GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in THCA-TP
Thyroid Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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 THCA-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1K64HJ9
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 "THCA-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: 705
Number of samples: 501
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 ] 158
pheno.type: 2 - 4 :[ clus2 ] 169
pheno.type: 3 - 4 :[ clus3 ] 59
pheno.type: 4 - 4 :[ clus4 ] 115

For the expression subtypes of 17991 genes in 502 samples, GSEA found enriched gene sets in each cluster using 501 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG DNA REPLICATION, KEGG LYSOSOME, KEGG CHRONIC MYELOID LEUKEMIA, BIOCARTA G1 PATHWAY, ST PHOSPHOINOSITIDE 3 KINASE PATHWAY, PID TNFPATHWAY, PID ECADHERIN NASCENTAJ PATHWAY, PID BARD1PATHWAY, REACTOME ORC1 REMOVAL FROM CHROMATIN, REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

    • And common core enriched genes are DDX58, HERC5, ISG15, STAT1, UBE2L6, ABI1, ARF6, CCND1, CDH1, CRK

  • clus2

    • Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM, KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG PROPANOATE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG INSULIN SIGNALING PATHWAY, KEGG ADIPOCYTOKINE SIGNALING PATHWAY

    • And common core enriched genes are ACAT1, ALDH1B1, ALDH2, ALDH7A1, ALDH9A1, ECHS1, EHHADH, HADH, OGDH, ABAT

  • clus3

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG PURINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG GLUTATHIONE METABOLISM

    • And common core enriched genes are PSMA8, PSMB9, B2M, HLA-A, PSMB10, PSMB8, PSME2, AP1S2, APOBEC3G, CD247

  • clus4

    • Top enriched gene sets are KEGG NOTCH SIGNALING PATHWAY, KEGG ADHERENS JUNCTION, KEGG THYROID CANCER, PID LKB1 PATHWAY, PID AJDISS 2PATHWAY, PID TRKRPATHWAY, PID NCADHERINPATHWAY, REACTOME CELL CELL COMMUNICATION, REACTOME NEGATIVE REGULATION OF FGFR SIGNALING, REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS

    • And common core enriched genes are CDH2, CLDN1, CLDN10, CLDN11, CLDN15, CLDN16, CLDN19, CLDN2, CLDN5, CLDN6

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 DNA REPLICATION 36 genes.ES.table 0.55 1.6 0.081 0.58 0.89 0.44 0.23 0.34 0.36 0.17
KEGG LYSOSOME 120 genes.ES.table 0.43 1.7 0.052 0.66 0.78 0.42 0.25 0.32 0.34 0.19
KEGG CHRONIC MYELOID LEUKEMIA 73 genes.ES.table 0.45 1.6 0.034 0.59 0.87 0.29 0.19 0.23 0.35 0.18
BIOCARTA G1 PATHWAY 28 genes.ES.table 0.59 1.6 0.014 0.68 0.84 0.32 0.16 0.27 0.38 0.2
ST PHOSPHOINOSITIDE 3 KINASE PATHWAY 37 genes.ES.table 0.55 1.6 0.024 0.6 0.88 0.38 0.21 0.3 0.36 0.18
PID TNFPATHWAY 46 genes.ES.table 0.53 1.8 0.014 0.78 0.52 0.54 0.28 0.4 0.25 0.22
PID ECADHERIN NASCENTAJ PATHWAY 39 genes.ES.table 0.56 2 0.0019 0.21 0.095 0.64 0.3 0.45 0 0.064
PID BARD1PATHWAY 29 genes.ES.table 0.63 1.7 0.014 0.73 0.71 0.62 0.27 0.45 0.35 0.21
REACTOME ORC1 REMOVAL FROM CHROMATIN 59 genes.ES.table 0.49 1.6 0.085 0.58 0.89 0.2 0.17 0.17 0.36 0.18
REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 65 genes.ES.table 0.46 1.8 0.028 1 0.48 0.52 0.3 0.37 0 0.27
genes ES table in pathway: KEGG DNA REPLICATION

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 ITGB7 ITGB7 ITGB7 1306 0.2 0.02 YES
2 TIAM1 TIAM1 TIAM1 1577 0.17 0.086 YES
3 PIK3CA PIK3CA PIK3CA 2003 0.14 0.13 YES
4 IQGAP1 IQGAP1 IQGAP1 2148 0.13 0.18 YES
5 ARF6 ARF6 ARF6 2380 0.12 0.22 YES
6 CCND1 CCND1 CCND1 2713 0.098 0.25 YES
7 CTTN CTTN CTTN 2796 0.094 0.29 YES
8 PIK3R1 PIK3R1 PIK3R1 3011 0.085 0.32 YES
9 NCKAP1 NCKAP1 NCKAP1 3115 0.081 0.35 YES
10 MLLT4 MLLT4 MLLT4 3216 0.078 0.38 YES
11 ENAH ENAH ENAH 3413 0.07 0.4 YES
12 JUP JUP JUP 3621 0.064 0.42 YES
13 ABI1 ABI1 ABI1 3668 0.063 0.45 YES
14 CTNNA1 CTNNA1 CTNNA1 4327 0.048 0.43 YES
15 KLHL20 KLHL20 KLHL20 4501 0.045 0.44 YES
16 CTNNB1 CTNNB1 CTNNB1 4732 0.04 0.45 YES
17 CDH1 CDH1 CDH1 4744 0.04 0.47 YES
18 CSNK2A2 CSNK2A2 CSNK2A2 4876 0.037 0.48 YES
19 SRC SRC SRC 4946 0.036 0.49 YES
20 CRK CRK CRK 5093 0.034 0.5 YES
21 CYFIP2 CYFIP2 CYFIP2 5134 0.033 0.51 YES
22 RAP1A RAP1A RAP1A 5164 0.033 0.53 YES
23 TJP1 TJP1 TJP1 5177 0.032 0.54 YES
24 CSNK2A1 CSNK2A1 CSNK2A1 5212 0.032 0.55 YES
25 WASF2 WASF2 WASF2 5332 0.03 0.56 YES
26 CDC42 CDC42 CDC42 5918 0.021 0.54 NO
27 RHOA RHOA RHOA 6027 0.019 0.54 NO
28 RAC1 RAC1 RAC1 6376 0.015 0.53 NO
29 CSNK2B CSNK2B CSNK2B 6735 0.011 0.51 NO
30 CTNND1 CTNND1 CTNND1 7058 0.0069 0.5 NO
31 RAP1B RAP1B RAP1B 7222 0.0051 0.49 NO
32 VAV2 VAV2 VAV2 7349 0.0036 0.49 NO
33 NME1 NME1 NME1 7835 -0.0017 0.46 NO
34 AP1M1 AP1M1 AP1M1 8455 -0.0091 0.43 NO
35 AKT1 AKT1 AKT1 8784 -0.013 0.42 NO
36 PIP5K1C PIP5K1C PIP5K1C 9380 -0.02 0.4 NO
37 RAPGEF1 RAPGEF1 RAPGEF1 9717 -0.024 0.39 NO
38 DLG1 DLG1 DLG1 10680 -0.037 0.35 NO
39 ITGAE ITGAE ITGAE 14065 -0.12 0.22 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 DNA REPLICATION.

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

genes ES table in pathway: KEGG LYSOSOME

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 IFIT1 IFIT1 IFIT1 1323 0.2 -0.0071 YES
2 STAT1 STAT1 STAT1 1548 0.17 0.039 YES
3 HERC5 HERC5 HERC5 1748 0.15 0.08 YES
4 MX1 MX1 MX1 1855 0.15 0.12 YES
5 ISG15 ISG15 ISG15 1918 0.14 0.17 YES
6 EIF2AK2 EIF2AK2 EIF2AK2 2121 0.13 0.2 YES
7 UBE2L6 UBE2L6 UBE2L6 2575 0.1 0.21 YES
8 NUP155 NUP155 NUP155 2889 0.09 0.22 YES
9 DDX58 DDX58 DDX58 3370 0.072 0.22 YES
10 KPNA2 KPNA2 KPNA2 3536 0.067 0.24 YES
11 JAK1 JAK1 JAK1 3878 0.058 0.24 YES
12 KPNA1 KPNA1 KPNA1 3886 0.058 0.26 YES
13 NUP93 NUP93 NUP93 3942 0.057 0.27 YES
14 NUP188 NUP188 NUP188 4010 0.055 0.29 YES
15 EIF4G1 EIF4G1 EIF4G1 4186 0.051 0.29 YES
16 NUP133 NUP133 NUP133 4315 0.048 0.3 YES
17 SEH1L SEH1L SEH1L 4503 0.045 0.31 YES
18 MX2 MX2 MX2 4631 0.042 0.32 YES
19 NUPL1 NUPL1 NUPL1 4648 0.042 0.33 YES
20 ARIH1 ARIH1 ARIH1 4772 0.039 0.34 YES
21 NUP85 NUP85 NUP85 4789 0.039 0.35 YES
22 KPNA3 KPNA3 KPNA3 4802 0.039 0.36 YES
23 NEDD4 NEDD4 NEDD4 4805 0.038 0.37 YES
24 EIF4A3 EIF4A3 EIF4A3 4900 0.037 0.38 YES
25 FLNB FLNB FLNB 4977 0.036 0.39 YES
26 NUP62 NUP62 NUP62 4989 0.036 0.4 YES
27 UBE2E1 UBE2E1 UBE2E1 5027 0.035 0.41 YES
28 NUP107 NUP107 NUP107 5065 0.034 0.42 YES
29 UBA52 UBA52 UBA52 5090 0.034 0.43 YES
30 EIF4A1 EIF4A1 EIF4A1 5101 0.034 0.44 YES
31 KPNA4 KPNA4 KPNA4 5125 0.033 0.45 YES
32 EIF4A2 EIF4A2 EIF4A2 5280 0.03 0.45 YES
33 TPR TPR TPR 5349 0.03 0.46 YES
34 KPNB1 KPNB1 KPNB1 5395 0.029 0.46 YES
35 NUP153 NUP153 NUP153 6191 0.017 0.43 NO
36 NUP54 NUP54 NUP54 6338 0.016 0.42 NO
37 NUP43 NUP43 NUP43 6504 0.014 0.42 NO
38 RPS27A RPS27A RPS27A 6554 0.013 0.42 NO
39 PIN1 PIN1 PIN1 6924 0.0085 0.4 NO
40 UBA7 UBA7 UBA7 6961 0.008 0.4 NO
41 NUP214 NUP214 NUP214 7123 0.006 0.4 NO
42 NUP205 NUP205 NUP205 7229 0.005 0.39 NO
43 EIF4G2 EIF4G2 EIF4G2 7253 0.0047 0.39 NO
44 IRF3 IRF3 IRF3 7294 0.0041 0.39 NO
45 RANBP2 RANBP2 RANBP2 7303 0.0041 0.39 NO
46 USP18 USP18 USP18 7475 0.0022 0.38 NO
47 MAPK3 MAPK3 MAPK3 7882 -0.0022 0.36 NO
48 PPM1B PPM1B PPM1B 8297 -0.0072 0.34 NO
49 EIF4E3 EIF4E3 EIF4E3 8505 -0.0098 0.33 NO
50 RAE1 RAE1 RAE1 8546 -0.01 0.33 NO
51 POM121 POM121 POM121 8552 -0.01 0.34 NO
52 EIF4E2 EIF4E2 EIF4E2 8839 -0.014 0.33 NO
53 NUP50 NUP50 NUP50 8861 -0.014 0.33 NO
54 TRIM25 TRIM25 TRIM25 9651 -0.024 0.29 NO
55 EIF4E EIF4E EIF4E 9654 -0.024 0.3 NO
56 UBE2N UBE2N UBE2N 9704 -0.024 0.31 NO
57 NUPL2 NUPL2 NUPL2 9807 -0.025 0.31 NO
58 NUP210 NUP210 NUP210 9968 -0.028 0.31 NO
59 NUP37 NUP37 NUP37 10145 -0.03 0.31 NO
60 EIF4G3 EIF4G3 EIF4G3 10820 -0.039 0.29 NO
61 PLCG1 PLCG1 PLCG1 11980 -0.059 0.24 NO
62 NUP88 NUP88 NUP88 11987 -0.059 0.26 NO
63 AAAS AAAS AAAS 12060 -0.061 0.28 NO
64 NUP35 NUP35 NUP35 12209 -0.064 0.29 NO
65 KPNA5 KPNA5 KPNA5 13176 -0.088 0.27 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 LYSOSOME.

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSOSOME, 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 CHRONIC MYELOID LEUKEMIA

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 BIRC3 BIRC3 BIRC3 304 0.42 0.13 YES
2 MAP3K5 MAP3K5 MAP3K5 976 0.24 0.17 YES
3 STAT1 STAT1 STAT1 1548 0.17 0.2 YES
4 CAV1 CAV1 CAV1 1627 0.16 0.25 YES
5 NRK NRK NRK 1930 0.14 0.28 YES
6 BAG4 BAG4 BAG4 2272 0.12 0.3 YES
7 MAP3K7 MAP3K7 MAP3K7 3005 0.086 0.29 YES
8 MAP3K1 MAP3K1 MAP3K1 3019 0.085 0.32 YES
9 TNFRSF1B TNFRSF1B TNFRSF1B 3073 0.083 0.35 YES
10 TNIK TNIK TNIK 3142 0.08 0.37 YES
11 SQSTM1 SQSTM1 SQSTM1 3601 0.065 0.37 YES
12 PRKCI PRKCI PRKCI 3925 0.057 0.37 YES
13 MAP2K3 MAP2K3 MAP2K3 3935 0.057 0.39 YES
14 MAP4K4 MAP4K4 MAP4K4 3950 0.056 0.41 YES
15 TXN TXN TXN 4022 0.055 0.42 YES
16 FADD FADD FADD 4107 0.053 0.43 YES
17 NFKB1 NFKB1 NFKB1 4127 0.052 0.45 YES
18 TNFRSF1A TNFRSF1A TNFRSF1A 4155 0.052 0.47 YES
19 NSMAF NSMAF NSMAF 4181 0.051 0.48 YES
20 RELA RELA RELA 4256 0.049 0.5 YES
21 BIRC2 BIRC2 BIRC2 4359 0.047 0.51 YES
22 TNF TNF TNF 4633 0.042 0.5 YES
23 ADAM17 ADAM17 ADAM17 4675 0.041 0.52 YES
24 GNB2L1 GNB2L1 GNB2L1 4737 0.04 0.53 YES
25 CHUK CHUK CHUK 4936 0.036 0.53 YES
26 MAP3K3 MAP3K3 MAP3K3 5241 0.031 0.52 NO
27 MAP4K3 MAP4K3 MAP4K3 5696 0.024 0.5 NO
28 TAB1 TAB1 TAB1 5708 0.024 0.51 NO
29 MAP4K5 MAP4K5 MAP4K5 6686 0.012 0.46 NO
30 MAP2K7 MAP2K7 MAP2K7 6806 0.0099 0.46 NO
31 TNFAIP3 TNFAIP3 TNFAIP3 6830 0.0096 0.46 NO
32 SMPD1 SMPD1 SMPD1 7809 -0.0014 0.41 NO
33 TRADD TRADD TRADD 7996 -0.0037 0.4 NO
34 TAB2 TAB2 TAB2 8147 -0.0055 0.39 NO
35 CASP8 CASP8 CASP8 8189 -0.0059 0.39 NO
36 PRKCZ PRKCZ PRKCZ 8377 -0.0081 0.38 NO
37 CYLD CYLD CYLD 8393 -0.0083 0.38 NO
38 RIPK1 RIPK1 RIPK1 9231 -0.018 0.34 NO
39 TRAF1 TRAF1 TRAF1 9716 -0.024 0.33 NO
40 SMPD2 SMPD2 SMPD2 10009 -0.028 0.32 NO
41 MADD MADD MADD 10909 -0.041 0.28 NO
42 IKBKB IKBKB IKBKB 11113 -0.044 0.29 NO
43 TRAF2 TRAF2 TRAF2 11234 -0.046 0.3 NO
44 IKBKG IKBKG IKBKG 12054 -0.06 0.27 NO
45 RFFL RFFL RFFL 12332 -0.066 0.28 NO
46 MAP4K2 MAP4K2 MAP4K2 13762 -0.1 0.24 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 CHRONIC MYELOID LEUKEMIA.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHRONIC MYELOID LEUKEMIA, 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 G1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HERC5 HERC5 HERC5 1748 0.15 0.023 YES
2 NLRC5 NLRC5 NLRC5 1904 0.14 0.13 YES
3 ISG15 ISG15 ISG15 1918 0.14 0.24 YES
4 RNF125 RNF125 RNF125 1927 0.14 0.35 YES
5 IFIH1 IFIH1 IFIH1 2220 0.12 0.43 YES
6 UBE2L6 UBE2L6 UBE2L6 2575 0.1 0.49 YES
7 DDX58 DDX58 DDX58 3370 0.072 0.5 YES
8 UBE2D1 UBE2D1 UBE2D1 3520 0.067 0.55 YES
9 ATG12 ATG12 ATG12 4654 0.042 0.52 NO
10 UBA52 UBA52 UBA52 5090 0.034 0.52 NO
11 TBK1 TBK1 TBK1 6018 0.02 0.48 NO
12 NLRX1 NLRX1 NLRX1 6020 0.02 0.5 NO
13 ATG5 ATG5 ATG5 6305 0.016 0.5 NO
14 TRAF3 TRAF3 TRAF3 6319 0.016 0.51 NO
15 TAX1BP1 TAX1BP1 TAX1BP1 6325 0.016 0.52 NO
16 RPS27A RPS27A RPS27A 6554 0.013 0.52 NO
17 TNFAIP3 TNFAIP3 TNFAIP3 6830 0.0096 0.51 NO
18 PIN1 PIN1 PIN1 6924 0.0085 0.51 NO
19 UBA7 UBA7 UBA7 6961 0.008 0.52 NO
20 OTUD5 OTUD5 OTUD5 7275 0.0044 0.5 NO
21 IRF3 IRF3 IRF3 7294 0.0041 0.5 NO
22 UBE2D3 UBE2D3 UBE2D3 7528 0.0016 0.49 NO
23 PCBP2 PCBP2 PCBP2 7900 -0.0024 0.47 NO
24 UBE2K UBE2K UBE2K 8157 -0.0056 0.46 NO
25 MAVS MAVS MAVS 8293 -0.0071 0.46 NO
26 CYLD CYLD CYLD 8393 -0.0083 0.46 NO
27 IKBKE IKBKE IKBKE 8847 -0.014 0.45 NO
28 RNF135 RNF135 RNF135 9554 -0.022 0.43 NO
29 TRIM25 TRIM25 TRIM25 9651 -0.024 0.44 NO
30 UBE2D2 UBE2D2 UBE2D2 10076 -0.029 0.44 NO

Figure S7.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST PHOSPHOINOSITIDE 3 KINASE PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PMAIP1 PMAIP1 PMAIP1 105 0.57 0.24 YES
2 BID BID BID 1015 0.23 0.3 YES
3 E2F1 E2F1 E2F1 1188 0.21 0.38 YES
4 BCL2L1 BCL2L1 BCL2L1 1515 0.18 0.44 YES
5 BBC3 BBC3 BBC3 1659 0.16 0.5 YES
6 BAX BAX BAX 3252 0.076 0.45 NO
7 CASP7 CASP7 CASP7 4872 0.038 0.37 NO
8 CASP3 CASP3 CASP3 6151 0.018 0.31 NO
9 APAF1 APAF1 APAF1 6327 0.016 0.31 NO
10 TP53 TP53 TP53 6435 0.014 0.31 NO
11 MAPK8 MAPK8 MAPK8 6449 0.014 0.31 NO
12 YWHAB YWHAB YWHAB 6486 0.014 0.32 NO
13 XIAP XIAP XIAP 6779 0.01 0.31 NO
14 PPP3R1 PPP3R1 PPP3R1 6997 0.0076 0.3 NO
15 NMT1 NMT1 NMT1 7323 0.0038 0.28 NO
16 DYNLL1 DYNLL1 DYNLL1 7415 0.0029 0.28 NO
17 BCL2L11 BCL2L11 BCL2L11 7942 -0.003 0.25 NO
18 CASP8 CASP8 CASP8 8189 -0.0059 0.24 NO
19 TFDP1 TFDP1 TFDP1 8587 -0.011 0.22 NO
20 AKT1 AKT1 AKT1 8784 -0.013 0.22 NO
21 DYNLL2 DYNLL2 DYNLL2 9347 -0.02 0.19 NO
22 GZMB GZMB GZMB 10586 -0.036 0.14 NO
23 DIABLO DIABLO DIABLO 10694 -0.037 0.15 NO
24 BAK1 BAK1 BAK1 11323 -0.048 0.14 NO
25 CYCS CYCS CYCS 12535 -0.071 0.099 NO
26 BMF BMF BMF 12692 -0.075 0.12 NO
27 BAD BAD BAD 12971 -0.082 0.14 NO
28 CASP9 CASP9 CASP9 13648 -0.1 0.15 NO
29 BCL2 BCL2 BCL2 15582 -0.2 0.13 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: ST PHOSPHOINOSITIDE 3 KINASE PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: ST PHOSPHOINOSITIDE 3 KINASE 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 TNFPATHWAY

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 RAD51 RAD51 RAD51 768 0.28 0.088 YES
2 FANCA FANCA FANCA 897 0.25 0.2 YES
3 FANCD2 FANCD2 FANCD2 1314 0.2 0.27 YES
4 BARD1 BARD1 BARD1 1526 0.17 0.34 YES
5 FANCE FANCE FANCE 1797 0.15 0.4 YES
6 RBBP8 RBBP8 RBBP8 2189 0.12 0.43 YES
7 CCNE1 CCNE1 CCNE1 2686 0.099 0.45 YES
8 CDK2 CDK2 CDK2 2858 0.092 0.48 YES
9 PCNA PCNA PCNA 3292 0.074 0.5 YES
10 PRKDC PRKDC PRKDC 3437 0.07 0.52 YES
11 MRE11A MRE11A MRE11A 3833 0.059 0.52 YES
12 TOPBP1 TOPBP1 TOPBP1 3868 0.058 0.55 YES
13 NBN NBN NBN 4055 0.054 0.57 YES
14 RAD50 RAD50 RAD50 4221 0.05 0.58 YES
15 XRCC6 XRCC6 XRCC6 4253 0.05 0.6 YES
16 NPM1 NPM1 NPM1 4283 0.049 0.62 YES
17 XRCC5 XRCC5 XRCC5 4641 0.042 0.62 YES
18 FANCG FANCG FANCG 4899 0.037 0.63 YES
19 TP53 TP53 TP53 6435 0.014 0.55 NO
20 FANCL FANCL FANCL 7047 0.007 0.52 NO
21 UBE2D3 UBE2D3 UBE2D3 7528 0.0016 0.49 NO
22 BRCA1 BRCA1 BRCA1 7808 -0.0014 0.48 NO
23 UBE2L3 UBE2L3 UBE2L3 8084 -0.0047 0.46 NO
24 ATM ATM ATM 8259 -0.0068 0.46 NO
25 CSTF1 CSTF1 CSTF1 9310 -0.019 0.41 NO
26 EWSR1 EWSR1 EWSR1 9658 -0.024 0.4 NO
27 FANCF FANCF FANCF 10058 -0.029 0.39 NO
28 ATR ATR ATR 10129 -0.03 0.4 NO
29 FANCC FANCC FANCC 12902 -0.08 0.28 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: PID TNFPATHWAY.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: PID TNFPATHWAY, 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 ECADHERIN NASCENTAJ 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 CCNA1 CCNA1 CCNA1 24 0.74 0.13 YES
2 CDC45 CDC45 CDC45 477 0.36 0.17 YES
3 POLE2 POLE2 POLE2 677 0.3 0.21 YES
4 CDT1 CDT1 CDT1 1023 0.23 0.23 YES
5 MCM4 MCM4 MCM4 1101 0.22 0.27 YES
6 GINS1 GINS1 GINS1 1341 0.2 0.29 YES
7 CDC6 CDC6 CDC6 1475 0.18 0.31 YES
8 PSMB9 PSMB9 PSMB9 1601 0.17 0.34 YES
9 POLD1 POLD1 POLD1 1920 0.14 0.34 YES
10 PSMB8 PSMB8 PSMB8 1928 0.14 0.37 YES
11 PRIM2 PRIM2 PRIM2 1936 0.14 0.39 YES
12 MCM6 MCM6 MCM6 2002 0.14 0.41 YES
13 MCM2 MCM2 MCM2 2038 0.14 0.43 YES
14 CDKN1A CDKN1A CDKN1A 2100 0.13 0.45 YES
15 GINS2 GINS2 GINS2 2223 0.12 0.47 YES
16 MCM5 MCM5 MCM5 2520 0.11 0.47 YES
17 GINS4 GINS4 GINS4 2690 0.099 0.48 YES
18 PRIM1 PRIM1 PRIM1 2828 0.093 0.49 YES
19 CDK2 CDK2 CDK2 2858 0.092 0.5 YES
20 MCM8 MCM8 MCM8 3105 0.082 0.5 YES
21 RFC3 RFC3 RFC3 3110 0.081 0.52 YES
22 PCNA PCNA PCNA 3292 0.074 0.52 YES
23 FEN1 FEN1 FEN1 3500 0.068 0.52 YES
24 POLA2 POLA2 POLA2 3757 0.061 0.52 YES
25 CCNA2 CCNA2 CCNA2 3786 0.06 0.53 YES
26 RFC4 RFC4 RFC4 3839 0.059 0.53 YES
27 POLE POLE POLE 3899 0.058 0.54 YES
28 RPA3 RPA3 RPA3 4110 0.053 0.54 YES
29 PSMD2 PSMD2 PSMD2 4235 0.05 0.54 YES
30 PSMA5 PSMA5 PSMA5 4333 0.048 0.54 YES
31 PSMD11 PSMD11 PSMD11 4698 0.041 0.53 NO
32 UBA52 UBA52 UBA52 5090 0.034 0.51 NO
33 PSMD1 PSMD1 PSMD1 5387 0.029 0.5 NO
34 POLA1 POLA1 POLA1 5408 0.029 0.51 NO
35 PSMA7 PSMA7 PSMA7 5472 0.028 0.51 NO
36 PSMD8 PSMD8 PSMD8 5477 0.028 0.51 NO
37 MCM3 MCM3 MCM3 5582 0.026 0.51 NO
38 MCM7 MCM7 MCM7 5645 0.025 0.51 NO
39 RFC5 RFC5 RFC5 5677 0.024 0.52 NO
40 PSMB5 PSMB5 PSMB5 5736 0.024 0.52 NO
41 LIG1 LIG1 LIG1 5818 0.022 0.52 NO
42 PSMC6 PSMC6 PSMC6 5828 0.022 0.52 NO
43 PSMB10 PSMB10 PSMB10 5893 0.021 0.52 NO
44 PSMA6 PSMA6 PSMA6 6090 0.018 0.51 NO
45 PSMA1 PSMA1 PSMA1 6142 0.018 0.51 NO
46 RPA1 RPA1 RPA1 6244 0.017 0.51 NO
47 PSMB2 PSMB2 PSMB2 6527 0.013 0.5 NO
48 RPS27A RPS27A RPS27A 6554 0.013 0.5 NO
49 PSMD7 PSMD7 PSMD7 6655 0.012 0.49 NO
50 RFC2 RFC2 RFC2 6691 0.011 0.49 NO
51 PSMD14 PSMD14 PSMD14 6714 0.011 0.49 NO
52 PSME1 PSME1 PSME1 6867 0.0093 0.49 NO
53 POLD4 POLD4 POLD4 6925 0.0085 0.48 NO
54 PSMA2 PSMA2 PSMA2 7008 0.0074 0.48 NO
55 POLD3 POLD3 POLD3 7014 0.0073 0.48 NO
56 PSMD5 PSMD5 PSMD5 7067 0.0068 0.48 NO
57 CDKN1B CDKN1B CDKN1B 7330 0.0037 0.47 NO
58 RB1 RB1 RB1 7546 0.0014 0.46 NO
59 PSMD4 PSMD4 PSMD4 7577 0.0011 0.45 NO
60 PSMD10 PSMD10 PSMD10 7667 0.00016 0.45 NO
61 PSMC2 PSMC2 PSMC2 7863 -0.0019 0.44 NO
62 PSMD12 PSMD12 PSMD12 7871 -0.002 0.44 NO
63 RPA2 RPA2 RPA2 8043 -0.0043 0.43 NO
64 PSMB4 PSMB4 PSMB4 8156 -0.0056 0.42 NO
65 PSMB7 PSMB7 PSMB7 8288 -0.007 0.42 NO
66 DNA2 DNA2 DNA2 8324 -0.0074 0.42 NO
67 PSMA3 PSMA3 PSMA3 8526 -0.01 0.41 NO
68 PSMD6 PSMD6 PSMD6 8621 -0.011 0.4 NO
69 PSMB1 PSMB1 PSMB1 8844 -0.014 0.4 NO
70 PSMD3 PSMD3 PSMD3 8856 -0.014 0.4 NO
71 PSMA4 PSMA4 PSMA4 8976 -0.016 0.39 NO
72 PSMD9 PSMD9 PSMD9 9297 -0.019 0.38 NO
73 PSMC1 PSMC1 PSMC1 9518 -0.022 0.37 NO
74 PSMC3 PSMC3 PSMC3 9623 -0.023 0.37 NO
75 PSMD13 PSMD13 PSMD13 9688 -0.024 0.37 NO
76 PSMB3 PSMB3 PSMB3 9707 -0.024 0.37 NO
77 PSME2 PSME2 PSME2 9835 -0.026 0.37 NO
78 PSME4 PSME4 PSME4 9916 -0.027 0.37 NO
79 PSMC4 PSMC4 PSMC4 9932 -0.027 0.37 NO
80 PSMF1 PSMF1 PSMF1 10002 -0.028 0.38 NO
81 PSMB6 PSMB6 PSMB6 10222 -0.031 0.37 NO
82 PSMC5 PSMC5 PSMC5 10923 -0.041 0.34 NO
83 POLD2 POLD2 POLD2 11956 -0.059 0.29 NO
84 PSMA8 PSMA8 PSMA8 16264 -0.26 0.095 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 ECADHERIN NASCENTAJ PATHWAY.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ECADHERIN NASCENTAJ 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 BARD1PATHWAY

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 CCNA1 CCNA1 CCNA1 24 0.74 0.11 YES
2 CDC45 CDC45 CDC45 477 0.36 0.14 YES
3 POLE2 POLE2 POLE2 677 0.3 0.17 YES
4 CDT1 CDT1 CDT1 1023 0.23 0.18 YES
5 MCM4 MCM4 MCM4 1101 0.22 0.21 YES
6 CCNE2 CCNE2 CCNE2 1153 0.22 0.24 YES
7 GINS1 GINS1 GINS1 1341 0.2 0.26 YES
8 CDC6 CDC6 CDC6 1475 0.18 0.28 YES
9 PSMB9 PSMB9 PSMB9 1601 0.17 0.3 YES
10 POLD1 POLD1 POLD1 1920 0.14 0.3 YES
11 PSMB8 PSMB8 PSMB8 1928 0.14 0.32 YES
12 PRIM2 PRIM2 PRIM2 1936 0.14 0.34 YES
13 MCM6 MCM6 MCM6 2002 0.14 0.36 YES
14 MCM2 MCM2 MCM2 2038 0.14 0.37 YES
15 CDKN1A CDKN1A CDKN1A 2100 0.13 0.39 YES
16 GINS2 GINS2 GINS2 2223 0.12 0.4 YES
17 CDC25B CDC25B CDC25B 2314 0.12 0.41 YES
18 MCM5 MCM5 MCM5 2520 0.11 0.42 YES
19 CCNE1 CCNE1 CCNE1 2686 0.099 0.42 YES
20 GINS4 GINS4 GINS4 2690 0.099 0.44 YES
21 CCND1 CCND1 CCND1 2713 0.098 0.45 YES
22 CDK7 CDK7 CDK7 2801 0.094 0.46 YES
23 CKS1B CKS1B CKS1B 2803 0.094 0.47 YES
24 PRIM1 PRIM1 PRIM1 2828 0.093 0.49 YES
25 CDK2 CDK2 CDK2 2858 0.092 0.5 YES
26 MCM8 MCM8 MCM8 3105 0.082 0.5 YES
27 RFC3 RFC3 RFC3 3110 0.081 0.51 YES
28 PCNA PCNA PCNA 3292 0.074 0.51 YES
29 FEN1 FEN1 FEN1 3500 0.068 0.51 YES
30 POLA2 POLA2 POLA2 3757 0.061 0.5 YES
31 CCNA2 CCNA2 CCNA2 3786 0.06 0.51 YES
32 RFC4 RFC4 RFC4 3839 0.059 0.52 YES
33 POLE POLE POLE 3899 0.058 0.52 YES
34 RPA3 RPA3 RPA3 4110 0.053 0.52 NO
35 PSMD2 PSMD2 PSMD2 4235 0.05 0.52 NO
36 PSMA5 PSMA5 PSMA5 4333 0.048 0.52 NO
37 PSMD11 PSMD11 PSMD11 4698 0.041 0.5 NO
38 CDK4 CDK4 CDK4 4720 0.04 0.51 NO
39 MYC MYC MYC 4759 0.04 0.51 NO
40 UBA52 UBA52 UBA52 5090 0.034 0.5 NO
41 PSMD1 PSMD1 PSMD1 5387 0.029 0.49 NO
42 POLA1 POLA1 POLA1 5408 0.029 0.49 NO
43 PSMA7 PSMA7 PSMA7 5472 0.028 0.49 NO
44 PSMD8 PSMD8 PSMD8 5477 0.028 0.49 NO
45 MCM3 MCM3 MCM3 5582 0.026 0.49 NO
46 MCM7 MCM7 MCM7 5645 0.025 0.49 NO
47 RFC5 RFC5 RFC5 5677 0.024 0.49 NO
48 PSMB5 PSMB5 PSMB5 5736 0.024 0.5 NO
49 LIG1 LIG1 LIG1 5818 0.022 0.49 NO
50 PSMC6 PSMC6 PSMC6 5828 0.022 0.5 NO
51 PSMB10 PSMB10 PSMB10 5893 0.021 0.5 NO
52 PSMA6 PSMA6 PSMA6 6090 0.018 0.49 NO
53 PSMA1 PSMA1 PSMA1 6142 0.018 0.49 NO
54 RPA1 RPA1 RPA1 6244 0.017 0.48 NO
55 CCNH CCNH CCNH 6335 0.016 0.48 NO
56 PSMB2 PSMB2 PSMB2 6527 0.013 0.47 NO
57 RPS27A RPS27A RPS27A 6554 0.013 0.47 NO
58 PSMD7 PSMD7 PSMD7 6655 0.012 0.47 NO
59 RFC2 RFC2 RFC2 6691 0.011 0.47 NO
60 PSMD14 PSMD14 PSMD14 6714 0.011 0.47 NO
61 PSME1 PSME1 PSME1 6867 0.0093 0.46 NO
62 WEE1 WEE1 WEE1 6898 0.0088 0.46 NO
63 POLD4 POLD4 POLD4 6925 0.0085 0.46 NO
64 PSMA2 PSMA2 PSMA2 7008 0.0074 0.46 NO
65 POLD3 POLD3 POLD3 7014 0.0073 0.46 NO
66 PSMD5 PSMD5 PSMD5 7067 0.0068 0.46 NO
67 CDKN1B CDKN1B CDKN1B 7330 0.0037 0.44 NO
68 RB1 RB1 RB1 7546 0.0014 0.43 NO
69 PSMD4 PSMD4 PSMD4 7577 0.0011 0.43 NO
70 PSMD10 PSMD10 PSMD10 7667 0.00016 0.42 NO
71 SKP1 SKP1 SKP1 7673 0.000074 0.42 NO
72 PSMC2 PSMC2 PSMC2 7863 -0.0019 0.41 NO
73 PSMD12 PSMD12 PSMD12 7871 -0.002 0.41 NO
74 RPA2 RPA2 RPA2 8043 -0.0043 0.4 NO
75 PSMB4 PSMB4 PSMB4 8156 -0.0056 0.4 NO
76 PSMB7 PSMB7 PSMB7 8288 -0.007 0.39 NO
77 CUL1 CUL1 CUL1 8304 -0.0072 0.39 NO
78 DNA2 DNA2 DNA2 8324 -0.0074 0.39 NO
79 MNAT1 MNAT1 MNAT1 8343 -0.0076 0.39 NO
80 MAX MAX MAX 8407 -0.0084 0.39 NO
81 PSMA3 PSMA3 PSMA3 8526 -0.01 0.39 NO
82 PSMD6 PSMD6 PSMD6 8621 -0.011 0.38 NO
83 PSMB1 PSMB1 PSMB1 8844 -0.014 0.37 NO
84 PSMD3 PSMD3 PSMD3 8856 -0.014 0.37 NO
85 PSMA4 PSMA4 PSMA4 8976 -0.016 0.37 NO
86 PSMD9 PSMD9 PSMD9 9297 -0.019 0.35 NO
87 PSMC1 PSMC1 PSMC1 9518 -0.022 0.34 NO
88 PSMC3 PSMC3 PSMC3 9623 -0.023 0.34 NO
89 PSMD13 PSMD13 PSMD13 9688 -0.024 0.34 NO
90 PSMB3 PSMB3 PSMB3 9707 -0.024 0.34 NO
91 PSME2 PSME2 PSME2 9835 -0.026 0.34 NO
92 PSME4 PSME4 PSME4 9916 -0.027 0.34 NO
93 PSMC4 PSMC4 PSMC4 9932 -0.027 0.34 NO
94 PSMF1 PSMF1 PSMF1 10002 -0.028 0.34 NO
95 PSMB6 PSMB6 PSMB6 10222 -0.031 0.34 NO
96 PSMC5 PSMC5 PSMC5 10923 -0.041 0.3 NO
97 POLD2 POLD2 POLD2 11956 -0.059 0.26 NO
98 SKP2 SKP2 SKP2 13319 -0.092 0.19 NO
99 CDC25A CDC25A CDC25A 15451 -0.19 0.1 NO
100 PSMA8 PSMA8 PSMA8 16264 -0.26 0.096 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 BARD1PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: PID BARD1PATHWAY, 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 ORC1 REMOVAL FROM CHROMATIN

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 CTSE CTSE CTSE 354 0.4 0.025 YES
2 NAPSA NAPSA NAPSA 448 0.37 0.062 YES
3 NPC1 NPC1 NPC1 778 0.28 0.074 YES
4 CTSL2 CTSL2 CTSL2 840 0.27 0.1 YES
5 CTSC CTSC CTSC 852 0.26 0.13 YES
6 ATP6V0D2 ATP6V0D2 ATP6V0D2 866 0.26 0.16 YES
7 ACP5 ACP5 ACP5 891 0.26 0.19 YES
8 SLC11A1 SLC11A1 SLC11A1 990 0.24 0.21 YES
9 CTSK CTSK CTSK 1198 0.21 0.22 YES
10 CTSH CTSH CTSH 1367 0.19 0.23 YES
11 CTSS CTSS CTSS 1418 0.18 0.25 YES
12 CD68 CD68 CD68 1469 0.18 0.27 YES
13 DNASE2B DNASE2B DNASE2B 1536 0.17 0.28 YES
14 LAMP3 LAMP3 LAMP3 1822 0.15 0.28 YES
15 IGF2R IGF2R IGF2R 1824 0.15 0.3 YES
16 SLC17A5 SLC17A5 SLC17A5 1929 0.14 0.31 YES
17 IDS IDS IDS 2110 0.13 0.31 YES
18 CTSA CTSA CTSA 2559 0.1 0.3 YES
19 HEXB HEXB HEXB 2797 0.094 0.3 YES
20 CTSD CTSD CTSD 2934 0.088 0.3 YES
21 AP3S1 AP3S1 AP3S1 2959 0.088 0.31 YES
22 PSAP PSAP PSAP 2985 0.086 0.32 YES
23 TCIRG1 TCIRG1 TCIRG1 2987 0.086 0.33 YES
24 LAPTM5 LAPTM5 LAPTM5 3072 0.083 0.33 YES
25 TPP1 TPP1 TPP1 3086 0.082 0.34 YES
26 GM2A GM2A GM2A 3133 0.081 0.35 YES
27 CTSB CTSB CTSB 3284 0.075 0.35 YES
28 MANBA MANBA MANBA 3303 0.074 0.35 YES
29 AP4E1 AP4E1 AP4E1 3332 0.073 0.36 YES
30 ENTPD4 ENTPD4 ENTPD4 3440 0.07 0.36 YES
31 NAGA NAGA NAGA 3460 0.069 0.37 YES
32 LAMP2 LAMP2 LAMP2 3489 0.068 0.38 YES
33 MAN2B1 MAN2B1 MAN2B1 3567 0.066 0.38 YES
34 AP1S3 AP1S3 AP1S3 3823 0.059 0.37 YES
35 NPC2 NPC2 NPC2 3844 0.059 0.38 YES
36 LIPA LIPA LIPA 3846 0.059 0.38 YES
37 GGA3 GGA3 GGA3 3851 0.059 0.39 YES
38 HGSNAT HGSNAT HGSNAT 3856 0.059 0.4 YES
39 FUCA1 FUCA1 FUCA1 3871 0.058 0.4 YES
40 CLTA CLTA CLTA 4007 0.055 0.4 YES
41 ATP6V0A2 ATP6V0A2 ATP6V0A2 4030 0.055 0.4 YES
42 SCARB2 SCARB2 SCARB2 4100 0.053 0.41 YES
43 LAPTM4B LAPTM4B LAPTM4B 4141 0.052 0.41 YES
44 AP1S1 AP1S1 AP1S1 4148 0.052 0.42 YES
45 ARSB ARSB ARSB 4249 0.05 0.42 YES
46 LAMP1 LAMP1 LAMP1 4329 0.048 0.42 YES
47 PPT1 PPT1 PPT1 4392 0.047 0.42 YES
48 GLB1 GLB1 GLB1 4434 0.046 0.42 YES
49 GNPTAB GNPTAB GNPTAB 4456 0.046 0.43 YES
50 ARSA ARSA ARSA 4471 0.045 0.43 YES
51 ASAH1 ASAH1 ASAH1 4513 0.044 0.43 YES
52 CTNS CTNS CTNS 4672 0.041 0.43 NO
53 CLTC CLTC CLTC 4796 0.039 0.43 NO
54 NEU1 NEU1 NEU1 4877 0.037 0.43 NO
55 SLC11A2 SLC11A2 SLC11A2 4964 0.036 0.42 NO
56 GBA GBA GBA 5075 0.034 0.42 NO
57 AP1M2 AP1M2 AP1M2 5231 0.032 0.42 NO
58 MCOLN1 MCOLN1 MCOLN1 5378 0.029 0.41 NO
59 GGA2 GGA2 GGA2 5621 0.025 0.4 NO
60 ABCB9 ABCB9 ABCB9 5628 0.025 0.4 NO
61 NAGPA NAGPA NAGPA 5635 0.025 0.41 NO
62 M6PR M6PR M6PR 5704 0.024 0.41 NO
63 AP4M1 AP4M1 AP4M1 5799 0.022 0.4 NO
64 CD63 CD63 CD63 5871 0.022 0.4 NO
65 LAPTM4A LAPTM4A LAPTM4A 5917 0.021 0.4 NO
66 AGA AGA AGA 6021 0.02 0.4 NO
67 AP1S2 AP1S2 AP1S2 6040 0.019 0.4 NO
68 GNS GNS GNS 6075 0.019 0.4 NO
69 GUSB GUSB GUSB 6163 0.018 0.4 NO
70 AP3D1 AP3D1 AP3D1 6471 0.014 0.38 NO
71 AP3M1 AP3M1 AP3M1 6495 0.014 0.38 NO
72 HEXA HEXA HEXA 6701 0.011 0.37 NO
73 GGA1 GGA1 GGA1 6728 0.011 0.37 NO
74 ATP6AP1 ATP6AP1 ATP6AP1 6954 0.0082 0.36 NO
75 CLN3 CLN3 CLN3 7013 0.0074 0.36 NO
76 AP1G1 AP1G1 AP1G1 7056 0.007 0.36 NO
77 MFSD8 MFSD8 MFSD8 7061 0.0069 0.36 NO
78 AP1B1 AP1B1 AP1B1 7121 0.0061 0.35 NO
79 CTSL1 CTSL1 CTSL1 7727 -0.00046 0.32 NO
80 SMPD1 SMPD1 SMPD1 7809 -0.0014 0.31 NO
81 ATP6V0A1 ATP6V0A1 ATP6V0A1 7814 -0.0014 0.31 NO
82 ATP6V0C ATP6V0C ATP6V0C 7954 -0.0031 0.31 NO
83 CTSG CTSG CTSG 7985 -0.0036 0.3 NO
84 ACP2 ACP2 ACP2 8005 -0.0038 0.3 NO
85 SUMF1 SUMF1 SUMF1 8192 -0.006 0.3 NO
86 SORT1 SORT1 SORT1 8228 -0.0064 0.29 NO
87 GALNS GALNS GALNS 8274 -0.0069 0.29 NO
88 AP1M1 AP1M1 AP1M1 8455 -0.0091 0.28 NO
89 ATP6V1H ATP6V1H ATP6V1H 8521 -0.01 0.28 NO
90 GAA GAA GAA 8556 -0.01 0.28 NO
91 GNPTG GNPTG GNPTG 8965 -0.016 0.26 NO
92 CLTB CLTB CLTB 9190 -0.018 0.25 NO
93 AP3B1 AP3B1 AP3B1 9218 -0.018 0.25 NO
94 SGSH SGSH SGSH 9395 -0.02 0.24 NO
95 DNASE2 DNASE2 DNASE2 9894 -0.027 0.22 NO
96 ATP6V0D1 ATP6V0D1 ATP6V0D1 9934 -0.027 0.22 NO
97 PLA2G15 PLA2G15 PLA2G15 10249 -0.031 0.2 NO
98 CD164 CD164 CD164 10272 -0.032 0.2 NO
99 CTSO CTSO CTSO 10428 -0.034 0.2 NO
100 CTSZ CTSZ CTSZ 10505 -0.035 0.2 NO
101 CTSF CTSF CTSF 10590 -0.036 0.2 NO
102 NAGLU NAGLU NAGLU 10644 -0.037 0.2 NO
103 CTSW CTSW CTSW 10647 -0.037 0.2 NO
104 AP3S2 AP3S2 AP3S2 11449 -0.05 0.16 NO
105 ATP6V0A4 ATP6V0A4 ATP6V0A4 11468 -0.05 0.17 NO
106 GALC GALC GALC 11766 -0.055 0.16 NO
107 ATP6V0B ATP6V0B ATP6V0B 11937 -0.059 0.16 NO
108 ABCA2 ABCA2 ABCA2 12021 -0.06 0.16 NO
109 AP3M2 AP3M2 AP3M2 12176 -0.063 0.16 NO
110 AP3B2 AP3B2 AP3B2 12253 -0.065 0.16 NO
111 CLN5 CLN5 CLN5 13026 -0.083 0.13 NO
112 LGMN LGMN LGMN 13415 -0.095 0.12 NO
113 GLA GLA GLA 13684 -0.1 0.11 NO
114 PPT2 PPT2 PPT2 14114 -0.12 0.1 NO
115 AP4B1 AP4B1 AP4B1 14416 -0.13 0.099 NO
116 CLTCL1 CLTCL1 CLTCL1 14430 -0.13 0.11 NO
117 AP4S1 AP4S1 AP4S1 14777 -0.15 0.11 NO
118 ARSG ARSG ARSG 15367 -0.19 0.099 NO
119 IDUA IDUA IDUA 15504 -0.2 0.11 NO
120 HYAL1 HYAL1 HYAL1 15751 -0.22 0.12 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 ORC1 REMOVAL FROM CHROMATIN.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ORC1 REMOVAL FROM CHROMATIN, 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 EIF3C EIF3C EIF3C 1619 0.17 -0.011 YES
2 RPS27 RPS27 RPS27 1916 0.14 0.041 YES
3 EIF4EBP1 EIF4EBP1 EIF4EBP1 2170 0.13 0.087 YES
4 RPS2 RPS2 RPS2 3443 0.07 0.049 YES
5 PABPC1 PABPC1 PABPC1 3581 0.065 0.073 YES
6 EIF3H EIF3H EIF3H 3675 0.063 0.098 YES
7 RPS12 RPS12 RPS12 3682 0.063 0.13 YES
8 RPS5 RPS5 RPS5 3705 0.062 0.16 YES
9 EIF3A EIF3A EIF3A 3855 0.059 0.18 YES
10 EIF3D EIF3D EIF3D 3984 0.056 0.2 YES
11 RPS29 RPS29 RPS29 4017 0.055 0.22 YES
12 RPS4X RPS4X RPS4X 4101 0.053 0.24 YES
13 EIF4G1 EIF4G1 EIF4G1 4186 0.051 0.26 YES
14 RPS8 RPS8 RPS8 4216 0.05 0.28 YES
15 EIF2S2 EIF2S2 EIF2S2 4386 0.047 0.3 YES
16 EIF4B EIF4B EIF4B 4490 0.045 0.31 YES
17 RPS9 RPS9 RPS9 4511 0.044 0.33 YES
18 EIF3F EIF3F EIF3F 4697 0.041 0.34 YES
19 EIF2S3 EIF2S3 EIF2S3 4721 0.04 0.36 YES
20 RPS15A RPS15A RPS15A 4857 0.038 0.37 YES
21 EIF4A1 EIF4A1 EIF4A1 5101 0.034 0.37 YES
22 RPS18 RPS18 RPS18 5104 0.034 0.39 YES
23 RPS19 RPS19 RPS19 5237 0.031 0.4 YES
24 RPS17 RPS17 RPS17 5242 0.031 0.41 YES
25 EIF4A2 EIF4A2 EIF4A2 5280 0.03 0.42 YES
26 EIF3E EIF3E EIF3E 5360 0.029 0.43 YES
27 RPS10 RPS10 RPS10 5446 0.028 0.44 YES
28 RPS23 RPS23 RPS23 5586 0.026 0.44 YES
29 EIF3G EIF3G EIF3G 5636 0.025 0.45 YES
30 RPS3A RPS3A RPS3A 5648 0.025 0.46 YES
31 RPS3 RPS3 RPS3 5699 0.024 0.47 YES
32 RPS26 RPS26 RPS26 5746 0.023 0.48 YES
33 RPS16 RPS16 RPS16 5770 0.023 0.49 YES
34 RPS13 RPS13 RPS13 5785 0.023 0.5 YES
35 RPS15 RPS15 RPS15 5921 0.021 0.5 YES
36 RPS25 RPS25 RPS25 5935 0.021 0.51 YES
37 RPS21 RPS21 RPS21 5936 0.021 0.52 YES
38 RPS7 RPS7 RPS7 5957 0.02 0.53 YES
39 RPS20 RPS20 RPS20 6032 0.019 0.54 YES
40 RPS14 RPS14 RPS14 6186 0.017 0.54 YES
41 RPS6 RPS6 RPS6 6229 0.017 0.54 YES
42 RPS24 RPS24 RPS24 6230 0.017 0.55 YES
43 EIF3B EIF3B EIF3B 6348 0.015 0.55 YES
44 EIF3I EIF3I EIF3I 6458 0.014 0.55 YES
45 RPS27A RPS27A RPS27A 6554 0.013 0.55 YES
46 RPSA RPSA RPSA 6555 0.013 0.56 YES
47 RPS11 RPS11 RPS11 6584 0.013 0.56 YES
48 EIF2S1 EIF2S1 EIF2S1 6695 0.011 0.56 NO
49 RPS4Y1 RPS4Y1 RPS4Y1 6886 0.009 0.56 NO
50 EIF3J EIF3J EIF3J 7041 0.007 0.55 NO
51 EIF4H EIF4H EIF4H 7895 -0.0024 0.51 NO
52 EIF3K EIF3K EIF3K 8029 -0.0041 0.5 NO
53 FAU FAU FAU 8062 -0.0045 0.5 NO
54 RPS28 RPS28 RPS28 9004 -0.016 0.46 NO
55 EIF1AX EIF1AX EIF1AX 9520 -0.022 0.44 NO
56 EIF4E EIF4E EIF4E 9654 -0.024 0.44 NO
57 RPSAP9 RPSAP9 RPSAP9 11291 -0.047 0.37 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 OXIDATIVE PHOSPHORYLATION 113 genes.ES.table 0.52 1.5 0.14 1 0.98 0.74 0.32 0.51 0.84 0.43
KEGG GLYCINE SERINE AND THREONINE METABOLISM 29 genes.ES.table 0.58 1.4 0.072 1 0.99 0.59 0.22 0.46 0.87 0.43
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 44 genes.ES.table 0.5 1.5 0.12 1 0.97 0.82 0.3 0.57 0.94 0.47
KEGG LYSINE DEGRADATION 44 genes.ES.table 0.49 1.8 0.019 1 0.53 0.48 0.28 0.34 0.34 0.29
KEGG ARGININE AND PROLINE METABOLISM 52 genes.ES.table 0.48 1.5 0.041 1 0.98 0.44 0.22 0.35 0.89 0.45
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS 25 genes.ES.table 0.41 1.4 0.14 1 1 0.64 0.42 0.37 0.81 0.38
KEGG PROPANOATE METABOLISM 32 genes.ES.table 0.62 1.7 0.018 0.82 0.64 0.81 0.3 0.57 0.32 0.23
KEGG BUTANOATE METABOLISM 31 genes.ES.table 0.65 1.7 0.0064 0.67 0.71 0.74 0.28 0.54 0.27 0.2
KEGG INSULIN SIGNALING PATHWAY 128 genes.ES.table 0.36 1.5 0.031 1 0.98 0.15 0.14 0.13 0.8 0.41
KEGG ADIPOCYTOKINE SIGNALING PATHWAY 64 genes.ES.table 0.39 1.4 0.079 1 1 0.27 0.16 0.22 0.83 0.4
genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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 OGDHL OGDHL OGDHL 110 0.77 0.17 YES
2 ALDH1B1 ALDH1B1 ALDH1B1 1443 0.26 0.15 YES
3 ALDH2 ALDH2 ALDH2 1554 0.25 0.2 YES
4 SETMAR SETMAR SETMAR 2191 0.19 0.21 YES
5 ACAT1 ACAT1 ACAT1 2270 0.18 0.25 YES
6 EHHADH EHHADH EHHADH 2392 0.17 0.28 YES
7 AASS AASS AASS 2726 0.15 0.3 YES
8 ALDH9A1 ALDH9A1 ALDH9A1 2746 0.15 0.33 YES
9 AADAT AADAT AADAT 2805 0.15 0.36 YES
10 SETD8 SETD8 SETD8 2954 0.14 0.38 YES
11 OGDH OGDH OGDH 3396 0.12 0.39 YES
12 GCDH GCDH GCDH 3531 0.11 0.4 YES
13 ALDH7A1 ALDH7A1 ALDH7A1 3765 0.1 0.42 YES
14 ECHS1 ECHS1 ECHS1 4088 0.094 0.42 YES
15 SUV420H1 SUV420H1 SUV420H1 4252 0.089 0.43 YES
16 SETDB2 SETDB2 SETDB2 4367 0.086 0.44 YES
17 AASDH AASDH AASDH 4672 0.077 0.44 YES
18 PLOD1 PLOD1 PLOD1 4676 0.077 0.46 YES
19 HADH HADH HADH 4919 0.071 0.46 YES
20 WHSC1 WHSC1 WHSC1 5023 0.068 0.47 YES
21 TMLHE TMLHE TMLHE 5036 0.068 0.49 YES
22 HADHA HADHA HADHA 5325 0.062 0.49 NO
23 SUV39H2 SUV39H2 SUV39H2 6029 0.048 0.46 NO
24 NSD1 NSD1 NSD1 6587 0.038 0.44 NO
25 SETD2 SETD2 SETD2 6996 0.031 0.42 NO
26 DLST DLST DLST 7091 0.03 0.42 NO
27 SETD1B SETD1B SETD1B 7371 0.026 0.41 NO
28 EHMT1 EHMT1 EHMT1 7439 0.025 0.41 NO
29 SUV39H1 SUV39H1 SUV39H1 7807 0.02 0.4 NO
30 DOT1L DOT1L DOT1L 7926 0.018 0.4 NO
31 PLOD3 PLOD3 PLOD3 8027 0.016 0.39 NO
32 SETD1A SETD1A SETD1A 8051 0.016 0.4 NO
33 AASDHPPT AASDHPPT AASDHPPT 8555 0.0094 0.37 NO
34 PLOD2 PLOD2 PLOD2 8716 0.0069 0.36 NO
35 WHSC1L1 WHSC1L1 WHSC1L1 9560 -0.0054 0.32 NO
36 SETDB1 SETDB1 SETDB1 10005 -0.011 0.29 NO
37 ALDH3A2 ALDH3A2 ALDH3A2 10274 -0.015 0.28 NO
38 ACAT2 ACAT2 ACAT2 10306 -0.016 0.28 NO
39 ASH1L ASH1L ASH1L 10781 -0.023 0.26 NO
40 BBOX1 BBOX1 BBOX1 11179 -0.029 0.25 NO
41 EHMT2 EHMT2 EHMT2 11324 -0.032 0.25 NO
42 SUV420H2 SUV420H2 SUV420H2 12324 -0.051 0.2 NO
43 SETD7 SETD7 SETD7 13956 -0.11 0.14 NO
44 PIPOX PIPOX PIPOX 16786 -0.38 0.066 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 OXIDATIVE PHOSPHORYLATION.

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACACB ACACB ACACB 848 0.38 0.049 YES
2 ALDH1B1 ALDH1B1 ALDH1B1 1443 0.26 0.084 YES
3 ALDH2 ALDH2 ALDH2 1554 0.25 0.14 YES
4 LDHAL6A LDHAL6A LDHAL6A 1764 0.22 0.19 YES
5 ALDH6A1 ALDH6A1 ALDH6A1 1814 0.22 0.24 YES
6 ACAT1 ACAT1 ACAT1 2270 0.18 0.26 YES
7 EHHADH EHHADH EHHADH 2392 0.17 0.3 YES
8 ACSS1 ACSS1 ACSS1 2578 0.16 0.33 YES
9 ALDH9A1 ALDH9A1 ALDH9A1 2746 0.15 0.36 YES
10 SUCLG1 SUCLG1 SUCLG1 3044 0.14 0.38 YES
11 ACADM ACADM ACADM 3246 0.13 0.4 YES
12 ABAT ABAT ABAT 3326 0.12 0.43 YES
13 LDHB LDHB LDHB 3451 0.12 0.45 YES
14 MLYCD MLYCD MLYCD 3497 0.12 0.48 YES
15 ALDH7A1 ALDH7A1 ALDH7A1 3765 0.1 0.49 YES
16 PCCB PCCB PCCB 3786 0.1 0.51 YES
17 PCCA PCCA PCCA 3870 0.1 0.54 YES
18 LDHC LDHC LDHC 3978 0.097 0.55 YES
19 ECHS1 ECHS1 ECHS1 4088 0.094 0.57 YES
20 SUCLA2 SUCLA2 SUCLA2 4189 0.091 0.59 YES
21 ACSS2 ACSS2 ACSS2 4872 0.072 0.57 YES
22 ACACA ACACA ACACA 5041 0.068 0.58 YES
23 HIBCH HIBCH HIBCH 5080 0.067 0.59 YES
24 SUCLG2 SUCLG2 SUCLG2 5281 0.063 0.6 YES
25 HADHA HADHA HADHA 5325 0.062 0.61 YES
26 MCEE MCEE MCEE 5443 0.059 0.62 YES
27 MUT MUT MUT 6076 0.047 0.6 NO
28 ACSS3 ACSS3 ACSS3 9167 0.00031 0.42 NO
29 ALDH3A2 ALDH3A2 ALDH3A2 10274 -0.015 0.37 NO
30 ACAT2 ACAT2 ACAT2 10306 -0.016 0.37 NO
31 LDHAL6B LDHAL6B LDHAL6B 13977 -0.11 0.19 NO
32 LDHA LDHA LDHA 14115 -0.12 0.22 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 GLYCINE SERINE AND THREONINE METABOLISM.

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

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

Table 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 HMGCS2 HMGCS2 HMGCS2 461 0.5 0.082 YES
2 ACSM5 ACSM5 ACSM5 496 0.48 0.18 YES
3 OXCT2 OXCT2 OXCT2 979 0.34 0.23 YES
4 ALDH1B1 ALDH1B1 ALDH1B1 1443 0.26 0.26 YES
5 ACSM3 ACSM3 ACSM3 1503 0.26 0.31 YES
6 ALDH2 ALDH2 ALDH2 1554 0.25 0.37 YES
7 BDH1 BDH1 BDH1 1669 0.24 0.41 YES
8 ACAT1 ACAT1 ACAT1 2270 0.18 0.42 YES
9 EHHADH EHHADH EHHADH 2392 0.17 0.45 YES
10 ACADS ACADS ACADS 2399 0.17 0.48 YES
11 AACS AACS AACS 2680 0.16 0.5 YES
12 ALDH9A1 ALDH9A1 ALDH9A1 2746 0.15 0.53 YES
13 L2HGDH L2HGDH L2HGDH 2824 0.15 0.56 YES
14 PDHA1 PDHA1 PDHA1 3228 0.13 0.56 YES
15 ABAT ABAT ABAT 3326 0.12 0.58 YES
16 HMGCS1 HMGCS1 HMGCS1 3627 0.11 0.59 YES
17 ALDH7A1 ALDH7A1 ALDH7A1 3765 0.1 0.6 YES
18 GAD1 GAD1 GAD1 3818 0.1 0.62 YES
19 ACSM2A ACSM2A ACSM2A 3997 0.096 0.64 YES
20 ECHS1 ECHS1 ECHS1 4088 0.094 0.65 YES
21 OXCT1 OXCT1 OXCT1 4477 0.083 0.65 YES
22 HADH HADH HADH 4919 0.071 0.64 YES
23 AKR1B10 AKR1B10 AKR1B10 4948 0.07 0.65 YES
24 HADHA HADHA HADHA 5325 0.062 0.64 NO
25 HMGCL HMGCL HMGCL 5723 0.054 0.63 NO
26 ALDH5A1 ALDH5A1 ALDH5A1 5867 0.051 0.64 NO
27 PDHB PDHB PDHB 6271 0.044 0.62 NO
28 BDH2 BDH2 BDH2 8225 0.013 0.52 NO
29 ALDH3A2 ALDH3A2 ALDH3A2 10274 -0.015 0.4 NO
30 ACAT2 ACAT2 ACAT2 10306 -0.016 0.41 NO
31 ACSM1 ACSM1 ACSM1 13662 -0.094 0.24 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

Table 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 PYGM PYGM PYGM 42 0.92 0.11 YES
2 PFKFB1 PFKFB1 PFKFB1 318 0.57 0.16 YES
3 GYS2 GYS2 GYS2 361 0.55 0.22 YES
4 ENO3 ENO3 ENO3 460 0.5 0.28 YES
5 PFKFB2 PFKFB2 PFKFB2 1128 0.32 0.28 YES
6 PRKACB PRKACB PRKACB 1150 0.31 0.32 YES
7 GYG2 GYG2 GYG2 1268 0.29 0.34 YES
8 PGAM2 PGAM2 PGAM2 1521 0.26 0.36 YES
9 PHKG1 PHKG1 PHKG1 1605 0.25 0.39 YES
10 GAPDHS GAPDHS GAPDHS 1678 0.24 0.41 YES
11 PCK1 PCK1 PCK1 2277 0.18 0.4 YES
12 PHKB PHKB PHKB 2484 0.16 0.41 YES
13 PFKM PFKM PFKM 2563 0.16 0.42 YES
14 AGL AGL AGL 2624 0.16 0.44 YES
15 GOT1 GOT1 GOT1 2841 0.15 0.44 YES
16 ALDOB ALDOB ALDOB 3137 0.13 0.44 YES
17 SLC25A10 SLC25A10 SLC25A10 3163 0.13 0.46 YES
18 ENO2 ENO2 ENO2 3577 0.11 0.45 YES
19 GOT2 GOT2 GOT2 3596 0.11 0.46 YES
20 MDH2 MDH2 MDH2 3920 0.099 0.45 NO
21 SLC25A13 SLC25A13 SLC25A13 4458 0.083 0.43 NO
22 GYS1 GYS1 GYS1 4908 0.071 0.42 NO
23 SLC25A11 SLC25A11 SLC25A11 5056 0.068 0.42 NO
24 SLC25A1 SLC25A1 SLC25A1 5101 0.067 0.42 NO
25 PPP2R5D PPP2R5D PPP2R5D 5353 0.061 0.42 NO
26 PPP2R1B PPP2R1B PPP2R1B 5358 0.061 0.42 NO
27 ALDOA ALDOA ALDOA 5472 0.058 0.42 NO
28 SLC25A12 SLC25A12 SLC25A12 5522 0.057 0.43 NO
29 PGK1 PGK1 PGK1 5643 0.055 0.43 NO
30 UGP2 UGP2 UGP2 5646 0.055 0.43 NO
31 GAPDH GAPDH GAPDH 6241 0.044 0.41 NO
32 TPI1 TPI1 TPI1 6249 0.044 0.41 NO
33 GPI GPI GPI 6469 0.04 0.4 NO
34 GBE1 GBE1 GBE1 6822 0.034 0.39 NO
35 PPP2CA PPP2CA PPP2CA 7264 0.027 0.37 NO
36 MDH1 MDH1 MDH1 7320 0.026 0.37 NO
37 PRKACA PRKACA PRKACA 7846 0.019 0.34 NO
38 PHKG2 PHKG2 PHKG2 8169 0.014 0.32 NO
39 CALM1 CALM1 CALM1 8355 0.012 0.31 NO
40 CALM3 CALM3 CALM3 8710 0.007 0.3 NO
41 PGM2 PGM2 PGM2 8799 0.0058 0.29 NO
42 PCK2 PCK2 PCK2 9151 0.00047 0.27 NO
43 PGAM1 PGAM1 PGAM1 9432 -0.0034 0.26 NO
44 PPP2R1A PPP2R1A PPP2R1A 10309 -0.016 0.21 NO
45 PPP2CB PPP2CB PPP2CB 10725 -0.022 0.19 NO
46 PKLR PKLR PKLR 11249 -0.031 0.16 NO
47 PFKP PFKP PFKP 11355 -0.032 0.16 NO
48 FBP1 FBP1 FBP1 11573 -0.036 0.15 NO
49 PFKL PFKL PFKL 11619 -0.037 0.16 NO
50 PHKA1 PHKA1 PHKA1 11642 -0.037 0.16 NO
51 ENO1 ENO1 ENO1 12035 -0.045 0.14 NO
52 PGM1 PGM1 PGM1 12266 -0.05 0.14 NO
53 PHKA2 PHKA2 PHKA2 12321 -0.051 0.14 NO
54 PFKFB4 PFKFB4 PFKFB4 12491 -0.056 0.14 NO
55 GYG1 GYG1 GYG1 12829 -0.065 0.12 NO
56 PYGB PYGB PYGB 13014 -0.071 0.12 NO
57 CALM2 CALM2 CALM2 13176 -0.076 0.12 NO
58 PKM2 PKM2 PKM2 14358 -0.13 0.072 NO
59 PYGL PYGL PYGL 15076 -0.18 0.054 NO
60 PC PC PC 15971 -0.26 0.036 NO
61 PFKFB3 PFKFB3 PFKFB3 16294 -0.31 0.055 NO
62 ALDOC ALDOC ALDOC 16380 -0.32 0.089 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 LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG ARGININE AND PROLINE 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 ADHFE1 ADHFE1 ADHFE1 2326 0.18 -0.11 YES
2 NDUFB1 NDUFB1 NDUFB1 2435 0.17 -0.1 YES
3 NNT NNT NNT 2482 0.17 -0.092 YES
4 ETFDH ETFDH ETFDH 2507 0.16 -0.079 YES
5 CYCS CYCS CYCS 2523 0.16 -0.064 YES
6 PDK4 PDK4 PDK4 2533 0.16 -0.05 YES
7 UCP3 UCP3 UCP3 2695 0.15 -0.045 YES
8 COX7B COX7B COX7B 2714 0.15 -0.032 YES
9 COX8A COX8A COX8A 2716 0.15 -0.018 YES
10 NDUFB2 NDUFB2 NDUFB2 2743 0.15 -0.0058 YES
11 ATP5G1 ATP5G1 ATP5G1 2802 0.15 0.0045 YES
12 L2HGDH L2HGDH L2HGDH 2824 0.15 0.017 YES
13 COX6A1 COX6A1 COX6A1 3030 0.14 0.018 YES
14 SUCLG1 SUCLG1 SUCLG1 3044 0.14 0.03 YES
15 ATP5H ATP5H ATP5H 3081 0.13 0.04 YES
16 NDUFA3 NDUFA3 NDUFA3 3101 0.13 0.051 YES
17 NDUFA5 NDUFA5 NDUFA5 3118 0.13 0.062 YES
18 COX6C COX6C COX6C 3140 0.13 0.073 YES
19 NDUFA1 NDUFA1 NDUFA1 3182 0.13 0.082 YES
20 D2HGDH D2HGDH D2HGDH 3191 0.13 0.094 YES
21 PDHA1 PDHA1 PDHA1 3228 0.13 0.1 YES
22 NDUFA8 NDUFA8 NDUFA8 3251 0.13 0.11 YES
23 FH FH FH 3273 0.13 0.12 YES
24 COX5B COX5B COX5B 3321 0.12 0.13 YES
25 CYC1 CYC1 CYC1 3362 0.12 0.14 YES
26 OGDH OGDH OGDH 3396 0.12 0.15 YES
27 LDHB LDHB LDHB 3451 0.12 0.16 YES
28 UQCRHL UQCRHL UQCRHL 3465 0.12 0.17 YES
29 ATP5I ATP5I ATP5I 3509 0.11 0.18 YES
30 ATP5J ATP5J ATP5J 3519 0.11 0.19 YES
31 NDUFA2 NDUFA2 NDUFA2 3520 0.11 0.2 YES
32 ATP5D ATP5D ATP5D 3618 0.11 0.2 YES
33 ETFB ETFB ETFB 3666 0.11 0.21 YES
34 NDUFV2 NDUFV2 NDUFV2 3675 0.11 0.22 YES
35 UQCRQ UQCRQ UQCRQ 3688 0.11 0.23 YES
36 NDUFA12 NDUFA12 NDUFA12 3739 0.11 0.23 YES
37 DLD DLD DLD 3766 0.1 0.24 YES
38 NDUFB3 NDUFB3 NDUFB3 3778 0.1 0.25 YES
39 NDUFB7 NDUFB7 NDUFB7 3796 0.1 0.26 YES
40 ATP5B ATP5B ATP5B 3815 0.1 0.27 YES
41 ATP5J2 ATP5J2 ATP5J2 3819 0.1 0.28 YES
42 UQCR11 UQCR11 UQCR11 3883 0.1 0.28 YES
43 MDH2 MDH2 MDH2 3920 0.099 0.29 YES
44 SDHD SDHD SDHD 3957 0.098 0.3 YES
45 NDUFC2 NDUFC2 NDUFC2 4019 0.096 0.3 YES
46 NDUFA6 NDUFA6 NDUFA6 4025 0.095 0.31 YES
47 NDUFS7 NDUFS7 NDUFS7 4070 0.094 0.32 YES
48 UQCRH UQCRH UQCRH 4081 0.094 0.32 YES
49 ATP5O ATP5O ATP5O 4162 0.091 0.33 YES
50 SUCLA2 SUCLA2 SUCLA2 4189 0.091 0.34 YES
51 COX5A COX5A COX5A 4230 0.09 0.34 YES
52 NDUFA7 NDUFA7 NDUFA7 4262 0.089 0.35 YES
53 IDH3B IDH3B IDH3B 4293 0.088 0.35 YES
54 ATP5E ATP5E ATP5E 4316 0.087 0.36 YES
55 ATP5C1 ATP5C1 ATP5C1 4331 0.087 0.37 YES
56 NDUFV3 NDUFV3 NDUFV3 4377 0.085 0.37 YES
57 COX4I1 COX4I1 COX4I1 4401 0.084 0.38 YES
58 NDUFS6 NDUFS6 NDUFS6 4460 0.083 0.38 YES
59 NDUFB6 NDUFB6 NDUFB6 4565 0.08 0.39 YES
60 NDUFB5 NDUFB5 NDUFB5 4600 0.079 0.39 YES
61 NDUFC1 NDUFC1 NDUFC1 4642 0.078 0.4 YES
62 PDPR PDPR PDPR 4650 0.077 0.4 YES
63 ATP5F1 ATP5F1 ATP5F1 4680 0.077 0.41 YES
64 NDUFB10 NDUFB10 NDUFB10 4691 0.076 0.41 YES
65 ATP5A1 ATP5A1 ATP5A1 4736 0.075 0.42 YES
66 NDUFS3 NDUFS3 NDUFS3 4761 0.075 0.42 YES
67 UQCRFS1 UQCRFS1 UQCRFS1 4812 0.074 0.43 YES
68 NDUFS2 NDUFS2 NDUFS2 4818 0.074 0.44 YES
69 COX6B1 COX6B1 COX6B1 4830 0.073 0.44 YES
70 ACO2 ACO2 ACO2 4842 0.073 0.45 YES
71 UQCRC2 UQCRC2 UQCRC2 4867 0.072 0.45 YES
72 SDHC SDHC SDHC 4927 0.071 0.46 YES
73 IDH3A IDH3A IDH3A 5073 0.067 0.45 YES
74 COX7C COX7C COX7C 5081 0.067 0.46 YES
75 NDUFA4 NDUFA4 NDUFA4 5098 0.067 0.46 YES
76 NDUFB8 NDUFB8 NDUFB8 5099 0.067 0.47 YES
77 UQCRB UQCRB UQCRB 5230 0.064 0.47 YES
78 NDUFA9 NDUFA9 NDUFA9 5257 0.063 0.47 YES
79 SUCLG2 SUCLG2 SUCLG2 5281 0.063 0.48 YES
80 ETFA ETFA ETFA 5301 0.062 0.48 YES
81 BSG BSG BSG 5342 0.061 0.49 YES
82 NDUFA10 NDUFA10 NDUFA10 5413 0.06 0.49 YES
83 NDUFB4 NDUFB4 NDUFB4 5421 0.059 0.49 YES
84 NDUFA13 NDUFA13 NDUFA13 5424 0.059 0.5 YES
85 NDUFS8 NDUFS8 NDUFS8 5485 0.058 0.5 YES
86 NDUFV1 NDUFV1 NDUFV1 5588 0.056 0.5 YES
87 SDHA SDHA SDHA 5665 0.055 0.5 YES
88 NDUFB9 NDUFB9 NDUFB9 5865 0.051 0.49 NO
89 NDUFS4 NDUFS4 NDUFS4 5938 0.049 0.49 NO
90 ATP5L ATP5L ATP5L 6083 0.047 0.49 NO
91 DLAT DLAT DLAT 6270 0.044 0.48 NO
92 PDHB PDHB PDHB 6271 0.044 0.49 NO
93 SDHB SDHB SDHB 6446 0.04 0.48 NO
94 UQCRC1 UQCRC1 UQCRC1 6460 0.04 0.48 NO
95 PDHX PDHX PDHX 6530 0.039 0.48 NO
96 NDUFS1 NDUFS1 NDUFS1 6568 0.038 0.48 NO
97 NDUFAB1 NDUFAB1 NDUFAB1 6594 0.038 0.49 NO
98 CS CS CS 6765 0.035 0.48 NO
99 DLST DLST DLST 7091 0.03 0.47 NO
100 NDUFA11 NDUFA11 NDUFA11 7141 0.029 0.47 NO
101 IDH2 IDH2 IDH2 7238 0.028 0.46 NO
102 IDH3G IDH3G IDH3G 7462 0.024 0.45 NO
103 UCP1 UCP1 UCP1 7577 0.023 0.45 NO
104 COX7A2L COX7A2L COX7A2L 9338 -0.002 0.35 NO
105 NDUFS5 NDUFS5 NDUFS5 9871 -0.0093 0.32 NO
106 PDP2 PDP2 PDP2 10709 -0.022 0.28 NO
107 PDK2 PDK2 PDK2 10844 -0.024 0.27 NO
108 SLC16A1 SLC16A1 SLC16A1 11879 -0.041 0.22 NO
109 IDH1 IDH1 IDH1 13350 -0.082 0.14 NO
110 SLC16A8 SLC16A8 SLC16A8 13419 -0.085 0.15 NO
111 PDK1 PDK1 PDK1 13539 -0.089 0.15 NO
112 LDHA LDHA LDHA 14115 -0.12 0.13 NO
113 PDP1 PDP1 PDP1 14698 -0.15 0.11 NO
114 UCP2 UCP2 UCP2 15224 -0.19 0.094 NO
115 SLC16A3 SLC16A3 SLC16A3 16071 -0.28 0.072 NO
116 PDK3 PDK3 PDK3 16718 -0.37 0.07 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 ARGININE AND PROLINE METABOLISM.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARGININE AND PROLINE 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 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 LDHD LDHD LDHD 192 0.66 0.18 YES
2 TIMM17B TIMM17B TIMM17B 1655 0.24 0.17 YES
3 ATP5G1 ATP5G1 ATP5G1 2802 0.15 0.15 YES
4 SLC25A4 SLC25A4 SLC25A4 3160 0.13 0.16 YES
5 FXN FXN FXN 3224 0.13 0.2 YES
6 CYC1 CYC1 CYC1 3362 0.12 0.22 YES
7 ATP5B ATP5B ATP5B 3815 0.1 0.23 YES
8 COX17 COX17 COX17 3888 0.1 0.25 YES
9 MTX2 MTX2 MTX2 4099 0.093 0.27 YES
10 C18orf55 C18orf55 C18orf55 4108 0.093 0.3 YES
11 TIMM13 TIMM13 TIMM13 4181 0.091 0.32 YES
12 SLC25A13 SLC25A13 SLC25A13 4458 0.083 0.33 YES
13 GRPEL2 GRPEL2 GRPEL2 4539 0.081 0.34 YES
14 ATP5A1 ATP5A1 ATP5A1 4736 0.075 0.36 YES
15 TIMM17A TIMM17A TIMM17A 4809 0.074 0.37 YES
16 ACO2 ACO2 ACO2 4842 0.073 0.39 YES
17 DNAJC19 DNAJC19 DNAJC19 4983 0.069 0.4 YES
18 MTX1 MTX1 MTX1 5020 0.068 0.42 YES
19 HSPA9 HSPA9 HSPA9 5280 0.063 0.43 YES
20 TIMM8B TIMM8B TIMM8B 5387 0.06 0.44 YES
21 SLC25A12 SLC25A12 SLC25A12 5522 0.057 0.45 YES
22 TOMM5 TOMM5 TOMM5 5623 0.055 0.46 YES
23 FXC1 FXC1 FXC1 5690 0.054 0.47 YES
24 GRPEL1 GRPEL1 GRPEL1 5901 0.05 0.47 YES
25 TOMM40 TOMM40 TOMM40 6095 0.047 0.47 YES
26 CHCHD4 CHCHD4 CHCHD4 6207 0.045 0.48 YES
27 BCS1L BCS1L BCS1L 6273 0.044 0.49 YES
28 TOMM70A TOMM70A TOMM70A 6297 0.043 0.5 YES
29 TIMM22 TIMM22 TIMM22 6382 0.042 0.51 YES
30 PMPCA PMPCA PMPCA 6503 0.039 0.51 YES
31 TIMM44 TIMM44 TIMM44 6535 0.039 0.52 YES
32 TIMM50 TIMM50 TIMM50 6639 0.037 0.53 YES
33 TIMM10 TIMM10 TIMM10 6710 0.036 0.53 YES
34 CS CS CS 6765 0.035 0.54 YES
35 TOMM7 TOMM7 TOMM7 6823 0.034 0.55 YES
36 SAMM50 SAMM50 SAMM50 6952 0.032 0.55 YES
37 TIMM9 TIMM9 TIMM9 7300 0.027 0.54 YES
38 PMPCB PMPCB PMPCB 7389 0.026 0.54 YES
39 TAZ TAZ TAZ 7435 0.025 0.55 YES
40 IDH3G IDH3G IDH3G 7462 0.024 0.55 YES
41 TOMM22 TOMM22 TOMM22 8784 0.0059 0.48 NO
42 SLC25A6 SLC25A6 SLC25A6 9160 0.00041 0.46 NO
43 TIMM8A TIMM8A TIMM8A 9168 0.00031 0.46 NO
44 GFER GFER GFER 9601 -0.0059 0.44 NO
45 HSPD1 HSPD1 HSPD1 9679 -0.0069 0.43 NO
46 TOMM20 TOMM20 TOMM20 9855 -0.0091 0.42 NO
47 VDAC1 VDAC1 VDAC1 10055 -0.012 0.42 NO
48 HSCB HSCB HSCB 10577 -0.02 0.4 NO
49 COQ2 COQ2 COQ2 12742 -0.062 0.29 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

Figure S32.  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 PROPANOATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HMGCS2 HMGCS2 HMGCS2 461 0.5 0.046 YES
2 AOX1 AOX1 AOX1 627 0.44 0.099 YES
3 OXCT2 OXCT2 OXCT2 979 0.34 0.13 YES
4 ALDH1B1 ALDH1B1 ALDH1B1 1443 0.26 0.14 YES
5 ALDH2 ALDH2 ALDH2 1554 0.25 0.17 YES
6 ALDH6A1 ALDH6A1 ALDH6A1 1814 0.22 0.19 YES
7 ACADSB ACADSB ACADSB 2091 0.19 0.2 YES
8 BCAT2 BCAT2 BCAT2 2177 0.19 0.22 YES
9 ACAT1 ACAT1 ACAT1 2270 0.18 0.24 YES
10 ACAD8 ACAD8 ACAD8 2314 0.18 0.26 YES
11 MCCC2 MCCC2 MCCC2 2349 0.17 0.29 YES
12 EHHADH EHHADH EHHADH 2392 0.17 0.31 YES
13 ACADS ACADS ACADS 2399 0.17 0.34 YES
14 ALDH9A1 ALDH9A1 ALDH9A1 2746 0.15 0.34 YES
15 DBT DBT DBT 2953 0.14 0.35 YES
16 BCKDHB BCKDHB BCKDHB 3112 0.13 0.36 YES
17 IVD IVD IVD 3220 0.13 0.37 YES
18 HSD17B10 HSD17B10 HSD17B10 3245 0.13 0.38 YES
19 ACADM ACADM ACADM 3246 0.13 0.4 YES
20 ABAT ABAT ABAT 3326 0.12 0.42 YES
21 HMGCS1 HMGCS1 HMGCS1 3627 0.11 0.42 YES
22 ALDH7A1 ALDH7A1 ALDH7A1 3765 0.1 0.42 YES
23 DLD DLD DLD 3766 0.1 0.44 YES
24 PCCB PCCB PCCB 3786 0.1 0.45 YES
25 PCCA PCCA PCCA 3870 0.1 0.46 YES
26 HIBADH HIBADH HIBADH 4002 0.096 0.47 YES
27 ECHS1 ECHS1 ECHS1 4088 0.094 0.48 YES
28 HADHB HADHB HADHB 4204 0.091 0.48 YES
29 BCKDHA BCKDHA BCKDHA 4224 0.09 0.5 YES
30 OXCT1 OXCT1 OXCT1 4477 0.083 0.49 YES
31 AUH AUH AUH 4886 0.072 0.48 YES
32 HADH HADH HADH 4919 0.071 0.49 YES
33 HIBCH HIBCH HIBCH 5080 0.067 0.49 YES
34 HADHA HADHA HADHA 5325 0.062 0.48 YES
35 MCCC1 MCCC1 MCCC1 5346 0.061 0.49 YES
36 MCEE MCEE MCEE 5443 0.059 0.5 YES
37 HMGCL HMGCL HMGCL 5723 0.054 0.49 NO
38 MUT MUT MUT 6076 0.047 0.48 NO
39 ACAA1 ACAA1 ACAA1 6218 0.045 0.47 NO
40 ALDH3A2 ALDH3A2 ALDH3A2 10274 -0.015 0.25 NO
41 ACAT2 ACAT2 ACAT2 10306 -0.016 0.25 NO
42 ACAA2 ACAA2 ACAA2 13840 -0.1 0.067 NO
43 BCAT1 BCAT1 BCAT1 17354 -0.51 -0.056 NO
44 IL4I1 IL4I1 IL4I1 17656 -0.63 0.018 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 PROPANOATE METABOLISM.

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table 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 SLC2A4 SLC2A4 SLC2A4 123 0.74 0.2 YES
2 GHR GHR GHR 566 0.46 0.3 YES
3 HNF1A HNF1A HNF1A 803 0.39 0.4 YES
4 IRS1 IRS1 IRS1 956 0.35 0.49 YES
5 PRKCA PRKCA PRKCA 1429 0.27 0.54 YES
6 RPS6KA1 RPS6KA1 RPS6KA1 4065 0.094 0.42 NO
7 SRF SRF SRF 5317 0.062 0.37 NO
8 SOS1 SOS1 SOS1 6348 0.042 0.32 NO
9 PRKCB PRKCB PRKCB 6648 0.037 0.32 NO
10 PLCG1 PLCG1 PLCG1 6834 0.034 0.31 NO
11 INSR INSR INSR 6930 0.032 0.32 NO
12 MAPK3 MAPK3 MAPK3 7407 0.025 0.3 NO
13 RAF1 RAF1 RAF1 7899 0.018 0.28 NO
14 HRAS HRAS HRAS 8157 0.014 0.27 NO
15 STAT5B STAT5B STAT5B 10116 -0.013 0.16 NO
16 SOCS1 SOCS1 SOCS1 10123 -0.013 0.16 NO
17 MAP2K1 MAP2K1 MAP2K1 10138 -0.013 0.17 NO
18 GRB2 GRB2 GRB2 10621 -0.02 0.14 NO
19 GH1 GH1 GH1 11881 -0.041 0.087 NO
20 SHC1 SHC1 SHC1 12833 -0.065 0.052 NO
21 JAK2 JAK2 JAK2 12997 -0.07 0.063 NO
22 PTPN6 PTPN6 PTPN6 13202 -0.077 0.073 NO
23 MAPK1 MAPK1 MAPK1 13273 -0.079 0.091 NO
24 PIK3R1 PIK3R1 PIK3R1 13741 -0.097 0.092 NO
25 STAT5A STAT5A STAT5A 14664 -0.15 0.082 NO
26 PIK3CA PIK3CA PIK3CA 14717 -0.15 0.12 NO
27 PIK3CG PIK3CG PIK3CG 15498 -0.22 0.14 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 BUTANOATE METABOLISM.

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

genes ES table in pathway: KEGG INSULIN SIGNALING PATHWAY

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 CKMT2 CKMT2 CKMT2 310 0.57 0.056 YES
2 AGMAT AGMAT AGMAT 516 0.47 0.1 YES
3 GATM GATM GATM 769 0.4 0.14 YES
4 CKMT1B CKMT1B CKMT1B 907 0.36 0.18 YES
5 ALDH4A1 ALDH4A1 ALDH4A1 945 0.35 0.22 YES
6 MAOB MAOB MAOB 1073 0.33 0.26 YES
7 CKB CKB CKB 1251 0.3 0.28 YES
8 ALDH1B1 ALDH1B1 ALDH1B1 1443 0.26 0.31 YES
9 NOS1 NOS1 NOS1 1450 0.26 0.34 YES
10 ALDH2 ALDH2 ALDH2 1554 0.25 0.37 YES
11 CKMT1A CKMT1A CKMT1A 1677 0.24 0.39 YES
12 SAT2 SAT2 SAT2 2508 0.16 0.37 YES
13 ARG1 ARG1 ARG1 2554 0.16 0.38 YES
14 GAMT GAMT GAMT 2631 0.16 0.4 YES
15 P4HA3 P4HA3 P4HA3 2639 0.16 0.42 YES
16 ALDH9A1 ALDH9A1 ALDH9A1 2746 0.15 0.43 YES
17 GOT1 GOT1 GOT1 2841 0.15 0.45 YES
18 CPS1 CPS1 CPS1 2978 0.14 0.46 YES
19 NAGS NAGS NAGS 3128 0.13 0.47 YES
20 GOT2 GOT2 GOT2 3596 0.11 0.45 YES
21 PYCRL PYCRL PYCRL 3659 0.11 0.46 YES
22 ALDH7A1 ALDH7A1 ALDH7A1 3765 0.1 0.47 YES
23 MAOA MAOA MAOA 3884 0.1 0.48 YES
24 ARG2 ARG2 ARG2 4492 0.082 0.46 NO
25 ASL ASL ASL 4630 0.078 0.46 NO
26 PYCR1 PYCR1 PYCR1 4633 0.078 0.47 NO
27 OAT OAT OAT 4984 0.069 0.46 NO
28 GLUL GLUL GLUL 5815 0.052 0.42 NO
29 ALDH18A1 ALDH18A1 ALDH18A1 6706 0.036 0.37 NO
30 AMD1 AMD1 AMD1 6833 0.034 0.37 NO
31 NOS3 NOS3 NOS3 7244 0.028 0.35 NO
32 ACY1 ACY1 ACY1 7534 0.024 0.34 NO
33 ADC ADC ADC 8868 0.0046 0.26 NO
34 NOS2 NOS2 NOS2 9255 -0.00078 0.24 NO
35 ALDH3A2 ALDH3A2 ALDH3A2 10274 -0.015 0.19 NO
36 P4HA1 P4HA1 P4HA1 10517 -0.019 0.18 NO
37 PYCR2 PYCR2 PYCR2 11323 -0.032 0.13 NO
38 GLUD1 GLUD1 GLUD1 12133 -0.047 0.095 NO
39 ASS1 ASS1 ASS1 12155 -0.048 0.1 NO
40 SMS SMS SMS 12506 -0.056 0.088 NO
41 ABP1 ABP1 ABP1 12682 -0.061 0.086 NO
42 DAO DAO DAO 12934 -0.068 0.08 NO
43 SRM SRM SRM 13026 -0.071 0.084 NO
44 LAP3 LAP3 LAP3 13400 -0.084 0.074 NO
45 GLUD2 GLUD2 GLUD2 13530 -0.089 0.079 NO
46 SAT1 SAT1 SAT1 13569 -0.09 0.088 NO
47 ODC1 ODC1 ODC1 13899 -0.1 0.083 NO
48 P4HA2 P4HA2 P4HA2 14630 -0.14 0.061 NO
49 GLS GLS GLS 15141 -0.18 0.056 NO
50 CKM CKM CKM 15567 -0.22 0.061 NO
51 PRODH PRODH PRODH 15857 -0.25 0.077 NO
52 GLS2 GLS2 GLS2 16385 -0.32 0.088 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 INSULIN SIGNALING PATHWAY.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG INSULIN 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 ADIPOCYTOKINE SIGNALING PATHWAY

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 ATP4A ATP4A ATP4A 227 0.63 0.04 YES
2 COX4I2 COX4I2 COX4I2 788 0.39 0.041 YES
3 ATP6V1G2 ATP6V1G2 ATP6V1G2 911 0.36 0.065 YES
4 COX7A1 COX7A1 COX7A1 1104 0.32 0.081 YES
5 ATP6V0E2 ATP6V0E2 ATP6V0E2 1253 0.3 0.097 YES
6 NDUFA4L2 NDUFA4L2 NDUFA4L2 1984 0.2 0.073 YES
7 ATP6V1E2 ATP6V1E2 ATP6V1E2 2352 0.17 0.067 YES
8 ATP6V1B1 ATP6V1B1 ATP6V1B1 2376 0.17 0.08 YES
9 NDUFB1 NDUFB1 NDUFB1 2435 0.17 0.091 YES
10 COX7B COX7B COX7B 2714 0.15 0.088 YES
11 COX10 COX10 COX10 2715 0.15 0.1 YES
12 COX8A COX8A COX8A 2716 0.15 0.11 YES
13 NDUFB2 NDUFB2 NDUFB2 2743 0.15 0.12 YES
14 ATP5G1 ATP5G1 ATP5G1 2802 0.15 0.14 YES
15 COX6A1 COX6A1 COX6A1 3030 0.14 0.13 YES
16 ATP5H ATP5H ATP5H 3081 0.13 0.14 YES
17 NDUFA3 NDUFA3 NDUFA3 3101 0.13 0.15 YES
18 NDUFA5 NDUFA5 NDUFA5 3118 0.13 0.16 YES
19 ATP4B ATP4B ATP4B 3139 0.13 0.17 YES
20 COX6C COX6C COX6C 3140 0.13 0.18 YES
21 NDUFA1 NDUFA1 NDUFA1 3182 0.13 0.19 YES
22 ATP6V1C2 ATP6V1C2 ATP6V1C2 3195 0.13 0.2 YES
23 NDUFA8 NDUFA8 NDUFA8 3251 0.13 0.21 YES
24 COX8C COX8C COX8C 3265 0.13 0.22 YES
25 COX5B COX5B COX5B 3321 0.12 0.23 YES
26 CYC1 CYC1 CYC1 3362 0.12 0.23 YES
27 UQCRHL UQCRHL UQCRHL 3465 0.12 0.24 YES
28 ATP5I ATP5I ATP5I 3509 0.11 0.25 YES
29 ATP5J ATP5J ATP5J 3519 0.11 0.26 YES
30 NDUFA2 NDUFA2 NDUFA2 3520 0.11 0.26 YES
31 ATP5D ATP5D ATP5D 3618 0.11 0.27 YES
32 NDUFV2 NDUFV2 NDUFV2 3675 0.11 0.27 YES
33 UQCRQ UQCRQ UQCRQ 3688 0.11 0.28 YES
34 NDUFB3 NDUFB3 NDUFB3 3778 0.1 0.29 YES
35 NDUFB7 NDUFB7 NDUFB7 3796 0.1 0.29 YES
36 ATP5B ATP5B ATP5B 3815 0.1 0.3 YES
37 ATP5J2 ATP5J2 ATP5J2 3819 0.1 0.31 YES
38 UQCR10 UQCR10 UQCR10 3829 0.1 0.32 YES
39 UQCR11 UQCR11 UQCR11 3883 0.1 0.32 YES
40 COX17 COX17 COX17 3888 0.1 0.33 YES
41 SDHD SDHD SDHD 3957 0.098 0.34 YES
42 NDUFC2 NDUFC2 NDUFC2 4019 0.096 0.34 YES
43 NDUFA6 NDUFA6 NDUFA6 4025 0.095 0.35 YES
44 NDUFS7 NDUFS7 NDUFS7 4070 0.094 0.35 YES
45 UQCRH UQCRH UQCRH 4081 0.094 0.36 YES
46 COX15 COX15 COX15 4138 0.092 0.37 YES
47 ATP5G3 ATP5G3 ATP5G3 4159 0.092 0.37 YES
48 ATP5O ATP5O ATP5O 4162 0.091 0.38 YES
49 COX5A COX5A COX5A 4230 0.09 0.38 YES
50 NDUFA7 NDUFA7 NDUFA7 4262 0.089 0.39 YES
51 ATP6V0B ATP6V0B ATP6V0B 4301 0.088 0.39 YES
52 ATP5E ATP5E ATP5E 4316 0.087 0.4 YES
53 ATP5C1 ATP5C1 ATP5C1 4331 0.087 0.41 YES
54 NDUFV3 NDUFV3 NDUFV3 4377 0.085 0.41 YES
55 COX4I1 COX4I1 COX4I1 4401 0.084 0.42 YES
56 NDUFS6 NDUFS6 NDUFS6 4460 0.083 0.42 YES
57 COX11 COX11 COX11 4549 0.08 0.42 YES
58 NDUFB6 NDUFB6 NDUFB6 4565 0.08 0.43 YES
59 COX7A2 COX7A2 COX7A2 4568 0.08 0.44 YES
60 NDUFB5 NDUFB5 NDUFB5 4600 0.079 0.44 YES
61 NDUFC1 NDUFC1 NDUFC1 4642 0.078 0.44 YES
62 ATP5F1 ATP5F1 ATP5F1 4680 0.077 0.45 YES
63 NDUFB10 NDUFB10 NDUFB10 4691 0.076 0.46 YES
64 ATP5A1 ATP5A1 ATP5A1 4736 0.075 0.46 YES
65 NDUFS3 NDUFS3 NDUFS3 4761 0.075 0.46 YES
66 ATP6V1H ATP6V1H ATP6V1H 4778 0.074 0.47 YES
67 UQCRFS1 UQCRFS1 UQCRFS1 4812 0.074 0.47 YES
68 LHPP LHPP LHPP 4813 0.074 0.48 YES
69 NDUFS2 NDUFS2 NDUFS2 4818 0.074 0.49 YES
70 COX6B1 COX6B1 COX6B1 4830 0.073 0.49 YES
71 UQCRC2 UQCRC2 UQCRC2 4867 0.072 0.5 YES
72 SDHC SDHC SDHC 4927 0.071 0.5 YES
73 ATP6V0D1 ATP6V0D1 ATP6V0D1 5039 0.068 0.5 YES
74 COX7C COX7C COX7C 5081 0.067 0.5 YES
75 NDUFA4 NDUFA4 NDUFA4 5098 0.067 0.5 YES
76 NDUFB8 NDUFB8 NDUFB8 5099 0.067 0.51 YES
77 UQCRB UQCRB UQCRB 5230 0.064 0.51 YES
78 NDUFA9 NDUFA9 NDUFA9 5257 0.063 0.51 YES
79 NDUFA10 NDUFA10 NDUFA10 5413 0.06 0.51 YES
80 NDUFB4 NDUFB4 NDUFB4 5421 0.059 0.51 YES
81 NDUFS8 NDUFS8 NDUFS8 5485 0.058 0.52 YES
82 ATP5G2 ATP5G2 ATP5G2 5506 0.057 0.52 YES
83 NDUFV1 NDUFV1 NDUFV1 5588 0.056 0.52 YES
84 SDHA SDHA SDHA 5665 0.055 0.52 YES
85 ATP6V1D ATP6V1D ATP6V1D 5834 0.051 0.51 NO
86 NDUFB9 NDUFB9 NDUFB9 5865 0.051 0.52 NO
87 NDUFS4 NDUFS4 NDUFS4 5938 0.049 0.52 NO
88 ATP6V0E1 ATP6V0E1 ATP6V0E1 6081 0.047 0.51 NO
89 ATP5L ATP5L ATP5L 6083 0.047 0.52 NO
90 SDHB SDHB SDHB 6446 0.04 0.5 NO
91 UQCRC1 UQCRC1 UQCRC1 6460 0.04 0.5 NO
92 NDUFS1 NDUFS1 NDUFS1 6568 0.038 0.5 NO
93 NDUFAB1 NDUFAB1 NDUFAB1 6594 0.038 0.5 NO
94 PPA2 PPA2 PPA2 6676 0.037 0.5 NO
95 ATP6AP1 ATP6AP1 ATP6AP1 6995 0.031 0.48 NO
96 NDUFA11 NDUFA11 NDUFA11 7141 0.029 0.48 NO
97 ATP6V1C1 ATP6V1C1 ATP6V1C1 7635 0.022 0.45 NO
98 ATP6V0C ATP6V0C ATP6V0C 8020 0.016 0.43 NO
99 ATP6V1G1 ATP6V1G1 ATP6V1G1 9071 0.0015 0.38 NO
100 ATP6V0A1 ATP6V0A1 ATP6V0A1 9295 -0.0013 0.36 NO
101 COX7A2L COX7A2L COX7A2L 9338 -0.002 0.36 NO
102 ATP6V1F ATP6V1F ATP6V1F 9700 -0.007 0.34 NO
103 NDUFS5 NDUFS5 NDUFS5 9871 -0.0093 0.33 NO
104 ATP6V0A4 ATP6V0A4 ATP6V0A4 11430 -0.034 0.25 NO
105 ATP6V1A ATP6V1A ATP6V1A 11458 -0.034 0.25 NO
106 ATP6V1E1 ATP6V1E1 ATP6V1E1 11877 -0.041 0.23 NO
107 ATP6V0A2 ATP6V0A2 ATP6V0A2 12906 -0.068 0.18 NO
108 PPA1 PPA1 PPA1 13401 -0.084 0.16 NO
109 ATP12A ATP12A ATP12A 13467 -0.087 0.16 NO
110 ATP6V1B2 ATP6V1B2 ATP6V1B2 14119 -0.12 0.13 NO
111 TCIRG1 TCIRG1 TCIRG1 15324 -0.2 0.082 NO
112 ATP6V0D2 ATP6V0D2 ATP6V0D2 16565 -0.35 0.042 NO
113 COX6B2 COX6B2 COX6B2 17075 -0.44 0.05 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype 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 GLYCOLYSIS GLUCONEOGENESIS 55 genes.ES.table 0.42 1.3 0.15 0.21 1 0.31 0.27 0.22 0.17 0
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.44 1.4 0.071 0.11 0.99 0.27 0.25 0.2 0.086 0
KEGG FATTY ACID METABOLISM 37 genes.ES.table 0.44 1.3 0.21 0.22 1 0.16 0.14 0.14 0.19 0
KEGG PURINE METABOLISM 154 genes.ES.table 0.42 1.7 0 0.042 0.68 0.23 0.26 0.18 0.019 0
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 29 genes.ES.table 0.49 1.5 0.038 0.098 0.98 0.1 0.041 0.099 0.072 0
KEGG CYSTEINE AND METHIONINE METABOLISM 33 genes.ES.table 0.45 1.4 0.092 0.15 1 0.3 0.27 0.22 0.11 0
KEGG HISTIDINE METABOLISM 29 genes.ES.table 0.53 1.4 0.085 0.14 1 0.38 0.23 0.29 0.11 0
KEGG TYROSINE METABOLISM 39 genes.ES.table 0.53 1.4 0.058 0.14 1 0.28 0.19 0.23 0.11 0
KEGG TRYPTOPHAN METABOLISM 39 genes.ES.table 0.62 1.6 0.0043 0.051 0.86 0.28 0.14 0.24 0.028 0
KEGG GLUTATHIONE METABOLISM 46 genes.ES.table 0.39 1.2 0.19 0.22 1 0.065 0.06 0.061 0.19 0
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 ASB2 ASB2 ASB2 169 0.87 0.038 YES
2 NCF4 NCF4 NCF4 583 0.64 0.05 YES
3 FCGR1A FCGR1A FCGR1A 620 0.63 0.082 YES
4 NCF2 NCF2 NCF2 684 0.6 0.11 YES
5 UBE2C UBE2C UBE2C 699 0.6 0.14 YES
6 CYBB CYBB CYBB 826 0.56 0.17 YES
7 PSMA8 PSMA8 PSMA8 909 0.54 0.19 YES
8 MRC1 MRC1 MRC1 992 0.52 0.21 YES
9 FCGR1B FCGR1B FCGR1B 1052 0.5 0.24 YES
10 FBXO17 FBXO17 FBXO17 1054 0.5 0.26 YES
11 SPSB4 SPSB4 SPSB4 1153 0.47 0.28 YES
12 CD207 CD207 CD207 1230 0.46 0.31 YES
13 PSMB9 PSMB9 PSMB9 1307 0.44 0.32 YES
14 HLA-G HLA-G HLA-G 1756 0.36 0.32 YES
15 CDC20 CDC20 CDC20 1800 0.35 0.34 YES
16 KLHL13 KLHL13 KLHL13 1897 0.33 0.35 YES
17 HLA-F HLA-F HLA-F 1911 0.33 0.36 YES
18 TAP1 TAP1 TAP1 1983 0.32 0.38 YES
19 TAP2 TAP2 TAP2 2164 0.29 0.38 YES
20 SOCS3 SOCS3 SOCS3 2483 0.25 0.38 YES
21 CTSS CTSS CTSS 2639 0.23 0.38 YES
22 SOCS1 SOCS1 SOCS1 2688 0.23 0.39 YES
23 PSMB10 PSMB10 PSMB10 2841 0.21 0.4 YES
24 FBXO27 FBXO27 FBXO27 2912 0.2 0.4 YES
25 UBE2L6 UBE2L6 UBE2L6 2913 0.2 0.41 YES
26 HLA-B HLA-B HLA-B 2932 0.2 0.42 YES
27 HLA-C HLA-C HLA-C 3069 0.19 0.43 YES
28 PSMB8 PSMB8 PSMB8 3225 0.18 0.43 YES
29 TRIM9 TRIM9 TRIM9 3278 0.17 0.43 YES
30 TRIM21 TRIM21 TRIM21 3309 0.17 0.44 YES
31 B2M B2M B2M 3410 0.16 0.44 YES
32 SPSB1 SPSB1 SPSB1 3447 0.16 0.45 YES
33 ERAP1 ERAP1 ERAP1 3536 0.16 0.46 YES
34 HLA-A HLA-A HLA-A 3615 0.15 0.46 YES
35 MRC2 MRC2 MRC2 3616 0.15 0.47 YES
36 PSME2 PSME2 PSME2 3636 0.15 0.48 YES
37 FBXO6 FBXO6 FBXO6 3640 0.15 0.48 YES
38 DTX3L DTX3L DTX3L 4133 0.12 0.46 NO
39 ASB13 ASB13 ASB13 4227 0.12 0.46 NO
40 UBA7 UBA7 UBA7 4356 0.11 0.46 NO
41 LNPEP LNPEP LNPEP 4391 0.11 0.46 NO
42 UBE2J1 UBE2J1 UBE2J1 4628 0.096 0.46 NO
43 SMURF2 SMURF2 SMURF2 4647 0.095 0.46 NO
44 SKP2 SKP2 SKP2 4675 0.094 0.46 NO
45 UBE2D1 UBE2D1 UBE2D1 4830 0.088 0.46 NO
46 PSME1 PSME1 PSME1 4860 0.087 0.46 NO
47 CYBA CYBA CYBA 4948 0.084 0.46 NO
48 UBA6 UBA6 UBA6 5020 0.081 0.46 NO
49 SEC23A SEC23A SEC23A 5134 0.078 0.46 NO
50 UBE2S UBE2S UBE2S 5372 0.069 0.45 NO
51 RNF138 RNF138 RNF138 5386 0.069 0.46 NO
52 TRIM36 TRIM36 TRIM36 5393 0.069 0.46 NO
53 PSMA4 PSMA4 PSMA4 5410 0.068 0.46 NO
54 FBXO2 FBXO2 FBXO2 5482 0.066 0.46 NO
55 SEC24D SEC24D SEC24D 5502 0.066 0.46 NO
56 CBLB CBLB CBLB 5513 0.065 0.47 NO
57 SMURF1 SMURF1 SMURF1 5569 0.063 0.47 NO
58 RNF34 RNF34 RNF34 5705 0.06 0.46 NO
59 ATG7 ATG7 ATG7 5802 0.057 0.46 NO
60 UBA3 UBA3 UBA3 5848 0.056 0.46 NO
61 UBE2N UBE2N UBE2N 5981 0.053 0.46 NO
62 TRIM63 TRIM63 TRIM63 5983 0.053 0.46 NO
63 KLHL20 KLHL20 KLHL20 6053 0.051 0.46 NO
64 PSMA3 PSMA3 PSMA3 6156 0.049 0.45 NO
65 ASB9 ASB9 ASB9 6162 0.049 0.46 NO
66 PSMA5 PSMA5 PSMA5 6365 0.045 0.45 NO
67 ASB12 ASB12 ASB12 6390 0.044 0.45 NO
68 VHL VHL VHL 6482 0.042 0.45 NO
69 UBE2E2 UBE2E2 UBE2E2 6483 0.042 0.45 NO
70 PSMA6 PSMA6 PSMA6 6509 0.042 0.45 NO
71 PSMB2 PSMB2 PSMB2 6656 0.039 0.44 NO
72 PSMD11 PSMD11 PSMD11 6680 0.039 0.44 NO
73 PSMD1 PSMD1 PSMD1 6886 0.035 0.43 NO
74 PSMD7 PSMD7 PSMD7 6901 0.035 0.44 NO
75 PSMD5 PSMD5 PSMD5 6976 0.034 0.43 NO
76 PSMA1 PSMA1 PSMA1 7037 0.033 0.43 NO
77 UBE2G1 UBE2G1 UBE2G1 7046 0.033 0.43 NO
78 TRIM11 TRIM11 TRIM11 7075 0.032 0.43 NO
79 UBE2L3 UBE2L3 UBE2L3 7111 0.032 0.43 NO
80 PSMC2 PSMC2 PSMC2 7116 0.032 0.43 NO
81 PSMA2 PSMA2 PSMA2 7223 0.03 0.43 NO
82 UBE3C UBE3C UBE3C 7322 0.028 0.43 NO
83 FBXW7 FBXW7 FBXW7 7375 0.028 0.42 NO
84 RNF6 RNF6 RNF6 7435 0.027 0.42 NO
85 ANAPC1 ANAPC1 ANAPC1 7462 0.027 0.42 NO
86 RBX1 RBX1 RBX1 7482 0.026 0.42 NO
87 ITGAV ITGAV ITGAV 7512 0.026 0.42 NO
88 PSMD12 PSMD12 PSMD12 7647 0.024 0.42 NO
89 PSMA7 PSMA7 PSMA7 7667 0.024 0.42 NO
90 PSME4 PSME4 PSME4 7736 0.023 0.41 NO
91 PSMD13 PSMD13 PSMD13 7764 0.023 0.41 NO
92 ASB3 ASB3 ASB3 7777 0.023 0.41 NO
93 TRIM32 TRIM32 TRIM32 7822 0.022 0.41 NO
94 WSB1 WSB1 WSB1 7853 0.022 0.41 NO
95 SEC31A SEC31A SEC31A 8036 0.02 0.4 NO
96 UBR2 UBR2 UBR2 8066 0.019 0.4 NO
97 TPP2 TPP2 TPP2 8069 0.019 0.4 NO
98 CDC26 CDC26 CDC26 8071 0.019 0.4 NO
99 ASB7 ASB7 ASB7 8088 0.019 0.4 NO
100 ASB16 ASB16 ASB16 8127 0.018 0.4 NO
101 CUL2 CUL2 CUL2 8189 0.018 0.4 NO
102 PSMB3 PSMB3 PSMB3 8242 0.017 0.4 NO
103 UBE2A UBE2A UBE2A 8246 0.017 0.4 NO
104 ITGB5 ITGB5 ITGB5 8302 0.017 0.4 NO
105 UBR1 UBR1 UBR1 8365 0.016 0.4 NO
106 PSMB4 PSMB4 PSMB4 8403 0.015 0.39 NO
107 UBE2W UBE2W UBE2W 8439 0.015 0.39 NO
108 ANAPC10 ANAPC10 ANAPC10 8500 0.014 0.39 NO
109 UBE2E1 UBE2E1 UBE2E1 8602 0.013 0.38 NO
110 CDC27 CDC27 CDC27 8605 0.013 0.39 NO
111 PSMD14 PSMD14 PSMD14 8607 0.013 0.39 NO
112 RNF4 RNF4 RNF4 8664 0.012 0.38 NO
113 CD36 CD36 CD36 8798 0.011 0.38 NO
114 TRIP12 TRIP12 TRIP12 8808 0.011 0.38 NO
115 WWP1 WWP1 WWP1 8843 0.011 0.38 NO
116 PSMB1 PSMB1 PSMB1 8909 0.01 0.37 NO
117 UBE2G2 UBE2G2 UBE2G2 8911 0.01 0.37 NO
118 UBA52 UBA52 UBA52 9051 0.0087 0.37 NO
119 ANAPC4 ANAPC4 ANAPC4 9058 0.0086 0.37 NO
120 RBCK1 RBCK1 RBCK1 9210 0.0072 0.36 NO
121 UBE2J2 UBE2J2 UBE2J2 9215 0.0071 0.36 NO
122 UBE2Z UBE2Z UBE2Z 9218 0.0071 0.36 NO
123 CUL1 CUL1 CUL1 9242 0.0069 0.36 NO
124 UBE2Q1 UBE2Q1 UBE2Q1 9243 0.0069 0.36 NO
125 NEDD4 NEDD4 NEDD4 9258 0.0067 0.36 NO
126 HECTD3 HECTD3 HECTD3 9272 0.0066 0.36 NO
127 PSMD3 PSMD3 PSMD3 9287 0.0065 0.36 NO
128 PSMD4 PSMD4 PSMD4 9326 0.0061 0.36 NO
129 SAR1B SAR1B SAR1B 9347 0.0059 0.35 NO
130 SEC13 SEC13 SEC13 9354 0.0059 0.35 NO
131 GAN GAN GAN 9381 0.0056 0.35 NO
132 UBE2Q2 UBE2Q2 UBE2Q2 9395 0.0054 0.35 NO
133 UBE2V2 UBE2V2 UBE2V2 9414 0.0053 0.35 NO
134 PSMD2 PSMD2 PSMD2 9438 0.005 0.35 NO
135 PSMF1 PSMF1 PSMF1 9454 0.0048 0.35 NO
136 SEC61A2 SEC61A2 SEC61A2 9520 0.0042 0.35 NO
137 SEC61B SEC61B SEC61B 9536 0.0041 0.35 NO
138 BLMH BLMH BLMH 9548 0.0039 0.34 NO
139 KLHL9 KLHL9 KLHL9 9585 0.0036 0.34 NO
140 PSMD6 PSMD6 PSMD6 9630 0.0031 0.34 NO
141 UBE2F UBE2F UBE2F 9741 0.0022 0.34 NO
142 RNF220 RNF220 RNF220 9761 0.002 0.33 NO
143 SEC61A1 SEC61A1 SEC61A1 9815 0.0016 0.33 NO
144 UBA2 UBA2 UBA2 9856 0.001 0.33 NO
145 ASB6 ASB6 ASB6 9874 0.00088 0.33 NO
146 PSMC6 PSMC6 PSMC6 9878 0.00086 0.33 NO
147 PSMB6 PSMB6 PSMB6 9986 -0.00029 0.32 NO
148 UBE2H UBE2H UBE2H 10013 -0.0005 0.32 NO
149 RPS27A RPS27A RPS27A 10076 -0.0011 0.32 NO
150 UBE2B UBE2B UBE2B 10177 -0.002 0.31 NO
151 HUWE1 HUWE1 HUWE1 10198 -0.0022 0.31 NO
152 NPEPPS NPEPPS NPEPPS 10224 -0.0023 0.31 NO
153 VPRBP VPRBP VPRBP 10244 -0.0026 0.31 NO
154 UBE2D3 UBE2D3 UBE2D3 10318 -0.0033 0.3 NO
155 MKRN1 MKRN1 MKRN1 10333 -0.0034 0.3 NO
156 PSMC4 PSMC4 PSMC4 10346 -0.0036 0.3 NO
157 RNF25 RNF25 RNF25 10362 -0.0038 0.3 NO
158 ANAPC5 ANAPC5 ANAPC5 10586 -0.0059 0.29 NO
159 UBE2K UBE2K UBE2K 10593 -0.0059 0.29 NO
160 TCEB1 TCEB1 TCEB1 10691 -0.0067 0.28 NO
161 TRIM37 TRIM37 TRIM37 10714 -0.007 0.28 NO
162 PSMC1 PSMC1 PSMC1 10749 -0.0073 0.28 NO
163 ANAPC7 ANAPC7 ANAPC7 10783 -0.0076 0.28 NO
164 SEC24B SEC24B SEC24B 10805 -0.0079 0.28 NO
165 ANAPC2 ANAPC2 ANAPC2 10815 -0.0079 0.28 NO
166 PSMD10 PSMD10 PSMD10 10860 -0.0083 0.28 NO
167 SEC24C SEC24C SEC24C 10864 -0.0084 0.28 NO
168 PSMC5 PSMC5 PSMC5 10973 -0.0094 0.27 NO
169 UBE2R2 UBE2R2 UBE2R2 10974 -0.0094 0.27 NO
170 UBE2D2 UBE2D2 UBE2D2 11014 -0.0098 0.27 NO
171 CUL3 CUL3 CUL3 11039 -0.01 0.27 NO
172 PDIA3 PDIA3 PDIA3 11062 -0.01 0.27 NO
173 SEC61G SEC61G SEC61G 11116 -0.011 0.27 NO
174 UBE3A UBE3A UBE3A 11196 -0.012 0.26 NO
175 ASB8 ASB8 ASB8 11262 -0.012 0.26 NO
176 FBXW11 FBXW11 FBXW11 11326 -0.013 0.26 NO
177 PSMC3 PSMC3 PSMC3 11355 -0.013 0.26 NO
178 HSPA5 HSPA5 HSPA5 11529 -0.014 0.25 NO
179 PSMB7 PSMB7 PSMB7 11552 -0.015 0.25 NO
180 CALR CALR CALR 11575 -0.015 0.25 NO
181 UBE4A UBE4A UBE4A 11659 -0.016 0.24 NO
182 UBR4 UBR4 UBR4 11762 -0.016 0.24 NO
183 CDC16 CDC16 CDC16 11805 -0.017 0.24 NO
184 CDC23 CDC23 CDC23 11807 -0.017 0.24 NO
185 UBA1 UBA1 UBA1 11915 -0.018 0.23 NO
186 CUL5 CUL5 CUL5 11916 -0.018 0.24 NO
187 KEAP1 KEAP1 KEAP1 11966 -0.018 0.23 NO
188 FBXO4 FBXO4 FBXO4 12013 -0.018 0.23 NO
189 BTRC BTRC BTRC 12032 -0.019 0.23 NO
190 LRSAM1 LRSAM1 LRSAM1 12215 -0.02 0.22 NO
191 RNF41 RNF41 RNF41 12264 -0.021 0.22 NO
192 UBE2E3 UBE2E3 UBE2E3 12337 -0.022 0.22 NO
193 HERC2 HERC2 HERC2 12382 -0.022 0.22 NO
194 PSMB5 PSMB5 PSMB5 12404 -0.022 0.22 NO
195 LRRC41 LRRC41 LRRC41 12500 -0.023 0.21 NO
196 PSMD9 PSMD9 PSMD9 12646 -0.025 0.2 NO
197 PSMD8 PSMD8 PSMD8 12657 -0.025 0.21 NO
198 CUL7 CUL7 CUL7 12754 -0.026 0.2 NO
199 PJA2 PJA2 PJA2 12985 -0.028 0.19 NO
200 ARIH2 ARIH2 ARIH2 13062 -0.029 0.19 NO
201 RNF123 RNF123 RNF123 13199 -0.031 0.18 NO
202 UBE2O UBE2O UBE2O 13360 -0.032 0.18 NO
203 UBE3B UBE3B UBE3B 13458 -0.034 0.17 NO
204 UBA5 UBA5 UBA5 13553 -0.035 0.17 NO
205 SKP1 SKP1 SKP1 13659 -0.036 0.16 NO
206 PJA1 PJA1 PJA1 13680 -0.036 0.16 NO
207 SAE1 SAE1 SAE1 13818 -0.038 0.16 NO
208 SPSB2 SPSB2 SPSB2 13822 -0.038 0.16 NO
209 RCHY1 RCHY1 RCHY1 13890 -0.039 0.16 NO
210 TCEB2 TCEB2 TCEB2 13902 -0.039 0.16 NO
211 ANAPC11 ANAPC11 ANAPC11 13915 -0.039 0.16 NO
212 DET1 DET1 DET1 13940 -0.039 0.16 NO
213 ANAPC13 ANAPC13 ANAPC13 13996 -0.04 0.16 NO
214 CDC34 CDC34 CDC34 14128 -0.042 0.16 NO
215 UBE2M UBE2M UBE2M 14247 -0.044 0.15 NO
216 CANX CANX CANX 14312 -0.044 0.15 NO
217 ASB1 ASB1 ASB1 14343 -0.045 0.15 NO
218 FBXW8 FBXW8 FBXW8 14364 -0.045 0.15 NO
219 DZIP3 DZIP3 DZIP3 14516 -0.047 0.15 NO
220 UBOX5 UBOX5 UBOX5 14555 -0.048 0.15 NO
221 FBXO3 FBXO3 FBXO3 14598 -0.049 0.15 NO
222 RNF144B RNF144B RNF144B 14746 -0.051 0.14 NO
223 ZBTB16 ZBTB16 ZBTB16 14841 -0.053 0.14 NO
224 UBE2D4 UBE2D4 UBE2D4 15146 -0.058 0.13 NO
225 FBXO44 FBXO44 FBXO44 15418 -0.064 0.11 NO
226 STUB1 STUB1 STUB1 15420 -0.064 0.12 NO
227 RNF182 RNF182 RNF182 16816 -0.11 0.045 NO
228 ASB4 ASB4 ASB4 17412 -0.16 0.02 NO
229 PARK2 PARK2 PARK2 17686 -0.2 0.016 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 GLYCOLYSIS GLUCONEOGENESIS.

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table 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 CD28 CD28 CD28 85 0.97 0.064 YES
2 CD247 CD247 CD247 124 0.92 0.13 YES
3 LCK LCK LCK 230 0.82 0.18 YES
4 CCR5 CCR5 CCR5 302 0.77 0.23 YES
5 DOCK2 DOCK2 DOCK2 337 0.75 0.28 YES
6 CD8B CD8B CD8B 532 0.66 0.32 YES
7 HCK HCK HCK 615 0.63 0.36 YES
8 PSMA8 PSMA8 PSMA8 909 0.54 0.38 YES
9 CXCR4 CXCR4 CXCR4 1176 0.47 0.4 YES
10 PSMB9 PSMB9 PSMB9 1307 0.44 0.42 YES
11 CD4 CD4 CD4 1371 0.42 0.45 YES
12 APOBEC3G APOBEC3G APOBEC3G 1728 0.36 0.45 YES
13 AP1S2 AP1S2 AP1S2 2745 0.22 0.41 YES
14 PSMB10 PSMB10 PSMB10 2841 0.21 0.42 YES
15 NUP210 NUP210 NUP210 2872 0.21 0.43 YES
16 PSMB8 PSMB8 PSMB8 3225 0.18 0.43 YES
17 B2M B2M B2M 3410 0.16 0.43 YES
18 TAF4B TAF4B TAF4B 3415 0.16 0.44 YES
19 RCC1 RCC1 RCC1 3503 0.16 0.44 YES
20 HLA-A HLA-A HLA-A 3615 0.15 0.45 YES
21 PSME2 PSME2 PSME2 3636 0.15 0.46 YES
22 ELMO1 ELMO1 ELMO1 3915 0.13 0.45 NO
23 TAF5 TAF5 TAF5 4273 0.11 0.44 NO
24 GTF2E1 GTF2E1 GTF2E1 4278 0.11 0.45 NO
25 PSME1 PSME1 PSME1 4860 0.087 0.42 NO
26 XRCC4 XRCC4 XRCC4 4928 0.084 0.42 NO
27 ELL ELL ELL 5011 0.082 0.42 NO
28 FEN1 FEN1 FEN1 5041 0.081 0.43 NO
29 RNGTT RNGTT RNGTT 5081 0.08 0.43 NO
30 NUP62 NUP62 NUP62 5152 0.077 0.43 NO
31 NUP107 NUP107 NUP107 5261 0.073 0.43 NO
32 NUP50 NUP50 NUP50 5316 0.071 0.44 NO
33 PSMA4 PSMA4 PSMA4 5410 0.068 0.43 NO
34 NUP93 NUP93 NUP93 5665 0.06 0.42 NO
35 POLR2D POLR2D POLR2D 5696 0.06 0.43 NO
36 AP1M1 AP1M1 AP1M1 5899 0.055 0.42 NO
37 CCNT1 CCNT1 CCNT1 5906 0.055 0.42 NO
38 NUP153 NUP153 NUP153 6058 0.051 0.42 NO
39 TAF13 TAF13 TAF13 6141 0.049 0.42 NO
40 PSMA3 PSMA3 PSMA3 6156 0.049 0.42 NO
41 GTF2A1 GTF2A1 GTF2A1 6213 0.048 0.42 NO
42 GTF2H2 GTF2H2 GTF2H2 6247 0.047 0.42 NO
43 NMT2 NMT2 NMT2 6306 0.046 0.42 NO
44 PSMA5 PSMA5 PSMA5 6365 0.045 0.42 NO
45 PAK2 PAK2 PAK2 6370 0.045 0.42 NO
46 FYN FYN FYN 6389 0.044 0.43 NO
47 NUP155 NUP155 NUP155 6428 0.043 0.43 NO
48 TAF4 TAF4 TAF4 6493 0.042 0.43 NO
49 PSMA6 PSMA6 PSMA6 6509 0.042 0.43 NO
50 PSMB2 PSMB2 PSMB2 6656 0.039 0.42 NO
51 AP2A2 AP2A2 AP2A2 6668 0.039 0.42 NO
52 PSMD11 PSMD11 PSMD11 6680 0.039 0.43 NO
53 AP1B1 AP1B1 AP1B1 6797 0.037 0.42 NO
54 NCBP1 NCBP1 NCBP1 6835 0.036 0.42 NO
55 PSMD1 PSMD1 PSMD1 6886 0.035 0.42 NO
56 PSMD7 PSMD7 PSMD7 6901 0.035 0.42 NO
57 NUP85 NUP85 NUP85 6971 0.034 0.42 NO
58 PSMD5 PSMD5 PSMD5 6976 0.034 0.43 NO
59 PSMA1 PSMA1 PSMA1 7037 0.033 0.42 NO
60 RAN RAN RAN 7061 0.032 0.43 NO
61 HMGA1 HMGA1 HMGA1 7085 0.032 0.43 NO
62 TAF12 TAF12 TAF12 7115 0.032 0.43 NO
63 PSMC2 PSMC2 PSMC2 7116 0.032 0.43 NO
64 NUP205 NUP205 NUP205 7131 0.031 0.43 NO
65 PSMA2 PSMA2 PSMA2 7223 0.03 0.43 NO
66 RANBP1 RANBP1 RANBP1 7264 0.029 0.43 NO
67 NUP37 NUP37 NUP37 7324 0.028 0.43 NO
68 AP2S1 AP2S1 AP2S1 7377 0.028 0.43 NO
69 PSIP1 PSIP1 PSIP1 7464 0.027 0.42 NO
70 RBX1 RBX1 RBX1 7482 0.026 0.42 NO
71 CCNT2 CCNT2 CCNT2 7487 0.026 0.42 NO
72 TPR TPR TPR 7494 0.026 0.43 NO
73 XPO1 XPO1 XPO1 7518 0.026 0.43 NO
74 RANGAP1 RANGAP1 RANGAP1 7601 0.025 0.42 NO
75 LIG4 LIG4 LIG4 7618 0.024 0.42 NO
76 PSMD12 PSMD12 PSMD12 7647 0.024 0.42 NO
77 PSMA7 PSMA7 PSMA7 7667 0.024 0.43 NO
78 CTDP1 CTDP1 CTDP1 7708 0.024 0.42 NO
79 GTF2H3 GTF2H3 GTF2H3 7735 0.023 0.43 NO
80 PSME4 PSME4 PSME4 7736 0.023 0.43 NO
81 PSMD13 PSMD13 PSMD13 7764 0.023 0.43 NO
82 NUPL2 NUPL2 NUPL2 7938 0.021 0.42 NO
83 NUP54 NUP54 NUP54 8060 0.019 0.41 NO
84 KPNB1 KPNB1 KPNB1 8079 0.019 0.41 NO
85 NUP35 NUP35 NUP35 8141 0.018 0.41 NO
86 POLR2B POLR2B POLR2B 8148 0.018 0.41 NO
87 SLC25A5 SLC25A5 SLC25A5 8202 0.018 0.41 NO
88 PSMB3 PSMB3 PSMB3 8242 0.017 0.41 NO
89 NUP88 NUP88 NUP88 8296 0.017 0.41 NO
90 PACS1 PACS1 PACS1 8303 0.017 0.41 NO
91 GTF2B GTF2B GTF2B 8399 0.015 0.4 NO
92 PSMB4 PSMB4 PSMB4 8403 0.015 0.41 NO
93 GTF2H2B GTF2H2B GTF2H2B 8472 0.014 0.4 NO
94 TBP TBP TBP 8562 0.014 0.4 NO
95 GTF2F2 GTF2F2 GTF2F2 8587 0.013 0.4 NO
96 PSMD14 PSMD14 PSMD14 8607 0.013 0.4 NO
97 RAC1 RAC1 RAC1 8644 0.013 0.4 NO
98 GTF2E2 GTF2E2 GTF2E2 8701 0.012 0.4 NO
99 PPIA PPIA PPIA 8795 0.011 0.39 NO
100 POLR2G POLR2G POLR2G 8865 0.011 0.39 NO
101 SUPT16H SUPT16H SUPT16H 8890 0.01 0.39 NO
102 CDK9 CDK9 CDK9 8908 0.01 0.39 NO
103 PSMB1 PSMB1 PSMB1 8909 0.01 0.39 NO
104 GTF2A2 GTF2A2 GTF2A2 8915 0.01 0.39 NO
105 POLR2K POLR2K POLR2K 8984 0.0094 0.38 NO
106 VPS37C VPS37C VPS37C 9007 0.0092 0.38 NO
107 UBA52 UBA52 UBA52 9051 0.0087 0.38 NO
108 XRCC6 XRCC6 XRCC6 9113 0.0081 0.38 NO
109 SUPT4H1 SUPT4H1 SUPT4H1 9206 0.0072 0.38 NO
110 PSMD3 PSMD3 PSMD3 9287 0.0065 0.37 NO
111 ERCC3 ERCC3 ERCC3 9293 0.0064 0.37 NO
112 PSMD4 PSMD4 PSMD4 9326 0.0061 0.37 NO
113 PSMD2 PSMD2 PSMD2 9438 0.005 0.36 NO
114 PSMF1 PSMF1 PSMF1 9454 0.0048 0.36 NO
115 XRCC5 XRCC5 XRCC5 9487 0.0045 0.36 NO
116 NUPL1 NUPL1 NUPL1 9491 0.0045 0.36 NO
117 PSMD6 PSMD6 PSMD6 9630 0.0031 0.35 NO
118 AP2M1 AP2M1 AP2M1 9636 0.0031 0.35 NO
119 NUP43 NUP43 NUP43 9645 0.003 0.35 NO
120 KPNA1 KPNA1 KPNA1 9675 0.0027 0.35 NO
121 TAF9 TAF9 TAF9 9728 0.0023 0.35 NO
122 RAE1 RAE1 RAE1 9777 0.0019 0.35 NO
123 AP2A1 AP2A1 AP2A1 9779 0.0019 0.35 NO
124 TAF1 TAF1 TAF1 9847 0.0011 0.34 NO
125 NUP214 NUP214 NUP214 9857 0.001 0.34 NO
126 PSMC6 PSMC6 PSMC6 9878 0.00086 0.34 NO
127 AAAS AAAS AAAS 9929 0.00034 0.34 NO
128 NUP188 NUP188 NUP188 9930 0.00033 0.34 NO
129 PSMB6 PSMB6 PSMB6 9986 -0.00029 0.34 NO
130 LIG1 LIG1 LIG1 10074 -0.0011 0.33 NO
131 RPS27A RPS27A RPS27A 10076 -0.0011 0.33 NO
132 AP1G1 AP1G1 AP1G1 10109 -0.0014 0.33 NO
133 NCBP2 NCBP2 NCBP2 10199 -0.0022 0.32 NO
134 NMT1 NMT1 NMT1 10294 -0.0031 0.32 NO
135 PSMC4 PSMC4 PSMC4 10346 -0.0036 0.32 NO
136 BANF1 BANF1 BANF1 10370 -0.0038 0.32 NO
137 TAF10 TAF10 TAF10 10372 -0.0038 0.32 NO
138 GTF2H1 GTF2H1 GTF2H1 10517 -0.0053 0.31 NO
139 SEH1L SEH1L SEH1L 10610 -0.006 0.3 NO
140 POM121 POM121 POM121 10622 -0.0061 0.3 NO
141 TCEB1 TCEB1 TCEB1 10691 -0.0067 0.3 NO
142 PSMC1 PSMC1 PSMC1 10749 -0.0073 0.3 NO
143 POLR2A POLR2A POLR2A 10801 -0.0078 0.3 NO
144 TCEB3 TCEB3 TCEB3 10818 -0.008 0.3 NO
145 PSMD10 PSMD10 PSMD10 10860 -0.0083 0.29 NO
146 PSMC5 PSMC5 PSMC5 10973 -0.0094 0.29 NO
147 VPS37A VPS37A VPS37A 11065 -0.01 0.28 NO
148 SUPT5H SUPT5H SUPT5H 11097 -0.01 0.28 NO
149 SSRP1 SSRP1 SSRP1 11109 -0.011 0.28 NO
150 RANBP2 RANBP2 RANBP2 11131 -0.011 0.28 NO
151 ARF1 ARF1 ARF1 11181 -0.011 0.28 NO
152 PSMC3 PSMC3 PSMC3 11355 -0.013 0.27 NO
153 PSMB7 PSMB7 PSMB7 11552 -0.015 0.26 NO
154 COBRA1 COBRA1 COBRA1 11567 -0.015 0.26 NO
155 POLR2F POLR2F POLR2F 11604 -0.015 0.26 NO
156 TAF11 TAF11 TAF11 11666 -0.016 0.26 NO
157 POLR2E POLR2E POLR2E 11734 -0.016 0.26 NO
158 POLR2H POLR2H POLR2H 11814 -0.017 0.25 NO
159 MNAT1 MNAT1 MNAT1 11857 -0.017 0.25 NO
160 CUL5 CUL5 CUL5 11916 -0.018 0.25 NO
161 BTRC BTRC BTRC 12032 -0.019 0.24 NO
162 TCEA1 TCEA1 TCEA1 12083 -0.019 0.24 NO
163 RNMT RNMT RNMT 12118 -0.019 0.24 NO
164 TSG101 TSG101 TSG101 12152 -0.02 0.24 NO
165 POLR2J POLR2J POLR2J 12155 -0.02 0.24 NO
166 CDK7 CDK7 CDK7 12179 -0.02 0.24 NO
167 VPS37B VPS37B VPS37B 12240 -0.021 0.24 NO
168 AP2B1 AP2B1 AP2B1 12255 -0.021 0.24 NO
169 PSMB5 PSMB5 PSMB5 12404 -0.022 0.24 NO
170 RDBP RDBP RDBP 12457 -0.023 0.23 NO
171 SLC25A6 SLC25A6 SLC25A6 12501 -0.024 0.23 NO
172 NUP133 NUP133 NUP133 12598 -0.024 0.23 NO
173 PSMD9 PSMD9 PSMD9 12646 -0.025 0.23 NO
174 PSMD8 PSMD8 PSMD8 12657 -0.025 0.23 NO
175 CCNH CCNH CCNH 12671 -0.025 0.23 NO
176 TAF6 TAF6 TAF6 12821 -0.027 0.22 NO
177 AP1S1 AP1S1 AP1S1 12990 -0.028 0.22 NO
178 GTF2F1 GTF2F1 GTF2F1 13262 -0.031 0.2 NO
179 WHSC2 WHSC2 WHSC2 13293 -0.032 0.2 NO
180 NPM1 NPM1 NPM1 13323 -0.032 0.2 NO
181 SKP1 SKP1 SKP1 13659 -0.036 0.19 NO
182 POLR2L POLR2L POLR2L 13681 -0.036 0.19 NO
183 GTF2H4 GTF2H4 GTF2H4 13763 -0.037 0.19 NO
184 VPS28 VPS28 VPS28 13875 -0.038 0.18 NO
185 TCEB2 TCEB2 TCEB2 13902 -0.039 0.18 NO
186 TH1L TH1L TH1L 14262 -0.044 0.17 NO
187 POLR2C POLR2C POLR2C 14372 -0.045 0.16 NO
188 POLR2I POLR2I POLR2I 14846 -0.053 0.14 NO
189 ATP6V1H ATP6V1H ATP6V1H 15622 -0.068 0.1 NO
190 ERCC2 ERCC2 ERCC2 16055 -0.08 0.085 NO
191 AP1M2 AP1M2 AP1M2 16399 -0.092 0.072 NO
192 SLC25A4 SLC25A4 SLC25A4 16831 -0.11 0.056 NO
193 VPS37D VPS37D VPS37D 16905 -0.12 0.06 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 FRUCTOSE AND MANNOSE METABOLISM.

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 IFNG IFNG IFNG 253 0.8 0.14 YES
2 PIF1 PIF1 PIF1 385 0.73 0.27 YES
3 IL2 IL2 IL2 571 0.65 0.38 YES
4 WT1 WT1 WT1 1511 0.4 0.4 YES
5 BLM BLM BLM 1600 0.38 0.47 YES
6 IRF1 IRF1 IRF1 1768 0.35 0.52 YES
7 MYC MYC MYC 2140 0.29 0.56 YES
8 IFNAR2 IFNAR2 IFNAR2 2968 0.2 0.55 NO
9 NR2F2 NR2F2 NR2F2 4044 0.13 0.51 NO
10 ATM ATM ATM 4182 0.12 0.53 NO
11 TGFB1 TGFB1 TGFB1 4438 0.1 0.53 NO
12 MXD1 MXD1 MXD1 5420 0.068 0.49 NO
13 NFKB1 NFKB1 NFKB1 5568 0.064 0.49 NO
14 ZNFX1 ZNFX1 ZNFX1 5720 0.059 0.5 NO
15 WRN WRN WRN 6076 0.051 0.49 NO
16 NBN NBN NBN 6447 0.043 0.47 NO
17 TINF2 TINF2 TINF2 6591 0.04 0.47 NO
18 SP1 SP1 SP1 6620 0.04 0.48 NO
19 MAX MAX MAX 6781 0.037 0.48 NO
20 MRE11A MRE11A MRE11A 6921 0.035 0.48 NO
21 SAP30 SAP30 SAP30 7244 0.03 0.46 NO
22 ESR1 ESR1 ESR1 7265 0.029 0.47 NO
23 FOS FOS FOS 7557 0.025 0.46 NO
24 RBBP4 RBBP4 RBBP4 7637 0.024 0.46 NO
25 HSP90AA1 HSP90AA1 HSP90AA1 7659 0.024 0.46 NO
26 CDKN1B CDKN1B CDKN1B 7713 0.024 0.46 NO
27 HUS1 HUS1 HUS1 7805 0.022 0.46 NO
28 ACD ACD ACD 7892 0.022 0.46 NO
29 HNRNPC HNRNPC HNRNPC 8146 0.018 0.45 NO
30 HDAC2 HDAC2 HDAC2 8193 0.018 0.45 NO
31 TERF1 TERF1 TERF1 8224 0.018 0.45 NO
32 RAD1 RAD1 RAD1 8253 0.017 0.45 NO
33 SP3 SP3 SP3 8751 0.012 0.43 NO
34 XRCC6 XRCC6 XRCC6 9113 0.0081 0.41 NO
35 PINX1 PINX1 PINX1 9255 0.0068 0.4 NO
36 RPS6KB1 RPS6KB1 RPS6KB1 9265 0.0066 0.4 NO
37 SIN3B SIN3B SIN3B 9338 0.006 0.4 NO
38 MTOR MTOR MTOR 9430 0.0051 0.4 NO
39 NCL NCL NCL 9466 0.0047 0.4 NO
40 XRCC5 XRCC5 XRCC5 9487 0.0045 0.4 NO
41 TERF2 TERF2 TERF2 9696 0.0026 0.38 NO
42 DKC1 DKC1 DKC1 9735 0.0022 0.38 NO
43 SIN3A SIN3A SIN3A 10231 -0.0024 0.36 NO
44 PTGES3 PTGES3 PTGES3 10331 -0.0034 0.35 NO
45 PARP2 PARP2 PARP2 10354 -0.0037 0.35 NO
46 MAPK1 MAPK1 MAPK1 10407 -0.0042 0.35 NO
47 TERF2IP TERF2IP TERF2IP 10575 -0.0058 0.34 NO
48 TNKS TNKS TNKS 10698 -0.0068 0.33 NO
49 JUN JUN JUN 10935 -0.0089 0.32 NO
50 AKT1 AKT1 AKT1 11079 -0.01 0.32 NO
51 RAD50 RAD50 RAD50 11081 -0.01 0.32 NO
52 ABL1 ABL1 ABL1 11137 -0.011 0.32 NO
53 UBE3A UBE3A UBE3A 11196 -0.012 0.32 NO
54 RBBP7 RBBP7 RBBP7 11210 -0.012 0.32 NO
55 SMG6 SMG6 SMG6 11483 -0.014 0.3 NO
56 SMG5 SMG5 SMG5 11538 -0.014 0.3 NO
57 SAP18 SAP18 SAP18 11569 -0.015 0.3 NO
58 RAD9A RAD9A RAD9A 11800 -0.017 0.3 NO
59 E2F1 E2F1 E2F1 12148 -0.02 0.28 NO
60 EGF EGF EGF 12182 -0.02 0.28 NO
61 POT1 POT1 POT1 12485 -0.023 0.27 NO
62 EGFR EGFR EGFR 12628 -0.025 0.27 NO
63 SMAD3 SMAD3 SMAD3 13310 -0.032 0.23 NO
64 YWHAE YWHAE YWHAE 13473 -0.034 0.23 NO
65 HDAC1 HDAC1 HDAC1 13505 -0.034 0.24 NO
66 CCND1 CCND1 CCND1 13617 -0.035 0.24 NO
67 MAPK3 MAPK3 MAPK3 13684 -0.036 0.24 NO

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

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

genes ES table in pathway: KEGG PURINE METABOLISM

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 CD19 CD19 CD19 50 1 0.069 YES
2 CD79A CD79A CD79A 59 1 0.14 YES
3 BLK BLK BLK 117 0.93 0.2 YES
4 CD79B CD79B CD79B 198 0.85 0.26 YES
5 BTK BTK BTK 231 0.82 0.31 YES
6 VAV1 VAV1 VAV1 341 0.75 0.36 YES
7 RASGRP1 RASGRP1 RASGRP1 355 0.74 0.41 YES
8 PRKCB PRKCB PRKCB 537 0.66 0.45 YES
9 CARD11 CARD11 CARD11 557 0.65 0.49 YES
10 PSMA8 PSMA8 PSMA8 909 0.54 0.51 YES
11 PSMB9 PSMB9 PSMB9 1307 0.44 0.52 YES
12 PIK3CD PIK3CD PIK3CD 1368 0.43 0.55 YES
13 PIK3AP1 PIK3AP1 PIK3AP1 1755 0.36 0.55 YES
14 REL REL REL 1898 0.33 0.56 YES
15 PLCG2 PLCG2 PLCG2 2054 0.3 0.58 YES
16 NFKBIE NFKBIE NFKBIE 2607 0.24 0.56 NO
17 PSMB10 PSMB10 PSMB10 2841 0.21 0.56 NO
18 PSMB8 PSMB8 PSMB8 3225 0.18 0.56 NO
19 PSME2 PSME2 PSME2 3636 0.15 0.54 NO
20 SH3KBP1 SH3KBP1 SH3KBP1 3657 0.15 0.55 NO
21 LYN LYN LYN 3685 0.15 0.56 NO
22 RASGRP3 RASGRP3 RASGRP3 3725 0.14 0.57 NO
23 NFKBIA NFKBIA NFKBIA 3969 0.13 0.56 NO
24 MALT1 MALT1 MALT1 4440 0.1 0.55 NO
25 PSME1 PSME1 PSME1 4860 0.087 0.53 NO
26 BCL10 BCL10 BCL10 4942 0.084 0.53 NO
27 NRAS NRAS NRAS 5231 0.074 0.52 NO
28 PSMA4 PSMA4 PSMA4 5410 0.068 0.51 NO
29 CBL CBL CBL 5492 0.066 0.51 NO
30 CBLB CBLB CBLB 5513 0.065 0.52 NO
31 KRAS KRAS KRAS 5529 0.065 0.52 NO
32 GRB2 GRB2 GRB2 5755 0.058 0.51 NO
33 IKBKG IKBKG IKBKG 5908 0.055 0.51 NO
34 PSMA3 PSMA3 PSMA3 6156 0.049 0.5 NO
35 NCK1 NCK1 NCK1 6311 0.046 0.49 NO
36 PSMA5 PSMA5 PSMA5 6365 0.045 0.49 NO
37 PIK3R1 PIK3R1 PIK3R1 6384 0.044 0.49 NO
38 FYN FYN FYN 6389 0.044 0.5 NO
39 RICTOR RICTOR RICTOR 6458 0.043 0.5 NO
40 PSMA6 PSMA6 PSMA6 6509 0.042 0.5 NO
41 SHC1 SHC1 SHC1 6625 0.04 0.49 NO
42 ITPR2 ITPR2 ITPR2 6637 0.04 0.49 NO
43 PSMB2 PSMB2 PSMB2 6656 0.039 0.5 NO
44 SOS1 SOS1 SOS1 6678 0.039 0.5 NO
45 PSMD11 PSMD11 PSMD11 6680 0.039 0.5 NO
46 PSMD1 PSMD1 PSMD1 6886 0.035 0.49 NO
47 PSMD7 PSMD7 PSMD7 6901 0.035 0.49 NO
48 PSMD5 PSMD5 PSMD5 6976 0.034 0.49 NO
49 PSMA1 PSMA1 PSMA1 7037 0.033 0.49 NO
50 PSMC2 PSMC2 PSMC2 7116 0.032 0.49 NO
51 PSMA2 PSMA2 PSMA2 7223 0.03 0.48 NO
52 CALM1 CALM1 CALM1 7274 0.029 0.48 NO
53 IKBKB IKBKB IKBKB 7353 0.028 0.48 NO
54 PTEN PTEN PTEN 7432 0.027 0.48 NO
55 CREB1 CREB1 CREB1 7508 0.026 0.48 NO
56 PSMD12 PSMD12 PSMD12 7647 0.024 0.47 NO
57 PSMA7 PSMA7 PSMA7 7667 0.024 0.47 NO
58 CDKN1B CDKN1B CDKN1B 7713 0.024 0.47 NO
59 RELA RELA RELA 7719 0.024 0.47 NO
60 FOXO3 FOXO3 FOXO3 7733 0.023 0.47 NO
61 PSME4 PSME4 PSME4 7736 0.023 0.47 NO
62 CHUK CHUK CHUK 7759 0.023 0.47 NO
63 PSMD13 PSMD13 PSMD13 7764 0.023 0.48 NO
64 SYK SYK SYK 7895 0.022 0.47 NO
65 MAP3K7 MAP3K7 MAP3K7 7995 0.02 0.47 NO
66 PSMB3 PSMB3 PSMB3 8242 0.017 0.45 NO
67 CALM3 CALM3 CALM3 8320 0.016 0.45 NO
68 PSMB4 PSMB4 PSMB4 8403 0.015 0.45 NO
69 ORAI1 ORAI1 ORAI1 8538 0.014 0.44 NO
70 PSMD14 PSMD14 PSMD14 8607 0.013 0.44 NO
71 MDM2 MDM2 MDM2 8726 0.012 0.43 NO
72 PSMB1 PSMB1 PSMB1 8909 0.01 0.42 NO
73 UBA52 UBA52 UBA52 9051 0.0087 0.41 NO
74 PLCG1 PLCG1 PLCG1 9080 0.0085 0.41 NO
75 CUL1 CUL1 CUL1 9242 0.0069 0.4 NO
76 PSMD3 PSMD3 PSMD3 9287 0.0065 0.4 NO
77 RPS6KB2 RPS6KB2 RPS6KB2 9294 0.0064 0.4 NO
78 PSMD4 PSMD4 PSMD4 9326 0.0061 0.4 NO
79 MTOR MTOR MTOR 9430 0.0051 0.4 NO
80 PSMD2 PSMD2 PSMD2 9438 0.005 0.4 NO
81 PSMF1 PSMF1 PSMF1 9454 0.0048 0.4 NO
82 PSMD6 PSMD6 PSMD6 9630 0.0031 0.39 NO
83 CDKN1A CDKN1A CDKN1A 9722 0.0023 0.38 NO
84 PSMC6 PSMC6 PSMC6 9878 0.00086 0.37 NO
85 PSMB6 PSMB6 PSMB6 9986 -0.00029 0.37 NO
86 CALM2 CALM2 CALM2 10048 -0.00084 0.36 NO
87 RPS27A RPS27A RPS27A 10076 -0.0011 0.36 NO
88 PSMC4 PSMC4 PSMC4 10346 -0.0036 0.35 NO
89 BLNK BLNK BLNK 10654 -0.0064 0.33 NO
90 PSMC1 PSMC1 PSMC1 10749 -0.0073 0.33 NO
91 NFKBIB NFKBIB NFKBIB 10857 -0.0083 0.32 NO
92 PSMD10 PSMD10 PSMD10 10860 -0.0083 0.32 NO
93 PSMC5 PSMC5 PSMC5 10973 -0.0094 0.32 NO
94 MAPKAP1 MAPKAP1 MAPKAP1 10989 -0.0096 0.32 NO
95 AKT1 AKT1 AKT1 11079 -0.01 0.31 NO
96 FBXW11 FBXW11 FBXW11 11326 -0.013 0.3 NO
97 ITPR3 ITPR3 ITPR3 11336 -0.013 0.3 NO
98 PSMC3 PSMC3 PSMC3 11355 -0.013 0.3 NO
99 PSMB7 PSMB7 PSMB7 11552 -0.015 0.29 NO
100 GSK3A GSK3A GSK3A 11806 -0.017 0.28 NO
101 BTRC BTRC BTRC 12032 -0.019 0.26 NO
102 AKT3 AKT3 AKT3 12067 -0.019 0.26 NO
103 FOXO1 FOXO1 FOXO1 12080 -0.019 0.26 NO
104 HRAS HRAS HRAS 12189 -0.02 0.26 NO
105 PSMB5 PSMB5 PSMB5 12404 -0.022 0.25 NO
106 PSMD9 PSMD9 PSMD9 12646 -0.025 0.24 NO
107 PSMD8 PSMD8 PSMD8 12657 -0.025 0.24 NO
108 CASP9 CASP9 CASP9 12720 -0.026 0.24 NO
109 PDPK1 PDPK1 PDPK1 12992 -0.028 0.22 NO
110 AKT1S1 AKT1S1 AKT1S1 13504 -0.034 0.2 NO
111 SKP1 SKP1 SKP1 13659 -0.036 0.19 NO
112 FOXO4 FOXO4 FOXO4 13845 -0.038 0.18 NO
113 NR4A1 NR4A1 NR4A1 14272 -0.044 0.16 NO
114 THEM4 THEM4 THEM4 14828 -0.052 0.14 NO
115 PHLPP1 PHLPP1 PHLPP1 15354 -0.062 0.11 NO
116 TSC2 TSC2 TSC2 15445 -0.064 0.11 NO
117 STIM1 STIM1 STIM1 15624 -0.068 0.1 NO
118 BAD BAD BAD 15714 -0.07 0.1 NO
119 MLST8 MLST8 MLST8 15777 -0.072 0.11 NO
120 AKT2 AKT2 AKT2 16561 -0.099 0.069 NO
121 TRIB3 TRIB3 TRIB3 17267 -0.14 0.039 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 PURINE METABOLISM.

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

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

Table 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 CD28 CD28 CD28 85 0.97 0.086 YES
2 CD247 CD247 CD247 124 0.92 0.17 YES
3 LCK LCK LCK 230 0.82 0.24 YES
4 DOCK2 DOCK2 DOCK2 337 0.75 0.3 YES
5 CD8B CD8B CD8B 532 0.66 0.36 YES
6 HCK HCK HCK 615 0.63 0.41 YES
7 PSMA8 PSMA8 PSMA8 909 0.54 0.44 YES
8 PSMB9 PSMB9 PSMB9 1307 0.44 0.46 YES
9 CD4 CD4 CD4 1371 0.42 0.5 YES
10 APOBEC3G APOBEC3G APOBEC3G 1728 0.36 0.51 YES
11 AP1S2 AP1S2 AP1S2 2745 0.22 0.48 YES
12 PSMB10 PSMB10 PSMB10 2841 0.21 0.49 YES
13 NUP210 NUP210 NUP210 2872 0.21 0.51 YES
14 PSMB8 PSMB8 PSMB8 3225 0.18 0.51 YES
15 B2M B2M B2M 3410 0.16 0.51 YES
16 RCC1 RCC1 RCC1 3503 0.16 0.52 YES
17 HLA-A HLA-A HLA-A 3615 0.15 0.53 YES
18 PSME2 PSME2 PSME2 3636 0.15 0.54 YES
19 ELMO1 ELMO1 ELMO1 3915 0.13 0.54 NO
20 PSME1 PSME1 PSME1 4860 0.087 0.49 NO
21 NUP62 NUP62 NUP62 5152 0.077 0.48 NO
22 NUP107 NUP107 NUP107 5261 0.073 0.48 NO
23 NUP50 NUP50 NUP50 5316 0.071 0.49 NO
24 PSMA4 PSMA4 PSMA4 5410 0.068 0.49 NO
25 NUP93 NUP93 NUP93 5665 0.06 0.48 NO
26 AP1M1 AP1M1 AP1M1 5899 0.055 0.47 NO
27 CCNT1 CCNT1 CCNT1 5906 0.055 0.48 NO
28 NUP153 NUP153 NUP153 6058 0.051 0.47 NO
29 PSMA3 PSMA3 PSMA3 6156 0.049 0.47 NO
30 PSMA5 PSMA5 PSMA5 6365 0.045 0.47 NO
31 PAK2 PAK2 PAK2 6370 0.045 0.47 NO
32 FYN FYN FYN 6389 0.044 0.47 NO
33 NUP155 NUP155 NUP155 6428 0.043 0.47 NO
34 PSMA6 PSMA6 PSMA6 6509 0.042 0.47 NO
35 PSMB2 PSMB2 PSMB2 6656 0.039 0.47 NO
36 AP2A2 AP2A2 AP2A2 6668 0.039 0.47 NO
37 PSMD11 PSMD11 PSMD11 6680 0.039 0.48 NO
38 AP1B1 AP1B1 AP1B1 6797 0.037 0.47 NO
39 PSMD1 PSMD1 PSMD1 6886 0.035 0.47 NO
40 PSMD7 PSMD7 PSMD7 6901 0.035 0.47 NO
41 NUP85 NUP85 NUP85 6971 0.034 0.47 NO
42 PSMD5 PSMD5 PSMD5 6976 0.034 0.48 NO
43 PSMA1 PSMA1 PSMA1 7037 0.033 0.48 NO
44 RAN RAN RAN 7061 0.032 0.48 NO
45 HMGA1 HMGA1 HMGA1 7085 0.032 0.48 NO
46 PSMC2 PSMC2 PSMC2 7116 0.032 0.48 NO
47 NUP205 NUP205 NUP205 7131 0.031 0.48 NO
48 PSMA2 PSMA2 PSMA2 7223 0.03 0.48 NO
49 RANBP1 RANBP1 RANBP1 7264 0.029 0.48 NO
50 NUP37 NUP37 NUP37 7324 0.028 0.48 NO
51 AP2S1 AP2S1 AP2S1 7377 0.028 0.48 NO
52 PSIP1 PSIP1 PSIP1 7464 0.027 0.48 NO
53 RBX1 RBX1 RBX1 7482 0.026 0.48 NO
54 TPR TPR TPR 7494 0.026 0.48 NO
55 XPO1 XPO1 XPO1 7518 0.026 0.48 NO
56 RANGAP1 RANGAP1 RANGAP1 7601 0.025 0.48 NO
57 PSMD12 PSMD12 PSMD12 7647 0.024 0.48 NO
58 PSMA7 PSMA7 PSMA7 7667 0.024 0.48 NO
59 PSME4 PSME4 PSME4 7736 0.023 0.48 NO
60 PSMD13 PSMD13 PSMD13 7764 0.023 0.48 NO
61 NUPL2 NUPL2 NUPL2 7938 0.021 0.47 NO
62 NUP54 NUP54 NUP54 8060 0.019 0.47 NO
63 KPNB1 KPNB1 KPNB1 8079 0.019 0.47 NO
64 NUP35 NUP35 NUP35 8141 0.018 0.46 NO
65 SLC25A5 SLC25A5 SLC25A5 8202 0.018 0.46 NO
66 PSMB3 PSMB3 PSMB3 8242 0.017 0.46 NO
67 NUP88 NUP88 NUP88 8296 0.017 0.46 NO
68 PACS1 PACS1 PACS1 8303 0.017 0.46 NO
69 PSMB4 PSMB4 PSMB4 8403 0.015 0.46 NO
70 PSMD14 PSMD14 PSMD14 8607 0.013 0.45 NO
71 RAC1 RAC1 RAC1 8644 0.013 0.45 NO
72 PPIA PPIA PPIA 8795 0.011 0.44 NO
73 CDK9 CDK9 CDK9 8908 0.01 0.44 NO
74 PSMB1 PSMB1 PSMB1 8909 0.01 0.44 NO
75 UBA52 UBA52 UBA52 9051 0.0087 0.43 NO
76 PSMD3 PSMD3 PSMD3 9287 0.0065 0.42 NO
77 PSMD4 PSMD4 PSMD4 9326 0.0061 0.42 NO
78 PSMD2 PSMD2 PSMD2 9438 0.005 0.41 NO
79 PSMF1 PSMF1 PSMF1 9454 0.0048 0.41 NO
80 NUPL1 NUPL1 NUPL1 9491 0.0045 0.41 NO
81 PSMD6 PSMD6 PSMD6 9630 0.0031 0.4 NO
82 AP2M1 AP2M1 AP2M1 9636 0.0031 0.4 NO
83 NUP43 NUP43 NUP43 9645 0.003 0.4 NO
84 KPNA1 KPNA1 KPNA1 9675 0.0027 0.4 NO
85 RAE1 RAE1 RAE1 9777 0.0019 0.39 NO
86 AP2A1 AP2A1 AP2A1 9779 0.0019 0.39 NO
87 NUP214 NUP214 NUP214 9857 0.001 0.39 NO
88 PSMC6 PSMC6 PSMC6 9878 0.00086 0.39 NO
89 AAAS AAAS AAAS 9929 0.00034 0.38 NO
90 NUP188 NUP188 NUP188 9930 0.00033 0.38 NO
91 PSMB6 PSMB6 PSMB6 9986 -0.00029 0.38 NO
92 RPS27A RPS27A RPS27A 10076 -0.0011 0.38 NO
93 AP1G1 AP1G1 AP1G1 10109 -0.0014 0.38 NO
94 PSMC4 PSMC4 PSMC4 10346 -0.0036 0.36 NO
95 BANF1 BANF1 BANF1 10370 -0.0038 0.36 NO
96 SEH1L SEH1L SEH1L 10610 -0.006 0.35 NO
97 POM121 POM121 POM121 10622 -0.0061 0.35 NO
98 TCEB1 TCEB1 TCEB1 10691 -0.0067 0.34 NO
99 PSMC1 PSMC1 PSMC1 10749 -0.0073 0.34 NO
100 PSMD10 PSMD10 PSMD10 10860 -0.0083 0.34 NO
101 PSMC5 PSMC5 PSMC5 10973 -0.0094 0.33 NO
102 RANBP2 RANBP2 RANBP2 11131 -0.011 0.32 NO
103 ARF1 ARF1 ARF1 11181 -0.011 0.32 NO
104 PSMC3 PSMC3 PSMC3 11355 -0.013 0.31 NO
105 PSMB7 PSMB7 PSMB7 11552 -0.015 0.3 NO
106 CUL5 CUL5 CUL5 11916 -0.018 0.29 NO
107 BTRC BTRC BTRC 12032 -0.019 0.28 NO
108 AP2B1 AP2B1 AP2B1 12255 -0.021 0.27 NO
109 PSMB5 PSMB5 PSMB5 12404 -0.022 0.26 NO
110 SLC25A6 SLC25A6 SLC25A6 12501 -0.024 0.26 NO
111 NUP133 NUP133 NUP133 12598 -0.024 0.26 NO
112 PSMD9 PSMD9 PSMD9 12646 -0.025 0.26 NO
113 PSMD8 PSMD8 PSMD8 12657 -0.025 0.26 NO
114 AP1S1 AP1S1 AP1S1 12990 -0.028 0.24 NO
115 NPM1 NPM1 NPM1 13323 -0.032 0.23 NO
116 SKP1 SKP1 SKP1 13659 -0.036 0.21 NO
117 TCEB2 TCEB2 TCEB2 13902 -0.039 0.2 NO
118 ATP6V1H ATP6V1H ATP6V1H 15622 -0.068 0.11 NO
119 AP1M2 AP1M2 AP1M2 16399 -0.092 0.078 NO
120 SLC25A4 SLC25A4 SLC25A4 16831 -0.11 0.064 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ASB2 ASB2 ASB2 169 0.87 0.066 YES
2 UBE2C UBE2C UBE2C 699 0.6 0.088 YES
3 PSMA8 PSMA8 PSMA8 909 0.54 0.12 YES
4 FBXO17 FBXO17 FBXO17 1054 0.5 0.16 YES
5 SPSB4 SPSB4 SPSB4 1153 0.47 0.19 YES
6 PSMB9 PSMB9 PSMB9 1307 0.44 0.22 YES
7 CDC20 CDC20 CDC20 1800 0.35 0.23 YES
8 KLHL13 KLHL13 KLHL13 1897 0.33 0.25 YES
9 SOCS3 SOCS3 SOCS3 2483 0.25 0.24 YES
10 SOCS1 SOCS1 SOCS1 2688 0.23 0.25 YES
11 PSMB10 PSMB10 PSMB10 2841 0.21 0.26 YES
12 FBXO27 FBXO27 FBXO27 2912 0.2 0.27 YES
13 UBE2L6 UBE2L6 UBE2L6 2913 0.2 0.29 YES
14 PSMB8 PSMB8 PSMB8 3225 0.18 0.28 YES
15 TRIM9 TRIM9 TRIM9 3278 0.17 0.3 YES
16 TRIM21 TRIM21 TRIM21 3309 0.17 0.31 YES
17 SPSB1 SPSB1 SPSB1 3447 0.16 0.32 YES
18 PSME2 PSME2 PSME2 3636 0.15 0.32 YES
19 FBXO6 FBXO6 FBXO6 3640 0.15 0.33 YES
20 DTX3L DTX3L DTX3L 4133 0.12 0.32 YES
21 ASB13 ASB13 ASB13 4227 0.12 0.32 YES
22 UBA7 UBA7 UBA7 4356 0.11 0.32 YES
23 LNPEP LNPEP LNPEP 4391 0.11 0.33 YES
24 UBE2J1 UBE2J1 UBE2J1 4628 0.096 0.32 YES
25 SMURF2 SMURF2 SMURF2 4647 0.095 0.33 YES
26 SKP2 SKP2 SKP2 4675 0.094 0.34 YES
27 UBE2D1 UBE2D1 UBE2D1 4830 0.088 0.34 YES
28 PSME1 PSME1 PSME1 4860 0.087 0.34 YES
29 UBA6 UBA6 UBA6 5020 0.081 0.34 YES
30 UBE2S UBE2S UBE2S 5372 0.069 0.33 YES
31 RNF138 RNF138 RNF138 5386 0.069 0.33 YES
32 TRIM36 TRIM36 TRIM36 5393 0.069 0.34 YES
33 PSMA4 PSMA4 PSMA4 5410 0.068 0.34 YES
34 FBXO2 FBXO2 FBXO2 5482 0.066 0.34 YES
35 CBLB CBLB CBLB 5513 0.065 0.35 YES
36 SMURF1 SMURF1 SMURF1 5569 0.063 0.35 YES
37 RNF34 RNF34 RNF34 5705 0.06 0.35 YES
38 ATG7 ATG7 ATG7 5802 0.057 0.35 YES
39 UBA3 UBA3 UBA3 5848 0.056 0.35 YES
40 UBE2N UBE2N UBE2N 5981 0.053 0.35 YES
41 TRIM63 TRIM63 TRIM63 5983 0.053 0.35 YES
42 KLHL20 KLHL20 KLHL20 6053 0.051 0.35 YES
43 PSMA3 PSMA3 PSMA3 6156 0.049 0.35 YES
44 ASB9 ASB9 ASB9 6162 0.049 0.36 YES
45 PSMA5 PSMA5 PSMA5 6365 0.045 0.35 NO
46 ASB12 ASB12 ASB12 6390 0.044 0.35 NO
47 VHL VHL VHL 6482 0.042 0.35 NO
48 UBE2E2 UBE2E2 UBE2E2 6483 0.042 0.35 NO
49 PSMA6 PSMA6 PSMA6 6509 0.042 0.36 NO
50 PSMB2 PSMB2 PSMB2 6656 0.039 0.35 NO
51 PSMD11 PSMD11 PSMD11 6680 0.039 0.35 NO
52 PSMD1 PSMD1 PSMD1 6886 0.035 0.34 NO
53 PSMD7 PSMD7 PSMD7 6901 0.035 0.35 NO
54 PSMD5 PSMD5 PSMD5 6976 0.034 0.34 NO
55 PSMA1 PSMA1 PSMA1 7037 0.033 0.34 NO
56 UBE2G1 UBE2G1 UBE2G1 7046 0.033 0.35 NO
57 TRIM11 TRIM11 TRIM11 7075 0.032 0.35 NO
58 UBE2L3 UBE2L3 UBE2L3 7111 0.032 0.35 NO
59 PSMC2 PSMC2 PSMC2 7116 0.032 0.35 NO
60 PSMA2 PSMA2 PSMA2 7223 0.03 0.35 NO
61 UBE3C UBE3C UBE3C 7322 0.028 0.34 NO
62 FBXW7 FBXW7 FBXW7 7375 0.028 0.34 NO
63 RNF6 RNF6 RNF6 7435 0.027 0.34 NO
64 ANAPC1 ANAPC1 ANAPC1 7462 0.027 0.34 NO
65 RBX1 RBX1 RBX1 7482 0.026 0.34 NO
66 PSMD12 PSMD12 PSMD12 7647 0.024 0.34 NO
67 PSMA7 PSMA7 PSMA7 7667 0.024 0.34 NO
68 PSME4 PSME4 PSME4 7736 0.023 0.34 NO
69 PSMD13 PSMD13 PSMD13 7764 0.023 0.34 NO
70 ASB3 ASB3 ASB3 7777 0.023 0.34 NO
71 TRIM32 TRIM32 TRIM32 7822 0.022 0.34 NO
72 WSB1 WSB1 WSB1 7853 0.022 0.34 NO
73 UBR2 UBR2 UBR2 8066 0.019 0.33 NO
74 TPP2 TPP2 TPP2 8069 0.019 0.33 NO
75 CDC26 CDC26 CDC26 8071 0.019 0.33 NO
76 ASB7 ASB7 ASB7 8088 0.019 0.33 NO
77 ASB16 ASB16 ASB16 8127 0.018 0.33 NO
78 CUL2 CUL2 CUL2 8189 0.018 0.33 NO
79 PSMB3 PSMB3 PSMB3 8242 0.017 0.33 NO
80 UBE2A UBE2A UBE2A 8246 0.017 0.33 NO
81 UBR1 UBR1 UBR1 8365 0.016 0.32 NO
82 PSMB4 PSMB4 PSMB4 8403 0.015 0.32 NO
83 UBE2W UBE2W UBE2W 8439 0.015 0.32 NO
84 ANAPC10 ANAPC10 ANAPC10 8500 0.014 0.32 NO
85 UBE2E1 UBE2E1 UBE2E1 8602 0.013 0.32 NO
86 CDC27 CDC27 CDC27 8605 0.013 0.32 NO
87 PSMD14 PSMD14 PSMD14 8607 0.013 0.32 NO
88 RNF4 RNF4 RNF4 8664 0.012 0.32 NO
89 TRIP12 TRIP12 TRIP12 8808 0.011 0.31 NO
90 WWP1 WWP1 WWP1 8843 0.011 0.31 NO
91 PSMB1 PSMB1 PSMB1 8909 0.01 0.3 NO
92 UBE2G2 UBE2G2 UBE2G2 8911 0.01 0.31 NO
93 UBA52 UBA52 UBA52 9051 0.0087 0.3 NO
94 ANAPC4 ANAPC4 ANAPC4 9058 0.0086 0.3 NO
95 RBCK1 RBCK1 RBCK1 9210 0.0072 0.29 NO
96 UBE2J2 UBE2J2 UBE2J2 9215 0.0071 0.29 NO
97 UBE2Z UBE2Z UBE2Z 9218 0.0071 0.29 NO
98 CUL1 CUL1 CUL1 9242 0.0069 0.29 NO
99 UBE2Q1 UBE2Q1 UBE2Q1 9243 0.0069 0.29 NO
100 NEDD4 NEDD4 NEDD4 9258 0.0067 0.29 NO
101 HECTD3 HECTD3 HECTD3 9272 0.0066 0.29 NO
102 PSMD3 PSMD3 PSMD3 9287 0.0065 0.29 NO
103 PSMD4 PSMD4 PSMD4 9326 0.0061 0.29 NO
104 GAN GAN GAN 9381 0.0056 0.29 NO
105 UBE2Q2 UBE2Q2 UBE2Q2 9395 0.0054 0.29 NO
106 UBE2V2 UBE2V2 UBE2V2 9414 0.0053 0.29 NO
107 PSMD2 PSMD2 PSMD2 9438 0.005 0.29 NO
108 PSMF1 PSMF1 PSMF1 9454 0.0048 0.29 NO
109 BLMH BLMH BLMH 9548 0.0039 0.28 NO
110 KLHL9 KLHL9 KLHL9 9585 0.0036 0.28 NO
111 PSMD6 PSMD6 PSMD6 9630 0.0031 0.28 NO
112 UBE2F UBE2F UBE2F 9741 0.0022 0.27 NO
113 RNF220 RNF220 RNF220 9761 0.002 0.27 NO
114 UBA2 UBA2 UBA2 9856 0.001 0.26 NO
115 ASB6 ASB6 ASB6 9874 0.00088 0.26 NO
116 PSMC6 PSMC6 PSMC6 9878 0.00086 0.26 NO
117 PSMB6 PSMB6 PSMB6 9986 -0.00029 0.26 NO
118 UBE2H UBE2H UBE2H 10013 -0.0005 0.26 NO
119 RPS27A RPS27A RPS27A 10076 -0.0011 0.25 NO
120 UBE2B UBE2B UBE2B 10177 -0.002 0.25 NO
121 HUWE1 HUWE1 HUWE1 10198 -0.0022 0.25 NO
122 NPEPPS NPEPPS NPEPPS 10224 -0.0023 0.24 NO
123 VPRBP VPRBP VPRBP 10244 -0.0026 0.24 NO
124 UBE2D3 UBE2D3 UBE2D3 10318 -0.0033 0.24 NO
125 MKRN1 MKRN1 MKRN1 10333 -0.0034 0.24 NO
126 PSMC4 PSMC4 PSMC4 10346 -0.0036 0.24 NO
127 RNF25 RNF25 RNF25 10362 -0.0038 0.24 NO
128 ANAPC5 ANAPC5 ANAPC5 10586 -0.0059 0.23 NO
129 UBE2K UBE2K UBE2K 10593 -0.0059 0.23 NO
130 TCEB1 TCEB1 TCEB1 10691 -0.0067 0.22 NO
131 TRIM37 TRIM37 TRIM37 10714 -0.007 0.22 NO
132 PSMC1 PSMC1 PSMC1 10749 -0.0073 0.22 NO
133 ANAPC7 ANAPC7 ANAPC7 10783 -0.0076 0.22 NO
134 ANAPC2 ANAPC2 ANAPC2 10815 -0.0079 0.22 NO
135 PSMD10 PSMD10 PSMD10 10860 -0.0083 0.22 NO
136 PSMC5 PSMC5 PSMC5 10973 -0.0094 0.21 NO
137 UBE2R2 UBE2R2 UBE2R2 10974 -0.0094 0.21 NO
138 UBE2D2 UBE2D2 UBE2D2 11014 -0.0098 0.21 NO
139 CUL3 CUL3 CUL3 11039 -0.01 0.21 NO
140 UBE3A UBE3A UBE3A 11196 -0.012 0.2 NO
141 ASB8 ASB8 ASB8 11262 -0.012 0.2 NO
142 FBXW11 FBXW11 FBXW11 11326 -0.013 0.2 NO
143 PSMC3 PSMC3 PSMC3 11355 -0.013 0.2 NO
144 PSMB7 PSMB7 PSMB7 11552 -0.015 0.19 NO
145 UBE4A UBE4A UBE4A 11659 -0.016 0.18 NO
146 UBR4 UBR4 UBR4 11762 -0.016 0.18 NO
147 CDC16 CDC16 CDC16 11805 -0.017 0.18 NO
148 CDC23 CDC23 CDC23 11807 -0.017 0.18 NO
149 UBA1 UBA1 UBA1 11915 -0.018 0.17 NO
150 CUL5 CUL5 CUL5 11916 -0.018 0.18 NO
151 KEAP1 KEAP1 KEAP1 11966 -0.018 0.17 NO
152 FBXO4 FBXO4 FBXO4 12013 -0.018 0.17 NO
153 BTRC BTRC BTRC 12032 -0.019 0.17 NO
154 LRSAM1 LRSAM1 LRSAM1 12215 -0.02 0.17 NO
155 RNF41 RNF41 RNF41 12264 -0.021 0.16 NO
156 UBE2E3 UBE2E3 UBE2E3 12337 -0.022 0.16 NO
157 HERC2 HERC2 HERC2 12382 -0.022 0.16 NO
158 PSMB5 PSMB5 PSMB5 12404 -0.022 0.16 NO
159 LRRC41 LRRC41 LRRC41 12500 -0.023 0.16 NO
160 PSMD9 PSMD9 PSMD9 12646 -0.025 0.15 NO
161 PSMD8 PSMD8 PSMD8 12657 -0.025 0.16 NO
162 CUL7 CUL7 CUL7 12754 -0.026 0.15 NO
163 PJA2 PJA2 PJA2 12985 -0.028 0.14 NO
164 ARIH2 ARIH2 ARIH2 13062 -0.029 0.14 NO
165 RNF123 RNF123 RNF123 13199 -0.031 0.14 NO
166 UBE2O UBE2O UBE2O 13360 -0.032 0.13 NO
167 UBE3B UBE3B UBE3B 13458 -0.034 0.13 NO
168 UBA5 UBA5 UBA5 13553 -0.035 0.12 NO
169 SKP1 SKP1 SKP1 13659 -0.036 0.12 NO
170 PJA1 PJA1 PJA1 13680 -0.036 0.12 NO
171 SAE1 SAE1 SAE1 13818 -0.038 0.12 NO
172 SPSB2 SPSB2 SPSB2 13822 -0.038 0.12 NO
173 RCHY1 RCHY1 RCHY1 13890 -0.039 0.12 NO
174 TCEB2 TCEB2 TCEB2 13902 -0.039 0.12 NO
175 ANAPC11 ANAPC11 ANAPC11 13915 -0.039 0.13 NO
176 DET1 DET1 DET1 13940 -0.039 0.13 NO
177 ANAPC13 ANAPC13 ANAPC13 13996 -0.04 0.13 NO
178 CDC34 CDC34 CDC34 14128 -0.042 0.12 NO
179 UBE2M UBE2M UBE2M 14247 -0.044 0.12 NO
180 ASB1 ASB1 ASB1 14343 -0.045 0.12 NO
181 FBXW8 FBXW8 FBXW8 14364 -0.045 0.12 NO
182 DZIP3 DZIP3 DZIP3 14516 -0.047 0.12 NO
183 UBOX5 UBOX5 UBOX5 14555 -0.048 0.12 NO
184 FBXO3 FBXO3 FBXO3 14598 -0.049 0.12 NO
185 RNF144B RNF144B RNF144B 14746 -0.051 0.12 NO
186 ZBTB16 ZBTB16 ZBTB16 14841 -0.053 0.12 NO
187 UBE2D4 UBE2D4 UBE2D4 15146 -0.058 0.11 NO
188 FBXO44 FBXO44 FBXO44 15418 -0.064 0.097 NO
189 STUB1 STUB1 STUB1 15420 -0.064 0.1 NO
190 RNF182 RNF182 RNF182 16816 -0.11 0.033 NO
191 ASB4 ASB4 ASB4 17412 -0.16 0.014 NO
192 PARK2 PARK2 PARK2 17686 -0.2 0.016 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 CYSTEINE AND METHIONINE METABOLISM.

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NOD2 NOD2 NOD2 227 0.82 0.098 YES
2 LY96 LY96 LY96 445 0.7 0.18 YES
3 S100B S100B S100B 468 0.69 0.27 YES
4 SAA1 SAA1 SAA1 780 0.58 0.33 YES
5 TICAM2 TICAM2 TICAM2 1301 0.44 0.36 YES
6 MAP2K6 MAP2K6 MAP2K6 1923 0.32 0.37 YES
7 TLR4 TLR4 TLR4 2196 0.28 0.4 YES
8 CDK1 CDK1 CDK1 2337 0.26 0.42 YES
9 TLR3 TLR3 TLR3 2342 0.26 0.46 YES
10 S100A12 S100A12 S100A12 2622 0.24 0.47 YES
11 CD14 CD14 CD14 2666 0.23 0.5 YES
12 RPS6KA5 RPS6KA5 RPS6KA5 3092 0.19 0.5 YES
13 NFKB2 NFKB2 NFKB2 3549 0.16 0.5 YES
14 DUSP4 DUSP4 DUSP4 3708 0.14 0.51 YES
15 IRAK2 IRAK2 IRAK2 3801 0.14 0.52 YES
16 NFKBIA NFKBIA NFKBIA 3969 0.13 0.53 YES
17 IRAK1 IRAK1 IRAK1 4165 0.12 0.54 YES
18 RIPK2 RIPK2 RIPK2 4295 0.11 0.55 YES
19 MAPK11 MAPK11 MAPK11 4327 0.11 0.56 YES
20 DUSP7 DUSP7 DUSP7 4501 0.1 0.56 YES
21 NOD1 NOD1 NOD1 4557 0.099 0.57 YES
22 MEF2C MEF2C MEF2C 4714 0.093 0.58 YES
23 MAP2K1 MAP2K1 MAP2K1 5735 0.059 0.53 NO
24 IKBKG IKBKG IKBKG 5908 0.055 0.52 NO
25 RPS6KA3 RPS6KA3 RPS6KA3 6626 0.04 0.49 NO
26 MEF2A MEF2A MEF2A 6820 0.036 0.48 NO
27 RIPK1 RIPK1 RIPK1 6951 0.034 0.48 NO
28 MAPKAPK2 MAPKAPK2 MAPKAPK2 6961 0.034 0.49 NO
29 TICAM1 TICAM1 TICAM1 7020 0.033 0.49 NO
30 DUSP6 DUSP6 DUSP6 7218 0.03 0.48 NO
31 MAPK7 MAPK7 MAPK7 7236 0.03 0.48 NO
32 IKBKB IKBKB IKBKB 7353 0.028 0.48 NO
33 CREB1 CREB1 CREB1 7508 0.026 0.48 NO
34 FOS FOS FOS 7557 0.025 0.48 NO
35 RPS6KA1 RPS6KA1 RPS6KA1 7657 0.024 0.47 NO
36 RELA RELA RELA 7719 0.024 0.47 NO
37 CHUK CHUK CHUK 7759 0.023 0.48 NO
38 ATF2 ATF2 ATF2 7894 0.022 0.47 NO
39 TRAF6 TRAF6 TRAF6 7943 0.021 0.47 NO
40 MAP3K7 MAP3K7 MAP3K7 7995 0.02 0.47 NO
41 PPP2R1B PPP2R1B PPP2R1B 8177 0.018 0.46 NO
42 ELK1 ELK1 ELK1 8257 0.017 0.46 NO
43 HMGB1 HMGB1 HMGB1 8451 0.015 0.45 NO
44 MAP2K3 MAP2K3 MAP2K3 8464 0.015 0.45 NO
45 TAB2 TAB2 TAB2 8656 0.012 0.44 NO
46 UBA52 UBA52 UBA52 9051 0.0087 0.42 NO
47 TAB3 TAB3 TAB3 9528 0.0041 0.4 NO
48 AGER AGER AGER 9659 0.0029 0.39 NO
49 PPP2R5D PPP2R5D PPP2R5D 10017 -0.00056 0.37 NO
50 RPS27A RPS27A RPS27A 10076 -0.0011 0.37 NO
51 TAB1 TAB1 TAB1 10285 -0.003 0.36 NO
52 MAPKAPK3 MAPKAPK3 MAPKAPK3 10287 -0.0031 0.36 NO
53 MAPK1 MAPK1 MAPK1 10407 -0.0042 0.35 NO
54 PPP2CA PPP2CA PPP2CA 10514 -0.0052 0.34 NO
55 NFKBIB NFKBIB NFKBIB 10857 -0.0083 0.33 NO
56 JUN JUN JUN 10935 -0.0089 0.32 NO
57 ATF1 ATF1 ATF1 10949 -0.009 0.32 NO
58 MAP2K7 MAP2K7 MAP2K7 11191 -0.011 0.31 NO
59 MAP2K2 MAP2K2 MAP2K2 11291 -0.012 0.31 NO
60 MAPK14 MAPK14 MAPK14 11358 -0.013 0.31 NO
61 MAP2K4 MAP2K4 MAP2K4 12064 -0.019 0.27 NO
62 DUSP3 DUSP3 DUSP3 12788 -0.026 0.23 NO
63 APP APP APP 12930 -0.028 0.23 NO
64 PPP2R1A PPP2R1A PPP2R1A 13320 -0.032 0.21 NO
65 PPP2CB PPP2CB PPP2CB 13608 -0.035 0.2 NO
66 MAPK3 MAPK3 MAPK3 13684 -0.036 0.2 NO
67 MAPK8 MAPK8 MAPK8 14058 -0.041 0.18 NO
68 MAPK9 MAPK9 MAPK9 14059 -0.041 0.19 NO
69 RPS6KA2 RPS6KA2 RPS6KA2 14079 -0.041 0.2 NO
70 MAPK10 MAPK10 MAPK10 17433 -0.16 0.03 NO

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

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

Table 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 TLR6 TLR6 TLR6 104 0.95 0.075 YES
2 NOD2 NOD2 NOD2 227 0.82 0.14 YES
3 BTK BTK BTK 231 0.82 0.21 YES
4 LY96 LY96 LY96 445 0.7 0.26 YES
5 S100B S100B S100B 468 0.69 0.31 YES
6 TLR1 TLR1 TLR1 658 0.62 0.36 YES
7 SAA1 SAA1 SAA1 780 0.58 0.4 YES
8 TICAM2 TICAM2 TICAM2 1301 0.44 0.41 YES
9 TLR2 TLR2 TLR2 1808 0.34 0.41 YES
10 IRAK3 IRAK3 IRAK3 1921 0.32 0.43 YES
11 MAP2K6 MAP2K6 MAP2K6 1923 0.32 0.46 YES
12 TLR4 TLR4 TLR4 2196 0.28 0.46 YES
13 CDK1 CDK1 CDK1 2337 0.26 0.48 YES
14 TLR3 TLR3 TLR3 2342 0.26 0.5 YES
15 S100A12 S100A12 S100A12 2622 0.24 0.51 YES
16 CD14 CD14 CD14 2666 0.23 0.52 YES
17 PELI1 PELI1 PELI1 2763 0.22 0.54 YES
18 RPS6KA5 RPS6KA5 RPS6KA5 3092 0.19 0.53 YES
19 MYD88 MYD88 MYD88 3212 0.18 0.54 YES
20 TRAF3 TRAF3 TRAF3 3274 0.18 0.55 YES
21 IRF7 IRF7 IRF7 3287 0.17 0.57 YES
22 NFKB2 NFKB2 NFKB2 3549 0.16 0.57 YES
23 DUSP4 DUSP4 DUSP4 3708 0.14 0.57 YES
24 IRAK2 IRAK2 IRAK2 3801 0.14 0.58 YES
25 PELI2 PELI2 PELI2 3952 0.13 0.58 YES
26 NFKBIA NFKBIA NFKBIA 3969 0.13 0.59 YES
27 IRAK1 IRAK1 IRAK1 4165 0.12 0.59 YES
28 RIPK2 RIPK2 RIPK2 4295 0.11 0.59 YES
29 MAPK11 MAPK11 MAPK11 4327 0.11 0.6 YES
30 DUSP7 DUSP7 DUSP7 4501 0.1 0.6 YES
31 NOD1 NOD1 NOD1 4557 0.099 0.6 YES
32 MEF2C MEF2C MEF2C 4714 0.093 0.6 NO
33 TBK1 TBK1 TBK1 5136 0.078 0.59 NO
34 MAP2K1 MAP2K1 MAP2K1 5735 0.059 0.56 NO
35 IKBKE IKBKE IKBKE 5803 0.057 0.56 NO
36 IKBKG IKBKG IKBKG 5908 0.055 0.56 NO
37 UBE2N UBE2N UBE2N 5981 0.053 0.56 NO
38 RPS6KA3 RPS6KA3 RPS6KA3 6626 0.04 0.52 NO
39 MEF2A MEF2A MEF2A 6820 0.036 0.52 NO
40 RIPK1 RIPK1 RIPK1 6951 0.034 0.51 NO
41 MAPKAPK2 MAPKAPK2 MAPKAPK2 6961 0.034 0.52 NO
42 IRF3 IRF3 IRF3 6966 0.034 0.52 NO
43 TICAM1 TICAM1 TICAM1 7020 0.033 0.52 NO
44 DUSP6 DUSP6 DUSP6 7218 0.03 0.51 NO
45 MAPK7 MAPK7 MAPK7 7236 0.03 0.51 NO
46 IKBKB IKBKB IKBKB 7353 0.028 0.51 NO
47 CREB1 CREB1 CREB1 7508 0.026 0.5 NO
48 FOS FOS FOS 7557 0.025 0.5 NO
49 RPS6KA1 RPS6KA1 RPS6KA1 7657 0.024 0.5 NO
50 RELA RELA RELA 7719 0.024 0.5 NO
51 CHUK CHUK CHUK 7759 0.023 0.5 NO
52 IRAK4 IRAK4 IRAK4 7882 0.022 0.49 NO
53 ATF2 ATF2 ATF2 7894 0.022 0.49 NO
54 TRAF6 TRAF6 TRAF6 7943 0.021 0.49 NO
55 MAP3K7 MAP3K7 MAP3K7 7995 0.02 0.49 NO
56 TIRAP TIRAP TIRAP 8134 0.018 0.48 NO
57 PPP2R1B PPP2R1B PPP2R1B 8177 0.018 0.48 NO
58 MAP3K1 MAP3K1 MAP3K1 8234 0.017 0.48 NO
59 ELK1 ELK1 ELK1 8257 0.017 0.48 NO
60 HMGB1 HMGB1 HMGB1 8451 0.015 0.47 NO
61 MAP2K3 MAP2K3 MAP2K3 8464 0.015 0.47 NO
62 TAB2 TAB2 TAB2 8656 0.012 0.46 NO
63 UBA52 UBA52 UBA52 9051 0.0087 0.44 NO
64 SIGIRR SIGIRR SIGIRR 9128 0.008 0.44 NO
65 TAB3 TAB3 TAB3 9528 0.0041 0.42 NO
66 AGER AGER AGER 9659 0.0029 0.41 NO
67 PPP2R5D PPP2R5D PPP2R5D 10017 -0.00056 0.39 NO
68 RPS27A RPS27A RPS27A 10076 -0.0011 0.38 NO
69 TAB1 TAB1 TAB1 10285 -0.003 0.37 NO
70 MAPKAPK3 MAPKAPK3 MAPKAPK3 10287 -0.0031 0.37 NO
71 MAPK1 MAPK1 MAPK1 10407 -0.0042 0.37 NO
72 PPP2CA PPP2CA PPP2CA 10514 -0.0052 0.36 NO
73 NFKBIB NFKBIB NFKBIB 10857 -0.0083 0.34 NO
74 JUN JUN JUN 10935 -0.0089 0.34 NO
75 ATF1 ATF1 ATF1 10949 -0.009 0.34 NO
76 MAP2K7 MAP2K7 MAP2K7 11191 -0.011 0.33 NO
77 MAP2K2 MAP2K2 MAP2K2 11291 -0.012 0.32 NO
78 MAPK14 MAPK14 MAPK14 11358 -0.013 0.32 NO
79 MAP2K4 MAP2K4 MAP2K4 12064 -0.019 0.28 NO
80 DUSP3 DUSP3 DUSP3 12788 -0.026 0.24 NO
81 APP APP APP 12930 -0.028 0.24 NO
82 PPP2R1A PPP2R1A PPP2R1A 13320 -0.032 0.22 NO
83 PPP2CB PPP2CB PPP2CB 13608 -0.035 0.21 NO
84 MAPK3 MAPK3 MAPK3 13684 -0.036 0.21 NO
85 MAPK8 MAPK8 MAPK8 14058 -0.041 0.19 NO
86 MAPK9 MAPK9 MAPK9 14059 -0.041 0.19 NO
87 RPS6KA2 RPS6KA2 RPS6KA2 14079 -0.041 0.19 NO
88 PELI3 PELI3 PELI3 14796 -0.052 0.16 NO
89 ECSIT ECSIT ECSIT 15130 -0.058 0.14 NO
90 MAPK10 MAPK10 MAPK10 17433 -0.16 0.03 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 TYROSINE METABOLISM.

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

genes ES table in pathway: KEGG TRYPTOPHAN METABOLISM

Table 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 TLR8 TLR8 TLR8 168 0.87 0.093 YES
2 NOD2 NOD2 NOD2 227 0.82 0.19 YES
3 TLR9 TLR9 TLR9 309 0.77 0.27 YES
4 TLR7 TLR7 TLR7 424 0.71 0.35 YES
5 S100B S100B S100B 468 0.69 0.43 YES
6 SAA1 SAA1 SAA1 780 0.58 0.48 YES
7 MAP2K6 MAP2K6 MAP2K6 1923 0.32 0.45 YES
8 CDK1 CDK1 CDK1 2337 0.26 0.46 YES
9 S100A12 S100A12 S100A12 2622 0.24 0.47 YES
10 PELI1 PELI1 PELI1 2763 0.22 0.49 YES
11 RPS6KA5 RPS6KA5 RPS6KA5 3092 0.19 0.49 YES
12 MYD88 MYD88 MYD88 3212 0.18 0.51 YES
13 NFKB2 NFKB2 NFKB2 3549 0.16 0.51 YES
14 DUSP4 DUSP4 DUSP4 3708 0.14 0.52 YES
15 IRAK2 IRAK2 IRAK2 3801 0.14 0.53 YES
16 PELI2 PELI2 PELI2 3952 0.13 0.53 YES
17 NFKBIA NFKBIA NFKBIA 3969 0.13 0.55 YES
18 IRAK1 IRAK1 IRAK1 4165 0.12 0.55 YES
19 RIPK2 RIPK2 RIPK2 4295 0.11 0.56 YES
20 MAPK11 MAPK11 MAPK11 4327 0.11 0.57 YES
21 DUSP7 DUSP7 DUSP7 4501 0.1 0.57 YES
22 NOD1 NOD1 NOD1 4557 0.099 0.58 YES
23 MEF2C MEF2C MEF2C 4714 0.093 0.58 YES
24 MAP2K1 MAP2K1 MAP2K1 5735 0.059 0.53 NO
25 IKBKG IKBKG IKBKG 5908 0.055 0.53 NO
26 UBE2N UBE2N UBE2N 5981 0.053 0.53 NO
27 RPS6KA3 RPS6KA3 RPS6KA3 6626 0.04 0.5 NO
28 MEF2A MEF2A MEF2A 6820 0.036 0.49 NO
29 MAPKAPK2 MAPKAPK2 MAPKAPK2 6961 0.034 0.49 NO
30 DUSP6 DUSP6 DUSP6 7218 0.03 0.48 NO
31 MAPK7 MAPK7 MAPK7 7236 0.03 0.48 NO
32 IKBKB IKBKB IKBKB 7353 0.028 0.48 NO
33 CREB1 CREB1 CREB1 7508 0.026 0.47 NO
34 FOS FOS FOS 7557 0.025 0.47 NO
35 RPS6KA1 RPS6KA1 RPS6KA1 7657 0.024 0.47 NO
36 RELA RELA RELA 7719 0.024 0.47 NO
37 CHUK CHUK CHUK 7759 0.023 0.47 NO
38 IRAK4 IRAK4 IRAK4 7882 0.022 0.46 NO
39 ATF2 ATF2 ATF2 7894 0.022 0.47 NO
40 TRAF6 TRAF6 TRAF6 7943 0.021 0.47 NO
41 MAP3K7 MAP3K7 MAP3K7 7995 0.02 0.47 NO
42 PPP2R1B PPP2R1B PPP2R1B 8177 0.018 0.46 NO
43 MAP3K1 MAP3K1 MAP3K1 8234 0.017 0.46 NO
44 ELK1 ELK1 ELK1 8257 0.017 0.46 NO
45 HMGB1 HMGB1 HMGB1 8451 0.015 0.45 NO
46 MAP2K3 MAP2K3 MAP2K3 8464 0.015 0.45 NO
47 TAB2 TAB2 TAB2 8656 0.012 0.44 NO
48 UBA52 UBA52 UBA52 9051 0.0087 0.42 NO
49 TAB3 TAB3 TAB3 9528 0.0041 0.39 NO
50 AGER AGER AGER 9659 0.0029 0.39 NO
51 PPP2R5D PPP2R5D PPP2R5D 10017 -0.00056 0.37 NO
52 RPS27A RPS27A RPS27A 10076 -0.0011 0.36 NO
53 TAB1 TAB1 TAB1 10285 -0.003 0.35 NO
54 MAPKAPK3 MAPKAPK3 MAPKAPK3 10287 -0.0031 0.35 NO
55 MAPK1 MAPK1 MAPK1 10407 -0.0042 0.35 NO
56 PPP2CA PPP2CA PPP2CA 10514 -0.0052 0.34 NO
57 NFKBIB NFKBIB NFKBIB 10857 -0.0083 0.32 NO
58 JUN JUN JUN 10935 -0.0089 0.32 NO
59 ATF1 ATF1 ATF1 10949 -0.009 0.32 NO
60 MAP2K7 MAP2K7 MAP2K7 11191 -0.011 0.31 NO
61 MAP2K2 MAP2K2 MAP2K2 11291 -0.012 0.3 NO
62 MAPK14 MAPK14 MAPK14 11358 -0.013 0.3 NO
63 MAP2K4 MAP2K4 MAP2K4 12064 -0.019 0.26 NO
64 DUSP3 DUSP3 DUSP3 12788 -0.026 0.23 NO
65 APP APP APP 12930 -0.028 0.22 NO
66 PPP2R1A PPP2R1A PPP2R1A 13320 -0.032 0.2 NO
67 PPP2CB PPP2CB PPP2CB 13608 -0.035 0.19 NO
68 MAPK3 MAPK3 MAPK3 13684 -0.036 0.19 NO
69 MAPK8 MAPK8 MAPK8 14058 -0.041 0.18 NO
70 MAPK9 MAPK9 MAPK9 14059 -0.041 0.18 NO
71 RPS6KA2 RPS6KA2 RPS6KA2 14079 -0.041 0.18 NO
72 PELI3 PELI3 PELI3 14796 -0.052 0.15 NO
73 ECSIT ECSIT ECSIT 15130 -0.058 0.14 NO
74 MAPK10 MAPK10 MAPK10 17433 -0.16 0.03 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 TRYPTOPHAN METABOLISM.

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

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TLR6 TLR6 TLR6 104 0.95 0.087 YES
2 NOD2 NOD2 NOD2 227 0.82 0.16 YES
3 BTK BTK BTK 231 0.82 0.24 YES
4 LY96 LY96 LY96 445 0.7 0.3 YES
5 S100B S100B S100B 468 0.69 0.36 YES
6 TLR1 TLR1 TLR1 658 0.62 0.41 YES
7 SAA1 SAA1 SAA1 780 0.58 0.46 YES
8 TLR2 TLR2 TLR2 1808 0.34 0.44 YES
9 IRAK3 IRAK3 IRAK3 1921 0.32 0.46 YES
10 MAP2K6 MAP2K6 MAP2K6 1923 0.32 0.5 YES
11 TLR4 TLR4 TLR4 2196 0.28 0.51 YES
12 CDK1 CDK1 CDK1 2337 0.26 0.53 YES
13 S100A12 S100A12 S100A12 2622 0.24 0.53 YES
14 PELI1 PELI1 PELI1 2763 0.22 0.55 YES
15 RPS6KA5 RPS6KA5 RPS6KA5 3092 0.19 0.55 YES
16 MYD88 MYD88 MYD88 3212 0.18 0.56 YES
17 NFKB2 NFKB2 NFKB2 3549 0.16 0.56 YES
18 DUSP4 DUSP4 DUSP4 3708 0.14 0.56 YES
19 IRAK2 IRAK2 IRAK2 3801 0.14 0.57 YES
20 PELI2 PELI2 PELI2 3952 0.13 0.57 YES
21 NFKBIA NFKBIA NFKBIA 3969 0.13 0.58 YES
22 IRAK1 IRAK1 IRAK1 4165 0.12 0.58 YES
23 RIPK2 RIPK2 RIPK2 4295 0.11 0.59 YES
24 MAPK11 MAPK11 MAPK11 4327 0.11 0.6 YES
25 DUSP7 DUSP7 DUSP7 4501 0.1 0.6 YES
26 NOD1 NOD1 NOD1 4557 0.099 0.6 YES
27 MEF2C MEF2C MEF2C 4714 0.093 0.6 YES
28 MAP2K1 MAP2K1 MAP2K1 5735 0.059 0.55 NO
29 IKBKG IKBKG IKBKG 5908 0.055 0.55 NO
30 UBE2N UBE2N UBE2N 5981 0.053 0.55 NO
31 RPS6KA3 RPS6KA3 RPS6KA3 6626 0.04 0.52 NO
32 MEF2A MEF2A MEF2A 6820 0.036 0.51 NO
33 MAPKAPK2 MAPKAPK2 MAPKAPK2 6961 0.034 0.51 NO
34 DUSP6 DUSP6 DUSP6 7218 0.03 0.5 NO
35 MAPK7 MAPK7 MAPK7 7236 0.03 0.5 NO
36 IKBKB IKBKB IKBKB 7353 0.028 0.49 NO
37 CREB1 CREB1 CREB1 7508 0.026 0.49 NO
38 FOS FOS FOS 7557 0.025 0.49 NO
39 RPS6KA1 RPS6KA1 RPS6KA1 7657 0.024 0.48 NO
40 RELA RELA RELA 7719 0.024 0.48 NO
41 CHUK CHUK CHUK 7759 0.023 0.48 NO
42 IRAK4 IRAK4 IRAK4 7882 0.022 0.48 NO
43 ATF2 ATF2 ATF2 7894 0.022 0.48 NO
44 TRAF6 TRAF6 TRAF6 7943 0.021 0.48 NO
45 MAP3K7 MAP3K7 MAP3K7 7995 0.02 0.48 NO
46 TIRAP TIRAP TIRAP 8134 0.018 0.47 NO
47 PPP2R1B PPP2R1B PPP2R1B 8177 0.018 0.47 NO
48 MAP3K1 MAP3K1 MAP3K1 8234 0.017 0.47 NO
49 ELK1 ELK1 ELK1 8257 0.017 0.47 NO
50 HMGB1 HMGB1 HMGB1 8451 0.015 0.46 NO
51 MAP2K3 MAP2K3 MAP2K3 8464 0.015 0.46 NO
52 TAB2 TAB2 TAB2 8656 0.012 0.45 NO
53 UBA52 UBA52 UBA52 9051 0.0087 0.43 NO
54 SIGIRR SIGIRR SIGIRR 9128 0.008 0.43 NO
55 TAB3 TAB3 TAB3 9528 0.0041 0.41 NO
56 AGER AGER AGER 9659 0.0029 0.4 NO
57 PPP2R5D PPP2R5D PPP2R5D 10017 -0.00056 0.38 NO
58 RPS27A RPS27A RPS27A 10076 -0.0011 0.38 NO
59 TAB1 TAB1 TAB1 10285 -0.003 0.36 NO
60 MAPKAPK3 MAPKAPK3 MAPKAPK3 10287 -0.0031 0.36 NO
61 MAPK1 MAPK1 MAPK1 10407 -0.0042 0.36 NO
62 PPP2CA PPP2CA PPP2CA 10514 -0.0052 0.35 NO
63 NFKBIB NFKBIB NFKBIB 10857 -0.0083 0.34 NO
64 JUN JUN JUN 10935 -0.0089 0.33 NO
65 ATF1 ATF1 ATF1 10949 -0.009 0.33 NO
66 MAP2K7 MAP2K7 MAP2K7 11191 -0.011 0.32 NO
67 MAP2K2 MAP2K2 MAP2K2 11291 -0.012 0.32 NO
68 MAPK14 MAPK14 MAPK14 11358 -0.013 0.31 NO
69 MAP2K4 MAP2K4 MAP2K4 12064 -0.019 0.28 NO
70 DUSP3 DUSP3 DUSP3 12788 -0.026 0.24 NO
71 APP APP APP 12930 -0.028 0.23 NO
72 PPP2R1A PPP2R1A PPP2R1A 13320 -0.032 0.21 NO
73 PPP2CB PPP2CB PPP2CB 13608 -0.035 0.2 NO
74 MAPK3 MAPK3 MAPK3 13684 -0.036 0.2 NO
75 MAPK8 MAPK8 MAPK8 14058 -0.041 0.18 NO
76 MAPK9 MAPK9 MAPK9 14059 -0.041 0.19 NO
77 RPS6KA2 RPS6KA2 RPS6KA2 14079 -0.041 0.19 NO
78 PELI3 PELI3 PELI3 14796 -0.052 0.16 NO
79 ECSIT ECSIT ECSIT 15130 -0.058 0.14 NO
80 MAPK10 MAPK10 MAPK10 17433 -0.16 0.03 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 GLUTATHIONE METABOLISM.

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

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 NOTCH SIGNALING PATHWAY 46 genes.ES.table 0.34 1.3 0.18 1 1 0.28 0.22 0.22 1 0.85
KEGG ADHERENS JUNCTION 73 genes.ES.table 0.36 1.3 0.17 1 1 0.33 0.22 0.26 1 0.86
KEGG THYROID CANCER 29 genes.ES.table 0.44 1.4 0.08 1 0.99 0.14 0.066 0.13 1 0.8
PID LKB1 PATHWAY 47 genes.ES.table 0.35 1.4 0.14 1 1 0.15 0.14 0.13 1 0.82
PID AJDISS 2PATHWAY 46 genes.ES.table 0.41 1.2 0.22 1 1 0.24 0.15 0.2 1 0.88
PID TRKRPATHWAY 61 genes.ES.table 0.45 1.6 0.038 1 0.94 0.082 0.038 0.079 1 0.74
PID NCADHERINPATHWAY 33 genes.ES.table 0.56 1.7 0 1 0.71 0.091 0.012 0.09 1 0.58
REACTOME CELL CELL COMMUNICATION 113 genes.ES.table 0.44 1.3 0.17 1 1 0.28 0.15 0.24 1 0.86
REACTOME NEGATIVE REGULATION OF FGFR SIGNALING 30 genes.ES.table 0.52 1.3 0.12 1 1 0.13 0.022 0.13 1 0.85
REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS 25 genes.ES.table 0.49 1.5 0.059 1 0.97 0.2 0.13 0.17 1 0.78
genes ES table in pathway: KEGG NOTCH 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 GRIA2 GRIA2 GRIA2 59 0.56 0.22 YES
2 GAP43 GAP43 GAP43 126 0.48 0.41 YES
3 CDH2 CDH2 CDH2 224 0.4 0.56 YES
4 GSN GSN GSN 2699 0.088 0.46 NO
5 GJA1 GJA1 GJA1 4064 0.054 0.41 NO
6 LRP5 LRP5 LRP5 4701 0.043 0.39 NO
7 CTNNB1 CTNNB1 CTNNB1 5396 0.034 0.36 NO
8 AXIN1 AXIN1 AXIN1 5405 0.034 0.38 NO
9 DAGLA DAGLA DAGLA 5828 0.029 0.36 NO
10 CTNNA1 CTNNA1 CTNNA1 5917 0.028 0.37 NO
11 PLCG1 PLCG1 PLCG1 6313 0.024 0.36 NO
12 CTTN CTTN CTTN 6783 0.019 0.34 NO
13 PIP5K1C PIP5K1C PIP5K1C 6810 0.019 0.35 NO
14 ROCK1 ROCK1 ROCK1 7128 0.016 0.34 NO
15 RAC1 RAC1 RAC1 7592 0.011 0.31 NO
16 JUP JUP JUP 7836 0.0092 0.3 NO
17 RHOA RHOA RHOA 7961 0.008 0.3 NO
18 DAGLB DAGLB DAGLB 8716 0.0013 0.26 NO
19 DCTN1 DCTN1 DCTN1 9731 -0.0079 0.2 NO
20 CDC42 CDC42 CDC42 9792 -0.0084 0.2 NO
21 PIK3R1 PIK3R1 PIK3R1 9836 -0.0088 0.21 NO
22 PIK3CA PIK3CA PIK3CA 10668 -0.017 0.17 NO
23 CTNND1 CTNND1 CTNND1 10771 -0.018 0.17 NO
24 MAPRE1 MAPRE1 MAPRE1 11172 -0.022 0.16 NO
25 CAMK2G CAMK2G CAMK2G 11334 -0.024 0.16 NO
26 FGFR1 FGFR1 FGFR1 11417 -0.025 0.16 NO
27 KIF5B KIF5B KIF5B 11687 -0.028 0.16 NO
28 PTPN11 PTPN11 PTPN11 12371 -0.037 0.13 NO
29 FER FER FER 12920 -0.045 0.12 NO
30 PTPN1 PTPN1 PTPN1 14005 -0.064 0.087 NO
31 MYL2 MYL2 MYL2 15397 -0.1 0.052 NO
32 CNR1 CNR1 CNR1 15550 -0.11 0.088 NO
33 MAPK8 MAPK8 MAPK8 15686 -0.12 0.13 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 NOTCH SIGNALING PATHWAY.

Figure S62.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH 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 ADHERENS JUNCTION

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 CLDN6 CLDN6 CLDN6 85 0.52 0.077 YES
2 CLDN10 CLDN10 CLDN10 167 0.44 0.14 YES
3 CLDN2 CLDN2 CLDN2 170 0.44 0.21 YES
4 CDH2 CDH2 CDH2 224 0.4 0.27 YES
5 CDH3 CDH3 CDH3 358 0.34 0.32 YES
6 CDH15 CDH15 CDH15 630 0.27 0.34 YES
7 PVRL4 PVRL4 PVRL4 666 0.26 0.38 YES
8 CLDN9 CLDN9 CLDN9 724 0.25 0.42 YES
9 CADM1 CADM1 CADM1 980 0.21 0.44 YES
10 PARD6B PARD6B PARD6B 1217 0.18 0.45 YES
11 CLDN1 CLDN1 CLDN1 1300 0.17 0.48 YES
12 CDH8 CDH8 CDH8 1388 0.16 0.5 YES
13 CLDN16 CLDN16 CLDN16 1420 0.16 0.52 YES
14 CDH24 CDH24 CDH24 1567 0.15 0.54 YES
15 CDH4 CDH4 CDH4 1656 0.14 0.55 YES
16 CLDN11 CLDN11 CLDN11 1685 0.14 0.57 YES
17 CDH11 CDH11 CDH11 1686 0.14 0.6 YES
18 PVRL1 PVRL1 PVRL1 1901 0.13 0.6 YES
19 CLDN15 CLDN15 CLDN15 2099 0.11 0.61 YES
20 CLDN19 CLDN19 CLDN19 2120 0.11 0.63 YES
21 CLDN5 CLDN5 CLDN5 2201 0.11 0.64 YES
22 CDH13 CDH13 CDH13 2414 0.099 0.64 YES
23 PVRL2 PVRL2 PVRL2 3317 0.071 0.6 NO
24 CLDN3 CLDN3 CLDN3 4117 0.053 0.57 NO
25 CLDN4 CLDN4 CLDN4 4461 0.047 0.56 NO
26 INADL INADL INADL 4494 0.046 0.56 NO
27 PARD6A PARD6A PARD6A 5213 0.036 0.53 NO
28 F11R F11R F11R 5385 0.034 0.52 NO
29 CTNNB1 CTNNB1 CTNNB1 5396 0.034 0.53 NO
30 CLDN7 CLDN7 CLDN7 5599 0.032 0.52 NO
31 CDH5 CDH5 CDH5 5646 0.031 0.52 NO
32 CTNNA1 CTNNA1 CTNNA1 5917 0.028 0.51 NO
33 CDH12 CDH12 CDH12 6229 0.025 0.5 NO
34 MPP5 MPP5 MPP5 7442 0.013 0.43 NO
35 JUP JUP JUP 7836 0.0092 0.41 NO
36 PARD3 PARD3 PARD3 8227 0.0057 0.39 NO
37 CDH1 CDH1 CDH1 8696 0.0015 0.37 NO
38 CRB3 CRB3 CRB3 10064 -0.011 0.29 NO
39 PVRL3 PVRL3 PVRL3 10365 -0.014 0.28 NO
40 CTNND1 CTNND1 CTNND1 10771 -0.018 0.26 NO
41 PARD6G PARD6G PARD6G 11129 -0.022 0.24 NO
42 CDH10 CDH10 CDH10 11305 -0.024 0.24 NO
43 PRKCI PRKCI PRKCI 11523 -0.026 0.23 NO
44 CDH6 CDH6 CDH6 13348 -0.052 0.13 NO
45 PVR PVR PVR 14101 -0.066 0.1 NO
46 CADM2 CADM2 CADM2 14300 -0.071 0.1 NO
47 CLDN18 CLDN18 CLDN18 14452 -0.075 0.1 NO
48 CLDN14 CLDN14 CLDN14 14520 -0.077 0.11 NO
49 CLDN12 CLDN12 CLDN12 14768 -0.084 0.11 NO
50 CLDN20 CLDN20 CLDN20 15978 -0.13 0.066 NO
51 CLDN8 CLDN8 CLDN8 17495 -0.28 0.027 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 ADHERENS JUNCTION.

Figure S64.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ADHERENS JUNCTION, 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 THYROID CANCER

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 RASGRF1 RASGRF1 RASGRF1 35 0.63 0.13 YES
2 NGFR NGFR NGFR 38 0.61 0.25 YES
3 BDNF BDNF BDNF 120 0.48 0.35 YES
4 NTRK3 NTRK3 NTRK3 212 0.4 0.42 YES
5 TIAM1 TIAM1 TIAM1 690 0.26 0.45 YES
6 NTF3 NTF3 NTF3 2289 0.1 0.38 NO
7 RASA1 RASA1 RASA1 3248 0.073 0.34 NO
8 FRS3 FRS3 FRS3 3256 0.073 0.36 NO
9 GAB2 GAB2 GAB2 3854 0.058 0.34 NO
10 NTRK2 NTRK2 NTRK2 4298 0.05 0.32 NO
11 HRAS HRAS HRAS 4300 0.05 0.33 NO
12 MCF2L MCF2L MCF2L 4338 0.049 0.34 NO
13 CCND1 CCND1 CCND1 4807 0.041 0.32 NO
14 DNM1 DNM1 DNM1 4814 0.041 0.33 NO
15 SHC1 SHC1 SHC1 5245 0.036 0.32 NO
16 SH2B1 SH2B1 SH2B1 5448 0.033 0.31 NO
17 RIT1 RIT1 RIT1 5620 0.031 0.31 NO
18 CRKL CRKL CRKL 5775 0.03 0.3 NO
19 GAB1 GAB1 GAB1 5951 0.028 0.3 NO
20 NEDD4L NEDD4L NEDD4L 6120 0.026 0.3 NO
21 STAT3 STAT3 STAT3 6201 0.025 0.3 NO
22 PLCG1 PLCG1 PLCG1 6313 0.024 0.3 NO
23 ABL1 ABL1 ABL1 6416 0.023 0.3 NO
24 EHD4 EHD4 EHD4 6436 0.023 0.3 NO
25 FAIM FAIM FAIM 7074 0.016 0.27 NO
26 PRKCZ PRKCZ PRKCZ 7375 0.013 0.25 NO
27 RHOG RHOG RHOG 7377 0.013 0.26 NO
28 RAC1 RAC1 RAC1 7592 0.011 0.24 NO
29 RHOA RHOA RHOA 7961 0.008 0.23 NO
30 RAP1B RAP1B RAP1B 8508 0.0033 0.2 NO
31 GIPC1 GIPC1 GIPC1 9319 -0.0042 0.15 NO
32 GRB2 GRB2 GRB2 9336 -0.0043 0.15 NO
33 RGS19 RGS19 RGS19 9498 -0.0059 0.14 NO
34 MAPK3 MAPK3 MAPK3 9755 -0.0081 0.13 NO
35 CDC42 CDC42 CDC42 9792 -0.0084 0.13 NO
36 PIK3R1 PIK3R1 PIK3R1 9836 -0.0088 0.13 NO
37 FRS2 FRS2 FRS2 9870 -0.0091 0.13 NO
38 MAPK1 MAPK1 MAPK1 10177 -0.012 0.12 NO
39 PIK3CA PIK3CA PIK3CA 10668 -0.017 0.092 NO
40 RAPGEF1 RAPGEF1 RAPGEF1 10683 -0.017 0.095 NO
41 DOCK1 DOCK1 DOCK1 10884 -0.019 0.088 NO
42 RAP1A RAP1A RAP1A 11198 -0.023 0.075 NO
43 SQSTM1 SQSTM1 SQSTM1 11513 -0.026 0.063 NO
44 PRKCI PRKCI PRKCI 11523 -0.026 0.068 NO
45 SOS1 SOS1 SOS1 11578 -0.027 0.07 NO
46 MATK MATK MATK 11581 -0.027 0.076 NO
47 MAGED1 MAGED1 MAGED1 11624 -0.027 0.079 NO
48 CRK CRK CRK 12126 -0.034 0.058 NO
49 MAP2K1 MAP2K1 MAP2K1 12341 -0.037 0.053 NO
50 PTPN11 PTPN11 PTPN11 12371 -0.037 0.059 NO
51 KRAS KRAS KRAS 12724 -0.042 0.048 NO
52 DNAJA3 DNAJA3 DNAJA3 13130 -0.048 0.035 NO
53 NGF NGF NGF 13335 -0.052 0.034 NO
54 DYNLT1 DYNLT1 DYNLT1 14411 -0.074 -0.01 NO
55 NRAS NRAS NRAS 14649 -0.081 -0.0071 NO
56 ARHGAP32 ARHGAP32 ARHGAP32 14780 -0.085 0.003 NO
57 SHC3 SHC3 SHC3 15849 -0.12 -0.031 NO
58 SHC2 SHC2 SHC2 15908 -0.13 -0.008 NO
59 NTRK1 NTRK1 NTRK1 16501 -0.16 -0.008 NO
60 NTF4 NTF4 NTF4 16906 -0.19 0.0087 NO
61 ELMO1 ELMO1 ELMO1 17341 -0.25 0.035 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 THYROID CANCER.

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID CANCER, 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 LKB1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NEURL NEURL NEURL 81 0.52 0.27 YES
2 DTX1 DTX1 DTX1 875 0.22 0.34 YES
3 DTX4 DTX4 DTX4 922 0.22 0.45 YES
4 DLL1 DLL1 DLL1 1880 0.13 0.47 YES
5 DLL4 DLL4 DLL4 2345 0.1 0.49 YES
6 JAG2 JAG2 JAG2 3866 0.058 0.44 NO
7 MIB2 MIB2 MIB2 4723 0.043 0.41 NO
8 APH1B APH1B APH1B 6224 0.025 0.34 NO
9 PSEN2 PSEN2 PSEN2 6729 0.02 0.33 NO
10 PSENEN PSENEN PSENEN 7281 0.014 0.3 NO
11 MIB1 MIB1 MIB1 7569 0.012 0.29 NO
12 NCSTN NCSTN NCSTN 8465 0.0037 0.24 NO
13 RPS27A RPS27A RPS27A 8574 0.0027 0.24 NO
14 PSEN1 PSEN1 PSEN1 9149 -0.0026 0.21 NO
15 JAG1 JAG1 JAG1 9422 -0.0051 0.2 NO
16 UBA52 UBA52 UBA52 9631 -0.0071 0.19 NO
17 APH1A APH1A APH1A 9632 -0.0071 0.19 NO
18 ARRB2 ARRB2 ARRB2 9925 -0.0097 0.18 NO
19 DTX2 DTX2 DTX2 10611 -0.016 0.15 NO
20 ADAM10 ADAM10 ADAM10 12037 -0.032 0.09 NO
21 NUMB NUMB NUMB 12607 -0.04 0.079 NO
22 ADAM17 ADAM17 ADAM17 12679 -0.041 0.097 NO
23 ARRB1 ARRB1 ARRB1 13243 -0.05 0.092 NO
24 DNER DNER DNER 16297 -0.15 -0.00053 NO
25 CNTN1 CNTN1 CNTN1 16758 -0.18 0.068 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: PID LKB1 PATHWAY.

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: PID LKB1 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 AJDISS 2PATHWAY

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 CLDN6 CLDN6 CLDN6 85 0.52 0.14 YES
2 CLDN10 CLDN10 CLDN10 167 0.44 0.26 YES
3 CLDN2 CLDN2 CLDN2 170 0.44 0.38 YES
4 CLDN9 CLDN9 CLDN9 724 0.25 0.42 YES
5 PARD6B PARD6B PARD6B 1217 0.18 0.44 YES
6 CLDN1 CLDN1 CLDN1 1300 0.17 0.48 YES
7 CLDN16 CLDN16 CLDN16 1420 0.16 0.52 YES
8 CLDN11 CLDN11 CLDN11 1685 0.14 0.54 YES
9 CLDN15 CLDN15 CLDN15 2099 0.11 0.55 YES
10 CLDN19 CLDN19 CLDN19 2120 0.11 0.58 YES
11 CLDN5 CLDN5 CLDN5 2201 0.11 0.61 YES
12 CLDN3 CLDN3 CLDN3 4117 0.053 0.52 NO
13 CLDN4 CLDN4 CLDN4 4461 0.047 0.51 NO
14 INADL INADL INADL 4494 0.046 0.52 NO
15 PARD6A PARD6A PARD6A 5213 0.036 0.49 NO
16 F11R F11R F11R 5385 0.034 0.49 NO
17 CLDN7 CLDN7 CLDN7 5599 0.032 0.49 NO
18 MPP5 MPP5 MPP5 7442 0.013 0.39 NO
19 PARD3 PARD3 PARD3 8227 0.0057 0.34 NO
20 CRB3 CRB3 CRB3 10064 -0.011 0.25 NO
21 PARD6G PARD6G PARD6G 11129 -0.022 0.19 NO
22 PRKCI PRKCI PRKCI 11523 -0.026 0.18 NO
23 CLDN18 CLDN18 CLDN18 14452 -0.075 0.036 NO
24 CLDN14 CLDN14 CLDN14 14520 -0.077 0.054 NO
25 CLDN12 CLDN12 CLDN12 14768 -0.084 0.063 NO
26 CLDN20 CLDN20 CLDN20 15978 -0.13 0.032 NO
27 CLDN8 CLDN8 CLDN8 17495 -0.28 0.026 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: PID AJDISS 2PATHWAY.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AJDISS 2PATHWAY, 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 TRKRPATHWAY

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 CLDN6 CLDN6 CLDN6 85 0.52 0.06 YES
2 CLDN10 CLDN10 CLDN10 167 0.44 0.11 YES
3 CLDN2 CLDN2 CLDN2 170 0.44 0.16 YES
4 CDH2 CDH2 CDH2 224 0.4 0.21 YES
5 CDH3 CDH3 CDH3 358 0.34 0.25 YES
6 LAMB3 LAMB3 LAMB3 552 0.29 0.27 YES
7 CDH15 CDH15 CDH15 630 0.27 0.3 YES
8 PVRL4 PVRL4 PVRL4 666 0.26 0.33 YES
9 CLDN9 CLDN9 CLDN9 724 0.25 0.36 YES
10 CADM1 CADM1 CADM1 980 0.21 0.37 YES
11 PARD6B PARD6B PARD6B 1217 0.18 0.38 YES
12 CLDN1 CLDN1 CLDN1 1300 0.17 0.4 YES
13 CDH8 CDH8 CDH8 1388 0.16 0.41 YES
14 CLDN16 CLDN16 CLDN16 1420 0.16 0.43 YES
15 CDH24 CDH24 CDH24 1567 0.15 0.44 YES
16 CDH4 CDH4 CDH4 1656 0.14 0.46 YES
17 CLDN11 CLDN11 CLDN11 1685 0.14 0.47 YES
18 CDH11 CDH11 CDH11 1686 0.14 0.49 YES
19 PVRL1 PVRL1 PVRL1 1901 0.13 0.49 YES
20 CD151 CD151 CD151 2098 0.11 0.5 YES
21 CLDN15 CLDN15 CLDN15 2099 0.11 0.51 YES
22 CLDN19 CLDN19 CLDN19 2120 0.11 0.52 YES
23 CLDN5 CLDN5 CLDN5 2201 0.11 0.53 YES
24 CDH13 CDH13 CDH13 2414 0.099 0.53 YES
25 ITGB4 ITGB4 ITGB4 2461 0.097 0.54 YES
26 PVRL2 PVRL2 PVRL2 3317 0.071 0.5 NO
27 LIMS3 LIMS3 LIMS3 3738 0.061 0.49 NO
28 VASP VASP VASP 4069 0.054 0.48 NO
29 CLDN3 CLDN3 CLDN3 4117 0.053 0.48 NO
30 CLDN4 CLDN4 CLDN4 4461 0.047 0.47 NO
31 INADL INADL INADL 4494 0.046 0.47 NO
32 ACTN1 ACTN1 ACTN1 4562 0.045 0.47 NO
33 PARD6A PARD6A PARD6A 5213 0.036 0.44 NO
34 F11R F11R F11R 5385 0.034 0.44 NO
35 CTNNB1 CTNNB1 CTNNB1 5396 0.034 0.44 NO
36 CLDN7 CLDN7 CLDN7 5599 0.032 0.43 NO
37 CDH5 CDH5 CDH5 5646 0.031 0.43 NO
38 CTNNA1 CTNNA1 CTNNA1 5917 0.028 0.42 NO
39 CDH12 CDH12 CDH12 6229 0.025 0.41 NO
40 PLEC PLEC PLEC 6377 0.023 0.4 NO
41 FERMT2 FERMT2 FERMT2 6477 0.022 0.4 NO
42 TESK1 TESK1 TESK1 7208 0.015 0.36 NO
43 MPP5 MPP5 MPP5 7442 0.013 0.35 NO
44 JUP JUP JUP 7836 0.0092 0.33 NO
45 ILK ILK ILK 7944 0.0082 0.32 NO
46 PARD3 PARD3 PARD3 8227 0.0057 0.31 NO
47 CDH1 CDH1 CDH1 8696 0.0015 0.28 NO
48 CRB3 CRB3 CRB3 10064 -0.011 0.21 NO
49 PVRL3 PVRL3 PVRL3 10365 -0.014 0.19 NO
50 PARVB PARVB PARVB 10499 -0.015 0.19 NO
51 ITGB1 ITGB1 ITGB1 10594 -0.016 0.18 NO
52 CTNND1 CTNND1 CTNND1 10771 -0.018 0.18 NO
53 PARD6G PARD6G PARD6G 11129 -0.022 0.16 NO
54 CDH10 CDH10 CDH10 11305 -0.024 0.15 NO
55 PRKCI PRKCI PRKCI 11523 -0.026 0.14 NO
56 PARVA PARVA PARVA 12098 -0.033 0.12 NO
57 FLNC FLNC FLNC 12603 -0.04 0.093 NO
58 LAMA3 LAMA3 LAMA3 12902 -0.045 0.082 NO
59 RSU1 RSU1 RSU1 13329 -0.051 0.065 NO
60 CDH6 CDH6 CDH6 13348 -0.052 0.07 NO
61 FBLIM1 FBLIM1 FBLIM1 13874 -0.061 0.048 NO
62 PVR PVR PVR 14101 -0.066 0.044 NO
63 ARHGEF6 ARHGEF6 ARHGEF6 14205 -0.069 0.047 NO
64 LAMC2 LAMC2 LAMC2 14295 -0.071 0.051 NO
65 CADM2 CADM2 CADM2 14300 -0.071 0.06 NO
66 CLDN18 CLDN18 CLDN18 14452 -0.075 0.06 NO
67 CLDN14 CLDN14 CLDN14 14520 -0.077 0.066 NO
68 CLDN12 CLDN12 CLDN12 14768 -0.084 0.063 NO
69 CLDN20 CLDN20 CLDN20 15978 -0.13 0.012 NO
70 LIMS1 LIMS1 LIMS1 17023 -0.2 -0.021 NO
71 CLDN8 CLDN8 CLDN8 17495 -0.28 -0.012 NO
72 COL17A1 COL17A1 COL17A1 17570 -0.3 0.022 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: PID TRKRPATHWAY.

Figure S72.  Get High-res Image For the top 5 core enriched genes in the pathway: PID TRKRPATHWAY, 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 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 RXRG RXRG RXRG 163 0.44 0.17 YES
2 RET RET RET 259 0.38 0.31 YES
3 TCF7 TCF7 TCF7 611 0.27 0.4 YES
4 LEF1 LEF1 LEF1 1183 0.18 0.44 YES
5 TCF7L2 TCF7L2 TCF7L2 3089 0.077 0.37 NO
6 MYC MYC MYC 4172 0.052 0.33 NO
7 HRAS HRAS HRAS 4300 0.05 0.34 NO
8 CCND1 CCND1 CCND1 4807 0.041 0.33 NO
9 CTNNB1 CTNNB1 CTNNB1 5396 0.034 0.31 NO
10 RXRB RXRB RXRB 6939 0.018 0.23 NO
11 TPM3 TPM3 TPM3 7660 0.011 0.19 NO
12 MAP2K2 MAP2K2 MAP2K2 8128 0.0065 0.17 NO
13 CDH1 CDH1 CDH1 8696 0.0015 0.14 NO
14 TP53 TP53 TP53 8903 -0.00031 0.13 NO
15 RXRA RXRA RXRA 9001 -0.0012 0.12 NO
16 MAPK3 MAPK3 MAPK3 9755 -0.0081 0.084 NO
17 PAX8 PAX8 PAX8 10121 -0.012 0.068 NO
18 MAPK1 MAPK1 MAPK1 10177 -0.012 0.069 NO
19 TPR TPR TPR 11281 -0.024 0.017 NO
20 TFG TFG TFG 11861 -0.03 -0.0031 NO
21 MAP2K1 MAP2K1 MAP2K1 12341 -0.037 -0.015 NO
22 KRAS KRAS KRAS 12724 -0.042 -0.02 NO
23 NCOA4 NCOA4 NCOA4 13290 -0.051 -0.032 NO
24 TCF7L1 TCF7L1 TCF7L1 13880 -0.062 -0.04 NO
25 CCDC6 CCDC6 CCDC6 14116 -0.067 -0.027 NO
26 NRAS NRAS NRAS 14649 -0.081 -0.024 NO
27 BRAF BRAF BRAF 14788 -0.085 0.0016 NO
28 NTRK1 NTRK1 NTRK1 16501 -0.16 -0.03 NO
29 PPARG PPARG PPARG 17491 -0.28 0.027 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: PID NCADHERINPATHWAY.

Figure S74.  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

genes ES table in pathway: REACTOME CELL CELL COMMUNICATION

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 SLIT2 SLIT2 SLIT2 330 0.35 0.18 YES
2 SRGAP3 SRGAP3 SRGAP3 2139 0.11 0.15 YES
3 SRGAP2 SRGAP2 SRGAP2 2168 0.11 0.21 YES
4 CAP2 CAP2 CAP2 2555 0.093 0.24 YES
5 NCK2 NCK2 NCK2 2916 0.082 0.26 YES
6 PAK7 PAK7 PAK7 3079 0.077 0.3 YES
7 PAK1 PAK1 PAK1 3213 0.074 0.33 YES
8 ROBO2 ROBO2 ROBO2 3668 0.062 0.34 YES
9 ROBO1 ROBO1 ROBO1 3874 0.058 0.37 YES
10 PAK4 PAK4 PAK4 3903 0.057 0.4 YES
11 VASP VASP VASP 4069 0.054 0.42 YES
12 SRGAP1 SRGAP1 SRGAP1 4107 0.053 0.45 YES
13 CLASP1 CLASP1 CLASP1 4836 0.041 0.43 NO
14 ABL1 ABL1 ABL1 6416 0.023 0.35 NO
15 RAC1 RAC1 RAC1 7592 0.011 0.3 NO
16 CAP1 CAP1 CAP1 8908 -0.00034 0.22 NO
17 ENAH ENAH ENAH 9120 -0.0023 0.21 NO
18 EVL EVL EVL 9512 -0.006 0.19 NO
19 CDC42 CDC42 CDC42 9792 -0.0084 0.18 NO
20 PFN1 PFN1 PFN1 10218 -0.012 0.16 NO
21 PFN2 PFN2 PFN2 10231 -0.012 0.17 NO
22 PAK2 PAK2 PAK2 10515 -0.015 0.16 NO
23 ROBO3 ROBO3 ROBO3 11006 -0.021 0.15 NO
24 SOS1 SOS1 SOS1 11578 -0.027 0.13 NO
25 ABL2 ABL2 ABL2 12050 -0.032 0.12 NO
26 NCK1 NCK1 NCK1 12437 -0.038 0.12 NO
27 SOS2 SOS2 SOS2 13943 -0.063 0.077 NO
28 PAK6 PAK6 PAK6 14574 -0.078 0.086 NO
29 GPC1 GPC1 GPC1 16784 -0.18 0.066 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: REACTOME CELL CELL COMMUNICATION.

Figure S76.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CELL CELL COMMUNICATION, 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 NEGATIVE REGULATION OF FGFR SIGNALING

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 FGF20 FGF20 FGF20 20 0.7 0.21 YES
2 FGF9 FGF9 FGF9 88 0.52 0.36 YES
3 FGFR3 FGFR3 FGFR3 264 0.38 0.47 YES
4 FGF1 FGF1 FGF1 2739 0.087 0.36 NO
5 FGF18 FGF18 FGF18 3778 0.06 0.32 NO
6 GAB2 GAB2 GAB2 3854 0.058 0.33 NO
7 HRAS HRAS HRAS 4300 0.05 0.32 NO
8 FGFR2 FGFR2 FGFR2 4399 0.048 0.33 NO
9 FGF2 FGF2 FGF2 4604 0.045 0.34 NO
10 STAT5A STAT5A STAT5A 5440 0.033 0.3 NO
11 STAT1 STAT1 STAT1 5642 0.031 0.3 NO
12 GAB1 GAB1 GAB1 5951 0.028 0.29 NO
13 STAT3 STAT3 STAT3 6201 0.025 0.28 NO
14 PLCG1 PLCG1 PLCG1 6313 0.024 0.28 NO
15 BCR BCR BCR 6786 0.019 0.26 NO
16 CPSF6 CPSF6 CPSF6 7274 0.014 0.24 NO
17 STAT5B STAT5B STAT5B 7440 0.013 0.24 NO
18 FGFR1OP2 FGFR1OP2 FGFR1OP2 7487 0.012 0.24 NO
19 ZMYM2 ZMYM2 ZMYM2 8533 0.0031 0.18 NO
20 GRB2 GRB2 GRB2 9336 -0.0043 0.14 NO
21 CUX1 CUX1 CUX1 9374 -0.0046 0.14 NO
22 PIK3R1 PIK3R1 PIK3R1 9836 -0.0088 0.11 NO
23 FRS2 FRS2 FRS2 9870 -0.0091 0.11 NO
24 FGF22 FGF22 FGF22 9964 -0.01 0.11 NO
25 PIK3CA PIK3CA PIK3CA 10668 -0.017 0.077 NO
26 MYO18A MYO18A MYO18A 10991 -0.021 0.066 NO
27 FGFR1 FGFR1 FGFR1 11417 -0.025 0.049 NO
28 SOS1 SOS1 SOS1 11578 -0.027 0.049 NO
29 FGFR1OP FGFR1OP FGFR1OP 12141 -0.034 0.028 NO
30 TRIM24 TRIM24 TRIM24 12408 -0.038 0.024 NO
31 KRAS KRAS KRAS 12724 -0.042 0.019 NO
32 NRAS NRAS NRAS 14649 -0.081 -0.063 NO
33 FGFR4 FGFR4 FGFR4 14990 -0.092 -0.054 NO
34 FGF17 FGF17 FGF17 17057 -0.21 -0.11 NO
35 FGF7 FGF7 FGF7 17230 -0.23 -0.046 NO
36 FGF10 FGF10 FGF10 17499 -0.29 0.026 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: REACTOME NEGATIVE REGULATION OF FGFR SIGNALING.

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME NEGATIVE REGULATION OF FGFR SIGNALING, 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 ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS

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 NEURL NEURL NEURL 81 0.52 0.11 YES
2 MAMLD1 MAMLD1 MAMLD1 454 0.31 0.16 YES
3 HEY2 HEY2 HEY2 658 0.26 0.21 YES
4 DTX1 DTX1 DTX1 875 0.22 0.25 YES
5 DTX4 DTX4 DTX4 922 0.22 0.29 YES
6 HEYL HEYL HEYL 1504 0.15 0.29 YES
7 DLL1 DLL1 DLL1 1880 0.13 0.3 YES
8 DLL4 DLL4 DLL4 2345 0.1 0.3 YES
9 HES5 HES5 HES5 2379 0.1 0.32 YES
10 MAML3 MAML3 MAML3 2418 0.099 0.34 YES
11 TLE4 TLE4 TLE4 2479 0.096 0.36 YES
12 TLE2 TLE2 TLE2 3111 0.076 0.34 NO
13 JAG2 JAG2 JAG2 3866 0.058 0.31 NO
14 HDAC8 HDAC8 HDAC8 3939 0.056 0.32 NO
15 MYC MYC MYC 4172 0.052 0.32 NO
16 HDAC7 HDAC7 HDAC7 4267 0.05 0.32 NO
17 MAML2 MAML2 MAML2 4295 0.05 0.33 NO
18 MIB2 MIB2 MIB2 4723 0.043 0.32 NO
19 SKP1 SKP1 SKP1 4913 0.04 0.32 NO
20 HDAC1 HDAC1 HDAC1 5060 0.038 0.32 NO
21 HDAC5 HDAC5 HDAC5 5589 0.032 0.29 NO
22 MAML1 MAML1 MAML1 5696 0.031 0.29 NO
23 KAT2A KAT2A KAT2A 6199 0.025 0.27 NO
24 APH1B APH1B APH1B 6224 0.025 0.28 NO
25 HDAC6 HDAC6 HDAC6 6530 0.022 0.26 NO
26 PSEN2 PSEN2 PSEN2 6729 0.02 0.26 NO
27 CREBBP CREBBP CREBBP 6805 0.019 0.26 NO
28 HDAC11 HDAC11 HDAC11 7115 0.016 0.24 NO
29 TBL1XR1 TBL1XR1 TBL1XR1 7209 0.015 0.24 NO
30 PSENEN PSENEN PSENEN 7281 0.014 0.24 NO
31 MIB1 MIB1 MIB1 7569 0.012 0.23 NO
32 RBX1 RBX1 RBX1 7627 0.011 0.23 NO
33 TLE3 TLE3 TLE3 7658 0.011 0.23 NO
34 RBPJ RBPJ RBPJ 8300 0.0052 0.19 NO
35 CUL1 CUL1 CUL1 8329 0.0048 0.19 NO
36 HIF1A HIF1A HIF1A 8369 0.0046 0.19 NO
37 NCSTN NCSTN NCSTN 8465 0.0037 0.19 NO
38 RPS27A RPS27A RPS27A 8574 0.0027 0.18 NO
39 EP300 EP300 EP300 8791 0.0006 0.17 NO
40 PSEN1 PSEN1 PSEN1 9149 -0.0026 0.15 NO
41 JAG1 JAG1 JAG1 9422 -0.0051 0.14 NO
42 HEY1 HEY1 HEY1 9575 -0.0066 0.13 NO
43 UBA52 UBA52 UBA52 9631 -0.0071 0.13 NO
44 APH1A APH1A APH1A 9632 -0.0071 0.13 NO
45 HDAC2 HDAC2 HDAC2 9744 -0.008 0.12 NO
46 NCOR1 NCOR1 NCOR1 9881 -0.0092 0.12 NO
47 ARRB2 ARRB2 ARRB2 9925 -0.0097 0.12 NO
48 NCOR2 NCOR2 NCOR2 10157 -0.012 0.11 NO
49 HDAC10 HDAC10 HDAC10 10235 -0.013 0.11 NO
50 SNW1 SNW1 SNW1 10417 -0.014 0.099 NO
51 DTX2 DTX2 DTX2 10611 -0.016 0.092 NO
52 HDAC3 HDAC3 HDAC3 10686 -0.017 0.092 NO
53 ADAM10 ADAM10 ADAM10 12037 -0.032 0.024 NO
54 KAT2B KAT2B KAT2B 12573 -0.04 0.0026 NO
55 NUMB NUMB NUMB 12607 -0.04 0.0098 NO
56 ADAM17 ADAM17 ADAM17 12679 -0.041 0.015 NO
57 FBXW7 FBXW7 FBXW7 12741 -0.042 0.021 NO
58 ARRB1 ARRB1 ARRB1 13243 -0.05 0.004 NO
59 TBL1X TBL1X TBL1X 13935 -0.063 -0.02 NO
60 CCNC CCNC CCNC 14594 -0.079 -0.04 NO
61 HDAC4 HDAC4 HDAC4 14801 -0.086 -0.032 NO
62 HDAC9 HDAC9 HDAC9 15003 -0.092 -0.023 NO
63 HES1 HES1 HES1 15977 -0.13 -0.048 NO
64 DNER DNER DNER 16297 -0.15 -0.032 NO
65 CDK8 CDK8 CDK8 16421 -0.16 -0.0045 NO
66 CNTN1 CNTN1 CNTN1 16758 -0.18 0.016 NO
67 TLE1 TLE1 TLE1 17232 -0.23 0.041 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: REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS, 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 = THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = THCA-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)