GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in MESO-TP
Mesothelioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1R78DP8
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in MESO-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1R78DP8
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 having more than three samples and the input expression file "MESO-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. 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: 717
Number of samples: 87
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 26
pheno.type: 2 - 4 :[ clus2 ] 21
pheno.type: 3 - 4 :[ clus3 ] 19
pheno.type: 4 - 4 :[ clus4 ] 21

For the expression subtypes of 18209 genes in 88 samples, GSEA found enriched gene sets in each cluster using 87 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FATTY ACID METABOLISM, KEGG TYROSINE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG PARKINSONS DISEASE, PID CASPASE PATHWAY, PID A6B1 A6B4 INTEGRIN PATHWAY, REACTOME TRANSLATION, REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

    • And common core enriched genes are ISG15, DDX58, HERC5, IFIH1, IFNB1, IRF2, IRF7, NLRC5, NLRX1, RNF125

  • clus2

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG PYRUVATE METABOLISM, KEGG PROPANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450, PID NCADHERINPATHWAY

    • And common core enriched genes are AP1M2, AP1S1, AP3B1, AP3S1, AP4E1, ARF1, ARRB1, BLOC1S1, CPD, DNAJC6

  • clus3

    • Top enriched gene sets are KEGG PROTEASOME, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG CELL CYCLE, KEGG APOPTOSIS, KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, KEGG CYTOSOLIC DNA SENSING PATHWAY, KEGG HEMATOPOIETIC CELL LINEAGE, KEGG T CELL RECEPTOR SIGNALING PATHWAY, KEGG B CELL RECEPTOR SIGNALING PATHWAY, KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS

    • And common core enriched genes are PSMA3, PSMA5, PSMA6, PSMA7, PSMA8, PSMB10, PSMB2, PSMB3, PSMB5, PSMB6

  • clus4

    • Top enriched gene sets are KEGG WNT SIGNALING PATHWAY, KEGG TGF BETA SIGNALING PATHWAY, KEGG LONG TERM POTENTIATION, KEGG MELANOGENESIS, KEGG BASAL CELL CARCINOMA, BIOCARTA ALK PATHWAY, ST WNT BETA CATENIN PATHWAY, PID EPHBFWDPATHWAY, PID P75NTRPATHWAY, PID HEDGEHOG GLIPATHWAY

    • And common core enriched genes are B3GAT1, B3GAT2, BCAN, BGN, CSPG4, GPC1, GPC2, GPC3, GPC4, GPC5

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
KEGG GLYCOLYSIS GLUCONEOGENESIS 56 genes.ES.table 0.46 1.5 0.053 1 0.99 0.21 0.098 0.19 1 0.6
KEGG FATTY ACID METABOLISM 38 genes.ES.table 0.63 1.9 0 0.54 0.26 0.34 0.12 0.3 0 0.13
KEGG TYROSINE METABOLISM 41 genes.ES.table 0.5 1.4 0.066 1 1 0.24 0.058 0.23 1 0.6
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.4 1.4 0.15 1 1 0.23 0.11 0.21 1 0.54
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS 25 genes.ES.table 0.39 1.5 0.086 1 0.98 0.4 0.21 0.32 1 0.54
KEGG PARKINSONS DISEASE 111 genes.ES.table 0.39 1.4 0.17 1 1 0.63 0.34 0.42 1 0.56
PID CASPASE PATHWAY 51 genes.ES.table 0.39 1.5 0.064 1 0.98 0.33 0.18 0.28 1 0.52
PID A6B1 A6B4 INTEGRIN PATHWAY 46 genes.ES.table 0.5 1.5 0.081 1 0.98 0.24 0.12 0.21 1 0.56
REACTOME TRANSLATION 146 genes.ES.table 0.43 1.4 0.2 1 1 0.6 0.37 0.38 1 0.58
REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 65 genes.ES.table 0.46 1.7 0.05 0.75 0.8 0.11 0.023 0.11 0.34 0.22
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 ADH6 ADH6 ADH6 1 1.3 0.17 YES
2 ADH1A ADH1A ADH1A 2 1.2 0.33 YES
3 ADH1B ADH1B ADH1B 13 0.8 0.44 YES
4 ACSL6 ACSL6 ACSL6 340 0.41 0.48 YES
5 ADH1C ADH1C ADH1C 595 0.32 0.51 YES
6 ADH4 ADH4 ADH4 666 0.3 0.54 YES
7 ALDH3A2 ALDH3A2 ALDH3A2 1053 0.23 0.55 YES
8 ACSL5 ACSL5 ACSL5 1151 0.22 0.58 YES
9 ACADS ACADS ACADS 1437 0.19 0.59 YES
10 ADH5 ADH5 ADH5 1724 0.16 0.6 YES
11 ALDH2 ALDH2 ALDH2 1786 0.16 0.61 YES
12 ACADM ACADM ACADM 2014 0.14 0.62 YES
13 ACSL1 ACSL1 ACSL1 2178 0.13 0.63 YES
14 CPT2 CPT2 CPT2 3209 0.086 0.58 NO
15 ALDH9A1 ALDH9A1 ALDH9A1 4274 0.057 0.53 NO
16 HADHB HADHB HADHB 4667 0.048 0.52 NO
17 ACAA2 ACAA2 ACAA2 4827 0.044 0.51 NO
18 ACADVL ACADVL ACADVL 4850 0.044 0.52 NO
19 HADH HADH HADH 5109 0.04 0.51 NO
20 CPT1B CPT1B CPT1B 5394 0.034 0.5 NO
21 ECHS1 ECHS1 ECHS1 5409 0.034 0.5 NO
22 ACAA1 ACAA1 ACAA1 6274 0.02 0.46 NO
23 HADHA HADHA HADHA 6875 0.012 0.43 NO
24 ACOX1 ACOX1 ACOX1 7042 0.0097 0.42 NO
25 CPT1A CPT1A CPT1A 7150 0.0081 0.41 NO
26 ACAT2 ACAT2 ACAT2 7323 0.006 0.41 NO
27 ALDH7A1 ALDH7A1 ALDH7A1 7455 0.0039 0.4 NO
28 ACAT1 ACAT1 ACAT1 8728 -0.014 0.33 NO
29 ACADSB ACADSB ACADSB 8866 -0.017 0.33 NO
30 GCDH GCDH GCDH 9514 -0.027 0.29 NO
31 ACSL3 ACSL3 ACSL3 10383 -0.042 0.25 NO
32 ACOX3 ACOX3 ACOX3 11823 -0.073 0.18 NO
33 ACADL ACADL ACADL 12655 -0.096 0.15 NO
34 ACSL4 ACSL4 ACSL4 13053 -0.11 0.14 NO
35 ALDH1B1 ALDH1B1 ALDH1B1 14871 -0.19 0.068 NO
36 CYP4A11 CYP4A11 CYP4A11 15549 -0.23 0.062 NO
37 EHHADH EHHADH EHHADH 16392 -0.29 0.055 NO
38 CPT1C CPT1C CPT1C 16725 -0.32 0.081 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: KEGG GLYCOLYSIS GLUCONEOGENESIS.

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 SAA1 SAA1 SAA1 95 0.57 0.083 YES
2 HERC5 HERC5 HERC5 158 0.5 0.16 YES
3 ISG15 ISG15 ISG15 238 0.45 0.22 YES
4 DDX58 DDX58 DDX58 412 0.38 0.27 YES
5 IFIH1 IFIH1 IFIH1 500 0.34 0.32 YES
6 IRF7 IRF7 IRF7 519 0.34 0.37 YES
7 IFNB1 IFNB1 IFNB1 611 0.32 0.41 YES
8 DHX58 DHX58 DHX58 816 0.27 0.44 YES
9 S100A12 S100A12 S100A12 1224 0.21 0.45 YES
10 TRIM25 TRIM25 TRIM25 1424 0.19 0.47 YES
11 IRF2 IRF2 IRF2 1671 0.16 0.48 YES
12 DAK DAK DAK 1675 0.16 0.51 YES
13 UBE2L6 UBE2L6 UBE2L6 1819 0.15 0.52 YES
14 CASP10 CASP10 CASP10 2426 0.12 0.51 YES
15 CASP8 CASP8 CASP8 2595 0.11 0.52 YES
16 UBE2D3 UBE2D3 UBE2D3 2902 0.095 0.52 YES
17 IRF1 IRF1 IRF1 2964 0.093 0.53 YES
18 RNF125 RNF125 RNF125 3183 0.086 0.53 YES
19 NFKBIA NFKBIA NFKBIA 3650 0.072 0.51 YES
20 RNF135 RNF135 RNF135 3653 0.072 0.52 YES
21 NLRX1 NLRX1 NLRX1 3742 0.069 0.53 YES
22 FADD FADD FADD 3774 0.068 0.54 YES
23 AGER AGER AGER 3875 0.066 0.54 YES
24 NLRC5 NLRC5 NLRC5 3915 0.065 0.55 YES
25 TANK TANK TANK 4263 0.057 0.54 NO
26 NFKB2 NFKB2 NFKB2 4424 0.053 0.54 NO
27 RIPK1 RIPK1 RIPK1 4723 0.046 0.53 NO
28 RPS27A RPS27A RPS27A 4792 0.045 0.53 NO
29 UBA7 UBA7 UBA7 4834 0.044 0.54 NO
30 SIKE1 SIKE1 SIKE1 4977 0.042 0.54 NO
31 MAVS MAVS MAVS 5207 0.038 0.53 NO
32 PCBP2 PCBP2 PCBP2 5397 0.034 0.52 NO
33 CHUK CHUK CHUK 5532 0.032 0.52 NO
34 APP APP APP 5643 0.03 0.52 NO
35 TRAF3 TRAF3 TRAF3 5752 0.028 0.52 NO
36 UBE2K UBE2K UBE2K 6656 0.015 0.47 NO
37 TBK1 TBK1 TBK1 6706 0.014 0.47 NO
38 TAX1BP1 TAX1BP1 TAX1BP1 6858 0.012 0.46 NO
39 OTUD5 OTUD5 OTUD5 6912 0.011 0.46 NO
40 RELA RELA RELA 6919 0.011 0.46 NO
41 IKBKE IKBKE IKBKE 7298 0.0063 0.45 NO
42 CYLD CYLD CYLD 7603 0.0017 0.43 NO
43 UBA52 UBA52 UBA52 7844 -0.0019 0.42 NO
44 UBE2D2 UBE2D2 UBE2D2 7879 -0.0023 0.42 NO
45 IRF3 IRF3 IRF3 7933 -0.0029 0.41 NO
46 IKBKB IKBKB IKBKB 8605 -0.013 0.38 NO
47 HMGB1 HMGB1 HMGB1 9050 -0.02 0.36 NO
48 CREBBP CREBBP CREBBP 9274 -0.023 0.35 NO
49 EP300 EP300 EP300 9451 -0.026 0.34 NO
50 ATG5 ATG5 ATG5 9660 -0.029 0.33 NO
51 PIN1 PIN1 PIN1 10310 -0.04 0.3 NO
52 MAP3K1 MAP3K1 MAP3K1 10410 -0.042 0.31 NO
53 ATG12 ATG12 ATG12 10490 -0.044 0.31 NO
54 IKBKG IKBKG IKBKG 11246 -0.06 0.28 NO
55 UBE2D1 UBE2D1 UBE2D1 11608 -0.068 0.27 NO
56 TRAF2 TRAF2 TRAF2 11880 -0.074 0.26 NO
57 TRAF6 TRAF6 TRAF6 12417 -0.088 0.25 NO
58 NFKBIB NFKBIB NFKBIB 12614 -0.095 0.25 NO
59 S100B S100B S100B 14063 -0.15 0.19 NO
60 TNFAIP3 TNFAIP3 TNFAIP3 15364 -0.22 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: KEGG FATTY ACID METABOLISM.

Figure S4.  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 TYROSINE METABOLISM

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 HERC5 HERC5 HERC5 158 0.5 0.15 YES
2 ISG15 ISG15 ISG15 238 0.45 0.3 YES
3 DDX58 DDX58 DDX58 412 0.38 0.41 YES
4 IFIH1 IFIH1 IFIH1 500 0.34 0.52 YES
5 TRIM25 TRIM25 TRIM25 1424 0.19 0.53 YES
6 UBE2L6 UBE2L6 UBE2L6 1819 0.15 0.56 YES
7 UBE2D3 UBE2D3 UBE2D3 2902 0.095 0.53 YES
8 RNF125 RNF125 RNF125 3183 0.086 0.54 YES
9 RNF135 RNF135 RNF135 3653 0.072 0.54 YES
10 NLRX1 NLRX1 NLRX1 3742 0.069 0.56 YES
11 NLRC5 NLRC5 NLRC5 3915 0.065 0.57 YES
12 RPS27A RPS27A RPS27A 4792 0.045 0.54 NO
13 UBA7 UBA7 UBA7 4834 0.044 0.55 NO
14 MAVS MAVS MAVS 5207 0.038 0.54 NO
15 PCBP2 PCBP2 PCBP2 5397 0.034 0.54 NO
16 TRAF3 TRAF3 TRAF3 5752 0.028 0.53 NO
17 UBE2K UBE2K UBE2K 6656 0.015 0.49 NO
18 TBK1 TBK1 TBK1 6706 0.014 0.49 NO
19 TAX1BP1 TAX1BP1 TAX1BP1 6858 0.012 0.48 NO
20 OTUD5 OTUD5 OTUD5 6912 0.011 0.48 NO
21 IKBKE IKBKE IKBKE 7298 0.0063 0.47 NO
22 CYLD CYLD CYLD 7603 0.0017 0.45 NO
23 UBA52 UBA52 UBA52 7844 -0.0019 0.44 NO
24 UBE2D2 UBE2D2 UBE2D2 7879 -0.0023 0.44 NO
25 IRF3 IRF3 IRF3 7933 -0.0029 0.43 NO
26 ATG5 ATG5 ATG5 9660 -0.029 0.35 NO
27 PIN1 PIN1 PIN1 10310 -0.04 0.33 NO
28 ATG12 ATG12 ATG12 10490 -0.044 0.33 NO
29 UBE2D1 UBE2D1 UBE2D1 11608 -0.068 0.29 NO
30 TNFAIP3 TNFAIP3 TNFAIP3 15364 -0.22 0.16 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: KEGG TYROSINE METABOLISM.

Figure S6.  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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 OASL OASL OASL 103 0.56 0.047 YES
2 IFIT1 IFIT1 IFIT1 111 0.55 0.098 YES
3 IFIT2 IFIT2 IFIT2 155 0.5 0.14 YES
4 IFIT3 IFIT3 IFIT3 165 0.49 0.19 YES
5 IFI6 IFI6 IFI6 213 0.46 0.23 YES
6 MX1 MX1 MX1 224 0.46 0.27 YES
7 ISG15 ISG15 ISG15 238 0.45 0.32 YES
8 USP18 USP18 USP18 264 0.44 0.36 YES
9 MX2 MX2 MX2 311 0.42 0.39 YES
10 OAS1 OAS1 OAS1 318 0.42 0.43 YES
11 OAS2 OAS2 OAS2 331 0.41 0.47 YES
12 IFI27 IFI27 IFI27 367 0.4 0.5 YES
13 ISG20 ISG20 ISG20 376 0.39 0.54 YES
14 HLA-G HLA-G HLA-G 451 0.36 0.57 YES
15 IRF7 IRF7 IRF7 519 0.34 0.6 YES
16 IFNB1 IFNB1 IFNB1 611 0.32 0.62 YES
17 OAS3 OAS3 OAS3 706 0.3 0.64 YES
18 XAF1 XAF1 XAF1 726 0.29 0.67 YES
19 HLA-F HLA-F HLA-F 859 0.26 0.69 YES
20 IFI35 IFI35 IFI35 951 0.25 0.71 YES
21 IFITM1 IFITM1 IFITM1 1204 0.21 0.71 YES
22 PSMB8 PSMB8 PSMB8 1504 0.18 0.71 YES
23 IRF9 IRF9 IRF9 1506 0.18 0.73 YES
24 IRF2 IRF2 IRF2 1671 0.16 0.74 YES
25 HLA-C HLA-C HLA-C 1962 0.14 0.73 YES
26 HLA-B HLA-B HLA-B 2103 0.13 0.74 YES
27 IFITM2 IFITM2 IFITM2 2235 0.13 0.74 YES
28 HLA-A HLA-A HLA-A 2327 0.12 0.75 YES
29 STAT1 STAT1 STAT1 2411 0.12 0.76 YES
30 STAT2 STAT2 STAT2 2877 0.096 0.74 NO
31 IRF1 IRF1 IRF1 2964 0.093 0.74 NO
32 IFITM3 IFITM3 IFITM3 3378 0.08 0.73 NO
33 PTPN6 PTPN6 PTPN6 3494 0.076 0.73 NO
34 IRF5 IRF5 IRF5 5136 0.039 0.64 NO
35 JAK1 JAK1 JAK1 5351 0.035 0.63 NO
36 IFNAR1 IFNAR1 IFNAR1 5671 0.03 0.62 NO
37 ADAR ADAR ADAR 6198 0.022 0.59 NO
38 EGR1 EGR1 EGR1 7054 0.0095 0.55 NO
39 RNASEL RNASEL RNASEL 7127 0.0085 0.54 NO
40 IFNAR2 IFNAR2 IFNAR2 7697 0.00024 0.51 NO
41 IRF3 IRF3 IRF3 7933 -0.0029 0.5 NO
42 IRF4 IRF4 IRF4 8530 -0.012 0.47 NO
43 GBP2 GBP2 GBP2 8726 -0.014 0.46 NO
44 TYK2 TYK2 TYK2 9069 -0.02 0.44 NO
45 SOCS3 SOCS3 SOCS3 9473 -0.027 0.42 NO
46 IP6K2 IP6K2 IP6K2 9606 -0.029 0.42 NO
47 IRF8 IRF8 IRF8 9859 -0.033 0.4 NO
48 PTPN1 PTPN1 PTPN1 11237 -0.06 0.34 NO
49 SOCS1 SOCS1 SOCS1 15615 -0.23 0.12 NO
50 IRF6 IRF6 IRF6 16252 -0.28 0.11 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: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

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

genes ES table in pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IFIT1 IFIT1 IFIT1 111 0.55 0.077 YES
2 HERC5 HERC5 HERC5 158 0.5 0.15 YES
3 MX1 MX1 MX1 224 0.46 0.22 YES
4 ISG15 ISG15 ISG15 238 0.45 0.28 YES
5 USP18 USP18 USP18 264 0.44 0.35 YES
6 MX2 MX2 MX2 311 0.42 0.41 YES
7 DDX58 DDX58 DDX58 412 0.38 0.46 YES
8 TRIM25 TRIM25 TRIM25 1424 0.19 0.43 NO
9 UBE2L6 UBE2L6 UBE2L6 1819 0.15 0.43 NO
10 EIF2AK2 EIF2AK2 EIF2AK2 2307 0.12 0.43 NO
11 STAT1 STAT1 STAT1 2411 0.12 0.44 NO
12 EIF4E3 EIF4E3 EIF4E3 3006 0.092 0.42 NO
13 NUP85 NUP85 NUP85 3943 0.064 0.38 NO
14 AAAS AAAS AAAS 4211 0.058 0.37 NO
15 MAPK3 MAPK3 MAPK3 4435 0.053 0.37 NO
16 EIF4G3 EIF4G3 EIF4G3 4464 0.052 0.37 NO
17 RPS27A RPS27A RPS27A 4792 0.045 0.36 NO
18 UBA7 UBA7 UBA7 4834 0.044 0.37 NO
19 NUP35 NUP35 NUP35 4886 0.043 0.37 NO
20 PPM1B PPM1B PPM1B 4899 0.043 0.38 NO
21 JAK1 JAK1 JAK1 5351 0.035 0.36 NO
22 EIF4E EIF4E EIF4E 5590 0.031 0.35 NO
23 NUP37 NUP37 NUP37 5817 0.027 0.34 NO
24 EIF4A1 EIF4A1 EIF4A1 6056 0.024 0.33 NO
25 POM121 POM121 POM121 6272 0.02 0.32 NO
26 NUP88 NUP88 NUP88 6551 0.017 0.31 NO
27 KPNB1 KPNB1 KPNB1 6589 0.016 0.31 NO
28 EIF4A3 EIF4A3 EIF4A3 6820 0.013 0.3 NO
29 TPR TPR TPR 6964 0.011 0.29 NO
30 EIF4G1 EIF4G1 EIF4G1 7103 0.0088 0.28 NO
31 EIF4A2 EIF4A2 EIF4A2 7125 0.0085 0.28 NO
32 EIF4G2 EIF4G2 EIF4G2 7260 0.0067 0.28 NO
33 EIF4E2 EIF4E2 EIF4E2 7456 0.0039 0.27 NO
34 NUP133 NUP133 NUP133 7521 0.0028 0.27 NO
35 NUP214 NUP214 NUP214 7600 0.0017 0.26 NO
36 UBA52 UBA52 UBA52 7844 -0.0019 0.25 NO
37 IRF3 IRF3 IRF3 7933 -0.0029 0.24 NO
38 RANBP2 RANBP2 RANBP2 8069 -0.0046 0.24 NO
39 UBE2E1 UBE2E1 UBE2E1 8146 -0.0057 0.23 NO
40 NUPL2 NUPL2 NUPL2 8177 -0.006 0.23 NO
41 NUP210 NUP210 NUP210 8539 -0.012 0.22 NO
42 NUP54 NUP54 NUP54 8611 -0.013 0.21 NO
43 KPNA1 KPNA1 KPNA1 8690 -0.014 0.21 NO
44 RAE1 RAE1 RAE1 8758 -0.015 0.21 NO
45 ARIH1 ARIH1 ARIH1 9410 -0.025 0.18 NO
46 NUP107 NUP107 NUP107 9435 -0.026 0.18 NO
47 NUP205 NUP205 NUP205 9938 -0.034 0.16 NO
48 KPNA4 KPNA4 KPNA4 10145 -0.038 0.15 NO
49 PIN1 PIN1 PIN1 10310 -0.04 0.15 NO
50 NUP50 NUP50 NUP50 10355 -0.041 0.15 NO
51 NUP153 NUP153 NUP153 10610 -0.046 0.14 NO
52 SEH1L SEH1L SEH1L 10764 -0.049 0.14 NO
53 NUP62 NUP62 NUP62 10885 -0.052 0.15 NO
54 UBE2N UBE2N UBE2N 11341 -0.062 0.13 NO
55 NUP155 NUP155 NUP155 11680 -0.07 0.12 NO
56 NUPL1 NUPL1 NUPL1 11816 -0.073 0.12 NO
57 PLCG1 PLCG1 PLCG1 12502 -0.091 0.1 NO
58 NUP188 NUP188 NUP188 12635 -0.096 0.11 NO
59 KPNA3 KPNA3 KPNA3 12841 -0.1 0.11 NO
60 NUP43 NUP43 NUP43 13039 -0.11 0.12 NO
61 NUP93 NUP93 NUP93 13676 -0.13 0.1 NO
62 KPNA2 KPNA2 KPNA2 14581 -0.17 0.079 NO
63 NEDD4 NEDD4 NEDD4 14658 -0.18 0.1 NO
64 FLNB FLNB FLNB 14987 -0.19 0.11 NO
65 KPNA5 KPNA5 KPNA5 17556 -0.43 0.035 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR 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 PARKINSONS DISEASE

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 OASL OASL OASL 103 0.56 0.026 YES
2 IFIT1 IFIT1 IFIT1 111 0.55 0.057 YES
3 IFIT2 IFIT2 IFIT2 155 0.5 0.083 YES
4 HERC5 HERC5 HERC5 158 0.5 0.11 YES
5 IFIT3 IFIT3 IFIT3 165 0.49 0.14 YES
6 IFI6 IFI6 IFI6 213 0.46 0.16 YES
7 MX1 MX1 MX1 224 0.46 0.19 YES
8 ISG15 ISG15 ISG15 238 0.45 0.21 YES
9 USP18 USP18 USP18 264 0.44 0.24 YES
10 MX2 MX2 MX2 311 0.42 0.26 YES
11 OAS1 OAS1 OAS1 318 0.42 0.28 YES
12 OAS2 OAS2 OAS2 331 0.41 0.3 YES
13 IFI27 IFI27 IFI27 367 0.4 0.32 YES
14 ISG20 ISG20 ISG20 376 0.39 0.35 YES
15 DDX58 DDX58 DDX58 412 0.38 0.37 YES
16 HLA-G HLA-G HLA-G 451 0.36 0.38 YES
17 IRF7 IRF7 IRF7 519 0.34 0.4 YES
18 IFNB1 IFNB1 IFNB1 611 0.32 0.41 YES
19 OAS3 OAS3 OAS3 706 0.3 0.42 YES
20 XAF1 XAF1 XAF1 726 0.29 0.44 YES
21 HLA-F HLA-F HLA-F 859 0.26 0.45 YES
22 IFI35 IFI35 IFI35 951 0.25 0.46 YES
23 IFITM1 IFITM1 IFITM1 1204 0.21 0.45 YES
24 TRIM25 TRIM25 TRIM25 1424 0.19 0.45 YES
25 PSMB8 PSMB8 PSMB8 1504 0.18 0.46 YES
26 IRF9 IRF9 IRF9 1506 0.18 0.47 YES
27 IRF2 IRF2 IRF2 1671 0.16 0.47 YES
28 UBE2L6 UBE2L6 UBE2L6 1819 0.15 0.47 YES
29 SP100 SP100 SP100 1912 0.15 0.47 YES
30 HLA-C HLA-C HLA-C 1962 0.14 0.48 YES
31 HLA-B HLA-B HLA-B 2103 0.13 0.48 YES
32 GBP4 GBP4 GBP4 2165 0.13 0.48 YES
33 CAMK2D CAMK2D CAMK2D 2214 0.13 0.49 YES
34 IFITM2 IFITM2 IFITM2 2235 0.13 0.49 YES
35 EIF2AK2 EIF2AK2 EIF2AK2 2307 0.12 0.5 YES
36 HLA-A HLA-A HLA-A 2327 0.12 0.5 YES
37 STAT1 STAT1 STAT1 2411 0.12 0.5 YES
38 MT2A MT2A MT2A 2797 0.1 0.49 NO
39 B2M B2M B2M 2836 0.098 0.49 NO
40 STAT2 STAT2 STAT2 2877 0.096 0.49 NO
41 IRF1 IRF1 IRF1 2964 0.093 0.5 NO
42 EIF4E3 EIF4E3 EIF4E3 3006 0.092 0.5 NO
43 IFITM3 IFITM3 IFITM3 3378 0.08 0.48 NO
44 PTPN6 PTPN6 PTPN6 3494 0.076 0.48 NO
45 PTPN2 PTPN2 PTPN2 3833 0.067 0.46 NO
46 NUP85 NUP85 NUP85 3943 0.064 0.46 NO
47 GBP1 GBP1 GBP1 4201 0.058 0.45 NO
48 AAAS AAAS AAAS 4211 0.058 0.45 NO
49 GBP7 GBP7 GBP7 4253 0.057 0.46 NO
50 MAPK3 MAPK3 MAPK3 4435 0.053 0.45 NO
51 EIF4G3 EIF4G3 EIF4G3 4464 0.052 0.45 NO
52 GBP6 GBP6 GBP6 4600 0.05 0.44 NO
53 RPS27A RPS27A RPS27A 4792 0.045 0.44 NO
54 UBA7 UBA7 UBA7 4834 0.044 0.44 NO
55 NUP35 NUP35 NUP35 4886 0.043 0.44 NO
56 PPM1B PPM1B PPM1B 4899 0.043 0.44 NO
57 IRF5 IRF5 IRF5 5136 0.039 0.43 NO
58 JAK1 JAK1 JAK1 5351 0.035 0.42 NO
59 EIF4E EIF4E EIF4E 5590 0.031 0.41 NO
60 JAK2 JAK2 JAK2 5601 0.031 0.41 NO
61 IFNAR1 IFNAR1 IFNAR1 5671 0.03 0.4 NO
62 NUP37 NUP37 NUP37 5817 0.027 0.4 NO
63 EIF4A1 EIF4A1 EIF4A1 6056 0.024 0.39 NO
64 ADAR ADAR ADAR 6198 0.022 0.38 NO
65 POM121 POM121 POM121 6272 0.02 0.38 NO
66 NUP88 NUP88 NUP88 6551 0.017 0.36 NO
67 KPNB1 KPNB1 KPNB1 6589 0.016 0.36 NO
68 EIF4A3 EIF4A3 EIF4A3 6820 0.013 0.35 NO
69 TPR TPR TPR 6964 0.011 0.34 NO
70 FCGR1A FCGR1A FCGR1A 6974 0.011 0.34 NO
71 GBP5 GBP5 GBP5 6987 0.01 0.34 NO
72 EGR1 EGR1 EGR1 7054 0.0095 0.34 NO
73 EIF4G1 EIF4G1 EIF4G1 7103 0.0088 0.34 NO
74 EIF4A2 EIF4A2 EIF4A2 7125 0.0085 0.34 NO
75 RNASEL RNASEL RNASEL 7127 0.0085 0.34 NO
76 EIF4G2 EIF4G2 EIF4G2 7260 0.0067 0.33 NO
77 FCGR1B FCGR1B FCGR1B 7290 0.0064 0.33 NO
78 EIF4E2 EIF4E2 EIF4E2 7456 0.0039 0.32 NO
79 NUP133 NUP133 NUP133 7521 0.0028 0.32 NO
80 NUP214 NUP214 NUP214 7600 0.0017 0.31 NO
81 SUMO1 SUMO1 SUMO1 7650 0.001 0.31 NO
82 IFNAR2 IFNAR2 IFNAR2 7697 0.00024 0.31 NO
83 UBA52 UBA52 UBA52 7844 -0.0019 0.3 NO
84 IRF3 IRF3 IRF3 7933 -0.0029 0.3 NO
85 RANBP2 RANBP2 RANBP2 8069 -0.0046 0.29 NO
86 UBE2E1 UBE2E1 UBE2E1 8146 -0.0057 0.28 NO
87 NUPL2 NUPL2 NUPL2 8177 -0.006 0.28 NO
88 IRF4 IRF4 IRF4 8530 -0.012 0.26 NO
89 NUP210 NUP210 NUP210 8539 -0.012 0.26 NO
90 NUP54 NUP54 NUP54 8611 -0.013 0.26 NO
91 HLA-DRB1 HLA-DRB1 HLA-DRB1 8671 -0.014 0.26 NO
92 KPNA1 KPNA1 KPNA1 8690 -0.014 0.26 NO
93 GBP2 GBP2 GBP2 8726 -0.014 0.26 NO
94 RAE1 RAE1 RAE1 8758 -0.015 0.26 NO
95 TYK2 TYK2 TYK2 9069 -0.02 0.24 NO
96 PML PML PML 9118 -0.021 0.24 NO
97 CAMK2B CAMK2B CAMK2B 9339 -0.024 0.23 NO
98 ARIH1 ARIH1 ARIH1 9410 -0.025 0.22 NO
99 NUP107 NUP107 NUP107 9435 -0.026 0.22 NO
100 SOCS3 SOCS3 SOCS3 9473 -0.027 0.22 NO
101 IP6K2 IP6K2 IP6K2 9606 -0.029 0.22 NO
102 IRF8 IRF8 IRF8 9859 -0.033 0.21 NO
103 NUP205 NUP205 NUP205 9938 -0.034 0.2 NO
104 KPNA4 KPNA4 KPNA4 10145 -0.038 0.2 NO
105 PTAFR PTAFR PTAFR 10189 -0.038 0.2 NO
106 PIN1 PIN1 PIN1 10310 -0.04 0.19 NO
107 NUP50 NUP50 NUP50 10355 -0.041 0.19 NO
108 NUP153 NUP153 NUP153 10610 -0.046 0.18 NO
109 HLA-DRB5 HLA-DRB5 HLA-DRB5 10627 -0.046 0.18 NO
110 SEH1L SEH1L SEH1L 10764 -0.049 0.18 NO
111 HLA-DPA1 HLA-DPA1 HLA-DPA1 10866 -0.051 0.17 NO
112 NUP62 NUP62 NUP62 10885 -0.052 0.18 NO
113 IFNGR1 IFNGR1 IFNGR1 10984 -0.054 0.17 NO
114 PTPN1 PTPN1 PTPN1 11237 -0.06 0.16 NO
115 UBE2N UBE2N UBE2N 11341 -0.062 0.16 NO
116 PIAS1 PIAS1 PIAS1 11348 -0.062 0.16 NO
117 ICAM1 ICAM1 ICAM1 11569 -0.067 0.16 NO
118 HLA-DPB1 HLA-DPB1 HLA-DPB1 11652 -0.069 0.15 NO
119 NUP155 NUP155 NUP155 11680 -0.07 0.16 NO
120 NUPL1 NUPL1 NUPL1 11816 -0.073 0.15 NO
121 PRKCD PRKCD PRKCD 12148 -0.081 0.14 NO
122 HLA-DQA2 HLA-DQA2 HLA-DQA2 12156 -0.082 0.14 NO
123 CIITA CIITA CIITA 12345 -0.086 0.14 NO
124 CD44 CD44 CD44 12467 -0.09 0.14 NO
125 PLCG1 PLCG1 PLCG1 12502 -0.091 0.14 NO
126 IFNGR2 IFNGR2 IFNGR2 12631 -0.095 0.14 NO
127 NUP188 NUP188 NUP188 12635 -0.096 0.14 NO
128 KPNA3 KPNA3 KPNA3 12841 -0.1 0.14 NO
129 NUP43 NUP43 NUP43 13039 -0.11 0.13 NO
130 IFNG IFNG IFNG 13659 -0.13 0.11 NO
131 NUP93 NUP93 NUP93 13676 -0.13 0.11 NO
132 HLA-DQA1 HLA-DQA1 HLA-DQA1 13934 -0.14 0.11 NO
133 VCAM1 VCAM1 VCAM1 14160 -0.15 0.1 NO
134 KPNA2 KPNA2 KPNA2 14581 -0.17 0.09 NO
135 NEDD4 NEDD4 NEDD4 14658 -0.18 0.095 NO
136 FLNB FLNB FLNB 14987 -0.19 0.088 NO
137 NCAM1 NCAM1 NCAM1 15355 -0.22 0.08 NO
138 SOCS1 SOCS1 SOCS1 15615 -0.23 0.079 NO
139 IRF6 IRF6 IRF6 16252 -0.28 0.06 NO
140 CAMK2A CAMK2A CAMK2A 17457 -0.41 0.016 NO
141 KPNA5 KPNA5 KPNA5 17556 -0.43 0.035 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 PARKINSONS DISEASE.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PARKINSONS DISEASE, 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: PID CASPASE PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NDUFC1 NDUFC1 NDUFC1 1454 0.18 -0.026 YES
2 NDUFB1 NDUFB1 NDUFB1 1904 0.15 -0.007 YES
3 NDUFB5 NDUFB5 NDUFB5 2498 0.11 -0.0063 YES
4 ETFB ETFB ETFB 2722 0.1 0.012 YES
5 ATP5H ATP5H ATP5H 3002 0.092 0.024 YES
6 ATP5G1 ATP5G1 ATP5G1 3017 0.091 0.05 YES
7 NDUFA2 NDUFA2 NDUFA2 3039 0.09 0.075 YES
8 NDUFA3 NDUFA3 NDUFA3 3336 0.082 0.083 YES
9 UCP2 UCP2 UCP2 3454 0.078 0.099 YES
10 NDUFB4 NDUFB4 NDUFB4 3485 0.077 0.12 YES
11 SDHD SDHD SDHD 3591 0.073 0.14 YES
12 COX7C COX7C COX7C 3651 0.072 0.15 YES
13 ATP5L ATP5L ATP5L 3701 0.07 0.17 YES
14 ATP5I ATP5I ATP5I 3722 0.07 0.19 YES
15 COX5B COX5B COX5B 3804 0.068 0.21 YES
16 NDUFB6 NDUFB6 NDUFB6 3854 0.066 0.22 YES
17 NDUFV3 NDUFV3 NDUFV3 3861 0.066 0.24 YES
18 NDUFA7 NDUFA7 NDUFA7 3925 0.064 0.26 YES
19 ATP5F1 ATP5F1 ATP5F1 3947 0.064 0.28 YES
20 NDUFS8 NDUFS8 NDUFS8 4092 0.061 0.29 YES
21 NDUFS4 NDUFS4 NDUFS4 4199 0.058 0.3 YES
22 UQCRFS1 UQCRFS1 UQCRFS1 4218 0.058 0.31 YES
23 ATP5A1 ATP5A1 ATP5A1 4243 0.057 0.33 YES
24 COX6A1 COX6A1 COX6A1 4342 0.055 0.34 YES
25 ATP5C1 ATP5C1 ATP5C1 4427 0.053 0.35 YES
26 ATP5B ATP5B ATP5B 4500 0.051 0.36 YES
27 UCP1 UCP1 UCP1 4629 0.049 0.37 YES
28 UQCRB UQCRB UQCRB 4702 0.047 0.38 YES
29 NDUFA13 NDUFA13 NDUFA13 4756 0.046 0.39 YES
30 ETFDH ETFDH ETFDH 4782 0.045 0.4 YES
31 COX7B COX7B COX7B 4793 0.045 0.42 YES
32 NDUFV1 NDUFV1 NDUFV1 4863 0.044 0.42 YES
33 NDUFB3 NDUFB3 NDUFB3 5000 0.041 0.43 YES
34 NDUFA10 NDUFA10 NDUFA10 5044 0.041 0.44 YES
35 ATP5O ATP5O ATP5O 5074 0.04 0.45 YES
36 UQCRQ UQCRQ UQCRQ 5075 0.04 0.46 YES
37 NDUFS5 NDUFS5 NDUFS5 5134 0.039 0.47 YES
38 NDUFA9 NDUFA9 NDUFA9 5308 0.036 0.47 YES
39 NDUFB10 NDUFB10 NDUFB10 5309 0.036 0.48 YES
40 COX4I1 COX4I1 COX4I1 5320 0.036 0.49 YES
41 NDUFB7 NDUFB7 NDUFB7 5408 0.034 0.5 YES
42 NDUFA8 NDUFA8 NDUFA8 5490 0.033 0.5 YES
43 UQCR11 UQCR11 UQCR11 5502 0.032 0.51 YES
44 ATP5J2 ATP5J2 ATP5J2 5622 0.03 0.51 YES
45 COX6C COX6C COX6C 5687 0.03 0.52 YES
46 NDUFS3 NDUFS3 NDUFS3 5730 0.029 0.52 YES
47 UQCRC2 UQCRC2 UQCRC2 5750 0.028 0.53 YES
48 ATP5J ATP5J ATP5J 5774 0.028 0.54 YES
49 COX8A COX8A COX8A 5779 0.028 0.55 YES
50 COX7A2L COX7A2L COX7A2L 5926 0.025 0.55 YES
51 SDHA SDHA SDHA 5937 0.025 0.55 YES
52 NDUFB2 NDUFB2 NDUFB2 6053 0.024 0.55 YES
53 NDUFB8 NDUFB8 NDUFB8 6119 0.022 0.56 YES
54 SDHB SDHB SDHB 6156 0.022 0.56 YES
55 NDUFV2 NDUFV2 NDUFV2 6233 0.021 0.56 YES
56 NDUFS1 NDUFS1 NDUFS1 6247 0.021 0.57 YES
57 NDUFA1 NDUFA1 NDUFA1 6418 0.018 0.56 NO
58 CYCS CYCS CYCS 6577 0.016 0.56 NO
59 NDUFS2 NDUFS2 NDUFS2 6590 0.016 0.56 NO
60 NDUFC2 NDUFC2 NDUFC2 6786 0.013 0.56 NO
61 NDUFA4 NDUFA4 NDUFA4 6905 0.011 0.55 NO
62 ATP5E ATP5E ATP5E 7043 0.0097 0.55 NO
63 CYC1 CYC1 CYC1 7083 0.0092 0.55 NO
64 NDUFA11 NDUFA11 NDUFA11 7186 0.0076 0.55 NO
65 ATP5D ATP5D ATP5D 7283 0.0064 0.54 NO
66 NDUFS7 NDUFS7 NDUFS7 7488 0.0034 0.53 NO
67 NDUFA5 NDUFA5 NDUFA5 7560 0.0024 0.53 NO
68 UQCRHL UQCRHL UQCRHL 7606 0.0017 0.53 NO
69 UQCRH UQCRH UQCRH 7632 0.0014 0.53 NO
70 ETFA ETFA ETFA 7853 -0.002 0.52 NO
71 COX5A COX5A COX5A 7898 -0.0026 0.51 NO
72 NDUFA12 NDUFA12 NDUFA12 7965 -0.0034 0.51 NO
73 SDHC SDHC SDHC 8108 -0.005 0.5 NO
74 NDUFAB1 NDUFAB1 NDUFAB1 8288 -0.0077 0.5 NO
75 COX6B1 COX6B1 COX6B1 8349 -0.0086 0.5 NO
76 NDUFB9 NDUFB9 NDUFB9 8378 -0.0093 0.5 NO
77 NDUFS6 NDUFS6 NDUFS6 8416 -0.0099 0.5 NO
78 NDUFA6 NDUFA6 NDUFA6 10418 -0.042 0.4 NO
79 UQCRC1 UQCRC1 UQCRC1 10445 -0.043 0.41 NO
80 UCP3 UCP3 UCP3 11041 -0.055 0.4 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: PID CASPASE PATHWAY.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: PID CASPASE 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: PID A6B1 A6B4 INTEGRIN PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GAS2 GAS2 GAS2 120 0.54 0.094 YES
2 CASP6 CASP6 CASP6 722 0.29 0.12 YES
3 TFAP2A TFAP2A TFAP2A 815 0.27 0.16 YES
4 GZMB GZMB GZMB 837 0.26 0.21 YES
5 CASP1 CASP1 CASP1 1067 0.23 0.24 YES
6 PRF1 PRF1 PRF1 1269 0.2 0.27 YES
7 CASP4 CASP4 CASP4 1851 0.15 0.26 YES
8 KRT18 KRT18 KRT18 2052 0.14 0.28 YES
9 CASP3 CASP3 CASP3 2146 0.13 0.3 YES
10 CASP10 CASP10 CASP10 2426 0.12 0.3 YES
11 CASP8 CASP8 CASP8 2595 0.11 0.32 YES
12 TRADD TRADD TRADD 2784 0.1 0.32 YES
13 TNF TNF TNF 2803 0.1 0.34 YES
14 SPTAN1 SPTAN1 SPTAN1 2875 0.096 0.36 YES
15 BIRC3 BIRC3 BIRC3 2883 0.096 0.37 YES
16 CASP9 CASP9 CASP9 3165 0.087 0.38 YES
17 TNFRSF1A TNFRSF1A TNFRSF1A 3180 0.086 0.39 YES
18 RIPK1 RIPK1 RIPK1 4723 0.046 0.31 NO
19 PTK2 PTK2 PTK2 4783 0.045 0.32 NO
20 APP APP APP 5643 0.03 0.28 NO
21 CRADD CRADD CRADD 6185 0.022 0.25 NO
22 MADD MADD MADD 6391 0.019 0.24 NO
23 NUMA1 NUMA1 NUMA1 6543 0.017 0.24 NO
24 CYCS CYCS CYCS 6577 0.016 0.24 NO
25 DIABLO DIABLO DIABLO 6615 0.016 0.24 NO
26 BID BID BID 6761 0.014 0.24 NO
27 TOP1 TOP1 TOP1 6859 0.012 0.23 NO
28 BIRC2 BIRC2 BIRC2 6949 0.011 0.23 NO
29 CASP7 CASP7 CASP7 8418 -0.0099 0.15 NO
30 CFL2 CFL2 CFL2 8919 -0.018 0.13 NO
31 BAX BAX BAX 9303 -0.024 0.11 NO
32 GSN GSN GSN 9764 -0.031 0.09 NO
33 SLK SLK SLK 9962 -0.035 0.086 NO
34 XIAP XIAP XIAP 10289 -0.04 0.075 NO
35 MAP3K1 MAP3K1 MAP3K1 10410 -0.042 0.076 NO
36 PARP1 PARP1 PARP1 11079 -0.056 0.05 NO
37 ARHGDIB ARHGDIB ARHGDIB 11153 -0.057 0.057 NO
38 DFFA DFFA DFFA 11361 -0.062 0.057 NO
39 SREBF1 SREBF1 SREBF1 11811 -0.073 0.046 NO
40 TRAF2 TRAF2 TRAF2 11880 -0.074 0.056 NO
41 LIMK1 LIMK1 LIMK1 11913 -0.075 0.069 NO
42 LMNB1 LMNB1 LMNB1 12304 -0.085 0.063 NO
43 LMNA LMNA LMNA 12331 -0.086 0.078 NO
44 CASP2 CASP2 CASP2 12562 -0.093 0.083 NO
45 DFFB DFFB DFFB 12834 -0.1 0.087 NO
46 APAF1 APAF1 APAF1 13027 -0.11 0.097 NO
47 LMNB2 LMNB2 LMNB2 14745 -0.18 0.036 NO
48 ACTA1 ACTA1 ACTA1 14902 -0.19 0.063 NO
49 BCL2 BCL2 BCL2 15120 -0.2 0.089 NO
50 VIM VIM VIM 15268 -0.21 0.12 NO
51 SATB1 SATB1 SATB1 15359 -0.22 0.16 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: PID A6B1 A6B4 INTEGRIN PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: PID A6B1 A6B4 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: REACTOME TRANSLATION

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 LAMB3 LAMB3 LAMB3 239 0.45 0.076 YES
2 CDH1 CDH1 CDH1 404 0.38 0.14 YES
3 LAMA3 LAMA3 LAMA3 435 0.37 0.21 YES
4 MST1R MST1R MST1R 438 0.36 0.28 YES
5 MET MET MET 502 0.34 0.34 YES
6 SFN SFN SFN 585 0.32 0.4 YES
7 ITGB4 ITGB4 ITGB4 773 0.28 0.45 YES
8 MST1 MST1 MST1 1160 0.22 0.47 YES
9 LAMA4 LAMA4 LAMA4 1866 0.15 0.46 YES
10 EGFR EGFR EGFR 1867 0.15 0.49 YES
11 ERBB2 ERBB2 ERBB2 2090 0.13 0.5 YES
12 CD9 CD9 CD9 3049 0.09 0.47 NO
13 ERBB3 ERBB3 ERBB3 3853 0.066 0.44 NO
14 LAMA5 LAMA5 LAMA5 4401 0.053 0.42 NO
15 RPS6KB1 RPS6KB1 RPS6KB1 4453 0.052 0.42 NO
16 RXRA RXRA RXRA 5060 0.04 0.4 NO
17 HRAS HRAS HRAS 5174 0.038 0.4 NO
18 PIK3R1 PIK3R1 PIK3R1 5467 0.033 0.39 NO
19 PIK3CA PIK3CA PIK3CA 5885 0.026 0.37 NO
20 EGF EGF EGF 6108 0.023 0.36 NO
21 GRB2 GRB2 GRB2 6636 0.015 0.34 NO
22 RXRG RXRG RXRG 6940 0.011 0.32 NO
23 YWHAZ YWHAZ YWHAZ 7261 0.0066 0.31 NO
24 LAMA1 LAMA1 LAMA1 7424 0.0044 0.3 NO
25 YWHAB YWHAB YWHAB 7929 -0.0028 0.27 NO
26 RXRB RXRB RXRB 8112 -0.0051 0.26 NO
27 CASP7 CASP7 CASP7 8418 -0.0099 0.25 NO
28 YWHAE YWHAE YWHAE 8897 -0.017 0.22 NO
29 YWHAH YWHAH YWHAH 8910 -0.017 0.23 NO
30 RAC1 RAC1 RAC1 9626 -0.029 0.19 NO
31 YWHAQ YWHAQ YWHAQ 9733 -0.031 0.19 NO
32 SHC1 SHC1 SHC1 10313 -0.04 0.17 NO
33 AKT1 AKT1 AKT1 10341 -0.041 0.18 NO
34 YWHAG YWHAG YWHAG 10556 -0.045 0.17 NO
35 ITGA6 ITGA6 ITGA6 10680 -0.047 0.18 NO
36 LAMB2 LAMB2 LAMB2 10905 -0.052 0.17 NO
37 COL17A1 COL17A1 COL17A1 11742 -0.071 0.14 NO
38 LAMA2 LAMA2 LAMA2 11855 -0.074 0.15 NO
39 ITGB1 ITGB1 ITGB1 11967 -0.076 0.16 NO
40 LAMC3 LAMC3 LAMC3 12129 -0.081 0.16 NO
41 PMP22 PMP22 PMP22 12231 -0.083 0.18 NO
42 LAMC1 LAMC1 LAMC1 13186 -0.11 0.14 NO
43 IL1A IL1A IL1A 13920 -0.14 0.13 NO
44 LAMC2 LAMC2 LAMC2 14341 -0.16 0.14 NO
45 LAMB1 LAMB1 LAMB1 14704 -0.18 0.16 NO
46 PRKCA PRKCA PRKCA 14943 -0.19 0.18 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: REACTOME TRANSLATION.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSLATION, 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: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

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 GPLD1 GPLD1 GPLD1 547 0.33 0.13 YES
2 PIGF PIGF PIGF 1656 0.17 0.14 YES
3 PIGZ PIGZ PIGZ 1729 0.16 0.22 YES
4 PIGP PIGP PIGP 2403 0.12 0.23 YES
5 PIGH PIGH PIGH 2507 0.11 0.28 YES
6 PIGY PIGY PIGY 3244 0.084 0.28 YES
7 PIGG PIGG PIGG 3361 0.081 0.31 YES
8 PIGB PIGB PIGB 3394 0.08 0.35 YES
9 PIGV PIGV PIGV 3644 0.072 0.37 YES
10 PIGO PIGO PIGO 3789 0.068 0.39 YES
11 PIGS PIGS PIGS 4305 0.056 0.39 NO
12 PIGL PIGL PIGL 5364 0.035 0.35 NO
13 PIGK PIGK PIGK 7395 0.0049 0.24 NO
14 PIGQ PIGQ PIGQ 7715 -0.000027 0.22 NO
15 PIGW PIGW PIGW 8564 -0.012 0.18 NO
16 PIGC PIGC PIGC 8781 -0.015 0.17 NO
17 PIGU PIGU PIGU 8943 -0.018 0.17 NO
18 PIGT PIGT PIGT 9649 -0.029 0.15 NO
19 GPAA1 GPAA1 GPAA1 10365 -0.041 0.13 NO
20 DPM2 DPM2 DPM2 10884 -0.052 0.12 NO
21 PIGM PIGM PIGM 11136 -0.057 0.14 NO
22 PIGN PIGN PIGN 11719 -0.071 0.14 NO
23 PIGX PIGX PIGX 11775 -0.072 0.17 NO
24 PIGA PIGA PIGA 12514 -0.092 0.17 NO
25 PGAP1 PGAP1 PGAP1 16494 -0.3 0.094 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: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES, 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 56 genes.ES.table 0.45 1.5 0.052 1 0.99 0.25 0.2 0.2 0.99 0.5
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.46 1.6 0.081 1 0.94 0.58 0.35 0.38 0.97 0.48
KEGG HISTIDINE METABOLISM 29 genes.ES.table 0.6 1.6 0.014 1 0.94 0.52 0.27 0.38 0.85 0.44
KEGG STARCH AND SUCROSE METABOLISM 35 genes.ES.table 0.58 1.5 0.041 1 0.97 0.31 0.11 0.28 0.85 0.44
KEGG PYRUVATE METABOLISM 38 genes.ES.table 0.43 1.5 0.038 1 0.97 0.47 0.33 0.32 0.8 0.4
KEGG PROPANOATE METABOLISM 32 genes.ES.table 0.51 1.5 0.072 1 0.97 0.53 0.34 0.35 0.83 0.41
KEGG AMINOACYL TRNA BIOSYNTHESIS 41 genes.ES.table 0.38 1.4 0.17 1 1 0.39 0.34 0.26 0.97 0.49
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 52 genes.ES.table 0.62 1.6 0.0067 1 0.96 0.54 0.2 0.43 0.89 0.46
KEGG DRUG METABOLISM CYTOCHROME P450 55 genes.ES.table 0.65 1.6 0 1 0.92 0.55 0.2 0.44 1 0.55
PID NCADHERINPATHWAY 33 genes.ES.table 0.5 1.7 0.014 1 0.81 0.46 0.28 0.33 1 0.52
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 ADHFE1 ADHFE1 ADHFE1 2056 0.18 -0.033 YES
2 PDP2 PDP2 PDP2 2179 0.18 0.037 YES
3 FH FH FH 2622 0.15 0.078 YES
4 PDK1 PDK1 PDK1 2788 0.14 0.13 YES
5 SLC16A1 SLC16A1 SLC16A1 3788 0.1 0.12 YES
6 IDH3A IDH3A IDH3A 4320 0.088 0.13 YES
7 NNT NNT NNT 4555 0.082 0.15 YES
8 BSG BSG BSG 4626 0.08 0.18 YES
9 SUCLA2 SUCLA2 SUCLA2 4671 0.079 0.21 YES
10 L2HGDH L2HGDH L2HGDH 5196 0.068 0.21 YES
11 SDHC SDHC SDHC 5240 0.066 0.24 YES
12 PDK2 PDK2 PDK2 5267 0.066 0.27 YES
13 PDHB PDHB PDHB 5455 0.062 0.28 YES
14 PDHA1 PDHA1 PDHA1 5550 0.061 0.3 YES
15 PDK3 PDK3 PDK3 5936 0.053 0.31 YES
16 PDHX PDHX PDHX 6003 0.052 0.33 YES
17 SUCLG2 SUCLG2 SUCLG2 6098 0.051 0.34 YES
18 DLD DLD DLD 6347 0.046 0.35 YES
19 PDP1 PDP1 PDP1 6562 0.043 0.36 YES
20 ACO2 ACO2 ACO2 6710 0.041 0.37 YES
21 SUCLG1 SUCLG1 SUCLG1 6787 0.04 0.38 YES
22 IDH3G IDH3G IDH3G 6809 0.04 0.4 YES
23 SLC16A3 SLC16A3 SLC16A3 6841 0.039 0.41 YES
24 LDHA LDHA LDHA 6964 0.037 0.42 YES
25 SDHA SDHA SDHA 7070 0.035 0.43 YES
26 PDPR PDPR PDPR 7594 0.028 0.41 NO
27 MDH2 MDH2 MDH2 7606 0.028 0.42 NO
28 SDHD SDHD SDHD 8290 0.019 0.4 NO
29 SLC16A8 SLC16A8 SLC16A8 8742 0.013 0.38 NO
30 D2HGDH D2HGDH D2HGDH 9045 0.0096 0.36 NO
31 LDHB LDHB LDHB 9091 0.009 0.36 NO
32 DLAT DLAT DLAT 9243 0.0071 0.36 NO
33 IDH1 IDH1 IDH1 9443 0.0046 0.35 NO
34 IDH3B IDH3B IDH3B 10243 -0.0052 0.31 NO
35 SDHB SDHB SDHB 11263 -0.019 0.26 NO
36 CS CS CS 11269 -0.019 0.27 NO
37 OGDH OGDH OGDH 12276 -0.033 0.23 NO
38 IDH2 IDH2 IDH2 12342 -0.034 0.24 NO
39 DLST DLST DLST 14659 -0.089 0.15 NO
40 PDK4 PDK4 PDK4 15118 -0.1 0.17 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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 CNR1 CNR1 CNR1 469 0.4 0.12 YES
2 GAP43 GAP43 GAP43 1553 0.23 0.15 YES
3 GRIA2 GRIA2 GRIA2 1949 0.19 0.2 YES
4 CDH2 CDH2 CDH2 2576 0.15 0.23 YES
5 FER FER FER 2943 0.14 0.26 YES
6 JUP JUP JUP 3249 0.12 0.29 YES
7 GJA1 GJA1 GJA1 3287 0.12 0.33 YES
8 MAPK8 MAPK8 MAPK8 3333 0.12 0.37 YES
9 MYL2 MYL2 MYL2 3594 0.11 0.4 YES
10 AXIN1 AXIN1 AXIN1 4168 0.092 0.4 YES
11 PTPN11 PTPN11 PTPN11 4219 0.091 0.43 YES
12 CTTN CTTN CTTN 4558 0.082 0.45 YES
13 LRP5 LRP5 LRP5 4585 0.081 0.48 YES
14 DAGLB DAGLB DAGLB 4892 0.074 0.49 YES
15 DAGLA DAGLA DAGLA 5092 0.07 0.5 YES
16 RHOA RHOA RHOA 6536 0.044 0.44 NO
17 PTPN1 PTPN1 PTPN1 6988 0.037 0.43 NO
18 PIK3R1 PIK3R1 PIK3R1 6996 0.037 0.44 NO
19 RAC1 RAC1 RAC1 8052 0.022 0.39 NO
20 PIK3CA PIK3CA PIK3CA 8717 0.014 0.36 NO
21 CTNND1 CTNND1 CTNND1 9534 0.0036 0.32 NO
22 CAMK2G CAMK2G CAMK2G 10063 -0.0029 0.29 NO
23 CTNNA1 CTNNA1 CTNNA1 10505 -0.0086 0.27 NO
24 CDC42 CDC42 CDC42 10724 -0.012 0.26 NO
25 PIP5K1C PIP5K1C PIP5K1C 10889 -0.014 0.26 NO
26 MAPRE1 MAPRE1 MAPRE1 11916 -0.028 0.21 NO
27 CTNNB1 CTNNB1 CTNNB1 11948 -0.028 0.22 NO
28 GSN GSN GSN 12013 -0.029 0.23 NO
29 DCTN1 DCTN1 DCTN1 12251 -0.033 0.23 NO
30 KIF5B KIF5B KIF5B 12923 -0.044 0.21 NO
31 ROCK1 ROCK1 ROCK1 13983 -0.069 0.17 NO
32 FGFR1 FGFR1 FGFR1 13987 -0.069 0.2 NO
33 PLCG1 PLCG1 PLCG1 14462 -0.082 0.2 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S24.  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 HISTIDINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AP1M2 AP1M2 AP1M2 525 0.38 0.098 YES
2 TBC1D8B TBC1D8B TBC1D8B 1048 0.28 0.16 YES
3 TPD52 TPD52 TPD52 1348 0.25 0.23 YES
4 SORT1 SORT1 SORT1 2910 0.14 0.19 YES
5 TPD52L1 TPD52L1 TPD52L1 3408 0.12 0.2 YES
6 TFRC TFRC TFRC 3635 0.11 0.22 YES
7 SH3D19 SH3D19 SH3D19 3719 0.1 0.25 YES
8 AP4E1 AP4E1 AP4E1 3989 0.098 0.27 YES
9 AP3S1 AP3S1 AP3S1 4013 0.097 0.3 YES
10 AP3B1 AP3B1 AP3B1 4391 0.086 0.31 YES
11 CPD CPD CPD 4804 0.076 0.31 YES
12 AP1S1 AP1S1 AP1S1 5480 0.062 0.29 YES
13 ARF1 ARF1 ARF1 5500 0.062 0.31 YES
14 ARRB1 ARRB1 ARRB1 5789 0.056 0.32 YES
15 PIK3C2A PIK3C2A PIK3C2A 5798 0.056 0.33 YES
16 SNX9 SNX9 SNX9 6124 0.05 0.33 YES
17 VAMP7 VAMP7 VAMP7 6178 0.049 0.35 YES
18 BLOC1S1 BLOC1S1 BLOC1S1 6247 0.048 0.36 YES
19 VAMP8 VAMP8 VAMP8 6458 0.045 0.36 YES
20 DNAJC6 DNAJC6 DNAJC6 6825 0.039 0.36 YES
21 SNAPIN SNAPIN SNAPIN 6847 0.039 0.37 YES
22 YIPF6 YIPF6 YIPF6 7013 0.036 0.37 YES
23 SNX2 SNX2 SNX2 7588 0.028 0.35 NO
24 PUM1 PUM1 PUM1 7799 0.026 0.34 NO
25 BLOC1S3 BLOC1S3 BLOC1S3 7939 0.024 0.34 NO
26 AP1M1 AP1M1 AP1M1 8705 0.014 0.31 NO
27 OCRL OCRL OCRL 8777 0.013 0.31 NO
28 HSPA8 HSPA8 HSPA8 8827 0.012 0.31 NO
29 AP4B1 AP4B1 AP4B1 9020 0.0099 0.3 NO
30 NAPA NAPA NAPA 9098 0.0088 0.3 NO
31 FTH1 FTH1 FTH1 9164 0.008 0.3 NO
32 DNM2 DNM2 DNM2 9331 0.0061 0.29 NO
33 AP1G1 AP1G1 AP1G1 9458 0.0044 0.29 NO
34 PLDN PLDN PLDN 9493 0.004 0.29 NO
35 PICALM PICALM PICALM 9530 0.0037 0.28 NO
36 RAB5C RAB5C RAB5C 9583 0.0031 0.28 NO
37 DTNBP1 DTNBP1 DTNBP1 9684 0.0019 0.28 NO
38 TXNDC5 TXNDC5 TXNDC5 9693 0.0017 0.28 NO
39 TGOLN2 TGOLN2 TGOLN2 9983 -0.0019 0.26 NO
40 CNO CNO CNO 10402 -0.0072 0.24 NO
41 CLTC CLTC CLTC 10423 -0.0076 0.24 NO
42 SNX5 SNX5 SNX5 10612 -0.01 0.24 NO
43 VAMP2 VAMP2 VAMP2 10757 -0.012 0.23 NO
44 GAK GAK GAK 10964 -0.015 0.23 NO
45 IGF2R IGF2R IGF2R 11092 -0.016 0.22 NO
46 NECAP1 NECAP1 NECAP1 11165 -0.017 0.23 NO
47 AP1S2 AP1S2 AP1S2 12431 -0.036 0.17 NO
48 CLTA CLTA CLTA 12802 -0.042 0.16 NO
49 AP1B1 AP1B1 AP1B1 12830 -0.043 0.18 NO
50 FTL FTL FTL 13755 -0.062 0.14 NO
51 HIP1R HIP1R HIP1R 13979 -0.069 0.16 NO
52 SH3GL2 SH3GL2 SH3GL2 17092 -0.23 0.061 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 HISTIDINE METABOLISM.

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

genes ES table in pathway: KEGG STARCH AND SUCROSE 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 MAOA MAOA MAOA 74 0.62 0.06 YES
2 AOX1 AOX1 AOX1 103 0.59 0.12 YES
3 MAOB MAOB MAOB 271 0.47 0.16 YES
4 UGT1A9 UGT1A9 UGT1A9 348 0.44 0.2 YES
5 CYP2E1 CYP2E1 CYP2E1 362 0.44 0.24 YES
6 ALDH1A3 ALDH1A3 ALDH1A3 460 0.4 0.28 YES
7 ADH1C ADH1C ADH1C 548 0.38 0.32 YES
8 ALDH3A1 ALDH3A1 ALDH3A1 588 0.37 0.35 YES
9 MGST1 MGST1 MGST1 684 0.35 0.38 YES
10 GSTM2 GSTM2 GSTM2 829 0.32 0.41 YES
11 CYP2C18 CYP2C18 CYP2C18 959 0.3 0.43 YES
12 UGT1A1 UGT1A1 UGT1A1 1002 0.29 0.46 YES
13 UGT1A6 UGT1A6 UGT1A6 1070 0.28 0.48 YES
14 UGT1A10 UGT1A10 UGT1A10 1165 0.27 0.51 YES
15 FMO4 FMO4 FMO4 1200 0.26 0.53 YES
16 GSTA4 GSTA4 GSTA4 1548 0.23 0.54 YES
17 UGT1A8 UGT1A8 UGT1A8 1566 0.23 0.56 YES
18 UGT2A1 UGT2A1 UGT2A1 1655 0.22 0.58 YES
19 GSTO2 GSTO2 GSTO2 1721 0.21 0.59 YES
20 GSTM3 GSTM3 GSTM3 1727 0.21 0.62 YES
21 GSTM4 GSTM4 GSTM4 2247 0.17 0.6 YES
22 GSTM1 GSTM1 GSTM1 2307 0.17 0.62 YES
23 CYP2C9 CYP2C9 CYP2C9 2951 0.13 0.6 YES
24 CYP3A7 CYP3A7 CYP3A7 3004 0.13 0.61 YES
25 MGST2 MGST2 MGST2 3084 0.13 0.62 YES
26 FMO5 FMO5 FMO5 3161 0.12 0.63 YES
27 CYP2C8 CYP2C8 CYP2C8 3301 0.12 0.63 YES
28 CYP2A7 CYP2A7 CYP2A7 3435 0.11 0.64 YES
29 CYP2A6 CYP2A6 CYP2A6 3513 0.11 0.64 YES
30 ALDH3B1 ALDH3B1 ALDH3B1 3621 0.11 0.65 YES
31 CYP3A5 CYP3A5 CYP3A5 4271 0.089 0.62 NO
32 ADH1B ADH1B ADH1B 4970 0.072 0.59 NO
33 MGST3 MGST3 MGST3 5017 0.071 0.6 NO
34 FMO1 FMO1 FMO1 5435 0.063 0.58 NO
35 CYP2D6 CYP2D6 CYP2D6 5457 0.062 0.58 NO
36 GSTK1 GSTK1 GSTK1 6437 0.045 0.53 NO
37 GSTP1 GSTP1 GSTP1 6496 0.044 0.54 NO
38 GSTT1 GSTT1 GSTT1 6561 0.043 0.54 NO
39 ALDH3B2 ALDH3B2 ALDH3B2 7541 0.029 0.48 NO
40 CYP2A13 CYP2A13 CYP2A13 8524 0.016 0.43 NO
41 GSTA1 GSTA1 GSTA1 10249 -0.0054 0.34 NO
42 CYP3A4 CYP3A4 CYP3A4 11305 -0.019 0.28 NO
43 ADH5 ADH5 ADH5 11306 -0.019 0.28 NO
44 GSTO1 GSTO1 GSTO1 11413 -0.021 0.28 NO
45 FMO3 FMO3 FMO3 11869 -0.027 0.26 NO
46 ADH6 ADH6 ADH6 12001 -0.029 0.25 NO
47 CYP3A43 CYP3A43 CYP3A43 13347 -0.053 0.18 NO
48 GSTM5 GSTM5 GSTM5 13556 -0.058 0.18 NO
49 CYP1A2 CYP1A2 CYP1A2 13661 -0.06 0.18 NO
50 GSTT2 GSTT2 GSTT2 14021 -0.07 0.17 NO
51 FMO2 FMO2 FMO2 14283 -0.077 0.16 NO
52 GSTA2 GSTA2 GSTA2 14846 -0.095 0.14 NO
53 ADH4 ADH4 ADH4 15310 -0.11 0.13 NO
54 ADH1A ADH1A ADH1A 15866 -0.14 0.11 NO
55 GSTZ1 GSTZ1 GSTZ1 16426 -0.18 0.097 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 STARCH AND SUCROSE METABOLISM.

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

genes ES table in pathway: KEGG PYRUVATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AP1M2 AP1M2 AP1M2 525 0.38 0.086 YES
2 TBC1D8B TBC1D8B TBC1D8B 1048 0.28 0.14 YES
3 TPD52 TPD52 TPD52 1348 0.25 0.2 YES
4 SORT1 SORT1 SORT1 2910 0.14 0.15 YES
5 TPD52L1 TPD52L1 TPD52L1 3408 0.12 0.16 YES
6 TFRC TFRC TFRC 3635 0.11 0.18 YES
7 SH3D19 SH3D19 SH3D19 3719 0.1 0.21 YES
8 DNASE2 DNASE2 DNASE2 3726 0.1 0.24 YES
9 AP4E1 AP4E1 AP4E1 3989 0.098 0.25 YES
10 AP3S1 AP3S1 AP3S1 4013 0.097 0.28 YES
11 AP3B1 AP3B1 AP3B1 4391 0.086 0.29 YES
12 CPD CPD CPD 4804 0.076 0.29 YES
13 AP1S1 AP1S1 AP1S1 5480 0.062 0.27 YES
14 ARF1 ARF1 ARF1 5500 0.062 0.28 YES
15 ARRB1 ARRB1 ARRB1 5789 0.056 0.28 YES
16 PIK3C2A PIK3C2A PIK3C2A 5798 0.056 0.3 YES
17 STX4 STX4 STX4 6018 0.052 0.3 YES
18 SNX9 SNX9 SNX9 6124 0.05 0.31 YES
19 VAMP7 VAMP7 VAMP7 6178 0.049 0.33 YES
20 BLOC1S1 BLOC1S1 BLOC1S1 6247 0.048 0.34 YES
21 VAMP8 VAMP8 VAMP8 6458 0.045 0.34 YES
22 DNAJC6 DNAJC6 DNAJC6 6825 0.039 0.33 YES
23 SNAPIN SNAPIN SNAPIN 6847 0.039 0.34 YES
24 YIPF6 YIPF6 YIPF6 7013 0.036 0.34 YES
25 SNAP23 SNAP23 SNAP23 7508 0.029 0.32 NO
26 SNX2 SNX2 SNX2 7588 0.028 0.33 NO
27 PUM1 PUM1 PUM1 7799 0.026 0.32 NO
28 BLOC1S3 BLOC1S3 BLOC1S3 7939 0.024 0.32 NO
29 AP1M1 AP1M1 AP1M1 8705 0.014 0.28 NO
30 OCRL OCRL OCRL 8777 0.013 0.28 NO
31 HSPA8 HSPA8 HSPA8 8827 0.012 0.29 NO
32 AP4B1 AP4B1 AP4B1 9020 0.0099 0.28 NO
33 NAPA NAPA NAPA 9098 0.0088 0.28 NO
34 FTH1 FTH1 FTH1 9164 0.008 0.28 NO
35 DNM2 DNM2 DNM2 9331 0.0061 0.27 NO
36 AP1G1 AP1G1 AP1G1 9458 0.0044 0.26 NO
37 PLDN PLDN PLDN 9493 0.004 0.26 NO
38 PICALM PICALM PICALM 9530 0.0037 0.26 NO
39 RAB5C RAB5C RAB5C 9583 0.0031 0.26 NO
40 DTNBP1 DTNBP1 DTNBP1 9684 0.0019 0.25 NO
41 TXNDC5 TXNDC5 TXNDC5 9693 0.0017 0.25 NO
42 TGOLN2 TGOLN2 TGOLN2 9983 -0.0019 0.24 NO
43 CNO CNO CNO 10402 -0.0072 0.22 NO
44 CLTC CLTC CLTC 10423 -0.0076 0.22 NO
45 GNS GNS GNS 10479 -0.0083 0.22 NO
46 SNX5 SNX5 SNX5 10612 -0.01 0.21 NO
47 VAMP2 VAMP2 VAMP2 10757 -0.012 0.21 NO
48 GAK GAK GAK 10964 -0.015 0.2 NO
49 IGF2R IGF2R IGF2R 11092 -0.016 0.2 NO
50 NECAP1 NECAP1 NECAP1 11165 -0.017 0.2 NO
51 CTSZ CTSZ CTSZ 12232 -0.033 0.15 NO
52 GBF1 GBF1 GBF1 12340 -0.034 0.16 NO
53 AP1S2 AP1S2 AP1S2 12431 -0.036 0.16 NO
54 CLTA CLTA CLTA 12802 -0.042 0.16 NO
55 AP1B1 AP1B1 AP1B1 12830 -0.043 0.17 NO
56 FTL FTL FTL 13755 -0.062 0.13 NO
57 M6PR M6PR M6PR 13940 -0.068 0.14 NO
58 HIP1R HIP1R HIP1R 13979 -0.069 0.16 NO
59 SH3GL2 SH3GL2 SH3GL2 17092 -0.23 0.061 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 PYRUVATE METABOLISM.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRUVATE 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 S16.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AOX1 AOX1 AOX1 103 0.59 0.14 YES
2 EHHADH EHHADH EHHADH 388 0.43 0.22 YES
3 AUH AUH AUH 1313 0.25 0.23 YES
4 ACADSB ACADSB ACADSB 1493 0.23 0.28 YES
5 BCKDHB BCKDHB BCKDHB 1599 0.22 0.33 YES
6 HIBCH HIBCH HIBCH 2063 0.18 0.35 YES
7 BCAT1 BCAT1 BCAT1 3296 0.12 0.31 YES
8 ALDH1B1 ALDH1B1 ALDH1B1 3331 0.12 0.34 YES
9 PCCA PCCA PCCA 3607 0.11 0.35 YES
10 ACAT1 ACAT1 ACAT1 3741 0.1 0.36 YES
11 HIBADH HIBADH HIBADH 3903 0.1 0.38 YES
12 ACAD8 ACAD8 ACAD8 3917 0.1 0.4 YES
13 MCEE MCEE MCEE 3969 0.098 0.42 YES
14 ABAT ABAT ABAT 4406 0.086 0.42 YES
15 OXCT1 OXCT1 OXCT1 4461 0.084 0.44 YES
16 ALDH7A1 ALDH7A1 ALDH7A1 4876 0.074 0.43 YES
17 HADH HADH HADH 5258 0.066 0.43 YES
18 MUT MUT MUT 5568 0.06 0.42 YES
19 ACAA2 ACAA2 ACAA2 5778 0.056 0.43 YES
20 ALDH3A2 ALDH3A2 ALDH3A2 6005 0.052 0.43 YES
21 HMGCS1 HMGCS1 HMGCS1 6017 0.052 0.44 YES
22 MCCC1 MCCC1 MCCC1 6273 0.048 0.44 YES
23 HSD17B10 HSD17B10 HSD17B10 6298 0.047 0.45 YES
24 DLD DLD DLD 6347 0.046 0.46 YES
25 MCCC2 MCCC2 MCCC2 6373 0.046 0.46 YES
26 BCKDHA BCKDHA BCKDHA 7426 0.03 0.41 NO
27 ALDH9A1 ALDH9A1 ALDH9A1 7507 0.029 0.42 NO
28 DBT DBT DBT 7630 0.028 0.42 NO
29 ALDH2 ALDH2 ALDH2 8041 0.022 0.4 NO
30 HMGCL HMGCL HMGCL 9040 0.0096 0.35 NO
31 ACAA1 ACAA1 ACAA1 9448 0.0046 0.32 NO
32 ACADM ACADM ACADM 9704 0.0016 0.31 NO
33 BCAT2 BCAT2 BCAT2 10570 -0.0095 0.27 NO
34 HADHB HADHB HADHB 10881 -0.014 0.25 NO
35 HADHA HADHA HADHA 11168 -0.017 0.24 NO
36 PCCB PCCB PCCB 11191 -0.018 0.24 NO
37 ACADS ACADS ACADS 11374 -0.02 0.24 NO
38 IL4I1 IL4I1 IL4I1 11749 -0.025 0.22 NO
39 ECHS1 ECHS1 ECHS1 12207 -0.032 0.21 NO
40 ALDH6A1 ALDH6A1 ALDH6A1 13412 -0.054 0.15 NO
41 IVD IVD IVD 14260 -0.076 0.12 NO
42 ACAT2 ACAT2 ACAT2 16363 -0.17 0.051 NO
43 OXCT2 OXCT2 OXCT2 16806 -0.21 0.076 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 PROPANOATE METABOLISM.

Figure S32.  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 AMINOACYL TRNA BIOSYNTHESIS

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 MAOA MAOA MAOA 74 0.62 0.15 YES
2 MAOB MAOB MAOB 271 0.47 0.26 YES
3 ALDH1A3 ALDH1A3 ALDH1A3 460 0.4 0.35 YES
4 ALDH3A1 ALDH3A1 ALDH3A1 588 0.37 0.44 YES
5 FTCD FTCD FTCD 827 0.32 0.51 YES
6 HAL HAL HAL 1887 0.2 0.5 YES
7 HEMK1 HEMK1 HEMK1 2014 0.19 0.54 YES
8 AMDHD1 AMDHD1 AMDHD1 2538 0.16 0.55 YES
9 HNMT HNMT HNMT 3306 0.12 0.54 YES
10 ALDH1B1 ALDH1B1 ALDH1B1 3331 0.12 0.57 YES
11 ALDH3B1 ALDH3B1 ALDH3B1 3621 0.11 0.58 YES
12 LCMT1 LCMT1 LCMT1 4058 0.096 0.58 YES
13 TRMT11 TRMT11 TRMT11 4291 0.089 0.59 YES
14 WBSCR22 WBSCR22 WBSCR22 4610 0.08 0.59 YES
15 ALDH7A1 ALDH7A1 ALDH7A1 4876 0.074 0.6 YES
16 ALDH3A2 ALDH3A2 ALDH3A2 6005 0.052 0.55 NO
17 UROC1 UROC1 UROC1 6906 0.038 0.51 NO
18 METTL2B METTL2B METTL2B 7081 0.035 0.51 NO
19 ALDH9A1 ALDH9A1 ALDH9A1 7507 0.029 0.49 NO
20 ALDH3B2 ALDH3B2 ALDH3B2 7541 0.029 0.5 NO
21 ALDH2 ALDH2 ALDH2 8041 0.022 0.47 NO
22 DDC DDC DDC 8799 0.013 0.44 NO
23 HDC HDC HDC 9501 0.0039 0.4 NO
24 LCMT2 LCMT2 LCMT2 10562 -0.0094 0.34 NO
25 ACY3 ACY3 ACY3 11370 -0.02 0.3 NO
26 CNDP1 CNDP1 CNDP1 12425 -0.036 0.25 NO
27 METTL6 METTL6 METTL6 13169 -0.049 0.22 NO
28 ABP1 ABP1 ABP1 14931 -0.098 0.15 NO
29 ASPA ASPA ASPA 15138 -0.11 0.17 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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450

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 UGT1A9 UGT1A9 UGT1A9 348 0.44 0.032 YES
2 CYP2S1 CYP2S1 CYP2S1 354 0.44 0.082 YES
3 CYP2E1 CYP2E1 CYP2E1 362 0.44 0.13 YES
4 ALDH1A3 ALDH1A3 ALDH1A3 460 0.4 0.17 YES
5 ADH1C ADH1C ADH1C 548 0.38 0.21 YES
6 ALDH3A1 ALDH3A1 ALDH3A1 588 0.37 0.25 YES
7 MGST1 MGST1 MGST1 684 0.35 0.28 YES
8 GSTM2 GSTM2 GSTM2 829 0.32 0.31 YES
9 AKR1C2 AKR1C2 AKR1C2 905 0.3 0.34 YES
10 CYP2C18 CYP2C18 CYP2C18 959 0.3 0.38 YES
11 UGT1A1 UGT1A1 UGT1A1 1002 0.29 0.41 YES
12 UGT1A6 UGT1A6 UGT1A6 1070 0.28 0.44 YES
13 UGT1A10 UGT1A10 UGT1A10 1165 0.27 0.46 YES
14 GSTA4 GSTA4 GSTA4 1548 0.23 0.47 YES
15 UGT1A8 UGT1A8 UGT1A8 1566 0.23 0.49 YES
16 UGT2A1 UGT2A1 UGT2A1 1655 0.22 0.51 YES
17 GSTO2 GSTO2 GSTO2 1721 0.21 0.53 YES
18 GSTM3 GSTM3 GSTM3 1727 0.21 0.56 YES
19 AKR1C1 AKR1C1 AKR1C1 1955 0.19 0.57 YES
20 GSTM4 GSTM4 GSTM4 2247 0.17 0.57 YES
21 GSTM1 GSTM1 GSTM1 2307 0.17 0.59 YES
22 CYP2F1 CYP2F1 CYP2F1 2646 0.15 0.58 YES
23 CYP2C9 CYP2C9 CYP2C9 2951 0.13 0.58 YES
24 CYP3A7 CYP3A7 CYP3A7 3004 0.13 0.6 YES
25 MGST2 MGST2 MGST2 3084 0.13 0.61 YES
26 CYP2C8 CYP2C8 CYP2C8 3301 0.12 0.61 YES
27 AKR1C3 AKR1C3 AKR1C3 3550 0.11 0.61 YES
28 ALDH3B1 ALDH3B1 ALDH3B1 3621 0.11 0.62 YES
29 CYP3A5 CYP3A5 CYP3A5 4271 0.089 0.59 NO
30 CYP1B1 CYP1B1 CYP1B1 4339 0.087 0.6 NO
31 EPHX1 EPHX1 EPHX1 4457 0.084 0.6 NO
32 ADH1B ADH1B ADH1B 4970 0.072 0.58 NO
33 MGST3 MGST3 MGST3 5017 0.071 0.59 NO
34 GSTK1 GSTK1 GSTK1 6437 0.045 0.51 NO
35 GSTP1 GSTP1 GSTP1 6496 0.044 0.52 NO
36 GSTT1 GSTT1 GSTT1 6561 0.043 0.52 NO
37 CYP1A1 CYP1A1 CYP1A1 6777 0.04 0.51 NO
38 ALDH3B2 ALDH3B2 ALDH3B2 7541 0.029 0.47 NO
39 GSTA1 GSTA1 GSTA1 10249 -0.0054 0.32 NO
40 CYP3A4 CYP3A4 CYP3A4 11305 -0.019 0.27 NO
41 ADH5 ADH5 ADH5 11306 -0.019 0.27 NO
42 GSTO1 GSTO1 GSTO1 11413 -0.021 0.26 NO
43 ADH6 ADH6 ADH6 12001 -0.029 0.24 NO
44 CYP3A43 CYP3A43 CYP3A43 13347 -0.053 0.17 NO
45 GSTM5 GSTM5 GSTM5 13556 -0.058 0.16 NO
46 CYP1A2 CYP1A2 CYP1A2 13661 -0.06 0.16 NO
47 GSTT2 GSTT2 GSTT2 14021 -0.07 0.15 NO
48 GSTA2 GSTA2 GSTA2 14846 -0.095 0.12 NO
49 ADH4 ADH4 ADH4 15310 -0.11 0.1 NO
50 ADH1A ADH1A ADH1A 15866 -0.14 0.09 NO
51 DHDH DHDH DHDH 16142 -0.16 0.093 NO
52 GSTZ1 GSTZ1 GSTZ1 16426 -0.18 0.097 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM CYTOCHROME P450

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 UGT1A9 UGT1A9 UGT1A9 348 0.44 0.077 YES
2 MGAM MGAM MGAM 445 0.41 0.16 YES
3 GCK GCK GCK 877 0.31 0.2 YES
4 UGT1A1 UGT1A1 UGT1A1 1002 0.29 0.26 YES
5 PYGM PYGM PYGM 1036 0.29 0.32 YES
6 UGT1A6 UGT1A6 UGT1A6 1070 0.28 0.38 YES
7 UGT1A10 UGT1A10 UGT1A10 1165 0.27 0.44 YES
8 AMY2B AMY2B AMY2B 1272 0.26 0.48 YES
9 UGT1A8 UGT1A8 UGT1A8 1566 0.23 0.52 YES
10 UGT2A1 UGT2A1 UGT2A1 1655 0.22 0.56 YES
11 GBA3 GBA3 GBA3 2083 0.18 0.58 YES
12 ENPP1 ENPP1 ENPP1 2684 0.15 0.58 NO
13 AGL AGL AGL 5027 0.071 0.46 NO
14 AMY1A AMY1A AMY1A 5586 0.06 0.45 NO
15 GPI GPI GPI 6248 0.048 0.42 NO
16 GBE1 GBE1 GBE1 6733 0.041 0.4 NO
17 UGP2 UGP2 UGP2 7545 0.029 0.36 NO
18 PGM2 PGM2 PGM2 7757 0.026 0.36 NO
19 UXS1 UXS1 UXS1 7760 0.026 0.36 NO
20 GUSB GUSB GUSB 7811 0.026 0.37 NO
21 AMY2A AMY2A AMY2A 7882 0.025 0.37 NO
22 HK2 HK2 HK2 8075 0.022 0.36 NO
23 GYS2 GYS2 GYS2 8765 0.013 0.33 NO
24 GAA GAA GAA 10412 -0.0074 0.24 NO
25 PYGB PYGB PYGB 12294 -0.034 0.14 NO
26 ENPP3 ENPP3 ENPP3 12591 -0.038 0.13 NO
27 UGDH UGDH UGDH 12708 -0.04 0.14 NO
28 GYS1 GYS1 GYS1 13140 -0.049 0.12 NO
29 PGM1 PGM1 PGM1 13562 -0.058 0.11 NO
30 HK1 HK1 HK1 14246 -0.076 0.091 NO
31 PYGL PYGL PYGL 14349 -0.08 0.1 NO
32 GANC GANC GANC 14789 -0.093 0.099 NO
33 TREH TREH TREH 15320 -0.11 0.094 NO
34 PGM2L1 PGM2L1 PGM2L1 15353 -0.12 0.12 NO
35 HK3 HK3 HK3 16456 -0.18 0.096 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 DRUG METABOLISM CYTOCHROME P450.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, 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: PID NCADHERINPATHWAY

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 LDHC LDHC LDHC 48 0.66 0.19 YES
2 ACSS3 ACSS3 ACSS3 184 0.51 0.33 YES
3 EHHADH EHHADH EHHADH 388 0.43 0.44 YES
4 LDHAL6A LDHAL6A LDHAL6A 1647 0.22 0.43 YES
5 HIBCH HIBCH HIBCH 2063 0.18 0.46 YES
6 ALDH1B1 ALDH1B1 ALDH1B1 3331 0.12 0.42 YES
7 PCCA PCCA PCCA 3607 0.11 0.44 YES
8 ACAT1 ACAT1 ACAT1 3741 0.1 0.46 YES
9 MCEE MCEE MCEE 3969 0.098 0.48 YES
10 ABAT ABAT ABAT 4406 0.086 0.48 YES
11 SUCLA2 SUCLA2 SUCLA2 4671 0.079 0.49 YES
12 ALDH7A1 ALDH7A1 ALDH7A1 4876 0.074 0.5 YES
13 MUT MUT MUT 5568 0.06 0.48 YES
14 ACACA ACACA ACACA 5966 0.053 0.47 YES
15 ALDH3A2 ALDH3A2 ALDH3A2 6005 0.052 0.48 YES
16 MLYCD MLYCD MLYCD 6052 0.052 0.5 YES
17 SUCLG2 SUCLG2 SUCLG2 6098 0.051 0.51 YES
18 SUCLG1 SUCLG1 SUCLG1 6787 0.04 0.48 NO
19 ACSS2 ACSS2 ACSS2 6917 0.038 0.48 NO
20 LDHA LDHA LDHA 6964 0.037 0.49 NO
21 ACSS1 ACSS1 ACSS1 7036 0.036 0.5 NO
22 ALDH9A1 ALDH9A1 ALDH9A1 7507 0.029 0.48 NO
23 ALDH2 ALDH2 ALDH2 8041 0.022 0.46 NO
24 LDHB LDHB LDHB 9091 0.009 0.4 NO
25 ACADM ACADM ACADM 9704 0.0016 0.37 NO
26 ACACB ACACB ACACB 10596 -0.0099 0.32 NO
27 HADHA HADHA HADHA 11168 -0.017 0.3 NO
28 PCCB PCCB PCCB 11191 -0.018 0.3 NO
29 LDHAL6B LDHAL6B LDHAL6B 12189 -0.032 0.26 NO
30 ECHS1 ECHS1 ECHS1 12207 -0.032 0.26 NO
31 ALDH6A1 ALDH6A1 ALDH6A1 13412 -0.054 0.21 NO
32 ACAT2 ACAT2 ACAT2 16363 -0.17 0.1 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: PID NCADHERINPATHWAY.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG PROTEASOME 43 genes.ES.table 0.58 1.6 0.074 0.18 0.9 0.79 0.37 0.5 0.1 0.021
KEGG CHEMOKINE SIGNALING PATHWAY 186 genes.ES.table 0.57 1.6 0.029 0.19 0.85 0.48 0.2 0.39 0.092 0.03
KEGG CELL CYCLE 118 genes.ES.table 0.48 1.7 0.049 0.2 0.76 0.4 0.27 0.29 0.082 0.043
KEGG APOPTOSIS 84 genes.ES.table 0.47 1.7 0.021 0.2 0.8 0.32 0.23 0.25 0.086 0.04
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY 89 genes.ES.table 0.56 1.7 0.037 0.19 0.84 0.29 0.14 0.25 0.095 0.035
KEGG CYTOSOLIC DNA SENSING PATHWAY 42 genes.ES.table 0.6 1.7 0.046 0.19 0.84 0.19 0.053 0.18 0.095 0.035
KEGG HEMATOPOIETIC CELL LINEAGE 79 genes.ES.table 0.67 1.6 0.023 0.2 0.95 0.65 0.15 0.55 0.12 0.016
KEGG T CELL RECEPTOR SIGNALING PATHWAY 105 genes.ES.table 0.59 1.6 0.036 0.19 0.88 0.42 0.2 0.34 0.097 0.023
KEGG B CELL RECEPTOR SIGNALING PATHWAY 74 genes.ES.table 0.57 1.7 0.025 0.22 0.75 0.42 0.2 0.34 0.089 0.047
KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS 94 genes.ES.table 0.45 1.7 0.026 0.2 0.83 0.42 0.21 0.33 0.093 0.037
genes ES table in pathway: KEGG PROTEASOME

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 CD28 CD28 CD28 272 0.48 0.018 YES
2 LCK LCK LCK 274 0.48 0.052 YES
3 CD8B CD8B CD8B 313 0.46 0.082 YES
4 CD247 CD247 CD247 594 0.39 0.094 YES
5 HMGA1 HMGA1 HMGA1 689 0.37 0.12 YES
6 CCR5 CCR5 CCR5 976 0.33 0.12 YES
7 HCK HCK HCK 1102 0.31 0.14 YES
8 TAF13 TAF13 TAF13 1137 0.31 0.16 YES
9 AP1S2 AP1S2 AP1S2 1339 0.28 0.17 YES
10 DOCK2 DOCK2 DOCK2 1348 0.28 0.18 YES
11 GTF2A1 GTF2A1 GTF2A1 1824 0.23 0.18 YES
12 CD4 CD4 CD4 1859 0.23 0.19 YES
13 ELMO1 ELMO1 ELMO1 1860 0.23 0.21 YES
14 APOBEC3G APOBEC3G APOBEC3G 1861 0.23 0.22 YES
15 NMT2 NMT2 NMT2 1908 0.23 0.24 YES
16 RCC1 RCC1 RCC1 2314 0.19 0.23 YES
17 PSME4 PSME4 PSME4 2414 0.18 0.23 YES
18 GTF2H2 GTF2H2 GTF2H2 2661 0.17 0.23 YES
19 CXCR4 CXCR4 CXCR4 2816 0.16 0.23 YES
20 PAK2 PAK2 PAK2 3574 0.12 0.2 YES
21 NUP93 NUP93 NUP93 3627 0.11 0.21 YES
22 AP1B1 AP1B1 AP1B1 3780 0.11 0.2 YES
23 AP2S1 AP2S1 AP2S1 3841 0.11 0.21 YES
24 RANGAP1 RANGAP1 RANGAP1 3873 0.1 0.22 YES
25 VPS37A VPS37A VPS37A 3908 0.1 0.22 YES
26 PSMA5 PSMA5 PSMA5 3922 0.1 0.23 YES
27 PSMA6 PSMA6 PSMA6 3951 0.1 0.23 YES
28 PSME2 PSME2 PSME2 3958 0.1 0.24 YES
29 FEN1 FEN1 FEN1 3985 0.1 0.24 YES
30 NUP188 NUP188 NUP188 3998 0.1 0.25 YES
31 RANBP1 RANBP1 RANBP1 4051 0.098 0.26 YES
32 PSMA8 PSMA8 PSMA8 4074 0.097 0.26 YES
33 PSMA3 PSMA3 PSMA3 4102 0.096 0.27 YES
34 NUP155 NUP155 NUP155 4155 0.093 0.27 YES
35 TAF5 TAF5 TAF5 4211 0.092 0.27 YES
36 NUP50 NUP50 NUP50 4222 0.092 0.28 YES
37 PSMD11 PSMD11 PSMD11 4237 0.091 0.28 YES
38 KPNB1 KPNB1 KPNB1 4249 0.091 0.29 YES
39 RNGTT RNGTT RNGTT 4333 0.088 0.29 YES
40 ERCC2 ERCC2 ERCC2 4390 0.087 0.3 YES
41 NUP205 NUP205 NUP205 4488 0.083 0.3 YES
42 LIG4 LIG4 LIG4 4489 0.083 0.3 YES
43 PSMD12 PSMD12 PSMD12 4502 0.083 0.31 YES
44 PSMB10 PSMB10 PSMB10 4534 0.082 0.31 YES
45 B2M B2M B2M 4536 0.082 0.32 YES
46 PSMC4 PSMC4 PSMC4 4681 0.077 0.31 YES
47 SLC25A5 SLC25A5 SLC25A5 4731 0.076 0.32 YES
48 TAF9 TAF9 TAF9 4761 0.075 0.32 YES
49 PSMC6 PSMC6 PSMC6 4795 0.074 0.32 YES
50 GTF2E1 GTF2E1 GTF2E1 4824 0.073 0.33 YES
51 PSMD2 PSMD2 PSMD2 4832 0.073 0.33 YES
52 PSMD13 PSMD13 PSMD13 4905 0.071 0.33 YES
53 PSMB5 PSMB5 PSMB5 5000 0.068 0.33 YES
54 NUPL1 NUPL1 NUPL1 5012 0.068 0.34 YES
55 PSMA7 PSMA7 PSMA7 5032 0.067 0.34 YES
56 CCNT1 CCNT1 CCNT1 5067 0.066 0.34 YES
57 NUP153 NUP153 NUP153 5081 0.066 0.35 YES
58 TAF12 TAF12 TAF12 5134 0.064 0.35 YES
59 POLR2D POLR2D POLR2D 5146 0.064 0.35 YES
60 PSMD14 PSMD14 PSMD14 5185 0.063 0.35 YES
61 PSMC1 PSMC1 PSMC1 5192 0.063 0.36 YES
62 GTF2H3 GTF2H3 GTF2H3 5321 0.06 0.36 YES
63 PSMB9 PSMB9 PSMB9 5349 0.059 0.36 YES
64 GTF2E2 GTF2E2 GTF2E2 5387 0.058 0.36 YES
65 TCEB3 TCEB3 TCEB3 5495 0.056 0.36 YES
66 CTDP1 CTDP1 CTDP1 5540 0.055 0.36 YES
67 PSMF1 PSMF1 PSMF1 5544 0.054 0.36 YES
68 RBX1 RBX1 RBX1 5551 0.054 0.37 YES
69 SUPT16H SUPT16H SUPT16H 5557 0.054 0.37 YES
70 PSMB6 PSMB6 PSMB6 5588 0.054 0.37 YES
71 NUP62 NUP62 NUP62 5617 0.053 0.38 YES
72 HLA-A HLA-A HLA-A 5675 0.052 0.38 YES
73 PSMD7 PSMD7 PSMD7 5687 0.052 0.38 YES
74 PSMD6 PSMD6 PSMD6 5692 0.052 0.38 YES
75 RAN RAN RAN 5716 0.051 0.38 YES
76 NCBP1 NCBP1 NCBP1 5733 0.051 0.39 YES
77 XRCC6 XRCC6 XRCC6 5741 0.051 0.39 YES
78 TCEB1 TCEB1 TCEB1 5758 0.051 0.39 YES
79 KPNA1 KPNA1 KPNA1 5792 0.05 0.39 YES
80 NUP54 NUP54 NUP54 5826 0.049 0.4 YES
81 PSMD1 PSMD1 PSMD1 5884 0.048 0.4 YES
82 LIG1 LIG1 LIG1 5896 0.048 0.4 YES
83 RANBP2 RANBP2 RANBP2 5906 0.047 0.4 YES
84 AP2A2 AP2A2 AP2A2 5937 0.046 0.4 YES
85 PSMB3 PSMB3 PSMB3 5953 0.046 0.41 YES
86 PSMB2 PSMB2 PSMB2 6010 0.045 0.41 YES
87 POLR2F POLR2F POLR2F 6074 0.043 0.4 YES
88 PSMD8 PSMD8 PSMD8 6101 0.043 0.41 YES
89 PSMD3 PSMD3 PSMD3 6211 0.04 0.4 NO
90 CDK7 CDK7 CDK7 6324 0.038 0.4 NO
91 GTF2H2B GTF2H2B GTF2H2B 6391 0.037 0.4 NO
92 GTF2B GTF2B GTF2B 6421 0.036 0.4 NO
93 NUP37 NUP37 NUP37 6437 0.036 0.4 NO
94 PACS1 PACS1 PACS1 6449 0.036 0.4 NO
95 PSME1 PSME1 PSME1 6462 0.036 0.4 NO
96 AP2A1 AP2A1 AP2A1 6544 0.034 0.4 NO
97 PSMD5 PSMD5 PSMD5 6566 0.033 0.4 NO
98 RAE1 RAE1 RAE1 6579 0.033 0.41 NO
99 PSMC3 PSMC3 PSMC3 6656 0.032 0.4 NO
100 SSRP1 SSRP1 SSRP1 6720 0.03 0.4 NO
101 PSMC2 PSMC2 PSMC2 6762 0.03 0.4 NO
102 PSMA1 PSMA1 PSMA1 6806 0.029 0.4 NO
103 GTF2H4 GTF2H4 GTF2H4 6940 0.026 0.4 NO
104 PSMD9 PSMD9 PSMD9 6960 0.026 0.4 NO
105 PSMA2 PSMA2 PSMA2 6996 0.025 0.4 NO
106 AP2M1 AP2M1 AP2M1 7009 0.025 0.4 NO
107 PPIA PPIA PPIA 7071 0.023 0.4 NO
108 POLR2B POLR2B POLR2B 7102 0.023 0.4 NO
109 NUP107 NUP107 NUP107 7171 0.022 0.39 NO
110 PSMA4 PSMA4 PSMA4 7225 0.021 0.39 NO
111 TBP TBP TBP 7246 0.02 0.39 NO
112 NUP88 NUP88 NUP88 7396 0.018 0.39 NO
113 NUP43 NUP43 NUP43 7437 0.018 0.38 NO
114 POLR2G POLR2G POLR2G 7452 0.017 0.39 NO
115 VPS37B VPS37B VPS37B 7487 0.017 0.38 NO
116 COBRA1 COBRA1 COBRA1 7525 0.016 0.38 NO
117 RDBP RDBP RDBP 7578 0.015 0.38 NO
118 POLR2A POLR2A POLR2A 7588 0.015 0.38 NO
119 TAF4B TAF4B TAF4B 7650 0.014 0.38 NO
120 XRCC4 XRCC4 XRCC4 7691 0.013 0.38 NO
121 PSMB4 PSMB4 PSMB4 7726 0.012 0.38 NO
122 MNAT1 MNAT1 MNAT1 7769 0.012 0.38 NO
123 PSMC5 PSMC5 PSMC5 7862 0.0099 0.37 NO
124 RAC1 RAC1 RAC1 7867 0.0098 0.37 NO
125 SUPT4H1 SUPT4H1 SUPT4H1 7903 0.0094 0.37 NO
126 AP1S1 AP1S1 AP1S1 7940 0.0087 0.37 NO
127 AP2B1 AP2B1 AP2B1 7986 0.0079 0.37 NO
128 CCNH CCNH CCNH 8008 0.0075 0.37 NO
129 PSMD4 PSMD4 PSMD4 8010 0.0075 0.37 NO
130 PSMB7 PSMB7 PSMB7 8065 0.0066 0.36 NO
131 POLR2K POLR2K POLR2K 8142 0.0051 0.36 NO
132 XRCC5 XRCC5 XRCC5 8195 0.0042 0.36 NO
133 PSMB1 PSMB1 PSMB1 8237 0.0036 0.36 NO
134 GTF2H1 GTF2H1 GTF2H1 8310 0.0025 0.35 NO
135 ELL ELL ELL 8383 0.001 0.35 NO
136 NUP85 NUP85 NUP85 8388 0.00095 0.35 NO
137 ARF1 ARF1 ARF1 8448 -0.000096 0.34 NO
138 GTF2F2 GTF2F2 GTF2F2 8504 -0.0011 0.34 NO
139 AP1G1 AP1G1 AP1G1 8523 -0.0013 0.34 NO
140 TAF1 TAF1 TAF1 8591 -0.0025 0.34 NO
141 BTRC BTRC BTRC 8603 -0.0027 0.34 NO
142 NPM1 NPM1 NPM1 8658 -0.0035 0.34 NO
143 TAF11 TAF11 TAF11 8813 -0.0061 0.33 NO
144 POLR2H POLR2H POLR2H 8862 -0.007 0.32 NO
145 PSIP1 PSIP1 PSIP1 9077 -0.011 0.31 NO
146 FYN FYN FYN 9108 -0.011 0.31 NO
147 TSG101 TSG101 TSG101 9262 -0.014 0.3 NO
148 XPO1 XPO1 XPO1 9287 -0.014 0.3 NO
149 TAF6 TAF6 TAF6 9312 -0.014 0.3 NO
150 SEH1L SEH1L SEH1L 9323 -0.015 0.3 NO
151 TCEA1 TCEA1 TCEA1 9352 -0.015 0.3 NO
152 POLR2C POLR2C POLR2C 9367 -0.016 0.3 NO
153 SUPT5H SUPT5H SUPT5H 9420 -0.016 0.3 NO
154 NMT1 NMT1 NMT1 9438 -0.017 0.3 NO
155 PSMB8 PSMB8 PSMB8 9607 -0.019 0.3 NO
156 PSMD10 PSMD10 PSMD10 9808 -0.023 0.29 NO
157 VPS37C VPS37C VPS37C 9919 -0.024 0.28 NO
158 BANF1 BANF1 BANF1 10009 -0.026 0.28 NO
159 NUP214 NUP214 NUP214 10106 -0.028 0.28 NO
160 AP1M1 AP1M1 AP1M1 10336 -0.032 0.26 NO
161 NUP210 NUP210 NUP210 10432 -0.033 0.26 NO
162 NCBP2 NCBP2 NCBP2 10433 -0.033 0.26 NO
163 TH1L TH1L TH1L 10533 -0.035 0.26 NO
164 NUPL2 NUPL2 NUPL2 10576 -0.036 0.26 NO
165 UBA52 UBA52 UBA52 10630 -0.037 0.26 NO
166 SKP1 SKP1 SKP1 10847 -0.041 0.25 NO
167 GTF2A2 GTF2A2 GTF2A2 10888 -0.042 0.25 NO
168 TAF4 TAF4 TAF4 11204 -0.049 0.24 NO
169 RPS27A RPS27A RPS27A 11209 -0.049 0.24 NO
170 POLR2L POLR2L POLR2L 11223 -0.049 0.24 NO
171 POLR2E POLR2E POLR2E 11360 -0.052 0.24 NO
172 AP1M2 AP1M2 AP1M2 11396 -0.052 0.24 NO
173 CDK9 CDK9 CDK9 11499 -0.055 0.24 NO
174 WHSC2 WHSC2 WHSC2 11556 -0.056 0.24 NO
175 CCNT2 CCNT2 CCNT2 11589 -0.057 0.24 NO
176 NUP133 NUP133 NUP133 11640 -0.058 0.24 NO
177 POLR2J POLR2J POLR2J 11714 -0.06 0.24 NO
178 ERCC3 ERCC3 ERCC3 11728 -0.06 0.25 NO
179 TAF10 TAF10 TAF10 11737 -0.06 0.25 NO
180 TCEB2 TCEB2 TCEB2 11905 -0.064 0.25 NO
181 CUL5 CUL5 CUL5 11947 -0.065 0.25 NO
182 RNMT RNMT RNMT 11976 -0.066 0.25 NO
183 TPR TPR TPR 12004 -0.067 0.26 NO
184 POM121 POM121 POM121 12182 -0.071 0.25 NO
185 VPS28 VPS28 VPS28 12323 -0.075 0.25 NO
186 ATP6V1H ATP6V1H ATP6V1H 12368 -0.076 0.25 NO
187 NUP35 NUP35 NUP35 12461 -0.079 0.25 NO
188 AAAS AAAS AAAS 12969 -0.093 0.23 NO
189 GTF2F1 GTF2F1 GTF2F1 13123 -0.097 0.23 NO
190 POLR2I POLR2I POLR2I 13263 -0.1 0.23 NO
191 SLC25A6 SLC25A6 SLC25A6 13760 -0.12 0.21 NO
192 SLC25A4 SLC25A4 SLC25A4 15264 -0.2 0.14 NO
193 VPS37D VPS37D VPS37D 16677 -0.33 0.084 NO

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

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING 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 AURKA AURKA AURKA 623 0.39 0.055 YES
2 SNAI1 SNAI1 SNAI1 773 0.36 0.13 YES
3 PPP1R14A PPP1R14A PPP1R14A 967 0.33 0.2 YES
4 ACTN1 ACTN1 ACTN1 1519 0.26 0.22 YES
5 ARHGEF6 ARHGEF6 ARHGEF6 1723 0.24 0.27 YES
6 PARVG PARVG PARVG 2080 0.21 0.3 YES
7 LIMS1 LIMS1 LIMS1 2117 0.21 0.34 YES
8 PARVB PARVB PARVB 2924 0.15 0.33 YES
9 TACC3 TACC3 TACC3 2953 0.15 0.37 YES
10 LIMS2 LIMS2 LIMS2 3094 0.14 0.39 YES
11 PXN PXN PXN 3200 0.14 0.42 YES
12 MYL9 MYL9 MYL9 3433 0.12 0.43 YES
13 RHOG RHOG RHOG 3476 0.12 0.46 YES
14 ZEB1 ZEB1 ZEB1 3847 0.11 0.46 YES
15 CCND1 CCND1 CCND1 3857 0.1 0.49 YES
16 ELMO2 ELMO2 ELMO2 4359 0.087 0.48 YES
17 CTNNB1 CTNNB1 CTNNB1 4528 0.082 0.49 YES
18 ILK ILK ILK 4586 0.08 0.5 YES
19 ZYX ZYX ZYX 5019 0.067 0.5 YES
20 TNS1 TNS1 TNS1 5029 0.067 0.51 YES
21 AKT1 AKT1 AKT1 5196 0.063 0.52 YES
22 CDC42 CDC42 CDC42 5592 0.054 0.51 YES
23 HSP90AA1 HSP90AA1 HSP90AA1 5684 0.052 0.51 YES
24 JUN JUN JUN 5693 0.052 0.52 YES
25 DIAPH1 DIAPH1 DIAPH1 5820 0.049 0.53 YES
26 CKAP5 CKAP5 CKAP5 5901 0.047 0.54 YES
27 CDC37 CDC37 CDC37 6110 0.043 0.53 NO
28 RUVBL2 RUVBL2 RUVBL2 6392 0.037 0.53 NO
29 PPP1R14B PPP1R14B PPP1R14B 6973 0.025 0.5 NO
30 PPP1R12A PPP1R12A PPP1R12A 7022 0.024 0.5 NO
31 GIT2 GIT2 GIT2 7191 0.021 0.5 NO
32 PARVA PARVA PARVA 7332 0.019 0.5 NO
33 IQGAP1 IQGAP1 IQGAP1 7366 0.019 0.5 NO
34 ILKAP ILKAP ILKAP 7444 0.017 0.5 NO
35 RUVBL1 RUVBL1 RUVBL1 7837 0.01 0.48 NO
36 RAC1 RAC1 RAC1 7867 0.0098 0.48 NO
37 GSK3B GSK3B GSK3B 8255 0.0034 0.46 NO
38 PARP1 PARP1 PARP1 8457 -0.00025 0.45 NO
39 CREB1 CREB1 CREB1 8492 -0.00088 0.45 NO
40 XPO1 XPO1 XPO1 9287 -0.014 0.41 NO
41 NCK2 NCK2 NCK2 9362 -0.015 0.41 NO
42 PPP1R14C PPP1R14C PPP1R14C 10918 -0.042 0.33 NO
43 ARHGEF7 ARHGEF7 ARHGEF7 11766 -0.061 0.3 NO
44 NACA NACA NACA 12143 -0.07 0.29 NO
45 RICTOR RICTOR RICTOR 14898 -0.18 0.18 NO

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

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHEMOKINE SIGNALING 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 CELL CYCLE

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 CD28 CD28 CD28 272 0.48 0.034 YES
2 LCK LCK LCK 274 0.48 0.082 YES
3 CD8B CD8B CD8B 313 0.46 0.13 YES
4 CD247 CD247 CD247 594 0.39 0.15 YES
5 HMGA1 HMGA1 HMGA1 689 0.37 0.18 YES
6 HCK HCK HCK 1102 0.31 0.19 YES
7 AP1S2 AP1S2 AP1S2 1339 0.28 0.21 YES
8 DOCK2 DOCK2 DOCK2 1348 0.28 0.24 YES
9 CD4 CD4 CD4 1859 0.23 0.23 YES
10 ELMO1 ELMO1 ELMO1 1860 0.23 0.26 YES
11 APOBEC3G APOBEC3G APOBEC3G 1861 0.23 0.28 YES
12 RCC1 RCC1 RCC1 2314 0.19 0.28 YES
13 PSME4 PSME4 PSME4 2414 0.18 0.29 YES
14 PAK2 PAK2 PAK2 3574 0.12 0.24 YES
15 NUP93 NUP93 NUP93 3627 0.11 0.25 YES
16 AP1B1 AP1B1 AP1B1 3780 0.11 0.25 YES
17 AP2S1 AP2S1 AP2S1 3841 0.11 0.26 YES
18 RANGAP1 RANGAP1 RANGAP1 3873 0.1 0.26 YES
19 PSMA5 PSMA5 PSMA5 3922 0.1 0.27 YES
20 PSMA6 PSMA6 PSMA6 3951 0.1 0.28 YES
21 PSME2 PSME2 PSME2 3958 0.1 0.29 YES
22 NUP188 NUP188 NUP188 3998 0.1 0.3 YES
23 RANBP1 RANBP1 RANBP1 4051 0.098 0.31 YES
24 PSMA8 PSMA8 PSMA8 4074 0.097 0.32 YES
25 PSMA3 PSMA3 PSMA3 4102 0.096 0.32 YES
26 NUP155 NUP155 NUP155 4155 0.093 0.33 YES
27 NUP50 NUP50 NUP50 4222 0.092 0.34 YES
28 PSMD11 PSMD11 PSMD11 4237 0.091 0.34 YES
29 KPNB1 KPNB1 KPNB1 4249 0.091 0.35 YES
30 NUP205 NUP205 NUP205 4488 0.083 0.35 YES
31 PSMD12 PSMD12 PSMD12 4502 0.083 0.36 YES
32 PSMB10 PSMB10 PSMB10 4534 0.082 0.36 YES
33 B2M B2M B2M 4536 0.082 0.37 YES
34 PSMC4 PSMC4 PSMC4 4681 0.077 0.37 YES
35 SLC25A5 SLC25A5 SLC25A5 4731 0.076 0.38 YES
36 PSMC6 PSMC6 PSMC6 4795 0.074 0.38 YES
37 PSMD2 PSMD2 PSMD2 4832 0.073 0.39 YES
38 PSMD13 PSMD13 PSMD13 4905 0.071 0.39 YES
39 PSMB5 PSMB5 PSMB5 5000 0.068 0.39 YES
40 NUPL1 NUPL1 NUPL1 5012 0.068 0.4 YES
41 PSMA7 PSMA7 PSMA7 5032 0.067 0.4 YES
42 CCNT1 CCNT1 CCNT1 5067 0.066 0.41 YES
43 NUP153 NUP153 NUP153 5081 0.066 0.41 YES
44 PSMD14 PSMD14 PSMD14 5185 0.063 0.42 YES
45 PSMC1 PSMC1 PSMC1 5192 0.063 0.42 YES
46 PSMB9 PSMB9 PSMB9 5349 0.059 0.42 YES
47 PSMF1 PSMF1 PSMF1 5544 0.054 0.41 YES
48 RBX1 RBX1 RBX1 5551 0.054 0.42 YES
49 PSMB6 PSMB6 PSMB6 5588 0.054 0.42 YES
50 NUP62 NUP62 NUP62 5617 0.053 0.43 YES
51 HLA-A HLA-A HLA-A 5675 0.052 0.43 YES
52 PSMD7 PSMD7 PSMD7 5687 0.052 0.43 YES
53 PSMD6 PSMD6 PSMD6 5692 0.052 0.44 YES
54 RAN RAN RAN 5716 0.051 0.44 YES
55 TCEB1 TCEB1 TCEB1 5758 0.051 0.44 YES
56 KPNA1 KPNA1 KPNA1 5792 0.05 0.45 YES
57 NUP54 NUP54 NUP54 5826 0.049 0.45 YES
58 PSMD1 PSMD1 PSMD1 5884 0.048 0.45 YES
59 RANBP2 RANBP2 RANBP2 5906 0.047 0.46 YES
60 AP2A2 AP2A2 AP2A2 5937 0.046 0.46 YES
61 PSMB3 PSMB3 PSMB3 5953 0.046 0.46 YES
62 PSMB2 PSMB2 PSMB2 6010 0.045 0.46 YES
63 PSMD8 PSMD8 PSMD8 6101 0.043 0.46 NO
64 PSMD3 PSMD3 PSMD3 6211 0.04 0.46 NO
65 NUP37 NUP37 NUP37 6437 0.036 0.45 NO
66 PACS1 PACS1 PACS1 6449 0.036 0.46 NO
67 PSME1 PSME1 PSME1 6462 0.036 0.46 NO
68 AP2A1 AP2A1 AP2A1 6544 0.034 0.46 NO
69 PSMD5 PSMD5 PSMD5 6566 0.033 0.46 NO
70 RAE1 RAE1 RAE1 6579 0.033 0.46 NO
71 PSMC3 PSMC3 PSMC3 6656 0.032 0.46 NO
72 PSMC2 PSMC2 PSMC2 6762 0.03 0.46 NO
73 PSMA1 PSMA1 PSMA1 6806 0.029 0.46 NO
74 PSMD9 PSMD9 PSMD9 6960 0.026 0.46 NO
75 PSMA2 PSMA2 PSMA2 6996 0.025 0.46 NO
76 AP2M1 AP2M1 AP2M1 7009 0.025 0.46 NO
77 PPIA PPIA PPIA 7071 0.023 0.46 NO
78 NUP107 NUP107 NUP107 7171 0.022 0.45 NO
79 PSMA4 PSMA4 PSMA4 7225 0.021 0.45 NO
80 NUP88 NUP88 NUP88 7396 0.018 0.44 NO
81 NUP43 NUP43 NUP43 7437 0.018 0.44 NO
82 PSMB4 PSMB4 PSMB4 7726 0.012 0.43 NO
83 PSMC5 PSMC5 PSMC5 7862 0.0099 0.42 NO
84 RAC1 RAC1 RAC1 7867 0.0098 0.42 NO
85 AP1S1 AP1S1 AP1S1 7940 0.0087 0.42 NO
86 AP2B1 AP2B1 AP2B1 7986 0.0079 0.42 NO
87 PSMD4 PSMD4 PSMD4 8010 0.0075 0.42 NO
88 PSMB7 PSMB7 PSMB7 8065 0.0066 0.42 NO
89 PSMB1 PSMB1 PSMB1 8237 0.0036 0.41 NO
90 NUP85 NUP85 NUP85 8388 0.00095 0.4 NO
91 ARF1 ARF1 ARF1 8448 -0.000096 0.4 NO
92 AP1G1 AP1G1 AP1G1 8523 -0.0013 0.39 NO
93 BTRC BTRC BTRC 8603 -0.0027 0.39 NO
94 NPM1 NPM1 NPM1 8658 -0.0035 0.38 NO
95 PSIP1 PSIP1 PSIP1 9077 -0.011 0.36 NO
96 FYN FYN FYN 9108 -0.011 0.36 NO
97 XPO1 XPO1 XPO1 9287 -0.014 0.36 NO
98 SEH1L SEH1L SEH1L 9323 -0.015 0.35 NO
99 PSMB8 PSMB8 PSMB8 9607 -0.019 0.34 NO
100 PSMD10 PSMD10 PSMD10 9808 -0.023 0.33 NO
101 BANF1 BANF1 BANF1 10009 -0.026 0.32 NO
102 NUP214 NUP214 NUP214 10106 -0.028 0.32 NO
103 AP1M1 AP1M1 AP1M1 10336 -0.032 0.31 NO
104 NUP210 NUP210 NUP210 10432 -0.033 0.31 NO
105 NUPL2 NUPL2 NUPL2 10576 -0.036 0.3 NO
106 UBA52 UBA52 UBA52 10630 -0.037 0.31 NO
107 SKP1 SKP1 SKP1 10847 -0.041 0.3 NO
108 RPS27A RPS27A RPS27A 11209 -0.049 0.28 NO
109 AP1M2 AP1M2 AP1M2 11396 -0.052 0.28 NO
110 CDK9 CDK9 CDK9 11499 -0.055 0.28 NO
111 NUP133 NUP133 NUP133 11640 -0.058 0.28 NO
112 TCEB2 TCEB2 TCEB2 11905 -0.064 0.27 NO
113 CUL5 CUL5 CUL5 11947 -0.065 0.27 NO
114 TPR TPR TPR 12004 -0.067 0.28 NO
115 POM121 POM121 POM121 12182 -0.071 0.27 NO
116 ATP6V1H ATP6V1H ATP6V1H 12368 -0.076 0.27 NO
117 NUP35 NUP35 NUP35 12461 -0.079 0.28 NO
118 AAAS AAAS AAAS 12969 -0.093 0.26 NO
119 SLC25A6 SLC25A6 SLC25A6 13760 -0.12 0.22 NO
120 SLC25A4 SLC25A4 SLC25A4 15264 -0.2 0.16 NO

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

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL 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 APOPTOSIS

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 RASGRP3 RASGRP3 RASGRP3 764 0.36 -0.0058 YES
2 PRKCB PRKCB PRKCB 937 0.34 0.018 YES
3 PIK3AP1 PIK3AP1 PIK3AP1 1009 0.32 0.047 YES
4 CD79B CD79B CD79B 1311 0.28 0.059 YES
5 ORAI1 ORAI1 ORAI1 1428 0.27 0.08 YES
6 CD19 CD19 CD19 1461 0.27 0.1 YES
7 BTK BTK BTK 1475 0.26 0.13 YES
8 VAV1 VAV1 VAV1 1548 0.26 0.15 YES
9 BCL10 BCL10 BCL10 1914 0.22 0.16 YES
10 AKT3 AKT3 AKT3 2102 0.21 0.17 YES
11 REL REL REL 2147 0.2 0.18 YES
12 LYN LYN LYN 2185 0.2 0.2 YES
13 TRIB3 TRIB3 TRIB3 2392 0.18 0.21 YES
14 PSME4 PSME4 PSME4 2414 0.18 0.23 YES
15 CD79A CD79A CD79A 2451 0.18 0.24 YES
16 SYK SYK SYK 2617 0.17 0.25 YES
17 BLK BLK BLK 2793 0.16 0.26 YES
18 BLNK BLNK BLNK 2903 0.15 0.27 YES
19 NFKBIE NFKBIE NFKBIE 3014 0.15 0.28 YES
20 PLCG2 PLCG2 PLCG2 3148 0.14 0.28 YES
21 NRAS NRAS NRAS 3244 0.13 0.29 YES
22 CDKN1A CDKN1A CDKN1A 3324 0.13 0.3 YES
23 MALT1 MALT1 MALT1 3359 0.13 0.31 YES
24 NFKBIB NFKBIB NFKBIB 3408 0.12 0.32 YES
25 CBL CBL CBL 3547 0.12 0.32 YES
26 SHC1 SHC1 SHC1 3580 0.12 0.34 YES
27 PSMA5 PSMA5 PSMA5 3922 0.1 0.33 YES
28 PSMA6 PSMA6 PSMA6 3951 0.1 0.34 YES
29 PSME2 PSME2 PSME2 3958 0.1 0.34 YES
30 PIK3CD PIK3CD PIK3CD 4067 0.097 0.35 YES
31 PSMA8 PSMA8 PSMA8 4074 0.097 0.36 YES
32 PSMA3 PSMA3 PSMA3 4102 0.096 0.37 YES
33 PSMD11 PSMD11 PSMD11 4237 0.091 0.37 YES
34 PSMD12 PSMD12 PSMD12 4502 0.083 0.36 YES
35 PSMB10 PSMB10 PSMB10 4534 0.082 0.37 YES
36 STIM1 STIM1 STIM1 4547 0.082 0.38 YES
37 PSMC4 PSMC4 PSMC4 4681 0.077 0.38 YES
38 PSMC6 PSMC6 PSMC6 4795 0.074 0.38 YES
39 CBLB CBLB CBLB 4827 0.073 0.38 YES
40 PSMD2 PSMD2 PSMD2 4832 0.073 0.39 YES
41 PSMD13 PSMD13 PSMD13 4905 0.071 0.39 YES
42 PSMB5 PSMB5 PSMB5 5000 0.068 0.4 YES
43 PSMA7 PSMA7 PSMA7 5032 0.067 0.4 YES
44 RASGRP1 RASGRP1 RASGRP1 5083 0.066 0.4 YES
45 PSMD14 PSMD14 PSMD14 5185 0.063 0.4 YES
46 PSMC1 PSMC1 PSMC1 5192 0.063 0.41 YES
47 AKT1 AKT1 AKT1 5196 0.063 0.42 YES
48 CHUK CHUK CHUK 5216 0.062 0.42 YES
49 CALM1 CALM1 CALM1 5304 0.06 0.42 YES
50 MTOR MTOR MTOR 5310 0.06 0.43 YES
51 GRB2 GRB2 GRB2 5323 0.06 0.44 YES
52 PSMB9 PSMB9 PSMB9 5349 0.059 0.44 YES
53 PSMF1 PSMF1 PSMF1 5544 0.054 0.44 YES
54 PSMB6 PSMB6 PSMB6 5588 0.054 0.44 YES
55 PSMD7 PSMD7 PSMD7 5687 0.052 0.44 YES
56 PSMD6 PSMD6 PSMD6 5692 0.052 0.44 YES
57 NFKBIA NFKBIA NFKBIA 5831 0.049 0.44 YES
58 PSMD1 PSMD1 PSMD1 5884 0.048 0.44 YES
59 FOXO1 FOXO1 FOXO1 5936 0.047 0.44 YES
60 PSMB3 PSMB3 PSMB3 5953 0.046 0.45 YES
61 PSMB2 PSMB2 PSMB2 6010 0.045 0.45 YES
62 KRAS KRAS KRAS 6089 0.043 0.45 YES
63 PSMD8 PSMD8 PSMD8 6101 0.043 0.45 YES
64 PSMD3 PSMD3 PSMD3 6211 0.04 0.45 NO
65 PSME1 PSME1 PSME1 6462 0.036 0.44 NO
66 PSMD5 PSMD5 PSMD5 6566 0.033 0.44 NO
67 PSMC3 PSMC3 PSMC3 6656 0.032 0.44 NO
68 SH3KBP1 SH3KBP1 SH3KBP1 6725 0.03 0.44 NO
69 PSMC2 PSMC2 PSMC2 6762 0.03 0.44 NO
70 PSMA1 PSMA1 PSMA1 6806 0.029 0.44 NO
71 CALM2 CALM2 CALM2 6902 0.027 0.43 NO
72 IKBKG IKBKG IKBKG 6912 0.026 0.44 NO
73 CALM3 CALM3 CALM3 6936 0.026 0.44 NO
74 PSMD9 PSMD9 PSMD9 6960 0.026 0.44 NO
75 PSMA2 PSMA2 PSMA2 6996 0.025 0.44 NO
76 PSMA4 PSMA4 PSMA4 7225 0.021 0.43 NO
77 NCK1 NCK1 NCK1 7228 0.021 0.43 NO
78 MAP3K7 MAP3K7 MAP3K7 7309 0.019 0.43 NO
79 PSMB4 PSMB4 PSMB4 7726 0.012 0.41 NO
80 CUL1 CUL1 CUL1 7741 0.012 0.41 NO
81 PSMC5 PSMC5 PSMC5 7862 0.0099 0.4 NO
82 PSMD4 PSMD4 PSMD4 8010 0.0075 0.4 NO
83 HRAS HRAS HRAS 8032 0.0071 0.39 NO
84 PSMB7 PSMB7 PSMB7 8065 0.0066 0.39 NO
85 GSK3A GSK3A GSK3A 8108 0.0058 0.39 NO
86 PHLPP1 PHLPP1 PHLPP1 8179 0.0045 0.39 NO
87 PSMB1 PSMB1 PSMB1 8237 0.0036 0.38 NO
88 PDPK1 PDPK1 PDPK1 8252 0.0034 0.38 NO
89 AKT1S1 AKT1S1 AKT1S1 8333 0.002 0.38 NO
90 MAPKAP1 MAPKAP1 MAPKAP1 8426 0.00023 0.38 NO
91 RELA RELA RELA 8468 -0.00039 0.37 NO
92 CREB1 CREB1 CREB1 8492 -0.00088 0.37 NO
93 BTRC BTRC BTRC 8603 -0.0027 0.37 NO
94 NR4A1 NR4A1 NR4A1 8713 -0.0045 0.36 NO
95 PLCG1 PLCG1 PLCG1 8947 -0.0085 0.35 NO
96 CDKN1B CDKN1B CDKN1B 9078 -0.011 0.34 NO
97 FYN FYN FYN 9108 -0.011 0.34 NO
98 MDM2 MDM2 MDM2 9172 -0.012 0.34 NO
99 RPS6KB2 RPS6KB2 RPS6KB2 9249 -0.014 0.34 NO
100 PSMB8 PSMB8 PSMB8 9607 -0.019 0.32 NO
101 PSMD10 PSMD10 PSMD10 9808 -0.023 0.31 NO
102 PTEN PTEN PTEN 9923 -0.025 0.31 NO
103 IKBKB IKBKB IKBKB 10285 -0.031 0.29 NO
104 TSC2 TSC2 TSC2 10290 -0.031 0.29 NO
105 AKT2 AKT2 AKT2 10369 -0.032 0.29 NO
106 UBA52 UBA52 UBA52 10630 -0.037 0.28 NO
107 SKP1 SKP1 SKP1 10847 -0.041 0.27 NO
108 FOXO3 FOXO3 FOXO3 11064 -0.045 0.27 NO
109 SOS1 SOS1 SOS1 11126 -0.047 0.27 NO
110 RPS27A RPS27A RPS27A 11209 -0.049 0.27 NO
111 ITPR2 ITPR2 ITPR2 11711 -0.06 0.25 NO
112 MLST8 MLST8 MLST8 11819 -0.062 0.25 NO
113 FBXW11 FBXW11 FBXW11 12087 -0.069 0.24 NO
114 ITPR3 ITPR3 ITPR3 12197 -0.072 0.24 NO
115 PIK3R1 PIK3R1 PIK3R1 12438 -0.078 0.23 NO
116 THEM4 THEM4 THEM4 13274 -0.1 0.2 NO
117 BAD BAD BAD 13782 -0.12 0.18 NO
118 CASP9 CASP9 CASP9 13795 -0.12 0.19 NO
119 FOXO4 FOXO4 FOXO4 13891 -0.13 0.2 NO
120 RICTOR RICTOR RICTOR 14898 -0.18 0.16 NO
121 CARD11 CARD11 CARD11 15051 -0.18 0.17 NO

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

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG APOPTOSIS, 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 TOLL LIKE RECEPTOR SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MECOM MECOM MECOM 156 0.54 0.069 YES
2 PIK3CG PIK3CG PIK3CG 407 0.44 0.12 YES
3 PIK3R5 PIK3R5 PIK3R5 835 0.35 0.14 YES
4 SHC3 SHC3 SHC3 1901 0.23 0.12 YES
5 TGFB1 TGFB1 TGFB1 1950 0.22 0.15 YES
6 AKT3 AKT3 AKT3 2102 0.21 0.17 YES
7 PIK3R3 PIK3R3 PIK3R3 2366 0.19 0.18 YES
8 TGFBR1 TGFBR1 TGFBR1 2488 0.18 0.2 YES
9 TGFBR2 TGFBR2 TGFBR2 2549 0.18 0.22 YES
10 E2F3 E2F3 E2F3 2799 0.16 0.23 YES
11 NRAS NRAS NRAS 3244 0.13 0.23 YES
12 SHC4 SHC4 SHC4 3263 0.13 0.24 YES
13 CDKN1A CDKN1A CDKN1A 3324 0.13 0.26 YES
14 CBL CBL CBL 3547 0.12 0.26 YES
15 MAP2K1 MAP2K1 MAP2K1 3548 0.12 0.28 YES
16 SHC1 SHC1 SHC1 3580 0.12 0.3 YES
17 GAB2 GAB2 GAB2 3746 0.11 0.3 YES
18 RUNX1 RUNX1 RUNX1 3795 0.11 0.32 YES
19 CCND1 CCND1 CCND1 3857 0.1 0.33 YES
20 PIK3CD PIK3CD PIK3CD 4067 0.097 0.33 YES
21 CRK CRK CRK 4274 0.09 0.33 YES
22 HDAC1 HDAC1 HDAC1 4452 0.085 0.34 YES
23 CDKN2A CDKN2A CDKN2A 4456 0.084 0.35 YES
24 E2F2 E2F2 E2F2 4462 0.084 0.36 YES
25 BRAF BRAF BRAF 4510 0.082 0.37 YES
26 CTBP2 CTBP2 CTBP2 4688 0.077 0.37 YES
27 E2F1 E2F1 E2F1 4750 0.075 0.38 YES
28 MAPK1 MAPK1 MAPK1 4758 0.075 0.39 YES
29 CBLB CBLB CBLB 4827 0.073 0.39 YES
30 CDK6 CDK6 CDK6 5071 0.066 0.39 YES
31 AKT1 AKT1 AKT1 5196 0.063 0.39 YES
32 BCL2L1 BCL2L1 BCL2L1 5214 0.062 0.4 YES
33 CHUK CHUK CHUK 5216 0.062 0.41 YES
34 GRB2 GRB2 GRB2 5323 0.06 0.41 YES
35 PTPN11 PTPN11 PTPN11 5342 0.06 0.42 YES
36 NFKB1 NFKB1 NFKB1 5404 0.058 0.42 YES
37 NFKBIA NFKBIA NFKBIA 5831 0.049 0.41 NO
38 KRAS KRAS KRAS 6089 0.043 0.4 NO
39 PIK3CA PIK3CA PIK3CA 6489 0.035 0.38 NO
40 RB1 RB1 RB1 6564 0.033 0.38 NO
41 IKBKG IKBKG IKBKG 6912 0.026 0.37 NO
42 HDAC2 HDAC2 HDAC2 7028 0.024 0.37 NO
43 SOS2 SOS2 SOS2 7492 0.016 0.34 NO
44 CRKL CRKL CRKL 7543 0.016 0.34 NO
45 RAF1 RAF1 RAF1 7585 0.015 0.34 NO
46 CBLC CBLC CBLC 8027 0.0072 0.32 NO
47 HRAS HRAS HRAS 8032 0.0071 0.32 NO
48 STAT5B STAT5B STAT5B 8067 0.0065 0.32 NO
49 CDK4 CDK4 CDK4 8254 0.0034 0.31 NO
50 ARAF ARAF ARAF 8262 0.0032 0.31 NO
51 MYC MYC MYC 8452 -0.00018 0.3 NO
52 RELA RELA RELA 8468 -0.00039 0.3 NO
53 MAP2K2 MAP2K2 MAP2K2 8724 -0.0046 0.28 NO
54 CDKN1B CDKN1B CDKN1B 9078 -0.011 0.27 NO
55 MDM2 MDM2 MDM2 9172 -0.012 0.26 NO
56 ABL1 ABL1 ABL1 9901 -0.024 0.23 NO
57 IKBKB IKBKB IKBKB 10285 -0.031 0.21 NO
58 CTBP1 CTBP1 CTBP1 10353 -0.032 0.21 NO
59 AKT2 AKT2 AKT2 10369 -0.032 0.22 NO
60 SMAD4 SMAD4 SMAD4 10599 -0.036 0.21 NO
61 SOS1 SOS1 SOS1 11126 -0.047 0.18 NO
62 PIK3CB PIK3CB PIK3CB 11271 -0.05 0.18 NO
63 STAT5A STAT5A STAT5A 11292 -0.05 0.19 NO
64 TP53 TP53 TP53 11310 -0.051 0.2 NO
65 SMAD3 SMAD3 SMAD3 11400 -0.053 0.2 NO
66 PIK3R1 PIK3R1 PIK3R1 12438 -0.078 0.15 NO
67 PIK3R2 PIK3R2 PIK3R2 12516 -0.08 0.16 NO
68 MAPK3 MAPK3 MAPK3 12813 -0.088 0.16 NO
69 TGFB2 TGFB2 TGFB2 13362 -0.1 0.14 NO
70 BCR BCR BCR 13714 -0.12 0.14 NO
71 BAD BAD BAD 13782 -0.12 0.15 NO
72 TGFB3 TGFB3 TGFB3 15241 -0.2 0.1 NO
73 SHC2 SHC2 SHC2 17270 -0.42 0.051 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 TOLL LIKE RECEPTOR SIGNALING PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TOLL LIKE RECEPTOR SIGNALING 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 CYTOSOLIC DNA SENSING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCA PRKCA PRKCA 1659 0.25 -0.034 YES
2 PSME4 PSME4 PSME4 2414 0.18 -0.032 YES
3 PRKCD PRKCD PRKCD 2883 0.15 -0.022 YES
4 MAPKAPK2 MAPKAPK2 MAPKAPK2 3484 0.12 -0.027 YES
5 MAPK11 MAPK11 MAPK11 3702 0.11 -0.013 YES
6 PSMA5 PSMA5 PSMA5 3922 0.1 -0.0011 YES
7 PSMA6 PSMA6 PSMA6 3951 0.1 0.021 YES
8 PSME2 PSME2 PSME2 3958 0.1 0.044 YES
9 PSMA8 PSMA8 PSMA8 4074 0.097 0.061 YES
10 PSMA3 PSMA3 PSMA3 4102 0.096 0.082 YES
11 PSMD11 PSMD11 PSMD11 4237 0.091 0.096 YES
12 EXOSC7 EXOSC7 EXOSC7 4449 0.085 0.1 YES
13 PSMD12 PSMD12 PSMD12 4502 0.083 0.12 YES
14 PSMB10 PSMB10 PSMB10 4534 0.082 0.14 YES
15 PSMC4 PSMC4 PSMC4 4681 0.077 0.15 YES
16 PSMC6 PSMC6 PSMC6 4795 0.074 0.16 YES
17 PSMD2 PSMD2 PSMD2 4832 0.073 0.17 YES
18 PSMD13 PSMD13 PSMD13 4905 0.071 0.19 YES
19 PSMB5 PSMB5 PSMB5 5000 0.068 0.2 YES
20 HSPA8 HSPA8 HSPA8 5020 0.067 0.21 YES
21 PSMA7 PSMA7 PSMA7 5032 0.067 0.23 YES
22 EIF4G1 EIF4G1 EIF4G1 5172 0.064 0.23 YES
23 PSMD14 PSMD14 PSMD14 5185 0.063 0.25 YES
24 PSMC1 PSMC1 PSMC1 5192 0.063 0.26 YES
25 AKT1 AKT1 AKT1 5196 0.063 0.28 YES
26 TNPO1 TNPO1 TNPO1 5299 0.06 0.29 YES
27 PSMB9 PSMB9 PSMB9 5349 0.059 0.3 YES
28 PSMF1 PSMF1 PSMF1 5544 0.054 0.3 YES
29 PSMB6 PSMB6 PSMB6 5588 0.054 0.31 YES
30 PSMD7 PSMD7 PSMD7 5687 0.052 0.32 YES
31 PSMD6 PSMD6 PSMD6 5692 0.052 0.33 YES
32 YWHAB YWHAB YWHAB 5760 0.051 0.34 YES
33 PSMD1 PSMD1 PSMD1 5884 0.048 0.34 YES
34 PSMB3 PSMB3 PSMB3 5953 0.046 0.35 YES
35 EXOSC3 EXOSC3 EXOSC3 5961 0.046 0.36 YES
36 MAPK14 MAPK14 MAPK14 5972 0.046 0.37 YES
37 PSMB2 PSMB2 PSMB2 6010 0.045 0.38 YES
38 PSMD8 PSMD8 PSMD8 6101 0.043 0.38 YES
39 HSPB1 HSPB1 HSPB1 6164 0.042 0.39 YES
40 PSMD3 PSMD3 PSMD3 6211 0.04 0.39 YES
41 PABPC1 PABPC1 PABPC1 6221 0.04 0.4 YES
42 ZFP36 ZFP36 ZFP36 6252 0.04 0.41 YES
43 XRN1 XRN1 XRN1 6376 0.037 0.41 YES
44 YWHAZ YWHAZ YWHAZ 6400 0.036 0.42 YES
45 EXOSC1 EXOSC1 EXOSC1 6448 0.036 0.43 YES
46 PSME1 PSME1 PSME1 6462 0.036 0.43 YES
47 HSPA1B HSPA1B HSPA1B 6537 0.034 0.44 YES
48 PSMD5 PSMD5 PSMD5 6566 0.033 0.44 YES
49 DCP2 DCP2 DCP2 6638 0.032 0.45 YES
50 PSMC3 PSMC3 PSMC3 6656 0.032 0.45 YES
51 PSMC2 PSMC2 PSMC2 6762 0.03 0.45 YES
52 PSMA1 PSMA1 PSMA1 6806 0.029 0.46 YES
53 PSMD9 PSMD9 PSMD9 6960 0.026 0.46 YES
54 PSMA2 PSMA2 PSMA2 6996 0.025 0.46 YES
55 EXOSC6 EXOSC6 EXOSC6 7175 0.022 0.46 NO
56 PSMA4 PSMA4 PSMA4 7225 0.021 0.46 NO
57 HNRNPD HNRNPD HNRNPD 7559 0.015 0.44 NO
58 PSMB4 PSMB4 PSMB4 7726 0.012 0.44 NO
59 PSMC5 PSMC5 PSMC5 7862 0.0099 0.43 NO
60 ZFP36L1 ZFP36L1 ZFP36L1 7947 0.0086 0.43 NO
61 PSMD4 PSMD4 PSMD4 8010 0.0075 0.43 NO
62 PSMB7 PSMB7 PSMB7 8065 0.0066 0.43 NO
63 EXOSC4 EXOSC4 EXOSC4 8132 0.0052 0.42 NO
64 EXOSC9 EXOSC9 EXOSC9 8170 0.0047 0.42 NO
65 PSMB1 PSMB1 PSMB1 8237 0.0036 0.42 NO
66 ANP32A ANP32A ANP32A 8432 0.00013 0.41 NO
67 XPO1 XPO1 XPO1 9287 -0.014 0.36 NO
68 EXOSC2 EXOSC2 EXOSC2 9447 -0.017 0.36 NO
69 DCP1A DCP1A DCP1A 9463 -0.017 0.36 NO
70 KHSRP KHSRP KHSRP 9547 -0.018 0.36 NO
71 PSMB8 PSMB8 PSMB8 9607 -0.019 0.36 NO
72 PSMD10 PSMD10 PSMD10 9808 -0.023 0.36 NO
73 ELAVL1 ELAVL1 ELAVL1 9858 -0.023 0.36 NO
74 TNFSF13 TNFSF13 TNFSF13 9971 -0.025 0.36 NO
75 NUP214 NUP214 NUP214 10106 -0.028 0.36 NO
76 EXOSC8 EXOSC8 EXOSC8 10561 -0.036 0.34 NO
77 UBA52 UBA52 UBA52 10630 -0.037 0.35 NO
78 RPS27A RPS27A RPS27A 11209 -0.049 0.33 NO
79 DIS3 DIS3 DIS3 11530 -0.056 0.32 NO
80 EXOSC5 EXOSC5 EXOSC5 12629 -0.083 0.28 NO
81 PARN PARN PARN 13453 -0.11 0.26 NO

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

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

genes ES table in pathway: KEGG HEMATOPOIETIC CELL LINEAGE

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 FOSL1 FOSL1 FOSL1 18 0.74 0.082 YES
2 MYCT1 MYCT1 MYCT1 116 0.56 0.14 YES
3 MMP9 MMP9 MMP9 239 0.49 0.19 YES
4 CDC25A CDC25A CDC25A 574 0.4 0.21 YES
5 CDCA7 CDCA7 CDCA7 613 0.39 0.25 YES
6 HMGA1 HMGA1 HMGA1 689 0.37 0.29 YES
7 SNAI1 SNAI1 SNAI1 773 0.36 0.33 YES
8 PMAIP1 PMAIP1 PMAIP1 1078 0.31 0.34 YES
9 BIRC5 BIRC5 BIRC5 1770 0.24 0.33 YES
10 CCNB1 CCNB1 CCNB1 1856 0.23 0.36 YES
11 TK1 TK1 TK1 2247 0.2 0.36 YES
12 RCC1 RCC1 RCC1 2314 0.19 0.37 YES
13 NDUFAF2 NDUFAF2 NDUFAF2 2388 0.19 0.39 YES
14 SUPT3H SUPT3H SUPT3H 2505 0.18 0.4 YES
15 TFRC TFRC TFRC 2734 0.16 0.41 YES
16 POLR3D POLR3D POLR3D 2789 0.16 0.42 YES
17 E2F3 E2F3 E2F3 2799 0.16 0.44 YES
18 EIF4E EIF4E EIF4E 3025 0.14 0.44 YES
19 EIF2S1 EIF2S1 EIF2S1 3039 0.14 0.46 YES
20 SLC2A1 SLC2A1 SLC2A1 3044 0.14 0.48 YES
21 BCAT1 BCAT1 BCAT1 3153 0.14 0.48 YES
22 NBN NBN NBN 3679 0.11 0.47 NO
23 PDCD10 PDCD10 PDCD10 3947 0.1 0.46 NO
24 BAX BAX BAX 4107 0.096 0.47 NO
25 HSPA4 HSPA4 HSPA4 4742 0.076 0.44 NO
26 TAF9 TAF9 TAF9 4761 0.075 0.45 NO
27 TERT TERT TERT 4891 0.071 0.45 NO
28 TAF12 TAF12 TAF12 5134 0.064 0.44 NO
29 EIF4G1 EIF4G1 EIF4G1 5172 0.064 0.45 NO
30 NME1 NME1 NME1 5448 0.057 0.44 NO
31 HSP90AA1 HSP90AA1 HSP90AA1 5684 0.052 0.43 NO
32 GAPDH GAPDH GAPDH 5793 0.05 0.43 NO
33 MINA MINA MINA 5888 0.048 0.43 NO
34 EIF4A1 EIF4A1 EIF4A1 6206 0.041 0.42 NO
35 LDHA LDHA LDHA 6249 0.04 0.42 NO
36 PIM1 PIM1 PIM1 6356 0.038 0.42 NO
37 RUVBL2 RUVBL2 RUVBL2 6392 0.037 0.42 NO
38 ENO1 ENO1 ENO1 6906 0.027 0.4 NO
39 DDX18 DDX18 DDX18 6944 0.026 0.4 NO
40 MAX MAX MAX 6961 0.026 0.4 NO
41 SUPT7L SUPT7L SUPT7L 7207 0.021 0.39 NO
42 CAD CAD CAD 7232 0.021 0.39 NO
43 MTDH MTDH MTDH 7282 0.02 0.39 NO
44 ACTL6A ACTL6A ACTL6A 7296 0.02 0.39 NO
45 EP300 EP300 EP300 7564 0.015 0.38 NO
46 TAF4B TAF4B TAF4B 7650 0.014 0.37 NO
47 RUVBL1 RUVBL1 RUVBL1 7837 0.01 0.36 NO
48 HUWE1 HUWE1 HUWE1 8058 0.0067 0.35 NO
49 CDK4 CDK4 CDK4 8254 0.0034 0.34 NO
50 GPAM GPAM GPAM 8364 0.0014 0.34 NO
51 MYC MYC MYC 8452 -0.00018 0.33 NO
52 NCL NCL NCL 8508 -0.0012 0.33 NO
53 NPM1 NPM1 NPM1 8658 -0.0035 0.32 NO
54 HSPD1 HSPD1 HSPD1 9302 -0.014 0.29 NO
55 MTA1 MTA1 MTA1 9752 -0.022 0.26 NO
56 BMI1 BMI1 BMI1 9855 -0.023 0.26 NO
57 TRRAP TRRAP TRRAP 9857 -0.023 0.26 NO
58 PRDX3 PRDX3 PRDX3 9895 -0.024 0.26 NO
59 NME2 NME2 NME2 10192 -0.029 0.25 NO
60 KAT5 KAT5 KAT5 10347 -0.032 0.25 NO
61 SMAD4 SMAD4 SMAD4 10599 -0.036 0.24 NO
62 IREB2 IREB2 IREB2 11077 -0.046 0.22 NO
63 KIR3DL1 KIR3DL1 KIR3DL1 11092 -0.046 0.22 NO
64 ODC1 ODC1 ODC1 11290 -0.05 0.21 NO
65 TP53 TP53 TP53 11310 -0.051 0.22 NO
66 SMAD3 SMAD3 SMAD3 11400 -0.053 0.22 NO
67 UBTF UBTF UBTF 11537 -0.056 0.22 NO
68 TAF10 TAF10 TAF10 11737 -0.06 0.21 NO
69 CREBBP CREBBP CREBBP 11796 -0.062 0.22 NO
70 PTMA PTMA PTMA 11854 -0.063 0.22 NO
71 RPL11 RPL11 RPL11 12296 -0.074 0.21 NO
72 PEG10 PEG10 PEG10 12544 -0.081 0.2 NO
73 ID2 ID2 ID2 12766 -0.086 0.2 NO
74 KAT2A KAT2A KAT2A 13993 -0.13 0.14 NO
75 SHMT1 SHMT1 SHMT1 14303 -0.14 0.14 NO
76 PFKM PFKM PFKM 14823 -0.17 0.14 NO
77 CCND2 CCND2 CCND2 15078 -0.19 0.14 NO
78 SERPINI1 SERPINI1 SERPINI1 16135 -0.27 0.11 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 HEMATOPOIETIC CELL LINEAGE.

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HEMATOPOIETIC CELL LINEAGE, 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 T CELL RECEPTOR SIGNALING PATHWAY

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 RASGRP3 RASGRP3 RASGRP3 764 0.36 0.016 YES
2 PRKCB PRKCB PRKCB 937 0.34 0.06 YES
3 BCL10 BCL10 BCL10 1914 0.22 0.042 YES
4 AKT3 AKT3 AKT3 2102 0.21 0.064 YES
5 REL REL REL 2147 0.2 0.095 YES
6 TRIB3 TRIB3 TRIB3 2392 0.18 0.11 YES
7 PSME4 PSME4 PSME4 2414 0.18 0.14 YES
8 NFKBIE NFKBIE NFKBIE 3014 0.15 0.13 YES
9 NRAS NRAS NRAS 3244 0.13 0.14 YES
10 CDKN1A CDKN1A CDKN1A 3324 0.13 0.15 YES
11 MALT1 MALT1 MALT1 3359 0.13 0.17 YES
12 NFKBIB NFKBIB NFKBIB 3408 0.12 0.19 YES
13 PSMA5 PSMA5 PSMA5 3922 0.1 0.18 YES
14 PSMA6 PSMA6 PSMA6 3951 0.1 0.19 YES
15 PSME2 PSME2 PSME2 3958 0.1 0.21 YES
16 PSMA8 PSMA8 PSMA8 4074 0.097 0.22 YES
17 PSMA3 PSMA3 PSMA3 4102 0.096 0.23 YES
18 PSMD11 PSMD11 PSMD11 4237 0.091 0.24 YES
19 PSMD12 PSMD12 PSMD12 4502 0.083 0.24 YES
20 PSMB10 PSMB10 PSMB10 4534 0.082 0.25 YES
21 PSMC4 PSMC4 PSMC4 4681 0.077 0.25 YES
22 PSMC6 PSMC6 PSMC6 4795 0.074 0.26 YES
23 PSMD2 PSMD2 PSMD2 4832 0.073 0.27 YES
24 PSMD13 PSMD13 PSMD13 4905 0.071 0.28 YES
25 PSMB5 PSMB5 PSMB5 5000 0.068 0.28 YES
26 PSMA7 PSMA7 PSMA7 5032 0.067 0.29 YES
27 RASGRP1 RASGRP1 RASGRP1 5083 0.066 0.3 YES
28 PSMD14 PSMD14 PSMD14 5185 0.063 0.3 YES
29 PSMC1 PSMC1 PSMC1 5192 0.063 0.31 YES
30 AKT1 AKT1 AKT1 5196 0.063 0.32 YES
31 CHUK CHUK CHUK 5216 0.062 0.33 YES
32 MTOR MTOR MTOR 5310 0.06 0.34 YES
33 PSMB9 PSMB9 PSMB9 5349 0.059 0.34 YES
34 PSMF1 PSMF1 PSMF1 5544 0.054 0.34 YES
35 PSMB6 PSMB6 PSMB6 5588 0.054 0.35 YES
36 PSMD7 PSMD7 PSMD7 5687 0.052 0.35 YES
37 PSMD6 PSMD6 PSMD6 5692 0.052 0.36 YES
38 NFKBIA NFKBIA NFKBIA 5831 0.049 0.36 YES
39 PSMD1 PSMD1 PSMD1 5884 0.048 0.36 YES
40 FOXO1 FOXO1 FOXO1 5936 0.047 0.37 YES
41 PSMB3 PSMB3 PSMB3 5953 0.046 0.38 YES
42 PSMB2 PSMB2 PSMB2 6010 0.045 0.38 YES
43 KRAS KRAS KRAS 6089 0.043 0.38 YES
44 PSMD8 PSMD8 PSMD8 6101 0.043 0.39 YES
45 PSMD3 PSMD3 PSMD3 6211 0.04 0.39 YES
46 PSME1 PSME1 PSME1 6462 0.036 0.38 NO
47 PSMD5 PSMD5 PSMD5 6566 0.033 0.38 NO
48 PSMC3 PSMC3 PSMC3 6656 0.032 0.38 NO
49 PSMC2 PSMC2 PSMC2 6762 0.03 0.38 NO
50 PSMA1 PSMA1 PSMA1 6806 0.029 0.38 NO
51 IKBKG IKBKG IKBKG 6912 0.026 0.38 NO
52 PSMD9 PSMD9 PSMD9 6960 0.026 0.38 NO
53 PSMA2 PSMA2 PSMA2 6996 0.025 0.38 NO
54 PSMA4 PSMA4 PSMA4 7225 0.021 0.37 NO
55 MAP3K7 MAP3K7 MAP3K7 7309 0.019 0.37 NO
56 PSMB4 PSMB4 PSMB4 7726 0.012 0.35 NO
57 CUL1 CUL1 CUL1 7741 0.012 0.35 NO
58 PSMC5 PSMC5 PSMC5 7862 0.0099 0.35 NO
59 PSMD4 PSMD4 PSMD4 8010 0.0075 0.34 NO
60 HRAS HRAS HRAS 8032 0.0071 0.34 NO
61 PSMB7 PSMB7 PSMB7 8065 0.0066 0.34 NO
62 GSK3A GSK3A GSK3A 8108 0.0058 0.34 NO
63 PHLPP1 PHLPP1 PHLPP1 8179 0.0045 0.34 NO
64 PSMB1 PSMB1 PSMB1 8237 0.0036 0.33 NO
65 PDPK1 PDPK1 PDPK1 8252 0.0034 0.33 NO
66 AKT1S1 AKT1S1 AKT1S1 8333 0.002 0.33 NO
67 MAPKAP1 MAPKAP1 MAPKAP1 8426 0.00023 0.32 NO
68 RELA RELA RELA 8468 -0.00039 0.32 NO
69 CREB1 CREB1 CREB1 8492 -0.00088 0.32 NO
70 BTRC BTRC BTRC 8603 -0.0027 0.31 NO
71 NR4A1 NR4A1 NR4A1 8713 -0.0045 0.31 NO
72 CDKN1B CDKN1B CDKN1B 9078 -0.011 0.29 NO
73 MDM2 MDM2 MDM2 9172 -0.012 0.29 NO
74 RPS6KB2 RPS6KB2 RPS6KB2 9249 -0.014 0.29 NO
75 PSMB8 PSMB8 PSMB8 9607 -0.019 0.27 NO
76 PSMD10 PSMD10 PSMD10 9808 -0.023 0.26 NO
77 PTEN PTEN PTEN 9923 -0.025 0.26 NO
78 IKBKB IKBKB IKBKB 10285 -0.031 0.24 NO
79 TSC2 TSC2 TSC2 10290 -0.031 0.25 NO
80 AKT2 AKT2 AKT2 10369 -0.032 0.25 NO
81 UBA52 UBA52 UBA52 10630 -0.037 0.24 NO
82 SKP1 SKP1 SKP1 10847 -0.041 0.24 NO
83 FOXO3 FOXO3 FOXO3 11064 -0.045 0.23 NO
84 RPS27A RPS27A RPS27A 11209 -0.049 0.23 NO
85 MLST8 MLST8 MLST8 11819 -0.062 0.21 NO
86 FBXW11 FBXW11 FBXW11 12087 -0.069 0.2 NO
87 THEM4 THEM4 THEM4 13274 -0.1 0.16 NO
88 BAD BAD BAD 13782 -0.12 0.15 NO
89 CASP9 CASP9 CASP9 13795 -0.12 0.16 NO
90 FOXO4 FOXO4 FOXO4 13891 -0.13 0.18 NO
91 RICTOR RICTOR RICTOR 14898 -0.18 0.15 NO
92 CARD11 CARD11 CARD11 15051 -0.18 0.17 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG T CELL RECEPTOR SIGNALING PATHWAY.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG T CELL RECEPTOR SIGNALING 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 B CELL RECEPTOR SIGNALING PATHWAY

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 MMP9 MMP9 MMP9 239 0.49 0.074 YES
2 THBS1 THBS1 THBS1 375 0.44 0.15 YES
3 ADAM12 ADAM12 ADAM12 377 0.44 0.22 YES
4 TFPI TFPI TFPI 639 0.38 0.28 YES
5 CCL5 CCL5 CCL5 848 0.35 0.33 YES
6 TNC TNC TNC 896 0.34 0.39 YES
7 ITGA5 ITGA5 ITGA5 932 0.34 0.44 YES
8 FGF2 FGF2 FGF2 1069 0.32 0.49 YES
9 ACTN1 ACTN1 ACTN1 1519 0.26 0.52 YES
10 FN1 FN1 FN1 1553 0.26 0.56 YES
11 PRKCA PRKCA PRKCA 1659 0.25 0.6 YES
12 F2 F2 F2 2126 0.2 0.61 YES
13 TNFRSF13B TNFRSF13B TNFRSF13B 2556 0.17 0.62 YES
14 ITGB1 ITGB1 ITGB1 2726 0.16 0.64 YES
15 CXCR4 CXCR4 CXCR4 2816 0.16 0.66 YES
16 PRKCD PRKCD PRKCD 2883 0.15 0.68 YES
17 LAMA1 LAMA1 LAMA1 3137 0.14 0.69 YES
18 RHOA RHOA RHOA 5381 0.058 0.58 NO
19 SDCBP SDCBP SDCBP 5988 0.045 0.56 NO
20 CXCL12 CXCL12 CXCL12 6007 0.045 0.56 NO
21 RAC1 RAC1 RAC1 7867 0.0098 0.46 NO
22 DNM2 DNM2 DNM2 8093 0.0061 0.45 NO
23 FGFR1 FGFR1 FGFR1 8845 -0.0067 0.41 NO
24 GIPC1 GIPC1 GIPC1 10019 -0.026 0.35 NO
25 SDC4 SDC4 SDC4 10125 -0.028 0.35 NO
26 PTK2 PTK2 PTK2 10817 -0.04 0.32 NO
27 MDK MDK MDK 11429 -0.053 0.29 NO
28 FZD7 FZD7 FZD7 11953 -0.065 0.28 NO
29 NUDT16L1 NUDT16L1 NUDT16L1 12964 -0.092 0.24 NO
30 LAMA3 LAMA3 LAMA3 16246 -0.28 0.11 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 B CELL RECEPTOR SIGNALING PATHWAY.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG B CELL RECEPTOR SIGNALING 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 FC GAMMA R MEDIATED PHAGOCYTOSIS

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 ITK ITK ITK 203 0.51 0.059 YES
2 LCK LCK LCK 274 0.48 0.12 YES
3 DAPP1 DAPP1 DAPP1 346 0.45 0.18 YES
4 PIK3CG PIK3CG PIK3CG 407 0.44 0.24 YES
5 ARAP3 ARAP3 ARAP3 478 0.42 0.29 YES
6 LAT LAT LAT 751 0.36 0.32 YES
7 ZAP70 ZAP70 ZAP70 770 0.36 0.37 YES
8 PIK3R5 PIK3R5 PIK3R5 835 0.35 0.42 YES
9 HCK HCK HCK 1102 0.31 0.44 YES
10 PIK3R6 PIK3R6 PIK3R6 1283 0.29 0.47 YES
11 FGR FGR FGR 1325 0.28 0.51 YES
12 BTK BTK BTK 1475 0.26 0.54 YES
13 LYN LYN LYN 2185 0.2 0.53 YES
14 PIK3R3 PIK3R3 PIK3R3 2366 0.19 0.54 YES
15 SYK SYK SYK 2617 0.17 0.55 YES
16 BLK BLK BLK 2793 0.16 0.56 YES
17 ARF6 ARF6 ARF6 2866 0.16 0.58 YES
18 ADAP1 ADAP1 ADAP1 2890 0.15 0.6 YES
19 BLNK BLNK BLNK 2903 0.15 0.62 YES
20 PLCG2 PLCG2 PLCG2 3148 0.14 0.63 YES
21 NRAS NRAS NRAS 3244 0.13 0.64 YES
22 RAP1A RAP1A RAP1A 3308 0.13 0.65 YES
23 PIK3CD PIK3CD PIK3CD 4067 0.097 0.63 NO
24 SGK1 SGK1 SGK1 4268 0.09 0.63 NO
25 CYTH1 CYTH1 CYTH1 4740 0.076 0.61 NO
26 RHOA RHOA RHOA 5381 0.058 0.58 NO
27 INPP5D INPP5D INPP5D 5542 0.055 0.58 NO
28 HSP90AA1 HSP90AA1 HSP90AA1 5684 0.052 0.58 NO
29 KRAS KRAS KRAS 6089 0.043 0.57 NO
30 PIK3CA PIK3CA PIK3CA 6489 0.035 0.55 NO
31 CYTH2 CYTH2 CYTH2 6886 0.027 0.53 NO
32 YES1 YES1 YES1 6969 0.025 0.53 NO
33 INPPL1 INPPL1 INPPL1 7792 0.011 0.49 NO
34 RAC1 RAC1 RAC1 7867 0.0098 0.48 NO
35 HRAS HRAS HRAS 8032 0.0071 0.48 NO
36 PDPK1 PDPK1 PDPK1 8252 0.0034 0.46 NO
37 ARF1 ARF1 ARF1 8448 -0.000096 0.45 NO
38 PLCG1 PLCG1 PLCG1 8947 -0.0085 0.43 NO
39 FYN FYN FYN 9108 -0.011 0.42 NO
40 SRC SRC SRC 9350 -0.015 0.41 NO
41 PLEKHA2 PLEKHA2 PLEKHA2 9423 -0.016 0.41 NO
42 PTEN PTEN PTEN 9923 -0.025 0.38 NO
43 ARF5 ARF5 ARF5 10473 -0.034 0.36 NO
44 FOXO3 FOXO3 FOXO3 11064 -0.045 0.33 NO
45 PIK3CB PIK3CB PIK3CB 11271 -0.05 0.33 NO
46 PIK3R1 PIK3R1 PIK3R1 12438 -0.078 0.27 NO
47 PIK3R2 PIK3R2 PIK3R2 12516 -0.08 0.28 NO
48 CYTH3 CYTH3 CYTH3 12818 -0.088 0.28 NO
49 PLEKHA1 PLEKHA1 PLEKHA1 14570 -0.16 0.2 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 FC GAMMA R MEDIATED PHAGOCYTOSIS.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS, 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
KEGG WNT SIGNALING PATHWAY 145 genes.ES.table 0.48 1.7 0.0058 1 0.85 0.29 0.19 0.24 0.55 0.29
KEGG TGF BETA SIGNALING PATHWAY 85 genes.ES.table 0.59 1.7 0.0021 0.98 0.86 0.33 0.13 0.29 0.53 0.28
KEGG LONG TERM POTENTIATION 68 genes.ES.table 0.49 1.6 0.0061 0.73 0.9 0.25 0.15 0.21 0.41 0.2
KEGG MELANOGENESIS 99 genes.ES.table 0.51 1.6 0.006 0.64 0.9 0.35 0.19 0.29 0.36 0.17
KEGG BASAL CELL CARCINOMA 54 genes.ES.table 0.61 1.7 0.01 0.69 0.87 0.5 0.19 0.41 0.38 0.19
BIOCARTA ALK PATHWAY 36 genes.ES.table 0.6 1.7 0.0063 1 0.83 0.22 0.078 0.2 0.57 0.32
ST WNT BETA CATENIN PATHWAY 31 genes.ES.table 0.58 1.6 0.012 0.53 0.91 0.23 0.07 0.21 0.3 0.14
PID EPHBFWDPATHWAY 40 genes.ES.table 0.45 1.6 0.0093 0.61 0.9 0.28 0.23 0.21 0.35 0.17
PID P75NTRPATHWAY 68 genes.ES.table 0.44 1.8 0 1 0.61 0.18 0.12 0.16 1 0.51
PID HEDGEHOG GLIPATHWAY 48 genes.ES.table 0.45 1.7 0.0083 0.89 0.87 0.33 0.28 0.24 0.49 0.25
genes ES table in pathway: KEGG WNT SIGNALING 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 MAG MAG MAG 125 0.6 0.075 YES
2 NGFR NGFR NGFR 227 0.53 0.14 YES
3 RTN4R RTN4R RTN4R 635 0.41 0.18 YES
4 BEX1 BEX1 BEX1 854 0.37 0.22 YES
5 MAPK10 MAPK10 MAPK10 1145 0.33 0.24 YES
6 NTF4 NTF4 NTF4 1306 0.3 0.28 YES
7 BDNF BDNF BDNF 1309 0.3 0.32 YES
8 NGF NGF NGF 1310 0.3 0.36 YES
9 NTRK1 NTRK1 NTRK1 1904 0.24 0.36 YES
10 NTF3 NTF3 NTF3 2038 0.24 0.39 YES
11 LINGO1 LINGO1 LINGO1 2222 0.22 0.41 YES
12 E2F1 E2F1 E2F1 2241 0.22 0.44 YES
13 MMP3 MMP3 MMP3 3893 0.13 0.36 NO
14 NGFRAP1 NGFRAP1 NGFRAP1 4459 0.11 0.35 NO
15 TP53 TP53 TP53 4609 0.11 0.35 NO
16 APAF1 APAF1 APAF1 4676 0.1 0.36 NO
17 BCL2L11 BCL2L11 BCL2L11 4888 0.097 0.36 NO
18 MMP7 MMP7 MMP7 5584 0.079 0.34 NO
19 OMG OMG OMG 6942 0.051 0.27 NO
20 APP APP APP 6970 0.05 0.28 NO
21 AKT1 AKT1 AKT1 7187 0.046 0.27 NO
22 FURIN FURIN FURIN 8045 0.032 0.23 NO
23 DIABLO DIABLO DIABLO 8064 0.032 0.23 NO
24 YWHAE YWHAE YWHAE 8149 0.03 0.23 NO
25 MAGED1 MAGED1 MAGED1 8469 0.025 0.22 NO
26 XIAP XIAP XIAP 8577 0.024 0.21 NO
27 IKBKG IKBKG IKBKG 9006 0.018 0.19 NO
28 CASP9 CASP9 CASP9 9318 0.014 0.18 NO
29 PRKACB PRKACB PRKACB 9537 0.011 0.17 NO
30 SHC1 SHC1 SHC1 9592 0.01 0.16 NO
31 IKBKB IKBKB IKBKB 9799 0.0074 0.15 NO
32 RAC1 RAC1 RAC1 10220 0.0013 0.13 NO
33 PIK3R1 PIK3R1 PIK3R1 10547 -0.0028 0.11 NO
34 MAPK8 MAPK8 MAPK8 10610 -0.0038 0.11 NO
35 PRKCI PRKCI PRKCI 10804 -0.0064 0.1 NO
36 PRDM4 PRDM4 PRDM4 10932 -0.0082 0.094 NO
37 NCSTN NCSTN NCSTN 11042 -0.0097 0.09 NO
38 NDN NDN NDN 11689 -0.019 0.057 NO
39 SMPD2 SMPD2 SMPD2 11720 -0.019 0.058 NO
40 APH1A APH1A APH1A 11722 -0.019 0.06 NO
41 PSEN1 PSEN1 PSEN1 11754 -0.02 0.061 NO
42 ADAM17 ADAM17 ADAM17 12341 -0.029 0.033 NO
43 ARHGDIA ARHGDIA ARHGDIA 12454 -0.03 0.031 NO
44 RHOC RHOC RHOC 12492 -0.031 0.033 NO
45 BIRC2 BIRC2 BIRC2 12967 -0.038 0.012 NO
46 BAD BAD BAD 13187 -0.042 0.006 NO
47 RTN4 RTN4 RTN4 13199 -0.043 0.011 NO
48 RHOA RHOA RHOA 13360 -0.046 0.0087 NO
49 SORT1 SORT1 SORT1 13510 -0.048 0.007 NO
50 RHOB RHOB RHOB 13521 -0.048 0.013 NO
51 NDNL2 NDNL2 NDNL2 13597 -0.05 0.016 NO
52 MAPK9 MAPK9 MAPK9 13611 -0.05 0.022 NO
53 CHUK CHUK CHUK 13670 -0.051 0.026 NO
54 MAGEH1 MAGEH1 MAGEH1 13758 -0.053 0.028 NO
55 IRAK1 IRAK1 IRAK1 13781 -0.053 0.034 NO
56 TRAF6 TRAF6 TRAF6 14029 -0.059 0.029 NO
57 PSENEN PSENEN PSENEN 14623 -0.072 0.0059 NO
58 SQSTM1 SQSTM1 SQSTM1 14784 -0.076 0.0075 NO
59 PIK3CA PIK3CA PIK3CA 14831 -0.077 0.016 NO
60 APH1B APH1B APH1B 15078 -0.083 0.013 NO
61 MYD88 MYD88 MYD88 15177 -0.086 0.02 NO
62 ZNF274 ZNF274 ZNF274 15640 -0.1 0.0082 NO
63 CYCS CYCS CYCS 15743 -0.11 0.017 NO
64 PRKCZ PRKCZ PRKCZ 15856 -0.11 0.026 NO
65 CASP3 CASP3 CASP3 15928 -0.11 0.038 NO
66 CASP6 CASP6 CASP6 16188 -0.13 0.041 NO
67 RIPK2 RIPK2 RIPK2 16283 -0.13 0.054 NO
68 BIRC3 BIRC3 BIRC3 18004 -0.38 0.01 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: KEGG WNT SIGNALING PATHWAY.

Figure S62.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG WNT SIGNALING 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 TGF BETA SIGNALING 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 GPC2 GPC2 GPC2 194 0.55 0.1 YES
2 B3GAT1 B3GAT1 B3GAT1 583 0.42 0.17 YES
3 GPC4 GPC4 GPC4 596 0.42 0.25 YES
4 GPC5 GPC5 GPC5 729 0.39 0.32 YES
5 CSPG4 CSPG4 CSPG4 848 0.37 0.4 YES
6 BCAN BCAN BCAN 1031 0.34 0.46 YES
7 GPC6 GPC6 GPC6 1253 0.31 0.51 YES
8 B3GAT2 B3GAT2 B3GAT2 1302 0.3 0.57 YES
9 SDC2 SDC2 SDC2 1324 0.3 0.63 YES
10 BGN BGN BGN 1920 0.24 0.64 YES
11 VCAN VCAN VCAN 2350 0.21 0.66 YES
12 SDC1 SDC1 SDC1 3260 0.16 0.65 YES
13 GPC1 GPC1 GPC1 3427 0.16 0.67 YES
14 GPC3 GPC3 GPC3 3521 0.15 0.69 YES
15 NCAN NCAN NCAN 4205 0.12 0.68 NO
16 DCN DCN DCN 4617 0.11 0.68 NO
17 HSPG2 HSPG2 HSPG2 4907 0.096 0.68 NO
18 B3GALT6 B3GALT6 B3GALT6 5256 0.087 0.68 NO
19 GXYLT1 GXYLT1 GXYLT1 6980 0.05 0.6 NO
20 SDC3 SDC3 SDC3 7986 0.033 0.55 NO
21 SDC4 SDC4 SDC4 9276 0.015 0.48 NO
22 B3GAT3 B3GAT3 B3GAT3 9916 0.0059 0.45 NO
23 AGRN AGRN AGRN 10246 0.00098 0.43 NO
24 B4GALT7 B4GALT7 B4GALT7 10282 0.00051 0.43 NO
25 GXYLT2 GXYLT2 GXYLT2 12868 -0.037 0.29 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: KEGG TGF BETA SIGNALING PATHWAY.

Figure S64.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TGF BETA SIGNALING 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 LONG TERM POTENTIATION

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 COL2A1 COL2A1 COL2A1 44 0.7 0.061 YES
2 COL9A1 COL9A1 COL9A1 75 0.64 0.12 YES
3 ST8SIA2 ST8SIA2 ST8SIA2 76 0.64 0.18 YES
4 CACNA1G CACNA1G CACNA1G 170 0.57 0.22 YES
5 CNTN2 CNTN2 CNTN2 221 0.54 0.27 YES
6 NCAM1 NCAM1 NCAM1 276 0.52 0.31 YES
7 GFRA2 GFRA2 GFRA2 316 0.5 0.36 YES
8 NRTN NRTN NRTN 369 0.48 0.4 YES
9 COL9A2 COL9A2 COL9A2 556 0.43 0.43 YES
10 CACNA1H CACNA1H CACNA1H 628 0.41 0.46 YES
11 COL9A3 COL9A3 COL9A3 688 0.4 0.49 YES
12 COL4A2 COL4A2 COL4A2 1351 0.3 0.48 YES
13 COL4A1 COL4A1 COL4A1 1386 0.29 0.51 YES
14 SPTBN5 SPTBN5 SPTBN5 1693 0.26 0.52 YES
15 GDNF GDNF GDNF 1724 0.26 0.54 YES
16 CACNA1I CACNA1I CACNA1I 1841 0.25 0.55 YES
17 GFRA1 GFRA1 GFRA1 2136 0.23 0.56 YES
18 CACNB1 CACNB1 CACNB1 2286 0.22 0.57 YES
19 COL6A3 COL6A3 COL6A3 2461 0.21 0.58 YES
20 SPTB SPTB SPTB 2481 0.2 0.6 YES
21 CACNB3 CACNB3 CACNB3 2496 0.2 0.61 YES
22 CDK1 CDK1 CDK1 3256 0.16 0.59 NO
23 COL5A1 COL5A1 COL5A1 3397 0.16 0.59 NO
24 COL3A1 COL3A1 COL3A1 3751 0.14 0.59 NO
25 COL1A2 COL1A2 COL1A2 3907 0.13 0.59 NO
26 SRC SRC SRC 4195 0.12 0.58 NO
27 NCAN NCAN NCAN 4205 0.12 0.6 NO
28 CACNA1S CACNA1S CACNA1S 4424 0.11 0.59 NO
29 COL6A1 COL6A1 COL6A1 4464 0.11 0.6 NO
30 CACNB4 CACNB4 CACNB4 4674 0.1 0.6 NO
31 COL5A2 COL5A2 COL5A2 4685 0.1 0.61 NO
32 COL6A2 COL6A2 COL6A2 5003 0.094 0.6 NO
33 FGFR1 FGFR1 FGFR1 5272 0.086 0.59 NO
34 COL1A1 COL1A1 COL1A1 5526 0.08 0.59 NO
35 COL4A5 COL4A5 COL4A5 5850 0.073 0.57 NO
36 RPS6KA5 RPS6KA5 RPS6KA5 6567 0.057 0.54 NO
37 KRAS KRAS KRAS 6691 0.055 0.54 NO
38 ARTN ARTN ARTN 6717 0.054 0.54 NO
39 SPTBN1 SPTBN1 SPTBN1 6862 0.052 0.54 NO
40 PSPN PSPN PSPN 7307 0.044 0.52 NO
41 CREB1 CREB1 CREB1 7706 0.038 0.5 NO
42 MAP2K2 MAP2K2 MAP2K2 7770 0.037 0.5 NO
43 SPTBN2 SPTBN2 SPTBN2 8696 0.022 0.45 NO
44 PTK2 PTK2 PTK2 8710 0.022 0.45 NO
45 AGRN AGRN AGRN 10246 0.00098 0.37 NO
46 RAF1 RAF1 RAF1 10267 0.00061 0.37 NO
47 MAPK1 MAPK1 MAPK1 10386 -0.00086 0.36 NO
48 SOS1 SOS1 SOS1 10627 -0.004 0.35 NO
49 COL4A4 COL4A4 COL4A4 11063 -0.01 0.32 NO
50 SPTAN1 SPTAN1 SPTAN1 11096 -0.01 0.32 NO
51 HRAS HRAS HRAS 11904 -0.022 0.28 NO
52 YWHAB YWHAB YWHAB 12066 -0.024 0.27 NO
53 NRAS NRAS NRAS 12115 -0.025 0.27 NO
54 ST8SIA4 ST8SIA4 ST8SIA4 12746 -0.035 0.24 NO
55 GRB2 GRB2 GRB2 13033 -0.04 0.23 NO
56 SPTBN4 SPTBN4 SPTBN4 13532 -0.048 0.21 NO
57 CACNB2 CACNB2 CACNB2 13727 -0.052 0.2 NO
58 MAPK3 MAPK3 MAPK3 13836 -0.055 0.2 NO
59 SPTA1 SPTA1 SPTA1 14280 -0.064 0.18 NO
60 MAP2K1 MAP2K1 MAP2K1 14342 -0.066 0.18 NO
61 PRNP PRNP PRNP 14432 -0.068 0.18 NO
62 COL4A3 COL4A3 COL4A3 14962 -0.08 0.16 NO
63 FYN FYN FYN 16837 -0.17 0.075 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: KEGG LONG TERM POTENTIATION.

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LONG TERM POTENTIATION, 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 MELANOGENESIS

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 GPC2 GPC2 GPC2 194 0.55 0.061 YES
2 UST UST UST 253 0.53 0.13 YES
3 CHST9 CHST9 CHST9 286 0.51 0.19 YES
4 B3GAT1 B3GAT1 B3GAT1 583 0.42 0.23 YES
5 GPC4 GPC4 GPC4 596 0.42 0.28 YES
6 CHSY3 CHSY3 CHSY3 709 0.4 0.33 YES
7 GPC5 GPC5 GPC5 729 0.39 0.38 YES
8 CSPG4 CSPG4 CSPG4 848 0.37 0.42 YES
9 BCAN BCAN BCAN 1031 0.34 0.46 YES
10 GPC6 GPC6 GPC6 1253 0.31 0.49 YES
11 B3GAT2 B3GAT2 B3GAT2 1302 0.3 0.52 YES
12 SDC2 SDC2 SDC2 1324 0.3 0.56 YES
13 BGN BGN BGN 1920 0.24 0.56 YES
14 VCAN VCAN VCAN 2350 0.21 0.56 YES
15 CHST13 CHST13 CHST13 2917 0.18 0.56 YES
16 SDC1 SDC1 SDC1 3260 0.16 0.56 YES
17 GPC1 GPC1 GPC1 3427 0.16 0.57 YES
18 GPC3 GPC3 GPC3 3521 0.15 0.58 YES
19 CHSY1 CHSY1 CHSY1 3713 0.14 0.59 YES
20 CHST14 CHST14 CHST14 4183 0.12 0.58 YES
21 NCAN NCAN NCAN 4205 0.12 0.6 YES
22 DCN DCN DCN 4617 0.11 0.59 NO
23 HSPG2 HSPG2 HSPG2 4907 0.096 0.59 NO
24 B3GALT6 B3GALT6 B3GALT6 5256 0.087 0.58 NO
25 CHST11 CHST11 CHST11 6251 0.064 0.53 NO
26 CSGALNACT2 CSGALNACT2 CSGALNACT2 6611 0.056 0.52 NO
27 ARSB ARSB ARSB 6634 0.056 0.52 NO
28 GXYLT1 GXYLT1 GXYLT1 6980 0.05 0.51 NO
29 CHST3 CHST3 CHST3 7022 0.049 0.52 NO
30 SDC3 SDC3 SDC3 7986 0.033 0.47 NO
31 CHST12 CHST12 CHST12 8637 0.023 0.44 NO
32 CHST15 CHST15 CHST15 8909 0.02 0.42 NO
33 IDS IDS IDS 9049 0.018 0.42 NO
34 SDC4 SDC4 SDC4 9276 0.015 0.41 NO
35 B3GAT3 B3GAT3 B3GAT3 9916 0.0059 0.37 NO
36 IDUA IDUA IDUA 9987 0.0048 0.37 NO
37 CHPF2 CHPF2 CHPF2 10034 0.0043 0.37 NO
38 AGRN AGRN AGRN 10246 0.00098 0.36 NO
39 B4GALT7 B4GALT7 B4GALT7 10282 0.00051 0.35 NO
40 DSE DSE DSE 11082 -0.01 0.31 NO
41 CHPF CHPF CHPF 12621 -0.033 0.23 NO
42 GXYLT2 GXYLT2 GXYLT2 12868 -0.037 0.22 NO
43 HEXA HEXA HEXA 13981 -0.058 0.17 NO
44 CHST7 CHST7 CHST7 14707 -0.074 0.14 NO
45 HEXB HEXB HEXB 15555 -0.098 0.1 NO
46 HYAL1 HYAL1 HYAL1 15639 -0.1 0.11 NO
47 CSGALNACT1 CSGALNACT1 CSGALNACT1 17298 -0.21 0.049 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: KEGG MELANOGENESIS.

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

genes ES table in pathway: KEGG BASAL CELL CARCINOMA

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 PRKAR2B PRKAR2B PRKAR2B 1418 0.29 -0.0062 YES
2 AZI1 AZI1 AZI1 2251 0.22 0.0025 YES
3 CENPJ CENPJ CENPJ 2615 0.2 0.031 YES
4 PLK4 PLK4 PLK4 2860 0.18 0.063 YES
5 TUBA1A TUBA1A TUBA1A 2978 0.18 0.1 YES
6 CDK1 CDK1 CDK1 3256 0.16 0.13 YES
7 PLK1 PLK1 PLK1 3266 0.16 0.16 YES
8 NEK2 NEK2 NEK2 3337 0.16 0.2 YES
9 ALMS1 ALMS1 ALMS1 3681 0.14 0.22 YES
10 CEP192 CEP192 CEP192 4133 0.12 0.22 YES
11 CSNK1E CSNK1E CSNK1E 4902 0.097 0.2 YES
12 CEP76 CEP76 CEP76 4962 0.095 0.22 YES
13 PCNT PCNT PCNT 5034 0.093 0.24 YES
14 CLASP1 CLASP1 CLASP1 5234 0.088 0.26 YES
15 CEP70 CEP70 CEP70 5907 0.072 0.24 YES
16 CCNB1 CCNB1 CCNB1 5929 0.071 0.25 YES
17 CEP135 CEP135 CEP135 5974 0.07 0.27 YES
18 CEP72 CEP72 CEP72 6010 0.069 0.28 YES
19 PRKACA PRKACA PRKACA 6057 0.068 0.3 YES
20 OFD1 OFD1 OFD1 6230 0.064 0.3 YES
21 TUBGCP3 TUBGCP3 TUBGCP3 6270 0.064 0.32 YES
22 NUMA1 NUMA1 NUMA1 6309 0.063 0.33 YES
23 CEP57 CEP57 CEP57 6431 0.06 0.34 YES
24 TUBGCP5 TUBGCP5 TUBGCP5 6452 0.06 0.35 YES
25 CKAP5 CKAP5 CKAP5 6453 0.06 0.37 YES
26 CEP250 CEP250 CEP250 6457 0.059 0.38 YES
27 SSNA1 SSNA1 SSNA1 6624 0.056 0.39 YES
28 CDK5RAP2 CDK5RAP2 CDK5RAP2 6683 0.055 0.4 YES
29 PPP2R1A PPP2R1A PPP2R1A 6739 0.054 0.41 YES
30 TUBGCP6 TUBGCP6 TUBGCP6 6826 0.053 0.42 YES
31 TUBG2 TUBG2 TUBG2 7088 0.048 0.41 NO
32 PAFAH1B1 PAFAH1B1 PAFAH1B1 7455 0.042 0.4 NO
33 CEP164 CEP164 CEP164 7615 0.039 0.4 NO
34 TUBB TUBB TUBB 7988 0.033 0.39 NO
35 YWHAE YWHAE YWHAE 8149 0.03 0.39 NO
36 NINL NINL NINL 8325 0.028 0.39 NO
37 DCTN2 DCTN2 DCTN2 8544 0.024 0.38 NO
38 PCM1 PCM1 PCM1 8695 0.022 0.38 NO
39 TUBGCP2 TUBGCP2 TUBGCP2 9078 0.017 0.36 NO
40 DCTN1 DCTN1 DCTN1 9226 0.015 0.36 NO
41 NEDD1 NEDD1 NEDD1 9504 0.011 0.35 NO
42 MAPRE1 MAPRE1 MAPRE1 9656 0.0094 0.34 NO
43 DYNC1I2 DYNC1I2 DYNC1I2 10183 0.0018 0.31 NO
44 DYNLL1 DYNLL1 DYNLL1 10362 -0.00054 0.3 NO
45 CEP290 CEP290 CEP290 10428 -0.0013 0.3 NO
46 SDCCAG8 SDCCAG8 SDCCAG8 10540 -0.0027 0.29 NO
47 AKAP9 AKAP9 AKAP9 10715 -0.0053 0.28 NO
48 CSNK1D CSNK1D CSNK1D 11391 -0.015 0.25 NO
49 CEP63 CEP63 CEP63 12321 -0.028 0.21 NO
50 HAUS2 HAUS2 HAUS2 12466 -0.031 0.21 NO
51 HSP90AA1 HSP90AA1 HSP90AA1 12486 -0.031 0.21 NO
52 DYNC1H1 DYNC1H1 DYNC1H1 12575 -0.032 0.22 NO
53 DCTN3 DCTN3 DCTN3 12831 -0.036 0.21 NO
54 TUBG1 TUBG1 TUBG1 12976 -0.038 0.21 NO
55 YWHAG YWHAG YWHAG 13261 -0.044 0.21 NO
56 ACTR1A ACTR1A ACTR1A 13285 -0.044 0.22 NO
57 FGFR1OP FGFR1OP FGFR1OP 13831 -0.054 0.2 NO
58 CETN2 CETN2 CETN2 14532 -0.07 0.18 NO
59 TUBA4A TUBA4A TUBA4A 15147 -0.085 0.17 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: KEGG BASAL CELL CARCINOMA.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASAL CELL CARCINOMA, 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 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 TGFB2 TGFB2 TGFB2 61 0.67 0.13 YES
2 CHRD CHRD CHRD 211 0.54 0.22 YES
3 BMP7 BMP7 BMP7 241 0.53 0.32 YES
4 SMAD6 SMAD6 SMAD6 582 0.42 0.38 YES
5 NKX2-5 NKX2-5 NKX2-5 749 0.39 0.45 YES
6 BMP5 BMP5 BMP5 885 0.37 0.51 YES
7 GATA4 GATA4 GATA4 1318 0.3 0.55 YES
8 TGFB3 TGFB3 TGFB3 1429 0.29 0.6 YES
9 FZD1 FZD1 FZD1 3261 0.16 0.53 NO
10 BMPR2 BMPR2 BMPR2 3465 0.15 0.55 NO
11 NPPB NPPB NPPB 3905 0.13 0.55 NO
12 BMPR1A BMPR1A BMPR1A 4570 0.11 0.53 NO
13 MAP3K7 MAP3K7 MAP3K7 4965 0.095 0.53 NO
14 NOG NOG NOG 5399 0.083 0.52 NO
15 TGFBR3 TGFBR3 TGFBR3 5571 0.079 0.52 NO
16 NPPA NPPA NPPA 5654 0.078 0.54 NO
17 SMAD4 SMAD4 SMAD4 6012 0.069 0.53 NO
18 CTNNB1 CTNNB1 CTNNB1 6448 0.06 0.52 NO
19 TGFB1 TGFB1 TGFB1 6618 0.056 0.52 NO
20 SMAD5 SMAD5 SMAD5 6687 0.055 0.52 NO
21 HNF1A HNF1A HNF1A 6703 0.055 0.53 NO
22 WNT1 WNT1 WNT1 7002 0.049 0.53 NO
23 BMP4 BMP4 BMP4 7173 0.046 0.53 NO
24 MEF2C MEF2C MEF2C 7697 0.038 0.5 NO
25 ACVR1 ACVR1 ACVR1 8591 0.023 0.46 NO
26 DVL1 DVL1 DVL1 8800 0.021 0.45 NO
27 MYL2 MYL2 MYL2 8953 0.019 0.45 NO
28 GSK3B GSK3B GSK3B 10205 0.0015 0.38 NO
29 TGFBR1 TGFBR1 TGFBR1 10411 -0.0012 0.37 NO
30 SMAD1 SMAD1 SMAD1 11308 -0.013 0.32 NO
31 AXIN1 AXIN1 AXIN1 11831 -0.021 0.3 NO
32 RFC1 RFC1 RFC1 11926 -0.022 0.3 NO
33 APC APC APC 13105 -0.041 0.24 NO
34 TGFBR2 TGFBR2 TGFBR2 13298 -0.044 0.24 NO
35 ATF2 ATF2 ATF2 13770 -0.053 0.22 NO
36 BMP2 BMP2 BMP2 15918 -0.11 0.12 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 ALK PATHWAY.

Figure S72.  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: ST WNT BETA CATENIN 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 SFRP5 SFRP5 SFRP5 92 0.62 0.027 YES
2 CAMK2B CAMK2B CAMK2B 105 0.61 0.058 YES
3 WNT11 WNT11 WNT11 158 0.57 0.084 YES
4 NKD1 NKD1 NKD1 167 0.57 0.11 YES
5 NKD2 NKD2 NKD2 295 0.51 0.13 YES
6 NFATC4 NFATC4 NFATC4 368 0.48 0.15 YES
7 WNT6 WNT6 WNT6 403 0.47 0.18 YES
8 WNT5B WNT5B WNT5B 581 0.42 0.19 YES
9 CXXC4 CXXC4 CXXC4 587 0.42 0.21 YES
10 WNT10B WNT10B WNT10B 815 0.38 0.22 YES
11 SFRP1 SFRP1 SFRP1 909 0.36 0.23 YES
12 FZD10 FZD10 FZD10 927 0.36 0.25 YES
13 APC2 APC2 APC2 976 0.35 0.26 YES
14 PRICKLE1 PRICKLE1 PRICKLE1 1032 0.34 0.28 YES
15 LEF1 LEF1 LEF1 1105 0.33 0.29 YES
16 FZD8 FZD8 FZD8 1110 0.33 0.31 YES
17 FZD3 FZD3 FZD3 1114 0.33 0.32 YES
18 MAPK10 MAPK10 MAPK10 1145 0.33 0.34 YES
19 WIF1 WIF1 WIF1 1215 0.32 0.35 YES
20 FZD2 FZD2 FZD2 1363 0.3 0.36 YES
21 PRKCG PRKCG PRKCG 1467 0.28 0.37 YES
22 DAAM2 DAAM2 DAAM2 1480 0.28 0.38 YES
23 TCF7L1 TCF7L1 TCF7L1 1703 0.26 0.38 YES
24 LRP6 LRP6 LRP6 1707 0.26 0.4 YES
25 VANGL2 VANGL2 VANGL2 1965 0.24 0.4 YES
26 RAC3 RAC3 RAC3 2021 0.24 0.4 YES
27 SFRP2 SFRP2 SFRP2 2073 0.23 0.41 YES
28 TBL1Y TBL1Y TBL1Y 2098 0.23 0.42 YES
29 TCF7 TCF7 TCF7 2209 0.22 0.43 YES
30 WNT9A WNT9A WNT9A 2335 0.22 0.43 YES
31 FZD7 FZD7 FZD7 2345 0.21 0.44 YES
32 DKK2 DKK2 DKK2 2442 0.21 0.45 YES
33 WNT7B WNT7B WNT7B 2619 0.2 0.45 YES
34 PLCB4 PLCB4 PLCB4 2644 0.2 0.46 YES
35 SOX17 SOX17 SOX17 2683 0.19 0.47 YES
36 CAMK2A CAMK2A CAMK2A 2712 0.19 0.48 YES
37 WNT8B WNT8B WNT8B 2953 0.18 0.47 YES
38 WNT7A WNT7A WNT7A 3021 0.17 0.48 YES
39 FZD9 FZD9 FZD9 3184 0.17 0.48 YES
40 FZD1 FZD1 FZD1 3261 0.16 0.48 YES
41 FZD4 FZD4 FZD4 3444 0.15 0.48 YES
42 CTNNBIP1 CTNNBIP1 CTNNBIP1 3480 0.15 0.48 YES
43 TBL1X TBL1X TBL1X 3829 0.14 0.47 NO
44 NFATC1 NFATC1 NFATC1 3938 0.13 0.47 NO
45 WNT3A WNT3A WNT3A 3991 0.13 0.48 NO
46 AXIN2 AXIN2 AXIN2 4107 0.12 0.48 NO
47 SMAD3 SMAD3 SMAD3 4173 0.12 0.48 NO
48 CAMK2G CAMK2G CAMK2G 4362 0.11 0.47 NO
49 CCND1 CCND1 CCND1 4492 0.11 0.47 NO
50 TP53 TP53 TP53 4609 0.11 0.47 NO
51 DVL2 DVL2 DVL2 4811 0.1 0.47 NO
52 CSNK1E CSNK1E CSNK1E 4902 0.097 0.47 NO
53 CREBBP CREBBP CREBBP 4912 0.096 0.47 NO
54 MAP3K7 MAP3K7 MAP3K7 4965 0.095 0.47 NO
55 PPP3CA PPP3CA PPP3CA 5231 0.088 0.46 NO
56 FRAT1 FRAT1 FRAT1 5312 0.086 0.46 NO
57 WNT2B WNT2B WNT2B 5518 0.081 0.46 NO
58 MMP7 MMP7 MMP7 5584 0.079 0.46 NO
59 WNT10A WNT10A WNT10A 5748 0.075 0.45 NO
60 SMAD4 SMAD4 SMAD4 6012 0.069 0.44 NO
61 PRKX PRKX PRKX 6045 0.069 0.44 NO
62 PRKACA PRKACA PRKACA 6057 0.068 0.44 NO
63 SFRP4 SFRP4 SFRP4 6260 0.064 0.44 NO
64 CTNNB1 CTNNB1 CTNNB1 6448 0.06 0.43 NO
65 PPP2R1A PPP2R1A PPP2R1A 6739 0.054 0.42 NO
66 ROCK1 ROCK1 ROCK1 6765 0.054 0.42 NO
67 PPARD PPARD PPARD 6856 0.052 0.41 NO
68 PPP2R5D PPP2R5D PPP2R5D 6993 0.05 0.41 NO
69 WNT1 WNT1 WNT1 7002 0.049 0.41 NO
70 CHD8 CHD8 CHD8 7066 0.048 0.41 NO
71 SIAH1 SIAH1 SIAH1 7162 0.047 0.41 NO
72 SMAD2 SMAD2 SMAD2 7337 0.044 0.4 NO
73 CAMK2D CAMK2D CAMK2D 7449 0.042 0.4 NO
74 PPP3CB PPP3CB PPP3CB 7887 0.034 0.37 NO
75 FZD6 FZD6 FZD6 7931 0.034 0.37 NO
76 EP300 EP300 EP300 8090 0.031 0.37 NO
77 PPP3R1 PPP3R1 PPP3R1 8286 0.028 0.36 NO
78 CTBP1 CTBP1 CTBP1 8422 0.026 0.35 NO
79 PPP2CB PPP2CB PPP2CB 8465 0.025 0.35 NO
80 CSNK2A1 CSNK2A1 CSNK2A1 8504 0.025 0.35 NO
81 NFATC2 NFATC2 NFATC2 8607 0.023 0.34 NO
82 PPP2R5B PPP2R5B PPP2R5B 8625 0.023 0.34 NO
83 WNT16 WNT16 WNT16 8633 0.023 0.34 NO
84 NFATC3 NFATC3 NFATC3 8666 0.022 0.34 NO
85 NFAT5 NFAT5 NFAT5 8789 0.021 0.34 NO
86 DVL1 DVL1 DVL1 8800 0.021 0.34 NO
87 PPP2R5C PPP2R5C PPP2R5C 9014 0.018 0.33 NO
88 CSNK2A2 CSNK2A2 CSNK2A2 9232 0.015 0.32 NO
89 CACYBP CACYBP CACYBP 9485 0.012 0.3 NO
90 PRKACB PRKACB PRKACB 9537 0.011 0.3 NO
91 CUL1 CUL1 CUL1 9542 0.011 0.3 NO
92 NLK NLK NLK 9710 0.0087 0.29 NO
93 LRP5 LRP5 LRP5 9911 0.0059 0.28 NO
94 GSK3B GSK3B GSK3B 10205 0.0015 0.27 NO
95 RAC1 RAC1 RAC1 10220 0.0013 0.27 NO
96 VANGL1 VANGL1 VANGL1 10412 -0.0012 0.26 NO
97 PPP2R5E PPP2R5E PPP2R5E 10461 -0.0017 0.25 NO
98 MAPK8 MAPK8 MAPK8 10610 -0.0038 0.24 NO
99 RUVBL1 RUVBL1 RUVBL1 10762 -0.0059 0.24 NO
100 CTBP2 CTBP2 CTBP2 10877 -0.0076 0.23 NO
101 FBXW11 FBXW11 FBXW11 11065 -0.01 0.22 NO
102 CSNK2B CSNK2B CSNK2B 11217 -0.012 0.21 NO
103 WNT5A WNT5A WNT5A 11268 -0.013 0.21 NO
104 JUN JUN JUN 11364 -0.014 0.21 NO
105 CSNK1A1 CSNK1A1 CSNK1A1 11368 -0.014 0.21 NO
106 PRICKLE2 PRICKLE2 PRICKLE2 11581 -0.017 0.2 NO
107 FOSL1 FOSL1 FOSL1 11743 -0.02 0.19 NO
108 PSEN1 PSEN1 PSEN1 11754 -0.02 0.19 NO
109 TBL1XR1 TBL1XR1 TBL1XR1 11759 -0.02 0.19 NO
110 AXIN1 AXIN1 AXIN1 11831 -0.021 0.19 NO
111 SKP1 SKP1 SKP1 11886 -0.022 0.18 NO
112 PPP2R5A PPP2R5A PPP2R5A 11928 -0.022 0.18 NO
113 RBX1 RBX1 RBX1 12075 -0.024 0.18 NO
114 BTRC BTRC BTRC 12124 -0.025 0.18 NO
115 ROCK2 ROCK2 ROCK2 12510 -0.031 0.16 NO
116 CHP2 CHP2 CHP2 12524 -0.032 0.16 NO
117 PPP2R1B PPP2R1B PPP2R1B 12906 -0.038 0.14 NO
118 WNT4 WNT4 WNT4 12921 -0.038 0.14 NO
119 PLCB3 PLCB3 PLCB3 12923 -0.038 0.14 NO
120 APC APC APC 13105 -0.041 0.13 NO
121 FZD5 FZD5 FZD5 13177 -0.042 0.13 NO
122 DKK1 DKK1 DKK1 13265 -0.044 0.13 NO
123 PPP2CA PPP2CA PPP2CA 13346 -0.045 0.13 NO
124 RHOA RHOA RHOA 13360 -0.046 0.13 NO
125 PORCN PORCN PORCN 13481 -0.048 0.12 NO
126 CCND3 CCND3 CCND3 13522 -0.048 0.12 NO
127 MAPK9 MAPK9 MAPK9 13611 -0.05 0.12 NO
128 PPP3CC PPP3CC PPP3CC 13753 -0.053 0.12 NO
129 TCF7L2 TCF7L2 TCF7L2 14097 -0.06 0.1 NO
130 FRAT2 FRAT2 FRAT2 14551 -0.07 0.079 NO
131 PRKCA PRKCA PRKCA 14773 -0.075 0.071 NO
132 SENP2 SENP2 SENP2 14801 -0.076 0.073 NO
133 DVL3 DVL3 DVL3 14829 -0.077 0.076 NO
134 PLCB1 PLCB1 PLCB1 15271 -0.089 0.056 NO
135 PLCB2 PLCB2 PLCB2 15291 -0.09 0.059 NO
136 CCND2 CCND2 CCND2 15578 -0.099 0.049 NO
137 RAC2 RAC2 RAC2 16241 -0.13 0.019 NO
138 CSNK1A1L CSNK1A1L CSNK1A1L 16587 -0.15 0.0073 NO
139 MYC MYC MYC 16802 -0.17 0.004 NO
140 WNT3 WNT3 WNT3 16816 -0.17 0.012 NO
141 WNT9B WNT9B WNT9B 16829 -0.17 0.02 NO
142 CHP CHP CHP 17043 -0.18 0.018 NO
143 DAAM1 DAAM1 DAAM1 17531 -0.25 0.0033 NO
144 PRKCB PRKCB PRKCB 17729 -0.29 0.0071 NO
145 WNT2 WNT2 WNT2 17958 -0.36 0.013 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: ST WNT BETA CATENIN PATHWAY.

Figure S74.  Get High-res Image For the top 5 core enriched genes in the pathway: ST WNT BETA CATENIN 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: PID EPHBFWDPATHWAY

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 TGFB2 TGFB2 TGFB2 61 0.67 0.042 YES
2 INHBC INHBC INHBC 107 0.61 0.081 YES
3 LEFTY1 LEFTY1 LEFTY1 162 0.57 0.12 YES
4 CHRD CHRD CHRD 211 0.54 0.15 YES
5 BMP7 BMP7 BMP7 241 0.53 0.18 YES
6 INHBE INHBE INHBE 247 0.53 0.22 YES
7 LEFTY2 LEFTY2 LEFTY2 249 0.53 0.26 YES
8 BMP6 BMP6 BMP6 378 0.48 0.28 YES
9 AMH AMH AMH 463 0.46 0.31 YES
10 NODAL NODAL NODAL 488 0.45 0.34 YES
11 SMAD6 SMAD6 SMAD6 582 0.42 0.36 YES
12 GDF7 GDF7 GDF7 700 0.4 0.38 YES
13 LTBP1 LTBP1 LTBP1 718 0.4 0.4 YES
14 AMHR2 AMHR2 AMHR2 827 0.38 0.42 YES
15 BMP5 BMP5 BMP5 885 0.37 0.45 YES
16 COMP COMP COMP 1135 0.33 0.45 YES
17 BMPR1B BMPR1B BMPR1B 1217 0.32 0.47 YES
18 FST FST FST 1360 0.3 0.48 YES
19 TGFB3 TGFB3 TGFB3 1429 0.29 0.5 YES
20 THBS4 THBS4 THBS4 1612 0.27 0.51 YES
21 ID3 ID3 ID3 1619 0.27 0.52 YES
22 BMP8A BMP8A BMP8A 1663 0.27 0.54 YES
23 ID1 ID1 ID1 1696 0.26 0.56 YES
24 SMAD7 SMAD7 SMAD7 1967 0.24 0.56 YES
25 INHBA INHBA INHBA 2141 0.23 0.56 YES
26 PITX2 PITX2 PITX2 2255 0.22 0.57 YES
27 BMP8B BMP8B BMP8B 2317 0.22 0.58 YES
28 SMAD9 SMAD9 SMAD9 2369 0.21 0.6 YES
29 GDF6 GDF6 GDF6 2618 0.2 0.59 NO
30 THBS1 THBS1 THBS1 3157 0.17 0.58 NO
31 BMPR2 BMPR2 BMPR2 3465 0.15 0.57 NO
32 ACVRL1 ACVRL1 ACVRL1 3832 0.14 0.56 NO
33 SMAD3 SMAD3 SMAD3 4173 0.12 0.55 NO
34 ZFYVE9 ZFYVE9 ZFYVE9 4276 0.12 0.55 NO
35 RBL1 RBL1 RBL1 4522 0.11 0.54 NO
36 BMPR1A BMPR1A BMPR1A 4570 0.11 0.55 NO
37 DCN DCN DCN 4617 0.11 0.55 NO
38 CREBBP CREBBP CREBBP 4912 0.096 0.54 NO
39 NOG NOG NOG 5399 0.083 0.52 NO
40 ACVR2B ACVR2B ACVR2B 6001 0.07 0.49 NO
41 SMAD4 SMAD4 SMAD4 6012 0.069 0.5 NO
42 TGFB1 TGFB1 TGFB1 6618 0.056 0.47 NO
43 ACVR2A ACVR2A ACVR2A 6636 0.056 0.47 NO
44 SMAD5 SMAD5 SMAD5 6687 0.055 0.47 NO
45 PPP2R1A PPP2R1A PPP2R1A 6739 0.054 0.47 NO
46 ROCK1 ROCK1 ROCK1 6765 0.054 0.48 NO
47 TFDP1 TFDP1 TFDP1 7006 0.049 0.46 NO
48 BMP4 BMP4 BMP4 7173 0.046 0.46 NO
49 SP1 SP1 SP1 7220 0.046 0.46 NO
50 THBS2 THBS2 THBS2 7225 0.046 0.46 NO
51 SMAD2 SMAD2 SMAD2 7337 0.044 0.46 NO
52 EP300 EP300 EP300 8090 0.031 0.42 NO
53 PPP2CB PPP2CB PPP2CB 8465 0.025 0.4 NO
54 ACVR1 ACVR1 ACVR1 8591 0.023 0.4 NO
55 SMURF1 SMURF1 SMURF1 8910 0.02 0.38 NO
56 THBS3 THBS3 THBS3 8944 0.019 0.38 NO
57 CUL1 CUL1 CUL1 9542 0.011 0.35 NO
58 E2F4 E2F4 E2F4 10349 -0.00036 0.3 NO
59 MAPK1 MAPK1 MAPK1 10386 -0.00086 0.3 NO
60 TGFBR1 TGFBR1 TGFBR1 10411 -0.0012 0.3 NO
61 ZFYVE16 ZFYVE16 ZFYVE16 11035 -0.0096 0.26 NO
62 SMURF2 SMURF2 SMURF2 11277 -0.013 0.25 NO
63 SMAD1 SMAD1 SMAD1 11308 -0.013 0.25 NO
64 ACVR1C ACVR1C ACVR1C 11710 -0.019 0.23 NO
65 SKP1 SKP1 SKP1 11886 -0.022 0.22 NO
66 RBX1 RBX1 RBX1 12075 -0.024 0.21 NO
67 ID4 ID4 ID4 12282 -0.028 0.2 NO
68 ROCK2 ROCK2 ROCK2 12510 -0.031 0.19 NO
69 PPP2R1B PPP2R1B PPP2R1B 12906 -0.038 0.18 NO
70 TGFBR2 TGFBR2 TGFBR2 13298 -0.044 0.16 NO
71 E2F5 E2F5 E2F5 13330 -0.045 0.16 NO
72 RPS6KB2 RPS6KB2 RPS6KB2 13333 -0.045 0.16 NO
73 PPP2CA PPP2CA PPP2CA 13346 -0.045 0.16 NO
74 RHOA RHOA RHOA 13360 -0.046 0.16 NO
75 RPS6KB1 RPS6KB1 RPS6KB1 13621 -0.05 0.15 NO
76 MAPK3 MAPK3 MAPK3 13836 -0.055 0.15 NO
77 RBL2 RBL2 RBL2 14122 -0.061 0.13 NO
78 BMP2 BMP2 BMP2 15918 -0.11 0.043 NO
79 INHBB INHBB INHBB 16014 -0.12 0.046 NO
80 ID2 ID2 ID2 16703 -0.16 0.018 NO
81 CDKN2B CDKN2B CDKN2B 16704 -0.16 0.029 NO
82 MYC MYC MYC 16802 -0.17 0.035 NO
83 GDF5 GDF5 GDF5 16929 -0.18 0.04 NO
84 IFNG IFNG IFNG 17268 -0.21 0.035 NO
85 TNF TNF TNF 17461 -0.24 0.04 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: PID EPHBFWDPATHWAY.

Figure S76.  Get High-res Image For the top 5 core enriched genes in the pathway: PID EPHBFWDPATHWAY, 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: PID P75NTRPATHWAY

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 GLI1 GLI1 GLI1 91 0.62 0.12 YES
2 PTCH1 PTCH1 PTCH1 202 0.55 0.22 YES
3 GNAO1 GNAO1 GNAO1 365 0.48 0.3 YES
4 SMO SMO SMO 1272 0.31 0.32 YES
5 GLI2 GLI2 GLI2 1883 0.25 0.33 YES
6 GNAZ GNAZ GNAZ 2254 0.22 0.35 YES
7 RAB23 RAB23 RAB23 2548 0.2 0.38 YES
8 SSPO SSPO SSPO 2839 0.18 0.4 YES
9 SHH SHH SHH 3141 0.17 0.41 YES
10 HDAC2 HDAC2 HDAC2 3743 0.14 0.41 YES
11 GLI3 GLI3 GLI3 4289 0.12 0.4 YES
12 IFT88 IFT88 IFT88 4487 0.11 0.41 YES
13 CSNK1E CSNK1E CSNK1E 4902 0.097 0.41 YES
14 CREBBP CREBBP CREBBP 4912 0.096 0.43 YES
15 SIN3B SIN3B SIN3B 5085 0.091 0.43 YES
16 STK36 STK36 STK36 5116 0.09 0.45 YES
17 KIF3A KIF3A KIF3A 5958 0.071 0.42 NO
18 PRKACA PRKACA PRKACA 6057 0.068 0.43 NO
19 HDAC1 HDAC1 HDAC1 6188 0.066 0.43 NO
20 CSNK1G2 CSNK1G2 CSNK1G2 6798 0.053 0.41 NO
21 MTSS1 MTSS1 MTSS1 6903 0.051 0.41 NO
22 SIN3A SIN3A SIN3A 7031 0.049 0.42 NO
23 AKT1 AKT1 AKT1 7187 0.046 0.42 NO
24 GNB1 GNB1 GNB1 8228 0.029 0.36 NO
25 GNG2 GNG2 GNG2 8356 0.027 0.36 NO
26 XPO1 XPO1 XPO1 8413 0.026 0.36 NO
27 SUFU SUFU SUFU 9172 0.016 0.33 NO
28 SPOP SPOP SPOP 9387 0.013 0.32 NO
29 CSNK1G3 CSNK1G3 CSNK1G3 9739 0.0082 0.3 NO
30 SAP18 SAP18 SAP18 9797 0.0074 0.3 NO
31 RBBP4 RBBP4 RBBP4 10002 0.0046 0.29 NO
32 GSK3B GSK3B GSK3B 10205 0.0015 0.28 NO
33 RBBP7 RBBP7 RBBP7 10871 -0.0076 0.24 NO
34 FBXW11 FBXW11 FBXW11 11065 -0.01 0.23 NO
35 CSNK1A1 CSNK1A1 CSNK1A1 11368 -0.014 0.22 NO
36 CSNK1D CSNK1D CSNK1D 11391 -0.015 0.22 NO
37 PRKCD PRKCD PRKCD 11701 -0.019 0.21 NO
38 GNAI2 GNAI2 GNAI2 12412 -0.03 0.17 NO
39 IFT172 IFT172 IFT172 12987 -0.039 0.15 NO
40 CSNK1G1 CSNK1G1 CSNK1G1 13148 -0.042 0.15 NO
41 SAP30 SAP30 SAP30 13372 -0.046 0.15 NO
42 PIAS1 PIAS1 PIAS1 13458 -0.047 0.15 NO
43 GNAI3 GNAI3 GNAI3 13617 -0.05 0.15 NO
44 MAP2K1 MAP2K1 MAP2K1 14342 -0.066 0.12 NO
45 ARRB2 ARRB2 ARRB2 15069 -0.083 0.1 NO
46 FOXA2 FOXA2 FOXA2 15206 -0.087 0.11 NO
47 LGALS3 LGALS3 LGALS3 15910 -0.11 0.094 NO
48 GNAI1 GNAI1 GNAI1 16753 -0.16 0.079 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: PID P75NTRPATHWAY.

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: PID P75NTRPATHWAY, 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: PID HEDGEHOG GLIPATHWAY

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 GRIK4 GRIK4 GRIK4 119 0.6 0.11 YES
2 GRIK3 GRIK3 GRIK3 579 0.43 0.16 YES
3 GNGT1 GNGT1 GNGT1 601 0.42 0.24 YES
4 NCALD NCALD NCALD 665 0.4 0.31 YES
5 GNG13 GNG13 GNG13 894 0.36 0.37 YES
6 GNB3 GNB3 GNB3 1068 0.34 0.42 YES
7 GRIK1 GRIK1 GRIK1 1124 0.33 0.48 YES
8 GRIK5 GRIK5 GRIK5 1276 0.31 0.53 YES
9 GNG8 GNG8 GNG8 1333 0.3 0.59 YES
10 GNG4 GNG4 GNG4 1702 0.26 0.62 YES
11 GNG3 GNG3 GNG3 2985 0.18 0.58 NO
12 DLG3 DLG3 DLG3 3570 0.15 0.57 NO
13 GNB5 GNB5 GNB5 3934 0.13 0.58 NO
14 GRIK2 GRIK2 GRIK2 4859 0.098 0.55 NO
15 CALM1 CALM1 CALM1 5854 0.073 0.51 NO
16 GNG11 GNG11 GNG11 6882 0.052 0.46 NO
17 CALM3 CALM3 CALM3 7960 0.033 0.41 NO
18 GNB1 GNB1 GNB1 8228 0.029 0.4 NO
19 GNG2 GNG2 GNG2 8356 0.027 0.4 NO
20 GNB4 GNB4 GNB4 8900 0.02 0.37 NO
21 GNG10 GNG10 GNG10 10178 0.0019 0.3 NO
22 GNB2 GNB2 GNB2 10884 -0.0077 0.26 NO
23 GNG12 GNG12 GNG12 11897 -0.022 0.21 NO
24 CALM2 CALM2 CALM2 11969 -0.023 0.21 NO
25 PLCB3 PLCB3 PLCB3 12923 -0.038 0.17 NO
26 GNG7 GNG7 GNG7 14120 -0.061 0.11 NO
27 DLG1 DLG1 DLG1 14440 -0.068 0.11 NO
28 PLCB1 PLCB1 PLCB1 15271 -0.089 0.078 NO
29 PLCB2 PLCB2 PLCB2 15291 -0.09 0.094 NO
30 GNG5 GNG5 GNG5 15867 -0.11 0.083 NO
31 GNGT2 GNGT2 GNGT2 17472 -0.24 0.04 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: PID HEDGEHOG GLIPATHWAY.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HEDGEHOG GLIPATHWAY, 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.v4.0.symbols.gmt

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

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

GSEA analysis

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

Download Results

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

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