GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PAAD-TP
Pancreatic Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C19K4990
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 PAAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C19K4990
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 PAAD-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: 195
Number of samples: 178
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 ] 83
pheno.type: 2 - 3 :[ clus2 ] 49
pheno.type: 3 - 3 :[ clus3 ] 46

For the expression subtypes of 18475 genes in 179 samples, GSEA found enriched gene sets in each cluster using 178 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA RHO PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG O GLYCAN BIOSYNTHESIS, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

    • And common core enriched genes are CCND1, CCNE1, CDK2, ACTR2, ACTR3, ARHGAP1, ARHGAP5, ARHGAP6, ARHGEF1, ARHGEF5

  • clus2

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA PPARA PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG GALACTOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM

    • And common core enriched genes are GGT1, GGT6, CBS, CTH, GGT7, MAT1A, SCLY, AASS, ACAT1, ACAT2

  • clus3

    • Top enriched gene sets are BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA GPCR PATHWAY, BIOCARTA CREB PATHWAY, BIOCARTA VEGF PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG LYSINE DEGRADATION, KEGG TRYPTOPHAN METABOLISM

    • And common core enriched genes are GNAI1, PRKCB, OGDHL, PIPOX, ACTC1, ATP1A2, ATP1A3, ATP1A4, ATP1B2, CACNA1D

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 FAS PATHWAY 29 genes.ES.table 0.37 1.2 0.28 0.82 1 0.45 0.23 0.34 0.72 0.3
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.31 1.3 0.25 0.8 0.99 0.42 0.26 0.31 0.68 0.28
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.34 1.1 0.35 0.92 1 0.53 0.23 0.41 0.84 0.37
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.43 1.6 0.065 0.31 0.76 0.48 0.32 0.33 0.2 0.059
BIOCARTA RHO PATHWAY 31 genes.ES.table 0.55 1.9 0.004 0.09 0.12 0.71 0.3 0.5 0 0.03
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.38 1.4 0.16 0.55 0.95 0.39 0.24 0.3 0.45 0.13
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS 25 genes.ES.table 0.57 1.2 0.27 0.89 1 0.36 0.07 0.34 0.8 0.35
KEGG STEROID HORMONE BIOSYNTHESIS 49 genes.ES.table 0.42 0.98 0.46 1 1 0.31 0.077 0.28 0.98 0.48
KEGG O GLYCAN BIOSYNTHESIS 28 genes.ES.table 0.43 1.1 0.39 1 1 0.39 0.09 0.36 0.98 0.48
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 37 genes.ES.table 0.44 1 0.41 1 1 0.22 0.055 0.2 0.95 0.45
genes ES table in pathway: BIOCARTA FAS 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 ARHGEF5 ARHGEF5 ARHGEF5 1793 0.12 -0.011 YES
2 SRC SRC SRC 1939 0.12 0.061 YES
3 PIP5K1B PIP5K1B PIP5K1B 1947 0.12 0.14 YES
4 MYL2 MYL2 MYL2 3050 0.072 0.13 YES
5 ARPC1A ARPC1A ARPC1A 3388 0.063 0.16 YES
6 DIAPH1 DIAPH1 DIAPH1 3473 0.06 0.19 YES
7 VCL VCL VCL 3511 0.06 0.23 YES
8 CFL1 CFL1 CFL1 3737 0.054 0.26 YES
9 BAIAP2 BAIAP2 BAIAP2 3757 0.054 0.3 YES
10 ARPC1B ARPC1B ARPC1B 3766 0.054 0.33 YES
11 ARHGAP6 ARHGAP6 ARHGAP6 3807 0.053 0.37 YES
12 ACTR3 ACTR3 ACTR3 3865 0.052 0.4 YES
13 ARHGAP5 ARHGAP5 ARHGAP5 4266 0.044 0.41 YES
14 ARPC2 ARPC2 ARPC2 4449 0.042 0.43 YES
15 ARPC3 ARPC3 ARPC3 4573 0.039 0.45 YES
16 ACTR2 ACTR2 ACTR2 4860 0.034 0.46 YES
17 ARHGEF1 ARHGEF1 ARHGEF1 5000 0.033 0.47 YES
18 LIMK1 LIMK1 LIMK1 5051 0.032 0.49 YES
19 MYLK MYLK MYLK 5154 0.03 0.51 YES
20 ARHGAP1 ARHGAP1 ARHGAP1 5190 0.03 0.52 YES
21 ARPC5 ARPC5 ARPC5 5312 0.029 0.54 YES
22 PFN1 PFN1 PFN1 5440 0.027 0.55 YES
23 RHOA RHOA RHOA 6196 0.018 0.52 NO
24 ARPC4 ARPC4 ARPC4 6378 0.016 0.52 NO
25 PIP5K1A PIP5K1A PIP5K1A 7165 0.0075 0.48 NO
26 ROCK1 ROCK1 ROCK1 7378 0.0055 0.48 NO
27 GSN GSN GSN 8316 -0.0041 0.43 NO
28 ARHGEF11 ARHGEF11 ARHGEF11 9155 -0.013 0.39 NO
29 PPP1R12B PPP1R12B PPP1R12B 9322 -0.015 0.39 NO
30 OPHN1 OPHN1 OPHN1 12731 -0.071 0.26 NO
31 ARHGAP4 ARHGAP4 ARHGAP4 12908 -0.075 0.3 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 FAS PATHWAY.

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

genes ES table in pathway: BIOCARTA HIVNEF 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 NEIL3 NEIL3 NEIL3 317 0.29 0.15 YES
2 POLE2 POLE2 POLE2 786 0.22 0.24 YES
3 PARP3 PARP3 PARP3 2080 0.11 0.24 YES
4 POLD4 POLD4 POLD4 2196 0.1 0.29 YES
5 NTHL1 NTHL1 NTHL1 2642 0.084 0.31 YES
6 POLB POLB POLB 3095 0.07 0.33 YES
7 MPG MPG MPG 3179 0.069 0.36 YES
8 PARP4 PARP4 PARP4 3210 0.068 0.4 YES
9 MUTYH MUTYH MUTYH 3250 0.067 0.43 YES
10 POLE POLE POLE 3412 0.062 0.46 YES
11 POLD1 POLD1 POLD1 3518 0.059 0.49 YES
12 FEN1 FEN1 FEN1 4222 0.045 0.48 YES
13 POLE4 POLE4 POLE4 4257 0.044 0.5 YES
14 POLD3 POLD3 POLD3 4314 0.043 0.52 YES
15 SMUG1 SMUG1 SMUG1 4390 0.042 0.54 YES
16 PCNA PCNA PCNA 4409 0.042 0.56 YES
17 LIG1 LIG1 LIG1 5245 0.029 0.54 NO
18 TDG TDG TDG 5325 0.028 0.55 NO
19 LIG3 LIG3 LIG3 5764 0.024 0.54 NO
20 UNG UNG UNG 5836 0.023 0.55 NO
21 POLE3 POLE3 POLE3 5889 0.022 0.56 NO
22 APEX2 APEX2 APEX2 6303 0.017 0.54 NO
23 MBD4 MBD4 MBD4 6482 0.015 0.54 NO
24 APEX1 APEX1 APEX1 7032 0.0087 0.52 NO
25 POLD2 POLD2 POLD2 7196 0.0071 0.51 NO
26 POLL POLL POLL 7507 0.0041 0.5 NO
27 OGG1 OGG1 OGG1 8356 -0.0045 0.45 NO
28 NEIL1 NEIL1 NEIL1 8986 -0.011 0.42 NO
29 PARP1 PARP1 PARP1 9184 -0.013 0.42 NO
30 PARP2 PARP2 PARP2 9346 -0.015 0.42 NO
31 XRCC1 XRCC1 XRCC1 10053 -0.023 0.4 NO
32 NEIL2 NEIL2 NEIL2 13849 -0.1 0.25 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 HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA DEATH 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 CDC25C CDC25C CDC25C 5 0.44 0.04 YES
2 SFN SFN SFN 159 0.34 0.061 YES
3 PKMYT1 PKMYT1 PKMYT1 219 0.32 0.086 YES
4 CDC45 CDC45 CDC45 227 0.32 0.11 YES
5 ESPL1 ESPL1 ESPL1 261 0.3 0.14 YES
6 TTK TTK TTK 264 0.3 0.17 YES
7 BUB1 BUB1 BUB1 330 0.29 0.19 YES
8 CDC20 CDC20 CDC20 340 0.29 0.22 YES
9 ORC6L ORC6L ORC6L 344 0.29 0.24 YES
10 CCNB2 CCNB2 CCNB2 448 0.27 0.26 YES
11 BUB1B BUB1B BUB1B 524 0.26 0.28 YES
12 PLK1 PLK1 PLK1 525 0.25 0.3 YES
13 E2F2 E2F2 E2F2 553 0.25 0.32 YES
14 CDK1 CDK1 CDK1 610 0.24 0.34 YES
15 CDC6 CDC6 CDC6 649 0.24 0.36 YES
16 PTTG1 PTTG1 PTTG1 683 0.23 0.38 YES
17 CCNA2 CCNA2 CCNA2 718 0.23 0.4 YES
18 E2F1 E2F1 E2F1 842 0.21 0.41 YES
19 ORC1L ORC1L ORC1L 942 0.2 0.42 YES
20 CCNE2 CCNE2 CCNE2 960 0.19 0.44 YES
21 MAD2L1 MAD2L1 MAD2L1 1131 0.18 0.44 YES
22 CCNB1 CCNB1 CCNB1 1306 0.16 0.45 YES
23 CDC25A CDC25A CDC25A 1328 0.16 0.46 YES
24 CHEK2 CHEK2 CHEK2 1733 0.13 0.45 YES
25 MCM2 MCM2 MCM2 1755 0.13 0.46 YES
26 CHEK1 CHEK1 CHEK1 2007 0.11 0.46 YES
27 CCNE1 CCNE1 CCNE1 2016 0.11 0.47 YES
28 SMC1B SMC1B SMC1B 2020 0.11 0.48 YES
29 SKP2 SKP2 SKP2 2147 0.1 0.48 YES
30 MCM4 MCM4 MCM4 2191 0.1 0.48 YES
31 SMAD3 SMAD3 SMAD3 2226 0.1 0.49 YES
32 CDK7 CDK7 CDK7 2300 0.097 0.5 YES
33 WEE1 WEE1 WEE1 2311 0.097 0.5 YES
34 E2F3 E2F3 E2F3 2493 0.09 0.5 YES
35 CDK2 CDK2 CDK2 2618 0.085 0.5 YES
36 PTTG2 PTTG2 PTTG2 2834 0.078 0.5 YES
37 HDAC1 HDAC1 HDAC1 2904 0.076 0.5 YES
38 ORC2L ORC2L ORC2L 3022 0.072 0.5 YES
39 YWHAZ YWHAZ YWHAZ 3045 0.072 0.51 YES
40 CDC25B CDC25B CDC25B 3160 0.069 0.51 YES
41 CCND1 CCND1 CCND1 3183 0.069 0.51 YES
42 MCM7 MCM7 MCM7 3406 0.062 0.51 NO
43 MAD1L1 MAD1L1 MAD1L1 3479 0.06 0.51 NO
44 CDK6 CDK6 CDK6 3787 0.053 0.5 NO
45 BUB3 BUB3 BUB3 3793 0.053 0.5 NO
46 MCM6 MCM6 MCM6 4050 0.048 0.49 NO
47 CDKN2D CDKN2D CDKN2D 4171 0.046 0.49 NO
48 MCM3 MCM3 MCM3 4229 0.045 0.49 NO
49 PCNA PCNA PCNA 4409 0.042 0.48 NO
50 ATR ATR ATR 4559 0.04 0.48 NO
51 ORC4L ORC4L ORC4L 4714 0.037 0.47 NO
52 MDM2 MDM2 MDM2 4742 0.036 0.48 NO
53 CDKN1A CDKN1A CDKN1A 4984 0.033 0.46 NO
54 MCM5 MCM5 MCM5 5728 0.024 0.43 NO
55 E2F4 E2F4 E2F4 5808 0.023 0.42 NO
56 TFDP2 TFDP2 TFDP2 5993 0.021 0.42 NO
57 ANAPC1 ANAPC1 ANAPC1 5999 0.021 0.42 NO
58 YWHAG YWHAG YWHAG 6030 0.02 0.42 NO
59 ANAPC11 ANAPC11 ANAPC11 6042 0.02 0.42 NO
60 TGFB2 TGFB2 TGFB2 6086 0.02 0.42 NO
61 CDC7 CDC7 CDC7 6529 0.014 0.4 NO
62 GSK3B GSK3B GSK3B 6639 0.013 0.39 NO
63 YWHAB YWHAB YWHAB 6708 0.012 0.39 NO
64 RAD21 RAD21 RAD21 6879 0.011 0.38 NO
65 YWHAH YWHAH YWHAH 7014 0.009 0.37 NO
66 ANAPC10 ANAPC10 ANAPC10 7516 0.004 0.35 NO
67 RBX1 RBX1 RBX1 7599 0.0033 0.34 NO
68 TFDP1 TFDP1 TFDP1 7737 0.0018 0.34 NO
69 PRKDC PRKDC PRKDC 7771 0.0015 0.33 NO
70 CDC23 CDC23 CDC23 7843 0.00066 0.33 NO
71 FZR1 FZR1 FZR1 7901 -7.3e-06 0.33 NO
72 ANAPC7 ANAPC7 ANAPC7 8137 -0.0025 0.31 NO
73 EP300 EP300 EP300 8212 -0.0032 0.31 NO
74 CDC14B CDC14B CDC14B 8254 -0.0035 0.31 NO
75 CDC26 CDC26 CDC26 8304 -0.004 0.31 NO
76 TGFB1 TGFB1 TGFB1 8308 -0.004 0.31 NO
77 CDK4 CDK4 CDK4 8584 -0.0071 0.29 NO
78 CREBBP CREBBP CREBBP 8590 -0.0072 0.29 NO
79 CCNH CCNH CCNH 8622 -0.0075 0.29 NO
80 ANAPC4 ANAPC4 ANAPC4 8678 -0.008 0.29 NO
81 STAG1 STAG1 STAG1 8815 -0.0094 0.28 NO
82 STAG2 STAG2 STAG2 8983 -0.011 0.27 NO
83 CDC27 CDC27 CDC27 9067 -0.012 0.27 NO
84 SKP1 SKP1 SKP1 9089 -0.012 0.27 NO
85 CDKN1B CDKN1B CDKN1B 9097 -0.012 0.27 NO
86 RBL1 RBL1 RBL1 9112 -0.012 0.27 NO
87 TP53 TP53 TP53 9141 -0.013 0.27 NO
88 ZBTB17 ZBTB17 ZBTB17 9213 -0.014 0.27 NO
89 RBL2 RBL2 RBL2 9448 -0.016 0.26 NO
90 ORC5L ORC5L ORC5L 9538 -0.017 0.25 NO
91 HDAC2 HDAC2 HDAC2 9654 -0.018 0.25 NO
92 CDC16 CDC16 CDC16 9674 -0.019 0.25 NO
93 CUL1 CUL1 CUL1 9950 -0.022 0.24 NO
94 YWHAE YWHAE YWHAE 10026 -0.023 0.24 NO
95 SMC1A SMC1A SMC1A 10028 -0.023 0.24 NO
96 MYC MYC MYC 10123 -0.024 0.23 NO
97 ABL1 ABL1 ABL1 10237 -0.026 0.23 NO
98 ANAPC5 ANAPC5 ANAPC5 10341 -0.027 0.23 NO
99 YWHAQ YWHAQ YWHAQ 10379 -0.028 0.23 NO
100 E2F5 E2F5 E2F5 10545 -0.03 0.22 NO
101 ANAPC13 ANAPC13 ANAPC13 10842 -0.034 0.21 NO
102 SMAD2 SMAD2 SMAD2 10956 -0.036 0.2 NO
103 GADD45A GADD45A GADD45A 11055 -0.037 0.2 NO
104 RB1 RB1 RB1 11079 -0.038 0.2 NO
105 ANAPC2 ANAPC2 ANAPC2 11123 -0.038 0.21 NO
106 CDKN2B CDKN2B CDKN2B 11170 -0.039 0.21 NO
107 SMC3 SMC3 SMC3 11469 -0.044 0.19 NO
108 CCND3 CCND3 CCND3 11748 -0.049 0.18 NO
109 MAD2L2 MAD2L2 MAD2L2 11901 -0.052 0.18 NO
110 CDKN2C CDKN2C CDKN2C 12356 -0.062 0.16 NO
111 CDKN2A CDKN2A CDKN2A 12522 -0.066 0.16 NO
112 ORC3L ORC3L ORC3L 12561 -0.067 0.16 NO
113 CCNB3 CCNB3 CCNB3 12640 -0.069 0.16 NO
114 GADD45B GADD45B GADD45B 12965 -0.077 0.15 NO
115 ATM ATM ATM 13113 -0.08 0.15 NO
116 CDKN1C CDKN1C CDKN1C 13639 -0.098 0.13 NO
117 CCND2 CCND2 CCND2 13910 -0.11 0.13 NO
118 CDC14A CDC14A CDC14A 14494 -0.13 0.11 NO
119 WEE2 WEE2 WEE2 14615 -0.14 0.11 NO
120 SMAD4 SMAD4 SMAD4 14905 -0.15 0.11 NO
121 TGFB3 TGFB3 TGFB3 15110 -0.16 0.11 NO
122 GADD45G GADD45G GADD45G 16950 -0.32 0.042 NO
123 CCNA1 CCNA1 CCNA1 17627 -0.45 0.045 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 DEATH PATHWAY.

Figure S6.  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 RACCYCD 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 HSPA1B HSPA1B HSPA1B 1386 0.15 -0.032 YES
2 HSPA6 HSPA6 HSPA6 1455 0.15 0.0056 YES
3 HSPA1A HSPA1A HSPA1A 1601 0.14 0.037 YES
4 HSPA2 HSPA2 HSPA2 2105 0.11 0.039 YES
5 THOC3 THOC3 THOC3 2606 0.086 0.036 YES
6 SNRPA1 SNRPA1 SNRPA1 2794 0.079 0.048 YES
7 SNRPD1 SNRPD1 SNRPD1 3134 0.07 0.049 YES
8 PPIH PPIH PPIH 3410 0.062 0.051 YES
9 SF3B4 SF3B4 SF3B4 3528 0.059 0.062 YES
10 SF3A2 SF3A2 SF3A2 3562 0.058 0.076 YES
11 SNRPA SNRPA SNRPA 3603 0.058 0.09 YES
12 TCERG1 TCERG1 TCERG1 3654 0.056 0.1 YES
13 SNRPG SNRPG SNRPG 3699 0.056 0.12 YES
14 SNRPB SNRPB SNRPB 3707 0.055 0.13 YES
15 SF3B14 SF3B14 SF3B14 3801 0.053 0.14 YES
16 LSM7 LSM7 LSM7 3973 0.05 0.15 YES
17 SNRPF SNRPF SNRPF 3998 0.049 0.16 YES
18 LSM4 LSM4 LSM4 4030 0.049 0.17 YES
19 BUD31 BUD31 BUD31 4167 0.046 0.18 YES
20 PRPF40A PRPF40A PRPF40A 4173 0.046 0.19 YES
21 NAA38 NAA38 NAA38 4364 0.043 0.19 YES
22 SF3B1 SF3B1 SF3B1 4374 0.043 0.2 YES
23 SMNDC1 SMNDC1 SMNDC1 4456 0.041 0.21 YES
24 RBM8A RBM8A RBM8A 4464 0.041 0.22 YES
25 SNRPD3 SNRPD3 SNRPD3 4511 0.04 0.23 YES
26 SFRS2 SFRS2 SFRS2 4592 0.039 0.24 YES
27 PRPF3 PRPF3 PRPF3 4729 0.037 0.24 YES
28 SR140 SR140 SR140 4736 0.037 0.25 YES
29 DHX15 DHX15 DHX15 4738 0.037 0.26 YES
30 SFRS7 SFRS7 SFRS7 4854 0.035 0.26 YES
31 SNRPE SNRPE SNRPE 4985 0.033 0.26 YES
32 USP39 USP39 USP39 5006 0.032 0.27 YES
33 PHF5A PHF5A PHF5A 5197 0.03 0.27 YES
34 THOC1 THOC1 THOC1 5318 0.028 0.27 YES
35 MAGOHB MAGOHB MAGOHB 5371 0.028 0.28 YES
36 PCBP1 PCBP1 PCBP1 5395 0.028 0.28 YES
37 ISY1 ISY1 ISY1 5474 0.027 0.29 YES
38 SFRS4 SFRS4 SFRS4 5519 0.026 0.29 YES
39 MAGOH MAGOH MAGOH 5552 0.026 0.3 YES
40 SFRS13A SFRS13A SFRS13A 5589 0.026 0.3 YES
41 RBM25 RBM25 RBM25 5628 0.025 0.31 YES
42 BAT1 BAT1 BAT1 5746 0.024 0.31 YES
43 LSM5 LSM5 LSM5 5756 0.024 0.31 YES
44 EIF4A3 EIF4A3 EIF4A3 5897 0.022 0.31 YES
45 SNRPB2 SNRPB2 SNRPB2 5939 0.021 0.32 YES
46 EFTUD2 EFTUD2 EFTUD2 5962 0.021 0.32 YES
47 SNRPD2 SNRPD2 SNRPD2 5978 0.021 0.32 YES
48 TRA2A TRA2A TRA2A 5990 0.021 0.33 YES
49 SNRPC SNRPC SNRPC 5992 0.021 0.34 YES
50 THOC4 THOC4 THOC4 6012 0.02 0.34 YES
51 HNRNPA3 HNRNPA3 HNRNPA3 6022 0.02 0.35 YES
52 CWC15 CWC15 CWC15 6049 0.02 0.35 YES
53 SFRS1 SFRS1 SFRS1 6126 0.019 0.35 YES
54 HNRNPC HNRNPC HNRNPC 6134 0.019 0.36 YES
55 SART1 SART1 SART1 6158 0.019 0.36 YES
56 TRA2B TRA2B TRA2B 6188 0.018 0.36 YES
57 SNRNP70 SNRNP70 SNRNP70 6191 0.018 0.37 YES
58 HNRNPU HNRNPU HNRNPU 6201 0.018 0.37 YES
59 SFRS3 SFRS3 SFRS3 6323 0.017 0.37 YES
60 SYF2 SYF2 SYF2 6349 0.016 0.38 YES
61 PRPF38A PRPF38A PRPF38A 6557 0.014 0.37 YES
62 CCDC12 CCDC12 CCDC12 6620 0.014 0.37 YES
63 PUF60 PUF60 PUF60 6634 0.013 0.37 YES
64 AQR AQR AQR 6675 0.013 0.37 YES
65 CTNNBL1 CTNNBL1 CTNNBL1 6749 0.012 0.37 YES
66 SNRNP27 SNRNP27 SNRNP27 6764 0.012 0.37 YES
67 SF3B3 SF3B3 SF3B3 6787 0.012 0.38 YES
68 CHERP CHERP CHERP 6826 0.011 0.38 YES
69 DHX16 DHX16 DHX16 6856 0.011 0.38 YES
70 DHX8 DHX8 DHX8 6881 0.011 0.38 YES
71 THOC2 THOC2 THOC2 6899 0.01 0.38 YES
72 U2AF1 U2AF1 U2AF1 6935 0.0099 0.38 YES
73 DHX38 DHX38 DHX38 6958 0.0097 0.38 YES
74 U2AF2 U2AF2 U2AF2 7215 0.007 0.37 NO
75 PRPF18 PRPF18 PRPF18 7295 0.0061 0.37 NO
76 DDX42 DDX42 DDX42 7308 0.006 0.37 NO
77 LSM6 LSM6 LSM6 7407 0.0051 0.37 NO
78 LSM2 LSM2 LSM2 7422 0.005 0.37 NO
79 PPIE PPIE PPIE 7424 0.005 0.37 NO
80 HNRNPK HNRNPK HNRNPK 7477 0.0045 0.37 NO
81 PRPF4 PRPF4 PRPF4 7510 0.0041 0.37 NO
82 PRPF6 PRPF6 PRPF6 7649 0.0027 0.36 NO
83 ZMAT2 ZMAT2 ZMAT2 7660 0.0026 0.36 NO
84 RBM17 RBM17 RBM17 7752 0.0017 0.36 NO
85 SFRS9 SFRS9 SFRS9 7767 0.0016 0.36 NO
86 SNRNP200 SNRNP200 SNRNP200 7776 0.0014 0.36 NO
87 PRPF38B PRPF38B PRPF38B 7820 0.00089 0.35 NO
88 DDX23 DDX23 DDX23 7822 0.00087 0.35 NO
89 SF3B2 SF3B2 SF3B2 7848 0.00059 0.35 NO
90 PPIL1 PPIL1 PPIL1 7904 -0.000066 0.35 NO
91 PRPF31 PRPF31 PRPF31 7912 -0.00013 0.35 NO
92 XAB2 XAB2 XAB2 7921 -0.00024 0.35 NO
93 CRNKL1 CRNKL1 CRNKL1 7925 -0.00026 0.35 NO
94 HNRNPA1 HNRNPA1 HNRNPA1 7975 -0.00076 0.35 NO
95 ACIN1 ACIN1 ACIN1 8004 -0.0011 0.34 NO
96 NCBP1 NCBP1 NCBP1 8009 -0.0011 0.34 NO
97 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 8283 -0.0038 0.33 NO
98 SNW1 SNW1 SNW1 8307 -0.004 0.33 NO
99 SFRS5 SFRS5 SFRS5 8459 -0.0057 0.32 NO
100 DDX46 DDX46 DDX46 8523 -0.0064 0.32 NO
101 PQBP1 PQBP1 PQBP1 8666 -0.0079 0.32 NO
102 BCAS2 BCAS2 BCAS2 8853 -0.0098 0.31 NO
103 PRPF19 PRPF19 PRPF19 8870 -0.01 0.31 NO
104 RBM22 RBM22 RBM22 9215 -0.014 0.3 NO
105 HNRNPM HNRNPM HNRNPM 9361 -0.015 0.29 NO
106 RBMX RBMX RBMX 9390 -0.015 0.3 NO
107 SLU7 SLU7 SLU7 9640 -0.018 0.29 NO
108 NHP2L1 NHP2L1 NHP2L1 9738 -0.02 0.29 NO
109 CDC5L CDC5L CDC5L 9786 -0.02 0.29 NO
110 SF3A1 SF3A1 SF3A1 9822 -0.02 0.29 NO
111 PLRG1 PLRG1 PLRG1 9880 -0.021 0.3 NO
112 SFRS6 SFRS6 SFRS6 9889 -0.021 0.3 NO
113 SNRNP40 SNRNP40 SNRNP40 9973 -0.022 0.3 NO
114 HSPA8 HSPA8 HSPA8 10222 -0.026 0.3 NO
115 SF3A3 SF3A3 SF3A3 10274 -0.026 0.3 NO
116 SF3B5 SF3B5 SF3B5 10285 -0.026 0.31 NO
117 SFRS2B SFRS2B SFRS2B 10539 -0.03 0.3 NO
118 LSM3 LSM3 LSM3 10631 -0.031 0.31 NO
119 WBP11 WBP11 WBP11 10653 -0.031 0.32 NO
120 PRPF40B PRPF40B PRPF40B 10770 -0.033 0.32 NO
121 DDX5 DDX5 DDX5 10949 -0.036 0.32 NO
122 PRPF8 PRPF8 PRPF8 12336 -0.062 0.26 NO
123 TXNL4A TXNL4A TXNL4A 12575 -0.067 0.27 NO
124 CDC40 CDC40 CDC40 13178 -0.083 0.26 NO
125 HSPA1L HSPA1L HSPA1L 14082 -0.11 0.24 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 RACCYCD PATHWAY.

Figure S8.  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 RHO PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CCNE1 CCNE1 CCNE1 2016 0.11 0.00076 YES
2 PAK1 PAK1 PAK1 2252 0.1 0.086 YES
3 MAPK3 MAPK3 MAPK3 2560 0.087 0.16 YES
4 CDK2 CDK2 CDK2 2618 0.085 0.24 YES
5 CCND1 CCND1 CCND1 3183 0.069 0.27 YES
6 RELA RELA RELA 3343 0.064 0.33 YES
7 RAC1 RAC1 RAC1 3370 0.064 0.39 YES
8 CDK6 CDK6 CDK6 3787 0.053 0.42 YES
9 IKBKB IKBKB IKBKB 4396 0.042 0.43 YES
10 CDKN1A CDKN1A CDKN1A 4984 0.033 0.43 YES
11 PIK3CA PIK3CA PIK3CA 5622 0.025 0.42 YES
12 AKT1 AKT1 AKT1 5830 0.023 0.43 YES
13 RHOA RHOA RHOA 6196 0.018 0.43 NO
14 RAF1 RAF1 RAF1 7218 0.007 0.38 NO
15 NFKB1 NFKB1 NFKB1 7450 0.0047 0.37 NO
16 TFDP1 TFDP1 TFDP1 7737 0.0018 0.36 NO
17 IKBKG IKBKG IKBKG 8084 -0.0019 0.34 NO
18 HRAS HRAS HRAS 8484 -0.006 0.33 NO
19 CDK4 CDK4 CDK4 8584 -0.0071 0.33 NO
20 CDKN1B CDKN1B CDKN1B 9097 -0.012 0.31 NO
21 MAPK1 MAPK1 MAPK1 9763 -0.02 0.3 NO
22 CHUK CHUK CHUK 10486 -0.029 0.28 NO
23 RB1 RB1 RB1 11079 -0.038 0.29 NO
24 NFKBIA NFKBIA NFKBIA 11212 -0.04 0.32 NO
25 PIK3R1 PIK3R1 PIK3R1 12784 -0.072 0.31 NO

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

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

genes ES table in pathway: BIOCARTA TNFR1 PATHWAY

Table S6.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RAD54L RAD54L RAD54L 137 0.34 0.12 YES
2 EME1 EME1 EME1 263 0.3 0.24 YES
3 XRCC2 XRCC2 XRCC2 286 0.3 0.35 YES
4 RAD51 RAD51 RAD51 445 0.27 0.44 YES
5 RAD54B RAD54B RAD54B 1496 0.15 0.44 YES
6 BRCA2 BRCA2 BRCA2 1535 0.14 0.5 YES
7 BLM BLM BLM 1635 0.14 0.55 YES
8 RPA4 RPA4 RPA4 1829 0.12 0.58 YES
9 XRCC3 XRCC3 XRCC3 2099 0.11 0.61 YES
10 POLD4 POLD4 POLD4 2196 0.1 0.64 YES
11 POLD1 POLD1 POLD1 3518 0.059 0.59 NO
12 RPA3 RPA3 RPA3 3525 0.059 0.62 NO
13 SHFM1 SHFM1 SHFM1 3590 0.058 0.64 NO
14 POLD3 POLD3 POLD3 4314 0.043 0.61 NO
15 MUS81 MUS81 MUS81 4547 0.04 0.62 NO
16 RAD51L1 RAD51L1 RAD51L1 4639 0.038 0.63 NO
17 SSBP1 SSBP1 SSBP1 4916 0.034 0.62 NO
18 TOP3B TOP3B TOP3B 5120 0.031 0.62 NO
19 MRE11A MRE11A MRE11A 5497 0.027 0.62 NO
20 POLD2 POLD2 POLD2 7196 0.0071 0.52 NO
21 RAD52 RAD52 RAD52 8076 -0.0018 0.48 NO
22 NBN NBN NBN 8535 -0.0066 0.46 NO
23 RAD50 RAD50 RAD50 9109 -0.012 0.43 NO
24 RPA2 RPA2 RPA2 11321 -0.041 0.33 NO
25 TOP3A TOP3A TOP3A 11644 -0.047 0.33 NO
26 RPA1 RPA1 RPA1 11890 -0.052 0.33 NO
27 RAD51L3 RAD51L3 RAD51L3 12300 -0.061 0.33 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TNFR1 PATHWAY.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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 TP73 TP73 TP73 6 0.44 0.063 YES
2 SERPINB5 SERPINB5 SERPINB5 135 0.34 0.1 YES
3 SFN SFN SFN 159 0.34 0.15 YES
4 GTSE1 GTSE1 GTSE1 389 0.28 0.18 YES
5 CCNB2 CCNB2 CCNB2 448 0.27 0.21 YES
6 RRM2 RRM2 RRM2 520 0.26 0.25 YES
7 CDK1 CDK1 CDK1 610 0.24 0.28 YES
8 PMAIP1 PMAIP1 PMAIP1 657 0.23 0.31 YES
9 CCNE2 CCNE2 CCNE2 960 0.19 0.32 YES
10 BBC3 BBC3 BBC3 1051 0.18 0.34 YES
11 CCNB1 CCNB1 CCNB1 1306 0.16 0.35 YES
12 TNFRSF10B TNFRSF10B TNFRSF10B 1387 0.15 0.37 YES
13 CASP8 CASP8 CASP8 1584 0.14 0.38 YES
14 CHEK2 CHEK2 CHEK2 1733 0.13 0.39 YES
15 CHEK1 CHEK1 CHEK1 2007 0.11 0.39 YES
16 CCNE1 CCNE1 CCNE1 2016 0.11 0.4 YES
17 PERP PERP PERP 2282 0.098 0.4 YES
18 CD82 CD82 CD82 2296 0.098 0.42 YES
19 IGFBP3 IGFBP3 IGFBP3 2368 0.095 0.42 YES
20 CDK2 CDK2 CDK2 2618 0.085 0.42 YES
21 BID BID BID 2779 0.08 0.43 YES
22 CCNG2 CCNG2 CCNG2 2861 0.077 0.43 YES
23 FAS FAS FAS 2907 0.076 0.44 YES
24 LRDD LRDD LRDD 2992 0.073 0.45 YES
25 CCND1 CCND1 CCND1 3183 0.069 0.45 YES
26 CASP3 CASP3 CASP3 3646 0.057 0.43 YES
27 SIAH1 SIAH1 SIAH1 3785 0.053 0.43 YES
28 CDK6 CDK6 CDK6 3787 0.053 0.44 YES
29 RFWD2 RFWD2 RFWD2 3872 0.052 0.44 YES
30 TP53I3 TP53I3 TP53I3 3894 0.052 0.45 YES
31 TP53AIP1 TP53AIP1 TP53AIP1 3897 0.052 0.45 YES
32 BAX BAX BAX 4208 0.045 0.44 NO
33 CYCS CYCS CYCS 4237 0.045 0.45 NO
34 SHISA5 SHISA5 SHISA5 4295 0.044 0.45 NO
35 ATR ATR ATR 4559 0.04 0.44 NO
36 MDM2 MDM2 MDM2 4742 0.036 0.44 NO
37 CDKN1A CDKN1A CDKN1A 4984 0.033 0.43 NO
38 DDB2 DDB2 DDB2 5435 0.027 0.41 NO
39 EI24 EI24 EI24 6302 0.017 0.36 NO
40 MDM4 MDM4 MDM4 7190 0.0071 0.32 NO
41 TSC2 TSC2 TSC2 7207 0.007 0.32 NO
42 APAF1 APAF1 APAF1 8435 -0.0054 0.25 NO
43 CDK4 CDK4 CDK4 8584 -0.0071 0.24 NO
44 CCNG1 CCNG1 CCNG1 9009 -0.011 0.22 NO
45 TP53 TP53 TP53 9141 -0.013 0.22 NO
46 CASP9 CASP9 CASP9 9869 -0.021 0.18 NO
47 BAI1 BAI1 BAI1 10496 -0.029 0.15 NO
48 THBS1 THBS1 THBS1 10567 -0.03 0.15 NO
49 RCHY1 RCHY1 RCHY1 10584 -0.03 0.16 NO
50 ZMAT3 ZMAT3 ZMAT3 10669 -0.031 0.16 NO
51 GADD45A GADD45A GADD45A 11055 -0.037 0.14 NO
52 PTEN PTEN PTEN 11710 -0.048 0.11 NO
53 CCND3 CCND3 CCND3 11748 -0.049 0.12 NO
54 RRM2B RRM2B RRM2B 11961 -0.053 0.11 NO
55 SERPINE1 SERPINE1 SERPINE1 11982 -0.054 0.12 NO
56 CDKN2A CDKN2A CDKN2A 12522 -0.066 0.098 NO
57 CCNB3 CCNB3 CCNB3 12640 -0.069 0.1 NO
58 GADD45B GADD45B GADD45B 12965 -0.077 0.095 NO
59 ATM ATM ATM 13113 -0.08 0.098 NO
60 RPRM RPRM RPRM 13423 -0.09 0.094 NO
61 PPM1D PPM1D PPM1D 13645 -0.098 0.096 NO
62 SESN2 SESN2 SESN2 13808 -0.1 0.1 NO
63 CCND2 CCND2 CCND2 13910 -0.11 0.11 NO
64 SESN3 SESN3 SESN3 14473 -0.13 0.1 NO
65 SESN1 SESN1 SESN1 15520 -0.19 0.071 NO
66 IGF1 IGF1 IGF1 16891 -0.31 0.04 NO
67 GADD45G GADD45G GADD45G 16950 -0.32 0.082 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, 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 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 POLE2 POLE2 POLE2 786 0.22 0.058 YES
2 DNA2 DNA2 DNA2 1418 0.15 0.095 YES
3 MCM2 MCM2 MCM2 1755 0.13 0.14 YES
4 RPA4 RPA4 RPA4 1829 0.12 0.19 YES
5 MCM4 MCM4 MCM4 2191 0.1 0.22 YES
6 POLD4 POLD4 POLD4 2196 0.1 0.27 YES
7 RFC4 RFC4 RFC4 2319 0.096 0.31 YES
8 PRIM2 PRIM2 PRIM2 3117 0.07 0.3 YES
9 MCM7 MCM7 MCM7 3406 0.062 0.31 YES
10 POLE POLE POLE 3412 0.062 0.34 YES
11 RNASEH1 RNASEH1 RNASEH1 3493 0.06 0.36 YES
12 POLD1 POLD1 POLD1 3518 0.059 0.39 YES
13 RNASEH2A RNASEH2A RNASEH2A 3521 0.059 0.42 YES
14 RPA3 RPA3 RPA3 3525 0.059 0.44 YES
15 MCM6 MCM6 MCM6 4050 0.048 0.44 YES
16 FEN1 FEN1 FEN1 4222 0.045 0.45 YES
17 MCM3 MCM3 MCM3 4229 0.045 0.47 YES
18 POLE4 POLE4 POLE4 4257 0.044 0.49 YES
19 POLD3 POLD3 POLD3 4314 0.043 0.51 YES
20 PCNA PCNA PCNA 4409 0.042 0.52 YES
21 POLA2 POLA2 POLA2 4531 0.04 0.53 YES
22 RFC5 RFC5 RFC5 4728 0.037 0.54 YES
23 SSBP1 SSBP1 SSBP1 4916 0.034 0.55 YES
24 LIG1 LIG1 LIG1 5245 0.029 0.54 NO
25 RFC2 RFC2 RFC2 5569 0.026 0.54 NO
26 MCM5 MCM5 MCM5 5728 0.024 0.54 NO
27 POLE3 POLE3 POLE3 5889 0.022 0.54 NO
28 POLD2 POLD2 POLD2 7196 0.0071 0.47 NO
29 RFC3 RFC3 RFC3 8963 -0.011 0.38 NO
30 PRIM1 PRIM1 PRIM1 10835 -0.034 0.3 NO
31 RPA2 RPA2 RPA2 11321 -0.041 0.29 NO
32 RNASEH2C RNASEH2C RNASEH2C 11379 -0.042 0.31 NO
33 RPA1 RPA1 RPA1 11890 -0.052 0.3 NO
34 RFC1 RFC1 RFC1 11974 -0.054 0.32 NO
35 RNASEH2B RNASEH2B RNASEH2B 12137 -0.057 0.34 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 STEROID HORMONE BIOSYNTHESIS.

Figure S16.  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 O GLYCAN BIOSYNTHESIS

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 CASP8 CASP8 CASP8 1584 0.14 0.012 YES
2 LMNB1 LMNB1 LMNB1 1850 0.12 0.082 YES
3 TRADD TRADD TRADD 1878 0.12 0.16 YES
4 PAK1 PAK1 PAK1 2252 0.1 0.21 YES
5 LMNA LMNA LMNA 2655 0.084 0.25 YES
6 LMNB2 LMNB2 LMNB2 3078 0.071 0.28 YES
7 BAG4 BAG4 BAG4 3442 0.061 0.3 YES
8 CASP3 CASP3 CASP3 3646 0.057 0.33 YES
9 PAK2 PAK2 PAK2 4146 0.046 0.34 YES
10 FADD FADD FADD 4301 0.044 0.36 YES
11 CASP2 CASP2 CASP2 4375 0.042 0.38 YES
12 TNFRSF1A TNFRSF1A TNFRSF1A 6326 0.017 0.29 NO
13 DFFA DFFA DFFA 7035 0.0086 0.26 NO
14 PRKDC PRKDC PRKDC 7771 0.0015 0.22 NO
15 SPTAN1 SPTAN1 SPTAN1 7823 0.00086 0.22 NO
16 MAPK8 MAPK8 MAPK8 8025 -0.0012 0.21 NO
17 JUN JUN JUN 8576 -0.007 0.18 NO
18 MAP3K1 MAP3K1 MAP3K1 8749 -0.0088 0.18 NO
19 PARP1 PARP1 PARP1 9184 -0.013 0.16 NO
20 DFFB DFFB DFFB 10064 -0.024 0.13 NO
21 MAP3K7 MAP3K7 MAP3K7 10167 -0.025 0.14 NO
22 RIPK1 RIPK1 RIPK1 10328 -0.027 0.15 NO
23 MADD MADD MADD 10899 -0.035 0.15 NO
24 RB1 RB1 RB1 11079 -0.038 0.16 NO
25 ARHGDIB ARHGDIB ARHGDIB 11573 -0.046 0.17 NO
26 TNF TNF TNF 12487 -0.065 0.17 NO
27 MAP2K4 MAP2K4 MAP2K4 13422 -0.09 0.18 NO
28 CRADD CRADD CRADD 14553 -0.14 0.21 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 O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

Table S10.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CASP8 CASP8 CASP8 1584 0.14 -0.038 YES
2 LMNB1 LMNB1 LMNB1 1850 0.12 -0.011 YES
3 TRADD TRADD TRADD 1878 0.12 0.028 YES
4 BIRC3 BIRC3 BIRC3 2258 0.099 0.042 YES
5 CASP6 CASP6 CASP6 2388 0.094 0.067 YES
6 LMNA LMNA LMNA 2655 0.084 0.081 YES
7 BID BID BID 2779 0.08 0.1 YES
8 FAS FAS FAS 2907 0.076 0.12 YES
9 LMNB2 LMNB2 LMNB2 3078 0.071 0.14 YES
10 PSEN1 PSEN1 PSEN1 3239 0.067 0.15 YES
11 RELA RELA RELA 3343 0.064 0.17 YES
12 BAG4 BAG4 BAG4 3442 0.061 0.18 YES
13 CASP7 CASP7 CASP7 3469 0.06 0.2 YES
14 CFLAR CFLAR CFLAR 3532 0.059 0.22 YES
15 CASP3 CASP3 CASP3 3646 0.057 0.23 YES
16 CDK11A CDK11A CDK11A 4072 0.048 0.22 YES
17 PAK2 PAK2 PAK2 4146 0.046 0.24 YES
18 TRAF2 TRAF2 TRAF2 4204 0.045 0.25 YES
19 CYCS CYCS CYCS 4237 0.045 0.26 YES
20 FADD FADD FADD 4301 0.044 0.28 YES
21 CASP2 CASP2 CASP2 4375 0.042 0.29 YES
22 MAP3K5 MAP3K5 MAP3K5 4538 0.04 0.29 YES
23 CDK11B CDK11B CDK11B 4550 0.04 0.3 YES
24 MDM2 MDM2 MDM2 4742 0.036 0.31 YES
25 PRKCD PRKCD PRKCD 5136 0.031 0.3 NO
26 ACTG1 ACTG1 ACTG1 5752 0.024 0.27 NO
27 DAXX DAXX DAXX 5774 0.023 0.28 NO
28 BIRC2 BIRC2 BIRC2 6172 0.019 0.26 NO
29 TNFRSF1A TNFRSF1A TNFRSF1A 6326 0.017 0.26 NO
30 RASA1 RASA1 RASA1 6993 0.0092 0.23 NO
31 DFFA DFFA DFFA 7035 0.0086 0.23 NO
32 NUMA1 NUMA1 NUMA1 7229 0.0068 0.22 NO
33 NFKB1 NFKB1 NFKB1 7450 0.0047 0.21 NO
34 PRKDC PRKDC PRKDC 7771 0.0015 0.19 NO
35 SPTAN1 SPTAN1 SPTAN1 7823 0.00086 0.19 NO
36 XIAP XIAP XIAP 7985 -0.00088 0.18 NO
37 MAPK8 MAPK8 MAPK8 8025 -0.0012 0.18 NO
38 MAP2K7 MAP2K7 MAP2K7 8302 -0.004 0.16 NO
39 GSN GSN GSN 8316 -0.0041 0.16 NO
40 PTK2 PTK2 PTK2 8385 -0.0048 0.16 NO
41 APAF1 APAF1 APAF1 8435 -0.0054 0.16 NO
42 MAP3K1 MAP3K1 MAP3K1 8749 -0.0088 0.15 NO
43 PARP1 PARP1 PARP1 9184 -0.013 0.13 NO
44 CASP9 CASP9 CASP9 9869 -0.021 0.1 NO
45 DFFB DFFB DFFB 10064 -0.024 0.097 NO
46 RIPK1 RIPK1 RIPK1 10328 -0.027 0.092 NO
47 CHUK CHUK CHUK 10486 -0.029 0.093 NO
48 RB1 RB1 RB1 11079 -0.038 0.074 NO
49 NFKBIA NFKBIA NFKBIA 11212 -0.04 0.081 NO
50 ARHGDIB ARHGDIB ARHGDIB 11573 -0.046 0.077 NO
51 TNFRSF1B TNFRSF1B TNFRSF1B 12256 -0.06 0.06 NO
52 TNF TNF TNF 12487 -0.065 0.07 NO
53 PSEN2 PSEN2 PSEN2 13161 -0.082 0.062 NO
54 MAP3K14 MAP3K14 MAP3K14 14233 -0.12 0.045 NO
55 TRAF1 TRAF1 TRAF1 14299 -0.12 0.084 NO
56 CRADD CRADD CRADD 14553 -0.14 0.12 NO
57 BCL2 BCL2 BCL2 16635 -0.28 0.099 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.56 1.7 0.0039 0.094 0.54 0.17 0.093 0.16 0.042 0.004
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.49 1.9 0.002 0.07 0.15 0.18 0.21 0.14 0 0.014
BIOCARTA PPARA PATHWAY 54 genes.ES.table 0.47 1.5 0.012 0.19 0.79 0.11 0.09 0.1 0.12 0.01
KEGG GLYCOLYSIS GLUCONEOGENESIS 58 genes.ES.table 0.49 1.5 0.024 0.18 0.79 0.21 0.11 0.19 0.12 0.007
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.45 1.5 0.091 0.23 0.84 0.28 0.31 0.19 0.15 0.015
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.53 1.7 0.012 0.099 0.42 0.21 0.12 0.19 0 0.006
KEGG GALACTOSE METABOLISM 25 genes.ES.table 0.62 1.8 0 0.061 0.17 0.16 0.096 0.14 0 0.009
KEGG FATTY ACID METABOLISM 39 genes.ES.table 0.6 1.7 0.0021 0.1 0.44 0.51 0.25 0.39 0 0.005
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 30 genes.ES.table 0.63 1.8 0 0.067 0.17 0.27 0.11 0.24 0 0.012
KEGG GLYCINE SERINE AND THREONINE METABOLISM 29 genes.ES.table 0.72 1.7 0.002 0.081 0.47 0.52 0.14 0.45 0 0.003
genes ES table in pathway: BIOCARTA AGR 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 MAT1A MAT1A MAT1A 146 0.6 0.21 YES
2 CBS CBS CBS 274 0.45 0.37 YES
3 GGT6 GGT6 GGT6 326 0.41 0.52 YES
4 GGT1 GGT1 GGT1 374 0.38 0.66 YES
5 CTH CTH CTH 1240 0.2 0.69 YES
6 SCLY SCLY SCLY 1699 0.15 0.72 YES
7 GGT7 GGT7 GGT7 2686 0.1 0.71 NO
8 AHCYL2 AHCYL2 AHCYL2 4303 0.056 0.64 NO
9 AHCYL1 AHCYL1 AHCYL1 4565 0.051 0.65 NO
10 MAT2A MAT2A MAT2A 5085 0.042 0.63 NO
11 LCMT2 LCMT2 LCMT2 5695 0.033 0.61 NO
12 MAT2B MAT2B MAT2B 6878 0.021 0.56 NO
13 LCMT1 LCMT1 LCMT1 7055 0.02 0.56 NO
14 PAPSS1 PAPSS1 PAPSS1 7080 0.02 0.56 NO
15 HEMK1 HEMK1 HEMK1 7629 0.015 0.54 NO
16 SEPHS1 SEPHS1 SEPHS1 8282 0.01 0.51 NO
17 MARS2 MARS2 MARS2 9241 0.0039 0.46 NO
18 AHCY AHCY AHCY 9313 0.0036 0.45 NO
19 GGT5 GGT5 GGT5 10329 -0.0027 0.4 NO
20 METTL6 METTL6 METTL6 10804 -0.0055 0.38 NO
21 MARS MARS MARS 12327 -0.016 0.3 NO
22 TRMT11 TRMT11 TRMT11 12417 -0.016 0.3 NO
23 METTL2B METTL2B METTL2B 13254 -0.023 0.26 NO
24 PAPSS2 PAPSS2 PAPSS2 13647 -0.026 0.25 NO
25 WBSCR22 WBSCR22 WBSCR22 13687 -0.027 0.26 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 AGR PATHWAY.

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

genes ES table in pathway: BIOCARTA CARM ER 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 BBOX1 BBOX1 BBOX1 205 0.51 0.2 YES
2 OGDHL OGDHL OGDHL 332 0.41 0.36 YES
3 ALDH3A2 ALDH3A2 ALDH3A2 1497 0.17 0.37 YES
4 ACAT1 ACAT1 ACAT1 2065 0.13 0.4 YES
5 AASS AASS AASS 3362 0.08 0.36 YES
6 ACAT2 ACAT2 ACAT2 3479 0.076 0.38 YES
7 TMLHE TMLHE TMLHE 3995 0.063 0.38 YES
8 SETDB2 SETDB2 SETDB2 4006 0.062 0.41 YES
9 ALDH2 ALDH2 ALDH2 4328 0.055 0.41 YES
10 ALDH7A1 ALDH7A1 ALDH7A1 4427 0.054 0.43 YES
11 SETMAR SETMAR SETMAR 4472 0.053 0.45 YES
12 HADH HADH HADH 4550 0.051 0.47 YES
13 AADAT AADAT AADAT 5149 0.041 0.45 NO
14 HADHA HADHA HADHA 6368 0.026 0.4 NO
15 AASDHPPT AASDHPPT AASDHPPT 6392 0.026 0.4 NO
16 SETD2 SETD2 SETD2 6694 0.023 0.4 NO
17 GCDH GCDH GCDH 6711 0.023 0.41 NO
18 WHSC1L1 WHSC1L1 WHSC1L1 7130 0.019 0.39 NO
19 NSD1 NSD1 NSD1 7158 0.019 0.4 NO
20 SETD1A SETD1A SETD1A 7464 0.016 0.39 NO
21 DOT1L DOT1L DOT1L 7476 0.016 0.4 NO
22 SETD7 SETD7 SETD7 8384 0.0095 0.35 NO
23 EHMT2 EHMT2 EHMT2 8409 0.0094 0.35 NO
24 SETDB1 SETDB1 SETDB1 8467 0.0089 0.35 NO
25 ECHS1 ECHS1 ECHS1 8771 0.007 0.34 NO
26 SUV420H1 SUV420H1 SUV420H1 8931 0.0059 0.33 NO
27 ALDH9A1 ALDH9A1 ALDH9A1 8946 0.0058 0.33 NO
28 ASH1L ASH1L ASH1L 9097 0.0048 0.33 NO
29 SETD1B SETD1B SETD1B 9271 0.0038 0.32 NO
30 EHMT1 EHMT1 EHMT1 9289 0.0037 0.32 NO
31 DLST DLST DLST 9675 0.001 0.3 NO
32 OGDH OGDH OGDH 10778 -0.0054 0.24 NO
33 PLOD1 PLOD1 PLOD1 12913 -0.02 0.14 NO
34 SUV39H2 SUV39H2 SUV39H2 13032 -0.021 0.14 NO
35 AASDH AASDH AASDH 13468 -0.025 0.12 NO
36 SUV39H1 SUV39H1 SUV39H1 13869 -0.028 0.11 NO
37 SETD8 SETD8 SETD8 13883 -0.029 0.13 NO
38 PIPOX PIPOX PIPOX 13925 -0.029 0.14 NO
39 PLOD3 PLOD3 PLOD3 14411 -0.034 0.12 NO
40 ALDH1B1 ALDH1B1 ALDH1B1 14652 -0.037 0.13 NO
41 WHSC1 WHSC1 WHSC1 15144 -0.044 0.12 NO
42 PLOD2 PLOD2 PLOD2 16375 -0.075 0.082 NO
43 SUV420H2 SUV420H2 SUV420H2 16389 -0.076 0.11 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 CARM ER PATHWAY.

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

genes ES table in pathway: BIOCARTA PPARA 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 PNLIPRP1 PNLIPRP1 PNLIPRP1 3 1.2 0.2 YES
2 CEL CEL CEL 19 1.1 0.38 YES
3 PNLIPRP2 PNLIPRP2 PNLIPRP2 26 1.1 0.55 YES
4 LIPC LIPC LIPC 209 0.5 0.62 YES
5 ALDH3A2 ALDH3A2 ALDH3A2 1497 0.17 0.58 NO
6 PPAP2C PPAP2C PPAP2C 1729 0.15 0.59 NO
7 DGKB DGKB DGKB 2073 0.13 0.6 NO
8 MBOAT1 MBOAT1 MBOAT1 2626 0.11 0.58 NO
9 LIPG LIPG LIPG 3369 0.08 0.56 NO
10 AGPAT2 AGPAT2 AGPAT2 3658 0.071 0.55 NO
11 ALDH2 ALDH2 ALDH2 4328 0.055 0.53 NO
12 AGPAT3 AGPAT3 AGPAT3 4406 0.054 0.53 NO
13 ALDH7A1 ALDH7A1 ALDH7A1 4427 0.054 0.54 NO
14 AGPAT6 AGPAT6 AGPAT6 4836 0.046 0.52 NO
15 DAK DAK DAK 5059 0.042 0.52 NO
16 GPAT2 GPAT2 GPAT2 5587 0.035 0.5 NO
17 AKR1A1 AKR1A1 AKR1A1 5901 0.031 0.48 NO
18 AKR1B1 AKR1B1 AKR1B1 6373 0.026 0.46 NO
19 PNPLA3 PNPLA3 PNPLA3 6594 0.024 0.45 NO
20 PPAP2B PPAP2B PPAP2B 7009 0.02 0.43 NO
21 GLA GLA GLA 7277 0.018 0.42 NO
22 AGPAT4 AGPAT4 AGPAT4 7439 0.017 0.42 NO
23 PPAP2A PPAP2A PPAP2A 7906 0.013 0.39 NO
24 DGKG DGKG DGKG 8908 0.006 0.34 NO
25 ALDH9A1 ALDH9A1 ALDH9A1 8946 0.0058 0.34 NO
26 MGLL MGLL MGLL 10271 -0.0024 0.27 NO
27 LCLAT1 LCLAT1 LCLAT1 10610 -0.0044 0.25 NO
28 DGKZ DGKZ DGKZ 10714 -0.005 0.24 NO
29 AGPAT1 AGPAT1 AGPAT1 11064 -0.0071 0.23 NO
30 DGKQ DGKQ DGKQ 12803 -0.019 0.14 NO
31 GPAM GPAM GPAM 12944 -0.02 0.13 NO
32 GLYCTK GLYCTK GLYCTK 13023 -0.021 0.13 NO
33 GK GK GK 13292 -0.023 0.12 NO
34 DGAT1 DGAT1 DGAT1 13817 -0.028 0.096 NO
35 DGKH DGKH DGKH 14170 -0.032 0.082 NO
36 AGK AGK AGK 14521 -0.036 0.069 NO
37 ALDH1B1 ALDH1B1 ALDH1B1 14652 -0.037 0.068 NO
38 DGKE DGKE DGKE 14731 -0.038 0.07 NO
39 DGKD DGKD DGKD 14815 -0.039 0.072 NO
40 LPL LPL LPL 14863 -0.04 0.076 NO
41 AWAT2 AWAT2 AWAT2 15854 -0.059 0.031 NO
42 DGKA DGKA DGKA 15901 -0.06 0.039 NO
43 AGPAT9 AGPAT9 AGPAT9 16102 -0.066 0.038 NO
44 LIPF LIPF LIPF 16161 -0.068 0.046 NO
45 MBOAT2 MBOAT2 MBOAT2 17374 -0.12 0.00033 NO
46 DGAT2 DGAT2 DGAT2 17813 -0.16 0.0024 NO
47 DGKI DGKI DGKI 18137 -0.2 0.017 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 PPARA PATHWAY.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PPARA 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 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 GSTA2 GSTA2 GSTA2 20 1.1 0.24 YES
2 GSTA1 GSTA1 GSTA1 180 0.53 0.35 YES
3 ANPEP ANPEP ANPEP 255 0.46 0.45 YES
4 GGT6 GGT6 GGT6 326 0.41 0.54 YES
5 GGT1 GGT1 GGT1 374 0.38 0.62 YES
6 IDH2 IDH2 IDH2 2367 0.12 0.54 YES
7 GGT7 GGT7 GGT7 2686 0.1 0.54 YES
8 MGST1 MGST1 MGST1 2702 0.1 0.56 YES
9 GSTM4 GSTM4 GSTM4 2802 0.1 0.58 YES
10 GPX2 GPX2 GPX2 2896 0.096 0.6 YES
11 GSTA4 GSTA4 GSTA4 3149 0.087 0.6 YES
12 OPLAH OPLAH OPLAH 3592 0.072 0.59 YES
13 GSTO2 GSTO2 GSTO2 3596 0.072 0.61 YES
14 GSR GSR GSR 3604 0.072 0.62 YES
15 MGST2 MGST2 MGST2 4075 0.061 0.61 NO
16 GSTM3 GSTM3 GSTM3 4234 0.058 0.62 NO
17 GSTP1 GSTP1 GSTP1 4723 0.048 0.6 NO
18 LAP3 LAP3 LAP3 5128 0.041 0.59 NO
19 GCLM GCLM GCLM 5219 0.04 0.59 NO
20 GSTZ1 GSTZ1 GSTZ1 5460 0.036 0.59 NO
21 GSTT1 GSTT1 GSTT1 6019 0.029 0.56 NO
22 ODC1 ODC1 ODC1 6451 0.025 0.55 NO
23 GSTK1 GSTK1 GSTK1 6468 0.025 0.55 NO
24 G6PD G6PD G6PD 6856 0.022 0.53 NO
25 GPX1 GPX1 GPX1 7290 0.018 0.51 NO
26 SRM SRM SRM 7342 0.018 0.52 NO
27 GSTO1 GSTO1 GSTO1 7498 0.016 0.51 NO
28 GCLC GCLC GCLC 8256 0.011 0.47 NO
29 MGST3 MGST3 MGST3 9022 0.0052 0.43 NO
30 GPX3 GPX3 GPX3 9064 0.005 0.43 NO
31 GSTM2 GSTM2 GSTM2 9257 0.0038 0.42 NO
32 IDH1 IDH1 IDH1 9738 0.00072 0.39 NO
33 SMS SMS SMS 10054 -0.0012 0.38 NO
34 GGT5 GGT5 GGT5 10329 -0.0027 0.36 NO
35 RRM1 RRM1 RRM1 10590 -0.0043 0.35 NO
36 TXNDC12 TXNDC12 TXNDC12 10644 -0.0046 0.35 NO
37 GSTM5 GSTM5 GSTM5 11083 -0.0072 0.33 NO
38 RRM2B RRM2B RRM2B 11737 -0.011 0.29 NO
39 GSS GSS GSS 13054 -0.021 0.23 NO
40 GPX7 GPX7 GPX7 13418 -0.024 0.21 NO
41 GPX4 GPX4 GPX4 13911 -0.029 0.19 NO
42 GSTM1 GSTM1 GSTM1 14260 -0.033 0.18 NO
43 GGCT GGCT GGCT 14374 -0.034 0.18 NO
44 RRM2 RRM2 RRM2 15924 -0.061 0.11 NO
45 GSTT2 GSTT2 GSTT2 17388 -0.12 0.058 NO

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

Figure S28.  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 CITRATE CYCLE TCA CYCLE

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 RBPJL RBPJL RBPJL 9 1.2 0.39 YES
2 PTCRA PTCRA PTCRA 1218 0.2 0.4 YES
3 DTX1 DTX1 DTX1 1745 0.15 0.42 YES
4 MAML3 MAML3 MAML3 2647 0.1 0.4 YES
5 KAT2B KAT2B KAT2B 2807 0.1 0.43 YES
6 PSEN2 PSEN2 PSEN2 2834 0.099 0.46 YES
7 NOTCH2 NOTCH2 NOTCH2 3256 0.084 0.47 YES
8 HES1 HES1 HES1 4062 0.061 0.44 NO
9 NOTCH1 NOTCH1 NOTCH1 4979 0.044 0.41 NO
10 DTX4 DTX4 DTX4 5504 0.036 0.39 NO
11 CREBBP CREBBP CREBBP 5509 0.036 0.4 NO
12 LFNG LFNG LFNG 5529 0.036 0.42 NO
13 CTBP2 CTBP2 CTBP2 6306 0.027 0.38 NO
14 DTX3L DTX3L DTX3L 7144 0.019 0.34 NO
15 NOTCH4 NOTCH4 NOTCH4 7350 0.018 0.34 NO
16 JAG2 JAG2 JAG2 7527 0.016 0.34 NO
17 APH1A APH1A APH1A 7690 0.015 0.33 NO
18 MAML1 MAML1 MAML1 8365 0.0097 0.3 NO
19 PSENEN PSENEN PSENEN 8706 0.0073 0.28 NO
20 NUMB NUMB NUMB 8826 0.0066 0.28 NO
21 EP300 EP300 EP300 8885 0.0062 0.28 NO
22 DVL1 DVL1 DVL1 9308 0.0036 0.26 NO
23 NCSTN NCSTN NCSTN 9796 0.00033 0.23 NO
24 HDAC2 HDAC2 HDAC2 10103 -0.0015 0.21 NO
25 JAG1 JAG1 JAG1 10126 -0.0016 0.21 NO
26 HDAC1 HDAC1 HDAC1 10193 -0.002 0.21 NO
27 NCOR2 NCOR2 NCOR2 10346 -0.0029 0.2 NO
28 PSEN1 PSEN1 PSEN1 10463 -0.0035 0.2 NO
29 CTBP1 CTBP1 CTBP1 11020 -0.0067 0.17 NO
30 SNW1 SNW1 SNW1 11081 -0.0072 0.17 NO
31 NOTCH3 NOTCH3 NOTCH3 11248 -0.0081 0.16 NO
32 CIR1 CIR1 CIR1 11783 -0.012 0.14 NO
33 MAML2 MAML2 MAML2 12140 -0.014 0.12 NO
34 RFNG RFNG RFNG 12165 -0.014 0.13 NO
35 DTX3 DTX3 DTX3 12535 -0.017 0.11 NO
36 DVL2 DVL2 DVL2 13001 -0.021 0.093 NO
37 RBPJ RBPJ RBPJ 13109 -0.022 0.095 NO
38 DTX2 DTX2 DTX2 13618 -0.026 0.076 NO
39 DVL3 DVL3 DVL3 14114 -0.031 0.06 NO
40 ADAM17 ADAM17 ADAM17 14343 -0.034 0.059 NO
41 DLL4 DLL4 DLL4 14473 -0.035 0.064 NO
42 KAT2A KAT2A KAT2A 15108 -0.044 0.044 NO
43 DLL1 DLL1 DLL1 15661 -0.054 0.032 NO
44 NUMBL NUMBL NUMBL 15935 -0.061 0.038 NO
45 HES5 HES5 HES5 16729 -0.088 0.025 NO
46 DLL3 DLL3 DLL3 18146 -0.2 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: KEGG CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AOX1 AOX1 AOX1 296 0.43 0.14 YES
2 ALDH3A2 ALDH3A2 ALDH3A2 1497 0.17 0.13 YES
3 ABAT ABAT ABAT 1715 0.15 0.18 YES
4 PCCA PCCA PCCA 1780 0.15 0.23 YES
5 ACAT1 ACAT1 ACAT1 2065 0.13 0.26 YES
6 MCCC1 MCCC1 MCCC1 2479 0.11 0.28 YES
7 ACADS ACADS ACADS 2810 0.099 0.29 YES
8 AUH AUH AUH 3022 0.092 0.32 YES
9 ACAA2 ACAA2 ACAA2 3182 0.086 0.34 YES
10 HIBCH HIBCH HIBCH 3225 0.085 0.36 YES
11 ACAT2 ACAT2 ACAT2 3479 0.076 0.38 YES
12 ACAA1 ACAA1 ACAA1 3708 0.07 0.39 YES
13 ALDH6A1 ALDH6A1 ALDH6A1 3844 0.066 0.41 YES
14 ALDH2 ALDH2 ALDH2 4328 0.055 0.4 YES
15 ALDH7A1 ALDH7A1 ALDH7A1 4427 0.054 0.41 YES
16 DBT DBT DBT 4514 0.052 0.43 YES
17 HADH HADH HADH 4550 0.051 0.44 YES
18 ACADSB ACADSB ACADSB 4605 0.05 0.46 YES
19 MCEE MCEE MCEE 4780 0.047 0.47 YES
20 BCAT2 BCAT2 BCAT2 4891 0.045 0.48 YES
21 ACAD8 ACAD8 ACAD8 5118 0.042 0.48 YES
22 IL4I1 IL4I1 IL4I1 5243 0.04 0.49 YES
23 BCKDHA BCKDHA BCKDHA 5329 0.038 0.5 YES
24 HMGCL HMGCL HMGCL 5411 0.037 0.5 YES
25 MCCC2 MCCC2 MCCC2 5616 0.034 0.5 YES
26 ACADM ACADM ACADM 5679 0.034 0.51 YES
27 IVD IVD IVD 5782 0.032 0.52 YES
28 HADHB HADHB HADHB 5912 0.03 0.52 YES
29 HADHA HADHA HADHA 6368 0.026 0.51 NO
30 MUT MUT MUT 6449 0.025 0.51 NO
31 EHHADH EHHADH EHHADH 6870 0.021 0.5 NO
32 PCCB PCCB PCCB 7247 0.018 0.48 NO
33 HIBADH HIBADH HIBADH 7490 0.016 0.48 NO
34 HSD17B10 HSD17B10 HSD17B10 8107 0.012 0.45 NO
35 DLD DLD DLD 8213 0.011 0.44 NO
36 ECHS1 ECHS1 ECHS1 8771 0.007 0.42 NO
37 ALDH9A1 ALDH9A1 ALDH9A1 8946 0.0058 0.41 NO
38 HMGCS1 HMGCS1 HMGCS1 11015 -0.0067 0.3 NO
39 BCKDHB BCKDHB BCKDHB 12883 -0.02 0.2 NO
40 ALDH1B1 ALDH1B1 ALDH1B1 14652 -0.037 0.12 NO
41 OXCT1 OXCT1 OXCT1 16020 -0.064 0.071 NO
42 HMGCS2 HMGCS2 HMGCS2 16585 -0.082 0.069 NO
43 OXCT2 OXCT2 OXCT2 16812 -0.091 0.089 NO

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

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

genes ES table in pathway: KEGG GALACTOSE 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 PPARGC1A PPARGC1A PPARGC1A 471 0.35 0.23 YES
2 NR0B1 NR0B1 NR0B1 1177 0.2 0.34 YES
3 ESR1 ESR1 ESR1 1598 0.16 0.44 YES
4 HDAC11 HDAC11 HDAC11 2441 0.12 0.48 YES
5 GRIP1 GRIP1 GRIP1 3565 0.073 0.47 YES
6 HIST2H3C HIST2H3C HIST2H3C 3946 0.064 0.49 YES
7 CREBBP CREBBP CREBBP 5509 0.036 0.44 NO
8 CCND1 CCND1 CCND1 6170 0.028 0.42 NO
9 HDAC5 HDAC5 HDAC5 7288 0.018 0.37 NO
10 POLR2A POLR2A POLR2A 7437 0.017 0.38 NO
11 SPEN SPEN SPEN 7830 0.014 0.37 NO
12 HDAC7 HDAC7 HDAC7 8574 0.0082 0.33 NO
13 PHB2 PHB2 PHB2 8751 0.0071 0.33 NO
14 NRIP1 NRIP1 NRIP1 8783 0.0069 0.33 NO
15 EP300 EP300 EP300 8885 0.0062 0.33 NO
16 GTF2F1 GTF2F1 GTF2F1 9870 -0.00012 0.28 NO
17 HDAC3 HDAC3 HDAC3 9946 -0.0006 0.27 NO
18 TBP TBP TBP 10070 -0.0013 0.27 NO
19 HDAC2 HDAC2 HDAC2 10103 -0.0015 0.27 NO
20 HDAC8 HDAC8 HDAC8 10133 -0.0017 0.27 NO
21 HDAC1 HDAC1 HDAC1 10193 -0.002 0.26 NO
22 HDAC6 HDAC6 HDAC6 10259 -0.0024 0.26 NO
23 NCOR2 NCOR2 NCOR2 10346 -0.0029 0.26 NO
24 HDAC10 HDAC10 HDAC10 11130 -0.0075 0.22 NO
25 GTF2A1 GTF2A1 GTF2A1 11542 -0.01 0.21 NO
26 PELP1 PELP1 PELP1 11625 -0.011 0.21 NO
27 HDAC4 HDAC4 HDAC4 12240 -0.015 0.19 NO
28 CARM1 CARM1 CARM1 12482 -0.017 0.19 NO
29 ERCC3 ERCC3 ERCC3 12725 -0.018 0.19 NO
30 SRA1 SRA1 SRA1 12886 -0.02 0.2 NO
31 MED1 MED1 MED1 13133 -0.022 0.2 NO
32 GTF2E1 GTF2E1 GTF2E1 13692 -0.027 0.19 NO
33 BRCA1 BRCA1 BRCA1 15136 -0.044 0.14 NO
34 HDAC9 HDAC9 HDAC9 15567 -0.052 0.16 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 GALACTOSE METABOLISM.

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 G6PC G6PC G6PC 282 0.44 0.081 YES
2 G6PC2 G6PC2 G6PC2 394 0.38 0.16 YES
3 PPARGC1A PPARGC1A PPARGC1A 471 0.35 0.23 YES
4 RXRG RXRG RXRG 638 0.3 0.28 YES
5 NPY NPY NPY 685 0.28 0.34 YES
6 POMC POMC POMC 811 0.26 0.39 YES
7 ACSL6 ACSL6 ACSL6 934 0.24 0.44 YES
8 PRKCQ PRKCQ PRKCQ 951 0.24 0.48 YES
9 CD36 CD36 CD36 1378 0.18 0.5 YES
10 IRS4 IRS4 IRS4 1427 0.18 0.54 YES
11 PRKAA2 PRKAA2 PRKAA2 1448 0.18 0.57 YES
12 ACACB ACACB ACACB 2577 0.11 0.54 NO
13 NFKBIE NFKBIE NFKBIE 4000 0.063 0.47 NO
14 ADIPOQ ADIPOQ ADIPOQ 4130 0.06 0.48 NO
15 TNFRSF1B TNFRSF1B TNFRSF1B 4462 0.053 0.47 NO
16 CPT1A CPT1A CPT1A 5174 0.041 0.44 NO
17 PCK2 PCK2 PCK2 5213 0.04 0.45 NO
18 RXRA RXRA RXRA 5330 0.038 0.45 NO
19 ACSL5 ACSL5 ACSL5 5530 0.036 0.45 NO
20 CAMKK2 CAMKK2 CAMKK2 6461 0.025 0.4 NO
21 ACSL4 ACSL4 ACSL4 6466 0.025 0.41 NO
22 CAMKK1 CAMKK1 CAMKK1 6499 0.025 0.41 NO
23 MAPK9 MAPK9 MAPK9 6575 0.024 0.41 NO
24 PRKAB1 PRKAB1 PRKAB1 6682 0.023 0.41 NO
25 PPARA PPARA PPARA 6722 0.022 0.41 NO
26 IKBKB IKBKB IKBKB 6773 0.022 0.42 NO
27 NFKBIA NFKBIA NFKBIA 6911 0.021 0.41 NO
28 AGRP AGRP AGRP 6920 0.021 0.42 NO
29 MAPK10 MAPK10 MAPK10 7101 0.019 0.41 NO
30 NFKB1 NFKB1 NFKB1 7676 0.015 0.38 NO
31 MTOR MTOR MTOR 7724 0.014 0.38 NO
32 NFKBIB NFKBIB NFKBIB 7912 0.013 0.38 NO
33 ADIPOR2 ADIPOR2 ADIPOR2 8222 0.011 0.36 NO
34 STK11 STK11 STK11 8299 0.01 0.36 NO
35 TNFRSF1A TNFRSF1A TNFRSF1A 8321 0.01 0.36 NO
36 STAT3 STAT3 STAT3 8579 0.0082 0.35 NO
37 IKBKG IKBKG IKBKG 8952 0.0058 0.33 NO
38 RELA RELA RELA 8953 0.0058 0.33 NO
39 TRADD TRADD TRADD 9021 0.0052 0.33 NO
40 RXRB RXRB RXRB 9546 0.002 0.3 NO
41 AKT2 AKT2 AKT2 9782 0.0004 0.29 NO
42 MAPK8 MAPK8 MAPK8 10265 -0.0024 0.26 NO
43 AKT1 AKT1 AKT1 10277 -0.0025 0.26 NO
44 PRKAG1 PRKAG1 PRKAG1 10685 -0.0048 0.24 NO
45 AKT3 AKT3 AKT3 10937 -0.0063 0.23 NO
46 ADIPOR1 ADIPOR1 ADIPOR1 11048 -0.007 0.22 NO
47 TRAF2 TRAF2 TRAF2 11108 -0.0073 0.22 NO
48 PRKAB2 PRKAB2 PRKAB2 11585 -0.01 0.2 NO
49 PTPN11 PTPN11 PTPN11 11884 -0.012 0.19 NO
50 IRS1 IRS1 IRS1 12438 -0.016 0.16 NO
51 CHUK CHUK CHUK 12458 -0.016 0.16 NO
52 JAK2 JAK2 JAK2 12480 -0.017 0.16 NO
53 ACSL1 ACSL1 ACSL1 13070 -0.021 0.14 NO
54 ACSL3 ACSL3 ACSL3 13096 -0.022 0.14 NO
55 LEPR LEPR LEPR 13250 -0.023 0.14 NO
56 PRKAA1 PRKAA1 PRKAA1 13319 -0.023 0.14 NO
57 PRKAG2 PRKAG2 PRKAG2 14048 -0.03 0.1 NO
58 SLC2A4 SLC2A4 SLC2A4 14784 -0.039 0.074 NO
59 CPT1B CPT1B CPT1B 15082 -0.043 0.067 NO
60 PCK1 PCK1 PCK1 15156 -0.044 0.073 NO
61 SOCS3 SOCS3 SOCS3 15375 -0.049 0.071 NO
62 CPT1C CPT1C CPT1C 15446 -0.05 0.078 NO
63 TNF TNF TNF 15597 -0.053 0.082 NO
64 IRS2 IRS2 IRS2 16542 -0.08 0.048 NO
65 SLC2A1 SLC2A1 SLC2A1 17020 -0.1 0.044 NO
66 LEP LEP LEP 17807 -0.16 0.035 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 FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

Table 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 GLS2 GLS2 GLS2 279 0.45 0.14 YES
2 GAD2 GAD2 GAD2 448 0.36 0.25 YES
3 DDO DDO DDO 583 0.31 0.35 YES
4 ACY3 ACY3 ACY3 634 0.3 0.45 YES
5 GPT GPT GPT 827 0.26 0.53 YES
6 GPT2 GPT2 GPT2 1359 0.18 0.57 YES
7 ABAT ABAT ABAT 1715 0.15 0.6 YES
8 ASPA ASPA ASPA 2056 0.13 0.63 YES
9 ALDH4A1 ALDH4A1 ALDH4A1 5165 0.041 0.47 NO
10 IL4I1 IL4I1 IL4I1 5243 0.04 0.48 NO
11 GLUL GLUL GLUL 5879 0.031 0.46 NO
12 GOT1 GOT1 GOT1 5904 0.031 0.47 NO
13 ASL ASL ASL 6010 0.03 0.47 NO
14 GLUD2 GLUD2 GLUD2 7521 0.016 0.4 NO
15 ADSL ADSL ADSL 7594 0.015 0.4 NO
16 GOT2 GOT2 GOT2 8131 0.012 0.37 NO
17 ALDH5A1 ALDH5A1 ALDH5A1 8811 0.0067 0.34 NO
18 GLUD1 GLUD1 GLUD1 10012 -0.00097 0.28 NO
19 NIT2 NIT2 NIT2 10664 -0.0047 0.24 NO
20 CAD CAD CAD 10723 -0.005 0.24 NO
21 ASS1 ASS1 ASS1 12092 -0.014 0.17 NO
22 GFPT2 GFPT2 GFPT2 12689 -0.018 0.14 NO
23 GFPT1 GFPT1 GFPT1 13452 -0.024 0.11 NO
24 ASNS ASNS ASNS 14239 -0.032 0.08 NO
25 ADSSL1 ADSSL1 ADSSL1 14259 -0.033 0.09 NO
26 GLS GLS GLS 14314 -0.033 0.098 NO
27 PPAT PPAT PPAT 15676 -0.055 0.043 NO
28 GAD1 GAD1 GAD1 16567 -0.081 0.023 NO
29 CPS1 CPS1 CPS1 17212 -0.11 0.027 NO
30 AGXT AGXT AGXT 17316 -0.12 0.062 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

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

Table 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 G6PC G6PC G6PC 282 0.44 0.26 YES
2 G6PC2 G6PC2 G6PC2 394 0.38 0.48 YES
3 GCK GCK GCK 1206 0.2 0.56 YES
4 HK3 HK3 HK3 1767 0.15 0.62 YES
5 PGM1 PGM1 PGM1 3249 0.084 0.59 NO
6 GALK1 GALK1 GALK1 4036 0.062 0.58 NO
7 GLB1 GLB1 GLB1 5925 0.03 0.5 NO
8 AKR1B1 AKR1B1 AKR1B1 6373 0.026 0.49 NO
9 GANC GANC GANC 6390 0.026 0.5 NO
10 GLA GLA GLA 7277 0.018 0.47 NO
11 GALK2 GALK2 GALK2 7752 0.014 0.45 NO
12 GALT GALT GALT 7925 0.013 0.45 NO
13 GALE GALE GALE 9144 0.0045 0.38 NO
14 UGP2 UGP2 UGP2 9598 0.0016 0.36 NO
15 PFKL PFKL PFKL 10205 -0.0021 0.33 NO
16 HK1 HK1 HK1 11119 -0.0074 0.28 NO
17 B4GALT1 B4GALT1 B4GALT1 11163 -0.0076 0.29 NO
18 GAA GAA GAA 11264 -0.0082 0.29 NO
19 MGAM MGAM MGAM 11554 -0.01 0.28 NO
20 B4GALT2 B4GALT2 B4GALT2 11983 -0.013 0.26 NO
21 LCT LCT LCT 12119 -0.014 0.26 NO
22 PFKP PFKP PFKP 12968 -0.021 0.23 NO
23 PFKM PFKM PFKM 13510 -0.025 0.22 NO
24 PGM2 PGM2 PGM2 13631 -0.026 0.22 NO
25 HK2 HK2 HK2 15966 -0.062 0.14 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 GLYCINE SERINE AND THREONINE METABOLISM.

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

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 BIOPEPTIDES PATHWAY 41 genes.ES.table 0.51 1.7 0.01 0.67 0.56 0.24 0.2 0.2 0.31 0.22
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.42 1.5 0.048 0.5 0.78 0.059 0.02 0.058 0.32 0.15
BIOCARTA HDAC PATHWAY 27 genes.ES.table 0.57 1.5 0.036 0.71 0.77 0.48 0.29 0.34 0.45 0.26
BIOCARTA CHREBP2 PATHWAY 40 genes.ES.table 0.45 1.5 0.057 0.62 0.77 0.1 0.084 0.092 0.39 0.2
BIOCARTA GPCR PATHWAY 32 genes.ES.table 0.51 1.6 0.019 0.77 0.75 0.47 0.33 0.32 0.47 0.28
BIOCARTA CREB PATHWAY 25 genes.ES.table 0.48 1.4 0.11 0.69 0.93 0.44 0.33 0.3 0.54 0.23
BIOCARTA VEGF PATHWAY 28 genes.ES.table 0.49 1.5 0.054 0.45 0.83 0.32 0.29 0.23 0.3 0.12
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.41 1.4 0.15 0.68 0.94 0.034 0.0072 0.034 0.57 0.21
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.43 1.9 0.0096 0.33 0.14 0.046 0.013 0.046 0 0.1
KEGG TRYPTOPHAN METABOLISM 39 genes.ES.table 0.5 1.4 0.11 0.69 0.96 0.41 0.22 0.32 0.59 0.22
genes ES table in pathway: BIOCARTA BIOPEPTIDES 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 OGDHL OGDHL OGDHL 132 0.77 0.23 YES
2 PIPOX PIPOX PIPOX 235 0.67 0.43 YES
3 ACAT1 ACAT1 ACAT1 3459 0.16 0.31 NO
4 AADAT AADAT AADAT 3806 0.14 0.33 NO
5 AASDH AASDH AASDH 4558 0.11 0.32 NO
6 HADH HADH HADH 5334 0.084 0.31 NO
7 SETMAR SETMAR SETMAR 5544 0.078 0.32 NO
8 SETDB2 SETDB2 SETDB2 5647 0.075 0.34 NO
9 SUV39H1 SUV39H1 SUV39H1 5987 0.066 0.34 NO
10 AASS AASS AASS 6087 0.064 0.35 NO
11 AASDHPPT AASDHPPT AASDHPPT 6459 0.057 0.35 NO
12 GCDH GCDH GCDH 6868 0.049 0.34 NO
13 ALDH9A1 ALDH9A1 ALDH9A1 7120 0.044 0.34 NO
14 NSD1 NSD1 NSD1 8413 0.024 0.28 NO
15 SUV39H2 SUV39H2 SUV39H2 8420 0.024 0.29 NO
16 SETD7 SETD7 SETD7 8551 0.022 0.29 NO
17 SETD2 SETD2 SETD2 10204 0.00038 0.2 NO
18 SETD1B SETD1B SETD1B 10283 -0.00055 0.2 NO
19 ASH1L ASH1L ASH1L 10522 -0.0032 0.18 NO
20 OGDH OGDH OGDH 10576 -0.0038 0.18 NO
21 PLOD2 PLOD2 PLOD2 10606 -0.0041 0.18 NO
22 HADHA HADHA HADHA 10623 -0.0044 0.18 NO
23 EHMT2 EHMT2 EHMT2 11662 -0.017 0.13 NO
24 PLOD1 PLOD1 PLOD1 11686 -0.018 0.13 NO
25 DLST DLST DLST 11825 -0.02 0.13 NO
26 SETD1A SETD1A SETD1A 11967 -0.021 0.13 NO
27 SUV420H1 SUV420H1 SUV420H1 11978 -0.021 0.14 NO
28 SETD8 SETD8 SETD8 11989 -0.022 0.14 NO
29 WHSC1 WHSC1 WHSC1 12021 -0.022 0.15 NO
30 SUV420H2 SUV420H2 SUV420H2 12091 -0.023 0.15 NO
31 EHMT1 EHMT1 EHMT1 12114 -0.023 0.16 NO
32 ECHS1 ECHS1 ECHS1 12374 -0.027 0.15 NO
33 DOT1L DOT1L DOT1L 12407 -0.028 0.16 NO
34 TMLHE TMLHE TMLHE 12582 -0.031 0.16 NO
35 WHSC1L1 WHSC1L1 WHSC1L1 12644 -0.032 0.17 NO
36 SETDB1 SETDB1 SETDB1 12741 -0.033 0.17 NO
37 PLOD3 PLOD3 PLOD3 12750 -0.034 0.18 NO
38 ACAT2 ACAT2 ACAT2 12883 -0.036 0.18 NO
39 ALDH1B1 ALDH1B1 ALDH1B1 13781 -0.053 0.15 NO
40 ALDH7A1 ALDH7A1 ALDH7A1 14347 -0.067 0.14 NO
41 ALDH3A2 ALDH3A2 ALDH3A2 14461 -0.07 0.16 NO
42 ALDH2 ALDH2 ALDH2 15152 -0.092 0.15 NO
43 BBOX1 BBOX1 BBOX1 15348 -0.1 0.17 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 BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA CARM ER PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CACNA2D2 CACNA2D2 CACNA2D2 48 0.88 0.067 YES
2 ATP1A3 ATP1A3 ATP1A3 302 0.63 0.1 YES
3 CACNB2 CACNB2 CACNB2 335 0.6 0.15 YES
4 CACNG5 CACNG5 CACNG5 389 0.57 0.19 YES
5 ATP1B2 ATP1B2 ATP1B2 392 0.57 0.24 YES
6 ACTC1 ACTC1 ACTC1 558 0.5 0.27 YES
7 CACNG2 CACNG2 CACNG2 590 0.49 0.3 YES
8 CACNA2D3 CACNA2D3 CACNA2D3 765 0.44 0.33 YES
9 ATP1A2 ATP1A2 ATP1A2 770 0.44 0.36 YES
10 CACNB4 CACNB4 CACNB4 971 0.4 0.38 YES
11 COX4I2 COX4I2 COX4I2 1224 0.35 0.4 YES
12 CACNA1S CACNA1S CACNA1S 1252 0.35 0.42 YES
13 MYL3 MYL3 MYL3 1294 0.34 0.45 YES
14 CACNA2D1 CACNA2D1 CACNA2D1 1331 0.33 0.47 YES
15 SLC8A1 SLC8A1 SLC8A1 1514 0.31 0.49 YES
16 CACNG1 CACNG1 CACNG1 1577 0.3 0.51 YES
17 CACNA1D CACNA1D CACNA1D 1601 0.3 0.53 YES
18 RYR2 RYR2 RYR2 1760 0.28 0.54 YES
19 CACNG7 CACNG7 CACNG7 1886 0.27 0.56 YES
20 FXYD2 FXYD2 FXYD2 1984 0.26 0.57 YES
21 ATP1A4 ATP1A4 ATP1A4 2051 0.25 0.59 YES
22 MYH6 MYH6 MYH6 2295 0.24 0.59 YES
23 CACNG4 CACNG4 CACNG4 2667 0.21 0.59 NO
24 CACNA1C CACNA1C CACNA1C 3052 0.18 0.58 NO
25 COX7A1 COX7A1 COX7A1 3616 0.15 0.56 NO
26 COX6A2 COX6A2 COX6A2 4989 0.095 0.5 NO
27 MYL2 MYL2 MYL2 6254 0.061 0.43 NO
28 SLC9A6 SLC9A6 SLC9A6 6478 0.056 0.43 NO
29 UQCR11 UQCR11 UQCR11 8787 0.019 0.3 NO
30 UQCRB UQCRB UQCRB 8841 0.018 0.3 NO
31 COX7A2 COX7A2 COX7A2 9014 0.016 0.29 NO
32 UQCRFS1 UQCRFS1 UQCRFS1 9249 0.013 0.28 NO
33 ATP2A2 ATP2A2 ATP2A2 9568 0.0086 0.26 NO
34 COX7A2L COX7A2L COX7A2L 9720 0.0065 0.26 NO
35 TNNC1 TNNC1 TNNC1 10040 0.0021 0.24 NO
36 COX8A COX8A COX8A 10678 -0.0049 0.2 NO
37 UQCR10 UQCR10 UQCR10 11197 -0.011 0.18 NO
38 COX6C COX6C COX6C 11385 -0.014 0.17 NO
39 CACNB1 CACNB1 CACNB1 11643 -0.017 0.16 NO
40 MYH7 MYH7 MYH7 11785 -0.019 0.15 NO
41 COX7C COX7C COX7C 11916 -0.021 0.14 NO
42 COX6A1 COX6A1 COX6A1 12237 -0.025 0.13 NO
43 CYC1 CYC1 CYC1 12442 -0.028 0.12 NO
44 UQCRQ UQCRQ UQCRQ 12656 -0.032 0.11 NO
45 CACNG3 CACNG3 CACNG3 12809 -0.034 0.1 NO
46 COX4I1 COX4I1 COX4I1 12855 -0.035 0.11 NO
47 UQCRH UQCRH UQCRH 13041 -0.038 0.099 NO
48 CACNG6 CACNG6 CACNG6 13191 -0.041 0.094 NO
49 COX6B1 COX6B1 COX6B1 13369 -0.044 0.088 NO
50 ATP1B3 ATP1B3 ATP1B3 13465 -0.046 0.086 NO
51 TPM3 TPM3 TPM3 13509 -0.047 0.088 NO
52 COX7B COX7B COX7B 13668 -0.051 0.083 NO
53 UQCRHL UQCRHL UQCRHL 13803 -0.053 0.08 NO
54 TPM4 TPM4 TPM4 13900 -0.056 0.079 NO
55 UQCRC1 UQCRC1 UQCRC1 13901 -0.056 0.084 NO
56 TPM2 TPM2 TPM2 14471 -0.07 0.058 NO
57 TPM1 TPM1 TPM1 14522 -0.072 0.061 NO
58 COX5A COX5A COX5A 14713 -0.077 0.057 NO
59 ATP1A1 ATP1A1 ATP1A1 14819 -0.08 0.057 NO
60 COX5B COX5B COX5B 14931 -0.084 0.058 NO
61 CACNA2D4 CACNA2D4 CACNA2D4 15599 -0.11 0.03 NO
62 TNNI3 TNNI3 TNNI3 15785 -0.12 0.03 NO
63 CACNB3 CACNB3 CACNB3 15855 -0.12 0.036 NO
64 SLC9A1 SLC9A1 SLC9A1 16150 -0.14 0.031 NO
65 ATP1B1 ATP1B1 ATP1B1 16313 -0.15 0.033 NO
66 COX6B2 COX6B2 COX6B2 16462 -0.16 0.038 NO
67 CACNG8 CACNG8 CACNG8 16834 -0.19 0.032 NO
68 TNNT2 TNNT2 TNNT2 17726 -0.29 0.0066 NO
69 CACNA1F CACNA1F CACNA1F 18275 -0.42 0.0099 NO

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

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

genes ES table in pathway: BIOCARTA HDAC PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CAMK2B CAMK2B CAMK2B 98 0.81 0.15 YES
2 MAPT MAPT MAPT 251 0.66 0.27 YES
3 STAT4 STAT4 STAT4 503 0.52 0.36 YES
4 AGTR2 AGTR2 AGTR2 876 0.41 0.42 YES
5 PRKCB PRKCB PRKCB 1499 0.31 0.44 YES
6 AGT AGT AGT 2520 0.22 0.43 YES
7 CAMK2A CAMK2A CAMK2A 2601 0.21 0.47 YES
8 F2 F2 F2 2758 0.2 0.5 YES
9 GNAI1 GNAI1 GNAI1 3119 0.18 0.51 YES
10 FYN FYN FYN 3647 0.15 0.51 YES
11 STAT5B STAT5B STAT5B 4320 0.12 0.5 NO
12 PLCG1 PLCG1 PLCG1 5330 0.084 0.46 NO
13 CALM1 CALM1 CALM1 5358 0.083 0.48 NO
14 JAK2 JAK2 JAK2 5404 0.082 0.49 NO
15 CDK5 CDK5 CDK5 6831 0.05 0.42 NO
16 STAT5A STAT5A STAT5A 7690 0.035 0.38 NO
17 STAT3 STAT3 STAT3 7814 0.033 0.38 NO
18 GRB2 GRB2 GRB2 7916 0.031 0.38 NO
19 PTK2B PTK2B PTK2B 7917 0.031 0.39 NO
20 MAPK1 MAPK1 MAPK1 8597 0.021 0.36 NO
21 STAT2 STAT2 STAT2 8857 0.018 0.34 NO
22 GNB1 GNB1 GNB1 8908 0.017 0.35 NO
23 MYLK MYLK MYLK 9087 0.015 0.34 NO
24 GNA11 GNA11 GNA11 9192 0.013 0.34 NO
25 CAMK2D CAMK2D CAMK2D 9197 0.013 0.34 NO
26 SOS1 SOS1 SOS1 9245 0.013 0.34 NO
27 CAMK2G CAMK2G CAMK2G 9323 0.012 0.34 NO
28 MAP2K1 MAP2K1 MAP2K1 9487 0.0096 0.33 NO
29 MAPK8 MAPK8 MAPK8 9883 0.0042 0.31 NO
30 MAP2K2 MAP2K2 MAP2K2 10318 -0.001 0.29 NO
31 CALM2 CALM2 CALM2 11100 -0.01 0.24 NO
32 CALM3 CALM3 CALM3 11303 -0.013 0.24 NO
33 MAPK14 MAPK14 MAPK14 11921 -0.021 0.21 NO
34 RAF1 RAF1 RAF1 12764 -0.034 0.17 NO
35 SHC1 SHC1 SHC1 13147 -0.04 0.16 NO
36 STAT1 STAT1 STAT1 13280 -0.043 0.16 NO
37 PRKCA PRKCA PRKCA 14523 -0.072 0.1 NO
38 MAPK3 MAPK3 MAPK3 15254 -0.096 0.082 NO
39 GNGT1 GNGT1 GNGT1 15795 -0.12 0.075 NO
40 STAT6 STAT6 STAT6 15911 -0.13 0.093 NO
41 KNG1 KNG1 KNG1 17284 -0.23 0.064 NO

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

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

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GRIA2 GRIA2 GRIA2 14 0.94 0.12 YES
2 NEFM NEFM NEFM 368 0.58 0.18 YES
3 NEFH NEFH NEFH 422 0.56 0.25 YES
4 PRPH PRPH PRPH 542 0.51 0.31 YES
5 NEFL NEFL NEFL 709 0.45 0.36 YES
6 GRIA1 GRIA1 GRIA1 1059 0.38 0.38 YES
7 MAPK12 MAPK12 MAPK12 1231 0.35 0.42 YES
8 GRIN2C GRIN2C GRIN2C 1470 0.31 0.45 YES
9 MAPK11 MAPK11 MAPK11 1574 0.3 0.48 YES
10 GRIN2A GRIN2A GRIN2A 1735 0.28 0.51 YES
11 PRPH2 PRPH2 PRPH2 1847 0.27 0.54 YES
12 BCL2 BCL2 BCL2 2301 0.24 0.55 YES
13 NOS1 NOS1 NOS1 3212 0.17 0.52 NO
14 TNF TNF TNF 3842 0.14 0.5 NO
15 SLC1A2 SLC1A2 SLC1A2 3847 0.14 0.52 NO
16 PPP3CB PPP3CB PPP3CB 4307 0.12 0.51 NO
17 PPP3CC PPP3CC PPP3CC 4495 0.11 0.51 NO
18 MAP2K6 MAP2K6 MAP2K6 7289 0.041 0.37 NO
19 TOMM40L TOMM40L TOMM40L 7954 0.031 0.34 NO
20 TNFRSF1B TNFRSF1B TNFRSF1B 8535 0.022 0.31 NO
21 CYCS CYCS CYCS 9835 0.0047 0.24 NO
22 TOMM40 TOMM40 TOMM40 9958 0.0032 0.23 NO
23 TP53 TP53 TP53 10191 0.00052 0.22 NO
24 GRIN1 GRIN1 GRIN1 10593 -0.004 0.2 NO
25 DERL1 DERL1 DERL1 10666 -0.0048 0.19 NO
26 APAF1 APAF1 APAF1 11004 -0.009 0.18 NO
27 PPP3R1 PPP3R1 PPP3R1 11244 -0.012 0.16 NO
28 DAXX DAXX DAXX 11542 -0.016 0.15 NO
29 RAB5A RAB5A RAB5A 11879 -0.02 0.14 NO
30 MAPK14 MAPK14 MAPK14 11921 -0.021 0.14 NO
31 BAX BAX BAX 12502 -0.029 0.11 NO
32 CCS CCS CCS 12516 -0.03 0.11 NO
33 CASP9 CASP9 CASP9 12558 -0.03 0.11 NO
34 TNFRSF1A TNFRSF1A TNFRSF1A 12699 -0.032 0.11 NO
35 CASP3 CASP3 CASP3 13015 -0.038 0.098 NO
36 SOD1 SOD1 SOD1 13084 -0.039 0.099 NO
37 PPP3CA PPP3CA PPP3CA 13115 -0.04 0.1 NO
38 PPP3R2 PPP3R2 PPP3R2 13269 -0.042 0.1 NO
39 CAT CAT CAT 13464 -0.046 0.095 NO
40 BID BID BID 13830 -0.054 0.082 NO
41 BAD BAD BAD 14084 -0.06 0.076 NO
42 MAP2K3 MAP2K3 MAP2K3 14153 -0.062 0.081 NO
43 RAC1 RAC1 RAC1 14254 -0.065 0.084 NO
44 GPX1 GPX1 GPX1 14879 -0.082 0.06 NO
45 MAP3K5 MAP3K5 MAP3K5 15047 -0.088 0.063 NO
46 BCL2L1 BCL2L1 BCL2L1 15092 -0.09 0.072 NO
47 GRIN2B GRIN2B GRIN2B 15255 -0.096 0.076 NO
48 MAPK13 MAPK13 MAPK13 15328 -0.099 0.085 NO
49 CHP CHP CHP 15677 -0.11 0.08 NO
50 CASP1 CASP1 CASP1 15711 -0.12 0.093 NO
51 GRIN2D GRIN2D GRIN2D 16862 -0.19 0.055 NO
52 CHP2 CHP2 CHP2 17378 -0.24 0.059 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CHREBP2 PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GPCR PATHWAY

Table 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 ADCY1 ADCY1 ADCY1 138 0.77 0.22 YES
2 PRKAR2B PRKAR2B PRKAR2B 1487 0.31 0.24 YES
3 PRKCB PRKCB PRKCB 1499 0.31 0.33 YES
4 NFATC1 NFATC1 NFATC1 2952 0.19 0.31 YES
5 GNAI1 GNAI1 GNAI1 3119 0.18 0.35 YES
6 NFATC2 NFATC2 NFATC2 3264 0.17 0.39 YES
7 GNAS GNAS GNAS 3527 0.15 0.42 YES
8 PRKAR1B PRKAR1B PRKAR1B 4260 0.12 0.42 YES
9 PPP3CB PPP3CB PPP3CB 4307 0.12 0.45 YES
10 PPP3CC PPP3CC PPP3CC 4495 0.11 0.47 YES
11 PRKAR1A PRKAR1A PRKAR1A 4841 0.1 0.48 YES
12 PLCG1 PLCG1 PLCG1 5330 0.084 0.48 YES
13 CALM1 CALM1 CALM1 5358 0.083 0.51 YES
14 PRKACB PRKACB PRKACB 5740 0.072 0.51 YES
15 PRKAR2A PRKAR2A PRKAR2A 6008 0.066 0.51 YES
16 NFATC4 NFATC4 NFATC4 6358 0.059 0.51 NO
17 RPS6KA3 RPS6KA3 RPS6KA3 7853 0.032 0.44 NO
18 GNB1 GNB1 GNB1 8908 0.017 0.39 NO
19 MAP2K1 MAP2K1 MAP2K1 9487 0.0096 0.36 NO
20 ELK1 ELK1 ELK1 9806 0.0051 0.34 NO
21 CREB1 CREB1 CREB1 10206 0.00038 0.32 NO
22 JUN JUN JUN 10331 -0.0012 0.32 NO
23 GNAQ GNAQ GNAQ 10952 -0.0085 0.28 NO
24 CALM2 CALM2 CALM2 11100 -0.01 0.28 NO
25 CALM3 CALM3 CALM3 11303 -0.013 0.27 NO
26 FOS FOS FOS 11528 -0.016 0.26 NO
27 NFATC3 NFATC3 NFATC3 11663 -0.017 0.26 NO
28 RAF1 RAF1 RAF1 12764 -0.034 0.21 NO
29 PPP3CA PPP3CA PPP3CA 13115 -0.04 0.2 NO
30 PRKCA PRKCA PRKCA 14523 -0.072 0.15 NO
31 MAPK3 MAPK3 MAPK3 15254 -0.096 0.14 NO
32 GNGT1 GNGT1 GNGT1 15795 -0.12 0.14 NO

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

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

genes ES table in pathway: BIOCARTA CREB PATHWAY

Table 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 IGF1 IGF1 IGF1 1125 0.36 0.083 YES
2 CAMK1G CAMK1G CAMK1G 1395 0.32 0.2 YES
3 INS INS INS 1988 0.26 0.27 YES
4 NFATC1 NFATC1 NFATC1 2952 0.19 0.29 YES
5 NFATC2 NFATC2 NFATC2 3264 0.17 0.34 YES
6 CAMK1 CAMK1 CAMK1 4009 0.13 0.35 YES
7 PPP3CB PPP3CB PPP3CB 4307 0.12 0.38 YES
8 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 4318 0.12 0.43 YES
9 HDAC5 HDAC5 HDAC5 4476 0.11 0.46 YES
10 PIK3CG PIK3CG PIK3CG 4482 0.11 0.51 YES
11 PPP3CC PPP3CC PPP3CC 4495 0.11 0.55 YES
12 PIK3R1 PIK3R1 PIK3R1 5344 0.084 0.54 YES
13 CALM1 CALM1 CALM1 5358 0.083 0.57 YES
14 MEF2A MEF2A MEF2A 6397 0.058 0.54 NO
15 MAP2K6 MAP2K6 MAP2K6 7289 0.041 0.51 NO
16 IGF1R IGF1R IGF1R 7398 0.039 0.52 NO
17 CABIN1 CABIN1 CABIN1 8330 0.025 0.48 NO
18 MEF2D MEF2D MEF2D 8851 0.018 0.45 NO
19 MAPK7 MAPK7 MAPK7 9419 0.011 0.43 NO
20 PIK3CA PIK3CA PIK3CA 10406 -0.0019 0.38 NO
21 YWHAH YWHAH YWHAH 10660 -0.0048 0.36 NO
22 CALM2 CALM2 CALM2 11100 -0.01 0.34 NO
23 CALM3 CALM3 CALM3 11303 -0.013 0.34 NO
24 MAPK14 MAPK14 MAPK14 11921 -0.021 0.31 NO
25 AKT1 AKT1 AKT1 12362 -0.027 0.3 NO
26 PPP3CA PPP3CA PPP3CA 13115 -0.04 0.27 NO
27 INSR INSR INSR 13132 -0.04 0.29 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: BIOCARTA CREB PATHWAY.

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

genes ES table in pathway: BIOCARTA VEGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GCK GCK GCK 36 0.89 0.23 YES
2 PPP2R2B PPP2R2B PPP2R2B 406 0.56 0.36 YES
3 PRKAR2B PRKAR2B PRKAR2B 1487 0.31 0.38 YES
4 MLXIPL MLXIPL MLXIPL 1548 0.3 0.45 YES
5 PPP2R2C PPP2R2C PPP2R2C 3235 0.17 0.41 NO
6 PRKAR1B PRKAR1B PRKAR1B 4260 0.12 0.38 NO
7 PPP2R3B PPP2R3B PPP2R3B 4507 0.11 0.4 NO
8 PRKAR1A PRKAR1A PRKAR1A 4841 0.1 0.41 NO
9 PKLR PKLR PKLR 5228 0.087 0.41 NO
10 PRKACA PRKACA PRKACA 5274 0.086 0.43 NO
11 PRKACB PRKACB PRKACB 5740 0.072 0.42 NO
12 PRKAR2A PRKAR2A PRKAR2A 6008 0.066 0.42 NO
13 PRKAG2 PRKAG2 PRKAG2 6261 0.061 0.43 NO
14 YWHAQ YWHAQ YWHAQ 7028 0.046 0.4 NO
15 YWHAE YWHAE YWHAE 7166 0.044 0.4 NO
16 ACACA ACACA ACACA 7174 0.043 0.41 NO
17 PPP2R5B PPP2R5B PPP2R5B 7184 0.043 0.42 NO
18 PPP2R1B PPP2R1B PPP2R1B 7586 0.036 0.41 NO
19 PPP2R5C PPP2R5C PPP2R5C 8116 0.028 0.39 NO
20 FASN FASN FASN 8376 0.025 0.38 NO
21 PRKAG1 PRKAG1 PRKAG1 8806 0.018 0.36 NO
22 YWHAG YWHAG YWHAG 8914 0.017 0.36 NO
23 PPP2R5D PPP2R5D PPP2R5D 9996 0.0027 0.3 NO
24 PPP2R4 PPP2R4 PPP2R4 10110 0.0013 0.3 NO
25 PPP2R1A PPP2R1A PPP2R1A 10282 -0.00054 0.29 NO
26 PPP2CB PPP2CB PPP2CB 10341 -0.0013 0.28 NO
27 YWHAH YWHAH YWHAH 10660 -0.0048 0.27 NO
28 YWHAB YWHAB YWHAB 10735 -0.0057 0.27 NO
29 PPP2CA PPP2CA PPP2CA 10794 -0.0064 0.26 NO
30 PPP2R5E PPP2R5E PPP2R5E 10928 -0.0081 0.26 NO
31 PRKAB2 PRKAB2 PRKAB2 11381 -0.014 0.24 NO
32 PPP2R2D PPP2R2D PPP2R2D 11655 -0.017 0.23 NO
33 MLX MLX MLX 12320 -0.026 0.2 NO
34 PPP2R2A PPP2R2A PPP2R2A 13666 -0.051 0.14 NO
35 PRKAA1 PRKAA1 PRKAA1 14111 -0.061 0.13 NO
36 PPP2R3A PPP2R3A PPP2R3A 14268 -0.065 0.14 NO
37 PPP2R5A PPP2R5A PPP2R5A 14274 -0.065 0.16 NO
38 PRKAB1 PRKAB1 PRKAB1 14753 -0.078 0.15 NO
39 YWHAZ YWHAZ YWHAZ 14884 -0.083 0.16 NO
40 PRKAA2 PRKAA2 PRKAA2 15661 -0.11 0.15 NO

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

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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 CACNA1A CACNA1A CACNA1A 31 0.9 0.085 YES
2 GCK GCK GCK 36 0.89 0.17 YES
3 CACNA1B CACNA1B CACNA1B 67 0.85 0.25 YES
4 ABCC8 ABCC8 ABCC8 106 0.8 0.33 YES
5 KCNJ11 KCNJ11 KCNJ11 255 0.66 0.38 YES
6 MAPK10 MAPK10 MAPK10 365 0.58 0.43 YES
7 CACNA1G CACNA1G CACNA1G 476 0.53 0.48 YES
8 ADIPOQ ADIPOQ ADIPOQ 547 0.5 0.52 YES
9 MAFA MAFA MAFA 670 0.47 0.56 YES
10 SOCS2 SOCS2 SOCS2 1319 0.34 0.56 YES
11 CACNA1D CACNA1D CACNA1D 1601 0.3 0.57 YES
12 INS INS INS 1988 0.26 0.58 YES
13 CACNA1E CACNA1E CACNA1E 2291 0.24 0.58 YES
14 SLC2A4 SLC2A4 SLC2A4 2368 0.23 0.6 YES
15 PIK3R3 PIK3R3 PIK3R3 2723 0.2 0.6 YES
16 PRKCE PRKCE PRKCE 2736 0.2 0.62 YES
17 CACNA1C CACNA1C CACNA1C 3052 0.18 0.62 YES
18 PIK3R5 PIK3R5 PIK3R5 3758 0.14 0.6 NO
19 TNF TNF TNF 3842 0.14 0.6 NO
20 PIK3CD PIK3CD PIK3CD 4139 0.13 0.6 NO
21 PIK3CG PIK3CG PIK3CG 4482 0.11 0.59 NO
22 SOCS1 SOCS1 SOCS1 4548 0.11 0.6 NO
23 PKLR PKLR PKLR 5228 0.087 0.57 NO
24 PIK3R1 PIK3R1 PIK3R1 5344 0.084 0.57 NO
25 IRS2 IRS2 IRS2 5955 0.067 0.55 NO
26 SOCS3 SOCS3 SOCS3 7023 0.046 0.49 NO
27 SOCS4 SOCS4 SOCS4 7075 0.045 0.49 NO
28 PIK3R2 PIK3R2 PIK3R2 7342 0.04 0.48 NO
29 MAPK9 MAPK9 MAPK9 7768 0.033 0.46 NO
30 SLC2A2 SLC2A2 SLC2A2 8575 0.022 0.42 NO
31 MAPK1 MAPK1 MAPK1 8597 0.021 0.42 NO
32 MAPK8 MAPK8 MAPK8 9883 0.0042 0.35 NO
33 PIK3CA PIK3CA PIK3CA 10406 -0.0019 0.32 NO
34 MTOR MTOR MTOR 10669 -0.0048 0.31 NO
35 HK3 HK3 HK3 12412 -0.028 0.22 NO
36 INSR INSR INSR 13132 -0.04 0.18 NO
37 PKM2 PKM2 PKM2 13361 -0.044 0.18 NO
38 PDX1 PDX1 PDX1 13409 -0.045 0.18 NO
39 IRS4 IRS4 IRS4 14747 -0.078 0.11 NO
40 IKBKB IKBKB IKBKB 14776 -0.079 0.12 NO
41 MAPK3 MAPK3 MAPK3 15254 -0.096 0.1 NO
42 HK1 HK1 HK1 15258 -0.096 0.11 NO
43 PRKCD PRKCD PRKCD 15436 -0.1 0.11 NO
44 PIK3CB PIK3CB PIK3CB 15490 -0.1 0.12 NO
45 IRS1 IRS1 IRS1 16158 -0.14 0.096 NO
46 HK2 HK2 HK2 17769 -0.29 0.037 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 CITRATE CYCLE TCA CYCLE.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG LYSINE DEGRADATION

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 NR0B1 NR0B1 NR0B1 152 0.75 0.24 YES
2 ESR1 ESR1 ESR1 364 0.58 0.42 YES
3 HDAC9 HDAC9 HDAC9 3290 0.17 0.32 NO
4 HDAC5 HDAC5 HDAC5 4476 0.11 0.29 NO
5 HDAC4 HDAC4 HDAC4 4663 0.11 0.31 NO
6 GRIP1 GRIP1 GRIP1 5421 0.081 0.3 NO
7 PELP1 PELP1 PELP1 6366 0.059 0.27 NO
8 TBP TBP TBP 7415 0.039 0.22 NO
9 HDAC6 HDAC6 HDAC6 7567 0.037 0.23 NO
10 BRCA1 BRCA1 BRCA1 8293 0.026 0.2 NO
11 HDAC2 HDAC2 HDAC2 8305 0.025 0.2 NO
12 GTF2F1 GTF2F1 GTF2F1 8627 0.021 0.19 NO
13 MED1 MED1 MED1 8663 0.02 0.2 NO
14 HDAC3 HDAC3 HDAC3 8688 0.02 0.2 NO
15 ERCC3 ERCC3 ERCC3 9023 0.016 0.19 NO
16 HDAC8 HDAC8 HDAC8 9125 0.014 0.19 NO
17 POLR2A POLR2A POLR2A 9305 0.012 0.18 NO
18 NCOR2 NCOR2 NCOR2 9652 0.0074 0.17 NO
19 GTF2E1 GTF2E1 GTF2E1 10240 -0.000049 0.14 NO
20 EP300 EP300 EP300 10448 -0.0023 0.12 NO
21 SRA1 SRA1 SRA1 10639 -0.0045 0.12 NO
22 NRIP1 NRIP1 NRIP1 10705 -0.0054 0.11 NO
23 SPEN SPEN SPEN 10862 -0.0073 0.11 NO
24 PHB2 PHB2 PHB2 11156 -0.011 0.096 NO
25 CARM1 CARM1 CARM1 11543 -0.016 0.08 NO
26 HDAC10 HDAC10 HDAC10 12359 -0.027 0.044 NO
27 GTF2A1 GTF2A1 GTF2A1 12381 -0.027 0.052 NO
28 CREBBP CREBBP CREBBP 12447 -0.028 0.058 NO
29 HDAC7 HDAC7 HDAC7 13921 -0.056 -0.0033 NO
30 HDAC11 HDAC11 HDAC11 14469 -0.07 -0.01 NO
31 HDAC1 HDAC1 HDAC1 15288 -0.097 -0.022 NO
32 CCND1 CCND1 CCND1 15812 -0.12 -0.011 NO
33 PPARGC1A PPARGC1A PPARGC1A 16081 -0.14 0.018 NO
34 HIST2H3C HIST2H3C HIST2H3C 17993 -0.34 0.025 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 LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG TRYPTOPHAN 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 GRIA2 GRIA2 GRIA2 14 0.94 0.1 YES
2 PPP1R1A PPP1R1A PPP1R1A 97 0.81 0.19 YES
3 CAMK2B CAMK2B CAMK2B 98 0.81 0.28 YES
4 GRM1 GRM1 GRM1 401 0.57 0.32 YES
5 GRIA1 GRIA1 GRIA1 1059 0.38 0.33 YES
6 GRIN2C GRIN2C GRIN2C 1470 0.31 0.34 YES
7 PRKCB PRKCB PRKCB 1499 0.31 0.38 YES
8 RPS6KA6 RPS6KA6 RPS6KA6 1683 0.29 0.4 YES
9 GRIN2A GRIN2A GRIN2A 1735 0.28 0.43 YES
10 ITPR1 ITPR1 ITPR1 2202 0.24 0.43 YES
11 CAMK2A CAMK2A CAMK2A 2601 0.21 0.43 YES
12 ADCY8 ADCY8 ADCY8 2766 0.2 0.44 YES
13 PLCB4 PLCB4 PLCB4 2885 0.19 0.46 YES
14 CACNA1C CACNA1C CACNA1C 3052 0.18 0.47 YES
15 PLCB1 PLCB1 PLCB1 4194 0.12 0.42 NO
16 PRKCG PRKCG PRKCG 4249 0.12 0.43 NO
17 PPP3CB PPP3CB PPP3CB 4307 0.12 0.44 NO
18 PPP3CC PPP3CC PPP3CC 4495 0.11 0.44 NO
19 PRKACA PRKACA PRKACA 5274 0.086 0.41 NO
20 CALM1 CALM1 CALM1 5358 0.083 0.41 NO
21 PRKACB PRKACB PRKACB 5740 0.072 0.4 NO
22 CAMK4 CAMK4 CAMK4 6416 0.058 0.37 NO
23 HRAS HRAS HRAS 7087 0.045 0.34 NO
24 PPP1R12A PPP1R12A PPP1R12A 7483 0.038 0.32 NO
25 RPS6KA3 RPS6KA3 RPS6KA3 7853 0.032 0.31 NO
26 MAPK1 MAPK1 MAPK1 8597 0.021 0.27 NO
27 PPP1CC PPP1CC PPP1CC 8747 0.019 0.26 NO
28 RPS6KA2 RPS6KA2 RPS6KA2 8885 0.017 0.26 NO
29 CAMK2D CAMK2D CAMK2D 9197 0.013 0.24 NO
30 CAMK2G CAMK2G CAMK2G 9323 0.012 0.24 NO
31 MAP2K1 MAP2K1 MAP2K1 9487 0.0096 0.23 NO
32 ITPR2 ITPR2 ITPR2 9502 0.0094 0.23 NO
33 GRM5 GRM5 GRM5 9933 0.0036 0.2 NO
34 PPP1CB PPP1CB PPP1CB 10145 0.001 0.19 NO
35 MAP2K2 MAP2K2 MAP2K2 10318 -0.001 0.18 NO
36 RAP1B RAP1B RAP1B 10326 -0.0011 0.18 NO
37 RAP1A RAP1A RAP1A 10359 -0.0015 0.18 NO
38 EP300 EP300 EP300 10448 -0.0023 0.18 NO
39 GRIN1 GRIN1 GRIN1 10593 -0.004 0.17 NO
40 PLCB2 PLCB2 PLCB2 10756 -0.0059 0.16 NO
41 GNAQ GNAQ GNAQ 10952 -0.0085 0.15 NO
42 ATF4 ATF4 ATF4 10974 -0.0087 0.15 NO
43 CALM2 CALM2 CALM2 11100 -0.01 0.15 NO
44 PPP3R1 PPP3R1 PPP3R1 11244 -0.012 0.14 NO
45 CALM3 CALM3 CALM3 11303 -0.013 0.14 NO
46 ARAF ARAF ARAF 12014 -0.022 0.1 NO
47 CREBBP CREBBP CREBBP 12447 -0.028 0.082 NO
48 RAF1 RAF1 RAF1 12764 -0.034 0.069 NO
49 PPP3CA PPP3CA PPP3CA 13115 -0.04 0.054 NO
50 PPP3R2 PPP3R2 PPP3R2 13269 -0.042 0.051 NO
51 NRAS NRAS NRAS 13316 -0.043 0.053 NO
52 BRAF BRAF BRAF 14025 -0.059 0.021 NO
53 CALML5 CALML5 CALML5 14102 -0.061 0.024 NO
54 RAPGEF3 RAPGEF3 RAPGEF3 14179 -0.063 0.026 NO
55 PRKX PRKX PRKX 14432 -0.069 0.02 NO
56 PRKCA PRKCA PRKCA 14523 -0.072 0.023 NO
57 KRAS KRAS KRAS 14589 -0.073 0.028 NO
58 PPP1CA PPP1CA PPP1CA 15004 -0.087 0.015 NO
59 MAPK3 MAPK3 MAPK3 15254 -0.096 0.012 NO
60 GRIN2B GRIN2B GRIN2B 15255 -0.096 0.023 NO
61 CALML3 CALML3 CALML3 15584 -0.11 0.017 NO
62 CHP CHP CHP 15677 -0.11 0.024 NO
63 RPS6KA1 RPS6KA1 RPS6KA1 15937 -0.13 0.024 NO
64 CALML6 CALML6 CALML6 16290 -0.15 0.021 NO
65 GRIN2D GRIN2D GRIN2D 16862 -0.19 0.011 NO
66 ITPR3 ITPR3 ITPR3 17178 -0.22 0.018 NO
67 PLCB3 PLCB3 PLCB3 17201 -0.22 0.042 NO
68 CHP2 CHP2 CHP2 17378 -0.24 0.059 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 TRYPTOPHAN METABOLISM.

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

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 = PAAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = PAAD-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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