GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in SKCM-TM

Skin Cutaneous Melanoma (Metastatic)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in SKCM-TM. Broad Institute of MIT and Harvard. doi:10.7908/C1WD4017

Overview

Introduction

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

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

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 708
Number of samples: 368
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 117
pheno.type: 2 - 4 :[ clus2 ] 73
pheno.type: 3 - 4 :[ clus3 ] 105
pheno.type: 4 - 4 :[ clus4 ] 73

For the expression subtypes of 18059 genes in 369 samples, GSEA found enriched gene sets in each cluster using 368 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG OXIDATIVE PHOSPHORYLATION, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG BASE EXCISION REPAIR, KEGG LYSOSOME, KEGG PARKINSONS DISEASE, PID MTOR 4PATHWAY, REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE

And common core enriched genes are ACO2, CS, IDH3G, SDHA, SDHB, SDHC, ATP5B, ATP5G1, CYC1, DLST

clus2

Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FATTY ACID METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

And common core enriched genes are PSMA8, PSMB10, PSMB8, PSMB9, PSME1, PSME2, B2M, HLA-A, APOBEC3G, CD247

clus3

Top enriched gene sets are KEGG TGF BETA SIGNALING PATHWAY, KEGG ECM RECEPTOR INTERACTION, BIOCARTA ERK PATHWAY, BIOCARTA MPR PATHWAY, WNT SIGNALING, ST INTEGRIN SIGNALING PATHWAY, PID INTEGRIN1 PATHWAY, PID EPHBFWDPATHWAY, PID RET PATHWAY, PID NCADHERINPATHWAY

And common core enriched genes are FGFR1, ACAN, B3GNT3, B3GNT7, B4GALT6, CHST1, CHST2, CHST5, CHST6, FMOD

clus4

Top enriched gene sets are KEGG LYSINE DEGRADATION, KEGG RIBOSOME, KEGG BASAL TRANSCRIPTION FACTORS, KEGG SPLICEOSOME, PID ATM PATHWAY, PID RETINOIC ACID PATHWAY, PID BARD1PATHWAY, PID P53REGULATIONPATHWAY, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

And common core enriched genes are HSPA1B, LSM2, MAGOH, NCBP1, RBM8A, AAAS, EIF4E, HNRNPD, LSM5, LSM6

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 CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.55	2	0.01	0.5	0.28	0.66	0.23	0.5	0	0.12
KEGG PENTOSE PHOSPHATE PATHWAY	27	genes.ES.table	0.39	1.3	0.17	1	1	0.44	0.13	0.39	1	0.72
KEGG OXIDATIVE PHOSPHORYLATION	114	genes.ES.table	0.52	1.9	0.025	0.56	0.49	0.61	0.25	0.46	0	0.15
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.4	1.5	0.081	1	0.98	0.37	0.14	0.32	0.69	0.35
KEGG AMINOACYL TRNA BIOSYNTHESIS	41	genes.ES.table	0.39	1.5	0.11	1	0.98	0.58	0.31	0.41	0.73	0.37
KEGG BASE EXCISION REPAIR	33	genes.ES.table	0.36	1.4	0.16	1	1	0.42	0.16	0.36	1	0.6
KEGG LYSOSOME	120	genes.ES.table	0.48	1.8	0.058	0.57	0.68	0.48	0.19	0.39	0.22	0.16
KEGG PARKINSONS DISEASE	111	genes.ES.table	0.33	1.3	0.24	1	1	0.53	0.25	0.4	1	0.64
PID MTOR 4PATHWAY	67	genes.ES.table	0.28	1.4	0.098	1	0.99	0.3	0.21	0.24	0.94	0.47
REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE	40	genes.ES.table	0.4	1.6	0.062	0.72	0.89	0.55	0.23	0.42	0.38	0.23

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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	OGDHL	OGDHL	OGDHL	674	0.21	0.056	YES
2	ACO2	ACO2	ACO2	1111	0.15	0.1	YES
3	SDHA	SDHA	SDHA	1330	0.14	0.15	YES
4	IDH3G	IDH3G	IDH3G	1742	0.12	0.18	YES
5	FH	FH	FH	1757	0.11	0.23	YES
6	PC	PC	PC	2166	0.099	0.25	YES
7	OGDH	OGDH	OGDH	2329	0.094	0.29	YES
8	DLST	DLST	DLST	2435	0.09	0.32	YES
9	SDHB	SDHB	SDHB	2604	0.085	0.35	YES
10	MDH2	MDH2	MDH2	2641	0.084	0.39	YES
11	IDH1	IDH1	IDH1	3071	0.072	0.4	YES
12	CS	CS	CS	3267	0.067	0.42	YES
13	MDH1	MDH1	MDH1	3345	0.066	0.44	YES
14	PCK2	PCK2	PCK2	3394	0.064	0.47	YES
15	SUCLG1	SUCLG1	SUCLG1	3465	0.062	0.49	YES
16	ACO1	ACO1	ACO1	3490	0.062	0.52	YES
17	SDHC	SDHC	SDHC	3604	0.059	0.54	YES
18	IDH3B	IDH3B	IDH3B	4021	0.05	0.54	YES
19	PDHA1	PDHA1	PDHA1	4203	0.046	0.55	YES
20	IDH3A	IDH3A	IDH3A	4915	0.033	0.52	NO
21	PDHB	PDHB	PDHB	5822	0.015	0.48	NO
22	ACLY	ACLY	ACLY	5857	0.014	0.48	NO
23	DLD	DLD	DLD	6664	-0.003	0.44	NO
24	IDH2	IDH2	IDH2	6874	-0.0073	0.43	NO
25	SUCLG2	SUCLG2	SUCLG2	6973	-0.0094	0.43	NO
26	DLAT	DLAT	DLAT	7701	-0.025	0.4	NO
27	SUCLA2	SUCLA2	SUCLA2	10898	-0.1	0.27	NO
28	SDHD	SDHD	SDHD	11602	-0.12	0.28	NO
29	PCK1	PCK1	PCK1	12994	-0.16	0.28	NO

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

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ATP6V0D2	ATP6V0D2	ATP6V0D2	102	0.42	0.041	YES
2	ATP6V0A4	ATP6V0A4	ATP6V0A4	104	0.42	0.087	YES
3	COX6A2	COX6A2	COX6A2	814	0.18	0.068	YES
4	ATP12A	ATP12A	ATP12A	850	0.18	0.086	YES
5	ATP6V0A1	ATP6V0A1	ATP6V0A1	865	0.18	0.1	YES
6	ATP6V0C	ATP6V0C	ATP6V0C	1046	0.16	0.11	YES
7	ATP6AP1	ATP6AP1	ATP6AP1	1052	0.16	0.13	YES
8	NDUFS8	NDUFS8	NDUFS8	1261	0.14	0.14	YES
9	UQCRC1	UQCRC1	UQCRC1	1307	0.14	0.15	YES
10	SDHA	SDHA	SDHA	1330	0.14	0.16	YES
11	ATP6V1F	ATP6V1F	ATP6V1F	1379	0.14	0.17	YES
12	ATP6V0B	ATP6V0B	ATP6V0B	1399	0.13	0.19	YES
13	NDUFS7	NDUFS7	NDUFS7	1490	0.13	0.2	YES
14	ATP6V0D1	ATP6V0D1	ATP6V0D1	1523	0.13	0.21	YES
15	NDUFA8	NDUFA8	NDUFA8	1529	0.13	0.22	YES
16	NDUFV1	NDUFV1	NDUFV1	1720	0.12	0.23	YES
17	NDUFB7	NDUFB7	NDUFB7	1722	0.12	0.24	YES
18	NDUFA7	NDUFA7	NDUFA7	1789	0.11	0.25	YES
19	NDUFB1	NDUFB1	NDUFB1	1811	0.11	0.26	YES
20	ATP5G1	ATP5G1	ATP5G1	1828	0.11	0.27	YES
21	NDUFA3	NDUFA3	NDUFA3	1850	0.11	0.28	YES
22	NDUFB4	NDUFB4	NDUFB4	1875	0.11	0.29	YES
23	ATP6V1D	ATP6V1D	ATP6V1D	1922	0.11	0.3	YES
24	COX6A1	COX6A1	COX6A1	1945	0.11	0.31	YES
25	ATP6V1B2	ATP6V1B2	ATP6V1B2	1959	0.11	0.32	YES
26	COX5A	COX5A	COX5A	1995	0.1	0.33	YES
27	NDUFV3	NDUFV3	NDUFV3	2013	0.1	0.34	YES
28	LHPP	LHPP	LHPP	2019	0.1	0.36	YES
29	NDUFS6	NDUFS6	NDUFS6	2093	0.1	0.36	YES
30	UQCR10	UQCR10	UQCR10	2251	0.096	0.36	YES
31	COX8A	COX8A	COX8A	2326	0.094	0.37	YES
32	ATP5B	ATP5B	ATP5B	2422	0.091	0.38	YES
33	NDUFS2	NDUFS2	NDUFS2	2593	0.086	0.38	YES
34	SDHB	SDHB	SDHB	2604	0.085	0.38	YES
35	ATP6V1E1	ATP6V1E1	ATP6V1E1	2621	0.085	0.39	YES
36	ATP5D	ATP5D	ATP5D	2637	0.084	0.4	YES
37	COX5B	COX5B	COX5B	2731	0.081	0.41	YES
38	ATP6V0E2	ATP6V0E2	ATP6V0E2	2733	0.081	0.42	YES
39	NDUFB10	NDUFB10	NDUFB10	2762	0.08	0.42	YES
40	NDUFC2	NDUFC2	NDUFC2	2804	0.079	0.43	YES
41	ATP5H	ATP5H	ATP5H	2819	0.079	0.44	YES
42	COX6B1	COX6B1	COX6B1	2935	0.076	0.44	YES
43	CYC1	CYC1	CYC1	2968	0.075	0.44	YES
44	NDUFS3	NDUFS3	NDUFS3	3106	0.071	0.45	YES
45	NDUFB8	NDUFB8	NDUFB8	3211	0.069	0.45	YES
46	NDUFA9	NDUFA9	NDUFA9	3290	0.067	0.45	YES
47	NDUFA11	NDUFA11	NDUFA11	3335	0.066	0.46	YES
48	UQCRQ	UQCRQ	UQCRQ	3446	0.063	0.46	YES
49	NDUFA6	NDUFA6	NDUFA6	3480	0.062	0.46	YES
50	ATP6V1E2	ATP6V1E2	ATP6V1E2	3584	0.06	0.46	YES
51	ATP5G3	ATP5G3	ATP5G3	3591	0.06	0.47	YES
52	SDHC	SDHC	SDHC	3604	0.059	0.48	YES
53	COX8C	COX8C	COX8C	3607	0.059	0.48	YES
54	UQCRFS1	UQCRFS1	UQCRFS1	3695	0.057	0.48	YES
55	COX7A2	COX7A2	COX7A2	3748	0.056	0.49	YES
56	ATP5I	ATP5I	ATP5I	3760	0.056	0.49	YES
57	ATP6V1H	ATP6V1H	ATP6V1H	3808	0.054	0.5	YES
58	COX15	COX15	COX15	3923	0.052	0.49	YES
59	NDUFA1	NDUFA1	NDUFA1	3925	0.052	0.5	YES
60	ATP5G2	ATP5G2	ATP5G2	3929	0.052	0.51	YES
61	ATP6V1G1	ATP6V1G1	ATP6V1G1	4183	0.047	0.5	YES
62	ATP6V1C1	ATP6V1C1	ATP6V1C1	4254	0.045	0.5	YES
63	NDUFB2	NDUFB2	NDUFB2	4276	0.045	0.5	YES
64	NDUFA2	NDUFA2	NDUFA2	4307	0.044	0.5	YES
65	NDUFB9	NDUFB9	NDUFB9	4343	0.044	0.51	YES
66	NDUFS5	NDUFS5	NDUFS5	4378	0.043	0.51	YES
67	NDUFV2	NDUFV2	NDUFV2	4452	0.041	0.51	YES
68	COX17	COX17	COX17	4461	0.041	0.52	YES
69	COX7A2L	COX7A2L	COX7A2L	4485	0.041	0.52	YES
70	TCIRG1	TCIRG1	TCIRG1	4511	0.04	0.52	YES
71	ATP5J2	ATP5J2	ATP5J2	4667	0.037	0.52	NO
72	COX6C	COX6C	COX6C	4732	0.036	0.52	NO
73	ATP6V0E1	ATP6V0E1	ATP6V0E1	4890	0.033	0.51	NO
74	NDUFA10	NDUFA10	NDUFA10	4996	0.031	0.51	NO
75	NDUFS1	NDUFS1	NDUFS1	5060	0.03	0.51	NO
76	NDUFAB1	NDUFAB1	NDUFAB1	5100	0.029	0.51	NO
77	COX4I1	COX4I1	COX4I1	5112	0.029	0.51	NO
78	ATP5J	ATP5J	ATP5J	5145	0.028	0.52	NO
79	NDUFC1	NDUFC1	NDUFC1	5206	0.027	0.52	NO
80	COX10	COX10	COX10	5384	0.023	0.51	NO
81	UQCR11	UQCR11	UQCR11	5446	0.022	0.51	NO
82	UQCRHL	UQCRHL	UQCRHL	5513	0.021	0.5	NO
83	UQCRH	UQCRH	UQCRH	5542	0.02	0.51	NO
84	ATP5A1	ATP5A1	ATP5A1	5577	0.02	0.51	NO
85	PPA2	PPA2	PPA2	5742	0.016	0.5	NO
86	NDUFB3	NDUFB3	NDUFB3	5816	0.015	0.5	NO
87	COX7C	COX7C	COX7C	5877	0.014	0.49	NO
88	ATP5C1	ATP5C1	ATP5C1	5917	0.013	0.49	NO
89	ATP5O	ATP5O	ATP5O	6259	0.006	0.48	NO
90	NDUFB6	NDUFB6	NDUFB6	6402	0.0031	0.47	NO
91	UQCRB	UQCRB	UQCRB	6467	0.0016	0.46	NO
92	ATP6V1A	ATP6V1A	ATP6V1A	6636	-0.0024	0.46	NO
93	ATP5F1	ATP5F1	ATP5F1	6936	-0.0086	0.44	NO
94	ATP4A	ATP4A	ATP4A	7071	-0.011	0.43	NO
95	ATP5E	ATP5E	ATP5E	7097	-0.012	0.43	NO
96	UQCRC2	UQCRC2	UQCRC2	7256	-0.016	0.43	NO
97	NDUFB5	NDUFB5	NDUFB5	7397	-0.018	0.42	NO
98	ATP5L	ATP5L	ATP5L	7423	-0.019	0.42	NO
99	NDUFA4	NDUFA4	NDUFA4	7472	-0.02	0.42	NO
100	COX7B	COX7B	COX7B	7610	-0.023	0.42	NO
101	COX6B2	COX6B2	COX6B2	7895	-0.029	0.4	NO
102	COX4I2	COX4I2	COX4I2	8358	-0.04	0.38	NO
103	ATP6V0A2	ATP6V0A2	ATP6V0A2	8947	-0.054	0.36	NO
104	COX11	COX11	COX11	9430	-0.065	0.34	NO
105	NDUFS4	NDUFS4	NDUFS4	9608	-0.07	0.33	NO
106	NDUFA5	NDUFA5	NDUFA5	9729	-0.073	0.34	NO
107	ATP6V1C2	ATP6V1C2	ATP6V1C2	10258	-0.085	0.32	NO
108	NDUFA4L2	NDUFA4L2	NDUFA4L2	10957	-0.1	0.29	NO
109	PPA1	PPA1	PPA1	11161	-0.11	0.29	NO
110	ATP6V1G2	ATP6V1G2	ATP6V1G2	11468	-0.12	0.28	NO
111	ATP6V1B1	ATP6V1B1	ATP6V1B1	11492	-0.12	0.3	NO
112	SDHD	SDHD	SDHD	11602	-0.12	0.3	NO
113	COX7A1	COX7A1	COX7A1	13044	-0.16	0.24	NO
114	ATP4B	ATP4B	ATP4B	16794	-0.34	0.07	NO

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

Figure S4. 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 OXIDATIVE PHOSPHORYLATION

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	PDK2	PDK2	PDK2	985	0.16	-0.033	YES
2	ACO2	ACO2	ACO2	1111	0.15	-0.02	YES
3	NDUFS8	NDUFS8	NDUFS8	1261	0.14	-0.009	YES
4	UQCRC1	UQCRC1	UQCRC1	1307	0.14	0.0071	YES
5	SDHA	SDHA	SDHA	1330	0.14	0.024	YES
6	NDUFS7	NDUFS7	NDUFS7	1490	0.13	0.033	YES
7	NDUFA8	NDUFA8	NDUFA8	1529	0.13	0.047	YES
8	NDUFV1	NDUFV1	NDUFV1	1720	0.12	0.052	YES
9	NDUFB7	NDUFB7	NDUFB7	1722	0.12	0.068	YES
10	IDH3G	IDH3G	IDH3G	1742	0.12	0.082	YES
11	FH	FH	FH	1757	0.11	0.096	YES
12	NDUFA7	NDUFA7	NDUFA7	1789	0.11	0.11	YES
13	NDUFB1	NDUFB1	NDUFB1	1811	0.11	0.12	YES
14	ATP5G1	ATP5G1	ATP5G1	1828	0.11	0.14	YES
15	NDUFA3	NDUFA3	NDUFA3	1850	0.11	0.15	YES
16	NDUFB4	NDUFB4	NDUFB4	1875	0.11	0.16	YES
17	COX6A1	COX6A1	COX6A1	1945	0.11	0.17	YES
18	COX5A	COX5A	COX5A	1995	0.1	0.18	YES
19	NDUFV3	NDUFV3	NDUFV3	2013	0.1	0.2	YES
20	NDUFS6	NDUFS6	NDUFS6	2093	0.1	0.21	YES
21	COX8A	COX8A	COX8A	2326	0.094	0.21	YES
22	OGDH	OGDH	OGDH	2329	0.094	0.22	YES
23	ATP5B	ATP5B	ATP5B	2422	0.091	0.23	YES
24	DLST	DLST	DLST	2435	0.09	0.24	YES
25	SLC16A3	SLC16A3	SLC16A3	2517	0.088	0.24	YES
26	NDUFS2	NDUFS2	NDUFS2	2593	0.086	0.25	YES
27	SDHB	SDHB	SDHB	2604	0.085	0.26	YES
28	ATP5D	ATP5D	ATP5D	2637	0.084	0.27	YES
29	MDH2	MDH2	MDH2	2641	0.084	0.28	YES
30	COX5B	COX5B	COX5B	2731	0.081	0.29	YES
31	NDUFB10	NDUFB10	NDUFB10	2762	0.08	0.3	YES
32	NDUFC2	NDUFC2	NDUFC2	2804	0.079	0.3	YES
33	BSG	BSG	BSG	2813	0.079	0.32	YES
34	ATP5H	ATP5H	ATP5H	2819	0.079	0.33	YES
35	PDK3	PDK3	PDK3	2865	0.078	0.33	YES
36	NDUFA13	NDUFA13	NDUFA13	2879	0.077	0.34	YES
37	COX6B1	COX6B1	COX6B1	2935	0.076	0.35	YES
38	CYC1	CYC1	CYC1	2968	0.075	0.36	YES
39	IDH1	IDH1	IDH1	3071	0.072	0.36	YES
40	NDUFS3	NDUFS3	NDUFS3	3106	0.071	0.37	YES
41	NDUFB8	NDUFB8	NDUFB8	3211	0.069	0.37	YES
42	CS	CS	CS	3267	0.067	0.38	YES
43	NDUFA9	NDUFA9	NDUFA9	3290	0.067	0.39	YES
44	NDUFA11	NDUFA11	NDUFA11	3335	0.066	0.39	YES
45	UQCRQ	UQCRQ	UQCRQ	3446	0.063	0.4	YES
46	SUCLG1	SUCLG1	SUCLG1	3465	0.062	0.4	YES
47	NDUFA6	NDUFA6	NDUFA6	3480	0.062	0.41	YES
48	ADHFE1	ADHFE1	ADHFE1	3517	0.061	0.42	YES
49	SDHC	SDHC	SDHC	3604	0.059	0.42	YES
50	UQCRFS1	UQCRFS1	UQCRFS1	3695	0.057	0.42	YES
51	ATP5I	ATP5I	ATP5I	3760	0.056	0.42	YES
52	NDUFA1	NDUFA1	NDUFA1	3925	0.052	0.42	YES
53	LDHA	LDHA	LDHA	3992	0.05	0.43	YES
54	IDH3B	IDH3B	IDH3B	4021	0.05	0.43	YES
55	PDP2	PDP2	PDP2	4039	0.05	0.44	YES
56	PDP1	PDP1	PDP1	4088	0.048	0.44	YES
57	PDHA1	PDHA1	PDHA1	4203	0.046	0.44	YES
58	NDUFB2	NDUFB2	NDUFB2	4276	0.045	0.44	YES
59	NDUFA2	NDUFA2	NDUFA2	4307	0.044	0.45	YES
60	NDUFB9	NDUFB9	NDUFB9	4343	0.044	0.45	YES
61	NDUFS5	NDUFS5	NDUFS5	4378	0.043	0.45	YES
62	NDUFV2	NDUFV2	NDUFV2	4452	0.041	0.46	YES
63	COX7A2L	COX7A2L	COX7A2L	4485	0.041	0.46	YES
64	ATP5J2	ATP5J2	ATP5J2	4667	0.037	0.45	YES
65	COX6C	COX6C	COX6C	4732	0.036	0.46	YES
66	NNT	NNT	NNT	4888	0.033	0.45	YES
67	IDH3A	IDH3A	IDH3A	4915	0.033	0.45	YES
68	NDUFA10	NDUFA10	NDUFA10	4996	0.031	0.45	YES
69	NDUFS1	NDUFS1	NDUFS1	5060	0.03	0.45	YES
70	NDUFAB1	NDUFAB1	NDUFAB1	5100	0.029	0.46	YES
71	COX4I1	COX4I1	COX4I1	5112	0.029	0.46	YES
72	ATP5J	ATP5J	ATP5J	5145	0.028	0.46	YES
73	NDUFA12	NDUFA12	NDUFA12	5187	0.027	0.46	YES
74	NDUFC1	NDUFC1	NDUFC1	5206	0.027	0.46	YES
75	UQCR11	UQCR11	UQCR11	5446	0.022	0.45	NO
76	UQCRHL	UQCRHL	UQCRHL	5513	0.021	0.45	NO
77	UQCRH	UQCRH	UQCRH	5542	0.02	0.45	NO
78	ATP5A1	ATP5A1	ATP5A1	5577	0.02	0.46	NO
79	LDHB	LDHB	LDHB	5683	0.017	0.45	NO
80	NDUFB3	NDUFB3	NDUFB3	5816	0.015	0.45	NO
81	PDHB	PDHB	PDHB	5822	0.015	0.45	NO
82	COX7C	COX7C	COX7C	5877	0.014	0.45	NO
83	ATP5C1	ATP5C1	ATP5C1	5917	0.013	0.45	NO
84	L2HGDH	L2HGDH	L2HGDH	5944	0.012	0.45	NO
85	ETFB	ETFB	ETFB	5979	0.011	0.45	NO
86	CYCS	CYCS	CYCS	6146	0.0083	0.44	NO
87	PDPR	PDPR	PDPR	6244	0.0063	0.43	NO
88	ATP5O	ATP5O	ATP5O	6259	0.006	0.43	NO
89	NDUFB6	NDUFB6	NDUFB6	6402	0.0031	0.42	NO
90	UQCRB	UQCRB	UQCRB	6467	0.0016	0.42	NO
91	DLD	DLD	DLD	6664	-0.003	0.41	NO
92	ETFDH	ETFDH	ETFDH	6748	-0.0047	0.41	NO
93	ETFA	ETFA	ETFA	6757	-0.0049	0.41	NO
94	IDH2	IDH2	IDH2	6874	-0.0073	0.4	NO
95	ATP5F1	ATP5F1	ATP5F1	6936	-0.0086	0.4	NO
96	SUCLG2	SUCLG2	SUCLG2	6973	-0.0094	0.4	NO
97	ATP5E	ATP5E	ATP5E	7097	-0.012	0.39	NO
98	SLC16A1	SLC16A1	SLC16A1	7246	-0.015	0.39	NO
99	UQCRC2	UQCRC2	UQCRC2	7256	-0.016	0.39	NO
100	NDUFB5	NDUFB5	NDUFB5	7397	-0.018	0.38	NO
101	ATP5L	ATP5L	ATP5L	7423	-0.019	0.38	NO
102	NDUFA4	NDUFA4	NDUFA4	7472	-0.02	0.38	NO
103	COX7B	COX7B	COX7B	7610	-0.023	0.38	NO
104	DLAT	DLAT	DLAT	7701	-0.025	0.38	NO
105	D2HGDH	D2HGDH	D2HGDH	7940	-0.03	0.37	NO
106	PDHX	PDHX	PDHX	9166	-0.059	0.31	NO
107	NDUFS4	NDUFS4	NDUFS4	9608	-0.07	0.29	NO
108	NDUFA5	NDUFA5	NDUFA5	9729	-0.073	0.3	NO
109	SLC16A8	SLC16A8	SLC16A8	10385	-0.089	0.27	NO
110	SUCLA2	SUCLA2	SUCLA2	10898	-0.1	0.26	NO
111	SDHD	SDHD	SDHD	11602	-0.12	0.23	NO
112	UCP2	UCP2	UCP2	12335	-0.14	0.21	NO
113	PDK1	PDK1	PDK1	14394	-0.21	0.12	NO
114	PDK4	PDK4	PDK4	15628	-0.27	0.091	NO
115	UCP3	UCP3	UCP3	16602	-0.33	0.08	NO

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

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

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

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	ARSG	ARSG	ARSG	40	0.52	0.041	YES
2	ATP6V0D2	ATP6V0D2	ATP6V0D2	102	0.42	0.072	YES
3	ATP6V0A4	ATP6V0A4	ATP6V0A4	104	0.42	0.11	YES
4	CTSL2	CTSL2	CTSL2	128	0.4	0.14	YES
5	GBA	GBA	GBA	560	0.22	0.13	YES
6	CTSF	CTSF	CTSF	733	0.19	0.14	YES
7	NAGLU	NAGLU	NAGLU	785	0.19	0.15	YES
8	ATP6V0A1	ATP6V0A1	ATP6V0A1	865	0.18	0.16	YES
9	PLA2G15	PLA2G15	PLA2G15	880	0.18	0.18	YES
10	CTSD	CTSD	CTSD	958	0.17	0.19	YES
11	ATP6V0C	ATP6V0C	ATP6V0C	1046	0.16	0.19	YES
12	ATP6AP1	ATP6AP1	ATP6AP1	1052	0.16	0.21	YES
13	CTNS	CTNS	CTNS	1071	0.16	0.22	YES
14	CTSH	CTSH	CTSH	1088	0.16	0.23	YES
15	PPT2	PPT2	PPT2	1147	0.15	0.24	YES
16	GLA	GLA	GLA	1152	0.15	0.25	YES
17	NPC1	NPC1	NPC1	1163	0.15	0.26	YES
18	MCOLN1	MCOLN1	MCOLN1	1199	0.15	0.28	YES
19	SORT1	SORT1	SORT1	1216	0.15	0.29	YES
20	GM2A	GM2A	GM2A	1227	0.15	0.3	YES
21	SMPD1	SMPD1	SMPD1	1252	0.14	0.31	YES
22	AP3B2	AP3B2	AP3B2	1339	0.14	0.32	YES
23	CTSK	CTSK	CTSK	1366	0.14	0.32	YES
24	ATP6V0B	ATP6V0B	ATP6V0B	1399	0.13	0.33	YES
25	ATP6V0D1	ATP6V0D1	ATP6V0D1	1523	0.13	0.34	YES
26	CTSA	CTSA	CTSA	1533	0.13	0.35	YES
27	ASAH1	ASAH1	ASAH1	1536	0.13	0.36	YES
28	HEXA	HEXA	HEXA	1577	0.12	0.37	YES
29	DNASE2B	DNASE2B	DNASE2B	1690	0.12	0.37	YES
30	CTSZ	CTSZ	CTSZ	1836	0.11	0.37	YES
31	NEU1	NEU1	NEU1	1843	0.11	0.38	YES
32	NAGA	NAGA	NAGA	1878	0.11	0.39	YES
33	CD63	CD63	CD63	1934	0.11	0.39	YES
34	GLB1	GLB1	GLB1	1953	0.11	0.4	YES
35	AP1S3	AP1S3	AP1S3	2111	0.1	0.4	YES
36	NAGPA	NAGPA	NAGPA	2147	0.099	0.41	YES
37	CLN3	CLN3	CLN3	2256	0.096	0.41	YES
38	ARSA	ARSA	ARSA	2314	0.094	0.41	YES
39	ACP5	ACP5	ACP5	2322	0.094	0.42	YES
40	GGA1	GGA1	GGA1	2330	0.094	0.43	YES
41	ABCB9	ABCB9	ABCB9	2442	0.09	0.43	YES
42	TPP1	TPP1	TPP1	2461	0.09	0.44	YES
43	CTSB	CTSB	CTSB	2531	0.087	0.44	YES
44	AP1M1	AP1M1	AP1M1	2555	0.087	0.44	YES
45	AP1M2	AP1M2	AP1M2	2693	0.082	0.44	YES
46	CTSL1	CTSL1	CTSL1	2870	0.077	0.44	YES
47	NPC2	NPC2	NPC2	2892	0.077	0.45	YES
48	IGF2R	IGF2R	IGF2R	2905	0.076	0.45	YES
49	SGSH	SGSH	SGSH	2922	0.076	0.46	YES
50	PSAP	PSAP	PSAP	3099	0.071	0.45	YES
51	ENTPD4	ENTPD4	ENTPD4	3109	0.071	0.46	YES
52	AP1S1	AP1S1	AP1S1	3115	0.071	0.46	YES
53	M6PR	M6PR	M6PR	3173	0.07	0.47	YES
54	GNPTG	GNPTG	GNPTG	3294	0.067	0.46	YES
55	AP3D1	AP3D1	AP3D1	3300	0.067	0.47	YES
56	DNASE2	DNASE2	DNASE2	3313	0.066	0.48	YES
57	GGA3	GGA3	GGA3	3403	0.064	0.48	YES
58	AP3S2	AP3S2	AP3S2	3437	0.063	0.48	YES
59	CLTB	CLTB	CLTB	3691	0.057	0.47	NO
60	ATP6V1H	ATP6V1H	ATP6V1H	3808	0.054	0.47	NO
61	CD68	CD68	CD68	4074	0.049	0.46	NO
62	AP1B1	AP1B1	AP1B1	4076	0.049	0.46	NO
63	AGA	AGA	AGA	4099	0.048	0.46	NO
64	LAMP1	LAMP1	LAMP1	4132	0.048	0.47	NO
65	SUMF1	SUMF1	SUMF1	4198	0.046	0.47	NO
66	AP3M2	AP3M2	AP3M2	4233	0.046	0.47	NO
67	HGSNAT	HGSNAT	HGSNAT	4238	0.046	0.47	NO
68	MAN2B1	MAN2B1	MAN2B1	4292	0.045	0.47	NO
69	GGA2	GGA2	GGA2	4329	0.044	0.47	NO
70	TCIRG1	TCIRG1	TCIRG1	4511	0.04	0.47	NO
71	CLTCL1	CLTCL1	CLTCL1	4569	0.039	0.47	NO
72	LAPTM4B	LAPTM4B	LAPTM4B	4718	0.036	0.46	NO
73	GALNS	GALNS	GALNS	4739	0.036	0.46	NO
74	GUSB	GUSB	GUSB	4801	0.035	0.46	NO
75	SLC11A1	SLC11A1	SLC11A1	4860	0.034	0.46	NO
76	LAMP2	LAMP2	LAMP2	4900	0.033	0.46	NO
77	SLC11A2	SLC11A2	SLC11A2	4981	0.031	0.46	NO
78	GNPTAB	GNPTAB	GNPTAB	5215	0.027	0.45	NO
79	ABCA2	ABCA2	ABCA2	5236	0.026	0.45	NO
80	AP4M1	AP4M1	AP4M1	5274	0.026	0.45	NO
81	GNS	GNS	GNS	5325	0.024	0.45	NO
82	CTSG	CTSG	CTSG	5536	0.02	0.44	NO
83	HEXB	HEXB	HEXB	5657	0.018	0.44	NO
84	GAA	GAA	GAA	5714	0.017	0.43	NO
85	SLC17A5	SLC17A5	SLC17A5	5932	0.012	0.42	NO
86	CLTC	CLTC	CLTC	5959	0.012	0.42	NO
87	AP3M1	AP3M1	AP3M1	6209	0.0071	0.41	NO
88	FUCA1	FUCA1	FUCA1	6317	0.0049	0.4	NO
89	LIPA	LIPA	LIPA	6662	-0.003	0.38	NO
90	LAPTM4A	LAPTM4A	LAPTM4A	6753	-0.0049	0.38	NO
91	CLTA	CLTA	CLTA	6862	-0.0071	0.38	NO
92	ACP2	ACP2	ACP2	7101	-0.012	0.36	NO
93	PPT1	PPT1	PPT1	7469	-0.02	0.34	NO
94	IDUA	IDUA	IDUA	7518	-0.021	0.34	NO
95	LGMN	LGMN	LGMN	7606	-0.023	0.34	NO
96	ARSB	ARSB	ARSB	7653	-0.024	0.34	NO
97	AP1G1	AP1G1	AP1G1	8193	-0.036	0.31	NO
98	SCARB2	SCARB2	SCARB2	8485	-0.044	0.3	NO
99	AP3S1	AP3S1	AP3S1	8534	-0.045	0.3	NO
100	AP4S1	AP4S1	AP4S1	8765	-0.05	0.29	NO
101	IDS	IDS	IDS	8788	-0.051	0.3	NO
102	ATP6V0A2	ATP6V0A2	ATP6V0A2	8947	-0.054	0.29	NO
103	AP4B1	AP4B1	AP4B1	9349	-0.063	0.27	NO
104	AP3B1	AP3B1	AP3B1	9710	-0.072	0.26	NO
105	CLN5	CLN5	CLN5	9941	-0.078	0.25	NO
106	AP1S2	AP1S2	AP1S2	10340	-0.088	0.24	NO
107	MANBA	MANBA	MANBA	10790	-0.099	0.22	NO
108	CD164	CD164	CD164	11334	-0.11	0.2	NO
109	CTSE	CTSE	CTSE	11351	-0.11	0.21	NO
110	AP4E1	AP4E1	AP4E1	11574	-0.12	0.21	NO
111	NAPSA	NAPSA	NAPSA	11670	-0.12	0.21	NO
112	HYAL1	HYAL1	HYAL1	12634	-0.15	0.17	NO
113	CTSO	CTSO	CTSO	12734	-0.15	0.18	NO
114	GALC	GALC	GALC	13474	-0.18	0.15	NO
115	MFSD8	MFSD8	MFSD8	13671	-0.18	0.16	NO
116	CTSC	CTSC	CTSC	13829	-0.19	0.16	NO
117	CTSS	CTSS	CTSS	14093	-0.2	0.16	NO
118	LAPTM5	LAPTM5	LAPTM5	14623	-0.22	0.15	NO
119	CTSW	CTSW	CTSW	14776	-0.23	0.16	NO
120	LAMP3	LAMP3	LAMP3	14953	-0.24	0.17	NO

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

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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	SAMM50	SAMM50	SAMM50	588	0.22	0.03	YES
2	TIMM50	TIMM50	TIMM50	889	0.17	0.063	YES
3	SLC25A4	SLC25A4	SLC25A4	1022	0.16	0.1	YES
4	LDHD	LDHD	LDHD	1049	0.16	0.15	YES
5	ACO2	ACO2	ACO2	1111	0.15	0.19	YES
6	MTX1	MTX1	MTX1	1430	0.13	0.21	YES
7	IDH3G	IDH3G	IDH3G	1742	0.12	0.22	YES
8	ATP5G1	ATP5G1	ATP5G1	1828	0.11	0.25	YES
9	PMPCA	PMPCA	PMPCA	2035	0.1	0.27	YES
10	FXN	FXN	FXN	2202	0.097	0.28	YES
11	ATP5B	ATP5B	ATP5B	2422	0.091	0.3	YES
12	VDAC1	VDAC1	VDAC1	2447	0.09	0.32	YES
13	SLC25A13	SLC25A13	SLC25A13	2502	0.088	0.34	YES
14	TOMM40	TOMM40	TOMM40	2598	0.086	0.36	YES
15	CYC1	CYC1	CYC1	2968	0.075	0.36	YES
16	GRPEL1	GRPEL1	GRPEL1	2969	0.075	0.39	YES
17	COQ2	COQ2	COQ2	3032	0.073	0.4	YES
18	CS	CS	CS	3267	0.067	0.41	YES
19	TOMM7	TOMM7	TOMM7	3386	0.065	0.42	YES
20	CHCHD4	CHCHD4	CHCHD4	3399	0.064	0.44	YES
21	BCS1L	BCS1L	BCS1L	3508	0.062	0.45	YES
22	TIMM44	TIMM44	TIMM44	3670	0.058	0.46	YES
23	TIMM10	TIMM10	TIMM10	3865	0.053	0.46	YES
24	TIMM13	TIMM13	TIMM13	3890	0.053	0.48	YES
25	SLC25A6	SLC25A6	SLC25A6	3951	0.051	0.49	YES
26	TAZ	TAZ	TAZ	4063	0.049	0.5	YES
27	COX17	COX17	COX17	4461	0.041	0.48	YES
28	TIMM17B	TIMM17B	TIMM17B	4516	0.04	0.49	YES
29	TIMM22	TIMM22	TIMM22	4698	0.036	0.49	YES
30	HSPA9	HSPA9	HSPA9	4710	0.036	0.5	YES
31	GFER	GFER	GFER	5271	0.026	0.48	NO
32	ATP5A1	ATP5A1	ATP5A1	5577	0.02	0.47	NO
33	TOMM22	TOMM22	TOMM22	5757	0.016	0.46	NO
34	TIMM17A	TIMM17A	TIMM17A	6355	0.0042	0.43	NO
35	TOMM5	TOMM5	TOMM5	6681	-0.0034	0.41	NO
36	TIMM8A	TIMM8A	TIMM8A	6919	-0.0083	0.4	NO
37	FXC1	FXC1	FXC1	7000	-0.01	0.4	NO
38	HSPD1	HSPD1	HSPD1	7154	-0.013	0.4	NO
39	TIMM9	TIMM9	TIMM9	7235	-0.015	0.4	NO
40	C18orf55	C18orf55	C18orf55	7372	-0.018	0.39	NO
41	TOMM20	TOMM20	TOMM20	8162	-0.035	0.36	NO
42	MTX2	MTX2	MTX2	8335	-0.04	0.36	NO
43	TOMM70A	TOMM70A	TOMM70A	8873	-0.053	0.35	NO
44	DNAJC19	DNAJC19	DNAJC19	9020	-0.056	0.36	NO
45	TIMM8B	TIMM8B	TIMM8B	9377	-0.064	0.35	NO
46	PMPCB	PMPCB	PMPCB	9450	-0.066	0.37	NO
47	SLC25A12	SLC25A12	SLC25A12	10539	-0.093	0.33	NO
48	HSCB	HSCB	HSCB	11099	-0.11	0.33	NO
49	GRPEL2	GRPEL2	GRPEL2	13637	-0.18	0.24	NO

Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG BASE EXCISION REPAIR

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	NDUFS8	NDUFS8	NDUFS8	1261	0.14	-0.034	YES
2	UQCRC1	UQCRC1	UQCRC1	1307	0.14	-0.0018	YES
3	SDHA	SDHA	SDHA	1330	0.14	0.032	YES
4	NDUFS7	NDUFS7	NDUFS7	1490	0.13	0.055	YES
5	NDUFA8	NDUFA8	NDUFA8	1529	0.13	0.085	YES
6	NDUFV1	NDUFV1	NDUFV1	1720	0.12	0.1	YES
7	NDUFB7	NDUFB7	NDUFB7	1722	0.12	0.13	YES
8	NDUFA7	NDUFA7	NDUFA7	1789	0.11	0.16	YES
9	NDUFB1	NDUFB1	NDUFB1	1811	0.11	0.18	YES
10	NDUFA3	NDUFA3	NDUFA3	1850	0.11	0.21	YES
11	NDUFB4	NDUFB4	NDUFB4	1875	0.11	0.24	YES
12	COX6A1	COX6A1	COX6A1	1945	0.11	0.26	YES
13	COX5A	COX5A	COX5A	1995	0.1	0.28	YES
14	NDUFV3	NDUFV3	NDUFV3	2013	0.1	0.31	YES
15	NDUFS6	NDUFS6	NDUFS6	2093	0.1	0.33	YES
16	COX8A	COX8A	COX8A	2326	0.094	0.34	YES
17	NDUFS2	NDUFS2	NDUFS2	2593	0.086	0.34	YES
18	SDHB	SDHB	SDHB	2604	0.085	0.36	YES
19	COX5B	COX5B	COX5B	2731	0.081	0.38	YES
20	NDUFB10	NDUFB10	NDUFB10	2762	0.08	0.4	YES
21	NDUFC2	NDUFC2	NDUFC2	2804	0.079	0.41	YES
22	NDUFA13	NDUFA13	NDUFA13	2879	0.077	0.43	YES
23	COX6B1	COX6B1	COX6B1	2935	0.076	0.44	YES
24	CYC1	CYC1	CYC1	2968	0.075	0.46	YES
25	NDUFS3	NDUFS3	NDUFS3	3106	0.071	0.47	YES
26	NDUFB8	NDUFB8	NDUFB8	3211	0.069	0.48	YES
27	NDUFA9	NDUFA9	NDUFA9	3290	0.067	0.5	YES
28	NDUFA11	NDUFA11	NDUFA11	3335	0.066	0.51	YES
29	UQCRQ	UQCRQ	UQCRQ	3446	0.063	0.52	YES
30	NDUFA6	NDUFA6	NDUFA6	3480	0.062	0.53	YES
31	SDHC	SDHC	SDHC	3604	0.059	0.54	YES
32	UQCRFS1	UQCRFS1	UQCRFS1	3695	0.057	0.55	YES
33	NDUFA1	NDUFA1	NDUFA1	3925	0.052	0.55	YES
34	NDUFB2	NDUFB2	NDUFB2	4276	0.045	0.54	YES
35	NDUFA2	NDUFA2	NDUFA2	4307	0.044	0.55	YES
36	NDUFB9	NDUFB9	NDUFB9	4343	0.044	0.56	YES
37	NDUFS5	NDUFS5	NDUFS5	4378	0.043	0.57	YES
38	NDUFV2	NDUFV2	NDUFV2	4452	0.041	0.58	YES
39	COX7A2L	COX7A2L	COX7A2L	4485	0.041	0.58	YES
40	COX6C	COX6C	COX6C	4732	0.036	0.58	YES
41	NDUFA10	NDUFA10	NDUFA10	4996	0.031	0.57	YES
42	NDUFS1	NDUFS1	NDUFS1	5060	0.03	0.58	YES
43	NDUFAB1	NDUFAB1	NDUFAB1	5100	0.029	0.58	YES
44	COX4I1	COX4I1	COX4I1	5112	0.029	0.59	YES
45	NDUFA12	NDUFA12	NDUFA12	5187	0.027	0.59	YES
46	NDUFC1	NDUFC1	NDUFC1	5206	0.027	0.6	YES
47	UQCR11	UQCR11	UQCR11	5446	0.022	0.59	NO
48	UQCRHL	UQCRHL	UQCRHL	5513	0.021	0.59	NO
49	UQCRH	UQCRH	UQCRH	5542	0.02	0.59	NO
50	NDUFB3	NDUFB3	NDUFB3	5816	0.015	0.58	NO
51	COX7C	COX7C	COX7C	5877	0.014	0.58	NO
52	ETFB	ETFB	ETFB	5979	0.011	0.58	NO
53	CYCS	CYCS	CYCS	6146	0.0083	0.57	NO
54	NDUFB6	NDUFB6	NDUFB6	6402	0.0031	0.56	NO
55	UQCRB	UQCRB	UQCRB	6467	0.0016	0.56	NO
56	ETFDH	ETFDH	ETFDH	6748	-0.0047	0.54	NO
57	ETFA	ETFA	ETFA	6757	-0.0049	0.54	NO
58	UQCRC2	UQCRC2	UQCRC2	7256	-0.016	0.52	NO
59	NDUFB5	NDUFB5	NDUFB5	7397	-0.018	0.52	NO
60	NDUFA4	NDUFA4	NDUFA4	7472	-0.02	0.52	NO
61	COX7B	COX7B	COX7B	7610	-0.023	0.51	NO
62	NDUFS4	NDUFS4	NDUFS4	9608	-0.07	0.42	NO
63	NDUFA5	NDUFA5	NDUFA5	9729	-0.073	0.43	NO
64	SDHD	SDHD	SDHD	11602	-0.12	0.36	NO

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

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

genes ES table in pathway: KEGG LYSOSOME

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	PDK2	PDK2	PDK2	985	0.16	0.002	YES
2	ACO2	ACO2	ACO2	1111	0.15	0.048	YES
3	SDHA	SDHA	SDHA	1330	0.14	0.084	YES
4	IDH3G	IDH3G	IDH3G	1742	0.12	0.1	YES
5	FH	FH	FH	1757	0.11	0.14	YES
6	OGDH	OGDH	OGDH	2329	0.094	0.14	YES
7	DLST	DLST	DLST	2435	0.09	0.16	YES
8	SLC16A3	SLC16A3	SLC16A3	2517	0.088	0.19	YES
9	SDHB	SDHB	SDHB	2604	0.085	0.22	YES
10	MDH2	MDH2	MDH2	2641	0.084	0.24	YES
11	BSG	BSG	BSG	2813	0.079	0.26	YES
12	PDK3	PDK3	PDK3	2865	0.078	0.28	YES
13	IDH1	IDH1	IDH1	3071	0.072	0.3	YES
14	CS	CS	CS	3267	0.067	0.31	YES
15	SUCLG1	SUCLG1	SUCLG1	3465	0.062	0.32	YES
16	ADHFE1	ADHFE1	ADHFE1	3517	0.061	0.34	YES
17	SDHC	SDHC	SDHC	3604	0.059	0.35	YES
18	LDHA	LDHA	LDHA	3992	0.05	0.35	YES
19	IDH3B	IDH3B	IDH3B	4021	0.05	0.36	YES
20	PDP2	PDP2	PDP2	4039	0.05	0.38	YES
21	PDP1	PDP1	PDP1	4088	0.048	0.4	YES
22	PDHA1	PDHA1	PDHA1	4203	0.046	0.4	YES
23	NNT	NNT	NNT	4888	0.033	0.38	NO
24	IDH3A	IDH3A	IDH3A	4915	0.033	0.39	NO
25	LDHB	LDHB	LDHB	5683	0.017	0.35	NO
26	PDHB	PDHB	PDHB	5822	0.015	0.35	NO
27	L2HGDH	L2HGDH	L2HGDH	5944	0.012	0.35	NO
28	PDPR	PDPR	PDPR	6244	0.0063	0.33	NO
29	DLD	DLD	DLD	6664	-0.003	0.31	NO
30	IDH2	IDH2	IDH2	6874	-0.0073	0.3	NO
31	SUCLG2	SUCLG2	SUCLG2	6973	-0.0094	0.3	NO
32	SLC16A1	SLC16A1	SLC16A1	7246	-0.015	0.29	NO
33	DLAT	DLAT	DLAT	7701	-0.025	0.27	NO
34	D2HGDH	D2HGDH	D2HGDH	7940	-0.03	0.27	NO
35	PDHX	PDHX	PDHX	9166	-0.059	0.22	NO
36	SLC16A8	SLC16A8	SLC16A8	10385	-0.089	0.18	NO
37	SUCLA2	SUCLA2	SUCLA2	10898	-0.1	0.19	NO
38	SDHD	SDHD	SDHD	11602	-0.12	0.19	NO
39	PDK1	PDK1	PDK1	14394	-0.21	0.11	NO
40	PDK4	PDK4	PDK4	15628	-0.27	0.13	NO

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

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

genes ES table in pathway: KEGG PARKINSONS DISEASE

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	NDUFS8	NDUFS8	NDUFS8	1261	0.14	-0.042	YES
2	UQCRC1	UQCRC1	UQCRC1	1307	0.14	-0.016	YES
3	SDHA	SDHA	SDHA	1330	0.14	0.01	YES
4	NDUFS7	NDUFS7	NDUFS7	1490	0.13	0.027	YES
5	NDUFA8	NDUFA8	NDUFA8	1529	0.13	0.05	YES
6	NDUFV1	NDUFV1	NDUFV1	1720	0.12	0.062	YES
7	NDUFB7	NDUFB7	NDUFB7	1722	0.12	0.086	YES
8	NDUFA7	NDUFA7	NDUFA7	1789	0.11	0.1	YES
9	NDUFB1	NDUFB1	NDUFB1	1811	0.11	0.12	YES
10	ATP5G1	ATP5G1	ATP5G1	1828	0.11	0.15	YES
11	NDUFA3	NDUFA3	NDUFA3	1850	0.11	0.17	YES
12	NDUFB4	NDUFB4	NDUFB4	1875	0.11	0.19	YES
13	COX6A1	COX6A1	COX6A1	1945	0.11	0.2	YES
14	COX5A	COX5A	COX5A	1995	0.1	0.22	YES
15	NDUFV3	NDUFV3	NDUFV3	2013	0.1	0.24	YES
16	NDUFS6	NDUFS6	NDUFS6	2093	0.1	0.26	YES
17	COX8A	COX8A	COX8A	2326	0.094	0.26	YES
18	ATP5B	ATP5B	ATP5B	2422	0.091	0.28	YES
19	NDUFS2	NDUFS2	NDUFS2	2593	0.086	0.28	YES
20	SDHB	SDHB	SDHB	2604	0.085	0.3	YES
21	ATP5D	ATP5D	ATP5D	2637	0.084	0.32	YES
22	COX5B	COX5B	COX5B	2731	0.081	0.33	YES
23	NDUFB10	NDUFB10	NDUFB10	2762	0.08	0.34	YES
24	NDUFC2	NDUFC2	NDUFC2	2804	0.079	0.36	YES
25	ATP5H	ATP5H	ATP5H	2819	0.079	0.37	YES
26	NDUFA13	NDUFA13	NDUFA13	2879	0.077	0.38	YES
27	COX6B1	COX6B1	COX6B1	2935	0.076	0.39	YES
28	CYC1	CYC1	CYC1	2968	0.075	0.41	YES
29	NDUFS3	NDUFS3	NDUFS3	3106	0.071	0.41	YES
30	NDUFB8	NDUFB8	NDUFB8	3211	0.069	0.42	YES
31	NDUFA9	NDUFA9	NDUFA9	3290	0.067	0.43	YES
32	NDUFA11	NDUFA11	NDUFA11	3335	0.066	0.44	YES
33	UQCRQ	UQCRQ	UQCRQ	3446	0.063	0.45	YES
34	NDUFA6	NDUFA6	NDUFA6	3480	0.062	0.46	YES
35	SDHC	SDHC	SDHC	3604	0.059	0.46	YES
36	UQCRFS1	UQCRFS1	UQCRFS1	3695	0.057	0.47	YES
37	ATP5I	ATP5I	ATP5I	3760	0.056	0.48	YES
38	NDUFA1	NDUFA1	NDUFA1	3925	0.052	0.48	YES
39	NDUFB2	NDUFB2	NDUFB2	4276	0.045	0.47	YES
40	NDUFA2	NDUFA2	NDUFA2	4307	0.044	0.47	YES
41	NDUFB9	NDUFB9	NDUFB9	4343	0.044	0.48	YES
42	NDUFS5	NDUFS5	NDUFS5	4378	0.043	0.49	YES
43	NDUFV2	NDUFV2	NDUFV2	4452	0.041	0.49	YES
44	COX7A2L	COX7A2L	COX7A2L	4485	0.041	0.5	YES
45	ATP5J2	ATP5J2	ATP5J2	4667	0.037	0.5	YES
46	COX6C	COX6C	COX6C	4732	0.036	0.5	YES
47	NDUFA10	NDUFA10	NDUFA10	4996	0.031	0.49	YES
48	NDUFS1	NDUFS1	NDUFS1	5060	0.03	0.49	YES
49	NDUFAB1	NDUFAB1	NDUFAB1	5100	0.029	0.5	YES
50	COX4I1	COX4I1	COX4I1	5112	0.029	0.5	YES
51	ATP5J	ATP5J	ATP5J	5145	0.028	0.5	YES
52	NDUFA12	NDUFA12	NDUFA12	5187	0.027	0.51	YES
53	NDUFC1	NDUFC1	NDUFC1	5206	0.027	0.51	YES
54	UQCR11	UQCR11	UQCR11	5446	0.022	0.5	NO
55	UQCRHL	UQCRHL	UQCRHL	5513	0.021	0.5	NO
56	UQCRH	UQCRH	UQCRH	5542	0.02	0.51	NO
57	ATP5A1	ATP5A1	ATP5A1	5577	0.02	0.51	NO
58	NDUFB3	NDUFB3	NDUFB3	5816	0.015	0.5	NO
59	COX7C	COX7C	COX7C	5877	0.014	0.5	NO
60	ATP5C1	ATP5C1	ATP5C1	5917	0.013	0.5	NO
61	ETFB	ETFB	ETFB	5979	0.011	0.5	NO
62	CYCS	CYCS	CYCS	6146	0.0083	0.49	NO
63	ATP5O	ATP5O	ATP5O	6259	0.006	0.48	NO
64	NDUFB6	NDUFB6	NDUFB6	6402	0.0031	0.48	NO
65	UQCRB	UQCRB	UQCRB	6467	0.0016	0.47	NO
66	ETFDH	ETFDH	ETFDH	6748	-0.0047	0.46	NO
67	ETFA	ETFA	ETFA	6757	-0.0049	0.46	NO
68	ATP5F1	ATP5F1	ATP5F1	6936	-0.0086	0.45	NO
69	ATP5E	ATP5E	ATP5E	7097	-0.012	0.44	NO
70	UQCRC2	UQCRC2	UQCRC2	7256	-0.016	0.44	NO
71	NDUFB5	NDUFB5	NDUFB5	7397	-0.018	0.44	NO
72	ATP5L	ATP5L	ATP5L	7423	-0.019	0.44	NO
73	NDUFA4	NDUFA4	NDUFA4	7472	-0.02	0.44	NO
74	COX7B	COX7B	COX7B	7610	-0.023	0.44	NO
75	NDUFS4	NDUFS4	NDUFS4	9608	-0.07	0.34	NO
76	NDUFA5	NDUFA5	NDUFA5	9729	-0.073	0.35	NO
77	SDHD	SDHD	SDHD	11602	-0.12	0.27	NO
78	UCP2	UCP2	UCP2	12335	-0.14	0.25	NO
79	UCP3	UCP3	UCP3	16602	-0.33	0.08	NO

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

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

genes ES table in pathway: PID MTOR 4PATHWAY

Table 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	PARS2	PARS2	PARS2	1014	0.16	0.011	YES
2	TARS2	TARS2	TARS2	1246	0.14	0.059	YES
3	LARS2	LARS2	LARS2	1930	0.11	0.066	YES
4	NARS2	NARS2	NARS2	1956	0.11	0.11	YES
5	SARS2	SARS2	SARS2	2040	0.1	0.15	YES
6	DARS2	DARS2	DARS2	2167	0.099	0.18	YES
7	AARS2	AARS2	AARS2	2232	0.096	0.22	YES
8	CARS2	CARS2	CARS2	2249	0.096	0.26	YES
9	VARS2	VARS2	VARS2	2615	0.085	0.27	YES
10	EARS2	EARS2	EARS2	2926	0.076	0.29	YES
11	MARS2	MARS2	MARS2	2998	0.074	0.31	YES
12	FARSA	FARSA	FARSA	3414	0.064	0.32	YES
13	VARS	VARS	VARS	3572	0.06	0.33	YES
14	QARS	QARS	QARS	3660	0.058	0.35	YES
15	YARS2	YARS2	YARS2	3751	0.056	0.37	YES
16	AARS	AARS	AARS	4097	0.048	0.37	YES
17	MTFMT	MTFMT	MTFMT	4380	0.043	0.37	YES
18	SARS	SARS	SARS	4529	0.04	0.38	YES
19	NARS	NARS	NARS	4929	0.032	0.37	YES
20	WARS	WARS	WARS	4999	0.031	0.38	YES
21	WARS2	WARS2	WARS2	5308	0.025	0.38	YES
22	IARS2	IARS2	IARS2	5432	0.022	0.38	YES
23	MARS	MARS	MARS	5519	0.021	0.38	YES
24	HARS2	HARS2	HARS2	5547	0.02	0.39	YES
25	YARS	YARS	YARS	5763	0.016	0.38	NO
26	FARS2	FARS2	FARS2	5798	0.015	0.39	NO
27	GARS	GARS	GARS	6055	0.01	0.38	NO
28	HARS	HARS	HARS	6307	0.0051	0.37	NO
29	CARS	CARS	CARS	6447	0.0022	0.36	NO
30	FARSB	FARSB	FARSB	6570	-0.00061	0.35	NO
31	IARS	IARS	IARS	7309	-0.017	0.32	NO
32	TARSL2	TARSL2	TARSL2	7428	-0.019	0.32	NO
33	EPRS	EPRS	EPRS	7544	-0.022	0.32	NO
34	RARS	RARS	RARS	7703	-0.025	0.32	NO
35	KARS	KARS	KARS	7767	-0.027	0.33	NO
36	TARS	TARS	TARS	7840	-0.028	0.34	NO
37	LARS	LARS	LARS	9005	-0.056	0.3	NO
38	PSTK	PSTK	PSTK	9275	-0.062	0.31	NO
39	DARS	DARS	DARS	10565	-0.093	0.28	NO
40	RARS2	RARS2	RARS2	11302	-0.11	0.28	NO
41	SEPSECS	SEPSECS	SEPSECS	14559	-0.22	0.19	NO

Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MTOR 4PATHWAY.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: PID MTOR 4PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE

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	MOCOS	MOCOS	MOCOS	316	0.3	0.038	YES
2	GSTO2	GSTO2	GSTO2	453	0.25	0.078	YES
3	QPRT	QPRT	QPRT	478	0.25	0.12	YES
4	GSTO1	GSTO1	GSTO1	587	0.22	0.16	YES
5	SLC19A2	SLC19A2	SLC19A2	894	0.17	0.17	YES
6	SLC19A1	SLC19A1	SLC19A1	1344	0.14	0.17	YES
7	CYB5R3	CYB5R3	CYB5R3	1453	0.13	0.19	YES
8	SLC25A16	SLC25A16	SLC25A16	1681	0.12	0.2	YES
9	SLC2A3	SLC2A3	SLC2A3	1777	0.11	0.22	YES
10	THTPA	THTPA	THTPA	1898	0.11	0.23	YES
11	MOCS1	MOCS1	MOCS1	1970	0.11	0.25	YES
12	FASN	FASN	FASN	2044	0.1	0.26	YES
13	NFS1	NFS1	NFS1	2190	0.098	0.27	YES
14	FLAD1	FLAD1	FLAD1	2279	0.095	0.29	YES
15	ACP5	ACP5	ACP5	2322	0.094	0.3	YES
16	PANK4	PANK4	PANK4	2403	0.092	0.32	YES
17	PNPO	PNPO	PNPO	2663	0.084	0.32	YES
18	COASY	COASY	COASY	2730	0.081	0.33	YES
19	NADSYN1	NADSYN1	NADSYN1	2831	0.078	0.34	YES
20	SLC46A1	SLC46A1	SLC46A1	3124	0.071	0.33	YES
21	MTHFD1	MTHFD1	MTHFD1	3171	0.07	0.34	YES
22	SLC19A3	SLC19A3	SLC19A3	3269	0.067	0.35	YES
23	MTHFR	MTHFR	MTHFR	3443	0.063	0.35	YES
24	PPCDC	PPCDC	PPCDC	3472	0.062	0.36	YES
25	SLC23A2	SLC23A2	SLC23A2	3557	0.06	0.37	YES
26	SLC2A1	SLC2A1	SLC2A1	3884	0.053	0.36	YES
27	ENPP1	ENPP1	ENPP1	4034	0.05	0.36	YES
28	MOCS3	MOCS3	MOCS3	4331	0.044	0.36	YES
29	FPGS	FPGS	FPGS	4363	0.043	0.36	YES
30	SLC5A6	SLC5A6	SLC5A6	4404	0.042	0.37	YES
31	NADK	NADK	NADK	4469	0.041	0.37	YES
32	GPHN	GPHN	GPHN	4510	0.04	0.38	YES
33	PDXK	PDXK	PDXK	4954	0.032	0.36	NO
34	PANK1	PANK1	PANK1	5500	0.021	0.33	NO
35	CYB5A	CYB5A	CYB5A	6461	0.0018	0.28	NO
36	PPCS	PPCS	PPCS	6808	-0.0061	0.26	NO
37	PANK2	PANK2	PANK2	6925	-0.0085	0.26	NO
38	NMNAT1	NMNAT1	NMNAT1	7845	-0.028	0.21	NO
39	PANK3	PANK3	PANK3	8420	-0.042	0.19	NO
40	SHMT1	SHMT1	SHMT1	8728	-0.049	0.18	NO
41	SLC25A32	SLC25A32	SLC25A32	8857	-0.052	0.18	NO
42	NAMPT	NAMPT	NAMPT	10252	-0.085	0.12	NO
43	DHFR	DHFR	DHFR	10335	-0.088	0.13	NO
44	RFK	RFK	RFK	11137	-0.11	0.11	NO
45	MOCS2	MOCS2	MOCS2	12402	-0.14	0.064	NO
46	AASDHPPT	AASDHPPT	AASDHPPT	12475	-0.14	0.087	NO
47	NMNAT3	NMNAT3	NMNAT3	13629	-0.18	0.057	NO
48	TPK1	TPK1	TPK1	15365	-0.25	0.0081	NO
49	NMNAT2	NMNAT2	NMNAT2	16525	-0.32	0.004	NO
50	SLC23A1	SLC23A1	SLC23A1	17538	-0.43	0.028	NO

Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA 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 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	0.4	1.3	0.11	0.24	1	0.088	0.075	0.081	0.2	0
KEGG FATTY ACID METABOLISM	37	genes.ES.table	0.49	1.6	0.041	0.1	0.96	0.32	0.28	0.24	0.065	0.001
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	30	genes.ES.table	0.44	1.3	0.14	0.24	1	0.17	0.13	0.15	0.21	0
KEGG GLYCINE SERINE AND THREONINE METABOLISM	30	genes.ES.table	0.52	1.4	0.082	0.21	1	0.33	0.14	0.29	0.18	0
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	43	genes.ES.table	0.52	1.8	0.0082	0.048	0.52	0.12	0.11	0.1	0.01	0.004
KEGG HISTIDINE METABOLISM	29	genes.ES.table	0.57	1.5	0.026	0.12	0.98	0.38	0.26	0.28	0.082	0
KEGG TYROSINE METABOLISM	40	genes.ES.table	0.55	1.6	0.018	0.098	0.96	0.28	0.18	0.23	0.058	0.001
KEGG TRYPTOPHAN METABOLISM	38	genes.ES.table	0.7	1.9	0	0.043	0.38	0.34	0.08	0.32	0	0.004
KEGG O GLYCAN BIOSYNTHESIS	28	genes.ES.table	0.48	1.3	0.12	0.25	1	0.14	0.076	0.13	0.21	0
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.34	1.3	0.17	0.24	1	0.07	0.1	0.063	0.21	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	CD247	CD247	CD247	104	0.87	0.069	YES
2	CD8B	CD8B	CD8B	129	0.85	0.14	YES
3	LCK	LCK	LCK	143	0.84	0.21	YES
4	CD28	CD28	CD28	232	0.78	0.27	YES
5	DOCK2	DOCK2	DOCK2	431	0.66	0.32	YES
6	HCK	HCK	HCK	648	0.56	0.36	YES
7	APOBEC3G	APOBEC3G	APOBEC3G	850	0.49	0.39	YES
8	ELMO1	ELMO1	ELMO1	901	0.47	0.43	YES
9	CD4	CD4	CD4	926	0.47	0.46	YES
10	PSMB9	PSMB9	PSMB9	1030	0.44	0.5	YES
11	PSMA8	PSMA8	PSMA8	1535	0.32	0.5	YES
12	PSMB10	PSMB10	PSMB10	1738	0.28	0.51	YES
13	NUP210	NUP210	NUP210	1833	0.27	0.53	YES
14	B2M	B2M	B2M	2091	0.24	0.53	YES
15	PSMB8	PSMB8	PSMB8	2154	0.23	0.55	YES
16	PSME2	PSME2	PSME2	2382	0.2	0.56	YES
17	PSME1	PSME1	PSME1	2709	0.18	0.55	YES
18	HLA-A	HLA-A	HLA-A	2779	0.17	0.56	YES
19	FYN	FYN	FYN	3958	0.1	0.51	NO
20	PSIP1	PSIP1	PSIP1	4484	0.085	0.48	NO
21	PACS1	PACS1	PACS1	4869	0.073	0.47	NO
22	PSMA3	PSMA3	PSMA3	5063	0.068	0.46	NO
23	PSMA4	PSMA4	PSMA4	5667	0.055	0.44	NO
24	PSMA5	PSMA5	PSMA5	5959	0.049	0.42	NO
25	PSMB1	PSMB1	PSMB1	6232	0.043	0.41	NO
26	PSMA6	PSMA6	PSMA6	6469	0.038	0.4	NO
27	AP1B1	AP1B1	AP1B1	6502	0.038	0.4	NO
28	CUL5	CUL5	CUL5	6669	0.035	0.4	NO
29	PSMB3	PSMB3	PSMB3	6696	0.034	0.4	NO
30	NUP54	NUP54	NUP54	6877	0.032	0.39	NO
31	AP1S2	AP1S2	AP1S2	6890	0.031	0.39	NO
32	NUPL2	NUPL2	NUPL2	6895	0.031	0.4	NO
33	PAK2	PAK2	PAK2	6974	0.03	0.39	NO
34	NUP43	NUP43	NUP43	7183	0.027	0.38	NO
35	PSMA2	PSMA2	PSMA2	7301	0.025	0.38	NO
36	PSME4	PSME4	PSME4	7503	0.022	0.37	NO
37	CDK9	CDK9	CDK9	7538	0.022	0.37	NO
38	PSMC6	PSMC6	PSMC6	7619	0.021	0.37	NO
39	RANBP2	RANBP2	RANBP2	7645	0.02	0.37	NO
40	RBX1	RBX1	RBX1	7930	0.017	0.35	NO
41	PSMD10	PSMD10	PSMD10	7998	0.016	0.35	NO
42	NUP37	NUP37	NUP37	8141	0.014	0.34	NO
43	AP1G1	AP1G1	AP1G1	8253	0.013	0.34	NO
44	PSMC2	PSMC2	PSMC2	8373	0.011	0.33	NO
45	NUP62	NUP62	NUP62	8448	0.0099	0.33	NO
46	NUP88	NUP88	NUP88	8494	0.0093	0.33	NO
47	NUP50	NUP50	NUP50	8627	0.0078	0.32	NO
48	PSMB6	PSMB6	PSMB6	8803	0.0055	0.31	NO
49	PSMB2	PSMB2	PSMB2	8874	0.0046	0.31	NO
50	PSMA1	PSMA1	PSMA1	8974	0.0034	0.3	NO
51	TPR	TPR	TPR	9011	0.0029	0.3	NO
52	RPS27A	RPS27A	RPS27A	9105	0.0018	0.3	NO
53	XPO1	XPO1	XPO1	9118	0.0016	0.3	NO
54	PSMD9	PSMD9	PSMD9	9245	0.0003	0.29	NO
55	PSMC5	PSMC5	PSMC5	9267	-0.000016	0.29	NO
56	PSMF1	PSMF1	PSMF1	9446	-0.0024	0.28	NO
57	NUP107	NUP107	NUP107	9601	-0.0038	0.27	NO
58	NUP85	NUP85	NUP85	9681	-0.0047	0.27	NO
59	ATP6V1H	ATP6V1H	ATP6V1H	9799	-0.0057	0.26	NO
60	NUP153	NUP153	NUP153	10004	-0.0081	0.25	NO
61	PSMD7	PSMD7	PSMD7	10012	-0.0082	0.25	NO
62	PSMD13	PSMD13	PSMD13	10104	-0.0093	0.25	NO
63	PSMD12	PSMD12	PSMD12	10107	-0.0093	0.25	NO
64	SKP1	SKP1	SKP1	10135	-0.0096	0.25	NO
65	PSMC1	PSMC1	PSMC1	10207	-0.01	0.24	NO
66	PSMD5	PSMD5	PSMD5	10249	-0.011	0.24	NO
67	KPNA1	KPNA1	KPNA1	10399	-0.012	0.24	NO
68	PSMD14	PSMD14	PSMD14	10573	-0.014	0.23	NO
69	PSMA7	PSMA7	PSMA7	10642	-0.015	0.22	NO
70	KPNB1	KPNB1	KPNB1	10689	-0.015	0.22	NO
71	AP2A2	AP2A2	AP2A2	10743	-0.016	0.22	NO
72	PSMD6	PSMD6	PSMD6	10761	-0.016	0.22	NO
73	AP2B1	AP2B1	AP2B1	10766	-0.016	0.22	NO
74	PSMD11	PSMD11	PSMD11	10815	-0.017	0.22	NO
75	PSMD1	PSMD1	PSMD1	10931	-0.018	0.22	NO
76	SLC25A4	SLC25A4	SLC25A4	11033	-0.019	0.21	NO
77	SLC25A5	SLC25A5	SLC25A5	11136	-0.02	0.21	NO
78	PSMC3	PSMC3	PSMC3	11140	-0.02	0.21	NO
79	BTRC	BTRC	BTRC	11191	-0.021	0.21	NO
80	AP2M1	AP2M1	AP2M1	11260	-0.021	0.21	NO
81	NUP205	NUP205	NUP205	11382	-0.022	0.2	NO
82	PPIA	PPIA	PPIA	11451	-0.023	0.2	NO
83	RAN	RAN	RAN	11817	-0.028	0.18	NO
84	SEH1L	SEH1L	SEH1L	11830	-0.028	0.18	NO
85	TCEB1	TCEB1	TCEB1	11865	-0.028	0.18	NO
86	PSMC4	PSMC4	PSMC4	12038	-0.03	0.18	NO
87	UBA52	UBA52	UBA52	12069	-0.03	0.18	NO
88	AAAS	AAAS	AAAS	12126	-0.031	0.18	NO
89	RANGAP1	RANGAP1	RANGAP1	12179	-0.032	0.18	NO
90	RAC1	RAC1	RAC1	12199	-0.032	0.18	NO
91	AP1M1	AP1M1	AP1M1	12284	-0.033	0.18	NO
92	AP2A1	AP2A1	AP2A1	12401	-0.035	0.17	NO
93	ARF1	ARF1	ARF1	12537	-0.036	0.17	NO
94	PSMD3	PSMD3	PSMD3	12584	-0.037	0.17	NO
95	BANF1	BANF1	BANF1	12672	-0.038	0.17	NO
96	PSMD2	PSMD2	PSMD2	12752	-0.039	0.17	NO
97	NUP188	NUP188	NUP188	12937	-0.041	0.16	NO
98	NUP214	NUP214	NUP214	13016	-0.042	0.16	NO
99	TCEB2	TCEB2	TCEB2	13126	-0.043	0.16	NO
100	POM121	POM121	POM121	13131	-0.044	0.16	NO
101	PSMB4	PSMB4	PSMB4	13132	-0.044	0.16	NO
102	SLC25A6	SLC25A6	SLC25A6	13306	-0.046	0.16	NO
103	NUP93	NUP93	NUP93	13355	-0.046	0.16	NO
104	NUPL1	NUPL1	NUPL1	13359	-0.046	0.16	NO
105	NPM1	NPM1	NPM1	13526	-0.049	0.16	NO
106	PSMD4	PSMD4	PSMD4	13869	-0.054	0.14	NO
107	AP2S1	AP2S1	AP2S1	13953	-0.055	0.15	NO
108	PSMD8	PSMD8	PSMD8	14061	-0.057	0.14	NO
109	RCC1	RCC1	RCC1	14146	-0.058	0.14	NO
110	NUP35	NUP35	NUP35	14497	-0.064	0.13	NO
111	PSMB7	PSMB7	PSMB7	14548	-0.065	0.13	NO
112	NUP133	NUP133	NUP133	14673	-0.068	0.13	NO
113	HMGA1	HMGA1	HMGA1	14722	-0.069	0.14	NO
114	AP1S1	AP1S1	AP1S1	14789	-0.07	0.14	NO
115	RAE1	RAE1	RAE1	14905	-0.072	0.14	NO
116	NUP155	NUP155	NUP155	15023	-0.074	0.14	NO
117	RANBP1	RANBP1	RANBP1	15538	-0.086	0.12	NO
118	CCNT1	CCNT1	CCNT1	15540	-0.086	0.12	NO
119	PSMB5	PSMB5	PSMB5	15570	-0.086	0.13	NO
120	AP1M2	AP1M2	AP1M2	15799	-0.093	0.12	NO

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

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	CD247	CD247	CD247	104	0.87	0.05	YES
2	CD8B	CD8B	CD8B	129	0.85	0.1	YES
3	LCK	LCK	LCK	143	0.84	0.16	YES
4	CD28	CD28	CD28	232	0.78	0.2	YES
5	CCR5	CCR5	CCR5	361	0.69	0.24	YES
6	DOCK2	DOCK2	DOCK2	431	0.66	0.28	YES
7	HCK	HCK	HCK	648	0.56	0.3	YES
8	APOBEC3G	APOBEC3G	APOBEC3G	850	0.49	0.32	YES
9	ELMO1	ELMO1	ELMO1	901	0.47	0.35	YES
10	CD4	CD4	CD4	926	0.47	0.38	YES
11	CXCR4	CXCR4	CXCR4	1020	0.44	0.4	YES
12	PSMB9	PSMB9	PSMB9	1030	0.44	0.43	YES
13	PSMA8	PSMA8	PSMA8	1535	0.32	0.42	YES
14	PSMB10	PSMB10	PSMB10	1738	0.28	0.43	YES
15	NUP210	NUP210	NUP210	1833	0.27	0.44	YES
16	B2M	B2M	B2M	2091	0.24	0.44	YES
17	PSMB8	PSMB8	PSMB8	2154	0.23	0.45	YES
18	PSME2	PSME2	PSME2	2382	0.2	0.46	YES
19	PSME1	PSME1	PSME1	2709	0.18	0.45	YES
20	HLA-A	HLA-A	HLA-A	2779	0.17	0.46	YES
21	RNGTT	RNGTT	RNGTT	3827	0.11	0.4	NO
22	FYN	FYN	FYN	3958	0.1	0.4	NO
23	NMT2	NMT2	NMT2	4168	0.096	0.4	NO
24	PSIP1	PSIP1	PSIP1	4484	0.085	0.38	NO
25	LIG4	LIG4	LIG4	4650	0.08	0.38	NO
26	TAF5	TAF5	TAF5	4746	0.077	0.38	NO
27	PACS1	PACS1	PACS1	4869	0.073	0.38	NO
28	PSMA3	PSMA3	PSMA3	5063	0.068	0.37	NO
29	GTF2H2	GTF2H2	GTF2H2	5118	0.067	0.37	NO
30	XRCC4	XRCC4	XRCC4	5215	0.064	0.37	NO
31	ELL	ELL	ELL	5521	0.058	0.36	NO
32	PSMA4	PSMA4	PSMA4	5667	0.055	0.35	NO
33	PSMA5	PSMA5	PSMA5	5959	0.049	0.34	NO
34	CCNT2	CCNT2	CCNT2	6060	0.046	0.34	NO
35	PSMB1	PSMB1	PSMB1	6232	0.043	0.33	NO
36	GTF2E2	GTF2E2	GTF2E2	6275	0.042	0.33	NO
37	GTF2E1	GTF2E1	GTF2E1	6291	0.042	0.33	NO
38	GTF2B	GTF2B	GTF2B	6452	0.039	0.33	NO
39	PSMA6	PSMA6	PSMA6	6469	0.038	0.33	NO
40	AP1B1	AP1B1	AP1B1	6502	0.038	0.33	NO
41	GTF2H2B	GTF2H2B	GTF2H2B	6617	0.036	0.33	NO
42	CUL5	CUL5	CUL5	6669	0.035	0.32	NO
43	PSMB3	PSMB3	PSMB3	6696	0.034	0.33	NO
44	NUP54	NUP54	NUP54	6877	0.032	0.32	NO
45	AP1S2	AP1S2	AP1S2	6890	0.031	0.32	NO
46	NUPL2	NUPL2	NUPL2	6895	0.031	0.32	NO
47	TBP	TBP	TBP	6936	0.031	0.32	NO
48	PAK2	PAK2	PAK2	6974	0.03	0.32	NO
49	NUP43	NUP43	NUP43	7183	0.027	0.31	NO
50	TAF12	TAF12	TAF12	7255	0.026	0.31	NO
51	PSMA2	PSMA2	PSMA2	7301	0.025	0.31	NO
52	TAF10	TAF10	TAF10	7396	0.024	0.3	NO
53	TAF1	TAF1	TAF1	7448	0.023	0.3	NO
54	PSME4	PSME4	PSME4	7503	0.022	0.3	NO
55	CDK9	CDK9	CDK9	7538	0.022	0.3	NO
56	PSMC6	PSMC6	PSMC6	7619	0.021	0.3	NO
57	RANBP2	RANBP2	RANBP2	7645	0.02	0.3	NO
58	CTDP1	CTDP1	CTDP1	7744	0.019	0.29	NO
59	RBX1	RBX1	RBX1	7930	0.017	0.28	NO
60	PSMD10	PSMD10	PSMD10	7998	0.016	0.28	NO
61	SUPT4H1	SUPT4H1	SUPT4H1	8057	0.015	0.28	NO
62	CCNH	CCNH	CCNH	8112	0.014	0.28	NO
63	NUP37	NUP37	NUP37	8141	0.014	0.28	NO
64	AP1G1	AP1G1	AP1G1	8253	0.013	0.27	NO
65	VPS37A	VPS37A	VPS37A	8304	0.012	0.27	NO
66	PSMC2	PSMC2	PSMC2	8373	0.011	0.26	NO
67	NUP62	NUP62	NUP62	8448	0.0099	0.26	NO
68	NUP88	NUP88	NUP88	8494	0.0093	0.26	NO
69	NUP50	NUP50	NUP50	8627	0.0078	0.25	NO
70	NMT1	NMT1	NMT1	8643	0.0076	0.25	NO
71	TAF9	TAF9	TAF9	8787	0.0056	0.24	NO
72	PSMB6	PSMB6	PSMB6	8803	0.0055	0.24	NO
73	PSMB2	PSMB2	PSMB2	8874	0.0046	0.24	NO
74	PSMA1	PSMA1	PSMA1	8974	0.0034	0.24	NO
75	TPR	TPR	TPR	9011	0.0029	0.23	NO
76	RPS27A	RPS27A	RPS27A	9105	0.0018	0.23	NO
77	XPO1	XPO1	XPO1	9118	0.0016	0.23	NO
78	CDK7	CDK7	CDK7	9225	0.00041	0.22	NO
79	PSMD9	PSMD9	PSMD9	9245	0.0003	0.22	NO
80	PSMC5	PSMC5	PSMC5	9267	-0.000016	0.22	NO
81	TCEA1	TCEA1	TCEA1	9283	-0.00024	0.22	NO
82	PSMF1	PSMF1	PSMF1	9446	-0.0024	0.21	NO
83	GTF2A2	GTF2A2	GTF2A2	9500	-0.0029	0.21	NO
84	GTF2H1	GTF2H1	GTF2H1	9529	-0.0031	0.21	NO
85	NUP107	NUP107	NUP107	9601	-0.0038	0.2	NO
86	NUP85	NUP85	NUP85	9681	-0.0047	0.2	NO
87	TCEB3	TCEB3	TCEB3	9684	-0.0047	0.2	NO
88	ATP6V1H	ATP6V1H	ATP6V1H	9799	-0.0057	0.19	NO
89	POLR2A	POLR2A	POLR2A	9914	-0.0071	0.19	NO
90	NUP153	NUP153	NUP153	10004	-0.0081	0.18	NO
91	PSMD7	PSMD7	PSMD7	10012	-0.0082	0.18	NO
92	POLR2K	POLR2K	POLR2K	10086	-0.0091	0.18	NO
93	PSMD13	PSMD13	PSMD13	10104	-0.0093	0.18	NO
94	PSMD12	PSMD12	PSMD12	10107	-0.0093	0.18	NO
95	TAF4B	TAF4B	TAF4B	10134	-0.0096	0.18	NO
96	SKP1	SKP1	SKP1	10135	-0.0096	0.18	NO
97	PSMC1	PSMC1	PSMC1	10207	-0.01	0.18	NO
98	PSMD5	PSMD5	PSMD5	10249	-0.011	0.17	NO
99	POLR2G	POLR2G	POLR2G	10295	-0.011	0.17	NO
100	LIG1	LIG1	LIG1	10304	-0.011	0.17	NO
101	KPNA1	KPNA1	KPNA1	10399	-0.012	0.17	NO
102	PSMD14	PSMD14	PSMD14	10573	-0.014	0.16	NO
103	TAF4	TAF4	TAF4	10581	-0.014	0.16	NO
104	POLR2B	POLR2B	POLR2B	10589	-0.014	0.16	NO
105	PSMA7	PSMA7	PSMA7	10642	-0.015	0.16	NO
106	POLR2J	POLR2J	POLR2J	10668	-0.015	0.16	NO
107	RNMT	RNMT	RNMT	10679	-0.015	0.16	NO
108	KPNB1	KPNB1	KPNB1	10689	-0.015	0.16	NO
109	AP2A2	AP2A2	AP2A2	10743	-0.016	0.16	NO
110	PSMD6	PSMD6	PSMD6	10761	-0.016	0.16	NO
111	AP2B1	AP2B1	AP2B1	10766	-0.016	0.16	NO
112	PSMD11	PSMD11	PSMD11	10815	-0.017	0.16	NO
113	PSMD1	PSMD1	PSMD1	10931	-0.018	0.15	NO
114	SLC25A4	SLC25A4	SLC25A4	11033	-0.019	0.15	NO
115	NCBP2	NCBP2	NCBP2	11072	-0.02	0.14	NO
116	SLC25A5	SLC25A5	SLC25A5	11136	-0.02	0.14	NO
117	PSMC3	PSMC3	PSMC3	11140	-0.02	0.14	NO
118	GTF2A1	GTF2A1	GTF2A1	11189	-0.021	0.14	NO
119	BTRC	BTRC	BTRC	11191	-0.021	0.14	NO
120	AP2M1	AP2M1	AP2M1	11260	-0.021	0.14	NO
121	TAF11	TAF11	TAF11	11339	-0.022	0.14	NO
122	NUP205	NUP205	NUP205	11382	-0.022	0.14	NO
123	PPIA	PPIA	PPIA	11451	-0.023	0.14	NO
124	TSG101	TSG101	TSG101	11583	-0.025	0.13	NO
125	TAF6	TAF6	TAF6	11748	-0.027	0.12	NO
126	VPS28	VPS28	VPS28	11789	-0.027	0.12	NO
127	RAN	RAN	RAN	11817	-0.028	0.12	NO
128	SEH1L	SEH1L	SEH1L	11830	-0.028	0.12	NO
129	POLR2C	POLR2C	POLR2C	11858	-0.028	0.12	NO
130	XRCC6	XRCC6	XRCC6	11860	-0.028	0.12	NO
131	TCEB1	TCEB1	TCEB1	11865	-0.028	0.13	NO
132	PSMC4	PSMC4	PSMC4	12038	-0.03	0.12	NO
133	UBA52	UBA52	UBA52	12069	-0.03	0.12	NO
134	ERCC3	ERCC3	ERCC3	12098	-0.031	0.12	NO
135	FEN1	FEN1	FEN1	12117	-0.031	0.12	NO
136	AAAS	AAAS	AAAS	12126	-0.031	0.12	NO
137	RANGAP1	RANGAP1	RANGAP1	12179	-0.032	0.12	NO
138	RAC1	RAC1	RAC1	12199	-0.032	0.12	NO
139	AP1M1	AP1M1	AP1M1	12284	-0.033	0.12	NO
140	XRCC5	XRCC5	XRCC5	12287	-0.033	0.12	NO
141	VPS37C	VPS37C	VPS37C	12336	-0.034	0.12	NO
142	POLR2L	POLR2L	POLR2L	12370	-0.034	0.12	NO
143	AP2A1	AP2A1	AP2A1	12401	-0.035	0.12	NO
144	ARF1	ARF1	ARF1	12537	-0.036	0.12	NO
145	PSMD3	PSMD3	PSMD3	12584	-0.037	0.12	NO
146	GTF2H3	GTF2H3	GTF2H3	12630	-0.037	0.12	NO
147	GTF2F2	GTF2F2	GTF2F2	12640	-0.037	0.12	NO
148	BANF1	BANF1	BANF1	12672	-0.038	0.12	NO
149	POLR2H	POLR2H	POLR2H	12673	-0.038	0.12	NO
150	COBRA1	COBRA1	COBRA1	12726	-0.038	0.12	NO
151	PSMD2	PSMD2	PSMD2	12752	-0.039	0.12	NO
152	SUPT16H	SUPT16H	SUPT16H	12886	-0.04	0.12	NO
153	SUPT5H	SUPT5H	SUPT5H	12925	-0.041	0.12	NO
154	RDBP	RDBP	RDBP	12926	-0.041	0.12	NO
155	NUP188	NUP188	NUP188	12937	-0.041	0.12	NO
156	NUP214	NUP214	NUP214	13016	-0.042	0.12	NO
157	MNAT1	MNAT1	MNAT1	13074	-0.043	0.12	NO
158	POLR2D	POLR2D	POLR2D	13098	-0.043	0.12	NO
159	TCEB2	TCEB2	TCEB2	13126	-0.043	0.12	NO
160	POM121	POM121	POM121	13131	-0.044	0.13	NO
161	PSMB4	PSMB4	PSMB4	13132	-0.044	0.13	NO
162	POLR2E	POLR2E	POLR2E	13219	-0.045	0.13	NO
163	NCBP1	NCBP1	NCBP1	13272	-0.045	0.13	NO
164	SLC25A6	SLC25A6	SLC25A6	13306	-0.046	0.13	NO
165	NUP93	NUP93	NUP93	13355	-0.046	0.13	NO
166	NUPL1	NUPL1	NUPL1	13359	-0.046	0.13	NO
167	NPM1	NPM1	NPM1	13526	-0.049	0.12	NO
168	VPS37B	VPS37B	VPS37B	13553	-0.049	0.13	NO
169	GTF2H4	GTF2H4	GTF2H4	13635	-0.05	0.13	NO
170	WHSC2	WHSC2	WHSC2	13854	-0.054	0.12	NO
171	PSMD4	PSMD4	PSMD4	13869	-0.054	0.12	NO
172	TAF13	TAF13	TAF13	13897	-0.054	0.12	NO
173	AP2S1	AP2S1	AP2S1	13953	-0.055	0.12	NO
174	SSRP1	SSRP1	SSRP1	14014	-0.056	0.12	NO
175	PSMD8	PSMD8	PSMD8	14061	-0.057	0.12	NO
176	TH1L	TH1L	TH1L	14136	-0.058	0.12	NO
177	RCC1	RCC1	RCC1	14146	-0.058	0.13	NO
178	NUP35	NUP35	NUP35	14497	-0.064	0.11	NO
179	GTF2F1	GTF2F1	GTF2F1	14501	-0.065	0.12	NO
180	PSMB7	PSMB7	PSMB7	14548	-0.065	0.12	NO
181	NUP133	NUP133	NUP133	14673	-0.068	0.11	NO
182	HMGA1	HMGA1	HMGA1	14722	-0.069	0.12	NO
183	AP1S1	AP1S1	AP1S1	14789	-0.07	0.12	NO
184	POLR2F	POLR2F	POLR2F	14892	-0.072	0.12	NO
185	RAE1	RAE1	RAE1	14905	-0.072	0.12	NO
186	NUP155	NUP155	NUP155	15023	-0.074	0.12	NO
187	ERCC2	ERCC2	ERCC2	15477	-0.084	0.098	NO
188	RANBP1	RANBP1	RANBP1	15538	-0.086	0.1	NO
189	CCNT1	CCNT1	CCNT1	15540	-0.086	0.1	NO
190	PSMB5	PSMB5	PSMB5	15570	-0.086	0.11	NO
191	AP1M2	AP1M2	AP1M2	15799	-0.093	0.1	NO
192	POLR2I	POLR2I	POLR2I	16417	-0.11	0.075	NO
193	VPS37D	VPS37D	VPS37D	17850	-0.24	0.011	NO

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

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE 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	CD19	CD19	CD19	32	0.96	0.054	YES
2	CD79A	CD79A	CD79A	90	0.89	0.1	YES
3	BLK	BLK	BLK	96	0.88	0.15	YES
4	BLNK	BLNK	BLNK	114	0.87	0.2	YES
5	CARD11	CARD11	CARD11	131	0.84	0.25	YES
6	RASGRP1	RASGRP1	RASGRP1	266	0.75	0.29	YES
7	VAV1	VAV1	VAV1	288	0.74	0.33	YES
8	CD79B	CD79B	CD79B	339	0.71	0.37	YES
9	PRKCB	PRKCB	PRKCB	348	0.7	0.41	YES
10	BTK	BTK	BTK	387	0.68	0.44	YES
11	PIK3AP1	PIK3AP1	PIK3AP1	587	0.58	0.47	YES
12	PLCG2	PLCG2	PLCG2	760	0.52	0.49	YES
13	SYK	SYK	SYK	771	0.52	0.52	YES
14	LYN	LYN	LYN	1007	0.44	0.53	YES
15	PSMB9	PSMB9	PSMB9	1030	0.44	0.55	YES
16	RASGRP3	RASGRP3	RASGRP3	1060	0.43	0.58	YES
17	PSMA8	PSMA8	PSMA8	1535	0.32	0.57	YES
18	PSMB10	PSMB10	PSMB10	1738	0.28	0.57	YES
19	NFKBIA	NFKBIA	NFKBIA	2005	0.25	0.57	YES
20	REL	REL	REL	2106	0.23	0.58	YES
21	PSMB8	PSMB8	PSMB8	2154	0.23	0.59	YES
22	PSME2	PSME2	PSME2	2382	0.2	0.59	YES
23	PIK3CD	PIK3CD	PIK3CD	2454	0.2	0.6	YES
24	MALT1	MALT1	MALT1	2679	0.18	0.6	YES
25	PSME1	PSME1	PSME1	2709	0.18	0.61	YES
26	CBLB	CBLB	CBLB	3062	0.15	0.6	NO
27	NFKBIE	NFKBIE	NFKBIE	3335	0.13	0.59	NO
28	NCK1	NCK1	NCK1	3419	0.13	0.59	NO
29	CDKN1B	CDKN1B	CDKN1B	3481	0.12	0.59	NO
30	ITPR2	ITPR2	ITPR2	3498	0.12	0.6	NO
31	GRB2	GRB2	GRB2	3813	0.11	0.59	NO
32	FYN	FYN	FYN	3958	0.1	0.59	NO
33	PTEN	PTEN	PTEN	4081	0.099	0.59	NO
34	FOXO1	FOXO1	FOXO1	4483	0.085	0.57	NO
35	RICTOR	RICTOR	RICTOR	4614	0.081	0.57	NO
36	PIK3R1	PIK3R1	PIK3R1	4687	0.078	0.57	NO
37	IKBKG	IKBKG	IKBKG	4881	0.073	0.56	NO
38	BCL10	BCL10	BCL10	4930	0.072	0.56	NO
39	PSMA3	PSMA3	PSMA3	5063	0.068	0.56	NO
40	SOS1	SOS1	SOS1	5293	0.062	0.55	NO
41	MAP3K7	MAP3K7	MAP3K7	5313	0.062	0.55	NO
42	CREB1	CREB1	CREB1	5420	0.06	0.55	NO
43	CBL	CBL	CBL	5456	0.059	0.55	NO
44	ORAI1	ORAI1	ORAI1	5481	0.059	0.55	NO
45	SH3KBP1	SH3KBP1	SH3KBP1	5570	0.057	0.55	NO
46	CHUK	CHUK	CHUK	5614	0.056	0.55	NO
47	IKBKB	IKBKB	IKBKB	5656	0.055	0.55	NO
48	PSMA4	PSMA4	PSMA4	5667	0.055	0.56	NO
49	KRAS	KRAS	KRAS	5737	0.053	0.55	NO
50	PSMA5	PSMA5	PSMA5	5959	0.049	0.55	NO
51	NFKBIB	NFKBIB	NFKBIB	6019	0.048	0.54	NO
52	PSMB1	PSMB1	PSMB1	6232	0.043	0.54	NO
53	ITPR3	ITPR3	ITPR3	6390	0.04	0.53	NO
54	PSMA6	PSMA6	PSMA6	6469	0.038	0.53	NO
55	STIM1	STIM1	STIM1	6657	0.035	0.52	NO
56	PSMB3	PSMB3	PSMB3	6696	0.034	0.52	NO
57	NRAS	NRAS	NRAS	7125	0.028	0.5	NO
58	PSMA2	PSMA2	PSMA2	7301	0.025	0.49	NO
59	PSME4	PSME4	PSME4	7503	0.022	0.48	NO
60	PSMC6	PSMC6	PSMC6	7619	0.021	0.47	NO
61	CALM1	CALM1	CALM1	7658	0.02	0.47	NO
62	CALM2	CALM2	CALM2	7817	0.018	0.46	NO
63	CUL1	CUL1	CUL1	7889	0.017	0.46	NO
64	PSMD10	PSMD10	PSMD10	7998	0.016	0.46	NO
65	FOXO3	FOXO3	FOXO3	8268	0.012	0.44	NO
66	CASP9	CASP9	CASP9	8352	0.011	0.44	NO
67	PSMC2	PSMC2	PSMC2	8373	0.011	0.44	NO
68	FOXO4	FOXO4	FOXO4	8534	0.0089	0.43	NO
69	RPS6KB2	RPS6KB2	RPS6KB2	8543	0.0087	0.43	NO
70	PSMB6	PSMB6	PSMB6	8803	0.0055	0.41	NO
71	PSMB2	PSMB2	PSMB2	8874	0.0046	0.41	NO
72	PSMA1	PSMA1	PSMA1	8974	0.0034	0.4	NO
73	RPS27A	RPS27A	RPS27A	9105	0.0018	0.4	NO
74	PSMD9	PSMD9	PSMD9	9245	0.0003	0.39	NO
75	PSMC5	PSMC5	PSMC5	9267	-0.000016	0.39	NO
76	CALM3	CALM3	CALM3	9278	-0.00018	0.39	NO
77	PSMF1	PSMF1	PSMF1	9446	-0.0024	0.38	NO
78	MDM2	MDM2	MDM2	9895	-0.0068	0.36	NO
79	PSMD7	PSMD7	PSMD7	10012	-0.0082	0.35	NO
80	PSMD13	PSMD13	PSMD13	10104	-0.0093	0.34	NO
81	PSMD12	PSMD12	PSMD12	10107	-0.0093	0.34	NO
82	SKP1	SKP1	SKP1	10135	-0.0096	0.34	NO
83	PSMC1	PSMC1	PSMC1	10207	-0.01	0.34	NO
84	MTOR	MTOR	MTOR	10211	-0.01	0.34	NO
85	PSMD5	PSMD5	PSMD5	10249	-0.011	0.34	NO
86	PSMD14	PSMD14	PSMD14	10573	-0.014	0.32	NO
87	PSMA7	PSMA7	PSMA7	10642	-0.015	0.32	NO
88	PDPK1	PDPK1	PDPK1	10699	-0.015	0.32	NO
89	PSMD6	PSMD6	PSMD6	10761	-0.016	0.32	NO
90	PSMD11	PSMD11	PSMD11	10815	-0.017	0.31	NO
91	MAPKAP1	MAPKAP1	MAPKAP1	10878	-0.018	0.31	NO
92	RELA	RELA	RELA	10903	-0.018	0.31	NO
93	PSMD1	PSMD1	PSMD1	10931	-0.018	0.31	NO
94	PSMC3	PSMC3	PSMC3	11140	-0.02	0.3	NO
95	BTRC	BTRC	BTRC	11191	-0.021	0.3	NO
96	THEM4	THEM4	THEM4	11698	-0.026	0.27	NO
97	PSMC4	PSMC4	PSMC4	12038	-0.03	0.25	NO
98	PLCG1	PLCG1	PLCG1	12039	-0.03	0.26	NO
99	UBA52	UBA52	UBA52	12069	-0.03	0.26	NO
100	AKT1	AKT1	AKT1	12293	-0.033	0.24	NO
101	FBXW11	FBXW11	FBXW11	12300	-0.033	0.25	NO
102	PSMD3	PSMD3	PSMD3	12584	-0.037	0.23	NO
103	PSMD2	PSMD2	PSMD2	12752	-0.039	0.23	NO
104	BAD	BAD	BAD	12804	-0.039	0.22	NO
105	PSMB4	PSMB4	PSMB4	13132	-0.044	0.21	NO
106	AKT2	AKT2	AKT2	13293	-0.046	0.2	NO
107	GSK3A	GSK3A	GSK3A	13654	-0.05	0.19	NO
108	AKT3	AKT3	AKT3	13795	-0.053	0.18	NO
109	PSMD4	PSMD4	PSMD4	13869	-0.054	0.18	NO
110	TSC2	TSC2	TSC2	13917	-0.055	0.18	NO
111	PSMD8	PSMD8	PSMD8	14061	-0.057	0.18	NO
112	PSMB7	PSMB7	PSMB7	14548	-0.065	0.15	NO
113	CDKN1A	CDKN1A	CDKN1A	14662	-0.068	0.15	NO
114	SHC1	SHC1	SHC1	14751	-0.069	0.15	NO
115	NR4A1	NR4A1	NR4A1	14797	-0.07	0.15	NO
116	PHLPP1	PHLPP1	PHLPP1	15049	-0.075	0.14	NO
117	MLST8	MLST8	MLST8	15368	-0.081	0.13	NO
118	TRIB3	TRIB3	TRIB3	15399	-0.082	0.13	NO
119	AKT1S1	AKT1S1	AKT1S1	15555	-0.086	0.13	NO
120	PSMB5	PSMB5	PSMB5	15570	-0.086	0.13	NO
121	HRAS	HRAS	HRAS	16012	-0.1	0.11	NO

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

Figure S26. 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 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	CARD11	CARD11	CARD11	131	0.84	0.097	YES
2	RASGRP1	RASGRP1	RASGRP1	266	0.75	0.18	YES
3	PRKCB	PRKCB	PRKCB	348	0.7	0.26	YES
4	PSMB9	PSMB9	PSMB9	1030	0.44	0.28	YES
5	RASGRP3	RASGRP3	RASGRP3	1060	0.43	0.33	YES
6	PSMA8	PSMA8	PSMA8	1535	0.32	0.34	YES
7	PSMB10	PSMB10	PSMB10	1738	0.28	0.37	YES
8	NFKBIA	NFKBIA	NFKBIA	2005	0.25	0.38	YES
9	REL	REL	REL	2106	0.23	0.41	YES
10	PSMB8	PSMB8	PSMB8	2154	0.23	0.43	YES
11	PSME2	PSME2	PSME2	2382	0.2	0.44	YES
12	MALT1	MALT1	MALT1	2679	0.18	0.45	YES
13	PSME1	PSME1	PSME1	2709	0.18	0.47	YES
14	NFKBIE	NFKBIE	NFKBIE	3335	0.13	0.45	NO
15	CDKN1B	CDKN1B	CDKN1B	3481	0.12	0.46	NO
16	PTEN	PTEN	PTEN	4081	0.099	0.44	NO
17	FOXO1	FOXO1	FOXO1	4483	0.085	0.43	NO
18	RICTOR	RICTOR	RICTOR	4614	0.081	0.43	NO
19	IKBKG	IKBKG	IKBKG	4881	0.073	0.42	NO
20	BCL10	BCL10	BCL10	4930	0.072	0.43	NO
21	PSMA3	PSMA3	PSMA3	5063	0.068	0.43	NO
22	MAP3K7	MAP3K7	MAP3K7	5313	0.062	0.42	NO
23	CREB1	CREB1	CREB1	5420	0.06	0.43	NO
24	CHUK	CHUK	CHUK	5614	0.056	0.42	NO
25	IKBKB	IKBKB	IKBKB	5656	0.055	0.43	NO
26	PSMA4	PSMA4	PSMA4	5667	0.055	0.43	NO
27	KRAS	KRAS	KRAS	5737	0.053	0.44	NO
28	PSMA5	PSMA5	PSMA5	5959	0.049	0.43	NO
29	NFKBIB	NFKBIB	NFKBIB	6019	0.048	0.43	NO
30	PSMB1	PSMB1	PSMB1	6232	0.043	0.43	NO
31	PSMA6	PSMA6	PSMA6	6469	0.038	0.42	NO
32	PSMB3	PSMB3	PSMB3	6696	0.034	0.41	NO
33	NRAS	NRAS	NRAS	7125	0.028	0.39	NO
34	PSMA2	PSMA2	PSMA2	7301	0.025	0.38	NO
35	PSME4	PSME4	PSME4	7503	0.022	0.37	NO
36	PSMC6	PSMC6	PSMC6	7619	0.021	0.37	NO
37	CUL1	CUL1	CUL1	7889	0.017	0.36	NO
38	PSMD10	PSMD10	PSMD10	7998	0.016	0.35	NO
39	FOXO3	FOXO3	FOXO3	8268	0.012	0.34	NO
40	CASP9	CASP9	CASP9	8352	0.011	0.34	NO
41	PSMC2	PSMC2	PSMC2	8373	0.011	0.34	NO
42	FOXO4	FOXO4	FOXO4	8534	0.0089	0.33	NO
43	RPS6KB2	RPS6KB2	RPS6KB2	8543	0.0087	0.33	NO
44	PSMB6	PSMB6	PSMB6	8803	0.0055	0.32	NO
45	PSMB2	PSMB2	PSMB2	8874	0.0046	0.31	NO
46	PSMA1	PSMA1	PSMA1	8974	0.0034	0.31	NO
47	RPS27A	RPS27A	RPS27A	9105	0.0018	0.3	NO
48	PSMD9	PSMD9	PSMD9	9245	0.0003	0.29	NO
49	PSMC5	PSMC5	PSMC5	9267	-0.000016	0.29	NO
50	PSMF1	PSMF1	PSMF1	9446	-0.0024	0.28	NO
51	MDM2	MDM2	MDM2	9895	-0.0068	0.26	NO
52	PSMD7	PSMD7	PSMD7	10012	-0.0082	0.25	NO
53	PSMD13	PSMD13	PSMD13	10104	-0.0093	0.25	NO
54	PSMD12	PSMD12	PSMD12	10107	-0.0093	0.25	NO
55	SKP1	SKP1	SKP1	10135	-0.0096	0.25	NO
56	PSMC1	PSMC1	PSMC1	10207	-0.01	0.25	NO
57	MTOR	MTOR	MTOR	10211	-0.01	0.25	NO
58	PSMD5	PSMD5	PSMD5	10249	-0.011	0.25	NO
59	PSMD14	PSMD14	PSMD14	10573	-0.014	0.23	NO
60	PSMA7	PSMA7	PSMA7	10642	-0.015	0.23	NO
61	PDPK1	PDPK1	PDPK1	10699	-0.015	0.23	NO
62	PSMD6	PSMD6	PSMD6	10761	-0.016	0.22	NO
63	PSMD11	PSMD11	PSMD11	10815	-0.017	0.22	NO
64	MAPKAP1	MAPKAP1	MAPKAP1	10878	-0.018	0.22	NO
65	RELA	RELA	RELA	10903	-0.018	0.22	NO
66	PSMD1	PSMD1	PSMD1	10931	-0.018	0.22	NO
67	PSMC3	PSMC3	PSMC3	11140	-0.02	0.22	NO
68	BTRC	BTRC	BTRC	11191	-0.021	0.22	NO
69	THEM4	THEM4	THEM4	11698	-0.026	0.19	NO
70	PSMC4	PSMC4	PSMC4	12038	-0.03	0.18	NO
71	UBA52	UBA52	UBA52	12069	-0.03	0.18	NO
72	AKT1	AKT1	AKT1	12293	-0.033	0.17	NO
73	FBXW11	FBXW11	FBXW11	12300	-0.033	0.17	NO
74	PSMD3	PSMD3	PSMD3	12584	-0.037	0.16	NO
75	PSMD2	PSMD2	PSMD2	12752	-0.039	0.16	NO
76	BAD	BAD	BAD	12804	-0.039	0.16	NO
77	PSMB4	PSMB4	PSMB4	13132	-0.044	0.15	NO
78	AKT2	AKT2	AKT2	13293	-0.046	0.14	NO
79	GSK3A	GSK3A	GSK3A	13654	-0.05	0.13	NO
80	AKT3	AKT3	AKT3	13795	-0.053	0.13	NO
81	PSMD4	PSMD4	PSMD4	13869	-0.054	0.13	NO
82	TSC2	TSC2	TSC2	13917	-0.055	0.13	NO
83	PSMD8	PSMD8	PSMD8	14061	-0.057	0.13	NO
84	PSMB7	PSMB7	PSMB7	14548	-0.065	0.11	NO
85	CDKN1A	CDKN1A	CDKN1A	14662	-0.068	0.12	NO
86	NR4A1	NR4A1	NR4A1	14797	-0.07	0.12	NO
87	PHLPP1	PHLPP1	PHLPP1	15049	-0.075	0.11	NO
88	MLST8	MLST8	MLST8	15368	-0.081	0.1	NO
89	TRIB3	TRIB3	TRIB3	15399	-0.082	0.11	NO
90	AKT1S1	AKT1S1	AKT1S1	15555	-0.086	0.12	NO
91	PSMB5	PSMB5	PSMB5	15570	-0.086	0.12	NO
92	HRAS	HRAS	HRAS	16012	-0.1	0.11	NO

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

Figure S28. 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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	SOCS1	SOCS1	SOCS1	393	0.68	0.012	YES
2	NCF4	NCF4	NCF4	497	0.62	0.037	YES
3	FCGR1A	FCGR1A	FCGR1A	623	0.57	0.058	YES
4	FCGR1B	FCGR1B	FCGR1B	626	0.57	0.086	YES
5	CYBB	CYBB	CYBB	677	0.55	0.11	YES
6	NCF2	NCF2	NCF2	728	0.53	0.13	YES
7	MRC1	MRC1	MRC1	977	0.45	0.14	YES
8	CTSS	CTSS	CTSS	981	0.45	0.16	YES
9	PSMB9	PSMB9	PSMB9	1030	0.44	0.18	YES
10	HLA-F	HLA-F	HLA-F	1235	0.39	0.19	YES
11	ASB2	ASB2	ASB2	1427	0.34	0.2	YES
12	ASB12	ASB12	ASB12	1436	0.34	0.22	YES
13	UBA7	UBA7	UBA7	1452	0.34	0.23	YES
14	PSMA8	PSMA8	PSMA8	1535	0.32	0.24	YES
15	FBXO6	FBXO6	FBXO6	1576	0.31	0.26	YES
16	TAP1	TAP1	TAP1	1724	0.29	0.26	YES
17	HLA-G	HLA-G	HLA-G	1734	0.28	0.27	YES
18	PSMB10	PSMB10	PSMB10	1738	0.28	0.29	YES
19	HLA-B	HLA-B	HLA-B	1796	0.27	0.3	YES
20	UBE2L6	UBE2L6	UBE2L6	1840	0.27	0.31	YES
21	CYBA	CYBA	CYBA	1912	0.26	0.32	YES
22	CD207	CD207	CD207	2057	0.24	0.32	YES
23	TRIM21	TRIM21	TRIM21	2069	0.24	0.33	YES
24	B2M	B2M	B2M	2091	0.24	0.34	YES
25	PSMB8	PSMB8	PSMB8	2154	0.23	0.35	YES
26	HLA-C	HLA-C	HLA-C	2224	0.22	0.36	YES
27	SOCS3	SOCS3	SOCS3	2239	0.22	0.37	YES
28	DTX3L	DTX3L	DTX3L	2287	0.21	0.38	YES
29	ERAP1	ERAP1	ERAP1	2325	0.21	0.38	YES
30	PSME2	PSME2	PSME2	2382	0.2	0.39	YES
31	LNPEP	LNPEP	LNPEP	2448	0.2	0.4	YES
32	TAP2	TAP2	TAP2	2571	0.19	0.4	YES
33	FBXO2	FBXO2	FBXO2	2574	0.19	0.41	YES
34	UBE2E2	UBE2E2	UBE2E2	2584	0.19	0.42	YES
35	ZBTB16	ZBTB16	ZBTB16	2634	0.18	0.42	YES
36	RNF144B	RNF144B	RNF144B	2704	0.18	0.43	YES
37	PSME1	PSME1	PSME1	2709	0.18	0.44	YES
38	UBE2D1	UBE2D1	UBE2D1	2735	0.17	0.45	YES
39	HLA-A	HLA-A	HLA-A	2779	0.17	0.45	YES
40	ASB16	ASB16	ASB16	2830	0.17	0.46	YES
41	UBE2J1	UBE2J1	UBE2J1	2845	0.16	0.46	YES
42	CBLB	CBLB	CBLB	3062	0.15	0.46	NO
43	FBXW7	FBXW7	FBXW7	3272	0.14	0.46	NO
44	DZIP3	DZIP3	DZIP3	3515	0.12	0.45	NO
45	SAR1B	SAR1B	SAR1B	3817	0.11	0.44	NO
46	FBXO27	FBXO27	FBXO27	4072	0.1	0.43	NO
47	CD36	CD36	CD36	4096	0.099	0.43	NO
48	PARK2	PARK2	PARK2	4211	0.094	0.43	NO
49	UBE2F	UBE2F	UBE2F	4429	0.086	0.42	NO
50	WSB1	WSB1	WSB1	4506	0.084	0.42	NO
51	CUL2	CUL2	CUL2	4523	0.083	0.42	NO
52	ASB9	ASB9	ASB9	4668	0.079	0.42	NO
53	WWP1	WWP1	WWP1	4806	0.075	0.42	NO
54	UBA6	UBA6	UBA6	4818	0.074	0.42	NO
55	SPSB2	SPSB2	SPSB2	4978	0.07	0.41	NO
56	FBXO4	FBXO4	FBXO4	5026	0.069	0.41	NO
57	PSMA3	PSMA3	PSMA3	5063	0.068	0.42	NO
58	UBR1	UBR1	UBR1	5120	0.067	0.42	NO
59	ASB8	ASB8	ASB8	5129	0.066	0.42	NO
60	RNF138	RNF138	RNF138	5135	0.066	0.42	NO
61	SEC24D	SEC24D	SEC24D	5267	0.063	0.42	NO
62	ANAPC10	ANAPC10	ANAPC10	5450	0.059	0.41	NO
63	ANAPC4	ANAPC4	ANAPC4	5577	0.057	0.41	NO
64	ATG7	ATG7	ATG7	5603	0.056	0.41	NO
65	PSMA4	PSMA4	PSMA4	5667	0.055	0.41	NO
66	UBE2A	UBE2A	UBE2A	5755	0.053	0.4	NO
67	UBA3	UBA3	UBA3	5879	0.05	0.4	NO
68	RNF34	RNF34	RNF34	5886	0.05	0.4	NO
69	ASB7	ASB7	ASB7	5934	0.049	0.4	NO
70	KLHL9	KLHL9	KLHL9	5938	0.049	0.4	NO
71	PSMA5	PSMA5	PSMA5	5959	0.049	0.4	NO
72	UBE2Q2	UBE2Q2	UBE2Q2	5995	0.048	0.41	NO
73	UBE2B	UBE2B	UBE2B	6012	0.048	0.41	NO
74	UBR2	UBR2	UBR2	6081	0.046	0.41	NO
75	PSMB1	PSMB1	PSMB1	6232	0.043	0.4	NO
76	VHL	VHL	VHL	6311	0.042	0.4	NO
77	RNF4	RNF4	RNF4	6443	0.039	0.39	NO
78	PSMA6	PSMA6	PSMA6	6469	0.038	0.39	NO
79	ITGAV	ITGAV	ITGAV	6492	0.038	0.39	NO
80	UBE2D2	UBE2D2	UBE2D2	6510	0.038	0.39	NO
81	FBXO44	FBXO44	FBXO44	6580	0.036	0.39	NO
82	CUL5	CUL5	CUL5	6669	0.035	0.39	NO
83	UBE2D3	UBE2D3	UBE2D3	6675	0.035	0.39	NO
84	PSMB3	PSMB3	PSMB3	6696	0.034	0.39	NO
85	RBCK1	RBCK1	RBCK1	6708	0.034	0.39	NO
86	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	6752	0.034	0.39	NO
87	SMURF2	SMURF2	SMURF2	6777	0.033	0.39	NO
88	CDC26	CDC26	CDC26	6797	0.033	0.39	NO
89	SPSB1	SPSB1	SPSB1	6856	0.032	0.39	NO
90	CUL3	CUL3	CUL3	6861	0.032	0.39	NO
91	PJA2	PJA2	PJA2	6924	0.031	0.39	NO
92	UBE2W	UBE2W	UBE2W	6958	0.03	0.39	NO
93	UBE2G1	UBE2G1	UBE2G1	7003	0.029	0.39	NO
94	RCHY1	RCHY1	RCHY1	7163	0.027	0.38	NO
95	NEDD4	NEDD4	NEDD4	7208	0.026	0.38	NO
96	PSMA2	PSMA2	PSMA2	7301	0.025	0.38	NO
97	SEC61B	SEC61B	SEC61B	7359	0.024	0.37	NO
98	MKRN1	MKRN1	MKRN1	7425	0.023	0.37	NO
99	ASB13	ASB13	ASB13	7444	0.023	0.37	NO
100	PSME4	PSME4	PSME4	7503	0.022	0.37	NO
101	UBA5	UBA5	UBA5	7532	0.022	0.37	NO
102	MRC2	MRC2	MRC2	7572	0.021	0.37	NO
103	PSMC6	PSMC6	PSMC6	7619	0.021	0.37	NO
104	TRIP12	TRIP12	TRIP12	7627	0.02	0.37	NO
105	UBE4A	UBE4A	UBE4A	7726	0.019	0.36	NO
106	TRIM63	TRIM63	TRIM63	7887	0.017	0.35	NO
107	CUL1	CUL1	CUL1	7889	0.017	0.36	NO
108	RBX1	RBX1	RBX1	7930	0.017	0.35	NO
109	PSMD10	PSMD10	PSMD10	7998	0.016	0.35	NO
110	UBE2N	UBE2N	UBE2N	8008	0.016	0.35	NO
111	RNF6	RNF6	RNF6	8075	0.015	0.35	NO
112	PDIA3	PDIA3	PDIA3	8111	0.014	0.35	NO
113	UBE3A	UBE3A	UBE3A	8260	0.012	0.34	NO
114	UBE2Z	UBE2Z	UBE2Z	8283	0.012	0.34	NO
115	TRIM37	TRIM37	TRIM37	8315	0.012	0.34	NO
116	PSMC2	PSMC2	PSMC2	8373	0.011	0.33	NO
117	HECTD3	HECTD3	HECTD3	8422	0.01	0.33	NO
118	FBXO3	FBXO3	FBXO3	8495	0.0093	0.33	NO
119	VPRBP	VPRBP	VPRBP	8640	0.0077	0.32	NO
120	SPSB4	SPSB4	SPSB4	8696	0.0069	0.32	NO
121	TPP2	TPP2	TPP2	8777	0.0058	0.31	NO
122	PSMB6	PSMB6	PSMB6	8803	0.0055	0.31	NO
123	UBE3B	UBE3B	UBE3B	8819	0.0053	0.31	NO
124	PSMB2	PSMB2	PSMB2	8874	0.0046	0.31	NO
125	ANAPC5	ANAPC5	ANAPC5	8882	0.0045	0.31	NO
126	CDC27	CDC27	CDC27	8930	0.0039	0.31	NO
127	SEC24C	SEC24C	SEC24C	8951	0.0036	0.31	NO
128	PSMA1	PSMA1	PSMA1	8974	0.0034	0.3	NO
129	UBE2K	UBE2K	UBE2K	8979	0.0033	0.3	NO
130	UBE2H	UBE2H	UBE2H	8989	0.0032	0.3	NO
131	CDC23	CDC23	CDC23	9059	0.0024	0.3	NO
132	RPS27A	RPS27A	RPS27A	9105	0.0018	0.3	NO
133	UBE2E1	UBE2E1	UBE2E1	9163	0.0011	0.3	NO
134	UBE2G2	UBE2G2	UBE2G2	9241	0.00033	0.29	NO
135	PSMD9	PSMD9	PSMD9	9245	0.0003	0.29	NO
136	PSMC5	PSMC5	PSMC5	9267	-0.000016	0.29	NO
137	ANAPC2	ANAPC2	ANAPC2	9360	-0.0013	0.28	NO
138	PSMF1	PSMF1	PSMF1	9446	-0.0024	0.28	NO
139	KEAP1	KEAP1	KEAP1	9621	-0.004	0.27	NO
140	SEC24B	SEC24B	SEC24B	9767	-0.0054	0.26	NO
141	PSMD7	PSMD7	PSMD7	10012	-0.0082	0.25	NO
142	ANAPC13	ANAPC13	ANAPC13	10050	-0.0086	0.25	NO
143	UBE2J2	UBE2J2	UBE2J2	10090	-0.0091	0.24	NO
144	PSMD13	PSMD13	PSMD13	10104	-0.0093	0.24	NO
145	PSMD12	PSMD12	PSMD12	10107	-0.0093	0.24	NO
146	SKP1	SKP1	SKP1	10135	-0.0096	0.24	NO
147	ANAPC7	ANAPC7	ANAPC7	10150	-0.0098	0.24	NO
148	UBE3C	UBE3C	UBE3C	10187	-0.01	0.24	NO
149	PSMC1	PSMC1	PSMC1	10207	-0.01	0.24	NO
150	PSMD5	PSMD5	PSMD5	10249	-0.011	0.24	NO
151	UBE2R2	UBE2R2	UBE2R2	10277	-0.011	0.24	NO
152	RNF220	RNF220	RNF220	10282	-0.011	0.24	NO
153	ASB3	ASB3	ASB3	10332	-0.012	0.24	NO
154	NPEPPS	NPEPPS	NPEPPS	10405	-0.012	0.23	NO
155	CALR	CALR	CALR	10431	-0.012	0.23	NO
156	PSMD14	PSMD14	PSMD14	10573	-0.014	0.23	NO
157	PSMA7	PSMA7	PSMA7	10642	-0.015	0.22	NO
158	UBR4	UBR4	UBR4	10685	-0.015	0.22	NO
159	HUWE1	HUWE1	HUWE1	10693	-0.015	0.22	NO
160	ARIH2	ARIH2	ARIH2	10751	-0.016	0.22	NO
161	PSMD6	PSMD6	PSMD6	10761	-0.016	0.22	NO
162	PSMD11	PSMD11	PSMD11	10815	-0.017	0.22	NO
163	PSMD1	PSMD1	PSMD1	10931	-0.018	0.21	NO
164	KLHL20	KLHL20	KLHL20	11106	-0.02	0.2	NO
165	PSMC3	PSMC3	PSMC3	11140	-0.02	0.2	NO
166	LRSAM1	LRSAM1	LRSAM1	11150	-0.02	0.2	NO
167	BTRC	BTRC	BTRC	11191	-0.021	0.2	NO
168	UBOX5	UBOX5	UBOX5	11224	-0.021	0.2	NO
169	UBE2V2	UBE2V2	UBE2V2	11348	-0.022	0.2	NO
170	UBE2L3	UBE2L3	UBE2L3	11373	-0.022	0.2	NO
171	CDC16	CDC16	CDC16	11442	-0.023	0.19	NO
172	SEC61A1	SEC61A1	SEC61A1	11538	-0.024	0.19	NO
173	SEC31A	SEC31A	SEC31A	11554	-0.025	0.19	NO
174	PJA1	PJA1	PJA1	11727	-0.027	0.18	NO
175	CANX	CANX	CANX	11751	-0.027	0.18	NO
176	SEC23A	SEC23A	SEC23A	11761	-0.027	0.18	NO
177	ANAPC11	ANAPC11	ANAPC11	11842	-0.028	0.18	NO
178	RNF182	RNF182	RNF182	11850	-0.028	0.18	NO
179	TCEB1	TCEB1	TCEB1	11865	-0.028	0.18	NO
180	UBA1	UBA1	UBA1	11932	-0.029	0.18	NO
181	HSPA5	HSPA5	HSPA5	12012	-0.03	0.17	NO
182	PSMC4	PSMC4	PSMC4	12038	-0.03	0.17	NO
183	UBA52	UBA52	UBA52	12069	-0.03	0.17	NO
184	SEC61G	SEC61G	SEC61G	12071	-0.03	0.18	NO
185	SEC13	SEC13	SEC13	12153	-0.032	0.17	NO
186	FBXW11	FBXW11	FBXW11	12300	-0.033	0.17	NO
187	RNF41	RNF41	RNF41	12326	-0.034	0.17	NO
188	PSMD3	PSMD3	PSMD3	12584	-0.037	0.15	NO
189	BLMH	BLMH	BLMH	12690	-0.038	0.15	NO
190	PSMD2	PSMD2	PSMD2	12752	-0.039	0.15	NO
191	SMURF1	SMURF1	SMURF1	12897	-0.04	0.14	NO
192	STUB1	STUB1	STUB1	12910	-0.041	0.14	NO
193	ASB11	ASB11	ASB11	13042	-0.042	0.14	NO
194	TCEB2	TCEB2	TCEB2	13126	-0.043	0.14	NO
195	PSMB4	PSMB4	PSMB4	13132	-0.044	0.14	NO
196	UBE2Q1	UBE2Q1	UBE2Q1	13165	-0.044	0.14	NO
197	RNF25	RNF25	RNF25	13175	-0.044	0.14	NO
198	UBE2O	UBE2O	UBE2O	13214	-0.045	0.14	NO
199	TRIM36	TRIM36	TRIM36	13247	-0.045	0.14	NO
200	CDC20	CDC20	CDC20	13333	-0.046	0.14	NO
201	SEC61A2	SEC61A2	SEC61A2	13395	-0.047	0.14	NO
202	TRIM11	TRIM11	TRIM11	13458	-0.048	0.14	NO
203	SAE1	SAE1	SAE1	13588	-0.05	0.13	NO
204	UBE2D4	UBE2D4	UBE2D4	13725	-0.052	0.13	NO
205	PSMD4	PSMD4	PSMD4	13869	-0.054	0.12	NO
206	ASB6	ASB6	ASB6	13885	-0.054	0.12	NO
207	HERC2	HERC2	HERC2	13979	-0.056	0.12	NO
208	UBA2	UBA2	UBA2	14046	-0.057	0.12	NO
209	PSMD8	PSMD8	PSMD8	14061	-0.057	0.12	NO
210	ANAPC1	ANAPC1	ANAPC1	14151	-0.058	0.12	NO
211	RNF123	RNF123	RNF123	14230	-0.06	0.12	NO
212	PSMB7	PSMB7	PSMB7	14548	-0.065	0.1	NO
213	UBE2M	UBE2M	UBE2M	14584	-0.066	0.1	NO
214	ASB4	ASB4	ASB4	14948	-0.073	0.087	NO
215	UBE2E3	UBE2E3	UBE2E3	14949	-0.073	0.091	NO
216	ASB1	ASB1	ASB1	15130	-0.076	0.085	NO
217	UBE2C	UBE2C	UBE2C	15144	-0.077	0.088	NO
218	LRRC41	LRRC41	LRRC41	15291	-0.08	0.083	NO
219	FBXW8	FBXW8	FBXW8	15520	-0.085	0.075	NO
220	CDC34	CDC34	CDC34	15546	-0.086	0.078	NO
221	UBE2S	UBE2S	UBE2S	15558	-0.086	0.081	NO
222	PSMB5	PSMB5	PSMB5	15570	-0.086	0.085	NO
223	DET1	DET1	DET1	15643	-0.088	0.085	NO
224	CUL7	CUL7	CUL7	15829	-0.094	0.08	NO
225	TRIM32	TRIM32	TRIM32	15872	-0.095	0.082	NO
226	GAN	GAN	GAN	15908	-0.096	0.085	NO
227	ITGB5	ITGB5	ITGB5	16004	-0.099	0.084	NO
228	KLHL13	KLHL13	KLHL13	16187	-0.1	0.079	NO
229	SKP2	SKP2	SKP2	16363	-0.11	0.075	NO
230	TRIM9	TRIM9	TRIM9	17216	-0.16	0.035	NO
231	FBXO17	FBXO17	FBXO17	17786	-0.22	0.014	NO

Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG HISTIDINE 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	FASLG	FASLG	FASLG	81	0.9	0.057	YES
2	PRKCQ	PRKCQ	PRKCQ	89	0.89	0.12	YES
3	TNF	TNF	TNF	202	0.8	0.17	YES
4	GZMB	GZMB	GZMB	252	0.76	0.22	YES
5	TNFSF10	TNFSF10	TNFSF10	537	0.6	0.24	YES
6	DAPK2	DAPK2	DAPK2	716	0.53	0.27	YES
7	CASP10	CASP10	CASP10	804	0.51	0.3	YES
8	PSMB9	PSMB9	PSMB9	1030	0.44	0.31	YES
9	MST4	MST4	MST4	1061	0.43	0.34	YES
10	FAS	FAS	FAS	1406	0.35	0.35	YES
11	UNC5A	UNC5A	UNC5A	1407	0.35	0.37	YES
12	HIST1H1D	HIST1H1D	HIST1H1D	1533	0.32	0.39	YES
13	PSMA8	PSMA8	PSMA8	1535	0.32	0.41	YES
14	PSMB10	PSMB10	PSMB10	1738	0.28	0.42	YES
15	CFLAR	CFLAR	CFLAR	2149	0.23	0.41	YES
16	PSMB8	PSMB8	PSMB8	2154	0.23	0.42	YES
17	BMX	BMX	BMX	2161	0.23	0.44	YES
18	SATB1	SATB1	SATB1	2282	0.21	0.45	YES
19	CASP8	CASP8	CASP8	2329	0.21	0.46	YES
20	CDH1	CDH1	CDH1	2378	0.2	0.47	YES
21	PSME2	PSME2	PSME2	2382	0.2	0.48	YES
22	PMAIP1	PMAIP1	PMAIP1	2592	0.19	0.48	YES
23	BCL2L11	BCL2L11	BCL2L11	2705	0.18	0.49	YES
24	PSME1	PSME1	PSME1	2709	0.18	0.5	YES
25	HIST1H1B	HIST1H1B	HIST1H1B	2730	0.17	0.51	YES
26	BMF	BMF	BMF	2882	0.16	0.52	YES
27	HMGB2	HMGB2	HMGB2	3394	0.13	0.5	NO
28	CASP7	CASP7	CASP7	3402	0.13	0.5	NO
29	CASP3	CASP3	CASP3	3414	0.13	0.51	NO
30	DAPK1	DAPK1	DAPK1	3688	0.12	0.51	NO
31	BCL2	BCL2	BCL2	3711	0.11	0.51	NO
32	TRADD	TRADD	TRADD	3783	0.11	0.52	NO
33	DCC	DCC	DCC	4070	0.1	0.51	NO
34	LMNB1	LMNB1	LMNB1	4686	0.078	0.48	NO
35	BIRC2	BIRC2	BIRC2	4826	0.074	0.48	NO
36	ROCK1	ROCK1	ROCK1	4855	0.074	0.48	NO
37	PSMA3	PSMA3	PSMA3	5063	0.068	0.47	NO
38	TJP2	TJP2	TJP2	5092	0.067	0.48	NO
39	CASP6	CASP6	CASP6	5113	0.067	0.48	NO
40	APAF1	APAF1	APAF1	5146	0.066	0.48	NO
41	XIAP	XIAP	XIAP	5363	0.061	0.47	NO
42	PRKCD	PRKCD	PRKCD	5526	0.058	0.47	NO
43	PSMA4	PSMA4	PSMA4	5667	0.055	0.46	NO
44	TRAF2	TRAF2	TRAF2	5740	0.053	0.46	NO
45	DBNL	DBNL	DBNL	5842	0.051	0.46	NO
46	PSMA5	PSMA5	PSMA5	5959	0.049	0.46	NO
47	PSMB1	PSMB1	PSMB1	6232	0.043	0.45	NO
48	LOC647859	LOC647859	LOC647859	6240	0.043	0.45	NO
49	PSMA6	PSMA6	PSMA6	6469	0.038	0.44	NO
50	BCL2L1	BCL2L1	BCL2L1	6483	0.038	0.44	NO
51	BID	BID	BID	6581	0.036	0.44	NO
52	PSMB3	PSMB3	PSMB3	6696	0.034	0.43	NO
53	BAK1	BAK1	BAK1	6772	0.033	0.43	NO
54	UNC5B	UNC5B	UNC5B	6847	0.032	0.43	NO
55	PAK2	PAK2	PAK2	6974	0.03	0.42	NO
56	APPL1	APPL1	APPL1	7000	0.029	0.43	NO
57	HIST1H1E	HIST1H1E	HIST1H1E	7092	0.028	0.42	NO
58	PSMA2	PSMA2	PSMA2	7301	0.025	0.41	NO
59	PSME4	PSME4	PSME4	7503	0.022	0.4	NO
60	HMGB1	HMGB1	HMGB1	7593	0.021	0.4	NO
61	PSMC6	PSMC6	PSMC6	7619	0.021	0.4	NO
62	RIPK1	RIPK1	RIPK1	7620	0.021	0.4	NO
63	PSMD10	PSMD10	PSMD10	7998	0.016	0.38	NO
64	APC	APC	APC	8330	0.012	0.36	NO
65	DFFB	DFFB	DFFB	8341	0.012	0.36	NO
66	CASP9	CASP9	CASP9	8352	0.011	0.36	NO
67	ARHGAP10	ARHGAP10	ARHGAP10	8372	0.011	0.36	NO
68	PSMC2	PSMC2	PSMC2	8373	0.011	0.36	NO
69	YWHAB	YWHAB	YWHAB	8455	0.0098	0.36	NO
70	OCLN	OCLN	OCLN	8620	0.0079	0.35	NO
71	NMT1	NMT1	NMT1	8643	0.0076	0.35	NO
72	TJP1	TJP1	TJP1	8680	0.0072	0.35	NO
73	FNTA	FNTA	FNTA	8718	0.0066	0.35	NO
74	PSMB6	PSMB6	PSMB6	8803	0.0055	0.34	NO
75	PSMB2	PSMB2	PSMB2	8874	0.0046	0.34	NO
76	TNFRSF1A	TNFRSF1A	TNFRSF1A	8906	0.0042	0.34	NO
77	PSMA1	PSMA1	PSMA1	8974	0.0034	0.34	NO
78	HIST1H1C	HIST1H1C	HIST1H1C	9049	0.0025	0.33	NO
79	RPS27A	RPS27A	RPS27A	9105	0.0018	0.33	NO
80	PSMD9	PSMD9	PSMD9	9245	0.0003	0.32	NO
81	PSMC5	PSMC5	PSMC5	9267	-0.000016	0.32	NO
82	ACIN1	ACIN1	ACIN1	9349	-0.0011	0.31	NO
83	PSMF1	PSMF1	PSMF1	9446	-0.0024	0.31	NO
84	PPP3R1	PPP3R1	PPP3R1	9489	-0.0028	0.31	NO
85	GSN	GSN	GSN	9748	-0.0052	0.29	NO
86	ADD1	ADD1	ADD1	9982	-0.0079	0.28	NO
87	PSMD7	PSMD7	PSMD7	10012	-0.0082	0.28	NO
88	PSMD13	PSMD13	PSMD13	10104	-0.0093	0.28	NO
89	PSMD12	PSMD12	PSMD12	10107	-0.0093	0.28	NO
90	PSMC1	PSMC1	PSMC1	10207	-0.01	0.27	NO
91	PSMD5	PSMD5	PSMD5	10249	-0.011	0.27	NO
92	KPNA1	KPNA1	KPNA1	10399	-0.012	0.26	NO
93	PSMD14	PSMD14	PSMD14	10573	-0.014	0.25	NO
94	PSMA7	PSMA7	PSMA7	10642	-0.015	0.25	NO
95	KPNB1	KPNB1	KPNB1	10689	-0.015	0.25	NO
96	PKP1	PKP1	PKP1	10746	-0.016	0.25	NO
97	PSMD6	PSMD6	PSMD6	10761	-0.016	0.25	NO
98	PSMD11	PSMD11	PSMD11	10815	-0.017	0.24	NO
99	SPTAN1	SPTAN1	SPTAN1	10840	-0.017	0.24	NO
100	PLEC	PLEC	PLEC	10886	-0.018	0.24	NO
101	PSMD1	PSMD1	PSMD1	10931	-0.018	0.24	NO
102	TP53	TP53	TP53	10990	-0.019	0.24	NO
103	PSMC3	PSMC3	PSMC3	11140	-0.02	0.23	NO
104	DYNLL1	DYNLL1	DYNLL1	11227	-0.021	0.23	NO
105	DSG3	DSG3	DSG3	11252	-0.021	0.23	NO
106	BAX	BAX	BAX	11301	-0.022	0.23	NO
107	BCAP31	BCAP31	BCAP31	11386	-0.022	0.23	NO
108	CYCS	CYCS	CYCS	11678	-0.026	0.21	NO
109	PSMC4	PSMC4	PSMC4	12038	-0.03	0.19	NO
110	UBA52	UBA52	UBA52	12069	-0.03	0.19	NO
111	DNM1L	DNM1L	DNM1L	12131	-0.031	0.19	NO
112	DYNLL2	DYNLL2	DYNLL2	12282	-0.033	0.19	NO
113	AKT1	AKT1	AKT1	12293	-0.033	0.19	NO
114	TFDP1	TFDP1	TFDP1	12400	-0.035	0.18	NO
115	DSP	DSP	DSP	12409	-0.035	0.19	NO
116	STK24	STK24	STK24	12554	-0.036	0.18	NO
117	PSMD3	PSMD3	PSMD3	12584	-0.037	0.18	NO
118	PSMD2	PSMD2	PSMD2	12752	-0.039	0.18	NO
119	BAD	BAD	BAD	12804	-0.039	0.18	NO
120	CTNNB1	CTNNB1	CTNNB1	12967	-0.042	0.17	NO
121	PSMB4	PSMB4	PSMB4	13132	-0.044	0.16	NO
122	BBC3	BBC3	BBC3	13192	-0.044	0.16	NO
123	MAPK8	MAPK8	MAPK8	13228	-0.045	0.16	NO
124	DIABLO	DIABLO	DIABLO	13235	-0.045	0.17	NO
125	VIM	VIM	VIM	13410	-0.047	0.16	NO
126	FADD	FADD	FADD	13534	-0.049	0.16	NO
127	E2F1	E2F1	E2F1	13667	-0.051	0.15	NO
128	PSMD4	PSMD4	PSMD4	13869	-0.054	0.14	NO
129	MAGED1	MAGED1	MAGED1	13892	-0.054	0.15	NO
130	DFFA	DFFA	DFFA	13915	-0.055	0.15	NO
131	PSMD8	PSMD8	PSMD8	14061	-0.057	0.15	NO
132	DAPK3	DAPK3	DAPK3	14206	-0.059	0.14	NO
133	PSMB7	PSMB7	PSMB7	14548	-0.065	0.13	NO
134	MAPT	MAPT	MAPT	15117	-0.076	0.1	NO
135	TNFRSF10B	TNFRSF10B	TNFRSF10B	15395	-0.082	0.091	NO
136	LMNA	LMNA	LMNA	15490	-0.084	0.091	NO
137	PSMB5	PSMB5	PSMB5	15570	-0.086	0.093	NO
138	PTK2	PTK2	PTK2	16021	-0.1	0.074	NO
139	DSG1	DSG1	DSG1	16110	-0.1	0.077	NO
140	H1F0	H1F0	H1F0	16347	-0.11	0.071	NO
141	GAS2	GAS2	GAS2	16975	-0.14	0.046	NO
142	DSG2	DSG2	DSG2	17639	-0.2	0.022	NO

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

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

Table 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	NCF4	NCF4	NCF4	497	0.62	0.038	YES
2	FCGR1A	FCGR1A	FCGR1A	623	0.57	0.091	YES
3	FCGR1B	FCGR1B	FCGR1B	626	0.57	0.15	YES
4	CYBB	CYBB	CYBB	677	0.55	0.2	YES
5	NCF2	NCF2	NCF2	728	0.53	0.26	YES
6	MRC1	MRC1	MRC1	977	0.45	0.29	YES
7	CTSS	CTSS	CTSS	981	0.45	0.34	YES
8	PSMB9	PSMB9	PSMB9	1030	0.44	0.38	YES
9	HLA-F	HLA-F	HLA-F	1235	0.39	0.41	YES
10	PSMA8	PSMA8	PSMA8	1535	0.32	0.43	YES
11	TAP1	TAP1	TAP1	1724	0.29	0.45	YES
12	HLA-G	HLA-G	HLA-G	1734	0.28	0.48	YES
13	PSMB10	PSMB10	PSMB10	1738	0.28	0.51	YES
14	HLA-B	HLA-B	HLA-B	1796	0.27	0.53	YES
15	CYBA	CYBA	CYBA	1912	0.26	0.55	YES
16	CD207	CD207	CD207	2057	0.24	0.57	YES
17	B2M	B2M	B2M	2091	0.24	0.59	YES
18	PSMB8	PSMB8	PSMB8	2154	0.23	0.61	YES
19	HLA-C	HLA-C	HLA-C	2224	0.22	0.63	YES
20	PSME2	PSME2	PSME2	2382	0.2	0.64	YES
21	LNPEP	LNPEP	LNPEP	2448	0.2	0.66	YES
22	TAP2	TAP2	TAP2	2571	0.19	0.68	YES
23	PSME1	PSME1	PSME1	2709	0.18	0.69	YES
24	HLA-A	HLA-A	HLA-A	2779	0.17	0.7	YES
25	CD36	CD36	CD36	4096	0.099	0.64	NO
26	PSMA3	PSMA3	PSMA3	5063	0.068	0.59	NO
27	PSMA4	PSMA4	PSMA4	5667	0.055	0.56	NO
28	PSMA5	PSMA5	PSMA5	5959	0.049	0.55	NO
29	PSMB1	PSMB1	PSMB1	6232	0.043	0.54	NO
30	PSMA6	PSMA6	PSMA6	6469	0.038	0.53	NO
31	ITGAV	ITGAV	ITGAV	6492	0.038	0.54	NO
32	PSMB3	PSMB3	PSMB3	6696	0.034	0.53	NO
33	PSMA2	PSMA2	PSMA2	7301	0.025	0.5	NO
34	SEC61B	SEC61B	SEC61B	7359	0.024	0.5	NO
35	PSME4	PSME4	PSME4	7503	0.022	0.49	NO
36	MRC2	MRC2	MRC2	7572	0.021	0.49	NO
37	PSMC6	PSMC6	PSMC6	7619	0.021	0.49	NO
38	PSMD10	PSMD10	PSMD10	7998	0.016	0.47	NO
39	PDIA3	PDIA3	PDIA3	8111	0.014	0.46	NO
40	PSMC2	PSMC2	PSMC2	8373	0.011	0.45	NO
41	PSMB6	PSMB6	PSMB6	8803	0.0055	0.43	NO
42	PSMB2	PSMB2	PSMB2	8874	0.0046	0.42	NO
43	PSMA1	PSMA1	PSMA1	8974	0.0034	0.42	NO
44	RPS27A	RPS27A	RPS27A	9105	0.0018	0.41	NO
45	PSMD9	PSMD9	PSMD9	9245	0.0003	0.4	NO
46	PSMC5	PSMC5	PSMC5	9267	-0.000016	0.4	NO
47	PSMF1	PSMF1	PSMF1	9446	-0.0024	0.39	NO
48	PSMD7	PSMD7	PSMD7	10012	-0.0082	0.36	NO
49	PSMD13	PSMD13	PSMD13	10104	-0.0093	0.36	NO
50	PSMD12	PSMD12	PSMD12	10107	-0.0093	0.36	NO
51	PSMC1	PSMC1	PSMC1	10207	-0.01	0.35	NO
52	PSMD5	PSMD5	PSMD5	10249	-0.011	0.35	NO
53	CALR	CALR	CALR	10431	-0.012	0.34	NO
54	PSMD14	PSMD14	PSMD14	10573	-0.014	0.34	NO
55	PSMA7	PSMA7	PSMA7	10642	-0.015	0.34	NO
56	PSMD6	PSMD6	PSMD6	10761	-0.016	0.33	NO
57	PSMD11	PSMD11	PSMD11	10815	-0.017	0.33	NO
58	PSMD1	PSMD1	PSMD1	10931	-0.018	0.32	NO
59	PSMC3	PSMC3	PSMC3	11140	-0.02	0.32	NO
60	SEC61A1	SEC61A1	SEC61A1	11538	-0.024	0.3	NO
61	PSMC4	PSMC4	PSMC4	12038	-0.03	0.27	NO
62	UBA52	UBA52	UBA52	12069	-0.03	0.27	NO
63	SEC61G	SEC61G	SEC61G	12071	-0.03	0.28	NO
64	PSMD3	PSMD3	PSMD3	12584	-0.037	0.25	NO
65	PSMD2	PSMD2	PSMD2	12752	-0.039	0.25	NO
66	PSMB4	PSMB4	PSMB4	13132	-0.044	0.23	NO
67	SEC61A2	SEC61A2	SEC61A2	13395	-0.047	0.22	NO
68	PSMD4	PSMD4	PSMD4	13869	-0.054	0.2	NO
69	PSMD8	PSMD8	PSMD8	14061	-0.057	0.2	NO
70	PSMB7	PSMB7	PSMB7	14548	-0.065	0.18	NO
71	PSMB5	PSMB5	PSMB5	15570	-0.086	0.13	NO
72	ITGB5	ITGB5	ITGB5	16004	-0.099	0.11	NO

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

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

genes ES table in pathway: KEGG TRYPTOPHAN 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	CARD11	CARD11	CARD11	131	0.84	0.15	YES
2	PRKCB	PRKCB	PRKCB	348	0.7	0.26	YES
3	PSMB9	PSMB9	PSMB9	1030	0.44	0.31	YES
4	PSMA8	PSMA8	PSMA8	1535	0.32	0.34	YES
5	PSMB10	PSMB10	PSMB10	1738	0.28	0.38	YES
6	NFKBIA	NFKBIA	NFKBIA	2005	0.25	0.41	YES
7	REL	REL	REL	2106	0.23	0.45	YES
8	PSMB8	PSMB8	PSMB8	2154	0.23	0.49	YES
9	PSME2	PSME2	PSME2	2382	0.2	0.51	YES
10	MALT1	MALT1	MALT1	2679	0.18	0.53	YES
11	PSME1	PSME1	PSME1	2709	0.18	0.56	YES
12	NFKBIE	NFKBIE	NFKBIE	3335	0.13	0.55	NO
13	IKBKG	IKBKG	IKBKG	4881	0.073	0.48	NO
14	BCL10	BCL10	BCL10	4930	0.072	0.49	NO
15	PSMA3	PSMA3	PSMA3	5063	0.068	0.49	NO
16	MAP3K7	MAP3K7	MAP3K7	5313	0.062	0.49	NO
17	CHUK	CHUK	CHUK	5614	0.056	0.48	NO
18	IKBKB	IKBKB	IKBKB	5656	0.055	0.49	NO
19	PSMA4	PSMA4	PSMA4	5667	0.055	0.5	NO
20	PSMA5	PSMA5	PSMA5	5959	0.049	0.49	NO
21	NFKBIB	NFKBIB	NFKBIB	6019	0.048	0.5	NO
22	PSMB1	PSMB1	PSMB1	6232	0.043	0.49	NO
23	PSMA6	PSMA6	PSMA6	6469	0.038	0.49	NO
24	PSMB3	PSMB3	PSMB3	6696	0.034	0.48	NO
25	PSMA2	PSMA2	PSMA2	7301	0.025	0.45	NO
26	PSME4	PSME4	PSME4	7503	0.022	0.45	NO
27	PSMC6	PSMC6	PSMC6	7619	0.021	0.44	NO
28	CUL1	CUL1	CUL1	7889	0.017	0.43	NO
29	PSMD10	PSMD10	PSMD10	7998	0.016	0.43	NO
30	PSMC2	PSMC2	PSMC2	8373	0.011	0.41	NO
31	PSMB6	PSMB6	PSMB6	8803	0.0055	0.39	NO
32	PSMB2	PSMB2	PSMB2	8874	0.0046	0.38	NO
33	PSMA1	PSMA1	PSMA1	8974	0.0034	0.38	NO
34	RPS27A	RPS27A	RPS27A	9105	0.0018	0.37	NO
35	PSMD9	PSMD9	PSMD9	9245	0.0003	0.36	NO
36	PSMC5	PSMC5	PSMC5	9267	-0.000016	0.36	NO
37	PSMF1	PSMF1	PSMF1	9446	-0.0024	0.35	NO
38	PSMD7	PSMD7	PSMD7	10012	-0.0082	0.32	NO
39	PSMD13	PSMD13	PSMD13	10104	-0.0093	0.32	NO
40	PSMD12	PSMD12	PSMD12	10107	-0.0093	0.32	NO
41	SKP1	SKP1	SKP1	10135	-0.0096	0.32	NO
42	PSMC1	PSMC1	PSMC1	10207	-0.01	0.32	NO
43	PSMD5	PSMD5	PSMD5	10249	-0.011	0.32	NO
44	PSMD14	PSMD14	PSMD14	10573	-0.014	0.3	NO
45	PSMA7	PSMA7	PSMA7	10642	-0.015	0.3	NO
46	PSMD6	PSMD6	PSMD6	10761	-0.016	0.3	NO
47	PSMD11	PSMD11	PSMD11	10815	-0.017	0.3	NO
48	RELA	RELA	RELA	10903	-0.018	0.3	NO
49	PSMD1	PSMD1	PSMD1	10931	-0.018	0.3	NO
50	PSMC3	PSMC3	PSMC3	11140	-0.02	0.29	NO
51	BTRC	BTRC	BTRC	11191	-0.021	0.29	NO
52	PSMC4	PSMC4	PSMC4	12038	-0.03	0.25	NO
53	UBA52	UBA52	UBA52	12069	-0.03	0.26	NO
54	FBXW11	FBXW11	FBXW11	12300	-0.033	0.25	NO
55	PSMD3	PSMD3	PSMD3	12584	-0.037	0.24	NO
56	PSMD2	PSMD2	PSMD2	12752	-0.039	0.24	NO
57	PSMB4	PSMB4	PSMB4	13132	-0.044	0.22	NO
58	PSMD4	PSMD4	PSMD4	13869	-0.054	0.19	NO
59	PSMD8	PSMD8	PSMD8	14061	-0.057	0.19	NO
60	PSMB7	PSMB7	PSMB7	14548	-0.065	0.18	NO
61	PSMB5	PSMB5	PSMB5	15570	-0.086	0.14	NO

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

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

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	PRKCQ	PRKCQ	PRKCQ	89	0.89	0.13	YES
2	AKAP5	AKAP5	AKAP5	270	0.75	0.24	YES
3	PRKCB	PRKCB	PRKCB	348	0.7	0.35	YES
4	MAP3K8	MAP3K8	MAP3K8	535	0.61	0.43	YES
5	PRKCH	PRKCH	PRKCH	1309	0.37	0.45	YES
6	PIM1	PIM1	PIM1	1329	0.36	0.5	YES
7	CAMK4	CAMK4	CAMK4	1414	0.34	0.55	YES
8	NFATC2	NFATC2	NFATC2	1809	0.27	0.57	YES
9	PRKCG	PRKCG	PRKCG	2148	0.23	0.59	YES
10	NFATC1	NFATC1	NFATC1	2625	0.18	0.59	YES
11	CASP3	CASP3	CASP3	3414	0.13	0.57	NO
12	BCL2	BCL2	BCL2	3711	0.11	0.57	NO
13	PRKCZ	PRKCZ	PRKCZ	3938	0.1	0.58	NO
14	NFATC3	NFATC3	NFATC3	4829	0.074	0.54	NO
15	MAP3K1	MAP3K1	MAP3K1	4925	0.072	0.54	NO
16	PPP3CB	PPP3CB	PPP3CB	5096	0.067	0.55	NO
17	PRKCD	PRKCD	PRKCD	5526	0.058	0.53	NO
18	RCAN2	RCAN2	RCAN2	5568	0.057	0.54	NO
19	BCL2L1	BCL2L1	BCL2L1	6483	0.038	0.49	NO
20	PPP3CA	PPP3CA	PPP3CA	6832	0.032	0.48	NO
21	YWHAH	YWHAH	YWHAH	6992	0.03	0.47	NO
22	MAPK9	MAPK9	MAPK9	7793	0.019	0.43	NO
23	YWHAB	YWHAB	YWHAB	8455	0.0098	0.4	NO
24	CSNK1A1	CSNK1A1	CSNK1A1	8555	0.0086	0.39	NO
25	XPO1	XPO1	XPO1	9118	0.0016	0.36	NO
26	MAPK14	MAPK14	MAPK14	9181	0.00082	0.36	NO
27	PPP3R1	PPP3R1	PPP3R1	9489	-0.0028	0.34	NO
28	MAPK3	MAPK3	MAPK3	9630	-0.0041	0.34	NO
29	SFN	SFN	SFN	9759	-0.0053	0.33	NO
30	RCAN1	RCAN1	RCAN1	9882	-0.0067	0.32	NO
31	FKBP1A	FKBP1A	FKBP1A	10039	-0.0085	0.32	NO
32	YWHAZ	YWHAZ	YWHAZ	10112	-0.0094	0.31	NO
33	CREBBP	CREBBP	CREBBP	10160	-0.0098	0.31	NO
34	CABIN1	CABIN1	CABIN1	10550	-0.014	0.29	NO
35	KPNB1	KPNB1	KPNB1	10689	-0.015	0.29	NO
36	EP300	EP300	EP300	10906	-0.018	0.28	NO
37	GSK3B	GSK3B	GSK3B	11111	-0.02	0.27	NO
38	BAX	BAX	BAX	11301	-0.022	0.26	NO
39	FKBP8	FKBP8	FKBP8	11403	-0.023	0.26	NO
40	KPNA2	KPNA2	KPNA2	11406	-0.023	0.26	NO
41	MEF2D	MEF2D	MEF2D	11419	-0.023	0.27	NO
42	PRKACA	PRKACA	PRKACA	11544	-0.024	0.26	NO
43	RAN	RAN	RAN	11817	-0.028	0.25	NO
44	CHP	CHP	CHP	11876	-0.028	0.26	NO
45	BAD	BAD	BAD	12804	-0.039	0.21	NO
46	NUP214	NUP214	NUP214	13016	-0.042	0.2	NO
47	YWHAG	YWHAG	YWHAG	13191	-0.044	0.2	NO
48	MAPK8	MAPK8	MAPK8	13228	-0.045	0.21	NO
49	YWHAQ	YWHAQ	YWHAQ	13295	-0.046	0.21	NO
50	YWHAE	YWHAE	YWHAE	13356	-0.046	0.21	NO
51	PRKCE	PRKCE	PRKCE	14440	-0.063	0.16	NO
52	NR4A1	NR4A1	NR4A1	14797	-0.07	0.16	NO
53	CSNK2A1	CSNK2A1	CSNK2A1	14812	-0.07	0.16	NO
54	PRKCA	PRKCA	PRKCA	15766	-0.092	0.13	NO

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

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

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR 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	ZBP1	ZBP1	ZBP1	47	0.94	0.13	YES
2	NOD2	NOD2	NOD2	442	0.65	0.2	YES
3	RIPK3	RIPK3	RIPK3	501	0.62	0.28	YES
4	IRAK2	IRAK2	IRAK2	1268	0.38	0.29	YES
5	IRF7	IRF7	IRF7	1845	0.27	0.29	YES
6	TLR3	TLR3	TLR3	1873	0.26	0.33	YES
7	IKBKE	IKBKE	IKBKE	1929	0.26	0.36	YES
8	NFKBIA	NFKBIA	NFKBIA	2005	0.25	0.39	YES
9	AGER	AGER	AGER	2158	0.23	0.41	YES
10	S100A12	S100A12	S100A12	2256	0.22	0.44	YES
11	NFKB2	NFKB2	NFKB2	2379	0.2	0.46	YES
12	RPS6KA1	RPS6KA1	RPS6KA1	2420	0.2	0.48	YES
13	MAP2K6	MAP2K6	MAP2K6	3174	0.14	0.46	YES
14	S100B	S100B	S100B	3334	0.13	0.47	YES
15	MEF2C	MEF2C	MEF2C	3416	0.13	0.48	YES
16	RPS6KA2	RPS6KA2	RPS6KA2	3428	0.13	0.5	YES
17	SAA1	SAA1	SAA1	3853	0.11	0.49	YES
18	NOD1	NOD1	NOD1	4068	0.1	0.49	YES
19	TAB2	TAB2	TAB2	4093	0.099	0.51	YES
20	TBK1	TBK1	TBK1	4385	0.088	0.5	YES
21	RIPK2	RIPK2	RIPK2	4414	0.087	0.51	YES
22	IRF3	IRF3	IRF3	4573	0.082	0.52	YES
23	IKBKG	IKBKG	IKBKG	4881	0.073	0.51	YES
24	TAB3	TAB3	TAB3	5244	0.064	0.5	YES
25	MAP3K7	MAP3K7	MAP3K7	5313	0.062	0.5	YES
26	CREB1	CREB1	CREB1	5420	0.06	0.5	YES
27	RPS6KA5	RPS6KA5	RPS6KA5	5445	0.06	0.51	YES
28	MAPK10	MAPK10	MAPK10	5471	0.059	0.52	YES
29	CHUK	CHUK	CHUK	5614	0.056	0.52	YES
30	IKBKB	IKBKB	IKBKB	5656	0.055	0.52	YES
31	MAP2K3	MAP2K3	MAP2K3	5962	0.049	0.51	YES
32	ATF1	ATF1	ATF1	5994	0.048	0.52	YES
33	NFKBIB	NFKBIB	NFKBIB	6019	0.048	0.52	YES
34	MEF2A	MEF2A	MEF2A	6059	0.046	0.53	YES
35	MAP2K1	MAP2K1	MAP2K1	6451	0.039	0.51	NO
36	FOS	FOS	FOS	6514	0.038	0.51	NO
37	MAPKAPK2	MAPKAPK2	MAPKAPK2	6552	0.037	0.52	NO
38	PPP2CA	PPP2CA	PPP2CA	6793	0.033	0.51	NO
39	RPS6KA3	RPS6KA3	RPS6KA3	7071	0.028	0.5	NO
40	MAP2K4	MAP2K4	MAP2K4	7210	0.026	0.49	NO
41	PPP2R1B	PPP2R1B	PPP2R1B	7487	0.022	0.48	NO
42	HMGB1	HMGB1	HMGB1	7593	0.021	0.48	NO
43	RIPK1	RIPK1	RIPK1	7620	0.021	0.48	NO
44	MAPK11	MAPK11	MAPK11	7707	0.02	0.48	NO
45	MAPK9	MAPK9	MAPK9	7793	0.019	0.47	NO
46	JUN	JUN	JUN	7979	0.016	0.46	NO
47	TICAM1	TICAM1	TICAM1	8297	0.012	0.45	NO
48	RPS27A	RPS27A	RPS27A	9105	0.0018	0.4	NO
49	ATF2	ATF2	ATF2	9155	0.0012	0.4	NO
50	MAPK14	MAPK14	MAPK14	9181	0.00082	0.4	NO
51	MAPKAPK3	MAPKAPK3	MAPKAPK3	9409	-0.0019	0.39	NO
52	MAPK3	MAPK3	MAPK3	9630	-0.0041	0.38	NO
53	DUSP6	DUSP6	DUSP6	9633	-0.0042	0.38	NO
54	IRAK1	IRAK1	IRAK1	10506	-0.013	0.33	NO
55	TRAF6	TRAF6	TRAF6	10774	-0.016	0.32	NO
56	DUSP3	DUSP3	DUSP3	10816	-0.017	0.32	NO
57	RELA	RELA	RELA	10903	-0.018	0.32	NO
58	CDK1	CDK1	CDK1	11248	-0.021	0.3	NO
59	ELK1	ELK1	ELK1	11556	-0.025	0.29	NO
60	MAP2K2	MAP2K2	MAP2K2	11676	-0.026	0.28	NO
61	UBA52	UBA52	UBA52	12069	-0.03	0.26	NO
62	APP	APP	APP	12137	-0.031	0.27	NO
63	TAB1	TAB1	TAB1	12299	-0.033	0.26	NO
64	MAPK1	MAPK1	MAPK1	12399	-0.035	0.26	NO
65	MAPK7	MAPK7	MAPK7	12616	-0.037	0.25	NO
66	PPP2CB	PPP2CB	PPP2CB	12722	-0.038	0.25	NO
67	MAPK8	MAPK8	MAPK8	13228	-0.045	0.23	NO
68	DUSP7	DUSP7	DUSP7	13658	-0.051	0.21	NO
69	PPP2R5D	PPP2R5D	PPP2R5D	13740	-0.052	0.22	NO
70	DUSP4	DUSP4	DUSP4	13758	-0.052	0.22	NO
71	MAP2K7	MAP2K7	MAP2K7	13805	-0.053	0.23	NO
72	PPP2R1A	PPP2R1A	PPP2R1A	13943	-0.055	0.23	NO

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

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

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 TGF BETA SIGNALING PATHWAY	85	genes.ES.table	0.56	1.7	0.004	0.82	0.84	0.4	0.21	0.32	0.36	0.23
KEGG ECM RECEPTOR INTERACTION	82	genes.ES.table	0.62	1.6	0.0079	0.62	0.91	0.66	0.22	0.52	0.33	0.17
BIOCARTA ERK PATHWAY	28	genes.ES.table	0.49	1.8	0.0097	1	0.63	0.18	0.094	0.16	0.3	0.24
BIOCARTA MPR PATHWAY	33	genes.ES.table	0.48	1.6	0.025	0.68	0.9	0.21	0.18	0.17	0.35	0.19
WNT SIGNALING	84	genes.ES.table	0.5	1.7	0.0039	0.69	0.9	0.29	0.16	0.24	0.35	0.19
ST INTEGRIN SIGNALING PATHWAY	80	genes.ES.table	0.43	1.6	0.017	0.64	0.9	0.38	0.26	0.28	0.33	0.18
PID INTEGRIN1 PATHWAY	64	genes.ES.table	0.68	1.7	0.0057	0.8	0.87	0.7	0.2	0.56	0.38	0.22
PID EPHBFWDPATHWAY	40	genes.ES.table	0.53	1.7	0.0061	0.83	0.79	0.52	0.33	0.35	0.31	0.22
PID RET PATHWAY	39	genes.ES.table	0.51	1.7	0.016	0.92	0.77	0.46	0.33	0.31	0.34	0.24
PID NCADHERINPATHWAY	33	genes.ES.table	0.59	1.9	0	1	0.46	0.36	0.25	0.27	0	0.38

genes ES table in pathway: KEGG TGF BETA SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GRIA2	GRIA2	GRIA2	14	0.7	0.16	YES
2	GAP43	GAP43	GAP43	20	0.68	0.31	YES
3	CDH2	CDH2	CDH2	181	0.5	0.42	YES
4	FGFR1	FGFR1	FGFR1	931	0.33	0.45	YES
5	GJA1	GJA1	GJA1	957	0.33	0.52	YES
6	CNR1	CNR1	CNR1	2254	0.22	0.5	YES
7	MAPK8	MAPK8	MAPK8	2521	0.2	0.53	YES
8	PIK3CA	PIK3CA	PIK3CA	3182	0.17	0.54	YES
9	DAGLA	DAGLA	DAGLA	3489	0.16	0.55	YES
10	LRP5	LRP5	LRP5	4264	0.13	0.54	YES
11	ROCK1	ROCK1	ROCK1	4469	0.12	0.56	YES
12	KIF5B	KIF5B	KIF5B	4488	0.12	0.58	YES
13	FER	FER	FER	5831	0.092	0.53	NO
14	GSN	GSN	GSN	6611	0.075	0.5	NO
15	PTPN11	PTPN11	PTPN11	7059	0.066	0.5	NO
16	CAMK2G	CAMK2G	CAMK2G	8760	0.035	0.41	NO
17	CTNNA1	CTNNA1	CTNNA1	8802	0.034	0.41	NO
18	PIK3R1	PIK3R1	PIK3R1	9562	0.021	0.38	NO
19	RAC1	RAC1	RAC1	9686	0.02	0.38	NO
20	CDC42	CDC42	CDC42	10252	0.011	0.35	NO
21	PIP5K1C	PIP5K1C	PIP5K1C	10676	0.0043	0.32	NO
22	DAGLB	DAGLB	DAGLB	11100	-0.0023	0.3	NO
23	RHOA	RHOA	RHOA	11198	-0.004	0.3	NO
24	MAPRE1	MAPRE1	MAPRE1	11277	-0.0054	0.29	NO
25	PLCG1	PLCG1	PLCG1	11531	-0.0092	0.28	NO
26	DCTN1	DCTN1	DCTN1	11668	-0.011	0.28	NO
27	JUP	JUP	JUP	12824	-0.029	0.22	NO
28	PTPN1	PTPN1	PTPN1	12853	-0.03	0.22	NO
29	CTTN	CTTN	CTTN	12954	-0.031	0.22	NO
30	CTNND1	CTNND1	CTNND1	13053	-0.033	0.23	NO
31	AXIN1	AXIN1	AXIN1	13659	-0.043	0.2	NO
32	CTNNB1	CTNNB1	CTNNB1	15295	-0.081	0.13	NO
33	MYL2	MYL2	MYL2	15760	-0.097	0.13	NO

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

Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TGF BETA 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 ECM RECEPTOR INTERACTION

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	CHST1	CHST1	CHST1	270	0.46	0.077	YES
2	ACAN	ACAN	ACAN	707	0.37	0.13	YES
3	B4GALT6	B4GALT6	B4GALT6	789	0.35	0.19	YES
4	CHST6	CHST6	CHST6	1131	0.31	0.23	YES
5	CHST5	CHST5	CHST5	1242	0.3	0.29	YES
6	CHST2	CHST2	CHST2	1334	0.29	0.34	YES
7	OGN	OGN	OGN	1352	0.29	0.4	YES
8	LUM	LUM	LUM	1465	0.28	0.44	YES
9	FMOD	FMOD	FMOD	1478	0.28	0.5	YES
10	KERA	KERA	KERA	1486	0.28	0.55	YES
11	B3GNT7	B3GNT7	B3GNT7	1537	0.27	0.6	YES
12	OMD	OMD	OMD	1833	0.25	0.64	YES
13	B3GNT3	B3GNT3	B3GNT3	1998	0.24	0.67	YES
14	B3GNT2	B3GNT2	B3GNT2	6582	0.075	0.43	NO
15	B4GALT4	B4GALT4	B4GALT4	6722	0.072	0.44	NO
16	ST3GAL2	ST3GAL2	ST3GAL2	7365	0.06	0.42	NO
17	B4GALT5	B4GALT5	B4GALT5	8346	0.042	0.37	NO
18	GNS	GNS	GNS	8427	0.04	0.37	NO
19	B4GALT2	B4GALT2	B4GALT2	9083	0.029	0.34	NO
20	ST3GAL1	ST3GAL1	ST3GAL1	9868	0.016	0.3	NO
21	HEXB	HEXB	HEXB	10555	0.0061	0.27	NO
22	B4GALT1	B4GALT1	B4GALT1	11053	-0.0015	0.24	NO
23	B3GNT1	B3GNT1	B3GNT1	11935	-0.015	0.19	NO
24	ST3GAL3	ST3GAL3	ST3GAL3	12461	-0.023	0.17	NO
25	B4GALT3	B4GALT3	B4GALT3	13250	-0.036	0.13	NO
26	B3GNT4	B3GNT4	B3GNT4	14030	-0.051	0.098	NO
27	GLB1	GLB1	GLB1	14524	-0.061	0.083	NO
28	HEXA	HEXA	HEXA	16319	-0.12	0.0079	NO
29	PRELP	PRELP	PRELP	17371	-0.22	-0.0068	NO
30	ST3GAL6	ST3GAL6	ST3GAL6	17376	-0.22	0.037	NO

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

Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ECM 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: BIOCARTA ERK PATHWAY

Table S23. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CHST1	CHST1	CHST1	270	0.46	0.082	YES
2	ACAN	ACAN	ACAN	707	0.37	0.13	YES
3	B4GALT6	B4GALT6	B4GALT6	789	0.35	0.2	YES
4	CHST6	CHST6	CHST6	1131	0.31	0.25	YES
5	CHST5	CHST5	CHST5	1242	0.3	0.3	YES
6	CHST2	CHST2	CHST2	1334	0.29	0.36	YES
7	OGN	OGN	OGN	1352	0.29	0.42	YES
8	LUM	LUM	LUM	1465	0.28	0.47	YES
9	FMOD	FMOD	FMOD	1478	0.28	0.52	YES
10	KERA	KERA	KERA	1486	0.28	0.58	YES
11	B3GNT7	B3GNT7	B3GNT7	1537	0.27	0.64	YES
12	OMD	OMD	OMD	1833	0.25	0.67	YES
13	B3GNT3	B3GNT3	B3GNT3	1998	0.24	0.71	YES
14	B3GNT2	B3GNT2	B3GNT2	6582	0.075	0.47	NO
15	B4GALT4	B4GALT4	B4GALT4	6722	0.072	0.48	NO
16	ST3GAL2	ST3GAL2	ST3GAL2	7365	0.06	0.46	NO
17	B4GALT5	B4GALT5	B4GALT5	8346	0.042	0.41	NO
18	B4GALT2	B4GALT2	B4GALT2	9083	0.029	0.38	NO
19	ST3GAL1	ST3GAL1	ST3GAL1	9868	0.016	0.34	NO
20	B4GALT1	B4GALT1	B4GALT1	11053	-0.0015	0.27	NO
21	B3GNT1	B3GNT1	B3GNT1	11935	-0.015	0.22	NO
22	ST3GAL3	ST3GAL3	ST3GAL3	12461	-0.023	0.2	NO
23	B4GALT3	B4GALT3	B4GALT3	13250	-0.036	0.16	NO
24	B3GNT4	B3GNT4	B3GNT4	14030	-0.051	0.13	NO
25	PRELP	PRELP	PRELP	17371	-0.22	-0.0089	NO
26	ST3GAL6	ST3GAL6	ST3GAL6	17376	-0.22	0.037	NO

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

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

genes ES table in pathway: BIOCARTA MPR PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NGFR	NGFR	NGFR	207	0.49	0.15	YES
2	PDGFRA	PDGFRA	PDGFRA	499	0.4	0.27	YES
3	EGFR	EGFR	EGFR	1209	0.3	0.33	YES
4	NGF	NGF	NGF	1313	0.29	0.43	YES
5	GNGT1	GNGT1	GNGT1	1688	0.26	0.49	YES
6	ITGB1	ITGB1	ITGB1	3599	0.15	0.44	NO
7	SHC1	SHC1	SHC1	4369	0.13	0.44	NO
8	MAP2K1	MAP2K1	MAP2K1	5996	0.088	0.38	NO
9	GNAS	GNAS	GNAS	6541	0.076	0.37	NO
10	PTPRR	PTPRR	PTPRR	7586	0.056	0.33	NO
11	STAT3	STAT3	STAT3	8278	0.043	0.31	NO
12	SOS1	SOS1	SOS1	10079	0.013	0.22	NO
13	IGF1R	IGF1R	IGF1R	10080	0.013	0.22	NO
14	RAF1	RAF1	RAF1	10243	0.011	0.21	NO
15	HRAS	HRAS	HRAS	10631	0.0049	0.19	NO
16	GNB1	GNB1	GNB1	10645	0.0047	0.2	NO
17	PPP2CA	PPP2CA	PPP2CA	10702	0.0039	0.19	NO
18	ELK1	ELK1	ELK1	10766	0.0029	0.19	NO
19	MAPK3	MAPK3	MAPK3	11492	-0.0085	0.15	NO
20	MAPK1	MAPK1	MAPK1	12197	-0.019	0.12	NO
21	RPS6KA1	RPS6KA1	RPS6KA1	12903	-0.03	0.092	NO
22	GRB2	GRB2	GRB2	12936	-0.031	0.1	NO
23	MKNK2	MKNK2	MKNK2	13335	-0.037	0.091	NO
24	MKNK1	MKNK1	MKNK1	13684	-0.044	0.086	NO
25	SRC	SRC	SRC	14012	-0.051	0.085	NO
26	MAP2K2	MAP2K2	MAP2K2	14101	-0.052	0.098	NO
27	MYC	MYC	MYC	16753	-0.15	0.0025	NO
28	RPS6KA5	RPS6KA5	RPS6KA5	17276	-0.2	0.042	NO

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

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

genes ES table in pathway: WNT SIGNALING

Table 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	FGF2	FGF2	FGF2	55	0.61	0.14	YES
2	FGF5	FGF5	FGF5	350	0.44	0.22	YES
3	FGF10	FGF10	FGF10	600	0.38	0.29	YES
4	FGF7	FGF7	FGF7	606	0.38	0.38	YES
5	KL	KL	KL	823	0.35	0.45	YES
6	FGFR1	FGFR1	FGFR1	931	0.33	0.52	YES
7	FGF18	FGF18	FGF18	1367	0.29	0.56	YES
8	SPRY2	SPRY2	SPRY2	1613	0.26	0.6	YES
9	FGF1	FGF1	FGF1	2376	0.21	0.61	YES
10	FGF23	FGF23	FGF23	2779	0.19	0.63	YES
11	KLB	KLB	KLB	4457	0.13	0.57	NO
12	BRAF	BRAF	BRAF	5208	0.11	0.55	NO
13	CBL	CBL	CBL	5223	0.11	0.57	NO
14	FGF8	FGF8	FGF8	6207	0.083	0.54	NO
15	FRS2	FRS2	FRS2	6692	0.073	0.53	NO
16	FGF22	FGF22	FGF22	7755	0.052	0.48	NO
17	FGF9	FGF9	FGF9	8025	0.048	0.48	NO
18	PPP2CB	PPP2CB	PPP2CB	8310	0.042	0.47	NO
19	FGF17	FGF17	FGF17	9436	0.023	0.41	NO
20	RPS27A	RPS27A	RPS27A	9842	0.017	0.4	NO
21	FGFR2	FGFR2	FGFR2	10151	0.012	0.38	NO
22	FGFR3	FGFR3	FGFR3	10526	0.0065	0.36	NO
23	PPP2CA	PPP2CA	PPP2CA	10702	0.0039	0.35	NO
24	MAPK3	MAPK3	MAPK3	11492	-0.0085	0.31	NO
25	MAPK1	MAPK1	MAPK1	12197	-0.019	0.28	NO
26	FGFR4	FGFR4	FGFR4	12659	-0.027	0.26	NO
27	PPP2R1A	PPP2R1A	PPP2R1A	12767	-0.028	0.26	NO
28	UBA52	UBA52	UBA52	12928	-0.031	0.26	NO
29	GRB2	GRB2	GRB2	12936	-0.031	0.26	NO
30	MKNK1	MKNK1	MKNK1	13684	-0.044	0.23	NO
31	SRC	SRC	SRC	14012	-0.051	0.22	NO

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

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

genes ES table in pathway: ST INTEGRIN SIGNALING 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	FGF2	FGF2	FGF2	55	0.61	0.15	YES
2	FGF5	FGF5	FGF5	350	0.44	0.24	YES
3	FGF10	FGF10	FGF10	600	0.38	0.32	YES
4	FGF7	FGF7	FGF7	606	0.38	0.41	YES
5	KL	KL	KL	823	0.35	0.49	YES
6	FGFR1	FGFR1	FGFR1	931	0.33	0.56	YES
7	FGF18	FGF18	FGF18	1367	0.29	0.61	YES
8	FGF1	FGF1	FGF1	2376	0.21	0.61	YES
9	FGF23	FGF23	FGF23	2779	0.19	0.63	YES
10	KLB	KLB	KLB	4457	0.13	0.57	NO
11	KRAS	KRAS	KRAS	5673	0.095	0.52	NO
12	MAP2K1	MAP2K1	MAP2K1	5996	0.088	0.53	NO
13	FGF8	FGF8	FGF8	6207	0.083	0.54	NO
14	FRS2	FRS2	FRS2	6692	0.073	0.53	NO
15	NRAS	NRAS	NRAS	7693	0.054	0.48	NO
16	FGF22	FGF22	FGF22	7755	0.052	0.5	NO
17	FGF9	FGF9	FGF9	8025	0.048	0.49	NO
18	FRS3	FRS3	FRS3	9412	0.024	0.42	NO
19	FGF17	FGF17	FGF17	9436	0.023	0.42	NO
20	SOS1	SOS1	SOS1	10079	0.013	0.39	NO
21	FGFR2	FGFR2	FGFR2	10151	0.012	0.39	NO
22	RAF1	RAF1	RAF1	10243	0.011	0.39	NO
23	FGFR3	FGFR3	FGFR3	10526	0.0065	0.38	NO
24	HRAS	HRAS	HRAS	10631	0.0049	0.37	NO
25	CDK1	CDK1	CDK1	11401	-0.0072	0.33	NO
26	MAPK3	MAPK3	MAPK3	11492	-0.0085	0.33	NO
27	YWHAB	YWHAB	YWHAB	12186	-0.019	0.29	NO
28	MAPK1	MAPK1	MAPK1	12197	-0.019	0.3	NO
29	FGFR4	FGFR4	FGFR4	12659	-0.027	0.28	NO
30	GRB2	GRB2	GRB2	12936	-0.031	0.27	NO
31	MAP2K2	MAP2K2	MAP2K2	14101	-0.052	0.22	NO

Figure S51. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST INTEGRIN SIGNALING PATHWAY.

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

genes ES table in pathway: PID INTEGRIN1 PATHWAY

Table S27. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GDNF	GDNF	GDNF	38	0.65	0.15	YES
2	GFRA1	GFRA1	GFRA1	652	0.37	0.2	YES
3	PRKCA	PRKCA	PRKCA	1326	0.29	0.23	YES
4	DOK6	DOK6	DOK6	2042	0.23	0.25	YES
5	RASA1	RASA1	RASA1	2375	0.21	0.28	YES
6	GRB7	GRB7	GRB7	2495	0.2	0.32	YES
7	MAPK8	MAPK8	MAPK8	2521	0.2	0.37	YES
8	DOK1	DOK1	DOK1	2710	0.19	0.4	YES
9	PIK3CA	PIK3CA	PIK3CA	3182	0.17	0.41	YES
10	DOK4	DOK4	DOK4	3296	0.16	0.45	YES
11	GRB10	GRB10	GRB10	3781	0.15	0.45	YES
12	SHC1	SHC1	SHC1	4369	0.13	0.45	YES
13	RAP1A	RAP1A	RAP1A	4527	0.12	0.47	YES
14	DOK5	DOK5	DOK5	4948	0.11	0.47	YES
15	CREB1	CREB1	CREB1	5356	0.1	0.48	YES
16	PDLIM7	PDLIM7	PDLIM7	5379	0.1	0.5	YES
17	CRK	CRK	CRK	5725	0.094	0.5	YES
18	JUN	JUN	JUN	5880	0.09	0.51	YES
19	FRS2	FRS2	FRS2	6692	0.073	0.48	NO
20	PTPN11	PTPN11	PTPN11	7059	0.066	0.48	NO
21	NCK1	NCK1	NCK1	7719	0.053	0.46	NO
22	PXN	PXN	PXN	7926	0.049	0.46	NO
23	IRS1	IRS1	IRS1	8065	0.047	0.46	NO
24	PTK2	PTK2	PTK2	8491	0.039	0.44	NO
25	PIK3R1	PIK3R1	PIK3R1	9562	0.021	0.39	NO
26	RAC1	RAC1	RAC1	9686	0.02	0.39	NO
27	PRKACA	PRKACA	PRKACA	9939	0.015	0.38	NO
28	SOS1	SOS1	SOS1	10079	0.013	0.37	NO
29	RET	RET	RET	10402	0.0084	0.36	NO
30	HRAS	HRAS	HRAS	10631	0.0049	0.34	NO
31	BCAR1	BCAR1	BCAR1	11087	-0.002	0.32	NO
32	RHOA	RHOA	RHOA	11198	-0.004	0.32	NO
33	MAPK3	MAPK3	MAPK3	11492	-0.0085	0.3	NO
34	MAPK1	MAPK1	MAPK1	12197	-0.019	0.27	NO
35	IRS2	IRS2	IRS2	12692	-0.027	0.24	NO
36	GRB2	GRB2	GRB2	12936	-0.031	0.24	NO
37	SRC	SRC	SRC	14012	-0.051	0.19	NO
38	GAB1	GAB1	GAB1	14505	-0.061	0.18	NO
39	SHANK3	SHANK3	SHANK3	15288	-0.081	0.15	NO

Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID INTEGRIN1 PATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: PID INTEGRIN1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID EPHBFWDPATHWAY

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	EPHB3	EPHB3	EPHB3	348	0.44	0.068	YES
2	KALRN	KALRN	KALRN	463	0.41	0.14	YES
3	DNM1	DNM1	DNM1	589	0.38	0.21	YES
4	EFNB2	EFNB2	EFNB2	595	0.38	0.29	YES
5	EFNA5	EFNA5	EFNA5	936	0.33	0.33	YES
6	GRIA1	GRIA1	GRIA1	1011	0.32	0.39	YES
7	RASA1	RASA1	RASA1	2375	0.21	0.36	YES
8	GRB7	GRB7	GRB7	2495	0.2	0.39	YES
9	EFNB1	EFNB1	EFNB1	2641	0.2	0.42	YES
10	PIK3CA	PIK3CA	PIK3CA	3182	0.17	0.43	YES
11	EPHB2	EPHB2	EPHB2	3197	0.17	0.46	YES
12	TF	TF	TF	4086	0.14	0.44	YES
13	SHC1	SHC1	SHC1	4369	0.13	0.45	YES
14	ROCK1	ROCK1	ROCK1	4469	0.12	0.46	YES
15	RAP1A	RAP1A	RAP1A	4527	0.12	0.49	YES
16	MAP4K4	MAP4K4	MAP4K4	4608	0.12	0.51	YES
17	EPHB4	EPHB4	EPHB4	5015	0.11	0.51	YES
18	EFNB3	EFNB3	EFNB3	5017	0.11	0.53	YES
19	KRAS	KRAS	KRAS	5673	0.095	0.51	YES
20	CRK	CRK	CRK	5725	0.094	0.53	YES
21	MAP2K1	MAP2K1	MAP2K1	5996	0.088	0.53	YES
22	EPHB1	EPHB1	EPHB1	6393	0.079	0.52	NO
23	ITSN1	ITSN1	ITSN1	6587	0.075	0.53	NO
24	RAP1B	RAP1B	RAP1B	7224	0.063	0.5	NO
25	RRAS	RRAS	RRAS	7442	0.058	0.5	NO
26	NRAS	NRAS	NRAS	7693	0.054	0.5	NO
27	NCK1	NCK1	NCK1	7719	0.053	0.51	NO
28	WASL	WASL	WASL	7720	0.053	0.52	NO
29	PXN	PXN	PXN	7926	0.049	0.52	NO
30	PTK2	PTK2	PTK2	8491	0.039	0.49	NO
31	PIK3R1	PIK3R1	PIK3R1	9562	0.021	0.44	NO
32	RAC1	RAC1	RAC1	9686	0.02	0.44	NO
33	CDC42	CDC42	CDC42	10252	0.011	0.41	NO
34	PAK1	PAK1	PAK1	10417	0.0082	0.4	NO
35	HRAS	HRAS	HRAS	10631	0.0049	0.39	NO
36	MAPK3	MAPK3	MAPK3	11492	-0.0085	0.34	NO
37	SYNJ1	SYNJ1	SYNJ1	11676	-0.011	0.33	NO
38	MAPK1	MAPK1	MAPK1	12197	-0.019	0.31	NO
39	GRB2	GRB2	GRB2	12936	-0.031	0.27	NO
40	SRC	SRC	SRC	14012	-0.051	0.22	NO

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

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: PID EPHBFWDPATHWAY, 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 RET PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CPE	CPE	CPE	86	0.57	0.04	YES
2	PCSK1	PCSK1	PCSK1	104	0.55	0.082	YES
3	PAPPA	PAPPA	PAPPA	183	0.5	0.12	YES
4	IGFBP6	IGFBP6	IGFBP6	287	0.46	0.15	YES
5	IGFBP3	IGFBP3	IGFBP3	416	0.42	0.17	YES
6	STX1A	STX1A	STX1A	456	0.41	0.2	YES
7	MMP1	MMP1	MMP1	547	0.39	0.23	YES
8	IGFBP5	IGFBP5	IGFBP5	604	0.38	0.25	YES
9	IL8	IL8	IL8	740	0.36	0.28	YES
10	ASNS	ASNS	ASNS	922	0.33	0.29	YES
11	IGFBP1	IGFBP1	IGFBP1	935	0.33	0.32	YES
12	IGFBP2	IGFBP2	IGFBP2	979	0.33	0.34	YES
13	IGF2BP1	IGF2BP1	IGF2BP1	1396	0.28	0.34	YES
14	FKBP14	FKBP14	FKBP14	1672	0.26	0.34	YES
15	PAPPA2	PAPPA2	PAPPA2	1895	0.24	0.35	YES
16	IGFBP4	IGFBP4	IGFBP4	3034	0.18	0.3	YES
17	CCL2	CCL2	CCL2	3367	0.16	0.29	YES
18	IGF2BP2	IGF2BP2	IGF2BP2	3417	0.16	0.3	YES
19	IGF2	IGF2	IGF2	3607	0.15	0.3	YES
20	NFYB	NFYB	NFYB	3855	0.14	0.3	YES
21	CTSG	CTSG	CTSG	4155	0.13	0.3	YES
22	SHC1	SHC1	SHC1	4369	0.13	0.29	YES
23	KIF5B	KIF5B	KIF5B	4488	0.12	0.3	YES
24	KLF4	KLF4	KLF4	4576	0.12	0.3	YES
25	SLC30A7	SLC30A7	SLC30A7	4675	0.12	0.31	YES
26	HYOU1	HYOU1	HYOU1	4722	0.12	0.31	YES
27	DNAJC3	DNAJC3	DNAJC3	4884	0.12	0.31	YES
28	IGF2BP3	IGF2BP3	IGF2BP3	4925	0.11	0.32	YES
29	SNAP25	SNAP25	SNAP25	4952	0.11	0.33	YES
30	PDIA6	PDIA6	PDIA6	5034	0.11	0.33	YES
31	MMP2	MMP2	MMP2	5137	0.11	0.33	YES
32	HSP90B1	HSP90B1	HSP90B1	5157	0.11	0.34	YES
33	KDELR3	KDELR3	KDELR3	5163	0.11	0.35	YES
34	EIF2AK3	EIF2AK3	EIF2AK3	5191	0.11	0.36	YES
35	DNAJB9	DNAJB9	DNAJB9	5265	0.1	0.36	YES
36	EDEM1	EDEM1	EDEM1	5469	0.1	0.36	YES
37	C19orf10	C19orf10	C19orf10	5491	0.1	0.36	YES
38	PDIA5	PDIA5	PDIA5	5535	0.099	0.37	YES
39	DIS3	DIS3	DIS3	5561	0.098	0.38	YES
40	HSPA5	HSPA5	HSPA5	5682	0.095	0.38	YES
41	DNAJB11	DNAJB11	DNAJB11	5742	0.093	0.38	YES
42	MBTPS1	MBTPS1	MBTPS1	5924	0.089	0.38	NO
43	ATF3	ATF3	ATF3	6370	0.08	0.36	NO
44	EXTL3	EXTL3	EXTL3	6568	0.075	0.35	NO
45	SRPRB	SRPRB	SRPRB	6690	0.073	0.35	NO
46	TSPYL2	TSPYL2	TSPYL2	6737	0.072	0.36	NO
47	SPCS3	SPCS3	SPCS3	6822	0.07	0.36	NO
48	SLC30A5	SLC30A5	SLC30A5	6938	0.068	0.35	NO
49	IGFALS	IGFALS	IGFALS	6939	0.068	0.36	NO
50	SERP1	SERP1	SERP1	7118	0.065	0.36	NO
51	EXOSC8	EXOSC8	EXOSC8	7169	0.064	0.36	NO
52	MBTPS2	MBTPS2	MBTPS2	7446	0.058	0.35	NO
53	LEP	LEP	LEP	7493	0.058	0.35	NO
54	EXOC5	EXOC5	EXOC5	7538	0.057	0.35	NO
55	EXOC1	EXOC1	EXOC1	7624	0.055	0.35	NO
56	DCP2	DCP2	DCP2	7728	0.053	0.35	NO
57	SULT1A3	SULT1A3	SULT1A3	7910	0.05	0.34	NO
58	EXOC6	EXOC6	EXOC6	7929	0.049	0.34	NO
59	EIF2S1	EIF2S1	EIF2S1	8246	0.044	0.33	NO
60	CTDSP2	CTDSP2	CTDSP2	8308	0.042	0.33	NO
61	SSR1	SSR1	SSR1	8680	0.036	0.31	NO
62	ACADVL	ACADVL	ACADVL	8873	0.033	0.3	NO
63	ATF6	ATF6	ATF6	8912	0.032	0.3	NO
64	XBP1	XBP1	XBP1	8959	0.031	0.3	NO
65	DDIT3	DDIT3	DDIT3	8997	0.031	0.3	NO
66	CALR	CALR	CALR	9029	0.03	0.31	NO
67	SPCS1	SPCS1	SPCS1	9155	0.028	0.3	NO
68	ATF4	ATF4	ATF4	9383	0.024	0.29	NO
69	ERN1	ERN1	ERN1	9454	0.023	0.29	NO
70	EXOSC3	EXOSC3	EXOSC3	9603	0.021	0.28	NO
71	SYVN1	SYVN1	SYVN1	9644	0.02	0.28	NO
72	SRPR	SRPR	SRPR	9673	0.02	0.28	NO
73	SEC11A	SEC11A	SEC11A	9818	0.017	0.27	NO
74	GOSR2	GOSR2	GOSR2	9873	0.016	0.27	NO
75	ZBTB17	ZBTB17	ZBTB17	10047	0.014	0.26	NO
76	BCHE	BCHE	BCHE	10098	0.013	0.26	NO
77	HDGF	HDGF	HDGF	10298	0.01	0.25	NO
78	CUL7	CUL7	CUL7	10318	0.0099	0.25	NO
79	EXOC4	EXOC4	EXOC4	10404	0.0083	0.25	NO
80	GHRL	GHRL	GHRL	10436	0.0079	0.25	NO
81	ERO1L	ERO1L	ERO1L	10514	0.0067	0.24	NO
82	PPP2R5B	PPP2R5B	PPP2R5B	10535	0.0064	0.24	NO
83	MBOAT4	MBOAT4	MBOAT4	10677	0.0042	0.23	NO
84	NFYA	NFYA	NFYA	10839	0.0019	0.22	NO
85	SEC31A	SEC31A	SEC31A	11118	-0.0025	0.21	NO
86	EXOSC2	EXOSC2	EXOSC2	11125	-0.0027	0.21	NO
87	EXOSC9	EXOSC9	EXOSC9	11404	-0.0073	0.2	NO
88	YIF1A	YIF1A	YIF1A	11442	-0.0079	0.19	NO
89	SPCS2	SPCS2	SPCS2	11497	-0.0086	0.19	NO
90	DCTN1	DCTN1	DCTN1	11668	-0.011	0.18	NO
91	EXOSC6	EXOSC6	EXOSC6	11674	-0.011	0.18	NO
92	LOC653566	LOC653566	LOC653566	11785	-0.013	0.18	NO
93	VAMP2	VAMP2	VAMP2	12068	-0.017	0.16	NO
94	ADD1	ADD1	ADD1	12146	-0.018	0.16	NO
95	PLA2G7	PLA2G7	PLA2G7	12157	-0.018	0.16	NO
96	GSK3A	GSK3A	GSK3A	12325	-0.021	0.15	NO
97	PREB	PREB	PREB	12410	-0.022	0.15	NO
98	TATDN2	TATDN2	TATDN2	12566	-0.025	0.14	NO
99	PCSK2	PCSK2	PCSK2	12940	-0.031	0.13	NO
100	EXOSC7	EXOSC7	EXOSC7	12958	-0.031	0.13	NO
101	EXOSC5	EXOSC5	EXOSC5	13121	-0.034	0.12	NO
102	EXOC8	EXOC8	EXOC8	13280	-0.036	0.12	NO
103	HERPUD1	HERPUD1	HERPUD1	13301	-0.037	0.12	NO
104	CXXC1	CXXC1	CXXC1	13375	-0.038	0.12	NO
105	TLN1	TLN1	TLN1	13511	-0.041	0.11	NO
106	KLHDC3	KLHDC3	KLHDC3	13628	-0.043	0.11	NO
107	LMNA	LMNA	LMNA	14103	-0.052	0.086	NO
108	WFS1	WFS1	WFS1	14189	-0.054	0.085	NO
109	KHSRP	KHSRP	KHSRP	14195	-0.054	0.089	NO
110	EXOC3	EXOC3	EXOC3	14228	-0.055	0.092	NO
111	PARN	PARN	PARN	14264	-0.056	0.094	NO
112	SEC11C	SEC11C	SEC11C	14267	-0.056	0.098	NO
113	ARFGAP1	ARFGAP1	ARFGAP1	14843	-0.069	0.072	NO
114	DDX11	DDX11	DDX11	15270	-0.08	0.054	NO
115	EXOSC1	EXOSC1	EXOSC1	15276	-0.081	0.06	NO
116	TPP1	TPP1	TPP1	15399	-0.085	0.06	NO
117	EXOSC4	EXOSC4	EXOSC4	15467	-0.087	0.063	NO
118	ATP6V0D1	ATP6V0D1	ATP6V0D1	15808	-0.099	0.052	NO
119	EXOC2	EXOC2	EXOC2	16177	-0.12	0.04	NO
120	MYO5A	MYO5A	MYO5A	16941	-0.17	0.011	NO
121	GH1	GH1	GH1	16984	-0.17	0.022	NO
122	WIPI1	WIPI1	WIPI1	17228	-0.2	0.024	NO
123	RAB27A	RAB27A	RAB27A	17638	-0.28	0.022	NO

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

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

genes ES table in pathway: PID NCADHERINPATHWAY

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	INHBA	INHBA	INHBA	52	0.62	0.045	YES
2	BMP2	BMP2	BMP2	130	0.53	0.082	YES
3	FST	FST	FST	226	0.48	0.11	YES
4	THBS2	THBS2	THBS2	422	0.42	0.14	YES
5	LTBP1	LTBP1	LTBP1	458	0.41	0.16	YES
6	ID1	ID1	ID1	610	0.38	0.19	YES
7	BMP6	BMP6	BMP6	646	0.37	0.21	YES
8	ID3	ID3	ID3	730	0.36	0.24	YES
9	DCN	DCN	DCN	791	0.35	0.26	YES
10	BMP8A	BMP8A	BMP8A	808	0.35	0.29	YES
11	BMP5	BMP5	BMP5	816	0.35	0.31	YES
12	INHBB	INHBB	INHBB	859	0.34	0.34	YES
13	THBS4	THBS4	THBS4	1060	0.32	0.35	YES
14	CHRD	CHRD	CHRD	1149	0.31	0.37	YES
15	ID4	ID4	ID4	1165	0.3	0.39	YES
16	THBS1	THBS1	THBS1	1224	0.3	0.41	YES
17	TGFB3	TGFB3	TGFB3	1273	0.3	0.43	YES
18	TGFB2	TGFB2	TGFB2	1381	0.28	0.45	YES
19	SMAD1	SMAD1	SMAD1	1416	0.28	0.47	YES
20	BMP8B	BMP8B	BMP8B	1462	0.28	0.49	YES
21	SMURF2	SMURF2	SMURF2	1787	0.25	0.49	YES
22	E2F5	E2F5	E2F5	2417	0.21	0.47	YES
23	SMAD9	SMAD9	SMAD9	2433	0.21	0.48	YES
24	ROCK2	ROCK2	ROCK2	2506	0.2	0.5	YES
25	GDF6	GDF6	GDF6	2619	0.2	0.5	YES
26	ACVR2A	ACVR2A	ACVR2A	2691	0.19	0.52	YES
27	COMP	COMP	COMP	2707	0.19	0.53	YES
28	ACVR1	ACVR1	ACVR1	2749	0.19	0.54	YES
29	BMP7	BMP7	BMP7	3193	0.17	0.53	YES
30	THBS3	THBS3	THBS3	3257	0.17	0.54	YES
31	AMH	AMH	AMH	3360	0.16	0.55	YES
32	NOG	NOG	NOG	3529	0.16	0.55	YES
33	BMPR1A	BMPR1A	BMPR1A	3647	0.15	0.56	YES
34	SMAD5	SMAD5	SMAD5	3805	0.15	0.56	YES
35	ID2	ID2	ID2	4372	0.13	0.54	NO
36	LEFTY1	LEFTY1	LEFTY1	4426	0.13	0.54	NO
37	ROCK1	ROCK1	ROCK1	4469	0.12	0.55	NO
38	TGFB1	TGFB1	TGFB1	4652	0.12	0.55	NO
39	SMAD7	SMAD7	SMAD7	4694	0.12	0.56	NO
40	GDF5	GDF5	GDF5	4870	0.12	0.56	NO
41	BMP4	BMP4	BMP4	5159	0.11	0.55	NO
42	TGFBR2	TGFBR2	TGFBR2	5402	0.1	0.54	NO
43	CDKN2B	CDKN2B	CDKN2B	5460	0.1	0.55	NO
44	PPP2R1B	PPP2R1B	PPP2R1B	5553	0.098	0.55	NO
45	ACVRL1	ACVRL1	ACVRL1	5785	0.093	0.54	NO
46	NODAL	NODAL	NODAL	5800	0.092	0.55	NO
47	RBL1	RBL1	RBL1	6259	0.082	0.53	NO
48	BMPR1B	BMPR1B	BMPR1B	6292	0.081	0.54	NO
49	SMAD4	SMAD4	SMAD4	6718	0.073	0.52	NO
50	RPS6KB1	RPS6KB1	RPS6KB1	6772	0.072	0.52	NO
51	LEFTY2	LEFTY2	LEFTY2	6812	0.071	0.52	NO
52	RBL2	RBL2	RBL2	7100	0.065	0.51	NO
53	INHBE	INHBE	INHBE	7407	0.059	0.5	NO
54	PPP2CB	PPP2CB	PPP2CB	8310	0.042	0.45	NO
55	ZFYVE9	ZFYVE9	ZFYVE9	8370	0.041	0.45	NO
56	ACVR1C	ACVR1C	ACVR1C	9119	0.028	0.41	NO
57	ACVR2B	ACVR2B	ACVR2B	9425	0.024	0.4	NO
58	CUL1	CUL1	CUL1	9479	0.023	0.4	NO
59	E2F4	E2F4	E2F4	9487	0.022	0.4	NO
60	SMAD6	SMAD6	SMAD6	9795	0.018	0.38	NO
61	BMPR2	BMPR2	BMPR2	10054	0.014	0.37	NO
62	SP1	SP1	SP1	10111	0.013	0.37	NO
63	SMAD3	SMAD3	SMAD3	10157	0.012	0.36	NO
64	TFDP1	TFDP1	TFDP1	10249	0.011	0.36	NO
65	INHBC	INHBC	INHBC	10467	0.0073	0.35	NO
66	SKP1	SKP1	SKP1	10617	0.0052	0.34	NO
67	PPP2CA	PPP2CA	PPP2CA	10702	0.0039	0.34	NO
68	SMAD2	SMAD2	SMAD2	10992	-0.00054	0.32	NO
69	RHOA	RHOA	RHOA	11198	-0.004	0.31	NO
70	MAPK3	MAPK3	MAPK3	11492	-0.0085	0.29	NO
71	PITX2	PITX2	PITX2	11524	-0.0091	0.29	NO
72	EP300	EP300	EP300	11820	-0.013	0.28	NO
73	CREBBP	CREBBP	CREBBP	11943	-0.015	0.27	NO
74	MAPK1	MAPK1	MAPK1	12197	-0.019	0.26	NO
75	TGFBR1	TGFBR1	TGFBR1	12281	-0.02	0.26	NO
76	RBX1	RBX1	RBX1	12376	-0.022	0.25	NO
77	PPP2R1A	PPP2R1A	PPP2R1A	12767	-0.028	0.23	NO
78	SMURF1	SMURF1	SMURF1	12771	-0.028	0.24	NO
79	GDF7	GDF7	GDF7	12834	-0.029	0.23	NO
80	ZFYVE16	ZFYVE16	ZFYVE16	14390	-0.058	0.15	NO
81	RPS6KB2	RPS6KB2	RPS6KB2	15110	-0.076	0.12	NO
82	TNF	TNF	TNF	15631	-0.092	0.096	NO
83	MYC	MYC	MYC	16753	-0.15	0.045	NO
84	AMHR2	AMHR2	AMHR2	16867	-0.16	0.051	NO
85	IFNG	IFNG	IFNG	17081	-0.18	0.053	NO

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

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: PID NCADHERINPATHWAY, 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 LYSINE DEGRADATION	44	genes.ES.table	0.37	1.6	0.033	0.25	0.95	0.5	0.29	0.36	0.15	0.027
KEGG RIBOSOME	85	genes.ES.table	0.64	1.7	0.046	0.22	0.77	0.87	0.33	0.59	0.095	0.039
KEGG BASAL TRANSCRIPTION FACTORS	34	genes.ES.table	0.52	1.7	0.021	0.19	0.82	0.62	0.33	0.41	0.084	0.024
KEGG SPLICEOSOME	114	genes.ES.table	0.42	1.9	0.023	0.17	0.35	0.57	0.39	0.35	0	0.036
PID ATM PATHWAY	34	genes.ES.table	0.52	1.7	0.042	0.19	0.8	0.59	0.32	0.4	0.085	0.027
PID RETINOIC ACID PATHWAY	30	genes.ES.table	0.45	1.6	0.039	0.23	0.95	0.43	0.26	0.32	0.15	0.02
PID BARD1PATHWAY	29	genes.ES.table	0.51	1.6	0.1	0.25	0.94	0.55	0.3	0.38	0.16	0.029
PID P53REGULATIONPATHWAY	58	genes.ES.table	0.36	1.6	0.035	0.2	0.91	0.4	0.3	0.28	0.11	0.021
REACTOME TRANSLATION	146	genes.ES.table	0.51	1.7	0.082	0.21	0.78	0.73	0.37	0.47	0.092	0.036
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX	49	genes.ES.table	0.6	1.7	0.051	0.18	0.83	0.8	0.34	0.52	0.083	0.019

genes ES table in pathway: KEGG LYSINE DEGRADATION

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	RPL36A	RPL36A	RPL36A	919	0.18	-0.037	YES
2	RPS27	RPS27	RPS27	1011	0.17	-0.028	YES
3	RPL7	RPL7	RPL7	1214	0.16	-0.027	YES
4	DCP2	DCP2	DCP2	1362	0.15	-0.023	YES
5	PRKCA	PRKCA	PRKCA	1378	0.15	-0.012	YES
6	SNRPE	SNRPE	SNRPE	1385	0.15	-0.00036	YES
7	RPL21	RPL21	RPL21	1606	0.13	-0.0019	YES
8	RPL9	RPL9	RPL9	1630	0.13	0.0076	YES
9	RPS3A	RPS3A	RPS3A	1684	0.13	0.015	YES
10	RPL39	RPL39	RPL39	1806	0.12	0.018	YES
11	PABPC1	PABPC1	PABPC1	1834	0.12	0.027	YES
12	EXOSC8	EXOSC8	EXOSC8	1968	0.12	0.029	YES
13	SMN1	SMN1	SMN1	2083	0.11	0.032	YES
14	TGS1	TGS1	TGS1	2088	0.11	0.041	YES
15	RPS7	RPS7	RPS7	2333	0.1	0.035	YES
16	NUP133	NUP133	NUP133	2383	0.1	0.041	YES
17	RPS12	RPS12	RPS12	2433	0.1	0.046	YES
18	SNRPD1	SNRPD1	SNRPD1	2442	0.1	0.054	YES
19	PAIP1	PAIP1	PAIP1	2524	0.099	0.058	YES
20	RPS18	RPS18	RPS18	2533	0.099	0.065	YES
21	UPF3B	UPF3B	UPF3B	2602	0.097	0.069	YES
22	RPSAP9	RPSAP9	RPSAP9	2706	0.094	0.071	YES
23	RPS23	RPS23	RPS23	2738	0.093	0.077	YES
24	RPL30	RPL30	RPL30	2787	0.092	0.081	YES
25	EIF4B	EIF4B	EIF4B	2852	0.09	0.085	YES
26	RPS10	RPS10	RPS10	2869	0.09	0.091	YES
27	RPL17	RPL17	RPL17	2876	0.09	0.098	YES
28	RPL22	RPL22	RPL22	2917	0.088	0.1	YES
29	RPS20	RPS20	RPS20	2996	0.086	0.11	YES
30	RPL26	RPL26	RPL26	3006	0.086	0.11	YES
31	RPL8	RPL8	RPL8	3011	0.086	0.12	YES
32	RPL10A	RPL10A	RPL10A	3034	0.085	0.12	YES
33	RPL34	RPL34	RPL34	3039	0.085	0.13	YES
34	DIS3	DIS3	DIS3	3045	0.085	0.14	YES
35	UPF3A	UPF3A	UPF3A	3049	0.085	0.14	YES
36	CNOT6	CNOT6	CNOT6	3056	0.085	0.15	YES
37	NUP153	NUP153	NUP153	3074	0.085	0.16	YES
38	RPL23	RPL23	RPL23	3186	0.082	0.16	YES
39	RPL5	RPL5	RPL5	3230	0.081	0.16	YES
40	RPL6	RPL6	RPL6	3280	0.08	0.16	YES
41	RPS8	RPS8	RPS8	3378	0.078	0.17	YES
42	CLNS1A	CLNS1A	CLNS1A	3381	0.078	0.17	YES
43	RPS6	RPS6	RPS6	3504	0.075	0.17	YES
44	RPS26	RPS26	RPS26	3519	0.074	0.18	YES
45	RPS24	RPS24	RPS24	3538	0.074	0.18	YES
46	ANP32A	ANP32A	ANP32A	3645	0.071	0.18	YES
47	GEMIN5	GEMIN5	GEMIN5	3663	0.071	0.19	YES
48	TPR	TPR	TPR	3674	0.071	0.19	YES
49	EXOSC2	EXOSC2	EXOSC2	3683	0.07	0.2	YES
50	EIF4A2	EIF4A2	EIF4A2	3688	0.07	0.2	YES
51	RPL13A	RPL13A	RPL13A	3735	0.069	0.2	YES
52	SMN2	SMN2	SMN2	3746	0.069	0.21	YES
53	RPS17	RPS17	RPS17	3826	0.068	0.21	YES
54	RPS4X	RPS4X	RPS4X	3829	0.068	0.22	YES
55	RPL4	RPL4	RPL4	3835	0.067	0.22	YES
56	GSPT2	GSPT2	GSPT2	3851	0.067	0.23	YES
57	UPF2	UPF2	UPF2	3877	0.067	0.23	YES
58	RPL3	RPL3	RPL3	3889	0.066	0.24	YES
59	LSM6	LSM6	LSM6	3944	0.066	0.24	YES
60	RPL31	RPL31	RPL31	3949	0.065	0.24	YES
61	RPL12	RPL12	RPL12	3978	0.065	0.25	YES
62	RPS3	RPS3	RPS3	3990	0.065	0.25	YES
63	PSMA8	PSMA8	PSMA8	4010	0.064	0.26	YES
64	RPL38	RPL38	RPL38	4039	0.064	0.26	YES
65	RPS14	RPS14	RPS14	4056	0.064	0.26	YES
66	RPS15A	RPS15A	RPS15A	4070	0.063	0.27	YES
67	RPS19	RPS19	RPS19	4166	0.061	0.27	YES
68	RPS27A	RPS27A	RPS27A	4186	0.061	0.27	YES
69	RPS21	RPS21	RPS21	4216	0.061	0.27	YES
70	NUP43	NUP43	NUP43	4261	0.06	0.28	YES
71	RPS29	RPS29	RPS29	4284	0.059	0.28	YES
72	NUP35	NUP35	NUP35	4302	0.059	0.28	YES
73	EXOSC4	EXOSC4	EXOSC4	4314	0.059	0.29	YES
74	RPS5	RPS5	RPS5	4329	0.058	0.29	YES
75	SEH1L	SEH1L	SEH1L	4336	0.058	0.3	YES
76	PSMC6	PSMC6	PSMC6	4339	0.058	0.3	YES
77	EXOSC5	EXOSC5	EXOSC5	4347	0.058	0.3	YES
78	RPL7A	RPL7A	RPL7A	4365	0.058	0.31	YES
79	MAPK14	MAPK14	MAPK14	4371	0.058	0.31	YES
80	RPL23A	RPL23A	RPL23A	4386	0.057	0.32	YES
81	DCP1B	DCP1B	DCP1B	4425	0.057	0.32	YES
82	NUPL1	NUPL1	NUPL1	4485	0.056	0.32	YES
83	RPL14	RPL14	RPL14	4551	0.055	0.32	YES
84	KHSRP	KHSRP	KHSRP	4578	0.054	0.32	YES
85	PPP2R2A	PPP2R2A	PPP2R2A	4603	0.054	0.33	YES
86	RPL37	RPL37	RPL37	4658	0.053	0.33	YES
87	NUP107	NUP107	NUP107	4673	0.053	0.33	YES
88	RPL24	RPL24	RPL24	4701	0.053	0.33	YES
89	LSM2	LSM2	LSM2	4703	0.052	0.34	YES
90	RPL35A	RPL35A	RPL35A	4720	0.052	0.34	YES
91	RPS16	RPS16	RPS16	4737	0.052	0.34	YES
92	EXOSC3	EXOSC3	EXOSC3	4751	0.052	0.35	YES
93	RPL29	RPL29	RPL29	4763	0.052	0.35	YES
94	RPS25	RPS25	RPS25	4769	0.051	0.36	YES
95	NUP54	NUP54	NUP54	4772	0.051	0.36	YES
96	GEMIN7	GEMIN7	GEMIN7	4827	0.05	0.36	YES
97	CNOT8	CNOT8	CNOT8	4835	0.05	0.36	YES
98	RPL18	RPL18	RPL18	4906	0.049	0.36	YES
99	RPL36	RPL36	RPL36	4907	0.049	0.37	YES
100	RBM8A	RBM8A	RBM8A	4912	0.049	0.37	YES
101	RPL37A	RPL37A	RPL37A	4981	0.048	0.37	YES
102	XPO1	XPO1	XPO1	4996	0.048	0.38	YES
103	PSMD10	PSMD10	PSMD10	4997	0.048	0.38	YES
104	RPL32	RPL32	RPL32	5021	0.048	0.38	YES
105	CNOT7	CNOT7	CNOT7	5039	0.047	0.38	YES
106	RPL11	RPL11	RPL11	5057	0.047	0.39	YES
107	RPS13	RPS13	RPS13	5119	0.046	0.39	YES
108	RPL19	RPL19	RPL19	5136	0.046	0.39	YES
109	PSMB4	PSMB4	PSMB4	5237	0.045	0.39	YES
110	RPLP1	RPLP1	RPLP1	5252	0.044	0.39	YES
111	RPS11	RPS11	RPS11	5255	0.044	0.4	YES
112	RPL18A	RPL18A	RPL18A	5283	0.044	0.4	YES
113	RPS2	RPS2	RPS2	5290	0.044	0.4	YES
114	PHAX	PHAX	PHAX	5324	0.043	0.4	YES
115	RPLP0	RPLP0	RPLP0	5343	0.043	0.4	YES
116	SNRPF	SNRPF	SNRPF	5362	0.043	0.41	YES
117	RPL15	RPL15	RPL15	5370	0.043	0.41	YES
118	HNRNPD	HNRNPD	HNRNPD	5462	0.041	0.41	YES
119	RPS9	RPS9	RPS9	5501	0.041	0.41	YES
120	RPL13	RPL13	RPL13	5526	0.04	0.41	YES
121	DDX20	DDX20	DDX20	5560	0.04	0.41	YES
122	DDX6	DDX6	DDX6	5589	0.04	0.41	YES
123	SNRPD3	SNRPD3	SNRPD3	5680	0.038	0.41	YES
124	DCP1A	DCP1A	DCP1A	5691	0.038	0.42	YES
125	MAGOH	MAGOH	MAGOH	5697	0.038	0.42	YES
126	RPL27	RPL27	RPL27	5712	0.038	0.42	YES
127	HSPA1B	HSPA1B	HSPA1B	5721	0.038	0.42	YES
128	PRMT5	PRMT5	PRMT5	5746	0.038	0.42	YES
129	RPL27A	RPL27A	RPL27A	5771	0.037	0.43	YES
130	NCBP1	NCBP1	NCBP1	5811	0.037	0.43	YES
131	RPS15	RPS15	RPS15	5875	0.036	0.43	YES
132	SMG5	SMG5	SMG5	5892	0.036	0.43	YES
133	GEMIN4	GEMIN4	GEMIN4	5895	0.036	0.43	YES
134	EIF4E	EIF4E	EIF4E	5918	0.035	0.43	YES
135	RPL35	RPL35	RPL35	5939	0.035	0.43	YES
136	LSM5	LSM5	LSM5	5945	0.035	0.44	YES
137	RPL41	RPL41	RPL41	5947	0.035	0.44	YES
138	ETF1	ETF1	ETF1	6067	0.033	0.44	YES
139	RPS28	RPS28	RPS28	6078	0.033	0.44	YES
140	NUPL2	NUPL2	NUPL2	6137	0.032	0.44	YES
141	PSMA4	PSMA4	PSMA4	6160	0.032	0.44	YES
142	RPSA	RPSA	RPSA	6191	0.032	0.44	YES
143	NUP88	NUP88	NUP88	6196	0.032	0.44	YES
144	SNRPB	SNRPB	SNRPB	6218	0.031	0.44	YES
145	AAAS	AAAS	AAAS	6275	0.03	0.44	YES
146	ZFP36L1	ZFP36L1	ZFP36L1	6326	0.03	0.44	YES
147	SNRPD2	SNRPD2	SNRPD2	6381	0.029	0.44	YES
148	SNUPN	SNUPN	SNUPN	6401	0.029	0.44	YES
149	EXOSC7	EXOSC7	EXOSC7	6431	0.028	0.44	YES
150	RPL10	RPL10	RPL10	6540	0.027	0.44	NO
151	SMG7	SMG7	SMG7	6721	0.024	0.43	NO
152	CNOT2	CNOT2	CNOT2	6736	0.024	0.43	NO
153	PSMD5	PSMD5	PSMD5	6789	0.024	0.43	NO
154	NUP85	NUP85	NUP85	6959	0.021	0.42	NO
155	PPP2CA	PPP2CA	PPP2CA	6970	0.021	0.42	NO
156	HSPA8	HSPA8	HSPA8	6986	0.021	0.42	NO
157	EIF4A3	EIF4A3	EIF4A3	7000	0.021	0.43	NO
158	ELAVL1	ELAVL1	ELAVL1	7068	0.02	0.42	NO
159	PSMF1	PSMF1	PSMF1	7099	0.02	0.42	NO
160	TNPO1	TNPO1	TNPO1	7122	0.019	0.42	NO
161	PSMA3	PSMA3	PSMA3	7222	0.018	0.42	NO
162	PSMB7	PSMB7	PSMB7	7234	0.018	0.42	NO
163	NUP214	NUP214	NUP214	7315	0.017	0.42	NO
164	RAE1	RAE1	RAE1	7320	0.016	0.42	NO
165	RNPS1	RNPS1	RNPS1	7328	0.016	0.42	NO
166	NUP37	NUP37	NUP37	7365	0.016	0.42	NO
167	YWHAZ	YWHAZ	YWHAZ	7397	0.015	0.42	NO
168	PPP2R1A	PPP2R1A	PPP2R1A	7427	0.015	0.42	NO
169	PSMD4	PSMD4	PSMD4	7536	0.014	0.41	NO
170	PSMA1	PSMA1	PSMA1	7581	0.013	0.41	NO
171	RPLP2	RPLP2	RPLP2	7610	0.013	0.41	NO
172	RPL28	RPL28	RPL28	7615	0.013	0.41	NO
173	LSM4	LSM4	LSM4	7726	0.012	0.41	NO
174	XRN1	XRN1	XRN1	7735	0.011	0.41	NO
175	PARN	PARN	PARN	7893	0.0093	0.4	NO
176	POM121	POM121	POM121	7942	0.0088	0.4	NO
177	EIF4A1	EIF4A1	EIF4A1	7945	0.0087	0.4	NO
178	PRKCD	PRKCD	PRKCD	7965	0.0086	0.4	NO
179	SMG1	SMG1	SMG1	8134	0.0063	0.39	NO
180	CASC3	CASC3	CASC3	8151	0.006	0.39	NO
181	EDC3	EDC3	EDC3	8162	0.0058	0.39	NO
182	CNOT4	CNOT4	CNOT4	8167	0.0058	0.39	NO
183	SMG6	SMG6	SMG6	8171	0.0057	0.39	NO
184	NCBP2	NCBP2	NCBP2	8179	0.0056	0.39	NO
185	UBA52	UBA52	UBA52	8183	0.0056	0.39	NO
186	RANBP2	RANBP2	RANBP2	8229	0.0051	0.39	NO
187	HSPB1	HSPB1	HSPB1	8305	0.0043	0.38	NO
188	NUP62	NUP62	NUP62	8411	0.0028	0.38	NO
189	NUP50	NUP50	NUP50	8461	0.0023	0.38	NO
190	PSMC1	PSMC1	PSMC1	8484	0.002	0.37	NO
191	PSMA6	PSMA6	PSMA6	8490	0.002	0.37	NO
192	SNRPG	SNRPG	SNRPG	8560	0.001	0.37	NO
193	PSMB1	PSMB1	PSMB1	8613	0.00026	0.37	NO
194	PSMB5	PSMB5	PSMB5	8669	-0.00052	0.36	NO
195	FAU	FAU	FAU	8710	-0.0012	0.36	NO
196	PSMA2	PSMA2	PSMA2	8764	-0.0018	0.36	NO
197	LSM3	LSM3	LSM3	8956	-0.0039	0.35	NO
198	WDR77	WDR77	WDR77	9102	-0.0058	0.34	NO
199	AKT1	AKT1	AKT1	9125	-0.0062	0.34	NO
200	EDC4	EDC4	EDC4	9130	-0.0063	0.34	NO
201	CNOT3	CNOT3	CNOT3	9131	-0.0063	0.34	NO
202	EXOSC9	EXOSC9	EXOSC9	9150	-0.0064	0.34	NO
203	C2orf29	C2orf29	C2orf29	9190	-0.007	0.34	NO
204	RPS4Y1	RPS4Y1	RPS4Y1	9221	-0.0074	0.34	NO
205	LSM1	LSM1	LSM1	9285	-0.0085	0.34	NO
206	YWHAB	YWHAB	YWHAB	9333	-0.0091	0.33	NO
207	PSMD12	PSMD12	PSMD12	9353	-0.0095	0.33	NO
208	NUP155	NUP155	NUP155	9409	-0.01	0.33	NO
209	GEMIN6	GEMIN6	GEMIN6	9444	-0.011	0.33	NO
210	PSMB2	PSMB2	PSMB2	9465	-0.011	0.33	NO
211	PSME1	PSME1	PSME1	9570	-0.012	0.32	NO
212	DCPS	DCPS	DCPS	9655	-0.014	0.32	NO
213	NUP205	NUP205	NUP205	9681	-0.014	0.32	NO
214	EXOSC6	EXOSC6	EXOSC6	9797	-0.016	0.32	NO
215	PSME2	PSME2	PSME2	10052	-0.019	0.3	NO
216	PSMD7	PSMD7	PSMD7	10056	-0.02	0.3	NO
217	PSME4	PSME4	PSME4	10085	-0.02	0.3	NO
218	EIF4G1	EIF4G1	EIF4G1	10099	-0.02	0.3	NO
219	PSMA5	PSMA5	PSMA5	10336	-0.023	0.29	NO
220	PSMC5	PSMC5	PSMC5	10338	-0.023	0.3	NO
221	PSMD14	PSMD14	PSMD14	10343	-0.024	0.3	NO
222	PSMD3	PSMD3	PSMD3	10357	-0.024	0.3	NO
223	PSMD6	PSMD6	PSMD6	10381	-0.024	0.3	NO
224	PSMA7	PSMA7	PSMA7	10387	-0.024	0.3	NO
225	PSMD13	PSMD13	PSMD13	10417	-0.025	0.3	NO
226	NUP188	NUP188	NUP188	10436	-0.025	0.3	NO
227	PSMC2	PSMC2	PSMC2	10726	-0.03	0.29	NO
228	PSMB10	PSMB10	PSMB10	10739	-0.03	0.29	NO
229	PSMD1	PSMD1	PSMD1	10787	-0.031	0.29	NO
230	PSMB8	PSMB8	PSMB8	10862	-0.032	0.29	NO
231	PSMB6	PSMB6	PSMB6	10893	-0.032	0.29	NO
232	RPL26L1	RPL26L1	RPL26L1	11064	-0.035	0.28	NO
233	PATL1	PATL1	PATL1	11202	-0.038	0.28	NO
234	CNOT10	CNOT10	CNOT10	11323	-0.04	0.27	NO
235	NUP93	NUP93	NUP93	11363	-0.041	0.28	NO
236	PSMD11	PSMD11	PSMD11	11408	-0.042	0.28	NO
237	MAPK11	MAPK11	MAPK11	11478	-0.043	0.28	NO
238	PSMD9	PSMD9	PSMD9	11542	-0.044	0.28	NO
239	PSMD8	PSMD8	PSMD8	11743	-0.048	0.27	NO
240	PSMC4	PSMC4	PSMC4	11745	-0.048	0.27	NO
241	PSMB3	PSMB3	PSMB3	11762	-0.048	0.28	NO
242	RQCD1	RQCD1	RQCD1	11959	-0.052	0.27	NO
243	MAPKAPK2	MAPKAPK2	MAPKAPK2	12015	-0.053	0.27	NO
244	TNFSF13	TNFSF13	TNFSF13	12152	-0.056	0.27	NO
245	PSMC3	PSMC3	PSMC3	12312	-0.059	0.26	NO
246	TNKS1BP1	TNKS1BP1	TNKS1BP1	12420	-0.062	0.26	NO
247	PSMD2	PSMD2	PSMD2	12871	-0.072	0.24	NO
248	NUP210	NUP210	NUP210	13232	-0.082	0.23	NO
249	EXOSC1	EXOSC1	EXOSC1	13951	-0.1	0.2	NO
250	PSMB9	PSMB9	PSMB9	14243	-0.11	0.19	NO
251	ZFP36	ZFP36	ZFP36	14718	-0.13	0.17	NO
252	FAM153A	FAM153A	FAM153A	15595	-0.17	0.14	NO

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

Figure S62. 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 RIBOSOME

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	LSM11	LSM11	LSM11	1072	0.17	-0.028	YES
2	SNRPE	SNRPE	SNRPE	1385	0.15	-0.017	YES
3	GTF2H2B	GTF2H2B	GTF2H2B	1625	0.13	-0.0051	YES
4	HNRNPA1	HNRNPA1	HNRNPA1	1942	0.12	-9e-05	YES
5	NUP133	NUP133	NUP133	2383	0.1	-0.0051	YES
6	GTF2H2	GTF2H2	GTF2H2	2436	0.1	0.011	YES
7	SNRPD1	SNRPD1	SNRPD1	2442	0.1	0.03	YES
8	UPF3B	UPF3B	UPF3B	2602	0.097	0.04	YES
9	GTF2F2	GTF2F2	GTF2F2	2617	0.097	0.057	YES
10	ZNF473	ZNF473	ZNF473	2872	0.09	0.06	YES
11	RBMX	RBMX	RBMX	3050	0.085	0.067	YES
12	NUP153	NUP153	NUP153	3074	0.085	0.082	YES
13	RBM5	RBM5	RBM5	3117	0.084	0.095	YES
14	TPR	TPR	TPR	3674	0.071	0.077	YES
15	HNRNPH1	HNRNPH1	HNRNPH1	3678	0.071	0.091	YES
16	POLR2K	POLR2K	POLR2K	3695	0.07	0.1	YES
17	HNRNPA3	HNRNPA3	HNRNPA3	4031	0.064	0.097	YES
18	MNAT1	MNAT1	MNAT1	4042	0.064	0.11	YES
19	GTF2H1	GTF2H1	GTF2H1	4232	0.06	0.11	YES
20	NUP43	NUP43	NUP43	4261	0.06	0.12	YES
21	NUP35	NUP35	NUP35	4302	0.059	0.13	YES
22	METTL3	METTL3	METTL3	4307	0.059	0.14	YES
23	SEH1L	SEH1L	SEH1L	4336	0.058	0.15	YES
24	ADARB1	ADARB1	ADARB1	4356	0.058	0.16	YES
25	CSTF3	CSTF3	CSTF3	4360	0.058	0.17	YES
26	CPSF1	CPSF1	CPSF1	4397	0.057	0.18	YES
27	HNRNPA0	HNRNPA0	HNRNPA0	4409	0.057	0.19	YES
28	SNRNP70	SNRNP70	SNRNP70	4438	0.056	0.2	YES
29	NUPL1	NUPL1	NUPL1	4485	0.056	0.21	YES
30	DHX9	DHX9	DHX9	4582	0.054	0.21	YES
31	ERCC2	ERCC2	ERCC2	4644	0.053	0.22	YES
32	NUP107	NUP107	NUP107	4673	0.053	0.23	YES
33	LSM2	LSM2	LSM2	4703	0.052	0.23	YES
34	PCF11	PCF11	PCF11	4728	0.052	0.24	YES
35	NUP54	NUP54	NUP54	4772	0.051	0.25	YES
36	NFX1	NFX1	NFX1	4859	0.05	0.26	YES
37	RBM8A	RBM8A	RBM8A	4912	0.049	0.26	YES
38	SMC1A	SMC1A	SMC1A	5007	0.048	0.26	YES
39	CDK7	CDK7	CDK7	5105	0.046	0.27	YES
40	HNRNPC	HNRNPC	HNRNPC	5125	0.046	0.28	YES
41	RNMT	RNMT	RNMT	5197	0.045	0.28	YES
42	PAPOLA	PAPOLA	PAPOLA	5248	0.044	0.29	YES
43	SNRPF	SNRPF	SNRPF	5362	0.043	0.29	YES
44	PABPN1	PABPN1	PABPN1	5387	0.042	0.3	YES
45	HNRNPM	HNRNPM	HNRNPM	5392	0.042	0.3	YES
46	CCAR1	CCAR1	CCAR1	5394	0.042	0.31	YES
47	PCBP2	PCBP2	PCBP2	5401	0.042	0.32	YES
48	NUDT21	NUDT21	NUDT21	5407	0.042	0.33	YES
49	HNRNPU	HNRNPU	HNRNPU	5423	0.042	0.33	YES
50	HNRNPD	HNRNPD	HNRNPD	5462	0.041	0.34	YES
51	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	5503	0.041	0.34	YES
52	SNRPD3	SNRPD3	SNRPD3	5680	0.038	0.34	YES
53	MAGOH	MAGOH	MAGOH	5697	0.038	0.35	YES
54	SF3B1	SF3B1	SF3B1	5735	0.038	0.35	YES
55	GTF2H4	GTF2H4	GTF2H4	5810	0.037	0.36	YES
56	NCBP1	NCBP1	NCBP1	5811	0.037	0.36	YES
57	HNRNPR	HNRNPR	HNRNPR	5834	0.037	0.37	YES
58	HNRNPK	HNRNPK	HNRNPK	5861	0.036	0.38	YES
59	EIF4E	EIF4E	EIF4E	5918	0.035	0.38	YES
60	FUS	FUS	FUS	5948	0.035	0.38	YES
61	SNRPB2	SNRPB2	SNRPB2	6105	0.033	0.38	YES
62	NUPL2	NUPL2	NUPL2	6137	0.032	0.39	YES
63	NUP88	NUP88	NUP88	6196	0.032	0.39	YES
64	SNRPB	SNRPB	SNRPB	6218	0.031	0.39	YES
65	SF3B14	SF3B14	SF3B14	6241	0.031	0.4	YES
66	AAAS	AAAS	AAAS	6275	0.03	0.4	YES
67	SLBP	SLBP	SLBP	6289	0.03	0.41	YES
68	GTF2H3	GTF2H3	GTF2H3	6374	0.029	0.41	YES
69	SNRPD2	SNRPD2	SNRPD2	6381	0.029	0.41	YES
70	NXF1	NXF1	NXF1	6481	0.028	0.41	YES
71	CCNH	CCNH	CCNH	6492	0.028	0.42	YES
72	SF3A3	SF3A3	SF3A3	6493	0.028	0.42	YES
73	CSTF1	CSTF1	CSTF1	6511	0.027	0.43	YES
74	SF3B3	SF3B3	SF3B3	6580	0.026	0.43	YES
75	YBX1	YBX1	YBX1	6612	0.026	0.43	YES
76	SNRPA1	SNRPA1	SNRPA1	6633	0.026	0.44	YES
77	RNGTT	RNGTT	RNGTT	6917	0.022	0.42	YES
78	NUP85	NUP85	NUP85	6959	0.021	0.42	YES
79	HNRNPH2	HNRNPH2	HNRNPH2	6979	0.021	0.43	YES
80	POLR2B	POLR2B	POLR2B	6982	0.021	0.43	YES
81	HNRNPF	HNRNPF	HNRNPF	7043	0.02	0.43	YES
82	HNRNPUL1	HNRNPUL1	HNRNPUL1	7214	0.018	0.43	YES
83	NUP214	NUP214	NUP214	7315	0.017	0.42	YES
84	RAE1	RAE1	RAE1	7320	0.016	0.43	YES
85	RNPS1	RNPS1	RNPS1	7328	0.016	0.43	YES
86	U2AF1	U2AF1	U2AF1	7354	0.016	0.43	YES
87	NUP37	NUP37	NUP37	7365	0.016	0.43	YES
88	HNRNPL	HNRNPL	HNRNPL	7390	0.016	0.44	YES
89	SNRPA	SNRPA	SNRPA	7491	0.014	0.43	YES
90	SNRNP200	SNRNP200	SNRNP200	7534	0.014	0.43	YES
91	POLR2G	POLR2G	POLR2G	7554	0.014	0.43	YES
92	PRPF4	PRPF4	PRPF4	7620	0.013	0.43	YES
93	PTBP1	PTBP1	PTBP1	7662	0.012	0.43	YES
94	PRPF6	PRPF6	PRPF6	7685	0.012	0.43	YES
95	POLR2D	POLR2D	POLR2D	7717	0.012	0.44	YES
96	CDC40	CDC40	CDC40	7784	0.011	0.43	YES
97	SF3A2	SF3A2	SF3A2	7798	0.01	0.43	YES
98	NHP2L1	NHP2L1	NHP2L1	7813	0.01	0.44	YES
99	CPSF3	CPSF3	CPSF3	7830	0.01	0.44	YES
100	CPSF7	CPSF7	CPSF7	7905	0.0092	0.43	NO
101	POM121	POM121	POM121	7942	0.0088	0.43	NO
102	CLP1	CLP1	CLP1	8068	0.007	0.43	NO
103	DNAJC8	DNAJC8	DNAJC8	8124	0.0065	0.43	NO
104	NCBP2	NCBP2	NCBP2	8179	0.0056	0.42	NO
105	ADAR	ADAR	ADAR	8198	0.0054	0.42	NO
106	RANBP2	RANBP2	RANBP2	8229	0.0051	0.42	NO
107	U2AF2	U2AF2	U2AF2	8289	0.0044	0.42	NO
108	PRPF8	PRPF8	PRPF8	8292	0.0044	0.42	NO
109	DDX23	DDX23	DDX23	8310	0.0042	0.42	NO
110	ERCC3	ERCC3	ERCC3	8344	0.0038	0.42	NO
111	GTF2F1	GTF2F1	GTF2F1	8371	0.0034	0.42	NO
112	EFTUD2	EFTUD2	EFTUD2	8402	0.003	0.42	NO
113	NUP62	NUP62	NUP62	8411	0.0028	0.42	NO
114	NUP50	NUP50	NUP50	8461	0.0023	0.42	NO
115	SNRPG	SNRPG	SNRPG	8560	0.001	0.41	NO
116	CPSF2	CPSF2	CPSF2	8739	-0.0015	0.4	NO
117	TXNL4A	TXNL4A	TXNL4A	8755	-0.0018	0.4	NO
118	SUPT5H	SUPT5H	SUPT5H	8819	-0.0024	0.4	NO
119	POLR2E	POLR2E	POLR2E	8851	-0.0029	0.4	NO
120	SRRM1	SRRM1	SRRM1	8870	-0.003	0.4	NO
121	SF3B4	SF3B4	SF3B4	8872	-0.003	0.4	NO
122	SNRNP40	SNRNP40	SNRNP40	8967	-0.0041	0.39	NO
123	POLR2I	POLR2I	POLR2I	9140	-0.0063	0.38	NO
124	POLR2F	POLR2F	POLR2F	9330	-0.0091	0.38	NO
125	THOC4	THOC4	THOC4	9367	-0.0097	0.38	NO
126	NUP155	NUP155	NUP155	9409	-0.01	0.38	NO
127	DHX38	DHX38	DHX38	9443	-0.011	0.38	NO
128	CSTF2	CSTF2	CSTF2	9466	-0.011	0.38	NO
129	SF3A1	SF3A1	SF3A1	9630	-0.013	0.37	NO
130	NUP205	NUP205	NUP205	9681	-0.014	0.37	NO
131	SF3B2	SF3B2	SF3B2	9729	-0.015	0.37	NO
132	SF3B5	SF3B5	SF3B5	9742	-0.015	0.37	NO
133	PHF5A	PHF5A	PHF5A	9914	-0.018	0.36	NO
134	POLR2H	POLR2H	POLR2H	9915	-0.018	0.37	NO
135	PCBP1	PCBP1	PCBP1	10196	-0.022	0.36	NO
136	CD2BP2	CD2BP2	CD2BP2	10411	-0.025	0.35	NO
137	NUP188	NUP188	NUP188	10436	-0.025	0.35	NO
138	POLR2L	POLR2L	POLR2L	10911	-0.032	0.33	NO
139	POLR2J	POLR2J	POLR2J	11204	-0.038	0.32	NO
140	NUP93	NUP93	NUP93	11363	-0.041	0.32	NO
141	POLR2C	POLR2C	POLR2C	11828	-0.05	0.31	NO
142	POLR2A	POLR2A	POLR2A	12478	-0.063	0.28	NO
143	LSM10	LSM10	LSM10	12758	-0.069	0.28	NO
144	NUP210	NUP210	NUP210	13232	-0.082	0.27	NO

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

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

genes ES table in pathway: KEGG BASAL TRANSCRIPTION FACTORS

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	RPL36A	RPL36A	RPL36A	919	0.18	-0.034	YES
2	RPS27	RPS27	RPS27	1011	0.17	-0.022	YES
3	RPL7	RPL7	RPL7	1214	0.16	-0.018	YES
4	DCP2	DCP2	DCP2	1362	0.15	-0.012	YES
5	PRKCA	PRKCA	PRKCA	1378	0.15	0.001	YES
6	RPL21	RPL21	RPL21	1606	0.13	0.0013	YES
7	RPL9	RPL9	RPL9	1630	0.13	0.013	YES
8	RPS3A	RPS3A	RPS3A	1684	0.13	0.022	YES
9	RPL39	RPL39	RPL39	1806	0.12	0.028	YES
10	PABPC1	PABPC1	PABPC1	1834	0.12	0.038	YES
11	EXOSC8	EXOSC8	EXOSC8	1968	0.12	0.042	YES
12	RPS7	RPS7	RPS7	2333	0.1	0.032	YES
13	RPS12	RPS12	RPS12	2433	0.1	0.036	YES
14	PAIP1	PAIP1	PAIP1	2524	0.099	0.041	YES
15	RPS18	RPS18	RPS18	2533	0.099	0.05	YES
16	UPF3B	UPF3B	UPF3B	2602	0.097	0.055	YES
17	RPSAP9	RPSAP9	RPSAP9	2706	0.094	0.058	YES
18	RPS23	RPS23	RPS23	2738	0.093	0.066	YES
19	RPL30	RPL30	RPL30	2787	0.092	0.072	YES
20	EIF4B	EIF4B	EIF4B	2852	0.09	0.077	YES
21	RPS10	RPS10	RPS10	2869	0.09	0.085	YES
22	RPL17	RPL17	RPL17	2876	0.09	0.093	YES
23	RPL22	RPL22	RPL22	2917	0.088	0.1	YES
24	RPS20	RPS20	RPS20	2996	0.086	0.1	YES
25	RPL26	RPL26	RPL26	3006	0.086	0.11	YES
26	RPL8	RPL8	RPL8	3011	0.086	0.12	YES
27	RPL10A	RPL10A	RPL10A	3034	0.085	0.13	YES
28	RPL34	RPL34	RPL34	3039	0.085	0.13	YES
29	DIS3	DIS3	DIS3	3045	0.085	0.14	YES
30	UPF3A	UPF3A	UPF3A	3049	0.085	0.15	YES
31	CNOT6	CNOT6	CNOT6	3056	0.085	0.16	YES
32	RPL23	RPL23	RPL23	3186	0.082	0.16	YES
33	RPL5	RPL5	RPL5	3230	0.081	0.16	YES
34	RPL6	RPL6	RPL6	3280	0.08	0.17	YES
35	RPS8	RPS8	RPS8	3378	0.078	0.17	YES
36	RPS6	RPS6	RPS6	3504	0.075	0.17	YES
37	RPS26	RPS26	RPS26	3519	0.074	0.18	YES
38	RPS24	RPS24	RPS24	3538	0.074	0.18	YES
39	ANP32A	ANP32A	ANP32A	3645	0.071	0.18	YES
40	EXOSC2	EXOSC2	EXOSC2	3683	0.07	0.19	YES
41	EIF4A2	EIF4A2	EIF4A2	3688	0.07	0.2	YES
42	RPL13A	RPL13A	RPL13A	3735	0.069	0.2	YES
43	RPS17	RPS17	RPS17	3826	0.068	0.2	YES
44	RPS4X	RPS4X	RPS4X	3829	0.068	0.21	YES
45	RPL4	RPL4	RPL4	3835	0.067	0.22	YES
46	GSPT2	GSPT2	GSPT2	3851	0.067	0.22	YES
47	UPF2	UPF2	UPF2	3877	0.067	0.22	YES
48	RPL3	RPL3	RPL3	3889	0.066	0.23	YES
49	LSM6	LSM6	LSM6	3944	0.066	0.23	YES
50	RPL31	RPL31	RPL31	3949	0.065	0.24	YES
51	RPL12	RPL12	RPL12	3978	0.065	0.24	YES
52	RPS3	RPS3	RPS3	3990	0.065	0.25	YES
53	PSMA8	PSMA8	PSMA8	4010	0.064	0.26	YES
54	RPL38	RPL38	RPL38	4039	0.064	0.26	YES
55	RPS14	RPS14	RPS14	4056	0.064	0.27	YES
56	RPS15A	RPS15A	RPS15A	4070	0.063	0.27	YES
57	RPS19	RPS19	RPS19	4166	0.061	0.27	YES
58	RPS27A	RPS27A	RPS27A	4186	0.061	0.28	YES
59	RPS21	RPS21	RPS21	4216	0.061	0.28	YES
60	RPS29	RPS29	RPS29	4284	0.059	0.28	YES
61	EXOSC4	EXOSC4	EXOSC4	4314	0.059	0.29	YES
62	RPS5	RPS5	RPS5	4329	0.058	0.29	YES
63	PSMC6	PSMC6	PSMC6	4339	0.058	0.3	YES
64	EXOSC5	EXOSC5	EXOSC5	4347	0.058	0.3	YES
65	RPL7A	RPL7A	RPL7A	4365	0.058	0.31	YES
66	MAPK14	MAPK14	MAPK14	4371	0.058	0.31	YES
67	RPL23A	RPL23A	RPL23A	4386	0.057	0.32	YES
68	DCP1B	DCP1B	DCP1B	4425	0.057	0.32	YES
69	RPL14	RPL14	RPL14	4551	0.055	0.32	YES
70	KHSRP	KHSRP	KHSRP	4578	0.054	0.32	YES
71	PPP2R2A	PPP2R2A	PPP2R2A	4603	0.054	0.33	YES
72	RPL37	RPL37	RPL37	4658	0.053	0.33	YES
73	RPL24	RPL24	RPL24	4701	0.053	0.33	YES
74	LSM2	LSM2	LSM2	4703	0.052	0.34	YES
75	RPL35A	RPL35A	RPL35A	4720	0.052	0.34	YES
76	RPS16	RPS16	RPS16	4737	0.052	0.34	YES
77	EXOSC3	EXOSC3	EXOSC3	4751	0.052	0.35	YES
78	RPL29	RPL29	RPL29	4763	0.052	0.35	YES
79	RPS25	RPS25	RPS25	4769	0.051	0.36	YES
80	CNOT8	CNOT8	CNOT8	4835	0.05	0.36	YES
81	RPL18	RPL18	RPL18	4906	0.049	0.36	YES
82	RPL36	RPL36	RPL36	4907	0.049	0.36	YES
83	RBM8A	RBM8A	RBM8A	4912	0.049	0.37	YES
84	RPL37A	RPL37A	RPL37A	4981	0.048	0.37	YES
85	XPO1	XPO1	XPO1	4996	0.048	0.37	YES
86	PSMD10	PSMD10	PSMD10	4997	0.048	0.38	YES
87	RPL32	RPL32	RPL32	5021	0.048	0.38	YES
88	CNOT7	CNOT7	CNOT7	5039	0.047	0.38	YES
89	RPL11	RPL11	RPL11	5057	0.047	0.39	YES
90	RPS13	RPS13	RPS13	5119	0.046	0.39	YES
91	RPL19	RPL19	RPL19	5136	0.046	0.39	YES
92	PSMB4	PSMB4	PSMB4	5237	0.045	0.39	YES
93	RPLP1	RPLP1	RPLP1	5252	0.044	0.4	YES
94	RPS11	RPS11	RPS11	5255	0.044	0.4	YES
95	RPL18A	RPL18A	RPL18A	5283	0.044	0.4	YES
96	RPS2	RPS2	RPS2	5290	0.044	0.41	YES
97	RPLP0	RPLP0	RPLP0	5343	0.043	0.41	YES
98	RPL15	RPL15	RPL15	5370	0.043	0.41	YES
99	HNRNPD	HNRNPD	HNRNPD	5462	0.041	0.41	YES
100	RPS9	RPS9	RPS9	5501	0.041	0.41	YES
101	RPL13	RPL13	RPL13	5526	0.04	0.41	YES
102	DDX6	DDX6	DDX6	5589	0.04	0.41	YES
103	DCP1A	DCP1A	DCP1A	5691	0.038	0.41	YES
104	MAGOH	MAGOH	MAGOH	5697	0.038	0.42	YES
105	RPL27	RPL27	RPL27	5712	0.038	0.42	YES
106	HSPA1B	HSPA1B	HSPA1B	5721	0.038	0.42	YES
107	RPL27A	RPL27A	RPL27A	5771	0.037	0.42	YES
108	NCBP1	NCBP1	NCBP1	5811	0.037	0.42	YES
109	RPS15	RPS15	RPS15	5875	0.036	0.42	YES
110	SMG5	SMG5	SMG5	5892	0.036	0.43	YES
111	EIF4E	EIF4E	EIF4E	5918	0.035	0.43	YES
112	RPL35	RPL35	RPL35	5939	0.035	0.43	YES
113	LSM5	LSM5	LSM5	5945	0.035	0.43	YES
114	RPL41	RPL41	RPL41	5947	0.035	0.44	YES
115	ETF1	ETF1	ETF1	6067	0.033	0.43	NO
116	RPS28	RPS28	RPS28	6078	0.033	0.44	NO
117	PSMA4	PSMA4	PSMA4	6160	0.032	0.43	NO
118	RPSA	RPSA	RPSA	6191	0.032	0.44	NO
119	ZFP36L1	ZFP36L1	ZFP36L1	6326	0.03	0.43	NO
120	EXOSC7	EXOSC7	EXOSC7	6431	0.028	0.43	NO
121	RPL10	RPL10	RPL10	6540	0.027	0.42	NO
122	SMG7	SMG7	SMG7	6721	0.024	0.42	NO
123	CNOT2	CNOT2	CNOT2	6736	0.024	0.42	NO
124	PSMD5	PSMD5	PSMD5	6789	0.024	0.42	NO
125	PPP2CA	PPP2CA	PPP2CA	6970	0.021	0.41	NO
126	HSPA8	HSPA8	HSPA8	6986	0.021	0.41	NO
127	EIF4A3	EIF4A3	EIF4A3	7000	0.021	0.41	NO
128	ELAVL1	ELAVL1	ELAVL1	7068	0.02	0.41	NO
129	PSMF1	PSMF1	PSMF1	7099	0.02	0.41	NO
130	TNPO1	TNPO1	TNPO1	7122	0.019	0.41	NO
131	PSMA3	PSMA3	PSMA3	7222	0.018	0.41	NO
132	PSMB7	PSMB7	PSMB7	7234	0.018	0.41	NO
133	NUP214	NUP214	NUP214	7315	0.017	0.4	NO
134	RNPS1	RNPS1	RNPS1	7328	0.016	0.41	NO
135	YWHAZ	YWHAZ	YWHAZ	7397	0.015	0.4	NO
136	PPP2R1A	PPP2R1A	PPP2R1A	7427	0.015	0.4	NO
137	PSMD4	PSMD4	PSMD4	7536	0.014	0.4	NO
138	PSMA1	PSMA1	PSMA1	7581	0.013	0.4	NO
139	RPLP2	RPLP2	RPLP2	7610	0.013	0.4	NO
140	RPL28	RPL28	RPL28	7615	0.013	0.4	NO
141	LSM4	LSM4	LSM4	7726	0.012	0.39	NO
142	XRN1	XRN1	XRN1	7735	0.011	0.39	NO
143	PARN	PARN	PARN	7893	0.0093	0.39	NO
144	EIF4A1	EIF4A1	EIF4A1	7945	0.0087	0.38	NO
145	PRKCD	PRKCD	PRKCD	7965	0.0086	0.38	NO
146	SMG1	SMG1	SMG1	8134	0.0063	0.38	NO
147	CASC3	CASC3	CASC3	8151	0.006	0.38	NO
148	EDC3	EDC3	EDC3	8162	0.0058	0.38	NO
149	CNOT4	CNOT4	CNOT4	8167	0.0058	0.38	NO
150	SMG6	SMG6	SMG6	8171	0.0057	0.38	NO
151	NCBP2	NCBP2	NCBP2	8179	0.0056	0.38	NO
152	UBA52	UBA52	UBA52	8183	0.0056	0.38	NO
153	HSPB1	HSPB1	HSPB1	8305	0.0043	0.37	NO
154	PSMC1	PSMC1	PSMC1	8484	0.002	0.36	NO
155	PSMA6	PSMA6	PSMA6	8490	0.002	0.36	NO
156	PSMB1	PSMB1	PSMB1	8613	0.00026	0.35	NO
157	PSMB5	PSMB5	PSMB5	8669	-0.00052	0.35	NO
158	FAU	FAU	FAU	8710	-0.0012	0.35	NO
159	PSMA2	PSMA2	PSMA2	8764	-0.0018	0.34	NO
160	LSM3	LSM3	LSM3	8956	-0.0039	0.34	NO
161	AKT1	AKT1	AKT1	9125	-0.0062	0.33	NO
162	EDC4	EDC4	EDC4	9130	-0.0063	0.33	NO
163	CNOT3	CNOT3	CNOT3	9131	-0.0063	0.33	NO
164	EXOSC9	EXOSC9	EXOSC9	9150	-0.0064	0.33	NO
165	C2orf29	C2orf29	C2orf29	9190	-0.007	0.32	NO
166	RPS4Y1	RPS4Y1	RPS4Y1	9221	-0.0074	0.32	NO
167	LSM1	LSM1	LSM1	9285	-0.0085	0.32	NO
168	YWHAB	YWHAB	YWHAB	9333	-0.0091	0.32	NO
169	PSMD12	PSMD12	PSMD12	9353	-0.0095	0.32	NO
170	PSMB2	PSMB2	PSMB2	9465	-0.011	0.31	NO
171	PSME1	PSME1	PSME1	9570	-0.012	0.31	NO
172	DCPS	DCPS	DCPS	9655	-0.014	0.31	NO
173	EXOSC6	EXOSC6	EXOSC6	9797	-0.016	0.3	NO
174	PSME2	PSME2	PSME2	10052	-0.019	0.29	NO
175	PSMD7	PSMD7	PSMD7	10056	-0.02	0.29	NO
176	PSME4	PSME4	PSME4	10085	-0.02	0.29	NO
177	EIF4G1	EIF4G1	EIF4G1	10099	-0.02	0.29	NO
178	PSMA5	PSMA5	PSMA5	10336	-0.023	0.28	NO
179	PSMC5	PSMC5	PSMC5	10338	-0.023	0.28	NO
180	PSMD14	PSMD14	PSMD14	10343	-0.024	0.28	NO
181	PSMD3	PSMD3	PSMD3	10357	-0.024	0.29	NO
182	PSMD6	PSMD6	PSMD6	10381	-0.024	0.29	NO
183	PSMA7	PSMA7	PSMA7	10387	-0.024	0.29	NO
184	PSMD13	PSMD13	PSMD13	10417	-0.025	0.29	NO
185	PSMC2	PSMC2	PSMC2	10726	-0.03	0.28	NO
186	PSMB10	PSMB10	PSMB10	10739	-0.03	0.28	NO
187	PSMD1	PSMD1	PSMD1	10787	-0.031	0.28	NO
188	PSMB8	PSMB8	PSMB8	10862	-0.032	0.28	NO
189	PSMB6	PSMB6	PSMB6	10893	-0.032	0.28	NO
190	RPL26L1	RPL26L1	RPL26L1	11064	-0.035	0.27	NO
191	PATL1	PATL1	PATL1	11202	-0.038	0.27	NO
192	CNOT10	CNOT10	CNOT10	11323	-0.04	0.26	NO
193	PSMD11	PSMD11	PSMD11	11408	-0.042	0.26	NO
194	MAPK11	MAPK11	MAPK11	11478	-0.043	0.26	NO
195	PSMD9	PSMD9	PSMD9	11542	-0.044	0.26	NO
196	PSMD8	PSMD8	PSMD8	11743	-0.048	0.26	NO
197	PSMC4	PSMC4	PSMC4	11745	-0.048	0.26	NO
198	PSMB3	PSMB3	PSMB3	11762	-0.048	0.27	NO
199	RQCD1	RQCD1	RQCD1	11959	-0.052	0.26	NO
200	MAPKAPK2	MAPKAPK2	MAPKAPK2	12015	-0.053	0.26	NO
201	TNFSF13	TNFSF13	TNFSF13	12152	-0.056	0.26	NO
202	PSMC3	PSMC3	PSMC3	12312	-0.059	0.26	NO
203	TNKS1BP1	TNKS1BP1	TNKS1BP1	12420	-0.062	0.26	NO
204	PSMD2	PSMD2	PSMD2	12871	-0.072	0.24	NO
205	EXOSC1	EXOSC1	EXOSC1	13951	-0.1	0.19	NO
206	PSMB9	PSMB9	PSMB9	14243	-0.11	0.18	NO
207	ZFP36	ZFP36	ZFP36	14718	-0.13	0.17	NO
208	FAM153A	FAM153A	FAM153A	15595	-0.17	0.14	NO

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

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

genes ES table in pathway: KEGG SPLICEOSOME

Table 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	SNRPE	SNRPE	SNRPE	1385	0.15	-0.042	YES
2	THOC1	THOC1	THOC1	1649	0.13	-0.025	YES
3	HSPA2	HSPA2	HSPA2	1790	0.13	-0.0023	YES
4	HNRNPA1	HNRNPA1	HNRNPA1	1942	0.12	0.018	YES
5	HNRNPA1L2	HNRNPA1L2	HNRNPA1L2	1993	0.12	0.043	YES
6	SNRPD1	SNRPD1	SNRPD1	2442	0.1	0.042	YES
7	PUF60	PUF60	PUF60	2816	0.091	0.044	YES
8	THOC2	THOC2	THOC2	2860	0.09	0.063	YES
9	PRPF40B	PRPF40B	PRPF40B	2871	0.09	0.084	YES
10	PRPF38A	PRPF38A	PRPF38A	3027	0.086	0.096	YES
11	RBMX	RBMX	RBMX	3050	0.085	0.12	YES
12	TCERG1	TCERG1	TCERG1	3139	0.083	0.13	YES
13	CDC5L	CDC5L	CDC5L	3520	0.074	0.13	YES
14	LSM6	LSM6	LSM6	3944	0.066	0.12	YES
15	SNRPC	SNRPC	SNRPC	3967	0.065	0.13	YES
16	HNRNPA3	HNRNPA3	HNRNPA3	4031	0.064	0.14	YES
17	PPIL1	PPIL1	PPIL1	4283	0.059	0.14	YES
18	SNRNP70	SNRNP70	SNRNP70	4438	0.056	0.15	YES
19	DHX15	DHX15	DHX15	4441	0.056	0.16	YES
20	RBM25	RBM25	RBM25	4588	0.054	0.17	YES
21	SNW1	SNW1	SNW1	4624	0.054	0.18	YES
22	DDX46	DDX46	DDX46	4684	0.053	0.19	YES
23	LSM2	LSM2	LSM2	4703	0.052	0.2	YES
24	CRNKL1	CRNKL1	CRNKL1	4761	0.052	0.21	YES
25	DDX42	DDX42	DDX42	4902	0.049	0.21	YES
26	RBM8A	RBM8A	RBM8A	4912	0.049	0.22	YES
27	TRA2B	TRA2B	TRA2B	5012	0.048	0.23	YES
28	HNRNPC	HNRNPC	HNRNPC	5125	0.046	0.24	YES
29	CWC15	CWC15	CWC15	5160	0.046	0.24	YES
30	PRPF40A	PRPF40A	PRPF40A	5187	0.045	0.25	YES
31	PRPF3	PRPF3	PRPF3	5294	0.044	0.26	YES
32	THOC3	THOC3	THOC3	5312	0.044	0.27	YES
33	SNRPF	SNRPF	SNRPF	5362	0.043	0.28	YES
34	HNRNPM	HNRNPM	HNRNPM	5392	0.042	0.28	YES
35	HNRNPU	HNRNPU	HNRNPU	5423	0.042	0.29	YES
36	PLRG1	PLRG1	PLRG1	5471	0.041	0.3	YES
37	LSM7	LSM7	LSM7	5578	0.04	0.3	YES
38	SLU7	SLU7	SLU7	5600	0.039	0.31	YES
39	SNRPD3	SNRPD3	SNRPD3	5680	0.038	0.32	YES
40	MAGOH	MAGOH	MAGOH	5697	0.038	0.32	YES
41	HSPA1B	HSPA1B	HSPA1B	5721	0.038	0.33	YES
42	SF3B1	SF3B1	SF3B1	5735	0.038	0.34	YES
43	PRPF38B	PRPF38B	PRPF38B	5762	0.037	0.35	YES
44	NCBP1	NCBP1	NCBP1	5811	0.037	0.36	YES
45	HNRNPK	HNRNPK	HNRNPK	5861	0.036	0.36	YES
46	ACIN1	ACIN1	ACIN1	5880	0.036	0.37	YES
47	LSM5	LSM5	LSM5	5945	0.035	0.37	YES
48	SNRPB2	SNRPB2	SNRPB2	6105	0.033	0.37	YES
49	ZMAT2	ZMAT2	ZMAT2	6113	0.033	0.38	YES
50	HSPA1A	HSPA1A	HSPA1A	6156	0.032	0.39	YES
51	SNRPB	SNRPB	SNRPB	6218	0.031	0.39	YES
52	SF3B14	SF3B14	SF3B14	6241	0.031	0.4	YES
53	SNRPD2	SNRPD2	SNRPD2	6381	0.029	0.4	YES
54	SF3A3	SF3A3	SF3A3	6493	0.028	0.4	YES
55	PRPF31	PRPF31	PRPF31	6559	0.026	0.4	YES
56	SF3B3	SF3B3	SF3B3	6580	0.026	0.4	YES
57	SNRPA1	SNRPA1	SNRPA1	6633	0.026	0.41	YES
58	TRA2A	TRA2A	TRA2A	6820	0.023	0.4	YES
59	PPIH	PPIH	PPIH	6898	0.022	0.4	YES
60	PQBP1	PQBP1	PQBP1	6958	0.021	0.4	YES
61	HSPA8	HSPA8	HSPA8	6986	0.021	0.41	YES
62	EIF4A3	EIF4A3	EIF4A3	7000	0.021	0.41	YES
63	MAGOHB	MAGOHB	MAGOHB	7066	0.02	0.41	YES
64	CHERP	CHERP	CHERP	7082	0.02	0.42	YES
65	SYF2	SYF2	SYF2	7083	0.02	0.42	YES
66	PRPF19	PRPF19	PRPF19	7276	0.017	0.42	NO
67	U2AF1	U2AF1	U2AF1	7354	0.016	0.42	NO
68	SNRPA	SNRPA	SNRPA	7491	0.014	0.41	NO
69	DHX16	DHX16	DHX16	7502	0.014	0.41	NO
70	SNRNP200	SNRNP200	SNRNP200	7534	0.014	0.42	NO
71	PRPF4	PRPF4	PRPF4	7620	0.013	0.41	NO
72	PRPF6	PRPF6	PRPF6	7685	0.012	0.41	NO
73	LSM4	LSM4	LSM4	7726	0.012	0.41	NO
74	CDC40	CDC40	CDC40	7784	0.011	0.41	NO
75	XAB2	XAB2	XAB2	7788	0.011	0.42	NO
76	SF3A2	SF3A2	SF3A2	7798	0.01	0.42	NO
77	NHP2L1	NHP2L1	NHP2L1	7813	0.01	0.42	NO
78	SMNDC1	SMNDC1	SMNDC1	7889	0.0093	0.42	NO
79	DDX5	DDX5	DDX5	7927	0.009	0.42	NO
80	RBM22	RBM22	RBM22	7936	0.0089	0.42	NO
81	NCBP2	NCBP2	NCBP2	8179	0.0056	0.41	NO
82	PPIE	PPIE	PPIE	8185	0.0055	0.41	NO
83	HSPA1L	HSPA1L	HSPA1L	8230	0.0051	0.41	NO
84	U2AF2	U2AF2	U2AF2	8289	0.0044	0.4	NO
85	PRPF8	PRPF8	PRPF8	8292	0.0044	0.41	NO
86	DDX23	DDX23	DDX23	8310	0.0042	0.41	NO
87	EFTUD2	EFTUD2	EFTUD2	8402	0.003	0.4	NO
88	RBM17	RBM17	RBM17	8469	0.0022	0.4	NO
89	WBP11	WBP11	WBP11	8492	0.0019	0.4	NO
90	SNRPG	SNRPG	SNRPG	8560	0.001	0.39	NO
91	TXNL4A	TXNL4A	TXNL4A	8755	-0.0018	0.38	NO
92	CCDC12	CCDC12	CCDC12	8789	-0.0021	0.38	NO
93	SF3B4	SF3B4	SF3B4	8872	-0.003	0.38	NO
94	LSM3	LSM3	LSM3	8956	-0.0039	0.38	NO
95	SNRNP40	SNRNP40	SNRNP40	8967	-0.0041	0.38	NO
96	BCAS2	BCAS2	BCAS2	9099	-0.0058	0.37	NO
97	CTNNBL1	CTNNBL1	CTNNBL1	9324	-0.009	0.36	NO
98	THOC4	THOC4	THOC4	9367	-0.0097	0.36	NO
99	SNRNP27	SNRNP27	SNRNP27	9407	-0.01	0.36	NO
100	DHX38	DHX38	DHX38	9443	-0.011	0.36	NO
101	SF3A1	SF3A1	SF3A1	9630	-0.013	0.35	NO
102	BUD31	BUD31	BUD31	9686	-0.014	0.35	NO
103	SF3B2	SF3B2	SF3B2	9729	-0.015	0.35	NO
104	AQR	AQR	AQR	9732	-0.015	0.36	NO
105	SF3B5	SF3B5	SF3B5	9742	-0.015	0.36	NO
106	SART1	SART1	SART1	9753	-0.015	0.36	NO
107	PHF5A	PHF5A	PHF5A	9914	-0.018	0.36	NO
108	USP39	USP39	USP39	9934	-0.018	0.36	NO
109	PCBP1	PCBP1	PCBP1	10196	-0.022	0.35	NO
110	ISY1	ISY1	ISY1	10439	-0.025	0.35	NO
111	NAA38	NAA38	NAA38	10993	-0.034	0.32	NO
112	PRPF18	PRPF18	PRPF18	11450	-0.042	0.31	NO
113	DHX8	DHX8	DHX8	11765	-0.048	0.3	NO
114	HSPA6	HSPA6	HSPA6	16227	-0.2	0.1	NO

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

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

genes ES table in pathway: PID ATM PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	RPL36A	RPL36A	RPL36A	919	0.18	-0.027	YES
2	RPS27	RPS27	RPS27	1011	0.17	-0.009	YES
3	RPL7	RPL7	RPL7	1214	0.16	0.00068	YES
4	RPL21	RPL21	RPL21	1606	0.13	-0.0033	YES
5	RPL9	RPL9	RPL9	1630	0.13	0.013	YES
6	RPS3A	RPS3A	RPS3A	1684	0.13	0.028	YES
7	RPL39	RPL39	RPL39	1806	0.12	0.038	YES
8	RPS7	RPS7	RPS7	2333	0.1	0.022	YES
9	NUP133	NUP133	NUP133	2383	0.1	0.033	YES
10	RPS12	RPS12	RPS12	2433	0.1	0.044	YES
11	RPS18	RPS18	RPS18	2533	0.099	0.051	YES
12	GTF2F2	GTF2F2	GTF2F2	2617	0.097	0.06	YES
13	RPSAP9	RPSAP9	RPSAP9	2706	0.094	0.067	YES
14	HSP90AA1	HSP90AA1	HSP90AA1	2713	0.094	0.079	YES
15	RPS23	RPS23	RPS23	2738	0.093	0.09	YES
16	RPL30	RPL30	RPL30	2787	0.092	0.1	YES
17	RPS10	RPS10	RPS10	2869	0.09	0.11	YES
18	RPL17	RPL17	RPL17	2876	0.09	0.12	YES
19	RPL22	RPL22	RPL22	2917	0.088	0.13	YES
20	RPS20	RPS20	RPS20	2996	0.086	0.14	YES
21	RPL26	RPL26	RPL26	3006	0.086	0.15	YES
22	RPL8	RPL8	RPL8	3011	0.086	0.16	YES
23	IPO5	IPO5	IPO5	3017	0.086	0.17	YES
24	RPL10A	RPL10A	RPL10A	3034	0.085	0.18	YES
25	RPL34	RPL34	RPL34	3039	0.085	0.19	YES
26	NUP153	NUP153	NUP153	3074	0.085	0.2	YES
27	RPL23	RPL23	RPL23	3186	0.082	0.2	YES
28	RPL5	RPL5	RPL5	3230	0.081	0.21	YES
29	RPL6	RPL6	RPL6	3280	0.08	0.22	YES
30	RPS8	RPS8	RPS8	3378	0.078	0.23	YES
31	RPS6	RPS6	RPS6	3504	0.075	0.23	YES
32	RPS26	RPS26	RPS26	3519	0.074	0.24	YES
33	RPS24	RPS24	RPS24	3538	0.074	0.25	YES
34	CLTA	CLTA	CLTA	3648	0.071	0.25	YES
35	TPR	TPR	TPR	3674	0.071	0.26	YES
36	POLR2K	POLR2K	POLR2K	3695	0.07	0.27	YES
37	RPL13A	RPL13A	RPL13A	3735	0.069	0.27	YES
38	RPS17	RPS17	RPS17	3826	0.068	0.28	YES
39	RPS4X	RPS4X	RPS4X	3829	0.068	0.29	YES
40	RPL4	RPL4	RPL4	3835	0.067	0.3	YES
41	RPL3	RPL3	RPL3	3889	0.066	0.3	YES
42	RPL31	RPL31	RPL31	3949	0.065	0.31	YES
43	RPL12	RPL12	RPL12	3978	0.065	0.31	YES
44	RPS3	RPS3	RPS3	3990	0.065	0.32	YES
45	RPL38	RPL38	RPL38	4039	0.064	0.33	YES
46	RPS14	RPS14	RPS14	4056	0.064	0.34	YES
47	RPS15A	RPS15A	RPS15A	4070	0.063	0.34	YES
48	RPS19	RPS19	RPS19	4166	0.061	0.34	YES
49	RPS27A	RPS27A	RPS27A	4186	0.061	0.35	YES
50	RPS21	RPS21	RPS21	4216	0.061	0.36	YES
51	NUP43	NUP43	NUP43	4261	0.06	0.36	YES
52	RPS29	RPS29	RPS29	4284	0.059	0.37	YES
53	NUP35	NUP35	NUP35	4302	0.059	0.38	YES
54	RPS5	RPS5	RPS5	4329	0.058	0.38	YES
55	SEH1L	SEH1L	SEH1L	4336	0.058	0.39	YES
56	RPL7A	RPL7A	RPL7A	4365	0.058	0.4	YES
57	RPL23A	RPL23A	RPL23A	4386	0.057	0.4	YES
58	NUPL1	NUPL1	NUPL1	4485	0.056	0.41	YES
59	RPL14	RPL14	RPL14	4551	0.055	0.41	YES
60	RPL37	RPL37	RPL37	4658	0.053	0.41	YES
61	NUP107	NUP107	NUP107	4673	0.053	0.42	YES
62	RPL24	RPL24	RPL24	4701	0.053	0.42	YES
63	RPL35A	RPL35A	RPL35A	4720	0.052	0.43	YES
64	RPS16	RPS16	RPS16	4737	0.052	0.44	YES
65	RPL29	RPL29	RPL29	4763	0.052	0.44	YES
66	RPS25	RPS25	RPS25	4769	0.051	0.45	YES
67	NUP54	NUP54	NUP54	4772	0.051	0.45	YES
68	RPL18	RPL18	RPL18	4906	0.049	0.45	YES
69	RPL36	RPL36	RPL36	4907	0.049	0.46	YES
70	RPL37A	RPL37A	RPL37A	4981	0.048	0.46	YES
71	XPO1	XPO1	XPO1	4996	0.048	0.47	YES
72	RPL32	RPL32	RPL32	5021	0.048	0.47	YES
73	RPL11	RPL11	RPL11	5057	0.047	0.48	YES
74	RPS13	RPS13	RPS13	5119	0.046	0.48	YES
75	RPL19	RPL19	RPL19	5136	0.046	0.48	YES
76	RPLP1	RPLP1	RPLP1	5252	0.044	0.48	YES
77	RPS11	RPS11	RPS11	5255	0.044	0.49	YES
78	RPL18A	RPL18A	RPL18A	5283	0.044	0.49	YES
79	RPS2	RPS2	RPS2	5290	0.044	0.5	YES
80	RPLP0	RPLP0	RPLP0	5343	0.043	0.5	YES
81	RPL15	RPL15	RPL15	5370	0.043	0.51	YES
82	RPS9	RPS9	RPS9	5501	0.041	0.5	YES
83	RPL13	RPL13	RPL13	5526	0.04	0.51	YES
84	RPL27	RPL27	RPL27	5712	0.038	0.5	YES
85	HSPA1B	HSPA1B	HSPA1B	5721	0.038	0.51	YES
86	RPL27A	RPL27A	RPL27A	5771	0.037	0.51	YES
87	RPS15	RPS15	RPS15	5875	0.036	0.51	YES
88	RPL35	RPL35	RPL35	5939	0.035	0.51	YES
89	RPL41	RPL41	RPL41	5947	0.035	0.52	YES
90	RPS28	RPS28	RPS28	6078	0.033	0.51	YES
91	NUPL2	NUPL2	NUPL2	6137	0.032	0.51	YES
92	RPSA	RPSA	RPSA	6191	0.032	0.51	YES
93	NUP88	NUP88	NUP88	6196	0.032	0.52	YES
94	AAAS	AAAS	AAAS	6275	0.03	0.52	YES
95	GRSF1	GRSF1	GRSF1	6312	0.03	0.52	YES
96	RAN	RAN	RAN	6341	0.029	0.52	YES
97	RPL10	RPL10	RPL10	6540	0.027	0.52	NO
98	CANX	CANX	CANX	6873	0.022	0.5	NO
99	NUP85	NUP85	NUP85	6959	0.021	0.5	NO
100	POLR2B	POLR2B	POLR2B	6982	0.021	0.5	NO
101	KPNB1	KPNB1	KPNB1	7147	0.019	0.49	NO
102	NUP214	NUP214	NUP214	7315	0.017	0.48	NO
103	RAE1	RAE1	RAE1	7320	0.016	0.49	NO
104	NUP37	NUP37	NUP37	7365	0.016	0.49	NO
105	POLR2G	POLR2G	POLR2G	7554	0.014	0.48	NO
106	RPLP2	RPLP2	RPLP2	7610	0.013	0.48	NO
107	RPL28	RPL28	RPL28	7615	0.013	0.48	NO
108	POLR2D	POLR2D	POLR2D	7717	0.012	0.47	NO
109	POM121	POM121	POM121	7942	0.0088	0.46	NO
110	UBA52	UBA52	UBA52	8183	0.0056	0.45	NO
111	RANBP2	RANBP2	RANBP2	8229	0.0051	0.45	NO
112	GTF2F1	GTF2F1	GTF2F1	8371	0.0034	0.44	NO
113	NUP62	NUP62	NUP62	8411	0.0028	0.44	NO
114	NUP50	NUP50	NUP50	8461	0.0023	0.44	NO
115	FAU	FAU	FAU	8710	-0.0012	0.42	NO
116	POLR2E	POLR2E	POLR2E	8851	-0.0029	0.42	NO
117	POLR2I	POLR2I	POLR2I	9140	-0.0063	0.4	NO
118	RPS4Y1	RPS4Y1	RPS4Y1	9221	-0.0074	0.4	NO
119	POLR2F	POLR2F	POLR2F	9330	-0.0091	0.39	NO
120	NUP155	NUP155	NUP155	9409	-0.01	0.39	NO
121	NUP205	NUP205	NUP205	9681	-0.014	0.38	NO
122	CLTC	CLTC	CLTC	9811	-0.016	0.37	NO
123	POLR2H	POLR2H	POLR2H	9915	-0.018	0.37	NO
124	DNAJC3	DNAJC3	DNAJC3	10432	-0.025	0.34	NO
125	NUP188	NUP188	NUP188	10436	-0.025	0.34	NO
126	POLR2L	POLR2L	POLR2L	10911	-0.032	0.32	NO
127	RPL26L1	RPL26L1	RPL26L1	11064	-0.035	0.32	NO
128	KPNA1	KPNA1	KPNA1	11123	-0.036	0.32	NO
129	POLR2J	POLR2J	POLR2J	11204	-0.038	0.32	NO
130	NUP93	NUP93	NUP93	11363	-0.041	0.32	NO
131	CALR	CALR	CALR	11725	-0.048	0.3	NO
132	POLR2C	POLR2C	POLR2C	11828	-0.05	0.3	NO
133	POLR2A	POLR2A	POLR2A	12478	-0.063	0.28	NO
134	NUP210	NUP210	NUP210	13232	-0.082	0.25	NO
135	FAM153A	FAM153A	FAM153A	15595	-0.17	0.14	NO

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

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

genes ES table in pathway: PID RETINOIC ACID PATHWAY

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	TAF4B	TAF4B	TAF4B	548	0.22	0.025	YES
2	LSM11	LSM11	LSM11	1072	0.17	0.038	YES
3	TAF11	TAF11	TAF11	1198	0.16	0.07	YES
4	SNRPE	SNRPE	SNRPE	1385	0.15	0.096	YES
5	GTF2H2B	GTF2H2B	GTF2H2B	1625	0.13	0.12	YES
6	GTF2H2	GTF2H2	GTF2H2	2436	0.1	0.095	YES
7	CCNT2	CCNT2	CCNT2	2455	0.1	0.12	YES
8	UPF3B	UPF3B	UPF3B	2602	0.097	0.14	YES
9	GTF2F2	GTF2F2	GTF2F2	2617	0.097	0.16	YES
10	TAF5	TAF5	TAF5	2836	0.09	0.17	YES
11	ZNF473	ZNF473	ZNF473	2872	0.09	0.19	YES
12	TCEA1	TCEA1	TCEA1	3022	0.086	0.2	YES
13	POLR2K	POLR2K	POLR2K	3695	0.07	0.18	YES
14	CCNT1	CCNT1	CCNT1	3986	0.065	0.18	YES
15	TBP	TBP	TBP	3998	0.064	0.2	YES
16	MNAT1	MNAT1	MNAT1	4042	0.064	0.21	YES
17	GTF2H1	GTF2H1	GTF2H1	4232	0.06	0.21	YES
18	CSTF3	CSTF3	CSTF3	4360	0.058	0.22	YES
19	CPSF1	CPSF1	CPSF1	4397	0.057	0.23	YES
20	GTF2B	GTF2B	GTF2B	4490	0.056	0.24	YES
21	ERCC2	ERCC2	ERCC2	4644	0.053	0.25	YES
22	PCF11	PCF11	PCF11	4728	0.052	0.25	YES
23	NFX1	NFX1	NFX1	4859	0.05	0.26	YES
24	RBM8A	RBM8A	RBM8A	4912	0.049	0.27	YES
25	CDK7	CDK7	CDK7	5105	0.046	0.27	YES
26	RNMT	RNMT	RNMT	5197	0.045	0.28	YES
27	PAPOLA	PAPOLA	PAPOLA	5248	0.044	0.28	YES
28	TAF9	TAF9	TAF9	5333	0.043	0.29	YES
29	SNRPF	SNRPF	SNRPF	5362	0.043	0.3	YES
30	PABPN1	PABPN1	PABPN1	5387	0.042	0.31	YES
31	NUDT21	NUDT21	NUDT21	5407	0.042	0.32	YES
32	SUPT16H	SUPT16H	SUPT16H	5659	0.039	0.31	YES
33	SNRPD3	SNRPD3	SNRPD3	5680	0.038	0.32	YES
34	MAGOH	MAGOH	MAGOH	5697	0.038	0.33	YES
35	GTF2H4	GTF2H4	GTF2H4	5810	0.037	0.33	YES
36	NCBP1	NCBP1	NCBP1	5811	0.037	0.34	YES
37	TAF1	TAF1	TAF1	5833	0.037	0.35	YES
38	GTF2A1	GTF2A1	GTF2A1	5921	0.035	0.35	YES
39	TAF4	TAF4	TAF4	5964	0.035	0.36	YES
40	SUPT4H1	SUPT4H1	SUPT4H1	6088	0.033	0.36	YES
41	TCEB1	TCEB1	TCEB1	6151	0.032	0.36	YES
42	SNRPB	SNRPB	SNRPB	6218	0.031	0.37	YES
43	TH1L	TH1L	TH1L	6224	0.031	0.38	YES
44	SLBP	SLBP	SLBP	6289	0.03	0.38	YES
45	GTF2H3	GTF2H3	GTF2H3	6374	0.029	0.38	YES
46	SSRP1	SSRP1	SSRP1	6458	0.028	0.38	YES
47	CCNH	CCNH	CCNH	6492	0.028	0.39	YES
48	CSTF1	CSTF1	CSTF1	6511	0.027	0.4	YES
49	RNGTT	RNGTT	RNGTT	6917	0.022	0.38	NO
50	WHSC2	WHSC2	WHSC2	6947	0.022	0.38	NO
51	POLR2B	POLR2B	POLR2B	6982	0.021	0.38	NO
52	RNPS1	RNPS1	RNPS1	7328	0.016	0.37	NO
53	U2AF1	U2AF1	U2AF1	7354	0.016	0.37	NO
54	TCEB2	TCEB2	TCEB2	7362	0.016	0.38	NO
55	POLR2G	POLR2G	POLR2G	7554	0.014	0.37	NO
56	RDBP	RDBP	RDBP	7667	0.012	0.37	NO
57	POLR2D	POLR2D	POLR2D	7717	0.012	0.37	NO
58	CDC40	CDC40	CDC40	7784	0.011	0.36	NO
59	CPSF3	CPSF3	CPSF3	7830	0.01	0.36	NO
60	CPSF7	CPSF7	CPSF7	7905	0.0092	0.36	NO
61	CLP1	CLP1	CLP1	8068	0.007	0.36	NO
62	NCBP2	NCBP2	NCBP2	8179	0.0056	0.35	NO
63	U2AF2	U2AF2	U2AF2	8289	0.0044	0.35	NO
64	ERCC3	ERCC3	ERCC3	8344	0.0038	0.34	NO
65	GTF2F1	GTF2F1	GTF2F1	8371	0.0034	0.34	NO
66	SNRPG	SNRPG	SNRPG	8560	0.001	0.33	NO
67	CPSF2	CPSF2	CPSF2	8739	-0.0015	0.32	NO
68	SUPT5H	SUPT5H	SUPT5H	8819	-0.0024	0.32	NO
69	POLR2E	POLR2E	POLR2E	8851	-0.0029	0.32	NO
70	SRRM1	SRRM1	SRRM1	8870	-0.003	0.32	NO
71	POLR2I	POLR2I	POLR2I	9140	-0.0063	0.3	NO
72	GTF2E1	GTF2E1	GTF2E1	9228	-0.0076	0.3	NO
73	POLR2F	POLR2F	POLR2F	9330	-0.0091	0.3	NO
74	THOC4	THOC4	THOC4	9367	-0.0097	0.3	NO
75	TCEB3	TCEB3	TCEB3	9396	-0.01	0.3	NO
76	DHX38	DHX38	DHX38	9443	-0.011	0.3	NO
77	CSTF2	CSTF2	CSTF2	9466	-0.011	0.3	NO
78	COBRA1	COBRA1	COBRA1	9803	-0.016	0.29	NO
79	GTF2A2	GTF2A2	GTF2A2	9857	-0.017	0.29	NO
80	POLR2H	POLR2H	POLR2H	9915	-0.018	0.29	NO
81	CDK9	CDK9	CDK9	10723	-0.03	0.25	NO
82	POLR2L	POLR2L	POLR2L	10911	-0.032	0.25	NO
83	TAF12	TAF12	TAF12	10912	-0.032	0.26	NO
84	POLR2J	POLR2J	POLR2J	11204	-0.038	0.25	NO
85	CTDP1	CTDP1	CTDP1	11289	-0.039	0.26	NO
86	TAF13	TAF13	TAF13	11645	-0.046	0.25	NO
87	POLR2C	POLR2C	POLR2C	11828	-0.05	0.25	NO
88	GTF2E2	GTF2E2	GTF2E2	11847	-0.05	0.26	NO
89	TAF6	TAF6	TAF6	12000	-0.053	0.26	NO
90	POLR2A	POLR2A	POLR2A	12478	-0.063	0.25	NO
91	LSM10	LSM10	LSM10	12758	-0.069	0.26	NO
92	ELL	ELL	ELL	12837	-0.071	0.27	NO
93	TAF10	TAF10	TAF10	13417	-0.087	0.26	NO

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

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

genes ES table in pathway: PID BARD1PATHWAY

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	SNRPE	SNRPE	SNRPE	1385	0.15	-0.0064	YES
2	SMN1	SMN1	SMN1	2083	0.11	0.0093	YES
3	TGS1	TGS1	TGS1	2088	0.11	0.064	YES
4	NUP133	NUP133	NUP133	2383	0.1	0.097	YES
5	SNRPD1	SNRPD1	SNRPD1	2442	0.1	0.14	YES
6	NUP153	NUP153	NUP153	3074	0.085	0.15	YES
7	CLNS1A	CLNS1A	CLNS1A	3381	0.078	0.17	YES
8	GEMIN5	GEMIN5	GEMIN5	3663	0.071	0.19	YES
9	TPR	TPR	TPR	3674	0.071	0.22	YES
10	SMN2	SMN2	SMN2	3746	0.069	0.25	YES
11	NUP43	NUP43	NUP43	4261	0.06	0.25	YES
12	NUP35	NUP35	NUP35	4302	0.059	0.28	YES
13	SEH1L	SEH1L	SEH1L	4336	0.058	0.3	YES
14	NUPL1	NUPL1	NUPL1	4485	0.056	0.32	YES
15	NUP107	NUP107	NUP107	4673	0.053	0.34	YES
16	NUP54	NUP54	NUP54	4772	0.051	0.35	YES
17	GEMIN7	GEMIN7	GEMIN7	4827	0.05	0.38	YES
18	PHAX	PHAX	PHAX	5324	0.043	0.37	YES
19	SNRPF	SNRPF	SNRPF	5362	0.043	0.39	YES
20	DDX20	DDX20	DDX20	5560	0.04	0.4	YES
21	SNRPD3	SNRPD3	SNRPD3	5680	0.038	0.41	YES
22	PRMT5	PRMT5	PRMT5	5746	0.038	0.42	YES
23	NCBP1	NCBP1	NCBP1	5811	0.037	0.44	YES
24	GEMIN4	GEMIN4	GEMIN4	5895	0.036	0.45	YES
25	NUPL2	NUPL2	NUPL2	6137	0.032	0.45	YES
26	NUP88	NUP88	NUP88	6196	0.032	0.46	YES
27	SNRPB	SNRPB	SNRPB	6218	0.031	0.48	YES
28	AAAS	AAAS	AAAS	6275	0.03	0.49	YES
29	SNRPD2	SNRPD2	SNRPD2	6381	0.029	0.5	YES
30	SNUPN	SNUPN	SNUPN	6401	0.029	0.51	YES
31	NUP85	NUP85	NUP85	6959	0.021	0.49	NO
32	NUP214	NUP214	NUP214	7315	0.017	0.48	NO
33	RAE1	RAE1	RAE1	7320	0.016	0.48	NO
34	NUP37	NUP37	NUP37	7365	0.016	0.49	NO
35	POM121	POM121	POM121	7942	0.0088	0.46	NO
36	NCBP2	NCBP2	NCBP2	8179	0.0056	0.45	NO
37	RANBP2	RANBP2	RANBP2	8229	0.0051	0.45	NO
38	NUP62	NUP62	NUP62	8411	0.0028	0.44	NO
39	NUP50	NUP50	NUP50	8461	0.0023	0.44	NO
40	SNRPG	SNRPG	SNRPG	8560	0.001	0.44	NO
41	WDR77	WDR77	WDR77	9102	-0.0058	0.41	NO
42	NUP155	NUP155	NUP155	9409	-0.01	0.4	NO
43	GEMIN6	GEMIN6	GEMIN6	9444	-0.011	0.4	NO
44	NUP205	NUP205	NUP205	9681	-0.014	0.39	NO
45	NUP188	NUP188	NUP188	10436	-0.025	0.36	NO
46	NUP93	NUP93	NUP93	11363	-0.041	0.33	NO
47	NUP210	NUP210	NUP210	13232	-0.082	0.27	NO

Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID BARD1PATHWAY.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: PID BARD1PATHWAY, 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 P53REGULATIONPATHWAY

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	POLR1C	POLR1C	POLR1C	1851	0.12	-0.0085	YES
2	POLR3B	POLR3B	POLR3B	1924	0.12	0.079	YES
3	POLR1D	POLR1D	POLR1D	2447	0.1	0.13	YES
4	NFIB	NFIB	NFIB	3346	0.078	0.14	YES
5	POLR3F	POLR3F	POLR3F	3435	0.076	0.19	YES
6	GTF3C4	GTF3C4	GTF3C4	3441	0.076	0.25	YES
7	SSB	SSB	SSB	3629	0.072	0.29	YES
8	POLR2K	POLR2K	POLR2K	3695	0.07	0.34	YES
9	TBP	TBP	TBP	3998	0.064	0.38	YES
10	GTF3C3	GTF3C3	GTF3C3	4713	0.052	0.38	YES
11	SNAPC1	SNAPC1	SNAPC1	4850	0.05	0.41	YES
12	POLR3C	POLR3C	POLR3C	5184	0.045	0.42	YES
13	POLR3E	POLR3E	POLR3E	5320	0.043	0.45	YES
14	SNAPC4	SNAPC4	SNAPC4	5900	0.036	0.44	YES
15	ZNF143	ZNF143	ZNF143	6404	0.029	0.44	YES
16	SNAPC3	SNAPC3	SNAPC3	6536	0.027	0.45	YES
17	BRF1	BRF1	BRF1	6738	0.024	0.46	YES
18	GTF3C5	GTF3C5	GTF3C5	7060	0.02	0.46	NO
19	SNAPC5	SNAPC5	SNAPC5	7452	0.015	0.45	NO
20	GTF3C2	GTF3C2	GTF3C2	7790	0.011	0.44	NO
21	POLR3K	POLR3K	POLR3K	7797	0.01	0.44	NO
22	POLR3D	POLR3D	POLR3D	8015	0.0078	0.44	NO
23	LZTS1	LZTS1	LZTS1	8025	0.0077	0.44	NO
24	BRF2	BRF2	BRF2	8367	0.0035	0.43	NO
25	POLR3A	POLR3A	POLR3A	8709	-0.0012	0.41	NO
26	POU2F1	POU2F1	POU2F1	8735	-0.0014	0.41	NO
27	POLR3H	POLR3H	POLR3H	8754	-0.0018	0.41	NO
28	POLR2E	POLR2E	POLR2E	8851	-0.0029	0.41	NO
29	POLR2F	POLR2F	POLR2F	9330	-0.0091	0.39	NO
30	POLR2H	POLR2H	POLR2H	9915	-0.018	0.37	NO
31	POLR3GL	POLR3GL	POLR3GL	9941	-0.018	0.38	NO
32	POLR2L	POLR2L	POLR2L	10911	-0.032	0.35	NO
33	SNAPC2	SNAPC2	SNAPC2	12281	-0.059	0.32	NO

Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID P53REGULATIONPATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: PID P53REGULATIONPATHWAY, 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 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	SNRPE	SNRPE	SNRPE	1385	0.15	-0.043	YES
2	HNRNPA1	HNRNPA1	HNRNPA1	1942	0.12	-0.046	YES
3	NUP133	NUP133	NUP133	2383	0.1	-0.046	YES
4	SNRPD1	SNRPD1	SNRPD1	2442	0.1	-0.025	YES
5	UPF3B	UPF3B	UPF3B	2602	0.097	-0.011	YES
6	GTF2F2	GTF2F2	GTF2F2	2617	0.097	0.011	YES
7	RBMX	RBMX	RBMX	3050	0.085	0.0068	YES
8	NUP153	NUP153	NUP153	3074	0.085	0.026	YES
9	RBM5	RBM5	RBM5	3117	0.084	0.043	YES
10	TPR	TPR	TPR	3674	0.071	0.029	YES
11	HNRNPH1	HNRNPH1	HNRNPH1	3678	0.071	0.045	YES
12	POLR2K	POLR2K	POLR2K	3695	0.07	0.061	YES
13	HNRNPA3	HNRNPA3	HNRNPA3	4031	0.064	0.057	YES
14	NUP43	NUP43	NUP43	4261	0.06	0.058	YES
15	NUP35	NUP35	NUP35	4302	0.059	0.07	YES
16	METTL3	METTL3	METTL3	4307	0.059	0.084	YES
17	SEH1L	SEH1L	SEH1L	4336	0.058	0.096	YES
18	CSTF3	CSTF3	CSTF3	4360	0.058	0.11	YES
19	CPSF1	CPSF1	CPSF1	4397	0.057	0.12	YES
20	HNRNPA0	HNRNPA0	HNRNPA0	4409	0.057	0.13	YES
21	SNRNP70	SNRNP70	SNRNP70	4438	0.056	0.14	YES
22	NUPL1	NUPL1	NUPL1	4485	0.056	0.16	YES
23	DHX9	DHX9	DHX9	4582	0.054	0.16	YES
24	NUP107	NUP107	NUP107	4673	0.053	0.17	YES
25	LSM2	LSM2	LSM2	4703	0.052	0.18	YES
26	PCF11	PCF11	PCF11	4728	0.052	0.19	YES
27	NUP54	NUP54	NUP54	4772	0.051	0.2	YES
28	NFX1	NFX1	NFX1	4859	0.05	0.21	YES
29	RBM8A	RBM8A	RBM8A	4912	0.049	0.22	YES
30	SMC1A	SMC1A	SMC1A	5007	0.048	0.22	YES
31	HNRNPC	HNRNPC	HNRNPC	5125	0.046	0.23	YES
32	PAPOLA	PAPOLA	PAPOLA	5248	0.044	0.23	YES
33	SNRPF	SNRPF	SNRPF	5362	0.043	0.24	YES
34	PABPN1	PABPN1	PABPN1	5387	0.042	0.24	YES
35	HNRNPM	HNRNPM	HNRNPM	5392	0.042	0.25	YES
36	CCAR1	CCAR1	CCAR1	5394	0.042	0.26	YES
37	PCBP2	PCBP2	PCBP2	5401	0.042	0.27	YES
38	NUDT21	NUDT21	NUDT21	5407	0.042	0.28	YES
39	HNRNPU	HNRNPU	HNRNPU	5423	0.042	0.29	YES
40	HNRNPD	HNRNPD	HNRNPD	5462	0.041	0.3	YES
41	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	5503	0.041	0.31	YES
42	SNRPD3	SNRPD3	SNRPD3	5680	0.038	0.31	YES
43	MAGOH	MAGOH	MAGOH	5697	0.038	0.31	YES
44	SF3B1	SF3B1	SF3B1	5735	0.038	0.32	YES
45	NCBP1	NCBP1	NCBP1	5811	0.037	0.33	YES
46	HNRNPR	HNRNPR	HNRNPR	5834	0.037	0.33	YES
47	HNRNPK	HNRNPK	HNRNPK	5861	0.036	0.34	YES
48	EIF4E	EIF4E	EIF4E	5918	0.035	0.34	YES
49	FUS	FUS	FUS	5948	0.035	0.35	YES
50	SNRPB2	SNRPB2	SNRPB2	6105	0.033	0.35	YES
51	NUPL2	NUPL2	NUPL2	6137	0.032	0.36	YES
52	NUP88	NUP88	NUP88	6196	0.032	0.36	YES
53	SNRPB	SNRPB	SNRPB	6218	0.031	0.37	YES
54	SF3B14	SF3B14	SF3B14	6241	0.031	0.37	YES
55	AAAS	AAAS	AAAS	6275	0.03	0.38	YES
56	SLBP	SLBP	SLBP	6289	0.03	0.38	YES
57	SNRPD2	SNRPD2	SNRPD2	6381	0.029	0.39	YES
58	NXF1	NXF1	NXF1	6481	0.028	0.39	YES
59	SF3A3	SF3A3	SF3A3	6493	0.028	0.39	YES
60	CSTF1	CSTF1	CSTF1	6511	0.027	0.4	YES
61	SF3B3	SF3B3	SF3B3	6580	0.026	0.4	YES
62	YBX1	YBX1	YBX1	6612	0.026	0.41	YES
63	SNRPA1	SNRPA1	SNRPA1	6633	0.026	0.41	YES
64	NUP85	NUP85	NUP85	6959	0.021	0.4	YES
65	HNRNPH2	HNRNPH2	HNRNPH2	6979	0.021	0.4	YES
66	POLR2B	POLR2B	POLR2B	6982	0.021	0.41	YES
67	HNRNPF	HNRNPF	HNRNPF	7043	0.02	0.41	YES
68	HNRNPUL1	HNRNPUL1	HNRNPUL1	7214	0.018	0.4	YES
69	NUP214	NUP214	NUP214	7315	0.017	0.4	YES
70	RAE1	RAE1	RAE1	7320	0.016	0.4	YES
71	RNPS1	RNPS1	RNPS1	7328	0.016	0.41	YES
72	U2AF1	U2AF1	U2AF1	7354	0.016	0.41	YES
73	NUP37	NUP37	NUP37	7365	0.016	0.41	YES
74	HNRNPL	HNRNPL	HNRNPL	7390	0.016	0.42	YES
75	SNRPA	SNRPA	SNRPA	7491	0.014	0.41	YES
76	SNRNP200	SNRNP200	SNRNP200	7534	0.014	0.42	YES
77	POLR2G	POLR2G	POLR2G	7554	0.014	0.42	YES
78	PRPF4	PRPF4	PRPF4	7620	0.013	0.42	YES
79	PTBP1	PTBP1	PTBP1	7662	0.012	0.42	YES
80	PRPF6	PRPF6	PRPF6	7685	0.012	0.42	YES
81	POLR2D	POLR2D	POLR2D	7717	0.012	0.42	YES
82	CDC40	CDC40	CDC40	7784	0.011	0.42	YES
83	SF3A2	SF3A2	SF3A2	7798	0.01	0.42	YES
84	NHP2L1	NHP2L1	NHP2L1	7813	0.01	0.42	YES
85	CPSF3	CPSF3	CPSF3	7830	0.01	0.42	YES
86	CPSF7	CPSF7	CPSF7	7905	0.0092	0.42	NO
87	POM121	POM121	POM121	7942	0.0088	0.42	NO
88	CLP1	CLP1	CLP1	8068	0.007	0.42	NO
89	DNAJC8	DNAJC8	DNAJC8	8124	0.0065	0.42	NO
90	NCBP2	NCBP2	NCBP2	8179	0.0056	0.41	NO
91	RANBP2	RANBP2	RANBP2	8229	0.0051	0.41	NO
92	U2AF2	U2AF2	U2AF2	8289	0.0044	0.41	NO
93	PRPF8	PRPF8	PRPF8	8292	0.0044	0.41	NO
94	DDX23	DDX23	DDX23	8310	0.0042	0.41	NO
95	GTF2F1	GTF2F1	GTF2F1	8371	0.0034	0.41	NO
96	EFTUD2	EFTUD2	EFTUD2	8402	0.003	0.41	NO
97	NUP62	NUP62	NUP62	8411	0.0028	0.41	NO
98	NUP50	NUP50	NUP50	8461	0.0023	0.4	NO
99	SNRPG	SNRPG	SNRPG	8560	0.001	0.4	NO
100	CPSF2	CPSF2	CPSF2	8739	-0.0015	0.39	NO
101	TXNL4A	TXNL4A	TXNL4A	8755	-0.0018	0.39	NO
102	POLR2E	POLR2E	POLR2E	8851	-0.0029	0.38	NO
103	SRRM1	SRRM1	SRRM1	8870	-0.003	0.38	NO
104	SF3B4	SF3B4	SF3B4	8872	-0.003	0.38	NO
105	SNRNP40	SNRNP40	SNRNP40	8967	-0.0041	0.38	NO
106	POLR2I	POLR2I	POLR2I	9140	-0.0063	0.37	NO
107	POLR2F	POLR2F	POLR2F	9330	-0.0091	0.36	NO
108	THOC4	THOC4	THOC4	9367	-0.0097	0.36	NO
109	NUP155	NUP155	NUP155	9409	-0.01	0.36	NO
110	DHX38	DHX38	DHX38	9443	-0.011	0.37	NO
111	CSTF2	CSTF2	CSTF2	9466	-0.011	0.37	NO
112	SF3A1	SF3A1	SF3A1	9630	-0.013	0.36	NO
113	NUP205	NUP205	NUP205	9681	-0.014	0.36	NO
114	SF3B2	SF3B2	SF3B2	9729	-0.015	0.36	NO
115	SF3B5	SF3B5	SF3B5	9742	-0.015	0.36	NO
116	PHF5A	PHF5A	PHF5A	9914	-0.018	0.36	NO
117	POLR2H	POLR2H	POLR2H	9915	-0.018	0.36	NO
118	PCBP1	PCBP1	PCBP1	10196	-0.022	0.35	NO
119	CD2BP2	CD2BP2	CD2BP2	10411	-0.025	0.35	NO
120	NUP188	NUP188	NUP188	10436	-0.025	0.35	NO
121	POLR2L	POLR2L	POLR2L	10911	-0.032	0.33	NO
122	POLR2J	POLR2J	POLR2J	11204	-0.038	0.33	NO
123	NUP93	NUP93	NUP93	11363	-0.041	0.33	NO
124	POLR2C	POLR2C	POLR2C	11828	-0.05	0.31	NO
125	POLR2A	POLR2A	POLR2A	12478	-0.063	0.29	NO
126	NUP210	NUP210	NUP210	13232	-0.082	0.27	NO

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

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

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

Table 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	LSM11	LSM11	LSM11	1072	0.17	0.068	YES
2	SNRPE	SNRPE	SNRPE	1385	0.15	0.16	YES
3	UPF3B	UPF3B	UPF3B	2602	0.097	0.17	YES
4	ZNF473	ZNF473	ZNF473	2872	0.09	0.22	YES
5	CSTF3	CSTF3	CSTF3	4360	0.058	0.18	YES
6	CPSF1	CPSF1	CPSF1	4397	0.057	0.22	YES
7	PCF11	PCF11	PCF11	4728	0.052	0.24	YES
8	NFX1	NFX1	NFX1	4859	0.05	0.27	YES
9	RBM8A	RBM8A	RBM8A	4912	0.049	0.31	YES
10	PAPOLA	PAPOLA	PAPOLA	5248	0.044	0.32	YES
11	SNRPF	SNRPF	SNRPF	5362	0.043	0.35	YES
12	PABPN1	PABPN1	PABPN1	5387	0.042	0.38	YES
13	NUDT21	NUDT21	NUDT21	5407	0.042	0.41	YES
14	SNRPD3	SNRPD3	SNRPD3	5680	0.038	0.42	YES
15	MAGOH	MAGOH	MAGOH	5697	0.038	0.45	YES
16	NCBP1	NCBP1	NCBP1	5811	0.037	0.47	YES
17	SNRPB	SNRPB	SNRPB	6218	0.031	0.47	YES
18	SLBP	SLBP	SLBP	6289	0.03	0.49	YES
19	CSTF1	CSTF1	CSTF1	6511	0.027	0.5	YES
20	RNPS1	RNPS1	RNPS1	7328	0.016	0.47	NO
21	U2AF1	U2AF1	U2AF1	7354	0.016	0.48	NO
22	CDC40	CDC40	CDC40	7784	0.011	0.46	NO
23	CPSF3	CPSF3	CPSF3	7830	0.01	0.47	NO
24	CPSF7	CPSF7	CPSF7	7905	0.0092	0.47	NO
25	CLP1	CLP1	CLP1	8068	0.007	0.47	NO
26	NCBP2	NCBP2	NCBP2	8179	0.0056	0.46	NO
27	U2AF2	U2AF2	U2AF2	8289	0.0044	0.46	NO
28	SNRPG	SNRPG	SNRPG	8560	0.001	0.45	NO
29	CPSF2	CPSF2	CPSF2	8739	-0.0015	0.44	NO
30	SRRM1	SRRM1	SRRM1	8870	-0.003	0.43	NO
31	THOC4	THOC4	THOC4	9367	-0.0097	0.41	NO
32	DHX38	DHX38	DHX38	9443	-0.011	0.42	NO
33	CSTF2	CSTF2	CSTF2	9466	-0.011	0.42	NO
34	LSM10	LSM10	LSM10	12758	-0.069	0.29	NO

Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

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

GSEA analysis

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

Download Results

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

References

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

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