB2	TAB2	TAB2	7522	0.052	0.49	NO
19	NFKBIA	NFKBIA	NFKBIA	8099	0.038	0.46	NO
20	JUN	JUN	JUN	8357	0.031	0.45	NO
21	TRAF6	TRAF6	TRAF6	8677	0.023	0.44	NO
22	PPARA	PPARA	PPARA	9726	0.00057	0.38	NO
23	MAPK14	MAPK14	MAPK14	9842	-0.0016	0.38	NO
24	RELA	RELA	RELA	9850	-0.0018	0.38	NO
25	ELK1	ELK1	ELK1	10073	-0.0066	0.37	NO
26	MYD88	MYD88	MYD88	10242	-0.01	0.36	NO
27	ECSIT	ECSIT	ECSIT	10451	-0.015	0.35	NO
28	MAP3K7	MAP3K7	MAP3K7	10559	-0.017	0.35	NO
29	IKBKG	IKBKG	IKBKG	11455	-0.034	0.3	NO
30	MAP2K4	MAP2K4	MAP2K4	11499	-0.035	0.31	NO
31	CHUK	CHUK	CHUK	11542	-0.036	0.31	NO
32	TOLLIP	TOLLIP	TOLLIP	12184	-0.049	0.28	NO
33	MAP2K6	MAP2K6	MAP2K6	12394	-0.054	0.28	NO
34	EIF2AK2	EIF2AK2	EIF2AK2	13957	-0.09	0.21	NO
35	MAPK8	MAPK8	MAPK8	14059	-0.093	0.22	NO
36	MAP2K3	MAP2K3	MAP2K3	14140	-0.095	0.23	NO
37	IRAK1	IRAK1	IRAK1	15253	-0.13	0.19	NO

Figure S95. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

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

genes ES table in pathway: KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION

Table S49. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ITGA8	ITGA8	ITGA8	135	0.95	0.03	YES
2	PIK3R6	PIK3R6	PIK3R6	287	0.85	0.056	YES
3	CXCL12	CXCL12	CXCL12	358	0.82	0.084	YES
4	ITGA9	ITGA9	ITGA9	425	0.78	0.11	YES
5	PIK3CG	PIK3CG	PIK3CG	466	0.77	0.14	YES
6	PIK3R5	PIK3R5	PIK3R5	589	0.72	0.16	YES
7	VAV1	VAV1	VAV1	625	0.71	0.19	YES
8	ITGA7	ITGA7	ITGA7	628	0.71	0.22	YES
9	GNAO1	GNAO1	GNAO1	646	0.7	0.24	YES
10	ITGA10	ITGA10	ITGA10	798	0.66	0.26	YES
11	CD3G	CD3G	CD3G	849	0.65	0.28	YES
12	FGR	FGR	FGR	902	0.64	0.3	YES
13	CD3E	CD3E	CD3E	990	0.62	0.32	YES
14	PTPRC	PTPRC	PTPRC	1016	0.62	0.35	YES
15	PLCB2	PLCB2	PLCB2	1048	0.61	0.37	YES
16	CD247	CD247	CD247	1126	0.59	0.39	YES
17	BLK	BLK	BLK	1195	0.58	0.41	YES
18	CD3D	CD3D	CD3D	1245	0.57	0.43	YES
19	ITGA4	ITGA4	ITGA4	1354	0.55	0.44	YES
20	CD4	CD4	CD4	1455	0.53	0.46	YES
21	LCK	LCK	LCK	1469	0.53	0.48	YES
22	GNG2	GNG2	GNG2	1498	0.52	0.5	YES
23	CXCR4	CXCR4	CXCR4	1555	0.51	0.52	YES
24	RGS1	RGS1	RGS1	1675	0.49	0.53	YES
25	INPP5D	INPP5D	INPP5D	1889	0.45	0.53	YES
26	HCK	HCK	HCK	1937	0.44	0.55	YES
27	GNAZ	GNAZ	GNAZ	2055	0.42	0.56	YES
28	ITGA11	ITGA11	ITGA11	2127	0.41	0.57	YES
29	ITGA1	ITGA1	ITGA1	2517	0.36	0.56	YES
30	HLA-DRB1	HLA-DRB1	HLA-DRB1	2649	0.34	0.57	YES
31	HLA-DRA	HLA-DRA	HLA-DRA	2698	0.34	0.58	YES
32	FYN	FYN	FYN	2797	0.33	0.59	YES
33	PIK3CD	PIK3CD	PIK3CD	2845	0.32	0.6	YES
34	PIK3R1	PIK3R1	PIK3R1	3194	0.28	0.59	YES
35	STAT5A	STAT5A	STAT5A	3423	0.26	0.59	YES
36	JAK2	JAK2	JAK2	3425	0.26	0.6	YES
37	MMP9	MMP9	MMP9	3622	0.24	0.6	NO
38	PAG1	PAG1	PAG1	4411	0.18	0.56	NO
39	STAT5B	STAT5B	STAT5B	4489	0.18	0.57	NO
40	FOXO1	FOXO1	FOXO1	4544	0.17	0.57	NO
41	PLCB1	PLCB1	PLCB1	4587	0.17	0.58	NO
42	ARRB2	ARRB2	ARRB2	4623	0.17	0.58	NO
43	PIK3R3	PIK3R3	PIK3R3	4641	0.17	0.59	NO
44	PTPN6	PTPN6	PTPN6	4889	0.15	0.58	NO
45	GNAI2	GNAI2	GNAI2	5053	0.14	0.58	NO
46	ITGAV	ITGAV	ITGAV	5316	0.13	0.57	NO
47	RHOB	RHOB	RHOB	5366	0.13	0.57	NO
48	STAT2	STAT2	STAT2	5379	0.13	0.57	NO
49	DNM1	DNM1	DNM1	6000	0.1	0.55	NO
50	SSH1	SSH1	SSH1	6023	0.1	0.55	NO
51	ITGA5	ITGA5	ITGA5	6119	0.096	0.55	NO
52	PIK3CA	PIK3CA	PIK3CA	6306	0.09	0.54	NO
53	RICTOR	RICTOR	RICTOR	6724	0.076	0.52	NO
54	ITGB1	ITGB1	ITGB1	6891	0.07	0.51	NO
55	PTK2B	PTK2B	PTK2B	6900	0.07	0.52	NO
56	PTEN	PTEN	PTEN	6974	0.068	0.52	NO
57	STAT1	STAT1	STAT1	7136	0.063	0.51	NO
58	GNA13	GNA13	GNA13	7330	0.058	0.5	NO
59	LYN	LYN	LYN	7450	0.055	0.5	NO
60	RAP1B	RAP1B	RAP1B	8087	0.038	0.46	NO
61	RHOA	RHOA	RHOA	8254	0.033	0.46	NO
62	MTOR	MTOR	MTOR	8400	0.03	0.45	NO
63	STAT3	STAT3	STAT3	8641	0.024	0.44	NO
64	GNB1	GNB1	GNB1	8671	0.023	0.44	NO
65	LIMK1	LIMK1	LIMK1	8732	0.021	0.44	NO
66	ADRBK1	ADRBK1	ADRBK1	8747	0.021	0.44	NO
67	PIK3CB	PIK3CB	PIK3CB	9191	0.011	0.41	NO
68	GRK6	GRK6	GRK6	9223	0.01	0.41	NO
69	PTPN11	PTPN11	PTPN11	9307	0.0089	0.41	NO
70	MAPKAP1	MAPKAP1	MAPKAP1	9570	0.0035	0.39	NO
71	BAD	BAD	BAD	9780	-0.00056	0.38	NO
72	GNAI1	GNAI1	GNAI1	10047	-0.0059	0.37	NO
73	CDC42	CDC42	CDC42	10168	-0.0086	0.36	NO
74	ITCH	ITCH	ITCH	10194	-0.0091	0.36	NO
75	GNB2L1	GNB2L1	GNB2L1	10375	-0.013	0.35	NO
76	CSK	CSK	CSK	10735	-0.02	0.33	NO
77	PDPK1	PDPK1	PDPK1	10781	-0.021	0.33	NO
78	CRK	CRK	CRK	10836	-0.022	0.33	NO
79	AKT1	AKT1	AKT1	10842	-0.022	0.33	NO
80	RHOC	RHOC	RHOC	11354	-0.032	0.3	NO
81	VPS4A	VPS4A	VPS4A	11366	-0.032	0.3	NO
82	PXN	PXN	PXN	11794	-0.041	0.28	NO
83	PAK1	PAK1	PAK1	12097	-0.047	0.27	NO
84	ARR3	ARR3	ARR3	12509	-0.056	0.25	NO
85	PTK2	PTK2	PTK2	12846	-0.064	0.23	NO
86	UBQLN1	UBQLN1	UBQLN1	13065	-0.069	0.22	NO
87	ITGA2	ITGA2	ITGA2	13103	-0.07	0.22	NO
88	CFL1	CFL1	CFL1	13239	-0.073	0.22	NO
89	GNAI3	GNAI3	GNAI3	13389	-0.076	0.22	NO
90	PIK3R2	PIK3R2	PIK3R2	13461	-0.078	0.22	NO
91	RALB	RALB	RALB	14415	-0.1	0.17	NO
92	HGS	HGS	HGS	14469	-0.1	0.17	NO
93	RAC1	RAC1	RAC1	14861	-0.12	0.15	NO
94	BCAR1	BCAR1	BCAR1	15014	-0.12	0.15	NO
95	VPS4B	VPS4B	VPS4B	15015	-0.12	0.15	NO
96	MLST8	MLST8	MLST8	15033	-0.12	0.16	NO
97	SRC	SRC	SRC	15611	-0.15	0.13	NO
98	ITGA3	ITGA3	ITGA3	15736	-0.15	0.13	NO
99	PRKCZ	PRKCZ	PRKCZ	16193	-0.17	0.11	NO
100	YES1	YES1	YES1	16269	-0.18	0.12	NO
101	ITGA6	ITGA6	ITGA6	16344	-0.18	0.12	NO
102	PLCB3	PLCB3	PLCB3	16755	-0.21	0.11	NO

Figure S97. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION.

Figure S98. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG LYSOSOME

Table S50. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PIK3R6	PIK3R6	PIK3R6	287	0.85	0.027	YES
2	MYOCD	MYOCD	MYOCD	298	0.84	0.068	YES
3	PIK3CG	PIK3CG	PIK3CG	466	0.77	0.097	YES
4	PIK3R5	PIK3R5	PIK3R5	589	0.72	0.13	YES
5	FGR	FGR	FGR	902	0.64	0.14	YES
6	S1PR1	S1PR1	S1PR1	975	0.63	0.17	YES
7	SLA	SLA	SLA	1027	0.62	0.2	YES
8	ITGB3	ITGB3	ITGB3	1140	0.59	0.22	YES
9	BLK	BLK	BLK	1195	0.58	0.25	YES
10	TAGLN	TAGLN	TAGLN	1325	0.55	0.27	YES
11	LCK	LCK	LCK	1469	0.53	0.28	YES
12	ACTA2	ACTA2	ACTA2	1543	0.51	0.31	YES
13	MAPK10	MAPK10	MAPK10	1557	0.51	0.33	YES
14	CYFIP2	CYFIP2	CYFIP2	1680	0.48	0.35	YES
15	HCK	HCK	HCK	1937	0.44	0.36	YES
16	PPP2R2B	PPP2R2B	PPP2R2B	2121	0.41	0.37	YES
17	FYN	FYN	FYN	2797	0.33	0.35	YES
18	PIK3CD	PIK3CD	PIK3CD	2845	0.32	0.36	YES
19	PDGFRB	PDGFRB	PDGFRB	3000	0.3	0.37	YES
20	PIK3R1	PIK3R1	PIK3R1	3194	0.28	0.37	YES
21	STAT5A	STAT5A	STAT5A	3423	0.26	0.37	YES
22	JAK2	JAK2	JAK2	3425	0.26	0.38	YES
23	DOCK4	DOCK4	DOCK4	3529	0.25	0.39	YES
24	GAB1	GAB1	GAB1	3792	0.23	0.39	YES
25	SIPA1	SIPA1	SIPA1	3829	0.22	0.4	YES
26	DOK1	DOK1	DOK1	4131	0.2	0.39	YES
27	RAP1A	RAP1A	RAP1A	4284	0.19	0.39	YES
28	PAG1	PAG1	PAG1	4411	0.18	0.4	YES
29	STAT5B	STAT5B	STAT5B	4489	0.18	0.4	YES
30	PIK3R3	PIK3R3	PIK3R3	4641	0.17	0.4	YES
31	PDGFB	PDGFB	PDGFB	4682	0.16	0.41	YES
32	RAPGEF1	RAPGEF1	RAPGEF1	4855	0.16	0.4	NO
33	PTPRJ	PTPRJ	PTPRJ	5024	0.15	0.4	NO
34	ITGAV	ITGAV	ITGAV	5316	0.13	0.39	NO
35	PRKCE	PRKCE	PRKCE	5438	0.12	0.39	NO
36	PLCG1	PLCG1	PLCG1	5718	0.11	0.38	NO
37	ABL1	ABL1	ABL1	5725	0.11	0.39	NO
38	LRP1	LRP1	LRP1	5833	0.11	0.39	NO
39	PRKCA	PRKCA	PRKCA	5896	0.1	0.39	NO
40	SLC9A3R2	SLC9A3R2	SLC9A3R2	6087	0.098	0.38	NO
41	FOS	FOS	FOS	6241	0.092	0.38	NO
42	PIK3CA	PIK3CA	PIK3CA	6306	0.09	0.38	NO
43	RPS6KA3	RPS6KA3	RPS6KA3	6506	0.083	0.38	NO
44	EPS8	EPS8	EPS8	6816	0.073	0.36	NO
45	ARAP1	ARAP1	ARAP1	6904	0.07	0.36	NO
46	CBL	CBL	CBL	6956	0.068	0.36	NO
47	PTEN	PTEN	PTEN	6974	0.068	0.36	NO
48	STAT1	STAT1	STAT1	7136	0.063	0.36	NO
49	YWHAH	YWHAH	YWHAH	7168	0.062	0.36	NO
50	LYN	LYN	LYN	7450	0.055	0.35	NO
51	MAP2K7	MAP2K7	MAP2K7	7493	0.053	0.35	NO
52	RASA1	RASA1	RASA1	7517	0.053	0.35	NO
53	BRAF	BRAF	BRAF	7839	0.044	0.34	NO
54	SRF	SRF	SRF	8083	0.038	0.32	NO
55	RAP1B	RAP1B	RAP1B	8087	0.038	0.32	NO
56	SPHK1	SPHK1	SPHK1	8215	0.034	0.32	NO
57	RHOA	RHOA	RHOA	8254	0.033	0.32	NO
58	NCK1	NCK1	NCK1	8310	0.032	0.32	NO
59	JUN	JUN	JUN	8357	0.031	0.32	NO
60	SOS1	SOS1	SOS1	8517	0.027	0.31	NO
61	JUND	JUND	JUND	8583	0.026	0.31	NO
62	STAT3	STAT3	STAT3	8641	0.024	0.31	NO
63	KSR1	KSR1	KSR1	8881	0.018	0.29	NO
64	RAF1	RAF1	RAF1	8957	0.016	0.29	NO
65	PTPN1	PTPN1	PTPN1	9051	0.014	0.29	NO
66	GRB2	GRB2	GRB2	9071	0.013	0.29	NO
67	PIN1	PIN1	PIN1	9116	0.012	0.28	NO
68	PIK3CB	PIK3CB	PIK3CB	9191	0.011	0.28	NO
69	PTPN11	PTPN11	PTPN11	9307	0.0089	0.28	NO
70	MAPK9	MAPK9	MAPK9	9618	0.0027	0.26	NO
71	ELK1	ELK1	ELK1	10073	-0.0066	0.24	NO
72	MAP2K2	MAP2K2	MAP2K2	10161	-0.0085	0.23	NO
73	WASF2	WASF2	WASF2	10211	-0.0095	0.23	NO
74	MAPK1	MAPK1	MAPK1	10237	-0.01	0.23	NO
75	IQGAP1	IQGAP1	IQGAP1	10404	-0.014	0.22	NO
76	ARPC1B	ARPC1B	ARPC1B	10434	-0.014	0.22	NO
77	RAB4A	RAB4A	RAB4A	10459	-0.015	0.22	NO
78	PTPN2	PTPN2	PTPN2	10513	-0.016	0.22	NO
79	RAB5A	RAB5A	RAB5A	10558	-0.017	0.21	NO
80	ARPC4	ARPC4	ARPC4	10587	-0.018	0.21	NO
81	CSK	CSK	CSK	10735	-0.02	0.21	NO
82	ACTR2	ACTR2	ACTR2	10791	-0.021	0.2	NO
83	CRK	CRK	CRK	10836	-0.022	0.2	NO
84	KRAS	KRAS	KRAS	10908	-0.023	0.2	NO
85	SHC1	SHC1	SHC1	11142	-0.028	0.19	NO
86	MAPK3	MAPK3	MAPK3	11157	-0.028	0.19	NO
87	ARPC5	ARPC5	ARPC5	11171	-0.028	0.19	NO
88	ARPC2	ARPC2	ARPC2	11249	-0.03	0.19	NO
89	ACTR3	ACTR3	ACTR3	11291	-0.031	0.19	NO
90	YWHAB	YWHAB	YWHAB	11329	-0.032	0.19	NO
91	ABI1	ABI1	ABI1	11461	-0.034	0.18	NO
92	MAP2K4	MAP2K4	MAP2K4	11499	-0.035	0.18	NO
93	DNM2	DNM2	DNM2	11520	-0.036	0.18	NO
94	WASL	WASL	WASL	11589	-0.037	0.18	NO
95	USP6NL	USP6NL	USP6NL	11605	-0.037	0.18	NO
96	PRKCD	PRKCD	PRKCD	11618	-0.038	0.18	NO
97	NCK2	NCK2	NCK2	11807	-0.041	0.18	NO
98	PPP2R1A	PPP2R1A	PPP2R1A	11863	-0.042	0.17	NO
99	PAK1	PAK1	PAK1	12097	-0.047	0.16	NO
100	ARHGDIA	ARHGDIA	ARHGDIA	12119	-0.047	0.16	NO
101	NCKAP1	NCKAP1	NCKAP1	12232	-0.05	0.16	NO
102	ARPC3	ARPC3	ARPC3	12258	-0.05	0.16	NO
103	ACTN4	ACTN4	ACTN4	12566	-0.057	0.15	NO
104	GRB10	GRB10	GRB10	12933	-0.066	0.13	NO
105	PPP2CA	PPP2CA	PPP2CA	13138	-0.07	0.12	NO
106	PIK3R2	PIK3R2	PIK3R2	13461	-0.078	0.11	NO
107	MLLT4	MLLT4	MLLT4	13793	-0.086	0.098	NO
108	MYC	MYC	MYC	13915	-0.089	0.096	NO
109	MAP2K1	MAP2K1	MAP2K1	13954	-0.09	0.099	NO
110	EIF2AK2	EIF2AK2	EIF2AK2	13957	-0.09	0.1	NO
111	MAPK8	MAPK8	MAPK8	14059	-0.093	0.1	NO
112	NRAS	NRAS	NRAS	14139	-0.095	0.1	NO
113	YWHAQ	YWHAQ	YWHAQ	14250	-0.098	0.1	NO
114	YWHAE	YWHAE	YWHAE	14808	-0.11	0.077	NO
115	RAC1	RAC1	RAC1	14861	-0.12	0.08	NO
116	BCAR1	BCAR1	BCAR1	15014	-0.12	0.078	NO
117	YWHAG	YWHAG	YWHAG	15414	-0.14	0.064	NO
118	SRC	SRC	SRC	15611	-0.15	0.06	NO
119	YWHAZ	YWHAZ	YWHAZ	15694	-0.15	0.063	NO
120	VAV2	VAV2	VAV2	15928	-0.16	0.059	NO
121	YES1	YES1	YES1	16269	-0.18	0.049	NO
122	SLC9A3R1	SLC9A3R1	SLC9A3R1	16558	-0.2	0.044	NO
123	HRAS	HRAS	HRAS	17024	-0.23	0.03	NO
124	CTTN	CTTN	CTTN	17050	-0.23	0.04	NO
125	PLA2G4A	PLA2G4A	PLA2G4A	17372	-0.26	0.036	NO
126	BAIAP2	BAIAP2	BAIAP2	17518	-0.28	0.042	NO
127	SFN	SFN	SFN	18560	-0.49	0.01	NO

Figure S99. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG LYSOSOME.

Figure S100. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus6 enriched pathways

Table 8. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus6. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES	26	genes.ES.table	0.65	1.7	0.0041	0.86	0.83	0.54	0.17	0.45	0.37	0.23
KEGG NOTCH SIGNALING PATHWAY	47	genes.ES.table	0.43	1.7	0.011	0.94	0.78	0.17	0.17	0.14	0.38	0.23
KEGG THYROID CANCER	29	genes.ES.table	0.51	1.8	0.0021	0.75	0.55	0.59	0.32	0.4	0.18	0.16
PID FOXOPATHWAY	49	genes.ES.table	0.37	1.7	0.024	0.93	0.83	0.39	0.32	0.27	0.39	0.24
PID ECADHERIN NASCENTAJ PATHWAY	39	genes.ES.table	0.46	1.9	0.0081	0.99	0.35	0.54	0.31	0.37	0	0.17
PID RETINOIC ACID PATHWAY	30	genes.ES.table	0.42	1.7	0.027	0.74	0.9	0.33	0.22	0.26	0.37	0.21
PID TAP63PATHWAY	54	genes.ES.table	0.48	1.7	0.014	0.72	0.84	0.24	0.14	0.21	0.32	0.2
PID MAPKTRKPATHWAY	33	genes.ES.table	0.41	1.7	0.027	0.77	0.84	0.58	0.32	0.39	0.34	0.21
REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS	38	genes.ES.table	0.51	1.8	0.012	0.91	0.54	0.34	0.2	0.27	0.22	0.18
REACTOME TRIF MEDIATED TLR3 SIGNALING	72	genes.ES.table	0.46	2	0.004	1	0.23	0.44	0.28	0.32	0	0.18

genes ES table in pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

Table S51. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	S100A12	S100A12	S100A12	122	0.87	0.13	YES
2	NOD2	NOD2	NOD2	471	0.51	0.19	YES
3	DUSP7	DUSP7	DUSP7	1431	0.26	0.17	YES
4	TLR3	TLR3	TLR3	1496	0.25	0.21	YES
5	TAB3	TAB3	TAB3	1716	0.22	0.23	YES
6	TICAM1	TICAM1	TICAM1	2166	0.18	0.23	YES
7	MAP2K4	MAP2K4	MAP2K4	2331	0.17	0.25	YES
8	RIPK3	RIPK3	RIPK3	2338	0.17	0.28	YES
9	SAA1	SAA1	SAA1	2445	0.16	0.3	YES
10	MAPK10	MAPK10	MAPK10	2583	0.15	0.31	YES
11	MAPK7	MAPK7	MAPK7	2596	0.15	0.33	YES
12	S100B	S100B	S100B	2766	0.14	0.35	YES
13	IKBKE	IKBKE	IKBKE	3032	0.13	0.35	YES
14	MAPKAPK3	MAPKAPK3	MAPKAPK3	3107	0.12	0.37	YES
15	AGER	AGER	AGER	3342	0.11	0.37	YES
16	IRF7	IRF7	IRF7	3551	0.1	0.38	YES
17	FOS	FOS	FOS	3710	0.099	0.38	YES
18	MAPK3	MAPK3	MAPK3	3788	0.096	0.39	YES
19	MAP2K6	MAP2K6	MAP2K6	3853	0.094	0.4	YES
20	IRAK2	IRAK2	IRAK2	3953	0.091	0.41	YES
21	TRAF6	TRAF6	TRAF6	4107	0.086	0.42	YES
22	MAP2K3	MAP2K3	MAP2K3	4681	0.068	0.4	YES
23	MAP2K1	MAP2K1	MAP2K1	4731	0.066	0.4	YES
24	IKBKB	IKBKB	IKBKB	4796	0.064	0.41	YES
25	TAB2	TAB2	TAB2	4850	0.063	0.42	YES
26	RIPK1	RIPK1	RIPK1	5003	0.06	0.42	YES
27	RPS6KA5	RPS6KA5	RPS6KA5	5029	0.059	0.43	YES
28	NFKBIA	NFKBIA	NFKBIA	5030	0.059	0.44	YES
29	DUSP4	DUSP4	DUSP4	5090	0.057	0.44	YES
30	PPP2CA	PPP2CA	PPP2CA	5103	0.057	0.45	YES
31	ZBP1	ZBP1	ZBP1	5109	0.056	0.46	YES
32	PPP2CB	PPP2CB	PPP2CB	5154	0.055	0.46	YES
33	PPP2R1A	PPP2R1A	PPP2R1A	5429	0.049	0.46	NO
34	MAPK14	MAPK14	MAPK14	5651	0.045	0.45	NO
35	MAPK1	MAPK1	MAPK1	5750	0.043	0.45	NO
36	MAP2K2	MAP2K2	MAP2K2	6043	0.037	0.44	NO
37	UBA52	UBA52	UBA52	6322	0.032	0.43	NO
38	MAPKAPK2	MAPKAPK2	MAPKAPK2	6596	0.027	0.42	NO
39	CREB1	CREB1	CREB1	6747	0.025	0.42	NO
40	RELA	RELA	RELA	7206	0.018	0.4	NO
41	PPP2R1B	PPP2R1B	PPP2R1B	7217	0.018	0.4	NO
42	NFKBIB	NFKBIB	NFKBIB	7341	0.016	0.4	NO
43	IKBKG	IKBKG	IKBKG	7381	0.015	0.4	NO
44	MAPK8	MAPK8	MAPK8	7737	0.01	0.38	NO
45	RPS6KA2	RPS6KA2	RPS6KA2	7750	0.01	0.38	NO
46	RPS27A	RPS27A	RPS27A	7799	0.0093	0.38	NO
47	MEF2A	MEF2A	MEF2A	7918	0.0077	0.37	NO
48	MAPK11	MAPK11	MAPK11	8375	0.00081	0.35	NO
49	MAP2K7	MAP2K7	MAP2K7	8710	-0.0035	0.33	NO
50	RPS6KA3	RPS6KA3	RPS6KA3	9158	-0.0093	0.31	NO
51	JUN	JUN	JUN	9203	-0.0098	0.31	NO
52	ATF1	ATF1	ATF1	9903	-0.019	0.27	NO
53	TAB1	TAB1	TAB1	10109	-0.022	0.26	NO
54	IRAK1	IRAK1	IRAK1	10151	-0.022	0.27	NO
55	TBK1	TBK1	TBK1	10974	-0.033	0.23	NO
56	DUSP3	DUSP3	DUSP3	11169	-0.036	0.22	NO
57	MAP3K7	MAP3K7	MAP3K7	11201	-0.036	0.23	NO
58	CHUK	CHUK	CHUK	11405	-0.039	0.22	NO
59	IRF3	IRF3	IRF3	11761	-0.044	0.21	NO
60	ELK1	ELK1	ELK1	11866	-0.046	0.21	NO
61	HMGB1	HMGB1	HMGB1	12445	-0.054	0.19	NO
62	NFKB2	NFKB2	NFKB2	12736	-0.058	0.18	NO
63	RPS6KA1	RPS6KA1	RPS6KA1	12831	-0.059	0.18	NO
64	NOD1	NOD1	NOD1	13148	-0.064	0.18	NO
65	PPP2R5D	PPP2R5D	PPP2R5D	13190	-0.065	0.19	NO
66	DUSP6	DUSP6	DUSP6	13946	-0.078	0.16	NO
67	APP	APP	APP	13997	-0.079	0.17	NO
68	MAPK9	MAPK9	MAPK9	14790	-0.096	0.14	NO
69	CDK1	CDK1	CDK1	15015	-0.1	0.14	NO
70	ATF2	ATF2	ATF2	15165	-0.1	0.15	NO
71	RIPK2	RIPK2	RIPK2	15633	-0.12	0.14	NO
72	MEF2C	MEF2C	MEF2C	16416	-0.15	0.12	NO

Figure S101. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

Figure S102. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, 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 NOTCH SIGNALING PATHWAY

Table S52. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TIAM1	TIAM1	TIAM1	266	0.64	0.16	YES
2	ITGB7	ITGB7	ITGB7	1400	0.26	0.18	YES
3	MLLT4	MLLT4	MLLT4	1828	0.21	0.21	YES
4	TJP1	TJP1	TJP1	2421	0.16	0.22	YES
5	JUP	JUP	JUP	2623	0.15	0.25	YES
6	ARF6	ARF6	ARF6	2844	0.14	0.28	YES
7	WASF2	WASF2	WASF2	3101	0.12	0.3	YES
8	CTNND1	CTNND1	CTNND1	3145	0.12	0.33	YES
9	CCND1	CCND1	CCND1	3243	0.12	0.36	YES
10	DLG1	DLG1	DLG1	3463	0.11	0.38	YES
11	ABI1	ABI1	ABI1	3485	0.11	0.4	YES
12	CTTN	CTTN	CTTN	3748	0.098	0.42	YES
13	CDH1	CDH1	CDH1	3805	0.096	0.44	YES
14	CTNNA1	CTNNA1	CTNNA1	4258	0.081	0.44	YES
15	RAC1	RAC1	RAC1	4795	0.064	0.43	YES
16	IQGAP1	IQGAP1	IQGAP1	4915	0.062	0.44	YES
17	CYFIP2	CYFIP2	CYFIP2	4972	0.06	0.45	YES
18	ITGAE	ITGAE	ITGAE	5191	0.054	0.46	YES
19	NCKAP1	NCKAP1	NCKAP1	5542	0.047	0.45	YES
20	RHOA	RHOA	RHOA	5703	0.044	0.46	YES
21	RAP1A	RAP1A	RAP1A	5747	0.043	0.46	YES
22	CDC42	CDC42	CDC42	7315	0.016	0.38	NO
23	PIP5K1C	PIP5K1C	PIP5K1C	7382	0.015	0.39	NO
24	CSNK2B	CSNK2B	CSNK2B	8033	0.0058	0.35	NO
25	PIK3CA	PIK3CA	PIK3CA	8331	0.0014	0.34	NO
26	KLHL20	KLHL20	KLHL20	8585	-0.0019	0.32	NO
27	CRK	CRK	CRK	8953	-0.0066	0.31	NO
28	CTNNB1	CTNNB1	CTNNB1	9385	-0.012	0.29	NO
29	CSNK2A1	CSNK2A1	CSNK2A1	10129	-0.022	0.25	NO
30	CSNK2A2	CSNK2A2	CSNK2A2	11236	-0.037	0.2	NO
31	SRC	SRC	SRC	11251	-0.037	0.21	NO
32	PIK3R1	PIK3R1	PIK3R1	11570	-0.041	0.21	NO
33	AKT1	AKT1	AKT1	12218	-0.05	0.19	NO
34	AP1M1	AP1M1	AP1M1	12532	-0.055	0.19	NO
35	RAP1B	RAP1B	RAP1B	12889	-0.06	0.18	NO
36	ENAH	ENAH	ENAH	12996	-0.062	0.2	NO
37	NME1	NME1	NME1	14536	-0.09	0.14	NO
38	RAPGEF1	RAPGEF1	RAPGEF1	15076	-0.1	0.14	NO
39	VAV2	VAV2	VAV2	17595	-0.21	0.062	NO

Figure S103. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NOTCH SIGNALING PATHWAY.

Figure S104. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG THYROID CANCER

Table S53. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	S100A12	S100A12	S100A12	122	0.87	0.12	YES
2	NOD2	NOD2	NOD2	471	0.51	0.18	YES
3	DUSP7	DUSP7	DUSP7	1431	0.26	0.17	YES
4	TAB3	TAB3	TAB3	1716	0.22	0.19	YES
5	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	1821	0.21	0.22	YES
6	MAP2K4	MAP2K4	MAP2K4	2331	0.17	0.21	YES
7	PELI1	PELI1	PELI1	2369	0.16	0.24	YES
8	SAA1	SAA1	SAA1	2445	0.16	0.26	YES
9	MAPK10	MAPK10	MAPK10	2583	0.15	0.27	YES
10	MAPK7	MAPK7	MAPK7	2596	0.15	0.3	YES
11	S100B	S100B	S100B	2766	0.14	0.31	YES
12	MYD88	MYD88	MYD88	2979	0.13	0.32	YES
13	MAPKAPK3	MAPKAPK3	MAPKAPK3	3107	0.12	0.33	YES
14	MAP3K1	MAP3K1	MAP3K1	3209	0.12	0.34	YES
15	AGER	AGER	AGER	3342	0.11	0.35	YES
16	IRAK4	IRAK4	IRAK4	3425	0.11	0.36	YES
17	FOS	FOS	FOS	3710	0.099	0.36	YES
18	MAPK3	MAPK3	MAPK3	3788	0.096	0.37	YES
19	MAP2K6	MAP2K6	MAP2K6	3853	0.094	0.38	YES
20	IRAK2	IRAK2	IRAK2	3953	0.091	0.39	YES
21	TRAF6	TRAF6	TRAF6	4107	0.086	0.4	YES
22	TLR9	TLR9	TLR9	4392	0.077	0.39	YES
23	MAP2K3	MAP2K3	MAP2K3	4681	0.068	0.39	YES
24	MAP2K1	MAP2K1	MAP2K1	4731	0.066	0.4	YES
25	IKBKB	IKBKB	IKBKB	4796	0.064	0.4	YES
26	TAB2	TAB2	TAB2	4850	0.063	0.41	YES
27	RPS6KA5	RPS6KA5	RPS6KA5	5029	0.059	0.41	YES
28	NFKBIA	NFKBIA	NFKBIA	5030	0.059	0.42	YES
29	DUSP4	DUSP4	DUSP4	5090	0.057	0.42	YES
30	PPP2CA	PPP2CA	PPP2CA	5103	0.057	0.43	YES
31	PPP2CB	PPP2CB	PPP2CB	5154	0.055	0.44	YES
32	PPP2R1A	PPP2R1A	PPP2R1A	5429	0.049	0.43	NO
33	MAPK14	MAPK14	MAPK14	5651	0.045	0.42	NO
34	MAPK1	MAPK1	MAPK1	5750	0.043	0.43	NO
35	MAP2K2	MAP2K2	MAP2K2	6043	0.037	0.42	NO
36	UBA52	UBA52	UBA52	6322	0.032	0.41	NO
37	MAPKAPK2	MAPKAPK2	MAPKAPK2	6596	0.027	0.4	NO
38	CREB1	CREB1	CREB1	6747	0.025	0.39	NO
39	RELA	RELA	RELA	7206	0.018	0.37	NO
40	PPP2R1B	PPP2R1B	PPP2R1B	7217	0.018	0.37	NO
41	PELI3	PELI3	PELI3	7251	0.017	0.37	NO
42	NFKBIB	NFKBIB	NFKBIB	7341	0.016	0.37	NO
43	IKBKG	IKBKG	IKBKG	7381	0.015	0.37	NO
44	UBE2N	UBE2N	UBE2N	7653	0.011	0.36	NO
45	MAPK8	MAPK8	MAPK8	7737	0.01	0.35	NO
46	RPS6KA2	RPS6KA2	RPS6KA2	7750	0.01	0.36	NO
47	RPS27A	RPS27A	RPS27A	7799	0.0093	0.35	NO
48	MEF2A	MEF2A	MEF2A	7918	0.0077	0.35	NO
49	MAPK11	MAPK11	MAPK11	8375	0.00081	0.32	NO
50	MAP2K7	MAP2K7	MAP2K7	8710	-0.0035	0.31	NO
51	RPS6KA3	RPS6KA3	RPS6KA3	9158	-0.0093	0.28	NO
52	JUN	JUN	JUN	9203	-0.0098	0.28	NO
53	ATF1	ATF1	ATF1	9903	-0.019	0.25	NO
54	TAB1	TAB1	TAB1	10109	-0.022	0.24	NO
55	IRAK1	IRAK1	IRAK1	10151	-0.022	0.24	NO
56	TLR7	TLR7	TLR7	10325	-0.024	0.24	NO
57	DUSP3	DUSP3	DUSP3	11169	-0.036	0.2	NO
58	MAP3K7	MAP3K7	MAP3K7	11201	-0.036	0.2	NO
59	CHUK	CHUK	CHUK	11405	-0.039	0.2	NO
60	ELK1	ELK1	ELK1	11866	-0.046	0.18	NO
61	ECSIT	ECSIT	ECSIT	12031	-0.048	0.18	NO
62	HMGB1	HMGB1	HMGB1	12445	-0.054	0.16	NO
63	TLR8	TLR8	TLR8	12515	-0.055	0.17	NO
64	NFKB2	NFKB2	NFKB2	12736	-0.058	0.16	NO
65	RPS6KA1	RPS6KA1	RPS6KA1	12831	-0.059	0.17	NO
66	NOD1	NOD1	NOD1	13148	-0.064	0.16	NO
67	PPP2R5D	PPP2R5D	PPP2R5D	13190	-0.065	0.17	NO
68	DUSP6	DUSP6	DUSP6	13946	-0.078	0.14	NO
69	APP	APP	APP	13997	-0.079	0.15	NO
70	MAPK9	MAPK9	MAPK9	14790	-0.096	0.12	NO
71	CDK1	CDK1	CDK1	15015	-0.1	0.13	NO
72	ATF2	ATF2	ATF2	15165	-0.1	0.13	NO
73	PELI2	PELI2	PELI2	15506	-0.12	0.13	NO
74	RIPK2	RIPK2	RIPK2	15633	-0.12	0.14	NO
75	MEF2C	MEF2C	MEF2C	16416	-0.15	0.12	NO

Figure S105. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG THYROID CANCER.

Figure S106. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID CANCER, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID FOXOPATHWAY

Table S54. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	DSG1	DSG1	DSG1	226	0.69	0.12	YES
2	DSG3	DSG3	DSG3	278	0.64	0.25	YES
3	PKP1	PKP1	PKP1	394	0.56	0.35	YES
4	MAPT	MAPT	MAPT	748	0.39	0.41	YES
5	DSP	DSP	DSP	1039	0.32	0.46	YES
6	GAS2	GAS2	GAS2	1980	0.19	0.44	YES
7	TJP1	TJP1	TJP1	2421	0.16	0.45	YES
8	OCLN	OCLN	OCLN	2706	0.14	0.46	YES
9	DBNL	DBNL	DBNL	2715	0.14	0.49	YES
10	GSN	GSN	GSN	3404	0.11	0.48	YES
11	STK24	STK24	STK24	3691	0.1	0.48	YES
12	APC	APC	APC	3782	0.096	0.5	YES
13	CDH1	CDH1	CDH1	3805	0.096	0.51	YES
14	SATB1	SATB1	SATB1	4122	0.085	0.51	NO
15	TJP2	TJP2	TJP2	4537	0.072	0.5	NO
16	BMX	BMX	BMX	5422	0.049	0.47	NO
17	PRKCD	PRKCD	PRKCD	6000	0.038	0.44	NO
18	PRKCQ	PRKCQ	PRKCQ	6479	0.029	0.42	NO
19	LMNA	LMNA	LMNA	6654	0.026	0.42	NO
20	MST4	MST4	MST4	6951	0.022	0.41	NO
21	ADD1	ADD1	ADD1	7332	0.016	0.39	NO
22	SPTAN1	SPTAN1	SPTAN1	8881	-0.0056	0.31	NO
23	BCAP31	BCAP31	BCAP31	9268	-0.011	0.29	NO
24	CTNNB1	CTNNB1	CTNNB1	9385	-0.012	0.29	NO
25	FNTA	FNTA	FNTA	9576	-0.015	0.28	NO
26	CASP3	CASP3	CASP3	9621	-0.015	0.28	NO
27	CASP7	CASP7	CASP7	9798	-0.018	0.28	NO
28	PLEC	PLEC	PLEC	10637	-0.028	0.24	NO
29	ACIN1	ACIN1	ACIN1	10831	-0.031	0.23	NO
30	BIRC2	BIRC2	BIRC2	12570	-0.056	0.15	NO
31	CASP8	CASP8	CASP8	13284	-0.066	0.12	NO
32	ROCK1	ROCK1	ROCK1	13398	-0.068	0.13	NO
33	LMNB1	LMNB1	LMNB1	14726	-0.095	0.08	NO
34	PTK2	PTK2	PTK2	15230	-0.11	0.074	NO
35	DSG2	DSG2	DSG2	15681	-0.12	0.073	NO
36	VIM	VIM	VIM	15896	-0.13	0.087	NO
37	LOC647859	LOC647859	LOC647859	16783	-0.16	0.072	NO
38	CASP6	CASP6	CASP6	16839	-0.17	0.1	NO

Figure S107. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FOXOPATHWAY.

Figure S108. Get High-res Image For the top 5 core enriched genes in the pathway: PID FOXOPATHWAY, 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 ECADHERIN NASCENTAJ PATHWAY

Table S55. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	RXRG	RXRG	RXRG	1421	0.26	0.07	YES
2	CCND1	CCND1	CCND1	3243	0.12	0.038	YES
3	LEF1	LEF1	LEF1	3510	0.11	0.084	YES
4	HRAS	HRAS	HRAS	3658	0.1	0.13	YES
5	TCF7L1	TCF7L1	TCF7L1	3771	0.097	0.18	YES
6	MAPK3	MAPK3	MAPK3	3788	0.096	0.24	YES
7	CDH1	CDH1	CDH1	3805	0.096	0.29	YES
8	CCDC6	CCDC6	CCDC6	3833	0.095	0.34	YES
9	RET	RET	RET	3981	0.09	0.38	YES
10	RXRA	RXRA	RXRA	4050	0.088	0.43	YES
11	MAP2K1	MAP2K1	MAP2K1	4731	0.066	0.43	YES
12	BRAF	BRAF	BRAF	5091	0.057	0.44	YES
13	NCOA4	NCOA4	NCOA4	5500	0.047	0.45	YES
14	MAPK1	MAPK1	MAPK1	5750	0.043	0.46	YES
15	PPARG	PPARG	PPARG	5879	0.04	0.48	YES
16	TFG	TFG	TFG	5941	0.039	0.49	YES
17	MAP2K2	MAP2K2	MAP2K2	6043	0.037	0.51	YES
18	NRAS	NRAS	NRAS	7695	0.011	0.43	NO
19	PAX8	PAX8	PAX8	8116	0.0044	0.41	NO
20	RXRB	RXRB	RXRB	8335	0.0014	0.4	NO
21	TP53	TP53	TP53	8497	-0.00087	0.39	NO
22	CTNNB1	CTNNB1	CTNNB1	9385	-0.012	0.35	NO
23	MYC	MYC	MYC	9670	-0.016	0.34	NO
24	KRAS	KRAS	KRAS	9959	-0.02	0.34	NO
25	NTRK1	NTRK1	NTRK1	10450	-0.026	0.32	NO
26	TPR	TPR	TPR	10623	-0.028	0.33	NO
27	TCF7	TCF7	TCF7	11719	-0.043	0.3	NO
28	TPM3	TPM3	TPM3	12017	-0.048	0.31	NO
29	TCF7L2	TCF7L2	TCF7L2	14525	-0.09	0.23	NO

Figure S109. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ECADHERIN NASCENTAJ PATHWAY.

Figure S110. Get High-res Image For the top 5 core enriched genes in the pathway: PID ECADHERIN NASCENTAJ PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID RETINOIC ACID PATHWAY

Table S56. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IL1RN	IL1RN	IL1RN	147	0.82	0.15	YES
2	IL1A	IL1A	IL1A	363	0.57	0.24	YES
3	NOD2	NOD2	NOD2	471	0.51	0.34	YES
4	TAB3	TAB3	TAB3	1716	0.22	0.31	YES
5	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	1821	0.21	0.34	YES
6	MAP3K8	MAP3K8	MAP3K8	1898	0.2	0.38	YES
7	IL1R2	IL1R2	IL1R2	1924	0.2	0.41	YES
8	TOLLIP	TOLLIP	TOLLIP	1988	0.19	0.45	YES
9	IL1RAP	IL1RAP	IL1RAP	2151	0.18	0.47	YES
10	MAP2K4	MAP2K4	MAP2K4	2331	0.17	0.49	YES
11	PELI1	PELI1	PELI1	2369	0.16	0.52	YES
12	BTRC	BTRC	BTRC	2900	0.13	0.52	YES
13	MYD88	MYD88	MYD88	2979	0.13	0.54	YES
14	IRAK4	IRAK4	IRAK4	3425	0.11	0.54	YES
15	MAP2K6	MAP2K6	MAP2K6	3853	0.094	0.53	YES
16	IRAK2	IRAK2	IRAK2	3953	0.091	0.54	YES
17	TRAF6	TRAF6	TRAF6	4107	0.086	0.55	YES
18	MAP2K1	MAP2K1	MAP2K1	4731	0.066	0.53	NO
19	IKBKB	IKBKB	IKBKB	4796	0.064	0.54	NO
20	TAB2	TAB2	TAB2	4850	0.063	0.55	NO
21	RBX1	RBX1	RBX1	5588	0.046	0.52	NO
22	SKP1	SKP1	SKP1	6990	0.021	0.45	NO
23	MAP3K3	MAP3K3	MAP3K3	7013	0.021	0.45	NO
24	PELI3	PELI3	PELI3	7251	0.017	0.44	NO
25	IKBKG	IKBKG	IKBKG	7381	0.015	0.44	NO
26	UBE2N	UBE2N	UBE2N	7653	0.011	0.42	NO
27	CUL1	CUL1	CUL1	9974	-0.02	0.3	NO
28	TAB1	TAB1	TAB1	10109	-0.022	0.3	NO
29	IRAK1	IRAK1	IRAK1	10151	-0.022	0.3	NO
30	MAP3K7	MAP3K7	MAP3K7	11201	-0.036	0.25	NO
31	CHUK	CHUK	CHUK	11405	-0.039	0.25	NO
32	TNIP2	TNIP2	TNIP2	11638	-0.042	0.25	NO
33	NOD1	NOD1	NOD1	13148	-0.064	0.18	NO
34	IL1R1	IL1R1	IL1R1	13976	-0.078	0.15	NO
35	SQSTM1	SQSTM1	SQSTM1	15160	-0.1	0.1	NO
36	IL1B	IL1B	IL1B	15359	-0.11	0.12	NO
37	IRAK3	IRAK3	IRAK3	15458	-0.11	0.13	NO
38	PELI2	PELI2	PELI2	15506	-0.12	0.15	NO
39	RIPK2	RIPK2	RIPK2	15633	-0.12	0.17	NO

Figure S111. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID RETINOIC ACID PATHWAY.

Figure S112. Get High-res Image For the top 5 core enriched genes in the pathway: PID RETINOIC ACID PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID TAP63PATHWAY

Table S57. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HES5	HES5	HES5	152	0.8	0.11	YES
2	KAT2B	KAT2B	KAT2B	733	0.4	0.14	YES
3	DLK1	DLK1	DLK1	847	0.37	0.19	YES
4	DTX1	DTX1	DTX1	1055	0.31	0.22	YES
5	NEURL	NEURL	NEURL	1139	0.3	0.26	YES
6	MAML3	MAML3	MAML3	1152	0.3	0.31	YES
7	TLE2	TLE2	TLE2	1236	0.28	0.35	YES
8	CNTN1	CNTN1	CNTN1	1758	0.22	0.35	YES
9	DTX2	DTX2	DTX2	1902	0.2	0.37	YES
10	TLE4	TLE4	TLE4	2271	0.17	0.38	YES
11	TLE3	TLE3	TLE3	2776	0.14	0.37	YES
12	TBL1X	TBL1X	TBL1X	2811	0.14	0.39	YES
13	FBXW7	FBXW7	FBXW7	2830	0.14	0.41	YES
14	HDAC11	HDAC11	HDAC11	3308	0.12	0.4	NO
15	DLL1	DLL1	DLL1	3768	0.097	0.39	NO
16	HDAC5	HDAC5	HDAC5	4118	0.085	0.39	NO
17	HDAC4	HDAC4	HDAC4	4376	0.077	0.38	NO
18	HES1	HES1	HES1	4519	0.072	0.39	NO
19	MAML2	MAML2	MAML2	4605	0.07	0.4	NO
20	CCNC	CCNC	CCNC	5341	0.051	0.36	NO
21	HDAC6	HDAC6	HDAC6	5540	0.047	0.36	NO
22	RBX1	RBX1	RBX1	5588	0.046	0.36	NO
23	MIB2	MIB2	MIB2	5720	0.043	0.36	NO
24	JAG1	JAG1	JAG1	5730	0.043	0.37	NO
25	PSEN2	PSEN2	PSEN2	5809	0.041	0.37	NO
26	EP300	EP300	EP300	5848	0.04	0.38	NO
27	PSENEN	PSENEN	PSENEN	6020	0.037	0.37	NO
28	ADAM17	ADAM17	ADAM17	6181	0.034	0.37	NO
29	DNER	DNER	DNER	6263	0.033	0.37	NO
30	UBA52	UBA52	UBA52	6322	0.032	0.37	NO
31	JAG2	JAG2	JAG2	6719	0.025	0.35	NO
32	HEY1	HEY1	HEY1	6937	0.022	0.34	NO
33	SKP1	SKP1	SKP1	6990	0.021	0.34	NO
34	HDAC3	HDAC3	HDAC3	7731	0.01	0.31	NO
35	RPS27A	RPS27A	RPS27A	7799	0.0093	0.3	NO
36	HEY2	HEY2	HEY2	7801	0.0093	0.31	NO
37	HDAC2	HDAC2	HDAC2	8187	0.0036	0.29	NO
38	HDAC1	HDAC1	HDAC1	8194	0.0035	0.29	NO
39	NUMB	NUMB	NUMB	8284	0.002	0.28	NO
40	CREBBP	CREBBP	CREBBP	8347	0.0012	0.28	NO
41	HDAC7	HDAC7	HDAC7	9305	-0.011	0.23	NO
42	CDK8	CDK8	CDK8	9407	-0.013	0.23	NO
43	MYC	MYC	MYC	9670	-0.016	0.21	NO
44	APH1A	APH1A	APH1A	9794	-0.018	0.21	NO
45	CUL1	CUL1	CUL1	9974	-0.02	0.2	NO
46	PSEN1	PSEN1	PSEN1	10029	-0.02	0.2	NO
47	NCOR1	NCOR1	NCOR1	10065	-0.021	0.2	NO
48	HIF1A	HIF1A	HIF1A	10251	-0.023	0.2	NO
49	ADAM10	ADAM10	ADAM10	10264	-0.023	0.2	NO
50	NCSTN	NCSTN	NCSTN	10476	-0.026	0.19	NO
51	ARRB1	ARRB1	ARRB1	10487	-0.026	0.2	NO
52	NCOR2	NCOR2	NCOR2	10542	-0.027	0.2	NO
53	TBL1XR1	TBL1XR1	TBL1XR1	11543	-0.041	0.15	NO
54	MAML1	MAML1	MAML1	11705	-0.043	0.15	NO
55	RBPJ	RBPJ	RBPJ	12048	-0.048	0.14	NO
56	SNW1	SNW1	SNW1	12348	-0.052	0.13	NO
57	HDAC9	HDAC9	HDAC9	12378	-0.053	0.14	NO
58	HDAC10	HDAC10	HDAC10	12536	-0.055	0.14	NO
59	HDAC8	HDAC8	HDAC8	12737	-0.058	0.13	NO
60	MIB1	MIB1	MIB1	13233	-0.065	0.12	NO
61	APH1B	APH1B	APH1B	13701	-0.073	0.1	NO
62	KAT2A	KAT2A	KAT2A	15016	-0.1	0.048	NO
63	ARRB2	ARRB2	ARRB2	15174	-0.1	0.055	NO
64	TLE1	TLE1	TLE1	15201	-0.11	0.07	NO
65	DTX4	DTX4	DTX4	15330	-0.11	0.079	NO
66	DLL4	DLL4	DLL4	16297	-0.14	0.049	NO
67	MAMLD1	MAMLD1	MAMLD1	17060	-0.18	0.035	NO
68	HEYL	HEYL	HEYL	18558	-0.37	0.01	NO

Figure S113. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TAP63PATHWAY.

Figure S114. Get High-res Image For the top 5 core enriched genes in the pathway: PID TAP63PATHWAY, 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 MAPKTRKPATHWAY

Table S58. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HES5	HES5	HES5	152	0.8	0.19	YES
2	KAT2B	KAT2B	KAT2B	733	0.4	0.26	YES
3	DTX1	DTX1	DTX1	1055	0.31	0.32	YES
4	MAML3	MAML3	MAML3	1152	0.3	0.39	YES
5	DTX2	DTX2	DTX2	1902	0.2	0.4	YES
6	NOTCH2	NOTCH2	NOTCH2	2351	0.16	0.41	YES
7	DLL3	DLL3	DLL3	3129	0.12	0.4	YES
8	NOTCH3	NOTCH3	NOTCH3	3197	0.12	0.43	YES
9	DLL1	DLL1	DLL1	3768	0.097	0.42	NO
10	HES1	HES1	HES1	4519	0.072	0.4	NO
11	MAML2	MAML2	MAML2	4605	0.07	0.41	NO
12	JAG1	JAG1	JAG1	5730	0.043	0.36	NO
13	PSEN2	PSEN2	PSEN2	5809	0.041	0.37	NO
14	EP300	EP300	EP300	5848	0.04	0.38	NO
15	PSENEN	PSENEN	PSENEN	6020	0.037	0.38	NO
16	DVL1	DVL1	DVL1	6109	0.036	0.38	NO
17	ADAM17	ADAM17	ADAM17	6181	0.034	0.39	NO
18	JAG2	JAG2	JAG2	6719	0.025	0.36	NO
19	PTCRA	PTCRA	PTCRA	6945	0.022	0.36	NO
20	MFNG	MFNG	MFNG	7438	0.014	0.34	NO
21	HDAC2	HDAC2	HDAC2	8187	0.0036	0.3	NO
22	HDAC1	HDAC1	HDAC1	8194	0.0035	0.3	NO
23	NUMB	NUMB	NUMB	8284	0.002	0.29	NO
24	CREBBP	CREBBP	CREBBP	8347	0.0012	0.29	NO
25	NOTCH1	NOTCH1	NOTCH1	9060	-0.0081	0.25	NO
26	RFNG	RFNG	RFNG	9302	-0.011	0.24	NO
27	DVL3	DVL3	DVL3	9468	-0.013	0.24	NO
28	APH1A	APH1A	APH1A	9794	-0.018	0.22	NO
29	DVL2	DVL2	DVL2	9839	-0.018	0.23	NO
30	DTX3	DTX3	DTX3	9893	-0.019	0.23	NO
31	PSEN1	PSEN1	PSEN1	10029	-0.02	0.23	NO
32	DTX3L	DTX3L	DTX3L	10352	-0.025	0.22	NO
33	NCSTN	NCSTN	NCSTN	10476	-0.026	0.22	NO
34	CTBP2	CTBP2	CTBP2	10520	-0.027	0.22	NO
35	NCOR2	NCOR2	NCOR2	10542	-0.027	0.22	NO
36	CTBP1	CTBP1	CTBP1	11578	-0.041	0.18	NO
37	MAML1	MAML1	MAML1	11705	-0.043	0.18	NO
38	NUMBL	NUMBL	NUMBL	11731	-0.044	0.19	NO
39	CIR1	CIR1	CIR1	11897	-0.046	0.2	NO
40	RBPJ	RBPJ	RBPJ	12048	-0.048	0.2	NO
41	SNW1	SNW1	SNW1	12348	-0.052	0.2	NO
42	LFNG	LFNG	LFNG	13183	-0.064	0.17	NO
43	NOTCH4	NOTCH4	NOTCH4	13320	-0.067	0.18	NO
44	RBPJL	RBPJL	RBPJL	14998	-0.1	0.11	NO
45	KAT2A	KAT2A	KAT2A	15016	-0.1	0.14	NO
46	DTX4	DTX4	DTX4	15330	-0.11	0.15	NO
47	DLL4	DLL4	DLL4	16297	-0.14	0.13	NO

Figure S115. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MAPKTRKPATHWAY.

Figure S116. Get High-res Image For the top 5 core enriched genes in the pathway: PID MAPKTRKPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS

Table S59. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PLA2G3	PLA2G3	PLA2G3	123	0.87	0.081	YES
2	PLA2G4D	PLA2G4D	PLA2G4D	387	0.56	0.12	YES
3	PLA2G4F	PLA2G4F	PLA2G4F	566	0.47	0.16	YES
4	MBOAT2	MBOAT2	MBOAT2	935	0.34	0.18	YES
5	MGLL	MGLL	MGLL	1022	0.32	0.2	YES
6	PLD2	PLD2	PLD2	1034	0.32	0.24	YES
7	DGAT2	DGAT2	DGAT2	1279	0.28	0.25	YES
8	AGPAT9	AGPAT9	AGPAT9	1413	0.26	0.27	YES
9	LPIN1	LPIN1	LPIN1	1487	0.25	0.29	YES
10	PLD1	PLD1	PLD1	1535	0.24	0.31	YES
11	ETNK2	ETNK2	ETNK2	1594	0.23	0.33	YES
12	PLD4	PLD4	PLD4	1634	0.23	0.35	YES
13	GPD1L	GPD1L	GPD1L	1912	0.2	0.36	YES
14	GPCPD1	GPCPD1	GPCPD1	1970	0.19	0.37	YES
15	CDS1	CDS1	CDS1	2053	0.19	0.39	YES
16	PLA2G2F	PLA2G2F	PLA2G2F	2107	0.18	0.4	YES
17	PNPLA3	PNPLA3	PNPLA3	2376	0.16	0.41	YES
18	PHOSPHO1	PHOSPHO1	PHOSPHO1	2401	0.16	0.42	YES
19	SLC44A3	SLC44A3	SLC44A3	2465	0.16	0.44	YES
20	AGPAT4	AGPAT4	AGPAT4	2658	0.15	0.44	YES
21	CHKB	CHKB	CHKB	2662	0.15	0.45	YES
22	PLBD1	PLBD1	PLBD1	2675	0.15	0.47	YES
23	PLA2G2D	PLA2G2D	PLA2G2D	2744	0.14	0.48	YES
24	SLC44A5	SLC44A5	SLC44A5	3244	0.12	0.46	YES
25	PLA2G2A	PLA2G2A	PLA2G2A	3259	0.12	0.48	YES
26	SLC44A2	SLC44A2	SLC44A2	3338	0.11	0.48	YES
27	PNPLA8	PNPLA8	PNPLA8	4159	0.084	0.45	NO
28	AGPAT3	AGPAT3	AGPAT3	4464	0.074	0.44	NO
29	PLA2G12A	PLA2G12A	PLA2G12A	4759	0.065	0.43	NO
30	GPAT2	GPAT2	GPAT2	5151	0.055	0.41	NO
31	LPCAT2	LPCAT2	LPCAT2	5626	0.045	0.39	NO
32	PLA2G4A	PLA2G4A	PLA2G4A	5962	0.039	0.38	NO
33	HADHB	HADHB	HADHB	6285	0.032	0.36	NO
34	CEPT1	CEPT1	CEPT1	6554	0.028	0.35	NO
35	LPIN3	LPIN3	LPIN3	6570	0.028	0.36	NO
36	PCYT1A	PCYT1A	PCYT1A	6800	0.024	0.34	NO
37	LPCAT4	LPCAT4	LPCAT4	6844	0.023	0.34	NO
38	PITPNB	PITPNB	PITPNB	7100	0.02	0.33	NO
39	PLA2G6	PLA2G6	PLA2G6	7137	0.019	0.33	NO
40	MBOAT1	MBOAT1	MBOAT1	7152	0.019	0.33	NO
41	HADHA	HADHA	HADHA	7583	0.012	0.31	NO
42	CHPT1	CHPT1	CHPT1	7610	0.012	0.31	NO
43	PLA2G5	PLA2G5	PLA2G5	8178	0.0036	0.28	NO
44	PEMT	PEMT	PEMT	8526	-0.0012	0.26	NO
45	PCYT1B	PCYT1B	PCYT1B	8553	-0.0015	0.26	NO
46	SLC44A4	SLC44A4	SLC44A4	9097	-0.0086	0.23	NO
47	PNPLA2	PNPLA2	PNPLA2	9175	-0.0095	0.23	NO
48	EPT1	EPT1	EPT1	9466	-0.013	0.22	NO
49	GPAM	GPAM	GPAM	9589	-0.015	0.21	NO
50	MBOAT7	MBOAT7	MBOAT7	10234	-0.023	0.18	NO
51	ACHE	ACHE	ACHE	10488	-0.026	0.17	NO
52	PLD3	PLD3	PLD3	10527	-0.027	0.17	NO
53	TAZ	TAZ	TAZ	10892	-0.032	0.15	NO
54	LPGAT1	LPGAT1	LPGAT1	11024	-0.034	0.15	NO
55	GNPAT	GNPAT	GNPAT	11518	-0.04	0.13	NO
56	AGPAT6	AGPAT6	AGPAT6	11549	-0.041	0.13	NO
57	ETNK1	ETNK1	ETNK1	11633	-0.042	0.13	NO
58	LCLAT1	LCLAT1	LCLAT1	11787	-0.044	0.13	NO
59	DGAT1	DGAT1	DGAT1	12093	-0.049	0.11	NO
60	PTDSS2	PTDSS2	PTDSS2	12272	-0.051	0.11	NO
61	LPCAT3	LPCAT3	LPCAT3	12381	-0.053	0.11	NO
62	LPIN2	LPIN2	LPIN2	12560	-0.055	0.11	NO
63	CDIPT	CDIPT	CDIPT	12693	-0.057	0.1	NO
64	SLC44A1	SLC44A1	SLC44A1	12696	-0.057	0.11	NO
65	PCYT2	PCYT2	PCYT2	12724	-0.058	0.11	NO
66	AGPAT5	AGPAT5	AGPAT5	13069	-0.063	0.1	NO
67	CDS2	CDS2	CDS2	13388	-0.068	0.092	NO
68	CHKA	CHKA	CHKA	13554	-0.07	0.09	NO
69	CRLS1	CRLS1	CRLS1	14190	-0.083	0.065	NO
70	AGPAT1	AGPAT1	AGPAT1	14217	-0.084	0.072	NO
71	PLA2G4C	PLA2G4C	PLA2G4C	14668	-0.093	0.057	NO
72	PGS1	PGS1	PGS1	15522	-0.12	0.023	NO
73	PTDSS1	PTDSS1	PTDSS1	15901	-0.13	0.016	NO
74	AGPAT2	AGPAT2	AGPAT2	16066	-0.13	0.02	NO
75	GPD1	GPD1	GPD1	16362	-0.15	0.019	NO
76	PLD6	PLD6	PLD6	16645	-0.16	0.02	NO
77	PLA2G16	PLA2G16	PLA2G16	17234	-0.19	0.0075	NO
78	PLA2G1B	PLA2G1B	PLA2G1B	17606	-0.21	0.0092	NO
79	LPCAT1	LPCAT1	LPCAT1	17941	-0.24	0.016	NO
80	PLA2G10	PLA2G10	PLA2G10	18140	-0.27	0.033	NO

Figure S117. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS.

Figure S118. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING

Table S60. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	KAT2B	KAT2B	KAT2B	733	0.4	0.078	YES
2	SFN	SFN	SFN	835	0.37	0.18	YES
3	G6PC	G6PC	G6PC	1505	0.25	0.22	YES
4	SGK1	SGK1	SGK1	1748	0.22	0.27	YES
5	FBXO32	FBXO32	FBXO32	2328	0.17	0.28	YES
6	MAPK10	MAPK10	MAPK10	2583	0.15	0.32	YES
7	FASLG	FASLG	FASLG	3566	0.1	0.29	YES
8	RALA	RALA	RALA	3817	0.095	0.31	YES
9	CSNK1A1	CSNK1A1	CSNK1A1	3969	0.09	0.33	YES
10	CSNK1G1	CSNK1G1	CSNK1G1	4213	0.082	0.34	YES
11	IKBKB	IKBKB	IKBKB	4796	0.064	0.33	YES
12	BCL6	BCL6	BCL6	5080	0.057	0.33	YES
13	YWHAQ	YWHAQ	YWHAQ	5159	0.055	0.34	YES
14	YWHAZ	YWHAZ	YWHAZ	5560	0.046	0.33	YES
15	FOXO3	FOXO3	FOXO3	5685	0.044	0.34	YES
16	FOXO1	FOXO1	FOXO1	5777	0.042	0.34	YES
17	EP300	EP300	EP300	5848	0.04	0.35	YES
18	FOXO4	FOXO4	FOXO4	5911	0.04	0.36	YES
19	RALB	RALB	RALB	5936	0.039	0.37	YES
20	USP7	USP7	USP7	6917	0.022	0.33	NO
21	CDKN1B	CDKN1B	CDKN1B	7113	0.019	0.32	NO
22	CSNK1E	CSNK1E	CSNK1E	7369	0.015	0.31	NO
23	MAPK8	MAPK8	MAPK8	7737	0.01	0.3	NO
24	ZFAND5	ZFAND5	ZFAND5	7829	0.0088	0.29	NO
25	CSNK1G3	CSNK1G3	CSNK1G3	8096	0.0048	0.28	NO
26	YWHAB	YWHAB	YWHAB	8192	0.0035	0.28	NO
27	BCL2L11	BCL2L11	BCL2L11	8228	0.003	0.28	NO
28	YWHAE	YWHAE	YWHAE	8267	0.0023	0.27	NO
29	CREBBP	CREBBP	CREBBP	8347	0.0012	0.27	NO
30	RBL2	RBL2	RBL2	8356	0.0011	0.27	NO
31	SIRT1	SIRT1	SIRT1	8461	-0.00038	0.26	NO
32	CSNK1G2	CSNK1G2	CSNK1G2	9140	-0.0091	0.23	NO
33	SOD2	SOD2	SOD2	9181	-0.0096	0.23	NO
34	CTNNB1	CTNNB1	CTNNB1	9385	-0.012	0.22	NO
35	GADD45A	GADD45A	GADD45A	9732	-0.017	0.21	NO
36	CSNK1D	CSNK1D	CSNK1D	10014	-0.02	0.2	NO
37	SKP2	SKP2	SKP2	10037	-0.021	0.21	NO
38	RAN	RAN	RAN	11339	-0.038	0.15	NO
39	CHUK	CHUK	CHUK	11405	-0.039	0.16	NO
40	XPO1	XPO1	XPO1	12004	-0.048	0.14	NO
41	YWHAG	YWHAG	YWHAG	12055	-0.048	0.15	NO
42	AKT1	AKT1	AKT1	12218	-0.05	0.16	NO
43	MST1	MST1	MST1	13172	-0.064	0.12	NO
44	YWHAH	YWHAH	YWHAH	13983	-0.079	0.1	NO
45	CAT	CAT	CAT	14657	-0.093	0.095	NO
46	CCNB1	CCNB1	CCNB1	14713	-0.094	0.12	NO
47	MAPK9	MAPK9	MAPK9	14790	-0.096	0.14	NO
48	CDK2	CDK2	CDK2	14956	-0.1	0.16	NO
49	PLK1	PLK1	PLK1	16023	-0.13	0.15	NO

Figure S119. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING.

Figure S120. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING, 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 = ESCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = ESCA-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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