GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UCEC-TP
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C10Z72DK
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 UCEC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C10Z72DK
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 UCEC-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: 545
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 ] 235
pheno.type: 2 - 3 :[ clus2 ] 154
pheno.type: 3 - 3 :[ clus3 ] 156

For the expression subtypes of 18545 genes in 546 samples, GSEA found enriched gene sets in each cluster using 545 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA CHREBP2 PATHWAY, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RNA DEGRADATION, KEGG BASAL TRANSCRIPTION FACTORS, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG PROTEASOME

    • And common core enriched genes are MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, PCNA, POLD1, RPA4, DNA2

  • clus2

    • Top enriched gene sets are BIOCARTA ALK PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA P38MAPK PATHWAY, BIOCARTA WNT PATHWAY, KEGG FATTY ACID METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG LINOLEIC ACID METABOLISM, KEGG SPHINGOLIPID METABOLISM

    • And common core enriched genes are CCND1, FZD1, LEF1, JMJD7-PLA2G4B, PLA2G2C, PLA2G3, PLA2G4A, PLA2G5, WIF1, TIRAP

  • clus3

    • Top enriched gene sets are BIOCARTA FMLP PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG BUTANOATE METABOLISM

    • And common core enriched genes are ADH1A, ADH1B, ADH1C, ADH4, ADH6, ADH7, GSTA1, GSTA2, GSTA3, GSTM1

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 G1 PATHWAY 27 genes.ES.table 0.44 1.3 0.17 1 0.99 0.37 0.18 0.3 0.86 0.43
BIOCARTA MPR PATHWAY 32 genes.ES.table 0.35 1.2 0.18 1 1 0.38 0.26 0.28 0.91 0.44
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.33 1.2 0.21 0.94 1 0.2 0.13 0.17 0.83 0.38
BIOCARTA CHREBP2 PATHWAY 40 genes.ES.table 0.33 1.3 0.12 1 0.98 0.12 0.11 0.11 0.95 0.47
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.31 1.2 0.28 1 1 0.57 0.43 0.33 0.93 0.45
KEGG RNA DEGRADATION 55 genes.ES.table 0.34 1.4 0.16 1 0.95 0.36 0.28 0.26 0.83 0.43
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.45 1.4 0.14 1 0.94 0.41 0.24 0.31 0.89 0.46
KEGG DNA REPLICATION 35 genes.ES.table 0.65 1.7 0.061 1 0.5 0.8 0.31 0.55 0 0.32
KEGG SPLICEOSOME 125 genes.ES.table 0.36 1.5 0.13 0.96 0.82 0.65 0.42 0.38 0.61 0.36
KEGG PROTEASOME 42 genes.ES.table 0.43 1.3 0.25 1 0.99 0.74 0.46 0.4 0.95 0.47
genes ES table in pathway: BIOCARTA G1 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 RFC4 RFC4 RFC4 973 0.27 0.02 YES
2 PRIM1 PRIM1 PRIM1 1090 0.26 0.082 YES
3 RPA4 RPA4 RPA4 1374 0.22 0.13 YES
4 MCM2 MCM2 MCM2 1497 0.21 0.18 YES
5 PRIM2 PRIM2 PRIM2 1659 0.2 0.22 YES
6 RNASEH1 RNASEH1 RNASEH1 1692 0.19 0.27 YES
7 DNA2 DNA2 DNA2 1788 0.18 0.31 YES
8 MCM4 MCM4 MCM4 2055 0.17 0.34 YES
9 POLE2 POLE2 POLE2 2320 0.15 0.37 YES
10 MCM6 MCM6 MCM6 2373 0.15 0.41 YES
11 RFC3 RFC3 RFC3 2727 0.13 0.42 YES
12 RFC5 RFC5 RFC5 2792 0.13 0.45 YES
13 MCM3 MCM3 MCM3 2875 0.12 0.48 YES
14 MCM7 MCM7 MCM7 2969 0.12 0.51 YES
15 RNASEH2A RNASEH2A RNASEH2A 2975 0.12 0.54 YES
16 POLD1 POLD1 POLD1 3006 0.12 0.57 YES
17 MCM5 MCM5 MCM5 3680 0.095 0.56 YES
18 FEN1 FEN1 FEN1 3779 0.092 0.58 YES
19 PCNA PCNA PCNA 4141 0.083 0.58 YES
20 RFC2 RFC2 RFC2 4262 0.08 0.6 YES
21 LIG1 LIG1 LIG1 4384 0.077 0.61 YES
22 POLE POLE POLE 4596 0.072 0.62 YES
23 RFC1 RFC1 RFC1 4650 0.071 0.64 YES
24 POLA2 POLA2 POLA2 4726 0.069 0.65 YES
25 RPA3 RPA3 RPA3 5154 0.06 0.64 YES
26 RNASEH2C RNASEH2C RNASEH2C 5567 0.054 0.64 YES
27 POLD2 POLD2 POLD2 5774 0.05 0.64 YES
28 RPA2 RPA2 RPA2 5788 0.05 0.65 YES
29 RPA1 RPA1 RPA1 6880 0.033 0.6 NO
30 RNASEH2B RNASEH2B RNASEH2B 7277 0.027 0.59 NO
31 POLE3 POLE3 POLE3 7504 0.023 0.58 NO
32 POLD3 POLD3 POLD3 7868 0.018 0.56 NO
33 POLE4 POLE4 POLE4 8715 0.0067 0.52 NO
34 SSBP1 SSBP1 SSBP1 9673 -0.0067 0.47 NO
35 POLD4 POLD4 POLD4 11012 -0.027 0.41 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 G1 PATHWAY.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA MPR 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 CDKN2A CDKN2A CDKN2A 113 0.5 0.027 YES
2 CCNE1 CCNE1 CCNE1 249 0.42 0.047 YES
3 SMC1B SMC1B SMC1B 276 0.41 0.072 YES
4 E2F1 E2F1 E2F1 502 0.35 0.083 YES
5 TTK TTK TTK 521 0.34 0.1 YES
6 ESPL1 ESPL1 ESPL1 668 0.32 0.12 YES
7 CDC7 CDC7 CDC7 734 0.31 0.13 YES
8 ORC1L ORC1L ORC1L 927 0.28 0.14 YES
9 CDC25B CDC25B CDC25B 964 0.27 0.16 YES
10 CDC25C CDC25C CDC25C 965 0.27 0.17 YES
11 BUB1 BUB1 BUB1 972 0.27 0.19 YES
12 CDKN2B CDKN2B CDKN2B 1001 0.26 0.21 YES
13 CDC25A CDC25A CDC25A 1052 0.26 0.22 YES
14 E2F2 E2F2 E2F2 1176 0.24 0.23 YES
15 MYC MYC MYC 1283 0.23 0.24 YES
16 CDC45 CDC45 CDC45 1449 0.22 0.24 YES
17 MCM2 MCM2 MCM2 1497 0.21 0.26 YES
18 CDC20 CDC20 CDC20 1502 0.21 0.27 YES
19 TFDP2 TFDP2 TFDP2 1563 0.2 0.28 YES
20 PLK1 PLK1 PLK1 1577 0.2 0.29 YES
21 MAD2L1 MAD2L1 MAD2L1 1591 0.2 0.3 YES
22 CDKN1B CDKN1B CDKN1B 1767 0.19 0.31 YES
23 CCNA2 CCNA2 CCNA2 1777 0.19 0.32 YES
24 PTTG1 PTTG1 PTTG1 1790 0.18 0.33 YES
25 CDK6 CDK6 CDK6 1832 0.18 0.34 YES
26 BUB1B BUB1B BUB1B 1920 0.18 0.35 YES
27 RBL1 RBL1 RBL1 1967 0.17 0.35 YES
28 CDKN2C CDKN2C CDKN2C 1995 0.17 0.36 YES
29 MCM4 MCM4 MCM4 2055 0.17 0.37 YES
30 CHEK1 CHEK1 CHEK1 2059 0.17 0.38 YES
31 E2F5 E2F5 E2F5 2067 0.17 0.39 YES
32 CCNB2 CCNB2 CCNB2 2168 0.16 0.4 YES
33 PKMYT1 PKMYT1 PKMYT1 2234 0.16 0.4 YES
34 MCM6 MCM6 MCM6 2373 0.15 0.41 YES
35 CDK2 CDK2 CDK2 2449 0.14 0.41 YES
36 PRKDC PRKDC PRKDC 2585 0.14 0.41 YES
37 RAD21 RAD21 RAD21 2682 0.13 0.42 YES
38 CCNB1 CCNB1 CCNB1 2687 0.13 0.42 YES
39 CHEK2 CHEK2 CHEK2 2777 0.13 0.43 YES
40 E2F3 E2F3 E2F3 2851 0.12 0.43 YES
41 MCM3 MCM3 MCM3 2875 0.12 0.44 YES
42 CDK1 CDK1 CDK1 2896 0.12 0.45 YES
43 MCM7 MCM7 MCM7 2969 0.12 0.45 YES
44 SMAD3 SMAD3 SMAD3 3086 0.12 0.45 YES
45 CDKN1C CDKN1C CDKN1C 3118 0.11 0.46 YES
46 SKP2 SKP2 SKP2 3289 0.11 0.46 YES
47 CDC6 CDC6 CDC6 3500 0.1 0.45 YES
48 CDKN2D CDKN2D CDKN2D 3575 0.099 0.45 YES
49 MCM5 MCM5 MCM5 3680 0.095 0.45 YES
50 CCND3 CCND3 CCND3 3957 0.088 0.44 YES
51 ORC4L ORC4L ORC4L 4077 0.085 0.44 YES
52 CDK4 CDK4 CDK4 4081 0.085 0.45 YES
53 CDC23 CDC23 CDC23 4113 0.084 0.45 YES
54 PCNA PCNA PCNA 4141 0.083 0.46 YES
55 STAG1 STAG1 STAG1 4171 0.082 0.46 YES
56 MAD2L2 MAD2L2 MAD2L2 4274 0.079 0.46 YES
57 YWHAB YWHAB YWHAB 4393 0.076 0.46 YES
58 ORC2L ORC2L ORC2L 4465 0.075 0.46 YES
59 HDAC2 HDAC2 HDAC2 4551 0.073 0.46 YES
60 SMC3 SMC3 SMC3 4582 0.072 0.46 YES
61 ORC3L ORC3L ORC3L 4585 0.072 0.47 YES
62 CCNE2 CCNE2 CCNE2 4799 0.068 0.46 NO
63 YWHAZ YWHAZ YWHAZ 5017 0.063 0.45 NO
64 GSK3B GSK3B GSK3B 5027 0.063 0.46 NO
65 SMC1A SMC1A SMC1A 5493 0.055 0.43 NO
66 CDC27 CDC27 CDC27 5686 0.052 0.43 NO
67 YWHAQ YWHAQ YWHAQ 5808 0.049 0.42 NO
68 CDC14B CDC14B CDC14B 6221 0.043 0.4 NO
69 ANAPC1 ANAPC1 ANAPC1 6290 0.042 0.4 NO
70 TGFB1 TGFB1 TGFB1 6753 0.034 0.38 NO
71 YWHAG YWHAG YWHAG 7106 0.029 0.36 NO
72 CUL1 CUL1 CUL1 7179 0.028 0.36 NO
73 TFDP1 TFDP1 TFDP1 7286 0.026 0.36 NO
74 STAG2 STAG2 STAG2 7422 0.024 0.35 NO
75 HDAC1 HDAC1 HDAC1 7502 0.023 0.35 NO
76 CREBBP CREBBP CREBBP 7965 0.017 0.32 NO
77 E2F4 E2F4 E2F4 8122 0.015 0.32 NO
78 PTTG2 PTTG2 PTTG2 8166 0.014 0.32 NO
79 SKP1 SKP1 SKP1 8206 0.014 0.31 NO
80 ANAPC10 ANAPC10 ANAPC10 8724 0.0066 0.29 NO
81 SMAD2 SMAD2 SMAD2 9063 0.0016 0.27 NO
82 ORC5L ORC5L ORC5L 9151 0.00063 0.26 NO
83 CCNB3 CCNB3 CCNB3 9202 -8e-05 0.26 NO
84 ANAPC7 ANAPC7 ANAPC7 9208 -0.00024 0.26 NO
85 EP300 EP300 EP300 9449 -0.0034 0.25 NO
86 BUB3 BUB3 BUB3 9737 -0.0078 0.23 NO
87 SMAD4 SMAD4 SMAD4 9965 -0.012 0.22 NO
88 ATR ATR ATR 10006 -0.012 0.22 NO
89 YWHAH YWHAH YWHAH 10009 -0.012 0.22 NO
90 ORC6L ORC6L ORC6L 10198 -0.015 0.21 NO
91 ANAPC13 ANAPC13 ANAPC13 10249 -0.016 0.21 NO
92 ANAPC5 ANAPC5 ANAPC5 10549 -0.02 0.19 NO
93 RBX1 RBX1 RBX1 10827 -0.024 0.18 NO
94 CDC16 CDC16 CDC16 11062 -0.028 0.17 NO
95 ATM ATM ATM 11239 -0.031 0.16 NO
96 MAD1L1 MAD1L1 MAD1L1 11268 -0.032 0.16 NO
97 YWHAE YWHAE YWHAE 11468 -0.035 0.15 NO
98 WEE2 WEE2 WEE2 11509 -0.036 0.15 NO
99 ZBTB17 ZBTB17 ZBTB17 11520 -0.036 0.16 NO
100 ANAPC11 ANAPC11 ANAPC11 11533 -0.037 0.16 NO
101 ABL1 ABL1 ABL1 11746 -0.04 0.15 NO
102 TGFB3 TGFB3 TGFB3 12011 -0.044 0.14 NO
103 FZR1 FZR1 FZR1 12368 -0.051 0.12 NO
104 WEE1 WEE1 WEE1 12721 -0.057 0.11 NO
105 ANAPC2 ANAPC2 ANAPC2 12754 -0.058 0.11 NO
106 CCND1 CCND1 CCND1 12771 -0.058 0.11 NO
107 RBL2 RBL2 RBL2 12991 -0.062 0.1 NO
108 CCNH CCNH CCNH 13460 -0.072 0.082 NO
109 TP53 TP53 TP53 13769 -0.08 0.071 NO
110 CDK7 CDK7 CDK7 13983 -0.085 0.064 NO
111 CCND2 CCND2 CCND2 14086 -0.087 0.065 NO
112 RB1 RB1 RB1 14230 -0.091 0.063 NO
113 GADD45A GADD45A GADD45A 15140 -0.12 0.021 NO
114 TGFB2 TGFB2 TGFB2 15177 -0.12 0.027 NO
115 CDC26 CDC26 CDC26 15478 -0.14 0.02 NO
116 GADD45B GADD45B GADD45B 16114 -0.16 -0.0039 NO
117 MDM2 MDM2 MDM2 16415 -0.18 -0.0084 NO
118 SFN SFN SFN 17229 -0.24 -0.037 NO
119 CDC14A CDC14A CDC14A 17265 -0.25 -0.022 NO
120 CDKN1A CDKN1A CDKN1A 17647 -0.3 -0.023 NO
121 GADD45G GADD45G GADD45G 17907 -0.36 -0.014 NO
122 CCNA1 CCNA1 CCNA1 17910 -0.36 0.0097 NO
123 ANAPC4 ANAPC4 ANAPC4 17913 -0.36 0.033 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 MPR PATHWAY.

Figure S4.  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 RACCYCD 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 RAD54L RAD54L RAD54L 1037 0.26 0.042 YES
2 BRCA2 BRCA2 BRCA2 1081 0.26 0.14 YES
3 RPA4 RPA4 RPA4 1374 0.22 0.2 YES
4 XRCC2 XRCC2 XRCC2 1429 0.22 0.28 YES
5 RAD51 RAD51 RAD51 1654 0.2 0.34 YES
6 RAD54B RAD54B RAD54B 1802 0.18 0.4 YES
7 BLM BLM BLM 1807 0.18 0.47 YES
8 EME1 EME1 EME1 2232 0.16 0.51 YES
9 XRCC3 XRCC3 XRCC3 2769 0.13 0.53 YES
10 POLD1 POLD1 POLD1 3006 0.12 0.56 YES
11 MRE11A MRE11A MRE11A 3487 0.1 0.57 YES
12 RPA3 RPA3 RPA3 5154 0.06 0.5 NO
13 POLD2 POLD2 POLD2 5774 0.05 0.49 NO
14 RPA2 RPA2 RPA2 5788 0.05 0.5 NO
15 RAD52 RAD52 RAD52 5895 0.048 0.52 NO
16 RPA1 RPA1 RPA1 6880 0.033 0.48 NO
17 MUS81 MUS81 MUS81 6883 0.032 0.49 NO
18 NBN NBN NBN 7381 0.025 0.47 NO
19 TOP3B TOP3B TOP3B 7488 0.023 0.47 NO
20 POLD3 POLD3 POLD3 7868 0.018 0.46 NO
21 RAD50 RAD50 RAD50 9109 0.0011 0.39 NO
22 SSBP1 SSBP1 SSBP1 9673 -0.0067 0.37 NO
23 TOP3A TOP3A TOP3A 10049 -0.013 0.35 NO
24 POLD4 POLD4 POLD4 11012 -0.027 0.31 NO
25 SHFM1 SHFM1 SHFM1 11785 -0.04 0.28 NO
26 RAD51L3 RAD51L3 RAD51L3 12442 -0.052 0.27 NO
27 RAD51L1 RAD51L1 RAD51L1 16154 -0.17 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 RACCYCD PATHWAY.

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

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

Table S4.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ISY1 ISY1 ISY1 2706 0.13 -0.13 YES
2 CTNNBL1 CTNNBL1 CTNNBL1 2856 0.12 -0.11 YES
3 SNRPB2 SNRPB2 SNRPB2 2883 0.12 -0.094 YES
4 THOC4 THOC4 THOC4 2884 0.12 -0.074 YES
5 EIF4A3 EIF4A3 EIF4A3 2987 0.12 -0.06 YES
6 SNRNP27 SNRNP27 SNRNP27 3276 0.11 -0.058 YES
7 LSM6 LSM6 LSM6 3304 0.11 -0.042 YES
8 PPIL1 PPIL1 PPIL1 3484 0.1 -0.035 YES
9 CHERP CHERP CHERP 3626 0.097 -0.027 YES
10 PRPF40A PRPF40A PRPF40A 3713 0.094 -0.016 YES
11 PUF60 PUF60 PUF60 3744 0.093 -0.0024 YES
12 THOC3 THOC3 THOC3 3805 0.091 0.0093 YES
13 SNRNP40 SNRNP40 SNRNP40 3866 0.09 0.021 YES
14 SNRPC SNRPC SNRPC 3935 0.088 0.032 YES
15 WBP11 WBP11 WBP11 3946 0.088 0.046 YES
16 SR140 SR140 SR140 3980 0.087 0.058 YES
17 SF3B14 SF3B14 SF3B14 4045 0.086 0.068 YES
18 SNRPD1 SNRPD1 SNRPD1 4059 0.085 0.082 YES
19 CDC5L CDC5L CDC5L 4080 0.085 0.095 YES
20 SNRNP200 SNRNP200 SNRNP200 4305 0.079 0.095 YES
21 SF3A3 SF3A3 SF3A3 4316 0.078 0.11 YES
22 RBM17 RBM17 RBM17 4490 0.074 0.11 YES
23 SNRPB SNRPB SNRPB 4591 0.072 0.12 YES
24 LSM5 LSM5 LSM5 4642 0.071 0.13 YES
25 USP39 USP39 USP39 4687 0.07 0.14 YES
26 TRA2B TRA2B TRA2B 4716 0.069 0.14 YES
27 SMNDC1 SMNDC1 SMNDC1 4742 0.069 0.16 YES
28 CDC40 CDC40 CDC40 4746 0.069 0.17 YES
29 BCAS2 BCAS2 BCAS2 4780 0.068 0.18 YES
30 LSM2 LSM2 LSM2 4822 0.067 0.18 YES
31 LSM4 LSM4 LSM4 4859 0.066 0.19 YES
32 LSM3 LSM3 LSM3 4884 0.066 0.2 YES
33 HSPA8 HSPA8 HSPA8 4941 0.065 0.21 YES
34 PRPF6 PRPF6 PRPF6 4990 0.064 0.22 YES
35 ZMAT2 ZMAT2 ZMAT2 5036 0.063 0.23 YES
36 RBM22 RBM22 RBM22 5054 0.062 0.24 YES
37 RBM8A RBM8A RBM8A 5065 0.062 0.24 YES
38 MAGOH MAGOH MAGOH 5208 0.059 0.25 YES
39 CRNKL1 CRNKL1 CRNKL1 5387 0.056 0.25 YES
40 PRPF38A PRPF38A PRPF38A 5393 0.056 0.26 YES
41 DHX16 DHX16 DHX16 5433 0.056 0.26 YES
42 SF3A1 SF3A1 SF3A1 5508 0.054 0.27 YES
43 PQBP1 PQBP1 PQBP1 5513 0.054 0.28 YES
44 DDX46 DDX46 DDX46 5538 0.054 0.28 YES
45 EFTUD2 EFTUD2 EFTUD2 5849 0.049 0.28 YES
46 SFRS3 SFRS3 SFRS3 5991 0.047 0.28 YES
47 PRPF3 PRPF3 PRPF3 5992 0.047 0.28 YES
48 SFRS2 SFRS2 SFRS2 6081 0.045 0.28 YES
49 SNRPE SNRPE SNRPE 6147 0.044 0.29 YES
50 SNRPD2 SNRPD2 SNRPD2 6161 0.044 0.3 YES
51 U2AF1 U2AF1 U2AF1 6241 0.042 0.3 YES
52 PPIH PPIH PPIH 6253 0.042 0.3 YES
53 SLU7 SLU7 SLU7 6254 0.042 0.31 YES
54 NAA38 NAA38 NAA38 6409 0.04 0.31 YES
55 SNRPD3 SNRPD3 SNRPD3 6421 0.04 0.32 YES
56 SF3B2 SF3B2 SF3B2 6555 0.037 0.31 YES
57 SF3B4 SF3B4 SF3B4 6670 0.036 0.31 YES
58 SNW1 SNW1 SNW1 6682 0.035 0.32 YES
59 SART1 SART1 SART1 6686 0.035 0.32 YES
60 DDX23 DDX23 DDX23 6843 0.033 0.32 YES
61 SNRPF SNRPF SNRPF 6905 0.032 0.32 YES
62 SNRPA1 SNRPA1 SNRPA1 6911 0.032 0.33 YES
63 PPIE PPIE PPIE 6971 0.031 0.33 YES
64 HNRNPM HNRNPM HNRNPM 7001 0.031 0.33 YES
65 SNRPG SNRPG SNRPG 7010 0.031 0.34 YES
66 RBMX RBMX RBMX 7073 0.03 0.34 YES
67 THOC1 THOC1 THOC1 7078 0.03 0.34 YES
68 PHF5A PHF5A PHF5A 7100 0.029 0.35 YES
69 SFRS7 SFRS7 SFRS7 7139 0.029 0.35 YES
70 HSPA1A HSPA1A HSPA1A 7176 0.028 0.35 YES
71 HNRNPU HNRNPU HNRNPU 7188 0.028 0.36 YES
72 U2AF2 U2AF2 U2AF2 7204 0.028 0.36 YES
73 MAGOHB MAGOHB MAGOHB 7264 0.027 0.36 YES
74 SFRS9 SFRS9 SFRS9 7333 0.026 0.36 YES
75 TCERG1 TCERG1 TCERG1 7416 0.025 0.36 YES
76 DHX15 DHX15 DHX15 7543 0.023 0.36 YES
77 SFRS1 SFRS1 SFRS1 7607 0.022 0.36 YES
78 PRPF19 PRPF19 PRPF19 7690 0.021 0.36 YES
79 PRPF18 PRPF18 PRPF18 7729 0.02 0.36 YES
80 SF3B3 SF3B3 SF3B3 7767 0.02 0.36 YES
81 PRPF31 PRPF31 PRPF31 7778 0.02 0.36 YES
82 SFRS6 SFRS6 SFRS6 7912 0.018 0.36 NO
83 PCBP1 PCBP1 PCBP1 8008 0.016 0.36 NO
84 THOC2 THOC2 THOC2 8134 0.015 0.35 NO
85 BAT1 BAT1 BAT1 8314 0.012 0.34 NO
86 PRPF38B PRPF38B PRPF38B 8386 0.011 0.34 NO
87 CWC15 CWC15 CWC15 8453 0.01 0.34 NO
88 SYF2 SYF2 SYF2 8577 0.0085 0.34 NO
89 HNRNPC HNRNPC HNRNPC 8676 0.0072 0.33 NO
90 PRPF4 PRPF4 PRPF4 8765 0.0061 0.33 NO
91 DDX42 DDX42 DDX42 8772 0.006 0.33 NO
92 HNRNPA3 HNRNPA3 HNRNPA3 8800 0.0057 0.33 NO
93 SF3B1 SF3B1 SF3B1 8887 0.0044 0.32 NO
94 DHX8 DHX8 DHX8 8924 0.0037 0.32 NO
95 SFRS13A SFRS13A SFRS13A 8934 0.0036 0.32 NO
96 PLRG1 PLRG1 PLRG1 8935 0.0036 0.32 NO
97 SFRS5 SFRS5 SFRS5 8960 0.0031 0.32 NO
98 NCBP1 NCBP1 NCBP1 9046 0.0018 0.32 NO
99 HNRNPK HNRNPK HNRNPK 9144 0.00068 0.31 NO
100 BUD31 BUD31 BUD31 9335 -0.002 0.3 NO
101 TXNL4A TXNL4A TXNL4A 9420 -0.0032 0.3 NO
102 SNRPA SNRPA SNRPA 9429 -0.0033 0.3 NO
103 ACIN1 ACIN1 ACIN1 9480 -0.0039 0.3 NO
104 SNRNP70 SNRNP70 SNRNP70 9928 -0.011 0.27 NO
105 DDX5 DDX5 DDX5 10055 -0.013 0.27 NO
106 RBM25 RBM25 RBM25 10073 -0.013 0.27 NO
107 SFRS4 SFRS4 SFRS4 10082 -0.013 0.27 NO
108 PRPF8 PRPF8 PRPF8 10089 -0.013 0.28 NO
109 SF3B5 SF3B5 SF3B5 10643 -0.022 0.25 NO
110 CCDC12 CCDC12 CCDC12 10707 -0.023 0.25 NO
111 PRPF40B PRPF40B PRPF40B 11136 -0.03 0.23 NO
112 NHP2L1 NHP2L1 NHP2L1 11158 -0.03 0.23 NO
113 DHX38 DHX38 DHX38 11291 -0.032 0.23 NO
114 XAB2 XAB2 XAB2 11586 -0.037 0.22 NO
115 HSPA6 HSPA6 HSPA6 11708 -0.039 0.22 NO
116 AQR AQR AQR 13004 -0.063 0.16 NO
117 HSPA2 HSPA2 HSPA2 13117 -0.065 0.17 NO
118 HSPA1B HSPA1B HSPA1B 13163 -0.066 0.18 NO
119 SF3A2 SF3A2 SF3A2 13185 -0.066 0.18 NO
120 HNRNPA1 HNRNPA1 HNRNPA1 13351 -0.07 0.19 NO
121 TRA2A TRA2A TRA2A 13361 -0.07 0.2 NO
122 SFRS2B SFRS2B SFRS2B 13744 -0.079 0.19 NO
123 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 15026 -0.12 0.14 NO
124 LSM7 LSM7 LSM7 15521 -0.14 0.14 NO
125 HSPA1L HSPA1L HSPA1L 16186 -0.17 0.13 NO

Figure S7.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CHREBP2 PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

Table S5.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GCK GCK GCK 68 0.55 0.1 YES
2 MAFA MAFA MAFA 150 0.48 0.19 YES
3 CACNA1B CACNA1B CACNA1B 159 0.47 0.28 YES
4 IRS2 IRS2 IRS2 183 0.46 0.36 YES
5 SLC2A4 SLC2A4 SLC2A4 319 0.4 0.43 YES
6 CACNA1A CACNA1A CACNA1A 950 0.27 0.45 YES
7 PIK3CA PIK3CA PIK3CA 1386 0.22 0.47 YES
8 SOCS3 SOCS3 SOCS3 1597 0.2 0.49 YES
9 PIK3CD PIK3CD PIK3CD 3009 0.12 0.44 NO
10 PRKCE PRKCE PRKCE 3120 0.11 0.46 NO
11 TNF TNF TNF 3945 0.088 0.43 NO
12 CACNA1G CACNA1G CACNA1G 4342 0.078 0.42 NO
13 MAPK3 MAPK3 MAPK3 4729 0.069 0.41 NO
14 PDX1 PDX1 PDX1 4978 0.064 0.41 NO
15 PIK3CB PIK3CB PIK3CB 5761 0.05 0.38 NO
16 IKBKB IKBKB IKBKB 6195 0.043 0.36 NO
17 MAPK10 MAPK10 MAPK10 6482 0.038 0.36 NO
18 SOCS2 SOCS2 SOCS2 6608 0.037 0.36 NO
19 PKLR PKLR PKLR 6736 0.035 0.36 NO
20 HK3 HK3 HK3 7192 0.028 0.34 NO
21 SOCS1 SOCS1 SOCS1 7789 0.02 0.31 NO
22 PKM2 PKM2 PKM2 8207 0.014 0.29 NO
23 PIK3R2 PIK3R2 PIK3R2 8529 0.0092 0.27 NO
24 MAPK1 MAPK1 MAPK1 9071 0.0015 0.24 NO
25 INSR INSR INSR 9252 -0.00084 0.23 NO
26 SOCS4 SOCS4 SOCS4 9645 -0.0063 0.21 NO
27 HK1 HK1 HK1 9939 -0.011 0.2 NO
28 IRS4 IRS4 IRS4 10052 -0.013 0.2 NO
29 HK2 HK2 HK2 10204 -0.015 0.19 NO
30 CACNA1E CACNA1E CACNA1E 10564 -0.021 0.17 NO
31 PIK3R5 PIK3R5 PIK3R5 10616 -0.021 0.18 NO
32 MAPK9 MAPK9 MAPK9 10617 -0.021 0.18 NO
33 IRS1 IRS1 IRS1 10811 -0.024 0.17 NO
34 MAPK8 MAPK8 MAPK8 10854 -0.025 0.18 NO
35 KCNJ11 KCNJ11 KCNJ11 10893 -0.026 0.18 NO
36 PRKCD PRKCD PRKCD 11028 -0.028 0.18 NO
37 MTOR MTOR MTOR 12214 -0.048 0.12 NO
38 ABCC8 ABCC8 ABCC8 13243 -0.067 0.079 NO
39 PIK3CG PIK3CG PIK3CG 14613 -0.1 0.025 NO
40 CACNA1D CACNA1D CACNA1D 15867 -0.15 -0.014 NO
41 PIK3R3 PIK3R3 PIK3R3 16564 -0.19 -0.015 NO
42 CACNA1C CACNA1C CACNA1C 17448 -0.27 -0.011 NO
43 PIK3R1 PIK3R1 PIK3R1 17912 -0.36 0.033 NO

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

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

genes ES table in pathway: KEGG RNA DEGRADATION

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 STON1 STON1 STON1 237 0.43 0.13 YES
2 TAF4B TAF4B TAF4B 680 0.31 0.21 YES
3 GTF2A1L GTF2A1L GTF2A1L 858 0.29 0.3 YES
4 TAF5 TAF5 TAF5 2109 0.16 0.28 YES
5 GTF2IRD1 GTF2IRD1 GTF2IRD1 3126 0.11 0.27 YES
6 TAF4 TAF4 TAF4 3670 0.095 0.27 YES
7 TAF2 TAF2 TAF2 3771 0.092 0.3 YES
8 GTF2H4 GTF2H4 GTF2H4 3853 0.09 0.32 YES
9 TAF11 TAF11 TAF11 3991 0.087 0.34 YES
10 GTF2E1 GTF2E1 GTF2E1 4039 0.086 0.37 YES
11 TBP TBP TBP 4192 0.082 0.39 YES
12 GTF2H3 GTF2H3 GTF2H3 4233 0.08 0.41 YES
13 TBPL1 TBPL1 TBPL1 4333 0.078 0.43 YES
14 TAF7L TAF7L TAF7L 4509 0.074 0.45 YES
15 GTF2A1 GTF2A1 GTF2A1 5241 0.059 0.43 NO
16 GTF2H1 GTF2H1 GTF2H1 7963 0.017 0.29 NO
17 GTF2B GTF2B GTF2B 8019 0.016 0.29 NO
18 TAF9B TAF9B TAF9B 8253 0.013 0.28 NO
19 TAF1 TAF1 TAF1 8366 0.012 0.28 NO
20 TAF6L TAF6L TAF6L 8932 0.0036 0.25 NO
21 TAF7 TAF7 TAF7 9407 -0.003 0.23 NO
22 GTF2F2 GTF2F2 GTF2F2 9448 -0.0034 0.22 NO
23 TAF5L TAF5L TAF5L 9525 -0.0045 0.22 NO
24 TAF12 TAF12 TAF12 10290 -0.017 0.19 NO
25 TAF6 TAF6 TAF6 10294 -0.017 0.19 NO
26 TAF13 TAF13 TAF13 10966 -0.027 0.16 NO
27 GTF2E2 GTF2E2 GTF2E2 12023 -0.045 0.12 NO
28 TAF10 TAF10 TAF10 12613 -0.055 0.11 NO
29 GTF2A2 GTF2A2 GTF2A2 12744 -0.058 0.12 NO
30 GTF2F1 GTF2F1 GTF2F1 13365 -0.07 0.11 NO
31 TAF9 TAF9 TAF9 13992 -0.085 0.1 NO
32 TAF1L TAF1L TAF1L 14280 -0.093 0.12 NO
33 GTF2I GTF2I GTF2I 15389 -0.13 0.1 NO
34 GTF2H2 GTF2H2 GTF2H2 16549 -0.19 0.11 NO

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

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

genes ES table in pathway: KEGG BASAL TRANSCRIPTION FACTORS

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 PAPD7 PAPD7 PAPD7 2522 0.14 -0.083 YES
2 EXOSC3 EXOSC3 EXOSC3 2955 0.12 -0.06 YES
3 LSM6 LSM6 LSM6 3304 0.11 -0.038 YES
4 EXOSC5 EXOSC5 EXOSC5 3475 0.1 -0.0083 YES
5 PNPT1 PNPT1 PNPT1 3480 0.1 0.03 YES
6 PAPOLG PAPOLG PAPOLG 3920 0.088 0.04 YES
7 XRN2 XRN2 XRN2 4291 0.079 0.051 YES
8 C1D C1D C1D 4304 0.079 0.08 YES
9 LSM5 LSM5 LSM5 4642 0.071 0.089 YES
10 EXOSC2 EXOSC2 EXOSC2 4696 0.07 0.11 YES
11 EXOSC10 EXOSC10 EXOSC10 4801 0.068 0.13 YES
12 LSM2 LSM2 LSM2 4822 0.067 0.16 YES
13 LSM4 LSM4 LSM4 4859 0.066 0.18 YES
14 LSM3 LSM3 LSM3 4884 0.066 0.2 YES
15 EXOSC9 EXOSC9 EXOSC9 4905 0.065 0.23 YES
16 ENO3 ENO3 ENO3 4919 0.065 0.25 YES
17 SKIV2L SKIV2L SKIV2L 4935 0.065 0.28 YES
18 DCP1A DCP1A DCP1A 4948 0.064 0.3 YES
19 XRN1 XRN1 XRN1 4989 0.064 0.32 YES
20 HSPD1 HSPD1 HSPD1 5108 0.061 0.34 YES
21 HSPA9 HSPA9 HSPA9 5793 0.05 0.32 NO
22 ENO1 ENO1 ENO1 6393 0.04 0.31 NO
23 EXOSC6 EXOSC6 EXOSC6 6401 0.04 0.32 NO
24 NAA38 NAA38 NAA38 6409 0.04 0.34 NO
25 EDC3 EDC3 EDC3 6826 0.033 0.33 NO
26 PAPOLA PAPOLA PAPOLA 6990 0.031 0.33 NO
27 DCP2 DCP2 DCP2 7125 0.029 0.33 NO
28 PATL1 PATL1 PATL1 7367 0.025 0.33 NO
29 DIS3 DIS3 DIS3 7736 0.02 0.32 NO
30 ZCCHC7 ZCCHC7 ZCCHC7 7908 0.018 0.32 NO
31 CNOT3 CNOT3 CNOT3 8165 0.014 0.31 NO
32 CNOT2 CNOT2 CNOT2 8318 0.012 0.3 NO
33 ENO2 ENO2 ENO2 8510 0.0095 0.3 NO
34 DCP1B DCP1B DCP1B 8518 0.0094 0.3 NO
35 EXOSC4 EXOSC4 EXOSC4 8525 0.0094 0.3 NO
36 EXOSC7 EXOSC7 EXOSC7 8553 0.0088 0.3 NO
37 RQCD1 RQCD1 RQCD1 8717 0.0067 0.3 NO
38 PARN PARN PARN 8751 0.0063 0.3 NO
39 CNOT10 CNOT10 CNOT10 8976 0.0028 0.29 NO
40 EXOSC8 EXOSC8 EXOSC8 8993 0.0026 0.29 NO
41 CNOT4 CNOT4 CNOT4 9052 0.0017 0.28 NO
42 SKIV2L2 SKIV2L2 SKIV2L2 9459 -0.0036 0.26 NO
43 CNOT6 CNOT6 CNOT6 9893 -0.01 0.24 NO
44 LSM1 LSM1 LSM1 10385 -0.018 0.23 NO
45 CNOT1 CNOT1 CNOT1 10519 -0.02 0.23 NO
46 DDX6 DDX6 DDX6 10536 -0.02 0.23 NO
47 CNOT7 CNOT7 CNOT7 10932 -0.026 0.22 NO
48 WDR61 WDR61 WDR61 11265 -0.032 0.22 NO
49 EDC4 EDC4 EDC4 11674 -0.039 0.21 NO
50 DCPS DCPS DCPS 12108 -0.046 0.2 NO
51 EXOSC1 EXOSC1 EXOSC1 12511 -0.053 0.2 NO
52 CNOT6L CNOT6L CNOT6L 12745 -0.058 0.21 NO
53 TTC37 TTC37 TTC37 12964 -0.062 0.22 NO
54 MPHOSPH6 MPHOSPH6 MPHOSPH6 13192 -0.066 0.24 NO
55 LSM7 LSM7 LSM7 15521 -0.14 0.16 NO

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

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

genes ES table in pathway: KEGG DNA REPLICATION

Table 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 GCK GCK GCK 68 0.55 0.16 YES
2 PPP2R2B PPP2R2B PPP2R2B 748 0.3 0.22 YES
3 PRKAR2B PRKAR2B PRKAR2B 961 0.27 0.29 YES
4 MLXIPL MLXIPL MLXIPL 2039 0.17 0.28 YES
5 PPP2R3A PPP2R3A PPP2R3A 2077 0.17 0.33 YES
6 PRKAR1B PRKAR1B PRKAR1B 3496 0.1 0.29 NO
7 YWHAB YWHAB YWHAB 4393 0.076 0.26 NO
8 FASN FASN FASN 4400 0.076 0.29 NO
9 PRKAA2 PRKAA2 PRKAA2 4692 0.07 0.29 NO
10 YWHAZ YWHAZ YWHAZ 5017 0.063 0.29 NO
11 PPP2R5D PPP2R5D PPP2R5D 5731 0.051 0.27 NO
12 YWHAQ YWHAQ YWHAQ 5808 0.049 0.28 NO
13 PRKACA PRKACA PRKACA 5881 0.048 0.29 NO
14 PRKAB2 PRKAB2 PRKAB2 5936 0.047 0.3 NO
15 PPP2R3B PPP2R3B PPP2R3B 6269 0.042 0.3 NO
16 PKLR PKLR PKLR 6736 0.035 0.28 NO
17 YWHAG YWHAG YWHAG 7106 0.029 0.27 NO
18 PRKAR1A PRKAR1A PRKAR1A 7496 0.023 0.26 NO
19 PPP2R2D PPP2R2D PPP2R2D 7725 0.02 0.25 NO
20 PPP2R5E PPP2R5E PPP2R5E 7991 0.017 0.24 NO
21 PRKAA1 PRKAA1 PRKAA1 8062 0.016 0.24 NO
22 PPP2CA PPP2CA PPP2CA 8478 0.01 0.22 NO
23 PPP2R1A PPP2R1A PPP2R1A 9431 -0.0033 0.18 NO
24 PPP2R5C PPP2R5C PPP2R5C 9469 -0.0037 0.17 NO
25 PRKACB PRKACB PRKACB 9865 -0.0098 0.16 NO
26 PPP2R5A PPP2R5A PPP2R5A 9904 -0.01 0.16 NO
27 YWHAH YWHAH YWHAH 10009 -0.012 0.16 NO
28 PPP2R2A PPP2R2A PPP2R2A 10083 -0.013 0.16 NO
29 PRKAG1 PRKAG1 PRKAG1 10158 -0.014 0.16 NO
30 ACACA ACACA ACACA 10452 -0.019 0.14 NO
31 PPP2CB PPP2CB PPP2CB 10472 -0.019 0.15 NO
32 PRKAR2A PRKAR2A PRKAR2A 11370 -0.034 0.11 NO
33 YWHAE YWHAE YWHAE 11468 -0.035 0.12 NO
34 PPP2R5B PPP2R5B PPP2R5B 12933 -0.061 0.057 NO
35 PPP2R4 PPP2R4 PPP2R4 13235 -0.067 0.061 NO
36 MLX MLX MLX 13494 -0.073 0.07 NO
37 PRKAB1 PRKAB1 PRKAB1 14990 -0.12 0.024 NO
38 PPP2R1B PPP2R1B PPP2R1B 15263 -0.13 0.048 NO
39 PRKAG2 PRKAG2 PRKAG2 15508 -0.14 0.077 NO
40 PPP2R2C PPP2R2C PPP2R2C 17515 -0.28 0.055 NO

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

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

genes ES table in pathway: KEGG SPLICEOSOME

Table 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 PSMD2 PSMD2 PSMD2 2872 0.12 -0.071 YES
2 PSMD12 PSMD12 PSMD12 3770 0.092 -0.056 YES
3 PSMA7 PSMA7 PSMA7 3811 0.091 0.0036 YES
4 PSMD3 PSMD3 PSMD3 4002 0.087 0.052 YES
5 PSMD11 PSMD11 PSMD11 4094 0.084 0.1 YES
6 PSMD1 PSMD1 PSMD1 4483 0.074 0.14 YES
7 PSMB2 PSMB2 PSMB2 5044 0.063 0.15 YES
8 PSMD8 PSMD8 PSMD8 5254 0.059 0.18 YES
9 PSMB11 PSMB11 PSMB11 5416 0.056 0.2 YES
10 PSMC4 PSMC4 PSMC4 5451 0.055 0.24 YES
11 PSMD14 PSMD14 PSMD14 5647 0.052 0.27 YES
12 PSMA2 PSMA2 PSMA2 5757 0.05 0.3 YES
13 PSMA6 PSMA6 PSMA6 5772 0.05 0.33 YES
14 PSMC2 PSMC2 PSMC2 6070 0.045 0.34 YES
15 PSMD4 PSMD4 PSMD4 6483 0.038 0.35 YES
16 PSMB4 PSMB4 PSMB4 6852 0.033 0.35 YES
17 PSMC6 PSMC6 PSMC6 7049 0.03 0.36 YES
18 PSME4 PSME4 PSME4 7239 0.027 0.37 YES
19 PSMA4 PSMA4 PSMA4 7550 0.023 0.37 YES
20 PSMB1 PSMB1 PSMB1 7636 0.021 0.38 YES
21 PSME1 PSME1 PSME1 7662 0.021 0.39 YES
22 PSMF1 PSMF1 PSMF1 7667 0.021 0.4 YES
23 PSME2 PSME2 PSME2 7809 0.019 0.41 YES
24 PSMA1 PSMA1 PSMA1 7838 0.019 0.42 YES
25 PSMC1 PSMC1 PSMC1 8005 0.016 0.42 YES
26 PSMA5 PSMA5 PSMA5 8337 0.012 0.41 YES
27 PSMB3 PSMB3 PSMB3 8342 0.012 0.42 YES
28 POMP POMP POMP 8457 0.01 0.42 YES
29 PSMB7 PSMB7 PSMB7 8523 0.0094 0.42 YES
30 PSMC5 PSMC5 PSMC5 8552 0.0088 0.43 YES
31 PSMB5 PSMB5 PSMB5 8587 0.0084 0.43 YES
32 PSMD6 PSMD6 PSMD6 8775 0.006 0.43 NO
33 PSMC3 PSMC3 PSMC3 8890 0.0043 0.42 NO
34 PSMA3 PSMA3 PSMA3 9176 0.00027 0.41 NO
35 PSMB6 PSMB6 PSMB6 9184 0.00019 0.41 NO
36 IFNG IFNG IFNG 9201 -0.000074 0.41 NO
37 PSMD13 PSMD13 PSMD13 9474 -0.0038 0.4 NO
38 PSMB9 PSMB9 PSMB9 9808 -0.009 0.38 NO
39 PSME3 PSME3 PSME3 9915 -0.011 0.38 NO
40 PSMB8 PSMB8 PSMB8 11247 -0.032 0.34 NO
41 SHFM1 SHFM1 SHFM1 11785 -0.04 0.33 NO
42 PSMD7 PSMD7 PSMD7 12080 -0.046 0.35 NO

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

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

genes ES table in pathway: KEGG PROTEASOME

Table 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 CDKN2A CDKN2A CDKN2A 113 0.5 0.13 YES
2 CCNE1 CCNE1 CCNE1 249 0.42 0.23 YES
3 CDKN2B CDKN2B CDKN2B 1001 0.26 0.26 YES
4 CDC25A CDC25A CDC25A 1052 0.26 0.33 YES
5 CDKN1B CDKN1B CDKN1B 1767 0.19 0.34 YES
6 CDK6 CDK6 CDK6 1832 0.18 0.39 YES
7 CDK2 CDK2 CDK2 2449 0.14 0.39 YES
8 CDK1 CDK1 CDK1 2896 0.12 0.4 YES
9 SMAD3 SMAD3 SMAD3 3086 0.12 0.42 YES
10 SKP2 SKP2 SKP2 3289 0.11 0.44 YES
11 CDK4 CDK4 CDK4 4081 0.085 0.42 NO
12 GSK3B GSK3B GSK3B 5027 0.063 0.38 NO
13 TGFB1 TGFB1 TGFB1 6753 0.034 0.3 NO
14 TFDP1 TFDP1 TFDP1 7286 0.026 0.28 NO
15 HDAC1 HDAC1 HDAC1 7502 0.023 0.27 NO
16 SMAD4 SMAD4 SMAD4 9965 -0.012 0.14 NO
17 ATR ATR ATR 10006 -0.012 0.14 NO
18 ATM ATM ATM 11239 -0.031 0.086 NO
19 ABL1 ABL1 ABL1 11746 -0.04 0.069 NO
20 TGFB3 TGFB3 TGFB3 12011 -0.044 0.067 NO
21 DHFR DHFR DHFR 12435 -0.052 0.058 NO
22 CCND1 CCND1 CCND1 12771 -0.058 0.055 NO
23 TP53 TP53 TP53 13769 -0.08 0.022 NO
24 RB1 RB1 RB1 14230 -0.091 0.022 NO
25 TGFB2 TGFB2 TGFB2 15177 -0.12 0.0034 NO
26 CDKN1A CDKN1A CDKN1A 17647 -0.3 -0.049 NO
27 CCNA1 CCNA1 CCNA1 17910 -0.36 0.033 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA ALK PATHWAY 35 genes.ES.table 0.49 1.4 0.069 1 0.94 0.2 0.041 0.19 0.99 0.5
BIOCARTA GSK3 PATHWAY 26 genes.ES.table 0.58 1.8 0.004 0.53 0.36 0.19 0.068 0.18 0 0.16
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.37 1.3 0.17 1 0.99 0.19 0.11 0.17 1 0.55
BIOCARTA INTEGRIN PATHWAY 37 genes.ES.table 0.35 1.4 0.15 1 0.97 0.054 0.016 0.053 1 0.56
BIOCARTA P38MAPK PATHWAY 39 genes.ES.table 0.36 1.4 0.11 1 0.97 0.1 0.06 0.097 1 0.52
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.6 2 0 0.15 0.056 0.16 0.068 0.15 0 0.041
KEGG FATTY ACID METABOLISM 41 genes.ES.table 0.4 1.2 0.22 1 1 0.2 0.12 0.17 1 0.71
KEGG ETHER LIPID METABOLISM 30 genes.ES.table 0.58 1.6 0.0098 0.88 0.66 0.23 0.08 0.22 0.5 0.29
KEGG LINOLEIC ACID METABOLISM 26 genes.ES.table 0.57 1.3 0.1 1 0.99 0.31 0.08 0.28 1 0.5
KEGG SPHINGOLIPID METABOLISM 37 genes.ES.table 0.39 1.2 0.23 1 1 0.35 0.2 0.28 1 0.65
genes ES table in pathway: BIOCARTA ALK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 WIF1 WIF1 WIF1 79 0.43 0.24 YES
2 LEF1 LEF1 LEF1 169 0.36 0.44 YES
3 FZD1 FZD1 FZD1 620 0.22 0.54 YES
4 CCND1 CCND1 CCND1 1263 0.16 0.6 YES
5 NLK NLK NLK 4075 0.054 0.48 NO
6 CSNK1A1 CSNK1A1 CSNK1A1 5030 0.039 0.45 NO
7 TLE1 TLE1 TLE1 5367 0.034 0.45 NO
8 APC APC APC 5968 0.027 0.43 NO
9 AXIN1 AXIN1 AXIN1 6403 0.022 0.42 NO
10 BTRC BTRC BTRC 6599 0.02 0.42 NO
11 CTNNB1 CTNNB1 CTNNB1 7319 0.013 0.39 NO
12 CTBP1 CTBP1 CTBP1 7373 0.012 0.39 NO
13 SMAD4 SMAD4 SMAD4 8002 0.006 0.36 NO
14 PPP2CA PPP2CA PPP2CA 8664 -0.00038 0.33 NO
15 TAB1 TAB1 TAB1 8818 -0.0019 0.32 NO
16 FRAT1 FRAT1 FRAT1 9351 -0.0068 0.3 NO
17 DVL1 DVL1 DVL1 9489 -0.008 0.29 NO
18 GSK3B GSK3B GSK3B 9605 -0.0091 0.29 NO
19 HDAC1 HDAC1 HDAC1 9829 -0.011 0.29 NO
20 CREBBP CREBBP CREBBP 10187 -0.015 0.28 NO
21 CSNK1D CSNK1D CSNK1D 11013 -0.023 0.24 NO
22 MAP3K7 MAP3K7 MAP3K7 12967 -0.048 0.16 NO
23 WNT1 WNT1 WNT1 13487 -0.056 0.17 NO
24 CSNK2A1 CSNK2A1 CSNK2A1 13491 -0.056 0.2 NO
25 MYC MYC MYC 15873 -0.12 0.14 NO

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

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ALK 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 GSK3 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TLR4 TLR4 TLR4 16 0.54 0.24 YES
2 LEF1 LEF1 LEF1 169 0.36 0.39 YES
3 FZD1 FZD1 FZD1 620 0.22 0.46 YES
4 TIRAP TIRAP TIRAP 721 0.2 0.54 YES
5 CCND1 CCND1 CCND1 1263 0.16 0.58 YES
6 GNAI1 GNAI1 GNAI1 4436 0.048 0.43 NO
7 PIK3R1 PIK3R1 PIK3R1 4571 0.046 0.44 NO
8 AKT1 AKT1 AKT1 5912 0.028 0.38 NO
9 APC APC APC 5968 0.027 0.39 NO
10 MYD88 MYD88 MYD88 6324 0.023 0.38 NO
11 AXIN1 AXIN1 AXIN1 6403 0.022 0.39 NO
12 CTNNB1 CTNNB1 CTNNB1 7319 0.013 0.34 NO
13 RELA RELA RELA 7324 0.013 0.35 NO
14 NFKB1 NFKB1 NFKB1 7711 0.009 0.33 NO
15 GJA1 GJA1 GJA1 7734 0.0087 0.34 NO
16 PDPK1 PDPK1 PDPK1 8168 0.0045 0.32 NO
17 PPP2CA PPP2CA PPP2CA 8664 -0.00038 0.29 NO
18 DVL1 DVL1 DVL1 9489 -0.008 0.25 NO
19 GSK3B GSK3B GSK3B 9605 -0.0091 0.24 NO
20 LY96 LY96 LY96 12808 -0.045 0.092 NO
21 IRAK1 IRAK1 IRAK1 13389 -0.054 0.084 NO
22 WNT1 WNT1 WNT1 13487 -0.056 0.1 NO
23 CD14 CD14 CD14 14011 -0.066 0.1 NO
24 LBP LBP LBP 14147 -0.068 0.13 NO
25 PIK3CA PIK3CA PIK3CA 15611 -0.11 0.098 NO
26 EIF2AK2 EIF2AK2 EIF2AK2 16109 -0.14 0.13 NO

Figure S23.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GSK3 PATHWAY.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GSK3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA DEATH PATHWAY

Table 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 PLA2G4A PLA2G4A PLA2G4A 26 0.51 0.16 YES
2 LPCAT2 LPCAT2 LPCAT2 130 0.38 0.28 YES
3 PLA2G2C PLA2G2C PLA2G2C 239 0.32 0.38 YES
4 PLA2G3 PLA2G3 PLA2G3 308 0.29 0.46 YES
5 PPAP2C PPAP2C PPAP2C 367 0.27 0.55 YES
6 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 1449 0.14 0.54 YES
7 PLA2G5 PLA2G5 PLA2G5 1483 0.14 0.58 YES
8 PPAP2A PPAP2A PPAP2A 3185 0.073 0.51 NO
9 PAFAH2 PAFAH2 PAFAH2 3814 0.059 0.5 NO
10 PLA2G10 PLA2G10 PLA2G10 3903 0.058 0.51 NO
11 PLA2G6 PLA2G6 PLA2G6 3969 0.056 0.52 NO
12 PLD2 PLD2 PLD2 4495 0.047 0.51 NO
13 PLA2G2F PLA2G2F PLA2G2F 5215 0.036 0.48 NO
14 PAFAH1B3 PAFAH1B3 PAFAH1B3 7292 0.013 0.38 NO
15 PLA2G4E PLA2G4E PLA2G4E 7887 0.0073 0.34 NO
16 PLA2G1B PLA2G1B PLA2G1B 8037 0.0056 0.34 NO
17 PAFAH1B1 PAFAH1B1 PAFAH1B1 8155 0.0046 0.33 NO
18 PLA2G7 PLA2G7 PLA2G7 8353 0.0027 0.32 NO
19 AGPS AGPS AGPS 8634 -0.000073 0.31 NO
20 CHPT1 CHPT1 CHPT1 10284 -0.016 0.22 NO
21 PLA2G12A PLA2G12A PLA2G12A 11480 -0.029 0.17 NO
22 LPCAT1 LPCAT1 LPCAT1 11886 -0.034 0.16 NO
23 PLA2G12B PLA2G12B PLA2G12B 13452 -0.055 0.091 NO
24 PAFAH1B2 PAFAH1B2 PAFAH1B2 13469 -0.055 0.11 NO
25 PLD1 PLD1 PLD1 13815 -0.061 0.11 NO
26 PLA2G2A PLA2G2A PLA2G2A 13852 -0.062 0.13 NO
27 LPCAT4 LPCAT4 LPCAT4 13912 -0.063 0.14 NO
28 PLA2G2D PLA2G2D PLA2G2D 14991 -0.091 0.11 NO
29 ENPP2 ENPP2 ENPP2 15460 -0.11 0.12 NO
30 PPAP2B PPAP2B PPAP2B 16001 -0.13 0.14 NO

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

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

genes ES table in pathway: BIOCARTA INTEGRIN PATHWAY

Table 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 GAD1 GAD1 GAD1 1 0.7 0.28 YES
2 ACSM1 ACSM1 ACSM1 876 0.19 0.31 YES
3 ALDH3A2 ALDH3A2 ALDH3A2 1025 0.17 0.38 YES
4 OXCT1 OXCT1 OXCT1 1249 0.16 0.43 YES
5 HMGCS2 HMGCS2 HMGCS2 1854 0.12 0.44 YES
6 ALDH2 ALDH2 ALDH2 2253 0.1 0.46 YES
7 ACSM3 ACSM3 ACSM3 2318 0.1 0.5 YES
8 ALDH9A1 ALDH9A1 ALDH9A1 3083 0.076 0.49 NO
9 AACS AACS AACS 3438 0.067 0.5 NO
10 ACADS ACADS ACADS 5148 0.037 0.42 NO
11 HADH HADH HADH 5188 0.037 0.44 NO
12 HMGCS1 HMGCS1 HMGCS1 6110 0.026 0.4 NO
13 ACAT2 ACAT2 ACAT2 6618 0.02 0.38 NO
14 HADHA HADHA HADHA 7296 0.013 0.34 NO
15 HMGCL HMGCL HMGCL 7442 0.012 0.34 NO
16 ALDH1B1 ALDH1B1 ALDH1B1 7462 0.012 0.34 NO
17 ECHS1 ECHS1 ECHS1 9003 -0.0036 0.26 NO
18 ACSM2A ACSM2A ACSM2A 9028 -0.0039 0.26 NO
19 BDH2 BDH2 BDH2 9399 -0.0072 0.25 NO
20 PDHB PDHB PDHB 9614 -0.0092 0.24 NO
21 ACAT1 ACAT1 ACAT1 9691 -0.01 0.24 NO
22 BDH1 BDH1 BDH1 10060 -0.014 0.22 NO
23 ALDH7A1 ALDH7A1 ALDH7A1 10643 -0.019 0.2 NO
24 L2HGDH L2HGDH L2HGDH 10793 -0.021 0.2 NO
25 OXCT2 OXCT2 OXCT2 11922 -0.034 0.15 NO
26 ABAT ABAT ABAT 12719 -0.044 0.13 NO
27 PDHA1 PDHA1 PDHA1 12966 -0.048 0.14 NO
28 AKR1B10 AKR1B10 AKR1B10 15456 -0.11 0.045 NO
29 ALDH5A1 ALDH5A1 ALDH5A1 16058 -0.13 0.067 NO
30 ACSM5 ACSM5 ACSM5 16581 -0.16 0.1 NO

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

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

genes ES table in pathway: BIOCARTA P38MAPK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PLA2G4A PLA2G4A PLA2G4A 26 0.51 0.058 YES
2 CALML3 CALML3 CALML3 84 0.42 0.1 YES
3 CACNA1S CACNA1S CACNA1S 195 0.34 0.14 YES
4 PLA2G2C PLA2G2C PLA2G2C 239 0.32 0.17 YES
5 PLA2G3 PLA2G3 PLA2G3 308 0.29 0.2 YES
6 CALML5 CALML5 CALML5 332 0.28 0.23 YES
7 MMP2 MMP2 MMP2 455 0.25 0.25 YES
8 PRKCA PRKCA PRKCA 604 0.22 0.27 YES
9 PLCB4 PLCB4 PLCB4 759 0.2 0.29 YES
10 ITPR2 ITPR2 ITPR2 828 0.19 0.3 YES
11 GNRH2 GNRH2 GNRH2 899 0.18 0.32 YES
12 MAP2K6 MAP2K6 MAP2K6 1103 0.17 0.33 YES
13 CAMK2D CAMK2D CAMK2D 1247 0.16 0.34 YES
14 CACNA1D CACNA1D CACNA1D 1366 0.15 0.35 YES
15 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 1449 0.14 0.36 YES
16 PLA2G5 PLA2G5 PLA2G5 1483 0.14 0.38 YES
17 CALML6 CALML6 CALML6 1677 0.13 0.38 YES
18 GNRHR GNRHR GNRHR 1701 0.13 0.4 YES
19 CACNA1C CACNA1C CACNA1C 2164 0.11 0.38 YES
20 MAPK13 MAPK13 MAPK13 2532 0.093 0.37 YES
21 PLCB1 PLCB1 PLCB1 2552 0.093 0.38 YES
22 ADCY2 ADCY2 ADCY2 2613 0.09 0.39 YES
23 ADCY4 ADCY4 ADCY4 2730 0.086 0.39 YES
24 GNRH1 GNRH1 GNRH1 2845 0.083 0.4 YES
25 CAMK2A CAMK2A CAMK2A 2848 0.083 0.41 YES
26 MAPK11 MAPK11 MAPK11 2888 0.082 0.41 YES
27 MAP2K4 MAP2K4 MAP2K4 3133 0.075 0.41 NO
28 GNAQ GNAQ GNAQ 3614 0.063 0.39 NO
29 HBEGF HBEGF HBEGF 3634 0.063 0.4 NO
30 PRKACB PRKACB PRKACB 3874 0.058 0.39 NO
31 PLA2G10 PLA2G10 PLA2G10 3903 0.058 0.4 NO
32 PLA2G6 PLA2G6 PLA2G6 3969 0.056 0.4 NO
33 MAPK7 MAPK7 MAPK7 4020 0.055 0.4 NO
34 ITPR1 ITPR1 ITPR1 4458 0.047 0.38 NO
35 PLD2 PLD2 PLD2 4495 0.047 0.39 NO
36 MAP2K1 MAP2K1 MAP2K1 4520 0.046 0.39 NO
37 MAP2K2 MAP2K2 MAP2K2 4749 0.043 0.38 NO
38 ADCY6 ADCY6 ADCY6 4762 0.043 0.39 NO
39 PLA2G2F PLA2G2F PLA2G2F 5215 0.036 0.37 NO
40 MAPK8 MAPK8 MAPK8 5431 0.034 0.36 NO
41 ITPR3 ITPR3 ITPR3 5545 0.032 0.36 NO
42 MAPK9 MAPK9 MAPK9 5716 0.03 0.35 NO
43 MAP2K3 MAP2K3 MAP2K3 5813 0.029 0.35 NO
44 ATF4 ATF4 ATF4 5839 0.029 0.35 NO
45 GNA11 GNA11 GNA11 6274 0.024 0.33 NO
46 HRAS HRAS HRAS 6323 0.023 0.33 NO
47 MAP3K4 MAP3K4 MAP3K4 6325 0.023 0.33 NO
48 MAPK1 MAPK1 MAPK1 6639 0.02 0.32 NO
49 MMP14 MMP14 MMP14 6732 0.019 0.32 NO
50 EGFR EGFR EGFR 6956 0.016 0.31 NO
51 PLCB3 PLCB3 PLCB3 7018 0.016 0.3 NO
52 GNAS GNAS GNAS 7550 0.01 0.28 NO
53 SRC SRC SRC 7791 0.0081 0.26 NO
54 PLA2G4E PLA2G4E PLA2G4E 7887 0.0073 0.26 NO
55 MAP2K7 MAP2K7 MAP2K7 7913 0.007 0.26 NO
56 JUN JUN JUN 7960 0.0065 0.26 NO
57 PLA2G1B PLA2G1B PLA2G1B 8037 0.0056 0.25 NO
58 MAPK12 MAPK12 MAPK12 8796 -0.0018 0.21 NO
59 PTK2B PTK2B PTK2B 9029 -0.0039 0.2 NO
60 CDC42 CDC42 CDC42 9490 -0.008 0.18 NO
61 CAMK2G CAMK2G CAMK2G 9730 -0.01 0.16 NO
62 MAP3K2 MAP3K2 MAP3K2 9882 -0.012 0.16 NO
63 ELK1 ELK1 ELK1 10183 -0.015 0.14 NO
64 SOS2 SOS2 SOS2 10269 -0.016 0.14 NO
65 KRAS KRAS KRAS 10401 -0.017 0.14 NO
66 PRKCB PRKCB PRKCB 10443 -0.017 0.14 NO
67 CALM1 CALM1 CALM1 10690 -0.02 0.12 NO
68 ADCY1 ADCY1 ADCY1 10935 -0.022 0.11 NO
69 RAF1 RAF1 RAF1 11252 -0.026 0.1 NO
70 PLA2G12A PLA2G12A PLA2G12A 11480 -0.029 0.091 NO
71 MAP3K3 MAP3K3 MAP3K3 11920 -0.034 0.071 NO
72 PRKACA PRKACA PRKACA 11928 -0.034 0.075 NO
73 GRB2 GRB2 GRB2 12151 -0.037 0.067 NO
74 MAPK14 MAPK14 MAPK14 12442 -0.041 0.056 NO
75 CALM3 CALM3 CALM3 12677 -0.044 0.048 NO
76 MAP3K1 MAP3K1 MAP3K1 12707 -0.044 0.052 NO
77 CALM2 CALM2 CALM2 13211 -0.051 0.03 NO
78 PRKX PRKX PRKX 13239 -0.052 0.035 NO
79 SOS1 SOS1 SOS1 13329 -0.053 0.036 NO
80 PLA2G12B PLA2G12B PLA2G12B 13452 -0.055 0.036 NO
81 NRAS NRAS NRAS 13512 -0.056 0.039 NO
82 PLD1 PLD1 PLD1 13815 -0.061 0.029 NO
83 PLA2G2A PLA2G2A PLA2G2A 13852 -0.062 0.035 NO
84 CGA CGA CGA 14167 -0.069 0.025 NO
85 MAPK3 MAPK3 MAPK3 14479 -0.077 0.017 NO
86 PLCB2 PLCB2 PLCB2 14757 -0.084 0.012 NO
87 CACNA1F CACNA1F CACNA1F 14774 -0.084 0.021 NO
88 PRKCD PRKCD PRKCD 14903 -0.088 0.024 NO
89 PLA2G2D PLA2G2D PLA2G2D 14991 -0.091 0.03 NO
90 LHB LHB LHB 15660 -0.12 0.0067 NO
91 ADCY7 ADCY7 ADCY7 16015 -0.13 0.0026 NO
92 CAMK2B CAMK2B CAMK2B 17226 -0.21 -0.038 NO
93 ADCY5 ADCY5 ADCY5 17681 -0.27 -0.032 NO
94 MAPK10 MAPK10 MAPK10 18052 -0.32 -0.016 NO
95 ADCY9 ADCY9 ADCY9 18219 -0.36 0.017 NO

Figure S29.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA P38MAPK PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA P38MAPK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA WNT PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DYNC1I1 DYNC1I1 DYNC1I1 9 0.57 0.14 YES
2 CREB3L1 CREB3L1 CREB3L1 13 0.55 0.27 YES
3 AQP3 AQP3 AQP3 494 0.24 0.3 YES
4 AQP2 AQP2 AQP2 669 0.21 0.35 YES
5 CREB3L4 CREB3L4 CREB3L4 857 0.19 0.38 YES
6 CREB5 CREB5 CREB5 1640 0.13 0.37 NO
7 VAMP2 VAMP2 VAMP2 2911 0.081 0.32 NO
8 CREB3L2 CREB3L2 CREB3L2 3102 0.075 0.33 NO
9 NSF NSF NSF 3467 0.066 0.33 NO
10 DYNC1LI2 DYNC1LI2 DYNC1LI2 3728 0.061 0.33 NO
11 PRKACB PRKACB PRKACB 3874 0.058 0.33 NO
12 DCTN6 DCTN6 DCTN6 4478 0.047 0.31 NO
13 ADCY6 ADCY6 ADCY6 4762 0.043 0.31 NO
14 RAB11A RAB11A RAB11A 4817 0.042 0.32 NO
15 DCTN4 DCTN4 DCTN4 5461 0.033 0.29 NO
16 CREB3 CREB3 CREB3 5746 0.03 0.28 NO
17 RAB5A RAB5A RAB5A 5760 0.03 0.29 NO
18 DYNC1LI1 DYNC1LI1 DYNC1LI1 6134 0.025 0.27 NO
19 ARHGDIA ARHGDIA ARHGDIA 6368 0.023 0.27 NO
20 DYNC1I2 DYNC1I2 DYNC1I2 7052 0.015 0.23 NO
21 GNAS GNAS GNAS 7550 0.01 0.21 NO
22 DYNC1H1 DYNC1H1 DYNC1H1 7561 0.01 0.21 NO
23 RAB11B RAB11B RAB11B 7706 0.009 0.2 NO
24 DCTN5 DCTN5 DCTN5 8899 -0.0027 0.14 NO
25 DCTN2 DCTN2 DCTN2 9108 -0.0048 0.13 NO
26 ARHGDIB ARHGDIB ARHGDIB 9362 -0.0069 0.12 NO
27 DYNLL2 DYNLL2 DYNLL2 10153 -0.014 0.08 NO
28 CREB3L3 CREB3L3 CREB3L3 10359 -0.016 0.073 NO
29 STX4 STX4 STX4 10417 -0.017 0.074 NO
30 RAB5C RAB5C RAB5C 10661 -0.02 0.066 NO
31 RAB5B RAB5B RAB5B 10725 -0.02 0.067 NO
32 DCTN1 DCTN1 DCTN1 11589 -0.03 0.028 NO
33 CREB1 CREB1 CREB1 11717 -0.032 0.028 NO
34 PRKACA PRKACA PRKACA 11928 -0.034 0.025 NO
35 DYNLL1 DYNLL1 DYNLL1 13236 -0.052 -0.033 NO
36 PRKX PRKX PRKX 13239 -0.052 -0.02 NO
37 DYNC2LI1 DYNC2LI1 DYNC2LI1 13652 -0.058 -0.028 NO
38 AQP4 AQP4 AQP4 17494 -0.24 -0.18 NO
39 DYNC2H1 DYNC2H1 DYNC2H1 17810 -0.28 -0.13 NO
40 AVPR2 AVPR2 AVPR2 18026 -0.32 -0.06 NO
41 ADCY9 ADCY9 ADCY9 18219 -0.36 0.017 NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BMP4 BMP4 BMP4 74 0.44 0.12 YES
2 TGFB2 TGFB2 TGFB2 362 0.27 0.19 YES
3 NOG NOG NOG 422 0.26 0.26 YES
4 FZD1 FZD1 FZD1 620 0.22 0.31 YES
5 BMP5 BMP5 BMP5 622 0.22 0.38 YES
6 BMP2 BMP2 BMP2 734 0.2 0.43 YES
7 HNF1A HNF1A HNF1A 757 0.2 0.49 YES
8 NPPA NPPA NPPA 2236 0.1 0.44 NO
9 ACVR1 ACVR1 ACVR1 3044 0.077 0.42 NO
10 BMPR1A BMPR1A BMPR1A 3737 0.061 0.4 NO
11 SMAD5 SMAD5 SMAD5 3831 0.059 0.41 NO
12 TGFB3 TGFB3 TGFB3 4138 0.053 0.41 NO
13 TGFB1 TGFB1 TGFB1 4476 0.047 0.4 NO
14 TGFBR1 TGFBR1 TGFBR1 5777 0.03 0.34 NO
15 APC APC APC 5968 0.027 0.34 NO
16 SMAD1 SMAD1 SMAD1 6393 0.022 0.32 NO
17 AXIN1 AXIN1 AXIN1 6403 0.022 0.33 NO
18 BMPR2 BMPR2 BMPR2 6927 0.017 0.31 NO
19 CTNNB1 CTNNB1 CTNNB1 7319 0.013 0.29 NO
20 SMAD4 SMAD4 SMAD4 8002 0.006 0.26 NO
21 ATF2 ATF2 ATF2 8681 -0.00056 0.22 NO
22 CHRD CHRD CHRD 8690 -0.00066 0.22 NO
23 SMAD6 SMAD6 SMAD6 9087 -0.0045 0.2 NO
24 DVL1 DVL1 DVL1 9489 -0.008 0.18 NO
25 GSK3B GSK3B GSK3B 9605 -0.0091 0.18 NO
26 TGFBR2 TGFBR2 TGFBR2 10387 -0.017 0.14 NO
27 RFC1 RFC1 RFC1 10452 -0.017 0.14 NO
28 MAP3K7 MAP3K7 MAP3K7 12967 -0.048 0.017 NO
29 NPPB NPPB NPPB 13320 -0.053 0.014 NO
30 WNT1 WNT1 WNT1 13487 -0.056 0.021 NO
31 BMP7 BMP7 BMP7 16014 -0.13 -0.077 NO
32 MYL2 MYL2 MYL2 16026 -0.13 -0.039 NO
33 NKX2-5 NKX2-5 NKX2-5 16666 -0.17 -0.024 NO
34 GATA4 GATA4 GATA4 16906 -0.18 0.017 NO
35 TGFBR3 TGFBR3 TGFBR3 17478 -0.24 0.057 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 FATTY ACID METABOLISM.

Figure S34.  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 ETHER LIPID 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 CAPNS2 CAPNS2 CAPNS2 142 0.38 0.2 YES
2 ITGA1 ITGA1 ITGA1 295 0.3 0.35 YES
3 ITGB1 ITGB1 ITGB1 3925 0.057 0.19 NO
4 PPP1R12B PPP1R12B PPP1R12B 4095 0.054 0.21 NO
5 BCAR1 BCAR1 BCAR1 4503 0.047 0.21 NO
6 MAP2K1 MAP2K1 MAP2K1 4520 0.046 0.24 NO
7 ACTA1 ACTA1 ACTA1 4734 0.044 0.25 NO
8 MAP2K2 MAP2K2 MAP2K2 4749 0.043 0.27 NO
9 ACTN1 ACTN1 ACTN1 5106 0.038 0.27 NO
10 CAV1 CAV1 CAV1 5190 0.037 0.29 NO
11 MAPK8 MAPK8 MAPK8 5431 0.034 0.3 NO
12 HRAS HRAS HRAS 6323 0.023 0.26 NO
13 MAPK1 MAPK1 MAPK1 6639 0.02 0.25 NO
14 FYN FYN FYN 7329 0.013 0.22 NO
15 SHC1 SHC1 SHC1 7393 0.012 0.23 NO
16 CSK CSK CSK 7511 0.011 0.23 NO
17 ZYX ZYX ZYX 7534 0.011 0.23 NO
18 ROCK1 ROCK1 ROCK1 7611 0.01 0.23 NO
19 CAPNS1 CAPNS1 CAPNS1 7712 0.009 0.23 NO
20 SRC SRC SRC 7791 0.0081 0.23 NO
21 JUN JUN JUN 7960 0.0065 0.23 NO
22 RHOA RHOA RHOA 8685 -0.00059 0.19 NO
23 TNS1 TNS1 TNS1 9666 -0.0097 0.14 NO
24 RAPGEF1 RAPGEF1 RAPGEF1 9700 -0.01 0.14 NO
25 RAP1A RAP1A RAP1A 9933 -0.012 0.14 NO
26 BCR BCR BCR 10189 -0.015 0.13 NO
27 PTK2 PTK2 PTK2 11230 -0.026 0.09 NO
28 RAF1 RAF1 RAF1 11252 -0.026 0.1 NO
29 CAPN1 CAPN1 CAPN1 11619 -0.03 0.1 NO
30 CRKL CRKL CRKL 11843 -0.033 0.11 NO
31 VCL VCL VCL 11997 -0.035 0.12 NO
32 GRB2 GRB2 GRB2 12151 -0.037 0.13 NO
33 SOS1 SOS1 SOS1 13329 -0.053 0.094 NO
34 PXN PXN PXN 13496 -0.056 0.12 NO
35 MAPK3 MAPK3 MAPK3 14479 -0.077 0.1 NO
36 ACTN3 ACTN3 ACTN3 14837 -0.086 0.13 NO
37 ACTN2 ACTN2 ACTN2 15814 -0.12 0.15 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 ETHER LIPID METABOLISM.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ETHER LIPID 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 LINOLEIC ACID 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 PLA2G4A PLA2G4A PLA2G4A 26 0.51 0.19 YES
2 TGFB2 TGFB2 TGFB2 362 0.27 0.28 YES
3 RPS6KA5 RPS6KA5 RPS6KA5 980 0.18 0.31 YES
4 MAP2K6 MAP2K6 MAP2K6 1103 0.17 0.36 YES
5 MAP3K9 MAP3K9 MAP3K9 2196 0.1 0.34 NO
6 MAP2K4 MAP2K4 MAP2K4 3133 0.075 0.32 NO
7 TRADD TRADD TRADD 3370 0.068 0.34 NO
8 MEF2C MEF2C MEF2C 3519 0.065 0.35 NO
9 TGFB3 TGFB3 TGFB3 4138 0.053 0.34 NO
10 RAPGEF2 RAPGEF2 RAPGEF2 4162 0.052 0.36 NO
11 TGFB1 TGFB1 TGFB1 4476 0.047 0.36 NO
12 MEF2D MEF2D MEF2D 5734 0.03 0.3 NO
13 TGFBR1 TGFBR1 TGFBR1 5777 0.03 0.31 NO
14 MAPKAPK2 MAPKAPK2 MAPKAPK2 6135 0.025 0.3 NO
15 MAP3K5 MAP3K5 MAP3K5 6201 0.024 0.3 NO
16 HRAS HRAS HRAS 6323 0.023 0.31 NO
17 SHC1 SHC1 SHC1 7393 0.012 0.25 NO
18 RAC1 RAC1 RAC1 7973 0.0064 0.22 NO
19 ATF2 ATF2 ATF2 8681 -0.00056 0.19 NO
20 RIPK1 RIPK1 RIPK1 8802 -0.0018 0.18 NO
21 CDC42 CDC42 CDC42 9490 -0.008 0.15 NO
22 MEF2A MEF2A MEF2A 9925 -0.012 0.13 NO
23 ELK1 ELK1 ELK1 10183 -0.015 0.12 NO
24 MAX MAX MAX 10665 -0.02 0.1 NO
25 MKNK1 MKNK1 MKNK1 10812 -0.021 0.1 NO
26 DAXX DAXX DAXX 11296 -0.027 0.084 NO
27 HSPB2 HSPB2 HSPB2 11451 -0.028 0.087 NO
28 CREB1 CREB1 CREB1 11717 -0.032 0.084 NO
29 TRAF2 TRAF2 TRAF2 11741 -0.032 0.095 NO
30 GRB2 GRB2 GRB2 12151 -0.037 0.086 NO
31 HSPB1 HSPB1 HSPB1 12195 -0.037 0.098 NO
32 MAPK14 MAPK14 MAPK14 12442 -0.041 0.1 NO
33 MAP3K1 MAP3K1 MAP3K1 12707 -0.044 0.1 NO
34 MAP3K7 MAP3K7 MAP3K7 12967 -0.048 0.11 NO
35 DDIT3 DDIT3 DDIT3 13359 -0.053 0.1 NO
36 MAPKAPK5 MAPKAPK5 MAPKAPK5 13687 -0.059 0.11 NO
37 STAT1 STAT1 STAT1 15642 -0.12 0.047 NO
38 MYC MYC MYC 15873 -0.12 0.081 NO
39 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 16612 -0.17 0.1 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 LINOLEIC ACID METABOLISM.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LINOLEIC 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 SPHINGOLIPID 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 BMP4 BMP4 BMP4 74 0.44 0.064 YES
2 INHBA INHBA INHBA 159 0.36 0.12 YES
3 SMAD9 SMAD9 SMAD9 315 0.29 0.15 YES
4 TGFB2 TGFB2 TGFB2 362 0.27 0.19 YES
5 AMH AMH AMH 370 0.27 0.23 YES
6 BMP5 BMP5 BMP5 622 0.22 0.25 YES
7 BMP8A BMP8A BMP8A 657 0.21 0.28 YES
8 BMP2 BMP2 BMP2 734 0.2 0.31 YES
9 NODAL NODAL NODAL 848 0.19 0.34 YES
10 THBS2 THBS2 THBS2 1141 0.16 0.34 YES
11 IFNG IFNG IFNG 1516 0.14 0.35 YES
12 BMPR1B BMPR1B BMPR1B 1618 0.13 0.36 YES
13 ACVR1C ACVR1C ACVR1C 2043 0.11 0.36 YES
14 THBS1 THBS1 THBS1 2083 0.11 0.37 YES
15 ID3 ID3 ID3 2086 0.11 0.39 YES
16 GDF5 GDF5 GDF5 2141 0.11 0.4 YES
17 PPP2R1B PPP2R1B PPP2R1B 2158 0.11 0.42 YES
18 ID4 ID4 ID4 2711 0.087 0.4 NO
19 ACVR1 ACVR1 ACVR1 3044 0.077 0.39 NO
20 ID2 ID2 ID2 3055 0.077 0.41 NO
21 FST FST FST 3404 0.068 0.4 NO
22 BMPR1A BMPR1A BMPR1A 3737 0.061 0.39 NO
23 SMAD5 SMAD5 SMAD5 3831 0.059 0.39 NO
24 TGFB3 TGFB3 TGFB3 4138 0.053 0.38 NO
25 TGFB1 TGFB1 TGFB1 4476 0.047 0.37 NO
26 ACVRL1 ACVRL1 ACVRL1 4737 0.044 0.37 NO
27 ROCK2 ROCK2 ROCK2 4971 0.04 0.36 NO
28 ID1 ID1 ID1 5011 0.04 0.36 NO
29 LTBP1 LTBP1 LTBP1 5059 0.039 0.37 NO
30 DCN DCN DCN 5178 0.037 0.37 NO
31 THBS4 THBS4 THBS4 5546 0.032 0.35 NO
32 BMP8B BMP8B BMP8B 5771 0.03 0.34 NO
33 TGFBR1 TGFBR1 TGFBR1 5777 0.03 0.35 NO
34 SP1 SP1 SP1 6189 0.024 0.33 NO
35 ZFYVE16 ZFYVE16 ZFYVE16 6285 0.023 0.33 NO
36 SMAD1 SMAD1 SMAD1 6393 0.022 0.33 NO
37 MAPK1 MAPK1 MAPK1 6639 0.02 0.32 NO
38 SMAD2 SMAD2 SMAD2 6828 0.018 0.31 NO
39 BMPR2 BMPR2 BMPR2 6927 0.017 0.31 NO
40 PPP2CB PPP2CB PPP2CB 7387 0.012 0.28 NO
41 RBX1 RBX1 RBX1 7497 0.011 0.28 NO
42 SMURF2 SMURF2 SMURF2 7546 0.011 0.28 NO
43 ROCK1 ROCK1 ROCK1 7611 0.01 0.28 NO
44 EP300 EP300 EP300 7732 0.0087 0.27 NO
45 RBL2 RBL2 RBL2 7792 0.0081 0.27 NO
46 SMAD4 SMAD4 SMAD4 8002 0.006 0.26 NO
47 COMP COMP COMP 8040 0.0056 0.26 NO
48 E2F4 E2F4 E2F4 8153 0.0046 0.25 NO
49 PPP2CA PPP2CA PPP2CA 8664 -0.00038 0.22 NO
50 RHOA RHOA RHOA 8685 -0.00059 0.22 NO
51 CHRD CHRD CHRD 8690 -0.00066 0.22 NO
52 RPS6KB1 RPS6KB1 RPS6KB1 8785 -0.0016 0.22 NO
53 SMAD6 SMAD6 SMAD6 9087 -0.0045 0.2 NO
54 INHBB INHBB INHBB 9757 -0.01 0.17 NO
55 TFDP1 TFDP1 TFDP1 9779 -0.011 0.17 NO
56 BMP6 BMP6 BMP6 10003 -0.013 0.16 NO
57 PPP2R1A PPP2R1A PPP2R1A 10068 -0.014 0.16 NO
58 CREBBP CREBBP CREBBP 10187 -0.015 0.15 NO
59 GDF7 GDF7 GDF7 10217 -0.015 0.15 NO
60 SKP1 SKP1 SKP1 10374 -0.017 0.15 NO
61 TGFBR2 TGFBR2 TGFBR2 10387 -0.017 0.15 NO
62 AMHR2 AMHR2 AMHR2 10698 -0.02 0.14 NO
63 CUL1 CUL1 CUL1 10843 -0.022 0.13 NO
64 SMAD7 SMAD7 SMAD7 11527 -0.029 0.099 NO
65 RBL1 RBL1 RBL1 11654 -0.031 0.097 NO
66 ACVR2A ACVR2A ACVR2A 12081 -0.036 0.079 NO
67 RPS6KB2 RPS6KB2 RPS6KB2 12283 -0.038 0.074 NO
68 PITX2 PITX2 PITX2 12425 -0.04 0.073 NO
69 ZFYVE9 ZFYVE9 ZFYVE9 12553 -0.042 0.072 NO
70 SMAD3 SMAD3 SMAD3 12841 -0.046 0.064 NO
71 SMURF1 SMURF1 SMURF1 13353 -0.053 0.044 NO
72 LEFTY2 LEFTY2 LEFTY2 13478 -0.055 0.046 NO
73 MAPK3 MAPK3 MAPK3 14479 -0.077 0.0039 NO
74 INHBC INHBC INHBC 15084 -0.094 -0.014 NO
75 THBS3 THBS3 THBS3 15190 -0.098 -0.0048 NO
76 LEFTY1 LEFTY1 LEFTY1 15482 -0.11 -0.0037 NO
77 ACVR2B ACVR2B ACVR2B 15718 -0.12 0.0019 NO
78 MYC MYC MYC 15873 -0.12 0.013 NO
79 CDKN2B CDKN2B CDKN2B 16002 -0.13 0.026 NO
80 BMP7 BMP7 BMP7 16014 -0.13 0.046 NO
81 E2F5 E2F5 E2F5 16145 -0.14 0.06 NO
82 GDF6 GDF6 GDF6 16206 -0.14 0.079 NO
83 TNF TNF TNF 16332 -0.15 0.095 NO
84 INHBE INHBE INHBE 16424 -0.15 0.11 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 SPHINGOLIPID METABOLISM.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPHINGOLIPID 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 FMLP PATHWAY 35 genes.ES.table 0.44 1.6 0.053 0.56 0.77 0.34 0.29 0.24 0.35 0.18
KEGG GLYCOLYSIS GLUCONEOGENESIS 59 genes.ES.table 0.52 1.7 0.0062 0.35 0.42 0.32 0.18 0.26 0 0.096
KEGG FATTY ACID METABOLISM 41 genes.ES.table 0.54 1.7 0.015 0.49 0.6 0.42 0.22 0.32 0.23 0.14
KEGG STEROID HORMONE BIOSYNTHESIS 38 genes.ES.table 0.56 1.4 0.057 0.66 0.94 0.34 0.12 0.3 0.5 0.19
KEGG HISTIDINE METABOLISM 28 genes.ES.table 0.5 1.4 0.1 0.7 0.97 0.32 0.12 0.28 0.57 0.21
KEGG TYROSINE METABOLISM 40 genes.ES.table 0.58 1.6 0.012 0.63 0.76 0.35 0.1 0.31 0.37 0.2
KEGG GLUTATHIONE METABOLISM 46 genes.ES.table 0.57 1.8 0.01 0.47 0.32 0.41 0.18 0.34 0 0.16
KEGG STARCH AND SUCROSE METABOLISM 35 genes.ES.table 0.54 1.5 0.033 0.59 0.88 0.26 0.1 0.23 0.41 0.16
KEGG ETHER LIPID METABOLISM 30 genes.ES.table 0.51 1.5 0.047 0.61 0.9 0.53 0.28 0.39 0.44 0.18
KEGG BUTANOATE METABOLISM 30 genes.ES.table 0.47 1.4 0.097 0.67 0.94 0.53 0.27 0.39 0.49 0.21
genes ES table in pathway: BIOCARTA FMLP 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 DNAI1 DNAI1 DNAI1 18 1.3 0.093 YES
2 DNAH3 DNAH3 DNAH3 73 1.1 0.17 YES
3 DNAI2 DNAI2 DNAI2 157 0.86 0.23 YES
4 DNAH2 DNAH2 DNAH2 277 0.65 0.27 YES
5 GRM5 GRM5 GRM5 333 0.57 0.31 YES
6 DNALI1 DNALI1 DNALI1 503 0.44 0.34 YES
7 GRIN1 GRIN1 GRIN1 841 0.32 0.34 YES
8 PLCB1 PLCB1 PLCB1 1039 0.28 0.35 YES
9 CREB3L1 CREB3L1 CREB3L1 1318 0.24 0.35 YES
10 DNAL1 DNAL1 DNAL1 1467 0.22 0.36 YES
11 PLCB4 PLCB4 PLCB4 1638 0.2 0.37 YES
12 DNAH1 DNAH1 DNAH1 1676 0.2 0.38 YES
13 CREB3L4 CREB3L4 CREB3L4 1828 0.19 0.39 YES
14 DNAL4 DNAL4 DNAL4 2142 0.16 0.38 YES
15 PLCB2 PLCB2 PLCB2 2201 0.16 0.39 YES
16 BDNF BDNF BDNF 2658 0.14 0.38 NO
17 CREB5 CREB5 CREB5 2833 0.12 0.38 NO
18 IFT57 IFT57 IFT57 3101 0.12 0.37 NO
19 ITPR1 ITPR1 ITPR1 3181 0.11 0.37 NO
20 UQCRHL UQCRHL UQCRHL 3448 0.1 0.37 NO
21 COX6B2 COX6B2 COX6B2 3549 0.099 0.37 NO
22 UQCR11 UQCR11 UQCR11 3677 0.094 0.37 NO
23 CREB3L2 CREB3L2 CREB3L2 3860 0.088 0.37 NO
24 UQCRH UQCRH UQCRH 3919 0.086 0.37 NO
25 POLR2J2 POLR2J2 POLR2J2 3940 0.086 0.37 NO
26 PPARG PPARG PPARG 4067 0.082 0.37 NO
27 POLR2I POLR2I POLR2I 4153 0.08 0.38 NO
28 NDUFS7 NDUFS7 NDUFS7 4358 0.074 0.37 NO
29 NDUFA7 NDUFA7 NDUFA7 4364 0.074 0.37 NO
30 COX8C COX8C COX8C 4435 0.072 0.38 NO
31 COX4I1 COX4I1 COX4I1 4520 0.07 0.38 NO
32 COX7A1 COX7A1 COX7A1 4621 0.067 0.38 NO
33 NDUFA3 NDUFA3 NDUFA3 4678 0.066 0.38 NO
34 ATP5D ATP5D ATP5D 4769 0.064 0.38 NO
35 NDUFC1 NDUFC1 NDUFC1 5025 0.058 0.37 NO
36 PPID PPID PPID 5058 0.057 0.37 NO
37 COX7C COX7C COX7C 5300 0.053 0.36 NO
38 BBC3 BBC3 BBC3 5328 0.052 0.36 NO
39 SLC25A6 SLC25A6 SLC25A6 5372 0.051 0.36 NO
40 COX6A1 COX6A1 COX6A1 5432 0.05 0.37 NO
41 NDUFA2 NDUFA2 NDUFA2 5557 0.048 0.36 NO
42 SLC25A4 SLC25A4 SLC25A4 5561 0.048 0.37 NO
43 UQCRQ UQCRQ UQCRQ 5659 0.046 0.36 NO
44 ATP5G2 ATP5G2 ATP5G2 5706 0.045 0.36 NO
45 GPX1 GPX1 GPX1 5838 0.043 0.36 NO
46 NDUFS5 NDUFS5 NDUFS5 5863 0.043 0.36 NO
47 AP2B1 AP2B1 AP2B1 6011 0.04 0.36 NO
48 COX5A COX5A COX5A 6041 0.04 0.36 NO
49 UQCR10 UQCR10 UQCR10 6121 0.038 0.36 NO
50 AP2A2 AP2A2 AP2A2 6198 0.037 0.36 NO
51 NDUFB1 NDUFB1 NDUFB1 6244 0.036 0.36 NO
52 SDHA SDHA SDHA 6251 0.036 0.36 NO
53 POLR2E POLR2E POLR2E 6292 0.036 0.36 NO
54 AP2S1 AP2S1 AP2S1 6381 0.034 0.36 NO
55 NDUFA8 NDUFA8 NDUFA8 6394 0.034 0.36 NO
56 ATP5F1 ATP5F1 ATP5F1 6404 0.034 0.36 NO
57 NDUFB8 NDUFB8 NDUFB8 6478 0.033 0.36 NO
58 TP53 TP53 TP53 6544 0.032 0.36 NO
59 POLR2G POLR2G POLR2G 6553 0.032 0.36 NO
60 CLTB CLTB CLTB 6554 0.032 0.36 NO
61 COX7B COX7B COX7B 6559 0.032 0.36 NO
62 NDUFA1 NDUFA1 NDUFA1 6605 0.032 0.36 NO
63 UQCRC2 UQCRC2 UQCRC2 6926 0.027 0.35 NO
64 NDUFS8 NDUFS8 NDUFS8 7028 0.025 0.35 NO
65 NRF1 NRF1 NRF1 7056 0.025 0.35 NO
66 POLR2J POLR2J POLR2J 7161 0.023 0.34 NO
67 NDUFV3 NDUFV3 NDUFV3 7162 0.023 0.34 NO
68 GNAQ GNAQ GNAQ 7274 0.022 0.34 NO
69 UQCRC1 UQCRC1 UQCRC1 7285 0.022 0.34 NO
70 ATP5C1 ATP5C1 ATP5C1 7287 0.022 0.34 NO
71 CLTA CLTA CLTA 7294 0.022 0.34 NO
72 UQCRB UQCRB UQCRB 7487 0.019 0.34 NO
73 NDUFS3 NDUFS3 NDUFS3 7599 0.018 0.33 NO
74 VDAC3 VDAC3 VDAC3 7663 0.017 0.33 NO
75 NDUFB10 NDUFB10 NDUFB10 7804 0.015 0.32 NO
76 CASP8 CASP8 CASP8 7835 0.015 0.32 NO
77 SOD1 SOD1 SOD1 7876 0.015 0.32 NO
78 DCTN1 DCTN1 DCTN1 7963 0.014 0.32 NO
79 POLR2J3 POLR2J3 POLR2J3 7979 0.013 0.32 NO
80 NDUFA10 NDUFA10 NDUFA10 7990 0.013 0.32 NO
81 CASP9 CASP9 CASP9 8098 0.012 0.31 NO
82 COX8A COX8A COX8A 8101 0.012 0.31 NO
83 SIN3A SIN3A SIN3A 8113 0.012 0.31 NO
84 NDUFA5 NDUFA5 NDUFA5 8115 0.012 0.31 NO
85 ATP5A1 ATP5A1 ATP5A1 8128 0.012 0.31 NO
86 COX7A2 COX7A2 COX7A2 8233 0.01 0.31 NO
87 NDUFA6 NDUFA6 NDUFA6 8254 0.01 0.31 NO
88 SOD2 SOD2 SOD2 8278 0.0097 0.31 NO
89 COX6C COX6C COX6C 8405 0.0084 0.3 NO
90 DCTN4 DCTN4 DCTN4 8484 0.0075 0.3 NO
91 NDUFC2 NDUFC2 NDUFC2 8601 0.0062 0.29 NO
92 NDUFB2 NDUFB2 NDUFB2 8611 0.0061 0.29 NO
93 NDUFS2 NDUFS2 NDUFS2 8621 0.006 0.29 NO
94 AP2A1 AP2A1 AP2A1 8629 0.0059 0.29 NO
95 BAX BAX BAX 8664 0.0056 0.29 NO
96 NDUFS4 NDUFS4 NDUFS4 8678 0.0054 0.29 NO
97 ATP5E ATP5E ATP5E 8682 0.0054 0.29 NO
98 HIP1 HIP1 HIP1 8782 0.0042 0.29 NO
99 CASP3 CASP3 CASP3 8837 0.0036 0.28 NO
100 POLR2L POLR2L POLR2L 8849 0.0035 0.28 NO
101 NDUFA9 NDUFA9 NDUFA9 8853 0.0034 0.28 NO
102 VDAC2 VDAC2 VDAC2 8979 0.002 0.28 NO
103 COX6B1 COX6B1 COX6B1 9057 0.0012 0.27 NO
104 NDUFA4 NDUFA4 NDUFA4 9486 -0.0031 0.25 NO
105 NDUFB4 NDUFB4 NDUFB4 9518 -0.0035 0.25 NO
106 CREB3 CREB3 CREB3 9538 -0.0037 0.25 NO
107 EP300 EP300 EP300 9596 -0.0045 0.24 NO
108 SP1 SP1 SP1 9647 -0.005 0.24 NO
109 COX7A2L COX7A2L COX7A2L 9671 -0.0054 0.24 NO
110 CREBBP CREBBP CREBBP 9717 -0.0059 0.24 NO
111 COX5B COX5B COX5B 9787 -0.0066 0.24 NO
112 VDAC1 VDAC1 VDAC1 9834 -0.007 0.23 NO
113 SDHC SDHC SDHC 10083 -0.0094 0.22 NO
114 CREB3L3 CREB3L3 CREB3L3 10163 -0.01 0.22 NO
115 ATP5G1 ATP5G1 ATP5G1 10201 -0.011 0.22 NO
116 CLTC CLTC CLTC 10230 -0.011 0.22 NO
117 NDUFV1 NDUFV1 NDUFV1 10264 -0.012 0.21 NO
118 ATP5O ATP5O ATP5O 10341 -0.012 0.21 NO
119 NDUFB7 NDUFB7 NDUFB7 10345 -0.012 0.21 NO
120 CYC1 CYC1 CYC1 10367 -0.013 0.21 NO
121 POLR2C POLR2C POLR2C 10377 -0.013 0.21 NO
122 NDUFB5 NDUFB5 NDUFB5 10424 -0.013 0.21 NO
123 DCTN2 DCTN2 DCTN2 10475 -0.014 0.21 NO
124 NDUFV2 NDUFV2 NDUFV2 10487 -0.014 0.21 NO
125 SDHB SDHB SDHB 10605 -0.015 0.2 NO
126 TGM2 TGM2 TGM2 10648 -0.015 0.2 NO
127 NDUFS6 NDUFS6 NDUFS6 10653 -0.016 0.2 NO
128 NDUFAB1 NDUFAB1 NDUFAB1 10703 -0.016 0.2 NO
129 HDAC1 HDAC1 HDAC1 10784 -0.017 0.2 NO
130 POLR2H POLR2H POLR2H 10938 -0.019 0.19 NO
131 POLR2A POLR2A POLR2A 11014 -0.019 0.19 NO
132 AP2M1 AP2M1 AP2M1 11210 -0.021 0.18 NO
133 POLR2B POLR2B POLR2B 11218 -0.021 0.18 NO
134 ATP5B ATP5B ATP5B 11547 -0.025 0.17 NO
135 ATP5H ATP5H ATP5H 11611 -0.026 0.16 NO
136 POLR2F POLR2F POLR2F 11687 -0.027 0.16 NO
137 NDUFS1 NDUFS1 NDUFS1 11827 -0.028 0.16 NO
138 SLC25A5 SLC25A5 SLC25A5 11869 -0.029 0.16 NO
139 NDUFB3 NDUFB3 NDUFB3 11922 -0.03 0.16 NO
140 ATP5G3 ATP5G3 ATP5G3 11964 -0.03 0.16 NO
141 POLR2K POLR2K POLR2K 12033 -0.031 0.16 NO
142 ATP5J ATP5J ATP5J 12145 -0.032 0.15 NO
143 SDHD SDHD SDHD 12149 -0.032 0.15 NO
144 TBPL1 TBPL1 TBPL1 12213 -0.033 0.15 NO
145 HTT HTT HTT 12329 -0.035 0.15 NO
146 TBP TBP TBP 12852 -0.041 0.12 NO
147 DLG4 DLG4 DLG4 12859 -0.041 0.13 NO
148 CREB1 CREB1 CREB1 13083 -0.044 0.12 NO
149 RCOR1 RCOR1 RCOR1 13139 -0.045 0.12 NO
150 NDUFB9 NDUFB9 NDUFB9 13242 -0.047 0.12 NO
151 REST REST REST 13257 -0.047 0.12 NO
152 HDAC2 HDAC2 HDAC2 13410 -0.049 0.11 NO
153 CYCS CYCS CYCS 13436 -0.049 0.12 NO
154 NDUFB6 NDUFB6 NDUFB6 13470 -0.05 0.12 NO
155 UQCRFS1 UQCRFS1 UQCRFS1 13488 -0.05 0.12 NO
156 APAF1 APAF1 APAF1 13835 -0.056 0.11 NO
157 TAF4 TAF4 TAF4 14350 -0.065 0.083 NO
158 PLCB3 PLCB3 PLCB3 14964 -0.078 0.055 NO
159 POLR2D POLR2D POLR2D 15214 -0.084 0.048 NO
160 SLC25A31 SLC25A31 SLC25A31 15506 -0.093 0.039 NO
161 TFAM TFAM TFAM 15570 -0.095 0.042 NO
162 CLTCL1 CLTCL1 CLTCL1 16120 -0.11 0.021 NO
163 UCP1 UCP1 UCP1 16580 -0.14 0.006 NO
164 COX6A2 COX6A2 COX6A2 16639 -0.14 0.013 NO
165 TAF4B TAF4B TAF4B 17081 -0.16 0.0014 NO
166 GRIN2B GRIN2B GRIN2B 17181 -0.17 0.0089 NO
167 PPARGC1A PPARGC1A PPARGC1A 17274 -0.18 0.017 NO
168 NDUFA4L2 NDUFA4L2 NDUFA4L2 17481 -0.2 0.021 NO
169 HAP1 HAP1 HAP1 17584 -0.21 0.03 NO
170 COX4I2 COX4I2 COX4I2 18126 -0.28 0.022 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 FMLP PATHWAY.

Figure S42.  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: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 GSTA3 GSTA3 GSTA3 43 1.2 0.23 YES
2 GSTA1 GSTA1 GSTA1 1196 0.26 0.21 YES
3 GSTA2 GSTA2 GSTA2 1381 0.23 0.25 YES
4 GGT6 GGT6 GGT6 1643 0.2 0.27 YES
5 ANPEP ANPEP ANPEP 1738 0.2 0.31 YES
6 GSTM5 GSTM5 GSTM5 1945 0.18 0.33 YES
7 GSTM1 GSTM1 GSTM1 2246 0.16 0.34 YES
8 MGST2 MGST2 MGST2 2302 0.15 0.37 YES
9 GPX2 GPX2 GPX2 2478 0.14 0.39 YES
10 GSR GSR GSR 2640 0.14 0.41 YES
11 GSTO2 GSTO2 GSTO2 2705 0.13 0.43 YES
12 GCLM GCLM GCLM 2831 0.12 0.45 YES
13 MGST1 MGST1 MGST1 2834 0.12 0.47 YES
14 GCLC GCLC GCLC 2846 0.12 0.5 YES
15 GSTZ1 GSTZ1 GSTZ1 2937 0.12 0.51 YES
16 IDH2 IDH2 IDH2 3080 0.12 0.53 YES
17 GGT1 GGT1 GGT1 3300 0.11 0.54 YES
18 GSTK1 GSTK1 GSTK1 3350 0.11 0.56 YES
19 GSTM2 GSTM2 GSTM2 3418 0.1 0.57 YES
20 GPX4 GPX4 GPX4 4401 0.073 0.53 NO
21 GSTT1 GSTT1 GSTT1 5524 0.048 0.48 NO
22 GSTM3 GSTM3 GSTM3 5532 0.048 0.49 NO
23 GPX1 GPX1 GPX1 5838 0.043 0.48 NO
24 G6PD G6PD G6PD 5939 0.041 0.49 NO
25 IDH1 IDH1 IDH1 6384 0.034 0.47 NO
26 SMS SMS SMS 6742 0.03 0.46 NO
27 GGT5 GGT5 GGT5 6765 0.029 0.46 NO
28 GSTP1 GSTP1 GSTP1 6823 0.028 0.46 NO
29 GSTO1 GSTO1 GSTO1 7066 0.024 0.45 NO
30 LAP3 LAP3 LAP3 7337 0.021 0.44 NO
31 GSTM4 GSTM4 GSTM4 7722 0.016 0.43 NO
32 GSTA4 GSTA4 GSTA4 7898 0.014 0.42 NO
33 GSS GSS GSS 8299 0.0095 0.4 NO
34 RRM2B RRM2B RRM2B 8333 0.0091 0.4 NO
35 TXNDC12 TXNDC12 TXNDC12 8537 0.0068 0.39 NO
36 GGCT GGCT GGCT 8677 0.0054 0.38 NO
37 GPX7 GPX7 GPX7 8788 0.0041 0.38 NO
38 OPLAH OPLAH OPLAH 8933 0.0025 0.37 NO
39 MGST3 MGST3 MGST3 10790 -0.017 0.27 NO
40 SRM SRM SRM 12759 -0.04 0.18 NO
41 GSTT2 GSTT2 GSTT2 13944 -0.058 0.12 NO
42 RRM1 RRM1 RRM1 15006 -0.079 0.08 NO
43 ODC1 ODC1 ODC1 15370 -0.089 0.077 NO
44 GGT7 GGT7 GGT7 16489 -0.13 0.042 NO
45 GPX3 GPX3 GPX3 17000 -0.16 0.046 NO
46 RRM2 RRM2 RRM2 17353 -0.19 0.063 NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 GSTA3 GSTA3 GSTA3 43 1.2 0.096 YES
2 ADH6 ADH6 ADH6 176 0.8 0.16 YES
3 FMO2 FMO2 FMO2 323 0.58 0.2 YES
4 FMO4 FMO4 FMO4 666 0.37 0.21 YES
5 ADH1B ADH1B ADH1B 682 0.37 0.24 YES
6 ALDH3A1 ALDH3A1 ALDH3A1 705 0.36 0.27 YES
7 FMO3 FMO3 FMO3 707 0.36 0.3 YES
8 ADH7 ADH7 ADH7 798 0.33 0.32 YES
9 ADH1C ADH1C ADH1C 810 0.33 0.35 YES
10 ADH1A ADH1A ADH1A 834 0.32 0.38 YES
11 MAOB MAOB MAOB 926 0.3 0.4 YES
12 CYP2D6 CYP2D6 CYP2D6 935 0.3 0.42 YES
13 UGT2B10 UGT2B10 UGT2B10 1032 0.28 0.44 YES
14 FMO5 FMO5 FMO5 1096 0.27 0.46 YES
15 ALDH1A3 ALDH1A3 ALDH1A3 1169 0.26 0.48 YES
16 GSTA1 GSTA1 GSTA1 1196 0.26 0.5 YES
17 UGT2B7 UGT2B7 UGT2B7 1261 0.24 0.51 YES
18 ALDH3B1 ALDH3B1 ALDH3B1 1353 0.23 0.53 YES
19 GSTA2 GSTA2 GSTA2 1381 0.23 0.55 YES
20 CYP2C8 CYP2C8 CYP2C8 1463 0.22 0.56 YES
21 UGT2B15 UGT2B15 UGT2B15 1505 0.22 0.58 YES
22 CYP2A6 CYP2A6 CYP2A6 1707 0.2 0.58 YES
23 MAOA MAOA MAOA 1735 0.2 0.6 YES
24 ADH4 ADH4 ADH4 1809 0.19 0.61 YES
25 UGT2B11 UGT2B11 UGT2B11 1870 0.18 0.62 YES
26 ALDH3B2 ALDH3B2 ALDH3B2 1931 0.18 0.63 YES
27 GSTM5 GSTM5 GSTM5 1945 0.18 0.65 YES
28 GSTM1 GSTM1 GSTM1 2246 0.16 0.64 YES
29 MGST2 MGST2 MGST2 2302 0.15 0.65 YES
30 CYP2E1 CYP2E1 CYP2E1 2400 0.15 0.66 YES
31 FMO1 FMO1 FMO1 2419 0.15 0.67 YES
32 GSTO2 GSTO2 GSTO2 2705 0.13 0.67 YES
33 CYP2A7 CYP2A7 CYP2A7 2745 0.13 0.68 YES
34 MGST1 MGST1 MGST1 2834 0.12 0.68 YES
35 GSTZ1 GSTZ1 GSTZ1 2937 0.12 0.69 YES
36 GSTK1 GSTK1 GSTK1 3350 0.11 0.67 NO
37 GSTM2 GSTM2 GSTM2 3418 0.1 0.68 NO
38 ADH5 ADH5 ADH5 5071 0.057 0.59 NO
39 GSTT1 GSTT1 GSTT1 5524 0.048 0.57 NO
40 GSTM3 GSTM3 GSTM3 5532 0.048 0.58 NO
41 GSTP1 GSTP1 GSTP1 6823 0.028 0.51 NO
42 GSTO1 GSTO1 GSTO1 7066 0.024 0.5 NO
43 CYP2A13 CYP2A13 CYP2A13 7070 0.024 0.5 NO
44 GSTM4 GSTM4 GSTM4 7722 0.016 0.47 NO
45 GSTA4 GSTA4 GSTA4 7898 0.014 0.46 NO
46 MGST3 MGST3 MGST3 10790 -0.017 0.3 NO
47 UGT1A6 UGT1A6 UGT1A6 12662 -0.039 0.2 NO
48 AOX1 AOX1 AOX1 13344 -0.048 0.17 NO
49 CYP2C18 CYP2C18 CYP2C18 13433 -0.049 0.17 NO
50 GSTT2 GSTT2 GSTT2 13944 -0.058 0.15 NO
51 CYP2C9 CYP2C9 CYP2C9 14432 -0.067 0.13 NO
52 CYP3A5 CYP3A5 CYP3A5 15341 -0.088 0.086 NO
53 CYP2C19 CYP2C19 CYP2C19 16288 -0.12 0.045 NO
54 CYP3A43 CYP3A43 CYP3A43 16495 -0.13 0.045 NO
55 UGT2B4 UGT2B4 UGT2B4 16815 -0.15 0.04 NO
56 CYP2B6 CYP2B6 CYP2B6 17143 -0.17 0.036 NO
57 CYP3A7 CYP3A7 CYP3A7 17680 -0.22 0.026 NO
58 CYP1A2 CYP1A2 CYP1A2 17864 -0.24 0.036 NO

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

Figure S46.  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 STEROID HORMONE BIOSYNTHESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADH6 ADH6 ADH6 176 0.8 0.11 YES
2 FBP1 FBP1 FBP1 643 0.38 0.14 YES
3 ADH1B ADH1B ADH1B 682 0.37 0.19 YES
4 ALDH3A1 ALDH3A1 ALDH3A1 705 0.36 0.24 YES
5 ADH7 ADH7 ADH7 798 0.33 0.29 YES
6 ADH1C ADH1C ADH1C 810 0.33 0.34 YES
7 ADH1A ADH1A ADH1A 834 0.32 0.38 YES
8 ALDH1A3 ALDH1A3 ALDH1A3 1169 0.26 0.4 YES
9 ALDH3B1 ALDH3B1 ALDH3B1 1353 0.23 0.43 YES
10 ADH4 ADH4 ADH4 1809 0.19 0.43 YES
11 ALDH3B2 ALDH3B2 ALDH3B2 1931 0.18 0.45 YES
12 GALM GALM GALM 2476 0.14 0.44 YES
13 PGK2 PGK2 PGK2 2653 0.14 0.45 YES
14 ALDOB ALDOB ALDOB 2697 0.13 0.47 YES
15 FBP2 FBP2 FBP2 2756 0.13 0.49 YES
16 G6PC G6PC G6PC 3131 0.11 0.48 YES
17 ACSS1 ACSS1 ACSS1 3168 0.11 0.5 YES
18 PGAM4 PGAM4 PGAM4 3242 0.11 0.51 YES
19 ALDH2 ALDH2 ALDH2 3327 0.11 0.52 YES
20 ADH5 ADH5 ADH5 5071 0.057 0.43 NO
21 PFKP PFKP PFKP 5812 0.044 0.4 NO
22 ALDH3A2 ALDH3A2 ALDH3A2 5900 0.042 0.4 NO
23 PFKL PFKL PFKL 6361 0.035 0.38 NO
24 AKR1A1 AKR1A1 AKR1A1 6444 0.034 0.38 NO
25 HK1 HK1 HK1 6464 0.034 0.39 NO
26 TPI1 TPI1 TPI1 6485 0.033 0.39 NO
27 ALDH9A1 ALDH9A1 ALDH9A1 7197 0.023 0.36 NO
28 PDHB PDHB PDHB 7444 0.02 0.34 NO
29 ALDH7A1 ALDH7A1 ALDH7A1 7477 0.019 0.35 NO
30 HK3 HK3 HK3 7478 0.019 0.35 NO
31 PGM2 PGM2 PGM2 8065 0.012 0.32 NO
32 PGAM1 PGAM1 PGAM1 8131 0.012 0.32 NO
33 LDHAL6B LDHAL6B LDHAL6B 8919 0.0026 0.28 NO
34 PKM2 PKM2 PKM2 9263 -0.00063 0.26 NO
35 ENO1 ENO1 ENO1 9662 -0.0053 0.24 NO
36 DLAT DLAT DLAT 9726 -0.006 0.23 NO
37 BPGM BPGM BPGM 10146 -0.01 0.21 NO
38 PGM1 PGM1 PGM1 10320 -0.012 0.2 NO
39 GAPDH GAPDH GAPDH 10504 -0.014 0.2 NO
40 LDHB LDHB LDHB 10540 -0.014 0.2 NO
41 DLD DLD DLD 10548 -0.014 0.2 NO
42 PCK1 PCK1 PCK1 10702 -0.016 0.19 NO
43 ALDOA ALDOA ALDOA 10936 -0.019 0.18 NO
44 PDHA1 PDHA1 PDHA1 11135 -0.02 0.18 NO
45 PGK1 PGK1 PGK1 11294 -0.022 0.17 NO
46 HK2 HK2 HK2 11558 -0.025 0.16 NO
47 LDHA LDHA LDHA 11649 -0.027 0.16 NO
48 ENO2 ENO2 ENO2 12729 -0.04 0.11 NO
49 GPI GPI GPI 12974 -0.043 0.099 NO
50 LDHAL6A LDHAL6A LDHAL6A 13639 -0.052 0.07 NO
51 PKLR PKLR PKLR 13973 -0.058 0.061 NO
52 ALDH1B1 ALDH1B1 ALDH1B1 14807 -0.074 0.027 NO
53 ACSS2 ACSS2 ACSS2 14860 -0.076 0.035 NO
54 PFKM PFKM PFKM 15386 -0.089 0.02 NO
55 ENO3 ENO3 ENO3 16257 -0.12 -0.0095 NO
56 PCK2 PCK2 PCK2 16299 -0.12 0.0063 NO
57 PGAM2 PGAM2 PGAM2 16721 -0.14 0.0047 NO
58 ALDOC ALDOC ALDOC 18231 -0.3 -0.032 NO
59 GCK GCK GCK 18314 -0.33 0.011 NO

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

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

Table S25.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADH6 ADH6 ADH6 176 0.8 0.15 YES
2 ADH1B ADH1B ADH1B 682 0.37 0.19 YES
3 ADH7 ADH7 ADH7 798 0.33 0.25 YES
4 ADH1C ADH1C ADH1C 810 0.33 0.31 YES
5 ADH1A ADH1A ADH1A 834 0.32 0.38 YES
6 PECI PECI PECI 1038 0.28 0.42 YES
7 ACADL ACADL ACADL 1306 0.24 0.45 YES
8 ACSL5 ACSL5 ACSL5 1795 0.19 0.46 YES
9 ADH4 ADH4 ADH4 1809 0.19 0.5 YES
10 ACADS ACADS ACADS 2430 0.15 0.49 YES
11 HADH HADH HADH 2491 0.14 0.52 YES
12 ALDH2 ALDH2 ALDH2 3327 0.11 0.5 YES
13 CPT1B CPT1B CPT1B 3378 0.1 0.51 YES
14 ACSL6 ACSL6 ACSL6 3589 0.097 0.52 YES
15 DCI DCI DCI 3843 0.089 0.52 YES
16 ACOX3 ACOX3 ACOX3 3869 0.088 0.54 YES
17 ECHS1 ECHS1 ECHS1 4109 0.081 0.54 YES
18 ACAT1 ACAT1 ACAT1 4802 0.063 0.52 NO
19 ADH5 ADH5 ADH5 5071 0.057 0.51 NO
20 ACAA1 ACAA1 ACAA1 5166 0.055 0.52 NO
21 ACADVL ACADVL ACADVL 5172 0.055 0.53 NO
22 ALDH3A2 ALDH3A2 ALDH3A2 5900 0.042 0.5 NO
23 ACSL4 ACSL4 ACSL4 5969 0.041 0.5 NO
24 CPT1A CPT1A CPT1A 6608 0.032 0.47 NO
25 ACADSB ACADSB ACADSB 6747 0.03 0.47 NO
26 ACSL3 ACSL3 ACSL3 7121 0.024 0.46 NO
27 ALDH9A1 ALDH9A1 ALDH9A1 7197 0.023 0.46 NO
28 ALDH7A1 ALDH7A1 ALDH7A1 7477 0.019 0.45 NO
29 HADHB HADHB HADHB 7982 0.013 0.42 NO
30 CYP4A11 CYP4A11 CYP4A11 7992 0.013 0.42 NO
31 HADHA HADHA HADHA 8556 0.0066 0.39 NO
32 CPT2 CPT2 CPT2 8688 0.0053 0.39 NO
33 CYP4A22 CYP4A22 CYP4A22 9093 0.00088 0.37 NO
34 ACADM ACADM ACADM 11953 -0.03 0.22 NO
35 EHHADH EHHADH EHHADH 12447 -0.036 0.2 NO
36 GCDH GCDH GCDH 12792 -0.04 0.19 NO
37 ALDH1B1 ALDH1B1 ALDH1B1 14807 -0.074 0.093 NO
38 ACSL1 ACSL1 ACSL1 15553 -0.094 0.071 NO
39 ACAT2 ACAT2 ACAT2 15772 -0.1 0.079 NO
40 CPT1C CPT1C CPT1C 17216 -0.18 0.035 NO
41 ACAA2 ACAA2 ACAA2 17307 -0.18 0.066 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 HISTIDINE METABOLISM.

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

Table 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 GSTA3 GSTA3 GSTA3 43 1.2 0.1 YES
2 ADH6 ADH6 ADH6 176 0.8 0.17 YES
3 AKR1C4 AKR1C4 AKR1C4 627 0.39 0.18 YES
4 AKR1C3 AKR1C3 AKR1C3 663 0.37 0.21 YES
5 ADH1B ADH1B ADH1B 682 0.37 0.25 YES
6 ALDH3A1 ALDH3A1 ALDH3A1 705 0.36 0.28 YES
7 ADH7 ADH7 ADH7 798 0.33 0.3 YES
8 ADH1C ADH1C ADH1C 810 0.33 0.33 YES
9 ADH1A ADH1A ADH1A 834 0.32 0.36 YES
10 AKR1C2 AKR1C2 AKR1C2 971 0.3 0.38 YES
11 UGT2B10 UGT2B10 UGT2B10 1032 0.28 0.4 YES
12 ALDH1A3 ALDH1A3 ALDH1A3 1169 0.26 0.42 YES
13 GSTA1 GSTA1 GSTA1 1196 0.26 0.44 YES
14 UGT2B7 UGT2B7 UGT2B7 1261 0.24 0.46 YES
15 ALDH3B1 ALDH3B1 ALDH3B1 1353 0.23 0.48 YES
16 GSTA2 GSTA2 GSTA2 1381 0.23 0.5 YES
17 AKR1C1 AKR1C1 AKR1C1 1395 0.23 0.52 YES
18 CYP2C8 CYP2C8 CYP2C8 1463 0.22 0.53 YES
19 UGT2B15 UGT2B15 UGT2B15 1505 0.22 0.55 YES
20 ADH4 ADH4 ADH4 1809 0.19 0.55 YES
21 UGT2B11 UGT2B11 UGT2B11 1870 0.18 0.56 YES
22 ALDH3B2 ALDH3B2 ALDH3B2 1931 0.18 0.58 YES
23 GSTM5 GSTM5 GSTM5 1945 0.18 0.59 YES
24 GSTM1 GSTM1 GSTM1 2246 0.16 0.59 YES
25 MGST2 MGST2 MGST2 2302 0.15 0.6 YES
26 CYP2E1 CYP2E1 CYP2E1 2400 0.15 0.61 YES
27 CYP2S1 CYP2S1 CYP2S1 2583 0.14 0.61 YES
28 GSTO2 GSTO2 GSTO2 2705 0.13 0.62 YES
29 MGST1 MGST1 MGST1 2834 0.12 0.62 YES
30 GSTZ1 GSTZ1 GSTZ1 2937 0.12 0.63 YES
31 EPHX1 EPHX1 EPHX1 3015 0.12 0.64 YES
32 GSTK1 GSTK1 GSTK1 3350 0.11 0.63 NO
33 GSTM2 GSTM2 GSTM2 3418 0.1 0.63 NO
34 CYP1B1 CYP1B1 CYP1B1 3547 0.099 0.64 NO
35 ADH5 ADH5 ADH5 5071 0.057 0.56 NO
36 GSTT1 GSTT1 GSTT1 5524 0.048 0.54 NO
37 GSTM3 GSTM3 GSTM3 5532 0.048 0.54 NO
38 GSTP1 GSTP1 GSTP1 6823 0.028 0.48 NO
39 GSTO1 GSTO1 GSTO1 7066 0.024 0.46 NO
40 GSTM4 GSTM4 GSTM4 7722 0.016 0.43 NO
41 GSTA4 GSTA4 GSTA4 7898 0.014 0.42 NO
42 CYP2F1 CYP2F1 CYP2F1 10780 -0.017 0.27 NO
43 MGST3 MGST3 MGST3 10790 -0.017 0.27 NO
44 UGT1A6 UGT1A6 UGT1A6 12662 -0.039 0.17 NO
45 CYP2C18 CYP2C18 CYP2C18 13433 -0.049 0.13 NO
46 GSTT2 GSTT2 GSTT2 13944 -0.058 0.11 NO
47 CYP2C9 CYP2C9 CYP2C9 14432 -0.067 0.091 NO
48 CYP1A1 CYP1A1 CYP1A1 14889 -0.076 0.073 NO
49 CYP3A5 CYP3A5 CYP3A5 15341 -0.088 0.057 NO
50 CYP2C19 CYP2C19 CYP2C19 16288 -0.12 0.016 NO
51 CYP3A43 CYP3A43 CYP3A43 16495 -0.13 0.017 NO
52 UGT2B4 UGT2B4 UGT2B4 16815 -0.15 0.014 NO
53 CYP2B6 CYP2B6 CYP2B6 17143 -0.17 0.011 NO
54 CYP3A7 CYP3A7 CYP3A7 17680 -0.22 0.0022 NO
55 DHDH DHDH DHDH 17849 -0.24 0.015 NO
56 CYP1A2 CYP1A2 CYP1A2 17864 -0.24 0.036 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 TYROSINE METABOLISM.

Figure S52.  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 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 ADH6 ADH6 ADH6 176 0.8 0.11 YES
2 HGD HGD HGD 413 0.49 0.17 YES
3 ADH1B ADH1B ADH1B 682 0.37 0.21 YES
4 ALDH3A1 ALDH3A1 ALDH3A1 705 0.36 0.26 YES
5 ADH7 ADH7 ADH7 798 0.33 0.3 YES
6 ADH1C ADH1C ADH1C 810 0.33 0.35 YES
7 ADH1A ADH1A ADH1A 834 0.32 0.4 YES
8 MAOB MAOB MAOB 926 0.3 0.44 YES
9 TAT TAT TAT 1113 0.27 0.47 YES
10 ALDH1A3 ALDH1A3 ALDH1A3 1169 0.26 0.5 YES
11 ALDH3B1 ALDH3B1 ALDH3B1 1353 0.23 0.53 YES
12 MAOA MAOA MAOA 1735 0.2 0.54 YES
13 ADH4 ADH4 ADH4 1809 0.19 0.56 YES
14 ALDH3B2 ALDH3B2 ALDH3B2 1931 0.18 0.58 YES
15 GSTZ1 GSTZ1 GSTZ1 2937 0.12 0.55 NO
16 AOC3 AOC3 AOC3 4334 0.075 0.48 NO
17 ADH5 ADH5 ADH5 5071 0.057 0.45 NO
18 COMT COMT COMT 5258 0.053 0.45 NO
19 HEMK1 HEMK1 HEMK1 5285 0.053 0.45 NO
20 GOT2 GOT2 GOT2 5697 0.046 0.44 NO
21 IL4I1 IL4I1 IL4I1 6785 0.029 0.38 NO
22 FAH FAH FAH 7048 0.025 0.37 NO
23 WBSCR22 WBSCR22 WBSCR22 7445 0.02 0.35 NO
24 MIF MIF MIF 7577 0.018 0.35 NO
25 LCMT1 LCMT1 LCMT1 7715 0.016 0.34 NO
26 AOC2 AOC2 AOC2 7756 0.016 0.34 NO
27 LCMT2 LCMT2 LCMT2 9643 -0.005 0.24 NO
28 GOT1 GOT1 GOT1 10168 -0.011 0.22 NO
29 TRMT11 TRMT11 TRMT11 12116 -0.032 0.12 NO
30 NAT6 NAT6 NAT6 12464 -0.036 0.1 NO
31 METTL2B METTL2B METTL2B 12664 -0.039 0.098 NO
32 AOX1 AOX1 AOX1 13344 -0.048 0.068 NO
33 METTL6 METTL6 METTL6 13495 -0.05 0.068 NO
34 DCT DCT DCT 14636 -0.07 0.016 NO
35 DBH DBH DBH 16232 -0.12 -0.052 NO
36 HPD HPD HPD 17456 -0.2 -0.09 NO
37 TPO TPO TPO 17710 -0.22 -0.071 NO
38 DDC DDC DDC 17865 -0.24 -0.044 NO
39 TH TH TH 18023 -0.26 -0.014 NO
40 PNMT PNMT PNMT 18101 -0.28 0.023 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 GLUTATHIONE METABOLISM.

Figure S54.  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 STARCH AND SUCROSE METABOLISM

Table S28.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PLCB1 PLCB1 PLCB1 1039 0.28 0.069 YES
2 NCF2 NCF2 NCF2 1178 0.26 0.18 YES
3 MAP2K6 MAP2K6 MAP2K6 1195 0.26 0.29 YES
4 PIK3C2G PIK3C2G PIK3C2G 1710 0.2 0.35 YES
5 NCF1C NCF1C NCF1C 2062 0.17 0.4 YES
6 FPR1 FPR1 FPR1 3381 0.1 0.38 YES
7 CALM1 CALM1 CALM1 4243 0.077 0.36 YES
8 MAP3K1 MAP3K1 MAP3K1 4288 0.076 0.4 YES
9 PAK1 PAK1 PAK1 4726 0.065 0.4 YES
10 GNGT1 GNGT1 GNGT1 4911 0.06 0.42 YES
11 NFATC3 NFATC3 NFATC3 5192 0.054 0.43 YES
12 MAP2K2 MAP2K2 MAP2K2 5422 0.05 0.44 YES
13 NFKB1 NFKB1 NFKB1 5811 0.044 0.44 NO
14 CAMK1G CAMK1G CAMK1G 6693 0.03 0.4 NO
15 RAC1 RAC1 RAC1 7003 0.025 0.4 NO
16 CALM3 CALM3 CALM3 7192 0.023 0.4 NO
17 NFKBIA NFKBIA NFKBIA 7467 0.02 0.39 NO
18 RELA RELA RELA 7508 0.019 0.4 NO
19 CALM2 CALM2 CALM2 7807 0.015 0.39 NO
20 MAP2K3 MAP2K3 MAP2K3 7911 0.014 0.39 NO
21 PPP3CB PPP3CB PPP3CB 8354 0.0089 0.37 NO
22 HRAS HRAS HRAS 8605 0.0062 0.36 NO
23 RAF1 RAF1 RAF1 8653 0.0057 0.36 NO
24 CAMK1 CAMK1 CAMK1 8654 0.0057 0.36 NO
25 NFATC1 NFATC1 NFATC1 9843 -0.007 0.3 NO
26 MAPK3 MAPK3 MAPK3 9918 -0.0077 0.3 NO
27 NFATC4 NFATC4 NFATC4 10069 -0.0094 0.29 NO
28 GNB1 GNB1 GNB1 10085 -0.0095 0.3 NO
29 PPP3CC PPP3CC PPP3CC 10418 -0.013 0.28 NO
30 MAPK1 MAPK1 MAPK1 11203 -0.021 0.25 NO
31 NFATC2 NFATC2 NFATC2 12990 -0.043 0.17 NO
32 MAP2K1 MAP2K1 MAP2K1 13868 -0.056 0.15 NO
33 MAPK14 MAPK14 MAPK14 14503 -0.068 0.15 NO
34 PPP3CA PPP3CA PPP3CA 14651 -0.071 0.17 NO
35 ELK1 ELK1 ELK1 15342 -0.088 0.17 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 STARCH AND SUCROSE METABOLISM.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STARCH AND SUCROSE 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 ETHER LIPID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DDO DDO DDO 431 0.49 0.058 YES
2 PEX11G PEX11G PEX11G 957 0.3 0.079 YES
3 PECI PECI PECI 1038 0.28 0.12 YES
4 SLC27A2 SLC27A2 SLC27A2 1336 0.24 0.14 YES
5 EPHX2 EPHX2 EPHX2 1563 0.21 0.17 YES
6 ACSL5 ACSL5 ACSL5 1795 0.19 0.19 YES
7 PEX11A PEX11A PEX11A 2000 0.18 0.2 YES
8 NUDT12 NUDT12 NUDT12 2040 0.17 0.23 YES
9 PEX7 PEX7 PEX7 2413 0.15 0.24 YES
10 ABCD2 ABCD2 ABCD2 2556 0.14 0.25 YES
11 DECR2 DECR2 DECR2 2683 0.13 0.27 YES
12 HMGCL HMGCL HMGCL 3052 0.12 0.27 YES
13 IDH2 IDH2 IDH2 3080 0.12 0.28 YES
14 PAOX PAOX PAOX 3208 0.11 0.3 YES
15 CAT CAT CAT 3278 0.11 0.31 YES
16 GSTK1 GSTK1 GSTK1 3350 0.11 0.32 YES
17 AGPS AGPS AGPS 3467 0.1 0.34 YES
18 ACSL6 ACSL6 ACSL6 3589 0.097 0.34 YES
19 MLYCD MLYCD MLYCD 3788 0.09 0.35 YES
20 ACOX3 ACOX3 ACOX3 3869 0.088 0.36 YES
21 PRDX5 PRDX5 PRDX5 4004 0.084 0.37 YES
22 HACL1 HACL1 HACL1 4169 0.079 0.37 YES
23 CRAT CRAT CRAT 4273 0.076 0.38 YES
24 PXMP4 PXMP4 PXMP4 4275 0.076 0.39 YES
25 PEX6 PEX6 PEX6 4312 0.076 0.4 YES
26 HSD17B4 HSD17B4 HSD17B4 4523 0.07 0.4 YES
27 ACAA1 ACAA1 ACAA1 5166 0.055 0.38 NO
28 PEX16 PEX16 PEX16 5237 0.054 0.38 NO
29 SCP2 SCP2 SCP2 5637 0.047 0.37 NO
30 CROT CROT CROT 5654 0.046 0.37 NO
31 PEX1 PEX1 PEX1 5691 0.046 0.38 NO
32 ABCD3 ABCD3 ABCD3 5896 0.042 0.38 NO
33 ACSL4 ACSL4 ACSL4 5969 0.041 0.38 NO
34 ABCD4 ABCD4 ABCD4 6108 0.039 0.38 NO
35 IDH1 IDH1 IDH1 6384 0.034 0.37 NO
36 ACOX1 ACOX1 ACOX1 6466 0.033 0.37 NO
37 GNPAT GNPAT GNPAT 6591 0.032 0.37 NO
38 DHRS4 DHRS4 DHRS4 6777 0.029 0.36 NO
39 PEX12 PEX12 PEX12 6973 0.026 0.36 NO
40 ACOT8 ACOT8 ACOT8 7012 0.025 0.36 NO
41 PEX14 PEX14 PEX14 7061 0.025 0.36 NO
42 ACSL3 ACSL3 ACSL3 7121 0.024 0.36 NO
43 PEX11B PEX11B PEX11B 7342 0.021 0.35 NO
44 PEX2 PEX2 PEX2 7437 0.02 0.35 NO
45 ECH1 ECH1 ECH1 7440 0.02 0.35 NO
46 PRDX1 PRDX1 PRDX1 7497 0.019 0.35 NO
47 MPV17 MPV17 MPV17 7539 0.019 0.36 NO
48 PIPOX PIPOX PIPOX 7610 0.018 0.35 NO
49 SOD1 SOD1 SOD1 7876 0.015 0.34 NO
50 PEX13 PEX13 PEX13 8070 0.012 0.33 NO
51 PEX10 PEX10 PEX10 8177 0.011 0.33 NO
52 PMVK PMVK PMVK 8252 0.01 0.33 NO
53 SOD2 SOD2 SOD2 8278 0.0097 0.33 NO
54 FAR1 FAR1 FAR1 8488 0.0075 0.32 NO
55 PEX26 PEX26 PEX26 8578 0.0064 0.31 NO
56 PEX3 PEX3 PEX3 9893 -0.0075 0.24 NO
57 SLC25A17 SLC25A17 SLC25A17 10235 -0.011 0.23 NO
58 MPV17L MPV17L MPV17L 10327 -0.012 0.22 NO
59 AMACR AMACR AMACR 10347 -0.012 0.22 NO
60 NUDT19 NUDT19 NUDT19 10751 -0.017 0.21 NO
61 DAO DAO DAO 11127 -0.02 0.19 NO
62 PEX5 PEX5 PEX5 11144 -0.021 0.19 NO
63 PXMP2 PXMP2 PXMP2 11939 -0.03 0.15 NO
64 MVK MVK MVK 12341 -0.035 0.14 NO
65 EHHADH EHHADH EHHADH 12447 -0.036 0.14 NO
66 PEX19 PEX19 PEX19 12509 -0.037 0.14 NO
67 PHYH PHYH PHYH 12562 -0.038 0.14 NO
68 PECR PECR PECR 14020 -0.059 0.076 NO
69 FAR2 FAR2 FAR2 14425 -0.067 0.065 NO
70 ACSL1 ACSL1 ACSL1 15553 -0.094 0.019 NO
71 HAO2 HAO2 HAO2 15917 -0.11 0.018 NO
72 NOS2 NOS2 NOS2 16274 -0.12 0.018 NO
73 AGXT AGXT AGXT 16403 -0.13 0.033 NO
74 ABCD1 ABCD1 ABCD1 16735 -0.14 0.039 NO
75 XDH XDH XDH 17118 -0.17 0.046 NO
76 BAAT BAAT BAAT 17291 -0.18 0.067 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 ETHER LIPID METABOLISM.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ETHER LIPID 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 BUTANOATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ABCB11 ABCB11 ABCB11 672 0.37 0.026 YES
2 ABCC6 ABCC6 ABCC6 720 0.36 0.084 YES
3 ABCA9 ABCA9 ABCA9 905 0.31 0.13 YES
4 ABCC11 ABCC11 ABCC11 915 0.31 0.18 YES
5 ABCB1 ABCB1 ABCB1 931 0.3 0.23 YES
6 ABCG2 ABCG2 ABCG2 1001 0.29 0.27 YES
7 ABCA10 ABCA10 ABCA10 1008 0.29 0.32 YES
8 ABCC12 ABCC12 ABCC12 1221 0.25 0.35 YES
9 ABCA6 ABCA6 ABCA6 1364 0.23 0.38 YES
10 ABCG1 ABCG1 ABCG1 1470 0.22 0.42 YES
11 ABCC2 ABCC2 ABCC2 1610 0.2 0.44 YES
12 ABCA5 ABCA5 ABCA5 1714 0.2 0.47 YES
13 CFTR CFTR CFTR 1762 0.19 0.5 YES
14 ABCA7 ABCA7 ABCA7 2237 0.16 0.5 YES
15 ABCB9 ABCB9 ABCB9 2311 0.15 0.52 YES
16 ABCD2 ABCD2 ABCD2 2556 0.14 0.53 YES
17 ABCC9 ABCC9 ABCC9 2622 0.14 0.55 YES
18 ABCA1 ABCA1 ABCA1 3308 0.11 0.54 NO
19 ABCA13 ABCA13 ABCA13 4002 0.084 0.51 NO
20 ABCA12 ABCA12 ABCA12 4449 0.072 0.5 NO
21 ABCB8 ABCB8 ABCB8 4629 0.067 0.5 NO
22 ABCC3 ABCC3 ABCC3 5292 0.053 0.47 NO
23 ABCB4 ABCB4 ABCB4 5436 0.05 0.48 NO
24 ABCD3 ABCD3 ABCD3 5896 0.042 0.46 NO
25 ABCD4 ABCD4 ABCD4 6108 0.039 0.45 NO
26 ABCC10 ABCC10 ABCC10 6172 0.038 0.46 NO
27 ABCB5 ABCB5 ABCB5 6242 0.036 0.46 NO
28 ABCA2 ABCA2 ABCA2 8219 0.01 0.35 NO
29 TAP1 TAP1 TAP1 8796 0.004 0.32 NO
30 ABCB10 ABCB10 ABCB10 9434 -0.0024 0.29 NO
31 ABCB6 ABCB6 ABCB6 9728 -0.006 0.27 NO
32 TAP2 TAP2 TAP2 10268 -0.012 0.25 NO
33 ABCC1 ABCC1 ABCC1 10831 -0.017 0.22 NO
34 ABCB7 ABCB7 ABCB7 11769 -0.028 0.17 NO
35 ABCC4 ABCC4 ABCC4 12166 -0.033 0.16 NO
36 ABCG5 ABCG5 ABCG5 13919 -0.057 0.071 NO
37 ABCG8 ABCG8 ABCG8 14262 -0.063 0.064 NO
38 ABCC8 ABCC8 ABCC8 15178 -0.083 0.028 NO
39 ABCC5 ABCC5 ABCC5 15490 -0.093 0.027 NO
40 ABCD1 ABCD1 ABCD1 16735 -0.14 -0.016 NO
41 ABCA4 ABCA4 ABCA4 16976 -0.16 -0.0024 NO
42 ABCA3 ABCA3 ABCA3 17940 -0.25 -0.012 NO
43 ABCG4 ABCG4 ABCG4 17982 -0.26 0.029 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 BUTANOATE METABOLISM.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

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

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

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

GSEA analysis

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

Download Results

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

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