GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LIHC-TP
Liver Hepatocellular Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LIHC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1348JFV
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 LIHC-TP. This pipeline has the following features:

  1. For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.

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

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

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

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

  6. Checks if the top core genes are significantly differently expressed genes.

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 192
Number of samples: 371
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 62
pheno.type: 2 - 5 :[ clus2 ] 99
pheno.type: 3 - 5 :[ clus3 ] 71
pheno.type: 4 - 5 :[ clus4 ] 69
pheno.type: 5 - 5 :[ clus5 ] 70

For the expression subtypes of 17745 genes in 372 samples, GSEA found enriched gene sets in each cluster using 371 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA TOLL PATHWAY, KEGG RNA DEGRADATION, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG BASE EXCISION REPAIR, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION

    • And common core enriched genes are MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, PCNA, POLD1, RPA4, ACIN1

  • clus2

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION

    • And common core enriched genes are ACAT1, ACAT2, ALDH2, ALDH7A1, ALDH9A1, LDHAL6B, PIPOX, ACACB, ACSS2, EHHADH

  • clus3

    • Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA WNT PATHWAY, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG SPHINGOLIPID METABOLISM, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG RIBOSOME, KEGG DNA REPLICATION

    • And common core enriched genes are ACTA1, CCNB1, CDC25C, CDK1, MYT1, SRC, RPL10A, RPL12, RPL13A, RPL14

  • clus4

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY

    • And common core enriched genes are PRKX, FZD1, FZD2, FZD7, FZD8, LEF1, WNT1, WNT10A, WNT11, WNT2

  • clus5

    • Top enriched gene sets are BIOCARTA WNT PATHWAY, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION, KEGG TYROSINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG PROPANOATE METABOLISM, KEGG BUTANOATE METABOLISM

    • And common core enriched genes are ACAA1, ACSL5, ACSL6, ADH1A, ADH1B, ADH1C, ADH4, ADH5, ADH6, ADH7

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA G1 PATHWAY 27 genes.ES.table 0.55 1.6 0.028 0.53 0.79 0.41 0.24 0.31 0.31 0.16
BIOCARTA FMLP PATHWAY 35 genes.ES.table 0.5 1.6 0.029 0.42 0.63 0.2 0.16 0.17 0.21 0.11
BIOCARTA MPR PATHWAY 32 genes.ES.table 0.53 1.7 0.012 0.41 0.57 0.31 0.18 0.26 0.18 0.11
BIOCARTA TOLL PATHWAY 36 genes.ES.table 0.48 1.5 0.068 0.5 0.88 0.19 0.11 0.17 0.31 0.14
KEGG RNA DEGRADATION 55 genes.ES.table 0.34 1.6 0.054 0.4 0.69 0.74 0.51 0.37 0.22 0.096
KEGG DNA REPLICATION 35 genes.ES.table 0.63 1.7 0.067 0.42 0.52 0.74 0.3 0.52 0.17 0.12
KEGG SPLICEOSOME 125 genes.ES.table 0.47 1.9 0.016 0.44 0.15 0.74 0.46 0.4 0 0.13
KEGG BASE EXCISION REPAIR 32 genes.ES.table 0.42 1.5 0.12 0.57 0.92 0.56 0.39 0.34 0.39 0.17
KEGG NUCLEOTIDE EXCISION REPAIR 43 genes.ES.table 0.39 1.5 0.11 0.54 0.84 0.51 0.41 0.3 0.33 0.16
KEGG HOMOLOGOUS RECOMBINATION 27 genes.ES.table 0.67 1.7 0.024 0.5 0.51 0.41 0.14 0.35 0.21 0.15
genes ES table in pathway: BIOCARTA G1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HSPA6 HSPA6 HSPA6 1121 0.3 -0.027 YES
2 PPIH PPIH PPIH 1829 0.24 -0.038 YES
3 SNRPD1 SNRPD1 SNRPD1 2795 0.18 -0.071 YES
4 THOC4 THOC4 THOC4 2991 0.17 -0.062 YES
5 SNRPA1 SNRPA1 SNRPA1 3139 0.16 -0.05 YES
6 HSPA1B HSPA1B HSPA1B 3291 0.16 -0.04 YES
7 SNRNP40 SNRNP40 SNRNP40 3482 0.15 -0.032 YES
8 SNRPA SNRPA SNRPA 3674 0.14 -0.026 YES
9 SNRPB SNRPB SNRPB 3683 0.14 -0.009 YES
10 SNRPD2 SNRPD2 SNRPD2 3857 0.14 -0.0024 YES
11 NAA38 NAA38 NAA38 3975 0.13 0.0069 YES
12 PRPF38A PRPF38A PRPF38A 4006 0.13 0.021 YES
13 SF3A3 SF3A3 SF3A3 4146 0.13 0.028 YES
14 SNRPF SNRPF SNRPF 4170 0.13 0.042 YES
15 EFTUD2 EFTUD2 EFTUD2 4277 0.12 0.051 YES
16 SF3B4 SF3B4 SF3B4 4292 0.12 0.065 YES
17 LSM2 LSM2 LSM2 4491 0.12 0.068 YES
18 PPIL1 PPIL1 PPIL1 4533 0.12 0.079 YES
19 SF3A2 SF3A2 SF3A2 4622 0.11 0.087 YES
20 TXNL4A TXNL4A TXNL4A 4762 0.11 0.092 YES
21 BUD31 BUD31 BUD31 4967 0.1 0.093 YES
22 PRPF4 PRPF4 PRPF4 5093 0.099 0.098 YES
23 SNRPC SNRPC SNRPC 5098 0.099 0.11 YES
24 PRPF3 PRPF3 PRPF3 5166 0.097 0.12 YES
25 PPIE PPIE PPIE 5167 0.097 0.13 YES
26 THOC1 THOC1 THOC1 5223 0.096 0.14 YES
27 EIF4A3 EIF4A3 EIF4A3 5335 0.093 0.14 YES
28 TCERG1 TCERG1 TCERG1 5379 0.092 0.15 YES
29 MAGOH MAGOH MAGOH 5493 0.089 0.16 YES
30 U2AF2 U2AF2 U2AF2 5536 0.088 0.16 YES
31 PRPF31 PRPF31 PRPF31 5562 0.088 0.17 YES
32 SNRPB2 SNRPB2 SNRPB2 5638 0.086 0.18 YES
33 SFRS9 SFRS9 SFRS9 5698 0.084 0.18 YES
34 SNRPG SNRPG SNRPG 5787 0.082 0.19 YES
35 RBM17 RBM17 RBM17 5808 0.082 0.2 YES
36 LSM7 LSM7 LSM7 5882 0.08 0.2 YES
37 HNRNPA3 HNRNPA3 HNRNPA3 5924 0.079 0.21 YES
38 SF3B5 SF3B5 SF3B5 5951 0.079 0.22 YES
39 SF3B3 SF3B3 SF3B3 6012 0.078 0.23 YES
40 RBMX RBMX RBMX 6033 0.077 0.23 YES
41 SNRPE SNRPE SNRPE 6077 0.076 0.24 YES
42 HSPA2 HSPA2 HSPA2 6134 0.075 0.25 YES
43 PRPF38B PRPF38B PRPF38B 6164 0.074 0.25 YES
44 THOC2 THOC2 THOC2 6167 0.074 0.26 YES
45 PRPF40B PRPF40B PRPF40B 6250 0.073 0.27 YES
46 LSM5 LSM5 LSM5 6274 0.072 0.27 YES
47 DDX23 DDX23 DDX23 6277 0.072 0.28 YES
48 SFRS13A SFRS13A SFRS13A 6334 0.071 0.29 YES
49 LSM4 LSM4 LSM4 6445 0.069 0.29 YES
50 SR140 SR140 SR140 6461 0.068 0.3 YES
51 U2AF1 U2AF1 U2AF1 6542 0.067 0.3 YES
52 ISY1 ISY1 ISY1 6551 0.067 0.31 YES
53 SART1 SART1 SART1 6560 0.067 0.32 YES
54 HNRNPM HNRNPM HNRNPM 6697 0.064 0.32 YES
55 PRPF19 PRPF19 PRPF19 6755 0.063 0.32 YES
56 BCAS2 BCAS2 BCAS2 6764 0.063 0.33 YES
57 SFRS3 SFRS3 SFRS3 6776 0.063 0.33 YES
58 RBM22 RBM22 RBM22 6786 0.063 0.34 YES
59 HNRNPA1 HNRNPA1 HNRNPA1 6787 0.063 0.35 YES
60 TRA2B TRA2B TRA2B 6908 0.06 0.35 YES
61 RBM8A RBM8A RBM8A 6925 0.06 0.36 YES
62 NCBP1 NCBP1 NCBP1 7004 0.058 0.36 YES
63 PUF60 PUF60 PUF60 7008 0.058 0.36 YES
64 CCDC12 CCDC12 CCDC12 7035 0.058 0.37 YES
65 THOC3 THOC3 THOC3 7045 0.058 0.38 YES
66 HNRNPU HNRNPU HNRNPU 7094 0.057 0.38 YES
67 PQBP1 PQBP1 PQBP1 7101 0.057 0.39 YES
68 SFRS7 SFRS7 SFRS7 7113 0.057 0.39 YES
69 DHX8 DHX8 DHX8 7148 0.056 0.4 YES
70 DHX15 DHX15 DHX15 7251 0.054 0.4 YES
71 SNRNP70 SNRNP70 SNRNP70 7285 0.054 0.4 YES
72 SF3B2 SF3B2 SF3B2 7292 0.054 0.41 YES
73 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 7468 0.051 0.41 YES
74 CRNKL1 CRNKL1 CRNKL1 7481 0.051 0.41 YES
75 BAT1 BAT1 BAT1 7564 0.05 0.41 YES
76 SFRS2 SFRS2 SFRS2 7647 0.048 0.41 YES
77 PHF5A PHF5A PHF5A 7682 0.048 0.42 YES
78 DHX38 DHX38 DHX38 7709 0.047 0.42 YES
79 PRPF6 PRPF6 PRPF6 7748 0.047 0.42 YES
80 PRPF40A PRPF40A PRPF40A 7765 0.046 0.43 YES
81 TRA2A TRA2A TRA2A 7807 0.046 0.43 YES
82 SFRS1 SFRS1 SFRS1 7830 0.045 0.44 YES
83 SNRNP200 SNRNP200 SNRNP200 7907 0.044 0.44 YES
84 PLRG1 PLRG1 PLRG1 7925 0.044 0.44 YES
85 SYF2 SYF2 SYF2 7948 0.043 0.45 YES
86 ACIN1 ACIN1 ACIN1 7973 0.043 0.45 YES
87 USP39 USP39 USP39 7977 0.043 0.46 YES
88 LSM6 LSM6 LSM6 7983 0.042 0.46 YES
89 HSPA1A HSPA1A HSPA1A 8075 0.041 0.46 YES
90 SFRS4 SFRS4 SFRS4 8170 0.039 0.46 YES
91 HNRNPC HNRNPC HNRNPC 8181 0.039 0.46 YES
92 HSPA8 HSPA8 HSPA8 8186 0.039 0.47 YES
93 SMNDC1 SMNDC1 SMNDC1 8207 0.039 0.47 YES
94 NHP2L1 NHP2L1 NHP2L1 8372 0.036 0.47 NO
95 MAGOHB MAGOHB MAGOHB 8510 0.034 0.46 NO
96 LSM3 LSM3 LSM3 8781 0.03 0.45 NO
97 SF3B14 SF3B14 SF3B14 8972 0.027 0.44 NO
98 SNRNP27 SNRNP27 SNRNP27 9139 0.024 0.44 NO
99 PRPF18 PRPF18 PRPF18 9283 0.022 0.43 NO
100 CDC40 CDC40 CDC40 9307 0.022 0.43 NO
101 HNRNPK HNRNPK HNRNPK 9311 0.022 0.44 NO
102 RBM25 RBM25 RBM25 9339 0.021 0.44 NO
103 SF3A1 SF3A1 SF3A1 9362 0.021 0.44 NO
104 DHX16 DHX16 DHX16 9553 0.018 0.43 NO
105 SF3B1 SF3B1 SF3B1 9564 0.018 0.43 NO
106 SNRPD3 SNRPD3 SNRPD3 9717 0.016 0.42 NO
107 SLU7 SLU7 SLU7 9741 0.015 0.42 NO
108 DDX46 DDX46 DDX46 9823 0.014 0.42 NO
109 DDX5 DDX5 DDX5 10079 0.01 0.41 NO
110 XAB2 XAB2 XAB2 10112 0.0096 0.41 NO
111 DDX42 DDX42 DDX42 10354 0.006 0.39 NO
112 SFRS6 SFRS6 SFRS6 10410 0.0052 0.39 NO
113 SNW1 SNW1 SNW1 10530 0.0035 0.38 NO
114 PRPF8 PRPF8 PRPF8 10681 0.0011 0.38 NO
115 CWC15 CWC15 CWC15 10695 0.00074 0.38 NO
116 AQR AQR AQR 10841 -0.0018 0.37 NO
117 WBP11 WBP11 WBP11 11073 -0.0052 0.36 NO
118 ZMAT2 ZMAT2 ZMAT2 11132 -0.0063 0.35 NO
119 PCBP1 PCBP1 PCBP1 11283 -0.0088 0.35 NO
120 CDC5L CDC5L CDC5L 11351 -0.01 0.34 NO
121 SFRS2B SFRS2B SFRS2B 11468 -0.012 0.34 NO
122 CHERP CHERP CHERP 11887 -0.02 0.32 NO
123 CTNNBL1 CTNNBL1 CTNNBL1 12228 -0.027 0.3 NO
124 HSPA1L HSPA1L HSPA1L 13019 -0.044 0.26 NO
125 SFRS5 SFRS5 SFRS5 13484 -0.054 0.24 NO

Figure S1.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

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

genes ES table in pathway: BIOCARTA FMLP 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 CARD18 CARD18 CARD18 150 0.51 0.048 YES
2 CASP5 CASP5 CASP5 267 0.46 0.092 YES
3 MAPK13 MAPK13 MAPK13 296 0.45 0.14 YES
4 IL1B IL1B IL1B 484 0.4 0.17 YES
5 CXCL1 CXCL1 CXCL1 493 0.4 0.22 YES
6 IL18 IL18 IL18 507 0.4 0.26 YES
7 CCL13 CCL13 CCL13 670 0.36 0.29 YES
8 PYCARD PYCARD PYCARD 866 0.33 0.32 YES
9 PSTPIP1 PSTPIP1 PSTPIP1 919 0.33 0.35 YES
10 CARD9 CARD9 CARD9 960 0.32 0.38 YES
11 IL8 IL8 IL8 961 0.32 0.42 YES
12 BIRC3 BIRC3 BIRC3 1069 0.31 0.45 YES
13 NLRC4 NLRC4 NLRC4 1118 0.3 0.48 YES
14 NOD2 NOD2 NOD2 1277 0.29 0.5 YES
15 TNF TNF TNF 1415 0.28 0.52 YES
16 CASP1 CASP1 CASP1 1440 0.27 0.55 YES
17 CARD6 CARD6 CARD6 1662 0.26 0.57 YES
18 CCL5 CCL5 CCL5 1712 0.25 0.59 YES
19 CCL8 CCL8 CCL8 1912 0.24 0.61 YES
20 RIPK2 RIPK2 RIPK2 1924 0.24 0.63 YES
21 NLRP3 NLRP3 NLRP3 2111 0.22 0.65 YES
22 MEFV MEFV MEFV 2200 0.22 0.66 YES
23 NAIP NAIP NAIP 3493 0.15 0.61 NO
24 NLRP1 NLRP1 NLRP1 4241 0.12 0.58 NO
25 CASP8 CASP8 CASP8 4782 0.11 0.56 NO
26 MAPK3 MAPK3 MAPK3 5160 0.097 0.55 NO
27 MAP3K7 MAP3K7 MAP3K7 5288 0.094 0.55 NO
28 MAPK12 MAPK12 MAPK12 5299 0.094 0.56 NO
29 NOD1 NOD1 NOD1 5551 0.088 0.56 NO
30 IKBKG IKBKG IKBKG 5602 0.086 0.57 NO
31 IL6 IL6 IL6 6099 0.076 0.55 NO
32 NFKBIB NFKBIB NFKBIB 6333 0.071 0.54 NO
33 HSP90AA1 HSP90AA1 HSP90AA1 7828 0.045 0.46 NO
34 HSP90B1 HSP90B1 HSP90B1 7979 0.042 0.46 NO
35 TNFAIP3 TNFAIP3 TNFAIP3 8261 0.038 0.44 NO
36 SUGT1 SUGT1 SUGT1 8658 0.032 0.43 NO
37 IKBKB IKBKB IKBKB 9388 0.02 0.39 NO
38 RELA RELA RELA 9629 0.017 0.38 NO
39 CCL2 CCL2 CCL2 10060 0.01 0.35 NO
40 CXCL2 CXCL2 CXCL2 10125 0.0093 0.35 NO
41 NFKB1 NFKB1 NFKB1 10302 0.0068 0.34 NO
42 XIAP XIAP XIAP 10333 0.0065 0.34 NO
43 MAPK14 MAPK14 MAPK14 11276 -0.0086 0.29 NO
44 MAPK9 MAPK9 MAPK9 11388 -0.011 0.28 NO
45 BIRC2 BIRC2 BIRC2 11472 -0.012 0.28 NO
46 MAPK1 MAPK1 MAPK1 11544 -0.014 0.28 NO
47 ERBB2IP ERBB2IP ERBB2IP 11785 -0.018 0.26 NO
48 CARD8 CARD8 CARD8 11806 -0.019 0.27 NO
49 TAB2 TAB2 TAB2 12081 -0.024 0.25 NO
50 TAB3 TAB3 TAB3 12197 -0.027 0.25 NO
51 TRIP6 TRIP6 TRIP6 12531 -0.033 0.23 NO
52 TAB1 TAB1 TAB1 12765 -0.038 0.22 NO
53 CHUK CHUK CHUK 13711 -0.061 0.18 NO
54 CCL11 CCL11 CCL11 13758 -0.062 0.18 NO
55 MAPK11 MAPK11 MAPK11 13806 -0.064 0.19 NO
56 TRAF6 TRAF6 TRAF6 13929 -0.068 0.19 NO
57 NFKBIA NFKBIA NFKBIA 13964 -0.069 0.19 NO
58 MAPK10 MAPK10 MAPK10 14152 -0.075 0.19 NO
59 MAPK8 MAPK8 MAPK8 14946 -0.1 0.16 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 FMLP PATHWAY.

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

genes ES table in pathway: BIOCARTA MPR 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 E2F2 E2F2 E2F2 32 0.61 0.026 YES
2 CDC20 CDC20 CDC20 37 0.61 0.053 YES
3 ORC1L ORC1L ORC1L 54 0.59 0.079 YES
4 TTK TTK TTK 72 0.56 0.1 YES
5 ORC6L ORC6L ORC6L 87 0.55 0.13 YES
6 CDC25A CDC25A CDC25A 107 0.54 0.15 YES
7 PLK1 PLK1 PLK1 109 0.53 0.18 YES
8 PKMYT1 PKMYT1 PKMYT1 115 0.53 0.2 YES
9 CDC45 CDC45 CDC45 121 0.52 0.22 YES
10 BUB1B BUB1B BUB1B 124 0.52 0.24 YES
11 BUB1 BUB1 BUB1 134 0.52 0.27 YES
12 PTTG1 PTTG1 PTTG1 138 0.51 0.29 YES
13 CDC25C CDC25C CDC25C 182 0.49 0.31 YES
14 CCNB2 CCNB2 CCNB2 276 0.45 0.33 YES
15 CDC6 CDC6 CDC6 285 0.45 0.35 YES
16 CDC7 CDC7 CDC7 315 0.44 0.36 YES
17 CDKN2A CDKN2A CDKN2A 417 0.42 0.38 YES
18 CDK1 CDK1 CDK1 427 0.41 0.4 YES
19 CCNB1 CCNB1 CCNB1 440 0.41 0.41 YES
20 CCNE1 CCNE1 CCNE1 461 0.41 0.43 YES
21 MAD2L1 MAD2L1 MAD2L1 464 0.41 0.45 YES
22 SFN SFN SFN 523 0.39 0.46 YES
23 PTTG2 PTTG2 PTTG2 592 0.38 0.48 YES
24 CCNE2 CCNE2 CCNE2 594 0.38 0.49 YES
25 CCNA2 CCNA2 CCNA2 761 0.35 0.5 YES
26 ESPL1 ESPL1 ESPL1 827 0.34 0.51 YES
27 SMC1B SMC1B SMC1B 840 0.34 0.53 YES
28 CHEK1 CHEK1 CHEK1 988 0.32 0.53 YES
29 MCM2 MCM2 MCM2 1208 0.3 0.53 YES
30 E2F5 E2F5 E2F5 1252 0.29 0.54 YES
31 E2F1 E2F1 E2F1 1302 0.29 0.55 YES
32 RBL1 RBL1 RBL1 1350 0.28 0.56 YES
33 CDC25B CDC25B CDC25B 1373 0.28 0.58 YES
34 CDC14A CDC14A CDC14A 1941 0.24 0.55 YES
35 CDKN2C CDKN2C CDKN2C 2020 0.23 0.56 YES
36 MCM4 MCM4 MCM4 2087 0.22 0.57 YES
37 MCM6 MCM6 MCM6 2125 0.22 0.57 YES
38 MCM7 MCM7 MCM7 2363 0.2 0.57 YES
39 CDKN2D CDKN2D CDKN2D 2541 0.2 0.57 YES
40 E2F3 E2F3 E2F3 2796 0.18 0.56 YES
41 CDKN2B CDKN2B CDKN2B 2900 0.18 0.56 YES
42 MAD2L2 MAD2L2 MAD2L2 2940 0.17 0.57 YES
43 MCM5 MCM5 MCM5 3202 0.16 0.56 YES
44 MCM3 MCM3 MCM3 3252 0.16 0.57 YES
45 CDK4 CDK4 CDK4 3642 0.14 0.55 YES
46 ZBTB17 ZBTB17 ZBTB17 3685 0.14 0.56 YES
47 SKP2 SKP2 SKP2 3712 0.14 0.56 YES
48 CCNA1 CCNA1 CCNA1 3776 0.14 0.56 YES
49 CHEK2 CHEK2 CHEK2 3777 0.14 0.57 YES
50 TGFB1 TGFB1 TGFB1 3846 0.14 0.57 YES
51 HDAC2 HDAC2 HDAC2 3995 0.13 0.57 YES
52 HDAC1 HDAC1 HDAC1 4063 0.13 0.57 YES
53 CDK2 CDK2 CDK2 4189 0.12 0.57 YES
54 YWHAZ YWHAZ YWHAZ 4191 0.12 0.58 YES
55 PCNA PCNA PCNA 4203 0.12 0.58 YES
56 ANAPC7 ANAPC7 ANAPC7 4525 0.12 0.57 NO
57 PRKDC PRKDC PRKDC 4906 0.1 0.55 NO
58 E2F4 E2F4 E2F4 5060 0.1 0.55 NO
59 CCND2 CCND2 CCND2 5106 0.098 0.55 NO
60 TFDP2 TFDP2 TFDP2 5126 0.098 0.55 NO
61 RAD21 RAD21 RAD21 5823 0.082 0.52 NO
62 CDC27 CDC27 CDC27 6213 0.074 0.5 NO
63 ANAPC11 ANAPC11 ANAPC11 6422 0.069 0.49 NO
64 CCND3 CCND3 CCND3 6557 0.067 0.48 NO
65 ANAPC4 ANAPC4 ANAPC4 6645 0.065 0.48 NO
66 BUB3 BUB3 BUB3 6709 0.064 0.48 NO
67 ORC2L ORC2L ORC2L 6785 0.063 0.48 NO
68 ATR ATR ATR 7043 0.058 0.47 NO
69 YWHAQ YWHAQ YWHAQ 7052 0.058 0.47 NO
70 TGFB2 TGFB2 TGFB2 7146 0.056 0.47 NO
71 SMC1A SMC1A SMC1A 7338 0.053 0.46 NO
72 ORC4L ORC4L ORC4L 7383 0.052 0.46 NO
73 ANAPC1 ANAPC1 ANAPC1 7388 0.052 0.46 NO
74 YWHAB YWHAB YWHAB 7528 0.05 0.46 NO
75 ANAPC5 ANAPC5 ANAPC5 7577 0.049 0.46 NO
76 SMAD2 SMAD2 SMAD2 7750 0.047 0.45 NO
77 RBX1 RBX1 RBX1 7795 0.046 0.45 NO
78 MYC MYC MYC 7910 0.044 0.44 NO
79 CDC26 CDC26 CDC26 8124 0.04 0.43 NO
80 YWHAH YWHAH YWHAH 8161 0.04 0.43 NO
81 ATM ATM ATM 8223 0.038 0.43 NO
82 TFDP1 TFDP1 TFDP1 8296 0.037 0.43 NO
83 CDK7 CDK7 CDK7 8447 0.035 0.42 NO
84 CDKN1C CDKN1C CDKN1C 8503 0.034 0.42 NO
85 ABL1 ABL1 ABL1 8520 0.034 0.42 NO
86 YWHAG YWHAG YWHAG 8613 0.032 0.42 NO
87 WEE1 WEE1 WEE1 8696 0.031 0.41 NO
88 CDC23 CDC23 CDC23 8771 0.03 0.41 NO
89 ORC5L ORC5L ORC5L 8875 0.028 0.41 NO
90 CDK6 CDK6 CDK6 9179 0.024 0.39 NO
91 YWHAE YWHAE YWHAE 9643 0.017 0.36 NO
92 ORC3L ORC3L ORC3L 9681 0.016 0.36 NO
93 MAD1L1 MAD1L1 MAD1L1 9918 0.013 0.35 NO
94 CDC16 CDC16 CDC16 9966 0.012 0.35 NO
95 CCNH CCNH CCNH 10134 0.0092 0.34 NO
96 STAG2 STAG2 STAG2 10240 0.0076 0.33 NO
97 SKP1 SKP1 SKP1 10464 0.0046 0.32 NO
98 ANAPC13 ANAPC13 ANAPC13 10774 -0.00071 0.3 NO
99 SMC3 SMC3 SMC3 10862 -0.0021 0.3 NO
100 CUL1 CUL1 CUL1 10916 -0.003 0.3 NO
101 GSK3B GSK3B GSK3B 11142 -0.0065 0.28 NO
102 ANAPC2 ANAPC2 ANAPC2 11446 -0.012 0.27 NO
103 SMAD4 SMAD4 SMAD4 11504 -0.013 0.26 NO
104 CREBBP CREBBP CREBBP 11627 -0.015 0.26 NO
105 MDM2 MDM2 MDM2 11919 -0.021 0.24 NO
106 WEE2 WEE2 WEE2 12026 -0.023 0.24 NO
107 ANAPC10 ANAPC10 ANAPC10 12098 -0.025 0.23 NO
108 RB1 RB1 RB1 12331 -0.029 0.22 NO
109 SMAD3 SMAD3 SMAD3 12611 -0.034 0.21 NO
110 CDKN1B CDKN1B CDKN1B 12914 -0.041 0.19 NO
111 FZR1 FZR1 FZR1 12932 -0.042 0.19 NO
112 STAG1 STAG1 STAG1 13002 -0.043 0.19 NO
113 EP300 EP300 EP300 13199 -0.048 0.18 NO
114 TGFB3 TGFB3 TGFB3 13305 -0.05 0.18 NO
115 TP53 TP53 TP53 13942 -0.068 0.14 NO
116 CDKN1A CDKN1A CDKN1A 14166 -0.076 0.14 NO
117 RBL2 RBL2 RBL2 15377 -0.12 0.073 NO
118 CCND1 CCND1 CCND1 15819 -0.14 0.054 NO
119 CCNB3 CCNB3 CCNB3 15847 -0.15 0.06 NO
120 GADD45B GADD45B GADD45B 16911 -0.25 0.01 NO
121 GADD45A GADD45A GADD45A 16946 -0.26 0.02 NO
122 GADD45G GADD45G GADD45G 16977 -0.26 0.03 NO
123 CDC14B CDC14B CDC14B 17064 -0.28 0.038 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 MPR PATHWAY.

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

genes ES table in pathway: BIOCARTA TOLL 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 RAD54L RAD54L RAD54L 17 0.64 0.13 YES
2 EME1 EME1 EME1 68 0.57 0.24 YES
3 RAD51 RAD51 RAD51 100 0.54 0.35 YES
4 BLM BLM BLM 187 0.49 0.44 YES
5 XRCC2 XRCC2 XRCC2 443 0.41 0.51 YES
6 RAD54B RAD54B RAD54B 791 0.34 0.56 YES
7 BRCA2 BRCA2 BRCA2 1998 0.23 0.53 YES
8 RAD51L1 RAD51L1 RAD51L1 2148 0.22 0.57 YES
9 XRCC3 XRCC3 XRCC3 2361 0.2 0.6 YES
10 RPA4 RPA4 RPA4 2393 0.2 0.64 YES
11 POLD1 POLD1 POLD1 2456 0.2 0.67 YES
12 POLD3 POLD3 POLD3 3632 0.14 0.64 NO
13 RPA2 RPA2 RPA2 4240 0.12 0.63 NO
14 MRE11A MRE11A MRE11A 4254 0.12 0.65 NO
15 RPA3 RPA3 RPA3 5228 0.095 0.62 NO
16 RAD51L3 RAD51L3 RAD51L3 5410 0.091 0.62 NO
17 NBN NBN NBN 6172 0.074 0.59 NO
18 SSBP1 SSBP1 SSBP1 6601 0.066 0.58 NO
19 RPA1 RPA1 RPA1 6975 0.059 0.57 NO
20 SHFM1 SHFM1 SHFM1 8539 0.034 0.49 NO
21 MUS81 MUS81 MUS81 8978 0.027 0.47 NO
22 POLD2 POLD2 POLD2 9017 0.026 0.48 NO
23 TOP3A TOP3A TOP3A 9301 0.022 0.46 NO
24 TOP3B TOP3B TOP3B 10567 0.003 0.39 NO
25 RAD50 RAD50 RAD50 10796 -0.0011 0.38 NO
26 POLD4 POLD4 POLD4 11493 -0.013 0.34 NO
27 RAD52 RAD52 RAD52 12851 -0.04 0.28 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 TOLL PATHWAY.

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

genes ES table in pathway: KEGG RNA DEGRADATION

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 POLE2 POLE2 POLE2 795 0.34 0.02 YES
2 MCM2 MCM2 MCM2 1208 0.3 0.052 YES
3 PRIM1 PRIM1 PRIM1 1446 0.27 0.09 YES
4 RFC4 RFC4 RFC4 1606 0.26 0.13 YES
5 DNA2 DNA2 DNA2 2035 0.23 0.15 YES
6 POLA2 POLA2 POLA2 2068 0.23 0.19 YES
7 MCM4 MCM4 MCM4 2087 0.22 0.23 YES
8 RNASEH2A RNASEH2A RNASEH2A 2123 0.22 0.27 YES
9 MCM6 MCM6 MCM6 2125 0.22 0.31 YES
10 PRIM2 PRIM2 PRIM2 2315 0.21 0.34 YES
11 MCM7 MCM7 MCM7 2363 0.2 0.38 YES
12 RPA4 RPA4 RPA4 2393 0.2 0.41 YES
13 FEN1 FEN1 FEN1 2445 0.2 0.45 YES
14 POLD1 POLD1 POLD1 2456 0.2 0.48 YES
15 POLE4 POLE4 POLE4 2998 0.17 0.49 YES
16 MCM5 MCM5 MCM5 3202 0.16 0.51 YES
17 MCM3 MCM3 MCM3 3252 0.16 0.53 YES
18 RFC3 RFC3 RFC3 3562 0.15 0.54 YES
19 POLD3 POLD3 POLD3 3632 0.14 0.57 YES
20 LIG1 LIG1 LIG1 4076 0.13 0.57 YES
21 RFC2 RFC2 RFC2 4126 0.13 0.59 YES
22 PCNA PCNA PCNA 4203 0.12 0.61 YES
23 RPA2 RPA2 RPA2 4240 0.12 0.63 YES
24 RFC5 RFC5 RFC5 4800 0.11 0.62 YES
25 POLE3 POLE3 POLE3 5119 0.098 0.62 YES
26 RPA3 RPA3 RPA3 5228 0.095 0.63 YES
27 RNASEH2B RNASEH2B RNASEH2B 5972 0.079 0.6 NO
28 RNASEH1 RNASEH1 RNASEH1 6474 0.068 0.59 NO
29 SSBP1 SSBP1 SSBP1 6601 0.066 0.59 NO
30 POLE POLE POLE 6647 0.065 0.6 NO
31 RPA1 RPA1 RPA1 6975 0.059 0.59 NO
32 RNASEH2C RNASEH2C RNASEH2C 8869 0.028 0.49 NO
33 POLD2 POLD2 POLD2 9017 0.026 0.49 NO
34 RFC1 RFC1 RFC1 10369 0.0057 0.41 NO
35 POLD4 POLD4 POLD4 11493 -0.013 0.35 NO

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

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

genes ES table in pathway: KEGG DNA REPLICATION

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 GNGT1 GNGT1 GNGT1 38 0.61 0.13 YES
2 CDC25C CDC25C CDC25C 182 0.49 0.23 YES
3 CDK1 CDK1 CDK1 427 0.41 0.3 YES
4 CCNB1 CCNB1 CCNB1 440 0.41 0.39 YES
5 PAQR5 PAQR5 PAQR5 1029 0.31 0.42 YES
6 PRKAR2B PRKAR2B PRKAR2B 1653 0.26 0.44 YES
7 SRC SRC SRC 2094 0.22 0.47 YES
8 RPS6KA1 RPS6KA1 RPS6KA1 2222 0.22 0.51 YES
9 HRAS HRAS HRAS 2849 0.18 0.51 YES
10 ARPC1B ARPC1B ARPC1B 3126 0.17 0.53 YES
11 ACTA1 ACTA1 ACTA1 4308 0.12 0.49 NO
12 PRKACB PRKACB PRKACB 4849 0.1 0.48 NO
13 ARPC3 ARPC3 ARPC3 4978 0.1 0.5 NO
14 MAPK3 MAPK3 MAPK3 5160 0.097 0.51 NO
15 CAP1 CAP1 CAP1 5279 0.094 0.52 NO
16 GNB1 GNB1 GNB1 5744 0.083 0.51 NO
17 ARPC4 ARPC4 ARPC4 6007 0.078 0.52 NO
18 ARPC2 ARPC2 ARPC2 6399 0.07 0.51 NO
19 ACTR3 ACTR3 ACTR3 6746 0.063 0.5 NO
20 ARPC1A ARPC1A ARPC1A 7816 0.045 0.45 NO
21 ACTR2 ACTR2 ACTR2 8561 0.033 0.42 NO
22 PGR PGR PGR 9435 0.02 0.37 NO
23 ARPC5 ARPC5 ARPC5 10158 0.0088 0.33 NO
24 PAQR7 PAQR7 PAQR7 10427 0.005 0.32 NO
25 PIN1 PIN1 PIN1 11221 -0.0077 0.28 NO
26 MAPK1 MAPK1 MAPK1 11544 -0.014 0.26 NO
27 PRKAR1A PRKAR1A PRKAR1A 12070 -0.024 0.24 NO
28 PRKAR2A PRKAR2A PRKAR2A 12373 -0.03 0.23 NO
29 GNAS GNAS GNAS 13197 -0.048 0.19 NO
30 GNAI1 GNAI1 GNAI1 13286 -0.05 0.2 NO
31 PRKAR1B PRKAR1B PRKAR1B 14035 -0.071 0.17 NO
32 MYT1 MYT1 MYT1 16310 -0.18 0.08 NO

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

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

genes ES table in pathway: KEGG SPLICEOSOME

Table 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 GNGT1 GNGT1 GNGT1 38 0.61 0.17 YES
2 PLCB1 PLCB1 PLCB1 535 0.39 0.26 YES
3 NCF2 NCF2 NCF2 1007 0.32 0.32 YES
4 FPR1 FPR1 FPR1 1246 0.29 0.39 YES
5 NCF1C NCF1C NCF1C 1487 0.27 0.46 YES
6 MAP2K6 MAP2K6 MAP2K6 1992 0.23 0.5 YES
7 HRAS HRAS HRAS 2849 0.18 0.5 YES
8 PAK1 PAK1 PAK1 4100 0.13 0.46 NO
9 PIK3C2G PIK3C2G PIK3C2G 4937 0.1 0.45 NO
10 NFATC4 NFATC4 NFATC4 4963 0.1 0.48 NO
11 MAPK3 MAPK3 MAPK3 5160 0.097 0.49 NO
12 GNB1 GNB1 GNB1 5744 0.083 0.48 NO
13 RAC1 RAC1 RAC1 6226 0.073 0.48 NO
14 MAP3K1 MAP3K1 MAP3K1 6381 0.07 0.49 NO
15 CAMK1G CAMK1G CAMK1G 7022 0.058 0.47 NO
16 MAP2K2 MAP2K2 MAP2K2 7689 0.048 0.44 NO
17 CALM3 CALM3 CALM3 8302 0.037 0.42 NO
18 CALM2 CALM2 CALM2 8639 0.032 0.41 NO
19 PPP3CA PPP3CA PPP3CA 8849 0.029 0.41 NO
20 NFATC1 NFATC1 NFATC1 8895 0.028 0.41 NO
21 CAMK1 CAMK1 CAMK1 9341 0.021 0.39 NO
22 PPP3CC PPP3CC PPP3CC 9383 0.021 0.4 NO
23 RELA RELA RELA 9629 0.017 0.39 NO
24 PPP3CB PPP3CB PPP3CB 10246 0.0076 0.36 NO
25 NFKB1 NFKB1 NFKB1 10302 0.0068 0.36 NO
26 ELK1 ELK1 ELK1 10634 0.0019 0.34 NO
27 RAF1 RAF1 RAF1 11143 -0.0065 0.31 NO
28 MAP2K1 MAP2K1 MAP2K1 11250 -0.0082 0.31 NO
29 MAPK14 MAPK14 MAPK14 11276 -0.0086 0.31 NO
30 MAPK1 MAPK1 MAPK1 11544 -0.014 0.3 NO
31 MAP2K3 MAP2K3 MAP2K3 11653 -0.016 0.3 NO
32 NFATC3 NFATC3 NFATC3 11672 -0.016 0.3 NO
33 CALM1 CALM1 CALM1 12528 -0.033 0.26 NO
34 NFATC2 NFATC2 NFATC2 13238 -0.049 0.23 NO
35 NFKBIA NFKBIA NFKBIA 13964 -0.069 0.21 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 SPLICEOSOME.

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

genes ES table in pathway: KEGG BASE EXCISION REPAIR

Table 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 CDC20 CDC20 CDC20 37 0.61 0.036 YES
2 SGOL1 SGOL1 SGOL1 84 0.55 0.069 YES
3 PLK1 PLK1 PLK1 109 0.53 0.1 YES
4 PKMYT1 PKMYT1 PKMYT1 115 0.53 0.13 YES
5 BUB1 BUB1 BUB1 134 0.52 0.17 YES
6 PTTG1 PTTG1 PTTG1 138 0.51 0.2 YES
7 CDC25C CDC25C CDC25C 182 0.49 0.23 YES
8 CCNB2 CCNB2 CCNB2 276 0.45 0.25 YES
9 CDK1 CDK1 CDK1 427 0.41 0.27 YES
10 FBXO43 FBXO43 FBXO43 430 0.41 0.29 YES
11 CCNB1 CCNB1 CCNB1 440 0.41 0.32 YES
12 CCNE1 CCNE1 CCNE1 461 0.41 0.34 YES
13 MAD2L1 MAD2L1 MAD2L1 464 0.41 0.37 YES
14 PTTG2 PTTG2 PTTG2 592 0.38 0.38 YES
15 FBXO5 FBXO5 FBXO5 593 0.38 0.41 YES
16 CCNE2 CCNE2 CCNE2 594 0.38 0.43 YES
17 ESPL1 ESPL1 ESPL1 827 0.34 0.44 YES
18 SMC1B SMC1B SMC1B 840 0.34 0.46 YES
19 ITPR3 ITPR3 ITPR3 1274 0.29 0.46 NO
20 AURKA AURKA AURKA 1861 0.24 0.44 NO
21 SPDYA SPDYA SPDYA 2031 0.23 0.44 NO
22 RPS6KA1 RPS6KA1 RPS6KA1 2222 0.22 0.44 NO
23 REC8 REC8 REC8 2431 0.2 0.45 NO
24 RPS6KA6 RPS6KA6 RPS6KA6 2691 0.19 0.44 NO
25 MAD2L2 MAD2L2 MAD2L2 2940 0.17 0.44 NO
26 CHP2 CHP2 CHP2 3053 0.17 0.44 NO
27 ADCY7 ADCY7 ADCY7 4061 0.13 0.4 NO
28 CDK2 CDK2 CDK2 4189 0.12 0.4 NO
29 YWHAZ YWHAZ YWHAZ 4191 0.12 0.4 NO
30 PPP1CC PPP1CC PPP1CC 4477 0.12 0.4 NO
31 ANAPC7 ANAPC7 ANAPC7 4525 0.12 0.4 NO
32 PRKACB PRKACB PRKACB 4849 0.1 0.39 NO
33 MAPK3 MAPK3 MAPK3 5160 0.097 0.38 NO
34 PRKX PRKX PRKX 5275 0.094 0.38 NO
35 MAPK12 MAPK12 MAPK12 5299 0.094 0.38 NO
36 CDC27 CDC27 CDC27 6213 0.074 0.33 NO
37 ITPR1 ITPR1 ITPR1 6264 0.072 0.34 NO
38 RPS6KA3 RPS6KA3 RPS6KA3 6306 0.072 0.34 NO
39 ANAPC11 ANAPC11 ANAPC11 6422 0.069 0.34 NO
40 PPP1CA PPP1CA PPP1CA 6492 0.068 0.34 NO
41 ANAPC4 ANAPC4 ANAPC4 6645 0.065 0.33 NO
42 CPEB1 CPEB1 CPEB1 6696 0.064 0.33 NO
43 YWHAQ YWHAQ YWHAQ 7052 0.058 0.32 NO
44 PPP2R1A PPP2R1A PPP2R1A 7316 0.053 0.3 NO
45 SMC1A SMC1A SMC1A 7338 0.053 0.31 NO
46 ANAPC1 ANAPC1 ANAPC1 7388 0.052 0.31 NO
47 YWHAB YWHAB YWHAB 7528 0.05 0.3 NO
48 ANAPC5 ANAPC5 ANAPC5 7577 0.049 0.3 NO
49 RBX1 RBX1 RBX1 7795 0.046 0.29 NO
50 CDC26 CDC26 CDC26 8124 0.04 0.28 NO
51 YWHAH YWHAH YWHAH 8161 0.04 0.28 NO
52 CALM3 CALM3 CALM3 8302 0.037 0.27 NO
53 PPP2CA PPP2CA PPP2CA 8472 0.035 0.26 NO
54 PPP1CB PPP1CB PPP1CB 8515 0.034 0.26 NO
55 YWHAG YWHAG YWHAG 8613 0.032 0.26 NO
56 CALM2 CALM2 CALM2 8639 0.032 0.26 NO
57 CDC23 CDC23 CDC23 8771 0.03 0.26 NO
58 PPP3CA PPP3CA PPP3CA 8849 0.029 0.25 NO
59 PPP2R5E PPP2R5E PPP2R5E 8859 0.028 0.25 NO
60 PPP2R5D PPP2R5D PPP2R5D 8998 0.026 0.25 NO
61 PPP2R5B PPP2R5B PPP2R5B 9309 0.022 0.23 NO
62 PPP3CC PPP3CC PPP3CC 9383 0.021 0.23 NO
63 PGR PGR PGR 9435 0.02 0.23 NO
64 YWHAE YWHAE YWHAE 9643 0.017 0.22 NO
65 CDC16 CDC16 CDC16 9966 0.012 0.2 NO
66 PPP3CB PPP3CB PPP3CB 10246 0.0076 0.18 NO
67 SKP1 SKP1 SKP1 10464 0.0046 0.17 NO
68 FBXW11 FBXW11 FBXW11 10468 0.0046 0.17 NO
69 IGF1R IGF1R IGF1R 10541 0.0033 0.17 NO
70 ANAPC13 ANAPC13 ANAPC13 10774 -0.00071 0.16 NO
71 ADCY6 ADCY6 ADCY6 10805 -0.0012 0.15 NO
72 SMC3 SMC3 SMC3 10862 -0.0021 0.15 NO
73 CUL1 CUL1 CUL1 10916 -0.003 0.15 NO
74 CALML3 CALML3 CALML3 11111 -0.0059 0.14 NO
75 MAP2K1 MAP2K1 MAP2K1 11250 -0.0082 0.13 NO
76 CAMK2D CAMK2D CAMK2D 11305 -0.0091 0.13 NO
77 ANAPC2 ANAPC2 ANAPC2 11446 -0.012 0.12 NO
78 MAPK1 MAPK1 MAPK1 11544 -0.014 0.12 NO
79 PPP3R1 PPP3R1 PPP3R1 11687 -0.016 0.11 NO
80 PPP2CB PPP2CB PPP2CB 12034 -0.023 0.09 NO
81 ANAPC10 ANAPC10 ANAPC10 12098 -0.025 0.088 NO
82 CALM1 CALM1 CALM1 12528 -0.033 0.065 NO
83 CAMK2G CAMK2G CAMK2G 12892 -0.041 0.047 NO
84 SLK SLK SLK 12928 -0.042 0.048 NO
85 BTRC BTRC BTRC 13100 -0.046 0.041 NO
86 PPP2R5C PPP2R5C PPP2R5C 13147 -0.046 0.042 NO
87 ADCY2 ADCY2 ADCY2 13629 -0.058 0.018 NO
88 PPP2R5A PPP2R5A PPP2R5A 14262 -0.078 -0.013 NO
89 PRKACA PRKACA PRKACA 14493 -0.086 -0.021 NO
90 ADCY9 ADCY9 ADCY9 14637 -0.09 -0.023 NO
91 ADCY5 ADCY5 ADCY5 15131 -0.11 -0.044 NO
92 CHP CHP CHP 15151 -0.11 -0.038 NO
93 PPP2R1B PPP2R1B PPP2R1B 15173 -0.11 -0.032 NO
94 CALML6 CALML6 CALML6 15807 -0.14 -0.059 NO
95 CAMK2A CAMK2A CAMK2A 15907 -0.15 -0.055 NO
96 ADCY8 ADCY8 ADCY8 15987 -0.16 -0.05 NO
97 STAG3 STAG3 STAG3 16042 -0.16 -0.042 NO
98 IGF1 IGF1 IGF1 16430 -0.2 -0.052 NO
99 ITPR2 ITPR2 ITPR2 16601 -0.21 -0.048 NO
100 ADCY1 ADCY1 ADCY1 16664 -0.22 -0.038 NO
101 RPS6KA2 RPS6KA2 RPS6KA2 16863 -0.24 -0.034 NO
102 SPDYC SPDYC SPDYC 16990 -0.26 -0.024 NO
103 AR AR AR 17279 -0.31 -0.021 NO
104 CAMK2B CAMK2B CAMK2B 17306 -0.32 -0.0022 NO
105 ADCY4 ADCY4 ADCY4 17572 -0.41 0.0088 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 BASE EXCISION REPAIR.

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

genes ES table in pathway: KEGG NUCLEOTIDE EXCISION REPAIR

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 ENO2 ENO2 ENO2 129 0.52 0.11 YES
2 ENO1 ENO1 ENO1 2345 0.21 0.036 YES
3 CNOT6 CNOT6 CNOT6 3311 0.16 0.018 YES
4 NAA38 NAA38 NAA38 3975 0.13 0.012 YES
5 MPHOSPH6 MPHOSPH6 MPHOSPH6 4124 0.13 0.033 YES
6 RQCD1 RQCD1 RQCD1 4220 0.12 0.057 YES
7 EXOSC2 EXOSC2 EXOSC2 4264 0.12 0.083 YES
8 LSM2 LSM2 LSM2 4491 0.12 0.097 YES
9 EXOSC3 EXOSC3 EXOSC3 4556 0.11 0.12 YES
10 EXOSC10 EXOSC10 EXOSC10 4567 0.11 0.15 YES
11 EXOSC9 EXOSC9 EXOSC9 5012 0.1 0.14 YES
12 EXOSC8 EXOSC8 EXOSC8 5056 0.1 0.16 YES
13 CNOT3 CNOT3 CNOT3 5186 0.096 0.18 YES
14 EDC4 EDC4 EDC4 5290 0.094 0.2 YES
15 DCP2 DCP2 DCP2 5369 0.092 0.21 YES
16 CNOT10 CNOT10 CNOT10 5383 0.091 0.23 YES
17 EXOSC4 EXOSC4 EXOSC4 5459 0.09 0.25 YES
18 EXOSC5 EXOSC5 EXOSC5 5532 0.088 0.27 YES
19 DCP1A DCP1A DCP1A 5743 0.084 0.28 YES
20 LSM7 LSM7 LSM7 5882 0.08 0.29 YES
21 LSM5 LSM5 LSM5 6274 0.072 0.28 YES
22 LSM4 LSM4 LSM4 6445 0.069 0.29 YES
23 EDC3 EDC3 EDC3 6563 0.067 0.3 YES
24 ZCCHC7 ZCCHC7 ZCCHC7 7014 0.058 0.28 YES
25 EXOSC7 EXOSC7 EXOSC7 7091 0.057 0.29 YES
26 CNOT2 CNOT2 CNOT2 7245 0.054 0.3 YES
27 PARN PARN PARN 7443 0.051 0.3 YES
28 EXOSC1 EXOSC1 EXOSC1 7487 0.051 0.31 YES
29 SKIV2L SKIV2L SKIV2L 7532 0.05 0.32 YES
30 EXOSC6 EXOSC6 EXOSC6 7681 0.048 0.32 YES
31 PNPT1 PNPT1 PNPT1 7732 0.047 0.33 YES
32 LSM6 LSM6 LSM6 7983 0.042 0.32 YES
33 HSPD1 HSPD1 HSPD1 8059 0.041 0.33 YES
34 PAPOLG PAPOLG PAPOLG 8106 0.04 0.34 YES
35 LSM1 LSM1 LSM1 8335 0.037 0.33 YES
36 CNOT1 CNOT1 CNOT1 8407 0.036 0.34 YES
37 SKIV2L2 SKIV2L2 SKIV2L2 8650 0.032 0.33 YES
38 CNOT7 CNOT7 CNOT7 8739 0.03 0.33 YES
39 LSM3 LSM3 LSM3 8781 0.03 0.34 YES
40 DCPS DCPS DCPS 8949 0.027 0.33 YES
41 PAPOLA PAPOLA PAPOLA 8976 0.027 0.34 YES
42 XRN2 XRN2 XRN2 9344 0.021 0.32 NO
43 PATL1 PATL1 PATL1 10432 0.005 0.26 NO
44 CNOT4 CNOT4 CNOT4 10698 0.00066 0.25 NO
45 DIS3 DIS3 DIS3 11265 -0.0085 0.22 NO
46 DDX6 DDX6 DDX6 11338 -0.0098 0.21 NO
47 HSPA9 HSPA9 HSPA9 11706 -0.017 0.2 NO
48 XRN1 XRN1 XRN1 12112 -0.025 0.18 NO
49 DCP1B DCP1B DCP1B 12338 -0.029 0.17 NO
50 C1D C1D C1D 12406 -0.03 0.18 NO
51 WDR61 WDR61 WDR61 12807 -0.039 0.16 NO
52 PAPD7 PAPD7 PAPD7 13426 -0.053 0.14 NO
53 TTC37 TTC37 TTC37 13831 -0.064 0.13 NO
54 CNOT6L CNOT6L CNOT6L 14602 -0.089 0.11 NO
55 ENO3 ENO3 ENO3 17127 -0.29 0.034 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 NUCLEOTIDE EXCISION REPAIR.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NUCLEOTIDE EXCISION REPAIR, 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 HOMOLOGOUS RECOMBINATION

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 CDC25A CDC25A CDC25A 107 0.54 0.15 YES
2 CDKN2A CDKN2A CDKN2A 417 0.42 0.25 YES
3 CDK1 CDK1 CDK1 427 0.41 0.37 YES
4 CCNE1 CCNE1 CCNE1 461 0.41 0.48 YES
5 CDKN2B CDKN2B CDKN2B 2900 0.18 0.39 YES
6 CDK4 CDK4 CDK4 3642 0.14 0.39 YES
7 SKP2 SKP2 SKP2 3712 0.14 0.43 YES
8 CCNA1 CCNA1 CCNA1 3776 0.14 0.47 YES
9 TGFB1 TGFB1 TGFB1 3846 0.14 0.5 YES
10 HDAC1 HDAC1 HDAC1 4063 0.13 0.53 YES
11 CDK2 CDK2 CDK2 4189 0.12 0.56 YES
12 ATR ATR ATR 7043 0.058 0.41 NO
13 TGFB2 TGFB2 TGFB2 7146 0.056 0.42 NO
14 ATM ATM ATM 8223 0.038 0.37 NO
15 TFDP1 TFDP1 TFDP1 8296 0.037 0.38 NO
16 ABL1 ABL1 ABL1 8520 0.034 0.37 NO
17 CDK6 CDK6 CDK6 9179 0.024 0.34 NO
18 DHFR DHFR DHFR 9211 0.023 0.35 NO
19 GSK3B GSK3B GSK3B 11142 -0.0065 0.24 NO
20 SMAD4 SMAD4 SMAD4 11504 -0.013 0.22 NO
21 RB1 RB1 RB1 12331 -0.029 0.19 NO
22 SMAD3 SMAD3 SMAD3 12611 -0.034 0.18 NO
23 CDKN1B CDKN1B CDKN1B 12914 -0.041 0.18 NO
24 TGFB3 TGFB3 TGFB3 13305 -0.05 0.17 NO
25 TP53 TP53 TP53 13942 -0.068 0.15 NO
26 CDKN1A CDKN1A CDKN1A 14166 -0.076 0.16 NO
27 CCND1 CCND1 CCND1 15819 -0.14 0.11 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 HOMOLOGOUS RECOMBINATION.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG GLYCOLYSIS GLUCONEOGENESIS 59 genes.ES.table 0.5 1.6 0.018 0.11 0.71 0.37 0.094 0.34 0.064 0.002
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.6 1.7 0.057 0.11 0.45 0.59 0.24 0.44 0 0.008
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS 26 genes.ES.table 0.72 1.5 0.097 0.19 0.9 0.58 0.15 0.49 0.14 0.004
KEGG FATTY ACID METABOLISM 41 genes.ES.table 0.68 1.6 0.055 0.12 0.69 0.71 0.18 0.58 0.064 0.002
KEGG STEROID HORMONE BIOSYNTHESIS 51 genes.ES.table 0.71 1.6 0.033 0.12 0.73 0.55 0.11 0.49 0.069 0.002
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 30 genes.ES.table 0.52 1.4 0.084 0.2 0.92 0.53 0.12 0.47 0.15 0.006
KEGG GLYCINE SERINE AND THREONINE METABOLISM 30 genes.ES.table 0.77 1.7 0.0041 0.093 0.51 0.8 0.18 0.66 0.038 0.002
KEGG CYSTEINE AND METHIONINE METABOLISM 33 genes.ES.table 0.57 1.8 0.0065 0.099 0.35 0.36 0.11 0.32 0 0.012
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.64 1.7 0.034 0.098 0.47 0.74 0.19 0.61 0 0.004
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.58 2 0.0062 0.051 0.043 0.3 0.11 0.27 0 0.019
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AADAT AADAT AADAT 32 0.62 0.12 YES
2 BBOX1 BBOX1 BBOX1 39 0.59 0.23 YES
3 AASS AASS AASS 165 0.44 0.31 YES
4 OGDHL OGDHL OGDHL 410 0.33 0.36 YES
5 PIPOX PIPOX PIPOX 530 0.3 0.41 YES
6 GCDH GCDH GCDH 1015 0.21 0.43 YES
7 ALDH7A1 ALDH7A1 ALDH7A1 1215 0.19 0.45 YES
8 ALDH2 ALDH2 ALDH2 1372 0.18 0.48 YES
9 ACAT1 ACAT1 ACAT1 1623 0.15 0.49 YES
10 SETD7 SETD7 SETD7 1740 0.14 0.52 YES
11 ACAT2 ACAT2 ACAT2 1797 0.14 0.54 YES
12 ALDH9A1 ALDH9A1 ALDH9A1 1944 0.13 0.56 YES
13 HADH HADH HADH 2029 0.13 0.58 YES
14 ALDH1B1 ALDH1B1 ALDH1B1 3156 0.08 0.53 NO
15 ECHS1 ECHS1 ECHS1 3249 0.077 0.54 NO
16 OGDH OGDH OGDH 3448 0.07 0.54 NO
17 TMLHE TMLHE TMLHE 3741 0.062 0.54 NO
18 PLOD1 PLOD1 PLOD1 4294 0.048 0.52 NO
19 HADHA HADHA HADHA 4376 0.046 0.52 NO
20 DLST DLST DLST 4728 0.039 0.51 NO
21 SETD2 SETD2 SETD2 4919 0.034 0.5 NO
22 AASDH AASDH AASDH 5559 0.023 0.47 NO
23 SUV39H1 SUV39H1 SUV39H1 5727 0.02 0.47 NO
24 SUV420H1 SUV420H1 SUV420H1 6009 0.015 0.45 NO
25 AASDHPPT AASDHPPT AASDHPPT 6845 0.0028 0.41 NO
26 ALDH3A2 ALDH3A2 ALDH3A2 8173 -0.016 0.34 NO
27 PLOD3 PLOD3 PLOD3 8245 -0.017 0.33 NO
28 EHMT1 EHMT1 EHMT1 8495 -0.02 0.32 NO
29 SETD1A SETD1A SETD1A 8557 -0.022 0.32 NO
30 DOT1L DOT1L DOT1L 8752 -0.025 0.32 NO
31 WHSC1L1 WHSC1L1 WHSC1L1 9117 -0.03 0.3 NO
32 ASH1L ASH1L ASH1L 9815 -0.04 0.27 NO
33 NSD1 NSD1 NSD1 9898 -0.041 0.28 NO
34 PLOD2 PLOD2 PLOD2 10451 -0.049 0.25 NO
35 SETMAR SETMAR SETMAR 10797 -0.055 0.25 NO
36 SETD1B SETD1B SETD1B 10937 -0.058 0.25 NO
37 SETDB2 SETDB2 SETDB2 11888 -0.075 0.21 NO
38 WHSC1 WHSC1 WHSC1 12125 -0.08 0.21 NO
39 SETD8 SETD8 SETD8 12301 -0.084 0.22 NO
40 SUV420H2 SUV420H2 SUV420H2 12367 -0.085 0.23 NO
41 SUV39H2 SUV39H2 SUV39H2 13582 -0.12 0.18 NO
42 SETDB1 SETDB1 SETDB1 13661 -0.12 0.2 NO
43 EHMT2 EHMT2 EHMT2 14254 -0.14 0.2 NO

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

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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 ACACB ACACB ACACB 391 0.34 0.054 YES
2 ALDH6A1 ALDH6A1 ALDH6A1 433 0.32 0.12 YES
3 ABAT ABAT ABAT 444 0.32 0.2 YES
4 EHHADH EHHADH EHHADH 518 0.3 0.26 YES
5 MUT MUT MUT 965 0.22 0.28 YES
6 ACADM ACADM ACADM 1075 0.2 0.32 YES
7 ALDH7A1 ALDH7A1 ALDH7A1 1215 0.19 0.36 YES
8 ACSS2 ACSS2 ACSS2 1245 0.19 0.4 YES
9 ALDH2 ALDH2 ALDH2 1372 0.18 0.43 YES
10 LDHAL6B LDHAL6B LDHAL6B 1489 0.16 0.46 YES
11 MLYCD MLYCD MLYCD 1545 0.16 0.49 YES
12 ACAT1 ACAT1 ACAT1 1623 0.15 0.52 YES
13 ACAT2 ACAT2 ACAT2 1797 0.14 0.55 YES
14 MCEE MCEE MCEE 1812 0.14 0.58 YES
15 SUCLG2 SUCLG2 SUCLG2 1865 0.14 0.6 YES
16 PCCA PCCA PCCA 1939 0.13 0.63 YES
17 ALDH9A1 ALDH9A1 ALDH9A1 1944 0.13 0.66 YES
18 PCCB PCCB PCCB 2299 0.12 0.67 YES
19 HIBCH HIBCH HIBCH 2444 0.11 0.68 YES
20 SUCLG1 SUCLG1 SUCLG1 2518 0.1 0.7 YES
21 ACSS3 ACSS3 ACSS3 2884 0.09 0.7 YES
22 ALDH1B1 ALDH1B1 ALDH1B1 3156 0.08 0.7 YES
23 ECHS1 ECHS1 ECHS1 3249 0.077 0.72 YES
24 HADHA HADHA HADHA 4376 0.046 0.66 NO
25 LDHA LDHA LDHA 7802 -0.011 0.47 NO
26 ALDH3A2 ALDH3A2 ALDH3A2 8173 -0.016 0.45 NO
27 SUCLA2 SUCLA2 SUCLA2 8485 -0.02 0.44 NO
28 LDHAL6A LDHAL6A LDHAL6A 9550 -0.036 0.39 NO
29 ACACA ACACA ACACA 11225 -0.063 0.31 NO
30 LDHB LDHB LDHB 13706 -0.12 0.2 NO
31 ACSS1 ACSS1 ACSS1 14462 -0.14 0.18 NO

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

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

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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 ACOT12 ACOT12 ACOT12 131 0.47 0.08 YES
2 PCK1 PCK1 PCK1 219 0.41 0.15 YES
3 ACACB ACACB ACACB 391 0.34 0.2 YES
4 PCK2 PCK2 PCK2 484 0.31 0.26 YES
5 LDHD LDHD LDHD 752 0.25 0.29 YES
6 PKLR PKLR PKLR 770 0.25 0.34 YES
7 HAGH HAGH HAGH 939 0.22 0.37 YES
8 ALDH7A1 ALDH7A1 ALDH7A1 1215 0.19 0.39 YES
9 ACSS2 ACSS2 ACSS2 1245 0.19 0.42 YES
10 ACYP2 ACYP2 ACYP2 1302 0.18 0.45 YES
11 ALDH2 ALDH2 ALDH2 1372 0.18 0.48 YES
12 LDHAL6B LDHAL6B LDHAL6B 1489 0.16 0.51 YES
13 GRHPR GRHPR GRHPR 1597 0.16 0.53 YES
14 ACAT1 ACAT1 ACAT1 1623 0.15 0.56 YES
15 ACAT2 ACAT2 ACAT2 1797 0.14 0.57 YES
16 ALDH9A1 ALDH9A1 ALDH9A1 1944 0.13 0.59 YES
17 PC PC PC 2328 0.11 0.59 NO
18 ALDH1B1 ALDH1B1 ALDH1B1 3156 0.08 0.56 NO
19 MDH1 MDH1 MDH1 4089 0.052 0.52 NO
20 DLD DLD DLD 4182 0.05 0.52 NO
21 PDHB PDHB PDHB 4843 0.036 0.49 NO
22 ME1 ME1 ME1 5265 0.028 0.47 NO
23 ME3 ME3 ME3 5324 0.027 0.47 NO
24 GLO1 GLO1 GLO1 5726 0.02 0.45 NO
25 PDHA1 PDHA1 PDHA1 5883 0.017 0.45 NO
26 LDHA LDHA LDHA 7802 -0.011 0.34 NO
27 DLAT DLAT DLAT 8055 -0.015 0.33 NO
28 ALDH3A2 ALDH3A2 ALDH3A2 8173 -0.016 0.33 NO
29 MDH2 MDH2 MDH2 8710 -0.024 0.3 NO
30 ME2 ME2 ME2 9546 -0.036 0.26 NO
31 LDHAL6A LDHAL6A LDHAL6A 9550 -0.036 0.27 NO
32 ACACA ACACA ACACA 11225 -0.063 0.18 NO
33 ACYP1 ACYP1 ACYP1 12162 -0.081 0.15 NO
34 AKR1B1 AKR1B1 AKR1B1 12989 -0.099 0.12 NO
35 LDHB LDHB LDHB 13706 -0.12 0.1 NO
36 ACSS1 ACSS1 ACSS1 14462 -0.14 0.084 NO
37 PKM2 PKM2 PKM2 16041 -0.22 0.036 NO
38 HAGHL HAGHL HAGHL 17036 -0.31 0.039 NO

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

Figure S26.  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 FATTY ACID METABOLISM

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 HAO2 HAO2 HAO2 7 0.79 0.07 YES
2 XDH XDH XDH 38 0.6 0.12 YES
3 DAO DAO DAO 94 0.51 0.16 YES
4 SLC27A2 SLC27A2 SLC27A2 269 0.38 0.19 YES
5 AGXT AGXT AGXT 276 0.38 0.22 YES
6 PEX11G PEX11G PEX11G 406 0.33 0.24 YES
7 HAO1 HAO1 HAO1 473 0.31 0.27 YES
8 EHHADH EHHADH EHHADH 518 0.3 0.29 YES
9 PIPOX PIPOX PIPOX 530 0.3 0.32 YES
10 EPHX2 EPHX2 EPHX2 552 0.29 0.34 YES
11 ACSL1 ACSL1 ACSL1 582 0.29 0.37 YES
12 PXMP2 PXMP2 PXMP2 605 0.28 0.39 YES
13 SCP2 SCP2 SCP2 760 0.25 0.4 YES
14 BAAT BAAT BAAT 824 0.24 0.42 YES
15 NUDT12 NUDT12 NUDT12 899 0.23 0.44 YES
16 NOS2 NOS2 NOS2 923 0.23 0.46 YES
17 CAT CAT CAT 991 0.22 0.47 YES
18 DHRS4 DHRS4 DHRS4 1275 0.18 0.47 YES
19 PHYH PHYH PHYH 1364 0.18 0.48 YES
20 ACOX1 ACOX1 ACOX1 1382 0.17 0.5 YES
21 MLYCD MLYCD MLYCD 1545 0.16 0.5 YES
22 HACL1 HACL1 HACL1 1602 0.16 0.52 YES
23 MPV17L MPV17L MPV17L 1676 0.15 0.52 YES
24 PECR PECR PECR 1816 0.14 0.53 YES
25 HMGCL HMGCL HMGCL 1952 0.13 0.53 YES
26 PECI PECI PECI 2114 0.12 0.54 YES
27 DDO DDO DDO 2115 0.12 0.55 YES
28 ACAA1 ACAA1 ACAA1 2133 0.12 0.56 YES
29 GSTK1 GSTK1 GSTK1 2156 0.12 0.56 YES
30 PEX1 PEX1 PEX1 2174 0.12 0.57 YES
31 PEX14 PEX14 PEX14 2289 0.12 0.58 YES
32 PEX7 PEX7 PEX7 2387 0.11 0.58 YES
33 PAOX PAOX PAOX 2392 0.11 0.59 YES
34 PXMP4 PXMP4 PXMP4 2551 0.1 0.59 YES
35 CRAT CRAT CRAT 2874 0.09 0.58 YES
36 SOD1 SOD1 SOD1 2920 0.089 0.59 YES
37 PEX3 PEX3 PEX3 2960 0.088 0.59 YES
38 ACOX3 ACOX3 ACOX3 2985 0.087 0.6 YES
39 SLC25A17 SLC25A17 SLC25A17 3041 0.085 0.6 YES
40 HSD17B4 HSD17B4 HSD17B4 3057 0.084 0.61 YES
41 PEX12 PEX12 PEX12 3070 0.083 0.62 YES
42 PEX16 PEX16 PEX16 3115 0.082 0.62 YES
43 CROT CROT CROT 3138 0.081 0.63 YES
44 PEX19 PEX19 PEX19 3141 0.08 0.64 YES
45 ACOT8 ACOT8 ACOT8 3717 0.063 0.61 NO
46 IDH1 IDH1 IDH1 3873 0.058 0.6 NO
47 ECH1 ECH1 ECH1 3896 0.057 0.61 NO
48 ABCD4 ABCD4 ABCD4 3977 0.055 0.61 NO
49 DECR2 DECR2 DECR2 4002 0.054 0.61 NO
50 PEX6 PEX6 PEX6 4119 0.052 0.61 NO
51 PEX13 PEX13 PEX13 4237 0.049 0.61 NO
52 ABCD3 ABCD3 ABCD3 4587 0.042 0.59 NO
53 PRDX5 PRDX5 PRDX5 5113 0.031 0.56 NO
54 PEX10 PEX10 PEX10 5182 0.03 0.56 NO
55 SOD2 SOD2 SOD2 5402 0.025 0.55 NO
56 ACSL5 ACSL5 ACSL5 5664 0.021 0.54 NO
57 PEX26 PEX26 PEX26 5688 0.021 0.54 NO
58 IDH2 IDH2 IDH2 5757 0.02 0.54 NO
59 PMVK PMVK PMVK 5874 0.018 0.53 NO
60 PRDX1 PRDX1 PRDX1 5970 0.016 0.53 NO
61 AMACR AMACR AMACR 6044 0.015 0.53 NO
62 MVK MVK MVK 6944 0.0013 0.48 NO
63 PEX5 PEX5 PEX5 7353 -0.0045 0.45 NO
64 PEX11A PEX11A PEX11A 7469 -0.0064 0.45 NO
65 NUDT19 NUDT19 NUDT19 7927 -0.013 0.42 NO
66 PEX11B PEX11B PEX11B 8755 -0.025 0.38 NO
67 PEX2 PEX2 PEX2 10033 -0.043 0.31 NO
68 AGPS AGPS AGPS 11463 -0.067 0.24 NO
69 FAR1 FAR1 FAR1 14034 -0.13 0.1 NO
70 ABCD1 ABCD1 ABCD1 14063 -0.13 0.11 NO
71 ACSL6 ACSL6 ACSL6 14264 -0.14 0.11 NO
72 GNPAT GNPAT GNPAT 14323 -0.14 0.12 NO
73 ACSL3 ACSL3 ACSL3 14440 -0.14 0.13 NO
74 MPV17 MPV17 MPV17 14758 -0.16 0.12 NO
75 ABCD2 ABCD2 ABCD2 14781 -0.16 0.14 NO
76 FAR2 FAR2 FAR2 15110 -0.17 0.13 NO
77 ACSL4 ACSL4 ACSL4 15355 -0.18 0.13 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 FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

Table 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 TAT TAT TAT 29 0.62 0.1 YES
2 SDS SDS SDS 34 0.62 0.21 YES
3 DNMT3L DNMT3L DNMT3L 54 0.57 0.31 YES
4 BHMT BHMT BHMT 110 0.49 0.39 YES
5 CTH CTH CTH 344 0.36 0.44 YES
6 CBS CBS CBS 568 0.29 0.47 YES
7 CDO1 CDO1 CDO1 615 0.28 0.52 YES
8 MAT1A MAT1A MAT1A 1070 0.21 0.53 YES
9 LDHAL6B LDHAL6B LDHAL6B 1489 0.16 0.53 YES
10 ADI1 ADI1 ADI1 1805 0.14 0.54 YES
11 GOT2 GOT2 GOT2 2004 0.13 0.55 YES
12 GOT1 GOT1 GOT1 2007 0.13 0.57 YES
13 AHCYL2 AHCYL2 AHCYL2 2853 0.091 0.54 NO
14 MAT2B MAT2B MAT2B 3838 0.059 0.49 NO
15 MPST MPST MPST 4519 0.043 0.46 NO
16 AHCY AHCY AHCY 4856 0.036 0.45 NO
17 MAT2A MAT2A MAT2A 5097 0.031 0.44 NO
18 MTAP MTAP MTAP 5943 0.016 0.4 NO
19 AHCYL1 AHCYL1 AHCYL1 6179 0.013 0.39 NO
20 LDHA LDHA LDHA 7802 -0.011 0.3 NO
21 LDHAL6A LDHAL6A LDHAL6A 9550 -0.036 0.2 NO
22 DNMT1 DNMT1 DNMT1 9612 -0.037 0.21 NO
23 APIP APIP APIP 10459 -0.049 0.17 NO
24 ENOPH1 ENOPH1 ENOPH1 10628 -0.052 0.17 NO
25 TRDMT1 TRDMT1 TRDMT1 11598 -0.07 0.12 NO
26 AMD1 AMD1 AMD1 11675 -0.071 0.13 NO
27 SRM SRM SRM 11779 -0.073 0.14 NO
28 SMS SMS SMS 12158 -0.081 0.13 NO
29 LDHB LDHB LDHB 13706 -0.12 0.064 NO
30 MTR MTR MTR 14136 -0.13 0.063 NO
31 DNMT3B DNMT3B DNMT3B 15367 -0.18 0.024 NO
32 DNMT3A DNMT3A DNMT3A 16547 -0.26 0.0022 NO
33 IL4I1 IL4I1 IL4I1 17380 -0.38 0.02 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 STEROID HORMONE BIOSYNTHESIS.

Figure S30.  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 ALANINE ASPARTATE AND GLUTAMATE 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 CYP2A7 CYP2A7 CYP2A7 1 1.1 0.095 YES
2 CYP2A13 CYP2A13 CYP2A13 2 0.87 0.17 YES
3 CYP2A6 CYP2A6 CYP2A6 6 0.82 0.24 YES
4 XDH XDH XDH 38 0.6 0.3 YES
5 CDA CDA CDA 100 0.5 0.34 YES
6 UPP2 UPP2 UPP2 121 0.48 0.38 YES
7 NAT2 NAT2 NAT2 179 0.43 0.41 YES
8 UGT2B10 UGT2B10 UGT2B10 249 0.39 0.44 YES
9 UGT2B7 UGT2B7 UGT2B7 254 0.39 0.48 YES
10 UPB1 UPB1 UPB1 315 0.37 0.51 YES
11 UGT2B15 UGT2B15 UGT2B15 376 0.34 0.54 YES
12 DPYS DPYS DPYS 422 0.33 0.56 YES
13 NAT1 NAT1 NAT1 563 0.29 0.58 YES
14 CES7 CES7 CES7 593 0.29 0.6 YES
15 UGT1A3 UGT1A3 UGT1A3 793 0.25 0.61 YES
16 CES2 CES2 CES2 803 0.24 0.64 YES
17 UGT2B28 UGT2B28 UGT2B28 850 0.24 0.65 YES
18 DPYD DPYD DPYD 905 0.23 0.67 YES
19 UGT2A1 UGT2A1 UGT2A1 950 0.22 0.69 YES
20 CYP3A43 CYP3A43 CYP3A43 966 0.22 0.71 YES
21 CYP3A5 CYP3A5 CYP3A5 1088 0.2 0.72 YES
22 CYP3A7 CYP3A7 CYP3A7 1165 0.19 0.73 YES
23 UGT1A9 UGT1A9 UGT1A9 1328 0.18 0.74 YES
24 UGT1A4 UGT1A4 UGT1A4 1528 0.16 0.74 YES
25 UGT2B4 UGT2B4 UGT2B4 1628 0.15 0.75 YES
26 CES1 CES1 CES1 1759 0.14 0.76 YES
27 UGT1A5 UGT1A5 UGT1A5 1834 0.14 0.76 YES
28 GUSB GUSB GUSB 2652 0.1 0.73 NO
29 TPMT TPMT TPMT 3123 0.081 0.71 NO
30 HPRT1 HPRT1 HPRT1 3261 0.076 0.7 NO
31 TYMP TYMP TYMP 3379 0.072 0.7 NO
32 UGT1A1 UGT1A1 UGT1A1 3874 0.058 0.68 NO
33 TK2 TK2 TK2 3915 0.057 0.68 NO
34 UGT1A8 UGT1A8 UGT1A8 4805 0.037 0.64 NO
35 UGT1A6 UGT1A6 UGT1A6 5275 0.028 0.61 NO
36 UGT1A7 UGT1A7 UGT1A7 5450 0.024 0.61 NO
37 UCK1 UCK1 UCK1 6471 0.0083 0.55 NO
38 UCKL1 UCKL1 UCKL1 6955 0.0011 0.52 NO
39 UPP1 UPP1 UPP1 7157 -0.0018 0.51 NO
40 UMPS UMPS UMPS 7354 -0.0045 0.5 NO
41 UGT2A3 UGT2A3 UGT2A3 7796 -0.011 0.48 NO
42 GMPS GMPS GMPS 10669 -0.053 0.32 NO
43 UGT2B11 UGT2B11 UGT2B11 11592 -0.07 0.27 NO
44 TK1 TK1 TK1 11686 -0.072 0.27 NO
45 UGT1A10 UGT1A10 UGT1A10 12920 -0.098 0.21 NO
46 IMPDH2 IMPDH2 IMPDH2 13043 -0.1 0.22 NO
47 ITPA ITPA ITPA 13531 -0.11 0.2 NO
48 UCK2 UCK2 UCK2 14192 -0.13 0.17 NO
49 IMPDH1 IMPDH1 IMPDH1 17067 -0.32 0.037 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S32.  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 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 PCK1 PCK1 PCK1 219 0.41 0.13 YES
2 OGDHL OGDHL OGDHL 410 0.33 0.24 YES
3 PCK2 PCK2 PCK2 484 0.31 0.35 YES
4 ACO1 ACO1 ACO1 1331 0.18 0.37 YES
5 SUCLG2 SUCLG2 SUCLG2 1865 0.14 0.39 YES
6 SDHD SDHD SDHD 2056 0.13 0.42 YES
7 PC PC PC 2328 0.11 0.45 YES
8 SDHB SDHB SDHB 2330 0.11 0.49 YES
9 SUCLG1 SUCLG1 SUCLG1 2518 0.1 0.52 YES
10 FH FH FH 2648 0.1 0.54 YES
11 OGDH OGDH OGDH 3448 0.07 0.52 YES
12 SDHA SDHA SDHA 3489 0.069 0.55 YES
13 IDH1 IDH1 IDH1 3873 0.058 0.55 YES
14 ACO2 ACO2 ACO2 3982 0.055 0.56 YES
15 MDH1 MDH1 MDH1 4089 0.052 0.57 YES
16 DLD DLD DLD 4182 0.05 0.59 YES
17 IDH3A IDH3A IDH3A 4286 0.048 0.6 YES
18 DLST DLST DLST 4728 0.039 0.59 NO
19 PDHB PDHB PDHB 4843 0.036 0.59 NO
20 SDHC SDHC SDHC 5232 0.029 0.58 NO
21 IDH2 IDH2 IDH2 5757 0.02 0.56 NO
22 PDHA1 PDHA1 PDHA1 5883 0.017 0.56 NO
23 IDH3B IDH3B IDH3B 7235 -0.0028 0.48 NO
24 DLAT DLAT DLAT 8055 -0.015 0.44 NO
25 SUCLA2 SUCLA2 SUCLA2 8485 -0.02 0.42 NO
26 MDH2 MDH2 MDH2 8710 -0.024 0.42 NO
27 IDH3G IDH3G IDH3G 9692 -0.038 0.38 NO
28 ACLY ACLY ACLY 11501 -0.068 0.3 NO
29 CS CS CS 14366 -0.14 0.19 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 GLYCINE SERINE AND THREONINE METABOLISM.

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

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE 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 ALDH6A1 ALDH6A1 ALDH6A1 433 0.32 0.028 YES
2 ABAT ABAT ABAT 444 0.32 0.079 YES
3 EHHADH EHHADH EHHADH 518 0.3 0.12 YES
4 HMGCS2 HMGCS2 HMGCS2 584 0.29 0.17 YES
5 BCKDHB BCKDHB BCKDHB 834 0.24 0.19 YES
6 ACAA2 ACAA2 ACAA2 916 0.23 0.22 YES
7 MUT MUT MUT 965 0.22 0.26 YES
8 ACADM ACADM ACADM 1075 0.2 0.28 YES
9 ALDH7A1 ALDH7A1 ALDH7A1 1215 0.19 0.3 YES
10 ALDH2 ALDH2 ALDH2 1372 0.18 0.32 YES
11 IVD IVD IVD 1434 0.17 0.35 YES
12 DBT DBT DBT 1488 0.16 0.37 YES
13 ACAT1 ACAT1 ACAT1 1623 0.15 0.39 YES
14 ACAT2 ACAT2 ACAT2 1797 0.14 0.4 YES
15 MCEE MCEE MCEE 1812 0.14 0.42 YES
16 ACADSB ACADSB ACADSB 1889 0.14 0.44 YES
17 PCCA PCCA PCCA 1939 0.13 0.46 YES
18 ALDH9A1 ALDH9A1 ALDH9A1 1944 0.13 0.48 YES
19 HMGCL HMGCL HMGCL 1952 0.13 0.5 YES
20 HADH HADH HADH 2029 0.13 0.52 YES
21 ACAA1 ACAA1 ACAA1 2133 0.12 0.53 YES
22 ACADS ACADS ACADS 2183 0.12 0.55 YES
23 HMGCS1 HMGCS1 HMGCS1 2251 0.12 0.56 YES
24 PCCB PCCB PCCB 2299 0.12 0.58 YES
25 HSD17B10 HSD17B10 HSD17B10 2329 0.11 0.6 YES
26 HIBCH HIBCH HIBCH 2444 0.11 0.61 YES
27 MCCC1 MCCC1 MCCC1 2560 0.1 0.62 YES
28 ACAD8 ACAD8 ACAD8 2603 0.1 0.63 YES
29 BCKDHA BCKDHA BCKDHA 3035 0.085 0.62 YES
30 ALDH1B1 ALDH1B1 ALDH1B1 3156 0.08 0.63 YES
31 ECHS1 ECHS1 ECHS1 3249 0.077 0.64 YES
32 MCCC2 MCCC2 MCCC2 3336 0.074 0.64 YES
33 BCAT2 BCAT2 BCAT2 3857 0.058 0.62 NO
34 HADHB HADHB HADHB 4052 0.053 0.62 NO
35 DLD DLD DLD 4182 0.05 0.62 NO
36 HIBADH HIBADH HIBADH 4264 0.049 0.62 NO
37 HADHA HADHA HADHA 4376 0.046 0.62 NO
38 AUH AUH AUH 5003 0.032 0.6 NO
39 ALDH3A2 ALDH3A2 ALDH3A2 8173 -0.016 0.42 NO
40 AOX1 AOX1 AOX1 9394 -0.034 0.36 NO
41 OXCT2 OXCT2 OXCT2 15021 -0.17 0.063 NO
42 OXCT1 OXCT1 OXCT1 15345 -0.18 0.074 NO
43 IL4I1 IL4I1 IL4I1 17380 -0.38 0.02 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 CYSTEINE AND METHIONINE METABOLISM.

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

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

Table 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 GBA3 GBA3 GBA3 13 0.7 0.073 YES
2 GCK GCK GCK 14 0.66 0.14 YES
3 GYS2 GYS2 GYS2 21 0.65 0.21 YES
4 AMY2B AMY2B AMY2B 217 0.41 0.24 YES
5 AMY1A AMY1A AMY1A 237 0.4 0.29 YES
6 AMY2A AMY2A AMY2A 245 0.39 0.33 YES
7 UGT2B10 UGT2B10 UGT2B10 249 0.39 0.37 YES
8 UGT2B7 UGT2B7 UGT2B7 254 0.39 0.41 YES
9 UGT2B15 UGT2B15 UGT2B15 376 0.34 0.44 YES
10 G6PC G6PC G6PC 494 0.31 0.47 YES
11 AGL AGL AGL 643 0.27 0.49 YES
12 UGT1A3 UGT1A3 UGT1A3 793 0.25 0.5 YES
13 UGT2B28 UGT2B28 UGT2B28 850 0.24 0.53 YES
14 TREH TREH TREH 880 0.23 0.55 YES
15 UGT2A1 UGT2A1 UGT2A1 950 0.22 0.57 YES
16 PGM2 PGM2 PGM2 1096 0.2 0.58 YES
17 UGP2 UGP2 UGP2 1123 0.2 0.6 YES
18 PYGL PYGL PYGL 1158 0.2 0.62 YES
19 UGT1A9 UGT1A9 UGT1A9 1328 0.18 0.63 YES
20 UGT1A4 UGT1A4 UGT1A4 1528 0.16 0.64 YES
21 PGM1 PGM1 PGM1 1605 0.16 0.65 YES
22 UGT2B4 UGT2B4 UGT2B4 1628 0.15 0.66 YES
23 UGT1A5 UGT1A5 UGT1A5 1834 0.14 0.67 YES
24 GBE1 GBE1 GBE1 1852 0.14 0.68 YES
25 GANC GANC GANC 1943 0.13 0.69 YES
26 ENPP1 ENPP1 ENPP1 2278 0.12 0.68 NO
27 GUSB GUSB GUSB 2652 0.1 0.67 NO
28 G6PC2 G6PC2 G6PC2 2688 0.098 0.68 NO
29 GAA GAA GAA 3403 0.072 0.65 NO
30 UGT1A1 UGT1A1 UGT1A1 3874 0.058 0.63 NO
31 UGT1A8 UGT1A8 UGT1A8 4805 0.037 0.58 NO
32 UGT1A6 UGT1A6 UGT1A6 5275 0.028 0.56 NO
33 UGT1A7 UGT1A7 UGT1A7 5450 0.024 0.55 NO
34 GPI GPI GPI 6786 0.0036 0.47 NO
35 UGT2A3 UGT2A3 UGT2A3 7796 -0.011 0.42 NO
36 HK1 HK1 HK1 8036 -0.014 0.4 NO
37 UGDH UGDH UGDH 8922 -0.028 0.36 NO
38 ENPP3 ENPP3 ENPP3 10124 -0.044 0.3 NO
39 PYGB PYGB PYGB 11275 -0.064 0.24 NO
40 UGT2B11 UGT2B11 UGT2B11 11592 -0.07 0.23 NO
41 GYS1 GYS1 GYS1 11891 -0.075 0.22 NO
42 PYGM PYGM PYGM 12596 -0.09 0.19 NO
43 UGT1A10 UGT1A10 UGT1A10 12920 -0.098 0.18 NO
44 MGAM MGAM MGAM 13833 -0.12 0.14 NO
45 HK3 HK3 HK3 15164 -0.17 0.084 NO
46 PGM2L1 PGM2L1 PGM2L1 15657 -0.2 0.077 NO
47 HK2 HK2 HK2 17388 -0.38 0.019 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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 SDS SDS SDS 34 0.62 0.088 YES
2 DAO DAO DAO 94 0.51 0.16 YES
3 BHMT BHMT BHMT 110 0.49 0.23 YES
4 GNMT GNMT GNMT 194 0.42 0.29 YES
5 AGXT AGXT AGXT 276 0.38 0.34 YES
6 GLDC GLDC GLDC 278 0.38 0.39 YES
7 DMGDH DMGDH DMGDH 343 0.36 0.44 YES
8 CTH CTH CTH 344 0.36 0.49 YES
9 AGXT2 AGXT2 AGXT2 363 0.35 0.54 YES
10 SARDH SARDH SARDH 524 0.3 0.58 YES
11 PIPOX PIPOX PIPOX 530 0.3 0.62 YES
12 CBS CBS CBS 568 0.29 0.66 YES
13 SHMT1 SHMT1 SHMT1 634 0.28 0.7 YES
14 GLYCTK GLYCTK GLYCTK 786 0.25 0.73 YES
15 GATM GATM GATM 1301 0.18 0.72 YES
16 AOC2 AOC2 AOC2 1596 0.16 0.73 YES
17 SRR SRR SRR 1685 0.15 0.75 YES
18 PHGDH PHGDH PHGDH 1828 0.14 0.76 YES
19 GCAT GCAT GCAT 2214 0.12 0.76 YES
20 GAMT GAMT GAMT 2366 0.11 0.76 YES
21 ALAS2 ALAS2 ALAS2 2716 0.097 0.76 YES
22 MAOB MAOB MAOB 2736 0.096 0.77 YES
23 MAOA MAOA MAOA 3046 0.084 0.76 YES
24 AOC3 AOC3 AOC3 3118 0.082 0.77 YES
25 ALAS1 ALAS1 ALAS1 3562 0.067 0.76 NO
26 PSAT1 PSAT1 PSAT1 3602 0.066 0.76 NO
27 DLD DLD DLD 4182 0.05 0.74 NO
28 SHMT2 SHMT2 SHMT2 4941 0.034 0.7 NO
29 CHDH CHDH CHDH 6163 0.013 0.64 NO
30 PSPH PSPH PSPH 14022 -0.13 0.21 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 LYSINE DEGRADATION.

Figure S40.  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

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 G1 PATHWAY 27 genes.ES.table 0.34 0.96 0.51 1 1 0.22 0.13 0.19 1 0.8
BIOCARTA MPR PATHWAY 32 genes.ES.table 0.46 1.5 0.076 1 0.92 0.19 0.065 0.18 1 0.84
BIOCARTA INTEGRIN PATHWAY 37 genes.ES.table 0.25 0.98 0.46 1 1 0.081 0.083 0.074 1 0.79
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.31 1.1 0.39 1 1 0.4 0.33 0.27 1 0.77
KEGG INOSITOL PHOSPHATE METABOLISM 53 genes.ES.table 0.3 0.99 0.49 1 1 0.19 0.16 0.16 1 0.8
KEGG ETHER LIPID METABOLISM 26 genes.ES.table 0.44 1.2 0.23 1 1 0.35 0.15 0.29 1 0.72
KEGG SPHINGOLIPID METABOLISM 36 genes.ES.table 0.35 1.1 0.36 1 1 0.11 0.04 0.11 1 0.81
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 25 genes.ES.table 0.37 0.95 0.52 1 1 0.28 0.13 0.24 1 0.81
KEGG RIBOSOME 85 genes.ES.table 0.57 1.4 0.21 1 0.95 0.73 0.26 0.55 1 0.8
KEGG DNA REPLICATION 35 genes.ES.table 0.52 1.4 0.21 1 0.96 0.6 0.28 0.43 1 0.67
genes ES table in pathway: BIOCARTA G1 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 MYT1 MYT1 MYT1 87 0.54 0.14 YES
2 ACTA1 ACTA1 ACTA1 327 0.39 0.23 YES
3 CDK1 CDK1 CDK1 597 0.32 0.3 YES
4 CDC25C CDC25C CDC25C 878 0.27 0.35 YES
5 SRC SRC SRC 1102 0.24 0.4 YES
6 CCNB1 CCNB1 CCNB1 1154 0.23 0.46 YES
7 GNAS GNAS GNAS 2731 0.13 0.41 NO
8 PAQR5 PAQR5 PAQR5 4020 0.087 0.36 NO
9 ARPC3 ARPC3 ARPC3 5455 0.057 0.29 NO
10 PAQR7 PAQR7 PAQR7 6123 0.045 0.26 NO
11 MAPK1 MAPK1 MAPK1 6795 0.034 0.24 NO
12 ARPC1A ARPC1A ARPC1A 6907 0.032 0.24 NO
13 ARPC4 ARPC4 ARPC4 7143 0.028 0.23 NO
14 PIN1 PIN1 PIN1 7383 0.025 0.22 NO
15 ARPC2 ARPC2 ARPC2 7719 0.02 0.21 NO
16 PRKAR2B PRKAR2B PRKAR2B 8848 0.0035 0.15 NO
17 ACTR2 ACTR2 ACTR2 9134 -0.0012 0.13 NO
18 ACTR3 ACTR3 ACTR3 9203 -0.0022 0.13 NO
19 ARPC5 ARPC5 ARPC5 9251 -0.0029 0.13 NO
20 MAPK3 MAPK3 MAPK3 9334 -0.0044 0.12 NO
21 ARPC1B ARPC1B ARPC1B 9731 -0.011 0.1 NO
22 HRAS HRAS HRAS 9801 -0.012 0.1 NO
23 PRKAR1B PRKAR1B PRKAR1B 9997 -0.015 0.097 NO
24 PRKAR1A PRKAR1A PRKAR1A 11606 -0.043 0.018 NO
25 GNB1 GNB1 GNB1 12939 -0.071 -0.039 NO
26 CAP1 CAP1 CAP1 13823 -0.094 -0.064 NO
27 GNAI1 GNAI1 GNAI1 14036 -0.1 -0.049 NO
28 PGR PGR PGR 14693 -0.12 -0.054 NO
29 PRKACB PRKACB PRKACB 15897 -0.18 -0.073 NO
30 PRKAR2A PRKAR2A PRKAR2A 15937 -0.19 -0.026 NO
31 GNGT1 GNGT1 GNGT1 16287 -0.21 0.0099 NO
32 RPS6KA1 RPS6KA1 RPS6KA1 16864 -0.27 0.049 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 G1 PATHWAY.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA MPR PATHWAY

Table 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 RPL21 RPL21 RPL21 1135 0.24 -0.036 YES
2 RPL22L1 RPL22L1 RPL22L1 1349 0.21 -0.023 YES
3 RPL36A RPL36A RPL36A 1551 0.2 -0.011 YES
4 RPL9 RPL9 RPL9 1974 0.17 -0.015 YES
5 RPS24 RPS24 RPS24 1994 0.16 0.0036 YES
6 RPSA RPSA RPSA 2282 0.15 0.005 YES
7 RPS19 RPS19 RPS19 2307 0.15 0.021 YES
8 RPLP0 RPLP0 RPLP0 2528 0.14 0.025 YES
9 RPS21 RPS21 RPS21 2641 0.13 0.034 YES
10 RPS10 RPS10 RPS10 2678 0.13 0.048 YES
11 RPS18 RPS18 RPS18 2743 0.13 0.059 YES
12 RPS12 RPS12 RPS12 2750 0.13 0.074 YES
13 RPS3 RPS3 RPS3 2784 0.13 0.087 YES
14 RPL27A RPL27A RPL27A 2805 0.12 0.1 YES
15 RPS7 RPS7 RPS7 2834 0.12 0.11 YES
16 RPL18A RPL18A RPL18A 2870 0.12 0.13 YES
17 RPS17 RPS17 RPS17 2892 0.12 0.14 YES
18 RPL39 RPL39 RPL39 2918 0.12 0.15 YES
19 RPS27 RPS27 RPS27 2921 0.12 0.17 YES
20 RPL26 RPL26 RPL26 2930 0.12 0.18 YES
21 RPS15 RPS15 RPS15 2940 0.12 0.2 YES
22 RPS27A RPS27A RPS27A 2953 0.12 0.21 YES
23 RPS5 RPS5 RPS5 2973 0.12 0.22 YES
24 RPL7 RPL7 RPL7 3006 0.12 0.23 YES
25 RPL23A RPL23A RPL23A 3022 0.12 0.25 YES
26 RPL28 RPL28 RPL28 3061 0.12 0.26 YES
27 RPS29 RPS29 RPS29 3211 0.11 0.26 YES
28 RPL7A RPL7A RPL7A 3227 0.11 0.28 YES
29 RPL36 RPL36 RPL36 3262 0.11 0.29 YES
30 RPS4X RPS4X RPS4X 3271 0.11 0.3 YES
31 RPL37A RPL37A RPL37A 3309 0.11 0.31 YES
32 RPL17 RPL17 RPL17 3321 0.11 0.32 YES
33 RPL31 RPL31 RPL31 3380 0.11 0.33 YES
34 RPL32 RPL32 RPL32 3385 0.1 0.34 YES
35 RPL3 RPL3 RPL3 3446 0.1 0.35 YES
36 RPL6 RPL6 RPL6 3450 0.1 0.36 YES
37 RPLP2 RPLP2 RPLP2 3457 0.1 0.38 YES
38 RPL13A RPL13A RPL13A 3476 0.1 0.39 YES
39 RPL27 RPL27 RPL27 3605 0.098 0.39 YES
40 RPL14 RPL14 RPL14 3661 0.097 0.4 YES
41 RPL38 RPL38 RPL38 3691 0.096 0.41 YES
42 RPL10A RPL10A RPL10A 3695 0.096 0.42 YES
43 RPS16 RPS16 RPS16 3777 0.094 0.43 YES
44 RPL4 RPL4 RPL4 3786 0.094 0.44 YES
45 RPL35A RPL35A RPL35A 3794 0.093 0.45 YES
46 RPS11 RPS11 RPS11 3810 0.093 0.46 YES
47 RPS28 RPS28 RPS28 4052 0.087 0.46 YES
48 RPL35 RPL35 RPL35 4059 0.086 0.47 YES
49 RPS6 RPS6 RPS6 4095 0.086 0.48 YES
50 RPL8 RPL8 RPL8 4118 0.085 0.48 YES
51 RPL23 RPL23 RPL23 4192 0.083 0.49 YES
52 RPS25 RPS25 RPS25 4209 0.083 0.5 YES
53 RPS9 RPS9 RPS9 4287 0.081 0.5 YES
54 RPL37 RPL37 RPL37 4309 0.08 0.51 YES
55 RPS2 RPS2 RPS2 4358 0.079 0.52 YES
56 RPL41 RPL41 RPL41 4375 0.079 0.53 YES
57 RPS23 RPS23 RPS23 4376 0.079 0.54 YES
58 RPL30 RPL30 RPL30 4396 0.078 0.55 YES
59 RPS13 RPS13 RPS13 4480 0.076 0.55 YES
60 RPL24 RPL24 RPL24 4503 0.076 0.56 YES
61 RPL29 RPL29 RPL29 4526 0.075 0.57 YES
62 RPL12 RPL12 RPL12 4528 0.075 0.57 YES
63 RPLP1 RPLP1 RPLP1 4804 0.07 0.57 NO
64 RPL15 RPL15 RPL15 4832 0.069 0.57 NO
65 RPS20 RPS20 RPS20 5006 0.066 0.57 NO
66 RPL10 RPL10 RPL10 5269 0.06 0.56 NO
67 RPS3A RPS3A RPS3A 5281 0.06 0.57 NO
68 RPL5 RPL5 RPL5 5438 0.058 0.57 NO
69 UBA52 UBA52 UBA52 5468 0.057 0.57 NO
70 RPL19 RPL19 RPL19 5826 0.05 0.56 NO
71 RPL34 RPL34 RPL34 5869 0.05 0.56 NO
72 RPS8 RPS8 RPS8 6048 0.046 0.56 NO
73 RSL24D1 RSL24D1 RSL24D1 6068 0.046 0.56 NO
74 RPL13 RPL13 RPL13 6101 0.045 0.57 NO
75 RPS15A RPS15A RPS15A 6400 0.041 0.56 NO
76 RPS26 RPS26 RPS26 6757 0.035 0.54 NO
77 FAU FAU FAU 6788 0.034 0.54 NO
78 RPL11 RPL11 RPL11 7181 0.028 0.52 NO
79 RPL22 RPL22 RPL22 7420 0.025 0.51 NO
80 MRPL13 MRPL13 MRPL13 7818 0.019 0.49 NO
81 RPL36AL RPL36AL RPL36AL 8160 0.013 0.47 NO
82 RPS27L RPS27L RPS27L 9733 -0.011 0.39 NO
83 RPL26L1 RPL26L1 RPL26L1 13955 -0.098 0.16 NO
84 RPL10L RPL10L RPL10L 16136 -0.2 0.059 NO
85 RPS4Y1 RPS4Y1 RPS4Y1 16812 -0.26 0.052 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 MPR PATHWAY.

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

genes ES table in pathway: BIOCARTA INTEGRIN 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 TUBB8 TUBB8 TUBB8 262 0.42 0.058 YES
2 TUBB4Q TUBB4Q TUBB4Q 320 0.39 0.12 YES
3 TUBB1 TUBB1 TUBB1 342 0.39 0.19 YES
4 NCK2 NCK2 NCK2 382 0.38 0.25 YES
5 TUBA8 TUBA8 TUBA8 456 0.35 0.31 YES
6 TLR5 TLR5 TLR5 725 0.29 0.35 YES
7 ARHGEF2 ARHGEF2 ARHGEF2 849 0.27 0.39 YES
8 CLDN1 CLDN1 CLDN1 2273 0.15 0.34 NO
9 TUBB4 TUBB4 TUBB4 2712 0.13 0.33 NO
10 CDH1 CDH1 CDH1 3126 0.11 0.33 NO
11 ARPC5L ARPC5L ARPC5L 4304 0.08 0.28 NO
12 TUBB3 TUBB3 TUBB3 4419 0.078 0.28 NO
13 OCLN OCLN OCLN 5235 0.061 0.25 NO
14 ARPC3 ARPC3 ARPC3 5455 0.057 0.25 NO
15 YWHAZ YWHAZ YWHAZ 5548 0.055 0.25 NO
16 YWHAQ YWHAQ YWHAQ 5609 0.054 0.26 NO
17 ABL1 ABL1 ABL1 6388 0.041 0.22 NO
18 TUBB TUBB TUBB 6428 0.04 0.22 NO
19 ACTG1 ACTG1 ACTG1 6558 0.038 0.22 NO
20 NCL NCL NCL 6639 0.037 0.23 NO
21 ARPC1A ARPC1A ARPC1A 6907 0.032 0.22 NO
22 TUBA1B TUBA1B TUBA1B 6920 0.032 0.22 NO
23 TUBB6 TUBB6 TUBB6 7047 0.03 0.22 NO
24 ARPC4 ARPC4 ARPC4 7143 0.028 0.22 NO
25 ARPC2 ARPC2 ARPC2 7719 0.02 0.19 NO
26 KRT18 KRT18 KRT18 8199 0.013 0.17 NO
27 TUBB2A TUBB2A TUBB2A 8226 0.012 0.17 NO
28 TUBB2C TUBB2C TUBB2C 8254 0.012 0.17 NO
29 ITGB1 ITGB1 ITGB1 8319 0.011 0.16 NO
30 TUBA1C TUBA1C TUBA1C 8513 0.0084 0.16 NO
31 EZR EZR EZR 8549 0.008 0.16 NO
32 TUBA1A TUBA1A TUBA1A 9007 0.0013 0.13 NO
33 TUBB2B TUBB2B TUBB2B 9045 0.00053 0.13 NO
34 ARPC5 ARPC5 ARPC5 9251 -0.0029 0.12 NO
35 ARPC1B ARPC1B ARPC1B 9731 -0.011 0.091 NO
36 CTTN CTTN CTTN 9781 -0.012 0.09 NO
37 CTNNB1 CTNNB1 CTNNB1 9917 -0.014 0.085 NO
38 PRKCA PRKCA PRKCA 10055 -0.016 0.08 NO
39 ACTB ACTB ACTB 10249 -0.02 0.073 NO
40 WASL WASL WASL 10408 -0.022 0.068 NO
41 ROCK1 ROCK1 ROCK1 11098 -0.034 0.035 NO
42 RHOA RHOA RHOA 11212 -0.036 0.035 NO
43 TUBA4A TUBA4A TUBA4A 11915 -0.049 0.0035 NO
44 WAS WAS WAS 12319 -0.058 -0.0092 NO
45 HCLS1 HCLS1 HCLS1 12397 -0.059 -0.0032 NO
46 TUBA3E TUBA3E TUBA3E 12440 -0.06 0.005 NO
47 TUBA3D TUBA3D TUBA3D 12747 -0.067 -0.00053 NO
48 CDC42 CDC42 CDC42 12940 -0.071 0.0011 NO
49 ROCK2 ROCK2 ROCK2 13246 -0.079 -0.0024 NO
50 NCK1 NCK1 NCK1 13809 -0.093 -0.018 NO
51 FYN FYN FYN 15153 -0.14 -0.069 NO
52 CD14 CD14 CD14 15680 -0.17 -0.069 NO
53 TUBAL3 TUBAL3 TUBAL3 15882 -0.18 -0.048 NO
54 TLR4 TLR4 TLR4 16615 -0.24 -0.047 NO
55 TUBA3C TUBA3C TUBA3C 17016 -0.29 -0.018 NO
56 LY96 LY96 LY96 17249 -0.33 0.027 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 INTEGRIN PATHWAY.

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

genes ES table in pathway: BIOCARTA WNT 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 POLE2 POLE2 POLE2 596 0.32 0.071 YES
2 DNA2 DNA2 DNA2 784 0.28 0.15 YES
3 LIG1 LIG1 LIG1 2090 0.16 0.13 YES
4 RFC4 RFC4 RFC4 2741 0.13 0.14 YES
5 MCM2 MCM2 MCM2 2863 0.12 0.17 YES
6 PRIM2 PRIM2 PRIM2 3103 0.12 0.2 YES
7 POLD1 POLD1 POLD1 3129 0.11 0.23 YES
8 PRIM1 PRIM1 PRIM1 3192 0.11 0.27 YES
9 FEN1 FEN1 FEN1 3393 0.1 0.29 YES
10 MCM5 MCM5 MCM5 3481 0.1 0.32 YES
11 MCM4 MCM4 MCM4 3628 0.098 0.34 YES
12 RNASEH2C RNASEH2C RNASEH2C 3705 0.096 0.37 YES
13 MCM3 MCM3 MCM3 3747 0.095 0.4 YES
14 RNASEH2B RNASEH2B RNASEH2B 4322 0.08 0.39 YES
15 MCM6 MCM6 MCM6 4339 0.08 0.42 YES
16 MCM7 MCM7 MCM7 4539 0.075 0.43 YES
17 POLD3 POLD3 POLD3 4817 0.069 0.44 YES
18 RNASEH2A RNASEH2A RNASEH2A 4820 0.069 0.46 YES
19 RFC2 RFC2 RFC2 4829 0.069 0.48 YES
20 RFC5 RFC5 RFC5 4913 0.067 0.5 YES
21 RFC1 RFC1 RFC1 5016 0.065 0.52 YES
22 RPA1 RPA1 RPA1 5719 0.052 0.5 NO
23 POLA2 POLA2 POLA2 6402 0.041 0.47 NO
24 POLE POLE POLE 6597 0.038 0.47 NO
25 RFC3 RFC3 RFC3 7222 0.027 0.44 NO
26 PCNA PCNA PCNA 8450 0.0091 0.38 NO
27 SSBP1 SSBP1 SSBP1 8517 0.0084 0.38 NO
28 POLE3 POLE3 POLE3 8970 0.0018 0.35 NO
29 RNASEH1 RNASEH1 RNASEH1 9847 -0.013 0.31 NO
30 POLD2 POLD2 POLD2 10622 -0.026 0.27 NO
31 POLD4 POLD4 POLD4 12254 -0.056 0.2 NO
32 RPA3 RPA3 RPA3 13092 -0.074 0.18 NO
33 RPA2 RPA2 RPA2 13282 -0.08 0.19 NO
34 RPA4 RPA4 RPA4 13563 -0.086 0.2 NO
35 POLE4 POLE4 POLE4 13834 -0.094 0.22 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 WNT PATHWAY.

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

genes ES table in pathway: KEGG INOSITOL PHOSPHATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ATP1B2 ATP1B2 ATP1B2 34 0.63 0.086 YES
2 TNNT2 TNNT2 TNNT2 51 0.6 0.17 YES
3 CACNA2D2 CACNA2D2 CACNA2D2 59 0.57 0.25 YES
4 FXYD2 FXYD2 FXYD2 91 0.54 0.32 YES
5 TNNC1 TNNC1 TNNC1 190 0.45 0.38 YES
6 CACNG4 CACNG4 CACNG4 304 0.4 0.43 YES
7 CACNA1D CACNA1D CACNA1D 576 0.32 0.46 YES
8 TNNI3 TNNI3 TNNI3 1488 0.2 0.43 NO
9 CACNB3 CACNB3 CACNB3 2040 0.16 0.42 NO
10 CACNA1F CACNA1F CACNA1F 2285 0.15 0.43 NO
11 CACNB2 CACNB2 CACNB2 2580 0.13 0.43 NO
12 CACNG1 CACNG1 CACNG1 2684 0.13 0.44 NO
13 CACNB1 CACNB1 CACNB1 3374 0.11 0.42 NO
14 MYL3 MYL3 MYL3 3965 0.089 0.4 NO
15 CACNB4 CACNB4 CACNB4 4166 0.084 0.4 NO
16 TPM4 TPM4 TPM4 4359 0.079 0.4 NO
17 COX6B1 COX6B1 COX6B1 5334 0.059 0.35 NO
18 ATP1B1 ATP1B1 ATP1B1 5833 0.05 0.33 NO
19 COX7A2L COX7A2L COX7A2L 5839 0.05 0.34 NO
20 TPM3 TPM3 TPM3 5988 0.047 0.34 NO
21 ATP1A1 ATP1A1 ATP1A1 6216 0.044 0.33 NO
22 COX4I2 COX4I2 COX4I2 6493 0.039 0.32 NO
23 TPM1 TPM1 TPM1 6541 0.039 0.32 NO
24 TPM2 TPM2 TPM2 6631 0.037 0.32 NO
25 CACNA1C CACNA1C CACNA1C 7509 0.023 0.28 NO
26 UQCR11 UQCR11 UQCR11 7869 0.018 0.26 NO
27 COX5A COX5A COX5A 7875 0.018 0.26 NO
28 UQCRB UQCRB UQCRB 7940 0.017 0.26 NO
29 UQCRFS1 UQCRFS1 UQCRFS1 8098 0.014 0.25 NO
30 UQCR10 UQCR10 UQCR10 8483 0.0087 0.23 NO
31 ATP2A2 ATP2A2 ATP2A2 8528 0.0082 0.23 NO
32 COX5B COX5B COX5B 8929 0.0024 0.21 NO
33 ATP1A4 ATP1A4 ATP1A4 9038 0.00061 0.2 NO
34 COX8A COX8A COX8A 9075 -0.000091 0.2 NO
35 COX6A1 COX6A1 COX6A1 9379 -0.0052 0.18 NO
36 COX6C COX6C COX6C 9385 -0.0053 0.18 NO
37 UQCRHL UQCRHL UQCRHL 9512 -0.0072 0.18 NO
38 COX7A2 COX7A2 COX7A2 9667 -0.0096 0.17 NO
39 CYC1 CYC1 CYC1 9949 -0.014 0.16 NO
40 COX7C COX7C COX7C 10084 -0.017 0.15 NO
41 CACNA1S CACNA1S CACNA1S 10107 -0.017 0.15 NO
42 UQCRH UQCRH UQCRH 10331 -0.021 0.14 NO
43 COX7A1 COX7A1 COX7A1 10986 -0.032 0.11 NO
44 CACNA2D4 CACNA2D4 CACNA2D4 11070 -0.033 0.11 NO
45 COX7B COX7B COX7B 11567 -0.042 0.087 NO
46 RYR2 RYR2 RYR2 11872 -0.048 0.077 NO
47 CACNA2D3 CACNA2D3 CACNA2D3 12022 -0.051 0.075 NO
48 CACNA2D1 CACNA2D1 CACNA2D1 12336 -0.058 0.066 NO
49 ATP1B3 ATP1B3 ATP1B3 12369 -0.059 0.072 NO
50 COX4I1 COX4I1 COX4I1 12512 -0.062 0.072 NO
51 SLC9A1 SLC9A1 SLC9A1 12665 -0.065 0.073 NO
52 COX6B2 COX6B2 COX6B2 12749 -0.067 0.078 NO
53 ATP1A2 ATP1A2 ATP1A2 12914 -0.07 0.078 NO
54 UQCRC1 UQCRC1 UQCRC1 13121 -0.075 0.077 NO
55 ATP1A3 ATP1A3 ATP1A3 13272 -0.079 0.079 NO
56 UQCRQ UQCRQ UQCRQ 14472 -0.12 0.028 NO
57 ACTC1 ACTC1 ACTC1 14559 -0.12 0.039 NO
58 SLC9A6 SLC9A6 SLC9A6 14882 -0.13 0.039 NO
59 SLC8A1 SLC8A1 SLC8A1 16520 -0.23 -0.021 NO
60 COX6A2 COX6A2 COX6A2 16863 -0.27 -0.0031 NO
61 COX7B2 COX7B2 COX7B2 17385 -0.37 0.019 NO

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

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

genes ES table in pathway: KEGG ETHER LIPID METABOLISM

Table S26.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SNRPA1 SNRPA1 SNRPA1 2271 0.15 -0.11 YES
2 SNRPE SNRPE SNRPE 2438 0.14 -0.093 YES
3 SF3A2 SF3A2 SF3A2 2510 0.14 -0.075 YES
4 THOC1 THOC1 THOC1 2687 0.13 -0.065 YES
5 SNRPD1 SNRPD1 SNRPD1 2749 0.13 -0.048 YES
6 HSPA1L HSPA1L HSPA1L 2846 0.12 -0.034 YES
7 LSM7 LSM7 LSM7 2859 0.12 -0.016 YES
8 SNRPF SNRPF SNRPF 3002 0.12 -0.0051 YES
9 LSM2 LSM2 LSM2 3379 0.11 -0.0098 YES
10 THOC4 THOC4 THOC4 3422 0.1 0.0042 YES
11 SNRPB SNRPB SNRPB 3539 0.1 0.013 YES
12 SR140 SR140 SR140 3633 0.098 0.024 YES
13 HNRNPA1 HNRNPA1 HNRNPA1 3667 0.097 0.037 YES
14 TCERG1 TCERG1 TCERG1 3684 0.096 0.051 YES
15 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 3697 0.096 0.066 YES
16 USP39 USP39 USP39 3962 0.089 0.065 YES
17 NHP2L1 NHP2L1 NHP2L1 4065 0.086 0.073 YES
18 SNRPG SNRPG SNRPG 4163 0.084 0.08 YES
19 PRPF3 PRPF3 PRPF3 4417 0.078 0.078 YES
20 U2AF1 U2AF1 U2AF1 4420 0.078 0.09 YES
21 ACIN1 ACIN1 ACIN1 4454 0.077 0.1 YES
22 RBM8A RBM8A RBM8A 4458 0.077 0.11 YES
23 PQBP1 PQBP1 PQBP1 4562 0.075 0.12 YES
24 SNRPA SNRPA SNRPA 4825 0.069 0.12 YES
25 SNRNP70 SNRNP70 SNRNP70 4872 0.068 0.12 YES
26 SNRPD3 SNRPD3 SNRPD3 4894 0.068 0.13 YES
27 RBMX RBMX RBMX 4898 0.068 0.14 YES
28 SFRS9 SFRS9 SFRS9 4899 0.068 0.15 YES
29 SF3B4 SF3B4 SF3B4 4907 0.067 0.16 YES
30 HNRNPA3 HNRNPA3 HNRNPA3 5058 0.064 0.16 YES
31 PHF5A PHF5A PHF5A 5253 0.061 0.16 YES
32 PRPF6 PRPF6 PRPF6 5256 0.061 0.17 YES
33 SFRS3 SFRS3 SFRS3 5270 0.06 0.18 YES
34 PPIL1 PPIL1 PPIL1 5274 0.06 0.19 YES
35 RBM17 RBM17 RBM17 5336 0.059 0.2 YES
36 SFRS6 SFRS6 SFRS6 5347 0.059 0.21 YES
37 SNRPD2 SNRPD2 SNRPD2 5373 0.059 0.21 YES
38 HNRNPU HNRNPU HNRNPU 5472 0.057 0.22 YES
39 MAGOHB MAGOHB MAGOHB 5623 0.054 0.22 YES
40 SFRS7 SFRS7 SFRS7 5701 0.052 0.22 YES
41 CCDC12 CCDC12 CCDC12 5789 0.051 0.22 YES
42 LSM4 LSM4 LSM4 5903 0.049 0.22 YES
43 SNRPB2 SNRPB2 SNRPB2 5910 0.049 0.23 YES
44 SMNDC1 SMNDC1 SMNDC1 6063 0.046 0.23 YES
45 HSPA2 HSPA2 HSPA2 6065 0.046 0.24 YES
46 RBM25 RBM25 RBM25 6147 0.045 0.24 YES
47 U2AF2 U2AF2 U2AF2 6168 0.044 0.25 YES
48 CRNKL1 CRNKL1 CRNKL1 6261 0.043 0.25 YES
49 WBP11 WBP11 WBP11 6338 0.042 0.25 YES
50 SNRPC SNRPC SNRPC 6363 0.041 0.26 YES
51 DDX42 DDX42 DDX42 6412 0.041 0.26 YES
52 XAB2 XAB2 XAB2 6419 0.04 0.27 YES
53 HNRNPC HNRNPC HNRNPC 6420 0.04 0.27 YES
54 CWC15 CWC15 CWC15 6443 0.04 0.28 YES
55 PRPF40B PRPF40B PRPF40B 6508 0.039 0.28 YES
56 TXNL4A TXNL4A TXNL4A 6509 0.039 0.29 YES
57 THOC3 THOC3 THOC3 6577 0.038 0.29 YES
58 BAT1 BAT1 BAT1 6589 0.038 0.29 YES
59 TRA2B TRA2B TRA2B 6616 0.037 0.3 YES
60 SFRS2 SFRS2 SFRS2 6660 0.036 0.3 YES
61 NAA38 NAA38 NAA38 6670 0.036 0.31 YES
62 TRA2A TRA2A TRA2A 6672 0.036 0.31 YES
63 SNW1 SNW1 SNW1 6714 0.035 0.32 YES
64 DDX46 DDX46 DDX46 6746 0.035 0.32 YES
65 HNRNPM HNRNPM HNRNPM 6791 0.034 0.32 YES
66 PRPF31 PRPF31 PRPF31 6845 0.033 0.32 YES
67 SF3B14 SF3B14 SF3B14 6918 0.032 0.32 YES
68 SFRS1 SFRS1 SFRS1 7019 0.03 0.32 NO
69 LSM3 LSM3 LSM3 7152 0.028 0.32 NO
70 THOC2 THOC2 THOC2 7419 0.025 0.31 NO
71 ISY1 ISY1 ISY1 7644 0.021 0.3 NO
72 PRPF40A PRPF40A PRPF40A 7664 0.021 0.3 NO
73 CHERP CHERP CHERP 7739 0.02 0.3 NO
74 SF3B5 SF3B5 SF3B5 7779 0.019 0.3 NO
75 DHX15 DHX15 DHX15 7780 0.019 0.3 NO
76 SF3B1 SF3B1 SF3B1 7817 0.019 0.31 NO
77 SART1 SART1 SART1 8013 0.015 0.3 NO
78 PRPF8 PRPF8 PRPF8 8071 0.015 0.3 NO
79 PUF60 PUF60 PUF60 8167 0.013 0.29 NO
80 EFTUD2 EFTUD2 EFTUD2 8260 0.012 0.29 NO
81 EIF4A3 EIF4A3 EIF4A3 8357 0.01 0.29 NO
82 BUD31 BUD31 BUD31 8378 0.01 0.29 NO
83 RBM22 RBM22 RBM22 8410 0.0096 0.29 NO
84 HSPA6 HSPA6 HSPA6 8449 0.0091 0.29 NO
85 DDX23 DDX23 DDX23 8539 0.0081 0.28 NO
86 PRPF38B PRPF38B PRPF38B 8631 0.0067 0.28 NO
87 SFRS5 SFRS5 SFRS5 8641 0.0065 0.28 NO
88 DHX16 DHX16 DHX16 8686 0.0059 0.28 NO
89 PRPF18 PRPF18 PRPF18 8704 0.0057 0.28 NO
90 PRPF4 PRPF4 PRPF4 8835 0.0038 0.27 NO
91 SF3B2 SF3B2 SF3B2 8905 0.0027 0.27 NO
92 PRPF19 PRPF19 PRPF19 8907 0.0027 0.27 NO
93 CTNNBL1 CTNNBL1 CTNNBL1 8915 0.0026 0.27 NO
94 LSM6 LSM6 LSM6 9109 -0.00064 0.26 NO
95 HNRNPK HNRNPK HNRNPK 9199 -0.0021 0.25 NO
96 PCBP1 PCBP1 PCBP1 9217 -0.0024 0.25 NO
97 SNRNP200 SNRNP200 SNRNP200 9324 -0.0042 0.24 NO
98 SNRNP40 SNRNP40 SNRNP40 9631 -0.0091 0.23 NO
99 SFRS13A SFRS13A SFRS13A 9965 -0.015 0.21 NO
100 HSPA8 HSPA8 HSPA8 10033 -0.016 0.21 NO
101 CDC5L CDC5L CDC5L 10046 -0.016 0.21 NO
102 NCBP1 NCBP1 NCBP1 10173 -0.018 0.21 NO
103 SF3A1 SF3A1 SF3A1 10438 -0.023 0.2 NO
104 DHX8 DHX8 DHX8 11174 -0.035 0.16 NO
105 PPIE PPIE PPIE 11280 -0.037 0.16 NO
106 DDX5 DDX5 DDX5 11307 -0.037 0.17 NO
107 SNRNP27 SNRNP27 SNRNP27 11400 -0.039 0.17 NO
108 AQR AQR AQR 11432 -0.04 0.17 NO
109 PRPF38A PRPF38A PRPF38A 11579 -0.042 0.17 NO
110 CDC40 CDC40 CDC40 11731 -0.045 0.17 NO
111 SLU7 SLU7 SLU7 11785 -0.046 0.17 NO
112 SF3B3 SF3B3 SF3B3 11832 -0.047 0.18 NO
113 SFRS4 SFRS4 SFRS4 11877 -0.048 0.18 NO
114 PPIH PPIH PPIH 11933 -0.049 0.19 NO
115 HSPA1A HSPA1A HSPA1A 11974 -0.05 0.19 NO
116 MAGOH MAGOH MAGOH 11985 -0.05 0.2 NO
117 ZMAT2 ZMAT2 ZMAT2 12115 -0.053 0.2 NO
118 LSM5 LSM5 LSM5 12330 -0.058 0.2 NO
119 SF3A3 SF3A3 SF3A3 12354 -0.058 0.2 NO
120 SYF2 SYF2 SYF2 12928 -0.071 0.18 NO
121 DHX38 DHX38 DHX38 13124 -0.076 0.18 NO
122 BCAS2 BCAS2 BCAS2 13626 -0.088 0.17 NO
123 PLRG1 PLRG1 PLRG1 13769 -0.092 0.18 NO
124 HSPA1B HSPA1B HSPA1B 15331 -0.15 0.11 NO
125 SFRS2B SFRS2B SFRS2B 15405 -0.15 0.13 NO

Figure S51.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ETHER LIPID METABOLISM.

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

genes ES table in pathway: KEGG SPHINGOLIPID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DTX1 DTX1 DTX1 519 0.34 0.06 YES
2 DTX3 DTX3 DTX3 621 0.31 0.14 YES
3 LFNG LFNG LFNG 1086 0.24 0.18 YES
4 CTBP2 CTBP2 CTBP2 1420 0.21 0.21 YES
5 DLL3 DLL3 DLL3 1764 0.18 0.24 YES
6 NOTCH1 NOTCH1 NOTCH1 2015 0.16 0.27 YES
7 DTX4 DTX4 DTX4 2126 0.16 0.3 YES
8 DVL2 DVL2 DVL2 2280 0.15 0.33 YES
9 KAT2A KAT2A KAT2A 3540 0.1 0.29 YES
10 HDAC2 HDAC2 HDAC2 3891 0.091 0.29 YES
11 HES1 HES1 HES1 4323 0.08 0.29 YES
12 JAG1 JAG1 JAG1 4439 0.078 0.3 YES
13 DVL3 DVL3 DVL3 4452 0.077 0.32 YES
14 MAML1 MAML1 MAML1 4584 0.074 0.34 YES
15 JAG2 JAG2 JAG2 4587 0.074 0.35 YES
16 APH1A APH1A APH1A 5197 0.062 0.34 YES
17 DLL4 DLL4 DLL4 5357 0.059 0.34 YES
18 EP300 EP300 EP300 5371 0.059 0.36 YES
19 CTBP1 CTBP1 CTBP1 5610 0.054 0.36 YES
20 HDAC1 HDAC1 HDAC1 5885 0.049 0.36 YES
21 RBPJ RBPJ RBPJ 6026 0.047 0.36 YES
22 DTX2 DTX2 DTX2 6035 0.047 0.37 YES
23 NCOR2 NCOR2 NCOR2 6712 0.036 0.34 NO
24 SNW1 SNW1 SNW1 6714 0.035 0.35 NO
25 NOTCH3 NOTCH3 NOTCH3 6741 0.035 0.36 NO
26 NCSTN NCSTN NCSTN 6829 0.034 0.36 NO
27 ADAM17 ADAM17 ADAM17 7760 0.02 0.32 NO
28 PSEN1 PSEN1 PSEN1 7893 0.018 0.31 NO
29 HES5 HES5 HES5 8205 0.013 0.3 NO
30 PSEN2 PSEN2 PSEN2 8264 0.012 0.3 NO
31 CIR1 CIR1 CIR1 8353 0.01 0.3 NO
32 NUMB NUMB NUMB 8689 0.0059 0.28 NO
33 NOTCH2 NOTCH2 NOTCH2 9369 -0.0051 0.24 NO
34 NOTCH4 NOTCH4 NOTCH4 10274 -0.02 0.2 NO
35 NUMBL NUMBL NUMBL 10628 -0.026 0.18 NO
36 DTX3L DTX3L DTX3L 10667 -0.026 0.19 NO
37 PSENEN PSENEN PSENEN 10729 -0.028 0.19 NO
38 DVL1 DVL1 DVL1 11678 -0.044 0.15 NO
39 PTCRA PTCRA PTCRA 12351 -0.058 0.13 NO
40 CREBBP CREBBP CREBBP 12617 -0.064 0.13 NO
41 RFNG RFNG RFNG 12658 -0.065 0.14 NO
42 DLL1 DLL1 DLL1 13691 -0.09 0.11 NO
43 MAML2 MAML2 MAML2 13804 -0.093 0.13 NO
44 MAML3 MAML3 MAML3 14963 -0.13 0.099 NO
45 KAT2B KAT2B KAT2B 16360 -0.22 0.077 NO

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

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

genes ES table in pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

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 MAPK13 MAPK13 MAPK13 125 0.5 0.052 YES
2 PLA2G1B PLA2G1B PLA2G1B 464 0.35 0.074 YES
3 CACNA1D CACNA1D CACNA1D 576 0.32 0.1 YES
4 PLA2G12B PLA2G12B PLA2G12B 724 0.29 0.13 YES
5 PRKX PRKX PRKX 754 0.29 0.16 YES
6 SRC SRC SRC 1102 0.24 0.17 YES
7 CALML6 CALML6 CALML6 1590 0.19 0.17 YES
8 PRKCD PRKCD PRKCD 1804 0.18 0.18 YES
9 PLD1 PLD1 PLD1 1930 0.17 0.19 YES
10 PLA2G10 PLA2G10 PLA2G10 2008 0.16 0.2 YES
11 ITPR3 ITPR3 ITPR3 2258 0.15 0.21 YES
12 CACNA1F CACNA1F CACNA1F 2285 0.15 0.22 YES
13 ADCY5 ADCY5 ADCY5 2286 0.15 0.24 YES
14 PLCB1 PLCB1 PLCB1 2364 0.14 0.25 YES
15 CAMK2B CAMK2B CAMK2B 2370 0.14 0.27 YES
16 CGA CGA CGA 2420 0.14 0.28 YES
17 PLCB4 PLCB4 PLCB4 2494 0.14 0.29 YES
18 MAP3K4 MAP3K4 MAP3K4 2515 0.14 0.31 YES
19 PLA2G6 PLA2G6 PLA2G6 2682 0.13 0.32 YES
20 GNRH1 GNRH1 GNRH1 2685 0.13 0.33 YES
21 LHB LHB LHB 2707 0.13 0.34 YES
22 GNAS GNAS GNAS 2731 0.13 0.36 YES
23 ADCY6 ADCY6 ADCY6 2934 0.12 0.36 YES
24 MAPK12 MAPK12 MAPK12 3617 0.098 0.33 NO
25 MAPK7 MAPK7 MAPK7 3749 0.095 0.34 NO
26 ATF4 ATF4 ATF4 3977 0.089 0.33 NO
27 PLCB3 PLCB3 PLCB3 4506 0.076 0.31 NO
28 KRAS KRAS KRAS 4510 0.076 0.32 NO
29 MAPK9 MAPK9 MAPK9 4597 0.074 0.33 NO
30 MAP2K7 MAP2K7 MAP2K7 4667 0.072 0.33 NO
31 PRKACA PRKACA PRKACA 4903 0.067 0.32 NO
32 MAP2K4 MAP2K4 MAP2K4 5112 0.063 0.32 NO
33 MAP2K2 MAP2K2 MAP2K2 5395 0.058 0.31 NO
34 MAP3K1 MAP3K1 MAP3K1 5458 0.057 0.32 NO
35 PLA2G2D PLA2G2D PLA2G2D 5570 0.055 0.32 NO
36 PLD2 PLD2 PLD2 5831 0.05 0.31 NO
37 RAF1 RAF1 RAF1 5999 0.047 0.3 NO
38 CAMK2G CAMK2G CAMK2G 6111 0.045 0.3 NO
39 MAPK14 MAPK14 MAPK14 6352 0.042 0.29 NO
40 CAMK2A CAMK2A CAMK2A 6682 0.036 0.28 NO
41 MAPK1 MAPK1 MAPK1 6795 0.034 0.28 NO
42 CALM2 CALM2 CALM2 6970 0.031 0.27 NO
43 GNAQ GNAQ GNAQ 7273 0.026 0.26 NO
44 PLA2G5 PLA2G5 PLA2G5 7274 0.026 0.26 NO
45 CALM3 CALM3 CALM3 7452 0.024 0.25 NO
46 CACNA1C CACNA1C CACNA1C 7509 0.023 0.25 NO
47 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 7564 0.022 0.25 NO
48 MAP2K6 MAP2K6 MAP2K6 7622 0.021 0.25 NO
49 CAMK2D CAMK2D CAMK2D 7746 0.02 0.24 NO
50 GRB2 GRB2 GRB2 7803 0.019 0.24 NO
51 MMP2 MMP2 MMP2 8229 0.012 0.22 NO
52 ELK1 ELK1 ELK1 9001 0.0014 0.18 NO
53 MMP14 MMP14 MMP14 9105 -0.00058 0.17 NO
54 CALM1 CALM1 CALM1 9200 -0.0021 0.17 NO
55 MAPK3 MAPK3 MAPK3 9334 -0.0044 0.16 NO
56 MAPK8 MAPK8 MAPK8 9533 -0.0075 0.15 NO
57 SOS2 SOS2 SOS2 9594 -0.0084 0.15 NO
58 HRAS HRAS HRAS 9801 -0.012 0.14 NO
59 ADCY7 ADCY7 ADCY7 9888 -0.014 0.13 NO
60 PRKCA PRKCA PRKCA 10055 -0.016 0.13 NO
61 GNRHR GNRHR GNRHR 10073 -0.016 0.13 NO
62 CACNA1S CACNA1S CACNA1S 10107 -0.017 0.13 NO
63 MAPK11 MAPK11 MAPK11 10775 -0.028 0.093 NO
64 SOS1 SOS1 SOS1 10789 -0.028 0.096 NO
65 MAP3K3 MAP3K3 MAP3K3 10819 -0.029 0.097 NO
66 MAP2K3 MAP2K3 MAP2K3 11044 -0.033 0.088 NO
67 NRAS NRAS NRAS 11057 -0.033 0.092 NO
68 ADCY2 ADCY2 ADCY2 11135 -0.034 0.091 NO
69 ADCY4 ADCY4 ADCY4 11340 -0.038 0.084 NO
70 PLA2G12A PLA2G12A PLA2G12A 11485 -0.041 0.081 NO
71 PLCB2 PLCB2 PLCB2 11530 -0.041 0.083 NO
72 MAP2K1 MAP2K1 MAP2K1 12327 -0.058 0.045 NO
73 ITPR2 ITPR2 ITPR2 12396 -0.059 0.048 NO
74 EGFR EGFR EGFR 12438 -0.06 0.053 NO
75 GNA11 GNA11 GNA11 12625 -0.064 0.05 NO
76 CDC42 CDC42 CDC42 12940 -0.071 0.04 NO
77 PRKCB PRKCB PRKCB 13209 -0.078 0.034 NO
78 ADCY1 ADCY1 ADCY1 13610 -0.088 0.022 NO
79 ADCY9 ADCY9 ADCY9 13852 -0.094 0.019 NO
80 CALML3 CALML3 CALML3 14040 -0.1 0.02 NO
81 JUN JUN JUN 14167 -0.1 0.026 NO
82 MAPK10 MAPK10 MAPK10 14342 -0.11 0.029 NO
83 PLA2G4A PLA2G4A PLA2G4A 14689 -0.12 0.023 NO
84 PTK2B PTK2B PTK2B 14719 -0.12 0.036 NO
85 HBEGF HBEGF HBEGF 14792 -0.13 0.047 NO
86 PLA2G2A PLA2G2A PLA2G2A 15814 -0.18 0.01 NO
87 PRKACB PRKACB PRKACB 15897 -0.18 0.027 NO
88 MAP3K2 MAP3K2 MAP3K2 16019 -0.19 0.043 NO
89 ITPR1 ITPR1 ITPR1 16035 -0.19 0.064 NO
90 ADCY8 ADCY8 ADCY8 16845 -0.27 0.05 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG RIBOSOME

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PLA2G1B PLA2G1B PLA2G1B 464 0.35 0.07 YES
2 PPAP2C PPAP2C PPAP2C 471 0.35 0.16 YES
3 PAFAH1B3 PAFAH1B3 PAFAH1B3 479 0.35 0.26 YES
4 PLA2G12B PLA2G12B PLA2G12B 724 0.29 0.32 YES
5 ENPP2 ENPP2 ENPP2 1208 0.23 0.36 YES
6 PLD1 PLD1 PLD1 1930 0.17 0.36 YES
7 PLA2G10 PLA2G10 PLA2G10 2008 0.16 0.4 YES
8 PLA2G7 PLA2G7 PLA2G7 2443 0.14 0.42 YES
9 PLA2G6 PLA2G6 PLA2G6 2682 0.13 0.44 YES
10 PLA2G2D PLA2G2D PLA2G2D 5570 0.055 0.29 NO
11 LPCAT1 LPCAT1 LPCAT1 5805 0.051 0.29 NO
12 PLD2 PLD2 PLD2 5831 0.05 0.3 NO
13 AGPS AGPS AGPS 6994 0.031 0.25 NO
14 LPCAT4 LPCAT4 LPCAT4 7245 0.027 0.24 NO
15 PLA2G5 PLA2G5 PLA2G5 7274 0.026 0.25 NO
16 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 7564 0.022 0.24 NO
17 PAFAH1B1 PAFAH1B1 PAFAH1B1 9268 -0.0031 0.14 NO
18 PLA2G12A PLA2G12A PLA2G12A 11485 -0.041 0.026 NO
19 CHPT1 CHPT1 CHPT1 12707 -0.066 -0.025 NO
20 PPAP2A PPAP2A PPAP2A 12959 -0.072 -0.019 NO
21 PAFAH1B2 PAFAH1B2 PAFAH1B2 13901 -0.096 -0.046 NO
22 PLA2G4A PLA2G4A PLA2G4A 14689 -0.12 -0.057 NO
23 PPAP2B PPAP2B PPAP2B 15325 -0.15 -0.052 NO
24 PLA2G2A PLA2G2A PLA2G2A 15814 -0.18 -0.031 NO
25 PAFAH2 PAFAH2 PAFAH2 16351 -0.22 -0.0023 NO
26 LPCAT2 LPCAT2 LPCAT2 17025 -0.29 0.04 NO

Figure S57.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RIBOSOME.

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

genes ES table in pathway: KEGG DNA REPLICATION

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 CDC25A CDC25A CDC25A 421 0.37 0.0042 YES
2 TTK TTK TTK 450 0.36 0.03 YES
3 CCNB2 CCNB2 CCNB2 523 0.34 0.051 YES
4 CDKN1C CDKN1C CDKN1C 552 0.33 0.075 YES
5 CDK1 CDK1 CDK1 597 0.32 0.097 YES
6 BUB1B BUB1B BUB1B 766 0.28 0.11 YES
7 ESPL1 ESPL1 ESPL1 797 0.28 0.13 YES
8 CDC25C CDC25C CDC25C 878 0.27 0.14 YES
9 PLK1 PLK1 PLK1 941 0.26 0.16 YES
10 BUB1 BUB1 BUB1 982 0.25 0.18 YES
11 PTTG1 PTTG1 PTTG1 1019 0.25 0.2 YES
12 CCNE1 CCNE1 CCNE1 1085 0.24 0.21 YES
13 CCNB1 CCNB1 CCNB1 1154 0.23 0.22 YES
14 CDC6 CDC6 CDC6 1241 0.22 0.24 YES
15 CCNB3 CCNB3 CCNB3 1294 0.22 0.25 YES
16 CCNA2 CCNA2 CCNA2 1331 0.22 0.26 YES
17 CDC20 CDC20 CDC20 1397 0.21 0.28 YES
18 SKP2 SKP2 SKP2 1572 0.19 0.28 YES
19 CDC45 CDC45 CDC45 1694 0.18 0.29 YES
20 CHEK2 CHEK2 CHEK2 1792 0.18 0.3 YES
21 ORC6L ORC6L ORC6L 1849 0.17 0.31 YES
22 TP53 TP53 TP53 1986 0.16 0.31 YES
23 TGFB1 TGFB1 TGFB1 2382 0.14 0.3 YES
24 CDK7 CDK7 CDK7 2439 0.14 0.31 YES
25 E2F1 E2F1 E2F1 2533 0.14 0.31 YES
26 SMC3 SMC3 SMC3 2608 0.13 0.32 YES
27 WEE1 WEE1 WEE1 2694 0.13 0.32 YES
28 MAD2L1 MAD2L1 MAD2L1 2771 0.13 0.33 YES
29 MCM2 MCM2 MCM2 2863 0.12 0.33 YES
30 CCNE2 CCNE2 CCNE2 3081 0.12 0.33 YES
31 CDK4 CDK4 CDK4 3164 0.11 0.33 YES
32 CHEK1 CHEK1 CHEK1 3218 0.11 0.34 YES
33 RBL1 RBL1 RBL1 3451 0.1 0.33 YES
34 MCM5 MCM5 MCM5 3481 0.1 0.34 YES
35 WEE2 WEE2 WEE2 3616 0.098 0.34 YES
36 MCM4 MCM4 MCM4 3628 0.098 0.35 YES
37 CDC7 CDC7 CDC7 3645 0.097 0.35 YES
38 PTTG2 PTTG2 PTTG2 3677 0.096 0.36 YES
39 MCM3 MCM3 MCM3 3747 0.095 0.36 YES
40 ANAPC4 ANAPC4 ANAPC4 3879 0.092 0.36 YES
41 HDAC2 HDAC2 HDAC2 3891 0.091 0.37 YES
42 ANAPC7 ANAPC7 ANAPC7 3995 0.088 0.37 YES
43 ORC2L ORC2L ORC2L 4056 0.087 0.37 YES
44 E2F3 E2F3 E2F3 4226 0.082 0.37 YES
45 TFDP1 TFDP1 TFDP1 4277 0.081 0.37 YES
46 FZR1 FZR1 FZR1 4289 0.081 0.38 YES
47 MCM6 MCM6 MCM6 4339 0.08 0.38 YES
48 SMC1B SMC1B SMC1B 4479 0.076 0.38 YES
49 MCM7 MCM7 MCM7 4539 0.075 0.38 YES
50 E2F2 E2F2 E2F2 4599 0.074 0.38 YES
51 ORC1L ORC1L ORC1L 4712 0.071 0.38 NO
52 ANAPC1 ANAPC1 ANAPC1 4917 0.067 0.38 NO
53 CDC16 CDC16 CDC16 4940 0.067 0.38 NO
54 RBX1 RBX1 RBX1 5113 0.063 0.38 NO
55 EP300 EP300 EP300 5371 0.059 0.37 NO
56 YWHAZ YWHAZ YWHAZ 5548 0.055 0.36 NO
57 BUB3 BUB3 BUB3 5562 0.055 0.36 NO
58 YWHAQ YWHAQ YWHAQ 5609 0.054 0.36 NO
59 HDAC1 HDAC1 HDAC1 5885 0.049 0.35 NO
60 YWHAH YWHAH YWHAH 6050 0.046 0.35 NO
61 CDC26 CDC26 CDC26 6106 0.045 0.35 NO
62 ANAPC5 ANAPC5 ANAPC5 6144 0.045 0.35 NO
63 SMAD3 SMAD3 SMAD3 6323 0.042 0.34 NO
64 ABL1 ABL1 ABL1 6388 0.041 0.34 NO
65 MAD1L1 MAD1L1 MAD1L1 6635 0.037 0.33 NO
66 CDC23 CDC23 CDC23 6848 0.033 0.32 NO
67 STAG1 STAG1 STAG1 7106 0.029 0.31 NO
68 CDK2 CDK2 CDK2 7162 0.028 0.31 NO
69 YWHAE YWHAE YWHAE 7249 0.027 0.3 NO
70 CDKN2D CDKN2D CDKN2D 7306 0.026 0.3 NO
71 RAD21 RAD21 RAD21 7350 0.025 0.3 NO
72 ORC3L ORC3L ORC3L 7592 0.022 0.29 NO
73 E2F5 E2F5 E2F5 7743 0.02 0.28 NO
74 ANAPC11 ANAPC11 ANAPC11 7943 0.017 0.27 NO
75 SMAD4 SMAD4 SMAD4 8018 0.015 0.27 NO
76 PRKDC PRKDC PRKDC 8262 0.012 0.26 NO
77 CDC27 CDC27 CDC27 8324 0.011 0.26 NO
78 ORC4L ORC4L ORC4L 8382 0.01 0.25 NO
79 PCNA PCNA PCNA 8450 0.0091 0.25 NO
80 ATM ATM ATM 8598 0.0072 0.24 NO
81 TGFB3 TGFB3 TGFB3 8750 0.0051 0.23 NO
82 ORC5L ORC5L ORC5L 8840 0.0038 0.23 NO
83 E2F4 E2F4 E2F4 9113 -0.00071 0.21 NO
84 CCND2 CCND2 CCND2 9267 -0.0031 0.2 NO
85 SKP1 SKP1 SKP1 9611 -0.0087 0.19 NO
86 CDC25B CDC25B CDC25B 9654 -0.0094 0.18 NO
87 PKMYT1 PKMYT1 PKMYT1 9746 -0.011 0.18 NO
88 YWHAB YWHAB YWHAB 9837 -0.013 0.18 NO
89 CCND1 CCND1 CCND1 9861 -0.013 0.18 NO
90 SMAD2 SMAD2 SMAD2 10108 -0.017 0.16 NO
91 ANAPC2 ANAPC2 ANAPC2 10182 -0.018 0.16 NO
92 CDC14A CDC14A CDC14A 10321 -0.021 0.15 NO
93 ATR ATR ATR 10330 -0.021 0.16 NO
94 ANAPC13 ANAPC13 ANAPC13 10343 -0.021 0.16 NO
95 STAG2 STAG2 STAG2 10756 -0.028 0.14 NO
96 SMC1A SMC1A SMC1A 10904 -0.03 0.13 NO
97 GSK3B GSK3B GSK3B 11562 -0.042 0.095 NO
98 YWHAG YWHAG YWHAG 11626 -0.043 0.095 NO
99 CDKN1B CDKN1B CDKN1B 11651 -0.044 0.097 NO
100 MDM2 MDM2 MDM2 11766 -0.046 0.094 NO
101 MYC MYC MYC 11947 -0.049 0.087 NO
102 TFDP2 TFDP2 TFDP2 12497 -0.061 0.061 NO
103 ZBTB17 ZBTB17 ZBTB17 12501 -0.062 0.065 NO
104 CUL1 CUL1 CUL1 12539 -0.062 0.068 NO
105 CREBBP CREBBP CREBBP 12617 -0.064 0.069 NO
106 RB1 RB1 RB1 13175 -0.077 0.043 NO
107 TGFB2 TGFB2 TGFB2 13288 -0.08 0.043 NO
108 GADD45B GADD45B GADD45B 13662 -0.089 0.028 NO
109 CCND3 CCND3 CCND3 13780 -0.092 0.029 NO
110 CDKN2C CDKN2C CDKN2C 13940 -0.097 0.027 NO
111 CCNH CCNH CCNH 13975 -0.098 0.033 NO
112 ANAPC10 ANAPC10 ANAPC10 14153 -0.1 0.03 NO
113 CCNA1 CCNA1 CCNA1 14508 -0.12 0.019 NO
114 CDKN1A CDKN1A CDKN1A 14538 -0.12 0.027 NO
115 CDK6 CDK6 CDK6 14608 -0.12 0.032 NO
116 SFN SFN SFN 15778 -0.18 -0.021 NO
117 MAD2L2 MAD2L2 MAD2L2 15825 -0.18 -0.01 NO
118 RBL2 RBL2 RBL2 16131 -0.2 -0.012 NO
119 GADD45A GADD45A GADD45A 16704 -0.25 -0.025 NO
120 GADD45G GADD45G GADD45G 16716 -0.25 -0.0066 NO
121 CDKN2B CDKN2B CDKN2B 16839 -0.27 0.0069 NO
122 CDC14B CDC14B CDC14B 16899 -0.28 0.025 NO
123 CDKN2A CDKN2A CDKN2A 17017 -0.29 0.04 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 DNA REPLICATION.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA NO1 PATHWAY 28 genes.ES.table 0.59 1.5 0.046 0.093 0.83 0.46 0.23 0.36 0.061 0
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.45 1.4 0.05 0.13 0.92 0.6 0.42 0.35 0.098 0
BIOCARTA ALK PATHWAY 33 genes.ES.table 0.5 1.5 0.051 0.1 0.87 0.48 0.3 0.34 0.072 0
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.51 1.4 0.11 0.13 0.93 0.24 0.14 0.21 0.098 0
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.34 1.3 0.18 0.24 0.99 0.18 0.27 0.13 0.2 0
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.46 1.4 0.11 0.14 0.93 0.15 0.1 0.14 0.11 0
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.38 1.3 0.24 0.24 0.99 0.5 0.41 0.3 0.21 0
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.53 1.6 0.028 0.06 0.67 0.18 0.11 0.16 0.035 0
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.42 1.4 0.16 0.15 0.95 0.66 0.48 0.34 0.12 0
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.61 1.7 0.012 0.053 0.56 0.27 0.12 0.24 0.026 0
genes ES table in pathway: BIOCARTA NO1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKAR2B PRKAR2B PRKAR2B 475 0.51 0.029 YES
2 ENDOD1 ENDOD1 ENDOD1 512 0.5 0.081 YES
3 IRAK3 IRAK3 IRAK3 536 0.49 0.13 YES
4 AKT3 AKT3 AKT3 748 0.44 0.17 YES
5 PRKX PRKX PRKX 766 0.44 0.22 YES
6 BCL2 BCL2 BCL2 912 0.41 0.25 YES
7 CSF2RB CSF2RB CSF2RB 1163 0.38 0.28 YES
8 IL1B IL1B IL1B 1250 0.37 0.32 YES
9 PIK3R5 PIK3R5 PIK3R5 1370 0.36 0.35 YES
10 NGF NGF NGF 1508 0.34 0.38 YES
11 BIRC3 BIRC3 BIRC3 1774 0.31 0.39 YES
12 TNF TNF TNF 1799 0.31 0.43 YES
13 PIK3CG PIK3CG PIK3CG 1828 0.31 0.46 YES
14 PIK3CD PIK3CD PIK3CD 1884 0.3 0.49 YES
15 TNFRSF10C TNFRSF10C TNFRSF10C 2157 0.28 0.5 YES
16 NTRK1 NTRK1 NTRK1 2427 0.26 0.52 YES
17 PRKAR1B PRKAR1B PRKAR1B 2672 0.24 0.53 YES
18 TNFRSF10A TNFRSF10A TNFRSF10A 2873 0.22 0.54 YES
19 IL3RA IL3RA IL3RA 3001 0.22 0.56 YES
20 CAPN2 CAPN2 CAPN2 3864 0.16 0.53 NO
21 TP53 TP53 TP53 4408 0.13 0.51 NO
22 PIK3R3 PIK3R3 PIK3R3 4569 0.12 0.51 NO
23 NFKB1 NFKB1 NFKB1 4811 0.11 0.51 NO
24 PPP3CC PPP3CC PPP3CC 5721 0.078 0.47 NO
25 PPP3CA PPP3CA PPP3CA 5725 0.078 0.48 NO
26 CFLAR CFLAR CFLAR 5922 0.072 0.47 NO
27 IL1R1 IL1R1 IL1R1 5938 0.072 0.48 NO
28 IKBKB IKBKB IKBKB 5986 0.07 0.49 NO
29 FAS FAS FAS 6001 0.07 0.49 NO
30 TRADD TRADD TRADD 6045 0.069 0.5 NO
31 CASP6 CASP6 CASP6 6081 0.068 0.5 NO
32 CASP10 CASP10 CASP10 6611 0.056 0.48 NO
33 CASP7 CASP7 CASP7 6615 0.056 0.49 NO
34 TNFRSF1A TNFRSF1A TNFRSF1A 6754 0.052 0.48 NO
35 CAPN1 CAPN1 CAPN1 6755 0.052 0.49 NO
36 IL1A IL1A IL1A 6924 0.049 0.48 NO
37 BID BID BID 7073 0.046 0.48 NO
38 BCL2L1 BCL2L1 BCL2L1 7085 0.045 0.49 NO
39 PRKACA PRKACA PRKACA 7142 0.044 0.49 NO
40 NFKBIA NFKBIA NFKBIA 7273 0.041 0.48 NO
41 CYCS CYCS CYCS 7422 0.038 0.48 NO
42 IRAK1 IRAK1 IRAK1 7500 0.037 0.48 NO
43 TNFRSF10B TNFRSF10B TNFRSF10B 7583 0.036 0.48 NO
44 AKT1 AKT1 AKT1 7775 0.032 0.47 NO
45 IRAK4 IRAK4 IRAK4 7924 0.03 0.47 NO
46 BAX BAX BAX 7969 0.029 0.47 NO
47 ATM ATM ATM 7989 0.029 0.47 NO
48 BAD BAD BAD 8004 0.029 0.47 NO
49 PIK3CA PIK3CA PIK3CA 8136 0.026 0.47 NO
50 CHP CHP CHP 8154 0.026 0.47 NO
51 PPP3CB PPP3CB PPP3CB 8192 0.026 0.47 NO
52 FADD FADD FADD 8409 0.023 0.46 NO
53 XIAP XIAP XIAP 8458 0.022 0.46 NO
54 CASP8 CASP8 CASP8 8991 0.014 0.43 NO
55 IL1RAP IL1RAP IL1RAP 9056 0.013 0.43 NO
56 DFFB DFFB DFFB 9593 0.0066 0.4 NO
57 AIFM1 AIFM1 AIFM1 9599 0.0066 0.4 NO
58 MAP3K14 MAP3K14 MAP3K14 9628 0.0061 0.4 NO
59 IKBKG IKBKG IKBKG 9663 0.0055 0.4 NO
60 PIK3CB PIK3CB PIK3CB 9781 0.0041 0.39 NO
61 CHP2 CHP2 CHP2 9981 0.0016 0.38 NO
62 CHUK CHUK CHUK 10385 -0.003 0.36 NO
63 CASP3 CASP3 CASP3 10465 -0.0041 0.35 NO
64 TRAF2 TRAF2 TRAF2 10663 -0.0065 0.34 NO
65 APAF1 APAF1 APAF1 10809 -0.0082 0.34 NO
66 PRKACB PRKACB PRKACB 10812 -0.0082 0.34 NO
67 PRKAR1A PRKAR1A PRKAR1A 10918 -0.0096 0.33 NO
68 RELA RELA RELA 11131 -0.012 0.32 NO
69 TNFRSF10D TNFRSF10D TNFRSF10D 11488 -0.016 0.3 NO
70 RIPK1 RIPK1 RIPK1 11493 -0.017 0.3 NO
71 DFFA DFFA DFFA 11507 -0.017 0.31 NO
72 PIK3R2 PIK3R2 PIK3R2 11746 -0.02 0.29 NO
73 TNFSF10 TNFSF10 TNFSF10 11893 -0.022 0.29 NO
74 EXOG EXOG EXOG 12035 -0.024 0.28 NO
75 BIRC2 BIRC2 BIRC2 12209 -0.026 0.28 NO
76 AKT2 AKT2 AKT2 12348 -0.028 0.27 NO
77 IRAK2 IRAK2 IRAK2 12372 -0.028 0.27 NO
78 PPP3R1 PPP3R1 PPP3R1 12388 -0.028 0.28 NO
79 MYD88 MYD88 MYD88 12856 -0.034 0.25 NO
80 CASP9 CASP9 CASP9 13049 -0.037 0.24 NO
81 ENDOG ENDOG ENDOG 13227 -0.04 0.24 NO
82 PIK3R1 PIK3R1 PIK3R1 14760 -0.07 0.16 NO
83 PRKAR2A PRKAR2A PRKAR2A 14856 -0.072 0.16 NO

Figure S61.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S62.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 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 AGR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRICKLE1 PRICKLE1 PRICKLE1 14 0.84 0.033 YES
2 SFRP4 SFRP4 SFRP4 61 0.73 0.059 YES
3 SFRP1 SFRP1 SFRP1 98 0.7 0.085 YES
4 MAPK10 MAPK10 MAPK10 102 0.7 0.11 YES
5 WNT4 WNT4 WNT4 162 0.65 0.14 YES
6 WNT2 WNT2 WNT2 171 0.64 0.16 YES
7 DKK2 DKK2 DKK2 180 0.64 0.18 YES
8 FZD2 FZD2 FZD2 198 0.63 0.21 YES
9 MMP7 MMP7 MMP7 264 0.59 0.23 YES
10 NKD2 NKD2 NKD2 298 0.57 0.25 YES
11 WNT2B WNT2B WNT2B 315 0.56 0.27 YES
12 PLCB4 PLCB4 PLCB4 362 0.54 0.29 YES
13 FZD10 FZD10 FZD10 377 0.54 0.31 YES
14 SFRP5 SFRP5 SFRP5 478 0.51 0.32 YES
15 VANGL2 VANGL2 VANGL2 497 0.5 0.34 YES
16 NFATC1 NFATC1 NFATC1 575 0.48 0.36 YES
17 WNT10A WNT10A WNT10A 605 0.48 0.38 YES
18 FZD1 FZD1 FZD1 695 0.46 0.39 YES
19 WNT9A WNT9A WNT9A 702 0.45 0.41 YES
20 FZD7 FZD7 FZD7 713 0.45 0.42 YES
21 FZD8 FZD8 FZD8 729 0.45 0.44 YES
22 PRKX PRKX PRKX 766 0.44 0.46 YES
23 CTBP2 CTBP2 CTBP2 868 0.42 0.47 YES
24 SFRP2 SFRP2 SFRP2 893 0.42 0.48 YES
25 WNT10B WNT10B WNT10B 901 0.41 0.5 YES
26 PRICKLE2 PRICKLE2 PRICKLE2 930 0.41 0.51 YES
27 WNT7B WNT7B WNT7B 1003 0.4 0.52 YES
28 SOX17 SOX17 SOX17 1102 0.39 0.54 YES
29 NFATC4 NFATC4 NFATC4 1297 0.36 0.54 YES
30 CCND2 CCND2 CCND2 1353 0.36 0.55 YES
31 PRKCB PRKCB PRKCB 1538 0.33 0.55 YES
32 PLCB2 PLCB2 PLCB2 1612 0.33 0.56 YES
33 FOSL1 FOSL1 FOSL1 1633 0.32 0.57 YES
34 RAC2 RAC2 RAC2 1875 0.3 0.57 YES
35 WNT7A WNT7A WNT7A 1877 0.3 0.58 YES
36 WNT11 WNT11 WNT11 2070 0.28 0.58 YES
37 WNT1 WNT1 WNT1 2139 0.28 0.59 YES
38 LEF1 LEF1 LEF1 2213 0.27 0.6 YES
39 WNT3A WNT3A WNT3A 2845 0.23 0.57 NO
40 CAMK2A CAMK2A CAMK2A 3350 0.19 0.55 NO
41 FZD6 FZD6 FZD6 3357 0.19 0.56 NO
42 WNT9B WNT9B WNT9B 3585 0.18 0.55 NO
43 WNT6 WNT6 WNT6 3803 0.16 0.55 NO
44 FZD3 FZD3 FZD3 3841 0.16 0.55 NO
45 MYC MYC MYC 3924 0.16 0.55 NO
46 CAMK2B CAMK2B CAMK2B 4018 0.15 0.55 NO
47 APC2 APC2 APC2 4125 0.15 0.55 NO
48 TP53 TP53 TP53 4408 0.13 0.54 NO
49 CCND3 CCND3 CCND3 4612 0.12 0.53 NO
50 CCND1 CCND1 CCND1 4814 0.11 0.53 NO
51 WNT16 WNT16 WNT16 4844 0.11 0.53 NO
52 NFATC2 NFATC2 NFATC2 4845 0.11 0.53 NO
53 VANGL1 VANGL1 VANGL1 5031 0.1 0.53 NO
54 PORCN PORCN PORCN 5043 0.1 0.53 NO
55 AXIN1 AXIN1 AXIN1 5274 0.094 0.52 NO
56 PPARD PPARD PPARD 5458 0.087 0.52 NO
57 PPP2CB PPP2CB PPP2CB 5634 0.081 0.51 NO
58 PPP3CC PPP3CC PPP3CC 5721 0.078 0.51 NO
59 PPP3CA PPP3CA PPP3CA 5725 0.078 0.51 NO
60 PLCB3 PLCB3 PLCB3 5773 0.077 0.51 NO
61 PPP2R5E PPP2R5E PPP2R5E 5912 0.073 0.5 NO
62 FBXW11 FBXW11 FBXW11 6207 0.065 0.49 NO
63 CSNK1E CSNK1E CSNK1E 6271 0.063 0.49 NO
64 NFAT5 NFAT5 NFAT5 6319 0.062 0.49 NO
65 DAAM1 DAAM1 DAAM1 6346 0.061 0.49 NO
66 PPP2R1A PPP2R1A PPP2R1A 6792 0.051 0.47 NO
67 DAAM2 DAAM2 DAAM2 6813 0.051 0.47 NO
68 SMAD2 SMAD2 SMAD2 6912 0.049 0.46 NO
69 PRKACA PRKACA PRKACA 7142 0.044 0.45 NO
70 RAC1 RAC1 RAC1 7148 0.044 0.46 NO
71 FZD4 FZD4 FZD4 7183 0.043 0.46 NO
72 WNT5A WNT5A WNT5A 7279 0.041 0.45 NO
73 CAMK2D CAMK2D CAMK2D 7283 0.041 0.45 NO
74 WNT5B WNT5B WNT5B 7290 0.041 0.45 NO
75 SKP1 SKP1 SKP1 7885 0.03 0.42 NO
76 ROCK1 ROCK1 ROCK1 7930 0.03 0.42 NO
77 CSNK1A1 CSNK1A1 CSNK1A1 7949 0.03 0.42 NO
78 APC APC APC 8023 0.028 0.42 NO
79 CHP CHP CHP 8154 0.026 0.41 NO
80 PPP3CB PPP3CB PPP3CB 8192 0.026 0.41 NO
81 JUN JUN JUN 8506 0.021 0.39 NO
82 CSNK2A1 CSNK2A1 CSNK2A1 8629 0.02 0.39 NO
83 SIAH1 SIAH1 SIAH1 8709 0.018 0.38 NO
84 MAPK9 MAPK9 MAPK9 8780 0.017 0.38 NO
85 TBL1XR1 TBL1XR1 TBL1XR1 9048 0.013 0.36 NO
86 PSEN1 PSEN1 PSEN1 9126 0.012 0.36 NO
87 TCF7L2 TCF7L2 TCF7L2 9172 0.012 0.36 NO
88 MAPK8 MAPK8 MAPK8 9184 0.012 0.36 NO
89 RHOA RHOA RHOA 9253 0.011 0.36 NO
90 CSNK2A2 CSNK2A2 CSNK2A2 9394 0.009 0.35 NO
91 RBX1 RBX1 RBX1 9482 0.0079 0.34 NO
92 CAMK2G CAMK2G CAMK2G 9541 0.0072 0.34 NO
93 CREBBP CREBBP CREBBP 9648 0.0058 0.33 NO
94 BTRC BTRC BTRC 9979 0.0016 0.32 NO
95 CHP2 CHP2 CHP2 9981 0.0016 0.32 NO
96 RUVBL1 RUVBL1 RUVBL1 10139 0.000041 0.31 NO
97 SMAD3 SMAD3 SMAD3 10237 -0.0012 0.3 NO
98 CTBP1 CTBP1 CTBP1 10395 -0.0031 0.29 NO
99 PPP2R5C PPP2R5C PPP2R5C 10424 -0.0035 0.29 NO
100 PPP2CA PPP2CA PPP2CA 10592 -0.0057 0.28 NO
101 TCF7L1 TCF7L1 TCF7L1 10620 -0.006 0.28 NO
102 FZD9 FZD9 FZD9 10675 -0.0067 0.28 NO
103 WNT3 WNT3 WNT3 10734 -0.0072 0.27 NO
104 PRKACB PRKACB PRKACB 10812 -0.0082 0.27 NO
105 LRP5 LRP5 LRP5 10843 -0.0087 0.27 NO
106 CUL1 CUL1 CUL1 10947 -0.0099 0.26 NO
107 CHD8 CHD8 CHD8 11055 -0.011 0.26 NO
108 SMAD4 SMAD4 SMAD4 11225 -0.013 0.25 NO
109 DVL3 DVL3 DVL3 11435 -0.016 0.24 NO
110 AXIN2 AXIN2 AXIN2 11458 -0.016 0.24 NO
111 EP300 EP300 EP300 11540 -0.017 0.23 NO
112 GSK3B GSK3B GSK3B 11610 -0.018 0.23 NO
113 PPP2R1B PPP2R1B PPP2R1B 12056 -0.024 0.2 NO
114 PPP3R1 PPP3R1 PPP3R1 12388 -0.028 0.19 NO
115 DVL1 DVL1 DVL1 12659 -0.032 0.17 NO
116 MAP3K7 MAP3K7 MAP3K7 12693 -0.032 0.17 NO
117 PRKCG PRKCG PRKCG 12717 -0.032 0.17 NO
118 DVL2 DVL2 DVL2 12767 -0.033 0.17 NO
119 CTNNB1 CTNNB1 CTNNB1 12896 -0.035 0.16 NO
120 FRAT2 FRAT2 FRAT2 13094 -0.038 0.16 NO
121 LRP6 LRP6 LRP6 13144 -0.038 0.15 NO
122 NFATC3 NFATC3 NFATC3 13325 -0.041 0.15 NO
123 CSNK1A1L CSNK1A1L CSNK1A1L 13468 -0.043 0.14 NO
124 ROCK2 ROCK2 ROCK2 13528 -0.044 0.14 NO
125 PPP2R5A PPP2R5A PPP2R5A 13662 -0.047 0.13 NO
126 NLK NLK NLK 13680 -0.047 0.13 NO
127 CACYBP CACYBP CACYBP 13906 -0.051 0.12 NO
128 DKK1 DKK1 DKK1 14104 -0.055 0.11 NO
129 TBL1X TBL1X TBL1X 14774 -0.07 0.078 NO
130 CSNK2B CSNK2B CSNK2B 14910 -0.073 0.073 NO
131 CXXC4 CXXC4 CXXC4 14924 -0.073 0.075 NO
132 SENP2 SENP2 SENP2 15004 -0.076 0.074 NO
133 FZD5 FZD5 FZD5 15131 -0.08 0.07 NO
134 FRAT1 FRAT1 FRAT1 15184 -0.081 0.07 NO
135 PPP2R5D PPP2R5D PPP2R5D 15205 -0.082 0.072 NO
136 PRKCA PRKCA PRKCA 15772 -0.1 0.044 NO
137 CTNNBIP1 CTNNBIP1 CTNNBIP1 15867 -0.11 0.043 NO
138 PLCB1 PLCB1 PLCB1 16037 -0.12 0.038 NO
139 DKK4 DKK4 DKK4 16334 -0.14 0.027 NO
140 TBL1Y TBL1Y TBL1Y 16446 -0.14 0.026 NO
141 NKD1 NKD1 NKD1 16488 -0.15 0.029 NO
142 WNT8B WNT8B WNT8B 17064 -0.19 0.0044 NO
143 TCF7 TCF7 TCF7 17245 -0.22 0.0029 NO
144 WIF1 WIF1 WIF1 17569 -0.3 -0.0038 NO
145 RAC3 RAC3 RAC3 17620 -0.32 0.0061 NO

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

Figure S64.  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 ALK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MAPK10 MAPK10 MAPK10 102 0.7 0.08 YES
2 CXCL1 CXCL1 CXCL1 468 0.51 0.12 YES
3 JAM2 JAM2 JAM2 545 0.49 0.18 YES
4 IL8 IL8 IL8 631 0.47 0.23 YES
5 PTPRZ1 PTPRZ1 PTPRZ1 883 0.42 0.27 YES
6 CXCR2 CXCR2 CXCR2 993 0.4 0.31 YES
7 IGSF5 IGSF5 IGSF5 1754 0.31 0.31 YES
8 JAM3 JAM3 JAM3 1860 0.3 0.34 YES
9 CXCR1 CXCR1 CXCR1 1866 0.3 0.37 YES
10 MAPK12 MAPK12 MAPK12 1899 0.3 0.41 YES
11 MAPK11 MAPK11 MAPK11 2005 0.29 0.44 YES
12 ATP6V1B1 ATP6V1B1 ATP6V1B1 2846 0.23 0.42 YES
13 CCL5 CCL5 CCL5 2848 0.23 0.45 YES
14 HBEGF HBEGF HBEGF 2975 0.22 0.47 YES
15 MAPK13 MAPK13 MAPK13 3056 0.21 0.49 YES
16 NOD1 NOD1 NOD1 3460 0.19 0.49 YES
17 LYN LYN LYN 3620 0.18 0.5 YES
18 ATP6V0D2 ATP6V0D2 ATP6V0D2 4052 0.15 0.49 YES
19 ADAM17 ADAM17 ADAM17 4316 0.14 0.5 YES
20 PLCG2 PLCG2 PLCG2 4644 0.12 0.49 YES
21 ATP6V1H ATP6V1H ATP6V1H 4656 0.12 0.51 YES
22 SRC SRC SRC 4700 0.12 0.52 YES
23 NFKB1 NFKB1 NFKB1 4811 0.11 0.53 YES
24 TCIRG1 TCIRG1 TCIRG1 4847 0.11 0.54 YES
25 EGFR EGFR EGFR 5445 0.088 0.52 NO
26 ATP6V1E2 ATP6V1E2 ATP6V1E2 5446 0.088 0.53 NO
27 ADAM10 ADAM10 ADAM10 5579 0.083 0.53 NO
28 IKBKB IKBKB IKBKB 5986 0.07 0.51 NO
29 GIT1 GIT1 GIT1 6114 0.067 0.52 NO
30 F11R F11R F11R 6149 0.066 0.52 NO
31 ATP6V1B2 ATP6V1B2 ATP6V1B2 6174 0.066 0.53 NO
32 ATP6V0D1 ATP6V0D1 ATP6V0D1 6509 0.058 0.52 NO
33 TJP1 TJP1 TJP1 6765 0.052 0.51 NO
34 ATP6V1E1 ATP6V1E1 ATP6V1E1 6944 0.048 0.5 NO
35 ATP6V1F ATP6V1F ATP6V1F 7028 0.047 0.5 NO
36 RAC1 RAC1 RAC1 7148 0.044 0.5 NO
37 MAP2K4 MAP2K4 MAP2K4 7250 0.042 0.5 NO
38 NFKBIA NFKBIA NFKBIA 7273 0.041 0.51 NO
39 ATP6V0C ATP6V0C ATP6V0C 7342 0.04 0.51 NO
40 PAK1 PAK1 PAK1 7355 0.04 0.51 NO
41 ATP6V1C1 ATP6V1C1 ATP6V1C1 7418 0.039 0.51 NO
42 ATP6V0B ATP6V0B ATP6V0B 7477 0.037 0.52 NO
43 ATP6V1D ATP6V1D ATP6V1D 7803 0.032 0.5 NO
44 CDC42 CDC42 CDC42 8025 0.028 0.49 NO
45 ATP6V1G2 ATP6V1G2 ATP6V1G2 8114 0.027 0.49 NO
46 ATP6V0A4 ATP6V0A4 ATP6V0A4 8263 0.025 0.48 NO
47 JUN JUN JUN 8506 0.021 0.47 NO
48 ATP6V1A ATP6V1A ATP6V1A 8524 0.021 0.48 NO
49 MAPK9 MAPK9 MAPK9 8780 0.017 0.46 NO
50 ATP6V1G1 ATP6V1G1 ATP6V1G1 9165 0.012 0.44 NO
51 MAPK8 MAPK8 MAPK8 9184 0.012 0.44 NO
52 ATP6V0A1 ATP6V0A1 ATP6V0A1 9203 0.011 0.44 NO
53 MAP3K14 MAP3K14 MAP3K14 9628 0.0061 0.42 NO
54 IKBKG IKBKG IKBKG 9663 0.0055 0.42 NO
55 CSK CSK CSK 9715 0.0049 0.42 NO
56 CHUK CHUK CHUK 10385 -0.003 0.38 NO
57 CASP3 CASP3 CASP3 10465 -0.0041 0.38 NO
58 ATP6AP1 ATP6AP1 ATP6AP1 10715 -0.007 0.36 NO
59 PTPN11 PTPN11 PTPN11 10976 -0.01 0.35 NO
60 RELA RELA RELA 11131 -0.012 0.34 NO
61 PLCG1 PLCG1 PLCG1 11593 -0.018 0.32 NO
62 ATP6V1C2 ATP6V1C2 ATP6V1C2 11990 -0.023 0.3 NO
63 MAPK14 MAPK14 MAPK14 12885 -0.035 0.25 NO
64 ATP6V0A2 ATP6V0A2 ATP6V0A2 13112 -0.038 0.24 NO
65 ATP6V0E2 ATP6V0E2 ATP6V0E2 14276 -0.059 0.18 NO
66 MET MET MET 15509 -0.093 0.13 NO

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

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ALK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA BCR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SFRP4 SFRP4 SFRP4 61 0.73 0.047 YES
2 SFRP1 SFRP1 SFRP1 98 0.7 0.093 YES
3 WNT4 WNT4 WNT4 162 0.65 0.13 YES
4 WNT2 WNT2 WNT2 171 0.64 0.18 YES
5 FZD2 FZD2 FZD2 198 0.63 0.22 YES
6 WNT2B WNT2B WNT2B 315 0.56 0.25 YES
7 WISP1 WISP1 WISP1 327 0.56 0.29 YES
8 WNT10A WNT10A WNT10A 605 0.48 0.31 YES
9 FRZB FRZB FRZB 609 0.47 0.34 YES
10 FZD1 FZD1 FZD1 695 0.46 0.37 YES
11 WNT9A WNT9A WNT9A 702 0.45 0.4 YES
12 FZD7 FZD7 FZD7 713 0.45 0.43 YES
13 FZD8 FZD8 FZD8 729 0.45 0.46 YES
14 CTBP2 CTBP2 CTBP2 868 0.42 0.48 YES
15 PYGO1 PYGO1 PYGO1 990 0.4 0.5 YES
16 WNT7B WNT7B WNT7B 1003 0.4 0.53 YES
17 SOX17 SOX17 SOX17 1102 0.39 0.55 YES
18 CCND2 CCND2 CCND2 1353 0.36 0.56 YES
19 FOSL1 FOSL1 FOSL1 1633 0.32 0.56 YES
20 WNT7A WNT7A WNT7A 1877 0.3 0.57 YES
21 WNT11 WNT11 WNT11 2070 0.28 0.58 YES
22 WNT1 WNT1 WNT1 2139 0.28 0.6 YES
23 LEF1 LEF1 LEF1 2213 0.27 0.61 YES
24 FZD6 FZD6 FZD6 3357 0.19 0.56 NO
25 WNT6 WNT6 WNT6 3803 0.16 0.55 NO
26 FZD3 FZD3 FZD3 3841 0.16 0.55 NO
27 MYC MYC MYC 3924 0.16 0.56 NO
28 CCND3 CCND3 CCND3 4612 0.12 0.53 NO
29 CCND1 CCND1 CCND1 4814 0.11 0.53 NO
30 WNT16 WNT16 WNT16 4844 0.11 0.53 NO
31 TLE2 TLE2 TLE2 4920 0.11 0.54 NO
32 PORCN PORCN PORCN 5043 0.1 0.54 NO
33 AXIN1 AXIN1 AXIN1 5274 0.094 0.53 NO
34 B2M B2M B2M 5567 0.083 0.52 NO
35 DIXDC1 DIXDC1 DIXDC1 5582 0.083 0.52 NO
36 FBXW11 FBXW11 FBXW11 6207 0.065 0.49 NO
37 DAAM1 DAAM1 DAAM1 6346 0.061 0.49 NO
38 PPP2R1A PPP2R1A PPP2R1A 6792 0.051 0.47 NO
39 AES AES AES 6951 0.048 0.46 NO
40 FZD4 FZD4 FZD4 7183 0.043 0.45 NO
41 WNT5A WNT5A WNT5A 7279 0.041 0.45 NO
42 WNT5B WNT5B WNT5B 7290 0.041 0.45 NO
43 KREMEN1 KREMEN1 KREMEN1 7331 0.04 0.45 NO
44 ACTB ACTB ACTB 7606 0.035 0.44 NO
45 CSNK1A1 CSNK1A1 CSNK1A1 7949 0.03 0.42 NO
46 APC APC APC 8023 0.028 0.42 NO
47 JUN JUN JUN 8506 0.021 0.39 NO
48 CSNK2A1 CSNK2A1 CSNK2A1 8629 0.02 0.39 NO
49 GSK3A GSK3A GSK3A 8644 0.019 0.39 NO
50 GAPDH GAPDH GAPDH 9243 0.011 0.36 NO
51 CSNK1G1 CSNK1G1 CSNK1G1 9355 0.0095 0.35 NO
52 FBXW4 FBXW4 FBXW4 9914 0.0023 0.32 NO
53 BTRC BTRC BTRC 9979 0.0016 0.31 NO
54 CTBP1 CTBP1 CTBP1 10395 -0.0031 0.29 NO
55 RPL13A RPL13A RPL13A 10437 -0.0037 0.29 NO
56 PPP2CA PPP2CA PPP2CA 10592 -0.0057 0.28 NO
57 TCF7L1 TCF7L1 TCF7L1 10620 -0.006 0.28 NO
58 WNT3 WNT3 WNT3 10734 -0.0072 0.27 NO
59 LRP5 LRP5 LRP5 10843 -0.0087 0.27 NO
60 BCL9 BCL9 BCL9 11272 -0.014 0.24 NO
61 EP300 EP300 EP300 11540 -0.017 0.23 NO
62 GSK3B GSK3B GSK3B 11610 -0.018 0.23 NO
63 FBXW2 FBXW2 FBXW2 11717 -0.02 0.22 NO
64 DVL1 DVL1 DVL1 12659 -0.032 0.17 NO
65 DVL2 DVL2 DVL2 12767 -0.033 0.17 NO
66 CTNNB1 CTNNB1 CTNNB1 12896 -0.035 0.16 NO
67 CSNK1D CSNK1D CSNK1D 13008 -0.036 0.16 NO
68 PITX2 PITX2 PITX2 13031 -0.037 0.16 NO
69 LRP6 LRP6 LRP6 13144 -0.038 0.16 NO
70 RHOU RHOU RHOU 13431 -0.043 0.14 NO
71 NLK NLK NLK 13680 -0.047 0.13 NO
72 DKK1 DKK1 DKK1 14104 -0.055 0.11 NO
73 CXXC4 CXXC4 CXXC4 14924 -0.073 0.071 NO
74 SENP2 SENP2 SENP2 15004 -0.076 0.072 NO
75 SLC9A3R1 SLC9A3R1 SLC9A3R1 15105 -0.079 0.072 NO
76 FZD5 FZD5 FZD5 15131 -0.08 0.076 NO
77 TLE1 TLE1 TLE1 15137 -0.08 0.081 NO
78 FRAT1 FRAT1 FRAT1 15184 -0.081 0.084 NO
79 HPRT1 HPRT1 HPRT1 15716 -0.1 0.061 NO
80 CTNNBIP1 CTNNBIP1 CTNNBIP1 15867 -0.11 0.06 NO
81 NKD1 NKD1 NKD1 16488 -0.15 0.035 NO
82 TCF7 TCF7 TCF7 17245 -0.22 0.007 NO
83 WIF1 WIF1 WIF1 17569 -0.3 0.009 NO

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

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BCR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CARM ER PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 WNT4 WNT4 WNT4 162 0.65 0.028 YES
2 WNT2 WNT2 WNT2 171 0.64 0.064 YES
3 ADCY5 ADCY5 ADCY5 196 0.63 0.098 YES
4 FZD2 FZD2 FZD2 198 0.63 0.13 YES
5 CREB3L1 CREB3L1 CREB3L1 206 0.63 0.17 YES
6 WNT2B WNT2B WNT2B 315 0.56 0.2 YES
7 PLCB4 PLCB4 PLCB4 362 0.54 0.22 YES
8 FZD10 FZD10 FZD10 377 0.54 0.25 YES
9 WNT10A WNT10A WNT10A 605 0.48 0.27 YES
10 FZD1 FZD1 FZD1 695 0.46 0.29 YES
11 WNT9A WNT9A WNT9A 702 0.45 0.31 YES
12 FZD7 FZD7 FZD7 713 0.45 0.34 YES
13 FZD8 FZD8 FZD8 729 0.45 0.36 YES
14 PRKX PRKX PRKX 766 0.44 0.38 YES
15 MITF MITF MITF 768 0.44 0.41 YES
16 ADCY2 ADCY2 ADCY2 778 0.44 0.43 YES
17 EDN1 EDN1 EDN1 780 0.44 0.46 YES
18 WNT10B WNT10B WNT10B 901 0.41 0.48 YES
19 WNT7B WNT7B WNT7B 1003 0.4 0.49 YES
20 ADCY4 ADCY4 ADCY4 1133 0.38 0.51 YES
21 POMC POMC POMC 1179 0.38 0.53 YES
22 PRKCB PRKCB PRKCB 1538 0.33 0.52 YES
23 PLCB2 PLCB2 PLCB2 1612 0.33 0.54 YES
24 WNT7A WNT7A WNT7A 1877 0.3 0.54 YES
25 KIT KIT KIT 1957 0.3 0.55 YES
26 ADCY7 ADCY7 ADCY7 1992 0.29 0.57 YES
27 WNT11 WNT11 WNT11 2070 0.28 0.58 YES
28 WNT1 WNT1 WNT1 2139 0.28 0.59 YES
29 LEF1 LEF1 LEF1 2213 0.27 0.6 YES
30 GNAO1 GNAO1 GNAO1 2369 0.26 0.61 YES
31 WNT3A WNT3A WNT3A 2845 0.23 0.6 YES
32 EDNRB EDNRB EDNRB 3006 0.22 0.6 YES
33 CAMK2A CAMK2A CAMK2A 3350 0.19 0.59 YES
34 FZD6 FZD6 FZD6 3357 0.19 0.6 YES
35 MC1R MC1R MC1R 3531 0.18 0.6 YES
36 WNT9B WNT9B WNT9B 3585 0.18 0.61 YES
37 WNT6 WNT6 WNT6 3803 0.16 0.6 YES
38 FZD3 FZD3 FZD3 3841 0.16 0.61 YES
39 CAMK2B CAMK2B CAMK2B 4018 0.15 0.61 NO
40 WNT16 WNT16 WNT16 4844 0.11 0.57 NO
41 PLCB3 PLCB3 PLCB3 5773 0.077 0.52 NO
42 CREB3 CREB3 CREB3 6068 0.068 0.51 NO
43 KITLG KITLG KITLG 6417 0.06 0.49 NO
44 MAPK3 MAPK3 MAPK3 6456 0.059 0.49 NO
45 MAP2K1 MAP2K1 MAP2K1 6763 0.052 0.48 NO
46 KRAS KRAS KRAS 7083 0.045 0.46 NO
47 PRKACA PRKACA PRKACA 7142 0.044 0.46 NO
48 FZD4 FZD4 FZD4 7183 0.043 0.46 NO
49 CALM2 CALM2 CALM2 7201 0.043 0.46 NO
50 WNT5A WNT5A WNT5A 7279 0.041 0.46 NO
51 CAMK2D CAMK2D CAMK2D 7283 0.041 0.46 NO
52 WNT5B WNT5B WNT5B 7290 0.041 0.47 NO
53 ADCY1 ADCY1 ADCY1 7396 0.039 0.46 NO
54 CALM1 CALM1 CALM1 7491 0.037 0.46 NO
55 ADCY9 ADCY9 ADCY9 7590 0.036 0.46 NO
56 CREB1 CREB1 CREB1 7857 0.031 0.44 NO
57 GNAI3 GNAI3 GNAI3 8086 0.027 0.43 NO
58 GNAS GNAS GNAS 8249 0.025 0.42 NO
59 GNAI2 GNAI2 GNAI2 8547 0.021 0.41 NO
60 ADCY6 ADCY6 ADCY6 9127 0.012 0.38 NO
61 TCF7L2 TCF7L2 TCF7L2 9172 0.012 0.37 NO
62 CAMK2G CAMK2G CAMK2G 9541 0.0072 0.35 NO
63 CREBBP CREBBP CREBBP 9648 0.0058 0.35 NO
64 MAP2K2 MAP2K2 MAP2K2 9712 0.0049 0.34 NO
65 GNAQ GNAQ GNAQ 9746 0.0044 0.34 NO
66 TYRP1 TYRP1 TYRP1 10258 -0.0015 0.31 NO
67 TCF7L1 TCF7L1 TCF7L1 10620 -0.006 0.29 NO
68 FZD9 FZD9 FZD9 10675 -0.0067 0.29 NO
69 WNT3 WNT3 WNT3 10734 -0.0072 0.29 NO
70 PRKACB PRKACB PRKACB 10812 -0.0082 0.28 NO
71 CALM3 CALM3 CALM3 10832 -0.0086 0.28 NO
72 HRAS HRAS HRAS 10983 -0.01 0.28 NO
73 ASIP ASIP ASIP 11017 -0.011 0.28 NO
74 MAPK1 MAPK1 MAPK1 11085 -0.012 0.27 NO
75 DVL3 DVL3 DVL3 11435 -0.016 0.25 NO
76 EP300 EP300 EP300 11540 -0.017 0.25 NO
77 GSK3B GSK3B GSK3B 11610 -0.018 0.24 NO
78 ADCY8 ADCY8 ADCY8 12247 -0.026 0.21 NO
79 DVL1 DVL1 DVL1 12659 -0.032 0.19 NO
80 PRKCG PRKCG PRKCG 12717 -0.032 0.19 NO
81 DVL2 DVL2 DVL2 12767 -0.033 0.19 NO
82 CTNNB1 CTNNB1 CTNNB1 12896 -0.035 0.18 NO
83 NRAS NRAS NRAS 13162 -0.039 0.17 NO
84 CREB3L2 CREB3L2 CREB3L2 13508 -0.044 0.15 NO
85 DCT DCT DCT 14132 -0.056 0.12 NO
86 RAF1 RAF1 RAF1 14790 -0.07 0.086 NO
87 FZD5 FZD5 FZD5 15131 -0.08 0.071 NO
88 CALML3 CALML3 CALML3 15209 -0.082 0.071 NO
89 CREB3L3 CREB3L3 CREB3L3 15592 -0.096 0.055 NO
90 PRKCA PRKCA PRKCA 15772 -0.1 0.051 NO
91 GNAI1 GNAI1 GNAI1 15958 -0.11 0.047 NO
92 PLCB1 PLCB1 PLCB1 16037 -0.12 0.049 NO
93 CREB3L4 CREB3L4 CREB3L4 16484 -0.14 0.032 NO
94 WNT8B WNT8B WNT8B 17064 -0.19 0.01 NO
95 TCF7 TCF7 TCF7 17245 -0.22 0.012 NO
96 CALML6 CALML6 CALML6 17488 -0.27 0.014 NO

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PDGFRA PDGFRA PDGFRA 146 0.66 0.026 YES
2 IGF1R IGF1R IGF1R 511 0.5 0.032 YES
3 EHD3 EHD3 EHD3 719 0.45 0.044 YES
4 IQSEC2 IQSEC2 IQSEC2 813 0.43 0.061 YES
5 RAB31 RAB31 RAB31 907 0.41 0.078 YES
6 F2R F2R F2R 973 0.4 0.095 YES
7 CXCR2 CXCR2 CXCR2 993 0.4 0.12 YES
8 DNM3 DNM3 DNM3 1037 0.4 0.13 YES
9 RET RET RET 1208 0.37 0.14 YES
10 CCR5 CCR5 CCR5 1251 0.37 0.16 YES
11 ACAP1 ACAP1 ACAP1 1463 0.34 0.17 YES
12 EPN3 EPN3 EPN3 1648 0.32 0.17 YES
13 FGFR2 FGFR2 FGFR2 1727 0.32 0.19 YES
14 EHD2 EHD2 EHD2 1788 0.31 0.2 YES
15 IL2RA IL2RA IL2RA 1816 0.31 0.21 YES
16 CXCR1 CXCR1 CXCR1 1866 0.3 0.23 YES
17 ARAP3 ARAP3 ARAP3 1878 0.3 0.24 YES
18 KIT KIT KIT 1957 0.3 0.25 YES
19 IL2RG IL2RG IL2RG 2106 0.28 0.26 YES
20 ERBB4 ERBB4 ERBB4 2173 0.28 0.27 YES
21 CSF1R CSF1R CSF1R 2182 0.28 0.28 YES
22 DNM1 DNM1 DNM1 2201 0.27 0.3 YES
23 DAB2 DAB2 DAB2 2339 0.26 0.3 YES
24 CXCR4 CXCR4 CXCR4 2362 0.26 0.32 YES
25 NTRK1 NTRK1 NTRK1 2427 0.26 0.33 YES
26 ARAP2 ARAP2 ARAP2 2525 0.25 0.33 YES
27 IL2RB IL2RB IL2RB 2558 0.25 0.34 YES
28 RAB11FIP5 RAB11FIP5 RAB11FIP5 2570 0.25 0.36 YES
29 PIP5K1B PIP5K1B PIP5K1B 2887 0.22 0.35 YES
30 PLD1 PLD1 PLD1 2930 0.22 0.36 YES
31 DNAJC6 DNAJC6 DNAJC6 2939 0.22 0.37 YES
32 HSPA2 HSPA2 HSPA2 3245 0.2 0.36 YES
33 ASAP1 ASAP1 ASAP1 3447 0.19 0.36 YES
34 KDR KDR KDR 3540 0.18 0.37 YES
35 GRK5 GRK5 GRK5 3656 0.17 0.37 YES
36 PLD2 PLD2 PLD2 3661 0.17 0.38 YES
37 EGF EGF EGF 3750 0.17 0.38 YES
38 ADRB3 ADRB3 ADRB3 3784 0.17 0.39 YES
39 ARRB1 ARRB1 ARRB1 3796 0.16 0.4 YES
40 HSPA6 HSPA6 HSPA6 3855 0.16 0.4 YES
41 CBL CBL CBL 3919 0.16 0.41 YES
42 PSD PSD PSD 3942 0.16 0.42 YES
43 PIP5K1C PIP5K1C PIP5K1C 4092 0.15 0.41 YES
44 RAB11FIP1 RAB11FIP1 RAB11FIP1 4256 0.14 0.41 YES
45 HLA-G HLA-G HLA-G 4428 0.13 0.41 YES
46 SH3GL2 SH3GL2 SH3GL2 4565 0.12 0.41 YES
47 SRC SRC SRC 4700 0.12 0.41 YES
48 VPS24 VPS24 VPS24 4727 0.12 0.41 YES
49 CBLB CBLB CBLB 4807 0.11 0.41 YES
50 HLA-B HLA-B HLA-B 4822 0.11 0.42 YES
51 CHMP4C CHMP4C CHMP4C 4903 0.11 0.42 YES
52 SH3KBP1 SH3KBP1 SH3KBP1 4957 0.11 0.42 YES
53 CLTB CLTB CLTB 4976 0.11 0.43 YES
54 HLA-F HLA-F HLA-F 5013 0.1 0.43 YES
55 AGAP2 AGAP2 AGAP2 5134 0.1 0.43 YES
56 AGAP1 AGAP1 AGAP1 5229 0.096 0.43 YES
57 VPS37B VPS37B VPS37B 5269 0.095 0.43 YES
58 FLT1 FLT1 FLT1 5322 0.092 0.43 YES
59 ASAP2 ASAP2 ASAP2 5330 0.092 0.44 YES
60 EGFR EGFR EGFR 5445 0.088 0.44 NO
61 VPS4A VPS4A VPS4A 5598 0.082 0.43 NO
62 SH3GLB1 SH3GLB1 SH3GLB1 5636 0.081 0.43 NO
63 EHD4 EHD4 EHD4 5822 0.075 0.43 NO
64 ARRB2 ARRB2 ARRB2 5899 0.073 0.43 NO
65 VPS4B VPS4B VPS4B 6049 0.069 0.42 NO
66 GIT1 GIT1 GIT1 6114 0.067 0.42 NO
67 HLA-C HLA-C HLA-C 6197 0.065 0.42 NO
68 GIT2 GIT2 GIT2 6205 0.065 0.42 NO
69 HLA-A HLA-A HLA-A 6259 0.064 0.42 NO
70 SMURF1 SMURF1 SMURF1 6348 0.061 0.42 NO
71 HLA-E HLA-E HLA-E 6362 0.061 0.42 NO
72 RAB11A RAB11A RAB11A 6378 0.061 0.43 NO
73 IQSEC3 IQSEC3 IQSEC3 6423 0.06 0.43 NO
74 FAM125B FAM125B FAM125B 6585 0.056 0.42 NO
75 CHMP4B CHMP4B CHMP4B 6677 0.054 0.42 NO
76 HSPA8 HSPA8 HSPA8 6814 0.051 0.41 NO
77 PSD2 PSD2 PSD2 6842 0.05 0.42 NO
78 VPS37A VPS37A VPS37A 6849 0.05 0.42 NO
79 RABEP1 RABEP1 RABEP1 6899 0.049 0.42 NO
80 PRKCZ PRKCZ PRKCZ 6904 0.049 0.42 NO
81 CHMP4A CHMP4A CHMP4A 7035 0.046 0.41 NO
82 ARFGAP3 ARFGAP3 ARFGAP3 7067 0.046 0.42 NO
83 TRAF6 TRAF6 TRAF6 7115 0.045 0.41 NO
84 VPS37C VPS37C VPS37C 7138 0.044 0.42 NO
85 PARD6B PARD6B PARD6B 7158 0.044 0.42 NO
86 ACAP2 ACAP2 ACAP2 7292 0.041 0.41 NO
87 EPN2 EPN2 EPN2 7309 0.041 0.41 NO
88 DNM2 DNM2 DNM2 7310 0.041 0.42 NO
89 DNM1L DNM1L DNM1L 7353 0.04 0.41 NO
90 PARD6G PARD6G PARD6G 7375 0.04 0.42 NO
91 VPS28 VPS28 VPS28 7403 0.039 0.42 NO
92 CHMP1B CHMP1B CHMP1B 7427 0.038 0.42 NO
93 RAB11FIP3 RAB11FIP3 RAB11FIP3 7671 0.034 0.4 NO
94 ARAP1 ARAP1 ARAP1 7678 0.034 0.41 NO
95 RAB5C RAB5C RAB5C 7921 0.03 0.39 NO
96 CDC42 CDC42 CDC42 8025 0.028 0.39 NO
97 EPS15 EPS15 EPS15 8036 0.028 0.39 NO
98 SH3GLB2 SH3GLB2 SH3GLB2 8048 0.028 0.39 NO
99 ARF6 ARF6 ARF6 8053 0.028 0.39 NO
100 CHMP5 CHMP5 CHMP5 8166 0.026 0.39 NO
101 ADRBK1 ADRBK1 ADRBK1 8206 0.026 0.39 NO
102 RUFY1 RUFY1 RUFY1 8226 0.025 0.39 NO
103 AP2A2 AP2A2 AP2A2 8244 0.025 0.39 NO
104 RAB22A RAB22A RAB22A 8334 0.024 0.38 NO
105 SMURF2 SMURF2 SMURF2 8362 0.023 0.38 NO
106 EHD1 EHD1 EHD1 8407 0.023 0.38 NO
107 FGFR3 FGFR3 FGFR3 8591 0.02 0.37 NO
108 CHMP2B CHMP2B CHMP2B 8674 0.019 0.37 NO
109 TFRC TFRC TFRC 8682 0.019 0.37 NO
110 CBLC CBLC CBLC 8701 0.018 0.37 NO
111 FAM125A FAM125A FAM125A 8746 0.018 0.37 NO
112 AP2B1 AP2B1 AP2B1 8749 0.018 0.37 NO
113 STAM STAM STAM 8815 0.017 0.36 NO
114 PIP5K1A PIP5K1A PIP5K1A 8836 0.016 0.36 NO
115 AP2M1 AP2M1 AP2M1 8849 0.016 0.36 NO
116 LDLR LDLR LDLR 8908 0.015 0.36 NO
117 PSD4 PSD4 PSD4 8915 0.015 0.36 NO
118 RNF41 RNF41 RNF41 9023 0.014 0.36 NO
119 STAM2 STAM2 STAM2 9379 0.0092 0.34 NO
120 ADRBK2 ADRBK2 ADRBK2 9428 0.0086 0.34 NO
121 SH3GL1 SH3GL1 SH3GL1 9463 0.0081 0.33 NO
122 VPS36 VPS36 VPS36 9629 0.0061 0.32 NO
123 VPS45 VPS45 VPS45 9771 0.0042 0.32 NO
124 SMAP1 SMAP1 SMAP1 9818 0.0036 0.32 NO
125 PRKCI PRKCI PRKCI 9941 0.002 0.31 NO
126 ADRB1 ADRB1 ADRB1 10090 0.00055 0.3 NO
127 RAB11B RAB11B RAB11B 10354 -0.0026 0.28 NO
128 PDCD6IP PDCD6IP PDCD6IP 10416 -0.0033 0.28 NO
129 RAB5A RAB5A RAB5A 10475 -0.0042 0.28 NO
130 USP8 USP8 USP8 10537 -0.005 0.28 NO
131 CHMP2A CHMP2A CHMP2A 10764 -0.0077 0.26 NO
132 PIKFYVE PIKFYVE PIKFYVE 10778 -0.0078 0.26 NO
133 CLTC CLTC CLTC 10783 -0.0079 0.26 NO
134 WWP1 WWP1 WWP1 10788 -0.008 0.26 NO
135 CLTA CLTA CLTA 11057 -0.011 0.25 NO
136 EPN1 EPN1 EPN1 11124 -0.012 0.24 NO
137 STAMBP STAMBP STAMBP 11141 -0.012 0.24 NO
138 LDLRAP1 LDLRAP1 LDLRAP1 11306 -0.014 0.24 NO
139 AP2A1 AP2A1 AP2A1 11308 -0.014 0.24 NO
140 AP2S1 AP2S1 AP2S1 11330 -0.015 0.24 NO
141 MDM2 MDM2 MDM2 11363 -0.015 0.24 NO
142 RAB5B RAB5B RAB5B 11486 -0.016 0.23 NO
143 TSG101 TSG101 TSG101 11868 -0.021 0.21 NO
144 ACAP3 ACAP3 ACAP3 12027 -0.024 0.2 NO
145 EEA1 EEA1 EEA1 12181 -0.025 0.19 NO
146 PIP4K2B PIP4K2B PIP4K2B 12331 -0.027 0.19 NO
147 SMAP2 SMAP2 SMAP2 12511 -0.03 0.18 NO
148 GRK4 GRK4 GRK4 12515 -0.03 0.18 NO
149 VTA1 VTA1 VTA1 12878 -0.035 0.16 NO
150 PARD3 PARD3 PARD3 12910 -0.035 0.16 NO
151 GRK6 GRK6 GRK6 13006 -0.036 0.16 NO
152 ARFGAP1 ARFGAP1 ARFGAP1 13117 -0.038 0.15 NO
153 SNF8 SNF8 SNF8 13182 -0.039 0.15 NO
154 RAB11FIP4 RAB11FIP4 RAB11FIP4 13294 -0.041 0.15 NO
155 PSD3 PSD3 PSD3 13425 -0.043 0.14 NO
156 RAB11FIP2 RAB11FIP2 RAB11FIP2 13527 -0.044 0.14 NO
157 VPS25 VPS25 VPS25 13538 -0.045 0.14 NO
158 ARFGAP2 ARFGAP2 ARFGAP2 13607 -0.046 0.14 NO
159 IQSEC1 IQSEC1 IQSEC1 13685 -0.047 0.14 NO
160 ASAP3 ASAP3 ASAP3 13737 -0.048 0.14 NO
161 CHMP6 CHMP6 CHMP6 13944 -0.052 0.13 NO
162 ZFYVE20 ZFYVE20 ZFYVE20 14102 -0.055 0.12 NO
163 ITCH ITCH ITCH 14124 -0.056 0.12 NO
164 RAB4A RAB4A RAB4A 14158 -0.056 0.12 NO
165 FGFR4 FGFR4 FGFR4 14374 -0.06 0.12 NO
166 PARD6A PARD6A PARD6A 14543 -0.064 0.11 NO
167 HSPA1B HSPA1B HSPA1B 14685 -0.068 0.1 NO
168 HGS HGS HGS 14951 -0.074 0.094 NO
169 CLTCL1 CLTCL1 CLTCL1 14976 -0.075 0.096 NO
170 HSPA1A HSPA1A HSPA1A 15039 -0.077 0.097 NO
171 NEDD4L NEDD4L NEDD4L 15368 -0.088 0.083 NO
172 MET MET MET 15509 -0.093 0.08 NO
173 NEDD4 NEDD4 NEDD4 15543 -0.094 0.083 NO
174 ERBB3 ERBB3 ERBB3 16026 -0.12 0.061 NO
175 HSPA1L HSPA1L HSPA1L 16628 -0.16 0.035 NO
176 ADRB2 ADRB2 ADRB2 16642 -0.16 0.043 NO
177 VPS37D VPS37D VPS37D 16688 -0.16 0.049 NO
178 SH3GL3 SH3GL3 SH3GL3 17083 -0.2 0.037 NO

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

Figure S72.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HDAC PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA EGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NTRK2 NTRK2 NTRK2 35 0.79 0.021 YES
2 MAPK10 MAPK10 MAPK10 102 0.7 0.038 YES
3 FGF1 FGF1 FGF1 130 0.67 0.056 YES
4 PDGFRA PDGFRA PDGFRA 146 0.66 0.074 YES
5 CACNA1C CACNA1C CACNA1C 189 0.64 0.09 YES
6 PLA2G4A PLA2G4A PLA2G4A 267 0.59 0.1 YES
7 PLA2G5 PLA2G5 PLA2G5 359 0.55 0.11 YES
8 FGF7 FGF7 FGF7 405 0.53 0.13 YES
9 CACNB3 CACNB3 CACNB3 441 0.52 0.14 YES
10 FGFR1 FGFR1 FGFR1 452 0.52 0.15 YES
11 FGF18 FGF18 FGF18 500 0.5 0.17 YES
12 NTF3 NTF3 NTF3 529 0.49 0.18 YES
13 TGFB3 TGFB3 TGFB3 550 0.49 0.19 YES
14 CACNA1H CACNA1H CACNA1H 622 0.47 0.2 YES
15 TGFB2 TGFB2 TGFB2 644 0.47 0.21 YES
16 AKT3 AKT3 AKT3 748 0.44 0.22 YES
17 RASGRP1 RASGRP1 RASGRP1 761 0.44 0.23 YES
18 PRKX PRKX PRKX 766 0.44 0.24 YES
19 MAP3K12 MAP3K12 MAP3K12 784 0.44 0.26 YES
20 DUSP4 DUSP4 DUSP4 925 0.41 0.26 YES
21 CACNA2D1 CACNA2D1 CACNA2D1 933 0.41 0.27 YES
22 PLA2G2A PLA2G2A PLA2G2A 1099 0.39 0.27 YES
23 CACNB1 CACNB1 CACNB1 1120 0.38 0.28 YES
24 FLNC FLNC FLNC 1205 0.37 0.29 YES
25 IL1B IL1B IL1B 1250 0.37 0.3 YES
26 NFATC4 NFATC4 NFATC4 1297 0.36 0.31 YES
27 NGF NGF NGF 1508 0.34 0.3 YES
28 PRKCB PRKCB PRKCB 1538 0.33 0.31 YES
29 MAP3K6 MAP3K6 MAP3K6 1560 0.33 0.32 YES
30 TGFB1 TGFB1 TGFB1 1575 0.33 0.33 YES
31 MAP4K1 MAP4K1 MAP4K1 1579 0.33 0.34 YES
32 DUSP5 DUSP5 DUSP5 1674 0.32 0.34 YES
33 MECOM MECOM MECOM 1699 0.32 0.35 YES
34 FGFR2 FGFR2 FGFR2 1727 0.32 0.36 YES
35 PDGFA PDGFA PDGFA 1768 0.31 0.36 YES
36 TNF TNF TNF 1799 0.31 0.37 YES
37 FLNA FLNA FLNA 1801 0.31 0.38 YES
38 MAP3K5 MAP3K5 MAP3K5 1836 0.31 0.39 YES
39 PTPN5 PTPN5 PTPN5 1848 0.3 0.4 YES
40 RASGRP4 RASGRP4 RASGRP4 1863 0.3 0.4 YES
41 RAC2 RAC2 RAC2 1875 0.3 0.41 YES
42 MAPK12 MAPK12 MAPK12 1899 0.3 0.42 YES
43 PTPRR PTPRR PTPRR 1918 0.3 0.43 YES
44 FGF14 FGF14 FGF14 1936 0.3 0.44 YES
45 FGF11 FGF11 FGF11 1941 0.3 0.44 YES
46 MAPK11 MAPK11 MAPK11 2005 0.29 0.45 YES
47 CACNA2D3 CACNA2D3 CACNA2D3 2015 0.29 0.46 YES
48 FOS FOS FOS 2116 0.28 0.46 YES
49 BDNF BDNF BDNF 2120 0.28 0.47 YES
50 RPS6KA2 RPS6KA2 RPS6KA2 2165 0.28 0.47 YES
51 PTPN7 PTPN7 PTPN7 2378 0.26 0.47 YES
52 PDGFRB PDGFRB PDGFRB 2413 0.26 0.47 YES
53 NTRK1 NTRK1 NTRK1 2427 0.26 0.48 YES
54 RASGRP2 RASGRP2 RASGRP2 2613 0.24 0.48 YES
55 RASGRP3 RASGRP3 RASGRP3 2718 0.24 0.48 YES
56 CACNA1A CACNA1A CACNA1A 2760 0.23 0.48 YES
57 DUSP2 DUSP2 DUSP2 2822 0.23 0.48 YES
58 MRAS MRAS MRAS 2891 0.22 0.49 YES
59 MAPK13 MAPK13 MAPK13 3056 0.21 0.48 YES
60 CACNA1F CACNA1F CACNA1F 3106 0.21 0.49 YES
61 CACNA1D CACNA1D CACNA1D 3219 0.2 0.49 YES
62 NR4A1 NR4A1 NR4A1 3228 0.2 0.49 YES
63 HSPA2 HSPA2 HSPA2 3245 0.2 0.5 YES
64 PLA2G2D PLA2G2D PLA2G2D 3456 0.19 0.49 YES
65 PDGFB PDGFB PDGFB 3570 0.18 0.49 YES
66 RPS6KA6 RPS6KA6 RPS6KA6 3594 0.18 0.49 YES
67 RRAS RRAS RRAS 3630 0.17 0.5 YES
68 RASGRF2 RASGRF2 RASGRF2 3681 0.17 0.5 YES
69 CACNA1G CACNA1G CACNA1G 3696 0.17 0.5 YES
70 EGF EGF EGF 3750 0.17 0.5 YES
71 FGF13 FGF13 FGF13 3793 0.16 0.51 YES
72 ARRB1 ARRB1 ARRB1 3796 0.16 0.51 YES
73 HSPA6 HSPA6 HSPA6 3855 0.16 0.51 YES
74 FGF12 FGF12 FGF12 3893 0.16 0.52 YES
75 MYC MYC MYC 3924 0.16 0.52 YES
76 CACNA2D2 CACNA2D2 CACNA2D2 4057 0.15 0.52 YES
77 CACNA2D4 CACNA2D4 CACNA2D4 4058 0.15 0.52 YES
78 RELB RELB RELB 4148 0.14 0.52 YES
79 FASLG FASLG FASLG 4193 0.14 0.52 YES
80 CACNA1E CACNA1E CACNA1E 4370 0.13 0.51 YES
81 FGF9 FGF9 FGF9 4394 0.13 0.52 YES
82 TP53 TP53 TP53 4408 0.13 0.52 YES
83 FGF19 FGF19 FGF19 4465 0.13 0.52 YES
84 CACNA1S CACNA1S CACNA1S 4486 0.13 0.52 YES
85 GADD45B GADD45B GADD45B 4591 0.12 0.52 NO
86 NFKB1 NFKB1 NFKB1 4811 0.11 0.51 NO
87 NFATC2 NFATC2 NFATC2 4845 0.11 0.51 NO
88 MAPT MAPT MAPT 5012 0.1 0.51 NO
89 DUSP1 DUSP1 DUSP1 5037 0.1 0.51 NO
90 GNG12 GNG12 GNG12 5086 0.1 0.51 NO
91 MAP4K3 MAP4K3 MAP4K3 5161 0.099 0.51 NO
92 ZAK ZAK ZAK 5190 0.098 0.51 NO
93 MAP3K8 MAP3K8 MAP3K8 5238 0.096 0.51 NO
94 RPS6KA5 RPS6KA5 RPS6KA5 5255 0.095 0.51 NO
95 MAP3K1 MAP3K1 MAP3K1 5333 0.092 0.51 NO
96 TGFBR1 TGFBR1 TGFBR1 5365 0.09 0.51 NO
97 MAPK7 MAPK7 MAPK7 5399 0.089 0.51 NO
98 EGFR EGFR EGFR 5445 0.088 0.51 NO
99 NFKB2 NFKB2 NFKB2 5556 0.084 0.51 NO
100 MAPKAPK2 MAPKAPK2 MAPKAPK2 5585 0.083 0.51 NO
101 PPP3CC PPP3CC PPP3CC 5721 0.078 0.5 NO
102 PPP3CA PPP3CA PPP3CA 5725 0.078 0.5 NO
103 TGFBR2 TGFBR2 TGFBR2 5799 0.076 0.5 NO
104 DUSP7 DUSP7 DUSP7 5854 0.074 0.5 NO
105 MAX MAX MAX 5872 0.074 0.5 NO
106 ARRB2 ARRB2 ARRB2 5899 0.073 0.5 NO
107 CRK CRK CRK 5901 0.073 0.5 NO
108 IL1R1 IL1R1 IL1R1 5938 0.072 0.5 NO
109 IKBKB IKBKB IKBKB 5986 0.07 0.5 NO
110 FAS FAS FAS 6001 0.07 0.5 NO
111 MAP3K2 MAP3K2 MAP3K2 6005 0.07 0.51 NO
112 MAPKSP1 MAPKSP1 MAPKSP1 6014 0.07 0.51 NO
113 RPS6KA4 RPS6KA4 RPS6KA4 6026 0.07 0.51 NO
114 GNA12 GNA12 GNA12 6147 0.066 0.5 NO
115 DUSP8 DUSP8 DUSP8 6163 0.066 0.51 NO
116 RPS6KA1 RPS6KA1 RPS6KA1 6164 0.066 0.51 NO
117 PLA2G12A PLA2G12A PLA2G12A 6237 0.064 0.5 NO
118 MAPK3 MAPK3 MAPK3 6456 0.059 0.5 NO
119 MAP2K3 MAP2K3 MAP2K3 6478 0.059 0.5 NO
120 CACNA1I CACNA1I CACNA1I 6487 0.059 0.5 NO
121 FGF2 FGF2 FGF2 6703 0.054 0.49 NO
122 DUSP6 DUSP6 DUSP6 6741 0.053 0.48 NO
123 TNFRSF1A TNFRSF1A TNFRSF1A 6754 0.052 0.49 NO
124 MAP2K1 MAP2K1 MAP2K1 6763 0.052 0.49 NO
125 HSPA8 HSPA8 HSPA8 6814 0.051 0.48 NO
126 IL1A IL1A IL1A 6924 0.049 0.48 NO
127 PLA2G10 PLA2G10 PLA2G10 7033 0.047 0.48 NO
128 KRAS KRAS KRAS 7083 0.045 0.47 NO
129 TRAF6 TRAF6 TRAF6 7115 0.045 0.47 NO
130 PPM1B PPM1B PPM1B 7133 0.044 0.47 NO
131 PRKACA PRKACA PRKACA 7142 0.044 0.48 NO
132 RAP1B RAP1B RAP1B 7143 0.044 0.48 NO
133 RAC1 RAC1 RAC1 7148 0.044 0.48 NO
134 MAP2K4 MAP2K4 MAP2K4 7250 0.042 0.47 NO
135 STK3 STK3 STK3 7269 0.041 0.47 NO
136 PAK1 PAK1 PAK1 7355 0.04 0.47 NO
137 CACNA1B CACNA1B CACNA1B 7518 0.037 0.46 NO
138 MAPK8IP3 MAPK8IP3 MAPK8IP3 7533 0.036 0.46 NO
139 RASA1 RASA1 RASA1 7550 0.036 0.46 NO
140 MAP3K3 MAP3K3 MAP3K3 7637 0.035 0.46 NO
141 DUSP10 DUSP10 DUSP10 7724 0.033 0.45 NO
142 AKT1 AKT1 AKT1 7775 0.032 0.45 NO
143 PPP5C PPP5C PPP5C 7839 0.031 0.45 NO
144 SOS2 SOS2 SOS2 7870 0.031 0.45 NO
145 PAK2 PAK2 PAK2 7916 0.03 0.45 NO
146 RASA2 RASA2 RASA2 7937 0.03 0.45 NO
147 CDC42 CDC42 CDC42 8025 0.028 0.44 NO
148 CHP CHP CHP 8154 0.026 0.44 NO
149 PPP3CB PPP3CB PPP3CB 8192 0.026 0.43 NO
150 HSPB1 HSPB1 HSPB1 8254 0.025 0.43 NO
151 MAPK8IP1 MAPK8IP1 MAPK8IP1 8405 0.023 0.42 NO
152 RAPGEF2 RAPGEF2 RAPGEF2 8406 0.023 0.42 NO
153 DUSP16 DUSP16 DUSP16 8453 0.022 0.42 NO
154 RAP1A RAP1A RAP1A 8484 0.022 0.42 NO
155 JUN JUN JUN 8506 0.021 0.42 NO
156 ATF4 ATF4 ATF4 8565 0.02 0.42 NO
157 TAOK1 TAOK1 TAOK1 8575 0.02 0.42 NO
158 FGFR3 FGFR3 FGFR3 8591 0.02 0.42 NO
159 CD14 CD14 CD14 8608 0.02 0.42 NO
160 MAP4K4 MAP4K4 MAP4K4 8645 0.019 0.42 NO
161 RASGRF1 RASGRF1 RASGRF1 8652 0.019 0.42 NO
162 TAOK2 TAOK2 TAOK2 8660 0.019 0.42 NO
163 MAPK9 MAPK9 MAPK9 8780 0.017 0.41 NO
164 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 8820 0.017 0.41 NO
165 MKNK1 MKNK1 MKNK1 9170 0.012 0.39 NO
166 MAPK8 MAPK8 MAPK8 9184 0.012 0.39 NO
167 MAPKAPK3 MAPKAPK3 MAPKAPK3 9251 0.011 0.38 NO
168 RRAS2 RRAS2 RRAS2 9444 0.0084 0.37 NO
169 MAP2K5 MAP2K5 MAP2K5 9604 0.0065 0.36 NO
170 MAP3K14 MAP3K14 MAP3K14 9628 0.0061 0.36 NO
171 IKBKG IKBKG IKBKG 9663 0.0055 0.36 NO
172 SRF SRF SRF 9699 0.005 0.36 NO
173 MAP2K2 MAP2K2 MAP2K2 9712 0.0049 0.36 NO
174 CHP2 CHP2 CHP2 9981 0.0016 0.34 NO
175 DDIT3 DDIT3 DDIT3 10215 -0.001 0.33 NO
176 CACNG4 CACNG4 CACNG4 10295 -0.002 0.33 NO
177 JUND JUND JUND 10312 -0.0022 0.33 NO
178 CHUK CHUK CHUK 10385 -0.003 0.32 NO
179 CASP3 CASP3 CASP3 10465 -0.0041 0.32 NO
180 DUSP14 DUSP14 DUSP14 10491 -0.0044 0.32 NO
181 ELK4 ELK4 ELK4 10544 -0.0051 0.31 NO
182 NF1 NF1 NF1 10574 -0.0055 0.31 NO
183 TRAF2 TRAF2 TRAF2 10663 -0.0065 0.31 NO
184 CDC25B CDC25B CDC25B 10750 -0.0075 0.3 NO
185 PLA2G6 PLA2G6 PLA2G6 10771 -0.0078 0.3 NO
186 MKNK2 MKNK2 MKNK2 10781 -0.0079 0.3 NO
187 PRKACB PRKACB PRKACB 10812 -0.0082 0.3 NO
188 DUSP3 DUSP3 DUSP3 10817 -0.0083 0.3 NO
189 HRAS HRAS HRAS 10983 -0.01 0.29 NO
190 STK4 STK4 STK4 11019 -0.011 0.29 NO
191 MAPK1 MAPK1 MAPK1 11085 -0.012 0.28 NO
192 RELA RELA RELA 11131 -0.012 0.28 NO
193 TAOK3 TAOK3 TAOK3 11362 -0.015 0.27 NO
194 SOS1 SOS1 SOS1 11408 -0.016 0.27 NO
195 FGF21 FGF21 FGF21 11605 -0.018 0.26 NO
196 ELK1 ELK1 ELK1 11676 -0.019 0.25 NO
197 MAP4K2 MAP4K2 MAP4K2 11830 -0.021 0.25 NO
198 PPM1A PPM1A PPM1A 12133 -0.025 0.23 NO
199 GADD45G GADD45G GADD45G 12174 -0.025 0.23 NO
200 ATF2 ATF2 ATF2 12223 -0.026 0.23 NO
201 GADD45A GADD45A GADD45A 12305 -0.027 0.22 NO
202 AKT2 AKT2 AKT2 12348 -0.028 0.22 NO
203 PPP3R1 PPP3R1 PPP3R1 12388 -0.028 0.22 NO
204 FGF22 FGF22 FGF22 12411 -0.028 0.22 NO
205 CACNB4 CACNB4 CACNB4 12417 -0.028 0.22 NO
206 FLNB FLNB FLNB 12471 -0.029 0.22 NO
207 TAB1 TAB1 TAB1 12490 -0.029 0.22 NO
208 IL1R2 IL1R2 IL1R2 12499 -0.029 0.22 NO
209 MAPK8IP2 MAPK8IP2 MAPK8IP2 12646 -0.031 0.21 NO
210 MAP3K7 MAP3K7 MAP3K7 12693 -0.032 0.21 NO
211 GRB2 GRB2 GRB2 12701 -0.032 0.21 NO
212 PRKCG PRKCG PRKCG 12717 -0.032 0.21 NO
213 MAP2K7 MAP2K7 MAP2K7 12844 -0.034 0.2 NO
214 MAPK14 MAPK14 MAPK14 12885 -0.035 0.2 NO
215 TAB2 TAB2 TAB2 12988 -0.036 0.2 NO
216 NRAS NRAS NRAS 13162 -0.039 0.19 NO
217 MAP3K11 MAP3K11 MAP3K11 13208 -0.04 0.19 NO
218 RPS6KA3 RPS6KA3 RPS6KA3 13269 -0.04 0.18 NO
219 DAXX DAXX DAXX 13356 -0.041 0.18 NO
220 MAPKAPK5 MAPKAPK5 MAPKAPK5 13371 -0.042 0.18 NO
221 MAP3K4 MAP3K4 MAP3K4 13419 -0.042 0.18 NO
222 CACNB2 CACNB2 CACNB2 13629 -0.046 0.17 NO
223 NLK NLK NLK 13680 -0.047 0.17 NO
224 ECSIT ECSIT ECSIT 13683 -0.047 0.17 NO
225 MAP3K13 MAP3K13 MAP3K13 13763 -0.049 0.16 NO
226 CRKL CRKL CRKL 14312 -0.059 0.14 NO
227 FGFR4 FGFR4 FGFR4 14374 -0.06 0.13 NO
228 HSPA1B HSPA1B HSPA1B 14685 -0.068 0.12 NO
229 RAF1 RAF1 RAF1 14790 -0.07 0.11 NO
230 BRAF BRAF BRAF 14793 -0.07 0.12 NO
231 HSPA1A HSPA1A HSPA1A 15039 -0.077 0.1 NO
232 STMN1 STMN1 STMN1 15094 -0.079 0.1 NO
233 PLA2G1B PLA2G1B PLA2G1B 15146 -0.08 0.1 NO
234 PRKCA PRKCA PRKCA 15772 -0.1 0.07 NO
235 CACNG1 CACNG1 CACNG1 15830 -0.11 0.07 NO
236 HSPA1L HSPA1L HSPA1L 16628 -0.16 0.029 NO
237 FGF17 FGF17 FGF17 16631 -0.16 0.033 NO
238 DUSP9 DUSP9 DUSP9 17193 -0.21 0.0073 NO
239 PLA2G12B PLA2G12B PLA2G12B 17315 -0.23 0.0071 NO
240 MAP2K6 MAP2K6 MAP2K6 17390 -0.24 0.0099 NO
241 RAC3 RAC3 RAC3 17620 -0.32 0.0062 NO

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

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

genes ES table in pathway: BIOCARTA ERK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HAND2 HAND2 HAND2 1 1 0.14 YES
2 LIF LIF LIF 402 0.53 0.19 YES
3 PRKAR2B PRKAR2B PRKAR2B 475 0.51 0.26 YES
4 NFATC1 NFATC1 NFATC1 575 0.48 0.32 YES
5 EDN1 EDN1 EDN1 780 0.44 0.37 YES
6 CAMK4 CAMK4 CAMK4 1016 0.4 0.41 YES
7 NFATC4 NFATC4 NFATC4 1297 0.36 0.44 YES
8 CTF1 CTF1 CTF1 1333 0.36 0.49 YES
9 CAMK1G CAMK1G CAMK1G 1392 0.35 0.53 YES
10 PIK3CG PIK3CG PIK3CG 1828 0.31 0.55 YES
11 MYH2 MYH2 MYH2 2308 0.27 0.56 YES
12 PRKAR1B PRKAR1B PRKAR1B 2672 0.24 0.57 YES
13 HBEGF HBEGF HBEGF 2975 0.22 0.59 YES
14 NFATC2 NFATC2 NFATC2 4845 0.11 0.5 NO
15 PPP3CC PPP3CC PPP3CC 5721 0.078 0.46 NO
16 PPP3CA PPP3CA PPP3CA 5725 0.078 0.47 NO
17 MAPK3 MAPK3 MAPK3 6456 0.059 0.44 NO
18 FGF2 FGF2 FGF2 6703 0.054 0.43 NO
19 FKBP1A FKBP1A FKBP1A 6739 0.053 0.43 NO
20 MAP2K1 MAP2K1 MAP2K1 6763 0.052 0.44 NO
21 IGF1 IGF1 IGF1 7046 0.046 0.43 NO
22 CALM2 CALM2 CALM2 7201 0.043 0.43 NO
23 CALM1 CALM1 CALM1 7491 0.037 0.42 NO
24 AKT1 AKT1 AKT1 7775 0.032 0.4 NO
25 CSNK1A1 CSNK1A1 CSNK1A1 7949 0.03 0.4 NO
26 PIK3CA PIK3CA PIK3CA 8136 0.026 0.39 NO
27 PPP3CB PPP3CB PPP3CB 8192 0.026 0.39 NO
28 MAPK8 MAPK8 MAPK8 9184 0.012 0.34 NO
29 CREBBP CREBBP CREBBP 9648 0.0058 0.31 NO
30 CALR CALR CALR 10507 -0.0046 0.26 NO
31 PRKACB PRKACB PRKACB 10812 -0.0082 0.25 NO
32 CALM3 CALM3 CALM3 10832 -0.0086 0.25 NO
33 PRKAR1A PRKAR1A PRKAR1A 10918 -0.0096 0.24 NO
34 HRAS HRAS HRAS 10983 -0.01 0.24 NO
35 MAPK1 MAPK1 MAPK1 11085 -0.012 0.24 NO
36 GATA4 GATA4 GATA4 11511 -0.017 0.22 NO
37 GSK3B GSK3B GSK3B 11610 -0.018 0.21 NO
38 MAPK14 MAPK14 MAPK14 12885 -0.035 0.15 NO
39 NFATC3 NFATC3 NFATC3 13325 -0.041 0.13 NO
40 CAMK1 CAMK1 CAMK1 14001 -0.053 0.096 NO
41 PIK3R1 PIK3R1 PIK3R1 14760 -0.07 0.063 NO
42 RAF1 RAF1 RAF1 14790 -0.07 0.071 NO
43 PRKAR2A PRKAR2A PRKAR2A 14856 -0.072 0.077 NO
44 RPS6KB1 RPS6KB1 RPS6KB1 14869 -0.072 0.087 NO
45 AGT AGT AGT 14875 -0.072 0.096 NO
46 ACTA1 ACTA1 ACTA1 15319 -0.086 0.083 NO
47 F2 F2 F2 16930 -0.18 0.017 NO
48 NPPA NPPA NPPA 17149 -0.2 0.033 NO

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

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

genes ES table in pathway: BIOCARTA FAS PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GLI2 GLI2 GLI2 5 0.92 0.018 YES
2 LAMA2 LAMA2 LAMA2 67 0.73 0.028 YES
3 MAPK10 MAPK10 MAPK10 102 0.7 0.039 YES
4 FGF1 FGF1 FGF1 130 0.67 0.051 YES
5 PDGFRA PDGFRA PDGFRA 146 0.66 0.063 YES
6 GLI3 GLI3 GLI3 161 0.65 0.074 YES
7 WNT4 WNT4 WNT4 162 0.65 0.087 YES
8 WNT2 WNT2 WNT2 171 0.64 0.099 YES
9 MMP2 MMP2 MMP2 193 0.63 0.11 YES
10 FZD2 FZD2 FZD2 198 0.63 0.12 YES
11 WNT2B WNT2B WNT2B 315 0.56 0.13 YES
12 LAMC2 LAMC2 LAMC2 332 0.56 0.14 YES
13 ITGA3 ITGA3 ITGA3 346 0.55 0.15 YES
14 PTGS2 PTGS2 PTGS2 372 0.54 0.16 YES
15 HHIP HHIP HHIP 374 0.54 0.16 YES
16 FZD10 FZD10 FZD10 377 0.54 0.18 YES
17 FGF7 FGF7 FGF7 405 0.53 0.18 YES
18 COL4A4 COL4A4 COL4A4 420 0.53 0.19 YES
19 FGFR1 FGFR1 FGFR1 452 0.52 0.2 YES
20 LAMC3 LAMC3 LAMC3 457 0.52 0.21 YES
21 FGF18 FGF18 FGF18 500 0.5 0.22 YES
22 IGF1R IGF1R IGF1R 511 0.5 0.23 YES
23 TGFB3 TGFB3 TGFB3 550 0.49 0.23 YES
24 WNT10A WNT10A WNT10A 605 0.48 0.24 YES
25 LAMA1 LAMA1 LAMA1 621 0.47 0.25 YES
26 IL8 IL8 IL8 631 0.47 0.26 YES
27 TGFB2 TGFB2 TGFB2 644 0.47 0.26 YES
28 FZD1 FZD1 FZD1 695 0.46 0.27 YES
29 TGFA TGFA TGFA 698 0.45 0.28 YES
30 GLI1 GLI1 GLI1 700 0.45 0.29 YES
31 WNT9A WNT9A WNT9A 702 0.45 0.3 YES
32 FZD7 FZD7 FZD7 713 0.45 0.3 YES
33 FZD8 FZD8 FZD8 729 0.45 0.31 YES
34 AKT3 AKT3 AKT3 748 0.44 0.32 YES
35 MITF MITF MITF 768 0.44 0.33 YES
36 RUNX1T1 RUNX1T1 RUNX1T1 793 0.43 0.34 YES
37 HGF HGF HGF 820 0.43 0.34 YES
38 ARNT2 ARNT2 ARNT2 838 0.42 0.35 YES
39 CTBP2 CTBP2 CTBP2 868 0.42 0.36 YES
40 WNT10B WNT10B WNT10B 901 0.41 0.36 YES
41 BCL2 BCL2 BCL2 912 0.41 0.37 YES
42 VEGFC VEGFC VEGFC 928 0.41 0.38 YES
43 IL6 IL6 IL6 959 0.41 0.38 YES
44 WNT7B WNT7B WNT7B 1003 0.4 0.39 YES
45 CSF2RA CSF2RA CSF2RA 1010 0.4 0.4 YES
46 GSTP1 GSTP1 GSTP1 1056 0.39 0.4 YES
47 RARB RARB RARB 1117 0.38 0.4 YES
48 RET RET RET 1208 0.37 0.41 YES
49 PGF PGF PGF 1244 0.37 0.41 YES
50 PIK3R5 PIK3R5 PIK3R5 1370 0.36 0.41 YES
51 PRKCB PRKCB PRKCB 1538 0.33 0.41 YES
52 TGFB1 TGFB1 TGFB1 1575 0.33 0.41 YES
53 CSF3R CSF3R CSF3R 1593 0.33 0.42 YES
54 FLT3 FLT3 FLT3 1603 0.33 0.42 YES
55 MECOM MECOM MECOM 1699 0.32 0.42 YES
56 FGFR2 FGFR2 FGFR2 1727 0.32 0.43 YES
57 PDGFA PDGFA PDGFA 1768 0.31 0.43 YES
58 BIRC3 BIRC3 BIRC3 1774 0.31 0.44 YES
59 PIK3CG PIK3CG PIK3CG 1828 0.31 0.44 YES
60 RAC2 RAC2 RAC2 1875 0.3 0.44 YES
61 WNT7A WNT7A WNT7A 1877 0.3 0.45 YES
62 MMP9 MMP9 MMP9 1879 0.3 0.46 YES
63 PIK3CD PIK3CD PIK3CD 1884 0.3 0.46 YES
64 FGF14 FGF14 FGF14 1936 0.3 0.46 YES
65 FGF11 FGF11 FGF11 1941 0.3 0.47 YES
66 KIT KIT KIT 1957 0.3 0.47 YES
67 WNT11 WNT11 WNT11 2070 0.28 0.47 YES
68 FOS FOS FOS 2116 0.28 0.48 YES
69 WNT1 WNT1 WNT1 2139 0.28 0.48 YES
70 CSF1R CSF1R CSF1R 2182 0.28 0.48 YES
71 LEF1 LEF1 LEF1 2213 0.27 0.49 YES
72 COL4A2 COL4A2 COL4A2 2289 0.27 0.49 YES
73 SPI1 SPI1 SPI1 2343 0.26 0.49 YES
74 LAMB1 LAMB1 LAMB1 2397 0.26 0.49 YES
75 PDGFRB PDGFRB PDGFRB 2413 0.26 0.5 YES
76 ITGA2 ITGA2 ITGA2 2421 0.26 0.5 YES
77 PTCH2 PTCH2 PTCH2 2426 0.26 0.5 YES
78 NTRK1 NTRK1 NTRK1 2427 0.26 0.51 YES
79 PTCH1 PTCH1 PTCH1 2471 0.25 0.51 YES
80 ETS1 ETS1 ETS1 2607 0.24 0.51 YES
81 ITGAV ITGAV ITGAV 2640 0.24 0.51 YES
82 COL4A1 COL4A1 COL4A1 2792 0.23 0.51 YES
83 WNT3A WNT3A WNT3A 2845 0.23 0.51 YES
84 EGLN3 EGLN3 EGLN3 2910 0.22 0.51 YES
85 PLD1 PLD1 PLD1 2930 0.22 0.51 YES
86 RUNX1 RUNX1 RUNX1 2950 0.22 0.52 YES
87 LAMA5 LAMA5 LAMA5 3030 0.21 0.52 YES
88 TRAF5 TRAF5 TRAF5 3036 0.21 0.52 YES
89 CCNA1 CCNA1 CCNA1 3178 0.2 0.51 YES
90 CDH1 CDH1 CDH1 3179 0.2 0.52 YES
91 FZD6 FZD6 FZD6 3357 0.19 0.51 YES
92 FLT3LG FLT3LG FLT3LG 3368 0.19 0.52 YES
93 HIF1A HIF1A HIF1A 3473 0.18 0.51 YES
94 BMP2 BMP2 BMP2 3522 0.18 0.51 YES
95 NOS2 NOS2 NOS2 3547 0.18 0.52 YES
96 PDGFB PDGFB PDGFB 3570 0.18 0.52 YES
97 WNT9B WNT9B WNT9B 3585 0.18 0.52 YES
98 EGF EGF EGF 3750 0.17 0.51 YES
99 FGF13 FGF13 FGF13 3793 0.16 0.52 YES
100 WNT6 WNT6 WNT6 3803 0.16 0.52 YES
101 FZD3 FZD3 FZD3 3841 0.16 0.52 YES
102 FGF12 FGF12 FGF12 3893 0.16 0.52 YES
103 CBL CBL CBL 3919 0.16 0.52 YES
104 MYC MYC MYC 3924 0.16 0.52 YES
105 RALGDS RALGDS RALGDS 3987 0.16 0.52 YES
106 LAMA4 LAMA4 LAMA4 4025 0.15 0.52 YES
107 ITGA2B ITGA2B ITGA2B 4081 0.15 0.52 YES
108 APC2 APC2 APC2 4125 0.15 0.52 YES
109 FASLG FASLG FASLG 4193 0.14 0.52 YES
110 RB1 RB1 RB1 4262 0.14 0.52 YES
111 FGF9 FGF9 FGF9 4394 0.13 0.52 YES
112 VEGFB VEGFB VEGFB 4400 0.13 0.52 YES
113 TP53 TP53 TP53 4408 0.13 0.52 YES
114 PML PML PML 4459 0.13 0.52 YES
115 FGF19 FGF19 FGF19 4465 0.13 0.52 YES
116 TRAF1 TRAF1 TRAF1 4528 0.13 0.52 YES
117 LAMB4 LAMB4 LAMB4 4544 0.12 0.52 YES
118 PIK3R3 PIK3R3 PIK3R3 4569 0.12 0.52 YES
119 PLCG2 PLCG2 PLCG2 4644 0.12 0.52 YES
120 SLC2A1 SLC2A1 SLC2A1 4664 0.12 0.52 YES
121 RASSF5 RASSF5 RASSF5 4728 0.12 0.52 YES
122 CBLB CBLB CBLB 4807 0.11 0.52 YES
123 RALB RALB RALB 4810 0.11 0.52 YES
124 NFKB1 NFKB1 NFKB1 4811 0.11 0.52 YES
125 CCND1 CCND1 CCND1 4814 0.11 0.53 YES
126 WNT16 WNT16 WNT16 4844 0.11 0.53 YES
127 DAPK1 DAPK1 DAPK1 4942 0.11 0.52 NO
128 STAT5A STAT5A STAT5A 4953 0.11 0.52 NO
129 CDKN1A CDKN1A CDKN1A 4955 0.11 0.53 NO
130 NKX3-1 NKX3-1 NKX3-1 5027 0.1 0.52 NO
131 E2F3 E2F3 E2F3 5144 0.1 0.52 NO
132 CDK6 CDK6 CDK6 5178 0.098 0.52 NO
133 AXIN1 AXIN1 AXIN1 5274 0.094 0.52 NO
134 ITGB1 ITGB1 ITGB1 5298 0.093 0.52 NO
135 TGFBR1 TGFBR1 TGFBR1 5365 0.09 0.51 NO
136 EGFR EGFR EGFR 5445 0.088 0.51 NO
137 PPARD PPARD PPARD 5458 0.087 0.51 NO
138 EPAS1 EPAS1 EPAS1 5477 0.086 0.51 NO
139 STAT3 STAT3 STAT3 5518 0.085 0.51 NO
140 NFKB2 NFKB2 NFKB2 5556 0.084 0.51 NO
141 LAMC1 LAMC1 LAMC1 5770 0.077 0.5 NO
142 TGFBR2 TGFBR2 TGFBR2 5799 0.076 0.5 NO
143 STAT1 STAT1 STAT1 5810 0.075 0.5 NO
144 ERBB2 ERBB2 ERBB2 5826 0.075 0.5 NO
145 MAX MAX MAX 5872 0.074 0.5 NO
146 CRK CRK CRK 5901 0.073 0.5 NO
147 CDKN2B CDKN2B CDKN2B 5927 0.072 0.5 NO
148 ABL1 ABL1 ABL1 5944 0.072 0.5 NO
149 JAK1 JAK1 JAK1 5965 0.071 0.5 NO
150 COL4A6 COL4A6 COL4A6 5968 0.071 0.5 NO
151 IKBKB IKBKB IKBKB 5986 0.07 0.5 NO
152 FAS FAS FAS 6001 0.07 0.5 NO
153 PAX8 PAX8 PAX8 6245 0.064 0.49 NO
154 KITLG KITLG KITLG 6417 0.06 0.48 NO
155 MAPK3 MAPK3 MAPK3 6456 0.059 0.48 NO
156 EGLN1 EGLN1 EGLN1 6650 0.055 0.47 NO
157 SUFU SUFU SUFU 6684 0.054 0.47 NO
158 FGF2 FGF2 FGF2 6703 0.054 0.47 NO
159 LAMB3 LAMB3 LAMB3 6740 0.053 0.47 NO
160 CCDC6 CCDC6 CCDC6 6752 0.052 0.47 NO
161 MAP2K1 MAP2K1 MAP2K1 6763 0.052 0.47 NO
162 BCR BCR BCR 6766 0.052 0.47 NO
163 PIAS3 PIAS3 PIAS3 6851 0.05 0.47 NO
164 SMAD2 SMAD2 SMAD2 6912 0.049 0.46 NO
165 DAPK3 DAPK3 DAPK3 6931 0.049 0.46 NO
166 TRAF3 TRAF3 TRAF3 6994 0.047 0.46 NO
167 IGF1 IGF1 IGF1 7046 0.046 0.46 NO
168 BID BID BID 7073 0.046 0.46 NO
169 KRAS KRAS KRAS 7083 0.045 0.46 NO
170 BCL2L1 BCL2L1 BCL2L1 7085 0.045 0.46 NO
171 TRAF6 TRAF6 TRAF6 7115 0.045 0.46 NO
172 RAC1 RAC1 RAC1 7148 0.044 0.46 NO
173 ZBTB16 ZBTB16 ZBTB16 7178 0.043 0.46 NO
174 FZD4 FZD4 FZD4 7183 0.043 0.46 NO
175 NFKBIA NFKBIA NFKBIA 7273 0.041 0.45 NO
176 WNT5A WNT5A WNT5A 7279 0.041 0.45 NO
177 WNT5B WNT5B WNT5B 7290 0.041 0.46 NO
178 LAMA3 LAMA3 LAMA3 7365 0.04 0.45 NO
179 FOXO1 FOXO1 FOXO1 7410 0.039 0.45 NO
180 CYCS CYCS CYCS 7422 0.038 0.45 NO
181 JUP JUP JUP 7587 0.036 0.44 NO
182 AKT1 AKT1 AKT1 7775 0.032 0.43 NO
183 LAMB2 LAMB2 LAMB2 7799 0.032 0.43 NO
184 PTK2 PTK2 PTK2 7848 0.031 0.43 NO
185 SOS2 SOS2 SOS2 7870 0.031 0.43 NO
186 CTNNA1 CTNNA1 CTNNA1 7942 0.03 0.42 NO
187 BAX BAX BAX 7969 0.029 0.42 NO
188 BAD BAD BAD 8004 0.029 0.42 NO
189 DAPK2 DAPK2 DAPK2 8009 0.028 0.42 NO
190 APC APC APC 8023 0.028 0.42 NO
191 CDC42 CDC42 CDC42 8025 0.028 0.42 NO
192 PIK3CA PIK3CA PIK3CA 8136 0.026 0.42 NO
193 FADD FADD FADD 8409 0.023 0.4 NO
194 XIAP XIAP XIAP 8458 0.022 0.4 NO
195 JUN JUN JUN 8506 0.021 0.4 NO
196 TPM3 TPM3 TPM3 8519 0.021 0.4 NO
197 FGFR3 FGFR3 FGFR3 8591 0.02 0.39 NO
198 CBLC CBLC CBLC 8701 0.018 0.39 NO
199 MAPK9 MAPK9 MAPK9 8780 0.017 0.38 NO
200 TCEB1 TCEB1 TCEB1 8818 0.017 0.38 NO
201 RALA RALA RALA 8891 0.015 0.38 NO
202 ARAF ARAF ARAF 8957 0.014 0.37 NO
203 CASP8 CASP8 CASP8 8991 0.014 0.37 NO
204 TCF7L2 TCF7L2 TCF7L2 9172 0.012 0.36 NO
205 MAPK8 MAPK8 MAPK8 9184 0.012 0.36 NO
206 RHOA RHOA RHOA 9253 0.011 0.36 NO
207 PTEN PTEN PTEN 9257 0.011 0.36 NO
208 MMP1 MMP1 MMP1 9298 0.01 0.36 NO
209 RBX1 RBX1 RBX1 9482 0.0079 0.34 NO
210 CREBBP CREBBP CREBBP 9648 0.0058 0.34 NO
211 IKBKG IKBKG IKBKG 9663 0.0055 0.34 NO
212 MAP2K2 MAP2K2 MAP2K2 9712 0.0049 0.33 NO
213 PIK3CB PIK3CB PIK3CB 9781 0.0041 0.33 NO
214 RASSF1 RASSF1 RASSF1 9809 0.0037 0.33 NO
215 FN1 FN1 FN1 9821 0.0036 0.33 NO
216 TCEB2 TCEB2 TCEB2 9877 0.0028 0.32 NO
217 HSP90AA1 HSP90AA1 HSP90AA1 10025 0.0012 0.32 NO
218 HDAC1 HDAC1 HDAC1 10089 0.00055 0.31 NO
219 SMAD3 SMAD3 SMAD3 10237 -0.0012 0.3 NO
220 APPL1 APPL1 APPL1 10346 -0.0026 0.3 NO
221 RALBP1 RALBP1 RALBP1 10383 -0.0029 0.3 NO
222 CHUK CHUK CHUK 10385 -0.003 0.3 NO
223 CTBP1 CTBP1 CTBP1 10395 -0.0031 0.29 NO
224 CASP3 CASP3 CASP3 10465 -0.0041 0.29 NO
225 PIAS2 PIAS2 PIAS2 10575 -0.0055 0.28 NO
226 TCF7L1 TCF7L1 TCF7L1 10620 -0.006 0.28 NO
227 TRAF2 TRAF2 TRAF2 10663 -0.0065 0.28 NO
228 FZD9 FZD9 FZD9 10675 -0.0067 0.28 NO
229 WNT3 WNT3 WNT3 10734 -0.0072 0.28 NO
230 HSP90B1 HSP90B1 HSP90B1 10851 -0.0088 0.27 NO
231 STK4 STK4 STK4 11019 -0.011 0.26 NO
232 HSP90AB1 HSP90AB1 HSP90AB1 11079 -0.012 0.26 NO
233 MAPK1 MAPK1 MAPK1 11085 -0.012 0.26 NO
234 RELA RELA RELA 11131 -0.012 0.25 NO
235 PIAS4 PIAS4 PIAS4 11137 -0.012 0.25 NO
236 HDAC2 HDAC2 HDAC2 11195 -0.013 0.25 NO
237 RARA RARA RARA 11221 -0.013 0.25 NO
238 SMAD4 SMAD4 SMAD4 11225 -0.013 0.25 NO
239 MLH1 MLH1 MLH1 11232 -0.014 0.25 NO
240 EGLN2 EGLN2 EGLN2 11291 -0.014 0.25 NO
241 MDM2 MDM2 MDM2 11363 -0.015 0.24 NO
242 SOS1 SOS1 SOS1 11408 -0.016 0.24 NO
243 DVL3 DVL3 DVL3 11435 -0.016 0.24 NO
244 AXIN2 AXIN2 AXIN2 11458 -0.016 0.24 NO
245 EP300 EP300 EP300 11540 -0.017 0.24 NO
246 PLCG1 PLCG1 PLCG1 11593 -0.018 0.23 NO
247 FGF21 FGF21 FGF21 11605 -0.018 0.23 NO
248 GSK3B GSK3B GSK3B 11610 -0.018 0.23 NO
249 FH FH FH 11669 -0.019 0.23 NO
250 PIK3R2 PIK3R2 PIK3R2 11746 -0.02 0.22 NO
251 RXRG RXRG RXRG 11870 -0.021 0.22 NO
252 MSH3 MSH3 MSH3 12083 -0.024 0.21 NO
253 BIRC2 BIRC2 BIRC2 12209 -0.026 0.2 NO
254 AKT2 AKT2 AKT2 12348 -0.028 0.19 NO
255 TFG TFG TFG 12362 -0.028 0.19 NO
256 FGF22 FGF22 FGF22 12411 -0.028 0.19 NO
257 TPR TPR TPR 12508 -0.03 0.18 NO
258 DVL1 DVL1 DVL1 12659 -0.032 0.18 NO
259 GRB2 GRB2 GRB2 12701 -0.032 0.18 NO
260 PRKCG PRKCG PRKCG 12717 -0.032 0.18 NO
261 DVL2 DVL2 DVL2 12767 -0.033 0.17 NO
262 CDKN1B CDKN1B CDKN1B 12895 -0.035 0.17 NO
263 CTNNB1 CTNNB1 CTNNB1 12896 -0.035 0.17 NO
264 MTOR MTOR MTOR 12905 -0.035 0.17 NO
265 CCNE1 CCNE1 CCNE1 12938 -0.036 0.17 NO
266 ITGA6 ITGA6 ITGA6 12983 -0.036 0.16 NO
267 CASP9 CASP9 CASP9 13049 -0.037 0.16 NO
268 STAT5B STAT5B STAT5B 13085 -0.038 0.16 NO
269 CDK4 CDK4 CDK4 13105 -0.038 0.16 NO
270 CUL2 CUL2 CUL2 13120 -0.038 0.16 NO
271 NRAS NRAS NRAS 13162 -0.039 0.16 NO
272 ARNT ARNT ARNT 13197 -0.039 0.16 NO
273 MSH6 MSH6 MSH6 13270 -0.04 0.15 NO
274 VHL VHL VHL 13398 -0.042 0.15 NO
275 RXRA RXRA RXRA 13551 -0.045 0.14 NO
276 VEGFA VEGFA VEGFA 13730 -0.048 0.13 NO
277 NCOA4 NCOA4 NCOA4 14022 -0.054 0.11 NO
278 TRAF4 TRAF4 TRAF4 14052 -0.054 0.11 NO
279 CRKL CRKL CRKL 14312 -0.059 0.1 NO
280 CKS1B CKS1B CKS1B 14373 -0.06 0.097 NO
281 STK36 STK36 STK36 14462 -0.063 0.093 NO
282 SHH SHH SHH 14717 -0.069 0.08 NO
283 PIK3R1 PIK3R1 PIK3R1 14760 -0.07 0.079 NO
284 PIAS1 PIAS1 PIAS1 14761 -0.07 0.08 NO
285 RAF1 RAF1 RAF1 14790 -0.07 0.08 NO
286 BRAF BRAF BRAF 14793 -0.07 0.081 NO
287 RXRB RXRB RXRB 14964 -0.075 0.073 NO
288 BMP4 BMP4 BMP4 15122 -0.08 0.066 NO
289 FZD5 FZD5 FZD5 15131 -0.08 0.067 NO
290 MSH2 MSH2 MSH2 15214 -0.082 0.064 NO
291 MET MET MET 15509 -0.093 0.048 NO
292 CDK2 CDK2 CDK2 15701 -0.1 0.039 NO
293 AR AR AR 15756 -0.1 0.038 NO
294 PRKCA PRKCA PRKCA 15772 -0.1 0.039 NO
295 E2F2 E2F2 E2F2 16011 -0.12 0.028 NO
296 CEBPA CEBPA CEBPA 16184 -0.12 0.02 NO
297 PPARG PPARG PPARG 16361 -0.14 0.013 NO
298 RAD51 RAD51 RAD51 16385 -0.14 0.014 NO
299 CCNE2 CCNE2 CCNE2 16531 -0.15 0.0088 NO
300 FGF17 FGF17 FGF17 16631 -0.16 0.0062 NO
301 CTNNA3 CTNNA3 CTNNA3 16715 -0.16 0.0045 NO
302 SMO SMO SMO 16853 -0.17 0.000022 NO
303 BRCA2 BRCA2 BRCA2 16871 -0.18 0.0024 NO
304 WNT8B WNT8B WNT8B 17064 -0.19 -0.0049 NO
305 FIGF FIGF FIGF 17088 -0.2 -0.0024 NO
306 CDKN2A CDKN2A CDKN2A 17201 -0.21 -0.0047 NO
307 TCF7 TCF7 TCF7 17245 -0.22 -0.003 NO
308 E2F1 E2F1 E2F1 17261 -0.22 0.00036 NO
309 BIRC5 BIRC5 BIRC5 17368 -0.24 -0.0011 NO
310 DCC DCC DCC 17432 -0.25 0.00014 NO
311 CTNNA2 CTNNA2 CTNNA2 17452 -0.26 0.004 NO
312 SKP2 SKP2 SKP2 17533 -0.29 0.0049 NO
313 RAC3 RAC3 RAC3 17620 -0.32 0.0062 NO

Figure S77.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FAS PATHWAY.

Figure S78.  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 FCER1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TGFB3 TGFB3 TGFB3 550 0.49 0.027 YES
2 TGFB2 TGFB2 TGFB2 644 0.47 0.078 YES
3 TGFA TGFA TGFA 698 0.45 0.13 YES
4 AKT3 AKT3 AKT3 748 0.44 0.18 YES
5 HGF HGF HGF 820 0.43 0.23 YES
6 ARNT2 ARNT2 ARNT2 838 0.42 0.28 YES
7 VEGFC VEGFC VEGFC 928 0.41 0.32 YES
8 PGF PGF PGF 1244 0.37 0.35 YES
9 PIK3R5 PIK3R5 PIK3R5 1370 0.36 0.38 YES
10 TGFB1 TGFB1 TGFB1 1575 0.33 0.41 YES
11 PIK3CG PIK3CG PIK3CG 1828 0.31 0.43 YES
12 PIK3CD PIK3CD PIK3CD 1884 0.3 0.47 YES
13 PAK7 PAK7 PAK7 2424 0.26 0.47 YES
14 ETS1 ETS1 ETS1 2607 0.24 0.48 YES
15 EGLN3 EGLN3 EGLN3 2910 0.22 0.5 YES
16 PAK3 PAK3 PAK3 3461 0.19 0.49 YES
17 HIF1A HIF1A HIF1A 3473 0.18 0.51 YES
18 PDGFB PDGFB PDGFB 3570 0.18 0.52 YES
19 PAK6 PAK6 PAK6 4254 0.14 0.5 NO
20 VEGFB VEGFB VEGFB 4400 0.13 0.51 NO
21 PIK3R3 PIK3R3 PIK3R3 4569 0.12 0.51 NO
22 SLC2A1 SLC2A1 SLC2A1 4664 0.12 0.52 NO
23 EPAS1 EPAS1 EPAS1 5477 0.086 0.49 NO
24 CRK CRK CRK 5901 0.073 0.47 NO
25 MAPK3 MAPK3 MAPK3 6456 0.059 0.45 NO
26 EGLN1 EGLN1 EGLN1 6650 0.055 0.44 NO
27 MAP2K1 MAP2K1 MAP2K1 6763 0.052 0.44 NO
28 KRAS KRAS KRAS 7083 0.045 0.43 NO
29 RAP1B RAP1B RAP1B 7143 0.044 0.43 NO
30 GAB1 GAB1 GAB1 7147 0.044 0.44 NO
31 RAC1 RAC1 RAC1 7148 0.044 0.44 NO
32 RAPGEF1 RAPGEF1 RAPGEF1 7289 0.041 0.44 NO
33 PAK1 PAK1 PAK1 7355 0.04 0.44 NO
34 AKT1 AKT1 AKT1 7775 0.032 0.42 NO
35 SOS2 SOS2 SOS2 7870 0.031 0.42 NO
36 PAK2 PAK2 PAK2 7916 0.03 0.42 NO
37 CDC42 CDC42 CDC42 8025 0.028 0.42 NO
38 PIK3CA PIK3CA PIK3CA 8136 0.026 0.42 NO
39 RAP1A RAP1A RAP1A 8484 0.022 0.4 NO
40 JUN JUN JUN 8506 0.021 0.4 NO
41 TCEB1 TCEB1 TCEB1 8818 0.017 0.38 NO
42 ARAF ARAF ARAF 8957 0.014 0.38 NO
43 RBX1 RBX1 RBX1 9482 0.0079 0.35 NO
44 CREBBP CREBBP CREBBP 9648 0.0058 0.34 NO
45 MAP2K2 MAP2K2 MAP2K2 9712 0.0049 0.34 NO
46 FLCN FLCN FLCN 9721 0.0048 0.34 NO
47 PIK3CB PIK3CB PIK3CB 9781 0.0041 0.34 NO
48 TCEB2 TCEB2 TCEB2 9877 0.0028 0.33 NO
49 PTPN11 PTPN11 PTPN11 10976 -0.01 0.27 NO
50 MAPK1 MAPK1 MAPK1 11085 -0.012 0.26 NO
51 EGLN2 EGLN2 EGLN2 11291 -0.014 0.25 NO
52 SOS1 SOS1 SOS1 11408 -0.016 0.25 NO
53 PAK4 PAK4 PAK4 11444 -0.016 0.25 NO
54 EP300 EP300 EP300 11540 -0.017 0.25 NO
55 FH FH FH 11669 -0.019 0.24 NO
56 PIK3R2 PIK3R2 PIK3R2 11746 -0.02 0.24 NO
57 AKT2 AKT2 AKT2 12348 -0.028 0.21 NO
58 GRB2 GRB2 GRB2 12701 -0.032 0.19 NO
59 CUL2 CUL2 CUL2 13120 -0.038 0.17 NO
60 NRAS NRAS NRAS 13162 -0.039 0.18 NO
61 ARNT ARNT ARNT 13197 -0.039 0.18 NO
62 VHL VHL VHL 13398 -0.042 0.17 NO
63 VEGFA VEGFA VEGFA 13730 -0.048 0.16 NO
64 CRKL CRKL CRKL 14312 -0.059 0.13 NO
65 PIK3R1 PIK3R1 PIK3R1 14760 -0.07 0.12 NO
66 RAF1 RAF1 RAF1 14790 -0.07 0.12 NO
67 BRAF BRAF BRAF 14793 -0.07 0.13 NO
68 MET MET MET 15509 -0.093 0.1 NO
69 FIGF FIGF FIGF 17088 -0.2 0.036 NO

Figure S79.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 clus5 enriched pathways

Table 7.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.35 1.2 0.29 0.6 1 0.28 0.14 0.24 0.54 0.13
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS 26 genes.ES.table 0.7 1.4 0.13 0.67 0.96 0.54 0.086 0.49 0.53 0.21
KEGG FATTY ACID METABOLISM 41 genes.ES.table 0.68 1.6 0.028 1 0.72 0.56 0.14 0.48 0.84 0.45
KEGG STEROID HORMONE BIOSYNTHESIS 51 genes.ES.table 0.65 1.4 0.086 0.67 0.95 0.53 0.093 0.48 0.52 0.22
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.53 1.4 0.19 0.62 0.97 0.63 0.21 0.5 0.49 0.18
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.38 1.3 0.25 0.62 0.99 0.35 0.19 0.28 0.54 0.16
KEGG TYROSINE METABOLISM 39 genes.ES.table 0.57 1.5 0.047 0.73 0.86 0.41 0.11 0.37 0.5 0.25
KEGG TRYPTOPHAN METABOLISM 38 genes.ES.table 0.48 1.2 0.22 0.61 1 0.34 0.087 0.31 0.53 0.14
KEGG PROPANOATE METABOLISM 31 genes.ES.table 0.43 1.1 0.36 0.69 1 0.48 0.17 0.4 0.64 0.17
KEGG BUTANOATE METABOLISM 30 genes.ES.table 0.55 1.4 0.15 0.58 0.97 0.57 0.17 0.47 0.46 0.15
genes ES table in pathway: BIOCARTA WNT PATHWAY

Table S41.  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 ACSL6 ACSL6 ACSL6 55 0.77 0.11 YES
2 ACSL5 ACSL5 ACSL5 174 0.48 0.18 YES
3 ADH1B ADH1B ADH1B 194 0.47 0.25 YES
4 ADH4 ADH4 ADH4 230 0.43 0.32 YES
5 ADH6 ADH6 ADH6 237 0.43 0.38 YES
6 EHHADH EHHADH EHHADH 627 0.26 0.4 YES
7 ADH1C ADH1C ADH1C 691 0.25 0.43 YES
8 ALDH3A2 ALDH3A2 ALDH3A2 878 0.22 0.46 YES
9 ACADL ACADL ACADL 1071 0.19 0.47 YES
10 ADH7 ADH7 ADH7 1082 0.19 0.5 YES
11 HADH HADH HADH 1253 0.17 0.52 YES
12 ALDH2 ALDH2 ALDH2 1357 0.16 0.54 YES
13 ALDH1B1 ALDH1B1 ALDH1B1 1361 0.16 0.56 YES
14 GCDH GCDH GCDH 1464 0.15 0.57 YES
15 ACADSB ACADSB ACADSB 1529 0.14 0.59 YES
16 ACAA1 ACAA1 ACAA1 1658 0.13 0.61 YES
17 PECI PECI PECI 1793 0.12 0.62 YES
18 ADH5 ADH5 ADH5 1876 0.12 0.63 YES
19 ADH1A ADH1A ADH1A 1914 0.12 0.64 YES
20 DCI DCI DCI 1958 0.11 0.66 YES
21 CPT2 CPT2 CPT2 2064 0.11 0.67 YES
22 ACADM ACADM ACADM 2401 0.09 0.66 YES
23 ECHS1 ECHS1 ECHS1 2429 0.088 0.68 YES
24 CYP4A11 CYP4A11 CYP4A11 2821 0.073 0.67 NO
25 ALDH7A1 ALDH7A1 ALDH7A1 2851 0.072 0.68 NO
26 ALDH9A1 ALDH9A1 ALDH9A1 3054 0.065 0.67 NO
27 CPT1C CPT1C CPT1C 3308 0.058 0.67 NO
28 CYP4A22 CYP4A22 CYP4A22 3394 0.056 0.67 NO
29 ACAA2 ACAA2 ACAA2 3577 0.051 0.67 NO
30 ACSL1 ACSL1 ACSL1 4345 0.034 0.63 NO
31 ACADVL ACADVL ACADVL 4486 0.032 0.63 NO
32 ACAT1 ACAT1 ACAT1 4859 0.024 0.61 NO
33 ACSL3 ACSL3 ACSL3 4948 0.022 0.61 NO
34 HADHB HADHB HADHB 5851 0.0068 0.56 NO
35 HADHA HADHA HADHA 5855 0.0068 0.56 NO
36 ACAT2 ACAT2 ACAT2 7881 -0.024 0.45 NO
37 ACADS ACADS ACADS 8671 -0.037 0.41 NO
38 ACOX3 ACOX3 ACOX3 8819 -0.04 0.41 NO
39 CPT1A CPT1A CPT1A 9156 -0.046 0.4 NO
40 CPT1B CPT1B CPT1B 12074 -0.13 0.25 NO
41 ACSL4 ACSL4 ACSL4 16983 -0.46 0.042 NO

Figure S81.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA WNT PATHWAY.

Figure S82.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA WNT PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

Table S42.  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 UGT1A3 UGT1A3 UGT1A3 49 0.78 0.1 YES
2 UGT1A5 UGT1A5 UGT1A5 56 0.76 0.21 YES
3 UGT1A4 UGT1A4 UGT1A4 74 0.69 0.3 YES
4 UGT1A1 UGT1A1 UGT1A1 181 0.48 0.36 YES
5 UGT1A9 UGT1A9 UGT1A9 302 0.38 0.41 YES
6 UGT1A6 UGT1A6 UGT1A6 469 0.31 0.44 YES
7 UGT2B28 UGT2B28 UGT2B28 496 0.31 0.48 YES
8 ALAS1 ALAS1 ALAS1 514 0.3 0.52 YES
9 UGT2B10 UGT2B10 UGT2B10 607 0.27 0.56 YES
10 UGT2B7 UGT2B7 UGT2B7 937 0.21 0.56 YES
11 ALAD ALAD ALAD 1068 0.19 0.58 YES
12 UGT1A8 UGT1A8 UGT1A8 1170 0.18 0.6 YES
13 UGT2B11 UGT2B11 UGT2B11 1269 0.16 0.62 YES
14 MMAB MMAB MMAB 1378 0.15 0.64 YES
15 UGT2B4 UGT2B4 UGT2B4 1532 0.14 0.65 YES
16 BLVRB BLVRB BLVRB 1820 0.12 0.65 YES
17 UGT2B15 UGT2B15 UGT2B15 2095 0.1 0.64 YES
18 HMOX2 HMOX2 HMOX2 2237 0.098 0.65 YES
19 EARS2 EARS2 EARS2 2398 0.09 0.65 YES
20 PPOX PPOX PPOX 2490 0.086 0.66 YES
21 FECH FECH FECH 2896 0.07 0.65 NO
22 UROS UROS UROS 3307 0.058 0.63 NO
23 COX15 COX15 COX15 3502 0.053 0.63 NO
24 UROD UROD UROD 5578 0.012 0.51 NO
25 EPRS EPRS EPRS 5931 0.0054 0.49 NO
26 CPOX CPOX CPOX 5987 0.0045 0.49 NO
27 COX10 COX10 COX10 6947 -0.01 0.44 NO
28 HMBS HMBS HMBS 7220 -0.014 0.42 NO
29 ALAS2 ALAS2 ALAS2 7664 -0.021 0.4 NO
30 UGT1A7 UGT1A7 UGT1A7 7830 -0.024 0.4 NO
31 FTH1 FTH1 FTH1 8529 -0.034 0.36 NO
32 GUSB GUSB GUSB 9575 -0.054 0.31 NO
33 HMOX1 HMOX1 HMOX1 11236 -0.097 0.23 NO
34 CP CP CP 11957 -0.12 0.21 NO
35 UGT2A1 UGT2A1 UGT2A1 12806 -0.16 0.18 NO
36 UGT1A10 UGT1A10 UGT1A10 13047 -0.17 0.19 NO
37 UGT2A3 UGT2A3 UGT2A3 13587 -0.2 0.19 NO
38 BLVRA BLVRA BLVRA 15959 -0.35 0.1 NO

Figure S83.  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 S84.  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 FATTY ACID METABOLISM

Table S43.  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 NARS2 NARS2 NARS2 1174 0.18 0.022 YES
2 FARS2 FARS2 FARS2 1363 0.16 0.09 YES
3 EARS2 EARS2 EARS2 2398 0.09 0.076 YES
4 PSTK PSTK PSTK 2409 0.089 0.12 YES
5 SEPSECS SEPSECS SEPSECS 2648 0.08 0.15 YES
6 PARS2 PARS2 PARS2 2995 0.067 0.16 YES
7 IARS2 IARS2 IARS2 3114 0.063 0.19 YES
8 VARS VARS VARS 3510 0.053 0.19 YES
9 KARS KARS KARS 3520 0.052 0.22 YES
10 HARS2 HARS2 HARS2 3549 0.052 0.24 YES
11 AARS AARS AARS 3580 0.051 0.26 YES
12 HARS HARS HARS 3973 0.042 0.26 YES
13 DARS DARS DARS 4200 0.037 0.27 YES
14 RARS RARS RARS 4283 0.035 0.28 YES
15 MTFMT MTFMT MTFMT 4555 0.03 0.28 YES
16 LARS2 LARS2 LARS2 4919 0.023 0.27 YES
17 QARS QARS QARS 5376 0.015 0.26 YES
18 AARS2 AARS2 AARS2 5826 0.0073 0.23 YES
19 FARSB FARSB FARSB 5870 0.0065 0.24 YES
20 EPRS EPRS EPRS 5931 0.0054 0.23 YES
21 VARS2 VARS2 VARS2 6163 0.0016 0.22 YES
22 NARS NARS NARS 6268 9.8e-06 0.22 YES
23 FARSA FARSA FARSA 6468 -0.003 0.21 YES
24 YARS2 YARS2 YARS2 7227 -0.015 0.17 YES
25 IARS IARS IARS 7233 -0.015 0.18 YES
26 DARS2 DARS2 DARS2 7364 -0.017 0.18 YES
27 WARS2 WARS2 WARS2 7956 -0.025 0.16 YES
28 TARSL2 TARSL2 TARSL2 8276 -0.031 0.16 YES
29 LARS LARS LARS 8524 -0.034 0.16 YES
30 WARS WARS WARS 9386 -0.05 0.14 YES
31 RARS2 RARS2 RARS2 9424 -0.051 0.16 YES
32 CARS2 CARS2 CARS2 9506 -0.052 0.18 YES
33 SARS SARS SARS 9863 -0.06 0.19 YES
34 YARS YARS YARS 9883 -0.061 0.22 YES
35 MARS MARS MARS 10114 -0.066 0.24 YES
36 GARS GARS GARS 10156 -0.067 0.27 YES
37 MARS2 MARS2 MARS2 10376 -0.072 0.3 YES
38 SARS2 SARS2 SARS2 10427 -0.073 0.33 YES
39 CARS CARS CARS 10774 -0.082 0.35 YES
40 TARS TARS TARS 10784 -0.082 0.39 YES

Figure S85.  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 S86.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FATTY ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

Table S44.  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 ALDH3A1 ALDH3A1 ALDH3A1 6 1.2 0.15 YES
2 AOX1 AOX1 AOX1 177 0.48 0.21 YES
3 ADH1B ADH1B ADH1B 194 0.47 0.27 YES
4 HPD HPD HPD 216 0.44 0.32 YES
5 ADH4 ADH4 ADH4 230 0.43 0.38 YES
6 ADH6 ADH6 ADH6 237 0.43 0.44 YES
7 ADH1C ADH1C ADH1C 691 0.25 0.44 YES
8 HGD HGD HGD 784 0.23 0.47 YES
9 NAT6 NAT6 NAT6 851 0.22 0.5 YES
10 ADH7 ADH7 ADH7 1082 0.19 0.51 YES
11 DDC DDC DDC 1147 0.18 0.53 YES
12 MAOA MAOA MAOA 1509 0.14 0.53 YES
13 MAOB MAOB MAOB 1541 0.14 0.54 YES
14 AOC2 AOC2 AOC2 1767 0.12 0.55 YES
15 ADH5 ADH5 ADH5 1876 0.12 0.56 YES
16 ADH1A ADH1A ADH1A 1914 0.12 0.57 YES
17 GSTZ1 GSTZ1 GSTZ1 2261 0.096 0.56 NO
18 TAT TAT TAT 2485 0.086 0.56 NO
19 LCMT2 LCMT2 LCMT2 2658 0.079 0.56 NO
20 HEMK1 HEMK1 HEMK1 3383 0.056 0.53 NO
21 DCT DCT DCT 3695 0.048 0.52 NO
22 PNMT PNMT PNMT 3746 0.047 0.52 NO
23 WBSCR22 WBSCR22 WBSCR22 4235 0.036 0.5 NO
24 COMT COMT COMT 4258 0.036 0.5 NO
25 GOT2 GOT2 GOT2 4496 0.031 0.49 NO
26 FAH FAH FAH 5555 0.012 0.43 NO
27 MIF MIF MIF 5583 0.012 0.43 NO
28 METTL2B METTL2B METTL2B 6408 -0.0021 0.39 NO
29 METTL6 METTL6 METTL6 6516 -0.0038 0.38 NO
30 TRMT11 TRMT11 TRMT11 6987 -0.011 0.36 NO
31 LCMT1 LCMT1 LCMT1 10010 -0.064 0.19 NO
32 AOC3 AOC3 AOC3 10692 -0.08 0.17 NO
33 DBH DBH DBH 12789 -0.16 0.069 NO
34 GOT1 GOT1 GOT1 13119 -0.17 0.073 NO
35 TH TH TH 13354 -0.19 0.084 NO
36 ALDH1A3 ALDH1A3 ALDH1A3 14455 -0.25 0.055 NO
37 ALDH3B1 ALDH3B1 ALDH3B1 14713 -0.26 0.075 NO
38 ALDH3B2 ALDH3B2 ALDH3B2 16070 -0.36 0.046 NO
39 IL4I1 IL4I1 IL4I1 16146 -0.36 0.089 NO

Figure S87.  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 S88.  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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION

Table S45.  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 ACSL6 ACSL6 ACSL6 55 0.77 0.077 YES
2 AMACR AMACR AMACR 130 0.57 0.13 YES
3 ACSL5 ACSL5 ACSL5 174 0.48 0.18 YES
4 HAO1 HAO1 HAO1 589 0.27 0.18 YES
5 EHHADH EHHADH EHHADH 627 0.26 0.21 YES
6 PEX11G PEX11G PEX11G 703 0.25 0.23 YES
7 PEX12 PEX12 PEX12 773 0.23 0.25 YES
8 BAAT BAAT BAAT 877 0.22 0.27 YES
9 HSD17B4 HSD17B4 HSD17B4 897 0.21 0.29 YES
10 PEX11A PEX11A PEX11A 967 0.2 0.31 YES
11 PECR PECR PECR 1167 0.18 0.31 YES
12 DAO DAO DAO 1171 0.18 0.33 YES
13 MLYCD MLYCD MLYCD 1379 0.15 0.34 YES
14 GNPAT GNPAT GNPAT 1487 0.14 0.34 YES
15 DECR2 DECR2 DECR2 1510 0.14 0.36 YES
16 SOD1 SOD1 SOD1 1548 0.14 0.37 YES
17 PIPOX PIPOX PIPOX 1568 0.14 0.38 YES
18 ACAA1 ACAA1 ACAA1 1658 0.13 0.39 YES
19 MVK MVK MVK 1690 0.13 0.4 YES
20 PEX5 PEX5 PEX5 1743 0.12 0.41 YES
21 PECI PECI PECI 1793 0.12 0.42 YES
22 PAOX PAOX PAOX 1881 0.12 0.43 YES
23 PEX6 PEX6 PEX6 2010 0.11 0.44 YES
24 CAT CAT CAT 2011 0.11 0.45 YES
25 HMGCL HMGCL HMGCL 2058 0.11 0.46 YES
26 SCP2 SCP2 SCP2 2167 0.1 0.46 YES
27 EPHX2 EPHX2 EPHX2 2236 0.098 0.46 YES
28 PEX14 PEX14 PEX14 2287 0.095 0.47 YES
29 IDH1 IDH1 IDH1 2327 0.093 0.48 YES
30 CRAT CRAT CRAT 2351 0.092 0.49 YES
31 PMVK PMVK PMVK 2692 0.078 0.48 YES
32 ABCD3 ABCD3 ABCD3 2709 0.077 0.48 YES
33 PEX19 PEX19 PEX19 2718 0.077 0.49 YES
34 PEX2 PEX2 PEX2 2824 0.073 0.49 YES
35 ACOX1 ACOX1 ACOX1 2833 0.073 0.5 YES
36 DHRS4 DHRS4 DHRS4 2890 0.071 0.5 YES
37 PEX10 PEX10 PEX10 3002 0.067 0.5 YES
38 GSTK1 GSTK1 GSTK1 3034 0.066 0.51 YES
39 HACL1 HACL1 HACL1 3275 0.059 0.5 NO
40 PEX1 PEX1 PEX1 3538 0.052 0.49 NO
41 PXMP2 PXMP2 PXMP2 3786 0.046 0.48 NO
42 PEX11B PEX11B PEX11B 3882 0.044 0.48 NO
43 ECH1 ECH1 ECH1 4190 0.037 0.47 NO
44 ACSL1 ACSL1 ACSL1 4345 0.034 0.46 NO
45 SLC27A2 SLC27A2 SLC27A2 4510 0.031 0.46 NO
46 ABCD2 ABCD2 ABCD2 4591 0.029 0.46 NO
47 PEX13 PEX13 PEX13 4835 0.024 0.45 NO
48 ACSL3 ACSL3 ACSL3 4948 0.022 0.44 NO
49 PRDX1 PRDX1 PRDX1 5005 0.021 0.44 NO
50 AGPS AGPS AGPS 5500 0.013 0.41 NO
51 NUDT12 NUDT12 NUDT12 5756 0.0086 0.4 NO
52 DDO DDO DDO 5831 0.0072 0.4 NO
53 PEX26 PEX26 PEX26 5899 0.0059 0.39 NO
54 ABCD1 ABCD1 ABCD1 6648 -0.0059 0.35 NO
55 NUDT19 NUDT19 NUDT19 6753 -0.0074 0.35 NO
56 PEX16 PEX16 PEX16 6822 -0.0084 0.34 NO
57 PEX3 PEX3 PEX3 7040 -0.011 0.33 NO
58 PEX7 PEX7 PEX7 7237 -0.015 0.32 NO
59 ABCD4 ABCD4 ABCD4 7389 -0.017 0.32 NO
60 IDH2 IDH2 IDH2 7601 -0.02 0.31 NO
61 ACOT8 ACOT8 ACOT8 7776 -0.023 0.3 NO
62 PXMP4 PXMP4 PXMP4 8488 -0.034 0.26 NO
63 SLC25A17 SLC25A17 SLC25A17 8704 -0.038 0.25 NO
64 ACOX3 ACOX3 ACOX3 8819 -0.04 0.25 NO
65 NOS2 NOS2 NOS2 8954 -0.042 0.25 NO
66 PRDX5 PRDX5 PRDX5 9621 -0.055 0.22 NO
67 AGXT AGXT AGXT 9655 -0.056 0.22 NO
68 PHYH PHYH PHYH 9780 -0.058 0.22 NO
69 SOD2 SOD2 SOD2 9787 -0.058 0.22 NO
70 MPV17 MPV17 MPV17 10449 -0.074 0.2 NO
71 MPV17L MPV17L MPV17L 11824 -0.12 0.13 NO
72 CROT CROT CROT 14066 -0.23 0.026 NO
73 XDH XDH XDH 14964 -0.28 0.0048 NO
74 HAO2 HAO2 HAO2 15025 -0.28 0.031 NO
75 FAR1 FAR1 FAR1 15562 -0.32 0.034 NO
76 FAR2 FAR2 FAR2 16571 -0.4 0.018 NO
77 ACSL4 ACSL4 ACSL4 16983 -0.46 0.042 NO

Figure S89.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S90.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG LYSINE DEGRADATION

Table S46.  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 ALDH3A1 ALDH3A1 ALDH3A1 6 1.2 0.066 YES
2 CYP1A1 CYP1A1 CYP1A1 15 1 0.12 YES
3 UGT1A3 UGT1A3 UGT1A3 49 0.78 0.17 YES
4 UGT1A5 UGT1A5 UGT1A5 56 0.76 0.21 YES
5 CYP1A2 CYP1A2 CYP1A2 64 0.74 0.25 YES
6 UGT1A4 UGT1A4 UGT1A4 74 0.69 0.29 YES
7 CYP2E1 CYP2E1 CYP2E1 92 0.64 0.33 YES
8 UGT1A1 UGT1A1 UGT1A1 181 0.48 0.35 YES
9 ADH1B ADH1B ADH1B 194 0.47 0.38 YES
10 ADH4 ADH4 ADH4 230 0.43 0.4 YES
11 ADH6 ADH6 ADH6 237 0.43 0.42 YES
12 UGT1A9 UGT1A9 UGT1A9 302 0.38 0.44 YES
13 CYP2C9 CYP2C9 CYP2C9 386 0.34 0.46 YES
14 AKR1C2 AKR1C2 AKR1C2 455 0.32 0.47 YES
15 UGT1A6 UGT1A6 UGT1A6 469 0.31 0.49 YES
16 CYP3A43 CYP3A43 CYP3A43 485 0.31 0.5 YES
17 UGT2B28 UGT2B28 UGT2B28 496 0.31 0.52 YES
18 AKR1C1 AKR1C1 AKR1C1 602 0.27 0.53 YES
19 UGT2B10 UGT2B10 UGT2B10 607 0.27 0.55 YES
20 ADH1C ADH1C ADH1C 691 0.25 0.56 YES
21 AKR1C4 AKR1C4 AKR1C4 707 0.25 0.57 YES
22 CYP2C19 CYP2C19 CYP2C19 723 0.24 0.58 YES
23 UGT2B7 UGT2B7 UGT2B7 937 0.21 0.58 YES
24 ADH7 ADH7 ADH7 1082 0.19 0.58 YES
25 EPHX1 EPHX1 EPHX1 1139 0.18 0.59 YES
26 UGT1A8 UGT1A8 UGT1A8 1170 0.18 0.6 YES
27 MGST1 MGST1 MGST1 1187 0.18 0.61 YES
28 GSTM4 GSTM4 GSTM4 1201 0.17 0.62 YES
29 UGT2B11 UGT2B11 UGT2B11 1269 0.16 0.62 YES
30 UGT2B4 UGT2B4 UGT2B4 1532 0.14 0.62 YES
31 MGST2 MGST2 MGST2 1551 0.14 0.62 YES
32 GSTM3 GSTM3 GSTM3 1586 0.14 0.63 YES
33 CYP2C8 CYP2C8 CYP2C8 1869 0.12 0.62 YES
34 ADH5 ADH5 ADH5 1876 0.12 0.63 YES
35 ADH1A ADH1A ADH1A 1914 0.12 0.63 YES
36 UGT2B15 UGT2B15 UGT2B15 2095 0.1 0.63 NO
37 GSTA4 GSTA4 GSTA4 2170 0.1 0.63 NO
38 GSTZ1 GSTZ1 GSTZ1 2261 0.096 0.63 NO
39 GSTM2 GSTM2 GSTM2 2385 0.09 0.63 NO
40 GSTO1 GSTO1 GSTO1 2462 0.087 0.63 NO
41 CYP1B1 CYP1B1 CYP1B1 2793 0.074 0.61 NO
42 GSTK1 GSTK1 GSTK1 3034 0.066 0.6 NO
43 GSTA1 GSTA1 GSTA1 3440 0.055 0.58 NO
44 GSTM1 GSTM1 GSTM1 3617 0.05 0.58 NO
45 CYP3A5 CYP3A5 CYP3A5 3725 0.047 0.57 NO
46 MGST3 MGST3 MGST3 3986 0.042 0.56 NO
47 GSTA2 GSTA2 GSTA2 4017 0.041 0.56 NO
48 GSTT1 GSTT1 GSTT1 4708 0.027 0.52 NO
49 AKR1C3 AKR1C3 AKR1C3 5091 0.02 0.5 NO
50 CYP2B6 CYP2B6 CYP2B6 5237 0.017 0.5 NO
51 GSTO2 GSTO2 GSTO2 6819 -0.0083 0.41 NO
52 UGT1A7 UGT1A7 UGT1A7 7830 -0.024 0.35 NO
53 UGT2A1 UGT2A1 UGT2A1 12806 -0.16 0.08 NO
54 UGT1A10 UGT1A10 UGT1A10 13047 -0.17 0.076 NO
55 UGT2A3 UGT2A3 UGT2A3 13587 -0.2 0.057 NO
56 ALDH1A3 ALDH1A3 ALDH1A3 14455 -0.25 0.022 NO
57 GSTT2 GSTT2 GSTT2 14598 -0.26 0.029 NO
58 CYP2C18 CYP2C18 CYP2C18 14698 -0.26 0.038 NO
59 ALDH3B1 ALDH3B1 ALDH3B1 14713 -0.26 0.053 NO
60 GSTM5 GSTM5 GSTM5 14930 -0.28 0.056 NO
61 CYP2S1 CYP2S1 CYP2S1 15444 -0.31 0.045 NO
62 GSTP1 GSTP1 GSTP1 16041 -0.35 0.032 NO
63 ALDH3B2 ALDH3B2 ALDH3B2 16070 -0.36 0.05 NO
64 DHDH DHDH DHDH 16152 -0.36 0.067 NO
65 CYP3A7 CYP3A7 CYP3A7 16474 -0.39 0.071 NO

Figure S91.  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 S92.  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 TYROSINE METABOLISM

Table S47.  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 CYP1A1 CYP1A1 CYP1A1 15 1 0.079 YES
2 UGT1A3 UGT1A3 UGT1A3 49 0.78 0.14 YES
3 UGT1A5 UGT1A5 UGT1A5 56 0.76 0.2 YES
4 UGT1A4 UGT1A4 UGT1A4 74 0.69 0.25 YES
5 HSD11B1 HSD11B1 HSD11B1 163 0.5 0.28 YES
6 UGT1A1 UGT1A1 UGT1A1 181 0.48 0.32 YES
7 SRD5A2 SRD5A2 SRD5A2 227 0.44 0.35 YES
8 SULT2B1 SULT2B1 SULT2B1 290 0.39 0.38 YES
9 UGT1A9 UGT1A9 UGT1A9 302 0.38 0.41 YES
10 CYP7B1 CYP7B1 CYP7B1 426 0.33 0.43 YES
11 AKR1C2 AKR1C2 AKR1C2 455 0.32 0.45 YES
12 UGT1A6 UGT1A6 UGT1A6 469 0.31 0.48 YES
13 CYP3A43 CYP3A43 CYP3A43 485 0.31 0.5 YES
14 UGT2B28 UGT2B28 UGT2B28 496 0.31 0.52 YES
15 AKR1C1 AKR1C1 AKR1C1 602 0.27 0.54 YES
16 UGT2B10 UGT2B10 UGT2B10 607 0.27 0.56 YES
17 AKR1C4 AKR1C4 AKR1C4 707 0.25 0.57 YES
18 UGT2B7 UGT2B7 UGT2B7 937 0.21 0.57 YES
19 HSD17B8 HSD17B8 HSD17B8 968 0.2 0.59 YES
20 CYP11A1 CYP11A1 CYP11A1 1017 0.2 0.6 YES
21 HSD17B3 HSD17B3 HSD17B3 1118 0.18 0.61 YES
22 UGT1A8 UGT1A8 UGT1A8 1170 0.18 0.62 YES
23 UGT2B11 UGT2B11 UGT2B11 1269 0.16 0.63 YES
24 CYP17A1 CYP17A1 CYP17A1 1370 0.15 0.64 YES
25 UGT2B4 UGT2B4 UGT2B4 1532 0.14 0.64 YES
26 HSD17B6 HSD17B6 HSD17B6 1550 0.14 0.65 YES
27 HSD17B7 HSD17B7 HSD17B7 1641 0.13 0.65 YES
28 CYP7A1 CYP7A1 CYP7A1 1871 0.12 0.65 NO
29 UGT2B15 UGT2B15 UGT2B15 2095 0.1 0.64 NO
30 SULT1E1 SULT1E1 SULT1E1 2500 0.086 0.63 NO
31 SRD5A1 SRD5A1 SRD5A1 2785 0.074 0.62 NO
32 CYP1B1 CYP1B1 CYP1B1 2793 0.074 0.62 NO
33 CYP3A5 CYP3A5 CYP3A5 3725 0.047 0.57 NO
34 COMT COMT COMT 4258 0.036 0.55 NO
35 HSD17B1 HSD17B1 HSD17B1 4284 0.035 0.55 NO
36 AKR1C3 AKR1C3 AKR1C3 5091 0.02 0.5 NO
37 HSD11B2 HSD11B2 HSD11B2 5171 0.018 0.5 NO
38 UGT1A7 UGT1A7 UGT1A7 7830 -0.024 0.35 NO
39 HSD17B12 HSD17B12 HSD17B12 8512 -0.034 0.32 NO
40 SRD5A3 SRD5A3 SRD5A3 9550 -0.054 0.26 NO
41 CYP21A2 CYP21A2 CYP21A2 11646 -0.11 0.15 NO
42 AKR1D1 AKR1D1 AKR1D1 12305 -0.14 0.13 NO
43 UGT2A1 UGT2A1 UGT2A1 12806 -0.16 0.11 NO
44 UGT1A10 UGT1A10 UGT1A10 13047 -0.17 0.11 NO
45 HSD17B2 HSD17B2 HSD17B2 13087 -0.17 0.12 NO
46 UGT2A3 UGT2A3 UGT2A3 13587 -0.2 0.11 NO
47 HSD3B2 HSD3B2 HSD3B2 14779 -0.27 0.062 NO
48 STS STS STS 14942 -0.28 0.075 NO
49 HSD3B1 HSD3B1 HSD3B1 15595 -0.32 0.063 NO
50 CYP19A1 CYP19A1 CYP19A1 15869 -0.34 0.074 NO
51 CYP3A7 CYP3A7 CYP3A7 16474 -0.39 0.071 NO

Figure S93.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TYROSINE METABOLISM.

Figure S94.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TYROSINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG TRYPTOPHAN METABOLISM

Table S48.  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 UGT1A3 UGT1A3 UGT1A3 49 0.78 0.12 YES
2 UGT1A5 UGT1A5 UGT1A5 56 0.76 0.23 YES
3 UGT1A4 UGT1A4 UGT1A4 74 0.69 0.33 YES
4 UGT1A1 UGT1A1 UGT1A1 181 0.48 0.4 YES
5 UGT1A9 UGT1A9 UGT1A9 302 0.38 0.45 YES
6 DCXR DCXR DCXR 392 0.34 0.5 YES
7 UGT1A6 UGT1A6 UGT1A6 469 0.31 0.54 YES
8 UGT2B28 UGT2B28 UGT2B28 496 0.31 0.58 YES
9 UGT2B10 UGT2B10 UGT2B10 607 0.27 0.62 YES
10 UGT2B7 UGT2B7 UGT2B7 937 0.21 0.63 YES
11 CRYL1 CRYL1 CRYL1 1141 0.18 0.65 YES
12 UGT1A8 UGT1A8 UGT1A8 1170 0.18 0.67 YES
13 UGT2B11 UGT2B11 UGT2B11 1269 0.16 0.69 YES
14 UGT2B4 UGT2B4 UGT2B4 1532 0.14 0.7 YES
15 UGT2B15 UGT2B15 UGT2B15 2095 0.1 0.68 NO
16 XYLB XYLB XYLB 2900 0.07 0.65 NO
17 LOC729020 LOC729020 LOC729020 4657 0.028 0.55 NO
18 RPE RPE RPE 6721 -0.0069 0.44 NO
19 UGT1A7 UGT1A7 UGT1A7 7830 -0.024 0.38 NO
20 UGP2 UGP2 UGP2 8856 -0.04 0.32 NO
21 GUSB GUSB GUSB 9575 -0.054 0.29 NO
22 UGT2A1 UGT2A1 UGT2A1 12806 -0.16 0.13 NO
23 UGT1A10 UGT1A10 UGT1A10 13047 -0.17 0.15 NO
24 UGT2A3 UGT2A3 UGT2A3 13587 -0.2 0.14 NO
25 AKR1B1 AKR1B1 AKR1B1 14039 -0.22 0.15 NO
26 DHDH DHDH DHDH 16152 -0.36 0.089 NO

Figure S95.  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 S96.  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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

Table S49.  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 177 0.48 0.085 YES
2 HIBADH HIBADH HIBADH 579 0.28 0.12 YES
3 ALDH6A1 ALDH6A1 ALDH6A1 604 0.27 0.17 YES
4 EHHADH EHHADH EHHADH 627 0.26 0.22 YES
5 ALDH3A2 ALDH3A2 ALDH3A2 878 0.22 0.25 YES
6 MCEE MCEE MCEE 1087 0.19 0.27 YES
7 HADH HADH HADH 1253 0.17 0.3 YES
8 ALDH2 ALDH2 ALDH2 1357 0.16 0.32 YES
9 ALDH1B1 ALDH1B1 ALDH1B1 1361 0.16 0.35 YES
10 ACADSB ACADSB ACADSB 1529 0.14 0.37 YES
11 ACAA1 ACAA1 ACAA1 1658 0.13 0.39 YES
12 ABAT ABAT ABAT 1674 0.13 0.41 YES
13 AUH AUH AUH 1874 0.12 0.42 YES
14 HMGCL HMGCL HMGCL 2058 0.11 0.44 YES
15 BCKDHB BCKDHB BCKDHB 2159 0.1 0.45 YES
16 ACADM ACADM ACADM 2401 0.09 0.45 YES
17 ECHS1 ECHS1 ECHS1 2429 0.088 0.47 YES
18 DBT DBT DBT 2571 0.083 0.48 YES
19 MCCC2 MCCC2 MCCC2 2586 0.082 0.49 YES
20 HIBCH HIBCH HIBCH 2622 0.081 0.51 YES
21 IVD IVD IVD 2657 0.079 0.52 YES
22 ALDH7A1 ALDH7A1 ALDH7A1 2851 0.072 0.52 YES
23 ALDH9A1 ALDH9A1 ALDH9A1 3054 0.065 0.52 YES
24 HSD17B10 HSD17B10 HSD17B10 3277 0.059 0.52 YES
25 HMGCS1 HMGCS1 HMGCS1 3561 0.052 0.52 YES
26 ACAA2 ACAA2 ACAA2 3577 0.051 0.53 YES
27 PCCA PCCA PCCA 3697 0.048 0.53 YES
28 BCKDHA BCKDHA BCKDHA 4220 0.037 0.51 NO
29 ACAT1 ACAT1 ACAT1 4859 0.024 0.48 NO
30 HADHB HADHB HADHB 5851 0.0068 0.42 NO
31 HADHA HADHA HADHA 5855 0.0068 0.42 NO
32 PCCB PCCB PCCB 6156 0.0018 0.41 NO
33 MUT MUT MUT 6570 -0.0044 0.38 NO
34 ACAD8 ACAD8 ACAD8 6777 -0.0077 0.37 NO
35 MCCC1 MCCC1 MCCC1 7104 -0.012 0.36 NO
36 DLD DLD DLD 7411 -0.018 0.34 NO
37 ACAT2 ACAT2 ACAT2 7881 -0.024 0.32 NO
38 ACADS ACADS ACADS 8671 -0.037 0.28 NO
39 HMGCS2 HMGCS2 HMGCS2 10405 -0.073 0.2 NO
40 OXCT1 OXCT1 OXCT1 10868 -0.085 0.19 NO
41 BCAT2 BCAT2 BCAT2 13492 -0.19 0.082 NO
42 IL4I1 IL4I1 IL4I1 16146 -0.36 0.003 NO
43 OXCT2 OXCT2 OXCT2 16868 -0.44 0.049 NO

Figure S97.  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 PROPANOATE METABOLISM.

Figure S98.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROPANOATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table S50.  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 ACSM3 ACSM3 ACSM3 344 0.37 0.078 YES
2 ACSM5 ACSM5 ACSM5 367 0.35 0.17 YES
3 ACSM2A ACSM2A ACSM2A 488 0.31 0.24 YES
4 ALDH3A2 ALDH3A2 ALDH3A2 878 0.22 0.28 YES
5 HADH HADH HADH 1253 0.17 0.3 YES
6 ALDH2 ALDH2 ALDH2 1357 0.16 0.34 YES
7 ALDH1B1 ALDH1B1 ALDH1B1 1361 0.16 0.38 YES
8 ALDH5A1 ALDH5A1 ALDH5A1 1515 0.14 0.41 YES
9 ABAT ABAT ABAT 1674 0.13 0.43 YES
10 BDH1 BDH1 BDH1 1865 0.12 0.45 YES
11 L2HGDH L2HGDH L2HGDH 1950 0.11 0.48 YES
12 HMGCL HMGCL HMGCL 2058 0.11 0.5 YES
13 ACSM1 ACSM1 ACSM1 2283 0.095 0.51 YES
14 ECHS1 ECHS1 ECHS1 2429 0.088 0.53 YES
15 ALDH7A1 ALDH7A1 ALDH7A1 2851 0.072 0.52 YES
16 GAD1 GAD1 GAD1 2970 0.068 0.54 YES
17 ALDH9A1 ALDH9A1 ALDH9A1 3054 0.065 0.55 YES
18 HMGCS1 HMGCS1 HMGCS1 3561 0.052 0.53 NO
19 ACAT1 ACAT1 ACAT1 4859 0.024 0.46 NO
20 HADHA HADHA HADHA 5855 0.0068 0.41 NO
21 PDHB PDHB PDHB 6150 0.0018 0.4 NO
22 ACAT2 ACAT2 ACAT2 7881 -0.024 0.3 NO
23 ACADS ACADS ACADS 8671 -0.037 0.27 NO
24 PDHA1 PDHA1 PDHA1 9009 -0.043 0.26 NO
25 BDH2 BDH2 BDH2 9936 -0.062 0.22 NO
26 AKR1B10 AKR1B10 AKR1B10 10202 -0.068 0.23 NO
27 HMGCS2 HMGCS2 HMGCS2 10405 -0.073 0.24 NO
28 OXCT1 OXCT1 OXCT1 10868 -0.085 0.23 NO
29 AACS AACS AACS 12555 -0.15 0.18 NO
30 OXCT2 OXCT2 OXCT2 16868 -0.44 0.049 NO

Figure S99.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BUTANOATE METABOLISM.

Figure S100.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BUTANOATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input
  • Gene set database = c2.cp.v3.0-2.symbols.gmt

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

  • Phenotype data file = LIHC-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)