Pathway_GSEA_mRNA - Uveal Melanoma (Primary solid tumor)

Pathway_GSEA_mRNA

Uveal Melanoma (Primary solid tumor)

13 July 2018 | None

Maintainer Information

Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)

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 mRNA_cNMF subtypes having more than three samples and the input expression file "TCGA-UVM-TP.mRNA_FPKM_log2_protein.coding.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: 2888
Number of samples: 80
Original number of Gene Sets: 4738
Maximum gene set size: 1972

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 11
pheno.type: 2 - 5 :[ clus2 ] 11
pheno.type: 3 - 5 :[ clus3 ] 29
pheno.type: 4 - 5 :[ clus4 ] 21
pheno.type: 5 - 5 :[ clus5 ] 8

For the expression subtypes of 18131 genes in 81 samples, GSEA found enriched gene sets in each cluster using 80 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG ABC TRANSPORTERS, KEGG HOMOLOGOUS RECOMBINATION, WANG LMO4 TARGETS DN, KIM WT1 TARGETS DN, BIDUS METASTASIS UP, MAYBURD RESPONSE TO L663536 DN, ENK UV RESPONSE KERATINOCYTE DN, SEIDEN ONCOGENESIS BY MET, DACOSTA UV RESPONSE VIA ERCC3 COMMON DN, NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON

And common core enriched genes are CDK1, EPS8, RRM1, UBA2, AURKA, BUB1, CCNA2, RRM2, TOP2A, CERS6

clus2

Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG GALACTOSE METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PURINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG LYSINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM

And common core enriched genes are SYT1, DUSP1, MAPK10, ACTC1, AK4, AKAP12, ALDOC, ALPL, AMH, ANGPTL4

clus3

Top enriched gene sets are KEGG RIBOSOME, PID P53 REGULATION PATHWAY, REACTOME TRANSLATION, 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 GENERIC TRANSCRIPTION PATHWAY, REACTOME PEPTIDE CHAIN ELONGATION, REACTOME MRNA PROCESSING, REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION, REACTOME INFLUENZA LIFE CYCLE

And common core enriched genes are ATR, KAT2B, UBE2D1, ZFP2, CCNG1, CDK2, CSNK1G3, DAXX, FBXO11, GSK3B

clus4

Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, SCHLOSSER MYC AND SERUM RESPONSE SYNERGY, DACOSTA UV RESPONSE VIA ERCC3 UP, DAIRKEE TERT TARGETS UP, SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP, LOCKWOOD AMPLIFIED IN LUNG CANCER, PENG LEUCINE DEPRIVATION DN, MOOTHA VOXPHOS, PENG GLUTAMINE DEPRIVATION DN, FAELT B CLL WITH VH3 21 UP

And common core enriched genes are CDK4, DDT, MRPS12, ANXA11, ATIC, CAD, CHAF1A, CLTA, CYC1, EIF4G1

clus5

Top enriched gene sets are KEGG PROTEASOME, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG APOPTOSIS, KEGG CELL ADHESION MOLECULES CAMS, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY, KEGG JAK STAT SIGNALING PATHWAY, KEGG HEMATOPOIETIC CELL LINEAGE, KEGG B CELL RECEPTOR SIGNALING PATHWAY

And common core enriched genes are PSMA1, PSMA2, PSMB8, PSMB9, BCL10, BLNK, CARD11, CDKN1A, CHUK, CREB1

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 ABC TRANSPORTERS	44	genes.ES.table	0.61	1.5	0.018	1	1	0.3	0.094	0.27	1	0.86
KEGG HOMOLOGOUS RECOMBINATION	28	genes.ES.table	0.52	1.5	0.063	1	1	0.32	0.25	0.24	1	0.89
WANG LMO4 TARGETS DN	329	genes.ES.table	0.32	1.5	0.031	1	1	0.44	0.37	0.28	1	0.87
KIM WT1 TARGETS DN	434	genes.ES.table	0.38	1.5	0.025	1	1	0.44	0.32	0.31	1	0.89
BIDUS METASTASIS UP	210	genes.ES.table	0.44	1.6	0.046	1	0.98	0.52	0.39	0.32	1	0.96
MAYBURD RESPONSE TO L663536 DN	53	genes.ES.table	0.44	1.5	0.053	1	1	0.6	0.4	0.36	1	0.89
ENK UV RESPONSE KERATINOCYTE DN	482	genes.ES.table	0.33	1.6	0.036	1	1	0.58	0.43	0.34	1	0.91
SEIDEN ONCOGENESIS BY MET	86	genes.ES.table	0.53	1.6	0.0066	1	0.96	0.77	0.4	0.46	1	0.96
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN	474	genes.ES.table	0.45	1.6	0.033	1	1	0.56	0.36	0.36	1	0.87
NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON	120	genes.ES.table	0.64	1.6	0.012	1	1	0.7	0.25	0.53	1	0.9

genes ES table in pathway: KEGG ABC TRANSPORTERS

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	EREG	EREG	EREG	390	0.42	0.033	YES
2	EEF1A2	EEF1A2	EEF1A2	1381	0.25	0.011	YES
3	LYPLA1	LYPLA1	LYPLA1	1655	0.22	0.026	YES
4	COMMD8	COMMD8	COMMD8	1860	0.21	0.042	YES
5	CXCL5	CXCL5	CXCL5	1939	0.2	0.064	YES
6	ADAM9	ADAM9	ADAM9	2307	0.18	0.067	YES
7	ITGA6	ITGA6	ITGA6	2390	0.18	0.085	YES
8	CDK1	CDK1	CDK1	2611	0.16	0.095	YES
9	SLC38A2	SLC38A2	SLC38A2	2899	0.15	0.099	YES
10	IFNGR1	IFNGR1	IFNGR1	2904	0.15	0.12	YES
11	CERS6	CERS6	CERS6	3079	0.14	0.13	YES
12	TRAM1	TRAM1	TRAM1	3096	0.14	0.15	YES
13	TCERG1	TCERG1	TCERG1	3192	0.14	0.16	YES
14	F2RL1	F2RL1	F2RL1	3218	0.14	0.18	YES
15	ANXA3	ANXA3	ANXA3	3254	0.14	0.19	YES
16	FAM208B	FAM208B	FAM208B	3418	0.13	0.2	YES
17	EPS8	EPS8	EPS8	3449	0.13	0.22	YES
18	TCEA1	TCEA1	TCEA1	3520	0.13	0.23	YES
19	CD46	CD46	CD46	3613	0.13	0.24	YES
20	CAPZA1	CAPZA1	CAPZA1	3661	0.12	0.25	YES
21	P4HA1	P4HA1	P4HA1	3843	0.12	0.26	YES
22	ACTR3	ACTR3	ACTR3	3865	0.12	0.27	YES
23	CLIC4	CLIC4	CLIC4	3868	0.12	0.29	YES
24	GBAS	GBAS	GBAS	3871	0.12	0.3	YES
25	ANXA4	ANXA4	ANXA4	3970	0.12	0.32	YES
26	UGDH	UGDH	UGDH	4116	0.11	0.32	YES
27	SEC23A	SEC23A	SEC23A	4272	0.11	0.33	YES
28	GLS	GLS	GLS	4309	0.11	0.34	YES
29	ATP2A1	ATP2A1	ATP2A1	4363	0.1	0.35	YES
30	HSP90AA1	HSP90AA1	HSP90AA1	4487	0.1	0.36	YES
31	NCKAP1	NCKAP1	NCKAP1	4624	0.098	0.36	YES
32	UBA2	UBA2	UBA2	4641	0.098	0.37	YES
33	TMEM123	TMEM123	TMEM123	4768	0.095	0.38	YES
34	HAT1	HAT1	HAT1	4786	0.095	0.39	YES
35	LAMB1	LAMB1	LAMB1	4924	0.091	0.4	YES
36	TMX1	TMX1	TMX1	5009	0.089	0.4	YES
37	SEP15	SEP15	SEP15	5013	0.089	0.41	YES
38	ZBED5	ZBED5	ZBED5	5435	0.079	0.4	YES
39	RIOK3	RIOK3	RIOK3	5453	0.079	0.41	YES
40	RRM1	RRM1	RRM1	5468	0.078	0.42	YES
41	PAPOLA	PAPOLA	PAPOLA	5503	0.078	0.43	YES
42	IPO7	IPO7	IPO7	5540	0.077	0.44	YES
43	PDE8A	PDE8A	PDE8A	5583	0.076	0.44	YES
44	PPP1CB	PPP1CB	PPP1CB	5734	0.072	0.44	YES
45	PCMT1	PCMT1	PCMT1	5736	0.072	0.46	YES
46	AASDHPPT	AASDHPPT	AASDHPPT	5777	0.072	0.46	YES
47	EIF5	EIF5	EIF5	5791	0.071	0.47	YES
48	MSMO1	MSMO1	MSMO1	5847	0.07	0.48	YES
49	SLC25A24	SLC25A24	SLC25A24	5864	0.07	0.48	YES
50	TAF1D	TAF1D	TAF1D	5911	0.069	0.49	YES
51	YME1L1	YME1L1	YME1L1	5942	0.068	0.5	YES
52	ARHGEF12	ARHGEF12	ARHGEF12	6018	0.066	0.5	YES
53	SPTLC1	SPTLC1	SPTLC1	6114	0.064	0.51	YES
54	SERINC1	SERINC1	SERINC1	6136	0.064	0.51	YES
55	SRP72	SRP72	SRP72	6140	0.064	0.52	YES
56	MBNL1	MBNL1	MBNL1	6259	0.061	0.52	YES
57	SUB1	SUB1	SUB1	6535	0.056	0.52	YES
58	C6orf62	C6orf62	C6orf62	6708	0.053	0.51	YES
59	HSPA4	HSPA4	HSPA4	6792	0.051	0.52	YES
60	PLS3	PLS3	PLS3	6856	0.05	0.52	YES
61	AIDA	AIDA	AIDA	6901	0.049	0.52	YES
62	MBIP	MBIP	MBIP	6916	0.049	0.53	YES
63	DPM1	DPM1	DPM1	7212	0.043	0.52	YES
64	RSL24D1	RSL24D1	RSL24D1	7224	0.043	0.52	YES
65	SH3BGRL	SH3BGRL	SH3BGRL	7233	0.043	0.53	YES
66	SLC39A6	SLC39A6	SLC39A6	7293	0.042	0.53	YES
67	CCT6A	CCT6A	CCT6A	8213	0.024	0.48	NO
68	SCP2	SCP2	SCP2	8527	0.018	0.47	NO
69	NPM1	NPM1	NPM1	8726	0.015	0.46	NO
70	GRSF1	GRSF1	GRSF1	8750	0.014	0.46	NO
71	COMMD3	COMMD3	COMMD3	8835	0.013	0.46	NO
72	PNRC2	PNRC2	PNRC2	8969	0.01	0.45	NO
73	HNRNPA3	HNRNPA3	HNRNPA3	9057	0.009	0.45	NO
74	HIGD1A	HIGD1A	HIGD1A	9189	0.0065	0.44	NO
75	PTEN	PTEN	PTEN	9208	0.0062	0.44	NO
76	MMADHC	MMADHC	MMADHC	9240	0.0055	0.44	NO
77	NSA2	NSA2	NSA2	9769	-0.0035	0.41	NO
78	HNRNPH2	HNRNPH2	HNRNPH2	9923	-0.0057	0.4	NO
79	STAT1	STAT1	STAT1	10081	-0.0088	0.39	NO
80	SERBP1	SERBP1	SERBP1	10107	-0.0091	0.39	NO
81	PLOD2	PLOD2	PLOD2	11051	-0.024	0.34	NO
82	GNAI3	GNAI3	GNAI3	11059	-0.024	0.35	NO
83	CSDE1	CSDE1	CSDE1	11648	-0.032	0.32	NO
84	IFITM1	IFITM1	IFITM1	14451	-0.076	0.17	NO
85	SERP1	SERP1	SERP1	14548	-0.078	0.18	NO
86	TSPAN8	TSPAN8	TSPAN8	16618	-0.14	0.082	NO

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

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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	ARX	ARX	ARX	46	0.66	0.038	YES
2	PPP1R14C	PPP1R14C	PPP1R14C	55	0.63	0.075	YES
3	SUMO4	SUMO4	SUMO4	430	0.41	0.079	YES
4	DEPDC1	DEPDC1	DEPDC1	847	0.32	0.075	YES
5	MPHOSPH9	MPHOSPH9	MPHOSPH9	1153	0.28	0.075	YES
6	CREB5	CREB5	CREB5	1246	0.26	0.086	YES
7	CASC5	CASC5	CASC5	1370	0.25	0.094	YES
8	DLGAP5	DLGAP5	DLGAP5	1617	0.23	0.094	YES
9	SMC4	SMC4	SMC4	1650	0.22	0.11	YES
10	MCM10	MCM10	MCM10	1723	0.22	0.12	YES
11	DBF4	DBF4	DBF4	1799	0.21	0.12	YES
12	SQLE	SQLE	SQLE	1902	0.2	0.13	YES
13	CENPF	CENPF	CENPF	2060	0.19	0.13	YES
14	MTDH	MTDH	MTDH	2079	0.19	0.14	YES
15	ERCC6L	ERCC6L	ERCC6L	2249	0.18	0.15	YES
16	KLHL23	KLHL23	KLHL23	2317	0.18	0.15	YES
17	STRN3	STRN3	STRN3	2365	0.18	0.16	YES
18	UBXN2B	UBXN2B	UBXN2B	2368	0.18	0.17	YES
19	PLK4	PLK4	PLK4	2370	0.18	0.18	YES
20	CDK1	CDK1	CDK1	2611	0.16	0.18	YES
21	GAS2L3	GAS2L3	GAS2L3	2637	0.16	0.19	YES
22	IFT81	IFT81	IFT81	2706	0.16	0.19	YES
23	PAGE2B	PAGE2B	PAGE2B	2739	0.16	0.2	YES
24	DNAAF2	DNAAF2	DNAAF2	2793	0.16	0.21	YES
25	PBK	PBK	PBK	2810	0.15	0.22	YES
26	KIF11	KIF11	KIF11	2819	0.15	0.23	YES
27	PRKDC	PRKDC	PRKDC	2824	0.15	0.24	YES
28	BUB1	BUB1	BUB1	2923	0.15	0.24	YES
29	CCNA2	CCNA2	CCNA2	2981	0.15	0.24	YES
30	LARP4	LARP4	LARP4	3033	0.15	0.25	YES
31	AZIN1	AZIN1	AZIN1	3165	0.14	0.25	YES
32	RRM2	RRM2	RRM2	3209	0.14	0.26	YES
33	MAD2L1	MAD2L1	MAD2L1	3286	0.14	0.26	YES
34	ATF2	ATF2	ATF2	3390	0.13	0.26	YES
35	SGMS2	SGMS2	SGMS2	3603	0.13	0.26	YES
36	FSD1L	FSD1L	FSD1L	3642	0.12	0.27	YES
37	WDHD1	WDHD1	WDHD1	3770	0.12	0.27	YES
38	CDC6	CDC6	CDC6	3820	0.12	0.27	YES
39	CENPA	CENPA	CENPA	3835	0.12	0.28	YES
40	NCAPH	NCAPH	NCAPH	3837	0.12	0.28	YES
41	P4HA1	P4HA1	P4HA1	3843	0.12	0.29	YES
42	ECT2	ECT2	ECT2	3859	0.12	0.3	YES
43	CEBPG	CEBPG	CEBPG	3965	0.12	0.3	YES
44	CBFB	CBFB	CBFB	3969	0.12	0.31	YES
45	ATP6V0A2	ATP6V0A2	ATP6V0A2	3977	0.12	0.31	YES
46	DDX21	DDX21	DDX21	3988	0.12	0.32	YES
47	EIF4E	EIF4E	EIF4E	4001	0.12	0.32	YES
48	CCNB2	CCNB2	CCNB2	4060	0.11	0.33	YES
49	DHFR	DHFR	DHFR	4075	0.11	0.34	YES
50	MRPL42	MRPL42	MRPL42	4199	0.11	0.34	YES
51	ZIC2	ZIC2	ZIC2	4210	0.11	0.34	YES
52	SEC23A	SEC23A	SEC23A	4272	0.11	0.34	YES
53	MLLT10	MLLT10	MLLT10	4278	0.11	0.35	YES
54	HMGXB4	HMGXB4	HMGXB4	4333	0.1	0.35	YES
55	CAND1	CAND1	CAND1	4340	0.1	0.36	YES
56	NUSAP1	NUSAP1	NUSAP1	4380	0.1	0.36	YES
57	TMEM33	TMEM33	TMEM33	4446	0.1	0.37	YES
58	HSP90AA1	HSP90AA1	HSP90AA1	4487	0.1	0.37	YES
59	LCA5L	LCA5L	LCA5L	4562	0.1	0.37	YES
60	FANCI	FANCI	FANCI	4598	0.099	0.38	YES
61	RNF138	RNF138	RNF138	4625	0.098	0.38	YES
62	SLMO2	SLMO2	SLMO2	4630	0.098	0.39	YES
63	SEC24B	SEC24B	SEC24B	4693	0.096	0.39	YES
64	PAIP1	PAIP1	PAIP1	4723	0.096	0.39	YES
65	NF1	NF1	NF1	4923	0.091	0.39	YES
66	CENPN	CENPN	CENPN	4925	0.091	0.39	YES
67	HBS1L	HBS1L	HBS1L	4962	0.09	0.4	YES
68	TYMS	TYMS	TYMS	5025	0.088	0.4	YES
69	WHSC1	WHSC1	WHSC1	5181	0.085	0.4	YES
70	RHBDL3	RHBDL3	RHBDL3	5219	0.084	0.4	YES
71	TMEM194A	TMEM194A	TMEM194A	5270	0.083	0.4	YES
72	GMNN	GMNN	GMNN	5332	0.082	0.4	YES
73	KDM6A	KDM6A	KDM6A	5374	0.08	0.4	YES
74	RRM1	RRM1	RRM1	5468	0.078	0.4	YES
75	AURKA	AURKA	AURKA	5686	0.074	0.4	YES
76	ARPP19	ARPP19	ARPP19	5747	0.072	0.4	YES
77	TFRC	TFRC	TFRC	5756	0.072	0.4	YES
78	PCNX	PCNX	PCNX	5815	0.071	0.4	YES
79	RACGAP1	RACGAP1	RACGAP1	5817	0.071	0.41	YES
80	DCTN4	DCTN4	DCTN4	5823	0.07	0.41	YES
81	VBP1	VBP1	VBP1	5833	0.07	0.42	YES
82	FBXO3	FBXO3	FBXO3	5842	0.07	0.42	YES
83	CCDC47	CCDC47	CCDC47	5846	0.07	0.42	YES
84	PHF10	PHF10	PHF10	5936	0.068	0.42	YES
85	RLIM	RLIM	RLIM	5955	0.068	0.42	YES
86	RCOR1	RCOR1	RCOR1	6173	0.063	0.42	YES
87	CEP57	CEP57	CEP57	6281	0.061	0.42	YES
88	RRN3	RRN3	RRN3	6304	0.06	0.42	YES
89	USP9X	USP9X	USP9X	6382	0.059	0.42	YES
90	RAB22A	RAB22A	RAB22A	6402	0.059	0.42	YES
91	BPTF	BPTF	BPTF	6414	0.058	0.42	YES
92	RAB28	RAB28	RAB28	6482	0.057	0.42	YES
93	WAC	WAC	WAC	6483	0.057	0.42	YES
94	CCDC15	CCDC15	CCDC15	6563	0.055	0.42	YES
95	SRSF2	SRSF2	SRSF2	6603	0.054	0.42	YES
96	ZNF550	ZNF550	ZNF550	6764	0.052	0.42	YES
97	MAPKAPK5	MAPKAPK5	MAPKAPK5	6800	0.051	0.42	YES
98	KLC1	KLC1	KLC1	6811	0.051	0.42	YES
99	BIRC5	BIRC5	BIRC5	6826	0.051	0.42	YES
100	SRSF1	SRSF1	SRSF1	6830	0.051	0.43	YES
101	EFHC1	EFHC1	EFHC1	6859	0.05	0.43	YES
102	C5orf22	C5orf22	C5orf22	6885	0.05	0.43	YES
103	MED14	MED14	MED14	6887	0.05	0.43	YES
104	MNS1	MNS1	MNS1	6933	0.049	0.44	YES
105	TLK2	TLK2	TLK2	6958	0.048	0.44	YES
106	PREPL	PREPL	PREPL	7017	0.047	0.44	YES
107	MAPK1	MAPK1	MAPK1	7042	0.046	0.44	YES
108	CDC23	CDC23	CDC23	7097	0.045	0.44	YES
109	CRY1	CRY1	CRY1	7106	0.045	0.44	YES
110	CDK2AP1	CDK2AP1	CDK2AP1	7118	0.045	0.44	YES
111	CCNB1	CCNB1	CCNB1	7222	0.043	0.44	NO
112	CSE1L	CSE1L	CSE1L	7287	0.042	0.44	NO
113	LMNB1	LMNB1	LMNB1	7315	0.041	0.44	NO
114	SFPQ	SFPQ	SFPQ	7372	0.04	0.44	NO
115	PSMD10	PSMD10	PSMD10	7471	0.038	0.44	NO
116	NRAS	NRAS	NRAS	7519	0.037	0.43	NO
117	COPS8	COPS8	COPS8	7581	0.036	0.43	NO
118	PPP2CA	PPP2CA	PPP2CA	7614	0.036	0.43	NO
119	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	7650	0.035	0.43	NO
120	TPX2	TPX2	TPX2	7743	0.033	0.43	NO
121	PTP4A1	PTP4A1	PTP4A1	7747	0.033	0.43	NO
122	SNRPD1	SNRPD1	SNRPD1	7828	0.031	0.43	NO
123	RFC5	RFC5	RFC5	7947	0.029	0.42	NO
124	KIF1B	KIF1B	KIF1B	8036	0.027	0.42	NO
125	ADNP	ADNP	ADNP	8098	0.026	0.42	NO
126	H2AFY	H2AFY	H2AFY	8166	0.025	0.42	NO
127	SRSF9	SRSF9	SRSF9	8184	0.025	0.42	NO
128	HNRNPR	HNRNPR	HNRNPR	8227	0.024	0.42	NO
129	TSR1	TSR1	TSR1	8259	0.023	0.42	NO
130	HNRNPH3	HNRNPH3	HNRNPH3	8302	0.022	0.42	NO
131	RABGAP1L	RABGAP1L	RABGAP1L	8303	0.022	0.42	NO
132	HSF2	HSF2	HSF2	8306	0.022	0.42	NO
133	RABGGTB	RABGGTB	RABGGTB	8315	0.022	0.42	NO
134	HMGB3	HMGB3	HMGB3	8321	0.022	0.42	NO
135	SLC35B4	SLC35B4	SLC35B4	8356	0.021	0.42	NO
136	BCL7A	BCL7A	BCL7A	8458	0.019	0.42	NO
137	G3BP1	G3BP1	G3BP1	8462	0.019	0.42	NO
138	CBLL1	CBLL1	CBLL1	8491	0.019	0.42	NO
139	SMS	SMS	SMS	8562	0.018	0.41	NO
140	CKAP5	CKAP5	CKAP5	8609	0.017	0.41	NO
141	AMD1	AMD1	AMD1	8613	0.017	0.41	NO
142	VDAC1	VDAC1	VDAC1	8640	0.016	0.41	NO
143	KIF4A	KIF4A	KIF4A	8766	0.014	0.41	NO
144	TTF2	TTF2	TTF2	8875	0.012	0.4	NO
145	WRB	WRB	WRB	8959	0.011	0.4	NO
146	SNRNP27	SNRNP27	SNRNP27	8974	0.01	0.4	NO
147	NUP153	NUP153	NUP153	8989	0.01	0.4	NO
148	PTGES3	PTGES3	PTGES3	9026	0.0095	0.4	NO
149	AZI2	AZI2	AZI2	9130	0.0076	0.39	NO
150	DKC1	DKC1	DKC1	9175	0.0067	0.39	NO
151	PNMA1	PNMA1	PNMA1	9180	0.0067	0.39	NO
152	AGAP1	AGAP1	AGAP1	9211	0.0061	0.39	NO
153	SRSF12	SRSF12	SRSF12	9277	0.0049	0.38	NO
154	TFDP1	TFDP1	TFDP1	9281	0.0048	0.38	NO
155	USP13	USP13	USP13	9348	0.0036	0.38	NO
156	ASF1B	ASF1B	ASF1B	9378	0.0031	0.38	NO
157	HNRNPK	HNRNPK	HNRNPK	9392	0.0028	0.38	NO
158	TUBGCP4	TUBGCP4	TUBGCP4	9446	0.002	0.38	NO
159	RBBP4	RBBP4	RBBP4	9476	0.0015	0.37	NO
160	YWHAE	YWHAE	YWHAE	9538	0.00025	0.37	NO
161	SMC1A	SMC1A	SMC1A	9540	0.00022	0.37	NO
162	CHEK1	CHEK1	CHEK1	9545	0.00017	0.37	NO
163	TRA2B	TRA2B	TRA2B	9572	-0.00021	0.37	NO
164	ZNF318	ZNF318	ZNF318	9606	-0.00072	0.37	NO
165	YTHDF1	YTHDF1	YTHDF1	9624	-0.0011	0.37	NO
166	RMND5A	RMND5A	RMND5A	9962	-0.0062	0.35	NO
167	KHDRBS1	KHDRBS1	KHDRBS1	9985	-0.0067	0.35	NO
168	NAP1L1	NAP1L1	NAP1L1	10032	-0.0079	0.34	NO
169	FEN1	FEN1	FEN1	10067	-0.0085	0.34	NO
170	EIF4A3	EIF4A3	EIF4A3	10077	-0.0086	0.34	NO
171	PLD6	PLD6	PLD6	10102	-0.0091	0.34	NO
172	CDYL	CDYL	CDYL	10110	-0.0092	0.34	NO
173	HNRNPU	HNRNPU	HNRNPU	10232	-0.011	0.34	NO
174	NDRG3	NDRG3	NDRG3	10250	-0.011	0.34	NO
175	RFC4	RFC4	RFC4	10318	-0.012	0.33	NO
176	WBP11	WBP11	WBP11	10322	-0.012	0.33	NO
177	UBQLN2	UBQLN2	UBQLN2	10409	-0.014	0.33	NO
178	UBE2C	UBE2C	UBE2C	10745	-0.019	0.31	NO
179	PNMAL1	PNMAL1	PNMAL1	10756	-0.019	0.31	NO
180	ODC1	ODC1	ODC1	10780	-0.019	0.31	NO
181	SRD5A1	SRD5A1	SRD5A1	10893	-0.021	0.31	NO
182	UNK	UNK	UNK	10925	-0.022	0.31	NO
183	PLOD2	PLOD2	PLOD2	11051	-0.024	0.3	NO
184	H2AFZ	H2AFZ	H2AFZ	11115	-0.024	0.3	NO
185	PCBP1	PCBP1	PCBP1	11226	-0.026	0.3	NO
186	YBX1	YBX1	YBX1	11430	-0.029	0.28	NO
187	PAK2	PAK2	PAK2	11496	-0.03	0.28	NO
188	PATL1	PATL1	PATL1	11613	-0.032	0.28	NO
189	TARDBP	TARDBP	TARDBP	11658	-0.032	0.28	NO
190	ELAVL1	ELAVL1	ELAVL1	11673	-0.033	0.28	NO
191	NCBP2	NCBP2	NCBP2	11736	-0.034	0.28	NO
192	CCNY	CCNY	CCNY	12058	-0.038	0.26	NO
193	CRKL	CRKL	CRKL	12085	-0.039	0.26	NO
194	MEAF6	MEAF6	MEAF6	12122	-0.039	0.26	NO
195	SSRP1	SSRP1	SSRP1	12127	-0.039	0.27	NO
196	HNRNPD	HNRNPD	HNRNPD	12193	-0.04	0.26	NO
197	NONO	NONO	NONO	12252	-0.041	0.26	NO
198	RAE1	RAE1	RAE1	12272	-0.041	0.27	NO
199	CCDC57	CCDC57	CCDC57	12308	-0.042	0.27	NO
200	HUWE1	HUWE1	HUWE1	13002	-0.052	0.23	NO
201	EIF1	EIF1	EIF1	13023	-0.052	0.23	NO
202	FEM1A	FEM1A	FEM1A	13671	-0.063	0.2	NO
203	ANKRD54	ANKRD54	ANKRD54	13809	-0.065	0.2	NO
204	KCTD6	KCTD6	KCTD6	14181	-0.071	0.18	NO
205	RAB7A	RAB7A	RAB7A	14855	-0.084	0.15	NO
206	MARCKS	MARCKS	MARCKS	14916	-0.085	0.15	NO
207	DSP	DSP	DSP	15514	-0.098	0.12	NO
208	NFIB	NFIB	NFIB	15945	-0.11	0.1	NO
209	STK24	STK24	STK24	15994	-0.11	0.11	NO
210	FNDC5	FNDC5	FNDC5	16465	-0.13	0.091	NO

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

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HOMOLOGOUS RECOMBINATION, 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: WANG LMO4 TARGETS DN

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	RAD54B	RAD54B	RAD54B	982	0.3	-0.04	YES
2	BAG2	BAG2	BAG2	1065	0.29	-0.03	YES
3	GTF2H2	GTF2H2	GTF2H2	1099	0.28	-0.017	YES
4	SACS	SACS	SACS	1378	0.25	-0.02	YES
5	HS3ST3B1	HS3ST3B1	HS3ST3B1	1578	0.23	-0.02	YES
6	FBXL7	FBXL7	FBXL7	1583	0.23	-0.008	YES
7	JMJD1C	JMJD1C	JMJD1C	1730	0.22	-0.0051	YES
8	TOP2A	TOP2A	TOP2A	1842	0.21	-0.00069	YES
9	SMARCA5	SMARCA5	SMARCA5	2126	0.19	-0.0069	YES
10	NLRC4	NLRC4	NLRC4	2194	0.19	-0.0012	YES
11	ANLN	ANLN	ANLN	2262	0.18	0.0044	YES
12	TBK1	TBK1	TBK1	2326	0.18	0.0099	YES
13	WEE1	WEE1	WEE1	2345	0.18	0.018	YES
14	VCAN	VCAN	VCAN	2527	0.17	0.016	YES
15	STK17B	STK17B	STK17B	2572	0.17	0.022	YES
16	CDK1	CDK1	CDK1	2611	0.16	0.028	YES
17	C8orf76	C8orf76	C8orf76	2680	0.16	0.033	YES
18	FNDC3A	FNDC3A	FNDC3A	2774	0.16	0.036	YES
19	NET1	NET1	NET1	2776	0.16	0.044	YES
20	DNAAF2	DNAAF2	DNAAF2	2793	0.16	0.05	YES
21	KIF11	KIF11	KIF11	2819	0.15	0.057	YES
22	PKN2	PKN2	PKN2	2850	0.15	0.063	YES
23	BUB1	BUB1	BUB1	2923	0.15	0.067	YES
24	JAG1	JAG1	JAG1	2927	0.15	0.074	YES
25	CCNA2	CCNA2	CCNA2	2981	0.15	0.079	YES
26	TDG	TDG	TDG	3011	0.15	0.085	YES
27	RBM25	RBM25	RBM25	3037	0.15	0.091	YES
28	TCERG1	TCERG1	TCERG1	3192	0.14	0.089	YES
29	BTAF1	BTAF1	BTAF1	3223	0.14	0.095	YES
30	MAP3K7	MAP3K7	MAP3K7	3283	0.14	0.098	YES
31	PSMD14	PSMD14	PSMD14	3295	0.14	0.1	YES
32	CEP55	CEP55	CEP55	3299	0.14	0.11	YES
33	RAP1B	RAP1B	RAP1B	3326	0.14	0.12	YES
34	DCK	DCK	DCK	3327	0.14	0.12	YES
35	OGT	OGT	OGT	3373	0.13	0.13	YES
36	ARFGEF2	ARFGEF2	ARFGEF2	3409	0.13	0.13	YES
37	EPS8	EPS8	EPS8	3449	0.13	0.14	YES
38	FRYL	FRYL	FRYL	3457	0.13	0.14	YES
39	RBM27	RBM27	RBM27	3459	0.13	0.15	YES
40	ZMYM2	ZMYM2	ZMYM2	3468	0.13	0.16	YES
41	TIAM2	TIAM2	TIAM2	3508	0.13	0.16	YES
42	MRPL1	MRPL1	MRPL1	3572	0.13	0.16	YES
43	BIRC2	BIRC2	BIRC2	3676	0.12	0.16	YES
44	RAB2A	RAB2A	RAB2A	3691	0.12	0.17	YES
45	PSMC6	PSMC6	PSMC6	3695	0.12	0.18	YES
46	TMPO	TMPO	TMPO	3737	0.12	0.18	YES
47	HERC4	HERC4	HERC4	3790	0.12	0.18	YES
48	TP53INP1	TP53INP1	TP53INP1	3823	0.12	0.19	YES
49	USP8	USP8	USP8	3891	0.12	0.19	YES
50	FBXL3	FBXL3	FBXL3	3936	0.12	0.19	YES
51	GOPC	GOPC	GOPC	3946	0.12	0.2	YES
52	ACSL3	ACSL3	ACSL3	3971	0.12	0.2	YES
53	DDX21	DDX21	DDX21	3988	0.12	0.21	YES
54	NOC3L	NOC3L	NOC3L	4050	0.11	0.21	YES
55	CDC27	CDC27	CDC27	4104	0.11	0.21	YES
56	CRLF3	CRLF3	CRLF3	4120	0.11	0.22	YES
57	PHF6	PHF6	PHF6	4122	0.11	0.22	YES
58	RSRC2	RSRC2	RSRC2	4204	0.11	0.22	YES
59	BLZF1	BLZF1	BLZF1	4225	0.11	0.23	YES
60	CXXC5	CXXC5	CXXC5	4228	0.11	0.24	YES
61	ELOVL6	ELOVL6	ELOVL6	4247	0.11	0.24	YES
62	CCNH	CCNH	CCNH	4288	0.11	0.24	YES
63	ATG5	ATG5	ATG5	4292	0.11	0.25	YES
64	STK17A	STK17A	STK17A	4295	0.11	0.25	YES
65	TARBP1	TARBP1	TARBP1	4349	0.1	0.26	YES
66	BIRC6	BIRC6	BIRC6	4383	0.1	0.26	YES
67	FOSL1	FOSL1	FOSL1	4412	0.1	0.26	YES
68	GCC2	GCC2	GCC2	4445	0.1	0.27	YES
69	PSMA4	PSMA4	PSMA4	4526	0.1	0.27	YES
70	SRPK2	SRPK2	SRPK2	4530	0.1	0.27	YES
71	CORO1C	CORO1C	CORO1C	4589	0.099	0.27	YES
72	PEX1	PEX1	PEX1	4612	0.098	0.28	YES
73	UBA2	UBA2	UBA2	4641	0.098	0.28	YES
74	CDC42BPA	CDC42BPA	CDC42BPA	4828	0.094	0.28	YES
75	HIST1H4B	HIST1H4B	HIST1H4B	4845	0.093	0.28	YES
76	SIRT1	SIRT1	SIRT1	4910	0.092	0.28	YES
77	PJA2	PJA2	PJA2	4927	0.091	0.28	YES
78	MRPL15	MRPL15	MRPL15	4955	0.09	0.29	YES
79	LBR	LBR	LBR	4974	0.09	0.29	YES
80	CDC25C	CDC25C	CDC25C	5056	0.088	0.29	YES
81	LHFPL2	LHFPL2	LHFPL2	5064	0.088	0.29	YES
82	TRIM24	TRIM24	TRIM24	5142	0.086	0.29	YES
83	GAPVD1	GAPVD1	GAPVD1	5189	0.085	0.3	YES
84	ATF1	ATF1	ATF1	5197	0.085	0.3	YES
85	SYNE1	SYNE1	SYNE1	5198	0.085	0.3	YES
86	DIS3	DIS3	DIS3	5237	0.084	0.31	YES
87	PTPRK	PTPRK	PTPRK	5247	0.084	0.31	YES
88	ZNF281	ZNF281	ZNF281	5295	0.083	0.31	YES
89	TXNRD1	TXNRD1	TXNRD1	5360	0.081	0.31	YES
90	GABPB2	GABPB2	GABPB2	5390	0.08	0.32	YES
91	CFLAR	CFLAR	CFLAR	5405	0.08	0.32	YES
92	HSPH1	HSPH1	HSPH1	5416	0.08	0.32	YES
93	MED17	MED17	MED17	5423	0.08	0.32	YES
94	UBE2T	UBE2T	UBE2T	5430	0.079	0.33	YES
95	ZMYND8	ZMYND8	ZMYND8	5528	0.077	0.33	YES
96	IPO7	IPO7	IPO7	5540	0.077	0.33	YES
97	SAMD4A	SAMD4A	SAMD4A	5570	0.076	0.33	YES
98	PPP2R5E	PPP2R5E	PPP2R5E	5597	0.076	0.34	YES
99	CDK7	CDK7	CDK7	5642	0.074	0.34	YES
100	AURKA	AURKA	AURKA	5686	0.074	0.34	YES
101	MRPS35	MRPS35	MRPS35	5746	0.072	0.34	YES
102	RSPRY1	RSPRY1	RSPRY1	5834	0.07	0.34	YES
103	RAB6A	RAB6A	RAB6A	5908	0.069	0.34	YES
104	FAM175B	FAM175B	FAM175B	5921	0.069	0.34	YES
105	DNAJA2	DNAJA2	DNAJA2	5945	0.068	0.34	YES
106	SSFA2	SSFA2	SSFA2	5961	0.068	0.34	YES
107	USP12	USP12	USP12	6014	0.066	0.34	YES
108	SLC4A1AP	SLC4A1AP	SLC4A1AP	6042	0.066	0.35	YES
109	C11orf30	C11orf30	C11orf30	6083	0.065	0.35	YES
110	MTIF2	MTIF2	MTIF2	6166	0.063	0.35	YES
111	RCOR1	RCOR1	RCOR1	6173	0.063	0.35	YES
112	CDC5L	CDC5L	CDC5L	6233	0.062	0.35	YES
113	GTF2H1	GTF2H1	GTF2H1	6283	0.061	0.35	YES
114	TOP1	TOP1	TOP1	6332	0.06	0.35	YES
115	MAP3K4	MAP3K4	MAP3K4	6353	0.059	0.35	YES
116	EPS15	EPS15	EPS15	6509	0.056	0.35	YES
117	HDAC2	HDAC2	HDAC2	6513	0.056	0.35	YES
118	PLAG1	PLAG1	PLAG1	6539	0.056	0.35	YES
119	DTL	DTL	DTL	6550	0.055	0.35	YES
120	EIF3A	EIF3A	EIF3A	6561	0.055	0.36	YES
121	HIST1H4C	HIST1H4C	HIST1H4C	6567	0.055	0.36	YES
122	PRKD3	PRKD3	PRKD3	6609	0.054	0.36	YES
123	RNF14	RNF14	RNF14	6724	0.052	0.35	YES
124	RAB1A	RAB1A	RAB1A	6732	0.052	0.36	YES
125	RAD23B	RAD23B	RAD23B	6741	0.052	0.36	YES
126	MAP7D3	MAP7D3	MAP7D3	6751	0.052	0.36	YES
127	GLRX	GLRX	GLRX	6761	0.052	0.36	YES
128	RABGAP1	RABGAP1	RABGAP1	6781	0.052	0.36	YES
129	MAPKAPK5	MAPKAPK5	MAPKAPK5	6800	0.051	0.37	YES
130	FZD1	FZD1	FZD1	6820	0.051	0.37	YES
131	PCNA	PCNA	PCNA	6844	0.05	0.37	YES
132	PANX1	PANX1	PANX1	6862	0.05	0.37	YES
133	UBR7	UBR7	UBR7	6875	0.05	0.37	YES
134	VEGFC	VEGFC	VEGFC	6920	0.049	0.37	YES
135	PSMC2	PSMC2	PSMC2	6935	0.049	0.37	YES
136	LRRC8C	LRRC8C	LRRC8C	6993	0.047	0.37	YES
137	SUPV3L1	SUPV3L1	SUPV3L1	6994	0.047	0.38	YES
138	EML4	EML4	EML4	7087	0.046	0.37	YES
139	CDC23	CDC23	CDC23	7097	0.045	0.37	YES
140	IMMP2L	IMMP2L	IMMP2L	7173	0.044	0.37	YES
141	CDK5R1	CDK5R1	CDK5R1	7187	0.044	0.37	YES
142	PRIM2	PRIM2	PRIM2	7322	0.041	0.37	YES
143	PRKACB	PRKACB	PRKACB	7350	0.04	0.37	YES
144	NPAS2	NPAS2	NPAS2	7361	0.04	0.37	YES
145	GGPS1	GGPS1	GGPS1	7399	0.04	0.37	YES
146	KIAA1279	KIAA1279	KIAA1279	7416	0.039	0.37	YES
147	CRK	CRK	CRK	7439	0.039	0.37	YES
148	HSPA8	HSPA8	HSPA8	7505	0.038	0.37	YES
149	MYCBP2	MYCBP2	MYCBP2	7599	0.036	0.37	YES
150	DDX20	DDX20	DDX20	7601	0.036	0.37	YES
151	CMPK1	CMPK1	CMPK1	7676	0.034	0.37	YES
152	MTMR4	MTMR4	MTMR4	7683	0.034	0.37	YES
153	ZNF345	ZNF345	ZNF345	7686	0.034	0.37	YES
154	POLD3	POLD3	POLD3	7723	0.033	0.37	YES
155	HSPE1	HSPE1	HSPE1	7726	0.033	0.37	YES
156	SRSF3	SRSF3	SRSF3	7753	0.033	0.37	YES
157	UCK2	UCK2	UCK2	7758	0.033	0.37	YES
158	C15orf41	C15orf41	C15orf41	7759	0.033	0.37	YES
159	SON	SON	SON	7775	0.032	0.38	YES
160	FNTA	FNTA	FNTA	7777	0.032	0.38	YES
161	TBL1XR1	TBL1XR1	TBL1XR1	7819	0.032	0.38	YES
162	FKBP15	FKBP15	FKBP15	7845	0.031	0.38	YES
163	B4GALT5	B4GALT5	B4GALT5	7856	0.031	0.38	YES
164	BUB3	BUB3	BUB3	7867	0.031	0.38	YES
165	PDGFB	PDGFB	PDGFB	7894	0.03	0.38	YES
166	GTF2B	GTF2B	GTF2B	7895	0.03	0.38	YES
167	GDI2	GDI2	GDI2	7898	0.03	0.38	YES
168	LSM14A	LSM14A	LSM14A	7907	0.03	0.38	YES
169	UBE2D3	UBE2D3	UBE2D3	7972	0.029	0.38	NO
170	RBM17	RBM17	RBM17	8029	0.028	0.38	NO
171	EGFR	EGFR	EGFR	8067	0.027	0.38	NO
172	SRSF9	SRSF9	SRSF9	8184	0.025	0.37	NO
173	ERCC3	ERCC3	ERCC3	8188	0.025	0.37	NO
174	SPIN1	SPIN1	SPIN1	8223	0.024	0.37	NO
175	RABGGTB	RABGGTB	RABGGTB	8315	0.022	0.37	NO
176	MAT2A	MAT2A	MAT2A	8350	0.022	0.37	NO
177	XRCC5	XRCC5	XRCC5	8430	0.02	0.36	NO
178	SLC25A17	SLC25A17	SLC25A17	8444	0.02	0.36	NO
179	DLG5	DLG5	DLG5	8449	0.02	0.37	NO
180	TSFM	TSFM	TSFM	8475	0.019	0.36	NO
181	USP3	USP3	USP3	8496	0.019	0.36	NO
182	PLK1	PLK1	PLK1	8673	0.016	0.36	NO
183	OSBP	OSBP	OSBP	8749	0.014	0.35	NO
184	MFAP1	MFAP1	MFAP1	8815	0.013	0.35	NO
185	MAPK14	MAPK14	MAPK14	8951	0.011	0.34	NO
186	TRIP4	TRIP4	TRIP4	8979	0.01	0.34	NO
187	PTGES3	PTGES3	PTGES3	9026	0.0095	0.34	NO
188	CCT4	CCT4	CCT4	9031	0.0094	0.34	NO
189	PSMB1	PSMB1	PSMB1	9115	0.0079	0.34	NO
190	DKC1	DKC1	DKC1	9175	0.0067	0.33	NO
191	UBE2D2	UBE2D2	UBE2D2	9210	0.0061	0.33	NO
192	OSBPL9	OSBPL9	OSBPL9	9220	0.0059	0.33	NO
193	PPP2R1B	PPP2R1B	PPP2R1B	9336	0.0037	0.32	NO
194	MID1IP1	MID1IP1	MID1IP1	9478	0.0014	0.32	NO
195	MYC	MYC	MYC	9503	0.00089	0.32	NO
196	MICAL2	MICAL2	MICAL2	9509	0.00078	0.32	NO
197	YWHAE	YWHAE	YWHAE	9538	0.00025	0.31	NO
198	ZDHHC5	ZDHHC5	ZDHHC5	9553	0.000053	0.31	NO
199	C5orf30	C5orf30	C5orf30	9558	-8.9e-06	0.31	NO
200	PPP1CC	PPP1CC	PPP1CC	9637	-0.0012	0.31	NO
201	PSMA5	PSMA5	PSMA5	9715	-0.0026	0.3	NO
202	NUFIP1	NUFIP1	NUFIP1	9752	-0.0031	0.3	NO
203	CSNK2A1	CSNK2A1	CSNK2A1	9774	-0.0036	0.3	NO
204	RIPK1	RIPK1	RIPK1	9787	-0.0038	0.3	NO
205	PAFAH2	PAFAH2	PAFAH2	9977	-0.0065	0.29	NO
206	SERBP1	SERBP1	SERBP1	10107	-0.0091	0.28	NO
207	MCTS1	MCTS1	MCTS1	10227	-0.011	0.28	NO
208	PSME3	PSME3	PSME3	10248	-0.011	0.28	NO
209	CYHR1	CYHR1	CYHR1	10280	-0.012	0.28	NO
210	ADSL	ADSL	ADSL	10284	-0.012	0.28	NO
211	CPSF7	CPSF7	CPSF7	10288	-0.012	0.28	NO
212	MCM3	MCM3	MCM3	10332	-0.012	0.28	NO
213	FOXK2	FOXK2	FOXK2	10374	-0.013	0.27	NO
214	FADD	FADD	FADD	10398	-0.014	0.27	NO
215	ARFGAP1	ARFGAP1	ARFGAP1	10539	-0.016	0.27	NO
216	EP400	EP400	EP400	10593	-0.017	0.26	NO
217	CDH11	CDH11	CDH11	10655	-0.018	0.26	NO
218	UBE2C	UBE2C	UBE2C	10745	-0.019	0.26	NO
219	RCC1	RCC1	RCC1	10758	-0.019	0.26	NO
220	ARPC5L	ARPC5L	ARPC5L	10791	-0.02	0.26	NO
221	PSMG2	PSMG2	PSMG2	10835	-0.02	0.26	NO
222	SRRM2	SRRM2	SRRM2	10889	-0.021	0.25	NO
223	ZNHIT3	ZNHIT3	ZNHIT3	10982	-0.022	0.25	NO
224	C16orf62	C16orf62	C16orf62	11057	-0.024	0.25	NO
225	EIF2A	EIF2A	EIF2A	11120	-0.025	0.24	NO
226	EPB41	EPB41	EPB41	11122	-0.025	0.24	NO
227	NMI	NMI	NMI	11212	-0.026	0.24	NO
228	USP22	USP22	USP22	11263	-0.027	0.24	NO
229	SPRY2	SPRY2	SPRY2	11345	-0.028	0.24	NO
230	CTGF	CTGF	CTGF	11360	-0.028	0.24	NO
231	FAF1	FAF1	FAF1	11539	-0.03	0.23	NO
232	TARDBP	TARDBP	TARDBP	11658	-0.032	0.22	NO
233	UBN1	UBN1	UBN1	11691	-0.033	0.22	NO
234	KDM1A	KDM1A	KDM1A	11800	-0.035	0.22	NO
235	RAB5A	RAB5A	RAB5A	11894	-0.036	0.22	NO
236	SRSF4	SRSF4	SRSF4	11951	-0.037	0.22	NO
237	LUZP1	LUZP1	LUZP1	12018	-0.038	0.21	NO
238	EIF4B	EIF4B	EIF4B	12036	-0.038	0.21	NO
239	RPP14	RPP14	RPP14	12065	-0.038	0.22	NO
240	THRAP3	THRAP3	THRAP3	12073	-0.039	0.22	NO
241	MEAF6	MEAF6	MEAF6	12122	-0.039	0.22	NO
242	ZDHHC16	ZDHHC16	ZDHHC16	12260	-0.041	0.21	NO
243	TGIF1	TGIF1	TGIF1	12262	-0.041	0.21	NO
244	STAU1	STAU1	STAU1	12343	-0.042	0.21	NO
245	NCOA6	NCOA6	NCOA6	12461	-0.044	0.2	NO
246	SNIP1	SNIP1	SNIP1	13009	-0.052	0.18	NO
247	BCL2L1	BCL2L1	BCL2L1	13085	-0.053	0.18	NO
248	TSPAN14	TSPAN14	TSPAN14	13091	-0.053	0.18	NO
249	IGF2BP2	IGF2BP2	IGF2BP2	13287	-0.056	0.17	NO
250	RBM14	RBM14	RBM14	13372	-0.058	0.17	NO
251	LRRC42	LRRC42	LRRC42	13561	-0.061	0.16	NO
252	SLC2A1	SLC2A1	SLC2A1	13669	-0.063	0.16	NO
253	METTL13	METTL13	METTL13	13755	-0.064	0.16	NO
254	ARHGEF2	ARHGEF2	ARHGEF2	14249	-0.073	0.13	NO
255	CLCN7	CLCN7	CLCN7	14280	-0.073	0.14	NO
256	SEC16A	SEC16A	SEC16A	14441	-0.076	0.13	NO
257	MAGEF1	MAGEF1	MAGEF1	15128	-0.09	0.096	NO
258	RNF220	RNF220	RNF220	15143	-0.09	0.1	NO
259	SIRPA	SIRPA	SIRPA	15276	-0.092	0.097	NO
260	KDM4B	KDM4B	KDM4B	15361	-0.094	0.097	NO
261	BTG1	BTG1	BTG1	15926	-0.11	0.071	NO
262	FYN	FYN	FYN	16207	-0.12	0.061	NO
263	TMEM53	TMEM53	TMEM53	16629	-0.14	0.045	NO
264	HSPA1L	HSPA1L	HSPA1L	16822	-0.15	0.042	NO
265	WNT5B	WNT5B	WNT5B	17002	-0.16	0.04	NO
266	NLRP2	NLRP2	NLRP2	17205	-0.18	0.038	NO
267	PAMR1	PAMR1	PAMR1	17458	-0.22	0.035	NO

Figure S5. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: WANG LMO4 TARGETS DN.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: WANG LMO4 TARGETS DN, 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: KIM WT1 TARGETS DN

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	ZNF878	ZNF878	ZNF878	167	0.51	0.0041	YES
2	GLRB	GLRB	GLRB	242	0.47	0.012	YES
3	EDAR	EDAR	EDAR	462	0.4	0.011	YES
4	NCAPG	NCAPG	NCAPG	813	0.32	-0.0005	YES
5	AP1S3	AP1S3	AP1S3	834	0.32	0.0068	YES
6	DEPDC1	DEPDC1	DEPDC1	847	0.32	0.014	YES
7	MATR3	MATR3	MATR3	858	0.31	0.022	YES
8	CDCA7	CDCA7	CDCA7	923	0.31	0.027	YES
9	RNF128	RNF128	RNF128	1050	0.29	0.027	YES
10	GTF2H2	GTF2H2	GTF2H2	1099	0.28	0.032	YES
11	KITLG	KITLG	KITLG	1188	0.27	0.034	YES
12	LCORL	LCORL	LCORL	1198	0.27	0.041	YES
13	TRIM59	TRIM59	TRIM59	1243	0.26	0.046	YES
14	TSPAN2	TSPAN2	TSPAN2	1255	0.26	0.052	YES
15	PLCB1	PLCB1	PLCB1	1256	0.26	0.059	YES
16	N4BP2	N4BP2	N4BP2	1266	0.26	0.066	YES
17	COL25A1	COL25A1	COL25A1	1287	0.26	0.072	YES
18	RPS6KA6	RPS6KA6	RPS6KA6	1379	0.25	0.073	YES
19	SGOL2	SGOL2	SGOL2	1385	0.25	0.079	YES
20	ESCO2	ESCO2	ESCO2	1534	0.24	0.077	YES
21	ATAD2	ATAD2	ATAD2	1576	0.23	0.081	YES
22	MYB	MYB	MYB	1585	0.23	0.087	YES
23	AKAP9	AKAP9	AKAP9	1629	0.23	0.09	YES
24	SMC4	SMC4	SMC4	1650	0.22	0.095	YES
25	CASP8AP2	CASP8AP2	CASP8AP2	1673	0.22	0.1	YES
26	TAF2	TAF2	TAF2	1745	0.22	0.1	YES
27	PUS7L	PUS7L	PUS7L	1789	0.21	0.1	YES
28	DBF4	DBF4	DBF4	1799	0.21	0.11	YES
29	PABPC4L	PABPC4L	PABPC4L	1837	0.21	0.11	YES
30	TOP2A	TOP2A	TOP2A	1842	0.21	0.12	YES
31	RELL1	RELL1	RELL1	1854	0.21	0.12	YES
32	ZNF799	ZNF799	ZNF799	1906	0.2	0.13	YES
33	PDK1	PDK1	PDK1	1920	0.2	0.13	YES
34	PPIP5K2	PPIP5K2	PPIP5K2	1928	0.2	0.14	YES
35	LRRC40	LRRC40	LRRC40	2005	0.2	0.14	YES
36	CENPF	CENPF	CENPF	2060	0.19	0.14	YES
37	MTDH	MTDH	MTDH	2079	0.19	0.14	YES
38	CEP192	CEP192	CEP192	2118	0.19	0.15	YES
39	SMARCA5	SMARCA5	SMARCA5	2126	0.19	0.15	YES
40	ANLN	ANLN	ANLN	2262	0.18	0.15	YES
41	SERTAD4	SERTAD4	SERTAD4	2273	0.18	0.15	YES
42	WEE1	WEE1	WEE1	2345	0.18	0.15	YES
43	NUDCD1	NUDCD1	NUDCD1	2346	0.18	0.16	YES
44	RBBP8	RBBP8	RBBP8	2361	0.18	0.16	YES
45	RBAK	RBAK	RBAK	2369	0.18	0.17	YES
46	EZH2	EZH2	EZH2	2371	0.18	0.17	YES
47	ANKRD26	ANKRD26	ANKRD26	2373	0.18	0.18	YES
48	MIS18BP1	MIS18BP1	MIS18BP1	2381	0.18	0.18	YES
49	ITGA6	ITGA6	ITGA6	2390	0.18	0.18	YES
50	ERI2	ERI2	ERI2	2514	0.17	0.18	YES
51	AHR	AHR	AHR	2537	0.17	0.18	YES
52	FAM76B	FAM76B	FAM76B	2542	0.17	0.19	YES
53	SMCHD1	SMCHD1	SMCHD1	2594	0.16	0.19	YES
54	SHCBP1	SHCBP1	SHCBP1	2618	0.16	0.19	YES
55	BCAP29	BCAP29	BCAP29	2621	0.16	0.2	YES
56	SAP30	SAP30	SAP30	2670	0.16	0.2	YES
57	IFT81	IFT81	IFT81	2706	0.16	0.2	YES
58	PROM1	PROM1	PROM1	2719	0.16	0.2	YES
59	GPSM2	GPSM2	GPSM2	2731	0.16	0.21	YES
60	PBK	PBK	PBK	2810	0.15	0.21	YES
61	HRSP12	HRSP12	HRSP12	2830	0.15	0.21	YES
62	POLA1	POLA1	POLA1	2861	0.15	0.21	YES
63	SMEK2	SMEK2	SMEK2	2913	0.15	0.21	YES
64	BUB1	BUB1	BUB1	2923	0.15	0.22	YES
65	CXorf23	CXorf23	CXorf23	2946	0.15	0.22	YES
66	CA12	CA12	CA12	2962	0.15	0.22	YES
67	CCNA2	CCNA2	CCNA2	2981	0.15	0.23	YES
68	TMEM209	TMEM209	TMEM209	2990	0.15	0.23	YES
69	ARL6IP6	ARL6IP6	ARL6IP6	2993	0.15	0.23	YES
70	UCHL5	UCHL5	UCHL5	2994	0.15	0.24	YES
71	FGFR1OP2	FGFR1OP2	FGFR1OP2	2995	0.15	0.24	YES
72	NEK1	NEK1	NEK1	3004	0.15	0.24	YES
73	XPO1	XPO1	XPO1	3018	0.15	0.25	YES
74	CDC40	CDC40	CDC40	3026	0.15	0.25	YES
75	GTPBP10	GTPBP10	GTPBP10	3056	0.14	0.25	YES
76	FGFR1OP	FGFR1OP	FGFR1OP	3067	0.14	0.26	YES
77	MOXD1	MOXD1	MOXD1	3113	0.14	0.26	YES
78	CD2AP	CD2AP	CD2AP	3138	0.14	0.26	YES
79	RAD21	RAD21	RAD21	3147	0.14	0.26	YES
80	AZIN1	AZIN1	AZIN1	3165	0.14	0.27	YES
81	RRM2	RRM2	RRM2	3209	0.14	0.27	YES
82	TRPS1	TRPS1	TRPS1	3221	0.14	0.27	YES
83	CEP55	CEP55	CEP55	3299	0.14	0.27	YES
84	RIF1	RIF1	RIF1	3303	0.14	0.27	YES
85	DCK	DCK	DCK	3327	0.14	0.28	YES
86	AEBP2	AEBP2	AEBP2	3342	0.14	0.28	YES
87	SEMA5A	SEMA5A	SEMA5A	3354	0.13	0.28	YES
88	PDS5B	PDS5B	PDS5B	3377	0.13	0.28	YES
89	ZNF770	ZNF770	ZNF770	3378	0.13	0.29	YES
90	RNF6	RNF6	RNF6	3402	0.13	0.29	YES
91	EPS8	EPS8	EPS8	3449	0.13	0.29	YES
92	CTDSPL2	CTDSPL2	CTDSPL2	3453	0.13	0.3	YES
93	TCEA1	TCEA1	TCEA1	3520	0.13	0.3	YES
94	SMC2	SMC2	SMC2	3605	0.13	0.29	YES
95	ANKRD32	ANKRD32	ANKRD32	3614	0.13	0.3	YES
96	CDC73	CDC73	CDC73	3619	0.13	0.3	YES
97	OXCT1	OXCT1	OXCT1	3621	0.13	0.3	YES
98	ZRANB2	ZRANB2	ZRANB2	3624	0.13	0.31	YES
99	BUB1B	BUB1B	BUB1B	3683	0.12	0.31	YES
100	CAPZA2	CAPZA2	CAPZA2	3685	0.12	0.31	YES
101	CLDN12	CLDN12	CLDN12	3700	0.12	0.31	YES
102	SSB	SSB	SSB	3711	0.12	0.31	YES
103	EFCAB7	EFCAB7	EFCAB7	3736	0.12	0.32	YES
104	TMPO	TMPO	TMPO	3737	0.12	0.32	YES
105	DSG2	DSG2	DSG2	3774	0.12	0.32	YES
106	USP34	USP34	USP34	3817	0.12	0.32	YES
107	CDC6	CDC6	CDC6	3820	0.12	0.32	YES
108	WDR11	WDR11	WDR11	3826	0.12	0.33	YES
109	CTTNBP2	CTTNBP2	CTTNBP2	3851	0.12	0.33	YES
110	ECT2	ECT2	ECT2	3859	0.12	0.33	YES
111	TRMT11	TRMT11	TRMT11	3884	0.12	0.33	YES
112	TAX1BP1	TAX1BP1	TAX1BP1	3904	0.12	0.34	YES
113	ZC3HAV1L	ZC3HAV1L	ZC3HAV1L	3931	0.12	0.34	YES
114	PPAT	PPAT	PPAT	3952	0.12	0.34	YES
115	ACSL3	ACSL3	ACSL3	3971	0.12	0.34	YES
116	MELK	MELK	MELK	4012	0.12	0.34	YES
117	PSAT1	PSAT1	PSAT1	4031	0.11	0.34	YES
118	C11orf54	C11orf54	C11orf54	4036	0.11	0.35	YES
119	FIGNL1	FIGNL1	FIGNL1	4061	0.11	0.35	YES
120	ALG13	ALG13	ALG13	4076	0.11	0.35	YES
121	SYDE2	SYDE2	SYDE2	4099	0.11	0.35	YES
122	UGDH	UGDH	UGDH	4116	0.11	0.36	YES
123	PHF6	PHF6	PHF6	4122	0.11	0.36	YES
124	MET	MET	MET	4123	0.11	0.36	YES
125	SLC39A10	SLC39A10	SLC39A10	4133	0.11	0.36	YES
126	SBNO1	SBNO1	SBNO1	4147	0.11	0.36	YES
127	WDR75	WDR75	WDR75	4148	0.11	0.37	YES
128	RBL1	RBL1	RBL1	4150	0.11	0.37	YES
129	EID1	EID1	EID1	4163	0.11	0.37	YES
130	MBNL3	MBNL3	MBNL3	4216	0.11	0.37	YES
131	C1orf131	C1orf131	C1orf131	4220	0.11	0.38	YES
132	UBLCP1	UBLCP1	UBLCP1	4229	0.11	0.38	YES
133	NUP107	NUP107	NUP107	4270	0.11	0.38	YES
134	NANP	NANP	NANP	4275	0.11	0.38	YES
135	C21orf91	C21orf91	C21orf91	4334	0.1	0.38	YES
136	GPM6B	GPM6B	GPM6B	4348	0.1	0.38	YES
137	PHF14	PHF14	PHF14	4438	0.1	0.38	YES
138	TMEM33	TMEM33	TMEM33	4446	0.1	0.38	YES
139	ACAT2	ACAT2	ACAT2	4466	0.1	0.38	YES
140	COL4A5	COL4A5	COL4A5	4488	0.1	0.39	YES
141	ZNF367	ZNF367	ZNF367	4490	0.1	0.39	YES
142	UHRF1	UHRF1	UHRF1	4499	0.1	0.39	YES
143	NCAPD3	NCAPD3	NCAPD3	4542	0.1	0.39	YES
144	DLAT	DLAT	DLAT	4570	0.1	0.39	YES
145	SGOL1	SGOL1	SGOL1	4583	0.099	0.4	YES
146	FAM13B	FAM13B	FAM13B	4590	0.099	0.4	YES
147	SLMO2	SLMO2	SLMO2	4630	0.098	0.4	YES
148	USP1	USP1	USP1	4637	0.098	0.4	YES
149	UBA2	UBA2	UBA2	4641	0.098	0.4	YES
150	ACTR6	ACTR6	ACTR6	4669	0.097	0.4	YES
151	POT1	POT1	POT1	4673	0.097	0.4	YES
152	SRSF10	SRSF10	SRSF10	4676	0.097	0.41	YES
153	APPBP2	APPBP2	APPBP2	4727	0.096	0.41	YES
154	HAT1	HAT1	HAT1	4786	0.095	0.41	YES
155	DNAJC9	DNAJC9	DNAJC9	4823	0.094	0.41	YES
156	MOB4	MOB4	MOB4	4904	0.092	0.4	YES
157	ADK	ADK	ADK	4920	0.091	0.41	YES
158	HACE1	HACE1	HACE1	4937	0.091	0.41	YES
159	TRDMT1	TRDMT1	TRDMT1	4946	0.091	0.41	YES
160	CETN3	CETN3	CETN3	4966	0.09	0.41	YES
161	STRBP	STRBP	STRBP	4968	0.09	0.41	YES
162	IDH3A	IDH3A	IDH3A	4971	0.09	0.42	YES
163	HMGB2	HMGB2	HMGB2	4995	0.089	0.42	YES
164	TSPAN13	TSPAN13	TSPAN13	5033	0.088	0.42	YES
165	PDZD8	PDZD8	PDZD8	5037	0.088	0.42	YES
166	TTC3	TTC3	TTC3	5050	0.088	0.42	YES
167	ZNF148	ZNF148	ZNF148	5073	0.088	0.42	YES
168	ANP32E	ANP32E	ANP32E	5093	0.087	0.42	YES
169	VPS54	VPS54	VPS54	5105	0.087	0.43	YES
170	CALM2	CALM2	CALM2	5193	0.085	0.42	YES
171	PAIP2	PAIP2	PAIP2	5214	0.084	0.42	YES
172	NFYB	NFYB	NFYB	5239	0.084	0.42	YES
173	RFX3	RFX3	RFX3	5255	0.084	0.43	YES
174	ARNT2	ARNT2	ARNT2	5258	0.084	0.43	YES
175	SEPHS2	SEPHS2	SEPHS2	5261	0.084	0.43	YES
176	GRHL2	GRHL2	GRHL2	5272	0.083	0.43	YES
177	GMNN	GMNN	GMNN	5332	0.082	0.43	YES
178	IPO8	IPO8	IPO8	5345	0.081	0.43	YES
179	G3BP2	G3BP2	G3BP2	5388	0.08	0.43	YES
180	SUCLA2	SUCLA2	SUCLA2	5419	0.08	0.43	YES
181	TIMM17A	TIMM17A	TIMM17A	5427	0.079	0.43	YES
182	RNMT	RNMT	RNMT	5460	0.079	0.44	YES
183	ORC5	ORC5	ORC5	5482	0.078	0.44	YES
184	ZFAND6	ZFAND6	ZFAND6	5492	0.078	0.44	YES
185	TGFA	TGFA	TGFA	5529	0.077	0.44	YES
186	RFC1	RFC1	RFC1	5532	0.077	0.44	YES
187	SKP2	SKP2	SKP2	5614	0.075	0.44	YES
188	SETX	SETX	SETX	5636	0.075	0.44	YES
189	ENPP3	ENPP3	ENPP3	5658	0.074	0.44	YES
190	AURKA	AURKA	AURKA	5686	0.074	0.44	YES
191	ZBTB44	ZBTB44	ZBTB44	5690	0.073	0.44	YES
192	NCBP1	NCBP1	NCBP1	5725	0.073	0.44	YES
193	AUTS2	AUTS2	AUTS2	5739	0.072	0.44	YES
194	CTNND2	CTNND2	CTNND2	5742	0.072	0.44	YES
195	ARPP19	ARPP19	ARPP19	5747	0.072	0.44	YES
196	CCDC90B	CCDC90B	CCDC90B	5748	0.072	0.45	YES
197	TFRC	TFRC	TFRC	5756	0.072	0.45	YES
198	HELLS	HELLS	HELLS	5799	0.071	0.45	YES
199	VBP1	VBP1	VBP1	5833	0.07	0.45	YES
200	E2F7	E2F7	E2F7	5888	0.069	0.45	YES
201	TAF1D	TAF1D	TAF1D	5911	0.069	0.45	YES
202	CNOT6	CNOT6	CNOT6	5962	0.068	0.45	YES
203	MDH1	MDH1	MDH1	5970	0.067	0.45	YES
204	ZNF841	ZNF841	ZNF841	5971	0.067	0.45	YES
205	TRIM37	TRIM37	TRIM37	5975	0.067	0.45	YES
206	PRIM1	PRIM1	PRIM1	6038	0.066	0.45	YES
207	NAE1	NAE1	NAE1	6040	0.066	0.45	YES
208	FAM199X	FAM199X	FAM199X	6076	0.065	0.45	YES
209	ZNF229	ZNF229	ZNF229	6107	0.064	0.45	YES
210	NFU1	NFU1	NFU1	6127	0.064	0.45	YES
211	TCEANC	TCEANC	TCEANC	6144	0.064	0.45	YES
212	NUP155	NUP155	NUP155	6171	0.063	0.45	YES
213	RBM45	RBM45	RBM45	6205	0.062	0.45	YES
214	ZNF24	ZNF24	ZNF24	6242	0.062	0.45	YES
215	NVL	NVL	NVL	6256	0.062	0.45	YES
216	PCM1	PCM1	PCM1	6285	0.061	0.45	YES
217	DPY30	DPY30	DPY30	6287	0.061	0.45	YES
218	ATXN1	ATXN1	ATXN1	6294	0.061	0.46	YES
219	MPHOSPH8	MPHOSPH8	MPHOSPH8	6315	0.06	0.46	YES
220	SYNCRIP	SYNCRIP	SYNCRIP	6330	0.06	0.46	YES
221	ACYP1	ACYP1	ACYP1	6357	0.059	0.46	YES
222	POLR2B	POLR2B	POLR2B	6426	0.058	0.46	YES
223	ATR	ATR	ATR	6441	0.058	0.46	YES
224	C1orf112	C1orf112	C1orf112	6449	0.058	0.46	YES
225	PAICS	PAICS	PAICS	6456	0.058	0.46	YES
226	TRIP13	TRIP13	TRIP13	6476	0.057	0.46	YES
227	MARCH6	MARCH6	MARCH6	6542	0.056	0.46	NO
228	ZNF239	ZNF239	ZNF239	6591	0.055	0.46	NO
229	C1D	C1D	C1D	6612	0.054	0.46	NO
230	ATAD1	ATAD1	ATAD1	6651	0.054	0.45	NO
231	LRBA	LRBA	LRBA	6652	0.054	0.46	NO
232	PRR14L	PRR14L	PRR14L	6681	0.053	0.46	NO
233	CRLS1	CRLS1	CRLS1	6703	0.053	0.46	NO
234	ZCCHC8	ZCCHC8	ZCCHC8	6744	0.052	0.46	NO
235	PCMTD2	PCMTD2	PCMTD2	6777	0.052	0.46	NO
236	PIGF	PIGF	PIGF	6794	0.051	0.46	NO
237	TRMT6	TRMT6	TRMT6	6833	0.051	0.45	NO
238	TOPBP1	TOPBP1	TOPBP1	6890	0.049	0.45	NO
239	KIF16B	KIF16B	KIF16B	6905	0.049	0.45	NO
240	ZNF846	ZNF846	ZNF846	6931	0.049	0.45	NO
241	PSPC1	PSPC1	PSPC1	6946	0.048	0.45	NO
242	BET1	BET1	BET1	7003	0.047	0.45	NO
243	UBE2B	UBE2B	UBE2B	7016	0.047	0.45	NO
244	ING3	ING3	ING3	7179	0.044	0.44	NO
245	SESN3	SESN3	SESN3	7197	0.044	0.44	NO
246	MLLT3	MLLT3	MLLT3	7228	0.043	0.44	NO
247	UTP15	UTP15	UTP15	7232	0.043	0.44	NO
248	NDUFS4	NDUFS4	NDUFS4	7251	0.043	0.44	NO
249	SHMT1	SHMT1	SHMT1	7321	0.041	0.44	NO
250	SFPQ	SFPQ	SFPQ	7372	0.04	0.44	NO
251	HUS1	HUS1	HUS1	7376	0.04	0.44	NO
252	ABHD13	ABHD13	ABHD13	7407	0.039	0.44	NO
253	BMI1	BMI1	BMI1	7463	0.038	0.44	NO
254	WIF1	WIF1	WIF1	7478	0.038	0.44	NO
255	SMNDC1	SMNDC1	SMNDC1	7493	0.038	0.44	NO
256	TRAPPC10	TRAPPC10	TRAPPC10	7517	0.037	0.44	NO
257	NRAS	NRAS	NRAS	7519	0.037	0.44	NO
258	UBA3	UBA3	UBA3	7585	0.036	0.44	NO
259	LYRM5	LYRM5	LYRM5	7612	0.036	0.44	NO
260	BRCA1	BRCA1	BRCA1	7649	0.035	0.44	NO
261	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	7650	0.035	0.44	NO
262	ANAPC1	ANAPC1	ANAPC1	7654	0.035	0.44	NO
263	PCYOX1	PCYOX1	PCYOX1	7701	0.034	0.44	NO
264	NUP85	NUP85	NUP85	7704	0.034	0.44	NO
265	CPSF6	CPSF6	CPSF6	7707	0.034	0.44	NO
266	POLD3	POLD3	POLD3	7723	0.033	0.44	NO
267	STARD7	STARD7	STARD7	7748	0.033	0.44	NO
268	SRSF3	SRSF3	SRSF3	7753	0.033	0.44	NO
269	MRPS31	MRPS31	MRPS31	7754	0.033	0.44	NO
270	BRD7	BRD7	BRD7	7768	0.033	0.44	NO
271	ACTR3B	ACTR3B	ACTR3B	7791	0.032	0.44	NO
272	SKA2	SKA2	SKA2	7793	0.032	0.44	NO
273	PPM1B	PPM1B	PPM1B	7915	0.03	0.43	NO
274	NDUFA4	NDUFA4	NDUFA4	8003	0.028	0.43	NO
275	STRAP	STRAP	STRAP	8051	0.027	0.43	NO
276	TMEM117	TMEM117	TMEM117	8078	0.027	0.42	NO
277	TP53BP1	TP53BP1	TP53BP1	8089	0.027	0.42	NO
278	DNAJA1	DNAJA1	DNAJA1	8115	0.026	0.42	NO
279	BCL2	BCL2	BCL2	8141	0.026	0.42	NO
280	SPIN1	SPIN1	SPIN1	8223	0.024	0.42	NO
281	SNRPB2	SNRPB2	SNRPB2	8367	0.021	0.41	NO
282	SLC38A1	SLC38A1	SLC38A1	8369	0.021	0.41	NO
283	MED6	MED6	MED6	8395	0.021	0.41	NO
284	XRCC5	XRCC5	XRCC5	8430	0.02	0.41	NO
285	IMMP1L	IMMP1L	IMMP1L	8602	0.017	0.4	NO
286	RBBP5	RBBP5	RBBP5	8621	0.017	0.4	NO
287	VDAC1	VDAC1	VDAC1	8640	0.016	0.4	NO
288	ANKLE2	ANKLE2	ANKLE2	8656	0.016	0.4	NO
289	RAD51	RAD51	RAD51	8668	0.016	0.4	NO
290	SNX5	SNX5	SNX5	8693	0.015	0.4	NO
291	WDR3	WDR3	WDR3	8717	0.015	0.4	NO
292	CAV2	CAV2	CAV2	8792	0.014	0.39	NO
293	NME7	NME7	NME7	8796	0.014	0.39	NO
294	GEMIN6	GEMIN6	GEMIN6	8830	0.013	0.39	NO
295	TTF2	TTF2	TTF2	8875	0.012	0.39	NO
296	TNIK	TNIK	TNIK	8881	0.012	0.39	NO
297	MTHFD1	MTHFD1	MTHFD1	8901	0.012	0.39	NO
298	ZNF22	ZNF22	ZNF22	8922	0.012	0.39	NO
299	YWHAB	YWHAB	YWHAB	8939	0.011	0.39	NO
300	PFN2	PFN2	PFN2	8949	0.011	0.39	NO
301	TASP1	TASP1	TASP1	8961	0.011	0.39	NO
302	PWP1	PWP1	PWP1	8970	0.01	0.39	NO
303	ADH5	ADH5	ADH5	8987	0.01	0.39	NO
304	DUSP11	DUSP11	DUSP11	9022	0.0095	0.38	NO
305	MRPS18C	MRPS18C	MRPS18C	9038	0.0093	0.38	NO
306	PRPS2	PRPS2	PRPS2	9049	0.0091	0.38	NO
307	HNRNPA3	HNRNPA3	HNRNPA3	9057	0.009	0.38	NO
308	FH	FH	FH	9140	0.0074	0.38	NO
309	UBE2D2	UBE2D2	UBE2D2	9210	0.0061	0.38	NO
310	ARMC10	ARMC10	ARMC10	9321	0.004	0.37	NO
311	SNAPIN	SNAPIN	SNAPIN	9340	0.0036	0.37	NO
312	VDAC3	VDAC3	VDAC3	9353	0.0035	0.37	NO
313	C1orf74	C1orf74	C1orf74	9375	0.0031	0.37	NO
314	FARSB	FARSB	FARSB	9397	0.0028	0.37	NO
315	CSTF2	CSTF2	CSTF2	9405	0.0027	0.37	NO
316	NAF1	NAF1	NAF1	9423	0.0024	0.36	NO
317	MPZL1	MPZL1	MPZL1	9504	0.00085	0.36	NO
318	IDUA	IDUA	IDUA	9506	0.00083	0.36	NO
319	IK	IK	IK	9533	0.00038	0.36	NO
320	CHEK1	CHEK1	CHEK1	9545	0.00017	0.36	NO
321	PTPN14	PTPN14	PTPN14	9607	-0.00072	0.36	NO
322	SSBP1	SSBP1	SSBP1	9631	-0.0011	0.35	NO
323	LPHN3	LPHN3	LPHN3	9680	-0.002	0.35	NO
324	CRYZ	CRYZ	CRYZ	9728	-0.0028	0.35	NO
325	PARP1	PARP1	PARP1	9795	-0.004	0.34	NO
326	CDCA8	CDCA8	CDCA8	9862	-0.0048	0.34	NO
327	KIF2C	KIF2C	KIF2C	9917	-0.0056	0.34	NO
328	EWSR1	EWSR1	EWSR1	9920	-0.0056	0.34	NO
329	EIF4H	EIF4H	EIF4H	10016	-0.0074	0.33	NO
330	RPRD2	RPRD2	RPRD2	10057	-0.0084	0.33	NO
331	SERBP1	SERBP1	SERBP1	10107	-0.0091	0.33	NO
332	DFNA5	DFNA5	DFNA5	10123	-0.0094	0.33	NO
333	PEX7	PEX7	PEX7	10138	-0.0096	0.33	NO
334	HNRNPU	HNRNPU	HNRNPU	10232	-0.011	0.32	NO
335	POLR3K	POLR3K	POLR3K	10285	-0.012	0.32	NO
336	TMTC4	TMTC4	TMTC4	10309	-0.012	0.32	NO
337	SLC7A1	SLC7A1	SLC7A1	10321	-0.012	0.32	NO
338	CAPRIN1	CAPRIN1	CAPRIN1	10390	-0.013	0.32	NO
339	LSM5	LSM5	LSM5	10472	-0.015	0.31	NO
340	ASXL1	ASXL1	ASXL1	10553	-0.016	0.31	NO
341	TRRAP	TRRAP	TRRAP	10609	-0.017	0.3	NO
342	METTL9	METTL9	METTL9	10643	-0.017	0.3	NO
343	RRAGD	RRAGD	RRAGD	10723	-0.018	0.3	NO
344	PARK7	PARK7	PARK7	10796	-0.02	0.3	NO
345	LSM7	LSM7	LSM7	11026	-0.023	0.28	NO
346	KBTBD8	KBTBD8	KBTBD8	11038	-0.023	0.28	NO
347	KCTD15	KCTD15	KCTD15	11091	-0.024	0.28	NO
348	H2AFZ	H2AFZ	H2AFZ	11115	-0.024	0.28	NO
349	STXBP6	STXBP6	STXBP6	11129	-0.025	0.28	NO
350	POLR1C	POLR1C	POLR1C	11204	-0.026	0.28	NO
351	PLEKHB1	PLEKHB1	PLEKHB1	11309	-0.027	0.27	NO
352	ACTL6A	ACTL6A	ACTL6A	11413	-0.029	0.27	NO
353	PKP4	PKP4	PKP4	11490	-0.03	0.26	NO
354	SLC20A2	SLC20A2	SLC20A2	11517	-0.03	0.26	NO
355	ILF3	ILF3	ILF3	11602	-0.032	0.26	NO
356	EFTUD2	EFTUD2	EFTUD2	11655	-0.032	0.26	NO
357	TOMM70A	TOMM70A	TOMM70A	11694	-0.033	0.26	NO
358	PANK1	PANK1	PANK1	11750	-0.034	0.25	NO
359	TP63	TP63	TP63	11752	-0.034	0.25	NO
360	MRPS33	MRPS33	MRPS33	11788	-0.034	0.25	NO
361	AHCY	AHCY	AHCY	11834	-0.035	0.25	NO
362	RPA3	RPA3	RPA3	11838	-0.035	0.25	NO
363	C11orf74	C11orf74	C11orf74	11925	-0.037	0.25	NO
364	EIF4B	EIF4B	EIF4B	12036	-0.038	0.24	NO
365	STMN1	STMN1	STMN1	12046	-0.038	0.24	NO
366	ZIK1	ZIK1	ZIK1	12134	-0.039	0.24	NO
367	CD24	CD24	CD24	12138	-0.039	0.24	NO
368	CTCF	CTCF	CTCF	12199	-0.04	0.24	NO
369	TULP3	TULP3	TULP3	12251	-0.041	0.24	NO
370	HARS	HARS	HARS	12255	-0.041	0.24	NO
371	NDUFC2	NDUFC2	NDUFC2	12280	-0.041	0.24	NO
372	NDUFC1	NDUFC1	NDUFC1	12294	-0.042	0.24	NO
373	ZNF317	ZNF317	ZNF317	12381	-0.043	0.23	NO
374	HNRNPA1	HNRNPA1	HNRNPA1	12476	-0.044	0.23	NO
375	EMID1	EMID1	EMID1	12651	-0.047	0.22	NO
376	RPA1	RPA1	RPA1	12707	-0.048	0.22	NO
377	SNRNP200	SNRNP200	SNRNP200	12755	-0.048	0.22	NO
378	RNF44	RNF44	RNF44	12844	-0.05	0.21	NO
379	NCAPD2	NCAPD2	NCAPD2	12920	-0.051	0.21	NO
380	UNG	UNG	UNG	12939	-0.051	0.21	NO
381	TRPM3	TRPM3	TRPM3	13017	-0.052	0.21	NO
382	CEP164	CEP164	CEP164	13141	-0.054	0.2	NO
383	TTC9C	TTC9C	TTC9C	13173	-0.055	0.2	NO
384	SEC22C	SEC22C	SEC22C	13306	-0.057	0.2	NO
385	PPP2R1A	PPP2R1A	PPP2R1A	13405	-0.058	0.19	NO
386	PIN1	PIN1	PIN1	13758	-0.064	0.17	NO
387	VPS26B	VPS26B	VPS26B	13786	-0.064	0.17	NO
388	PHB2	PHB2	PHB2	13956	-0.067	0.17	NO
389	RNF7	RNF7	RNF7	14030	-0.069	0.16	NO
390	DDR1	DDR1	DDR1	14207	-0.072	0.16	NO
391	CHCHD4	CHCHD4	CHCHD4	14392	-0.075	0.15	NO
392	MAP7D2	MAP7D2	MAP7D2	14476	-0.077	0.14	NO
393	POLR3H	POLR3H	POLR3H	14495	-0.077	0.15	NO
394	PCDH18	PCDH18	PCDH18	14828	-0.083	0.13	NO
395	ST6GAL1	ST6GAL1	ST6GAL1	15003	-0.087	0.12	NO
396	PATZ1	PATZ1	PATZ1	15179	-0.09	0.12	NO
397	RPS3	RPS3	RPS3	15277	-0.092	0.11	NO
398	ARAP2	ARAP2	ARAP2	15746	-0.1	0.088	NO
399	RPL15	RPL15	RPL15	16129	-0.12	0.069	NO
400	HOOK1	HOOK1	HOOK1	16233	-0.12	0.067	NO
401	ZNF532	ZNF532	ZNF532	16347	-0.13	0.064	NO
402	CDC25A	CDC25A	CDC25A	16387	-0.13	0.065	NO
403	NEO1	NEO1	NEO1	16454	-0.13	0.065	NO
404	ZNF362	ZNF362	ZNF362	16496	-0.13	0.066	NO
405	CTH	CTH	CTH	16903	-0.16	0.047	NO
406	MCM2	MCM2	MCM2	16950	-0.16	0.049	NO
407	NFIA	NFIA	NFIA	17546	-0.24	0.021	NO
408	BCL11A	BCL11A	BCL11A	17865	-0.34	0.012	NO

Figure S7. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KIM WT1 TARGETS DN.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: KIM WT1 TARGETS DN, 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: BIDUS METASTASIS UP

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	ABCC2	ABCC2	ABCC2	427	0.41	0.0014	YES
2	ASIP	ASIP	ASIP	530	0.38	0.019	YES
3	ANKRD18A	ANKRD18A	ANKRD18A	711	0.34	0.03	YES
4	TRIM73	TRIM73	TRIM73	768	0.33	0.047	YES
5	E2F8	E2F8	E2F8	885	0.31	0.06	YES
6	REEP1	REEP1	REEP1	887	0.31	0.079	YES
7	ANKRD36	ANKRD36	ANKRD36	1067	0.29	0.087	YES
8	ADAM22	ADAM22	ADAM22	1098	0.28	0.1	YES
9	DNA2	DNA2	DNA2	1218	0.27	0.11	YES
10	GOLGA8B	GOLGA8B	GOLGA8B	1352	0.25	0.12	YES
11	CCDC150	CCDC150	CCDC150	1354	0.25	0.14	YES
12	GOLGA8A	GOLGA8A	GOLGA8A	1366	0.25	0.15	YES
13	ESCO2	ESCO2	ESCO2	1534	0.24	0.16	YES
14	ATAD2	ATAD2	ATAD2	1576	0.23	0.17	YES
15	DEPDC7	DEPDC7	DEPDC7	1594	0.23	0.18	YES
16	RAD51AP1	RAD51AP1	RAD51AP1	1626	0.23	0.19	YES
17	PILRB	PILRB	PILRB	1667	0.22	0.2	YES
18	PHTF2	PHTF2	PHTF2	1788	0.21	0.21	YES
19	TTLL7	TTLL7	TTLL7	1822	0.21	0.22	YES
20	GPR126	GPR126	GPR126	1828	0.21	0.24	YES
21	TOP2A	TOP2A	TOP2A	1842	0.21	0.25	YES
22	SH3GL2	SH3GL2	SH3GL2	1970	0.2	0.25	YES
23	BRIP1	BRIP1	BRIP1	2070	0.19	0.26	YES
24	SLC22A3	SLC22A3	SLC22A3	2133	0.19	0.27	YES
25	C5orf42	C5orf42	C5orf42	2159	0.19	0.28	YES
26	CREBZF	CREBZF	CREBZF	2274	0.18	0.28	YES
27	LYRM7	LYRM7	LYRM7	2313	0.18	0.29	YES
28	CDH24	CDH24	CDH24	2319	0.18	0.3	YES
29	PHIP	PHIP	PHIP	2359	0.18	0.31	YES
30	RBBP8	RBBP8	RBBP8	2361	0.18	0.32	YES
31	EZH2	EZH2	EZH2	2371	0.18	0.33	YES
32	KIAA1598	KIAA1598	KIAA1598	2468	0.17	0.34	YES
33	MASTL	MASTL	MASTL	2478	0.17	0.35	YES
34	DMXL2	DMXL2	DMXL2	2549	0.17	0.35	YES
35	CPNE8	CPNE8	CPNE8	2651	0.16	0.36	YES
36	CENPQ	CENPQ	CENPQ	2664	0.16	0.37	YES
37	MAP3K2	MAP3K2	MAP3K2	2701	0.16	0.38	YES
38	POLA1	POLA1	POLA1	2861	0.15	0.38	YES
39	SLC38A2	SLC38A2	SLC38A2	2899	0.15	0.38	YES
40	PHTF1	PHTF1	PHTF1	2935	0.15	0.39	YES
41	RMI1	RMI1	RMI1	2971	0.15	0.4	YES
42	CDKN2AIP	CDKN2AIP	CDKN2AIP	3077	0.14	0.4	YES
43	CERS6	CERS6	CERS6	3079	0.14	0.41	YES
44	DNAJC6	DNAJC6	DNAJC6	3135	0.14	0.41	YES
45	RRM2	RRM2	RRM2	3209	0.14	0.42	YES
46	DSCC1	DSCC1	DSCC1	3329	0.14	0.42	YES
47	OGT	OGT	OGT	3373	0.13	0.43	YES
48	OSGIN2	OSGIN2	OSGIN2	3417	0.13	0.43	YES
49	CDC7	CDC7	CDC7	3471	0.13	0.44	YES
50	ENOSF1	ENOSF1	ENOSF1	3708	0.12	0.43	YES
51	IFIT1	IFIT1	IFIT1	3751	0.12	0.44	YES
52	DONSON	DONSON	DONSON	3831	0.12	0.44	YES
53	KIFC2	KIFC2	KIFC2	3928	0.12	0.44	YES
54	DHFR	DHFR	DHFR	4075	0.11	0.44	YES
55	NAB1	NAB1	NAB1	4086	0.11	0.45	YES
56	DNAJB4	DNAJB4	DNAJB4	4170	0.11	0.45	YES
57	RSRC2	RSRC2	RSRC2	4204	0.11	0.45	YES
58	ARHGAP42	ARHGAP42	ARHGAP42	4208	0.11	0.46	YES
59	MCM8	MCM8	MCM8	4214	0.11	0.47	YES
60	CCDC84	CCDC84	CCDC84	4239	0.11	0.47	YES
61	GCLM	GCLM	GCLM	4307	0.11	0.48	YES
62	PTAR1	PTAR1	PTAR1	4425	0.1	0.48	YES
63	DYNC1LI2	DYNC1LI2	DYNC1LI2	4573	0.1	0.47	YES
64	FANCI	FANCI	FANCI	4598	0.099	0.48	YES
65	USP1	USP1	USP1	4637	0.098	0.48	YES
66	SRSF10	SRSF10	SRSF10	4676	0.097	0.48	YES
67	FAM178A	FAM178A	FAM178A	4696	0.096	0.49	YES
68	RHOBTB3	RHOBTB3	RHOBTB3	4728	0.096	0.49	YES
69	HIST1H4B	HIST1H4B	HIST1H4B	4845	0.093	0.49	YES
70	TYMS	TYMS	TYMS	5025	0.088	0.49	YES
71	CALM2	CALM2	CALM2	5193	0.085	0.48	YES
72	ORC3	ORC3	ORC3	5196	0.085	0.49	YES
73	SLC25A27	SLC25A27	SLC25A27	5238	0.084	0.49	YES
74	HSPB8	HSPB8	HSPB8	5267	0.083	0.5	YES
75	NUP160	NUP160	NUP160	5300	0.082	0.5	YES
76	UBE2T	UBE2T	UBE2T	5430	0.079	0.5	YES
77	ZBED5	ZBED5	ZBED5	5435	0.079	0.5	YES
78	ACPP	ACPP	ACPP	5440	0.079	0.51	YES
79	RRM1	RRM1	RRM1	5468	0.078	0.51	YES
80	KAT2A	KAT2A	KAT2A	5516	0.078	0.51	YES
81	CHML	CHML	CHML	5577	0.076	0.51	YES
82	NFE2L2	NFE2L2	NFE2L2	5631	0.075	0.52	YES
83	CCDC14	CCDC14	CCDC14	5664	0.074	0.52	YES
84	DCAF16	DCAF16	DCAF16	5703	0.073	0.52	YES
85	HELLS	HELLS	HELLS	5799	0.071	0.52	YES
86	CALD1	CALD1	CALD1	5901	0.069	0.52	YES
87	MAN1A2	MAN1A2	MAN1A2	5964	0.068	0.52	YES
88	INTS7	INTS7	INTS7	5979	0.067	0.52	YES
89	PRIM1	PRIM1	PRIM1	6038	0.066	0.52	YES
90	BLM	BLM	BLM	6072	0.065	0.52	YES
91	PHOSPHO2	PHOSPHO2	PHOSPHO2	6446	0.058	0.51	NO
92	CDC45	CDC45	CDC45	6457	0.058	0.51	NO
93	BIVM	BIVM	BIVM	6518	0.056	0.51	NO
94	HIST1H4C	HIST1H4C	HIST1H4C	6567	0.055	0.51	NO
95	SRSF5	SRSF5	SRSF5	6649	0.054	0.51	NO
96	CRLS1	CRLS1	CRLS1	6703	0.053	0.51	NO
97	EFHC1	EFHC1	EFHC1	6859	0.05	0.51	NO
98	SVIP	SVIP	SVIP	6883	0.05	0.51	NO
99	NT5DC1	NT5DC1	NT5DC1	6962	0.048	0.51	NO
100	INSIG2	INSIG2	INSIG2	7049	0.046	0.5	NO
101	DCUN1D3	DCUN1D3	DCUN1D3	7071	0.046	0.51	NO
102	BBS2	BBS2	BBS2	7083	0.046	0.51	NO
103	PRIM2	PRIM2	PRIM2	7322	0.041	0.5	NO
104	COL7A1	COL7A1	COL7A1	7412	0.039	0.5	NO
105	BMI1	BMI1	BMI1	7463	0.038	0.49	NO
106	MYCBP2	MYCBP2	MYCBP2	7599	0.036	0.49	NO
107	HIST1H2AM	HIST1H2AM	HIST1H2AM	7636	0.035	0.49	NO
108	BRCA1	BRCA1	BRCA1	7649	0.035	0.49	NO
109	MZF1	MZF1	MZF1	7681	0.034	0.49	NO
110	ZWINT	ZWINT	ZWINT	7724	0.033	0.49	NO
111	NRD1	NRD1	NRD1	7760	0.033	0.49	NO
112	UBL3	UBL3	UBL3	7825	0.032	0.49	NO
113	NSUN3	NSUN3	NSUN3	8313	0.022	0.46	NO
114	RAD18	RAD18	RAD18	8355	0.021	0.46	NO
115	EXO1	EXO1	EXO1	8368	0.021	0.46	NO
116	CAPS	CAPS	CAPS	8373	0.021	0.46	NO
117	HIST1H2BC	HIST1H2BC	HIST1H2BC	8415	0.02	0.46	NO
118	SHC1	SHC1	SHC1	8498	0.019	0.46	NO
119	RAD51	RAD51	RAD51	8668	0.016	0.45	NO
120	KAT2B	KAT2B	KAT2B	8684	0.016	0.45	NO
121	C4BPB	C4BPB	C4BPB	8742	0.015	0.45	NO
122	COQ9	COQ9	COQ9	8980	0.01	0.44	NO
123	ASF1B	ASF1B	ASF1B	9378	0.0031	0.41	NO
124	MITF	MITF	MITF	9398	0.0027	0.41	NO
125	RAD54L	RAD54L	RAD54L	9494	0.0011	0.41	NO
126	FANCA	FANCA	FANCA	9625	-0.0011	0.4	NO
127	RHPN1	RHPN1	RHPN1	9626	-0.0011	0.4	NO
128	RFC2	RFC2	RFC2	9853	-0.0047	0.39	NO
129	FEN1	FEN1	FEN1	10067	-0.0085	0.38	NO
130	TRIM45	TRIM45	TRIM45	10186	-0.01	0.37	NO
131	CENPM	CENPM	CENPM	10478	-0.015	0.36	NO
132	CDCA5	CDCA5	CDCA5	10540	-0.016	0.35	NO
133	PKMYT1	PKMYT1	PKMYT1	10763	-0.019	0.34	NO
134	SP1	SP1	SP1	10801	-0.02	0.34	NO
135	ABCC5	ABCC5	ABCC5	10860	-0.02	0.34	NO
136	MBD4	MBD4	MBD4	11028	-0.023	0.33	NO
137	TTC31	TTC31	TTC31	11311	-0.027	0.32	NO
138	TMCC1	TMCC1	TMCC1	11506	-0.03	0.31	NO
139	RPA2	RPA2	RPA2	11739	-0.034	0.3	NO
140	ABHD10	ABHD10	ABHD10	11873	-0.036	0.29	NO
141	EIF4EBP2	EIF4EBP2	EIF4EBP2	12131	-0.039	0.28	NO
142	SAP30BP	SAP30BP	SAP30BP	12310	-0.042	0.27	NO
143	LIPH	LIPH	LIPH	13011	-0.052	0.24	NO
144	ZNF217	ZNF217	ZNF217	13403	-0.058	0.22	NO
145	LMO4	LMO4	LMO4	13801	-0.065	0.2	NO
146	HIST1H4H	HIST1H4H	HIST1H4H	14083	-0.07	0.19	NO
147	CASP2	CASP2	CASP2	14307	-0.074	0.18	NO
148	H1F0	H1F0	H1F0	14887	-0.085	0.16	NO
149	HIST3H2A	HIST3H2A	HIST3H2A	15225	-0.092	0.14	NO
150	KDELC1	KDELC1	KDELC1	16446	-0.13	0.082	NO
151	HIST1H2AC	HIST1H2AC	HIST1H2AC	16852	-0.15	0.069	NO

Figure S9. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: BIDUS METASTASIS UP.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: BIDUS METASTASIS UP, 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: MAYBURD RESPONSE TO L663536 DN

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	MATR3	MATR3	MATR3	858	0.31	-0.024	YES
2	MPHOSPH9	MPHOSPH9	MPHOSPH9	1153	0.28	-0.019	YES
3	OTUD6B	OTUD6B	OTUD6B	1200	0.27	-0.00039	YES
4	SGOL2	SGOL2	SGOL2	1385	0.25	0.0086	YES
5	ABHD3	ABHD3	ABHD3	1489	0.24	0.021	YES
6	TAF2	TAF2	TAF2	1745	0.22	0.024	YES
7	DBF4	DBF4	DBF4	1799	0.21	0.037	YES
8	PPP1R12A	PPP1R12A	PPP1R12A	1836	0.21	0.051	YES
9	DNAJB14	DNAJB14	DNAJB14	1881	0.2	0.065	YES
10	PPIP5K2	PPIP5K2	PPIP5K2	1928	0.2	0.078	YES
11	CEP152	CEP152	CEP152	1982	0.2	0.09	YES
12	LRRC40	LRRC40	LRRC40	2005	0.2	0.1	YES
13	TERF1	TERF1	TERF1	2124	0.19	0.11	YES
14	C5orf28	C5orf28	C5orf28	2281	0.18	0.12	YES
15	EZH2	EZH2	EZH2	2371	0.18	0.13	YES
16	ZNF567	ZNF567	ZNF567	2401	0.17	0.14	YES
17	ASF1A	ASF1A	ASF1A	2440	0.17	0.15	YES
18	TMEM165	TMEM165	TMEM165	2577	0.16	0.15	YES
19	CDK1	CDK1	CDK1	2611	0.16	0.16	YES
20	ANKRD49	ANKRD49	ANKRD49	2661	0.16	0.18	YES
21	SPAST	SPAST	SPAST	2773	0.16	0.18	YES
22	PRKDC	PRKDC	PRKDC	2824	0.15	0.19	YES
23	KRIT1	KRIT1	KRIT1	3013	0.15	0.19	YES
24	STAM2	STAM2	STAM2	3088	0.14	0.2	YES
25	NOL8	NOL8	NOL8	3101	0.14	0.21	YES
26	TRIB1	TRIB1	TRIB1	3388	0.13	0.2	YES
27	BARD1	BARD1	BARD1	3488	0.13	0.21	YES
28	NNT	NNT	NNT	3699	0.12	0.2	YES
29	IFT74	IFT74	IFT74	3743	0.12	0.21	YES
30	DENND4A	DENND4A	DENND4A	3910	0.12	0.21	YES
31	DHX29	DHX29	DHX29	4015	0.11	0.22	YES
32	C11orf54	C11orf54	C11orf54	4036	0.11	0.22	YES
33	IREB2	IREB2	IREB2	4085	0.11	0.23	YES
34	PAPD4	PAPD4	PAPD4	4095	0.11	0.24	YES
35	MET	MET	MET	4123	0.11	0.24	YES
36	HAUS1	HAUS1	HAUS1	4157	0.11	0.25	YES
37	ZCCHC10	ZCCHC10	ZCCHC10	4161	0.11	0.26	YES
38	ZNF131	ZNF131	ZNF131	4171	0.11	0.27	YES
39	RFX7	RFX7	RFX7	4212	0.11	0.27	YES
40	C1orf131	C1orf131	C1orf131	4220	0.11	0.28	YES
41	BTBD1	BTBD1	BTBD1	4238	0.11	0.29	YES
42	LEMD3	LEMD3	LEMD3	4243	0.11	0.3	YES
43	IARS	IARS	IARS	4369	0.1	0.3	YES
44	FAM188A	FAM188A	FAM188A	4389	0.1	0.3	YES
45	FANCL	FANCL	FANCL	4461	0.1	0.31	YES
46	TATDN1	TATDN1	TATDN1	4489	0.1	0.32	YES
47	ZNF367	ZNF367	ZNF367	4490	0.1	0.32	YES
48	LAP3	LAP3	LAP3	4527	0.1	0.33	YES
49	NCAPD3	NCAPD3	NCAPD3	4542	0.1	0.34	YES
50	RSF1	RSF1	RSF1	4565	0.1	0.34	YES
51	PEX1	PEX1	PEX1	4612	0.098	0.35	YES
52	DDX1	DDX1	DDX1	4653	0.097	0.35	YES
53	ACTR6	ACTR6	ACTR6	4669	0.097	0.36	YES
54	PAIP1	PAIP1	PAIP1	4723	0.096	0.36	YES
55	MRPL19	MRPL19	MRPL19	4809	0.094	0.37	YES
56	PSMA3	PSMA3	PSMA3	4824	0.094	0.37	YES
57	MINPP1	MINPP1	MINPP1	4853	0.093	0.38	YES
58	TYMS	TYMS	TYMS	5025	0.088	0.38	YES
59	PAK1IP1	PAK1IP1	PAK1IP1	5174	0.085	0.37	YES
60	ANAPC10	ANAPC10	ANAPC10	5254	0.084	0.38	YES
61	SPATA5L1	SPATA5L1	SPATA5L1	5290	0.083	0.38	YES
62	TMEM135	TMEM135	TMEM135	5327	0.082	0.38	YES
63	FEM1B	FEM1B	FEM1B	5361	0.081	0.39	YES
64	ZNF277	ZNF277	ZNF277	5415	0.08	0.39	YES
65	ORC5	ORC5	ORC5	5482	0.078	0.39	YES
66	SLC25A36	SLC25A36	SLC25A36	5486	0.078	0.4	YES
67	PAPOLA	PAPOLA	PAPOLA	5503	0.078	0.4	YES
68	NUDCD2	NUDCD2	NUDCD2	5572	0.076	0.41	YES
69	UPF3A	UPF3A	UPF3A	5762	0.072	0.4	YES
70	AASDHPPT	AASDHPPT	AASDHPPT	5777	0.072	0.41	YES
71	RACGAP1	RACGAP1	RACGAP1	5817	0.071	0.41	YES
72	MRPL50	MRPL50	MRPL50	5891	0.069	0.41	YES
73	CYP2R1	CYP2R1	CYP2R1	5893	0.069	0.42	YES
74	PFDN4	PFDN4	PFDN4	6054	0.066	0.41	YES
75	NASP	NASP	NASP	6106	0.064	0.42	YES
76	DDX18	DDX18	DDX18	6213	0.062	0.41	YES
77	CCT2	CCT2	CCT2	6247	0.062	0.42	YES
78	CEP57	CEP57	CEP57	6281	0.061	0.42	YES
79	RPL26L1	RPL26L1	RPL26L1	6314	0.06	0.42	YES
80	AVL9	AVL9	AVL9	6397	0.059	0.42	NO
81	DARS	DARS	DARS	6739	0.052	0.41	NO
82	RNF111	RNF111	RNF111	7064	0.046	0.39	NO
83	SLC33A1	SLC33A1	SLC33A1	7088	0.046	0.4	NO
84	CDC23	CDC23	CDC23	7097	0.045	0.4	NO
85	WDR61	WDR61	WDR61	7203	0.043	0.4	NO
86	FAM98B	FAM98B	FAM98B	7364	0.04	0.39	NO
87	ELAC1	ELAC1	ELAC1	7377	0.04	0.39	NO
88	CHMP4A	CHMP4A	CHMP4A	7507	0.038	0.39	NO
89	CCT5	CCT5	CCT5	7554	0.037	0.39	NO
90	TLE4	TLE4	TLE4	7557	0.036	0.39	NO
91	PPP2R5C	PPP2R5C	PPP2R5C	7597	0.036	0.39	NO
92	PDCD6	PDCD6	PDCD6	7671	0.034	0.39	NO
93	SNX19	SNX19	SNX19	7695	0.034	0.39	NO
94	C15orf41	C15orf41	C15orf41	7759	0.033	0.39	NO
95	SNRPD1	SNRPD1	SNRPD1	7828	0.031	0.39	NO
96	BUB3	BUB3	BUB3	7867	0.031	0.39	NO
97	TMEM126A	TMEM126A	TMEM126A	8013	0.028	0.38	NO
98	GCSH	GCSH	GCSH	8142	0.026	0.38	NO
99	TDP2	TDP2	TDP2	8347	0.022	0.37	NO
100	SLC38A1	SLC38A1	SLC38A1	8369	0.021	0.37	NO
101	G3BP1	G3BP1	G3BP1	8462	0.019	0.37	NO
102	C1QBP	C1QBP	C1QBP	8648	0.016	0.36	NO
103	NUDT5	NUDT5	NUDT5	9016	0.0096	0.34	NO
104	KLF13	KLF13	KLF13	9154	0.0072	0.33	NO
105	DKC1	DKC1	DKC1	9175	0.0067	0.33	NO
106	RAN	RAN	RAN	9179	0.0067	0.33	NO
107	NAA50	NAA50	NAA50	9206	0.0063	0.33	NO
108	GEMIN5	GEMIN5	GEMIN5	9346	0.0036	0.32	NO
109	DDX31	DDX31	DDX31	9355	0.0034	0.32	NO
110	CMC1	CMC1	CMC1	9515	0.00071	0.31	NO
111	IK	IK	IK	9533	0.00038	0.31	NO
112	CHEK1	CHEK1	CHEK1	9545	0.00017	0.31	NO
113	C11orf73	C11orf73	C11orf73	9615	-0.00084	0.31	NO
114	SSBP1	SSBP1	SSBP1	9631	-0.0011	0.31	NO
115	PAAF1	PAAF1	PAAF1	9686	-0.0022	0.3	NO
116	THYN1	THYN1	THYN1	9738	-0.0029	0.3	NO
117	TSHZ1	TSHZ1	TSHZ1	9784	-0.0038	0.3	NO
118	MCM3AP	MCM3AP	MCM3AP	9876	-0.005	0.29	NO
119	CHCHD1	CHCHD1	CHCHD1	9904	-0.0054	0.29	NO
120	C19orf52	C19orf52	C19orf52	10205	-0.01	0.28	NO
121	SLC16A1	SLC16A1	SLC16A1	10319	-0.012	0.27	NO
122	PTPMT1	PTPMT1	PTPMT1	10338	-0.013	0.27	NO
123	NMT1	NMT1	NMT1	10416	-0.014	0.27	NO
124	SHFM1	SHFM1	SHFM1	10442	-0.014	0.27	NO
125	LSM5	LSM5	LSM5	10472	-0.015	0.27	NO
126	EBNA1BP2	EBNA1BP2	EBNA1BP2	10589	-0.017	0.26	NO
127	PSMC4	PSMC4	PSMC4	10914	-0.021	0.25	NO
128	GLT8D1	GLT8D1	GLT8D1	10936	-0.022	0.25	NO
129	FANCF	FANCF	FANCF	10950	-0.022	0.25	NO
130	EIF3M	EIF3M	EIF3M	10969	-0.022	0.25	NO
131	MBD4	MBD4	MBD4	11028	-0.023	0.25	NO
132	AIMP2	AIMP2	AIMP2	11137	-0.025	0.24	NO
133	MYLIP	MYLIP	MYLIP	11314	-0.027	0.24	NO
134	TBCB	TBCB	TBCB	11379	-0.028	0.23	NO
135	ACTL6A	ACTL6A	ACTL6A	11413	-0.029	0.23	NO
136	NCLN	NCLN	NCLN	11505	-0.03	0.23	NO
137	MINA	MINA	MINA	11525	-0.03	0.23	NO
138	IFT57	IFT57	IFT57	11597	-0.031	0.23	NO
139	ILF3	ILF3	ILF3	11602	-0.032	0.23	NO
140	EFTUD2	EFTUD2	EFTUD2	11655	-0.032	0.23	NO
141	KEAP1	KEAP1	KEAP1	11742	-0.034	0.23	NO
142	PSMD8	PSMD8	PSMD8	11815	-0.035	0.23	NO
143	LSM4	LSM4	LSM4	11851	-0.036	0.23	NO
144	ATP5L	ATP5L	ATP5L	11960	-0.037	0.23	NO
145	CIRH1A	CIRH1A	CIRH1A	12353	-0.042	0.21	NO
146	MRPS12	MRPS12	MRPS12	12405	-0.043	0.21	NO
147	SMARCA4	SMARCA4	SMARCA4	12770	-0.048	0.19	NO
148	SF3B2	SF3B2	SF3B2	12875	-0.05	0.19	NO
149	TIMM50	TIMM50	TIMM50	13554	-0.061	0.16	NO
150	RUVBL2	RUVBL2	RUVBL2	13791	-0.065	0.15	NO
151	RNF7	RNF7	RNF7	14030	-0.069	0.14	NO
152	MRPL43	MRPL43	MRPL43	14086	-0.07	0.14	NO
153	NDUFA13	NDUFA13	NDUFA13	14190	-0.072	0.14	NO
154	FIBP	FIBP	FIBP	14250	-0.073	0.14	NO
155	COMMD4	COMMD4	COMMD4	14851	-0.084	0.12	NO
156	CCDC94	CCDC94	CCDC94	15192	-0.091	0.11	NO
157	NADSYN1	NADSYN1	NADSYN1	15319	-0.094	0.11	NO
158	ERCC1	ERCC1	ERCC1	15474	-0.097	0.1	NO
159	IP6K2	IP6K2	IP6K2	15684	-0.1	0.1	NO
160	EIF3G	EIF3G	EIF3G	16066	-0.12	0.089	NO
161	ACD	ACD	ACD	16728	-0.14	0.063	NO
162	MCM2	MCM2	MCM2	16950	-0.16	0.063	NO

Figure S11. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: MAYBURD RESPONSE TO L663536 DN.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: MAYBURD RESPONSE TO L663536 DN, 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: ENK UV RESPONSE KERATINOCYTE DN

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	SOCS2	SOCS2	SOCS2	1148	0.28	-0.045	YES
2	GAS2	GAS2	GAS2	1473	0.24	-0.047	YES
3	PHTF2	PHTF2	PHTF2	1788	0.21	-0.049	YES
4	MAP4K3	MAP4K3	MAP4K3	1803	0.21	-0.036	YES
5	ADAM9	ADAM9	ADAM9	2307	0.18	-0.051	YES
6	STRN3	STRN3	STRN3	2365	0.18	-0.042	YES
7	F2R	F2R	F2R	2387	0.18	-0.031	YES
8	ITGA6	ITGA6	ITGA6	2390	0.18	-0.02	YES
9	TGS1	TGS1	TGS1	2501	0.17	-0.014	YES
10	MPHOSPH10	MPHOSPH10	MPHOSPH10	2544	0.17	-0.0047	YES
11	ESF1	ESF1	ESF1	2709	0.16	-0.0028	YES
12	NOP58	NOP58	NOP58	2728	0.16	0.0071	YES
13	HRSP12	HRSP12	HRSP12	2830	0.15	0.012	YES
14	CHD1	CHD1	CHD1	2834	0.15	0.022	YES
15	SLC38A2	SLC38A2	SLC38A2	2899	0.15	0.029	YES
16	SMARCAD1	SMARCAD1	SMARCAD1	2977	0.15	0.035	YES
17	XPO1	XPO1	XPO1	3018	0.15	0.043	YES
18	SLC4A7	SLC4A7	SLC4A7	3110	0.14	0.048	YES
19	XPOT	XPOT	XPOT	3117	0.14	0.058	YES
20	BACH1	BACH1	BACH1	3234	0.14	0.061	YES
21	TBC1D15	TBC1D15	TBC1D15	3321	0.14	0.065	YES
22	STXBP3	STXBP3	STXBP3	3404	0.13	0.07	YES
23	WDR43	WDR43	WDR43	3421	0.13	0.078	YES
24	MARCH7	MARCH7	MARCH7	3445	0.13	0.086	YES
25	PACRGL	PACRGL	PACRGL	3597	0.13	0.086	YES
26	PTPN2	PTPN2	PTPN2	3620	0.13	0.094	YES
27	RNFT1	RNFT1	RNFT1	3637	0.12	0.1	YES
28	TXNDC9	TXNDC9	TXNDC9	3641	0.12	0.11	YES
29	DICER1	DICER1	DICER1	3656	0.12	0.12	YES
30	CWC22	CWC22	CWC22	3670	0.12	0.13	YES
31	KRAS	KRAS	KRAS	3701	0.12	0.13	YES
32	MTMR10	MTMR10	MTMR10	3734	0.12	0.14	YES
33	IMPAD1	IMPAD1	IMPAD1	3747	0.12	0.15	YES
34	PSMD12	PSMD12	PSMD12	4072	0.11	0.14	YES
35	ZCCHC10	ZCCHC10	ZCCHC10	4161	0.11	0.14	YES
36	RSRC2	RSRC2	RSRC2	4204	0.11	0.14	YES
37	TNPO1	TNPO1	TNPO1	4219	0.11	0.15	YES
38	ZFX	ZFX	ZFX	4222	0.11	0.16	YES
39	BLZF1	BLZF1	BLZF1	4225	0.11	0.17	YES
40	MDFIC	MDFIC	MDFIC	4237	0.11	0.17	YES
41	ELOVL6	ELOVL6	ELOVL6	4247	0.11	0.18	YES
42	SEC23A	SEC23A	SEC23A	4272	0.11	0.19	YES
43	GCLM	GCLM	GCLM	4307	0.11	0.19	YES
44	IARS	IARS	IARS	4369	0.1	0.2	YES
45	GAB1	GAB1	GAB1	4415	0.1	0.2	YES
46	PCF11	PCF11	PCF11	4426	0.1	0.21	YES
47	EIF3J	EIF3J	EIF3J	4447	0.1	0.21	YES
48	SRSF6	SRSF6	SRSF6	4458	0.1	0.22	YES
49	ACAT2	ACAT2	ACAT2	4466	0.1	0.23	YES
50	KIF2A	KIF2A	KIF2A	4610	0.098	0.22	YES
51	RNF138	RNF138	RNF138	4625	0.098	0.23	YES
52	DDX1	DDX1	DDX1	4653	0.097	0.24	YES
53	RAB18	RAB18	RAB18	4683	0.097	0.24	YES
54	PKD2	PKD2	PKD2	4757	0.095	0.24	YES
55	MED23	MED23	MED23	4787	0.095	0.25	YES
56	PLA2G6	PLA2G6	PLA2G6	4807	0.094	0.25	YES
57	FBXO38	FBXO38	FBXO38	4822	0.094	0.26	YES
58	RASA1	RASA1	RASA1	4867	0.093	0.26	YES
59	SEC23IP	SEC23IP	SEC23IP	4881	0.092	0.27	YES
60	ROCK2	ROCK2	ROCK2	4936	0.091	0.27	YES
61	ACADM	ACADM	ACADM	4985	0.09	0.28	YES
62	PPIC	PPIC	PPIC	4989	0.09	0.28	YES
63	ZNF644	ZNF644	ZNF644	4993	0.09	0.29	YES
64	EPRS	EPRS	EPRS	5020	0.089	0.29	YES
65	LIMA1	LIMA1	LIMA1	5032	0.088	0.3	YES
66	KLHL7	KLHL7	KLHL7	5202	0.085	0.29	YES
67	TBRG1	TBRG1	TBRG1	5218	0.084	0.3	YES
68	ZNF281	ZNF281	ZNF281	5295	0.083	0.3	YES
69	TXNRD1	TXNRD1	TXNRD1	5360	0.081	0.3	YES
70	UBE2T	UBE2T	UBE2T	5430	0.079	0.3	YES
71	MSH2	MSH2	MSH2	5497	0.078	0.31	YES
72	STAM	STAM	STAM	5508	0.078	0.31	YES
73	ZC3H14	ZC3H14	ZC3H14	5629	0.075	0.31	YES
74	RNF145	RNF145	RNF145	5693	0.073	0.31	YES
75	RARS2	RARS2	RARS2	5699	0.073	0.32	YES
76	UTP20	UTP20	UTP20	5713	0.073	0.32	YES
77	FHL1	FHL1	FHL1	5784	0.072	0.32	YES
78	YAP1	YAP1	YAP1	5824	0.07	0.32	YES
79	TOM1L1	TOM1L1	TOM1L1	5994	0.067	0.32	YES
80	YES1	YES1	YES1	6105	0.064	0.32	YES
81	ITGB1	ITGB1	ITGB1	6191	0.063	0.32	YES
82	SLC7A6	SLC7A6	SLC7A6	6240	0.062	0.32	YES
83	IARS2	IARS2	IARS2	6241	0.062	0.32	YES
84	ANKRD17	ANKRD17	ANKRD17	6297	0.061	0.32	YES
85	RRN3	RRN3	RRN3	6304	0.06	0.33	YES
86	USP9X	USP9X	USP9X	6382	0.059	0.33	YES
87	ARIH1	ARIH1	ARIH1	6458	0.058	0.33	YES
88	COPS4	COPS4	COPS4	6554	0.055	0.33	YES
89	CTBP2	CTBP2	CTBP2	6589	0.055	0.33	YES
90	GNL2	GNL2	GNL2	6633	0.054	0.33	YES
91	ELP2	ELP2	ELP2	6689	0.053	0.33	YES
92	NUP35	NUP35	NUP35	6695	0.053	0.33	YES
93	C5orf51	C5orf51	C5orf51	6711	0.053	0.34	YES
94	RAD23B	RAD23B	RAD23B	6741	0.052	0.34	YES
95	LAPTM4B	LAPTM4B	LAPTM4B	6778	0.052	0.34	YES
96	HSPA4	HSPA4	HSPA4	6792	0.051	0.34	YES
97	ZMYM4	ZMYM4	ZMYM4	6809	0.051	0.34	YES
98	TPP2	TPP2	TPP2	6843	0.05	0.35	YES
99	NDUFAF1	NDUFAF1	NDUFAF1	6852	0.05	0.35	YES
100	PLS3	PLS3	PLS3	6856	0.05	0.35	YES
101	FKBP11	FKBP11	FKBP11	6922	0.049	0.35	NO
102	PPA1	PPA1	PPA1	7020	0.047	0.35	NO
103	FCF1	FCF1	FCF1	7096	0.045	0.35	NO
104	CDK2AP1	CDK2AP1	CDK2AP1	7118	0.045	0.35	NO
105	FBXO8	FBXO8	FBXO8	7166	0.044	0.35	NO
106	WBP5	WBP5	WBP5	7379	0.04	0.34	NO
107	EIF4G2	EIF4G2	EIF4G2	7430	0.039	0.34	NO
108	WDR55	WDR55	WDR55	7535	0.037	0.34	NO
109	RNF4	RNF4	RNF4	7587	0.036	0.34	NO
110	PPP1R2	PPP1R2	PPP1R2	7595	0.036	0.34	NO
111	SRSF3	SRSF3	SRSF3	7753	0.033	0.33	NO
112	MRPS31	MRPS31	MRPS31	7754	0.033	0.34	NO
113	SMAD1	SMAD1	SMAD1	8121	0.026	0.32	NO
114	ZZZ3	ZZZ3	ZZZ3	8127	0.026	0.32	NO
115	ARCN1	ARCN1	ARCN1	8130	0.026	0.32	NO
116	GCSH	GCSH	GCSH	8142	0.026	0.32	NO
117	RYK	RYK	RYK	8224	0.024	0.32	NO
118	SH3D19	SH3D19	SH3D19	8287	0.023	0.32	NO
119	RABGGTB	RABGGTB	RABGGTB	8315	0.022	0.32	NO
120	CTTN	CTTN	CTTN	8324	0.022	0.32	NO
121	UPP1	UPP1	UPP1	8361	0.021	0.32	NO
122	NDUFAF4	NDUFAF4	NDUFAF4	8374	0.021	0.32	NO
123	PSMD11	PSMD11	PSMD11	8423	0.02	0.32	NO
124	XRCC5	XRCC5	XRCC5	8430	0.02	0.32	NO
125	LAPTM4A	LAPTM4A	LAPTM4A	8523	0.018	0.32	NO
126	RSL1D1	RSL1D1	RSL1D1	8525	0.018	0.32	NO
127	SUCLG2	SUCLG2	SUCLG2	8689	0.015	0.31	NO
128	ALDH7A1	ALDH7A1	ALDH7A1	8743	0.014	0.31	NO
129	NDUFAB1	NDUFAB1	NDUFAB1	8760	0.014	0.31	NO
130	LRRC58	LRRC58	LRRC58	8850	0.013	0.3	NO
131	CDKN1A	CDKN1A	CDKN1A	8903	0.012	0.3	NO
132	YWHAB	YWHAB	YWHAB	8939	0.011	0.3	NO
133	TJP1	TJP1	TJP1	9093	0.0082	0.29	NO
134	UBE2D2	UBE2D2	UBE2D2	9210	0.0061	0.28	NO
135	ZNF639	ZNF639	ZNF639	9225	0.0058	0.28	NO
136	NOP56	NOP56	NOP56	9268	0.005	0.28	NO
137	GARS	GARS	GARS	9290	0.0046	0.28	NO
138	PPP2R1B	PPP2R1B	PPP2R1B	9336	0.0037	0.28	NO
139	YWHAH	YWHAH	YWHAH	9427	0.0023	0.27	NO
140	MRPL34	MRPL34	MRPL34	9483	0.0013	0.27	NO
141	CCND1	CCND1	CCND1	9518	0.00061	0.27	NO
142	PDCD2	PDCD2	PDCD2	9551	0.000087	0.27	NO
143	DTYMK	DTYMK	DTYMK	9611	-0.00078	0.26	NO
144	ERCC5	ERCC5	ERCC5	9651	-0.0014	0.26	NO
145	GHR	GHR	GHR	9660	-0.0016	0.26	NO
146	TARS2	TARS2	TARS2	9695	-0.0023	0.26	NO
147	DNAJB6	DNAJB6	DNAJB6	9796	-0.004	0.26	NO
148	MRPS10	MRPS10	MRPS10	9837	-0.0045	0.25	NO
149	GLO1	GLO1	GLO1	9864	-0.0048	0.25	NO
150	PAFAH2	PAFAH2	PAFAH2	9977	-0.0065	0.25	NO
151	PEX7	PEX7	PEX7	10138	-0.0096	0.24	NO
152	USP10	USP10	USP10	10202	-0.01	0.24	NO
153	SMAD2	SMAD2	SMAD2	10230	-0.011	0.23	NO
154	GSTA4	GSTA4	GSTA4	10561	-0.016	0.22	NO
155	CBR3	CBR3	CBR3	10692	-0.018	0.21	NO
156	COPS7A	COPS7A	COPS7A	10718	-0.018	0.21	NO
157	MRPL17	MRPL17	MRPL17	10767	-0.019	0.21	NO
158	RCN1	RCN1	RCN1	10927	-0.022	0.2	NO
159	LAS1L	LAS1L	LAS1L	10990	-0.023	0.2	NO
160	KCNAB3	KCNAB3	KCNAB3	11054	-0.024	0.2	NO
161	MRPL3	MRPL3	MRPL3	11312	-0.027	0.19	NO
162	MRPL45	MRPL45	MRPL45	11707	-0.033	0.17	NO
163	TMEM183A	TMEM183A	TMEM183A	11809	-0.035	0.16	NO
164	PIGX	PIGX	PIGX	11880	-0.036	0.16	NO
165	RPP14	RPP14	RPP14	12065	-0.038	0.15	NO
166	CAD	CAD	CAD	12082	-0.039	0.16	NO
167	MPDU1	MPDU1	MPDU1	12194	-0.04	0.15	NO
168	GNB1	GNB1	GNB1	12218	-0.04	0.15	NO
169	DCTPP1	DCTPP1	DCTPP1	12234	-0.041	0.16	NO
170	CIRH1A	CIRH1A	CIRH1A	12353	-0.042	0.15	NO
171	PRPSAP1	PRPSAP1	PRPSAP1	12483	-0.044	0.15	NO
172	DPH5	DPH5	DPH5	12740	-0.048	0.14	NO
173	TGIF2	TGIF2	TGIF2	13071	-0.053	0.12	NO
174	SNX12	SNX12	SNX12	13144	-0.054	0.12	NO
175	FKBP9	FKBP9	FKBP9	13242	-0.056	0.12	NO
176	INTS5	INTS5	INTS5	13267	-0.056	0.12	NO
177	MRPS2	MRPS2	MRPS2	13360	-0.058	0.12	NO
178	RCL1	RCL1	RCL1	13457	-0.059	0.12	NO
179	SNRPC	SNRPC	SNRPC	13468	-0.059	0.12	NO
180	MDFI	MDFI	MDFI	13566	-0.061	0.12	NO
181	C12orf45	C12orf45	C12orf45	13581	-0.061	0.13	NO
182	LSG1	LSG1	LSG1	13627	-0.062	0.13	NO
183	GCAT	GCAT	GCAT	14321	-0.074	0.094	NO
184	TRIP6	TRIP6	TRIP6	14349	-0.075	0.098	NO
185	CRTAP	CRTAP	CRTAP	14359	-0.075	0.1	NO
186	BYSL	BYSL	BYSL	14363	-0.075	0.11	NO
187	RPUSD4	RPUSD4	RPUSD4	14537	-0.078	0.1	NO
188	GRWD1	GRWD1	GRWD1	14625	-0.079	0.1	NO
189	UMPS	UMPS	UMPS	14668	-0.08	0.11	NO
190	GFER	GFER	GFER	14749	-0.082	0.11	NO
191	PRPF6	PRPF6	PRPF6	15181	-0.09	0.09	NO
192	RPL22	RPL22	RPL22	15418	-0.096	0.084	NO
193	ZMAT3	ZMAT3	ZMAT3	15575	-0.1	0.082	NO
194	CPXM1	CPXM1	CPXM1	15589	-0.1	0.088	NO
195	TEAD2	TEAD2	TEAD2	16013	-0.11	0.072	NO
196	ZNF213	ZNF213	ZNF213	16034	-0.11	0.079	NO
197	LSM2	LSM2	LSM2	16053	-0.11	0.086	NO
198	EIF4EBP1	EIF4EBP1	EIF4EBP1	16220	-0.12	0.085	NO
199	JAGN1	JAGN1	JAGN1	16573	-0.14	0.075	NO
200	KANK3	KANK3	KANK3	16623	-0.14	0.082	NO

Figure S13. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: ENK UV RESPONSE KERATINOCYTE DN.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: ENK UV RESPONSE KERATINOCYTE DN, 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: SEIDEN ONCOGENESIS BY MET

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	SLCO5A1	SLCO5A1	SLCO5A1	102	0.56	0.021	YES
2	CDH17	CDH17	CDH17	160	0.51	0.042	YES
3	PI15	PI15	PI15	210	0.49	0.062	YES
4	SLC26A7	SLC26A7	SLC26A7	254	0.47	0.082	YES
5	MMP16	MMP16	MMP16	274	0.45	0.1	YES
6	PMP2	PMP2	PMP2	282	0.45	0.12	YES
7	CCNE2	CCNE2	CCNE2	303	0.44	0.14	YES
8	TTPA	TTPA	TTPA	413	0.41	0.16	YES
9	OSR2	OSR2	OSR2	455	0.4	0.17	YES
10	CLVS1	CLVS1	CLVS1	521	0.38	0.19	YES
11	CALB1	CALB1	CALB1	541	0.38	0.2	YES
12	JPH1	JPH1	JPH1	579	0.37	0.22	YES
13	RIMS2	RIMS2	RIMS2	600	0.36	0.24	YES
14	FBXO43	FBXO43	FBXO43	614	0.36	0.25	YES
15	IL7	IL7	IL7	654	0.35	0.27	YES
16	SDC2	SDC2	SDC2	715	0.34	0.28	YES
17	KCNB2	KCNB2	KCNB2	731	0.34	0.29	YES
18	XKR9	XKR9	XKR9	824	0.32	0.3	YES
19	C8orf37	C8orf37	C8orf37	863	0.31	0.32	YES
20	TPD52	TPD52	TPD52	889	0.31	0.33	YES
21	RGS22	RGS22	RGS22	957	0.3	0.34	YES
22	GEM	GEM	GEM	972	0.3	0.35	YES
23	RAD54B	RAD54B	RAD54B	982	0.3	0.37	YES
24	OTUD6B	OTUD6B	OTUD6B	1200	0.27	0.37	YES
25	PRDM14	PRDM14	PRDM14	1212	0.27	0.38	YES
26	SLC10A5	SLC10A5	SLC10A5	1358	0.25	0.38	YES
27	SPAG1	SPAG1	SPAG1	1427	0.24	0.39	YES
28	IMPA1	IMPA1	IMPA1	1502	0.24	0.4	YES
29	PKIA	PKIA	PKIA	1547	0.23	0.41	YES
30	SNX31	SNX31	SNX31	1570	0.23	0.42	YES
31	TMEM67	TMEM67	TMEM67	1698	0.22	0.42	YES
32	DPY19L4	DPY19L4	DPY19L4	1808	0.21	0.42	YES
33	CYP7A1	CYP7A1	CYP7A1	1812	0.21	0.43	YES
34	ZFHX4	ZFHX4	ZFHX4	1988	0.2	0.43	YES
35	UBE2W	UBE2W	UBE2W	2037	0.2	0.44	YES
36	MTDH	MTDH	MTDH	2079	0.19	0.45	YES
37	SNX16	SNX16	SNX16	2109	0.19	0.46	YES
38	TERF1	TERF1	TERF1	2124	0.19	0.46	YES
39	LACTB2	LACTB2	LACTB2	2156	0.19	0.47	YES
40	TMEM64	TMEM64	TMEM64	2162	0.19	0.48	YES
41	YTHDF3	YTHDF3	YTHDF3	2193	0.19	0.49	YES
42	PLEKHF2	PLEKHF2	PLEKHF2	2258	0.18	0.49	YES
43	LY96	LY96	LY96	2350	0.18	0.49	YES
44	NBN	NBN	NBN	2352	0.18	0.5	YES
45	UBXN2B	UBXN2B	UBXN2B	2368	0.18	0.51	YES
46	RNF19A	RNF19A	RNF19A	2505	0.17	0.51	YES
47	NIPAL2	NIPAL2	NIPAL2	2593	0.16	0.51	YES
48	ASPH	ASPH	ASPH	2672	0.16	0.52	YES
49	FABP5	FABP5	FABP5	2692	0.16	0.52	YES
50	VPS13B	VPS13B	VPS13B	2699	0.16	0.53	YES
51	TMEM70	TMEM70	TMEM70	2708	0.16	0.54	YES
52	STAU2	STAU2	STAU2	2741	0.16	0.54	YES
53	INTS8	INTS8	INTS8	2750	0.16	0.55	YES
54	HRSP12	HRSP12	HRSP12	2830	0.15	0.55	YES
55	FAM92A1	FAM92A1	FAM92A1	2878	0.15	0.56	YES
56	STK3	STK3	STK3	2928	0.15	0.56	YES
57	MRPS28	MRPS28	MRPS28	3047	0.15	0.56	YES
58	TRAM1	TRAM1	TRAM1	3096	0.14	0.57	YES
59	TMEM55A	TMEM55A	TMEM55A	3150	0.14	0.57	YES
60	AZIN1	AZIN1	AZIN1	3165	0.14	0.57	YES
61	PDP1	PDP1	PDP1	3174	0.14	0.58	YES
62	RUNX1T1	RUNX1T1	RUNX1T1	3248	0.14	0.58	YES
63	SLC25A32	SLC25A32	SLC25A32	3335	0.14	0.59	YES
64	DCAF13	DCAF13	DCAF13	3338	0.14	0.59	YES
65	CHD7	CHD7	CHD7	3344	0.14	0.6	YES
66	NCOA2	NCOA2	NCOA2	3370	0.13	0.6	YES
67	BAALC	BAALC	BAALC	3383	0.13	0.61	YES
68	OSGIN2	OSGIN2	OSGIN2	3417	0.13	0.61	YES
69	NSMAF	NSMAF	NSMAF	3524	0.13	0.61	YES
70	ZNF704	ZNF704	ZNF704	3586	0.13	0.62	YES
71	ATP6V1C1	ATP6V1C1	ATP6V1C1	3627	0.13	0.62	YES
72	TSPYL5	TSPYL5	TSPYL5	3662	0.12	0.62	YES
73	RAB2A	RAB2A	RAB2A	3691	0.12	0.63	YES
74	KIAA1429	KIAA1429	KIAA1429	3755	0.12	0.63	YES
75	TP53INP1	TP53INP1	TP53INP1	3823	0.12	0.63	YES
76	PAG1	PAG1	PAG1	3895	0.12	0.63	YES
77	TCEB1	TCEB1	TCEB1	4142	0.11	0.62	YES
78	KCNS2	KCNS2	KCNS2	4165	0.11	0.63	YES
79	ZBTB10	ZBTB10	ZBTB10	4233	0.11	0.63	YES
80	RDH10	RDH10	RDH10	4339	0.1	0.63	YES
81	RBM12B	RBM12B	RBM12B	4347	0.1	0.63	YES
82	GDF6	GDF6	GDF6	4359	0.1	0.64	YES
83	GGH	GGH	GGH	4402	0.1	0.64	YES
84	GDAP1	GDAP1	GDAP1	4486	0.1	0.64	YES
85	PEX2	PEX2	PEX2	4857	0.093	0.62	NO
86	POLR2K	POLR2K	POLR2K	4970	0.09	0.62	NO
87	HEY1	HEY1	HEY1	4987	0.09	0.63	NO
88	ZFAND1	ZFAND1	ZFAND1	5040	0.088	0.63	NO
89	GRHL2	GRHL2	GRHL2	5272	0.083	0.62	NO
90	YWHAZ	YWHAZ	YWHAZ	5526	0.077	0.61	NO
91	ANKRD46	ANKRD46	ANKRD46	5648	0.074	0.6	NO
92	POP1	POP1	POP1	5675	0.074	0.61	NO
93	DECR1	DECR1	DECR1	5741	0.072	0.61	NO
94	SDCBP	SDCBP	SDCBP	5940	0.068	0.6	NO
95	COX6C	COX6C	COX6C	6523	0.056	0.57	NO
96	FABP4	FABP4	FABP4	6707	0.053	0.56	NO
97	RALYL	RALYL	RALYL	6727	0.052	0.56	NO
98	LAPTM4B	LAPTM4B	LAPTM4B	6778	0.052	0.56	NO
99	NECAB1	NECAB1	NECAB1	6951	0.048	0.56	NO
100	FZD6	FZD6	FZD6	7155	0.044	0.55	NO
101	PABPC1	PABPC1	PABPC1	7365	0.04	0.54	NO
102	ZNF706	ZNF706	ZNF706	7467	0.038	0.53	NO
103	UQCRB	UQCRB	UQCRB	8105	0.026	0.5	NO
104	ESRP1	ESRP1	ESRP1	8185	0.025	0.5	NO
105	RIPK2	RIPK2	RIPK2	8210	0.024	0.5	NO
106	NKAIN3	NKAIN3	NKAIN3	8243	0.024	0.49	NO
107	RPL7	RPL7	RPL7	8666	0.016	0.47	NO
108	KLF10	KLF10	KLF10	8955	0.011	0.46	NO
109	PTDSS1	PTDSS1	PTDSS1	9099	0.0081	0.45	NO
110	CRISPLD1	CRISPLD1	CRISPLD1	9102	0.008	0.45	NO
111	STMN2	STMN2	STMN2	9121	0.0078	0.45	NO
112	MATN2	MATN2	MATN2	10978	-0.022	0.35	NO
113	RPL30	RPL30	RPL30	11102	-0.024	0.34	NO
114	HNF4G	HNF4G	HNF4G	11135	-0.025	0.34	NO
115	CTHRC1	CTHRC1	CTHRC1	12525	-0.045	0.26	NO
116	SULF1	SULF1	SULF1	14074	-0.07	0.18	NO
117	EYA1	EYA1	EYA1	15373	-0.095	0.11	NO
118	TRPA1	TRPA1	TRPA1	15519	-0.098	0.11	NO
119	CHMP4C	CHMP4C	CHMP4C	17036	-0.17	0.034	NO
120	MSC	MSC	MSC	18065	-0.52	0.0011	NO

Figure S15. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: SEIDEN ONCOGENESIS BY MET.

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: SEIDEN ONCOGENESIS BY MET, 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: DACOSTA UV RESPONSE VIA ERCC3 COMMON DN

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	IGF2BP3	IGF2BP3	IGF2BP3	109	0.56	0.0092	YES
2	DKK1	DKK1	DKK1	474	0.4	-0.00056	YES
3	PTHLH	PTHLH	PTHLH	505	0.39	0.0084	YES
4	BIRC3	BIRC3	BIRC3	956	0.3	-0.0088	YES
5	HSPA4L	HSPA4L	HSPA4L	1167	0.27	-0.013	YES
6	GOLGA8A	GOLGA8A	GOLGA8A	1366	0.25	-0.018	YES
7	NRG1	NRG1	NRG1	1417	0.25	-0.014	YES
8	PAWR	PAWR	PAWR	1464	0.24	-0.0094	YES
9	IMPA1	IMPA1	IMPA1	1502	0.24	-0.0049	YES
10	USP6	USP6	USP6	1503	0.24	0.0016	YES
11	FLRT2	FLRT2	FLRT2	1522	0.24	0.0071	YES
12	PYROXD1	PYROXD1	PYROXD1	1706	0.22	0.0028	YES
13	CD58	CD58	CD58	1809	0.21	0.0028	YES
14	ARFGEF1	ARFGEF1	ARFGEF1	1816	0.21	0.0083	YES
15	TOP2A	TOP2A	TOP2A	1842	0.21	0.013	YES
16	FKBP5	FKBP5	FKBP5	1849	0.21	0.018	YES
17	PTPRZ1	PTPRZ1	PTPRZ1	1885	0.2	0.022	YES
18	SQLE	SQLE	SQLE	1902	0.2	0.026	YES
19	VSNL1	VSNL1	VSNL1	1933	0.2	0.03	YES
20	KTN1	KTN1	KTN1	1957	0.2	0.034	YES
21	CYP51A1	CYP51A1	CYP51A1	2035	0.2	0.036	YES
22	FOS	FOS	FOS	2050	0.19	0.04	YES
23	SRSF11	SRSF11	SRSF11	2099	0.19	0.043	YES
24	TERF1	TERF1	TERF1	2124	0.19	0.046	YES
25	FEZ1	FEZ1	FEZ1	2235	0.18	0.045	YES
26	RDX	RDX	RDX	2306	0.18	0.046	YES
27	CTAGE5	CTAGE5	CTAGE5	2347	0.18	0.049	YES
28	NBN	NBN	NBN	2352	0.18	0.054	YES
29	RBBP8	RBBP8	RBBP8	2361	0.18	0.058	YES
30	STRN3	STRN3	STRN3	2365	0.18	0.063	YES
31	HOXA9	HOXA9	HOXA9	2379	0.18	0.067	YES
32	ACADSB	ACADSB	ACADSB	2402	0.17	0.07	YES
33	MAP3K5	MAP3K5	MAP3K5	2429	0.17	0.074	YES
34	RGS2	RGS2	RGS2	2470	0.17	0.076	YES
35	MAN2A1	MAN2A1	MAN2A1	2524	0.17	0.078	YES
36	TSNAX	TSNAX	TSNAX	2609	0.16	0.078	YES
37	LUC7L3	LUC7L3	LUC7L3	2662	0.16	0.079	YES
38	UBR5	UBR5	UBR5	2770	0.16	0.077	YES
39	FPGT	FPGT	FPGT	2784	0.16	0.081	YES
40	PRKDC	PRKDC	PRKDC	2824	0.15	0.083	YES
41	SCAF11	SCAF11	SCAF11	2839	0.15	0.086	YES
42	TROVE2	TROVE2	TROVE2	2882	0.15	0.088	YES
43	STK3	STK3	STK3	2928	0.15	0.09	YES
44	AUH	AUH	AUH	2941	0.15	0.093	YES
45	IFI44L	IFI44L	IFI44L	2969	0.15	0.096	YES
46	XPO1	XPO1	XPO1	3018	0.15	0.097	YES
47	CLIP1	CLIP1	CLIP1	3039	0.15	0.1	YES
48	CD2AP	CD2AP	CD2AP	3138	0.14	0.098	YES
49	AZIN1	AZIN1	AZIN1	3165	0.14	0.1	YES
50	TCERG1	TCERG1	TCERG1	3192	0.14	0.1	YES
51	ZNF638	ZNF638	ZNF638	3201	0.14	0.11	YES
52	TPR	TPR	TPR	3257	0.14	0.11	YES
53	MAD2L1	MAD2L1	MAD2L1	3286	0.14	0.11	YES
54	PPIG	PPIG	PPIG	3313	0.14	0.11	YES
55	ME2	ME2	ME2	3341	0.14	0.11	YES
56	OGT	OGT	OGT	3373	0.13	0.12	YES
57	STXBP3	STXBP3	STXBP3	3404	0.13	0.12	YES
58	TRIM23	TRIM23	TRIM23	3408	0.13	0.12	YES
59	MARCH7	MARCH7	MARCH7	3445	0.13	0.12	YES
60	ZMYM2	ZMYM2	ZMYM2	3468	0.13	0.12	YES
61	CDC7	CDC7	CDC7	3471	0.13	0.13	YES
62	RP2	RP2	RP2	3491	0.13	0.13	YES
63	KLF9	KLF9	KLF9	3545	0.13	0.13	YES
64	CD46	CD46	CD46	3613	0.13	0.13	YES
65	ZFR	ZFR	ZFR	3615	0.13	0.14	YES
66	AKAP10	AKAP10	AKAP10	3647	0.12	0.14	YES
67	PRPF4B	PRPF4B	PRPF4B	3658	0.12	0.14	YES
68	CEBPD	CEBPD	CEBPD	3659	0.12	0.14	YES
69	BIRC2	BIRC2	BIRC2	3676	0.12	0.14	YES
70	KRAS	KRAS	KRAS	3701	0.12	0.15	YES
71	CPNE3	CPNE3	CPNE3	3702	0.12	0.15	YES
72	ATRX	ATRX	ATRX	3705	0.12	0.15	YES
73	ENOSF1	ENOSF1	ENOSF1	3708	0.12	0.16	YES
74	SSB	SSB	SSB	3711	0.12	0.16	YES
75	IFIT1	IFIT1	IFIT1	3751	0.12	0.16	YES
76	IFI44	IFI44	IFI44	3825	0.12	0.16	YES
77	VAMP4	VAMP4	VAMP4	3844	0.12	0.16	YES
78	ACTR3	ACTR3	ACTR3	3865	0.12	0.16	YES
79	GBAS	GBAS	GBAS	3871	0.12	0.17	YES
80	ITSN2	ITSN2	ITSN2	3893	0.12	0.17	YES
81	EBAG9	EBAG9	EBAG9	3896	0.12	0.17	YES
82	TOPORS	TOPORS	TOPORS	3922	0.12	0.18	YES
83	SCFD1	SCFD1	SCFD1	3966	0.12	0.18	YES
84	ACSL3	ACSL3	ACSL3	3971	0.12	0.18	YES
85	DYRK2	DYRK2	DYRK2	3990	0.12	0.18	YES
86	CREB1	CREB1	CREB1	3994	0.12	0.18	YES
87	UGDH	UGDH	UGDH	4116	0.11	0.18	YES
88	CTNNAL1	CTNNAL1	CTNNAL1	4119	0.11	0.18	YES
89	FAT2	FAT2	FAT2	4128	0.11	0.19	YES
90	EID1	EID1	EID1	4163	0.11	0.19	YES
91	CSNK1A1	CSNK1A1	CSNK1A1	4188	0.11	0.19	YES
92	SEC23A	SEC23A	SEC23A	4272	0.11	0.19	YES
93	PCGF3	PCGF3	PCGF3	4284	0.11	0.19	YES
94	NDUFS1	NDUFS1	NDUFS1	4286	0.11	0.19	YES
95	ABCE1	ABCE1	ABCE1	4293	0.11	0.2	YES
96	SLC11A2	SLC11A2	SLC11A2	4306	0.11	0.2	YES
97	AKAP11	AKAP11	AKAP11	4322	0.11	0.2	YES
98	TARBP1	TARBP1	TARBP1	4349	0.1	0.2	YES
99	RPGR	RPGR	RPGR	4408	0.1	0.2	YES
100	YAF2	YAF2	YAF2	4421	0.1	0.2	YES
101	PCF11	PCF11	PCF11	4426	0.1	0.2	YES
102	WWTR1	WWTR1	WWTR1	4434	0.1	0.21	YES
103	EIF3J	EIF3J	EIF3J	4447	0.1	0.21	YES
104	TGDS	TGDS	TGDS	4465	0.1	0.21	YES
105	COPB1	COPB1	COPB1	4520	0.1	0.21	YES
106	MARK3	MARK3	MARK3	4539	0.1	0.21	YES
107	VRK1	VRK1	VRK1	4593	0.099	0.21	YES
108	KIF2A	KIF2A	KIF2A	4610	0.098	0.21	YES
109	AGL	AGL	AGL	4622	0.098	0.22	YES
110	MED7	MED7	MED7	4626	0.098	0.22	YES
111	MALT1	MALT1	MALT1	4634	0.098	0.22	YES
112	MYO5A	MYO5A	MYO5A	4635	0.098	0.22	YES
113	USP1	USP1	USP1	4637	0.098	0.23	YES
114	UBA2	UBA2	UBA2	4641	0.098	0.23	YES
115	DEK	DEK	DEK	4666	0.097	0.23	YES
116	MTF2	MTF2	MTF2	4682	0.097	0.23	YES
117	SEC24B	SEC24B	SEC24B	4693	0.096	0.23	YES
118	PURA	PURA	PURA	4712	0.096	0.24	YES
119	PKD2	PKD2	PKD2	4757	0.095	0.24	YES
120	COPS2	COPS2	COPS2	4783	0.095	0.24	YES
121	CAP2	CAP2	CAP2	4785	0.095	0.24	YES
122	RASA1	RASA1	RASA1	4867	0.093	0.24	YES
123	USP14	USP14	USP14	4892	0.092	0.24	YES
124	CBX3	CBX3	CBX3	4915	0.091	0.24	YES
125	ROCK2	ROCK2	ROCK2	4936	0.091	0.24	YES
126	PEX3	PEX3	PEX3	4964	0.09	0.24	YES
127	CETN3	CETN3	CETN3	4966	0.09	0.24	YES
128	LBR	LBR	LBR	4974	0.09	0.25	YES
129	SNTB2	SNTB2	SNTB2	4976	0.09	0.25	YES
130	ACADM	ACADM	ACADM	4985	0.09	0.25	YES
131	ADCY7	ADCY7	ADCY7	4994	0.09	0.25	YES
132	TMX1	TMX1	TMX1	5009	0.089	0.26	YES
133	GMFB	GMFB	GMFB	5010	0.089	0.26	YES
134	EPRS	EPRS	EPRS	5020	0.089	0.26	YES
135	TYMS	TYMS	TYMS	5025	0.088	0.26	YES
136	SLC35A1	SLC35A1	SLC35A1	5063	0.088	0.26	YES
137	ZNF148	ZNF148	ZNF148	5073	0.088	0.26	YES
138	CDK14	CDK14	CDK14	5119	0.087	0.26	YES
139	HES1	HES1	HES1	5172	0.085	0.26	YES
140	DHX15	DHX15	DHX15	5216	0.084	0.26	YES
141	DLD	DLD	DLD	5266	0.084	0.26	YES
142	FAT1	FAT1	FAT1	5310	0.082	0.26	YES
143	RANBP2	RANBP2	RANBP2	5359	0.081	0.26	YES
144	ACBD3	ACBD3	ACBD3	5370	0.081	0.26	YES
145	G3BP2	G3BP2	G3BP2	5388	0.08	0.26	YES
146	RRM1	RRM1	RRM1	5468	0.078	0.26	YES
147	ZNF146	ZNF146	ZNF146	5470	0.078	0.26	YES
148	TCEAL1	TCEAL1	TCEAL1	5500	0.078	0.26	YES
149	ZMYND8	ZMYND8	ZMYND8	5528	0.077	0.27	YES
150	IPO7	IPO7	IPO7	5540	0.077	0.27	YES
151	AGPS	AGPS	AGPS	5559	0.076	0.27	YES
152	PPP2R5E	PPP2R5E	PPP2R5E	5597	0.076	0.27	YES
153	CUL1	CUL1	CUL1	5621	0.075	0.27	YES
154	PAFAH1B1	PAFAH1B1	PAFAH1B1	5627	0.075	0.27	YES
155	SMAD4	SMAD4	SMAD4	5645	0.074	0.27	YES
156	SCML2	SCML2	SCML2	5691	0.073	0.27	YES
157	CDKN1B	CDKN1B	CDKN1B	5692	0.073	0.27	YES
158	SERPINE2	SERPINE2	SERPINE2	5698	0.073	0.28	YES
159	ACTR2	ACTR2	ACTR2	5712	0.073	0.28	YES
160	PCMT1	PCMT1	PCMT1	5736	0.072	0.28	YES
161	UPF3A	UPF3A	UPF3A	5762	0.072	0.28	YES
162	AASDHPPT	AASDHPPT	AASDHPPT	5777	0.072	0.28	YES
163	SORL1	SORL1	SORL1	5785	0.071	0.28	YES
164	ZMYND11	ZMYND11	ZMYND11	5789	0.071	0.28	YES
165	FMR1	FMR1	FMR1	5809	0.071	0.28	YES
166	DDX17	DDX17	DDX17	5827	0.07	0.28	YES
167	MSMO1	MSMO1	MSMO1	5847	0.07	0.28	YES
168	JAG2	JAG2	JAG2	5879	0.069	0.28	YES
169	SLC2A3	SLC2A3	SLC2A3	5920	0.069	0.28	YES
170	YME1L1	YME1L1	YME1L1	5942	0.068	0.29	YES
171	COG5	COG5	COG5	5943	0.068	0.29	YES
172	MDH1	MDH1	MDH1	5970	0.067	0.29	YES
173	MCM6	MCM6	MCM6	6013	0.066	0.29	YES
174	NPEPPS	NPEPPS	NPEPPS	6022	0.066	0.29	YES
175	PSMD5	PSMD5	PSMD5	6037	0.066	0.29	YES
176	NAE1	NAE1	NAE1	6040	0.066	0.29	YES
177	PFDN4	PFDN4	PFDN4	6054	0.066	0.29	YES
178	XPA	XPA	XPA	6071	0.065	0.29	YES
179	DUSP5	DUSP5	DUSP5	6089	0.065	0.29	YES
180	YES1	YES1	YES1	6105	0.064	0.3	YES
181	UBE4A	UBE4A	UBE4A	6141	0.064	0.3	YES
182	PAPD7	PAPD7	PAPD7	6192	0.062	0.29	YES
183	RB1	RB1	RB1	6195	0.062	0.3	YES
184	GNAQ	GNAQ	GNAQ	6209	0.062	0.3	YES
185	STX7	STX7	STX7	6218	0.062	0.3	YES
186	DLEU1	DLEU1	DLEU1	6228	0.062	0.3	YES
187	MCL1	MCL1	MCL1	6243	0.062	0.3	YES
188	MBNL1	MBNL1	MBNL1	6259	0.061	0.3	YES
189	PCDH7	PCDH7	PCDH7	6262	0.061	0.3	YES
190	COL16A1	COL16A1	COL16A1	6263	0.061	0.3	YES
191	SLBP	SLBP	SLBP	6275	0.061	0.3	YES
192	H2AFV	H2AFV	H2AFV	6303	0.06	0.3	YES
193	GOLGA4	GOLGA4	GOLGA4	6349	0.06	0.3	YES
194	ACYP1	ACYP1	ACYP1	6357	0.059	0.3	YES
195	RGS20	RGS20	RGS20	6363	0.059	0.31	YES
196	SP100	SP100	SP100	6371	0.059	0.31	YES
197	RBFOX2	RBFOX2	RBFOX2	6393	0.059	0.31	YES
198	SDHD	SDHD	SDHD	6395	0.059	0.31	YES
199	BPTF	BPTF	BPTF	6414	0.058	0.31	YES
200	PUM2	PUM2	PUM2	6415	0.058	0.31	YES
201	POLR2B	POLR2B	POLR2B	6426	0.058	0.31	YES
202	ATR	ATR	ATR	6441	0.058	0.31	YES
203	CLTC	CLTC	CLTC	6444	0.058	0.32	YES
204	PAICS	PAICS	PAICS	6456	0.058	0.32	YES
205	TRIP13	TRIP13	TRIP13	6476	0.057	0.32	YES
206	LYST	LYST	LYST	6488	0.057	0.32	YES
207	NCOA3	NCOA3	NCOA3	6492	0.057	0.32	YES
208	ARHGEF4	ARHGEF4	ARHGEF4	6503	0.056	0.32	YES
209	EPS15	EPS15	EPS15	6509	0.056	0.32	YES
210	CPOX	CPOX	CPOX	6540	0.056	0.32	YES
211	GNE	GNE	GNE	6549	0.055	0.32	YES
212	HIST1H4C	HIST1H4C	HIST1H4C	6567	0.055	0.32	YES
213	CDC123	CDC123	CDC123	6569	0.055	0.32	YES
214	CRIM1	CRIM1	CRIM1	6579	0.055	0.33	YES
215	C1D	C1D	C1D	6612	0.054	0.32	YES
216	CDH13	CDH13	CDH13	6706	0.053	0.32	YES
217	AFF1	AFF1	AFF1	6725	0.052	0.32	YES
218	BRD8	BRD8	BRD8	6737	0.052	0.32	YES
219	RABGAP1	RABGAP1	RABGAP1	6781	0.052	0.32	YES
220	RAPGEF5	RAPGEF5	RAPGEF5	6788	0.051	0.32	YES
221	MAPKAPK5	MAPKAPK5	MAPKAPK5	6800	0.051	0.32	YES
222	SIAH1	SIAH1	SIAH1	6818	0.051	0.32	YES
223	DUT	DUT	DUT	6824	0.051	0.32	YES
224	SRSF1	SRSF1	SRSF1	6830	0.051	0.33	YES
225	HSPD1	HSPD1	HSPD1	6929	0.049	0.32	YES
226	TLK2	TLK2	TLK2	6958	0.048	0.32	YES
227	TACC1	TACC1	TACC1	6963	0.048	0.32	YES
228	SFRP1	SFRP1	SFRP1	7001	0.047	0.32	YES
229	BET1	BET1	BET1	7003	0.047	0.32	YES
230	SUGP2	SUGP2	SUGP2	7030	0.047	0.32	YES
231	WNK1	WNK1	WNK1	7040	0.046	0.32	YES
232	ATP2A2	ATP2A2	ATP2A2	7055	0.046	0.32	YES
233	ANXA7	ANXA7	ANXA7	7084	0.046	0.32	YES
234	CDC23	CDC23	CDC23	7097	0.045	0.32	YES
235	HPS5	HPS5	HPS5	7108	0.045	0.32	YES
236	MACF1	MACF1	MACF1	7109	0.045	0.33	YES
237	PICALM	PICALM	PICALM	7150	0.044	0.32	YES
238	FZD6	FZD6	FZD6	7155	0.044	0.33	YES
239	ATXN2	ATXN2	ATXN2	7181	0.044	0.33	YES
240	MBD2	MBD2	MBD2	7194	0.044	0.33	YES
241	DNMT1	DNMT1	DNMT1	7218	0.043	0.33	YES
242	SYPL1	SYPL1	SYPL1	7238	0.043	0.33	YES
243	LAMP3	LAMP3	LAMP3	7248	0.043	0.33	YES
244	SNX7	SNX7	SNX7	7270	0.042	0.33	YES
245	CSE1L	CSE1L	CSE1L	7287	0.042	0.33	YES
246	CNOT4	CNOT4	CNOT4	7303	0.041	0.33	YES
247	CNOT2	CNOT2	CNOT2	7335	0.041	0.33	YES
248	ARL6IP5	ARL6IP5	ARL6IP5	7367	0.04	0.33	YES
249	RPP38	RPP38	RPP38	7417	0.039	0.32	YES
250	KLF7	KLF7	KLF7	7445	0.039	0.32	YES
251	SLC31A1	SLC31A1	SLC31A1	7456	0.039	0.32	YES
252	RARS	RARS	RARS	7459	0.039	0.33	YES
253	BMI1	BMI1	BMI1	7463	0.038	0.33	YES
254	ELOVL5	ELOVL5	ELOVL5	7489	0.038	0.33	YES
255	SNX4	SNX4	SNX4	7539	0.037	0.32	YES
256	TMEM5	TMEM5	TMEM5	7540	0.037	0.33	YES
257	NPTN	NPTN	NPTN	7549	0.037	0.33	YES
258	CRADD	CRADD	CRADD	7550	0.037	0.33	YES
259	UTP3	UTP3	UTP3	7551	0.037	0.33	YES
260	KDM5A	KDM5A	KDM5A	7560	0.036	0.33	YES
261	TRIP12	TRIP12	TRIP12	7568	0.036	0.33	YES
262	KIFAP3	KIFAP3	KIFAP3	7584	0.036	0.33	YES
263	GNPAT	GNPAT	GNPAT	7624	0.035	0.33	YES
264	CCDC6	CCDC6	CCDC6	7633	0.035	0.33	YES
265	CXADR	CXADR	CXADR	7635	0.035	0.33	YES
266	ADCY3	ADCY3	ADCY3	7643	0.035	0.33	YES
267	SNRPG	SNRPG	SNRPG	7664	0.034	0.33	YES
268	MTMR4	MTMR4	MTMR4	7683	0.034	0.33	YES
269	PRRG1	PRRG1	PRRG1	7715	0.034	0.33	YES
270	ZWINT	ZWINT	ZWINT	7724	0.033	0.33	YES
271	AFAP1	AFAP1	AFAP1	7725	0.033	0.33	YES
272	HSPE1	HSPE1	HSPE1	7726	0.033	0.33	YES
273	PSPH	PSPH	PSPH	7739	0.033	0.33	YES
274	TPX2	TPX2	TPX2	7743	0.033	0.33	YES
275	STARD7	STARD7	STARD7	7748	0.033	0.33	YES
276	TCFL5	TCFL5	TCFL5	7762	0.033	0.33	YES
277	SUMO1	SUMO1	SUMO1	7778	0.032	0.33	YES
278	NOLC1	NOLC1	NOLC1	7790	0.032	0.33	YES
279	YTHDC1	YTHDC1	YTHDC1	7794	0.032	0.33	YES
280	ERAP1	ERAP1	ERAP1	7836	0.031	0.33	NO
281	BUB3	BUB3	BUB3	7867	0.031	0.33	NO
282	RAB14	RAB14	RAB14	7945	0.029	0.33	NO
283	RBM6	RBM6	RBM6	7963	0.029	0.33	NO
284	UBE2D3	UBE2D3	UBE2D3	7972	0.029	0.33	NO
285	MPHOSPH6	MPHOSPH6	MPHOSPH6	7998	0.028	0.33	NO
286	AFG3L2	AFG3L2	AFG3L2	8066	0.027	0.32	NO
287	RNF13	RNF13	RNF13	8076	0.027	0.32	NO
288	IKBKAP	IKBKAP	IKBKAP	8081	0.027	0.33	NO
289	TP53BP1	TP53BP1	TP53BP1	8089	0.027	0.33	NO
290	DNAJA1	DNAJA1	DNAJA1	8115	0.026	0.32	NO
291	SLC9A6	SLC9A6	SLC9A6	8123	0.026	0.33	NO
292	GCSH	GCSH	GCSH	8142	0.026	0.32	NO
293	PSMG1	PSMG1	PSMG1	8164	0.025	0.32	NO
294	TRIM13	TRIM13	TRIM13	8204	0.024	0.32	NO
295	LAMP2	LAMP2	LAMP2	8221	0.024	0.32	NO
296	HNRNPR	HNRNPR	HNRNPR	8227	0.024	0.32	NO
297	DHX9	DHX9	DHX9	8248	0.023	0.32	NO
298	UBE2N	UBE2N	UBE2N	8299	0.022	0.32	NO
299	DLG5	DLG5	DLG5	8449	0.02	0.31	NO
300	G3BP1	G3BP1	G3BP1	8462	0.019	0.31	NO
301	ATP1B3	ATP1B3	ATP1B3	8596	0.017	0.31	NO
302	CAMKK2	CAMKK2	CAMKK2	8607	0.017	0.3	NO
303	TM9SF2	TM9SF2	TM9SF2	8636	0.016	0.3	NO
304	PRKAR1A	PRKAR1A	PRKAR1A	8663	0.016	0.3	NO
305	GOSR1	GOSR1	GOSR1	8725	0.015	0.3	NO
306	GRSF1	GRSF1	GRSF1	8750	0.014	0.3	NO
307	BCAR3	BCAR3	BCAR3	8767	0.014	0.3	NO
308	PIK3R3	PIK3R3	PIK3R3	8768	0.014	0.3	NO
309	BNIP3L	BNIP3L	BNIP3L	8824	0.013	0.3	NO
310	TRIM38	TRIM38	TRIM38	8836	0.013	0.3	NO
311	PTP4A2	PTP4A2	PTP4A2	8839	0.013	0.3	NO
312	MTHFD1	MTHFD1	MTHFD1	8901	0.012	0.29	NO
313	DDX42	DDX42	DDX42	8940	0.011	0.29	NO
314	ADH5	ADH5	ADH5	8987	0.01	0.29	NO
315	PGRMC2	PGRMC2	PGRMC2	8992	0.01	0.29	NO
316	MT1H	MT1H	MT1H	8993	0.01	0.29	NO
317	DCAF8	DCAF8	DCAF8	8994	0.0099	0.29	NO
318	FH	FH	FH	9140	0.0074	0.28	NO
319	DKC1	DKC1	DKC1	9175	0.0067	0.28	NO
320	SRI	SRI	SRI	9209	0.0062	0.28	NO
321	TOMM20	TOMM20	TOMM20	9222	0.0058	0.28	NO
322	DOPEY2	DOPEY2	DOPEY2	9235	0.0056	0.28	NO
323	GTF2F2	GTF2F2	GTF2F2	9269	0.005	0.28	NO
324	PRKCI	PRKCI	PRKCI	9280	0.0048	0.28	NO
325	TNFRSF1A	TNFRSF1A	TNFRSF1A	9329	0.0038	0.27	NO
326	ENTPD4	ENTPD4	ENTPD4	9337	0.0037	0.27	NO
327	CCNG2	CCNG2	CCNG2	9377	0.0031	0.27	NO
328	ZFAND5	ZFAND5	ZFAND5	9424	0.0023	0.27	NO
329	PRPF4	PRPF4	PRPF4	9439	0.0022	0.27	NO
330	CPD	CPD	CPD	9440	0.0021	0.27	NO
331	STT3A	STT3A	STT3A	9451	0.0019	0.27	NO
332	GOT1	GOT1	GOT1	9458	0.0019	0.27	NO
333	NOL7	NOL7	NOL7	9459	0.0018	0.27	NO
334	EEF1E1	EEF1E1	EEF1E1	9468	0.0016	0.26	NO
335	ERH	ERH	ERH	9472	0.0016	0.26	NO
336	STX6	STX6	STX6	9507	0.00081	0.26	NO
337	SMC1A	SMC1A	SMC1A	9540	0.00022	0.26	NO
338	ARHGEF7	ARHGEF7	ARHGEF7	9557	-2.6e-06	0.26	NO
339	TRA2B	TRA2B	TRA2B	9572	-0.00021	0.26	NO
340	ITSN1	ITSN1	ITSN1	9612	-0.0008	0.26	NO
341	ATP6V1A	ATP6V1A	ATP6V1A	9629	-0.0011	0.26	NO
342	ATP5B	ATP5B	ATP5B	9636	-0.0012	0.26	NO
343	ERCC5	ERCC5	ERCC5	9651	-0.0014	0.26	NO
344	RPP30	RPP30	RPP30	9678	-0.002	0.25	NO
345	RBM8A	RBM8A	RBM8A	9693	-0.0023	0.25	NO
346	RNF2	RNF2	RNF2	9705	-0.0025	0.25	NO
347	CTNNA1	CTNNA1	CTNNA1	9772	-0.0035	0.25	NO
348	PARP1	PARP1	PARP1	9795	-0.004	0.25	NO
349	RABIF	RABIF	RABIF	9800	-0.0041	0.25	NO
350	TBL2	TBL2	TBL2	9842	-0.0046	0.25	NO
351	IPO5	IPO5	IPO5	9845	-0.0046	0.25	NO
352	TOR1A	TOR1A	TOR1A	9857	-0.0047	0.24	NO
353	MCM3AP	MCM3AP	MCM3AP	9876	-0.005	0.24	NO
354	RBMX	RBMX	RBMX	9893	-0.0052	0.24	NO
355	CNN3	CNN3	CNN3	9912	-0.0055	0.24	NO
356	PFKM	PFKM	PFKM	9927	-0.0057	0.24	NO
357	CBX1	CBX1	CBX1	9934	-0.0058	0.24	NO
358	ZNF133	ZNF133	ZNF133	9938	-0.0059	0.24	NO
359	CTBP1	CTBP1	CTBP1	9947	-0.006	0.24	NO
360	TRIM44	TRIM44	TRIM44	9950	-0.0061	0.24	NO
361	EIF4H	EIF4H	EIF4H	10016	-0.0074	0.24	NO
362	BCAT2	BCAT2	BCAT2	10062	-0.0084	0.24	NO
363	FEN1	FEN1	FEN1	10067	-0.0085	0.24	NO
364	TOP2B	TOP2B	TOP2B	10094	-0.009	0.24	NO
365	ANP32A	ANP32A	ANP32A	10097	-0.009	0.24	NO
366	HSPB11	HSPB11	HSPB11	10116	-0.0093	0.23	NO
367	DFNA5	DFNA5	DFNA5	10123	-0.0094	0.23	NO
368	DSCR3	DSCR3	DSCR3	10132	-0.0095	0.23	NO
369	KAT6A	KAT6A	KAT6A	10157	-0.0098	0.23	NO
370	CYB5B	CYB5B	CYB5B	10176	-0.01	0.23	NO
371	USP7	USP7	USP7	10178	-0.01	0.23	NO
372	RABEPK	RABEPK	RABEPK	10211	-0.011	0.23	NO
373	IRS1	IRS1	IRS1	10291	-0.012	0.23	NO
374	ADCY9	ADCY9	ADCY9	10316	-0.012	0.23	NO
375	SLC16A1	SLC16A1	SLC16A1	10319	-0.012	0.23	NO
376	CCND2	CCND2	CCND2	10405	-0.014	0.22	NO
377	SMARCA1	SMARCA1	SMARCA1	10495	-0.015	0.22	NO
378	CUX1	CUX1	CUX1	10503	-0.015	0.22	NO
379	GSK3B	GSK3B	GSK3B	10551	-0.016	0.22	NO
380	MYO10	MYO10	MYO10	10620	-0.017	0.21	NO
381	PHB	PHB	PHB	10724	-0.018	0.21	NO
382	UBE2C	UBE2C	UBE2C	10745	-0.019	0.2	NO
383	NMT2	NMT2	NMT2	10810	-0.02	0.2	NO
384	PTPN1	PTPN1	PTPN1	10825	-0.02	0.2	NO
385	MMS19	MMS19	MMS19	10834	-0.02	0.2	NO
386	ABCC5	ABCC5	ABCC5	10860	-0.02	0.2	NO
387	MECP2	MECP2	MECP2	10967	-0.022	0.2	NO
388	GTF3C2	GTF3C2	GTF3C2	10968	-0.022	0.2	NO
389	MBD4	MBD4	MBD4	11028	-0.023	0.19	NO
390	PLSCR1	PLSCR1	PLSCR1	11053	-0.024	0.19	NO
391	PTMA	PTMA	PTMA	11126	-0.025	0.19	NO
392	GAPDH	GAPDH	GAPDH	11170	-0.025	0.19	NO
393	NMI	NMI	NMI	11212	-0.026	0.19	NO
394	ELAC2	ELAC2	ELAC2	11229	-0.026	0.19	NO
395	IL10RB	IL10RB	IL10RB	11305	-0.027	0.18	NO
396	MRPL3	MRPL3	MRPL3	11312	-0.027	0.18	NO
397	GBE1	GBE1	GBE1	11324	-0.027	0.18	NO
398	ACTL6A	ACTL6A	ACTL6A	11413	-0.029	0.18	NO
399	CD44	CD44	CD44	11448	-0.029	0.18	NO
400	SLC25A5	SLC25A5	SLC25A5	11456	-0.029	0.18	NO
401	SMARCA2	SMARCA2	SMARCA2	11472	-0.029	0.18	NO
402	TPST2	TPST2	TPST2	11551	-0.031	0.17	NO
403	RND3	RND3	RND3	11588	-0.031	0.17	NO
404	ITGB5	ITGB5	ITGB5	11615	-0.032	0.17	NO
405	BCL6	BCL6	BCL6	11639	-0.032	0.17	NO
406	TP63	TP63	TP63	11752	-0.034	0.17	NO
407	RPA3	RPA3	RPA3	11838	-0.035	0.16	NO
408	TMEM187	TMEM187	TMEM187	11876	-0.036	0.16	NO
409	HNRNPA0	HNRNPA0	HNRNPA0	11883	-0.036	0.16	NO
410	DUSP4	DUSP4	DUSP4	12120	-0.039	0.15	NO
411	FOXO3	FOXO3	FOXO3	12182	-0.04	0.15	NO
412	HNRNPD	HNRNPD	HNRNPD	12193	-0.04	0.15	NO
413	CTCF	CTCF	CTCF	12199	-0.04	0.15	NO
414	MKRN1	MKRN1	MKRN1	12249	-0.041	0.15	NO
415	BLMH	BLMH	BLMH	12296	-0.042	0.15	NO
416	WASF1	WASF1	WASF1	12322	-0.042	0.15	NO
417	STAU1	STAU1	STAU1	12343	-0.042	0.15	NO
418	FASN	FASN	FASN	12457	-0.044	0.14	NO
419	TBXA2R	TBXA2R	TBXA2R	12472	-0.044	0.14	NO
420	PIP4K2B	PIP4K2B	PIP4K2B	12473	-0.044	0.14	NO
421	LPCAT3	LPCAT3	LPCAT3	12662	-0.047	0.13	NO
422	RCBTB2	RCBTB2	RCBTB2	12665	-0.047	0.13	NO
423	ASH2L	ASH2L	ASH2L	12708	-0.048	0.13	NO
424	SNRNP200	SNRNP200	SNRNP200	12755	-0.048	0.13	NO
425	SNRPF	SNRPF	SNRPF	12792	-0.049	0.13	NO
426	IFNGR2	IFNGR2	IFNGR2	12822	-0.049	0.13	NO
427	PEX11B	PEX11B	PEX11B	12919	-0.051	0.13	NO
428	RGS19	RGS19	RGS19	12944	-0.051	0.13	NO
429	KHSRP	KHSRP	KHSRP	13093	-0.053	0.12	NO
430	TGFBR2	TGFBR2	TGFBR2	13161	-0.054	0.12	NO
431	FNTB	FNTB	FNTB	13570	-0.061	0.096	NO
432	NME6	NME6	NME6	13656	-0.062	0.093	NO
433	SLC2A1	SLC2A1	SLC2A1	13669	-0.063	0.094	NO
434	RRBP1	RRBP1	RRBP1	13724	-0.064	0.093	NO
435	MTMR3	MTMR3	MTMR3	13783	-0.064	0.091	NO
436	GAS2L1	GAS2L1	GAS2L1	13806	-0.065	0.092	NO
437	TFAP4	TFAP4	TFAP4	13954	-0.067	0.085	NO
438	MICB	MICB	MICB	13955	-0.067	0.087	NO
439	ATP2C1	ATP2C1	ATP2C1	14055	-0.069	0.083	NO
440	SEMA3F	SEMA3F	SEMA3F	14288	-0.074	0.072	NO
441	BAIAP2	BAIAP2	BAIAP2	14317	-0.074	0.073	NO
442	GCAT	GCAT	GCAT	14321	-0.074	0.074	NO
443	CPSF4	CPSF4	CPSF4	14335	-0.074	0.076	NO
444	PTOV1	PTOV1	PTOV1	14394	-0.075	0.075	NO
445	GSK3A	GSK3A	GSK3A	14449	-0.076	0.074	NO
446	MT1G	MT1G	MT1G	14468	-0.077	0.075	NO
447	TUBGCP2	TUBGCP2	TUBGCP2	14471	-0.077	0.077	NO
448	UMPS	UMPS	UMPS	14668	-0.08	0.068	NO
449	GNB2L1	GNB2L1	GNB2L1	14680	-0.081	0.07	NO
450	BHLHE40	BHLHE40	BHLHE40	14748	-0.082	0.068	NO
451	SRF	SRF	SRF	14862	-0.084	0.064	NO
452	SVIL	SVIL	SVIL	14874	-0.084	0.066	NO
453	H1F0	H1F0	H1F0	14887	-0.085	0.067	NO
454	KATNB1	KATNB1	KATNB1	15075	-0.088	0.059	NO
455	ENTPD6	ENTPD6	ENTPD6	15233	-0.092	0.053	NO
456	PAK1	PAK1	PAK1	15235	-0.092	0.055	NO
457	MAP4	MAP4	MAP4	15422	-0.096	0.047	NO
458	WNT5A	WNT5A	WNT5A	15562	-0.099	0.042	NO
459	CDK2	CDK2	CDK2	15604	-0.1	0.042	NO
460	ZDHHC3	ZDHHC3	ZDHHC3	15606	-0.1	0.045	NO
461	TNC	TNC	TNC	15797	-0.11	0.037	NO
462	CELSR2	CELSR2	CELSR2	15813	-0.11	0.039	NO
463	EFEMP1	EFEMP1	EFEMP1	15840	-0.11	0.041	NO
464	WWOX	WWOX	WWOX	15948	-0.11	0.038	NO
465	EXTL3	EXTL3	EXTL3	16006	-0.11	0.038	NO
466	STEAP1	STEAP1	STEAP1	16169	-0.12	0.032	NO
467	B4GALT2	B4GALT2	B4GALT2	16181	-0.12	0.034	NO
468	RUVBL1	RUVBL1	RUVBL1	16256	-0.12	0.034	NO
469	IGSF3	IGSF3	IGSF3	16382	-0.13	0.03	NO
470	TJP2	TJP2	TJP2	16413	-0.13	0.032	NO
471	PEX6	PEX6	PEX6	16445	-0.13	0.034	NO
472	ID1	ID1	ID1	16455	-0.13	0.037	NO
473	TUSC2	TUSC2	TUSC2	16611	-0.14	0.032	NO
474	DHRS3	DHRS3	DHRS3	16617	-0.14	0.036	NO
475	SEMA3C	SEMA3C	SEMA3C	16626	-0.14	0.039	NO
476	FDFT1	FDFT1	FDFT1	16657	-0.14	0.041	NO
477	MT3	MT3	MT3	16883	-0.16	0.033	NO
478	MAOA	MAOA	MAOA	17440	-0.22	0.007	NO
479	PPP1R3C	PPP1R3C	PPP1R3C	17447	-0.22	0.013	NO
480	ADRB2	ADRB2	ADRB2	17502	-0.23	0.016	NO
481	DDX3Y	DDX3Y	DDX3Y	17712	-0.27	0.012	NO
482	CNTN1	CNTN1	CNTN1	17880	-0.35	0.012	NO

Figure S17. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: DACOSTA UV RESPONSE VIA ERCC3 COMMON DN.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: DACOSTA UV RESPONSE VIA ERCC3 COMMON DN, 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: NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON

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	DLX2	DLX2	DLX2	113	0.55	0.018	YES
2	KIF18A	KIF18A	KIF18A	450	0.4	0.018	YES
3	TMEFF1	TMEFF1	TMEFF1	557	0.37	0.028	YES
4	PTGS2	PTGS2	PTGS2	781	0.33	0.03	YES
5	BIRC3	BIRC3	BIRC3	956	0.3	0.034	YES
6	GEM	GEM	GEM	972	0.3	0.047	YES
7	SCG5	SCG5	SCG5	1091	0.28	0.053	YES
8	CREB5	CREB5	CREB5	1246	0.26	0.056	YES
9	GAD1	GAD1	GAD1	1264	0.26	0.067	YES
10	ZNF107	ZNF107	ZNF107	1293	0.26	0.077	YES
11	TRPC1	TRPC1	TRPC1	1332	0.26	0.086	YES
12	CHAC1	CHAC1	CHAC1	1527	0.24	0.086	YES
13	CLK4	CLK4	CLK4	1588	0.23	0.093	YES
14	ZNF23	ZNF23	ZNF23	1614	0.23	0.1	YES
15	PYROXD1	PYROXD1	PYROXD1	1706	0.22	0.11	YES
16	SREK1	SREK1	SREK1	1725	0.22	0.12	YES
17	JMJD1C	JMJD1C	JMJD1C	1730	0.22	0.12	YES
18	TAF2	TAF2	TAF2	1745	0.22	0.13	YES
19	PPP1R12A	PPP1R12A	PPP1R12A	1836	0.21	0.14	YES
20	LIG4	LIG4	LIG4	1841	0.21	0.15	YES
21	DMTF1	DMTF1	DMTF1	1922	0.2	0.15	YES
22	LIF	LIF	LIF	1965	0.2	0.16	YES
23	FOS	FOS	FOS	2050	0.19	0.16	YES
24	BDKRB1	BDKRB1	BDKRB1	2072	0.19	0.17	YES
25	C1orf27	C1orf27	C1orf27	2102	0.19	0.18	YES
26	SNX16	SNX16	SNX16	2109	0.19	0.18	YES
27	CHD9	CHD9	CHD9	2143	0.19	0.19	YES
28	ZNF267	ZNF267	ZNF267	2205	0.18	0.2	YES
29	PIBF1	PIBF1	PIBF1	2291	0.18	0.2	YES
30	ATAD2B	ATAD2B	ATAD2B	2312	0.18	0.21	YES
31	TBK1	TBK1	TBK1	2326	0.18	0.21	YES
32	CCNT2	CCNT2	CCNT2	2335	0.18	0.22	YES
33	STRN3	STRN3	STRN3	2365	0.18	0.23	YES
34	DAAM1	DAAM1	DAAM1	2398	0.17	0.23	YES
35	THUMPD2	THUMPD2	THUMPD2	2473	0.17	0.24	YES
36	DCLRE1C	DCLRE1C	DCLRE1C	2559	0.17	0.24	YES
37	ARID4B	ARID4B	ARID4B	2591	0.16	0.25	YES
38	SMCHD1	SMCHD1	SMCHD1	2594	0.16	0.25	YES
39	CLK1	CLK1	CLK1	2619	0.16	0.26	YES
40	NEMF	NEMF	NEMF	2625	0.16	0.27	YES
41	TBX3	TBX3	TBX3	2803	0.16	0.26	YES
42	IFRD1	IFRD1	IFRD1	2908	0.15	0.26	YES
43	ZNF451	ZNF451	ZNF451	2936	0.15	0.27	YES
44	VEGFA	VEGFA	VEGFA	2975	0.15	0.27	YES
45	ZNF468	ZNF468	ZNF468	3000	0.15	0.28	YES
46	NEK1	NEK1	NEK1	3004	0.15	0.29	YES
47	ZNF195	ZNF195	ZNF195	3010	0.15	0.29	YES
48	TDG	TDG	TDG	3011	0.15	0.3	YES
49	CLEC4A	CLEC4A	CLEC4A	3044	0.15	0.3	YES
50	CDKN2AIP	CDKN2AIP	CDKN2AIP	3077	0.14	0.31	YES
51	KRCC1	KRCC1	KRCC1	3152	0.14	0.31	YES
52	ZNF432	ZNF432	ZNF432	3166	0.14	0.32	YES
53	SEC24A	SEC24A	SEC24A	3182	0.14	0.32	YES
54	PPWD1	PPWD1	PPWD1	3189	0.14	0.33	YES
55	PELI1	PELI1	PELI1	3208	0.14	0.33	YES
56	SOX30	SOX30	SOX30	3227	0.14	0.34	YES
57	BACH1	BACH1	BACH1	3234	0.14	0.34	YES
58	MTHFD2L	MTHFD2L	MTHFD2L	3294	0.14	0.35	YES
59	PPIG	PPIG	PPIG	3313	0.14	0.35	YES
60	DNAJC2	DNAJC2	DNAJC2	3356	0.13	0.36	YES
61	MORC3	MORC3	MORC3	3420	0.13	0.36	YES
62	PTBP2	PTBP2	PTBP2	3422	0.13	0.36	YES
63	MARCH7	MARCH7	MARCH7	3445	0.13	0.37	YES
64	FNBP4	FNBP4	FNBP4	3478	0.13	0.37	YES
65	ZNF136	ZNF136	ZNF136	3496	0.13	0.38	YES
66	ZNF180	ZNF180	ZNF180	3575	0.13	0.38	YES
67	PTPN2	PTPN2	PTPN2	3620	0.13	0.38	YES
68	AKAP10	AKAP10	AKAP10	3647	0.12	0.39	YES
69	ATF3	ATF3	ATF3	3665	0.12	0.39	YES
70	BIRC2	BIRC2	BIRC2	3676	0.12	0.4	YES
71	NSUN6	NSUN6	NSUN6	3693	0.12	0.4	YES
72	CREM	CREM	CREM	3745	0.12	0.4	YES
73	TANK	TANK	TANK	3802	0.12	0.4	YES
74	ZNF14	ZNF14	ZNF14	3849	0.12	0.41	YES
75	CEBPG	CEBPG	CEBPG	3965	0.12	0.41	YES
76	EGR1	EGR1	EGR1	4000	0.12	0.41	YES
77	INTS6	INTS6	INTS6	4040	0.11	0.41	YES
78	NOC3L	NOC3L	NOC3L	4050	0.11	0.42	YES
79	ALG13	ALG13	ALG13	4076	0.11	0.42	YES
80	ZCCHC10	ZCCHC10	ZCCHC10	4161	0.11	0.42	YES
81	ZNF131	ZNF131	ZNF131	4171	0.11	0.42	YES
82	RSRC2	RSRC2	RSRC2	4204	0.11	0.43	YES
83	KLF5	KLF5	KLF5	4332	0.1	0.43	YES
84	C21orf91	C21orf91	C21orf91	4334	0.1	0.43	YES
85	GPATCH2	GPATCH2	GPATCH2	4367	0.1	0.43	YES
86	ASNS	ASNS	ASNS	4496	0.1	0.43	YES
87	TNFRSF9	TNFRSF9	TNFRSF9	4519	0.1	0.43	YES
88	TSC22D1	TSC22D1	TSC22D1	4536	0.1	0.44	YES
89	MARK3	MARK3	MARK3	4539	0.1	0.44	YES
90	RLF	RLF	RLF	4576	0.1	0.44	YES
91	FAM13B	FAM13B	FAM13B	4590	0.099	0.45	YES
92	FEM1C	FEM1C	FEM1C	4600	0.099	0.45	YES
93	RBM39	RBM39	RBM39	4616	0.098	0.46	YES
94	SRSF10	SRSF10	SRSF10	4676	0.097	0.46	YES
95	CASP3	CASP3	CASP3	4689	0.096	0.46	YES
96	CDK17	CDK17	CDK17	4743	0.096	0.46	YES
97	ZNF280D	ZNF280D	ZNF280D	4755	0.095	0.47	YES
98	ZNF44	ZNF44	ZNF44	4780	0.095	0.47	YES
99	FBXO38	FBXO38	FBXO38	4822	0.094	0.47	YES
100	PRPF38B	PRPF38B	PRPF38B	4980	0.09	0.47	YES
101	CEP76	CEP76	CEP76	5035	0.088	0.47	YES
102	ZNF557	ZNF557	ZNF557	5061	0.088	0.47	YES
103	CCNL1	CCNL1	CCNL1	5205	0.085	0.46	YES
104	SPATA5L1	SPATA5L1	SPATA5L1	5290	0.083	0.46	YES
105	ZNF222	ZNF222	ZNF222	5294	0.083	0.47	YES
106	DPP8	DPP8	DPP8	5316	0.082	0.47	YES
107	TAF1A	TAF1A	TAF1A	5321	0.082	0.47	YES
108	RBBP6	RBBP6	RBBP6	5434	0.079	0.47	YES
109	PMAIP1	PMAIP1	PMAIP1	5491	0.078	0.47	YES
110	KIAA0907	KIAA0907	KIAA0907	5551	0.077	0.47	YES
111	IFI16	IFI16	IFI16	5589	0.076	0.47	YES
112	CDK7	CDK7	CDK7	5642	0.074	0.47	YES
113	RIC8B	RIC8B	RIC8B	5652	0.074	0.48	YES
114	CAB39	CAB39	CAB39	5671	0.074	0.48	YES
115	NUPL1	NUPL1	NUPL1	5718	0.073	0.48	YES
116	ZNF45	ZNF45	ZNF45	5722	0.073	0.48	YES
117	ARNTL	ARNTL	ARNTL	5743	0.072	0.48	YES
118	ZNF331	ZNF331	ZNF331	5773	0.072	0.49	YES
119	ZNF184	ZNF184	ZNF184	5778	0.072	0.49	YES
120	EIF5	EIF5	EIF5	5791	0.071	0.49	YES
121	AGTPBP1	AGTPBP1	AGTPBP1	5863	0.07	0.49	YES
122	TAF1D	TAF1D	TAF1D	5911	0.069	0.49	YES
123	ZNF274	ZNF274	ZNF274	5989	0.067	0.49	YES
124	DUSP5	DUSP5	DUSP5	6089	0.065	0.49	YES
125	KIN	KIN	KIN	6143	0.064	0.49	YES
126	RCHY1	RCHY1	RCHY1	6210	0.062	0.49	YES
127	MCL1	MCL1	MCL1	6243	0.062	0.49	YES
128	BCL10	BCL10	BCL10	6254	0.062	0.49	YES
129	LRIF1	LRIF1	LRIF1	6279	0.061	0.49	YES
130	ZNF227	ZNF227	ZNF227	6309	0.06	0.49	YES
131	POLR3F	POLR3F	POLR3F	6329	0.06	0.49	YES
132	AVL9	AVL9	AVL9	6397	0.059	0.49	YES
133	NFIL3	NFIL3	NFIL3	6418	0.058	0.49	YES
134	ARIH1	ARIH1	ARIH1	6458	0.058	0.49	YES
135	AKIRIN1	AKIRIN1	AKIRIN1	6474	0.057	0.5	YES
136	WAC	WAC	WAC	6483	0.057	0.5	YES
137	NCOA3	NCOA3	NCOA3	6492	0.057	0.5	YES
138	NRBF2	NRBF2	NRBF2	6494	0.057	0.5	YES
139	BTN2A1	BTN2A1	BTN2A1	6669	0.053	0.5	NO
140	KDM3A	KDM3A	KDM3A	6678	0.053	0.5	NO
141	C6orf62	C6orf62	C6orf62	6708	0.053	0.5	NO
142	ZCCHC8	ZCCHC8	ZCCHC8	6744	0.052	0.5	NO
143	STC2	STC2	STC2	6823	0.051	0.5	NO
144	SUV420H1	SUV420H1	SUV420H1	6894	0.049	0.49	NO
145	PSPC1	PSPC1	PSPC1	6946	0.048	0.49	NO
146	TLK2	TLK2	TLK2	6958	0.048	0.5	NO
147	ZCCHC6	ZCCHC6	ZCCHC6	7022	0.047	0.49	NO
148	RNF111	RNF111	RNF111	7064	0.046	0.49	NO
149	CRY1	CRY1	CRY1	7106	0.045	0.49	NO
150	ING3	ING3	ING3	7179	0.044	0.49	NO
151	LINS	LINS	LINS	7196	0.044	0.49	NO
152	SLTM	SLTM	SLTM	7250	0.043	0.49	NO
153	RBM15	RBM15	RBM15	7299	0.042	0.49	NO
154	CNOT4	CNOT4	CNOT4	7303	0.041	0.49	NO
155	CNOT2	CNOT2	CNOT2	7335	0.041	0.49	NO
156	SFPQ	SFPQ	SFPQ	7372	0.04	0.49	NO
157	SCYL3	SCYL3	SCYL3	7441	0.039	0.49	NO
158	KLF6	KLF6	KLF6	7722	0.033	0.48	NO
159	JUNB	JUNB	JUNB	7974	0.029	0.46	NO
160	UIMC1	UIMC1	UIMC1	8090	0.027	0.46	NO
161	ADNP	ADNP	ADNP	8098	0.026	0.46	NO
162	ZZZ3	ZZZ3	ZZZ3	8127	0.026	0.46	NO
163	RCAN1	RCAN1	RCAN1	8167	0.025	0.46	NO
164	ZSCAN16	ZSCAN16	ZSCAN16	8197	0.024	0.46	NO
165	RIPK2	RIPK2	RIPK2	8210	0.024	0.46	NO
166	RABGGTB	RABGGTB	RABGGTB	8315	0.022	0.45	NO
167	PRPF3	PRPF3	PRPF3	8581	0.017	0.44	NO
168	RBM5	RBM5	RBM5	8680	0.016	0.43	NO
169	SNX5	SNX5	SNX5	8693	0.015	0.43	NO
170	ZNF426	ZNF426	ZNF426	8924	0.011	0.42	NO
171	KLF10	KLF10	KLF10	8955	0.011	0.42	NO
172	PNRC2	PNRC2	PNRC2	8969	0.01	0.42	NO
173	ZNF155	ZNF155	ZNF155	9092	0.0082	0.41	NO
174	HLX	HLX	HLX	9502	0.00089	0.39	NO
175	IER2	IER2	IER2	9527	0.00049	0.39	NO
176	TSC22D2	TSC22D2	TSC22D2	9699	-0.0024	0.38	NO
177	ZNF3	ZNF3	ZNF3	9822	-0.0044	0.37	NO
178	PRKRIP1	PRKRIP1	PRKRIP1	10129	-0.0095	0.36	NO
179	TNFRSF10B	TNFRSF10B	TNFRSF10B	10470	-0.015	0.34	NO
180	C2orf42	C2orf42	C2orf42	10510	-0.015	0.34	NO
181	PTN	PTN	PTN	10703	-0.018	0.33	NO
182	HRH1	HRH1	HRH1	10732	-0.019	0.32	NO
183	CEBPB	CEBPB	CEBPB	10733	-0.019	0.33	NO
184	GADD45B	GADD45B	GADD45B	10802	-0.02	0.32	NO
185	ETS2	ETS2	ETS2	10838	-0.02	0.32	NO
186	FAM53C	FAM53C	FAM53C	11152	-0.025	0.31	NO
187	FOSL2	FOSL2	FOSL2	11183	-0.025	0.3	NO
188	CARS	CARS	CARS	11274	-0.027	0.3	NO
189	RELB	RELB	RELB	11407	-0.029	0.3	NO
190	NFKBIA	NFKBIA	NFKBIA	11409	-0.029	0.3	NO
191	ZNF165	ZNF165	ZNF165	11420	-0.029	0.3	NO
192	IRF7	IRF7	IRF7	11460	-0.029	0.3	NO
193	JUN	JUN	JUN	11660	-0.032	0.29	NO
194	DUSP6	DUSP6	DUSP6	11821	-0.035	0.28	NO
195	FOXO3	FOXO3	FOXO3	12182	-0.04	0.26	NO
196	PGS1	PGS1	PGS1	12269	-0.041	0.26	NO
197	SAT1	SAT1	SAT1	12297	-0.042	0.26	NO
198	RYBP	RYBP	RYBP	12635	-0.047	0.24	NO
199	SETDB1	SETDB1	SETDB1	13054	-0.053	0.22	NO
200	TUFT1	TUFT1	TUFT1	13379	-0.058	0.2	NO
201	MAFF	MAFF	MAFF	13493	-0.06	0.2	NO
202	NFKBIE	NFKBIE	NFKBIE	14005	-0.068	0.18	NO
203	F3	F3	F3	14339	-0.074	0.16	NO
204	SNAI2	SNAI2	SNAI2	14723	-0.082	0.14	NO
205	YY1AP1	YY1AP1	YY1AP1	14814	-0.083	0.14	NO
206	TNFAIP3	TNFAIP3	TNFAIP3	15159	-0.09	0.13	NO
207	IP6K2	IP6K2	IP6K2	15684	-0.1	0.1	NO
208	TIPARP	TIPARP	TIPARP	16166	-0.12	0.08	NO
209	FOSB	FOSB	FOSB	16409	-0.13	0.072	NO
210	DUSP8	DUSP8	DUSP8	16531	-0.14	0.072	NO
211	CTH	CTH	CTH	16903	-0.16	0.058	NO
212	NEDD9	NEDD9	NEDD9	17196	-0.18	0.05	NO

Figure S19. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON, 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 GLYCOLYSIS GLUCONEOGENESIS	57	genes.ES.table	0.42	1.2	0.13	0.23	1	0.26	0.25	0.2	0.19	0
KEGG PENTOSE PHOSPHATE PATHWAY	25	genes.ES.table	0.47	1.4	0.09	0.12	1	0.36	0.32	0.25	0.084	0
KEGG FRUCTOSE AND MANNOSE METABOLISM	34	genes.ES.table	0.44	1.5	0.059	0.085	1	0.24	0.25	0.18	0.058	0
KEGG GALACTOSE METABOLISM	25	genes.ES.table	0.57	1.5	0.042	0.077	1	0.12	0.055	0.11	0.051	0
KEGG STEROID HORMONE BIOSYNTHESIS	36	genes.ES.table	0.61	1.4	0.042	0.12	1	0.28	0.12	0.24	0.085	0
KEGG PURINE METABOLISM	154	genes.ES.table	0.49	1.8	0.0057	0.047	0.75	0.23	0.24	0.18	0.017	0
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	31	genes.ES.table	0.52	1.5	0.047	0.091	1	0.36	0.26	0.26	0.063	0
KEGG GLYCINE SERINE AND THREONINE METABOLISM	30	genes.ES.table	0.69	1.7	0.0041	0.053	0.95	0.37	0.15	0.31	0.027	0
KEGG LYSINE DEGRADATION	44	genes.ES.table	0.43	1.9	0.023	0.052	0.61	0.046	0.073	0.042	0.015	0.003
KEGG ARGININE AND PROLINE METABOLISM	52	genes.ES.table	0.49	1.5	0.049	0.091	1	0.36	0.3	0.26	0.064	0

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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	SYT1	SYT1	SYT1	37	0.97	0.41	YES
2	MAPK10	MAPK10	MAPK10	551	0.54	0.62	YES
3	MAPK8IP3	MAPK8IP3	MAPK8IP3	4457	0.09	0.44	NO
4	MAPK8IP1	MAPK8IP1	MAPK8IP1	4508	0.088	0.47	NO
5	DUSP1	DUSP1	DUSP1	4548	0.087	0.51	NO
6	CD40	CD40	CD40	5523	0.052	0.48	NO
7	MAPK3	MAPK3	MAPK3	5934	0.042	0.47	NO
8	MAPK11	MAPK11	MAPK11	6173	0.037	0.47	NO
9	NFKBIA	NFKBIA	NFKBIA	6978	0.025	0.44	NO
10	MAPK13	MAPK13	MAPK13	7751	0.018	0.4	NO
11	NFKBIB	NFKBIB	NFKBIB	7899	0.016	0.4	NO
12	TRAF3	TRAF3	TRAF3	8040	0.015	0.4	NO
13	IKBKG	IKBKG	IKBKG	8100	0.014	0.4	NO
14	NFKB2	NFKB2	NFKB2	8297	0.013	0.4	NO
15	GORASP1	GORASP1	GORASP1	8820	0.0088	0.37	NO
16	NFKBIE	NFKBIE	NFKBIE	9057	0.0072	0.36	NO
17	PIK3R1	PIK3R1	PIK3R1	9201	0.0061	0.36	NO
18	TRAF2	TRAF2	TRAF2	9205	0.0061	0.36	NO
19	MAP2K4	MAP2K4	MAP2K4	9245	0.0058	0.36	NO
20	MAPK12	MAPK12	MAPK12	9570	0.0035	0.34	NO
21	MAP2K7	MAP2K7	MAP2K7	10392	-0.0021	0.3	NO
22	MAPK8	MAPK8	MAPK8	11038	-0.0064	0.27	NO
23	NFKBIL1	NFKBIL1	NFKBIL1	11078	-0.0067	0.27	NO
24	MAPK1	MAPK1	MAPK1	11428	-0.0091	0.25	NO
25	MAPKAPK5	MAPKAPK5	MAPKAPK5	11694	-0.011	0.24	NO
26	NFKB1	NFKB1	NFKB1	12083	-0.013	0.23	NO
27	TRAF5	TRAF5	TRAF5	12282	-0.015	0.22	NO
28	MAPK9	MAPK9	MAPK9	12340	-0.015	0.22	NO
29	TONSL	TONSL	TONSL	13320	-0.022	0.18	NO
30	PIK3CD	PIK3CD	PIK3CD	14377	-0.031	0.14	NO
31	MAPK14	MAPK14	MAPK14	14720	-0.034	0.13	NO
32	TRAF6	TRAF6	TRAF6	14823	-0.035	0.14	NO
33	MAPK8IP2	MAPK8IP2	MAPK8IP2	15166	-0.039	0.14	NO
34	PIK3CA	PIK3CA	PIK3CA	16220	-0.057	0.1	NO

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

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

Table 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	ACTC1	ACTC1	ACTC1	57	0.92	0.052	YES
2	CDCP1	CDCP1	CDCP1	847	0.44	0.034	YES
3	NEFL	NEFL	NEFL	860	0.44	0.059	YES
4	CLDN3	CLDN3	CLDN3	954	0.41	0.078	YES
5	KCNMA1	KCNMA1	KCNMA1	1044	0.39	0.097	YES
6	MYOD1	MYOD1	MYOD1	1066	0.39	0.12	YES
7	STC2	STC2	STC2	1251	0.36	0.13	YES
8	GPR39	GPR39	GPR39	1275	0.35	0.15	YES
9	CA12	CA12	CA12	1448	0.32	0.16	YES
10	CCNJL	CCNJL	CCNJL	1450	0.32	0.18	YES
11	ANGPTL4	ANGPTL4	ANGPTL4	1552	0.31	0.19	YES
12	MAOA	MAOA	MAOA	1644	0.3	0.2	YES
13	HEMGN	HEMGN	HEMGN	1727	0.29	0.22	YES
14	SYT13	SYT13	SYT13	1728	0.29	0.23	YES
15	ENO2	ENO2	ENO2	1838	0.27	0.24	YES
16	DPP4	DPP4	DPP4	1912	0.26	0.25	YES
17	HLF	HLF	HLF	1955	0.26	0.27	YES
18	FEZ1	FEZ1	FEZ1	2460	0.21	0.25	YES
19	SERPINE1	SERPINE1	SERPINE1	2529	0.2	0.26	YES
20	ITGB4	ITGB4	ITGB4	2617	0.2	0.27	YES
21	CAPG	CAPG	CAPG	2677	0.19	0.28	YES
22	PDGFC	PDGFC	PDGFC	2837	0.18	0.28	YES
23	ARHGAP8	ARHGAP8	ARHGAP8	2947	0.17	0.28	YES
24	SLC2A3	SLC2A3	SLC2A3	2950	0.17	0.29	YES
25	ALDOC	ALDOC	ALDOC	3020	0.17	0.3	YES
26	GPRC5A	GPRC5A	GPRC5A	3046	0.17	0.31	YES
27	MDK	MDK	MDK	3185	0.16	0.31	YES
28	CORO1A	CORO1A	CORO1A	3253	0.15	0.31	YES
29	SLC2A1	SLC2A1	SLC2A1	3306	0.15	0.32	YES
30	CFD	CFD	CFD	3330	0.15	0.33	YES
31	IL9R	IL9R	IL9R	3455	0.14	0.33	YES
32	ASB15	ASB15	ASB15	3645	0.13	0.32	YES
33	CKB	CKB	CKB	3708	0.13	0.33	YES
34	AK4	AK4	AK4	3756	0.12	0.33	YES
35	NT5E	NT5E	NT5E	3783	0.12	0.34	YES
36	HMOX1	HMOX1	HMOX1	3807	0.12	0.35	YES
37	AMH	AMH	AMH	3814	0.12	0.35	YES
38	TIMP1	TIMP1	TIMP1	4056	0.11	0.34	YES
39	TGM2	TGM2	TGM2	4180	0.1	0.34	YES
40	CITED2	CITED2	CITED2	4346	0.095	0.34	YES
41	ALPL	ALPL	ALPL	4347	0.095	0.35	YES
42	PLOD2	PLOD2	PLOD2	4392	0.093	0.35	YES
43	AKAP12	AKAP12	AKAP12	4401	0.093	0.36	YES
44	LGALSL	LGALSL	LGALSL	4416	0.093	0.36	YES
45	JUN	JUN	JUN	4433	0.092	0.36	YES
46	CCND2	CCND2	CCND2	4479	0.09	0.37	YES
47	TSC22D3	TSC22D3	TSC22D3	4492	0.089	0.37	YES
48	GAL3ST1	GAL3ST1	GAL3ST1	4519	0.088	0.38	YES
49	DUSP1	DUSP1	DUSP1	4548	0.087	0.38	YES
50	PTPRU	PTPRU	PTPRU	4560	0.086	0.38	YES
51	PFKFB4	PFKFB4	PFKFB4	4581	0.085	0.39	YES
52	LGALS1	LGALS1	LGALS1	4582	0.085	0.39	YES
53	IGFBP3	IGFBP3	IGFBP3	4597	0.084	0.4	YES
54	NDRG2	NDRG2	NDRG2	4600	0.084	0.4	YES
55	MAP2K6	MAP2K6	MAP2K6	4684	0.08	0.4	YES
56	LARP6	LARP6	LARP6	4740	0.078	0.4	YES
57	FAM84A	FAM84A	FAM84A	4755	0.078	0.41	YES
58	SESN2	SESN2	SESN2	4771	0.077	0.41	YES
59	PEA15	PEA15	PEA15	4783	0.076	0.42	YES
60	EHD2	EHD2	EHD2	4800	0.076	0.42	YES
61	LRP1	LRP1	LRP1	4971	0.069	0.41	NO
62	SGCE	SGCE	SGCE	5147	0.063	0.41	NO
63	UPP1	UPP1	UPP1	5223	0.061	0.41	NO
64	IFI30	IFI30	IFI30	5433	0.054	0.4	NO
65	ZFP36	ZFP36	ZFP36	5469	0.053	0.4	NO
66	TMEM38A	TMEM38A	TMEM38A	5519	0.052	0.4	NO
67	MESDC1	MESDC1	MESDC1	5534	0.051	0.4	NO
68	GADD45B	GADD45B	GADD45B	5661	0.048	0.4	NO
69	PRODH	PRODH	PRODH	5687	0.047	0.4	NO
70	PIGU	PIGU	PIGU	5857	0.043	0.39	NO
71	PI4K2A	PI4K2A	PI4K2A	5861	0.043	0.39	NO
72	PLIN2	PLIN2	PLIN2	5869	0.043	0.4	NO
73	CD9	CD9	CD9	5911	0.042	0.4	NO
74	SNX10	SNX10	SNX10	5967	0.041	0.4	NO
75	GSTA1	GSTA1	GSTA1	5968	0.041	0.4	NO
76	SEPT2	SEPT2	SEPT2	5977	0.041	0.4	NO
77	CPNE1	CPNE1	CPNE1	5990	0.04	0.4	NO
78	SOD2	SOD2	SOD2	5995	0.04	0.4	NO
79	SPRYD3	SPRYD3	SPRYD3	6049	0.039	0.4	NO
80	SNTA1	SNTA1	SNTA1	6067	0.039	0.4	NO
81	CC2D1A	CC2D1A	CC2D1A	6080	0.039	0.41	NO
82	PIN4	PIN4	PIN4	6180	0.037	0.4	NO
83	SYNC	SYNC	SYNC	6205	0.036	0.4	NO
84	H3F3B	H3F3B	H3F3B	6352	0.034	0.4	NO
85	ARHGAP19	ARHGAP19	ARHGAP19	6379	0.033	0.4	NO
86	CD2BP2	CD2BP2	CD2BP2	6451	0.032	0.4	NO
87	RAB20	RAB20	RAB20	6487	0.032	0.4	NO
88	MSMO1	MSMO1	MSMO1	6517	0.031	0.4	NO
89	PSMB10	PSMB10	PSMB10	6540	0.031	0.4	NO
90	SPATA20	SPATA20	SPATA20	6722	0.029	0.39	NO
91	MAP1LC3B	MAP1LC3B	MAP1LC3B	6836	0.027	0.38	NO
92	SERGEF	SERGEF	SERGEF	6855	0.027	0.38	NO
93	BNIP3L	BNIP3L	BNIP3L	6971	0.025	0.38	NO
94	ALKBH5	ALKBH5	ALKBH5	6977	0.025	0.38	NO
95	NFKBIA	NFKBIA	NFKBIA	6978	0.025	0.38	NO
96	TSKU	TSKU	TSKU	6981	0.025	0.38	NO
97	HOXA4	HOXA4	HOXA4	6989	0.025	0.38	NO
98	SDC4	SDC4	SDC4	7000	0.025	0.38	NO
99	TRNAU1AP	TRNAU1AP	TRNAU1AP	7137	0.024	0.38	NO
100	SAP30BP	SAP30BP	SAP30BP	7154	0.023	0.38	NO
101	C1orf35	C1orf35	C1orf35	7175	0.023	0.38	NO
102	RHBDD3	RHBDD3	RHBDD3	7178	0.023	0.38	NO
103	FAM162A	FAM162A	FAM162A	7222	0.023	0.38	NO
104	PEX26	PEX26	PEX26	7231	0.023	0.38	NO
105	NUCKS1	NUCKS1	NUCKS1	7254	0.022	0.38	NO
106	NUPR1	NUPR1	NUPR1	7282	0.022	0.38	NO
107	ASPH	ASPH	ASPH	7286	0.022	0.38	NO
108	PPP1R15A	PPP1R15A	PPP1R15A	7342	0.022	0.38	NO
109	SPAG7	SPAG7	SPAG7	7347	0.022	0.38	NO
110	DTX3L	DTX3L	DTX3L	7429	0.021	0.38	NO
111	DHCR7	DHCR7	DHCR7	7561	0.019	0.37	NO
112	TCEA3	TCEA3	TCEA3	7670	0.018	0.37	NO
113	FOSL2	FOSL2	FOSL2	7675	0.018	0.37	NO
114	SLC3A2	SLC3A2	SLC3A2	7681	0.018	0.37	NO
115	GM2A	GM2A	GM2A	7695	0.018	0.37	NO
116	ZNF395	ZNF395	ZNF395	7739	0.018	0.37	NO
117	C19orf53	C19orf53	C19orf53	7773	0.017	0.37	NO
118	STOM	STOM	STOM	7800	0.017	0.37	NO
119	OBSL1	OBSL1	OBSL1	7811	0.017	0.37	NO
120	HSP90B1	HSP90B1	HSP90B1	7830	0.017	0.37	NO
121	SQLE	SQLE	SQLE	7839	0.017	0.37	NO
122	FTH1	FTH1	FTH1	7884	0.016	0.36	NO
123	RFX3	RFX3	RFX3	7943	0.016	0.36	NO
124	IMP3	IMP3	IMP3	7973	0.016	0.36	NO
125	HSPA5	HSPA5	HSPA5	8020	0.015	0.36	NO
126	CDK8	CDK8	CDK8	8027	0.015	0.36	NO
127	DDX19B	DDX19B	DDX19B	8106	0.014	0.36	NO
128	AGPAT2	AGPAT2	AGPAT2	8183	0.014	0.35	NO
129	CDC34	CDC34	CDC34	8209	0.014	0.35	NO
130	DDX41	DDX41	DDX41	8258	0.013	0.35	NO
131	CNNM4	CNNM4	CNNM4	8264	0.013	0.35	NO
132	C14orf2	C14orf2	C14orf2	8312	0.013	0.35	NO
133	MVK	MVK	MVK	8325	0.013	0.35	NO
134	RER1	RER1	RER1	8363	0.012	0.35	NO
135	PLCD1	PLCD1	PLCD1	8493	0.012	0.34	NO
136	FASN	FASN	FASN	8547	0.011	0.34	NO
137	LAMC1	LAMC1	LAMC1	8560	0.011	0.34	NO
138	PIM2	PIM2	PIM2	8563	0.011	0.34	NO
139	LSR	LSR	LSR	8564	0.011	0.34	NO
140	PIP4K2B	PIP4K2B	PIP4K2B	8570	0.011	0.34	NO
141	P4HB	P4HB	P4HB	8639	0.01	0.34	NO
142	AP3M2	AP3M2	AP3M2	8642	0.01	0.34	NO
143	BLVRB	BLVRB	BLVRB	8664	0.01	0.34	NO
144	CTSO	CTSO	CTSO	8746	0.0095	0.34	NO
145	NIT1	NIT1	NIT1	8785	0.0091	0.33	NO
146	PLAGL2	PLAGL2	PLAGL2	8801	0.0089	0.33	NO
147	ARHGEF2	ARHGEF2	ARHGEF2	8802	0.0089	0.33	NO
148	SLC30A1	SLC30A1	SLC30A1	8942	0.008	0.33	NO
149	MAPK7	MAPK7	MAPK7	8953	0.0078	0.33	NO
150	MCL1	MCL1	MCL1	8970	0.0077	0.32	NO
151	ARPC1A	ARPC1A	ARPC1A	9111	0.0068	0.32	NO
152	RBKS	RBKS	RBKS	9128	0.0066	0.32	NO
153	GNPDA1	GNPDA1	GNPDA1	9157	0.0064	0.32	NO
154	ZFP36L1	ZFP36L1	ZFP36L1	9196	0.0061	0.31	NO
155	MYH9	MYH9	MYH9	9219	0.006	0.31	NO
156	VAPB	VAPB	VAPB	9228	0.0059	0.31	NO
157	MLF1	MLF1	MLF1	9286	0.0055	0.31	NO
158	GXYLT1	GXYLT1	GXYLT1	9320	0.0052	0.31	NO
159	MOAP1	MOAP1	MOAP1	9390	0.0048	0.3	NO
160	ADAR	ADAR	ADAR	9463	0.0042	0.3	NO
161	TUBA1B	TUBA1B	TUBA1B	9466	0.0042	0.3	NO
162	SNX9	SNX9	SNX9	9545	0.0036	0.3	NO
163	AP2B1	AP2B1	AP2B1	9599	0.0033	0.3	NO
164	RALGDS	RALGDS	RALGDS	9623	0.0031	0.29	NO
165	UBE2O	UBE2O	UBE2O	9678	0.0028	0.29	NO
166	MUT	MUT	MUT	9808	0.0018	0.28	NO
167	ADAM10	ADAM10	ADAM10	9935	0.00098	0.28	NO
168	SERTAD2	SERTAD2	SERTAD2	10070	-0.000052	0.27	NO
169	NCL	NCL	NCL	10179	-0.00073	0.26	NO
170	STAU1	STAU1	STAU1	10191	-0.00078	0.26	NO
171	PFDN1	PFDN1	PFDN1	10197	-0.00081	0.26	NO
172	HIF1A	HIF1A	HIF1A	10285	-0.0014	0.26	NO
173	YWHAZ	YWHAZ	YWHAZ	10331	-0.0017	0.26	NO
174	RNF114	RNF114	RNF114	10333	-0.0018	0.26	NO
175	PTP4A2	PTP4A2	PTP4A2	10337	-0.0018	0.26	NO
176	SDCBP	SDCBP	SDCBP	10353	-0.0019	0.25	NO
177	BSG	BSG	BSG	10367	-0.0019	0.25	NO
178	GRB10	GRB10	GRB10	10440	-0.0025	0.25	NO
179	ADD3	ADD3	ADD3	10450	-0.0026	0.25	NO
180	SYF2	SYF2	SYF2	10470	-0.0027	0.25	NO
181	ATF7IP	ATF7IP	ATF7IP	10481	-0.0027	0.25	NO
182	RPL29	RPL29	RPL29	10492	-0.0029	0.25	NO
183	UBE2H	UBE2H	UBE2H	10606	-0.0036	0.24	NO
184	XPNPEP1	XPNPEP1	XPNPEP1	10628	-0.0037	0.24	NO
185	NARS	NARS	NARS	10672	-0.004	0.24	NO
186	KDM2B	KDM2B	KDM2B	10705	-0.0042	0.24	NO
187	SGPL1	SGPL1	SGPL1	10728	-0.0044	0.24	NO
188	PKD1	PKD1	PKD1	10778	-0.0046	0.23	NO
189	RPS27L	RPS27L	RPS27L	10782	-0.0046	0.23	NO
190	CDC42	CDC42	CDC42	10785	-0.0047	0.23	NO
191	PPP1R11	PPP1R11	PPP1R11	10792	-0.0047	0.23	NO
192	RYBP	RYBP	RYBP	10901	-0.0055	0.23	NO
193	ZCCHC3	ZCCHC3	ZCCHC3	11146	-0.0072	0.22	NO
194	YPEL5	YPEL5	YPEL5	11214	-0.0078	0.21	NO
195	SLC35E1	SLC35E1	SLC35E1	11247	-0.008	0.21	NO
196	CECR5	CECR5	CECR5	11295	-0.0082	0.21	NO
197	TMEM30A	TMEM30A	TMEM30A	11304	-0.0083	0.21	NO
198	AFF4	AFF4	AFF4	11353	-0.0086	0.21	NO
199	CANX	CANX	CANX	11362	-0.0087	0.21	NO
200	NMT1	NMT1	NMT1	11389	-0.0088	0.2	NO
201	MED10	MED10	MED10	11392	-0.0089	0.2	NO
202	KLHL36	KLHL36	KLHL36	11413	-0.009	0.2	NO
203	USP9X	USP9X	USP9X	11462	-0.0093	0.2	NO
204	IFNGR1	IFNGR1	IFNGR1	11520	-0.0097	0.2	NO
205	HNRNPU	HNRNPU	HNRNPU	11559	-0.01	0.2	NO
206	WIPF2	WIPF2	WIPF2	11591	-0.01	0.2	NO
207	NOL3	NOL3	NOL3	11642	-0.011	0.2	NO
208	SIRPA	SIRPA	SIRPA	11703	-0.011	0.19	NO
209	KCMF1	KCMF1	KCMF1	11722	-0.011	0.19	NO
210	ORMDL1	ORMDL1	ORMDL1	11724	-0.011	0.19	NO
211	SCD	SCD	SCD	11873	-0.012	0.18	NO
212	RPL12	RPL12	RPL12	11897	-0.012	0.18	NO
213	EIF2S2	EIF2S2	EIF2S2	11903	-0.012	0.18	NO
214	IMMP2L	IMMP2L	IMMP2L	11958	-0.012	0.18	NO
215	ARL1	ARL1	ARL1	11971	-0.013	0.18	NO
216	MFGE8	MFGE8	MFGE8	11980	-0.013	0.18	NO
217	ANKRD17	ANKRD17	ANKRD17	11990	-0.013	0.18	NO
218	STAMBP	STAMBP	STAMBP	12001	-0.013	0.18	NO
219	KPNB1	KPNB1	KPNB1	12170	-0.014	0.18	NO
220	SERBP1	SERBP1	SERBP1	12249	-0.014	0.17	NO
221	A2M	A2M	A2M	12276	-0.015	0.17	NO
222	RNF146	RNF146	RNF146	12421	-0.016	0.16	NO
223	NAP1L1	NAP1L1	NAP1L1	12560	-0.016	0.16	NO
224	RPL10	RPL10	RPL10	12575	-0.017	0.16	NO
225	ATP1B3	ATP1B3	ATP1B3	12603	-0.017	0.16	NO
226	KHDRBS3	KHDRBS3	KHDRBS3	12655	-0.017	0.15	NO
227	FBXO8	FBXO8	FBXO8	12691	-0.017	0.15	NO
228	AK2	AK2	AK2	12694	-0.017	0.15	NO
229	ANXA4	ANXA4	ANXA4	12716	-0.018	0.15	NO
230	RDH14	RDH14	RDH14	12732	-0.018	0.16	NO
231	ZFP91	ZFP91	ZFP91	12736	-0.018	0.16	NO
232	CSDE1	CSDE1	CSDE1	12824	-0.018	0.15	NO
233	PSMD6	PSMD6	PSMD6	12931	-0.019	0.15	NO
234	PJA2	PJA2	PJA2	12938	-0.019	0.15	NO
235	FAM189A2	FAM189A2	FAM189A2	12970	-0.02	0.15	NO
236	ARHGEF1	ARHGEF1	ARHGEF1	12993	-0.02	0.15	NO
237	CPD	CPD	CPD	13256	-0.022	0.13	NO
238	MARCKS	MARCKS	MARCKS	13306	-0.022	0.13	NO
239	KLF6	KLF6	KLF6	13323	-0.022	0.13	NO
240	UGP2	UGP2	UGP2	13380	-0.023	0.13	NO
241	EIF4B	EIF4B	EIF4B	13459	-0.023	0.13	NO
242	CHPT1	CHPT1	CHPT1	13467	-0.023	0.13	NO
243	SRRM2	SRRM2	SRRM2	13476	-0.023	0.13	NO
244	RPL30	RPL30	RPL30	13495	-0.023	0.13	NO
245	ANAPC10	ANAPC10	ANAPC10	13551	-0.024	0.13	NO
246	ZBTB47	ZBTB47	ZBTB47	13568	-0.024	0.13	NO
247	KPNA4	KPNA4	KPNA4	13570	-0.024	0.13	NO
248	HNRNPC	HNRNPC	HNRNPC	13617	-0.024	0.13	NO
249	LOX	LOX	LOX	13665	-0.025	0.13	NO
250	TOMM20	TOMM20	TOMM20	13668	-0.025	0.13	NO
251	IGF2BP2	IGF2BP2	IGF2BP2	13682	-0.025	0.13	NO
252	G3BP2	G3BP2	G3BP2	13696	-0.025	0.13	NO
253	GRSF1	GRSF1	GRSF1	13719	-0.025	0.13	NO
254	GNA13	GNA13	GNA13	13741	-0.025	0.13	NO
255	DCAF6	DCAF6	DCAF6	13747	-0.025	0.13	NO
256	TFG	TFG	TFG	13809	-0.026	0.13	NO
257	RPS3	RPS3	RPS3	13881	-0.027	0.13	NO
258	RBM12	RBM12	RBM12	13912	-0.027	0.13	NO
259	ARIH2	ARIH2	ARIH2	13924	-0.027	0.13	NO
260	CD164	CD164	CD164	14002	-0.028	0.13	NO
261	BNIP3	BNIP3	BNIP3	14037	-0.028	0.13	NO
262	MXI1	MXI1	MXI1	14075	-0.028	0.13	NO
263	UGCG	UGCG	UGCG	14139	-0.029	0.12	NO
264	CAV1	CAV1	CAV1	14193	-0.029	0.12	NO
265	C2orf49	C2orf49	C2orf49	14194	-0.029	0.12	NO
266	EEF1A1	EEF1A1	EEF1A1	14297	-0.03	0.12	NO
267	SIKE1	SIKE1	SIKE1	14399	-0.031	0.12	NO
268	PTER	PTER	PTER	14411	-0.031	0.12	NO
269	GTPBP2	GTPBP2	GTPBP2	14444	-0.031	0.12	NO
270	PGRMC2	PGRMC2	PGRMC2	14532	-0.032	0.12	NO
271	P4HA1	P4HA1	P4HA1	14554	-0.033	0.12	NO
272	UBE2E1	UBE2E1	UBE2E1	14629	-0.033	0.11	NO
273	WAPAL	WAPAL	WAPAL	14650	-0.034	0.12	NO
274	YAP1	YAP1	YAP1	14828	-0.035	0.11	NO
275	SMG1	SMG1	SMG1	14882	-0.036	0.11	NO
276	TXNIP	TXNIP	TXNIP	14894	-0.036	0.11	NO
277	SNX4	SNX4	SNX4	15152	-0.039	0.095	NO
278	BTG1	BTG1	BTG1	15198	-0.04	0.095	NO
279	PTPN12	PTPN12	PTPN12	15218	-0.04	0.096	NO
280	SAT1	SAT1	SAT1	15268	-0.04	0.096	NO
281	HOOK2	HOOK2	HOOK2	15292	-0.041	0.097	NO
282	SLC30A9	SLC30A9	SLC30A9	15380	-0.042	0.095	NO
283	GPATCH8	GPATCH8	GPATCH8	15413	-0.042	0.095	NO
284	NEK6	NEK6	NEK6	15607	-0.045	0.087	NO
285	STXBP2	STXBP2	STXBP2	15622	-0.045	0.089	NO
286	EIF1AX	EIF1AX	EIF1AX	15733	-0.047	0.086	NO
287	TSNAX	TSNAX	TSNAX	15773	-0.048	0.086	NO
288	RHOF	RHOF	RHOF	15914	-0.05	0.082	NO
289	RIPK4	RIPK4	RIPK4	16052	-0.053	0.077	NO
290	RSL24D1	RSL24D1	RSL24D1	16137	-0.055	0.076	NO
291	MAGT1	MAGT1	MAGT1	16265	-0.058	0.072	NO
292	NDRG1	NDRG1	NDRG1	16271	-0.058	0.075	NO
293	CIDEB	CIDEB	CIDEB	16281	-0.058	0.078	NO
294	RPL9	RPL9	RPL9	16331	-0.059	0.079	NO
295	IKBIP	IKBIP	IKBIP	16459	-0.063	0.075	NO
296	PPP1R3C	PPP1R3C	PPP1R3C	16734	-0.073	0.064	NO
297	ENOSF1	ENOSF1	ENOSF1	17035	-0.087	0.053	NO
298	ELL2	ELL2	ELL2	17265	-0.11	0.046	NO

Figure S23. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY.

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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	ADCY8	ADCY8	ADCY8	322	0.66	0.061	YES
2	ADCYAP1R1	ADCYAP1R1	ADCYAP1R1	379	0.62	0.13	YES
3	PRKCG	PRKCG	PRKCG	765	0.47	0.17	YES
4	NTRK1	NTRK1	NTRK1	934	0.42	0.21	YES
5	NGF	NGF	NGF	1095	0.38	0.25	YES
6	NTRK2	NTRK2	NTRK2	1244	0.36	0.28	YES
7	SH3GL2	SH3GL2	SH3GL2	1246	0.36	0.32	YES
8	SHC3	SHC3	SHC3	1314	0.35	0.36	YES
9	PDE1A	PDE1A	PDE1A	1404	0.33	0.4	YES
10	ADCY1	ADCY1	ADCY1	1439	0.32	0.44	YES
11	ADCYAP1	ADCYAP1	ADCYAP1	1742	0.29	0.45	YES
12	RIT2	RIT2	RIT2	1872	0.27	0.48	YES
13	ADCY5	ADCY5	ADCY5	2073	0.25	0.5	YES
14	ADCY2	ADCY2	ADCY2	2124	0.24	0.52	YES
15	RPS6KA2	RPS6KA2	RPS6KA2	2919	0.18	0.5	NO
16	CDKN1A	CDKN1A	CDKN1A	3643	0.13	0.48	NO
17	PRKAR2B	PRKAR2B	PRKAR2B	3999	0.11	0.47	NO
18	ADCY4	ADCY4	ADCY4	4291	0.098	0.46	NO
19	ITPR2	ITPR2	ITPR2	5111	0.064	0.43	NO
20	PIK3R2	PIK3R2	PIK3R2	5353	0.056	0.42	NO
21	BAD	BAD	BAD	5511	0.052	0.42	NO
22	PDE1B	PDE1B	PDE1B	5526	0.052	0.42	NO
23	MAPK3	MAPK3	MAPK3	5934	0.042	0.41	NO
24	MAPK11	MAPK11	MAPK11	6173	0.037	0.4	NO
25	CAMK4	CAMK4	CAMK4	6187	0.036	0.4	NO
26	CALM1	CALM1	CALM1	6339	0.034	0.4	NO
27	SHC1	SHC1	SHC1	6374	0.033	0.4	NO
28	PRKACA	PRKACA	PRKACA	6545	0.031	0.39	NO
29	MLST8	MLST8	MLST8	6607	0.03	0.39	NO
30	ADCY3	ADCY3	ADCY3	6689	0.029	0.39	NO
31	AP2S1	AP2S1	AP2S1	6885	0.026	0.38	NO
32	DNM1	DNM1	DNM1	6911	0.026	0.39	NO
33	PPP2R1A	PPP2R1A	PPP2R1A	6924	0.026	0.39	NO
34	CALM3	CALM3	CALM3	7065	0.024	0.38	NO
35	DUSP4	DUSP4	DUSP4	7079	0.024	0.39	NO
36	YWHAB	YWHAB	YWHAB	7174	0.023	0.38	NO
37	AKT1S1	AKT1S1	AKT1S1	7177	0.023	0.39	NO
38	AKT3	AKT3	AKT3	7192	0.023	0.39	NO
39	HRAS	HRAS	HRAS	7301	0.022	0.38	NO
40	GSK3A	GSK3A	GSK3A	7625	0.019	0.37	NO
41	SRC	SRC	SRC	7673	0.018	0.37	NO
42	ADCY7	ADCY7	ADCY7	7742	0.018	0.37	NO
43	MAPK13	MAPK13	MAPK13	7751	0.018	0.37	NO
44	MAPKAPK2	MAPKAPK2	MAPKAPK2	7872	0.016	0.36	NO
45	AP2A1	AP2A1	AP2A1	7968	0.016	0.36	NO
46	PLCG1	PLCG1	PLCG1	8052	0.015	0.36	NO
47	DNAL4	DNAL4	DNAL4	8107	0.014	0.36	NO
48	AP2M1	AP2M1	AP2M1	8324	0.013	0.35	NO
49	PRKAR1B	PRKAR1B	PRKAR1B	8425	0.012	0.34	NO
50	ADRBK1	ADRBK1	ADRBK1	8446	0.012	0.34	NO
51	MDM2	MDM2	MDM2	8545	0.011	0.34	NO
52	RPS6KA1	RPS6KA1	RPS6KA1	8574	0.011	0.34	NO
53	STAT3	STAT3	STAT3	8832	0.0088	0.32	NO
54	MAPK7	MAPK7	MAPK7	8953	0.0078	0.32	NO
55	RALB	RALB	RALB	9065	0.0071	0.31	NO
56	AKT1	AKT1	AKT1	9099	0.0069	0.31	NO
57	PIK3R1	PIK3R1	PIK3R1	9201	0.0061	0.31	NO
58	RPS6KB2	RPS6KB2	RPS6KB2	9226	0.0059	0.31	NO
59	MAPKAPK3	MAPKAPK3	MAPKAPK3	9336	0.0052	0.3	NO
60	MAPKAP1	MAPKAP1	MAPKAP1	9479	0.0041	0.29	NO
61	MAPK12	MAPK12	MAPK12	9570	0.0035	0.29	NO
62	AP2A2	AP2A2	AP2A2	9578	0.0034	0.29	NO
63	AP2B1	AP2B1	AP2B1	9599	0.0033	0.29	NO
64	CASP9	CASP9	CASP9	9617	0.0032	0.29	NO
65	RALGDS	RALGDS	RALGDS	9623	0.0031	0.29	NO
66	GRB2	GRB2	GRB2	9778	0.0021	0.28	NO
67	FOXO3	FOXO3	FOXO3	9791	0.002	0.28	NO
68	RIT1	RIT1	RIT1	9820	0.0018	0.28	NO
69	IRS2	IRS2	IRS2	9829	0.0017	0.28	NO
70	FOXO1	FOXO1	FOXO1	10081	-0.00012	0.26	NO
71	PTEN	PTEN	PTEN	10413	-0.0023	0.25	NO
72	MAP2K5	MAP2K5	MAP2K5	10431	-0.0024	0.24	NO
73	RAPGEF1	RAPGEF1	RAPGEF1	10436	-0.0024	0.24	NO
74	MAP2K2	MAP2K2	MAP2K2	10520	-0.003	0.24	NO
75	SHC2	SHC2	SHC2	10760	-0.0045	0.23	NO
76	MEF2C	MEF2C	MEF2C	10835	-0.0051	0.22	NO
77	TRIB3	TRIB3	TRIB3	10853	-0.0052	0.22	NO
78	KIDINS220	KIDINS220	KIDINS220	10898	-0.0055	0.22	NO
79	AKT2	AKT2	AKT2	10968	-0.0059	0.22	NO
80	MEF2A	MEF2A	MEF2A	11071	-0.0067	0.22	NO
81	DUSP7	DUSP7	DUSP7	11086	-0.0068	0.22	NO
82	CLTA	CLTA	CLTA	11199	-0.0077	0.21	NO
83	MAPK1	MAPK1	MAPK1	11428	-0.0091	0.2	NO
84	PPP2CB	PPP2CB	PPP2CB	11605	-0.01	0.19	NO
85	MAP2K1	MAP2K1	MAP2K1	11622	-0.01	0.19	NO
86	PPP2CA	PPP2CA	PPP2CA	11696	-0.011	0.19	NO
87	RHOA	RHOA	RHOA	11701	-0.011	0.19	NO
88	CLTC	CLTC	CLTC	11702	-0.011	0.19	NO
89	SOS1	SOS1	SOS1	11772	-0.011	0.19	NO
90	FOXO4	FOXO4	FOXO4	11934	-0.012	0.18	NO
91	CALM2	CALM2	CALM2	11981	-0.013	0.18	NO
92	DNM2	DNM2	DNM2	12212	-0.014	0.17	NO
93	ADCY9	ADCY9	ADCY9	12328	-0.015	0.16	NO
94	DUSP6	DUSP6	DUSP6	12357	-0.015	0.16	NO
95	PPP2R5D	PPP2R5D	PPP2R5D	12361	-0.015	0.16	NO
96	RAF1	RAF1	RAF1	12375	-0.015	0.17	NO
97	ELK1	ELK1	ELK1	12450	-0.016	0.16	NO
98	PPP2R1B	PPP2R1B	PPP2R1B	12533	-0.016	0.16	NO
99	KRAS	KRAS	KRAS	12551	-0.016	0.16	NO
100	RALA	RALA	RALA	12606	-0.017	0.16	NO
101	PRKCA	PRKCA	PRKCA	12632	-0.017	0.16	NO
102	PRKAR2A	PRKAR2A	PRKAR2A	12708	-0.018	0.16	NO
103	PDPK1	PDPK1	PDPK1	12850	-0.019	0.15	NO
104	THEM4	THEM4	THEM4	12873	-0.019	0.16	NO
105	BRAF	BRAF	BRAF	13058	-0.02	0.15	NO
106	CRK	CRK	CRK	13231	-0.022	0.14	NO
107	CDKN1B	CDKN1B	CDKN1B	13470	-0.023	0.13	NO
108	RAP1A	RAP1A	RAP1A	13477	-0.023	0.13	NO
109	MTOR	MTOR	MTOR	13656	-0.025	0.12	NO
110	NRAS	NRAS	NRAS	13674	-0.025	0.13	NO
111	RICTOR	RICTOR	RICTOR	13808	-0.026	0.12	NO
112	PRKACB	PRKACB	PRKACB	13822	-0.026	0.12	NO
113	IRS1	IRS1	IRS1	13944	-0.027	0.12	NO
114	TSC2	TSC2	TSC2	14010	-0.028	0.12	NO
115	CHUK	CHUK	CHUK	14156	-0.029	0.12	NO
116	PRKCD	PRKCD	PRKCD	14188	-0.029	0.12	NO
117	PHLPP1	PHLPP1	PHLPP1	14209	-0.029	0.12	NO
118	CDK1	CDK1	CDK1	14228	-0.029	0.12	NO
119	MAPK14	MAPK14	MAPK14	14720	-0.034	0.1	NO
120	FRS2	FRS2	FRS2	14956	-0.037	0.092	NO
121	ATF1	ATF1	ATF1	15099	-0.038	0.088	NO
122	PRKCE	PRKCE	PRKCE	15102	-0.038	0.093	NO
123	DUSP3	DUSP3	DUSP3	15202	-0.04	0.092	NO
124	NR4A1	NR4A1	NR4A1	15312	-0.041	0.091	NO
125	RPS6KA3	RPS6KA3	RPS6KA3	15319	-0.041	0.096	NO
126	CREB1	CREB1	CREB1	15370	-0.042	0.098	NO
127	PRKAR1A	PRKAR1A	PRKAR1A	15550	-0.044	0.093	NO
128	ITPR3	ITPR3	ITPR3	15575	-0.045	0.097	NO
129	ADCY6	ADCY6	ADCY6	16150	-0.055	0.072	NO
130	PIK3CB	PIK3CB	PIK3CB	16165	-0.056	0.078	NO
131	PIK3CA	PIK3CA	PIK3CA	16220	-0.057	0.082	NO
132	RPS6KA5	RPS6KA5	RPS6KA5	16829	-0.077	0.057	NO
133	ADORA2A	ADORA2A	ADORA2A	17244	-0.1	0.047	NO

Figure S25. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM.

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

genes ES table in pathway: KEGG GALACTOSE METABOLISM

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	MYOC	MYOC	MYOC	177	0.77	0.25	YES
2	KCNJ9	KCNJ9	KCNJ9	507	0.56	0.42	YES
3	SCG5	SCG5	SCG5	543	0.54	0.6	YES
4	MAP1B	MAP1B	MAP1B	1000	0.41	0.71	YES
5	FOLH1	FOLH1	FOLH1	4029	0.11	0.58	NO
6	PAM	PAM	PAM	4892	0.072	0.56	NO
7	COL4A1	COL4A1	COL4A1	5494	0.052	0.54	NO
8	GNB1	GNB1	GNB1	5809	0.044	0.54	NO
9	PRDX2	PRDX2	PRDX2	6576	0.03	0.5	NO
10	RGS19	RGS19	RGS19	7296	0.022	0.47	NO
11	PTTG1	PTTG1	PTTG1	8160	0.014	0.43	NO
12	OCEL1	OCEL1	OCEL1	8196	0.014	0.43	NO
13	ALAD	ALAD	ALAD	10178	-0.00072	0.32	NO
14	CAP1	CAP1	CAP1	10199	-0.00083	0.32	NO
15	MEF2C	MEF2C	MEF2C	10835	-0.0051	0.29	NO
16	C4orf3	C4orf3	C4orf3	10945	-0.0058	0.28	NO
17	TOX4	TOX4	TOX4	11147	-0.0072	0.28	NO
18	PSTK	PSTK	PSTK	11344	-0.0085	0.27	NO
19	MTIF2	MTIF2	MTIF2	11382	-0.0088	0.27	NO
20	ALDH7A1	ALDH7A1	ALDH7A1	12333	-0.015	0.22	NO
21	ACAA1	ACAA1	ACAA1	12501	-0.016	0.22	NO
22	BCAT2	BCAT2	BCAT2	12986	-0.02	0.2	NO
23	TULP3	TULP3	TULP3	13199	-0.021	0.19	NO
24	THUMPD1	THUMPD1	THUMPD1	13518	-0.024	0.18	NO
25	CPSF2	CPSF2	CPSF2	13931	-0.027	0.17	NO
26	VPS52	VPS52	VPS52	14018	-0.028	0.17	NO
27	RPP14	RPP14	RPP14	14638	-0.034	0.15	NO
28	PDXDC1	PDXDC1	PDXDC1	15008	-0.037	0.14	NO
29	C5orf34	C5orf34	C5orf34	15029	-0.038	0.15	NO
30	PHLDA1	PHLDA1	PHLDA1	15599	-0.045	0.14	NO

Figure S27. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG GALACTOSE METABOLISM.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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	GRIA1	GRIA1	GRIA1	27	1	0.23	YES
2	SYT1	SYT1	SYT1	37	0.97	0.46	YES
3	VSNL1	VSNL1	VSNL1	915	0.42	0.51	YES
4	PTGDS	PTGDS	PTGDS	1241	0.36	0.58	YES
5	ACHE	ACHE	ACHE	1972	0.26	0.6	YES
6	CPE	CPE	CPE	2174	0.24	0.64	YES
7	ATP1B2	ATP1B2	ATP1B2	2338	0.22	0.69	YES
8	DLG4	DLG4	DLG4	3673	0.13	0.64	NO
9	EPAS1	EPAS1	EPAS1	5998	0.04	0.52	NO
10	ATP9A	ATP9A	ATP9A	6162	0.037	0.52	NO
11	GDI1	GDI1	GDI1	6168	0.037	0.53	NO
12	GNAI2	GNAI2	GNAI2	6228	0.036	0.54	NO
13	APOE	APOE	APOE	6386	0.033	0.54	NO
14	DNM1	DNM1	DNM1	6911	0.026	0.51	NO
15	PPP2R1A	PPP2R1A	PPP2R1A	6924	0.026	0.52	NO
16	UBC	UBC	UBC	7091	0.024	0.52	NO
17	MAGED1	MAGED1	MAGED1	7207	0.023	0.51	NO
18	PLD3	PLD3	PLD3	7302	0.022	0.51	NO
19	GPX4	GPX4	GPX4	7325	0.022	0.52	NO
20	ATP6AP1	ATP6AP1	ATP6AP1	7494	0.02	0.51	NO
21	STIP1	STIP1	STIP1	7892	0.016	0.5	NO
22	ATP6V0C	ATP6V0C	ATP6V0C	7909	0.016	0.5	NO
23	CAMK2G	CAMK2G	CAMK2G	7933	0.016	0.5	NO
24	AP2M1	AP2M1	AP2M1	8324	0.013	0.48	NO
25	SARS	SARS	SARS	8652	0.01	0.47	NO
26	DNAJA2	DNAJA2	DNAJA2	8744	0.0095	0.46	NO
27	EPRS	EPRS	EPRS	8849	0.0086	0.46	NO
28	DHX30	DHX30	DHX30	8999	0.0075	0.45	NO
29	ATP6V1E1	ATP6V1E1	ATP6V1E1	9021	0.0073	0.45	NO
30	DDB1	DDB1	DDB1	10035	0.0002	0.4	NO
31	CS	CS	CS	10631	-0.0037	0.37	NO
32	ATP2A2	ATP2A2	ATP2A2	10997	-0.0061	0.35	NO
33	CANX	CANX	CANX	11362	-0.0087	0.33	NO
34	VTI1B	VTI1B	VTI1B	11948	-0.012	0.3	NO
35	ACO2	ACO2	ACO2	12625	-0.017	0.27	NO
36	PRKACB	PRKACB	PRKACB	13822	-0.026	0.21	NO
37	MGAT2	MGAT2	MGAT2	14229	-0.029	0.19	NO
38	EEF1A1	EEF1A1	EEF1A1	14297	-0.03	0.19	NO
39	RAB18	RAB18	RAB18	14590	-0.033	0.18	NO
40	KIF5B	KIF5B	KIF5B	14948	-0.037	0.17	NO

Figure S29. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS.

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

genes ES table in pathway: KEGG PURINE METABOLISM

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	GFAP	GFAP	GFAP	113	0.84	0.043	YES
2	PCP4	PCP4	PCP4	209	0.74	0.082	YES
3	RGN	RGN	RGN	279	0.69	0.12	YES
4	CHI3L1	CHI3L1	CHI3L1	365	0.63	0.15	YES
5	WFDC2	WFDC2	WFDC2	369	0.63	0.19	YES
6	PVALB	PVALB	PVALB	458	0.58	0.22	YES
7	DKK3	DKK3	DKK3	533	0.55	0.25	YES
8	TRDN	TRDN	TRDN	553	0.54	0.28	YES
9	PSG1	PSG1	PSG1	778	0.46	0.29	YES
10	CLDN10	CLDN10	CLDN10	806	0.45	0.32	YES
11	BDNF	BDNF	BDNF	862	0.44	0.34	YES
12	BCL2A1	BCL2A1	BCL2A1	890	0.43	0.36	YES
13	DDAH1	DDAH1	DDAH1	1261	0.35	0.36	YES
14	ALAS2	ALAS2	ALAS2	1519	0.31	0.37	YES
15	CYP3A7	CYP3A7	CYP3A7	1910	0.26	0.36	YES
16	ROPN1L	ROPN1L	ROPN1L	1932	0.26	0.38	YES
17	MNDA	MNDA	MNDA	1968	0.26	0.39	YES
18	FGR	FGR	FGR	1987	0.26	0.4	YES
19	CD8A	CD8A	CD8A	2074	0.25	0.41	YES
20	CACNA1D	CACNA1D	CACNA1D	2104	0.24	0.42	YES
21	SLAMF8	SLAMF8	SLAMF8	2265	0.23	0.43	YES
22	IGFBP6	IGFBP6	IGFBP6	2298	0.22	0.44	YES
23	ROBO2	ROBO2	ROBO2	2303	0.22	0.45	YES
24	CSF3R	CSF3R	CSF3R	2423	0.21	0.46	YES
25	TUBA4A	TUBA4A	TUBA4A	2457	0.21	0.47	YES
26	IL2RB	IL2RB	IL2RB	2511	0.2	0.48	YES
27	SLC6A12	SLC6A12	SLC6A12	2553	0.2	0.49	YES
28	PBX1	PBX1	PBX1	2705	0.19	0.49	YES
29	SPINT2	SPINT2	SPINT2	2891	0.18	0.49	YES
30	IGF2	IGF2	IGF2	2937	0.17	0.5	YES
31	EPB42	EPB42	EPB42	3084	0.16	0.5	YES
32	GGT5	GGT5	GGT5	3469	0.14	0.49	NO
33	SLC16A2	SLC16A2	SLC16A2	3569	0.14	0.49	NO
34	PDE6G	PDE6G	PDE6G	3651	0.13	0.49	NO
35	TM4SF1	TM4SF1	TM4SF1	3891	0.12	0.49	NO
36	ECE1	ECE1	ECE1	3949	0.12	0.49	NO
37	CCL14	CCL14	CCL14	4148	0.1	0.49	NO
38	SGK1	SGK1	SGK1	4150	0.1	0.49	NO
39	PLEKHG5	PLEKHG5	PLEKHG5	4982	0.069	0.45	NO
40	HS6ST1	HS6ST1	HS6ST1	5079	0.065	0.45	NO
41	LRRC17	LRRC17	LRRC17	5177	0.062	0.45	NO
42	ARHGDIB	ARHGDIB	ARHGDIB	5390	0.056	0.44	NO
43	DGKA	DGKA	DGKA	5399	0.055	0.44	NO
44	ST14	ST14	ST14	5498	0.052	0.44	NO
45	DHCR24	DHCR24	DHCR24	5598	0.049	0.44	NO
46	TIAF1	TIAF1	TIAF1	5666	0.048	0.44	NO
47	AMMECR1	AMMECR1	AMMECR1	5672	0.048	0.44	NO
48	ITSN1	ITSN1	ITSN1	5835	0.044	0.43	NO
49	APOL6	APOL6	APOL6	5932	0.042	0.43	NO
50	RND3	RND3	RND3	6076	0.039	0.42	NO
51	TMSB10	TMSB10	TMSB10	6109	0.038	0.42	NO
52	H3F3B	H3F3B	H3F3B	6352	0.034	0.41	NO
53	RALY	RALY	RALY	6357	0.034	0.41	NO
54	IL13RA1	IL13RA1	IL13RA1	6389	0.033	0.41	NO
55	PTOV1	PTOV1	PTOV1	6457	0.032	0.41	NO
56	DRAP1	DRAP1	DRAP1	6470	0.032	0.41	NO
57	WWTR1	WWTR1	WWTR1	6528	0.031	0.41	NO
58	CDC20	CDC20	CDC20	6580	0.03	0.41	NO
59	AIP	AIP	AIP	6590	0.03	0.41	NO
60	GABBR1	GABBR1	GABBR1	6690	0.029	0.41	NO
61	SMARCB1	SMARCB1	SMARCB1	6696	0.029	0.41	NO
62	POLR2J	POLR2J	POLR2J	6732	0.028	0.41	NO
63	USP6NL	USP6NL	USP6NL	6788	0.028	0.41	NO
64	TNRC6B	TNRC6B	TNRC6B	6867	0.027	0.4	NO
65	PDAP1	PDAP1	PDAP1	6980	0.025	0.4	NO
66	RALGAPA2	RALGAPA2	RALGAPA2	6996	0.025	0.4	NO
67	SDC4	SDC4	SDC4	7000	0.025	0.4	NO
68	NHSL1	NHSL1	NHSL1	7006	0.025	0.4	NO
69	BEX2	BEX2	BEX2	7109	0.024	0.4	NO
70	IRF9	IRF9	IRF9	7147	0.023	0.4	NO
71	MADD	MADD	MADD	7255	0.022	0.39	NO
72	C17orf99	C17orf99	C17orf99	7318	0.022	0.39	NO
73	SNRNP27	SNRNP27	SNRNP27	7367	0.021	0.39	NO
74	CYTH1	CYTH1	CYTH1	7487	0.02	0.38	NO
75	ZNF629	ZNF629	ZNF629	7566	0.019	0.38	NO
76	GM2A	GM2A	GM2A	7695	0.018	0.38	NO
77	ADCY7	ADCY7	ADCY7	7742	0.018	0.37	NO
78	MYL6	MYL6	MYL6	7770	0.017	0.37	NO
79	ZBTB4	ZBTB4	ZBTB4	7813	0.017	0.37	NO
80	PRCC	PRCC	PRCC	7901	0.016	0.37	NO
81	INPPL1	INPPL1	INPPL1	7922	0.016	0.37	NO
82	CDC27	CDC27	CDC27	8188	0.014	0.35	NO
83	DAD1	DAD1	DAD1	8356	0.012	0.34	NO
84	POLR2A	POLR2A	POLR2A	8365	0.012	0.34	NO
85	MIA3	MIA3	MIA3	8386	0.012	0.34	NO
86	MEF2BNB	MEF2BNB	MEF2BNB	8418	0.012	0.34	NO
87	RPL28	RPL28	RPL28	8489	0.012	0.34	NO
88	DDT	DDT	DDT	8578	0.011	0.34	NO
89	LGMN	LGMN	LGMN	8775	0.0091	0.33	NO
90	FGFR2	FGFR2	FGFR2	8778	0.0091	0.33	NO
91	GSTO1	GSTO1	GSTO1	8783	0.0091	0.33	NO
92	NUCB1	NUCB1	NUCB1	8904	0.0083	0.32	NO
93	SMARCA1	SMARCA1	SMARCA1	9037	0.0072	0.31	NO
94	DPF2	DPF2	DPF2	9063	0.0071	0.31	NO
95	ARPC1A	ARPC1A	ARPC1A	9111	0.0068	0.31	NO
96	AAMP	AAMP	AAMP	9154	0.0065	0.31	NO
97	MAP2K4	MAP2K4	MAP2K4	9245	0.0058	0.3	NO
98	DYRK4	DYRK4	DYRK4	9326	0.0052	0.3	NO
99	BRE	BRE	BRE	9360	0.005	0.3	NO
100	VEZF1	VEZF1	VEZF1	9383	0.0049	0.3	NO
101	ADAR	ADAR	ADAR	9463	0.0042	0.29	NO
102	RNPS1	RNPS1	RNPS1	9529	0.0037	0.29	NO
103	GSTM4	GSTM4	GSTM4	9547	0.0036	0.29	NO
104	MED22	MED22	MED22	9550	0.0036	0.29	NO
105	KARS	KARS	KARS	9703	0.0026	0.28	NO
106	ARPC2	ARPC2	ARPC2	9777	0.0021	0.28	NO
107	GRB2	GRB2	GRB2	9778	0.0021	0.28	NO
108	TGFBR2	TGFBR2	TGFBR2	9798	0.0019	0.28	NO
109	RIT1	RIT1	RIT1	9820	0.0018	0.27	NO
110	SNRPD2	SNRPD2	SNRPD2	9832	0.0017	0.27	NO
111	CLK2	CLK2	CLK2	9873	0.0014	0.27	NO
112	NPAS2	NPAS2	NPAS2	9878	0.0014	0.27	NO
113	AMFR	AMFR	AMFR	9903	0.0012	0.27	NO
114	MCFD2	MCFD2	MCFD2	9963	0.00072	0.27	NO
115	UFD1L	UFD1L	UFD1L	9973	0.00064	0.27	NO
116	PSEN1	PSEN1	PSEN1	10027	0.00025	0.26	NO
117	LRBA	LRBA	LRBA	10030	0.00023	0.26	NO
118	CKAP5	CKAP5	CKAP5	10043	0.00014	0.26	NO
119	TMEM187	TMEM187	TMEM187	10045	0.00011	0.26	NO
120	AKAP17A	AKAP17A	AKAP17A	10099	-0.00025	0.26	NO
121	WDR48	WDR48	WDR48	10406	-0.0022	0.24	NO
122	CDC123	CDC123	CDC123	10442	-0.0025	0.24	NO
123	ATP6V0A1	ATP6V0A1	ATP6V0A1	10549	-0.0032	0.24	NO
124	PPP6C	PPP6C	PPP6C	10577	-0.0034	0.23	NO
125	METTL2A	METTL2A	METTL2A	10587	-0.0034	0.23	NO
126	STX5	STX5	STX5	10661	-0.004	0.23	NO
127	MTCH2	MTCH2	MTCH2	10690	-0.0041	0.23	NO
128	SUMO1	SUMO1	SUMO1	10692	-0.0041	0.23	NO
129	SLC22A9	SLC22A9	SLC22A9	10704	-0.0042	0.23	NO
130	HDHD1	HDHD1	HDHD1	10744	-0.0045	0.23	NO
131	COG2	COG2	COG2	10753	-0.0045	0.23	NO
132	INSR	INSR	INSR	10951	-0.0058	0.22	NO
133	STK38	STK38	STK38	11056	-0.0066	0.21	NO
134	MPI	MPI	MPI	11192	-0.0076	0.2	NO
135	COASY	COASY	COASY	11503	-0.0096	0.19	NO
136	POLRMT	POLRMT	POLRMT	11512	-0.0097	0.19	NO
137	TJP2	TJP2	TJP2	11532	-0.0098	0.19	NO
138	TXNRD1	TXNRD1	TXNRD1	11679	-0.011	0.18	NO
139	HCCS	HCCS	HCCS	11709	-0.011	0.18	NO
140	PSMD14	PSMD14	PSMD14	11719	-0.011	0.18	NO
141	NEDD4	NEDD4	NEDD4	11924	-0.012	0.17	NO
142	METTL1	METTL1	METTL1	11957	-0.012	0.17	NO
143	ABR	ABR	ABR	12019	-0.013	0.16	NO
144	CNN2	CNN2	CNN2	12118	-0.014	0.16	NO
145	ZFP36L2	ZFP36L2	ZFP36L2	12120	-0.014	0.16	NO
146	CDK2AP1	CDK2AP1	CDK2AP1	12122	-0.014	0.16	NO
147	BAZ2A	BAZ2A	BAZ2A	12422	-0.016	0.14	NO
148	ZNF32	ZNF32	ZNF32	12481	-0.016	0.14	NO
149	ATP1B3	ATP1B3	ATP1B3	12603	-0.017	0.14	NO
150	SLC30A7	SLC30A7	SLC30A7	12676	-0.017	0.13	NO
151	PSMA5	PSMA5	PSMA5	12803	-0.018	0.13	NO
152	UBE2N	UBE2N	UBE2N	12818	-0.018	0.13	NO
153	MRPL4	MRPL4	MRPL4	12825	-0.018	0.13	NO
154	CYFIP1	CYFIP1	CYFIP1	12842	-0.018	0.13	NO
155	SRSF1	SRSF1	SRSF1	12904	-0.019	0.13	NO
156	DPM1	DPM1	DPM1	12912	-0.019	0.13	NO
157	BZW1	BZW1	BZW1	12921	-0.019	0.13	NO
158	IGF2R	IGF2R	IGF2R	12978	-0.02	0.12	NO
159	VKORC1L1	VKORC1L1	VKORC1L1	13095	-0.02	0.12	NO
160	ZNF449	ZNF449	ZNF449	13129	-0.021	0.12	NO
161	FAM120A	FAM120A	FAM120A	13439	-0.023	0.1	NO
162	BAP1	BAP1	BAP1	13623	-0.024	0.095	NO
163	ZNF440	ZNF440	ZNF440	13828	-0.026	0.085	NO
164	TFDP2	TFDP2	TFDP2	13971	-0.027	0.079	NO
165	THOC1	THOC1	THOC1	13987	-0.028	0.079	NO
166	COPS5	COPS5	COPS5	14091	-0.028	0.075	NO
167	TMED1	TMED1	TMED1	14106	-0.028	0.076	NO
168	PWP1	PWP1	PWP1	14195	-0.029	0.073	NO
169	MGAT2	MGAT2	MGAT2	14229	-0.029	0.073	NO
170	KCTD4	KCTD4	KCTD4	14291	-0.03	0.071	NO
171	MTMR3	MTMR3	MTMR3	14381	-0.031	0.068	NO
172	MED13L	MED13L	MED13L	14382	-0.031	0.07	NO
173	LPIN1	LPIN1	LPIN1	14409	-0.031	0.07	NO
174	FXN	FXN	FXN	14485	-0.032	0.068	NO
175	GALC	GALC	GALC	14513	-0.032	0.068	NO
176	CBX3	CBX3	CBX3	14584	-0.033	0.066	NO
177	MCM2	MCM2	MCM2	14613	-0.033	0.067	NO
178	STAM	STAM	STAM	14770	-0.035	0.06	NO
179	HNRNPF	HNRNPF	HNRNPF	14773	-0.035	0.062	NO
180	CAPZA1	CAPZA1	CAPZA1	14911	-0.036	0.056	NO
181	USP34	USP34	USP34	14925	-0.036	0.058	NO
182	USP4	USP4	USP4	14932	-0.037	0.06	NO
183	KIF5B	KIF5B	KIF5B	14948	-0.037	0.061	NO
184	CABLES1	CABLES1	CABLES1	14983	-0.037	0.061	NO
185	GPATCH2	GPATCH2	GPATCH2	15004	-0.037	0.062	NO
186	PDXDC1	PDXDC1	PDXDC1	15008	-0.037	0.064	NO
187	HINT1	HINT1	HINT1	15162	-0.039	0.058	NO
188	FOXM1	FOXM1	FOXM1	15233	-0.04	0.057	NO
189	SAV1	SAV1	SAV1	15306	-0.041	0.055	NO
190	HNRNPH1	HNRNPH1	HNRNPH1	15377	-0.042	0.054	NO
191	GPATCH8	GPATCH8	GPATCH8	15413	-0.042	0.054	NO
192	ALG13	ALG13	ALG13	15455	-0.043	0.054	NO
193	MCM9	MCM9	MCM9	15541	-0.044	0.052	NO
194	DDX17	DDX17	DDX17	15593	-0.045	0.052	NO
195	BECN1	BECN1	BECN1	15606	-0.045	0.054	NO
196	ATP7A	ATP7A	ATP7A	15616	-0.045	0.056	NO
197	CTDSPL	CTDSPL	CTDSPL	15623	-0.045	0.058	NO
198	PFDN4	PFDN4	PFDN4	15669	-0.046	0.059	NO
199	PAN3	PAN3	PAN3	15718	-0.047	0.059	NO
200	LPP	LPP	LPP	15737	-0.047	0.061	NO
201	CUL2	CUL2	CUL2	15741	-0.047	0.063	NO
202	CCT2	CCT2	CCT2	15784	-0.048	0.064	NO
203	SLC35A1	SLC35A1	SLC35A1	15792	-0.048	0.066	NO
204	EIF2AK1	EIF2AK1	EIF2AK1	15798	-0.048	0.069	NO
205	C11orf58	C11orf58	C11orf58	15838	-0.049	0.07	NO
206	PHKB	PHKB	PHKB	15842	-0.049	0.072	NO
207	SLC25A16	SLC25A16	SLC25A16	15883	-0.05	0.073	NO
208	USO1	USO1	USO1	15904	-0.05	0.075	NO
209	FAIM3	FAIM3	FAIM3	15942	-0.051	0.076	NO
210	MORC3	MORC3	MORC3	16182	-0.056	0.066	NO
211	AADAC	AADAC	AADAC	16260	-0.058	0.065	NO
212	ALDH6A1	ALDH6A1	ALDH6A1	16264	-0.058	0.068	NO
213	SFTPA2	SFTPA2	SFTPA2	16270	-0.058	0.071	NO
214	LTBP1	LTBP1	LTBP1	17063	-0.089	0.032	NO
215	ZC3HAV1L	ZC3HAV1L	ZC3HAV1L	17101	-0.092	0.035	NO
216	LRRIQ3	LRRIQ3	LRRIQ3	17961	-0.33	0.0069	NO

Figure S31. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG PURINE METABOLISM.

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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	HP	HP	HP	345	0.64	0.036	YES
2	CAMP	CAMP	CAMP	530	0.55	0.073	YES
3	GDF5	GDF5	GDF5	594	0.52	0.12	YES
4	CA2	CA2	CA2	724	0.48	0.15	YES
5	RETN	RETN	RETN	879	0.43	0.18	YES
6	THRSP	THRSP	THRSP	888	0.43	0.22	YES
7	LUM	LUM	LUM	921	0.42	0.25	YES
8	ABCD2	ABCD2	ABCD2	1049	0.39	0.28	YES
9	G0S2	G0S2	G0S2	1303	0.35	0.29	YES
10	HSD11B1	HSD11B1	HSD11B1	1328	0.34	0.32	YES
11	GPD1	GPD1	GPD1	1344	0.34	0.35	YES
12	LCN2	LCN2	LCN2	1512	0.31	0.37	YES
13	AOC3	AOC3	AOC3	1879	0.27	0.37	YES
14	PARM1	PARM1	PARM1	1922	0.26	0.39	YES
15	NNMT	NNMT	NNMT	1994	0.26	0.41	YES
16	CA3	CA3	CA3	2111	0.24	0.42	YES
17	ME1	ME1	ME1	2220	0.23	0.44	YES
18	S100A8	S100A8	S100A8	2346	0.22	0.45	YES
19	RARRES2	RARRES2	RARRES2	2401	0.22	0.46	YES
20	LTC4S	LTC4S	LTC4S	2486	0.21	0.48	YES
21	CD1D	CD1D	CD1D	3006	0.17	0.46	NO
22	CFD	CFD	CFD	3330	0.15	0.46	NO
23	COL15A1	COL15A1	COL15A1	4025	0.11	0.43	NO
24	UNC119	UNC119	UNC119	4042	0.11	0.44	NO
25	APOC1	APOC1	APOC1	4520	0.088	0.42	NO
26	ORM2	ORM2	ORM2	4596	0.084	0.42	NO
27	CDKN2C	CDKN2C	CDKN2C	4765	0.077	0.42	NO
28	ACADL	ACADL	ACADL	4844	0.074	0.42	NO
29	MGST1	MGST1	MGST1	4935	0.071	0.42	NO
30	MGLL	MGLL	MGLL	5152	0.063	0.42	NO
31	NDUFB8	NDUFB8	NDUFB8	5380	0.056	0.41	NO
32	C9orf16	C9orf16	C9orf16	5576	0.05	0.4	NO
33	AGPAT3	AGPAT3	AGPAT3	5704	0.046	0.4	NO
34	PGM1	PGM1	PGM1	5716	0.046	0.4	NO
35	ITGA6	ITGA6	ITGA6	5757	0.045	0.4	NO
36	TP53INP2	TP53INP2	TP53INP2	5782	0.045	0.41	NO
37	SFXN1	SFXN1	SFXN1	5831	0.044	0.41	NO
38	ADIPOQ	ADIPOQ	ADIPOQ	5836	0.044	0.41	NO
39	FAH	FAH	FAH	5904	0.042	0.41	NO
40	PSAT1	PSAT1	PSAT1	6315	0.034	0.39	NO
41	IMPDH1	IMPDH1	IMPDH1	6342	0.034	0.39	NO
42	UQCR10	UQCR10	UQCR10	6370	0.033	0.39	NO
43	APOE	APOE	APOE	6386	0.033	0.4	NO
44	RBPMS	RBPMS	RBPMS	6561	0.031	0.39	NO
45	REEP6	REEP6	REEP6	6632	0.03	0.39	NO
46	MRAP	MRAP	MRAP	6655	0.029	0.39	NO
47	PPP2R5A	PPP2R5A	PPP2R5A	6886	0.026	0.38	NO
48	PLIN4	PLIN4	PLIN4	6901	0.026	0.38	NO
49	PDAP1	PDAP1	PDAP1	6980	0.025	0.38	NO
50	CIB2	CIB2	CIB2	7070	0.024	0.37	NO
51	QDPR	QDPR	QDPR	7103	0.024	0.38	NO
52	C20orf27	C20orf27	C20orf27	7194	0.023	0.37	NO
53	NDUFC1	NDUFC1	NDUFC1	7305	0.022	0.37	NO
54	CD151	CD151	CD151	7427	0.021	0.36	NO
55	CCRN4L	CCRN4L	CCRN4L	7436	0.02	0.36	NO
56	MCAM	MCAM	MCAM	7442	0.02	0.36	NO
57	PEMT	PEMT	PEMT	7543	0.02	0.36	NO
58	DHCR7	DHCR7	DHCR7	7561	0.019	0.36	NO
59	MPDU1	MPDU1	MPDU1	7651	0.018	0.36	NO
60	NDUFB7	NDUFB7	NDUFB7	7672	0.018	0.36	NO
61	COX5B	COX5B	COX5B	7743	0.018	0.36	NO
62	SLC25A1	SLC25A1	SLC25A1	7825	0.017	0.35	NO
63	ACAA2	ACAA2	ACAA2	7844	0.017	0.35	NO
64	PSEN2	PSEN2	PSEN2	7868	0.016	0.35	NO
65	EHD1	EHD1	EHD1	7944	0.016	0.35	NO
66	UCK1	UCK1	UCK1	8131	0.014	0.34	NO
67	NDUFS3	NDUFS3	NDUFS3	8137	0.014	0.34	NO
68	DLST	DLST	DLST	8156	0.014	0.34	NO
69	DGAT1	DGAT1	DGAT1	8169	0.014	0.34	NO
70	GSR	GSR	GSR	8354	0.012	0.34	NO
71	UQCRC1	UQCRC1	UQCRC1	8532	0.011	0.33	NO
72	FASN	FASN	FASN	8547	0.011	0.33	NO
73	DDT	DDT	DDT	8578	0.011	0.32	NO
74	RTN3	RTN3	RTN3	8646	0.01	0.32	NO
75	UQCRQ	UQCRQ	UQCRQ	8711	0.0097	0.32	NO
76	SCARB1	SCARB1	SCARB1	8731	0.0095	0.32	NO
77	NDUFB9	NDUFB9	NDUFB9	8770	0.0092	0.32	NO
78	ALAS1	ALAS1	ALAS1	8842	0.0087	0.32	NO
79	PNPLA2	PNPLA2	PNPLA2	9023	0.0073	0.3	NO
80	TSPAN12	TSPAN12	TSPAN12	9088	0.0069	0.3	NO
81	ATP5O	ATP5O	ATP5O	9233	0.0058	0.3	NO
82	C9orf72	C9orf72	C9orf72	9274	0.0056	0.29	NO
83	CIDEC	CIDEC	CIDEC	9292	0.0054	0.29	NO
84	CYB5B	CYB5B	CYB5B	9356	0.005	0.29	NO
85	COX7A2	COX7A2	COX7A2	9501	0.0039	0.28	NO
86	MRPL51	MRPL51	MRPL51	9533	0.0037	0.28	NO
87	CBR1	CBR1	CBR1	9594	0.0034	0.28	NO
88	CYB5A	CYB5A	CYB5A	9669	0.0028	0.27	NO
89	ACYP2	ACYP2	ACYP2	9713	0.0025	0.27	NO
90	C6orf136	C6orf136	C6orf136	9745	0.0022	0.27	NO
91	REEP5	REEP5	REEP5	9810	0.0018	0.27	NO
92	S100A1	S100A1	S100A1	9833	0.0017	0.26	NO
93	PEX19	PEX19	PEX19	9856	0.0015	0.26	NO
94	NDUFA9	NDUFA9	NDUFA9	9962	0.00072	0.26	NO
95	MAP4K4	MAP4K4	MAP4K4	9986	0.00058	0.26	NO
96	PXMP2	PXMP2	PXMP2	10025	0.00026	0.26	NO
97	DNAJC15	DNAJC15	DNAJC15	10066	-0.000031	0.25	NO
98	ALAD	ALAD	ALAD	10178	-0.00072	0.25	NO
99	ATP5D	ATP5D	ATP5D	10218	-0.00097	0.24	NO
100	SDHA	SDHA	SDHA	10293	-0.0015	0.24	NO
101	PCYOX1	PCYOX1	PCYOX1	10310	-0.0016	0.24	NO
102	ETFDH	ETFDH	ETFDH	10360	-0.0019	0.24	NO
103	CS	CS	CS	10631	-0.0037	0.22	NO
104	SLC19A1	SLC19A1	SLC19A1	10682	-0.0041	0.22	NO
105	OGDH	OGDH	OGDH	10863	-0.0052	0.21	NO
106	LONP2	LONP2	LONP2	10872	-0.0053	0.21	NO
107	DECR1	DECR1	DECR1	10925	-0.0056	0.21	NO
108	QKI	QKI	QKI	11203	-0.0077	0.19	NO
109	TUFM	TUFM	TUFM	11230	-0.0079	0.19	NO
110	GSTZ1	GSTZ1	GSTZ1	11340	-0.0085	0.19	NO
111	NDUFB3	NDUFB3	NDUFB3	11358	-0.0086	0.19	NO
112	TAB3	TAB3	TAB3	11367	-0.0087	0.19	NO
113	ACADS	ACADS	ACADS	11442	-0.0092	0.18	NO
114	PDHB	PDHB	PDHB	11562	-0.01	0.18	NO
115	NDUFB6	NDUFB6	NDUFB6	11595	-0.01	0.18	NO
116	SDHB	SDHB	SDHB	11685	-0.011	0.17	NO
117	ISCA1	ISCA1	ISCA1	11765	-0.011	0.17	NO
118	ACAD9	ACAD9	ACAD9	11859	-0.012	0.16	NO
119	UQCRB	UQCRB	UQCRB	11871	-0.012	0.17	NO
120	SCD	SCD	SCD	11873	-0.012	0.17	NO
121	HIPK2	HIPK2	HIPK2	11953	-0.012	0.16	NO
122	DHRS7B	DHRS7B	DHRS7B	11962	-0.013	0.16	NO
123	RAB3D	RAB3D	RAB3D	11965	-0.013	0.16	NO
124	RETSAT	RETSAT	RETSAT	12040	-0.013	0.16	NO
125	LDHB	LDHB	LDHB	12057	-0.013	0.16	NO
126	SETD8	SETD8	SETD8	12088	-0.013	0.16	NO
127	SDHC	SDHC	SDHC	12146	-0.014	0.16	NO
128	SAMM50	SAMM50	SAMM50	12671	-0.017	0.13	NO
129	RNF11	RNF11	RNF11	12765	-0.018	0.13	NO
130	HSD17B4	HSD17B4	HSD17B4	12783	-0.018	0.13	NO
131	CMBL	CMBL	CMBL	12964	-0.02	0.12	NO
132	BCAT2	BCAT2	BCAT2	12986	-0.02	0.12	NO
133	LPL	LPL	LPL	13077	-0.02	0.12	NO
134	COX7B	COX7B	COX7B	13078	-0.02	0.12	NO
135	HIBCH	HIBCH	HIBCH	13205	-0.021	0.12	NO
136	SGCD	SGCD	SGCD	13228	-0.021	0.12	NO
137	CCNG2	CCNG2	CCNG2	13266	-0.022	0.12	NO
138	CHPT1	CHPT1	CHPT1	13467	-0.023	0.11	NO
139	SUCLG1	SUCLG1	SUCLG1	13484	-0.023	0.11	NO
140	NDUFA5	NDUFA5	NDUFA5	13584	-0.024	0.1	NO
141	SLC2A4	SLC2A4	SLC2A4	13598	-0.024	0.1	NO
142	NR1H3	NR1H3	NR1H3	13640	-0.024	0.1	NO
143	TKT	TKT	TKT	13642	-0.024	0.11	NO
144	SDPR	SDPR	SDPR	13677	-0.025	0.11	NO
145	TANK	TANK	TANK	13695	-0.025	0.11	NO
146	NDUFS1	NDUFS1	NDUFS1	13758	-0.026	0.11	NO
147	FAM49B	FAM49B	FAM49B	13904	-0.027	0.1	NO
148	KAT2B	KAT2B	KAT2B	13946	-0.027	0.1	NO
149	DLD	DLD	DLD	13960	-0.027	0.1	NO
150	BNIP3	BNIP3	BNIP3	14037	-0.028	0.1	NO
151	UQCRC2	UQCRC2	UQCRC2	14082	-0.028	0.1	NO
152	COQ5	COQ5	COQ5	14123	-0.028	0.1	NO
153	HSD17B12	HSD17B12	HSD17B12	14303	-0.03	0.094	NO
154	FXN	FXN	FXN	14485	-0.032	0.086	NO
155	CHCHD3	CHCHD3	CHCHD3	14492	-0.032	0.089	NO
156	SLC25A5	SLC25A5	SLC25A5	14599	-0.033	0.086	NO
157	DLAT	DLAT	DLAT	14707	-0.034	0.083	NO
158	SCP2	SCP2	SCP2	14723	-0.034	0.085	NO
159	TST	TST	TST	14747	-0.034	0.087	NO
160	NDUFB5	NDUFB5	NDUFB5	14832	-0.036	0.085	NO
161	HIBADH	HIBADH	HIBADH	15027	-0.037	0.077	NO
162	PLA2G6	PLA2G6	PLA2G6	15059	-0.038	0.079	NO
163	HADHB	HADHB	HADHB	15085	-0.038	0.081	NO
164	ISOC1	ISOC1	ISOC1	15156	-0.039	0.08	NO
165	HADH	HADH	HADH	15291	-0.041	0.076	NO
166	MCCC1	MCCC1	MCCC1	15313	-0.041	0.079	NO
167	ARL4A	ARL4A	ARL4A	15415	-0.042	0.077	NO
168	PON2	PON2	PON2	15421	-0.042	0.08	NO
169	PHTF2	PHTF2	PHTF2	15545	-0.044	0.077	NO
170	GBE1	GBE1	GBE1	15549	-0.044	0.081	NO
171	ABCA1	ABCA1	ABCA1	15573	-0.045	0.083	NO
172	FAM132A	FAM132A	FAM132A	15688	-0.047	0.081	NO
173	DBT	DBT	DBT	16016	-0.052	0.067	NO
174	LIAS	LIAS	LIAS	16131	-0.055	0.065	NO
175	ADCY6	ADCY6	ADCY6	16150	-0.055	0.069	NO
176	AQP7	AQP7	AQP7	16565	-0.066	0.052	NO
177	BCKDHB	BCKDHB	BCKDHB	16566	-0.066	0.058	NO
178	GCSH	GCSH	GCSH	16587	-0.067	0.062	NO
179	CAT	CAT	CAT	16998	-0.085	0.047	NO
180	SLC25A10	SLC25A10	SLC25A10	17621	-0.16	0.026	NO

Figure S33. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

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

Table 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	NTRK1	NTRK1	NTRK1	934	0.42	0.16	YES
2	NGF	NGF	NGF	1095	0.38	0.35	YES
3	SHC3	SHC3	SHC3	1314	0.35	0.52	YES
4	RIT2	RIT2	RIT2	1872	0.27	0.62	YES
5	MAPK3	MAPK3	MAPK3	5934	0.042	0.42	NO
6	MAPK11	MAPK11	MAPK11	6173	0.037	0.43	NO
7	SHC1	SHC1	SHC1	6374	0.033	0.43	NO
8	YWHAB	YWHAB	YWHAB	7174	0.023	0.4	NO
9	HRAS	HRAS	HRAS	7301	0.022	0.4	NO
10	SRC	SRC	SRC	7673	0.018	0.39	NO
11	MAPK13	MAPK13	MAPK13	7751	0.018	0.4	NO
12	MAPKAPK2	MAPKAPK2	MAPKAPK2	7872	0.016	0.4	NO
13	PLCG1	PLCG1	PLCG1	8052	0.015	0.4	NO
14	RALB	RALB	RALB	9065	0.0071	0.34	NO
15	MAPKAPK3	MAPKAPK3	MAPKAPK3	9336	0.0052	0.33	NO
16	MAPK12	MAPK12	MAPK12	9570	0.0035	0.32	NO
17	RALGDS	RALGDS	RALGDS	9623	0.0031	0.32	NO
18	GRB2	GRB2	GRB2	9778	0.0021	0.31	NO
19	RIT1	RIT1	RIT1	9820	0.0018	0.31	NO
20	RAPGEF1	RAPGEF1	RAPGEF1	10436	-0.0024	0.28	NO
21	MAP2K2	MAP2K2	MAP2K2	10520	-0.003	0.28	NO
22	SHC2	SHC2	SHC2	10760	-0.0045	0.26	NO
23	KIDINS220	KIDINS220	KIDINS220	10898	-0.0055	0.26	NO
24	MAPK1	MAPK1	MAPK1	11428	-0.0091	0.24	NO
25	MAP2K1	MAP2K1	MAP2K1	11622	-0.01	0.23	NO
26	SOS1	SOS1	SOS1	11772	-0.011	0.23	NO
27	RAF1	RAF1	RAF1	12375	-0.015	0.2	NO
28	KRAS	KRAS	KRAS	12551	-0.016	0.2	NO
29	RALA	RALA	RALA	12606	-0.017	0.21	NO
30	BRAF	BRAF	BRAF	13058	-0.02	0.19	NO
31	CRK	CRK	CRK	13231	-0.022	0.19	NO
32	RAP1A	RAP1A	RAP1A	13477	-0.023	0.19	NO
33	NRAS	NRAS	NRAS	13674	-0.025	0.19	NO
34	CDK1	CDK1	CDK1	14228	-0.029	0.18	NO
35	MAPK14	MAPK14	MAPK14	14720	-0.034	0.17	NO
36	FRS2	FRS2	FRS2	14956	-0.037	0.17	NO

Figure S35. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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	WIF1	WIF1	WIF1	34	0.98	0.54	YES
2	WNT1	WNT1	WNT1	1379	0.33	0.65	YES
3	LEF1	LEF1	LEF1	3798	0.12	0.59	NO
4	TLE1	TLE1	TLE1	7270	0.022	0.41	NO
5	MAP3K7	MAP3K7	MAP3K7	7632	0.019	0.4	NO
6	DVL1	DVL1	DVL1	8023	0.015	0.38	NO
7	TAB1	TAB1	TAB1	8469	0.012	0.36	NO
8	PPARD	PPARD	PPARD	8658	0.01	0.36	NO
9	CTBP1	CTBP1	CTBP1	9069	0.0071	0.34	NO
10	NLK	NLK	NLK	9288	0.0055	0.33	NO
11	BTRC	BTRC	BTRC	9400	0.0047	0.33	NO
12	CCND1	CCND1	CCND1	9425	0.0045	0.33	NO
13	CSNK2A1	CSNK2A1	CSNK2A1	9554	0.0036	0.32	NO
14	FRAT1	FRAT1	FRAT1	10584	-0.0034	0.27	NO
15	HDAC1	HDAC1	HDAC1	10590	-0.0035	0.27	NO
16	CREBBP	CREBBP	CREBBP	10865	-0.0052	0.26	NO
17	FZD1	FZD1	FZD1	11028	-0.0064	0.25	NO
18	AXIN1	AXIN1	AXIN1	11339	-0.0085	0.24	NO
19	PPP2CA	PPP2CA	PPP2CA	11696	-0.011	0.23	NO
20	GSK3B	GSK3B	GSK3B	11809	-0.012	0.23	NO
21	CSNK1D	CSNK1D	CSNK1D	12564	-0.016	0.2	NO
22	CSNK1A1	CSNK1A1	CSNK1A1	13349	-0.022	0.16	NO
23	APC	APC	APC	13691	-0.025	0.16	NO
24	SMAD4	SMAD4	SMAD4	14573	-0.033	0.13	NO
25	MYC	MYC	MYC	16184	-0.056	0.07	NO
26	CTNNB1	CTNNB1	CTNNB1	16446	-0.063	0.091	NO

Figure S37. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

Table S20. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SYT1	SYT1	SYT1	37	0.97	0.21	YES
2	CCK	CCK	CCK	75	0.88	0.39	YES
3	GABRA1	GABRA1	GABRA1	752	0.47	0.46	YES
4	KCNMA1	KCNMA1	KCNMA1	1044	0.39	0.53	YES
5	PTGDS	PTGDS	PTGDS	1241	0.36	0.59	YES
6	NPTX1	NPTX1	NPTX1	2208	0.23	0.59	YES
7	ATP1B2	ATP1B2	ATP1B2	2338	0.22	0.63	YES
8	TUBB3	TUBB3	TUBB3	3917	0.12	0.57	NO
9	MAG	MAG	MAG	4857	0.073	0.53	NO
10	MGLL	MGLL	MGLL	5152	0.063	0.53	NO
11	CPLX1	CPLX1	CPLX1	5490	0.052	0.52	NO
12	EEF1G	EEF1G	EEF1G	6023	0.04	0.5	NO
13	NME1	NME1	NME1	6332	0.034	0.49	NO
14	TUBB4B	TUBB4B	TUBB4B	6344	0.034	0.5	NO
15	APOE	APOE	APOE	6386	0.033	0.5	NO
16	CDK16	CDK16	CDK16	6846	0.027	0.48	NO
17	DNM1	DNM1	DNM1	6911	0.026	0.48	NO
18	NSF	NSF	NSF	7027	0.025	0.48	NO
19	OAZ2	OAZ2	OAZ2	7221	0.023	0.48	NO
20	PLD3	PLD3	PLD3	7302	0.022	0.48	NO
21	ATP6AP1	ATP6AP1	ATP6AP1	7494	0.02	0.47	NO
22	PFN1	PFN1	PFN1	7674	0.018	0.46	NO
23	DYNC1H1	DYNC1H1	DYNC1H1	7801	0.017	0.46	NO
24	DCTN1	DCTN1	DCTN1	8136	0.014	0.45	NO
25	AP2M1	AP2M1	AP2M1	8324	0.013	0.44	NO
26	DAD1	DAD1	DAD1	8356	0.012	0.44	NO
27	EIF4G3	EIF4G3	EIF4G3	8482	0.012	0.44	NO
28	ATP6V1E1	ATP6V1E1	ATP6V1E1	9021	0.0073	0.41	NO
29	RAB2A	RAB2A	RAB2A	9720	0.0024	0.37	NO
30	NCL	NCL	NCL	10179	-0.00073	0.34	NO
31	DNAJB11	DNAJB11	DNAJB11	10454	-0.0026	0.33	NO
32	CS	CS	CS	10631	-0.0037	0.32	NO
33	GORASP2	GORASP2	GORASP2	10638	-0.0038	0.32	NO
34	SEPT7	SEPT7	SEPT7	10908	-0.0055	0.31	NO
35	ATP2A2	ATP2A2	ATP2A2	10997	-0.0061	0.3	NO
36	PPP2CA	PPP2CA	PPP2CA	11696	-0.011	0.27	NO
37	SKP1	SKP1	SKP1	11824	-0.012	0.26	NO
38	CALM2	CALM2	CALM2	11981	-0.013	0.26	NO
39	RAB14	RAB14	RAB14	11987	-0.013	0.26	NO
40	PGK1	PGK1	PGK1	12049	-0.013	0.26	NO
41	ATP1A1	ATP1A1	ATP1A1	12341	-0.015	0.24	NO
42	ACO2	ACO2	ACO2	12625	-0.017	0.23	NO
43	ARPP19	ARPP19	ARPP19	12718	-0.018	0.23	NO
44	CSDE1	CSDE1	CSDE1	12824	-0.018	0.23	NO
45	HSP90AB1	HSP90AB1	HSP90AB1	12929	-0.019	0.23	NO
46	CSNK1A1	CSNK1A1	CSNK1A1	13349	-0.022	0.21	NO
47	PPP1CB	PPP1CB	PPP1CB	13418	-0.023	0.21	NO
48	EEF2	EEF2	EEF2	13778	-0.026	0.2	NO
49	PRKACB	PRKACB	PRKACB	13822	-0.026	0.2	NO
50	PPM1A	PPM1A	PPM1A	14100	-0.028	0.19	NO
51	ACTR3	ACTR3	ACTR3	14248	-0.03	0.19	NO
52	DDX3X	DDX3X	DDX3X	14859	-0.036	0.16	NO
53	SRSF5	SRSF5	SRSF5	14942	-0.037	0.17	NO
54	TIA1	TIA1	TIA1	15300	-0.041	0.15	NO

Figure S39. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG ARGININE AND PROLINE METABOLISM.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus3 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG RIBOSOME	87	genes.ES.table	0.59	1.4	0.22	1	1	0.78	0.34	0.52	1	0.78
PID P53 REGULATION PATHWAY	59	genes.ES.table	0.41	1.9	0.027	1	0.57	0.34	0.27	0.25	0.25	0.23
REACTOME TRANSLATION	145	genes.ES.table	0.49	1.4	0.18	1	1	0.58	0.34	0.39	1	0.82
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	108	genes.ES.table	0.54	1.4	0.17	1	1	0.67	0.34	0.44	1	0.78
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S	56	genes.ES.table	0.53	1.4	0.19	1	1	0.8	0.39	0.49	1	0.78
REACTOME GENERIC TRANSCRIPTION PATHWAY	333	genes.ES.table	0.53	1.8	0.0083	1	0.84	0.5	0.23	0.39	0.62	0.37
REACTOME PEPTIDE CHAIN ELONGATION	85	genes.ES.table	0.61	1.4	0.19	1	1	0.8	0.34	0.53	1	0.79
REACTOME MRNA PROCESSING	152	genes.ES.table	0.25	1.4	0.14	1	1	1	0.75	0.25	1	0.8
REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION	105	genes.ES.table	0.57	1.4	0.17	1	1	0.71	0.34	0.48	1	0.79
REACTOME INFLUENZA LIFE CYCLE	135	genes.ES.table	0.44	1.4	0.22	1	1	0.56	0.34	0.38	1	0.78

genes ES table in pathway: KEGG RIBOSOME

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	TP53AIP1	TP53AIP1	TP53AIP1	134	0.45	0.14	YES
2	KAT2B	KAT2B	KAT2B	1154	0.19	0.14	YES
3	ATR	ATR	ATR	1468	0.16	0.18	YES
4	PPP1R13L	PPP1R13L	PPP1R13L	1916	0.14	0.2	YES
5	PRKCD	PRKCD	PRKCD	1961	0.13	0.24	YES
6	CDK2	CDK2	CDK2	2672	0.1	0.23	YES
7	RPL5	RPL5	RPL5	2860	0.096	0.25	YES
8	UBE2D1	UBE2D1	UBE2D1	2904	0.094	0.28	YES
9	CCNG1	CCNG1	CCNG1	3305	0.082	0.28	YES
10	RCHY1	RCHY1	RCHY1	3585	0.074	0.29	YES
11	SKP2	SKP2	SKP2	3873	0.068	0.3	YES
12	MAPK8	MAPK8	MAPK8	4064	0.064	0.31	YES
13	DAXX	DAXX	DAXX	4197	0.061	0.32	YES
14	RPL11	RPL11	RPL11	4262	0.06	0.34	YES
15	SMYD2	SMYD2	SMYD2	4416	0.056	0.35	YES
16	RPL23	RPL23	RPL23	4461	0.056	0.36	YES
17	GSK3B	GSK3B	GSK3B	4494	0.055	0.38	YES
18	CSNK1G3	CSNK1G3	CSNK1G3	4572	0.054	0.39	YES
19	HIPK2	HIPK2	HIPK2	4666	0.052	0.4	YES
20	RASSF1	RASSF1	RASSF1	4834	0.049	0.41	YES
21	MDM4	MDM4	MDM4	5386	0.041	0.39	NO
22	RFWD2	RFWD2	RFWD2	5418	0.04	0.4	NO
23	FBXO11	FBXO11	FBXO11	6017	0.032	0.38	NO
24	MAPK9	MAPK9	MAPK9	6260	0.029	0.38	NO
25	MAPK14	MAPK14	MAPK14	6291	0.028	0.38	NO
26	CSNK1A1	CSNK1A1	CSNK1A1	7058	0.019	0.35	NO
27	YY1	YY1	YY1	7166	0.018	0.35	NO
28	CSNK1D	CSNK1D	CSNK1D	7282	0.016	0.34	NO
29	TTC5	TTC5	TTC5	7807	0.01	0.32	NO
30	KAT8	KAT8	KAT8	8008	0.0078	0.31	NO
31	PPP2CA	PPP2CA	PPP2CA	8062	0.0073	0.31	NO
32	PPM1D	PPM1D	PPM1D	8196	0.0059	0.3	NO
33	TRIM28	TRIM28	TRIM28	8720	-0.00025	0.28	NO
34	CSNK1G2	CSNK1G2	CSNK1G2	9131	-0.0051	0.26	NO
35	PIN1	PIN1	PIN1	9138	-0.0051	0.26	NO
36	HUWE1	HUWE1	HUWE1	9278	-0.0069	0.25	NO
37	CSE1L	CSE1L	CSE1L	9507	-0.0096	0.24	NO
38	CSNK1G1	CSNK1G1	CSNK1G1	9526	-0.0097	0.24	NO
39	SETD8	SETD8	SETD8	9611	-0.011	0.24	NO
40	EP300	EP300	EP300	9615	-0.011	0.24	NO
41	PRMT5	PRMT5	PRMT5	9665	-0.012	0.25	NO
42	CREBBP	CREBBP	CREBBP	9738	-0.012	0.25	NO
43	ATM	ATM	ATM	10055	-0.016	0.23	NO
44	USP7	USP7	USP7	10260	-0.018	0.23	NO
45	CHEK1	CHEK1	CHEK1	10375	-0.02	0.23	NO
46	E4F1	E4F1	E4F1	10460	-0.021	0.23	NO
47	KAT5	KAT5	KAT5	10525	-0.022	0.23	NO
48	AKT1	AKT1	AKT1	10567	-0.022	0.24	NO
49	CCNA2	CCNA2	CCNA2	10990	-0.028	0.22	NO
50	ABL1	ABL1	ABL1	11633	-0.036	0.2	NO
51	NEDD8	NEDD8	NEDD8	11708	-0.037	0.21	NO
52	CSNK1E	CSNK1E	CSNK1E	11789	-0.039	0.22	NO
53	DYRK2	DYRK2	DYRK2	12261	-0.045	0.2	NO
54	TP53	TP53	TP53	12471	-0.049	0.21	NO
55	SETD7	SETD7	SETD7	12621	-0.052	0.22	NO
56	CDKN2A	CDKN2A	CDKN2A	12842	-0.055	0.22	NO
57	MDM2	MDM2	MDM2	13289	-0.064	0.22	NO
58	CHEK2	CHEK2	CHEK2	13622	-0.072	0.22	NO
59	PPP2R4	PPP2R4	PPP2R4	13796	-0.076	0.24	NO

Figure S41. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG RIBOSOME.

Figure S42. 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: PID P53 REGULATION PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ZNF492	ZNF492	ZNF492	6	0.78	0.022	YES
2	ZNF415	ZNF415	ZNF415	39	0.61	0.038	YES
3	ZNF454	ZNF454	ZNF454	48	0.58	0.055	YES
4	ZNF382	ZNF382	ZNF382	59	0.55	0.07	YES
5	ZNF98	ZNF98	ZNF98	80	0.52	0.084	YES
6	RORC	RORC	RORC	95	0.49	0.097	YES
7	NR6A1	NR6A1	NR6A1	112	0.48	0.11	YES
8	ZIM2	ZIM2	ZIM2	120	0.46	0.12	YES
9	ZNF208	ZNF208	ZNF208	149	0.44	0.13	YES
10	ESRRG	ESRRG	ESRRG	183	0.42	0.14	YES
11	ZNF560	ZNF560	ZNF560	209	0.4	0.16	YES
12	ZNF154	ZNF154	ZNF154	336	0.35	0.16	YES
13	ZNF285	ZNF285	ZNF285	360	0.34	0.17	YES
14	ZNF215	ZNF215	ZNF215	393	0.34	0.17	YES
15	ZNF471	ZNF471	ZNF471	401	0.33	0.18	YES
16	PPARG	PPARG	PPARG	423	0.32	0.19	YES
17	ZFP2	ZFP2	ZFP2	461	0.32	0.2	YES
18	ZNF433	ZNF433	ZNF433	463	0.32	0.21	YES
19	ZNF157	ZNF157	ZNF157	475	0.31	0.22	YES
20	NR5A1	NR5A1	NR5A1	513	0.3	0.22	YES
21	NPPA	NPPA	NPPA	518	0.3	0.23	YES
22	ZNF214	ZNF214	ZNF214	547	0.29	0.24	YES
23	ZFP37	ZFP37	ZFP37	558	0.29	0.25	YES
24	ZNF610	ZNF610	ZNF610	661	0.27	0.25	YES
25	ZNF439	ZNF439	ZNF439	773	0.24	0.25	YES
26	ZNF114	ZNF114	ZNF114	812	0.24	0.25	YES
27	ZNF334	ZNF334	ZNF334	855	0.23	0.26	YES
28	ZNF354C	ZNF354C	ZNF354C	873	0.23	0.26	YES
29	ZIM3	ZIM3	ZIM3	895	0.22	0.27	YES
30	ZNF311	ZNF311	ZNF311	922	0.22	0.27	YES
31	ZNF544	ZNF544	ZNF544	931	0.22	0.28	YES
32	ZNF577	ZNF577	ZNF577	964	0.21	0.28	YES
33	ZIK1	ZIK1	ZIK1	982	0.21	0.29	YES
34	ZNF197	ZNF197	ZNF197	983	0.21	0.3	YES
35	ZNF287	ZNF287	ZNF287	1101	0.2	0.29	YES
36	KAT2B	KAT2B	KAT2B	1154	0.19	0.3	YES
37	ZNF620	ZNF620	ZNF620	1162	0.19	0.3	YES
38	ZNF23	ZNF23	ZNF23	1168	0.19	0.31	YES
39	ZNF300	ZNF300	ZNF300	1169	0.19	0.31	YES
40	ZNF619	ZNF619	ZNF619	1187	0.19	0.32	YES
41	ZNF221	ZNF221	ZNF221	1277	0.18	0.32	YES
42	ZNF621	ZNF621	ZNF621	1312	0.18	0.32	YES
43	ZNF599	ZNF599	ZNF599	1335	0.18	0.32	YES
44	ZNF773	ZNF773	ZNF773	1369	0.17	0.33	YES
45	ZNF33B	ZNF33B	ZNF33B	1505	0.16	0.32	YES
46	ZNF649	ZNF649	ZNF649	1506	0.16	0.33	YES
47	ZNF540	ZNF540	ZNF540	1518	0.16	0.33	YES
48	ZNF418	ZNF418	ZNF418	1527	0.16	0.34	YES
49	ZNF442	ZNF442	ZNF442	1533	0.16	0.34	YES
50	ZNF493	ZNF493	ZNF493	1544	0.16	0.35	YES
51	ZNF354B	ZNF354B	ZNF354B	1548	0.16	0.35	YES
52	ZNF607	ZNF607	ZNF607	1551	0.16	0.36	YES
53	NR1D2	NR1D2	NR1D2	1553	0.16	0.36	YES
54	ZNF519	ZNF519	ZNF519	1621	0.15	0.36	YES
55	ZNF419	ZNF419	ZNF419	1626	0.15	0.36	YES
56	ZNF347	ZNF347	ZNF347	1689	0.15	0.37	YES
57	ZNF551	ZNF551	ZNF551	1780	0.14	0.36	YES
58	ZNF320	ZNF320	ZNF320	1870	0.14	0.36	YES
59	NR0B2	NR0B2	NR0B2	1872	0.14	0.37	YES
60	ZNF184	ZNF184	ZNF184	1900	0.14	0.37	YES
61	ZNF614	ZNF614	ZNF614	1910	0.14	0.37	YES
62	ZNF528	ZNF528	ZNF528	1917	0.14	0.38	YES
63	ZNF570	ZNF570	ZNF570	1970	0.13	0.38	YES
64	ZNF286A	ZNF286A	ZNF286A	1975	0.13	0.38	YES
65	ZKSCAN3	ZKSCAN3	ZKSCAN3	1992	0.13	0.38	YES
66	ZNF354A	ZNF354A	ZNF354A	2070	0.13	0.38	YES
67	ZNF559	ZNF559	ZNF559	2081	0.13	0.39	YES
68	ZNF615	ZNF615	ZNF615	2096	0.13	0.39	YES
69	ZNF627	ZNF627	ZNF627	2126	0.12	0.39	YES
70	ZNF564	ZNF564	ZNF564	2155	0.12	0.39	YES
71	ZKSCAN4	ZKSCAN4	ZKSCAN4	2180	0.12	0.4	YES
72	ZNF569	ZNF569	ZNF569	2208	0.12	0.4	YES
73	ZNF445	ZNF445	ZNF445	2214	0.12	0.4	YES
74	ZNF211	ZNF211	ZNF211	2221	0.12	0.4	YES
75	ZNF529	ZNF529	ZNF529	2235	0.12	0.41	YES
76	ZNF443	ZNF443	ZNF443	2248	0.12	0.41	YES
77	ZNF441	ZNF441	ZNF441	2262	0.12	0.41	YES
78	ZNF10	ZNF10	ZNF10	2269	0.12	0.42	YES
79	ZNF235	ZNF235	ZNF235	2296	0.12	0.42	YES
80	ZNF440	ZNF440	ZNF440	2298	0.12	0.42	YES
81	ZFP28	ZFP28	ZFP28	2321	0.12	0.42	YES
82	ZNF30	ZNF30	ZNF30	2350	0.12	0.42	YES
83	ZNF616	ZNF616	ZNF616	2359	0.11	0.43	YES
84	ZNF583	ZNF583	ZNF583	2401	0.11	0.43	YES
85	ZNF558	ZNF558	ZNF558	2421	0.11	0.43	YES
86	ZNF223	ZNF223	ZNF223	2458	0.11	0.43	YES
87	ZNF555	ZNF555	ZNF555	2463	0.11	0.44	YES
88	ZNF160	ZNF160	ZNF160	2470	0.11	0.44	YES
89	ZNF514	ZNF514	ZNF514	2486	0.11	0.44	YES
90	ZNF613	ZNF613	ZNF613	2512	0.11	0.44	YES
91	ZNF530	ZNF530	ZNF530	2513	0.11	0.44	YES
92	ZNF14	ZNF14	ZNF14	2533	0.11	0.45	YES
93	ZNF606	ZNF606	ZNF606	2563	0.11	0.45	YES
94	ZNF548	ZNF548	ZNF548	2564	0.11	0.45	YES
95	ZNF155	ZNF155	ZNF155	2577	0.11	0.45	YES
96	ZNF600	ZNF600	ZNF600	2620	0.1	0.46	YES
97	RORA	RORA	RORA	2651	0.1	0.46	YES
98	ZNF563	ZNF563	ZNF563	2657	0.1	0.46	YES
99	MED20	MED20	MED20	2689	0.1	0.46	YES
100	ZNF20	ZNF20	ZNF20	2712	0.1	0.46	YES
101	ZNF552	ZNF552	ZNF552	2718	0.1	0.46	YES
102	SKIL	SKIL	SKIL	2789	0.098	0.46	YES
103	ZNF658	ZNF658	ZNF658	2805	0.098	0.46	YES
104	ZNF304	ZNF304	ZNF304	2850	0.096	0.46	YES
105	ZNF605	ZNF605	ZNF605	2865	0.096	0.47	YES
106	ZNF587	ZNF587	ZNF587	2878	0.095	0.47	YES
107	ZNF426	ZNF426	ZNF426	2889	0.095	0.47	YES
108	UBE2D1	UBE2D1	UBE2D1	2904	0.094	0.47	YES
109	NR3C2	NR3C2	NR3C2	2914	0.094	0.48	YES
110	ZNF169	ZNF169	ZNF169	2930	0.093	0.48	YES
111	ZNF567	ZNF567	ZNF567	2934	0.093	0.48	YES
112	ZNF611	ZNF611	ZNF611	2939	0.093	0.48	YES
113	ZNF625	ZNF625	ZNF625	2954	0.093	0.48	YES
114	ZNF19	ZNF19	ZNF19	2980	0.092	0.49	YES
115	ZNF350	ZNF350	ZNF350	2988	0.092	0.49	YES
116	ZNF431	ZNF431	ZNF431	3001	0.091	0.49	YES
117	ZNF141	ZNF141	ZNF141	3054	0.09	0.49	YES
118	ZNF582	ZNF582	ZNF582	3057	0.09	0.49	YES
119	NR4A3	NR4A3	NR4A3	3108	0.088	0.49	YES
120	ZNF230	ZNF230	ZNF230	3114	0.088	0.49	YES
121	ZNF571	ZNF571	ZNF571	3116	0.088	0.5	YES
122	ZNF585A	ZNF585A	ZNF585A	3171	0.086	0.5	YES
123	ZNF543	ZNF543	ZNF543	3176	0.086	0.5	YES
124	ZNF506	ZNF506	ZNF506	3206	0.085	0.5	YES
125	ZNF561	ZNF561	ZNF561	3257	0.084	0.5	YES
126	RXRB	RXRB	RXRB	3306	0.082	0.5	YES
127	ZNF589	ZNF589	ZNF589	3318	0.082	0.5	YES
128	ZNF425	ZNF425	ZNF425	3339	0.081	0.5	YES
129	NR3C1	NR3C1	NR3C1	3340	0.081	0.5	YES
130	ZNF274	ZNF274	ZNF274	3366	0.08	0.5	YES
131	ZNF254	ZNF254	ZNF254	3442	0.078	0.5	YES
132	ZNF224	ZNF224	ZNF224	3465	0.078	0.5	YES
133	ZFP90	ZFP90	ZFP90	3503	0.077	0.5	YES
134	ZNF28	ZNF28	ZNF28	3527	0.076	0.5	YES
135	ZNF26	ZNF26	ZNF26	3539	0.076	0.51	YES
136	ZNF383	ZNF383	ZNF383	3553	0.075	0.51	YES
137	ZNF547	ZNF547	ZNF547	3579	0.075	0.51	YES
138	NR1I2	NR1I2	NR1I2	3597	0.074	0.51	YES
139	SMURF2	SMURF2	SMURF2	3614	0.074	0.51	YES
140	ZNF175	ZNF175	ZNF175	3668	0.072	0.51	YES
141	ZNF490	ZNF490	ZNF490	3683	0.072	0.51	YES
142	ZNF432	ZNF432	ZNF432	3697	0.072	0.51	YES
143	ZNF416	ZNF416	ZNF416	3706	0.072	0.51	YES
144	ZNF655	ZNF655	ZNF655	3752	0.071	0.51	YES
145	ZNF331	ZNF331	ZNF331	3778	0.07	0.51	YES
146	ZNF202	ZNF202	ZNF202	3784	0.07	0.52	YES
147	ZNF337	ZNF337	ZNF337	3802	0.07	0.52	YES
148	ZNF266	ZNF266	ZNF266	3838	0.069	0.52	YES
149	ZNF485	ZNF485	ZNF485	3855	0.068	0.52	YES
150	NR1I3	NR1I3	NR1I3	3863	0.068	0.52	YES
151	ZNF624	ZNF624	ZNF624	3879	0.068	0.52	YES
152	ZNF180	ZNF180	ZNF180	3907	0.067	0.52	YES
153	RPS27A	RPS27A	RPS27A	3935	0.067	0.52	YES
154	ZNF566	ZNF566	ZNF566	3942	0.066	0.52	YES
155	ZNF227	ZNF227	ZNF227	3967	0.066	0.52	YES
156	ZNF45	ZNF45	ZNF45	3978	0.066	0.52	YES
157	TEAD1	TEAD1	TEAD1	4027	0.065	0.52	YES
158	ZNF484	ZNF484	ZNF484	4081	0.064	0.52	YES
159	ZNF417	ZNF417	ZNF417	4094	0.063	0.52	YES
160	ZNF17	ZNF17	ZNF17	4126	0.062	0.52	YES
161	ZNF394	ZNF394	ZNF394	4181	0.062	0.52	YES
162	MYC	MYC	MYC	4190	0.061	0.52	YES
163	ZNF420	ZNF420	ZNF420	4193	0.061	0.53	YES
164	ZNF333	ZNF333	ZNF333	4198	0.061	0.53	YES
165	ZNF430	ZNF430	ZNF430	4203	0.061	0.53	YES
166	ZNF136	ZNF136	ZNF136	4238	0.06	0.53	NO
167	TGIF1	TGIF1	TGIF1	4327	0.058	0.53	NO
168	ZNF234	ZNF234	ZNF234	4361	0.058	0.52	NO
169	CCNC	CCNC	CCNC	4518	0.055	0.52	NO
170	NOTCH2	NOTCH2	NOTCH2	4565	0.054	0.52	NO
171	ZNF468	ZNF468	ZNF468	4584	0.054	0.52	NO
172	ZNF264	ZNF264	ZNF264	4592	0.053	0.52	NO
173	ZNF225	ZNF225	ZNF225	4625	0.053	0.52	NO
174	TEAD3	TEAD3	TEAD3	4632	0.052	0.52	NO
175	ZNF256	ZNF256	ZNF256	4656	0.052	0.52	NO
176	ZNF460	ZNF460	ZNF460	4657	0.052	0.52	NO
177	ZNF595	ZNF595	ZNF595	4660	0.052	0.52	NO
178	ZNF222	ZNF222	ZNF222	4726	0.051	0.52	NO
179	ZNF473	ZNF473	ZNF473	4737	0.05	0.52	NO
180	ZKSCAN1	ZKSCAN1	ZKSCAN1	4778	0.05	0.52	NO
181	CCNT2	CCNT2	CCNT2	4800	0.05	0.52	NO
182	ZFP1	ZFP1	ZFP1	4874	0.048	0.52	NO
183	TBL1XR1	TBL1XR1	TBL1XR1	4945	0.047	0.52	NO
184	TEAD2	TEAD2	TEAD2	5005	0.046	0.51	NO
185	ZNF343	ZNF343	ZNF343	5028	0.046	0.51	NO
186	ZNF37A	ZNF37A	ZNF37A	5051	0.046	0.51	NO
187	ZNF248	ZNF248	ZNF248	5065	0.045	0.51	NO
188	TGIF2	TGIF2	TGIF2	5084	0.045	0.52	NO
189	TRIM33	TRIM33	TRIM33	5168	0.044	0.51	NO
190	ZNF3	ZNF3	ZNF3	5175	0.044	0.51	NO
191	ZNF189	ZNF189	ZNF189	5235	0.043	0.51	NO
192	ZNF708	ZNF708	ZNF708	5255	0.042	0.51	NO
193	MED23	MED23	MED23	5281	0.042	0.51	NO
194	SMAD4	SMAD4	SMAD4	5310	0.042	0.51	NO
195	ZNF140	ZNF140	ZNF140	5313	0.042	0.51	NO
196	PPM1A	PPM1A	PPM1A	5446	0.04	0.5	NO
197	NCOA1	NCOA1	NCOA1	5497	0.039	0.5	NO
198	ZNF556	ZNF556	ZNF556	5498	0.039	0.5	NO
199	RXRG	RXRG	RXRG	5521	0.038	0.5	NO
200	ZNF500	ZNF500	ZNF500	5612	0.037	0.5	NO
201	ZNF101	ZNF101	ZNF101	5618	0.037	0.5	NO
202	SMAD7	SMAD7	SMAD7	5682	0.036	0.5	NO
203	ZNF33A	ZNF33A	ZNF33A	5701	0.036	0.5	NO
204	ZNF12	ZNF12	ZNF12	5711	0.036	0.5	NO
205	ZNF597	ZNF597	ZNF597	5733	0.036	0.5	NO
206	MED17	MED17	MED17	5774	0.035	0.5	NO
207	ZNF510	ZNF510	ZNF510	5860	0.034	0.49	NO
208	ZNF324	ZNF324	ZNF324	5954	0.032	0.49	NO
209	ZNF585B	ZNF585B	ZNF585B	6096	0.031	0.48	NO
210	TBL1X	TBL1X	TBL1X	6103	0.03	0.48	NO
211	ZNF496	ZNF496	ZNF496	6117	0.03	0.48	NO
212	CDKN2B	CDKN2B	CDKN2B	6221	0.029	0.48	NO
213	ZNF138	ZNF138	ZNF138	6258	0.029	0.48	NO
214	ZNF273	ZNF273	ZNF273	6546	0.025	0.46	NO
215	ESRRA	ESRRA	ESRRA	6549	0.025	0.46	NO
216	MED10	MED10	MED10	6565	0.025	0.46	NO
217	ZNF596	ZNF596	ZNF596	6625	0.024	0.46	NO
218	ZNF226	ZNF226	ZNF226	6626	0.024	0.46	NO
219	SKI	SKI	SKI	6677	0.024	0.46	NO
220	THRB	THRB	THRB	6703	0.023	0.46	NO
221	ZNF200	ZNF200	ZNF200	6729	0.023	0.46	NO
222	SP1	SP1	SP1	6764	0.023	0.46	NO
223	ZNF557	ZNF557	ZNF557	6871	0.021	0.45	NO
224	NR4A2	NR4A2	NR4A2	7016	0.019	0.44	NO
225	RBL1	RBL1	RBL1	7150	0.018	0.44	NO
226	MED14	MED14	MED14	7155	0.018	0.44	NO
227	ZNF2	ZNF2	ZNF2	7172	0.017	0.44	NO
228	ZNF480	ZNF480	ZNF480	7221	0.017	0.43	NO
229	ZNF25	ZNF25	ZNF25	7233	0.017	0.43	NO
230	SMAD2	SMAD2	SMAD2	7267	0.016	0.43	NO
231	ZNF250	ZNF250	ZNF250	7304	0.016	0.43	NO
232	PPARD	PPARD	PPARD	7333	0.016	0.43	NO
233	E2F4	E2F4	E2F4	7375	0.015	0.43	NO
234	ZNF43	ZNF43	ZNF43	7391	0.015	0.43	NO
235	ZNF641	ZNF641	ZNF641	7443	0.014	0.42	NO
236	ZNF565	ZNF565	ZNF565	7485	0.014	0.42	NO
237	ZNF317	ZNF317	ZNF317	7501	0.014	0.42	NO
238	ZKSCAN5	ZKSCAN5	ZKSCAN5	7620	0.012	0.42	NO
239	ZNF398	ZNF398	ZNF398	7665	0.012	0.41	NO
240	NRBF2	NRBF2	NRBF2	7700	0.011	0.41	NO
241	MED4	MED4	MED4	7728	0.011	0.41	NO
242	CCNT1	CCNT1	CCNT1	7736	0.011	0.41	NO
243	NR2C2AP	NR2C2AP	NR2C2AP	7750	0.011	0.41	NO
244	ZNF212	ZNF212	ZNF212	7760	0.01	0.41	NO
245	PPARA	PPARA	PPARA	7817	0.01	0.41	NO
246	ZNF436	ZNF436	ZNF436	7835	0.0099	0.41	NO
247	ZNF205	ZNF205	ZNF205	7850	0.0097	0.4	NO
248	MAML1	MAML1	MAML1	7886	0.0093	0.4	NO
249	MED7	MED7	MED7	7996	0.008	0.4	NO
250	ZNF546	ZNF546	ZNF546	8003	0.0079	0.4	NO
251	UBE2D3	UBE2D3	UBE2D3	8050	0.0074	0.4	NO
252	UBA52	UBA52	UBA52	8081	0.0071	0.39	NO
253	ZNF92	ZNF92	ZNF92	8082	0.0071	0.39	NO
254	ZNF584	ZNF584	ZNF584	8123	0.0067	0.39	NO
255	MED1	MED1	MED1	8178	0.0061	0.39	NO
256	NR2E1	NR2E1	NR2E1	8186	0.006	0.39	NO
257	NR1H2	NR1H2	NR1H2	8287	0.0047	0.38	NO
258	USP9X	USP9X	USP9X	8405	0.0034	0.38	NO
259	YAP1	YAP1	YAP1	8438	0.0031	0.38	NO
260	ZNF263	ZNF263	ZNF263	8446	0.003	0.38	NO
261	CDK8	CDK8	CDK8	8450	0.0029	0.38	NO
262	MAMLD1	MAMLD1	MAMLD1	8483	0.0025	0.37	NO
263	TRIM28	TRIM28	TRIM28	8720	-0.00025	0.36	NO
264	NCOA6	NCOA6	NCOA6	9030	-0.0039	0.34	NO
265	NCOA3	NCOA3	NCOA3	9096	-0.0046	0.34	NO
266	TFDP1	TFDP1	TFDP1	9101	-0.0047	0.34	NO
267	ZNF100	ZNF100	ZNF100	9558	-0.01	0.31	NO
268	CREBBP	CREBBP	CREBBP	9738	-0.012	0.3	NO
269	ZNF267	ZNF267	ZNF267	9750	-0.012	0.3	NO
270	ZNF446	ZNF446	ZNF446	9788	-0.013	0.3	NO
271	RXRA	RXRA	RXRA	9793	-0.013	0.3	NO
272	MED27	MED27	MED27	9848	-0.014	0.3	NO
273	NRBP1	NRBP1	NRBP1	9970	-0.015	0.29	NO
274	MED8	MED8	MED8	10262	-0.018	0.28	NO
275	MED26	MED26	MED26	10275	-0.019	0.28	NO
276	MED12	MED12	MED12	10293	-0.019	0.28	NO
277	MED31	MED31	MED31	10352	-0.02	0.27	NO
278	MED30	MED30	MED30	10517	-0.022	0.26	NO
279	NR4A1	NR4A1	NR4A1	10536	-0.022	0.26	NO
280	ZNF282	ZNF282	ZNF282	10687	-0.024	0.26	NO
281	ZNF18	ZNF18	ZNF18	10751	-0.025	0.25	NO
282	MAML2	MAML2	MAML2	10781	-0.025	0.25	NO
283	SNW1	SNW1	SNW1	10793	-0.025	0.25	NO
284	MED6	MED6	MED6	10800	-0.026	0.25	NO
285	RARA	RARA	RARA	10819	-0.026	0.25	NO
286	THRA	THRA	THRA	10832	-0.026	0.25	NO
287	HDAC1	HDAC1	HDAC1	10867	-0.026	0.25	NO
288	NOTCH4	NOTCH4	NOTCH4	10925	-0.027	0.25	NO
289	NCOR1	NCOR1	NCOR1	10931	-0.027	0.25	NO
290	KAT2A	KAT2A	KAT2A	11035	-0.028	0.24	NO
291	CTGF	CTGF	CTGF	11122	-0.03	0.24	NO
292	PARP1	PARP1	PARP1	11372	-0.033	0.23	NO
293	NR2F6	NR2F6	NR2F6	11409	-0.033	0.23	NO
294	ZNF213	ZNF213	ZNF213	11475	-0.034	0.22	NO
295	CDK9	CDK9	CDK9	11741	-0.038	0.21	NO
296	RARG	RARG	RARG	11852	-0.039	0.21	NO
297	MED24	MED24	MED24	12069	-0.042	0.2	NO
298	NCOR2	NCOR2	NCOR2	12133	-0.044	0.19	NO
299	MAML3	MAML3	MAML3	12197	-0.044	0.19	NO
300	NCOA2	NCOA2	NCOA2	12211	-0.044	0.19	NO
301	E2F5	E2F5	E2F5	12234	-0.045	0.19	NO
302	SMAD3	SMAD3	SMAD3	12254	-0.045	0.19	NO
303	RBPJ	RBPJ	RBPJ	12759	-0.054	0.16	NO
304	NR1D1	NR1D1	NR1D1	12821	-0.055	0.16	NO
305	MED16	MED16	MED16	12913	-0.057	0.16	NO
306	ZNF517	ZNF517	ZNF517	12926	-0.057	0.16	NO
307	MEN1	MEN1	MEN1	13104	-0.061	0.15	NO
308	MED25	MED25	MED25	13438	-0.068	0.14	NO
309	NR1H3	NR1H3	NR1H3	13495	-0.069	0.13	NO
310	TGS1	TGS1	TGS1	13526	-0.07	0.13	NO
311	JUNB	JUNB	JUNB	13584	-0.071	0.13	NO
312	ESRRB	ESRRB	ESRRB	13643	-0.072	0.13	NO
313	MED15	MED15	MED15	14537	-0.097	0.084	NO
314	TEAD4	TEAD4	TEAD4	14896	-0.11	0.067	NO
315	SMARCD3	SMARCD3	SMARCD3	14974	-0.12	0.066	NO
316	ZNF483	ZNF483	ZNF483	15145	-0.12	0.06	NO
317	RORB	RORB	RORB	15269	-0.13	0.057	NO
318	TBX5	TBX5	TBX5	15465	-0.14	0.05	NO
319	WWTR1	WWTR1	WWTR1	15472	-0.14	0.054	NO
320	ESR1	ESR1	ESR1	15495	-0.14	0.056	NO
321	AR	AR	AR	15633	-0.15	0.053	NO
322	VDR	VDR	VDR	15913	-0.16	0.042	NO
323	NOTCH3	NOTCH3	NOTCH3	15918	-0.16	0.047	NO
324	ESR2	ESR2	ESR2	16320	-0.19	0.03	NO
325	NR2F1	NR2F1	NR2F1	16439	-0.2	0.029	NO
326	RUNX2	RUNX2	RUNX2	16701	-0.22	0.02	NO
327	PGR	PGR	PGR	16865	-0.24	0.018	NO
328	HNF4A	HNF4A	HNF4A	16901	-0.24	0.023	NO
329	NR2E3	NR2E3	NR2E3	16963	-0.24	0.027	NO
330	HNF4G	HNF4G	HNF4G	17271	-0.28	0.018	NO
331	SERPINE1	SERPINE1	SERPINE1	17292	-0.28	0.025	NO
332	NR5A2	NR5A2	NR5A2	17487	-0.32	0.023	NO
333	NR0B1	NR0B1	NR0B1	17745	-0.38	0.019	NO

Figure S43. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: PID P53 REGULATION PATHWAY.

Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: PID P53 REGULATION 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 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	EFS	EFS	EFS	299	0.36	0.095	YES
2	SLC25A38	SLC25A38	SLC25A38	973	0.21	0.12	YES
3	PSD3	PSD3	PSD3	1289	0.18	0.16	YES
4	TSC22D2	TSC22D2	TSC22D2	1304	0.18	0.22	YES
5	PRUNE2	PRUNE2	PRUNE2	1866	0.14	0.23	YES
6	PTP4A1	PTP4A1	PTP4A1	2917	0.094	0.2	YES
7	TBPL1	TBPL1	TBPL1	3329	0.082	0.2	YES
8	ERCC6	ERCC6	ERCC6	3477	0.078	0.22	YES
9	CCHCR1	CCHCR1	CCHCR1	3536	0.076	0.24	YES
10	TMEM231	TMEM231	TMEM231	3786	0.07	0.24	YES
11	TRMT61B	TRMT61B	TRMT61B	3841	0.069	0.26	YES
12	NPRL2	NPRL2	NPRL2	4093	0.063	0.27	YES
13	U2AF1	U2AF1	U2AF1	4140	0.062	0.28	YES
14	TIMM9	TIMM9	TIMM9	4300	0.059	0.29	YES
15	RNF138	RNF138	RNF138	4408	0.057	0.3	YES
16	FBXO21	FBXO21	FBXO21	4428	0.056	0.32	YES
17	VEZT	VEZT	VEZT	4739	0.05	0.32	YES
18	PCF11	PCF11	PCF11	4856	0.049	0.33	YES
19	EIF1AX	EIF1AX	EIF1AX	4918	0.048	0.34	YES
20	NAP1L3	NAP1L3	NAP1L3	5004	0.046	0.35	YES
21	DDX10	DDX10	DDX10	5530	0.038	0.33	YES
22	NAA16	NAA16	NAA16	5730	0.036	0.33	YES
23	TRAPPC2	TRAPPC2	TRAPPC2	5878	0.034	0.33	YES
24	TMPO	TMPO	TMPO	5973	0.032	0.34	YES
25	FBXO11	FBXO11	FBXO11	6017	0.032	0.34	YES
26	VEZF1	VEZF1	VEZF1	6225	0.029	0.34	YES
27	SRSF3	SRSF3	SRSF3	6278	0.028	0.35	YES
28	CARS2	CARS2	CARS2	6301	0.028	0.36	YES
29	ZFP64	ZFP64	ZFP64	6387	0.027	0.36	YES
30	RBBP6	RBBP6	RBBP6	6421	0.027	0.36	YES
31	PAPOLA	PAPOLA	PAPOLA	6470	0.026	0.37	YES
32	UBQLN4	UBQLN4	UBQLN4	6997	0.02	0.35	NO
33	RBBP7	RBBP7	RBBP7	7352	0.015	0.33	NO
34	HIC2	HIC2	HIC2	7742	0.011	0.31	NO
35	PTPN2	PTPN2	PTPN2	8137	0.0066	0.29	NO
36	TTC27	TTC27	TTC27	8284	0.0048	0.29	NO
37	FARP1	FARP1	FARP1	8288	0.0047	0.29	NO
38	MIA3	MIA3	MIA3	8328	0.0042	0.29	NO
39	CNOT2	CNOT2	CNOT2	8354	0.004	0.29	NO
40	EIF5B	EIF5B	EIF5B	8485	0.0024	0.28	NO
41	ZDHHC6	ZDHHC6	ZDHHC6	8661	0.00052	0.27	NO
42	STX18	STX18	STX18	8835	-0.0017	0.26	NO
43	RAD51C	RAD51C	RAD51C	8929	-0.0028	0.26	NO
44	GON4L	GON4L	GON4L	9051	-0.0041	0.25	NO
45	UBR7	UBR7	UBR7	9152	-0.0053	0.25	NO
46	YTHDF1	YTHDF1	YTHDF1	9320	-0.0074	0.24	NO
47	CSE1L	CSE1L	CSE1L	9507	-0.0096	0.24	NO
48	RAD23B	RAD23B	RAD23B	9627	-0.011	0.23	NO
49	EMG1	EMG1	EMG1	9952	-0.015	0.22	NO
50	MAX	MAX	MAX	10485	-0.021	0.2	NO
51	HCFC1	HCFC1	HCFC1	10594	-0.023	0.2	NO
52	NXT1	NXT1	NXT1	10669	-0.024	0.2	NO
53	PCMT1	PCMT1	PCMT1	10775	-0.025	0.2	NO
54	ISG20L2	ISG20L2	ISG20L2	11144	-0.03	0.19	NO
55	GOSR2	GOSR2	GOSR2	11437	-0.034	0.18	NO
56	ANP32E	ANP32E	ANP32E	11652	-0.037	0.18	NO
57	SMARCA4	SMARCA4	SMARCA4	12259	-0.045	0.16	NO
58	BCS1L	BCS1L	BCS1L	12420	-0.048	0.17	NO
59	SLC35A2	SLC35A2	SLC35A2	12447	-0.049	0.18	NO
60	RUVBL2	RUVBL2	RUVBL2	12841	-0.055	0.18	NO
61	TCEA1	TCEA1	TCEA1	13207	-0.063	0.18	NO
62	IGFBP5	IGFBP5	IGFBP5	13730	-0.074	0.17	NO
63	PHGDH	PHGDH	PHGDH	14902	-0.11	0.14	NO
64	TNFAIP8	TNFAIP8	TNFAIP8	15021	-0.12	0.17	NO

Figure S45. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME TRANSLATION.

Figure S46. 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 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE

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	PDGFD	PDGFD	PDGFD	357	0.34	0.082	YES
2	COX6A2	COX6A2	COX6A2	382	0.34	0.18	YES
3	FAM129A	FAM129A	FAM129A	808	0.24	0.23	YES
4	ID2	ID2	ID2	946	0.22	0.28	YES
5	H2AFY2	H2AFY2	H2AFY2	999	0.21	0.34	YES
6	PTPRN2	PTPRN2	PTPRN2	1405	0.17	0.37	YES
7	ATR	ATR	ATR	1468	0.16	0.42	YES
8	MBNL1	MBNL1	MBNL1	1965	0.13	0.43	YES
9	CCP110	CCP110	CCP110	2287	0.12	0.44	YES
10	EEF1A1	EEF1A1	EEF1A1	2749	0.1	0.45	YES
11	CLK4	CLK4	CLK4	2949	0.093	0.46	YES
12	RPL9	RPL9	RPL9	3179	0.086	0.48	YES
13	MRPS25	MRPS25	MRPS25	3266	0.083	0.5	YES
14	HAUS4	HAUS4	HAUS4	3627	0.073	0.5	YES
15	ALDH3A2	ALDH3A2	ALDH3A2	3898	0.068	0.5	YES
16	GLTSCR2	GLTSCR2	GLTSCR2	4130	0.062	0.51	YES
17	ALOX5AP	ALOX5AP	ALOX5AP	4460	0.056	0.51	YES
18	RABGGTB	RABGGTB	RABGGTB	4568	0.054	0.52	YES
19	TMEM47	TMEM47	TMEM47	4769	0.05	0.52	YES
20	EXTL2	EXTL2	EXTL2	4860	0.049	0.53	YES
21	BCL2L2	BCL2L2	BCL2L2	4868	0.048	0.54	YES
22	PHTF2	PHTF2	PHTF2	4990	0.047	0.55	YES
23	RWDD2B	RWDD2B	RWDD2B	5075	0.045	0.56	YES
24	CGRRF1	CGRRF1	CGRRF1	5370	0.041	0.55	YES
25	ERMAP	ERMAP	ERMAP	5649	0.037	0.55	YES
26	RASIP1	RASIP1	RASIP1	5679	0.036	0.56	YES
27	HDGFRP3	HDGFRP3	HDGFRP3	5714	0.036	0.57	YES
28	FERMT2	FERMT2	FERMT2	5961	0.032	0.56	YES
29	PTEN	PTEN	PTEN	6037	0.031	0.57	YES
30	CWC27	CWC27	CWC27	6460	0.026	0.55	YES
31	RPF2	RPF2	RPF2	6485	0.026	0.56	YES
32	NEK1	NEK1	NEK1	6537	0.025	0.56	YES
33	SCAF11	SCAF11	SCAF11	6617	0.024	0.57	YES
34	SPG20	SPG20	SPG20	6639	0.024	0.57	YES
35	FBXO33	FBXO33	FBXO33	7111	0.018	0.55	NO
36	FNDC3A	FNDC3A	FNDC3A	7378	0.015	0.54	NO
37	TUBGCP3	TUBGCP3	TUBGCP3	7435	0.014	0.54	NO
38	PNMA1	PNMA1	PNMA1	9517	-0.0096	0.43	NO
39	CAST	CAST	CAST	11514	-0.035	0.33	NO
40	FKBP3	FKBP3	FKBP3	11539	-0.035	0.34	NO
41	RHOC	RHOC	RHOC	14004	-0.081	0.23	NO

Figure S47. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S48. 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 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	RNASE4	RNASE4	RNASE4	243	0.39	0.098	YES
2	ZFP2	ZFP2	ZFP2	461	0.32	0.18	YES
3	C11orf63	C11orf63	C11orf63	1064	0.2	0.2	YES
4	DYNC2H1	DYNC2H1	DYNC2H1	1359	0.18	0.24	YES
5	DIXDC1	DIXDC1	DIXDC1	1384	0.17	0.28	YES
6	WDR19	WDR19	WDR19	1796	0.14	0.3	YES
7	NYNRIN	NYNRIN	NYNRIN	2246	0.12	0.31	YES
8	SYNC	SYNC	SYNC	2294	0.12	0.34	YES
9	DZANK1	DZANK1	DZANK1	2485	0.11	0.36	YES
10	SESN1	SESN1	SESN1	2808	0.098	0.37	YES
11	ZNF395	ZNF395	ZNF395	2995	0.091	0.39	YES
12	ECHDC2	ECHDC2	ECHDC2	3581	0.074	0.38	YES
13	NME5	NME5	NME5	3670	0.072	0.39	YES
14	MARCH8	MARCH8	MARCH8	3704	0.072	0.41	YES
15	ZNF862	ZNF862	ZNF862	3924	0.067	0.42	YES
16	KIF13B	KIF13B	KIF13B	3989	0.066	0.43	YES
17	LAMB2	LAMB2	LAMB2	4049	0.064	0.45	YES
18	BBS1	BBS1	BBS1	4305	0.059	0.45	YES
19	TPT1	TPT1	TPT1	4675	0.052	0.45	YES
20	CRY2	CRY2	CRY2	4746	0.05	0.46	YES
21	CYBRD1	CYBRD1	CYBRD1	5232	0.043	0.44	NO
22	CX3CR1	CX3CR1	CX3CR1	5292	0.042	0.45	NO
23	CASP9	CASP9	CASP9	5693	0.036	0.44	NO
24	IFT88	IFT88	IFT88	6018	0.032	0.43	NO
25	MPHOSPH8	MPHOSPH8	MPHOSPH8	6145	0.03	0.43	NO
26	SIRT3	SIRT3	SIRT3	6314	0.028	0.43	NO
27	CIRBP	CIRBP	CIRBP	6584	0.025	0.42	NO
28	CRTC3	CRTC3	CRTC3	6591	0.025	0.43	NO
29	AKAP11	AKAP11	AKAP11	6860	0.021	0.42	NO
30	AASS	AASS	AASS	7335	0.016	0.4	NO
31	SLC24A1	SLC24A1	SLC24A1	7572	0.013	0.39	NO
32	SMARCA2	SMARCA2	SMARCA2	7841	0.0098	0.38	NO
33	NBR1	NBR1	NBR1	8104	0.0068	0.36	NO
34	IFT46	IFT46	IFT46	8237	0.0054	0.36	NO
35	ARHGEF12	ARHGEF12	ARHGEF12	8522	0.0018	0.34	NO
36	STAT5B	STAT5B	STAT5B	8559	0.0015	0.34	NO
37	TUBGCP4	TUBGCP4	TUBGCP4	9209	-0.006	0.31	NO
38	TBC1D17	TBC1D17	TBC1D17	9362	-0.008	0.3	NO
39	ARHGEF40	ARHGEF40	ARHGEF40	9776	-0.013	0.28	NO
40	NF1	NF1	NF1	9972	-0.015	0.28	NO
41	PIGV	PIGV	PIGV	10506	-0.022	0.25	NO
42	CTDSP1	CTDSP1	CTDSP1	10682	-0.024	0.25	NO
43	SNX1	SNX1	SNX1	11049	-0.029	0.24	NO
44	LTBP3	LTBP3	LTBP3	11564	-0.035	0.22	NO
45	DEAF1	DEAF1	DEAF1	12286	-0.046	0.19	NO
46	STARD13	STARD13	STARD13	12807	-0.055	0.18	NO
47	FOS	FOS	FOS	13404	-0.067	0.17	NO
48	FRY	FRY	FRY	15100	-0.12	0.11	NO
49	RUNX1	RUNX1	RUNX1	16511	-0.2	0.087	NO

Figure S49. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S50. 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 GENERIC TRANSCRIPTION PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	EHHADH	EHHADH	EHHADH	749	0.25	-0.006	YES
2	CELSR3	CELSR3	CELSR3	917	0.22	0.016	YES
3	TFDP2	TFDP2	TFDP2	1068	0.2	0.037	YES
4	SPICE1	SPICE1	SPICE1	1094	0.2	0.064	YES
5	GTPBP8	GTPBP8	GTPBP8	1115	0.2	0.091	YES
6	RNF32	RNF32	RNF32	1120	0.2	0.12	YES
7	WNK3	WNK3	WNK3	1306	0.18	0.13	YES
8	ZFR2	ZFR2	ZFR2	1374	0.17	0.16	YES
9	HLTF	HLTF	HLTF	1549	0.16	0.17	YES
10	NR1D2	NR1D2	NR1D2	1553	0.16	0.19	YES
11	RAD18	RAD18	RAD18	1627	0.15	0.21	YES
12	MEIS1	MEIS1	MEIS1	1808	0.14	0.22	YES
13	PDCD10	PDCD10	PDCD10	1836	0.14	0.24	YES
14	TMEM41A	TMEM41A	TMEM41A	1868	0.14	0.26	YES
15	KIAA2022	KIAA2022	KIAA2022	1960	0.13	0.27	YES
16	MYNN	MYNN	MYNN	2003	0.13	0.29	YES
17	TBCCD1	TBCCD1	TBCCD1	2026	0.13	0.3	YES
18	GK5	GK5	GK5	2188	0.12	0.31	YES
19	ACTL6A	ACTL6A	ACTL6A	2284	0.12	0.32	YES
20	SENP5	SENP5	SENP5	2334	0.12	0.34	YES
21	MSL2	MSL2	MSL2	2361	0.11	0.35	YES
22	SYCP2	SYCP2	SYCP2	2402	0.11	0.36	YES
23	TOPBP1	TOPBP1	TOPBP1	2582	0.11	0.37	YES
24	RFC4	RFC4	RFC4	2607	0.1	0.38	YES
25	RNF168	RNF168	RNF168	2633	0.1	0.4	YES
26	WDR53	WDR53	WDR53	2679	0.1	0.41	YES
27	NDUFB5	NDUFB5	NDUFB5	2757	0.1	0.42	YES
28	RMI1	RMI1	RMI1	2872	0.095	0.43	YES
29	OPA1	OPA1	OPA1	3241	0.084	0.42	YES
30	MCM2	MCM2	MCM2	3284	0.083	0.43	YES
31	STMN1	STMN1	STMN1	3451	0.078	0.43	YES
32	ANKRD32	ANKRD32	ANKRD32	3497	0.077	0.44	YES
33	EIF2B5	EIF2B5	EIF2B5	3518	0.076	0.45	YES
34	SYCE2	SYCE2	SYCE2	3586	0.074	0.46	YES
35	RAP2B	RAP2B	RAP2B	3621	0.073	0.46	YES
36	KCNS1	KCNS1	KCNS1	3701	0.072	0.47	YES
37	MLH1	MLH1	MLH1	3813	0.069	0.47	YES
38	FMR1	FMR1	FMR1	3891	0.068	0.48	YES
39	CENPK	CENPK	CENPK	4256	0.06	0.47	NO
40	PRPF38A	PRPF38A	PRPF38A	4662	0.052	0.45	NO
41	POLR2H	POLR2H	POLR2H	4929	0.048	0.44	NO
42	RMI2	RMI2	RMI2	5262	0.042	0.43	NO
43	MRPL47	MRPL47	MRPL47	5286	0.042	0.44	NO
44	CXCL17	CXCL17	CXCL17	6326	0.028	0.38	NO
45	RPA2	RPA2	RPA2	6433	0.027	0.38	NO
46	ING2	ING2	ING2	6571	0.025	0.38	NO
47	USP1	USP1	USP1	6732	0.023	0.37	NO
48	INPP5B	INPP5B	INPP5B	6929	0.02	0.36	NO
49	TAF7L	TAF7L	TAF7L	6995	0.02	0.36	NO
50	MORN2	MORN2	MORN2	7187	0.017	0.35	NO
51	CDC7	CDC7	CDC7	7292	0.016	0.35	NO
52	HAUS5	HAUS5	HAUS5	7537	0.013	0.34	NO
53	NR2C2AP	NR2C2AP	NR2C2AP	7750	0.011	0.33	NO
54	KIF15	KIF15	KIF15	7788	0.01	0.33	NO
55	NUP210	NUP210	NUP210	8086	0.007	0.31	NO
56	DHFR	DHFR	DHFR	8263	0.0051	0.3	NO
57	SLFN13	SLFN13	SLFN13	8330	0.0042	0.3	NO
58	C9orf40	C9orf40	C9orf40	9625	-0.011	0.23	NO
59	ALG6	ALG6	ALG6	9775	-0.013	0.22	NO
60	NMU	NMU	NMU	10152	-0.017	0.2	NO
61	CENPW	CENPW	CENPW	10721	-0.024	0.18	NO
62	C5orf34	C5orf34	C5orf34	11066	-0.029	0.16	NO
63	EZH2	EZH2	EZH2	11842	-0.039	0.12	NO
64	LIG1	LIG1	LIG1	12068	-0.042	0.12	NO
65	MCM6	MCM6	MCM6	12811	-0.055	0.084	NO
66	CDKN2A	CDKN2A	CDKN2A	12842	-0.055	0.09	NO
67	HES1	HES1	HES1	12960	-0.058	0.092	NO
68	HS6ST2	HS6ST2	HS6ST2	13011	-0.059	0.098	NO
69	YBX2	YBX2	YBX2	13628	-0.072	0.074	NO
70	WEE1	WEE1	WEE1	13961	-0.08	0.067	NO
71	CDKN2C	CDKN2C	CDKN2C	13976	-0.08	0.078	NO
72	DNAJC13	DNAJC13	DNAJC13	14190	-0.087	0.078	NO
73	RIBC2	RIBC2	RIBC2	14723	-0.1	0.064	NO
74	FAM111B	FAM111B	FAM111B	15007	-0.12	0.064	NO
75	C11orf85	C11orf85	C11orf85	15466	-0.14	0.059	NO
76	ASS1	ASS1	ASS1	15557	-0.14	0.074	NO
77	SYNGR3	SYNGR3	SYNGR3	15621	-0.15	0.092	NO
78	MEI1	MEI1	MEI1	15771	-0.16	0.11	NO
79	NEFH	NEFH	NEFH	15805	-0.16	0.13	NO

Figure S51. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME GENERIC TRANSCRIPTION PATHWAY.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME GENERIC TRANSCRIPTION 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 PEPTIDE CHAIN ELONGATION

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	BEX1	BEX1	BEX1	181	0.42	0.011	YES
2	RNASE4	RNASE4	RNASE4	243	0.39	0.028	YES
3	BEX5	BEX5	BEX5	310	0.36	0.042	YES
4	SHE	SHE	SHE	404	0.33	0.054	YES
5	LNP1	LNP1	LNP1	498	0.31	0.064	YES
6	ANG	ANG	ANG	512	0.3	0.079	YES
7	GXYLT2	GXYLT2	GXYLT2	557	0.29	0.092	YES
8	SLC16A10	SLC16A10	SLC16A10	686	0.26	0.098	YES
9	PAIP2B	PAIP2B	PAIP2B	829	0.23	0.1	YES
10	TFDP2	TFDP2	TFDP2	1068	0.2	0.099	YES
11	LMLN	LMLN	LMLN	1106	0.2	0.11	YES
12	MARVELD2	MARVELD2	MARVELD2	1163	0.19	0.11	YES
13	ZNF711	ZNF711	ZNF711	1248	0.18	0.12	YES
14	ZNF621	ZNF621	ZNF621	1312	0.18	0.12	YES
15	MEST	MEST	MEST	1525	0.16	0.12	YES
16	MFAP3L	MFAP3L	MFAP3L	1582	0.16	0.12	YES
17	SFMBT1	SFMBT1	SFMBT1	1662	0.15	0.13	YES
18	ZNF789	ZNF789	ZNF789	1671	0.15	0.14	YES
19	JAM3	JAM3	JAM3	1743	0.15	0.14	YES
20	C3orf17	C3orf17	C3orf17	1758	0.15	0.15	YES
21	TIGD7	TIGD7	TIGD7	1776	0.14	0.15	YES
22	BOC	BOC	BOC	1786	0.14	0.16	YES
23	FAM161A	FAM161A	FAM161A	1793	0.14	0.17	YES
24	SENP2	SENP2	SENP2	1825	0.14	0.17	YES
25	CAND2	CAND2	CAND2	1831	0.14	0.18	YES
26	DCUN1D1	DCUN1D1	DCUN1D1	1946	0.13	0.18	YES
27	MDM1	MDM1	MDM1	1962	0.13	0.18	YES
28	BEX4	BEX4	BEX4	2044	0.13	0.19	YES
29	TSPAN6	TSPAN6	TSPAN6	2142	0.12	0.19	YES
30	ARL17A	ARL17A	ARL17A	2177	0.12	0.19	YES
31	BHLHB9	BHLHB9	BHLHB9	2189	0.12	0.2	YES
32	BEX2	BEX2	BEX2	2226	0.12	0.2	YES
33	CCP110	CCP110	CCP110	2287	0.12	0.2	YES
34	VHL	VHL	VHL	2315	0.12	0.21	YES
35	MSL2	MSL2	MSL2	2361	0.11	0.21	YES
36	ITGA9	ITGA9	ITGA9	2442	0.11	0.21	YES
37	SPATA7	SPATA7	SPATA7	2474	0.11	0.22	YES
38	ALDH6A1	ALDH6A1	ALDH6A1	2487	0.11	0.22	YES
39	GPRASP2	GPRASP2	GPRASP2	2500	0.11	0.23	YES
40	ZNF606	ZNF606	ZNF606	2563	0.11	0.23	YES
41	USP13	USP13	USP13	2666	0.1	0.23	YES
42	SEC62	SEC62	SEC62	2674	0.1	0.23	YES
43	TMEM97	TMEM97	TMEM97	2776	0.099	0.23	YES
44	SNED1	SNED1	SNED1	2922	0.094	0.23	YES
45	MAGEH1	MAGEH1	MAGEH1	2926	0.093	0.23	YES
46	MAGEF1	MAGEF1	MAGEF1	3109	0.088	0.23	YES
47	ACVR2A	ACVR2A	ACVR2A	3132	0.087	0.23	YES
48	ARMCX1	ARMCX1	ARMCX1	3235	0.084	0.23	YES
49	PASK	PASK	PASK	3248	0.084	0.23	YES
50	PNN	PNN	PNN	3258	0.084	0.24	YES
51	TFAM	TFAM	TFAM	3268	0.083	0.24	YES
52	RASSF8	RASSF8	RASSF8	3293	0.082	0.24	YES
53	ARMCX6	ARMCX6	ARMCX6	3313	0.082	0.25	YES
54	NKAP	NKAP	NKAP	3365	0.08	0.25	YES
55	NUP54	NUP54	NUP54	3439	0.078	0.25	YES
56	CCNB1IP1	CCNB1IP1	CCNB1IP1	3448	0.078	0.25	YES
57	ZFP90	ZFP90	ZFP90	3503	0.077	0.25	YES
58	LRP6	LRP6	LRP6	3506	0.077	0.26	YES
59	EPM2AIP1	EPM2AIP1	EPM2AIP1	3540	0.076	0.26	YES
60	TMEM5	TMEM5	TMEM5	3566	0.075	0.26	YES
61	LRP4	LRP4	LRP4	3598	0.074	0.26	YES
62	ETV5	ETV5	ETV5	3700	0.072	0.26	YES
63	RPL22	RPL22	RPL22	3771	0.07	0.26	YES
64	SLC25A14	SLC25A14	SLC25A14	3791	0.07	0.26	YES
65	SMARCA1	SMARCA1	SMARCA1	3816	0.069	0.26	YES
66	ST13	ST13	ST13	3820	0.069	0.27	YES
67	ALS2	ALS2	ALS2	3866	0.068	0.27	YES
68	JAGN1	JAGN1	JAGN1	3878	0.068	0.27	YES
69	TIGD1	TIGD1	TIGD1	3903	0.067	0.28	YES
70	PLEKHA5	PLEKHA5	PLEKHA5	3910	0.067	0.28	YES
71	PKP4	PKP4	PKP4	3993	0.065	0.28	YES
72	PRCP	PRCP	PRCP	4004	0.065	0.28	YES
73	NUDT7	NUDT7	NUDT7	4020	0.065	0.28	YES
74	TAF9B	TAF9B	TAF9B	4053	0.064	0.28	YES
75	EPC2	EPC2	EPC2	4246	0.06	0.28	YES
76	SVIP	SVIP	SVIP	4272	0.059	0.28	YES
77	MAGEE1	MAGEE1	MAGEE1	4284	0.059	0.28	YES
78	CETN2	CETN2	CETN2	4329	0.058	0.28	YES
79	CCDC43	CCDC43	CCDC43	4333	0.058	0.28	YES
80	EEF1B2	EEF1B2	EEF1B2	4375	0.057	0.28	YES
81	SLC25A33	SLC25A33	SLC25A33	4420	0.056	0.28	YES
82	PILRB	PILRB	PILRB	4552	0.054	0.28	YES
83	MMGT1	MMGT1	MMGT1	4563	0.054	0.28	YES
84	MOB1B	MOB1B	MOB1B	4628	0.053	0.28	YES
85	APOOL	APOOL	APOOL	4692	0.052	0.28	YES
86	PPIG	PPIG	PPIG	4696	0.052	0.28	YES
87	FAM13B	FAM13B	FAM13B	4782	0.05	0.28	YES
88	PARL	PARL	PARL	4803	0.05	0.28	YES
89	ZNF449	ZNF449	ZNF449	4826	0.049	0.28	YES
90	TCEAL8	TCEAL8	TCEAL8	4827	0.049	0.28	YES
91	ETV4	ETV4	ETV4	4886	0.048	0.28	YES
92	HNRNPH1	HNRNPH1	HNRNPH1	4979	0.047	0.28	YES
93	C2orf44	C2orf44	C2orf44	5034	0.046	0.28	YES
94	IFT52	IFT52	IFT52	5039	0.046	0.28	YES
95	SNRPN	SNRPN	SNRPN	5056	0.046	0.28	YES
96	TMED8	TMED8	TMED8	5121	0.045	0.28	YES
97	C18orf21	C18orf21	C18orf21	5138	0.044	0.28	YES
98	ZNF75A	ZNF75A	ZNF75A	5173	0.044	0.28	YES
99	PPWD1	PPWD1	PPWD1	5186	0.044	0.29	YES
100	NGFRAP1	NGFRAP1	NGFRAP1	5231	0.043	0.29	YES
101	ANKRD40	ANKRD40	ANKRD40	5243	0.043	0.29	YES
102	ZNF133	ZNF133	ZNF133	5270	0.042	0.29	YES
103	FAM133B	FAM133B	FAM133B	5280	0.042	0.29	YES
104	NAT9	NAT9	NAT9	5291	0.042	0.29	YES
105	ZMYND11	ZMYND11	ZMYND11	5340	0.041	0.29	YES
106	IDH1	IDH1	IDH1	5417	0.04	0.29	YES
107	CREB1	CREB1	CREB1	5519	0.038	0.28	YES
108	NAP1L5	NAP1L5	NAP1L5	5528	0.038	0.29	YES
109	KIAA1467	KIAA1467	KIAA1467	5560	0.038	0.29	YES
110	CTCF	CTCF	CTCF	5593	0.038	0.29	YES
111	LRRC23	LRRC23	LRRC23	5750	0.035	0.28	YES
112	GGT7	GGT7	GGT7	5776	0.035	0.28	YES
113	ITGBL1	ITGBL1	ITGBL1	5832	0.034	0.28	YES
114	STAG2	STAG2	STAG2	5846	0.034	0.28	YES
115	PSMD10	PSMD10	PSMD10	5877	0.034	0.28	YES
116	ZNF24	ZNF24	ZNF24	5919	0.033	0.28	YES
117	BBS9	BBS9	BBS9	5933	0.033	0.28	YES
118	DNAJB11	DNAJB11	DNAJB11	5955	0.032	0.28	YES
119	TXNDC15	TXNDC15	TXNDC15	5956	0.032	0.28	YES
120	HSD17B11	HSD17B11	HSD17B11	5963	0.032	0.28	YES
121	DHX35	DHX35	DHX35	5980	0.032	0.28	YES
122	E2F6	E2F6	E2F6	5991	0.032	0.28	YES
123	TCEAL4	TCEAL4	TCEAL4	5995	0.032	0.29	YES
124	PLCB4	PLCB4	PLCB4	6024	0.032	0.29	YES
125	SH3BGRL2	SH3BGRL2	SH3BGRL2	6098	0.031	0.28	YES
126	YTHDC1	YTHDC1	YTHDC1	6134	0.03	0.28	YES
127	BEND7	BEND7	BEND7	6152	0.03	0.28	YES
128	COX11	COX11	COX11	6157	0.03	0.29	YES
129	MAGI2	MAGI2	MAGI2	6192	0.03	0.28	YES
130	METTL9	METTL9	METTL9	6204	0.029	0.29	YES
131	SALL4	SALL4	SALL4	6220	0.029	0.29	YES
132	ZNF397	ZNF397	ZNF397	6222	0.029	0.29	YES
133	INO80D	INO80D	INO80D	6250	0.029	0.29	YES
134	LAMA2	LAMA2	LAMA2	6275	0.029	0.29	YES
135	RLIM	RLIM	RLIM	6288	0.028	0.29	YES
136	PRR3	PRR3	PRR3	6294	0.028	0.29	YES
137	TAF1C	TAF1C	TAF1C	6356	0.028	0.29	YES
138	SRSF6	SRSF6	SRSF6	6386	0.027	0.29	YES
139	RBMX2	RBMX2	RBMX2	6396	0.027	0.29	YES
140	TP53BP1	TP53BP1	TP53BP1	6407	0.027	0.29	YES
141	RBBP6	RBBP6	RBBP6	6421	0.027	0.29	YES
142	MUTYH	MUTYH	MUTYH	6436	0.027	0.29	YES
143	C17orf80	C17orf80	C17orf80	6458	0.026	0.29	YES
144	PAPOLA	PAPOLA	PAPOLA	6470	0.026	0.29	YES
145	UPF3B	UPF3B	UPF3B	6530	0.025	0.29	NO
146	AHI1	AHI1	AHI1	6561	0.025	0.29	NO
147	TMLHE	TMLHE	TMLHE	6570	0.025	0.29	NO
148	TMEM18	TMEM18	TMEM18	6628	0.024	0.29	NO
149	ACP1	ACP1	ACP1	6667	0.024	0.29	NO
150	EFHD1	EFHD1	EFHD1	6692	0.023	0.29	NO
151	ARMCX3	ARMCX3	ARMCX3	6722	0.023	0.29	NO
152	VPS45	VPS45	VPS45	6741	0.023	0.29	NO
153	RAD17	RAD17	RAD17	6775	0.022	0.29	NO
154	SDAD1	SDAD1	SDAD1	6782	0.022	0.29	NO
155	NUDT4	NUDT4	NUDT4	6787	0.022	0.29	NO
156	MPDZ	MPDZ	MPDZ	6793	0.022	0.29	NO
157	MGA	MGA	MGA	6813	0.022	0.29	NO
158	LOH12CR1	LOH12CR1	LOH12CR1	6869	0.021	0.29	NO
159	MRPS35	MRPS35	MRPS35	6908	0.02	0.29	NO
160	MTA3	MTA3	MTA3	6949	0.02	0.28	NO
161	LMAN2L	LMAN2L	LMAN2L	6991	0.02	0.28	NO
162	NUP107	NUP107	NUP107	6994	0.02	0.28	NO
163	YY1AP1	YY1AP1	YY1AP1	7009	0.019	0.28	NO
164	LMTK2	LMTK2	LMTK2	7036	0.019	0.28	NO
165	ARL16	ARL16	ARL16	7044	0.019	0.28	NO
166	ZBTB33	ZBTB33	ZBTB33	7046	0.019	0.28	NO
167	CENPBD1	CENPBD1	CENPBD1	7095	0.018	0.28	NO
168	EFCAB11	EFCAB11	EFCAB11	7175	0.017	0.28	NO
169	MORN2	MORN2	MORN2	7187	0.017	0.28	NO
170	WDR12	WDR12	WDR12	7192	0.017	0.28	NO
171	METTL21A	METTL21A	METTL21A	7234	0.017	0.28	NO
172	FARP2	FARP2	FARP2	7244	0.016	0.28	NO
173	RBM15	RBM15	RBM15	7245	0.016	0.28	NO
174	TTC17	TTC17	TTC17	7250	0.016	0.28	NO
175	SALL2	SALL2	SALL2	7359	0.015	0.28	NO
176	THOC2	THOC2	THOC2	7370	0.015	0.28	NO
177	ATAD2B	ATAD2B	ATAD2B	7388	0.015	0.28	NO
178	PDRG1	PDRG1	PDRG1	7397	0.015	0.28	NO
179	CAND1	CAND1	CAND1	7431	0.014	0.28	NO
180	ATXN3	ATXN3	ATXN3	7471	0.014	0.27	NO
181	OSCP1	OSCP1	OSCP1	7482	0.014	0.27	NO
182	PABPN1	PABPN1	PABPN1	7562	0.013	0.27	NO
183	PHC1	PHC1	PHC1	7657	0.012	0.26	NO
184	ERCC8	ERCC8	ERCC8	7731	0.011	0.26	NO
185	TTC5	TTC5	TTC5	7807	0.01	0.26	NO
186	PRKD1	PRKD1	PRKD1	7825	0.01	0.26	NO
187	TTLL5	TTLL5	TTLL5	7853	0.0097	0.26	NO
188	CHST10	CHST10	CHST10	7895	0.0093	0.26	NO
189	FIP1L1	FIP1L1	FIP1L1	7962	0.0084	0.25	NO
190	KAT8	KAT8	KAT8	8008	0.0078	0.25	NO
191	ABCD4	ABCD4	ABCD4	8009	0.0078	0.25	NO
192	VBP1	VBP1	VBP1	8057	0.0074	0.25	NO
193	ZNF92	ZNF92	ZNF92	8082	0.0071	0.25	NO
194	NBR1	NBR1	NBR1	8104	0.0068	0.24	NO
195	MPHOSPH10	MPHOSPH10	MPHOSPH10	8151	0.0064	0.24	NO
196	PPM1D	PPM1D	PPM1D	8196	0.0059	0.24	NO
197	ATRX	ATRX	ATRX	8283	0.0048	0.24	NO
198	IFT43	IFT43	IFT43	8389	0.0036	0.23	NO
199	RBM25	RBM25	RBM25	8420	0.0033	0.23	NO
200	LCLAT1	LCLAT1	LCLAT1	8422	0.0032	0.23	NO
201	SUPT7L	SUPT7L	SUPT7L	8445	0.003	0.23	NO
202	ZNF263	ZNF263	ZNF263	8446	0.003	0.23	NO
203	NDUFS1	NDUFS1	NDUFS1	8494	0.0022	0.23	NO
204	MTHFSD	MTHFSD	MTHFSD	8495	0.0022	0.23	NO
205	ISCA2	ISCA2	ISCA2	8499	0.0022	0.23	NO
206	PGRMC1	PGRMC1	PGRMC1	8503	0.0021	0.23	NO
207	GLRX5	GLRX5	GLRX5	8543	0.0016	0.22	NO
208	BOLA1	BOLA1	BOLA1	8551	0.0015	0.22	NO
209	ZMYM3	ZMYM3	ZMYM3	8585	0.0012	0.22	NO
210	SUMO1	SUMO1	SUMO1	8619	0.00088	0.22	NO
211	APBA2	APBA2	APBA2	8685	0.00021	0.22	NO
212	GATC	GATC	GATC	8715	-0.00018	0.21	NO
213	HSD17B12	HSD17B12	HSD17B12	8732	-0.00037	0.21	NO
214	APPBP2	APPBP2	APPBP2	8765	-0.00067	0.21	NO
215	TRIP12	TRIP12	TRIP12	8783	-0.00094	0.21	NO
216	ADAM17	ADAM17	ADAM17	8807	-0.0013	0.21	NO
217	AKAP1	AKAP1	AKAP1	8809	-0.0013	0.21	NO
218	MRPL1	MRPL1	MRPL1	8823	-0.0015	0.21	NO
219	TMEM128	TMEM128	TMEM128	8887	-0.0023	0.21	NO
220	YIPF6	YIPF6	YIPF6	8921	-0.0027	0.2	NO
221	B4GALT5	B4GALT5	B4GALT5	8946	-0.003	0.2	NO
222	DTX3	DTX3	DTX3	8950	-0.0031	0.2	NO
223	SLC37A3	SLC37A3	SLC37A3	8953	-0.0031	0.2	NO
224	DYRK4	DYRK4	DYRK4	8982	-0.0034	0.2	NO
225	IPO8	IPO8	IPO8	8991	-0.0035	0.2	NO
226	USP51	USP51	USP51	9006	-0.0037	0.2	NO
227	UBFD1	UBFD1	UBFD1	9009	-0.0037	0.2	NO
228	RPE	RPE	RPE	9022	-0.0038	0.2	NO
229	NOL9	NOL9	NOL9	9045	-0.0041	0.2	NO
230	TCTN3	TCTN3	TCTN3	9180	-0.0056	0.19	NO
231	TUBGCP4	TUBGCP4	TUBGCP4	9209	-0.006	0.19	NO
232	PSMD1	PSMD1	PSMD1	9483	-0.0093	0.18	NO
233	HEBP1	HEBP1	HEBP1	9497	-0.0094	0.18	NO
234	ABI2	ABI2	ABI2	9510	-0.0096	0.18	NO
235	APOLD1	APOLD1	APOLD1	9544	-0.01	0.17	NO
236	NCL	NCL	NCL	9582	-0.01	0.17	NO
237	ITGB5	ITGB5	ITGB5	9587	-0.01	0.17	NO
238	ABCB7	ABCB7	ABCB7	9606	-0.011	0.17	NO
239	ELP2	ELP2	ELP2	9628	-0.011	0.17	NO
240	QPCT	QPCT	QPCT	9708	-0.012	0.17	NO
241	DPY30	DPY30	DPY30	9725	-0.012	0.17	NO
242	DDR2	DDR2	DDR2	9753	-0.012	0.17	NO
243	ACVR1B	ACVR1B	ACVR1B	9864	-0.014	0.16	NO
244	CKAP5	CKAP5	CKAP5	9941	-0.015	0.16	NO
245	PDXDC1	PDXDC1	PDXDC1	9982	-0.015	0.16	NO
246	DNAJC18	DNAJC18	DNAJC18	10187	-0.017	0.14	NO
247	PFKM	PFKM	PFKM	10272	-0.018	0.14	NO
248	MECP2	MECP2	MECP2	10349	-0.02	0.14	NO
249	GNAS	GNAS	GNAS	10434	-0.02	0.14	NO
250	GIGYF2	GIGYF2	GIGYF2	10514	-0.022	0.13	NO
251	BDH2	BDH2	BDH2	10540	-0.022	0.13	NO
252	EP400	EP400	EP400	10544	-0.022	0.13	NO
253	CDK5RAP3	CDK5RAP3	CDK5RAP3	10642	-0.023	0.13	NO
254	AGFG1	AGFG1	AGFG1	10668	-0.024	0.13	NO
255	MGP	MGP	MGP	10677	-0.024	0.13	NO
256	YARS2	YARS2	YARS2	10752	-0.025	0.12	NO
257	VKORC1L1	VKORC1L1	VKORC1L1	10830	-0.026	0.12	NO
258	NOP58	NOP58	NOP58	10896	-0.027	0.12	NO
259	ZNF764	ZNF764	ZNF764	10917	-0.027	0.12	NO
260	NEK9	NEK9	NEK9	10922	-0.027	0.12	NO
261	MRPL44	MRPL44	MRPL44	11091	-0.029	0.11	NO
262	PDZD11	PDZD11	PDZD11	11117	-0.03	0.11	NO
263	C11orf49	C11orf49	C11orf49	11118	-0.03	0.12	NO
264	PDIA4	PDIA4	PDIA4	11130	-0.03	0.12	NO
265	FASTKD2	FASTKD2	FASTKD2	11244	-0.031	0.11	NO
266	EDAR	EDAR	EDAR	11450	-0.034	0.1	NO
267	AMZ2	AMZ2	AMZ2	11713	-0.037	0.089	NO
268	SCFD2	SCFD2	SCFD2	11721	-0.038	0.09	NO
269	PHB	PHB	PHB	11750	-0.038	0.091	NO
270	FAM134A	FAM134A	FAM134A	11800	-0.039	0.09	NO
271	NMT1	NMT1	NMT1	11841	-0.039	0.09	NO
272	TMX4	TMX4	TMX4	11866	-0.04	0.09	NO
273	CNPY2	CNPY2	CNPY2	11889	-0.04	0.091	NO
274	SEC14L4	SEC14L4	SEC14L4	12033	-0.042	0.085	NO
275	NAT10	NAT10	NAT10	12037	-0.042	0.087	NO
276	GPRC5B	GPRC5B	GPRC5B	12089	-0.043	0.086	NO
277	TPST1	TPST1	TPST1	12177	-0.044	0.084	NO
278	TMEM201	TMEM201	TMEM201	12225	-0.045	0.083	NO
279	DYRK2	DYRK2	DYRK2	12261	-0.045	0.084	NO
280	RNF25	RNF25	RNF25	12313	-0.046	0.083	NO
281	DHX8	DHX8	DHX8	12360	-0.047	0.083	NO
282	COPS8	COPS8	COPS8	12376	-0.047	0.085	NO
283	DDIT3	DDIT3	DDIT3	12478	-0.049	0.082	NO
284	NUDT9	NUDT9	NUDT9	12491	-0.049	0.083	NO
285	WBSCR22	WBSCR22	WBSCR22	12496	-0.049	0.086	NO
286	DIS3L2	DIS3L2	DIS3L2	12509	-0.05	0.088	NO
287	MFF	MFF	MFF	12575	-0.051	0.086	NO
288	C1orf56	C1orf56	C1orf56	13008	-0.059	0.065	NO
289	DNAL1	DNAL1	DNAL1	13111	-0.061	0.062	NO
290	SH3RF3	SH3RF3	SH3RF3	13174	-0.062	0.062	NO
291	SNF8	SNF8	SNF8	13198	-0.063	0.064	NO
292	FGF19	FGF19	FGF19	13402	-0.067	0.056	NO
293	HIRIP3	HIRIP3	HIRIP3	13692	-0.073	0.044	NO
294	ATP9A	ATP9A	ATP9A	13733	-0.074	0.045	NO
295	SEPHS2	SEPHS2	SEPHS2	13882	-0.078	0.041	NO
296	DTX4	DTX4	DTX4	13948	-0.08	0.041	NO
297	ZNF704	ZNF704	ZNF704	14025	-0.082	0.041	NO
298	GCAT	GCAT	GCAT	14026	-0.082	0.045	NO
299	ILKAP	ILKAP	ILKAP	14031	-0.082	0.049	NO
300	SLC11A2	SLC11A2	SLC11A2	14092	-0.084	0.05	NO
301	FAM19A5	FAM19A5	FAM19A5	14319	-0.09	0.042	NO
302	ACACB	ACACB	ACACB	14627	-0.1	0.03	NO
303	HJURP	HJURP	HJURP	14648	-0.1	0.034	NO
304	HIST1H2BG	HIST1H2BG	HIST1H2BG	14825	-0.11	0.03	NO
305	GAS7	GAS7	GAS7	14827	-0.11	0.035	NO
306	CDCA3	CDCA3	CDCA3	14915	-0.11	0.036	NO
307	APITD1	APITD1	APITD1	15014	-0.12	0.036	NO
308	RASL12	RASL12	RASL12	15724	-0.15	0.0043	NO
309	VSTM4	VSTM4	VSTM4	15744	-0.16	0.011	NO
310	METTL7B	METTL7B	METTL7B	16062	-0.17	0.0021	NO
311	GPR19	GPR19	GPR19	16195	-0.18	0.004	NO
312	FRZB	FRZB	FRZB	16250	-0.19	0.01	NO
313	SLC22A17	SLC22A17	SLC22A17	16614	-0.21	0.00091	NO
314	ADAMTS9	ADAMTS9	ADAMTS9	16669	-0.22	0.009	NO
315	PXDN	PXDN	PXDN	17443	-0.31	-0.019	NO
316	LGR6	LGR6	LGR6	17503	-0.32	-0.0057	NO
317	GEM	GEM	GEM	17699	-0.36	0.0016	NO
318	CADM1	CADM1	CADM1	17789	-0.39	0.017	NO

Figure S53. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME PEPTIDE CHAIN ELONGATION.

Figure S54. 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

genes ES table in pathway: REACTOME MRNA PROCESSING

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	FAM153A	FAM153A	FAM153A	171	0.42	0.064	YES
2	RPL3L	RPL3L	RPL3L	1067	0.2	0.049	YES
3	RPL35A	RPL35A	RPL35A	1790	0.14	0.034	YES
4	RPL15	RPL15	RPL15	1873	0.14	0.054	YES
5	RPL24	RPL24	RPL24	2091	0.13	0.063	YES
6	RPSA	RPSA	RPSA	2101	0.13	0.084	YES
7	RPL32	RPL32	RPL32	2306	0.12	0.093	YES
8	RPL14	RPL14	RPL14	2343	0.12	0.11	YES
9	RPS3A	RPS3A	RPS3A	2351	0.12	0.13	YES
10	RPS10	RPS10	RPS10	2727	0.1	0.13	YES
11	RPS18	RPS18	RPS18	2815	0.097	0.14	YES
12	RPL5	RPL5	RPL5	2860	0.096	0.15	YES
13	RPS7	RPS7	RPS7	2933	0.093	0.17	YES
14	RPS12	RPS12	RPS12	2965	0.092	0.18	YES
15	RPL10A	RPL10A	RPL10A	2969	0.092	0.2	YES
16	NCBP2	NCBP2	NCBP2	3097	0.088	0.2	YES
17	RPL9	RPL9	RPL9	3179	0.086	0.21	YES
18	RPS6	RPS6	RPS6	3252	0.084	0.22	YES
19	RPL17	RPL17	RPL17	3264	0.083	0.24	YES
20	RPL29	RPL29	RPL29	3363	0.08	0.25	YES
21	RPL26	RPL26	RPL26	3475	0.078	0.25	YES
22	RPS15A	RPS15A	RPS15A	3592	0.074	0.26	YES
23	RPL31	RPL31	RPL31	3742	0.071	0.26	YES
24	RPL21	RPL21	RPL21	3755	0.07	0.28	YES
25	RPL22	RPL22	RPL22	3771	0.07	0.29	YES
26	RPS8	RPS8	RPS8	3840	0.069	0.3	YES
27	RPL34	RPL34	RPL34	3875	0.068	0.3	YES
28	RPS23	RPS23	RPS23	3933	0.067	0.31	YES
29	RPS27A	RPS27A	RPS27A	3935	0.067	0.32	YES
30	RPS17	RPS17	RPS17	4062	0.064	0.33	YES
31	RPL36A	RPL36A	RPL36A	4091	0.063	0.34	YES
32	RPS24	RPS24	RPS24	4096	0.063	0.35	YES
33	RPL3	RPL3	RPL3	4125	0.062	0.36	YES
34	RPL39	RPL39	RPL39	4188	0.061	0.37	YES
35	PPP2R2A	PPP2R2A	PPP2R2A	4245	0.06	0.37	YES
36	RPL11	RPL11	RPL11	4262	0.06	0.38	YES
37	RPS29	RPS29	RPS29	4266	0.06	0.39	YES
38	RPL12	RPL12	RPL12	4386	0.057	0.4	YES
39	RPL13A	RPL13A	RPL13A	4390	0.057	0.41	YES
40	RPS3	RPS3	RPS3	4443	0.056	0.41	YES
41	RPL23	RPL23	RPL23	4461	0.056	0.42	YES
42	RPS27	RPS27	RPS27	4594	0.053	0.42	YES
43	RPS25	RPS25	RPS25	4613	0.053	0.43	YES
44	RPS19	RPS19	RPS19	4712	0.051	0.44	YES
45	RPLP1	RPLP1	RPLP1	4714	0.051	0.44	YES
46	RPS4Y1	RPS4Y1	RPS4Y1	4718	0.051	0.45	YES
47	RPL38	RPL38	RPL38	4734	0.051	0.46	YES
48	SMG1	SMG1	SMG1	4753	0.05	0.47	YES
49	RPLP0	RPLP0	RPLP0	4777	0.05	0.48	YES
50	RPL4	RPL4	RPL4	4798	0.05	0.48	YES
51	RPL6	RPL6	RPL6	4932	0.048	0.48	YES
52	SMG8	SMG8	SMG8	4993	0.046	0.49	YES
53	RPS9	RPS9	RPS9	5177	0.044	0.48	YES
54	RPL7A	RPL7A	RPL7A	5194	0.044	0.49	YES
55	EIF4G1	EIF4G1	EIF4G1	5311	0.042	0.49	YES
56	RPS14	RPS14	RPS14	5427	0.04	0.49	YES
57	RPS5	RPS5	RPS5	5485	0.039	0.5	YES
58	RPS4X	RPS4X	RPS4X	5510	0.039	0.5	YES
59	RPL18	RPL18	RPL18	5615	0.037	0.5	YES
60	RPS13	RPS13	RPS13	5631	0.037	0.51	YES
61	RPL27	RPL27	RPL27	5643	0.037	0.51	YES
62	RPL13	RPL13	RPL13	5684	0.036	0.52	YES
63	RPL10	RPL10	RPL10	5695	0.036	0.52	YES
64	RPS21	RPS21	RPS21	5728	0.036	0.53	YES
65	RPL27A	RPL27A	RPL27A	5751	0.035	0.53	YES
66	RPL41	RPL41	RPL41	5839	0.034	0.53	YES
67	RPS28	RPS28	RPS28	5856	0.034	0.54	YES
68	RPL37	RPL37	RPL37	5859	0.034	0.55	YES
69	RPS2	RPS2	RPS2	5894	0.033	0.55	YES
70	RPL37A	RPL37A	RPL37A	5936	0.033	0.55	YES
71	RPL35	RPL35	RPL35	6061	0.031	0.55	YES
72	RPL18A	RPL18A	RPL18A	6112	0.03	0.55	YES
73	RPLP2	RPLP2	RPLP2	6479	0.026	0.54	NO
74	UPF3B	UPF3B	UPF3B	6530	0.025	0.54	NO
75	RPS16	RPS16	RPS16	6545	0.025	0.54	NO
76	RPS11	RPS11	RPS11	6717	0.023	0.54	NO
77	PABPC1	PABPC1	PABPC1	6719	0.023	0.54	NO
78	UPF3A	UPF3A	UPF3A	6844	0.021	0.54	NO
79	FAU	FAU	FAU	6968	0.02	0.53	NO
80	RPL19	RPL19	RPL19	7035	0.019	0.53	NO
81	RPS15	RPS15	RPS15	7048	0.019	0.54	NO
82	RPL7	RPL7	RPL7	7334	0.016	0.52	NO
83	RPL36	RPL36	RPL36	7419	0.015	0.52	NO
84	RPL23A	RPL23A	RPL23A	7663	0.012	0.51	NO
85	RPL30	RPL30	RPL30	7712	0.011	0.51	NO
86	PPP2CA	PPP2CA	PPP2CA	8062	0.0073	0.49	NO
87	ETF1	ETF1	ETF1	8068	0.0073	0.49	NO
88	RBM8A	RBM8A	RBM8A	8070	0.0072	0.49	NO
89	UBA52	UBA52	UBA52	8081	0.0071	0.49	NO
90	UPF2	UPF2	UPF2	8255	0.0051	0.48	NO
91	RPL28	RPL28	RPL28	8581	0.0013	0.47	NO
92	RPL8	RPL8	RPL8	8857	-0.002	0.45	NO
93	GSPT2	GSPT2	GSPT2	9288	-0.007	0.43	NO
94	RNPS1	RNPS1	RNPS1	9398	-0.0085	0.42	NO
95	SMG7	SMG7	SMG7	9456	-0.009	0.42	NO
96	SMG6	SMG6	SMG6	9458	-0.009	0.42	NO
97	RPS20	RPS20	RPS20	9586	-0.01	0.42	NO
98	MAGOH	MAGOH	MAGOH	9922	-0.015	0.4	NO
99	NCBP1	NCBP1	NCBP1	10026	-0.016	0.4	NO
100	RPS26	RPS26	RPS26	10232	-0.018	0.39	NO
101	CASC3	CASC3	CASC3	11286	-0.032	0.34	NO
102	PPP2R1A	PPP2R1A	PPP2R1A	11859	-0.04	0.31	NO
103	EIF4A3	EIF4A3	EIF4A3	11886	-0.04	0.32	NO
104	RPL26L1	RPL26L1	RPL26L1	11970	-0.041	0.32	NO
105	SMG5	SMG5	SMG5	12622	-0.052	0.3	NO
106	SMG9	SMG9	SMG9	12646	-0.052	0.3	NO

Figure S55. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME MRNA PROCESSING.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MRNA PROCESSING, 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 3 UTR MEDIATED TRANSLATIONAL REGULATION

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	FAM153A	FAM153A	FAM153A	171	0.42	0.05	YES
2	RPL3L	RPL3L	RPL3L	1067	0.2	0.029	YES
3	EIF4A2	EIF4A2	EIF4A2	1268	0.18	0.044	YES
4	RPL35A	RPL35A	RPL35A	1790	0.14	0.035	YES
5	RPL15	RPL15	RPL15	1873	0.14	0.05	YES
6	RPL24	RPL24	RPL24	2091	0.13	0.056	YES
7	RPSA	RPSA	RPSA	2101	0.13	0.073	YES
8	RPL32	RPL32	RPL32	2306	0.12	0.078	YES
9	RPL14	RPL14	RPL14	2343	0.12	0.092	YES
10	RPS3A	RPS3A	RPS3A	2351	0.12	0.11	YES
11	RPS10	RPS10	RPS10	2727	0.1	0.1	YES
12	EEF1A1	EEF1A1	EEF1A1	2749	0.1	0.11	YES
13	RPS18	RPS18	RPS18	2815	0.097	0.12	YES
14	RPL5	RPL5	RPL5	2860	0.096	0.14	YES
15	RPS7	RPS7	RPS7	2933	0.093	0.14	YES
16	RPS12	RPS12	RPS12	2965	0.092	0.16	YES
17	RPL10A	RPL10A	RPL10A	2969	0.092	0.17	YES
18	RPL9	RPL9	RPL9	3179	0.086	0.17	YES
19	RPS6	RPS6	RPS6	3252	0.084	0.18	YES
20	RPL17	RPL17	RPL17	3264	0.083	0.19	YES
21	RPL29	RPL29	RPL29	3363	0.08	0.19	YES
22	RPL26	RPL26	RPL26	3475	0.078	0.2	YES
23	EIF2B5	EIF2B5	EIF2B5	3518	0.076	0.21	YES
24	SSR3	SSR3	SSR3	3557	0.075	0.22	YES
25	RPS15A	RPS15A	RPS15A	3592	0.074	0.22	YES
26	EIF2S3	EIF2S3	EIF2S3	3732	0.071	0.23	YES
27	RPL31	RPL31	RPL31	3742	0.071	0.24	YES
28	RPL21	RPL21	RPL21	3755	0.07	0.25	YES
29	RPL22	RPL22	RPL22	3771	0.07	0.26	YES
30	RPS8	RPS8	RPS8	3840	0.069	0.26	YES
31	RPL34	RPL34	RPL34	3875	0.068	0.27	YES
32	RPS23	RPS23	RPS23	3933	0.067	0.27	YES
33	RPS27A	RPS27A	RPS27A	3935	0.067	0.28	YES
34	RPS17	RPS17	RPS17	4062	0.064	0.29	YES
35	RPL36A	RPL36A	RPL36A	4091	0.063	0.29	YES
36	RPS24	RPS24	RPS24	4096	0.063	0.3	YES
37	RPL3	RPL3	RPL3	4125	0.062	0.31	YES
38	RPL39	RPL39	RPL39	4188	0.061	0.31	YES
39	RPL11	RPL11	RPL11	4262	0.06	0.32	YES
40	RPS29	RPS29	RPS29	4266	0.06	0.33	YES
41	EEF1B2	EEF1B2	EEF1B2	4375	0.057	0.33	YES
42	RPL12	RPL12	RPL12	4386	0.057	0.34	YES
43	RPL13A	RPL13A	RPL13A	4390	0.057	0.34	YES
44	RPS3	RPS3	RPS3	4443	0.056	0.35	YES
45	RPL23	RPL23	RPL23	4461	0.056	0.36	YES
46	RPS27	RPS27	RPS27	4594	0.053	0.36	YES
47	RPS25	RPS25	RPS25	4613	0.053	0.36	YES
48	RPS19	RPS19	RPS19	4712	0.051	0.36	YES
49	RPLP1	RPLP1	RPLP1	4714	0.051	0.37	YES
50	RPS4Y1	RPS4Y1	RPS4Y1	4718	0.051	0.38	YES
51	EIF4B	EIF4B	EIF4B	4730	0.051	0.38	YES
52	RPL38	RPL38	RPL38	4734	0.051	0.39	YES
53	RPLP0	RPLP0	RPLP0	4777	0.05	0.4	YES
54	RPL4	RPL4	RPL4	4798	0.05	0.4	YES
55	SRPRB	SRPRB	SRPRB	4871	0.048	0.41	YES
56	EIF1AX	EIF1AX	EIF1AX	4918	0.048	0.41	YES
57	RPL6	RPL6	RPL6	4932	0.048	0.42	YES
58	RPS9	RPS9	RPS9	5177	0.044	0.41	YES
59	SPCS1	SPCS1	SPCS1	5181	0.044	0.42	YES
60	RPL7A	RPL7A	RPL7A	5194	0.044	0.42	YES
61	EIF5	EIF5	EIF5	5297	0.042	0.42	YES
62	EIF4G1	EIF4G1	EIF4G1	5311	0.042	0.42	YES
63	RPS14	RPS14	RPS14	5427	0.04	0.42	YES
64	RPS5	RPS5	RPS5	5485	0.039	0.43	YES
65	RPS4X	RPS4X	RPS4X	5510	0.039	0.43	YES
66	SEC11A	SEC11A	SEC11A	5548	0.038	0.43	YES
67	RPL18	RPL18	RPL18	5615	0.037	0.44	YES
68	RPS13	RPS13	RPS13	5631	0.037	0.44	YES
69	RPL27	RPL27	RPL27	5643	0.037	0.44	YES
70	RPL13	RPL13	RPL13	5684	0.036	0.45	YES
71	RPL10	RPL10	RPL10	5695	0.036	0.45	YES
72	RPS21	RPS21	RPS21	5728	0.036	0.46	YES
73	RPL27A	RPL27A	RPL27A	5751	0.035	0.46	YES
74	SSR1	SSR1	SSR1	5790	0.035	0.46	YES
75	RPL41	RPL41	RPL41	5839	0.034	0.46	YES
76	RPS28	RPS28	RPS28	5856	0.034	0.47	YES
77	RPL37	RPL37	RPL37	5859	0.034	0.47	YES
78	RPS2	RPS2	RPS2	5894	0.033	0.48	YES
79	RPL37A	RPL37A	RPL37A	5936	0.033	0.48	YES
80	EIF3D	EIF3D	EIF3D	5964	0.032	0.48	YES
81	EIF3A	EIF3A	EIF3A	6012	0.032	0.48	YES
82	RPL35	RPL35	RPL35	6061	0.031	0.48	YES
83	RPL18A	RPL18A	RPL18A	6112	0.03	0.49	YES
84	EIF3C	EIF3C	EIF3C	6119	0.03	0.49	YES
85	EIF3H	EIF3H	EIF3H	6304	0.028	0.48	NO
86	EEF2	EEF2	EEF2	6332	0.028	0.49	NO
87	RPLP2	RPLP2	RPLP2	6479	0.026	0.48	NO
88	EIF3F	EIF3F	EIF3F	6492	0.026	0.48	NO
89	EIF3E	EIF3E	EIF3E	6509	0.026	0.49	NO
90	RPS16	RPS16	RPS16	6545	0.025	0.49	NO
91	RPS11	RPS11	RPS11	6717	0.023	0.48	NO
92	PABPC1	PABPC1	PABPC1	6719	0.023	0.49	NO
93	EIF4A1	EIF4A1	EIF4A1	6809	0.022	0.48	NO
94	FAU	FAU	FAU	6968	0.02	0.48	NO
95	RPL19	RPL19	RPL19	7035	0.019	0.48	NO
96	RPS15	RPS15	RPS15	7048	0.019	0.48	NO
97	EIF3G	EIF3G	EIF3G	7054	0.019	0.48	NO
98	SRP19	SRP19	SRP19	7123	0.018	0.48	NO
99	EIF3K	EIF3K	EIF3K	7252	0.016	0.48	NO
100	RPL7	RPL7	RPL7	7334	0.016	0.47	NO
101	RPL36	RPL36	RPL36	7419	0.015	0.47	NO
102	RPL23A	RPL23A	RPL23A	7663	0.012	0.46	NO
103	RPL30	RPL30	RPL30	7712	0.011	0.46	NO
104	EEF1G	EEF1G	EEF1G	7729	0.011	0.46	NO
105	SSR2	SSR2	SSR2	7803	0.01	0.46	NO
106	RPN1	RPN1	RPN1	7861	0.0096	0.45	NO
107	SRP9	SRP9	SRP9	7980	0.0082	0.45	NO
108	EIF2B1	EIF2B1	EIF2B1	8044	0.0074	0.45	NO
109	ETF1	ETF1	ETF1	8068	0.0073	0.45	NO
110	UBA52	UBA52	UBA52	8081	0.0071	0.45	NO
111	EIF4E	EIF4E	EIF4E	8171	0.0062	0.44	NO
112	EIF2S2	EIF2S2	EIF2S2	8212	0.0057	0.44	NO
113	EIF5B	EIF5B	EIF5B	8485	0.0024	0.43	NO
114	RPL28	RPL28	RPL28	8581	0.0013	0.42	NO
115	SRP72	SRP72	SRP72	8590	0.0012	0.42	NO
116	EIF4H	EIF4H	EIF4H	8770	-0.00075	0.41	NO
117	DDOST	DDOST	DDOST	8771	-0.00076	0.41	NO
118	EIF3J	EIF3J	EIF3J	8772	-0.00076	0.41	NO
119	RPL8	RPL8	RPL8	8857	-0.002	0.41	NO
120	SEC61A1	SEC61A1	SEC61A1	8877	-0.0022	0.4	NO
121	EIF2B3	EIF2B3	EIF2B3	9041	-0.004	0.4	NO
122	EIF3I	EIF3I	EIF3I	9272	-0.0068	0.38	NO
123	GSPT2	GSPT2	GSPT2	9288	-0.007	0.38	NO
124	RPS20	RPS20	RPS20	9586	-0.01	0.37	NO
125	SRP54	SRP54	SRP54	9592	-0.01	0.37	NO
126	SEC61B	SEC61B	SEC61B	9910	-0.014	0.36	NO
127	SRP14	SRP14	SRP14	10142	-0.017	0.34	NO
128	SSR4	SSR4	SSR4	10147	-0.017	0.35	NO
129	SRP68	SRP68	SRP68	10211	-0.018	0.35	NO
130	RPS26	RPS26	RPS26	10232	-0.018	0.35	NO
131	SPCS3	SPCS3	SPCS3	10284	-0.019	0.35	NO
132	EEF1D	EEF1D	EEF1D	10294	-0.019	0.35	NO
133	EIF2B2	EIF2B2	EIF2B2	10398	-0.02	0.35	NO
134	SEC61A2	SEC61A2	SEC61A2	11053	-0.029	0.31	NO
135	RPN2	RPN2	RPN2	11397	-0.033	0.3	NO
136	EIF2S1	EIF2S1	EIF2S1	11538	-0.035	0.3	NO
137	SRPR	SRPR	SRPR	11648	-0.036	0.3	NO
138	RPL26L1	RPL26L1	RPL26L1	11970	-0.041	0.28	NO
139	SEC11C	SEC11C	SEC11C	12222	-0.045	0.28	NO
140	SEC61G	SEC61G	SEC61G	12440	-0.048	0.27	NO
141	EIF2B4	EIF2B4	EIF2B4	12676	-0.052	0.26	NO
142	EIF4EBP1	EIF4EBP1	EIF4EBP1	12818	-0.055	0.26	NO
143	EIF3B	EIF3B	EIF3B	13153	-0.062	0.26	NO
144	TRAM1	TRAM1	TRAM1	13252	-0.064	0.26	NO
145	SPCS2	SPCS2	SPCS2	13699	-0.074	0.24	NO

Figure S57. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION, 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 INFLUENZA LIFE CYCLE

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	TARDBP	TARDBP	TARDBP	301	0.36	0.12	YES
2	ZNF544	ZNF544	ZNF544	931	0.22	0.17	YES
3	FAM60A	FAM60A	FAM60A	1920	0.14	0.17	YES
4	TOMM70A	TOMM70A	TOMM70A	2342	0.12	0.19	YES
5	CMTM6	CMTM6	CMTM6	2432	0.11	0.22	YES
6	UBE2E1	UBE2E1	UBE2E1	2704	0.1	0.25	YES
7	NAP1L1	NAP1L1	NAP1L1	3121	0.088	0.26	YES
8	ST13	ST13	ST13	3820	0.069	0.24	YES
9	CCDC90B	CCDC90B	CCDC90B	3865	0.068	0.27	YES
10	PLEKHA5	PLEKHA5	PLEKHA5	3910	0.067	0.29	YES
11	PUM2	PUM2	PUM2	4220	0.061	0.3	YES
12	PPP2R2A	PPP2R2A	PPP2R2A	4245	0.06	0.32	YES
13	COMMD3	COMMD3	COMMD3	4288	0.059	0.34	YES
14	PRPF4B	PRPF4B	PRPF4B	4334	0.058	0.36	YES
15	RAPGEF2	RAPGEF2	RAPGEF2	4456	0.056	0.37	YES
16	RRAGC	RRAGC	RRAGC	4680	0.052	0.38	YES
17	SRPRB	SRPRB	SRPRB	4871	0.048	0.39	YES
18	RBBP4	RBBP4	RBBP4	4981	0.047	0.4	YES
19	SEC11A	SEC11A	SEC11A	5548	0.038	0.38	YES
20	DUT	DUT	DUT	5576	0.038	0.4	YES
21	SLC25A46	SLC25A46	SLC25A46	5678	0.036	0.4	YES
22	MRFAP1L1	MRFAP1L1	MRFAP1L1	5873	0.034	0.41	YES
23	RALA	RALA	RALA	6292	0.028	0.39	NO
24	TSPO	TSPO	TSPO	7541	0.013	0.33	NO
25	GMFB	GMFB	GMFB	7566	0.013	0.33	NO
26	SEC23B	SEC23B	SEC23B	7831	0.0099	0.32	NO
27	MTRF1L	MTRF1L	MTRF1L	7944	0.0086	0.32	NO
28	GORASP2	GORASP2	GORASP2	8824	-0.0015	0.27	NO
29	ATP5A1	ATP5A1	ATP5A1	9157	-0.0054	0.26	NO
30	HSPA4	HSPA4	HSPA4	9429	-0.0088	0.24	NO
31	PLEKHJ1	PLEKHJ1	PLEKHJ1	9487	-0.0094	0.24	NO
32	CCT3	CCT3	CCT3	9816	-0.013	0.23	NO
33	R3HDM1	R3HDM1	R3HDM1	10634	-0.023	0.19	NO
34	TTYH2	TTYH2	TTYH2	10951	-0.027	0.19	NO
35	IL17RA	IL17RA	IL17RA	12212	-0.044	0.13	NO
36	C20orf24	C20orf24	C20orf24	12417	-0.048	0.14	NO
37	FTL	FTL	FTL	13066	-0.06	0.13	NO
38	C11orf21	C11orf21	C11orf21	15645	-0.15	0.041	NO
39	CD52	CD52	CD52	16994	-0.25	0.06	NO

Figure S59. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME INFLUENZA LIFE CYCLE.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus4 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG OXIDATIVE PHOSPHORYLATION	114	genes.ES.table	0.46	1.7	0.033	0.44	0.9	0.67	0.32	0.46	0.19	0.11
SCHLOSSER MYC AND SERUM RESPONSE SYNERGY	32	genes.ES.table	0.62	1.7	0.0039	0.41	0.9	0.66	0.2	0.53	0.18	0.1
DACOSTA UV RESPONSE VIA ERCC3 UP	300	genes.ES.table	0.44	1.8	0.002	0.53	0.7	0.56	0.26	0.42	0.18	0.11
DAIRKEE TERT TARGETS UP	349	genes.ES.table	0.38	1.7	0.002	0.44	0.88	0.59	0.25	0.45	0.19	0.1
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP	469	genes.ES.table	0.36	1.8	0.012	0.44	0.83	0.5	0.25	0.38	0.17	0.1
LOCKWOOD AMPLIFIED IN LUNG CANCER	207	genes.ES.table	0.26	1.7	0.0061	0.4	0.9	0.45	0.25	0.34	0.17	0.096
PENG LEUCINE DEPRIVATION DN	183	genes.ES.table	0.35	1.7	0.032	0.4	0.91	0.51	0.31	0.36	0.18	0.095
MOOTHA VOXPHOS	86	genes.ES.table	0.57	1.7	0.018	0.47	0.86	0.74	0.32	0.51	0.2	0.11
PENG GLUTAMINE DEPRIVATION DN	327	genes.ES.table	0.3	1.8	0.036	0.43	0.8	0.49	0.31	0.34	0.16	0.093
FAELT B CLL WITH VH3 21 UP	42	genes.ES.table	0.59	1.7	0.018	0.44	0.89	0.76	0.27	0.56	0.19	0.1

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SLC19A1	SLC19A1	SLC19A1	452	0.16	-0.0098	YES
2	FASN	FASN	FASN	504	0.16	0.0022	YES
3	BOP1	BOP1	BOP1	517	0.16	0.016	YES
4	GAL	GAL	GAL	567	0.15	0.028	YES
5	PKN1	PKN1	PKN1	659	0.15	0.036	YES
6	GALK1	GALK1	GALK1	694	0.14	0.048	YES
7	CDC25B	CDC25B	CDC25B	711	0.14	0.06	YES
8	FARSA	FARSA	FARSA	759	0.14	0.071	YES
9	CCDC85B	CCDC85B	CCDC85B	762	0.14	0.084	YES
10	SLC1A5	SLC1A5	SLC1A5	768	0.14	0.097	YES
11	SRM	SRM	SRM	805	0.14	0.11	YES
12	CAD	CAD	CAD	858	0.14	0.12	YES
13	TRAP1	TRAP1	TRAP1	913	0.13	0.13	YES
14	RELA	RELA	RELA	972	0.13	0.14	YES
15	NOS2	NOS2	NOS2	1030	0.13	0.14	YES
16	ALG3	ALG3	ALG3	1248	0.12	0.14	YES
17	CYC1	CYC1	CYC1	1282	0.12	0.15	YES
18	HRAS	HRAS	HRAS	1298	0.12	0.16	YES
19	POLRMT	POLRMT	POLRMT	1315	0.12	0.17	YES
20	MRPS12	MRPS12	MRPS12	1319	0.12	0.19	YES
21	HSF1	HSF1	HSF1	1345	0.12	0.2	YES
22	EIF3B	EIF3B	EIF3B	1392	0.12	0.2	YES
23	ANXA11	ANXA11	ANXA11	1464	0.12	0.21	YES
24	CHAF1A	CHAF1A	CHAF1A	1536	0.11	0.22	YES
25	SMARCA4	SMARCA4	SMARCA4	1566	0.11	0.23	YES
26	AIMP2	AIMP2	AIMP2	1568	0.11	0.24	YES
27	PRKACA	PRKACA	PRKACA	1672	0.11	0.24	YES
28	PWP2	PWP2	PWP2	1709	0.11	0.25	YES
29	FKBP4	FKBP4	FKBP4	1763	0.11	0.26	YES
30	USP5	USP5	USP5	1986	0.1	0.25	YES
31	NAT6	NAT6	NAT6	1992	0.1	0.26	YES
32	HDLBP	HDLBP	HDLBP	2016	0.1	0.27	YES
33	PHKG2	PHKG2	PHKG2	2065	0.1	0.28	YES
34	NME3	NME3	NME3	2127	0.1	0.28	YES
35	NUP214	NUP214	NUP214	2249	0.098	0.29	YES
36	HCFC1	HCFC1	HCFC1	2253	0.098	0.3	YES
37	ATIC	ATIC	ATIC	2297	0.097	0.3	YES
38	PPM1F	PPM1F	PPM1F	2311	0.097	0.31	YES
39	PRRC2A	PRRC2A	PRRC2A	2316	0.097	0.32	YES
40	DHCR24	DHCR24	DHCR24	2394	0.095	0.32	YES
41	PIEZO1	PIEZO1	PIEZO1	2609	0.091	0.32	YES
42	SCAP	SCAP	SCAP	2641	0.09	0.33	YES
43	BYSL	BYSL	BYSL	2695	0.089	0.33	YES
44	P2RX4	P2RX4	P2RX4	2739	0.088	0.34	YES
45	LMNB2	LMNB2	LMNB2	2906	0.085	0.34	YES
46	NSDHL	NSDHL	NSDHL	2934	0.085	0.34	YES
47	MOGS	MOGS	MOGS	2974	0.084	0.35	YES
48	PDCD11	PDCD11	PDCD11	3063	0.082	0.35	YES
49	SF3B2	SF3B2	SF3B2	3091	0.081	0.36	YES
50	CDK4	CDK4	CDK4	3156	0.08	0.36	YES
51	POLD1	POLD1	POLD1	3291	0.077	0.36	YES
52	EIF4G1	EIF4G1	EIF4G1	3321	0.076	0.37	YES
53	UBL4A	UBL4A	UBL4A	3330	0.076	0.38	YES
54	RXRA	RXRA	RXRA	3340	0.076	0.38	YES
55	PMPCA	PMPCA	PMPCA	3359	0.076	0.39	YES
56	SCRIB	SCRIB	SCRIB	3360	0.076	0.4	YES
57	SSRP1	SSRP1	SSRP1	3378	0.075	0.4	YES
58	CDC37	CDC37	CDC37	3477	0.074	0.4	YES
59	KDM5C	KDM5C	KDM5C	3491	0.073	0.41	YES
60	FGFR3	FGFR3	FGFR3	3509	0.073	0.41	YES
61	PABPC4	PABPC4	PABPC4	3527	0.072	0.42	YES
62	NUP188	NUP188	NUP188	3625	0.07	0.42	YES
63	AP3D1	AP3D1	AP3D1	3684	0.069	0.42	YES
64	GTF3C2	GTF3C2	GTF3C2	3829	0.067	0.42	YES
65	SKIV2L	SKIV2L	SKIV2L	3848	0.066	0.43	YES
66	DDT	DDT	DDT	3853	0.066	0.43	YES
67	AGPAT2	AGPAT2	AGPAT2	3917	0.065	0.44	YES
68	NDRG1	NDRG1	NDRG1	3923	0.065	0.44	YES
69	SEC24C	SEC24C	SEC24C	3947	0.065	0.45	YES
70	H1FX	H1FX	H1FX	3950	0.064	0.45	YES
71	HK1	HK1	HK1	3960	0.064	0.46	YES
72	TCOF1	TCOF1	TCOF1	3995	0.064	0.46	YES
73	EIF2B2	EIF2B2	EIF2B2	4006	0.064	0.47	YES
74	VDAC1	VDAC1	VDAC1	4080	0.062	0.47	YES
75	FDFT1	FDFT1	FDFT1	4100	0.062	0.47	YES
76	SMAD6	SMAD6	SMAD6	4214	0.06	0.47	YES
77	SLC6A8	SLC6A8	SLC6A8	4242	0.059	0.48	YES
78	POLG	POLG	POLG	4359	0.057	0.48	YES
79	NMT1	NMT1	NMT1	4417	0.056	0.48	YES
80	MCM2	MCM2	MCM2	4501	0.054	0.48	YES
81	RAE1	RAE1	RAE1	4536	0.053	0.48	YES
82	EMG1	EMG1	EMG1	4684	0.05	0.48	YES
83	CLTA	CLTA	CLTA	4689	0.05	0.48	YES
84	MANF	MANF	MANF	4697	0.05	0.49	YES
85	UBAP2L	UBAP2L	UBAP2L	4810	0.048	0.49	YES
86	MAP2K5	MAP2K5	MAP2K5	4838	0.048	0.49	YES
87	SSBP1	SSBP1	SSBP1	5147	0.042	0.48	YES
88	SLC7A5	SLC7A5	SLC7A5	5149	0.042	0.48	YES
89	CKAP4	CKAP4	CKAP4	5152	0.042	0.48	YES
90	SAFB	SAFB	SAFB	5234	0.041	0.48	YES
91	SLC39A7	SLC39A7	SLC39A7	5241	0.04	0.49	YES
92	MTHFD1	MTHFD1	MTHFD1	5294	0.04	0.49	YES
93	CHD4	CHD4	CHD4	5326	0.039	0.49	YES
94	RRP1B	RRP1B	RRP1B	5373	0.038	0.49	YES
95	RCC1	RCC1	RCC1	5476	0.036	0.49	NO
96	EDC4	EDC4	EDC4	5530	0.035	0.49	NO
97	RABEPK	RABEPK	RABEPK	5589	0.034	0.49	NO
98	NOLC1	NOLC1	NOLC1	5794	0.03	0.48	NO
99	APEX1	APEX1	APEX1	5807	0.03	0.48	NO
100	SLC29A1	SLC29A1	SLC29A1	6063	0.024	0.47	NO
101	CCND1	CCND1	CCND1	6088	0.024	0.47	NO
102	EIF4H	EIF4H	EIF4H	6109	0.024	0.47	NO
103	CCNE1	CCNE1	CCNE1	6128	0.023	0.47	NO
104	SNRNP70	SNRNP70	SNRNP70	6188	0.022	0.47	NO
105	RASSF7	RASSF7	RASSF7	6341	0.019	0.46	NO
106	SF3A3	SF3A3	SF3A3	6400	0.018	0.46	NO
107	MLEC	MLEC	MLEC	6696	0.012	0.45	NO
108	XRCC5	XRCC5	XRCC5	6748	0.011	0.45	NO
109	RPIA	RPIA	RPIA	6792	0.01	0.44	NO
110	KAT2A	KAT2A	KAT2A	6808	0.01	0.44	NO
111	BRD2	BRD2	BRD2	7124	0.003	0.43	NO
112	TAF1C	TAF1C	TAF1C	7217	0.001	0.42	NO
113	CDC123	CDC123	CDC123	7257	-0.000062	0.42	NO
114	PSMD1	PSMD1	PSMD1	7280	-0.00037	0.42	NO
115	MYC	MYC	MYC	7768	-0.011	0.39	NO
116	RARS	RARS	RARS	7958	-0.015	0.38	NO
117	DNAJC7	DNAJC7	DNAJC7	7996	-0.016	0.38	NO
118	NARS	NARS	NARS	8061	-0.017	0.38	NO
119	BMS1	BMS1	BMS1	8243	-0.021	0.37	NO
120	EZR	EZR	EZR	8286	-0.022	0.37	NO
121	MCL1	MCL1	MCL1	8897	-0.034	0.34	NO
122	HSP90B1	HSP90B1	HSP90B1	8957	-0.036	0.34	NO
123	SON	SON	SON	9097	-0.039	0.34	NO
124	GCSH	GCSH	GCSH	9215	-0.042	0.34	NO
125	STC1	STC1	STC1	9355	-0.044	0.33	NO
126	EIF3E	EIF3E	EIF3E	9474	-0.047	0.33	NO
127	KRT6B	KRT6B	KRT6B	9966	-0.058	0.31	NO
128	SNRPA1	SNRPA1	SNRPA1	10110	-0.061	0.3	NO
129	MGST1	MGST1	MGST1	10215	-0.064	0.31	NO
130	U2AF1	U2AF1	U2AF1	10361	-0.067	0.3	NO
131	SRPK1	SRPK1	SRPK1	10729	-0.075	0.29	NO
132	DUSP1	DUSP1	DUSP1	11194	-0.086	0.27	NO
133	SOX4	SOX4	SOX4	11239	-0.087	0.28	NO
134	PPAT	PPAT	PPAT	11891	-0.1	0.25	NO
135	DDX10	DDX10	DDX10	12747	-0.12	0.22	NO
136	DNTTIP2	DNTTIP2	DNTTIP2	14485	-0.18	0.14	NO
137	HIST1H4C	HIST1H4C	HIST1H4C	15244	-0.21	0.11	NO
138	SRSF11	SRSF11	SRSF11	15476	-0.23	0.12	NO
139	SLC1A3	SLC1A3	SLC1A3	15876	-0.25	0.12	NO

Figure S61. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION.

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

genes ES table in pathway: SCHLOSSER MYC AND SERUM RESPONSE SYNERGY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MRPL23	MRPL23	MRPL23	416	0.17	-0.0031	YES
2	NDUFS8	NDUFS8	NDUFS8	480	0.16	0.012	YES
3	PHGDH	PHGDH	PHGDH	524	0.16	0.029	YES
4	NT5DC2	NT5DC2	NT5DC2	525	0.16	0.047	YES
5	DCXR	DCXR	DCXR	542	0.16	0.065	YES
6	SCO2	SCO2	SCO2	597	0.15	0.08	YES
7	DGCR6	DGCR6	DGCR6	719	0.14	0.09	YES
8	EXOSC4	EXOSC4	EXOSC4	724	0.14	0.11	YES
9	TST	TST	TST	738	0.14	0.12	YES
10	RUVBL2	RUVBL2	RUVBL2	900	0.13	0.13	YES
11	C12orf10	C12orf10	C12orf10	903	0.13	0.14	YES
12	DEAF1	DEAF1	DEAF1	919	0.13	0.16	YES
13	ETFB	ETFB	ETFB	950	0.13	0.17	YES
14	NDUFS7	NDUFS7	NDUFS7	951	0.13	0.19	YES
15	AP2S1	AP2S1	AP2S1	1013	0.13	0.2	YES
16	NDUFB7	NDUFB7	NDUFB7	1015	0.13	0.22	YES
17	MAP2K2	MAP2K2	MAP2K2	1016	0.13	0.23	YES
18	MTX1	MTX1	MTX1	1128	0.13	0.24	YES
19	CYC1	CYC1	CYC1	1282	0.12	0.25	YES
20	MRPS12	MRPS12	MRPS12	1319	0.12	0.26	YES
21	EIF3G	EIF3G	EIF3G	1342	0.12	0.27	YES
22	ENO1	ENO1	ENO1	1424	0.12	0.28	YES
23	APRT	APRT	APRT	1517	0.11	0.29	YES
24	DGCR14	DGCR14	DGCR14	1532	0.11	0.3	YES
25	CHAF1A	CHAF1A	CHAF1A	1536	0.11	0.32	YES
26	CUEDC2	CUEDC2	CUEDC2	1567	0.11	0.33	YES
27	IDH3G	IDH3G	IDH3G	1603	0.11	0.34	YES
28	TRIB3	TRIB3	TRIB3	1636	0.11	0.35	YES
29	WDR74	WDR74	WDR74	1652	0.11	0.36	YES
30	CHMP2A	CHMP2A	CHMP2A	1688	0.11	0.37	YES
31	UQCRC1	UQCRC1	UQCRC1	1749	0.11	0.38	YES
32	TCEB2	TCEB2	TCEB2	1811	0.11	0.39	YES
33	MRPL12	MRPL12	MRPL12	1879	0.11	0.4	YES
34	UBXN6	UBXN6	UBXN6	1889	0.1	0.41	YES
35	DUS1L	DUS1L	DUS1L	1900	0.1	0.43	YES
36	ZNF593	ZNF593	ZNF593	1928	0.1	0.44	YES
37	FLII	FLII	FLII	1939	0.1	0.45	YES
38	HSD17B10	HSD17B10	HSD17B10	2175	0.1	0.45	YES
39	WDR45	WDR45	WDR45	2229	0.098	0.46	YES
40	NDUFA13	NDUFA13	NDUFA13	2301	0.097	0.46	YES
41	POLR2L	POLR2L	POLR2L	2409	0.095	0.47	YES
42	PPIB	PPIB	PPIB	2430	0.094	0.48	YES
43	RPS5	RPS5	RPS5	2458	0.094	0.49	YES
44	HMOX2	HMOX2	HMOX2	2459	0.094	0.5	YES
45	EEF1D	EEF1D	EEF1D	2495	0.093	0.51	YES
46	PDXK	PDXK	PDXK	2830	0.087	0.5	YES
47	APEH	APEH	APEH	2994	0.084	0.5	YES
48	PPP1R7	PPP1R7	PPP1R7	3012	0.083	0.51	YES
49	PSMC3	PSMC3	PSMC3	3029	0.083	0.52	YES
50	TRAPPC2L	TRAPPC2L	TRAPPC2L	3052	0.082	0.53	YES
51	PSMC5	PSMC5	PSMC5	3070	0.082	0.54	YES
52	EDF1	EDF1	EDF1	3105	0.081	0.54	YES
53	TACO1	TACO1	TACO1	3162	0.08	0.55	YES
54	GLTSCR2	GLTSCR2	GLTSCR2	3217	0.079	0.56	YES
55	RFC2	RFC2	RFC2	3309	0.077	0.56	YES
56	STRA13	STRA13	STRA13	3320	0.076	0.57	YES
57	FAM50A	FAM50A	FAM50A	3747	0.068	0.55	NO
58	ADA	ADA	ADA	3858	0.066	0.56	NO
59	MRPS11	MRPS11	MRPS11	3865	0.066	0.56	NO
60	UFC1	UFC1	UFC1	4087	0.062	0.56	NO
61	NARF	NARF	NARF	4234	0.059	0.56	NO
62	FAHD2A	FAHD2A	FAHD2A	4313	0.057	0.56	NO
63	MRTO4	MRTO4	MRTO4	4742	0.05	0.54	NO
64	NOP56	NOP56	NOP56	4755	0.049	0.55	NO
65	SAP30BP	SAP30BP	SAP30BP	4885	0.047	0.55	NO
66	LSM3	LSM3	LSM3	5521	0.035	0.51	NO
67	SRRM2	SRRM2	SRRM2	5907	0.028	0.5	NO
68	RPSA	RPSA	RPSA	5944	0.027	0.5	NO
69	PITRM1	PITRM1	PITRM1	6206	0.022	0.48	NO
70	SPEN	SPEN	SPEN	6659	0.013	0.46	NO
71	NQO2	NQO2	NQO2	6694	0.012	0.46	NO
72	BID	BID	BID	6883	0.0078	0.45	NO
73	JMJD6	JMJD6	JMJD6	7735	-0.0099	0.41	NO
74	MAT1A	MAT1A	MAT1A	8460	-0.025	0.37	NO
75	NOL7	NOL7	NOL7	8461	-0.025	0.37	NO
76	NME6	NME6	NME6	8470	-0.025	0.37	NO
77	HSP90B1	HSP90B1	HSP90B1	8957	-0.036	0.35	NO
78	GATAD1	GATAD1	GATAD1	9492	-0.048	0.33	NO
79	ACBD3	ACBD3	ACBD3	10651	-0.073	0.27	NO
80	TPR	TPR	TPR	11689	-0.097	0.23	NO
81	TTC3	TTC3	TTC3	11849	-0.1	0.23	NO
82	NAA15	NAA15	NAA15	12337	-0.11	0.22	NO
83	SMC3	SMC3	SMC3	12434	-0.12	0.22	NO
84	PRPF40A	PRPF40A	PRPF40A	12962	-0.13	0.21	NO
85	BAZ1A	BAZ1A	BAZ1A	14160	-0.17	0.16	NO
86	DNTTIP2	DNTTIP2	DNTTIP2	14485	-0.18	0.17	NO
87	DLEC1	DLEC1	DLEC1	16262	-0.28	0.1	NO

Figure S63. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: SCHLOSSER MYC AND SERUM RESPONSE SYNERGY.

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: SCHLOSSER MYC AND SERUM RESPONSE SYNERGY, 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: DACOSTA UV RESPONSE VIA ERCC3 UP

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TMEM160	TMEM160	TMEM160	598	0.15	-0.021	YES
2	KRTCAP2	KRTCAP2	KRTCAP2	800	0.14	-0.021	YES
3	C8orf82	C8orf82	C8orf82	828	0.14	-0.011	YES
4	TAF10	TAF10	TAF10	850	0.14	-0.001	YES
5	CLPB	CLPB	CLPB	914	0.13	0.0064	YES
6	NDUFB7	NDUFB7	NDUFB7	1015	0.13	0.012	YES
7	UBE2S	UBE2S	UBE2S	1096	0.13	0.018	YES
8	IMPDH2	IMPDH2	IMPDH2	1237	0.12	0.02	YES
9	MRPL2	MRPL2	MRPL2	1257	0.12	0.029	YES
10	MRPS12	MRPS12	MRPS12	1319	0.12	0.035	YES
11	DDX54	DDX54	DDX54	1361	0.12	0.043	YES
12	CENPB	CENPB	CENPB	1391	0.12	0.051	YES
13	TIMM13	TIMM13	TIMM13	1453	0.12	0.057	YES
14	SLC25A39	SLC25A39	SLC25A39	1560	0.11	0.06	YES
15	SLC39A4	SLC39A4	SLC39A4	1575	0.11	0.069	YES
16	PRELID1	PRELID1	PRELID1	1584	0.11	0.078	YES
17	NDUFA11	NDUFA11	NDUFA11	1614	0.11	0.085	YES
18	RPS6KA4	RPS6KA4	RPS6KA4	1658	0.11	0.092	YES
19	AURKAIP1	AURKAIP1	AURKAIP1	1693	0.11	0.099	YES
20	NDUFS6	NDUFS6	NDUFS6	1752	0.11	0.1	YES
21	UBA1	UBA1	UBA1	1806	0.11	0.11	YES
22	MRPL21	MRPL21	MRPL21	1842	0.11	0.12	YES
23	MRPS34	MRPS34	MRPS34	1848	0.11	0.13	YES
24	MDH2	MDH2	MDH2	1852	0.11	0.14	YES
25	LMNA	LMNA	LMNA	1862	0.11	0.14	YES
26	COPS6	COPS6	COPS6	1965	0.1	0.15	YES
27	FKBP1A	FKBP1A	FKBP1A	2094	0.1	0.15	YES
28	COPE	COPE	COPE	2178	0.099	0.15	YES
29	LRPAP1	LRPAP1	LRPAP1	2187	0.099	0.16	YES
30	AKT1	AKT1	AKT1	2208	0.099	0.16	YES
31	PUF60	PUF60	PUF60	2279	0.097	0.17	YES
32	PSMD8	PSMD8	PSMD8	2381	0.095	0.17	YES
33	NR2F6	NR2F6	NR2F6	2386	0.095	0.18	YES
34	N6AMT2	N6AMT2	N6AMT2	2393	0.095	0.19	YES
35	VPS25	VPS25	VPS25	2442	0.094	0.19	YES
36	TUBB	TUBB	TUBB	2444	0.094	0.2	YES
37	PC	PC	PC	2494	0.093	0.2	YES
38	LSM4	LSM4	LSM4	2543	0.092	0.21	YES
39	NDUFS3	NDUFS3	NDUFS3	2580	0.091	0.22	YES
40	DLGAP4	DLGAP4	DLGAP4	2598	0.091	0.22	YES
41	TALDO1	TALDO1	TALDO1	2599	0.091	0.23	YES
42	NAA10	NAA10	NAA10	2610	0.091	0.24	YES
43	EXOC7	EXOC7	EXOC7	2637	0.09	0.24	YES
44	RAMP2	RAMP2	RAMP2	2645	0.09	0.25	YES
45	TGFB1I1	TGFB1I1	TGFB1I1	2703	0.089	0.25	YES
46	STUB1	STUB1	STUB1	2751	0.088	0.26	YES
47	CSNK2B	CSNK2B	CSNK2B	2798	0.087	0.26	YES
48	IFI35	IFI35	IFI35	2852	0.086	0.27	YES
49	TMEM109	TMEM109	TMEM109	2942	0.085	0.27	YES
50	DPP3	DPP3	DPP3	2944	0.085	0.28	YES
51	HMBS	HMBS	HMBS	2971	0.084	0.28	YES
52	ACTB	ACTB	ACTB	2987	0.084	0.29	YES
53	RUVBL1	RUVBL1	RUVBL1	3039	0.082	0.29	YES
54	PSMB6	PSMB6	PSMB6	3048	0.082	0.3	YES
55	NDUFB9	NDUFB9	NDUFB9	3064	0.082	0.3	YES
56	MRPL51	MRPL51	MRPL51	3074	0.082	0.31	YES
57	ERP29	ERP29	ERP29	3108	0.081	0.31	YES
58	TOR2A	TOR2A	TOR2A	3114	0.081	0.32	YES
59	CDK4	CDK4	CDK4	3156	0.08	0.32	YES
60	ROMO1	ROMO1	ROMO1	3181	0.08	0.33	YES
61	TWF2	TWF2	TWF2	3244	0.078	0.33	YES
62	SAMM50	SAMM50	SAMM50	3272	0.078	0.34	YES
63	MRPL36	MRPL36	MRPL36	3327	0.076	0.34	YES
64	UBL4A	UBL4A	UBL4A	3330	0.076	0.35	YES
65	PTDSS1	PTDSS1	PTDSS1	3444	0.074	0.35	YES
66	LAMTOR1	LAMTOR1	LAMTOR1	3462	0.074	0.35	YES
67	POLR3K	POLR3K	POLR3K	3612	0.071	0.35	YES
68	PHB2	PHB2	PHB2	3641	0.07	0.35	YES
69	MARCKSL1	MARCKSL1	MARCKSL1	3660	0.07	0.36	YES
70	DRAP1	DRAP1	DRAP1	3667	0.07	0.36	YES
71	SLIRP	SLIRP	SLIRP	3680	0.07	0.37	YES
72	GRPEL1	GRPEL1	GRPEL1	3707	0.069	0.37	YES
73	EI24	EI24	EI24	3762	0.068	0.38	YES
74	DDT	DDT	DDT	3853	0.066	0.38	YES
75	MRPS11	MRPS11	MRPS11	3865	0.066	0.38	YES
76	PDAP1	PDAP1	PDAP1	3911	0.065	0.38	YES
77	ADSL	ADSL	ADSL	4070	0.062	0.38	YES
78	LSM7	LSM7	LSM7	4073	0.062	0.39	YES
79	PSMD13	PSMD13	PSMD13	4076	0.062	0.39	YES
80	UFC1	UFC1	UFC1	4087	0.062	0.4	YES
81	GSTP1	GSTP1	GSTP1	4093	0.062	0.4	YES
82	HNRNPD	HNRNPD	HNRNPD	4142	0.06	0.4	YES
83	DDOST	DDOST	DDOST	4231	0.059	0.4	YES
84	EIF4A3	EIF4A3	EIF4A3	4288	0.058	0.4	YES
85	MAPKAPK2	MAPKAPK2	MAPKAPK2	4326	0.057	0.41	YES
86	CYB5R1	CYB5R1	CYB5R1	4402	0.056	0.41	YES
87	EVL	EVL	EVL	4459	0.055	0.41	YES
88	SAE1	SAE1	SAE1	4468	0.055	0.41	YES
89	EIF4E2	EIF4E2	EIF4E2	4499	0.054	0.42	YES
90	DCTN2	DCTN2	DCTN2	4530	0.053	0.42	YES
91	BAG1	BAG1	BAG1	4666	0.051	0.42	YES
92	CKB	CKB	CKB	4702	0.05	0.42	YES
93	CRYGD	CRYGD	CRYGD	4758	0.049	0.42	YES
94	MRPS7	MRPS7	MRPS7	4967	0.046	0.41	YES
95	UQCRQ	UQCRQ	UQCRQ	4999	0.045	0.41	YES
96	FAM96B	FAM96B	FAM96B	5048	0.044	0.41	YES
97	SRSF9	SRSF9	SRSF9	5052	0.044	0.42	YES
98	VDAC3	VDAC3	VDAC3	5093	0.043	0.42	YES
99	PARL	PARL	PARL	5104	0.043	0.42	YES
100	GOSR2	GOSR2	GOSR2	5274	0.04	0.41	NO
101	TRAPPC4	TRAPPC4	TRAPPC4	5553	0.035	0.4	NO
102	TNFAIP1	TNFAIP1	TNFAIP1	5556	0.035	0.4	NO
103	ALDH9A1	ALDH9A1	ALDH9A1	5762	0.031	0.4	NO
104	ALG5	ALG5	ALG5	5912	0.027	0.39	NO
105	NDUFAB1	NDUFAB1	NDUFAB1	5917	0.027	0.39	NO
106	ICT1	ICT1	ICT1	5928	0.027	0.39	NO
107	SLC39A9	SLC39A9	SLC39A9	6169	0.022	0.38	NO
108	CCDC12	CCDC12	CCDC12	6226	0.021	0.38	NO
109	INPP5A	INPP5A	INPP5A	6378	0.018	0.37	NO
110	PIAS3	PIAS3	PIAS3	6402	0.018	0.37	NO
111	NDUFV2	NDUFV2	NDUFV2	6409	0.018	0.38	NO
112	RPN2	RPN2	RPN2	6471	0.017	0.37	NO
113	FAM162A	FAM162A	FAM162A	6553	0.015	0.37	NO
114	MRPS15	MRPS15	MRPS15	6625	0.014	0.37	NO
115	PSMG1	PSMG1	PSMG1	6653	0.013	0.37	NO
116	PSMB7	PSMB7	PSMB7	6681	0.012	0.37	NO
117	CKS1B	CKS1B	CKS1B	6699	0.012	0.37	NO
118	XRCC5	XRCC5	XRCC5	6748	0.011	0.36	NO
119	STARD7	STARD7	STARD7	6894	0.0075	0.36	NO
120	CALM1	CALM1	CALM1	7018	0.005	0.35	NO
121	ARL2BP	ARL2BP	ARL2BP	7063	0.0039	0.35	NO
122	KRT10	KRT10	KRT10	7105	0.0032	0.35	NO
123	FAF1	FAF1	FAF1	7193	0.0016	0.34	NO
124	TMED10	TMED10	TMED10	7208	0.0013	0.34	NO
125	MRPS14	MRPS14	MRPS14	7279	-0.00037	0.34	NO
126	NDUFB6	NDUFB6	NDUFB6	7284	-0.00047	0.34	NO
127	MRPL18	MRPL18	MRPL18	7344	-0.0019	0.33	NO
128	MRPL16	MRPL16	MRPL16	7347	-0.0019	0.33	NO
129	RNF7	RNF7	RNF7	7516	-0.0055	0.32	NO
130	SDHB	SDHB	SDHB	7520	-0.0055	0.32	NO
131	TPM4	TPM4	TPM4	7605	-0.007	0.32	NO
132	MRPL34	MRPL34	MRPL34	7608	-0.007	0.32	NO
133	TCP1	TCP1	TCP1	7766	-0.01	0.31	NO
134	ARF4	ARF4	ARF4	7773	-0.011	0.31	NO
135	CAPN2	CAPN2	CAPN2	7803	-0.011	0.31	NO
136	PPAP2A	PPAP2A	PPAP2A	8055	-0.017	0.3	NO
137	CMBL	CMBL	CMBL	8157	-0.019	0.3	NO
138	BPGM	BPGM	BPGM	8213	-0.02	0.3	NO
139	PSMA7	PSMA7	PSMA7	8289	-0.022	0.29	NO
140	CORO1C	CORO1C	CORO1C	8355	-0.023	0.29	NO
141	SET	SET	SET	8459	-0.025	0.29	NO
142	ERCC3	ERCC3	ERCC3	8584	-0.028	0.28	NO
143	COQ7	COQ7	COQ7	8641	-0.029	0.28	NO
144	FUCA1	FUCA1	FUCA1	8840	-0.033	0.27	NO
145	MRPS22	MRPS22	MRPS22	9075	-0.038	0.26	NO
146	HSD17B4	HSD17B4	HSD17B4	9096	-0.039	0.27	NO
147	TCEA1	TCEA1	TCEA1	9337	-0.044	0.26	NO
148	LIAS	LIAS	LIAS	9357	-0.045	0.26	NO
149	ARL3	ARL3	ARL3	9378	-0.045	0.26	NO
150	NAP1L1	NAP1L1	NAP1L1	9467	-0.047	0.26	NO
151	PDCD2	PDCD2	PDCD2	9851	-0.056	0.24	NO
152	ARPC5	ARPC5	ARPC5	9912	-0.057	0.24	NO
153	TOMM70A	TOMM70A	TOMM70A	10089	-0.061	0.24	NO
154	TRAM1	TRAM1	TRAM1	10136	-0.062	0.24	NO
155	GNG10	GNG10	GNG10	10156	-0.062	0.25	NO
156	DDX1	DDX1	DDX1	10164	-0.063	0.25	NO
157	DNAJC19	DNAJC19	DNAJC19	10321	-0.066	0.25	NO
158	TMEM5	TMEM5	TMEM5	10338	-0.066	0.25	NO
159	MTIF2	MTIF2	MTIF2	10402	-0.068	0.25	NO
160	PTPLAD1	PTPLAD1	PTPLAD1	10526	-0.07	0.25	NO
161	COPS5	COPS5	COPS5	10560	-0.071	0.26	NO
162	TXNRD1	TXNRD1	TXNRD1	10703	-0.074	0.26	NO
163	YIPF5	YIPF5	YIPF5	10788	-0.076	0.26	NO
164	HSD17B12	HSD17B12	HSD17B12	11091	-0.084	0.25	NO
165	CMPK1	CMPK1	CMPK1	11593	-0.095	0.23	NO
166	SMAP1	SMAP1	SMAP1	11631	-0.096	0.23	NO
167	PSMD14	PSMD14	PSMD14	12024	-0.1	0.22	NO
168	WTAP	WTAP	WTAP	12122	-0.11	0.22	NO
169	BCAP29	BCAP29	BCAP29	12128	-0.11	0.23	NO
170	HMGCS1	HMGCS1	HMGCS1	12718	-0.12	0.21	NO
171	C11orf54	C11orf54	C11orf54	12765	-0.12	0.22	NO
172	USP1	USP1	USP1	13154	-0.14	0.21	NO
173	LYPLA1	LYPLA1	LYPLA1	13368	-0.14	0.21	NO
174	GCLM	GCLM	GCLM	13928	-0.16	0.19	NO
175	MAP3K7	MAP3K7	MAP3K7	14948	-0.2	0.15	NO
176	AQP4	AQP4	AQP4	16812	-0.34	0.071	NO

Figure S65. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: DACOSTA UV RESPONSE VIA ERCC3 UP.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: DACOSTA UV RESPONSE VIA ERCC3 UP, 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: DAIRKEE TERT TARGETS UP

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MTRNR2L8	MTRNR2L8	MTRNR2L8	53	0.29	0.0088	YES
2	CCND2	CCND2	CCND2	257	0.2	0.0055	YES
3	UBE2C	UBE2C	UBE2C	271	0.2	0.013	YES
4	EEF1G	EEF1G	EEF1G	395	0.17	0.013	YES
5	FMOD	FMOD	FMOD	468	0.16	0.015	YES
6	PDLIM1	PDLIM1	PDLIM1	484	0.16	0.021	YES
7	MGST2	MGST2	MGST2	787	0.14	0.0097	YES
8	ARHGAP1	ARHGAP1	ARHGAP1	892	0.13	0.0093	YES
9	GAPDH	GAPDH	GAPDH	937	0.13	0.012	YES
10	ALDOA	ALDOA	ALDOA	981	0.13	0.015	YES
11	CST3	CST3	CST3	994	0.13	0.02	YES
12	CAPNS1	CAPNS1	CAPNS1	1014	0.13	0.024	YES
13	GPS1	GPS1	GPS1	1036	0.13	0.028	YES
14	CD81	CD81	CD81	1047	0.13	0.033	YES
15	RPL28	RPL28	RPL28	1053	0.13	0.038	YES
16	USP11	USP11	USP11	1105	0.13	0.04	YES
17	NCOR2	NCOR2	NCOR2	1162	0.12	0.042	YES
18	RPL18A	RPL18A	RPL18A	1193	0.12	0.046	YES
19	LGALS1	LGALS1	LGALS1	1239	0.12	0.048	YES
20	COMT	COMT	COMT	1338	0.12	0.047	YES
21	TRIM28	TRIM28	TRIM28	1360	0.12	0.051	YES
22	MAZ	MAZ	MAZ	1387	0.12	0.054	YES
23	ENO1	ENO1	ENO1	1424	0.12	0.057	YES
24	ANXA11	ANXA11	ANXA11	1464	0.12	0.06	YES
25	UBA52	UBA52	UBA52	1515	0.11	0.062	YES
26	ARAF	ARAF	ARAF	1516	0.11	0.066	YES
27	RPS15	RPS15	RPS15	1550	0.11	0.069	YES
28	CFL1	CFL1	CFL1	1556	0.11	0.073	YES
29	ILK	ILK	ILK	1595	0.11	0.076	YES
30	ATP5G2	ATP5G2	ATP5G2	1635	0.11	0.078	YES
31	GPX4	GPX4	GPX4	1644	0.11	0.082	YES
32	ATP5G1	ATP5G1	ATP5G1	1647	0.11	0.087	YES
33	IFITM1	IFITM1	IFITM1	1734	0.11	0.086	YES
34	FKBP4	FKBP4	FKBP4	1763	0.11	0.089	YES
35	UBA1	UBA1	UBA1	1806	0.11	0.091	YES
36	RBPMS	RBPMS	RBPMS	1810	0.11	0.095	YES
37	LASP1	LASP1	LASP1	1877	0.11	0.096	YES
38	RPS28	RPS28	RPS28	1886	0.11	0.1	YES
39	CD34	CD34	CD34	1911	0.1	0.1	YES
40	COPS6	COPS6	COPS6	1965	0.1	0.1	YES
41	MLF2	MLF2	MLF2	2001	0.1	0.11	YES
42	GUSB	GUSB	GUSB	2051	0.1	0.11	YES
43	ARF3	ARF3	ARF3	2054	0.1	0.11	YES
44	FKBP1A	FKBP1A	FKBP1A	2094	0.1	0.11	YES
45	ITPK1	ITPK1	ITPK1	2104	0.1	0.12	YES
46	AARS	AARS	AARS	2123	0.1	0.12	YES
47	CD151	CD151	CD151	2135	0.1	0.12	YES
48	RPLP2	RPLP2	RPLP2	2212	0.099	0.12	YES
49	JUND	JUND	JUND	2220	0.099	0.13	YES
50	TAGLN2	TAGLN2	TAGLN2	2235	0.098	0.13	YES
51	SLC25A6	SLC25A6	SLC25A6	2267	0.098	0.13	YES
52	MSN	MSN	MSN	2278	0.097	0.14	YES
53	ATIC	ATIC	ATIC	2297	0.097	0.14	YES
54	RPL18	RPL18	RPL18	2304	0.097	0.14	YES
55	ATP6V1F	ATP6V1F	ATP6V1F	2354	0.096	0.14	YES
56	SF1	SF1	SF1	2362	0.096	0.15	YES
57	HSPB1	HSPB1	HSPB1	2366	0.096	0.15	YES
58	PFN1	PFN1	PFN1	2372	0.096	0.16	YES
59	DHPS	DHPS	DHPS	2378	0.095	0.16	YES
60	PSMD8	PSMD8	PSMD8	2381	0.095	0.16	YES
61	CASC3	CASC3	CASC3	2407	0.095	0.16	YES
62	POLR2L	POLR2L	POLR2L	2409	0.095	0.17	YES
63	CSTB	CSTB	CSTB	2410	0.095	0.17	YES
64	TUBB	TUBB	TUBB	2444	0.094	0.17	YES
65	RPS5	RPS5	RPS5	2458	0.094	0.18	YES
66	RPL13	RPL13	RPL13	2489	0.093	0.18	YES
67	EEF1D	EEF1D	EEF1D	2495	0.093	0.18	YES
68	COX8A	COX8A	COX8A	2502	0.093	0.19	YES
69	RPS26	RPS26	RPS26	2544	0.092	0.19	YES
70	COX6B1	COX6B1	COX6B1	2555	0.092	0.19	YES
71	EIF3F	EIF3F	EIF3F	2617	0.091	0.19	YES
72	BCAP31	BCAP31	BCAP31	2636	0.09	0.19	YES
73	LAMP1	LAMP1	LAMP1	2717	0.089	0.19	YES
74	FBL	FBL	FBL	2725	0.089	0.2	YES
75	OS9	OS9	OS9	2779	0.088	0.2	YES
76	MYH9	MYH9	MYH9	2781	0.088	0.2	YES
77	DDB1	DDB1	DDB1	2783	0.088	0.2	YES
78	RPS9	RPS9	RPS9	2797	0.087	0.21	YES
79	CSNK2B	CSNK2B	CSNK2B	2798	0.087	0.21	YES
80	RPS2	RPS2	RPS2	2804	0.087	0.21	YES
81	RPL37A	RPL37A	RPL37A	2817	0.087	0.22	YES
82	RPS19	RPS19	RPS19	2834	0.086	0.22	YES
83	EEF2	EEF2	EEF2	2874	0.086	0.22	YES
84	NEDD8	NEDD8	NEDD8	2895	0.085	0.22	YES
85	VPS72	VPS72	VPS72	2948	0.084	0.22	YES
86	ACTB	ACTB	ACTB	2987	0.084	0.22	YES
87	NCSTN	NCSTN	NCSTN	3001	0.083	0.23	YES
88	DYNLL1	DYNLL1	DYNLL1	3002	0.083	0.23	YES
89	SSR2	SSR2	SSR2	3009	0.083	0.23	YES
90	RPL8	RPL8	RPL8	3015	0.083	0.24	YES
91	DVL3	DVL3	DVL3	3030	0.083	0.24	YES
92	PSMB6	PSMB6	PSMB6	3048	0.082	0.24	YES
93	SURF1	SURF1	SURF1	3065	0.082	0.24	YES
94	FCGRT	FCGRT	FCGRT	3079	0.082	0.25	YES
95	CYB5R3	CYB5R3	CYB5R3	3082	0.082	0.25	YES
96	ACTG1	ACTG1	ACTG1	3087	0.082	0.25	YES
97	AAMP	AAMP	AAMP	3088	0.082	0.26	YES
98	SF3B2	SF3B2	SF3B2	3091	0.081	0.26	YES
99	WARS	WARS	WARS	3123	0.08	0.26	YES
100	GPX1	GPX1	GPX1	3127	0.08	0.26	YES
101	AGPAT1	AGPAT1	AGPAT1	3138	0.08	0.27	YES
102	GNB2L1	GNB2L1	GNB2L1	3148	0.08	0.27	YES
103	ATOX1	ATOX1	ATOX1	3155	0.08	0.27	YES
104	PSMB3	PSMB3	PSMB3	3222	0.079	0.27	YES
105	SQSTM1	SQSTM1	SQSTM1	3233	0.078	0.28	YES
106	ISG20	ISG20	ISG20	3252	0.078	0.28	YES
107	RPS16	RPS16	RPS16	3281	0.077	0.28	YES
108	PSMB5	PSMB5	PSMB5	3305	0.077	0.28	YES
109	PI4KA	PI4KA	PI4KA	3338	0.076	0.28	YES
110	SCN1B	SCN1B	SCN1B	3341	0.076	0.28	YES
111	ATP5B	ATP5B	ATP5B	3349	0.076	0.29	YES
112	COX6A1	COX6A1	COX6A1	3351	0.076	0.29	YES
113	UBB	UBB	UBB	3383	0.075	0.29	YES
114	FTL	FTL	FTL	3436	0.074	0.29	YES
115	PGAM1	PGAM1	PGAM1	3443	0.074	0.3	YES
116	PTDSS1	PTDSS1	PTDSS1	3444	0.074	0.3	YES
117	FLNA	FLNA	FLNA	3502	0.073	0.3	YES
118	IRAK1	IRAK1	IRAK1	3525	0.072	0.3	YES
119	RPL29	RPL29	RPL29	3542	0.072	0.3	YES
120	TRAF4	TRAF4	TRAF4	3546	0.072	0.3	YES
121	CD63	CD63	CD63	3582	0.071	0.31	YES
122	FTH1	FTH1	FTH1	3606	0.071	0.31	YES
123	PHB2	PHB2	PHB2	3641	0.07	0.31	YES
124	CIRBP	CIRBP	CIRBP	3659	0.07	0.31	YES
125	YWHAH	YWHAH	YWHAH	3666	0.07	0.31	YES
126	AES	AES	AES	3690	0.069	0.31	YES
127	RPS11	RPS11	RPS11	3718	0.069	0.32	YES
128	ECHS1	ECHS1	ECHS1	3724	0.069	0.32	YES
129	PCBP2	PCBP2	PCBP2	3739	0.068	0.32	YES
130	PLP2	PLP2	PLP2	3755	0.068	0.32	YES
131	HTRA1	HTRA1	HTRA1	3763	0.068	0.32	YES
132	PRDX6	PRDX6	PRDX6	3828	0.067	0.32	YES
133	DDT	DDT	DDT	3853	0.066	0.32	YES
134	RPL27A	RPL27A	RPL27A	3855	0.066	0.33	YES
135	FUS	FUS	FUS	3900	0.065	0.33	YES
136	RPS29	RPS29	RPS29	3909	0.065	0.33	YES
137	NDRG1	NDRG1	NDRG1	3923	0.065	0.33	YES
138	RPL35	RPL35	RPL35	3964	0.064	0.33	YES
139	SNRPD2	SNRPD2	SNRPD2	3968	0.064	0.33	YES
140	QARS	QARS	QARS	4010	0.063	0.34	YES
141	GSTP1	GSTP1	GSTP1	4093	0.062	0.33	YES
142	RPS3	RPS3	RPS3	4135	0.061	0.33	YES
143	RAC1	RAC1	RAC1	4180	0.06	0.33	YES
144	SPTBN1	SPTBN1	SPTBN1	4197	0.06	0.33	YES
145	CD3E	CD3E	CD3E	4208	0.06	0.34	YES
146	RPL41	RPL41	RPL41	4209	0.06	0.34	YES
147	ARF1	ARF1	ARF1	4227	0.059	0.34	YES
148	OAZ1	OAZ1	OAZ1	4238	0.059	0.34	YES
149	SLC6A8	SLC6A8	SLC6A8	4242	0.059	0.34	YES
150	RPLP1	RPLP1	RPLP1	4263	0.059	0.34	YES
151	PPIA	PPIA	PPIA	4283	0.058	0.35	YES
152	EIF4A3	EIF4A3	EIF4A3	4288	0.058	0.35	YES
153	COX4I1	COX4I1	COX4I1	4312	0.058	0.35	YES
154	CLIC1	CLIC1	CLIC1	4330	0.057	0.35	YES
155	RPS14	RPS14	RPS14	4331	0.057	0.35	YES
156	PSMD2	PSMD2	PSMD2	4340	0.057	0.36	YES
157	VIM	VIM	VIM	4385	0.056	0.36	YES
158	RPL19	RPL19	RPL19	4392	0.056	0.36	YES
159	MT2A	MT2A	MT2A	4473	0.054	0.36	YES
160	NDUFA12	NDUFA12	NDUFA12	4508	0.054	0.36	YES
161	PSMB4	PSMB4	PSMB4	4512	0.054	0.36	YES
162	RPL23	RPL23	RPL23	4524	0.054	0.36	YES
163	DCTN2	DCTN2	DCTN2	4530	0.053	0.36	YES
164	RPL12	RPL12	RPL12	4547	0.053	0.36	YES
165	RER1	RER1	RER1	4564	0.053	0.36	YES
166	NPC2	NPC2	NPC2	4593	0.052	0.36	YES
167	RPL38	RPL38	RPL38	4640	0.051	0.36	YES
168	CTDSP2	CTDSP2	CTDSP2	4649	0.051	0.36	YES
169	ATP5G3	ATP5G3	ATP5G3	4685	0.05	0.36	YES
170	CLTA	CLTA	CLTA	4689	0.05	0.37	YES
171	SARS	SARS	SARS	4710	0.05	0.37	YES
172	SEC61B	SEC61B	SEC61B	4729	0.05	0.37	YES
173	RPL36AL	RPL36AL	RPL36AL	4731	0.05	0.37	YES
174	HLA-A	HLA-A	HLA-A	4766	0.049	0.37	YES
175	RPL7A	RPL7A	RPL7A	4792	0.049	0.37	YES
176	COPA	COPA	COPA	4799	0.049	0.37	YES
177	PARP1	PARP1	PARP1	4816	0.048	0.37	YES
178	ANXA2	ANXA2	ANXA2	4823	0.048	0.38	YES
179	C1QBP	C1QBP	C1QBP	4847	0.048	0.38	YES
180	MPRIP	MPRIP	MPRIP	4852	0.048	0.38	YES
181	SLC25A3	SLC25A3	SLC25A3	4856	0.048	0.38	YES
182	UBC	UBC	UBC	4865	0.047	0.38	YES
183	RHOA	RHOA	RHOA	4874	0.047	0.38	YES
184	EIF1	EIF1	EIF1	4884	0.047	0.38	YES
185	RPS21	RPS21	RPS21	4887	0.047	0.39	YES
186	ARPC2	ARPC2	ARPC2	4892	0.047	0.39	YES
187	UQCRH	UQCRH	UQCRH	4920	0.046	0.39	YES
188	COX7A2	COX7A2	COX7A2	4956	0.046	0.39	YES
189	FAM193A	FAM193A	FAM193A	4959	0.046	0.39	YES
190	S100A10	S100A10	S100A10	4985	0.045	0.39	YES
191	RPL32	RPL32	RPL32	4994	0.045	0.39	YES
192	APLP2	APLP2	APLP2	5023	0.044	0.39	YES
193	COX6C	COX6C	COX6C	5067	0.044	0.39	YES
194	H2AFZ	H2AFZ	H2AFZ	5099	0.043	0.39	YES
195	VDAC2	VDAC2	VDAC2	5105	0.043	0.39	YES
196	ERH	ERH	ERH	5115	0.043	0.39	YES
197	SOD1	SOD1	SOD1	5151	0.042	0.39	YES
198	COX7C	COX7C	COX7C	5204	0.041	0.39	YES
199	RPL27	RPL27	RPL27	5248	0.04	0.39	YES
200	PSAP	PSAP	PSAP	5273	0.04	0.39	YES
201	CES2	CES2	CES2	5276	0.04	0.39	YES
202	GNAS	GNAS	GNAS	5390	0.038	0.39	YES
203	LDHA	LDHA	LDHA	5407	0.038	0.39	YES
204	RPS17	RPS17	RPS17	5417	0.037	0.39	YES
205	PSME1	PSME1	PSME1	5418	0.037	0.39	YES
206	TMSB10	TMSB10	TMSB10	5431	0.037	0.39	YES
207	RPL3	RPL3	RPL3	5482	0.036	0.39	YES
208	CHKB	CHKB	CHKB	5483	0.036	0.39	YES
209	RPL13A	RPL13A	RPL13A	5496	0.036	0.39	YES
210	RPL39	RPL39	RPL39	5503	0.036	0.4	YES
211	PSMB2	PSMB2	PSMB2	5570	0.034	0.39	YES
212	ATP5O	ATP5O	ATP5O	5579	0.034	0.39	YES
213	NACA	NACA	NACA	5591	0.034	0.39	YES
214	TXN	TXN	TXN	5594	0.034	0.4	YES
215	SLC25A5	SLC25A5	SLC25A5	5614	0.034	0.4	YES
216	ATF4	ATF4	ATF4	5615	0.034	0.4	YES
217	LDHB	LDHB	LDHB	5639	0.033	0.4	YES
218	HNRNPL	HNRNPL	HNRNPL	5645	0.033	0.4	YES
219	SEPW1	SEPW1	SEPW1	5654	0.033	0.4	YES
220	RPS25	RPS25	RPS25	5723	0.032	0.4	NO
221	COX10	COX10	COX10	5755	0.031	0.4	NO
222	KARS	KARS	KARS	5756	0.031	0.4	NO
223	APEX1	APEX1	APEX1	5807	0.03	0.4	NO
224	RPS10	RPS10	RPS10	5821	0.029	0.4	NO
225	RPL36A	RPL36A	RPL36A	5824	0.029	0.4	NO
226	RPL14	RPL14	RPL14	5827	0.029	0.4	NO
227	GSTO1	GSTO1	GSTO1	5869	0.028	0.4	NO
228	CD74	CD74	CD74	5871	0.028	0.4	NO
229	PRDX1	PRDX1	PRDX1	5920	0.027	0.4	NO
230	RPLP0	RPLP0	RPLP0	5940	0.027	0.4	NO
231	RPSA	RPSA	RPSA	5944	0.027	0.4	NO
232	PEBP1	PEBP1	PEBP1	5973	0.026	0.4	NO
233	RPL11	RPL11	RPL11	5977	0.026	0.4	NO
234	ANP32B	ANP32B	ANP32B	6003	0.026	0.4	NO
235	RPS18	RPS18	RPS18	6015	0.025	0.4	NO
236	RPL10A	RPL10A	RPL10A	6034	0.025	0.4	NO
237	PSEN1	PSEN1	PSEN1	6055	0.025	0.4	NO
238	JOSD1	JOSD1	JOSD1	6096	0.024	0.4	NO
239	CETN2	CETN2	CETN2	6105	0.024	0.4	NO
240	EIF4H	EIF4H	EIF4H	6109	0.024	0.4	NO
241	YBX1	YBX1	YBX1	6133	0.023	0.4	NO
242	SNRNP70	SNRNP70	SNRNP70	6188	0.022	0.4	NO
243	HDAC1	HDAC1	HDAC1	6200	0.022	0.4	NO
244	SERPINB6	SERPINB6	SERPINB6	6237	0.021	0.4	NO
245	NONO	NONO	NONO	6276	0.02	0.39	NO
246	RPS23	RPS23	RPS23	6288	0.02	0.39	NO
247	CCNI	CCNI	CCNI	6336	0.019	0.39	NO
248	TMBIM6	TMBIM6	TMBIM6	6369	0.019	0.39	NO
249	HLA-E	HLA-E	HLA-E	6372	0.019	0.39	NO
250	NDUFV2	NDUFV2	NDUFV2	6409	0.018	0.39	NO
251	STAT3	STAT3	STAT3	6425	0.017	0.39	NO
252	PFDN5	PFDN5	PFDN5	6426	0.017	0.39	NO
253	PTPN6	PTPN6	PTPN6	6446	0.017	0.39	NO
254	RPS27A	RPS27A	RPS27A	6462	0.017	0.39	NO
255	RPN2	RPN2	RPN2	6471	0.017	0.39	NO
256	DAZAP2	DAZAP2	DAZAP2	6526	0.016	0.39	NO
257	RPL21	RPL21	RPL21	6533	0.015	0.39	NO
258	HNRNPC	HNRNPC	HNRNPC	6582	0.014	0.39	NO
259	HYAL2	HYAL2	HYAL2	6597	0.014	0.39	NO
260	NFKBIA	NFKBIA	NFKBIA	6648	0.013	0.38	NO
261	CLU	CLU	CLU	6658	0.013	0.38	NO
262	HSP90AB1	HSP90AB1	HSP90AB1	6677	0.012	0.38	NO
263	UQCRB	UQCRB	UQCRB	6692	0.012	0.38	NO
264	RPS15A	RPS15A	RPS15A	6702	0.012	0.38	NO
265	RPL4	RPL4	RPL4	6756	0.011	0.38	NO
266	GNB1	GNB1	GNB1	6770	0.011	0.38	NO
267	H3F3B	H3F3B	H3F3B	6809	0.01	0.38	NO
268	RFTN1	RFTN1	RFTN1	6876	0.008	0.38	NO
269	HLA-DQB1	HLA-DQB1	HLA-DQB1	6919	0.007	0.37	NO
270	NCL	NCL	NCL	6926	0.0068	0.37	NO
271	PTMA	PTMA	PTMA	6936	0.0066	0.37	NO
272	RPS8	RPS8	RPS8	6971	0.0059	0.37	NO
273	RPL34	RPL34	RPL34	6990	0.0055	0.37	NO
274	RPL31	RPL31	RPL31	7032	0.0046	0.37	NO
275	ATP5A1	ATP5A1	ATP5A1	7069	0.0038	0.37	NO
276	HINT1	HINT1	HINT1	7070	0.0037	0.37	NO
277	BUD31	BUD31	BUD31	7074	0.0037	0.37	NO
278	ATP5C1	ATP5C1	ATP5C1	7078	0.0036	0.37	NO
279	ESD	ESD	ESD	7094	0.0034	0.36	NO
280	HNRNPA1	HNRNPA1	HNRNPA1	7120	0.003	0.36	NO
281	BRD2	BRD2	BRD2	7124	0.003	0.36	NO
282	GLUL	GLUL	GLUL	7132	0.0028	0.36	NO
283	NDUFA4	NDUFA4	NDUFA4	7152	0.0025	0.36	NO
284	HNRNPK	HNRNPK	HNRNPK	7160	0.0024	0.36	NO
285	BECN1	BECN1	BECN1	7173	0.0021	0.36	NO
286	HMGN2	HMGN2	HMGN2	7194	0.0016	0.36	NO
287	AP3S1	AP3S1	AP3S1	7195	0.0016	0.36	NO
288	TMED10	TMED10	TMED10	7208	0.0013	0.36	NO
289	RPL24	RPL24	RPL24	7293	-0.00072	0.36	NO
290	B2M	B2M	B2M	7392	-0.0028	0.35	NO
291	ARL6IP1	ARL6IP1	ARL6IP1	7407	-0.0031	0.35	NO
292	TPT1	TPT1	TPT1	7414	-0.0031	0.35	NO
293	PSMC1	PSMC1	PSMC1	7429	-0.0034	0.35	NO
294	CCT4	CCT4	CCT4	7449	-0.0038	0.35	NO
295	RPL35A	RPL35A	RPL35A	7467	-0.0042	0.35	NO
296	RPL7	RPL7	RPL7	7501	-0.0051	0.34	NO
297	HNRNPF	HNRNPF	HNRNPF	7517	-0.0055	0.34	NO
298	CAP1	CAP1	CAP1	7527	-0.0057	0.34	NO
299	SRP14	SRP14	SRP14	7659	-0.0083	0.34	NO
300	RPL6	RPL6	RPL6	7663	-0.0083	0.34	NO
301	YWHAB	YWHAB	YWHAB	7693	-0.0091	0.34	NO
302	PSD	PSD	PSD	7749	-0.01	0.33	NO
303	ARF4	ARF4	ARF4	7773	-0.011	0.33	NO
304	MGP	MGP	MGP	7799	-0.011	0.33	NO
305	CAPN2	CAPN2	CAPN2	7803	-0.011	0.33	NO
306	HLA-DPA1	HLA-DPA1	HLA-DPA1	7827	-0.012	0.33	NO
307	YWHAQ	YWHAQ	YWHAQ	7900	-0.013	0.33	NO
308	JUNB	JUNB	JUNB	7904	-0.013	0.33	NO
309	MDH1	MDH1	MDH1	7918	-0.014	0.33	NO
310	TXNIP	TXNIP	TXNIP	7964	-0.015	0.33	NO
311	ARHGDIB	ARHGDIB	ARHGDIB	7998	-0.016	0.32	NO
312	MORF4L2	MORF4L2	MORF4L2	8060	-0.017	0.32	NO
313	ZFP36	ZFP36	ZFP36	8100	-0.018	0.32	NO
314	RPA2	RPA2	RPA2	8101	-0.018	0.32	NO
315	LTA4H	LTA4H	LTA4H	8125	-0.018	0.32	NO
316	FHL1	FHL1	FHL1	8149	-0.019	0.32	NO
317	YWHAZ	YWHAZ	YWHAZ	8246	-0.021	0.32	NO
318	EZR	EZR	EZR	8286	-0.022	0.31	NO
319	PGK1	PGK1	PGK1	8354	-0.023	0.31	NO
320	SET	SET	SET	8459	-0.025	0.31	NO
321	UBE2D3	UBE2D3	UBE2D3	8468	-0.025	0.31	NO
322	MLH1	MLH1	MLH1	8518	-0.026	0.3	NO
323	GDI2	GDI2	GDI2	8531	-0.026	0.31	NO
324	CANX	CANX	CANX	8625	-0.028	0.3	NO
325	CALM2	CALM2	CALM2	8667	-0.03	0.3	NO
326	DSTN	DSTN	DSTN	8668	-0.03	0.3	NO
327	CLTC	CLTC	CLTC	8705	-0.03	0.3	NO
328	EEF1B2	EEF1B2	EEF1B2	8728	-0.031	0.3	NO
329	RPS6	RPS6	RPS6	8735	-0.031	0.3	NO
330	FUCA1	FUCA1	FUCA1	8840	-0.033	0.3	NO
331	GPS2	GPS2	GPS2	8858	-0.034	0.3	NO
332	BTG2	BTG2	BTG2	9044	-0.038	0.29	NO
333	STMN1	STMN1	STMN1	9085	-0.039	0.29	NO
334	SON	SON	SON	9097	-0.039	0.29	NO
335	PABPC1	PABPC1	PABPC1	9114	-0.04	0.29	NO
336	RPL17	RPL17	RPL17	9131	-0.04	0.29	NO
337	FYN	FYN	FYN	9207	-0.041	0.29	NO
338	RPL9	RPL9	RPL9	9234	-0.042	0.29	NO
339	TMSB4X	TMSB4X	TMSB4X	9307	-0.044	0.29	NO
340	TCEA1	TCEA1	TCEA1	9337	-0.044	0.29	NO
341	NPM1	NPM1	NPM1	9421	-0.046	0.28	NO
342	HSPD1	HSPD1	HSPD1	9426	-0.046	0.28	NO
343	LGALS3	LGALS3	LGALS3	9445	-0.047	0.29	NO
344	NAP1L1	NAP1L1	NAP1L1	9467	-0.047	0.29	NO
345	EIF3E	EIF3E	EIF3E	9474	-0.047	0.29	NO
346	KAT6A	KAT6A	KAT6A	9478	-0.047	0.29	NO
347	PSMD7	PSMD7	PSMD7	9546	-0.049	0.29	NO
348	PTP4A2	PTP4A2	PTP4A2	9554	-0.049	0.29	NO
349	RPS7	RPS7	RPS7	9590	-0.05	0.29	NO
350	ATP5F1	ATP5F1	ATP5F1	9623	-0.051	0.29	NO
351	STOM	STOM	STOM	9791	-0.055	0.28	NO
352	EEF1A1	EEF1A1	EEF1A1	9792	-0.055	0.28	NO
353	SEPT2	SEPT2	SEPT2	9986	-0.058	0.28	NO
354	HLA-DRA	HLA-DRA	HLA-DRA	10015	-0.059	0.28	NO
355	HSP90AA1	HSP90AA1	HSP90AA1	10314	-0.066	0.26	NO
356	ITGB1	ITGB1	ITGB1	10550	-0.071	0.25	NO
357	IQGAP1	IQGAP1	IQGAP1	10579	-0.072	0.26	NO
358	NFIB	NFIB	NFIB	10645	-0.073	0.25	NO
359	HMGB1	HMGB1	HMGB1	10662	-0.074	0.26	NO
360	HLA-DOA	HLA-DOA	HLA-DOA	10691	-0.074	0.26	NO
361	EIF4G2	EIF4G2	EIF4G2	10974	-0.082	0.24	NO
362	CAST	CAST	CAST	11151	-0.085	0.24	NO
363	DUSP1	DUSP1	DUSP1	11194	-0.086	0.24	NO
364	FNTA	FNTA	FNTA	11206	-0.086	0.24	NO
365	CTNNB1	CTNNB1	CTNNB1	11215	-0.086	0.25	NO
366	EIF4A1	EIF4A1	EIF4A1	11354	-0.09	0.24	NO
367	DDX5	DDX5	DDX5	11393	-0.09	0.24	NO
368	CAPZA1	CAPZA1	CAPZA1	11398	-0.091	0.25	NO
369	TPR	TPR	TPR	11689	-0.097	0.23	NO
370	BCLAF1	BCLAF1	BCLAF1	11738	-0.098	0.24	NO
371	MARCKS	MARCKS	MARCKS	11744	-0.098	0.24	NO
372	RPS3A	RPS3A	RPS3A	11771	-0.099	0.24	NO
373	EIF4A2	EIF4A2	EIF4A2	12099	-0.11	0.23	NO
374	PIM1	PIM1	PIM1	12177	-0.11	0.23	NO
375	SSB	SSB	SSB	12265	-0.11	0.23	NO
376	CD164	CD164	CD164	12653	-0.12	0.21	NO
377	ABLIM1	ABLIM1	ABLIM1	12946	-0.13	0.2	NO
378	XPO1	XPO1	XPO1	13006	-0.13	0.2	NO
379	PAX6	PAX6	PAX6	13307	-0.14	0.19	NO
380	DDX39B	DDX39B	DDX39B	13465	-0.14	0.19	NO
381	TAX1BP1	TAX1BP1	TAX1BP1	13831	-0.16	0.17	NO
382	ZNF91	ZNF91	ZNF91	14640	-0.19	0.14	NO
383	CHI3L2	CHI3L2	CHI3L2	14709	-0.19	0.14	NO
384	FAS	FAS	FAS	15115	-0.21	0.12	NO
385	NEFL	NEFL	NEFL	15864	-0.25	0.092	NO
386	SERPINA3	SERPINA3	SERPINA3	16996	-0.36	0.043	NO
387	CCR9	CCR9	CCR9	17509	-0.45	0.032	NO

Figure S67. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: DAIRKEE TERT TARGETS UP.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: DAIRKEE TERT TARGETS UP, 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: SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NKAIN1	NKAIN1	NKAIN1	322	0.18	-0.00076	YES
2	GALK1	GALK1	GALK1	694	0.14	-0.008	YES
3	C9orf16	C9orf16	C9orf16	794	0.14	-0.00064	YES
4	ARHGDIA	ARHGDIA	ARHGDIA	830	0.14	0.01	YES
5	CAD	CAD	CAD	858	0.14	0.021	YES
6	GAPDH	GAPDH	GAPDH	937	0.13	0.029	YES
7	ACTA1	ACTA1	ACTA1	954	0.13	0.041	YES
8	PPP1R14B	PPP1R14B	PPP1R14B	978	0.13	0.052	YES
9	GPS1	GPS1	GPS1	1036	0.13	0.06	YES
10	IPO4	IPO4	IPO4	1092	0.13	0.069	YES
11	BAX	BAX	BAX	1114	0.13	0.08	YES
12	ASL	ASL	ASL	1117	0.13	0.092	YES
13	DDX41	DDX41	DDX41	1157	0.12	0.1	YES
14	MYBBP1A	MYBBP1A	MYBBP1A	1161	0.12	0.11	YES
15	CARM1	CARM1	CARM1	1292	0.12	0.12	YES
16	PTOV1	PTOV1	PTOV1	1304	0.12	0.13	YES
17	UBE2M	UBE2M	UBE2M	1308	0.12	0.14	YES
18	JAG2	JAG2	JAG2	1312	0.12	0.15	YES
19	PTP4A3	PTP4A3	PTP4A3	1435	0.12	0.15	YES
20	CTSD	CTSD	CTSD	1498	0.12	0.16	YES
21	PES1	PES1	PES1	1505	0.12	0.17	YES
22	ERGIC1	ERGIC1	ERGIC1	1519	0.11	0.18	YES
23	PIGQ	PIGQ	PIGQ	1555	0.11	0.19	YES
24	SMARCA4	SMARCA4	SMARCA4	1566	0.11	0.2	YES
25	WDR74	WDR74	WDR74	1652	0.11	0.2	YES
26	NME1	NME1	NME1	1790	0.11	0.21	YES
27	VARS	VARS	VARS	1827	0.11	0.22	YES
28	PTH1R	PTH1R	PTH1R	1859	0.11	0.22	YES
29	MRPL12	MRPL12	MRPL12	1879	0.11	0.23	YES
30	RAB34	RAB34	RAB34	1926	0.1	0.24	YES
31	COL18A1	COL18A1	COL18A1	1934	0.1	0.25	YES
32	TMEM147	TMEM147	TMEM147	1971	0.1	0.26	YES
33	HDLBP	HDLBP	HDLBP	2016	0.1	0.26	YES
34	NDE1	NDE1	NDE1	2082	0.1	0.27	YES
35	SND1	SND1	SND1	2103	0.1	0.28	YES
36	HTRA2	HTRA2	HTRA2	2259	0.098	0.28	YES
37	GGA1	GGA1	GGA1	2320	0.097	0.28	YES
38	FKBP11	FKBP11	FKBP11	2404	0.095	0.29	YES
39	PRMT1	PRMT1	PRMT1	2467	0.094	0.29	YES
40	EFTUD2	EFTUD2	EFTUD2	2548	0.092	0.3	YES
41	BANF1	BANF1	BANF1	2553	0.092	0.31	YES
42	GATAD2A	GATAD2A	GATAD2A	2570	0.091	0.31	YES
43	FBL	FBL	FBL	2725	0.089	0.31	YES
44	PADI2	PADI2	PADI2	2752	0.088	0.32	YES
45	CS	CS	CS	2864	0.086	0.32	YES
46	CLPTM1L	CLPTM1L	CLPTM1L	2926	0.085	0.33	YES
47	SSR2	SSR2	SSR2	3009	0.083	0.33	YES
48	NHP2	NHP2	NHP2	3034	0.083	0.34	YES
49	LMAN2	LMAN2	LMAN2	3057	0.082	0.34	YES
50	CDK4	CDK4	CDK4	3156	0.08	0.34	YES
51	TUBB3	TUBB3	TUBB3	3209	0.079	0.35	YES
52	PSMB3	PSMB3	PSMB3	3222	0.079	0.36	YES
53	PSMB5	PSMB5	PSMB5	3305	0.077	0.36	YES
54	RGS19	RGS19	RGS19	3317	0.077	0.36	YES
55	EIF4G1	EIF4G1	EIF4G1	3321	0.076	0.37	YES
56	SERPINH1	SERPINH1	SERPINH1	3409	0.075	0.37	YES
57	IRAK1	IRAK1	IRAK1	3525	0.072	0.37	YES
58	YKT6	YKT6	YKT6	3539	0.072	0.38	YES
59	TBCB	TBCB	TBCB	3550	0.072	0.39	YES
60	MRPL20	MRPL20	MRPL20	3717	0.069	0.38	YES
61	DCTPP1	DCTPP1	DCTPP1	3873	0.066	0.38	YES
62	MRPS18B	MRPS18B	MRPS18B	3914	0.065	0.38	YES
63	SEC61A1	SEC61A1	SEC61A1	3951	0.064	0.39	YES
64	DTYMK	DTYMK	DTYMK	4027	0.063	0.39	YES
65	CCT3	CCT3	CCT3	4319	0.057	0.38	YES
66	RPN1	RPN1	RPN1	4337	0.057	0.38	YES
67	ATF6B	ATF6B	ATF6B	4369	0.056	0.39	YES
68	THOP1	THOP1	THOP1	4483	0.054	0.39	YES
69	PDIA3	PDIA3	PDIA3	4538	0.053	0.39	YES
70	TMEM97	TMEM97	TMEM97	4555	0.053	0.39	YES
71	SEC61B	SEC61B	SEC61B	4729	0.05	0.39	NO
72	PKDCC	PKDCC	PKDCC	5031	0.044	0.38	NO
73	NUBP1	NUBP1	NUBP1	5129	0.043	0.37	NO
74	SNRPD3	SNRPD3	SNRPD3	5180	0.042	0.37	NO
75	SLC39A7	SLC39A7	SLC39A7	5241	0.04	0.38	NO
76	CALCA	CALCA	CALCA	5242	0.04	0.38	NO
77	C6orf136	C6orf136	C6orf136	5401	0.038	0.37	NO
78	PDIA4	PDIA4	PDIA4	5488	0.036	0.37	NO
79	SEC13	SEC13	SEC13	5559	0.035	0.37	NO
80	RAN	RAN	RAN	5564	0.034	0.37	NO
81	SLC25A5	SLC25A5	SLC25A5	5614	0.034	0.38	NO
82	GORASP2	GORASP2	GORASP2	5725	0.032	0.37	NO
83	CCT8	CCT8	CCT8	5736	0.031	0.37	NO
84	RANBP1	RANBP1	RANBP1	5738	0.031	0.38	NO
85	UBFD1	UBFD1	UBFD1	5740	0.031	0.38	NO
86	APEX1	APEX1	APEX1	5807	0.03	0.38	NO
87	TUBB6	TUBB6	TUBB6	5926	0.027	0.38	NO
88	SERPINE2	SERPINE2	SERPINE2	6020	0.025	0.37	NO
89	CDK2AP1	CDK2AP1	CDK2AP1	6142	0.023	0.37	NO
90	EIF2B5	EIF2B5	EIF2B5	6254	0.021	0.36	NO
91	ODC1	ODC1	ODC1	6294	0.02	0.36	NO
92	TUBA1A	TUBA1A	TUBA1A	6403	0.018	0.36	NO
93	RCN1	RCN1	RCN1	6459	0.017	0.36	NO
94	NSUN2	NSUN2	NSUN2	6498	0.016	0.36	NO
95	PREP	PREP	PREP	6641	0.013	0.35	NO
96	UBE2N	UBE2N	UBE2N	7012	0.0051	0.33	NO
97	VCL	VCL	VCL	7051	0.0042	0.33	NO
98	CCT6A	CCT6A	CCT6A	7275	-0.00027	0.32	NO
99	PSMD1	PSMD1	PSMD1	7280	-0.00037	0.32	NO
100	METAP1	METAP1	METAP1	7658	-0.0083	0.3	NO
101	RARS	RARS	RARS	7958	-0.015	0.28	NO
102	MORF4L2	MORF4L2	MORF4L2	8060	-0.017	0.28	NO
103	NARS	NARS	NARS	8061	-0.017	0.28	NO
104	SRSF1	SRSF1	SRSF1	8234	-0.021	0.27	NO
105	TMEM14C	TMEM14C	TMEM14C	8647	-0.029	0.25	NO
106	CISD1	CISD1	CISD1	8716	-0.031	0.25	NO
107	PSMD6	PSMD6	PSMD6	8772	-0.032	0.25	NO
108	GALM	GALM	GALM	8806	-0.033	0.25	NO
109	SSR1	SSR1	SSR1	8915	-0.035	0.25	NO
110	EBNA1BP2	EBNA1BP2	EBNA1BP2	8925	-0.035	0.25	NO
111	MRPS10	MRPS10	MRPS10	9042	-0.038	0.25	NO
112	IPO5	IPO5	IPO5	9233	-0.042	0.24	NO
113	MRPS28	MRPS28	MRPS28	9258	-0.042	0.24	NO
114	TCEA1	TCEA1	TCEA1	9337	-0.044	0.24	NO
115	SYNCRIP	SYNCRIP	SYNCRIP	9385	-0.045	0.24	NO
116	PPA1	PPA1	PPA1	9799	-0.055	0.23	NO
117	PRRC1	PRRC1	PRRC1	9883	-0.057	0.23	NO
118	TOMM70A	TOMM70A	TOMM70A	10089	-0.061	0.22	NO
119	SNRPA1	SNRPA1	SNRPA1	10110	-0.061	0.22	NO
120	SMYD2	SMYD2	SMYD2	10225	-0.064	0.22	NO
121	SSR3	SSR3	SSR3	10242	-0.064	0.23	NO
122	GSTM2	GSTM2	GSTM2	10362	-0.067	0.23	NO
123	PDLIM3	PDLIM3	PDLIM3	10710	-0.074	0.22	NO
124	MME	MME	MME	10805	-0.077	0.22	NO
125	PSME4	PSME4	PSME4	11114	-0.084	0.21	NO
126	GOLGA5	GOLGA5	GOLGA5	11189	-0.086	0.21	NO
127	GNPNAT1	GNPNAT1	GNPNAT1	12066	-0.11	0.18	NO
128	RB1	RB1	RB1	12157	-0.11	0.18	NO
129	TMEM167A	TMEM167A	TMEM167A	12368	-0.11	0.18	NO
130	SLMO2	SLMO2	SLMO2	12441	-0.12	0.18	NO
131	DNAJC2	DNAJC2	DNAJC2	13095	-0.13	0.16	NO
132	SLAIN1	SLAIN1	SLAIN1	13432	-0.14	0.16	NO
133	TCERG1	TCERG1	TCERG1	13769	-0.15	0.15	NO
134	TANK	TANK	TANK	15366	-0.22	0.083	NO
135	HMGN5	HMGN5	HMGN5	15509	-0.23	0.097	NO
136	FGF1	FGF1	FGF1	15739	-0.24	0.11	NO
137	IRG1	IRG1	IRG1	15914	-0.26	0.12	NO

Figure S69. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP, 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: LOCKWOOD AMPLIFIED IN LUNG CANCER

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	C21orf33	C21orf33	C21orf33	83	0.26	0.0058	YES
2	MYBL2	MYBL2	MYBL2	112	0.24	0.014	YES
3	KCNJ4	KCNJ4	KCNJ4	158	0.23	0.02	YES
4	CDT1	CDT1	CDT1	179	0.22	0.028	YES
5	PKMYT1	PKMYT1	PKMYT1	208	0.21	0.035	YES
6	TK1	TK1	TK1	218	0.21	0.043	YES
7	SULT1A1	SULT1A1	SULT1A1	301	0.19	0.046	YES
8	MRPL23	MRPL23	MRPL23	416	0.17	0.046	YES
9	PLTP	PLTP	PLTP	458	0.16	0.05	YES
10	MPDU1	MPDU1	MPDU1	568	0.15	0.05	YES
11	PGF	PGF	PGF	590	0.15	0.055	YES
12	SCO2	SCO2	SCO2	597	0.15	0.061	YES
13	BTBD2	BTBD2	BTBD2	603	0.15	0.066	YES
14	E2F1	E2F1	E2F1	613	0.15	0.072	YES
15	GCAT	GCAT	GCAT	617	0.15	0.078	YES
16	PAFAH1B3	PAFAH1B3	PAFAH1B3	621	0.15	0.083	YES
17	TNFSF9	TNFSF9	TNFSF9	633	0.15	0.089	YES
18	LY6E	LY6E	LY6E	700	0.14	0.091	YES
19	LMF2	LMF2	LMF2	722	0.14	0.095	YES
20	EIF4EBP1	EIF4EBP1	EIF4EBP1	726	0.14	0.1	YES
21	TST	TST	TST	738	0.14	0.11	YES
22	CCDC85B	CCDC85B	CCDC85B	762	0.14	0.11	YES
23	SLC1A5	SLC1A5	SLC1A5	768	0.14	0.12	YES
24	IFITM2	IFITM2	IFITM2	785	0.14	0.12	YES
25	ERBB2	ERBB2	ERBB2	815	0.14	0.12	YES
26	SHMT2	SHMT2	SHMT2	895	0.13	0.12	YES
27	ERCC2	ERCC2	ERCC2	920	0.13	0.13	YES
28	NDUFS7	NDUFS7	NDUFS7	951	0.13	0.13	YES
29	RELA	RELA	RELA	972	0.13	0.14	YES
30	TCIRG1	TCIRG1	TCIRG1	974	0.13	0.14	YES
31	ALDOA	ALDOA	ALDOA	981	0.13	0.15	YES
32	ABHD14A	ABHD14A	ABHD14A	990	0.13	0.15	YES
33	RNF40	RNF40	RNF40	1002	0.13	0.16	YES
34	AP2S1	AP2S1	AP2S1	1013	0.13	0.16	YES
35	NDUFB7	NDUFB7	NDUFB7	1015	0.13	0.17	YES
36	SAC3D1	SAC3D1	SAC3D1	1018	0.13	0.17	YES
37	NDUFV1	NDUFV1	NDUFV1	1066	0.13	0.17	YES
38	ASL	ASL	ASL	1117	0.13	0.18	YES
39	MCM5	MCM5	MCM5	1154	0.12	0.18	YES
40	ERCC1	ERCC1	ERCC1	1165	0.12	0.18	YES
41	ZFPL1	ZFPL1	ZFPL1	1172	0.12	0.19	YES
42	FDXR	FDXR	FDXR	1176	0.12	0.19	YES
43	SLC30A3	SLC30A3	SLC30A3	1197	0.12	0.2	YES
44	ECI1	ECI1	ECI1	1202	0.12	0.2	YES
45	CBX2	CBX2	CBX2	1210	0.12	0.21	YES
46	GRINA	GRINA	GRINA	1215	0.12	0.21	YES
47	BSG	BSG	BSG	1223	0.12	0.22	YES
48	DGAT1	DGAT1	DGAT1	1235	0.12	0.22	YES
49	BRMS1	BRMS1	BRMS1	1268	0.12	0.22	YES
50	MRPL28	MRPL28	MRPL28	1280	0.12	0.23	YES
51	BAD	BAD	BAD	1299	0.12	0.23	YES
52	MRPS12	MRPS12	MRPS12	1319	0.12	0.23	YES
53	LIN37	LIN37	LIN37	1325	0.12	0.24	YES
54	EPHX1	EPHX1	EPHX1	1351	0.12	0.24	YES
55	MAZ	MAZ	MAZ	1387	0.12	0.24	YES
56	PHLDA2	PHLDA2	PHLDA2	1420	0.12	0.25	YES
57	NCLN	NCLN	NCLN	1452	0.12	0.25	YES
58	PPP1CA	PPP1CA	PPP1CA	1460	0.12	0.26	YES
59	SNRPA	SNRPA	SNRPA	1481	0.12	0.26	YES
60	SMARCD3	SMARCD3	SMARCD3	1530	0.11	0.26	YES
61	DGCR14	DGCR14	DGCR14	1532	0.11	0.26	YES
62	PLD3	PLD3	PLD3	1582	0.11	0.27	YES
63	TP53	TP53	TP53	1585	0.11	0.27	YES
64	ABCB6	ABCB6	ABCB6	1631	0.11	0.27	YES
65	ERGIC3	ERGIC3	ERGIC3	1671	0.11	0.28	YES
66	NOP2	NOP2	NOP2	1691	0.11	0.28	YES
67	PDLIM7	PDLIM7	PDLIM7	1731	0.11	0.28	YES
68	UQCRC1	UQCRC1	UQCRC1	1749	0.11	0.28	YES
69	MBOAT7	MBOAT7	MBOAT7	1799	0.11	0.28	YES
70	UBA1	UBA1	UBA1	1806	0.11	0.29	YES
71	POLR2A	POLR2A	POLR2A	1868	0.11	0.29	YES
72	ZNHIT1	ZNHIT1	ZNHIT1	1947	0.1	0.29	YES
73	CNP	CNP	CNP	1973	0.1	0.29	YES
74	ISG15	ISG15	ISG15	1983	0.1	0.3	YES
75	CDK16	CDK16	CDK16	2017	0.1	0.3	YES
76	IDH2	IDH2	IDH2	2028	0.1	0.3	YES
77	CLTB	CLTB	CLTB	2036	0.1	0.31	YES
78	SMPD1	SMPD1	SMPD1	2039	0.1	0.31	YES
79	LHX2	LHX2	LHX2	2047	0.1	0.31	YES
80	PQBP1	PQBP1	PQBP1	2059	0.1	0.32	YES
81	RPS6KB2	RPS6KB2	RPS6KB2	2084	0.1	0.32	YES
82	FKBP1A	FKBP1A	FKBP1A	2094	0.1	0.32	YES
83	NME3	NME3	NME3	2127	0.1	0.32	YES
84	IGFBP6	IGFBP6	IGFBP6	2164	0.1	0.33	YES
85	TMED1	TMED1	TMED1	2174	0.1	0.33	YES
86	SPR	SPR	SPR	2188	0.099	0.33	YES
87	S100A13	S100A13	S100A13	2210	0.099	0.34	YES
88	SIGMAR1	SIGMAR1	SIGMAR1	2329	0.096	0.33	YES
89	ATP6V1F	ATP6V1F	ATP6V1F	2354	0.096	0.34	YES
90	PSMD8	PSMD8	PSMD8	2381	0.095	0.34	YES
91	EEF1D	EEF1D	EEF1D	2495	0.093	0.34	YES
92	OGFR	OGFR	OGFR	2573	0.091	0.34	YES
93	NCDN	NCDN	NCDN	2667	0.09	0.33	YES
94	CCND3	CCND3	CCND3	2715	0.089	0.34	YES
95	OSR2	OSR2	OSR2	2718	0.089	0.34	YES
96	GRHPR	GRHPR	GRHPR	2753	0.088	0.34	YES
97	STK25	STK25	STK25	2777	0.088	0.34	YES
98	ABCF3	ABCF3	ABCF3	2807	0.087	0.34	YES
99	ASNA1	ASNA1	ASNA1	2826	0.087	0.35	YES
100	GNL1	GNL1	GNL1	2838	0.086	0.35	YES
101	PPP2R5D	PPP2R5D	PPP2R5D	2925	0.085	0.35	YES
102	CDC34	CDC34	CDC34	2927	0.085	0.35	YES
103	TMEM109	TMEM109	TMEM109	2942	0.085	0.35	YES
104	FRAT2	FRAT2	FRAT2	2990	0.084	0.36	YES
105	NR4A1	NR4A1	NR4A1	3016	0.083	0.36	YES
106	PSMC3	PSMC3	PSMC3	3029	0.083	0.36	YES
107	AAMP	AAMP	AAMP	3088	0.082	0.36	YES
108	PLXNA3	PLXNA3	PLXNA3	3093	0.081	0.36	YES
109	PPIF	PPIF	PPIF	3094	0.081	0.36	YES
110	MVD	MVD	MVD	3095	0.081	0.37	YES
111	TYK2	TYK2	TYK2	3110	0.081	0.37	YES
112	MEA1	MEA1	MEA1	3177	0.08	0.37	YES
113	RBM38	RBM38	RBM38	3202	0.079	0.37	YES
114	TUBB3	TUBB3	TUBB3	3209	0.079	0.38	YES
115	THAP3	THAP3	THAP3	3226	0.078	0.38	YES
116	SQSTM1	SQSTM1	SQSTM1	3233	0.078	0.38	YES
117	RPUSD2	RPUSD2	RPUSD2	3257	0.078	0.38	YES
118	BAK1	BAK1	BAK1	3295	0.077	0.38	YES
119	RFC2	RFC2	RFC2	3309	0.077	0.39	YES
120	GPRC5B	GPRC5B	GPRC5B	3316	0.077	0.39	YES
121	RBM4	RBM4	RBM4	3401	0.075	0.39	YES
122	PAQR4	PAQR4	PAQR4	3405	0.075	0.39	YES
123	SERPINH1	SERPINH1	SERPINH1	3409	0.075	0.39	YES
124	MDK	MDK	MDK	3416	0.075	0.4	YES
125	CBR3	CBR3	CBR3	3496	0.073	0.39	YES
126	FLNA	FLNA	FLNA	3502	0.073	0.4	YES
127	FGFR3	FGFR3	FGFR3	3509	0.073	0.4	YES
128	CDKN1C	CDKN1C	CDKN1C	3512	0.073	0.4	YES
129	CBX4	CBX4	CBX4	3526	0.072	0.4	YES
130	YKT6	YKT6	YKT6	3539	0.072	0.41	YES
131	IL11RA	IL11RA	IL11RA	3554	0.072	0.41	YES
132	ARPC4	ARPC4	ARPC4	3688	0.069	0.4	YES
133	U2AF2	U2AF2	U2AF2	3770	0.068	0.4	YES
134	UROS	UROS	UROS	3795	0.067	0.4	YES
135	RABAC1	RABAC1	RABAC1	3827	0.067	0.4	YES
136	KLHDC3	KLHDC3	KLHDC3	3850	0.066	0.4	YES
137	ADA	ADA	ADA	3858	0.066	0.41	YES
138	PDAP1	PDAP1	PDAP1	3911	0.065	0.41	YES
139	AGPAT2	AGPAT2	AGPAT2	3917	0.065	0.41	YES
140	PLEKHO2	PLEKHO2	PLEKHO2	3963	0.064	0.41	YES
141	FEN1	FEN1	FEN1	3985	0.064	0.41	YES
142	SDF2	SDF2	SDF2	4004	0.064	0.41	YES
143	TP53I3	TP53I3	TP53I3	4009	0.063	0.42	YES
144	C2CD2L	C2CD2L	C2CD2L	4062	0.062	0.41	YES
145	PLCB3	PLCB3	PLCB3	4063	0.062	0.42	YES
146	OAZ2	OAZ2	OAZ2	4090	0.062	0.42	YES
147	GSTP1	GSTP1	GSTP1	4093	0.062	0.42	YES
148	SHMT1	SHMT1	SHMT1	4106	0.061	0.42	YES
149	TERF2	TERF2	TERF2	4144	0.06	0.42	YES
150	RNF113A	RNF113A	RNF113A	4230	0.059	0.42	YES
151	WBSCR22	WBSCR22	WBSCR22	4236	0.059	0.42	YES
152	SLC6A8	SLC6A8	SLC6A8	4242	0.059	0.42	YES
153	TNFRSF10D	TNFRSF10D	TNFRSF10D	4271	0.058	0.42	YES
154	RPN1	RPN1	RPN1	4337	0.057	0.42	YES
155	UROD	UROD	UROD	4372	0.056	0.42	YES
156	RAB8A	RAB8A	RAB8A	4387	0.056	0.42	YES
157	CYB5R1	CYB5R1	CYB5R1	4402	0.056	0.43	YES
158	GALNT2	GALNT2	GALNT2	4408	0.056	0.43	YES
159	HSPA1A	HSPA1A	HSPA1A	4434	0.055	0.43	YES
160	ARRB2	ARRB2	ARRB2	4437	0.055	0.43	YES
161	PSMB10	PSMB10	PSMB10	4495	0.054	0.43	YES
162	PPIE	PPIE	PPIE	4580	0.052	0.43	YES
163	SAP18	SAP18	SAP18	4626	0.052	0.43	YES
164	NEU1	NEU1	NEU1	4653	0.051	0.43	YES
165	DNASE2	DNASE2	DNASE2	4661	0.051	0.43	YES
166	BAG1	BAG1	BAG1	4666	0.051	0.43	YES
167	PVR	PVR	PVR	4681	0.051	0.43	YES
168	CDC6	CDC6	CDC6	4696	0.05	0.43	YES
169	TRIM25	TRIM25	TRIM25	4700	0.05	0.44	YES
170	HLA-A	HLA-A	HLA-A	4766	0.049	0.43	NO
171	MGAT1	MGAT1	MGAT1	4772	0.049	0.44	NO
172	TYMS	TYMS	TYMS	4831	0.048	0.43	NO
173	RAD9A	RAD9A	RAD9A	4891	0.047	0.43	NO
174	CYB5B	CYB5B	CYB5B	5025	0.044	0.43	NO
175	ALAS1	ALAS1	ALAS1	5054	0.044	0.43	NO
176	C1orf123	C1orf123	C1orf123	5059	0.044	0.43	NO
177	CEBPD	CEBPD	CEBPD	5266	0.04	0.42	NO
178	TRIM21	TRIM21	TRIM21	5452	0.037	0.41	NO
179	RHOB	RHOB	RHOB	5464	0.036	0.41	NO
180	NFE2L1	NFE2L1	NFE2L1	5501	0.036	0.41	NO
181	DMPK	DMPK	DMPK	5560	0.035	0.41	NO
182	ALDH1B1	ALDH1B1	ALDH1B1	5583	0.034	0.41	NO
183	EIF3I	EIF3I	EIF3I	5587	0.034	0.41	NO
184	NFKBIE	NFKBIE	NFKBIE	5644	0.033	0.41	NO
185	SEPW1	SEPW1	SEPW1	5654	0.033	0.41	NO
186	TM7SF2	TM7SF2	TM7SF2	5679	0.032	0.41	NO
187	NPRL2	NPRL2	NPRL2	5747	0.031	0.41	NO
188	PRPF4	PRPF4	PRPF4	5764	0.031	0.41	NO
189	CDKN2C	CDKN2C	CDKN2C	5867	0.028	0.4	NO
190	DUSP3	DUSP3	DUSP3	5992	0.026	0.4	NO
191	HEXIM1	HEXIM1	HEXIM1	6021	0.025	0.4	NO
192	ZNF263	ZNF263	ZNF263	6032	0.025	0.4	NO
193	PIM2	PIM2	PIM2	6035	0.025	0.4	NO
194	HNRNPU	HNRNPU	HNRNPU	6100	0.024	0.39	NO
195	CCNE1	CCNE1	CCNE1	6128	0.023	0.39	NO
196	FADS1	FADS1	FADS1	6218	0.021	0.39	NO
197	TBCC	TBCC	TBCC	6295	0.02	0.39	NO
198	PROSC	PROSC	PROSC	6322	0.02	0.38	NO
199	TMBIM6	TMBIM6	TMBIM6	6369	0.019	0.38	NO
200	HLA-E	HLA-E	HLA-E	6372	0.019	0.38	NO
201	PSMC3IP	PSMC3IP	PSMC3IP	6444	0.017	0.38	NO
202	DAXX	DAXX	DAXX	6473	0.017	0.38	NO
203	CLK3	CLK3	CLK3	6475	0.016	0.38	NO
204	EWSR1	EWSR1	EWSR1	6507	0.016	0.38	NO
205	ACAA1	ACAA1	ACAA1	6542	0.015	0.38	NO
206	EPOR	EPOR	EPOR	6561	0.015	0.38	NO
207	PER2	PER2	PER2	6567	0.015	0.38	NO
208	HYAL2	HYAL2	HYAL2	6597	0.014	0.38	NO
209	TUBA4A	TUBA4A	TUBA4A	6598	0.014	0.38	NO
210	RPS15A	RPS15A	RPS15A	6702	0.012	0.37	NO
211	THBS1	THBS1	THBS1	6752	0.011	0.37	NO
212	PITX2	PITX2	PITX2	6761	0.011	0.37	NO
213	CEP68	CEP68	CEP68	6906	0.0072	0.36	NO
214	RFC5	RFC5	RFC5	6967	0.006	0.36	NO
215	BRD2	BRD2	BRD2	7124	0.003	0.35	NO
216	GLUL	GLUL	GLUL	7132	0.0028	0.35	NO
217	TRIM13	TRIM13	TRIM13	7175	0.0021	0.35	NO
218	TPM2	TPM2	TPM2	7219	0.00097	0.34	NO
219	NAT1	NAT1	NAT1	7227	0.00069	0.34	NO
220	MCM4	MCM4	MCM4	7253	0.000045	0.34	NO
221	MED6	MED6	MED6	7398	-0.003	0.34	NO
222	CDK2	CDK2	CDK2	7423	-0.0033	0.33	NO
223	PNRC1	PNRC1	PNRC1	7462	-0.0041	0.33	NO
224	TRIAP1	TRIAP1	TRIAP1	7522	-0.0056	0.33	NO
225	OGG1	OGG1	OGG1	7523	-0.0056	0.33	NO
226	IRF1	IRF1	IRF1	7580	-0.0066	0.33	NO
227	NXF1	NXF1	NXF1	7638	-0.0079	0.32	NO
228	FBXL14	FBXL14	FBXL14	7669	-0.0085	0.32	NO
229	TSPYL2	TSPYL2	TSPYL2	7724	-0.0097	0.32	NO
230	JUNB	JUNB	JUNB	7904	-0.013	0.31	NO
231	BTG1	BTG1	BTG1	7915	-0.014	0.31	NO
232	NPTXR	NPTXR	NPTXR	7978	-0.015	0.31	NO
233	CLCN2	CLCN2	CLCN2	7981	-0.015	0.31	NO
234	SAT1	SAT1	SAT1	8081	-0.018	0.3	NO
235	MAT2A	MAT2A	MAT2A	8097	-0.018	0.3	NO
236	ZNF330	ZNF330	ZNF330	8207	-0.02	0.3	NO
237	AP3M2	AP3M2	AP3M2	8251	-0.021	0.3	NO
238	HLA-G	HLA-G	HLA-G	8282	-0.022	0.3	NO
239	PCNA	PCNA	PCNA	8296	-0.022	0.3	NO
240	ADO	ADO	ADO	8305	-0.022	0.3	NO
241	ATF3	ATF3	ATF3	8527	-0.026	0.28	NO
242	GDI2	GDI2	GDI2	8531	-0.026	0.28	NO
243	HLA-F	HLA-F	HLA-F	8634	-0.029	0.28	NO
244	EIF2S3	EIF2S3	EIF2S3	8707	-0.031	0.28	NO
245	EFNA1	EFNA1	EFNA1	8711	-0.031	0.28	NO
246	CTH	CTH	CTH	8904	-0.034	0.27	NO
247	BTG2	BTG2	BTG2	9044	-0.038	0.26	NO
248	PNP	PNP	PNP	9116	-0.04	0.26	NO
249	SLC25A4	SLC25A4	SLC25A4	9163	-0.04	0.26	NO
250	GABARAPL1	GABARAPL1	GABARAPL1	9203	-0.041	0.26	NO
251	TOB1	TOB1	TOB1	9235	-0.042	0.26	NO
252	ITM2B	ITM2B	ITM2B	9240	-0.042	0.26	NO
253	RNF103	RNF103	RNF103	9242	-0.042	0.26	NO
254	RSL1D1	RSL1D1	RSL1D1	9383	-0.045	0.26	NO
255	IFI30	IFI30	IFI30	9514	-0.048	0.25	NO
256	HSPA2	HSPA2	HSPA2	9722	-0.053	0.24	NO
257	MOAP1	MOAP1	MOAP1	9751	-0.054	0.24	NO
258	TMX4	TMX4	TMX4	9806	-0.055	0.24	NO
259	CSRNP2	CSRNP2	CSRNP2	9815	-0.055	0.24	NO
260	GLUD1	GLUD1	GLUD1	9903	-0.057	0.24	NO
261	MICB	MICB	MICB	10018	-0.059	0.24	NO
262	NCBP2	NCBP2	NCBP2	10261	-0.065	0.22	NO
263	PDCL	PDCL	PDCL	10387	-0.068	0.22	NO
264	HOXD9	HOXD9	HOXD9	10422	-0.068	0.22	NO
265	ZKSCAN1	ZKSCAN1	ZKSCAN1	10440	-0.069	0.22	NO
266	GAS1	GAS1	GAS1	10522	-0.07	0.22	NO
267	TREX1	TREX1	TREX1	10553	-0.071	0.22	NO
268	CREM	CREM	CREM	10594	-0.072	0.22	NO
269	PTPN11	PTPN11	PTPN11	10615	-0.072	0.22	NO
270	CREG1	CREG1	CREG1	10755	-0.076	0.22	NO
271	CCNG2	CCNG2	CCNG2	11168	-0.086	0.2	NO
272	CASP3	CASP3	CASP3	11281	-0.088	0.2	NO
273	STX16	STX16	STX16	11387	-0.09	0.2	NO
274	ACYP1	ACYP1	ACYP1	11454	-0.092	0.2	NO
275	MFAP3	MFAP3	MFAP3	11736	-0.098	0.18	NO
276	RGS2	RGS2	RGS2	11755	-0.098	0.19	NO
277	HHEX	HHEX	HHEX	11909	-0.1	0.18	NO
278	MLLT11	MLLT11	MLLT11	11940	-0.1	0.18	NO
279	SIX1	SIX1	SIX1	12078	-0.11	0.18	NO
280	SYNM	SYNM	SYNM	12242	-0.11	0.18	NO
281	CDKN2B	CDKN2B	CDKN2B	12484	-0.12	0.17	NO
282	SHOX2	SHOX2	SHOX2	12618	-0.12	0.16	NO
283	FAM8A1	FAM8A1	FAM8A1	12804	-0.12	0.16	NO
284	MBD4	MBD4	MBD4	12831	-0.13	0.16	NO
285	GCH1	GCH1	GCH1	12837	-0.13	0.17	NO
286	GLS	GLS	GLS	12956	-0.13	0.17	NO
287	TPBG	TPBG	TPBG	13131	-0.13	0.16	NO
288	TFAM	TFAM	TFAM	13701	-0.15	0.14	NO
289	SMPDL3A	SMPDL3A	SMPDL3A	14096	-0.16	0.12	NO
290	IFIT1	IFIT1	IFIT1	14134	-0.17	0.12	NO
291	ZNF510	ZNF510	ZNF510	14427	-0.18	0.12	NO
292	CREBZF	CREBZF	CREBZF	14463	-0.18	0.12	NO
293	HAUS3	HAUS3	HAUS3	14624	-0.19	0.12	NO
294	CYP1B1	CYP1B1	CYP1B1	14765	-0.19	0.12	NO
295	ICAM3	ICAM3	ICAM3	14808	-0.19	0.12	NO
296	CDO1	CDO1	CDO1	14911	-0.2	0.13	NO
297	CLK1	CLK1	CLK1	15630	-0.24	0.096	NO
298	PMAIP1	PMAIP1	PMAIP1	16604	-0.32	0.053	NO
299	CCNE2	CCNE2	CCNE2	16620	-0.32	0.065	NO
300	PCDH9	PCDH9	PCDH9	17415	-0.43	0.038	NO

Figure S71. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: LOCKWOOD AMPLIFIED IN LUNG CANCER.

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: LOCKWOOD AMPLIFIED IN LUNG 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: PENG LEUCINE DEPRIVATION DN

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	POLD2	POLD2	POLD2	557	0.15	0.0036	YES
2	FARSA	FARSA	FARSA	759	0.14	0.024	YES
3	RUVBL2	RUVBL2	RUVBL2	900	0.13	0.046	YES
4	TRAP1	TRAP1	TRAP1	913	0.13	0.076	YES
5	ERCC2	ERCC2	ERCC2	920	0.13	0.1	YES
6	SSSCA1	SSSCA1	SSSCA1	924	0.13	0.14	YES
7	PFKL	PFKL	PFKL	1371	0.12	0.14	YES
8	EIF3B	EIF3B	EIF3B	1392	0.12	0.16	YES
9	SNRPA	SNRPA	SNRPA	1481	0.12	0.18	YES
10	ATP5G2	ATP5G2	ATP5G2	1635	0.11	0.2	YES
11	TIMM17B	TIMM17B	TIMM17B	1690	0.11	0.22	YES
12	TUBG1	TUBG1	TUBG1	1795	0.11	0.24	YES
13	FANCG	FANCG	FANCG	2035	0.1	0.25	YES
14	RHOC	RHOC	RHOC	2181	0.099	0.26	YES
15	SLC25A6	SLC25A6	SLC25A6	2267	0.098	0.28	YES
16	EEF1D	EEF1D	EEF1D	2495	0.093	0.29	YES
17	NDUFS3	NDUFS3	NDUFS3	2580	0.091	0.3	YES
18	TKT	TKT	TKT	2714	0.089	0.32	YES
19	EML2	EML2	EML2	2980	0.084	0.32	YES
20	CDK4	CDK4	CDK4	3156	0.08	0.33	YES
21	MCM7	MCM7	MCM7	3167	0.08	0.35	YES
22	QDPR	QDPR	QDPR	3390	0.075	0.35	YES
23	PGAM1	PGAM1	PGAM1	3443	0.074	0.36	YES
24	RPL29	RPL29	RPL29	3542	0.072	0.38	YES
25	RRM2	RRM2	RRM2	3738	0.068	0.38	YES
26	PA2G4	PA2G4	PA2G4	4017	0.063	0.38	YES
27	COX4I1	COX4I1	COX4I1	4312	0.058	0.38	YES
28	RPS14	RPS14	RPS14	4331	0.057	0.39	YES
29	NOP16	NOP16	NOP16	4605	0.052	0.38	YES
30	ATP5G3	ATP5G3	ATP5G3	4685	0.05	0.39	YES
31	HADHA	HADHA	HADHA	4730	0.05	0.4	YES
32	POLR2H	POLR2H	POLR2H	4749	0.049	0.41	YES
33	NOP56	NOP56	NOP56	4755	0.049	0.42	YES
34	FARSB	FARSB	FARSB	4790	0.049	0.43	YES
35	SNRPC	SNRPC	SNRPC	4807	0.048	0.44	YES
36	UQCRH	UQCRH	UQCRH	4920	0.046	0.44	YES
37	TIMM23	TIMM23	TIMM23	5181	0.042	0.44	YES
38	NDUFB2	NDUFB2	NDUFB2	5194	0.042	0.45	YES
39	MTHFD1	MTHFD1	MTHFD1	5294	0.04	0.45	YES
40	RPSA	RPSA	RPSA	5944	0.027	0.42	NO
41	FABP5	FABP5	FABP5	5960	0.026	0.43	NO
42	SNRPD1	SNRPD1	SNRPD1	6487	0.016	0.4	NO
43	HNRNPC	HNRNPC	HNRNPC	6582	0.014	0.4	NO
44	HARS2	HARS2	HARS2	6603	0.014	0.4	NO
45	ABCA3	ABCA3	ABCA3	6665	0.013	0.4	NO
46	ZFYVE26	ZFYVE26	ZFYVE26	6738	0.011	0.4	NO
47	RPL4	RPL4	RPL4	6756	0.011	0.4	NO
48	AKAP13	AKAP13	AKAP13	6829	0.0095	0.4	NO
49	RFC5	RFC5	RFC5	6967	0.006	0.39	NO
50	NDUFB6	NDUFB6	NDUFB6	7284	-0.00047	0.38	NO
51	GTF3A	GTF3A	GTF3A	7410	-0.0031	0.37	NO
52	RPL15	RPL15	RPL15	7491	-0.0049	0.36	NO
53	SUPT16H	SUPT16H	SUPT16H	7662	-0.0083	0.36	NO
54	MYC	MYC	MYC	7768	-0.011	0.35	NO
55	RRM1	RRM1	RRM1	7860	-0.013	0.35	NO
56	ABCC4	ABCC4	ABCC4	8009	-0.016	0.35	NO
57	MRPL3	MRPL3	MRPL3	8087	-0.018	0.35	NO
58	MSH6	MSH6	MSH6	8554	-0.027	0.33	NO
59	GTF2H4	GTF2H4	GTF2H4	9086	-0.039	0.31	NO
60	SNRPA1	SNRPA1	SNRPA1	10110	-0.061	0.26	NO
61	SLC27A2	SLC27A2	SLC27A2	10165	-0.063	0.28	NO
62	ZNF200	ZNF200	ZNF200	10843	-0.078	0.25	NO
63	MYB	MYB	MYB	11806	-0.1	0.22	NO
64	IDH3A	IDH3A	IDH3A	11980	-0.1	0.24	NO
65	PRIM1	PRIM1	PRIM1	12457	-0.12	0.24	NO
66	SLK	SLK	SLK	12593	-0.12	0.26	NO
67	PIK3CA	PIK3CA	PIK3CA	15296	-0.22	0.16	NO

Figure S73. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: PENG LEUCINE DEPRIVATION DN.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: PENG LEUCINE DEPRIVATION DN, 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: MOOTHA VOXPHOS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NRGN	NRGN	NRGN	176	0.22	0.0073	YES
2	COX7A1	COX7A1	COX7A1	310	0.19	0.014	YES
3	MRPL23	MRPL23	MRPL23	416	0.17	0.022	YES
4	COL9A3	COL9A3	COL9A3	477	0.16	0.031	YES
5	NDUFS8	NDUFS8	NDUFS8	480	0.16	0.044	YES
6	SEC14L5	SEC14L5	SEC14L5	515	0.16	0.054	YES
7	DCXR	DCXR	DCXR	542	0.16	0.065	YES
8	PAFAH1B3	PAFAH1B3	PAFAH1B3	621	0.15	0.072	YES
9	ENDOG	ENDOG	ENDOG	702	0.14	0.079	YES
10	C9orf16	C9orf16	C9orf16	794	0.14	0.085	YES
11	ACTL6B	ACTL6B	ACTL6B	804	0.14	0.095	YES
12	ECSIT	ECSIT	ECSIT	810	0.14	0.1	YES
13	NTHL1	NTHL1	NTHL1	874	0.14	0.11	YES
14	RUVBL2	RUVBL2	RUVBL2	900	0.13	0.12	YES
15	TRAP1	TRAP1	TRAP1	913	0.13	0.13	YES
16	ETFB	ETFB	ETFB	950	0.13	0.14	YES
17	NDUFS7	NDUFS7	NDUFS7	951	0.13	0.15	YES
18	NBL1	NBL1	NBL1	960	0.13	0.16	YES
19	MAL	MAL	MAL	967	0.13	0.17	YES
20	HCFC1R1	HCFC1R1	HCFC1R1	1017	0.13	0.18	YES
21	SAC3D1	SAC3D1	SAC3D1	1018	0.13	0.19	YES
22	TPI1	TPI1	TPI1	1028	0.13	0.2	YES
23	MAPK3	MAPK3	MAPK3	1041	0.13	0.21	YES
24	CX3CL1	CX3CL1	CX3CL1	1058	0.13	0.22	YES
25	EXOC3	EXOC3	EXOC3	1109	0.13	0.22	YES
26	VPS28	VPS28	VPS28	1140	0.13	0.23	YES
27	ECI1	ECI1	ECI1	1202	0.12	0.24	YES
28	IMPDH2	IMPDH2	IMPDH2	1237	0.12	0.24	YES
29	EIF6	EIF6	EIF6	1285	0.12	0.25	YES
30	HRAS	HRAS	HRAS	1298	0.12	0.26	YES
31	EIF3G	EIF3G	EIF3G	1342	0.12	0.27	YES
32	SLC25A11	SLC25A11	SLC25A11	1366	0.12	0.28	YES
33	CTDNEP1	CTDNEP1	CTDNEP1	1402	0.12	0.28	YES
34	SNRPA	SNRPA	SNRPA	1481	0.12	0.29	YES
35	RNH1	RNH1	RNH1	1503	0.12	0.3	YES
36	PES1	PES1	PES1	1505	0.12	0.3	YES
37	ATP6AP1	ATP6AP1	ATP6AP1	1605	0.11	0.31	YES
38	NDUFAF3	NDUFAF3	NDUFAF3	1634	0.11	0.32	YES
39	ATP5G1	ATP5G1	ATP5G1	1647	0.11	0.32	YES
40	CHMP2A	CHMP2A	CHMP2A	1688	0.11	0.33	YES
41	TUFM	TUFM	TUFM	1872	0.11	0.33	YES
42	DTX4	DTX4	DTX4	1881	0.11	0.34	YES
43	TMEM147	TMEM147	TMEM147	1971	0.1	0.34	YES
44	PUF60	PUF60	PUF60	2279	0.097	0.33	YES
45	RBM10	RBM10	RBM10	2284	0.097	0.34	YES
46	DHPS	DHPS	DHPS	2378	0.095	0.34	YES
47	CRYAB	CRYAB	CRYAB	2391	0.095	0.34	YES
48	HAX1	HAX1	HAX1	2418	0.095	0.35	YES
49	ESYT1	ESYT1	ESYT1	2428	0.094	0.36	YES
50	RPL13	RPL13	RPL13	2489	0.093	0.36	YES
51	PIN1	PIN1	PIN1	2493	0.093	0.37	YES
52	COX8A	COX8A	COX8A	2502	0.093	0.38	YES
53	HDGF	HDGF	HDGF	2575	0.091	0.38	YES
54	SFXN3	SFXN3	SFXN3	2582	0.091	0.39	YES
55	NUDC	NUDC	NUDC	2583	0.091	0.39	YES
56	TALDO1	TALDO1	TALDO1	2599	0.091	0.4	YES
57	CCT7	CCT7	CCT7	2627	0.091	0.4	YES
58	BCAP31	BCAP31	BCAP31	2636	0.09	0.41	YES
59	ACOT7	ACOT7	ACOT7	2748	0.088	0.41	YES
60	GRHPR	GRHPR	GRHPR	2753	0.088	0.42	YES
61	OS9	OS9	OS9	2779	0.088	0.42	YES
62	CREB3	CREB3	CREB3	2829	0.087	0.43	YES
63	GDI1	GDI1	GDI1	2869	0.086	0.43	YES
64	NDUFA7	NDUFA7	NDUFA7	2898	0.085	0.44	YES
65	GTF3C1	GTF3C1	GTF3C1	3071	0.082	0.44	YES
66	SF3B2	SF3B2	SF3B2	3091	0.081	0.44	YES
67	GPX1	GPX1	GPX1	3127	0.08	0.44	YES
68	ATOX1	ATOX1	ATOX1	3155	0.08	0.45	YES
69	SPAG7	SPAG7	SPAG7	3218	0.079	0.45	YES
70	AMPD2	AMPD2	AMPD2	3229	0.078	0.46	YES
71	CDIPT	CDIPT	CDIPT	3234	0.078	0.46	YES
72	ATP6V0B	ATP6V0B	ATP6V0B	3283	0.077	0.47	YES
73	PSMB5	PSMB5	PSMB5	3305	0.077	0.47	YES
74	AKR1A1	AKR1A1	AKR1A1	3449	0.074	0.47	YES
75	ACTR1A	ACTR1A	ACTR1A	3547	0.072	0.47	YES
76	STOML1	STOML1	STOML1	3557	0.072	0.48	YES
77	DHX30	DHX30	DHX30	3558	0.072	0.48	YES
78	MARCKSL1	MARCKSL1	MARCKSL1	3660	0.07	0.48	YES
79	ACD	ACD	ACD	3692	0.069	0.48	YES
80	PMM1	PMM1	PMM1	3700	0.069	0.49	YES
81	AKR1B1	AKR1B1	AKR1B1	3767	0.068	0.49	YES
82	RABAC1	RABAC1	RABAC1	3827	0.067	0.49	YES
83	DPF2	DPF2	DPF2	3847	0.066	0.5	YES
84	PEF1	PEF1	PEF1	3849	0.066	0.5	YES
85	RPS29	RPS29	RPS29	3909	0.065	0.5	YES
86	DNAJB2	DNAJB2	DNAJB2	4033	0.063	0.5	YES
87	ATP6V0E2	ATP6V0E2	ATP6V0E2	4039	0.063	0.51	YES
88	MADD	MADD	MADD	4215	0.06	0.5	YES
89	NUP93	NUP93	NUP93	4222	0.059	0.51	YES
90	PPIA	PPIA	PPIA	4283	0.058	0.51	YES
91	COX4I1	COX4I1	COX4I1	4312	0.058	0.51	YES
92	SUMO3	SUMO3	SUMO3	4429	0.055	0.51	YES
93	ARRB2	ARRB2	ARRB2	4437	0.055	0.51	YES
94	GNPDA1	GNPDA1	GNPDA1	4470	0.054	0.51	YES
95	DCTN2	DCTN2	DCTN2	4530	0.053	0.52	YES
96	NDUFA1	NDUFA1	NDUFA1	4535	0.053	0.52	YES
97	CLTA	CLTA	CLTA	4689	0.05	0.52	YES
98	CKB	CKB	CKB	4702	0.05	0.52	YES
99	PARP1	PARP1	PARP1	4816	0.048	0.52	YES
100	ARPC2	ARPC2	ARPC2	4892	0.047	0.52	YES
101	NCALD	NCALD	NCALD	4978	0.045	0.51	YES
102	UQCRQ	UQCRQ	UQCRQ	4999	0.045	0.52	YES
103	AHSA1	AHSA1	AHSA1	5038	0.044	0.52	YES
104	NDUFC1	NDUFC1	NDUFC1	5060	0.044	0.52	YES
105	COX7C	COX7C	COX7C	5204	0.041	0.52	NO
106	LMAN2L	LMAN2L	LMAN2L	5214	0.041	0.52	NO
107	RAP1GAP2	RAP1GAP2	RAP1GAP2	5318	0.039	0.52	NO
108	RNPS1	RNPS1	RNPS1	5413	0.037	0.51	NO
109	KLHL21	KLHL21	KLHL21	5489	0.036	0.51	NO
110	FNDC4	FNDC4	FNDC4	5769	0.031	0.5	NO
111	MAST3	MAST3	MAST3	5779	0.03	0.5	NO
112	NDUFB1	NDUFB1	NDUFB1	5805	0.03	0.5	NO
113	NIPSNAP1	NIPSNAP1	NIPSNAP1	5846	0.029	0.5	NO
114	FTO	FTO	FTO	6104	0.024	0.49	NO
115	PLA2G16	PLA2G16	PLA2G16	6315	0.02	0.48	NO
116	GNAZ	GNAZ	GNAZ	6421	0.018	0.47	NO
117	TUBA4A	TUBA4A	TUBA4A	6598	0.014	0.46	NO
118	UQCRB	UQCRB	UQCRB	6692	0.012	0.46	NO
119	GPR37	GPR37	GPR37	6815	0.0098	0.46	NO
120	STARD7	STARD7	STARD7	6894	0.0075	0.45	NO
121	RPS8	RPS8	RPS8	6971	0.0059	0.45	NO
122	SUCLG1	SUCLG1	SUCLG1	7490	-0.0049	0.42	NO
123	DEGS1	DEGS1	DEGS1	7627	-0.0075	0.41	NO
124	PFDN1	PFDN1	PFDN1	7804	-0.011	0.4	NO
125	ZMAT4	ZMAT4	ZMAT4	8214	-0.02	0.38	NO
126	PTGDS	PTGDS	PTGDS	8274	-0.022	0.38	NO
127	FXYD7	FXYD7	FXYD7	8498	-0.026	0.37	NO
128	PMP22	PMP22	PMP22	8947	-0.036	0.35	NO
129	ARL4A	ARL4A	ARL4A	9128	-0.04	0.34	NO
130	B3GAT1	B3GAT1	B3GAT1	9650	-0.052	0.32	NO
131	FBXO9	FBXO9	FBXO9	10580	-0.072	0.27	NO
132	C16orf45	C16orf45	C16orf45	11379	-0.09	0.23	NO
133	STX7	STX7	STX7	11801	-0.099	0.22	NO
134	CLASP2	CLASP2	CLASP2	12486	-0.12	0.19	NO
135	SNX6	SNX6	SNX6	12701	-0.12	0.18	NO
136	CACNG3	CACNG3	CACNG3	13449	-0.14	0.16	NO
137	GABBR1	GABBR1	GABBR1	13543	-0.15	0.16	NO
138	TAX1BP1	TAX1BP1	TAX1BP1	13831	-0.16	0.16	NO
139	CX3CR1	CX3CR1	CX3CR1	14328	-0.17	0.14	NO
140	PAK6	PAK6	PAK6	15282	-0.22	0.11	NO
141	KLK6	KLK6	KLK6	16367	-0.29	0.07	NO
142	HMP19	HMP19	HMP19	16751	-0.33	0.074	NO

Figure S75. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: MOOTHA VOXPHOS.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: MOOTHA VOXPHOS, 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: PENG GLUTAMINE DEPRIVATION DN

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SYT5	SYT5	SYT5	113	0.24	0.0043	YES
2	MAD1L1	MAD1L1	MAD1L1	226	0.21	0.007	YES
3	LHB	LHB	LHB	292	0.19	0.012	YES
4	EHD2	EHD2	EHD2	434	0.17	0.011	YES
5	G6PC3	G6PC3	G6PC3	451	0.16	0.017	YES
6	SPATA20	SPATA20	SPATA20	642	0.15	0.013	YES
7	PLOD3	PLOD3	PLOD3	667	0.14	0.018	YES
8	EXOSC4	EXOSC4	EXOSC4	724	0.14	0.021	YES
9	GYS1	GYS1	GYS1	744	0.14	0.026	YES
10	SLC1A5	SLC1A5	SLC1A5	768	0.14	0.031	YES
11	NOSIP	NOSIP	NOSIP	786	0.14	0.036	YES
12	EPN1	EPN1	EPN1	806	0.14	0.041	YES
13	OPLAH	OPLAH	OPLAH	846	0.14	0.045	YES
14	SHARPIN	SHARPIN	SHARPIN	877	0.14	0.049	YES
15	RUVBL2	RUVBL2	RUVBL2	900	0.13	0.054	YES
16	GPR124	GPR124	GPR124	959	0.13	0.056	YES
17	ZNF787	ZNF787	ZNF787	977	0.13	0.061	YES
18	TSTA3	TSTA3	TSTA3	999	0.13	0.066	YES
19	GRWD1	GRWD1	GRWD1	1009	0.13	0.071	YES
20	AP2S1	AP2S1	AP2S1	1013	0.13	0.076	YES
21	ZC3H3	ZC3H3	ZC3H3	1027	0.13	0.081	YES
22	DBP	DBP	DBP	1048	0.13	0.086	YES
23	GPAA1	GPAA1	GPAA1	1084	0.13	0.089	YES
24	GRN	GRN	GRN	1094	0.13	0.094	YES
25	EXOC3	EXOC3	EXOC3	1109	0.13	0.099	YES
26	BAX	BAX	BAX	1114	0.13	0.1	YES
27	ASL	ASL	ASL	1117	0.13	0.11	YES
28	FIS1	FIS1	FIS1	1137	0.13	0.11	YES
29	VPS28	VPS28	VPS28	1140	0.13	0.12	YES
30	ZNF444	ZNF444	ZNF444	1152	0.12	0.12	YES
31	PAK4	PAK4	PAK4	1204	0.12	0.13	YES
32	KAT7	KAT7	KAT7	1206	0.12	0.13	YES
33	DGAT1	DGAT1	DGAT1	1235	0.12	0.14	YES
34	INTS1	INTS1	INTS1	1278	0.12	0.14	YES
35	CYC1	CYC1	CYC1	1282	0.12	0.14	YES
36	MRPS12	MRPS12	MRPS12	1319	0.12	0.15	YES
37	CASKIN2	CASKIN2	CASKIN2	1333	0.12	0.15	YES
38	NUCB1	NUCB1	NUCB1	1383	0.12	0.15	YES
39	SARS2	SARS2	SARS2	1407	0.12	0.16	YES
40	SLC12A9	SLC12A9	SLC12A9	1497	0.12	0.16	YES
41	PRKD2	PRKD2	PRKD2	1544	0.11	0.16	YES
42	SLC39A4	SLC39A4	SLC39A4	1575	0.11	0.16	YES
43	TLN1	TLN1	TLN1	1583	0.11	0.17	YES
44	GNB2	GNB2	GNB2	1642	0.11	0.17	YES
45	ATP5G1	ATP5G1	ATP5G1	1647	0.11	0.18	YES
46	CNOT3	CNOT3	CNOT3	1675	0.11	0.18	YES
47	ZDHHC24	ZDHHC24	ZDHHC24	1727	0.11	0.18	YES
48	NDUFS6	NDUFS6	NDUFS6	1752	0.11	0.18	YES
49	STRN4	STRN4	STRN4	1753	0.11	0.19	YES
50	NME1	NME1	NME1	1790	0.11	0.19	YES
51	MBOAT7	MBOAT7	MBOAT7	1799	0.11	0.2	YES
52	NAPA	NAPA	NAPA	1836	0.11	0.2	YES
53	LIG1	LIG1	LIG1	1923	0.1	0.2	YES
54	SIX5	SIX5	SIX5	1929	0.1	0.2	YES
55	KDELR1	KDELR1	KDELR1	1933	0.1	0.21	YES
56	ZNHIT1	ZNHIT1	ZNHIT1	1947	0.1	0.21	YES
57	SNF8	SNF8	SNF8	2041	0.1	0.21	YES
58	MPP2	MPP2	MPP2	2072	0.1	0.21	YES
59	KIAA0195	KIAA0195	KIAA0195	2172	0.1	0.21	YES
60	ATP6V0A1	ATP6V0A1	ATP6V0A1	2193	0.099	0.21	YES
61	TSEN34	TSEN34	TSEN34	2228	0.098	0.22	YES
62	ARFRP1	ARFRP1	ARFRP1	2268	0.098	0.22	YES
63	GSDMD	GSDMD	GSDMD	2274	0.098	0.22	YES
64	ZNF580	ZNF580	ZNF580	2283	0.097	0.23	YES
65	RPL18	RPL18	RPL18	2304	0.097	0.23	YES
66	PDK2	PDK2	PDK2	2306	0.097	0.23	YES
67	PSME3	PSME3	PSME3	2313	0.097	0.24	YES
68	PSMD8	PSMD8	PSMD8	2381	0.095	0.24	YES
69	ORAI2	ORAI2	ORAI2	2431	0.094	0.24	YES
70	PRPF6	PRPF6	PRPF6	2440	0.094	0.24	YES
71	PRMT1	PRMT1	PRMT1	2467	0.094	0.25	YES
72	EEF1D	EEF1D	EEF1D	2495	0.093	0.25	YES
73	SIRT2	SIRT2	SIRT2	2551	0.092	0.25	YES
74	NUDC	NUDC	NUDC	2583	0.091	0.25	YES
75	LRRC59	LRRC59	LRRC59	2612	0.091	0.25	YES
76	PHB	PHB	PHB	2699	0.089	0.25	YES
77	RPS9	RPS9	RPS9	2797	0.087	0.25	YES
78	CREB3	CREB3	CREB3	2829	0.087	0.25	YES
79	PPP2R5D	PPP2R5D	PPP2R5D	2925	0.085	0.25	YES
80	EML2	EML2	EML2	2980	0.084	0.25	YES
81	PAF1	PAF1	PAF1	3006	0.083	0.25	YES
82	CNPY3	CNPY3	CNPY3	3019	0.083	0.26	YES
83	RCN3	RCN3	RCN3	3022	0.083	0.26	YES
84	NKIRAS2	NKIRAS2	NKIRAS2	3027	0.083	0.26	YES
85	NR1H2	NR1H2	NR1H2	3081	0.082	0.26	YES
86	SDHA	SDHA	SDHA	3106	0.081	0.27	YES
87	IRF3	IRF3	IRF3	3150	0.08	0.27	YES
88	CYHR1	CYHR1	CYHR1	3207	0.079	0.27	YES
89	TMUB2	TMUB2	TMUB2	3225	0.078	0.27	YES
90	MICALL2	MICALL2	MICALL2	3285	0.077	0.27	YES
91	SCRIB	SCRIB	SCRIB	3360	0.076	0.27	YES
92	XYLT2	XYLT2	XYLT2	3607	0.071	0.26	YES
93	RAB5C	RAB5C	RAB5C	3621	0.071	0.26	YES
94	TRRAP	TRRAP	TRRAP	3664	0.07	0.26	YES
95	TAF6	TAF6	TAF6	3675	0.07	0.26	YES
96	EIF3K	EIF3K	EIF3K	3713	0.069	0.27	YES
97	PLEKHG3	PLEKHG3	PLEKHG3	3732	0.069	0.27	YES
98	LAMA5	LAMA5	LAMA5	3754	0.068	0.27	YES
99	U2AF2	U2AF2	U2AF2	3770	0.068	0.27	YES
100	MYL6	MYL6	MYL6	3786	0.067	0.27	YES
101	SPAG8	SPAG8	SPAG8	3801	0.067	0.28	YES
102	OPA3	OPA3	OPA3	3805	0.067	0.28	YES
103	FUT1	FUT1	FUT1	3834	0.067	0.28	YES
104	DDT	DDT	DDT	3853	0.066	0.28	YES
105	MYL10	MYL10	MYL10	3868	0.066	0.28	YES
106	ITGA3	ITGA3	ITGA3	3884	0.066	0.29	YES
107	NDRG1	NDRG1	NDRG1	3923	0.065	0.29	YES
108	SNRPD2	SNRPD2	SNRPD2	3968	0.064	0.29	YES
109	PLEKHA4	PLEKHA4	PLEKHA4	4013	0.063	0.29	YES
110	CD3EAP	CD3EAP	CD3EAP	4015	0.063	0.29	YES
111	AARSD1	AARSD1	AARSD1	4095	0.062	0.29	YES
112	MLX	MLX	MLX	4165	0.06	0.29	YES
113	FAM117A	FAM117A	FAM117A	4194	0.06	0.29	YES
114	ZGPAT	ZGPAT	ZGPAT	4211	0.06	0.29	YES
115	SHFM1	SHFM1	SHFM1	4219	0.059	0.29	YES
116	SLC35B1	SLC35B1	SLC35B1	4239	0.059	0.29	YES
117	SNX11	SNX11	SNX11	4248	0.059	0.3	YES
118	CPSF1	CPSF1	CPSF1	4270	0.058	0.3	YES
119	TMEM8B	TMEM8B	TMEM8B	4300	0.058	0.3	YES
120	FAM134C	FAM134C	FAM134C	4350	0.057	0.3	YES
121	RGP1	RGP1	RGP1	4368	0.057	0.3	YES
122	NUP62	NUP62	NUP62	4374	0.056	0.3	YES
123	NPR2	NPR2	NPR2	4377	0.056	0.3	YES
124	NMT1	NMT1	NMT1	4417	0.056	0.3	YES
125	DPF1	DPF1	DPF1	4566	0.053	0.3	NO
126	CLTA	CLTA	CLTA	4689	0.05	0.29	NO
127	RPS21	RPS21	RPS21	4887	0.047	0.28	NO
128	SMURF1	SMURF1	SMURF1	4889	0.047	0.29	NO
129	PNPO	PNPO	PNPO	4952	0.046	0.28	NO
130	MAP4K1	MAP4K1	MAP4K1	4977	0.045	0.29	NO
131	ARPC1B	ARPC1B	ARPC1B	5029	0.044	0.28	NO
132	ID1	ID1	ID1	5070	0.044	0.28	NO
133	MAFK	MAFK	MAFK	5092	0.043	0.28	NO
134	ACLY	ACLY	ACLY	5207	0.041	0.28	NO
135	UBE2Z	UBE2Z	UBE2Z	5213	0.041	0.28	NO
136	RPL27	RPL27	RPL27	5248	0.04	0.28	NO
137	BRD9	BRD9	BRD9	5256	0.04	0.28	NO
138	CEP72	CEP72	CEP72	5352	0.039	0.28	NO
139	SLC25A13	SLC25A13	SLC25A13	5389	0.038	0.28	NO
140	ARPC1A	ARPC1A	ARPC1A	5400	0.038	0.28	NO
141	GARS	GARS	GARS	5469	0.036	0.28	NO
142	RPL13A	RPL13A	RPL13A	5496	0.036	0.28	NO
143	BRF2	BRF2	BRF2	5545	0.035	0.28	NO
144	DMPK	DMPK	DMPK	5560	0.035	0.28	NO
145	HNRNPL	HNRNPL	HNRNPL	5645	0.033	0.27	NO
146	LPCAT1	LPCAT1	LPCAT1	5675	0.032	0.27	NO
147	STAT5B	STAT5B	STAT5B	5742	0.031	0.27	NO
148	CDKN2A	CDKN2A	CDKN2A	5774	0.031	0.27	NO
149	RABGEF1	RABGEF1	RABGEF1	5870	0.028	0.27	NO
150	PCTP	PCTP	PCTP	5898	0.028	0.27	NO
151	TPD52L2	TPD52L2	TPD52L2	5952	0.027	0.26	NO
152	DUSP3	DUSP3	DUSP3	5992	0.026	0.26	NO
153	HEXIM1	HEXIM1	HEXIM1	6021	0.025	0.26	NO
154	AP4M1	AP4M1	AP4M1	6040	0.025	0.26	NO
155	PDCD6	PDCD6	PDCD6	6069	0.024	0.26	NO
156	NFKBIB	NFKBIB	NFKBIB	6168	0.022	0.26	NO
157	SNRNP70	SNRNP70	SNRNP70	6188	0.022	0.26	NO
158	PQLC3	PQLC3	PQLC3	6314	0.02	0.25	NO
159	MAPK1IP1L	MAPK1IP1L	MAPK1IP1L	6358	0.019	0.25	NO
160	SAMD4A	SAMD4A	SAMD4A	6364	0.019	0.25	NO
161	RSAD1	RSAD1	RSAD1	6435	0.017	0.25	NO
162	PSMC3IP	PSMC3IP	PSMC3IP	6444	0.017	0.25	NO
163	DERL1	DERL1	DERL1	6457	0.017	0.25	NO
164	ARHGAP35	ARHGAP35	ARHGAP35	6647	0.013	0.24	NO
165	KPNB1	KPNB1	KPNB1	6690	0.012	0.24	NO
166	EZH1	EZH1	EZH1	6812	0.01	0.23	NO
167	EPN3	EPN3	EPN3	6859	0.0085	0.23	NO
168	WDYHV1	WDYHV1	WDYHV1	6899	0.0075	0.23	NO
169	YTHDF1	YTHDF1	YTHDF1	7044	0.0044	0.22	NO
170	CABYR	CABYR	CABYR	7101	0.0033	0.22	NO
171	KRT10	KRT10	KRT10	7105	0.0032	0.22	NO
172	ATP5E	ATP5E	ATP5E	7144	0.0026	0.21	NO
173	BECN1	BECN1	BECN1	7173	0.0021	0.21	NO
174	BMP4	BMP4	BMP4	7199	0.0015	0.21	NO
175	TCFL5	TCFL5	TCFL5	7205	0.0014	0.21	NO
176	TPM2	TPM2	TPM2	7219	0.00097	0.21	NO
177	UCKL1	UCKL1	UCKL1	7325	-0.0014	0.2	NO
178	CBLL1	CBLL1	CBLL1	7330	-0.0015	0.2	NO
179	NSF	NSF	NSF	7352	-0.002	0.2	NO
180	TAF4	TAF4	TAF4	7365	-0.0022	0.2	NO
181	ASH2L	ASH2L	ASH2L	7395	-0.003	0.2	NO
182	NPC1	NPC1	NPC1	7483	-0.0047	0.2	NO
183	PPP1R3D	PPP1R3D	PPP1R3D	7549	-0.006	0.19	NO
184	MYC	MYC	MYC	7768	-0.011	0.18	NO
185	C18orf8	C18orf8	C18orf8	7805	-0.011	0.18	NO
186	SYPL1	SYPL1	SYPL1	7875	-0.013	0.18	NO
187	PPP1R13L	PPP1R13L	PPP1R13L	7893	-0.013	0.18	NO
188	NBR1	NBR1	NBR1	7916	-0.014	0.18	NO
189	ANKRD40	ANKRD40	ANKRD40	7966	-0.015	0.17	NO
190	UTP18	UTP18	UTP18	8014	-0.016	0.17	NO
191	ATXN7L1	ATXN7L1	ATXN7L1	8059	-0.017	0.17	NO
192	DKKL1	DKKL1	DKKL1	8092	-0.018	0.17	NO
193	LSM1	LSM1	LSM1	8184	-0.02	0.16	NO
194	PSMA7	PSMA7	PSMA7	8289	-0.022	0.16	NO
195	DLD	DLD	DLD	8443	-0.025	0.15	NO
196	WDR3	WDR3	WDR3	8464	-0.025	0.15	NO
197	ZNF623	ZNF623	ZNF623	8491	-0.026	0.15	NO
198	PTK2	PTK2	PTK2	8513	-0.026	0.15	NO
199	ACTR10	ACTR10	ACTR10	8585	-0.028	0.15	NO
200	LMTK2	LMTK2	LMTK2	8774	-0.032	0.14	NO
201	CMAS	CMAS	CMAS	8860	-0.034	0.14	NO
202	OSBPL2	OSBPL2	OSBPL2	8893	-0.034	0.14	NO
203	WHSC1L1	WHSC1L1	WHSC1L1	8969	-0.036	0.13	NO
204	CRCP	CRCP	CRCP	8996	-0.036	0.13	NO
205	ZNF460	ZNF460	ZNF460	9023	-0.037	0.13	NO
206	SMARCE1	SMARCE1	SMARCE1	9174	-0.041	0.13	NO
207	KIAA0196	KIAA0196	KIAA0196	9179	-0.041	0.13	NO
208	ZNF134	ZNF134	ZNF134	9182	-0.041	0.13	NO
209	BET1	BET1	BET1	9219	-0.042	0.13	NO
210	ACSF2	ACSF2	ACSF2	9266	-0.042	0.13	NO
211	CBX1	CBX1	CBX1	9332	-0.044	0.13	NO
212	ZNF264	ZNF264	ZNF264	9363	-0.045	0.13	NO
213	ZKSCAN5	ZKSCAN5	ZKSCAN5	9416	-0.046	0.13	NO
214	RNF139	RNF139	RNF139	9441	-0.047	0.13	NO
215	DLGAP5	DLGAP5	DLGAP5	9486	-0.048	0.13	NO
216	NPEPPS	NPEPPS	NPEPPS	9530	-0.049	0.13	NO
217	EAPP	EAPP	EAPP	9582	-0.05	0.13	NO
218	OSBPL1A	OSBPL1A	OSBPL1A	9626	-0.051	0.12	NO
219	MTAP	MTAP	MTAP	9667	-0.052	0.12	NO
220	COX11	COX11	COX11	9779	-0.054	0.12	NO
221	CDC27	CDC27	CDC27	9811	-0.055	0.12	NO
222	GPATCH8	GPATCH8	GPATCH8	9834	-0.056	0.12	NO
223	RNF38	RNF38	RNF38	9949	-0.058	0.12	NO
224	ZNF652	ZNF652	ZNF652	10025	-0.059	0.12	NO
225	KCTD7	KCTD7	KCTD7	10053	-0.06	0.12	NO
226	PRKCH	PRKCH	PRKCH	10190	-0.063	0.11	NO
227	NUBPL	NUBPL	NUBPL	10340	-0.066	0.11	NO
228	MRPL13	MRPL13	MRPL13	10412	-0.068	0.11	NO
229	NPAS3	NPAS3	NPAS3	10414	-0.068	0.11	NO
230	C5AR1	C5AR1	C5AR1	10565	-0.072	0.1	NO
231	SPOP	SPOP	SPOP	10570	-0.072	0.11	NO
232	PARP4	PARP4	PARP4	10589	-0.072	0.11	NO
233	ASNS	ASNS	ASNS	10685	-0.074	0.11	NO
234	SPAG9	SPAG9	SPAG9	10708	-0.074	0.11	NO
235	MPP3	MPP3	MPP3	10715	-0.075	0.11	NO
236	FAM49B	FAM49B	FAM49B	10725	-0.075	0.12	NO
237	AP4S1	AP4S1	AP4S1	10825	-0.077	0.11	NO
238	DDHD2	DDHD2	DDHD2	10891	-0.079	0.11	NO
239	ACN9	ACN9	ACN9	10893	-0.079	0.12	NO
240	UPF3A	UPF3A	UPF3A	10941	-0.08	0.12	NO
241	PON2	PON2	PON2	10962	-0.081	0.12	NO
242	FBXO34	FBXO34	FBXO34	11286	-0.088	0.11	NO
243	ZNF146	ZNF146	ZNF146	11374	-0.09	0.1	NO
244	ZNF304	ZNF304	ZNF304	11482	-0.092	0.1	NO
245	SCFD1	SCFD1	SCFD1	11943	-0.1	0.082	NO
246	ARHGAP5	ARHGAP5	ARHGAP5	12042	-0.11	0.081	NO
247	CASD1	CASD1	CASD1	12054	-0.11	0.085	NO
248	RIOK3	RIOK3	RIOK3	12224	-0.11	0.08	NO
249	HIF1A	HIF1A	HIF1A	12267	-0.11	0.083	NO
250	WDHD1	WDHD1	WDHD1	12341	-0.11	0.084	NO
251	ZNF211	ZNF211	ZNF211	12349	-0.11	0.088	NO
252	SLMO2	SLMO2	SLMO2	12441	-0.12	0.088	NO
253	BAG4	BAG4	BAG4	12503	-0.12	0.09	NO
254	ZNF573	ZNF573	ZNF573	12681	-0.12	0.085	NO
255	SNX6	SNX6	SNX6	12701	-0.12	0.09	NO
256	TAF2	TAF2	TAF2	13139	-0.13	0.071	NO
257	RASA4	RASA4	RASA4	13187	-0.14	0.074	NO
258	SS18L1	SS18L1	SS18L1	13273	-0.14	0.075	NO
259	PDK4	PDK4	PDK4	13448	-0.14	0.072	NO
260	TTF2	TTF2	TTF2	13519	-0.15	0.074	NO
261	MTMR6	MTMR6	MTMR6	13524	-0.15	0.08	NO
262	DOCK4	DOCK4	DOCK4	13644	-0.15	0.08	NO
263	SNAPC1	SNAPC1	SNAPC1	13797	-0.16	0.079	NO
264	PON3	PON3	PON3	13855	-0.16	0.082	NO
265	PHF20L1	PHF20L1	PHF20L1	13885	-0.16	0.088	NO
266	ZNF419	ZNF419	ZNF419	13912	-0.16	0.093	NO
267	EXOC5	EXOC5	EXOC5	13959	-0.16	0.098	NO
268	HAS2	HAS2	HAS2	14039	-0.16	0.1	NO
269	RNF6	RNF6	RNF6	14131	-0.17	0.1	NO
270	ZNF331	ZNF331	ZNF331	14155	-0.17	0.11	NO
271	LUC7L3	LUC7L3	LUC7L3	14534	-0.18	0.095	NO
272	HLF	HLF	HLF	14792	-0.19	0.089	NO
273	AOC2	AOC2	AOC2	14877	-0.2	0.093	NO
274	KTN1	KTN1	KTN1	15048	-0.2	0.092	NO
275	ZBTB1	ZBTB1	ZBTB1	15100	-0.21	0.099	NO
276	CYP3A5	CYP3A5	CYP3A5	15847	-0.25	0.068	NO
277	SLC26A4	SLC26A4	SLC26A4	15955	-0.26	0.073	NO
278	KLK13	KLK13	KLK13	16688	-0.32	0.046	NO
279	GIPR	GIPR	GIPR	16970	-0.36	0.046	NO
280	ANXA13	ANXA13	ANXA13	17101	-0.38	0.055	NO

Figure S77. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: PENG GLUTAMINE DEPRIVATION DN.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: PENG GLUTAMINE DEPRIVATION DN, 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: FAELT B CLL WITH VH3 21 UP

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	EHD2	EHD2	EHD2	434	0.17	0.032	YES
2	G6PC3	G6PC3	G6PC3	451	0.16	0.086	YES
3	PCDHGC3	PCDHGC3	PCDHGC3	527	0.16	0.13	YES
4	ANPEP	ANPEP	ANPEP	831	0.14	0.16	YES
5	PPAP2C	PPAP2C	PPAP2C	1005	0.13	0.2	YES
6	INO80B	INO80B	INO80B	1141	0.13	0.23	YES
7	H2AFX	H2AFX	H2AFX	1449	0.12	0.25	YES
8	MYL9	MYL9	MYL9	1637	0.11	0.28	YES
9	FJX1	FJX1	FJX1	1905	0.1	0.3	YES
10	KDELR1	KDELR1	KDELR1	1933	0.1	0.34	YES
11	ST6GALNAC4	ST6GALNAC4	ST6GALNAC4	2061	0.1	0.36	YES
12	WNT5B	WNT5B	WNT5B	2153	0.1	0.39	YES
13	GEMIN4	GEMIN4	GEMIN4	2385	0.095	0.41	YES
14	FAM127A	FAM127A	FAM127A	2767	0.088	0.42	YES
15	UBTF	UBTF	UBTF	3297	0.077	0.41	YES
16	TOMM22	TOMM22	TOMM22	3373	0.075	0.44	YES
17	SERPINH1	SERPINH1	SERPINH1	3409	0.075	0.46	YES
18	SYNGR2	SYNGR2	SYNGR2	3428	0.074	0.48	YES
19	DDT	DDT	DDT	3853	0.066	0.48	YES
20	HMGB3	HMGB3	HMGB3	3921	0.065	0.5	YES
21	FEN1	FEN1	FEN1	3985	0.064	0.52	YES
22	AP1S1	AP1S1	AP1S1	3987	0.064	0.54	YES
23	LOXL1	LOXL1	LOXL1	4002	0.064	0.56	YES
24	PRR16	PRR16	PRR16	4475	0.054	0.55	YES
25	TMEM97	TMEM97	TMEM97	4555	0.053	0.56	YES
26	GM2A	GM2A	GM2A	4927	0.046	0.56	YES
27	CBX6	CBX6	CBX6	5014	0.045	0.57	YES
28	SV2A	SV2A	SV2A	5061	0.044	0.58	YES
29	ANP32A	ANP32A	ANP32A	5126	0.043	0.59	YES
30	CKAP4	CKAP4	CKAP4	5152	0.042	0.6	YES
31	GLG1	GLG1	GLG1	5198	0.041	0.62	YES
32	LPCAT1	LPCAT1	LPCAT1	5675	0.032	0.6	NO
33	SLC29A1	SLC29A1	SLC29A1	6063	0.024	0.59	NO
34	FZD2	FZD2	FZD2	6344	0.019	0.58	NO
35	AKAP1	AKAP1	AKAP1	7377	-0.0024	0.52	NO
36	MAT2A	MAT2A	MAT2A	8097	-0.018	0.49	NO
37	SKP2	SKP2	SKP2	11626	-0.096	0.32	NO
38	MARCKS	MARCKS	MARCKS	11744	-0.098	0.35	NO

Figure S79. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: FAELT B CLL WITH VH3 21 UP.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: FAELT B CLL WITH VH3 21 UP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus5 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG PROTEASOME	44	genes.ES.table	0.54	1.6	0.028	0.19	0.97	0.34	0.27	0.25	0.1	0.021
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION	236	genes.ES.table	0.74	1.7	0	0.23	0.93	0.51	0.12	0.46	0.1	0.037
KEGG CHEMOKINE SIGNALING PATHWAY	184	genes.ES.table	0.65	1.6	0.0041	0.19	0.98	0.32	0.11	0.28	0.1	0.02
KEGG APOPTOSIS	84	genes.ES.table	0.54	1.7	0.0039	0.25	0.9	0.27	0.18	0.22	0.11	0.041
KEGG CELL ADHESION MOLECULES CAMS	128	genes.ES.table	0.65	1.5	0.0038	0.2	1	0.49	0.18	0.41	0.13	0.014
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY	60	genes.ES.table	0.63	1.6	0.027	0.19	1	0.28	0.066	0.26	0.11	0.014
KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY	58	genes.ES.table	0.55	1.7	0.018	0.21	0.96	0.34	0.24	0.26	0.11	0.028
KEGG JAK STAT SIGNALING PATHWAY	131	genes.ES.table	0.63	1.7	0	0.22	0.96	0.37	0.13	0.33	0.11	0.034
KEGG HEMATOPOIETIC CELL LINEAGE	83	genes.ES.table	0.78	1.6	0	0.19	0.98	0.66	0.14	0.57	0.1	0.02
KEGG B CELL RECEPTOR SIGNALING PATHWAY	74	genes.ES.table	0.55	1.7	0.02	0.23	0.9	0.32	0.18	0.27	0.098	0.036

genes ES table in pathway: KEGG PROTEASOME

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PSMA1	PSMA1	PSMA1	48	1	0.077	YES
2	RASGRP1	RASGRP1	RASGRP1	202	0.75	0.13	YES
3	PSMB9	PSMB9	PSMB9	463	0.57	0.16	YES
4	CD79A	CD79A	CD79A	827	0.45	0.17	YES
5	VAV1	VAV1	VAV1	843	0.44	0.21	YES
6	BLNK	BLNK	BLNK	907	0.43	0.24	YES
7	PSMA2	PSMA2	PSMA2	1121	0.39	0.26	YES
8	PIK3AP1	PIK3AP1	PIK3AP1	1402	0.34	0.27	YES
9	ITPR2	ITPR2	ITPR2	1523	0.33	0.29	YES
10	CARD11	CARD11	CARD11	1571	0.32	0.31	YES
11	BLK	BLK	BLK	1774	0.3	0.32	YES
12	PSMB8	PSMB8	PSMB8	1900	0.28	0.34	YES
13	BTK	BTK	BTK	1985	0.27	0.35	YES
14	PRKCB	PRKCB	PRKCB	2506	0.22	0.34	YES
15	CD19	CD19	CD19	2561	0.21	0.36	YES
16	PSMB10	PSMB10	PSMB10	2806	0.19	0.36	YES
17	SYK	SYK	SYK	2950	0.18	0.36	YES
18	MDM2	MDM2	MDM2	3085	0.18	0.37	YES
19	PSME2	PSME2	PSME2	3309	0.16	0.37	YES
20	LYN	LYN	LYN	3311	0.16	0.38	YES
21	CD79B	CD79B	CD79B	3740	0.14	0.37	YES
22	PSMA3	PSMA3	PSMA3	3757	0.14	0.38	YES
23	PSMA4	PSMA4	PSMA4	3809	0.14	0.39	YES
24	RICTOR	RICTOR	RICTOR	3827	0.14	0.4	YES
25	PSME4	PSME4	PSME4	3830	0.14	0.41	YES
26	BCL10	BCL10	BCL10	3960	0.13	0.41	YES
27	PLCG2	PLCG2	PLCG2	4066	0.13	0.42	YES
28	PSMD14	PSMD14	PSMD14	4117	0.12	0.42	YES
29	CDKN1A	CDKN1A	CDKN1A	4411	0.11	0.42	YES
30	PSMA5	PSMA5	PSMA5	4534	0.11	0.42	YES
31	PSMA6	PSMA6	PSMA6	4713	0.1	0.42	YES
32	PSME1	PSME1	PSME1	4764	0.1	0.42	YES
33	PSMC6	PSMC6	PSMC6	4926	0.096	0.42	YES
34	CREB1	CREB1	CREB1	4987	0.095	0.42	YES
35	MALT1	MALT1	MALT1	5195	0.089	0.42	YES
36	KRAS	KRAS	KRAS	5250	0.087	0.42	YES
37	SH3KBP1	SH3KBP1	SH3KBP1	5254	0.087	0.43	YES
38	NFKBIA	NFKBIA	NFKBIA	5278	0.086	0.44	YES
39	MAP3K7	MAP3K7	MAP3K7	5345	0.085	0.44	YES
40	SOS1	SOS1	SOS1	5572	0.079	0.43	YES
41	PIK3R1	PIK3R1	PIK3R1	5635	0.078	0.44	YES
42	PSMD12	PSMD12	PSMD12	5705	0.076	0.44	YES
43	CHUK	CHUK	CHUK	5716	0.076	0.44	YES
44	NRAS	NRAS	NRAS	5741	0.075	0.45	YES
45	CDKN1B	CDKN1B	CDKN1B	6180	0.066	0.43	NO
46	CUL1	CUL1	CUL1	6182	0.066	0.44	NO
47	PSMA7	PSMA7	PSMA7	6580	0.057	0.42	NO
48	NCK1	NCK1	NCK1	6636	0.056	0.42	NO
49	PSMD7	PSMD7	PSMD7	6717	0.054	0.42	NO
50	PSMB2	PSMB2	PSMB2	6742	0.054	0.42	NO
51	CALM1	CALM1	CALM1	6897	0.051	0.42	NO
52	PSMC2	PSMC2	PSMC2	6949	0.05	0.42	NO
53	ITPR3	ITPR3	ITPR3	6950	0.05	0.42	NO
54	CALM2	CALM2	CALM2	6990	0.049	0.42	NO
55	PTEN	PTEN	PTEN	7167	0.046	0.42	NO
56	PSMC1	PSMC1	PSMC1	7331	0.043	0.41	NO
57	ORAI1	ORAI1	ORAI1	7476	0.04	0.41	NO
58	REL	REL	REL	7712	0.036	0.4	NO
59	MTOR	MTOR	MTOR	7906	0.032	0.39	NO
60	PSMD5	PSMD5	PSMD5	7928	0.032	0.39	NO
61	SHC1	SHC1	SHC1	8213	0.027	0.38	NO
62	PSMB3	PSMB3	PSMB3	8251	0.026	0.38	NO
63	PSMB1	PSMB1	PSMB1	8257	0.026	0.38	NO
64	CBLB	CBLB	CBLB	8315	0.026	0.38	NO
65	NFKBIE	NFKBIE	NFKBIE	8333	0.025	0.38	NO
66	PSMD11	PSMD11	PSMD11	8401	0.024	0.38	NO
67	PSMD10	PSMD10	PSMD10	8914	0.016	0.35	NO
68	GRB2	GRB2	GRB2	9080	0.013	0.34	NO
69	PSMA8	PSMA8	PSMA8	9540	0.007	0.32	NO
70	STIM1	STIM1	STIM1	9622	0.0057	0.31	NO
71	PDPK1	PDPK1	PDPK1	9634	0.0054	0.31	NO
72	SKP1	SKP1	SKP1	9662	0.005	0.31	NO
73	PSMC4	PSMC4	PSMC4	9796	0.0029	0.3	NO
74	PSMD1	PSMD1	PSMD1	9820	0.0026	0.3	NO
75	NFKBIB	NFKBIB	NFKBIB	9852	0.0021	0.3	NO
76	PSMC3	PSMC3	PSMC3	9891	0.0015	0.3	NO
77	PIK3CD	PIK3CD	PIK3CD	10253	-0.0038	0.28	NO
78	PSMD13	PSMD13	PSMD13	10277	-0.0043	0.28	NO
79	PSMC5	PSMC5	PSMC5	10429	-0.0064	0.27	NO
80	PSMB6	PSMB6	PSMB6	10559	-0.0085	0.26	NO
81	PSMD3	PSMD3	PSMD3	10590	-0.0091	0.26	NO
82	AKT3	AKT3	AKT3	10665	-0.01	0.26	NO
83	PSMB7	PSMB7	PSMB7	10709	-0.011	0.26	NO
84	CBL	CBL	CBL	10752	-0.012	0.26	NO
85	RASGRP3	RASGRP3	RASGRP3	10912	-0.013	0.25	NO
86	PSMD8	PSMD8	PSMD8	11103	-0.016	0.24	NO
87	PSMB4	PSMB4	PSMB4	11164	-0.017	0.24	NO
88	FBXW11	FBXW11	FBXW11	11172	-0.017	0.24	NO
89	IKBKB	IKBKB	IKBKB	11311	-0.019	0.23	NO
90	PSMB5	PSMB5	PSMB5	11414	-0.02	0.23	NO
91	CASP9	CASP9	CASP9	11514	-0.021	0.22	NO
92	MAPKAP1	MAPKAP1	MAPKAP1	11527	-0.022	0.22	NO
93	THEM4	THEM4	THEM4	11813	-0.026	0.21	NO
94	PSMD4	PSMD4	PSMD4	12032	-0.029	0.2	NO
95	PSMD9	PSMD9	PSMD9	12076	-0.03	0.2	NO
96	BTRC	BTRC	BTRC	12089	-0.03	0.2	NO
97	PLCG1	PLCG1	PLCG1	12268	-0.032	0.2	NO
98	PSMD6	PSMD6	PSMD6	12416	-0.035	0.19	NO
99	IKBKG	IKBKG	IKBKG	12564	-0.037	0.18	NO
100	FOXO4	FOXO4	FOXO4	12784	-0.041	0.18	NO
101	BAD	BAD	BAD	12966	-0.044	0.17	NO
102	PHLPP1	PHLPP1	PHLPP1	13022	-0.044	0.17	NO
103	HRAS	HRAS	HRAS	13052	-0.045	0.17	NO
104	CALM3	CALM3	CALM3	13185	-0.047	0.17	NO
105	MLST8	MLST8	MLST8	13868	-0.058	0.14	NO
106	GSK3A	GSK3A	GSK3A	13892	-0.059	0.14	NO
107	AKT1S1	AKT1S1	AKT1S1	14088	-0.062	0.13	NO
108	FYN	FYN	FYN	14091	-0.062	0.14	NO
109	FOXO1	FOXO1	FOXO1	14202	-0.064	0.14	NO
110	RPS6KB2	RPS6KB2	RPS6KB2	14302	-0.066	0.14	NO
111	AKT2	AKT2	AKT2	14395	-0.067	0.14	NO
112	AKT1	AKT1	AKT1	14488	-0.069	0.14	NO
113	PSMD2	PSMD2	PSMD2	14824	-0.076	0.12	NO
114	TSC2	TSC2	TSC2	14943	-0.079	0.12	NO
115	PSMF1	PSMF1	PSMF1	15085	-0.082	0.12	NO
116	NR4A1	NR4A1	NR4A1	15125	-0.084	0.13	NO
117	TRIB3	TRIB3	TRIB3	15304	-0.088	0.12	NO
118	RELA	RELA	RELA	15341	-0.09	0.13	NO
119	RPS27A	RPS27A	RPS27A	15344	-0.09	0.14	NO
120	FOXO3	FOXO3	FOXO3	15765	-0.1	0.12	NO
121	UBA52	UBA52	UBA52	16002	-0.11	0.12	NO

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

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

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	RHOH	RHOH	RHOH	97	0.88	0.037	YES
2	PTPN22	PTPN22	PTPN22	126	0.84	0.077	YES
3	PTPN7	PTPN7	PTPN7	181	0.78	0.11	YES
4	PTPRC	PTPRC	PTPRC	204	0.75	0.15	YES
5	SAMSN1	SAMSN1	SAMSN1	226	0.73	0.18	YES
6	PIK3CG	PIK3CG	PIK3CG	323	0.65	0.21	YES
7	LRMP	LRMP	LRMP	339	0.64	0.24	YES
8	NKG7	NKG7	NKG7	386	0.61	0.26	YES
9	BIN2	BIN2	BIN2	507	0.55	0.29	YES
10	IKZF1	IKZF1	IKZF1	508	0.55	0.31	YES
11	MYB	MYB	MYB	588	0.52	0.33	YES
12	SLA	SLA	SLA	592	0.52	0.36	YES
13	NCKAP1L	NCKAP1L	NCKAP1L	819	0.45	0.37	YES
14	CORO1A	CORO1A	CORO1A	846	0.44	0.39	YES
15	CD53	CD53	CD53	975	0.42	0.4	YES
16	INPP5D	INPP5D	INPP5D	1187	0.38	0.41	YES
17	ARHGAP15	ARHGAP15	ARHGAP15	1200	0.38	0.42	YES
18	HCLS1	HCLS1	HCLS1	1211	0.37	0.44	YES
19	RAC2	RAC2	RAC2	1427	0.34	0.45	YES
20	GMFG	GMFG	GMFG	1456	0.33	0.46	YES
21	SELPLG	SELPLG	SELPLG	1480	0.33	0.48	YES
22	ATP2A3	ATP2A3	ATP2A3	2512	0.22	0.43	NO
23	ARHGAP29	ARHGAP29	ARHGAP29	2518	0.22	0.44	NO
24	KIF21B	KIF21B	KIF21B	2654	0.21	0.44	NO
25	ARHGAP4	ARHGAP4	ARHGAP4	3213	0.17	0.42	NO
26	WWTR1	WWTR1	WWTR1	3253	0.17	0.43	NO
27	STIL	STIL	STIL	3505	0.15	0.42	NO
28	MYOF	MYOF	MYOF	3818	0.14	0.41	NO
29	NASP	NASP	NASP	3912	0.13	0.41	NO
30	CD93	CD93	CD93	4082	0.12	0.41	NO
31	FZD7	FZD7	FZD7	4092	0.12	0.41	NO
32	HMHA1	HMHA1	HMHA1	4236	0.12	0.41	NO
33	DEF6	DEF6	DEF6	4293	0.12	0.41	NO
34	TNFRSF12A	TNFRSF12A	TNFRSF12A	4336	0.12	0.42	NO
35	SCAF11	SCAF11	SCAF11	4564	0.11	0.41	NO
36	CAPRIN2	CAPRIN2	CAPRIN2	4579	0.11	0.41	NO
37	PLCD4	PLCD4	PLCD4	4830	0.099	0.4	NO
38	CNTRL	CNTRL	CNTRL	4886	0.097	0.4	NO
39	ELF1	ELF1	ELF1	4908	0.097	0.41	NO
40	FAM114A1	FAM114A1	FAM114A1	4978	0.095	0.41	NO
41	TMPO	TMPO	TMPO	5002	0.094	0.41	NO
42	ITGAV	ITGAV	ITGAV	5025	0.094	0.42	NO
43	TPP2	TPP2	TPP2	5294	0.086	0.4	NO
44	TRIM14	TRIM14	TRIM14	5481	0.081	0.4	NO
45	CALD1	CALD1	CALD1	5521	0.08	0.4	NO
46	YIPF6	YIPF6	YIPF6	6013	0.069	0.38	NO
47	USP14	USP14	USP14	6146	0.066	0.37	NO
48	TAF4B	TAF4B	TAF4B	6191	0.065	0.37	NO
49	LAMB1	LAMB1	LAMB1	6224	0.065	0.37	NO
50	PDSS1	PDSS1	PDSS1	6238	0.064	0.38	NO
51	INTS7	INTS7	INTS7	6413	0.06	0.37	NO
52	CAMSAP2	CAMSAP2	CAMSAP2	6561	0.058	0.36	NO
53	LINS	LINS	LINS	6566	0.058	0.37	NO
54	OTUD4	OTUD4	OTUD4	6644	0.056	0.37	NO
55	RBFOX2	RBFOX2	RBFOX2	6699	0.055	0.36	NO
56	DOCK1	DOCK1	DOCK1	6842	0.052	0.36	NO
57	ZNF200	ZNF200	ZNF200	6963	0.05	0.36	NO
58	ZFHX3	ZFHX3	ZFHX3	7293	0.044	0.34	NO
59	S100A13	S100A13	S100A13	7463	0.041	0.33	NO
60	ZBTB33	ZBTB33	ZBTB33	7582	0.039	0.33	NO
61	LAPTM4B	LAPTM4B	LAPTM4B	7669	0.037	0.32	NO
62	RNASEH2B	RNASEH2B	RNASEH2B	7742	0.035	0.32	NO
63	PTK2B	PTK2B	PTK2B	7798	0.034	0.32	NO
64	SNRPG	SNRPG	SNRPG	7843	0.033	0.32	NO
65	SRSF1	SRSF1	SRSF1	7892	0.032	0.32	NO
66	ORC1	ORC1	ORC1	8006	0.03	0.31	NO
67	S100A10	S100A10	S100A10	8067	0.029	0.31	NO
68	PFN2	PFN2	PFN2	8441	0.024	0.29	NO
69	RBBP4	RBBP4	RBBP4	8525	0.022	0.29	NO
70	ULK2	ULK2	ULK2	8839	0.018	0.27	NO
71	PLS3	PLS3	PLS3	8964	0.015	0.27	NO
72	DIP2C	DIP2C	DIP2C	8982	0.015	0.27	NO
73	LAPTM4A	LAPTM4A	LAPTM4A	9002	0.014	0.26	NO
74	TMEM184B	TMEM184B	TMEM184B	9198	0.012	0.26	NO
75	C2orf43	C2orf43	C2orf43	9280	0.011	0.25	NO
76	RHBDF1	RHBDF1	RHBDF1	9294	0.01	0.25	NO
77	HIP1	HIP1	HIP1	9315	0.01	0.25	NO
78	ANXA2	ANXA2	ANXA2	9385	0.0091	0.25	NO
79	ADCY9	ADCY9	ADCY9	9509	0.0074	0.24	NO
80	ZNF22	ZNF22	ZNF22	9569	0.0065	0.24	NO
81	ZNF207	ZNF207	ZNF207	9628	0.0056	0.23	NO
82	ENAH	ENAH	ENAH	9800	0.0028	0.22	NO
83	CTTN	CTTN	CTTN	9893	0.0015	0.22	NO
84	LAMC1	LAMC1	LAMC1	9921	0.001	0.22	NO
85	CNN3	CNN3	CNN3	9970	0.00034	0.22	NO
86	C9orf78	C9orf78	C9orf78	10106	-0.0018	0.21	NO
87	SMARCA1	SMARCA1	SMARCA1	10126	-0.0021	0.21	NO
88	DUT	DUT	DUT	10146	-0.0024	0.21	NO
89	CCND1	CCND1	CCND1	10254	-0.0038	0.2	NO
90	POLR3E	POLR3E	POLR3E	10348	-0.0053	0.2	NO
91	ELL	ELL	ELL	10432	-0.0065	0.19	NO
92	PLK2	PLK2	PLK2	10492	-0.0074	0.19	NO
93	NFYA	NFYA	NFYA	10513	-0.0078	0.19	NO
94	ITGB1BP1	ITGB1BP1	ITGB1BP1	10581	-0.0089	0.18	NO
95	PTMS	PTMS	PTMS	10734	-0.011	0.18	NO
96	USP7	USP7	USP7	10966	-0.014	0.16	NO
97	MFSD11	MFSD11	MFSD11	11007	-0.014	0.16	NO
98	VAMP3	VAMP3	VAMP3	11078	-0.015	0.16	NO
99	LPPR2	LPPR2	LPPR2	11228	-0.018	0.15	NO
100	ANXA5	ANXA5	ANXA5	11233	-0.018	0.15	NO
101	LPP	LPP	LPP	11345	-0.019	0.15	NO
102	GPC1	GPC1	GPC1	11468	-0.021	0.14	NO
103	ANP32A	ANP32A	ANP32A	11480	-0.021	0.14	NO
104	AMD1	AMD1	AMD1	11482	-0.021	0.14	NO
105	MXD1	MXD1	MXD1	11675	-0.024	0.13	NO
106	RAB13	RAB13	RAB13	11752	-0.025	0.13	NO
107	RAD51	RAD51	RAD51	11783	-0.025	0.13	NO
108	CDC42BPB	CDC42BPB	CDC42BPB	11948	-0.028	0.12	NO
109	TCEAL4	TCEAL4	TCEAL4	12094	-0.03	0.12	NO
110	LMNA	LMNA	LMNA	12172	-0.031	0.11	NO
111	ITGB1	ITGB1	ITGB1	12218	-0.032	0.11	NO
112	SLC25A12	SLC25A12	SLC25A12	12222	-0.032	0.11	NO
113	OCRL	OCRL	OCRL	12326	-0.033	0.11	NO
114	HNRNPD	HNRNPD	HNRNPD	12474	-0.036	0.1	NO
115	HDLBP	HDLBP	HDLBP	12587	-0.038	0.098	NO
116	DLG5	DLG5	DLG5	12589	-0.038	0.1	NO
117	DAZAP1	DAZAP1	DAZAP1	12671	-0.039	0.097	NO
118	RPIA	RPIA	RPIA	12749	-0.04	0.095	NO
119	ALDH7A1	ALDH7A1	ALDH7A1	12872	-0.042	0.09	NO
120	ANP32B	ANP32B	ANP32B	12891	-0.043	0.091	NO
121	CDK16	CDK16	CDK16	13002	-0.044	0.087	NO
122	CD63	CD63	CD63	13005	-0.044	0.089	NO
123	TJP1	TJP1	TJP1	13054	-0.045	0.089	NO
124	MAPRE2	MAPRE2	MAPRE2	13055	-0.045	0.091	NO
125	TSPAN4	TSPAN4	TSPAN4	13069	-0.045	0.092	NO
126	AGRN	AGRN	AGRN	13149	-0.046	0.09	NO
127	ABT1	ABT1	ABT1	13198	-0.047	0.09	NO
128	SSBP3	SSBP3	SSBP3	13381	-0.05	0.082	NO
129	PPP6R1	PPP6R1	PPP6R1	13403	-0.05	0.084	NO
130	PCGF2	PCGF2	PCGF2	13443	-0.051	0.084	NO
131	VRK3	VRK3	VRK3	13510	-0.052	0.083	NO
132	RPS8	RPS8	RPS8	13883	-0.058	0.065	NO
133	NOC4L	NOC4L	NOC4L	13891	-0.059	0.067	NO
134	SIK2	SIK2	SIK2	13924	-0.059	0.068	NO
135	TRIM27	TRIM27	TRIM27	14066	-0.062	0.063	NO
136	FKBP9	FKBP9	FKBP9	14100	-0.062	0.065	NO
137	MYC	MYC	MYC	14208	-0.064	0.062	NO
138	SH3BP4	SH3BP4	SH3BP4	14229	-0.064	0.064	NO
139	SLC19A1	SLC19A1	SLC19A1	14277	-0.065	0.064	NO
140	CSK	CSK	CSK	14511	-0.069	0.055	NO
141	PML	PML	PML	14527	-0.07	0.057	NO
142	DDX51	DDX51	DDX51	14837	-0.076	0.044	NO
143	TXNRD3	TXNRD3	TXNRD3	14946	-0.079	0.042	NO
144	DAG1	DAG1	DAG1	15097	-0.083	0.037	NO
145	DST	DST	DST	15122	-0.084	0.04	NO
146	NXN	NXN	NXN	15408	-0.092	0.028	NO
147	NFIB	NFIB	NFIB	15435	-0.093	0.032	NO
148	SYDE1	SYDE1	SYDE1	15470	-0.094	0.034	NO
149	ATN1	ATN1	ATN1	15581	-0.097	0.033	NO
150	CRTAP	CRTAP	CRTAP	15636	-0.099	0.035	NO
151	POLD1	POLD1	POLD1	15675	-0.1	0.037	NO
152	KIF1C	KIF1C	KIF1C	15689	-0.1	0.042	NO
153	ZNF532	ZNF532	ZNF532	15718	-0.1	0.045	NO
154	KANK2	KANK2	KANK2	15746	-0.1	0.048	NO
155	KATNB1	KATNB1	KATNB1	15855	-0.11	0.048	NO
156	REXO4	REXO4	REXO4	16077	-0.12	0.041	NO
157	APBB1	APBB1	APBB1	16087	-0.12	0.046	NO
158	PRMT7	PRMT7	PRMT7	16238	-0.12	0.044	NO
159	CCNJL	CCNJL	CCNJL	16280	-0.13	0.048	NO
160	GNG11	GNG11	GNG11	16556	-0.14	0.039	NO
161	LAMB2	LAMB2	LAMB2	16677	-0.15	0.04	NO
162	AMOTL2	AMOTL2	AMOTL2	16706	-0.16	0.046	NO
163	ADCY6	ADCY6	ADCY6	16778	-0.16	0.05	NO
164	PCBP4	PCBP4	PCBP4	16780	-0.16	0.058	NO
165	MID1	MID1	MID1	17583	-0.3	0.028	NO

Figure S83. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

Figure S84. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PSMA1	PSMA1	PSMA1	48	1	0.12	YES
2	RASGRP1	RASGRP1	RASGRP1	202	0.75	0.19	YES
3	PSMB9	PSMB9	PSMB9	463	0.57	0.25	YES
4	PSMA2	PSMA2	PSMA2	1121	0.39	0.26	YES
5	CARD11	CARD11	CARD11	1571	0.32	0.27	YES
6	PSMB8	PSMB8	PSMB8	1900	0.28	0.28	YES
7	PRKCB	PRKCB	PRKCB	2506	0.22	0.27	YES
8	PSMB10	PSMB10	PSMB10	2806	0.19	0.28	YES
9	MDM2	MDM2	MDM2	3085	0.18	0.29	YES
10	PSME2	PSME2	PSME2	3309	0.16	0.29	YES
11	PSMA3	PSMA3	PSMA3	3757	0.14	0.28	YES
12	PSMA4	PSMA4	PSMA4	3809	0.14	0.3	YES
13	RICTOR	RICTOR	RICTOR	3827	0.14	0.31	YES
14	PSME4	PSME4	PSME4	3830	0.14	0.33	YES
15	BCL10	BCL10	BCL10	3960	0.13	0.34	YES
16	PSMD14	PSMD14	PSMD14	4117	0.12	0.34	YES
17	CDKN1A	CDKN1A	CDKN1A	4411	0.11	0.34	YES
18	PSMA5	PSMA5	PSMA5	4534	0.11	0.34	YES
19	PSMA6	PSMA6	PSMA6	4713	0.1	0.35	YES
20	PSME1	PSME1	PSME1	4764	0.1	0.36	YES
21	PSMC6	PSMC6	PSMC6	4926	0.096	0.36	YES
22	CREB1	CREB1	CREB1	4987	0.095	0.37	YES
23	MALT1	MALT1	MALT1	5195	0.089	0.36	YES
24	KRAS	KRAS	KRAS	5250	0.087	0.37	YES
25	NFKBIA	NFKBIA	NFKBIA	5278	0.086	0.38	YES
26	MAP3K7	MAP3K7	MAP3K7	5345	0.085	0.39	YES
27	PSMD12	PSMD12	PSMD12	5705	0.076	0.38	YES
28	CHUK	CHUK	CHUK	5716	0.076	0.38	YES
29	NRAS	NRAS	NRAS	5741	0.075	0.39	YES
30	CDKN1B	CDKN1B	CDKN1B	6180	0.066	0.38	NO
31	CUL1	CUL1	CUL1	6182	0.066	0.38	NO
32	PSMA7	PSMA7	PSMA7	6580	0.057	0.37	NO
33	PSMD7	PSMD7	PSMD7	6717	0.054	0.37	NO
34	PSMB2	PSMB2	PSMB2	6742	0.054	0.37	NO
35	PSMC2	PSMC2	PSMC2	6949	0.05	0.36	NO
36	PTEN	PTEN	PTEN	7167	0.046	0.36	NO
37	PSMC1	PSMC1	PSMC1	7331	0.043	0.36	NO
38	REL	REL	REL	7712	0.036	0.34	NO
39	MTOR	MTOR	MTOR	7906	0.032	0.33	NO
40	PSMD5	PSMD5	PSMD5	7928	0.032	0.33	NO
41	PSMB3	PSMB3	PSMB3	8251	0.026	0.32	NO
42	PSMB1	PSMB1	PSMB1	8257	0.026	0.32	NO
43	NFKBIE	NFKBIE	NFKBIE	8333	0.025	0.32	NO
44	PSMD11	PSMD11	PSMD11	8401	0.024	0.32	NO
45	PSMD10	PSMD10	PSMD10	8914	0.016	0.29	NO
46	PSMA8	PSMA8	PSMA8	9540	0.007	0.26	NO
47	PDPK1	PDPK1	PDPK1	9634	0.0054	0.25	NO
48	SKP1	SKP1	SKP1	9662	0.005	0.25	NO
49	PSMC4	PSMC4	PSMC4	9796	0.0029	0.25	NO
50	PSMD1	PSMD1	PSMD1	9820	0.0026	0.24	NO
51	NFKBIB	NFKBIB	NFKBIB	9852	0.0021	0.24	NO
52	PSMC3	PSMC3	PSMC3	9891	0.0015	0.24	NO
53	PSMD13	PSMD13	PSMD13	10277	-0.0043	0.22	NO
54	PSMC5	PSMC5	PSMC5	10429	-0.0064	0.21	NO
55	PSMB6	PSMB6	PSMB6	10559	-0.0085	0.21	NO
56	PSMD3	PSMD3	PSMD3	10590	-0.0091	0.21	NO
57	AKT3	AKT3	AKT3	10665	-0.01	0.2	NO
58	PSMB7	PSMB7	PSMB7	10709	-0.011	0.2	NO
59	RASGRP3	RASGRP3	RASGRP3	10912	-0.013	0.19	NO
60	PSMD8	PSMD8	PSMD8	11103	-0.016	0.18	NO
61	PSMB4	PSMB4	PSMB4	11164	-0.017	0.18	NO
62	FBXW11	FBXW11	FBXW11	11172	-0.017	0.18	NO
63	IKBKB	IKBKB	IKBKB	11311	-0.019	0.18	NO
64	PSMB5	PSMB5	PSMB5	11414	-0.02	0.18	NO
65	CASP9	CASP9	CASP9	11514	-0.021	0.17	NO
66	MAPKAP1	MAPKAP1	MAPKAP1	11527	-0.022	0.17	NO
67	THEM4	THEM4	THEM4	11813	-0.026	0.16	NO
68	PSMD4	PSMD4	PSMD4	12032	-0.029	0.15	NO
69	PSMD9	PSMD9	PSMD9	12076	-0.03	0.15	NO
70	BTRC	BTRC	BTRC	12089	-0.03	0.16	NO
71	PSMD6	PSMD6	PSMD6	12416	-0.035	0.14	NO
72	IKBKG	IKBKG	IKBKG	12564	-0.037	0.14	NO
73	FOXO4	FOXO4	FOXO4	12784	-0.041	0.13	NO
74	BAD	BAD	BAD	12966	-0.044	0.13	NO
75	PHLPP1	PHLPP1	PHLPP1	13022	-0.044	0.13	NO
76	HRAS	HRAS	HRAS	13052	-0.045	0.13	NO
77	MLST8	MLST8	MLST8	13868	-0.058	0.094	NO
78	GSK3A	GSK3A	GSK3A	13892	-0.059	0.099	NO
79	AKT1S1	AKT1S1	AKT1S1	14088	-0.062	0.096	NO
80	FOXO1	FOXO1	FOXO1	14202	-0.064	0.097	NO
81	RPS6KB2	RPS6KB2	RPS6KB2	14302	-0.066	0.099	NO
82	AKT2	AKT2	AKT2	14395	-0.067	0.1	NO
83	AKT1	AKT1	AKT1	14488	-0.069	0.1	NO
84	PSMD2	PSMD2	PSMD2	14824	-0.076	0.095	NO
85	TSC2	TSC2	TSC2	14943	-0.079	0.098	NO
86	PSMF1	PSMF1	PSMF1	15085	-0.082	0.1	NO
87	NR4A1	NR4A1	NR4A1	15125	-0.084	0.11	NO
88	TRIB3	TRIB3	TRIB3	15304	-0.088	0.11	NO
89	RELA	RELA	RELA	15341	-0.09	0.12	NO
90	RPS27A	RPS27A	RPS27A	15344	-0.09	0.13	NO
91	FOXO3	FOXO3	FOXO3	15765	-0.1	0.12	NO
92	UBA52	UBA52	UBA52	16002	-0.11	0.12	NO

Figure S85. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG APOPTOSIS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PSMA1	PSMA1	PSMA1	48	1	0.077	YES
2	CD8B	CD8B	CD8B	104	0.87	0.14	YES
3	LCK	LCK	LCK	149	0.81	0.2	YES
4	CD247	CD247	CD247	228	0.73	0.26	YES
5	PSMB9	PSMB9	PSMB9	463	0.57	0.29	YES
6	DOCK2	DOCK2	DOCK2	659	0.5	0.32	YES
7	CD28	CD28	CD28	979	0.42	0.33	YES
8	PSMA2	PSMA2	PSMA2	1121	0.39	0.36	YES
9	HCK	HCK	HCK	1463	0.33	0.36	YES
10	AP1M2	AP1M2	AP1M2	1499	0.33	0.39	YES
11	B2M	B2M	B2M	1883	0.28	0.39	YES
12	PSMB8	PSMB8	PSMB8	1900	0.28	0.41	YES
13	ELMO1	ELMO1	ELMO1	1935	0.27	0.43	YES
14	APOBEC3G	APOBEC3G	APOBEC3G	2013	0.27	0.45	YES
15	CD4	CD4	CD4	2531	0.22	0.43	NO
16	PSMB10	PSMB10	PSMB10	2806	0.19	0.43	NO
17	HLA-A	HLA-A	HLA-A	3039	0.18	0.44	NO
18	PSME2	PSME2	PSME2	3309	0.16	0.43	NO
19	PSMA3	PSMA3	PSMA3	3757	0.14	0.42	NO
20	PSMA4	PSMA4	PSMA4	3809	0.14	0.43	NO
21	PSME4	PSME4	PSME4	3830	0.14	0.44	NO
22	PSMD14	PSMD14	PSMD14	4117	0.12	0.43	NO
23	TPR	TPR	TPR	4140	0.12	0.44	NO
24	TCEB1	TCEB1	TCEB1	4471	0.11	0.43	NO
25	PSMA5	PSMA5	PSMA5	4534	0.11	0.44	NO
26	PSMA6	PSMA6	PSMA6	4713	0.1	0.43	NO
27	PSME1	PSME1	PSME1	4764	0.1	0.44	NO
28	XPO1	XPO1	XPO1	4911	0.097	0.44	NO
29	PSMC6	PSMC6	PSMC6	4926	0.096	0.44	NO
30	ATP6V1H	ATP6V1H	ATP6V1H	5322	0.085	0.43	NO
31	CUL5	CUL5	CUL5	5421	0.083	0.43	NO
32	NUPL2	NUPL2	NUPL2	5528	0.08	0.43	NO
33	PSMD12	PSMD12	PSMD12	5705	0.076	0.43	NO
34	NUP88	NUP88	NUP88	6290	0.063	0.4	NO
35	NUP50	NUP50	NUP50	6291	0.063	0.4	NO
36	NUP107	NUP107	NUP107	6464	0.06	0.4	NO
37	PSMA7	PSMA7	PSMA7	6580	0.057	0.4	NO
38	PSMD7	PSMD7	PSMD7	6717	0.054	0.4	NO
39	PSMB2	PSMB2	PSMB2	6742	0.054	0.4	NO
40	PSMC2	PSMC2	PSMC2	6949	0.05	0.39	NO
41	RANBP2	RANBP2	RANBP2	7028	0.049	0.39	NO
42	NUP54	NUP54	NUP54	7046	0.048	0.39	NO
43	PSIP1	PSIP1	PSIP1	7319	0.043	0.38	NO
44	PSMC1	PSMC1	PSMC1	7331	0.043	0.38	NO
45	CCNT1	CCNT1	CCNT1	7489	0.04	0.38	NO
46	NUP43	NUP43	NUP43	7512	0.04	0.38	NO
47	NUPL1	NUPL1	NUPL1	7523	0.04	0.38	NO
48	AP1G1	AP1G1	AP1G1	7783	0.034	0.37	NO
49	PSMD5	PSMD5	PSMD5	7928	0.032	0.37	NO
50	NUP85	NUP85	NUP85	8043	0.03	0.36	NO
51	RBX1	RBX1	RBX1	8095	0.029	0.36	NO
52	SEH1L	SEH1L	SEH1L	8173	0.028	0.36	NO
53	PSMB3	PSMB3	PSMB3	8251	0.026	0.36	NO
54	PSMB1	PSMB1	PSMB1	8257	0.026	0.36	NO
55	PSMD11	PSMD11	PSMD11	8401	0.024	0.35	NO
56	KPNB1	KPNB1	KPNB1	8422	0.024	0.35	NO
57	NUP155	NUP155	NUP155	8910	0.016	0.33	NO
58	PSMD10	PSMD10	PSMD10	8914	0.016	0.33	NO
59	NUP205	NUP205	NUP205	9376	0.0091	0.3	NO
60	PSMA8	PSMA8	PSMA8	9540	0.007	0.3	NO
61	SKP1	SKP1	SKP1	9662	0.005	0.29	NO
62	PSMC4	PSMC4	PSMC4	9796	0.0029	0.28	NO
63	NUP37	NUP37	NUP37	9807	0.0027	0.28	NO
64	PSMD1	PSMD1	PSMD1	9820	0.0026	0.28	NO
65	SLC25A4	SLC25A4	SLC25A4	9868	0.0019	0.28	NO
66	PSMC3	PSMC3	PSMC3	9891	0.0015	0.28	NO
67	CDK9	CDK9	CDK9	10119	-0.002	0.26	NO
68	AP2A2	AP2A2	AP2A2	10203	-0.003	0.26	NO
69	PSMD13	PSMD13	PSMD13	10277	-0.0043	0.26	NO
70	NUP35	NUP35	NUP35	10404	-0.0062	0.25	NO
71	PSMC5	PSMC5	PSMC5	10429	-0.0064	0.25	NO
72	AP1S2	AP1S2	AP1S2	10471	-0.0071	0.25	NO
73	PSMB6	PSMB6	PSMB6	10559	-0.0085	0.24	NO
74	PSMD3	PSMD3	PSMD3	10590	-0.0091	0.24	NO
75	NUP210	NUP210	NUP210	10642	-0.0099	0.24	NO
76	ARF1	ARF1	ARF1	10666	-0.01	0.24	NO
77	PSMB7	PSMB7	PSMB7	10709	-0.011	0.24	NO
78	RAN	RAN	RAN	10991	-0.014	0.22	NO
79	NUP133	NUP133	NUP133	11041	-0.015	0.22	NO
80	PSMD8	PSMD8	PSMD8	11103	-0.016	0.22	NO
81	NUP188	NUP188	NUP188	11140	-0.016	0.22	NO
82	PSMB4	PSMB4	PSMB4	11164	-0.017	0.22	NO
83	PSMB5	PSMB5	PSMB5	11414	-0.02	0.21	NO
84	NUP62	NUP62	NUP62	11433	-0.02	0.21	NO
85	AP2B1	AP2B1	AP2B1	11562	-0.022	0.2	NO
86	KPNA1	KPNA1	KPNA1	11635	-0.023	0.2	NO
87	PAK2	PAK2	PAK2	11766	-0.025	0.2	NO
88	AP1S1	AP1S1	AP1S1	11858	-0.026	0.19	NO
89	PPIA	PPIA	PPIA	11867	-0.027	0.19	NO
90	RCC1	RCC1	RCC1	11876	-0.027	0.2	NO
91	PSMD4	PSMD4	PSMD4	12032	-0.029	0.19	NO
92	NUP153	NUP153	NUP153	12054	-0.029	0.19	NO
93	PSMD9	PSMD9	PSMD9	12076	-0.03	0.19	NO
94	BTRC	BTRC	BTRC	12089	-0.03	0.19	NO
95	AP1M1	AP1M1	AP1M1	12354	-0.034	0.18	NO
96	PSMD6	PSMD6	PSMD6	12416	-0.035	0.18	NO
97	SLC25A5	SLC25A5	SLC25A5	12434	-0.036	0.18	NO
98	RAC1	RAC1	RAC1	12511	-0.036	0.18	NO
99	NPM1	NPM1	NPM1	12549	-0.037	0.18	NO
100	RANBP1	RANBP1	RANBP1	12640	-0.038	0.18	NO
101	AP1B1	AP1B1	AP1B1	12772	-0.04	0.18	NO
102	TCEB2	TCEB2	TCEB2	13312	-0.049	0.15	NO
103	AAAS	AAAS	AAAS	13390	-0.05	0.15	NO
104	AP2A1	AP2A1	AP2A1	13477	-0.052	0.15	NO
105	RAE1	RAE1	RAE1	13491	-0.052	0.15	NO
106	AP2S1	AP2S1	AP2S1	13652	-0.054	0.15	NO
107	FYN	FYN	FYN	14091	-0.062	0.13	NO
108	NUP93	NUP93	NUP93	14315	-0.066	0.12	NO
109	NUP214	NUP214	NUP214	14487	-0.069	0.12	NO
110	BANF1	BANF1	BANF1	14660	-0.072	0.11	NO
111	RANGAP1	RANGAP1	RANGAP1	14734	-0.074	0.12	NO
112	PSMD2	PSMD2	PSMD2	14824	-0.076	0.12	NO
113	PSMF1	PSMF1	PSMF1	15085	-0.082	0.11	NO
114	POM121	POM121	POM121	15123	-0.084	0.11	NO
115	RPS27A	RPS27A	RPS27A	15344	-0.09	0.11	NO
116	AP2M1	AP2M1	AP2M1	15657	-0.1	0.098	NO
117	PACS1	PACS1	PACS1	15739	-0.1	0.1	NO
118	HMGA1	HMGA1	HMGA1	15943	-0.11	0.099	NO
119	UBA52	UBA52	UBA52	16002	-0.11	0.1	NO
120	SLC25A6	SLC25A6	SLC25A6	16532	-0.14	0.086	NO

Figure S87. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG APOPTOSIS.

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG APOPTOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CELL ADHESION MOLECULES CAMS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	LCK	LCK	LCK	149	0.81	0.038	YES
2	IL7R	IL7R	IL7R	217	0.74	0.077	YES
3	IL2RB	IL2RB	IL2RB	380	0.62	0.1	YES
4	IL2RA	IL2RA	IL2RA	385	0.62	0.14	YES
5	NOD2	NOD2	NOD2	404	0.6	0.17	YES
6	CSF2	CSF2	CSF2	406	0.6	0.21	YES
7	IL2RG	IL2RG	IL2RG	438	0.58	0.24	YES
8	IL1B	IL1B	IL1B	454	0.57	0.27	YES
9	IL1R2	IL1R2	IL1R2	462	0.57	0.3	YES
10	IL7	IL7	IL7	476	0.56	0.33	YES
11	IL18	IL18	IL18	558	0.53	0.36	YES
12	CSF2RB	CSF2RB	CSF2RB	579	0.52	0.39	YES
13	VAV1	VAV1	VAV1	843	0.44	0.4	YES
14	IL6	IL6	IL6	878	0.44	0.42	YES
15	BLNK	BLNK	BLNK	907	0.43	0.44	YES
16	CASP1	CASP1	CASP1	961	0.42	0.46	YES
17	PTPN6	PTPN6	PTPN6	1036	0.4	0.48	YES
18	STAT1	STAT1	STAT1	1132	0.39	0.5	YES
19	IRAK3	IRAK3	IRAK3	1190	0.38	0.52	YES
20	IL5RA	IL5RA	IL5RA	1379	0.35	0.53	YES
21	IL1RN	IL1RN	IL1RN	1389	0.34	0.55	YES
22	IL1A	IL1A	IL1A	1457	0.33	0.56	YES
23	HCK	HCK	HCK	1463	0.33	0.58	YES
24	JAK3	JAK3	JAK3	1618	0.31	0.59	YES
25	IL1R1	IL1R1	IL1R1	1945	0.27	0.59	YES
26	HGF	HGF	HGF	2068	0.26	0.6	YES
27	PELI1	PELI1	PELI1	2138	0.26	0.61	YES
28	JAK2	JAK2	JAK2	2164	0.25	0.62	YES
29	MAP3K8	MAP3K8	MAP3K8	2331	0.23	0.62	YES
30	IL5	IL5	IL5	2355	0.23	0.64	YES
31	CSF2RA	CSF2RA	CSF2RA	2504	0.22	0.64	YES
32	SYK	SYK	SYK	2950	0.18	0.63	NO
33	PIK3R3	PIK3R3	PIK3R3	3232	0.17	0.62	NO
34	SOCS3	SOCS3	SOCS3	3284	0.16	0.63	NO
35	LYN	LYN	LYN	3311	0.16	0.64	NO
36	IRAK2	IRAK2	IRAK2	3825	0.14	0.62	NO
37	IRAK4	IRAK4	IRAK4	4325	0.12	0.59	NO
38	IL6R	IL6R	IL6R	4663	0.1	0.58	NO
39	STAT3	STAT3	STAT3	5153	0.09	0.56	NO
40	KRAS	KRAS	KRAS	5250	0.087	0.56	NO
41	MAP3K7	MAP3K7	MAP3K7	5345	0.085	0.56	NO
42	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	5548	0.08	0.55	NO
43	SOS1	SOS1	SOS1	5572	0.079	0.56	NO
44	PIK3CA	PIK3CA	PIK3CA	5611	0.078	0.56	NO
45	PIK3R1	PIK3R1	PIK3R1	5635	0.078	0.56	NO
46	IL6ST	IL6ST	IL6ST	5661	0.077	0.56	NO
47	YWHAZ	YWHAZ	YWHAZ	5664	0.077	0.57	NO
48	CHUK	CHUK	CHUK	5716	0.076	0.57	NO
49	NRAS	NRAS	NRAS	5741	0.075	0.57	NO
50	CUL1	CUL1	CUL1	6182	0.066	0.55	NO
51	PRKACB	PRKACB	PRKACB	6385	0.061	0.54	NO
52	RIPK2	RIPK2	RIPK2	6847	0.052	0.52	NO
53	TEC	TEC	TEC	7422	0.041	0.49	NO
54	MAPK1	MAPK1	MAPK1	7460	0.041	0.49	NO
55	MAP2K4	MAP2K4	MAP2K4	7722	0.036	0.48	NO
56	PTK2B	PTK2B	PTK2B	7798	0.034	0.48	NO
57	RBX1	RBX1	RBX1	8095	0.029	0.46	NO
58	MAP2K1	MAP2K1	MAP2K1	8121	0.028	0.46	NO
59	SHC1	SHC1	SHC1	8213	0.027	0.46	NO
60	CRK	CRK	CRK	8287	0.026	0.46	NO
61	IRAK1	IRAK1	IRAK1	8416	0.024	0.45	NO
62	TAB2	TAB2	TAB2	8419	0.024	0.45	NO
63	CDK1	CDK1	CDK1	8444	0.024	0.45	NO
64	MAP2K6	MAP2K6	MAP2K6	8478	0.023	0.45	NO
65	MYD88	MYD88	MYD88	8783	0.018	0.44	NO
66	JAK1	JAK1	JAK1	8835	0.018	0.43	NO
67	TRAF6	TRAF6	TRAF6	8887	0.017	0.43	NO
68	TAB3	TAB3	TAB3	8936	0.016	0.43	NO
69	NFKB2	NFKB2	NFKB2	8994	0.015	0.43	NO
70	GRB2	GRB2	GRB2	9080	0.013	0.42	NO
71	YWHAB	YWHAB	YWHAB	9223	0.012	0.42	NO
72	UBE2N	UBE2N	UBE2N	9344	0.0096	0.41	NO
73	IL3RA	IL3RA	IL3RA	9586	0.0062	0.4	NO
74	SKP1	SKP1	SKP1	9662	0.005	0.39	NO
75	YES1	YES1	YES1	9663	0.005	0.39	NO
76	NOD1	NOD1	NOD1	9856	0.0021	0.38	NO
77	SQSTM1	SQSTM1	SQSTM1	10048	-0.00088	0.37	NO
78	STAT5B	STAT5B	STAT5B	10100	-0.0016	0.37	NO
79	RAPGEF1	RAPGEF1	RAPGEF1	10221	-0.0034	0.36	NO
80	PIK3CD	PIK3CD	PIK3CD	10253	-0.0038	0.36	NO
81	PIK3CB	PIK3CB	PIK3CB	10313	-0.0048	0.36	NO
82	CBL	CBL	CBL	10752	-0.012	0.34	NO
83	TNIP2	TNIP2	TNIP2	10961	-0.014	0.32	NO
84	TYK2	TYK2	TYK2	11019	-0.015	0.32	NO
85	IKBKB	IKBKB	IKBKB	11311	-0.019	0.31	NO
86	INPPL1	INPPL1	INPPL1	11316	-0.019	0.31	NO
87	BTRC	BTRC	BTRC	12089	-0.03	0.27	NO
88	IKBKG	IKBKG	IKBKG	12564	-0.037	0.24	NO
89	MAP3K3	MAP3K3	MAP3K3	12809	-0.041	0.23	NO
90	CRKL	CRKL	CRKL	12892	-0.043	0.23	NO
91	STAT5A	STAT5A	STAT5A	12930	-0.043	0.23	NO
92	GAB2	GAB2	GAB2	13006	-0.044	0.23	NO
93	HRAS	HRAS	HRAS	13052	-0.045	0.23	NO
94	TAB1	TAB1	TAB1	13130	-0.046	0.23	NO
95	TOLLIP	TOLLIP	TOLLIP	13406	-0.05	0.21	NO
96	FYN	FYN	FYN	14091	-0.062	0.18	NO
97	MAPK3	MAPK3	MAPK3	14380	-0.067	0.17	NO
98	MAP2K2	MAP2K2	MAP2K2	14942	-0.079	0.14	NO
99	PELI2	PELI2	PELI2	14965	-0.079	0.14	NO
100	RAF1	RAF1	RAF1	15263	-0.087	0.13	NO
101	RELA	RELA	RELA	15341	-0.09	0.13	NO
102	PIK3R2	PIK3R2	PIK3R2	15774	-0.1	0.12	NO
103	IL1RAP	IL1RAP	IL1RAP	15978	-0.11	0.11	NO
104	PELI3	PELI3	PELI3	16265	-0.12	0.1	NO

Figure S89. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG CELL ADHESION MOLECULES CAMS.

Figure S90. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL ADHESION MOLECULES CAMS, 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 NOD LIKE RECEPTOR SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	STAP1	STAP1	STAP1	79	0.91	0.031	YES
2	TNFRSF17	TNFRSF17	TNFRSF17	89	0.89	0.066	YES
3	IGJ	IGJ	IGJ	95	0.88	0.1	YES
4	PTPN22	PTPN22	PTPN22	126	0.84	0.13	YES
5	LCK	LCK	LCK	149	0.81	0.16	YES
6	TOX	TOX	TOX	160	0.81	0.19	YES
7	PTPRC	PTPRC	PTPRC	204	0.75	0.22	YES
8	CD38	CD38	CD38	225	0.73	0.25	YES
9	LY9	LY9	LY9	240	0.72	0.28	YES
10	RGS13	RGS13	RGS13	295	0.68	0.3	YES
11	LRMP	LRMP	LRMP	339	0.64	0.32	YES
12	IRF8	IRF8	IRF8	518	0.55	0.33	YES
13	ADAM19	ADAM19	ADAM19	684	0.49	0.34	YES
14	VAV1	VAV1	VAV1	843	0.44	0.35	YES
15	CD86	CD86	CD86	883	0.43	0.37	YES
16	TUBB3	TUBB3	TUBB3	1027	0.41	0.38	YES
17	IFI30	IFI30	IFI30	1167	0.38	0.38	YES
18	LEF1	LEF1	LEF1	1293	0.36	0.39	YES
19	EAF2	EAF2	EAF2	1383	0.35	0.4	YES
20	RAC2	RAC2	RAC2	1427	0.34	0.41	YES
21	RUNX3	RUNX3	RUNX3	1590	0.32	0.41	YES
22	MAP4K1	MAP4K1	MAP4K1	1612	0.32	0.42	YES
23	BLK	BLK	BLK	1774	0.3	0.43	YES
24	MEIS2	MEIS2	MEIS2	1788	0.29	0.44	YES
25	SNX10	SNX10	SNX10	1910	0.28	0.44	YES
26	BTK	BTK	BTK	1985	0.27	0.45	YES
27	LAP3	LAP3	LAP3	2101	0.26	0.45	YES
28	CCDC109B	CCDC109B	CCDC109B	2281	0.24	0.45	YES
29	KCNN3	KCNN3	KCNN3	2328	0.24	0.46	YES
30	PLEKHF2	PLEKHF2	PLEKHF2	2970	0.18	0.43	NO
31	ITGB7	ITGB7	ITGB7	3103	0.18	0.43	NO
32	RFTN1	RFTN1	RFTN1	3123	0.18	0.44	NO
33	CAB39L	CAB39L	CAB39L	3705	0.14	0.41	NO
34	PRKCA	PRKCA	PRKCA	4001	0.13	0.4	NO
35	MAPK6	MAPK6	MAPK6	4028	0.13	0.4	NO
36	RNF19B	RNF19B	RNF19B	4037	0.13	0.4	NO
37	CDK14	CDK14	CDK14	4046	0.13	0.41	NO
38	MYBL1	MYBL1	MYBL1	4151	0.12	0.41	NO
39	COTL1	COTL1	COTL1	4195	0.12	0.41	NO
40	SMC4	SMC4	SMC4	4308	0.12	0.41	NO
41	SERINC5	SERINC5	SERINC5	4377	0.12	0.41	NO
42	RAP1B	RAP1B	RAP1B	4386	0.11	0.41	NO
43	SGCB	SGCB	SGCB	4392	0.11	0.42	NO
44	CREM	CREM	CREM	4545	0.11	0.41	NO
45	TMEM194A	TMEM194A	TMEM194A	4782	0.1	0.4	NO
46	PITX1	PITX1	PITX1	5045	0.093	0.39	NO
47	TCEA1	TCEA1	TCEA1	5080	0.092	0.4	NO
48	PEX3	PEX3	PEX3	5121	0.09	0.4	NO
49	HSPH1	HSPH1	HSPH1	5135	0.09	0.4	NO
50	DEPTOR	DEPTOR	DEPTOR	5144	0.09	0.4	NO
51	ZNF93	ZNF93	ZNF93	5344	0.085	0.4	NO
52	NR3C1	NR3C1	NR3C1	5454	0.082	0.39	NO
53	CPNE3	CPNE3	CPNE3	5501	0.081	0.39	NO
54	SYNE1	SYNE1	SYNE1	5720	0.076	0.38	NO
55	PPP3CC	PPP3CC	PPP3CC	5824	0.073	0.38	NO
56	MBD2	MBD2	MBD2	5851	0.073	0.38	NO
57	ENDOD1	ENDOD1	ENDOD1	5980	0.07	0.38	NO
58	SHMT1	SHMT1	SHMT1	6034	0.069	0.38	NO
59	BASP1	BASP1	BASP1	6074	0.068	0.38	NO
60	SRP54	SRP54	SRP54	6133	0.066	0.38	NO
61	EMP3	EMP3	EMP3	6296	0.063	0.37	NO
62	HMGB1	HMGB1	HMGB1	6355	0.062	0.37	NO
63	HBS1L	HBS1L	HBS1L	6405	0.061	0.37	NO
64	USP34	USP34	USP34	6435	0.06	0.37	NO
65	MAST2	MAST2	MAST2	6452	0.06	0.37	NO
66	SS18	SS18	SS18	6582	0.057	0.37	NO
67	SDHB	SDHB	SDHB	6741	0.054	0.36	NO
68	LSR	LSR	LSR	6776	0.053	0.36	NO
69	TIMELESS	TIMELESS	TIMELESS	6983	0.049	0.35	NO
70	ARPP19	ARPP19	ARPP19	6991	0.049	0.35	NO
71	HDAC1	HDAC1	HDAC1	6995	0.049	0.35	NO
72	COPS2	COPS2	COPS2	7036	0.048	0.35	NO
73	CAP1	CAP1	CAP1	7194	0.046	0.35	NO
74	TBC1D1	TBC1D1	TBC1D1	7294	0.043	0.34	NO
75	ALDH4A1	ALDH4A1	ALDH4A1	7543	0.039	0.33	NO
76	ARPC1B	ARPC1B	ARPC1B	7630	0.038	0.33	NO
77	AGPAT5	AGPAT5	AGPAT5	7710	0.036	0.32	NO
78	PCMT1	PCMT1	PCMT1	7716	0.036	0.32	NO
79	PCM1	PCM1	PCM1	7953	0.031	0.31	NO
80	GCHFR	GCHFR	GCHFR	8292	0.026	0.3	NO
81	GM2A	GM2A	GM2A	8332	0.025	0.29	NO
82	RHEB	RHEB	RHEB	8406	0.024	0.29	NO
83	SYPL1	SYPL1	SYPL1	8428	0.024	0.29	NO
84	NUSAP1	NUSAP1	NUSAP1	8437	0.024	0.29	NO
85	NQO2	NQO2	NQO2	8448	0.023	0.29	NO
86	COPS3	COPS3	COPS3	8466	0.023	0.29	NO
87	XRCC5	XRCC5	XRCC5	8498	0.023	0.29	NO
88	PEX1	PEX1	PEX1	8676	0.02	0.28	NO
89	ARPC2	ARPC2	ARPC2	8691	0.02	0.28	NO
90	G3BP1	G3BP1	G3BP1	8815	0.018	0.28	NO
91	FOXN3	FOXN3	FOXN3	8841	0.018	0.27	NO
92	PRPSAP2	PRPSAP2	PRPSAP2	8918	0.016	0.27	NO
93	DDX39A	DDX39A	DDX39A	8922	0.016	0.27	NO
94	CD22	CD22	CD22	8973	0.015	0.27	NO
95	ALDH2	ALDH2	ALDH2	9254	0.011	0.25	NO
96	TSFM	TSFM	TSFM	9317	0.01	0.25	NO
97	MAK16	MAK16	MAK16	9396	0.0089	0.25	NO
98	SNX19	SNX19	SNX19	9522	0.0073	0.24	NO
99	ISCU	ISCU	ISCU	9549	0.0069	0.24	NO
100	EPB41L2	EPB41L2	EPB41L2	9601	0.006	0.24	NO
101	PARN	PARN	PARN	9866	0.0019	0.22	NO
102	TRMT12	TRMT12	TRMT12	10008	-0.0003	0.21	NO
103	PFDN2	PFDN2	PFDN2	10063	-0.0011	0.21	NO
104	GSR	GSR	GSR	10098	-0.0015	0.21	NO
105	ATP8A1	ATP8A1	ATP8A1	10139	-0.0022	0.21	NO
106	DUT	DUT	DUT	10146	-0.0024	0.21	NO
107	TACC1	TACC1	TACC1	10209	-0.0031	0.2	NO
108	CLSTN1	CLSTN1	CLSTN1	10258	-0.0039	0.2	NO
109	BIN3	BIN3	BIN3	10270	-0.0041	0.2	NO
110	SNRPD1	SNRPD1	SNRPD1	10274	-0.0042	0.2	NO
111	ETS2	ETS2	ETS2	10298	-0.0046	0.2	NO
112	FNTA	FNTA	FNTA	10366	-0.0056	0.2	NO
113	CHMP7	CHMP7	CHMP7	10859	-0.013	0.17	NO
114	NBEAL2	NBEAL2	NBEAL2	10942	-0.014	0.16	NO
115	PARP1	PARP1	PARP1	10947	-0.014	0.16	NO
116	NRGN	NRGN	NRGN	10979	-0.014	0.16	NO
117	MRPS22	MRPS22	MRPS22	11225	-0.018	0.15	NO
118	CKAP4	CKAP4	CKAP4	11254	-0.018	0.15	NO
119	ENSA	ENSA	ENSA	11287	-0.018	0.15	NO
120	SH2B2	SH2B2	SH2B2	11365	-0.02	0.14	NO
121	LGALSL	LGALSL	LGALSL	11529	-0.022	0.14	NO
122	GNAS	GNAS	GNAS	11678	-0.024	0.13	NO
123	MEF2C	MEF2C	MEF2C	11759	-0.025	0.13	NO
124	PAK2	PAK2	PAK2	11766	-0.025	0.13	NO
125	DENND1C	DENND1C	DENND1C	11829	-0.026	0.12	NO
126	MRPL34	MRPL34	MRPL34	11838	-0.026	0.12	NO
127	DEDD	DEDD	DEDD	11951	-0.028	0.12	NO
128	NUDT11	NUDT11	NUDT11	12004	-0.029	0.12	NO
129	HMGB3	HMGB3	HMGB3	12042	-0.029	0.12	NO
130	FANCA	FANCA	FANCA	12096	-0.03	0.12	NO
131	ITGB1	ITGB1	ITGB1	12218	-0.032	0.11	NO
132	ARF3	ARF3	ARF3	12360	-0.034	0.1	NO
133	CYB5R1	CYB5R1	CYB5R1	12389	-0.035	0.1	NO
134	ADCK2	ADCK2	ADCK2	12394	-0.035	0.1	NO
135	KIAA0226	KIAA0226	KIAA0226	12465	-0.036	0.1	NO
136	CNOT7	CNOT7	CNOT7	12477	-0.036	0.1	NO
137	PPP2R2A	PPP2R2A	PPP2R2A	12676	-0.039	0.093	NO
138	GRK6	GRK6	GRK6	12726	-0.04	0.092	NO
139	LSM4	LSM4	LSM4	12748	-0.04	0.092	NO
140	TMEM147	TMEM147	TMEM147	12925	-0.043	0.084	NO
141	LSM1	LSM1	LSM1	13159	-0.046	0.073	NO
142	CDKN3	CDKN3	CDKN3	13176	-0.046	0.074	NO
143	ATP6V1B2	ATP6V1B2	ATP6V1B2	13178	-0.046	0.076	NO
144	C6orf106	C6orf106	C6orf106	13253	-0.048	0.073	NO
145	MAGEH1	MAGEH1	MAGEH1	13259	-0.048	0.075	NO
146	HGSNAT	HGSNAT	HGSNAT	13324	-0.049	0.073	NO
147	TUBB2A	TUBB2A	TUBB2A	13325	-0.049	0.075	NO
148	MAP4K4	MAP4K4	MAP4K4	13331	-0.049	0.077	NO
149	TUBA1B	TUBA1B	TUBA1B	13384	-0.05	0.076	NO
150	PPP6R1	PPP6R1	PPP6R1	13403	-0.05	0.077	NO
151	TUBA1C	TUBA1C	TUBA1C	13404	-0.05	0.079	NO
152	CLTB	CLTB	CLTB	13459	-0.051	0.078	NO
153	FLII	FLII	FLII	13515	-0.052	0.077	NO
154	RNF126	RNF126	RNF126	13545	-0.053	0.077	NO
155	SBF1	SBF1	SBF1	13573	-0.053	0.078	NO
156	XPO7	XPO7	XPO7	13720	-0.056	0.072	NO
157	ACAT1	ACAT1	ACAT1	13747	-0.056	0.073	NO
158	NCOR2	NCOR2	NCOR2	13897	-0.059	0.067	NO
159	NHP2L1	NHP2L1	NHP2L1	13962	-0.06	0.065	NO
160	KIAA0930	KIAA0930	KIAA0930	14160	-0.063	0.057	NO
161	COPS6	COPS6	COPS6	14276	-0.065	0.053	NO
162	DDX3Y	DDX3Y	DDX3Y	14292	-0.066	0.055	NO
163	CUX1	CUX1	CUX1	14328	-0.066	0.055	NO
164	MFHAS1	MFHAS1	MFHAS1	14416	-0.068	0.053	NO
165	MYH10	MYH10	MYH10	14614	-0.071	0.045	NO
166	PARD6A	PARD6A	PARD6A	14649	-0.072	0.046	NO
167	MRPS33	MRPS33	MRPS33	14703	-0.073	0.046	NO
168	PXMP4	PXMP4	PXMP4	14745	-0.074	0.046	NO
169	ASH2L	ASH2L	ASH2L	14810	-0.076	0.046	NO
170	PPP2CB	PPP2CB	PPP2CB	14874	-0.077	0.045	NO
171	DST	DST	DST	15122	-0.084	0.035	NO
172	HSPBP1	HSPBP1	HSPBP1	15161	-0.084	0.036	NO
173	TMEM106C	TMEM106C	TMEM106C	15387	-0.091	0.027	NO
174	NFIB	NFIB	NFIB	15435	-0.093	0.028	NO
175	INTS9	INTS9	INTS9	15454	-0.093	0.031	NO
176	MYO1E	MYO1E	MYO1E	15510	-0.095	0.031	NO
177	PDLIM2	PDLIM2	PDLIM2	15580	-0.097	0.031	NO
178	PEMT	PEMT	PEMT	15596	-0.098	0.034	NO
179	USP13	USP13	USP13	15623	-0.098	0.037	NO
180	E2F1	E2F1	E2F1	15643	-0.099	0.04	NO
181	GTF2F1	GTF2F1	GTF2F1	15660	-0.1	0.043	NO
182	GTF2IRD1	GTF2IRD1	GTF2IRD1	16004	-0.11	0.028	NO
183	GTPBP6	GTPBP6	GTPBP6	16056	-0.12	0.03	NO
184	CD99	CD99	CD99	16057	-0.12	0.034	NO
185	KDM5D	KDM5D	KDM5D	16150	-0.12	0.034	NO
186	DPYSL2	DPYSL2	DPYSL2	16197	-0.12	0.036	NO
187	D4S234E	D4S234E	D4S234E	16377	-0.13	0.031	NO
188	SLCO4A1	SLCO4A1	SLCO4A1	16490	-0.14	0.03	NO
189	CYP39A1	CYP39A1	CYP39A1	16502	-0.14	0.035	NO
190	SLC25A6	SLC25A6	SLC25A6	16532	-0.14	0.039	NO
191	LTBP1	LTBP1	LTBP1	17151	-0.2	0.013	NO
192	PEG10	PEG10	PEG10	17269	-0.23	0.015	NO
193	RPS4Y1	RPS4Y1	RPS4Y1	17318	-0.24	0.022	NO
194	MEST	MEST	MEST	17404	-0.26	0.027	NO
195	PDGFD	PDGFD	PDGFD	17500	-0.28	0.033	NO

Figure S91. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY.

Figure S92. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOD LIKE RECEPTOR 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 RIG I LIKE RECEPTOR SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PSMA1	PSMA1	PSMA1	48	1	0.14	YES
2	PSMB9	PSMB9	PSMB9	463	0.57	0.21	YES
3	TAP1	TAP1	TAP1	1000	0.41	0.24	YES
4	PSMA2	PSMA2	PSMA2	1121	0.39	0.29	YES
5	HLA-B	HLA-B	HLA-B	1484	0.33	0.32	YES
6	ERAP2	ERAP2	ERAP2	1578	0.32	0.36	YES
7	TAP2	TAP2	TAP2	1751	0.3	0.39	YES
8	PSMB8	PSMB8	PSMB8	1900	0.28	0.43	YES
9	HLA-C	HLA-C	HLA-C	2116	0.26	0.45	YES
10	TAPBPL	TAPBPL	TAPBPL	2419	0.23	0.47	YES
11	PSMB10	PSMB10	PSMB10	2806	0.19	0.48	YES
12	HLA-A	HLA-A	HLA-A	3039	0.18	0.49	YES
13	ERAP1	ERAP1	ERAP1	3175	0.17	0.51	YES
14	PSME2	PSME2	PSME2	3309	0.16	0.52	YES
15	PSMA3	PSMA3	PSMA3	3757	0.14	0.52	YES
16	PSMA4	PSMA4	PSMA4	3809	0.14	0.54	YES
17	PSME4	PSME4	PSME4	3830	0.14	0.56	YES
18	DERL1	DERL1	DERL1	3899	0.13	0.57	YES
19	PSMD14	PSMD14	PSMD14	4117	0.12	0.58	YES
20	TAPBP	TAPBP	TAPBP	4292	0.12	0.58	YES
21	PSMA6	PSMA6	PSMA6	4713	0.1	0.58	YES
22	PSME1	PSME1	PSME1	4764	0.1	0.59	YES
23	PSMC6	PSMC6	PSMC6	4926	0.096	0.59	YES
24	PSMA7	PSMA7	PSMA7	6580	0.057	0.51	NO
25	PSMD7	PSMD7	PSMD7	6717	0.054	0.51	NO
26	PSMB2	PSMB2	PSMB2	6742	0.054	0.52	NO
27	PSMC2	PSMC2	PSMC2	6949	0.05	0.51	NO
28	PSMC1	PSMC1	PSMC1	7331	0.043	0.5	NO
29	PDIA3	PDIA3	PDIA3	7718	0.036	0.48	NO
30	PSMD5	PSMD5	PSMD5	7928	0.032	0.48	NO
31	CANX	CANX	CANX	7996	0.03	0.48	NO
32	PSMD11	PSMD11	PSMD11	8401	0.024	0.46	NO
33	HMGCS1	HMGCS1	HMGCS1	9099	0.013	0.42	NO
34	PDIA6	PDIA6	PDIA6	9636	0.0054	0.39	NO
35	PSMC3	PSMC3	PSMC3	9891	0.0015	0.38	NO
36	PSMC5	PSMC5	PSMC5	10429	-0.0064	0.35	NO
37	PSMB6	PSMB6	PSMB6	10559	-0.0085	0.34	NO
38	PSMD8	PSMD8	PSMD8	11103	-0.016	0.32	NO
39	NGLY1	NGLY1	NGLY1	11290	-0.018	0.31	NO
40	PSME3	PSME3	PSME3	11322	-0.019	0.31	NO
41	PSMB5	PSMB5	PSMB5	11414	-0.02	0.31	NO
42	TMED4	TMED4	TMED4	12203	-0.032	0.27	NO
43	KDELR1	KDELR1	KDELR1	12224	-0.032	0.27	NO
44	PDIA5	PDIA5	PDIA5	12601	-0.038	0.26	NO
45	GGA3	GGA3	GGA3	13186	-0.047	0.23	NO
46	ATF4	ATF4	ATF4	13656	-0.055	0.21	NO
47	SERP1	SERP1	SERP1	13665	-0.055	0.22	NO
48	SEC22C	SEC22C	SEC22C	14992	-0.08	0.16	NO
49	PSMF1	PSMF1	PSMF1	15085	-0.082	0.17	NO

Figure S93. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY.

Figure S94. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIG I LIKE RECEPTOR 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 JAK STAT SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PSMA1	PSMA1	PSMA1	48	1	0.056	YES
2	CD8B	CD8B	CD8B	104	0.87	0.1	YES
3	LCK	LCK	LCK	149	0.81	0.15	YES
4	CCR5	CCR5	CCR5	185	0.77	0.19	YES
5	CD247	CD247	CD247	228	0.73	0.23	YES
6	PSMB9	PSMB9	PSMB9	463	0.57	0.25	YES
7	DOCK2	DOCK2	DOCK2	659	0.5	0.27	YES
8	CD28	CD28	CD28	979	0.42	0.28	YES
9	PSMA2	PSMA2	PSMA2	1121	0.39	0.29	YES
10	HCK	HCK	HCK	1463	0.33	0.29	YES
11	AP1M2	AP1M2	AP1M2	1499	0.33	0.31	YES
12	B2M	B2M	B2M	1883	0.28	0.3	YES
13	PSMB8	PSMB8	PSMB8	1900	0.28	0.32	YES
14	ELMO1	ELMO1	ELMO1	1935	0.27	0.33	YES
15	APOBEC3G	APOBEC3G	APOBEC3G	2013	0.27	0.34	YES
16	CD4	CD4	CD4	2531	0.22	0.33	YES
17	PSMB10	PSMB10	PSMB10	2806	0.19	0.32	YES
18	HLA-A	HLA-A	HLA-A	3039	0.18	0.32	YES
19	LIG4	LIG4	LIG4	3181	0.17	0.32	YES
20	PSME2	PSME2	PSME2	3309	0.16	0.32	YES
21	CXCR4	CXCR4	CXCR4	3512	0.15	0.32	YES
22	PSMA3	PSMA3	PSMA3	3757	0.14	0.32	YES
23	PSMA4	PSMA4	PSMA4	3809	0.14	0.32	YES
24	PSME4	PSME4	PSME4	3830	0.14	0.33	YES
25	CCNT2	CCNT2	CCNT2	4109	0.12	0.32	YES
26	PSMD14	PSMD14	PSMD14	4117	0.12	0.33	YES
27	TPR	TPR	TPR	4140	0.12	0.33	YES
28	TAF13	TAF13	TAF13	4289	0.12	0.33	YES
29	TAF5	TAF5	TAF5	4368	0.12	0.33	YES
30	TCEB1	TCEB1	TCEB1	4471	0.11	0.34	YES
31	POLR2F	POLR2F	POLR2F	4514	0.11	0.34	YES
32	PSMA5	PSMA5	PSMA5	4534	0.11	0.34	YES
33	XRCC4	XRCC4	XRCC4	4686	0.1	0.34	YES
34	PSMA6	PSMA6	PSMA6	4713	0.1	0.35	YES
35	PSME1	PSME1	PSME1	4764	0.1	0.35	YES
36	XPO1	XPO1	XPO1	4911	0.097	0.35	YES
37	PSMC6	PSMC6	PSMC6	4926	0.096	0.35	YES
38	POLR2K	POLR2K	POLR2K	4998	0.094	0.35	YES
39	TCEA1	TCEA1	TCEA1	5080	0.092	0.35	YES
40	CCNH	CCNH	CCNH	5165	0.089	0.36	YES
41	GTF2A1	GTF2A1	GTF2A1	5212	0.088	0.36	YES
42	ATP6V1H	ATP6V1H	ATP6V1H	5322	0.085	0.36	YES
43	CUL5	CUL5	CUL5	5421	0.083	0.36	YES
44	NUPL2	NUPL2	NUPL2	5528	0.08	0.35	YES
45	GTF2B	GTF2B	GTF2B	5626	0.078	0.35	YES
46	GTF2F2	GTF2F2	GTF2F2	5690	0.076	0.35	YES
47	PSMD12	PSMD12	PSMD12	5705	0.076	0.36	YES
48	GTF2H3	GTF2H3	GTF2H3	5906	0.071	0.35	NO
49	RNGTT	RNGTT	RNGTT	6051	0.068	0.35	NO
50	TAF4B	TAF4B	TAF4B	6191	0.065	0.34	NO
51	NUP88	NUP88	NUP88	6290	0.063	0.34	NO
52	NUP50	NUP50	NUP50	6291	0.063	0.34	NO
53	NCBP1	NCBP1	NCBP1	6369	0.062	0.34	NO
54	NUP107	NUP107	NUP107	6464	0.06	0.34	NO
55	PSMA7	PSMA7	PSMA7	6580	0.057	0.34	NO
56	PSMD7	PSMD7	PSMD7	6717	0.054	0.34	NO
57	PSMB2	PSMB2	PSMB2	6742	0.054	0.34	NO
58	PSMC2	PSMC2	PSMC2	6949	0.05	0.33	NO
59	TCEB3	TCEB3	TCEB3	7007	0.049	0.33	NO
60	RANBP2	RANBP2	RANBP2	7028	0.049	0.33	NO
61	POLR2B	POLR2B	POLR2B	7038	0.048	0.33	NO
62	NUP54	NUP54	NUP54	7046	0.048	0.33	NO
63	TAF9	TAF9	TAF9	7130	0.047	0.33	NO
64	PSIP1	PSIP1	PSIP1	7319	0.043	0.32	NO
65	PSMC1	PSMC1	PSMC1	7331	0.043	0.33	NO
66	RNMT	RNMT	RNMT	7344	0.042	0.33	NO
67	CCNT1	CCNT1	CCNT1	7489	0.04	0.32	NO
68	NUP43	NUP43	NUP43	7512	0.04	0.32	NO
69	NUPL1	NUPL1	NUPL1	7523	0.04	0.32	NO
70	GTF2H1	GTF2H1	GTF2H1	7706	0.036	0.32	NO
71	AP1G1	AP1G1	AP1G1	7783	0.034	0.32	NO
72	PSMD5	PSMD5	PSMD5	7928	0.032	0.31	NO
73	TAF12	TAF12	TAF12	8037	0.03	0.3	NO
74	NUP85	NUP85	NUP85	8043	0.03	0.31	NO
75	SUPT16H	SUPT16H	SUPT16H	8081	0.029	0.3	NO
76	GTF2H2	GTF2H2	GTF2H2	8094	0.029	0.31	NO
77	RBX1	RBX1	RBX1	8095	0.029	0.31	NO
78	SEH1L	SEH1L	SEH1L	8173	0.028	0.3	NO
79	PSMB3	PSMB3	PSMB3	8251	0.026	0.3	NO
80	PSMB1	PSMB1	PSMB1	8257	0.026	0.3	NO
81	PSMD11	PSMD11	PSMD11	8401	0.024	0.3	NO
82	KPNB1	KPNB1	KPNB1	8422	0.024	0.3	NO
83	CDK7	CDK7	CDK7	8481	0.023	0.3	NO
84	XRCC5	XRCC5	XRCC5	8498	0.023	0.3	NO
85	GTF2A2	GTF2A2	GTF2A2	8508	0.023	0.3	NO
86	TAF1	TAF1	TAF1	8574	0.021	0.29	NO
87	NUP155	NUP155	NUP155	8910	0.016	0.28	NO
88	PSMD10	PSMD10	PSMD10	8914	0.016	0.28	NO
89	POLR2D	POLR2D	POLR2D	9151	0.012	0.26	NO
90	VPS37A	VPS37A	VPS37A	9259	0.011	0.26	NO
91	NMT1	NMT1	NMT1	9300	0.01	0.26	NO
92	NUP205	NUP205	NUP205	9376	0.0091	0.25	NO
93	VPS28	VPS28	VPS28	9423	0.0086	0.25	NO
94	PSMA8	PSMA8	PSMA8	9540	0.007	0.25	NO
95	GTF2E2	GTF2E2	GTF2E2	9607	0.0059	0.24	NO
96	SKP1	SKP1	SKP1	9662	0.005	0.24	NO
97	PSMC4	PSMC4	PSMC4	9796	0.0029	0.23	NO
98	NUP37	NUP37	NUP37	9807	0.0027	0.23	NO
99	PSMD1	PSMD1	PSMD1	9820	0.0026	0.23	NO
100	SLC25A4	SLC25A4	SLC25A4	9868	0.0019	0.23	NO
101	PSMC3	PSMC3	PSMC3	9891	0.0015	0.23	NO
102	CDK9	CDK9	CDK9	10119	-0.002	0.22	NO
103	AP2A2	AP2A2	AP2A2	10203	-0.003	0.21	NO
104	PSMD13	PSMD13	PSMD13	10277	-0.0043	0.21	NO
105	ERCC3	ERCC3	ERCC3	10316	-0.0048	0.21	NO
106	POLR2A	POLR2A	POLR2A	10350	-0.0053	0.2	NO
107	NUP35	NUP35	NUP35	10404	-0.0062	0.2	NO
108	PSMC5	PSMC5	PSMC5	10429	-0.0064	0.2	NO
109	ELL	ELL	ELL	10432	-0.0065	0.2	NO
110	AP1S2	AP1S2	AP1S2	10471	-0.0071	0.2	NO
111	FEN1	FEN1	FEN1	10547	-0.0084	0.2	NO
112	PSMB6	PSMB6	PSMB6	10559	-0.0085	0.2	NO
113	PSMD3	PSMD3	PSMD3	10590	-0.0091	0.19	NO
114	NUP210	NUP210	NUP210	10642	-0.0099	0.19	NO
115	ARF1	ARF1	ARF1	10666	-0.01	0.19	NO
116	MNAT1	MNAT1	MNAT1	10679	-0.01	0.19	NO
117	PSMB7	PSMB7	PSMB7	10709	-0.011	0.19	NO
118	TSG101	TSG101	TSG101	10898	-0.013	0.18	NO
119	RAN	RAN	RAN	10991	-0.014	0.18	NO
120	NUP133	NUP133	NUP133	11041	-0.015	0.17	NO
121	PSMD8	PSMD8	PSMD8	11103	-0.016	0.17	NO
122	NUP188	NUP188	NUP188	11140	-0.016	0.17	NO
123	PSMB4	PSMB4	PSMB4	11164	-0.017	0.17	NO
124	TBP	TBP	TBP	11293	-0.018	0.16	NO
125	POLR2C	POLR2C	POLR2C	11372	-0.02	0.16	NO
126	PSMB5	PSMB5	PSMB5	11414	-0.02	0.16	NO
127	POLR2G	POLR2G	POLR2G	11425	-0.02	0.16	NO
128	NUP62	NUP62	NUP62	11433	-0.02	0.16	NO
129	AP2B1	AP2B1	AP2B1	11562	-0.022	0.16	NO
130	KPNA1	KPNA1	KPNA1	11635	-0.023	0.15	NO
131	PAK2	PAK2	PAK2	11766	-0.025	0.15	NO
132	AP1S1	AP1S1	AP1S1	11858	-0.026	0.14	NO
133	PPIA	PPIA	PPIA	11867	-0.027	0.14	NO
134	RCC1	RCC1	RCC1	11876	-0.027	0.14	NO
135	PSMD4	PSMD4	PSMD4	12032	-0.029	0.14	NO
136	CTDP1	CTDP1	CTDP1	12044	-0.029	0.14	NO
137	NUP153	NUP153	NUP153	12054	-0.029	0.14	NO
138	PSMD9	PSMD9	PSMD9	12076	-0.03	0.14	NO
139	BTRC	BTRC	BTRC	12089	-0.03	0.14	NO
140	TAF4	TAF4	TAF4	12159	-0.031	0.14	NO
141	NCBP2	NCBP2	NCBP2	12230	-0.032	0.14	NO
142	GTF2E1	GTF2E1	GTF2E1	12246	-0.032	0.14	NO
143	AP1M1	AP1M1	AP1M1	12354	-0.034	0.14	NO
144	PSMD6	PSMD6	PSMD6	12416	-0.035	0.13	NO
145	SLC25A5	SLC25A5	SLC25A5	12434	-0.036	0.14	NO
146	TAF11	TAF11	TAF11	12436	-0.036	0.14	NO
147	POLR2E	POLR2E	POLR2E	12438	-0.036	0.14	NO
148	RAC1	RAC1	RAC1	12511	-0.036	0.14	NO
149	NPM1	NPM1	NPM1	12549	-0.037	0.14	NO
150	XRCC6	XRCC6	XRCC6	12605	-0.038	0.14	NO
151	POLR2J	POLR2J	POLR2J	12607	-0.038	0.14	NO
152	RANBP1	RANBP1	RANBP1	12640	-0.038	0.14	NO
153	AP1B1	AP1B1	AP1B1	12772	-0.04	0.13	NO
154	GTF2H4	GTF2H4	GTF2H4	12881	-0.042	0.13	NO
155	LIG1	LIG1	LIG1	13150	-0.046	0.12	NO
156	TCEB2	TCEB2	TCEB2	13312	-0.049	0.11	NO
157	AAAS	AAAS	AAAS	13390	-0.05	0.11	NO
158	AP2A1	AP2A1	AP2A1	13477	-0.052	0.11	NO
159	RAE1	RAE1	RAE1	13491	-0.052	0.11	NO
160	NMT2	NMT2	NMT2	13509	-0.052	0.11	NO
161	POLR2L	POLR2L	POLR2L	13561	-0.053	0.11	NO
162	AP2S1	AP2S1	AP2S1	13652	-0.054	0.11	NO
163	SSRP1	SSRP1	SSRP1	13834	-0.058	0.1	NO
164	VPS37B	VPS37B	VPS37B	14036	-0.061	0.097	NO
165	FYN	FYN	FYN	14091	-0.062	0.098	NO
166	SUPT4H1	SUPT4H1	SUPT4H1	14125	-0.062	0.1	NO
167	TAF10	TAF10	TAF10	14260	-0.065	0.096	NO
168	NUP93	NUP93	NUP93	14315	-0.066	0.097	NO
169	NUP214	NUP214	NUP214	14487	-0.069	0.091	NO
170	BANF1	BANF1	BANF1	14660	-0.072	0.086	NO
171	POLR2I	POLR2I	POLR2I	14685	-0.073	0.089	NO
172	RANGAP1	RANGAP1	RANGAP1	14734	-0.074	0.09	NO
173	PSMD2	PSMD2	PSMD2	14824	-0.076	0.09	NO
174	VPS37C	VPS37C	VPS37C	14957	-0.079	0.087	NO
175	SUPT5H	SUPT5H	SUPT5H	14989	-0.08	0.09	NO
176	PSMF1	PSMF1	PSMF1	15085	-0.082	0.09	NO
177	POM121	POM121	POM121	15123	-0.084	0.092	NO
178	TAF6	TAF6	TAF6	15218	-0.086	0.092	NO
179	RPS27A	RPS27A	RPS27A	15344	-0.09	0.09	NO
180	POLR2H	POLR2H	POLR2H	15373	-0.091	0.094	NO
181	AP2M1	AP2M1	AP2M1	15657	-0.1	0.084	NO
182	GTF2F1	GTF2F1	GTF2F1	15660	-0.1	0.09	NO
183	PACS1	PACS1	PACS1	15739	-0.1	0.091	NO
184	HMGA1	HMGA1	HMGA1	15943	-0.11	0.086	NO
185	UBA52	UBA52	UBA52	16002	-0.11	0.09	NO
186	SLC25A6	SLC25A6	SLC25A6	16532	-0.14	0.068	NO
187	VPS37D	VPS37D	VPS37D	16698	-0.16	0.068	NO
188	ERCC2	ERCC2	ERCC2	16737	-0.16	0.075	NO

Figure S95. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG JAK STAT SIGNALING PATHWAY.

Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG JAK STAT 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 HEMATOPOIETIC CELL LINEAGE

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PSMA1	PSMA1	PSMA1	48	1	0.042	YES
2	FCGR1B	FCGR1B	FCGR1B	211	0.75	0.066	YES
3	FCGR1A	FCGR1A	FCGR1A	443	0.58	0.078	YES
4	PSMB9	PSMB9	PSMB9	463	0.57	0.1	YES
5	HLA-F	HLA-F	HLA-F	940	0.42	0.095	YES
6	TAP1	TAP1	TAP1	1000	0.41	0.11	YES
7	TRIM36	TRIM36	TRIM36	1065	0.4	0.12	YES
8	PSMA2	PSMA2	PSMA2	1121	0.39	0.14	YES
9	CTSS	CTSS	CTSS	1161	0.38	0.15	YES
10	CYBB	CYBB	CYBB	1171	0.38	0.17	YES
11	ASB2	ASB2	ASB2	1410	0.34	0.17	YES
12	UBE2L6	UBE2L6	UBE2L6	1436	0.34	0.18	YES
13	ASB15	ASB15	ASB15	1481	0.33	0.2	YES
14	HLA-B	HLA-B	HLA-B	1484	0.33	0.21	YES
15	NCF4	NCF4	NCF4	1706	0.3	0.21	YES
16	MRC1	MRC1	MRC1	1714	0.3	0.22	YES
17	TAP2	TAP2	TAP2	1751	0.3	0.24	YES
18	B2M	B2M	B2M	1883	0.28	0.24	YES
19	PSMB8	PSMB8	PSMB8	1900	0.28	0.25	YES
20	HLA-C	HLA-C	HLA-C	2116	0.26	0.25	YES
21	DTX3L	DTX3L	DTX3L	2117	0.26	0.26	YES
22	MRC2	MRC2	MRC2	2134	0.26	0.27	YES
23	SEC24D	SEC24D	SEC24D	2179	0.25	0.28	YES
24	NCF2	NCF2	NCF2	2291	0.24	0.29	YES
25	UBA7	UBA7	UBA7	2458	0.22	0.29	YES
26	TRIM9	TRIM9	TRIM9	2486	0.22	0.3	YES
27	CD207	CD207	CD207	2751	0.2	0.29	YES
28	PSMB10	PSMB10	PSMB10	2806	0.19	0.3	YES
29	UBE2W	UBE2W	UBE2W	2959	0.18	0.3	YES
30	HLA-A	HLA-A	HLA-A	3039	0.18	0.3	YES
31	RNF182	RNF182	RNF182	3151	0.17	0.3	YES
32	ERAP1	ERAP1	ERAP1	3175	0.17	0.31	YES
33	WSB1	WSB1	WSB1	3244	0.17	0.31	YES
34	SOCS3	SOCS3	SOCS3	3284	0.16	0.32	YES
35	PSME2	PSME2	PSME2	3309	0.16	0.32	YES
36	UBR1	UBR1	UBR1	3527	0.15	0.32	YES
37	UBE2V2	UBE2V2	UBE2V2	3554	0.15	0.32	YES
38	HLA-G	HLA-G	HLA-G	3610	0.15	0.32	YES
39	FBXO6	FBXO6	FBXO6	3613	0.15	0.33	YES
40	PSMA3	PSMA3	PSMA3	3757	0.14	0.33	YES
41	SAR1B	SAR1B	SAR1B	3787	0.14	0.33	YES
42	PSMA4	PSMA4	PSMA4	3809	0.14	0.34	YES
43	PSME4	PSME4	PSME4	3830	0.14	0.34	YES
44	TRIM21	TRIM21	TRIM21	3875	0.13	0.35	YES
45	ASB5	ASB5	ASB5	3893	0.13	0.35	YES
46	SOCS1	SOCS1	SOCS1	3905	0.13	0.36	YES
47	UBA6	UBA6	UBA6	4088	0.12	0.35	YES
48	PSMD14	PSMD14	PSMD14	4117	0.12	0.36	YES
49	WWP1	WWP1	WWP1	4395	0.11	0.34	YES
50	TCEB1	TCEB1	TCEB1	4471	0.11	0.35	YES
51	CDC27	CDC27	CDC27	4505	0.11	0.35	YES
52	RNF6	RNF6	RNF6	4511	0.11	0.35	YES
53	PSMA5	PSMA5	PSMA5	4534	0.11	0.36	YES
54	CUL2	CUL2	CUL2	4585	0.11	0.36	YES
55	PSMA6	PSMA6	PSMA6	4713	0.1	0.36	YES
56	NEDD4	NEDD4	NEDD4	4715	0.1	0.36	YES
57	PSME1	PSME1	PSME1	4764	0.1	0.36	YES
58	SEC61A2	SEC61A2	SEC61A2	4922	0.096	0.36	NO
59	PSMC6	PSMC6	PSMC6	4926	0.096	0.36	NO
60	ITGAV	ITGAV	ITGAV	5025	0.094	0.36	NO
61	UBE2A	UBE2A	UBE2A	5131	0.09	0.36	NO
62	ANAPC4	ANAPC4	ANAPC4	5155	0.09	0.36	NO
63	TPP2	TPP2	TPP2	5294	0.086	0.36	NO
64	ASB11	ASB11	ASB11	5407	0.083	0.36	NO
65	CUL5	CUL5	CUL5	5421	0.083	0.36	NO
66	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	5548	0.08	0.35	NO
67	FBXW7	FBXW7	FBXW7	5579	0.079	0.36	NO
68	UBE2J1	UBE2J1	UBE2J1	5630	0.078	0.36	NO
69	PSMD12	PSMD12	PSMD12	5705	0.076	0.36	NO
70	SEC23A	SEC23A	SEC23A	5717	0.076	0.36	NO
71	LNPEP	LNPEP	LNPEP	5739	0.075	0.36	NO
72	UBE2Q2	UBE2Q2	UBE2Q2	5904	0.071	0.36	NO
73	UBE3A	UBE3A	UBE3A	5994	0.07	0.35	NO
74	UBA2	UBA2	UBA2	5996	0.069	0.36	NO
75	HERC2	HERC2	HERC2	6099	0.067	0.35	NO
76	CUL1	CUL1	CUL1	6182	0.066	0.35	NO
77	LRR1	LRR1	LRR1	6190	0.065	0.35	NO
78	ASB9	ASB9	ASB9	6235	0.064	0.35	NO
79	UBR2	UBR2	UBR2	6244	0.064	0.36	NO
80	UBE2K	UBE2K	UBE2K	6273	0.064	0.36	NO
81	CD36	CD36	CD36	6303	0.063	0.36	NO
82	HSPA5	HSPA5	HSPA5	6445	0.06	0.35	NO
83	PSMA7	PSMA7	PSMA7	6580	0.057	0.35	NO
84	CUL3	CUL3	CUL3	6660	0.056	0.35	NO
85	FBXO3	FBXO3	FBXO3	6703	0.055	0.35	NO
86	PJA2	PJA2	PJA2	6716	0.054	0.35	NO
87	PSMD7	PSMD7	PSMD7	6717	0.054	0.35	NO
88	PSMB2	PSMB2	PSMB2	6742	0.054	0.35	NO
89	ASB7	ASB7	ASB7	6791	0.053	0.35	NO
90	UBE2D1	UBE2D1	UBE2D1	6889	0.051	0.35	NO
91	FBXO4	FBXO4	FBXO4	6898	0.051	0.35	NO
92	ANAPC10	ANAPC10	ANAPC10	6907	0.051	0.35	NO
93	PSMC2	PSMC2	PSMC2	6949	0.05	0.35	NO
94	FBXO2	FBXO2	FBXO2	7055	0.048	0.35	NO
95	ASB8	ASB8	ASB8	7084	0.048	0.35	NO
96	PSMC1	PSMC1	PSMC1	7331	0.043	0.34	NO
97	UBE2F	UBE2F	UBE2F	7352	0.042	0.34	NO
98	KLHL20	KLHL20	KLHL20	7547	0.039	0.33	NO
99	SEC24B	SEC24B	SEC24B	7597	0.038	0.33	NO
100	RNF138	RNF138	RNF138	7607	0.038	0.33	NO
101	PDIA3	PDIA3	PDIA3	7718	0.036	0.32	NO
102	UBE2B	UBE2B	UBE2B	7850	0.033	0.32	NO
103	UBA3	UBA3	UBA3	7851	0.033	0.32	NO
104	NPEPPS	NPEPPS	NPEPPS	7882	0.033	0.32	NO
105	PSMD5	PSMD5	PSMD5	7928	0.032	0.32	NO
106	SPSB1	SPSB1	SPSB1	7955	0.031	0.32	NO
107	CANX	CANX	CANX	7996	0.03	0.32	NO
108	CDC26	CDC26	CDC26	8025	0.03	0.32	NO
109	RBX1	RBX1	RBX1	8095	0.029	0.32	NO
110	PSMB3	PSMB3	PSMB3	8251	0.026	0.31	NO
111	UBE4A	UBE4A	UBE4A	8255	0.026	0.31	NO
112	PSMB1	PSMB1	PSMB1	8257	0.026	0.31	NO
113	CBLB	CBLB	CBLB	8315	0.026	0.31	NO
114	UBE2Z	UBE2Z	UBE2Z	8323	0.025	0.31	NO
115	RCHY1	RCHY1	RCHY1	8328	0.025	0.31	NO
116	UBE2D3	UBE2D3	UBE2D3	8370	0.025	0.31	NO
117	PSMD11	PSMD11	PSMD11	8401	0.024	0.31	NO
118	KEAP1	KEAP1	KEAP1	8430	0.024	0.31	NO
119	TRIP12	TRIP12	TRIP12	8473	0.023	0.3	NO
120	SMURF2	SMURF2	SMURF2	8520	0.022	0.3	NO
121	RNF34	RNF34	RNF34	8545	0.022	0.3	NO
122	UBE2G1	UBE2G1	UBE2G1	8549	0.022	0.3	NO
123	TRIM37	TRIM37	TRIM37	8702	0.02	0.3	NO
124	UBA5	UBA5	UBA5	8831	0.018	0.29	NO
125	UBE3C	UBE3C	UBE3C	8882	0.017	0.29	NO
126	PSMD10	PSMD10	PSMD10	8914	0.016	0.29	NO
127	UBE2J2	UBE2J2	UBE2J2	9133	0.013	0.28	NO
128	KLHL9	KLHL9	KLHL9	9178	0.012	0.27	NO
129	ANAPC7	ANAPC7	ANAPC7	9265	0.011	0.27	NO
130	UBE2N	UBE2N	UBE2N	9344	0.0096	0.26	NO
131	SEC31A	SEC31A	SEC31A	9410	0.0088	0.26	NO
132	RNF4	RNF4	RNF4	9465	0.0081	0.26	NO
133	SKP2	SKP2	SKP2	9528	0.0072	0.26	NO
134	PSMA8	PSMA8	PSMA8	9540	0.007	0.26	NO
135	SKP1	SKP1	SKP1	9662	0.005	0.25	NO
136	CALR	CALR	CALR	9694	0.0046	0.25	NO
137	CDC16	CDC16	CDC16	9710	0.0043	0.25	NO
138	CYBA	CYBA	CYBA	9754	0.0037	0.24	NO
139	PSMC4	PSMC4	PSMC4	9796	0.0029	0.24	NO
140	PSMD1	PSMD1	PSMD1	9820	0.0026	0.24	NO
141	CDC23	CDC23	CDC23	9821	0.0026	0.24	NO
142	PSMC3	PSMC3	PSMC3	9891	0.0015	0.24	NO
143	UBE2H	UBE2H	UBE2H	9910	0.0013	0.24	NO
144	HECTD3	HECTD3	HECTD3	9916	0.0011	0.24	NO
145	ANAPC5	ANAPC5	ANAPC5	10170	-0.0027	0.22	NO
146	UBR4	UBR4	UBR4	10196	-0.0029	0.22	NO
147	UBE2D2	UBE2D2	UBE2D2	10247	-0.0038	0.22	NO
148	PSMD13	PSMD13	PSMD13	10277	-0.0043	0.22	NO
149	RNF220	RNF220	RNF220	10414	-0.0063	0.21	NO
150	PSMC5	PSMC5	PSMC5	10429	-0.0064	0.21	NO
151	TRIM32	TRIM32	TRIM32	10457	-0.0069	0.21	NO
152	VHL	VHL	VHL	10534	-0.0082	0.2	NO
153	PSMB6	PSMB6	PSMB6	10559	-0.0085	0.2	NO
154	PSMD3	PSMD3	PSMD3	10590	-0.0091	0.2	NO
155	PSMB7	PSMB7	PSMB7	10709	-0.011	0.2	NO
156	ITGB5	ITGB5	ITGB5	10785	-0.012	0.19	NO
157	DZIP3	DZIP3	DZIP3	10789	-0.012	0.19	NO
158	SAE1	SAE1	SAE1	10870	-0.013	0.19	NO
159	FBXO44	FBXO44	FBXO44	10998	-0.014	0.18	NO
160	GAN	GAN	GAN	11086	-0.016	0.18	NO
161	PSMD8	PSMD8	PSMD8	11103	-0.016	0.18	NO
162	PSMB4	PSMB4	PSMB4	11164	-0.017	0.18	NO
163	FBXW11	FBXW11	FBXW11	11172	-0.017	0.18	NO
164	MKRN1	MKRN1	MKRN1	11189	-0.017	0.18	NO
165	SEC61B	SEC61B	SEC61B	11318	-0.019	0.17	NO
166	SEC61G	SEC61G	SEC61G	11351	-0.019	0.17	NO
167	PSMB5	PSMB5	PSMB5	11414	-0.02	0.16	NO
168	ASB16	ASB16	ASB16	11457	-0.021	0.16	NO
169	UBE2G2	UBE2G2	UBE2G2	11553	-0.022	0.16	NO
170	PARK2	PARK2	PARK2	11591	-0.022	0.16	NO
171	UBE3B	UBE3B	UBE3B	11663	-0.024	0.16	NO
172	RNF41	RNF41	RNF41	11937	-0.028	0.14	NO
173	RNF25	RNF25	RNF25	11976	-0.028	0.14	NO
174	PJA1	PJA1	PJA1	11995	-0.029	0.14	NO
175	PSMD4	PSMD4	PSMD4	12032	-0.029	0.14	NO
176	UBA1	UBA1	UBA1	12047	-0.029	0.14	NO
177	UBE2L3	UBE2L3	UBE2L3	12056	-0.029	0.14	NO
178	PSMD9	PSMD9	PSMD9	12076	-0.03	0.14	NO
179	BTRC	BTRC	BTRC	12089	-0.03	0.14	NO
180	SEC24C	SEC24C	SEC24C	12158	-0.031	0.14	NO
181	UBE2M	UBE2M	UBE2M	12188	-0.031	0.14	NO
182	ARIH2	ARIH2	ARIH2	12195	-0.031	0.14	NO
183	UBE2Q1	UBE2Q1	UBE2Q1	12197	-0.031	0.14	NO
184	LRRC41	LRRC41	LRRC41	12274	-0.032	0.14	NO
185	LRSAM1	LRSAM1	LRSAM1	12368	-0.034	0.14	NO
186	CDC20	CDC20	CDC20	12386	-0.035	0.14	NO
187	PSMD6	PSMD6	PSMD6	12416	-0.035	0.14	NO
188	ANAPC11	ANAPC11	ANAPC11	12523	-0.037	0.13	NO
189	TRIM63	TRIM63	TRIM63	12814	-0.041	0.12	NO
190	ANAPC1	ANAPC1	ANAPC1	12841	-0.042	0.12	NO
191	HUWE1	HUWE1	HUWE1	12899	-0.043	0.12	NO
192	UBE2E3	UBE2E3	UBE2E3	12951	-0.043	0.12	NO
193	SEC61A1	SEC61A1	SEC61A1	13152	-0.046	0.11	NO
194	TRIM11	TRIM11	TRIM11	13219	-0.047	0.1	NO
195	TCEB2	TCEB2	TCEB2	13312	-0.049	0.1	NO
196	RBCK1	RBCK1	RBCK1	13358	-0.049	0.1	NO
197	ASB1	ASB1	ASB1	13412	-0.05	0.1	NO
198	ATG7	ATG7	ATG7	13444	-0.051	0.1	NO
199	UBE2E1	UBE2E1	UBE2E1	13445	-0.051	0.1	NO
200	ASB6	ASB6	ASB6	13484	-0.052	0.1	NO
201	UBE2S	UBE2S	UBE2S	13546	-0.053	0.1	NO
202	UBE2E2	UBE2E2	UBE2E2	13557	-0.053	0.1	NO
203	UBOX5	UBOX5	UBOX5	13627	-0.054	0.1	NO
204	SEC13	SEC13	SEC13	13697	-0.055	0.1	NO
205	BLMH	BLMH	BLMH	13798	-0.057	0.099	NO
206	ASB13	ASB13	ASB13	13859	-0.058	0.098	NO
207	UBE2C	UBE2C	UBE2C	13986	-0.06	0.093	NO
208	UBE2D4	UBE2D4	UBE2D4	14012	-0.06	0.095	NO
209	ANAPC2	ANAPC2	ANAPC2	14085	-0.062	0.093	NO
210	CDC34	CDC34	CDC34	14123	-0.062	0.094	NO
211	SPSB2	SPSB2	SPSB2	14154	-0.063	0.095	NO
212	SMURF1	SMURF1	SMURF1	14368	-0.067	0.086	NO
213	FBXW8	FBXW8	FBXW8	14674	-0.073	0.072	NO
214	UBE2O	UBE2O	UBE2O	14747	-0.074	0.072	NO
215	ANAPC13	ANAPC13	ANAPC13	14765	-0.075	0.074	NO
216	SPSB4	SPSB4	SPSB4	14768	-0.075	0.077	NO
217	PSMD2	PSMD2	PSMD2	14824	-0.076	0.078	NO
218	UBE2R2	UBE2R2	UBE2R2	14928	-0.079	0.075	NO
219	PSMF1	PSMF1	PSMF1	15085	-0.082	0.07	NO
220	STUB1	STUB1	STUB1	15099	-0.083	0.073	NO
221	VPRBP	VPRBP	VPRBP	15108	-0.083	0.076	NO
222	RPS27A	RPS27A	RPS27A	15344	-0.09	0.067	NO
223	CUL7	CUL7	CUL7	15431	-0.092	0.066	NO
224	RNF144B	RNF144B	RNF144B	15441	-0.093	0.07	NO
225	FBXO27	FBXO27	FBXO27	15696	-0.1	0.06	NO
226	UBE2U	UBE2U	UBE2U	15759	-0.1	0.061	NO
227	DET1	DET1	DET1	15784	-0.1	0.065	NO
228	UBA52	UBA52	UBA52	16002	-0.11	0.058	NO
229	ASB12	ASB12	ASB12	16263	-0.12	0.048	NO
230	RNF123	RNF123	RNF123	16505	-0.14	0.041	NO
231	ZBTB16	ZBTB16	ZBTB16	16739	-0.16	0.035	NO
232	KLHL13	KLHL13	KLHL13	16838	-0.17	0.037	NO
233	ASB4	ASB4	ASB4	17730	-0.35	0.0027	NO
234	FBXO17	FBXO17	FBXO17	17813	-0.39	0.015	NO

Figure S97. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG HEMATOPOIETIC CELL LINEAGE.

Figure S98. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HEMATOPOIETIC CELL LINEAGE, 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 B CELL RECEPTOR SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PSMA1	PSMA1	PSMA1	48	1	0.091	YES
2	FCGR1B	FCGR1B	FCGR1B	211	0.75	0.15	YES
3	FCGR1A	FCGR1A	FCGR1A	443	0.58	0.19	YES
4	PSMB9	PSMB9	PSMB9	463	0.57	0.24	YES
5	HLA-F	HLA-F	HLA-F	940	0.42	0.26	YES
6	TAP1	TAP1	TAP1	1000	0.41	0.29	YES
7	PSMA2	PSMA2	PSMA2	1121	0.39	0.32	YES
8	CTSS	CTSS	CTSS	1161	0.38	0.36	YES
9	CYBB	CYBB	CYBB	1171	0.38	0.39	YES
10	HLA-B	HLA-B	HLA-B	1484	0.33	0.4	YES
11	NCF4	NCF4	NCF4	1706	0.3	0.42	YES
12	MRC1	MRC1	MRC1	1714	0.3	0.45	YES
13	TAP2	TAP2	TAP2	1751	0.3	0.47	YES
14	B2M	B2M	B2M	1883	0.28	0.49	YES
15	PSMB8	PSMB8	PSMB8	1900	0.28	0.52	YES
16	HLA-C	HLA-C	HLA-C	2116	0.26	0.53	YES
17	MRC2	MRC2	MRC2	2134	0.26	0.55	YES
18	NCF2	NCF2	NCF2	2291	0.24	0.56	YES
19	CD207	CD207	CD207	2751	0.2	0.56	YES
20	PSMB10	PSMB10	PSMB10	2806	0.19	0.57	YES
21	HLA-A	HLA-A	HLA-A	3039	0.18	0.58	YES
22	PSME2	PSME2	PSME2	3309	0.16	0.58	YES
23	HLA-G	HLA-G	HLA-G	3610	0.15	0.57	YES
24	PSMA3	PSMA3	PSMA3	3757	0.14	0.58	YES
25	PSMA4	PSMA4	PSMA4	3809	0.14	0.59	YES
26	PSME4	PSME4	PSME4	3830	0.14	0.6	YES
27	PSMD14	PSMD14	PSMD14	4117	0.12	0.6	YES
28	PSMA5	PSMA5	PSMA5	4534	0.11	0.58	YES
29	PSMA6	PSMA6	PSMA6	4713	0.1	0.58	YES
30	PSME1	PSME1	PSME1	4764	0.1	0.59	YES
31	SEC61A2	SEC61A2	SEC61A2	4922	0.096	0.59	YES
32	PSMC6	PSMC6	PSMC6	4926	0.096	0.6	YES
33	ITGAV	ITGAV	ITGAV	5025	0.094	0.6	YES
34	PSMD12	PSMD12	PSMD12	5705	0.076	0.57	NO
35	LNPEP	LNPEP	LNPEP	5739	0.075	0.58	NO
36	CD36	CD36	CD36	6303	0.063	0.55	NO
37	PSMA7	PSMA7	PSMA7	6580	0.057	0.54	NO
38	PSMD7	PSMD7	PSMD7	6717	0.054	0.54	NO
39	PSMB2	PSMB2	PSMB2	6742	0.054	0.54	NO
40	PSMC2	PSMC2	PSMC2	6949	0.05	0.54	NO
41	PSMC1	PSMC1	PSMC1	7331	0.043	0.52	NO
42	PDIA3	PDIA3	PDIA3	7718	0.036	0.5	NO
43	PSMD5	PSMD5	PSMD5	7928	0.032	0.49	NO
44	PSMB3	PSMB3	PSMB3	8251	0.026	0.48	NO
45	PSMB1	PSMB1	PSMB1	8257	0.026	0.48	NO
46	PSMD11	PSMD11	PSMD11	8401	0.024	0.47	NO
47	PSMD10	PSMD10	PSMD10	8914	0.016	0.45	NO
48	PSMA8	PSMA8	PSMA8	9540	0.007	0.41	NO
49	CALR	CALR	CALR	9694	0.0046	0.4	NO
50	CYBA	CYBA	CYBA	9754	0.0037	0.4	NO
51	PSMC4	PSMC4	PSMC4	9796	0.0029	0.4	NO
52	PSMD1	PSMD1	PSMD1	9820	0.0026	0.4	NO
53	PSMC3	PSMC3	PSMC3	9891	0.0015	0.39	NO
54	PSMD13	PSMD13	PSMD13	10277	-0.0043	0.37	NO
55	PSMC5	PSMC5	PSMC5	10429	-0.0064	0.36	NO
56	PSMB6	PSMB6	PSMB6	10559	-0.0085	0.36	NO
57	PSMD3	PSMD3	PSMD3	10590	-0.0091	0.36	NO
58	PSMB7	PSMB7	PSMB7	10709	-0.011	0.35	NO
59	ITGB5	ITGB5	ITGB5	10785	-0.012	0.35	NO
60	PSMD8	PSMD8	PSMD8	11103	-0.016	0.33	NO
61	PSMB4	PSMB4	PSMB4	11164	-0.017	0.33	NO
62	SEC61B	SEC61B	SEC61B	11318	-0.019	0.32	NO
63	SEC61G	SEC61G	SEC61G	11351	-0.019	0.32	NO
64	PSMB5	PSMB5	PSMB5	11414	-0.02	0.32	NO
65	PSMD4	PSMD4	PSMD4	12032	-0.029	0.29	NO
66	PSMD9	PSMD9	PSMD9	12076	-0.03	0.29	NO
67	PSMD6	PSMD6	PSMD6	12416	-0.035	0.28	NO
68	SEC61A1	SEC61A1	SEC61A1	13152	-0.046	0.24	NO
69	PSMD2	PSMD2	PSMD2	14824	-0.076	0.15	NO
70	PSMF1	PSMF1	PSMF1	15085	-0.082	0.15	NO
71	RPS27A	RPS27A	RPS27A	15344	-0.09	0.14	NO
72	UBA52	UBA52	UBA52	16002	-0.11	0.12	NO

Figure S99. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG B CELL RECEPTOR SIGNALING PATHWAY.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

Gene set database = c2.all.v6.1.symbols.gmt
Expression data file = TCGA-UVM-TP.mRNA_FPKM_log2_protein.coding.txt
Phenotype data file = TCGA-UVM-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA),Broad GSEA-P-R.1.0 version is used with class2: canonical pathways genes from MSigDB v6.1.Further details about statistics are available inThe Broad GSEA website.

MSigDB releases (v6.0 and above) are available under a Creative Commons style license, plus additional terms for some gene sets. The full license terms are available

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)

Made with Nozzle