GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LUAD-TP
Lung Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C18K7845
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LUAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C18K7845
Overview
Introduction

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

  1. 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.

  2. Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).

  3. Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).

  4. Checks if the top core genes are up-regulated or down-regulated.

  5. Checks if the top core genes are high expressed or low expressed.

  6. 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: 192
Number of samples: 515
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 167
pheno.type: 2 - 3 :[ clus2 ] 197
pheno.type: 3 - 3 :[ clus3 ] 151

For the expression subtypes of 18319 genes in 516 samples, GSEA found enriched gene sets in each cluster using 515 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA RHO PATHWAY, BIOCARTA CREB PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CARDIAC MUSCLE CONTRACTION, KEGG CELL ADHESION MOLECULES CAMS

    • And common core enriched genes are PRKCA, PRKCB, BTK, VAV1, PIK3R1, ADCY9, AQP2, AQP3, AQP4, ARHGDIB

  • clus2

    • Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA IL1R PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG PYRIMIDINE METABOLISM, KEGG BASAL TRANSCRIPTION FACTORS, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG PROTEASOME

    • And common core enriched genes are CCNE1, CDK2, CDK4, CDK6, CDC25A, CDK1, CDKN2A, MCM2, MCM4, MCM5

  • clus3

    • Top enriched gene sets are BIOCARTA WNT PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG OXIDATIVE PHOSPHORYLATION, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG GLUTATHIONE METABOLISM

    • And common core enriched genes are DLAT, DLD, MDH2, PC, PCK1, PDHA1, PDHB, SUCLA2, SUCLG1, SUCLG2

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.51 1.6 0.023 0.52 0.8 0.17 0.1 0.15 0.32 0.15
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.54 1.7 0.018 0.99 0.6 0.46 0.3 0.32 0.47 0.31
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.49 1.6 0.053 0.59 0.69 0.35 0.28 0.26 0.32 0.18
BIOCARTA KERATINOCYTE PATHWAY 45 genes.ES.table 0.45 1.5 0.042 0.43 0.83 0.49 0.33 0.33 0.27 0.11
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.38 1.5 0.065 0.46 0.83 0.22 0.26 0.16 0.29 0.13
BIOCARTA RHO PATHWAY 31 genes.ES.table 0.4 1.5 0.08 0.4 0.87 0.26 0.29 0.18 0.26 0.092
BIOCARTA CREB PATHWAY 25 genes.ES.table 0.5 1.6 0.022 0.8 0.62 0.32 0.26 0.24 0.39 0.25
KEGG ERBB SIGNALING PATHWAY 86 genes.ES.table 0.42 1.6 0.014 0.66 0.68 0.28 0.26 0.21 0.35 0.2
KEGG CARDIAC MUSCLE CONTRACTION 64 genes.ES.table 0.56 1.7 0.0061 1 0.52 0.25 0.095 0.23 0.5 0.34
KEGG CELL ADHESION MOLECULES CAMS 128 genes.ES.table 0.6 1.6 0.026 0.48 0.8 0.6 0.26 0.45 0.3 0.14
genes ES table in pathway: BIOCARTA AGR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AQP4 AQP4 AQP4 221 0.52 0.13 YES
2 AQP2 AQP2 AQP2 719 0.37 0.21 YES
3 DYNC2H1 DYNC2H1 DYNC2H1 820 0.35 0.31 YES
4 AQP3 AQP3 AQP3 1556 0.26 0.34 YES
5 AVPR2 AVPR2 AVPR2 1832 0.24 0.39 YES
6 ADCY9 ADCY9 ADCY9 2178 0.21 0.43 YES
7 ARHGDIB ARHGDIB ARHGDIB 3404 0.15 0.4 YES
8 CREB3L1 CREB3L1 CREB3L1 3621 0.14 0.43 YES
9 CREB5 CREB5 CREB5 3724 0.13 0.46 YES
10 VAMP2 VAMP2 VAMP2 4233 0.12 0.47 YES
11 DYNC2LI1 DYNC2LI1 DYNC2LI1 4967 0.092 0.46 NO
12 ADCY6 ADCY6 ADCY6 6185 0.062 0.41 NO
13 RAB11B RAB11B RAB11B 7023 0.046 0.37 NO
14 DCTN4 DCTN4 DCTN4 7245 0.043 0.37 NO
15 CREB3L3 CREB3L3 CREB3L3 7676 0.036 0.36 NO
16 DYNLL2 DYNLL2 DYNLL2 7975 0.032 0.35 NO
17 DYNC1LI2 DYNC1LI2 DYNC1LI2 8016 0.031 0.36 NO
18 PRKACA PRKACA PRKACA 8314 0.026 0.35 NO
19 PRKACB PRKACB PRKACB 8637 0.022 0.34 NO
20 PRKX PRKX PRKX 8766 0.02 0.34 NO
21 CREB1 CREB1 CREB1 8842 0.019 0.34 NO
22 STX4 STX4 STX4 9003 0.017 0.33 NO
23 RAB5B RAB5B RAB5B 9681 0.0075 0.3 NO
24 RAB5A RAB5A RAB5A 10434 -0.0024 0.26 NO
25 CREB3 CREB3 CREB3 10485 -0.003 0.26 NO
26 DCTN6 DCTN6 DCTN6 10535 -0.0036 0.26 NO
27 DCTN1 DCTN1 DCTN1 10711 -0.006 0.25 NO
28 DYNC1LI1 DYNC1LI1 DYNC1LI1 10878 -0.008 0.24 NO
29 RAB5C RAB5C RAB5C 11101 -0.011 0.23 NO
30 DCTN5 DCTN5 DCTN5 11185 -0.012 0.23 NO
31 RAB11A RAB11A RAB11A 11275 -0.013 0.23 NO
32 ARHGDIA ARHGDIA ARHGDIA 11782 -0.019 0.21 NO
33 DYNC1H1 DYNC1H1 DYNC1H1 11922 -0.021 0.2 NO
34 GNAS GNAS GNAS 12324 -0.026 0.19 NO
35 DYNC1I2 DYNC1I2 DYNC1I2 12574 -0.029 0.18 NO
36 CREB3L2 CREB3L2 CREB3L2 12597 -0.03 0.19 NO
37 NSF NSF NSF 12831 -0.033 0.19 NO
38 CREB3L4 CREB3L4 CREB3L4 13995 -0.051 0.14 NO
39 DCTN2 DCTN2 DCTN2 14181 -0.054 0.14 NO
40 DYNLL1 DYNLL1 DYNLL1 15238 -0.077 0.11 NO
41 DYNC1I1 DYNC1I1 DYNC1I1 17458 -0.21 0.046 NO

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

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

genes ES table in pathway: BIOCARTA BCR 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 ATP1A2 ATP1A2 ATP1A2 28 0.66 0.073 YES
2 CACNA2D2 CACNA2D2 CACNA2D2 237 0.51 0.12 YES
3 TNNC1 TNNC1 TNNC1 412 0.45 0.16 YES
4 CACNG6 CACNG6 CACNG6 437 0.44 0.21 YES
5 CACNB4 CACNB4 CACNB4 599 0.4 0.24 YES
6 ATP1B2 ATP1B2 ATP1B2 648 0.39 0.28 YES
7 MYL3 MYL3 MYL3 735 0.37 0.32 YES
8 RYR2 RYR2 RYR2 772 0.36 0.36 YES
9 ATP1A4 ATP1A4 ATP1A4 811 0.36 0.4 YES
10 CACNB1 CACNB1 CACNB1 852 0.35 0.43 YES
11 CACNA2D3 CACNA2D3 CACNA2D3 1038 0.32 0.46 YES
12 COX4I2 COX4I2 COX4I2 1458 0.27 0.47 YES
13 CACNA1D CACNA1D CACNA1D 1528 0.26 0.49 YES
14 TNNT2 TNNT2 TNNT2 1718 0.24 0.51 YES
15 CACNA1C CACNA1C CACNA1C 1722 0.24 0.54 YES
16 CACNA1F CACNA1F CACNA1F 1732 0.24 0.56 YES
17 COX7A1 COX7A1 COX7A1 3042 0.16 0.51 NO
18 CACNA2D4 CACNA2D4 CACNA2D4 3845 0.13 0.48 NO
19 ACTC1 ACTC1 ACTC1 3848 0.13 0.5 NO
20 CACNG4 CACNG4 CACNG4 3882 0.13 0.51 NO
21 SLC9A1 SLC9A1 SLC9A1 4612 0.1 0.48 NO
22 SLC8A1 SLC8A1 SLC8A1 5402 0.08 0.44 NO
23 ATP1A1 ATP1A1 ATP1A1 5505 0.078 0.45 NO
24 CACNA1S CACNA1S CACNA1S 5669 0.074 0.45 NO
25 ATP1A3 ATP1A3 ATP1A3 6996 0.046 0.38 NO
26 SLC9A6 SLC9A6 SLC9A6 7295 0.042 0.37 NO
27 MYL2 MYL2 MYL2 7441 0.04 0.36 NO
28 FXYD2 FXYD2 FXYD2 7793 0.034 0.35 NO
29 UQCR10 UQCR10 UQCR10 7880 0.033 0.35 NO
30 CACNB3 CACNB3 CACNB3 8084 0.03 0.34 NO
31 CACNG1 CACNG1 CACNG1 8548 0.023 0.32 NO
32 COX7C COX7C COX7C 9066 0.016 0.29 NO
33 UQCR11 UQCR11 UQCR11 9351 0.012 0.28 NO
34 TPM1 TPM1 TPM1 9393 0.011 0.28 NO
35 MYH7 MYH7 MYH7 9452 0.011 0.27 NO
36 ATP1B1 ATP1B1 ATP1B1 10113 0.0018 0.24 NO
37 TPM4 TPM4 TPM4 11091 -0.011 0.18 NO
38 COX4I1 COX4I1 COX4I1 11292 -0.013 0.18 NO
39 UQCRQ UQCRQ UQCRQ 11804 -0.019 0.15 NO
40 CACNB2 CACNB2 CACNB2 12231 -0.025 0.13 NO
41 UQCRB UQCRB UQCRB 12562 -0.029 0.11 NO
42 COX7B COX7B COX7B 13173 -0.038 0.085 NO
43 CACNA2D1 CACNA2D1 CACNA2D1 13279 -0.04 0.084 NO
44 ATP1B3 ATP1B3 ATP1B3 13591 -0.044 0.072 NO
45 COX7A2L COX7A2L COX7A2L 13823 -0.048 0.065 NO
46 COX8A COX8A COX8A 13925 -0.05 0.065 NO
47 UQCRC1 UQCRC1 UQCRC1 14015 -0.051 0.066 NO
48 TPM3 TPM3 TPM3 14276 -0.056 0.058 NO
49 COX8C COX8C COX8C 14279 -0.056 0.064 NO
50 COX5A COX5A COX5A 14352 -0.058 0.066 NO
51 UQCRFS1 UQCRFS1 UQCRFS1 14450 -0.06 0.068 NO
52 COX6B1 COX6B1 COX6B1 14680 -0.064 0.062 NO
53 COX6C COX6C COX6C 14689 -0.064 0.069 NO
54 COX7A2 COX7A2 COX7A2 15089 -0.073 0.056 NO
55 UQCRH UQCRH UQCRH 15143 -0.075 0.061 NO
56 COX5B COX5B COX5B 15245 -0.077 0.064 NO
57 ATP2A2 ATP2A2 ATP2A2 15360 -0.08 0.067 NO
58 TPM2 TPM2 TPM2 15607 -0.086 0.063 NO
59 COX6A1 COX6A1 COX6A1 16055 -0.1 0.05 NO
60 UQCRHL UQCRHL UQCRHL 16230 -0.11 0.053 NO
61 COX6B2 COX6B2 COX6B2 16317 -0.12 0.061 NO
62 CYC1 CYC1 CYC1 16504 -0.12 0.065 NO
63 TNNI3 TNNI3 TNNI3 16608 -0.13 0.074 NO
64 MYH6 MYH6 MYH6 17126 -0.17 0.064 NO

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

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BTK BTK BTK 1266 0.29 0.025 YES
2 PRKCB PRKCB PRKCB 1537 0.26 0.095 YES
3 CD79B CD79B CD79B 1539 0.26 0.18 YES
4 NFATC2 NFATC2 NFATC2 1648 0.25 0.26 YES
5 BLNK BLNK BLNK 1942 0.23 0.31 YES
6 FOS FOS FOS 2497 0.19 0.34 YES
7 NFATC1 NFATC1 NFATC1 2734 0.18 0.39 YES
8 VAV1 VAV1 VAV1 2977 0.17 0.43 YES
9 CD79A CD79A CD79A 3364 0.15 0.46 YES
10 PRKCA PRKCA PRKCA 3732 0.13 0.48 YES
11 NFATC3 NFATC3 NFATC3 4475 0.11 0.48 YES
12 MAP3K1 MAP3K1 MAP3K1 4509 0.11 0.51 YES
13 JUN JUN JUN 4718 0.1 0.53 YES
14 SYK SYK SYK 5058 0.089 0.54 YES
15 PPP3CC PPP3CC PPP3CC 5485 0.078 0.54 YES
16 PPP3CA PPP3CA PPP3CA 6698 0.052 0.49 NO
17 CALM1 CALM1 CALM1 8064 0.03 0.43 NO
18 MAPK3 MAPK3 MAPK3 9008 0.017 0.38 NO
19 LYN LYN LYN 9127 0.015 0.38 NO
20 MAPK14 MAPK14 MAPK14 9288 0.013 0.38 NO
21 PPP3CB PPP3CB PPP3CB 9464 0.01 0.37 NO
22 PLCG1 PLCG1 PLCG1 9647 0.008 0.36 NO
23 RAF1 RAF1 RAF1 10304 -0.0005 0.33 NO
24 CALM2 CALM2 CALM2 10366 -0.0013 0.32 NO
25 CALM3 CALM3 CALM3 10456 -0.0026 0.32 NO
26 GRB2 GRB2 GRB2 10483 -0.003 0.32 NO
27 MAP2K1 MAP2K1 MAP2K1 11170 -0.012 0.29 NO
28 RAC1 RAC1 RAC1 11536 -0.016 0.27 NO
29 SOS1 SOS1 SOS1 12765 -0.032 0.21 NO
30 ELK1 ELK1 ELK1 13373 -0.041 0.19 NO
31 NFATC4 NFATC4 NFATC4 13987 -0.051 0.18 NO
32 SHC1 SHC1 SHC1 14951 -0.07 0.15 NO
33 MAPK8 MAPK8 MAPK8 16258 -0.11 0.11 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA KERATINOCYTE PATHWAY

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 CAMK2A CAMK2A CAMK2A 1407 0.27 0.078 YES
2 PRKCB PRKCB PRKCB 1537 0.26 0.22 YES
3 RPS6KA5 RPS6KA5 RPS6KA5 3069 0.16 0.23 YES
4 PIK3R1 PIK3R1 PIK3R1 3456 0.14 0.29 YES
5 CAMK2D CAMK2D CAMK2D 3465 0.14 0.37 YES
6 PRKCA PRKCA PRKCA 3732 0.13 0.43 YES
7 RPS6KA1 RPS6KA1 RPS6KA1 4123 0.12 0.48 YES
8 PRKAR2B PRKAR2B PRKAR2B 4687 0.1 0.5 YES
9 PRKAR1A PRKAR1A PRKAR1A 7558 0.037 0.37 NO
10 CAMK2G CAMK2G CAMK2G 8228 0.028 0.34 NO
11 PRKAR2A PRKAR2A PRKAR2A 8286 0.027 0.36 NO
12 PRKACB PRKACB PRKACB 8637 0.022 0.35 NO
13 CREB1 CREB1 CREB1 8842 0.019 0.35 NO
14 MAPK3 MAPK3 MAPK3 9008 0.017 0.35 NO
15 MAPK1 MAPK1 MAPK1 9109 0.015 0.35 NO
16 MAPK14 MAPK14 MAPK14 9288 0.013 0.35 NO
17 GRB2 GRB2 GRB2 10483 -0.003 0.29 NO
18 AKT1 AKT1 AKT1 10511 -0.0033 0.29 NO
19 RAC1 RAC1 RAC1 11536 -0.016 0.24 NO
20 GNAS GNAS GNAS 12324 -0.026 0.21 NO
21 CAMK2B CAMK2B CAMK2B 12724 -0.031 0.21 NO
22 SOS1 SOS1 SOS1 12765 -0.032 0.22 NO
23 PIK3CA PIK3CA PIK3CA 13089 -0.037 0.23 NO
24 PRKAR1B PRKAR1B PRKAR1B 13391 -0.042 0.23 NO
25 HRAS HRAS HRAS 14503 -0.061 0.21 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: BIOCARTA KERATINOCYTE PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

Table 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 MAPK10 MAPK10 MAPK10 3 0.74 0.077 YES
2 FCER1A FCER1A FCER1A 11 0.7 0.15 YES
3 MS4A2 MS4A2 MS4A2 39 0.64 0.22 YES
4 PLA2G1B PLA2G1B PLA2G1B 319 0.48 0.25 YES
5 CSF2 CSF2 CSF2 1153 0.3 0.24 YES
6 PLA2G3 PLA2G3 PLA2G3 1252 0.29 0.26 YES
7 BTK BTK BTK 1266 0.29 0.29 YES
8 PLA2G10 PLA2G10 PLA2G10 1294 0.29 0.32 YES
9 PRKCB PRKCB PRKCB 1537 0.26 0.33 YES
10 PLA2G4E PLA2G4E PLA2G4E 1579 0.26 0.36 YES
11 PLA2G12B PLA2G12B PLA2G12B 1660 0.25 0.38 YES
12 PIK3CG PIK3CG PIK3CG 1731 0.24 0.4 YES
13 PIK3R5 PIK3R5 PIK3R5 2103 0.22 0.4 YES
14 PRKCE PRKCE PRKCE 2451 0.2 0.4 YES
15 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 2578 0.19 0.42 YES
16 TNF TNF TNF 2960 0.17 0.41 YES
17 VAV1 VAV1 VAV1 2977 0.17 0.43 YES
18 PLCG2 PLCG2 PLCG2 2987 0.17 0.45 YES
19 INPP5D INPP5D INPP5D 3118 0.16 0.46 YES
20 PLA2G2A PLA2G2A PLA2G2A 3233 0.16 0.47 YES
21 PIK3R1 PIK3R1 PIK3R1 3456 0.14 0.47 YES
22 PLA2G5 PLA2G5 PLA2G5 3461 0.14 0.48 YES
23 LAT LAT LAT 3722 0.13 0.48 YES
24 PRKCA PRKCA PRKCA 3732 0.13 0.5 YES
25 PIK3CD PIK3CD PIK3CD 3817 0.13 0.51 YES
26 IL13 IL13 IL13 3929 0.13 0.51 YES
27 RAC2 RAC2 RAC2 4160 0.12 0.51 YES
28 PLA2G2D PLA2G2D PLA2G2D 4557 0.1 0.5 YES
29 FYN FYN FYN 4581 0.1 0.51 YES
30 LCP2 LCP2 LCP2 4601 0.1 0.52 YES
31 SYK SYK SYK 5058 0.089 0.51 NO
32 PRKCD PRKCD PRKCD 5712 0.072 0.48 NO
33 MAPK11 MAPK11 MAPK11 5871 0.069 0.48 NO
34 FCER1G FCER1G FCER1G 6298 0.06 0.46 NO
35 VAV3 VAV3 VAV3 6551 0.054 0.45 NO
36 PLA2G6 PLA2G6 PLA2G6 6861 0.049 0.44 NO
37 MAPK9 MAPK9 MAPK9 7342 0.041 0.42 NO
38 GAB2 GAB2 GAB2 7449 0.039 0.42 NO
39 MAP2K7 MAP2K7 MAP2K7 7707 0.035 0.41 NO
40 PIK3R3 PIK3R3 PIK3R3 7750 0.035 0.41 NO
41 MAP2K3 MAP2K3 MAP2K3 8166 0.028 0.39 NO
42 PLA2G12A PLA2G12A PLA2G12A 8198 0.028 0.39 NO
43 SOS2 SOS2 SOS2 8626 0.022 0.37 NO
44 MAPK3 MAPK3 MAPK3 9008 0.017 0.35 NO
45 MAPK1 MAPK1 MAPK1 9109 0.015 0.34 NO
46 LYN LYN LYN 9127 0.015 0.34 NO
47 MAPK14 MAPK14 MAPK14 9288 0.013 0.34 NO
48 PIK3CB PIK3CB PIK3CB 9530 0.0097 0.32 NO
49 PLCG1 PLCG1 PLCG1 9647 0.008 0.32 NO
50 RAF1 RAF1 RAF1 10304 -0.0005 0.28 NO
51 GRB2 GRB2 GRB2 10483 -0.003 0.27 NO
52 AKT1 AKT1 AKT1 10511 -0.0033 0.27 NO
53 MAPK13 MAPK13 MAPK13 10823 -0.0074 0.26 NO
54 MAP2K4 MAP2K4 MAP2K4 10842 -0.0076 0.26 NO
55 PIK3R2 PIK3R2 PIK3R2 10942 -0.0088 0.25 NO
56 MAP2K1 MAP2K1 MAP2K1 11170 -0.012 0.24 NO
57 MAP2K2 MAP2K2 MAP2K2 11440 -0.015 0.23 NO
58 RAC1 RAC1 RAC1 11536 -0.016 0.22 NO
59 VAV2 VAV2 VAV2 12250 -0.025 0.19 NO
60 AKT2 AKT2 AKT2 12576 -0.029 0.17 NO
61 SOS1 SOS1 SOS1 12765 -0.032 0.17 NO
62 AKT3 AKT3 AKT3 13059 -0.036 0.15 NO
63 PIK3CA PIK3CA PIK3CA 13089 -0.037 0.16 NO
64 KRAS KRAS KRAS 14894 -0.069 0.064 NO
65 PLA2G2F PLA2G2F PLA2G2F 15619 -0.087 0.034 NO
66 NRAS NRAS NRAS 15766 -0.092 0.035 NO
67 MAPK8 MAPK8 MAPK8 16258 -0.11 0.02 NO
68 PLA2G4A PLA2G4A PLA2G4A 16381 -0.12 0.025 NO
69 MAPK12 MAPK12 MAPK12 16650 -0.13 0.025 NO
70 PDK1 PDK1 PDK1 16887 -0.15 0.027 NO
71 MAP2K6 MAP2K6 MAP2K6 17185 -0.18 0.03 NO
72 RAC3 RAC3 RAC3 17897 -0.3 0.022 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: BIOCARTA PYK2 PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RHO PATHWAY

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 MAPK10 MAPK10 MAPK10 3 0.74 0.091 YES
2 ERBB4 ERBB4 ERBB4 42 0.64 0.17 YES
3 SHC3 SHC3 SHC3 411 0.45 0.2 YES
4 NRG2 NRG2 NRG2 1357 0.28 0.18 YES
5 CAMK2A CAMK2A CAMK2A 1407 0.27 0.22 YES
6 BTC BTC BTC 1452 0.27 0.25 YES
7 PRKCB PRKCB PRKCB 1537 0.26 0.27 YES
8 PIK3CG PIK3CG PIK3CG 1731 0.24 0.29 YES
9 PAK7 PAK7 PAK7 1848 0.23 0.32 YES
10 PIK3R5 PIK3R5 PIK3R5 2103 0.22 0.33 YES
11 NRG3 NRG3 NRG3 2581 0.19 0.33 YES
12 PLCG2 PLCG2 PLCG2 2987 0.17 0.32 YES
13 AREG AREG AREG 3170 0.16 0.33 YES
14 SHC2 SHC2 SHC2 3320 0.15 0.34 YES
15 PIK3R1 PIK3R1 PIK3R1 3456 0.14 0.35 YES
16 CAMK2D CAMK2D CAMK2D 3465 0.14 0.37 YES
17 HBEGF HBEGF HBEGF 3620 0.14 0.38 YES
18 PRKCA PRKCA PRKCA 3732 0.13 0.39 YES
19 GAB1 GAB1 GAB1 3795 0.13 0.4 YES
20 PIK3CD PIK3CD PIK3CD 3817 0.13 0.42 YES
21 STAT5A STAT5A STAT5A 4026 0.12 0.42 YES
22 EGFR EGFR EGFR 4379 0.11 0.42 YES
23 NRG1 NRG1 NRG1 4646 0.1 0.41 YES
24 JUN JUN JUN 4718 0.1 0.42 YES
25 SHC4 SHC4 SHC4 5198 0.085 0.41 NO
26 PAK6 PAK6 PAK6 5916 0.068 0.38 NO
27 ERBB3 ERBB3 ERBB3 6864 0.049 0.33 NO
28 ARAF ARAF ARAF 6885 0.049 0.33 NO
29 STAT5B STAT5B STAT5B 7174 0.044 0.32 NO
30 MAPK9 MAPK9 MAPK9 7342 0.041 0.32 NO
31 CDKN1A CDKN1A CDKN1A 7695 0.035 0.3 NO
32 MAP2K7 MAP2K7 MAP2K7 7707 0.035 0.31 NO
33 BAD BAD BAD 7749 0.035 0.31 NO
34 PIK3R3 PIK3R3 PIK3R3 7750 0.035 0.32 NO
35 CAMK2G CAMK2G CAMK2G 8228 0.028 0.29 NO
36 CDKN1B CDKN1B CDKN1B 8485 0.024 0.28 NO
37 SOS2 SOS2 SOS2 8626 0.022 0.28 NO
38 MAPK3 MAPK3 MAPK3 9008 0.017 0.26 NO
39 ERBB2 ERBB2 ERBB2 9055 0.016 0.26 NO
40 EREG EREG EREG 9091 0.016 0.26 NO
41 MAPK1 MAPK1 MAPK1 9109 0.015 0.26 NO
42 TGFA TGFA TGFA 9154 0.015 0.26 NO
43 PIK3CB PIK3CB PIK3CB 9530 0.0097 0.24 NO
44 PLCG1 PLCG1 PLCG1 9647 0.008 0.23 NO
45 CBL CBL CBL 10001 0.0033 0.21 NO
46 CRK CRK CRK 10179 0.00094 0.2 NO
47 RAF1 RAF1 RAF1 10304 -0.0005 0.2 NO
48 GRB2 GRB2 GRB2 10483 -0.003 0.19 NO
49 AKT1 AKT1 AKT1 10511 -0.0033 0.19 NO
50 NCK2 NCK2 NCK2 10818 -0.0073 0.17 NO
51 MAP2K4 MAP2K4 MAP2K4 10842 -0.0076 0.17 NO
52 PIK3R2 PIK3R2 PIK3R2 10942 -0.0088 0.17 NO
53 CRKL CRKL CRKL 11077 -0.01 0.16 NO
54 MAP2K1 MAP2K1 MAP2K1 11170 -0.012 0.16 NO
55 PTK2 PTK2 PTK2 11384 -0.014 0.15 NO
56 MAP2K2 MAP2K2 MAP2K2 11440 -0.015 0.14 NO
57 MTOR MTOR MTOR 11535 -0.016 0.14 NO
58 EGF EGF EGF 11975 -0.021 0.12 NO
59 CBLB CBLB CBLB 11997 -0.022 0.12 NO
60 ABL1 ABL1 ABL1 12174 -0.024 0.12 NO
61 AKT2 AKT2 AKT2 12576 -0.029 0.097 NO
62 CAMK2B CAMK2B CAMK2B 12724 -0.031 0.093 NO
63 SOS1 SOS1 SOS1 12765 -0.032 0.094 NO
64 NCK1 NCK1 NCK1 12860 -0.033 0.093 NO
65 SRC SRC SRC 12879 -0.033 0.096 NO
66 PAK1 PAK1 PAK1 13014 -0.036 0.093 NO
67 AKT3 AKT3 AKT3 13059 -0.036 0.095 NO
68 PIK3CA PIK3CA PIK3CA 13089 -0.037 0.098 NO
69 ELK1 ELK1 ELK1 13373 -0.041 0.088 NO
70 GSK3B GSK3B GSK3B 13429 -0.042 0.09 NO
71 ABL2 ABL2 ABL2 13775 -0.048 0.077 NO
72 PAK2 PAK2 PAK2 13822 -0.048 0.08 NO
73 PAK4 PAK4 PAK4 13875 -0.049 0.084 NO
74 BRAF BRAF BRAF 14079 -0.052 0.079 NO
75 RPS6KB1 RPS6KB1 RPS6KB1 14166 -0.054 0.081 NO
76 RPS6KB2 RPS6KB2 RPS6KB2 14291 -0.056 0.081 NO
77 PAK3 PAK3 PAK3 14545 -0.061 0.074 NO
78 NRG4 NRG4 NRG4 14888 -0.069 0.064 NO
79 KRAS KRAS KRAS 14894 -0.069 0.072 NO
80 SHC1 SHC1 SHC1 14951 -0.07 0.078 NO
81 MYC MYC MYC 15528 -0.084 0.057 NO
82 NRAS NRAS NRAS 15766 -0.092 0.055 NO
83 MAPK8 MAPK8 MAPK8 16258 -0.11 0.042 NO
84 CBLC CBLC CBLC 16861 -0.15 0.027 NO
85 PRKCG PRKCG PRKCG 17044 -0.16 0.037 NO
86 EIF4EBP1 EIF4EBP1 EIF4EBP1 17741 -0.26 0.031 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: BIOCARTA RHO PATHWAY.

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

genes ES table in pathway: BIOCARTA CREB PATHWAY

Table S7.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FCER1A FCER1A FCER1A 11 0.7 0.19 YES
2 BTK BTK BTK 1266 0.29 0.2 YES
3 PRKCB PRKCB PRKCB 1537 0.26 0.26 YES
4 NFATC2 NFATC2 NFATC2 1648 0.25 0.32 YES
5 PIK3CG PIK3CG PIK3CG 1731 0.24 0.38 YES
6 FOS FOS FOS 2497 0.19 0.39 YES
7 NFATC1 NFATC1 NFATC1 2734 0.18 0.42 YES
8 VAV1 VAV1 VAV1 2977 0.17 0.46 YES
9 PIK3R1 PIK3R1 PIK3R1 3456 0.14 0.47 YES
10 NFATC3 NFATC3 NFATC3 4475 0.11 0.44 YES
11 MAP3K1 MAP3K1 MAP3K1 4509 0.11 0.47 YES
12 JUN JUN JUN 4718 0.1 0.49 YES
13 SYK SYK SYK 5058 0.089 0.49 YES
14 PPP3CC PPP3CC PPP3CC 5485 0.078 0.49 NO
15 FCER1G FCER1G FCER1G 6298 0.06 0.46 NO
16 PPP3CA PPP3CA PPP3CA 6698 0.052 0.45 NO
17 MAP2K7 MAP2K7 MAP2K7 7707 0.035 0.41 NO
18 CALM1 CALM1 CALM1 8064 0.03 0.4 NO
19 MAPK3 MAPK3 MAPK3 9008 0.017 0.35 NO
20 MAPK1 MAPK1 MAPK1 9109 0.015 0.35 NO
21 LYN LYN LYN 9127 0.015 0.35 NO
22 PPP3CB PPP3CB PPP3CB 9464 0.01 0.34 NO
23 PLCG1 PLCG1 PLCG1 9647 0.008 0.33 NO
24 RAF1 RAF1 RAF1 10304 -0.0005 0.29 NO
25 CALM2 CALM2 CALM2 10366 -0.0013 0.29 NO
26 CALM3 CALM3 CALM3 10456 -0.0026 0.28 NO
27 GRB2 GRB2 GRB2 10483 -0.003 0.28 NO
28 MAP2K4 MAP2K4 MAP2K4 10842 -0.0076 0.27 NO
29 MAP2K1 MAP2K1 MAP2K1 11170 -0.012 0.25 NO
30 SOS1 SOS1 SOS1 12765 -0.032 0.17 NO
31 PIK3CA PIK3CA PIK3CA 13089 -0.037 0.17 NO
32 ELK1 ELK1 ELK1 13373 -0.041 0.16 NO
33 PAK2 PAK2 PAK2 13822 -0.048 0.15 NO
34 NFATC4 NFATC4 NFATC4 13987 -0.051 0.16 NO
35 SHC1 SHC1 SHC1 14951 -0.07 0.12 NO
36 MAPK8 MAPK8 MAPK8 16258 -0.11 0.08 NO
37 PLA2G4A PLA2G4A PLA2G4A 16381 -0.12 0.1 NO

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

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CREB 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 ERBB SIGNALING PATHWAY

Table S8.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MAPK10 MAPK10 MAPK10 3 0.74 0.067 YES
2 NTRK3 NTRK3 NTRK3 298 0.49 0.096 YES
3 SHC3 SHC3 SHC3 411 0.45 0.13 YES
4 NTRK2 NTRK2 NTRK2 444 0.44 0.17 YES
5 NGFR NGFR NGFR 569 0.4 0.2 YES
6 NTF4 NTF4 NTF4 1043 0.32 0.2 YES
7 CAMK2A CAMK2A CAMK2A 1407 0.27 0.21 YES
8 NTRK1 NTRK1 NTRK1 1565 0.26 0.22 YES
9 CAMK4 CAMK4 CAMK4 1652 0.25 0.24 YES
10 PIK3CG PIK3CG PIK3CG 1731 0.24 0.26 YES
11 PIK3R5 PIK3R5 PIK3R5 2103 0.22 0.26 YES
12 TP73 TP73 TP73 2416 0.2 0.26 YES
13 PLCG2 PLCG2 PLCG2 2987 0.17 0.24 YES
14 RPS6KA5 RPS6KA5 RPS6KA5 3069 0.16 0.25 YES
15 RPS6KA2 RPS6KA2 RPS6KA2 3273 0.15 0.25 YES
16 SHC2 SHC2 SHC2 3320 0.15 0.27 YES
17 IRAK3 IRAK3 IRAK3 3344 0.15 0.28 YES
18 ARHGDIB ARHGDIB ARHGDIB 3404 0.15 0.29 YES
19 PIK3R1 PIK3R1 PIK3R1 3456 0.14 0.3 YES
20 CAMK2D CAMK2D CAMK2D 3465 0.14 0.31 YES
21 BCL2 BCL2 BCL2 3593 0.14 0.32 YES
22 MAP3K3 MAP3K3 MAP3K3 3741 0.13 0.32 YES
23 GAB1 GAB1 GAB1 3795 0.13 0.33 YES
24 PIK3CD PIK3CD PIK3CD 3817 0.13 0.34 YES
25 NTF3 NTF3 NTF3 3927 0.13 0.35 YES
26 CALML6 CALML6 CALML6 3999 0.12 0.35 YES
27 MAP3K5 MAP3K5 MAP3K5 4018 0.12 0.36 YES
28 RPS6KA1 RPS6KA1 RPS6KA1 4123 0.12 0.37 YES
29 IKBKB IKBKB IKBKB 4153 0.12 0.38 YES
30 MAP3K1 MAP3K1 MAP3K1 4509 0.11 0.37 NO
31 JUN JUN JUN 4718 0.1 0.37 NO
32 BDNF BDNF BDNF 5054 0.09 0.36 NO
33 RPS6KA3 RPS6KA3 RPS6KA3 5150 0.087 0.36 NO
34 SHC4 SHC4 SHC4 5198 0.085 0.36 NO
35 SH2B1 SH2B1 SH2B1 5276 0.083 0.37 NO
36 SH2B3 SH2B3 SH2B3 5319 0.082 0.37 NO
37 SORT1 SORT1 SORT1 5358 0.081 0.38 NO
38 PRKCD PRKCD PRKCD 5712 0.072 0.36 NO
39 MAPK11 MAPK11 MAPK11 5871 0.069 0.36 NO
40 NFKB1 NFKB1 NFKB1 5994 0.066 0.36 NO
41 MAP2K5 MAP2K5 MAP2K5 6107 0.064 0.36 NO
42 TRAF6 TRAF6 TRAF6 6315 0.059 0.36 NO
43 FOXO3 FOXO3 FOXO3 6492 0.056 0.35 NO
44 IRAK2 IRAK2 IRAK2 6818 0.05 0.34 NO
45 RAP1A RAP1A RAP1A 6840 0.049 0.34 NO
46 KIDINS220 KIDINS220 KIDINS220 7205 0.043 0.32 NO
47 MAPK9 MAPK9 MAPK9 7342 0.041 0.32 NO
48 RPS6KA6 RPS6KA6 RPS6KA6 7673 0.036 0.31 NO
49 MAP2K7 MAP2K7 MAP2K7 7707 0.035 0.31 NO
50 BAD BAD BAD 7749 0.035 0.31 NO
51 PIK3R3 PIK3R3 PIK3R3 7750 0.035 0.31 NO
52 CALM1 CALM1 CALM1 8064 0.03 0.3 NO
53 IRS4 IRS4 IRS4 8074 0.03 0.3 NO
54 TP53 TP53 TP53 8102 0.03 0.3 NO
55 CDC42 CDC42 CDC42 8213 0.028 0.3 NO
56 CAMK2G CAMK2G CAMK2G 8228 0.028 0.3 NO
57 IRAK4 IRAK4 IRAK4 8418 0.025 0.29 NO
58 NFKBIE NFKBIE NFKBIE 8588 0.023 0.28 NO
59 SOS2 SOS2 SOS2 8626 0.022 0.28 NO
60 NFKBIA NFKBIA NFKBIA 8774 0.02 0.28 NO
61 MAPK3 MAPK3 MAPK3 9008 0.017 0.27 NO
62 RAPGEF1 RAPGEF1 RAPGEF1 9032 0.016 0.27 NO
63 MAPK1 MAPK1 MAPK1 9109 0.015 0.26 NO
64 ZNF274 ZNF274 ZNF274 9140 0.015 0.26 NO
65 RHOA RHOA RHOA 9248 0.013 0.26 NO
66 MAPK14 MAPK14 MAPK14 9288 0.013 0.26 NO
67 FASLG FASLG FASLG 9358 0.012 0.25 NO
68 CSK CSK CSK 9435 0.011 0.25 NO
69 PIK3CB PIK3CB PIK3CB 9530 0.0097 0.25 NO
70 PLCG1 PLCG1 PLCG1 9647 0.008 0.24 NO
71 MAPKAPK2 MAPKAPK2 MAPKAPK2 9809 0.0058 0.23 NO
72 FRS2 FRS2 FRS2 9995 0.0034 0.22 NO
73 YWHAH YWHAH YWHAH 9999 0.0033 0.22 NO
74 CRK CRK CRK 10179 0.00094 0.21 NO
75 RAF1 RAF1 RAF1 10304 -0.0005 0.21 NO
76 CALM2 CALM2 CALM2 10366 -0.0013 0.2 NO
77 RAP1B RAP1B RAP1B 10447 -0.0025 0.2 NO
78 CALM3 CALM3 CALM3 10456 -0.0026 0.2 NO
79 GRB2 GRB2 GRB2 10483 -0.003 0.2 NO
80 AKT1 AKT1 AKT1 10511 -0.0033 0.2 NO
81 MAPK13 MAPK13 MAPK13 10823 -0.0074 0.18 NO
82 PIK3R2 PIK3R2 PIK3R2 10942 -0.0088 0.18 NO
83 RPS6KA4 RPS6KA4 RPS6KA4 11004 -0.0097 0.17 NO
84 BAX BAX BAX 11050 -0.01 0.17 NO
85 CRKL CRKL CRKL 11077 -0.01 0.17 NO
86 PSEN1 PSEN1 PSEN1 11086 -0.01 0.17 NO
87 MAP2K1 MAP2K1 MAP2K1 11170 -0.012 0.17 NO
88 MAP2K2 MAP2K2 MAP2K2 11440 -0.015 0.15 NO
89 NGFRAP1 NGFRAP1 NGFRAP1 11481 -0.015 0.15 NO
90 RAC1 RAC1 RAC1 11536 -0.016 0.15 NO
91 RELA RELA RELA 11657 -0.018 0.15 NO
92 ARHGDIA ARHGDIA ARHGDIA 11782 -0.019 0.14 NO
93 YWHAB YWHAB YWHAB 11904 -0.02 0.14 NO
94 IRS1 IRS1 IRS1 12076 -0.023 0.13 NO
95 ABL1 ABL1 ABL1 12174 -0.024 0.13 NO
96 AKT2 AKT2 AKT2 12576 -0.029 0.11 NO
97 MAPK7 MAPK7 MAPK7 12653 -0.03 0.1 NO
98 CAMK2B CAMK2B CAMK2B 12724 -0.031 0.1 NO
99 SOS1 SOS1 SOS1 12765 -0.032 0.1 NO
100 MAGED1 MAGED1 MAGED1 12829 -0.033 0.1 NO
101 AKT3 AKT3 AKT3 13059 -0.036 0.095 NO
102 PIK3CA PIK3CA PIK3CA 13089 -0.037 0.097 NO
103 YWHAE YWHAE YWHAE 13171 -0.038 0.096 NO
104 GSK3B GSK3B GSK3B 13429 -0.042 0.086 NO
105 ATF4 ATF4 ATF4 13498 -0.043 0.086 NO
106 NGF NGF NGF 13620 -0.045 0.083 NO
107 NFKBIB NFKBIB NFKBIB 13793 -0.048 0.078 NO
108 BRAF BRAF BRAF 14079 -0.052 0.067 NO
109 YWHAQ YWHAQ YWHAQ 14669 -0.064 0.041 NO
110 KRAS KRAS KRAS 14894 -0.069 0.034 NO
111 IRS2 IRS2 IRS2 14899 -0.069 0.041 NO
112 SHC1 SHC1 SHC1 14951 -0.07 0.044 NO
113 PRDM4 PRDM4 PRDM4 15096 -0.074 0.043 NO
114 PTPN11 PTPN11 PTPN11 15105 -0.074 0.049 NO
115 YWHAZ YWHAZ YWHAZ 15332 -0.079 0.044 NO
116 IRAK1 IRAK1 IRAK1 15672 -0.089 0.033 NO
117 NRAS NRAS NRAS 15766 -0.092 0.037 NO
118 YWHAG YWHAG YWHAG 16066 -0.1 0.03 NO
119 MAPK8 MAPK8 MAPK8 16258 -0.11 0.029 NO
120 CALML5 CALML5 CALML5 16424 -0.12 0.031 NO
121 RIPK2 RIPK2 RIPK2 16571 -0.13 0.035 NO
122 MAPK12 MAPK12 MAPK12 16650 -0.13 0.042 NO
123 PDK1 PDK1 PDK1 16887 -0.15 0.043 NO
124 SH2B2 SH2B2 SH2B2 17197 -0.18 0.042 NO
125 CALML3 CALML3 CALML3 17378 -0.2 0.051 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 ERBB SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG CARDIAC MUSCLE CONTRACTION

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 DES DES DES 155 0.55 0.033 YES
2 SGCA SGCA SGCA 184 0.53 0.071 YES
3 CACNA2D2 CACNA2D2 CACNA2D2 237 0.51 0.11 YES
4 TNNC1 TNNC1 TNNC1 412 0.45 0.13 YES
5 CACNG6 CACNG6 CACNG6 437 0.44 0.16 YES
6 ITGA8 ITGA8 ITGA8 454 0.44 0.2 YES
7 ITGA10 ITGA10 ITGA10 506 0.42 0.22 YES
8 SGCG SGCG SGCG 557 0.41 0.25 YES
9 CACNB4 CACNB4 CACNB4 599 0.4 0.28 YES
10 ADRB1 ADRB1 ADRB1 607 0.4 0.31 YES
11 MYL3 MYL3 MYL3 735 0.37 0.33 YES
12 RYR2 RYR2 RYR2 772 0.36 0.36 YES
13 CACNB1 CACNB1 CACNB1 852 0.35 0.38 YES
14 ITGA9 ITGA9 ITGA9 907 0.34 0.4 YES
15 CACNA2D3 CACNA2D3 CACNA2D3 1038 0.32 0.42 YES
16 ADCY2 ADCY2 ADCY2 1382 0.28 0.42 YES
17 LAMA2 LAMA2 LAMA2 1404 0.27 0.44 YES
18 CACNA1D CACNA1D CACNA1D 1528 0.26 0.45 YES
19 TNNT2 TNNT2 TNNT2 1718 0.24 0.46 YES
20 CACNA1C CACNA1C CACNA1C 1722 0.24 0.48 YES
21 CACNA1F CACNA1F CACNA1F 1732 0.24 0.5 YES
22 DMD DMD DMD 1765 0.24 0.51 YES
23 ITGB6 ITGB6 ITGB6 1833 0.24 0.53 YES
24 ADCY8 ADCY8 ADCY8 1952 0.23 0.54 YES
25 ADCY9 ADCY9 ADCY9 2178 0.21 0.54 YES
26 SGCD SGCD SGCD 2719 0.18 0.52 YES
27 TNF TNF TNF 2960 0.17 0.52 YES
28 TGFB2 TGFB2 TGFB2 2967 0.17 0.54 YES
29 ADCY4 ADCY4 ADCY4 3050 0.16 0.55 YES
30 ITGB3 ITGB3 ITGB3 3101 0.16 0.55 YES
31 ITGA2 ITGA2 ITGA2 3253 0.15 0.56 YES
32 ITGA4 ITGA4 ITGA4 3406 0.15 0.56 YES
33 TTN TTN TTN 3421 0.15 0.57 YES
34 ITGB8 ITGB8 ITGB8 3525 0.14 0.58 YES
35 ITGA7 ITGA7 ITGA7 3656 0.14 0.58 YES
36 IGF1 IGF1 IGF1 3697 0.14 0.59 YES
37 CACNA2D4 CACNA2D4 CACNA2D4 3845 0.13 0.59 YES
38 ACTC1 ACTC1 ACTC1 3848 0.13 0.6 YES
39 CACNG4 CACNG4 CACNG4 3882 0.13 0.61 YES
40 ADCY5 ADCY5 ADCY5 4147 0.12 0.6 NO
41 ITGB4 ITGB4 ITGB4 4329 0.11 0.6 NO
42 TGFB1 TGFB1 TGFB1 4711 0.1 0.59 NO
43 MYBPC3 MYBPC3 MYBPC3 4998 0.091 0.58 NO
44 SLC8A1 SLC8A1 SLC8A1 5402 0.08 0.56 NO
45 CACNA1S CACNA1S CACNA1S 5669 0.074 0.55 NO
46 ITGA2B ITGA2B ITGA2B 5843 0.07 0.55 NO
47 ADCY6 ADCY6 ADCY6 6185 0.062 0.53 NO
48 ITGA1 ITGA1 ITGA1 6433 0.057 0.52 NO
49 PLN PLN PLN 6835 0.05 0.51 NO
50 ITGB7 ITGB7 ITGB7 6866 0.049 0.51 NO
51 ITGA3 ITGA3 ITGA3 6896 0.048 0.51 NO
52 ADCY1 ADCY1 ADCY1 6999 0.046 0.51 NO
53 MYL2 MYL2 MYL2 7441 0.04 0.49 NO
54 ITGA6 ITGA6 ITGA6 7886 0.033 0.46 NO
55 CACNB3 CACNB3 CACNB3 8084 0.03 0.46 NO
56 PRKACA PRKACA PRKACA 8314 0.026 0.45 NO
57 LMNA LMNA LMNA 8400 0.025 0.44 NO
58 ADCY7 ADCY7 ADCY7 8516 0.024 0.44 NO
59 CACNG1 CACNG1 CACNG1 8548 0.023 0.44 NO
60 PRKACB PRKACB PRKACB 8637 0.022 0.44 NO
61 PRKX PRKX PRKX 8766 0.02 0.43 NO
62 TPM1 TPM1 TPM1 9393 0.011 0.4 NO
63 MYH7 MYH7 MYH7 9452 0.011 0.39 NO
64 SGCB SGCB SGCB 10844 -0.0076 0.32 NO
65 ACTB ACTB ACTB 10861 -0.0078 0.32 NO
66 TPM4 TPM4 TPM4 11091 -0.011 0.31 NO
67 TGFB3 TGFB3 TGFB3 11146 -0.011 0.3 NO
68 ITGAV ITGAV ITGAV 11611 -0.017 0.28 NO
69 EMD EMD EMD 11898 -0.02 0.27 NO
70 ITGB5 ITGB5 ITGB5 12115 -0.023 0.26 NO
71 CACNB2 CACNB2 CACNB2 12231 -0.025 0.25 NO
72 GNAS GNAS GNAS 12324 -0.026 0.25 NO
73 DAG1 DAG1 DAG1 12592 -0.03 0.24 NO
74 ACTG1 ACTG1 ACTG1 13180 -0.038 0.21 NO
75 CACNA2D1 CACNA2D1 CACNA2D1 13279 -0.04 0.2 NO
76 TPM3 TPM3 TPM3 14276 -0.056 0.15 NO
77 ITGB1 ITGB1 ITGB1 15291 -0.078 0.1 NO
78 ATP2A2 ATP2A2 ATP2A2 15360 -0.08 0.11 NO
79 TPM2 TPM2 TPM2 15607 -0.086 0.099 NO
80 ITGA5 ITGA5 ITGA5 16562 -0.13 0.056 NO
81 TNNI3 TNNI3 TNNI3 16608 -0.13 0.064 NO
82 MYH6 MYH6 MYH6 17126 -0.17 0.048 NO
83 ITGA11 ITGA11 ITGA11 17493 -0.22 0.044 NO

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

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

genes ES table in pathway: KEGG CELL ADHESION MOLECULES CAMS

Table 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 ATP1A2 ATP1A2 ATP1A2 28 0.66 0.12 YES
2 NR3C2 NR3C2 NR3C2 451 0.44 0.18 YES
3 ATP1B2 ATP1B2 ATP1B2 648 0.39 0.24 YES
4 ATP1A4 ATP1A4 ATP1A4 811 0.36 0.3 YES
5 SCNN1B SCNN1B SCNN1B 872 0.35 0.36 YES
6 PRKCB PRKCB PRKCB 1537 0.26 0.38 YES
7 SCNN1G SCNN1G SCNN1G 1583 0.26 0.42 YES
8 PIK3CG PIK3CG PIK3CG 1731 0.24 0.46 YES
9 PIK3R5 PIK3R5 PIK3R5 2103 0.22 0.48 YES
10 HSD11B2 HSD11B2 HSD11B2 2179 0.21 0.51 YES
11 SGK1 SGK1 SGK1 3304 0.15 0.48 YES
12 PIK3R1 PIK3R1 PIK3R1 3456 0.14 0.5 YES
13 IGF1 IGF1 IGF1 3697 0.14 0.51 YES
14 PRKCA PRKCA PRKCA 3732 0.13 0.53 YES
15 PIK3CD PIK3CD PIK3CD 3817 0.13 0.55 YES
16 PDPK1 PDPK1 PDPK1 5070 0.089 0.5 NO
17 SLC9A3R2 SLC9A3R2 SLC9A3R2 5294 0.083 0.5 NO
18 HSD11B1 HSD11B1 HSD11B1 5384 0.08 0.52 NO
19 ATP1A1 ATP1A1 ATP1A1 5505 0.078 0.52 NO
20 NEDD4L NEDD4L NEDD4L 6078 0.064 0.5 NO
21 KCNJ1 KCNJ1 KCNJ1 6351 0.058 0.5 NO
22 ATP1A3 ATP1A3 ATP1A3 6996 0.046 0.47 NO
23 PIK3R3 PIK3R3 PIK3R3 7750 0.035 0.44 NO
24 IRS4 IRS4 IRS4 8074 0.03 0.43 NO
25 MAPK3 MAPK3 MAPK3 9008 0.017 0.38 NO
26 MAPK1 MAPK1 MAPK1 9109 0.015 0.38 NO
27 SFN SFN SFN 9436 0.011 0.36 NO
28 PIK3CB PIK3CB PIK3CB 9530 0.0097 0.36 NO
29 ATP1B1 ATP1B1 ATP1B1 10113 0.0018 0.32 NO
30 INSR INSR INSR 10345 -0.001 0.31 NO
31 PIK3R2 PIK3R2 PIK3R2 10942 -0.0088 0.28 NO
32 IRS1 IRS1 IRS1 12076 -0.023 0.22 NO
33 PIK3CA PIK3CA PIK3CA 13089 -0.037 0.18 NO
34 SCNN1A SCNN1A SCNN1A 13093 -0.037 0.18 NO
35 ATP1B3 ATP1B3 ATP1B3 13591 -0.044 0.16 NO
36 KRAS KRAS KRAS 14894 -0.069 0.1 NO
37 IRS2 IRS2 IRS2 14899 -0.069 0.12 NO
38 PRKCG PRKCG PRKCG 17044 -0.16 0.031 NO
39 FXYD4 FXYD4 FXYD4 17400 -0.2 0.049 NO

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

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

Fold change

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

Expression level

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA G1 PATHWAY 27 genes.ES.table 0.63 1.8 0.0061 0.17 0.38 0.44 0.19 0.36 0 0.031
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.42 1.5 0.074 0.25 0.83 0.48 0.28 0.35 0.17 0.03
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.52 2 0 0.079 0.066 0.36 0.26 0.26 0 0.029
BIOCARTA IL1R PATHWAY 31 genes.ES.table 0.49 1.4 0.13 0.41 0.96 0.36 0.18 0.29 0.32 0.063
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.39 1.5 0.068 0.24 0.84 0.43 0.28 0.31 0.16 0.024
KEGG PYRIMIDINE METABOLISM 97 genes.ES.table 0.4 1.6 0.053 0.19 0.74 0.4 0.23 0.31 0.12 0.015
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.39 1.4 0.15 0.43 0.96 0.53 0.34 0.35 0.34 0.08
KEGG DNA REPLICATION 35 genes.ES.table 0.75 1.8 0 0.12 0.25 0.77 0.2 0.62 0 0.021
KEGG SPLICEOSOME 125 genes.ES.table 0.42 1.7 0.042 0.14 0.48 0.5 0.34 0.33 0 0.015
KEGG PROTEASOME 42 genes.ES.table 0.59 1.7 0.037 0.14 0.44 0.88 0.37 0.56 0 0.02
genes ES table in pathway: BIOCARTA G1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CCNE1 CCNE1 CCNE1 50 0.44 0.32 YES
2 CDK6 CDK6 CDK6 1524 0.14 0.34 YES
3 CDK2 CDK2 CDK2 1992 0.12 0.4 YES
4 CDK4 CDK4 CDK4 2405 0.099 0.45 YES
5 PIK3CA PIK3CA PIK3CA 3194 0.076 0.46 YES
6 RAC1 RAC1 RAC1 3686 0.065 0.48 YES
7 IKBKG IKBKG IKBKG 4312 0.053 0.48 YES
8 TFDP1 TFDP1 TFDP1 4474 0.05 0.51 YES
9 CDKN1A CDKN1A CDKN1A 4858 0.045 0.52 YES
10 RELA RELA RELA 5774 0.032 0.5 NO
11 PAK1 PAK1 PAK1 6011 0.029 0.5 NO
12 HRAS HRAS HRAS 7352 0.013 0.44 NO
13 RHOA RHOA RHOA 7528 0.011 0.44 NO
14 CCND1 CCND1 CCND1 7555 0.011 0.45 NO
15 CDKN1B CDKN1B CDKN1B 8314 0.0025 0.41 NO
16 MAPK1 MAPK1 MAPK1 8557 -0.00036 0.39 NO
17 AKT1 AKT1 AKT1 8627 -0.0014 0.39 NO
18 NFKB1 NFKB1 NFKB1 8695 -0.0021 0.39 NO
19 NFKBIA NFKBIA NFKBIA 9002 -0.0057 0.38 NO
20 MAPK3 MAPK3 MAPK3 9118 -0.007 0.38 NO
21 RAF1 RAF1 RAF1 9192 -0.0078 0.38 NO
22 CHUK CHUK CHUK 10349 -0.02 0.33 NO
23 RB1 RB1 RB1 11172 -0.031 0.3 NO
24 PIK3R1 PIK3R1 PIK3R1 11697 -0.038 0.3 NO
25 IKBKB IKBKB IKBKB 13921 -0.08 0.24 NO

Figure S21.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA FAS PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TTK TTK TTK 48 0.44 0.027 YES
2 CCNE1 CCNE1 CCNE1 50 0.44 0.056 YES
3 ORC1L ORC1L ORC1L 106 0.4 0.079 YES
4 CDC45 CDC45 CDC45 108 0.4 0.11 YES
5 PKMYT1 PKMYT1 PKMYT1 113 0.39 0.13 YES
6 CDC25C CDC25C CDC25C 134 0.38 0.16 YES
7 CDC20 CDC20 CDC20 171 0.36 0.18 YES
8 SMC1B SMC1B SMC1B 201 0.34 0.2 YES
9 CDC25A CDC25A CDC25A 202 0.34 0.22 YES
10 CDC6 CDC6 CDC6 204 0.34 0.24 YES
11 ESPL1 ESPL1 ESPL1 206 0.34 0.27 YES
12 CCNA2 CCNA2 CCNA2 211 0.34 0.29 YES
13 BUB1 BUB1 BUB1 232 0.33 0.31 YES
14 BUB1B BUB1B BUB1B 236 0.33 0.33 YES
15 PLK1 PLK1 PLK1 252 0.32 0.35 YES
16 MAD2L1 MAD2L1 MAD2L1 255 0.32 0.37 YES
17 CCNB2 CCNB2 CCNB2 257 0.32 0.4 YES
18 ORC6L ORC6L ORC6L 272 0.31 0.42 YES
19 CHEK1 CHEK1 CHEK1 300 0.3 0.43 YES
20 CCNE2 CCNE2 CCNE2 306 0.3 0.45 YES
21 CDK1 CDK1 CDK1 403 0.28 0.47 YES
22 CCNB1 CCNB1 CCNB1 493 0.26 0.48 YES
23 CDKN2A CDKN2A CDKN2A 533 0.25 0.49 YES
24 MCM2 MCM2 MCM2 623 0.23 0.5 YES
25 CDC7 CDC7 CDC7 627 0.23 0.52 YES
26 SKP2 SKP2 SKP2 631 0.23 0.53 YES
27 E2F2 E2F2 E2F2 699 0.22 0.55 YES
28 RBL1 RBL1 RBL1 712 0.22 0.56 YES
29 PTTG1 PTTG1 PTTG1 772 0.21 0.57 YES
30 E2F1 E2F1 E2F1 850 0.2 0.58 YES
31 MCM4 MCM4 MCM4 906 0.19 0.59 YES
32 GADD45A GADD45A GADD45A 910 0.19 0.6 YES
33 MCM6 MCM6 MCM6 938 0.19 0.61 YES
34 MAD2L2 MAD2L2 MAD2L2 1333 0.16 0.6 YES
35 TGFB2 TGFB2 TGFB2 1340 0.16 0.61 YES
36 CDK6 CDK6 CDK6 1524 0.14 0.61 YES
37 MCM5 MCM5 MCM5 1570 0.14 0.62 YES
38 MCM7 MCM7 MCM7 1682 0.13 0.62 YES
39 CDKN2C CDKN2C CDKN2C 1813 0.13 0.62 YES
40 MYC MYC MYC 1896 0.12 0.63 YES
41 CDK2 CDK2 CDK2 1992 0.12 0.63 YES
42 SFN SFN SFN 2310 0.1 0.62 YES
43 ORC5L ORC5L ORC5L 2336 0.1 0.62 YES
44 PTTG2 PTTG2 PTTG2 2349 0.1 0.63 YES
45 CDK4 CDK4 CDK4 2405 0.099 0.63 YES
46 CHEK2 CHEK2 CHEK2 2432 0.098 0.64 YES
47 YWHAG YWHAG YWHAG 2442 0.098 0.64 YES
48 TGFB1 TGFB1 TGFB1 2992 0.081 0.62 NO
49 TGFB3 TGFB3 TGFB3 3066 0.079 0.62 NO
50 E2F3 E2F3 E2F3 3257 0.074 0.62 NO
51 PCNA PCNA PCNA 3379 0.072 0.61 NO
52 ANAPC11 ANAPC11 ANAPC11 3388 0.071 0.62 NO
53 CCNA1 CCNA1 CCNA1 3460 0.069 0.62 NO
54 MCM3 MCM3 MCM3 3567 0.067 0.62 NO
55 MAD1L1 MAD1L1 MAD1L1 3676 0.065 0.62 NO
56 CDC27 CDC27 CDC27 3745 0.064 0.62 NO
57 BUB3 BUB3 BUB3 3981 0.059 0.61 NO
58 PRKDC PRKDC PRKDC 4029 0.058 0.61 NO
59 CDKN2D CDKN2D CDKN2D 4092 0.057 0.61 NO
60 YWHAQ YWHAQ YWHAQ 4138 0.056 0.61 NO
61 CDKN2B CDKN2B CDKN2B 4143 0.056 0.61 NO
62 TFDP2 TFDP2 TFDP2 4243 0.054 0.61 NO
63 YWHAZ YWHAZ YWHAZ 4288 0.054 0.61 NO
64 ORC3L ORC3L ORC3L 4314 0.053 0.61 NO
65 ANAPC10 ANAPC10 ANAPC10 4351 0.053 0.62 NO
66 HDAC2 HDAC2 HDAC2 4356 0.053 0.62 NO
67 TFDP1 TFDP1 TFDP1 4474 0.05 0.62 NO
68 E2F4 E2F4 E2F4 4752 0.047 0.6 NO
69 CDKN1A CDKN1A CDKN1A 4858 0.045 0.6 NO
70 FZR1 FZR1 FZR1 4947 0.044 0.6 NO
71 YWHAH YWHAH YWHAH 5149 0.04 0.59 NO
72 ANAPC1 ANAPC1 ANAPC1 5377 0.037 0.58 NO
73 RAD21 RAD21 RAD21 5659 0.034 0.57 NO
74 SMC3 SMC3 SMC3 5882 0.031 0.56 NO
75 GSK3B GSK3B GSK3B 5905 0.03 0.56 NO
76 ATR ATR ATR 5911 0.03 0.56 NO
77 ANAPC7 ANAPC7 ANAPC7 6347 0.025 0.54 NO
78 CUL1 CUL1 CUL1 6403 0.024 0.54 NO
79 RBX1 RBX1 RBX1 6422 0.024 0.54 NO
80 YWHAB YWHAB YWHAB 6497 0.023 0.54 NO
81 SMAD3 SMAD3 SMAD3 6512 0.023 0.54 NO
82 ZBTB17 ZBTB17 ZBTB17 6663 0.021 0.53 NO
83 ANAPC5 ANAPC5 ANAPC5 6837 0.019 0.52 NO
84 SMC1A SMC1A SMC1A 6919 0.018 0.52 NO
85 ANAPC13 ANAPC13 ANAPC13 6952 0.018 0.52 NO
86 CDC26 CDC26 CDC26 7000 0.017 0.52 NO
87 CCNB3 CCNB3 CCNB3 7029 0.017 0.52 NO
88 ORC4L ORC4L ORC4L 7337 0.014 0.5 NO
89 CDK7 CDK7 CDK7 7395 0.013 0.5 NO
90 CCND1 CCND1 CCND1 7555 0.011 0.49 NO
91 STAG1 STAG1 STAG1 7558 0.011 0.49 NO
92 CDC25B CDC25B CDC25B 7834 0.008 0.47 NO
93 WEE1 WEE1 WEE1 7950 0.0066 0.47 NO
94 CDKN1B CDKN1B CDKN1B 8314 0.0025 0.45 NO
95 YWHAE YWHAE YWHAE 8346 0.0021 0.45 NO
96 ORC2L ORC2L ORC2L 8461 0.001 0.44 NO
97 CDC23 CDC23 CDC23 8631 -0.0014 0.43 NO
98 HDAC1 HDAC1 HDAC1 8643 -0.0015 0.43 NO
99 STAG2 STAG2 STAG2 8955 -0.0052 0.41 NO
100 ABL1 ABL1 ABL1 9346 -0.0095 0.39 NO
101 ANAPC2 ANAPC2 ANAPC2 9354 -0.0096 0.39 NO
102 ANAPC4 ANAPC4 ANAPC4 10085 -0.018 0.36 NO
103 CCNH CCNH CCNH 10197 -0.019 0.35 NO
104 CCND2 CCND2 CCND2 10403 -0.021 0.34 NO
105 GADD45B GADD45B GADD45B 10515 -0.022 0.34 NO
106 EP300 EP300 EP300 10656 -0.024 0.33 NO
107 CREBBP CREBBP CREBBP 10958 -0.028 0.32 NO
108 SKP1 SKP1 SKP1 11086 -0.03 0.31 NO
109 RB1 RB1 RB1 11172 -0.031 0.31 NO
110 CDKN1C CDKN1C CDKN1C 11587 -0.036 0.29 NO
111 CDC16 CDC16 CDC16 11681 -0.038 0.28 NO
112 ATM ATM ATM 11792 -0.039 0.28 NO
113 SMAD2 SMAD2 SMAD2 12151 -0.044 0.26 NO
114 CDC14B CDC14B CDC14B 12691 -0.053 0.24 NO
115 SMAD4 SMAD4 SMAD4 12720 -0.054 0.24 NO
116 CDC14A CDC14A CDC14A 13447 -0.069 0.2 NO
117 TP53 TP53 TP53 13635 -0.073 0.2 NO
118 MDM2 MDM2 MDM2 13831 -0.077 0.19 NO
119 RBL2 RBL2 RBL2 13968 -0.081 0.19 NO
120 E2F5 E2F5 E2F5 14354 -0.091 0.18 NO
121 CCND3 CCND3 CCND3 14944 -0.11 0.15 NO
122 WEE2 WEE2 WEE2 16160 -0.17 0.095 NO
123 GADD45G GADD45G GADD45G 17860 -0.34 0.024 NO

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

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

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 POLE2 POLE2 POLE2 187 0.35 0.079 YES
2 RFC4 RFC4 RFC4 566 0.24 0.12 YES
3 MCM2 MCM2 MCM2 623 0.23 0.18 YES
4 PRIM1 PRIM1 PRIM1 759 0.21 0.22 YES
5 RNASEH2A RNASEH2A RNASEH2A 893 0.2 0.26 YES
6 MCM4 MCM4 MCM4 906 0.19 0.31 YES
7 MCM6 MCM6 MCM6 938 0.19 0.36 YES
8 FEN1 FEN1 FEN1 1277 0.16 0.38 YES
9 RPA3 RPA3 RPA3 1324 0.16 0.42 YES
10 PRIM2 PRIM2 PRIM2 1406 0.15 0.45 YES
11 RFC2 RFC2 RFC2 1507 0.14 0.48 YES
12 MCM5 MCM5 MCM5 1570 0.14 0.52 YES
13 RFC5 RFC5 RFC5 1610 0.14 0.55 YES
14 MCM7 MCM7 MCM7 1682 0.13 0.58 YES
15 POLA2 POLA2 POLA2 1891 0.12 0.6 YES
16 DNA2 DNA2 DNA2 2011 0.12 0.62 YES
17 RFC3 RFC3 RFC3 2347 0.1 0.63 YES
18 POLD1 POLD1 POLD1 2393 0.099 0.65 YES
19 POLD2 POLD2 POLD2 2396 0.099 0.68 YES
20 RNASEH1 RNASEH1 RNASEH1 2833 0.085 0.67 YES
21 SSBP1 SSBP1 SSBP1 2995 0.081 0.68 YES
22 POLE3 POLE3 POLE3 3197 0.076 0.69 YES
23 POLE POLE POLE 3333 0.072 0.7 YES
24 PCNA PCNA PCNA 3379 0.072 0.72 YES
25 MCM3 MCM3 MCM3 3567 0.067 0.73 YES
26 LIG1 LIG1 LIG1 3624 0.066 0.74 YES
27 POLE4 POLE4 POLE4 3678 0.065 0.75 YES
28 POLD3 POLD3 POLD3 5196 0.04 0.68 NO
29 RNASEH2C RNASEH2C RNASEH2C 5450 0.036 0.68 NO
30 RPA2 RPA2 RPA2 5668 0.034 0.67 NO
31 RPA1 RPA1 RPA1 6223 0.026 0.65 NO
32 POLD4 POLD4 POLD4 6895 0.018 0.62 NO
33 RFC1 RFC1 RFC1 6991 0.017 0.62 NO
34 RPA4 RPA4 RPA4 8342 0.0022 0.54 NO
35 RNASEH2B RNASEH2B RNASEH2B 9222 -0.0081 0.5 NO

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

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA RACCYCD 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 IL1R PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CCNE1 CCNE1 CCNE1 50 0.44 0.16 YES
2 CDC25A CDC25A CDC25A 202 0.34 0.27 YES
3 CDK1 CDK1 CDK1 403 0.28 0.36 YES
4 CDKN2A CDKN2A CDKN2A 533 0.25 0.44 YES
5 SKP2 SKP2 SKP2 631 0.23 0.52 YES
6 TGFB2 TGFB2 TGFB2 1340 0.16 0.54 YES
7 CDK6 CDK6 CDK6 1524 0.14 0.58 YES
8 CDK2 CDK2 CDK2 1992 0.12 0.59 YES
9 CDK4 CDK4 CDK4 2405 0.099 0.61 YES
10 TGFB1 TGFB1 TGFB1 2992 0.081 0.6 YES
11 TGFB3 TGFB3 TGFB3 3066 0.079 0.63 YES
12 CCNA1 CCNA1 CCNA1 3460 0.069 0.63 YES
13 CDKN2B CDKN2B CDKN2B 4143 0.056 0.61 NO
14 TFDP1 TFDP1 TFDP1 4474 0.05 0.61 NO
15 DHFR DHFR DHFR 4708 0.047 0.62 NO
16 CDKN1A CDKN1A CDKN1A 4858 0.045 0.63 NO
17 GSK3B GSK3B GSK3B 5905 0.03 0.58 NO
18 ATR ATR ATR 5911 0.03 0.59 NO
19 SMAD3 SMAD3 SMAD3 6512 0.023 0.56 NO
20 CCND1 CCND1 CCND1 7555 0.011 0.51 NO
21 CDKN1B CDKN1B CDKN1B 8314 0.0025 0.47 NO
22 HDAC1 HDAC1 HDAC1 8643 -0.0015 0.45 NO
23 ABL1 ABL1 ABL1 9346 -0.0095 0.42 NO
24 RB1 RB1 RB1 11172 -0.031 0.33 NO
25 ATM ATM ATM 11792 -0.039 0.31 NO
26 SMAD4 SMAD4 SMAD4 12720 -0.054 0.28 NO
27 TP53 TP53 TP53 13635 -0.073 0.26 NO

Figure S27.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL1R PATHWAY.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R 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 TNFR1 PATHWAY

Table S15.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 POLE2 POLE2 POLE2 187 0.35 0.12 YES
2 RFC4 RFC4 RFC4 566 0.24 0.19 YES
3 RPA3 RPA3 RPA3 1324 0.16 0.21 YES
4 RFC2 RFC2 RFC2 1507 0.14 0.25 YES
5 RFC5 RFC5 RFC5 1610 0.14 0.3 YES
6 GTF2H3 GTF2H3 GTF2H3 2315 0.1 0.3 YES
7 RFC3 RFC3 RFC3 2347 0.1 0.33 YES
8 POLD1 POLD1 POLD1 2393 0.099 0.37 YES
9 POLD2 POLD2 POLD2 2396 0.099 0.4 YES
10 POLE3 POLE3 POLE3 3197 0.076 0.39 YES
11 POLE POLE POLE 3333 0.072 0.41 YES
12 PCNA PCNA PCNA 3379 0.072 0.43 YES
13 LIG1 LIG1 LIG1 3624 0.066 0.44 YES
14 ERCC8 ERCC8 ERCC8 3648 0.066 0.46 YES
15 POLE4 POLE4 POLE4 3678 0.065 0.49 YES
16 GTF2H2 GTF2H2 GTF2H2 3755 0.064 0.51 YES
17 GTF2H4 GTF2H4 GTF2H4 4628 0.048 0.48 YES
18 ERCC2 ERCC2 ERCC2 4700 0.048 0.49 YES
19 RAD23A RAD23A RAD23A 5011 0.042 0.49 YES
20 CUL4B CUL4B CUL4B 5156 0.04 0.5 YES
21 POLD3 POLD3 POLD3 5196 0.04 0.51 YES
22 RPA2 RPA2 RPA2 5668 0.034 0.5 NO
23 ERCC1 ERCC1 ERCC1 5695 0.034 0.51 NO
24 ERCC4 ERCC4 ERCC4 6050 0.029 0.5 NO
25 MNAT1 MNAT1 MNAT1 6207 0.027 0.5 NO
26 RPA1 RPA1 RPA1 6223 0.026 0.51 NO
27 RBX1 RBX1 RBX1 6422 0.024 0.51 NO
28 CETN2 CETN2 CETN2 6777 0.02 0.5 NO
29 POLD4 POLD4 POLD4 6895 0.018 0.5 NO
30 RFC1 RFC1 RFC1 6991 0.017 0.5 NO
31 CDK7 CDK7 CDK7 7395 0.013 0.48 NO
32 ERCC3 ERCC3 ERCC3 7607 0.011 0.47 NO
33 GTF2H1 GTF2H1 GTF2H1 7783 0.0087 0.46 NO
34 DDB1 DDB1 DDB1 8147 0.0044 0.45 NO
35 RPA4 RPA4 RPA4 8342 0.0022 0.44 NO
36 GTF2H5 GTF2H5 GTF2H5 8780 -0.0031 0.41 NO
37 DDB2 DDB2 DDB2 9698 -0.013 0.37 NO
38 CCNH CCNH CCNH 10197 -0.019 0.35 NO
39 CUL4A CUL4A CUL4A 10297 -0.02 0.35 NO
40 ERCC6 ERCC6 ERCC6 11104 -0.03 0.32 NO
41 ERCC5 ERCC5 ERCC5 12952 -0.058 0.24 NO
42 XPA XPA XPA 13452 -0.069 0.24 NO
43 XPC XPC XPC 13881 -0.078 0.24 NO

Figure S29.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TNFR1 PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 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 PYRIMIDINE 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 IFNG IFNG IFNG 617 0.23 0.062 YES
2 PSMB9 PSMB9 PSMB9 1066 0.18 0.11 YES
3 PSMD12 PSMD12 PSMD12 2177 0.11 0.093 YES
4 PSMC2 PSMC2 PSMC2 2360 0.1 0.12 YES
5 PSMD2 PSMD2 PSMD2 2370 0.1 0.16 YES
6 PSMD11 PSMD11 PSMD11 2623 0.092 0.19 YES
7 PSMB3 PSMB3 PSMB3 2713 0.09 0.22 YES
8 PSME2 PSME2 PSME2 2806 0.086 0.25 YES
9 PSMA2 PSMA2 PSMA2 2852 0.085 0.28 YES
10 PSMA6 PSMA6 PSMA6 2969 0.082 0.31 YES
11 PSMC4 PSMC4 PSMC4 3485 0.069 0.31 YES
12 PSMA5 PSMA5 PSMA5 3487 0.069 0.34 YES
13 SHFM1 SHFM1 SHFM1 3554 0.067 0.36 YES
14 PSMB2 PSMB2 PSMB2 3716 0.064 0.38 YES
15 PSMB8 PSMB8 PSMB8 3825 0.062 0.4 YES
16 PSMD3 PSMD3 PSMD3 3982 0.059 0.41 YES
17 PSMC1 PSMC1 PSMC1 3999 0.059 0.44 YES
18 PSMB7 PSMB7 PSMB7 4002 0.059 0.46 YES
19 PSMD14 PSMD14 PSMD14 4047 0.058 0.48 YES
20 PSMA7 PSMA7 PSMA7 4332 0.053 0.49 YES
21 PSMB1 PSMB1 PSMB1 4571 0.049 0.49 YES
22 PSMC6 PSMC6 PSMC6 4608 0.049 0.51 YES
23 PSMC5 PSMC5 PSMC5 4617 0.048 0.53 YES
24 PSMC3 PSMC3 PSMC3 4675 0.048 0.55 YES
25 PSMB4 PSMB4 PSMB4 4804 0.046 0.56 YES
26 PSME3 PSME3 PSME3 4990 0.043 0.57 YES
27 PSMB5 PSMB5 PSMB5 5044 0.042 0.58 YES
28 PSMD8 PSMD8 PSMD8 5214 0.04 0.59 YES
29 PSMD13 PSMD13 PSMD13 5807 0.032 0.57 YES
30 PSMD6 PSMD6 PSMD6 5915 0.03 0.57 YES
31 PSMD4 PSMD4 PSMD4 5962 0.03 0.58 YES
32 PSME1 PSME1 PSME1 6370 0.025 0.57 YES
33 PSMD1 PSMD1 PSMD1 6374 0.025 0.58 YES
34 PSMD7 PSMD7 PSMD7 6432 0.024 0.59 YES
35 PSMA3 PSMA3 PSMA3 6644 0.021 0.59 YES
36 POMP POMP POMP 6685 0.021 0.59 YES
37 PSME4 PSME4 PSME4 6795 0.02 0.59 YES
38 PSMA1 PSMA1 PSMA1 7198 0.015 0.58 NO
39 PSMB6 PSMB6 PSMB6 7312 0.014 0.58 NO
40 PSMA4 PSMA4 PSMA4 7988 0.0063 0.54 NO
41 PSMF1 PSMF1 PSMF1 9102 -0.0068 0.48 NO
42 PSMA8 PSMA8 PSMA8 12192 -0.045 0.34 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 PYRIMIDINE METABOLISM.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRIMIDINE 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 BASAL TRANSCRIPTION FACTORS

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 HSPA6 HSPA6 HSPA6 516 0.25 0.024 YES
2 THOC4 THOC4 THOC4 1214 0.16 0.02 YES
3 PPIH PPIH PPIH 2079 0.11 -0.0033 YES
4 LSM5 LSM5 LSM5 2128 0.11 0.017 YES
5 LSM6 LSM6 LSM6 2870 0.084 -0.0057 YES
6 ISY1 ISY1 ISY1 2917 0.083 0.0091 YES
7 PRPF4 PRPF4 PRPF4 2960 0.082 0.024 YES
8 MAGOH MAGOH MAGOH 3013 0.081 0.038 YES
9 SNRPG SNRPG SNRPG 3176 0.076 0.045 YES
10 EIF4A3 EIF4A3 EIF4A3 3190 0.076 0.06 YES
11 SNRPA1 SNRPA1 SNRPA1 3214 0.075 0.075 YES
12 EFTUD2 EFTUD2 EFTUD2 3331 0.073 0.084 YES
13 BCAS2 BCAS2 BCAS2 3338 0.072 0.099 YES
14 PHF5A PHF5A PHF5A 3404 0.071 0.11 YES
15 SNRNP40 SNRNP40 SNRNP40 3505 0.068 0.12 YES
16 BUD31 BUD31 BUD31 3529 0.068 0.13 YES
17 SF3B14 SF3B14 SF3B14 3547 0.068 0.14 YES
18 SNRPF SNRPF SNRPF 3606 0.066 0.16 YES
19 CTNNBL1 CTNNBL1 CTNNBL1 3616 0.066 0.17 YES
20 SNRPD1 SNRPD1 SNRPD1 3719 0.064 0.18 YES
21 PPIL1 PPIL1 PPIL1 3822 0.062 0.18 YES
22 SNRPD2 SNRPD2 SNRPD2 3836 0.062 0.2 YES
23 PLRG1 PLRG1 PLRG1 4034 0.058 0.2 YES
24 LSM7 LSM7 LSM7 4036 0.058 0.21 YES
25 WBP11 WBP11 WBP11 4048 0.058 0.22 YES
26 THOC3 THOC3 THOC3 4104 0.057 0.23 YES
27 MAGOHB MAGOHB MAGOHB 4176 0.056 0.24 YES
28 SF3A2 SF3A2 SF3A2 4237 0.054 0.25 YES
29 HSPA2 HSPA2 HSPA2 4295 0.054 0.26 YES
30 SNRPB SNRPB SNRPB 4352 0.053 0.26 YES
31 SMNDC1 SMNDC1 SMNDC1 4376 0.052 0.27 YES
32 SNRPC SNRPC SNRPC 4466 0.051 0.28 YES
33 SF3B4 SF3B4 SF3B4 4568 0.049 0.28 YES
34 HSPA1B HSPA1B HSPA1B 4596 0.049 0.29 YES
35 HSPA1A HSPA1A HSPA1A 4666 0.048 0.3 YES
36 SNRNP27 SNRNP27 SNRNP27 4767 0.046 0.3 YES
37 SFRS9 SFRS9 SFRS9 4852 0.045 0.31 YES
38 NAA38 NAA38 NAA38 4896 0.044 0.31 YES
39 SNW1 SNW1 SNW1 4901 0.044 0.32 YES
40 SART1 SART1 SART1 5002 0.043 0.33 YES
41 NCBP1 NCBP1 NCBP1 5005 0.043 0.34 YES
42 LSM2 LSM2 LSM2 5042 0.042 0.34 YES
43 USP39 USP39 USP39 5049 0.042 0.35 YES
44 LSM3 LSM3 LSM3 5057 0.042 0.36 YES
45 CHERP CHERP CHERP 5110 0.041 0.36 YES
46 SF3A3 SF3A3 SF3A3 5176 0.04 0.37 YES
47 PRPF19 PRPF19 PRPF19 5183 0.04 0.38 YES
48 PRPF38A PRPF38A PRPF38A 5370 0.037 0.38 YES
49 U2AF1 U2AF1 U2AF1 5442 0.036 0.38 YES
50 PUF60 PUF60 PUF60 5480 0.036 0.38 YES
51 CWC15 CWC15 CWC15 5497 0.036 0.39 YES
52 SR140 SR140 SR140 5540 0.035 0.4 YES
53 PRPF40A PRPF40A PRPF40A 5556 0.035 0.4 YES
54 HNRNPC HNRNPC HNRNPC 5867 0.031 0.39 YES
55 HSPA8 HSPA8 HSPA8 5904 0.031 0.4 YES
56 SNRPB2 SNRPB2 SNRPB2 5912 0.03 0.4 YES
57 U2AF2 U2AF2 U2AF2 5992 0.03 0.4 YES
58 RBM17 RBM17 RBM17 6004 0.029 0.41 YES
59 PRPF31 PRPF31 PRPF31 6045 0.029 0.41 YES
60 LSM4 LSM4 LSM4 6116 0.028 0.42 YES
61 SNRPA SNRPA SNRPA 6180 0.027 0.42 YES
62 THOC1 THOC1 THOC1 6307 0.025 0.42 YES
63 TRA2B TRA2B TRA2B 6309 0.025 0.42 YES
64 CDC5L CDC5L CDC5L 6513 0.023 0.42 NO
65 SF3B5 SF3B5 SF3B5 6631 0.022 0.41 NO
66 SNRPD3 SNRPD3 SNRPD3 6666 0.021 0.42 NO
67 SF3B2 SF3B2 SF3B2 6679 0.021 0.42 NO
68 DHX8 DHX8 DHX8 6775 0.02 0.42 NO
69 DDX23 DDX23 DDX23 6851 0.019 0.42 NO
70 SFRS2 SFRS2 SFRS2 6912 0.018 0.42 NO
71 XAB2 XAB2 XAB2 7109 0.016 0.41 NO
72 SNRPE SNRPE SNRPE 7153 0.016 0.41 NO
73 PPIE PPIE PPIE 7179 0.015 0.41 NO
74 SF3B3 SF3B3 SF3B3 7275 0.014 0.41 NO
75 PQBP1 PQBP1 PQBP1 7305 0.014 0.41 NO
76 SFRS7 SFRS7 SFRS7 7314 0.014 0.42 NO
77 SFRS3 SFRS3 SFRS3 7491 0.012 0.41 NO
78 HNRNPK HNRNPK HNRNPK 7547 0.011 0.41 NO
79 DHX15 DHX15 DHX15 7563 0.011 0.41 NO
80 PRPF3 PRPF3 PRPF3 7564 0.011 0.41 NO
81 RBM8A RBM8A RBM8A 7601 0.011 0.41 NO
82 HNRNPM HNRNPM HNRNPM 7628 0.01 0.41 NO
83 TCERG1 TCERG1 TCERG1 7839 0.008 0.4 NO
84 DHX16 DHX16 DHX16 8136 0.0045 0.39 NO
85 NHP2L1 NHP2L1 NHP2L1 8220 0.0036 0.38 NO
86 SNRNP200 SNRNP200 SNRNP200 8292 0.0027 0.38 NO
87 PCBP1 PCBP1 PCBP1 8310 0.0026 0.38 NO
88 SFRS1 SFRS1 SFRS1 8459 0.0011 0.37 NO
89 RBM22 RBM22 RBM22 8523 9e-05 0.37 NO
90 HNRNPU HNRNPU HNRNPU 8612 -0.0011 0.36 NO
91 DHX38 DHX38 DHX38 8724 -0.0024 0.36 NO
92 CDC40 CDC40 CDC40 8832 -0.0038 0.35 NO
93 RBMX RBMX RBMX 8932 -0.0049 0.35 NO
94 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 8950 -0.0052 0.35 NO
95 ZMAT2 ZMAT2 ZMAT2 9133 -0.0071 0.34 NO
96 SFRS13A SFRS13A SFRS13A 9183 -0.0077 0.34 NO
97 SFRS4 SFRS4 SFRS4 9186 -0.0077 0.34 NO
98 DDX42 DDX42 DDX42 9244 -0.0083 0.34 NO
99 PRPF6 PRPF6 PRPF6 9299 -0.009 0.34 NO
100 HNRNPA1 HNRNPA1 HNRNPA1 9402 -0.01 0.34 NO
101 TRA2A TRA2A TRA2A 9788 -0.014 0.32 NO
102 AQR AQR AQR 9882 -0.015 0.32 NO
103 HNRNPA3 HNRNPA3 HNRNPA3 10099 -0.018 0.31 NO
104 SF3A1 SF3A1 SF3A1 10191 -0.019 0.3 NO
105 RBM25 RBM25 RBM25 10209 -0.019 0.31 NO
106 PRPF38B PRPF38B PRPF38B 10225 -0.019 0.31 NO
107 TXNL4A TXNL4A TXNL4A 10279 -0.02 0.31 NO
108 THOC2 THOC2 THOC2 10367 -0.021 0.31 NO
109 DDX5 DDX5 DDX5 10670 -0.025 0.3 NO
110 BAT1 BAT1 BAT1 10707 -0.025 0.3 NO
111 HSPA1L HSPA1L HSPA1L 10813 -0.026 0.3 NO
112 CRNKL1 CRNKL1 CRNKL1 10837 -0.027 0.31 NO
113 PRPF18 PRPF18 PRPF18 10846 -0.027 0.31 NO
114 PRPF40B PRPF40B PRPF40B 10954 -0.028 0.31 NO
115 ACIN1 ACIN1 ACIN1 10978 -0.028 0.32 NO
116 SF3B1 SF3B1 SF3B1 11052 -0.029 0.32 NO
117 SYF2 SYF2 SYF2 11129 -0.03 0.32 NO
118 SLU7 SLU7 SLU7 11155 -0.03 0.33 NO
119 SNRNP70 SNRNP70 SNRNP70 11156 -0.03 0.33 NO
120 DDX46 DDX46 DDX46 11488 -0.035 0.32 NO
121 CCDC12 CCDC12 CCDC12 11496 -0.035 0.33 NO
122 SFRS6 SFRS6 SFRS6 11857 -0.04 0.32 NO
123 PRPF8 PRPF8 PRPF8 12458 -0.049 0.3 NO
124 SFRS2B SFRS2B SFRS2B 12648 -0.053 0.3 NO
125 SFRS5 SFRS5 SFRS5 13457 -0.069 0.27 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 BASAL TRANSCRIPTION FACTORS.

Figure S34.  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 DNA REPLICATION

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 UBE2C UBE2C UBE2C 43 0.45 0.056 YES
2 CDC20 CDC20 CDC20 171 0.36 0.096 YES
3 BRCA1 BRCA1 BRCA1 447 0.26 0.12 YES
4 UBE2S UBE2S UBE2S 555 0.24 0.14 YES
5 SKP2 SKP2 SKP2 631 0.23 0.17 YES
6 UBE2QL1 UBE2QL1 UBE2QL1 942 0.19 0.17 YES
7 NEDD4 NEDD4 NEDD4 1580 0.14 0.16 YES
8 NHLRC1 NHLRC1 NHLRC1 1675 0.13 0.17 YES
9 UBE2E2 UBE2E2 UBE2E2 1730 0.13 0.18 YES
10 SMURF2 SMURF2 SMURF2 1946 0.12 0.19 YES
11 UBE2L6 UBE2L6 UBE2L6 2032 0.12 0.2 YES
12 BIRC3 BIRC3 BIRC3 2237 0.11 0.2 YES
13 UBA6 UBA6 UBA6 2253 0.1 0.21 YES
14 CDC34 CDC34 CDC34 2317 0.1 0.22 YES
15 UBE2E3 UBE2E3 UBE2E3 2459 0.097 0.23 YES
16 PML PML PML 2936 0.082 0.21 YES
17 FANCL FANCL FANCL 3027 0.08 0.22 YES
18 UBE2D1 UBE2D1 UBE2D1 3357 0.072 0.21 YES
19 ANAPC11 ANAPC11 ANAPC11 3388 0.071 0.22 YES
20 RNF7 RNF7 RNF7 3544 0.068 0.22 YES
21 SOCS1 SOCS1 SOCS1 3603 0.067 0.22 YES
22 ERCC8 ERCC8 ERCC8 3648 0.066 0.23 YES
23 UBA2 UBA2 UBA2 3683 0.065 0.24 YES
24 CDC27 CDC27 CDC27 3745 0.064 0.24 YES
25 CUL2 CUL2 CUL2 3936 0.06 0.24 YES
26 UBE2F UBE2F UBE2F 4046 0.058 0.24 YES
27 CBL CBL CBL 4091 0.057 0.24 YES
28 BIRC2 BIRC2 BIRC2 4187 0.056 0.25 YES
29 CBLB CBLB CBLB 4212 0.055 0.25 YES
30 UBE2Z UBE2Z UBE2Z 4261 0.054 0.26 YES
31 ANAPC10 ANAPC10 ANAPC10 4351 0.053 0.26 YES
32 TCEB1 TCEB1 TCEB1 4430 0.051 0.26 YES
33 UBE2H UBE2H UBE2H 4490 0.05 0.26 YES
34 UBE3C UBE3C UBE3C 4560 0.049 0.27 YES
35 UBE2O UBE2O UBE2O 4721 0.047 0.26 YES
36 FBXO4 FBXO4 FBXO4 4743 0.047 0.27 YES
37 FZR1 FZR1 FZR1 4947 0.044 0.26 YES
38 UBE2R2 UBE2R2 UBE2R2 4959 0.043 0.27 YES
39 UBE2M UBE2M UBE2M 5060 0.042 0.27 YES
40 ITCH ITCH ITCH 5068 0.042 0.27 YES
41 CUL4B CUL4B CUL4B 5156 0.04 0.27 YES
42 PRPF19 PRPF19 PRPF19 5183 0.04 0.28 YES
43 FBXO2 FBXO2 FBXO2 5249 0.039 0.28 YES
44 UBE2I UBE2I UBE2I 5336 0.038 0.28 YES
45 ANAPC1 ANAPC1 ANAPC1 5377 0.037 0.28 YES
46 UBE2K UBE2K UBE2K 5379 0.037 0.29 YES
47 TCEB2 TCEB2 TCEB2 5538 0.035 0.28 NO
48 SMURF1 SMURF1 SMURF1 5664 0.034 0.28 NO
49 SAE1 SAE1 SAE1 5692 0.034 0.28 NO
50 FBXW8 FBXW8 FBXW8 5711 0.033 0.29 NO
51 UBE2NL UBE2NL UBE2NL 5978 0.03 0.28 NO
52 UBE2A UBE2A UBE2A 6144 0.027 0.27 NO
53 UBE2N UBE2N UBE2N 6335 0.025 0.26 NO
54 ANAPC7 ANAPC7 ANAPC7 6347 0.025 0.26 NO
55 STUB1 STUB1 STUB1 6393 0.024 0.27 NO
56 CUL1 CUL1 CUL1 6403 0.024 0.27 NO
57 RBX1 RBX1 RBX1 6422 0.024 0.27 NO
58 UBA3 UBA3 UBA3 6425 0.024 0.27 NO
59 UBE2D4 UBE2D4 UBE2D4 6454 0.024 0.28 NO
60 KLHL13 KLHL13 KLHL13 6509 0.023 0.28 NO
61 UBE2J2 UBE2J2 UBE2J2 6568 0.022 0.28 NO
62 TRIP12 TRIP12 TRIP12 6591 0.022 0.28 NO
63 CUL7 CUL7 CUL7 6612 0.022 0.28 NO
64 UBE2E1 UBE2E1 UBE2E1 6635 0.022 0.28 NO
65 PIAS4 PIAS4 PIAS4 6702 0.021 0.28 NO
66 UBE2L3 UBE2L3 UBE2L3 6714 0.021 0.28 NO
67 ANAPC5 ANAPC5 ANAPC5 6837 0.019 0.28 NO
68 ANAPC13 ANAPC13 ANAPC13 6952 0.018 0.27 NO
69 CDC26 CDC26 CDC26 7000 0.017 0.27 NO
70 UBE2D3 UBE2D3 UBE2D3 7019 0.017 0.27 NO
71 SOCS3 SOCS3 SOCS3 7032 0.017 0.28 NO
72 PIAS3 PIAS3 PIAS3 7550 0.011 0.25 NO
73 UBE2Q2 UBE2Q2 UBE2Q2 7587 0.011 0.25 NO
74 UBE4A UBE4A UBE4A 7696 0.0096 0.24 NO
75 UBR5 UBR5 UBR5 7928 0.0068 0.23 NO
76 UBA1 UBA1 UBA1 8003 0.0061 0.23 NO
77 DDB1 DDB1 DDB1 8147 0.0044 0.22 NO
78 UBE2W UBE2W UBE2W 8355 0.0021 0.21 NO
79 MID1 MID1 MID1 8387 0.0017 0.21 NO
80 UBE3B UBE3B UBE3B 8593 -0.0008 0.2 NO
81 CDC23 CDC23 CDC23 8631 -0.0014 0.2 NO
82 HUWE1 HUWE1 HUWE1 8710 -0.0022 0.19 NO
83 TRIM32 TRIM32 TRIM32 8884 -0.0044 0.18 NO
84 TRIM37 TRIM37 TRIM37 8901 -0.0046 0.18 NO
85 UBE2D2 UBE2D2 UBE2D2 8931 -0.0049 0.18 NO
86 HERC4 HERC4 HERC4 9217 -0.008 0.17 NO
87 KEAP1 KEAP1 KEAP1 9308 -0.0091 0.16 NO
88 ANAPC2 ANAPC2 ANAPC2 9354 -0.0096 0.16 NO
89 UBA7 UBA7 UBA7 9364 -0.0097 0.16 NO
90 PIAS2 PIAS2 PIAS2 9419 -0.01 0.16 NO
91 UBE2G1 UBE2G1 UBE2G1 9580 -0.012 0.15 NO
92 UBE2Q1 UBE2Q1 UBE2Q1 9597 -0.012 0.15 NO
93 HERC3 HERC3 HERC3 9599 -0.012 0.16 NO
94 UBE4B UBE4B UBE4B 9651 -0.013 0.15 NO
95 DDB2 DDB2 DDB2 9698 -0.013 0.15 NO
96 CUL3 CUL3 CUL3 9832 -0.015 0.15 NO
97 UBE2B UBE2B UBE2B 9956 -0.016 0.14 NO
98 UBE3A UBE3A UBE3A 9988 -0.016 0.14 NO
99 UBE2J1 UBE2J1 UBE2J1 10055 -0.017 0.14 NO
100 ANAPC4 ANAPC4 ANAPC4 10085 -0.018 0.14 NO
101 FBXW11 FBXW11 FBXW11 10218 -0.019 0.14 NO
102 CUL4A CUL4A CUL4A 10297 -0.02 0.14 NO
103 BIRC6 BIRC6 BIRC6 10317 -0.02 0.14 NO
104 CUL5 CUL5 CUL5 10326 -0.02 0.14 NO
105 KLHL9 KLHL9 KLHL9 10332 -0.02 0.14 NO
106 SIAH1 SIAH1 SIAH1 10503 -0.022 0.14 NO
107 FBXW7 FBXW7 FBXW7 10826 -0.027 0.12 NO
108 RCHY1 RCHY1 RCHY1 10968 -0.028 0.12 NO
109 PPIL2 PPIL2 PPIL2 10992 -0.028 0.12 NO
110 SKP1 SKP1 SKP1 11086 -0.03 0.12 NO
111 XIAP XIAP XIAP 11427 -0.034 0.1 NO
112 VHL VHL VHL 11432 -0.034 0.11 NO
113 RFWD2 RFWD2 RFWD2 11436 -0.034 0.11 NO
114 CDC16 CDC16 CDC16 11681 -0.038 0.1 NO
115 SYVN1 SYVN1 SYVN1 11847 -0.04 0.1 NO
116 UBE2G2 UBE2G2 UBE2G2 11871 -0.04 0.1 NO
117 MAP3K1 MAP3K1 MAP3K1 11916 -0.041 0.11 NO
118 PIAS1 PIAS1 PIAS1 12011 -0.042 0.11 NO
119 TRAF6 TRAF6 TRAF6 12159 -0.044 0.1 NO
120 UBOX5 UBOX5 UBOX5 12377 -0.048 0.1 NO
121 HERC2 HERC2 HERC2 12513 -0.05 0.099 NO
122 WWP1 WWP1 WWP1 12660 -0.053 0.098 NO
123 CBLC CBLC CBLC 12955 -0.058 0.089 NO
124 MGRN1 MGRN1 MGRN1 13315 -0.066 0.078 NO
125 MDM2 MDM2 MDM2 13831 -0.077 0.059 NO
126 WWP2 WWP2 WWP2 14360 -0.091 0.042 NO
127 HERC1 HERC1 HERC1 14798 -0.1 0.032 NO
128 DET1 DET1 DET1 15765 -0.14 -0.0027 NO
129 NEDD4L NEDD4L NEDD4L 16626 -0.2 -0.024 NO
130 AIRE AIRE AIRE 16973 -0.22 -0.015 NO
131 RHOBTB2 RHOBTB2 RHOBTB2 17532 -0.28 -0.009 NO
132 PARK2 PARK2 PARK2 18072 -0.39 0.012 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 DNA REPLICATION.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DNA REPLICATION, 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 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 CCNE1 CCNE1 CCNE1 50 0.44 0.036 YES
2 SGOL1 SGOL1 SGOL1 60 0.42 0.073 YES
3 PKMYT1 PKMYT1 PKMYT1 113 0.39 0.1 YES
4 CDC25C CDC25C CDC25C 134 0.38 0.14 YES
5 CDC20 CDC20 CDC20 171 0.36 0.17 YES
6 SMC1B SMC1B SMC1B 201 0.34 0.2 YES
7 ESPL1 ESPL1 ESPL1 206 0.34 0.23 YES
8 BUB1 BUB1 BUB1 232 0.33 0.26 YES
9 FBXO43 FBXO43 FBXO43 243 0.32 0.28 YES
10 PLK1 PLK1 PLK1 252 0.32 0.31 YES
11 MAD2L1 MAD2L1 MAD2L1 255 0.32 0.34 YES
12 CCNB2 CCNB2 CCNB2 257 0.32 0.37 YES
13 CCNE2 CCNE2 CCNE2 306 0.3 0.39 YES
14 CDK1 CDK1 CDK1 403 0.28 0.41 YES
15 CCNB1 CCNB1 CCNB1 493 0.26 0.43 YES
16 AURKA AURKA AURKA 642 0.23 0.44 YES
17 PTTG1 PTTG1 PTTG1 772 0.21 0.45 YES
18 FBXO5 FBXO5 FBXO5 855 0.2 0.46 YES
19 CALML5 CALML5 CALML5 891 0.2 0.48 YES
20 STAG3 STAG3 STAG3 1284 0.16 0.47 YES
21 MAD2L2 MAD2L2 MAD2L2 1333 0.16 0.48 YES
22 MAPK12 MAPK12 MAPK12 1906 0.12 0.46 NO
23 CDK2 CDK2 CDK2 1992 0.12 0.47 NO
24 PTTG2 PTTG2 PTTG2 2349 0.1 0.46 NO
25 YWHAG YWHAG YWHAG 2442 0.098 0.46 NO
26 PPP2R5B PPP2R5B PPP2R5B 2952 0.082 0.44 NO
27 ANAPC11 ANAPC11 ANAPC11 3388 0.071 0.42 NO
28 PPP2R5E PPP2R5E PPP2R5E 3412 0.071 0.43 NO
29 CDC27 CDC27 CDC27 3745 0.064 0.42 NO
30 YWHAQ YWHAQ YWHAQ 4138 0.056 0.4 NO
31 YWHAZ YWHAZ YWHAZ 4288 0.054 0.4 NO
32 ANAPC10 ANAPC10 ANAPC10 4351 0.053 0.4 NO
33 SPDYA SPDYA SPDYA 4916 0.044 0.37 NO
34 YWHAH YWHAH YWHAH 5149 0.04 0.36 NO
35 ANAPC1 ANAPC1 ANAPC1 5377 0.037 0.35 NO
36 SMC3 SMC3 SMC3 5882 0.031 0.33 NO
37 PPP1CC PPP1CC PPP1CC 6041 0.029 0.32 NO
38 PPP2R5D PPP2R5D PPP2R5D 6042 0.029 0.32 NO
39 CALM2 CALM2 CALM2 6217 0.027 0.32 NO
40 CALM3 CALM3 CALM3 6323 0.025 0.31 NO
41 ANAPC7 ANAPC7 ANAPC7 6347 0.025 0.31 NO
42 PPP1CB PPP1CB PPP1CB 6354 0.025 0.32 NO
43 CUL1 CUL1 CUL1 6403 0.024 0.32 NO
44 PPP2CA PPP2CA PPP2CA 6404 0.024 0.32 NO
45 MAP2K1 MAP2K1 MAP2K1 6406 0.024 0.32 NO
46 RBX1 RBX1 RBX1 6422 0.024 0.32 NO
47 YWHAB YWHAB YWHAB 6497 0.023 0.32 NO
48 PPP1CA PPP1CA PPP1CA 6503 0.023 0.32 NO
49 PRKACA PRKACA PRKACA 6523 0.023 0.32 NO
50 PPP3CA PPP3CA PPP3CA 6614 0.022 0.32 NO
51 ANAPC5 ANAPC5 ANAPC5 6837 0.019 0.31 NO
52 SMC1A SMC1A SMC1A 6919 0.018 0.3 NO
53 ANAPC13 ANAPC13 ANAPC13 6952 0.018 0.3 NO
54 PPP3R1 PPP3R1 PPP3R1 6973 0.018 0.3 NO
55 CDC26 CDC26 CDC26 7000 0.017 0.3 NO
56 CPEB1 CPEB1 CPEB1 7113 0.016 0.3 NO
57 SPDYC SPDYC SPDYC 7447 0.012 0.28 NO
58 YWHAE YWHAE YWHAE 8346 0.0021 0.23 NO
59 MAPK1 MAPK1 MAPK1 8557 -0.00036 0.22 NO
60 CDC23 CDC23 CDC23 8631 -0.0014 0.22 NO
61 PPP2R1A PPP2R1A PPP2R1A 8650 -0.0016 0.22 NO
62 CAMK2G CAMK2G CAMK2G 8963 -0.0054 0.2 NO
63 MAPK3 MAPK3 MAPK3 9118 -0.007 0.19 NO
64 ANAPC2 ANAPC2 ANAPC2 9354 -0.0096 0.18 NO
65 CAMK2A CAMK2A CAMK2A 9710 -0.013 0.16 NO
66 SLK SLK SLK 9894 -0.015 0.15 NO
67 PPP2R1B PPP2R1B PPP2R1B 10049 -0.017 0.15 NO
68 ANAPC4 ANAPC4 ANAPC4 10085 -0.018 0.15 NO
69 FBXW11 FBXW11 FBXW11 10218 -0.019 0.14 NO
70 CALM1 CALM1 CALM1 10222 -0.019 0.14 NO
71 CALML6 CALML6 CALML6 10428 -0.021 0.13 NO
72 PPP2R5C PPP2R5C PPP2R5C 10902 -0.027 0.11 NO
73 SKP1 SKP1 SKP1 11086 -0.03 0.1 NO
74 PPP3CB PPP3CB PPP3CB 11470 -0.035 0.085 NO
75 CAMK2D CAMK2D CAMK2D 11553 -0.036 0.083 NO
76 BTRC BTRC BTRC 11625 -0.037 0.083 NO
77 CDC16 CDC16 CDC16 11681 -0.038 0.083 NO
78 RPS6KA1 RPS6KA1 RPS6KA1 11799 -0.039 0.08 NO
79 PPP2CB PPP2CB PPP2CB 11901 -0.041 0.078 NO
80 RPS6KA3 RPS6KA3 RPS6KA3 11981 -0.042 0.077 NO
81 RPS6KA6 RPS6KA6 RPS6KA6 12360 -0.048 0.061 NO
82 ITPR3 ITPR3 ITPR3 12625 -0.052 0.051 NO
83 ADCY7 ADCY7 ADCY7 13082 -0.061 0.031 NO
84 ADCY8 ADCY8 ADCY8 13268 -0.065 0.027 NO
85 PRKX PRKX PRKX 13474 -0.07 0.022 NO
86 IGF1R IGF1R IGF1R 13546 -0.071 0.024 NO
87 ADCY1 ADCY1 ADCY1 13834 -0.077 0.015 NO
88 PPP3CC PPP3CC PPP3CC 13871 -0.078 0.02 NO
89 ITPR2 ITPR2 ITPR2 14120 -0.085 0.014 NO
90 IGF1 IGF1 IGF1 14250 -0.088 0.015 NO
91 PPP2R5A PPP2R5A PPP2R5A 14330 -0.09 0.018 NO
92 ADCY6 ADCY6 ADCY6 14351 -0.091 0.025 NO
93 CHP CHP CHP 14517 -0.096 0.025 NO
94 PRKACB PRKACB PRKACB 14724 -0.1 0.023 NO
95 CAMK2B CAMK2B CAMK2B 14749 -0.1 0.03 NO
96 ADCY9 ADCY9 ADCY9 14801 -0.1 0.037 NO
97 RPS6KA2 RPS6KA2 RPS6KA2 14966 -0.11 0.038 NO
98 CALML3 CALML3 CALML3 15141 -0.12 0.038 NO
99 REC8 REC8 REC8 15475 -0.13 0.032 NO
100 ADCY4 ADCY4 ADCY4 15719 -0.14 0.031 NO
101 CHP2 CHP2 CHP2 15771 -0.14 0.041 NO
102 ITPR1 ITPR1 ITPR1 16176 -0.17 0.034 NO
103 PGR PGR PGR 16416 -0.18 0.036 NO
104 ADCY5 ADCY5 ADCY5 16968 -0.22 0.026 NO
105 ADCY2 ADCY2 ADCY2 17130 -0.23 0.038 NO
106 AR AR AR 17667 -0.3 0.035 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 SPLICEOSOME.

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

genes ES table in pathway: KEGG PROTEASOME

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 CCNE1 CCNE1 CCNE1 50 0.44 0.057 YES
2 GTSE1 GTSE1 GTSE1 158 0.36 0.1 YES
3 PMAIP1 PMAIP1 PMAIP1 216 0.34 0.14 YES
4 CCNB2 CCNB2 CCNB2 257 0.32 0.18 YES
5 RRM2 RRM2 RRM2 282 0.31 0.23 YES
6 CHEK1 CHEK1 CHEK1 300 0.3 0.27 YES
7 CCNE2 CCNE2 CCNE2 306 0.3 0.31 YES
8 CDK1 CDK1 CDK1 403 0.28 0.34 YES
9 CCNB1 CCNB1 CCNB1 493 0.26 0.37 YES
10 CDKN2A CDKN2A CDKN2A 533 0.25 0.4 YES
11 SERPINE1 SERPINE1 SERPINE1 852 0.2 0.41 YES
12 GADD45A GADD45A GADD45A 910 0.19 0.44 YES
13 IGFBP3 IGFBP3 IGFBP3 1199 0.17 0.44 YES
14 FAS FAS FAS 1361 0.16 0.46 YES
15 CDK6 CDK6 CDK6 1524 0.14 0.46 YES
16 BID BID BID 1982 0.12 0.46 YES
17 CDK2 CDK2 CDK2 1992 0.12 0.47 YES
18 SFN SFN SFN 2310 0.1 0.47 YES
19 CDK4 CDK4 CDK4 2405 0.099 0.48 YES
20 CHEK2 CHEK2 CHEK2 2432 0.098 0.49 YES
21 PERP PERP PERP 2599 0.093 0.49 YES
22 THBS1 THBS1 THBS1 2736 0.089 0.5 YES
23 SERPINB5 SERPINB5 SERPINB5 3499 0.069 0.46 NO
24 TP73 TP73 TP73 3525 0.068 0.47 NO
25 CYCS CYCS CYCS 4158 0.056 0.45 NO
26 CCNG2 CCNG2 CCNG2 4724 0.047 0.42 NO
27 CDKN1A CDKN1A CDKN1A 4858 0.045 0.42 NO
28 CASP3 CASP3 CASP3 4982 0.043 0.42 NO
29 SHISA5 SHISA5 SHISA5 5413 0.037 0.4 NO
30 TP53I3 TP53I3 TP53I3 5468 0.036 0.4 NO
31 ATR ATR ATR 5911 0.03 0.38 NO
32 CCNB3 CCNB3 CCNB3 7029 0.017 0.32 NO
33 CASP8 CASP8 CASP8 7114 0.016 0.32 NO
34 APAF1 APAF1 APAF1 7349 0.013 0.31 NO
35 CCND1 CCND1 CCND1 7555 0.011 0.3 NO
36 EI24 EI24 EI24 7888 0.0073 0.28 NO
37 BAX BAX BAX 8325 0.0023 0.26 NO
38 SESN2 SESN2 SESN2 8563 -0.00043 0.25 NO
39 TNFRSF10B TNFRSF10B TNFRSF10B 8953 -0.0052 0.23 NO
40 CD82 CD82 CD82 9355 -0.0096 0.2 NO
41 DDB2 DDB2 DDB2 9698 -0.013 0.19 NO
42 ZMAT3 ZMAT3 ZMAT3 9994 -0.016 0.17 NO
43 PTEN PTEN PTEN 10071 -0.017 0.17 NO
44 CCND2 CCND2 CCND2 10403 -0.021 0.16 NO
45 SIAH1 SIAH1 SIAH1 10503 -0.022 0.16 NO
46 GADD45B GADD45B GADD45B 10515 -0.022 0.16 NO
47 RCHY1 RCHY1 RCHY1 10968 -0.028 0.14 NO
48 LRDD LRDD LRDD 11071 -0.03 0.14 NO
49 BBC3 BBC3 BBC3 11076 -0.03 0.14 NO
50 RFWD2 RFWD2 RFWD2 11436 -0.034 0.12 NO
51 ATM ATM ATM 11792 -0.039 0.11 NO
52 TP53AIP1 TP53AIP1 TP53AIP1 11818 -0.04 0.11 NO
53 TSC2 TSC2 TSC2 12251 -0.046 0.096 NO
54 CASP9 CASP9 CASP9 12398 -0.048 0.095 NO
55 PPM1D PPM1D PPM1D 13305 -0.066 0.054 NO
56 TP53 TP53 TP53 13635 -0.073 0.046 NO
57 MDM2 MDM2 MDM2 13831 -0.077 0.046 NO
58 SESN3 SESN3 SESN3 14237 -0.088 0.036 NO
59 IGF1 IGF1 IGF1 14250 -0.088 0.047 NO
60 CCNG1 CCNG1 CCNG1 14383 -0.092 0.052 NO
61 RRM2B RRM2B RRM2B 14490 -0.095 0.059 NO
62 CCND3 CCND3 CCND3 14944 -0.11 0.05 NO
63 MDM4 MDM4 MDM4 15293 -0.12 0.047 NO
64 SESN1 SESN1 SESN1 15810 -0.15 0.039 NO
65 RPRM RPRM RPRM 16466 -0.18 0.028 NO
66 BAI1 BAI1 BAI1 16561 -0.19 0.05 NO
67 GADD45G GADD45G GADD45G 17860 -0.34 0.024 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 PROTEASOME.

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

Fold change

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

Expression level

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

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.36 1.3 0.2 0.7 0.99 0.12 0.07 0.11 0.61 0.2
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.63 2.1 0.008 0.039 0.03 0.66 0.26 0.48 0 0.02
KEGG OXIDATIVE PHOSPHORYLATION 112 genes.ES.table 0.42 1.5 0.16 0.49 0.92 0.57 0.34 0.38 0.35 0.13
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 28 genes.ES.table 0.48 1.4 0.055 0.53 0.94 0.18 0.056 0.17 0.41 0.14
KEGG CYSTEINE AND METHIONINE METABOLISM 32 genes.ES.table 0.41 1.3 0.15 0.76 0.99 0.34 0.21 0.27 0.66 0.26
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.44 1.6 0.099 0.35 0.8 0.51 0.25 0.38 0.21 0.071
KEGG ARGININE AND PROLINE METABOLISM 52 genes.ES.table 0.5 1.6 0.026 0.4 0.8 0.31 0.14 0.27 0.24 0.096
KEGG HISTIDINE METABOLISM 28 genes.ES.table 0.58 1.6 0.029 0.46 0.8 0.29 0.056 0.27 0.28 0.13
KEGG TYROSINE METABOLISM 40 genes.ES.table 0.48 1.3 0.14 0.8 0.99 0.3 0.12 0.26 0.69 0.28
KEGG GLUTATHIONE METABOLISM 47 genes.ES.table 0.44 1.3 0.16 0.76 0.99 0.3 0.11 0.26 0.65 0.26
genes ES table in pathway: BIOCARTA WNT 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 PCK1 PCK1 PCK1 69 0.49 0.25 YES
2 IDH2 IDH2 IDH2 1241 0.15 0.27 YES
3 IDH1 IDH1 IDH1 2033 0.11 0.28 YES
4 SUCLG2 SUCLG2 SUCLG2 2409 0.092 0.31 YES
5 OGDHL OGDHL OGDHL 2455 0.09 0.36 YES
6 FH FH FH 2766 0.08 0.38 YES
7 SDHC SDHC SDHC 3189 0.07 0.39 YES
8 IDH3B IDH3B IDH3B 3445 0.064 0.41 YES
9 PDHB PDHB PDHB 3450 0.064 0.45 YES
10 PDHA1 PDHA1 PDHA1 3871 0.056 0.45 YES
11 PC PC PC 3987 0.054 0.48 YES
12 CS CS CS 4149 0.051 0.49 YES
13 DLAT DLAT DLAT 4159 0.051 0.52 YES
14 DLD DLD DLD 4223 0.05 0.54 YES
15 DLST DLST DLST 4231 0.05 0.57 YES
16 SUCLG1 SUCLG1 SUCLG1 4336 0.048 0.59 YES
17 IDH3A IDH3A IDH3A 4533 0.046 0.6 YES
18 SUCLA2 SUCLA2 SUCLA2 4553 0.045 0.62 YES
19 MDH2 MDH2 MDH2 4788 0.042 0.63 YES
20 ACLY ACLY ACLY 5288 0.035 0.62 NO
21 SDHA SDHA SDHA 5707 0.03 0.62 NO
22 PCK2 PCK2 PCK2 5880 0.028 0.62 NO
23 ACO2 ACO2 ACO2 6781 0.018 0.58 NO
24 MDH1 MDH1 MDH1 7752 0.0067 0.53 NO
25 SDHB SDHB SDHB 7848 0.0057 0.53 NO
26 IDH3G IDH3G IDH3G 8980 -0.0066 0.47 NO
27 ACO1 ACO1 ACO1 9393 -0.011 0.46 NO
28 SDHD SDHD SDHD 10072 -0.019 0.43 NO
29 OGDH OGDH OGDH 11573 -0.04 0.37 NO

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

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table 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 DARS2 DARS2 DARS2 1286 0.15 0.0083 YES
2 MARS2 MARS2 MARS2 1543 0.13 0.063 YES
3 SARS2 SARS2 SARS2 1687 0.12 0.12 YES
4 NARS2 NARS2 NARS2 2063 0.1 0.15 YES
5 NARS NARS NARS 2235 0.098 0.2 YES
6 AARS AARS AARS 2717 0.082 0.21 YES
7 MARS MARS MARS 2889 0.077 0.24 YES
8 TARSL2 TARSL2 TARSL2 2967 0.075 0.28 YES
9 PSTK PSTK PSTK 3298 0.067 0.3 YES
10 MTFMT MTFMT MTFMT 3338 0.066 0.33 YES
11 YARS2 YARS2 YARS2 3470 0.064 0.35 YES
12 IARS2 IARS2 IARS2 3593 0.061 0.38 YES
13 VARS VARS VARS 3716 0.059 0.4 YES
14 EPRS EPRS EPRS 4103 0.052 0.41 YES
15 EARS2 EARS2 EARS2 4283 0.049 0.43 YES
16 VARS2 VARS2 VARS2 4339 0.048 0.45 YES
17 PARS2 PARS2 PARS2 4653 0.044 0.45 YES
18 SEPSECS SEPSECS SEPSECS 4669 0.044 0.48 YES
19 LARS2 LARS2 LARS2 4843 0.041 0.49 YES
20 WARS2 WARS2 WARS2 5014 0.039 0.5 YES
21 IARS IARS IARS 5346 0.035 0.5 YES
22 TARS TARS TARS 5381 0.034 0.52 YES
23 CARS CARS CARS 5483 0.033 0.53 YES
24 GARS GARS GARS 5660 0.031 0.53 YES
25 HARS2 HARS2 HARS2 6014 0.026 0.53 YES
26 LARS LARS LARS 6103 0.025 0.54 YES
27 YARS YARS YARS 6294 0.023 0.54 YES
28 AARS2 AARS2 AARS2 6375 0.022 0.55 YES
29 FARSB FARSB FARSB 6390 0.022 0.56 YES
30 QARS QARS QARS 6715 0.019 0.55 NO
31 DARS DARS DARS 7115 0.014 0.54 NO
32 HARS HARS HARS 7803 0.0062 0.5 NO
33 KARS KARS KARS 8045 0.0033 0.49 NO
34 FARS2 FARS2 FARS2 8636 -0.0031 0.46 NO
35 CARS2 CARS2 CARS2 8872 -0.0055 0.45 NO
36 RARS2 RARS2 RARS2 9040 -0.0073 0.44 NO
37 FARSA FARSA FARSA 9270 -0.0096 0.44 NO
38 RARS RARS RARS 9555 -0.013 0.43 NO
39 WARS WARS WARS 11911 -0.045 0.32 NO
40 SARS SARS SARS 12372 -0.054 0.32 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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

Table 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 ACSS3 ACSS3 ACSS3 793 0.2 0.058 YES
2 ALDH3A2 ALDH3A2 ALDH3A2 815 0.2 0.16 YES
3 ACAT1 ACAT1 ACAT1 1604 0.13 0.18 YES
4 ALDH6A1 ALDH6A1 ALDH6A1 1802 0.12 0.22 YES
5 HIBCH HIBCH HIBCH 2108 0.1 0.26 YES
6 SUCLG2 SUCLG2 SUCLG2 2409 0.092 0.29 YES
7 MLYCD MLYCD MLYCD 2575 0.086 0.32 YES
8 MCEE MCEE MCEE 2832 0.078 0.34 YES
9 ACADM ACADM ACADM 3061 0.073 0.37 YES
10 PCCB PCCB PCCB 3068 0.073 0.4 YES
11 LDHAL6A LDHAL6A LDHAL6A 3233 0.069 0.43 YES
12 ACAT2 ACAT2 ACAT2 3386 0.065 0.45 YES
13 MUT MUT MUT 3462 0.064 0.48 YES
14 ACACB ACACB ACACB 3507 0.063 0.51 YES
15 ALDH2 ALDH2 ALDH2 3870 0.056 0.52 YES
16 ECHS1 ECHS1 ECHS1 3976 0.054 0.54 YES
17 SUCLG1 SUCLG1 SUCLG1 4336 0.048 0.54 YES
18 ACACA ACACA ACACA 4465 0.046 0.56 YES
19 ABAT ABAT ABAT 4499 0.046 0.58 YES
20 SUCLA2 SUCLA2 SUCLA2 4553 0.045 0.6 YES
21 ACSS1 ACSS1 ACSS1 4754 0.043 0.61 YES
22 PCCA PCCA PCCA 5295 0.035 0.6 NO
23 LDHB LDHB LDHB 6040 0.026 0.57 NO
24 HADHA HADHA HADHA 6560 0.02 0.55 NO
25 ALDH7A1 ALDH7A1 ALDH7A1 6727 0.019 0.55 NO
26 LDHAL6B LDHAL6B LDHAL6B 6877 0.017 0.55 NO
27 ALDH9A1 ALDH9A1 ALDH9A1 7066 0.015 0.55 NO
28 LDHA LDHA LDHA 8943 -0.0062 0.45 NO
29 ACSS2 ACSS2 ACSS2 8945 -0.0062 0.45 NO
30 ALDH1B1 ALDH1B1 ALDH1B1 12038 -0.048 0.31 NO
31 EHHADH EHHADH EHHADH 13083 -0.07 0.29 NO

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

Figure S46.  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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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 ENO3 ENO3 ENO3 13 0.68 0.26 YES
2 HSPD1 HSPD1 HSPD1 2009 0.11 0.19 YES
3 PAPOLA PAPOLA PAPOLA 2059 0.1 0.23 YES
4 PAPOLB PAPOLB PAPOLB 2560 0.087 0.23 YES
5 PNPT1 PNPT1 PNPT1 2704 0.082 0.26 YES
6 CNOT7 CNOT7 CNOT7 3006 0.074 0.27 YES
7 HSPA9 HSPA9 HSPA9 3031 0.073 0.29 YES
8 LSM1 LSM1 LSM1 3176 0.07 0.31 YES
9 CNOT2 CNOT2 CNOT2 3311 0.067 0.33 YES
10 EXOSC1 EXOSC1 EXOSC1 3512 0.063 0.34 YES
11 EXOSC8 EXOSC8 EXOSC8 3873 0.056 0.34 YES
12 EXOSC4 EXOSC4 EXOSC4 4108 0.052 0.35 YES
13 LSM4 LSM4 LSM4 4272 0.05 0.36 YES
14 CNOT3 CNOT3 CNOT3 4399 0.048 0.37 YES
15 XRN2 XRN2 XRN2 4649 0.044 0.38 YES
16 WDR61 WDR61 WDR61 4745 0.043 0.39 YES
17 EDC4 EDC4 EDC4 5186 0.037 0.38 YES
18 EXOSC3 EXOSC3 EXOSC3 5188 0.037 0.39 YES
19 LSM2 LSM2 LSM2 5208 0.036 0.4 YES
20 EXOSC6 EXOSC6 EXOSC6 5252 0.036 0.41 YES
21 NAA38 NAA38 NAA38 5257 0.036 0.43 YES
22 PARN PARN PARN 5279 0.036 0.44 YES
23 EXOSC5 EXOSC5 EXOSC5 6109 0.025 0.4 NO
24 EDC3 EDC3 EDC3 6336 0.023 0.4 NO
25 TTC37 TTC37 TTC37 6345 0.023 0.41 NO
26 CNOT1 CNOT1 CNOT1 6593 0.02 0.4 NO
27 C1D C1D C1D 6670 0.019 0.4 NO
28 CNOT6 CNOT6 CNOT6 6671 0.019 0.41 NO
29 MPHOSPH6 MPHOSPH6 MPHOSPH6 6744 0.018 0.42 NO
30 DCP1B DCP1B DCP1B 6820 0.018 0.42 NO
31 PATL1 PATL1 PATL1 6905 0.017 0.42 NO
32 RQCD1 RQCD1 RQCD1 6974 0.016 0.42 NO
33 ZCCHC7 ZCCHC7 ZCCHC7 7407 0.011 0.4 NO
34 EXOSC2 EXOSC2 EXOSC2 7541 0.0091 0.4 NO
35 CNOT10 CNOT10 CNOT10 7596 0.0084 0.4 NO
36 DCP1A DCP1A DCP1A 7880 0.0053 0.39 NO
37 EXOSC7 EXOSC7 EXOSC7 8103 0.0027 0.38 NO
38 DDX6 DDX6 DDX6 8163 0.0021 0.37 NO
39 DCPS DCPS DCPS 8651 -0.0032 0.35 NO
40 SKIV2L2 SKIV2L2 SKIV2L2 8721 -0.004 0.34 NO
41 EXOSC10 EXOSC10 EXOSC10 8834 -0.0051 0.34 NO
42 SKIV2L SKIV2L SKIV2L 9001 -0.0069 0.33 NO
43 CNOT6L CNOT6L CNOT6L 9123 -0.0081 0.33 NO
44 LSM3 LSM3 LSM3 9203 -0.0088 0.33 NO
45 PAPOLG PAPOLG PAPOLG 9592 -0.013 0.31 NO
46 DIS3 DIS3 DIS3 9624 -0.014 0.32 NO
47 PAPD7 PAPD7 PAPD7 9814 -0.016 0.31 NO
48 XRN1 XRN1 XRN1 10253 -0.021 0.3 NO
49 LSM7 LSM7 LSM7 10448 -0.024 0.3 NO
50 LSM5 LSM5 LSM5 11002 -0.032 0.28 NO
51 EXOSC9 EXOSC9 EXOSC9 11020 -0.032 0.29 NO
52 CNOT4 CNOT4 CNOT4 11022 -0.032 0.3 NO
53 ENO1 ENO1 ENO1 12591 -0.058 0.24 NO
54 DCP2 DCP2 DCP2 12717 -0.061 0.25 NO
55 ENO2 ENO2 ENO2 12981 -0.068 0.26 NO
56 LSM6 LSM6 LSM6 13185 -0.073 0.28 NO

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

Figure S48.  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 CYSTEINE AND METHIONINE METABOLISM

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 PCK1 PCK1 PCK1 69 0.49 0.18 YES
2 LDHD LDHD LDHD 506 0.26 0.25 YES
3 ME1 ME1 ME1 679 0.22 0.32 YES
4 ALDH3A2 ALDH3A2 ALDH3A2 815 0.2 0.39 YES
5 ACAT1 ACAT1 ACAT1 1604 0.13 0.39 YES
6 ACYP1 ACYP1 ACYP1 2887 0.077 0.35 YES
7 PKLR PKLR PKLR 3154 0.071 0.36 YES
8 LDHAL6A LDHAL6A LDHAL6A 3233 0.069 0.38 YES
9 ACAT2 ACAT2 ACAT2 3386 0.065 0.4 YES
10 PDHB PDHB PDHB 3450 0.064 0.42 YES
11 ACACB ACACB ACACB 3507 0.063 0.44 YES
12 ALDH2 ALDH2 ALDH2 3870 0.056 0.44 YES
13 PDHA1 PDHA1 PDHA1 3871 0.056 0.46 YES
14 PC PC PC 3987 0.054 0.47 YES
15 DLAT DLAT DLAT 4159 0.051 0.48 YES
16 DLD DLD DLD 4223 0.05 0.5 YES
17 ACACA ACACA ACACA 4465 0.046 0.5 YES
18 ACSS1 ACSS1 ACSS1 4754 0.043 0.5 YES
19 MDH2 MDH2 MDH2 4788 0.042 0.52 YES
20 HAGH HAGH HAGH 5561 0.032 0.49 NO
21 PCK2 PCK2 PCK2 5880 0.028 0.48 NO
22 LDHB LDHB LDHB 6040 0.026 0.48 NO
23 ALDH7A1 ALDH7A1 ALDH7A1 6727 0.019 0.45 NO
24 LDHAL6B LDHAL6B LDHAL6B 6877 0.017 0.45 NO
25 ALDH9A1 ALDH9A1 ALDH9A1 7066 0.015 0.44 NO
26 MDH1 MDH1 MDH1 7752 0.0067 0.41 NO
27 LDHA LDHA LDHA 8943 -0.0062 0.34 NO
28 ACSS2 ACSS2 ACSS2 8945 -0.0062 0.35 NO
29 GRHPR GRHPR GRHPR 9016 -0.0071 0.34 NO
30 ACYP2 ACYP2 ACYP2 9837 -0.016 0.31 NO
31 AKR1B1 AKR1B1 AKR1B1 10401 -0.023 0.28 NO
32 ME3 ME3 ME3 10704 -0.028 0.28 NO
33 PKM2 PKM2 PKM2 10731 -0.028 0.29 NO
34 ALDH1B1 ALDH1B1 ALDH1B1 12038 -0.048 0.23 NO
35 GLO1 GLO1 GLO1 12531 -0.057 0.23 NO
36 ME2 ME2 ME2 12972 -0.067 0.23 NO
37 HAGHL HAGHL HAGHL 16038 -0.17 0.12 NO

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

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

genes ES table in pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION

Table 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 DDC DDC DDC 22 0.64 0.15 YES
2 HAL HAL HAL 37 0.57 0.29 YES
3 ABP1 ABP1 ABP1 147 0.4 0.38 YES
4 ALDH3A1 ALDH3A1 ALDH3A1 565 0.24 0.41 YES
5 ALDH3B2 ALDH3B2 ALDH3B2 604 0.24 0.46 YES
6 MAOA MAOA MAOA 699 0.22 0.51 YES
7 ALDH3A2 ALDH3A2 ALDH3A2 815 0.2 0.55 YES
8 ACY3 ACY3 ACY3 1024 0.17 0.58 YES
9 ALDH3B1 ALDH3B1 ALDH3B1 1898 0.11 0.56 NO
10 AMDHD1 AMDHD1 AMDHD1 2728 0.082 0.54 NO
11 ALDH2 ALDH2 ALDH2 3870 0.056 0.48 NO
12 LCMT2 LCMT2 LCMT2 5225 0.036 0.42 NO
13 WBSCR22 WBSCR22 WBSCR22 6000 0.027 0.38 NO
14 ALDH7A1 ALDH7A1 ALDH7A1 6727 0.019 0.35 NO
15 ALDH9A1 ALDH9A1 ALDH9A1 7066 0.015 0.33 NO
16 LCMT1 LCMT1 LCMT1 7201 0.013 0.33 NO
17 METTL6 METTL6 METTL6 8407 -0.00039 0.26 NO
18 HEMK1 HEMK1 HEMK1 10006 -0.018 0.18 NO
19 METTL2B METTL2B METTL2B 10367 -0.023 0.17 NO
20 TRMT11 TRMT11 TRMT11 10447 -0.024 0.17 NO
21 ASPA ASPA ASPA 11766 -0.043 0.11 NO
22 ALDH1B1 ALDH1B1 ALDH1B1 12038 -0.048 0.1 NO
23 FTCD FTCD FTCD 12600 -0.058 0.085 NO
24 MAOB MAOB MAOB 13914 -0.092 0.035 NO
25 HNMT HNMT HNMT 14387 -0.11 0.035 NO
26 UROC1 UROC1 UROC1 15376 -0.14 0.014 NO
27 ALDH1A3 ALDH1A3 ALDH1A3 17322 -0.26 -0.031 NO
28 HDC HDC HDC 17994 -0.36 0.017 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: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S52.  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 ARGININE AND PROLINE METABOLISM

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 CPS1 CPS1 CPS1 12 0.69 0.11 YES
2 ABP1 ABP1 ABP1 147 0.4 0.17 YES
3 ODC1 ODC1 ODC1 180 0.38 0.23 YES
4 CKMT1A CKMT1A CKMT1A 205 0.36 0.29 YES
5 AGMAT AGMAT AGMAT 226 0.35 0.34 YES
6 CKMT1B CKMT1B CKMT1B 244 0.34 0.4 YES
7 MAOA MAOA MAOA 699 0.22 0.41 YES
8 ALDH3A2 ALDH3A2 ALDH3A2 815 0.2 0.43 YES
9 OAT OAT OAT 832 0.2 0.46 YES
10 ARG2 ARG2 ARG2 863 0.19 0.49 YES
11 GOT1 GOT1 GOT1 1744 0.12 0.46 YES
12 PYCR1 PYCR1 PYCR1 1844 0.11 0.48 YES
13 ALDH18A1 ALDH18A1 ALDH18A1 1934 0.11 0.49 YES
14 NOS2 NOS2 NOS2 2217 0.099 0.49 YES
15 NOS3 NOS3 NOS3 2538 0.088 0.49 YES
16 NOS1 NOS1 NOS1 2553 0.087 0.5 YES
17 SAT2 SAT2 SAT2 2852 0.078 0.5 NO
18 ACY1 ACY1 ACY1 3192 0.07 0.49 NO
19 GLS2 GLS2 GLS2 3408 0.065 0.49 NO
20 ALDH2 ALDH2 ALDH2 3870 0.056 0.47 NO
21 GOT2 GOT2 GOT2 3889 0.055 0.48 NO
22 DAO DAO DAO 4143 0.052 0.48 NO
23 ARG1 ARG1 ARG1 4494 0.046 0.46 NO
24 PYCRL PYCRL PYCRL 5089 0.038 0.44 NO
25 P4HA3 P4HA3 P4HA3 5291 0.035 0.43 NO
26 ALDH4A1 ALDH4A1 ALDH4A1 6295 0.023 0.38 NO
27 GLUL GLUL GLUL 6503 0.021 0.37 NO
28 PYCR2 PYCR2 PYCR2 6696 0.019 0.37 NO
29 ALDH7A1 ALDH7A1 ALDH7A1 6727 0.019 0.37 NO
30 SRM SRM SRM 6760 0.018 0.37 NO
31 ALDH9A1 ALDH9A1 ALDH9A1 7066 0.015 0.35 NO
32 AMD1 AMD1 AMD1 8215 0.0015 0.29 NO
33 P4HA1 P4HA1 P4HA1 8934 -0.0062 0.25 NO
34 GLUD2 GLUD2 GLUD2 9239 -0.0091 0.24 NO
35 GLUD1 GLUD1 GLUD1 9260 -0.0095 0.24 NO
36 SMS SMS SMS 10460 -0.024 0.18 NO
37 CKM CKM CKM 11195 -0.034 0.14 NO
38 PRODH PRODH PRODH 11937 -0.046 0.11 NO
39 ALDH1B1 ALDH1B1 ALDH1B1 12038 -0.048 0.11 NO
40 CKB CKB CKB 12274 -0.052 0.11 NO
41 ASS1 ASS1 ASS1 12330 -0.053 0.11 NO
42 ASL ASL ASL 12553 -0.058 0.11 NO
43 CKMT2 CKMT2 CKMT2 12810 -0.063 0.11 NO
44 LAP3 LAP3 LAP3 13079 -0.07 0.1 NO
45 OTC OTC OTC 13467 -0.08 0.094 NO
46 P4HA2 P4HA2 P4HA2 13863 -0.09 0.087 NO
47 MAOB MAOB MAOB 13914 -0.092 0.1 NO
48 GATM GATM GATM 14497 -0.11 0.085 NO
49 GAMT GAMT GAMT 15838 -0.16 0.038 NO
50 ADC ADC ADC 15906 -0.16 0.061 NO
51 GLS GLS GLS 16764 -0.21 0.049 NO
52 NAGS NAGS NAGS 16802 -0.22 0.082 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: KEGG ARGININE AND PROLINE METABOLISM.

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

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 HMGCS2 HMGCS2 HMGCS2 146 0.4 0.12 YES
2 ALDH3A2 ALDH3A2 ALDH3A2 815 0.2 0.16 YES
3 OXCT2 OXCT2 OXCT2 1374 0.14 0.17 YES
4 ACAT1 ACAT1 ACAT1 1604 0.13 0.2 YES
5 ALDH6A1 ALDH6A1 ALDH6A1 1802 0.12 0.23 YES
6 MCCC2 MCCC2 MCCC2 2055 0.1 0.25 YES
7 HIBCH HIBCH HIBCH 2108 0.1 0.28 YES
8 ACADSB ACADSB ACADSB 2634 0.084 0.28 YES
9 MCEE MCEE MCEE 2832 0.078 0.29 YES
10 ACADM ACADM ACADM 3061 0.073 0.3 YES
11 PCCB PCCB PCCB 3068 0.073 0.33 YES
12 ACAT2 ACAT2 ACAT2 3386 0.065 0.33 YES
13 BCAT2 BCAT2 BCAT2 3395 0.065 0.35 YES
14 MUT MUT MUT 3462 0.064 0.37 YES
15 BCKDHB BCKDHB BCKDHB 3668 0.06 0.38 YES
16 ALDH2 ALDH2 ALDH2 3870 0.056 0.39 YES
17 AUH AUH AUH 3942 0.054 0.4 YES
18 ECHS1 ECHS1 ECHS1 3976 0.054 0.42 YES
19 DLD DLD DLD 4223 0.05 0.42 YES
20 ABAT ABAT ABAT 4499 0.046 0.42 YES
21 HSD17B10 HSD17B10 HSD17B10 4650 0.044 0.43 YES
22 AOX1 AOX1 AOX1 4652 0.044 0.44 YES
23 HADHB HADHB HADHB 4985 0.039 0.44 NO
24 PCCA PCCA PCCA 5295 0.035 0.43 NO
25 HADHA HADHA HADHA 6560 0.02 0.37 NO
26 ALDH7A1 ALDH7A1 ALDH7A1 6727 0.019 0.36 NO
27 ACADS ACADS ACADS 6923 0.016 0.36 NO
28 HMGCS1 HMGCS1 HMGCS1 6977 0.016 0.36 NO
29 ACAA2 ACAA2 ACAA2 6985 0.016 0.37 NO
30 ALDH9A1 ALDH9A1 ALDH9A1 7066 0.015 0.37 NO
31 DBT DBT DBT 7258 0.012 0.36 NO
32 MCCC1 MCCC1 MCCC1 7314 0.012 0.36 NO
33 BCKDHA BCKDHA BCKDHA 8209 0.0016 0.31 NO
34 HMGCL HMGCL HMGCL 8931 -0.0061 0.28 NO
35 HADH HADH HADH 9003 -0.0069 0.28 NO
36 IVD IVD IVD 9381 -0.011 0.26 NO
37 ACAA1 ACAA1 ACAA1 10526 -0.025 0.2 NO
38 ALDH1B1 ALDH1B1 ALDH1B1 12038 -0.048 0.14 NO
39 HIBADH HIBADH HIBADH 12564 -0.058 0.13 NO
40 EHHADH EHHADH EHHADH 13083 -0.07 0.12 NO
41 ACAD8 ACAD8 ACAD8 15556 -0.15 0.035 NO
42 OXCT1 OXCT1 OXCT1 15876 -0.16 0.071 NO
43 IL4I1 IL4I1 IL4I1 16319 -0.19 0.11 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: KEGG HISTIDINE METABOLISM.

Figure S56.  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 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 UGT2B4 UGT2B4 UGT2B4 45 0.54 0.18 YES
2 UGT2B11 UGT2B11 UGT2B11 523 0.25 0.25 YES
3 UGT1A1 UGT1A1 UGT1A1 634 0.23 0.32 YES
4 FECH FECH FECH 956 0.18 0.36 YES
5 UGT2B28 UGT2B28 UGT2B28 969 0.18 0.42 YES
6 UGT2B15 UGT2B15 UGT2B15 1062 0.17 0.48 YES
7 UGT1A9 UGT1A9 UGT1A9 1500 0.13 0.5 YES
8 UGT2B10 UGT2B10 UGT2B10 1965 0.11 0.51 YES
9 UGT1A6 UGT1A6 UGT1A6 2026 0.11 0.54 YES
10 COX10 COX10 COX10 2305 0.095 0.56 YES
11 COX15 COX15 COX15 2699 0.082 0.57 YES
12 UGT2A1 UGT2A1 UGT2A1 2724 0.082 0.6 YES
13 MMAB MMAB MMAB 3129 0.071 0.6 YES
14 UGT2B7 UGT2B7 UGT2B7 3422 0.065 0.6 YES
15 EPRS EPRS EPRS 4103 0.052 0.58 NO
16 EARS2 EARS2 EARS2 4283 0.049 0.59 NO
17 HMBS HMBS HMBS 5773 0.029 0.52 NO
18 ALAS1 ALAS1 ALAS1 5905 0.028 0.52 NO
19 UGT1A10 UGT1A10 UGT1A10 6434 0.022 0.5 NO
20 ALAS2 ALAS2 ALAS2 6821 0.018 0.49 NO
21 ALAD ALAD ALAD 7251 0.012 0.47 NO
22 PPOX PPOX PPOX 7591 0.0085 0.45 NO
23 CP CP CP 7685 0.0073 0.45 NO
24 UROS UROS UROS 8962 -0.0064 0.38 NO
25 CPOX CPOX CPOX 9292 -0.0098 0.37 NO
26 GUSB GUSB GUSB 9510 -0.013 0.36 NO
27 FTH1 FTH1 FTH1 9854 -0.016 0.35 NO
28 BLVRB BLVRB BLVRB 10328 -0.022 0.33 NO
29 HMOX1 HMOX1 HMOX1 13346 -0.077 0.19 NO
30 BLVRA BLVRA BLVRA 13377 -0.077 0.21 NO
31 UROD UROD UROD 13485 -0.08 0.24 NO
32 HMOX2 HMOX2 HMOX2 13587 -0.082 0.26 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: KEGG TYROSINE METABOLISM.

Figure S58.  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 GLUTATHIONE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ATP6V1B1 ATP6V1B1 ATP6V1B1 113 0.43 0.065 YES
2 ATP6V0A4 ATP6V0A4 ATP6V0A4 500 0.26 0.087 YES
3 ATP4B ATP4B ATP4B 538 0.25 0.13 YES
4 ATP6V1C2 ATP6V1C2 ATP6V1C2 560 0.24 0.16 YES
5 NDUFA4L2 NDUFA4L2 NDUFA4L2 1343 0.14 0.15 YES
6 NDUFS1 NDUFS1 NDUFS1 1895 0.11 0.13 YES
7 NDUFV2 NDUFV2 NDUFV2 1976 0.11 0.15 YES
8 COX4I2 COX4I2 COX4I2 2000 0.11 0.16 YES
9 COX6A1 COX6A1 COX6A1 2253 0.098 0.17 YES
10 CYC1 CYC1 CYC1 2260 0.097 0.18 YES
11 COX5A COX5A COX5A 2283 0.096 0.2 YES
12 COX10 COX10 COX10 2305 0.095 0.21 YES
13 COX17 COX17 COX17 2513 0.088 0.21 YES
14 COX15 COX15 COX15 2699 0.082 0.22 YES
15 COX6C COX6C COX6C 2779 0.08 0.23 YES
16 UQCRB UQCRB UQCRB 2843 0.078 0.24 YES
17 NDUFA9 NDUFA9 NDUFA9 2890 0.077 0.25 YES
18 COX7A2 COX7A2 COX7A2 2917 0.076 0.26 YES
19 ATP5G1 ATP5G1 ATP5G1 2951 0.075 0.27 YES
20 ATP5B ATP5B ATP5B 2975 0.074 0.28 YES
21 NDUFA10 NDUFA10 NDUFA10 3042 0.073 0.29 YES
22 ATP5A1 ATP5A1 ATP5A1 3063 0.073 0.3 YES
23 NDUFB9 NDUFB9 NDUFB9 3127 0.071 0.31 YES
24 ATP5G3 ATP5G3 ATP5G3 3137 0.071 0.32 YES
25 SDHC SDHC SDHC 3189 0.07 0.33 YES
26 NDUFS2 NDUFS2 NDUFS2 3226 0.069 0.34 YES
27 COX5B COX5B COX5B 3360 0.066 0.34 YES
28 LHPP LHPP LHPP 3394 0.065 0.35 YES
29 ATP6V1G2 ATP6V1G2 ATP6V1G2 3455 0.064 0.36 YES
30 UQCRHL UQCRHL UQCRHL 3618 0.06 0.36 YES
31 UQCRFS1 UQCRFS1 UQCRFS1 3754 0.058 0.36 YES
32 NDUFA8 NDUFA8 NDUFA8 3886 0.055 0.36 YES
33 NDUFB8 NDUFB8 NDUFB8 3953 0.054 0.37 YES
34 ATP5C1 ATP5C1 ATP5C1 4206 0.05 0.36 YES
35 COX7B COX7B COX7B 4321 0.049 0.36 YES
36 COX6B1 COX6B1 COX6B1 4368 0.048 0.37 YES
37 UQCRH UQCRH UQCRH 4380 0.048 0.38 YES
38 ATP6V1H ATP6V1H ATP6V1H 4489 0.046 0.38 YES
39 ATP6V1E2 ATP6V1E2 ATP6V1E2 4622 0.044 0.38 YES
40 NDUFB3 NDUFB3 NDUFB3 4629 0.044 0.38 YES
41 ATP5G2 ATP5G2 ATP5G2 4643 0.044 0.39 YES
42 UQCRC2 UQCRC2 UQCRC2 4675 0.044 0.4 YES
43 UQCRQ UQCRQ UQCRQ 4866 0.041 0.39 YES
44 NDUFA1 NDUFA1 NDUFA1 4899 0.04 0.4 YES
45 UQCRC1 UQCRC1 UQCRC1 5141 0.037 0.39 YES
46 COX8A COX8A COX8A 5267 0.036 0.39 YES
47 NDUFA7 NDUFA7 NDUFA7 5276 0.036 0.39 YES
48 NDUFA5 NDUFA5 NDUFA5 5289 0.035 0.4 YES
49 NDUFC2 NDUFC2 NDUFC2 5292 0.035 0.4 YES
50 NDUFAB1 NDUFAB1 NDUFAB1 5367 0.034 0.41 YES
51 COX4I1 COX4I1 COX4I1 5471 0.033 0.41 YES
52 COX7C COX7C COX7C 5489 0.033 0.41 YES
53 ATP5E ATP5E ATP5E 5651 0.031 0.41 YES
54 NDUFV1 NDUFV1 NDUFV1 5703 0.03 0.41 YES
55 SDHA SDHA SDHA 5707 0.03 0.41 YES
56 NDUFB1 NDUFB1 NDUFB1 5739 0.03 0.42 YES
57 ATP6V0A2 ATP6V0A2 ATP6V0A2 5805 0.029 0.42 YES
58 PPA2 PPA2 PPA2 5863 0.028 0.42 YES
59 COX7A2L COX7A2L COX7A2L 6033 0.026 0.42 YES
60 ATP6V1G1 ATP6V1G1 ATP6V1G1 6088 0.026 0.42 YES
61 ATP6AP1 ATP6AP1 ATP6AP1 6148 0.025 0.42 YES
62 ATP5J2 ATP5J2 ATP5J2 6157 0.025 0.42 YES
63 ATP6V1C1 ATP6V1C1 ATP6V1C1 6226 0.024 0.42 YES
64 NDUFS5 NDUFS5 NDUFS5 6283 0.023 0.42 YES
65 NDUFA3 NDUFA3 NDUFA3 6438 0.022 0.42 NO
66 NDUFS6 NDUFS6 NDUFS6 6522 0.021 0.42 NO
67 ATP6V0B ATP6V0B ATP6V0B 6536 0.02 0.42 NO
68 NDUFB4 NDUFB4 NDUFB4 7050 0.015 0.39 NO
69 NDUFS8 NDUFS8 NDUFS8 7104 0.014 0.39 NO
70 NDUFC1 NDUFC1 NDUFC1 7126 0.014 0.39 NO
71 NDUFS3 NDUFS3 NDUFS3 7147 0.014 0.39 NO
72 ATP5I ATP5I ATP5I 7533 0.0092 0.37 NO
73 ATP5D ATP5D ATP5D 7589 0.0085 0.37 NO
74 NDUFA4 NDUFA4 NDUFA4 7768 0.0065 0.36 NO
75 SDHB SDHB SDHB 7848 0.0057 0.36 NO
76 NDUFB6 NDUFB6 NDUFB6 7885 0.0053 0.36 NO
77 ATP5L ATP5L ATP5L 8013 0.0037 0.35 NO
78 PPA1 PPA1 PPA1 8020 0.0036 0.35 NO
79 COX11 COX11 COX11 8134 0.0024 0.35 NO
80 ATP5J ATP5J ATP5J 8149 0.0023 0.35 NO
81 ATP6V1A ATP6V1A ATP6V1A 8258 0.001 0.34 NO
82 ATP5F1 ATP5F1 ATP5F1 8299 0.00066 0.34 NO
83 NDUFB10 NDUFB10 NDUFB10 8584 -0.0025 0.32 NO
84 NDUFA2 NDUFA2 NDUFA2 8634 -0.0031 0.32 NO
85 NDUFS4 NDUFS4 NDUFS4 8716 -0.0039 0.32 NO
86 TCIRG1 TCIRG1 TCIRG1 8814 -0.0049 0.31 NO
87 COX6B2 COX6B2 COX6B2 9603 -0.014 0.27 NO
88 NDUFB2 NDUFB2 NDUFB2 9694 -0.015 0.27 NO
89 NDUFV3 NDUFV3 NDUFV3 9832 -0.016 0.26 NO
90 ATP6V1E1 ATP6V1E1 ATP6V1E1 9964 -0.018 0.26 NO
91 ATP6V0C ATP6V0C ATP6V0C 10010 -0.018 0.26 NO
92 SDHD SDHD SDHD 10072 -0.019 0.26 NO
93 ATP6V1D ATP6V1D ATP6V1D 10082 -0.019 0.26 NO
94 NDUFA6 NDUFA6 NDUFA6 10142 -0.02 0.26 NO
95 ATP5H ATP5H ATP5H 10306 -0.022 0.26 NO
96 ATP6V0E2 ATP6V0E2 ATP6V0E2 10338 -0.023 0.26 NO
97 ATP5O ATP5O ATP5O 10574 -0.026 0.25 NO
98 UQCR10 UQCR10 UQCR10 10716 -0.028 0.25 NO
99 NDUFB5 NDUFB5 NDUFB5 10741 -0.028 0.25 NO
100 UQCR11 UQCR11 UQCR11 10765 -0.028 0.26 NO
101 COX8C COX8C COX8C 11232 -0.035 0.24 NO
102 ATP6V0D1 ATP6V0D1 ATP6V0D1 11600 -0.04 0.22 NO
103 ATP6V0E1 ATP6V0E1 ATP6V0E1 11639 -0.041 0.23 NO
104 ATP6V1F ATP6V1F ATP6V1F 11710 -0.042 0.23 NO
105 ATP6V0A1 ATP6V0A1 ATP6V0A1 12049 -0.048 0.22 NO
106 NDUFA11 NDUFA11 NDUFA11 12206 -0.051 0.22 NO
107 ATP6V1B2 ATP6V1B2 ATP6V1B2 12332 -0.053 0.22 NO
108 NDUFB7 NDUFB7 NDUFB7 12850 -0.064 0.2 NO
109 NDUFS7 NDUFS7 NDUFS7 13154 -0.072 0.2 NO
110 ATP12A ATP12A ATP12A 14725 -0.12 0.13 NO
111 COX7A1 COX7A1 COX7A1 16101 -0.17 0.084 NO
112 ATP6V0D2 ATP6V0D2 ATP6V0D2 16862 -0.22 0.079 NO

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

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

Fold change

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

Expression level

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

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

Methods & Data
Input

  • Gene set database = c2.cp.v3.0-2.symbols.gmt

  • Expression data file = LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = LUAD-TP.mergedcluster.txt

GSEA analysis

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

Download Results

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

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