GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PRAD-TP
Prostate Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
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 PRAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1959GTJ
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 PRAD-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: 193
Number of samples: 497
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 147
pheno.type: 2 - 3 :[ clus2 ] 175
pheno.type: 3 - 3 :[ clus3 ] 175

For the expression subtypes of 18274 genes in 498 samples, GSEA found enriched gene sets in each cluster using 497 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY

    • And common core enriched genes are PLCG2, ATP6V0A4, ATP6V0D2, ATP6V1B1, ATP6V1G3, CXCR1, CXCR2, EGFR, MET, NTRK1

  • clus2

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG TYROSINE METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

    • And common core enriched genes are ACAT2, ALDH2, ALDH3A2, ALDH7A1, ECHS1, ABAT, ACAA1, ACAA2, ACADSB, EHHADH

  • clus3

    • Top enriched gene sets are BIOCARTA CARM ER PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG N GLYCAN BIOSYNTHESIS, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA DEGRADATION

    • And common core enriched genes are CARS2, DARS, DARS2, EARS2, EPRS, FARSB, GARS, IARS, IARS2, LARS

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 0.61 1.5 0.048 0.22 0.85 0.4 0.22 0.31 0.15 0.015
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.54 1.4 0.088 0.17 0.92 0.33 0.23 0.26 0.13 0.001
BIOCARTA BIOPEPTIDES PATHWAY 39 genes.ES.table 0.4 1.3 0.17 0.23 0.99 0.31 0.26 0.23 0.19 0
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.44 1.3 0.17 0.21 0.98 0.62 0.4 0.37 0.17 0
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.51 1.4 0.085 0.18 0.94 0.53 0.36 0.34 0.14 0.002
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.56 1.5 0.075 0.18 0.9 0.3 0.2 0.24 0.13 0.003
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.46 1.5 0.082 0.18 0.9 0.41 0.36 0.26 0.13 0.003
BIOCARTA GH PATHWAY 26 genes.ES.table 0.54 1.5 0.07 0.17 0.9 0.5 0.32 0.34 0.13 0.002
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.35 1.4 0.14 0.19 0.95 0.37 0.4 0.22 0.15 0.004
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.58 1.5 0.073 0.17 0.91 0.43 0.21 0.34 0.13 0.001
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 CXCR2 CXCR2 CXCR2 59 0.74 0.09 YES
2 ATP6V0A4 ATP6V0A4 ATP6V0A4 187 0.6 0.16 YES
3 PTPRZ1 PTPRZ1 PTPRZ1 247 0.57 0.23 YES
4 CXCL1 CXCL1 CXCL1 304 0.54 0.29 YES
5 ATP6V1G3 ATP6V1G3 ATP6V1G3 342 0.52 0.36 YES
6 ATP6V0D2 ATP6V0D2 ATP6V0D2 469 0.48 0.41 YES
7 MET MET MET 692 0.42 0.45 YES
8 IL8 IL8 IL8 1858 0.27 0.42 YES
9 PLCG2 PLCG2 PLCG2 2063 0.25 0.44 YES
10 CCL5 CCL5 CCL5 2197 0.24 0.46 YES
11 ATP6V1B1 ATP6V1B1 ATP6V1B1 2221 0.24 0.49 YES
12 EGFR EGFR EGFR 2751 0.2 0.49 YES
13 MAP3K14 MAP3K14 MAP3K14 2881 0.2 0.51 YES
14 JAM2 JAM2 JAM2 2913 0.19 0.53 YES
15 CXCR1 CXCR1 CXCR1 3005 0.19 0.55 YES
16 HBEGF HBEGF HBEGF 3103 0.18 0.56 YES
17 JAM3 JAM3 JAM3 3421 0.17 0.57 YES
18 PAK1 PAK1 PAK1 4017 0.14 0.55 NO
19 TCIRG1 TCIRG1 TCIRG1 4604 0.11 0.54 NO
20 NFKB1 NFKB1 NFKB1 5345 0.085 0.51 NO
21 F11R F11R F11R 5389 0.084 0.51 NO
22 JUN JUN JUN 5675 0.076 0.51 NO
23 NFKBIA NFKBIA NFKBIA 5963 0.068 0.5 NO
24 ATP6V1G2 ATP6V1G2 ATP6V1G2 6717 0.05 0.47 NO
25 ADAM17 ADAM17 ADAM17 6766 0.049 0.47 NO
26 ADAM10 ADAM10 ADAM10 6804 0.049 0.47 NO
27 NOD1 NOD1 NOD1 7336 0.039 0.45 NO
28 ATP6V1C2 ATP6V1C2 ATP6V1C2 7451 0.037 0.45 NO
29 SRC SRC SRC 7509 0.036 0.45 NO
30 IGSF5 IGSF5 IGSF5 7572 0.035 0.45 NO
31 IKBKB IKBKB IKBKB 7763 0.032 0.44 NO
32 MAPK10 MAPK10 MAPK10 7764 0.032 0.45 NO
33 MAPK14 MAPK14 MAPK14 7767 0.032 0.45 NO
34 MAPK13 MAPK13 MAPK13 7964 0.029 0.44 NO
35 ATP6V0A2 ATP6V0A2 ATP6V0A2 8133 0.027 0.44 NO
36 ATP6V0D1 ATP6V0D1 ATP6V0D1 8215 0.026 0.44 NO
37 MAPK8 MAPK8 MAPK8 8275 0.025 0.44 NO
38 PTPN11 PTPN11 PTPN11 8456 0.022 0.43 NO
39 LYN LYN LYN 8481 0.022 0.43 NO
40 ATP6V1B2 ATP6V1B2 ATP6V1B2 8965 0.016 0.41 NO
41 CHUK CHUK CHUK 9057 0.015 0.4 NO
42 MAP2K4 MAP2K4 MAP2K4 9215 0.013 0.4 NO
43 MAPK11 MAPK11 MAPK11 9273 0.012 0.4 NO
44 ATP6V0A1 ATP6V0A1 ATP6V0A1 9673 0.0077 0.37 NO
45 PLCG1 PLCG1 PLCG1 9689 0.0076 0.37 NO
46 RELA RELA RELA 9970 0.0046 0.36 NO
47 IKBKG IKBKG IKBKG 9995 0.0042 0.36 NO
48 CDC42 CDC42 CDC42 10545 -0.0019 0.33 NO
49 CASP3 CASP3 CASP3 11537 -0.012 0.28 NO
50 ATP6V1H ATP6V1H ATP6V1H 11558 -0.012 0.28 NO
51 ATP6V1D ATP6V1D ATP6V1D 11582 -0.012 0.28 NO
52 ATP6V1E1 ATP6V1E1 ATP6V1E1 11879 -0.015 0.26 NO
53 RAC1 RAC1 RAC1 11885 -0.015 0.26 NO
54 CSK CSK CSK 12373 -0.02 0.24 NO
55 GIT1 GIT1 GIT1 12558 -0.022 0.23 NO
56 TJP1 TJP1 TJP1 13135 -0.029 0.2 NO
57 ATP6AP1 ATP6AP1 ATP6AP1 13384 -0.031 0.2 NO
58 ATP6V1A ATP6V1A ATP6V1A 13453 -0.032 0.2 NO
59 ATP6V1C1 ATP6V1C1 ATP6V1C1 13508 -0.033 0.2 NO
60 ATP6V0C ATP6V0C ATP6V0C 14278 -0.042 0.16 NO
61 ATP6V1E2 ATP6V1E2 ATP6V1E2 14448 -0.044 0.16 NO
62 MAPK9 MAPK9 MAPK9 14539 -0.045 0.16 NO
63 ATP6V0B ATP6V0B ATP6V0B 15198 -0.056 0.13 NO
64 ATP6V1F ATP6V1F ATP6V1F 15288 -0.058 0.13 NO
65 ATP6V1G1 ATP6V1G1 ATP6V1G1 15661 -0.064 0.12 NO
66 ATP6V0E2 ATP6V0E2 ATP6V0E2 16306 -0.082 0.092 NO
67 MAPK12 MAPK12 MAPK12 17086 -0.12 0.064 NO

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

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

genes ES table in pathway: BIOCARTA BCR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NTF4 NTF4 NTF4 33 0.79 0.063 YES
2 CALML3 CALML3 CALML3 79 0.71 0.12 YES
3 TP73 TP73 TP73 192 0.6 0.16 YES
4 NTRK3 NTRK3 NTRK3 207 0.6 0.21 YES
5 NTF3 NTF3 NTF3 432 0.49 0.24 YES
6 BDNF BDNF BDNF 548 0.46 0.27 YES
7 NGFR NGFR NGFR 710 0.42 0.29 YES
8 NTRK2 NTRK2 NTRK2 844 0.39 0.32 YES
9 NTRK1 NTRK1 NTRK1 1124 0.35 0.33 YES
10 PIK3CD PIK3CD PIK3CD 1291 0.32 0.35 YES
11 BCL2 BCL2 BCL2 1377 0.32 0.37 YES
12 IRAK3 IRAK3 IRAK3 1539 0.3 0.38 YES
13 FASLG FASLG FASLG 1579 0.3 0.4 YES
14 PIK3CG PIK3CG PIK3CG 1880 0.26 0.41 YES
15 SHC3 SHC3 SHC3 2004 0.26 0.42 YES
16 IRS1 IRS1 IRS1 2052 0.25 0.44 YES
17 PLCG2 PLCG2 PLCG2 2063 0.25 0.46 YES
18 IRAK2 IRAK2 IRAK2 2211 0.24 0.47 YES
19 CAMK4 CAMK4 CAMK4 2283 0.23 0.49 YES
20 IRS4 IRS4 IRS4 3532 0.16 0.43 NO
21 PIK3R1 PIK3R1 PIK3R1 3640 0.16 0.44 NO
22 CAMK2A CAMK2A CAMK2A 3918 0.14 0.43 NO
23 MAP3K1 MAP3K1 MAP3K1 4267 0.13 0.42 NO
24 TRAF6 TRAF6 TRAF6 4412 0.12 0.43 NO
25 CAMK2G CAMK2G CAMK2G 4507 0.12 0.43 NO
26 SH2B3 SH2B3 SH2B3 4574 0.11 0.44 NO
27 PIK3R5 PIK3R5 PIK3R5 4684 0.11 0.44 NO
28 RPS6KA5 RPS6KA5 RPS6KA5 5110 0.093 0.42 NO
29 NFKB1 NFKB1 NFKB1 5345 0.085 0.42 NO
30 MAPK7 MAPK7 MAPK7 5666 0.076 0.41 NO
31 JUN JUN JUN 5675 0.076 0.41 NO
32 MAP3K3 MAP3K3 MAP3K3 5778 0.074 0.41 NO
33 CALM1 CALM1 CALM1 5943 0.069 0.41 NO
34 NFKBIA NFKBIA NFKBIA 5963 0.068 0.41 NO
35 GAB1 GAB1 GAB1 6086 0.065 0.41 NO
36 MAP3K5 MAP3K5 MAP3K5 6308 0.06 0.4 NO
37 PIK3CA PIK3CA PIK3CA 6344 0.059 0.41 NO
38 SHC4 SHC4 SHC4 6407 0.057 0.41 NO
39 CALML6 CALML6 CALML6 6430 0.057 0.41 NO
40 NFKBIE NFKBIE NFKBIE 6532 0.054 0.41 NO
41 SOS1 SOS1 SOS1 6586 0.053 0.41 NO
42 NGF NGF NGF 6666 0.052 0.41 NO
43 SOS2 SOS2 SOS2 6925 0.046 0.4 NO
44 IRAK4 IRAK4 IRAK4 6938 0.046 0.4 NO
45 RAPGEF1 RAPGEF1 RAPGEF1 7004 0.045 0.4 NO
46 CRKL CRKL CRKL 7381 0.038 0.39 NO
47 MAPK3 MAPK3 MAPK3 7510 0.036 0.38 NO
48 CRK CRK CRK 7526 0.036 0.38 NO
49 RAP1B RAP1B RAP1B 7621 0.034 0.38 NO
50 PRDM4 PRDM4 PRDM4 7665 0.034 0.38 NO
51 IKBKB IKBKB IKBKB 7763 0.032 0.38 NO
52 MAPK10 MAPK10 MAPK10 7764 0.032 0.38 NO
53 MAPK14 MAPK14 MAPK14 7767 0.032 0.39 NO
54 RPS6KA2 RPS6KA2 RPS6KA2 7778 0.032 0.39 NO
55 FOXO3 FOXO3 FOXO3 7792 0.032 0.39 NO
56 ARHGDIB ARHGDIB ARHGDIB 7853 0.031 0.39 NO
57 RAP1A RAP1A RAP1A 7914 0.03 0.39 NO
58 YWHAH YWHAH YWHAH 7929 0.029 0.39 NO
59 KIDINS220 KIDINS220 KIDINS220 7946 0.029 0.39 NO
60 MAPK13 MAPK13 MAPK13 7964 0.029 0.39 NO
61 CAMK2D CAMK2D CAMK2D 7978 0.029 0.39 NO
62 SORT1 SORT1 SORT1 8022 0.028 0.39 NO
63 IRS2 IRS2 IRS2 8181 0.026 0.39 NO
64 CALML5 CALML5 CALML5 8266 0.025 0.38 NO
65 MAPK8 MAPK8 MAPK8 8275 0.025 0.39 NO
66 TP53 TP53 TP53 8348 0.024 0.38 NO
67 MAPKAPK2 MAPKAPK2 MAPKAPK2 8420 0.023 0.38 NO
68 PTPN11 PTPN11 PTPN11 8456 0.022 0.38 NO
69 SHC1 SHC1 SHC1 8477 0.022 0.38 NO
70 AKT3 AKT3 AKT3 8806 0.018 0.37 NO
71 PSEN1 PSEN1 PSEN1 8989 0.016 0.36 NO
72 FRS2 FRS2 FRS2 9049 0.015 0.36 NO
73 MAPK1 MAPK1 MAPK1 9197 0.013 0.35 NO
74 MAPK11 MAPK11 MAPK11 9273 0.012 0.34 NO
75 ZNF274 ZNF274 ZNF274 9368 0.012 0.34 NO
76 ABL1 ABL1 ABL1 9540 0.0094 0.33 NO
77 PLCG1 PLCG1 PLCG1 9689 0.0076 0.32 NO
78 MAP2K7 MAP2K7 MAP2K7 9779 0.0066 0.32 NO
79 MAP2K5 MAP2K5 MAP2K5 9847 0.006 0.32 NO
80 RELA RELA RELA 9970 0.0046 0.31 NO
81 YWHAB YWHAB YWHAB 10027 0.0038 0.31 NO
82 RHOA RHOA RHOA 10131 0.0025 0.3 NO
83 SH2B1 SH2B1 SH2B1 10207 0.0017 0.3 NO
84 RPS6KA3 RPS6KA3 RPS6KA3 10256 0.0012 0.3 NO
85 CDC42 CDC42 CDC42 10545 -0.0019 0.28 NO
86 GRB2 GRB2 GRB2 10644 -0.0028 0.28 NO
87 CALM3 CALM3 CALM3 11009 -0.0063 0.26 NO
88 NRAS NRAS NRAS 11024 -0.0065 0.26 NO
89 RAF1 RAF1 RAF1 11040 -0.0066 0.26 NO
90 NGFRAP1 NGFRAP1 NGFRAP1 11061 -0.0068 0.26 NO
91 AKT2 AKT2 AKT2 11216 -0.0087 0.25 NO
92 KRAS KRAS KRAS 11547 -0.012 0.23 NO
93 NFKBIB NFKBIB NFKBIB 11684 -0.013 0.22 NO
94 RAC1 RAC1 RAC1 11885 -0.015 0.21 NO
95 PRKCD PRKCD PRKCD 12025 -0.017 0.21 NO
96 SHC2 SHC2 SHC2 12319 -0.02 0.19 NO
97 CALM2 CALM2 CALM2 12360 -0.02 0.19 NO
98 CSK CSK CSK 12373 -0.02 0.19 NO
99 RPS6KA1 RPS6KA1 RPS6KA1 12407 -0.021 0.19 NO
100 AKT1 AKT1 AKT1 12627 -0.023 0.18 NO
101 RPS6KA6 RPS6KA6 RPS6KA6 13034 -0.028 0.16 NO
102 MAP2K2 MAP2K2 MAP2K2 13165 -0.029 0.16 NO
103 PIK3R2 PIK3R2 PIK3R2 13482 -0.032 0.14 NO
104 YWHAE YWHAE YWHAE 13897 -0.037 0.12 NO
105 GSK3B GSK3B GSK3B 13902 -0.037 0.13 NO
106 YWHAQ YWHAQ YWHAQ 13922 -0.038 0.13 NO
107 ATF4 ATF4 ATF4 13971 -0.038 0.13 NO
108 PIK3R3 PIK3R3 PIK3R3 14025 -0.039 0.13 NO
109 YWHAZ YWHAZ YWHAZ 14058 -0.039 0.13 NO
110 PIK3CB PIK3CB PIK3CB 14073 -0.039 0.13 NO
111 MAP2K1 MAP2K1 MAP2K1 14380 -0.043 0.12 NO
112 MAPK9 MAPK9 MAPK9 14539 -0.045 0.11 NO
113 ARHGDIA ARHGDIA ARHGDIA 14559 -0.045 0.12 NO
114 IRAK1 IRAK1 IRAK1 14991 -0.052 0.097 NO
115 YWHAG YWHAG YWHAG 15077 -0.054 0.097 NO
116 MAGED1 MAGED1 MAGED1 15122 -0.054 0.099 NO
117 BAX BAX BAX 15244 -0.057 0.097 NO
118 BAD BAD BAD 15633 -0.064 0.08 NO
119 RPS6KA4 RPS6KA4 RPS6KA4 15973 -0.072 0.068 NO
120 BRAF BRAF BRAF 16009 -0.073 0.072 NO
121 PDK1 PDK1 PDK1 16259 -0.08 0.064 NO
122 MAPK12 MAPK12 MAPK12 17086 -0.12 0.029 NO
123 RIPK2 RIPK2 RIPK2 17111 -0.12 0.037 NO
124 SH2B2 SH2B2 SH2B2 17407 -0.15 0.033 NO
125 CAMK2B CAMK2B CAMK2B 17615 -0.17 0.035 NO

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

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES 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 TMLHE TMLHE TMLHE 216 0.59 0.22 YES
2 PIPOX PIPOX PIPOX 254 0.56 0.43 YES
3 BBOX1 BBOX1 BBOX1 2813 0.2 0.36 NO
4 ALDH2 ALDH2 ALDH2 3065 0.18 0.42 NO
5 ALDH3A2 ALDH3A2 ALDH3A2 4461 0.12 0.39 NO
6 WHSC1L1 WHSC1L1 WHSC1L1 6060 0.066 0.33 NO
7 SETDB2 SETDB2 SETDB2 6817 0.048 0.31 NO
8 ASH1L ASH1L ASH1L 6862 0.047 0.32 NO
9 ALDH1B1 ALDH1B1 ALDH1B1 7110 0.043 0.32 NO
10 AASS AASS AASS 7539 0.036 0.32 NO
11 PLOD2 PLOD2 PLOD2 7558 0.035 0.33 NO
12 AASDH AASDH AASDH 7841 0.031 0.32 NO
13 ALDH9A1 ALDH9A1 ALDH9A1 8744 0.019 0.28 NO
14 SETD2 SETD2 SETD2 8815 0.018 0.28 NO
15 NSD1 NSD1 NSD1 8819 0.018 0.29 NO
16 SETD1A SETD1A SETD1A 8852 0.018 0.3 NO
17 OGDHL OGDHL OGDHL 8929 0.016 0.3 NO
18 ACAT2 ACAT2 ACAT2 9100 0.014 0.3 NO
19 OGDH OGDH OGDH 9193 0.013 0.3 NO
20 SETD1B SETD1B SETD1B 9229 0.013 0.3 NO
21 ALDH7A1 ALDH7A1 ALDH7A1 9874 0.0056 0.26 NO
22 DLST DLST DLST 10208 0.0017 0.25 NO
23 EHMT2 EHMT2 EHMT2 10291 0.00078 0.24 NO
24 SETD8 SETD8 SETD8 10415 -0.00064 0.24 NO
25 SUV420H1 SUV420H1 SUV420H1 10535 -0.0018 0.23 NO
26 PLOD1 PLOD1 PLOD1 10546 -0.0019 0.23 NO
27 HADHA HADHA HADHA 10587 -0.0023 0.23 NO
28 SETD7 SETD7 SETD7 10652 -0.0029 0.23 NO
29 EHMT1 EHMT1 EHMT1 10766 -0.0041 0.22 NO
30 AASDHPPT AASDHPPT AASDHPPT 10805 -0.0045 0.22 NO
31 SETDB1 SETDB1 SETDB1 11532 -0.012 0.19 NO
32 SETMAR SETMAR SETMAR 12408 -0.021 0.15 NO
33 DOT1L DOT1L DOT1L 12469 -0.021 0.15 NO
34 SUV39H2 SUV39H2 SUV39H2 12704 -0.024 0.15 NO
35 SUV39H1 SUV39H1 SUV39H1 12786 -0.025 0.15 NO
36 HADH HADH HADH 12902 -0.026 0.16 NO
37 AADAT AADAT AADAT 13035 -0.028 0.16 NO
38 GCDH GCDH GCDH 13654 -0.034 0.14 NO
39 PLOD3 PLOD3 PLOD3 14164 -0.04 0.13 NO
40 SUV420H2 SUV420H2 SUV420H2 15136 -0.055 0.095 NO
41 ECHS1 ECHS1 ECHS1 15444 -0.06 0.1 NO
42 ACAT1 ACAT1 ACAT1 15814 -0.068 0.11 NO
43 WHSC1 WHSC1 WHSC1 15819 -0.068 0.13 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 BIOPEPTIDES PATHWAY.

Figure S6.  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 HDAC 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 CFTR CFTR CFTR 65 0.72 0.14 YES
2 ATP6V0A4 ATP6V0A4 ATP6V0A4 187 0.6 0.25 YES
3 ATP6V1G3 ATP6V1G3 ATP6V1G3 342 0.52 0.34 YES
4 ATP6V0D2 ATP6V0D2 ATP6V0D2 469 0.48 0.42 YES
5 PRKCB PRKCB PRKCB 798 0.4 0.48 YES
6 PLCG2 PLCG2 PLCG2 2063 0.25 0.46 YES
7 ATP6V1B1 ATP6V1B1 ATP6V1B1 2221 0.24 0.5 YES
8 PRKCA PRKCA PRKCA 2960 0.19 0.5 NO
9 KCNQ1 KCNQ1 KCNQ1 4348 0.12 0.44 NO
10 TCIRG1 TCIRG1 TCIRG1 4604 0.11 0.45 NO
11 ADCY9 ADCY9 ADCY9 5104 0.093 0.44 NO
12 ERO1L ERO1L ERO1L 5901 0.07 0.41 NO
13 ATP6V1G2 ATP6V1G2 ATP6V1G2 6717 0.05 0.38 NO
14 KDELR3 KDELR3 KDELR3 7031 0.044 0.37 NO
15 ACTB ACTB ACTB 7269 0.04 0.36 NO
16 PRKCG PRKCG PRKCG 7414 0.038 0.36 NO
17 TJP2 TJP2 TJP2 7427 0.038 0.37 NO
18 ATP6V1C2 ATP6V1C2 ATP6V1C2 7451 0.037 0.38 NO
19 SLC12A2 SLC12A2 SLC12A2 8078 0.028 0.35 NO
20 ATP6V0A2 ATP6V0A2 ATP6V0A2 8133 0.027 0.35 NO
21 ATP6V0D1 ATP6V0D1 ATP6V0D1 8215 0.026 0.35 NO
22 PRKX PRKX PRKX 8754 0.019 0.32 NO
23 ATP6V1B2 ATP6V1B2 ATP6V1B2 8965 0.016 0.32 NO
24 MUC2 MUC2 MUC2 9444 0.01 0.29 NO
25 ATP6V0A1 ATP6V0A1 ATP6V0A1 9673 0.0077 0.28 NO
26 PLCG1 PLCG1 PLCG1 9689 0.0076 0.28 NO
27 PRKACA PRKACA PRKACA 9770 0.0066 0.28 NO
28 ATP6V0E1 ATP6V0E1 ATP6V0E1 11349 -0.01 0.19 NO
29 ATP6V1H ATP6V1H ATP6V1H 11558 -0.012 0.18 NO
30 ATP6V1D ATP6V1D ATP6V1D 11582 -0.012 0.18 NO
31 ATP6V1E1 ATP6V1E1 ATP6V1E1 11879 -0.015 0.17 NO
32 KDELR1 KDELR1 KDELR1 12279 -0.019 0.15 NO
33 SEC61A2 SEC61A2 SEC61A2 12573 -0.023 0.14 NO
34 PRKACB PRKACB PRKACB 13109 -0.029 0.12 NO
35 TJP1 TJP1 TJP1 13135 -0.029 0.12 NO
36 ACTG1 ACTG1 ACTG1 13191 -0.029 0.12 NO
37 ATP6AP1 ATP6AP1 ATP6AP1 13384 -0.031 0.12 NO
38 SEC61A1 SEC61A1 SEC61A1 13386 -0.031 0.13 NO
39 PDIA4 PDIA4 PDIA4 13450 -0.032 0.13 NO
40 ATP6V1A ATP6V1A ATP6V1A 13453 -0.032 0.14 NO
41 ATP6V1C1 ATP6V1C1 ATP6V1C1 13508 -0.033 0.14 NO
42 ARF1 ARF1 ARF1 13892 -0.037 0.12 NO
43 GNAS GNAS GNAS 13963 -0.038 0.13 NO
44 ATP6V0C ATP6V0C ATP6V0C 14278 -0.042 0.12 NO
45 ATP6V1E2 ATP6V1E2 ATP6V1E2 14448 -0.044 0.12 NO
46 KDELR2 KDELR2 KDELR2 14715 -0.048 0.11 NO
47 ATP6V0B ATP6V0B ATP6V0B 15198 -0.056 0.097 NO
48 ATP6V1F ATP6V1F ATP6V1F 15288 -0.058 0.1 NO
49 ATP6V1G1 ATP6V1G1 ATP6V1G1 15661 -0.064 0.095 NO
50 SEC61B SEC61B SEC61B 15787 -0.068 0.1 NO
51 ATP6V0E2 ATP6V0E2 ATP6V0E2 16306 -0.082 0.089 NO
52 SEC61G SEC61G SEC61G 16630 -0.095 0.089 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 HDAC PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HDAC 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 EGF 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 CXCR2 CXCR2 CXCR2 59 0.74 0.048 YES
2 FGFR2 FGFR2 FGFR2 284 0.55 0.073 YES
3 PSD2 PSD2 PSD2 471 0.48 0.096 YES
4 PIP5K1B PIP5K1B PIP5K1B 591 0.45 0.12 YES
5 SH3GL3 SH3GL3 SH3GL3 662 0.43 0.15 YES
6 MET MET MET 692 0.42 0.17 YES
7 IQSEC3 IQSEC3 IQSEC3 834 0.39 0.19 YES
8 KIT KIT KIT 990 0.36 0.21 YES
9 IL2RB IL2RB IL2RB 1085 0.35 0.23 YES
10 NTRK1 NTRK1 NTRK1 1124 0.35 0.25 YES
11 CCR5 CCR5 CCR5 1653 0.29 0.24 YES
12 PLD1 PLD1 PLD1 1818 0.27 0.25 YES
13 ACAP1 ACAP1 ACAP1 1873 0.27 0.26 YES
14 HLA-G HLA-G HLA-G 1885 0.26 0.28 YES
15 ERBB4 ERBB4 ERBB4 1993 0.26 0.3 YES
16 EHD2 EHD2 EHD2 2425 0.22 0.29 YES
17 EGFR EGFR EGFR 2751 0.2 0.28 YES
18 DNM3 DNM3 DNM3 2888 0.2 0.29 YES
19 CXCR1 CXCR1 CXCR1 3005 0.19 0.3 YES
20 HLA-F HLA-F HLA-F 3189 0.18 0.3 YES
21 CSF1R CSF1R CSF1R 3211 0.18 0.31 YES
22 IL2RG IL2RG IL2RG 3243 0.18 0.32 YES
23 GRK5 GRK5 GRK5 3290 0.17 0.33 YES
24 SH3GL2 SH3GL2 SH3GL2 3424 0.17 0.33 YES
25 PARD6G PARD6G PARD6G 3494 0.16 0.34 YES
26 ARAP3 ARAP3 ARAP3 3496 0.16 0.35 YES
27 HSPA2 HSPA2 HSPA2 3526 0.16 0.36 YES
28 AGAP2 AGAP2 AGAP2 3546 0.16 0.37 YES
29 PDGFRA PDGFRA PDGFRA 3653 0.16 0.38 YES
30 RAB31 RAB31 RAB31 3711 0.15 0.38 YES
31 KDR KDR KDR 3810 0.15 0.39 YES
32 CLTCL1 CLTCL1 CLTCL1 3855 0.14 0.39 YES
33 DNM1 DNM1 DNM1 4141 0.13 0.39 YES
34 ASAP1 ASAP1 ASAP1 4205 0.13 0.39 YES
35 HLA-E HLA-E HLA-E 4290 0.13 0.4 YES
36 NEDD4 NEDD4 NEDD4 4350 0.12 0.4 YES
37 ARAP2 ARAP2 ARAP2 4372 0.12 0.41 YES
38 TRAF6 TRAF6 TRAF6 4412 0.12 0.42 YES
39 HLA-A HLA-A HLA-A 4547 0.11 0.42 YES
40 CXCR4 CXCR4 CXCR4 4575 0.11 0.42 YES
41 TFRC TFRC TFRC 4697 0.11 0.42 YES
42 FLT1 FLT1 FLT1 4899 0.1 0.42 YES
43 VPS36 VPS36 VPS36 5257 0.088 0.41 YES
44 PSD PSD PSD 5290 0.087 0.41 YES
45 ADRB3 ADRB3 ADRB3 5406 0.084 0.41 YES
46 ASAP3 ASAP3 ASAP3 5434 0.083 0.41 YES
47 ARRB1 ARRB1 ARRB1 5470 0.082 0.42 YES
48 EHD3 EHD3 EHD3 5533 0.08 0.42 YES
49 HLA-B HLA-B HLA-B 5542 0.08 0.42 YES
50 FAM125B FAM125B FAM125B 5551 0.08 0.43 YES
51 IL2RA IL2RA IL2RA 5691 0.076 0.43 YES
52 ARAP1 ARAP1 ARAP1 5750 0.074 0.43 YES
53 RAB11FIP2 RAB11FIP2 RAB11FIP2 5774 0.074 0.43 YES
54 GRK7 GRK7 GRK7 5840 0.072 0.43 YES
55 EHD4 EHD4 EHD4 5994 0.067 0.43 NO
56 IQSEC2 IQSEC2 IQSEC2 6093 0.065 0.43 NO
57 PIP5K1C PIP5K1C PIP5K1C 6124 0.064 0.43 NO
58 PLD2 PLD2 PLD2 6222 0.062 0.43 NO
59 SH3KBP1 SH3KBP1 SH3KBP1 6274 0.06 0.43 NO
60 SMURF1 SMURF1 SMURF1 6357 0.058 0.43 NO
61 CBL CBL CBL 6489 0.055 0.43 NO
62 VPS37D VPS37D VPS37D 6562 0.054 0.43 NO
63 VPS37A VPS37A VPS37A 6577 0.053 0.43 NO
64 HLA-C HLA-C HLA-C 6831 0.048 0.42 NO
65 VPS4B VPS4B VPS4B 6840 0.048 0.42 NO
66 IGF1R IGF1R IGF1R 6867 0.047 0.42 NO
67 RET RET RET 6951 0.046 0.42 NO
68 LDLR LDLR LDLR 6956 0.046 0.43 NO
69 FGFR3 FGFR3 FGFR3 7002 0.045 0.43 NO
70 SH3GLB1 SH3GLB1 SH3GLB1 7260 0.04 0.42 NO
71 ZFYVE20 ZFYVE20 ZFYVE20 7390 0.038 0.41 NO
72 CHMP1B CHMP1B CHMP1B 7401 0.038 0.41 NO
73 ADRBK2 ADRBK2 ADRBK2 7407 0.038 0.42 NO
74 SRC SRC SRC 7509 0.036 0.41 NO
75 PARD3 PARD3 PARD3 8042 0.028 0.38 NO
76 EPN2 EPN2 EPN2 8064 0.028 0.39 NO
77 CHMP4A CHMP4A CHMP4A 8091 0.027 0.39 NO
78 GIT2 GIT2 GIT2 8107 0.027 0.39 NO
79 ACAP2 ACAP2 ACAP2 8162 0.026 0.39 NO
80 CHMP2B CHMP2B CHMP2B 8279 0.025 0.38 NO
81 DAB2 DAB2 DAB2 8352 0.024 0.38 NO
82 RAB5C RAB5C RAB5C 8561 0.021 0.37 NO
83 EGF EGF EGF 8570 0.021 0.37 NO
84 EHD1 EHD1 EHD1 8632 0.02 0.37 NO
85 MDM2 MDM2 MDM2 8702 0.019 0.37 NO
86 EEA1 EEA1 EEA1 8740 0.019 0.36 NO
87 STAM2 STAM2 STAM2 8793 0.018 0.36 NO
88 AP2A1 AP2A1 AP2A1 8834 0.018 0.36 NO
89 HSPA1L HSPA1L HSPA1L 8846 0.018 0.36 NO
90 USP8 USP8 USP8 8865 0.017 0.36 NO
91 RAB11FIP5 RAB11FIP5 RAB11FIP5 8945 0.016 0.36 NO
92 ARRB2 ARRB2 ARRB2 9086 0.014 0.35 NO
93 ARFGAP2 ARFGAP2 ARFGAP2 9401 0.011 0.34 NO
94 RAB11B RAB11B RAB11B 9486 0.01 0.33 NO
95 VPS24 VPS24 VPS24 9533 0.0094 0.33 NO
96 RAB11FIP1 RAB11FIP1 RAB11FIP1 9596 0.0088 0.33 NO
97 PIKFYVE PIKFYVE PIKFYVE 9664 0.0079 0.32 NO
98 RABEP1 RABEP1 RABEP1 9668 0.0078 0.32 NO
99 ITCH ITCH ITCH 9782 0.0065 0.32 NO
100 PIP4K2B PIP4K2B PIP4K2B 9796 0.0065 0.32 NO
101 HSPA6 HSPA6 HSPA6 9825 0.0062 0.32 NO
102 IQSEC1 IQSEC1 IQSEC1 9914 0.0052 0.31 NO
103 STAM STAM STAM 9924 0.0051 0.31 NO
104 AP2B1 AP2B1 AP2B1 10001 0.004 0.31 NO
105 AP2M1 AP2M1 AP2M1 10227 0.0015 0.3 NO
106 CHMP6 CHMP6 CHMP6 10270 0.001 0.3 NO
107 DNAJC6 DNAJC6 DNAJC6 10272 0.001 0.3 NO
108 SMAP1 SMAP1 SMAP1 10374 -0.00023 0.29 NO
109 PDCD6IP PDCD6IP PDCD6IP 10411 -0.0006 0.29 NO
110 RAB4A RAB4A RAB4A 10420 -0.00071 0.29 NO
111 VPS4A VPS4A VPS4A 10427 -0.00081 0.29 NO
112 LDLRAP1 LDLRAP1 LDLRAP1 10474 -0.0012 0.28 NO
113 DNM2 DNM2 DNM2 10487 -0.0013 0.28 NO
114 CHMP4B CHMP4B CHMP4B 10502 -0.0015 0.28 NO
115 VTA1 VTA1 VTA1 10516 -0.0016 0.28 NO
116 PRKCI PRKCI PRKCI 10528 -0.0018 0.28 NO
117 CDC42 CDC42 CDC42 10545 -0.0019 0.28 NO
118 VPS45 VPS45 VPS45 10591 -0.0023 0.28 NO
119 CHMP5 CHMP5 CHMP5 10641 -0.0028 0.28 NO
120 PSD4 PSD4 PSD4 10749 -0.0039 0.27 NO
121 SMURF2 SMURF2 SMURF2 10767 -0.0041 0.27 NO
122 ASAP2 ASAP2 ASAP2 10778 -0.0042 0.27 NO
123 RUFY1 RUFY1 RUFY1 10850 -0.0049 0.27 NO
124 RAB11FIP4 RAB11FIP4 RAB11FIP4 10923 -0.0056 0.26 NO
125 DNM1L DNM1L DNM1L 10930 -0.0056 0.26 NO
126 VPS37B VPS37B VPS37B 10979 -0.0061 0.26 NO
127 EPS15 EPS15 EPS15 11160 -0.0079 0.25 NO
128 HSPA1A HSPA1A HSPA1A 11281 -0.0094 0.24 NO
129 PRKCZ PRKCZ PRKCZ 11295 -0.0096 0.24 NO
130 RAB5B RAB5B RAB5B 11394 -0.01 0.24 NO
131 STAMBP STAMBP STAMBP 11431 -0.011 0.24 NO
132 SH3GL1 SH3GL1 SH3GL1 11438 -0.011 0.24 NO
133 AP2A2 AP2A2 AP2A2 11522 -0.012 0.24 NO
134 VPS25 VPS25 VPS25 11675 -0.013 0.23 NO
135 RAB22A RAB22A RAB22A 11946 -0.016 0.21 NO
136 CLTB CLTB CLTB 11978 -0.016 0.21 NO
137 ERBB3 ERBB3 ERBB3 12012 -0.016 0.21 NO
138 EPN3 EPN3 EPN3 12075 -0.017 0.21 NO
139 PSD3 PSD3 PSD3 12088 -0.017 0.21 NO
140 HGS HGS HGS 12207 -0.019 0.21 NO
141 ARFGAP3 ARFGAP3 ARFGAP3 12247 -0.019 0.2 NO
142 FGFR4 FGFR4 FGFR4 12285 -0.019 0.2 NO
143 F2R F2R F2R 12372 -0.02 0.2 NO
144 CLTC CLTC CLTC 12433 -0.021 0.2 NO
145 GRK6 GRK6 GRK6 12479 -0.022 0.2 NO
146 CBLB CBLB CBLB 12509 -0.022 0.2 NO
147 GIT1 GIT1 GIT1 12558 -0.022 0.2 NO
148 PIP5K1A PIP5K1A PIP5K1A 12689 -0.024 0.19 NO
149 ARFGAP1 ARFGAP1 ARFGAP1 12735 -0.024 0.19 NO
150 RAB5A RAB5A RAB5A 12835 -0.026 0.19 NO
151 HSPA1B HSPA1B HSPA1B 13078 -0.028 0.18 NO
152 SMAP2 SMAP2 SMAP2 13272 -0.03 0.17 NO
153 CBLC CBLC CBLC 13337 -0.031 0.16 NO
154 FAM125A FAM125A FAM125A 13470 -0.032 0.16 NO
155 EPN1 EPN1 EPN1 13577 -0.034 0.16 NO
156 RNF41 RNF41 RNF41 13625 -0.034 0.16 NO
157 CHMP2A CHMP2A CHMP2A 13685 -0.035 0.16 NO
158 HSPA8 HSPA8 HSPA8 13697 -0.035 0.16 NO
159 SH3GLB2 SH3GLB2 SH3GLB2 13767 -0.036 0.16 NO
160 SNF8 SNF8 SNF8 13856 -0.037 0.15 NO
161 CLTA CLTA CLTA 13972 -0.038 0.15 NO
162 TSG101 TSG101 TSG101 14173 -0.04 0.14 NO
163 ADRBK1 ADRBK1 ADRBK1 14288 -0.042 0.14 NO
164 ADRB2 ADRB2 ADRB2 14350 -0.043 0.14 NO
165 ARF6 ARF6 ARF6 14577 -0.046 0.13 NO
166 PARD6B PARD6B PARD6B 14586 -0.046 0.13 NO
167 RAB11A RAB11A RAB11A 14594 -0.046 0.13 NO
168 VPS28 VPS28 VPS28 14642 -0.046 0.14 NO
169 ACAP3 ACAP3 ACAP3 14763 -0.048 0.13 NO
170 RAB11FIP3 RAB11FIP3 RAB11FIP3 14942 -0.051 0.12 NO
171 WWP1 WWP1 WWP1 14986 -0.052 0.13 NO
172 NEDD4L NEDD4L NEDD4L 15794 -0.068 0.086 NO
173 AP2S1 AP2S1 AP2S1 15911 -0.07 0.085 NO
174 AGAP1 AGAP1 AGAP1 16052 -0.074 0.082 NO
175 VPS37C VPS37C VPS37C 16132 -0.076 0.083 NO
176 PARD6A PARD6A PARD6A 16789 -0.1 0.054 NO
177 ADRB1 ADRB1 ADRB1 17096 -0.12 0.045 NO
178 GRK4 GRK4 GRK4 17209 -0.13 0.048 NO
179 CHMP4C CHMP4C CHMP4C 17381 -0.14 0.048 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 EGF PATHWAY.

Figure S10.  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 FCER1 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 CHP2 CHP2 CHP2 1 1 0.15 YES
2 GRIN2A GRIN2A GRIN2A 106 0.67 0.24 YES
3 NOS1 NOS1 NOS1 170 0.61 0.32 YES
4 PRPH2 PRPH2 PRPH2 420 0.5 0.38 YES
5 NEFH NEFH NEFH 466 0.48 0.45 YES
6 CASP1 CASP1 CASP1 746 0.41 0.5 YES
7 BCL2 BCL2 BCL2 1377 0.32 0.51 YES
8 GRIA2 GRIA2 GRIA2 1408 0.31 0.55 YES
9 TNF TNF TNF 1644 0.29 0.58 YES
10 NEFM NEFM NEFM 3249 0.18 0.52 NO
11 GRIN2D GRIN2D GRIN2D 3359 0.17 0.54 NO
12 GRIA1 GRIA1 GRIA1 3644 0.16 0.54 NO
13 TNFRSF1B TNFRSF1B TNFRSF1B 3859 0.14 0.55 NO
14 NEFL NEFL NEFL 4823 0.1 0.51 NO
15 TNFRSF1A TNFRSF1A TNFRSF1A 5649 0.077 0.48 NO
16 PRPH PRPH PRPH 5986 0.068 0.47 NO
17 CAT CAT CAT 6190 0.062 0.47 NO
18 MAP3K5 MAP3K5 MAP3K5 6308 0.06 0.47 NO
19 GRIN2C GRIN2C GRIN2C 6529 0.054 0.47 NO
20 PPP3CC PPP3CC PPP3CC 6550 0.054 0.47 NO
21 PPP3CB PPP3CB PPP3CB 7331 0.039 0.44 NO
22 MAPK14 MAPK14 MAPK14 7767 0.032 0.42 NO
23 MAPK13 MAPK13 MAPK13 7964 0.029 0.41 NO
24 APAF1 APAF1 APAF1 8260 0.025 0.4 NO
25 TP53 TP53 TP53 8348 0.024 0.4 NO
26 CASP9 CASP9 CASP9 8365 0.024 0.4 NO
27 MAPK11 MAPK11 MAPK11 9273 0.012 0.35 NO
28 DAXX DAXX DAXX 10330 0.00033 0.29 NO
29 CHP CHP CHP 10651 -0.0029 0.28 NO
30 BID BID BID 10983 -0.0061 0.26 NO
31 BCL2L1 BCL2L1 BCL2L1 11149 -0.0078 0.25 NO
32 CASP3 CASP3 CASP3 11537 -0.012 0.23 NO
33 MAP2K3 MAP2K3 MAP2K3 11646 -0.013 0.23 NO
34 PPP3R1 PPP3R1 PPP3R1 11767 -0.014 0.22 NO
35 RAC1 RAC1 RAC1 11885 -0.015 0.22 NO
36 CCS CCS CCS 11918 -0.016 0.22 NO
37 SLC1A2 SLC1A2 SLC1A2 11985 -0.016 0.22 NO
38 MAP2K6 MAP2K6 MAP2K6 12458 -0.021 0.2 NO
39 DERL1 DERL1 DERL1 12797 -0.025 0.18 NO
40 GPX1 GPX1 GPX1 12812 -0.025 0.18 NO
41 RAB5A RAB5A RAB5A 12835 -0.026 0.19 NO
42 GRIN1 GRIN1 GRIN1 13067 -0.028 0.18 NO
43 TOMM40L TOMM40L TOMM40L 13230 -0.03 0.17 NO
44 SOD1 SOD1 SOD1 14141 -0.04 0.13 NO
45 BAX BAX BAX 15244 -0.057 0.077 NO
46 BAD BAD BAD 15633 -0.064 0.065 NO
47 CYCS CYCS CYCS 15986 -0.072 0.056 NO
48 TOMM40 TOMM40 TOMM40 16020 -0.073 0.065 NO
49 PPP3CA PPP3CA PPP3CA 16237 -0.079 0.064 NO
50 MAPK12 MAPK12 MAPK12 17086 -0.12 0.035 NO
51 PPP3R2 PPP3R2 PPP3R2 17801 -0.2 0.025 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 FCER1 PATHWAY.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA FMLP PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PAK7 PAK7 PAK7 4 0.93 0.092 YES
2 NRG2 NRG2 NRG2 5 0.92 0.18 YES
3 NRG1 NRG1 NRG1 18 0.86 0.27 YES
4 PAK3 PAK3 PAK3 398 0.5 0.3 YES
5 PRKCB PRKCB PRKCB 798 0.4 0.31 YES
6 PIK3CD PIK3CD PIK3CD 1291 0.32 0.32 YES
7 TGFA TGFA TGFA 1339 0.32 0.35 YES
8 AREG AREG AREG 1582 0.29 0.36 YES
9 PIK3CG PIK3CG PIK3CG 1880 0.26 0.37 YES
10 EREG EREG EREG 1938 0.26 0.4 YES
11 ERBB4 ERBB4 ERBB4 1993 0.26 0.42 YES
12 SHC3 SHC3 SHC3 2004 0.26 0.44 YES
13 PLCG2 PLCG2 PLCG2 2063 0.25 0.46 YES
14 NRG4 NRG4 NRG4 2260 0.24 0.48 YES
15 PAK6 PAK6 PAK6 2300 0.23 0.5 YES
16 EGFR EGFR EGFR 2751 0.2 0.49 YES
17 PRKCA PRKCA PRKCA 2960 0.19 0.5 YES
18 HBEGF HBEGF HBEGF 3103 0.18 0.51 YES
19 NRG3 NRG3 NRG3 3254 0.18 0.52 YES
20 PIK3R1 PIK3R1 PIK3R1 3640 0.16 0.51 YES
21 STAT5A STAT5A STAT5A 3885 0.14 0.51 YES
22 CAMK2A CAMK2A CAMK2A 3918 0.14 0.53 YES
23 PAK1 PAK1 PAK1 4017 0.14 0.54 YES
24 BTC BTC BTC 4506 0.12 0.52 NO
25 CAMK2G CAMK2G CAMK2G 4507 0.12 0.53 NO
26 PIK3R5 PIK3R5 PIK3R5 4684 0.11 0.53 NO
27 CDKN1A CDKN1A CDKN1A 5086 0.094 0.52 NO
28 STAT5B STAT5B STAT5B 5324 0.086 0.51 NO
29 JUN JUN JUN 5675 0.076 0.5 NO
30 GAB1 GAB1 GAB1 6086 0.065 0.49 NO
31 PIK3CA PIK3CA PIK3CA 6344 0.059 0.48 NO
32 SHC4 SHC4 SHC4 6407 0.057 0.48 NO
33 CBL CBL CBL 6489 0.055 0.48 NO
34 SOS1 SOS1 SOS1 6586 0.053 0.48 NO
35 SOS2 SOS2 SOS2 6925 0.046 0.47 NO
36 CRKL CRKL CRKL 7381 0.038 0.45 NO
37 PRKCG PRKCG PRKCG 7414 0.038 0.45 NO
38 ARAF ARAF ARAF 7500 0.036 0.45 NO
39 SRC SRC SRC 7509 0.036 0.45 NO
40 MAPK3 MAPK3 MAPK3 7510 0.036 0.45 NO
41 CRK CRK CRK 7526 0.036 0.46 NO
42 ERBB2 ERBB2 ERBB2 7598 0.035 0.46 NO
43 CDKN1B CDKN1B CDKN1B 7620 0.034 0.46 NO
44 MAPK10 MAPK10 MAPK10 7764 0.032 0.45 NO
45 CAMK2D CAMK2D CAMK2D 7978 0.029 0.44 NO
46 MAPK8 MAPK8 MAPK8 8275 0.025 0.43 NO
47 SHC1 SHC1 SHC1 8477 0.022 0.42 NO
48 EGF EGF EGF 8570 0.021 0.42 NO
49 AKT3 AKT3 AKT3 8806 0.018 0.41 NO
50 MAPK1 MAPK1 MAPK1 9197 0.013 0.39 NO
51 MAP2K4 MAP2K4 MAP2K4 9215 0.013 0.39 NO
52 NCK1 NCK1 NCK1 9353 0.012 0.38 NO
53 ABL1 ABL1 ABL1 9540 0.0094 0.37 NO
54 NCK2 NCK2 NCK2 9682 0.0076 0.36 NO
55 PLCG1 PLCG1 PLCG1 9689 0.0076 0.37 NO
56 MAP2K7 MAP2K7 MAP2K7 9779 0.0066 0.36 NO
57 GRB2 GRB2 GRB2 10644 -0.0028 0.31 NO
58 MTOR MTOR MTOR 10821 -0.0046 0.3 NO
59 NRAS NRAS NRAS 11024 -0.0065 0.3 NO
60 RAF1 RAF1 RAF1 11040 -0.0066 0.29 NO
61 ABL2 ABL2 ABL2 11076 -0.007 0.29 NO
62 AKT2 AKT2 AKT2 11216 -0.0087 0.29 NO
63 KRAS KRAS KRAS 11547 -0.012 0.27 NO
64 PAK2 PAK2 PAK2 11588 -0.012 0.27 NO
65 ERBB3 ERBB3 ERBB3 12012 -0.016 0.25 NO
66 PTK2 PTK2 PTK2 12295 -0.02 0.23 NO
67 SHC2 SHC2 SHC2 12319 -0.02 0.23 NO
68 CBLB CBLB CBLB 12509 -0.022 0.23 NO
69 AKT1 AKT1 AKT1 12627 -0.023 0.22 NO
70 RPS6KB1 RPS6KB1 RPS6KB1 13084 -0.028 0.2 NO
71 RPS6KB2 RPS6KB2 RPS6KB2 13116 -0.029 0.2 NO
72 MAP2K2 MAP2K2 MAP2K2 13165 -0.029 0.2 NO
73 CBLC CBLC CBLC 13337 -0.031 0.19 NO
74 PAK4 PAK4 PAK4 13475 -0.032 0.19 NO
75 PIK3R2 PIK3R2 PIK3R2 13482 -0.032 0.19 NO
76 ELK1 ELK1 ELK1 13526 -0.033 0.19 NO
77 GSK3B GSK3B GSK3B 13902 -0.037 0.18 NO
78 PIK3R3 PIK3R3 PIK3R3 14025 -0.039 0.17 NO
79 PIK3CB PIK3CB PIK3CB 14073 -0.039 0.18 NO
80 MAP2K1 MAP2K1 MAP2K1 14380 -0.043 0.16 NO
81 MAPK9 MAPK9 MAPK9 14539 -0.045 0.16 NO
82 MYC MYC MYC 15261 -0.057 0.12 NO
83 BAD BAD BAD 15633 -0.064 0.11 NO
84 BRAF BRAF BRAF 16009 -0.073 0.097 NO
85 EIF4EBP1 EIF4EBP1 EIF4EBP1 16737 -0.1 0.066 NO
86 CAMK2B CAMK2B CAMK2B 17615 -0.17 0.035 NO

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PAK7 PAK7 PAK7 4 0.93 0.14 YES
2 PAK3 PAK3 PAK3 398 0.5 0.19 YES
3 MET MET MET 692 0.42 0.24 YES
4 PIK3CD PIK3CD PIK3CD 1291 0.32 0.26 YES
5 TGFA TGFA TGFA 1339 0.32 0.3 YES
6 TGFB3 TGFB3 TGFB3 1575 0.3 0.33 YES
7 PIK3CG PIK3CG PIK3CG 1880 0.26 0.36 YES
8 PAK6 PAK6 PAK6 2300 0.23 0.37 YES
9 HGF HGF HGF 2713 0.2 0.38 YES
10 EGLN3 EGLN3 EGLN3 2906 0.19 0.4 YES
11 PGF PGF PGF 3053 0.18 0.41 YES
12 VEGFA VEGFA VEGFA 3410 0.17 0.42 YES
13 EPAS1 EPAS1 EPAS1 3539 0.16 0.44 YES
14 PIK3R1 PIK3R1 PIK3R1 3640 0.16 0.46 YES
15 TGFB2 TGFB2 TGFB2 3888 0.14 0.46 YES
16 PAK1 PAK1 PAK1 4017 0.14 0.48 YES
17 ETS1 ETS1 ETS1 4079 0.14 0.49 YES
18 PIK3R5 PIK3R5 PIK3R5 4684 0.11 0.48 NO
19 TGFB1 TGFB1 TGFB1 4802 0.1 0.49 NO
20 JUN JUN JUN 5675 0.076 0.45 NO
21 VEGFC VEGFC VEGFC 5755 0.074 0.46 NO
22 GAB1 GAB1 GAB1 6086 0.065 0.45 NO
23 PIK3CA PIK3CA PIK3CA 6344 0.059 0.44 NO
24 SOS1 SOS1 SOS1 6586 0.053 0.44 NO
25 SOS2 SOS2 SOS2 6925 0.046 0.43 NO
26 CREBBP CREBBP CREBBP 6985 0.045 0.43 NO
27 RAPGEF1 RAPGEF1 RAPGEF1 7004 0.045 0.44 NO
28 CRKL CRKL CRKL 7381 0.038 0.42 NO
29 ARAF ARAF ARAF 7500 0.036 0.42 NO
30 MAPK3 MAPK3 MAPK3 7510 0.036 0.42 NO
31 CRK CRK CRK 7526 0.036 0.43 NO
32 ARNT2 ARNT2 ARNT2 7527 0.036 0.43 NO
33 EGLN2 EGLN2 EGLN2 7531 0.036 0.44 NO
34 RAP1B RAP1B RAP1B 7621 0.034 0.44 NO
35 RAP1A RAP1A RAP1A 7914 0.03 0.43 NO
36 EP300 EP300 EP300 8075 0.028 0.42 NO
37 SLC2A1 SLC2A1 SLC2A1 8291 0.025 0.42 NO
38 ARNT ARNT ARNT 8341 0.024 0.42 NO
39 PTPN11 PTPN11 PTPN11 8456 0.022 0.41 NO
40 AKT3 AKT3 AKT3 8806 0.018 0.4 NO
41 FLCN FLCN FLCN 8836 0.018 0.4 NO
42 FIGF FIGF FIGF 8862 0.017 0.4 NO
43 MAPK1 MAPK1 MAPK1 9197 0.013 0.38 NO
44 HIF1A HIF1A HIF1A 9218 0.013 0.38 NO
45 CUL2 CUL2 CUL2 10003 0.004 0.34 NO
46 PDGFB PDGFB PDGFB 10199 0.0018 0.33 NO
47 CDC42 CDC42 CDC42 10545 -0.0019 0.31 NO
48 GRB2 GRB2 GRB2 10644 -0.0028 0.31 NO
49 NRAS NRAS NRAS 11024 -0.0065 0.29 NO
50 RAF1 RAF1 RAF1 11040 -0.0066 0.29 NO
51 AKT2 AKT2 AKT2 11216 -0.0087 0.28 NO
52 VEGFB VEGFB VEGFB 11544 -0.012 0.26 NO
53 KRAS KRAS KRAS 11547 -0.012 0.26 NO
54 PAK2 PAK2 PAK2 11588 -0.012 0.26 NO
55 VHL VHL VHL 11749 -0.014 0.26 NO
56 RAC1 RAC1 RAC1 11885 -0.015 0.25 NO
57 EGLN1 EGLN1 EGLN1 12623 -0.023 0.22 NO
58 AKT1 AKT1 AKT1 12627 -0.023 0.22 NO
59 MAP2K2 MAP2K2 MAP2K2 13165 -0.029 0.19 NO
60 PAK4 PAK4 PAK4 13475 -0.032 0.18 NO
61 PIK3R2 PIK3R2 PIK3R2 13482 -0.032 0.19 NO
62 PIK3R3 PIK3R3 PIK3R3 14025 -0.039 0.16 NO
63 PIK3CB PIK3CB PIK3CB 14073 -0.039 0.16 NO
64 MAP2K1 MAP2K1 MAP2K1 14380 -0.043 0.16 NO
65 RBX1 RBX1 RBX1 14952 -0.051 0.13 NO
66 TCEB2 TCEB2 TCEB2 15829 -0.069 0.093 NO
67 FH FH FH 15907 -0.07 0.1 NO
68 BRAF BRAF BRAF 16009 -0.073 0.1 NO
69 TCEB1 TCEB1 TCEB1 17126 -0.12 0.062 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: BIOCARTA GH PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GH 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 HIVNEF PATHWAY

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 CALML3 CALML3 CALML3 79 0.71 0.056 YES
2 PPARGC1A PPARGC1A PPARGC1A 181 0.61 0.1 YES
3 SLC2A4 SLC2A4 SLC2A4 403 0.5 0.13 YES
4 PYGM PYGM PYGM 611 0.44 0.16 YES
5 LIPE LIPE LIPE 641 0.43 0.2 YES
6 PPP1R3C PPP1R3C PPP1R3C 1159 0.34 0.2 YES
7 GCK GCK GCK 1172 0.34 0.22 YES
8 INPP5D INPP5D INPP5D 1198 0.34 0.25 YES
9 PIK3CD PIK3CD PIK3CD 1291 0.32 0.27 YES
10 PHKG1 PHKG1 PHKG1 1559 0.3 0.28 YES
11 ACACB ACACB ACACB 1604 0.29 0.31 YES
12 PCK1 PCK1 PCK1 1698 0.28 0.33 YES
13 SORBS1 SORBS1 SORBS1 1823 0.27 0.34 YES
14 PIK3CG PIK3CG PIK3CG 1880 0.26 0.36 YES
15 SHC3 SHC3 SHC3 2004 0.26 0.38 YES
16 SOCS3 SOCS3 SOCS3 2034 0.25 0.4 YES
17 IRS1 IRS1 IRS1 2052 0.25 0.42 YES
18 SOCS1 SOCS1 SOCS1 2210 0.24 0.43 YES
19 GYS2 GYS2 GYS2 2628 0.21 0.42 NO
20 PYGL PYGL PYGL 2843 0.2 0.43 NO
21 FOXO1 FOXO1 FOXO1 3197 0.18 0.42 NO
22 IRS4 IRS4 IRS4 3532 0.16 0.42 NO
23 PIK3R1 PIK3R1 PIK3R1 3640 0.16 0.43 NO
24 TRIP10 TRIP10 TRIP10 3854 0.14 0.43 NO
25 PDE3A PDE3A PDE3A 4081 0.14 0.43 NO
26 PIK3R5 PIK3R5 PIK3R5 4684 0.11 0.4 NO
27 PPP1R3B PPP1R3B PPP1R3B 5006 0.097 0.39 NO
28 PRKAR2A PRKAR2A PRKAR2A 5263 0.088 0.39 NO
29 CALM1 CALM1 CALM1 5943 0.069 0.36 NO
30 HK1 HK1 HK1 6085 0.065 0.35 NO
31 PRKAR1B PRKAR1B PRKAR1B 6088 0.065 0.36 NO
32 G6PC2 G6PC2 G6PC2 6273 0.06 0.35 NO
33 RPTOR RPTOR RPTOR 6331 0.059 0.36 NO
34 PIK3CA PIK3CA PIK3CA 6344 0.059 0.36 NO
35 SHC4 SHC4 SHC4 6407 0.057 0.36 NO
36 PYGB PYGB PYGB 6420 0.057 0.37 NO
37 MKNK1 MKNK1 MKNK1 6429 0.057 0.37 NO
38 CALML6 CALML6 CALML6 6430 0.057 0.38 NO
39 CBL CBL CBL 6489 0.055 0.38 NO
40 SOS1 SOS1 SOS1 6586 0.053 0.38 NO
41 SOS2 SOS2 SOS2 6925 0.046 0.36 NO
42 INSR INSR INSR 6978 0.045 0.36 NO
43 RAPGEF1 RAPGEF1 RAPGEF1 7004 0.045 0.36 NO
44 SOCS2 SOCS2 SOCS2 7297 0.04 0.35 NO
45 CRKL CRKL CRKL 7381 0.038 0.35 NO
46 ARAF ARAF ARAF 7500 0.036 0.35 NO
47 MAPK3 MAPK3 MAPK3 7510 0.036 0.35 NO
48 CRK CRK CRK 7526 0.036 0.35 NO
49 FLOT2 FLOT2 FLOT2 7582 0.035 0.35 NO
50 PRKAR1A PRKAR1A PRKAR1A 7622 0.034 0.35 NO
51 RHOQ RHOQ RHOQ 7650 0.034 0.35 NO
52 PPP1R3D PPP1R3D PPP1R3D 7722 0.033 0.35 NO
53 IKBKB IKBKB IKBKB 7763 0.032 0.35 NO
54 MAPK10 MAPK10 MAPK10 7764 0.032 0.36 NO
55 PRKAA2 PRKAA2 PRKAA2 8134 0.027 0.34 NO
56 PRKAB1 PRKAB1 PRKAB1 8175 0.026 0.34 NO
57 IRS2 IRS2 IRS2 8181 0.026 0.34 NO
58 CALML5 CALML5 CALML5 8266 0.025 0.34 NO
59 MAPK8 MAPK8 MAPK8 8275 0.025 0.34 NO
60 SHC1 SHC1 SHC1 8477 0.022 0.33 NO
61 HK3 HK3 HK3 8656 0.02 0.32 NO
62 PTPRF PTPRF PTPRF 8715 0.019 0.32 NO
63 PTPN1 PTPN1 PTPN1 8739 0.019 0.32 NO
64 PRKX PRKX PRKX 8754 0.019 0.32 NO
65 AKT3 AKT3 AKT3 8806 0.018 0.32 NO
66 PRKAB2 PRKAB2 PRKAB2 9073 0.015 0.31 NO
67 MAPK1 MAPK1 MAPK1 9197 0.013 0.3 NO
68 INPP5K INPP5K INPP5K 9255 0.013 0.3 NO
69 PRKAG3 PRKAG3 PRKAG3 9670 0.0078 0.28 NO
70 TSC1 TSC1 TSC1 9729 0.0072 0.27 NO
71 PRKACA PRKACA PRKACA 9770 0.0066 0.27 NO
72 PRKAR2B PRKAR2B PRKAR2B 9800 0.0064 0.27 NO
73 PHKA2 PHKA2 PHKA2 10065 0.0033 0.26 NO
74 SOCS4 SOCS4 SOCS4 10163 0.0022 0.25 NO
75 TSC2 TSC2 TSC2 10456 -0.001 0.24 NO
76 PRKCI PRKCI PRKCI 10528 -0.0018 0.23 NO
77 GRB2 GRB2 GRB2 10644 -0.0028 0.23 NO
78 PDPK1 PDPK1 PDPK1 10728 -0.0037 0.22 NO
79 MTOR MTOR MTOR 10821 -0.0046 0.22 NO
80 HK2 HK2 HK2 10943 -0.0057 0.21 NO
81 CALM3 CALM3 CALM3 11009 -0.0063 0.21 NO
82 NRAS NRAS NRAS 11024 -0.0065 0.21 NO
83 RAF1 RAF1 RAF1 11040 -0.0066 0.21 NO
84 FLOT1 FLOT1 FLOT1 11046 -0.0066 0.21 NO
85 AKT2 AKT2 AKT2 11216 -0.0087 0.2 NO
86 PCK2 PCK2 PCK2 11247 -0.009 0.2 NO
87 GYS1 GYS1 GYS1 11288 -0.0095 0.2 NO
88 PRKCZ PRKCZ PRKCZ 11295 -0.0096 0.2 NO
89 EXOC7 EXOC7 EXOC7 11317 -0.0097 0.2 NO
90 KRAS KRAS KRAS 11547 -0.012 0.18 NO
91 PHKG2 PHKG2 PHKG2 11617 -0.013 0.18 NO
92 PPP1CB PPP1CB PPP1CB 11619 -0.013 0.18 NO
93 MKNK2 MKNK2 MKNK2 11664 -0.013 0.18 NO
94 PRKAG2 PRKAG2 PRKAG2 11798 -0.014 0.18 NO
95 RHEB RHEB RHEB 11980 -0.016 0.17 NO
96 SHC2 SHC2 SHC2 12319 -0.02 0.15 NO
97 CALM2 CALM2 CALM2 12360 -0.02 0.15 NO
98 CBLB CBLB CBLB 12509 -0.022 0.14 NO
99 AKT1 AKT1 AKT1 12627 -0.023 0.14 NO
100 PRKAA1 PRKAA1 PRKAA1 12703 -0.024 0.14 NO
101 EIF4E2 EIF4E2 EIF4E2 12791 -0.025 0.14 NO
102 PPP1CC PPP1CC PPP1CC 12882 -0.026 0.13 NO
103 RPS6KB1 RPS6KB1 RPS6KB1 13084 -0.028 0.12 NO
104 PRKACB PRKACB PRKACB 13109 -0.029 0.12 NO
105 RPS6KB2 RPS6KB2 RPS6KB2 13116 -0.029 0.13 NO
106 MAP2K2 MAP2K2 MAP2K2 13165 -0.029 0.13 NO
107 CBLC CBLC CBLC 13337 -0.031 0.12 NO
108 PHKA1 PHKA1 PHKA1 13343 -0.031 0.12 NO
109 PIK3R2 PIK3R2 PIK3R2 13482 -0.032 0.12 NO
110 ELK1 ELK1 ELK1 13526 -0.033 0.12 NO
111 EIF4E EIF4E EIF4E 13570 -0.034 0.12 NO
112 G6PC G6PC G6PC 13655 -0.034 0.12 NO
113 PPP1CA PPP1CA PPP1CA 13690 -0.035 0.12 NO
114 PRKAG1 PRKAG1 PRKAG1 13708 -0.035 0.12 NO
115 PHKB PHKB PHKB 13730 -0.035 0.12 NO
116 RPS6 RPS6 RPS6 13809 -0.036 0.12 NO
117 GSK3B GSK3B GSK3B 13902 -0.037 0.12 NO
118 PIK3R3 PIK3R3 PIK3R3 14025 -0.039 0.12 NO
119 PIK3CB PIK3CB PIK3CB 14073 -0.039 0.12 NO
120 MAP2K1 MAP2K1 MAP2K1 14380 -0.043 0.1 NO
121 MAPK9 MAPK9 MAPK9 14539 -0.045 0.098 NO
122 FBP1 FBP1 FBP1 15078 -0.054 0.073 NO
123 BAD BAD BAD 15633 -0.064 0.048 NO
124 SREBF1 SREBF1 SREBF1 15879 -0.07 0.04 NO
125 BRAF BRAF BRAF 16009 -0.073 0.039 NO
126 PDE3B PDE3B PDE3B 16624 -0.095 0.013 NO
127 EIF4EBP1 EIF4EBP1 EIF4EBP1 16737 -0.1 0.016 NO
128 ACACA ACACA ACACA 16774 -0.1 0.022 NO
129 FASN FASN FASN 16910 -0.11 0.024 NO
130 SH2B2 SH2B2 SH2B2 17407 -0.15 0.0094 NO
131 PKLR PKLR PKLR 17784 -0.2 0.0055 NO
132 FBP2 FBP2 FBP2 17972 -0.24 0.016 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: BIOCARTA HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

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 SCNN1B SCNN1B SCNN1B 194 0.6 0.076 YES
2 SCNN1G SCNN1G SCNN1G 214 0.59 0.16 YES
3 ATP1A2 ATP1A2 ATP1A2 628 0.44 0.2 YES
4 ATP1A4 ATP1A4 ATP1A4 629 0.44 0.26 YES
5 KCNJ1 KCNJ1 KCNJ1 761 0.4 0.31 YES
6 PRKCB PRKCB PRKCB 798 0.4 0.37 YES
7 SCNN1A SCNN1A SCNN1A 1021 0.36 0.41 YES
8 ATP1B2 ATP1B2 ATP1B2 1232 0.33 0.44 YES
9 PIK3CD PIK3CD PIK3CD 1291 0.32 0.49 YES
10 SGK1 SGK1 SGK1 1630 0.29 0.51 YES
11 PIK3CG PIK3CG PIK3CG 1880 0.26 0.53 YES
12 IRS1 IRS1 IRS1 2052 0.25 0.56 YES
13 HSD11B1 HSD11B1 HSD11B1 2393 0.22 0.57 YES
14 SFN SFN SFN 2619 0.21 0.59 YES
15 HSD11B2 HSD11B2 HSD11B2 2787 0.2 0.61 YES
16 PRKCA PRKCA PRKCA 2960 0.19 0.63 YES
17 ATP1B1 ATP1B1 ATP1B1 3015 0.19 0.65 YES
18 IRS4 IRS4 IRS4 3532 0.16 0.65 YES
19 PIK3R1 PIK3R1 PIK3R1 3640 0.16 0.66 YES
20 NR3C2 NR3C2 NR3C2 4050 0.14 0.66 NO
21 PIK3R5 PIK3R5 PIK3R5 4684 0.11 0.64 NO
22 IGF1 IGF1 IGF1 5515 0.081 0.61 NO
23 PIK3CA PIK3CA PIK3CA 6344 0.059 0.57 NO
24 INSR INSR INSR 6978 0.045 0.54 NO
25 ATP1A1 ATP1A1 ATP1A1 7293 0.04 0.53 NO
26 PRKCG PRKCG PRKCG 7414 0.038 0.53 NO
27 MAPK3 MAPK3 MAPK3 7510 0.036 0.53 NO
28 IRS2 IRS2 IRS2 8181 0.026 0.5 NO
29 MAPK1 MAPK1 MAPK1 9197 0.013 0.44 NO
30 ATP1A3 ATP1A3 ATP1A3 9840 0.006 0.41 NO
31 ATP1B3 ATP1B3 ATP1B3 9957 0.0047 0.4 NO
32 PDPK1 PDPK1 PDPK1 10728 -0.0037 0.36 NO
33 KRAS KRAS KRAS 11547 -0.012 0.32 NO
34 PIK3R2 PIK3R2 PIK3R2 13482 -0.032 0.22 NO
35 PIK3R3 PIK3R3 PIK3R3 14025 -0.039 0.19 NO
36 PIK3CB PIK3CB PIK3CB 14073 -0.039 0.2 NO
37 FXYD4 FXYD4 FXYD4 14127 -0.04 0.2 NO
38 SLC9A3R2 SLC9A3R2 SLC9A3R2 14716 -0.048 0.17 NO
39 NEDD4L NEDD4L NEDD4L 15794 -0.068 0.12 NO
40 ATP1B4 ATP1B4 ATP1B4 16396 -0.085 0.1 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: BIOCARTA IL2RB PATHWAY.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB 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 clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG GLYCOLYSIS GLUCONEOGENESIS 58 genes.ES.table 0.37 1.1 0.27 1 1 0.31 0.17 0.26 0.93 0.45
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.46 1.5 0.051 0.76 0.9 0.36 0.19 0.3 0.57 0.25
KEGG FATTY ACID METABOLISM 39 genes.ES.table 0.55 1.7 0.018 0.25 0.5 0.56 0.21 0.45 0.11 0.054
KEGG OXIDATIVE PHOSPHORYLATION 114 genes.ES.table 0.45 1.4 0.17 0.7 0.96 0.68 0.28 0.49 0.56 0.22
KEGG PYRIMIDINE METABOLISM 97 genes.ES.table 0.4 1.7 0.018 0.32 0.46 0.28 0.17 0.23 0 0.09
KEGG GLYCINE SERINE AND THREONINE METABOLISM 28 genes.ES.table 0.5 1.4 0.09 0.76 0.97 0.43 0.15 0.36 0.61 0.25
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.57 1.9 0.016 0.15 0.14 0.58 0.26 0.43 0 0.052
KEGG TYROSINE METABOLISM 39 genes.ES.table 0.42 1.1 0.34 0.89 1 0.56 0.22 0.44 0.8 0.33
KEGG GLUTATHIONE METABOLISM 47 genes.ES.table 0.39 1.1 0.35 0.9 1 0.38 0.18 0.31 0.8 0.33
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 42 genes.ES.table 0.32 1.1 0.32 1 1 0.31 0.17 0.26 0.89 0.41
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 EHHADH EHHADH EHHADH 170 0.32 0.11 YES
2 ACAD8 ACAD8 ACAD8 491 0.22 0.18 YES
3 MCCC2 MCCC2 MCCC2 1083 0.15 0.2 YES
4 ALDH2 ALDH2 ALDH2 1143 0.14 0.25 YES
5 AUH AUH AUH 1441 0.12 0.28 YES
6 ABAT ABAT ABAT 1495 0.12 0.32 YES
7 ECHS1 ECHS1 ECHS1 1930 0.1 0.34 YES
8 ACAA1 ACAA1 ACAA1 2281 0.088 0.35 YES
9 BCAT2 BCAT2 BCAT2 2478 0.082 0.37 YES
10 ALDH7A1 ALDH7A1 ALDH7A1 2629 0.078 0.39 YES
11 ACAT2 ACAT2 ACAT2 3179 0.064 0.38 YES
12 HSD17B10 HSD17B10 HSD17B10 3226 0.063 0.41 YES
13 ALDH6A1 ALDH6A1 ALDH6A1 3259 0.062 0.43 YES
14 MCEE MCEE MCEE 3373 0.06 0.44 YES
15 OXCT1 OXCT1 OXCT1 3573 0.056 0.45 YES
16 MCCC1 MCCC1 MCCC1 3598 0.055 0.47 YES
17 ACAA2 ACAA2 ACAA2 3733 0.053 0.49 YES
18 ALDH3A2 ALDH3A2 ALDH3A2 3771 0.052 0.5 YES
19 ACADSB ACADSB ACADSB 3819 0.051 0.52 YES
20 HMGCL HMGCL HMGCL 3864 0.05 0.54 YES
21 PCCB PCCB PCCB 3962 0.048 0.55 YES
22 DBT DBT DBT 4077 0.046 0.56 YES
23 HADH HADH HADH 4214 0.044 0.57 YES
24 HIBADH HIBADH HIBADH 4541 0.039 0.57 YES
25 PCCA PCCA PCCA 4655 0.037 0.57 YES
26 ACADS ACADS ACADS 6175 0.018 0.5 NO
27 ACAT1 ACAT1 ACAT1 6431 0.015 0.49 NO
28 HIBCH HIBCH HIBCH 6477 0.014 0.49 NO
29 IL4I1 IL4I1 IL4I1 6657 0.012 0.49 NO
30 DLD DLD DLD 6677 0.012 0.49 NO
31 IVD IVD IVD 6855 0.01 0.48 NO
32 ALDH1B1 ALDH1B1 ALDH1B1 7281 0.0055 0.46 NO
33 BCKDHA BCKDHA BCKDHA 7417 0.0036 0.46 NO
34 MUT MUT MUT 7582 0.0021 0.45 NO
35 HMGCS1 HMGCS1 HMGCS1 8183 -0.0047 0.42 NO
36 HADHA HADHA HADHA 8203 -0.0049 0.42 NO
37 HADHB HADHB HADHB 8593 -0.0089 0.4 NO
38 ACADM ACADM ACADM 8743 -0.01 0.4 NO
39 HMGCS2 HMGCS2 HMGCS2 9190 -0.015 0.38 NO
40 BCKDHB BCKDHB BCKDHB 10550 -0.03 0.31 NO
41 ALDH9A1 ALDH9A1 ALDH9A1 10754 -0.033 0.31 NO
42 OXCT2 OXCT2 OXCT2 13542 -0.072 0.19 NO
43 AOX1 AOX1 AOX1 16679 -0.19 0.087 NO

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

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRIM2 PRIM2 PRIM2 191 0.32 0.041 YES
2 NME5 NME5 NME5 497 0.22 0.06 YES
3 NT5M NT5M NT5M 532 0.22 0.093 YES
4 NT5C NT5C NT5C 534 0.21 0.13 YES
5 NT5C1A NT5C1A NT5C1A 556 0.21 0.16 YES
6 UPP2 UPP2 UPP2 586 0.21 0.19 YES
7 UPB1 UPB1 UPB1 656 0.2 0.22 YES
8 POLE2 POLE2 POLE2 802 0.18 0.24 YES
9 POLD4 POLD4 POLD4 1062 0.15 0.25 YES
10 TK1 TK1 TK1 1274 0.13 0.26 YES
11 NT5C3 NT5C3 NT5C3 1329 0.13 0.28 YES
12 ENTPD8 ENTPD8 ENTPD8 1885 0.1 0.26 YES
13 POLE4 POLE4 POLE4 1962 0.099 0.28 YES
14 RRM2 RRM2 RRM2 1963 0.099 0.29 YES
15 POLR2J POLR2J POLR2J 2126 0.093 0.3 YES
16 TXNRD2 TXNRD2 TXNRD2 2216 0.09 0.31 YES
17 DTYMK DTYMK DTYMK 2244 0.089 0.32 YES
18 CDA CDA CDA 2369 0.085 0.33 YES
19 NME1 NME1 NME1 2560 0.079 0.33 YES
20 POLR3K POLR3K POLR3K 2610 0.078 0.34 YES
21 POLR2F POLR2F POLR2F 2822 0.073 0.34 YES
22 ITPA ITPA ITPA 2832 0.072 0.35 YES
23 POLR2I POLR2I POLR2I 2863 0.072 0.36 YES
24 POLR2L POLR2L POLR2L 2892 0.071 0.37 YES
25 DPYS DPYS DPYS 3006 0.068 0.38 YES
26 PNP PNP PNP 3037 0.068 0.39 YES
27 POLR2K POLR2K POLR2K 3079 0.066 0.4 YES
28 POLD2 POLD2 POLD2 3637 0.055 0.37 NO
29 DHODH DHODH DHODH 3845 0.051 0.37 NO
30 POLR2G POLR2G POLR2G 3951 0.049 0.37 NO
31 ENTPD6 ENTPD6 ENTPD6 4084 0.046 0.37 NO
32 POLR2H POLR2H POLR2H 4115 0.046 0.38 NO
33 NME1-NME2 NME1-NME2 NME1-NME2 4151 0.045 0.38 NO
34 POLR1E POLR1E POLR1E 4322 0.042 0.38 NO
35 NME2 NME2 NME2 4440 0.04 0.38 NO
36 POLR1C POLR1C POLR1C 4608 0.038 0.38 NO
37 POLR3H POLR3H POLR3H 5072 0.032 0.36 NO
38 POLR2E POLR2E POLR2E 5077 0.032 0.36 NO
39 NUDT2 NUDT2 NUDT2 5087 0.032 0.37 NO
40 NT5C2 NT5C2 NT5C2 5125 0.031 0.37 NO
41 PNPT1 PNPT1 PNPT1 5290 0.029 0.37 NO
42 UCK1 UCK1 UCK1 5307 0.028 0.37 NO
43 NME3 NME3 NME3 5474 0.026 0.36 NO
44 UPP1 UPP1 UPP1 5668 0.024 0.36 NO
45 POLR1D POLR1D POLR1D 5812 0.022 0.35 NO
46 POLR3D POLR3D POLR3D 5866 0.021 0.35 NO
47 ENTPD1 ENTPD1 ENTPD1 6176 0.018 0.34 NO
48 RRM2B RRM2B RRM2B 6681 0.012 0.31 NO
49 NME6 NME6 NME6 6711 0.012 0.32 NO
50 CANT1 CANT1 CANT1 6802 0.011 0.31 NO
51 CMPK2 CMPK2 CMPK2 6844 0.01 0.31 NO
52 CTPS2 CTPS2 CTPS2 6949 0.009 0.31 NO
53 ZNRD1 ZNRD1 ZNRD1 7066 0.0077 0.3 NO
54 UMPS UMPS UMPS 7319 0.0049 0.29 NO
55 POLR2J3 POLR2J3 POLR2J3 7656 0.0012 0.27 NO
56 DCK DCK DCK 7782 -0.00038 0.26 NO
57 NME4 NME4 NME4 7834 -0.00093 0.26 NO
58 DCTD DCTD DCTD 7935 -0.0022 0.26 NO
59 POLR3C POLR3C POLR3C 7941 -0.0022 0.26 NO
60 POLR3B POLR3B POLR3B 8072 -0.0036 0.25 NO
61 RRM1 RRM1 RRM1 8201 -0.0049 0.24 NO
62 CMPK1 CMPK1 CMPK1 8391 -0.0068 0.23 NO
63 UCK2 UCK2 UCK2 8567 -0.0087 0.22 NO
64 POLR2J2 POLR2J2 POLR2J2 8683 -0.0099 0.22 NO
65 TK2 TK2 TK2 8758 -0.011 0.22 NO
66 NME7 NME7 NME7 9009 -0.013 0.21 NO
67 UPRT UPRT UPRT 9034 -0.013 0.21 NO
68 POLA2 POLA2 POLA2 9041 -0.013 0.21 NO
69 POLR3GL POLR3GL POLR3GL 9227 -0.015 0.2 NO
70 AK3 AK3 AK3 9296 -0.016 0.2 NO
71 POLE POLE POLE 9417 -0.018 0.2 NO
72 POLD1 POLD1 POLD1 9460 -0.018 0.2 NO
73 TYMS TYMS TYMS 9551 -0.019 0.2 NO
74 POLR3F POLR3F POLR3F 9829 -0.022 0.18 NO
75 TXNRD1 TXNRD1 TXNRD1 10232 -0.027 0.17 NO
76 POLR2C POLR2C POLR2C 10458 -0.029 0.16 NO
77 POLE3 POLE3 POLE3 10685 -0.032 0.15 NO
78 POLR2A POLR2A POLR2A 10821 -0.033 0.15 NO
79 DUT DUT DUT 10848 -0.034 0.15 NO
80 UCKL1 UCKL1 UCKL1 10851 -0.034 0.16 NO
81 ENTPD5 ENTPD5 ENTPD5 10998 -0.035 0.16 NO
82 POLR3A POLR3A POLR3A 11004 -0.036 0.16 NO
83 POLR1A POLR1A POLR1A 11124 -0.037 0.16 NO
84 POLD3 POLD3 POLD3 11380 -0.04 0.15 NO
85 POLR2B POLR2B POLR2B 11586 -0.043 0.15 NO
86 POLA1 POLA1 POLA1 11631 -0.043 0.15 NO
87 POLR2D POLR2D POLR2D 11790 -0.045 0.15 NO
88 POLR1B POLR1B POLR1B 11974 -0.048 0.15 NO
89 ENTPD4 ENTPD4 ENTPD4 12548 -0.056 0.13 NO
90 TYMP TYMP TYMP 13084 -0.064 0.11 NO
91 PRIM1 PRIM1 PRIM1 13725 -0.076 0.085 NO
92 CAD CAD CAD 14115 -0.084 0.078 NO
93 NT5E NT5E NT5E 15098 -0.11 0.042 NO
94 DPYD DPYD DPYD 15323 -0.12 0.049 NO
95 ENTPD3 ENTPD3 ENTPD3 15975 -0.15 0.037 NO
96 NT5C1B NT5C1B NT5C1B 16772 -0.2 0.025 NO
97 POLR3G POLR3G POLR3G 17870 -0.35 0.021 NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACADL ACADL ACADL 79 0.4 0.1 YES
2 EHHADH EHHADH EHHADH 170 0.32 0.19 YES
3 ADH1C ADH1C ADH1C 196 0.31 0.27 YES
4 ADH1B ADH1B ADH1B 658 0.2 0.3 YES
5 ADH1A ADH1A ADH1A 1026 0.15 0.32 YES
6 ALDH2 ALDH2 ALDH2 1143 0.14 0.36 YES
7 ADH6 ADH6 ADH6 1741 0.11 0.36 YES
8 ECHS1 ECHS1 ECHS1 1930 0.1 0.37 YES
9 ADH4 ADH4 ADH4 2199 0.09 0.38 YES
10 ACAA1 ACAA1 ACAA1 2281 0.088 0.4 YES
11 ACOX3 ACOX3 ACOX3 2318 0.087 0.42 YES
12 DCI DCI DCI 2321 0.087 0.45 YES
13 PECI PECI PECI 2364 0.085 0.47 YES
14 CPT1B CPT1B CPT1B 2365 0.085 0.49 YES
15 ALDH7A1 ALDH7A1 ALDH7A1 2629 0.078 0.5 YES
16 GCDH GCDH GCDH 2894 0.071 0.51 YES
17 ACSL6 ACSL6 ACSL6 3070 0.067 0.51 YES
18 ADH5 ADH5 ADH5 3133 0.066 0.53 YES
19 ACAT2 ACAT2 ACAT2 3179 0.064 0.54 YES
20 ACAA2 ACAA2 ACAA2 3733 0.053 0.53 YES
21 ALDH3A2 ALDH3A2 ALDH3A2 3771 0.052 0.54 YES
22 ACADSB ACADSB ACADSB 3819 0.051 0.55 YES
23 HADH HADH HADH 4214 0.044 0.54 NO
24 CPT2 CPT2 CPT2 4708 0.037 0.53 NO
25 ACADVL ACADVL ACADVL 5218 0.03 0.51 NO
26 ACSL1 ACSL1 ACSL1 5965 0.02 0.47 NO
27 ACADS ACADS ACADS 6175 0.018 0.46 NO
28 ACAT1 ACAT1 ACAT1 6431 0.015 0.45 NO
29 CYP4A11 CYP4A11 CYP4A11 6620 0.013 0.45 NO
30 ALDH1B1 ALDH1B1 ALDH1B1 7281 0.0055 0.41 NO
31 HADHA HADHA HADHA 8203 -0.0049 0.36 NO
32 HADHB HADHB HADHB 8593 -0.0089 0.34 NO
33 ACADM ACADM ACADM 8743 -0.01 0.34 NO
34 ALDH9A1 ALDH9A1 ALDH9A1 10754 -0.033 0.24 NO
35 ACSL3 ACSL3 ACSL3 12894 -0.061 0.14 NO
36 CPT1A CPT1A CPT1A 14404 -0.092 0.08 NO
37 ACSL4 ACSL4 ACSL4 14634 -0.098 0.095 NO
38 CPT1C CPT1C CPT1C 15579 -0.13 0.079 NO
39 ACSL5 ACSL5 ACSL5 17297 -0.25 0.053 NO

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

Figure S26.  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 OXIDATIVE PHOSPHORYLATION

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 PFKFB1 PFKFB1 PFKFB1 96 0.38 0.16 YES
2 GMDS GMDS GMDS 828 0.17 0.2 YES
3 PFKFB4 PFKFB4 PFKFB4 1048 0.15 0.25 YES
4 FBP2 FBP2 FBP2 1347 0.13 0.29 YES
5 AKR1B10 AKR1B10 AKR1B10 1363 0.13 0.34 YES
6 PMM1 PMM1 PMM1 1887 0.1 0.36 YES
7 KHK KHK KHK 2270 0.088 0.38 YES
8 HK3 HK3 HK3 2733 0.075 0.38 YES
9 HK2 HK2 HK2 2941 0.07 0.4 YES
10 PHPT1 PHPT1 PHPT1 3090 0.066 0.42 YES
11 GMPPA GMPPA GMPPA 3180 0.064 0.45 YES
12 SORD SORD SORD 3466 0.058 0.46 YES
13 MPI MPI MPI 4272 0.043 0.43 NO
14 PFKFB2 PFKFB2 PFKFB2 4583 0.038 0.43 NO
15 MTMR2 MTMR2 MTMR2 5022 0.032 0.42 NO
16 PMM2 PMM2 PMM2 5026 0.032 0.44 NO
17 TPI1 TPI1 TPI1 5295 0.029 0.43 NO
18 GMPPB GMPPB GMPPB 5818 0.022 0.42 NO
19 PFKL PFKL PFKL 6463 0.014 0.39 NO
20 FUK FUK FUK 6865 0.01 0.37 NO
21 MTMR7 MTMR7 MTMR7 7310 0.005 0.35 NO
22 MTMR6 MTMR6 MTMR6 7699 0.00071 0.33 NO
23 AKR1B1 AKR1B1 AKR1B1 7837 -0.00096 0.32 NO
24 HK1 HK1 HK1 9279 -0.016 0.25 NO
25 MTMR1 MTMR1 MTMR1 9683 -0.021 0.23 NO
26 ALDOC ALDOC ALDOC 9886 -0.023 0.23 NO
27 PFKP PFKP PFKP 10609 -0.031 0.21 NO
28 FPGT FPGT FPGT 10773 -0.033 0.21 NO
29 FBP1 FBP1 FBP1 11479 -0.041 0.19 NO
30 TSTA3 TSTA3 TSTA3 11713 -0.044 0.2 NO
31 ALDOB ALDOB ALDOB 14291 -0.089 0.095 NO
32 PFKM PFKM PFKM 15474 -0.13 0.085 NO
33 PFKFB3 PFKFB3 PFKFB3 16091 -0.15 0.12 NO

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

Figure S28.  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 PYRIMIDINE METABOLISM

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 ACSM1 ACSM1 ACSM1 901 0.16 0.044 YES
2 ALDH2 ALDH2 ALDH2 1143 0.14 0.11 YES
3 AKR1B10 AKR1B10 AKR1B10 1363 0.13 0.17 YES
4 ABAT ABAT ABAT 1495 0.12 0.23 YES
5 ACSM5 ACSM5 ACSM5 1613 0.11 0.29 YES
6 ECHS1 ECHS1 ECHS1 1930 0.1 0.33 YES
7 BDH1 BDH1 BDH1 2317 0.087 0.36 YES
8 ALDH7A1 ALDH7A1 ALDH7A1 2629 0.078 0.39 YES
9 ACAT2 ACAT2 ACAT2 3179 0.064 0.39 YES
10 OXCT1 OXCT1 OXCT1 3573 0.056 0.4 YES
11 ALDH3A2 ALDH3A2 ALDH3A2 3771 0.052 0.42 YES
12 HMGCL HMGCL HMGCL 3864 0.05 0.44 YES
13 HADH HADH HADH 4214 0.044 0.45 YES
14 BDH2 BDH2 BDH2 4217 0.044 0.48 YES
15 L2HGDH L2HGDH L2HGDH 5559 0.026 0.42 NO
16 AACS AACS AACS 5897 0.021 0.41 NO
17 ACADS ACADS ACADS 6175 0.018 0.4 NO
18 ACAT1 ACAT1 ACAT1 6431 0.015 0.4 NO
19 PDHB PDHB PDHB 6561 0.014 0.4 NO
20 ALDH1B1 ALDH1B1 ALDH1B1 7281 0.0055 0.36 NO
21 PDHA1 PDHA1 PDHA1 8178 -0.0046 0.32 NO
22 HMGCS1 HMGCS1 HMGCS1 8183 -0.0047 0.32 NO
23 HADHA HADHA HADHA 8203 -0.0049 0.32 NO
24 ACSM2A ACSM2A ACSM2A 8901 -0.012 0.29 NO
25 HMGCS2 HMGCS2 HMGCS2 9190 -0.015 0.28 NO
26 ACSM3 ACSM3 ACSM3 10319 -0.028 0.24 NO
27 ALDH9A1 ALDH9A1 ALDH9A1 10754 -0.033 0.23 NO
28 ALDH5A1 ALDH5A1 ALDH5A1 11386 -0.04 0.22 NO
29 OXCT2 OXCT2 OXCT2 13542 -0.072 0.14 NO
30 GAD1 GAD1 GAD1 16926 -0.21 0.073 NO

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

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

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

Table S16.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SLC6A3 SLC6A3 SLC6A3 135 0.35 0.039 YES
2 COX6A2 COX6A2 COX6A2 292 0.28 0.068 YES
3 COX4I2 COX4I2 COX4I2 366 0.25 0.098 YES
4 SNCA SNCA SNCA 964 0.16 0.086 YES
5 NDUFA4L2 NDUFA4L2 NDUFA4L2 1067 0.15 0.1 YES
6 NDUFA3 NDUFA3 NDUFA3 1471 0.12 0.095 YES
7 COX6C COX6C COX6C 1749 0.11 0.094 YES
8 NDUFS8 NDUFS8 NDUFS8 1827 0.1 0.1 YES
9 NDUFB1 NDUFB1 NDUFB1 1891 0.1 0.11 YES
10 COX6A1 COX6A1 COX6A1 1936 0.1 0.12 YES
11 NDUFB9 NDUFB9 NDUFB9 1949 0.1 0.14 YES
12 UQCR11 UQCR11 UQCR11 1952 0.1 0.15 YES
13 NDUFB7 NDUFB7 NDUFB7 1970 0.099 0.16 YES
14 NDUFA2 NDUFA2 NDUFA2 1995 0.098 0.18 YES
15 COX5B COX5B COX5B 2015 0.098 0.19 YES
16 ATP5D ATP5D ATP5D 2280 0.088 0.18 YES
17 NDUFA7 NDUFA7 NDUFA7 2326 0.086 0.19 YES
18 NDUFC2 NDUFC2 NDUFC2 2374 0.085 0.2 YES
19 UQCR10 UQCR10 UQCR10 2381 0.085 0.21 YES
20 COX7B COX7B COX7B 2412 0.084 0.22 YES
21 COX8C COX8C COX8C 2507 0.081 0.23 YES
22 GPR37 GPR37 GPR37 2510 0.081 0.24 YES
23 UQCRB UQCRB UQCRB 2516 0.08 0.25 YES
24 NDUFA1 NDUFA1 NDUFA1 2572 0.079 0.26 YES
25 COX7A1 COX7A1 COX7A1 2625 0.078 0.26 YES
26 COX8A COX8A COX8A 2687 0.076 0.27 YES
27 NDUFB10 NDUFB10 NDUFB10 2698 0.076 0.28 YES
28 UQCRQ UQCRQ UQCRQ 2736 0.075 0.29 YES
29 ATP5E ATP5E ATP5E 2845 0.072 0.29 YES
30 TH TH TH 2868 0.072 0.3 YES
31 NDUFB8 NDUFB8 NDUFB8 2878 0.071 0.31 YES
32 NDUFV3 NDUFV3 NDUFV3 2904 0.071 0.32 YES
33 NDUFB3 NDUFB3 NDUFB3 2923 0.07 0.33 YES
34 NDUFV2 NDUFV2 NDUFV2 2930 0.07 0.34 YES
35 ATP5G1 ATP5G1 ATP5G1 2959 0.069 0.34 YES
36 COX6B1 COX6B1 COX6B1 2997 0.068 0.35 YES
37 NDUFS6 NDUFS6 NDUFS6 3015 0.068 0.36 YES
38 NDUFB6 NDUFB6 NDUFB6 3053 0.067 0.37 YES
39 NDUFS7 NDUFS7 NDUFS7 3217 0.063 0.37 YES
40 PINK1 PINK1 PINK1 3218 0.063 0.37 YES
41 NDUFV1 NDUFV1 NDUFV1 3399 0.059 0.37 YES
42 NDUFA8 NDUFA8 NDUFA8 3475 0.058 0.38 YES
43 COX4I1 COX4I1 COX4I1 3566 0.056 0.38 YES
44 COX5A COX5A COX5A 3655 0.054 0.38 YES
45 NDUFB2 NDUFB2 NDUFB2 3664 0.054 0.39 YES
46 UQCRHL UQCRHL UQCRHL 3675 0.054 0.39 YES
47 UBB UBB UBB 3886 0.05 0.39 YES
48 NDUFC1 NDUFC1 NDUFC1 3937 0.049 0.39 YES
49 UBE2G2 UBE2G2 UBE2G2 4060 0.047 0.39 YES
50 NDUFAB1 NDUFAB1 NDUFAB1 4062 0.047 0.4 YES
51 PARK7 PARK7 PARK7 4210 0.044 0.4 YES
52 UQCRH UQCRH UQCRH 4294 0.043 0.4 YES
53 SLC25A4 SLC25A4 SLC25A4 4340 0.042 0.4 YES
54 COX7A2 COX7A2 COX7A2 4400 0.041 0.4 YES
55 NDUFA9 NDUFA9 NDUFA9 4511 0.039 0.4 YES
56 NDUFA6 NDUFA6 NDUFA6 4683 0.037 0.4 YES
57 UBE2L3 UBE2L3 UBE2L3 4749 0.036 0.4 YES
58 VDAC3 VDAC3 VDAC3 4788 0.036 0.4 YES
59 ATP5O ATP5O ATP5O 4853 0.035 0.4 YES
60 ATP5J ATP5J ATP5J 4858 0.035 0.41 YES
61 NDUFA5 NDUFA5 NDUFA5 4881 0.034 0.41 YES
62 NDUFS5 NDUFS5 NDUFS5 4895 0.034 0.42 YES
63 COX7C COX7C COX7C 4976 0.033 0.42 YES
64 NDUFA10 NDUFA10 NDUFA10 5048 0.032 0.42 YES
65 CYC1 CYC1 CYC1 5076 0.032 0.42 YES
66 UQCRC1 UQCRC1 UQCRC1 5089 0.032 0.42 YES
67 ATP5H ATP5H ATP5H 5197 0.03 0.42 YES
68 NDUFA4 NDUFA4 NDUFA4 5212 0.03 0.42 YES
69 CYCS CYCS CYCS 5312 0.028 0.42 NO
70 NDUFS3 NDUFS3 NDUFS3 5422 0.027 0.42 NO
71 NDUFB4 NDUFB4 NDUFB4 5558 0.026 0.42 NO
72 ATP5C1 ATP5C1 ATP5C1 5570 0.025 0.42 NO
73 UBA1 UBA1 UBA1 5658 0.024 0.42 NO
74 VDAC1 VDAC1 VDAC1 5684 0.024 0.42 NO
75 COX7A2L COX7A2L COX7A2L 5918 0.021 0.41 NO
76 ATP5G2 ATP5G2 ATP5G2 6100 0.019 0.4 NO
77 SDHB SDHB SDHB 6356 0.016 0.39 NO
78 NDUFB5 NDUFB5 NDUFB5 6438 0.015 0.39 NO
79 SDHA SDHA SDHA 6455 0.015 0.39 NO
80 HTRA2 HTRA2 HTRA2 6622 0.013 0.38 NO
81 UQCRFS1 UQCRFS1 UQCRFS1 6707 0.012 0.38 NO
82 NDUFS4 NDUFS4 NDUFS4 6821 0.011 0.37 NO
83 NDUFS2 NDUFS2 NDUFS2 6910 0.0094 0.37 NO
84 ATP5G3 ATP5G3 ATP5G3 6990 0.0085 0.36 NO
85 ATP5A1 ATP5A1 ATP5A1 7015 0.0083 0.36 NO
86 UBE2J2 UBE2J2 UBE2J2 7026 0.0081 0.36 NO
87 SDHC SDHC SDHC 7055 0.0078 0.36 NO
88 VDAC2 VDAC2 VDAC2 7212 0.0062 0.36 NO
89 ATP5B ATP5B ATP5B 7302 0.0051 0.35 NO
90 ATP5F1 ATP5F1 ATP5F1 7449 0.0033 0.34 NO
91 PPID PPID PPID 7847 -0.0011 0.32 NO
92 CASP9 CASP9 CASP9 8262 -0.0055 0.3 NO
93 UBE2G1 UBE2G1 UBE2G1 9158 -0.015 0.25 NO
94 UCHL1 UCHL1 UCHL1 9388 -0.017 0.24 NO
95 UBE2J1 UBE2J1 UBE2J1 9568 -0.02 0.24 NO
96 SLC25A6 SLC25A6 SLC25A6 10336 -0.028 0.2 NO
97 SDHD SDHD SDHD 10530 -0.03 0.19 NO
98 APAF1 APAF1 APAF1 10669 -0.032 0.19 NO
99 UQCRC2 UQCRC2 UQCRC2 10884 -0.034 0.18 NO
100 NDUFS1 NDUFS1 NDUFS1 10990 -0.035 0.18 NO
101 CASP3 CASP3 CASP3 11348 -0.04 0.16 NO
102 UBA7 UBA7 UBA7 12178 -0.05 0.13 NO
103 SLC25A5 SLC25A5 SLC25A5 12315 -0.052 0.13 NO
104 UBE2L6 UBE2L6 UBE2L6 12475 -0.055 0.12 NO
105 PARK2 PARK2 PARK2 13401 -0.07 0.083 NO
106 LRRK2 LRRK2 LRRK2 15706 -0.14 -0.026 NO
107 SLC18A2 SLC18A2 SLC18A2 16853 -0.2 -0.062 NO
108 COX6B2 COX6B2 COX6B2 17228 -0.24 -0.051 NO
109 SNCAIP SNCAIP SNCAIP 17923 -0.36 -0.04 NO
110 SLC18A1 SLC18A1 SLC18A1 18098 -0.44 0.0087 NO

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

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

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

Table 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 COX6A2 COX6A2 COX6A2 292 0.28 0.019 YES
2 COX4I2 COX4I2 COX4I2 366 0.25 0.046 YES
3 NDUFA4L2 NDUFA4L2 NDUFA4L2 1067 0.15 0.027 YES
4 COX17 COX17 COX17 1134 0.14 0.041 YES
5 NDUFA3 NDUFA3 NDUFA3 1471 0.12 0.038 YES
6 ATP6V1G2 ATP6V1G2 ATP6V1G2 1498 0.12 0.051 YES
7 ATP6V0E2 ATP6V0E2 ATP6V0E2 1539 0.12 0.064 YES
8 TCIRG1 TCIRG1 TCIRG1 1617 0.11 0.074 YES
9 ATP5I ATP5I ATP5I 1655 0.11 0.086 YES
10 COX6C COX6C COX6C 1749 0.11 0.094 YES
11 NDUFS8 NDUFS8 NDUFS8 1827 0.1 0.1 YES
12 ATP6V1E2 ATP6V1E2 ATP6V1E2 1842 0.1 0.12 YES
13 ATP5J2 ATP5J2 ATP5J2 1872 0.1 0.13 YES
14 NDUFB1 NDUFB1 NDUFB1 1891 0.1 0.14 YES
15 COX6A1 COX6A1 COX6A1 1936 0.1 0.15 YES
16 NDUFB9 NDUFB9 NDUFB9 1949 0.1 0.16 YES
17 UQCR11 UQCR11 UQCR11 1952 0.1 0.17 YES
18 NDUFB7 NDUFB7 NDUFB7 1970 0.099 0.18 YES
19 NDUFA2 NDUFA2 NDUFA2 1995 0.098 0.19 YES
20 COX5B COX5B COX5B 2015 0.098 0.21 YES
21 ATP5D ATP5D ATP5D 2280 0.088 0.2 YES
22 ATP6V1C2 ATP6V1C2 ATP6V1C2 2286 0.088 0.21 YES
23 NDUFA7 NDUFA7 NDUFA7 2326 0.086 0.22 YES
24 NDUFC2 NDUFC2 NDUFC2 2374 0.085 0.23 YES
25 UQCR10 UQCR10 UQCR10 2381 0.085 0.24 YES
26 COX7B COX7B COX7B 2412 0.084 0.25 YES
27 ATP6V0B ATP6V0B ATP6V0B 2413 0.084 0.26 YES
28 COX8C COX8C COX8C 2507 0.081 0.26 YES
29 UQCRB UQCRB UQCRB 2516 0.08 0.27 YES
30 ATP6V1F ATP6V1F ATP6V1F 2536 0.08 0.28 YES
31 NDUFA1 NDUFA1 NDUFA1 2572 0.079 0.29 YES
32 COX7A1 COX7A1 COX7A1 2625 0.078 0.3 YES
33 COX8A COX8A COX8A 2687 0.076 0.3 YES
34 NDUFB10 NDUFB10 NDUFB10 2698 0.076 0.31 YES
35 UQCRQ UQCRQ UQCRQ 2736 0.075 0.32 YES
36 ATP5E ATP5E ATP5E 2845 0.072 0.32 YES
37 NDUFB8 NDUFB8 NDUFB8 2878 0.071 0.33 YES
38 NDUFV3 NDUFV3 NDUFV3 2904 0.071 0.34 YES
39 NDUFB3 NDUFB3 NDUFB3 2923 0.07 0.34 YES
40 NDUFV2 NDUFV2 NDUFV2 2930 0.07 0.35 YES
41 ATP5G1 ATP5G1 ATP5G1 2959 0.069 0.36 YES
42 COX6B1 COX6B1 COX6B1 2997 0.068 0.37 YES
43 NDUFS6 NDUFS6 NDUFS6 3015 0.068 0.38 YES
44 NDUFB6 NDUFB6 NDUFB6 3053 0.067 0.38 YES
45 NDUFS7 NDUFS7 NDUFS7 3217 0.063 0.38 YES
46 NDUFA11 NDUFA11 NDUFA11 3392 0.06 0.38 YES
47 NDUFV1 NDUFV1 NDUFV1 3399 0.059 0.38 YES
48 ATP6V0C ATP6V0C ATP6V0C 3411 0.059 0.39 YES
49 NDUFA8 NDUFA8 NDUFA8 3475 0.058 0.4 YES
50 ATP6V1H ATP6V1H ATP6V1H 3550 0.056 0.4 YES
51 COX4I1 COX4I1 COX4I1 3566 0.056 0.4 YES
52 COX5A COX5A COX5A 3655 0.054 0.41 YES
53 NDUFB2 NDUFB2 NDUFB2 3664 0.054 0.41 YES
54 UQCRHL UQCRHL UQCRHL 3675 0.054 0.42 YES
55 ATP6V1C1 ATP6V1C1 ATP6V1C1 3693 0.054 0.42 YES
56 NDUFC1 NDUFC1 NDUFC1 3937 0.049 0.42 YES
57 NDUFAB1 NDUFAB1 NDUFAB1 4062 0.047 0.42 YES
58 ATP6V0A1 ATP6V0A1 ATP6V0A1 4105 0.046 0.42 YES
59 LHPP LHPP LHPP 4187 0.045 0.42 YES
60 UQCRH UQCRH UQCRH 4294 0.043 0.42 YES
61 COX7A2 COX7A2 COX7A2 4400 0.041 0.42 YES
62 NDUFA9 NDUFA9 NDUFA9 4511 0.039 0.42 YES
63 ATP6V1D ATP6V1D ATP6V1D 4543 0.039 0.42 YES
64 ATP5L ATP5L ATP5L 4637 0.038 0.42 YES
65 PPA2 PPA2 PPA2 4670 0.037 0.42 YES
66 NDUFA6 NDUFA6 NDUFA6 4683 0.037 0.43 YES
67 ATP5O ATP5O ATP5O 4853 0.035 0.42 YES
68 ATP5J ATP5J ATP5J 4858 0.035 0.43 YES
69 NDUFA5 NDUFA5 NDUFA5 4881 0.034 0.43 YES
70 NDUFS5 NDUFS5 NDUFS5 4895 0.034 0.43 YES
71 ATP6V0A2 ATP6V0A2 ATP6V0A2 4910 0.034 0.44 YES
72 COX7C COX7C COX7C 4976 0.033 0.44 YES
73 NDUFA10 NDUFA10 NDUFA10 5048 0.032 0.44 YES
74 CYC1 CYC1 CYC1 5076 0.032 0.44 YES
75 UQCRC1 UQCRC1 UQCRC1 5089 0.032 0.44 YES
76 COX15 COX15 COX15 5181 0.03 0.44 YES
77 ATP5H ATP5H ATP5H 5197 0.03 0.45 YES
78 NDUFA4 NDUFA4 NDUFA4 5212 0.03 0.45 YES
79 NDUFS3 NDUFS3 NDUFS3 5422 0.027 0.44 NO
80 ATP6V1E1 ATP6V1E1 ATP6V1E1 5492 0.026 0.44 NO
81 NDUFB4 NDUFB4 NDUFB4 5558 0.026 0.44 NO
82 ATP5C1 ATP5C1 ATP5C1 5570 0.025 0.44 NO
83 COX7A2L COX7A2L COX7A2L 5918 0.021 0.43 NO
84 ATP6V0E1 ATP6V0E1 ATP6V0E1 6045 0.019 0.42 NO
85 ATP6V0D1 ATP6V0D1 ATP6V0D1 6092 0.019 0.42 NO
86 ATP5G2 ATP5G2 ATP5G2 6100 0.019 0.42 NO
87 SDHB SDHB SDHB 6356 0.016 0.41 NO
88 NDUFB5 NDUFB5 NDUFB5 6438 0.015 0.41 NO
89 ATP6AP1 ATP6AP1 ATP6AP1 6448 0.015 0.41 NO
90 SDHA SDHA SDHA 6455 0.015 0.41 NO
91 UQCRFS1 UQCRFS1 UQCRFS1 6707 0.012 0.4 NO
92 NDUFS4 NDUFS4 NDUFS4 6821 0.011 0.39 NO
93 NDUFS2 NDUFS2 NDUFS2 6910 0.0094 0.39 NO
94 ATP5G3 ATP5G3 ATP5G3 6990 0.0085 0.39 NO
95 ATP5A1 ATP5A1 ATP5A1 7015 0.0083 0.39 NO
96 SDHC SDHC SDHC 7055 0.0078 0.39 NO
97 ATP5B ATP5B ATP5B 7302 0.0051 0.37 NO
98 PPA1 PPA1 PPA1 7329 0.0047 0.37 NO
99 ATP5F1 ATP5F1 ATP5F1 7449 0.0033 0.37 NO
100 COX10 COX10 COX10 7695 0.00077 0.35 NO
101 ATP6V1B2 ATP6V1B2 ATP6V1B2 8008 -0.0029 0.34 NO
102 ATP6V1G1 ATP6V1G1 ATP6V1G1 8642 -0.0096 0.3 NO
103 ATP6V1A ATP6V1A ATP6V1A 9866 -0.023 0.24 NO
104 COX11 COX11 COX11 9897 -0.023 0.24 NO
105 SDHD SDHD SDHD 10530 -0.03 0.21 NO
106 UQCRC2 UQCRC2 UQCRC2 10884 -0.034 0.19 NO
107 NDUFS1 NDUFS1 NDUFS1 10990 -0.035 0.19 NO
108 ATP4B ATP4B ATP4B 12262 -0.052 0.13 NO
109 ATP6V0D2 ATP6V0D2 ATP6V0D2 15907 -0.14 -0.056 NO
110 ATP6V1G3 ATP6V1G3 ATP6V1G3 17030 -0.22 -0.09 NO
111 COX6B2 COX6B2 COX6B2 17228 -0.24 -0.072 NO
112 ATP6V1B1 ATP6V1B1 ATP6V1B1 17243 -0.24 -0.042 NO
113 ATP6V0A4 ATP6V0A4 ATP6V0A4 17459 -0.27 -0.021 NO
114 ATP12A ATP12A ATP12A 18183 -0.52 0.004 NO

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

Figure S34.  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 TYROSINE METABOLISM

Table S18.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GNMT GNMT GNMT 30 0.48 0.16 YES
2 GAMT GAMT GAMT 543 0.21 0.2 YES
3 CBS CBS CBS 545 0.21 0.27 YES
4 AOC2 AOC2 AOC2 593 0.21 0.33 YES
5 SDS SDS SDS 939 0.16 0.37 YES
6 PSAT1 PSAT1 PSAT1 959 0.16 0.42 YES
7 CHDH CHDH CHDH 1324 0.13 0.44 YES
8 MAOA MAOA MAOA 1993 0.098 0.44 YES
9 SARDH SARDH SARDH 2156 0.092 0.46 YES
10 DMGDH DMGDH DMGDH 2448 0.083 0.47 YES
11 GCAT GCAT GCAT 2758 0.075 0.48 YES
12 ALAS2 ALAS2 ALAS2 2811 0.073 0.5 YES
13 PSPH PSPH PSPH 4263 0.043 0.44 NO
14 CTH CTH CTH 5495 0.026 0.38 NO
15 ALAS1 ALAS1 ALAS1 5823 0.022 0.36 NO
16 SRR SRR SRR 5980 0.02 0.36 NO
17 DLD DLD DLD 6677 0.012 0.33 NO
18 BHMT BHMT BHMT 6881 0.0098 0.32 NO
19 SHMT2 SHMT2 SHMT2 7727 0.00029 0.28 NO
20 GLYCTK GLYCTK GLYCTK 7909 -0.0018 0.26 NO
21 MAOB MAOB MAOB 8371 -0.0066 0.24 NO
22 PHGDH PHGDH PHGDH 8870 -0.012 0.22 NO
23 SHMT1 SHMT1 SHMT1 11001 -0.035 0.11 NO
24 AGXT AGXT AGXT 13549 -0.072 -0.0022 NO
25 AOC3 AOC3 AOC3 14138 -0.085 -0.0064 NO
26 GATM GATM GATM 15458 -0.13 -0.037 NO
27 PIPOX PIPOX PIPOX 15777 -0.14 -0.0094 NO
28 GLDC GLDC GLDC 18104 -0.44 0.0083 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 TYROSINE METABOLISM.

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

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

Table 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 SHFM1 SHFM1 SHFM1 1680 0.11 0.0052 YES
2 PSMC1 PSMC1 PSMC1 3194 0.064 -0.021 YES
3 PSMB6 PSMB6 PSMB6 3410 0.059 0.019 YES
4 PSME2 PSME2 PSME2 3616 0.055 0.057 YES
5 PSMB7 PSMB7 PSMB7 3718 0.053 0.098 YES
6 PSMA4 PSMA4 PSMA4 3835 0.051 0.14 YES
7 PSMB3 PSMB3 PSMB3 3837 0.051 0.18 YES
8 PSMB11 PSMB11 PSMB11 4121 0.046 0.21 YES
9 POMP POMP POMP 4315 0.042 0.23 YES
10 PSMB5 PSMB5 PSMB5 4736 0.036 0.24 YES
11 PSMC2 PSMC2 PSMC2 4789 0.036 0.27 YES
12 PSMA2 PSMA2 PSMA2 5070 0.032 0.28 YES
13 PSMB4 PSMB4 PSMB4 5149 0.03 0.31 YES
14 PSMA3 PSMA3 PSMA3 5173 0.03 0.33 YES
15 PSMC3 PSMC3 PSMC3 5268 0.029 0.35 YES
16 PSMD4 PSMD4 PSMD4 5321 0.028 0.38 YES
17 PSMA6 PSMA6 PSMA6 5716 0.024 0.37 YES
18 PSMB2 PSMB2 PSMB2 5854 0.022 0.39 YES
19 PSMD8 PSMD8 PSMD8 5931 0.021 0.4 YES
20 PSMA5 PSMA5 PSMA5 5933 0.021 0.42 YES
21 PSMC5 PSMC5 PSMC5 6000 0.02 0.43 YES
22 PSMA7 PSMA7 PSMA7 6425 0.015 0.42 YES
23 PSMD14 PSMD14 PSMD14 6598 0.013 0.42 YES
24 PSMC6 PSMC6 PSMC6 6637 0.013 0.43 YES
25 PSMB1 PSMB1 PSMB1 7304 0.0051 0.4 NO
26 PSMD11 PSMD11 PSMD11 7315 0.0049 0.4 NO
27 PSMD13 PSMD13 PSMD13 7362 0.0044 0.41 NO
28 PSME1 PSME1 PSME1 7552 0.0024 0.4 NO
29 PSMC4 PSMC4 PSMC4 7623 0.0017 0.4 NO
30 PSMD7 PSMD7 PSMD7 7648 0.0013 0.4 NO
31 PSMD3 PSMD3 PSMD3 7666 0.0011 0.4 NO
32 PSMD1 PSMD1 PSMD1 7747 0.000038 0.39 NO
33 PSME3 PSME3 PSME3 8028 -0.0032 0.38 NO
34 PSMD6 PSMD6 PSMD6 8078 -0.0037 0.38 NO
35 PSMD12 PSMD12 PSMD12 8088 -0.0038 0.38 NO
36 PSME4 PSME4 PSME4 8461 -0.0076 0.37 NO
37 PSMA1 PSMA1 PSMA1 8560 -0.0086 0.37 NO
38 PSMF1 PSMF1 PSMF1 8581 -0.0088 0.38 NO
39 PSMD2 PSMD2 PSMD2 8624 -0.0094 0.38 NO
40 IFNG IFNG IFNG 10546 -0.03 0.3 NO
41 PSMB9 PSMB9 PSMB9 12471 -0.055 0.25 NO
42 PSMB8 PSMB8 PSMB8 13909 -0.08 0.24 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 GLUTATHIONE METABOLISM.

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL3L RPL3L RPL3L 102 0.37 0.13 YES
2 RPL22L1 RPL22L1 RPL22L1 1557 0.12 0.088 YES
3 RPL36A RPL36A RPL36A 2452 0.083 0.068 YES
4 RPL9 RPL9 RPL9 2456 0.083 0.097 YES
5 RPS27L RPS27L RPS27L 2721 0.075 0.11 YES
6 RPS20 RPS20 RPS20 3051 0.067 0.12 YES
7 MRPL13 MRPL13 MRPL13 3242 0.063 0.13 YES
8 RPS10 RPS10 RPS10 3788 0.052 0.12 YES
9 RPS15 RPS15 RPS15 3818 0.051 0.13 YES
10 RPL28 RPL28 RPL28 3933 0.049 0.14 YES
11 RPL26 RPL26 RPL26 4097 0.046 0.15 YES
12 RPL13 RPL13 RPL13 4161 0.045 0.16 YES
13 RPL39 RPL39 RPL39 4274 0.043 0.17 YES
14 RPL36AL RPL36AL RPL36AL 4288 0.043 0.19 YES
15 RPL12 RPL12 RPL12 4290 0.043 0.2 YES
16 RPL35 RPL35 RPL35 4428 0.041 0.21 YES
17 RPL37A RPL37A RPL37A 4451 0.04 0.22 YES
18 RPLP2 RPLP2 RPLP2 4461 0.04 0.24 YES
19 RPL26L1 RPL26L1 RPL26L1 4482 0.04 0.25 YES
20 RPL32 RPL32 RPL32 4570 0.038 0.26 YES
21 FAU FAU FAU 4601 0.038 0.27 YES
22 RPS26 RPS26 RPS26 4606 0.038 0.28 YES
23 RPS19 RPS19 RPS19 4631 0.038 0.29 YES
24 RPS21 RPS21 RPS21 4634 0.038 0.31 YES
25 RPL23 RPL23 RPL23 4641 0.038 0.32 YES
26 RPL38 RPL38 RPL38 4654 0.037 0.33 YES
27 RPL14 RPL14 RPL14 4717 0.036 0.34 YES
28 RPL30 RPL30 RPL30 4768 0.036 0.35 YES
29 RPL8 RPL8 RPL8 4901 0.034 0.36 YES
30 RPL36 RPL36 RPL36 4906 0.034 0.37 YES
31 UBA52 UBA52 UBA52 4919 0.034 0.38 YES
32 RPL37 RPL37 RPL37 4992 0.033 0.39 YES
33 RPS16 RPS16 RPS16 5219 0.03 0.38 YES
34 RPL27 RPL27 RPL27 5244 0.029 0.4 YES
35 RPSA RPSA RPSA 5311 0.028 0.4 YES
36 RPS24 RPS24 RPS24 5318 0.028 0.41 YES
37 RPL35A RPL35A RPL35A 5331 0.028 0.42 YES
38 RPS25 RPS25 RPS25 5365 0.028 0.43 YES
39 RPL24 RPL24 RPL24 5395 0.027 0.44 YES
40 RPL23A RPL23A RPL23A 5453 0.027 0.44 YES
41 RPL29 RPL29 RPL29 5463 0.027 0.45 YES
42 RPLP1 RPLP1 RPLP1 5480 0.026 0.46 YES
43 RPS6 RPS6 RPS6 5502 0.026 0.47 YES
44 RPL19 RPL19 RPL19 5596 0.025 0.47 YES
45 RPS9 RPS9 RPS9 5657 0.024 0.48 YES
46 RPS5 RPS5 RPS5 5686 0.024 0.48 YES
47 RPL31 RPL31 RPL31 5722 0.023 0.49 YES
48 RPS8 RPS8 RPS8 5753 0.023 0.5 YES
49 RPL34 RPL34 RPL34 5775 0.022 0.5 YES
50 RPS29 RPS29 RPS29 6015 0.02 0.5 YES
51 RPL18A RPL18A RPL18A 6137 0.018 0.5 YES
52 RPS27A RPS27A RPS27A 6161 0.018 0.5 YES
53 RPL27A RPL27A RPL27A 6322 0.016 0.5 YES
54 RPL15 RPL15 RPL15 6327 0.016 0.5 YES
55 RPLP0 RPLP0 RPLP0 6382 0.015 0.51 YES
56 RPS2 RPS2 RPS2 6454 0.015 0.51 YES
57 RPS13 RPS13 RPS13 6469 0.014 0.51 YES
58 RPL41 RPL41 RPL41 6523 0.014 0.52 YES
59 RPS11 RPS11 RPS11 6526 0.014 0.52 YES
60 RPL7A RPL7A RPL7A 6528 0.014 0.52 YES
61 RPS23 RPS23 RPS23 6586 0.013 0.53 YES
62 RPL13A RPL13A RPL13A 6687 0.012 0.52 NO
63 RPL7 RPL7 RPL7 6830 0.01 0.52 NO
64 RPS18 RPS18 RPS18 6880 0.0098 0.52 NO
65 RPS4X RPS4X RPS4X 6955 0.0089 0.52 NO
66 RPS17 RPS17 RPS17 7022 0.0082 0.52 NO
67 RPL4 RPL4 RPL4 7032 0.008 0.52 NO
68 RPL3 RPL3 RPL3 7086 0.0074 0.52 NO
69 RPL10 RPL10 RPL10 7306 0.0051 0.51 NO
70 RPS4Y1 RPS4Y1 RPS4Y1 7324 0.0049 0.51 NO
71 RPS7 RPS7 RPS7 7403 0.0038 0.51 NO
72 RPS12 RPS12 RPS12 7539 0.0025 0.5 NO
73 RPL11 RPL11 RPL11 7662 0.0011 0.5 NO
74 RSL24D1 RSL24D1 RSL24D1 7797 -0.00054 0.49 NO
75 RPL10A RPL10A RPL10A 7850 -0.0011 0.49 NO
76 RPL17 RPL17 RPL17 8038 -0.0033 0.48 NO
77 RPS3 RPS3 RPS3 8104 -0.0039 0.48 NO
78 RPL6 RPL6 RPL6 8162 -0.0046 0.47 NO
79 RPS15A RPS15A RPS15A 8317 -0.0061 0.47 NO
80 RPL5 RPL5 RPL5 8881 -0.012 0.44 NO
81 RPS3A RPS3A RPS3A 9403 -0.017 0.42 NO
82 RPL22 RPL22 RPL22 9442 -0.018 0.42 NO
83 RPS28 RPS28 RPS28 10798 -0.033 0.36 NO
84 RPS27 RPS27 RPS27 13076 -0.064 0.26 NO
85 RPL21 RPL21 RPL21 13807 -0.078 0.24 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.29 1 0.42 0.91 1 0.41 0.28 0.3 0.85 0.33
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.24 0.96 0.51 0.91 1 0.39 0.27 0.28 0.86 0.33
BIOCARTA MPR PATHWAY 31 genes.ES.table 0.34 1.1 0.3 0.99 1 0.19 0.12 0.17 0.89 0.39
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.36 1.2 0.29 0.92 1 0.39 0.21 0.31 0.82 0.34
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.49 1.6 0.059 0.19 0.68 0.034 0.00077 0.034 0.11 0.017
KEGG PENTOSE PHOSPHATE PATHWAY 25 genes.ES.table 0.35 1.1 0.34 0.87 1 0.32 0.17 0.27 0.78 0.29
KEGG N GLYCAN BIOSYNTHESIS 45 genes.ES.table 0.47 1.6 0.051 0.25 0.67 0.4 0.26 0.3 0.14 0.048
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.51 1.7 0.042 0.28 0.37 0.62 0.36 0.4 0 0.081
KEGG RIBOSOME 85 genes.ES.table 0.39 0.92 0.55 0.86 1 0.86 0.42 0.5 0.82 0.26
KEGG RNA DEGRADATION 56 genes.ES.table 0.33 1.6 0.053 0.33 0.64 0.54 0.36 0.35 0.18 0.081
genes ES table in pathway: BIOCARTA CARM ER PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DARS2 DARS2 DARS2 1732 0.1 -0.015 YES
2 NARS2 NARS2 NARS2 1892 0.096 0.052 YES
3 EPRS EPRS EPRS 2208 0.084 0.1 YES
4 RARS2 RARS2 RARS2 2502 0.074 0.14 YES
5 VARS VARS VARS 2986 0.064 0.17 YES
6 IARS IARS IARS 3722 0.051 0.17 YES
7 FARSB FARSB FARSB 3899 0.048 0.2 YES
8 PARS2 PARS2 PARS2 4033 0.046 0.22 YES
9 RARS RARS RARS 4301 0.043 0.24 YES
10 LARS LARS LARS 4314 0.043 0.28 YES
11 IARS2 IARS2 IARS2 4445 0.041 0.3 YES
12 VARS2 VARS2 VARS2 4532 0.04 0.33 YES
13 YARS2 YARS2 YARS2 4535 0.04 0.36 YES
14 SEPSECS SEPSECS SEPSECS 4602 0.039 0.39 YES
15 EARS2 EARS2 EARS2 4651 0.039 0.41 YES
16 QARS QARS QARS 5183 0.032 0.41 YES
17 MARS2 MARS2 MARS2 5184 0.032 0.44 YES
18 WARS2 WARS2 WARS2 5273 0.031 0.46 YES
19 YARS YARS YARS 5536 0.028 0.46 YES
20 TARSL2 TARSL2 TARSL2 5546 0.028 0.48 YES
21 LARS2 LARS2 LARS2 5657 0.027 0.5 YES
22 GARS GARS GARS 6129 0.022 0.49 YES
23 TARS TARS TARS 6233 0.021 0.5 YES
24 CARS2 CARS2 CARS2 6524 0.018 0.5 YES
25 DARS DARS DARS 6637 0.017 0.51 YES
26 NARS NARS NARS 7053 0.013 0.5 NO
27 FARSA FARSA FARSA 7095 0.013 0.5 NO
28 HARS2 HARS2 HARS2 7279 0.011 0.5 NO
29 WARS WARS WARS 7770 0.0063 0.48 NO
30 MARS MARS MARS 7821 0.0058 0.48 NO
31 AARS2 AARS2 AARS2 7919 0.0049 0.48 NO
32 MTFMT MTFMT MTFMT 8313 0.00086 0.46 NO
33 SARS2 SARS2 SARS2 8479 -0.0008 0.45 NO
34 SARS SARS SARS 8512 -0.0011 0.45 NO
35 CARS CARS CARS 8587 -0.0018 0.45 NO
36 AARS AARS AARS 8893 -0.0049 0.44 NO
37 PSTK PSTK PSTK 9022 -0.0062 0.43 NO
38 KARS KARS KARS 9511 -0.012 0.42 NO
39 HARS HARS HARS 10632 -0.026 0.38 NO
40 FARS2 FARS2 FARS2 12319 -0.054 0.33 NO

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

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CARM ER 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 HIVNEF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RQCD1 RQCD1 RQCD1 1823 0.098 -0.046 YES
2 CNOT6 CNOT6 CNOT6 2145 0.086 -0.015 YES
3 DCPS DCPS DCPS 3069 0.062 -0.032 YES
4 ZCCHC7 ZCCHC7 ZCCHC7 3272 0.058 -0.01 YES
5 XRN2 XRN2 XRN2 3367 0.057 0.016 YES
6 HSPD1 HSPD1 HSPD1 3576 0.053 0.034 YES
7 TTC37 TTC37 TTC37 3592 0.053 0.063 YES
8 ENO1 ENO1 ENO1 3782 0.05 0.08 YES
9 PATL1 PATL1 PATL1 3887 0.048 0.1 YES
10 CNOT10 CNOT10 CNOT10 4106 0.045 0.11 YES
11 DCP2 DCP2 DCP2 4298 0.043 0.13 YES
12 EDC3 EDC3 EDC3 4338 0.042 0.15 YES
13 DCP1A DCP1A DCP1A 4400 0.042 0.17 YES
14 EXOSC3 EXOSC3 EXOSC3 4508 0.04 0.18 YES
15 HSPA9 HSPA9 HSPA9 4658 0.039 0.2 YES
16 EXOSC10 EXOSC10 EXOSC10 4708 0.038 0.22 YES
17 PAPOLG PAPOLG PAPOLG 4837 0.036 0.23 YES
18 EXOSC4 EXOSC4 EXOSC4 4916 0.036 0.25 YES
19 CNOT1 CNOT1 CNOT1 5146 0.033 0.25 YES
20 CNOT2 CNOT2 CNOT2 5271 0.031 0.26 YES
21 CNOT3 CNOT3 CNOT3 5331 0.031 0.28 YES
22 DDX6 DDX6 DDX6 5337 0.03 0.29 YES
23 LSM2 LSM2 LSM2 5504 0.029 0.3 YES
24 PARN PARN PARN 5808 0.026 0.3 YES
25 EXOSC9 EXOSC9 EXOSC9 6051 0.023 0.3 YES
26 NAA38 NAA38 NAA38 6100 0.023 0.31 YES
27 PAPOLA PAPOLA PAPOLA 6135 0.022 0.32 YES
28 EXOSC2 EXOSC2 EXOSC2 6292 0.021 0.32 YES
29 PAPOLB PAPOLB PAPOLB 6413 0.019 0.32 YES
30 EXOSC5 EXOSC5 EXOSC5 6511 0.018 0.33 YES
31 DIS3 DIS3 DIS3 6776 0.016 0.32 NO
32 PNPT1 PNPT1 PNPT1 6977 0.014 0.32 NO
33 CNOT6L CNOT6L CNOT6L 7411 0.0098 0.3 NO
34 PAPD7 PAPD7 PAPD7 7489 0.009 0.3 NO
35 SKIV2L SKIV2L SKIV2L 7724 0.0066 0.29 NO
36 EDC4 EDC4 EDC4 7808 0.0059 0.29 NO
37 DCP1B DCP1B DCP1B 7896 0.0052 0.29 NO
38 XRN1 XRN1 XRN1 7911 0.005 0.29 NO
39 LSM7 LSM7 LSM7 8081 0.0033 0.28 NO
40 EXOSC8 EXOSC8 EXOSC8 8203 0.0023 0.28 NO
41 CNOT7 CNOT7 CNOT7 8242 0.0018 0.28 NO
42 LSM4 LSM4 LSM4 8387 0.0001 0.27 NO
43 EXOSC7 EXOSC7 EXOSC7 8435 -0.00039 0.27 NO
44 SKIV2L2 SKIV2L2 SKIV2L2 8820 -0.0043 0.25 NO
45 LSM5 LSM5 LSM5 8854 -0.0045 0.25 NO
46 LSM3 LSM3 LSM3 8965 -0.0057 0.25 NO
47 CNOT4 CNOT4 CNOT4 9520 -0.012 0.22 NO
48 LSM6 LSM6 LSM6 9721 -0.014 0.22 NO
49 WDR61 WDR61 WDR61 10470 -0.024 0.19 NO
50 EXOSC6 EXOSC6 EXOSC6 11109 -0.033 0.18 NO
51 C1D C1D C1D 11455 -0.038 0.18 NO
52 MPHOSPH6 MPHOSPH6 MPHOSPH6 11461 -0.038 0.2 NO
53 EXOSC1 EXOSC1 EXOSC1 11722 -0.042 0.21 NO
54 ENO2 ENO2 ENO2 12000 -0.048 0.22 NO
55 LSM1 LSM1 LSM1 14223 -0.11 0.16 NO
56 ENO3 ENO3 ENO3 14608 -0.12 0.2 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: BIOCARTA HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA MPR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MGAT5B MGAT5B MGAT5B 10 0.72 0.26 YES
2 ALG11 ALG11 ALG11 491 0.22 0.32 YES
3 MAN2A1 MAN2A1 MAN2A1 913 0.16 0.35 YES
4 MGAT5 MGAT5 MGAT5 1257 0.13 0.38 YES
5 ALG10B ALG10B ALG10B 1729 0.1 0.39 YES
6 MGAT4B MGAT4B MGAT4B 2569 0.073 0.37 YES
7 MAN2A2 MAN2A2 MAN2A2 3122 0.061 0.36 YES
8 ST6GAL1 ST6GAL1 ST6GAL1 3154 0.061 0.39 YES
9 ALG6 ALG6 ALG6 3287 0.058 0.4 YES
10 MOGS MOGS MOGS 3293 0.058 0.42 YES
11 GANAB GANAB GANAB 3307 0.058 0.44 YES
12 STT3A STT3A STT3A 3663 0.052 0.44 YES
13 ALG10 ALG10 ALG10 3741 0.05 0.45 YES
14 ALG13 ALG13 ALG13 4355 0.042 0.44 YES
15 B4GALT3 B4GALT3 B4GALT3 4484 0.041 0.44 YES
16 DDOST DDOST DDOST 4678 0.038 0.45 YES
17 FUT8 FUT8 FUT8 4691 0.038 0.46 YES
18 STT3B STT3B STT3B 4707 0.038 0.47 YES
19 MAN1B1 MAN1B1 MAN1B1 5302 0.031 0.45 NO
20 DPAGT1 DPAGT1 DPAGT1 5482 0.029 0.45 NO
21 RPN2 RPN2 RPN2 5700 0.027 0.45 NO
22 B4GALT2 B4GALT2 B4GALT2 6303 0.02 0.43 NO
23 MGAT4A MGAT4A MGAT4A 6543 0.018 0.42 NO
24 DOLPP1 DOLPP1 DOLPP1 6947 0.014 0.4 NO
25 DPM1 DPM1 DPM1 6976 0.014 0.41 NO
26 MAN1A2 MAN1A2 MAN1A2 7089 0.013 0.4 NO
27 ALG9 ALG9 ALG9 7720 0.0067 0.37 NO
28 RPN1 RPN1 RPN1 7850 0.0056 0.37 NO
29 ALG2 ALG2 ALG2 8780 -0.0038 0.32 NO
30 MGAT2 MGAT2 MGAT2 9172 -0.0078 0.3 NO
31 MAN1C1 MAN1C1 MAN1C1 9209 -0.0081 0.3 NO
32 ALG14 ALG14 ALG14 9421 -0.011 0.29 NO
33 ALG1 ALG1 ALG1 9991 -0.017 0.27 NO
34 ALG8 ALG8 ALG8 10430 -0.023 0.25 NO
35 DPM3 DPM3 DPM3 10513 -0.024 0.26 NO
36 DAD1 DAD1 DAD1 10815 -0.028 0.25 NO
37 ALG12 ALG12 ALG12 11130 -0.033 0.24 NO
38 ALG3 ALG3 ALG3 11180 -0.034 0.25 NO
39 B4GALT1 B4GALT1 B4GALT1 11417 -0.037 0.26 NO
40 MGAT1 MGAT1 MGAT1 11638 -0.041 0.26 NO
41 MGAT3 MGAT3 MGAT3 11710 -0.042 0.27 NO
42 DPM2 DPM2 DPM2 12359 -0.055 0.25 NO
43 ALG5 ALG5 ALG5 12526 -0.059 0.27 NO
44 TUSC3 TUSC3 TUSC3 12749 -0.063 0.28 NO
45 MAN1A1 MAN1A1 MAN1A1 12930 -0.068 0.29 NO

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

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

genes ES table in pathway: BIOCARTA TNFR1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 OGDHL OGDHL OGDHL 14 0.68 0.49 YES
2 DLAT DLAT DLAT 2412 0.077 0.41 NO
3 CS CS CS 4653 0.039 0.32 NO
4 MDH2 MDH2 MDH2 4943 0.035 0.33 NO
5 PDHA1 PDHA1 PDHA1 5244 0.032 0.33 NO
6 FH FH FH 5299 0.031 0.35 NO
7 SUCLG1 SUCLG1 SUCLG1 5820 0.026 0.34 NO
8 SDHB SDHB SDHB 6173 0.022 0.34 NO
9 SDHC SDHC SDHC 6911 0.015 0.31 NO
10 OGDH OGDH OGDH 7483 0.0091 0.28 NO
11 SDHD SDHD SDHD 7637 0.0076 0.28 NO
12 DLD DLD DLD 7638 0.0076 0.29 NO
13 PDHB PDHB PDHB 7665 0.0074 0.29 NO
14 ACO2 ACO2 ACO2 8190 0.0024 0.26 NO
15 PCK2 PCK2 PCK2 8399 -0.000021 0.25 NO
16 ACLY ACLY ACLY 8455 -0.00051 0.25 NO
17 SDHA SDHA SDHA 8490 -0.00092 0.25 NO
18 SUCLG2 SUCLG2 SUCLG2 8875 -0.0048 0.23 NO
19 IDH1 IDH1 IDH1 8911 -0.0051 0.23 NO
20 IDH3G IDH3G IDH3G 9075 -0.0067 0.23 NO
21 MDH1 MDH1 MDH1 9231 -0.0084 0.22 NO
22 ACO1 ACO1 ACO1 9919 -0.017 0.2 NO
23 IDH2 IDH2 IDH2 10181 -0.02 0.2 NO
24 IDH3B IDH3B IDH3B 10351 -0.022 0.21 NO
25 SUCLA2 SUCLA2 SUCLA2 10706 -0.027 0.21 NO
26 DLST DLST DLST 10905 -0.03 0.22 NO
27 IDH3A IDH3A IDH3A 11580 -0.04 0.21 NO
28 PCK1 PCK1 PCK1 14244 -0.11 0.14 NO
29 PC PC PC 14481 -0.12 0.21 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TNFR1 PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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 CBLC CBLC CBLC 517 0.22 0.0075 YES
2 CDC20 CDC20 CDC20 527 0.22 0.043 YES
3 UBE2C UBE2C UBE2C 563 0.21 0.075 YES
4 UBE2E3 UBE2E3 UBE2E3 731 0.18 0.096 YES
5 SKP2 SKP2 SKP2 896 0.16 0.11 YES
6 NHLRC1 NHLRC1 NHLRC1 936 0.16 0.14 YES
7 UBE2NL UBE2NL UBE2NL 972 0.15 0.16 YES
8 ANAPC1 ANAPC1 ANAPC1 1486 0.11 0.15 YES
9 CUL7 CUL7 CUL7 2070 0.089 0.13 YES
10 MID1 MID1 MID1 2236 0.083 0.14 YES
11 WWP2 WWP2 WWP2 2368 0.078 0.14 YES
12 TRIM37 TRIM37 TRIM37 2587 0.072 0.14 YES
13 ERCC8 ERCC8 ERCC8 2630 0.072 0.15 YES
14 UBE2I UBE2I UBE2I 2756 0.069 0.16 YES
15 PIAS3 PIAS3 PIAS3 2774 0.068 0.17 YES
16 CUL4B CUL4B CUL4B 2806 0.068 0.18 YES
17 BRCA1 BRCA1 BRCA1 2865 0.067 0.19 YES
18 CBLB CBLB CBLB 2880 0.066 0.2 YES
19 TRIM32 TRIM32 TRIM32 2890 0.066 0.21 YES
20 VHL VHL VHL 3251 0.059 0.2 YES
21 SIAH1 SIAH1 SIAH1 3436 0.056 0.2 YES
22 ITCH ITCH ITCH 3504 0.054 0.2 YES
23 XIAP XIAP XIAP 3520 0.054 0.21 YES
24 RCHY1 RCHY1 RCHY1 3564 0.053 0.22 YES
25 UBE3C UBE3C UBE3C 3616 0.052 0.22 YES
26 UBA2 UBA2 UBA2 3646 0.052 0.23 YES
27 RFWD2 RFWD2 RFWD2 3731 0.05 0.23 YES
28 HERC2 HERC2 HERC2 3733 0.05 0.24 YES
29 UBR5 UBR5 UBR5 3907 0.048 0.24 YES
30 UBA3 UBA3 UBA3 3926 0.048 0.25 YES
31 UBE2K UBE2K UBE2K 4066 0.046 0.25 YES
32 UBE2G1 UBE2G1 UBE2G1 4307 0.043 0.24 YES
33 CDC26 CDC26 CDC26 4415 0.041 0.24 YES
34 UBE2W UBE2W UBE2W 4519 0.04 0.24 YES
35 UBE2Q1 UBE2Q1 UBE2Q1 4554 0.04 0.25 YES
36 HERC1 HERC1 HERC1 4565 0.04 0.25 YES
37 BIRC2 BIRC2 BIRC2 4715 0.038 0.25 YES
38 UBE2J1 UBE2J1 UBE2J1 4893 0.036 0.25 YES
39 BIRC6 BIRC6 BIRC6 4957 0.035 0.25 YES
40 UBE3A UBE3A UBE3A 4993 0.034 0.25 YES
41 UBE2J2 UBE2J2 UBE2J2 5024 0.034 0.26 YES
42 UBE2H UBE2H UBE2H 5063 0.034 0.26 YES
43 KEAP1 KEAP1 KEAP1 5136 0.033 0.26 YES
44 HUWE1 HUWE1 HUWE1 5242 0.032 0.26 YES
45 UBE2R2 UBE2R2 UBE2R2 5297 0.031 0.26 YES
46 FBXO4 FBXO4 FBXO4 5360 0.03 0.26 YES
47 CUL5 CUL5 CUL5 5388 0.03 0.27 YES
48 PIAS4 PIAS4 PIAS4 5433 0.03 0.27 YES
49 UBE2N UBE2N UBE2N 5533 0.028 0.27 YES
50 UBE2Z UBE2Z UBE2Z 5621 0.028 0.27 YES
51 FANCL FANCL FANCL 5719 0.026 0.27 YES
52 UBE2S UBE2S UBE2S 5736 0.026 0.27 YES
53 KLHL9 KLHL9 KLHL9 5760 0.026 0.28 YES
54 HERC4 HERC4 HERC4 5851 0.025 0.27 YES
55 MGRN1 MGRN1 MGRN1 5901 0.025 0.28 YES
56 UBE2O UBE2O UBE2O 5951 0.024 0.28 YES
57 FBXW8 FBXW8 FBXW8 6101 0.022 0.27 YES
58 FBXW11 FBXW11 FBXW11 6177 0.022 0.27 YES
59 TRIP12 TRIP12 TRIP12 6194 0.022 0.28 YES
60 TCEB1 TCEB1 TCEB1 6253 0.021 0.28 YES
61 DDB1 DDB1 DDB1 6275 0.021 0.28 YES
62 SYVN1 SYVN1 SYVN1 6316 0.02 0.28 YES
63 ANAPC10 ANAPC10 ANAPC10 6362 0.02 0.28 YES
64 UBE2A UBE2A UBE2A 6434 0.019 0.28 NO
65 PIAS2 PIAS2 PIAS2 6522 0.018 0.28 NO
66 UBE2E1 UBE2E1 UBE2E1 6843 0.015 0.26 NO
67 UBE2D2 UBE2D2 UBE2D2 6876 0.015 0.26 NO
68 UBE2Q2 UBE2Q2 UBE2Q2 7044 0.013 0.26 NO
69 UBA6 UBA6 UBA6 7102 0.013 0.25 NO
70 UBE2D3 UBE2D3 UBE2D3 7208 0.012 0.25 NO
71 UBE4B UBE4B UBE4B 7322 0.011 0.25 NO
72 CUL2 CUL2 CUL2 7509 0.0088 0.24 NO
73 PRPF19 PRPF19 PRPF19 7672 0.0074 0.23 NO
74 CUL3 CUL3 CUL3 7731 0.0066 0.23 NO
75 CDC16 CDC16 CDC16 7783 0.0062 0.23 NO
76 CDC27 CDC27 CDC27 7831 0.0057 0.22 NO
77 DET1 DET1 DET1 7934 0.0048 0.22 NO
78 NEDD4L NEDD4L NEDD4L 8027 0.0038 0.22 NO
79 SKP1 SKP1 SKP1 8033 0.0038 0.22 NO
80 UBE2E2 UBE2E2 UBE2E2 8079 0.0034 0.21 NO
81 WWP1 WWP1 WWP1 8121 0.0029 0.21 NO
82 ANAPC7 ANAPC7 ANAPC7 8235 0.0018 0.2 NO
83 HERC3 HERC3 HERC3 8284 0.0013 0.2 NO
84 ANAPC5 ANAPC5 ANAPC5 8339 0.00064 0.2 NO
85 MAP3K1 MAP3K1 MAP3K1 8381 0.00016 0.2 NO
86 BIRC3 BIRC3 BIRC3 8669 -0.0027 0.18 NO
87 CUL4A CUL4A CUL4A 8736 -0.0034 0.18 NO
88 UBE4A UBE4A UBE4A 8807 -0.0042 0.18 NO
89 MDM2 MDM2 MDM2 9084 -0.0068 0.16 NO
90 PARK2 PARK2 PARK2 9107 -0.0071 0.16 NO
91 UBA1 UBA1 UBA1 9118 -0.0071 0.16 NO
92 TRAF6 TRAF6 TRAF6 9189 -0.0079 0.16 NO
93 ANAPC2 ANAPC2 ANAPC2 9235 -0.0084 0.16 NO
94 UBE2D1 UBE2D1 UBE2D1 9468 -0.011 0.15 NO
95 UBE2M UBE2M UBE2M 9486 -0.012 0.15 NO
96 RBX1 RBX1 RBX1 9500 -0.012 0.15 NO
97 UBE2B UBE2B UBE2B 9502 -0.012 0.15 NO
98 RNF7 RNF7 RNF7 9580 -0.012 0.15 NO
99 PML PML PML 9672 -0.014 0.15 NO
100 SMURF2 SMURF2 SMURF2 9928 -0.017 0.14 NO
101 FBXW7 FBXW7 FBXW7 9933 -0.017 0.14 NO
102 PPIL2 PPIL2 PPIL2 10055 -0.018 0.14 NO
103 UBE3B UBE3B UBE3B 10113 -0.019 0.14 NO
104 CUL1 CUL1 CUL1 10282 -0.021 0.13 NO
105 STUB1 STUB1 STUB1 10350 -0.022 0.13 NO
106 ANAPC11 ANAPC11 ANAPC11 10395 -0.023 0.13 NO
107 PIAS1 PIAS1 PIAS1 10518 -0.024 0.13 NO
108 ANAPC4 ANAPC4 ANAPC4 10571 -0.025 0.13 NO
109 AIRE AIRE AIRE 10577 -0.025 0.13 NO
110 UBOX5 UBOX5 UBOX5 10589 -0.026 0.14 NO
111 UBE2F UBE2F UBE2F 10612 -0.026 0.14 NO
112 FZR1 FZR1 FZR1 10614 -0.026 0.14 NO
113 TCEB2 TCEB2 TCEB2 10693 -0.027 0.14 NO
114 UBE2L3 UBE2L3 UBE2L3 11042 -0.032 0.13 NO
115 CBL CBL CBL 11158 -0.033 0.13 NO
116 SAE1 SAE1 SAE1 11237 -0.034 0.13 NO
117 UBE2L6 UBE2L6 UBE2L6 11240 -0.035 0.14 NO
118 UBE2G2 UBE2G2 UBE2G2 11310 -0.036 0.14 NO
119 CDC23 CDC23 CDC23 11368 -0.037 0.14 NO
120 CDC34 CDC34 CDC34 11758 -0.043 0.13 NO
121 ANAPC13 ANAPC13 ANAPC13 11987 -0.047 0.12 NO
122 UBE2D4 UBE2D4 UBE2D4 12053 -0.049 0.13 NO
123 SMURF1 SMURF1 SMURF1 13193 -0.075 0.076 NO
124 FBXO2 FBXO2 FBXO2 13889 -0.094 0.054 NO
125 RHOBTB2 RHOBTB2 RHOBTB2 14320 -0.11 0.048 NO
126 DDB2 DDB2 DDB2 14617 -0.12 0.052 NO
127 UBE2QL1 UBE2QL1 UBE2QL1 14689 -0.12 0.068 NO
128 NEDD4 NEDD4 NEDD4 14711 -0.12 0.087 NO
129 SOCS1 SOCS1 SOCS1 15061 -0.14 0.091 NO
130 UBA7 UBA7 UBA7 15242 -0.14 0.1 NO
131 KLHL13 KLHL13 KLHL13 16091 -0.18 0.088 NO
132 SOCS3 SOCS3 SOCS3 16198 -0.19 0.11 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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

Table 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 SNRNP40 SNRNP40 SNRNP40 1228 0.13 -0.03 YES
2 CDC40 CDC40 CDC40 2109 0.087 -0.054 YES
3 SNRPB2 SNRPB2 SNRPB2 2580 0.073 -0.06 YES
4 THOC2 THOC2 THOC2 2598 0.072 -0.04 YES
5 AQR AQR AQR 2856 0.067 -0.036 YES
6 PRPF3 PRPF3 PRPF3 3417 0.056 -0.051 YES
7 SNRPA1 SNRPA1 SNRPA1 3551 0.054 -0.043 YES
8 DHX15 DHX15 DHX15 3571 0.053 -0.029 YES
9 PRPF40A PRPF40A PRPF40A 3610 0.053 -0.016 YES
10 RBMX RBMX RBMX 3626 0.052 -0.0022 YES
11 THOC3 THOC3 THOC3 3659 0.052 0.011 YES
12 SNRPE SNRPE SNRPE 3696 0.051 0.023 YES
13 TRA2A TRA2A TRA2A 3729 0.051 0.036 YES
14 SNRPF SNRPF SNRPF 3837 0.049 0.044 YES
15 SFRS1 SFRS1 SFRS1 4105 0.045 0.042 YES
16 SNRPD3 SNRPD3 SNRPD3 4121 0.045 0.054 YES
17 SNRPG SNRPG SNRPG 4156 0.045 0.064 YES
18 PRPF38A PRPF38A PRPF38A 4196 0.044 0.075 YES
19 HSPA8 HSPA8 HSPA8 4349 0.042 0.078 YES
20 NCBP1 NCBP1 NCBP1 4363 0.042 0.089 YES
21 SF3B3 SF3B3 SF3B3 4556 0.04 0.09 YES
22 SNRNP200 SNRNP200 SNRNP200 4585 0.039 0.1 YES
23 SFRS6 SFRS6 SFRS6 4592 0.039 0.11 YES
24 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 4635 0.039 0.12 YES
25 U2AF2 U2AF2 U2AF2 4662 0.038 0.13 YES
26 THOC4 THOC4 THOC4 4675 0.038 0.14 YES
27 DDX46 DDX46 DDX46 4732 0.038 0.15 YES
28 HNRNPK HNRNPK HNRNPK 4740 0.038 0.16 YES
29 RBM8A RBM8A RBM8A 4841 0.036 0.16 YES
30 SF3B14 SF3B14 SF3B14 4931 0.035 0.17 YES
31 ISY1 ISY1 ISY1 4932 0.035 0.18 YES
32 SF3B1 SF3B1 SF3B1 4966 0.035 0.18 YES
33 HNRNPC HNRNPC HNRNPC 4992 0.034 0.19 YES
34 SFRS2 SFRS2 SFRS2 5070 0.034 0.2 YES
35 SFRS13A SFRS13A SFRS13A 5126 0.033 0.2 YES
36 HNRNPU HNRNPU HNRNPU 5143 0.033 0.21 YES
37 SNRPD1 SNRPD1 SNRPD1 5294 0.031 0.21 YES
38 CDC5L CDC5L CDC5L 5394 0.03 0.22 YES
39 SFRS9 SFRS9 SFRS9 5416 0.03 0.22 YES
40 SMNDC1 SMNDC1 SMNDC1 5452 0.029 0.23 YES
41 PRPF4 PRPF4 PRPF4 5472 0.029 0.24 YES
42 SNRPB SNRPB SNRPB 5493 0.029 0.24 YES
43 LSM2 LSM2 LSM2 5504 0.029 0.25 YES
44 SF3A2 SF3A2 SF3A2 5557 0.028 0.26 YES
45 CHERP CHERP CHERP 5573 0.028 0.26 YES
46 PPIH PPIH PPIH 5616 0.028 0.27 YES
47 SNRNP27 SNRNP27 SNRNP27 5632 0.027 0.28 YES
48 DDX42 DDX42 DDX42 5633 0.027 0.28 YES
49 SLU7 SLU7 SLU7 5666 0.027 0.29 YES
50 HNRNPA1 HNRNPA1 HNRNPA1 5676 0.027 0.3 YES
51 RBM22 RBM22 RBM22 5825 0.025 0.3 YES
52 THOC1 THOC1 THOC1 5839 0.025 0.3 YES
53 TCERG1 TCERG1 TCERG1 5943 0.024 0.3 YES
54 SYF2 SYF2 SYF2 6003 0.023 0.31 YES
55 BCAS2 BCAS2 BCAS2 6028 0.023 0.31 YES
56 NAA38 NAA38 NAA38 6100 0.023 0.31 YES
57 MAGOH MAGOH MAGOH 6104 0.022 0.32 YES
58 PRPF8 PRPF8 PRPF8 6326 0.02 0.31 YES
59 SF3B4 SF3B4 SF3B4 6352 0.02 0.32 YES
60 PRPF6 PRPF6 PRPF6 6366 0.02 0.32 YES
61 U2AF1 U2AF1 U2AF1 6438 0.019 0.32 YES
62 SNRPD2 SNRPD2 SNRPD2 6569 0.018 0.32 YES
63 EIF4A3 EIF4A3 EIF4A3 6683 0.017 0.32 YES
64 RBM17 RBM17 RBM17 6728 0.016 0.32 YES
65 PRPF38B PRPF38B PRPF38B 6752 0.016 0.33 YES
66 PLRG1 PLRG1 PLRG1 6789 0.016 0.33 YES
67 RBM25 RBM25 RBM25 6796 0.016 0.33 YES
68 PQBP1 PQBP1 PQBP1 6866 0.015 0.33 YES
69 SF3A3 SF3A3 SF3A3 6886 0.015 0.34 YES
70 BAT1 BAT1 BAT1 6895 0.015 0.34 YES
71 PCBP1 PCBP1 PCBP1 6910 0.015 0.34 YES
72 SNRNP70 SNRNP70 SNRNP70 6916 0.014 0.35 YES
73 SNW1 SNW1 SNW1 6946 0.014 0.35 YES
74 SNRPC SNRPC SNRPC 6963 0.014 0.35 YES
75 SFRS3 SFRS3 SFRS3 7008 0.014 0.36 YES
76 PUF60 PUF60 PUF60 7091 0.013 0.35 YES
77 CWC15 CWC15 CWC15 7182 0.012 0.35 YES
78 SF3B2 SF3B2 SF3B2 7225 0.012 0.35 YES
79 USP39 USP39 USP39 7251 0.011 0.36 YES
80 DDX23 DDX23 DDX23 7258 0.011 0.36 YES
81 PHF5A PHF5A PHF5A 7289 0.011 0.36 YES
82 SF3A1 SF3A1 SF3A1 7308 0.011 0.36 YES
83 SR140 SR140 SR140 7348 0.01 0.36 YES
84 DDX5 DDX5 DDX5 7416 0.0097 0.36 YES
85 CRNKL1 CRNKL1 CRNKL1 7447 0.0094 0.36 YES
86 PRPF19 PRPF19 PRPF19 7672 0.0074 0.35 NO
87 HNRNPA3 HNRNPA3 HNRNPA3 7759 0.0064 0.35 NO
88 DHX8 DHX8 DHX8 7816 0.0058 0.35 NO
89 HNRNPM HNRNPM HNRNPM 8015 0.0039 0.34 NO
90 SFRS7 SFRS7 SFRS7 8073 0.0034 0.34 NO
91 LSM7 LSM7 LSM7 8081 0.0033 0.34 NO
92 ACIN1 ACIN1 ACIN1 8196 0.0023 0.33 NO
93 EFTUD2 EFTUD2 EFTUD2 8220 0.002 0.33 NO
94 PRPF18 PRPF18 PRPF18 8279 0.0014 0.33 NO
95 LSM4 LSM4 LSM4 8387 0.0001 0.32 NO
96 TRA2B TRA2B TRA2B 8493 -0.00095 0.32 NO
97 SNRPA SNRPA SNRPA 8624 -0.0022 0.31 NO
98 SFRS5 SFRS5 SFRS5 8723 -0.0032 0.3 NO
99 DHX16 DHX16 DHX16 8752 -0.0035 0.3 NO
100 LSM5 LSM5 LSM5 8854 -0.0045 0.3 NO
101 MAGOHB MAGOHB MAGOHB 8910 -0.0051 0.3 NO
102 WBP11 WBP11 WBP11 8944 -0.0054 0.3 NO
103 LSM3 LSM3 LSM3 8965 -0.0057 0.3 NO
104 PRPF31 PRPF31 PRPF31 8977 -0.0058 0.3 NO
105 XAB2 XAB2 XAB2 8980 -0.0058 0.3 NO
106 PPIE PPIE PPIE 9021 -0.0062 0.3 NO
107 SFRS4 SFRS4 SFRS4 9149 -0.0075 0.3 NO
108 SFRS2B SFRS2B SFRS2B 9185 -0.0079 0.3 NO
109 PPIL1 PPIL1 PPIL1 9295 -0.0093 0.29 NO
110 CTNNBL1 CTNNBL1 CTNNBL1 9432 -0.011 0.29 NO
111 TXNL4A TXNL4A TXNL4A 9636 -0.013 0.28 NO
112 LSM6 LSM6 LSM6 9721 -0.014 0.28 NO
113 PRPF40B PRPF40B PRPF40B 9806 -0.015 0.28 NO
114 SART1 SART1 SART1 9924 -0.017 0.28 NO
115 ZMAT2 ZMAT2 ZMAT2 9957 -0.017 0.28 NO
116 NHP2L1 NHP2L1 NHP2L1 10180 -0.02 0.27 NO
117 BUD31 BUD31 BUD31 10267 -0.021 0.28 NO
118 DHX38 DHX38 DHX38 10285 -0.022 0.28 NO
119 HSPA6 HSPA6 HSPA6 10348 -0.022 0.28 NO
120 HSPA1L HSPA1L HSPA1L 10635 -0.026 0.28 NO
121 CCDC12 CCDC12 CCDC12 11000 -0.031 0.26 NO
122 HSPA1B HSPA1B HSPA1B 11415 -0.037 0.25 NO
123 SF3B5 SF3B5 SF3B5 11618 -0.041 0.25 NO
124 HSPA1A HSPA1A HSPA1A 12864 -0.067 0.2 NO
125 HSPA2 HSPA2 HSPA2 17779 -0.34 0.026 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 PENTOSE PHOSPHATE PATHWAY.

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

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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 CDC45 CDC45 CDC45 354 0.26 0.0083 YES
2 BUB1B BUB1B BUB1B 355 0.26 0.036 YES
3 CCNE2 CCNE2 CCNE2 374 0.26 0.062 YES
4 CDKN2A CDKN2A CDKN2A 406 0.24 0.086 YES
5 TTK TTK TTK 453 0.23 0.11 YES
6 CDC20 CDC20 CDC20 527 0.22 0.13 YES
7 SMC1B SMC1B SMC1B 571 0.21 0.15 YES
8 CCNB2 CCNB2 CCNB2 621 0.2 0.16 YES
9 BUB1 BUB1 BUB1 653 0.2 0.18 YES
10 ESPL1 ESPL1 ESPL1 764 0.18 0.2 YES
11 CDC25C CDC25C CDC25C 783 0.18 0.21 YES
12 PLK1 PLK1 PLK1 853 0.17 0.23 YES
13 CCNA2 CCNA2 CCNA2 856 0.17 0.24 YES
14 SKP2 SKP2 SKP2 896 0.16 0.26 YES
15 E2F3 E2F3 E2F3 1047 0.15 0.27 YES
16 ORC1L ORC1L ORC1L 1062 0.15 0.28 YES
17 HDAC1 HDAC1 HDAC1 1276 0.13 0.28 YES
18 CDK1 CDK1 CDK1 1344 0.12 0.29 YES
19 ANAPC1 ANAPC1 ANAPC1 1486 0.11 0.3 YES
20 E2F2 E2F2 E2F2 1535 0.11 0.31 YES
21 HDAC2 HDAC2 HDAC2 1552 0.11 0.32 YES
22 MAD2L1 MAD2L1 MAD2L1 1606 0.11 0.33 YES
23 CCNB1 CCNB1 CCNB1 1610 0.11 0.34 YES
24 E2F5 E2F5 E2F5 1733 0.1 0.34 YES
25 ORC6L ORC6L ORC6L 1791 0.099 0.35 YES
26 ATR ATR ATR 1908 0.095 0.35 YES
27 ORC3L ORC3L ORC3L 2097 0.088 0.35 YES
28 GSK3B GSK3B GSK3B 2217 0.084 0.35 YES
29 PKMYT1 PKMYT1 PKMYT1 2226 0.083 0.36 YES
30 TFDP1 TFDP1 TFDP1 2258 0.082 0.37 YES
31 MCM2 MCM2 MCM2 2315 0.08 0.37 YES
32 PTTG1 PTTG1 PTTG1 2342 0.079 0.38 YES
33 WEE1 WEE1 WEE1 2451 0.076 0.38 YES
34 CDK7 CDK7 CDK7 2968 0.064 0.36 YES
35 STAG2 STAG2 STAG2 2975 0.064 0.37 YES
36 CDC6 CDC6 CDC6 3225 0.059 0.36 YES
37 MYC MYC MYC 3228 0.059 0.37 YES
38 ORC2L ORC2L ORC2L 3229 0.059 0.37 YES
39 ORC4L ORC4L ORC4L 3313 0.058 0.37 YES
40 MCM4 MCM4 MCM4 3347 0.057 0.38 YES
41 PRKDC PRKDC PRKDC 3350 0.057 0.38 YES
42 CDK4 CDK4 CDK4 3438 0.056 0.39 YES
43 CHEK2 CHEK2 CHEK2 3456 0.055 0.39 YES
44 MCM6 MCM6 MCM6 3490 0.055 0.39 YES
45 SMC3 SMC3 SMC3 3636 0.052 0.39 YES
46 RAD21 RAD21 RAD21 3685 0.051 0.4 YES
47 BUB3 BUB3 BUB3 3737 0.05 0.4 YES
48 ATM ATM ATM 3900 0.048 0.39 NO
49 CDC26 CDC26 CDC26 4415 0.041 0.37 NO
50 CDC7 CDC7 CDC7 4689 0.038 0.36 NO
51 E2F1 E2F1 E2F1 4748 0.038 0.36 NO
52 SMAD2 SMAD2 SMAD2 4771 0.037 0.36 NO
53 EP300 EP300 EP300 5042 0.034 0.35 NO
54 YWHAQ YWHAQ YWHAQ 5280 0.031 0.34 NO
55 CDC14A CDC14A CDC14A 5332 0.031 0.34 NO
56 RBL1 RBL1 RBL1 5395 0.03 0.34 NO
57 MCM7 MCM7 MCM7 5428 0.03 0.34 NO
58 PCNA PCNA PCNA 5807 0.026 0.32 NO
59 YWHAZ YWHAZ YWHAZ 5905 0.025 0.32 NO
60 ANAPC10 ANAPC10 ANAPC10 6362 0.02 0.3 NO
61 RB1 RB1 RB1 6369 0.02 0.3 NO
62 YWHAB YWHAB YWHAB 6402 0.019 0.3 NO
63 ABL1 ABL1 ABL1 6484 0.019 0.3 NO
64 CCNB3 CCNB3 CCNB3 6507 0.018 0.3 NO
65 CREBBP CREBBP CREBBP 6523 0.018 0.3 NO
66 YWHAE YWHAE YWHAE 6553 0.018 0.3 NO
67 STAG1 STAG1 STAG1 6769 0.016 0.29 NO
68 SMC1A SMC1A SMC1A 7023 0.013 0.28 NO
69 YWHAG YWHAG YWHAG 7065 0.013 0.28 NO
70 ORC5L ORC5L ORC5L 7188 0.012 0.27 NO
71 MCM3 MCM3 MCM3 7227 0.012 0.27 NO
72 CDK2 CDK2 CDK2 7428 0.0096 0.26 NO
73 CDC16 CDC16 CDC16 7783 0.0062 0.24 NO
74 CDC27 CDC27 CDC27 7831 0.0057 0.24 NO
75 CCNH CCNH CCNH 7937 0.0048 0.23 NO
76 SKP1 SKP1 SKP1 8033 0.0038 0.23 NO
77 CHEK1 CHEK1 CHEK1 8074 0.0034 0.23 NO
78 ANAPC7 ANAPC7 ANAPC7 8235 0.0018 0.22 NO
79 CDKN1B CDKN1B CDKN1B 8258 0.0016 0.22 NO
80 ANAPC5 ANAPC5 ANAPC5 8339 0.00064 0.21 NO
81 ZBTB17 ZBTB17 ZBTB17 8651 -0.0026 0.2 NO
82 E2F4 E2F4 E2F4 8747 -0.0034 0.19 NO
83 RBL2 RBL2 RBL2 8837 -0.0044 0.19 NO
84 MDM2 MDM2 MDM2 9084 -0.0068 0.17 NO
85 TP53 TP53 TP53 9093 -0.0069 0.18 NO
86 MCM5 MCM5 MCM5 9170 -0.0078 0.17 NO
87 ANAPC2 ANAPC2 ANAPC2 9235 -0.0084 0.17 NO
88 TFDP2 TFDP2 TFDP2 9458 -0.011 0.16 NO
89 WEE2 WEE2 WEE2 9463 -0.011 0.16 NO
90 RBX1 RBX1 RBX1 9500 -0.012 0.16 NO
91 MAD2L2 MAD2L2 MAD2L2 9551 -0.012 0.16 NO
92 CCND3 CCND3 CCND3 9670 -0.014 0.15 NO
93 CUL1 CUL1 CUL1 10282 -0.021 0.12 NO
94 ANAPC11 ANAPC11 ANAPC11 10395 -0.023 0.12 NO
95 ANAPC4 ANAPC4 ANAPC4 10571 -0.025 0.11 NO
96 FZR1 FZR1 FZR1 10614 -0.026 0.11 NO
97 CDKN2B CDKN2B CDKN2B 10794 -0.028 0.1 NO
98 CCNE1 CCNE1 CCNE1 10886 -0.029 0.1 NO
99 SMAD3 SMAD3 SMAD3 11051 -0.032 0.095 NO
100 TGFB1 TGFB1 TGFB1 11196 -0.034 0.091 NO
101 CDC23 CDC23 CDC23 11368 -0.037 0.085 NO
102 SMAD4 SMAD4 SMAD4 11397 -0.037 0.088 NO
103 CDC25B CDC25B CDC25B 11613 -0.04 0.08 NO
104 YWHAH YWHAH YWHAH 11867 -0.045 0.071 NO
105 ANAPC13 ANAPC13 ANAPC13 11987 -0.047 0.069 NO
106 PTTG2 PTTG2 PTTG2 12459 -0.057 0.049 NO
107 CCND1 CCND1 CCND1 12651 -0.062 0.045 NO
108 SFN SFN SFN 13070 -0.072 0.03 NO
109 GADD45A GADD45A GADD45A 13553 -0.084 0.012 NO
110 CDC25A CDC25A CDC25A 13570 -0.085 0.02 NO
111 GADD45G GADD45G GADD45G 13960 -0.097 0.0089 NO
112 MAD1L1 MAD1L1 MAD1L1 14040 -0.099 0.015 NO
113 TGFB2 TGFB2 TGFB2 14184 -0.1 0.018 NO
114 CCNA1 CCNA1 CCNA1 14928 -0.13 -0.0088 NO
115 CDKN2D CDKN2D CDKN2D 15153 -0.14 -0.0063 NO
116 CCND2 CCND2 CCND2 15429 -0.15 -0.0054 NO
117 CDC14B CDC14B CDC14B 15556 -0.16 0.0043 NO
118 GADD45B GADD45B GADD45B 15777 -0.17 0.0099 NO
119 CDKN1C CDKN1C CDKN1C 16092 -0.18 0.012 NO
120 CDKN2C CDKN2C CDKN2C 16217 -0.19 0.025 NO
121 CDKN1A CDKN1A CDKN1A 16223 -0.19 0.045 NO
122 CDK6 CDK6 CDK6 17609 -0.31 0.0014 NO
123 TGFB3 TGFB3 TGFB3 17709 -0.32 0.03 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 N GLYCAN BIOSYNTHESIS.

Figure S54.  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 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 TAF4B TAF4B TAF4B 1036 0.15 0.028 YES
2 TAF1L TAF1L TAF1L 1350 0.12 0.082 YES
3 GTF2H2 GTF2H2 GTF2H2 1645 0.11 0.13 YES
4 TAF2 TAF2 TAF2 2264 0.082 0.14 YES
5 TAF4 TAF4 TAF4 2418 0.077 0.18 YES
6 TAF1 TAF1 TAF1 2428 0.077 0.22 YES
7 GTF2E1 GTF2E1 GTF2E1 2441 0.076 0.26 YES
8 GTF2H3 GTF2H3 GTF2H3 2505 0.074 0.3 YES
9 STON1 STON1 STON1 2707 0.07 0.33 YES
10 GTF2I GTF2I GTF2I 3585 0.053 0.31 YES
11 GTF2IRD1 GTF2IRD1 GTF2IRD1 3675 0.051 0.34 YES
12 TAF9 TAF9 TAF9 4325 0.042 0.32 YES
13 GTF2A1L GTF2A1L GTF2A1L 4406 0.042 0.34 YES
14 TAF7 TAF7 TAF7 4618 0.039 0.36 YES
15 GTF2A1 GTF2A1 GTF2A1 4652 0.039 0.38 YES
16 TAF5L TAF5L TAF5L 5020 0.034 0.38 NO
17 GTF2A2 GTF2A2 GTF2A2 5815 0.026 0.35 NO
18 GTF2H1 GTF2H1 GTF2H1 5835 0.025 0.36 NO
19 TAF9B TAF9B TAF9B 5911 0.025 0.37 NO
20 TAF6L TAF6L TAF6L 6325 0.02 0.36 NO
21 GTF2E2 GTF2E2 GTF2E2 7326 0.011 0.31 NO
22 TAF11 TAF11 TAF11 7452 0.0093 0.31 NO
23 GTF2H4 GTF2H4 GTF2H4 7900 0.0051 0.29 NO
24 TAF5 TAF5 TAF5 7948 0.0047 0.29 NO
25 TBP TBP TBP 8044 0.0037 0.28 NO
26 TAF12 TAF12 TAF12 9030 -0.0063 0.23 NO
27 GTF2F2 GTF2F2 GTF2F2 9147 -0.0074 0.23 NO
28 TAF10 TAF10 TAF10 9234 -0.0084 0.23 NO
29 GTF2F1 GTF2F1 GTF2F1 9714 -0.014 0.21 NO
30 TAF13 TAF13 TAF13 9810 -0.015 0.22 NO
31 TAF6 TAF6 TAF6 9958 -0.017 0.22 NO
32 GTF2B GTF2B GTF2B 11880 -0.045 0.14 NO
33 TBPL1 TBPL1 TBPL1 14566 -0.12 0.059 NO
34 TAF7L TAF7L TAF7L 17102 -0.25 0.063 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 AMINOACYL TRNA BIOSYNTHESIS.

Figure S56.  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 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 ARHGDIB ARHGDIB ARHGDIB 704 0.19 0.064 YES
2 CASP2 CASP2 CASP2 875 0.16 0.14 YES
3 LMNB1 LMNB1 LMNB1 979 0.15 0.22 YES
4 MAPK8 MAPK8 MAPK8 1388 0.12 0.27 YES
5 DFFB DFFB DFFB 2233 0.083 0.27 YES
6 PARP1 PARP1 PARP1 2727 0.07 0.28 YES
7 PRKDC PRKDC PRKDC 3350 0.057 0.27 YES
8 MAP3K7 MAP3K7 MAP3K7 3383 0.056 0.3 YES
9 CASP8 CASP8 CASP8 3604 0.053 0.32 YES
10 CASP3 CASP3 CASP3 3750 0.05 0.34 YES
11 LMNB2 LMNB2 LMNB2 3889 0.048 0.36 YES
12 MADD MADD MADD 6156 0.022 0.25 NO
13 RB1 RB1 RB1 6369 0.02 0.25 NO
14 PAK2 PAK2 PAK2 7430 0.0096 0.19 NO
15 PAK1 PAK1 PAK1 7676 0.0074 0.18 NO
16 SPTAN1 SPTAN1 SPTAN1 8360 0.00042 0.15 NO
17 DFFA DFFA DFFA 8378 0.0002 0.14 NO
18 MAP3K1 MAP3K1 MAP3K1 8381 0.00016 0.14 NO
19 BAG4 BAG4 BAG4 10688 -0.027 0.033 NO
20 CRADD CRADD CRADD 10861 -0.029 0.04 NO
21 FADD FADD FADD 11208 -0.034 0.04 NO
22 RIPK1 RIPK1 RIPK1 11675 -0.041 0.037 NO
23 TRADD TRADD TRADD 11862 -0.045 0.052 NO
24 MAP2K4 MAP2K4 MAP2K4 12800 -0.065 0.036 NO
25 TNFRSF1A TNFRSF1A TNFRSF1A 13268 -0.077 0.052 NO
26 LMNA LMNA LMNA 13935 -0.096 0.068 NO
27 JUN JUN JUN 13978 -0.097 0.12 NO
28 TNF TNF TNF 16582 -0.21 0.092 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 RIBOSOME.

Figure S58.  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 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 MYT1 MYT1 MYT1 41 0.53 0.22 YES
2 CDC25C CDC25C CDC25C 783 0.18 0.25 YES
3 CDK1 CDK1 CDK1 1344 0.12 0.27 YES
4 CCNB1 CCNB1 CCNB1 1610 0.11 0.3 YES
5 PAQR5 PAQR5 PAQR5 2138 0.086 0.31 YES
6 PRKAR1B PRKAR1B PRKAR1B 2201 0.084 0.34 YES
7 GNAI1 GNAI1 GNAI1 2949 0.065 0.32 NO
8 ACTR3 ACTR3 ACTR3 4694 0.038 0.24 NO
9 PRKACB PRKACB PRKACB 5285 0.031 0.23 NO
10 ARPC3 ARPC3 ARPC3 5317 0.031 0.24 NO
11 GNB1 GNB1 GNB1 5320 0.031 0.25 NO
12 PRKAR2A PRKAR2A PRKAR2A 6134 0.022 0.21 NO
13 RPS6KA1 RPS6KA1 RPS6KA1 6411 0.019 0.21 NO
14 ACTR2 ACTR2 ACTR2 6655 0.017 0.2 NO
15 GNAS GNAS GNAS 6880 0.015 0.2 NO
16 ARPC5 ARPC5 ARPC5 7057 0.013 0.19 NO
17 PRKAR1A PRKAR1A PRKAR1A 7168 0.012 0.19 NO
18 ARPC1B ARPC1B ARPC1B 9369 -0.01 0.073 NO
19 ARPC1A ARPC1A ARPC1A 9414 -0.011 0.075 NO
20 ARPC2 ARPC2 ARPC2 9443 -0.011 0.078 NO
21 MAPK1 MAPK1 MAPK1 9459 -0.011 0.082 NO
22 SRC SRC SRC 9754 -0.015 0.072 NO
23 ARPC4 ARPC4 ARPC4 9992 -0.018 0.066 NO
24 CAP1 CAP1 CAP1 10773 -0.028 0.035 NO
25 PIN1 PIN1 PIN1 11370 -0.037 0.017 NO
26 HRAS HRAS HRAS 11878 -0.045 0.0084 NO
27 MAPK3 MAPK3 MAPK3 12256 -0.053 0.0098 NO
28 PAQR7 PAQR7 PAQR7 12476 -0.058 0.022 NO
29 PRKAR2B PRKAR2B PRKAR2B 14218 -0.1 -0.03 NO
30 PGR PGR PGR 17092 -0.25 -0.084 NO
31 ACTA1 ACTA1 ACTA1 17870 -0.36 0.021 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 RNA DEGRADATION.

Figure S60.  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

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 = PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = PRAD-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)