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

Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in KIPAN-TP. Broad Institute of MIT and Harvard. doi:10.7908/C17080F3

Overview

Introduction

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

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

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 194
Number of samples: 889
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus4 ] 271
pheno.type: 2 - 4 :[ clus1 ] 122
pheno.type: 3 - 4 :[ clus2 ] 196
pheno.type: 4 - 4 :[ clus3 ] 300

For the expression subtypes of 18216 genes in 890 samples, GSEA found enriched gene sets in each cluster using 889 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA RHO PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG OXIDATIVE PHOSPHORYLATION, KEGG O GLYCAN BIOSYNTHESIS, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG SPLICEOSOME, KEGG ERBB SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

And common core enriched genes are ATP5A1, ATP5B, ATP5D, ATP5E, ATP5G1, ATP5G3, ATP5J, ATP5O, COX4I1, COX5A

clus2

Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA G1 PATHWAY, BIOCARTA INFLAM PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY

And common core enriched genes are CCL4, CCL5, CXCL10, IFNB1, IKBKE, IL1B, IL6, IRF7, CCNB1, CCNB2

clus3

Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA MET PATHWAY, BIOCARTA TCR PATHWAY, BIOCARTA PAR1 PATHWAY, BIOCARTA TOLL PATHWAY, BIOCARTA VEGF PATHWAY, KEGG TRYPTOPHAN METABOLISM

And common core enriched genes are ARHGDIB, CYP4A11, CYP4A22, AQP3, AQP4, AVPR2, CREB3L3, DYNC1I1, DYNC2H1, ACADL

clus4

Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG OXIDATIVE PHOSPHORYLATION, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

And common core enriched genes are APEX2, LIG1, MPG, MUTYH, NEIL1, NEIL2, NTHL1, OGG1, PARP3, PARP4

Results

Subtype clus1 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA NO1 PATHWAY	28	genes.ES.table	0.47	1	0.44	1	1	0.29	0.18	0.24	1	0.55
BIOCARTA AGR PATHWAY	34	genes.ES.table	0.45	1.4	0.063	0.65	0.9	0.12	0.025	0.12	0.51	0.22
BIOCARTA RHO PATHWAY	31	genes.ES.table	0.29	1.1	0.31	1	1	0.23	0.18	0.18	0.93	0.45
KEGG CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.54	1.3	0.22	0.87	0.96	0.59	0.18	0.48	0.75	0.34
KEGG OXIDATIVE PHOSPHORYLATION	113	genes.ES.table	0.63	1.7	0.033	0.4	0.52	0.74	0.23	0.57	0.18	0.13
KEGG O GLYCAN BIOSYNTHESIS	28	genes.ES.table	0.35	1	0.41	1	1	0.21	0.068	0.2	1	0.52
KEGG INOSITOL PHOSPHATE METABOLISM	53	genes.ES.table	0.37	1.3	0.19	0.82	0.98	0.23	0.13	0.2	0.71	0.3
KEGG SPLICEOSOME	125	genes.ES.table	0.24	1.1	0.36	1	1	0.97	0.66	0.33	1	0.54
KEGG ERBB SIGNALING PATHWAY	86	genes.ES.table	0.32	1.3	0.13	0.76	0.98	0.1	0.044	0.1	0.66	0.26
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM	74	genes.ES.table	0.33	1.2	0.23	0.86	1	0.2	0.11	0.18	0.78	0.33

genes ES table in pathway: BIOCARTA NO1 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ATP6V0A4	ATP6V0A4	ATP6V0A4	19	1.4	0.092	YES
2	ATP6V1B1	ATP6V1B1	ATP6V1B1	31	1.3	0.18	YES
3	CFTR	CFTR	CFTR	44	1.2	0.26	YES
4	ATP6V0D2	ATP6V0D2	ATP6V0D2	68	1.1	0.33	YES
5	PLCG2	PLCG2	PLCG2	172	0.89	0.38	YES
6	KCNQ1	KCNQ1	KCNQ1	194	0.86	0.44	YES
7	ATP6V1C2	ATP6V1C2	ATP6V1C2	221	0.81	0.49	YES
8	ATP6V1A	ATP6V1A	ATP6V1A	888	0.43	0.48	YES
9	ATP6V1H	ATP6V1H	ATP6V1H	1229	0.34	0.48	YES
10	SLC12A2	SLC12A2	SLC12A2	1331	0.32	0.5	YES
11	ATP6V0B	ATP6V0B	ATP6V0B	1366	0.32	0.52	YES
12	ATP6V0E2	ATP6V0E2	ATP6V0E2	1433	0.31	0.53	YES
13	ATP6V1D	ATP6V1D	ATP6V1D	1502	0.3	0.55	YES
14	ATP6V0C	ATP6V0C	ATP6V0C	1620	0.28	0.56	YES
15	ATP6AP1	ATP6AP1	ATP6AP1	2129	0.22	0.55	NO
16	ATP6V1E1	ATP6V1E1	ATP6V1E1	2289	0.21	0.55	NO
17	ATP6V1F	ATP6V1F	ATP6V1F	2848	0.17	0.54	NO
18	GNAS	GNAS	GNAS	3266	0.14	0.52	NO
19	ATP6V0D1	ATP6V0D1	ATP6V0D1	3271	0.14	0.53	NO
20	ATP6V1G1	ATP6V1G1	ATP6V1G1	3783	0.12	0.51	NO
21	ATP6V0A2	ATP6V0A2	ATP6V0A2	4094	0.11	0.5	NO
22	ATP6V0E1	ATP6V0E1	ATP6V0E1	4180	0.1	0.5	NO
23	ERO1L	ERO1L	ERO1L	4409	0.095	0.5	NO
24	PRKACA	PRKACA	PRKACA	4871	0.079	0.48	NO
25	PRKCA	PRKCA	PRKCA	5081	0.072	0.47	NO
26	MUC2	MUC2	MUC2	5156	0.07	0.47	NO
27	TJP2	TJP2	TJP2	5292	0.065	0.47	NO
28	KDELR1	KDELR1	KDELR1	5526	0.058	0.46	NO
29	PRKACB	PRKACB	PRKACB	5752	0.052	0.45	NO
30	SEC61B	SEC61B	SEC61B	6099	0.041	0.43	NO
31	ATP6V1C1	ATP6V1C1	ATP6V1C1	6186	0.038	0.43	NO
32	SEC61A1	SEC61A1	SEC61A1	6191	0.038	0.43	NO
33	ATP6V1E2	ATP6V1E2	ATP6V1E2	6491	0.03	0.42	NO
34	TJP1	TJP1	TJP1	7412	0.005	0.37	NO
35	ARF1	ARF1	ARF1	7863	-0.007	0.34	NO
36	ACTB	ACTB	ACTB	8486	-0.024	0.31	NO
37	ACTG1	ACTG1	ACTG1	8837	-0.034	0.29	NO
38	TCIRG1	TCIRG1	TCIRG1	9744	-0.058	0.25	NO
39	SEC61G	SEC61G	SEC61G	10214	-0.073	0.23	NO
40	KDELR2	KDELR2	KDELR2	10310	-0.076	0.23	NO
41	PLCG1	PLCG1	PLCG1	11606	-0.12	0.16	NO
42	ATP6V1B2	ATP6V1B2	ATP6V1B2	12485	-0.16	0.12	NO
43	PDIA4	PDIA4	PDIA4	13019	-0.18	0.11	NO
44	ADCY9	ADCY9	ADCY9	13120	-0.19	0.11	NO
45	PRKCG	PRKCG	PRKCG	14342	-0.26	0.063	NO
46	SEC61A2	SEC61A2	SEC61A2	14353	-0.26	0.08	NO
47	ATP6V0A1	ATP6V0A1	ATP6V0A1	14609	-0.28	0.084	NO
48	ATP6V1G2	ATP6V1G2	ATP6V1G2	14739	-0.29	0.096	NO
49	PRKX	PRKX	PRKX	14861	-0.3	0.11	NO
50	KDELR3	KDELR3	KDELR3	16876	-0.53	0.033	NO
51	PRKCB	PRKCB	PRKCB	17308	-0.61	0.049	NO

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

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

genes ES table in pathway: BIOCARTA AGR PATHWAY

Table S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ATP6V0A4	ATP6V0A4	ATP6V0A4	19	1.4	0.056	YES
2	ATP6V1B1	ATP6V1B1	ATP6V1B1	31	1.3	0.11	YES
3	ATP6V0D2	ATP6V0D2	ATP6V0D2	68	1.1	0.15	YES
4	ATP6V1C2	ATP6V1C2	ATP6V1C2	221	0.81	0.18	YES
5	ATP4B	ATP4B	ATP4B	669	0.5	0.17	YES
6	COX7A1	COX7A1	COX7A1	762	0.46	0.18	YES
7	ATP6V1A	ATP6V1A	ATP6V1A	888	0.43	0.2	YES
8	ATP6V1H	ATP6V1H	ATP6V1H	1229	0.34	0.19	YES
9	COX5A	COX5A	COX5A	1257	0.34	0.2	YES
10	UQCRFS1	UQCRFS1	UQCRFS1	1342	0.32	0.21	YES
11	ATP6V0B	ATP6V0B	ATP6V0B	1366	0.32	0.22	YES
12	NDUFA4	NDUFA4	NDUFA4	1428	0.31	0.23	YES
13	ATP6V0E2	ATP6V0E2	ATP6V0E2	1433	0.31	0.24	YES
14	NDUFA6	NDUFA6	NDUFA6	1457	0.3	0.25	YES
15	ATP12A	ATP12A	ATP12A	1467	0.3	0.27	YES
16	ATP6V1D	ATP6V1D	ATP6V1D	1502	0.3	0.28	YES
17	COX7B	COX7B	COX7B	1551	0.29	0.28	YES
18	COX8A	COX8A	COX8A	1561	0.29	0.3	YES
19	COX6C	COX6C	COX6C	1599	0.29	0.31	YES
20	ATP6V0C	ATP6V0C	ATP6V0C	1620	0.28	0.32	YES
21	UQCRC1	UQCRC1	UQCRC1	1655	0.28	0.33	YES
22	ATP5A1	ATP5A1	ATP5A1	1798	0.26	0.33	YES
23	NDUFS7	NDUFS7	NDUFS7	1837	0.26	0.34	YES
24	NDUFS8	NDUFS8	NDUFS8	1920	0.25	0.34	YES
25	UQCR10	UQCR10	UQCR10	1942	0.24	0.35	YES
26	SDHD	SDHD	SDHD	1970	0.24	0.36	YES
27	NDUFA3	NDUFA3	NDUFA3	1987	0.24	0.37	YES
28	PPA2	PPA2	PPA2	1991	0.24	0.38	YES
29	NDUFA8	NDUFA8	NDUFA8	2004	0.24	0.39	YES
30	UQCR11	UQCR11	UQCR11	2016	0.24	0.4	YES
31	COX6A1	COX6A1	COX6A1	2058	0.23	0.4	YES
32	CYC1	CYC1	CYC1	2071	0.23	0.41	YES
33	NDUFB1	NDUFB1	NDUFB1	2108	0.23	0.42	YES
34	ATP6AP1	ATP6AP1	ATP6AP1	2129	0.22	0.43	YES
35	NDUFV1	NDUFV1	NDUFV1	2175	0.22	0.43	YES
36	ATP5B	ATP5B	ATP5B	2207	0.22	0.44	YES
37	NDUFC2	NDUFC2	NDUFC2	2232	0.22	0.45	YES
38	ATP5L	ATP5L	ATP5L	2239	0.21	0.46	YES
39	ATP6V1E1	ATP6V1E1	ATP6V1E1	2289	0.21	0.46	YES
40	COX17	COX17	COX17	2295	0.21	0.47	YES
41	ATP5D	ATP5D	ATP5D	2353	0.2	0.47	YES
42	UQCRHL	UQCRHL	UQCRHL	2369	0.2	0.48	YES
43	SDHA	SDHA	SDHA	2412	0.2	0.49	YES
44	NDUFB7	NDUFB7	NDUFB7	2444	0.2	0.49	YES
45	COX7A2	COX7A2	COX7A2	2470	0.19	0.5	YES
46	UQCRH	UQCRH	UQCRH	2489	0.19	0.51	YES
47	NDUFA9	NDUFA9	NDUFA9	2569	0.19	0.51	YES
48	NDUFB2	NDUFB2	NDUFB2	2619	0.18	0.52	YES
49	NDUFB9	NDUFB9	NDUFB9	2679	0.18	0.52	YES
50	UQCRQ	UQCRQ	UQCRQ	2769	0.18	0.52	YES
51	NDUFA7	NDUFA7	NDUFA7	2786	0.17	0.53	YES
52	NDUFS3	NDUFS3	NDUFS3	2819	0.17	0.53	YES
53	NDUFB6	NDUFB6	NDUFB6	2838	0.17	0.54	YES
54	ATP6V1F	ATP6V1F	ATP6V1F	2848	0.17	0.54	YES
55	COX7C	COX7C	COX7C	2854	0.17	0.55	YES
56	COX6B1	COX6B1	COX6B1	2874	0.17	0.56	YES
57	UQCRC2	UQCRC2	UQCRC2	2938	0.16	0.56	YES
58	NDUFA5	NDUFA5	NDUFA5	2958	0.16	0.56	YES
59	COX4I1	COX4I1	COX4I1	2959	0.16	0.57	YES
60	ATP5I	ATP5I	ATP5I	2976	0.16	0.58	YES
61	NDUFS6	NDUFS6	NDUFS6	3107	0.15	0.58	YES
62	NDUFA1	NDUFA1	NDUFA1	3116	0.15	0.58	YES
63	NDUFS1	NDUFS1	NDUFS1	3158	0.15	0.59	YES
64	ATP5J	ATP5J	ATP5J	3223	0.15	0.59	YES
65	ATP6V0D1	ATP6V0D1	ATP6V0D1	3271	0.14	0.59	YES
66	ATP5E	ATP5E	ATP5E	3278	0.14	0.6	YES
67	NDUFAB1	NDUFAB1	NDUFAB1	3280	0.14	0.6	YES
68	NDUFA11	NDUFA11	NDUFA11	3375	0.14	0.6	YES
69	COX5B	COX5B	COX5B	3386	0.14	0.61	YES
70	UQCRB	UQCRB	UQCRB	3400	0.14	0.61	YES
71	NDUFB5	NDUFB5	NDUFB5	3423	0.14	0.62	YES
72	NDUFV2	NDUFV2	NDUFV2	3516	0.13	0.62	YES
73	ATP5G3	ATP5G3	ATP5G3	3547	0.13	0.62	YES
74	ATP5G1	ATP5G1	ATP5G1	3703	0.12	0.62	YES
75	ATP5J2	ATP5J2	ATP5J2	3705	0.12	0.62	YES
76	ATP5O	ATP5O	ATP5O	3734	0.12	0.63	YES
77	ATP6V1G1	ATP6V1G1	ATP6V1G1	3783	0.12	0.63	YES
78	NDUFS2	NDUFS2	NDUFS2	3955	0.11	0.62	YES
79	ATP6V0A2	ATP6V0A2	ATP6V0A2	4094	0.11	0.62	YES
80	NDUFB8	NDUFB8	NDUFB8	4138	0.1	0.62	YES
81	ATP6V0E1	ATP6V0E1	ATP6V0E1	4180	0.1	0.62	YES
82	NDUFS4	NDUFS4	NDUFS4	4231	0.1	0.62	YES
83	COX7A2L	COX7A2L	COX7A2L	4239	0.1	0.63	YES
84	NDUFA10	NDUFA10	NDUFA10	4362	0.097	0.63	NO
85	NDUFB10	NDUFB10	NDUFB10	4438	0.094	0.63	NO
86	NDUFB4	NDUFB4	NDUFB4	4660	0.086	0.62	NO
87	SDHB	SDHB	SDHB	4826	0.081	0.61	NO
88	NDUFA2	NDUFA2	NDUFA2	4984	0.075	0.61	NO
89	ATP5F1	ATP5F1	ATP5F1	5111	0.071	0.6	NO
90	NDUFC1	NDUFC1	NDUFC1	5192	0.068	0.6	NO
91	ATP5C1	ATP5C1	ATP5C1	5305	0.065	0.6	NO
92	ATP5H	ATP5H	ATP5H	5355	0.064	0.6	NO
93	NDUFV3	NDUFV3	NDUFV3	5427	0.061	0.6	NO
94	NDUFB3	NDUFB3	NDUFB3	5882	0.047	0.57	NO
95	COX10	COX10	COX10	5923	0.046	0.57	NO
96	ATP6V1C1	ATP6V1C1	ATP6V1C1	6186	0.038	0.56	NO
97	SDHC	SDHC	SDHC	6201	0.038	0.56	NO
98	ATP6V1E2	ATP6V1E2	ATP6V1E2	6491	0.03	0.54	NO
99	COX4I2	COX4I2	COX4I2	6750	0.023	0.53	NO
100	NDUFS5	NDUFS5	NDUFS5	6971	0.017	0.52	NO
101	ATP5G2	ATP5G2	ATP5G2	7305	0.0081	0.5	NO
102	PPA1	PPA1	PPA1	9612	-0.055	0.38	NO
103	COX11	COX11	COX11	9661	-0.056	0.38	NO
104	TCIRG1	TCIRG1	TCIRG1	9744	-0.058	0.37	NO
105	COX15	COX15	COX15	10360	-0.077	0.34	NO
106	COX6B2	COX6B2	COX6B2	10947	-0.096	0.31	NO
107	ATP6V1B2	ATP6V1B2	ATP6V1B2	12485	-0.16	0.24	NO
108	ATP6V0A1	ATP6V0A1	ATP6V0A1	14609	-0.28	0.13	NO
109	ATP6V1G2	ATP6V1G2	ATP6V1G2	14739	-0.29	0.13	NO
110	LHPP	LHPP	LHPP	15234	-0.33	0.12	NO
111	NDUFA4L2	NDUFA4L2	NDUFA4L2	15380	-0.34	0.13	NO
112	COX6A2	COX6A2	COX6A2	15527	-0.36	0.13	NO
113	COX8C	COX8C	COX8C	15792	-0.38	0.13	NO

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

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

genes ES table in pathway: BIOCARTA RHO PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GPR37	GPR37	GPR37	497	0.59	0.0014	YES
2	COX7A1	COX7A1	COX7A1	762	0.46	0.0096	YES
3	SLC25A4	SLC25A4	SLC25A4	954	0.41	0.019	YES
4	SNCAIP	SNCAIP	SNCAIP	1004	0.39	0.036	YES
5	SLC25A5	SLC25A5	SLC25A5	1073	0.38	0.05	YES
6	UCHL1	UCHL1	UCHL1	1124	0.36	0.065	YES
7	CYCS	CYCS	CYCS	1198	0.35	0.078	YES
8	COX5A	COX5A	COX5A	1257	0.34	0.092	YES
9	UQCRFS1	UQCRFS1	UQCRFS1	1342	0.32	0.1	YES
10	SNCA	SNCA	SNCA	1419	0.31	0.11	YES
11	NDUFA4	NDUFA4	NDUFA4	1428	0.31	0.13	YES
12	NDUFA6	NDUFA6	NDUFA6	1457	0.3	0.14	YES
13	COX7B	COX7B	COX7B	1551	0.29	0.15	YES
14	COX8A	COX8A	COX8A	1561	0.29	0.16	YES
15	COX6C	COX6C	COX6C	1599	0.29	0.18	YES
16	UQCRC1	UQCRC1	UQCRC1	1655	0.28	0.19	YES
17	ATP5A1	ATP5A1	ATP5A1	1798	0.26	0.19	YES
18	NDUFS7	NDUFS7	NDUFS7	1837	0.26	0.2	YES
19	NDUFS8	NDUFS8	NDUFS8	1920	0.25	0.21	YES
20	UQCR10	UQCR10	UQCR10	1942	0.24	0.22	YES
21	SDHD	SDHD	SDHD	1970	0.24	0.23	YES
22	NDUFA3	NDUFA3	NDUFA3	1987	0.24	0.24	YES
23	NDUFA8	NDUFA8	NDUFA8	2004	0.24	0.25	YES
24	UQCR11	UQCR11	UQCR11	2016	0.24	0.26	YES
25	COX6A1	COX6A1	COX6A1	2058	0.23	0.27	YES
26	CYC1	CYC1	CYC1	2071	0.23	0.28	YES
27	NDUFB1	NDUFB1	NDUFB1	2108	0.23	0.29	YES
28	NDUFV1	NDUFV1	NDUFV1	2175	0.22	0.3	YES
29	ATP5B	ATP5B	ATP5B	2207	0.22	0.31	YES
30	NDUFC2	NDUFC2	NDUFC2	2232	0.22	0.32	YES
31	ATP5D	ATP5D	ATP5D	2353	0.2	0.32	YES
32	UQCRHL	UQCRHL	UQCRHL	2369	0.2	0.33	YES
33	SDHA	SDHA	SDHA	2412	0.2	0.34	YES
34	NDUFB7	NDUFB7	NDUFB7	2444	0.2	0.35	YES
35	COX7A2	COX7A2	COX7A2	2470	0.19	0.35	YES
36	UQCRH	UQCRH	UQCRH	2489	0.19	0.36	YES
37	NDUFA9	NDUFA9	NDUFA9	2569	0.19	0.37	YES
38	NDUFB2	NDUFB2	NDUFB2	2619	0.18	0.37	YES
39	NDUFB9	NDUFB9	NDUFB9	2679	0.18	0.38	YES
40	UQCRQ	UQCRQ	UQCRQ	2769	0.18	0.38	YES
41	NDUFA7	NDUFA7	NDUFA7	2786	0.17	0.39	YES
42	NDUFS3	NDUFS3	NDUFS3	2819	0.17	0.4	YES
43	NDUFB6	NDUFB6	NDUFB6	2838	0.17	0.4	YES
44	COX7C	COX7C	COX7C	2854	0.17	0.41	YES
45	COX6B1	COX6B1	COX6B1	2874	0.17	0.42	YES
46	UQCRC2	UQCRC2	UQCRC2	2938	0.16	0.42	YES
47	NDUFA5	NDUFA5	NDUFA5	2958	0.16	0.43	YES
48	COX4I1	COX4I1	COX4I1	2959	0.16	0.44	YES
49	NDUFS6	NDUFS6	NDUFS6	3107	0.15	0.44	YES
50	NDUFA1	NDUFA1	NDUFA1	3116	0.15	0.44	YES
51	NDUFS1	NDUFS1	NDUFS1	3158	0.15	0.45	YES
52	PPID	PPID	PPID	3174	0.15	0.46	YES
53	ATP5J	ATP5J	ATP5J	3223	0.15	0.46	YES
54	ATP5E	ATP5E	ATP5E	3278	0.14	0.46	YES
55	NDUFAB1	NDUFAB1	NDUFAB1	3280	0.14	0.47	YES
56	UBA1	UBA1	UBA1	3306	0.14	0.48	YES
57	SLC25A6	SLC25A6	SLC25A6	3315	0.14	0.48	YES
58	COX5B	COX5B	COX5B	3386	0.14	0.49	YES
59	UQCRB	UQCRB	UQCRB	3400	0.14	0.49	YES
60	NDUFB5	NDUFB5	NDUFB5	3423	0.14	0.5	YES
61	TH	TH	TH	3464	0.14	0.5	YES
62	NDUFV2	NDUFV2	NDUFV2	3516	0.13	0.51	YES
63	ATP5G3	ATP5G3	ATP5G3	3547	0.13	0.51	YES
64	ATP5G1	ATP5G1	ATP5G1	3703	0.12	0.51	YES
65	ATP5O	ATP5O	ATP5O	3734	0.12	0.51	YES
66	PINK1	PINK1	PINK1	3860	0.12	0.51	YES
67	NDUFS2	NDUFS2	NDUFS2	3955	0.11	0.51	YES
68	NDUFB8	NDUFB8	NDUFB8	4138	0.1	0.51	YES
69	NDUFS4	NDUFS4	NDUFS4	4231	0.1	0.51	YES
70	COX7A2L	COX7A2L	COX7A2L	4239	0.1	0.51	YES
71	SLC18A2	SLC18A2	SLC18A2	4324	0.098	0.51	YES
72	VDAC1	VDAC1	VDAC1	4336	0.098	0.52	YES
73	NDUFA10	NDUFA10	NDUFA10	4362	0.097	0.52	YES
74	NDUFB10	NDUFB10	NDUFB10	4438	0.094	0.52	YES
75	PARK2	PARK2	PARK2	4550	0.09	0.52	YES
76	VDAC2	VDAC2	VDAC2	4576	0.089	0.52	YES
77	NDUFB4	NDUFB4	NDUFB4	4660	0.086	0.52	NO
78	SDHB	SDHB	SDHB	4826	0.081	0.52	NO
79	VDAC3	VDAC3	VDAC3	4942	0.077	0.51	NO
80	NDUFA2	NDUFA2	NDUFA2	4984	0.075	0.52	NO
81	ATP5F1	ATP5F1	ATP5F1	5111	0.071	0.51	NO
82	NDUFC1	NDUFC1	NDUFC1	5192	0.068	0.51	NO
83	ATP5C1	ATP5C1	ATP5C1	5305	0.065	0.51	NO
84	ATP5H	ATP5H	ATP5H	5355	0.064	0.51	NO
85	NDUFV3	NDUFV3	NDUFV3	5427	0.061	0.51	NO
86	UBE2L6	UBE2L6	UBE2L6	5685	0.054	0.5	NO
87	NDUFB3	NDUFB3	NDUFB3	5882	0.047	0.49	NO
88	SDHC	SDHC	SDHC	6201	0.038	0.47	NO
89	UBE2L3	UBE2L3	UBE2L3	6270	0.036	0.47	NO
90	COX4I2	COX4I2	COX4I2	6750	0.023	0.44	NO
91	NDUFS5	NDUFS5	NDUFS5	6971	0.017	0.43	NO
92	ATP5G2	ATP5G2	ATP5G2	7305	0.0081	0.41	NO
93	UBB	UBB	UBB	7801	-0.005	0.39	NO
94	CASP3	CASP3	CASP3	7836	-0.0063	0.39	NO
95	UBE2G1	UBE2G1	UBE2G1	9175	-0.042	0.31	NO
96	UBE2G2	UBE2G2	UBE2G2	9435	-0.05	0.3	NO
97	PARK7	PARK7	PARK7	9438	-0.05	0.3	NO
98	CASP9	CASP9	CASP9	10412	-0.078	0.25	NO
99	COX6B2	COX6B2	COX6B2	10947	-0.096	0.23	NO
100	UBE2J2	UBE2J2	UBE2J2	10976	-0.098	0.23	NO
101	SLC18A1	SLC18A1	SLC18A1	11285	-0.11	0.22	NO
102	UBA7	UBA7	UBA7	11344	-0.11	0.22	NO
103	APAF1	APAF1	APAF1	11880	-0.13	0.2	NO
104	UBE2J1	UBE2J1	UBE2J1	12864	-0.17	0.15	NO
105	HTRA2	HTRA2	HTRA2	13335	-0.2	0.14	NO
106	NDUFA4L2	NDUFA4L2	NDUFA4L2	15380	-0.34	0.042	NO
107	COX6A2	COX6A2	COX6A2	15527	-0.36	0.051	NO
108	COX8C	COX8C	COX8C	15792	-0.38	0.055	NO
109	SLC6A3	SLC6A3	SLC6A3	17631	-0.69	-0.012	NO
110	LRRK2	LRRK2	LRRK2	17968	-0.89	0.013	NO

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

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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	BACE2	BACE2	BACE2	658	0.5	-0.018	YES
2	ITPR1	ITPR1	ITPR1	709	0.48	-0.0024	YES
3	ITPR2	ITPR2	ITPR2	742	0.47	0.014	YES
4	COX7A1	COX7A1	COX7A1	762	0.46	0.03	YES
5	CACNA1D	CACNA1D	CACNA1D	1065	0.38	0.027	YES
6	GRIN1	GRIN1	GRIN1	1067	0.38	0.042	YES
7	CYCS	CYCS	CYCS	1198	0.35	0.047	YES
8	COX5A	COX5A	COX5A	1257	0.34	0.057	YES
9	UQCRFS1	UQCRFS1	UQCRFS1	1342	0.32	0.064	YES
10	SNCA	SNCA	SNCA	1419	0.31	0.072	YES
11	NDUFA4	NDUFA4	NDUFA4	1428	0.31	0.083	YES
12	NDUFA6	NDUFA6	NDUFA6	1457	0.3	0.093	YES
13	COX7B	COX7B	COX7B	1551	0.29	0.099	YES
14	COX8A	COX8A	COX8A	1561	0.29	0.11	YES
15	COX6C	COX6C	COX6C	1599	0.29	0.12	YES
16	UQCRC1	UQCRC1	UQCRC1	1655	0.28	0.12	YES
17	ATP5A1	ATP5A1	ATP5A1	1798	0.26	0.13	YES
18	NDUFS7	NDUFS7	NDUFS7	1837	0.26	0.13	YES
19	NDUFS8	NDUFS8	NDUFS8	1920	0.25	0.14	YES
20	UQCR10	UQCR10	UQCR10	1942	0.24	0.15	YES
21	SDHD	SDHD	SDHD	1970	0.24	0.16	YES
22	NDUFA3	NDUFA3	NDUFA3	1987	0.24	0.16	YES
23	NDUFA8	NDUFA8	NDUFA8	2004	0.24	0.17	YES
24	UQCR11	UQCR11	UQCR11	2016	0.24	0.18	YES
25	COX6A1	COX6A1	COX6A1	2058	0.23	0.19	YES
26	CYC1	CYC1	CYC1	2071	0.23	0.19	YES
27	NDUFB1	NDUFB1	NDUFB1	2108	0.23	0.2	YES
28	NDUFV1	NDUFV1	NDUFV1	2175	0.22	0.2	YES
29	ATP5B	ATP5B	ATP5B	2207	0.22	0.21	YES
30	NDUFC2	NDUFC2	NDUFC2	2232	0.22	0.22	YES
31	ATP5D	ATP5D	ATP5D	2353	0.2	0.22	YES
32	UQCRHL	UQCRHL	UQCRHL	2369	0.2	0.23	YES
33	SDHA	SDHA	SDHA	2412	0.2	0.23	YES
34	NDUFB7	NDUFB7	NDUFB7	2444	0.2	0.24	YES
35	COX7A2	COX7A2	COX7A2	2470	0.19	0.24	YES
36	UQCRH	UQCRH	UQCRH	2489	0.19	0.25	YES
37	NDUFA9	NDUFA9	NDUFA9	2569	0.19	0.25	YES
38	NDUFB2	NDUFB2	NDUFB2	2619	0.18	0.26	YES
39	NDUFB9	NDUFB9	NDUFB9	2679	0.18	0.26	YES
40	UQCRQ	UQCRQ	UQCRQ	2769	0.18	0.26	YES
41	NDUFA7	NDUFA7	NDUFA7	2786	0.17	0.27	YES
42	NDUFS3	NDUFS3	NDUFS3	2819	0.17	0.27	YES
43	NDUFB6	NDUFB6	NDUFB6	2838	0.17	0.28	YES
44	NOS1	NOS1	NOS1	2846	0.17	0.28	YES
45	COX7C	COX7C	COX7C	2854	0.17	0.29	YES
46	COX6B1	COX6B1	COX6B1	2874	0.17	0.29	YES
47	UQCRC2	UQCRC2	UQCRC2	2938	0.16	0.3	YES
48	NDUFA5	NDUFA5	NDUFA5	2958	0.16	0.3	YES
49	COX4I1	COX4I1	COX4I1	2959	0.16	0.31	YES
50	NDUFS6	NDUFS6	NDUFS6	3107	0.15	0.3	YES
51	NDUFA1	NDUFA1	NDUFA1	3116	0.15	0.31	YES
52	NDUFS1	NDUFS1	NDUFS1	3158	0.15	0.31	YES
53	CAPN2	CAPN2	CAPN2	3162	0.15	0.32	YES
54	PSEN2	PSEN2	PSEN2	3173	0.15	0.32	YES
55	ATP5J	ATP5J	ATP5J	3223	0.15	0.33	YES
56	ATP5E	ATP5E	ATP5E	3278	0.14	0.33	YES
57	NDUFAB1	NDUFAB1	NDUFAB1	3280	0.14	0.34	YES
58	PPP3CA	PPP3CA	PPP3CA	3302	0.14	0.34	YES
59	COX5B	COX5B	COX5B	3386	0.14	0.34	YES
60	UQCRB	UQCRB	UQCRB	3400	0.14	0.34	YES
61	NDUFB5	NDUFB5	NDUFB5	3423	0.14	0.35	YES
62	NDUFV2	NDUFV2	NDUFV2	3516	0.13	0.35	YES
63	ATP5G3	ATP5G3	ATP5G3	3547	0.13	0.35	YES
64	CHP	CHP	CHP	3558	0.13	0.36	YES
65	PLCB4	PLCB4	PLCB4	3663	0.13	0.36	YES
66	ATP5G1	ATP5G1	ATP5G1	3703	0.12	0.36	YES
67	ATP5O	ATP5O	ATP5O	3734	0.12	0.36	YES
68	NDUFS2	NDUFS2	NDUFS2	3955	0.11	0.35	NO
69	NDUFB8	NDUFB8	NDUFB8	4138	0.1	0.35	NO
70	NDUFS4	NDUFS4	NDUFS4	4231	0.1	0.34	NO
71	COX7A2L	COX7A2L	COX7A2L	4239	0.1	0.35	NO
72	RYR3	RYR3	RYR3	4274	0.1	0.35	NO
73	EIF2AK3	EIF2AK3	EIF2AK3	4289	0.099	0.35	NO
74	NDUFA10	NDUFA10	NDUFA10	4362	0.097	0.35	NO
75	PPP3CC	PPP3CC	PPP3CC	4400	0.095	0.35	NO
76	NDUFB10	NDUFB10	NDUFB10	4438	0.094	0.36	NO
77	CAPN1	CAPN1	CAPN1	4633	0.087	0.35	NO
78	NDUFB4	NDUFB4	NDUFB4	4660	0.086	0.35	NO
79	SDHB	SDHB	SDHB	4826	0.081	0.34	NO
80	PSEN1	PSEN1	PSEN1	4849	0.08	0.34	NO
81	GSK3B	GSK3B	GSK3B	4962	0.076	0.34	NO
82	NDUFA2	NDUFA2	NDUFA2	4984	0.075	0.34	NO
83	ATP5F1	ATP5F1	ATP5F1	5111	0.071	0.34	NO
84	GNAQ	GNAQ	GNAQ	5142	0.07	0.34	NO
85	CALM3	CALM3	CALM3	5162	0.07	0.34	NO
86	NDUFC1	NDUFC1	NDUFC1	5192	0.068	0.34	NO
87	CALM2	CALM2	CALM2	5259	0.066	0.34	NO
88	ATP5C1	ATP5C1	ATP5C1	5305	0.065	0.34	NO
89	ATP5H	ATP5H	ATP5H	5355	0.064	0.34	NO
90	NDUFV3	NDUFV3	NDUFV3	5427	0.061	0.34	NO
91	BACE1	BACE1	BACE1	5782	0.051	0.32	NO
92	NDUFB3	NDUFB3	NDUFB3	5882	0.047	0.32	NO
93	SDHC	SDHC	SDHC	6201	0.038	0.3	NO
94	BAD	BAD	BAD	6286	0.036	0.3	NO
95	NAE1	NAE1	NAE1	6562	0.028	0.28	NO
96	COX4I2	COX4I2	COX4I2	6750	0.023	0.28	NO
97	NDUFS5	NDUFS5	NDUFS5	6971	0.017	0.26	NO
98	ATP5G2	ATP5G2	ATP5G2	7305	0.0081	0.24	NO
99	PLCB3	PLCB3	PLCB3	7504	0.003	0.23	NO
100	PPP3CB	PPP3CB	PPP3CB	7592	0.00076	0.23	NO
101	APP	APP	APP	7787	-0.0045	0.22	NO
102	APH1A	APH1A	APH1A	7830	-0.006	0.22	NO
103	CASP3	CASP3	CASP3	7836	-0.0063	0.22	NO
104	CACNA1S	CACNA1S	CACNA1S	7865	-0.007	0.22	NO
105	ERN1	ERN1	ERN1	7933	-0.0094	0.21	NO
106	CALML6	CALML6	CALML6	7937	-0.0095	0.21	NO
107	ATF6	ATF6	ATF6	7940	-0.0096	0.21	NO
108	MAPK1	MAPK1	MAPK1	7984	-0.011	0.21	NO
109	APBB1	APBB1	APBB1	8159	-0.015	0.2	NO
110	CALM1	CALM1	CALM1	8433	-0.023	0.19	NO
111	ATP2A2	ATP2A2	ATP2A2	8611	-0.028	0.18	NO
112	ADAM10	ADAM10	ADAM10	8766	-0.032	0.17	NO
113	PSENEN	PSENEN	PSENEN	8957	-0.036	0.16	NO
114	LPL	LPL	LPL	9536	-0.053	0.13	NO
115	CALML3	CALML3	CALML3	9620	-0.055	0.13	NO
116	IDE	IDE	IDE	9672	-0.056	0.13	NO
117	MAPK3	MAPK3	MAPK3	9692	-0.057	0.13	NO
118	CHP2	CHP2	CHP2	9748	-0.058	0.13	NO
119	ATP2A1	ATP2A1	ATP2A1	9970	-0.065	0.12	NO
120	HSD17B10	HSD17B10	HSD17B10	9995	-0.066	0.12	NO
121	NCSTN	NCSTN	NCSTN	10362	-0.077	0.1	NO
122	CASP9	CASP9	CASP9	10412	-0.078	0.1	NO
123	PPP3R2	PPP3R2	PPP3R2	10537	-0.083	0.099	NO
124	GAPDH	GAPDH	GAPDH	10641	-0.086	0.097	NO
125	COX6B2	COX6B2	COX6B2	10947	-0.096	0.084	NO
126	CDK5	CDK5	CDK5	11116	-0.1	0.078	NO
127	CASP7	CASP7	CASP7	11176	-0.1	0.079	NO
128	CACNA1C	CACNA1C	CACNA1C	11239	-0.11	0.079	NO
129	CDK5R1	CDK5R1	CDK5R1	11776	-0.13	0.054	NO
130	APAF1	APAF1	APAF1	11880	-0.13	0.054	NO
131	ADAM17	ADAM17	ADAM17	11895	-0.13	0.058	NO
132	FADD	FADD	FADD	12262	-0.14	0.043	NO
133	PPP3R1	PPP3R1	PPP3R1	12291	-0.15	0.047	NO
134	GRIN2C	GRIN2C	GRIN2C	12427	-0.15	0.045	NO
135	GRIN2A	GRIN2A	GRIN2A	12977	-0.18	0.021	NO
136	APOE	APOE	APOE	13157	-0.19	0.018	NO
137	ATP2A3	ATP2A3	ATP2A3	13406	-0.2	0.012	NO
138	GRIN2B	GRIN2B	GRIN2B	13822	-0.22	-0.0023	NO
139	ITPR3	ITPR3	ITPR3	14192	-0.25	-0.013	NO
140	CASP8	CASP8	CASP8	14504	-0.27	-0.02	NO
141	TNFRSF1A	TNFRSF1A	TNFRSF1A	14577	-0.28	-0.014	NO
142	LRP1	LRP1	LRP1	14690	-0.29	-0.0095	NO
143	IL1B	IL1B	IL1B	14786	-0.29	-0.0037	NO
144	GRIN2D	GRIN2D	GRIN2D	14922	-0.31	0.00027	NO
145	BID	BID	BID	15131	-0.32	0.00082	NO
146	NDUFA4L2	NDUFA4L2	NDUFA4L2	15380	-0.34	-6.6e-06	NO
147	TNF	TNF	TNF	15399	-0.35	0.012	NO
148	COX6A2	COX6A2	COX6A2	15527	-0.36	0.018	NO
149	MAPT	MAPT	MAPT	15635	-0.37	0.026	NO
150	COX8C	COX8C	COX8C	15792	-0.38	0.032	NO
151	PLCB1	PLCB1	PLCB1	16400	-0.46	0.016	NO
152	CACNA1F	CACNA1F	CACNA1F	16656	-0.5	0.02	NO
153	FAS	FAS	FAS	17026	-0.56	0.02	NO
154	PLCB2	PLCB2	PLCB2	17110	-0.57	0.037	NO
155	MME	MME	MME	17343	-0.62	0.047	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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

Table 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	UBE2QL1	UBE2QL1	UBE2QL1	142	0.94	0.047	YES
2	FBXO2	FBXO2	FBXO2	201	0.84	0.093	YES
3	SOCS1	SOCS1	SOCS1	491	0.59	0.11	YES
4	NEDD4L	NEDD4L	NEDD4L	689	0.49	0.13	YES
5	CBLC	CBLC	CBLC	804	0.45	0.15	YES
6	PIAS2	PIAS2	PIAS2	1584	0.29	0.12	YES
7	KLHL13	KLHL13	KLHL13	1586	0.29	0.14	YES
8	UBE2S	UBE2S	UBE2S	2332	0.21	0.11	YES
9	UBOX5	UBOX5	UBOX5	2524	0.19	0.11	YES
10	CUL5	CUL5	CUL5	2545	0.19	0.12	YES
11	WWP1	WWP1	WWP1	2609	0.18	0.13	YES
12	HERC1	HERC1	HERC1	2697	0.18	0.14	YES
13	SMURF1	SMURF1	SMURF1	2845	0.17	0.14	YES
14	WWP2	WWP2	WWP2	2973	0.16	0.14	YES
15	DET1	DET1	DET1	2984	0.16	0.15	YES
16	HERC3	HERC3	HERC3	3041	0.16	0.15	YES
17	DDB1	DDB1	DDB1	3159	0.15	0.16	YES
18	RHOBTB2	RHOBTB2	RHOBTB2	3269	0.14	0.16	YES
19	UBA1	UBA1	UBA1	3306	0.14	0.16	YES
20	UBE3C	UBE3C	UBE3C	3333	0.14	0.17	YES
21	UBE2H	UBE2H	UBE2H	3342	0.14	0.18	YES
22	VHL	VHL	VHL	3563	0.13	0.18	YES
23	UBE2M	UBE2M	UBE2M	3674	0.13	0.18	YES
24	ANAPC13	ANAPC13	ANAPC13	3717	0.12	0.18	YES
25	SYVN1	SYVN1	SYVN1	3760	0.12	0.19	YES
26	RCHY1	RCHY1	RCHY1	3905	0.12	0.19	YES
27	HERC2	HERC2	HERC2	3932	0.12	0.19	YES
28	UBE2Q2	UBE2Q2	UBE2Q2	4188	0.1	0.18	YES
29	XIAP	XIAP	XIAP	4268	0.1	0.18	YES
30	PIAS4	PIAS4	PIAS4	4285	0.1	0.19	YES
31	PIAS1	PIAS1	PIAS1	4311	0.099	0.19	YES
32	UBE2D4	UBE2D4	UBE2D4	4322	0.098	0.2	YES
33	PPIL2	PPIL2	PPIL2	4329	0.098	0.2	YES
34	TRAF6	TRAF6	TRAF6	4394	0.095	0.21	YES
35	KLHL9	KLHL9	KLHL9	4459	0.093	0.21	YES
36	STUB1	STUB1	STUB1	4532	0.09	0.21	YES
37	PARK2	PARK2	PARK2	4550	0.09	0.21	YES
38	FBXW11	FBXW11	FBXW11	4604	0.088	0.22	YES
39	UBE2K	UBE2K	UBE2K	4608	0.088	0.22	YES
40	ERCC8	ERCC8	ERCC8	4611	0.088	0.23	YES
41	UBA6	UBA6	UBA6	4706	0.085	0.23	YES
42	SAE1	SAE1	SAE1	4791	0.082	0.23	YES
43	CDC34	CDC34	CDC34	4802	0.081	0.23	YES
44	FZR1	FZR1	FZR1	4813	0.081	0.23	YES
45	UBE3A	UBE3A	UBE3A	5008	0.074	0.23	YES
46	ANAPC10	ANAPC10	ANAPC10	5044	0.073	0.23	YES
47	UBE3B	UBE3B	UBE3B	5124	0.071	0.23	YES
48	SIAH1	SIAH1	SIAH1	5141	0.07	0.23	YES
49	UBE2N	UBE2N	UBE2N	5165	0.069	0.24	YES
50	UBE2E1	UBE2E1	UBE2E1	5221	0.068	0.24	YES
51	UBE2D3	UBE2D3	UBE2D3	5230	0.067	0.24	YES
52	TCEB1	TCEB1	TCEB1	5231	0.067	0.24	YES
53	SKP1	SKP1	SKP1	5265	0.066	0.25	YES
54	UBE2NL	UBE2NL	UBE2NL	5314	0.065	0.25	YES
55	UBE2C	UBE2C	UBE2C	5425	0.061	0.24	YES
56	UBE2W	UBE2W	UBE2W	5472	0.06	0.25	YES
57	HUWE1	HUWE1	HUWE1	5478	0.06	0.25	YES
58	UBE2D1	UBE2D1	UBE2D1	5481	0.06	0.25	YES
59	NHLRC1	NHLRC1	NHLRC1	5492	0.059	0.26	YES
60	UBR5	UBR5	UBR5	5519	0.058	0.26	YES
61	UBE2L6	UBE2L6	UBE2L6	5685	0.054	0.25	NO
62	UBE2A	UBE2A	UBE2A	5744	0.052	0.25	NO
63	ANAPC11	ANAPC11	ANAPC11	5768	0.051	0.25	NO
64	CUL1	CUL1	CUL1	5873	0.047	0.25	NO
65	TCEB2	TCEB2	TCEB2	5878	0.047	0.25	NO
66	UBA3	UBA3	UBA3	6032	0.043	0.25	NO
67	UBE4A	UBE4A	UBE4A	6076	0.041	0.25	NO
68	UBE2B	UBE2B	UBE2B	6221	0.038	0.24	NO
69	UBE2L3	UBE2L3	UBE2L3	6270	0.036	0.24	NO
70	ANAPC5	ANAPC5	ANAPC5	6313	0.035	0.24	NO
71	KEAP1	KEAP1	KEAP1	6443	0.032	0.24	NO
72	TRIM32	TRIM32	TRIM32	6514	0.029	0.23	NO
73	RBX1	RBX1	RBX1	6647	0.026	0.23	NO
74	ITCH	ITCH	ITCH	6666	0.025	0.23	NO
75	UBA2	UBA2	UBA2	6733	0.024	0.22	NO
76	CUL4A	CUL4A	CUL4A	7079	0.014	0.21	NO
77	ANAPC2	ANAPC2	ANAPC2	7091	0.014	0.21	NO
78	CUL4B	CUL4B	CUL4B	7095	0.013	0.21	NO
79	PRPF19	PRPF19	PRPF19	7218	0.01	0.2	NO
80	UBE2I	UBE2I	UBE2I	7275	0.0089	0.2	NO
81	CUL2	CUL2	CUL2	7798	-0.0049	0.17	NO
82	CUL3	CUL3	CUL3	8038	-0.012	0.16	NO
83	CDC23	CDC23	CDC23	8059	-0.012	0.16	NO
84	FBXW8	FBXW8	FBXW8	8096	-0.013	0.16	NO
85	UBE2O	UBE2O	UBE2O	8257	-0.018	0.15	NO
86	ANAPC7	ANAPC7	ANAPC7	8336	-0.02	0.14	NO
87	UBE2R2	UBE2R2	UBE2R2	8581	-0.027	0.13	NO
88	CUL7	CUL7	CUL7	8623	-0.028	0.13	NO
89	BIRC6	BIRC6	BIRC6	8659	-0.029	0.13	NO
90	UBE2F	UBE2F	UBE2F	8772	-0.032	0.13	NO
91	CDC26	CDC26	CDC26	8928	-0.036	0.12	NO
92	TRIM37	TRIM37	TRIM37	9054	-0.039	0.12	NO
93	FBXW7	FBXW7	FBXW7	9065	-0.039	0.12	NO
94	RNF7	RNF7	RNF7	9129	-0.041	0.12	NO
95	UBE2G1	UBE2G1	UBE2G1	9175	-0.042	0.12	NO
96	ANAPC1	ANAPC1	ANAPC1	9250	-0.045	0.12	NO
97	UBE2G2	UBE2G2	UBE2G2	9435	-0.05	0.11	NO
98	CBL	CBL	CBL	9528	-0.052	0.11	NO
99	RFWD2	RFWD2	RFWD2	9577	-0.054	0.11	NO
100	MGRN1	MGRN1	MGRN1	9582	-0.054	0.11	NO
101	TRIP12	TRIP12	TRIP12	9850	-0.062	0.099	NO
102	ANAPC4	ANAPC4	ANAPC4	9866	-0.062	0.1	NO
103	UBE2D2	UBE2D2	UBE2D2	10150	-0.071	0.091	NO
104	UBE4B	UBE4B	UBE4B	10220	-0.073	0.091	NO
105	BIRC2	BIRC2	BIRC2	10233	-0.073	0.095	NO
106	PIAS3	PIAS3	PIAS3	10734	-0.089	0.072	NO
107	CDC27	CDC27	CDC27	10827	-0.092	0.073	NO
108	UBE2Q1	UBE2Q1	UBE2Q1	10905	-0.095	0.074	NO
109	MAP3K1	MAP3K1	MAP3K1	10943	-0.096	0.078	NO
110	UBE2J2	UBE2J2	UBE2J2	10976	-0.098	0.081	NO
111	UBA7	UBA7	UBA7	11344	-0.11	0.068	NO
112	UBE2Z	UBE2Z	UBE2Z	11603	-0.12	0.06	NO
113	HERC4	HERC4	HERC4	11920	-0.13	0.051	NO
114	CDC16	CDC16	CDC16	12109	-0.14	0.048	NO
115	SKP2	SKP2	SKP2	12198	-0.14	0.052	NO
116	UBE2E3	UBE2E3	UBE2E3	12330	-0.15	0.053	NO
117	MDM2	MDM2	MDM2	12596	-0.16	0.048	NO
118	PML	PML	PML	12624	-0.16	0.056	NO
119	UBE2J1	UBE2J1	UBE2J1	12864	-0.17	0.053	NO
120	CBLB	CBLB	CBLB	12962	-0.18	0.058	NO
121	SMURF2	SMURF2	SMURF2	13011	-0.18	0.066	NO
122	UBE2E2	UBE2E2	UBE2E2	13235	-0.19	0.065	NO
123	FBXO4	FBXO4	FBXO4	13322	-0.2	0.072	NO
124	FANCL	FANCL	FANCL	13340	-0.2	0.082	NO
125	CDC20	CDC20	CDC20	13819	-0.22	0.069	NO
126	SOCS3	SOCS3	SOCS3	15272	-0.34	0.0082	NO
127	AIRE	AIRE	AIRE	15453	-0.35	0.019	NO
128	DDB2	DDB2	DDB2	15454	-0.35	0.039	NO
129	BRCA1	BRCA1	BRCA1	15769	-0.38	0.044	NO
130	NEDD4	NEDD4	NEDD4	15966	-0.4	0.057	NO
131	MID1	MID1	MID1	16319	-0.45	0.064	NO
132	BIRC3	BIRC3	BIRC3	17610	-0.68	0.032	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 OXIDATIVE PHOSPHORYLATION.

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

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	ATP6V0A4	ATP6V0A4	ATP6V0A4	19	1.4	0.084	YES
2	ATP6V1B1	ATP6V1B1	ATP6V1B1	31	1.3	0.16	YES
3	ATP6V0D2	ATP6V0D2	ATP6V0D2	68	1.1	0.23	YES
4	PLCG2	PLCG2	PLCG2	172	0.89	0.28	YES
5	ATP6V1C2	ATP6V1C2	ATP6V1C2	221	0.81	0.32	YES
6	ATP6V1A	ATP6V1A	ATP6V1A	888	0.43	0.31	YES
7	ATP6V1H	ATP6V1H	ATP6V1H	1229	0.34	0.31	YES
8	ATP6V0B	ATP6V0B	ATP6V0B	1366	0.32	0.33	YES
9	ATP6V0E2	ATP6V0E2	ATP6V0E2	1433	0.31	0.34	YES
10	ATP6V1D	ATP6V1D	ATP6V1D	1502	0.3	0.36	YES
11	ATP6V0C	ATP6V0C	ATP6V0C	1620	0.28	0.37	YES
12	ATP6AP1	ATP6AP1	ATP6AP1	2129	0.22	0.35	YES
13	MAPK13	MAPK13	MAPK13	2205	0.22	0.36	YES
14	ATP6V1E1	ATP6V1E1	ATP6V1E1	2289	0.21	0.37	YES
15	ATP6V1F	ATP6V1F	ATP6V1F	2848	0.17	0.35	NO
16	ATP6V0D1	ATP6V0D1	ATP6V0D1	3271	0.14	0.33	NO
17	ATP6V1G1	ATP6V1G1	ATP6V1G1	3783	0.12	0.31	NO
18	ATP6V0A2	ATP6V0A2	ATP6V0A2	4094	0.11	0.3	NO
19	MAPK8	MAPK8	MAPK8	4935	0.077	0.26	NO
20	PTPN11	PTPN11	PTPN11	5005	0.075	0.26	NO
21	IKBKG	IKBKG	IKBKG	5225	0.068	0.25	NO
22	ATP6V1C1	ATP6V1C1	ATP6V1C1	6186	0.038	0.2	NO
23	CHUK	CHUK	CHUK	6334	0.035	0.2	NO
24	ATP6V1E2	ATP6V1E2	ATP6V1E2	6491	0.03	0.19	NO
25	PAK1	PAK1	PAK1	6593	0.027	0.18	NO
26	RELA	RELA	RELA	6604	0.027	0.19	NO
27	PTPRZ1	PTPRZ1	PTPRZ1	6797	0.022	0.18	NO
28	MAPK9	MAPK9	MAPK9	7298	0.0082	0.15	NO
29	TJP1	TJP1	TJP1	7412	0.005	0.14	NO
30	CASP3	CASP3	CASP3	7836	-0.0063	0.12	NO
31	ADAM10	ADAM10	ADAM10	8766	-0.032	0.072	NO
32	JAM3	JAM3	JAM3	8802	-0.033	0.072	NO
33	IKBKB	IKBKB	IKBKB	8969	-0.037	0.065	NO
34	MET	MET	MET	9091	-0.04	0.061	NO
35	SRC	SRC	SRC	9607	-0.055	0.036	NO
36	CDC42	CDC42	CDC42	9621	-0.055	0.038	NO
37	TCIRG1	TCIRG1	TCIRG1	9744	-0.058	0.035	NO
38	CSK	CSK	CSK	9881	-0.062	0.031	NO
39	F11R	F11R	F11R	9935	-0.064	0.032	NO
40	NFKB1	NFKB1	NFKB1	9960	-0.065	0.035	NO
41	RAC1	RAC1	RAC1	10654	-0.086	0.0019	NO
42	PLCG1	PLCG1	PLCG1	11606	-0.12	-0.043	NO
43	JAM2	JAM2	JAM2	11656	-0.12	-0.039	NO
44	NOD1	NOD1	NOD1	11693	-0.12	-0.033	NO
45	ADAM17	ADAM17	ADAM17	11895	-0.13	-0.036	NO
46	GIT1	GIT1	GIT1	11960	-0.13	-0.032	NO
47	MAP2K4	MAP2K4	MAP2K4	11999	-0.13	-0.026	NO
48	HBEGF	HBEGF	HBEGF	12354	-0.15	-0.036	NO
49	MAPK14	MAPK14	MAPK14	12402	-0.15	-0.03	NO
50	ATP6V1B2	ATP6V1B2	ATP6V1B2	12485	-0.16	-0.025	NO
51	NFKBIA	NFKBIA	NFKBIA	13035	-0.18	-0.044	NO
52	EGFR	EGFR	EGFR	13435	-0.2	-0.054	NO
53	JUN	JUN	JUN	13440	-0.2	-0.042	NO
54	LYN	LYN	LYN	13765	-0.22	-0.047	NO
55	MAPK11	MAPK11	MAPK11	14119	-0.24	-0.051	NO
56	CXCR1	CXCR1	CXCR1	14491	-0.27	-0.055	NO
57	ATP6V0A1	ATP6V0A1	ATP6V0A1	14609	-0.28	-0.045	NO
58	IGSF5	IGSF5	IGSF5	14719	-0.29	-0.033	NO
59	ATP6V1G2	ATP6V1G2	ATP6V1G2	14739	-0.29	-0.017	NO
60	MAPK10	MAPK10	MAPK10	15038	-0.32	-0.014	NO
61	CXCR2	CXCR2	CXCR2	15309	-0.34	-0.0086	NO
62	IL8	IL8	IL8	15919	-0.4	-0.018	NO
63	CCL5	CCL5	CCL5	16806	-0.52	-0.036	NO
64	MAPK12	MAPK12	MAPK12	17091	-0.57	-0.017	NO
65	MAP3K14	MAP3K14	MAP3K14	17281	-0.6	0.0088	NO
66	CXCL1	CXCL1	CXCL1	17622	-0.69	0.032	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 O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG INOSITOL PHOSPHATE METABOLISM

Table 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	PAK6	PAK6	PAK6	17	1.4	0.18	YES
2	PAK7	PAK7	PAK7	176	0.89	0.29	YES
3	NRG2	NRG2	NRG2	216	0.82	0.39	YES
4	CHRM1	CHRM1	CHRM1	457	0.61	0.46	YES
5	PAK4	PAK4	PAK4	1971	0.24	0.4	NO
6	DAG1	DAG1	DAG1	2820	0.17	0.38	NO
7	RAPSN	RAPSN	RAPSN	3287	0.14	0.37	NO
8	LAMA2	LAMA2	LAMA2	3832	0.12	0.36	NO
9	PXN	PXN	PXN	4059	0.11	0.36	NO
10	DVL1	DVL1	DVL1	4677	0.086	0.34	NO
11	MAPK8	MAPK8	MAPK8	4935	0.077	0.33	NO
12	LAMA3	LAMA3	LAMA3	5661	0.054	0.3	NO
13	DMD	DMD	DMD	5815	0.05	0.3	NO
14	PTK2	PTK2	PTK2	6322	0.035	0.27	NO
15	CTTN	CTTN	CTTN	6461	0.031	0.27	NO
16	PAK1	PAK1	PAK1	6593	0.027	0.26	NO
17	MAPK1	MAPK1	MAPK1	7984	-0.011	0.19	NO
18	ITGA1	ITGA1	ITGA1	8891	-0.035	0.14	NO
19	SRC	SRC	SRC	9607	-0.055	0.11	NO
20	CDC42	CDC42	CDC42	9621	-0.055	0.12	NO
21	ACTA1	ACTA1	ACTA1	9637	-0.055	0.12	NO
22	MAPK3	MAPK3	MAPK3	9692	-0.057	0.13	NO
23	PAK2	PAK2	PAK2	10303	-0.075	0.1	NO
24	RAC1	RAC1	RAC1	10654	-0.086	0.097	NO
25	LAMA4	LAMA4	LAMA4	11692	-0.12	0.056	NO
26	UTRN	UTRN	UTRN	11910	-0.13	0.061	NO
27	SP1	SP1	SP1	12028	-0.14	0.072	NO
28	ITGB1	ITGB1	ITGB1	12964	-0.18	0.043	NO
29	EGFR	EGFR	EGFR	13435	-0.2	0.044	NO
30	JUN	JUN	JUN	13440	-0.2	0.069	NO
31	GIT2	GIT2	GIT2	13771	-0.22	0.08	NO
32	CHRNA1	CHRNA1	CHRNA1	15756	-0.38	0.02	NO
33	PAK3	PAK3	PAK3	15778	-0.38	0.068	NO
34	NRG1	NRG1	NRG1	16747	-0.51	0.08	NO

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

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

genes ES table in pathway: KEGG SPLICEOSOME

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	OGDHL	OGDHL	OGDHL	547	0.55	0.067	YES
2	IDH3A	IDH3A	IDH3A	1144	0.36	0.098	YES
3	IDH2	IDH2	IDH2	1203	0.35	0.16	YES
4	DLAT	DLAT	DLAT	1947	0.24	0.16	YES
5	SDHD	SDHD	SDHD	1970	0.24	0.2	YES
6	PDHA1	PDHA1	PDHA1	2061	0.23	0.24	YES
7	PDHB	PDHB	PDHB	2185	0.22	0.27	YES
8	OGDH	OGDH	OGDH	2252	0.21	0.3	YES
9	DLD	DLD	DLD	2330	0.21	0.33	YES
10	FH	FH	FH	2367	0.2	0.37	YES
11	SDHA	SDHA	SDHA	2412	0.2	0.4	YES
12	DLST	DLST	DLST	2481	0.19	0.43	YES
13	CS	CS	CS	2532	0.19	0.46	YES
14	SUCLG2	SUCLG2	SUCLG2	2577	0.19	0.49	YES
15	ACO2	ACO2	ACO2	2589	0.19	0.52	YES
16	SUCLG1	SUCLG1	SUCLG1	3122	0.15	0.52	YES
17	MDH2	MDH2	MDH2	3178	0.15	0.54	YES
18	SUCLA2	SUCLA2	SUCLA2	4505	0.091	0.49	NO
19	SDHB	SDHB	SDHB	4826	0.081	0.48	NO
20	IDH3G	IDH3G	IDH3G	5022	0.074	0.49	NO
21	MDH1	MDH1	MDH1	5075	0.073	0.5	NO
22	IDH3B	IDH3B	IDH3B	5749	0.052	0.47	NO
23	SDHC	SDHC	SDHC	6201	0.038	0.45	NO
24	ACO1	ACO1	ACO1	6280	0.036	0.45	NO
25	PCK2	PCK2	PCK2	9733	-0.058	0.27	NO
26	IDH1	IDH1	IDH1	11774	-0.13	0.18	NO
27	PC	PC	PC	14791	-0.29	0.068	NO
28	PCK1	PCK1	PCK1	14865	-0.3	0.12	NO
29	ACLY	ACLY	ACLY	15737	-0.38	0.14	NO

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

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

genes ES table in pathway: KEGG ERBB SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CREB3L1	CREB3L1	CREB3L1	249	0.78	0.012	YES
2	HAP1	HAP1	HAP1	380	0.66	0.026	YES
3	PPARGC1A	PPARGC1A	PPARGC1A	570	0.54	0.033	YES
4	ITPR1	ITPR1	ITPR1	709	0.48	0.041	YES
5	COX7A1	COX7A1	COX7A1	762	0.46	0.053	YES
6	SLC25A4	SLC25A4	SLC25A4	954	0.41	0.056	YES
7	GRIN1	GRIN1	GRIN1	1067	0.38	0.062	YES
8	SLC25A5	SLC25A5	SLC25A5	1073	0.38	0.074	YES
9	CYCS	CYCS	CYCS	1198	0.35	0.078	YES
10	COX5A	COX5A	COX5A	1257	0.34	0.086	YES
11	UQCRFS1	UQCRFS1	UQCRFS1	1342	0.32	0.092	YES
12	NDUFA4	NDUFA4	NDUFA4	1428	0.31	0.097	YES
13	NDUFA6	NDUFA6	NDUFA6	1457	0.3	0.11	YES
14	COX7B	COX7B	COX7B	1551	0.29	0.11	YES
15	COX8A	COX8A	COX8A	1561	0.29	0.12	YES
16	COX6C	COX6C	COX6C	1599	0.29	0.13	YES
17	UQCRC1	UQCRC1	UQCRC1	1655	0.28	0.13	YES
18	ATP5A1	ATP5A1	ATP5A1	1798	0.26	0.13	YES
19	NDUFS7	NDUFS7	NDUFS7	1837	0.26	0.14	YES
20	NDUFS8	NDUFS8	NDUFS8	1920	0.25	0.14	YES
21	UQCR10	UQCR10	UQCR10	1942	0.24	0.15	YES
22	SDHD	SDHD	SDHD	1970	0.24	0.16	YES
23	NDUFA3	NDUFA3	NDUFA3	1987	0.24	0.16	YES
24	NDUFA8	NDUFA8	NDUFA8	2004	0.24	0.17	YES
25	UQCR11	UQCR11	UQCR11	2016	0.24	0.18	YES
26	COX6A1	COX6A1	COX6A1	2058	0.23	0.18	YES
27	REST	REST	REST	2059	0.23	0.19	YES
28	CYC1	CYC1	CYC1	2071	0.23	0.2	YES
29	NDUFB1	NDUFB1	NDUFB1	2108	0.23	0.2	YES
30	NDUFV1	NDUFV1	NDUFV1	2175	0.22	0.2	YES
31	ATP5B	ATP5B	ATP5B	2207	0.22	0.21	YES
32	NDUFC2	NDUFC2	NDUFC2	2232	0.22	0.22	YES
33	ATP5D	ATP5D	ATP5D	2353	0.2	0.22	YES
34	UQCRHL	UQCRHL	UQCRHL	2369	0.2	0.22	YES
35	SDHA	SDHA	SDHA	2412	0.2	0.23	YES
36	NDUFB7	NDUFB7	NDUFB7	2444	0.2	0.23	YES
37	COX7A2	COX7A2	COX7A2	2470	0.19	0.24	YES
38	UQCRH	UQCRH	UQCRH	2489	0.19	0.24	YES
39	NDUFA9	NDUFA9	NDUFA9	2569	0.19	0.24	YES
40	NDUFB2	NDUFB2	NDUFB2	2619	0.18	0.25	YES
41	NDUFB9	NDUFB9	NDUFB9	2679	0.18	0.25	YES
42	UQCRQ	UQCRQ	UQCRQ	2769	0.18	0.25	YES
43	NDUFA7	NDUFA7	NDUFA7	2786	0.17	0.25	YES
44	NDUFS3	NDUFS3	NDUFS3	2819	0.17	0.26	YES
45	NDUFB6	NDUFB6	NDUFB6	2838	0.17	0.26	YES
46	PPARG	PPARG	PPARG	2844	0.17	0.27	YES
47	COX7C	COX7C	COX7C	2854	0.17	0.27	YES
48	COX6B1	COX6B1	COX6B1	2874	0.17	0.28	YES
49	UQCRC2	UQCRC2	UQCRC2	2938	0.16	0.28	YES
50	NDUFA5	NDUFA5	NDUFA5	2958	0.16	0.28	YES
51	COX4I1	COX4I1	COX4I1	2959	0.16	0.29	YES
52	NDUFS6	NDUFS6	NDUFS6	3107	0.15	0.28	YES
53	NDUFA1	NDUFA1	NDUFA1	3116	0.15	0.29	YES
54	NDUFS1	NDUFS1	NDUFS1	3158	0.15	0.29	YES
55	PPID	PPID	PPID	3174	0.15	0.3	YES
56	ATP5J	ATP5J	ATP5J	3223	0.15	0.3	YES
57	ATP5E	ATP5E	ATP5E	3278	0.14	0.3	YES
58	NDUFAB1	NDUFAB1	NDUFAB1	3280	0.14	0.3	YES
59	SLC25A6	SLC25A6	SLC25A6	3315	0.14	0.31	YES
60	COX5B	COX5B	COX5B	3386	0.14	0.31	YES
61	UQCRB	UQCRB	UQCRB	3400	0.14	0.31	YES
62	NDUFB5	NDUFB5	NDUFB5	3423	0.14	0.32	YES
63	TFAM	TFAM	TFAM	3455	0.14	0.32	YES
64	HTT	HTT	HTT	3456	0.14	0.32	YES
65	NDUFV2	NDUFV2	NDUFV2	3516	0.13	0.32	YES
66	ATP5G3	ATP5G3	ATP5G3	3547	0.13	0.33	YES
67	PLCB4	PLCB4	PLCB4	3663	0.13	0.32	YES
68	ATP5G1	ATP5G1	ATP5G1	3703	0.12	0.33	YES
69	POLR2K	POLR2K	POLR2K	3706	0.12	0.33	YES
70	ATP5O	ATP5O	ATP5O	3734	0.12	0.33	YES
71	POLR2F	POLR2F	POLR2F	3819	0.12	0.33	NO
72	NDUFS2	NDUFS2	NDUFS2	3955	0.11	0.33	NO
73	POLR2L	POLR2L	POLR2L	4050	0.11	0.33	NO
74	NDUFB8	NDUFB8	NDUFB8	4138	0.1	0.32	NO
75	NDUFS4	NDUFS4	NDUFS4	4231	0.1	0.32	NO
76	COX7A2L	COX7A2L	COX7A2L	4239	0.1	0.33	NO
77	VDAC1	VDAC1	VDAC1	4336	0.098	0.32	NO
78	NDUFA10	NDUFA10	NDUFA10	4362	0.097	0.32	NO
79	NDUFB10	NDUFB10	NDUFB10	4438	0.094	0.32	NO
80	DNAL4	DNAL4	DNAL4	4463	0.093	0.33	NO
81	VDAC2	VDAC2	VDAC2	4576	0.089	0.32	NO
82	RCOR1	RCOR1	RCOR1	4628	0.087	0.32	NO
83	NDUFB4	NDUFB4	NDUFB4	4660	0.086	0.32	NO
84	SDHB	SDHB	SDHB	4826	0.081	0.32	NO
85	SIN3A	SIN3A	SIN3A	4855	0.08	0.32	NO
86	VDAC3	VDAC3	VDAC3	4942	0.077	0.32	NO
87	NDUFA2	NDUFA2	NDUFA2	4984	0.075	0.32	NO
88	TAF4	TAF4	TAF4	5006	0.075	0.32	NO
89	ATP5F1	ATP5F1	ATP5F1	5111	0.071	0.31	NO
90	GNAQ	GNAQ	GNAQ	5142	0.07	0.32	NO
91	EP300	EP300	EP300	5171	0.069	0.32	NO
92	NDUFC1	NDUFC1	NDUFC1	5192	0.068	0.32	NO
93	ATP5C1	ATP5C1	ATP5C1	5305	0.065	0.31	NO
94	CLTB	CLTB	CLTB	5352	0.064	0.31	NO
95	ATP5H	ATP5H	ATP5H	5355	0.064	0.31	NO
96	NDUFV3	NDUFV3	NDUFV3	5427	0.061	0.31	NO
97	CLTCL1	CLTCL1	CLTCL1	5639	0.055	0.3	NO
98	POLR2B	POLR2B	POLR2B	5726	0.053	0.3	NO
99	POLR2J	POLR2J	POLR2J	5823	0.049	0.3	NO
100	NDUFB3	NDUFB3	NDUFB3	5882	0.047	0.29	NO
101	CREBBP	CREBBP	CREBBP	6121	0.04	0.28	NO
102	SDHC	SDHC	SDHC	6201	0.038	0.28	NO
103	AP2S1	AP2S1	AP2S1	6427	0.032	0.27	NO
104	GPX1	GPX1	GPX1	6640	0.026	0.26	NO
105	POLR2E	POLR2E	POLR2E	6643	0.026	0.26	NO
106	COX4I2	COX4I2	COX4I2	6750	0.023	0.25	NO
107	CLTA	CLTA	CLTA	6917	0.018	0.24	NO
108	NDUFS5	NDUFS5	NDUFS5	6971	0.017	0.24	NO
109	POLR2J3	POLR2J3	POLR2J3	7010	0.016	0.24	NO
110	CREB3	CREB3	CREB3	7073	0.014	0.24	NO
111	POLR2A	POLR2A	POLR2A	7116	0.013	0.23	NO
112	TBPL1	TBPL1	TBPL1	7221	0.01	0.23	NO
113	DCTN2	DCTN2	DCTN2	7250	0.0098	0.23	NO
114	ATP5G2	ATP5G2	ATP5G2	7305	0.0081	0.22	NO
115	PLCB3	PLCB3	PLCB3	7504	0.003	0.21	NO
116	POLR2I	POLR2I	POLR2I	7732	-0.0028	0.2	NO
117	BBC3	BBC3	BBC3	7760	-0.0038	0.2	NO
118	CASP3	CASP3	CASP3	7836	-0.0063	0.2	NO
119	POLR2J2	POLR2J2	POLR2J2	8062	-0.012	0.18	NO
120	DCTN4	DCTN4	DCTN4	8222	-0.017	0.18	NO
121	AP2B1	AP2B1	AP2B1	8307	-0.019	0.17	NO
122	POLR2G	POLR2G	POLR2G	8646	-0.028	0.15	NO
123	POLR2C	POLR2C	POLR2C	9021	-0.038	0.13	NO
124	CLTC	CLTC	CLTC	9026	-0.038	0.14	NO
125	POLR2H	POLR2H	POLR2H	9046	-0.039	0.14	NO
126	AP2A2	AP2A2	AP2A2	9061	-0.039	0.14	NO
127	DCTN1	DCTN1	DCTN1	9223	-0.044	0.13	NO
128	SOD1	SOD1	SOD1	9244	-0.044	0.13	NO
129	TBP	TBP	TBP	9479	-0.051	0.12	NO
130	CREB3L2	CREB3L2	CREB3L2	9549	-0.053	0.12	NO
131	AP2M1	AP2M1	AP2M1	9991	-0.066	0.093	NO
132	NRF1	NRF1	NRF1	10176	-0.071	0.085	NO
133	HDAC2	HDAC2	HDAC2	10187	-0.072	0.087	NO
134	CASP9	CASP9	CASP9	10412	-0.078	0.077	NO
135	DNAL1	DNAL1	DNAL1	10556	-0.083	0.072	NO
136	HDAC1	HDAC1	HDAC1	10640	-0.086	0.07	NO
137	POLR2D	POLR2D	POLR2D	10887	-0.094	0.06	NO
138	COX6B2	COX6B2	COX6B2	10947	-0.096	0.059	NO
139	DNAI2	DNAI2	DNAI2	11060	-0.1	0.056	NO
140	AP2A1	AP2A1	AP2A1	11568	-0.12	0.032	NO
141	CREB1	CREB1	CREB1	11648	-0.12	0.032	NO
142	APAF1	APAF1	APAF1	11880	-0.13	0.023	NO
143	IFT57	IFT57	IFT57	11922	-0.13	0.025	NO
144	SP1	SP1	SP1	12028	-0.14	0.024	NO
145	DLG4	DLG4	DLG4	12837	-0.17	-0.016	NO
146	BAX	BAX	BAX	12838	-0.17	-0.0099	NO
147	TAF4B	TAF4B	TAF4B	12990	-0.18	-0.012	NO
148	TP53	TP53	TP53	13586	-0.21	-0.039	NO
149	GRIN2B	GRIN2B	GRIN2B	13822	-0.22	-0.044	NO
150	HIP1	HIP1	HIP1	14262	-0.25	-0.06	NO
151	SOD2	SOD2	SOD2	14329	-0.26	-0.056	NO
152	CASP8	CASP8	CASP8	14504	-0.27	-0.057	NO
153	DNAH3	DNAH3	DNAH3	15052	-0.32	-0.077	NO
154	CREB3L4	CREB3L4	CREB3L4	15370	-0.34	-0.083	NO
155	NDUFA4L2	NDUFA4L2	NDUFA4L2	15380	-0.34	-0.072	NO
156	DNAH2	DNAH2	DNAH2	15392	-0.34	-0.062	NO
157	COX6A2	COX6A2	COX6A2	15527	-0.36	-0.058	NO
158	DNAH1	DNAH1	DNAH1	15619	-0.37	-0.051	NO
159	COX8C	COX8C	COX8C	15792	-0.38	-0.048	NO
160	BDNF	BDNF	BDNF	16344	-0.45	-0.064	NO
161	PLCB1	PLCB1	PLCB1	16400	-0.46	-0.052	NO
162	DNAI1	DNAI1	DNAI1	16642	-0.49	-0.049	NO
163	TGM2	TGM2	TGM2	16716	-0.5	-0.037	NO
164	DNALI1	DNALI1	DNALI1	16968	-0.55	-0.033	NO
165	PLCB2	PLCB2	PLCB2	17110	-0.57	-0.022	NO
166	GRM5	GRM5	GRM5	17846	-0.8	-0.037	NO
167	CREB5	CREB5	CREB5	17848	-0.8	-0.011	NO
168	CREB3L3	CREB3L3	CREB3L3	18007	-0.94	0.01	NO

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

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ERBB 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 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	HSD11B2	HSD11B2	HSD11B2	126	0.97	0.082	YES
2	FXYD4	FXYD4	FXYD4	202	0.84	0.16	YES
3	SCNN1A	SCNN1A	SCNN1A	215	0.82	0.23	YES
4	NR3C2	NR3C2	NR3C2	275	0.75	0.3	YES
5	KCNJ1	KCNJ1	KCNJ1	549	0.55	0.33	YES
6	NEDD4L	NEDD4L	NEDD4L	689	0.49	0.37	YES
7	IRS1	IRS1	IRS1	842	0.44	0.4	YES
8	IRS2	IRS2	IRS2	848	0.44	0.44	YES
9	IGF1	IGF1	IGF1	864	0.44	0.48	YES
10	SCNN1G	SCNN1G	SCNN1G	1900	0.25	0.45	YES
11	ATP1A3	ATP1A3	ATP1A3	1948	0.24	0.47	YES
12	ATP1A1	ATP1A1	ATP1A1	2072	0.23	0.48	YES
13	SCNN1B	SCNN1B	SCNN1B	2633	0.18	0.47	NO
14	ATP1A4	ATP1A4	ATP1A4	3903	0.12	0.41	NO
15	ATP1B1	ATP1B1	ATP1B1	3999	0.11	0.41	NO
16	PDPK1	PDPK1	PDPK1	4018	0.11	0.42	NO
17	KRAS	KRAS	KRAS	4749	0.083	0.39	NO
18	PRKCA	PRKCA	PRKCA	5081	0.072	0.38	NO
19	ATP1B3	ATP1B3	ATP1B3	5408	0.062	0.37	NO
20	PIK3CA	PIK3CA	PIK3CA	5879	0.047	0.34	NO
21	PIK3R3	PIK3R3	PIK3R3	5953	0.045	0.34	NO
22	PIK3R2	PIK3R2	PIK3R2	6299	0.036	0.33	NO
23	HSD11B1	HSD11B1	HSD11B1	6502	0.03	0.32	NO
24	MAPK1	MAPK1	MAPK1	7984	-0.011	0.24	NO
25	INSR	INSR	INSR	8240	-0.018	0.23	NO
26	MAPK3	MAPK3	MAPK3	9692	-0.057	0.15	NO
27	ATP1B2	ATP1B2	ATP1B2	9729	-0.058	0.16	NO
28	ATP1A2	ATP1A2	ATP1A2	10250	-0.074	0.14	NO
29	SLC9A3R2	SLC9A3R2	SLC9A3R2	10354	-0.077	0.14	NO
30	PIK3CB	PIK3CB	PIK3CB	11545	-0.12	0.082	NO
31	SFN	SFN	SFN	13164	-0.19	0.01	NO
32	PRKCG	PRKCG	PRKCG	14342	-0.26	-0.031	NO
33	PIK3R1	PIK3R1	PIK3R1	14661	-0.28	-0.022	NO
34	SGK1	SGK1	SGK1	15547	-0.36	-0.038	NO
35	PIK3CD	PIK3CD	PIK3CD	15839	-0.39	-0.018	NO
36	PIK3CG	PIK3CG	PIK3CG	16064	-0.41	0.0078	NO
37	PIK3R5	PIK3R5	PIK3R5	17190	-0.58	-0.00057	NO
38	PRKCB	PRKCB	PRKCB	17308	-0.61	0.049	NO

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

Figure S20. 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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA NO1 PATHWAY	28	genes.ES.table	0.57	1.3	0.17	0.24	0.98	0.36	0.16	0.3	0.21	0
BIOCARTA ALK PATHWAY	34	genes.ES.table	0.45	1.3	0.14	0.24	0.98	0.26	0.21	0.21	0.21	0.001
BIOCARTA BCR PATHWAY	33	genes.ES.table	0.53	1.5	0.078	0.17	0.89	0.27	0.17	0.23	0.12	0.002
BIOCARTA BIOPEPTIDES PATHWAY	40	genes.ES.table	0.4	1.4	0.086	0.18	0.93	0.3	0.27	0.22	0.14	0.001
BIOCARTA G1 PATHWAY	27	genes.ES.table	0.56	1.6	0.029	0.3	0.72	0.3	0.12	0.26	0.18	0.058
BIOCARTA INFLAM PATHWAY	26	genes.ES.table	0.72	1.5	0.01	0.23	0.8	0.81	0.22	0.63	0.14	0.022
BIOCARTA EGF PATHWAY	30	genes.ES.table	0.4	1.3	0.18	0.24	0.98	0.5	0.38	0.31	0.21	0
BIOCARTA ERK PATHWAY	27	genes.ES.table	0.48	1.4	0.098	0.19	0.93	0.41	0.29	0.29	0.14	0.001
BIOCARTA FAS PATHWAY	29	genes.ES.table	0.44	1.4	0.13	0.19	0.92	0.52	0.39	0.31	0.14	0.001
BIOCARTA FCER1 PATHWAY	37	genes.ES.table	0.51	1.4	0.17	0.2	0.96	0.57	0.38	0.35	0.16	0

genes ES table in pathway: BIOCARTA NO1 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	AIM2	AIM2	AIM2	26	0.78	0.095	YES
2	IL6	IL6	IL6	42	0.72	0.18	YES
3	ZBP1	ZBP1	ZBP1	470	0.5	0.22	YES
4	CCL5	CCL5	CCL5	885	0.43	0.25	YES
5	CCL4	CCL4	CCL4	968	0.41	0.3	YES
6	CXCL10	CXCL10	CXCL10	1113	0.39	0.34	YES
7	TMEM173	TMEM173	TMEM173	1149	0.39	0.39	YES
8	IL33	IL33	IL33	1459	0.35	0.42	YES
9	IL1B	IL1B	IL1B	1638	0.33	0.45	YES
10	RIPK3	RIPK3	RIPK3	1823	0.31	0.48	YES
11	POLR3G	POLR3G	POLR3G	2132	0.29	0.5	YES
12	CASP1	CASP1	CASP1	2208	0.28	0.52	YES
13	CCL4L2	CCL4L2	CCL4L2	2271	0.27	0.56	YES
14	IFNB1	IFNB1	IFNB1	2300	0.27	0.59	YES
15	IKBKE	IKBKE	IKBKE	2506	0.26	0.61	YES
16	PYCARD	PYCARD	PYCARD	2542	0.25	0.64	YES
17	IRF7	IRF7	IRF7	2813	0.23	0.65	YES
18	DDX58	DDX58	DDX58	4716	0.12	0.56	NO
19	POLR3C	POLR3C	POLR3C	5550	0.094	0.53	NO
20	TBK1	TBK1	TBK1	6469	0.07	0.49	NO
21	POLR3D	POLR3D	POLR3D	6522	0.069	0.49	NO
22	POLR3GL	POLR3GL	POLR3GL	6780	0.063	0.49	NO
23	ADAR	ADAR	ADAR	6875	0.061	0.49	NO
24	POLR3A	POLR3A	POLR3A	7424	0.05	0.46	NO
25	POLR3H	POLR3H	POLR3H	7608	0.047	0.46	NO
26	RIPK1	RIPK1	RIPK1	7732	0.044	0.46	NO
27	NFKBIA	NFKBIA	NFKBIA	8423	0.033	0.43	NO
28	RELA	RELA	RELA	8457	0.032	0.43	NO
29	POLR1D	POLR1D	POLR1D	9181	0.021	0.39	NO
30	IRF3	IRF3	IRF3	9282	0.019	0.39	NO
31	IKBKG	IKBKG	IKBKG	10133	0.0064	0.34	NO
32	NFKB1	NFKB1	NFKB1	10837	-0.0048	0.3	NO
33	IL18	IL18	IL18	11130	-0.009	0.29	NO
34	POLR3F	POLR3F	POLR3F	11582	-0.016	0.27	NO
35	IKBKB	IKBKB	IKBKB	11677	-0.018	0.26	NO
36	POLR1C	POLR1C	POLR1C	12186	-0.026	0.24	NO
37	MAVS	MAVS	MAVS	13243	-0.046	0.18	NO
38	POLR3K	POLR3K	POLR3K	13496	-0.051	0.18	NO
39	TREX1	TREX1	TREX1	13972	-0.061	0.16	NO
40	CHUK	CHUK	CHUK	14180	-0.066	0.16	NO
41	NFKBIB	NFKBIB	NFKBIB	14740	-0.081	0.14	NO
42	POLR3B	POLR3B	POLR3B	14973	-0.088	0.13	NO
43	IFNA13	IFNA13	IFNA13	16360	-0.15	0.076	NO
44	IFNA1	IFNA1	IFNA1	17068	-0.2	0.062	NO

Figure S21. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA ALK PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	BLM	BLM	BLM	388	0.52	0.11	YES
2	RAD54B	RAD54B	RAD54B	930	0.42	0.19	YES
3	RAD51	RAD51	RAD51	961	0.41	0.29	YES
4	RAD54L	RAD54L	RAD54L	1025	0.4	0.39	YES
5	EME1	EME1	EME1	1137	0.39	0.49	YES
6	BRCA2	BRCA2	BRCA2	1199	0.38	0.58	YES
7	RPA4	RPA4	RPA4	1779	0.32	0.63	YES
8	XRCC2	XRCC2	XRCC2	1824	0.31	0.71	YES
9	POLD3	POLD3	POLD3	4801	0.12	0.57	NO
10	NBN	NBN	NBN	5557	0.094	0.56	NO
11	MRE11A	MRE11A	MRE11A	5599	0.093	0.58	NO
12	POLD4	POLD4	POLD4	6499	0.07	0.55	NO
13	RAD51L3	RAD51L3	RAD51L3	6757	0.064	0.55	NO
14	RAD51L1	RAD51L1	RAD51L1	7794	0.044	0.5	NO
15	RPA2	RPA2	RPA2	8203	0.036	0.49	NO
16	SHFM1	SHFM1	SHFM1	8800	0.027	0.46	NO
17	SSBP1	SSBP1	SSBP1	9529	0.015	0.43	NO
18	RPA1	RPA1	RPA1	9751	0.012	0.42	NO
19	RAD50	RAD50	RAD50	10302	0.0039	0.39	NO
20	TOP3A	TOP3A	TOP3A	10630	-0.0015	0.37	NO
21	RAD52	RAD52	RAD52	10666	-0.002	0.37	NO
22	POLD1	POLD1	POLD1	10869	-0.0053	0.36	NO
23	POLD2	POLD2	POLD2	11465	-0.014	0.33	NO
24	XRCC3	XRCC3	XRCC3	12129	-0.025	0.3	NO
25	MUS81	MUS81	MUS81	12223	-0.027	0.3	NO
26	RPA3	RPA3	RPA3	12567	-0.033	0.29	NO
27	TOP3B	TOP3B	TOP3B	14267	-0.068	0.22	NO

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

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

genes ES table in pathway: BIOCARTA BCR PATHWAY

Table S13. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SERPINE1	SERPINE1	SERPINE1	69	0.67	0.066	YES
2	GTSE1	GTSE1	GTSE1	230	0.57	0.12	YES
3	RRM2	RRM2	RRM2	233	0.57	0.18	YES
4	CCNB2	CCNB2	CCNB2	309	0.55	0.23	YES
5	CCNE2	CCNE2	CCNE2	673	0.46	0.26	YES
6	CDK1	CDK1	CDK1	976	0.41	0.28	YES
7	IGFBP3	IGFBP3	IGFBP3	1244	0.38	0.31	YES
8	TP73	TP73	TP73	1596	0.34	0.32	YES
9	CDKN2A	CDKN2A	CDKN2A	1903	0.31	0.34	YES
10	IGF1	IGF1	IGF1	1946	0.3	0.37	YES
11	BAI1	BAI1	BAI1	1974	0.3	0.4	YES
12	CCNB1	CCNB1	CCNB1	2136	0.29	0.42	YES
13	CCNE1	CCNE1	CCNE1	2265	0.28	0.44	YES
14	PMAIP1	PMAIP1	PMAIP1	2269	0.28	0.47	YES
15	CD82	CD82	CD82	2716	0.24	0.47	YES
16	BID	BID	BID	2830	0.23	0.49	YES
17	CHEK2	CHEK2	CHEK2	3126	0.21	0.5	YES
18	THBS1	THBS1	THBS1	3312	0.2	0.51	YES
19	FAS	FAS	FAS	4327	0.14	0.46	YES
20	CASP3	CASP3	CASP3	4794	0.12	0.45	YES
21	CCND1	CCND1	CCND1	4869	0.12	0.46	YES
22	CASP8	CASP8	CASP8	4905	0.12	0.47	YES
23	SESN3	SESN3	SESN3	5213	0.1	0.46	YES
24	CHEK1	CHEK1	CHEK1	5219	0.1	0.48	YES
25	SERPINB5	SERPINB5	SERPINB5	5351	0.1	0.48	YES
26	APAF1	APAF1	APAF1	5383	0.099	0.49	YES
27	ZMAT3	ZMAT3	ZMAT3	5564	0.094	0.49	YES
28	GADD45B	GADD45B	GADD45B	5570	0.094	0.5	YES
29	CDK2	CDK2	CDK2	5622	0.092	0.5	YES
30	CCND3	CCND3	CCND3	5673	0.09	0.51	YES
31	PTEN	PTEN	PTEN	5883	0.085	0.51	YES
32	SFN	SFN	SFN	5924	0.084	0.51	YES
33	MDM2	MDM2	MDM2	5934	0.084	0.52	YES
34	CDK6	CDK6	CDK6	6642	0.067	0.49	NO
35	ATM	ATM	ATM	6893	0.061	0.48	NO
36	TP53	TP53	TP53	6934	0.06	0.49	NO
37	RRM2B	RRM2B	RRM2B	7654	0.046	0.45	NO
38	CDK4	CDK4	CDK4	7850	0.042	0.45	NO
39	TP53AIP1	TP53AIP1	TP53AIP1	8045	0.039	0.44	NO
40	DDB2	DDB2	DDB2	8314	0.035	0.43	NO
41	SHISA5	SHISA5	SHISA5	8506	0.031	0.42	NO
42	EI24	EI24	EI24	8741	0.027	0.41	NO
43	RFWD2	RFWD2	RFWD2	8795	0.027	0.41	NO
44	TP53I3	TP53I3	TP53I3	8978	0.024	0.4	NO
45	TNFRSF10B	TNFRSF10B	TNFRSF10B	9145	0.021	0.4	NO
46	PERP	PERP	PERP	9268	0.019	0.39	NO
47	SESN1	SESN1	SESN1	9297	0.019	0.39	NO
48	MDM4	MDM4	MDM4	9481	0.016	0.38	NO
49	CCND2	CCND2	CCND2	9556	0.015	0.38	NO
50	BAX	BAX	BAX	9730	0.012	0.37	NO
51	SIAH1	SIAH1	SIAH1	10141	0.0062	0.35	NO
52	PPM1D	PPM1D	PPM1D	10783	-0.004	0.32	NO
53	ATR	ATR	ATR	11140	-0.0092	0.3	NO
54	CCNG2	CCNG2	CCNG2	11239	-0.011	0.29	NO
55	CCNG1	CCNG1	CCNG1	11325	-0.012	0.29	NO
56	SESN2	SESN2	SESN2	11452	-0.014	0.28	NO
57	CASP9	CASP9	CASP9	12026	-0.023	0.26	NO
58	RCHY1	RCHY1	RCHY1	12303	-0.028	0.24	NO
59	GADD45A	GADD45A	GADD45A	12326	-0.028	0.24	NO
60	CDKN1A	CDKN1A	CDKN1A	12347	-0.029	0.25	NO
61	TSC2	TSC2	TSC2	12935	-0.04	0.22	NO
62	LRDD	LRDD	LRDD	13580	-0.053	0.19	NO
63	CCNB3	CCNB3	CCNB3	14923	-0.087	0.12	NO
64	RPRM	RPRM	RPRM	15555	-0.11	0.1	NO
65	BBC3	BBC3	BBC3	15665	-0.11	0.1	NO
66	CYCS	CYCS	CYCS	16193	-0.14	0.091	NO
67	GADD45G	GADD45G	GADD45G	16923	-0.19	0.07	NO

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

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BCR 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 BIOPEPTIDES PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	LBP	LBP	LBP	24	0.78	0.048	YES
2	IL6	IL6	IL6	42	0.72	0.092	YES
3	CD80	CD80	CD80	216	0.58	0.12	YES
4	LY96	LY96	LY96	295	0.55	0.15	YES
5	TLR6	TLR6	TLR6	310	0.55	0.18	YES
6	CXCL9	CXCL9	CXCL9	406	0.52	0.21	YES
7	TLR8	TLR8	TLR8	658	0.47	0.23	YES
8	CCL5	CCL5	CCL5	885	0.43	0.24	YES
9	CXCL11	CXCL11	CXCL11	933	0.42	0.26	YES
10	PIK3CG	PIK3CG	PIK3CG	942	0.42	0.29	YES
11	TICAM2	TICAM2	TICAM2	953	0.42	0.32	YES
12	CCL4	CCL4	CCL4	968	0.41	0.34	YES
13	CXCL10	CXCL10	CXCL10	1113	0.39	0.36	YES
14	TLR7	TLR7	TLR7	1364	0.36	0.37	YES
15	TLR9	TLR9	TLR9	1453	0.35	0.38	YES
16	CD86	CD86	CD86	1464	0.35	0.41	YES
17	IL1B	IL1B	IL1B	1638	0.33	0.42	YES
18	PIK3R5	PIK3R5	PIK3R5	1785	0.32	0.43	YES
19	TLR5	TLR5	TLR5	1900	0.31	0.44	YES
20	CTSK	CTSK	CTSK	1966	0.3	0.46	YES
21	TLR1	TLR1	TLR1	2045	0.3	0.47	YES
22	IL12A	IL12A	IL12A	2223	0.28	0.48	YES
23	IFNB1	IFNB1	IFNB1	2300	0.27	0.49	YES
24	CCL3	CCL3	CCL3	2373	0.27	0.51	YES
25	IL12B	IL12B	IL12B	2470	0.26	0.52	YES
26	CD14	CD14	CD14	2494	0.26	0.53	YES
27	IKBKE	IKBKE	IKBKE	2506	0.26	0.55	YES
28	MAP3K8	MAP3K8	MAP3K8	2557	0.25	0.56	YES
29	IL8	IL8	IL8	2560	0.25	0.58	YES
30	TLR2	TLR2	TLR2	2632	0.25	0.59	YES
31	IRF7	IRF7	IRF7	2813	0.23	0.59	YES
32	TLR3	TLR3	TLR3	3017	0.22	0.6	YES
33	IFNAR2	IFNAR2	IFNAR2	3266	0.2	0.6	YES
34	MAPK11	MAPK11	MAPK11	3341	0.2	0.6	YES
35	FOS	FOS	FOS	3907	0.16	0.58	NO
36	TLR4	TLR4	TLR4	4153	0.15	0.58	NO
37	CD40	CD40	CD40	4258	0.14	0.58	NO
38	STAT1	STAT1	STAT1	4449	0.14	0.58	NO
39	PIK3CD	PIK3CD	PIK3CD	4544	0.13	0.58	NO
40	MYD88	MYD88	MYD88	4694	0.13	0.58	NO
41	PIK3R1	PIK3R1	PIK3R1	4819	0.12	0.58	NO
42	CASP8	CASP8	CASP8	4905	0.12	0.59	NO
43	JUN	JUN	JUN	4934	0.12	0.59	NO
44	TRAF3	TRAF3	TRAF3	4939	0.12	0.6	NO
45	TNF	TNF	TNF	5356	0.1	0.58	NO
46	MAPK12	MAPK12	MAPK12	6101	0.08	0.55	NO
47	MAP2K1	MAP2K1	MAP2K1	6441	0.071	0.53	NO
48	PIK3CA	PIK3CA	PIK3CA	6853	0.062	0.51	NO
49	PIK3R3	PIK3R3	PIK3R3	7472	0.049	0.48	NO
50	MAPK14	MAPK14	MAPK14	7581	0.047	0.48	NO
51	TAB2	TAB2	TAB2	7639	0.046	0.48	NO
52	RIPK1	RIPK1	RIPK1	7732	0.044	0.48	NO
53	MAP2K6	MAP2K6	MAP2K6	7856	0.042	0.47	NO
54	IFNAR1	IFNAR1	IFNAR1	7857	0.042	0.48	NO
55	IRAK1	IRAK1	IRAK1	8095	0.038	0.46	NO
56	MAPK9	MAPK9	MAPK9	8199	0.037	0.46	NO
57	MAPK1	MAPK1	MAPK1	8248	0.036	0.46	NO
58	NFKBIA	NFKBIA	NFKBIA	8423	0.033	0.45	NO
59	RELA	RELA	RELA	8457	0.032	0.45	NO
60	TIRAP	TIRAP	TIRAP	8588	0.03	0.45	NO
61	AKT3	AKT3	AKT3	8763	0.027	0.44	NO
62	IRAK4	IRAK4	IRAK4	9132	0.022	0.42	NO
63	RAC1	RAC1	RAC1	9180	0.021	0.42	NO
64	MAPK3	MAPK3	MAPK3	9228	0.02	0.42	NO
65	IRF3	IRF3	IRF3	9282	0.019	0.42	NO
66	MAP3K7	MAP3K7	MAP3K7	9699	0.012	0.39	NO
67	FADD	FADD	FADD	10060	0.0074	0.38	NO
68	IKBKG	IKBKG	IKBKG	10133	0.0064	0.37	NO
69	PIK3CB	PIK3CB	PIK3CB	10414	0.002	0.36	NO
70	NFKB1	NFKB1	NFKB1	10837	-0.0048	0.33	NO
71	MAP2K2	MAP2K2	MAP2K2	10865	-0.0052	0.33	NO
72	TICAM1	TICAM1	TICAM1	11066	-0.0083	0.32	NO
73	MAP2K3	MAP2K3	MAP2K3	11390	-0.013	0.3	NO
74	MAP2K4	MAP2K4	MAP2K4	11433	-0.014	0.3	NO
75	IKBKB	IKBKB	IKBKB	11677	-0.018	0.29	NO
76	AKT1	AKT1	AKT1	11810	-0.02	0.28	NO
77	TRAF6	TRAF6	TRAF6	12065	-0.024	0.27	NO
78	MAPK13	MAPK13	MAPK13	12716	-0.036	0.24	NO
79	TAB1	TAB1	TAB1	12920	-0.04	0.23	NO
80	PIK3R2	PIK3R2	PIK3R2	12986	-0.041	0.23	NO
81	SPP1	SPP1	SPP1	13093	-0.043	0.22	NO
82	MAP2K7	MAP2K7	MAP2K7	13197	-0.045	0.22	NO
83	IRF5	IRF5	IRF5	13255	-0.046	0.22	NO
84	MAPK8	MAPK8	MAPK8	13551	-0.052	0.21	NO
85	CHUK	CHUK	CHUK	14180	-0.066	0.18	NO
86	AKT2	AKT2	AKT2	14390	-0.071	0.17	NO
87	MAPK10	MAPK10	MAPK10	15852	-0.12	0.099	NO
88	TOLLIP	TOLLIP	TOLLIP	16132	-0.14	0.092	NO
89	IFNA13	IFNA13	IFNA13	16360	-0.15	0.089	NO
90	IFNA1	IFNA1	IFNA1	17068	-0.2	0.062	NO

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

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BIOPEPTIDES 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 G1 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	CDC25C	CDC25C	CDC25C	141	0.61	0.028	YES
2	BUB1	BUB1	BUB1	217	0.58	0.057	YES
3	CCNB2	CCNB2	CCNB2	309	0.55	0.084	YES
4	PTTG1	PTTG1	PTTG1	317	0.55	0.12	YES
5	TTK	TTK	TTK	531	0.49	0.13	YES
6	PLK1	PLK1	PLK1	580	0.48	0.16	YES
7	BUB1B	BUB1B	BUB1B	612	0.48	0.18	YES
8	CDC20	CDC20	CDC20	624	0.47	0.21	YES
9	CCNE2	CCNE2	CCNE2	673	0.46	0.23	YES
10	E2F2	E2F2	E2F2	852	0.43	0.25	YES
11	CCNA2	CCNA2	CCNA2	901	0.42	0.27	YES
12	CDC45	CDC45	CDC45	947	0.42	0.29	YES
13	CDK1	CDK1	CDK1	976	0.41	0.32	YES
14	TGFB3	TGFB3	TGFB3	1194	0.38	0.33	YES
15	ORC1L	ORC1L	ORC1L	1443	0.36	0.33	YES
16	CDC6	CDC6	CDC6	1538	0.34	0.35	YES
17	ESPL1	ESPL1	ESPL1	1810	0.32	0.35	YES
18	PKMYT1	PKMYT1	PKMYT1	1833	0.31	0.37	YES
19	CCNA1	CCNA1	CCNA1	1846	0.31	0.39	YES
20	CDKN2A	CDKN2A	CDKN2A	1903	0.31	0.4	YES
21	TGFB1	TGFB1	TGFB1	1929	0.3	0.42	YES
22	CCNB1	CCNB1	CCNB1	2136	0.29	0.42	YES
23	MAD2L1	MAD2L1	MAD2L1	2170	0.28	0.44	YES
24	CDKN2B	CDKN2B	CDKN2B	2190	0.28	0.45	YES
25	TGFB2	TGFB2	TGFB2	2194	0.28	0.47	YES
26	CDC7	CDC7	CDC7	2235	0.28	0.48	YES
27	CCNE1	CCNE1	CCNE1	2265	0.28	0.5	YES
28	ORC6L	ORC6L	ORC6L	2762	0.24	0.48	YES
29	RBL1	RBL1	RBL1	2915	0.22	0.49	YES
30	CHEK2	CHEK2	CHEK2	3126	0.21	0.49	YES
31	SKP2	SKP2	SKP2	3346	0.2	0.49	YES
32	CDKN2C	CDKN2C	CDKN2C	3386	0.19	0.5	YES
33	MCM6	MCM6	MCM6	3492	0.19	0.5	YES
34	SMC1B	SMC1B	SMC1B	3658	0.18	0.5	YES
35	MYC	MYC	MYC	3735	0.17	0.51	YES
36	CDC25B	CDC25B	CDC25B	3751	0.17	0.52	YES
37	CCND1	CCND1	CCND1	4869	0.12	0.46	NO
38	E2F1	E2F1	E2F1	4926	0.12	0.47	NO
39	E2F3	E2F3	E2F3	5154	0.11	0.46	NO
40	CHEK1	CHEK1	CHEK1	5219	0.1	0.46	NO
41	WEE1	WEE1	WEE1	5452	0.097	0.46	NO
42	MCM5	MCM5	MCM5	5477	0.097	0.46	NO
43	GADD45B	GADD45B	GADD45B	5570	0.094	0.46	NO
44	CDK2	CDK2	CDK2	5622	0.092	0.46	NO
45	CCND3	CCND3	CCND3	5673	0.09	0.47	NO
46	PTTG2	PTTG2	PTTG2	5729	0.089	0.47	NO
47	CDC27	CDC27	CDC27	5904	0.084	0.46	NO
48	SFN	SFN	SFN	5924	0.084	0.47	NO
49	MDM2	MDM2	MDM2	5934	0.084	0.47	NO
50	ANAPC1	ANAPC1	ANAPC1	6000	0.082	0.47	NO
51	YWHAG	YWHAG	YWHAG	6045	0.081	0.48	NO
52	MAD2L2	MAD2L2	MAD2L2	6053	0.081	0.48	NO
53	HDAC1	HDAC1	HDAC1	6169	0.078	0.48	NO
54	CDKN2D	CDKN2D	CDKN2D	6212	0.077	0.48	NO
55	RB1	RB1	RB1	6294	0.074	0.48	NO
56	CDK7	CDK7	CDK7	6302	0.074	0.48	NO
57	STAG1	STAG1	STAG1	6345	0.073	0.48	NO
58	BUB3	BUB3	BUB3	6348	0.073	0.49	NO
59	MCM4	MCM4	MCM4	6581	0.068	0.48	NO
60	CDKN1B	CDKN1B	CDKN1B	6620	0.067	0.48	NO
61	YWHAZ	YWHAZ	YWHAZ	6627	0.067	0.49	NO
62	CDK6	CDK6	CDK6	6642	0.067	0.49	NO
63	YWHAQ	YWHAQ	YWHAQ	6802	0.063	0.48	NO
64	ATM	ATM	ATM	6893	0.061	0.48	NO
65	TP53	TP53	TP53	6934	0.06	0.48	NO
66	SMC3	SMC3	SMC3	6942	0.06	0.49	NO
67	PCNA	PCNA	PCNA	7064	0.057	0.48	NO
68	CCNH	CCNH	CCNH	7099	0.056	0.48	NO
69	ANAPC5	ANAPC5	ANAPC5	7143	0.055	0.49	NO
70	PRKDC	PRKDC	PRKDC	7153	0.055	0.49	NO
71	CUL1	CUL1	CUL1	7372	0.051	0.48	NO
72	MCM2	MCM2	MCM2	7509	0.048	0.48	NO
73	ANAPC10	ANAPC10	ANAPC10	7697	0.045	0.47	NO
74	CDK4	CDK4	CDK4	7850	0.042	0.46	NO
75	ORC2L	ORC2L	ORC2L	7934	0.041	0.46	NO
76	RBX1	RBX1	RBX1	8001	0.04	0.46	NO
77	CDC25A	CDC25A	CDC25A	8873	0.025	0.41	NO
78	SMC1A	SMC1A	SMC1A	8949	0.024	0.41	NO
79	STAG2	STAG2	STAG2	9204	0.02	0.4	NO
80	EP300	EP300	EP300	9231	0.02	0.4	NO
81	YWHAH	YWHAH	YWHAH	9262	0.02	0.39	NO
82	HDAC2	HDAC2	HDAC2	9336	0.018	0.39	NO
83	ORC3L	ORC3L	ORC3L	9348	0.018	0.39	NO
84	RAD21	RAD21	RAD21	9373	0.018	0.39	NO
85	ORC5L	ORC5L	ORC5L	9549	0.015	0.38	NO
86	CCND2	CCND2	CCND2	9556	0.015	0.38	NO
87	CDC16	CDC16	CDC16	9579	0.014	0.38	NO
88	SMAD2	SMAD2	SMAD2	9612	0.014	0.38	NO
89	YWHAB	YWHAB	YWHAB	9937	0.009	0.36	NO
90	MCM7	MCM7	MCM7	10264	0.0044	0.35	NO
91	ZBTB17	ZBTB17	ZBTB17	10372	0.0026	0.34	NO
92	ANAPC4	ANAPC4	ANAPC4	10672	-0.0021	0.32	NO
93	E2F4	E2F4	E2F4	10698	-0.0025	0.32	NO
94	CREBBP	CREBBP	CREBBP	10790	-0.0041	0.32	NO
95	ABL1	ABL1	ABL1	10857	-0.0051	0.32	NO
96	CDC14A	CDC14A	CDC14A	10916	-0.0059	0.31	NO
97	SKP1	SKP1	SKP1	11076	-0.0084	0.3	NO
98	ATR	ATR	ATR	11140	-0.0092	0.3	NO
99	TFDP1	TFDP1	TFDP1	11174	-0.0097	0.3	NO
100	FZR1	FZR1	FZR1	11487	-0.015	0.28	NO
101	MCM3	MCM3	MCM3	11924	-0.022	0.26	NO
102	CDC23	CDC23	CDC23	11933	-0.022	0.26	NO
103	ANAPC7	ANAPC7	ANAPC7	12132	-0.025	0.25	NO
104	RBL2	RBL2	RBL2	12217	-0.027	0.25	NO
105	GADD45A	GADD45A	GADD45A	12326	-0.028	0.24	NO
106	CDKN1A	CDKN1A	CDKN1A	12347	-0.029	0.24	NO
107	CDC26	CDC26	CDC26	12606	-0.034	0.23	NO
108	CDKN1C	CDKN1C	CDKN1C	12823	-0.038	0.22	NO
109	MAD1L1	MAD1L1	MAD1L1	12881	-0.039	0.22	NO
110	YWHAE	YWHAE	YWHAE	12887	-0.039	0.22	NO
111	E2F5	E2F5	E2F5	13240	-0.046	0.21	NO
112	TFDP2	TFDP2	TFDP2	13277	-0.047	0.21	NO
113	SMAD4	SMAD4	SMAD4	13444	-0.05	0.2	NO
114	ANAPC11	ANAPC11	ANAPC11	13768	-0.057	0.19	NO
115	GSK3B	GSK3B	GSK3B	13812	-0.058	0.19	NO
116	SMAD3	SMAD3	SMAD3	14203	-0.066	0.17	NO
117	ORC4L	ORC4L	ORC4L	14668	-0.079	0.15	NO
118	CCNB3	CCNB3	CCNB3	14923	-0.087	0.14	NO
119	WEE2	WEE2	WEE2	14924	-0.087	0.14	NO
120	ANAPC2	ANAPC2	ANAPC2	15452	-0.1	0.12	NO
121	ANAPC13	ANAPC13	ANAPC13	15958	-0.13	0.1	NO
122	CDC14B	CDC14B	CDC14B	16917	-0.19	0.06	NO
123	GADD45G	GADD45G	GADD45G	16923	-0.19	0.07	NO

Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA INFLAM PATHWAY

Table 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	IBSP	IBSP	IBSP	19	0.8	0.022	YES
2	COL11A1	COL11A1	COL11A1	20	0.8	0.046	YES
3	COL5A1	COL5A1	COL5A1	61	0.68	0.063	YES
4	COL6A3	COL6A3	COL6A3	92	0.64	0.08	YES
5	PGF	PGF	PGF	170	0.6	0.093	YES
6	ITGA11	ITGA11	ITGA11	176	0.59	0.11	YES
7	COL5A2	COL5A2	COL5A2	181	0.59	0.13	YES
8	COL5A3	COL5A3	COL5A3	264	0.56	0.14	YES
9	COL1A1	COL1A1	COL1A1	294	0.55	0.15	YES
10	SHC4	SHC4	SHC4	311	0.55	0.17	YES
11	COL3A1	COL3A1	COL3A1	385	0.52	0.18	YES
12	HGF	HGF	HGF	425	0.52	0.19	YES
13	COMP	COMP	COMP	437	0.51	0.2	YES
14	LAMB3	LAMB3	LAMB3	480	0.5	0.22	YES
15	PDGFRA	PDGFRA	PDGFRA	500	0.5	0.23	YES
16	COL1A2	COL1A2	COL1A2	678	0.46	0.24	YES
17	THBS2	THBS2	THBS2	784	0.44	0.24	YES
18	MYLK2	MYLK2	MYLK2	793	0.44	0.25	YES
19	ACTN2	ACTN2	ACTN2	815	0.44	0.26	YES
20	ITGA10	ITGA10	ITGA10	827	0.44	0.28	YES
21	PAK3	PAK3	PAK3	828	0.44	0.29	YES
22	ITGA4	ITGA4	ITGA4	928	0.42	0.3	YES
23	PIK3CG	PIK3CG	PIK3CG	942	0.42	0.31	YES
24	ITGA5	ITGA5	ITGA5	1005	0.41	0.32	YES
25	PDGFRB	PDGFRB	PDGFRB	1035	0.4	0.33	YES
26	BIRC3	BIRC3	BIRC3	1067	0.4	0.34	YES
27	FN1	FN1	FN1	1079	0.4	0.35	YES
28	COL6A2	COL6A2	COL6A2	1150	0.39	0.36	YES
29	PRKCB	PRKCB	PRKCB	1171	0.39	0.36	YES
30	VTN	VTN	VTN	1250	0.38	0.37	YES
31	CAV1	CAV1	CAV1	1279	0.38	0.38	YES
32	VAV1	VAV1	VAV1	1288	0.37	0.39	YES
33	RAC2	RAC2	RAC2	1601	0.34	0.38	YES
34	MYL2	MYL2	MYL2	1687	0.33	0.39	YES
35	LAMA4	LAMA4	LAMA4	1689	0.33	0.4	YES
36	PIK3R5	PIK3R5	PIK3R5	1785	0.32	0.4	YES
37	VEGFA	VEGFA	VEGFA	1798	0.32	0.41	YES
38	PARVG	PARVG	PARVG	1912	0.31	0.41	YES
39	VEGFC	VEGFC	VEGFC	1923	0.3	0.42	YES
40	IGF1	IGF1	IGF1	1946	0.3	0.43	YES
41	ITGA1	ITGA1	ITGA1	2006	0.3	0.43	YES
42	COL4A1	COL4A1	COL4A1	2049	0.3	0.44	YES
43	ITGA8	ITGA8	ITGA8	2129	0.29	0.44	YES
44	ITGA9	ITGA9	ITGA9	2148	0.29	0.45	YES
45	FLT1	FLT1	FLT1	2236	0.28	0.45	YES
46	TNC	TNC	TNC	2363	0.27	0.46	YES
47	FLT4	FLT4	FLT4	2367	0.27	0.46	YES
48	MYLK	MYLK	MYLK	2521	0.25	0.46	YES
49	KDR	KDR	KDR	2546	0.25	0.47	YES
50	TNR	TNR	TNR	2595	0.25	0.47	YES
51	FLNC	FLNC	FLNC	2617	0.25	0.48	YES
52	ACTN1	ACTN1	ACTN1	2651	0.24	0.48	YES
53	ACTN3	ACTN3	ACTN3	2702	0.24	0.49	YES
54	MYL9	MYL9	MYL9	2724	0.24	0.49	YES
55	ITGA2B	ITGA2B	ITGA2B	3007	0.22	0.48	YES
56	SHC1	SHC1	SHC1	3071	0.21	0.49	YES
57	SHC3	SHC3	SHC3	3108	0.21	0.49	YES
58	COL6A1	COL6A1	COL6A1	3176	0.21	0.49	YES
59	THBS1	THBS1	THBS1	3312	0.2	0.49	YES
60	LAMA2	LAMA2	LAMA2	3330	0.2	0.5	YES
61	EGFR	EGFR	EGFR	3400	0.19	0.5	YES
62	VWF	VWF	VWF	3407	0.19	0.5	YES
63	COL4A2	COL4A2	COL4A2	3513	0.19	0.5	YES
64	FLNA	FLNA	FLNA	3519	0.19	0.51	YES
65	PDGFB	PDGFB	PDGFB	3619	0.18	0.51	YES
66	FYN	FYN	FYN	3638	0.18	0.51	YES
67	ITGB3	ITGB3	ITGB3	3753	0.17	0.51	NO
68	PARVB	PARVB	PARVB	4135	0.15	0.49	NO
69	ITGB1	ITGB1	ITGB1	4214	0.15	0.49	NO
70	TNXB	TNXB	TNXB	4291	0.14	0.49	NO
71	ITGAV	ITGAV	ITGAV	4473	0.14	0.49	NO
72	COL6A6	COL6A6	COL6A6	4506	0.13	0.49	NO
73	PIK3CD	PIK3CD	PIK3CD	4544	0.13	0.49	NO
74	THBS3	THBS3	THBS3	4563	0.13	0.49	NO
75	RASGRF1	RASGRF1	RASGRF1	4667	0.13	0.49	NO
76	ROCK2	ROCK2	ROCK2	4709	0.12	0.49	NO
77	THBS4	THBS4	THBS4	4802	0.12	0.49	NO
78	PIK3R1	PIK3R1	PIK3R1	4819	0.12	0.49	NO
79	CCND1	CCND1	CCND1	4869	0.12	0.5	NO
80	ITGB4	ITGB4	ITGB4	4899	0.12	0.5	NO
81	ITGB5	ITGB5	ITGB5	4929	0.12	0.5	NO
82	JUN	JUN	JUN	4934	0.12	0.5	NO
83	ELK1	ELK1	ELK1	5102	0.11	0.5	NO
84	PARVA	PARVA	PARVA	5203	0.1	0.49	NO
85	CAV2	CAV2	CAV2	5255	0.1	0.49	NO
86	PXN	PXN	PXN	5401	0.099	0.49	NO
87	TNN	TNN	TNN	5489	0.096	0.48	NO
88	CRKL	CRKL	CRKL	5562	0.094	0.48	NO
89	VASP	VASP	VASP	5624	0.092	0.48	NO
90	VCL	VCL	VCL	5661	0.091	0.48	NO
91	CCND3	CCND3	CCND3	5673	0.09	0.49	NO
92	RAP1B	RAP1B	RAP1B	5718	0.09	0.49	NO
93	RAP1A	RAP1A	RAP1A	5877	0.085	0.48	NO
94	PTEN	PTEN	PTEN	5883	0.085	0.48	NO
95	LAMC1	LAMC1	LAMC1	5958	0.083	0.48	NO
96	PPP1R12A	PPP1R12A	PPP1R12A	5981	0.082	0.48	NO
97	ITGA2	ITGA2	ITGA2	5988	0.082	0.48	NO
98	ITGA3	ITGA3	ITGA3	6233	0.076	0.47	NO
99	MAP2K1	MAP2K1	MAP2K1	6441	0.071	0.46	NO
100	BIRC2	BIRC2	BIRC2	6483	0.07	0.46	NO
101	PPP1CC	PPP1CC	PPP1CC	6535	0.069	0.46	NO
102	ITGA7	ITGA7	ITGA7	6565	0.068	0.46	NO
103	SOS1	SOS1	SOS1	6664	0.066	0.46	NO
104	ROCK1	ROCK1	ROCK1	6726	0.065	0.46	NO
105	PIK3CA	PIK3CA	PIK3CA	6853	0.062	0.45	NO
106	PAK2	PAK2	PAK2	6871	0.061	0.45	NO
107	LAMC3	LAMC3	LAMC3	7031	0.058	0.44	NO
108	ZYX	ZYX	ZYX	7104	0.056	0.44	NO
109	PIK3R3	PIK3R3	PIK3R3	7472	0.049	0.42	NO
110	TLN1	TLN1	TLN1	7556	0.048	0.42	NO
111	ACTB	ACTB	ACTB	7765	0.044	0.41	NO
112	MYLK3	MYLK3	MYLK3	8019	0.039	0.4	NO
113	PTK2	PTK2	PTK2	8194	0.037	0.39	NO
114	MAPK9	MAPK9	MAPK9	8199	0.037	0.39	NO
115	MAPK1	MAPK1	MAPK1	8248	0.036	0.39	NO
116	MYLPF	MYLPF	MYLPF	8358	0.034	0.38	NO
117	PPP1CB	PPP1CB	PPP1CB	8576	0.03	0.37	NO
118	AKT3	AKT3	AKT3	8763	0.027	0.36	NO
119	CDC42	CDC42	CDC42	8920	0.025	0.36	NO
120	PRKCG	PRKCG	PRKCG	8972	0.024	0.35	NO
121	MYL12A	MYL12A	MYL12A	9161	0.021	0.34	NO
122	RAC1	RAC1	RAC1	9180	0.021	0.34	NO
123	PIP5K1C	PIP5K1C	PIP5K1C	9187	0.021	0.34	NO
124	ILK	ILK	ILK	9215	0.02	0.34	NO
125	MAPK3	MAPK3	MAPK3	9228	0.02	0.34	NO
126	ACTG1	ACTG1	ACTG1	9541	0.015	0.32	NO
127	CCND2	CCND2	CCND2	9556	0.015	0.32	NO
128	XIAP	XIAP	XIAP	9560	0.014	0.32	NO
129	CTNNB1	CTNNB1	CTNNB1	9727	0.012	0.32	NO
130	CRK	CRK	CRK	9769	0.011	0.31	NO
131	RAPGEF1	RAPGEF1	RAPGEF1	9781	0.011	0.31	NO
132	PAK1	PAK1	PAK1	9870	0.0099	0.31	NO
133	GRB2	GRB2	GRB2	9931	0.0091	0.31	NO
134	PDGFA	PDGFA	PDGFA	10061	0.0073	0.3	NO
135	DOCK1	DOCK1	DOCK1	10320	0.0035	0.28	NO
136	ACTN4	ACTN4	ACTN4	10369	0.0026	0.28	NO
137	PIK3CB	PIK3CB	PIK3CB	10414	0.002	0.28	NO
138	LAMB2	LAMB2	LAMB2	10714	-0.0028	0.26	NO
139	LAMA3	LAMA3	LAMA3	11175	-0.0097	0.24	NO
140	GRLF1	GRLF1	GRLF1	11297	-0.012	0.23	NO
141	COL11A2	COL11A2	COL11A2	11424	-0.014	0.22	NO
142	COL2A1	COL2A1	COL2A1	11532	-0.015	0.22	NO
143	AKT1	AKT1	AKT1	11810	-0.02	0.2	NO
144	DIAPH1	DIAPH1	DIAPH1	11902	-0.021	0.2	NO
145	PPP1CA	PPP1CA	PPP1CA	11917	-0.022	0.2	NO
146	RHOA	RHOA	RHOA	11939	-0.022	0.2	NO
147	BAD	BAD	BAD	11974	-0.022	0.2	NO
148	CAPN2	CAPN2	CAPN2	12106	-0.025	0.19	NO
149	FLNB	FLNB	FLNB	12120	-0.025	0.19	NO
150	LAMC2	LAMC2	LAMC2	12203	-0.026	0.19	NO
151	RAF1	RAF1	RAF1	12210	-0.026	0.19	NO
152	SRC	SRC	SRC	12257	-0.027	0.19	NO
153	PDGFD	PDGFD	PDGFD	12269	-0.028	0.19	NO
154	ITGB6	ITGB6	ITGB6	12674	-0.035	0.16	NO
155	ITGB7	ITGB7	ITGB7	12701	-0.035	0.16	NO
156	VEGFB	VEGFB	VEGFB	12714	-0.036	0.16	NO
157	MET	MET	MET	12769	-0.037	0.16	NO
158	LAMA5	LAMA5	LAMA5	12856	-0.038	0.16	NO
159	MYL12B	MYL12B	MYL12B	12925	-0.04	0.16	NO
160	PIK3R2	PIK3R2	PIK3R2	12986	-0.041	0.16	NO
161	SPP1	SPP1	SPP1	13093	-0.043	0.15	NO
162	FIGF	FIGF	FIGF	13196	-0.045	0.15	NO
163	PDGFC	PDGFC	PDGFC	13211	-0.045	0.15	NO
164	MAPK8	MAPK8	MAPK8	13551	-0.052	0.13	NO
165	TLN2	TLN2	TLN2	13626	-0.054	0.13	NO
166	GSK3B	GSK3B	GSK3B	13812	-0.058	0.12	NO
167	BRAF	BRAF	BRAF	14042	-0.062	0.11	NO
168	SHC2	SHC2	SHC2	14158	-0.065	0.1	NO
169	PRKCA	PRKCA	PRKCA	14245	-0.067	0.099	NO
170	AKT2	AKT2	AKT2	14390	-0.071	0.094	NO
171	PDPK1	PDPK1	PDPK1	14399	-0.071	0.095	NO
172	SOS2	SOS2	SOS2	14564	-0.076	0.088	NO
173	LAMB1	LAMB1	LAMB1	14593	-0.077	0.089	NO
174	MYL5	MYL5	MYL5	14741	-0.081	0.083	NO
175	ARHGAP5	ARHGAP5	ARHGAP5	14959	-0.088	0.074	NO
176	VAV2	VAV2	VAV2	15084	-0.092	0.069	NO
177	PAK4	PAK4	PAK4	15753	-0.12	0.036	NO
178	IGF1R	IGF1R	IGF1R	15783	-0.12	0.037	NO
179	BCAR1	BCAR1	BCAR1	15812	-0.12	0.039	NO
180	MAPK10	MAPK10	MAPK10	15852	-0.12	0.04	NO
181	RELN	RELN	RELN	16118	-0.14	0.03	NO
182	ITGB8	ITGB8	ITGB8	16123	-0.14	0.033	NO
183	ITGA6	ITGA6	ITGA6	16224	-0.14	0.032	NO
184	BCL2	BCL2	BCL2	16260	-0.14	0.034	NO
185	LAMA1	LAMA1	LAMA1	16350	-0.15	0.033	NO
186	PAK6	PAK6	PAK6	16364	-0.15	0.037	NO
187	COL4A6	COL4A6	COL4A6	16479	-0.16	0.035	NO
188	VAV3	VAV3	VAV3	16908	-0.19	0.017	NO
189	CHAD	CHAD	CHAD	17029	-0.2	0.016	NO
190	RAC3	RAC3	RAC3	17132	-0.21	0.016	NO
191	LAMB4	LAMB4	LAMB4	17379	-0.24	0.0097	NO
192	EGF	EGF	EGF	17446	-0.25	0.013	NO
193	ERBB2	ERBB2	ERBB2	17512	-0.26	0.017	NO
194	PAK7	PAK7	PAK7	17630	-0.28	0.019	NO
195	COL4A4	COL4A4	COL4A4	18060	-0.43	0.0076	NO

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

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

genes ES table in pathway: BIOCARTA EGF 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	CASP5	CASP5	CASP5	41	0.72	0.06	YES
2	IL6	IL6	IL6	42	0.72	0.12	YES
3	MEFV	MEFV	MEFV	129	0.62	0.17	YES
4	CCL11	CCL11	CCL11	431	0.51	0.2	YES
5	NOD2	NOD2	NOD2	434	0.51	0.24	YES
6	NLRC4	NLRC4	NLRC4	548	0.48	0.28	YES
7	CCL13	CCL13	CCL13	573	0.48	0.32	YES
8	CCL8	CCL8	CCL8	668	0.46	0.35	YES
9	CCL5	CCL5	CCL5	885	0.43	0.38	YES
10	PSTPIP1	PSTPIP1	PSTPIP1	929	0.42	0.41	YES
11	BIRC3	BIRC3	BIRC3	1067	0.4	0.44	YES
12	NAIP	NAIP	NAIP	1381	0.36	0.45	YES
13	NLRP1	NLRP1	NLRP1	1435	0.36	0.48	YES
14	CCL7	CCL7	CCL7	1510	0.35	0.5	YES
15	CARD9	CARD9	CARD9	1533	0.35	0.53	YES
16	IL1B	IL1B	IL1B	1638	0.33	0.55	YES
17	NLRP3	NLRP3	NLRP3	1915	0.31	0.56	YES
18	CASP1	CASP1	CASP1	2208	0.28	0.57	YES
19	PYCARD	PYCARD	PYCARD	2542	0.25	0.58	YES
20	IL8	IL8	IL8	2560	0.25	0.6	YES
21	RIPK2	RIPK2	RIPK2	2714	0.24	0.61	YES
22	CXCL2	CXCL2	CXCL2	2831	0.23	0.62	YES
23	TNFAIP3	TNFAIP3	TNFAIP3	2864	0.23	0.64	YES
24	MAPK11	MAPK11	MAPK11	3341	0.2	0.63	YES
25	PYDC1	PYDC1	PYDC1	3504	0.19	0.64	YES
26	CARD6	CARD6	CARD6	3825	0.17	0.64	YES
27	CARD8	CARD8	CARD8	3948	0.16	0.64	YES
28	CASP8	CASP8	CASP8	4905	0.12	0.6	NO
29	CXCL1	CXCL1	CXCL1	5200	0.1	0.59	NO
30	TNF	TNF	TNF	5356	0.1	0.59	NO
31	HSP90B1	HSP90B1	HSP90B1	5410	0.098	0.6	NO
32	NOD1	NOD1	NOD1	5708	0.09	0.59	NO
33	CCL2	CCL2	CCL2	5744	0.088	0.6	NO
34	MAPK12	MAPK12	MAPK12	6101	0.08	0.58	NO
35	BIRC2	BIRC2	BIRC2	6483	0.07	0.57	NO
36	MAPK14	MAPK14	MAPK14	7581	0.047	0.51	NO
37	TAB2	TAB2	TAB2	7639	0.046	0.51	NO
38	MAPK9	MAPK9	MAPK9	8199	0.037	0.48	NO
39	MAPK1	MAPK1	MAPK1	8248	0.036	0.48	NO
40	NFKBIA	NFKBIA	NFKBIA	8423	0.033	0.48	NO
41	RELA	RELA	RELA	8457	0.032	0.48	NO
42	SUGT1	SUGT1	SUGT1	8821	0.026	0.46	NO
43	ERBB2IP	ERBB2IP	ERBB2IP	9094	0.022	0.45	NO
44	MAPK3	MAPK3	MAPK3	9228	0.02	0.44	NO
45	XIAP	XIAP	XIAP	9560	0.014	0.42	NO
46	MAP3K7	MAP3K7	MAP3K7	9699	0.012	0.42	NO
47	IKBKG	IKBKG	IKBKG	10133	0.0064	0.4	NO
48	NFKB1	NFKB1	NFKB1	10837	-0.0048	0.36	NO
49	TRIP6	TRIP6	TRIP6	10981	-0.007	0.35	NO
50	IL18	IL18	IL18	11130	-0.009	0.34	NO
51	IKBKB	IKBKB	IKBKB	11677	-0.018	0.31	NO
52	TRAF6	TRAF6	TRAF6	12065	-0.024	0.29	NO
53	MAPK13	MAPK13	MAPK13	12716	-0.036	0.26	NO
54	TAB1	TAB1	TAB1	12920	-0.04	0.25	NO
55	TAB3	TAB3	TAB3	13119	-0.043	0.25	NO
56	MAPK8	MAPK8	MAPK8	13551	-0.052	0.23	NO
57	CHUK	CHUK	CHUK	14180	-0.066	0.2	NO
58	HSP90AA1	HSP90AA1	HSP90AA1	14469	-0.073	0.19	NO
59	NFKBIB	NFKBIB	NFKBIB	14740	-0.081	0.18	NO
60	MAPK10	MAPK10	MAPK10	15852	-0.12	0.13	NO

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

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

genes ES table in pathway: BIOCARTA ERK PATHWAY

Table 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	HGF	HGF	HGF	425	0.52	0.12	YES
2	MAP4K1	MAP4K1	MAP4K1	866	0.43	0.22	YES
3	PIK3CG	PIK3CG	PIK3CG	942	0.42	0.33	YES
4	ITGA1	ITGA1	ITGA1	2006	0.3	0.36	YES
5	FOS	FOS	FOS	3907	0.16	0.3	YES
6	ACTA1	ACTA1	ACTA1	4201	0.15	0.33	YES
7	ITGB1	ITGB1	ITGB1	4214	0.15	0.37	YES
8	PIK3R1	PIK3R1	PIK3R1	4819	0.12	0.37	YES
9	JUN	JUN	JUN	4934	0.12	0.4	YES
10	ELK1	ELK1	ELK1	5102	0.11	0.42	YES
11	PXN	PXN	PXN	5401	0.099	0.43	YES
12	CRKL	CRKL	CRKL	5562	0.094	0.45	YES
13	RAP1B	RAP1B	RAP1B	5718	0.09	0.46	YES
14	RAP1A	RAP1A	RAP1A	5877	0.085	0.48	YES
15	PTEN	PTEN	PTEN	5883	0.085	0.5	YES
16	MAP2K1	MAP2K1	MAP2K1	6441	0.071	0.49	YES
17	SOS1	SOS1	SOS1	6664	0.066	0.5	YES
18	STAT3	STAT3	STAT3	6775	0.063	0.51	YES
19	PIK3CA	PIK3CA	PIK3CA	6853	0.062	0.52	YES
20	PTK2	PTK2	PTK2	8194	0.037	0.46	NO
21	MAPK1	MAPK1	MAPK1	8248	0.036	0.47	NO
22	RASA1	RASA1	RASA1	8347	0.034	0.47	NO
23	PTK2B	PTK2B	PTK2B	8754	0.027	0.46	NO
24	MAPK3	MAPK3	MAPK3	9228	0.02	0.44	NO
25	CRK	CRK	CRK	9769	0.011	0.41	NO
26	RAPGEF1	RAPGEF1	RAPGEF1	9781	0.011	0.41	NO
27	PAK1	PAK1	PAK1	9870	0.0099	0.41	NO
28	GRB2	GRB2	GRB2	9931	0.0091	0.41	NO
29	PTPN11	PTPN11	PTPN11	10196	0.0055	0.4	NO
30	DOCK1	DOCK1	DOCK1	10320	0.0035	0.39	NO
31	GAB1	GAB1	GAB1	10715	-0.0028	0.37	NO
32	MAP2K2	MAP2K2	MAP2K2	10865	-0.0052	0.36	NO
33	RAF1	RAF1	RAF1	12210	-0.026	0.3	NO
34	SRC	SRC	SRC	12257	-0.027	0.3	NO
35	MET	MET	MET	12769	-0.037	0.28	NO
36	MAPK8	MAPK8	MAPK8	13551	-0.052	0.26	NO

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

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

genes ES table in pathway: BIOCARTA FAS 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	LBP	LBP	LBP	24	0.78	0.19	YES
2	LEF1	LEF1	LEF1	30	0.76	0.38	YES
3	LY96	LY96	LY96	295	0.55	0.5	YES
4	WNT1	WNT1	WNT1	2456	0.26	0.44	YES
5	CD14	CD14	CD14	2494	0.26	0.5	YES
6	GJA1	GJA1	GJA1	3214	0.2	0.51	YES
7	EIF2AK2	EIF2AK2	EIF2AK2	4107	0.15	0.5	YES
8	TLR4	TLR4	TLR4	4153	0.15	0.54	YES
9	MYD88	MYD88	MYD88	4694	0.13	0.54	YES
10	PIK3R1	PIK3R1	PIK3R1	4819	0.12	0.56	YES
11	CCND1	CCND1	CCND1	4869	0.12	0.59	YES
12	PIK3CA	PIK3CA	PIK3CA	6853	0.062	0.49	NO
13	IRAK1	IRAK1	IRAK1	8095	0.038	0.43	NO
14	APC	APC	APC	8206	0.036	0.44	NO
15	RELA	RELA	RELA	8457	0.032	0.43	NO
16	TIRAP	TIRAP	TIRAP	8588	0.03	0.43	NO
17	CTNNB1	CTNNB1	CTNNB1	9727	0.012	0.37	NO
18	PPP2CA	PPP2CA	PPP2CA	10233	0.005	0.34	NO
19	NFKB1	NFKB1	NFKB1	10837	-0.0048	0.31	NO
20	AKT1	AKT1	AKT1	11810	-0.02	0.26	NO
21	FZD1	FZD1	FZD1	12765	-0.037	0.22	NO
22	DVL1	DVL1	DVL1	13644	-0.054	0.18	NO
23	GNAI1	GNAI1	GNAI1	13667	-0.055	0.2	NO
24	GSK3B	GSK3B	GSK3B	13812	-0.058	0.2	NO
25	PDPK1	PDPK1	PDPK1	14399	-0.071	0.19	NO
26	AXIN1	AXIN1	AXIN1	14746	-0.081	0.19	NO

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

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

Table 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	SHC4	SHC4	SHC4	311	0.55	0.056	YES
2	RUNX1	RUNX1	RUNX1	596	0.48	0.1	YES
3	E2F2	E2F2	E2F2	852	0.43	0.15	YES
4	PIK3CG	PIK3CG	PIK3CG	942	0.42	0.2	YES
5	TGFB3	TGFB3	TGFB3	1194	0.38	0.24	YES
6	PIK3R5	PIK3R5	PIK3R5	1785	0.32	0.25	YES
7	CDKN2A	CDKN2A	CDKN2A	1903	0.31	0.28	YES
8	TGFB1	TGFB1	TGFB1	1929	0.3	0.32	YES
9	TGFB2	TGFB2	TGFB2	2194	0.28	0.34	YES
10	SHC1	SHC1	SHC1	3071	0.21	0.33	YES
11	SHC3	SHC3	SHC3	3108	0.21	0.35	YES
12	MYC	MYC	MYC	3735	0.17	0.34	YES
13	CBLB	CBLB	CBLB	4052	0.15	0.34	YES
14	MECOM	MECOM	MECOM	4318	0.14	0.35	YES
15	PIK3CD	PIK3CD	PIK3CD	4544	0.13	0.35	YES
16	PIK3R1	PIK3R1	PIK3R1	4819	0.12	0.36	YES
17	CCND1	CCND1	CCND1	4869	0.12	0.37	YES
18	TGFBR1	TGFBR1	TGFBR1	4994	0.11	0.38	YES
19	E2F3	E2F3	E2F3	5154	0.11	0.38	YES
20	CRKL	CRKL	CRKL	5562	0.094	0.37	YES
21	NRAS	NRAS	NRAS	5639	0.092	0.38	YES
22	MDM2	MDM2	MDM2	5934	0.084	0.38	YES
23	CBL	CBL	CBL	6076	0.081	0.38	YES
24	HDAC1	HDAC1	HDAC1	6169	0.078	0.38	YES
25	RB1	RB1	RB1	6294	0.074	0.39	YES
26	MAP2K1	MAP2K1	MAP2K1	6441	0.071	0.39	YES
27	CDKN1B	CDKN1B	CDKN1B	6620	0.067	0.39	YES
28	CDK6	CDK6	CDK6	6642	0.067	0.4	YES
29	SOS1	SOS1	SOS1	6664	0.066	0.4	YES
30	STAT5A	STAT5A	STAT5A	6758	0.064	0.41	YES
31	PIK3CA	PIK3CA	PIK3CA	6853	0.062	0.41	YES
32	TP53	TP53	TP53	6934	0.06	0.41	YES
33	PIK3R3	PIK3R3	PIK3R3	7472	0.049	0.39	NO
34	CDK4	CDK4	CDK4	7850	0.042	0.38	NO
35	TGFBR2	TGFBR2	TGFBR2	8002	0.04	0.37	NO
36	MAPK1	MAPK1	MAPK1	8248	0.036	0.36	NO
37	NFKBIA	NFKBIA	NFKBIA	8423	0.033	0.36	NO
38	RELA	RELA	RELA	8457	0.032	0.36	NO
39	AKT3	AKT3	AKT3	8763	0.027	0.35	NO
40	MAPK3	MAPK3	MAPK3	9228	0.02	0.32	NO
41	HDAC2	HDAC2	HDAC2	9336	0.018	0.32	NO
42	CRK	CRK	CRK	9769	0.011	0.3	NO
43	GRB2	GRB2	GRB2	9931	0.0091	0.29	NO
44	IKBKG	IKBKG	IKBKG	10133	0.0064	0.28	NO
45	PTPN11	PTPN11	PTPN11	10196	0.0055	0.28	NO
46	GAB2	GAB2	GAB2	10245	0.0048	0.28	NO
47	PIK3CB	PIK3CB	PIK3CB	10414	0.002	0.27	NO
48	NFKB1	NFKB1	NFKB1	10837	-0.0048	0.24	NO
49	ABL1	ABL1	ABL1	10857	-0.0051	0.24	NO
50	MAP2K2	MAP2K2	MAP2K2	10865	-0.0052	0.24	NO
51	IKBKB	IKBKB	IKBKB	11677	-0.018	0.2	NO
52	STAT5B	STAT5B	STAT5B	11743	-0.019	0.2	NO
53	AKT1	AKT1	AKT1	11810	-0.02	0.2	NO
54	CTBP1	CTBP1	CTBP1	11847	-0.02	0.2	NO
55	BAD	BAD	BAD	11974	-0.022	0.2	NO
56	CTBP2	CTBP2	CTBP2	12145	-0.025	0.19	NO
57	RAF1	RAF1	RAF1	12210	-0.026	0.19	NO
58	CDKN1A	CDKN1A	CDKN1A	12347	-0.029	0.19	NO
59	ARAF	ARAF	ARAF	12348	-0.029	0.19	NO
60	HRAS	HRAS	HRAS	12375	-0.029	0.19	NO
61	PIK3R2	PIK3R2	PIK3R2	12986	-0.041	0.17	NO
62	SMAD4	SMAD4	SMAD4	13444	-0.05	0.15	NO
63	KRAS	KRAS	KRAS	13479	-0.051	0.15	NO
64	BCL2L1	BCL2L1	BCL2L1	13509	-0.052	0.16	NO
65	BRAF	BRAF	BRAF	14042	-0.062	0.14	NO
66	SHC2	SHC2	SHC2	14158	-0.065	0.14	NO
67	CHUK	CHUK	CHUK	14180	-0.066	0.15	NO
68	SMAD3	SMAD3	SMAD3	14203	-0.066	0.16	NO
69	AKT2	AKT2	AKT2	14390	-0.071	0.15	NO
70	SOS2	SOS2	SOS2	14564	-0.076	0.16	NO
71	BCR	BCR	BCR	15526	-0.11	0.12	NO
72	CBLC	CBLC	CBLC	17287	-0.23	0.05	NO

Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus3 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
BIOCARTA NO1 PATHWAY	28	genes.ES.table	0.64	1.4	0.08	0.97	0.94	0.29	0.031	0.28	0.72	0.37
BIOCARTA ERK PATHWAY	27	genes.ES.table	0.49	1.5	0.088	0.98	0.92	0.18	0.084	0.17	0.73	0.38
BIOCARTA FAS PATHWAY	29	genes.ES.table	0.45	1.5	0.073	1	0.86	0.31	0.24	0.24	0.98	0.5
BIOCARTA FCER1 PATHWAY	37	genes.ES.table	0.5	1.4	0.17	0.78	0.95	0.6	0.34	0.39	0.6	0.27
BIOCARTA MET PATHWAY	36	genes.ES.table	0.46	1.5	0.11	1	0.91	0.58	0.32	0.4	0.79	0.41
BIOCARTA TCR PATHWAY	43	genes.ES.table	0.56	1.4	0.18	0.76	0.96	0.54	0.28	0.39	0.59	0.25
BIOCARTA PAR1 PATHWAY	36	genes.ES.table	0.48	1.4	0.099	0.84	0.95	0.42	0.24	0.32	0.64	0.3
BIOCARTA TOLL PATHWAY	36	genes.ES.table	0.52	1.5	0.078	1	0.89	0.39	0.24	0.3	0.97	0.48
BIOCARTA VEGF PATHWAY	28	genes.ES.table	0.63	1.6	0.024	1	0.68	0.21	0.048	0.2	0.7	0.37
KEGG TRYPTOPHAN METABOLISM	38	genes.ES.table	0.5	1.4	0.08	0.91	0.94	0.29	0.11	0.26	0.69	0.34

genes ES table in pathway: BIOCARTA NO1 PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CREB3L3	CREB3L3	CREB3L3	23	0.89	0.17	YES
2	AQP4	AQP4	AQP4	655	0.47	0.23	YES
3	DYNC1I1	DYNC1I1	DYNC1I1	741	0.45	0.31	YES
4	AQP3	AQP3	AQP3	975	0.4	0.37	YES
5	AVPR2	AVPR2	AVPR2	1100	0.38	0.44	YES
6	DYNC2H1	DYNC2H1	DYNC2H1	2306	0.24	0.42	YES
7	ARHGDIB	ARHGDIB	ARHGDIB	2344	0.23	0.46	YES
8	DCTN6	DCTN6	DCTN6	3350	0.17	0.44	NO
9	CREB1	CREB1	CREB1	4226	0.13	0.41	NO
10	CREB3L4	CREB3L4	CREB3L4	4697	0.11	0.41	NO
11	ADCY9	ADCY9	ADCY9	5407	0.092	0.39	NO
12	DCTN4	DCTN4	DCTN4	5561	0.088	0.4	NO
13	DYNC1I2	DYNC1I2	DYNC1I2	5885	0.08	0.39	NO
14	VAMP2	VAMP2	VAMP2	6186	0.072	0.39	NO
15	CREB5	CREB5	CREB5	7331	0.046	0.34	NO
16	DCTN1	DCTN1	DCTN1	7611	0.04	0.33	NO
17	CREB3L2	CREB3L2	CREB3L2	7807	0.035	0.32	NO
18	CREB3	CREB3	CREB3	7842	0.035	0.33	NO
19	PRKACB	PRKACB	PRKACB	8730	0.016	0.28	NO
20	DYNC1LI2	DYNC1LI2	DYNC1LI2	8766	0.016	0.28	NO
21	RAB11A	RAB11A	RAB11A	8922	0.012	0.28	NO
22	STX4	STX4	STX4	9361	0.0033	0.26	NO
23	RAB5B	RAB5B	RAB5B	10101	-0.011	0.22	NO
24	DYNLL1	DYNLL1	DYNLL1	10109	-0.012	0.22	NO
25	DYNC1H1	DYNC1H1	DYNC1H1	10899	-0.028	0.18	NO
26	PRKACA	PRKACA	PRKACA	11050	-0.032	0.18	NO
27	DYNLL2	DYNLL2	DYNLL2	11212	-0.035	0.18	NO
28	DYNC1LI1	DYNC1LI1	DYNC1LI1	11356	-0.038	0.18	NO
29	DCTN5	DCTN5	DCTN5	11490	-0.041	0.18	NO
30	RAB5C	RAB5C	RAB5C	11529	-0.042	0.18	NO
31	AQP2	AQP2	AQP2	11560	-0.043	0.19	NO
32	ARHGDIA	ARHGDIA	ARHGDIA	12177	-0.057	0.17	NO
33	NSF	NSF	NSF	12186	-0.058	0.18	NO
34	ADCY6	ADCY6	ADCY6	12358	-0.062	0.18	NO
35	RAB5A	RAB5A	RAB5A	12546	-0.066	0.18	NO
36	PRKX	PRKX	PRKX	12664	-0.069	0.19	NO
37	DCTN2	DCTN2	DCTN2	13321	-0.087	0.17	NO
38	DYNC2LI1	DYNC2LI1	DYNC2LI1	13440	-0.091	0.18	NO
39	RAB11B	RAB11B	RAB11B	13568	-0.095	0.19	NO
40	GNAS	GNAS	GNAS	14032	-0.11	0.19	NO
41	CREB3L1	CREB3L1	CREB3L1	16185	-0.22	0.11	NO

Figure S41. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA 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	CYP4A11	CYP4A11	CYP4A11	2	1.2	0.079	YES
2	CD36	CD36	CD36	62	0.75	0.13	YES
3	FABP7	FABP7	FABP7	105	0.7	0.17	YES
4	ANGPTL4	ANGPTL4	ANGPTL4	132	0.68	0.22	YES
5	CYP4A22	CYP4A22	CYP4A22	186	0.65	0.26	YES
6	HMGCS2	HMGCS2	HMGCS2	244	0.62	0.3	YES
7	FABP4	FABP4	FABP4	263	0.6	0.34	YES
8	PCK1	PCK1	PCK1	506	0.51	0.36	YES
9	FABP6	FABP6	FABP6	510	0.5	0.39	YES
10	CPT1C	CPT1C	CPT1C	581	0.49	0.42	YES
11	LPL	LPL	LPL	625	0.48	0.45	YES
12	PLIN1	PLIN1	PLIN1	685	0.46	0.48	YES
13	SLC27A2	SLC27A2	SLC27A2	695	0.46	0.51	YES
14	ACADL	ACADL	ACADL	893	0.41	0.52	YES
15	FABP1	FABP1	FABP1	1464	0.32	0.51	YES
16	EHHADH	EHHADH	EHHADH	1477	0.32	0.54	YES
17	RXRG	RXRG	RXRG	1547	0.31	0.55	YES
18	FADS2	FADS2	FADS2	1730	0.29	0.56	YES
19	AQP7	AQP7	AQP7	1806	0.28	0.58	YES
20	MMP1	MMP1	MMP1	2120	0.25	0.58	YES
21	ACSL5	ACSL5	ACSL5	2172	0.25	0.59	YES
22	SCD	SCD	SCD	2181	0.25	0.61	YES
23	FABP5	FABP5	FABP5	2351	0.23	0.61	YES
24	SORBS1	SORBS1	SORBS1	2869	0.2	0.6	NO
25	CYP7A1	CYP7A1	CYP7A1	3437	0.16	0.58	NO
26	CYP8B1	CYP8B1	CYP8B1	3469	0.16	0.59	NO
27	CYP27A1	CYP27A1	CYP27A1	3653	0.15	0.59	NO
28	ACADM	ACADM	ACADM	4088	0.13	0.57	NO
29	ACSL1	ACSL1	ACSL1	4240	0.13	0.57	NO
30	RXRA	RXRA	RXRA	4364	0.12	0.57	NO
31	CPT1A	CPT1A	CPT1A	5201	0.098	0.53	NO
32	GK	GK	GK	5599	0.087	0.52	NO
33	CPT2	CPT2	CPT2	5755	0.083	0.52	NO
34	NR1H3	NR1H3	NR1H3	6327	0.069	0.49	NO
35	PCK2	PCK2	PCK2	6362	0.068	0.49	NO
36	UBC	UBC	UBC	6694	0.06	0.48	NO
37	ILK	ILK	ILK	6869	0.056	0.47	NO
38	SCP2	SCP2	SCP2	7187	0.049	0.46	NO
39	ACSL6	ACSL6	ACSL6	7216	0.048	0.46	NO
40	OLR1	OLR1	OLR1	7287	0.047	0.46	NO
41	ADIPOQ	ADIPOQ	ADIPOQ	7821	0.035	0.43	NO
42	PPARA	PPARA	PPARA	7822	0.035	0.43	NO
43	FABP2	FABP2	FABP2	8036	0.031	0.42	NO
44	SCD5	SCD5	SCD5	8081	0.03	0.42	NO
45	RXRB	RXRB	RXRB	8558	0.02	0.4	NO
46	ME1	ME1	ME1	8764	0.016	0.39	NO
47	PDPK1	PDPK1	PDPK1	9309	0.0044	0.36	NO
48	PPARG	PPARG	PPARG	9444	0.0018	0.35	NO
49	PPARD	PPARD	PPARD	9597	-0.0013	0.34	NO
50	FABP3	FABP3	FABP3	9825	-0.0059	0.33	NO
51	ACOX1	ACOX1	ACOX1	9985	-0.0091	0.32	NO
52	ACSL3	ACSL3	ACSL3	10444	-0.018	0.3	NO
53	APOC3	APOC3	APOC3	11146	-0.034	0.26	NO
54	ACSL4	ACSL4	ACSL4	11513	-0.042	0.24	NO
55	APOA2	APOA2	APOA2	12322	-0.061	0.2	NO
56	APOA1	APOA1	APOA1	12800	-0.072	0.18	NO
57	SLC27A1	SLC27A1	SLC27A1	12966	-0.077	0.18	NO
58	ACAA1	ACAA1	ACAA1	13910	-0.11	0.13	NO
59	ACOX3	ACOX3	ACOX3	13966	-0.11	0.14	NO
60	DBI	DBI	DBI	14215	-0.12	0.13	NO
61	SLC27A4	SLC27A4	SLC27A4	16621	-0.26	0.017	NO
62	CPT1B	CPT1B	CPT1B	16805	-0.28	0.026	NO
63	PLTP	PLTP	PLTP	17395	-0.37	0.018	NO
64	SLC27A5	SLC27A5	SLC27A5	17428	-0.38	0.042	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: BIOCARTA FAS PATHWAY

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	KDR	KDR	KDR	110	0.7	0.13	YES
2	FLT1	FLT1	FLT1	164	0.66	0.26	YES
3	FLT4	FLT4	FLT4	296	0.59	0.37	YES
4	VEGFA	VEGFA	VEGFA	320	0.58	0.48	YES
5	NOS3	NOS3	NOS3	522	0.5	0.57	YES
6	PIK3CG	PIK3CG	PIK3CG	867	0.42	0.63	YES
7	PRKCB	PRKCB	PRKCB	2133	0.25	0.61	NO
8	PIK3CA	PIK3CA	PIK3CA	4005	0.14	0.53	NO
9	ARNT	ARNT	ARNT	4972	0.1	0.5	NO
10	PIK3R1	PIK3R1	PIK3R1	5006	0.1	0.52	NO
11	EIF1AX	EIF1AX	EIF1AX	5594	0.087	0.5	NO
12	PTK2	PTK2	PTK2	5745	0.083	0.51	NO
13	EIF2S3	EIF2S3	EIF2S3	5971	0.078	0.51	NO
14	SHC1	SHC1	SHC1	6185	0.072	0.52	NO
15	EIF2S1	EIF2S1	EIF2S1	6390	0.067	0.52	NO
16	EIF1	EIF1	EIF1	8360	0.024	0.41	NO
17	EIF2B4	EIF2B4	EIF2B4	8731	0.016	0.4	NO
18	PXN	PXN	PXN	9529	0.000039	0.35	NO
19	PLCG1	PLCG1	PLCG1	9690	-0.0033	0.34	NO
20	EIF2B3	EIF2B3	EIF2B3	9738	-0.0042	0.34	NO
21	EIF2B2	EIF2B2	EIF2B2	9775	-0.005	0.34	NO
22	EIF2B5	EIF2B5	EIF2B5	10561	-0.02	0.3	NO
23	EIF2B1	EIF2B1	EIF2B1	10843	-0.028	0.29	NO
24	EIF2S2	EIF2S2	EIF2S2	11232	-0.036	0.28	NO
25	ELAVL1	ELAVL1	ELAVL1	11987	-0.053	0.25	NO
26	HIF1A	HIF1A	HIF1A	14102	-0.11	0.15	NO
27	VHL	VHL	VHL	14812	-0.14	0.14	NO
28	PRKCA	PRKCA	PRKCA	16353	-0.23	0.1	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: BIOCARTA FAS PATHWAY.

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

Table 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	CYP4A11	CYP4A11	CYP4A11	2	1.2	0.049	YES
2	AGTR1	AGTR1	AGTR1	9	0.96	0.089	YES
3	AVPR1B	AVPR1B	AVPR1B	16	0.93	0.13	YES
4	CYP4A22	CYP4A22	CYP4A22	186	0.65	0.14	YES
5	RAMP3	RAMP3	RAMP3	251	0.61	0.17	YES
6	ADCY4	ADCY4	ADCY4	261	0.61	0.19	YES
7	CALCRL	CALCRL	CALCRL	330	0.58	0.21	YES
8	PLCB1	PLCB1	PLCB1	344	0.57	0.24	YES
9	EDNRA	EDNRA	EDNRA	358	0.57	0.26	YES
10	CACNA1C	CACNA1C	CACNA1C	390	0.55	0.28	YES
11	ADRA1B	ADRA1B	ADRA1B	394	0.55	0.3	YES
12	PLA2G12B	PLA2G12B	PLA2G12B	415	0.54	0.32	YES
13	RAMP2	RAMP2	RAMP2	485	0.51	0.34	YES
14	ADORA2A	ADORA2A	ADORA2A	553	0.5	0.36	YES
15	PRKG1	PRKG1	PRKG1	560	0.5	0.38	YES
16	KCNMA1	KCNMA1	KCNMA1	561	0.5	0.4	YES
17	ADCY5	ADCY5	ADCY5	579	0.49	0.42	YES
18	GUCY1A2	GUCY1A2	GUCY1A2	645	0.47	0.44	YES
19	ACTG2	ACTG2	ACTG2	731	0.45	0.45	YES
20	PRKCH	PRKCH	PRKCH	826	0.43	0.46	YES
21	ADRA1A	ADRA1A	ADRA1A	920	0.41	0.48	YES
22	MYH11	MYH11	MYH11	939	0.41	0.49	YES
23	MRVI1	MRVI1	MRVI1	1086	0.38	0.5	YES
24	PTGIR	PTGIR	PTGIR	1135	0.37	0.51	YES
25	AVPR1A	AVPR1A	AVPR1A	1342	0.34	0.51	YES
26	KCNMB1	KCNMB1	KCNMB1	1472	0.32	0.52	YES
27	ADORA2B	ADORA2B	ADORA2B	1487	0.32	0.53	YES
28	GUCY1A3	GUCY1A3	GUCY1A3	1587	0.3	0.54	YES
29	MYLK	MYLK	MYLK	1714	0.29	0.55	YES
30	ADCY1	ADCY1	ADCY1	1814	0.28	0.55	YES
31	ACTA2	ACTA2	ACTA2	1897	0.27	0.56	YES
32	PRKCB	PRKCB	PRKCB	2133	0.25	0.56	YES
33	ROCK2	ROCK2	ROCK2	2237	0.24	0.56	YES
34	PRKCE	PRKCE	PRKCE	2295	0.24	0.57	YES
35	GUCY1B3	GUCY1B3	GUCY1B3	2366	0.23	0.57	YES
36	CACNA1F	CACNA1F	CACNA1F	2481	0.22	0.58	YES
37	PLA2G5	PLA2G5	PLA2G5	2514	0.22	0.58	YES
38	CALD1	CALD1	CALD1	2593	0.22	0.59	YES
39	ADCY8	ADCY8	ADCY8	2820	0.2	0.58	NO
40	PPP1R14A	PPP1R14A	PPP1R14A	3279	0.17	0.57	NO
41	CACNA1S	CACNA1S	CACNA1S	3391	0.17	0.57	NO
42	MAPK1	MAPK1	MAPK1	3636	0.16	0.56	NO
43	ROCK1	ROCK1	ROCK1	3788	0.15	0.56	NO
44	PPP1R12B	PPP1R12B	PPP1R12B	4311	0.13	0.53	NO
45	ITPR1	ITPR1	ITPR1	4997	0.1	0.5	NO
46	GNA13	GNA13	GNA13	5048	0.1	0.5	NO
47	MYL9	MYL9	MYL9	5341	0.094	0.49	NO
48	ADCY9	ADCY9	ADCY9	5407	0.092	0.49	NO
49	KCNMB2	KCNMB2	KCNMB2	5445	0.091	0.49	NO
50	MAPK3	MAPK3	MAPK3	5491	0.09	0.49	NO
51	ARHGEF12	ARHGEF12	ARHGEF12	5609	0.087	0.49	NO
52	PLCB4	PLCB4	PLCB4	5661	0.085	0.49	NO
53	BRAF	BRAF	BRAF	5684	0.085	0.49	NO
54	PLCB2	PLCB2	PLCB2	5700	0.084	0.5	NO
55	PPP1R12A	PPP1R12A	PPP1R12A	5818	0.082	0.49	NO
56	CALM1	CALM1	CALM1	6065	0.075	0.48	NO
57	PLA2G1B	PLA2G1B	PLA2G1B	6485	0.065	0.46	NO
58	CALM3	CALM3	CALM3	6564	0.063	0.46	NO
59	NPR1	NPR1	NPR1	6644	0.061	0.46	NO
60	GNAQ	GNAQ	GNAQ	6838	0.056	0.45	NO
61	MYL6B	MYL6B	MYL6B	7295	0.047	0.43	NO
62	MAP2K1	MAP2K1	MAP2K1	7341	0.046	0.43	NO
63	PPP1CC	PPP1CC	PPP1CC	7566	0.04	0.42	NO
64	GNA11	GNA11	GNA11	7640	0.039	0.41	NO
65	PPP1CB	PPP1CB	PPP1CB	7843	0.035	0.4	NO
66	ARHGEF1	ARHGEF1	ARHGEF1	7857	0.034	0.4	NO
67	PRKACB	PRKACB	PRKACB	8730	0.016	0.36	NO
68	ADCY7	ADCY7	ADCY7	10136	-0.012	0.28	NO
69	GNA12	GNA12	GNA12	10201	-0.013	0.28	NO
70	CALML6	CALML6	CALML6	10829	-0.027	0.24	NO
71	PRKACA	PRKACA	PRKACA	11050	-0.032	0.23	NO
72	RHOA	RHOA	RHOA	11062	-0.032	0.23	NO
73	PLA2G12A	PLA2G12A	PLA2G12A	11235	-0.036	0.22	NO
74	MYL6	MYL6	MYL6	11283	-0.037	0.22	NO
75	ITPR3	ITPR3	ITPR3	11342	-0.038	0.22	NO
76	ADCY2	ADCY2	ADCY2	11432	-0.04	0.22	NO
77	MYLK2	MYLK2	MYLK2	11752	-0.047	0.2	NO
78	ARAF	ARAF	ARAF	11945	-0.052	0.2	NO
79	PLCB3	PLCB3	PLCB3	11957	-0.052	0.2	NO
80	CALML3	CALML3	CALML3	12134	-0.057	0.19	NO
81	MYLK3	MYLK3	MYLK3	12206	-0.058	0.19	NO
82	ADCY6	ADCY6	ADCY6	12358	-0.062	0.18	NO
83	ADRA1D	ADRA1D	ADRA1D	12389	-0.062	0.18	NO
84	PRKX	PRKX	PRKX	12664	-0.069	0.17	NO
85	CALM2	CALM2	CALM2	12730	-0.071	0.17	NO
86	ARHGEF11	ARHGEF11	ARHGEF11	12778	-0.072	0.17	NO
87	RAMP1	RAMP1	RAMP1	12790	-0.072	0.17	NO
88	KCNMB3	KCNMB3	KCNMB3	12843	-0.073	0.17	NO
89	PPP1CA	PPP1CA	PPP1CA	12853	-0.074	0.18	NO
90	PLA2G4A	PLA2G4A	PLA2G4A	13143	-0.081	0.16	NO
91	JMJD7-PLA2G4B	JMJD7-PLA2G4B	JMJD7-PLA2G4B	13350	-0.088	0.16	NO
92	RAF1	RAF1	RAF1	13367	-0.088	0.16	NO
93	PRKCQ	PRKCQ	PRKCQ	13455	-0.091	0.16	NO
94	PLA2G10	PLA2G10	PLA2G10	13799	-0.1	0.14	NO
95	GNAS	GNAS	GNAS	14032	-0.11	0.13	NO
96	ITPR2	ITPR2	ITPR2	14050	-0.11	0.14	NO
97	MAP2K2	MAP2K2	MAP2K2	14129	-0.11	0.14	NO
98	PLA2G2A	PLA2G2A	PLA2G2A	15481	-0.17	0.071	NO
99	PLA2G6	PLA2G6	PLA2G6	15486	-0.17	0.078	NO
100	PRKCD	PRKCD	PRKCD	15716	-0.19	0.073	NO
101	NPR2	NPR2	NPR2	15717	-0.19	0.081	NO
102	KCNMB4	KCNMB4	KCNMB4	15810	-0.19	0.084	NO
103	CACNA1D	CACNA1D	CACNA1D	16028	-0.21	0.08	NO
104	PRKCA	PRKCA	PRKCA	16353	-0.23	0.072	NO
105	PLA2G2D	PLA2G2D	PLA2G2D	16845	-0.28	0.057	NO
106	PRKCG	PRKCG	PRKCG	17598	-0.42	0.033	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: BIOCARTA FCER1 PATHWAY.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA MET PATHWAY

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	FASLG	FASLG	FASLG	608	0.48	0.15	YES
2	ARHGDIB	ARHGDIB	ARHGDIB	2344	0.23	0.14	YES
3	CASP10	CASP10	CASP10	2758	0.2	0.2	YES
4	MAPK8	MAPK8	MAPK8	3182	0.18	0.24	YES
5	CASP7	CASP7	CASP7	3249	0.18	0.31	YES
6	RB1	RB1	RB1	3593	0.16	0.35	YES
7	CFLAR	CFLAR	CFLAR	3916	0.14	0.38	YES
8	FAS	FAS	FAS	4390	0.12	0.4	YES
9	JUN	JUN	JUN	4404	0.12	0.45	YES
10	CASP8	CASP8	CASP8	6992	0.053	0.33	NO
11	DAXX	DAXX	DAXX	6994	0.053	0.35	NO
12	LMNA	LMNA	LMNA	7702	0.038	0.32	NO
13	PAK2	PAK2	PAK2	7918	0.033	0.32	NO
14	PAK1	PAK1	PAK1	8432	0.022	0.3	NO
15	DFFB	DFFB	DFFB	8698	0.017	0.3	NO
16	MAP2K4	MAP2K4	MAP2K4	8829	0.014	0.29	NO
17	PTPN13	PTPN13	PTPN13	8947	0.012	0.29	NO
18	FAF1	FAF1	FAF1	9276	0.0052	0.28	NO
19	MAP3K7	MAP3K7	MAP3K7	9892	-0.0071	0.24	NO
20	RIPK2	RIPK2	RIPK2	9911	-0.0075	0.25	NO
21	PARP1	PARP1	PARP1	9941	-0.008	0.25	NO
22	DFFA	DFFA	DFFA	10518	-0.02	0.22	NO
23	PRKDC	PRKDC	PRKDC	10639	-0.023	0.23	NO
24	MAP3K1	MAP3K1	MAP3K1	11151	-0.034	0.21	NO
25	SPTAN1	SPTAN1	SPTAN1	11713	-0.046	0.2	NO
26	FADD	FADD	FADD	11964	-0.052	0.2	NO
27	CASP3	CASP3	CASP3	13228	-0.084	0.17	NO
28	LMNB2	LMNB2	LMNB2	14827	-0.14	0.13	NO
29	CASP6	CASP6	CASP6	14882	-0.14	0.18	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: BIOCARTA MET PATHWAY.

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

genes ES table in pathway: BIOCARTA TCR 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	TLR3	TLR3	TLR3	257	0.61	0.13	YES
2	TLR4	TLR4	TLR4	1612	0.3	0.13	YES
3	TLR7	TLR7	TLR7	1920	0.27	0.18	YES
4	FOS	FOS	FOS	1929	0.27	0.25	YES
5	PGLYRP1	PGLYRP1	PGLYRP1	2873	0.2	0.24	YES
6	MAP3K14	MAP3K14	MAP3K14	3006	0.19	0.28	YES
7	TLR6	TLR6	TLR6	3041	0.19	0.33	YES
8	TRAF6	TRAF6	TRAF6	3157	0.18	0.36	YES
9	MAPK8	MAPK8	MAPK8	3182	0.18	0.4	YES
10	NFKBIA	NFKBIA	NFKBIA	3320	0.17	0.44	YES
11	TLR10	TLR10	TLR10	3324	0.17	0.48	YES
12	TIRAP	TIRAP	TIRAP	3546	0.16	0.51	YES
13	EIF2AK2	EIF2AK2	EIF2AK2	4047	0.14	0.51	YES
14	JUN	JUN	JUN	4404	0.12	0.52	YES
15	NFKB1	NFKB1	NFKB1	6027	0.076	0.45	NO
16	MYD88	MYD88	MYD88	6985	0.053	0.41	NO
17	LY96	LY96	LY96	7186	0.049	0.41	NO
18	MAPK14	MAPK14	MAPK14	7255	0.048	0.42	NO
19	CD14	CD14	CD14	7372	0.045	0.43	NO
20	TAB2	TAB2	TAB2	7679	0.038	0.42	NO
21	TLR2	TLR2	TLR2	8185	0.027	0.4	NO
22	MAP2K3	MAP2K3	MAP2K3	8191	0.027	0.4	NO
23	RELA	RELA	RELA	8627	0.019	0.38	NO
24	MAP2K4	MAP2K4	MAP2K4	8829	0.014	0.38	NO
25	MAP2K6	MAP2K6	MAP2K6	9376	0.0031	0.35	NO
26	CHUK	CHUK	CHUK	9483	0.001	0.34	NO
27	TOLLIP	TOLLIP	TOLLIP	9659	-0.0027	0.33	NO
28	MAP3K7	MAP3K7	MAP3K7	9892	-0.0071	0.32	NO
29	TAB1	TAB1	TAB1	10435	-0.018	0.3	NO
30	IKBKB	IKBKB	IKBKB	10874	-0.028	0.28	NO
31	MAP3K1	MAP3K1	MAP3K1	11151	-0.034	0.27	NO
32	ELK1	ELK1	ELK1	11975	-0.053	0.24	NO
33	ECSIT	ECSIT	ECSIT	13330	-0.087	0.19	NO
34	IRAK1	IRAK1	IRAK1	14042	-0.11	0.17	NO
35	IKBKG	IKBKG	IKBKG	14122	-0.11	0.2	NO
36	TLR9	TLR9	TLR9	14124	-0.11	0.22	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: BIOCARTA TCR PATHWAY.

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

genes ES table in pathway: BIOCARTA PAR1 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	VEGFA	VEGFA	VEGFA	320	0.58	0.045	YES
2	PGF	PGF	PGF	544	0.5	0.086	YES
3	PIK3CG	PIK3CG	PIK3CG	867	0.42	0.11	YES
4	CCND1	CCND1	CCND1	923	0.41	0.15	YES
5	TGFA	TGFA	TGFA	1023	0.39	0.19	YES
6	BRCA2	BRCA2	BRCA2	1091	0.38	0.23	YES
7	PIK3R3	PIK3R3	PIK3R3	1493	0.32	0.24	YES
8	EGFR	EGFR	EGFR	1520	0.31	0.27	YES
9	VEGFC	VEGFC	VEGFC	2032	0.26	0.27	YES
10	TGFB2	TGFB2	TGFB2	2304	0.24	0.28	YES
11	TGFBR2	TGFBR2	TGFBR2	2343	0.23	0.3	YES
12	PIK3R5	PIK3R5	PIK3R5	2543	0.22	0.32	YES
13	AKT3	AKT3	AKT3	2959	0.19	0.31	YES
14	PLD1	PLD1	PLD1	3012	0.19	0.33	YES
15	MAPK8	MAPK8	MAPK8	3182	0.18	0.34	YES
16	ARHGEF6	ARHGEF6	ARHGEF6	3209	0.18	0.36	YES
17	TGFB3	TGFB3	TGFB3	3339	0.17	0.37	YES
18	TGFB1	TGFB1	TGFB1	3411	0.17	0.38	YES
19	RB1	RB1	RB1	3593	0.16	0.39	YES
20	RALB	RALB	RALB	3601	0.16	0.41	YES
21	MAPK1	MAPK1	MAPK1	3636	0.16	0.42	YES
22	PIK3CA	PIK3CA	PIK3CA	4005	0.14	0.42	NO
23	MAPK10	MAPK10	MAPK10	4280	0.13	0.41	NO
24	PIK3R1	PIK3R1	PIK3R1	5006	0.1	0.38	NO
25	E2F2	E2F2	E2F2	5134	0.1	0.39	NO
26	RALGDS	RALGDS	RALGDS	5176	0.099	0.4	NO
27	CDKN2A	CDKN2A	CDKN2A	5483	0.09	0.39	NO
28	MAPK3	MAPK3	MAPK3	5491	0.09	0.4	NO
29	PIK3CB	PIK3CB	PIK3CB	5525	0.089	0.41	NO
30	BRAF	BRAF	BRAF	5684	0.085	0.41	NO
31	NFKB1	NFKB1	NFKB1	6027	0.076	0.4	NO
32	JAK1	JAK1	JAK1	6030	0.076	0.4	NO
33	FIGF	FIGF	FIGF	6070	0.075	0.41	NO
34	RAC2	RAC2	RAC2	6196	0.072	0.41	NO
35	SMAD4	SMAD4	SMAD4	6403	0.067	0.41	NO
36	CDC42	CDC42	CDC42	7016	0.052	0.38	NO
37	MAPK9	MAPK9	MAPK9	7059	0.052	0.38	NO
38	PIK3CD	PIK3CD	PIK3CD	7279	0.047	0.38	NO
39	MAP2K1	MAP2K1	MAP2K1	7341	0.046	0.38	NO
40	STAT1	STAT1	STAT1	7395	0.044	0.38	NO
41	STAT3	STAT3	STAT3	7508	0.042	0.38	NO
42	SMAD2	SMAD2	SMAD2	7978	0.032	0.35	NO
43	TGFBR1	TGFBR1	TGFBR1	8421	0.023	0.33	NO
44	RAD51	RAD51	RAD51	8547	0.02	0.33	NO
45	RELA	RELA	RELA	8627	0.019	0.32	NO
46	KRAS	KRAS	KRAS	8686	0.017	0.32	NO
47	CHUK	CHUK	CHUK	9483	0.001	0.28	NO
48	RALBP1	RALBP1	RALBP1	10397	-0.017	0.23	NO
49	TP53	TP53	TP53	10430	-0.018	0.23	NO
50	CDK6	CDK6	CDK6	10576	-0.021	0.23	NO
51	SMAD3	SMAD3	SMAD3	10851	-0.028	0.21	NO
52	IKBKB	IKBKB	IKBKB	10874	-0.028	0.22	NO
53	RALA	RALA	RALA	11083	-0.032	0.21	NO
54	E2F3	E2F3	E2F3	11137	-0.033	0.21	NO
55	RAC1	RAC1	RAC1	11416	-0.04	0.2	NO
56	ARAF	ARAF	ARAF	11945	-0.052	0.17	NO
57	AKT1	AKT1	AKT1	12098	-0.055	0.17	NO
58	VEGFB	VEGFB	VEGFB	12631	-0.068	0.15	NO
59	EGF	EGF	EGF	12829	-0.073	0.15	NO
60	RAF1	RAF1	RAF1	13367	-0.088	0.13	NO
61	BAD	BAD	BAD	13449	-0.091	0.13	NO
62	CDK4	CDK4	CDK4	13476	-0.092	0.14	NO
63	CASP9	CASP9	CASP9	13490	-0.092	0.15	NO
64	AKT2	AKT2	AKT2	13926	-0.11	0.14	NO
65	ERBB2	ERBB2	ERBB2	14017	-0.11	0.14	NO
66	PIK3R2	PIK3R2	PIK3R2	14107	-0.11	0.15	NO
67	IKBKG	IKBKG	IKBKG	14122	-0.11	0.16	NO
68	BCL2L1	BCL2L1	BCL2L1	14208	-0.12	0.17	NO
69	RAC3	RAC3	RAC3	17755	-0.48	0.024	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: BIOCARTA PAR1 PATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PAR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TOLL PATHWAY

Table 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	KIR3DL1	KIR3DL1	KIR3DL1	366	0.56	0.027	YES
2	KIR2DL1	KIR2DL1	KIR2DL1	593	0.48	0.056	YES
3	KIR3DL2	KIR3DL2	KIR3DL2	860	0.42	0.076	YES
4	KIR2DL3	KIR2DL3	KIR2DL3	882	0.42	0.11	YES
5	KIR2DL4	KIR2DL4	KIR2DL4	916	0.41	0.14	YES
6	CD8B	CD8B	CD8B	945	0.4	0.18	YES
7	CD8A	CD8A	CD8A	983	0.4	0.21	YES
8	KLRD1	KLRD1	KLRD1	1015	0.39	0.24	YES
9	KIR2DS4	KIR2DS4	KIR2DS4	1272	0.34	0.25	YES
10	HLA-G	HLA-G	HLA-G	1500	0.32	0.27	YES
11	KLRC4	KLRC4	KLRC4	1548	0.31	0.29	YES
12	LTA	LTA	LTA	1552	0.31	0.32	YES
13	HLA-DQA2	HLA-DQA2	HLA-DQA2	1556	0.31	0.34	YES
14	KLRC3	KLRC3	KLRC3	1815	0.28	0.35	YES
15	HLA-DOB	HLA-DOB	HLA-DOB	1829	0.28	0.37	YES
16	HLA-DOA	HLA-DOA	HLA-DOA	2112	0.25	0.38	YES
17	HLA-DQA1	HLA-DQA1	HLA-DQA1	2136	0.25	0.4	YES
18	HLA-DQB1	HLA-DQB1	HLA-DQB1	2167	0.25	0.42	YES
19	HLA-DRB5	HLA-DRB5	HLA-DRB5	2198	0.25	0.44	YES
20	KLRC1	KLRC1	KLRC1	2238	0.24	0.46	YES
21	HLA-F	HLA-F	HLA-F	2534	0.22	0.46	YES
22	CIITA	CIITA	CIITA	2619	0.21	0.47	YES
23	HLA-DPA1	HLA-DPA1	HLA-DPA1	2656	0.21	0.49	YES
24	HLA-DRB1	HLA-DRB1	HLA-DRB1	2857	0.2	0.49	YES
25	HLA-E	HLA-E	HLA-E	2879	0.2	0.51	YES
26	HLA-DRA	HLA-DRA	HLA-DRA	2943	0.19	0.52	YES
27	HLA-DPB1	HLA-DPB1	HLA-DPB1	3047	0.19	0.53	YES
28	RFXAP	RFXAP	RFXAP	3098	0.18	0.54	YES
29	HLA-DMA	HLA-DMA	HLA-DMA	3212	0.18	0.55	YES
30	KLRC2	KLRC2	KLRC2	3551	0.16	0.55	YES
31	HSPA1L	HSPA1L	HSPA1L	3563	0.16	0.56	YES
32	CD4	CD4	CD4	3701	0.15	0.57	YES
33	TAP2	TAP2	TAP2	3731	0.15	0.58	YES
34	TAP1	TAP1	TAP1	3920	0.14	0.58	YES
35	HLA-DMB	HLA-DMB	HLA-DMB	4204	0.13	0.57	YES
36	CREB1	CREB1	CREB1	4226	0.13	0.58	YES
37	CTSS	CTSS	CTSS	4324	0.13	0.59	YES
38	CD74	CD74	CD74	4622	0.12	0.58	NO
39	HLA-B	HLA-B	HLA-B	4832	0.11	0.58	NO
40	B2M	B2M	B2M	4996	0.1	0.58	NO
41	CANX	CANX	CANX	5211	0.097	0.58	NO
42	HLA-C	HLA-C	HLA-C	5659	0.085	0.56	NO
43	HLA-A	HLA-A	HLA-A	7228	0.048	0.48	NO
44	NFYA	NFYA	NFYA	7839	0.035	0.44	NO
45	TAPBP	TAPBP	TAPBP	8403	0.023	0.42	NO
46	PDIA3	PDIA3	PDIA3	8436	0.022	0.42	NO
47	HSPA5	HSPA5	HSPA5	8568	0.02	0.41	NO
48	PSME1	PSME1	PSME1	9144	0.0081	0.38	NO
49	CTSL1	CTSL1	CTSL1	9362	0.0033	0.37	NO
50	NFYB	NFYB	NFYB	9553	-0.00033	0.36	NO
51	HSPA8	HSPA8	HSPA8	10075	-0.011	0.33	NO
52	CALR	CALR	CALR	10257	-0.014	0.32	NO
53	RFX5	RFX5	RFX5	10273	-0.015	0.32	NO
54	NFYC	NFYC	NFYC	10455	-0.018	0.31	NO
55	HSPA6	HSPA6	HSPA6	10732	-0.025	0.3	NO
56	HSPA4	HSPA4	HSPA4	11192	-0.035	0.28	NO
57	LGMN	LGMN	LGMN	12027	-0.054	0.24	NO
58	RFXANK	RFXANK	RFXANK	12136	-0.057	0.23	NO
59	HSPA1A	HSPA1A	HSPA1A	12390	-0.062	0.23	NO
60	CTSB	CTSB	CTSB	12397	-0.063	0.23	NO
61	PSME2	PSME2	PSME2	12464	-0.064	0.23	NO
62	HSP90AA1	HSP90AA1	HSP90AA1	13830	-0.1	0.17	NO
63	PSME3	PSME3	PSME3	13996	-0.11	0.17	NO
64	IFI30	IFI30	IFI30	14056	-0.11	0.17	NO
65	IFNA13	IFNA13	IFNA13	14188	-0.12	0.17	NO
66	IFNA1	IFNA1	IFNA1	15155	-0.16	0.13	NO
67	HSPA1B	HSPA1B	HSPA1B	15371	-0.17	0.14	NO
68	HSPA2	HSPA2	HSPA2	16358	-0.23	0.1	NO

Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TOLL PATHWAY.

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

genes ES table in pathway: BIOCARTA VEGF PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ITGA1	ITGA1	ITGA1	665	0.46	0.066	YES
2	PIK3CG	PIK3CG	PIK3CG	867	0.42	0.15	YES
3	HGF	HGF	HGF	1175	0.36	0.21	YES
4	FOS	FOS	FOS	1929	0.27	0.23	YES
5	MAPK8	MAPK8	MAPK8	3182	0.18	0.2	YES
6	MAP4K1	MAP4K1	MAP4K1	3245	0.18	0.23	YES
7	GAB1	GAB1	GAB1	3522	0.16	0.25	YES
8	MAPK1	MAPK1	MAPK1	3636	0.16	0.28	YES
9	PIK3CA	PIK3CA	PIK3CA	4005	0.14	0.29	YES
10	JUN	JUN	JUN	4404	0.12	0.3	YES
11	CRK	CRK	CRK	4573	0.12	0.31	YES
12	PTEN	PTEN	PTEN	4628	0.12	0.34	YES
13	SOS1	SOS1	SOS1	4768	0.11	0.35	YES
14	RAPGEF1	RAPGEF1	RAPGEF1	4989	0.1	0.36	YES
15	PIK3R1	PIK3R1	PIK3R1	5006	0.1	0.38	YES
16	ITGB1	ITGB1	ITGB1	5193	0.098	0.4	YES
17	DOCK1	DOCK1	DOCK1	5420	0.092	0.4	YES
18	CRKL	CRKL	CRKL	5450	0.091	0.42	YES
19	MAPK3	MAPK3	MAPK3	5491	0.09	0.44	YES
20	RAP1A	RAP1A	RAP1A	5501	0.089	0.46	YES
21	PTK2	PTK2	PTK2	5745	0.083	0.46	YES
22	RAP1B	RAP1B	RAP1B	6924	0.055	0.41	NO
23	MAP2K1	MAP2K1	MAP2K1	7341	0.046	0.4	NO
24	STAT3	STAT3	STAT3	7508	0.042	0.4	NO
25	RASA1	RASA1	RASA1	7614	0.04	0.4	NO
26	PAK1	PAK1	PAK1	8432	0.022	0.36	NO
27	PXN	PXN	PXN	9529	0.000039	0.3	NO
28	PTPN11	PTPN11	PTPN11	11120	-0.033	0.22	NO
29	ELK1	ELK1	ELK1	11975	-0.053	0.19	NO
30	ACTA1	ACTA1	ACTA1	12454	-0.064	0.17	NO
31	GRB2	GRB2	GRB2	12864	-0.074	0.17	NO
32	RAF1	RAF1	RAF1	13367	-0.088	0.16	NO
33	MET	MET	MET	13945	-0.11	0.15	NO
34	MAP2K2	MAP2K2	MAP2K2	14129	-0.11	0.17	NO
35	PTK2B	PTK2B	PTK2B	14453	-0.13	0.18	NO
36	SRC	SRC	SRC	14760	-0.14	0.19	NO

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

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA VEGF 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 TRYPTOPHAN METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NGF	NGF	NGF	135	0.68	0.15	YES
2	NGFR	NGFR	NGFR	429	0.53	0.26	YES
3	PTPRR	PTPRR	PTPRR	501	0.51	0.37	YES
4	RPS6KA5	RPS6KA5	RPS6KA5	664	0.46	0.47	YES
5	EGFR	EGFR	EGFR	1520	0.31	0.49	YES
6	MYC	MYC	MYC	2754	0.2	0.47	NO
7	MAPK1	MAPK1	MAPK1	3636	0.16	0.46	NO
8	SOS1	SOS1	SOS1	4768	0.11	0.42	NO
9	ITGB1	ITGB1	ITGB1	5193	0.098	0.42	NO
10	MAPK3	MAPK3	MAPK3	5491	0.09	0.42	NO
11	SHC1	SHC1	SHC1	6185	0.072	0.4	NO
12	GNB1	GNB1	GNB1	6608	0.062	0.39	NO
13	IGF1R	IGF1R	IGF1R	6788	0.058	0.4	NO
14	MAP2K1	MAP2K1	MAP2K1	7341	0.046	0.38	NO
15	STAT3	STAT3	STAT3	7508	0.042	0.38	NO
16	PPP2CA	PPP2CA	PPP2CA	8203	0.027	0.35	NO
17	MKNK1	MKNK1	MKNK1	9272	0.0052	0.29	NO
18	GNGT1	GNGT1	GNGT1	10302	-0.015	0.24	NO
19	MKNK2	MKNK2	MKNK2	11894	-0.051	0.16	NO
20	ELK1	ELK1	ELK1	11975	-0.053	0.17	NO
21	GRB2	GRB2	GRB2	12864	-0.074	0.14	NO
22	PDGFRA	PDGFRA	PDGFRA	12962	-0.076	0.15	NO
23	RAF1	RAF1	RAF1	13367	-0.088	0.15	NO
24	GNAS	GNAS	GNAS	14032	-0.11	0.13	NO
25	MAP2K2	MAP2K2	MAP2K2	14129	-0.11	0.16	NO
26	SRC	SRC	SRC	14760	-0.14	0.15	NO
27	RPS6KA1	RPS6KA1	RPS6KA1	15265	-0.16	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: KEGG TRYPTOPHAN METABOLISM.

Figure S60. 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

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 CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.49	1.2	0.36	0.87	1	0.69	0.39	0.42	0.76	0.32
KEGG OXIDATIVE PHOSPHORYLATION	113	genes.ES.table	0.37	0.99	0.52	0.94	1	0.64	0.31	0.44	0.89	0.39
KEGG GLYCINE SERINE AND THREONINE METABOLISM	30	genes.ES.table	0.51	1.1	0.31	0.76	1	0.47	0.16	0.39	0.68	0.24
KEGG CYSTEINE AND METHIONINE METABOLISM	33	genes.ES.table	0.31	0.96	0.52	0.96	1	0.21	0.17	0.18	0.91	0.41
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	43	genes.ES.table	0.46	1.2	0.33	0.93	1	0.58	0.32	0.4	0.82	0.37
KEGG LYSINE DEGRADATION	43	genes.ES.table	0.28	1.1	0.35	0.79	1	0.49	0.37	0.31	0.71	0.26
KEGG HISTIDINE METABOLISM	28	genes.ES.table	0.53	1.3	0.24	0.96	0.99	0.5	0.22	0.39	0.8	0.38
KEGG TYROSINE METABOLISM	40	genes.ES.table	0.35	0.99	0.43	0.99	1	0.42	0.22	0.33	0.93	0.43
KEGG SELENOAMINO ACID METABOLISM	25	genes.ES.table	0.43	1.3	0.14	1	0.97	0.64	0.35	0.42	1	0.64
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.27	0.94	0.51	0.97	1	0.19	0.16	0.16	0.93	0.42

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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	NEIL1	NEIL1	NEIL1	994	0.39	0.052	YES
2	OGG1	OGG1	OGG1	1336	0.33	0.12	YES
3	NTHL1	NTHL1	NTHL1	1339	0.33	0.21	YES
4	PARP3	PARP3	PARP3	1340	0.33	0.3	YES
5	MUTYH	MUTYH	MUTYH	1856	0.27	0.35	YES
6	POLD1	POLD1	POLD1	2483	0.22	0.37	YES
7	MPG	MPG	MPG	2996	0.18	0.4	YES
8	POLD2	POLD2	POLD2	3359	0.16	0.42	YES
9	LIG1	LIG1	LIG1	4406	0.12	0.4	YES
10	NEIL2	NEIL2	NEIL2	4679	0.11	0.41	YES
11	UNG	UNG	UNG	4802	0.1	0.43	YES
12	PARP4	PARP4	PARP4	4921	0.1	0.45	YES
13	POLE	POLE	POLE	5120	0.093	0.47	YES
14	SMUG1	SMUG1	SMUG1	5444	0.082	0.47	YES
15	APEX2	APEX2	APEX2	5588	0.078	0.48	YES
16	POLD4	POLD4	POLD4	6143	0.061	0.47	YES
17	POLL	POLL	POLL	6257	0.058	0.48	YES
18	XRCC1	XRCC1	XRCC1	6315	0.056	0.49	YES
19	LIG3	LIG3	LIG3	7070	0.035	0.46	NO
20	PCNA	PCNA	PCNA	7697	0.018	0.43	NO
21	PARP2	PARP2	PARP2	8612	-0.0053	0.38	NO
22	POLE3	POLE3	POLE3	8700	-0.0071	0.38	NO
23	APEX1	APEX1	APEX1	9019	-0.015	0.37	NO
24	POLB	POLB	POLB	9195	-0.02	0.36	NO
25	MBD4	MBD4	MBD4	9217	-0.02	0.37	NO
26	FEN1	FEN1	FEN1	9622	-0.031	0.35	NO
27	PARP1	PARP1	PARP1	9803	-0.035	0.35	NO
28	POLE4	POLE4	POLE4	9842	-0.036	0.36	NO
29	TDG	TDG	TDG	10869	-0.063	0.32	NO
30	POLE2	POLE2	POLE2	10971	-0.066	0.33	NO
31	POLD3	POLD3	POLD3	12088	-0.1	0.3	NO
32	NEIL3	NEIL3	NEIL3	13076	-0.14	0.28	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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

Table 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	NAPSA	NAPSA	NAPSA	195	0.7	0.032	YES
2	CTSL2	CTSL2	CTSL2	271	0.64	0.068	YES
3	AP3B2	AP3B2	AP3B2	409	0.57	0.096	YES
4	CTSC	CTSC	CTSC	958	0.4	0.09	YES
5	AP1M2	AP1M2	AP1M2	960	0.4	0.12	YES
6	IDUA	IDUA	IDUA	1154	0.36	0.13	YES
7	DNASE2B	DNASE2B	DNASE2B	1581	0.3	0.12	YES
8	GLB1	GLB1	GLB1	1682	0.29	0.13	YES
9	AP1S3	AP1S3	AP1S3	1692	0.29	0.15	YES
10	NAGLU	NAGLU	NAGLU	1711	0.28	0.17	YES
11	NEU1	NEU1	NEU1	1728	0.28	0.18	YES
12	ACP5	ACP5	ACP5	1879	0.27	0.19	YES
13	ATP6V0A1	ATP6V0A1	ATP6V0A1	1994	0.26	0.2	YES
14	SMPD1	SMPD1	SMPD1	2203	0.24	0.2	YES
15	SUMF1	SUMF1	SUMF1	2301	0.23	0.21	YES
16	NAGPA	NAGPA	NAGPA	2304	0.23	0.23	YES
17	ABCB9	ABCB9	ABCB9	2340	0.23	0.24	YES
18	PPT2	PPT2	PPT2	2343	0.23	0.25	YES
19	LAPTM4B	LAPTM4B	LAPTM4B	2433	0.22	0.26	YES
20	GALNS	GALNS	GALNS	2631	0.21	0.26	YES
21	PLA2G15	PLA2G15	PLA2G15	2717	0.2	0.27	YES
22	GAA	GAA	GAA	2855	0.19	0.28	YES
23	GNPTG	GNPTG	GNPTG	2992	0.18	0.28	YES
24	SGSH	SGSH	SGSH	3195	0.17	0.28	YES
25	ATP6V0C	ATP6V0C	ATP6V0C	3208	0.17	0.29	YES
26	CTSH	CTSH	CTSH	3233	0.17	0.3	YES
27	AP1S1	AP1S1	AP1S1	3312	0.16	0.31	YES
28	AP4M1	AP4M1	AP4M1	3447	0.16	0.31	YES
29	CTSA	CTSA	CTSA	3814	0.14	0.3	YES
30	CTNS	CTNS	CTNS	3902	0.14	0.3	YES
31	GGA3	GGA3	GGA3	3947	0.14	0.31	YES
32	ACP2	ACP2	ACP2	3982	0.14	0.31	YES
33	GGA1	GGA1	GGA1	4069	0.13	0.32	YES
34	CTSF	CTSF	CTSF	4083	0.13	0.32	YES
35	GLA	GLA	GLA	4196	0.13	0.33	YES
36	ARSA	ARSA	ARSA	4198	0.13	0.33	YES
37	CTSG	CTSG	CTSG	4202	0.12	0.34	YES
38	ATP6V0D1	ATP6V0D1	ATP6V0D1	4282	0.12	0.34	YES
39	CLN3	CLN3	CLN3	4436	0.12	0.34	YES
40	ATP6V0A4	ATP6V0A4	ATP6V0A4	4549	0.11	0.34	YES
41	CTSB	CTSB	CTSB	5037	0.096	0.32	YES
42	CTSK	CTSK	CTSK	5051	0.095	0.33	YES
43	CTSD	CTSD	CTSD	5082	0.094	0.33	YES
44	ARSG	ARSG	ARSG	5146	0.092	0.34	YES
45	CTSZ	CTSZ	CTSZ	5178	0.091	0.34	YES
46	CLTA	CLTA	CLTA	5183	0.091	0.34	YES
47	MCOLN1	MCOLN1	MCOLN1	5211	0.09	0.35	YES
48	GUSB	GUSB	GUSB	5373	0.084	0.34	YES
49	GNS	GNS	GNS	5414	0.083	0.35	YES
50	AGA	AGA	AGA	5436	0.082	0.35	YES
51	CD63	CD63	CD63	5470	0.081	0.35	YES
52	CD68	CD68	CD68	5500	0.08	0.36	YES
53	CTSL1	CTSL1	CTSL1	5575	0.078	0.36	YES
54	SORT1	SORT1	SORT1	5671	0.075	0.36	YES
55	LAPTM4A	LAPTM4A	LAPTM4A	5686	0.075	0.36	YES
56	LAMP1	LAMP1	LAMP1	5746	0.073	0.36	YES
57	PSAP	PSAP	PSAP	5832	0.07	0.36	NO
58	ATP6V1H	ATP6V1H	ATP6V1H	6010	0.065	0.36	NO
59	NPC2	NPC2	NPC2	6027	0.065	0.36	NO
60	AP1M1	AP1M1	AP1M1	6207	0.059	0.35	NO
61	SLC11A1	SLC11A1	SLC11A1	6306	0.056	0.35	NO
62	MAN2B1	MAN2B1	MAN2B1	6620	0.048	0.34	NO
63	AP1G1	AP1G1	AP1G1	6683	0.046	0.34	NO
64	AP3D1	AP3D1	AP3D1	6684	0.046	0.34	NO
65	ATP6V0B	ATP6V0B	ATP6V0B	6712	0.046	0.34	NO
66	AP3S2	AP3S2	AP3S2	6761	0.044	0.34	NO
67	FUCA1	FUCA1	FUCA1	6836	0.042	0.34	NO
68	SLC11A2	SLC11A2	SLC11A2	6873	0.041	0.34	NO
69	CLTB	CLTB	CLTB	6878	0.041	0.34	NO
70	ATP6V0A2	ATP6V0A2	ATP6V0A2	7006	0.037	0.34	NO
71	ENTPD4	ENTPD4	ENTPD4	7162	0.033	0.33	NO
72	CLTC	CLTC	CLTC	7180	0.032	0.33	NO
73	GBA	GBA	GBA	7377	0.028	0.32	NO
74	HEXA	HEXA	HEXA	7459	0.025	0.32	NO
75	HEXB	HEXB	HEXB	7570	0.022	0.32	NO
76	AP1B1	AP1B1	AP1B1	7578	0.022	0.32	NO
77	ARSB	ARSB	ARSB	7589	0.021	0.32	NO
78	HYAL1	HYAL1	HYAL1	7600	0.021	0.32	NO
79	GM2A	GM2A	GM2A	7628	0.02	0.32	NO
80	NPC1	NPC1	NPC1	7927	0.012	0.3	NO
81	GGA2	GGA2	GGA2	7951	0.012	0.3	NO
82	AP4S1	AP4S1	AP4S1	8106	0.008	0.29	NO
83	SLC17A5	SLC17A5	SLC17A5	8299	0.0031	0.28	NO
84	ATP6AP1	ATP6AP1	ATP6AP1	8696	-0.007	0.26	NO
85	NAGA	NAGA	NAGA	8834	-0.011	0.26	NO
86	CLTCL1	CLTCL1	CLTCL1	9216	-0.02	0.24	NO
87	M6PR	M6PR	M6PR	9285	-0.022	0.23	NO
88	ASAH1	ASAH1	ASAH1	9406	-0.025	0.23	NO
89	CLN5	CLN5	CLN5	9463	-0.026	0.23	NO
90	ABCA2	ABCA2	ABCA2	9484	-0.027	0.23	NO
91	AP3B1	AP3B1	AP3B1	9501	-0.028	0.23	NO
92	IGF2R	IGF2R	IGF2R	9540	-0.028	0.23	NO
93	DNASE2	DNASE2	DNASE2	9643	-0.031	0.22	NO
94	CD164	CD164	CD164	9836	-0.036	0.22	NO
95	LIPA	LIPA	LIPA	9885	-0.038	0.22	NO
96	TPP1	TPP1	TPP1	10040	-0.042	0.21	NO
97	AP3M1	AP3M1	AP3M1	10095	-0.043	0.21	NO
98	LAMP2	LAMP2	LAMP2	10474	-0.053	0.19	NO
99	TCIRG1	TCIRG1	TCIRG1	10490	-0.053	0.19	NO
100	AP3M2	AP3M2	AP3M2	10647	-0.058	0.19	NO
101	AP4B1	AP4B1	AP4B1	10784	-0.061	0.18	NO
102	PPT1	PPT1	PPT1	10823	-0.062	0.19	NO
103	AP4E1	AP4E1	AP4E1	11793	-0.09	0.14	NO
104	SCARB2	SCARB2	SCARB2	11811	-0.091	0.14	NO
105	LGMN	LGMN	LGMN	11878	-0.093	0.14	NO
106	MFSD8	MFSD8	MFSD8	11915	-0.094	0.15	NO
107	MANBA	MANBA	MANBA	12134	-0.1	0.14	NO
108	ATP6V0D2	ATP6V0D2	ATP6V0D2	12582	-0.12	0.13	NO
109	GNPTAB	GNPTAB	GNPTAB	12666	-0.12	0.13	NO
110	LAPTM5	LAPTM5	LAPTM5	12678	-0.12	0.14	NO
111	CTSS	CTSS	CTSS	13246	-0.14	0.11	NO
112	CTSE	CTSE	CTSE	13567	-0.16	0.1	NO
113	CTSO	CTSO	CTSO	13818	-0.17	0.1	NO
114	AP3S1	AP3S1	AP3S1	14147	-0.19	0.095	NO
115	GALC	GALC	GALC	14230	-0.19	0.1	NO
116	IDS	IDS	IDS	15150	-0.25	0.067	NO
117	AP1S2	AP1S2	AP1S2	16540	-0.4	0.015	NO
118	CTSW	CTSW	CTSW	17137	-0.52	0.014	NO
119	LAMP3	LAMP3	LAMP3	17637	-0.71	0.031	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 OXIDATIVE PHOSPHORYLATION.

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

genes ES table in pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CBS	CBS	CBS	220	0.68	0.17	YES
2	GGT1	GGT1	GGT1	1182	0.36	0.22	YES
3	HEMK1	HEMK1	HEMK1	1928	0.26	0.25	YES
4	SCLY	SCLY	SCLY	2244	0.24	0.3	YES
5	PAPSS2	PAPSS2	PAPSS2	2805	0.2	0.32	YES
6	WBSCR22	WBSCR22	WBSCR22	3180	0.17	0.35	YES
7	LCMT1	LCMT1	LCMT1	3367	0.16	0.38	YES
8	TRMT11	TRMT11	TRMT11	3476	0.16	0.42	YES
9	LCMT2	LCMT2	LCMT2	4939	0.099	0.37	YES
10	METTL6	METTL6	METTL6	5007	0.097	0.39	YES
11	SEPHS1	SEPHS1	SEPHS1	5106	0.094	0.41	YES
12	CTH	CTH	CTH	5757	0.072	0.39	YES
13	AHCY	AHCY	AHCY	5914	0.068	0.4	YES
14	MARS	MARS	MARS	5999	0.066	0.42	YES
15	PAPSS1	PAPSS1	PAPSS1	6211	0.059	0.42	YES
16	MARS2	MARS2	MARS2	6308	0.056	0.43	YES
17	METTL2B	METTL2B	METTL2B	6608	0.048	0.43	NO
18	GGT7	GGT7	GGT7	7532	0.023	0.38	NO
19	MAT2A	MAT2A	MAT2A	7556	0.022	0.39	NO
20	GGT6	GGT6	GGT6	7760	0.016	0.38	NO
21	AHCYL1	AHCYL1	AHCYL1	8337	0.0022	0.35	NO
22	AHCYL2	AHCYL2	AHCYL2	8928	-0.013	0.32	NO
23	MAT2B	MAT2B	MAT2B	10480	-0.053	0.25	NO
24	MAT1A	MAT1A	MAT1A	14413	-0.2	0.09	NO
25	GGT5	GGT5	GGT5	16732	-0.43	0.081	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 GLYCINE SERINE AND THREONINE METABOLISM.

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

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE METABOLISM

Table 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	LDHD	LDHD	LDHD	327	0.6	0.095	YES
2	HAGHL	HAGHL	HAGHL	482	0.53	0.19	YES
3	ACSS2	ACSS2	ACSS2	1251	0.34	0.21	YES
4	ALDH2	ALDH2	ALDH2	1469	0.31	0.26	YES
5	ACYP1	ACYP1	ACYP1	2570	0.21	0.24	YES
6	PDHA1	PDHA1	PDHA1	2573	0.21	0.27	YES
7	PC	PC	PC	2579	0.21	0.31	YES
8	HAGH	HAGH	HAGH	3040	0.18	0.32	YES
9	LDHB	LDHB	LDHB	3042	0.18	0.36	YES
10	ACACA	ACACA	ACACA	3526	0.16	0.36	YES
11	DLD	DLD	DLD	3705	0.15	0.38	YES
12	PDHB	PDHB	PDHB	3925	0.14	0.39	YES
13	ALDH1B1	ALDH1B1	ALDH1B1	4000	0.13	0.41	YES
14	AKR1B1	AKR1B1	AKR1B1	4210	0.12	0.42	YES
15	MDH2	MDH2	MDH2	4317	0.12	0.44	YES
16	MDH1	MDH1	MDH1	4398	0.12	0.46	YES
17	ACAT1	ACAT1	ACAT1	5032	0.096	0.44	NO
18	ALDH3A2	ALDH3A2	ALDH3A2	5790	0.072	0.41	NO
19	ACOT12	ACOT12	ACOT12	6131	0.061	0.4	NO
20	GRHPR	GRHPR	GRHPR	6259	0.058	0.41	NO
21	PCK2	PCK2	PCK2	6311	0.056	0.42	NO
22	PKLR	PKLR	PKLR	6333	0.055	0.43	NO
23	ACAT2	ACAT2	ACAT2	8033	0.0094	0.33	NO
24	PKM2	PKM2	PKM2	8611	-0.0052	0.3	NO
25	PCK1	PCK1	PCK1	8718	-0.0076	0.3	NO
26	DLAT	DLAT	DLAT	8775	-0.0089	0.3	NO
27	ACSS1	ACSS1	ACSS1	8918	-0.013	0.29	NO
28	ACACB	ACACB	ACACB	9319	-0.023	0.27	NO
29	LDHAL6A	LDHAL6A	LDHAL6A	9370	-0.024	0.28	NO
30	ALDH7A1	ALDH7A1	ALDH7A1	9751	-0.034	0.26	NO
31	ACYP2	ACYP2	ACYP2	10001	-0.04	0.26	NO
32	ALDH9A1	ALDH9A1	ALDH9A1	10018	-0.041	0.26	NO
33	GLO1	GLO1	GLO1	11020	-0.067	0.22	NO
34	ME2	ME2	ME2	12619	-0.12	0.15	NO
35	ME3	ME3	ME3	13291	-0.15	0.14	NO
36	ME1	ME1	ME1	14648	-0.22	0.11	NO
37	LDHAL6B	LDHAL6B	LDHAL6B	14762	-0.22	0.14	NO
38	LDHA	LDHA	LDHA	14938	-0.23	0.18	NO

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

Figure S68. 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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	TUBB4	TUBB4	TUBB4	94	0.82	0.064	YES
2	TUBB3	TUBB3	TUBB3	175	0.71	0.12	YES
3	TUBB2B	TUBB2B	TUBB2B	188	0.7	0.18	YES
4	TUBB8	TUBB8	TUBB8	530	0.52	0.2	YES
5	OCLN	OCLN	OCLN	533	0.52	0.25	YES
6	TUBB4Q	TUBB4Q	TUBB4Q	547	0.51	0.29	YES
7	CLDN1	CLDN1	CLDN1	616	0.49	0.33	YES
8	TUBB2A	TUBB2A	TUBB2A	1166	0.36	0.33	YES
9	TUBAL3	TUBAL3	TUBAL3	1784	0.28	0.32	YES
10	ARPC1B	ARPC1B	ARPC1B	1962	0.26	0.33	YES
11	PRKCA	PRKCA	PRKCA	2078	0.25	0.35	YES
12	TUBA8	TUBA8	TUBA8	2345	0.23	0.35	YES
13	EZR	EZR	EZR	3276	0.17	0.32	NO
14	KRT18	KRT18	KRT18	3662	0.15	0.31	NO
15	CTTN	CTTN	CTTN	4098	0.13	0.29	NO
16	TUBB2C	TUBB2C	TUBB2C	4316	0.12	0.29	NO
17	TUBA1C	TUBA1C	TUBA1C	5193	0.091	0.25	NO
18	TUBA1A	TUBA1A	TUBA1A	5447	0.082	0.24	NO
19	WASL	WASL	WASL	5493	0.08	0.25	NO
20	ACTG1	ACTG1	ACTG1	5623	0.076	0.25	NO
21	ARPC4	ARPC4	ARPC4	5882	0.069	0.24	NO
22	ARPC3	ARPC3	ARPC3	6177	0.06	0.23	NO
23	RHOA	RHOA	RHOA	6718	0.046	0.2	NO
24	ACTB	ACTB	ACTB	7049	0.036	0.19	NO
25	ABL1	ABL1	ABL1	7258	0.031	0.18	NO
26	ARHGEF2	ARHGEF2	ARHGEF2	7730	0.017	0.15	NO
27	TUBA1B	TUBA1B	TUBA1B	8453	-0.0012	0.11	NO
28	TUBB6	TUBB6	TUBB6	8486	-0.002	0.11	NO
29	ARPC1A	ARPC1A	ARPC1A	8534	-0.0036	0.11	NO
30	ARPC5L	ARPC5L	ARPC5L	8732	-0.0079	0.1	NO
31	TUBB	TUBB	TUBB	8761	-0.0087	0.099	NO
32	YWHAQ	YWHAQ	YWHAQ	8967	-0.014	0.089	NO
33	ARPC2	ARPC2	ARPC2	9207	-0.02	0.078	NO
34	NCK2	NCK2	NCK2	9590	-0.03	0.059	NO
35	ARPC5	ARPC5	ARPC5	9608	-0.03	0.061	NO
36	YWHAZ	YWHAZ	YWHAZ	10013	-0.041	0.042	NO
37	NCL	NCL	NCL	10038	-0.042	0.044	NO
38	CDC42	CDC42	CDC42	10181	-0.045	0.04	NO
39	CD14	CD14	CD14	10636	-0.057	0.02	NO
40	TLR5	TLR5	TLR5	11083	-0.069	0.0013	NO
41	CTNNB1	CTNNB1	CTNNB1	12147	-0.1	-0.049	NO
42	WAS	WAS	WAS	12218	-0.1	-0.044	NO
43	ITGB1	ITGB1	ITGB1	12911	-0.13	-0.071	NO
44	TUBA4A	TUBA4A	TUBA4A	13166	-0.14	-0.073	NO
45	NCK1	NCK1	NCK1	13167	-0.14	-0.061	NO
46	CDH1	CDH1	CDH1	14456	-0.2	-0.12	NO
47	ROCK1	ROCK1	ROCK1	15063	-0.24	-0.13	NO
48	LY96	LY96	LY96	15069	-0.24	-0.11	NO
49	TUBB1	TUBB1	TUBB1	15145	-0.25	-0.09	NO
50	HCLS1	HCLS1	HCLS1	15254	-0.26	-0.074	NO
51	ROCK2	ROCK2	ROCK2	16164	-0.34	-0.095	NO
52	FYN	FYN	FYN	16363	-0.37	-0.075	NO
53	TLR4	TLR4	TLR4	16749	-0.43	-0.059	NO
54	TUBA3E	TUBA3E	TUBA3E	17129	-0.52	-0.036	NO
55	TUBA3C	TUBA3C	TUBA3C	17153	-0.52	0.0077	NO
56	TUBA3D	TUBA3D	TUBA3D	17353	-0.59	0.046	NO

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

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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	ACSM1	ACSM1	ACSM1	25	1	0.14	YES
2	BDH1	BDH1	BDH1	321	0.61	0.2	YES
3	OXCT2	OXCT2	OXCT2	362	0.59	0.28	YES
4	AKR1B10	AKR1B10	AKR1B10	504	0.53	0.34	YES
5	ABAT	ABAT	ABAT	793	0.44	0.39	YES
6	ACSM2A	ACSM2A	ACSM2A	867	0.42	0.44	YES
7	ALDH2	ALDH2	ALDH2	1469	0.31	0.45	YES
8	PDHA1	PDHA1	PDHA1	2573	0.21	0.42	YES
9	ACSM5	ACSM5	ACSM5	2630	0.21	0.44	YES
10	ACSM3	ACSM3	ACSM3	3073	0.18	0.44	YES
11	AACS	AACS	AACS	3199	0.17	0.46	YES
12	HMGCL	HMGCL	HMGCL	3392	0.16	0.47	YES
13	PDHB	PDHB	PDHB	3925	0.14	0.46	YES
14	ALDH1B1	ALDH1B1	ALDH1B1	4000	0.13	0.47	YES
15	OXCT1	OXCT1	OXCT1	4174	0.13	0.48	YES
16	ECHS1	ECHS1	ECHS1	4259	0.12	0.49	YES
17	BDH2	BDH2	BDH2	4272	0.12	0.5	YES
18	ALDH5A1	ALDH5A1	ALDH5A1	4716	0.11	0.5	NO
19	ACAT1	ACAT1	ACAT1	5032	0.096	0.49	NO
20	L2HGDH	L2HGDH	L2HGDH	5376	0.084	0.48	NO
21	ALDH3A2	ALDH3A2	ALDH3A2	5790	0.072	0.47	NO
22	HADH	HADH	HADH	6641	0.048	0.43	NO
23	HMGCS1	HMGCS1	HMGCS1	6655	0.047	0.44	NO
24	ACADS	ACADS	ACADS	6762	0.044	0.44	NO
25	HADHA	HADHA	HADHA	7506	0.024	0.4	NO
26	ACAT2	ACAT2	ACAT2	8033	0.0094	0.37	NO
27	ALDH7A1	ALDH7A1	ALDH7A1	9751	-0.034	0.28	NO
28	ALDH9A1	ALDH9A1	ALDH9A1	10018	-0.041	0.27	NO
29	GAD1	GAD1	GAD1	17141	-0.52	-0.052	NO
30	HMGCS2	HMGCS2	HMGCS2	17797	-0.82	0.022	NO

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

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

Table 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	ALDH3A1	ALDH3A1	ALDH3A1	572	0.51	0.078	YES
2	ALDH3B1	ALDH3B1	ALDH3B1	1274	0.34	0.11	YES
3	ALDH2	ALDH2	ALDH2	1469	0.31	0.17	YES
4	FTCD	FTCD	FTCD	1614	0.3	0.22	YES
5	UROC1	UROC1	UROC1	1720	0.28	0.28	YES
6	ACY3	ACY3	ACY3	1884	0.26	0.33	YES
7	HEMK1	HEMK1	HEMK1	1928	0.26	0.38	YES
8	DDC	DDC	DDC	2315	0.23	0.41	YES
9	AMDHD1	AMDHD1	AMDHD1	2832	0.19	0.42	YES
10	WBSCR22	WBSCR22	WBSCR22	3180	0.17	0.44	YES
11	LCMT1	LCMT1	LCMT1	3367	0.16	0.47	YES
12	TRMT11	TRMT11	TRMT11	3476	0.16	0.5	YES
13	ALDH1A3	ALDH1A3	ALDH1A3	3741	0.14	0.51	YES
14	ALDH1B1	ALDH1B1	ALDH1B1	4000	0.13	0.53	YES
15	LCMT2	LCMT2	LCMT2	4939	0.099	0.5	NO
16	METTL6	METTL6	METTL6	5007	0.097	0.52	NO
17	MAOA	MAOA	MAOA	5418	0.083	0.51	NO
18	ALDH3A2	ALDH3A2	ALDH3A2	5790	0.072	0.5	NO
19	HDC	HDC	HDC	6517	0.05	0.48	NO
20	MAOB	MAOB	MAOB	6532	0.05	0.49	NO
21	METTL2B	METTL2B	METTL2B	6608	0.048	0.49	NO
22	HAL	HAL	HAL	8277	0.0037	0.4	NO
23	ALDH7A1	ALDH7A1	ALDH7A1	9751	-0.034	0.33	NO
24	ALDH9A1	ALDH9A1	ALDH9A1	10018	-0.041	0.32	NO
25	ALDH3B2	ALDH3B2	ALDH3B2	10928	-0.065	0.29	NO
26	ABP1	ABP1	ABP1	11152	-0.071	0.29	NO
27	ASPA	ASPA	ASPA	13604	-0.16	0.19	NO
28	HNMT	HNMT	HNMT	15712	-0.3	0.14	NO

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

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

Table 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	PARS2	PARS2	PARS2	1116	0.37	0.03	YES
2	VARS2	VARS2	VARS2	1927	0.26	0.05	YES
3	PSTK	PSTK	PSTK	1956	0.26	0.11	YES
4	LARS2	LARS2	LARS2	2236	0.24	0.16	YES
5	SARS2	SARS2	SARS2	2536	0.21	0.19	YES
6	VARS	VARS	VARS	2762	0.2	0.23	YES
7	QARS	QARS	QARS	3472	0.16	0.23	YES
8	NARS2	NARS2	NARS2	3663	0.15	0.26	YES
9	EARS2	EARS2	EARS2	4300	0.12	0.25	YES
10	CARS2	CARS2	CARS2	4479	0.12	0.27	YES
11	DARS2	DARS2	DARS2	4553	0.11	0.29	YES
12	AARS2	AARS2	AARS2	4746	0.1	0.31	YES
13	HARS2	HARS2	HARS2	4941	0.099	0.32	YES
14	YARS2	YARS2	YARS2	5092	0.094	0.34	YES
15	MARS	MARS	MARS	5999	0.066	0.3	YES
16	NARS	NARS	NARS	6052	0.064	0.32	YES
17	GARS	GARS	GARS	6250	0.058	0.32	YES
18	MARS2	MARS2	MARS2	6308	0.056	0.33	YES
19	FARSA	FARSA	FARSA	6320	0.056	0.34	YES
20	AARS	AARS	AARS	7023	0.036	0.32	NO
21	KARS	KARS	KARS	7116	0.034	0.32	NO
22	FARS2	FARS2	FARS2	7562	0.022	0.3	NO
23	FARSB	FARSB	FARSB	7904	0.013	0.28	NO
24	WARS2	WARS2	WARS2	7944	0.012	0.28	NO
25	SEPSECS	SEPSECS	SEPSECS	8433	-0.00036	0.26	NO
26	IARS2	IARS2	IARS2	8437	-0.00048	0.26	NO
27	MTFMT	MTFMT	MTFMT	8864	-0.012	0.24	NO
28	HARS	HARS	HARS	9172	-0.02	0.22	NO
29	IARS	IARS	IARS	9523	-0.028	0.21	NO
30	RARS2	RARS2	RARS2	10298	-0.048	0.18	NO
31	SARS	SARS	SARS	11038	-0.068	0.16	NO
32	YARS	YARS	YARS	11375	-0.078	0.16	NO
33	CARS	CARS	CARS	11456	-0.08	0.17	NO
34	TARSL2	TARSL2	TARSL2	11478	-0.08	0.19	NO
35	LARS	LARS	LARS	11565	-0.083	0.21	NO
36	RARS	RARS	RARS	11586	-0.084	0.23	NO
37	TARS	TARS	TARS	12200	-0.1	0.22	NO
38	EPRS	EPRS	EPRS	12958	-0.13	0.21	NO
39	WARS	WARS	WARS	13452	-0.15	0.22	NO
40	DARS	DARS	DARS	13606	-0.16	0.25	NO

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

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

genes ES table in pathway: KEGG SELENOAMINO ACID METABOLISM

Table 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	CLDN3	CLDN3	CLDN3	45	0.92	0.032	YES
2	TJP3	TJP3	TJP3	49	0.9	0.067	YES
3	RAB3B	RAB3B	RAB3B	254	0.65	0.08	YES
4	IGSF5	IGSF5	IGSF5	354	0.6	0.098	YES
5	CLDN7	CLDN7	CLDN7	525	0.52	0.11	YES
6	OCLN	OCLN	OCLN	533	0.52	0.13	YES
7	CLDN1	CLDN1	CLDN1	616	0.49	0.14	YES
8	CLDN23	CLDN23	CLDN23	697	0.47	0.16	YES
9	PARD6A	PARD6A	PARD6A	698	0.47	0.17	YES
10	CLDN4	CLDN4	CLDN4	714	0.46	0.19	YES
11	PRKCG	PRKCG	PRKCG	834	0.43	0.2	YES
12	MYH14	MYH14	MYH14	963	0.4	0.21	YES
13	LLGL2	LLGL2	LLGL2	1009	0.39	0.22	YES
14	MYH3	MYH3	MYH3	1037	0.38	0.23	YES
15	MYH8	MYH8	MYH8	1231	0.35	0.24	YES
16	CLDN16	CLDN16	CLDN16	1241	0.34	0.25	YES
17	MYLPF	MYLPF	MYLPF	1279	0.34	0.26	YES
18	CLDN6	CLDN6	CLDN6	1345	0.33	0.27	YES
19	MRAS	MRAS	MRAS	1555	0.3	0.27	YES
20	CLDN14	CLDN14	CLDN14	1777	0.28	0.27	YES
21	MYH7	MYH7	MYH7	1781	0.28	0.28	YES
22	PRKCQ	PRKCQ	PRKCQ	1793	0.28	0.29	YES
23	CLDN2	CLDN2	CLDN2	1810	0.27	0.3	YES
24	CLDN9	CLDN9	CLDN9	1919	0.26	0.3	YES
25	PRKCA	PRKCA	PRKCA	2078	0.25	0.3	YES
26	EPB41L1	EPB41L1	EPB41L1	2458	0.22	0.29	NO
27	CLDN10	CLDN10	CLDN10	2515	0.22	0.29	NO
28	PRKCZ	PRKCZ	PRKCZ	2601	0.21	0.3	NO
29	SRC	SRC	SRC	2861	0.19	0.29	NO
30	CRB3	CRB3	CRB3	2997	0.18	0.29	NO
31	RRAS2	RRAS2	RRAS2	3024	0.18	0.3	NO
32	PARD6B	PARD6B	PARD6B	3411	0.16	0.28	NO
33	MYH10	MYH10	MYH10	3636	0.15	0.27	NO
34	TJP2	TJP2	TJP2	3735	0.14	0.27	NO
35	CLDN15	CLDN15	CLDN15	3753	0.14	0.28	NO
36	MAGI2	MAGI2	MAGI2	3770	0.14	0.28	NO
37	CTTN	CTTN	CTTN	4098	0.13	0.27	NO
38	CGN	CGN	CGN	4119	0.13	0.27	NO
39	MYL5	MYL5	MYL5	4164	0.13	0.28	NO
40	SYMPK	SYMPK	SYMPK	4428	0.12	0.26	NO
41	GNAI1	GNAI1	GNAI1	4431	0.12	0.27	NO
42	PARD3	PARD3	PARD3	4465	0.12	0.27	NO
43	LLGL1	LLGL1	LLGL1	4576	0.11	0.27	NO
44	CASK	CASK	CASK	4837	0.1	0.26	NO
45	PRKCI	PRKCI	PRKCI	4924	0.1	0.26	NO
46	EXOC4	EXOC4	EXOC4	4964	0.098	0.26	NO
47	AKT2	AKT2	AKT2	5250	0.089	0.25	NO
48	PPP2R2D	PPP2R2D	PPP2R2D	5579	0.078	0.23	NO
49	EPB41L2	EPB41L2	EPB41L2	5581	0.078	0.24	NO
50	ACTG1	ACTG1	ACTG1	5623	0.076	0.24	NO
51	PPP2R1A	PPP2R1A	PPP2R1A	5967	0.067	0.22	NO
52	F11R	F11R	F11R	6114	0.062	0.21	NO
53	SPTAN1	SPTAN1	SPTAN1	6174	0.06	0.21	NO
54	MYL12B	MYL12B	MYL12B	6434	0.053	0.2	NO
55	RHOA	RHOA	RHOA	6718	0.046	0.19	NO
56	INADL	INADL	INADL	6855	0.041	0.18	NO
57	CDK4	CDK4	CDK4	6864	0.041	0.18	NO
58	CTNNA1	CTNNA1	CTNNA1	6960	0.038	0.18	NO
59	ACTB	ACTB	ACTB	7049	0.036	0.18	NO
60	CSNK2B	CSNK2B	CSNK2B	7087	0.035	0.17	NO
61	CLDN19	CLDN19	CLDN19	7238	0.031	0.17	NO
62	EPB41L3	EPB41L3	EPB41L3	7243	0.031	0.17	NO
63	PPP2CB	PPP2CB	PPP2CB	7629	0.02	0.15	NO
64	TJAP1	TJAP1	TJAP1	7636	0.02	0.15	NO
65	RAB13	RAB13	RAB13	7698	0.018	0.14	NO
66	MPP5	MPP5	MPP5	7900	0.013	0.14	NO
67	MYH1	MYH1	MYH1	7929	0.012	0.13	NO
68	MLLT4	MLLT4	MLLT4	7936	0.012	0.13	NO
69	MYH7B	MYH7B	MYH7B	8112	0.0078	0.12	NO
70	CSNK2A1	CSNK2A1	CSNK2A1	8117	0.0076	0.12	NO
71	RRAS	RRAS	RRAS	8406	0.00036	0.11	NO
72	CSNK2A2	CSNK2A2	CSNK2A2	8422	8e-05	0.11	NO
73	CSDA	CSDA	CSDA	8518	-0.0031	0.1	NO
74	AKT1	AKT1	AKT1	8814	-0.0099	0.087	NO
75	MYL12A	MYL12A	MYL12A	8868	-0.012	0.084	NO
76	CLDN18	CLDN18	CLDN18	9152	-0.019	0.069	NO
77	KRAS	KRAS	KRAS	9365	-0.024	0.058	NO
78	ACTN4	ACTN4	ACTN4	9627	-0.031	0.045	NO
79	TJP1	TJP1	TJP1	9944	-0.039	0.029	NO
80	AMOTL1	AMOTL1	AMOTL1	10063	-0.042	0.024	NO
81	CDC42	CDC42	CDC42	10181	-0.045	0.02	NO
82	PPP2CA	PPP2CA	PPP2CA	10249	-0.047	0.018	NO
83	PPP2R2C	PPP2R2C	PPP2R2C	10500	-0.054	0.0059	NO
84	GNAI3	GNAI3	GNAI3	10691	-0.059	-0.0024	NO
85	GNAI2	GNAI2	GNAI2	10722	-0.06	-0.0018	NO
86	VAPA	VAPA	VAPA	10791	-0.061	-0.0032	NO
87	EPB41	EPB41	EPB41	10895	-0.064	-0.0065	NO
88	ACTN2	ACTN2	ACTN2	10972	-0.066	-0.0082	NO
89	CLDN20	CLDN20	CLDN20	11195	-0.072	-0.018	NO
90	PRKCD	PRKCD	PRKCD	11212	-0.073	-0.016	NO
91	CTNNA2	CTNNA2	CTNNA2	11932	-0.095	-0.052	NO
92	YES1	YES1	YES1	12040	-0.099	-0.054	NO
93	ACTN1	ACTN1	ACTN1	12059	-0.099	-0.051	NO
94	CTNNB1	CTNNB1	CTNNB1	12147	-0.1	-0.052	NO
95	MAGI3	MAGI3	MAGI3	12182	-0.1	-0.05	NO
96	EXOC3	EXOC3	EXOC3	12667	-0.12	-0.072	NO
97	ASH1L	ASH1L	ASH1L	12694	-0.12	-0.069	NO
98	MYL2	MYL2	MYL2	12763	-0.12	-0.068	NO
99	MPDZ	MPDZ	MPDZ	12924	-0.13	-0.072	NO
100	PTEN	PTEN	PTEN	12991	-0.13	-0.071	NO
101	NRAS	NRAS	NRAS	13060	-0.14	-0.069	NO
102	PPP2R1B	PPP2R1B	PPP2R1B	13217	-0.14	-0.072	NO
103	MYH9	MYH9	MYH9	13490	-0.16	-0.082	NO
104	PPP2R2A	PPP2R2A	PPP2R2A	13609	-0.16	-0.082	NO
105	ACTN3	ACTN3	ACTN3	13676	-0.16	-0.079	NO
106	AKT3	AKT3	AKT3	13785	-0.17	-0.079	NO
107	MYL9	MYL9	MYL9	13994	-0.18	-0.084	NO
108	MAGI1	MAGI1	MAGI1	14636	-0.21	-0.11	NO
109	PRKCB	PRKCB	PRKCB	15033	-0.24	-0.12	NO
110	HCLS1	HCLS1	HCLS1	15254	-0.26	-0.13	NO
111	MYH15	MYH15	MYH15	15553	-0.28	-0.13	NO
112	CLDN11	CLDN11	CLDN11	15954	-0.32	-0.14	NO
113	MYH13	MYH13	MYH13	15970	-0.32	-0.13	NO
114	CLDN8	CLDN8	CLDN8	16045	-0.33	-0.12	NO
115	ZAK	ZAK	ZAK	16277	-0.36	-0.12	NO
116	PRKCE	PRKCE	PRKCE	16848	-0.46	-0.14	NO
117	PARD6G	PARD6G	PARD6G	16958	-0.48	-0.12	NO
118	PPP2R2B	PPP2R2B	PPP2R2B	17034	-0.49	-0.11	NO
119	CLDN5	CLDN5	CLDN5	17101	-0.51	-0.092	NO
120	JAM3	JAM3	JAM3	17579	-0.68	-0.092	NO
121	PRKCH	PRKCH	PRKCH	17703	-0.74	-0.071	NO
122	CTNNA3	CTNNA3	CTNNA3	17761	-0.79	-0.044	NO
123	MYH11	MYH11	MYH11	17775	-0.8	-0.014	NO
124	JAM2	JAM2	JAM2	17953	-0.97	0.014	NO

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

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

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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	OXCT2	OXCT2	OXCT2	362	0.59	0.084	YES
2	ABAT	ABAT	ABAT	793	0.44	0.14	YES
3	ALDH2	ALDH2	ALDH2	1469	0.31	0.15	YES
4	BCAT2	BCAT2	BCAT2	2068	0.25	0.16	YES
5	ACAA1	ACAA1	ACAA1	2187	0.24	0.2	YES
6	BCKDHB	BCKDHB	BCKDHB	2311	0.23	0.23	YES
7	HSD17B10	HSD17B10	HSD17B10	2923	0.19	0.23	YES
8	PCCB	PCCB	PCCB	3020	0.18	0.26	YES
9	MCCC1	MCCC1	MCCC1	3288	0.17	0.28	YES
10	HIBADH	HIBADH	HIBADH	3322	0.16	0.3	YES
11	PCCA	PCCA	PCCA	3382	0.16	0.33	YES
12	HMGCL	HMGCL	HMGCL	3392	0.16	0.36	YES
13	DLD	DLD	DLD	3705	0.15	0.36	YES
14	ACAD8	ACAD8	ACAD8	3939	0.14	0.37	YES
15	ALDH1B1	ALDH1B1	ALDH1B1	4000	0.13	0.39	YES
16	OXCT1	OXCT1	OXCT1	4174	0.13	0.41	YES
17	ECHS1	ECHS1	ECHS1	4259	0.12	0.42	YES
18	ALDH6A1	ALDH6A1	ALDH6A1	4608	0.11	0.42	YES
19	AOX1	AOX1	AOX1	4722	0.11	0.44	YES
20	HIBCH	HIBCH	HIBCH	4990	0.097	0.44	YES
21	ACAT1	ACAT1	ACAT1	5032	0.096	0.45	YES
22	MCEE	MCEE	MCEE	5464	0.082	0.44	YES
23	AUH	AUH	AUH	5607	0.077	0.45	YES
24	IVD	IVD	IVD	5775	0.072	0.45	YES
25	ALDH3A2	ALDH3A2	ALDH3A2	5790	0.072	0.46	YES
26	HADH	HADH	HADH	6641	0.048	0.42	NO
27	HMGCS1	HMGCS1	HMGCS1	6655	0.047	0.43	NO
28	MCCC2	MCCC2	MCCC2	6727	0.045	0.44	NO
29	ACADS	ACADS	ACADS	6762	0.044	0.44	NO
30	HADHA	HADHA	HADHA	7506	0.024	0.41	NO
31	DBT	DBT	DBT	7516	0.024	0.41	NO
32	MUT	MUT	MUT	7940	0.012	0.39	NO
33	ACADM	ACADM	ACADM	7969	0.011	0.39	NO
34	ACAT2	ACAT2	ACAT2	8033	0.0094	0.39	NO
35	HADHB	HADHB	HADHB	8207	0.0052	0.38	NO
36	BCKDHA	BCKDHA	BCKDHA	8257	0.0041	0.38	NO
37	ACAA2	ACAA2	ACAA2	8615	-0.0054	0.36	NO
38	ACADSB	ACADSB	ACADSB	9016	-0.015	0.34	NO
39	EHHADH	EHHADH	EHHADH	9328	-0.023	0.32	NO
40	ALDH7A1	ALDH7A1	ALDH7A1	9751	-0.034	0.31	NO
41	ALDH9A1	ALDH9A1	ALDH9A1	10018	-0.041	0.3	NO
42	IL4I1	IL4I1	IL4I1	10102	-0.043	0.3	NO
43	HMGCS2	HMGCS2	HMGCS2	17797	-0.82	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: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

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