GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in HNSC-TP
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1MK6C8X
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 HNSC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1MK6C8X
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 "HNSC-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: 716
Number of samples: 520
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 ] 136
pheno.type: 2 - 4 :[ clus2 ] 114
pheno.type: 3 - 4 :[ clus3 ] 172
pheno.type: 4 - 4 :[ clus4 ] 98

For the expression subtypes of 18378 genes in 521 samples, GSEA found enriched gene sets in each cluster using 520 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are PID INTEGRIN3 PATHWAY, PID ILK PATHWAY, PID SYNDECAN 2 PATHWAY, REACTOME ER PHAGOSOME PATHWAY, REACTOME EXTRACELLULAR MATRIX ORGANIZATION, REACTOME COLLAGEN FORMATION, REACTOME CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM, REACTOME MRNA CAPPING, REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS, REACTOME PROTEIN FOLDING

    • And common core enriched genes are ARFGAP1, C19orf10, CUL7, DDX11, DNAJB11, EXTL3, FKBP14, HYOU1, KDELR3, PDIA5

  • clus2

    • Top enriched gene sets are KEGG PROTEASOME, KEGG CYTOSOLIC DNA SENSING PATHWAY, BIOCARTA PROTEASOME PATHWAY, PID MTOR 4PATHWAY, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME SIGNALING BY WNT, REACTOME TRIF MEDIATED TLR3 SIGNALING, REACTOME ER PHAGOSOME PATHWAY, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, REACTOME REGULATION OF ORNITHINE DECARBOXYLASE ODC

    • And common core enriched genes are RPS27A, EIF4A1, EIF4E, EIF4EBP1, EIF1AX, EIF2S1, EIF2S2, EIF2S3, EIF3A, EIF3B

  • clus3

    • Top enriched gene sets are KEGG FATTY ACID METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG STARCH AND SUCROSE METABOLISM, KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG BUTANOATE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450, PID FANCONI PATHWAY

    • And common core enriched genes are UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT2A1, UGT2B15

  • clus4

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG PURINE METABOLISM, KEGG ARGININE AND PROLINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG GLYCEROLIPID METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG ABC TRANSPORTERS, KEGG RNA DEGRADATION

    • And common core enriched genes are ASB11, ASB12, ASB15, ASB16, ASB4, ASB5, PARK2, TRIM63, ZBTB16, ASB2

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
PID INTEGRIN3 PATHWAY 43 genes.ES.table 0.64 1.6 0.042 0.71 0.92 0.7 0.17 0.58 0.36 0.21
PID ILK PATHWAY 45 genes.ES.table 0.51 1.9 0.016 0.53 0.31 0.49 0.3 0.34 0 0.11
PID SYNDECAN 2 PATHWAY 33 genes.ES.table 0.55 1.7 0.025 0.71 0.77 0.36 0.14 0.31 0.25 0.18
REACTOME ER PHAGOSOME PATHWAY 58 genes.ES.table 0.52 1.6 0.11 0.67 0.95 0.76 0.4 0.46 0.38 0.2
REACTOME EXTRACELLULAR MATRIX ORGANIZATION 83 genes.ES.table 0.64 1.6 0.041 0.76 0.94 0.68 0.12 0.59 0.42 0.23
REACTOME COLLAGEN FORMATION 58 genes.ES.table 0.67 1.6 0.036 0.72 0.94 0.71 0.12 0.62 0.4 0.22
REACTOME CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 47 genes.ES.table 0.58 1.6 0.012 0.8 0.9 0.62 0.2 0.5 0.37 0.22
REACTOME MRNA CAPPING 29 genes.ES.table 0.52 1.7 0.029 0.82 0.76 0.52 0.28 0.37 0.28 0.2
REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS 26 genes.ES.table 0.4 1.6 0.042 0.9 0.88 0.58 0.36 0.37 0.41 0.25
REACTOME PROTEIN FOLDING 49 genes.ES.table 0.44 1.9 0.012 0.39 0.4 0.55 0.34 0.36 0 0.091
genes ES table in pathway: PID INTEGRIN3 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 KDELR3 KDELR3 KDELR3 257 0.25 0.056 YES
2 FKBP14 FKBP14 FKBP14 688 0.19 0.085 YES
3 IGFBP1 IGFBP1 IGFBP1 750 0.18 0.13 YES
4 PDIA5 PDIA5 PDIA5 1447 0.13 0.13 YES
5 IL8 IL8 IL8 1464 0.13 0.17 YES
6 C19orf10 C19orf10 C19orf10 1880 0.11 0.17 YES
7 ARFGAP1 ARFGAP1 ARFGAP1 2220 0.096 0.18 YES
8 EXOSC6 EXOSC6 EXOSC6 2391 0.09 0.2 YES
9 YIF1A YIF1A YIF1A 2409 0.09 0.22 YES
10 EXOSC4 EXOSC4 EXOSC4 2593 0.085 0.24 YES
11 SHC1 SHC1 SHC1 2758 0.08 0.25 YES
12 DDIT3 DDIT3 DDIT3 3264 0.069 0.24 YES
13 HSP90B1 HSP90B1 HSP90B1 3298 0.068 0.26 YES
14 EXOSC9 EXOSC9 EXOSC9 3444 0.066 0.27 YES
15 EXOSC1 EXOSC1 EXOSC1 3788 0.059 0.27 YES
16 HSPA5 HSPA5 HSPA5 3910 0.058 0.28 YES
17 PARN PARN PARN 3993 0.056 0.29 YES
18 EXOSC2 EXOSC2 EXOSC2 3997 0.056 0.3 YES
19 EXTL3 EXTL3 EXTL3 4067 0.055 0.32 YES
20 CALR CALR CALR 4173 0.054 0.33 YES
21 HYOU1 HYOU1 HYOU1 4188 0.054 0.34 YES
22 ASNS ASNS ASNS 4206 0.053 0.36 YES
23 EXOSC8 EXOSC8 EXOSC8 4316 0.051 0.36 YES
24 CUL7 CUL7 CUL7 4595 0.048 0.36 YES
25 PDIA6 PDIA6 PDIA6 4697 0.046 0.37 YES
26 SULT1A3 SULT1A3 SULT1A3 4740 0.046 0.38 YES
27 ZBTB17 ZBTB17 ZBTB17 4893 0.044 0.38 YES
28 TPP1 TPP1 TPP1 5140 0.041 0.38 YES
29 DNAJB11 DNAJB11 DNAJB11 5275 0.039 0.38 YES
30 DDX11 DDX11 DDX11 5510 0.036 0.38 YES
31 WFS1 WFS1 WFS1 5715 0.034 0.38 YES
32 MBTPS2 MBTPS2 MBTPS2 5949 0.031 0.38 YES
33 MBTPS1 MBTPS1 MBTPS1 5989 0.031 0.38 YES
34 SRPRB SRPRB SRPRB 6003 0.031 0.39 YES
35 EIF2S1 EIF2S1 EIF2S1 6340 0.028 0.38 YES
36 LMNA LMNA LMNA 6354 0.027 0.39 YES
37 TSPYL2 TSPYL2 TSPYL2 6542 0.026 0.38 YES
38 EXOSC7 EXOSC7 EXOSC7 6546 0.026 0.39 YES
39 PPP2R5B PPP2R5B PPP2R5B 6754 0.024 0.39 NO
40 SYVN1 SYVN1 SYVN1 7302 0.018 0.36 NO
41 DNAJC3 DNAJC3 DNAJC3 7405 0.017 0.36 NO
42 KLHDC3 KLHDC3 KLHDC3 7566 0.016 0.36 NO
43 DCTN1 DCTN1 DCTN1 7590 0.015 0.36 NO
44 TLN1 TLN1 TLN1 7756 0.014 0.36 NO
45 ATP6V0D1 ATP6V0D1 ATP6V0D1 7786 0.013 0.36 NO
46 ADD1 ADD1 ADD1 7884 0.012 0.36 NO
47 GSK3A GSK3A GSK3A 8012 0.011 0.35 NO
48 GOSR2 GOSR2 GOSR2 8441 0.0073 0.33 NO
49 EXOSC5 EXOSC5 EXOSC5 8477 0.0069 0.33 NO
50 PREB PREB PREB 8515 0.0065 0.33 NO
51 SRPR SRPR SRPR 8523 0.0065 0.33 NO
52 SEC31A SEC31A SEC31A 8556 0.0061 0.33 NO
53 NFYA NFYA NFYA 8745 0.0043 0.32 NO
54 ATF6 ATF6 ATF6 8776 0.004 0.32 NO
55 HDGF HDGF HDGF 8780 0.004 0.32 NO
56 ATF4 ATF4 ATF4 9159 0.00046 0.3 NO
57 SSR1 SSR1 SSR1 9191 0.00023 0.3 NO
58 EDEM1 EDEM1 EDEM1 9257 -0.00046 0.3 NO
59 KHSRP KHSRP KHSRP 9606 -0.0037 0.28 NO
60 NFYB NFYB NFYB 10037 -0.0084 0.26 NO
61 SERP1 SERP1 SERP1 11049 -0.019 0.21 NO
62 EXOSC3 EXOSC3 EXOSC3 11059 -0.019 0.21 NO
63 DIS3 DIS3 DIS3 11235 -0.022 0.21 NO
64 TATDN2 TATDN2 TATDN2 11266 -0.022 0.22 NO
65 ACADVL ACADVL ACADVL 11430 -0.024 0.21 NO
66 CCL2 CCL2 CCL2 11736 -0.028 0.2 NO
67 CTDSP2 CTDSP2 CTDSP2 11911 -0.03 0.2 NO
68 DCP2 DCP2 DCP2 11975 -0.031 0.21 NO
69 ATF3 ATF3 ATF3 12022 -0.032 0.21 NO
70 CXXC1 CXXC1 CXXC1 12054 -0.032 0.22 NO
71 HERPUD1 HERPUD1 HERPUD1 12647 -0.04 0.2 NO
72 DNAJB9 DNAJB9 DNAJB9 12705 -0.041 0.21 NO
73 WIPI1 WIPI1 WIPI1 13251 -0.05 0.19 NO
74 XBP1 XBP1 XBP1 14753 -0.085 0.14 NO
75 EIF2AK3 EIF2AK3 EIF2AK3 15034 -0.094 0.15 NO
76 ERN1 ERN1 ERN1 15872 -0.13 0.14 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: PID INTEGRIN3 PATHWAY.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: PID INTEGRIN3 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 ILK PATHWAY

Table S2.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MYL9 MYL9 MYL9 393 0.22 0.061 YES
2 PPP1R14A PPP1R14A PPP1R14A 458 0.21 0.14 YES
3 SNAI1 SNAI1 SNAI1 736 0.18 0.19 YES
4 PARVB PARVB PARVB 764 0.18 0.25 YES
5 CCND1 CCND1 CCND1 958 0.16 0.3 YES
6 ACTN1 ACTN1 ACTN1 1194 0.14 0.34 YES
7 PXN PXN PXN 1488 0.13 0.37 YES
8 PPP1R14C PPP1R14C PPP1R14C 2106 0.1 0.38 YES
9 PARVA PARVA PARVA 2138 0.099 0.41 YES
10 PPP1R14B PPP1R14B PPP1R14B 2143 0.099 0.45 YES
11 AURKA AURKA AURKA 2202 0.097 0.48 YES
12 ILK ILK ILK 2645 0.084 0.48 YES
13 ZYX ZYX ZYX 3269 0.069 0.48 YES
14 RUVBL2 RUVBL2 RUVBL2 3487 0.065 0.49 YES
15 TACC3 TACC3 TACC3 3844 0.059 0.49 YES
16 JUN JUN JUN 4072 0.055 0.5 YES
17 AKT1 AKT1 AKT1 4438 0.05 0.5 YES
18 HSP90AA1 HSP90AA1 HSP90AA1 4715 0.046 0.5 YES
19 ILKAP ILKAP ILKAP 4958 0.043 0.5 YES
20 CDC37 CDC37 CDC37 5443 0.037 0.49 YES
21 CTNNB1 CTNNB1 CTNNB1 5488 0.036 0.5 YES
22 RUVBL1 RUVBL1 RUVBL1 5563 0.036 0.51 YES
23 LIMS2 LIMS2 LIMS2 6670 0.024 0.46 NO
24 CKAP5 CKAP5 CKAP5 6714 0.024 0.46 NO
25 CDC42 CDC42 CDC42 7214 0.019 0.44 NO
26 RHOG RHOG RHOG 7753 0.014 0.42 NO
27 LIMS1 LIMS1 LIMS1 7948 0.012 0.41 NO
28 ZEB1 ZEB1 ZEB1 8015 0.011 0.41 NO
29 PARP1 PARP1 PARP1 8113 0.01 0.41 NO
30 RICTOR RICTOR RICTOR 8225 0.0093 0.41 NO
31 XPO1 XPO1 XPO1 9027 0.0016 0.37 NO
32 ARHGEF7 ARHGEF7 ARHGEF7 9084 0.0011 0.36 NO
33 NACA NACA NACA 9570 -0.0034 0.34 NO
34 IQGAP1 IQGAP1 IQGAP1 10022 -0.0081 0.32 NO
35 GIT2 GIT2 GIT2 10067 -0.0087 0.32 NO
36 RAC1 RAC1 RAC1 10124 -0.0092 0.32 NO
37 PPP1R12A PPP1R12A PPP1R12A 10269 -0.011 0.31 NO
38 ELMO2 ELMO2 ELMO2 10394 -0.012 0.31 NO
39 DIAPH1 DIAPH1 DIAPH1 11304 -0.022 0.27 NO
40 PARVG PARVG PARVG 11670 -0.027 0.26 NO
41 CREB1 CREB1 CREB1 12210 -0.034 0.24 NO
42 GSK3B GSK3B GSK3B 12710 -0.041 0.23 NO
43 NCK2 NCK2 NCK2 12812 -0.043 0.24 NO
44 TNS1 TNS1 TNS1 14184 -0.07 0.19 NO
45 ARHGEF6 ARHGEF6 ARHGEF6 15166 -0.099 0.17 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: PID ILK PATHWAY.

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ILK 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 SYNDECAN 2 PATHWAY

Table S3.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GFPT2 GFPT2 GFPT2 260 0.25 0.17 YES
2 DPM2 DPM2 DPM2 3187 0.07 0.067 YES
3 GMPPA GMPPA GMPPA 3498 0.065 0.099 YES
4 PMM2 PMM2 PMM2 3552 0.064 0.14 YES
5 DPM3 DPM3 DPM3 3621 0.062 0.19 YES
6 PMM1 PMM1 PMM1 3664 0.062 0.23 YES
7 ALG3 ALG3 ALG3 3689 0.061 0.28 YES
8 ALG11 ALG11 ALG11 3894 0.058 0.31 YES
9 ALG14 ALG14 ALG14 4059 0.056 0.34 YES
10 PGM3 PGM3 PGM3 4383 0.05 0.36 YES
11 RFT1 RFT1 RFT1 4491 0.049 0.39 YES
12 ALG5 ALG5 ALG5 4722 0.046 0.42 YES
13 ALG8 ALG8 ALG8 4753 0.046 0.45 YES
14 ALG1 ALG1 ALG1 4844 0.044 0.48 YES
15 DPAGT1 DPAGT1 DPAGT1 5188 0.04 0.49 YES
16 DPM1 DPM1 DPM1 5403 0.038 0.51 YES
17 ALG2 ALG2 ALG2 6056 0.03 0.49 YES
18 DOLK DOLK DOLK 6409 0.027 0.5 YES
19 GNPNAT1 GNPNAT1 GNPNAT1 6554 0.026 0.51 YES
20 ALG9 ALG9 ALG9 6923 0.022 0.5 YES
21 MPI MPI MPI 6926 0.022 0.52 YES
22 ALG12 ALG12 ALG12 7811 0.013 0.48 NO
23 DOLPP1 DOLPP1 DOLPP1 8541 0.0063 0.45 NO
24 ALG10B ALG10B ALG10B 9918 -0.0072 0.38 NO
25 ALG10 ALG10 ALG10 10907 -0.018 0.34 NO
26 ALG13 ALG13 ALG13 11108 -0.02 0.34 NO
27 GMPPB GMPPB GMPPB 11913 -0.03 0.32 NO
28 ALG6 ALG6 ALG6 12876 -0.044 0.3 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: PID SYNDECAN 2 PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: PID SYNDECAN 2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME ER PHAGOSOME 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 TUBB3 TUBB3 TUBB3 851 0.17 0.029 YES
2 KIFC3 KIFC3 KIFC3 1346 0.13 0.061 YES
3 SPHK1 SPHK1 SPHK1 1900 0.11 0.079 YES
4 PFDN4 PFDN4 PFDN4 1953 0.11 0.12 YES
5 TUBB6 TUBB6 TUBB6 2088 0.1 0.16 YES
6 TUBA1A TUBA1A TUBA1A 2192 0.097 0.2 YES
7 FKBP9 FKBP9 FKBP9 2236 0.095 0.24 YES
8 PFDN2 PFDN2 PFDN2 2583 0.085 0.26 YES
9 PFDN6 PFDN6 PFDN6 2754 0.08 0.28 YES
10 TBCE TBCE TBCE 3576 0.063 0.26 YES
11 CCT6A CCT6A CCT6A 3996 0.056 0.27 YES
12 CCT3 CCT3 CCT3 4040 0.056 0.29 YES
13 CCT5 CCT5 CCT5 4053 0.056 0.31 YES
14 TUBA1B TUBA1B TUBA1B 4226 0.053 0.33 YES
15 TBCA TBCA TBCA 4244 0.052 0.35 YES
16 ACTB ACTB ACTB 4488 0.049 0.36 YES
17 TBCB TBCB TBCB 4525 0.049 0.38 YES
18 CCT2 CCT2 CCT2 4735 0.046 0.38 YES
19 CCT4 CCT4 CCT4 4906 0.044 0.39 YES
20 FBXO4 FBXO4 FBXO4 5172 0.04 0.4 YES
21 USP11 USP11 USP11 5415 0.037 0.4 YES
22 PFDN5 PFDN5 PFDN5 5511 0.036 0.41 YES
23 CCT7 CCT7 CCT7 5518 0.036 0.43 YES
24 PFDN1 PFDN1 PFDN1 5620 0.035 0.44 YES
25 NOP56 NOP56 NOP56 5811 0.033 0.44 YES
26 LONP2 LONP2 LONP2 6190 0.029 0.43 YES
27 TCP1 TCP1 TCP1 6251 0.028 0.44 YES
28 CCT8 CCT8 CCT8 6573 0.025 0.44 NO
29 TUBA1C TUBA1C TUBA1C 6890 0.022 0.43 NO
30 VBP1 VBP1 VBP1 7970 0.012 0.38 NO
31 TUBA3C TUBA3C TUBA3C 7989 0.011 0.38 NO
32 TUBA3D TUBA3D TUBA3D 9168 0.00041 0.32 NO
33 FBXW7 FBXW7 FBXW7 9219 -0.00013 0.31 NO
34 XRN2 XRN2 XRN2 9283 -0.0007 0.31 NO
35 FBXW2 FBXW2 FBXW2 9644 -0.0041 0.29 NO
36 FBXW4 FBXW4 FBXW4 9891 -0.0068 0.28 NO
37 FBXO6 FBXO6 FBXO6 9896 -0.0068 0.28 NO
38 TUBB2A TUBB2A TUBB2A 10151 -0.0095 0.27 NO
39 TBCD TBCD TBCD 10388 -0.012 0.27 NO
40 TUBA4A TUBA4A TUBA4A 10615 -0.014 0.26 NO
41 FBXW5 FBXW5 FBXW5 11423 -0.024 0.23 NO
42 TBCC TBCC TBCC 11451 -0.024 0.24 NO
43 AP3M1 AP3M1 AP3M1 11696 -0.027 0.23 NO
44 TUBB1 TUBB1 TUBB1 11782 -0.028 0.24 NO
45 FBXL3 FBXL3 FBXL3 13006 -0.046 0.2 NO
46 KIF13A KIF13A KIF13A 13007 -0.046 0.22 NO
47 FBXL5 FBXL5 FBXL5 13036 -0.046 0.23 NO
48 ARFGEF2 ARFGEF2 ARFGEF2 13375 -0.052 0.24 NO
49 TUBB2B TUBB2B TUBB2B 14508 -0.077 0.21 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: REACTOME ER PHAGOSOME PATHWAY.

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

genes ES table in pathway: REACTOME EXTRACELLULAR MATRIX ORGANIZATION

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 KDELR3 KDELR3 KDELR3 257 0.25 0.11 YES
2 FKBP14 FKBP14 FKBP14 688 0.19 0.19 YES
3 PDIA5 PDIA5 PDIA5 1447 0.13 0.21 YES
4 C19orf10 C19orf10 C19orf10 1880 0.11 0.24 YES
5 ARFGAP1 ARFGAP1 ARFGAP1 2220 0.096 0.28 YES
6 YIF1A YIF1A YIF1A 2409 0.09 0.31 YES
7 SHC1 SHC1 SHC1 2758 0.08 0.33 YES
8 EXTL3 EXTL3 EXTL3 4067 0.055 0.29 YES
9 HYOU1 HYOU1 HYOU1 4188 0.054 0.31 YES
10 CUL7 CUL7 CUL7 4595 0.048 0.31 YES
11 PDIA6 PDIA6 PDIA6 4697 0.046 0.33 YES
12 SULT1A3 SULT1A3 SULT1A3 4740 0.046 0.35 YES
13 ZBTB17 ZBTB17 ZBTB17 4893 0.044 0.37 YES
14 TPP1 TPP1 TPP1 5140 0.041 0.38 YES
15 DNAJB11 DNAJB11 DNAJB11 5275 0.039 0.39 YES
16 DDX11 DDX11 DDX11 5510 0.036 0.4 YES
17 WFS1 WFS1 WFS1 5715 0.034 0.4 YES
18 SRPRB SRPRB SRPRB 6003 0.031 0.4 YES
19 LMNA LMNA LMNA 6354 0.027 0.4 NO
20 TSPYL2 TSPYL2 TSPYL2 6542 0.026 0.4 NO
21 PPP2R5B PPP2R5B PPP2R5B 6754 0.024 0.4 NO
22 SYVN1 SYVN1 SYVN1 7302 0.018 0.38 NO
23 DNAJC3 DNAJC3 DNAJC3 7405 0.017 0.38 NO
24 KLHDC3 KLHDC3 KLHDC3 7566 0.016 0.38 NO
25 DCTN1 DCTN1 DCTN1 7590 0.015 0.39 NO
26 TLN1 TLN1 TLN1 7756 0.014 0.39 NO
27 ATP6V0D1 ATP6V0D1 ATP6V0D1 7786 0.013 0.39 NO
28 ADD1 ADD1 ADD1 7884 0.012 0.39 NO
29 GSK3A GSK3A GSK3A 8012 0.011 0.39 NO
30 GOSR2 GOSR2 GOSR2 8441 0.0073 0.37 NO
31 PREB PREB PREB 8515 0.0065 0.37 NO
32 SRPR SRPR SRPR 8523 0.0065 0.38 NO
33 SEC31A SEC31A SEC31A 8556 0.0061 0.38 NO
34 HDGF HDGF HDGF 8780 0.004 0.37 NO
35 SSR1 SSR1 SSR1 9191 0.00023 0.34 NO
36 EDEM1 EDEM1 EDEM1 9257 -0.00046 0.34 NO
37 SERP1 SERP1 SERP1 11049 -0.019 0.25 NO
38 TATDN2 TATDN2 TATDN2 11266 -0.022 0.25 NO
39 ACADVL ACADVL ACADVL 11430 -0.024 0.26 NO
40 CTDSP2 CTDSP2 CTDSP2 11911 -0.03 0.24 NO
41 CXXC1 CXXC1 CXXC1 12054 -0.032 0.25 NO
42 DNAJB9 DNAJB9 DNAJB9 12705 -0.041 0.24 NO
43 WIPI1 WIPI1 WIPI1 13251 -0.05 0.24 NO
44 XBP1 XBP1 XBP1 14753 -0.085 0.2 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: REACTOME EXTRACELLULAR MATRIX ORGANIZATION.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME EXTRACELLULAR MATRIX ORGANIZATION, 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 COLLAGEN FORMATION

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 GTF2H2B GTF2H2B GTF2H2B 2273 0.094 -0.04 YES
2 GTF2H4 GTF2H4 GTF2H4 2766 0.08 0.0038 YES
3 ERCC2 ERCC2 ERCC2 3128 0.072 0.048 YES
4 MNAT1 MNAT1 MNAT1 3200 0.07 0.11 YES
5 POLR2L POLR2L POLR2L 3333 0.068 0.16 YES
6 POLR2H POLR2H POLR2H 3471 0.065 0.21 YES
7 POLR2F POLR2F POLR2F 3517 0.064 0.26 YES
8 GTF2F2 GTF2F2 GTF2F2 3672 0.062 0.31 YES
9 POLR2C POLR2C POLR2C 4114 0.055 0.34 YES
10 POLR2G POLR2G POLR2G 4602 0.048 0.35 YES
11 GTF2H2 GTF2H2 GTF2H2 4807 0.045 0.38 YES
12 NCBP2 NCBP2 NCBP2 4809 0.045 0.42 YES
13 POLR2J POLR2J POLR2J 4847 0.044 0.46 YES
14 POLR2K POLR2K POLR2K 4907 0.044 0.49 YES
15 POLR2D POLR2D POLR2D 5100 0.042 0.52 YES
16 CCNH CCNH CCNH 6726 0.024 0.45 NO
17 CDK7 CDK7 CDK7 7198 0.02 0.44 NO
18 GTF2F1 GTF2F1 GTF2F1 7577 0.016 0.44 NO
19 ERCC3 ERCC3 ERCC3 7941 0.012 0.43 NO
20 POLR2I POLR2I POLR2I 8175 0.0097 0.42 NO
21 SUPT5H SUPT5H SUPT5H 8256 0.009 0.43 NO
22 RNGTT RNGTT RNGTT 8294 0.0086 0.43 NO
23 POLR2E POLR2E POLR2E 8347 0.0082 0.44 NO
24 GTF2H1 GTF2H1 GTF2H1 9835 -0.0062 0.36 NO
25 NCBP1 NCBP1 NCBP1 10522 -0.013 0.34 NO
26 GTF2H3 GTF2H3 GTF2H3 11014 -0.019 0.33 NO
27 POLR2B POLR2B POLR2B 11093 -0.02 0.34 NO
28 POLR2A POLR2A POLR2A 11574 -0.025 0.34 NO
29 RNMT RNMT RNMT 12558 -0.039 0.32 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: REACTOME COLLAGEN FORMATION.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME COLLAGEN FORMATION, 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 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM

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 CSF2 CSF2 CSF2 175 0.27 0.082 YES
2 ITGA5 ITGA5 ITGA5 213 0.26 0.17 YES
3 LAMA1 LAMA1 LAMA1 255 0.25 0.25 YES
4 FN1 FN1 FN1 335 0.23 0.32 YES
5 SDC2 SDC2 SDC2 431 0.22 0.39 YES
6 EPHB2 EPHB2 EPHB2 717 0.18 0.43 YES
7 MMP2 MMP2 MMP2 1309 0.14 0.45 YES
8 IL8 IL8 IL8 1464 0.13 0.48 YES
9 LAMA3 LAMA3 LAMA3 1511 0.12 0.52 YES
10 CAV2 CAV2 CAV2 1888 0.11 0.54 YES
11 ITGB1 ITGB1 ITGB1 2338 0.092 0.54 YES
12 TGFB1 TGFB1 TGFB1 2665 0.083 0.55 YES
13 TRAPPC4 TRAPPC4 TRAPPC4 4156 0.054 0.49 NO
14 SDCBP SDCBP SDCBP 4580 0.048 0.48 NO
15 BAX BAX BAX 4593 0.048 0.5 NO
16 HRAS HRAS HRAS 4985 0.043 0.49 NO
17 GNB2L1 GNB2L1 GNB2L1 6047 0.03 0.44 NO
18 RHOA RHOA RHOA 9068 0.0012 0.28 NO
19 CASK CASK CASK 9174 0.00036 0.27 NO
20 SRC SRC SRC 9516 -0.0029 0.26 NO
21 CASP3 CASP3 CASP3 10071 -0.0087 0.23 NO
22 EZR EZR EZR 10152 -0.0095 0.23 NO
23 PRKACA PRKACA PRKACA 10243 -0.01 0.22 NO
24 ITGA2 ITGA2 ITGA2 10360 -0.012 0.22 NO
25 RASA1 RASA1 RASA1 10729 -0.016 0.21 NO
26 MAPK8 MAPK8 MAPK8 10782 -0.016 0.21 NO
27 NF1 NF1 NF1 10957 -0.018 0.21 NO
28 KNG1 KNG1 KNG1 11137 -0.02 0.2 NO
29 MAPK1 MAPK1 MAPK1 11966 -0.031 0.17 NO
30 PRKCD PRKCD PRKCD 12104 -0.033 0.17 NO
31 MAPK3 MAPK3 MAPK3 12674 -0.04 0.16 NO
32 EPB41 EPB41 EPB41 15932 -0.13 0.02 NO
33 TNFRSF13B TNFRSF13B TNFRSF13B 18071 -0.34 0.016 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: REACTOME CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CHONDROITIN SULFATE DERMATAN SULFATE 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: REACTOME MRNA CAPPING

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 SNAPC1 SNAPC1 SNAPC1 1563 0.12 0.037 YES
2 SNAPC2 SNAPC2 SNAPC2 2480 0.088 0.074 YES
3 POLR2L POLR2L POLR2L 3333 0.068 0.095 YES
4 POLR2H POLR2H POLR2H 3471 0.065 0.15 YES
5 POLR2F POLR2F POLR2F 3517 0.064 0.21 YES
6 LZTS1 LZTS1 LZTS1 3779 0.06 0.26 YES
7 SNAPC4 SNAPC4 SNAPC4 3877 0.058 0.31 YES
8 POLR2K POLR2K POLR2K 4907 0.044 0.3 YES
9 POLR3D POLR3D POLR3D 4915 0.044 0.34 YES
10 POLR3GL POLR3GL POLR3GL 5129 0.041 0.37 YES
11 POLR3K POLR3K POLR3K 5633 0.035 0.38 YES
12 POLR1C POLR1C POLR1C 5667 0.034 0.41 YES
13 POLR3H POLR3H POLR3H 5960 0.031 0.42 YES
14 POLR3C POLR3C POLR3C 6252 0.028 0.44 YES
15 TBP TBP TBP 7019 0.021 0.42 NO
16 POLR1D POLR1D POLR1D 7351 0.018 0.42 NO
17 BRF2 BRF2 BRF2 7475 0.016 0.43 NO
18 POLR3A POLR3A POLR3A 8295 0.0086 0.39 NO
19 POLR2E POLR2E POLR2E 8347 0.0082 0.4 NO
20 POLR3F POLR3F POLR3F 8355 0.0082 0.4 NO
21 SNAPC5 SNAPC5 SNAPC5 9582 -0.0035 0.34 NO
22 ZNF143 ZNF143 ZNF143 10055 -0.0086 0.32 NO
23 POLR3E POLR3E POLR3E 10253 -0.01 0.32 NO
24 SNAPC3 SNAPC3 SNAPC3 10657 -0.015 0.32 NO
25 POLR3B POLR3B POLR3B 12967 -0.045 0.23 NO
26 POU2F1 POU2F1 POU2F1 13765 -0.06 0.25 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: REACTOME MRNA CAPPING.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MRNA CAPPING, 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 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS

Table S9.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 KIFC3 KIFC3 KIFC3 1346 0.13 0.05 YES
2 SPHK1 SPHK1 SPHK1 1900 0.11 0.12 YES
3 FKBP9 FKBP9 FKBP9 2236 0.095 0.19 YES
4 CCT6A CCT6A CCT6A 3996 0.056 0.15 YES
5 CCT3 CCT3 CCT3 4040 0.056 0.2 YES
6 CCT5 CCT5 CCT5 4053 0.056 0.25 YES
7 CCT2 CCT2 CCT2 4735 0.046 0.25 YES
8 CCT4 CCT4 CCT4 4906 0.044 0.28 YES
9 FBXO4 FBXO4 FBXO4 5172 0.04 0.3 YES
10 USP11 USP11 USP11 5415 0.037 0.33 YES
11 CCT7 CCT7 CCT7 5518 0.036 0.35 YES
12 NOP56 NOP56 NOP56 5811 0.033 0.37 YES
13 LONP2 LONP2 LONP2 6190 0.029 0.38 YES
14 TCP1 TCP1 TCP1 6251 0.028 0.4 YES
15 CCT8 CCT8 CCT8 6573 0.025 0.4 YES
16 FBXW7 FBXW7 FBXW7 9219 -0.00013 0.26 NO
17 XRN2 XRN2 XRN2 9283 -0.0007 0.26 NO
18 FBXW2 FBXW2 FBXW2 9644 -0.0041 0.24 NO
19 FBXW4 FBXW4 FBXW4 9891 -0.0068 0.23 NO
20 FBXO6 FBXO6 FBXO6 9896 -0.0068 0.24 NO
21 FBXW5 FBXW5 FBXW5 11423 -0.024 0.18 NO
22 AP3M1 AP3M1 AP3M1 11696 -0.027 0.19 NO
23 FBXL3 FBXL3 FBXL3 13006 -0.046 0.16 NO
24 KIF13A KIF13A KIF13A 13007 -0.046 0.2 NO
25 FBXL5 FBXL5 FBXL5 13036 -0.046 0.24 NO
26 ARFGEF2 ARFGEF2 ARFGEF2 13375 -0.052 0.27 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 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING 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: REACTOME PROTEIN FOLDING

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 GTF2H2B GTF2H2B GTF2H2B 2273 0.094 -0.037 YES
2 GTF2H4 GTF2H4 GTF2H4 2766 0.08 0.01 YES
3 ERCC2 ERCC2 ERCC2 3128 0.072 0.057 YES
4 MNAT1 MNAT1 MNAT1 3200 0.07 0.12 YES
5 POLR2L POLR2L POLR2L 3333 0.068 0.17 YES
6 POLR2H POLR2H POLR2H 3471 0.065 0.23 YES
7 POLR2F POLR2F POLR2F 3517 0.064 0.28 YES
8 POLR2C POLR2C POLR2C 4114 0.055 0.3 YES
9 POLR2G POLR2G POLR2G 4602 0.048 0.32 YES
10 GTF2H2 GTF2H2 GTF2H2 4807 0.045 0.35 YES
11 POLR2J POLR2J POLR2J 4847 0.044 0.39 YES
12 POLR2K POLR2K POLR2K 4907 0.044 0.42 YES
13 POLR2D POLR2D POLR2D 5100 0.042 0.45 YES
14 ERCC1 ERCC1 ERCC1 5256 0.039 0.48 YES
15 XAB2 XAB2 XAB2 6465 0.026 0.44 NO
16 CCNH CCNH CCNH 6726 0.024 0.45 NO
17 CDK7 CDK7 CDK7 7198 0.02 0.44 NO
18 TCEA1 TCEA1 TCEA1 7412 0.017 0.44 NO
19 ERCC8 ERCC8 ERCC8 7425 0.017 0.46 NO
20 ERCC3 ERCC3 ERCC3 7941 0.012 0.44 NO
21 POLR2I POLR2I POLR2I 8175 0.0097 0.44 NO
22 POLR2E POLR2E POLR2E 8347 0.0082 0.44 NO
23 ERCC6 ERCC6 ERCC6 8499 0.0067 0.43 NO
24 ERCC5 ERCC5 ERCC5 9310 -0.00097 0.39 NO
25 GTF2H1 GTF2H1 GTF2H1 9835 -0.0062 0.37 NO
26 GTF2H3 GTF2H3 GTF2H3 11014 -0.019 0.32 NO
27 POLR2B POLR2B POLR2B 11093 -0.02 0.34 NO
28 POLR2A POLR2A POLR2A 11574 -0.025 0.33 NO
29 ERCC4 ERCC4 ERCC4 12687 -0.041 0.31 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 PROTEIN FOLDING.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PROTEIN FOLDING, 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 PROTEASOME 43 genes.ES.table 0.53 1.5 0.099 1 0.98 0.79 0.27 0.58 0.77 0.41
KEGG CYTOSOLIC DNA SENSING PATHWAY 44 genes.ES.table 0.57 1.6 0.078 1 0.97 0.34 0.14 0.3 0.8 0.43
BIOCARTA PROTEASOME PATHWAY 28 genes.ES.table 0.59 1.5 0.049 1 0.98 0.68 0.23 0.52 0.81 0.43
PID MTOR 4PATHWAY 67 genes.ES.table 0.32 1.7 0.049 1 0.85 0.42 0.2 0.33 1 0.73
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 49 genes.ES.table 0.63 1.7 0.047 1 0.86 0.92 0.25 0.69 1 0.56
REACTOME SIGNALING BY WNT 63 genes.ES.table 0.42 1.6 0.072 1 0.9 0.6 0.23 0.46 1 0.5
REACTOME TRIF MEDIATED TLR3 SIGNALING 72 genes.ES.table 0.38 1.6 0.069 1 0.97 0.26 0.14 0.23 0.88 0.45
REACTOME ER PHAGOSOME PATHWAY 58 genes.ES.table 0.5 1.5 0.13 1 0.99 0.64 0.23 0.49 0.79 0.4
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 57 genes.ES.table 0.57 1.6 0.08 1 0.91 0.88 0.25 0.66 0.86 0.44
REACTOME REGULATION OF ORNITHINE DECARBOXYLASE ODC 48 genes.ES.table 0.51 1.6 0.091 1 0.93 0.67 0.25 0.5 0.81 0.42
genes ES table in pathway: KEGG PROTEASOME

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 PLD2 PLD2 PLD2 486 0.27 0.036 YES
2 SFN SFN SFN 561 0.24 0.089 YES
3 BNIP3 BNIP3 BNIP3 908 0.17 0.11 YES
4 MAPK3 MAPK3 MAPK3 1080 0.15 0.13 YES
5 HRAS HRAS HRAS 1203 0.13 0.16 YES
6 CLIP1 CLIP1 CLIP1 1499 0.11 0.17 YES
7 YWHAZ YWHAZ YWHAZ 1606 0.099 0.18 YES
8 EIF4E EIF4E EIF4E 1674 0.095 0.2 YES
9 RRAGC RRAGC RRAGC 1794 0.088 0.22 YES
10 CCNE1 CCNE1 CCNE1 1838 0.085 0.24 YES
11 IRS1 IRS1 IRS1 2008 0.077 0.24 YES
12 RRAGA RRAGA RRAGA 2460 0.06 0.23 YES
13 AKT1S1 AKT1S1 AKT1S1 2675 0.054 0.24 YES
14 EIF4EBP1 EIF4EBP1 EIF4EBP1 2684 0.054 0.25 YES
15 YWHAQ YWHAQ YWHAQ 2707 0.053 0.26 YES
16 EIF4A1 EIF4A1 EIF4A1 2709 0.053 0.27 YES
17 PML PML PML 2722 0.053 0.28 YES
18 RAC1 RAC1 RAC1 2746 0.052 0.29 YES
19 CYCS CYCS CYCS 2988 0.046 0.29 YES
20 YWHAB YWHAB YWHAB 3078 0.043 0.3 YES
21 PDCD4 PDCD4 PDCD4 3082 0.043 0.31 YES
22 RPTOR RPTOR RPTOR 3143 0.042 0.31 YES
23 PLD1 PLD1 PLD1 3287 0.038 0.31 YES
24 NRAS NRAS NRAS 3442 0.035 0.31 YES
25 PXN PXN PXN 3594 0.032 0.31 YES
26 MAP2K2 MAP2K2 MAP2K2 3723 0.029 0.31 YES
27 RHOA RHOA RHOA 3748 0.028 0.32 YES
28 RPS6KB1 RPS6KB1 RPS6KB1 3753 0.028 0.32 YES
29 RPS6KA1 RPS6KA1 RPS6KA1 3925 0.025 0.32 NO
30 YWHAE YWHAE YWHAE 4538 0.014 0.29 NO
31 DDIT4 DDIT4 DDIT4 4821 0.0096 0.28 NO
32 MAPKAP1 MAPKAP1 MAPKAP1 4831 0.0094 0.28 NO
33 MTOR MTOR MTOR 4845 0.0091 0.28 NO
34 ULK1 ULK1 ULK1 4856 0.0089 0.28 NO
35 FBXW11 FBXW11 FBXW11 4931 0.0078 0.28 NO
36 MAPK1 MAPK1 MAPK1 4985 0.0071 0.28 NO
37 MLST8 MLST8 MLST8 5256 0.0026 0.26 NO
38 YWHAG YWHAG YWHAG 5408 0.00022 0.26 NO
39 EEF2 EEF2 EEF2 5476 -0.00079 0.25 NO
40 PDPK1 PDPK1 PDPK1 5659 -0.0035 0.24 NO
41 MAP2K1 MAP2K1 MAP2K1 5711 -0.0042 0.24 NO
42 RAF1 RAF1 RAF1 5780 -0.0053 0.24 NO
43 TSC1 TSC1 TSC1 5950 -0.0082 0.23 NO
44 KRAS KRAS KRAS 6233 -0.012 0.22 NO
45 EIF4B EIF4B EIF4B 6443 -0.015 0.21 NO
46 SGK1 SGK1 SGK1 6558 -0.017 0.21 NO
47 YY1 YY1 YY1 7290 -0.028 0.18 NO
48 PRR5 PRR5 PRR5 7414 -0.03 0.18 NO
49 TSC2 TSC2 TSC2 7661 -0.034 0.17 NO
50 BRAF BRAF BRAF 7802 -0.036 0.17 NO
51 RB1CC1 RB1CC1 RB1CC1 7900 -0.038 0.18 NO
52 SREBF1 SREBF1 SREBF1 7922 -0.038 0.18 NO
53 AKT1 AKT1 AKT1 7990 -0.039 0.19 NO
54 RRN3 RRN3 RRN3 8197 -0.043 0.19 NO
55 YWHAH YWHAH YWHAH 8198 -0.043 0.2 NO
56 ULK2 ULK2 ULK2 8434 -0.046 0.2 NO
57 POLDIP3 POLDIP3 POLDIP3 8661 -0.05 0.2 NO
58 IKBKB IKBKB IKBKB 8809 -0.053 0.2 NO
59 RICTOR RICTOR RICTOR 9204 -0.06 0.19 NO
60 EEF2K EEF2K EEF2K 9583 -0.068 0.19 NO
61 RHEB RHEB RHEB 9594 -0.068 0.2 NO
62 CDK2 CDK2 CDK2 11421 -0.11 0.13 NO
63 PRKCA PRKCA PRKCA 12396 -0.14 0.11 NO
64 RRAGB RRAGB RRAGB 13145 -0.16 0.1 NO
65 RRAGD RRAGD RRAGD 14187 -0.2 0.094 NO
66 SSPO SSPO SSPO 14937 -0.23 0.11 NO
67 PPARGC1A PPARGC1A PPARGC1A 17007 -0.34 0.074 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 PROTEASOME.

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

genes ES table in pathway: KEGG CYTOSOLIC DNA SENSING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 EIF2S1 EIF2S1 EIF2S1 2178 0.07 -0.079 YES
2 RPS13 RPS13 RPS13 2249 0.067 -0.045 YES
3 RPS12 RPS12 RPS12 2499 0.059 -0.025 YES
4 RPS10 RPS10 RPS10 2655 0.055 -0.0029 YES
5 EIF3I EIF3I EIF3I 2690 0.054 0.026 YES
6 RPS3 RPS3 RPS3 2803 0.051 0.048 YES
7 EIF3J EIF3J EIF3J 2856 0.049 0.073 YES
8 EIF3B EIF3B EIF3B 2910 0.048 0.097 YES
9 RPS24 RPS24 RPS24 3039 0.044 0.12 YES
10 RPS16 RPS16 RPS16 3084 0.043 0.14 YES
11 EIF1AX EIF1AX EIF1AX 3093 0.043 0.16 YES
12 RPS15 RPS15 RPS15 3096 0.043 0.18 YES
13 RPS6 RPS6 RPS6 3097 0.043 0.21 YES
14 RPSA RPSA RPSA 3103 0.043 0.23 YES
15 RPS29 RPS29 RPS29 3165 0.041 0.25 YES
16 RPS25 RPS25 RPS25 3166 0.041 0.28 YES
17 EIF2S3 EIF2S3 EIF2S3 3181 0.041 0.3 YES
18 RPS14 RPS14 RPS14 3236 0.039 0.32 YES
19 RPS18 RPS18 RPS18 3335 0.037 0.33 YES
20 RPS2 RPS2 RPS2 3413 0.036 0.35 YES
21 RPS9 RPS9 RPS9 3517 0.033 0.36 YES
22 RPS15A RPS15A RPS15A 3523 0.033 0.38 YES
23 RPS7 RPS7 RPS7 3577 0.032 0.4 YES
24 FAU FAU FAU 3596 0.032 0.41 YES
25 RPS3A RPS3A RPS3A 3629 0.031 0.43 YES
26 RPS17 RPS17 RPS17 3644 0.031 0.45 YES
27 RPS4X RPS4X RPS4X 3673 0.03 0.46 YES
28 RPS21 RPS21 RPS21 3701 0.029 0.48 YES
29 EIF2S2 EIF2S2 EIF2S2 3705 0.029 0.49 YES
30 RPS5 RPS5 RPS5 3751 0.028 0.51 YES
31 EIF3H EIF3H EIF3H 3759 0.028 0.52 YES
32 EIF3E EIF3E EIF3E 3783 0.028 0.54 YES
33 RPS8 RPS8 RPS8 3866 0.026 0.55 YES
34 RPS27A RPS27A RPS27A 3887 0.026 0.56 YES
35 EIF3F EIF3F EIF3F 3944 0.024 0.57 YES
36 RPS26 RPS26 RPS26 4005 0.023 0.58 YES
37 RPS23 RPS23 RPS23 4116 0.021 0.59 YES
38 EIF3D EIF3D EIF3D 4233 0.019 0.59 YES
39 EIF3A EIF3A EIF3A 4343 0.018 0.6 YES
40 RPS19 RPS19 RPS19 4466 0.015 0.6 YES
41 EIF3K EIF3K EIF3K 4494 0.015 0.6 YES
42 EIF3G EIF3G EIF3G 4513 0.015 0.61 YES
43 RPS20 RPS20 RPS20 4574 0.014 0.62 YES
44 RPS28 RPS28 RPS28 4610 0.013 0.62 YES
45 RPS11 RPS11 RPS11 4611 0.013 0.63 YES
46 RPSAP9 RPSAP9 RPSAP9 5001 0.0068 0.61 NO
47 EIF3C EIF3C EIF3C 6222 -0.012 0.55 NO
48 RPS27 RPS27 RPS27 6396 -0.015 0.55 NO
49 RPS4Y1 RPS4Y1 RPS4Y1 13743 -0.18 0.25 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 CYTOSOLIC DNA SENSING PATHWAY.

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

genes ES table in pathway: BIOCARTA PROTEASOME PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CSNK1A1 CSNK1A1 CSNK1A1 1354 0.12 -0.026 YES
2 BTRC BTRC BTRC 1742 0.091 -0.011 YES
3 PPP2R5B PPP2R5B PPP2R5B 1899 0.083 0.014 YES
4 PPP2R1B PPP2R1B PPP2R1B 1928 0.081 0.045 YES
5 PSMD6 PSMD6 PSMD6 2062 0.074 0.067 YES
6 PPP2CA PPP2CA PPP2CA 2190 0.07 0.088 YES
7 PSMB10 PSMB10 PSMB10 2260 0.067 0.11 YES
8 PSMB8 PSMB8 PSMB8 2554 0.058 0.12 YES
9 PSMA5 PSMA5 PSMA5 2635 0.055 0.14 YES
10 PSMB7 PSMB7 PSMB7 2636 0.055 0.16 YES
11 PSMD13 PSMD13 PSMD13 2750 0.052 0.17 YES
12 PSMB6 PSMB6 PSMB6 2857 0.049 0.19 YES
13 PSMA6 PSMA6 PSMA6 2922 0.047 0.2 YES
14 PSME2 PSME2 PSME2 2937 0.047 0.22 YES
15 PPP2R1A PPP2R1A PPP2R1A 3045 0.044 0.23 YES
16 PSMB5 PSMB5 PSMB5 3170 0.041 0.24 YES
17 PPP2R5E PPP2R5E PPP2R5E 3204 0.04 0.26 YES
18 PSMD12 PSMD12 PSMD12 3443 0.035 0.26 YES
19 PSME1 PSME1 PSME1 3504 0.034 0.27 YES
20 PSMB2 PSMB2 PSMB2 3607 0.032 0.28 YES
21 PSMC3 PSMC3 PSMC3 3619 0.031 0.29 YES
22 UBA52 UBA52 UBA52 3666 0.03 0.3 YES
23 PSMD7 PSMD7 PSMD7 3699 0.029 0.31 YES
24 PSMA2 PSMA2 PSMA2 3711 0.029 0.32 YES
25 PSMD1 PSMD1 PSMD1 3712 0.029 0.33 YES
26 PSMC6 PSMC6 PSMC6 3755 0.028 0.34 YES
27 PSMA4 PSMA4 PSMA4 3792 0.028 0.35 YES
28 PSMD8 PSMD8 PSMD8 3820 0.027 0.36 YES
29 RPS27A RPS27A RPS27A 3887 0.026 0.36 YES
30 SKP1 SKP1 SKP1 3975 0.024 0.37 YES
31 PSMF1 PSMF1 PSMF1 4009 0.023 0.38 YES
32 PSMD9 PSMD9 PSMD9 4053 0.023 0.38 YES
33 PSMB1 PSMB1 PSMB1 4079 0.022 0.39 YES
34 CUL1 CUL1 CUL1 4167 0.02 0.39 YES
35 PPP2CB PPP2CB PPP2CB 4205 0.02 0.4 YES
36 PSMA1 PSMA1 PSMA1 4220 0.02 0.41 YES
37 PSMA7 PSMA7 PSMA7 4255 0.019 0.41 YES
38 PSMA3 PSMA3 PSMA3 4289 0.019 0.42 YES
39 PSMB9 PSMB9 PSMB9 4490 0.015 0.41 NO
40 PSMC1 PSMC1 PSMC1 4562 0.014 0.42 NO
41 PPP2R5A PPP2R5A PPP2R5A 4728 0.011 0.41 NO
42 PSMD14 PSMD14 PSMD14 4815 0.0097 0.41 NO
43 PSMC5 PSMC5 PSMC5 4888 0.0085 0.41 NO
44 PSMB3 PSMB3 PSMB3 4889 0.0084 0.41 NO
45 PSMD3 PSMD3 PSMD3 4927 0.0079 0.41 NO
46 PSMC4 PSMC4 PSMC4 5278 0.0022 0.4 NO
47 AXIN1 AXIN1 AXIN1 5340 0.0011 0.39 NO
48 PPP2R5C PPP2R5C PPP2R5C 5418 0.00013 0.39 NO
49 PSMD11 PSMD11 PSMD11 5705 -0.0042 0.37 NO
50 PSMD4 PSMD4 PSMD4 5966 -0.0084 0.36 NO
51 PSMD5 PSMD5 PSMD5 6083 -0.01 0.36 NO
52 PSMB4 PSMB4 PSMB4 6583 -0.018 0.34 NO
53 PSMC2 PSMC2 PSMC2 6681 -0.019 0.34 NO
54 PSMD10 PSMD10 PSMD10 6927 -0.023 0.34 NO
55 PSME4 PSME4 PSME4 7055 -0.025 0.34 NO
56 PPP2R5D PPP2R5D PPP2R5D 7103 -0.026 0.35 NO
57 PSMD2 PSMD2 PSMD2 7170 -0.026 0.36 NO
58 CTNNB1 CTNNB1 CTNNB1 8440 -0.047 0.31 NO
59 APC APC APC 8961 -0.056 0.3 NO
60 FRAT2 FRAT2 FRAT2 9686 -0.07 0.29 NO
61 FRAT1 FRAT1 FRAT1 9803 -0.072 0.31 NO
62 PSMA8 PSMA8 PSMA8 13641 -0.18 0.17 NO
63 FAM123B FAM123B FAM123B 14609 -0.21 0.2 NO

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

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PROTEASOME 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 MTOR 4PATHWAY

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 EIF4E EIF4E EIF4E 1674 0.095 -0.048 YES
2 EIF2S1 EIF2S1 EIF2S1 2178 0.07 -0.044 YES
3 RPS13 RPS13 RPS13 2249 0.067 -0.017 YES
4 RPS12 RPS12 RPS12 2499 0.059 -0.004 YES
5 RPS10 RPS10 RPS10 2655 0.055 0.012 YES
6 EIF4EBP1 EIF4EBP1 EIF4EBP1 2684 0.054 0.035 YES
7 EIF3I EIF3I EIF3I 2690 0.054 0.059 YES
8 EIF4A1 EIF4A1 EIF4A1 2709 0.053 0.082 YES
9 RPS3 RPS3 RPS3 2803 0.051 0.1 YES
10 EIF3J EIF3J EIF3J 2856 0.049 0.12 YES
11 EIF3B EIF3B EIF3B 2910 0.048 0.14 YES
12 RPS24 RPS24 RPS24 3039 0.044 0.15 YES
13 RPS16 RPS16 RPS16 3084 0.043 0.17 YES
14 EIF1AX EIF1AX EIF1AX 3093 0.043 0.19 YES
15 RPS15 RPS15 RPS15 3096 0.043 0.21 YES
16 RPS6 RPS6 RPS6 3097 0.043 0.23 YES
17 RPSA RPSA RPSA 3103 0.043 0.25 YES
18 RPS29 RPS29 RPS29 3165 0.041 0.26 YES
19 RPS25 RPS25 RPS25 3166 0.041 0.28 YES
20 EIF2S3 EIF2S3 EIF2S3 3181 0.041 0.3 YES
21 RPS14 RPS14 RPS14 3236 0.039 0.31 YES
22 RPS18 RPS18 RPS18 3335 0.037 0.32 YES
23 RPS2 RPS2 RPS2 3413 0.036 0.34 YES
24 RPS9 RPS9 RPS9 3517 0.033 0.35 YES
25 RPS15A RPS15A RPS15A 3523 0.033 0.36 YES
26 EIF4H EIF4H EIF4H 3557 0.032 0.37 YES
27 RPS7 RPS7 RPS7 3577 0.032 0.39 YES
28 FAU FAU FAU 3596 0.032 0.4 YES
29 RPS3A RPS3A RPS3A 3629 0.031 0.41 YES
30 RPS17 RPS17 RPS17 3644 0.031 0.43 YES
31 RPS4X RPS4X RPS4X 3673 0.03 0.44 YES
32 RPS21 RPS21 RPS21 3701 0.029 0.45 YES
33 EIF2S2 EIF2S2 EIF2S2 3705 0.029 0.46 YES
34 RPS5 RPS5 RPS5 3751 0.028 0.47 YES
35 EIF3H EIF3H EIF3H 3759 0.028 0.48 YES
36 EIF3E EIF3E EIF3E 3783 0.028 0.5 YES
37 RPS8 RPS8 RPS8 3866 0.026 0.5 YES
38 RPS27A RPS27A RPS27A 3887 0.026 0.51 YES
39 PABPC1 PABPC1 PABPC1 3898 0.025 0.52 YES
40 EIF3F EIF3F EIF3F 3944 0.024 0.53 YES
41 RPS26 RPS26 RPS26 4005 0.023 0.54 YES
42 RPS23 RPS23 RPS23 4116 0.021 0.55 YES
43 EIF3D EIF3D EIF3D 4233 0.019 0.55 YES
44 EIF3A EIF3A EIF3A 4343 0.018 0.55 YES
45 RPS19 RPS19 RPS19 4466 0.015 0.55 YES
46 EIF3K EIF3K EIF3K 4494 0.015 0.56 YES
47 EIF3G EIF3G EIF3G 4513 0.015 0.56 YES
48 RPS20 RPS20 RPS20 4574 0.014 0.56 YES
49 RPS28 RPS28 RPS28 4610 0.013 0.57 YES
50 RPS11 RPS11 RPS11 4611 0.013 0.57 YES
51 EIF4G1 EIF4G1 EIF4G1 4834 0.0094 0.57 NO
52 RPSAP9 RPSAP9 RPSAP9 5001 0.0068 0.56 NO
53 EIF3C EIF3C EIF3C 6222 -0.012 0.5 NO
54 RPS27 RPS27 RPS27 6396 -0.015 0.5 NO
55 EIF4B EIF4B EIF4B 6443 -0.015 0.5 NO
56 EIF4A2 EIF4A2 EIF4A2 12899 -0.15 0.22 NO
57 RPS4Y1 RPS4Y1 RPS4Y1 13743 -0.18 0.25 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: PID MTOR 4PATHWAY.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: PID MTOR 4PATHWAY, 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 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

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 OAZ3 OAZ3 OAZ3 579 0.24 0.099 YES
2 PSMD6 PSMD6 PSMD6 2062 0.074 0.06 YES
3 PSMB10 PSMB10 PSMB10 2260 0.067 0.086 YES
4 PSMB8 PSMB8 PSMB8 2554 0.058 0.1 YES
5 PSMA5 PSMA5 PSMA5 2635 0.055 0.13 YES
6 PSMB7 PSMB7 PSMB7 2636 0.055 0.16 YES
7 ODC1 ODC1 ODC1 2745 0.052 0.18 YES
8 PSMD13 PSMD13 PSMD13 2750 0.052 0.21 YES
9 NQO1 NQO1 NQO1 2829 0.05 0.24 YES
10 PSMB6 PSMB6 PSMB6 2857 0.049 0.26 YES
11 PSMA6 PSMA6 PSMA6 2922 0.047 0.28 YES
12 PSME2 PSME2 PSME2 2937 0.047 0.31 YES
13 PSMB5 PSMB5 PSMB5 3170 0.041 0.32 YES
14 PSMD12 PSMD12 PSMD12 3443 0.035 0.32 YES
15 PSME1 PSME1 PSME1 3504 0.034 0.34 YES
16 PSMB2 PSMB2 PSMB2 3607 0.032 0.35 YES
17 PSMC3 PSMC3 PSMC3 3619 0.031 0.37 YES
18 PSMD7 PSMD7 PSMD7 3699 0.029 0.38 YES
19 PSMA2 PSMA2 PSMA2 3711 0.029 0.4 YES
20 PSMD1 PSMD1 PSMD1 3712 0.029 0.41 YES
21 PSMC6 PSMC6 PSMC6 3755 0.028 0.42 YES
22 PSMA4 PSMA4 PSMA4 3792 0.028 0.44 YES
23 PSMD8 PSMD8 PSMD8 3820 0.027 0.45 YES
24 PSMF1 PSMF1 PSMF1 4009 0.023 0.45 YES
25 PSMD9 PSMD9 PSMD9 4053 0.023 0.46 YES
26 PSMB1 PSMB1 PSMB1 4079 0.022 0.48 YES
27 PSMA1 PSMA1 PSMA1 4220 0.02 0.48 YES
28 PSMA7 PSMA7 PSMA7 4255 0.019 0.49 YES
29 PSMA3 PSMA3 PSMA3 4289 0.019 0.5 YES
30 OAZ1 OAZ1 OAZ1 4324 0.018 0.5 YES
31 PSMB9 PSMB9 PSMB9 4490 0.015 0.5 YES
32 PSMC1 PSMC1 PSMC1 4562 0.014 0.51 YES
33 PSMD14 PSMD14 PSMD14 4815 0.0097 0.5 NO
34 PSMC5 PSMC5 PSMC5 4888 0.0085 0.5 NO
35 PSMB3 PSMB3 PSMB3 4889 0.0084 0.5 NO
36 PSMD3 PSMD3 PSMD3 4927 0.0079 0.51 NO
37 PSMC4 PSMC4 PSMC4 5278 0.0022 0.49 NO
38 PSMD11 PSMD11 PSMD11 5705 -0.0042 0.47 NO
39 PSMD4 PSMD4 PSMD4 5966 -0.0084 0.46 NO
40 PSMD5 PSMD5 PSMD5 6083 -0.01 0.46 NO
41 PSMB4 PSMB4 PSMB4 6583 -0.018 0.44 NO
42 PSMC2 PSMC2 PSMC2 6681 -0.019 0.45 NO
43 PSMD10 PSMD10 PSMD10 6927 -0.023 0.44 NO
44 PSME4 PSME4 PSME4 7055 -0.025 0.45 NO
45 PSMD2 PSMD2 PSMD2 7170 -0.026 0.46 NO
46 OAZ2 OAZ2 OAZ2 7653 -0.034 0.45 NO
47 AZIN1 AZIN1 AZIN1 9175 -0.059 0.4 NO
48 PSMA8 PSMA8 PSMA8 13641 -0.18 0.26 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: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, 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 SIGNALING BY WNT

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 POLR2L POLR2L POLR2L 1201 0.13 0.045 YES
2 CDK7 CDK7 CDK7 1283 0.12 0.14 YES
3 ERCC1 ERCC1 ERCC1 2244 0.067 0.15 YES
4 ERCC6 ERCC6 ERCC6 2682 0.054 0.17 YES
5 GTF2H1 GTF2H1 GTF2H1 3537 0.033 0.15 YES
6 POLR2A POLR2A POLR2A 4073 0.022 0.14 YES
7 CCNH CCNH CCNH 4540 0.014 0.13 YES
8 ERCC5 ERCC5 ERCC5 4572 0.014 0.14 YES
9 POLR2E POLR2E POLR2E 4603 0.013 0.15 YES
10 POLR2G POLR2G POLR2G 5257 0.0026 0.11 YES
11 POLR2I POLR2I POLR2I 5311 0.0017 0.11 YES
12 POLR2F POLR2F POLR2F 6206 -0.012 0.073 YES
13 GTF2H3 GTF2H3 GTF2H3 6316 -0.014 0.079 YES
14 XAB2 XAB2 XAB2 6704 -0.019 0.074 YES
15 POLR2C POLR2C POLR2C 6958 -0.023 0.079 YES
16 POLR2K POLR2K POLR2K 6965 -0.023 0.098 YES
17 POLR2B POLR2B POLR2B 7019 -0.024 0.12 YES
18 GTF2H2 GTF2H2 GTF2H2 7022 -0.024 0.14 YES
19 POLR2J POLR2J POLR2J 7552 -0.032 0.13 YES
20 TCEA1 TCEA1 TCEA1 7587 -0.033 0.16 YES
21 GTF2H4 GTF2H4 GTF2H4 7926 -0.038 0.17 YES
22 ERCC8 ERCC8 ERCC8 8202 -0.043 0.19 YES
23 ERCC3 ERCC3 ERCC3 8800 -0.052 0.21 YES
24 ERCC4 ERCC4 ERCC4 8833 -0.053 0.25 YES
25 MNAT1 MNAT1 MNAT1 8887 -0.054 0.29 YES
26 POLR2D POLR2D POLR2D 8965 -0.056 0.33 YES
27 GTF2H2B GTF2H2B GTF2H2B 9367 -0.063 0.36 YES
28 ERCC2 ERCC2 ERCC2 9661 -0.069 0.41 YES
29 POLR2H POLR2H POLR2H 10251 -0.082 0.44 YES

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: REACTOME SIGNALING BY WNT.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SIGNALING BY WNT, 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 TRIF MEDIATED TLR3 SIGNALING

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 S100A12 S100A12 S100A12 21 0.74 0.14 YES
2 NOD2 NOD2 NOD2 269 0.38 0.19 YES
3 IRF7 IRF7 IRF7 774 0.19 0.2 YES
4 MAPK3 MAPK3 MAPK3 1080 0.15 0.21 YES
5 ZBP1 ZBP1 ZBP1 1316 0.12 0.22 YES
6 FOS FOS FOS 1337 0.12 0.24 YES
7 DUSP7 DUSP7 DUSP7 1368 0.12 0.26 YES
8 DUSP6 DUSP6 DUSP6 1469 0.11 0.28 YES
9 MAP2K4 MAP2K4 MAP2K4 1542 0.1 0.29 YES
10 MAPKAPK3 MAPKAPK3 MAPKAPK3 1737 0.091 0.3 YES
11 IRAK2 IRAK2 IRAK2 1781 0.089 0.31 YES
12 PPP2R1B PPP2R1B PPP2R1B 1928 0.081 0.32 YES
13 MAPK14 MAPK14 MAPK14 1988 0.078 0.33 YES
14 RIPK3 RIPK3 RIPK3 2090 0.073 0.34 YES
15 SAA1 SAA1 SAA1 2188 0.07 0.34 YES
16 PPP2CA PPP2CA PPP2CA 2190 0.07 0.36 YES
17 MAPK7 MAPK7 MAPK7 2295 0.065 0.36 YES
18 TICAM1 TICAM1 TICAM1 2349 0.063 0.37 YES
19 MAP2K3 MAP2K3 MAP2K3 2473 0.06 0.38 YES
20 PPP2R1A PPP2R1A PPP2R1A 3045 0.044 0.35 NO
21 JUN JUN JUN 3105 0.043 0.36 NO
22 TAB2 TAB2 TAB2 3503 0.034 0.34 NO
23 UBA52 UBA52 UBA52 3666 0.03 0.34 NO
24 MAP2K2 MAP2K2 MAP2K2 3723 0.029 0.34 NO
25 RPS27A RPS27A RPS27A 3887 0.026 0.34 NO
26 RPS6KA1 RPS6KA1 RPS6KA1 3925 0.025 0.34 NO
27 RELA RELA RELA 4184 0.02 0.33 NO
28 PPP2CB PPP2CB PPP2CB 4205 0.02 0.33 NO
29 TLR3 TLR3 TLR3 4230 0.02 0.33 NO
30 TAB3 TAB3 TAB3 4243 0.019 0.34 NO
31 RIPK1 RIPK1 RIPK1 4275 0.019 0.34 NO
32 RIPK2 RIPK2 RIPK2 4446 0.016 0.33 NO
33 MEF2A MEF2A MEF2A 4722 0.011 0.32 NO
34 CHUK CHUK CHUK 4861 0.0088 0.31 NO
35 NFKBIB NFKBIB NFKBIB 4925 0.0079 0.31 NO
36 MAPK1 MAPK1 MAPK1 4985 0.0071 0.31 NO
37 NFKBIA NFKBIA NFKBIA 5147 0.0042 0.3 NO
38 DUSP4 DUSP4 DUSP4 5456 -0.00046 0.28 NO
39 IRAK1 IRAK1 IRAK1 5505 -0.0012 0.28 NO
40 NOD1 NOD1 NOD1 5634 -0.0031 0.28 NO
41 MAP2K1 MAP2K1 MAP2K1 5711 -0.0042 0.27 NO
42 DUSP3 DUSP3 DUSP3 5712 -0.0042 0.27 NO
43 MAP3K7 MAP3K7 MAP3K7 5755 -0.0048 0.27 NO
44 IRF3 IRF3 IRF3 5803 -0.0057 0.27 NO
45 MAP2K7 MAP2K7 MAP2K7 6000 -0.0089 0.26 NO
46 CREB1 CREB1 CREB1 6043 -0.0095 0.26 NO
47 IKBKG IKBKG IKBKG 6193 -0.012 0.25 NO
48 S100B S100B S100B 6227 -0.012 0.25 NO
49 MAPK11 MAPK11 MAPK11 6463 -0.016 0.24 NO
50 APP APP APP 6653 -0.018 0.24 NO
51 IKBKE IKBKE IKBKE 7035 -0.024 0.22 NO
52 PPP2R5D PPP2R5D PPP2R5D 7103 -0.026 0.22 NO
53 TRAF6 TRAF6 TRAF6 7311 -0.029 0.22 NO
54 RPS6KA3 RPS6KA3 RPS6KA3 7458 -0.031 0.21 NO
55 TBK1 TBK1 TBK1 7686 -0.034 0.21 NO
56 MAPK9 MAPK9 MAPK9 8009 -0.04 0.2 NO
57 HMGB1 HMGB1 HMGB1 8116 -0.042 0.2 NO
58 MAPKAPK2 MAPKAPK2 MAPKAPK2 8501 -0.048 0.19 NO
59 NFKB2 NFKB2 NFKB2 8593 -0.049 0.19 NO
60 IKBKB IKBKB IKBKB 8809 -0.053 0.19 NO
61 AGER AGER AGER 9798 -0.072 0.15 NO
62 RPS6KA2 RPS6KA2 RPS6KA2 9886 -0.074 0.16 NO
63 TAB1 TAB1 TAB1 10264 -0.082 0.15 NO
64 RPS6KA5 RPS6KA5 RPS6KA5 10489 -0.086 0.16 NO
65 CDK1 CDK1 CDK1 10550 -0.088 0.17 NO
66 ATF1 ATF1 ATF1 10820 -0.094 0.17 NO
67 ELK1 ELK1 ELK1 11295 -0.11 0.16 NO
68 MAPK8 MAPK8 MAPK8 12445 -0.14 0.13 NO
69 ATF2 ATF2 ATF2 13632 -0.18 0.094 NO
70 MAPK10 MAPK10 MAPK10 13726 -0.18 0.12 NO
71 MEF2C MEF2C MEF2C 16398 -0.3 0.032 NO
72 MAP2K6 MAP2K6 MAP2K6 17730 -0.41 0.034 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: REACTOME TRIF MEDIATED TLR3 SIGNALING.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRIF MEDIATED TLR3 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 ER PHAGOSOME PATHWAY

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 IL18 IL18 IL18 414 0.3 0.066 YES
2 IL1B IL1B IL1B 426 0.29 0.15 YES
3 POLR3G POLR3G POLR3G 503 0.26 0.22 YES
4 PYCARD PYCARD PYCARD 760 0.19 0.27 YES
5 IRF7 IRF7 IRF7 774 0.19 0.32 YES
6 CASP1 CASP1 CASP1 855 0.18 0.37 YES
7 DDX58 DDX58 DDX58 972 0.16 0.41 YES
8 AIM2 AIM2 AIM2 1006 0.16 0.46 YES
9 IFNA13 IFNA13 IFNA13 1114 0.14 0.49 YES
10 CXCL10 CXCL10 CXCL10 1185 0.13 0.53 YES
11 ZBP1 ZBP1 ZBP1 1316 0.12 0.56 YES
12 IFNA1 IFNA1 IFNA1 1813 0.087 0.56 YES
13 RIPK3 RIPK3 RIPK3 2090 0.073 0.56 YES
14 IL33 IL33 IL33 2273 0.066 0.57 YES
15 POLR3B POLR3B POLR3B 2516 0.058 0.57 YES
16 POLR1D POLR1D POLR1D 3369 0.037 0.54 NO
17 POLR3H POLR3H POLR3H 4036 0.023 0.51 NO
18 POLR3A POLR3A POLR3A 4092 0.022 0.51 NO
19 RELA RELA RELA 4184 0.02 0.51 NO
20 RIPK1 RIPK1 RIPK1 4275 0.019 0.52 NO
21 CHUK CHUK CHUK 4861 0.0088 0.48 NO
22 NFKBIB NFKBIB NFKBIB 4925 0.0079 0.48 NO
23 NFKBIA NFKBIA NFKBIA 5147 0.0042 0.47 NO
24 NFKB1 NFKB1 NFKB1 5181 0.0037 0.47 NO
25 TMEM173 TMEM173 TMEM173 5272 0.0023 0.47 NO
26 CCL5 CCL5 CCL5 5722 -0.0044 0.44 NO
27 IRF3 IRF3 IRF3 5803 -0.0057 0.44 NO
28 IKBKG IKBKG IKBKG 6193 -0.012 0.42 NO
29 POLR1C POLR1C POLR1C 6241 -0.012 0.43 NO
30 POLR3F POLR3F POLR3F 6356 -0.014 0.42 NO
31 ADAR ADAR ADAR 6381 -0.015 0.43 NO
32 IKBKE IKBKE IKBKE 7035 -0.024 0.4 NO
33 TREX1 TREX1 TREX1 7127 -0.026 0.4 NO
34 MAVS MAVS MAVS 7371 -0.03 0.4 NO
35 TBK1 TBK1 TBK1 7686 -0.034 0.39 NO
36 IL6 IL6 IL6 7929 -0.038 0.39 NO
37 CCL4 CCL4 CCL4 8208 -0.043 0.38 NO
38 IFNB1 IFNB1 IFNB1 8464 -0.047 0.38 NO
39 IKBKB IKBKB IKBKB 8809 -0.053 0.38 NO
40 POLR3C POLR3C POLR3C 9677 -0.069 0.36 NO
41 POLR3K POLR3K POLR3K 9706 -0.07 0.37 NO
42 POLR3D POLR3D POLR3D 9894 -0.074 0.39 NO
43 CCL4L2 CCL4L2 CCL4L2 11129 -0.1 0.35 NO
44 POLR3GL POLR3GL POLR3GL 13035 -0.16 0.29 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: REACTOME ER PHAGOSOME PATHWAY.

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

genes ES table in pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

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 PSMD6 PSMD6 PSMD6 2062 0.074 -0.02 YES
2 PSMA5 PSMA5 PSMA5 2635 0.055 0.018 YES
3 PSMB7 PSMB7 PSMB7 2636 0.055 0.087 YES
4 PSMB6 PSMB6 PSMB6 2857 0.049 0.14 YES
5 PSMA6 PSMA6 PSMA6 2922 0.047 0.19 YES
6 PSMB5 PSMB5 PSMB5 3170 0.041 0.23 YES
7 PSMD12 PSMD12 PSMD12 3443 0.035 0.26 YES
8 PSMB2 PSMB2 PSMB2 3607 0.032 0.29 YES
9 PSMC3 PSMC3 PSMC3 3619 0.031 0.33 YES
10 PSMA2 PSMA2 PSMA2 3711 0.029 0.36 YES
11 PSMC6 PSMC6 PSMC6 3755 0.028 0.39 YES
12 UBA1 UBA1 UBA1 3789 0.028 0.42 YES
13 PSMA4 PSMA4 PSMA4 3792 0.028 0.46 YES
14 PSMD8 PSMD8 PSMD8 3820 0.027 0.49 YES
15 UBE2A UBE2A UBE2A 3990 0.024 0.51 YES
16 PSMB1 PSMB1 PSMB1 4079 0.022 0.53 YES
17 PSMA1 PSMA1 PSMA1 4220 0.02 0.55 YES
18 PSMA7 PSMA7 PSMA7 4255 0.019 0.57 YES
19 PSMA3 PSMA3 PSMA3 4289 0.019 0.59 YES
20 PSMD14 PSMD14 PSMD14 4815 0.0097 0.58 NO
21 PSMB3 PSMB3 PSMB3 4889 0.0084 0.58 NO
22 PSMC4 PSMC4 PSMC4 5278 0.0022 0.56 NO
23 PSMD11 PSMD11 PSMD11 5705 -0.0042 0.55 NO
24 PSMB4 PSMB4 PSMB4 6583 -0.018 0.52 NO
25 PSMC2 PSMC2 PSMC2 6681 -0.019 0.54 NO
26 RPN1 RPN1 RPN1 6804 -0.021 0.56 NO
27 UBE3A UBE3A UBE3A 7125 -0.026 0.57 NO
28 RPN2 RPN2 RPN2 7481 -0.031 0.59 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: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, 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 REGULATION OF ORNITHINE DECARBOXYLASE ODC

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 PSMD6 PSMD6 PSMD6 2062 0.074 -0.067 YES
2 HSPB1 HSPB1 HSPB1 2169 0.071 -0.03 YES
3 PSMB10 PSMB10 PSMB10 2260 0.067 0.006 YES
4 PSMB8 PSMB8 PSMB8 2554 0.058 0.025 YES
5 PSMA5 PSMA5 PSMA5 2635 0.055 0.054 YES
6 PSMB7 PSMB7 PSMB7 2636 0.055 0.088 YES
7 PSMD13 PSMD13 PSMD13 2750 0.052 0.11 YES
8 PSMB6 PSMB6 PSMB6 2857 0.049 0.14 YES
9 PSMA6 PSMA6 PSMA6 2922 0.047 0.16 YES
10 PSME2 PSME2 PSME2 2937 0.047 0.19 YES
11 HSPA8 HSPA8 HSPA8 3034 0.044 0.21 YES
12 PSMB5 PSMB5 PSMB5 3170 0.041 0.23 YES
13 PSMD12 PSMD12 PSMD12 3443 0.035 0.24 YES
14 PSME1 PSME1 PSME1 3504 0.034 0.26 YES
15 PSMB2 PSMB2 PSMB2 3607 0.032 0.27 YES
16 PSMC3 PSMC3 PSMC3 3619 0.031 0.29 YES
17 UBA52 UBA52 UBA52 3666 0.03 0.3 YES
18 PSMD7 PSMD7 PSMD7 3699 0.029 0.32 YES
19 PSMA2 PSMA2 PSMA2 3711 0.029 0.34 YES
20 PSMD1 PSMD1 PSMD1 3712 0.029 0.35 YES
21 PSMC6 PSMC6 PSMC6 3755 0.028 0.37 YES
22 PSMA4 PSMA4 PSMA4 3792 0.028 0.38 YES
23 PSMD8 PSMD8 PSMD8 3820 0.027 0.4 YES
24 RPS27A RPS27A RPS27A 3887 0.026 0.41 YES
25 PABPC1 PABPC1 PABPC1 3898 0.025 0.42 YES
26 PSMF1 PSMF1 PSMF1 4009 0.023 0.43 YES
27 PSMD9 PSMD9 PSMD9 4053 0.023 0.44 YES
28 PSMB1 PSMB1 PSMB1 4079 0.022 0.46 YES
29 PSMA1 PSMA1 PSMA1 4220 0.02 0.46 YES
30 PSMA7 PSMA7 PSMA7 4255 0.019 0.47 YES
31 PSMA3 PSMA3 PSMA3 4289 0.019 0.48 YES
32 PSMB9 PSMB9 PSMB9 4490 0.015 0.48 YES
33 PSMC1 PSMC1 PSMC1 4562 0.014 0.48 YES
34 PSMD14 PSMD14 PSMD14 4815 0.0097 0.48 YES
35 EIF4G1 EIF4G1 EIF4G1 4834 0.0094 0.48 YES
36 PSMC5 PSMC5 PSMC5 4888 0.0085 0.48 YES
37 PSMB3 PSMB3 PSMB3 4889 0.0084 0.49 YES
38 PSMD3 PSMD3 PSMD3 4927 0.0079 0.49 YES
39 PSMC4 PSMC4 PSMC4 5278 0.0022 0.47 NO
40 PSMD11 PSMD11 PSMD11 5705 -0.0042 0.45 NO
41 PSMD4 PSMD4 PSMD4 5966 -0.0084 0.44 NO
42 PSMD5 PSMD5 PSMD5 6083 -0.01 0.44 NO
43 PSMB4 PSMB4 PSMB4 6583 -0.018 0.43 NO
44 PSMC2 PSMC2 PSMC2 6681 -0.019 0.43 NO
45 PSMD10 PSMD10 PSMD10 6927 -0.023 0.43 NO
46 PSME4 PSME4 PSME4 7055 -0.025 0.44 NO
47 PSMD2 PSMD2 PSMD2 7170 -0.026 0.45 NO
48 HNRNPD HNRNPD HNRNPD 8003 -0.04 0.43 NO
49 HSPA1B HSPA1B HSPA1B 8286 -0.044 0.44 NO
50 PSMA8 PSMA8 PSMA8 13641 -0.18 0.26 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: REACTOME REGULATION OF ORNITHINE DECARBOXYLASE ODC.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME REGULATION OF ORNITHINE DECARBOXYLASE ODC, 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 FATTY ACID METABOLISM 39 genes.ES.table 0.5 1.5 0.082 1 0.98 0.46 0.32 0.32 0.88 0.46
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 44 genes.ES.table 0.44 1.5 0.077 1 0.99 0.48 0.34 0.32 0.93 0.47
KEGG STARCH AND SUCROSE METABOLISM 40 genes.ES.table 0.65 1.7 0.0041 1 0.84 0.42 0.14 0.36 1 0.54
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS 25 genes.ES.table 0.43 1.5 0.11 1 0.99 0.2 0.22 0.16 0.89 0.46
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 26 genes.ES.table 0.63 1.7 0.004 1 0.82 0.31 0.088 0.28 1 0.76
KEGG BUTANOATE METABOLISM 30 genes.ES.table 0.52 1.6 0.037 1 0.96 0.47 0.3 0.33 1 0.5
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 33 genes.ES.table 0.65 1.6 0.025 1 0.9 0.33 0.14 0.29 1 0.57
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 59 genes.ES.table 0.73 1.6 0.014 1 0.92 0.56 0.14 0.48 1 0.51
KEGG DRUG METABOLISM CYTOCHROME P450 60 genes.ES.table 0.75 1.7 0.0062 1 0.82 0.57 0.14 0.49 1 0.59
PID FANCONI PATHWAY 46 genes.ES.table 0.54 1.6 0.1 1 0.96 0.7 0.36 0.45 1 0.54
genes ES table in pathway: KEGG FATTY ACID METABOLISM

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 GCNT2 GCNT2 GCNT2 33 0.72 0.14 YES
2 B3GALT5 B3GALT5 B3GALT5 64 0.67 0.27 YES
3 FUT6 FUT6 FUT6 165 0.56 0.38 YES
4 ABO ABO ABO 519 0.44 0.44 YES
5 FUT3 FUT3 FUT3 1201 0.33 0.47 YES
6 B3GALT2 B3GALT2 B3GALT2 1242 0.33 0.53 YES
7 FUT5 FUT5 FUT5 1576 0.3 0.57 YES
8 B4GALT4 B4GALT4 B4GALT4 1614 0.29 0.63 YES
9 FUT2 FUT2 FUT2 3398 0.18 0.57 NO
10 FUT9 FUT9 FUT9 4151 0.14 0.55 NO
11 FUT4 FUT4 FUT4 7147 0.066 0.4 NO
12 B3GNT3 B3GNT3 B3GNT3 7689 0.056 0.38 NO
13 B3GALT1 B3GALT1 B3GALT1 8470 0.041 0.35 NO
14 ST8SIA1 ST8SIA1 ST8SIA1 8539 0.04 0.35 NO
15 ST3GAL3 ST3GAL3 ST3GAL3 10152 0.016 0.27 NO
16 FUT1 FUT1 FUT1 10203 0.015 0.27 NO
17 B3GNT2 B3GNT2 B3GNT2 10602 0.0092 0.25 NO
18 FUT7 FUT7 FUT7 10870 0.005 0.24 NO
19 ST3GAL4 ST3GAL4 ST3GAL4 11497 -0.0039 0.2 NO
20 B4GALT3 B4GALT3 B4GALT3 11541 -0.0047 0.2 NO
21 B3GNT5 B3GNT5 B3GNT5 12903 -0.027 0.13 NO
22 B4GALT1 B4GALT1 B4GALT1 14497 -0.06 0.057 NO
23 B4GALT2 B4GALT2 B4GALT2 15125 -0.078 0.038 NO
24 B3GNT1 B3GNT1 B3GNT1 15570 -0.095 0.033 NO
25 ST3GAL6 ST3GAL6 ST3GAL6 17684 -0.28 -0.027 NO
26 B3GNT4 B3GNT4 B3GNT4 17909 -0.32 0.025 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 FATTY ACID METABOLISM.

Figure S42.  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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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 GSTA1 GSTA1 GSTA1 20 0.78 0.048 YES
2 ADH7 ADH7 ADH7 47 0.7 0.09 YES
3 UGT1A6 UGT1A6 UGT1A6 70 0.66 0.13 YES
4 ALDH3A1 ALDH3A1 ALDH3A1 89 0.63 0.17 YES
5 UGT1A9 UGT1A9 UGT1A9 100 0.62 0.21 YES
6 ADH1C ADH1C ADH1C 120 0.61 0.24 YES
7 GSTA2 GSTA2 GSTA2 139 0.59 0.28 YES
8 UGT2A1 UGT2A1 UGT2A1 187 0.55 0.31 YES
9 UGT1A7 UGT1A7 UGT1A7 196 0.55 0.34 YES
10 UGT1A8 UGT1A8 UGT1A8 215 0.54 0.38 YES
11 ADH6 ADH6 ADH6 267 0.52 0.41 YES
12 UGT1A3 UGT1A3 UGT1A3 424 0.47 0.43 YES
13 CYP2C19 CYP2C19 CYP2C19 438 0.46 0.46 YES
14 CYP2E1 CYP2E1 CYP2E1 454 0.46 0.48 YES
15 CYP2C18 CYP2C18 CYP2C18 714 0.4 0.49 YES
16 CYP2C9 CYP2C9 CYP2C9 739 0.4 0.52 YES
17 FMO3 FMO3 FMO3 753 0.4 0.54 YES
18 CYP2A6 CYP2A6 CYP2A6 758 0.39 0.56 YES
19 GSTM4 GSTM4 GSTM4 1158 0.34 0.56 YES
20 GSTM2 GSTM2 GSTM2 1210 0.33 0.58 YES
21 MGST1 MGST1 MGST1 1275 0.32 0.6 YES
22 MAOB MAOB MAOB 1443 0.31 0.61 YES
23 UGT1A4 UGT1A4 UGT1A4 1491 0.3 0.62 YES
24 CYP3A5 CYP3A5 CYP3A5 1531 0.3 0.64 YES
25 GSTM3 GSTM3 GSTM3 1538 0.3 0.66 YES
26 UGT1A10 UGT1A10 UGT1A10 1747 0.28 0.67 YES
27 CYP2D6 CYP2D6 CYP2D6 1792 0.28 0.68 YES
28 FMO2 FMO2 FMO2 1796 0.28 0.7 YES
29 MAOA MAOA MAOA 1889 0.27 0.71 YES
30 UGT1A1 UGT1A1 UGT1A1 2054 0.25 0.72 YES
31 ADH1A ADH1A ADH1A 2233 0.24 0.72 YES
32 GSTA3 GSTA3 GSTA3 2377 0.23 0.73 YES
33 GSTA4 GSTA4 GSTA4 2449 0.23 0.74 YES
34 UGT2B15 UGT2B15 UGT2B15 2565 0.22 0.75 YES
35 CYP3A7 CYP3A7 CYP3A7 3023 0.19 0.73 NO
36 UGT2B7 UGT2B7 UGT2B7 3981 0.15 0.69 NO
37 ADH1B ADH1B ADH1B 4082 0.15 0.69 NO
38 CYP2C8 CYP2C8 CYP2C8 4171 0.14 0.7 NO
39 FMO5 FMO5 FMO5 4332 0.14 0.7 NO
40 GSTM1 GSTM1 GSTM1 5013 0.12 0.67 NO
41 ADH4 ADH4 ADH4 5324 0.11 0.66 NO
42 MGST2 MGST2 MGST2 6075 0.09 0.62 NO
43 GSTT1 GSTT1 GSTT1 6329 0.084 0.61 NO
44 FMO4 FMO4 FMO4 6765 0.074 0.59 NO
45 CYP2B6 CYP2B6 CYP2B6 7726 0.055 0.55 NO
46 ADH5 ADH5 ADH5 8616 0.039 0.5 NO
47 CYP3A4 CYP3A4 CYP3A4 8674 0.038 0.5 NO
48 GSTM5 GSTM5 GSTM5 8852 0.035 0.49 NO
49 ALDH3B1 ALDH3B1 ALDH3B1 9129 0.031 0.48 NO
50 GSTO2 GSTO2 GSTO2 10394 0.012 0.41 NO
51 ALDH1A3 ALDH1A3 ALDH1A3 11244 -0.00036 0.36 NO
52 MGST3 MGST3 MGST3 11968 -0.012 0.32 NO
53 GSTZ1 GSTZ1 GSTZ1 12195 -0.015 0.31 NO
54 GSTT2 GSTT2 GSTT2 12311 -0.017 0.31 NO
55 AOX1 AOX1 AOX1 13172 -0.032 0.26 NO
56 GSTK1 GSTK1 GSTK1 13767 -0.043 0.23 NO
57 FMO1 FMO1 FMO1 13862 -0.045 0.23 NO
58 GSTP1 GSTP1 GSTP1 14076 -0.05 0.22 NO
59 GSTO1 GSTO1 GSTO1 14866 -0.07 0.18 NO
60 ALDH3B2 ALDH3B2 ALDH3B2 16098 -0.12 0.12 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S44.  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 STARCH AND SUCROSE 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 UGT1A6 UGT1A6 UGT1A6 70 0.66 0.072 YES
2 UGT1A9 UGT1A9 UGT1A9 100 0.62 0.14 YES
3 UGT2A1 UGT2A1 UGT2A1 187 0.55 0.2 YES
4 UGT1A7 UGT1A7 UGT1A7 196 0.55 0.26 YES
5 UGT1A8 UGT1A8 UGT1A8 215 0.54 0.32 YES
6 UGT1A3 UGT1A3 UGT1A3 424 0.47 0.37 YES
7 GCK GCK GCK 484 0.45 0.41 YES
8 AMY2B AMY2B AMY2B 603 0.42 0.46 YES
9 ENPP3 ENPP3 ENPP3 893 0.37 0.48 YES
10 AMY1A AMY1A AMY1A 943 0.37 0.52 YES
11 AMY2A AMY2A AMY2A 1075 0.35 0.56 YES
12 UGT1A4 UGT1A4 UGT1A4 1491 0.3 0.57 YES
13 UGT1A10 UGT1A10 UGT1A10 1747 0.28 0.58 YES
14 GBA3 GBA3 GBA3 1778 0.28 0.62 YES
15 UGT1A1 UGT1A1 UGT1A1 2054 0.25 0.63 YES
16 UGT2B15 UGT2B15 UGT2B15 2565 0.22 0.63 YES
17 TREH TREH TREH 2610 0.22 0.65 YES
18 UGT2B7 UGT2B7 UGT2B7 3981 0.15 0.59 NO
19 UGDH UGDH UGDH 4216 0.14 0.59 NO
20 AGL AGL AGL 5138 0.11 0.56 NO
21 UXS1 UXS1 UXS1 5829 0.095 0.53 NO
22 GUSB GUSB GUSB 6487 0.08 0.5 NO
23 GYS2 GYS2 GYS2 7083 0.067 0.48 NO
24 GPI GPI GPI 8096 0.048 0.43 NO
25 GAA GAA GAA 8545 0.04 0.41 NO
26 GBE1 GBE1 GBE1 10820 0.0056 0.29 NO
27 HK1 HK1 HK1 11153 0.0011 0.27 NO
28 PGM2 PGM2 PGM2 11441 -0.0033 0.25 NO
29 ENPP1 ENPP1 ENPP1 12036 -0.012 0.22 NO
30 UGP2 UGP2 UGP2 12215 -0.015 0.21 NO
31 PGM2L1 PGM2L1 PGM2L1 13038 -0.03 0.17 NO
32 HK2 HK2 HK2 13355 -0.036 0.16 NO
33 PYGB PYGB PYGB 14935 -0.072 0.081 NO
34 PGM1 PGM1 PGM1 15097 -0.077 0.081 NO
35 HK3 HK3 HK3 15231 -0.082 0.083 NO
36 GYS1 GYS1 GYS1 15372 -0.087 0.085 NO
37 GANC GANC GANC 15390 -0.088 0.094 NO
38 MGAM MGAM MGAM 16030 -0.12 0.073 NO
39 PYGM PYGM PYGM 16926 -0.18 0.044 NO
40 PYGL PYGL PYGL 17762 -0.3 0.033 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 STARCH AND SUCROSE METABOLISM.

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

genes ES table in pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 UGT1A6 UGT1A6 UGT1A6 70 0.66 0.1 YES
2 UGT1A9 UGT1A9 UGT1A9 100 0.62 0.2 YES
3 CP CP CP 133 0.59 0.29 YES
4 UGT2A1 UGT2A1 UGT2A1 187 0.55 0.37 YES
5 UGT1A7 UGT1A7 UGT1A7 196 0.55 0.46 YES
6 UGT1A8 UGT1A8 UGT1A8 215 0.54 0.54 YES
7 UGT1A3 UGT1A3 UGT1A3 424 0.47 0.6 YES
8 UGT1A4 UGT1A4 UGT1A4 1491 0.3 0.59 YES
9 UGT1A10 UGT1A10 UGT1A10 1747 0.28 0.62 YES
10 UGT1A1 UGT1A1 UGT1A1 2054 0.25 0.64 YES
11 UGT2B15 UGT2B15 UGT2B15 2565 0.22 0.65 YES
12 UGT2B7 UGT2B7 UGT2B7 3981 0.15 0.6 NO
13 FECH FECH FECH 4693 0.13 0.58 NO
14 PPOX PPOX PPOX 5282 0.11 0.56 NO
15 CPOX CPOX CPOX 5807 0.096 0.55 NO
16 GUSB GUSB GUSB 6487 0.08 0.53 NO
17 MMAB MMAB MMAB 6635 0.076 0.53 NO
18 BLVRB BLVRB BLVRB 8175 0.047 0.45 NO
19 ALAD ALAD ALAD 8738 0.037 0.43 NO
20 EARS2 EARS2 EARS2 8868 0.035 0.43 NO
21 EPRS EPRS EPRS 9204 0.03 0.41 NO
22 COX10 COX10 COX10 9542 0.025 0.4 NO
23 COX15 COX15 COX15 9702 0.022 0.39 NO
24 ALAS1 ALAS1 ALAS1 9709 0.022 0.4 NO
25 FTH1 FTH1 FTH1 12130 -0.014 0.27 NO
26 HCCS HCCS HCCS 12279 -0.016 0.26 NO
27 UROS UROS UROS 12611 -0.022 0.25 NO
28 HMOX1 HMOX1 HMOX1 13025 -0.029 0.23 NO
29 BLVRA BLVRA BLVRA 13546 -0.039 0.21 NO
30 HMBS HMBS HMBS 13847 -0.045 0.2 NO
31 UROD UROD UROD 14919 -0.071 0.15 NO
32 ALAS2 ALAS2 ALAS2 15409 -0.088 0.14 NO
33 HMOX2 HMOX2 HMOX2 16567 -0.15 0.098 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

Figure S48.  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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

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 CLDN3 CLDN3 CLDN3 8 0.87 0.14 YES
2 PARD6A PARD6A PARD6A 137 0.59 0.22 YES
3 CLDN10 CLDN10 CLDN10 217 0.54 0.3 YES
4 CLDN7 CLDN7 CLDN7 447 0.46 0.36 YES
5 CLDN20 CLDN20 CLDN20 451 0.46 0.43 YES
6 CLDN8 CLDN8 CLDN8 506 0.44 0.49 YES
7 CLDN16 CLDN16 CLDN16 1310 0.32 0.5 YES
8 CLDN4 CLDN4 CLDN4 1320 0.32 0.55 YES
9 PARD6B PARD6B PARD6B 1327 0.32 0.6 YES
10 CLDN18 CLDN18 CLDN18 2026 0.26 0.6 YES
11 CLDN2 CLDN2 CLDN2 2252 0.24 0.62 YES
12 CLDN15 CLDN15 CLDN15 2482 0.22 0.65 YES
13 CRB3 CRB3 CRB3 2638 0.22 0.67 YES
14 CLDN11 CLDN11 CLDN11 3850 0.16 0.63 NO
15 PARD3 PARD3 PARD3 3893 0.15 0.65 NO
16 CLDN1 CLDN1 CLDN1 4466 0.14 0.64 NO
17 PRKCI PRKCI PRKCI 5225 0.11 0.62 NO
18 CLDN6 CLDN6 CLDN6 6022 0.091 0.59 NO
19 F11R F11R F11R 6188 0.087 0.59 NO
20 CLDN19 CLDN19 CLDN19 6808 0.073 0.57 NO
21 CLDN9 CLDN9 CLDN9 7646 0.057 0.53 NO
22 PARD6G PARD6G PARD6G 7683 0.056 0.54 NO
23 CLDN5 CLDN5 CLDN5 7712 0.056 0.55 NO
24 INADL INADL INADL 8872 0.035 0.49 NO
25 CLDN14 CLDN14 CLDN14 9716 0.022 0.45 NO
26 CLDN12 CLDN12 CLDN12 10768 0.0066 0.39 NO
27 MPP5 MPP5 MPP5 13317 -0.035 0.26 NO
28 CLDN17 CLDN17 CLDN17 16187 -0.12 0.12 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG BUTANOATE 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 GSTA1 GSTA1 GSTA1 20 0.78 0.047 YES
2 ADH7 ADH7 ADH7 47 0.7 0.089 YES
3 UGT1A6 UGT1A6 UGT1A6 70 0.66 0.13 YES
4 ALDH3A1 ALDH3A1 ALDH3A1 89 0.63 0.17 YES
5 UGT1A9 UGT1A9 UGT1A9 100 0.62 0.2 YES
6 ADH1C ADH1C ADH1C 120 0.61 0.24 YES
7 CYP2F1 CYP2F1 CYP2F1 127 0.6 0.28 YES
8 GSTA2 GSTA2 GSTA2 139 0.59 0.31 YES
9 UGT2A1 UGT2A1 UGT2A1 187 0.55 0.34 YES
10 UGT1A7 UGT1A7 UGT1A7 196 0.55 0.38 YES
11 UGT1A8 UGT1A8 UGT1A8 215 0.54 0.41 YES
12 ADH6 ADH6 ADH6 267 0.52 0.44 YES
13 UGT1A3 UGT1A3 UGT1A3 424 0.47 0.46 YES
14 CYP2C19 CYP2C19 CYP2C19 438 0.46 0.49 YES
15 CYP2E1 CYP2E1 CYP2E1 454 0.46 0.52 YES
16 CYP2C18 CYP2C18 CYP2C18 714 0.4 0.53 YES
17 CYP2C9 CYP2C9 CYP2C9 739 0.4 0.55 YES
18 CYP2S1 CYP2S1 CYP2S1 772 0.39 0.57 YES
19 GSTM4 GSTM4 GSTM4 1158 0.34 0.57 YES
20 GSTM2 GSTM2 GSTM2 1210 0.33 0.59 YES
21 MGST1 MGST1 MGST1 1275 0.32 0.61 YES
22 UGT1A4 UGT1A4 UGT1A4 1491 0.3 0.61 YES
23 CYP3A5 CYP3A5 CYP3A5 1531 0.3 0.63 YES
24 GSTM3 GSTM3 GSTM3 1538 0.3 0.65 YES
25 UGT1A10 UGT1A10 UGT1A10 1747 0.28 0.65 YES
26 UGT1A1 UGT1A1 UGT1A1 2054 0.25 0.65 YES
27 ADH1A ADH1A ADH1A 2233 0.24 0.66 YES
28 EPHX1 EPHX1 EPHX1 2265 0.24 0.67 YES
29 DHDH DHDH DHDH 2268 0.24 0.69 YES
30 GSTA3 GSTA3 GSTA3 2377 0.23 0.69 YES
31 GSTA4 GSTA4 GSTA4 2449 0.23 0.7 YES
32 AKR1C1 AKR1C1 AKR1C1 2554 0.22 0.71 YES
33 UGT2B15 UGT2B15 UGT2B15 2565 0.22 0.72 YES
34 CYP3A7 CYP3A7 CYP3A7 3023 0.19 0.71 NO
35 AKR1C2 AKR1C2 AKR1C2 3254 0.18 0.71 NO
36 CYP1B1 CYP1B1 CYP1B1 3342 0.18 0.72 NO
37 CYP1A1 CYP1A1 CYP1A1 3973 0.15 0.69 NO
38 UGT2B7 UGT2B7 UGT2B7 3981 0.15 0.7 NO
39 ADH1B ADH1B ADH1B 4082 0.15 0.7 NO
40 CYP2C8 CYP2C8 CYP2C8 4171 0.14 0.71 NO
41 AKR1C3 AKR1C3 AKR1C3 4735 0.13 0.69 NO
42 GSTM1 GSTM1 GSTM1 5013 0.12 0.68 NO
43 ADH4 ADH4 ADH4 5324 0.11 0.67 NO
44 MGST2 MGST2 MGST2 6075 0.09 0.63 NO
45 GSTT1 GSTT1 GSTT1 6329 0.084 0.62 NO
46 CYP2B6 CYP2B6 CYP2B6 7726 0.055 0.55 NO
47 ADH5 ADH5 ADH5 8616 0.039 0.5 NO
48 CYP3A4 CYP3A4 CYP3A4 8674 0.038 0.5 NO
49 GSTM5 GSTM5 GSTM5 8852 0.035 0.5 NO
50 ALDH3B1 ALDH3B1 ALDH3B1 9129 0.031 0.48 NO
51 GSTO2 GSTO2 GSTO2 10394 0.012 0.42 NO
52 ALDH1A3 ALDH1A3 ALDH1A3 11244 -0.00036 0.37 NO
53 MGST3 MGST3 MGST3 11968 -0.012 0.33 NO
54 GSTZ1 GSTZ1 GSTZ1 12195 -0.015 0.32 NO
55 GSTT2 GSTT2 GSTT2 12311 -0.017 0.31 NO
56 GSTK1 GSTK1 GSTK1 13767 -0.043 0.24 NO
57 GSTP1 GSTP1 GSTP1 14076 -0.05 0.22 NO
58 GSTO1 GSTO1 GSTO1 14866 -0.07 0.18 NO
59 ALDH3B2 ALDH3B2 ALDH3B2 16098 -0.12 0.12 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 BUTANOATE METABOLISM.

Figure S52.  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 PORPHYRIN AND CHLOROPHYLL 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 BARD1 BARD1 BARD1 1228 0.33 0.052 YES
2 FANCL FANCL FANCL 1776 0.28 0.12 YES
3 TP53 TP53 TP53 2997 0.2 0.12 YES
4 TOPBP1 TOPBP1 TOPBP1 3367 0.18 0.17 YES
5 BRCA1 BRCA1 BRCA1 3423 0.17 0.23 YES
6 FANCD2 FANCD2 FANCD2 3447 0.17 0.29 YES
7 FANCC FANCC FANCC 3919 0.15 0.32 YES
8 RBBP8 RBBP8 RBBP8 4577 0.13 0.33 YES
9 FANCE FANCE FANCE 4636 0.13 0.37 YES
10 ATR ATR ATR 5216 0.11 0.38 YES
11 ATM ATM ATM 5434 0.11 0.41 YES
12 FANCA FANCA FANCA 5498 0.1 0.44 YES
13 CDK2 CDK2 CDK2 5590 0.1 0.47 YES
14 PCNA PCNA PCNA 5852 0.094 0.49 YES
15 RAD51 RAD51 RAD51 6356 0.083 0.5 YES
16 FANCG FANCG FANCG 6422 0.081 0.52 YES
17 MRE11A MRE11A MRE11A 6621 0.076 0.54 YES
18 PRKDC PRKDC PRKDC 9029 0.033 0.42 NO
19 XRCC5 XRCC5 XRCC5 9527 0.025 0.4 NO
20 CSTF1 CSTF1 CSTF1 9722 0.022 0.4 NO
21 CCNE1 CCNE1 CCNE1 9729 0.022 0.4 NO
22 NBN NBN NBN 10272 0.014 0.38 NO
23 EWSR1 EWSR1 EWSR1 10736 0.0071 0.36 NO
24 XRCC6 XRCC6 XRCC6 11260 -0.00057 0.33 NO
25 RAD50 RAD50 RAD50 12384 -0.018 0.28 NO
26 FANCF FANCF FANCF 12669 -0.023 0.27 NO
27 UBE2D3 UBE2D3 UBE2D3 13486 -0.038 0.24 NO
28 NPM1 NPM1 NPM1 13566 -0.039 0.25 NO
29 UBE2L3 UBE2L3 UBE2L3 13695 -0.042 0.26 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

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

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

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 BRIP1 BRIP1 BRIP1 1564 0.3 -0.03 YES
2 SSPO SSPO SSPO 1703 0.28 0.016 YES
3 FANCL FANCL FANCL 1776 0.28 0.064 YES
4 BRCA2 BRCA2 BRCA2 2196 0.24 0.086 YES
5 FANCB FANCB FANCB 2642 0.22 0.1 YES
6 RFC5 RFC5 RFC5 2840 0.2 0.13 YES
7 BLM BLM BLM 3170 0.19 0.15 YES
8 RMI1 RMI1 RMI1 3172 0.19 0.18 YES
9 RFC4 RFC4 RFC4 3180 0.19 0.22 YES
10 UBE2T UBE2T UBE2T 3223 0.18 0.25 YES
11 APITD1 APITD1 APITD1 3355 0.18 0.27 YES
12 TOPBP1 TOPBP1 TOPBP1 3367 0.18 0.31 YES
13 BRCA1 BRCA1 BRCA1 3423 0.17 0.34 YES
14 FANCD2 FANCD2 FANCD2 3447 0.17 0.37 YES
15 FANCC FANCC FANCC 3919 0.15 0.37 YES
16 FANCE FANCE FANCE 4636 0.13 0.36 YES
17 C19orf40 C19orf40 C19orf40 4804 0.12 0.37 YES
18 FANCI FANCI FANCI 4852 0.12 0.39 YES
19 ATR ATR ATR 5216 0.11 0.39 YES
20 RFC3 RFC3 RFC3 5376 0.11 0.4 YES
21 RAD1 RAD1 RAD1 5430 0.11 0.42 YES
22 ATM ATM ATM 5434 0.11 0.44 YES
23 USP1 USP1 USP1 5468 0.1 0.46 YES
24 FANCA FANCA FANCA 5498 0.1 0.47 YES
25 RPA2 RPA2 RPA2 5579 0.1 0.49 YES
26 WDR48 WDR48 WDR48 5735 0.097 0.5 YES
27 FANCM FANCM FANCM 6001 0.091 0.5 YES
28 RFC2 RFC2 RFC2 6047 0.09 0.52 YES
29 FANCG FANCG FANCG 6422 0.081 0.51 YES
30 RPA1 RPA1 RPA1 6501 0.08 0.52 YES
31 HES1 HES1 HES1 6565 0.078 0.53 YES
32 MRE11A MRE11A MRE11A 6621 0.076 0.54 YES
33 PALB2 PALB2 PALB2 7082 0.067 0.53 NO
34 TOP3A TOP3A TOP3A 7323 0.063 0.53 NO
35 XRCC3 XRCC3 XRCC3 7375 0.062 0.54 NO
36 H2AFX H2AFX H2AFX 7660 0.057 0.53 NO
37 RAD17 RAD17 RAD17 8155 0.047 0.52 NO
38 CHEK1 CHEK1 CHEK1 8301 0.044 0.52 NO
39 FBXW11 FBXW11 FBXW11 8758 0.037 0.5 NO
40 RAD9A RAD9A RAD9A 9395 0.027 0.47 NO
41 NBN NBN NBN 10272 0.014 0.42 NO
42 ATRIP ATRIP ATRIP 11768 -0.0081 0.34 NO
43 C17orf70 C17orf70 C17orf70 11992 -0.012 0.33 NO
44 RAD50 RAD50 RAD50 12384 -0.018 0.32 NO
45 FANCF FANCF FANCF 12669 -0.023 0.3 NO
46 HUS1 HUS1 HUS1 13548 -0.039 0.26 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM CYTOCHROME P450

Table 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 ACSM3 ACSM3 ACSM3 365 0.49 0.11 YES
2 ALDH5A1 ALDH5A1 ALDH5A1 392 0.48 0.24 YES
3 ABAT ABAT ABAT 1840 0.27 0.24 YES
4 ACSM1 ACSM1 ACSM1 2306 0.24 0.28 YES
5 GAD1 GAD1 GAD1 2661 0.21 0.32 YES
6 HMGCS2 HMGCS2 HMGCS2 3111 0.19 0.35 YES
7 ACAT2 ACAT2 ACAT2 3184 0.19 0.4 YES
8 L2HGDH L2HGDH L2HGDH 3965 0.15 0.39 YES
9 ALDH3A2 ALDH3A2 ALDH3A2 4030 0.15 0.43 YES
10 HADH HADH HADH 4662 0.13 0.43 YES
11 ACADS ACADS ACADS 4682 0.13 0.47 YES
12 EHHADH EHHADH EHHADH 4811 0.12 0.49 YES
13 BDH1 BDH1 BDH1 5107 0.12 0.51 YES
14 BDH2 BDH2 BDH2 5429 0.11 0.52 YES
15 ALDH9A1 ALDH9A1 ALDH9A1 7270 0.064 0.44 NO
16 OXCT1 OXCT1 OXCT1 7508 0.059 0.44 NO
17 PDHA1 PDHA1 PDHA1 8323 0.044 0.41 NO
18 ALDH2 ALDH2 ALDH2 8544 0.04 0.41 NO
19 ACSM5 ACSM5 ACSM5 8799 0.036 0.4 NO
20 HMGCS1 HMGCS1 HMGCS1 9258 0.029 0.39 NO
21 PDHB PDHB PDHB 9538 0.025 0.38 NO
22 AACS AACS AACS 9615 0.023 0.38 NO
23 ECHS1 ECHS1 ECHS1 10840 0.0054 0.32 NO
24 ALDH1B1 ALDH1B1 ALDH1B1 11270 -0.00071 0.29 NO
25 AKR1B10 AKR1B10 AKR1B10 11899 -0.01 0.26 NO
26 OXCT2 OXCT2 OXCT2 12646 -0.022 0.23 NO
27 ACAT1 ACAT1 ACAT1 12925 -0.028 0.22 NO
28 HADHA HADHA HADHA 13253 -0.034 0.21 NO
29 HMGCL HMGCL HMGCL 13417 -0.036 0.21 NO
30 ALDH7A1 ALDH7A1 ALDH7A1 17268 -0.21 0.06 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 DRUG METABOLISM CYTOCHROME P450.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID FANCONI PATHWAY

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 NUP210 NUP210 NUP210 594 0.42 0.16 YES
2 SLC25A4 SLC25A4 SLC25A4 2649 0.22 0.14 YES
3 PSIP1 PSIP1 PSIP1 2722 0.21 0.24 YES
4 SEH1L SEH1L SEH1L 6320 0.084 0.078 YES
5 NUP43 NUP43 NUP43 6398 0.082 0.11 YES
6 NUP35 NUP35 NUP35 6489 0.08 0.14 YES
7 TPR TPR TPR 6563 0.078 0.17 YES
8 NUP205 NUP205 NUP205 6603 0.077 0.21 YES
9 NUP155 NUP155 NUP155 6823 0.072 0.23 YES
10 NUP153 NUP153 NUP153 7188 0.066 0.24 YES
11 POM121 POM121 POM121 7369 0.062 0.26 YES
12 HMGA1 HMGA1 HMGA1 7478 0.06 0.28 YES
13 NUP107 NUP107 NUP107 7781 0.054 0.28 YES
14 NUP62 NUP62 NUP62 7895 0.052 0.3 YES
15 NUP133 NUP133 NUP133 7911 0.052 0.32 YES
16 NUP88 NUP88 NUP88 7922 0.052 0.35 YES
17 NUPL2 NUPL2 NUPL2 7936 0.051 0.37 YES
18 NUP50 NUP50 NUP50 8113 0.048 0.38 YES
19 NUP188 NUP188 NUP188 8244 0.045 0.4 YES
20 NUP214 NUP214 NUP214 8531 0.04 0.4 YES
21 SLC25A6 SLC25A6 SLC25A6 8679 0.038 0.41 YES
22 AAAS AAAS AAAS 8739 0.037 0.42 YES
23 KPNA1 KPNA1 KPNA1 8817 0.036 0.43 YES
24 NUP54 NUP54 NUP54 8875 0.035 0.45 YES
25 NUP85 NUP85 NUP85 9346 0.028 0.43 NO
26 RANBP2 RANBP2 RANBP2 9573 0.024 0.43 NO
27 SLC25A5 SLC25A5 SLC25A5 9753 0.021 0.43 NO
28 RAE1 RAE1 RAE1 9858 0.02 0.44 NO
29 NUPL1 NUPL1 NUPL1 10869 0.005 0.38 NO
30 NUP37 NUP37 NUP37 11862 -0.0096 0.33 NO
31 NUP93 NUP93 NUP93 11891 -0.01 0.34 NO
32 BANF1 BANF1 BANF1 13501 -0.038 0.26 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: PID FANCONI PATHWAY.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: PID FANCONI 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 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 GLYCOLYSIS GLUCONEOGENESIS 58 genes.ES.table 0.47 1.5 0.053 0.12 0.98 0.22 0.17 0.19 0.077 0
KEGG PURINE METABOLISM 154 genes.ES.table 0.43 1.7 0.002 0.067 0.84 0.16 0.13 0.14 0.027 0.001
KEGG ARGININE AND PROLINE METABOLISM 52 genes.ES.table 0.48 1.6 0.0042 0.086 0.93 0.14 0.11 0.12 0.042 0
KEGG TYROSINE METABOLISM 41 genes.ES.table 0.47 1.3 0.18 0.25 1 0.27 0.17 0.22 0.21 0
KEGG GLYCEROLIPID METABOLISM 43 genes.ES.table 0.41 1.4 0.071 0.18 1 0.3 0.22 0.24 0.14 0
KEGG INOSITOL PHOSPHATE METABOLISM 54 genes.ES.table 0.36 1.3 0.11 0.21 1 0.43 0.32 0.29 0.17 0
KEGG GLYCEROPHOSPHOLIPID METABOLISM 73 genes.ES.table 0.49 1.8 0.0021 0.043 0.52 0.22 0.19 0.18 0.011 0.001
KEGG ETHER LIPID METABOLISM 29 genes.ES.table 0.46 1.3 0.12 0.22 1 0.34 0.21 0.27 0.18 0
KEGG ABC TRANSPORTERS 43 genes.ES.table 0.48 1.3 0.13 0.24 1 0.23 0.14 0.2 0.2 0
KEGG RNA DEGRADATION 57 genes.ES.table 0.31 1.4 0.16 0.18 1 0.018 0.0059 0.018 0.14 0
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 ASB5 ASB5 ASB5 21 1.5 0.1 YES
2 TRIM63 TRIM63 TRIM63 59 1.3 0.2 YES
3 ASB15 ASB15 ASB15 122 1.1 0.27 YES
4 ASB11 ASB11 ASB11 176 0.85 0.33 YES
5 ASB12 ASB12 ASB12 234 0.7 0.38 YES
6 ZBTB16 ZBTB16 ZBTB16 251 0.66 0.42 YES
7 ASB16 ASB16 ASB16 310 0.58 0.46 YES
8 PARK2 PARK2 PARK2 404 0.5 0.49 YES
9 ASB4 ASB4 ASB4 519 0.43 0.51 YES
10 SPSB4 SPSB4 SPSB4 1226 0.28 0.5 NO
11 ASB2 ASB2 ASB2 1719 0.22 0.48 NO
12 DET1 DET1 DET1 2530 0.16 0.45 NO
13 NEDD4 NEDD4 NEDD4 2806 0.14 0.45 NO
14 TRIM9 TRIM9 TRIM9 3210 0.12 0.43 NO
15 CBLB CBLB CBLB 3477 0.11 0.43 NO
16 UBE2D4 UBE2D4 UBE2D4 3536 0.11 0.43 NO
17 LNPEP LNPEP LNPEP 3864 0.096 0.42 NO
18 FBXO2 FBXO2 FBXO2 3952 0.092 0.42 NO
19 SPSB1 SPSB1 SPSB1 4040 0.089 0.42 NO
20 TRIM21 TRIM21 TRIM21 4161 0.084 0.42 NO
21 ASB8 ASB8 ASB8 4174 0.084 0.43 NO
22 UBR1 UBR1 UBR1 4378 0.077 0.42 NO
23 UBR2 UBR2 UBR2 4468 0.074 0.42 NO
24 TRIM32 TRIM32 TRIM32 4600 0.07 0.42 NO
25 TRIM36 TRIM36 TRIM36 4781 0.066 0.42 NO
26 PSMB9 PSMB9 PSMB9 4886 0.062 0.41 NO
27 UBE2L6 UBE2L6 UBE2L6 4968 0.06 0.41 NO
28 ASB1 ASB1 ASB1 5045 0.058 0.41 NO
29 PJA2 PJA2 PJA2 5182 0.055 0.41 NO
30 DZIP3 DZIP3 DZIP3 5263 0.053 0.41 NO
31 FBXO17 FBXO17 FBXO17 5319 0.052 0.41 NO
32 UBA7 UBA7 UBA7 5407 0.049 0.41 NO
33 DTX3L DTX3L DTX3L 5409 0.049 0.41 NO
34 SMURF2 SMURF2 SMURF2 5504 0.047 0.41 NO
35 UBE2D1 UBE2D1 UBE2D1 5581 0.045 0.41 NO
36 RNF123 RNF123 RNF123 5643 0.044 0.41 NO
37 UBE2H UBE2H UBE2H 5675 0.043 0.41 NO
38 WWP1 WWP1 WWP1 5759 0.042 0.41 NO
39 HECTD3 HECTD3 HECTD3 5792 0.041 0.41 NO
40 UBE2Q2 UBE2Q2 UBE2Q2 5794 0.041 0.41 NO
41 CUL5 CUL5 CUL5 5873 0.04 0.41 NO
42 SOCS3 SOCS3 SOCS3 6036 0.037 0.41 NO
43 TRIP12 TRIP12 TRIP12 6053 0.037 0.41 NO
44 TPP2 TPP2 TPP2 6186 0.035 0.4 NO
45 CDC27 CDC27 CDC27 6246 0.034 0.4 NO
46 PSMB10 PSMB10 PSMB10 6253 0.034 0.4 NO
47 SMURF1 SMURF1 SMURF1 6418 0.031 0.4 NO
48 KLHL20 KLHL20 KLHL20 6457 0.031 0.4 NO
49 HERC2 HERC2 HERC2 6501 0.03 0.4 NO
50 FBXW7 FBXW7 FBXW7 6645 0.028 0.39 NO
51 UBOX5 UBOX5 UBOX5 6686 0.027 0.39 NO
52 CUL7 CUL7 CUL7 6693 0.027 0.39 NO
53 UBE4A UBE4A UBE4A 6830 0.025 0.39 NO
54 UBE2R2 UBE2R2 UBE2R2 6840 0.025 0.39 NO
55 PSMD1 PSMD1 PSMD1 6850 0.025 0.39 NO
56 UBE3B UBE3B UBE3B 6890 0.024 0.39 NO
57 ASB13 ASB13 ASB13 6891 0.024 0.39 NO
58 UBR4 UBR4 UBR4 6930 0.024 0.39 NO
59 PSMB8 PSMB8 PSMB8 6938 0.024 0.39 NO
60 UBE3C UBE3C UBE3C 7117 0.021 0.38 NO
61 FBXO3 FBXO3 FBXO3 7147 0.021 0.38 NO
62 FBXW8 FBXW8 FBXW8 7182 0.02 0.38 NO
63 PSMF1 PSMF1 PSMF1 7186 0.02 0.38 NO
64 RNF41 RNF41 RNF41 7291 0.019 0.38 NO
65 UBE2W UBE2W UBE2W 7303 0.019 0.38 NO
66 LRSAM1 LRSAM1 LRSAM1 7336 0.018 0.38 NO
67 PSMD5 PSMD5 PSMD5 7513 0.016 0.37 NO
68 RBCK1 RBCK1 RBCK1 7547 0.016 0.37 NO
69 RNF4 RNF4 RNF4 7561 0.016 0.37 NO
70 ASB7 ASB7 ASB7 7595 0.016 0.37 NO
71 FBXO27 FBXO27 FBXO27 7601 0.016 0.37 NO
72 RNF34 RNF34 RNF34 7668 0.015 0.37 NO
73 HUWE1 HUWE1 HUWE1 7692 0.014 0.37 NO
74 PJA1 PJA1 PJA1 7697 0.014 0.37 NO
75 RNF6 RNF6 RNF6 7770 0.013 0.37 NO
76 UBE2F UBE2F UBE2F 7847 0.012 0.36 NO
77 PSMD2 PSMD2 PSMD2 7872 0.012 0.36 NO
78 BTRC BTRC BTRC 7934 0.011 0.36 NO
79 UBE2G1 UBE2G1 UBE2G1 7950 0.011 0.36 NO
80 KLHL9 KLHL9 KLHL9 8056 0.01 0.36 NO
81 PSME2 PSME2 PSME2 8059 0.0099 0.36 NO
82 PSME1 PSME1 PSME1 8360 0.0065 0.34 NO
83 FBXO6 FBXO6 FBXO6 8415 0.0059 0.34 NO
84 PSMC2 PSMC2 PSMC2 8478 0.0052 0.33 NO
85 RNF25 RNF25 RNF25 8492 0.0051 0.33 NO
86 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 8499 0.005 0.33 NO
87 PSMD7 PSMD7 PSMD7 8578 0.0042 0.33 NO
88 KLHL13 KLHL13 KLHL13 8618 0.0039 0.33 NO
89 UBE2Z UBE2Z UBE2Z 8623 0.0038 0.33 NO
90 RNF144B RNF144B RNF144B 8627 0.0038 0.33 NO
91 UBE2J1 UBE2J1 UBE2J1 8681 0.0033 0.32 NO
92 RCHY1 RCHY1 RCHY1 8854 0.0016 0.32 NO
93 TRIM37 TRIM37 TRIM37 8896 0.0011 0.31 NO
94 UBE3A UBE3A UBE3A 9096 -0.00097 0.3 NO
95 ARIH2 ARIH2 ARIH2 9141 -0.0014 0.3 NO
96 PSMD13 PSMD13 PSMD13 9144 -0.0014 0.3 NO
97 PSMD11 PSMD11 PSMD11 9178 -0.0017 0.3 NO
98 UBE2L3 UBE2L3 UBE2L3 9189 -0.0018 0.3 NO
99 PSMA7 PSMA7 PSMA7 9213 -0.0021 0.3 NO
100 CUL2 CUL2 CUL2 9224 -0.0022 0.3 NO
101 ATG7 ATG7 ATG7 9239 -0.0023 0.3 NO
102 CUL3 CUL3 CUL3 9265 -0.0025 0.3 NO
103 CUL1 CUL1 CUL1 9266 -0.0025 0.3 NO
104 MKRN1 MKRN1 MKRN1 9314 -0.003 0.29 NO
105 PSME4 PSME4 PSME4 9336 -0.0032 0.29 NO
106 VPRBP VPRBP VPRBP 9381 -0.0036 0.29 NO
107 PSMB5 PSMB5 PSMB5 9384 -0.0036 0.29 NO
108 UBE2A UBE2A UBE2A 9401 -0.0038 0.29 NO
109 FBXW11 FBXW11 FBXW11 9406 -0.0038 0.29 NO
110 PSMC3 PSMC3 PSMC3 9536 -0.0051 0.28 NO
111 LRRC41 LRRC41 LRRC41 9591 -0.0057 0.28 NO
112 ANAPC1 ANAPC1 ANAPC1 9661 -0.0064 0.28 NO
113 SPSB2 SPSB2 SPSB2 9668 -0.0064 0.28 NO
114 CDC16 CDC16 CDC16 9691 -0.0066 0.28 NO
115 ANAPC5 ANAPC5 ANAPC5 9733 -0.0071 0.27 NO
116 PSMB2 PSMB2 PSMB2 9779 -0.0075 0.27 NO
117 UBE2G2 UBE2G2 UBE2G2 9814 -0.0078 0.27 NO
118 RNF220 RNF220 RNF220 9920 -0.0088 0.27 NO
119 PSMC6 PSMC6 PSMC6 9972 -0.0092 0.26 NO
120 UBE2D3 UBE2D3 UBE2D3 9986 -0.0094 0.26 NO
121 PSMA8 PSMA8 PSMA8 9989 -0.0094 0.26 NO
122 UBE2K UBE2K UBE2K 10005 -0.0096 0.26 NO
123 UBE2B UBE2B UBE2B 10016 -0.0097 0.26 NO
124 PSMA1 PSMA1 PSMA1 10180 -0.011 0.26 NO
125 PSMB6 PSMB6 PSMB6 10261 -0.012 0.25 NO
126 UBA1 UBA1 UBA1 10312 -0.012 0.25 NO
127 PSMC1 PSMC1 PSMC1 10585 -0.015 0.24 NO
128 PSMC5 PSMC5 PSMC5 10654 -0.016 0.23 NO
129 PSMD12 PSMD12 PSMD12 10658 -0.016 0.24 NO
130 PSMA5 PSMA5 PSMA5 10753 -0.017 0.23 NO
131 UBE2O UBE2O UBE2O 10774 -0.017 0.23 NO
132 SKP1 SKP1 SKP1 10800 -0.017 0.23 NO
133 PSMD8 PSMD8 PSMD8 10808 -0.017 0.23 NO
134 PSMD9 PSMD9 PSMD9 10879 -0.018 0.23 NO
135 PSMA6 PSMA6 PSMA6 10928 -0.018 0.23 NO
136 PSMC4 PSMC4 PSMC4 10961 -0.019 0.23 NO
137 CDC26 CDC26 CDC26 11006 -0.019 0.23 NO
138 PSMA3 PSMA3 PSMA3 11012 -0.019 0.23 NO
139 PSMD3 PSMD3 PSMD3 11028 -0.019 0.23 NO
140 UBE2V2 UBE2V2 UBE2V2 11155 -0.021 0.22 NO
141 PSMD10 PSMD10 PSMD10 11158 -0.021 0.22 NO
142 UBA3 UBA3 UBA3 11190 -0.021 0.22 NO
143 NPEPPS NPEPPS NPEPPS 11272 -0.022 0.22 NO
144 ANAPC13 ANAPC13 ANAPC13 11277 -0.022 0.22 NO
145 UBE2Q1 UBE2Q1 UBE2Q1 11397 -0.023 0.22 NO
146 PSMB1 PSMB1 PSMB1 11401 -0.023 0.22 NO
147 ANAPC2 ANAPC2 ANAPC2 11422 -0.023 0.22 NO
148 CDC23 CDC23 CDC23 11493 -0.024 0.22 NO
149 UBE2E3 UBE2E3 UBE2E3 11722 -0.026 0.21 NO
150 UBE2E2 UBE2E2 UBE2E2 11825 -0.027 0.2 NO
151 PSMD4 PSMD4 PSMD4 11831 -0.027 0.2 NO
152 UBA6 UBA6 UBA6 11841 -0.027 0.21 NO
153 KEAP1 KEAP1 KEAP1 11842 -0.027 0.21 NO
154 STUB1 STUB1 STUB1 11898 -0.028 0.21 NO
155 UBE2D2 UBE2D2 UBE2D2 11910 -0.028 0.21 NO
156 ANAPC4 ANAPC4 ANAPC4 11932 -0.028 0.21 NO
157 CDC34 CDC34 CDC34 11959 -0.029 0.21 NO
158 PSMD14 PSMD14 PSMD14 11987 -0.029 0.21 NO
159 RBX1 RBX1 RBX1 12031 -0.029 0.21 NO
160 PSMD6 PSMD6 PSMD6 12047 -0.03 0.21 NO
161 GAN GAN GAN 12094 -0.03 0.21 NO
162 ASB3 ASB3 ASB3 12097 -0.03 0.21 NO
163 TCEB1 TCEB1 TCEB1 12101 -0.03 0.22 NO
164 PSMA2 PSMA2 PSMA2 12188 -0.031 0.21 NO
165 UBE2J2 UBE2J2 UBE2J2 12217 -0.031 0.21 NO
166 ASB6 ASB6 ASB6 12228 -0.031 0.22 NO
167 PSMB7 PSMB7 PSMB7 12319 -0.032 0.21 NO
168 SAE1 SAE1 SAE1 12340 -0.032 0.21 NO
169 SOCS1 SOCS1 SOCS1 12370 -0.033 0.21 NO
170 PSMA4 PSMA4 PSMA4 12474 -0.034 0.21 NO
171 FBXO4 FBXO4 FBXO4 12498 -0.034 0.21 NO
172 UBA2 UBA2 UBA2 12558 -0.035 0.21 NO
173 FBXO44 FBXO44 FBXO44 12708 -0.037 0.2 NO
174 PSMB3 PSMB3 PSMB3 12830 -0.038 0.2 NO
175 ANAPC11 ANAPC11 ANAPC11 13077 -0.041 0.19 NO
176 VHL VHL VHL 13227 -0.043 0.19 NO
177 TCEB2 TCEB2 TCEB2 13240 -0.043 0.19 NO
178 UBE2N UBE2N UBE2N 13256 -0.043 0.19 NO
179 PSMB4 PSMB4 PSMB4 13266 -0.043 0.19 NO
180 UBA5 UBA5 UBA5 13362 -0.044 0.19 NO
181 UBA52 UBA52 UBA52 13505 -0.046 0.19 NO
182 UBE2E1 UBE2E1 UBE2E1 13553 -0.047 0.19 NO
183 WSB1 WSB1 WSB1 13865 -0.051 0.17 NO
184 ANAPC7 ANAPC7 ANAPC7 14016 -0.054 0.17 NO
185 UBE2M UBE2M UBE2M 14027 -0.054 0.17 NO
186 SKP2 SKP2 SKP2 14074 -0.054 0.17 NO
187 RNF182 RNF182 RNF182 14075 -0.054 0.18 NO
188 BLMH BLMH BLMH 14086 -0.055 0.18 NO
189 TRIM11 TRIM11 TRIM11 14578 -0.063 0.16 NO
190 ANAPC10 ANAPC10 ANAPC10 14810 -0.067 0.15 NO
191 CDC20 CDC20 CDC20 14817 -0.068 0.16 NO
192 RPS27A RPS27A RPS27A 14964 -0.07 0.15 NO
193 UBE2C UBE2C UBE2C 15955 -0.098 0.1 NO
194 RNF138 RNF138 RNF138 16095 -0.1 0.1 NO
195 UBE2S UBE2S UBE2S 16635 -0.12 0.084 NO
196 ASB9 ASB9 ASB9 17274 -0.16 0.06 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 GLYCOLYSIS GLUCONEOGENESIS.

Figure S62.  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 PURINE METABOLISM

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 PRKAG3 PRKAG3 PRKAG3 53 1.4 0.5 YES
2 PRKAA2 PRKAA2 PRKAA2 280 0.61 0.72 YES
3 PRKAB2 PRKAB2 PRKAB2 2997 0.14 0.62 NO
4 CAB39 CAB39 CAB39 4958 0.06 0.53 NO
5 MTOR MTOR MTOR 5870 0.04 0.5 NO
6 PPM1A PPM1A PPM1A 6282 0.033 0.49 NO
7 STRADB STRADB STRADB 6593 0.029 0.48 NO
8 PRKAA1 PRKAA1 PRKAA1 7130 0.021 0.46 NO
9 CAB39L CAB39L CAB39L 7281 0.019 0.46 NO
10 RPTOR RPTOR RPTOR 7448 0.017 0.46 NO
11 EEF2K EEF2K EEF2K 7877 0.012 0.44 NO
12 AKT2 AKT2 AKT2 7952 0.011 0.44 NO
13 PRKAG1 PRKAG1 PRKAG1 8584 0.0042 0.4 NO
14 PRKAG2 PRKAG2 PRKAG2 8622 0.0038 0.4 NO
15 EIF4G1 EIF4G1 EIF4G1 8637 0.0037 0.4 NO
16 TSC2 TSC2 TSC2 9158 -0.0015 0.38 NO
17 RHEB RHEB RHEB 9538 -0.0051 0.36 NO
18 TSC1 TSC1 TSC1 9555 -0.0053 0.36 NO
19 EIF4B EIF4B EIF4B 9894 -0.0086 0.34 NO
20 STRADA STRADA STRADA 10568 -0.015 0.31 NO
21 STK11 STK11 STK11 10624 -0.016 0.32 NO
22 RPS6KB1 RPS6KB1 RPS6KB1 10955 -0.019 0.3 NO
23 PDE3B PDE3B PDE3B 12049 -0.03 0.26 NO
24 PRKAB1 PRKAB1 PRKAB1 12224 -0.031 0.26 NO
25 MLST8 MLST8 MLST8 12483 -0.034 0.26 NO
26 EIF4E EIF4E EIF4E 13167 -0.042 0.24 NO
27 RPS6 RPS6 RPS6 13588 -0.047 0.23 NO
28 EIF4EBP1 EIF4EBP1 EIF4EBP1 15371 -0.081 0.16 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 PURINE METABOLISM.

Figure S64.  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 ARGININE AND PROLINE METABOLISM

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 ASB5 ASB5 ASB5 21 1.5 0.085 YES
2 TRIM63 TRIM63 TRIM63 59 1.3 0.16 YES
3 ASB15 ASB15 ASB15 122 1.1 0.22 YES
4 ASB11 ASB11 ASB11 176 0.85 0.26 YES
5 ASB12 ASB12 ASB12 234 0.7 0.3 YES
6 ZBTB16 ZBTB16 ZBTB16 251 0.66 0.34 YES
7 ASB16 ASB16 ASB16 310 0.58 0.37 YES
8 PARK2 PARK2 PARK2 404 0.5 0.39 YES
9 ASB4 ASB4 ASB4 519 0.43 0.41 YES
10 MRC1 MRC1 MRC1 1010 0.31 0.4 YES
11 FCGR1A FCGR1A FCGR1A 1166 0.29 0.41 YES
12 SPSB4 SPSB4 SPSB4 1226 0.28 0.42 YES
13 CYBB CYBB CYBB 1259 0.28 0.44 YES
14 FCGR1B FCGR1B FCGR1B 1415 0.26 0.44 YES
15 ASB2 ASB2 ASB2 1719 0.22 0.44 YES
16 CD36 CD36 CD36 1796 0.22 0.45 YES
17 CD207 CD207 CD207 2140 0.19 0.44 NO
18 MRC2 MRC2 MRC2 2391 0.17 0.44 NO
19 DET1 DET1 DET1 2530 0.16 0.44 NO
20 CTSS CTSS CTSS 2722 0.15 0.44 NO
21 NEDD4 NEDD4 NEDD4 2806 0.14 0.44 NO
22 ITGAV ITGAV ITGAV 3044 0.13 0.44 NO
23 TRIM9 TRIM9 TRIM9 3210 0.12 0.43 NO
24 NCF4 NCF4 NCF4 3228 0.12 0.44 NO
25 CBLB CBLB CBLB 3477 0.11 0.43 NO
26 UBE2D4 UBE2D4 UBE2D4 3536 0.11 0.44 NO
27 SEC23A SEC23A SEC23A 3767 0.099 0.43 NO
28 ITGB5 ITGB5 ITGB5 3830 0.097 0.43 NO
29 NCF2 NCF2 NCF2 3831 0.097 0.44 NO
30 LNPEP LNPEP LNPEP 3864 0.096 0.44 NO
31 FBXO2 FBXO2 FBXO2 3952 0.092 0.44 NO
32 SPSB1 SPSB1 SPSB1 4040 0.089 0.44 NO
33 TRIM21 TRIM21 TRIM21 4161 0.084 0.44 NO
34 ASB8 ASB8 ASB8 4174 0.084 0.44 NO
35 UBR1 UBR1 UBR1 4378 0.077 0.44 NO
36 HLA-F HLA-F HLA-F 4462 0.074 0.44 NO
37 UBR2 UBR2 UBR2 4468 0.074 0.44 NO
38 SEC24D SEC24D SEC24D 4479 0.074 0.44 NO
39 HLA-C HLA-C HLA-C 4556 0.072 0.44 NO
40 TRIM32 TRIM32 TRIM32 4600 0.07 0.44 NO
41 HLA-B HLA-B HLA-B 4655 0.069 0.45 NO
42 TRIM36 TRIM36 TRIM36 4781 0.066 0.44 NO
43 PSMB9 PSMB9 PSMB9 4886 0.062 0.44 NO
44 TAP1 TAP1 TAP1 4960 0.06 0.44 NO
45 UBE2L6 UBE2L6 UBE2L6 4968 0.06 0.44 NO
46 ASB1 ASB1 ASB1 5045 0.058 0.44 NO
47 TAP2 TAP2 TAP2 5050 0.058 0.45 NO
48 HLA-A HLA-A HLA-A 5092 0.057 0.45 NO
49 PJA2 PJA2 PJA2 5182 0.055 0.44 NO
50 DZIP3 DZIP3 DZIP3 5263 0.053 0.44 NO
51 FBXO17 FBXO17 FBXO17 5319 0.052 0.44 NO
52 UBA7 UBA7 UBA7 5407 0.049 0.44 NO
53 DTX3L DTX3L DTX3L 5409 0.049 0.44 NO
54 B2M B2M B2M 5457 0.048 0.44 NO
55 SMURF2 SMURF2 SMURF2 5504 0.047 0.44 NO
56 UBE2D1 UBE2D1 UBE2D1 5581 0.045 0.44 NO
57 RNF123 RNF123 RNF123 5643 0.044 0.44 NO
58 UBE2H UBE2H UBE2H 5675 0.043 0.44 NO
59 WWP1 WWP1 WWP1 5759 0.042 0.44 NO
60 HECTD3 HECTD3 HECTD3 5792 0.041 0.44 NO
61 UBE2Q2 UBE2Q2 UBE2Q2 5794 0.041 0.44 NO
62 SEC31A SEC31A SEC31A 5854 0.04 0.44 NO
63 CUL5 CUL5 CUL5 5873 0.04 0.44 NO
64 ERAP1 ERAP1 ERAP1 5904 0.039 0.44 NO
65 SOCS3 SOCS3 SOCS3 6036 0.037 0.44 NO
66 TRIP12 TRIP12 TRIP12 6053 0.037 0.44 NO
67 TPP2 TPP2 TPP2 6186 0.035 0.44 NO
68 CDC27 CDC27 CDC27 6246 0.034 0.44 NO
69 PSMB10 PSMB10 PSMB10 6253 0.034 0.44 NO
70 SMURF1 SMURF1 SMURF1 6418 0.031 0.43 NO
71 KLHL20 KLHL20 KLHL20 6457 0.031 0.43 NO
72 HERC2 HERC2 HERC2 6501 0.03 0.43 NO
73 FBXW7 FBXW7 FBXW7 6645 0.028 0.42 NO
74 UBOX5 UBOX5 UBOX5 6686 0.027 0.42 NO
75 CUL7 CUL7 CUL7 6693 0.027 0.42 NO
76 UBE4A UBE4A UBE4A 6830 0.025 0.42 NO
77 UBE2R2 UBE2R2 UBE2R2 6840 0.025 0.42 NO
78 PSMD1 PSMD1 PSMD1 6850 0.025 0.42 NO
79 UBE3B UBE3B UBE3B 6890 0.024 0.42 NO
80 ASB13 ASB13 ASB13 6891 0.024 0.42 NO
81 UBR4 UBR4 UBR4 6930 0.024 0.42 NO
82 PSMB8 PSMB8 PSMB8 6938 0.024 0.42 NO
83 UBE3C UBE3C UBE3C 7117 0.021 0.41 NO
84 FBXO3 FBXO3 FBXO3 7147 0.021 0.41 NO
85 FBXW8 FBXW8 FBXW8 7182 0.02 0.41 NO
86 PSMF1 PSMF1 PSMF1 7186 0.02 0.41 NO
87 RNF41 RNF41 RNF41 7291 0.019 0.41 NO
88 UBE2W UBE2W UBE2W 7303 0.019 0.41 NO
89 LRSAM1 LRSAM1 LRSAM1 7336 0.018 0.41 NO
90 PSMD5 PSMD5 PSMD5 7513 0.016 0.4 NO
91 HSPA5 HSPA5 HSPA5 7524 0.016 0.4 NO
92 RBCK1 RBCK1 RBCK1 7547 0.016 0.4 NO
93 RNF4 RNF4 RNF4 7561 0.016 0.4 NO
94 ASB7 ASB7 ASB7 7595 0.016 0.4 NO
95 FBXO27 FBXO27 FBXO27 7601 0.016 0.4 NO
96 RNF34 RNF34 RNF34 7668 0.015 0.39 NO
97 HUWE1 HUWE1 HUWE1 7692 0.014 0.39 NO
98 PJA1 PJA1 PJA1 7697 0.014 0.39 NO
99 SEC24B SEC24B SEC24B 7732 0.014 0.39 NO
100 CALR CALR CALR 7761 0.013 0.39 NO
101 RNF6 RNF6 RNF6 7770 0.013 0.39 NO
102 UBE2F UBE2F UBE2F 7847 0.012 0.39 NO
103 PSMD2 PSMD2 PSMD2 7872 0.012 0.39 NO
104 BTRC BTRC BTRC 7934 0.011 0.39 NO
105 UBE2G1 UBE2G1 UBE2G1 7950 0.011 0.39 NO
106 CANX CANX CANX 8032 0.01 0.38 NO
107 KLHL9 KLHL9 KLHL9 8056 0.01 0.38 NO
108 PSME2 PSME2 PSME2 8059 0.0099 0.38 NO
109 SEC24C SEC24C SEC24C 8078 0.0097 0.38 NO
110 SAR1B SAR1B SAR1B 8287 0.0074 0.37 NO
111 PSME1 PSME1 PSME1 8360 0.0065 0.37 NO
112 FBXO6 FBXO6 FBXO6 8415 0.0059 0.36 NO
113 PSMC2 PSMC2 PSMC2 8478 0.0052 0.36 NO
114 RNF25 RNF25 RNF25 8492 0.0051 0.36 NO
115 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 8499 0.005 0.36 NO
116 PSMD7 PSMD7 PSMD7 8578 0.0042 0.36 NO
117 KLHL13 KLHL13 KLHL13 8618 0.0039 0.36 NO
118 UBE2Z UBE2Z UBE2Z 8623 0.0038 0.36 NO
119 RNF144B RNF144B RNF144B 8627 0.0038 0.36 NO
120 UBE2J1 UBE2J1 UBE2J1 8681 0.0033 0.35 NO
121 SEC61A1 SEC61A1 SEC61A1 8778 0.0024 0.35 NO
122 RCHY1 RCHY1 RCHY1 8854 0.0016 0.34 NO
123 TRIM37 TRIM37 TRIM37 8896 0.0011 0.34 NO
124 UBE3A UBE3A UBE3A 9096 -0.00097 0.33 NO
125 ARIH2 ARIH2 ARIH2 9141 -0.0014 0.33 NO
126 PSMD13 PSMD13 PSMD13 9144 -0.0014 0.33 NO
127 PSMD11 PSMD11 PSMD11 9178 -0.0017 0.32 NO
128 UBE2L3 UBE2L3 UBE2L3 9189 -0.0018 0.32 NO
129 PSMA7 PSMA7 PSMA7 9213 -0.0021 0.32 NO
130 CUL2 CUL2 CUL2 9224 -0.0022 0.32 NO
131 ATG7 ATG7 ATG7 9239 -0.0023 0.32 NO
132 PDIA3 PDIA3 PDIA3 9257 -0.0024 0.32 NO
133 CUL3 CUL3 CUL3 9265 -0.0025 0.32 NO
134 CUL1 CUL1 CUL1 9266 -0.0025 0.32 NO
135 MKRN1 MKRN1 MKRN1 9314 -0.003 0.32 NO
136 PSME4 PSME4 PSME4 9336 -0.0032 0.32 NO
137 VPRBP VPRBP VPRBP 9381 -0.0036 0.32 NO
138 PSMB5 PSMB5 PSMB5 9384 -0.0036 0.32 NO
139 UBE2A UBE2A UBE2A 9401 -0.0038 0.32 NO
140 FBXW11 FBXW11 FBXW11 9406 -0.0038 0.32 NO
141 PSMC3 PSMC3 PSMC3 9536 -0.0051 0.31 NO
142 LRRC41 LRRC41 LRRC41 9591 -0.0057 0.31 NO
143 ANAPC1 ANAPC1 ANAPC1 9661 -0.0064 0.3 NO
144 SPSB2 SPSB2 SPSB2 9668 -0.0064 0.3 NO
145 CDC16 CDC16 CDC16 9691 -0.0066 0.3 NO
146 ANAPC5 ANAPC5 ANAPC5 9733 -0.0071 0.3 NO
147 PSMB2 PSMB2 PSMB2 9779 -0.0075 0.3 NO
148 UBE2G2 UBE2G2 UBE2G2 9814 -0.0078 0.3 NO
149 RNF220 RNF220 RNF220 9920 -0.0088 0.29 NO
150 PSMC6 PSMC6 PSMC6 9972 -0.0092 0.29 NO
151 UBE2D3 UBE2D3 UBE2D3 9986 -0.0094 0.29 NO
152 PSMA8 PSMA8 PSMA8 9989 -0.0094 0.29 NO
153 UBE2K UBE2K UBE2K 10005 -0.0096 0.29 NO
154 UBE2B UBE2B UBE2B 10016 -0.0097 0.29 NO
155 SEC13 SEC13 SEC13 10073 -0.01 0.29 NO
156 PSMA1 PSMA1 PSMA1 10180 -0.011 0.28 NO
157 PSMB6 PSMB6 PSMB6 10261 -0.012 0.28 NO
158 UBA1 UBA1 UBA1 10312 -0.012 0.28 NO
159 CYBA CYBA CYBA 10420 -0.014 0.27 NO
160 HLA-G HLA-G HLA-G 10581 -0.015 0.26 NO
161 PSMC1 PSMC1 PSMC1 10585 -0.015 0.26 NO
162 PSMC5 PSMC5 PSMC5 10654 -0.016 0.26 NO
163 PSMD12 PSMD12 PSMD12 10658 -0.016 0.26 NO
164 PSMA5 PSMA5 PSMA5 10753 -0.017 0.26 NO
165 UBE2O UBE2O UBE2O 10774 -0.017 0.26 NO
166 SKP1 SKP1 SKP1 10800 -0.017 0.26 NO
167 PSMD8 PSMD8 PSMD8 10808 -0.017 0.26 NO
168 PSMD9 PSMD9 PSMD9 10879 -0.018 0.25 NO
169 PSMA6 PSMA6 PSMA6 10928 -0.018 0.25 NO
170 PSMC4 PSMC4 PSMC4 10961 -0.019 0.25 NO
171 CDC26 CDC26 CDC26 11006 -0.019 0.25 NO
172 PSMA3 PSMA3 PSMA3 11012 -0.019 0.25 NO
173 PSMD3 PSMD3 PSMD3 11028 -0.019 0.25 NO
174 UBE2V2 UBE2V2 UBE2V2 11155 -0.021 0.25 NO
175 PSMD10 PSMD10 PSMD10 11158 -0.021 0.25 NO
176 UBA3 UBA3 UBA3 11190 -0.021 0.25 NO
177 NPEPPS NPEPPS NPEPPS 11272 -0.022 0.24 NO
178 ANAPC13 ANAPC13 ANAPC13 11277 -0.022 0.24 NO
179 UBE2Q1 UBE2Q1 UBE2Q1 11397 -0.023 0.24 NO
180 PSMB1 PSMB1 PSMB1 11401 -0.023 0.24 NO
181 ANAPC2 ANAPC2 ANAPC2 11422 -0.023 0.24 NO
182 CDC23 CDC23 CDC23 11493 -0.024 0.24 NO
183 UBE2E3 UBE2E3 UBE2E3 11722 -0.026 0.23 NO
184 UBE2E2 UBE2E2 UBE2E2 11825 -0.027 0.22 NO
185 PSMD4 PSMD4 PSMD4 11831 -0.027 0.22 NO
186 UBA6 UBA6 UBA6 11841 -0.027 0.22 NO
187 KEAP1 KEAP1 KEAP1 11842 -0.027 0.23 NO
188 STUB1 STUB1 STUB1 11898 -0.028 0.23 NO
189 UBE2D2 UBE2D2 UBE2D2 11910 -0.028 0.23 NO
190 ANAPC4 ANAPC4 ANAPC4 11932 -0.028 0.23 NO
191 CDC34 CDC34 CDC34 11959 -0.029 0.23 NO
192 PSMD14 PSMD14 PSMD14 11987 -0.029 0.23 NO
193 RBX1 RBX1 RBX1 12031 -0.029 0.23 NO
194 PSMD6 PSMD6 PSMD6 12047 -0.03 0.23 NO
195 GAN GAN GAN 12094 -0.03 0.23 NO
196 ASB3 ASB3 ASB3 12097 -0.03 0.23 NO
197 TCEB1 TCEB1 TCEB1 12101 -0.03 0.23 NO
198 PSMA2 PSMA2 PSMA2 12188 -0.031 0.23 NO
199 UBE2J2 UBE2J2 UBE2J2 12217 -0.031 0.23 NO
200 ASB6 ASB6 ASB6 12228 -0.031 0.23 NO
201 PSMB7 PSMB7 PSMB7 12319 -0.032 0.23 NO
202 SAE1 SAE1 SAE1 12340 -0.032 0.23 NO
203 SOCS1 SOCS1 SOCS1 12370 -0.033 0.23 NO
204 PSMA4 PSMA4 PSMA4 12474 -0.034 0.22 NO
205 FBXO4 FBXO4 FBXO4 12498 -0.034 0.22 NO
206 UBA2 UBA2 UBA2 12558 -0.035 0.22 NO
207 FBXO44 FBXO44 FBXO44 12708 -0.037 0.22 NO
208 PSMB3 PSMB3 PSMB3 12830 -0.038 0.21 NO
209 SEC61A2 SEC61A2 SEC61A2 12855 -0.038 0.21 NO
210 ANAPC11 ANAPC11 ANAPC11 13077 -0.041 0.2 NO
211 VHL VHL VHL 13227 -0.043 0.2 NO
212 TCEB2 TCEB2 TCEB2 13240 -0.043 0.2 NO
213 UBE2N UBE2N UBE2N 13256 -0.043 0.2 NO
214 PSMB4 PSMB4 PSMB4 13266 -0.043 0.2 NO
215 UBA5 UBA5 UBA5 13362 -0.044 0.2 NO
216 UBA52 UBA52 UBA52 13505 -0.046 0.2 NO
217 UBE2E1 UBE2E1 UBE2E1 13553 -0.047 0.2 NO
218 SEC61B SEC61B SEC61B 13691 -0.049 0.19 NO
219 WSB1 WSB1 WSB1 13865 -0.051 0.18 NO
220 ANAPC7 ANAPC7 ANAPC7 14016 -0.054 0.18 NO
221 UBE2M UBE2M UBE2M 14027 -0.054 0.18 NO
222 SKP2 SKP2 SKP2 14074 -0.054 0.18 NO
223 RNF182 RNF182 RNF182 14075 -0.054 0.18 NO
224 BLMH BLMH BLMH 14086 -0.055 0.19 NO
225 TRIM11 TRIM11 TRIM11 14578 -0.063 0.16 NO
226 ANAPC10 ANAPC10 ANAPC10 14810 -0.067 0.16 NO
227 CDC20 CDC20 CDC20 14817 -0.068 0.16 NO
228 RPS27A RPS27A RPS27A 14964 -0.07 0.16 NO
229 SEC61G SEC61G SEC61G 15276 -0.078 0.14 NO
230 UBE2C UBE2C UBE2C 15955 -0.098 0.11 NO
231 RNF138 RNF138 RNF138 16095 -0.1 0.11 NO
232 UBE2S UBE2S UBE2S 16635 -0.12 0.086 NO
233 ASB9 ASB9 ASB9 17274 -0.16 0.06 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 ARGININE AND PROLINE METABOLISM.

Figure S66.  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 TYROSINE METABOLISM

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 CKM CKM CKM 66 1.3 0.18 YES
2 MYOD1 MYOD1 MYOD1 84 1.2 0.34 YES
3 MEF2C MEF2C MEF2C 208 0.76 0.44 YES
4 MITF MITF MITF 503 0.44 0.49 YES
5 GSC GSC GSC 1067 0.3 0.5 YES
6 PAX3 PAX3 PAX3 1704 0.23 0.5 YES
7 TGFB2 TGFB2 TGFB2 1745 0.22 0.52 YES
8 RUNX2 RUNX2 RUNX2 1823 0.22 0.55 YES
9 SPI1 SPI1 SPI1 1895 0.21 0.57 YES
10 CDK6 CDK6 CDK6 4053 0.089 0.47 NO
11 PPARG PPARG PPARG 4232 0.082 0.47 NO
12 MET MET MET 4583 0.071 0.46 NO
13 CCND1 CCND1 CCND1 4768 0.066 0.46 NO
14 ATF2 ATF2 ATF2 4836 0.064 0.46 NO
15 ABL1 ABL1 ABL1 5088 0.057 0.46 NO
16 PPP2R3B PPP2R3B PPP2R3B 5325 0.052 0.45 NO
17 ATF7 ATF7 ATF7 5343 0.051 0.46 NO
18 SFTPD SFTPD SFTPD 5829 0.041 0.44 NO
19 CCND2 CCND2 CCND2 5923 0.039 0.44 NO
20 EP300 EP300 EP300 6038 0.037 0.44 NO
21 ELF1 ELF1 ELF1 6141 0.035 0.44 NO
22 SIRT1 SIRT1 SIRT1 6192 0.034 0.44 NO
23 RB1 RB1 RB1 6454 0.031 0.43 NO
24 CEBPB CEBPB CEBPB 6481 0.03 0.43 NO
25 CTBP1 CTBP1 CTBP1 6498 0.03 0.44 NO
26 CSF2 CSF2 CSF2 6665 0.028 0.43 NO
27 CREBBP CREBBP CREBBP 7288 0.019 0.4 NO
28 JUN JUN JUN 7587 0.016 0.38 NO
29 TAF1 TAF1 TAF1 7639 0.015 0.38 NO
30 CCND3 CCND3 CCND3 7834 0.012 0.37 NO
31 CDKN2A CDKN2A CDKN2A 7845 0.012 0.38 NO
32 CDKN1B CDKN1B CDKN1B 8121 0.0092 0.36 NO
33 MAPK14 MAPK14 MAPK14 9242 -0.0023 0.3 NO
34 CDKN1A CDKN1A CDKN1A 9260 -0.0025 0.3 NO
35 UBTF UBTF UBTF 9274 -0.0026 0.3 NO
36 MAPK11 MAPK11 MAPK11 9707 -0.0068 0.28 NO
37 SMARCB1 SMARCB1 SMARCB1 10075 -0.01 0.26 NO
38 E2F4 E2F4 E2F4 10233 -0.012 0.25 NO
39 RAF1 RAF1 RAF1 10240 -0.012 0.25 NO
40 AATF AATF AATF 10266 -0.012 0.25 NO
41 MAPK9 MAPK9 MAPK9 10639 -0.016 0.24 NO
42 BRD2 BRD2 BRD2 10662 -0.016 0.24 NO
43 TBP TBP TBP 10863 -0.018 0.23 NO
44 E2F3 E2F3 E2F3 10906 -0.018 0.23 NO
45 PPP2CA PPP2CA PPP2CA 11056 -0.02 0.22 NO
46 HDAC1 HDAC1 HDAC1 12115 -0.03 0.17 NO
47 HDAC3 HDAC3 HDAC3 12247 -0.032 0.17 NO
48 RBBP4 RBBP4 RBBP4 12278 -0.032 0.17 NO
49 DNMT1 DNMT1 DNMT1 12329 -0.032 0.17 NO
50 CEBPA CEBPA CEBPA 12553 -0.035 0.16 NO
51 TFDP1 TFDP1 TFDP1 12678 -0.036 0.16 NO
52 BGLAP BGLAP BGLAP 12866 -0.038 0.16 NO
53 SMARCA4 SMARCA4 SMARCA4 13015 -0.04 0.15 NO
54 MDM2 MDM2 MDM2 13114 -0.041 0.15 NO
55 CDK4 CDK4 CDK4 13914 -0.052 0.12 NO
56 SKP2 SKP2 SKP2 14074 -0.054 0.12 NO
57 CDK2 CDK2 CDK2 14094 -0.055 0.12 NO
58 CBX4 CBX4 CBX4 14462 -0.061 0.11 NO
59 SUV39H1 SUV39H1 SUV39H1 15633 -0.088 0.06 NO
60 CEBPD CEBPD CEBPD 15821 -0.093 0.062 NO
61 CCNA2 CCNA2 CCNA2 15842 -0.094 0.074 NO
62 E2F1 E2F1 E2F1 16779 -0.13 0.041 NO
63 E2F2 E2F2 E2F2 16961 -0.14 0.051 NO
64 CCNE1 CCNE1 CCNE1 17587 -0.18 0.042 NO

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

Figure S68.  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 GLYCEROLIPID METABOLISM

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 PPP1R3A PPP1R3A PPP1R3A 19 1.5 0.52 YES
2 SLC2A4 SLC2A4 SLC2A4 423 0.48 0.66 YES
3 RHOQ RHOQ RHOQ 3565 0.11 0.53 NO
4 ASIP ASIP ASIP 3838 0.097 0.55 NO
5 LNPEP LNPEP LNPEP 3864 0.096 0.58 NO
6 INSR INSR INSR 4414 0.076 0.58 NO
7 TBC1D4 TBC1D4 TBC1D4 5240 0.054 0.55 NO
8 GYS1 GYS1 GYS1 6100 0.036 0.52 NO
9 YWHAG YWHAG YWHAG 6342 0.032 0.52 NO
10 YWHAH YWHAH YWHAH 6621 0.028 0.51 NO
11 VAMP2 VAMP2 VAMP2 6833 0.025 0.51 NO
12 YWHAZ YWHAZ YWHAZ 7204 0.02 0.5 NO
13 STX4 STX4 STX4 7318 0.019 0.5 NO
14 GSK3B GSK3B GSK3B 7370 0.018 0.5 NO
15 AKT2 AKT2 AKT2 7952 0.011 0.47 NO
16 YWHAB YWHAB YWHAB 8016 0.01 0.47 NO
17 SFN SFN SFN 8022 0.01 0.48 NO
18 AKT1 AKT1 AKT1 8190 0.0086 0.47 NO
19 YWHAQ YWHAQ YWHAQ 9215 -0.0021 0.41 NO
20 YWHAE YWHAE YWHAE 10973 -0.019 0.32 NO
21 PPP1CC PPP1CC PPP1CC 11114 -0.02 0.32 NO
22 PRKCI PRKCI PRKCI 12639 -0.036 0.25 NO
23 TRIP10 TRIP10 TRIP10 12761 -0.037 0.26 NO
24 PRKCZ PRKCZ PRKCZ 14592 -0.064 0.18 NO
25 STXBP4 STXBP4 STXBP4 14828 -0.068 0.19 NO

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

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROLIPID 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 INOSITOL PHOSPHATE METABOLISM

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 MYLPF MYLPF MYLPF 49 1.4 0.21 YES
2 MEF2C MEF2C MEF2C 208 0.76 0.32 YES
3 EGF EGF EGF 323 0.56 0.4 YES
4 F2RL2 F2RL2 F2RL2 439 0.47 0.46 YES
5 CHN2 CHN2 CHN2 732 0.36 0.5 YES
6 PIK3R1 PIK3R1 PIK3R1 2109 0.19 0.46 NO
7 PRKCA PRKCA PRKCA 2649 0.15 0.45 NO
8 PIK3CD PIK3CD PIK3CD 3369 0.12 0.43 NO
9 EPS8 EPS8 EPS8 3680 0.1 0.43 NO
10 STAT1 STAT1 STAT1 3976 0.091 0.43 NO
11 DUSP6 DUSP6 DUSP6 4412 0.076 0.42 NO
12 MAP3K2 MAP3K2 MAP3K2 4446 0.075 0.43 NO
13 CYFIP2 CYFIP2 CYFIP2 4581 0.071 0.43 NO
14 ATF2 ATF2 ATF2 4836 0.064 0.42 NO
15 ARPC1B ARPC1B ARPC1B 4871 0.063 0.43 NO
16 GAB1 GAB1 GAB1 5317 0.052 0.42 NO
17 VAV2 VAV2 VAV2 5406 0.049 0.42 NO
18 RICTOR RICTOR RICTOR 5453 0.048 0.42 NO
19 MAP3K1 MAP3K1 MAP3K1 5748 0.042 0.42 NO
20 MTOR MTOR MTOR 5870 0.04 0.41 NO
21 EGFR EGFR EGFR 6109 0.036 0.41 NO
22 RIN1 RIN1 RIN1 6152 0.035 0.41 NO
23 MAPK8 MAPK8 MAPK8 6171 0.035 0.41 NO
24 SRC SRC SRC 6226 0.034 0.42 NO
25 YWHAG YWHAG YWHAG 6342 0.032 0.42 NO
26 IQGAP1 IQGAP1 IQGAP1 6550 0.029 0.41 NO
27 RPS6KA4 RPS6KA4 RPS6KA4 6556 0.029 0.41 NO
28 YWHAH YWHAH YWHAH 6621 0.028 0.41 NO
29 PDPK1 PDPK1 PDPK1 6876 0.025 0.4 NO
30 SOS1 SOS1 SOS1 6914 0.024 0.4 NO
31 ARF4 ARF4 ARF4 7004 0.023 0.4 NO
32 PIK3CA PIK3CA PIK3CA 7181 0.02 0.4 NO
33 YWHAZ YWHAZ YWHAZ 7204 0.02 0.4 NO
34 MAPK1 MAPK1 MAPK1 7233 0.02 0.4 NO
35 CAPN2 CAPN2 CAPN2 7287 0.019 0.4 NO
36 CREB1 CREB1 CREB1 7337 0.018 0.4 NO
37 SRF SRF SRF 7430 0.018 0.4 NO
38 SMAD1 SMAD1 SMAD1 7460 0.017 0.4 NO
39 NCKAP1 NCKAP1 NCKAP1 7527 0.016 0.4 NO
40 JUN JUN JUN 7587 0.016 0.4 NO
41 ATF1 ATF1 ATF1 7708 0.014 0.39 NO
42 NRAS NRAS NRAS 7718 0.014 0.4 NO
43 ACTR2 ACTR2 ACTR2 7833 0.012 0.39 NO
44 ARPC2 ARPC2 ARPC2 7899 0.012 0.39 NO
45 SH2D2A SH2D2A SH2D2A 8001 0.011 0.38 NO
46 YWHAB YWHAB YWHAB 8016 0.01 0.39 NO
47 SFN SFN SFN 8022 0.01 0.39 NO
48 MAP2K4 MAP2K4 MAP2K4 8151 0.0091 0.38 NO
49 AKT1 AKT1 AKT1 8190 0.0086 0.38 NO
50 RALA RALA RALA 8306 0.0072 0.38 NO
51 SLC9A1 SLC9A1 SLC9A1 8485 0.0051 0.37 NO
52 EGR1 EGR1 EGR1 8547 0.0045 0.36 NO
53 ACTR3 ACTR3 ACTR3 8614 0.0039 0.36 NO
54 STAT3 STAT3 STAT3 8748 0.0027 0.36 NO
55 RPS6KA3 RPS6KA3 RPS6KA3 8749 0.0027 0.36 NO
56 PLD1 PLD1 PLD1 8889 0.0012 0.35 NO
57 RPS6KA5 RPS6KA5 RPS6KA5 8924 0.00079 0.35 NO
58 GRB2 GRB2 GRB2 9018 -0.00015 0.34 NO
59 WASL WASL WASL 9128 -0.0012 0.34 NO
60 MAPK7 MAPK7 MAPK7 9174 -0.0017 0.33 NO
61 YWHAQ YWHAQ YWHAQ 9215 -0.0021 0.33 NO
62 ELK1 ELK1 ELK1 9238 -0.0023 0.33 NO
63 CDC42 CDC42 CDC42 9447 -0.0042 0.32 NO
64 ARPC4 ARPC4 ARPC4 9454 -0.0043 0.32 NO
65 MAPKAP1 MAPKAP1 MAPKAP1 9497 -0.0047 0.32 NO
66 KSR1 KSR1 KSR1 9735 -0.0071 0.31 NO
67 PPP2R1A PPP2R1A PPP2R1A 9776 -0.0074 0.3 NO
68 FOS FOS FOS 9816 -0.0078 0.3 NO
69 KRAS KRAS KRAS 10060 -0.01 0.29 NO
70 PIK3R2 PIK3R2 PIK3R2 10143 -0.011 0.29 NO
71 MAP2K1 MAP2K1 MAP2K1 10189 -0.011 0.29 NO
72 RAF1 RAF1 RAF1 10240 -0.012 0.29 NO
73 HRAS HRAS HRAS 10288 -0.012 0.29 NO
74 WASF2 WASF2 WASF2 10628 -0.016 0.27 NO
75 PLD2 PLD2 PLD2 10636 -0.016 0.27 NO
76 MAPK9 MAPK9 MAPK9 10639 -0.016 0.28 NO
77 MAP2K5 MAP2K5 MAP2K5 10670 -0.016 0.28 NO
78 YWHAE YWHAE YWHAE 10973 -0.019 0.26 NO
79 ABI1 ABI1 ABI1 10992 -0.019 0.26 NO
80 PPP2CA PPP2CA PPP2CA 11056 -0.02 0.26 NO
81 BCL2L1 BCL2L1 BCL2L1 11060 -0.02 0.27 NO
82 MAP2K2 MAP2K2 MAP2K2 11179 -0.021 0.26 NO
83 PPP5C PPP5C PPP5C 11448 -0.023 0.25 NO
84 PIK3CB PIK3CB PIK3CB 11583 -0.025 0.25 NO
85 ARPC5 ARPC5 ARPC5 11661 -0.026 0.25 NO
86 RAB5A RAB5A RAB5A 11669 -0.026 0.25 NO
87 MAPK3 MAPK3 MAPK3 11690 -0.026 0.26 NO
88 PEBP1 PEBP1 PEBP1 11785 -0.027 0.26 NO
89 RAC1 RAC1 RAC1 11884 -0.028 0.25 NO
90 PRKCD PRKCD PRKCD 11992 -0.029 0.25 NO
91 ARPC3 ARPC3 ARPC3 12033 -0.029 0.25 NO
92 ZFP36 ZFP36 ZFP36 12123 -0.03 0.25 NO
93 BAD BAD BAD 12361 -0.033 0.25 NO
94 MLST8 MLST8 MLST8 12483 -0.034 0.24 NO
95 DIAPH3 DIAPH3 DIAPH3 12501 -0.034 0.25 NO
96 PIK3R3 PIK3R3 PIK3R3 12662 -0.036 0.25 NO
97 BAIAP2 BAIAP2 BAIAP2 12843 -0.038 0.24 NO
98 BRAF BRAF BRAF 13102 -0.041 0.23 NO
99 RPS6 RPS6 RPS6 13588 -0.047 0.22 NO
100 RALGDS RALGDS RALGDS 13722 -0.049 0.22 NO
101 PPP2R2A PPP2R2A PPP2R2A 13801 -0.05 0.22 NO
102 DUSP1 DUSP1 DUSP1 14270 -0.058 0.2 NO
103 PRKCZ PRKCZ PRKCZ 14592 -0.064 0.2 NO
104 USP6NL USP6NL USP6NL 15205 -0.076 0.17 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: KEGG INOSITOL PHOSPHATE METABOLISM.

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

genes ES table in pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM

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 PPP1R3A PPP1R3A PPP1R3A 19 1.5 0.094 YES
2 PRKAG3 PRKAG3 PRKAG3 53 1.4 0.18 YES
3 PHKG1 PHKG1 PHKG1 133 1 0.24 YES
4 PYGM PYGM PYGM 134 1 0.3 YES
5 PRKAA2 PRKAA2 PRKAA2 280 0.61 0.34 YES
6 SORBS1 SORBS1 SORBS1 283 0.61 0.37 YES
7 FBP2 FBP2 FBP2 356 0.54 0.4 YES
8 PPARGC1A PPARGC1A PPARGC1A 386 0.51 0.43 YES
9 SLC2A4 SLC2A4 SLC2A4 423 0.48 0.46 YES
10 PPP1R3C PPP1R3C PPP1R3C 502 0.44 0.49 YES
11 ACACB ACACB ACACB 767 0.35 0.5 YES
12 PDE3A PDE3A PDE3A 774 0.35 0.52 YES
13 HK3 HK3 HK3 1184 0.29 0.51 YES
14 PIK3CG PIK3CG PIK3CG 1200 0.28 0.53 YES
15 PIK3R5 PIK3R5 PIK3R5 1873 0.21 0.51 YES
16 PIK3R1 PIK3R1 PIK3R1 2109 0.19 0.51 YES
17 SHC3 SHC3 SHC3 2158 0.19 0.52 YES
18 SHC2 SHC2 SHC2 2259 0.18 0.52 YES
19 IRS1 IRS1 IRS1 2411 0.17 0.52 YES
20 SH2B2 SH2B2 SH2B2 2729 0.15 0.52 YES
21 PRKAR2B PRKAR2B PRKAR2B 2747 0.15 0.52 YES
22 AKT3 AKT3 AKT3 2790 0.15 0.53 YES
23 FBP1 FBP1 FBP1 2945 0.14 0.53 YES
24 PRKAB2 PRKAB2 PRKAB2 2997 0.14 0.54 YES
25 FOXO1 FOXO1 FOXO1 3182 0.13 0.54 YES
26 PIK3CD PIK3CD PIK3CD 3369 0.12 0.53 YES
27 CBLB CBLB CBLB 3477 0.11 0.53 YES
28 SHC4 SHC4 SHC4 3497 0.11 0.54 YES
29 RAPGEF1 RAPGEF1 RAPGEF1 3522 0.11 0.55 YES
30 RHOQ RHOQ RHOQ 3565 0.11 0.55 YES
31 PRKACB PRKACB PRKACB 3921 0.093 0.54 NO
32 PRKAR2A PRKAR2A PRKAR2A 3928 0.093 0.54 NO
33 PCK1 PCK1 PCK1 4345 0.078 0.52 NO
34 PHKA1 PHKA1 PHKA1 4377 0.077 0.53 NO
35 INSR INSR INSR 4414 0.076 0.53 NO
36 IRS2 IRS2 IRS2 4645 0.069 0.52 NO
37 INPP5D INPP5D INPP5D 5203 0.054 0.5 NO
38 PYGL PYGL PYGL 5326 0.051 0.49 NO
39 SOS2 SOS2 SOS2 5432 0.048 0.49 NO
40 PRKACA PRKACA PRKACA 5448 0.048 0.49 NO
41 GYS2 GYS2 GYS2 5510 0.047 0.49 NO
42 SOCS4 SOCS4 SOCS4 5513 0.047 0.49 NO
43 INPP5K INPP5K INPP5K 5540 0.046 0.5 NO
44 CRK CRK CRK 5558 0.046 0.5 NO
45 CALML6 CALML6 CALML6 5697 0.043 0.49 NO
46 CBL CBL CBL 5706 0.043 0.49 NO
47 CALM1 CALM1 CALM1 5813 0.041 0.49 NO
48 MTOR MTOR MTOR 5870 0.04 0.49 NO
49 SOCS2 SOCS2 SOCS2 5902 0.039 0.49 NO
50 PRKAR1A PRKAR1A PRKAR1A 6019 0.037 0.49 NO
51 SOCS3 SOCS3 SOCS3 6036 0.037 0.49 NO
52 GYS1 GYS1 GYS1 6100 0.036 0.49 NO
53 MAPK8 MAPK8 MAPK8 6171 0.035 0.49 NO
54 ARAF ARAF ARAF 6346 0.032 0.48 NO
55 PYGB PYGB PYGB 6355 0.032 0.48 NO
56 FLOT1 FLOT1 FLOT1 6732 0.027 0.46 NO
57 PHKB PHKB PHKB 6734 0.027 0.46 NO
58 SHC1 SHC1 SHC1 6804 0.026 0.46 NO
59 HK1 HK1 HK1 6831 0.025 0.46 NO
60 PDPK1 PDPK1 PDPK1 6876 0.025 0.46 NO
61 SOS1 SOS1 SOS1 6914 0.024 0.46 NO
62 CALML3 CALML3 CALML3 7077 0.022 0.45 NO
63 PRKAA1 PRKAA1 PRKAA1 7130 0.021 0.45 NO
64 PIK3CA PIK3CA PIK3CA 7181 0.02 0.45 NO
65 MAPK1 MAPK1 MAPK1 7233 0.02 0.45 NO
66 PTPN1 PTPN1 PTPN1 7238 0.02 0.45 NO
67 GSK3B GSK3B GSK3B 7370 0.018 0.44 NO
68 RPTOR RPTOR RPTOR 7448 0.017 0.44 NO
69 NRAS NRAS NRAS 7718 0.014 0.43 NO
70 EIF4E2 EIF4E2 EIF4E2 7923 0.012 0.42 NO
71 AKT2 AKT2 AKT2 7952 0.011 0.41 NO
72 AKT1 AKT1 AKT1 8190 0.0086 0.4 NO
73 PRKAG1 PRKAG1 PRKAG1 8584 0.0042 0.38 NO
74 PRKAG2 PRKAG2 PRKAG2 8622 0.0038 0.38 NO
75 EXOC7 EXOC7 EXOC7 8815 0.0019 0.37 NO
76 MKNK1 MKNK1 MKNK1 8818 0.0019 0.37 NO
77 PPP1CA PPP1CA PPP1CA 8835 0.0017 0.37 NO
78 IKBKB IKBKB IKBKB 8906 0.001 0.36 NO
79 GRB2 GRB2 GRB2 9018 -0.00015 0.36 NO
80 CRKL CRKL CRKL 9038 -0.0003 0.36 NO
81 TSC2 TSC2 TSC2 9158 -0.0015 0.35 NO
82 ELK1 ELK1 ELK1 9238 -0.0023 0.35 NO
83 PPP1CB PPP1CB PPP1CB 9450 -0.0042 0.34 NO
84 RHEB RHEB RHEB 9538 -0.0051 0.33 NO
85 TSC1 TSC1 TSC1 9555 -0.0053 0.33 NO
86 PTPRF PTPRF PTPRF 9872 -0.0084 0.31 NO
87 PPP1R3B PPP1R3B PPP1R3B 9980 -0.0094 0.31 NO
88 KRAS KRAS KRAS 10060 -0.01 0.3 NO
89 CALM3 CALM3 CALM3 10112 -0.011 0.3 NO
90 PIK3R2 PIK3R2 PIK3R2 10143 -0.011 0.3 NO
91 MAP2K1 MAP2K1 MAP2K1 10189 -0.011 0.3 NO
92 RAF1 RAF1 RAF1 10240 -0.012 0.3 NO
93 HRAS HRAS HRAS 10288 -0.012 0.3 NO
94 RPS6KB2 RPS6KB2 RPS6KB2 10532 -0.015 0.28 NO
95 MAPK9 MAPK9 MAPK9 10639 -0.016 0.28 NO
96 RPS6KB1 RPS6KB1 RPS6KB1 10955 -0.019 0.26 NO
97 PPP1CC PPP1CC PPP1CC 11114 -0.02 0.26 NO
98 PKLR PKLR PKLR 11120 -0.02 0.26 NO
99 MAP2K2 MAP2K2 MAP2K2 11179 -0.021 0.25 NO
100 PIK3CB PIK3CB PIK3CB 11583 -0.025 0.23 NO
101 MAPK3 MAPK3 MAPK3 11690 -0.026 0.23 NO
102 CALM2 CALM2 CALM2 11748 -0.026 0.23 NO
103 PDE3B PDE3B PDE3B 12049 -0.03 0.21 NO
104 PRKAB1 PRKAB1 PRKAB1 12224 -0.031 0.2 NO
105 BAD BAD BAD 12361 -0.033 0.2 NO
106 SOCS1 SOCS1 SOCS1 12370 -0.033 0.2 NO
107 PRKCI PRKCI PRKCI 12639 -0.036 0.19 NO
108 PIK3R3 PIK3R3 PIK3R3 12662 -0.036 0.19 NO
109 FLOT2 FLOT2 FLOT2 12669 -0.036 0.19 NO
110 TRIP10 TRIP10 TRIP10 12761 -0.037 0.19 NO
111 ACACA ACACA ACACA 12935 -0.039 0.18 NO
112 BRAF BRAF BRAF 13102 -0.041 0.18 NO
113 EIF4E EIF4E EIF4E 13167 -0.042 0.18 NO
114 RPS6 RPS6 RPS6 13588 -0.047 0.16 NO
115 HK2 HK2 HK2 13726 -0.049 0.15 NO
116 PHKA2 PHKA2 PHKA2 13814 -0.05 0.15 NO
117 PCK2 PCK2 PCK2 14235 -0.057 0.13 NO
118 FASN FASN FASN 14430 -0.061 0.12 NO
119 PRKCZ PRKCZ PRKCZ 14592 -0.064 0.12 NO
120 MKNK2 MKNK2 MKNK2 14842 -0.068 0.11 NO
121 PHKG2 PHKG2 PHKG2 14874 -0.068 0.11 NO
122 PPP1R3D PPP1R3D PPP1R3D 15009 -0.071 0.11 NO
123 SREBF1 SREBF1 SREBF1 15153 -0.075 0.11 NO
124 LIPE LIPE LIPE 15182 -0.076 0.11 NO
125 CALML5 CALML5 CALML5 15314 -0.079 0.11 NO
126 EIF4EBP1 EIF4EBP1 EIF4EBP1 15371 -0.081 0.11 NO
127 PRKAR1B PRKAR1B PRKAR1B 15835 -0.094 0.09 NO
128 PRKX PRKX PRKX 16528 -0.12 0.059 NO
129 CBLC CBLC CBLC 16725 -0.13 0.057 NO
130 GCK GCK GCK 17189 -0.16 0.041 NO
131 MAPK10 MAPK10 MAPK10 17343 -0.17 0.043 NO
132 IRS4 IRS4 IRS4 17738 -0.2 0.034 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: KEGG GLYCEROPHOSPHOLIPID METABOLISM.

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

genes ES table in pathway: KEGG ETHER LIPID METABOLISM

Table 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 MYL2 MYL2 MYL2 33 1.4 0.38 YES
2 ARHGAP6 ARHGAP6 ARHGAP6 422 0.48 0.49 YES
3 PIP5K1B PIP5K1B PIP5K1B 894 0.33 0.56 YES
4 PPP1R12B PPP1R12B PPP1R12B 1341 0.27 0.61 YES
5 MYLK MYLK MYLK 2148 0.19 0.61 YES
6 TLN1 TLN1 TLN1 3448 0.11 0.57 NO
7 GSN GSN GSN 4496 0.074 0.54 NO
8 ARHGAP1 ARHGAP1 ARHGAP1 4647 0.069 0.55 NO
9 OPHN1 OPHN1 OPHN1 4692 0.068 0.56 NO
10 VCL VCL VCL 4757 0.066 0.58 NO
11 ARPC1B ARPC1B ARPC1B 4871 0.063 0.59 NO
12 LIMK1 LIMK1 LIMK1 4983 0.06 0.6 NO
13 ROCK1 ROCK1 ROCK1 5631 0.044 0.58 NO
14 SRC SRC SRC 6226 0.034 0.55 NO
15 ARHGAP5 ARHGAP5 ARHGAP5 6828 0.025 0.53 NO
16 DIAPH1 DIAPH1 DIAPH1 7239 0.02 0.51 NO
17 CFL1 CFL1 CFL1 7681 0.015 0.49 NO
18 PFN1 PFN1 PFN1 7693 0.014 0.49 NO
19 RHOA RHOA RHOA 7750 0.014 0.49 NO
20 ACTR2 ACTR2 ACTR2 7833 0.012 0.49 NO
21 ARPC2 ARPC2 ARPC2 7899 0.012 0.49 NO
22 ARHGEF1 ARHGEF1 ARHGEF1 7928 0.011 0.49 NO
23 ACTR3 ACTR3 ACTR3 8614 0.0039 0.46 NO
24 ARHGEF11 ARHGEF11 ARHGEF11 8866 0.0014 0.44 NO
25 ARPC4 ARPC4 ARPC4 9454 -0.0043 0.41 NO
26 ARPC1A ARPC1A ARPC1A 11495 -0.024 0.31 NO
27 ARPC5 ARPC5 ARPC5 11661 -0.026 0.31 NO
28 PIP5K1A PIP5K1A PIP5K1A 11830 -0.027 0.3 NO
29 ARPC3 ARPC3 ARPC3 12033 -0.029 0.3 NO
30 BAIAP2 BAIAP2 BAIAP2 12843 -0.038 0.27 NO
31 ARHGEF5 ARHGEF5 ARHGEF5 13797 -0.05 0.23 NO
32 ARHGAP4 ARHGAP4 ARHGAP4 14840 -0.068 0.19 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: KEGG ETHER LIPID METABOLISM.

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

genes ES table in pathway: KEGG ABC TRANSPORTERS

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 ENO3 ENO3 ENO3 109 1.1 0.14 YES
2 PHKG1 PHKG1 PHKG1 133 1 0.28 YES
3 PYGM PYGM PYGM 134 1 0.42 YES
4 PGAM2 PGAM2 PGAM2 218 0.73 0.51 YES
5 FBP2 FBP2 FBP2 356 0.54 0.58 YES
6 FBP1 FBP1 FBP1 2945 0.14 0.46 NO
7 PFKM PFKM PFKM 3084 0.13 0.47 NO
8 PRKACB PRKACB PRKACB 3921 0.093 0.43 NO
9 GBE1 GBE1 GBE1 4002 0.09 0.44 NO
10 GYG1 GYG1 GYG1 4339 0.079 0.43 NO
11 PCK1 PCK1 PCK1 4345 0.078 0.44 NO
12 PHKA1 PHKA1 PHKA1 4377 0.077 0.45 NO
13 AGL AGL AGL 4688 0.068 0.44 NO
14 GYG2 GYG2 GYG2 4790 0.065 0.45 NO
15 PFKFB1 PFKFB1 PFKFB1 4943 0.061 0.45 NO
16 PGM1 PGM1 PGM1 5265 0.053 0.44 NO
17 PYGL PYGL PYGL 5326 0.051 0.44 NO
18 PRKACA PRKACA PRKACA 5448 0.048 0.44 NO
19 GYS2 GYS2 GYS2 5510 0.047 0.44 NO
20 SLC25A12 SLC25A12 SLC25A12 5779 0.042 0.44 NO
21 CALM1 CALM1 CALM1 5813 0.041 0.44 NO
22 GYS1 GYS1 GYS1 6100 0.036 0.43 NO
23 PYGB PYGB PYGB 6355 0.032 0.42 NO
24 PC PC PC 6388 0.032 0.42 NO
25 UGP2 UGP2 UGP2 6642 0.028 0.41 NO
26 PHKB PHKB PHKB 6734 0.027 0.41 NO
27 PKM2 PKM2 PKM2 7220 0.02 0.39 NO
28 PFKFB3 PFKFB3 PFKFB3 7565 0.016 0.37 NO
29 PFKFB2 PFKFB2 PFKFB2 7663 0.015 0.37 NO
30 PPP2R5D PPP2R5D PPP2R5D 8304 0.0072 0.33 NO
31 SLC25A11 SLC25A11 SLC25A11 8392 0.0062 0.33 NO
32 PPP2R1B PPP2R1B PPP2R1B 8777 0.0024 0.31 NO
33 PPP2R1A PPP2R1A PPP2R1A 9776 -0.0074 0.25 NO
34 PGAM1 PGAM1 PGAM1 9901 -0.0086 0.25 NO
35 GOT1 GOT1 GOT1 10030 -0.0098 0.24 NO
36 CALM3 CALM3 CALM3 10112 -0.011 0.24 NO
37 ENO1 ENO1 ENO1 10579 -0.015 0.22 NO
38 MDH2 MDH2 MDH2 10727 -0.016 0.21 NO
39 PPP2CA PPP2CA PPP2CA 11056 -0.02 0.2 NO
40 PKLR PKLR PKLR 11120 -0.02 0.19 NO
41 GAPDH GAPDH GAPDH 11131 -0.02 0.2 NO
42 PGK1 PGK1 PGK1 11496 -0.024 0.18 NO
43 CALM2 CALM2 CALM2 11748 -0.026 0.17 NO
44 PPP2CB PPP2CB PPP2CB 11782 -0.027 0.17 NO
45 ALDOA ALDOA ALDOA 11857 -0.028 0.17 NO
46 GOT2 GOT2 GOT2 12195 -0.031 0.16 NO
47 PFKL PFKL PFKL 12223 -0.031 0.16 NO
48 PFKP PFKP PFKP 12821 -0.038 0.13 NO
49 SLC25A13 SLC25A13 SLC25A13 13180 -0.042 0.12 NO
50 MDH1 MDH1 MDH1 13359 -0.044 0.11 NO
51 GPI GPI GPI 13391 -0.045 0.12 NO
52 TPI1 TPI1 TPI1 13439 -0.045 0.12 NO
53 PHKA2 PHKA2 PHKA2 13814 -0.05 0.11 NO
54 PGM2 PGM2 PGM2 13897 -0.052 0.11 NO
55 PCK2 PCK2 PCK2 14235 -0.057 0.1 NO
56 SLC25A1 SLC25A1 SLC25A1 14624 -0.064 0.088 NO
57 PHKG2 PHKG2 PHKG2 14874 -0.068 0.084 NO
58 PFKFB4 PFKFB4 PFKFB4 15742 -0.091 0.049 NO
59 SLC25A10 SLC25A10 SLC25A10 16387 -0.11 0.029 NO
60 ALDOB ALDOB ALDOB 16467 -0.12 0.04 NO
61 ENO2 ENO2 ENO2 16638 -0.12 0.048 NO
62 GAPDHS GAPDHS GAPDHS 17184 -0.15 0.039 NO
63 ALDOC ALDOC ALDOC 17630 -0.19 0.04 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: KEGG ABC TRANSPORTERS.

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ABC TRANSPORTERS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG RNA DEGRADATION

Table 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 MYH1 MYH1 MYH1 27 1.4 0.053 YES
2 MYH8 MYH8 MYH8 31 1.4 0.11 YES
3 ACTN2 ACTN2 ACTN2 32 1.4 0.16 YES
4 MYL2 MYL2 MYL2 33 1.4 0.21 YES
5 MYH7 MYH7 MYH7 45 1.4 0.26 YES
6 MYH2 MYH2 MYH2 47 1.4 0.31 YES
7 MYLPF MYLPF MYLPF 49 1.4 0.36 YES
8 MYH6 MYH6 MYH6 67 1.3 0.41 YES
9 MYH4 MYH4 MYH4 71 1.3 0.46 YES
10 MYH3 MYH3 MYH3 120 1.1 0.5 YES
11 CTNNA3 CTNNA3 CTNNA3 141 0.99 0.54 YES
12 MYH13 MYH13 MYH13 159 0.92 0.57 YES
13 JAM2 JAM2 JAM2 345 0.54 0.58 YES
14 MYH7B MYH7B MYH7B 444 0.47 0.59 YES
15 ACTN3 ACTN3 ACTN3 478 0.45 0.61 YES
16 MRAS MRAS MRAS 479 0.45 0.62 YES
17 PRKCQ PRKCQ PRKCQ 575 0.41 0.63 YES
18 MYH11 MYH11 MYH11 845 0.34 0.63 YES
19 CLDN11 CLDN11 CLDN11 1084 0.3 0.63 YES
20 CLDN5 CLDN5 CLDN5 1176 0.29 0.64 YES
21 MYH15 MYH15 MYH15 1177 0.29 0.65 YES
22 MPDZ MPDZ MPDZ 1312 0.27 0.65 YES
23 JAM3 JAM3 JAM3 1375 0.26 0.66 YES
24 PRKCB PRKCB PRKCB 1644 0.23 0.65 NO
25 MYL9 MYL9 MYL9 2036 0.2 0.64 NO
26 CLDN14 CLDN14 CLDN14 2344 0.17 0.63 NO
27 EPB41L3 EPB41L3 EPB41L3 2557 0.16 0.62 NO
28 ZAK ZAK ZAK 2570 0.16 0.63 NO
29 PRKCA PRKCA PRKCA 2649 0.15 0.63 NO
30 PPP2R2C PPP2R2C PPP2R2C 2743 0.15 0.63 NO
31 AKT3 AKT3 AKT3 2790 0.15 0.63 NO
32 CTNNA2 CTNNA2 CTNNA2 3233 0.12 0.61 NO
33 CLDN19 CLDN19 CLDN19 3527 0.11 0.6 NO
34 ACTN1 ACTN1 ACTN1 3533 0.11 0.6 NO
35 HCLS1 HCLS1 HCLS1 3766 0.099 0.59 NO
36 MYH10 MYH10 MYH10 4324 0.079 0.57 NO
37 AMOTL1 AMOTL1 AMOTL1 4547 0.072 0.56 NO
38 EPB41L2 EPB41L2 EPB41L2 4952 0.06 0.54 NO
39 PTEN PTEN PTEN 5285 0.052 0.52 NO
40 RRAS RRAS RRAS 5292 0.052 0.52 NO
41 GNAI2 GNAI2 GNAI2 5353 0.051 0.52 NO
42 CSDA CSDA CSDA 5397 0.049 0.52 NO
43 MYH9 MYH9 MYH9 5484 0.047 0.52 NO
44 CLDN9 CLDN9 CLDN9 5953 0.038 0.49 NO
45 MAGI2 MAGI2 MAGI2 6169 0.035 0.48 NO
46 SRC SRC SRC 6226 0.034 0.48 NO
47 MYL12A MYL12A MYL12A 6270 0.033 0.48 NO
48 CLDN23 CLDN23 CLDN23 6487 0.03 0.47 NO
49 TJAP1 TJAP1 TJAP1 6533 0.03 0.47 NO
50 SPTAN1 SPTAN1 SPTAN1 7019 0.023 0.44 NO
51 MAGI1 MAGI1 MAGI1 7143 0.021 0.44 NO
52 CTNNB1 CTNNB1 CTNNB1 7191 0.02 0.43 NO
53 CLDN17 CLDN17 CLDN17 7329 0.019 0.43 NO
54 LLGL1 LLGL1 LLGL1 7551 0.016 0.42 NO
55 ASH1L ASH1L ASH1L 7577 0.016 0.42 NO
56 NRAS NRAS NRAS 7718 0.014 0.41 NO
57 RHOA RHOA RHOA 7750 0.014 0.41 NO
58 ACTB ACTB ACTB 7878 0.012 0.4 NO
59 GNAI1 GNAI1 GNAI1 7925 0.012 0.4 NO
60 AKT2 AKT2 AKT2 7952 0.011 0.4 NO
61 EXOC4 EXOC4 EXOC4 8049 0.01 0.39 NO
62 CTTN CTTN CTTN 8136 0.0092 0.39 NO
63 AKT1 AKT1 AKT1 8190 0.0086 0.39 NO
64 CSNK2A2 CSNK2A2 CSNK2A2 8434 0.0057 0.37 NO
65 MPP5 MPP5 MPP5 8468 0.0054 0.37 NO
66 PPP2R1B PPP2R1B PPP2R1B 8777 0.0024 0.35 NO
67 TJP1 TJP1 TJP1 8917 0.0009 0.35 NO
68 ACTN4 ACTN4 ACTN4 9165 -0.0016 0.33 NO
69 EXOC3 EXOC3 EXOC3 9197 -0.0019 0.33 NO
70 CSNK2A1 CSNK2A1 CSNK2A1 9441 -0.0042 0.32 NO
71 CDC42 CDC42 CDC42 9447 -0.0042 0.32 NO
72 PPP2R2D PPP2R2D PPP2R2D 9580 -0.0055 0.31 NO
73 CASK CASK CASK 9645 -0.0062 0.31 NO
74 CTNNA1 CTNNA1 CTNNA1 9752 -0.0072 0.3 NO
75 PPP2R1A PPP2R1A PPP2R1A 9776 -0.0074 0.3 NO
76 GNAI3 GNAI3 GNAI3 9885 -0.0085 0.3 NO
77 PRKCH PRKCH PRKCH 9908 -0.0087 0.3 NO
78 MYH14 MYH14 MYH14 9968 -0.0092 0.29 NO
79 PARD3 PARD3 PARD3 9976 -0.0093 0.29 NO
80 KRAS KRAS KRAS 10060 -0.01 0.29 NO
81 SYMPK SYMPK SYMPK 10168 -0.011 0.28 NO
82 INADL INADL INADL 10177 -0.011 0.28 NO
83 HRAS HRAS HRAS 10288 -0.012 0.28 NO
84 VAPA VAPA VAPA 10609 -0.015 0.26 NO
85 PPP2R2B PPP2R2B PPP2R2B 10730 -0.016 0.25 NO
86 RRAS2 RRAS2 RRAS2 10960 -0.019 0.24 NO
87 PPP2CA PPP2CA PPP2CA 11056 -0.02 0.24 NO
88 ACTG1 ACTG1 ACTG1 11105 -0.02 0.24 NO
89 RAB13 RAB13 RAB13 11235 -0.021 0.23 NO
90 MLLT4 MLLT4 MLLT4 11286 -0.022 0.23 NO
91 MYL12B MYL12B MYL12B 11436 -0.023 0.22 NO
92 PARD6G PARD6G PARD6G 11531 -0.024 0.22 NO
93 EPB41L1 EPB41L1 EPB41L1 11551 -0.024 0.22 NO
94 YES1 YES1 YES1 11630 -0.025 0.21 NO
95 CLDN15 CLDN15 CLDN15 11671 -0.026 0.21 NO
96 PPP2CB PPP2CB PPP2CB 11782 -0.027 0.21 NO
97 PRKCD PRKCD PRKCD 11992 -0.029 0.2 NO
98 TJP2 TJP2 TJP2 12484 -0.034 0.17 NO
99 PRKCI PRKCI PRKCI 12639 -0.036 0.16 NO
100 CSNK2B CSNK2B CSNK2B 12771 -0.037 0.16 NO
101 EPB41 EPB41 EPB41 12872 -0.038 0.15 NO
102 RAB3B RAB3B RAB3B 12945 -0.039 0.15 NO
103 F11R F11R F11R 13027 -0.04 0.15 NO
104 PRKCE PRKCE PRKCE 13181 -0.042 0.14 NO
105 PPP2R2A PPP2R2A PPP2R2A 13801 -0.05 0.11 NO
106 CDK4 CDK4 CDK4 13914 -0.052 0.1 NO
107 MYL7 MYL7 MYL7 13998 -0.053 0.1 NO
108 CLDN2 CLDN2 CLDN2 14326 -0.059 0.086 NO
109 MAGI3 MAGI3 MAGI3 14575 -0.063 0.075 NO
110 PRKCZ PRKCZ PRKCZ 14592 -0.064 0.076 NO
111 CLDN8 CLDN8 CLDN8 15103 -0.074 0.051 NO
112 CLDN18 CLDN18 CLDN18 15380 -0.081 0.039 NO
113 CLDN1 CLDN1 CLDN1 15394 -0.081 0.042 NO
114 PARD6A PARD6A PARD6A 15544 -0.086 0.037 NO
115 CLDN20 CLDN20 CLDN20 15957 -0.098 0.018 NO
116 MYL5 MYL5 MYL5 16046 -0.1 0.017 NO
117 LLGL2 LLGL2 LLGL2 16808 -0.13 -0.02 NO
118 CLDN4 CLDN4 CLDN4 16940 -0.14 -0.022 NO
119 IGSF5 IGSF5 IGSF5 17090 -0.15 -0.025 NO
120 CRB3 CRB3 CRB3 17296 -0.16 -0.03 NO
121 CLDN6 CLDN6 CLDN6 17392 -0.17 -0.029 NO
122 PRKCG PRKCG PRKCG 17725 -0.2 -0.039 NO
123 OCLN OCLN OCLN 17779 -0.2 -0.035 NO
124 CGN CGN CGN 17900 -0.21 -0.033 NO
125 CLDN16 CLDN16 CLDN16 18006 -0.23 -0.031 NO
126 CLDN7 CLDN7 CLDN7 18035 -0.23 -0.023 NO
127 PARD6B PARD6B PARD6B 18055 -0.24 -0.016 NO
128 CLDN10 CLDN10 CLDN10 18109 -0.25 -0.0092 NO
129 TJP3 TJP3 TJP3 18222 -0.28 -0.005 NO
130 CLDN3 CLDN3 CLDN3 18327 -0.33 0.0019 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: KEGG RNA DEGRADATION.

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

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 = HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

GSEA analysis

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

Download Results

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

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