GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in KICH-TP
Kidney Chromophobe (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1833R2Q
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 KICH-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1833R2Q
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 KICH-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: 191
Number of samples: 66
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 19
pheno.type: 2 - 4 :[ clus2 ] 22
pheno.type: 3 - 4 :[ clus3 ] 15
pheno.type: 4 - 4 :[ clus4 ] 10

For the expression subtypes of 17843 genes in 67 samples, GSEA found enriched gene sets in each cluster using 66 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA P38MAPK PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA GPCR PATHWAY, BIOCARTA CREB PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FATTY ACID METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG INOSITOL PHOSPHATE METABOLISM

    • And common core enriched genes are CALM3, PRKACB, GNAI1, NFATC2, NFATC4, ACAA1, ACSL1, ACSL6, ADRBK2, CAMK2B

  • clus2

    • Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA RHO PATHWAY, BIOCARTA MET PATHWAY, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG CYTOSOLIC DNA SENSING PATHWAY

    • And common core enriched genes are NFKB1, NFKBIA, ARPC1B, JUN, MAP2K1, SRC, APAF1, BCL2, BIRC2, BIRC3

  • clus3

    • Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG OXIDATIVE PHOSPHORYLATION, KEGG N GLYCAN BIOSYNTHESIS, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA DEGRADATION, KEGG RNA POLYMERASE, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG BASE EXCISION REPAIR

    • And common core enriched genes are LIG1, POLD1, POLD2, POLE2, POLE3, POLE4, RFC1, RFC2, RFC4, RFC5

  • clus4

    • Top enriched gene sets are BIOCARTA EGF PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA PDGF PATHWAY, BIOCARTA EDG1 PATHWAY, BIOCARTA IL1R PATHWAY, BIOCARTA TNFR1 PATHWAY, BIOCARTA TOLL PATHWAY, BIOCARTA VEGF PATHWAY, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG ARGININE AND PROLINE METABOLISM

    • And common core enriched genes are MAP2K4, ARHGDIB, CASP8, DFFA, DFFB, LMNA, MAP3K7, PAK2, PARP1, PRKDC

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 0.37 1.1 0.31 1 1 0.14 0.1 0.13 1 0.82
BIOCARTA BIOPEPTIDES PATHWAY 39 genes.ES.table 0.31 1.1 0.31 1 1 0.15 0.16 0.13 1 0.87
BIOCARTA P38MAPK PATHWAY 39 genes.ES.table 0.28 1.1 0.39 1 1 0.051 0.049 0.049 1 0.74
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.27 1.1 0.37 1 1 0.2 0.2 0.16 1 0.7
BIOCARTA GPCR PATHWAY 33 genes.ES.table 0.39 1.3 0.17 1 0.97 0.39 0.2 0.31 1 0.96
BIOCARTA CREB PATHWAY 26 genes.ES.table 0.37 1.1 0.3 1 1 0.15 0.086 0.14 1 0.84
KEGG GLYCOLYSIS GLUCONEOGENESIS 58 genes.ES.table 0.36 1.1 0.32 1 1 0.28 0.17 0.23 1 0.8
KEGG FATTY ACID METABOLISM 40 genes.ES.table 0.44 1.2 0.23 1 0.98 0.4 0.23 0.31 1 0.95
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.38 1.2 0.33 1 0.99 0.3 0.25 0.23 1 0.89
KEGG INOSITOL PHOSPHATE METABOLISM 53 genes.ES.table 0.36 1.2 0.22 1 0.98 0.23 0.16 0.19 1 0.88
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 OR1N1 OR1N1 OR1N1 6 1.1 0.1 YES
2 OR1L8 OR1L8 OR1L8 30 0.82 0.17 YES
3 OR1N2 OR1N2 OR1N2 67 0.66 0.23 YES
4 OR5B12 OR5B12 OR5B12 84 0.61 0.29 YES
5 OR1B1 OR1B1 OR1B1 108 0.57 0.34 YES
6 CAMK2B CAMK2B CAMK2B 201 0.5 0.38 YES
7 PDE1C PDE1C PDE1C 853 0.29 0.37 YES
8 OR2A1 OR2A1 OR2A1 1095 0.25 0.38 YES
9 OR1J1 OR1J1 OR1J1 1116 0.25 0.4 YES
10 OR13J1 OR13J1 OR13J1 1165 0.24 0.42 YES
11 PRKACB PRKACB PRKACB 1289 0.23 0.43 YES
12 CAMK2D CAMK2D CAMK2D 1453 0.21 0.44 YES
13 OR7D2 OR7D2 OR7D2 1862 0.18 0.44 YES
14 ADRBK2 ADRBK2 ADRBK2 1925 0.18 0.45 YES
15 CNGA4 CNGA4 CNGA4 2071 0.17 0.46 YES
16 OR1Q1 OR1Q1 OR1Q1 2162 0.16 0.46 YES
17 OR51E1 OR51E1 OR51E1 2254 0.16 0.47 YES
18 OR1J2 OR1J2 OR1J2 2467 0.14 0.47 YES
19 OR2A25 OR2A25 OR2A25 2776 0.13 0.47 YES
20 CALM3 CALM3 CALM3 2808 0.13 0.48 YES
21 OR56B4 OR56B4 OR56B4 2825 0.13 0.49 YES
22 OR2W3 OR2W3 OR2W3 3106 0.12 0.48 YES
23 OR2A4 OR2A4 OR2A4 3160 0.11 0.49 YES
24 OR2A7 OR2A7 OR2A7 3669 0.097 0.47 NO
25 OR2A5 OR2A5 OR2A5 3884 0.091 0.47 NO
26 PRKX PRKX PRKX 4542 0.074 0.44 NO
27 CALML3 CALML3 CALML3 4926 0.066 0.42 NO
28 OR6T1 OR6T1 OR6T1 5215 0.06 0.41 NO
29 OR2A14 OR2A14 OR2A14 5662 0.053 0.39 NO
30 GUCA1B GUCA1B GUCA1B 5667 0.053 0.4 NO
31 ARRB2 ARRB2 ARRB2 6093 0.045 0.38 NO
32 OR5K2 OR5K2 OR5K2 6281 0.042 0.37 NO
33 CALM1 CALM1 CALM1 7697 0.02 0.29 NO
34 OR51E2 OR51E2 OR51E2 8221 0.012 0.26 NO
35 PRKACA PRKACA PRKACA 8520 0.0084 0.25 NO
36 OR2A2 OR2A2 OR2A2 8564 0.0077 0.24 NO
37 PRKACG PRKACG PRKACG 9516 -0.0067 0.19 NO
38 CALM2 CALM2 CALM2 9824 -0.011 0.18 NO
39 OR3A2 OR3A2 OR3A2 9940 -0.013 0.17 NO
40 CAMK2A CAMK2A CAMK2A 10239 -0.017 0.16 NO
41 OR10AD1 OR10AD1 OR10AD1 10399 -0.02 0.15 NO
42 CNGB1 CNGB1 CNGB1 12644 -0.059 0.027 NO
43 CAMK2G CAMK2G CAMK2G 13799 -0.086 -0.03 NO
44 ADCY3 ADCY3 ADCY3 14684 -0.11 -0.069 NO
45 OR2C1 OR2C1 OR2C1 14892 -0.12 -0.07 NO
46 GNAL GNAL GNAL 15348 -0.14 -0.082 NO
47 CALML6 CALML6 CALML6 15532 -0.15 -0.079 NO
48 GUCY2D GUCY2D GUCY2D 16471 -0.21 -0.11 NO
49 OR52R1 OR52R1 OR52R1 16648 -0.23 -0.1 NO
50 CLCA2 CLCA2 CLCA2 16816 -0.24 -0.089 NO
51 OR52N4 OR52N4 OR52N4 16958 -0.26 -0.072 NO
52 PRKG2 PRKG2 PRKG2 17156 -0.29 -0.057 NO
53 OR51T1 OR51T1 OR51T1 17253 -0.31 -0.034 NO
54 PRKG1 PRKG1 PRKG1 17333 -0.33 -0.0085 NO
55 OR13A1 OR13A1 OR13A1 17548 -0.4 0.016 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 BIOPEPTIDES 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 NFATC2 NFATC2 NFATC2 1010 0.26 0.019 YES
2 PRKACB PRKACB PRKACB 1289 0.23 0.07 YES
3 NFATC4 NFATC4 NFATC4 1528 0.21 0.12 YES
4 PRKAR2B PRKAR2B PRKAR2B 1541 0.2 0.17 YES
5 GNAQ GNAQ GNAQ 1775 0.19 0.21 YES
6 GNAI1 GNAI1 GNAI1 2216 0.16 0.23 YES
7 GNGT1 GNGT1 GNGT1 2274 0.16 0.28 YES
8 FOS FOS FOS 2656 0.13 0.29 YES
9 CALM3 CALM3 CALM3 2808 0.13 0.32 YES
10 RAF1 RAF1 RAF1 3473 0.1 0.31 YES
11 PPP3CA PPP3CA PPP3CA 3574 0.099 0.34 YES
12 RPS6KA3 RPS6KA3 RPS6KA3 3632 0.098 0.36 YES
13 PRKAR2A PRKAR2A PRKAR2A 3649 0.098 0.39 YES
14 NFATC3 NFATC3 NFATC3 4938 0.066 0.33 NO
15 GNAS GNAS GNAS 7547 0.022 0.19 NO
16 CALM1 CALM1 CALM1 7697 0.02 0.19 NO
17 ELK1 ELK1 ELK1 8828 0.004 0.13 NO
18 PLCG1 PLCG1 PLCG1 9399 -0.0048 0.098 NO
19 PRKACG PRKACG PRKACG 9516 -0.0067 0.093 NO
20 CALM2 CALM2 CALM2 9824 -0.011 0.079 NO
21 PRKCB PRKCB PRKCB 10230 -0.017 0.061 NO
22 PRKAR1B PRKAR1B PRKAR1B 10284 -0.018 0.063 NO
23 MAPK3 MAPK3 MAPK3 10920 -0.029 0.036 NO
24 CREB1 CREB1 CREB1 11193 -0.033 0.03 NO
25 PRKAR1A PRKAR1A PRKAR1A 12338 -0.053 -0.019 NO
26 PPP3CB PPP3CB PPP3CB 13740 -0.084 -0.074 NO
27 GNB1 GNB1 GNB1 13760 -0.085 -0.05 NO
28 ADCY1 ADCY1 ADCY1 14845 -0.12 -0.077 NO
29 MAP2K1 MAP2K1 MAP2K1 15316 -0.14 -0.063 NO
30 NFATC1 NFATC1 NFATC1 15425 -0.15 -0.027 NO
31 PRKCA PRKCA PRKCA 15873 -0.17 -0.0031 NO
32 JUN JUN JUN 16125 -0.19 0.036 NO
33 PPP3CC PPP3CC PPP3CC 16377 -0.2 0.081 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 BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA P38MAPK 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 ADH1C ADH1C ADH1C 110 0.57 0.14 YES
2 ADH7 ADH7 ADH7 715 0.32 0.18 YES
3 ADH6 ADH6 ADH6 1273 0.23 0.21 YES
4 CYP4A11 CYP4A11 CYP4A11 1616 0.2 0.24 YES
5 ADH4 ADH4 ADH4 1849 0.18 0.27 YES
6 ACADL ACADL ACADL 2273 0.16 0.28 YES
7 CPT1C CPT1C CPT1C 2493 0.14 0.3 YES
8 CPT1B CPT1B CPT1B 2711 0.13 0.32 YES
9 ALDH7A1 ALDH7A1 ALDH7A1 2782 0.13 0.35 YES
10 ADH1A ADH1A ADH1A 2995 0.12 0.37 YES
11 GCDH GCDH GCDH 3358 0.11 0.38 YES
12 ACSL6 ACSL6 ACSL6 3859 0.092 0.37 YES
13 ACSL1 ACSL1 ACSL1 3899 0.091 0.39 YES
14 ACAA1 ACAA1 ACAA1 4001 0.087 0.41 YES
15 ACAT1 ACAT1 ACAT1 4038 0.086 0.43 YES
16 ALDH2 ALDH2 ALDH2 4097 0.084 0.44 YES
17 ACSL5 ACSL5 ACSL5 5723 0.052 0.37 NO
18 EHHADH EHHADH EHHADH 6218 0.043 0.35 NO
19 ACSL3 ACSL3 ACSL3 7694 0.02 0.27 NO
20 ACAT2 ACAT2 ACAT2 7720 0.02 0.28 NO
21 ADH5 ADH5 ADH5 7769 0.019 0.28 NO
22 ALDH1B1 ALDH1B1 ALDH1B1 7924 0.017 0.27 NO
23 HADH HADH HADH 8860 0.0033 0.22 NO
24 DCI DCI DCI 8886 0.003 0.22 NO
25 ACOX3 ACOX3 ACOX3 9370 -0.0043 0.19 NO
26 ACAA2 ACAA2 ACAA2 9620 -0.0081 0.18 NO
27 ACADS ACADS ACADS 10090 -0.015 0.16 NO
28 CPT2 CPT2 CPT2 11406 -0.037 0.094 NO
29 ALDH9A1 ALDH9A1 ALDH9A1 12330 -0.053 0.056 NO
30 ECHS1 ECHS1 ECHS1 12527 -0.056 0.059 NO
31 ACADSB ACADSB ACADSB 12897 -0.064 0.054 NO
32 CPT1A CPT1A CPT1A 13140 -0.07 0.058 NO
33 HADHA HADHA HADHA 13563 -0.08 0.054 NO
34 PECI PECI PECI 13590 -0.08 0.072 NO
35 ACSL4 ACSL4 ACSL4 13761 -0.085 0.084 NO
36 ACADVL ACADVL ACADVL 13948 -0.09 0.096 NO
37 ACADM ACADM ACADM 14021 -0.092 0.11 NO
38 ALDH3A2 ALDH3A2 ALDH3A2 14266 -0.098 0.12 NO
39 HADHB HADHB HADHB 15196 -0.14 0.11 NO
40 ADH1B ADH1B ADH1B 15792 -0.17 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 P38MAPK PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA P38MAPK 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 CHREBP2 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 UNC5D UNC5D UNC5D 21 0.86 0.05 YES
2 NTNG1 NTNG1 NTNG1 43 0.76 0.093 YES
3 EPHA6 EPHA6 EPHA6 55 0.72 0.13 YES
4 PAK7 PAK7 PAK7 57 0.7 0.18 YES
5 SEMA5A SEMA5A SEMA5A 323 0.42 0.18 YES
6 DPYSL5 DPYSL5 DPYSL5 334 0.42 0.21 YES
7 UNC5A UNC5A UNC5A 546 0.35 0.22 YES
8 EPHB2 EPHB2 EPHB2 786 0.3 0.22 YES
9 PLXNC1 PLXNC1 PLXNC1 815 0.29 0.24 YES
10 EPHB6 EPHB6 EPHB6 997 0.27 0.24 YES
11 SEMA6A SEMA6A SEMA6A 998 0.27 0.26 YES
12 NFATC2 NFATC2 NFATC2 1010 0.26 0.27 YES
13 ROBO1 ROBO1 ROBO1 1061 0.26 0.29 YES
14 SEMA4D SEMA4D SEMA4D 1155 0.24 0.3 YES
15 SEMA3B SEMA3B SEMA3B 1236 0.24 0.3 YES
16 SEMA3F SEMA3F SEMA3F 1245 0.24 0.32 YES
17 EPHA1 EPHA1 EPHA1 1284 0.23 0.33 YES
18 PPP3R2 PPP3R2 PPP3R2 1361 0.22 0.34 YES
19 NFATC4 NFATC4 NFATC4 1528 0.21 0.34 YES
20 NGEF NGEF NGEF 1699 0.19 0.34 YES
21 EPHB1 EPHB1 EPHB1 1793 0.18 0.35 YES
22 PAK6 PAK6 PAK6 1840 0.18 0.36 YES
23 GNAI1 GNAI1 GNAI1 2216 0.16 0.34 YES
24 EFNA3 EFNA3 EFNA3 2413 0.15 0.34 YES
25 ROBO3 ROBO3 ROBO3 2463 0.14 0.35 YES
26 EFNA5 EFNA5 EFNA5 2515 0.14 0.35 YES
27 SEMA7A SEMA7A SEMA7A 2733 0.13 0.35 YES
28 SRGAP3 SRGAP3 SRGAP3 2757 0.13 0.36 YES
29 NTN4 NTN4 NTN4 2786 0.13 0.36 YES
30 PLXNA1 PLXNA1 PLXNA1 2891 0.12 0.36 YES
31 RAC3 RAC3 RAC3 2930 0.12 0.37 YES
32 PLXNB2 PLXNB2 PLXNB2 3122 0.11 0.36 NO
33 EFNA4 EFNA4 EFNA4 3187 0.11 0.37 NO
34 SEMA3D SEMA3D SEMA3D 3451 0.1 0.36 NO
35 PPP3CA PPP3CA PPP3CA 3574 0.099 0.36 NO
36 MET MET MET 3680 0.097 0.36 NO
37 DCC DCC DCC 3931 0.09 0.35 NO
38 NTN1 NTN1 NTN1 3995 0.088 0.35 NO
39 CFL2 CFL2 CFL2 4048 0.086 0.35 NO
40 PAK4 PAK4 PAK4 4233 0.081 0.34 NO
41 SEMA3A SEMA3A SEMA3A 4459 0.076 0.34 NO
42 EFNA1 EFNA1 EFNA1 4702 0.071 0.33 NO
43 NFAT5 NFAT5 NFAT5 4752 0.07 0.33 NO
44 NFATC3 NFATC3 NFATC3 4938 0.066 0.32 NO
45 RASA1 RASA1 RASA1 5085 0.063 0.32 NO
46 NCK1 NCK1 NCK1 5275 0.059 0.31 NO
47 RHOA RHOA RHOA 5469 0.056 0.3 NO
48 PLXNA3 PLXNA3 PLXNA3 5788 0.05 0.29 NO
49 PLXNB3 PLXNB3 PLXNB3 5858 0.05 0.29 NO
50 EFNB3 EFNB3 EFNB3 5962 0.048 0.28 NO
51 GSK3B GSK3B GSK3B 6265 0.043 0.27 NO
52 GNAI2 GNAI2 GNAI2 7113 0.029 0.22 NO
53 CHP CHP CHP 7311 0.026 0.21 NO
54 PAK2 PAK2 PAK2 7868 0.018 0.18 NO
55 SEMA3C SEMA3C SEMA3C 8176 0.013 0.17 NO
56 SEMA4F SEMA4F SEMA4F 8188 0.013 0.17 NO
57 ROCK1 ROCK1 ROCK1 8287 0.011 0.16 NO
58 FYN FYN FYN 8433 0.0095 0.15 NO
59 LIMK2 LIMK2 LIMK2 8476 0.009 0.15 NO
60 RND1 RND1 RND1 8658 0.0065 0.14 NO
61 SEMA3G SEMA3G SEMA3G 8679 0.0062 0.14 NO
62 SEMA4B SEMA4B SEMA4B 8741 0.0052 0.14 NO
63 ABLIM3 ABLIM3 ABLIM3 9116 -0.00064 0.12 NO
64 CDK5 CDK5 CDK5 9629 -0.0082 0.089 NO
65 RAC1 RAC1 RAC1 9664 -0.0088 0.088 NO
66 ARHGEF12 ARHGEF12 ARHGEF12 9676 -0.0089 0.088 NO
67 SEMA5B SEMA5B SEMA5B 9919 -0.013 0.075 NO
68 CDC42 CDC42 CDC42 10196 -0.017 0.06 NO
69 KRAS KRAS KRAS 10338 -0.019 0.053 NO
70 UNC5C UNC5C UNC5C 10436 -0.02 0.049 NO
71 UNC5B UNC5B UNC5B 10595 -0.023 0.041 NO
72 CFL1 CFL1 CFL1 10812 -0.026 0.031 NO
73 MAPK1 MAPK1 MAPK1 10821 -0.027 0.032 NO
74 PLXNB1 PLXNB1 PLXNB1 10853 -0.027 0.032 NO
75 MAPK3 MAPK3 MAPK3 10920 -0.029 0.03 NO
76 NRP1 NRP1 NRP1 11237 -0.034 0.014 NO
77 SEMA4C SEMA4C SEMA4C 11361 -0.036 0.0089 NO
78 PAK3 PAK3 PAK3 11534 -0.039 0.0015 NO
79 PAK1 PAK1 PAK1 11891 -0.045 -0.016 NO
80 ABL1 ABL1 ABL1 11908 -0.046 -0.014 NO
81 ABLIM2 ABLIM2 ABLIM2 12086 -0.048 -0.021 NO
82 DPYSL2 DPYSL2 DPYSL2 12174 -0.05 -0.023 NO
83 LRRC4C LRRC4C LRRC4C 12220 -0.051 -0.023 NO
84 SEMA3E SEMA3E SEMA3E 12274 -0.052 -0.023 NO
85 PPP3R1 PPP3R1 PPP3R1 12728 -0.061 -0.045 NO
86 NTN3 NTN3 NTN3 12810 -0.062 -0.046 NO
87 FES FES FES 12937 -0.065 -0.049 NO
88 NRAS NRAS NRAS 12973 -0.066 -0.047 NO
89 EPHB4 EPHB4 EPHB4 12991 -0.066 -0.044 NO
90 PTK2 PTK2 PTK2 12996 -0.066 -0.04 NO
91 SLIT3 SLIT3 SLIT3 13021 -0.067 -0.038 NO
92 EPHA2 EPHA2 EPHA2 13060 -0.068 -0.036 NO
93 NCK2 NCK2 NCK2 13438 -0.077 -0.053 NO
94 ITGB1 ITGB1 ITGB1 13442 -0.077 -0.048 NO
95 EFNB1 EFNB1 EFNB1 13534 -0.079 -0.049 NO
96 EPHA3 EPHA3 EPHA3 13724 -0.084 -0.055 NO
97 PPP3CB PPP3CB PPP3CB 13740 -0.084 -0.05 NO
98 ROCK2 ROCK2 ROCK2 13874 -0.088 -0.053 NO
99 LIMK1 LIMK1 LIMK1 13990 -0.091 -0.054 NO
100 RAC2 RAC2 RAC2 14016 -0.092 -0.05 NO
101 CXCR4 CXCR4 CXCR4 14086 -0.094 -0.048 NO
102 EFNB2 EFNB2 EFNB2 14123 -0.094 -0.045 NO
103 SEMA6B SEMA6B SEMA6B 14255 -0.098 -0.046 NO
104 GNAI3 GNAI3 GNAI3 14259 -0.098 -0.041 NO
105 SRGAP1 SRGAP1 SRGAP1 14436 -0.1 -0.045 NO
106 SRGAP2 SRGAP2 SRGAP2 14451 -0.1 -0.039 NO
107 SEMA6D SEMA6D SEMA6D 14532 -0.11 -0.038 NO
108 EPHA4 EPHA4 EPHA4 14744 -0.12 -0.043 NO
109 RGS3 RGS3 RGS3 15100 -0.13 -0.055 NO
110 SLIT1 SLIT1 SLIT1 15338 -0.14 -0.06 NO
111 SEMA6C SEMA6C SEMA6C 15417 -0.15 -0.056 NO
112 NFATC1 NFATC1 NFATC1 15425 -0.15 -0.048 NO
113 SLIT2 SLIT2 SLIT2 15438 -0.15 -0.04 NO
114 SEMA4A SEMA4A SEMA4A 15468 -0.15 -0.032 NO
115 PLXNA2 PLXNA2 PLXNA2 15673 -0.16 -0.035 NO
116 PPP3CC PPP3CC PPP3CC 16377 -0.2 -0.062 NO
117 CXCL12 CXCL12 CXCL12 16594 -0.22 -0.061 NO
118 ABLIM1 ABLIM1 ABLIM1 16631 -0.23 -0.05 NO
119 L1CAM L1CAM L1CAM 16642 -0.23 -0.037 NO
120 RHOD RHOD RHOD 16726 -0.24 -0.028 NO
121 EPHA7 EPHA7 EPHA7 16824 -0.24 -0.019 NO
122 EPHA8 EPHA8 EPHA8 16834 -0.25 -0.0053 NO
123 ROBO2 ROBO2 ROBO2 17101 -0.28 -0.0036 NO
124 EPHB3 EPHB3 EPHB3 17497 -0.38 -0.0038 NO
125 SEMA4G SEMA4G SEMA4G 17500 -0.38 0.018 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 CHREBP2 PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 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 GPCR 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 FAR2 FAR2 FAR2 205 0.5 0.065 YES
2 AMACR AMACR AMACR 555 0.35 0.1 YES
3 BAAT BAAT BAAT 851 0.29 0.13 YES
4 HACL1 HACL1 HACL1 1404 0.22 0.13 YES
5 PEX11G PEX11G PEX11G 1490 0.21 0.16 YES
6 MPV17L MPV17L MPV17L 1534 0.2 0.19 YES
7 HAO2 HAO2 HAO2 1584 0.2 0.22 YES
8 NUDT12 NUDT12 NUDT12 1811 0.18 0.23 YES
9 AGXT AGXT AGXT 1823 0.18 0.26 YES
10 PXMP4 PXMP4 PXMP4 2429 0.15 0.25 YES
11 MLYCD MLYCD MLYCD 2453 0.14 0.27 YES
12 DAO DAO DAO 2457 0.14 0.29 YES
13 PEX26 PEX26 PEX26 2965 0.12 0.28 YES
14 PEX11A PEX11A PEX11A 3001 0.12 0.3 YES
15 FAR1 FAR1 FAR1 3795 0.094 0.27 YES
16 ACSL6 ACSL6 ACSL6 3859 0.092 0.28 YES
17 ACSL1 ACSL1 ACSL1 3899 0.091 0.29 YES
18 ACAA1 ACAA1 ACAA1 4001 0.087 0.3 YES
19 HSD17B4 HSD17B4 HSD17B4 4005 0.087 0.31 YES
20 PEX12 PEX12 PEX12 4021 0.087 0.32 YES
21 ACOT8 ACOT8 ACOT8 5314 0.058 0.26 NO
22 ACSL5 ACSL5 ACSL5 5723 0.052 0.24 NO
23 PEX1 PEX1 PEX1 6000 0.047 0.24 NO
24 CRAT CRAT CRAT 6075 0.046 0.24 NO
25 EHHADH EHHADH EHHADH 6218 0.043 0.24 NO
26 GSTK1 GSTK1 GSTK1 6309 0.042 0.24 NO
27 SLC25A17 SLC25A17 SLC25A17 6313 0.042 0.24 NO
28 PEX7 PEX7 PEX7 6327 0.042 0.25 NO
29 CAT CAT CAT 6370 0.041 0.25 NO
30 PEX5 PEX5 PEX5 6454 0.04 0.26 NO
31 PRDX1 PRDX1 PRDX1 6701 0.036 0.25 NO
32 PEX6 PEX6 PEX6 6864 0.033 0.24 NO
33 IDH1 IDH1 IDH1 6996 0.031 0.24 NO
34 DHRS4 DHRS4 DHRS4 7383 0.025 0.22 NO
35 PECR PECR PECR 7527 0.023 0.22 NO
36 ACSL3 ACSL3 ACSL3 7694 0.02 0.21 NO
37 PRDX5 PRDX5 PRDX5 8894 0.0028 0.14 NO
38 PEX16 PEX16 PEX16 8950 0.0021 0.14 NO
39 EPHX2 EPHX2 EPHX2 9083 -0.000087 0.14 NO
40 PEX14 PEX14 PEX14 9101 -0.00033 0.13 NO
41 PEX2 PEX2 PEX2 9185 -0.0018 0.13 NO
42 ACOX3 ACOX3 ACOX3 9370 -0.0043 0.12 NO
43 PEX19 PEX19 PEX19 9595 -0.0078 0.11 NO
44 MVK MVK MVK 9969 -0.014 0.089 NO
45 ABCD1 ABCD1 ABCD1 10066 -0.015 0.086 NO
46 SCP2 SCP2 SCP2 10166 -0.016 0.083 NO
47 SOD1 SOD1 SOD1 10168 -0.016 0.086 NO
48 ABCD3 ABCD3 ABCD3 10169 -0.016 0.088 NO
49 PHYH PHYH PHYH 10209 -0.017 0.089 NO
50 ABCD4 ABCD4 ABCD4 10309 -0.018 0.086 NO
51 PEX11B PEX11B PEX11B 10455 -0.021 0.081 NO
52 PMVK PMVK PMVK 10665 -0.024 0.073 NO
53 ACOX1 ACOX1 ACOX1 11140 -0.032 0.051 NO
54 NUDT19 NUDT19 NUDT19 11661 -0.041 0.028 NO
55 NOS2 NOS2 NOS2 11894 -0.045 0.022 NO
56 PEX10 PEX10 PEX10 12146 -0.05 0.016 NO
57 MPV17 MPV17 MPV17 12259 -0.052 0.017 NO
58 HMGCL HMGCL HMGCL 12508 -0.056 0.012 NO
59 AGPS AGPS AGPS 12521 -0.056 0.02 NO
60 ABCD2 ABCD2 ABCD2 12591 -0.058 0.025 NO
61 IDH2 IDH2 IDH2 12679 -0.06 0.03 NO
62 PIPOX PIPOX PIPOX 12748 -0.061 0.035 NO
63 GNPAT GNPAT GNPAT 12752 -0.061 0.044 NO
64 DECR2 DECR2 DECR2 13082 -0.068 0.036 NO
65 PEX13 PEX13 PEX13 13129 -0.07 0.044 NO
66 PEX3 PEX3 PEX3 13580 -0.08 0.032 NO
67 PECI PECI PECI 13590 -0.08 0.043 NO
68 SOD2 SOD2 SOD2 13635 -0.081 0.054 NO
69 ACSL4 ACSL4 ACSL4 13761 -0.085 0.06 NO
70 CROT CROT CROT 14146 -0.095 0.053 NO
71 SLC27A2 SLC27A2 SLC27A2 14190 -0.096 0.065 NO
72 PAOX PAOX PAOX 14279 -0.099 0.075 NO
73 ECH1 ECH1 ECH1 14366 -0.1 0.086 NO
74 DDO DDO DDO 14984 -0.12 0.071 NO
75 PXMP2 PXMP2 PXMP2 16937 -0.26 0.00095 NO
76 XDH XDH XDH 17281 -0.32 0.031 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 GPCR PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GPCR 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 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 INPP4B INPP4B INPP4B 177 0.51 0.072 YES
2 PLCE1 PLCE1 PLCE1 333 0.42 0.13 YES
3 PLCB4 PLCB4 PLCB4 397 0.4 0.19 YES
4 PIK3C2G PIK3C2G PIK3C2G 534 0.36 0.24 YES
5 INPP5J INPP5J INPP5J 930 0.28 0.26 YES
6 ALDH6A1 ALDH6A1 ALDH6A1 1125 0.25 0.29 YES
7 PLCG2 PLCG2 PLCG2 1396 0.22 0.31 YES
8 ITPK1 ITPK1 ITPK1 1710 0.19 0.32 YES
9 PIP5K1B PIP5K1B PIP5K1B 1981 0.17 0.34 YES
10 PLCD4 PLCD4 PLCD4 2202 0.16 0.35 YES
11 INPP4A INPP4A INPP4A 2501 0.14 0.35 YES
12 PIK3CA PIK3CA PIK3CA 2806 0.13 0.36 YES
13 IPPK IPPK IPPK 4819 0.068 0.26 NO
14 PIK3C3 PIK3C3 PIK3C3 5202 0.061 0.24 NO
15 PLCD1 PLCD1 PLCD1 6086 0.046 0.2 NO
16 PIK3CB PIK3CB PIK3CB 6500 0.039 0.18 NO
17 INPP5E INPP5E INPP5E 6566 0.038 0.19 NO
18 OCRL OCRL OCRL 6991 0.031 0.17 NO
19 PIK3C2B PIK3C2B PIK3C2B 7294 0.026 0.15 NO
20 INPP5K INPP5K INPP5K 7863 0.018 0.12 NO
21 PI4KA PI4KA PI4KA 8406 0.0097 0.096 NO
22 INPPL1 INPPL1 INPPL1 8445 0.0093 0.096 NO
23 PIP5K1C PIP5K1C PIP5K1C 8559 0.0078 0.091 NO
24 PIK3C2A PIK3C2A PIK3C2A 9073 0.000027 0.062 NO
25 TPI1 TPI1 TPI1 9205 -0.002 0.055 NO
26 PLCB1 PLCB1 PLCB1 9305 -0.0034 0.05 NO
27 PLCG1 PLCG1 PLCG1 9399 -0.0048 0.045 NO
28 MINPP1 MINPP1 MINPP1 10139 -0.016 0.0062 NO
29 PTEN PTEN PTEN 10559 -0.022 -0.014 NO
30 CDIPT CDIPT CDIPT 10934 -0.029 -0.03 NO
31 PIP4K2A PIP4K2A PIP4K2A 11272 -0.034 -0.044 NO
32 PIK3CG PIK3CG PIK3CG 11342 -0.035 -0.042 NO
33 PIP4K2C PIP4K2C PIP4K2C 11402 -0.037 -0.039 NO
34 IMPA2 IMPA2 IMPA2 11972 -0.047 -0.064 NO
35 PIKFYVE PIKFYVE PIKFYVE 12197 -0.05 -0.068 NO
36 PI4KB PI4KB PI4KB 12281 -0.052 -0.065 NO
37 INPP5B INPP5B INPP5B 12417 -0.054 -0.064 NO
38 INPP1 INPP1 INPP1 13071 -0.068 -0.09 NO
39 ITPKB ITPKB ITPKB 13130 -0.07 -0.082 NO
40 PIP4K2B PIP4K2B PIP4K2B 13545 -0.079 -0.092 NO
41 PLCB3 PLCB3 PLCB3 13655 -0.082 -0.085 NO
42 PIP5K1A PIP5K1A PIP5K1A 13689 -0.083 -0.074 NO
43 INPP5A INPP5A INPP5A 13721 -0.084 -0.062 NO
44 PLCB2 PLCB2 PLCB2 14413 -0.1 -0.085 NO
45 SYNJ1 SYNJ1 SYNJ1 14717 -0.12 -0.084 NO
46 IMPA1 IMPA1 IMPA1 15207 -0.14 -0.089 NO
47 ITPKA ITPKA ITPKA 15521 -0.15 -0.083 NO
48 MIOX MIOX MIOX 15679 -0.16 -0.066 NO
49 ISYNA1 ISYNA1 ISYNA1 15779 -0.16 -0.045 NO
50 SYNJ2 SYNJ2 SYNJ2 15984 -0.18 -0.028 NO
51 PIK3CD PIK3CD PIK3CD 16617 -0.22 -0.028 NO
52 IPMK IPMK IPMK 16934 -0.26 -0.004 NO
53 PLCD3 PLCD3 PLCD3 17370 -0.34 0.026 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 CREB PATHWAY.

Figure S12.  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 GLYCOLYSIS GLUCONEOGENESIS

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 AR AR AR 100 0.58 0.042 YES
2 CPEB1 CPEB1 CPEB1 119 0.56 0.087 YES
3 CAMK2B CAMK2B CAMK2B 201 0.5 0.12 YES
4 SPDYC SPDYC SPDYC 357 0.41 0.15 YES
5 PTTG2 PTTG2 PTTG2 863 0.29 0.14 YES
6 CCNB1 CCNB1 CCNB1 900 0.28 0.16 YES
7 CCNB2 CCNB2 CCNB2 962 0.27 0.18 YES
8 CDC20 CDC20 CDC20 1062 0.26 0.2 YES
9 PTTG1 PTTG1 PTTG1 1161 0.24 0.21 YES
10 CDC25C CDC25C CDC25C 1253 0.24 0.23 YES
11 PRKACB PRKACB PRKACB 1289 0.23 0.25 YES
12 PPP3R2 PPP3R2 PPP3R2 1361 0.22 0.26 YES
13 CAMK2D CAMK2D CAMK2D 1453 0.21 0.27 YES
14 BUB1 BUB1 BUB1 1493 0.21 0.29 YES
15 ITPR2 ITPR2 ITPR2 1502 0.21 0.3 YES
16 SGOL1 SGOL1 SGOL1 1507 0.21 0.32 YES
17 PLK1 PLK1 PLK1 1567 0.2 0.34 YES
18 ANAPC2 ANAPC2 ANAPC2 1607 0.2 0.35 YES
19 ADCY4 ADCY4 ADCY4 2031 0.17 0.34 YES
20 MAD2L1 MAD2L1 MAD2L1 2221 0.16 0.34 YES
21 IGF1 IGF1 IGF1 2401 0.15 0.34 YES
22 SMC1B SMC1B SMC1B 2619 0.14 0.34 YES
23 CALM3 CALM3 CALM3 2808 0.13 0.34 YES
24 ADCY8 ADCY8 ADCY8 2928 0.12 0.34 YES
25 CDC26 CDC26 CDC26 3419 0.1 0.33 YES
26 SKP1 SKP1 SKP1 3431 0.1 0.33 YES
27 FBXO43 FBXO43 FBXO43 3460 0.1 0.34 YES
28 PPP3CA PPP3CA PPP3CA 3574 0.099 0.34 YES
29 RPS6KA3 RPS6KA3 RPS6KA3 3632 0.098 0.35 YES
30 CDK1 CDK1 CDK1 3790 0.094 0.35 YES
31 ITPR1 ITPR1 ITPR1 3816 0.093 0.35 YES
32 RPS6KA2 RPS6KA2 RPS6KA2 4102 0.084 0.34 YES
33 RBX1 RBX1 RBX1 4115 0.084 0.35 YES
34 PKMYT1 PKMYT1 PKMYT1 4192 0.082 0.35 YES
35 CCNE2 CCNE2 CCNE2 4226 0.082 0.36 YES
36 PRKX PRKX PRKX 4542 0.074 0.35 NO
37 CALML3 CALML3 CALML3 4926 0.066 0.33 NO
38 RPS6KA6 RPS6KA6 RPS6KA6 4935 0.066 0.33 NO
39 ANAPC13 ANAPC13 ANAPC13 5123 0.062 0.33 NO
40 PPP2CA PPP2CA PPP2CA 5165 0.061 0.33 NO
41 PPP1CC PPP1CC PPP1CC 6238 0.043 0.28 NO
42 ADCY6 ADCY6 ADCY6 6328 0.042 0.27 NO
43 FBXW11 FBXW11 FBXW11 6471 0.04 0.27 NO
44 YWHAE YWHAE YWHAE 6552 0.038 0.27 NO
45 CCNE1 CCNE1 CCNE1 6599 0.038 0.27 NO
46 YWHAB YWHAB YWHAB 6643 0.037 0.27 NO
47 PPP2R5A PPP2R5A PPP2R5A 6661 0.037 0.27 NO
48 IGF1R IGF1R IGF1R 6891 0.033 0.26 NO
49 PLCZ1 PLCZ1 PLCZ1 7071 0.03 0.25 NO
50 CUL1 CUL1 CUL1 7184 0.028 0.25 NO
51 SPDYA SPDYA SPDYA 7186 0.028 0.25 NO
52 ESPL1 ESPL1 ESPL1 7268 0.027 0.25 NO
53 CHP CHP CHP 7311 0.026 0.25 NO
54 CDC23 CDC23 CDC23 7389 0.025 0.25 NO
55 CALM1 CALM1 CALM1 7697 0.02 0.23 NO
56 PPP2R5C PPP2R5C PPP2R5C 7881 0.017 0.22 NO
57 ANAPC7 ANAPC7 ANAPC7 7953 0.016 0.22 NO
58 SMC1A SMC1A SMC1A 8036 0.015 0.22 NO
59 PPP2R1A PPP2R1A PPP2R1A 8118 0.014 0.21 NO
60 PRKACA PRKACA PRKACA 8520 0.0084 0.19 NO
61 PPP2R5E PPP2R5E PPP2R5E 8788 0.0046 0.18 NO
62 YWHAZ YWHAZ YWHAZ 8821 0.0041 0.17 NO
63 PRKACG PRKACG PRKACG 9516 -0.0067 0.14 NO
64 ADCY2 ADCY2 ADCY2 9556 -0.0074 0.13 NO
65 ANAPC10 ANAPC10 ANAPC10 9559 -0.0074 0.13 NO
66 CALM2 CALM2 CALM2 9824 -0.011 0.12 NO
67 YWHAH YWHAH YWHAH 10185 -0.017 0.1 NO
68 PPP2R5B PPP2R5B PPP2R5B 10197 -0.017 0.1 NO
69 AURKA AURKA AURKA 10208 -0.017 0.1 NO
70 CAMK2A CAMK2A CAMK2A 10239 -0.017 0.1 NO
71 ANAPC5 ANAPC5 ANAPC5 10562 -0.022 0.086 NO
72 REC8 REC8 REC8 10762 -0.026 0.077 NO
73 MAPK1 MAPK1 MAPK1 10821 -0.027 0.076 NO
74 MAPK3 MAPK3 MAPK3 10920 -0.029 0.073 NO
75 ANAPC1 ANAPC1 ANAPC1 11021 -0.03 0.07 NO
76 MAD2L2 MAD2L2 MAD2L2 11218 -0.033 0.061 NO
77 PPP1CA PPP1CA PPP1CA 11499 -0.038 0.049 NO
78 BTRC BTRC BTRC 11755 -0.043 0.038 NO
79 CDC16 CDC16 CDC16 11760 -0.043 0.041 NO
80 ANAPC4 ANAPC4 ANAPC4 11769 -0.043 0.044 NO
81 ANAPC11 ANAPC11 ANAPC11 12307 -0.053 0.018 NO
82 YWHAG YWHAG YWHAG 12308 -0.053 0.023 NO
83 CDK2 CDK2 CDK2 12313 -0.053 0.027 NO
84 PPP1CB PPP1CB PPP1CB 12634 -0.059 0.014 NO
85 PPP3R1 PPP3R1 PPP3R1 12728 -0.061 0.013 NO
86 PPP2R1B PPP2R1B PPP2R1B 12750 -0.061 0.017 NO
87 FBXO5 FBXO5 FBXO5 12789 -0.062 0.02 NO
88 MAPK12 MAPK12 MAPK12 12905 -0.065 0.019 NO
89 YWHAQ YWHAQ YWHAQ 13230 -0.072 0.0066 NO
90 SMC3 SMC3 SMC3 13233 -0.072 0.012 NO
91 CDC27 CDC27 CDC27 13342 -0.074 0.012 NO
92 ADCY9 ADCY9 ADCY9 13427 -0.077 0.014 NO
93 PPP2CB PPP2CB PPP2CB 13453 -0.077 0.019 NO
94 STAG3 STAG3 STAG3 13679 -0.083 0.013 NO
95 PPP3CB PPP3CB PPP3CB 13740 -0.084 0.017 NO
96 CAMK2G CAMK2G CAMK2G 13799 -0.086 0.02 NO
97 PPP2R5D PPP2R5D PPP2R5D 14039 -0.093 0.015 NO
98 SLK SLK SLK 14285 -0.099 0.009 NO
99 ADCY1 ADCY1 ADCY1 14845 -0.12 -0.013 NO
100 MAP2K1 MAP2K1 MAP2K1 15316 -0.14 -0.028 NO
101 CALML6 CALML6 CALML6 15532 -0.15 -0.027 NO
102 RPS6KA1 RPS6KA1 RPS6KA1 15909 -0.17 -0.034 NO
103 ADCY7 ADCY7 ADCY7 15939 -0.18 -0.022 NO
104 PPP3CC PPP3CC PPP3CC 16377 -0.2 -0.029 NO
105 ITPR3 ITPR3 ITPR3 16587 -0.22 -0.023 NO
106 ADCY5 ADCY5 ADCY5 17757 -0.53 -0.045 NO
107 PGR PGR PGR 17785 -0.59 0.0022 NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 CFTR CFTR CFTR 485 0.37 0.062 YES
2 ATP6V1G3 ATP6V1G3 ATP6V1G3 731 0.31 0.12 YES
3 PRKACB PRKACB PRKACB 1289 0.23 0.15 YES
4 PLCG2 PLCG2 PLCG2 1396 0.22 0.2 YES
5 ATP6V1A ATP6V1A ATP6V1A 2213 0.16 0.19 YES
6 ATP6V0D2 ATP6V0D2 ATP6V0D2 2508 0.14 0.2 YES
7 SLC12A2 SLC12A2 SLC12A2 2855 0.12 0.22 YES
8 TJP2 TJP2 TJP2 2902 0.12 0.24 YES
9 SEC61B SEC61B SEC61B 2903 0.12 0.27 YES
10 ATP6V1C2 ATP6V1C2 ATP6V1C2 2950 0.12 0.3 YES
11 ATP6V0E1 ATP6V0E1 ATP6V0E1 2985 0.12 0.33 YES
12 ATP6V1B1 ATP6V1B1 ATP6V1B1 3990 0.088 0.29 NO
13 ATP6V1E1 ATP6V1E1 ATP6V1E1 4214 0.082 0.3 NO
14 PRKX PRKX PRKX 4542 0.074 0.3 NO
15 ATP6V0C ATP6V0C ATP6V0C 4941 0.066 0.29 NO
16 ATP6V0A4 ATP6V0A4 ATP6V0A4 4950 0.066 0.31 NO
17 ERO1L ERO1L ERO1L 5021 0.064 0.32 NO
18 TCIRG1 TCIRG1 TCIRG1 5555 0.054 0.3 NO
19 ATP6V1D ATP6V1D ATP6V1D 5687 0.052 0.31 NO
20 ATP6V1G1 ATP6V1G1 ATP6V1G1 5847 0.05 0.31 NO
21 ATP6V0B ATP6V0B ATP6V0B 6038 0.046 0.31 NO
22 ATP6AP1 ATP6AP1 ATP6AP1 6211 0.044 0.31 NO
23 ATP6V0D1 ATP6V0D1 ATP6V0D1 6292 0.042 0.32 NO
24 SEC61A1 SEC61A1 SEC61A1 6648 0.037 0.31 NO
25 ATP6V0E2 ATP6V0E2 ATP6V0E2 7007 0.031 0.29 NO
26 SEC61G SEC61G SEC61G 7454 0.024 0.27 NO
27 GNAS GNAS GNAS 7547 0.022 0.28 NO
28 ATP6V1C1 ATP6V1C1 ATP6V1C1 7645 0.021 0.27 NO
29 KCNQ1 KCNQ1 KCNQ1 7708 0.02 0.28 NO
30 TJP1 TJP1 TJP1 8293 0.011 0.25 NO
31 PRKACA PRKACA PRKACA 8520 0.0084 0.24 NO
32 KDELR1 KDELR1 KDELR1 8578 0.0075 0.23 NO
33 ATP6V1F ATP6V1F ATP6V1F 8629 0.0069 0.23 NO
34 ACTB ACTB ACTB 8795 0.0045 0.22 NO
35 ATP6V0A2 ATP6V0A2 ATP6V0A2 9330 -0.0038 0.2 NO
36 ARF1 ARF1 ARF1 9340 -0.0039 0.2 NO
37 PLCG1 PLCG1 PLCG1 9399 -0.0048 0.19 NO
38 ATP6V1H ATP6V1H ATP6V1H 9401 -0.0048 0.19 NO
39 KDELR2 KDELR2 KDELR2 9472 -0.0061 0.19 NO
40 PRKACG PRKACG PRKACG 9516 -0.0067 0.19 NO
41 ATP6V0A1 ATP6V0A1 ATP6V0A1 10056 -0.015 0.16 NO
42 PDIA4 PDIA4 PDIA4 10115 -0.016 0.16 NO
43 PRKCB PRKCB PRKCB 10230 -0.017 0.16 NO
44 KDELR3 KDELR3 KDELR3 10453 -0.021 0.16 NO
45 ATP6V1E2 ATP6V1E2 ATP6V1E2 10915 -0.029 0.14 NO
46 ATP6V1B2 ATP6V1B2 ATP6V1B2 11787 -0.044 0.098 NO
47 ACTG1 ACTG1 ACTG1 12488 -0.056 0.072 NO
48 ADCY9 ADCY9 ADCY9 13427 -0.077 0.038 NO
49 PRKCA PRKCA PRKCA 15873 -0.17 -0.059 NO
50 ATP6V1G2 ATP6V1G2 ATP6V1G2 15902 -0.17 -0.018 NO
51 PRKCG PRKCG PRKCG 16925 -0.26 -0.014 NO
52 SEC61A2 SEC61A2 SEC61A2 16966 -0.26 0.048 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 FATTY ACID METABOLISM.

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

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

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 OXCT1 OXCT1 OXCT1 499 0.36 0.084 YES
2 ABAT ABAT ABAT 653 0.33 0.18 YES
3 ALDH6A1 ALDH6A1 ALDH6A1 1125 0.25 0.23 YES
4 AOX1 AOX1 AOX1 1570 0.2 0.26 YES
5 HMGCS2 HMGCS2 HMGCS2 2543 0.14 0.25 YES
6 ALDH7A1 ALDH7A1 ALDH7A1 2782 0.13 0.28 YES
7 BCKDHB BCKDHB BCKDHB 3623 0.098 0.26 YES
8 MCCC2 MCCC2 MCCC2 3724 0.096 0.28 YES
9 MCCC1 MCCC1 MCCC1 3823 0.093 0.31 YES
10 ACAA1 ACAA1 ACAA1 4001 0.087 0.32 YES
11 ACAT1 ACAT1 ACAT1 4038 0.086 0.35 YES
12 ALDH2 ALDH2 ALDH2 4097 0.084 0.37 YES
13 BCKDHA BCKDHA BCKDHA 4421 0.077 0.38 YES
14 HMGCS1 HMGCS1 HMGCS1 5335 0.058 0.34 NO
15 PCCB PCCB PCCB 5778 0.051 0.34 NO
16 OXCT2 OXCT2 OXCT2 6180 0.044 0.33 NO
17 EHHADH EHHADH EHHADH 6218 0.043 0.34 NO
18 AUH AUH AUH 6873 0.033 0.31 NO
19 ACAT2 ACAT2 ACAT2 7720 0.02 0.27 NO
20 MUT MUT MUT 7760 0.019 0.27 NO
21 IL4I1 IL4I1 IL4I1 7859 0.018 0.27 NO
22 ALDH1B1 ALDH1B1 ALDH1B1 7924 0.017 0.27 NO
23 HADH HADH HADH 8860 0.0033 0.22 NO
24 BCAT2 BCAT2 BCAT2 8940 0.0022 0.22 NO
25 IVD IVD IVD 9026 0.00077 0.22 NO
26 HIBADH HIBADH HIBADH 9280 -0.003 0.2 NO
27 DBT DBT DBT 9486 -0.0063 0.19 NO
28 ACAA2 ACAA2 ACAA2 9620 -0.0081 0.19 NO
29 ACADS ACADS ACADS 10090 -0.015 0.16 NO
30 ACAD8 ACAD8 ACAD8 10743 -0.025 0.14 NO
31 HSD17B10 HSD17B10 HSD17B10 10938 -0.029 0.13 NO
32 HIBCH HIBCH HIBCH 11226 -0.034 0.13 NO
33 PCCA PCCA PCCA 11240 -0.034 0.14 NO
34 DLD DLD DLD 11587 -0.04 0.13 NO
35 ALDH9A1 ALDH9A1 ALDH9A1 12330 -0.053 0.1 NO
36 HMGCL HMGCL HMGCL 12508 -0.056 0.11 NO
37 ECHS1 ECHS1 ECHS1 12527 -0.056 0.13 NO
38 ACADSB ACADSB ACADSB 12897 -0.064 0.13 NO
39 MCEE MCEE MCEE 13449 -0.077 0.12 NO
40 HADHA HADHA HADHA 13563 -0.08 0.14 NO
41 ACADM ACADM ACADM 14021 -0.092 0.14 NO
42 ALDH3A2 ALDH3A2 ALDH3A2 14266 -0.098 0.16 NO
43 HADHB HADHB HADHB 15196 -0.14 0.15 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S18.  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 INOSITOL PHOSPHATE METABOLISM

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 OXCT1 OXCT1 OXCT1 499 0.36 0.093 YES
2 ABAT ABAT ABAT 653 0.33 0.19 YES
3 ACSM1 ACSM1 ACSM1 1371 0.22 0.23 YES
4 ACSM2A ACSM2A ACSM2A 1939 0.18 0.25 YES
5 BDH2 BDH2 BDH2 2009 0.17 0.31 YES
6 HMGCS2 HMGCS2 HMGCS2 2543 0.14 0.32 YES
7 ALDH7A1 ALDH7A1 ALDH7A1 2782 0.13 0.35 YES
8 BDH1 BDH1 BDH1 2850 0.12 0.39 YES
9 ACSM3 ACSM3 ACSM3 3715 0.096 0.37 YES
10 ACAT1 ACAT1 ACAT1 4038 0.086 0.38 YES
11 ALDH2 ALDH2 ALDH2 4097 0.084 0.41 YES
12 HMGCS1 HMGCS1 HMGCS1 5335 0.058 0.36 NO
13 AKR1B10 AKR1B10 AKR1B10 6146 0.044 0.33 NO
14 OXCT2 OXCT2 OXCT2 6180 0.044 0.34 NO
15 ACAT2 ACAT2 ACAT2 7720 0.02 0.26 NO
16 PDHB PDHB PDHB 7823 0.018 0.26 NO
17 ALDH1B1 ALDH1B1 ALDH1B1 7924 0.017 0.26 NO
18 HADH HADH HADH 8860 0.0033 0.21 NO
19 ACADS ACADS ACADS 10090 -0.015 0.14 NO
20 L2HGDH L2HGDH L2HGDH 10114 -0.016 0.15 NO
21 PDHA1 PDHA1 PDHA1 10960 -0.029 0.11 NO
22 ALDH5A1 ALDH5A1 ALDH5A1 11699 -0.042 0.083 NO
23 ALDH9A1 ALDH9A1 ALDH9A1 12330 -0.053 0.065 NO
24 HMGCL HMGCL HMGCL 12508 -0.056 0.074 NO
25 ECHS1 ECHS1 ECHS1 12527 -0.056 0.091 NO
26 HADHA HADHA HADHA 13563 -0.08 0.06 NO
27 AACS AACS AACS 14214 -0.097 0.055 NO
28 ALDH3A2 ALDH3A2 ALDH3A2 14266 -0.098 0.085 NO
29 ACSM5 ACSM5 ACSM5 15329 -0.14 0.072 NO
30 GAD1 GAD1 GAD1 16355 -0.2 0.083 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 INOSITOL PHOSPHATE METABOLISM.

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

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 AT1R PATHWAY 32 genes.ES.table 0.33 1.3 0.14 1 0.97 0.16 0.14 0.13 0.81 0.38
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.53 1.7 0.025 1 0.54 0.62 0.32 0.43 0.9 0.46
BIOCARTA INTEGRIN PATHWAY 37 genes.ES.table 0.38 1.6 0.052 1 0.78 0.51 0.36 0.33 0.92 0.48
BIOCARTA KERATINOCYTE PATHWAY 45 genes.ES.table 0.45 1.5 0.086 1 0.88 0.31 0.16 0.26 1 0.56
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.33 1.4 0.11 1 0.95 0.41 0.36 0.26 0.81 0.4
BIOCARTA RHO PATHWAY 30 genes.ES.table 0.34 1.5 0.051 1 0.88 0.33 0.29 0.24 0.94 0.48
BIOCARTA MET PATHWAY 36 genes.ES.table 0.4 1.3 0.26 1 0.99 0.25 0.19 0.2 0.82 0.36
KEGG DRUG METABOLISM OTHER ENZYMES 39 genes.ES.table 0.48 1.3 0.098 1 0.98 0.44 0.18 0.36 0.8 0.36
KEGG ANTIGEN PROCESSING AND PRESENTATION 66 genes.ES.table 0.51 1.3 0.27 1 0.99 0.36 0.19 0.3 0.85 0.4
KEGG CYTOSOLIC DNA SENSING PATHWAY 41 genes.ES.table 0.5 1.3 0.23 1 0.98 0.39 0.23 0.3 0.81 0.37
genes ES table in pathway: BIOCARTA AT1R 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 BIRC3 BIRC3 BIRC3 320 0.37 0.11 YES
2 GAS2 GAS2 GAS2 708 0.28 0.18 YES
3 TNFRSF10A TNFRSF10A TNFRSF10A 1060 0.23 0.24 YES
4 CASP3 CASP3 CASP3 1478 0.2 0.28 YES
5 NFKBIA NFKBIA NFKBIA 1942 0.16 0.31 YES
6 CASP6 CASP6 CASP6 2233 0.14 0.34 YES
7 TNFRSF10B TNFRSF10B TNFRSF10B 2447 0.13 0.37 YES
8 NFKB1 NFKB1 NFKB1 2885 0.12 0.39 YES
9 TNFSF12 TNFSF12 TNFSF12 2942 0.11 0.42 YES
10 RELA RELA RELA 3372 0.098 0.43 YES
11 TNFSF10 TNFSF10 TNFSF10 3418 0.097 0.46 YES
12 TRADD TRADD TRADD 3533 0.094 0.49 YES
13 CASP7 CASP7 CASP7 3951 0.082 0.49 YES
14 BCL2 BCL2 BCL2 3988 0.081 0.52 YES
15 CFLAR CFLAR CFLAR 4999 0.058 0.48 YES
16 BIRC2 BIRC2 BIRC2 5119 0.055 0.49 YES
17 FADD FADD FADD 5397 0.05 0.49 YES
18 TRAF2 TRAF2 TRAF2 5438 0.049 0.51 YES
19 MAP3K14 MAP3K14 MAP3K14 5536 0.047 0.52 YES
20 APAF1 APAF1 APAF1 5647 0.045 0.53 YES
21 CYCS CYCS CYCS 5907 0.04 0.52 NO
22 SPTAN1 SPTAN1 SPTAN1 6171 0.035 0.52 NO
23 XIAP XIAP XIAP 6754 0.025 0.5 NO
24 RIPK1 RIPK1 RIPK1 6973 0.022 0.49 NO
25 CHUK CHUK CHUK 7636 0.012 0.46 NO
26 CASP10 CASP10 CASP10 10070 -0.022 0.33 NO
27 LMNA LMNA LMNA 10254 -0.025 0.33 NO
28 DFFA DFFA DFFA 10345 -0.026 0.33 NO
29 CASP9 CASP9 CASP9 10860 -0.034 0.32 NO
30 TNFRSF25 TNFRSF25 TNFRSF25 10981 -0.036 0.32 NO
31 CASP8 CASP8 CASP8 12431 -0.062 0.26 NO
32 DFFB DFFB DFFB 14667 -0.13 0.18 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 AT1R PATHWAY.

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R 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 DEATH 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 TUBB3 TUBB3 TUBB3 59 0.58 0.13 YES
2 TUBB8 TUBB8 TUBB8 826 0.26 0.15 YES
3 TUBB2B TUBB2B TUBB2B 1119 0.23 0.18 YES
4 CDH1 CDH1 CDH1 1442 0.2 0.21 YES
5 TUBB1 TUBB1 TUBB1 1467 0.2 0.26 YES
6 WAS WAS WAS 1669 0.18 0.29 YES
7 TUBB4Q TUBB4Q TUBB4Q 1685 0.18 0.33 YES
8 LY96 LY96 LY96 1840 0.17 0.36 YES
9 TUBB2A TUBB2A TUBB2A 2200 0.15 0.37 YES
10 KRT18 KRT18 KRT18 2519 0.13 0.39 YES
11 ARPC1B ARPC1B ARPC1B 2745 0.12 0.4 YES
12 HCLS1 HCLS1 HCLS1 2822 0.12 0.43 YES
13 TUBA1A TUBA1A TUBA1A 2943 0.11 0.44 YES
14 TUBA8 TUBA8 TUBA8 3089 0.11 0.46 YES
15 TUBA4A TUBA4A TUBA4A 3512 0.095 0.46 NO
16 CTTN CTTN CTTN 4063 0.079 0.45 NO
17 ARPC5 ARPC5 ARPC5 4714 0.063 0.43 NO
18 TUBA1C TUBA1C TUBA1C 4777 0.062 0.44 NO
19 TLR5 TLR5 TLR5 5671 0.045 0.4 NO
20 FYN FYN FYN 5719 0.044 0.4 NO
21 CD14 CD14 CD14 5906 0.04 0.4 NO
22 TUBA1B TUBA1B TUBA1B 6119 0.036 0.4 NO
23 TUBB6 TUBB6 TUBB6 6258 0.034 0.4 NO
24 CDC42 CDC42 CDC42 6498 0.03 0.39 NO
25 ACTB ACTB ACTB 6775 0.025 0.38 NO
26 TLR4 TLR4 TLR4 6815 0.024 0.39 NO
27 OCLN OCLN OCLN 7016 0.021 0.38 NO
28 ARHGEF2 ARHGEF2 ARHGEF2 7341 0.016 0.37 NO
29 ARPC3 ARPC3 ARPC3 7665 0.012 0.35 NO
30 ACTG1 ACTG1 ACTG1 7784 0.0097 0.35 NO
31 ARPC1A ARPC1A ARPC1A 7855 0.0085 0.34 NO
32 WASL WASL WASL 7912 0.0078 0.34 NO
33 ITGB1 ITGB1 ITGB1 8721 -0.0039 0.3 NO
34 TUBB2C TUBB2C TUBB2C 9077 -0.0089 0.28 NO
35 YWHAZ YWHAZ YWHAZ 9089 -0.009 0.28 NO
36 ARPC2 ARPC2 ARPC2 9678 -0.016 0.25 NO
37 ABL1 ABL1 ABL1 9732 -0.017 0.26 NO
38 TUBA3D TUBA3D TUBA3D 9797 -0.018 0.26 NO
39 ROCK1 ROCK1 ROCK1 9801 -0.018 0.26 NO
40 ROCK2 ROCK2 ROCK2 9938 -0.02 0.26 NO
41 ARPC5L ARPC5L ARPC5L 10104 -0.023 0.25 NO
42 YWHAQ YWHAQ YWHAQ 10259 -0.025 0.25 NO
43 NCL NCL NCL 10604 -0.03 0.24 NO
44 EZR EZR EZR 10899 -0.035 0.23 NO
45 TUBB TUBB TUBB 11450 -0.044 0.21 NO
46 PRKCA PRKCA PRKCA 11660 -0.048 0.21 NO
47 NCK2 NCK2 NCK2 11762 -0.049 0.21 NO
48 ARPC4 ARPC4 ARPC4 11802 -0.05 0.22 NO
49 RHOA RHOA RHOA 12687 -0.068 0.19 NO
50 CTNNB1 CTNNB1 CTNNB1 13608 -0.091 0.16 NO
51 CLDN1 CLDN1 CLDN1 13943 -0.1 0.16 NO
52 TUBB4 TUBB4 TUBB4 14151 -0.11 0.18 NO
53 NCK1 NCK1 NCK1 14773 -0.13 0.17 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 DEATH PATHWAY.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA DEATH 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 INTEGRIN 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 JUN JUN JUN 743 0.27 0.077 YES
2 ACTA1 ACTA1 ACTA1 1278 0.21 0.14 YES
3 SRC SRC SRC 2267 0.14 0.14 YES
4 MAP2K1 MAP2K1 MAP2K1 2520 0.13 0.19 YES
5 CAPN1 CAPN1 CAPN1 2849 0.12 0.22 YES
6 CSK CSK CSK 3320 0.1 0.24 YES
7 BCAR1 BCAR1 BCAR1 3369 0.098 0.28 YES
8 PXN PXN PXN 3378 0.098 0.32 YES
9 HRAS HRAS HRAS 4684 0.064 0.27 YES
10 ACTN3 ACTN3 ACTN3 4706 0.064 0.3 YES
11 RAPGEF1 RAPGEF1 RAPGEF1 4707 0.064 0.33 YES
12 PTK2 PTK2 PTK2 5448 0.049 0.31 YES
13 MAPK3 MAPK3 MAPK3 5525 0.047 0.32 YES
14 ZYX ZYX ZYX 5689 0.044 0.33 YES
15 FYN FYN FYN 5719 0.044 0.35 YES
16 VCL VCL VCL 5814 0.042 0.36 YES
17 MAPK8 MAPK8 MAPK8 6076 0.037 0.37 YES
18 CAPNS1 CAPNS1 CAPNS1 6147 0.036 0.38 YES
19 MAPK1 MAPK1 MAPK1 6376 0.032 0.38 YES
20 MAP2K2 MAP2K2 MAP2K2 7487 0.014 0.32 NO
21 RAP1A RAP1A RAP1A 7923 0.0076 0.3 NO
22 SHC1 SHC1 SHC1 8249 0.0028 0.28 NO
23 CAV1 CAV1 CAV1 8406 0.00058 0.28 NO
24 PPP1R12B PPP1R12B PPP1R12B 8410 0.00051 0.28 NO
25 TNS1 TNS1 TNS1 8626 -0.0025 0.26 NO
26 ITGB1 ITGB1 ITGB1 8721 -0.0039 0.26 NO
27 CRKL CRKL CRKL 8876 -0.0061 0.26 NO
28 GRB2 GRB2 GRB2 9749 -0.018 0.21 NO
29 ROCK1 ROCK1 ROCK1 9801 -0.018 0.22 NO
30 BCR BCR BCR 9953 -0.021 0.22 NO
31 SOS1 SOS1 SOS1 10158 -0.024 0.22 NO
32 RAF1 RAF1 RAF1 10640 -0.031 0.2 NO
33 ITGA1 ITGA1 ITGA1 10710 -0.032 0.21 NO
34 ACTN2 ACTN2 ACTN2 12060 -0.055 0.16 NO
35 RHOA RHOA RHOA 12687 -0.068 0.16 NO
36 CAPNS2 CAPNS2 CAPNS2 13918 -0.1 0.13 NO
37 ACTN1 ACTN1 ACTN1 16096 -0.2 0.097 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 INTEGRIN PATHWAY.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INTEGRIN 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 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 PRKCG PRKCG PRKCG 245 0.4 0.077 YES
2 JUN JUN JUN 743 0.27 0.11 YES
3 FASLG FASLG FASLG 898 0.25 0.16 YES
4 TNF TNF TNF 912 0.25 0.21 YES
5 CEBPA CEBPA CEBPA 1212 0.22 0.25 YES
6 EGFR EGFR EGFR 1659 0.18 0.26 YES
7 MAPK13 MAPK13 MAPK13 1748 0.17 0.3 YES
8 NFKBIA NFKBIA NFKBIA 1942 0.16 0.32 YES
9 EGF EGF EGF 1943 0.16 0.36 YES
10 HOXA7 HOXA7 HOXA7 2334 0.14 0.37 YES
11 FAS FAS FAS 2455 0.13 0.39 YES
12 MAP2K1 MAP2K1 MAP2K1 2520 0.13 0.42 YES
13 TNFRSF1B TNFRSF1B TNFRSF1B 2533 0.13 0.44 YES
14 NFKB1 NFKB1 NFKB1 2885 0.12 0.45 YES
15 RELA RELA RELA 3372 0.098 0.45 NO
16 BCL2 BCL2 BCL2 3988 0.081 0.43 NO
17 MAP2K3 MAP2K3 MAP2K3 4669 0.064 0.41 NO
18 HRAS HRAS HRAS 4684 0.064 0.42 NO
19 ETS1 ETS1 ETS1 5275 0.052 0.4 NO
20 MAPK3 MAPK3 MAPK3 5525 0.047 0.39 NO
21 MAP3K14 MAP3K14 MAP3K14 5536 0.047 0.4 NO
22 PRKCD PRKCD PRKCD 5780 0.043 0.4 NO
23 IKBKB IKBKB IKBKB 5782 0.043 0.41 NO
24 PRKCE PRKCE PRKCE 5999 0.039 0.41 NO
25 MAPK8 MAPK8 MAPK8 6076 0.037 0.41 NO
26 PRKCH PRKCH PRKCH 6332 0.032 0.4 NO
27 MAPK1 MAPK1 MAPK1 6376 0.032 0.41 NO
28 MAP3K5 MAP3K5 MAP3K5 6422 0.031 0.41 NO
29 SP1 SP1 SP1 6664 0.027 0.4 NO
30 MAP2K7 MAP2K7 MAP2K7 6730 0.026 0.41 NO
31 RIPK1 RIPK1 RIPK1 6973 0.022 0.4 NO
32 CHUK CHUK CHUK 7636 0.012 0.36 NO
33 DAXX DAXX DAXX 7791 0.0096 0.36 NO
34 TNFRSF1A TNFRSF1A TNFRSF1A 8824 -0.0053 0.3 NO
35 PRKCB PRKCB PRKCB 9934 -0.02 0.24 NO
36 MAP2K4 MAP2K4 MAP2K4 10043 -0.022 0.24 NO
37 MAPK14 MAPK14 MAPK14 10498 -0.029 0.22 NO
38 RAF1 RAF1 RAF1 10640 -0.031 0.22 NO
39 PRKCA PRKCA PRKCA 11660 -0.048 0.18 NO
40 MAP3K1 MAP3K1 MAP3K1 12018 -0.054 0.17 NO
41 ETS2 ETS2 ETS2 12445 -0.062 0.16 NO
42 PPP2CA PPP2CA PPP2CA 14364 -0.12 0.075 NO
43 FOS FOS FOS 14554 -0.12 0.092 NO
44 PRKCQ PRKCQ PRKCQ 16004 -0.2 0.055 NO
45 MAP2K6 MAP2K6 MAP2K6 16155 -0.21 0.094 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 KERATINOCYTE PATHWAY.

Figure S28.  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 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 BAIAP2 BAIAP2 BAIAP2 1178 0.22 0.061 YES
2 SRC SRC SRC 2267 0.14 0.082 YES
3 MYLK MYLK MYLK 2325 0.14 0.16 YES
4 ARHGAP4 ARHGAP4 ARHGAP4 2527 0.13 0.22 YES
5 ARPC1B ARPC1B ARPC1B 2745 0.12 0.28 YES
6 OPHN1 OPHN1 OPHN1 3067 0.11 0.32 YES
7 ARPC5 ARPC5 ARPC5 4714 0.063 0.27 YES
8 CFL1 CFL1 CFL1 4748 0.063 0.3 YES
9 LIMK1 LIMK1 LIMK1 5030 0.057 0.32 YES
10 ARHGEF5 ARHGEF5 ARHGEF5 5199 0.053 0.34 YES
11 VCL VCL VCL 5814 0.042 0.33 NO
12 ARHGAP1 ARHGAP1 ARHGAP1 6050 0.038 0.34 NO
13 ARHGEF11 ARHGEF11 ARHGEF11 6434 0.031 0.34 NO
14 ARHGEF1 ARHGEF1 ARHGEF1 6679 0.027 0.34 NO
15 ARHGAP5 ARHGAP5 ARHGAP5 7550 0.013 0.3 NO
16 ARPC3 ARPC3 ARPC3 7665 0.012 0.3 NO
17 ARPC1A ARPC1A ARPC1A 7855 0.0085 0.29 NO
18 PIP5K1A PIP5K1A PIP5K1A 8034 0.006 0.28 NO
19 PPP1R12B PPP1R12B PPP1R12B 8410 0.00051 0.26 NO
20 PFN1 PFN1 PFN1 8681 -0.0033 0.25 NO
21 ARHGAP6 ARHGAP6 ARHGAP6 8975 -0.0076 0.24 NO
22 ACTR3 ACTR3 ACTR3 9269 -0.012 0.23 NO
23 DIAPH1 DIAPH1 DIAPH1 9450 -0.014 0.22 NO
24 ARPC2 ARPC2 ARPC2 9678 -0.016 0.22 NO
25 ROCK1 ROCK1 ROCK1 9801 -0.018 0.22 NO
26 ACTR2 ACTR2 ACTR2 11613 -0.047 0.15 NO
27 GSN GSN GSN 11779 -0.05 0.17 NO
28 ARPC4 ARPC4 ARPC4 11802 -0.05 0.2 NO
29 RHOA RHOA RHOA 12687 -0.068 0.19 NO
30 PIP5K1B PIP5K1B PIP5K1B 15707 -0.18 0.12 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 PYK2 PATHWAY.

Figure S30.  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 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 ULBP3 ULBP3 ULBP3 96 0.51 0.03 YES
2 PRKCG PRKCG PRKCG 245 0.4 0.049 YES
3 RAET1L RAET1L RAET1L 271 0.39 0.074 YES
4 ULBP1 ULBP1 ULBP1 318 0.37 0.097 YES
5 NCR1 NCR1 NCR1 341 0.36 0.12 YES
6 KLRC3 KLRC3 KLRC3 478 0.32 0.14 YES
7 KIR2DL3 KIR2DL3 KIR2DL3 535 0.31 0.15 YES
8 KIR2DS4 KIR2DS4 KIR2DS4 617 0.3 0.17 YES
9 KIR2DL4 KIR2DL4 KIR2DL4 677 0.28 0.19 YES
10 TNFRSF10C TNFRSF10C TNFRSF10C 770 0.27 0.2 YES
11 NCR3 NCR3 NCR3 823 0.26 0.21 YES
12 KLRK1 KLRK1 KLRK1 834 0.26 0.23 YES
13 FASLG FASLG FASLG 898 0.25 0.25 YES
14 TNF TNF TNF 912 0.25 0.26 YES
15 LCK LCK LCK 1009 0.24 0.27 YES
16 TNFRSF10A TNFRSF10A TNFRSF10A 1060 0.23 0.29 YES
17 ITGAL ITGAL ITGAL 1094 0.23 0.3 YES
18 CD244 CD244 CD244 1203 0.22 0.31 YES
19 KIR3DL1 KIR3DL1 KIR3DL1 1259 0.22 0.32 YES
20 KIR3DL2 KIR3DL2 KIR3DL2 1297 0.21 0.33 YES
21 PIK3CG PIK3CG PIK3CG 1328 0.21 0.35 YES
22 ZAP70 ZAP70 ZAP70 1380 0.2 0.36 YES
23 ICAM1 ICAM1 ICAM1 1469 0.2 0.37 YES
24 CASP3 CASP3 CASP3 1478 0.2 0.38 YES
25 PIK3R5 PIK3R5 PIK3R5 1590 0.19 0.38 YES
26 CD247 CD247 CD247 1593 0.19 0.4 YES
27 CD48 CD48 CD48 1616 0.18 0.41 YES
28 FCGR3A FCGR3A FCGR3A 1638 0.18 0.42 YES
29 PRF1 PRF1 PRF1 1643 0.18 0.43 YES
30 RAC3 RAC3 RAC3 1738 0.18 0.44 YES
31 KIR2DL1 KIR2DL1 KIR2DL1 1758 0.17 0.45 YES
32 VAV1 VAV1 VAV1 1780 0.17 0.46 YES
33 RAET1G RAET1G RAET1G 1862 0.17 0.47 YES
34 SH2D1A SH2D1A SH2D1A 1899 0.16 0.48 YES
35 FCGR3B FCGR3B FCGR3B 1946 0.16 0.49 YES
36 GZMB GZMB GZMB 1954 0.16 0.5 YES
37 PAK1 PAK1 PAK1 2252 0.14 0.49 YES
38 TYROBP TYROBP TYROBP 2255 0.14 0.5 YES
39 LCP2 LCP2 LCP2 2310 0.14 0.51 YES
40 KLRC1 KLRC1 KLRC1 2339 0.14 0.51 YES
41 IFNG IFNG IFNG 2373 0.14 0.52 YES
42 SYK SYK SYK 2387 0.14 0.53 YES
43 TNFRSF10B TNFRSF10B TNFRSF10B 2447 0.13 0.54 YES
44 FAS FAS FAS 2455 0.13 0.55 YES
45 MAP2K1 MAP2K1 MAP2K1 2520 0.13 0.55 YES
46 FCER1G FCER1G FCER1G 2677 0.12 0.55 YES
47 SH2D1B SH2D1B SH2D1B 2919 0.11 0.54 YES
48 PPP3CC PPP3CC PPP3CC 2994 0.11 0.55 YES
49 NFAT5 NFAT5 NFAT5 3062 0.11 0.55 YES
50 ITGB2 ITGB2 ITGB2 3275 0.1 0.55 YES
51 SH3BP2 SH3BP2 SH3BP2 3277 0.1 0.55 YES
52 HCST HCST HCST 3387 0.098 0.55 YES
53 TNFSF10 TNFSF10 TNFSF10 3418 0.097 0.56 YES
54 ICAM2 ICAM2 ICAM2 3774 0.087 0.55 NO
55 NCR2 NCR2 NCR2 3815 0.085 0.55 NO
56 RAC2 RAC2 RAC2 4224 0.074 0.53 NO
57 PTPN6 PTPN6 PTPN6 4248 0.074 0.54 NO
58 KLRC2 KLRC2 KLRC2 4297 0.073 0.54 NO
59 ULBP2 ULBP2 ULBP2 4619 0.065 0.52 NO
60 HRAS HRAS HRAS 4684 0.064 0.52 NO
61 HLA-E HLA-E HLA-E 4836 0.061 0.52 NO
62 PTK2B PTK2B PTK2B 5419 0.049 0.49 NO
63 HLA-C HLA-C HLA-C 5483 0.048 0.49 NO
64 TNFRSF10D TNFRSF10D TNFRSF10D 5501 0.048 0.49 NO
65 MAPK3 MAPK3 MAPK3 5525 0.047 0.5 NO
66 KRAS KRAS KRAS 5526 0.047 0.5 NO
67 VAV3 VAV3 VAV3 5623 0.046 0.5 NO
68 NFATC3 NFATC3 NFATC3 5696 0.044 0.5 NO
69 NRAS NRAS NRAS 5708 0.044 0.5 NO
70 FYN FYN FYN 5719 0.044 0.5 NO
71 IFNAR2 IFNAR2 IFNAR2 5898 0.041 0.49 NO
72 HLA-B HLA-B HLA-B 5979 0.039 0.49 NO
73 PLCG2 PLCG2 PLCG2 6116 0.036 0.48 NO
74 PLCG1 PLCG1 PLCG1 6280 0.033 0.48 NO
75 MAPK1 MAPK1 MAPK1 6376 0.032 0.48 NO
76 ARAF ARAF ARAF 6553 0.029 0.47 NO
77 HLA-A HLA-A HLA-A 6572 0.028 0.47 NO
78 SOS2 SOS2 SOS2 6656 0.027 0.46 NO
79 RAC1 RAC1 RAC1 6945 0.022 0.45 NO
80 MAP2K2 MAP2K2 MAP2K2 7487 0.014 0.42 NO
81 PTPN11 PTPN11 PTPN11 7562 0.013 0.42 NO
82 PIK3CD PIK3CD PIK3CD 7763 0.01 0.41 NO
83 BID BID BID 7852 0.0085 0.4 NO
84 HLA-G HLA-G HLA-G 7856 0.0085 0.4 NO
85 SHC1 SHC1 SHC1 8249 0.0028 0.38 NO
86 PPP3CA PPP3CA PPP3CA 8487 -0.00061 0.37 NO
87 IFNGR2 IFNGR2 IFNGR2 8501 -0.00074 0.37 NO
88 PIK3R3 PIK3R3 PIK3R3 8575 -0.0019 0.36 NO
89 SHC2 SHC2 SHC2 9073 -0.0088 0.34 NO
90 IFNGR1 IFNGR1 IFNGR1 9290 -0.012 0.32 NO
91 PIK3R2 PIK3R2 PIK3R2 9581 -0.015 0.31 NO
92 GRB2 GRB2 GRB2 9749 -0.018 0.3 NO
93 PRKCB PRKCB PRKCB 9934 -0.02 0.29 NO
94 PPP3CB PPP3CB PPP3CB 9968 -0.021 0.29 NO
95 SOS1 SOS1 SOS1 10158 -0.024 0.28 NO
96 IFNAR1 IFNAR1 IFNAR1 10290 -0.026 0.28 NO
97 VAV2 VAV2 VAV2 10521 -0.029 0.27 NO
98 RAF1 RAF1 RAF1 10640 -0.031 0.26 NO
99 CHP CHP CHP 10692 -0.032 0.26 NO
100 RAET1E RAET1E RAET1E 11396 -0.043 0.22 NO
101 LAT LAT LAT 11483 -0.044 0.22 NO
102 MICA MICA MICA 11548 -0.046 0.22 NO
103 PRKCA PRKCA PRKCA 11660 -0.048 0.22 NO
104 PIK3R1 PIK3R1 PIK3R1 11910 -0.052 0.21 NO
105 PPP3R1 PPP3R1 PPP3R1 12963 -0.073 0.15 NO
106 PIK3CB PIK3CB PIK3CB 13996 -0.1 0.1 NO
107 KLRD1 KLRD1 KLRD1 14078 -0.1 0.1 NO
108 BRAF BRAF BRAF 14267 -0.11 0.1 NO
109 PIK3CA PIK3CA PIK3CA 14815 -0.13 0.08 NO
110 PPP3R2 PPP3R2 PPP3R2 15712 -0.18 0.042 NO
111 NFATC4 NFATC4 NFATC4 15863 -0.19 0.046 NO
112 SHC3 SHC3 SHC3 15908 -0.19 0.057 NO
113 SHC4 SHC4 SHC4 15981 -0.2 0.067 NO
114 NFATC1 NFATC1 NFATC1 16395 -0.23 0.059 NO
115 NFATC2 NFATC2 NFATC2 17009 -0.31 0.046 NO

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

Figure S32.  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 MET PATHWAY

Table S17.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RXRG RXRG RXRG 156 0.46 0.09 YES
2 PRKCG PRKCG PRKCG 245 0.4 0.17 YES
3 PIK3CG PIK3CG PIK3CG 1328 0.21 0.16 YES
4 CDKN2A CDKN2A CDKN2A 1362 0.21 0.2 YES
5 PIK3R5 PIK3R5 PIK3R5 1590 0.19 0.22 YES
6 EGFR EGFR EGFR 1659 0.18 0.26 YES
7 RASSF5 RASSF5 RASSF5 1906 0.16 0.28 YES
8 EGF EGF EGF 1943 0.16 0.31 YES
9 AKT1 AKT1 AKT1 2355 0.14 0.32 YES
10 MAP2K1 MAP2K1 MAP2K1 2520 0.13 0.34 YES
11 ERBB2 ERBB2 ERBB2 2545 0.13 0.37 YES
12 AKT3 AKT3 AKT3 3101 0.11 0.36 YES
13 RASSF1 RASSF1 RASSF1 3115 0.11 0.38 YES
14 PDPK1 PDPK1 PDPK1 4343 0.072 0.33 NO
15 BAD BAD BAD 4680 0.064 0.32 NO
16 HRAS HRAS HRAS 4684 0.064 0.34 NO
17 RARB RARB RARB 4837 0.061 0.34 NO
18 TP53 TP53 TP53 5243 0.052 0.33 NO
19 MAPK3 MAPK3 MAPK3 5525 0.047 0.32 NO
20 KRAS KRAS KRAS 5526 0.047 0.33 NO
21 NRAS NRAS NRAS 5708 0.044 0.33 NO
22 PLCG2 PLCG2 PLCG2 6116 0.036 0.32 NO
23 PLCG1 PLCG1 PLCG1 6280 0.033 0.31 NO
24 MAPK1 MAPK1 MAPK1 6376 0.032 0.32 NO
25 ARAF ARAF ARAF 6553 0.029 0.31 NO
26 SOS2 SOS2 SOS2 6656 0.027 0.31 NO
27 CCND1 CCND1 CCND1 7313 0.016 0.28 NO
28 TGFA TGFA TGFA 7457 0.014 0.27 NO
29 MAP2K2 MAP2K2 MAP2K2 7487 0.014 0.28 NO
30 STK4 STK4 STK4 7630 0.012 0.27 NO
31 AKT2 AKT2 AKT2 7657 0.012 0.27 NO
32 PIK3CD PIK3CD PIK3CD 7763 0.01 0.27 NO
33 FOXO3 FOXO3 FOXO3 8267 0.0025 0.24 NO
34 PIK3R3 PIK3R3 PIK3R3 8575 -0.0019 0.22 NO
35 CDK4 CDK4 CDK4 9491 -0.014 0.17 NO
36 PIK3R2 PIK3R2 PIK3R2 9581 -0.015 0.17 NO
37 GRB2 GRB2 GRB2 9749 -0.018 0.17 NO
38 PRKCB PRKCB PRKCB 9934 -0.02 0.16 NO
39 SOS1 SOS1 SOS1 10158 -0.024 0.15 NO
40 RAF1 RAF1 RAF1 10640 -0.031 0.13 NO
41 CASP9 CASP9 CASP9 10860 -0.034 0.13 NO
42 E2F3 E2F3 E2F3 10953 -0.036 0.13 NO
43 CDK6 CDK6 CDK6 11304 -0.042 0.12 NO
44 RXRB RXRB RXRB 11507 -0.045 0.12 NO
45 PRKCA PRKCA PRKCA 11660 -0.048 0.12 NO
46 PIK3R1 PIK3R1 PIK3R1 11910 -0.052 0.12 NO
47 RXRA RXRA RXRA 12269 -0.059 0.11 NO
48 PIK3CB PIK3CB PIK3CB 13996 -0.1 0.034 NO
49 BRAF BRAF BRAF 14267 -0.11 0.043 NO
50 PIK3CA PIK3CA PIK3CA 14815 -0.13 0.041 NO
51 RB1 RB1 RB1 14928 -0.14 0.064 NO
52 FHIT FHIT FHIT 16326 -0.22 0.034 NO
53 E2F2 E2F2 E2F2 16445 -0.24 0.078 NO

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

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

genes ES table in pathway: KEGG DRUG METABOLISM OTHER ENZYMES

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 IL1A IL1A IL1A 191 0.43 0.069 YES
2 HLA-DOB HLA-DOB HLA-DOB 367 0.36 0.12 YES
3 KIR2DL3 KIR2DL3 KIR2DL3 535 0.31 0.17 YES
4 HLA-DQA2 HLA-DQA2 HLA-DQA2 544 0.31 0.23 YES
5 FASLG FASLG FASLG 898 0.25 0.26 YES
6 TNF TNF TNF 912 0.25 0.3 YES
7 HLA-DOA HLA-DOA HLA-DOA 1074 0.23 0.34 YES
8 KIR3DL1 KIR3DL1 KIR3DL1 1259 0.22 0.36 YES
9 KIR3DL2 KIR3DL2 KIR3DL2 1297 0.21 0.4 YES
10 HLA-DQA1 HLA-DQA1 HLA-DQA1 1452 0.2 0.43 YES
11 HLA-DMB HLA-DMB HLA-DMB 1461 0.2 0.47 YES
12 PRF1 PRF1 PRF1 1643 0.18 0.49 YES
13 HLA-DMA HLA-DMA HLA-DMA 1652 0.18 0.52 YES
14 KIR2DL1 KIR2DL1 KIR2DL1 1758 0.17 0.55 YES
15 GZMB GZMB GZMB 1954 0.16 0.57 YES
16 KLRC1 KLRC1 KLRC1 2339 0.14 0.57 YES
17 IFNG IFNG IFNG 2373 0.14 0.6 YES
18 FAS FAS FAS 2455 0.13 0.62 YES
19 HLA-DPB1 HLA-DPB1 HLA-DPB1 2564 0.13 0.63 YES
20 HLA-DRA HLA-DRA HLA-DRA 2861 0.12 0.64 YES
21 IL6 IL6 IL6 2923 0.11 0.66 YES
22 CD80 CD80 CD80 2948 0.11 0.68 YES
23 CD86 CD86 CD86 2963 0.11 0.7 YES
24 HLA-DRB1 HLA-DRB1 HLA-DRB1 3032 0.11 0.71 YES
25 HLA-DRB5 HLA-DRB5 HLA-DRB5 3350 0.099 0.71 YES
26 HLA-DPA1 HLA-DPA1 HLA-DPA1 3374 0.098 0.73 YES
27 IL1B IL1B IL1B 3987 0.081 0.71 NO
28 HLA-E HLA-E HLA-E 4836 0.061 0.67 NO
29 HLA-F HLA-F HLA-F 5160 0.054 0.66 NO
30 HLA-C HLA-C HLA-C 5483 0.048 0.66 NO
31 HLA-B HLA-B HLA-B 5979 0.039 0.64 NO
32 HLA-A HLA-A HLA-A 6572 0.028 0.61 NO
33 HLA-G HLA-G HLA-G 7856 0.0085 0.54 NO
34 CD28 CD28 CD28 10064 -0.022 0.42 NO
35 KLRD1 KLRD1 KLRD1 14078 -0.1 0.21 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 DRUG METABOLISM OTHER ENZYMES.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM OTHER ENZYMES, 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 ANTIGEN PROCESSING AND PRESENTATION

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 IL1A IL1A IL1A 191 0.43 0.068 YES
2 IL12B IL12B IL12B 217 0.42 0.14 YES
3 HLA-DOB HLA-DOB HLA-DOB 367 0.36 0.2 YES
4 GAD1 GAD1 GAD1 401 0.35 0.26 YES
5 HLA-DQA2 HLA-DQA2 HLA-DQA2 544 0.31 0.31 YES
6 FASLG FASLG FASLG 898 0.25 0.33 YES
7 TNF TNF TNF 912 0.25 0.38 YES
8 HLA-DOA HLA-DOA HLA-DOA 1074 0.23 0.41 YES
9 HLA-DQA1 HLA-DQA1 HLA-DQA1 1452 0.2 0.43 YES
10 HLA-DMB HLA-DMB HLA-DMB 1461 0.2 0.46 YES
11 PRF1 PRF1 PRF1 1643 0.18 0.48 YES
12 HLA-DMA HLA-DMA HLA-DMA 1652 0.18 0.52 YES
13 GZMB GZMB GZMB 1954 0.16 0.53 YES
14 ICA1 ICA1 ICA1 2157 0.15 0.55 YES
15 IFNG IFNG IFNG 2373 0.14 0.56 YES
16 FAS FAS FAS 2455 0.13 0.58 YES
17 HLA-DPB1 HLA-DPB1 HLA-DPB1 2564 0.13 0.6 YES
18 HLA-DRA HLA-DRA HLA-DRA 2861 0.12 0.6 YES
19 CD80 CD80 CD80 2948 0.11 0.62 YES
20 CD86 CD86 CD86 2963 0.11 0.64 YES
21 HLA-DRB1 HLA-DRB1 HLA-DRB1 3032 0.11 0.65 YES
22 HLA-DRB5 HLA-DRB5 HLA-DRB5 3350 0.099 0.65 YES
23 HLA-DPA1 HLA-DPA1 HLA-DPA1 3374 0.098 0.67 YES
24 IL1B IL1B IL1B 3987 0.081 0.65 NO
25 LTA LTA LTA 4379 0.071 0.64 NO
26 HLA-E HLA-E HLA-E 4836 0.061 0.63 NO
27 HLA-F HLA-F HLA-F 5160 0.054 0.62 NO
28 HLA-C HLA-C HLA-C 5483 0.048 0.61 NO
29 HLA-B HLA-B HLA-B 5979 0.039 0.59 NO
30 HLA-A HLA-A HLA-A 6572 0.028 0.56 NO
31 HLA-G HLA-G HLA-G 7856 0.0085 0.49 NO
32 CD28 CD28 CD28 10064 -0.022 0.37 NO
33 HSPD1 HSPD1 HSPD1 10600 -0.03 0.34 NO
34 IL12A IL12A IL12A 11026 -0.037 0.33 NO
35 CPE CPE CPE 11760 -0.049 0.3 NO
36 PTPRN2 PTPRN2 PTPRN2 13764 -0.096 0.2 NO
37 PTPRN PTPRN PTPRN 15417 -0.16 0.14 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 ANTIGEN PROCESSING AND PRESENTATION.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION, 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 CYTOSOLIC DNA SENSING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL12B IL12B IL12B 217 0.42 0.082 YES
2 HLA-DOB HLA-DOB HLA-DOB 367 0.36 0.15 YES
3 HLA-DQA2 HLA-DQA2 HLA-DQA2 544 0.31 0.21 YES
4 FASLG FASLG FASLG 898 0.25 0.25 YES
5 TNF TNF TNF 912 0.25 0.31 YES
6 CD40LG CD40LG CD40LG 1035 0.23 0.35 YES
7 HLA-DOA HLA-DOA HLA-DOA 1074 0.23 0.4 YES
8 HLA-DQA1 HLA-DQA1 HLA-DQA1 1452 0.2 0.43 YES
9 HLA-DMB HLA-DMB HLA-DMB 1461 0.2 0.47 YES
10 PRF1 PRF1 PRF1 1643 0.18 0.5 YES
11 HLA-DMA HLA-DMA HLA-DMA 1652 0.18 0.54 YES
12 GZMB GZMB GZMB 1954 0.16 0.56 YES
13 IFNG IFNG IFNG 2373 0.14 0.57 YES
14 FAS FAS FAS 2455 0.13 0.59 YES
15 HLA-DPB1 HLA-DPB1 HLA-DPB1 2564 0.13 0.62 YES
16 HLA-DRA HLA-DRA HLA-DRA 2861 0.12 0.63 YES
17 CD80 CD80 CD80 2948 0.11 0.65 YES
18 CD86 CD86 CD86 2963 0.11 0.67 YES
19 HLA-DRB1 HLA-DRB1 HLA-DRB1 3032 0.11 0.69 YES
20 HLA-DRB5 HLA-DRB5 HLA-DRB5 3350 0.099 0.7 YES
21 HLA-DPA1 HLA-DPA1 HLA-DPA1 3374 0.098 0.72 YES
22 HLA-E HLA-E HLA-E 4836 0.061 0.65 NO
23 HLA-F HLA-F HLA-F 5160 0.054 0.64 NO
24 HLA-C HLA-C HLA-C 5483 0.048 0.64 NO
25 HLA-B HLA-B HLA-B 5979 0.039 0.62 NO
26 HLA-A HLA-A HLA-A 6572 0.028 0.59 NO
27 HLA-G HLA-G HLA-G 7856 0.0085 0.52 NO
28 CD28 CD28 CD28 10064 -0.022 0.4 NO
29 IL12A IL12A IL12A 11026 -0.037 0.36 NO
30 CD40 CD40 CD40 11476 -0.044 0.34 NO
31 IL10 IL10 IL10 12844 -0.071 0.28 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 CYTOSOLIC DNA SENSING PATHWAY.

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

Fold change

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

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
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.52 1.5 0.11 0.23 0.78 0.66 0.38 0.41 0.16 0.03
KEGG OXIDATIVE PHOSPHORYLATION 113 genes.ES.table 0.46 1.5 0.18 0.26 0.85 0.68 0.34 0.45 0.19 0.032
KEGG N GLYCAN BIOSYNTHESIS 45 genes.ES.table 0.25 1 0.42 0.79 1 0.42 0.3 0.29 0.72 0.23
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.51 1.8 0.026 0.23 0.28 0.6 0.37 0.38 0 0.067
KEGG RIBOSOME 84 genes.ES.table 0.63 1.7 0.049 0.085 0.42 0.8 0.25 0.6 0 0.004
KEGG RNA DEGRADATION 56 genes.ES.table 0.38 1.8 0.039 0.16 0.35 0.45 0.28 0.32 0 0.034
KEGG RNA POLYMERASE 28 genes.ES.table 0.32 1.2 0.26 0.51 1 0.43 0.35 0.28 0.43 0.1
KEGG DNA REPLICATION 35 genes.ES.table 0.65 1.7 0.029 0.087 0.37 0.63 0.2 0.5 0 0.009
KEGG SPLICEOSOME 125 genes.ES.table 0.35 1.6 0.048 0.17 0.67 0.54 0.4 0.33 0.1 0.015
KEGG BASE EXCISION REPAIR 32 genes.ES.table 0.38 1.2 0.3 0.54 1 0.5 0.29 0.36 0.46 0.11
genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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 TARSL2 TARSL2 TARSL2 2114 0.13 -0.046 YES
2 TARS TARS TARS 2257 0.12 0.015 YES
3 LARS LARS LARS 2717 0.1 0.047 YES
4 IARS IARS IARS 2845 0.097 0.096 YES
5 RARS RARS RARS 2909 0.095 0.15 YES
6 LARS2 LARS2 LARS2 3010 0.092 0.19 YES
7 MTFMT MTFMT MTFMT 3283 0.084 0.23 YES
8 FARSA FARSA FARSA 3359 0.082 0.27 YES
9 CARS CARS CARS 3450 0.079 0.31 YES
10 MARS MARS MARS 3752 0.072 0.33 YES
11 HARS HARS HARS 3887 0.069 0.36 YES
12 EPRS EPRS EPRS 4391 0.06 0.37 YES
13 RARS2 RARS2 RARS2 4937 0.051 0.37 YES
14 QARS QARS QARS 5381 0.044 0.37 YES
15 CARS2 CARS2 CARS2 5447 0.043 0.39 YES
16 AARS2 AARS2 AARS2 5451 0.043 0.42 YES
17 FARS2 FARS2 FARS2 5552 0.042 0.43 YES
18 YARS YARS YARS 5785 0.039 0.44 YES
19 SARS SARS SARS 5820 0.038 0.46 YES
20 IARS2 IARS2 IARS2 5934 0.037 0.48 YES
21 PSTK PSTK PSTK 5960 0.036 0.5 YES
22 EARS2 EARS2 EARS2 6117 0.034 0.51 YES
23 MARS2 MARS2 MARS2 6452 0.03 0.51 YES
24 GARS GARS GARS 6626 0.027 0.51 YES
25 HARS2 HARS2 HARS2 7419 0.017 0.48 NO
26 FARSB FARSB FARSB 7447 0.017 0.48 NO
27 WARS WARS WARS 7881 0.011 0.47 NO
28 NARS2 NARS2 NARS2 8154 0.0079 0.46 NO
29 DARS2 DARS2 DARS2 8214 0.0071 0.46 NO
30 AARS AARS AARS 8575 0.0022 0.44 NO
31 NARS NARS NARS 8620 0.0017 0.44 NO
32 PARS2 PARS2 PARS2 8626 0.0016 0.44 NO
33 SEPSECS SEPSECS SEPSECS 8987 -0.0028 0.42 NO
34 DARS DARS DARS 9391 -0.0084 0.4 NO
35 KARS KARS KARS 9680 -0.013 0.39 NO
36 VARS2 VARS2 VARS2 10153 -0.019 0.38 NO
37 WARS2 WARS2 WARS2 10166 -0.019 0.39 NO
38 SARS2 SARS2 SARS2 10304 -0.021 0.39 NO
39 VARS VARS VARS 10448 -0.023 0.4 NO
40 YARS2 YARS2 YARS2 11032 -0.033 0.38 NO

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

Figure S42.  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 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 EXOSC5 EXOSC5 EXOSC5 289 0.35 0.073 YES
2 ENO2 ENO2 ENO2 361 0.33 0.15 YES
3 EXOSC7 EXOSC7 EXOSC7 1141 0.2 0.16 YES
4 LSM3 LSM3 LSM3 2085 0.13 0.14 YES
5 ZCCHC7 ZCCHC7 ZCCHC7 2087 0.13 0.17 YES
6 HSPA9 HSPA9 HSPA9 2377 0.12 0.18 YES
7 CNOT10 CNOT10 CNOT10 2577 0.11 0.2 YES
8 EXOSC3 EXOSC3 EXOSC3 2675 0.1 0.22 YES
9 EDC3 EDC3 EDC3 3054 0.09 0.22 YES
10 PAPD7 PAPD7 PAPD7 3214 0.086 0.23 YES
11 SKIV2L2 SKIV2L2 SKIV2L2 3422 0.08 0.24 YES
12 LSM5 LSM5 LSM5 3439 0.08 0.26 YES
13 DCP1B DCP1B DCP1B 3618 0.075 0.27 YES
14 DCP1A DCP1A DCP1A 3729 0.072 0.28 YES
15 EXOSC2 EXOSC2 EXOSC2 3832 0.071 0.29 YES
16 ENO3 ENO3 ENO3 3957 0.068 0.3 YES
17 DCP2 DCP2 DCP2 4013 0.067 0.32 YES
18 CNOT7 CNOT7 CNOT7 4114 0.065 0.33 YES
19 HSPD1 HSPD1 HSPD1 4189 0.064 0.34 YES
20 LSM6 LSM6 LSM6 4213 0.063 0.35 YES
21 EXOSC4 EXOSC4 EXOSC4 4295 0.062 0.36 YES
22 LSM4 LSM4 LSM4 4537 0.058 0.37 YES
23 LSM2 LSM2 LSM2 4733 0.054 0.37 YES
24 TTC37 TTC37 TTC37 4973 0.051 0.37 YES
25 CNOT6L CNOT6L CNOT6L 4980 0.05 0.38 YES
26 NAA38 NAA38 NAA38 5507 0.043 0.36 NO
27 WDR61 WDR61 WDR61 5751 0.039 0.36 NO
28 EXOSC9 EXOSC9 EXOSC9 5772 0.039 0.37 NO
29 RQCD1 RQCD1 RQCD1 5970 0.036 0.36 NO
30 XRN1 XRN1 XRN1 5998 0.036 0.37 NO
31 DDX6 DDX6 DDX6 6679 0.026 0.34 NO
32 DIS3 DIS3 DIS3 6982 0.023 0.33 NO
33 XRN2 XRN2 XRN2 7168 0.02 0.32 NO
34 ENO1 ENO1 ENO1 7624 0.014 0.3 NO
35 CNOT3 CNOT3 CNOT3 7659 0.014 0.3 NO
36 EXOSC8 EXOSC8 EXOSC8 7680 0.014 0.3 NO
37 LSM1 LSM1 LSM1 7718 0.013 0.31 NO
38 PNPT1 PNPT1 PNPT1 7727 0.013 0.31 NO
39 LSM7 LSM7 LSM7 7959 0.01 0.3 NO
40 PATL1 PATL1 PATL1 7987 0.0099 0.3 NO
41 CNOT4 CNOT4 CNOT4 8050 0.0092 0.3 NO
42 CNOT2 CNOT2 CNOT2 8202 0.0073 0.29 NO
43 CNOT6 CNOT6 CNOT6 8423 0.0044 0.28 NO
44 SKIV2L SKIV2L SKIV2L 8427 0.0044 0.28 NO
45 PAPOLA PAPOLA PAPOLA 8444 0.0041 0.28 NO
46 EXOSC10 EXOSC10 EXOSC10 8823 -0.00071 0.26 NO
47 C1D C1D C1D 10058 -0.018 0.2 NO
48 CNOT1 CNOT1 CNOT1 10262 -0.02 0.19 NO
49 PAPOLG PAPOLG PAPOLG 10747 -0.028 0.17 NO
50 EXOSC1 EXOSC1 EXOSC1 11284 -0.037 0.15 NO
51 PARN PARN PARN 11790 -0.047 0.13 NO
52 EDC4 EDC4 EDC4 12114 -0.053 0.13 NO
53 DCPS DCPS DCPS 14155 -0.12 0.041 NO
54 MPHOSPH6 MPHOSPH6 MPHOSPH6 14693 -0.14 0.046 NO
55 EXOSC6 EXOSC6 EXOSC6 15105 -0.16 0.063 NO
56 PAPOLB PAPOLB PAPOLB 17236 -0.36 0.033 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 OXIDATIVE PHOSPHORYLATION.

Figure S44.  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 N GLYCAN BIOSYNTHESIS

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 POLE2 POLE2 POLE2 884 0.23 0.027 YES
2 GTF2H2 GTF2H2 GTF2H2 909 0.23 0.1 YES
3 RFC4 RFC4 RFC4 1377 0.18 0.13 YES
4 RPA3 RPA3 RPA3 1940 0.14 0.15 YES
5 ERCC8 ERCC8 ERCC8 1944 0.14 0.19 YES
6 LIG1 LIG1 LIG1 2251 0.12 0.21 YES
7 POLD2 POLD2 POLD2 2295 0.12 0.25 YES
8 POLE3 POLE3 POLE3 2416 0.11 0.28 YES
9 ERCC1 ERCC1 ERCC1 2448 0.11 0.32 YES
10 POLD1 POLD1 POLD1 2741 0.1 0.33 YES
11 RFC5 RFC5 RFC5 2773 0.1 0.37 YES
12 RFC1 RFC1 RFC1 2860 0.096 0.39 YES
13 RFC2 RFC2 RFC2 3109 0.089 0.41 YES
14 POLE4 POLE4 POLE4 3362 0.082 0.42 YES
15 RFC3 RFC3 RFC3 4394 0.06 0.38 YES
16 MNAT1 MNAT1 MNAT1 4655 0.056 0.39 YES
17 ERCC2 ERCC2 ERCC2 4770 0.054 0.4 YES
18 DDB1 DDB1 DDB1 4793 0.053 0.41 YES
19 XPA XPA XPA 4901 0.052 0.42 YES
20 CETN2 CETN2 CETN2 4968 0.051 0.44 YES
21 CUL4B CUL4B CUL4B 5055 0.049 0.45 YES
22 CDK7 CDK7 CDK7 5095 0.049 0.46 YES
23 PCNA PCNA PCNA 5117 0.048 0.48 YES
24 RPA1 RPA1 RPA1 5573 0.042 0.47 NO
25 RAD23A RAD23A RAD23A 5962 0.036 0.46 NO
26 CCNH CCNH CCNH 6727 0.026 0.42 NO
27 GTF2H3 GTF2H3 GTF2H3 7607 0.015 0.38 NO
28 RBX1 RBX1 RBX1 7700 0.014 0.38 NO
29 RPA2 RPA2 RPA2 8027 0.0094 0.36 NO
30 XPC XPC XPC 8593 0.0021 0.33 NO
31 POLD3 POLD3 POLD3 8651 0.0012 0.33 NO
32 POLE POLE POLE 8727 0.00048 0.32 NO
33 ERCC4 ERCC4 ERCC4 8736 0.00038 0.32 NO
34 ERCC3 ERCC3 ERCC3 8892 -0.0016 0.32 NO
35 GTF2H5 GTF2H5 GTF2H5 10253 -0.02 0.25 NO
36 DDB2 DDB2 DDB2 11409 -0.039 0.19 NO
37 GTF2H4 GTF2H4 GTF2H4 11545 -0.042 0.2 NO
38 ERCC5 ERCC5 ERCC5 12110 -0.053 0.19 NO
39 CUL4A CUL4A CUL4A 12250 -0.056 0.2 NO
40 GTF2H1 GTF2H1 GTF2H1 12361 -0.058 0.21 NO
41 RPA4 RPA4 RPA4 13149 -0.079 0.19 NO
42 ERCC6 ERCC6 ERCC6 13689 -0.098 0.19 NO
43 POLD4 POLD4 POLD4 14213 -0.12 0.2 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 N GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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 POLE2 POLE2 POLE2 884 0.23 0.023 YES
2 MCM2 MCM2 MCM2 1168 0.2 0.069 YES
3 PRIM1 PRIM1 PRIM1 1331 0.18 0.12 YES
4 RFC4 RFC4 RFC4 1377 0.18 0.17 YES
5 RNASEH2A RNASEH2A RNASEH2A 1459 0.17 0.22 YES
6 RPA3 RPA3 RPA3 1940 0.14 0.24 YES
7 FEN1 FEN1 FEN1 1948 0.14 0.28 YES
8 LIG1 LIG1 LIG1 2251 0.12 0.3 YES
9 POLD2 POLD2 POLD2 2295 0.12 0.33 YES
10 PRIM2 PRIM2 PRIM2 2301 0.12 0.37 YES
11 POLE3 POLE3 POLE3 2416 0.11 0.4 YES
12 MCM7 MCM7 MCM7 2556 0.11 0.42 YES
13 POLA2 POLA2 POLA2 2607 0.1 0.45 YES
14 MCM4 MCM4 MCM4 2722 0.1 0.48 YES
15 POLD1 POLD1 POLD1 2741 0.1 0.51 YES
16 RFC5 RFC5 RFC5 2773 0.1 0.54 YES
17 RFC1 RFC1 RFC1 2860 0.096 0.56 YES
18 RFC2 RFC2 RFC2 3109 0.089 0.58 YES
19 RNASEH2C RNASEH2C RNASEH2C 3278 0.084 0.6 YES
20 POLE4 POLE4 POLE4 3362 0.082 0.62 YES
21 SSBP1 SSBP1 SSBP1 3384 0.081 0.64 YES
22 MCM6 MCM6 MCM6 3659 0.074 0.65 YES
23 RFC3 RFC3 RFC3 4394 0.06 0.63 NO
24 PCNA PCNA PCNA 5117 0.048 0.6 NO
25 RPA1 RPA1 RPA1 5573 0.042 0.59 NO
26 MCM5 MCM5 MCM5 5780 0.039 0.59 NO
27 MCM3 MCM3 MCM3 6403 0.03 0.56 NO
28 RPA2 RPA2 RPA2 8027 0.0094 0.48 NO
29 RNASEH1 RNASEH1 RNASEH1 8083 0.0087 0.48 NO
30 POLD3 POLD3 POLD3 8651 0.0012 0.44 NO
31 POLE POLE POLE 8727 0.00048 0.44 NO
32 RNASEH2B RNASEH2B RNASEH2B 9610 -0.012 0.39 NO
33 DNA2 DNA2 DNA2 10301 -0.021 0.36 NO
34 RPA4 RPA4 RPA4 13149 -0.079 0.23 NO
35 POLD4 POLD4 POLD4 14213 -0.12 0.2 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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RIBOSOME

Table 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 RPL36A RPL36A RPL36A 1291 0.19 -0.047 YES
2 RPL7 RPL7 RPL7 1522 0.17 -0.036 YES
3 RPSA RPSA RPSA 1715 0.15 -0.026 YES
4 RPS26 RPS26 RPS26 1736 0.15 -0.0056 YES
5 RPS27 RPS27 RPS27 1773 0.15 0.013 YES
6 RPL24 RPL24 RPL24 1925 0.14 0.024 YES
7 RPS17 RPS17 RPS17 1942 0.14 0.042 YES
8 RPL9 RPL9 RPL9 2115 0.13 0.05 YES
9 RPS4Y1 RPS4Y1 RPS4Y1 2193 0.12 0.063 YES
10 RPL32 RPL32 RPL32 2206 0.12 0.08 YES
11 RPL15 RPL15 RPL15 2266 0.12 0.093 YES
12 RPS23 RPS23 RPS23 2273 0.12 0.11 YES
13 RPL7A RPL7A RPL7A 2331 0.12 0.12 YES
14 RPS5 RPS5 RPS5 2408 0.11 0.14 YES
15 RPS6 RPS6 RPS6 2445 0.11 0.15 YES
16 RPL14 RPL14 RPL14 2509 0.11 0.16 YES
17 RPL18A RPL18A RPL18A 2519 0.11 0.18 YES
18 RPL17 RPL17 RPL17 2598 0.1 0.18 YES
19 RPL35 RPL35 RPL35 2599 0.1 0.2 YES
20 RPL29 RPL29 RPL29 2628 0.1 0.21 YES
21 RPL35A RPL35A RPL35A 2668 0.1 0.22 YES
22 RPS15 RPS15 RPS15 2685 0.1 0.24 YES
23 RPL6 RPL6 RPL6 2698 0.1 0.25 YES
24 RPS3A RPS3A RPS3A 2732 0.1 0.26 YES
25 RPL41 RPL41 RPL41 2733 0.1 0.28 YES
26 RPL38 RPL38 RPL38 2736 0.1 0.29 YES
27 RSL24D1 RSL24D1 RSL24D1 2903 0.095 0.3 YES
28 RPL37 RPL37 RPL37 2910 0.095 0.31 YES
29 RPS16 RPS16 RPS16 3038 0.091 0.32 YES
30 RPS29 RPS29 RPS29 3063 0.09 0.33 YES
31 RPLP0 RPLP0 RPLP0 3100 0.089 0.34 YES
32 RPS10 RPS10 RPS10 3136 0.088 0.35 YES
33 RPL3 RPL3 RPL3 3175 0.087 0.36 YES
34 RPL39 RPL39 RPL39 3234 0.086 0.37 YES
35 RPS18 RPS18 RPS18 3267 0.084 0.38 YES
36 RPL8 RPL8 RPL8 3298 0.083 0.39 YES
37 UBA52 UBA52 UBA52 3302 0.083 0.4 YES
38 RPL26 RPL26 RPL26 3367 0.081 0.41 YES
39 RPL4 RPL4 RPL4 3381 0.081 0.42 YES
40 RPS8 RPS8 RPS8 3397 0.081 0.43 YES
41 RPL34 RPL34 RPL34 3525 0.078 0.43 YES
42 RPS9 RPS9 RPS9 3557 0.077 0.44 YES
43 RPL10A RPL10A RPL10A 3579 0.076 0.45 YES
44 RPS25 RPS25 RPS25 3600 0.076 0.46 YES
45 RPL22L1 RPL22L1 RPL22L1 3613 0.075 0.47 YES
46 RPL5 RPL5 RPL5 3661 0.074 0.48 YES
47 RPL30 RPL30 RPL30 3683 0.074 0.49 YES
48 RPS11 RPS11 RPS11 3702 0.073 0.5 YES
49 RPL12 RPL12 RPL12 3711 0.073 0.5 YES
50 RPS3 RPS3 RPS3 3716 0.073 0.52 YES
51 RPL27 RPL27 RPL27 3734 0.072 0.52 YES
52 RPS4X RPS4X RPS4X 3755 0.072 0.53 YES
53 RPL36AL RPL36AL RPL36AL 3778 0.072 0.54 YES
54 RPL28 RPL28 RPL28 3824 0.071 0.55 YES
55 RPL10 RPL10 RPL10 3844 0.07 0.56 YES
56 RPL22 RPL22 RPL22 3866 0.07 0.57 YES
57 RPL13A RPL13A RPL13A 3918 0.069 0.57 YES
58 RPS2 RPS2 RPS2 3992 0.068 0.58 YES
59 RPL36 RPL36 RPL36 4044 0.067 0.59 YES
60 RPL11 RPL11 RPL11 4103 0.066 0.59 YES
61 RPS24 RPS24 RPS24 4128 0.065 0.6 YES
62 RPL37A RPL37A RPL37A 4153 0.065 0.61 YES
63 RPLP1 RPLP1 RPLP1 4334 0.061 0.61 YES
64 RPL23 RPL23 RPL23 4371 0.06 0.61 YES
65 RPS21 RPS21 RPS21 4386 0.06 0.62 YES
66 RPS20 RPS20 RPS20 4446 0.059 0.62 YES
67 RPL26L1 RPL26L1 RPL26L1 4453 0.059 0.63 YES
68 RPS15A RPS15A RPS15A 4857 0.052 0.62 NO
69 RPL31 RPL31 RPL31 4925 0.051 0.62 NO
70 RPS7 RPS7 RPS7 5019 0.05 0.62 NO
71 RPS27A RPS27A RPS27A 5102 0.049 0.62 NO
72 FAU FAU FAU 5202 0.047 0.63 NO
73 RPS19 RPS19 RPS19 5417 0.044 0.62 NO
74 RPL13 RPL13 RPL13 5548 0.042 0.62 NO
75 RPL23A RPL23A RPL23A 5629 0.041 0.62 NO
76 MRPL13 MRPL13 MRPL13 5713 0.04 0.62 NO
77 RPS13 RPS13 RPS13 5760 0.039 0.62 NO
78 RPS12 RPS12 RPS12 5858 0.038 0.62 NO
79 RPL19 RPL19 RPL19 5865 0.038 0.63 NO
80 RPL21 RPL21 RPL21 6488 0.029 0.6 NO
81 RPL27A RPL27A RPL27A 6646 0.027 0.59 NO
82 RPLP2 RPLP2 RPLP2 7634 0.014 0.54 NO
83 RPS27L RPS27L RPS27L 12967 -0.073 0.25 NO
84 RPS28 RPS28 RPS28 15398 -0.18 0.14 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 RIBOSOME.

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

genes ES table in pathway: KEGG RNA 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 THOC3 THOC3 THOC3 1732 0.15 -0.064 YES
2 LSM3 LSM3 LSM3 2085 0.13 -0.055 YES
3 SLU7 SLU7 SLU7 2458 0.11 -0.051 YES
4 TCERG1 TCERG1 TCERG1 3191 0.087 -0.072 YES
5 ZMAT2 ZMAT2 ZMAT2 3199 0.086 -0.054 YES
6 SNRPD2 SNRPD2 SNRPD2 3403 0.081 -0.047 YES
7 LSM5 LSM5 LSM5 3439 0.08 -0.031 YES
8 HSPA1L HSPA1L HSPA1L 3609 0.076 -0.023 YES
9 DDX46 DDX46 DDX46 3785 0.071 -0.017 YES
10 THOC4 THOC4 THOC4 3860 0.07 -0.0055 YES
11 RBM22 RBM22 RBM22 4125 0.065 -0.0058 YES
12 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 4211 0.063 0.0037 YES
13 LSM6 LSM6 LSM6 4213 0.063 0.018 YES
14 HNRNPA1 HNRNPA1 HNRNPA1 4220 0.063 0.032 YES
15 PPIH PPIH PPIH 4345 0.061 0.039 YES
16 MAGOHB MAGOHB MAGOHB 4405 0.06 0.049 YES
17 PRPF4 PRPF4 PRPF4 4523 0.058 0.055 YES
18 LSM4 LSM4 LSM4 4537 0.058 0.068 YES
19 SFRS5 SFRS5 SFRS5 4599 0.056 0.077 YES
20 SNRPE SNRPE SNRPE 4616 0.056 0.089 YES
21 RBMX RBMX RBMX 4621 0.056 0.1 YES
22 NCBP1 NCBP1 NCBP1 4632 0.056 0.11 YES
23 SF3A2 SF3A2 SF3A2 4687 0.055 0.12 YES
24 HSPA2 HSPA2 HSPA2 4705 0.055 0.13 YES
25 WBP11 WBP11 WBP11 4711 0.055 0.15 YES
26 LSM2 LSM2 LSM2 4733 0.054 0.16 YES
27 ISY1 ISY1 ISY1 4887 0.052 0.16 YES
28 U2AF1 U2AF1 U2AF1 5033 0.05 0.16 YES
29 PRPF31 PRPF31 PRPF31 5068 0.049 0.17 YES
30 PHF5A PHF5A PHF5A 5124 0.048 0.18 YES
31 CCDC12 CCDC12 CCDC12 5158 0.048 0.19 YES
32 TRA2B TRA2B TRA2B 5223 0.047 0.2 YES
33 SNRPB SNRPB SNRPB 5251 0.047 0.2 YES
34 SNRNP27 SNRNP27 SNRNP27 5262 0.046 0.22 YES
35 DDX23 DDX23 DDX23 5424 0.044 0.22 YES
36 PRPF3 PRPF3 PRPF3 5469 0.043 0.22 YES
37 NAA38 NAA38 NAA38 5507 0.043 0.23 YES
38 NHP2L1 NHP2L1 NHP2L1 5608 0.041 0.23 YES
39 SNRPA SNRPA SNRPA 5651 0.041 0.24 YES
40 CHERP CHERP CHERP 5755 0.039 0.24 YES
41 SNRPD3 SNRPD3 SNRPD3 5791 0.039 0.25 YES
42 BUD31 BUD31 BUD31 5885 0.038 0.25 YES
43 SF3A3 SF3A3 SF3A3 5917 0.037 0.26 YES
44 SF3A1 SF3A1 SF3A1 5937 0.037 0.27 YES
45 U2AF2 U2AF2 U2AF2 6021 0.036 0.27 YES
46 AQR AQR AQR 6036 0.035 0.28 YES
47 SNRPF SNRPF SNRPF 6213 0.033 0.28 YES
48 PRPF8 PRPF8 PRPF8 6250 0.032 0.28 YES
49 PPIE PPIE PPIE 6280 0.032 0.29 YES
50 PRPF19 PRPF19 PRPF19 6348 0.031 0.29 YES
51 XAB2 XAB2 XAB2 6463 0.029 0.29 YES
52 SNRNP70 SNRNP70 SNRNP70 6476 0.029 0.3 YES
53 SNRPG SNRPG SNRPG 6565 0.028 0.3 YES
54 HNRNPK HNRNPK HNRNPK 6594 0.028 0.3 YES
55 SR140 SR140 SR140 6612 0.027 0.31 YES
56 SFRS9 SFRS9 SFRS9 6613 0.027 0.31 YES
57 HSPA8 HSPA8 HSPA8 6736 0.026 0.31 YES
58 PLRG1 PLRG1 PLRG1 6792 0.025 0.31 YES
59 HNRNPM HNRNPM HNRNPM 6838 0.024 0.32 YES
60 SNRPD1 SNRPD1 SNRPD1 6893 0.024 0.32 YES
61 SNW1 SNW1 SNW1 6897 0.024 0.32 YES
62 PRPF6 PRPF6 PRPF6 6899 0.024 0.33 YES
63 SNRNP40 SNRNP40 SNRNP40 6908 0.024 0.34 YES
64 SNRPB2 SNRPB2 SNRPB2 6920 0.024 0.34 YES
65 EIF4A3 EIF4A3 EIF4A3 6997 0.023 0.34 YES
66 SNRNP200 SNRNP200 SNRNP200 7015 0.022 0.34 YES
67 SNRPC SNRPC SNRPC 7044 0.022 0.35 YES
68 PQBP1 PQBP1 PQBP1 7135 0.021 0.35 NO
69 SF3B14 SF3B14 SF3B14 7335 0.018 0.34 NO
70 CWC15 CWC15 CWC15 7405 0.017 0.34 NO
71 PUF60 PUF60 PUF60 7450 0.017 0.34 NO
72 HSPA6 HSPA6 HSPA6 7473 0.016 0.34 NO
73 HNRNPC HNRNPC HNRNPC 7821 0.012 0.33 NO
74 SF3B5 SF3B5 SF3B5 7828 0.012 0.33 NO
75 LSM7 LSM7 LSM7 7959 0.01 0.32 NO
76 RBM25 RBM25 RBM25 7973 0.01 0.33 NO
77 SYF2 SYF2 SYF2 8109 0.0084 0.32 NO
78 SFRS2 SFRS2 SFRS2 8216 0.0071 0.32 NO
79 PRPF40B PRPF40B PRPF40B 8337 0.0056 0.31 NO
80 MAGOH MAGOH MAGOH 8382 0.005 0.31 NO
81 BAT1 BAT1 BAT1 8400 0.0047 0.31 NO
82 USP39 USP39 USP39 8474 0.0038 0.31 NO
83 THOC2 THOC2 THOC2 8508 0.0034 0.3 NO
84 RBM8A RBM8A RBM8A 8515 0.0033 0.3 NO
85 DDX42 DDX42 DDX42 8528 0.0031 0.3 NO
86 DHX15 DHX15 DHX15 8539 0.0029 0.3 NO
87 ACIN1 ACIN1 ACIN1 8623 0.0017 0.3 NO
88 CDC5L CDC5L CDC5L 8663 0.0011 0.3 NO
89 SFRS3 SFRS3 SFRS3 8713 0.00061 0.3 NO
90 TRA2A TRA2A TRA2A 8775 -0.00011 0.29 NO
91 BCAS2 BCAS2 BCAS2 8895 -0.0016 0.29 NO
92 SF3B2 SF3B2 SF3B2 8939 -0.0021 0.28 NO
93 PPIL1 PPIL1 PPIL1 8984 -0.0027 0.28 NO
94 SFRS6 SFRS6 SFRS6 9102 -0.0043 0.28 NO
95 SART1 SART1 SART1 9128 -0.0047 0.28 NO
96 HNRNPU HNRNPU HNRNPU 9259 -0.0064 0.27 NO
97 SF3B3 SF3B3 SF3B3 9328 -0.0075 0.27 NO
98 TXNL4A TXNL4A TXNL4A 9468 -0.0095 0.26 NO
99 PRPF38B PRPF38B PRPF38B 9497 -0.01 0.26 NO
100 SFRS13A SFRS13A SFRS13A 9601 -0.012 0.26 NO
101 SF3B1 SF3B1 SF3B1 9664 -0.012 0.26 NO
102 PRPF38A PRPF38A PRPF38A 9668 -0.012 0.26 NO
103 CRNKL1 CRNKL1 CRNKL1 9783 -0.014 0.26 NO
104 EFTUD2 EFTUD2 EFTUD2 9881 -0.015 0.26 NO
105 SFRS1 SFRS1 SFRS1 9904 -0.016 0.26 NO
106 PRPF18 PRPF18 PRPF18 9954 -0.016 0.26 NO
107 RBM17 RBM17 RBM17 9995 -0.017 0.26 NO
108 SFRS2B SFRS2B SFRS2B 10383 -0.022 0.24 NO
109 SNRPA1 SNRPA1 SNRPA1 10384 -0.022 0.25 NO
110 CTNNBL1 CTNNBL1 CTNNBL1 10464 -0.024 0.25 NO
111 DDX5 DDX5 DDX5 10715 -0.028 0.24 NO
112 SF3B4 SF3B4 SF3B4 10754 -0.028 0.25 NO
113 THOC1 THOC1 THOC1 11091 -0.034 0.24 NO
114 PRPF40A PRPF40A PRPF40A 11101 -0.034 0.24 NO
115 CDC40 CDC40 CDC40 11222 -0.036 0.24 NO
116 SFRS7 SFRS7 SFRS7 11232 -0.036 0.25 NO
117 PCBP1 PCBP1 PCBP1 11475 -0.04 0.25 NO
118 DHX16 DHX16 DHX16 11476 -0.04 0.26 NO
119 HNRNPA3 HNRNPA3 HNRNPA3 11726 -0.045 0.25 NO
120 SMNDC1 SMNDC1 SMNDC1 12426 -0.059 0.23 NO
121 DHX38 DHX38 DHX38 12544 -0.062 0.23 NO
122 SFRS4 SFRS4 SFRS4 12555 -0.062 0.25 NO
123 DHX8 DHX8 DHX8 12913 -0.072 0.24 NO
124 HSPA1B HSPA1B HSPA1B 12925 -0.072 0.26 NO
125 HSPA1A HSPA1A HSPA1A 13186 -0.08 0.26 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 RNA DEGRADATION.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA 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 RNA POLYMERASE

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 PCK1 PCK1 PCK1 291 0.35 0.2 YES
2 PCK2 PCK2 PCK2 1747 0.15 0.21 YES
3 SDHA SDHA SDHA 2302 0.12 0.26 YES
4 ACO1 ACO1 ACO1 2677 0.1 0.3 YES
5 IDH3A IDH3A IDH3A 2778 0.099 0.35 YES
6 MDH1 MDH1 MDH1 3104 0.089 0.39 YES
7 MDH2 MDH2 MDH2 3922 0.069 0.39 YES
8 PDHB PDHB PDHB 4644 0.056 0.38 YES
9 FH FH FH 5015 0.05 0.39 YES
10 DLAT DLAT DLAT 5059 0.049 0.42 YES
11 IDH2 IDH2 IDH2 5196 0.047 0.44 YES
12 CS CS CS 5322 0.045 0.46 YES
13 DLD DLD DLD 5486 0.043 0.48 YES
14 OGDHL OGDHL OGDHL 5748 0.039 0.49 YES
15 SUCLA2 SUCLA2 SUCLA2 5874 0.038 0.5 YES
16 ACO2 ACO2 ACO2 6018 0.036 0.52 YES
17 SDHB SDHB SDHB 6521 0.029 0.51 YES
18 SDHC SDHC SDHC 6750 0.026 0.51 YES
19 SUCLG2 SUCLG2 SUCLG2 6800 0.025 0.52 YES
20 DLST DLST DLST 7089 0.021 0.52 NO
21 OGDH OGDH OGDH 7552 0.016 0.5 NO
22 IDH3B IDH3B IDH3B 7554 0.016 0.51 NO
23 PC PC PC 7762 0.013 0.51 NO
24 PDHA1 PDHA1 PDHA1 7887 0.011 0.51 NO
25 SDHD SDHD SDHD 8012 0.0096 0.51 NO
26 SUCLG1 SUCLG1 SUCLG1 8742 0.00027 0.47 NO
27 ACLY ACLY ACLY 9608 -0.012 0.43 NO
28 IDH3G IDH3G IDH3G 10165 -0.019 0.41 NO
29 IDH1 IDH1 IDH1 11288 -0.037 0.37 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 RNA POLYMERASE.

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

genes ES table in pathway: KEGG DNA REPLICATION

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 COX7A1 COX7A1 COX7A1 280 0.36 0.031 YES
2 ATP6V1G2 ATP6V1G2 ATP6V1G2 1248 0.19 0.00077 YES
3 ATP6V1C2 ATP6V1C2 ATP6V1C2 1428 0.17 0.013 YES
4 ATP6V1G3 ATP6V1G3 ATP6V1G3 1441 0.17 0.035 YES
5 ATP4A ATP4A ATP4A 1509 0.17 0.053 YES
6 NDUFS4 NDUFS4 NDUFS4 1636 0.16 0.066 YES
7 NDUFS6 NDUFS6 NDUFS6 1862 0.14 0.072 YES
8 NDUFB6 NDUFB6 NDUFB6 2009 0.13 0.08 YES
9 ATP6V1E2 ATP6V1E2 ATP6V1E2 2165 0.12 0.088 YES
10 NDUFA2 NDUFA2 NDUFA2 2171 0.12 0.1 YES
11 ATP6V0A4 ATP6V0A4 ATP6V0A4 2262 0.12 0.11 YES
12 SDHA SDHA SDHA 2302 0.12 0.13 YES
13 COX17 COX17 COX17 2492 0.11 0.13 YES
14 NDUFV3 NDUFV3 NDUFV3 2521 0.11 0.14 YES
15 ATP5O ATP5O ATP5O 2688 0.1 0.15 YES
16 ATP6V1D ATP6V1D ATP6V1D 2712 0.1 0.16 YES
17 COX7C COX7C COX7C 2757 0.1 0.17 YES
18 ATP5J ATP5J ATP5J 2777 0.099 0.18 YES
19 UQCRB UQCRB UQCRB 2815 0.098 0.19 YES
20 COX5B COX5B COX5B 2861 0.096 0.2 YES
21 NDUFA8 NDUFA8 NDUFA8 2916 0.095 0.21 YES
22 NDUFB5 NDUFB5 NDUFB5 3079 0.09 0.21 YES
23 ATP6V0D2 ATP6V0D2 ATP6V0D2 3080 0.09 0.22 YES
24 NDUFA4 NDUFA4 NDUFA4 3209 0.086 0.23 YES
25 COX5A COX5A COX5A 3219 0.086 0.24 YES
26 ATP5G2 ATP5G2 ATP5G2 3246 0.085 0.25 YES
27 ATP5G1 ATP5G1 ATP5G1 3304 0.083 0.26 YES
28 NDUFS7 NDUFS7 NDUFS7 3400 0.081 0.26 YES
29 UQCRHL UQCRHL UQCRHL 3449 0.079 0.27 YES
30 UQCR11 UQCR11 UQCR11 3507 0.078 0.28 YES
31 ATP5H ATP5H ATP5H 3530 0.077 0.28 YES
32 UQCRQ UQCRQ UQCRQ 3574 0.076 0.29 YES
33 NDUFB4 NDUFB4 NDUFB4 3607 0.076 0.3 YES
34 NDUFB7 NDUFB7 NDUFB7 3626 0.075 0.31 YES
35 ATP6V1B1 ATP6V1B1 ATP6V1B1 3674 0.074 0.32 YES
36 COX6B1 COX6B1 COX6B1 3836 0.07 0.32 YES
37 NDUFB2 NDUFB2 NDUFB2 3915 0.069 0.32 YES
38 ATP6V1G1 ATP6V1G1 ATP6V1G1 3995 0.068 0.32 YES
39 NDUFB1 NDUFB1 NDUFB1 4178 0.064 0.32 YES
40 COX6C COX6C COX6C 4192 0.064 0.33 YES
41 ATP6V0E2 ATP6V0E2 ATP6V0E2 4207 0.064 0.34 YES
42 NDUFAB1 NDUFAB1 NDUFAB1 4275 0.062 0.34 YES
43 NDUFA11 NDUFA11 NDUFA11 4289 0.062 0.35 YES
44 ATP5L ATP5L ATP5L 4326 0.061 0.36 YES
45 NDUFA1 NDUFA1 NDUFA1 4340 0.061 0.36 YES
46 UQCRC1 UQCRC1 UQCRC1 4362 0.061 0.37 YES
47 COX7A2L COX7A2L COX7A2L 4402 0.06 0.38 YES
48 UQCRH UQCRH UQCRH 4461 0.059 0.38 YES
49 NDUFA5 NDUFA5 NDUFA5 4467 0.059 0.39 YES
50 NDUFC1 NDUFC1 NDUFC1 4514 0.058 0.39 YES
51 NDUFA7 NDUFA7 NDUFA7 4548 0.058 0.4 YES
52 COX7A2 COX7A2 COX7A2 4554 0.057 0.4 YES
53 UQCRFS1 UQCRFS1 UQCRFS1 4557 0.057 0.41 YES
54 NDUFA9 NDUFA9 NDUFA9 4683 0.055 0.41 YES
55 NDUFA3 NDUFA3 NDUFA3 4728 0.054 0.42 YES
56 NDUFB3 NDUFB3 NDUFB3 4872 0.052 0.42 YES
57 ATP5D ATP5D ATP5D 4879 0.052 0.42 YES
58 ATP5G3 ATP5G3 ATP5G3 5013 0.05 0.42 YES
59 CYC1 CYC1 CYC1 5180 0.048 0.42 YES
60 ATP6V1H ATP6V1H ATP6V1H 5212 0.047 0.42 YES
61 NDUFS3 NDUFS3 NDUFS3 5289 0.046 0.42 YES
62 NDUFA6 NDUFA6 NDUFA6 5346 0.045 0.43 YES
63 ATP5B ATP5B ATP5B 5352 0.045 0.43 YES
64 NDUFV1 NDUFV1 NDUFV1 5472 0.043 0.43 YES
65 UQCR10 UQCR10 UQCR10 5475 0.043 0.44 YES
66 COX8A COX8A COX8A 5614 0.041 0.43 YES
67 NDUFB9 NDUFB9 NDUFB9 5616 0.041 0.44 YES
68 ATP6V1F ATP6V1F ATP6V1F 5693 0.04 0.44 YES
69 ATP6V1A ATP6V1A ATP6V1A 5714 0.04 0.44 YES
70 COX7B COX7B COX7B 5759 0.039 0.45 YES
71 ATP5I ATP5I ATP5I 5794 0.039 0.45 YES
72 ATP6V1E1 ATP6V1E1 ATP6V1E1 5882 0.038 0.45 YES
73 ATP5J2 ATP5J2 ATP5J2 5924 0.037 0.45 YES
74 COX6A1 COX6A1 COX6A1 5976 0.036 0.45 YES
75 ATP6V0B ATP6V0B ATP6V0B 5995 0.036 0.46 YES
76 ATP5A1 ATP5A1 ATP5A1 6038 0.035 0.46 YES
77 NDUFS2 NDUFS2 NDUFS2 6074 0.035 0.46 YES
78 ATP6V0E1 ATP6V0E1 ATP6V0E1 6192 0.033 0.46 NO
79 NDUFC2 NDUFC2 NDUFC2 6370 0.031 0.45 NO
80 NDUFB10 NDUFB10 NDUFB10 6514 0.029 0.45 NO
81 SDHB SDHB SDHB 6521 0.029 0.45 NO
82 NDUFS5 NDUFS5 NDUFS5 6707 0.026 0.45 NO
83 SDHC SDHC SDHC 6750 0.026 0.45 NO
84 NDUFA10 NDUFA10 NDUFA10 6822 0.025 0.45 NO
85 ATP5E ATP5E ATP5E 7073 0.022 0.43 NO
86 UQCRC2 UQCRC2 UQCRC2 7223 0.02 0.43 NO
87 PPA2 PPA2 PPA2 7381 0.018 0.42 NO
88 ATP6V1C1 ATP6V1C1 ATP6V1C1 7565 0.015 0.41 NO
89 ATP5F1 ATP5F1 ATP5F1 7673 0.014 0.41 NO
90 ATP6V0C ATP6V0C ATP6V0C 7788 0.012 0.4 NO
91 NDUFV2 NDUFV2 NDUFV2 8005 0.0097 0.39 NO
92 SDHD SDHD SDHD 8012 0.0096 0.39 NO
93 ATP6V1B2 ATP6V1B2 ATP6V1B2 8065 0.009 0.39 NO
94 COX15 COX15 COX15 8095 0.0085 0.39 NO
95 NDUFS1 NDUFS1 NDUFS1 8320 0.0058 0.38 NO
96 NDUFS8 NDUFS8 NDUFS8 8494 0.0035 0.37 NO
97 ATP5C1 ATP5C1 ATP5C1 8761 8e-05 0.36 NO
98 COX11 COX11 COX11 8862 -0.0013 0.35 NO
99 ATP6AP1 ATP6AP1 ATP6AP1 9264 -0.0065 0.33 NO
100 COX10 COX10 COX10 9339 -0.0076 0.33 NO
101 NDUFB8 NDUFB8 NDUFB8 9629 -0.012 0.31 NO
102 COX4I1 COX4I1 COX4I1 9634 -0.012 0.31 NO
103 NDUFA4L2 NDUFA4L2 NDUFA4L2 9940 -0.016 0.3 NO
104 PPA1 PPA1 PPA1 10187 -0.02 0.29 NO
105 COX4I2 COX4I2 COX4I2 10250 -0.02 0.28 NO
106 ATP4B ATP4B ATP4B 10987 -0.032 0.25 NO
107 ATP6V0A1 ATP6V0A1 ATP6V0A1 11290 -0.037 0.24 NO
108 ATP6V0D1 ATP6V0D1 ATP6V0D1 11582 -0.042 0.22 NO
109 ATP6V0A2 ATP6V0A2 ATP6V0A2 11975 -0.05 0.21 NO
110 COX6A2 COX6A2 COX6A2 13311 -0.084 0.14 NO
111 COX6B2 COX6B2 COX6B2 16091 -0.23 0.017 NO
112 LHPP LHPP LHPP 16611 -0.28 0.024 NO
113 TCIRG1 TCIRG1 TCIRG1 17139 -0.34 0.039 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 DNA REPLICATION.

Figure S56.  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 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 HAP1 HAP1 HAP1 218 0.39 0.018 YES
2 COX7A1 COX7A1 COX7A1 280 0.36 0.042 YES
3 PLCB4 PLCB4 PLCB4 507 0.3 0.052 YES
4 DNAI1 DNAI1 DNAI1 680 0.26 0.063 YES
5 DNAH3 DNAH3 DNAH3 912 0.23 0.068 YES
6 BDNF BDNF BDNF 1132 0.2 0.071 YES
7 UCP1 UCP1 UCP1 1135 0.2 0.087 YES
8 CLTCL1 CLTCL1 CLTCL1 1372 0.18 0.087 YES
9 NDUFS4 NDUFS4 NDUFS4 1636 0.16 0.085 YES
10 ITPR1 ITPR1 ITPR1 1703 0.15 0.093 YES
11 NDUFS6 NDUFS6 NDUFS6 1862 0.14 0.095 YES
12 NDUFB6 NDUFB6 NDUFB6 2009 0.13 0.097 YES
13 SLC25A5 SLC25A5 SLC25A5 2140 0.13 0.099 YES
14 NDUFA2 NDUFA2 NDUFA2 2171 0.12 0.11 YES
15 SDHA SDHA SDHA 2302 0.12 0.11 YES
16 PPARGC1A PPARGC1A PPARGC1A 2337 0.12 0.12 YES
17 NDUFV3 NDUFV3 NDUFV3 2521 0.11 0.11 YES
18 ATP5O ATP5O ATP5O 2688 0.1 0.11 YES
19 COX7C COX7C COX7C 2757 0.1 0.12 YES
20 ATP5J ATP5J ATP5J 2777 0.099 0.12 YES
21 UQCRB UQCRB UQCRB 2815 0.098 0.13 YES
22 COX5B COX5B COX5B 2861 0.096 0.13 YES
23 NDUFA8 NDUFA8 NDUFA8 2916 0.095 0.14 YES
24 SLC25A4 SLC25A4 SLC25A4 2977 0.093 0.14 YES
25 NDUFB5 NDUFB5 NDUFB5 3079 0.09 0.14 YES
26 NDUFA4 NDUFA4 NDUFA4 3209 0.086 0.14 YES
27 COX5A COX5A COX5A 3219 0.086 0.15 YES
28 ATP5G2 ATP5G2 ATP5G2 3246 0.085 0.15 YES
29 ATP5G1 ATP5G1 ATP5G1 3304 0.083 0.16 YES
30 NDUFS7 NDUFS7 NDUFS7 3400 0.081 0.16 YES
31 POLR2I POLR2I POLR2I 3406 0.08 0.16 YES
32 UQCRHL UQCRHL UQCRHL 3449 0.079 0.17 YES
33 UQCR11 UQCR11 UQCR11 3507 0.078 0.17 YES
34 ATP5H ATP5H ATP5H 3530 0.077 0.18 YES
35 CLTA CLTA CLTA 3544 0.077 0.18 YES
36 UQCRQ UQCRQ UQCRQ 3574 0.076 0.18 YES
37 VDAC1 VDAC1 VDAC1 3598 0.076 0.19 YES
38 NDUFB4 NDUFB4 NDUFB4 3607 0.076 0.2 YES
39 NDUFB7 NDUFB7 NDUFB7 3626 0.075 0.2 YES
40 CREB3L2 CREB3L2 CREB3L2 3708 0.073 0.2 YES
41 COX6B1 COX6B1 COX6B1 3836 0.07 0.2 YES
42 NDUFB2 NDUFB2 NDUFB2 3915 0.069 0.2 YES
43 NDUFB1 NDUFB1 NDUFB1 4178 0.064 0.19 YES
44 COX6C COX6C COX6C 4192 0.064 0.2 YES
45 DNAL4 DNAL4 DNAL4 4249 0.063 0.2 YES
46 NDUFAB1 NDUFAB1 NDUFAB1 4275 0.062 0.2 YES
47 CREB3 CREB3 CREB3 4287 0.062 0.2 YES
48 SOD1 SOD1 SOD1 4292 0.062 0.21 YES
49 VDAC3 VDAC3 VDAC3 4320 0.061 0.21 YES
50 POLR2F POLR2F POLR2F 4321 0.061 0.22 YES
51 POLR2K POLR2K POLR2K 4337 0.061 0.22 YES
52 NDUFA1 NDUFA1 NDUFA1 4340 0.061 0.22 YES
53 UQCRC1 UQCRC1 UQCRC1 4362 0.061 0.23 YES
54 COX7A2L COX7A2L COX7A2L 4402 0.06 0.23 YES
55 UQCRH UQCRH UQCRH 4461 0.059 0.23 YES
56 NDUFA5 NDUFA5 NDUFA5 4467 0.059 0.24 YES
57 DCTN4 DCTN4 DCTN4 4473 0.059 0.24 YES
58 POLR2J POLR2J POLR2J 4475 0.059 0.25 YES
59 NDUFC1 NDUFC1 NDUFC1 4514 0.058 0.25 YES
60 NDUFA7 NDUFA7 NDUFA7 4548 0.058 0.25 YES
61 COX7A2 COX7A2 COX7A2 4554 0.057 0.26 YES
62 UQCRFS1 UQCRFS1 UQCRFS1 4557 0.057 0.26 YES
63 GNAQ GNAQ GNAQ 4608 0.056 0.26 YES
64 NDUFA9 NDUFA9 NDUFA9 4683 0.055 0.26 YES
65 NDUFA3 NDUFA3 NDUFA3 4728 0.054 0.26 YES
66 TBPL1 TBPL1 TBPL1 4731 0.054 0.27 YES
67 VDAC2 VDAC2 VDAC2 4830 0.053 0.26 YES
68 POLR2E POLR2E POLR2E 4854 0.052 0.27 YES
69 NDUFB3 NDUFB3 NDUFB3 4872 0.052 0.27 YES
70 ATP5D ATP5D ATP5D 4879 0.052 0.28 YES
71 ATP5G3 ATP5G3 ATP5G3 5013 0.05 0.27 YES
72 CLTB CLTB CLTB 5139 0.048 0.27 YES
73 CYC1 CYC1 CYC1 5180 0.048 0.27 YES
74 NDUFS3 NDUFS3 NDUFS3 5289 0.046 0.27 YES
75 NDUFA6 NDUFA6 NDUFA6 5346 0.045 0.27 YES
76 ATP5B ATP5B ATP5B 5352 0.045 0.27 YES
77 POLR2J3 POLR2J3 POLR2J3 5393 0.044 0.27 YES
78 NDUFV1 NDUFV1 NDUFV1 5472 0.043 0.27 YES
79 UQCR10 UQCR10 UQCR10 5475 0.043 0.27 YES
80 COX8A COX8A COX8A 5614 0.041 0.27 YES
81 NDUFB9 NDUFB9 NDUFB9 5616 0.041 0.27 YES
82 DNAL1 DNAL1 DNAL1 5655 0.041 0.27 YES
83 POLR2J2 POLR2J2 POLR2J2 5688 0.04 0.28 YES
84 COX7B COX7B COX7B 5759 0.039 0.27 YES
85 POLR2H POLR2H POLR2H 5819 0.038 0.27 YES
86 POLR2L POLR2L POLR2L 5840 0.038 0.28 YES
87 COX6A1 COX6A1 COX6A1 5976 0.036 0.27 NO
88 ATP5A1 ATP5A1 ATP5A1 6038 0.035 0.27 NO
89 NDUFS2 NDUFS2 NDUFS2 6074 0.035 0.27 NO
90 POLR2B POLR2B POLR2B 6264 0.032 0.26 NO
91 CYCS CYCS CYCS 6308 0.032 0.26 NO
92 NDUFC2 NDUFC2 NDUFC2 6370 0.031 0.26 NO
93 PPID PPID PPID 6389 0.03 0.26 NO
94 SLC25A6 SLC25A6 SLC25A6 6500 0.029 0.26 NO
95 NDUFB10 NDUFB10 NDUFB10 6514 0.029 0.26 NO
96 SDHB SDHB SDHB 6521 0.029 0.26 NO
97 NDUFS5 NDUFS5 NDUFS5 6707 0.026 0.25 NO
98 SDHC SDHC SDHC 6750 0.026 0.25 NO
99 REST REST REST 6755 0.025 0.26 NO
100 PPARG PPARG PPARG 6799 0.025 0.25 NO
101 NDUFA10 NDUFA10 NDUFA10 6822 0.025 0.26 NO
102 SIN3A SIN3A SIN3A 6883 0.024 0.25 NO
103 TFAM TFAM TFAM 6922 0.024 0.25 NO
104 AP2S1 AP2S1 AP2S1 6931 0.023 0.25 NO
105 ATP5E ATP5E ATP5E 7073 0.022 0.25 NO
106 UQCRC2 UQCRC2 UQCRC2 7223 0.02 0.24 NO
107 DCTN2 DCTN2 DCTN2 7514 0.016 0.23 NO
108 POLR2C POLR2C POLR2C 7568 0.015 0.22 NO
109 ATP5F1 ATP5F1 ATP5F1 7673 0.014 0.22 NO
110 NRF1 NRF1 NRF1 7730 0.013 0.22 NO
111 POLR2G POLR2G POLR2G 7776 0.012 0.22 NO
112 GRM5 GRM5 GRM5 7958 0.01 0.21 NO
113 NDUFV2 NDUFV2 NDUFV2 8005 0.0097 0.2 NO
114 SDHD SDHD SDHD 8012 0.0096 0.2 NO
115 AP2M1 AP2M1 AP2M1 8062 0.009 0.2 NO
116 NDUFS1 NDUFS1 NDUFS1 8320 0.0058 0.19 NO
117 NDUFS8 NDUFS8 NDUFS8 8494 0.0035 0.18 NO
118 GPX1 GPX1 GPX1 8543 0.0029 0.18 NO
119 AP2B1 AP2B1 AP2B1 8709 0.00064 0.17 NO
120 ATP5C1 ATP5C1 ATP5C1 8761 8e-05 0.16 NO
121 GRIN1 GRIN1 GRIN1 9008 -0.003 0.15 NO
122 HDAC2 HDAC2 HDAC2 9485 -0.0097 0.12 NO
123 IFT57 IFT57 IFT57 9541 -0.011 0.12 NO
124 NDUFB8 NDUFB8 NDUFB8 9629 -0.012 0.12 NO
125 COX4I1 COX4I1 COX4I1 9634 -0.012 0.12 NO
126 CREBBP CREBBP CREBBP 9646 -0.012 0.12 NO
127 SP1 SP1 SP1 9653 -0.012 0.12 NO
128 TBP TBP TBP 9689 -0.013 0.12 NO
129 NDUFA4L2 NDUFA4L2 NDUFA4L2 9940 -0.016 0.11 NO
130 AP2A1 AP2A1 AP2A1 10049 -0.017 0.1 NO
131 EP300 EP300 EP300 10128 -0.019 0.098 NO
132 COX4I2 COX4I2 COX4I2 10250 -0.02 0.093 NO
133 CLTC CLTC CLTC 10263 -0.02 0.094 NO
134 SOD2 SOD2 SOD2 10288 -0.021 0.094 NO
135 DCTN1 DCTN1 DCTN1 10350 -0.022 0.092 NO
136 POLR2A POLR2A POLR2A 10430 -0.023 0.09 NO
137 RCOR1 RCOR1 RCOR1 10521 -0.024 0.086 NO
138 HDAC1 HDAC1 HDAC1 10683 -0.027 0.079 NO
139 CREB1 CREB1 CREB1 10735 -0.028 0.079 NO
140 POLR2D POLR2D POLR2D 11345 -0.038 0.047 NO
141 CREB3L4 CREB3L4 CREB3L4 11441 -0.039 0.045 NO
142 APAF1 APAF1 APAF1 11858 -0.048 0.025 NO
143 CASP9 CASP9 CASP9 12241 -0.056 0.0078 NO
144 TGM2 TGM2 TGM2 12295 -0.057 0.0092 NO
145 TAF4 TAF4 TAF4 12403 -0.059 0.0077 NO
146 HTT HTT HTT 12529 -0.062 0.0054 NO
147 PLCB3 PLCB3 PLCB3 12603 -0.064 0.0062 NO
148 TP53 TP53 TP53 12772 -0.068 0.002 NO
149 AP2A2 AP2A2 AP2A2 12802 -0.068 0.0057 NO
150 DNAH1 DNAH1 DNAH1 13197 -0.08 -0.01 NO
151 CASP8 CASP8 CASP8 13310 -0.084 -0.01 NO
152 COX6A2 COX6A2 COX6A2 13311 -0.084 -0.0036 NO
153 BAX BAX BAX 13405 -0.088 -0.002 NO
154 TAF4B TAF4B TAF4B 13609 -0.095 -0.0062 NO
155 CASP3 CASP3 CASP3 13764 -0.1 -0.0071 NO
156 CREB3L1 CREB3L1 CREB3L1 14092 -0.11 -0.017 NO
157 BBC3 BBC3 BBC3 14093 -0.11 -0.0082 NO
158 HIP1 HIP1 HIP1 14743 -0.14 -0.034 NO
159 DNALI1 DNALI1 DNALI1 15631 -0.2 -0.069 NO
160 DLG4 DLG4 DLG4 15711 -0.2 -0.058 NO
161 CREB3L3 CREB3L3 CREB3L3 15789 -0.21 -0.046 NO
162 COX6B2 COX6B2 COX6B2 16091 -0.23 -0.045 NO
163 DNAH2 DNAH2 DNAH2 16915 -0.31 -0.067 NO
164 PLCB2 PLCB2 PLCB2 17632 -0.45 -0.073 NO
165 PLCB1 PLCB1 PLCB1 17716 -0.49 -0.04 NO
166 CREB5 CREB5 CREB5 17805 -0.59 0.0011 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 SPLICEOSOME.

Figure S58.  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 BASE EXCISION REPAIR

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 COX7A1 COX7A1 COX7A1 280 0.36 0.033 YES
2 UBE2L6 UBE2L6 UBE2L6 650 0.27 0.049 YES
3 NDUFS4 NDUFS4 NDUFS4 1636 0.16 0.014 YES
4 NDUFS6 NDUFS6 NDUFS6 1862 0.14 0.021 YES
5 NDUFB6 NDUFB6 NDUFB6 2009 0.13 0.031 YES
6 SLC25A5 SLC25A5 SLC25A5 2140 0.13 0.04 YES
7 NDUFA2 NDUFA2 NDUFA2 2171 0.12 0.056 YES
8 SDHA SDHA SDHA 2302 0.12 0.065 YES
9 SNCA SNCA SNCA 2490 0.11 0.069 YES
10 NDUFV3 NDUFV3 NDUFV3 2521 0.11 0.082 YES
11 ATP5O ATP5O ATP5O 2688 0.1 0.087 YES
12 COX7C COX7C COX7C 2757 0.1 0.096 YES
13 ATP5J ATP5J ATP5J 2777 0.099 0.11 YES
14 UQCRB UQCRB UQCRB 2815 0.098 0.12 YES
15 COX5B COX5B COX5B 2861 0.096 0.13 YES
16 NDUFA8 NDUFA8 NDUFA8 2916 0.095 0.14 YES
17 SLC25A4 SLC25A4 SLC25A4 2977 0.093 0.15 YES
18 NDUFB5 NDUFB5 NDUFB5 3079 0.09 0.16 YES
19 NDUFA4 NDUFA4 NDUFA4 3209 0.086 0.16 YES
20 COX5A COX5A COX5A 3219 0.086 0.17 YES
21 ATP5G2 ATP5G2 ATP5G2 3246 0.085 0.18 YES
22 ATP5G1 ATP5G1 ATP5G1 3304 0.083 0.19 YES
23 NDUFS7 NDUFS7 NDUFS7 3400 0.081 0.2 YES
24 UQCRHL UQCRHL UQCRHL 3449 0.079 0.2 YES
25 UQCR11 UQCR11 UQCR11 3507 0.078 0.21 YES
26 ATP5H ATP5H ATP5H 3530 0.077 0.22 YES
27 UQCRQ UQCRQ UQCRQ 3574 0.076 0.23 YES
28 VDAC1 VDAC1 VDAC1 3598 0.076 0.24 YES
29 NDUFB4 NDUFB4 NDUFB4 3607 0.076 0.25 YES
30 NDUFB7 NDUFB7 NDUFB7 3626 0.075 0.26 YES
31 COX6B1 COX6B1 COX6B1 3836 0.07 0.25 YES
32 NDUFB2 NDUFB2 NDUFB2 3915 0.069 0.26 YES
33 NDUFB1 NDUFB1 NDUFB1 4178 0.064 0.25 YES
34 COX6C COX6C COX6C 4192 0.064 0.26 YES
35 NDUFAB1 NDUFAB1 NDUFAB1 4275 0.062 0.26 YES
36 VDAC3 VDAC3 VDAC3 4320 0.061 0.27 YES
37 NDUFA1 NDUFA1 NDUFA1 4340 0.061 0.28 YES
38 UQCRC1 UQCRC1 UQCRC1 4362 0.061 0.28 YES
39 COX7A2L COX7A2L COX7A2L 4402 0.06 0.29 YES
40 UQCRH UQCRH UQCRH 4461 0.059 0.3 YES
41 NDUFA5 NDUFA5 NDUFA5 4467 0.059 0.3 YES
42 NDUFC1 NDUFC1 NDUFC1 4514 0.058 0.31 YES
43 NDUFA7 NDUFA7 NDUFA7 4548 0.058 0.32 YES
44 COX7A2 COX7A2 COX7A2 4554 0.057 0.32 YES
45 UQCRFS1 UQCRFS1 UQCRFS1 4557 0.057 0.33 YES
46 NDUFA9 NDUFA9 NDUFA9 4683 0.055 0.33 YES
47 NDUFA3 NDUFA3 NDUFA3 4728 0.054 0.34 YES
48 VDAC2 VDAC2 VDAC2 4830 0.053 0.34 YES
49 NDUFB3 NDUFB3 NDUFB3 4872 0.052 0.34 YES
50 ATP5D ATP5D ATP5D 4879 0.052 0.35 YES
51 ATP5G3 ATP5G3 ATP5G3 5013 0.05 0.35 YES
52 CYC1 CYC1 CYC1 5180 0.048 0.34 YES
53 UBB UBB UBB 5288 0.046 0.34 YES
54 NDUFS3 NDUFS3 NDUFS3 5289 0.046 0.35 YES
55 UBE2G2 UBE2G2 UBE2G2 5321 0.045 0.36 YES
56 NDUFA6 NDUFA6 NDUFA6 5346 0.045 0.36 YES
57 ATP5B ATP5B ATP5B 5352 0.045 0.37 YES
58 NDUFV1 NDUFV1 NDUFV1 5472 0.043 0.37 YES
59 UQCR10 UQCR10 UQCR10 5475 0.043 0.37 YES
60 COX8A COX8A COX8A 5614 0.041 0.37 YES
61 NDUFB9 NDUFB9 NDUFB9 5616 0.041 0.38 YES
62 COX7B COX7B COX7B 5759 0.039 0.37 NO
63 COX6A1 COX6A1 COX6A1 5976 0.036 0.36 NO
64 ATP5A1 ATP5A1 ATP5A1 6038 0.035 0.37 NO
65 NDUFS2 NDUFS2 NDUFS2 6074 0.035 0.37 NO
66 CYCS CYCS CYCS 6308 0.032 0.36 NO
67 NDUFC2 NDUFC2 NDUFC2 6370 0.031 0.36 NO
68 PPID PPID PPID 6389 0.03 0.36 NO
69 SLC25A6 SLC25A6 SLC25A6 6500 0.029 0.36 NO
70 NDUFB10 NDUFB10 NDUFB10 6514 0.029 0.36 NO
71 SDHB SDHB SDHB 6521 0.029 0.37 NO
72 NDUFS5 NDUFS5 NDUFS5 6707 0.026 0.36 NO
73 UCHL1 UCHL1 UCHL1 6711 0.026 0.36 NO
74 SDHC SDHC SDHC 6750 0.026 0.37 NO
75 NDUFA10 NDUFA10 NDUFA10 6822 0.025 0.37 NO
76 PARK7 PARK7 PARK7 6834 0.024 0.37 NO
77 ATP5E ATP5E ATP5E 7073 0.022 0.36 NO
78 PARK2 PARK2 PARK2 7099 0.021 0.36 NO
79 UQCRC2 UQCRC2 UQCRC2 7223 0.02 0.36 NO
80 ATP5F1 ATP5F1 ATP5F1 7673 0.014 0.33 NO
81 SLC18A2 SLC18A2 SLC18A2 7968 0.01 0.32 NO
82 NDUFV2 NDUFV2 NDUFV2 8005 0.0097 0.32 NO
83 SDHD SDHD SDHD 8012 0.0096 0.32 NO
84 NDUFS1 NDUFS1 NDUFS1 8320 0.0058 0.3 NO
85 NDUFS8 NDUFS8 NDUFS8 8494 0.0035 0.29 NO
86 ATP5C1 ATP5C1 ATP5C1 8761 8e-05 0.28 NO
87 UBE2L3 UBE2L3 UBE2L3 8783 -0.0002 0.28 NO
88 UBA1 UBA1 UBA1 8814 -0.00064 0.27 NO
89 PINK1 PINK1 PINK1 9046 -0.0035 0.26 NO
90 NDUFB8 NDUFB8 NDUFB8 9629 -0.012 0.23 NO
91 COX4I1 COX4I1 COX4I1 9634 -0.012 0.23 NO
92 UBE2G1 UBE2G1 UBE2G1 9884 -0.015 0.22 NO
93 NDUFA4L2 NDUFA4L2 NDUFA4L2 9940 -0.016 0.22 NO
94 COX4I2 COX4I2 COX4I2 10250 -0.02 0.2 NO
95 GPR37 GPR37 GPR37 10298 -0.021 0.2 NO
96 UBE2J2 UBE2J2 UBE2J2 10838 -0.03 0.18 NO
97 UBA7 UBA7 UBA7 11843 -0.048 0.13 NO
98 APAF1 APAF1 APAF1 11858 -0.048 0.13 NO
99 CASP9 CASP9 CASP9 12241 -0.056 0.12 NO
100 LRRK2 LRRK2 LRRK2 12313 -0.057 0.12 NO
101 HTRA2 HTRA2 HTRA2 12389 -0.059 0.13 NO
102 SNCAIP SNCAIP SNCAIP 12758 -0.067 0.12 NO
103 UBE2J1 UBE2J1 UBE2J1 13119 -0.078 0.1 NO
104 COX6A2 COX6A2 COX6A2 13311 -0.084 0.11 NO
105 CASP3 CASP3 CASP3 13764 -0.1 0.094 NO
106 TH TH TH 15156 -0.16 0.038 NO
107 SLC18A1 SLC18A1 SLC18A1 15762 -0.2 0.032 NO
108 COX6B2 COX6B2 COX6B2 16091 -0.23 0.044 NO
109 SLC6A3 SLC6A3 SLC6A3 17424 -0.39 0.023 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 BASE EXCISION REPAIR.

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

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 clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.4 1.4 0.15 1 0.93 0.5 0.31 0.34 1 0.8
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.49 1.6 0.068 1 0.69 0.62 0.38 0.38 0.79 0.42
BIOCARTA PDGF PATHWAY 31 genes.ES.table 0.53 1.6 0.035 1 0.68 0.58 0.31 0.4 1 0.53
BIOCARTA EDG1 PATHWAY 26 genes.ES.table 0.47 1.3 0.14 1 0.97 0.27 0.14 0.23 1 0.77
BIOCARTA IL1R PATHWAY 30 genes.ES.table 0.51 1.2 0.27 1 0.98 0.47 0.28 0.34 1 0.72
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.51 1.8 0.01 0.73 0.26 0.57 0.35 0.37 0 0.21
BIOCARTA TOLL PATHWAY 36 genes.ES.table 0.43 1.2 0.34 1 0.99 0.44 0.32 0.3 1 0.77
BIOCARTA VEGF PATHWAY 28 genes.ES.table 0.39 1.3 0.25 1 0.97 0.43 0.38 0.27 1 0.74
KEGG GLYCINE SERINE AND THREONINE METABOLISM 30 genes.ES.table 0.47 1.2 0.2 1 0.98 0.37 0.17 0.3 1 0.77
KEGG ARGININE AND PROLINE METABOLISM 53 genes.ES.table 0.38 1.2 0.14 1 0.98 0.23 0.16 0.19 1 0.73
genes ES table in pathway: BIOCARTA EGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TNF TNF TNF 697 0.5 0.096 YES
2 DFFB DFFB DFFB 1411 0.39 0.16 YES
3 RB1 RB1 RB1 1972 0.32 0.22 YES
4 LMNB1 LMNB1 LMNB1 3309 0.23 0.2 YES
5 LMNA LMNA LMNA 3364 0.22 0.26 YES
6 MAP3K7 MAP3K7 MAP3K7 4148 0.18 0.26 YES
7 MAP2K4 MAP2K4 MAP2K4 4171 0.18 0.31 YES
8 PARP1 PARP1 PARP1 4299 0.17 0.35 YES
9 TNFRSF1A TNFRSF1A TNFRSF1A 4498 0.16 0.38 YES
10 BAG4 BAG4 BAG4 4613 0.16 0.42 YES
11 CASP8 CASP8 CASP8 4796 0.15 0.45 YES
12 PRKDC PRKDC PRKDC 5509 0.12 0.44 YES
13 DFFA DFFA DFFA 5745 0.12 0.46 YES
14 PAK2 PAK2 PAK2 5931 0.11 0.48 YES
15 ARHGDIB ARHGDIB ARHGDIB 6176 0.1 0.49 YES
16 RIPK1 RIPK1 RIPK1 6245 0.097 0.52 YES
17 LMNB2 LMNB2 LMNB2 6779 0.078 0.51 NO
18 MAPK8 MAPK8 MAPK8 7144 0.064 0.5 NO
19 CASP2 CASP2 CASP2 9263 -0.0042 0.38 NO
20 MADD MADD MADD 9583 -0.014 0.37 NO
21 CRADD CRADD CRADD 9697 -0.017 0.37 NO
22 JUN JUN JUN 9888 -0.023 0.36 NO
23 FADD FADD FADD 10005 -0.026 0.36 NO
24 TRADD TRADD TRADD 10190 -0.032 0.36 NO
25 MAP3K1 MAP3K1 MAP3K1 10417 -0.038 0.36 NO
26 PAK1 PAK1 PAK1 11345 -0.065 0.33 NO
27 CASP3 CASP3 CASP3 11375 -0.066 0.34 NO
28 SPTAN1 SPTAN1 SPTAN1 11742 -0.076 0.34 NO

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

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

genes ES table in pathway: BIOCARTA FAS PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PDGFRA PDGFRA PDGFRA 178 0.73 0.13 YES
2 PDGFA PDGFA PDGFA 769 0.49 0.19 YES
3 PRKCB PRKCB PRKCB 836 0.48 0.27 YES
4 PIK3R1 PIK3R1 PIK3R1 1038 0.44 0.35 YES
5 STAT4 STAT4 STAT4 2472 0.28 0.32 YES
6 PIK3CG PIK3CG PIK3CG 2558 0.27 0.37 YES
7 STAT3 STAT3 STAT3 3724 0.2 0.34 YES
8 MAP2K4 MAP2K4 MAP2K4 4171 0.18 0.35 YES
9 PRKCA PRKCA PRKCA 4402 0.17 0.37 YES
10 STAT1 STAT1 STAT1 4567 0.16 0.39 YES
11 STAT5A STAT5A STAT5A 4748 0.15 0.41 YES
12 SHC1 SHC1 SHC1 5058 0.14 0.42 YES
13 JAK1 JAK1 JAK1 5250 0.13 0.43 YES
14 FOS FOS FOS 5433 0.13 0.45 YES
15 SRF SRF SRF 5456 0.13 0.47 YES
16 PIK3CA PIK3CA PIK3CA 5511 0.12 0.49 YES
17 SOS1 SOS1 SOS1 5556 0.12 0.51 YES
18 GRB2 GRB2 GRB2 5602 0.12 0.53 YES
19 RASA1 RASA1 RASA1 6692 0.08 0.48 NO
20 STAT5B STAT5B STAT5B 6996 0.069 0.48 NO
21 MAPK8 MAPK8 MAPK8 7144 0.064 0.48 NO
22 PLCG1 PLCG1 PLCG1 8561 0.018 0.41 NO
23 STAT2 STAT2 STAT2 9750 -0.018 0.34 NO
24 MAPK3 MAPK3 MAPK3 9792 -0.02 0.35 NO
25 CSNK2A1 CSNK2A1 CSNK2A1 9797 -0.02 0.35 NO
26 JUN JUN JUN 9888 -0.023 0.35 NO
27 MAP3K1 MAP3K1 MAP3K1 10417 -0.038 0.33 NO
28 MAP2K1 MAP2K1 MAP2K1 11410 -0.067 0.28 NO
29 ELK1 ELK1 ELK1 12627 -0.1 0.24 NO
30 RAF1 RAF1 RAF1 13583 -0.14 0.21 NO
31 STAT6 STAT6 STAT6 14242 -0.16 0.2 NO

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

Figure S64.  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 PDGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PTPN13 PTPN13 PTPN13 807 0.48 0.064 YES
2 FAS FAS FAS 824 0.48 0.17 YES
3 CASP10 CASP10 CASP10 881 0.47 0.28 YES
4 DFFB DFFB DFFB 1411 0.39 0.33 YES
5 RB1 RB1 RB1 1972 0.32 0.38 YES
6 LMNA LMNA LMNA 3364 0.22 0.35 YES
7 MAP3K7 MAP3K7 MAP3K7 4148 0.18 0.35 YES
8 MAP2K4 MAP2K4 MAP2K4 4171 0.18 0.39 YES
9 PARP1 PARP1 PARP1 4299 0.17 0.42 YES
10 CASP8 CASP8 CASP8 4796 0.15 0.42 YES
11 PRKDC PRKDC PRKDC 5509 0.12 0.41 YES
12 DFFA DFFA DFFA 5745 0.12 0.43 YES
13 PAK2 PAK2 PAK2 5931 0.11 0.44 YES
14 ARHGDIB ARHGDIB ARHGDIB 6176 0.1 0.45 YES
15 CFLAR CFLAR CFLAR 6179 0.1 0.47 YES
16 DAXX DAXX DAXX 6270 0.096 0.49 YES
17 LMNB2 LMNB2 LMNB2 6779 0.078 0.48 YES
18 FAF1 FAF1 FAF1 6819 0.076 0.49 YES
19 MAPK8 MAPK8 MAPK8 7144 0.064 0.49 NO
20 CASP7 CASP7 CASP7 7943 0.036 0.45 NO
21 RIPK2 RIPK2 RIPK2 9389 -0.0078 0.37 NO
22 JUN JUN JUN 9888 -0.023 0.35 NO
23 FASLG FASLG FASLG 9970 -0.025 0.35 NO
24 FADD FADD FADD 10005 -0.026 0.36 NO
25 MAP3K1 MAP3K1 MAP3K1 10417 -0.038 0.34 NO
26 PAK1 PAK1 PAK1 11345 -0.065 0.3 NO
27 CASP3 CASP3 CASP3 11375 -0.066 0.32 NO
28 SPTAN1 SPTAN1 SPTAN1 11742 -0.076 0.32 NO
29 CASP6 CASP6 CASP6 13062 -0.12 0.27 NO

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

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PDGF 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 EDG1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GGT1 GGT1 GGT1 113 0.79 0.16 YES
2 GGT5 GGT5 GGT5 711 0.5 0.23 YES
3 PAPSS2 PAPSS2 PAPSS2 765 0.49 0.33 YES
4 CTH CTH CTH 796 0.48 0.43 YES
5 SCLY SCLY SCLY 1368 0.4 0.49 YES
6 CBS CBS CBS 1858 0.34 0.53 YES
7 MAT1A MAT1A MAT1A 4047 0.18 0.45 NO
8 TRMT11 TRMT11 TRMT11 4434 0.17 0.46 NO
9 PAPSS1 PAPSS1 PAPSS1 5064 0.14 0.45 NO
10 MAT2A MAT2A MAT2A 5538 0.12 0.45 NO
11 AHCYL1 AHCYL1 AHCYL1 6388 0.092 0.42 NO
12 SEPHS1 SEPHS1 SEPHS1 8050 0.034 0.34 NO
13 MARS2 MARS2 MARS2 8093 0.032 0.34 NO
14 METTL2B METTL2B METTL2B 8237 0.028 0.34 NO
15 METTL6 METTL6 METTL6 8874 0.0078 0.31 NO
16 GGT7 GGT7 GGT7 9323 -0.0059 0.28 NO
17 MAT2B MAT2B MAT2B 10848 -0.051 0.21 NO
18 AHCY AHCY AHCY 11104 -0.059 0.21 NO
19 MARS MARS MARS 11166 -0.06 0.22 NO
20 HEMK1 HEMK1 HEMK1 11212 -0.062 0.23 NO
21 LCMT2 LCMT2 LCMT2 11826 -0.079 0.21 NO
22 WBSCR22 WBSCR22 WBSCR22 13011 -0.12 0.17 NO
23 GGT6 GGT6 GGT6 13246 -0.12 0.18 NO
24 LCMT1 LCMT1 LCMT1 13283 -0.13 0.2 NO
25 AHCYL2 AHCYL2 AHCYL2 15434 -0.24 0.13 NO

Figure S67.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA EDG1 PATHWAY.

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EDG1 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 S35.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 836 0.48 0.068 YES
2 PIK3R1 PIK3R1 PIK3R1 1038 0.44 0.16 YES
3 STAT4 STAT4 STAT4 2472 0.28 0.15 YES
4 STAT3 STAT3 STAT3 3724 0.2 0.13 YES
5 MAP2K4 MAP2K4 MAP2K4 4171 0.18 0.15 YES
6 PRKCA PRKCA PRKCA 4402 0.17 0.18 YES
7 STAT1 STAT1 STAT1 4567 0.16 0.2 YES
8 STAT5A STAT5A STAT5A 4748 0.15 0.23 YES
9 SHC1 SHC1 SHC1 5058 0.14 0.25 YES
10 JAK1 JAK1 JAK1 5250 0.13 0.27 YES
11 FOS FOS FOS 5433 0.13 0.29 YES
12 SRF SRF SRF 5456 0.13 0.32 YES
13 PIK3CA PIK3CA PIK3CA 5511 0.12 0.35 YES
14 SOS1 SOS1 SOS1 5556 0.12 0.38 YES
15 GRB2 GRB2 GRB2 5602 0.12 0.4 YES
16 RASA1 RASA1 RASA1 6692 0.08 0.36 NO
17 STAT5B STAT5B STAT5B 6996 0.069 0.36 NO
18 MAPK8 MAPK8 MAPK8 7144 0.064 0.37 NO
19 PLCG1 PLCG1 PLCG1 8561 0.018 0.29 NO
20 EGFR EGFR EGFR 9327 -0.006 0.25 NO
21 STAT2 STAT2 STAT2 9750 -0.018 0.23 NO
22 MAPK3 MAPK3 MAPK3 9792 -0.02 0.23 NO
23 CSNK2A1 CSNK2A1 CSNK2A1 9797 -0.02 0.24 NO
24 JUN JUN JUN 9888 -0.023 0.24 NO
25 MAP3K1 MAP3K1 MAP3K1 10417 -0.038 0.22 NO
26 MAP2K1 MAP2K1 MAP2K1 11410 -0.067 0.18 NO
27 ELK1 ELK1 ELK1 12627 -0.1 0.14 NO
28 RAF1 RAF1 RAF1 13583 -0.14 0.12 NO
29 STAT6 STAT6 STAT6 14242 -0.16 0.12 NO
30 EGF EGF EGF 16320 -0.35 0.084 NO

Figure S69.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL1R PATHWAY.

Figure S70.  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 S36.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AGPAT4 AGPAT4 AGPAT4 95 0.81 0.073 YES
2 DGAT2 DGAT2 DGAT2 343 0.62 0.12 YES
3 PPAP2C PPAP2C PPAP2C 465 0.57 0.17 YES
4 DGKA DGKA DGKA 477 0.57 0.22 YES
5 PNPLA3 PNPLA3 PNPLA3 569 0.54 0.27 YES
6 MBOAT2 MBOAT2 MBOAT2 1062 0.44 0.28 YES
7 LIPF LIPF LIPF 1186 0.42 0.31 YES
8 ALDH2 ALDH2 ALDH2 1715 0.35 0.32 YES
9 DGKG DGKG DGKG 1774 0.35 0.35 YES
10 LPL LPL LPL 1953 0.33 0.37 YES
11 LIPC LIPC LIPC 2082 0.32 0.39 YES
12 DGKH DGKH DGKH 2211 0.3 0.42 YES
13 LIPG LIPG LIPG 2329 0.29 0.44 YES
14 ALDH1B1 ALDH1B1 ALDH1B1 2765 0.26 0.44 YES
15 DGKD DGKD DGKD 3388 0.22 0.42 YES
16 GPAT2 GPAT2 GPAT2 3495 0.21 0.44 YES
17 LCLAT1 LCLAT1 LCLAT1 4214 0.18 0.41 NO
18 ALDH9A1 ALDH9A1 ALDH9A1 4237 0.18 0.43 NO
19 CEL CEL CEL 4435 0.17 0.44 NO
20 AGPAT1 AGPAT1 AGPAT1 5266 0.13 0.4 NO
21 DGKE DGKE DGKE 5799 0.11 0.38 NO
22 ALDH3A2 ALDH3A2 ALDH3A2 6045 0.1 0.38 NO
23 DGKQ DGKQ DGKQ 6257 0.097 0.38 NO
24 GPAM GPAM GPAM 7335 0.058 0.32 NO
25 PPAP2A PPAP2A PPAP2A 7414 0.055 0.32 NO
26 ALDH7A1 ALDH7A1 ALDH7A1 7981 0.035 0.29 NO
27 DAK DAK DAK 8059 0.033 0.29 NO
28 AGPAT6 AGPAT6 AGPAT6 8525 0.02 0.27 NO
29 AKR1B1 AKR1B1 AKR1B1 9006 0.0039 0.24 NO
30 AKR1A1 AKR1A1 AKR1A1 9171 -0.0013 0.23 NO
31 PPAP2B PPAP2B PPAP2B 9283 -0.0048 0.23 NO
32 AGK AGK AGK 9381 -0.0076 0.22 NO
33 AGPAT3 AGPAT3 AGPAT3 12321 -0.094 0.065 NO
34 GLYCTK GLYCTK GLYCTK 12800 -0.11 0.049 NO
35 DGAT1 DGAT1 DGAT1 12959 -0.12 0.051 NO
36 DGKB DGKB DGKB 13584 -0.14 0.029 NO
37 GLA GLA GLA 14088 -0.16 0.016 NO
38 MBOAT1 MBOAT1 MBOAT1 14374 -0.17 0.017 NO
39 DGKZ DGKZ DGKZ 14566 -0.18 0.023 NO
40 MGLL MGLL MGLL 14967 -0.21 0.021 NO
41 GK GK GK 15906 -0.29 -0.0043 NO
42 AGPAT2 AGPAT2 AGPAT2 15910 -0.29 0.023 NO
43 AGPAT9 AGPAT9 AGPAT9 16179 -0.32 0.04 NO
44 DGKI DGKI DGKI 17187 -0.55 0.036 NO

Figure S71.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TNFR1 PATHWAY.

Figure S72.  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: BIOCARTA TOLL PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MAPK10 MAPK10 MAPK10 261 0.67 0.035 YES
2 NLRP3 NLRP3 NLRP3 421 0.59 0.069 YES
3 PYCARD PYCARD PYCARD 476 0.57 0.11 YES
4 IL1B IL1B IL1B 578 0.54 0.14 YES
5 CCL11 CCL11 CCL11 584 0.54 0.18 YES
6 CCL2 CCL2 CCL2 627 0.52 0.22 YES
7 MAPK12 MAPK12 MAPK12 630 0.52 0.26 YES
8 TNF TNF TNF 697 0.5 0.29 YES
9 MEFV MEFV MEFV 747 0.49 0.32 YES
10 CXCL1 CXCL1 CXCL1 788 0.48 0.36 YES
11 CCL8 CCL8 CCL8 835 0.48 0.39 YES
12 CXCL2 CXCL2 CXCL2 913 0.46 0.42 YES
13 NOD2 NOD2 NOD2 972 0.45 0.45 YES
14 NLRP1 NLRP1 NLRP1 982 0.45 0.48 YES
15 IL6 IL6 IL6 1315 0.4 0.49 YES
16 CARD9 CARD9 CARD9 1579 0.37 0.5 YES
17 CCL7 CCL7 CCL7 1863 0.34 0.51 YES
18 CASP1 CASP1 CASP1 2094 0.31 0.52 YES
19 PSTPIP1 PSTPIP1 PSTPIP1 2410 0.28 0.53 YES
20 CCL13 CCL13 CCL13 2535 0.28 0.54 YES
21 IL8 IL8 IL8 2752 0.26 0.55 YES
22 SUGT1 SUGT1 SUGT1 3335 0.22 0.53 YES
23 CASP5 CASP5 CASP5 3362 0.22 0.55 YES
24 MAPK11 MAPK11 MAPK11 3407 0.22 0.56 YES
25 NLRC4 NLRC4 NLRC4 4037 0.19 0.54 YES
26 TAB2 TAB2 TAB2 4095 0.18 0.55 YES
27 MAP3K7 MAP3K7 MAP3K7 4148 0.18 0.56 YES
28 CHUK CHUK CHUK 4248 0.18 0.57 YES
29 MAPK14 MAPK14 MAPK14 4597 0.16 0.56 YES
30 TRIP6 TRIP6 TRIP6 4723 0.16 0.56 YES
31 CASP8 CASP8 CASP8 4796 0.15 0.57 YES
32 BIRC3 BIRC3 BIRC3 6028 0.1 0.51 NO
33 MAPK8 MAPK8 MAPK8 7144 0.064 0.45 NO
34 BIRC2 BIRC2 BIRC2 7307 0.059 0.45 NO
35 NAIP NAIP NAIP 7352 0.057 0.45 NO
36 CARD8 CARD8 CARD8 7396 0.056 0.45 NO
37 TRAF6 TRAF6 TRAF6 8310 0.026 0.4 NO
38 IKBKB IKBKB IKBKB 8553 0.018 0.39 NO
39 MAPK9 MAPK9 MAPK9 8921 0.0065 0.37 NO
40 ERBB2IP ERBB2IP ERBB2IP 9287 -0.0048 0.35 NO
41 CCL5 CCL5 CCL5 9339 -0.0064 0.35 NO
42 RIPK2 RIPK2 RIPK2 9389 -0.0078 0.34 NO
43 MAPK1 MAPK1 MAPK1 9785 -0.02 0.32 NO
44 MAPK3 MAPK3 MAPK3 9792 -0.02 0.32 NO
45 HSP90B1 HSP90B1 HSP90B1 10246 -0.033 0.3 NO
46 NFKBIA NFKBIA NFKBIA 10268 -0.034 0.3 NO
47 NFKBIB NFKBIB NFKBIB 10326 -0.035 0.3 NO
48 NOD1 NOD1 NOD1 10606 -0.044 0.29 NO
49 TAB3 TAB3 TAB3 10820 -0.05 0.28 NO
50 XIAP XIAP XIAP 10927 -0.053 0.28 NO
51 TNFAIP3 TNFAIP3 TNFAIP3 11907 -0.081 0.23 NO
52 CARD6 CARD6 CARD6 12045 -0.085 0.23 NO
53 NFKB1 NFKB1 NFKB1 12207 -0.09 0.23 NO
54 TAB1 TAB1 TAB1 12310 -0.093 0.23 NO
55 RELA RELA RELA 13077 -0.12 0.19 NO
56 HSP90AA1 HSP90AA1 HSP90AA1 13345 -0.13 0.19 NO
57 IKBKG IKBKG IKBKG 13537 -0.14 0.19 NO
58 MAPK13 MAPK13 MAPK13 14211 -0.16 0.16 NO
59 IL18 IL18 IL18 17244 -0.58 0.033 NO

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

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

genes ES table in pathway: BIOCARTA VEGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GGT1 GGT1 GGT1 113 0.79 0.067 YES
2 MGST1 MGST1 MGST1 181 0.73 0.13 YES
3 GSTM2 GSTM2 GSTM2 187 0.72 0.2 YES
4 GSTM1 GSTM1 GSTM1 382 0.6 0.24 YES
5 ANPEP ANPEP ANPEP 431 0.59 0.29 YES
6 GSTM3 GSTM3 GSTM3 491 0.56 0.34 YES
7 GGT5 GGT5 GGT5 711 0.5 0.38 YES
8 RRM2 RRM2 RRM2 1137 0.43 0.39 YES
9 GSTM5 GSTM5 GSTM5 1365 0.4 0.42 YES
10 GSTT2 GSTT2 GSTT2 1666 0.36 0.43 YES
11 GSTA4 GSTA4 GSTA4 1949 0.33 0.45 YES
12 GSTT1 GSTT1 GSTT1 2229 0.3 0.46 YES
13 GPX7 GPX7 GPX7 2705 0.26 0.46 NO
14 GSTM4 GSTM4 GSTM4 3617 0.21 0.42 NO
15 TXNDC12 TXNDC12 TXNDC12 4294 0.17 0.4 NO
16 ODC1 ODC1 ODC1 4509 0.16 0.4 NO
17 GCLM GCLM GCLM 5373 0.13 0.37 NO
18 GGCT GGCT GGCT 5378 0.13 0.38 NO
19 GSTO2 GSTO2 GSTO2 5616 0.12 0.38 NO
20 GSR GSR GSR 5648 0.12 0.39 NO
21 IDH1 IDH1 IDH1 6311 0.095 0.36 NO
22 SRM SRM SRM 6420 0.091 0.36 NO
23 GSS GSS GSS 6786 0.077 0.35 NO
24 GCLC GCLC GCLC 7104 0.066 0.34 NO
25 GSTO1 GSTO1 GSTO1 7277 0.06 0.33 NO
26 GSTA1 GSTA1 GSTA1 7952 0.036 0.3 NO
27 GPX3 GPX3 GPX3 8099 0.032 0.29 NO
28 GSTP1 GSTP1 GSTP1 8272 0.027 0.28 NO
29 MGST3 MGST3 MGST3 8559 0.018 0.27 NO
30 OPLAH OPLAH OPLAH 8748 0.012 0.26 NO
31 GGT7 GGT7 GGT7 9323 -0.0059 0.23 NO
32 RRM2B RRM2B RRM2B 9802 -0.02 0.2 NO
33 RRM1 RRM1 RRM1 9942 -0.024 0.2 NO
34 LAP3 LAP3 LAP3 11059 -0.057 0.14 NO
35 GPX4 GPX4 GPX4 11203 -0.062 0.14 NO
36 SMS SMS SMS 11970 -0.083 0.1 NO
37 IDH2 IDH2 IDH2 12683 -0.1 0.073 NO
38 G6PD G6PD G6PD 13028 -0.12 0.064 NO
39 GGT6 GGT6 GGT6 13246 -0.12 0.064 NO
40 GPX1 GPX1 GPX1 13851 -0.15 0.043 NO
41 GSTK1 GSTK1 GSTK1 14043 -0.16 0.047 NO
42 GSTA2 GSTA2 GSTA2 14448 -0.18 0.04 NO
43 GSTZ1 GSTZ1 GSTZ1 15371 -0.24 0.01 NO
44 GPX2 GPX2 GPX2 16098 -0.31 -0.0018 NO
45 MGST2 MGST2 MGST2 16378 -0.36 0.015 NO
46 GSTA3 GSTA3 GSTA3 17547 -0.71 0.016 NO

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

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PDGFRA PDGFRA PDGFRA 178 0.73 0.13 YES
2 PDGFA PDGFA PDGFA 769 0.49 0.19 YES
3 PRKCB PRKCB PRKCB 836 0.48 0.28 YES
4 SPHK1 SPHK1 SPHK1 850 0.47 0.37 YES
5 PIK3R1 PIK3R1 PIK3R1 1038 0.44 0.45 YES
6 SMPD2 SMPD2 SMPD2 2299 0.29 0.44 YES
7 PIK3CG PIK3CG PIK3CG 2558 0.27 0.47 YES
8 PRKCA PRKCA PRKCA 4402 0.17 0.4 NO
9 PLCB1 PLCB1 PLCB1 4605 0.16 0.42 NO
10 S1PR1 S1PR1 S1PR1 4851 0.15 0.44 NO
11 PIK3CA PIK3CA PIK3CA 5511 0.12 0.42 NO
12 GNB1 GNB1 GNB1 6236 0.098 0.4 NO
13 ASAH1 ASAH1 ASAH1 6839 0.075 0.38 NO
14 SRC SRC SRC 7439 0.054 0.36 NO
15 ITGAV ITGAV ITGAV 7633 0.048 0.36 NO
16 RHOA RHOA RHOA 8639 0.015 0.31 NO
17 RAC1 RAC1 RAC1 9254 -0.004 0.27 NO
18 MAPK1 MAPK1 MAPK1 9785 -0.02 0.25 NO
19 MAPK3 MAPK3 MAPK3 9792 -0.02 0.25 NO
20 PTK2 PTK2 PTK2 9840 -0.021 0.25 NO
21 GNAI1 GNAI1 GNAI1 9988 -0.026 0.25 NO
22 ITGB3 ITGB3 ITGB3 10749 -0.048 0.22 NO
23 SMPD1 SMPD1 SMPD1 11271 -0.063 0.2 NO
24 SPHKAP SPHKAP SPHKAP 13647 -0.14 0.091 NO
25 AKT1 AKT1 AKT1 14124 -0.16 0.096 NO
26 GNGT1 GNGT1 GNGT1 17243 -0.58 0.033 NO

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

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

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL1R1 IL1R1 IL1R1 267 0.66 0.028 YES
2 IL1B IL1B IL1B 578 0.54 0.046 YES
3 TNFRSF10A TNFRSF10A TNFRSF10A 585 0.54 0.08 YES
4 TNF TNF TNF 697 0.5 0.11 YES
5 PIK3CD PIK3CD PIK3CD 709 0.5 0.14 YES
6 FAS FAS FAS 824 0.48 0.16 YES
7 CASP10 CASP10 CASP10 881 0.47 0.19 YES
8 NGF NGF NGF 918 0.46 0.22 YES
9 PIK3R1 PIK3R1 PIK3R1 1038 0.44 0.24 YES
10 IRAK3 IRAK3 IRAK3 1040 0.44 0.27 YES
11 IRAK2 IRAK2 IRAK2 1383 0.39 0.28 YES
12 DFFB DFFB DFFB 1411 0.39 0.3 YES
13 MYD88 MYD88 MYD88 1413 0.39 0.32 YES
14 CSF2RB CSF2RB CSF2RB 1522 0.38 0.34 YES
15 PIK3R5 PIK3R5 PIK3R5 1681 0.36 0.36 YES
16 IL1RAP IL1RAP IL1RAP 2018 0.32 0.36 YES
17 MAP3K14 MAP3K14 MAP3K14 2455 0.28 0.35 YES
18 PIK3CG PIK3CG PIK3CG 2558 0.27 0.36 YES
19 NTRK1 NTRK1 NTRK1 2766 0.26 0.37 YES
20 PPP3R1 PPP3R1 PPP3R1 3112 0.24 0.36 YES
21 PRKX PRKX PRKX 3130 0.24 0.38 YES
22 TNFRSF10C TNFRSF10C TNFRSF10C 4039 0.18 0.34 NO
23 TNFSF10 TNFSF10 TNFSF10 4082 0.18 0.35 NO
24 IL1A IL1A IL1A 4137 0.18 0.36 NO
25 CHUK CHUK CHUK 4248 0.18 0.36 NO
26 CASP9 CASP9 CASP9 4461 0.17 0.36 NO
27 TNFRSF1A TNFRSF1A TNFRSF1A 4498 0.16 0.37 NO
28 CASP8 CASP8 CASP8 4796 0.15 0.36 NO
29 TNFRSF10D TNFRSF10D TNFRSF10D 5111 0.14 0.36 NO
30 PPP3CB PPP3CB PPP3CB 5249 0.13 0.36 NO
31 PIK3CA PIK3CA PIK3CA 5511 0.12 0.35 NO
32 DFFA DFFA DFFA 5745 0.12 0.34 NO
33 PRKAR1A PRKAR1A PRKAR1A 5959 0.11 0.34 NO
34 BIRC3 BIRC3 BIRC3 6028 0.1 0.34 NO
35 CFLAR CFLAR CFLAR 6179 0.1 0.34 NO
36 RIPK1 RIPK1 RIPK1 6245 0.097 0.34 NO
37 TP53 TP53 TP53 6359 0.093 0.34 NO
38 PRKACG PRKACG PRKACG 6504 0.088 0.34 NO
39 BAX BAX BAX 6993 0.069 0.32 NO
40 BIRC2 BIRC2 BIRC2 7307 0.059 0.3 NO
41 APAF1 APAF1 APAF1 7372 0.056 0.3 NO
42 BID BID BID 7467 0.053 0.3 NO
43 PIK3R2 PIK3R2 PIK3R2 7487 0.053 0.3 NO
44 PIK3CB PIK3CB PIK3CB 7542 0.051 0.3 NO
45 PPP3CC PPP3CC PPP3CC 7587 0.049 0.3 NO
46 PRKAR2A PRKAR2A PRKAR2A 7606 0.048 0.31 NO
47 ATM ATM ATM 7891 0.038 0.29 NO
48 CASP7 CASP7 CASP7 7943 0.036 0.29 NO
49 IKBKB IKBKB IKBKB 8553 0.018 0.26 NO
50 PIK3R3 PIK3R3 PIK3R3 8583 0.017 0.26 NO
51 EXOG EXOG EXOG 8700 0.013 0.25 NO
52 TNFRSF10B TNFRSF10B TNFRSF10B 8842 0.009 0.25 NO
53 CAPN2 CAPN2 CAPN2 9169 -0.0013 0.23 NO
54 IRAK1 IRAK1 IRAK1 9559 -0.013 0.21 NO
55 PRKAR1B PRKAR1B PRKAR1B 9866 -0.022 0.19 NO
56 FADD FADD FADD 10005 -0.026 0.18 NO
57 PRKACB PRKACB PRKACB 10113 -0.029 0.18 NO
58 TRADD TRADD TRADD 10190 -0.032 0.18 NO
59 BAD BAD BAD 10209 -0.032 0.18 NO
60 NFKBIA NFKBIA NFKBIA 10268 -0.034 0.18 NO
61 BCL2L1 BCL2L1 BCL2L1 10690 -0.046 0.16 NO
62 CHP CHP CHP 10777 -0.049 0.16 NO
63 XIAP XIAP XIAP 10927 -0.053 0.15 NO
64 PRKACA PRKACA PRKACA 11337 -0.065 0.13 NO
65 CASP3 CASP3 CASP3 11375 -0.066 0.13 NO
66 NFKB1 NFKB1 NFKB1 12207 -0.09 0.094 NO
67 AIFM1 AIFM1 AIFM1 12699 -0.11 0.073 NO
68 TRAF2 TRAF2 TRAF2 12735 -0.11 0.078 NO
69 ENDOD1 ENDOD1 ENDOD1 12810 -0.11 0.081 NO
70 CASP6 CASP6 CASP6 13062 -0.12 0.074 NO
71 RELA RELA RELA 13077 -0.12 0.081 NO
72 AKT2 AKT2 AKT2 13450 -0.13 0.069 NO
73 PPP3CA PPP3CA PPP3CA 13518 -0.14 0.074 NO
74 IKBKG IKBKG IKBKG 13537 -0.14 0.081 NO
75 CAPN1 CAPN1 CAPN1 13544 -0.14 0.09 NO
76 IL3RA IL3RA IL3RA 13887 -0.15 0.08 NO
77 CYCS CYCS CYCS 13938 -0.15 0.087 NO
78 AKT1 AKT1 AKT1 14124 -0.16 0.087 NO
79 IRAK4 IRAK4 IRAK4 15096 -0.22 0.046 NO
80 ENDOG ENDOG ENDOG 15359 -0.23 0.047 NO
81 AKT3 AKT3 AKT3 15637 -0.26 0.048 NO
82 PRKAR2B PRKAR2B PRKAR2B 15965 -0.3 0.049 NO
83 BCL2 BCL2 BCL2 16457 -0.37 0.045 NO
84 PPP3R2 PPP3R2 PPP3R2 17011 -0.49 0.046 NO

Figure S79.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ARGININE AND PROLINE METABOLISM.

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

Fold change

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

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 = KICH-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = KICH-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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