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

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

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LAML-TB. Broad Institute of MIT and Harvard. doi:10.7908/C1R78DNT

Overview

Introduction

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

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

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 692
Number of samples: 173
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 75
pheno.type: 2 - 3 :[ clus2 ] 52
pheno.type: 3 - 3 :[ clus3 ] 46

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

clus1

Top enriched gene sets are KEGG N GLYCAN BIOSYNTHESIS, KEGG MTOR SIGNALING PATHWAY, KEGG ADHERENS JUNCTION, KEGG RENAL CELL CARCINOMA, KEGG PANCREATIC CANCER, KEGG ENDOMETRIAL CANCER, KEGG PROSTATE CANCER, KEGG THYROID CANCER, KEGG MELANOMA, KEGG NON SMALL CELL LUNG CANCER

And common core enriched genes are EGF, EGFR, CCND1, CDH1, MGAT3, ESR1, IFNG, NR2F2, TERT, AKT3

clus2

Top enriched gene sets are KEGG LYSOSOME, KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS, BIOCARTA HIVNEF PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA TOLL PATHWAY, ST TUMOR NECROSIS FACTOR PATHWAY, PID IL1PATHWAY, PID IFNGPATHWAY, PID IL8CXCR2 PATHWAY, PID MAPKTRKPATHWAY

And common core enriched genes are FOS, MAP2K1, MAP2K6, MAPK7, MEF2C, DUSP6, IRAK3, LY96, MYD88, NFKB2

clus3

Top enriched gene sets are KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA POLYMERASE, PID MYC PATHWAY, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, REACTOME PEPTIDE CHAIN ELONGATION

And common core enriched genes are POLR1C, POLR1D, POLR2F, POLR2H, POLR2L, POLR3B, POLR3D, POLR3H, POLR3K, CDKN2A

Results

Subtype clus1 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG N GLYCAN BIOSYNTHESIS	46	genes.ES.table	0.48	1.9	0.002	0.53	0.26	0.28	0.28	0.2	0	0.1
KEGG MTOR SIGNALING PATHWAY	49	genes.ES.table	0.48	1.7	0.012	0.47	0.65	0.2	0.17	0.17	0.16	0.12
KEGG ADHERENS JUNCTION	72	genes.ES.table	0.57	1.7	0.0061	0.68	0.61	0.24	0.092	0.22	0.22	0.16
KEGG RENAL CELL CARCINOMA	69	genes.ES.table	0.46	1.7	0.004	0.48	0.73	0.23	0.18	0.19	0.19	0.12
KEGG PANCREATIC CANCER	70	genes.ES.table	0.43	1.7	0.0019	0.55	0.62	0.17	0.15	0.15	0.18	0.13
KEGG ENDOMETRIAL CANCER	51	genes.ES.table	0.54	1.9	0.002	0.79	0.26	0.2	0.15	0.17	0	0.15
KEGG PROSTATE CANCER	87	genes.ES.table	0.5	1.8	0.004	0.5	0.42	0.23	0.17	0.19	0	0.11
KEGG THYROID CANCER	28	genes.ES.table	0.57	1.7	0.002	0.45	0.65	0.18	0.14	0.15	0.16	0.12
KEGG MELANOMA	60	genes.ES.table	0.58	1.7	0.0019	0.47	0.69	0.35	0.17	0.29	0.17	0.13
KEGG NON SMALL CELL LUNG CANCER	53	genes.ES.table	0.45	1.7	0.0039	0.6	0.61	0.15	0.15	0.13	0.19	0.14

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCND1	CCND1	CCND1	63	0.61	0.1	YES
2	TERT	TERT	TERT	143	0.56	0.19	YES
3	EGFR	EGFR	EGFR	177	0.54	0.28	YES
4	EGF	EGF	EGF	253	0.51	0.36	YES
5	ESR1	ESR1	ESR1	652	0.42	0.41	YES
6	NR2F2	NR2F2	NR2F2	881	0.38	0.46	YES
7	IFNG	IFNG	IFNG	1523	0.31	0.47	YES
8	PIF1	PIF1	PIF1	2377	0.23	0.46	NO
9	WRN	WRN	WRN	4085	0.14	0.39	NO
10	MYC	MYC	MYC	5427	0.09	0.32	NO
11	PARP2	PARP2	PARP2	5487	0.089	0.34	NO
12	DKC1	DKC1	DKC1	6217	0.071	0.31	NO
13	MRE11A	MRE11A	MRE11A	6287	0.07	0.31	NO
14	TNKS	TNKS	TNKS	6339	0.069	0.32	NO
15	POT1	POT1	POT1	7074	0.054	0.29	NO
16	RBBP4	RBBP4	RBBP4	7161	0.053	0.29	NO
17	NBN	NBN	NBN	7211	0.052	0.3	NO
18	WT1	WT1	WT1	7320	0.05	0.3	NO
19	HDAC2	HDAC2	HDAC2	7479	0.048	0.3	NO
20	SIN3A	SIN3A	SIN3A	7537	0.047	0.3	NO
21	SMAD3	SMAD3	SMAD3	7609	0.046	0.31	NO
22	SP3	SP3	SP3	7672	0.045	0.31	NO
23	RAD9A	RAD9A	RAD9A	7969	0.04	0.3	NO
24	TERF1	TERF1	TERF1	7990	0.04	0.31	NO
25	SMG6	SMG6	SMG6	8042	0.04	0.31	NO
26	IRF1	IRF1	IRF1	8060	0.039	0.32	NO
27	E2F1	E2F1	E2F1	8092	0.039	0.32	NO
28	MAX	MAX	MAX	8131	0.038	0.32	NO
29	ABL1	ABL1	ABL1	8189	0.038	0.33	NO
30	ATM	ATM	ATM	8222	0.037	0.33	NO
31	RAD1	RAD1	RAD1	8267	0.037	0.34	NO
32	TERF2IP	TERF2IP	TERF2IP	8441	0.034	0.33	NO
33	UBE3A	UBE3A	UBE3A	8508	0.033	0.33	NO
34	BLM	BLM	BLM	8557	0.033	0.34	NO
35	SIN3B	SIN3B	SIN3B	8587	0.032	0.34	NO
36	HDAC1	HDAC1	HDAC1	8625	0.032	0.34	NO
37	NCL	NCL	NCL	8824	0.029	0.34	NO
38	SMG5	SMG5	SMG5	8854	0.029	0.34	NO
39	RPS6KB1	RPS6KB1	RPS6KB1	8933	0.028	0.34	NO
40	RBBP7	RBBP7	RBBP7	9094	0.026	0.34	NO
41	XRCC5	XRCC5	XRCC5	9106	0.026	0.34	NO
42	MTOR	MTOR	MTOR	9420	0.022	0.32	NO
43	MAPK1	MAPK1	MAPK1	10305	0.011	0.28	NO
44	XRCC6	XRCC6	XRCC6	10472	0.0086	0.27	NO
45	CDKN1B	CDKN1B	CDKN1B	10668	0.0064	0.26	NO
46	HSP90AA1	HSP90AA1	HSP90AA1	10748	0.0052	0.25	NO
47	RAD50	RAD50	RAD50	10917	0.0032	0.24	NO
48	SP1	SP1	SP1	11371	-0.0029	0.22	NO
49	HNRNPC	HNRNPC	HNRNPC	11479	-0.0043	0.21	NO
50	TERF2	TERF2	TERF2	11563	-0.0054	0.21	NO
51	ZNFX1	ZNFX1	ZNFX1	11635	-0.0066	0.21	NO
52	SAP18	SAP18	SAP18	12010	-0.012	0.19	NO
53	PTGES3	PTGES3	PTGES3	12348	-0.017	0.17	NO
54	IFNAR2	IFNAR2	IFNAR2	12351	-0.017	0.17	NO
55	MAPK3	MAPK3	MAPK3	12736	-0.023	0.15	NO
56	TINF2	TINF2	TINF2	12819	-0.025	0.15	NO
57	HUS1	HUS1	HUS1	12925	-0.027	0.15	NO
58	NFKB1	NFKB1	NFKB1	13189	-0.031	0.14	NO
59	YWHAE	YWHAE	YWHAE	13424	-0.036	0.13	NO
60	ACD	ACD	ACD	13800	-0.044	0.12	NO
61	FOS	FOS	FOS	13848	-0.045	0.12	NO
62	PINX1	PINX1	PINX1	13893	-0.046	0.13	NO
63	TGFB1	TGFB1	TGFB1	14565	-0.064	0.1	NO
64	AKT1	AKT1	AKT1	14735	-0.07	0.1	NO
65	JUN	JUN	JUN	14997	-0.078	0.1	NO
66	MXD1	MXD1	MXD1	15005	-0.078	0.11	NO
67	SAP30	SAP30	SAP30	15505	-0.1	0.1	NO

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

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG N 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 MTOR SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCND1	CCND1	CCND1	63	0.61	0.1	YES
2	CDH1	CDH1	CDH1	140	0.56	0.2	YES
3	EGFR	EGFR	EGFR	177	0.54	0.29	YES
4	EGF	EGF	EGF	253	0.51	0.38	YES
5	LEF1	LEF1	LEF1	642	0.42	0.43	YES
6	TCF7	TCF7	TCF7	1589	0.3	0.42	YES
7	AXIN2	AXIN2	AXIN2	1885	0.27	0.45	YES
8	AKT3	AKT3	AKT3	2347	0.24	0.47	YES
9	PIK3R3	PIK3R3	PIK3R3	2395	0.23	0.51	YES
10	ERBB2	ERBB2	ERBB2	2526	0.22	0.54	YES
11	CTNNA3	CTNNA3	CTNNA3	3921	0.14	0.48	NO
12	PIK3CA	PIK3CA	PIK3CA	5255	0.095	0.42	NO
13	MYC	MYC	MYC	5427	0.09	0.43	NO
14	FOXO3	FOXO3	FOXO3	5514	0.088	0.44	NO
15	SOS1	SOS1	SOS1	5782	0.081	0.44	NO
16	BRAF	BRAF	BRAF	6025	0.075	0.44	NO
17	TCF7L2	TCF7L2	TCF7L2	6035	0.075	0.45	NO
18	PIK3R1	PIK3R1	PIK3R1	6522	0.065	0.43	NO
19	APC	APC	APC	8151	0.038	0.34	NO
20	NRAS	NRAS	NRAS	8475	0.034	0.33	NO
21	AXIN1	AXIN1	AXIN1	8762	0.03	0.32	NO
22	PTEN	PTEN	PTEN	8964	0.028	0.31	NO
23	PIK3CG	PIK3CG	PIK3CG	9829	0.017	0.26	NO
24	GSK3B	GSK3B	GSK3B	10065	0.014	0.25	NO
25	MAPK1	MAPK1	MAPK1	10305	0.011	0.24	NO
26	MAP2K2	MAP2K2	MAP2K2	10714	0.0058	0.22	NO
27	AKT2	AKT2	AKT2	11099	0.0008	0.2	NO
28	MLH1	MLH1	MLH1	11261	-0.0013	0.19	NO
29	PIK3CD	PIK3CD	PIK3CD	11292	-0.0018	0.19	NO
30	RAF1	RAF1	RAF1	11328	-0.0022	0.18	NO
31	ELK1	ELK1	ELK1	11412	-0.0034	0.18	NO
32	PDPK1	PDPK1	PDPK1	11511	-0.0048	0.18	NO
33	KRAS	KRAS	KRAS	11523	-0.0049	0.18	NO
34	APC2	APC2	APC2	11737	-0.008	0.16	NO
35	TP53	TP53	TP53	11867	-0.0098	0.16	NO
36	SOS2	SOS2	SOS2	12356	-0.017	0.13	NO
37	CTNNB1	CTNNB1	CTNNB1	12367	-0.018	0.14	NO
38	MAPK3	MAPK3	MAPK3	12736	-0.023	0.12	NO
39	ARAF	ARAF	ARAF	12866	-0.026	0.12	NO
40	PIK3R2	PIK3R2	PIK3R2	12876	-0.026	0.12	NO
41	TCF7L1	TCF7L1	TCF7L1	13041	-0.028	0.12	NO
42	HRAS	HRAS	HRAS	14457	-0.061	0.044	NO
43	BAD	BAD	BAD	14488	-0.062	0.053	NO
44	PIK3CB	PIK3CB	PIK3CB	14720	-0.069	0.052	NO
45	AKT1	AKT1	AKT1	14735	-0.07	0.063	NO
46	PIK3R5	PIK3R5	PIK3R5	14762	-0.07	0.074	NO
47	GRB2	GRB2	GRB2	14763	-0.07	0.086	NO
48	MAP2K1	MAP2K1	MAP2K1	14788	-0.071	0.097	NO
49	CASP9	CASP9	CASP9	14790	-0.072	0.11	NO
50	ILK	ILK	ILK	14911	-0.075	0.12	NO
51	CTNNA1	CTNNA1	CTNNA1	15811	-0.12	0.084	NO

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

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

genes ES table in pathway: KEGG ADHERENS JUNCTION

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MGAT5B	MGAT5B	MGAT5B	379	0.48	0.096	YES
2	TUSC3	TUSC3	TUSC3	635	0.42	0.18	YES
3	MAN1A1	MAN1A1	MAN1A1	683	0.41	0.28	YES
4	MGAT3	MGAT3	MGAT3	830	0.39	0.37	YES
5	MAN1C1	MAN1C1	MAN1C1	2381	0.23	0.34	YES
6	ALG11	ALG11	ALG11	2649	0.22	0.38	YES
7	MGAT4A	MGAT4A	MGAT4A	2656	0.22	0.43	YES
8	FUT8	FUT8	FUT8	4002	0.14	0.39	YES
9	ALG10B	ALG10B	ALG10B	4364	0.13	0.4	YES
10	MGAT5	MGAT5	MGAT5	4738	0.11	0.4	YES
11	ALG10	ALG10	ALG10	4828	0.11	0.43	YES
12	STT3B	STT3B	STT3B	4859	0.11	0.45	YES
13	ST6GAL1	ST6GAL1	ST6GAL1	4885	0.11	0.48	YES
14	ALG14	ALG14	ALG14	5754	0.082	0.45	NO
15	ALG9	ALG9	ALG9	5935	0.078	0.46	NO
16	MAN1A2	MAN1A2	MAN1A2	6416	0.067	0.44	NO
17	ALG13	ALG13	ALG13	7480	0.048	0.4	NO
18	MAN2A2	MAN2A2	MAN2A2	8725	0.031	0.33	NO
19	B4GALT3	B4GALT3	B4GALT3	8994	0.027	0.32	NO
20	GANAB	GANAB	GANAB	9154	0.025	0.32	NO
21	ALG12	ALG12	ALG12	9264	0.024	0.32	NO
22	STT3A	STT3A	STT3A	9421	0.022	0.31	NO
23	ALG6	ALG6	ALG6	9753	0.018	0.3	NO
24	MAN1B1	MAN1B1	MAN1B1	10415	0.0093	0.26	NO
25	DOLPP1	DOLPP1	DOLPP1	10894	0.0034	0.24	NO
26	ALG3	ALG3	ALG3	11016	0.0019	0.23	NO
27	ALG2	ALG2	ALG2	11114	0.00064	0.22	NO
28	B4GALT2	B4GALT2	B4GALT2	11144	0.00024	0.22	NO
29	DPAGT1	DPAGT1	DPAGT1	11443	-0.0038	0.21	NO
30	DPM1	DPM1	DPM1	11584	-0.0057	0.2	NO
31	RPN1	RPN1	RPN1	11601	-0.006	0.2	NO
32	DDOST	DDOST	DDOST	11611	-0.0062	0.2	NO
33	RPN2	RPN2	RPN2	11711	-0.0077	0.2	NO
34	ALG5	ALG5	ALG5	11834	-0.0095	0.19	NO
35	RFT1	RFT1	RFT1	11950	-0.011	0.19	NO
36	DPM2	DPM2	DPM2	12120	-0.014	0.18	NO
37	DPM3	DPM3	DPM3	12196	-0.015	0.18	NO
38	MAN2A1	MAN2A1	MAN2A1	12276	-0.016	0.18	NO
39	ALG8	ALG8	ALG8	13317	-0.033	0.13	NO
40	MOGS	MOGS	MOGS	13384	-0.035	0.13	NO
41	MGAT2	MGAT2	MGAT2	13674	-0.041	0.13	NO
42	ALG1	ALG1	ALG1	13998	-0.048	0.12	NO
43	DAD1	DAD1	DAD1	14564	-0.064	0.1	NO
44	B4GALT1	B4GALT1	B4GALT1	14731	-0.069	0.11	NO
45	MGAT1	MGAT1	MGAT1	14769	-0.071	0.13	NO
46	MGAT4B	MGAT4B	MGAT4B	14806	-0.072	0.14	NO

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

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ADHERENS JUNCTION, 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 RENAL CELL CARCINOMA

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	EFNA1	EFNA1	EFNA1	97	0.58	0.076	YES
2	CDH1	CDH1	CDH1	140	0.56	0.15	YES
3	EGFR	EGFR	EGFR	177	0.54	0.22	YES
4	EGF	EGF	EGF	253	0.51	0.29	YES
5	NCKAP1	NCKAP1	NCKAP1	279	0.5	0.36	YES
6	IGF1	IGF1	IGF1	303	0.49	0.43	YES
7	MET	MET	MET	676	0.41	0.46	YES
8	MGAT3	MGAT3	MGAT3	830	0.39	0.51	YES
9	EPHA2	EPHA2	EPHA2	846	0.38	0.56	YES
10	IGF1R	IGF1R	IGF1R	1338	0.32	0.58	YES
11	MLLT4	MLLT4	MLLT4	1552	0.3	0.61	YES
12	ENAH	ENAH	ENAH	1569	0.3	0.65	YES
13	MYO6	MYO6	MYO6	1895	0.27	0.67	YES
14	HGF	HGF	HGF	1998	0.26	0.7	YES
15	CYFIP2	CYFIP2	CYFIP2	3423	0.17	0.64	NO
16	LIMA1	LIMA1	LIMA1	4705	0.11	0.58	NO
17	NCK1	NCK1	NCK1	5874	0.079	0.52	NO
18	PVRL2	PVRL2	PVRL2	5898	0.078	0.53	NO
19	VCL	VCL	VCL	7723	0.044	0.43	NO
20	KIFC3	KIFC3	KIFC3	9476	0.021	0.33	NO
21	GIT1	GIT1	GIT1	9582	0.02	0.33	NO
22	ABI1	ABI1	ABI1	10350	0.01	0.29	NO
23	ROCK1	ROCK1	ROCK1	10445	0.0089	0.28	NO
24	CTNND1	CTNND1	CTNND1	11596	-0.0059	0.22	NO
25	DIAPH1	DIAPH1	DIAPH1	11675	-0.0072	0.21	NO
26	EXOC4	EXOC4	EXOC4	12044	-0.013	0.19	NO
27	ACTN1	ACTN1	ACTN1	12073	-0.013	0.19	NO
28	CTNNB1	CTNNB1	CTNNB1	12367	-0.018	0.18	NO
29	EXOC3	EXOC3	EXOC3	12836	-0.025	0.16	NO
30	PIP5K1C	PIP5K1C	PIP5K1C	13328	-0.034	0.13	NO
31	AQP3	AQP3	AQP3	13411	-0.036	0.13	NO
32	STX4	STX4	STX4	13984	-0.048	0.1	NO
33	RHOA	RHOA	RHOA	14076	-0.05	0.11	NO
34	ARF6	ARF6	ARF6	14406	-0.06	0.096	NO
35	LPP	LPP	LPP	14440	-0.06	0.1	NO
36	VASP	VASP	VASP	14643	-0.066	0.1	NO
37	ZYX	ZYX	ZYX	15455	-0.097	0.066	NO
38	CTNNA1	CTNNA1	CTNNA1	15811	-0.12	0.062	NO
39	PLEKHA7	PLEKHA7	PLEKHA7	16259	-0.16	0.058	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 RENAL CELL CARCINOMA.

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

genes ES table in pathway: KEGG PANCREATIC CANCER

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FLT4	FLT4	FLT4	114	0.58	0.16	YES
2	KDR	KDR	KDR	437	0.46	0.28	YES
3	PTK2	PTK2	PTK2	483	0.45	0.41	YES
4	FLT1	FLT1	FLT1	624	0.42	0.53	YES
5	PLCG1	PLCG1	PLCG1	686	0.41	0.65	YES
6	VEGFA	VEGFA	VEGFA	1915	0.27	0.66	YES
7	NOS3	NOS3	NOS3	3357	0.17	0.62	NO
8	PIK3CA	PIK3CA	PIK3CA	5255	0.095	0.54	NO
9	HIF1A	HIF1A	HIF1A	6016	0.076	0.52	NO
10	PIK3R1	PIK3R1	PIK3R1	6522	0.065	0.51	NO
11	PRKCB	PRKCB	PRKCB	7241	0.052	0.48	NO
12	EIF1AX	EIF1AX	EIF1AX	8181	0.038	0.44	NO
13	EIF2S1	EIF2S1	EIF2S1	8669	0.032	0.42	NO
14	ELAVL1	ELAVL1	ELAVL1	9051	0.027	0.41	NO
15	PXN	PXN	PXN	9697	0.018	0.38	NO
16	PIK3CG	PIK3CG	PIK3CG	9829	0.017	0.37	NO
17	EIF2B5	EIF2B5	EIF2B5	10791	0.0047	0.32	NO
18	SHC1	SHC1	SHC1	10856	0.0039	0.32	NO
19	EIF2B3	EIF2B3	EIF2B3	11005	0.0021	0.31	NO
20	VHL	VHL	VHL	11033	0.0017	0.31	NO
21	EIF2S3	EIF2S3	EIF2S3	11203	-0.00066	0.3	NO
22	PRKCA	PRKCA	PRKCA	11637	-0.0066	0.27	NO
23	EIF2S2	EIF2S2	EIF2S2	11692	-0.0074	0.27	NO
24	EIF2B4	EIF2B4	EIF2B4	11756	-0.0082	0.27	NO
25	EIF2B1	EIF2B1	EIF2B1	12294	-0.016	0.25	NO
26	EIF2B2	EIF2B2	EIF2B2	12737	-0.023	0.23	NO
27	ARNT	ARNT	ARNT	12811	-0.024	0.23	NO
28	EIF1	EIF1	EIF1	13335	-0.034	0.21	NO
29	HRAS	HRAS	HRAS	14457	-0.061	0.16	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 PANCREATIC CANCER.

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

genes ES table in pathway: KEGG ENDOMETRIAL CANCER

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCND1	CCND1	CCND1	63	0.61	0.056	YES
2	EGFR	EGFR	EGFR	177	0.54	0.1	YES
3	EGF	EGF	EGF	253	0.51	0.15	YES
4	IGF1	IGF1	IGF1	303	0.49	0.19	YES
5	FGFR2	FGFR2	FGFR2	509	0.44	0.22	YES
6	LEF1	LEF1	LEF1	642	0.42	0.26	YES
7	PDGFRA	PDGFRA	PDGFRA	718	0.4	0.29	YES
8	FGFR1	FGFR1	FGFR1	776	0.4	0.32	YES
9	IGF1R	IGF1R	IGF1R	1338	0.32	0.32	YES
10	PDGFB	PDGFB	PDGFB	1444	0.31	0.35	YES
11	PDGFRB	PDGFRB	PDGFRB	1498	0.31	0.37	YES
12	FOXO1	FOXO1	FOXO1	1581	0.3	0.4	YES
13	TCF7	TCF7	TCF7	1589	0.3	0.43	YES
14	CREB3L3	CREB3L3	CREB3L3	1888	0.27	0.44	YES
15	AR	AR	AR	2130	0.25	0.45	YES
16	AKT3	AKT3	AKT3	2347	0.24	0.46	YES
17	PIK3R3	PIK3R3	PIK3R3	2395	0.23	0.48	YES
18	ERBB2	ERBB2	ERBB2	2526	0.22	0.49	YES
19	PDGFC	PDGFC	PDGFC	2757	0.21	0.5	YES
20	PDGFA	PDGFA	PDGFA	3008	0.19	0.5	YES
21	CREB3L1	CREB3L1	CREB3L1	3380	0.17	0.5	NO
22	BCL2	BCL2	BCL2	3993	0.14	0.47	NO
23	CREB3L4	CREB3L4	CREB3L4	4227	0.13	0.47	NO
24	PIK3CA	PIK3CA	PIK3CA	5255	0.095	0.42	NO
25	E2F2	E2F2	E2F2	5441	0.09	0.42	NO
26	SRD5A2	SRD5A2	SRD5A2	5723	0.083	0.41	NO
27	SOS1	SOS1	SOS1	5782	0.081	0.42	NO
28	BRAF	BRAF	BRAF	6025	0.075	0.41	NO
29	TCF7L2	TCF7L2	TCF7L2	6035	0.075	0.42	NO
30	CCNE2	CCNE2	CCNE2	6124	0.073	0.42	NO
31	CCNE1	CCNE1	CCNE1	6133	0.073	0.42	NO
32	PIK3R1	PIK3R1	PIK3R1	6522	0.065	0.41	NO
33	RB1	RB1	RB1	7562	0.047	0.35	NO
34	CREB1	CREB1	CREB1	7684	0.045	0.35	NO
35	E2F1	E2F1	E2F1	8092	0.039	0.33	NO
36	CREBBP	CREBBP	CREBBP	8220	0.037	0.33	NO
37	NRAS	NRAS	NRAS	8475	0.034	0.32	NO
38	CREB3L2	CREB3L2	CREB3L2	8600	0.032	0.31	NO
39	PTEN	PTEN	PTEN	8964	0.028	0.29	NO
40	CDK2	CDK2	CDK2	9134	0.025	0.28	NO
41	HSP90AB1	HSP90AB1	HSP90AB1	9180	0.025	0.28	NO
42	MTOR	MTOR	MTOR	9420	0.022	0.27	NO
43	EP300	EP300	EP300	9530	0.02	0.27	NO
44	E2F3	E2F3	E2F3	9827	0.017	0.25	NO
45	PIK3CG	PIK3CG	PIK3CG	9829	0.017	0.25	NO
46	IKBKB	IKBKB	IKBKB	9869	0.016	0.25	NO
47	GSK3B	GSK3B	GSK3B	10065	0.014	0.24	NO
48	ATF4	ATF4	ATF4	10071	0.014	0.24	NO
49	HSP90B1	HSP90B1	HSP90B1	10267	0.011	0.24	NO
50	MAPK1	MAPK1	MAPK1	10305	0.011	0.23	NO
51	INSRR	INSRR	INSRR	10609	0.007	0.22	NO
52	CDKN1B	CDKN1B	CDKN1B	10668	0.0064	0.21	NO
53	MAP2K2	MAP2K2	MAP2K2	10714	0.0058	0.21	NO
54	HSP90AA1	HSP90AA1	HSP90AA1	10748	0.0052	0.21	NO
55	AKT2	AKT2	AKT2	11099	0.0008	0.19	NO
56	NKX3-1	NKX3-1	NKX3-1	11234	-0.001	0.18	NO
57	PIK3CD	PIK3CD	PIK3CD	11292	-0.0018	0.18	NO
58	RAF1	RAF1	RAF1	11328	-0.0022	0.18	NO
59	PDPK1	PDPK1	PDPK1	11511	-0.0048	0.17	NO
60	KRAS	KRAS	KRAS	11523	-0.0049	0.17	NO
61	CHUK	CHUK	CHUK	11693	-0.0075	0.16	NO
62	TP53	TP53	TP53	11867	-0.0098	0.15	NO
63	RELA	RELA	RELA	12337	-0.017	0.12	NO
64	SOS2	SOS2	SOS2	12356	-0.017	0.12	NO
65	CTNNB1	CTNNB1	CTNNB1	12367	-0.018	0.12	NO
66	TGFA	TGFA	TGFA	12532	-0.02	0.12	NO
67	MAPK3	MAPK3	MAPK3	12736	-0.023	0.11	NO
68	ARAF	ARAF	ARAF	12866	-0.026	0.1	NO
69	PIK3R2	PIK3R2	PIK3R2	12876	-0.026	0.1	NO
70	TCF7L1	TCF7L1	TCF7L1	13041	-0.028	0.098	NO
71	NFKB1	NFKB1	NFKB1	13189	-0.031	0.092	NO
72	CREB3	CREB3	CREB3	13260	-0.033	0.091	NO
73	GSTP1	GSTP1	GSTP1	13655	-0.041	0.072	NO
74	IKBKG	IKBKG	IKBKG	13709	-0.042	0.073	NO
75	NFKBIA	NFKBIA	NFKBIA	13967	-0.048	0.063	NO
76	HRAS	HRAS	HRAS	14457	-0.061	0.04	NO
77	BAD	BAD	BAD	14488	-0.062	0.044	NO
78	PIK3CB	PIK3CB	PIK3CB	14720	-0.069	0.038	NO
79	AKT1	AKT1	AKT1	14735	-0.07	0.044	NO
80	PIK3R5	PIK3R5	PIK3R5	14762	-0.07	0.049	NO
81	GRB2	GRB2	GRB2	14763	-0.07	0.056	NO
82	MAP2K1	MAP2K1	MAP2K1	14788	-0.071	0.061	NO
83	CASP9	CASP9	CASP9	14790	-0.072	0.068	NO
84	MDM2	MDM2	MDM2	15207	-0.086	0.052	NO
85	PDGFD	PDGFD	PDGFD	16598	-0.2	-0.0091	NO
86	CREB5	CREB5	CREB5	16768	-0.24	0.004	NO
87	CDKN1A	CDKN1A	CDKN1A	16840	-0.25	0.024	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 ENDOMETRIAL CANCER.

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

genes ES table in pathway: KEGG PROSTATE CANCER

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	HEY2	HEY2	HEY2	99	0.58	0.14	YES
2	MAMLD1	MAMLD1	MAMLD1	278	0.5	0.24	YES
3	HES1	HES1	HES1	617	0.42	0.33	YES
4	HES5	HES5	HES5	1048	0.36	0.39	YES
5	TLE2	TLE2	TLE2	1503	0.31	0.44	YES
6	MAML2	MAML2	MAML2	1689	0.29	0.5	YES
7	HEY1	HEY1	HEY1	2862	0.2	0.48	NO
8	CDK8	CDK8	CDK8	5176	0.098	0.36	NO
9	MYC	MYC	MYC	5427	0.09	0.37	NO
10	HDAC7	HDAC7	HDAC7	5712	0.083	0.38	NO
11	HIF1A	HIF1A	HIF1A	6016	0.076	0.38	NO
12	CUL1	CUL1	CUL1	6296	0.07	0.38	NO
13	FBXW7	FBXW7	FBXW7	6399	0.067	0.39	NO
14	TBL1XR1	TBL1XR1	TBL1XR1	6863	0.058	0.37	NO
15	CCNC	CCNC	CCNC	7382	0.049	0.36	NO
16	HDAC2	HDAC2	HDAC2	7479	0.048	0.36	NO
17	CREBBP	CREBBP	CREBBP	8220	0.037	0.33	NO
18	HDAC6	HDAC6	HDAC6	8295	0.036	0.33	NO
19	HDAC1	HDAC1	HDAC1	8625	0.032	0.32	NO
20	KAT2B	KAT2B	KAT2B	9079	0.026	0.3	NO
21	HDAC8	HDAC8	HDAC8	9460	0.021	0.28	NO
22	EP300	EP300	EP300	9530	0.02	0.28	NO
23	RPS27A	RPS27A	RPS27A	9596	0.019	0.29	NO
24	TLE3	TLE3	TLE3	10001	0.015	0.27	NO
25	MAML3	MAML3	MAML3	10014	0.014	0.27	NO
26	KAT2A	KAT2A	KAT2A	10048	0.014	0.27	NO
27	RBX1	RBX1	RBX1	10054	0.014	0.27	NO
28	HEYL	HEYL	HEYL	10070	0.014	0.28	NO
29	HDAC9	HDAC9	HDAC9	10240	0.012	0.27	NO
30	MAML1	MAML1	MAML1	10694	0.006	0.24	NO
31	SNW1	SNW1	SNW1	11150	0.0002	0.22	NO
32	NCOR1	NCOR1	NCOR1	11391	-0.0031	0.2	NO
33	HDAC5	HDAC5	HDAC5	11489	-0.0044	0.2	NO
34	NCOR2	NCOR2	NCOR2	11644	-0.0067	0.19	NO
35	UBA52	UBA52	UBA52	11762	-0.0084	0.19	NO
36	RBPJ	RBPJ	RBPJ	12492	-0.02	0.15	NO
37	SKP1	SKP1	SKP1	13004	-0.028	0.13	NO
38	HDAC3	HDAC3	HDAC3	13428	-0.036	0.11	NO
39	TLE4	TLE4	TLE4	13532	-0.038	0.11	NO
40	HDAC10	HDAC10	HDAC10	14187	-0.053	0.089	NO
41	TBL1X	TBL1X	TBL1X	14360	-0.058	0.093	NO
42	HDAC11	HDAC11	HDAC11	14921	-0.075	0.078	NO
43	HDAC4	HDAC4	HDAC4	15729	-0.11	0.059	NO
44	TLE1	TLE1	TLE1	15915	-0.13	0.078	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 PROSTATE CANCER.

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

genes ES table in pathway: KEGG THYROID CANCER

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	SORBS1	SORBS1	SORBS1	50	0.63	0.058	YES
2	CDH1	CDH1	CDH1	140	0.56	0.11	YES
3	EGFR	EGFR	EGFR	177	0.54	0.16	YES
4	SNAI2	SNAI2	SNAI2	409	0.46	0.19	YES
5	TJP1	TJP1	TJP1	475	0.45	0.23	YES
6	LEF1	LEF1	LEF1	642	0.42	0.26	YES
7	MET	MET	MET	676	0.41	0.3	YES
8	FGFR1	FGFR1	FGFR1	776	0.4	0.33	YES
9	WASF1	WASF1	WASF1	894	0.38	0.36	YES
10	PTPRB	PTPRB	PTPRB	941	0.37	0.39	YES
11	WASF3	WASF3	WASF3	980	0.36	0.42	YES
12	PVRL3	PVRL3	PVRL3	1224	0.34	0.44	YES
13	PTPRM	PTPRM	PTPRM	1299	0.33	0.47	YES
14	IGF1R	IGF1R	IGF1R	1338	0.32	0.5	YES
15	PARD3	PARD3	PARD3	1378	0.32	0.53	YES
16	MLLT4	MLLT4	MLLT4	1552	0.3	0.55	YES
17	TCF7	TCF7	TCF7	1589	0.3	0.57	YES
18	RAC3	RAC3	RAC3	2504	0.22	0.54	NO
19	ERBB2	ERBB2	ERBB2	2526	0.22	0.56	NO
20	LMO7	LMO7	LMO7	3470	0.17	0.52	NO
21	SNAI1	SNAI1	SNAI1	3820	0.15	0.52	NO
22	CTNNA3	CTNNA3	CTNNA3	3921	0.14	0.52	NO
23	YES1	YES1	YES1	4089	0.14	0.53	NO
24	PVRL2	PVRL2	PVRL2	5898	0.078	0.43	NO
25	TCF7L2	TCF7L2	TCF7L2	6035	0.075	0.43	NO
26	CSNK2A1	CSNK2A1	CSNK2A1	6943	0.056	0.38	NO
27	CSNK2A2	CSNK2A2	CSNK2A2	7040	0.055	0.38	NO
28	ACP1	ACP1	ACP1	7085	0.054	0.38	NO
29	MAP3K7	MAP3K7	MAP3K7	7290	0.051	0.38	NO
30	SMAD4	SMAD4	SMAD4	7333	0.05	0.38	NO
31	TGFBR1	TGFBR1	TGFBR1	7542	0.047	0.37	NO
32	SMAD3	SMAD3	SMAD3	7609	0.046	0.37	NO
33	PVRL1	PVRL1	PVRL1	7704	0.045	0.37	NO
34	VCL	VCL	VCL	7723	0.044	0.38	NO
35	CREBBP	CREBBP	CREBBP	8220	0.037	0.35	NO
36	SMAD2	SMAD2	SMAD2	8772	0.03	0.32	NO
37	WASL	WASL	WASL	8782	0.03	0.32	NO
38	FYN	FYN	FYN	8850	0.029	0.32	NO
39	NLK	NLK	NLK	8852	0.029	0.32	NO
40	WASF2	WASF2	WASF2	9261	0.024	0.3	NO
41	ACTN3	ACTN3	ACTN3	9390	0.022	0.3	NO
42	FARP2	FARP2	FARP2	9413	0.022	0.3	NO
43	TGFBR2	TGFBR2	TGFBR2	9510	0.02	0.3	NO
44	PTPRF	PTPRF	PTPRF	9520	0.02	0.3	NO
45	EP300	EP300	EP300	9530	0.02	0.3	NO
46	BAIAP2	BAIAP2	BAIAP2	9676	0.019	0.29	NO
47	MAPK1	MAPK1	MAPK1	10305	0.011	0.26	NO
48	ACTN2	ACTN2	ACTN2	11532	-0.005	0.18	NO
49	CTNND1	CTNND1	CTNND1	11596	-0.0059	0.18	NO
50	FER	FER	FER	11748	-0.0081	0.17	NO
51	ACTN1	ACTN1	ACTN1	12073	-0.013	0.16	NO
52	CTNNB1	CTNNB1	CTNNB1	12367	-0.018	0.14	NO
53	PTPN1	PTPN1	PTPN1	12373	-0.018	0.14	NO
54	CSNK2B	CSNK2B	CSNK2B	12513	-0.02	0.14	NO
55	MAPK3	MAPK3	MAPK3	12736	-0.023	0.12	NO
56	TCF7L1	TCF7L1	TCF7L1	13041	-0.028	0.11	NO
57	RAC2	RAC2	RAC2	13438	-0.036	0.091	NO
58	ACTB	ACTB	ACTB	13587	-0.039	0.086	NO
59	ACTG1	ACTG1	ACTG1	13649	-0.041	0.086	NO
60	ACTN4	ACTN4	ACTN4	13712	-0.042	0.087	NO
61	CDC42	CDC42	CDC42	14018	-0.049	0.074	NO
62	INSR	INSR	INSR	14031	-0.049	0.078	NO
63	RHOA	RHOA	RHOA	14076	-0.05	0.08	NO
64	IQGAP1	IQGAP1	IQGAP1	14182	-0.053	0.079	NO
65	SSX2IP	SSX2IP	SSX2IP	14210	-0.054	0.082	NO
66	RAC1	RAC1	RAC1	14572	-0.064	0.068	NO
67	SRC	SRC	SRC	15443	-0.096	0.026	NO
68	WAS	WAS	WAS	15453	-0.097	0.035	NO
69	PTPRJ	PTPRJ	PTPRJ	15756	-0.12	0.029	NO
70	CTNNA1	CTNNA1	CTNNA1	15811	-0.12	0.037	NO
71	PTPN6	PTPN6	PTPN6	16139	-0.14	0.032	NO
72	PVRL4	PVRL4	PVRL4	17081	-0.35	0.01	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 THYROID CANCER.

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

genes ES table in pathway: KEGG MELANOMA

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	CCND1	CCND1	CCND1	63	0.61	0.12	YES
2	EGFR	EGFR	EGFR	177	0.54	0.22	YES
3	EGF	EGF	EGF	253	0.51	0.32	YES
4	PLCG1	PLCG1	PLCG1	686	0.41	0.37	YES
5	FHIT	FHIT	FHIT	2256	0.24	0.33	YES
6	AKT3	AKT3	AKT3	2347	0.24	0.37	YES
7	PIK3R3	PIK3R3	PIK3R3	2395	0.23	0.42	YES
8	ERBB2	ERBB2	ERBB2	2526	0.22	0.45	YES
9	CDK6	CDK6	CDK6	3866	0.15	0.4	NO
10	PIK3CA	PIK3CA	PIK3CA	5255	0.095	0.34	NO
11	E2F2	E2F2	E2F2	5441	0.09	0.35	NO
12	FOXO3	FOXO3	FOXO3	5514	0.088	0.36	NO
13	SOS1	SOS1	SOS1	5782	0.081	0.36	NO
14	BRAF	BRAF	BRAF	6025	0.075	0.36	NO
15	PIK3R1	PIK3R1	PIK3R1	6522	0.065	0.35	NO
16	PRKCB	PRKCB	PRKCB	7241	0.052	0.32	NO
17	RARB	RARB	RARB	7281	0.051	0.32	NO
18	RB1	RB1	RB1	7562	0.047	0.32	NO
19	CDK4	CDK4	CDK4	7826	0.043	0.31	NO
20	E2F1	E2F1	E2F1	8092	0.039	0.3	NO
21	NRAS	NRAS	NRAS	8475	0.034	0.29	NO
22	PLCG2	PLCG2	PLCG2	8675	0.032	0.28	NO
23	E2F3	E2F3	E2F3	9827	0.017	0.22	NO
24	PIK3CG	PIK3CG	PIK3CG	9829	0.017	0.22	NO
25	MAPK1	MAPK1	MAPK1	10305	0.011	0.2	NO
26	RXRB	RXRB	RXRB	10507	0.0082	0.19	NO
27	MAP2K2	MAP2K2	MAP2K2	10714	0.0058	0.18	NO
28	RASSF1	RASSF1	RASSF1	11085	0.001	0.15	NO
29	AKT2	AKT2	AKT2	11099	0.0008	0.15	NO
30	PIK3CD	PIK3CD	PIK3CD	11292	-0.0018	0.14	NO
31	RAF1	RAF1	RAF1	11328	-0.0022	0.14	NO
32	PDPK1	PDPK1	PDPK1	11511	-0.0048	0.13	NO
33	KRAS	KRAS	KRAS	11523	-0.0049	0.13	NO
34	PRKCA	PRKCA	PRKCA	11637	-0.0066	0.13	NO
35	TP53	TP53	TP53	11867	-0.0098	0.12	NO
36	PRKCG	PRKCG	PRKCG	12322	-0.017	0.092	NO
37	STK4	STK4	STK4	12335	-0.017	0.095	NO
38	SOS2	SOS2	SOS2	12356	-0.017	0.097	NO
39	TGFA	TGFA	TGFA	12532	-0.02	0.091	NO
40	MAPK3	MAPK3	MAPK3	12736	-0.023	0.084	NO
41	ARAF	ARAF	ARAF	12866	-0.026	0.082	NO
42	PIK3R2	PIK3R2	PIK3R2	12876	-0.026	0.086	NO
43	RASSF5	RASSF5	RASSF5	13131	-0.03	0.078	NO
44	HRAS	HRAS	HRAS	14457	-0.061	0.013	NO
45	BAD	BAD	BAD	14488	-0.062	0.023	NO
46	PIK3CB	PIK3CB	PIK3CB	14720	-0.069	0.024	NO
47	AKT1	AKT1	AKT1	14735	-0.07	0.037	NO
48	PIK3R5	PIK3R5	PIK3R5	14762	-0.07	0.049	NO
49	GRB2	GRB2	GRB2	14763	-0.07	0.063	NO
50	MAP2K1	MAP2K1	MAP2K1	14788	-0.071	0.076	NO
51	CASP9	CASP9	CASP9	14790	-0.072	0.09	NO
52	CDKN2A	CDKN2A	CDKN2A	15760	-0.12	0.057	NO
53	RXRA	RXRA	RXRA	16210	-0.15	0.061	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 MELANOMA.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MELANOMA, 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 NON SMALL CELL LUNG CANCER

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCND1	CCND1	CCND1	63	0.61	0.084	YES
2	EGFR	EGFR	EGFR	177	0.54	0.16	YES
3	EGF	EGF	EGF	253	0.51	0.22	YES
4	PGF	PGF	PGF	920	0.37	0.24	YES
5	TGFB2	TGFB2	TGFB2	1632	0.3	0.24	YES
6	VEGFA	VEGFA	VEGFA	1915	0.27	0.26	YES
7	VEGFC	VEGFC	VEGFC	2162	0.25	0.28	YES
8	FIGF	FIGF	FIGF	2170	0.25	0.32	YES
9	AKT3	AKT3	AKT3	2347	0.24	0.34	YES
10	PIK3R3	PIK3R3	PIK3R3	2395	0.23	0.37	YES
11	RAC3	RAC3	RAC3	2504	0.22	0.4	YES
12	ERBB2	ERBB2	ERBB2	2526	0.22	0.43	YES
13	TGFB3	TGFB3	TGFB3	3038	0.19	0.42	NO
14	BCL2L1	BCL2L1	BCL2L1	3673	0.16	0.41	NO
15	CDK6	CDK6	CDK6	3866	0.15	0.42	NO
16	STAT1	STAT1	STAT1	5119	0.099	0.36	NO
17	MAPK8	MAPK8	MAPK8	5228	0.096	0.37	NO
18	PIK3CA	PIK3CA	PIK3CA	5255	0.095	0.38	NO
19	E2F2	E2F2	E2F2	5441	0.09	0.38	NO
20	JAK1	JAK1	JAK1	5494	0.089	0.39	NO
21	MAPK10	MAPK10	MAPK10	6004	0.076	0.37	NO
22	BRAF	BRAF	BRAF	6025	0.075	0.38	NO
23	ARHGEF6	ARHGEF6	ARHGEF6	6032	0.075	0.39	NO
24	PIK3R1	PIK3R1	PIK3R1	6522	0.065	0.37	NO
25	SMAD4	SMAD4	SMAD4	7333	0.05	0.33	NO
26	TGFBR1	TGFBR1	TGFBR1	7542	0.047	0.33	NO
27	RB1	RB1	RB1	7562	0.047	0.33	NO
28	SMAD3	SMAD3	SMAD3	7609	0.046	0.34	NO
29	BRCA2	BRCA2	BRCA2	7761	0.044	0.34	NO
30	CDK4	CDK4	CDK4	7826	0.043	0.34	NO
31	E2F1	E2F1	E2F1	8092	0.039	0.33	NO
32	VEGFB	VEGFB	VEGFB	8280	0.036	0.32	NO
33	RALA	RALA	RALA	8314	0.036	0.33	NO
34	RALBP1	RALBP1	RALBP1	8502	0.034	0.32	NO
35	RALGDS	RALGDS	RALGDS	8570	0.033	0.32	NO
36	SMAD2	SMAD2	SMAD2	8772	0.03	0.31	NO
37	TGFBR2	TGFBR2	TGFBR2	9510	0.02	0.27	NO
38	E2F3	E2F3	E2F3	9827	0.017	0.26	NO
39	PIK3CG	PIK3CG	PIK3CG	9829	0.017	0.26	NO
40	STAT3	STAT3	STAT3	9858	0.016	0.26	NO
41	IKBKB	IKBKB	IKBKB	9869	0.016	0.26	NO
42	MAPK1	MAPK1	MAPK1	10305	0.011	0.24	NO
43	AKT2	AKT2	AKT2	11099	0.0008	0.19	NO
44	PIK3CD	PIK3CD	PIK3CD	11292	-0.0018	0.18	NO
45	RAF1	RAF1	RAF1	11328	-0.0022	0.18	NO
46	KRAS	KRAS	KRAS	11523	-0.0049	0.17	NO
47	CHUK	CHUK	CHUK	11693	-0.0075	0.16	NO
48	TP53	TP53	TP53	11867	-0.0098	0.15	NO
49	RAD51	RAD51	RAD51	12001	-0.012	0.14	NO
50	RELA	RELA	RELA	12337	-0.017	0.13	NO
51	TGFA	TGFA	TGFA	12532	-0.02	0.12	NO
52	MAPK9	MAPK9	MAPK9	12618	-0.022	0.12	NO
53	MAPK3	MAPK3	MAPK3	12736	-0.023	0.11	NO
54	ARAF	ARAF	ARAF	12866	-0.026	0.11	NO
55	PIK3R2	PIK3R2	PIK3R2	12876	-0.026	0.11	NO
56	NFKB1	NFKB1	NFKB1	13189	-0.031	0.1	NO
57	RAC2	RAC2	RAC2	13438	-0.036	0.091	NO
58	IKBKG	IKBKG	IKBKG	13709	-0.042	0.081	NO
59	CDC42	CDC42	CDC42	14018	-0.049	0.07	NO
60	PLD1	PLD1	PLD1	14316	-0.057	0.061	NO
61	BAD	BAD	BAD	14488	-0.062	0.06	NO
62	TGFB1	TGFB1	TGFB1	14565	-0.064	0.065	NO
63	RAC1	RAC1	RAC1	14572	-0.064	0.073	NO
64	PIK3CB	PIK3CB	PIK3CB	14720	-0.069	0.075	NO
65	AKT1	AKT1	AKT1	14735	-0.07	0.084	NO
66	PIK3R5	PIK3R5	PIK3R5	14762	-0.07	0.092	NO
67	MAP2K1	MAP2K1	MAP2K1	14788	-0.071	0.1	NO
68	CASP9	CASP9	CASP9	14790	-0.072	0.11	NO
69	RALB	RALB	RALB	15693	-0.11	0.075	NO
70	CDKN2A	CDKN2A	CDKN2A	15760	-0.12	0.087	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 NON SMALL CELL LUNG CANCER.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG LYSOSOME	118	genes.ES.table	0.55	1.8	0.002	0.39	0.46	0.45	0.14	0.39	0	0.093
KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS	92	genes.ES.table	0.54	1.8	0	0.32	0.59	0.42	0.16	0.36	0.1	0.079
BIOCARTA HIVNEF PATHWAY	58	genes.ES.table	0.42	1.8	0.0099	0.37	0.5	0.41	0.19	0.34	0	0.091
BIOCARTA PYK2 PATHWAY	28	genes.ES.table	0.54	1.7	0.016	0.32	0.63	0.64	0.23	0.5	0.12	0.086
BIOCARTA TOLL PATHWAY	37	genes.ES.table	0.62	1.8	0.0096	0.38	0.53	0.49	0.18	0.4	0.097	0.097
ST TUMOR NECROSIS FACTOR PATHWAY	28	genes.ES.table	0.54	1.7	0.029	0.32	0.7	0.5	0.22	0.39	0.12	0.084
PID IL1PATHWAY	34	genes.ES.table	0.57	1.8	0.0098	0.35	0.57	0.38	0.17	0.32	0.098	0.087
PID IFNGPATHWAY	40	genes.ES.table	0.53	1.7	0.02	0.32	0.66	0.55	0.25	0.41	0.12	0.086
PID IL8CXCR2 PATHWAY	34	genes.ES.table	0.6	1.7	0.01	0.31	0.67	0.59	0.2	0.47	0.12	0.08
PID MAPKTRKPATHWAY	32	genes.ES.table	0.6	2	0	0.39	0.1	0.59	0.23	0.46	0	0.075

genes ES table in pathway: KEGG LYSOSOME

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	EHD4	EHD4	EHD4	492	0.4	0.098	YES
2	PRKCD	PRKCD	PRKCD	906	0.27	0.16	YES
3	MAPK7	MAPK7	MAPK7	925	0.26	0.24	YES
4	MAP2K6	MAP2K6	MAP2K6	1062	0.24	0.31	YES
5	MAP2K1	MAP2K1	MAP2K1	1187	0.22	0.37	YES
6	FOS	FOS	FOS	1620	0.16	0.4	YES
7	CDK5	CDK5	CDK5	1630	0.16	0.45	YES
8	MEF2C	MEF2C	MEF2C	1850	0.14	0.48	YES
9	RAP1A	RAP1A	RAP1A	1908	0.14	0.52	YES
10	MAP2K3	MAP2K3	MAP2K3	2376	0.1	0.53	YES
11	EGR1	EGR1	EGR1	2873	0.079	0.52	YES
12	MAPK3	MAPK3	MAPK3	2933	0.076	0.54	YES
13	RPS6KA1	RPS6KA1	RPS6KA1	3013	0.072	0.56	YES
14	RIT1	RIT1	RIT1	3192	0.066	0.57	YES
15	MAPKAPK2	MAPKAPK2	MAPKAPK2	3527	0.054	0.57	YES
16	MAP3K2	MAP3K2	MAP3K2	3598	0.051	0.58	YES
17	MAPK14	MAPK14	MAPK14	3883	0.043	0.58	YES
18	RAP1B	RAP1B	RAP1B	3933	0.042	0.59	YES
19	MAPK1	MAPK1	MAPK1	3962	0.041	0.6	YES
20	RUSC1	RUSC1	RUSC1	4236	0.034	0.6	NO
21	RAF1	RAF1	RAF1	4606	0.025	0.58	NO
22	RPS6KA5	RPS6KA5	RPS6KA5	5244	0.012	0.55	NO
23	KRAS	KRAS	KRAS	5734	0.0021	0.52	NO
24	SRF	SRF	SRF	5822	0.00036	0.52	NO
25	NRAS	NRAS	NRAS	6219	-0.0071	0.5	NO
26	CDK5R1	CDK5R1	CDK5R1	7384	-0.028	0.44	NO
27	CREB1	CREB1	CREB1	7723	-0.033	0.43	NO
28	HRAS	HRAS	HRAS	7785	-0.034	0.44	NO
29	ELK1	ELK1	ELK1	7912	-0.036	0.44	NO
30	MAP2K5	MAP2K5	MAP2K5	8859	-0.052	0.4	NO
31	BRAF	BRAF	BRAF	10291	-0.079	0.34	NO
32	TRPV1	TRPV1	TRPV1	13783	-0.19	0.2	NO

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

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

genes ES table in pathway: KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS

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	TLR8	TLR8	TLR8	15	0.92	0.048	YES
2	TLR5	TLR5	TLR5	16	0.92	0.097	YES
3	CD14	CD14	CD14	36	0.84	0.14	YES
4	S100A12	S100A12	S100A12	55	0.8	0.18	YES
5	TLR7	TLR7	TLR7	60	0.79	0.22	YES
6	LY86	LY86	LY86	112	0.7	0.26	YES
7	TICAM2	TICAM2	TICAM2	118	0.69	0.29	YES
8	LY96	LY96	LY96	135	0.67	0.33	YES
9	NOD2	NOD2	NOD2	166	0.63	0.36	YES
10	CTSL1	CTSL1	CTSL1	205	0.59	0.39	YES
11	TLR4	TLR4	TLR4	270	0.54	0.41	YES
12	CD180	CD180	CD180	286	0.52	0.44	YES
13	CTSS	CTSS	CTSS	499	0.4	0.45	YES
14	PELI3	PELI3	PELI3	518	0.39	0.47	YES
15	TLR6	TLR6	TLR6	584	0.37	0.48	YES
16	TLR2	TLR2	TLR2	656	0.34	0.5	YES
17	TLR1	TLR1	TLR1	700	0.33	0.51	YES
18	DUSP6	DUSP6	DUSP6	702	0.33	0.53	YES
19	UNC93B1	UNC93B1	UNC93B1	807	0.3	0.54	YES
20	CTSB	CTSB	CTSB	911	0.27	0.55	YES
21	MAPK7	MAPK7	MAPK7	925	0.26	0.56	YES
22	PELI1	PELI1	PELI1	1031	0.24	0.57	YES
23	MAP2K6	MAP2K6	MAP2K6	1062	0.24	0.58	YES
24	MAP2K1	MAP2K1	MAP2K1	1187	0.22	0.58	YES
25	MYD88	MYD88	MYD88	1291	0.2	0.59	YES
26	FOS	FOS	FOS	1620	0.16	0.58	YES
27	NFKB2	NFKB2	NFKB2	1695	0.15	0.58	YES
28	MEF2C	MEF2C	MEF2C	1850	0.14	0.58	YES
29	TIRAP	TIRAP	TIRAP	1963	0.13	0.58	YES
30	TICAM1	TICAM1	TICAM1	1992	0.13	0.58	YES
31	IRAK3	IRAK3	IRAK3	2010	0.13	0.59	YES
32	EEA1	EEA1	EEA1	2117	0.12	0.59	YES
33	MAP2K3	MAP2K3	MAP2K3	2376	0.1	0.58	NO
34	CTSK	CTSK	CTSK	2442	0.1	0.58	NO
35	DUSP7	DUSP7	DUSP7	2585	0.093	0.58	NO
36	NFKBIA	NFKBIA	NFKBIA	2653	0.09	0.58	NO
37	CNPY3	CNPY3	CNPY3	2691	0.088	0.58	NO
38	CHUK	CHUK	CHUK	2910	0.078	0.57	NO
39	TLR10	TLR10	TLR10	2919	0.077	0.58	NO
40	MAPK3	MAPK3	MAPK3	2933	0.076	0.58	NO
41	IKBKG	IKBKG	IKBKG	2970	0.074	0.58	NO
42	RPS6KA1	RPS6KA1	RPS6KA1	3013	0.072	0.58	NO
43	TBK1	TBK1	TBK1	3306	0.062	0.57	NO
44	IRAK4	IRAK4	IRAK4	3430	0.058	0.57	NO
45	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	3481	0.056	0.57	NO
46	MAPKAPK2	MAPKAPK2	MAPKAPK2	3527	0.054	0.57	NO
47	PPP2CA	PPP2CA	PPP2CA	3533	0.054	0.57	NO
48	MAP3K1	MAP3K1	MAP3K1	3562	0.052	0.57	NO
49	TRAF3	TRAF3	TRAF3	3575	0.052	0.57	NO
50	IRAK1	IRAK1	IRAK1	3643	0.05	0.57	NO
51	JUN	JUN	JUN	3719	0.048	0.57	NO
52	IRF7	IRF7	IRF7	3829	0.045	0.56	NO
53	MAPK14	MAPK14	MAPK14	3883	0.043	0.56	NO
54	MAPK1	MAPK1	MAPK1	3962	0.041	0.56	NO
55	ATF1	ATF1	ATF1	3964	0.041	0.56	NO
56	DUSP3	DUSP3	DUSP3	4256	0.033	0.55	NO
57	UBE2N	UBE2N	UBE2N	4444	0.028	0.54	NO
58	RPS6KA3	RPS6KA3	RPS6KA3	4467	0.028	0.54	NO
59	MAP2K4	MAP2K4	MAP2K4	4595	0.025	0.53	NO
60	RIPK2	RIPK2	RIPK2	4619	0.025	0.53	NO
61	BTK	BTK	BTK	4725	0.022	0.53	NO
62	NFKBIB	NFKBIB	NFKBIB	4784	0.021	0.53	NO
63	MAPK9	MAPK9	MAPK9	5022	0.016	0.51	NO
64	MAPKAPK3	MAPKAPK3	MAPKAPK3	5165	0.013	0.51	NO
65	DNM2	DNM2	DNM2	5193	0.013	0.5	NO
66	RPS6KA5	RPS6KA5	RPS6KA5	5244	0.012	0.5	NO
67	PPP2CB	PPP2CB	PPP2CB	5384	0.0088	0.5	NO
68	IKBKE	IKBKE	IKBKE	5516	0.0063	0.49	NO
69	MAP2K2	MAP2K2	MAP2K2	5602	0.0045	0.48	NO
70	HSP90B1	HSP90B1	HSP90B1	5658	0.0033	0.48	NO
71	CDK1	CDK1	CDK1	5829	0.00029	0.47	NO
72	MEF2A	MEF2A	MEF2A	5888	-0.0011	0.47	NO
73	PLCG2	PLCG2	PLCG2	5915	-0.0015	0.46	NO
74	RELA	RELA	RELA	6026	-0.0035	0.46	NO
75	PPP2R1A	PPP2R1A	PPP2R1A	6098	-0.0048	0.46	NO
76	UBA52	UBA52	UBA52	6462	-0.012	0.43	NO
77	PPP2R1B	PPP2R1B	PPP2R1B	6548	-0.013	0.43	NO
78	PIK3R4	PIK3R4	PIK3R4	6617	-0.014	0.43	NO
79	MAPK10	MAPK10	MAPK10	6625	-0.014	0.43	NO
80	RIPK1	RIPK1	RIPK1	6771	-0.017	0.42	NO
81	IRF3	IRF3	IRF3	7002	-0.021	0.41	NO
82	PPP2R5D	PPP2R5D	PPP2R5D	7028	-0.022	0.41	NO
83	TAB2	TAB2	TAB2	7098	-0.023	0.4	NO
84	IKBKB	IKBKB	IKBKB	7288	-0.026	0.39	NO
85	ECSIT	ECSIT	ECSIT	7296	-0.026	0.4	NO
86	MAP3K7	MAP3K7	MAP3K7	7426	-0.028	0.39	NO
87	CREB1	CREB1	CREB1	7723	-0.033	0.37	NO
88	MAP2K7	MAP2K7	MAP2K7	7853	-0.035	0.37	NO
89	ELK1	ELK1	ELK1	7912	-0.036	0.37	NO
90	HMGB1	HMGB1	HMGB1	8037	-0.039	0.36	NO
91	S100B	S100B	S100B	8093	-0.04	0.36	NO
92	AGER	AGER	AGER	8162	-0.041	0.36	NO
93	ZFYVE20	ZFYVE20	ZFYVE20	8501	-0.046	0.34	NO
94	TRAF6	TRAF6	TRAF6	8541	-0.047	0.34	NO
95	TAB1	TAB1	TAB1	8543	-0.047	0.34	NO
96	NOD1	NOD1	NOD1	8872	-0.053	0.33	NO
97	SIGIRR	SIGIRR	SIGIRR	8907	-0.053	0.33	NO
98	TAB3	TAB3	TAB3	8990	-0.054	0.33	NO
99	RPS27A	RPS27A	RPS27A	9037	-0.055	0.33	NO
100	PELI2	PELI2	PELI2	9054	-0.056	0.33	NO
101	ATF2	ATF2	ATF2	9567	-0.066	0.3	NO
102	PIK3C3	PIK3C3	PIK3C3	9661	-0.068	0.3	NO
103	LGMN	LGMN	LGMN	10111	-0.076	0.28	NO
104	IRAK2	IRAK2	IRAK2	10996	-0.095	0.23	NO
105	TLR9	TLR9	TLR9	11686	-0.11	0.2	NO
106	DUSP4	DUSP4	DUSP4	12626	-0.14	0.15	NO
107	MAPK8	MAPK8	MAPK8	12703	-0.15	0.15	NO
108	RPS6KA2	RPS6KA2	RPS6KA2	13091	-0.16	0.14	NO
109	APP	APP	APP	15575	-0.29	0.011	NO
110	LBP	LBP	LBP	16040	-0.33	0.0014	NO
111	DNM1	DNM1	DNM1	16384	-0.37	0.001	NO
112	TLR3	TLR3	TLR3	16390	-0.37	0.02	NO
113	MAPK11	MAPK11	MAPK11	17156	-0.57	0.006	NO

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

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table 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	CD14	CD14	CD14	36	0.84	0.067	YES
2	S100A12	S100A12	S100A12	55	0.8	0.13	YES
3	TICAM2	TICAM2	TICAM2	118	0.69	0.19	YES
4	LY96	LY96	LY96	135	0.67	0.24	YES
5	NOD2	NOD2	NOD2	166	0.63	0.29	YES
6	TLR4	TLR4	TLR4	270	0.54	0.33	YES
7	PELI3	PELI3	PELI3	518	0.39	0.35	YES
8	TLR6	TLR6	TLR6	584	0.37	0.37	YES
9	TLR2	TLR2	TLR2	656	0.34	0.4	YES
10	TLR1	TLR1	TLR1	700	0.33	0.42	YES
11	DUSP6	DUSP6	DUSP6	702	0.33	0.45	YES
12	MAPK7	MAPK7	MAPK7	925	0.26	0.46	YES
13	PELI1	PELI1	PELI1	1031	0.24	0.47	YES
14	MAP2K6	MAP2K6	MAP2K6	1062	0.24	0.49	YES
15	MAP2K1	MAP2K1	MAP2K1	1187	0.22	0.5	YES
16	MYD88	MYD88	MYD88	1291	0.2	0.51	YES
17	FOS	FOS	FOS	1620	0.16	0.51	YES
18	NFKB2	NFKB2	NFKB2	1695	0.15	0.52	YES
19	MEF2C	MEF2C	MEF2C	1850	0.14	0.52	YES
20	TIRAP	TIRAP	TIRAP	1963	0.13	0.52	YES
21	TICAM1	TICAM1	TICAM1	1992	0.13	0.53	YES
22	IRAK3	IRAK3	IRAK3	2010	0.13	0.54	YES
23	MAP2K3	MAP2K3	MAP2K3	2376	0.1	0.53	NO
24	DUSP7	DUSP7	DUSP7	2585	0.093	0.52	NO
25	NFKBIA	NFKBIA	NFKBIA	2653	0.09	0.53	NO
26	CHUK	CHUK	CHUK	2910	0.078	0.52	NO
27	MAPK3	MAPK3	MAPK3	2933	0.076	0.52	NO
28	IKBKG	IKBKG	IKBKG	2970	0.074	0.53	NO
29	RPS6KA1	RPS6KA1	RPS6KA1	3013	0.072	0.53	NO
30	TBK1	TBK1	TBK1	3306	0.062	0.52	NO
31	IRAK4	IRAK4	IRAK4	3430	0.058	0.52	NO
32	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	3481	0.056	0.52	NO
33	MAPKAPK2	MAPKAPK2	MAPKAPK2	3527	0.054	0.52	NO
34	PPP2CA	PPP2CA	PPP2CA	3533	0.054	0.52	NO
35	MAP3K1	MAP3K1	MAP3K1	3562	0.052	0.53	NO
36	TRAF3	TRAF3	TRAF3	3575	0.052	0.53	NO
37	IRAK1	IRAK1	IRAK1	3643	0.05	0.53	NO
38	JUN	JUN	JUN	3719	0.048	0.53	NO
39	IRF7	IRF7	IRF7	3829	0.045	0.53	NO
40	MAPK14	MAPK14	MAPK14	3883	0.043	0.53	NO
41	MAPK1	MAPK1	MAPK1	3962	0.041	0.53	NO
42	ATF1	ATF1	ATF1	3964	0.041	0.53	NO
43	DUSP3	DUSP3	DUSP3	4256	0.033	0.52	NO
44	UBE2N	UBE2N	UBE2N	4444	0.028	0.51	NO
45	RPS6KA3	RPS6KA3	RPS6KA3	4467	0.028	0.51	NO
46	MAP2K4	MAP2K4	MAP2K4	4595	0.025	0.5	NO
47	RIPK2	RIPK2	RIPK2	4619	0.025	0.5	NO
48	BTK	BTK	BTK	4725	0.022	0.5	NO
49	NFKBIB	NFKBIB	NFKBIB	4784	0.021	0.5	NO
50	MAPK9	MAPK9	MAPK9	5022	0.016	0.49	NO
51	MAPKAPK3	MAPKAPK3	MAPKAPK3	5165	0.013	0.48	NO
52	RPS6KA5	RPS6KA5	RPS6KA5	5244	0.012	0.48	NO
53	PPP2CB	PPP2CB	PPP2CB	5384	0.0088	0.47	NO
54	IKBKE	IKBKE	IKBKE	5516	0.0063	0.46	NO
55	MAP2K2	MAP2K2	MAP2K2	5602	0.0045	0.46	NO
56	CDK1	CDK1	CDK1	5829	0.00029	0.44	NO
57	MEF2A	MEF2A	MEF2A	5888	-0.0011	0.44	NO
58	RELA	RELA	RELA	6026	-0.0035	0.43	NO
59	PPP2R1A	PPP2R1A	PPP2R1A	6098	-0.0048	0.43	NO
60	UBA52	UBA52	UBA52	6462	-0.012	0.41	NO
61	PPP2R1B	PPP2R1B	PPP2R1B	6548	-0.013	0.4	NO
62	MAPK10	MAPK10	MAPK10	6625	-0.014	0.4	NO
63	RIPK1	RIPK1	RIPK1	6771	-0.017	0.4	NO
64	IRF3	IRF3	IRF3	7002	-0.021	0.38	NO
65	PPP2R5D	PPP2R5D	PPP2R5D	7028	-0.022	0.38	NO
66	TAB2	TAB2	TAB2	7098	-0.023	0.38	NO
67	IKBKB	IKBKB	IKBKB	7288	-0.026	0.37	NO
68	ECSIT	ECSIT	ECSIT	7296	-0.026	0.37	NO
69	MAP3K7	MAP3K7	MAP3K7	7426	-0.028	0.37	NO
70	CREB1	CREB1	CREB1	7723	-0.033	0.36	NO
71	MAP2K7	MAP2K7	MAP2K7	7853	-0.035	0.35	NO
72	ELK1	ELK1	ELK1	7912	-0.036	0.35	NO
73	HMGB1	HMGB1	HMGB1	8037	-0.039	0.35	NO
74	S100B	S100B	S100B	8093	-0.04	0.35	NO
75	AGER	AGER	AGER	8162	-0.041	0.34	NO
76	TRAF6	TRAF6	TRAF6	8541	-0.047	0.33	NO
77	TAB1	TAB1	TAB1	8543	-0.047	0.33	NO
78	NOD1	NOD1	NOD1	8872	-0.053	0.32	NO
79	SIGIRR	SIGIRR	SIGIRR	8907	-0.053	0.32	NO
80	TAB3	TAB3	TAB3	8990	-0.054	0.32	NO
81	RPS27A	RPS27A	RPS27A	9037	-0.055	0.32	NO
82	PELI2	PELI2	PELI2	9054	-0.056	0.32	NO
83	ATF2	ATF2	ATF2	9567	-0.066	0.3	NO
84	IRAK2	IRAK2	IRAK2	10996	-0.095	0.22	NO
85	DUSP4	DUSP4	DUSP4	12626	-0.14	0.14	NO
86	MAPK8	MAPK8	MAPK8	12703	-0.15	0.15	NO
87	RPS6KA2	RPS6KA2	RPS6KA2	13091	-0.16	0.14	NO
88	APP	APP	APP	15575	-0.29	0.02	NO
89	TLR3	TLR3	TLR3	16390	-0.37	0.0033	NO
90	MAPK11	MAPK11	MAPK11	17156	-0.57	0.006	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 HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

Table 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	S100A12	S100A12	S100A12	55	0.8	0.078	YES
2	LY96	LY96	LY96	135	0.67	0.14	YES
3	NOD2	NOD2	NOD2	166	0.63	0.2	YES
4	TLR4	TLR4	TLR4	270	0.54	0.25	YES
5	PELI3	PELI3	PELI3	518	0.39	0.28	YES
6	TLR6	TLR6	TLR6	584	0.37	0.31	YES
7	TLR2	TLR2	TLR2	656	0.34	0.34	YES
8	TLR1	TLR1	TLR1	700	0.33	0.37	YES
9	DUSP6	DUSP6	DUSP6	702	0.33	0.41	YES
10	MAPK7	MAPK7	MAPK7	925	0.26	0.42	YES
11	PELI1	PELI1	PELI1	1031	0.24	0.44	YES
12	MAP2K6	MAP2K6	MAP2K6	1062	0.24	0.46	YES
13	MAP2K1	MAP2K1	MAP2K1	1187	0.22	0.48	YES
14	MYD88	MYD88	MYD88	1291	0.2	0.49	YES
15	FOS	FOS	FOS	1620	0.16	0.49	YES
16	NFKB2	NFKB2	NFKB2	1695	0.15	0.5	YES
17	MEF2C	MEF2C	MEF2C	1850	0.14	0.5	YES
18	TIRAP	TIRAP	TIRAP	1963	0.13	0.51	YES
19	IRAK3	IRAK3	IRAK3	2010	0.13	0.52	YES
20	MAP2K3	MAP2K3	MAP2K3	2376	0.1	0.51	YES
21	DUSP7	DUSP7	DUSP7	2585	0.093	0.51	YES
22	NFKBIA	NFKBIA	NFKBIA	2653	0.09	0.51	YES
23	CHUK	CHUK	CHUK	2910	0.078	0.51	YES
24	MAPK3	MAPK3	MAPK3	2933	0.076	0.51	YES
25	IKBKG	IKBKG	IKBKG	2970	0.074	0.52	YES
26	RPS6KA1	RPS6KA1	RPS6KA1	3013	0.072	0.52	YES
27	IRAK4	IRAK4	IRAK4	3430	0.058	0.5	NO
28	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	3481	0.056	0.51	NO
29	MAPKAPK2	MAPKAPK2	MAPKAPK2	3527	0.054	0.51	NO
30	PPP2CA	PPP2CA	PPP2CA	3533	0.054	0.52	NO
31	MAP3K1	MAP3K1	MAP3K1	3562	0.052	0.52	NO
32	IRAK1	IRAK1	IRAK1	3643	0.05	0.52	NO
33	JUN	JUN	JUN	3719	0.048	0.52	NO
34	MAPK14	MAPK14	MAPK14	3883	0.043	0.52	NO
35	MAPK1	MAPK1	MAPK1	3962	0.041	0.52	NO
36	ATF1	ATF1	ATF1	3964	0.041	0.52	NO
37	DUSP3	DUSP3	DUSP3	4256	0.033	0.51	NO
38	UBE2N	UBE2N	UBE2N	4444	0.028	0.5	NO
39	RPS6KA3	RPS6KA3	RPS6KA3	4467	0.028	0.5	NO
40	MAP2K4	MAP2K4	MAP2K4	4595	0.025	0.49	NO
41	RIPK2	RIPK2	RIPK2	4619	0.025	0.5	NO
42	BTK	BTK	BTK	4725	0.022	0.49	NO
43	NFKBIB	NFKBIB	NFKBIB	4784	0.021	0.49	NO
44	MAPK9	MAPK9	MAPK9	5022	0.016	0.48	NO
45	MAPKAPK3	MAPKAPK3	MAPKAPK3	5165	0.013	0.47	NO
46	RPS6KA5	RPS6KA5	RPS6KA5	5244	0.012	0.47	NO
47	PPP2CB	PPP2CB	PPP2CB	5384	0.0088	0.46	NO
48	MAP2K2	MAP2K2	MAP2K2	5602	0.0045	0.45	NO
49	CDK1	CDK1	CDK1	5829	0.00029	0.44	NO
50	MEF2A	MEF2A	MEF2A	5888	-0.0011	0.43	NO
51	RELA	RELA	RELA	6026	-0.0035	0.42	NO
52	PPP2R1A	PPP2R1A	PPP2R1A	6098	-0.0048	0.42	NO
53	UBA52	UBA52	UBA52	6462	-0.012	0.4	NO
54	PPP2R1B	PPP2R1B	PPP2R1B	6548	-0.013	0.4	NO
55	MAPK10	MAPK10	MAPK10	6625	-0.014	0.4	NO
56	PPP2R5D	PPP2R5D	PPP2R5D	7028	-0.022	0.37	NO
57	TAB2	TAB2	TAB2	7098	-0.023	0.37	NO
58	IKBKB	IKBKB	IKBKB	7288	-0.026	0.36	NO
59	ECSIT	ECSIT	ECSIT	7296	-0.026	0.37	NO
60	MAP3K7	MAP3K7	MAP3K7	7426	-0.028	0.36	NO
61	CREB1	CREB1	CREB1	7723	-0.033	0.35	NO
62	MAP2K7	MAP2K7	MAP2K7	7853	-0.035	0.34	NO
63	ELK1	ELK1	ELK1	7912	-0.036	0.34	NO
64	HMGB1	HMGB1	HMGB1	8037	-0.039	0.34	NO
65	S100B	S100B	S100B	8093	-0.04	0.34	NO
66	AGER	AGER	AGER	8162	-0.041	0.34	NO
67	TRAF6	TRAF6	TRAF6	8541	-0.047	0.32	NO
68	TAB1	TAB1	TAB1	8543	-0.047	0.33	NO
69	NOD1	NOD1	NOD1	8872	-0.053	0.32	NO
70	SIGIRR	SIGIRR	SIGIRR	8907	-0.053	0.32	NO
71	TAB3	TAB3	TAB3	8990	-0.054	0.32	NO
72	RPS27A	RPS27A	RPS27A	9037	-0.055	0.32	NO
73	PELI2	PELI2	PELI2	9054	-0.056	0.33	NO
74	ATF2	ATF2	ATF2	9567	-0.066	0.3	NO
75	IRAK2	IRAK2	IRAK2	10996	-0.095	0.23	NO
76	DUSP4	DUSP4	DUSP4	12626	-0.14	0.15	NO
77	MAPK8	MAPK8	MAPK8	12703	-0.15	0.16	NO
78	RPS6KA2	RPS6KA2	RPS6KA2	13091	-0.16	0.16	NO
79	APP	APP	APP	15575	-0.29	0.04	NO
80	MAPK11	MAPK11	MAPK11	17156	-0.57	0.006	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 PYK2 PATHWAY.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TOLL 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	MEFV	MEFV	MEFV	12	0.93	0.026	YES
2	TLR8	TLR8	TLR8	15	0.92	0.053	YES
3	TLR5	TLR5	TLR5	16	0.92	0.08	YES
4	CD14	CD14	CD14	36	0.84	0.1	YES
5	S100A12	S100A12	S100A12	55	0.8	0.12	YES
6	TLR7	TLR7	TLR7	60	0.79	0.15	YES
7	NLRC4	NLRC4	NLRC4	66	0.78	0.17	YES
8	CCR2	CCR2	CCR2	98	0.72	0.19	YES
9	LGALS3	LGALS3	LGALS3	110	0.7	0.21	YES
10	LY86	LY86	LY86	112	0.7	0.23	YES
11	TICAM2	TICAM2	TICAM2	118	0.69	0.25	YES
12	LY96	LY96	LY96	135	0.67	0.27	YES
13	NOD2	NOD2	NOD2	166	0.63	0.28	YES
14	CTSL1	CTSL1	CTSL1	205	0.59	0.3	YES
15	CR1	CR1	CR1	246	0.56	0.31	YES
16	C3	C3	C3	257	0.55	0.33	YES
17	AIM2	AIM2	AIM2	263	0.54	0.34	YES
18	C2	C2	C2	266	0.54	0.36	YES
19	TLR4	TLR4	TLR4	270	0.54	0.37	YES
20	CD180	CD180	CD180	286	0.52	0.39	YES
21	CD4	CD4	CD4	353	0.48	0.4	YES
22	P2RX7	P2RX7	P2RX7	475	0.41	0.4	YES
23	CTSS	CTSS	CTSS	499	0.4	0.41	YES
24	PELI3	PELI3	PELI3	518	0.39	0.42	YES
25	CASP1	CASP1	CASP1	578	0.37	0.43	YES
26	NLRP3	NLRP3	NLRP3	580	0.37	0.44	YES
27	TLR6	TLR6	TLR6	584	0.37	0.45	YES
28	TLR2	TLR2	TLR2	656	0.34	0.46	YES
29	CFB	CFB	CFB	697	0.33	0.46	YES
30	TLR1	TLR1	TLR1	700	0.33	0.47	YES
31	DUSP6	DUSP6	DUSP6	702	0.33	0.48	YES
32	CARD9	CARD9	CARD9	735	0.32	0.49	YES
33	UNC93B1	UNC93B1	UNC93B1	807	0.3	0.49	YES
34	NLRP1	NLRP1	NLRP1	845	0.29	0.5	YES
35	C1QA	C1QA	C1QA	851	0.29	0.51	YES
36	UBE2D1	UBE2D1	UBE2D1	904	0.27	0.51	YES
37	CTSB	CTSB	CTSB	911	0.27	0.52	YES
38	PSTPIP1	PSTPIP1	PSTPIP1	912	0.27	0.53	YES
39	MAPK7	MAPK7	MAPK7	925	0.26	0.54	YES
40	PELI1	PELI1	PELI1	1031	0.24	0.54	YES
41	MAP2K6	MAP2K6	MAP2K6	1062	0.24	0.54	YES
42	DEFB1	DEFB1	DEFB1	1065	0.24	0.55	YES
43	CFD	CFD	CFD	1128	0.23	0.55	YES
44	PYCARD	PYCARD	PYCARD	1182	0.22	0.55	YES
45	MAP2K1	MAP2K1	MAP2K1	1187	0.22	0.56	YES
46	MYD88	MYD88	MYD88	1291	0.2	0.56	YES
47	RNF135	RNF135	RNF135	1337	0.2	0.56	YES
48	FOS	FOS	FOS	1620	0.16	0.55	YES
49	C4BPA	C4BPA	C4BPA	1646	0.16	0.56	YES
50	NFKB2	NFKB2	NFKB2	1695	0.15	0.56	YES
51	CAPZA2	CAPZA2	CAPZA2	1716	0.15	0.56	YES
52	MEF2C	MEF2C	MEF2C	1850	0.14	0.56	YES
53	RIPK3	RIPK3	RIPK3	1910	0.14	0.56	YES
54	TIRAP	TIRAP	TIRAP	1963	0.13	0.56	YES
55	TICAM1	TICAM1	TICAM1	1992	0.13	0.56	YES
56	IRAK3	IRAK3	IRAK3	2010	0.13	0.56	YES
57	EEA1	EEA1	EEA1	2117	0.12	0.56	YES
58	C1QC	C1QC	C1QC	2168	0.12	0.56	YES
59	C5	C5	C5	2285	0.11	0.56	YES
60	IRF2	IRF2	IRF2	2345	0.11	0.56	YES
61	CD55	CD55	CD55	2370	0.1	0.56	YES
62	MAP2K3	MAP2K3	MAP2K3	2376	0.1	0.56	YES
63	CAPZA1	CAPZA1	CAPZA1	2385	0.1	0.56	YES
64	CTSK	CTSK	CTSK	2442	0.1	0.56	YES
65	C1QB	C1QB	C1QB	2455	0.1	0.56	YES
66	TANK	TANK	TANK	2539	0.096	0.56	YES
67	DUSP7	DUSP7	DUSP7	2585	0.093	0.56	YES
68	MAPK13	MAPK13	MAPK13	2590	0.093	0.56	YES
69	NFKBIA	NFKBIA	NFKBIA	2653	0.09	0.56	NO
70	CNPY3	CNPY3	CNPY3	2691	0.088	0.56	NO
71	BIRC3	BIRC3	BIRC3	2767	0.084	0.56	NO
72	DEFA4	DEFA4	DEFA4	2782	0.083	0.56	NO
73	TXNIP	TXNIP	TXNIP	2867	0.079	0.56	NO
74	CHUK	CHUK	CHUK	2910	0.078	0.56	NO
75	TLR10	TLR10	TLR10	2919	0.077	0.56	NO
76	MAPK3	MAPK3	MAPK3	2933	0.076	0.56	NO
77	IKBKG	IKBKG	IKBKG	2970	0.074	0.56	NO
78	RPS6KA1	RPS6KA1	RPS6KA1	3013	0.072	0.56	NO
79	ZBP1	ZBP1	ZBP1	3067	0.071	0.56	NO
80	PANX1	PANX1	PANX1	3089	0.07	0.56	NO
81	TNFAIP3	TNFAIP3	TNFAIP3	3174	0.066	0.56	NO
82	FADD	FADD	FADD	3265	0.063	0.56	NO
83	TBK1	TBK1	TBK1	3306	0.062	0.56	NO
84	IRAK4	IRAK4	IRAK4	3430	0.058	0.55	NO
85	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	3481	0.056	0.55	NO
86	MAPKAPK2	MAPKAPK2	MAPKAPK2	3527	0.054	0.55	NO
87	PPP2CA	PPP2CA	PPP2CA	3533	0.054	0.55	NO
88	MAP3K1	MAP3K1	MAP3K1	3562	0.052	0.55	NO
89	TRAF3	TRAF3	TRAF3	3575	0.052	0.55	NO
90	IRAK1	IRAK1	IRAK1	3643	0.05	0.55	NO
91	JUN	JUN	JUN	3719	0.048	0.55	NO
92	IRF7	IRF7	IRF7	3829	0.045	0.54	NO
93	TRIM25	TRIM25	TRIM25	3872	0.043	0.54	NO
94	MAPK14	MAPK14	MAPK14	3883	0.043	0.54	NO
95	MAPK1	MAPK1	MAPK1	3962	0.041	0.54	NO
96	ATF1	ATF1	ATF1	3964	0.041	0.54	NO
97	HERC5	HERC5	HERC5	4120	0.037	0.53	NO
98	DUSP3	DUSP3	DUSP3	4256	0.033	0.52	NO
99	ISG15	ISG15	ISG15	4259	0.033	0.52	NO
100	IRF1	IRF1	IRF1	4276	0.033	0.52	NO
101	CD46	CD46	CD46	4286	0.032	0.52	NO
102	TAX1BP1	TAX1BP1	TAX1BP1	4399	0.03	0.52	NO
103	UBE2N	UBE2N	UBE2N	4444	0.028	0.52	NO
104	RPS6KA3	RPS6KA3	RPS6KA3	4467	0.028	0.52	NO
105	ATG5	ATG5	ATG5	4561	0.026	0.51	NO
106	MAP2K4	MAP2K4	MAP2K4	4595	0.025	0.51	NO
107	RIPK2	RIPK2	RIPK2	4619	0.025	0.51	NO
108	CASP10	CASP10	CASP10	4628	0.025	0.51	NO
109	DAK	DAK	DAK	4650	0.024	0.51	NO
110	BIRC2	BIRC2	BIRC2	4666	0.024	0.51	NO
111	BTK	BTK	BTK	4725	0.022	0.51	NO
112	NFKBIB	NFKBIB	NFKBIB	4784	0.021	0.5	NO
113	UBE2D3	UBE2D3	UBE2D3	4844	0.02	0.5	NO
114	CREBBP	CREBBP	CREBBP	4926	0.018	0.5	NO
115	MAPK9	MAPK9	MAPK9	5022	0.016	0.49	NO
116	EP300	EP300	EP300	5126	0.014	0.48	NO
117	CASP9	CASP9	CASP9	5131	0.014	0.48	NO
118	MAPKAPK3	MAPKAPK3	MAPKAPK3	5165	0.013	0.48	NO
119	NLRC5	NLRC5	NLRC5	5188	0.013	0.48	NO
120	DNM2	DNM2	DNM2	5193	0.013	0.48	NO
121	RPS6KA5	RPS6KA5	RPS6KA5	5244	0.012	0.48	NO
122	PPP2CB	PPP2CB	PPP2CB	5384	0.0088	0.47	NO
123	DDOST	DDOST	DDOST	5391	0.0087	0.47	NO
124	ATG12	ATG12	ATG12	5452	0.0076	0.47	NO
125	DEFA1B	DEFA1B	DEFA1B	5496	0.0067	0.47	NO
126	IKBKE	IKBKE	IKBKE	5516	0.0063	0.47	NO
127	UBE2D2	UBE2D2	UBE2D2	5579	0.0049	0.46	NO
128	MAP2K2	MAP2K2	MAP2K2	5602	0.0045	0.46	NO
129	HSP90B1	HSP90B1	HSP90B1	5658	0.0033	0.46	NO
130	DDX58	DDX58	DDX58	5685	0.0028	0.46	NO
131	CASP4	CASP4	CASP4	5765	0.0015	0.45	NO
132	CDK1	CDK1	CDK1	5829	0.00029	0.45	NO
133	MEF2A	MEF2A	MEF2A	5888	-0.0011	0.44	NO
134	PLCG2	PLCG2	PLCG2	5915	-0.0015	0.44	NO
135	NLRX1	NLRX1	NLRX1	5958	-0.0022	0.44	NO
136	RELA	RELA	RELA	6026	-0.0035	0.44	NO
137	PPP2R1A	PPP2R1A	PPP2R1A	6098	-0.0048	0.43	NO
138	C4BPB	C4BPB	C4BPB	6283	-0.0079	0.42	NO
139	UBE2K	UBE2K	UBE2K	6422	-0.011	0.42	NO
140	UBA52	UBA52	UBA52	6462	-0.012	0.41	NO
141	DHX58	DHX58	DHX58	6490	-0.012	0.41	NO
142	PPP2R1B	PPP2R1B	PPP2R1B	6548	-0.013	0.41	NO
143	PIK3R4	PIK3R4	PIK3R4	6617	-0.014	0.4	NO
144	PCBP2	PCBP2	PCBP2	6622	-0.014	0.4	NO
145	MAPK10	MAPK10	MAPK10	6625	-0.014	0.4	NO
146	RIPK1	RIPK1	RIPK1	6771	-0.017	0.4	NO
147	IRF3	IRF3	IRF3	7002	-0.021	0.38	NO
148	PPP2R5D	PPP2R5D	PPP2R5D	7028	-0.022	0.38	NO
149	TAB2	TAB2	TAB2	7098	-0.023	0.38	NO
150	CASP8	CASP8	CASP8	7222	-0.025	0.37	NO
151	IKBKB	IKBKB	IKBKB	7288	-0.026	0.37	NO
152	ECSIT	ECSIT	ECSIT	7296	-0.026	0.37	NO
153	MAP3K7	MAP3K7	MAP3K7	7426	-0.028	0.36	NO
154	CYLD	CYLD	CYLD	7531	-0.03	0.36	NO
155	CREB1	CREB1	CREB1	7723	-0.033	0.35	NO
156	UBA7	UBA7	UBA7	7772	-0.034	0.35	NO
157	PRKCSH	PRKCSH	PRKCSH	7822	-0.035	0.34	NO
158	MAP2K7	MAP2K7	MAP2K7	7853	-0.035	0.34	NO
159	ELK1	ELK1	ELK1	7912	-0.036	0.34	NO
160	MAVS	MAVS	MAVS	7974	-0.038	0.34	NO
161	HMGB1	HMGB1	HMGB1	8037	-0.039	0.34	NO
162	OTUD5	OTUD5	OTUD5	8088	-0.04	0.34	NO
163	S100B	S100B	S100B	8093	-0.04	0.34	NO
164	CASP2	CASP2	CASP2	8112	-0.04	0.34	NO
165	PIN1	PIN1	PIN1	8117	-0.04	0.34	NO
166	AGER	AGER	AGER	8162	-0.041	0.34	NO
167	IFIH1	IFIH1	IFIH1	8214	-0.042	0.33	NO
168	UBE2L6	UBE2L6	UBE2L6	8337	-0.044	0.33	NO
169	SIKE1	SIKE1	SIKE1	8391	-0.045	0.33	NO
170	ZFYVE20	ZFYVE20	ZFYVE20	8501	-0.046	0.32	NO
171	TRAF6	TRAF6	TRAF6	8541	-0.047	0.32	NO
172	TAB1	TAB1	TAB1	8543	-0.047	0.32	NO
173	TXN	TXN	TXN	8768	-0.051	0.31	NO
174	NOD1	NOD1	NOD1	8872	-0.053	0.3	NO
175	SIGIRR	SIGIRR	SIGIRR	8907	-0.053	0.3	NO
176	TAB3	TAB3	TAB3	8990	-0.054	0.3	NO
177	RPS27A	RPS27A	RPS27A	9037	-0.055	0.3	NO
178	PELI2	PELI2	PELI2	9054	-0.056	0.3	NO
179	ATF2	ATF2	ATF2	9567	-0.066	0.27	NO
180	PIK3C3	PIK3C3	PIK3C3	9661	-0.068	0.27	NO
181	LGMN	LGMN	LGMN	10111	-0.076	0.25	NO
182	HSP90AB1	HSP90AB1	HSP90AB1	10218	-0.078	0.24	NO
183	IRAK2	IRAK2	IRAK2	10996	-0.095	0.2	NO
184	ART1	ART1	ART1	11130	-0.099	0.19	NO
185	C4A	C4A	C4A	11397	-0.11	0.18	NO
186	TLR9	TLR9	TLR9	11686	-0.11	0.17	NO
187	TRAF2	TRAF2	TRAF2	11789	-0.12	0.16	NO
188	CCR6	CCR6	CCR6	11935	-0.12	0.16	NO
189	PROS1	PROS1	PROS1	12123	-0.13	0.15	NO
190	MASP2	MASP2	MASP2	12471	-0.14	0.14	NO
191	C7	C7	C7	12599	-0.14	0.13	NO
192	DUSP4	DUSP4	DUSP4	12626	-0.14	0.14	NO
193	MAPK8	MAPK8	MAPK8	12703	-0.15	0.14	NO
194	RNF125	RNF125	RNF125	12704	-0.15	0.14	NO
195	RPS6KA2	RPS6KA2	RPS6KA2	13091	-0.16	0.12	NO
196	C8G	C8G	C8G	13288	-0.17	0.12	NO
197	BCL2L1	BCL2L1	BCL2L1	13818	-0.19	0.09	NO
198	BCL2	BCL2	BCL2	14661	-0.23	0.047	NO
199	CFI	CFI	CFI	14719	-0.24	0.051	NO
200	IFNA21	IFNA21	IFNA21	15133	-0.26	0.034	NO
201	CFH	CFH	CFH	15423	-0.28	0.025	NO
202	MAPK12	MAPK12	MAPK12	15521	-0.29	0.028	NO
203	APP	APP	APP	15575	-0.29	0.033	NO
204	C1S	C1S	C1S	15615	-0.3	0.04	NO
205	IFNB1	IFNB1	IFNB1	15680	-0.3	0.045	NO
206	LBP	LBP	LBP	16040	-0.33	0.033	NO
207	DNM1	DNM1	DNM1	16384	-0.37	0.024	NO
208	TLR3	TLR3	TLR3	16390	-0.37	0.034	NO
209	MAPK11	MAPK11	MAPK11	17156	-0.57	0.006	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 TOLL PATHWAY.

Figure S30. 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: ST TUMOR NECROSIS FACTOR 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	TLR8	TLR8	TLR8	15	0.92	0.1	YES
2	S100A12	S100A12	S100A12	55	0.8	0.19	YES
3	TLR7	TLR7	TLR7	60	0.79	0.27	YES
4	NOD2	NOD2	NOD2	166	0.63	0.34	YES
5	PELI3	PELI3	PELI3	518	0.39	0.36	YES
6	DUSP6	DUSP6	DUSP6	702	0.33	0.38	YES
7	MAPK7	MAPK7	MAPK7	925	0.26	0.4	YES
8	PELI1	PELI1	PELI1	1031	0.24	0.42	YES
9	MAP2K6	MAP2K6	MAP2K6	1062	0.24	0.45	YES
10	MAP2K1	MAP2K1	MAP2K1	1187	0.22	0.46	YES
11	MYD88	MYD88	MYD88	1291	0.2	0.48	YES
12	FOS	FOS	FOS	1620	0.16	0.48	YES
13	NFKB2	NFKB2	NFKB2	1695	0.15	0.49	YES
14	MEF2C	MEF2C	MEF2C	1850	0.14	0.5	YES
15	MAP2K3	MAP2K3	MAP2K3	2376	0.1	0.48	NO
16	DUSP7	DUSP7	DUSP7	2585	0.093	0.48	NO
17	NFKBIA	NFKBIA	NFKBIA	2653	0.09	0.48	NO
18	CHUK	CHUK	CHUK	2910	0.078	0.48	NO
19	MAPK3	MAPK3	MAPK3	2933	0.076	0.48	NO
20	IKBKG	IKBKG	IKBKG	2970	0.074	0.49	NO
21	RPS6KA1	RPS6KA1	RPS6KA1	3013	0.072	0.49	NO
22	IRAK4	IRAK4	IRAK4	3430	0.058	0.48	NO
23	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	3481	0.056	0.48	NO
24	MAPKAPK2	MAPKAPK2	MAPKAPK2	3527	0.054	0.48	NO
25	PPP2CA	PPP2CA	PPP2CA	3533	0.054	0.49	NO
26	MAP3K1	MAP3K1	MAP3K1	3562	0.052	0.49	NO
27	IRAK1	IRAK1	IRAK1	3643	0.05	0.49	NO
28	JUN	JUN	JUN	3719	0.048	0.49	NO
29	MAPK14	MAPK14	MAPK14	3883	0.043	0.49	NO
30	MAPK1	MAPK1	MAPK1	3962	0.041	0.49	NO
31	ATF1	ATF1	ATF1	3964	0.041	0.49	NO
32	DUSP3	DUSP3	DUSP3	4256	0.033	0.48	NO
33	UBE2N	UBE2N	UBE2N	4444	0.028	0.47	NO
34	RPS6KA3	RPS6KA3	RPS6KA3	4467	0.028	0.48	NO
35	MAP2K4	MAP2K4	MAP2K4	4595	0.025	0.47	NO
36	RIPK2	RIPK2	RIPK2	4619	0.025	0.47	NO
37	NFKBIB	NFKBIB	NFKBIB	4784	0.021	0.46	NO
38	MAPK9	MAPK9	MAPK9	5022	0.016	0.45	NO
39	MAPKAPK3	MAPKAPK3	MAPKAPK3	5165	0.013	0.45	NO
40	RPS6KA5	RPS6KA5	RPS6KA5	5244	0.012	0.44	NO
41	PPP2CB	PPP2CB	PPP2CB	5384	0.0088	0.44	NO
42	MAP2K2	MAP2K2	MAP2K2	5602	0.0045	0.42	NO
43	CDK1	CDK1	CDK1	5829	0.00029	0.41	NO
44	MEF2A	MEF2A	MEF2A	5888	-0.0011	0.41	NO
45	RELA	RELA	RELA	6026	-0.0035	0.4	NO
46	PPP2R1A	PPP2R1A	PPP2R1A	6098	-0.0048	0.4	NO
47	UBA52	UBA52	UBA52	6462	-0.012	0.38	NO
48	PPP2R1B	PPP2R1B	PPP2R1B	6548	-0.013	0.37	NO
49	MAPK10	MAPK10	MAPK10	6625	-0.014	0.37	NO
50	PPP2R5D	PPP2R5D	PPP2R5D	7028	-0.022	0.35	NO
51	TAB2	TAB2	TAB2	7098	-0.023	0.35	NO
52	IKBKB	IKBKB	IKBKB	7288	-0.026	0.34	NO
53	ECSIT	ECSIT	ECSIT	7296	-0.026	0.34	NO
54	MAP3K7	MAP3K7	MAP3K7	7426	-0.028	0.34	NO
55	CREB1	CREB1	CREB1	7723	-0.033	0.32	NO
56	MAP2K7	MAP2K7	MAP2K7	7853	-0.035	0.32	NO
57	ELK1	ELK1	ELK1	7912	-0.036	0.32	NO
58	HMGB1	HMGB1	HMGB1	8037	-0.039	0.32	NO
59	S100B	S100B	S100B	8093	-0.04	0.32	NO
60	AGER	AGER	AGER	8162	-0.041	0.32	NO
61	TRAF6	TRAF6	TRAF6	8541	-0.047	0.3	NO
62	TAB1	TAB1	TAB1	8543	-0.047	0.31	NO
63	NOD1	NOD1	NOD1	8872	-0.053	0.29	NO
64	TAB3	TAB3	TAB3	8990	-0.054	0.29	NO
65	RPS27A	RPS27A	RPS27A	9037	-0.055	0.3	NO
66	PELI2	PELI2	PELI2	9054	-0.056	0.3	NO
67	ATF2	ATF2	ATF2	9567	-0.066	0.28	NO
68	IRAK2	IRAK2	IRAK2	10996	-0.095	0.21	NO
69	TLR9	TLR9	TLR9	11686	-0.11	0.18	NO
70	DUSP4	DUSP4	DUSP4	12626	-0.14	0.14	NO
71	MAPK8	MAPK8	MAPK8	12703	-0.15	0.15	NO
72	RPS6KA2	RPS6KA2	RPS6KA2	13091	-0.16	0.15	NO
73	APP	APP	APP	15575	-0.29	0.035	NO
74	MAPK11	MAPK11	MAPK11	17156	-0.57	0.006	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: ST TUMOR NECROSIS FACTOR PATHWAY.

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

genes ES table in pathway: PID IL1PATHWAY

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	SLC11A1	SLC11A1	SLC11A1	32	0.85	0.041	YES
2	SORT1	SORT1	SORT1	131	0.67	0.069	YES
3	CTSL1	CTSL1	CTSL1	205	0.59	0.095	YES
4	CTSH	CTSH	CTSH	207	0.59	0.12	YES
5	SGSH	SGSH	SGSH	239	0.56	0.15	YES
6	CTSL2	CTSL2	CTSL2	291	0.52	0.18	YES
7	CD68	CD68	CD68	321	0.5	0.2	YES
8	AP1S2	AP1S2	AP1S2	462	0.42	0.21	YES
9	CTSS	CTSS	CTSS	499	0.4	0.23	YES
10	IGF2R	IGF2R	IGF2R	506	0.4	0.25	YES
11	AP1S3	AP1S3	AP1S3	531	0.39	0.27	YES
12	CTSZ	CTSZ	CTSZ	601	0.36	0.28	YES
13	ARSG	ARSG	ARSG	616	0.36	0.3	YES
14	NAGA	NAGA	NAGA	689	0.33	0.31	YES
15	GAA	GAA	GAA	731	0.32	0.32	YES
16	HEXB	HEXB	HEXB	742	0.32	0.34	YES
17	CLTCL1	CLTCL1	CLTCL1	802	0.3	0.35	YES
18	PSAP	PSAP	PSAP	894	0.28	0.36	YES
19	CTSB	CTSB	CTSB	911	0.27	0.37	YES
20	GNS	GNS	GNS	940	0.26	0.38	YES
21	FUCA1	FUCA1	FUCA1	969	0.25	0.4	YES
22	ATP6V0D1	ATP6V0D1	ATP6V0D1	1024	0.24	0.4	YES
23	CTSD	CTSD	CTSD	1140	0.23	0.41	YES
24	TCIRG1	TCIRG1	TCIRG1	1181	0.22	0.42	YES
25	NPC2	NPC2	NPC2	1190	0.22	0.43	YES
26	GM2A	GM2A	GM2A	1216	0.21	0.44	YES
27	ATP6V0A1	ATP6V0A1	ATP6V0A1	1327	0.2	0.44	YES
28	MCOLN1	MCOLN1	MCOLN1	1368	0.19	0.45	YES
29	LIPA	LIPA	LIPA	1481	0.18	0.45	YES
30	PPT1	PPT1	PPT1	1586	0.17	0.45	YES
31	LAPTM5	LAPTM5	LAPTM5	1680	0.16	0.46	YES
32	PLA2G15	PLA2G15	PLA2G15	1682	0.16	0.46	YES
33	AP1S1	AP1S1	AP1S1	1782	0.15	0.46	YES
34	SLC17A5	SLC17A5	SLC17A5	1844	0.14	0.47	YES
35	GBA	GBA	GBA	1859	0.14	0.48	YES
36	MAN2B1	MAN2B1	MAN2B1	1861	0.14	0.48	YES
37	ASAH1	ASAH1	ASAH1	1918	0.14	0.48	YES
38	ARSB	ARSB	ARSB	1947	0.13	0.49	YES
39	TPP1	TPP1	TPP1	1955	0.13	0.5	YES
40	GUSB	GUSB	GUSB	1998	0.13	0.5	YES
41	CD63	CD63	CD63	2027	0.13	0.5	YES
42	ACP2	ACP2	ACP2	2049	0.13	0.51	YES
43	GGA2	GGA2	GGA2	2071	0.12	0.52	YES
44	SMPD1	SMPD1	SMPD1	2116	0.12	0.52	YES
45	GLB1	GLB1	GLB1	2122	0.12	0.52	YES
46	ATP6V0B	ATP6V0B	ATP6V0B	2147	0.12	0.53	YES
47	NAGPA	NAGPA	NAGPA	2167	0.12	0.54	YES
48	NEU1	NEU1	NEU1	2189	0.12	0.54	YES
49	ATP6V0C	ATP6V0C	ATP6V0C	2193	0.12	0.55	YES
50	CTSA	CTSA	CTSA	2197	0.12	0.55	YES
51	CLTB	CLTB	CLTB	2355	0.11	0.55	YES
52	CTSO	CTSO	CTSO	2427	0.1	0.55	YES
53	CTSK	CTSK	CTSK	2442	0.1	0.55	YES
54	SUMF1	SUMF1	SUMF1	2744	0.086	0.54	NO
55	CLTA	CLTA	CLTA	2809	0.082	0.54	NO
56	HYAL1	HYAL1	HYAL1	2831	0.081	0.54	NO
57	ARSA	ARSA	ARSA	2837	0.081	0.55	NO
58	GLA	GLA	GLA	2866	0.079	0.55	NO
59	GALC	GALC	GALC	2966	0.075	0.55	NO
60	AP1M1	AP1M1	AP1M1	3119	0.068	0.54	NO
61	AGA	AGA	AGA	3153	0.067	0.54	NO
62	AP3B1	AP3B1	AP3B1	3215	0.065	0.54	NO
63	AP3S1	AP3S1	AP3S1	3317	0.061	0.54	NO
64	M6PR	M6PR	M6PR	3338	0.061	0.54	NO
65	LAMP1	LAMP1	LAMP1	3356	0.06	0.54	NO
66	ACP5	ACP5	ACP5	3402	0.059	0.54	NO
67	CTSG	CTSG	CTSG	3416	0.058	0.55	NO
68	SCARB2	SCARB2	SCARB2	3417	0.058	0.55	NO
69	CLN3	CLN3	CLN3	3458	0.056	0.55	NO
70	GALNS	GALNS	GALNS	3791	0.046	0.53	NO
71	CLTC	CLTC	CLTC	3792	0.046	0.53	NO
72	HEXA	HEXA	HEXA	3817	0.045	0.54	NO
73	MANBA	MANBA	MANBA	3942	0.042	0.53	NO
74	AP3S2	AP3S2	AP3S2	3952	0.041	0.53	NO
75	CLN5	CLN5	CLN5	4050	0.039	0.53	NO
76	NPC1	NPC1	NPC1	4261	0.033	0.52	NO
77	ATP6AP1	ATP6AP1	ATP6AP1	4396	0.03	0.51	NO
78	AP3D1	AP3D1	AP3D1	4411	0.029	0.51	NO
79	GNPTG	GNPTG	GNPTG	4460	0.028	0.51	NO
80	LAMP2	LAMP2	LAMP2	4617	0.025	0.5	NO
81	AP4E1	AP4E1	AP4E1	4770	0.022	0.5	NO
82	AP3M1	AP3M1	AP3M1	5038	0.016	0.48	NO
83	ATP6V1H	ATP6V1H	ATP6V1H	5073	0.015	0.48	NO
84	AP1B1	AP1B1	AP1B1	5152	0.014	0.48	NO
85	ENTPD4	ENTPD4	ENTPD4	5303	0.01	0.47	NO
86	CTSC	CTSC	CTSC	5497	0.0067	0.46	NO
87	NAGLU	NAGLU	NAGLU	5761	0.0016	0.44	NO
88	CTNS	CTNS	CTNS	5812	0.0005	0.44	NO
89	AP1G1	AP1G1	AP1G1	5914	-0.0015	0.43	NO
90	LAPTM4A	LAPTM4A	LAPTM4A	6061	-0.0041	0.42	NO
91	GGA3	GGA3	GGA3	6083	-0.0046	0.42	NO
92	GGA1	GGA1	GGA1	6561	-0.013	0.4	NO
93	HGSNAT	HGSNAT	HGSNAT	7469	-0.029	0.34	NO
94	AP4M1	AP4M1	AP4M1	7668	-0.032	0.33	NO
95	SLC11A2	SLC11A2	SLC11A2	7679	-0.032	0.34	NO
96	AP4B1	AP4B1	AP4B1	7819	-0.035	0.33	NO
97	GNPTAB	GNPTAB	GNPTAB	8818	-0.052	0.27	NO
98	IDS	IDS	IDS	9595	-0.066	0.23	NO
99	DNASE2	DNASE2	DNASE2	9617	-0.067	0.23	NO
100	CD164	CD164	CD164	9758	-0.069	0.23	NO
101	LGMN	LGMN	LGMN	10111	-0.076	0.21	NO
102	ATP6V0D2	ATP6V0D2	ATP6V0D2	10596	-0.086	0.19	NO
103	AP3B2	AP3B2	AP3B2	11149	-0.1	0.16	NO
104	IDUA	IDUA	IDUA	11557	-0.11	0.14	NO
105	ATP6V0A2	ATP6V0A2	ATP6V0A2	11852	-0.12	0.13	NO
106	AP1M2	AP1M2	AP1M2	12231	-0.13	0.12	NO
107	MFSD8	MFSD8	MFSD8	12569	-0.14	0.1	NO
108	AP4S1	AP4S1	AP4S1	13620	-0.18	0.051	NO
109	AP3M2	AP3M2	AP3M2	13748	-0.19	0.054	NO
110	NAPSA	NAPSA	NAPSA	14485	-0.22	0.022	NO
111	LAMP3	LAMP3	LAMP3	14832	-0.24	0.014	NO
112	CTSW	CTSW	CTSW	15259	-0.27	0.0027	NO
113	ABCA2	ABCA2	ABCA2	15517	-0.29	0.0023	NO
114	ABCB9	ABCB9	ABCB9	15752	-0.31	0.0041	NO
115	PPT2	PPT2	PPT2	15999	-0.33	0.0064	NO
116	CTSE	CTSE	CTSE	16315	-0.36	0.0063	NO
117	LAPTM4B	LAPTM4B	LAPTM4B	16911	-0.47	-0.0048	NO
118	CTSF	CTSF	CTSF	17000	-0.5	0.015	NO

Figure S33. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID IL1PATHWAY.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: PID IL1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID IFNGPATHWAY

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	TNFRSF1B	TNFRSF1B	TNFRSF1B	282	0.53	0.08	YES
2	LMNA	LMNA	LMNA	850	0.29	0.1	YES
3	PRKCD	PRKCD	PRKCD	906	0.27	0.15	YES
4	TNF	TNF	TNF	927	0.26	0.19	YES
5	APAF1	APAF1	APAF1	1530	0.17	0.19	YES
6	GSN	GSN	GSN	1765	0.15	0.2	YES
7	PTK2	PTK2	PTK2	1791	0.14	0.23	YES
8	FAS	FAS	FAS	1961	0.13	0.24	YES
9	MDM2	MDM2	MDM2	2078	0.12	0.26	YES
10	PSEN2	PSEN2	PSEN2	2175	0.12	0.28	YES
11	BID	BID	BID	2320	0.11	0.29	YES
12	PSEN1	PSEN1	PSEN1	2415	0.1	0.3	YES
13	LMNB1	LMNB1	LMNB1	2466	0.099	0.32	YES
14	NFKB1	NFKB1	NFKB1	2508	0.097	0.33	YES
15	NFKBIA	NFKBIA	NFKBIA	2653	0.09	0.34	YES
16	BIRC3	BIRC3	BIRC3	2767	0.084	0.35	YES
17	CHUK	CHUK	CHUK	2910	0.078	0.35	YES
18	ARHGDIB	ARHGDIB	ARHGDIB	2939	0.076	0.37	YES
19	CFLAR	CFLAR	CFLAR	2998	0.073	0.38	YES
20	MAP3K14	MAP3K14	MAP3K14	3070	0.07	0.38	YES
21	RB1	RB1	RB1	3166	0.067	0.39	YES
22	CYCS	CYCS	CYCS	3233	0.064	0.4	YES
23	FADD	FADD	FADD	3265	0.063	0.41	YES
24	PAK2	PAK2	PAK2	3332	0.061	0.42	YES
25	MAP3K1	MAP3K1	MAP3K1	3562	0.052	0.41	NO
26	BAG4	BAG4	BAG4	3667	0.049	0.42	NO
27	ACTG1	ACTG1	ACTG1	4331	0.032	0.38	NO
28	TRADD	TRADD	TRADD	4575	0.026	0.37	NO
29	BIRC2	BIRC2	BIRC2	4666	0.024	0.37	NO
30	CDK11B	CDK11B	CDK11B	4722	0.023	0.37	NO
31	MAP3K5	MAP3K5	MAP3K5	4872	0.019	0.37	NO
32	TNFRSF1A	TNFRSF1A	TNFRSF1A	4873	0.019	0.37	NO
33	CASP7	CASP7	CASP7	4882	0.019	0.38	NO
34	CASP9	CASP9	CASP9	5131	0.014	0.36	NO
35	CDK11A	CDK11A	CDK11A	5140	0.014	0.37	NO
36	XIAP	XIAP	XIAP	5226	0.012	0.36	NO
37	RASA1	RASA1	RASA1	5295	0.011	0.36	NO
38	RELA	RELA	RELA	6026	-0.0035	0.32	NO
39	TRAF1	TRAF1	TRAF1	6461	-0.011	0.3	NO
40	DAXX	DAXX	DAXX	6685	-0.015	0.29	NO
41	RIPK1	RIPK1	RIPK1	6771	-0.017	0.28	NO
42	CASP8	CASP8	CASP8	7222	-0.025	0.26	NO
43	MAP2K7	MAP2K7	MAP2K7	7853	-0.035	0.23	NO
44	CASP2	CASP2	CASP2	8112	-0.04	0.22	NO
45	PRKDC	PRKDC	PRKDC	8621	-0.049	0.2	NO
46	LMNB2	LMNB2	LMNB2	8760	-0.051	0.2	NO
47	SPTAN1	SPTAN1	SPTAN1	9110	-0.057	0.2	NO
48	NUMA1	NUMA1	NUMA1	9665	-0.068	0.18	NO
49	PARP1	PARP1	PARP1	10406	-0.082	0.15	NO
50	DFFA	DFFA	DFFA	10744	-0.09	0.14	NO
51	TRAF2	TRAF2	TRAF2	11789	-0.12	0.1	NO
52	CRADD	CRADD	CRADD	12040	-0.12	0.11	NO
53	DFFB	DFFB	DFFB	12097	-0.13	0.13	NO
54	CASP3	CASP3	CASP3	12426	-0.14	0.14	NO
55	MAPK8	MAPK8	MAPK8	12703	-0.15	0.15	NO
56	FASLG	FASLG	FASLG	12758	-0.15	0.17	NO
57	BCL2	BCL2	BCL2	14661	-0.23	0.11	NO
58	CASP6	CASP6	CASP6	14885	-0.24	0.14	NO

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

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

genes ES table in pathway: PID IL8CXCR2 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	CD14	CD14	CD14	36	0.84	0.13	YES
2	TLR7	TLR7	TLR7	60	0.79	0.26	YES
3	LY96	LY96	LY96	135	0.67	0.36	YES
4	TLR4	TLR4	TLR4	270	0.54	0.43	YES
5	TLR6	TLR6	TLR6	584	0.37	0.47	YES
6	TLR2	TLR2	TLR2	656	0.34	0.52	YES
7	MAP2K6	MAP2K6	MAP2K6	1062	0.24	0.54	YES
8	MYD88	MYD88	MYD88	1291	0.2	0.56	YES
9	FOS	FOS	FOS	1620	0.16	0.56	YES
10	TIRAP	TIRAP	TIRAP	1963	0.13	0.56	YES
11	TOLLIP	TOLLIP	TOLLIP	1982	0.13	0.58	YES
12	MAP2K3	MAP2K3	MAP2K3	2376	0.1	0.58	YES
13	NFKB1	NFKB1	NFKB1	2508	0.097	0.59	YES
14	NFKBIA	NFKBIA	NFKBIA	2653	0.09	0.59	YES
15	CHUK	CHUK	CHUK	2910	0.078	0.59	YES
16	TLR10	TLR10	TLR10	2919	0.077	0.6	YES
17	IKBKG	IKBKG	IKBKG	2970	0.074	0.61	YES
18	MAP3K14	MAP3K14	MAP3K14	3070	0.07	0.62	YES
19	MAP3K1	MAP3K1	MAP3K1	3562	0.052	0.6	NO
20	IRAK1	IRAK1	IRAK1	3643	0.05	0.6	NO
21	JUN	JUN	JUN	3719	0.048	0.6	NO
22	MAPK14	MAPK14	MAPK14	3883	0.043	0.6	NO
23	MAP2K4	MAP2K4	MAP2K4	4595	0.025	0.56	NO
24	RELA	RELA	RELA	6026	-0.0035	0.48	NO
25	TAB2	TAB2	TAB2	7098	-0.023	0.42	NO
26	PGLYRP1	PGLYRP1	PGLYRP1	7198	-0.024	0.42	NO
27	IKBKB	IKBKB	IKBKB	7288	-0.026	0.42	NO
28	ECSIT	ECSIT	ECSIT	7296	-0.026	0.42	NO
29	MAP3K7	MAP3K7	MAP3K7	7426	-0.028	0.42	NO
30	ELK1	ELK1	ELK1	7912	-0.036	0.4	NO
31	TRAF6	TRAF6	TRAF6	8541	-0.047	0.37	NO
32	TAB1	TAB1	TAB1	8543	-0.047	0.38	NO
33	EIF2AK2	EIF2AK2	EIF2AK2	10813	-0.091	0.26	NO
34	PPARA	PPARA	PPARA	11097	-0.098	0.26	NO
35	TLR9	TLR9	TLR9	11686	-0.11	0.24	NO
36	MAPK8	MAPK8	MAPK8	12703	-0.15	0.2	NO
37	TLR3	TLR3	TLR3	16390	-0.37	0.05	NO

Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID IL8CXCR2 PATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: PID IL8CXCR2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID MAPKTRKPATHWAY

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	IL1RN	IL1RN	IL1RN	56	0.8	0.16	YES
2	NOD2	NOD2	NOD2	166	0.63	0.28	YES
3	PELI3	PELI3	PELI3	518	0.39	0.34	YES
4	IL1R2	IL1R2	IL1R2	695	0.33	0.4	YES
5	PELI1	PELI1	PELI1	1031	0.24	0.42	YES
6	MAP2K6	MAP2K6	MAP2K6	1062	0.24	0.47	YES
7	MAP2K1	MAP2K1	MAP2K1	1187	0.22	0.51	YES
8	MYD88	MYD88	MYD88	1291	0.2	0.54	YES
9	MAP3K3	MAP3K3	MAP3K3	1307	0.2	0.58	YES
10	TOLLIP	TOLLIP	TOLLIP	1982	0.13	0.57	YES
11	IRAK3	IRAK3	IRAK3	2010	0.13	0.59	YES
12	IL1A	IL1A	IL1A	2498	0.098	0.58	YES
13	CHUK	CHUK	CHUK	2910	0.078	0.58	YES
14	IKBKG	IKBKG	IKBKG	2970	0.074	0.59	YES
15	IRAK4	IRAK4	IRAK4	3430	0.058	0.57	YES
16	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	3481	0.056	0.58	YES
17	TNIP2	TNIP2	TNIP2	3516	0.054	0.59	YES
18	IRAK1	IRAK1	IRAK1	3643	0.05	0.59	YES
19	SQSTM1	SQSTM1	SQSTM1	3828	0.045	0.59	NO
20	UBE2N	UBE2N	UBE2N	4444	0.028	0.56	NO
21	MAP2K4	MAP2K4	MAP2K4	4595	0.025	0.56	NO
22	RIPK2	RIPK2	RIPK2	4619	0.025	0.56	NO
23	CUL1	CUL1	CUL1	5409	0.0083	0.52	NO
24	RBX1	RBX1	RBX1	5641	0.0035	0.51	NO
25	IL1RAP	IL1RAP	IL1RAP	5654	0.0033	0.51	NO
26	MAP3K8	MAP3K8	MAP3K8	6162	-0.006	0.48	NO
27	SKP1	SKP1	SKP1	6594	-0.013	0.46	NO
28	TAB2	TAB2	TAB2	7098	-0.023	0.43	NO
29	IKBKB	IKBKB	IKBKB	7288	-0.026	0.42	NO
30	MAP3K7	MAP3K7	MAP3K7	7426	-0.028	0.42	NO
31	TRAF6	TRAF6	TRAF6	8541	-0.047	0.37	NO
32	TAB1	TAB1	TAB1	8543	-0.047	0.38	NO
33	NOD1	NOD1	NOD1	8872	-0.053	0.37	NO
34	TAB3	TAB3	TAB3	8990	-0.054	0.37	NO
35	PELI2	PELI2	PELI2	9054	-0.056	0.38	NO
36	IL1R1	IL1R1	IL1R1	10985	-0.095	0.29	NO
37	IRAK2	IRAK2	IRAK2	10996	-0.095	0.31	NO
38	BTRC	BTRC	BTRC	11931	-0.12	0.28	NO
39	IL1B	IL1B	IL1B	13055	-0.16	0.24	NO

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

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus3 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS	25	genes.ES.table	0.54	1.8	0.0076	0.3	0.47	0.64	0.37	0.4	0	0.068
KEGG AMINOACYL TRNA BIOSYNTHESIS	41	genes.ES.table	0.36	1.2	0.26	1	1	0.51	0.36	0.33	0.89	0.43
KEGG RIBOSOME	85	genes.ES.table	0.54	1.4	0.21	1	0.98	0.89	0.4	0.54	0.89	0.44
KEGG RNA POLYMERASE	29	genes.ES.table	0.5	1.7	0.035	0.6	0.77	0.69	0.41	0.41	0.25	0.17
PID MYC PATHWAY	25	genes.ES.table	0.5	1.9	0.0019	0.36	0.33	0.48	0.31	0.33	0	0.075
REACTOME TRANSLATION	146	genes.ES.table	0.41	1.4	0.25	1	0.98	0.62	0.39	0.38	0.82	0.4
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX	49	genes.ES.table	0.4	1.2	0.34	1	1	0.71	0.41	0.42	0.99	0.49
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	109	genes.ES.table	0.44	1.3	0.27	1	0.99	0.73	0.39	0.45	0.79	0.38
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S	57	genes.ES.table	0.4	1.2	0.32	0.99	1	0.67	0.41	0.4	0.84	0.39
REACTOME PEPTIDE CHAIN ELONGATION	85	genes.ES.table	0.49	1.3	0.26	0.97	0.99	0.88	0.39	0.54	0.76	0.36

genes ES table in pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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	KAT2A	KAT2A	KAT2A	1829	0.14	0.02	YES
2	SUPT3H	SUPT3H	SUPT3H	2229	0.12	0.1	YES
3	MYC	MYC	MYC	2347	0.12	0.2	YES
4	RUVBL2	RUVBL2	RUVBL2	3226	0.085	0.23	YES
5	RUVBL1	RUVBL1	RUVBL1	3821	0.07	0.25	YES
6	CDKN2A	CDKN2A	CDKN2A	3831	0.07	0.31	YES
7	PIN1	PIN1	PIN1	3923	0.067	0.37	YES
8	PML	PML	PML	4520	0.055	0.38	YES
9	SUPT7L	SUPT7L	SUPT7L	4705	0.052	0.42	YES
10	ZBTB17	ZBTB17	ZBTB17	4717	0.052	0.46	YES
11	MAX	MAX	MAX	5246	0.043	0.47	YES
12	TAF9	TAF9	TAF9	5330	0.041	0.5	YES
13	TAF12	TAF12	TAF12	7198	0.018	0.41	NO
14	AXIN1	AXIN1	AXIN1	7426	0.014	0.41	NO
15	ACTL6A	ACTL6A	ACTL6A	8467	0.002	0.35	NO
16	PPP2CA	PPP2CA	PPP2CA	8501	0.0016	0.35	NO
17	SKP2	SKP2	SKP2	8715	-0.0011	0.34	NO
18	TAF10	TAF10	TAF10	8824	-0.0024	0.34	NO
19	KAT5	KAT5	KAT5	8891	-0.0031	0.33	NO
20	HBP1	HBP1	HBP1	9076	-0.0053	0.33	NO
21	GSK3B	GSK3B	GSK3B	9919	-0.016	0.29	NO
22	TRRAP	TRRAP	TRRAP	10202	-0.02	0.3	NO
23	PAK2	PAK2	PAK2	11101	-0.034	0.27	NO
24	PPP2R5A	PPP2R5A	PPP2R5A	11244	-0.036	0.3	NO
25	FBXW7	FBXW7	FBXW7	12239	-0.059	0.29	NO

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

Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR 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 AMINOACYL TRNA BIOSYNTHESIS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PIGZ	PIGZ	PIGZ	860	0.22	0.16	YES
2	PIGU	PIGU	PIGU	2351	0.12	0.18	YES
3	PIGV	PIGV	PIGV	3255	0.084	0.2	YES
4	PIGM	PIGM	PIGM	3948	0.067	0.22	YES
5	PIGG	PIGG	PIGG	4486	0.056	0.24	YES
6	PIGT	PIGT	PIGT	4681	0.052	0.28	YES
7	PIGF	PIGF	PIGF	4726	0.052	0.32	YES
8	DPM2	DPM2	DPM2	4798	0.05	0.36	YES
9	PIGX	PIGX	PIGX	5027	0.046	0.39	YES
10	PIGQ	PIGQ	PIGQ	5088	0.045	0.43	YES
11	GPAA1	GPAA1	GPAA1	5200	0.043	0.46	YES
12	PIGO	PIGO	PIGO	5510	0.039	0.48	YES
13	PIGW	PIGW	PIGW	6018	0.032	0.48	YES
14	PIGC	PIGC	PIGC	6109	0.031	0.5	YES
15	PIGS	PIGS	PIGS	6309	0.028	0.52	YES
16	PIGH	PIGH	PIGH	6414	0.027	0.54	YES
17	PIGA	PIGA	PIGA	7540	0.013	0.48	NO
18	PIGL	PIGL	PIGL	7544	0.013	0.5	NO
19	PIGN	PIGN	PIGN	7696	0.011	0.5	NO
20	PIGY	PIGY	PIGY	7860	0.0093	0.5	NO
21	PIGB	PIGB	PIGB	8676	-0.00063	0.45	NO
22	PIGK	PIGK	PIGK	9363	-0.0088	0.42	NO
23	PGAP1	PGAP1	PGAP1	9704	-0.013	0.41	NO
24	PIGP	PIGP	PIGP	9863	-0.015	0.42	NO
25	GPLD1	GPLD1	GPLD1	9865	-0.015	0.43	NO

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

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

genes ES table in pathway: KEGG RIBOSOME

Table 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	POLR3G	POLR3G	POLR3G	1925	0.14	-0.01	YES
2	POLR2H	POLR2H	POLR2H	1990	0.13	0.086	YES
3	POLR1C	POLR1C	POLR1C	2057	0.13	0.18	YES
4	POLR2I	POLR2I	POLR2I	2124	0.13	0.27	YES
5	ZNRD1	ZNRD1	ZNRD1	2336	0.12	0.34	YES
6	POLR2F	POLR2F	POLR2F	3781	0.071	0.31	YES
7	POLR2J3	POLR2J3	POLR2J3	3790	0.07	0.37	YES
8	POLR2J2	POLR2J2	POLR2J2	4082	0.064	0.4	YES
9	POLR3H	POLR3H	POLR3H	4835	0.049	0.39	YES
10	POLR3B	POLR3B	POLR3B	5158	0.044	0.4	YES
11	POLR3D	POLR3D	POLR3D	5235	0.043	0.43	YES
12	POLR2L	POLR2L	POLR2L	5300	0.042	0.46	YES
13	POLR1D	POLR1D	POLR1D	5685	0.036	0.46	YES
14	POLR2A	POLR2A	POLR2A	5779	0.035	0.48	YES
15	POLR3K	POLR3K	POLR3K	6559	0.025	0.46	YES
16	POLR2D	POLR2D	POLR2D	6756	0.023	0.46	YES
17	POLR2J	POLR2J	POLR2J	6798	0.022	0.48	YES
18	POLR1B	POLR1B	POLR1B	7004	0.02	0.48	YES
19	POLR3F	POLR3F	POLR3F	7023	0.02	0.5	YES
20	POLR1E	POLR1E	POLR1E	7128	0.018	0.5	YES
21	POLR2C	POLR2C	POLR2C	7765	0.01	0.47	NO
22	POLR2G	POLR2G	POLR2G	7844	0.0095	0.48	NO
23	POLR1A	POLR1A	POLR1A	8227	0.0048	0.46	NO
24	POLR3GL	POLR3GL	POLR3GL	8621	0.00018	0.44	NO
25	POLR2E	POLR2E	POLR2E	9135	-0.0061	0.41	NO
26	POLR3A	POLR3A	POLR3A	10138	-0.019	0.37	NO
27	POLR3C	POLR3C	POLR3C	10249	-0.02	0.38	NO
28	POLR2B	POLR2B	POLR2B	10287	-0.021	0.39	NO
29	POLR2K	POLR2K	POLR2K	10313	-0.021	0.4	NO

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

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

genes ES table in pathway: KEGG RNA POLYMERASE

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	LZTS1	LZTS1	LZTS1	1965	0.14	-0.0096	YES
2	POLR2H	POLR2H	POLR2H	1990	0.13	0.092	YES
3	POLR1C	POLR1C	POLR1C	2057	0.13	0.19	YES
4	SNAPC4	SNAPC4	SNAPC4	2736	0.1	0.23	YES
5	POLR3E	POLR3E	POLR3E	3755	0.071	0.22	YES
6	POLR2F	POLR2F	POLR2F	3781	0.071	0.28	YES
7	SNAPC1	SNAPC1	SNAPC1	4359	0.058	0.29	YES
8	POLR3H	POLR3H	POLR3H	4835	0.049	0.3	YES
9	POLR3B	POLR3B	POLR3B	5158	0.044	0.32	YES
10	POLR3D	POLR3D	POLR3D	5235	0.043	0.34	YES
11	SNAPC2	SNAPC2	SNAPC2	5269	0.042	0.38	YES
12	POLR2L	POLR2L	POLR2L	5300	0.042	0.41	YES
13	POLR1D	POLR1D	POLR1D	5685	0.036	0.41	YES
14	POLR3K	POLR3K	POLR3K	6559	0.025	0.38	YES
15	BRF2	BRF2	BRF2	6586	0.025	0.4	YES
16	POU2F1	POU2F1	POU2F1	6597	0.025	0.42	YES
17	POLR3F	POLR3F	POLR3F	7023	0.02	0.41	NO
18	TBP	TBP	TBP	8175	0.0056	0.35	NO
19	POLR3GL	POLR3GL	POLR3GL	8621	0.00018	0.32	NO
20	POLR2E	POLR2E	POLR2E	9135	-0.0061	0.3	NO
21	POLR3A	POLR3A	POLR3A	10138	-0.019	0.25	NO
22	POLR3C	POLR3C	POLR3C	10249	-0.02	0.26	NO
23	POLR2K	POLR2K	POLR2K	10313	-0.021	0.27	NO
24	SNAPC5	SNAPC5	SNAPC5	11477	-0.041	0.24	NO
25	SNAPC3	SNAPC3	SNAPC3	11727	-0.046	0.26	NO
26	ZNF143	ZNF143	ZNF143	12863	-0.079	0.26	NO

Figure S47. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA POLYMERASE.

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

genes ES table in pathway: PID MYC PATHWAY

Table 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	RPSAP9	RPSAP9	RPSAP9	981	0.21	-0.017	YES
2	RPS26	RPS26	RPS26	1570	0.16	-0.02	YES
3	RPL9	RPL9	RPL9	1646	0.15	0.0049	YES
4	RPL36A	RPL36A	RPL36A	2319	0.12	-0.011	YES
5	RPL21	RPL21	RPL21	2469	0.11	0.0017	YES
6	RPL37	RPL37	RPL37	2989	0.092	-0.011	YES
7	GSPT2	GSPT2	GSPT2	3108	0.088	-0.00035	YES
8	RPL36	RPL36	RPL36	3302	0.083	0.0044	YES
9	RPL12	RPL12	RPL12	3427	0.079	0.013	YES
10	RPS15	RPS15	RPS15	3447	0.079	0.027	YES
11	RPL35A	RPL35A	RPL35A	3459	0.079	0.042	YES
12	RPL39	RPL39	RPL39	3594	0.075	0.048	YES
13	UPF3A	UPF3A	UPF3A	3665	0.073	0.058	YES
14	RPL31	RPL31	RPL31	3739	0.072	0.068	YES
15	RPS17	RPS17	RPS17	3843	0.069	0.076	YES
16	RPL29	RPL29	RPL29	3854	0.069	0.088	YES
17	RPL10A	RPL10A	RPL10A	3899	0.068	0.099	YES
18	RPL23	RPL23	RPL23	3936	0.067	0.11	YES
19	RPS28	RPS28	RPS28	4069	0.064	0.12	YES
20	NCBP2	NCBP2	NCBP2	4102	0.064	0.12	YES
21	RPL28	RPL28	RPL28	4148	0.063	0.14	YES
22	RPL26	RPL26	RPL26	4178	0.062	0.14	YES
23	RPL13	RPL13	RPL13	4188	0.062	0.16	YES
24	RPS4X	RPS4X	RPS4X	4284	0.06	0.16	YES
25	RPL18	RPL18	RPL18	4314	0.059	0.17	YES
26	RPS10	RPS10	RPS10	4324	0.059	0.18	YES
27	RPL41	RPL41	RPL41	4385	0.058	0.19	YES
28	RPL17	RPL17	RPL17	4475	0.056	0.2	YES
29	RPS15A	RPS15A	RPS15A	4511	0.055	0.2	YES
30	RPL34	RPL34	RPL34	4515	0.055	0.22	YES
31	RPL32	RPL32	RPL32	4525	0.055	0.23	YES
32	RPL38	RPL38	RPL38	4542	0.055	0.24	YES
33	UPF3B	UPF3B	UPF3B	4602	0.054	0.24	YES
34	RPL22	RPL22	RPL22	4610	0.053	0.25	YES
35	RPL37A	RPL37A	RPL37A	4626	0.053	0.26	YES
36	RPL18A	RPL18A	RPL18A	4743	0.051	0.26	YES
37	RPS14	RPS14	RPS14	4763	0.051	0.27	YES
38	RPS24	RPS24	RPS24	4772	0.051	0.28	YES
39	RPS20	RPS20	RPS20	4802	0.05	0.29	YES
40	RPL35	RPL35	RPL35	4891	0.048	0.3	YES
41	RPL27	RPL27	RPL27	4987	0.047	0.3	YES
42	RPLP2	RPLP2	RPLP2	4996	0.047	0.31	YES
43	RPS2	RPS2	RPS2	5025	0.046	0.32	YES
44	RPSA	RPSA	RPSA	5045	0.046	0.32	YES
45	RPS23	RPS23	RPS23	5068	0.045	0.33	YES
46	RPS18	RPS18	RPS18	5225	0.043	0.33	YES
47	RPL23A	RPL23A	RPL23A	5256	0.043	0.34	YES
48	RPS5	RPS5	RPS5	5278	0.042	0.34	YES
49	RPL14	RPL14	RPL14	5284	0.042	0.35	YES
50	RPS9	RPS9	RPS9	5288	0.042	0.36	YES
51	RPLP1	RPLP1	RPLP1	5334	0.041	0.36	YES
52	RPS7	RPS7	RPS7	5348	0.041	0.37	YES
53	RNPS1	RNPS1	RNPS1	5407	0.04	0.38	YES
54	RPL10	RPL10	RPL10	5428	0.04	0.38	YES
55	RPL24	RPL24	RPL24	5429	0.04	0.39	YES
56	RPS13	RPS13	RPS13	5577	0.038	0.39	YES
57	RPS11	RPS11	RPS11	5664	0.037	0.39	YES
58	RPL11	RPL11	RPL11	5717	0.036	0.4	YES
59	RPS21	RPS21	RPS21	5720	0.036	0.4	YES
60	RPL30	RPL30	RPL30	5769	0.035	0.41	YES
61	RPS16	RPS16	RPS16	5783	0.035	0.41	YES
62	RPS27A	RPS27A	RPS27A	5809	0.035	0.42	YES
63	RPL27A	RPL27A	RPL27A	5854	0.034	0.42	YES
64	RPS3	RPS3	RPS3	5858	0.034	0.43	YES
65	RPS6	RPS6	RPS6	5872	0.034	0.44	YES
66	RPS19	RPS19	RPS19	5890	0.034	0.44	YES
67	RPL15	RPL15	RPL15	5903	0.034	0.45	YES
68	FAU	FAU	FAU	5975	0.033	0.45	YES
69	RPLP0	RPLP0	RPLP0	5994	0.033	0.45	YES
70	RPS29	RPS29	RPS29	6231	0.03	0.45	YES
71	RPL3	RPL3	RPL3	6266	0.029	0.45	YES
72	RPL6	RPL6	RPL6	6307	0.028	0.45	YES
73	RPL8	RPL8	RPL8	6322	0.028	0.46	YES
74	RPS8	RPS8	RPS8	6342	0.028	0.46	YES
75	PPP2R2A	PPP2R2A	PPP2R2A	6399	0.027	0.46	YES
76	ETF1	ETF1	ETF1	6410	0.027	0.47	YES
77	RPS12	RPS12	RPS12	6519	0.026	0.47	YES
78	SMG6	SMG6	SMG6	6621	0.025	0.47	YES
79	RPL13A	RPL13A	RPL13A	6646	0.024	0.47	YES
80	UBA52	UBA52	UBA52	6773	0.023	0.47	YES
81	RPL5	RPL5	RPL5	6803	0.022	0.47	YES
82	RPS3A	RPS3A	RPS3A	6807	0.022	0.47	YES
83	MAGOH	MAGOH	MAGOH	6858	0.022	0.47	YES
84	CASC3	CASC3	CASC3	7461	0.014	0.44	NO
85	RBM8A	RBM8A	RBM8A	7521	0.013	0.44	NO
86	RPL7A	RPL7A	RPL7A	7555	0.013	0.44	NO
87	SMG5	SMG5	SMG5	7595	0.012	0.44	NO
88	RPS25	RPS25	RPS25	7786	0.01	0.43	NO
89	RPL4	RPL4	RPL4	7983	0.0078	0.42	NO
90	RPL19	RPL19	RPL19	8017	0.0073	0.42	NO
91	RPL26L1	RPL26L1	RPL26L1	8488	0.0017	0.4	NO
92	PPP2CA	PPP2CA	PPP2CA	8501	0.0016	0.4	NO
93	PPP2R1A	PPP2R1A	PPP2R1A	9151	-0.0063	0.36	NO
94	SMG1	SMG1	SMG1	9390	-0.0092	0.35	NO
95	PABPC1	PABPC1	PABPC1	9502	-0.011	0.34	NO
96	EIF4A3	EIF4A3	EIF4A3	9572	-0.012	0.34	NO
97	SMG7	SMG7	SMG7	9673	-0.013	0.34	NO
98	EIF4G1	EIF4G1	EIF4G1	9722	-0.014	0.34	NO
99	RPL7	RPL7	RPL7	9782	-0.014	0.34	NO
100	UPF2	UPF2	UPF2	10331	-0.022	0.31	NO
101	NCBP1	NCBP1	NCBP1	10966	-0.032	0.28	NO
102	RPS27	RPS27	RPS27	13088	-0.088	0.17	NO
103	RPS4Y1	RPS4Y1	RPS4Y1	14512	-0.16	0.12	NO
104	FAM153A	FAM153A	FAM153A	15115	-0.21	0.12	NO

Figure S49. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MYC PATHWAY.

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

genes ES table in pathway: REACTOME TRANSLATION

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	RPSAP9	RPSAP9	RPSAP9	981	0.21	-0.017	YES
2	RPS26	RPS26	RPS26	1570	0.16	-0.021	YES
3	RPL9	RPL9	RPL9	1646	0.15	0.0037	YES
4	POLR2H	POLR2H	POLR2H	1990	0.13	0.0093	YES
5	POLR2I	POLR2I	POLR2I	2124	0.13	0.026	YES
6	RPL36A	RPL36A	RPL36A	2319	0.12	0.037	YES
7	RPL21	RPL21	RPL21	2469	0.11	0.05	YES
8	RPL37	RPL37	RPL37	2989	0.092	0.037	YES
9	RPL36	RPL36	RPL36	3302	0.083	0.035	YES
10	RPL12	RPL12	RPL12	3427	0.079	0.043	YES
11	RPS15	RPS15	RPS15	3447	0.079	0.057	YES
12	RPL35A	RPL35A	RPL35A	3459	0.079	0.071	YES
13	RPL39	RPL39	RPL39	3594	0.075	0.078	YES
14	RPL31	RPL31	RPL31	3739	0.072	0.083	YES
15	POLR2F	POLR2F	POLR2F	3781	0.071	0.094	YES
16	RPS17	RPS17	RPS17	3843	0.069	0.1	YES
17	RPL29	RPL29	RPL29	3854	0.069	0.12	YES
18	RPL10A	RPL10A	RPL10A	3899	0.068	0.13	YES
19	RPL23	RPL23	RPL23	3936	0.067	0.14	YES
20	RPS28	RPS28	RPS28	4069	0.064	0.14	YES
21	RPL28	RPL28	RPL28	4148	0.063	0.15	YES
22	RPL26	RPL26	RPL26	4178	0.062	0.16	YES
23	RPL13	RPL13	RPL13	4188	0.062	0.17	YES
24	RPS4X	RPS4X	RPS4X	4284	0.06	0.18	YES
25	RPL18	RPL18	RPL18	4314	0.059	0.19	YES
26	RPS10	RPS10	RPS10	4324	0.059	0.2	YES
27	RPL41	RPL41	RPL41	4385	0.058	0.21	YES
28	RPL17	RPL17	RPL17	4475	0.056	0.21	YES
29	RPS15A	RPS15A	RPS15A	4511	0.055	0.22	YES
30	RPL34	RPL34	RPL34	4515	0.055	0.23	YES
31	RPL32	RPL32	RPL32	4525	0.055	0.24	YES
32	RPL38	RPL38	RPL38	4542	0.055	0.25	YES
33	RPL22	RPL22	RPL22	4610	0.053	0.26	YES
34	RPL37A	RPL37A	RPL37A	4626	0.053	0.26	YES
35	GTF2F1	GTF2F1	GTF2F1	4704	0.052	0.27	YES
36	RPL18A	RPL18A	RPL18A	4743	0.051	0.28	YES
37	RPS14	RPS14	RPS14	4763	0.051	0.29	YES
38	RPS24	RPS24	RPS24	4772	0.051	0.3	YES
39	RPS20	RPS20	RPS20	4802	0.05	0.3	YES
40	RPL35	RPL35	RPL35	4891	0.048	0.31	YES
41	RPL27	RPL27	RPL27	4987	0.047	0.31	YES
42	RPLP2	RPLP2	RPLP2	4996	0.047	0.32	YES
43	RPS2	RPS2	RPS2	5025	0.046	0.33	YES
44	RPSA	RPSA	RPSA	5045	0.046	0.34	YES
45	RPS23	RPS23	RPS23	5068	0.045	0.34	YES
46	RPS18	RPS18	RPS18	5225	0.043	0.34	YES
47	RPL23A	RPL23A	RPL23A	5256	0.043	0.35	YES
48	RPS5	RPS5	RPS5	5278	0.042	0.36	YES
49	RPL14	RPL14	RPL14	5284	0.042	0.36	YES
50	RPS9	RPS9	RPS9	5288	0.042	0.37	YES
51	POLR2L	POLR2L	POLR2L	5300	0.042	0.38	YES
52	RPLP1	RPLP1	RPLP1	5334	0.041	0.38	YES
53	RPS7	RPS7	RPS7	5348	0.041	0.39	YES
54	RPL10	RPL10	RPL10	5428	0.04	0.4	YES
55	RPL24	RPL24	RPL24	5429	0.04	0.4	YES
56	RPS13	RPS13	RPS13	5577	0.038	0.4	YES
57	RPS11	RPS11	RPS11	5664	0.037	0.4	YES
58	RPL11	RPL11	RPL11	5717	0.036	0.41	YES
59	RPS21	RPS21	RPS21	5720	0.036	0.41	YES
60	RPL30	RPL30	RPL30	5769	0.035	0.42	YES
61	POLR2A	POLR2A	POLR2A	5779	0.035	0.42	YES
62	RPS16	RPS16	RPS16	5783	0.035	0.43	YES
63	RPS27A	RPS27A	RPS27A	5809	0.035	0.44	YES
64	RPL27A	RPL27A	RPL27A	5854	0.034	0.44	YES
65	RPS3	RPS3	RPS3	5858	0.034	0.45	YES
66	RPS6	RPS6	RPS6	5872	0.034	0.45	YES
67	RPS19	RPS19	RPS19	5890	0.034	0.46	YES
68	RPL15	RPL15	RPL15	5903	0.034	0.46	YES
69	FAU	FAU	FAU	5975	0.033	0.46	YES
70	RPLP0	RPLP0	RPLP0	5994	0.033	0.47	YES
71	RPS29	RPS29	RPS29	6231	0.03	0.46	YES
72	RPL3	RPL3	RPL3	6266	0.029	0.47	YES
73	RPL6	RPL6	RPL6	6307	0.028	0.47	YES
74	RPL8	RPL8	RPL8	6322	0.028	0.47	YES
75	RPS8	RPS8	RPS8	6342	0.028	0.48	YES
76	RPS12	RPS12	RPS12	6519	0.026	0.47	YES
77	RPL13A	RPL13A	RPL13A	6646	0.024	0.47	YES
78	POLR2D	POLR2D	POLR2D	6756	0.023	0.47	YES
79	UBA52	UBA52	UBA52	6773	0.023	0.47	YES
80	POLR2J	POLR2J	POLR2J	6798	0.022	0.47	YES
81	RPL5	RPL5	RPL5	6803	0.022	0.48	YES
82	RPS3A	RPS3A	RPS3A	6807	0.022	0.48	YES
83	HSP90AA1	HSP90AA1	HSP90AA1	7134	0.018	0.47	NO
84	RPL7A	RPL7A	RPL7A	7555	0.013	0.44	NO
85	POLR2C	POLR2C	POLR2C	7765	0.01	0.44	NO
86	RPS25	RPS25	RPS25	7786	0.01	0.44	NO
87	POLR2G	POLR2G	POLR2G	7844	0.0095	0.43	NO
88	RPL4	RPL4	RPL4	7983	0.0078	0.43	NO
89	RPL19	RPL19	RPL19	8017	0.0073	0.43	NO
90	GRSF1	GRSF1	GRSF1	8480	0.0018	0.4	NO
91	RPL26L1	RPL26L1	RPL26L1	8488	0.0017	0.4	NO
92	IPO5	IPO5	IPO5	8737	-0.0013	0.39	NO
93	POLR2E	POLR2E	POLR2E	9135	-0.0061	0.36	NO
94	RPL7	RPL7	RPL7	9782	-0.014	0.33	NO
95	GTF2F2	GTF2F2	GTF2F2	9819	-0.015	0.33	NO
96	POLR2B	POLR2B	POLR2B	10287	-0.021	0.31	NO
97	POLR2K	POLR2K	POLR2K	10313	-0.021	0.31	NO
98	DNAJC3	DNAJC3	DNAJC3	11174	-0.035	0.27	NO
99	RPS27	RPS27	RPS27	13088	-0.088	0.17	NO
100	RPS4Y1	RPS4Y1	RPS4Y1	14512	-0.16	0.12	NO
101	FAM153A	FAM153A	FAM153A	15115	-0.21	0.12	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: REACTOME TRANSLATION.

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

genes ES table in pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

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	RPS26	RPS26	RPS26	1570	0.16	-0.054	YES
2	RPL9	RPL9	RPL9	1646	0.15	-0.023	YES
3	RPL36A	RPL36A	RPL36A	2319	0.12	-0.035	YES
4	RPL21	RPL21	RPL21	2469	0.11	-0.017	YES
5	RPL22L1	RPL22L1	RPL22L1	2763	0.1	-0.011	YES
6	RPL37	RPL37	RPL37	2989	0.092	-0.0024	YES
7	RPL36	RPL36	RPL36	3302	0.083	-0.0013	YES
8	RPL12	RPL12	RPL12	3427	0.079	0.01	YES
9	RPS15	RPS15	RPS15	3447	0.079	0.027	YES
10	RPL35A	RPL35A	RPL35A	3459	0.079	0.045	YES
11	RPL39	RPL39	RPL39	3594	0.075	0.055	YES
12	RPL31	RPL31	RPL31	3739	0.072	0.063	YES
13	RPS17	RPS17	RPS17	3843	0.069	0.073	YES
14	RPL29	RPL29	RPL29	3854	0.069	0.089	YES
15	RPL10A	RPL10A	RPL10A	3899	0.068	0.1	YES
16	RPL23	RPL23	RPL23	3936	0.067	0.12	YES
17	RPS28	RPS28	RPS28	4069	0.064	0.12	YES
18	RPL28	RPL28	RPL28	4148	0.063	0.13	YES
19	RPL26	RPL26	RPL26	4178	0.062	0.15	YES
20	RPL13	RPL13	RPL13	4188	0.062	0.16	YES
21	RPS4X	RPS4X	RPS4X	4284	0.06	0.17	YES
22	RPL18	RPL18	RPL18	4314	0.059	0.18	YES
23	RPS10	RPS10	RPS10	4324	0.059	0.19	YES
24	RPL41	RPL41	RPL41	4385	0.058	0.2	YES
25	RPL17	RPL17	RPL17	4475	0.056	0.21	YES
26	RPS15A	RPS15A	RPS15A	4511	0.055	0.22	YES
27	RPL34	RPL34	RPL34	4515	0.055	0.24	YES
28	RPL32	RPL32	RPL32	4525	0.055	0.25	YES
29	RPL38	RPL38	RPL38	4542	0.055	0.26	YES
30	RPL22	RPL22	RPL22	4610	0.053	0.27	YES
31	RPL37A	RPL37A	RPL37A	4626	0.053	0.28	YES
32	RPL18A	RPL18A	RPL18A	4743	0.051	0.28	YES
33	RPS24	RPS24	RPS24	4772	0.051	0.3	YES
34	RPS20	RPS20	RPS20	4802	0.05	0.3	YES
35	RPL35	RPL35	RPL35	4891	0.048	0.31	YES
36	RPL27	RPL27	RPL27	4987	0.047	0.32	YES
37	RPLP2	RPLP2	RPLP2	4996	0.047	0.33	YES
38	RPS2	RPS2	RPS2	5025	0.046	0.34	YES
39	RPSA	RPSA	RPSA	5045	0.046	0.35	YES
40	RPS23	RPS23	RPS23	5068	0.045	0.36	YES
41	RPS18	RPS18	RPS18	5225	0.043	0.36	YES
42	RPL23A	RPL23A	RPL23A	5256	0.043	0.36	YES
43	RPS5	RPS5	RPS5	5278	0.042	0.37	YES
44	RPL14	RPL14	RPL14	5284	0.042	0.38	YES
45	RPS9	RPS9	RPS9	5288	0.042	0.39	YES
46	RPLP1	RPLP1	RPLP1	5334	0.041	0.4	YES
47	RPS7	RPS7	RPS7	5348	0.041	0.41	YES
48	RPL10	RPL10	RPL10	5428	0.04	0.41	YES
49	RPL24	RPL24	RPL24	5429	0.04	0.42	YES
50	RPS13	RPS13	RPS13	5577	0.038	0.42	YES
51	RPS11	RPS11	RPS11	5664	0.037	0.43	YES
52	RPL11	RPL11	RPL11	5717	0.036	0.43	YES
53	RPS21	RPS21	RPS21	5720	0.036	0.44	YES
54	RPL30	RPL30	RPL30	5769	0.035	0.44	YES
55	RPS16	RPS16	RPS16	5783	0.035	0.45	YES
56	RPS27A	RPS27A	RPS27A	5809	0.035	0.46	YES
57	RPL27A	RPL27A	RPL27A	5854	0.034	0.46	YES
58	RPS3	RPS3	RPS3	5858	0.034	0.47	YES
59	RPS6	RPS6	RPS6	5872	0.034	0.48	YES
60	RPS19	RPS19	RPS19	5890	0.034	0.49	YES
61	RPL15	RPL15	RPL15	5903	0.034	0.49	YES
62	FAU	FAU	FAU	5975	0.033	0.5	YES
63	RPLP0	RPLP0	RPLP0	5994	0.033	0.5	YES
64	RPS29	RPS29	RPS29	6231	0.03	0.5	YES
65	RPL3	RPL3	RPL3	6266	0.029	0.5	YES
66	RPL6	RPL6	RPL6	6307	0.028	0.51	YES
67	RPL8	RPL8	RPL8	6322	0.028	0.51	YES
68	RPL36AL	RPL36AL	RPL36AL	6332	0.028	0.52	YES
69	RPS8	RPS8	RPS8	6342	0.028	0.52	YES
70	RPS12	RPS12	RPS12	6519	0.026	0.52	YES
71	RPL13A	RPL13A	RPL13A	6646	0.024	0.52	YES
72	RSL24D1	RSL24D1	RSL24D1	6713	0.024	0.52	YES
73	UBA52	UBA52	UBA52	6773	0.023	0.52	YES
74	RPL5	RPL5	RPL5	6803	0.022	0.53	YES
75	RPS3A	RPS3A	RPS3A	6807	0.022	0.53	YES
76	RPS27L	RPS27L	RPS27L	6822	0.022	0.54	YES
77	RPL7A	RPL7A	RPL7A	7555	0.013	0.5	NO
78	RPS25	RPS25	RPS25	7786	0.01	0.48	NO
79	RPL4	RPL4	RPL4	7983	0.0078	0.48	NO
80	RPL19	RPL19	RPL19	8017	0.0073	0.48	NO
81	RPL26L1	RPL26L1	RPL26L1	8488	0.0017	0.45	NO
82	MRPL13	MRPL13	MRPL13	9041	-0.0048	0.42	NO
83	RPL7	RPL7	RPL7	9782	-0.014	0.38	NO
84	RPS27	RPS27	RPS27	13088	-0.088	0.2	NO
85	RPS4Y1	RPS4Y1	RPS4Y1	14512	-0.16	0.16	NO

Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE

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	RPSAP9	RPSAP9	RPSAP9	981	0.21	-0.024	YES
2	RPS26	RPS26	RPS26	1570	0.16	-0.032	YES
3	RPL9	RPL9	RPL9	1646	0.15	-0.012	YES
4	POLR2H	POLR2H	POLR2H	1990	0.13	-0.01	YES
5	POLR2I	POLR2I	POLR2I	2124	0.13	0.0024	YES
6	RPL36A	RPL36A	RPL36A	2319	0.12	0.01	YES
7	RPL21	RPL21	RPL21	2469	0.11	0.02	YES
8	CALR	CALR	CALR	2851	0.096	0.013	YES
9	RPL37	RPL37	RPL37	2989	0.092	0.02	YES
10	RPL36	RPL36	RPL36	3302	0.083	0.015	YES
11	RPL12	RPL12	RPL12	3427	0.079	0.021	YES
12	RPS15	RPS15	RPS15	3447	0.079	0.032	YES
13	RPL35A	RPL35A	RPL35A	3459	0.079	0.044	YES
14	RPL39	RPL39	RPL39	3594	0.075	0.049	YES
15	RPL31	RPL31	RPL31	3739	0.072	0.052	YES
16	POLR2F	POLR2F	POLR2F	3781	0.071	0.061	YES
17	RPS17	RPS17	RPS17	3843	0.069	0.069	YES
18	RPL29	RPL29	RPL29	3854	0.069	0.079	YES
19	RPL10A	RPL10A	RPL10A	3899	0.068	0.088	YES
20	RPL23	RPL23	RPL23	3936	0.067	0.096	YES
21	RPS28	RPS28	RPS28	4069	0.064	0.099	YES
22	RPL28	RPL28	RPL28	4148	0.063	0.1	YES
23	RPL26	RPL26	RPL26	4178	0.062	0.11	YES
24	RPL13	RPL13	RPL13	4188	0.062	0.12	YES
25	HSPA1B	HSPA1B	HSPA1B	4224	0.061	0.13	YES
26	RPS4X	RPS4X	RPS4X	4284	0.06	0.14	YES
27	RPL18	RPL18	RPL18	4314	0.059	0.14	YES
28	RPS10	RPS10	RPS10	4324	0.059	0.15	YES
29	RPL41	RPL41	RPL41	4385	0.058	0.16	YES
30	RPL17	RPL17	RPL17	4475	0.056	0.16	YES
31	RPS15A	RPS15A	RPS15A	4511	0.055	0.17	YES
32	RPL34	RPL34	RPL34	4515	0.055	0.18	YES
33	RPL32	RPL32	RPL32	4525	0.055	0.19	YES
34	RPL38	RPL38	RPL38	4542	0.055	0.2	YES
35	RPL22	RPL22	RPL22	4610	0.053	0.2	YES
36	RPL37A	RPL37A	RPL37A	4626	0.053	0.21	YES
37	GTF2F1	GTF2F1	GTF2F1	4704	0.052	0.21	YES
38	RPL18A	RPL18A	RPL18A	4743	0.051	0.22	YES
39	RPS14	RPS14	RPS14	4763	0.051	0.22	YES
40	RPS24	RPS24	RPS24	4772	0.051	0.23	YES
41	RPS20	RPS20	RPS20	4802	0.05	0.24	YES
42	RPL35	RPL35	RPL35	4891	0.048	0.24	YES
43	RPL27	RPL27	RPL27	4987	0.047	0.24	YES
44	RPLP2	RPLP2	RPLP2	4996	0.047	0.25	YES
45	RPS2	RPS2	RPS2	5025	0.046	0.26	YES
46	RPSA	RPSA	RPSA	5045	0.046	0.26	YES
47	RPS23	RPS23	RPS23	5068	0.045	0.27	YES
48	RPS18	RPS18	RPS18	5225	0.043	0.27	YES
49	RPL23A	RPL23A	RPL23A	5256	0.043	0.27	YES
50	RPS5	RPS5	RPS5	5278	0.042	0.28	YES
51	RPL14	RPL14	RPL14	5284	0.042	0.28	YES
52	AAAS	AAAS	AAAS	5285	0.042	0.29	YES
53	RPS9	RPS9	RPS9	5288	0.042	0.3	YES
54	POLR2L	POLR2L	POLR2L	5300	0.042	0.3	YES
55	RPLP1	RPLP1	RPLP1	5334	0.041	0.31	YES
56	RPS7	RPS7	RPS7	5348	0.041	0.32	YES
57	RPL10	RPL10	RPL10	5428	0.04	0.32	YES
58	RPL24	RPL24	RPL24	5429	0.04	0.32	YES
59	RPS13	RPS13	RPS13	5577	0.038	0.32	YES
60	RPS11	RPS11	RPS11	5664	0.037	0.32	YES
61	RPL11	RPL11	RPL11	5717	0.036	0.32	YES
62	RPS21	RPS21	RPS21	5720	0.036	0.33	YES
63	RPL30	RPL30	RPL30	5769	0.035	0.33	YES
64	POLR2A	POLR2A	POLR2A	5779	0.035	0.34	YES
65	POM121	POM121	POM121	5781	0.035	0.34	YES
66	RPS16	RPS16	RPS16	5783	0.035	0.35	YES
67	RPS27A	RPS27A	RPS27A	5809	0.035	0.35	YES
68	RPL27A	RPL27A	RPL27A	5854	0.034	0.36	YES
69	RPS3	RPS3	RPS3	5858	0.034	0.36	YES
70	RPS6	RPS6	RPS6	5872	0.034	0.37	YES
71	RPS19	RPS19	RPS19	5890	0.034	0.37	YES
72	RPL15	RPL15	RPL15	5903	0.034	0.38	YES
73	FAU	FAU	FAU	5975	0.033	0.38	YES
74	RPLP0	RPLP0	RPLP0	5994	0.033	0.38	YES
75	RPS29	RPS29	RPS29	6231	0.03	0.37	YES
76	RPL3	RPL3	RPL3	6266	0.029	0.38	YES
77	RPL6	RPL6	RPL6	6307	0.028	0.38	YES
78	RPL8	RPL8	RPL8	6322	0.028	0.38	YES
79	RPS8	RPS8	RPS8	6342	0.028	0.38	YES
80	RPS12	RPS12	RPS12	6519	0.026	0.38	YES
81	RAN	RAN	RAN	6539	0.026	0.38	YES
82	NUP188	NUP188	NUP188	6590	0.025	0.38	YES
83	RPL13A	RPL13A	RPL13A	6646	0.024	0.38	YES
84	RAE1	RAE1	RAE1	6726	0.023	0.38	YES
85	POLR2D	POLR2D	POLR2D	6756	0.023	0.38	YES
86	UBA52	UBA52	UBA52	6773	0.023	0.39	YES
87	SEH1L	SEH1L	SEH1L	6777	0.023	0.39	YES
88	NUP214	NUP214	NUP214	6792	0.023	0.39	YES
89	POLR2J	POLR2J	POLR2J	6798	0.022	0.4	YES
90	RPL5	RPL5	RPL5	6803	0.022	0.4	YES
91	RPS3A	RPS3A	RPS3A	6807	0.022	0.4	YES
92	NUP85	NUP85	NUP85	7033	0.02	0.39	NO
93	HSP90AA1	HSP90AA1	HSP90AA1	7134	0.018	0.39	NO
94	RPL7A	RPL7A	RPL7A	7555	0.013	0.37	NO
95	NUP107	NUP107	NUP107	7609	0.012	0.37	NO
96	POLR2C	POLR2C	POLR2C	7765	0.01	0.36	NO
97	NUP54	NUP54	NUP54	7773	0.01	0.36	NO
98	RPS25	RPS25	RPS25	7786	0.01	0.36	NO
99	NUP153	NUP153	NUP153	7800	0.01	0.36	NO
100	POLR2G	POLR2G	POLR2G	7844	0.0095	0.36	NO
101	XPO1	XPO1	XPO1	7854	0.0093	0.36	NO
102	NUP35	NUP35	NUP35	7961	0.008	0.36	NO
103	RPL4	RPL4	RPL4	7983	0.0078	0.36	NO
104	RPL19	RPL19	RPL19	8017	0.0073	0.36	NO
105	NUPL2	NUPL2	NUPL2	8384	0.003	0.34	NO
106	GRSF1	GRSF1	GRSF1	8480	0.0018	0.33	NO
107	RPL26L1	RPL26L1	RPL26L1	8488	0.0017	0.33	NO
108	IPO5	IPO5	IPO5	8737	-0.0013	0.32	NO
109	NUP88	NUP88	NUP88	9031	-0.0047	0.3	NO
110	POLR2E	POLR2E	POLR2E	9135	-0.0061	0.3	NO
111	NUP43	NUP43	NUP43	9251	-0.0074	0.29	NO
112	NUP62	NUP62	NUP62	9261	-0.0076	0.29	NO
113	CLTA	CLTA	CLTA	9539	-0.011	0.28	NO
114	KPNB1	KPNB1	KPNB1	9551	-0.011	0.28	NO
115	CANX	CANX	CANX	9634	-0.012	0.28	NO
116	RPL7	RPL7	RPL7	9782	-0.014	0.27	NO
117	GTF2F2	GTF2F2	GTF2F2	9819	-0.015	0.27	NO
118	NUP93	NUP93	NUP93	9857	-0.015	0.27	NO
119	NUP205	NUP205	NUP205	9905	-0.016	0.27	NO
120	NUP133	NUP133	NUP133	10258	-0.021	0.25	NO
121	POLR2B	POLR2B	POLR2B	10287	-0.021	0.25	NO
122	POLR2K	POLR2K	POLR2K	10313	-0.021	0.26	NO
123	NUP37	NUP37	NUP37	10623	-0.026	0.24	NO
124	TPR	TPR	TPR	10637	-0.027	0.25	NO
125	DNAJC3	DNAJC3	DNAJC3	11174	-0.035	0.22	NO
126	KPNA1	KPNA1	KPNA1	11259	-0.037	0.22	NO
127	NUP210	NUP210	NUP210	11480	-0.041	0.22	NO
128	RANBP2	RANBP2	RANBP2	11779	-0.048	0.2	NO
129	NUP50	NUP50	NUP50	11823	-0.048	0.21	NO
130	NUPL1	NUPL1	NUPL1	12304	-0.061	0.19	NO
131	NUP155	NUP155	NUP155	12495	-0.066	0.19	NO
132	CLTC	CLTC	CLTC	12602	-0.07	0.2	NO
133	RPS27	RPS27	RPS27	13088	-0.088	0.18	NO
134	RPS4Y1	RPS4Y1	RPS4Y1	14512	-0.16	0.13	NO
135	FAM153A	FAM153A	FAM153A	15115	-0.21	0.12	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: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

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	RPSAP9	RPSAP9	RPSAP9	981	0.21	-0.022	YES
2	RPS26	RPS26	RPS26	1570	0.16	-0.03	YES
3	RPL9	RPL9	RPL9	1646	0.15	-0.0089	YES
4	RPL36A	RPL36A	RPL36A	2319	0.12	-0.028	YES
5	RPL21	RPL21	RPL21	2469	0.11	-0.018	YES
6	RPL37	RPL37	RPL37	2989	0.092	-0.033	YES
7	GSPT2	GSPT2	GSPT2	3108	0.088	-0.025	YES
8	RPL36	RPL36	RPL36	3302	0.083	-0.023	YES
9	RPL12	RPL12	RPL12	3427	0.079	-0.016	YES
10	RPS15	RPS15	RPS15	3447	0.079	-0.0044	YES
11	RPL35A	RPL35A	RPL35A	3459	0.079	0.0082	YES
12	RPL39	RPL39	RPL39	3594	0.075	0.013	YES
13	RPL31	RPL31	RPL31	3739	0.072	0.017	YES
14	RPS17	RPS17	RPS17	3843	0.069	0.022	YES
15	RPL29	RPL29	RPL29	3854	0.069	0.033	YES
16	RPL10A	RPL10A	RPL10A	3899	0.068	0.042	YES
17	RPL23	RPL23	RPL23	3936	0.067	0.051	YES
18	RPS28	RPS28	RPS28	4069	0.064	0.054	YES
19	SEC61A2	SEC61A2	SEC61A2	4075	0.064	0.065	YES
20	RPL28	RPL28	RPL28	4148	0.063	0.071	YES
21	RPL26	RPL26	RPL26	4178	0.062	0.08	YES
22	RPL13	RPL13	RPL13	4188	0.062	0.09	YES
23	EIF4EBP1	EIF4EBP1	EIF4EBP1	4232	0.061	0.097	YES
24	RPS4X	RPS4X	RPS4X	4284	0.06	0.1	YES
25	RPL18	RPL18	RPL18	4314	0.059	0.11	YES
26	RPS10	RPS10	RPS10	4324	0.059	0.12	YES
27	RPL41	RPL41	RPL41	4385	0.058	0.13	YES
28	RPL17	RPL17	RPL17	4475	0.056	0.13	YES
29	SRPRB	SRPRB	SRPRB	4478	0.056	0.14	YES
30	RPS15A	RPS15A	RPS15A	4511	0.055	0.15	YES
31	RPL34	RPL34	RPL34	4515	0.055	0.16	YES
32	RPL32	RPL32	RPL32	4525	0.055	0.17	YES
33	RPL38	RPL38	RPL38	4542	0.055	0.18	YES
34	EEF1B2	EEF1B2	EEF1B2	4595	0.054	0.18	YES
35	RPL22	RPL22	RPL22	4610	0.053	0.19	YES
36	RPL37A	RPL37A	RPL37A	4626	0.053	0.2	YES
37	EIF2B4	EIF2B4	EIF2B4	4668	0.052	0.2	YES
38	EIF4A2	EIF4A2	EIF4A2	4714	0.052	0.21	YES
39	RPL18A	RPL18A	RPL18A	4743	0.051	0.22	YES
40	RPS14	RPS14	RPS14	4763	0.051	0.22	YES
41	RPS24	RPS24	RPS24	4772	0.051	0.23	YES
42	RPS20	RPS20	RPS20	4802	0.05	0.24	YES
43	RPL35	RPL35	RPL35	4891	0.048	0.24	YES
44	RPL27	RPL27	RPL27	4987	0.047	0.24	YES
45	RPLP2	RPLP2	RPLP2	4996	0.047	0.25	YES
46	RPS2	RPS2	RPS2	5025	0.046	0.26	YES
47	RPSA	RPSA	RPSA	5045	0.046	0.26	YES
48	RPS23	RPS23	RPS23	5068	0.045	0.27	YES
49	RPS18	RPS18	RPS18	5225	0.043	0.27	YES
50	RPL23A	RPL23A	RPL23A	5256	0.043	0.27	YES
51	RPS5	RPS5	RPS5	5278	0.042	0.28	YES
52	RPL14	RPL14	RPL14	5284	0.042	0.29	YES
53	RPS9	RPS9	RPS9	5288	0.042	0.29	YES
54	RPLP1	RPLP1	RPLP1	5334	0.041	0.3	YES
55	RPS7	RPS7	RPS7	5348	0.041	0.3	YES
56	RPL10	RPL10	RPL10	5428	0.04	0.31	YES
57	RPL24	RPL24	RPL24	5429	0.04	0.31	YES
58	RPS13	RPS13	RPS13	5577	0.038	0.31	YES
59	RPS11	RPS11	RPS11	5664	0.037	0.31	YES
60	RPL11	RPL11	RPL11	5717	0.036	0.32	YES
61	RPS21	RPS21	RPS21	5720	0.036	0.32	YES
62	RPL30	RPL30	RPL30	5769	0.035	0.32	YES
63	RPS16	RPS16	RPS16	5783	0.035	0.33	YES
64	RPS27A	RPS27A	RPS27A	5809	0.035	0.33	YES
65	EIF5	EIF5	EIF5	5812	0.035	0.34	YES
66	RPL27A	RPL27A	RPL27A	5854	0.034	0.34	YES
67	RPS3	RPS3	RPS3	5858	0.034	0.35	YES
68	RPS6	RPS6	RPS6	5872	0.034	0.35	YES
69	SEC61G	SEC61G	SEC61G	5882	0.034	0.36	YES
70	EIF3B	EIF3B	EIF3B	5887	0.034	0.36	YES
71	RPS19	RPS19	RPS19	5890	0.034	0.37	YES
72	RPL15	RPL15	RPL15	5903	0.034	0.38	YES
73	FAU	FAU	FAU	5975	0.033	0.38	YES
74	RPLP0	RPLP0	RPLP0	5994	0.033	0.38	YES
75	RPS29	RPS29	RPS29	6231	0.03	0.37	YES
76	SSR4	SSR4	SSR4	6264	0.029	0.38	YES
77	RPL3	RPL3	RPL3	6266	0.029	0.38	YES
78	RPL6	RPL6	RPL6	6307	0.028	0.38	YES
79	RPL8	RPL8	RPL8	6322	0.028	0.39	YES
80	SEC61B	SEC61B	SEC61B	6339	0.028	0.39	YES
81	RPS8	RPS8	RPS8	6342	0.028	0.39	YES
82	ETF1	ETF1	ETF1	6410	0.027	0.4	YES
83	SPCS1	SPCS1	SPCS1	6431	0.027	0.4	YES
84	RPS12	RPS12	RPS12	6519	0.026	0.4	YES
85	EIF2S3	EIF2S3	EIF2S3	6596	0.025	0.4	YES
86	RPL13A	RPL13A	RPL13A	6646	0.024	0.4	YES
87	EIF4A1	EIF4A1	EIF4A1	6651	0.024	0.4	YES
88	UBA52	UBA52	UBA52	6773	0.023	0.4	YES
89	EEF2	EEF2	EEF2	6781	0.023	0.4	YES
90	RPL5	RPL5	RPL5	6803	0.022	0.4	YES
91	RPS3A	RPS3A	RPS3A	6807	0.022	0.41	YES
92	EIF2B5	EIF2B5	EIF2B5	7000	0.02	0.4	NO
93	SSR2	SSR2	SSR2	7043	0.02	0.4	NO
94	EIF3E	EIF3E	EIF3E	7047	0.02	0.4	NO
95	EIF3I	EIF3I	EIF3I	7060	0.019	0.41	NO
96	EIF1AX	EIF1AX	EIF1AX	7314	0.016	0.4	NO
97	EEF1D	EEF1D	EEF1D	7412	0.014	0.39	NO
98	SRP14	SRP14	SRP14	7519	0.013	0.39	NO
99	RPL7A	RPL7A	RPL7A	7555	0.013	0.39	NO
100	EIF3J	EIF3J	EIF3J	7564	0.013	0.39	NO
101	EIF4E	EIF4E	EIF4E	7590	0.012	0.39	NO
102	EIF3F	EIF3F	EIF3F	7677	0.012	0.39	NO
103	EIF3H	EIF3H	EIF3H	7733	0.011	0.39	NO
104	EIF3G	EIF3G	EIF3G	7762	0.01	0.39	NO
105	RPS25	RPS25	RPS25	7786	0.01	0.39	NO
106	EEF1A1	EEF1A1	EEF1A1	7810	0.0099	0.39	NO
107	EEF1G	EEF1G	EEF1G	7916	0.0086	0.38	NO
108	RPL4	RPL4	RPL4	7983	0.0078	0.38	NO
109	RPL19	RPL19	RPL19	8017	0.0073	0.38	NO
110	EIF4H	EIF4H	EIF4H	8270	0.0044	0.36	NO
111	EIF2B2	EIF2B2	EIF2B2	8318	0.0038	0.36	NO
112	SEC11C	SEC11C	SEC11C	8373	0.0032	0.36	NO
113	RPL26L1	RPL26L1	RPL26L1	8488	0.0017	0.35	NO
114	RPN2	RPN2	RPN2	8505	0.0015	0.35	NO
115	EIF3C	EIF3C	EIF3C	8519	0.0014	0.35	NO
116	SEC61A1	SEC61A1	SEC61A1	8673	-0.00061	0.34	NO
117	EIF2B3	EIF2B3	EIF2B3	8726	-0.0012	0.34	NO
118	DDOST	DDOST	DDOST	8762	-0.0016	0.34	NO
119	EIF3A	EIF3A	EIF3A	8812	-0.0022	0.34	NO
120	EIF3K	EIF3K	EIF3K	8873	-0.0029	0.33	NO
121	SRP19	SRP19	SRP19	8951	-0.0037	0.33	NO
122	EIF2B1	EIF2B1	EIF2B1	9012	-0.0044	0.33	NO
123	EIF5B	EIF5B	EIF5B	9099	-0.0056	0.32	NO
124	SRP72	SRP72	SRP72	9228	-0.0072	0.32	NO
125	EIF4B	EIF4B	EIF4B	9319	-0.0082	0.31	NO
126	TRAM1	TRAM1	TRAM1	9397	-0.0092	0.31	NO
127	SRP68	SRP68	SRP68	9450	-0.01	0.31	NO
128	PABPC1	PABPC1	PABPC1	9502	-0.011	0.31	NO
129	SRP9	SRP9	SRP9	9640	-0.012	0.3	NO
130	EIF4G1	EIF4G1	EIF4G1	9722	-0.014	0.3	NO
131	EIF3D	EIF3D	EIF3D	9728	-0.014	0.3	NO
132	RPL7	RPL7	RPL7	9782	-0.014	0.3	NO
133	RPN1	RPN1	RPN1	9967	-0.017	0.29	NO
134	SRPR	SRPR	SRPR	9999	-0.017	0.29	NO
135	EIF2S2	EIF2S2	EIF2S2	10207	-0.02	0.28	NO
136	SSR3	SSR3	SSR3	10486	-0.024	0.27	NO
137	SPCS3	SPCS3	SPCS3	10664	-0.027	0.27	NO
138	LOC653566	LOC653566	LOC653566	10887	-0.03	0.26	NO
139	SPCS2	SPCS2	SPCS2	10943	-0.031	0.26	NO
140	SEC11A	SEC11A	SEC11A	11625	-0.044	0.23	NO
141	SRP54	SRP54	SRP54	11644	-0.045	0.24	NO
142	EIF2S1	EIF2S1	EIF2S1	11703	-0.046	0.24	NO
143	SSR1	SSR1	SSR1	11875	-0.049	0.24	NO
144	RPS27	RPS27	RPS27	13088	-0.088	0.18	NO
145	RPS4Y1	RPS4Y1	RPS4Y1	14512	-0.16	0.12	NO
146	FAM153A	FAM153A	FAM153A	15115	-0.21	0.12	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: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME PEPTIDE CHAIN ELONGATION

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	RPSAP9	RPSAP9	RPSAP9	981	0.21	-0.015	YES
2	RPS26	RPS26	RPS26	1570	0.16	-0.017	YES
3	RPL9	RPL9	RPL9	1646	0.15	0.0092	YES
4	RPL36A	RPL36A	RPL36A	2319	0.12	-0.006	YES
5	RPL21	RPL21	RPL21	2469	0.11	0.0078	YES
6	RPL37	RPL37	RPL37	2989	0.092	-0.0038	YES
7	RPL36	RPL36	RPL36	3302	0.083	-0.0052	YES
8	RPL12	RPL12	RPL12	3427	0.079	0.0036	YES
9	RPS15	RPS15	RPS15	3447	0.079	0.018	YES
10	RPL35A	RPL35A	RPL35A	3459	0.079	0.034	YES
11	RPL39	RPL39	RPL39	3594	0.075	0.041	YES
12	RPL31	RPL31	RPL31	3739	0.072	0.047	YES
13	RPS17	RPS17	RPS17	3843	0.069	0.055	YES
14	RPL29	RPL29	RPL29	3854	0.069	0.069	YES
15	RPL10A	RPL10A	RPL10A	3899	0.068	0.08	YES
16	RPL23	RPL23	RPL23	3936	0.067	0.091	YES
17	RPS28	RPS28	RPS28	4069	0.064	0.096	YES
18	RPL28	RPL28	RPL28	4148	0.063	0.1	YES
19	RPL26	RPL26	RPL26	4178	0.062	0.12	YES
20	RPL13	RPL13	RPL13	4188	0.062	0.13	YES
21	RPS4X	RPS4X	RPS4X	4284	0.06	0.13	YES
22	RPL18	RPL18	RPL18	4314	0.059	0.14	YES
23	RPS10	RPS10	RPS10	4324	0.059	0.16	YES
24	RPL41	RPL41	RPL41	4385	0.058	0.16	YES
25	RPL17	RPL17	RPL17	4475	0.056	0.17	YES
26	RPS15A	RPS15A	RPS15A	4511	0.055	0.18	YES
27	RPL34	RPL34	RPL34	4515	0.055	0.19	YES
28	RPL32	RPL32	RPL32	4525	0.055	0.2	YES
29	RPL38	RPL38	RPL38	4542	0.055	0.21	YES
30	RPL22	RPL22	RPL22	4610	0.053	0.22	YES
31	RPL37A	RPL37A	RPL37A	4626	0.053	0.23	YES
32	EIF4A2	EIF4A2	EIF4A2	4714	0.052	0.23	YES
33	RPL18A	RPL18A	RPL18A	4743	0.051	0.24	YES
34	RPS14	RPS14	RPS14	4763	0.051	0.25	YES
35	RPS24	RPS24	RPS24	4772	0.051	0.26	YES
36	RPS20	RPS20	RPS20	4802	0.05	0.27	YES
37	RPL35	RPL35	RPL35	4891	0.048	0.27	YES
38	RPL27	RPL27	RPL27	4987	0.047	0.28	YES
39	RPLP2	RPLP2	RPLP2	4996	0.047	0.29	YES
40	RPS2	RPS2	RPS2	5025	0.046	0.3	YES
41	RPSA	RPSA	RPSA	5045	0.046	0.3	YES
42	RPS23	RPS23	RPS23	5068	0.045	0.31	YES
43	RPS18	RPS18	RPS18	5225	0.043	0.31	YES
44	RPL23A	RPL23A	RPL23A	5256	0.043	0.32	YES
45	RPS5	RPS5	RPS5	5278	0.042	0.32	YES
46	RPL14	RPL14	RPL14	5284	0.042	0.33	YES
47	RPS9	RPS9	RPS9	5288	0.042	0.34	YES
48	RPLP1	RPLP1	RPLP1	5334	0.041	0.35	YES
49	RPS7	RPS7	RPS7	5348	0.041	0.36	YES
50	RPL10	RPL10	RPL10	5428	0.04	0.36	YES
51	RPL24	RPL24	RPL24	5429	0.04	0.37	YES
52	RPS13	RPS13	RPS13	5577	0.038	0.36	YES
53	RPS11	RPS11	RPS11	5664	0.037	0.37	YES
54	RPL11	RPL11	RPL11	5717	0.036	0.37	YES
55	RPS21	RPS21	RPS21	5720	0.036	0.38	YES
56	RPL30	RPL30	RPL30	5769	0.035	0.38	YES
57	RPS16	RPS16	RPS16	5783	0.035	0.39	YES
58	RPS27A	RPS27A	RPS27A	5809	0.035	0.4	YES
59	RPL27A	RPL27A	RPL27A	5854	0.034	0.4	YES
60	RPS3	RPS3	RPS3	5858	0.034	0.41	YES
61	RPS6	RPS6	RPS6	5872	0.034	0.41	YES
62	EIF3B	EIF3B	EIF3B	5887	0.034	0.42	YES
63	RPS19	RPS19	RPS19	5890	0.034	0.43	YES
64	RPL15	RPL15	RPL15	5903	0.034	0.43	YES
65	FAU	FAU	FAU	5975	0.033	0.43	YES
66	RPLP0	RPLP0	RPLP0	5994	0.033	0.44	YES
67	RPS29	RPS29	RPS29	6231	0.03	0.43	YES
68	RPL3	RPL3	RPL3	6266	0.029	0.44	YES
69	RPL6	RPL6	RPL6	6307	0.028	0.44	YES
70	RPL8	RPL8	RPL8	6322	0.028	0.44	YES
71	RPS8	RPS8	RPS8	6342	0.028	0.45	YES
72	RPS12	RPS12	RPS12	6519	0.026	0.44	YES
73	EIF2S3	EIF2S3	EIF2S3	6596	0.025	0.44	YES
74	RPL13A	RPL13A	RPL13A	6646	0.024	0.45	YES
75	EIF4A1	EIF4A1	EIF4A1	6651	0.024	0.45	YES
76	UBA52	UBA52	UBA52	6773	0.023	0.45	YES
77	RPL5	RPL5	RPL5	6803	0.022	0.45	YES
78	RPS3A	RPS3A	RPS3A	6807	0.022	0.46	YES
79	EIF3E	EIF3E	EIF3E	7047	0.02	0.45	NO
80	EIF3I	EIF3I	EIF3I	7060	0.019	0.45	NO
81	EIF1AX	EIF1AX	EIF1AX	7314	0.016	0.44	NO
82	RPL7A	RPL7A	RPL7A	7555	0.013	0.43	NO
83	EIF3J	EIF3J	EIF3J	7564	0.013	0.43	NO
84	EIF4E	EIF4E	EIF4E	7590	0.012	0.43	NO
85	EIF3F	EIF3F	EIF3F	7677	0.012	0.43	NO
86	EIF3H	EIF3H	EIF3H	7733	0.011	0.43	NO
87	EIF3G	EIF3G	EIF3G	7762	0.01	0.43	NO
88	RPS25	RPS25	RPS25	7786	0.01	0.43	NO
89	RPL4	RPL4	RPL4	7983	0.0078	0.42	NO
90	RPL19	RPL19	RPL19	8017	0.0073	0.42	NO
91	EIF4H	EIF4H	EIF4H	8270	0.0044	0.4	NO
92	RPL26L1	RPL26L1	RPL26L1	8488	0.0017	0.39	NO
93	EIF3C	EIF3C	EIF3C	8519	0.0014	0.39	NO
94	EIF3A	EIF3A	EIF3A	8812	-0.0022	0.37	NO
95	EIF3K	EIF3K	EIF3K	8873	-0.0029	0.37	NO
96	EIF4B	EIF4B	EIF4B	9319	-0.0082	0.34	NO
97	PABPC1	PABPC1	PABPC1	9502	-0.011	0.34	NO
98	EIF4G1	EIF4G1	EIF4G1	9722	-0.014	0.33	NO
99	EIF3D	EIF3D	EIF3D	9728	-0.014	0.33	NO
100	RPL7	RPL7	RPL7	9782	-0.014	0.33	NO
101	EIF2S2	EIF2S2	EIF2S2	10207	-0.02	0.31	NO
102	EIF2S1	EIF2S1	EIF2S1	11703	-0.046	0.23	NO
103	RPS27	RPS27	RPS27	13088	-0.088	0.17	NO
104	RPS4Y1	RPS4Y1	RPS4Y1	14512	-0.16	0.12	NO
105	FAM153A	FAM153A	FAM153A	15115	-0.21	0.12	NO

Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PEPTIDE CHAIN ELONGATION.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

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

GSEA analysis

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

Download Results

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

References

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

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