GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PRAD-TP
Prostate Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PRAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C19886GD
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 "PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 717
Number of samples: 497
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 ] 96
pheno.type: 2 - 4 :[ clus2 ] 142
pheno.type: 3 - 4 :[ clus3 ] 151
pheno.type: 4 - 4 :[ clus4 ] 108

For the expression subtypes of 18274 genes in 498 samples, GSEA found enriched gene sets in each cluster using 497 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG PROPANOATE METABOLISM, KEGG ADHERENS JUNCTION, KEGG INSULIN SIGNALING PATHWAY, KEGG THYROID CANCER, BIOCARTA AGR PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA MYOSIN PATHWAY

    • And common core enriched genes are ACTN1, ACTN2, ACTN3, MAPK1, VCL, ABAT, ACACB, ACAT2, ACSS2, ACSS3

  • clus2

    • Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG N GLYCAN BIOSYNTHESIS, KEGG UBIQUITIN MEDIATED PROTEOLYSIS, PID ECADHERIN NASCENTAJ PATHWAY, PID LIS1PATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER, REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, REACTOME RNA POL II TRANSCRIPTION, REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES

    • And common core enriched genes are NCBP1, NUP107, NUP133, NUP153, NUP155, NUP188, NUP205, NUP210, NUP214, NUP37

  • clus3

    • Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG RIBOSOME, KEGG DNA REPLICATION, KEGG PROTEASOME, KEGG BASE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG CELL CYCLE, KEGG PARKINSONS DISEASE

    • And common core enriched genes are MCM7, POLE2, PRIM2, RPA3, CDC45, CDC6, CDT1, DNA2, FEN1, MCM5

  • clus4

    • Top enriched gene sets are KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG LYSINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG GLYCEROLIPID METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM

    • And common core enriched genes are BDNF, BEX1, BIRC3, MMP7, NGFR, NTF3, NTF4, NTRK1, BBOX1, PIPOX

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 44 genes.ES.table 0.55 1.7 0.025 0.46 0.66 0.5 0.26 0.37 0.13 0.11
KEGG PROPANOATE METABOLISM 32 genes.ES.table 0.63 1.9 0.004 1 0.22 0.59 0.26 0.44 0 0.19
KEGG ADHERENS JUNCTION 73 genes.ES.table 0.51 1.8 0.002 0.64 0.47 0.33 0.24 0.25 0 0.14
KEGG INSULIN SIGNALING PATHWAY 133 genes.ES.table 0.42 1.7 0.0041 0.45 0.8 0.33 0.24 0.25 0.16 0.12
KEGG THYROID CANCER 29 genes.ES.table 0.54 1.7 0.014 0.41 0.75 0.17 0.11 0.15 0.14 0.11
BIOCARTA AGR PATHWAY 36 genes.ES.table 0.69 1.8 0 0.54 0.61 0.36 0.14 0.31 0.13 0.13
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.64 1.8 0 0.76 0.44 0.46 0.26 0.34 0 0.16
BIOCARTA INTEGRIN PATHWAY 38 genes.ES.table 0.59 1.9 0 0.64 0.33 0.37 0.24 0.28 0 0.14
BIOCARTA PYK2 PATHWAY 28 genes.ES.table 0.46 1.7 0.0078 0.51 0.62 0.29 0.26 0.21 0.12 0.13
BIOCARTA MYOSIN PATHWAY 29 genes.ES.table 0.61 1.8 0 0.57 0.58 0.45 0.19 0.36 0.13 0.14
genes ES table in pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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 ACSS3 ACSS3 ACSS3 181 0.44 0.14 YES
2 EHHADH EHHADH EHHADH 530 0.33 0.24 YES
3 LDHAL6A LDHAL6A LDHAL6A 1128 0.23 0.28 YES
4 ABAT ABAT ABAT 1442 0.2 0.34 YES
5 ACACB ACACB ACACB 2119 0.15 0.35 YES
6 ALDH2 ALDH2 ALDH2 2276 0.14 0.39 YES
7 ALDH6A1 ALDH6A1 ALDH6A1 2584 0.13 0.42 YES
8 LDHC LDHC LDHC 2901 0.11 0.44 YES
9 ALDH3A2 ALDH3A2 ALDH3A2 2986 0.11 0.47 YES
10 MLYCD MLYCD MLYCD 3265 0.095 0.49 YES
11 SUCLA2 SUCLA2 SUCLA2 3413 0.089 0.51 YES
12 LDHB LDHB LDHB 3498 0.086 0.54 YES
13 PCCA PCCA PCCA 3575 0.084 0.56 YES
14 ACAT2 ACAT2 ACAT2 3629 0.082 0.58 YES
15 ALDH1B1 ALDH1B1 ALDH1B1 3877 0.074 0.6 YES
16 MCEE MCEE MCEE 4352 0.062 0.59 YES
17 ALDH7A1 ALDH7A1 ALDH7A1 4437 0.06 0.61 YES
18 ACSS2 ACSS2 ACSS2 4528 0.058 0.62 YES
19 ALDH9A1 ALDH9A1 ALDH9A1 4797 0.052 0.62 YES
20 ACADM ACADM ACADM 5495 0.04 0.6 NO
21 SUCLG2 SUCLG2 SUCLG2 6439 0.027 0.56 NO
22 LDHAL6B LDHAL6B LDHAL6B 6950 0.02 0.54 NO
23 HIBCH HIBCH HIBCH 8274 0.0052 0.47 NO
24 MUT MUT MUT 9393 -0.0064 0.41 NO
25 HADHA HADHA HADHA 9777 -0.01 0.39 NO
26 ACACA ACACA ACACA 10658 -0.02 0.35 NO
27 PCCB PCCB PCCB 11114 -0.025 0.33 NO
28 ECHS1 ECHS1 ECHS1 11160 -0.025 0.34 NO
29 SUCLG1 SUCLG1 SUCLG1 11218 -0.026 0.34 NO
30 ACSS1 ACSS1 ACSS1 11326 -0.027 0.35 NO
31 ACAT1 ACAT1 ACAT1 12444 -0.04 0.3 NO
32 LDHA LDHA LDHA 13675 -0.056 0.25 NO

Figure S1.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S2.  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 PROPANOATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PAK3 PAK3 PAK3 5 0.73 0.2 YES
2 FLNC FLNC FLNC 477 0.34 0.27 YES
3 MYLK MYLK MYLK 800 0.28 0.33 YES
4 MYH2 MYH2 MYH2 839 0.27 0.4 YES
5 ACTG2 ACTG2 ACTG2 1011 0.25 0.46 YES
6 PAK7 PAK7 PAK7 1189 0.23 0.51 YES
7 FLNA FLNA FLNA 1304 0.22 0.57 YES
8 ROCK2 ROCK2 ROCK2 1370 0.21 0.62 YES
9 CFL2 CFL2 CFL2 1528 0.2 0.67 YES
10 MYLK2 MYLK2 MYLK2 2881 0.11 0.62 NO
11 ROCK1 ROCK1 ROCK1 4263 0.064 0.56 NO
12 ANGPTL2 ANGPTL2 ANGPTL2 5020 0.049 0.54 NO
13 PAK1 PAK1 PAK1 6748 0.023 0.45 NO
14 ACTR2 ACTR2 ACTR2 7092 0.019 0.43 NO
15 PAK2 PAK2 PAK2 7954 0.0086 0.39 NO
16 ACTR3 ACTR3 ACTR3 8415 0.0039 0.36 NO
17 WASL WASL WASL 8438 0.0036 0.36 NO
18 VASP VASP VASP 8568 0.0023 0.36 NO
19 PFN2 PFN2 PFN2 8616 0.0018 0.36 NO
20 AKT1 AKT1 AKT1 8881 -0.0011 0.34 NO
21 CDC42 CDC42 CDC42 9838 -0.011 0.29 NO
22 PFN1 PFN1 PFN1 10331 -0.016 0.27 NO
23 FSCN3 FSCN3 FSCN3 10526 -0.018 0.26 NO
24 GDI2 GDI2 GDI2 10920 -0.022 0.25 NO
25 PAK4 PAK4 PAK4 10973 -0.023 0.25 NO
26 CFL1 CFL1 CFL1 11779 -0.032 0.22 NO
27 ACTG1 ACTG1 ACTG1 11852 -0.033 0.22 NO
28 GDI1 GDI1 GDI1 11911 -0.034 0.23 NO
29 RPS4X RPS4X RPS4X 12167 -0.036 0.22 NO
30 RHO RHO RHO 12182 -0.037 0.23 NO
31 FSCN1 FSCN1 FSCN1 12200 -0.037 0.24 NO
32 PAK6 PAK6 PAK6 13444 -0.053 0.19 NO
33 LIMK1 LIMK1 LIMK1 13799 -0.058 0.19 NO
34 WASF1 WASF1 WASF1 14340 -0.068 0.18 NO
35 FSCN2 FSCN2 FSCN2 16592 -0.15 0.091 NO

Figure S3.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PROPANOATE METABOLISM.

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

genes ES table in pathway: KEGG ADHERENS JUNCTION

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 ACTA1 ACTA1 ACTA1 204 0.43 0.12 YES
2 ACTN2 ACTN2 ACTN2 523 0.33 0.21 YES
3 CAV1 CAV1 CAV1 988 0.25 0.27 YES
4 ITGA1 ITGA1 ITGA1 1022 0.25 0.34 YES
5 VCL VCL VCL 1215 0.22 0.41 YES
6 ACTN3 ACTN3 ACTN3 1331 0.21 0.47 YES
7 PPP1R12B PPP1R12B PPP1R12B 1444 0.2 0.53 YES
8 TNS1 TNS1 TNS1 1505 0.2 0.59 YES
9 ACTN1 ACTN1 ACTN1 2592 0.12 0.57 YES
10 TLN1 TLN1 TLN1 3154 0.1 0.57 YES
11 JUN JUN JUN 3467 0.087 0.58 YES
12 SOS1 SOS1 SOS1 4197 0.066 0.56 YES
13 ROCK1 ROCK1 ROCK1 4263 0.064 0.57 YES
14 MAPK1 MAPK1 MAPK1 4310 0.063 0.59 YES
15 ITGB1 ITGB1 ITGB1 5128 0.047 0.56 NO
16 ZYX ZYX ZYX 5487 0.041 0.56 NO
17 RAP1A RAP1A RAP1A 5716 0.037 0.56 NO
18 MAPK8 MAPK8 MAPK8 6660 0.024 0.51 NO
19 MAP2K1 MAP2K1 MAP2K1 7035 0.019 0.5 NO
20 CRKL CRKL CRKL 7072 0.019 0.5 NO
21 RAPGEF1 RAPGEF1 RAPGEF1 7131 0.018 0.5 NO
22 GRB2 GRB2 GRB2 7569 0.013 0.48 NO
23 BCAR1 BCAR1 BCAR1 7759 0.011 0.48 NO
24 PXN PXN PXN 8011 0.008 0.46 NO
25 CAPNS2 CAPNS2 CAPNS2 8217 0.006 0.46 NO
26 FYN FYN FYN 8432 0.0037 0.44 NO
27 RHOA RHOA RHOA 8975 -0.0021 0.42 NO
28 RAF1 RAF1 RAF1 9259 -0.0051 0.4 NO
29 MAPK3 MAPK3 MAPK3 9285 -0.0054 0.4 NO
30 SHC1 SHC1 SHC1 9297 -0.0055 0.4 NO
31 CAPN1 CAPN1 CAPN1 9939 -0.012 0.37 NO
32 SRC SRC SRC 10220 -0.015 0.36 NO
33 CAPNS1 CAPNS1 CAPNS1 10615 -0.019 0.35 NO
34 MAP2K2 MAP2K2 MAP2K2 11396 -0.028 0.31 NO
35 PTK2 PTK2 PTK2 11585 -0.03 0.31 NO
36 CSK CSK CSK 12196 -0.037 0.29 NO
37 BCR BCR BCR 13098 -0.048 0.26 NO
38 HRAS HRAS HRAS 15206 -0.086 0.17 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ADHERENS JUNCTION.

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

genes ES table in pathway: KEGG INSULIN SIGNALING 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 CAMK1G CAMK1G CAMK1G 201 0.43 0.2 YES
2 NFATC2 NFATC2 NFATC2 845 0.27 0.3 YES
3 IGF1 IGF1 IGF1 886 0.27 0.43 YES
4 MEF2C MEF2C MEF2C 1683 0.18 0.47 YES
5 PIK3CG PIK3CG PIK3CG 2292 0.14 0.51 YES
6 PIK3R1 PIK3R1 PIK3R1 2618 0.12 0.55 YES
7 CALM1 CALM1 CALM1 3402 0.089 0.55 YES
8 MEF2A MEF2A MEF2A 3535 0.085 0.59 YES
9 PIK3CA PIK3CA PIK3CA 3567 0.084 0.63 YES
10 MEF2D MEF2D MEF2D 4323 0.063 0.62 YES
11 PPP3CC PPP3CC PPP3CC 4350 0.062 0.64 YES
12 PPP3CB PPP3CB PPP3CB 4802 0.052 0.64 YES
13 MAPK7 MAPK7 MAPK7 5849 0.035 0.6 NO
14 INSR INSR INSR 6550 0.025 0.58 NO
15 IGF1R IGF1R IGF1R 6955 0.02 0.57 NO
16 NFATC1 NFATC1 NFATC1 7051 0.019 0.57 NO
17 CABIN1 CABIN1 CABIN1 7410 0.015 0.56 NO
18 CAMK1 CAMK1 CAMK1 7573 0.013 0.56 NO
19 HDAC5 HDAC5 HDAC5 8103 0.0069 0.53 NO
20 YWHAH YWHAH YWHAH 8264 0.0054 0.52 NO
21 CALM2 CALM2 CALM2 8591 0.0021 0.51 NO
22 AKT1 AKT1 AKT1 8881 -0.0011 0.49 NO
23 CALM3 CALM3 CALM3 8915 -0.0016 0.49 NO
24 MAPK14 MAPK14 MAPK14 9149 -0.004 0.48 NO
25 MAP2K6 MAP2K6 MAP2K6 9517 -0.0077 0.46 NO
26 PPP3CA PPP3CA PPP3CA 11885 -0.034 0.35 NO

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

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

genes ES table in pathway: KEGG THYROID CANCER

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 ACTN2 ACTN2 ACTN2 523 0.33 0.041 YES
2 SNAI2 SNAI2 SNAI2 685 0.3 0.094 YES
3 SORBS1 SORBS1 SORBS1 794 0.28 0.15 YES
4 VCL VCL VCL 1215 0.22 0.17 YES
5 ACTN3 ACTN3 ACTN3 1331 0.21 0.21 YES
6 FER FER FER 1571 0.19 0.24 YES
7 CTNNA3 CTNNA3 CTNNA3 1834 0.17 0.26 YES
8 PTPRM PTPRM PTPRM 1972 0.16 0.28 YES
9 TCF7 TCF7 TCF7 2000 0.16 0.32 YES
10 TCF7L1 TCF7L1 TCF7L1 2070 0.16 0.35 YES
11 LMO7 LMO7 LMO7 2182 0.15 0.37 YES
12 FGFR1 FGFR1 FGFR1 2200 0.15 0.4 YES
13 TGFBR2 TGFBR2 TGFBR2 2386 0.14 0.42 YES
14 EGFR EGFR EGFR 2471 0.13 0.44 YES
15 ACTN1 ACTN1 ACTN1 2592 0.12 0.46 YES
16 PTPRB PTPRB PTPRB 3429 0.088 0.44 YES
17 CTNNA2 CTNNA2 CTNNA2 3475 0.087 0.45 YES
18 SMAD4 SMAD4 SMAD4 3667 0.081 0.46 YES
19 SSX2IP SSX2IP SSX2IP 3705 0.079 0.47 YES
20 IQGAP1 IQGAP1 IQGAP1 3987 0.07 0.47 YES
21 TGFBR1 TGFBR1 TGFBR1 4126 0.067 0.48 YES
22 SNAI1 SNAI1 SNAI1 4182 0.066 0.49 YES
23 MAPK1 MAPK1 MAPK1 4310 0.063 0.5 YES
24 EP300 EP300 EP300 4311 0.063 0.51 YES
25 PVRL3 PVRL3 PVRL3 4775 0.053 0.49 NO
26 PTPN1 PTPN1 PTPN1 4921 0.05 0.5 NO
27 MET MET MET 5095 0.047 0.5 NO
28 SMAD3 SMAD3 SMAD3 5297 0.044 0.5 NO
29 BAIAP2 BAIAP2 BAIAP2 5544 0.04 0.49 NO
30 TCF7L2 TCF7L2 TCF7L2 5771 0.036 0.48 NO
31 CREBBP CREBBP CREBBP 5796 0.036 0.49 NO
32 CDH1 CDH1 CDH1 6263 0.029 0.47 NO
33 CTNNB1 CTNNB1 CTNNB1 6338 0.028 0.47 NO
34 WASF3 WASF3 WASF3 6392 0.028 0.48 NO
35 INSR INSR INSR 6550 0.025 0.47 NO
36 MAP3K7 MAP3K7 MAP3K7 6595 0.025 0.48 NO
37 ACTB ACTB ACTB 6663 0.024 0.48 NO
38 PARD3 PARD3 PARD3 6736 0.023 0.48 NO
39 CTNND1 CTNND1 CTNND1 6833 0.022 0.48 NO
40 IGF1R IGF1R IGF1R 6955 0.02 0.48 NO
41 MLLT4 MLLT4 MLLT4 7362 0.015 0.46 NO
42 ACTN4 ACTN4 ACTN4 7443 0.014 0.45 NO
43 TJP1 TJP1 TJP1 7533 0.013 0.45 NO
44 PTPRF PTPRF PTPRF 7577 0.013 0.45 NO
45 ERBB2 ERBB2 ERBB2 7804 0.01 0.44 NO
46 PVRL4 PVRL4 PVRL4 7846 0.0098 0.44 NO
47 WASF2 WASF2 WASF2 7854 0.0097 0.44 NO
48 CTNNA1 CTNNA1 CTNNA1 8219 0.006 0.42 NO
49 SMAD2 SMAD2 SMAD2 8250 0.0055 0.42 NO
50 FYN FYN FYN 8432 0.0037 0.42 NO
51 WASL WASL WASL 8438 0.0036 0.42 NO
52 CSNK2A2 CSNK2A2 CSNK2A2 8759 0.000045 0.4 NO
53 RHOA RHOA RHOA 8975 -0.0021 0.39 NO
54 NLK NLK NLK 9125 -0.0038 0.38 NO
55 PTPRJ PTPRJ PTPRJ 9267 -0.0052 0.37 NO
56 MAPK3 MAPK3 MAPK3 9285 -0.0054 0.37 NO
57 YES1 YES1 YES1 9462 -0.0073 0.36 NO
58 PTPN6 PTPN6 PTPN6 9756 -0.01 0.35 NO
59 PVRL2 PVRL2 PVRL2 9802 -0.01 0.35 NO
60 CDC42 CDC42 CDC42 9838 -0.011 0.35 NO
61 PVRL1 PVRL1 PVRL1 10036 -0.013 0.34 NO
62 SRC SRC SRC 10220 -0.015 0.34 NO
63 CSNK2A1 CSNK2A1 CSNK2A1 10443 -0.017 0.33 NO
64 RAC1 RAC1 RAC1 10867 -0.022 0.31 NO
65 RAC2 RAC2 RAC2 11154 -0.025 0.3 NO
66 ACP1 ACP1 ACP1 11562 -0.03 0.28 NO
67 LEF1 LEF1 LEF1 11583 -0.03 0.29 NO
68 ACTG1 ACTG1 ACTG1 11852 -0.033 0.28 NO
69 CSNK2B CSNK2B CSNK2B 12664 -0.042 0.24 NO
70 FARP2 FARP2 FARP2 13572 -0.055 0.2 NO
71 WAS WAS WAS 13892 -0.06 0.2 NO
72 WASF1 WASF1 WASF1 14340 -0.068 0.19 NO
73 RAC3 RAC3 RAC3 16208 -0.12 0.11 NO

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

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

genes ES table in pathway: BIOCARTA AGR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 152 0.46 0.099 YES
2 ITGB3 ITGB3 ITGB3 195 0.44 0.2 YES
3 CAV1 CAV1 CAV1 988 0.25 0.22 YES
4 VCL VCL VCL 1215 0.22 0.26 YES
5 PRKCA PRKCA PRKCA 1470 0.2 0.29 YES
6 KDR KDR KDR 1480 0.2 0.34 YES
7 NEDD4 NEDD4 NEDD4 1796 0.18 0.36 YES
8 MYOF MYOF MYOF 2017 0.16 0.39 YES
9 PRKAA2 PRKAA2 PRKAA2 2469 0.13 0.39 YES
10 PIK3R1 PIK3R1 PIK3R1 2618 0.12 0.41 YES
11 FLT1 FLT1 FLT1 2653 0.12 0.44 YES
12 PIK3CA PIK3CA PIK3CA 3567 0.084 0.41 YES
13 CDH5 CDH5 CDH5 3944 0.072 0.41 YES
14 IQGAP1 IQGAP1 IQGAP1 3987 0.07 0.42 YES
15 ITGAV ITGAV ITGAV 4029 0.069 0.44 YES
16 PTPN11 PTPN11 PTPN11 4205 0.065 0.44 YES
17 ROCK1 ROCK1 ROCK1 4263 0.064 0.45 YES
18 CBL CBL CBL 4265 0.064 0.47 YES
19 MAPK1 MAPK1 MAPK1 4310 0.063 0.48 YES
20 PTK2B PTK2B PTK2B 4747 0.054 0.47 NO
21 AKAP1 AKAP1 AKAP1 4835 0.052 0.48 NO
22 GAB1 GAB1 GAB1 5615 0.038 0.44 NO
23 FBXW11 FBXW11 FBXW11 5873 0.034 0.44 NO
24 GRB10 GRB10 GRB10 5994 0.033 0.44 NO
25 VEGFA VEGFA VEGFA 6160 0.03 0.44 NO
26 SHB SHB SHB 6186 0.03 0.44 NO
27 PDPK1 PDPK1 PDPK1 6296 0.029 0.44 NO
28 CTNNB1 CTNNB1 CTNNB1 6338 0.028 0.45 NO
29 NOS3 NOS3 NOS3 6518 0.026 0.44 NO
30 MAP2K1 MAP2K1 MAP2K1 7035 0.019 0.42 NO
31 HSP90AA1 HSP90AA1 HSP90AA1 7402 0.015 0.4 NO
32 PRKACA PRKACA PRKACA 7495 0.014 0.4 NO
33 GRB2 GRB2 GRB2 7569 0.013 0.4 NO
34 PAK2 PAK2 PAK2 7954 0.0086 0.38 NO
35 PXN PXN PXN 8011 0.008 0.38 NO
36 CTNNA1 CTNNA1 CTNNA1 8219 0.006 0.37 NO
37 CAMKK2 CAMKK2 CAMKK2 8411 0.0039 0.36 NO
38 FYN FYN FYN 8432 0.0037 0.36 NO
39 PRKAA1 PRKAA1 PRKAA1 8599 0.002 0.35 NO
40 DNM2 DNM2 DNM2 8717 0.00053 0.34 NO
41 AKT1 AKT1 AKT1 8881 -0.0011 0.34 NO
42 PRKAB1 PRKAB1 PRKAB1 8890 -0.0012 0.34 NO
43 RHOA RHOA RHOA 8975 -0.0021 0.33 NO
44 ARF1 ARF1 ARF1 9113 -0.0037 0.32 NO
45 MAPK14 MAPK14 MAPK14 9149 -0.004 0.32 NO
46 RAF1 RAF1 RAF1 9259 -0.0051 0.32 NO
47 PTPRJ PTPRJ PTPRJ 9267 -0.0052 0.32 NO
48 MAPK3 MAPK3 MAPK3 9285 -0.0054 0.32 NO
49 PRKAG1 PRKAG1 PRKAG1 9415 -0.0067 0.31 NO
50 MAP2K6 MAP2K6 MAP2K6 9517 -0.0077 0.31 NO
51 NCK2 NCK2 NCK2 9660 -0.0092 0.3 NO
52 PTPN6 PTPN6 PTPN6 9756 -0.01 0.3 NO
53 CDC42 CDC42 CDC42 9838 -0.011 0.3 NO
54 SRC SRC SRC 10220 -0.015 0.28 NO
55 HGS HGS HGS 10404 -0.017 0.28 NO
56 MAPK11 MAPK11 MAPK11 10414 -0.017 0.28 NO
57 FES FES FES 10497 -0.018 0.28 NO
58 MAP2K2 MAP2K2 MAP2K2 11396 -0.028 0.24 NO
59 PTK2 PTK2 PTK2 11585 -0.03 0.23 NO
60 MAP2K3 MAP2K3 MAP2K3 11737 -0.032 0.23 NO
61 NCK1 NCK1 NCK1 11856 -0.033 0.23 NO
62 MAPKAPK2 MAPKAPK2 MAPKAPK2 11941 -0.034 0.24 NO
63 PLCG1 PLCG1 PLCG1 12034 -0.035 0.24 NO
64 BRAF BRAF BRAF 12356 -0.039 0.23 NO
65 HSP90AB1 HSP90AB1 HSP90AB1 12818 -0.044 0.22 NO
66 PTPN2 PTPN2 PTPN2 14011 -0.062 0.17 NO
67 SH2D2A SH2D2A SH2D2A 14495 -0.07 0.16 NO
68 PRKCD PRKCD PRKCD 14667 -0.074 0.16 NO
69 VTN VTN VTN 16531 -0.14 0.095 NO

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

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

genes ES table in pathway: BIOCARTA HDAC PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 152 0.46 0.2 YES
2 CAMK2A CAMK2A CAMK2A 164 0.45 0.4 YES
3 PRKCA PRKCA PRKCA 1470 0.2 0.42 YES
4 PRKAR2A PRKAR2A PRKAR2A 1486 0.2 0.51 YES
5 CAMK2G CAMK2G CAMK2G 2549 0.13 0.51 YES
6 PIK3R1 PIK3R1 PIK3R1 2618 0.12 0.56 YES
7 PIK3CA PIK3CA PIK3CA 3567 0.084 0.55 YES
8 SOS1 SOS1 SOS1 4197 0.066 0.54 YES
9 PRKAR2B PRKAR2B PRKAR2B 4273 0.064 0.56 YES
10 MAPK1 MAPK1 MAPK1 4310 0.063 0.59 YES
11 RPS6KA5 RPS6KA5 RPS6KA5 5482 0.041 0.55 NO
12 PRKACB PRKACB PRKACB 5519 0.04 0.56 NO
13 PRKAR1A PRKAR1A PRKAR1A 6282 0.029 0.53 NO
14 CREB1 CREB1 CREB1 7163 0.018 0.49 NO
15 GRB2 GRB2 GRB2 7569 0.013 0.48 NO
16 CAMK2D CAMK2D CAMK2D 8838 -0.00074 0.41 NO
17 AKT1 AKT1 AKT1 8881 -0.0011 0.4 NO
18 MAPK14 MAPK14 MAPK14 9149 -0.004 0.39 NO
19 MAPK3 MAPK3 MAPK3 9285 -0.0054 0.39 NO
20 CAMK2B CAMK2B CAMK2B 9476 -0.0074 0.38 NO
21 ADCY1 ADCY1 ADCY1 10231 -0.015 0.34 NO
22 RAC1 RAC1 RAC1 10867 -0.022 0.32 NO
23 GNAS GNAS GNAS 11117 -0.025 0.32 NO
24 RPS6KA1 RPS6KA1 RPS6KA1 11294 -0.027 0.32 NO
25 PRKAR1B PRKAR1B PRKAR1B 13330 -0.052 0.23 NO
26 HRAS HRAS HRAS 15206 -0.086 0.17 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: BIOCARTA HDAC PATHWAY.

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

genes ES table in pathway: BIOCARTA INTEGRIN PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 152 0.46 0.15 YES
2 MYL2 MYL2 MYL2 647 0.3 0.23 YES
3 MYLK MYLK MYLK 800 0.28 0.32 YES
4 PPP1R12B PPP1R12B PPP1R12B 1444 0.2 0.35 YES
5 PRKCA PRKCA PRKCA 1470 0.2 0.42 YES
6 ARHGEF4 ARHGEF4 ARHGEF4 2152 0.15 0.44 YES
7 ARHGEF7 ARHGEF7 ARHGEF7 2833 0.11 0.44 YES
8 ARHGEF17 ARHGEF17 ARHGEF17 2962 0.11 0.47 YES
9 ARHGEF6 ARHGEF6 ARHGEF6 3099 0.1 0.5 YES
10 ARHGEF9 ARHGEF9 ARHGEF9 3119 0.1 0.53 YES
11 ARHGEF10 ARHGEF10 ARHGEF10 3137 0.1 0.57 YES
12 PLCB1 PLCB1 PLCB1 3235 0.096 0.6 YES
13 ARHGEF15 ARHGEF15 ARHGEF15 3502 0.086 0.61 YES
14 ROCK1 ROCK1 ROCK1 4263 0.064 0.59 NO
15 ARHGEF2 ARHGEF2 ARHGEF2 5686 0.037 0.53 NO
16 ARHGEF12 ARHGEF12 ARHGEF12 5818 0.035 0.53 NO
17 GNAQ GNAQ GNAQ 5836 0.035 0.54 NO
18 GNA12 GNA12 GNA12 6515 0.026 0.52 NO
19 ARHGEF18 ARHGEF18 ARHGEF18 6644 0.024 0.52 NO
20 ARHGAP5 ARHGAP5 ARHGAP5 6675 0.024 0.52 NO
21 ARHGEF11 ARHGEF11 ARHGEF11 6677 0.024 0.53 NO
22 ARHGEF5 ARHGEF5 ARHGEF5 6996 0.02 0.52 NO
23 GNA13 GNA13 GNA13 8311 0.0049 0.45 NO
24 GNB1 GNB1 GNB1 8425 0.0038 0.44 NO
25 ARHGEF3 ARHGEF3 ARHGEF3 12361 -0.039 0.24 NO
26 ARHGEF1 ARHGEF1 ARHGEF1 12509 -0.04 0.25 NO
27 ARHGEF19 ARHGEF19 ARHGEF19 13032 -0.048 0.24 NO
28 ARHGEF16 ARHGEF16 ARHGEF16 13204 -0.05 0.24 NO
29 PKN1 PKN1 PKN1 15439 -0.093 0.16 NO

Figure S15.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA INTEGRIN PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

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 PAK3 PAK3 PAK3 5 0.73 0.17 YES
2 ACTA1 ACTA1 ACTA1 204 0.43 0.26 YES
3 NRG2 NRG2 NRG2 239 0.42 0.35 YES
4 NRG1 NRG1 NRG1 498 0.34 0.41 YES
5 DMD DMD DMD 775 0.28 0.46 YES
6 ITGA1 ITGA1 ITGA1 1022 0.25 0.5 YES
7 PAK7 PAK7 PAK7 1189 0.23 0.55 YES
8 MUSK MUSK MUSK 1340 0.21 0.59 YES
9 CHRM1 CHRM1 CHRM1 1544 0.19 0.62 YES
10 LAMA2 LAMA2 LAMA2 2010 0.16 0.63 YES
11 EGFR EGFR EGFR 2471 0.13 0.64 YES
12 LAMA4 LAMA4 LAMA4 2526 0.13 0.67 YES
13 CHRNA1 CHRNA1 CHRNA1 2598 0.12 0.69 YES
14 JUN JUN JUN 3467 0.087 0.66 NO
15 MAPK1 MAPK1 MAPK1 4310 0.063 0.63 NO
16 RAPSN RAPSN RAPSN 4534 0.058 0.63 NO
17 ITGB1 ITGB1 ITGB1 5128 0.047 0.61 NO
18 MAPK8 MAPK8 MAPK8 6660 0.024 0.53 NO
19 SP1 SP1 SP1 6700 0.024 0.54 NO
20 PAK1 PAK1 PAK1 6748 0.023 0.54 NO
21 DAG1 DAG1 DAG1 7036 0.019 0.53 NO
22 LAMA3 LAMA3 LAMA3 7428 0.014 0.51 NO
23 PAK2 PAK2 PAK2 7954 0.0086 0.48 NO
24 PXN PXN PXN 8011 0.008 0.48 NO
25 UTRN UTRN UTRN 8112 0.0069 0.48 NO
26 GIT2 GIT2 GIT2 8287 0.0051 0.47 NO
27 MAPK3 MAPK3 MAPK3 9285 -0.0054 0.42 NO
28 CTTN CTTN CTTN 9436 -0.0069 0.41 NO
29 CDC42 CDC42 CDC42 9838 -0.011 0.39 NO
30 SRC SRC SRC 10220 -0.015 0.37 NO
31 RAC1 RAC1 RAC1 10867 -0.022 0.34 NO
32 PAK4 PAK4 PAK4 10973 -0.023 0.34 NO
33 PTK2 PTK2 PTK2 11585 -0.03 0.31 NO
34 PAK6 PAK6 PAK6 13444 -0.053 0.22 NO
35 DVL1 DVL1 DVL1 14683 -0.074 0.17 NO
36 NRG3 NRG3 NRG3 15645 -0.1 0.14 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: BIOCARTA PYK2 PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 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 MYOSIN PATHWAY

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 PRKCB PRKCB PRKCB 152 0.46 0.3 YES
2 PRKCA PRKCA PRKCA 1470 0.2 0.36 YES
3 CALM1 CALM1 CALM1 3402 0.089 0.31 YES
4 JUN JUN JUN 3467 0.087 0.37 YES
5 MAP2K4 MAP2K4 MAP2K4 4056 0.069 0.38 YES
6 SOS1 SOS1 SOS1 4197 0.066 0.42 YES
7 MAPK1 MAPK1 MAPK1 4310 0.063 0.45 YES
8 PTK2B PTK2B PTK2B 4747 0.054 0.46 YES
9 GNAQ GNAQ GNAQ 5836 0.035 0.43 NO
10 MAP3K1 MAP3K1 MAP3K1 6134 0.031 0.43 NO
11 MAPK8 MAPK8 MAPK8 6660 0.024 0.42 NO
12 PAK1 PAK1 PAK1 6748 0.023 0.43 NO
13 MAP2K1 MAP2K1 MAP2K1 7035 0.019 0.43 NO
14 CRKL CRKL CRKL 7072 0.019 0.44 NO
15 GRB2 GRB2 GRB2 7569 0.013 0.42 NO
16 BCAR1 BCAR1 BCAR1 7759 0.011 0.41 NO
17 CALM2 CALM2 CALM2 8591 0.0021 0.37 NO
18 CALM3 CALM3 CALM3 8915 -0.0016 0.35 NO
19 MAPK14 MAPK14 MAPK14 9149 -0.004 0.34 NO
20 RAF1 RAF1 RAF1 9259 -0.0051 0.34 NO
21 MAPK3 MAPK3 MAPK3 9285 -0.0054 0.34 NO
22 SHC1 SHC1 SHC1 9297 -0.0055 0.35 NO
23 SRC SRC SRC 10220 -0.015 0.3 NO
24 RAC1 RAC1 RAC1 10867 -0.022 0.28 NO
25 MAP2K2 MAP2K2 MAP2K2 11396 -0.028 0.27 NO
26 MAP2K3 MAP2K3 MAP2K3 11737 -0.032 0.28 NO
27 PLCG1 PLCG1 PLCG1 12034 -0.035 0.28 NO
28 HRAS HRAS HRAS 15206 -0.086 0.17 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: BIOCARTA MYOSIN PATHWAY.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MYOSIN 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 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 CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.51 1.7 0.029 0.44 0.75 0.034 0.00038 0.034 0.17 0.12
KEGG N GLYCAN BIOSYNTHESIS 46 genes.ES.table 0.49 1.6 0.031 0.55 0.9 0.46 0.29 0.32 0.26 0.15
KEGG UBIQUITIN MEDIATED PROTEOLYSIS 133 genes.ES.table 0.31 1.8 0.0019 0.71 0.56 0.44 0.3 0.32 0.17 0.16
PID ECADHERIN NASCENTAJ PATHWAY 39 genes.ES.table 0.38 1.6 0.032 0.54 0.9 0.33 0.24 0.25 0.27 0.16
PID LIS1PATHWAY 28 genes.ES.table 0.58 1.8 0.0063 0.43 0.62 0.21 0.087 0.2 0.12 0.1
REACTOME METABOLISM OF NON CODING RNA 47 genes.ES.table 0.5 1.8 0.042 0.55 0.57 0.68 0.37 0.43 0.14 0.14
REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 36 genes.ES.table 0.55 1.6 0.016 0.57 0.89 0.5 0.25 0.38 0.27 0.16
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM 44 genes.ES.table 0.53 1.9 0.004 0.55 0.36 0.61 0.33 0.41 0 0.12
REACTOME RNA POL II TRANSCRIPTION 93 genes.ES.table 0.34 1.6 0.066 0.6 0.94 0.38 0.32 0.26 0.33 0.18
REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES 59 genes.ES.table 0.41 1.6 0.089 0.62 0.95 0.32 0.22 0.25 0.37 0.18
genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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 CCNT1 CCNT1 CCNT1 534 0.23 0.023 YES
2 TAF4B TAF4B TAF4B 808 0.18 0.05 YES
3 GTF2A1 GTF2A1 GTF2A1 845 0.18 0.088 YES
4 GTF2H2 GTF2H2 GTF2H2 1117 0.15 0.11 YES
5 NUP210 NUP210 NUP210 1167 0.15 0.14 YES
6 GTF2H3 GTF2H3 GTF2H3 1408 0.13 0.16 YES
7 RCC1 RCC1 RCC1 1622 0.12 0.17 YES
8 TAF1 TAF1 TAF1 1789 0.11 0.18 YES
9 GTF2E1 GTF2E1 GTF2E1 1841 0.11 0.21 YES
10 NUP155 NUP155 NUP155 2195 0.092 0.21 YES
11 RANBP2 RANBP2 RANBP2 2435 0.086 0.22 YES
12 CCNT2 CCNT2 CCNT2 2543 0.083 0.23 YES
13 TAF4 TAF4 TAF4 2743 0.077 0.23 YES
14 NUP54 NUP54 NUP54 2756 0.077 0.25 YES
15 TPR TPR TPR 2985 0.071 0.26 YES
16 NUPL1 NUPL1 NUPL1 3073 0.069 0.27 YES
17 CDK7 CDK7 CDK7 3142 0.068 0.28 YES
18 POM121 POM121 POM121 3241 0.065 0.29 YES
19 NUP133 NUP133 NUP133 3284 0.064 0.3 YES
20 NUP153 NUP153 NUP153 3387 0.062 0.31 YES
21 POLR2B POLR2B POLR2B 3577 0.059 0.31 YES
22 TAF9 TAF9 TAF9 3631 0.058 0.32 YES
23 XPO1 XPO1 XPO1 3662 0.057 0.33 YES
24 POLR2D POLR2D POLR2D 3706 0.056 0.34 YES
25 NUP205 NUP205 NUP205 3924 0.052 0.34 YES
26 SEH1L SEH1L SEH1L 3927 0.052 0.35 YES
27 RNGTT RNGTT RNGTT 4072 0.05 0.36 YES
28 TAF13 TAF13 TAF13 4226 0.048 0.36 YES
29 NCBP1 NCBP1 NCBP1 4246 0.048 0.37 YES
30 NUP188 NUP188 NUP188 4343 0.046 0.38 YES
31 NUP50 NUP50 NUP50 4709 0.041 0.36 YES
32 RNMT RNMT RNMT 4763 0.04 0.37 YES
33 GTF2H2B GTF2H2B GTF2H2B 4963 0.036 0.37 YES
34 SSRP1 SSRP1 SSRP1 5029 0.036 0.37 YES
35 ERCC3 ERCC3 ERCC3 5072 0.035 0.38 YES
36 TSG101 TSG101 TSG101 5236 0.033 0.38 YES
37 SUPT16H SUPT16H SUPT16H 5336 0.032 0.38 YES
38 NUP43 NUP43 NUP43 5341 0.032 0.38 YES
39 RANBP1 RANBP1 RANBP1 5423 0.03 0.39 YES
40 GTF2H1 GTF2H1 GTF2H1 5431 0.03 0.39 YES
41 NUP107 NUP107 NUP107 5505 0.029 0.4 YES
42 NUPL2 NUPL2 NUPL2 5570 0.028 0.4 YES
43 GTF2A2 GTF2A2 GTF2A2 5800 0.025 0.39 YES
44 NUP37 NUP37 NUP37 5914 0.023 0.39 YES
45 MNAT1 MNAT1 MNAT1 5965 0.022 0.39 YES
46 NUP214 NUP214 NUP214 6006 0.022 0.4 YES
47 VPS37A VPS37A VPS37A 6018 0.022 0.4 YES
48 RAN RAN RAN 6225 0.019 0.39 NO
49 RAE1 RAE1 RAE1 6332 0.018 0.39 NO
50 CCNH CCNH CCNH 6509 0.016 0.39 NO
51 NCBP2 NCBP2 NCBP2 6679 0.014 0.38 NO
52 NUP62 NUP62 NUP62 6823 0.012 0.38 NO
53 POLR2A POLR2A POLR2A 6936 0.01 0.37 NO
54 TCEA1 TCEA1 TCEA1 6953 0.0099 0.37 NO
55 TCEB3 TCEB3 TCEB3 7236 0.0065 0.36 NO
56 POLR2C POLR2C POLR2C 7468 0.0038 0.35 NO
57 GTF2E2 GTF2E2 GTF2E2 7543 0.0027 0.34 NO
58 WHSC2 WHSC2 WHSC2 7621 0.0017 0.34 NO
59 CTDP1 CTDP1 CTDP1 7891 -0.0016 0.32 NO
60 NMT1 NMT1 NMT1 7934 -0.0023 0.32 NO
61 COBRA1 COBRA1 COBRA1 7989 -0.0028 0.32 NO
62 TBP TBP TBP 8031 -0.0032 0.32 NO
63 ERCC2 ERCC2 ERCC2 8157 -0.005 0.31 NO
64 RANGAP1 RANGAP1 RANGAP1 8191 -0.0053 0.31 NO
65 NUP88 NUP88 NUP88 8218 -0.0057 0.31 NO
66 RPS27A RPS27A RPS27A 8342 -0.0071 0.31 NO
67 AAAS AAAS AAAS 8506 -0.0094 0.3 NO
68 VPS37D VPS37D VPS37D 8535 -0.0099 0.3 NO
69 TH1L TH1L TH1L 8562 -0.01 0.3 NO
70 POLR2H POLR2H POLR2H 8577 -0.01 0.3 NO
71 NMT2 NMT2 NMT2 8684 -0.012 0.3 NO
72 TAF5 TAF5 TAF5 8709 -0.012 0.3 NO
73 NUP35 NUP35 NUP35 8846 -0.014 0.3 NO
74 TAF12 TAF12 TAF12 8897 -0.014 0.3 NO
75 NUP93 NUP93 NUP93 9030 -0.016 0.3 NO
76 TCEB1 TCEB1 TCEB1 9057 -0.016 0.3 NO
77 TAF11 TAF11 TAF11 9111 -0.017 0.3 NO
78 NUP85 NUP85 NUP85 9155 -0.018 0.3 NO
79 GTF2F2 GTF2F2 GTF2F2 9403 -0.021 0.29 NO
80 GTF2F1 GTF2F1 GTF2F1 9438 -0.021 0.29 NO
81 POLR2K POLR2K POLR2K 9532 -0.022 0.29 NO
82 CDK9 CDK9 CDK9 9572 -0.023 0.3 NO
83 UBA52 UBA52 UBA52 9623 -0.024 0.3 NO
84 TAF6 TAF6 TAF6 9660 -0.024 0.3 NO
85 SUPT4H1 SUPT4H1 SUPT4H1 9920 -0.028 0.3 NO
86 GTF2H4 GTF2H4 GTF2H4 9932 -0.028 0.3 NO
87 ELL ELL ELL 9970 -0.029 0.3 NO
88 SUPT5H SUPT5H SUPT5H 9981 -0.029 0.31 NO
89 VPS37C VPS37C VPS37C 10056 -0.03 0.31 NO
90 POLR2F POLR2F POLR2F 10472 -0.036 0.3 NO
91 VPS37B VPS37B VPS37B 10562 -0.037 0.3 NO
92 RDBP RDBP RDBP 10609 -0.038 0.31 NO
93 POLR2E POLR2E POLR2E 10610 -0.038 0.32 NO
94 TAF10 TAF10 TAF10 10632 -0.039 0.33 NO
95 VPS28 VPS28 VPS28 11012 -0.044 0.32 NO
96 POLR2G POLR2G POLR2G 11172 -0.047 0.32 NO
97 GTF2B GTF2B GTF2B 11558 -0.054 0.31 NO
98 POLR2L POLR2L POLR2L 11891 -0.06 0.3 NO
99 POLR2I POLR2I POLR2I 12011 -0.063 0.31 NO
100 POLR2J POLR2J POLR2J 12325 -0.069 0.31 NO
101 TCEB2 TCEB2 TCEB2 12641 -0.076 0.31 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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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 NUP210 NUP210 NUP210 1167 0.15 0.022 YES
2 CDC40 CDC40 CDC40 1643 0.12 0.064 YES
3 NUP155 NUP155 NUP155 2195 0.092 0.088 YES
4 RANBP2 RANBP2 RANBP2 2435 0.086 0.12 YES
5 NUP54 NUP54 NUP54 2756 0.077 0.15 YES
6 TPR TPR TPR 2985 0.071 0.18 YES
7 NUPL1 NUPL1 NUPL1 3073 0.069 0.22 YES
8 POM121 POM121 POM121 3241 0.065 0.25 YES
9 NUP133 NUP133 NUP133 3284 0.064 0.28 YES
10 NUP153 NUP153 NUP153 3387 0.062 0.31 YES
11 NUP205 NUP205 NUP205 3924 0.052 0.31 YES
12 SEH1L SEH1L SEH1L 3927 0.052 0.34 YES
13 CPSF2 CPSF2 CPSF2 4117 0.049 0.36 YES
14 NCBP1 NCBP1 NCBP1 4246 0.048 0.38 YES
15 NUP188 NUP188 NUP188 4343 0.046 0.41 YES
16 EIF4E EIF4E EIF4E 4414 0.045 0.43 YES
17 NUP50 NUP50 NUP50 4709 0.041 0.44 YES
18 CPSF3 CPSF3 CPSF3 5144 0.034 0.43 YES
19 NFX1 NFX1 NFX1 5163 0.034 0.45 YES
20 NUP43 NUP43 NUP43 5341 0.032 0.46 YES
21 NUP107 NUP107 NUP107 5505 0.029 0.47 YES
22 RBM8A RBM8A RBM8A 5565 0.028 0.48 YES
23 NUPL2 NUPL2 NUPL2 5570 0.028 0.5 YES
24 UPF3B UPF3B UPF3B 5751 0.026 0.5 YES
25 NUP37 NUP37 NUP37 5914 0.023 0.51 YES
26 NUP214 NUP214 NUP214 6006 0.022 0.52 YES
27 U2AF2 U2AF2 U2AF2 6014 0.022 0.53 YES
28 RAE1 RAE1 RAE1 6332 0.018 0.52 NO
29 NCBP2 NCBP2 NCBP2 6679 0.014 0.51 NO
30 NUP62 NUP62 NUP62 6823 0.012 0.51 NO
31 THOC4 THOC4 THOC4 7518 0.0031 0.47 NO
32 SLBP SLBP SLBP 7547 0.0027 0.47 NO
33 U2AF1 U2AF1 U2AF1 8180 -0.0052 0.44 NO
34 NUP88 NUP88 NUP88 8218 -0.0057 0.44 NO
35 MAGOH MAGOH MAGOH 8457 -0.0086 0.43 NO
36 AAAS AAAS AAAS 8506 -0.0094 0.44 NO
37 NUP35 NUP35 NUP35 8846 -0.014 0.43 NO
38 RNPS1 RNPS1 RNPS1 8939 -0.015 0.43 NO
39 NUP93 NUP93 NUP93 9030 -0.016 0.44 NO
40 NUP85 NUP85 NUP85 9155 -0.018 0.44 NO
41 SRRM1 SRRM1 SRRM1 9259 -0.019 0.44 NO
42 DHX38 DHX38 DHX38 9535 -0.023 0.44 NO
43 CPSF1 CPSF1 CPSF1 9996 -0.029 0.43 NO
44 NXF1 NXF1 NXF1 10311 -0.034 0.44 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 N GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS

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 CBLC CBLC CBLC 558 0.23 0.0016 YES
2 UBE2NL UBE2NL UBE2NL 826 0.18 0.012 YES
3 SKP2 SKP2 SKP2 852 0.18 0.036 YES
4 UBE2E3 UBE2E3 UBE2E3 884 0.17 0.06 YES
5 ANAPC1 ANAPC1 ANAPC1 1258 0.14 0.059 YES
6 NHLRC1 NHLRC1 NHLRC1 1270 0.14 0.078 YES
7 MID1 MID1 MID1 1860 0.11 0.061 YES
8 ERCC8 ERCC8 ERCC8 2067 0.098 0.063 YES
9 PARK2 PARK2 PARK2 2087 0.097 0.076 YES
10 TRIM37 TRIM37 TRIM37 2127 0.095 0.087 YES
11 WWP2 WWP2 WWP2 2320 0.089 0.09 YES
12 XIAP XIAP XIAP 2472 0.085 0.093 YES
13 CDC20 CDC20 CDC20 2547 0.083 0.1 YES
14 BIRC6 BIRC6 BIRC6 2578 0.082 0.11 YES
15 HERC2 HERC2 HERC2 2725 0.078 0.11 YES
16 HERC1 HERC1 HERC1 2770 0.077 0.12 YES
17 VHL VHL VHL 2777 0.076 0.13 YES
18 CUL7 CUL7 CUL7 2878 0.074 0.14 YES
19 ITCH ITCH ITCH 2905 0.073 0.15 YES
20 UBE2C UBE2C UBE2C 2975 0.072 0.15 YES
21 HERC3 HERC3 HERC3 2980 0.071 0.16 YES
22 CUL4B CUL4B CUL4B 3046 0.07 0.17 YES
23 UBE3C UBE3C UBE3C 3063 0.07 0.18 YES
24 RCHY1 RCHY1 RCHY1 3097 0.069 0.19 YES
25 UBE2J1 UBE2J1 UBE2J1 3170 0.067 0.19 YES
26 UBA2 UBA2 UBA2 3186 0.066 0.2 YES
27 PIAS2 PIAS2 PIAS2 3204 0.066 0.21 YES
28 KLHL9 KLHL9 KLHL9 3215 0.066 0.22 YES
29 UBE2G1 UBE2G1 UBE2G1 3255 0.065 0.22 YES
30 UBE2H UBE2H UBE2H 3314 0.064 0.23 YES
31 CBLB CBLB CBLB 3334 0.063 0.24 YES
32 SIAH1 SIAH1 SIAH1 3380 0.063 0.25 YES
33 UBE2W UBE2W UBE2W 3425 0.062 0.25 YES
34 BRCA1 BRCA1 BRCA1 3447 0.062 0.26 YES
35 PIAS3 PIAS3 PIAS3 3583 0.059 0.26 YES
36 TRIM32 TRIM32 TRIM32 3621 0.058 0.27 YES
37 UBR5 UBR5 UBR5 3931 0.052 0.26 YES
38 UBE2K UBE2K UBE2K 3952 0.052 0.26 YES
39 FBXW11 FBXW11 FBXW11 4042 0.05 0.27 YES
40 CUL5 CUL5 CUL5 4075 0.05 0.27 YES
41 UBE3A UBE3A UBE3A 4080 0.05 0.28 YES
42 NEDD4L NEDD4L NEDD4L 4218 0.048 0.28 YES
43 HUWE1 HUWE1 HUWE1 4249 0.048 0.28 YES
44 RFWD2 RFWD2 RFWD2 4555 0.043 0.27 YES
45 BIRC2 BIRC2 BIRC2 4594 0.043 0.28 YES
46 UBE2I UBE2I UBE2I 4608 0.042 0.28 YES
47 UBA3 UBA3 UBA3 4638 0.042 0.28 YES
48 UBE2Q2 UBE2Q2 UBE2Q2 4654 0.042 0.29 YES
49 TRIP12 TRIP12 TRIP12 4663 0.041 0.3 YES
50 UBE2N UBE2N UBE2N 4795 0.039 0.29 YES
51 PIAS1 PIAS1 PIAS1 4943 0.037 0.29 YES
52 MAP3K1 MAP3K1 MAP3K1 4967 0.036 0.3 YES
53 UBE2R2 UBE2R2 UBE2R2 5044 0.035 0.3 YES
54 DET1 DET1 DET1 5107 0.035 0.3 YES
55 TRAF6 TRAF6 TRAF6 5140 0.034 0.3 YES
56 UBE4B UBE4B UBE4B 5277 0.032 0.3 YES
57 FBXO4 FBXO4 FBXO4 5294 0.032 0.3 YES
58 HERC4 HERC4 HERC4 5360 0.031 0.3 YES
59 CDC27 CDC27 CDC27 5390 0.031 0.3 YES
60 UBE2Q1 UBE2Q1 UBE2Q1 5634 0.027 0.3 NO
61 ANAPC10 ANAPC10 ANAPC10 5668 0.027 0.3 NO
62 DDB1 DDB1 DDB1 5764 0.026 0.3 NO
63 CUL2 CUL2 CUL2 5831 0.025 0.3 NO
64 FBXW8 FBXW8 FBXW8 5855 0.024 0.3 NO
65 UBA6 UBA6 UBA6 5983 0.022 0.29 NO
66 CUL3 CUL3 CUL3 6239 0.019 0.28 NO
67 UBE2O UBE2O UBE2O 6255 0.019 0.28 NO
68 UBE2A UBE2A UBE2A 6258 0.019 0.29 NO
69 PIAS4 PIAS4 PIAS4 6262 0.019 0.29 NO
70 UBE2Z UBE2Z UBE2Z 6294 0.018 0.29 NO
71 SYVN1 SYVN1 SYVN1 6326 0.018 0.29 NO
72 UBE2E2 UBE2E2 UBE2E2 6508 0.016 0.28 NO
73 CUL4A CUL4A CUL4A 6575 0.015 0.28 NO
74 KEAP1 KEAP1 KEAP1 6625 0.014 0.28 NO
75 UBE2D3 UBE2D3 UBE2D3 6642 0.014 0.28 NO
76 CBL CBL CBL 6690 0.013 0.28 NO
77 MGRN1 MGRN1 MGRN1 6768 0.012 0.28 NO
78 UBE2E1 UBE2E1 UBE2E1 6876 0.011 0.28 NO
79 MDM2 MDM2 MDM2 6951 0.0099 0.27 NO
80 SMURF2 SMURF2 SMURF2 7018 0.0091 0.27 NO
81 UBE2J2 UBE2J2 UBE2J2 7092 0.0083 0.27 NO
82 UBE2D2 UBE2D2 UBE2D2 7171 0.0073 0.26 NO
83 FANCL FANCL FANCL 7210 0.0068 0.26 NO
84 UBE4A UBE4A UBE4A 7280 0.006 0.26 NO
85 CDC26 CDC26 CDC26 7302 0.0058 0.26 NO
86 WWP1 WWP1 WWP1 7322 0.0055 0.26 NO
87 SKP1 SKP1 SKP1 7451 0.0039 0.25 NO
88 BTRC BTRC BTRC 7719 0.00054 0.24 NO
89 CDC16 CDC16 CDC16 7966 -0.0026 0.22 NO
90 UBE2D1 UBE2D1 UBE2D1 7996 -0.0028 0.22 NO
91 PRPF19 PRPF19 PRPF19 8521 -0.0097 0.2 NO
92 UBE3B UBE3B UBE3B 8546 -0.01 0.2 NO
93 BIRC3 BIRC3 BIRC3 8609 -0.011 0.2 NO
94 ANAPC7 ANAPC7 ANAPC7 8617 -0.011 0.2 NO
95 PML PML PML 8764 -0.013 0.19 NO
96 UBA1 UBA1 UBA1 8784 -0.013 0.19 NO
97 FBXW7 FBXW7 FBXW7 8913 -0.015 0.18 NO
98 ANAPC5 ANAPC5 ANAPC5 8984 -0.016 0.18 NO
99 TCEB1 TCEB1 TCEB1 9057 -0.016 0.18 NO
100 UBE2B UBE2B UBE2B 9120 -0.017 0.18 NO
101 CUL1 CUL1 CUL1 9236 -0.019 0.18 NO
102 CDC23 CDC23 CDC23 9412 -0.021 0.17 NO
103 NEDD4 NEDD4 NEDD4 9875 -0.028 0.15 NO
104 RBX1 RBX1 RBX1 9961 -0.029 0.15 NO
105 RNF7 RNF7 RNF7 10044 -0.03 0.15 NO
106 PPIL2 PPIL2 PPIL2 10122 -0.031 0.15 NO
107 UBE2F UBE2F UBE2F 10212 -0.032 0.15 NO
108 UBE2L3 UBE2L3 UBE2L3 10504 -0.036 0.14 NO
109 ANAPC2 ANAPC2 ANAPC2 10747 -0.04 0.13 NO
110 UBE2M UBE2M UBE2M 10802 -0.041 0.13 NO
111 SAE1 SAE1 SAE1 10873 -0.042 0.14 NO
112 UBE2L6 UBE2L6 UBE2L6 11022 -0.044 0.13 NO
113 UBE2G2 UBE2G2 UBE2G2 11128 -0.047 0.13 NO
114 ANAPC13 ANAPC13 ANAPC13 11151 -0.047 0.14 NO
115 FZR1 FZR1 FZR1 11422 -0.051 0.13 NO
116 UBOX5 UBOX5 UBOX5 11439 -0.052 0.14 NO
117 UBE2S UBE2S UBE2S 11453 -0.052 0.14 NO
118 AIRE AIRE AIRE 11572 -0.054 0.15 NO
119 ANAPC4 ANAPC4 ANAPC4 11608 -0.055 0.15 NO
120 UBE2D4 UBE2D4 UBE2D4 11618 -0.055 0.16 NO
121 STUB1 STUB1 STUB1 12019 -0.063 0.15 NO
122 ANAPC11 ANAPC11 ANAPC11 12278 -0.068 0.14 NO
123 TCEB2 TCEB2 TCEB2 12641 -0.076 0.13 NO
124 SMURF1 SMURF1 SMURF1 12661 -0.076 0.14 NO
125 UBE2QL1 UBE2QL1 UBE2QL1 13276 -0.091 0.12 NO
126 CDC34 CDC34 CDC34 13327 -0.092 0.13 NO
127 RHOBTB2 RHOBTB2 RHOBTB2 13543 -0.098 0.13 NO
128 FBXO2 FBXO2 FBXO2 13998 -0.11 0.12 NO
129 KLHL13 KLHL13 KLHL13 14154 -0.12 0.13 NO
130 DDB2 DDB2 DDB2 14444 -0.13 0.14 NO
131 SOCS3 SOCS3 SOCS3 15311 -0.16 0.11 NO
132 UBA7 UBA7 UBA7 15887 -0.18 0.1 NO
133 SOCS1 SOCS1 SOCS1 15982 -0.19 0.12 NO

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

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

genes ES table in pathway: PID ECADHERIN NASCENTAJ PATHWAY

Table 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 SMN1 SMN1 SMN1 501 0.24 0.093 YES
2 NUP210 NUP210 NUP210 1167 0.15 0.13 YES
3 NUP155 NUP155 NUP155 2195 0.092 0.12 YES
4 RANBP2 RANBP2 RANBP2 2435 0.086 0.15 YES
5 NUP54 NUP54 NUP54 2756 0.077 0.17 YES
6 TPR TPR TPR 2985 0.071 0.2 YES
7 NUPL1 NUPL1 NUPL1 3073 0.069 0.23 YES
8 POM121 POM121 POM121 3241 0.065 0.25 YES
9 NUP133 NUP133 NUP133 3284 0.064 0.28 YES
10 NUP153 NUP153 NUP153 3387 0.062 0.31 YES
11 SMN2 SMN2 SMN2 3840 0.054 0.31 YES
12 NUP205 NUP205 NUP205 3924 0.052 0.33 YES
13 SEH1L SEH1L SEH1L 3927 0.052 0.36 YES
14 NCBP1 NCBP1 NCBP1 4246 0.048 0.36 YES
15 PHAX PHAX PHAX 4260 0.047 0.39 YES
16 GEMIN5 GEMIN5 GEMIN5 4327 0.046 0.41 YES
17 NUP188 NUP188 NUP188 4343 0.046 0.43 YES
18 CLNS1A CLNS1A CLNS1A 4481 0.044 0.44 YES
19 NUP50 NUP50 NUP50 4709 0.041 0.45 YES
20 NUP43 NUP43 NUP43 5341 0.032 0.43 YES
21 NUP107 NUP107 NUP107 5505 0.029 0.44 YES
22 SNRPD3 SNRPD3 SNRPD3 5547 0.029 0.45 YES
23 PRMT5 PRMT5 PRMT5 5561 0.028 0.47 YES
24 NUPL2 NUPL2 NUPL2 5570 0.028 0.48 YES
25 TGS1 TGS1 TGS1 5582 0.028 0.49 YES
26 NUP37 NUP37 NUP37 5914 0.023 0.49 YES
27 NUP214 NUP214 NUP214 6006 0.022 0.49 YES
28 RAE1 RAE1 RAE1 6332 0.018 0.48 YES
29 SNRPE SNRPE SNRPE 6357 0.017 0.49 YES
30 SNRPG SNRPG SNRPG 6462 0.016 0.49 YES
31 GEMIN4 GEMIN4 GEMIN4 6669 0.014 0.49 YES
32 NCBP2 NCBP2 NCBP2 6679 0.014 0.5 YES
33 NUP62 NUP62 NUP62 6823 0.012 0.49 NO
34 SNRPD1 SNRPD1 SNRPD1 7272 0.0061 0.47 NO
35 SNRPF SNRPF SNRPF 7644 0.0014 0.45 NO
36 SNRPB SNRPB SNRPB 7963 -0.0026 0.44 NO
37 NUP88 NUP88 NUP88 8218 -0.0057 0.43 NO
38 DDX20 DDX20 DDX20 8490 -0.0092 0.42 NO
39 AAAS AAAS AAAS 8506 -0.0094 0.42 NO
40 NUP35 NUP35 NUP35 8846 -0.014 0.41 NO
41 SNRPD2 SNRPD2 SNRPD2 8965 -0.015 0.41 NO
42 NUP93 NUP93 NUP93 9030 -0.016 0.41 NO
43 NUP85 NUP85 NUP85 9155 -0.018 0.42 NO
44 SNUPN SNUPN SNUPN 9322 -0.02 0.42 NO
45 WDR77 WDR77 WDR77 9988 -0.029 0.4 NO
46 GEMIN6 GEMIN6 GEMIN6 10120 -0.031 0.4 NO
47 GEMIN7 GEMIN7 GEMIN7 13065 -0.086 0.28 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 ECADHERIN NASCENTAJ PATHWAY.

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

genes ES table in pathway: PID LIS1PATHWAY

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 NUP210 NUP210 NUP210 1167 0.15 0.04 YES
2 NUP155 NUP155 NUP155 2195 0.092 0.049 YES
3 RANBP2 RANBP2 RANBP2 2435 0.086 0.097 YES
4 NUP54 NUP54 NUP54 2756 0.077 0.13 YES
5 TPR TPR TPR 2985 0.071 0.17 YES
6 NUPL1 NUPL1 NUPL1 3073 0.069 0.22 YES
7 POM121 POM121 POM121 3241 0.065 0.25 YES
8 NUP133 NUP133 NUP133 3284 0.064 0.3 YES
9 NUP153 NUP153 NUP153 3387 0.062 0.34 YES
10 NUP205 NUP205 NUP205 3924 0.052 0.34 YES
11 SEH1L SEH1L SEH1L 3927 0.052 0.38 YES
12 CPSF2 CPSF2 CPSF2 4117 0.049 0.41 YES
13 NCBP1 NCBP1 NCBP1 4246 0.048 0.43 YES
14 NUP188 NUP188 NUP188 4343 0.046 0.46 YES
15 EIF4E EIF4E EIF4E 4414 0.045 0.49 YES
16 NUP50 NUP50 NUP50 4709 0.041 0.5 YES
17 CPSF3 CPSF3 CPSF3 5144 0.034 0.5 YES
18 NUP43 NUP43 NUP43 5341 0.032 0.51 YES
19 NUP107 NUP107 NUP107 5505 0.029 0.52 YES
20 NUPL2 NUPL2 NUPL2 5570 0.028 0.54 YES
21 NUP37 NUP37 NUP37 5914 0.023 0.54 YES
22 NUP214 NUP214 NUP214 6006 0.022 0.55 YES
23 RAE1 RAE1 RAE1 6332 0.018 0.54 NO
24 NCBP2 NCBP2 NCBP2 6679 0.014 0.54 NO
25 NUP62 NUP62 NUP62 6823 0.012 0.54 NO
26 THOC4 THOC4 THOC4 7518 0.0031 0.5 NO
27 NUP88 NUP88 NUP88 8218 -0.0057 0.46 NO
28 AAAS AAAS AAAS 8506 -0.0094 0.46 NO
29 NUP35 NUP35 NUP35 8846 -0.014 0.45 NO
30 NUP93 NUP93 NUP93 9030 -0.016 0.45 NO
31 NUP85 NUP85 NUP85 9155 -0.018 0.46 NO
32 CPSF1 CPSF1 CPSF1 9996 -0.029 0.43 NO
33 NXF1 NXF1 NXF1 10311 -0.034 0.44 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: PID LIS1PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: PID LIS1PATHWAY, 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 METABOLISM OF NON CODING RNA

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 PLA2G7 PLA2G7 PLA2G7 102 0.47 0.21 YES
2 CDK5R2 CDK5R2 CDK5R2 364 0.27 0.32 YES
3 VLDLR VLDLR VLDLR 385 0.27 0.45 YES
4 LRP8 LRP8 LRP8 877 0.17 0.5 YES
5 DAB1 DAB1 DAB1 1516 0.12 0.53 YES
6 PAFAH1B2 PAFAH1B2 PAFAH1B2 1590 0.12 0.58 YES
7 CSNK2A1 CSNK2A1 CSNK2A1 2648 0.08 0.56 NO
8 CDK5R1 CDK5R1 CDK5R1 3917 0.052 0.51 NO
9 DYNC1H1 DYNC1H1 DYNC1H1 5222 0.033 0.46 NO
10 KATNA1 KATNA1 KATNA1 5609 0.028 0.45 NO
11 ABL1 ABL1 ABL1 5611 0.028 0.46 NO
12 YWHAE YWHAE YWHAE 6543 0.015 0.42 NO
13 CDC42 CDC42 CDC42 6822 0.012 0.41 NO
14 RHOA RHOA RHOA 6939 0.01 0.4 NO
15 CLIP1 CLIP1 CLIP1 7066 0.0086 0.4 NO
16 IQGAP1 IQGAP1 IQGAP1 7593 0.002 0.37 NO
17 CDK5 CDK5 CDK5 7739 0.00029 0.37 NO
18 PAFAH1B1 PAFAH1B1 PAFAH1B1 8042 -0.0034 0.35 NO
19 PPP2R5D PPP2R5D PPP2R5D 8214 -0.0056 0.34 NO
20 RAC1 RAC1 RAC1 8754 -0.013 0.32 NO
21 DYNLT1 DYNLT1 DYNLT1 9729 -0.025 0.28 NO
22 LRPAP1 LRPAP1 LRPAP1 9788 -0.026 0.29 NO
23 MAP1B MAP1B MAP1B 10426 -0.035 0.27 NO
24 NUDC NUDC NUDC 10698 -0.04 0.27 NO
25 NDEL1 NDEL1 NDEL1 10752 -0.04 0.29 NO
26 PAFAH1B3 PAFAH1B3 PAFAH1B3 12142 -0.066 0.24 NO
27 DCX DCX DCX 12301 -0.068 0.27 NO
28 RELN RELN RELN 14501 -0.13 0.21 NO

Figure S31.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME METABOLISM OF NON CODING RNA.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF NON CODING RNA, 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 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER

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 NUP210 NUP210 NUP210 1167 0.15 0.056 YES
2 NUP155 NUP155 NUP155 2195 0.092 0.076 YES
3 RANBP2 RANBP2 RANBP2 2435 0.086 0.13 YES
4 NUP54 NUP54 NUP54 2756 0.077 0.18 YES
5 TPR TPR TPR 2985 0.071 0.22 YES
6 NUPL1 NUPL1 NUPL1 3073 0.069 0.28 YES
7 POM121 POM121 POM121 3241 0.065 0.32 YES
8 NUP133 NUP133 NUP133 3284 0.064 0.37 YES
9 NUP153 NUP153 NUP153 3387 0.062 0.42 YES
10 KPNB1 KPNB1 KPNB1 3464 0.061 0.46 YES
11 NUP205 NUP205 NUP205 3924 0.052 0.48 YES
12 SEH1L SEH1L SEH1L 3927 0.052 0.52 YES
13 NUP188 NUP188 NUP188 4343 0.046 0.54 YES
14 NUP50 NUP50 NUP50 4709 0.041 0.55 YES
15 NUP43 NUP43 NUP43 5341 0.032 0.54 YES
16 NUP107 NUP107 NUP107 5505 0.029 0.56 YES
17 NUPL2 NUPL2 NUPL2 5570 0.028 0.58 YES
18 NUP37 NUP37 NUP37 5914 0.023 0.58 YES
19 NUP214 NUP214 NUP214 6006 0.022 0.59 YES
20 RAE1 RAE1 RAE1 6332 0.018 0.59 NO
21 NUP62 NUP62 NUP62 6823 0.012 0.57 NO
22 KPNA1 KPNA1 KPNA1 7412 0.0044 0.54 NO
23 NUP88 NUP88 NUP88 8218 -0.0057 0.5 NO
24 AAAS AAAS AAAS 8506 -0.0094 0.5 NO
25 NUP35 NUP35 NUP35 8846 -0.014 0.49 NO
26 NUP93 NUP93 NUP93 9030 -0.016 0.49 NO
27 NUP85 NUP85 NUP85 9155 -0.018 0.5 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 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER, 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 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM

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 NUP210 NUP210 NUP210 1167 0.15 0.055 YES
2 NUP155 NUP155 NUP155 2195 0.092 0.074 YES
3 RANBP2 RANBP2 RANBP2 2435 0.086 0.13 YES
4 NUP54 NUP54 NUP54 2756 0.077 0.18 YES
5 TPR TPR TPR 2985 0.071 0.22 YES
6 NUPL1 NUPL1 NUPL1 3073 0.069 0.27 YES
7 POM121 POM121 POM121 3241 0.065 0.32 YES
8 NUP133 NUP133 NUP133 3284 0.064 0.37 YES
9 NUP153 NUP153 NUP153 3387 0.062 0.41 YES
10 XPO1 XPO1 XPO1 3662 0.057 0.44 YES
11 NUP205 NUP205 NUP205 3924 0.052 0.47 YES
12 SEH1L SEH1L SEH1L 3927 0.052 0.52 YES
13 NUP188 NUP188 NUP188 4343 0.046 0.53 YES
14 NUP50 NUP50 NUP50 4709 0.041 0.54 YES
15 NUP43 NUP43 NUP43 5341 0.032 0.53 YES
16 NUP107 NUP107 NUP107 5505 0.029 0.55 YES
17 NUPL2 NUPL2 NUPL2 5570 0.028 0.57 YES
18 NUP37 NUP37 NUP37 5914 0.023 0.57 YES
19 NUP214 NUP214 NUP214 6006 0.022 0.58 YES
20 RAN RAN RAN 6225 0.019 0.58 YES
21 RAE1 RAE1 RAE1 6332 0.018 0.59 YES
22 NUP62 NUP62 NUP62 6823 0.012 0.58 NO
23 NUP88 NUP88 NUP88 8218 -0.0057 0.5 NO
24 AAAS AAAS AAAS 8506 -0.0094 0.5 NO
25 NUP35 NUP35 NUP35 8846 -0.014 0.49 NO
26 NUP93 NUP93 NUP93 9030 -0.016 0.49 NO
27 NUP85 NUP85 NUP85 9155 -0.018 0.5 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 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, 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 RNA POL II TRANSCRIPTION

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 OGDHL OGDHL OGDHL 7 0.82 0.51 YES
2 DLAT DLAT DLAT 1966 0.1 0.47 NO
3 CS CS CS 4658 0.042 0.35 NO
4 SDHD SDHD SDHD 5496 0.029 0.32 NO
5 ACLY ACLY ACLY 5839 0.024 0.32 NO
6 FH FH FH 6009 0.022 0.32 NO
7 DLD DLD DLD 6099 0.021 0.33 NO
8 MDH2 MDH2 MDH2 6129 0.021 0.34 NO
9 OGDH OGDH OGDH 6137 0.02 0.35 NO
10 SUCLG1 SUCLG1 SUCLG1 6351 0.018 0.35 NO
11 IDH1 IDH1 IDH1 6549 0.015 0.35 NO
12 PDHB PDHB PDHB 6709 0.013 0.35 NO
13 SDHC SDHC SDHC 6716 0.013 0.36 NO
14 SDHB SDHB SDHB 6725 0.013 0.37 NO
15 SUCLG2 SUCLG2 SUCLG2 6820 0.012 0.37 NO
16 PDHA1 PDHA1 PDHA1 6848 0.011 0.37 NO
17 ACO1 ACO1 ACO1 6976 0.0096 0.37 NO
18 ACO2 ACO2 ACO2 6988 0.0095 0.38 NO
19 SUCLA2 SUCLA2 SUCLA2 7439 0.0041 0.36 NO
20 MDH1 MDH1 MDH1 7680 0.0009 0.34 NO
21 SDHA SDHA SDHA 8712 -0.012 0.29 NO
22 DLST DLST DLST 9434 -0.021 0.27 NO
23 IDH3A IDH3A IDH3A 9488 -0.022 0.28 NO
24 IDH3G IDH3G IDH3G 9947 -0.028 0.27 NO
25 PCK2 PCK2 PCK2 10253 -0.033 0.28 NO
26 IDH2 IDH2 IDH2 10532 -0.037 0.28 NO
27 IDH3B IDH3B IDH3B 10880 -0.042 0.29 NO
28 PCK1 PCK1 PCK1 11708 -0.057 0.28 NO
29 PC PC PC 14460 -0.13 0.21 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 RNA POL II TRANSCRIPTION.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RNA POL II TRANSCRIPTION, 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 RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES

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 GTF2H2 GTF2H2 GTF2H2 1117 0.15 -0.033 YES
2 NUP210 NUP210 NUP210 1167 0.15 -0.0076 YES
3 SNRNP40 SNRNP40 SNRNP40 1388 0.13 0.0053 YES
4 GTF2H3 GTF2H3 GTF2H3 1408 0.13 0.029 YES
5 CDC40 CDC40 CDC40 1643 0.12 0.038 YES
6 NUP155 NUP155 NUP155 2195 0.092 0.026 YES
7 ZNF473 ZNF473 ZNF473 2380 0.087 0.032 YES
8 RANBP2 RANBP2 RANBP2 2435 0.086 0.046 YES
9 NUP54 NUP54 NUP54 2756 0.077 0.043 YES
10 TPR TPR TPR 2985 0.071 0.044 YES
11 NUPL1 NUPL1 NUPL1 3073 0.069 0.052 YES
12 CDK7 CDK7 CDK7 3142 0.068 0.061 YES
13 CCAR1 CCAR1 CCAR1 3222 0.066 0.07 YES
14 POM121 POM121 POM121 3241 0.065 0.081 YES
15 NUP133 NUP133 NUP133 3284 0.064 0.091 YES
16 HNRNPR HNRNPR HNRNPR 3351 0.063 0.099 YES
17 NUP153 NUP153 NUP153 3387 0.062 0.11 YES
18 HNRNPUL1 HNRNPUL1 HNRNPUL1 3395 0.062 0.12 YES
19 NUDT21 NUDT21 NUDT21 3398 0.062 0.13 YES
20 POLR2B POLR2B POLR2B 3577 0.059 0.13 YES
21 CPSF7 CPSF7 CPSF7 3586 0.059 0.14 YES
22 DHX9 DHX9 DHX9 3634 0.058 0.15 YES
23 SNRPB2 SNRPB2 SNRPB2 3700 0.056 0.16 YES
24 POLR2D POLR2D POLR2D 3706 0.056 0.17 YES
25 HNRNPF HNRNPF HNRNPF 3842 0.054 0.17 YES
26 NUP205 NUP205 NUP205 3924 0.052 0.18 YES
27 SEH1L SEH1L SEH1L 3927 0.052 0.19 YES
28 PCF11 PCF11 PCF11 3947 0.052 0.2 YES
29 SNRNP200 SNRNP200 SNRNP200 4025 0.051 0.2 YES
30 RNGTT RNGTT RNGTT 4072 0.05 0.21 YES
31 CPSF2 CPSF2 CPSF2 4117 0.049 0.22 YES
32 NCBP1 NCBP1 NCBP1 4246 0.048 0.22 YES
33 NUP188 NUP188 NUP188 4343 0.046 0.22 YES
34 RBMX RBMX RBMX 4385 0.046 0.23 YES
35 EIF4E EIF4E EIF4E 4414 0.045 0.24 YES
36 HNRNPA0 HNRNPA0 HNRNPA0 4447 0.045 0.24 YES
37 HNRNPK HNRNPK HNRNPK 4513 0.044 0.25 YES
38 PAPOLA PAPOLA PAPOLA 4686 0.041 0.25 YES
39 NUP50 NUP50 NUP50 4709 0.041 0.25 YES
40 ADAR ADAR ADAR 4725 0.04 0.26 YES
41 RNMT RNMT RNMT 4763 0.04 0.27 YES
42 SF3B3 SF3B3 SF3B3 4824 0.039 0.27 YES
43 SF3A1 SF3A1 SF3A1 4849 0.038 0.28 YES
44 SMC1A SMC1A SMC1A 4859 0.038 0.28 YES
45 SF3B1 SF3B1 SF3B1 4879 0.038 0.29 YES
46 HNRNPL HNRNPL HNRNPL 4884 0.038 0.3 YES
47 PRPF8 PRPF8 PRPF8 4922 0.037 0.3 YES
48 GTF2H2B GTF2H2B GTF2H2B 4963 0.036 0.31 YES
49 PCBP2 PCBP2 PCBP2 4986 0.036 0.31 YES
50 ERCC3 ERCC3 ERCC3 5072 0.035 0.31 YES
51 CPSF3 CPSF3 CPSF3 5144 0.034 0.32 YES
52 NFX1 NFX1 NFX1 5163 0.034 0.32 YES
53 HNRNPU HNRNPU HNRNPU 5197 0.033 0.33 YES
54 NUP43 NUP43 NUP43 5341 0.032 0.32 YES
55 HNRNPH2 HNRNPH2 HNRNPH2 5370 0.031 0.33 YES
56 GTF2H1 GTF2H1 GTF2H1 5431 0.03 0.33 YES
57 HNRNPC HNRNPC HNRNPC 5468 0.03 0.34 YES
58 NUP107 NUP107 NUP107 5505 0.029 0.34 YES
59 SNRPD3 SNRPD3 SNRPD3 5547 0.029 0.34 YES
60 RBM8A RBM8A RBM8A 5565 0.028 0.35 YES
61 NUPL2 NUPL2 NUPL2 5570 0.028 0.35 YES
62 UPF3B UPF3B UPF3B 5751 0.026 0.35 YES
63 SNRPA1 SNRPA1 SNRPA1 5842 0.024 0.35 YES
64 NUP37 NUP37 NUP37 5914 0.023 0.35 YES
65 PCBP1 PCBP1 PCBP1 5917 0.023 0.35 YES
66 PTBP1 PTBP1 PTBP1 5926 0.023 0.36 YES
67 MNAT1 MNAT1 MNAT1 5965 0.022 0.36 YES
68 NUP214 NUP214 NUP214 6006 0.022 0.36 YES
69 U2AF2 U2AF2 U2AF2 6014 0.022 0.36 YES
70 HNRNPA2B1 HNRNPA2B1 HNRNPA2B1 6260 0.019 0.35 NO
71 SF3B14 SF3B14 SF3B14 6329 0.018 0.35 NO
72 RAE1 RAE1 RAE1 6332 0.018 0.36 NO
73 SNRPE SNRPE SNRPE 6357 0.017 0.36 NO
74 HNRNPD HNRNPD HNRNPD 6440 0.016 0.36 NO
75 SNRPG SNRPG SNRPG 6462 0.016 0.36 NO
76 CCNH CCNH CCNH 6509 0.016 0.36 NO
77 SF3B4 SF3B4 SF3B4 6581 0.015 0.36 NO
78 PRPF4 PRPF4 PRPF4 6649 0.014 0.36 NO
79 NCBP2 NCBP2 NCBP2 6679 0.014 0.36 NO
80 SF3A3 SF3A3 SF3A3 6781 0.012 0.35 NO
81 NUP62 NUP62 NUP62 6823 0.012 0.35 NO
82 HNRNPA1 HNRNPA1 HNRNPA1 6860 0.011 0.36 NO
83 CSTF3 CSTF3 CSTF3 6866 0.011 0.36 NO
84 POLR2A POLR2A POLR2A 6936 0.01 0.36 NO
85 DDX23 DDX23 DDX23 7051 0.0087 0.35 NO
86 HNRNPA3 HNRNPA3 HNRNPA3 7071 0.0085 0.35 NO
87 SF3B2 SF3B2 SF3B2 7248 0.0064 0.34 NO
88 SNRPD1 SNRPD1 SNRPD1 7272 0.0061 0.34 NO
89 FUS FUS FUS 7321 0.0055 0.34 NO
90 HNRNPH1 HNRNPH1 HNRNPH1 7403 0.0045 0.34 NO
91 PHF5A PHF5A PHF5A 7408 0.0044 0.34 NO
92 POLR2C POLR2C POLR2C 7468 0.0038 0.34 NO
93 THOC4 THOC4 THOC4 7518 0.0031 0.33 NO
94 SLBP SLBP SLBP 7547 0.0027 0.33 NO
95 YBX1 YBX1 YBX1 7557 0.0026 0.33 NO
96 CSTF1 CSTF1 CSTF1 7636 0.0015 0.33 NO
97 SNRPF SNRPF SNRPF 7644 0.0014 0.33 NO
98 SNRPB SNRPB SNRPB 7963 -0.0026 0.31 NO
99 PRPF6 PRPF6 PRPF6 7978 -0.0027 0.31 NO
100 ERCC2 ERCC2 ERCC2 8157 -0.005 0.3 NO
101 SF3A2 SF3A2 SF3A2 8178 -0.0052 0.3 NO
102 U2AF1 U2AF1 U2AF1 8180 -0.0052 0.3 NO
103 NUP88 NUP88 NUP88 8218 -0.0057 0.3 NO
104 CLP1 CLP1 CLP1 8224 -0.0058 0.3 NO
105 METTL3 METTL3 METTL3 8388 -0.0077 0.29 NO
106 MAGOH MAGOH MAGOH 8457 -0.0086 0.29 NO
107 AAAS AAAS AAAS 8506 -0.0094 0.29 NO
108 POLR2H POLR2H POLR2H 8577 -0.01 0.29 NO
109 HNRNPM HNRNPM HNRNPM 8666 -0.012 0.29 NO
110 EFTUD2 EFTUD2 EFTUD2 8708 -0.012 0.29 NO
111 DNAJC8 DNAJC8 DNAJC8 8820 -0.014 0.28 NO
112 NUP35 NUP35 NUP35 8846 -0.014 0.28 NO
113 PABPN1 PABPN1 PABPN1 8925 -0.015 0.28 NO
114 RNPS1 RNPS1 RNPS1 8939 -0.015 0.29 NO
115 SNRPD2 SNRPD2 SNRPD2 8965 -0.015 0.29 NO
116 LSM2 LSM2 LSM2 8999 -0.016 0.29 NO
117 NUP93 NUP93 NUP93 9030 -0.016 0.29 NO
118 NUP85 NUP85 NUP85 9155 -0.018 0.29 NO
119 SRRM1 SRRM1 SRRM1 9259 -0.019 0.28 NO
120 GTF2F2 GTF2F2 GTF2F2 9403 -0.021 0.28 NO
121 GTF2F1 GTF2F1 GTF2F1 9438 -0.021 0.28 NO
122 POLR2K POLR2K POLR2K 9532 -0.022 0.28 NO
123 DHX38 DHX38 DHX38 9535 -0.023 0.29 NO
124 RBM5 RBM5 RBM5 9545 -0.023 0.29 NO
125 TXNL4A TXNL4A TXNL4A 9885 -0.028 0.28 NO
126 GTF2H4 GTF2H4 GTF2H4 9932 -0.028 0.28 NO
127 A1CF A1CF A1CF 9948 -0.028 0.28 NO
128 SUPT5H SUPT5H SUPT5H 9981 -0.029 0.29 NO
129 CPSF1 CPSF1 CPSF1 9996 -0.029 0.29 NO
130 NHP2L1 NHP2L1 NHP2L1 10052 -0.03 0.3 NO
131 CSTF2 CSTF2 CSTF2 10089 -0.031 0.3 NO
132 NXF1 NXF1 NXF1 10311 -0.034 0.29 NO
133 SNRNP70 SNRNP70 SNRNP70 10372 -0.035 0.3 NO
134 POLR2F POLR2F POLR2F 10472 -0.036 0.3 NO
135 SNRPA SNRPA SNRPA 10526 -0.037 0.3 NO
136 POLR2E POLR2E POLR2E 10610 -0.038 0.3 NO
137 CD2BP2 CD2BP2 CD2BP2 11087 -0.046 0.29 NO
138 POLR2G POLR2G POLR2G 11172 -0.047 0.29 NO
139 POLR2L POLR2L POLR2L 11891 -0.06 0.26 NO
140 POLR2I POLR2I POLR2I 12011 -0.063 0.27 NO
141 POLR2J POLR2J POLR2J 12325 -0.069 0.26 NO
142 SF3B5 SF3B5 SF3B5 12331 -0.069 0.28 NO
143 LSM11 LSM11 LSM11 12433 -0.071 0.29 NO
144 LSM10 LSM10 LSM10 13311 -0.092 0.26 NO
145 ADARB1 ADARB1 ADARB1 13370 -0.094 0.27 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 RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES, 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 OXIDATIVE PHOSPHORYLATION 114 genes.ES.table 0.52 1.6 0.036 0.21 0.88 0.64 0.28 0.46 0.11 0.031
KEGG PYRIMIDINE METABOLISM 98 genes.ES.table 0.38 1.7 0.013 0.18 0.78 0.44 0.27 0.32 0.078 0.034
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 33 genes.ES.table 0.63 1.5 0.047 0.22 0.98 0.52 0.2 0.41 0.14 0.017
KEGG RIBOSOME 86 genes.ES.table 0.64 1.5 0.098 0.21 0.96 0.85 0.32 0.58 0.13 0.019
KEGG DNA REPLICATION 36 genes.ES.table 0.6 1.8 0.022 0.47 0.41 0.5 0.22 0.39 0 0.1
KEGG PROTEASOME 43 genes.ES.table 0.56 1.7 0.036 0.28 0.68 0.74 0.37 0.47 0.096 0.069
KEGG BASE EXCISION REPAIR 33 genes.ES.table 0.52 1.7 0.045 0.19 0.73 0.7 0.35 0.45 0.073 0.034
KEGG HOMOLOGOUS RECOMBINATION 26 genes.ES.table 0.64 1.5 0.074 0.21 0.98 0.58 0.22 0.45 0.14 0.014
KEGG CELL CYCLE 118 genes.ES.table 0.51 1.6 0.063 0.21 0.93 0.26 0.13 0.23 0.12 0.023
KEGG PARKINSONS DISEASE 111 genes.ES.table 0.42 1.5 0.12 0.23 0.98 0.63 0.28 0.45 0.16 0.012
genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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 CDT1 CDT1 CDT1 59 0.43 0.067 YES
2 GINS2 GINS2 GINS2 248 0.32 0.11 YES
3 CDC6 CDC6 CDC6 376 0.29 0.15 YES
4 CCNA2 CCNA2 CCNA2 506 0.26 0.18 YES
5 CDC45 CDC45 CDC45 551 0.26 0.22 YES
6 POLE2 POLE2 POLE2 597 0.25 0.26 YES
7 GINS1 GINS1 GINS1 829 0.21 0.28 YES
8 DNA2 DNA2 DNA2 998 0.19 0.3 YES
9 PRIM2 PRIM2 PRIM2 1064 0.18 0.33 YES
10 RFC4 RFC4 RFC4 1169 0.17 0.35 YES
11 GINS4 GINS4 GINS4 1212 0.17 0.38 YES
12 RFC3 RFC3 RFC3 1654 0.14 0.38 YES
13 POLD4 POLD4 POLD4 1834 0.13 0.39 YES
14 RPA3 RPA3 RPA3 2175 0.11 0.39 YES
15 RFC2 RFC2 RFC2 2242 0.11 0.4 YES
16 PSMC1 PSMC1 PSMC1 2564 0.097 0.4 YES
17 PSME2 PSME2 PSME2 2596 0.096 0.41 YES
18 FEN1 FEN1 FEN1 2686 0.094 0.42 YES
19 PSMB7 PSMB7 PSMB7 2861 0.089 0.43 YES
20 PSMB3 PSMB3 PSMB3 2925 0.087 0.44 YES
21 POLD2 POLD2 POLD2 3118 0.082 0.44 YES
22 MCM7 MCM7 MCM7 3337 0.078 0.44 YES
23 PSMD9 PSMD9 PSMD9 3516 0.074 0.44 YES
24 PSMB4 PSMB4 PSMB4 3775 0.068 0.44 YES
25 UBA52 UBA52 UBA52 3903 0.065 0.44 YES
26 PCNA PCNA PCNA 3917 0.065 0.45 YES
27 PSMD4 PSMD4 PSMD4 3919 0.065 0.46 YES
28 PSMA3 PSMA3 PSMA3 3929 0.065 0.48 YES
29 POLD1 POLD1 POLD1 3948 0.064 0.48 YES
30 PSMB1 PSMB1 PSMB1 4032 0.063 0.49 YES
31 PSMB6 PSMB6 PSMB6 4124 0.061 0.5 YES
32 PSMA4 PSMA4 PSMA4 4132 0.06 0.5 YES
33 PSMA6 PSMA6 PSMA6 4173 0.06 0.51 YES
34 PSMB5 PSMB5 PSMB5 4332 0.057 0.51 YES
35 PSMA7 PSMA7 PSMA7 4443 0.055 0.52 YES
36 PSMA5 PSMA5 PSMA5 4474 0.054 0.52 YES
37 PSMA2 PSMA2 PSMA2 4513 0.053 0.53 YES
38 PSMD13 PSMD13 PSMD13 4563 0.052 0.54 YES
39 LIG1 LIG1 LIG1 4702 0.05 0.54 YES
40 CDKN1A CDKN1A CDKN1A 4721 0.05 0.54 YES
41 PSMC2 PSMC2 PSMC2 4913 0.046 0.54 YES
42 PSMB2 PSMB2 PSMB2 5057 0.044 0.54 YES
43 POLA2 POLA2 POLA2 5084 0.044 0.55 YES
44 RPS27A RPS27A RPS27A 5181 0.042 0.55 YES
45 PSMC3 PSMC3 PSMC3 5230 0.041 0.55 YES
46 MCM5 MCM5 MCM5 5318 0.04 0.55 YES
47 PSMC5 PSMC5 PSMC5 5584 0.036 0.54 NO
48 MCM2 MCM2 MCM2 5820 0.032 0.54 NO
49 PSME1 PSME1 PSME1 5831 0.032 0.54 NO
50 PSMC6 PSMC6 PSMC6 5960 0.031 0.54 NO
51 PSMD3 PSMD3 PSMD3 6167 0.027 0.53 NO
52 POLE POLE POLE 6400 0.024 0.52 NO
53 MCM4 MCM4 MCM4 6480 0.023 0.52 NO
54 RPA2 RPA2 RPA2 6548 0.022 0.52 NO
55 PSMD14 PSMD14 PSMD14 6592 0.021 0.52 NO
56 PSMC4 PSMC4 PSMC4 6606 0.021 0.52 NO
57 PSMD6 PSMD6 PSMD6 6652 0.02 0.53 NO
58 MCM3 MCM3 MCM3 6679 0.02 0.53 NO
59 PSMA1 PSMA1 PSMA1 6765 0.019 0.53 NO
60 RFC5 RFC5 RFC5 6768 0.019 0.53 NO
61 PSMD8 PSMD8 PSMD8 6780 0.019 0.53 NO
62 PSMD11 PSMD11 PSMD11 7003 0.016 0.52 NO
63 PSMB10 PSMB10 PSMB10 7416 0.0097 0.5 NO
64 PSMD12 PSMD12 PSMD12 7542 0.0078 0.5 NO
65 CDK2 CDK2 CDK2 7776 0.0047 0.48 NO
66 PSMF1 PSMF1 PSMF1 7778 0.0046 0.48 NO
67 PSMD2 PSMD2 PSMD2 8193 -0.0013 0.46 NO
68 PSME4 PSME4 PSME4 8241 -0.0018 0.46 NO
69 PSMB9 PSMB9 PSMB9 8664 -0.0073 0.44 NO
70 CCNA1 CCNA1 CCNA1 8702 -0.0077 0.44 NO
71 PSMD7 PSMD7 PSMD7 8770 -0.0086 0.43 NO
72 PSMD1 PSMD1 PSMD1 8998 -0.012 0.42 NO
73 POLD3 POLD3 POLD3 9619 -0.02 0.39 NO
74 PSMD10 PSMD10 PSMD10 9843 -0.023 0.38 NO
75 CDKN1B CDKN1B CDKN1B 10343 -0.031 0.36 NO
76 MCM6 MCM6 MCM6 10350 -0.031 0.37 NO
77 POLA1 POLA1 POLA1 10639 -0.035 0.36 NO
78 RPA1 RPA1 RPA1 10860 -0.039 0.35 NO
79 PRIM1 PRIM1 PRIM1 10904 -0.04 0.36 NO
80 PSMB8 PSMB8 PSMB8 11588 -0.05 0.32 NO
81 MCM8 MCM8 MCM8 11995 -0.057 0.31 NO
82 PSMD5 PSMD5 PSMD5 13662 -0.094 0.24 NO
83 RB1 RB1 RB1 14004 -0.1 0.23 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 OXIDATIVE PHOSPHORYLATION.

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

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 POLE2 POLE2 POLE2 597 0.25 0.058 YES
2 DNA2 DNA2 DNA2 998 0.19 0.1 YES
3 PRIM2 PRIM2 PRIM2 1064 0.18 0.17 YES
4 RFC4 RFC4 RFC4 1169 0.17 0.22 YES
5 RNASEH2A RNASEH2A RNASEH2A 1356 0.16 0.27 YES
6 RPA4 RPA4 RPA4 1444 0.15 0.32 YES
7 RFC3 RFC3 RFC3 1654 0.14 0.36 YES
8 POLE4 POLE4 POLE4 1741 0.13 0.4 YES
9 POLD4 POLD4 POLD4 1834 0.13 0.44 YES
10 RPA3 RPA3 RPA3 2175 0.11 0.47 YES
11 RFC2 RFC2 RFC2 2242 0.11 0.5 YES
12 FEN1 FEN1 FEN1 2686 0.094 0.51 YES
13 POLD2 POLD2 POLD2 3118 0.082 0.52 YES
14 MCM7 MCM7 MCM7 3337 0.078 0.54 YES
15 SSBP1 SSBP1 SSBP1 3395 0.076 0.56 YES
16 RNASEH2C RNASEH2C RNASEH2C 3652 0.071 0.57 YES
17 PCNA PCNA PCNA 3917 0.065 0.58 YES
18 POLD1 POLD1 POLD1 3948 0.064 0.6 YES
19 LIG1 LIG1 LIG1 4702 0.05 0.58 NO
20 POLA2 POLA2 POLA2 5084 0.044 0.57 NO
21 MCM5 MCM5 MCM5 5318 0.04 0.58 NO
22 MCM2 MCM2 MCM2 5820 0.032 0.56 NO
23 POLE POLE POLE 6400 0.024 0.54 NO
24 MCM4 MCM4 MCM4 6480 0.023 0.54 NO
25 RPA2 RPA2 RPA2 6548 0.022 0.55 NO
26 MCM3 MCM3 MCM3 6679 0.02 0.55 NO
27 RFC5 RFC5 RFC5 6768 0.019 0.55 NO
28 POLE3 POLE3 POLE3 7804 0.0042 0.49 NO
29 RNASEH1 RNASEH1 RNASEH1 8463 -0.0048 0.46 NO
30 RNASEH2B RNASEH2B RNASEH2B 9600 -0.02 0.4 NO
31 POLD3 POLD3 POLD3 9619 -0.02 0.41 NO
32 RFC1 RFC1 RFC1 10184 -0.028 0.39 NO
33 MCM6 MCM6 MCM6 10350 -0.031 0.39 NO
34 POLA1 POLA1 POLA1 10639 -0.035 0.39 NO
35 RPA1 RPA1 RPA1 10860 -0.039 0.39 NO
36 PRIM1 PRIM1 PRIM1 10904 -0.04 0.4 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 PYRIMIDINE METABOLISM.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRIMIDINE 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 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 CDT1 CDT1 CDT1 59 0.43 0.056 YES
2 GINS2 GINS2 GINS2 248 0.32 0.09 YES
3 CDC6 CDC6 CDC6 376 0.29 0.12 YES
4 CCNA2 CCNA2 CCNA2 506 0.26 0.15 YES
5 CDC45 CDC45 CDC45 551 0.26 0.18 YES
6 POLE2 POLE2 POLE2 597 0.25 0.22 YES
7 CCNE1 CCNE1 CCNE1 772 0.22 0.24 YES
8 GINS1 GINS1 GINS1 829 0.21 0.26 YES
9 CDC25A CDC25A CDC25A 872 0.21 0.29 YES
10 CCNE2 CCNE2 CCNE2 920 0.2 0.31 YES
11 DNA2 DNA2 DNA2 998 0.19 0.33 YES
12 PRIM2 PRIM2 PRIM2 1064 0.18 0.36 YES
13 RFC4 RFC4 RFC4 1169 0.17 0.37 YES
14 GINS4 GINS4 GINS4 1212 0.17 0.39 YES
15 RFC3 RFC3 RFC3 1654 0.14 0.39 YES
16 POLD4 POLD4 POLD4 1834 0.13 0.4 YES
17 RPA3 RPA3 RPA3 2175 0.11 0.39 YES
18 RFC2 RFC2 RFC2 2242 0.11 0.4 YES
19 PSMC1 PSMC1 PSMC1 2564 0.097 0.4 YES
20 PSME2 PSME2 PSME2 2596 0.096 0.41 YES
21 FEN1 FEN1 FEN1 2686 0.094 0.42 YES
22 PSMB7 PSMB7 PSMB7 2861 0.089 0.42 YES
23 PSMB3 PSMB3 PSMB3 2925 0.087 0.43 YES
24 POLD2 POLD2 POLD2 3118 0.082 0.43 YES
25 CKS1B CKS1B CKS1B 3330 0.078 0.43 YES
26 MCM7 MCM7 MCM7 3337 0.078 0.44 YES
27 PSMD9 PSMD9 PSMD9 3516 0.074 0.44 YES
28 PSMB4 PSMB4 PSMB4 3775 0.068 0.44 YES
29 UBA52 UBA52 UBA52 3903 0.065 0.44 YES
30 PCNA PCNA PCNA 3917 0.065 0.45 YES
31 PSMD4 PSMD4 PSMD4 3919 0.065 0.46 YES
32 PSMA3 PSMA3 PSMA3 3929 0.065 0.46 YES
33 CDC25B CDC25B CDC25B 3945 0.064 0.47 YES
34 POLD1 POLD1 POLD1 3948 0.064 0.48 YES
35 PSMB1 PSMB1 PSMB1 4032 0.063 0.48 YES
36 PSMB6 PSMB6 PSMB6 4124 0.061 0.49 YES
37 PSMA4 PSMA4 PSMA4 4132 0.06 0.5 YES
38 PSMA6 PSMA6 PSMA6 4173 0.06 0.5 YES
39 PSMB5 PSMB5 PSMB5 4332 0.057 0.5 YES
40 PSMA7 PSMA7 PSMA7 4443 0.055 0.5 YES
41 PSMA5 PSMA5 PSMA5 4474 0.054 0.51 YES
42 PSMA2 PSMA2 PSMA2 4513 0.053 0.51 YES
43 PSMD13 PSMD13 PSMD13 4563 0.052 0.52 YES
44 LIG1 LIG1 LIG1 4702 0.05 0.52 YES
45 CDKN1A CDKN1A CDKN1A 4721 0.05 0.52 YES
46 MNAT1 MNAT1 MNAT1 4796 0.048 0.52 YES
47 PSMC2 PSMC2 PSMC2 4913 0.046 0.52 YES
48 PSMB2 PSMB2 PSMB2 5057 0.044 0.52 YES
49 POLA2 POLA2 POLA2 5084 0.044 0.53 YES
50 RPS27A RPS27A RPS27A 5181 0.042 0.53 YES
51 PSMC3 PSMC3 PSMC3 5230 0.041 0.53 YES
52 MCM5 MCM5 MCM5 5318 0.04 0.53 YES
53 PSMC5 PSMC5 PSMC5 5584 0.036 0.52 NO
54 CCND1 CCND1 CCND1 5735 0.034 0.52 NO
55 MCM2 MCM2 MCM2 5820 0.032 0.52 NO
56 PSME1 PSME1 PSME1 5831 0.032 0.52 NO
57 CDK4 CDK4 CDK4 5865 0.032 0.52 NO
58 PSMC6 PSMC6 PSMC6 5960 0.031 0.52 NO
59 PSMD3 PSMD3 PSMD3 6167 0.027 0.52 NO
60 POLE POLE POLE 6400 0.024 0.51 NO
61 MCM4 MCM4 MCM4 6480 0.023 0.5 NO
62 RPA2 RPA2 RPA2 6548 0.022 0.5 NO
63 PSMD14 PSMD14 PSMD14 6592 0.021 0.5 NO
64 PSMC4 PSMC4 PSMC4 6606 0.021 0.51 NO
65 PSMD6 PSMD6 PSMD6 6652 0.02 0.51 NO
66 MCM3 MCM3 MCM3 6679 0.02 0.51 NO
67 PSMA1 PSMA1 PSMA1 6765 0.019 0.51 NO
68 RFC5 RFC5 RFC5 6768 0.019 0.51 NO
69 PSMD8 PSMD8 PSMD8 6780 0.019 0.51 NO
70 PSMD11 PSMD11 PSMD11 7003 0.016 0.5 NO
71 PSMB10 PSMB10 PSMB10 7416 0.0097 0.48 NO
72 CCNH CCNH CCNH 7441 0.0094 0.48 NO
73 MAX MAX MAX 7448 0.0093 0.48 NO
74 PSMD12 PSMD12 PSMD12 7542 0.0078 0.48 NO
75 CDK2 CDK2 CDK2 7776 0.0047 0.46 NO
76 PSMF1 PSMF1 PSMF1 7778 0.0046 0.46 NO
77 CUL1 CUL1 CUL1 7921 0.0026 0.46 NO
78 SKP1 SKP1 SKP1 7936 0.0023 0.46 NO
79 PSMD2 PSMD2 PSMD2 8193 -0.0013 0.44 NO
80 PSME4 PSME4 PSME4 8241 -0.0018 0.44 NO
81 CDK7 CDK7 CDK7 8495 -0.0054 0.43 NO
82 PSMB9 PSMB9 PSMB9 8664 -0.0073 0.42 NO
83 CCNA1 CCNA1 CCNA1 8702 -0.0077 0.42 NO
84 PSMD7 PSMD7 PSMD7 8770 -0.0086 0.42 NO
85 PSMD1 PSMD1 PSMD1 8998 -0.012 0.4 NO
86 MYC MYC MYC 9306 -0.016 0.39 NO
87 POLD3 POLD3 POLD3 9619 -0.02 0.38 NO
88 PSMD10 PSMD10 PSMD10 9843 -0.023 0.37 NO
89 CDKN1B CDKN1B CDKN1B 10343 -0.031 0.34 NO
90 MCM6 MCM6 MCM6 10350 -0.031 0.35 NO
91 POLA1 POLA1 POLA1 10639 -0.035 0.34 NO
92 RPA1 RPA1 RPA1 10860 -0.039 0.33 NO
93 PRIM1 PRIM1 PRIM1 10904 -0.04 0.33 NO
94 PSMB8 PSMB8 PSMB8 11588 -0.05 0.3 NO
95 MCM8 MCM8 MCM8 11995 -0.057 0.29 NO
96 PSMD5 PSMD5 PSMD5 13662 -0.094 0.21 NO
97 WEE1 WEE1 WEE1 13681 -0.094 0.22 NO
98 RB1 RB1 RB1 14004 -0.1 0.22 NO
99 SKP2 SKP2 SKP2 14650 -0.12 0.2 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

Figure S46.  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 RIBOSOME

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 COX17 COX17 COX17 1351 0.16 -0.023 YES
2 LDHD LDHD LDHD 1381 0.15 0.026 YES
3 TAZ TAZ TAZ 1886 0.12 0.039 YES
4 MTX1 MTX1 MTX1 1887 0.12 0.079 YES
5 TIMM10 TIMM10 TIMM10 1888 0.12 0.12 YES
6 BCS1L BCS1L BCS1L 2150 0.11 0.14 YES
7 TIMM8B TIMM8B TIMM8B 2160 0.11 0.18 YES
8 TIMM13 TIMM13 TIMM13 2227 0.11 0.21 YES
9 GFER GFER GFER 2237 0.11 0.25 YES
10 TIMM8A TIMM8A TIMM8A 2295 0.11 0.28 YES
11 ATP5G1 ATP5G1 ATP5G1 2382 0.1 0.31 YES
12 TOMM7 TOMM7 TOMM7 2696 0.093 0.32 YES
13 TOMM5 TOMM5 TOMM5 2798 0.091 0.35 YES
14 TIMM50 TIMM50 TIMM50 2974 0.086 0.36 YES
15 DNAJC19 DNAJC19 DNAJC19 2982 0.086 0.39 YES
16 TIMM17B TIMM17B TIMM17B 3091 0.083 0.41 YES
17 TOMM40 TOMM40 TOMM40 3513 0.074 0.42 YES
18 CYC1 CYC1 CYC1 3728 0.069 0.43 YES
19 TIMM44 TIMM44 TIMM44 3729 0.069 0.45 YES
20 PMPCB PMPCB PMPCB 4063 0.062 0.45 YES
21 PMPCA PMPCA PMPCA 4076 0.062 0.47 YES
22 GRPEL1 GRPEL1 GRPEL1 4097 0.061 0.49 YES
23 TIMM9 TIMM9 TIMM9 4264 0.058 0.5 YES
24 HSPD1 HSPD1 HSPD1 4270 0.058 0.52 YES
25 CHCHD4 CHCHD4 CHCHD4 4295 0.057 0.54 YES
26 MTX2 MTX2 MTX2 4564 0.052 0.54 YES
27 IDH3G IDH3G IDH3G 4642 0.051 0.55 YES
28 COQ2 COQ2 COQ2 4704 0.05 0.56 YES
29 TIMM17A TIMM17A TIMM17A 4844 0.048 0.57 YES
30 HSCB HSCB HSCB 4881 0.047 0.58 YES
31 TOMM70A TOMM70A TOMM70A 5149 0.042 0.58 YES
32 GRPEL2 GRPEL2 GRPEL2 5415 0.038 0.58 YES
33 VDAC1 VDAC1 VDAC1 5485 0.037 0.59 YES
34 FXN FXN FXN 5673 0.035 0.59 YES
35 TOMM22 TOMM22 TOMM22 5697 0.034 0.6 YES
36 TIMM22 TIMM22 TIMM22 5904 0.032 0.6 NO
37 HSPA9 HSPA9 HSPA9 7104 0.014 0.54 NO
38 ATP5B ATP5B ATP5B 7312 0.011 0.53 NO
39 SLC25A13 SLC25A13 SLC25A13 7588 0.0072 0.52 NO
40 SLC25A6 SLC25A6 SLC25A6 7790 0.0045 0.51 NO
41 CS CS CS 8126 -0.00031 0.49 NO
42 SLC25A4 SLC25A4 SLC25A4 8247 -0.0019 0.49 NO
43 TOMM20 TOMM20 TOMM20 8290 -0.0024 0.48 NO
44 ATP5A1 ATP5A1 ATP5A1 8296 -0.0024 0.48 NO
45 ACO2 ACO2 ACO2 8473 -0.005 0.48 NO
46 SAMM50 SAMM50 SAMM50 8903 -0.01 0.46 NO
47 C18orf55 C18orf55 C18orf55 9386 -0.017 0.44 NO
48 FXC1 FXC1 FXC1 12117 -0.06 0.31 NO
49 SLC25A12 SLC25A12 SLC25A12 13750 -0.096 0.25 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 RIBOSOME.

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

genes ES table in pathway: KEGG DNA REPLICATION

Table 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 CDT1 CDT1 CDT1 59 0.43 0.082 YES
2 E2F1 E2F1 E2F1 274 0.32 0.13 YES
3 E2F2 E2F2 E2F2 313 0.3 0.19 YES
4 CDC6 CDC6 CDC6 376 0.29 0.24 YES
5 CDC45 CDC45 CDC45 551 0.26 0.28 YES
6 POLE2 POLE2 POLE2 597 0.25 0.33 YES
7 MCM10 MCM10 MCM10 648 0.24 0.37 YES
8 PRIM2 PRIM2 PRIM2 1064 0.18 0.39 YES
9 RPA4 RPA4 RPA4 1444 0.15 0.4 YES
10 RPA3 RPA3 RPA3 2175 0.11 0.38 YES
11 PSMC1 PSMC1 PSMC1 2564 0.097 0.38 YES
12 PSME2 PSME2 PSME2 2596 0.096 0.39 YES
13 DBF4 DBF4 DBF4 2852 0.089 0.4 YES
14 PSMB7 PSMB7 PSMB7 2861 0.089 0.41 YES
15 PSMB3 PSMB3 PSMB3 2925 0.087 0.43 YES
16 MCM7 MCM7 MCM7 3337 0.078 0.42 YES
17 CDC7 CDC7 CDC7 3448 0.075 0.43 YES
18 PSMD9 PSMD9 PSMD9 3516 0.074 0.44 YES
19 PSMB4 PSMB4 PSMB4 3775 0.068 0.44 YES
20 UBA52 UBA52 UBA52 3903 0.065 0.44 YES
21 PSMD4 PSMD4 PSMD4 3919 0.065 0.46 YES
22 PSMA3 PSMA3 PSMA3 3929 0.065 0.47 YES
23 PSMB1 PSMB1 PSMB1 4032 0.063 0.48 YES
24 PSMB6 PSMB6 PSMB6 4124 0.061 0.48 YES
25 PSMA4 PSMA4 PSMA4 4132 0.06 0.49 YES
26 PSMA6 PSMA6 PSMA6 4173 0.06 0.5 YES
27 PSMB5 PSMB5 PSMB5 4332 0.057 0.5 YES
28 PSMA7 PSMA7 PSMA7 4443 0.055 0.51 YES
29 PSMA5 PSMA5 PSMA5 4474 0.054 0.52 YES
30 PSMA2 PSMA2 PSMA2 4513 0.053 0.53 YES
31 PSMD13 PSMD13 PSMD13 4563 0.052 0.54 YES
32 PSMC2 PSMC2 PSMC2 4913 0.046 0.52 YES
33 PSMB2 PSMB2 PSMB2 5057 0.044 0.53 YES
34 POLA2 POLA2 POLA2 5084 0.044 0.53 YES
35 RPS27A RPS27A RPS27A 5181 0.042 0.54 YES
36 PSMC3 PSMC3 PSMC3 5230 0.041 0.54 YES
37 MCM5 MCM5 MCM5 5318 0.04 0.54 YES
38 GMNN GMNN GMNN 5386 0.039 0.55 YES
39 PSMC5 PSMC5 PSMC5 5584 0.036 0.54 NO
40 MCM2 MCM2 MCM2 5820 0.032 0.54 NO
41 PSME1 PSME1 PSME1 5831 0.032 0.54 NO
42 PSMC6 PSMC6 PSMC6 5960 0.031 0.54 NO
43 PSMD3 PSMD3 PSMD3 6167 0.027 0.54 NO
44 POLE POLE POLE 6400 0.024 0.53 NO
45 MCM4 MCM4 MCM4 6480 0.023 0.53 NO
46 RPA2 RPA2 RPA2 6548 0.022 0.53 NO
47 PSMD14 PSMD14 PSMD14 6592 0.021 0.53 NO
48 PSMC4 PSMC4 PSMC4 6606 0.021 0.54 NO
49 PSMD6 PSMD6 PSMD6 6652 0.02 0.54 NO
50 MCM3 MCM3 MCM3 6679 0.02 0.54 NO
51 PSMA1 PSMA1 PSMA1 6765 0.019 0.54 NO
52 PSMD8 PSMD8 PSMD8 6780 0.019 0.54 NO
53 PSMD11 PSMD11 PSMD11 7003 0.016 0.53 NO
54 PSMB10 PSMB10 PSMB10 7416 0.0097 0.51 NO
55 PSMD12 PSMD12 PSMD12 7542 0.0078 0.5 NO
56 CDK2 CDK2 CDK2 7776 0.0047 0.49 NO
57 PSMF1 PSMF1 PSMF1 7778 0.0046 0.49 NO
58 PSMD2 PSMD2 PSMD2 8193 -0.0013 0.47 NO
59 PSME4 PSME4 PSME4 8241 -0.0018 0.47 NO
60 PSMB9 PSMB9 PSMB9 8664 -0.0073 0.45 NO
61 PSMD7 PSMD7 PSMD7 8770 -0.0086 0.44 NO
62 E2F3 E2F3 E2F3 8991 -0.012 0.43 NO
63 PSMD1 PSMD1 PSMD1 8998 -0.012 0.44 NO
64 PSMD10 PSMD10 PSMD10 9843 -0.023 0.39 NO
65 MCM6 MCM6 MCM6 10350 -0.031 0.37 NO
66 POLA1 POLA1 POLA1 10639 -0.035 0.36 NO
67 RPA1 RPA1 RPA1 10860 -0.039 0.36 NO
68 PRIM1 PRIM1 PRIM1 10904 -0.04 0.36 NO
69 PSMB8 PSMB8 PSMB8 11588 -0.05 0.34 NO
70 MCM8 MCM8 MCM8 11995 -0.057 0.33 NO
71 PSMD5 PSMD5 PSMD5 13662 -0.094 0.25 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 DNA REPLICATION.

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

genes ES table in pathway: KEGG PROTEASOME

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 CDT1 CDT1 CDT1 59 0.43 0.13 YES
2 CDC6 CDC6 CDC6 376 0.29 0.2 YES
3 CCNA2 CCNA2 CCNA2 506 0.26 0.27 YES
4 PSMC1 PSMC1 PSMC1 2564 0.097 0.19 YES
5 PSME2 PSME2 PSME2 2596 0.096 0.21 YES
6 PSMB7 PSMB7 PSMB7 2861 0.089 0.22 YES
7 PSMB3 PSMB3 PSMB3 2925 0.087 0.25 YES
8 MCM7 MCM7 MCM7 3337 0.078 0.25 YES
9 PSMD9 PSMD9 PSMD9 3516 0.074 0.26 YES
10 PSMB4 PSMB4 PSMB4 3775 0.068 0.27 YES
11 UBA52 UBA52 UBA52 3903 0.065 0.28 YES
12 PSMD4 PSMD4 PSMD4 3919 0.065 0.3 YES
13 PSMA3 PSMA3 PSMA3 3929 0.065 0.32 YES
14 PSMB1 PSMB1 PSMB1 4032 0.063 0.33 YES
15 PSMB6 PSMB6 PSMB6 4124 0.061 0.34 YES
16 PSMA4 PSMA4 PSMA4 4132 0.06 0.36 YES
17 PSMA6 PSMA6 PSMA6 4173 0.06 0.38 YES
18 PSMB5 PSMB5 PSMB5 4332 0.057 0.39 YES
19 PSMA7 PSMA7 PSMA7 4443 0.055 0.4 YES
20 PSMA5 PSMA5 PSMA5 4474 0.054 0.41 YES
21 PSMA2 PSMA2 PSMA2 4513 0.053 0.42 YES
22 PSMD13 PSMD13 PSMD13 4563 0.052 0.44 YES
23 CDKN1A CDKN1A CDKN1A 4721 0.05 0.44 YES
24 PSMC2 PSMC2 PSMC2 4913 0.046 0.45 YES
25 PSMB2 PSMB2 PSMB2 5057 0.044 0.45 YES
26 RPS27A RPS27A RPS27A 5181 0.042 0.46 YES
27 PSMC3 PSMC3 PSMC3 5230 0.041 0.47 YES
28 MCM5 MCM5 MCM5 5318 0.04 0.48 YES
29 PSMC5 PSMC5 PSMC5 5584 0.036 0.47 YES
30 MCM2 MCM2 MCM2 5820 0.032 0.47 YES
31 PSME1 PSME1 PSME1 5831 0.032 0.48 YES
32 PSMC6 PSMC6 PSMC6 5960 0.031 0.48 YES
33 PSMD3 PSMD3 PSMD3 6167 0.027 0.48 YES
34 MCM4 MCM4 MCM4 6480 0.023 0.47 YES
35 PSMD14 PSMD14 PSMD14 6592 0.021 0.47 YES
36 PSMC4 PSMC4 PSMC4 6606 0.021 0.47 YES
37 PSMD6 PSMD6 PSMD6 6652 0.02 0.48 YES
38 MCM3 MCM3 MCM3 6679 0.02 0.48 YES
39 PSMA1 PSMA1 PSMA1 6765 0.019 0.48 YES
40 PSMD8 PSMD8 PSMD8 6780 0.019 0.49 YES
41 PSMD11 PSMD11 PSMD11 7003 0.016 0.48 NO
42 PSMB10 PSMB10 PSMB10 7416 0.0097 0.46 NO
43 PSMD12 PSMD12 PSMD12 7542 0.0078 0.46 NO
44 CDK2 CDK2 CDK2 7776 0.0047 0.44 NO
45 PSMF1 PSMF1 PSMF1 7778 0.0046 0.45 NO
46 PSMD2 PSMD2 PSMD2 8193 -0.0013 0.42 NO
47 PSME4 PSME4 PSME4 8241 -0.0018 0.42 NO
48 PSMB9 PSMB9 PSMB9 8664 -0.0073 0.4 NO
49 CCNA1 CCNA1 CCNA1 8702 -0.0077 0.4 NO
50 PSMD7 PSMD7 PSMD7 8770 -0.0086 0.4 NO
51 PSMD1 PSMD1 PSMD1 8998 -0.012 0.39 NO
52 PSMD10 PSMD10 PSMD10 9843 -0.023 0.35 NO
53 CDKN1B CDKN1B CDKN1B 10343 -0.031 0.33 NO
54 MCM6 MCM6 MCM6 10350 -0.031 0.34 NO
55 PSMB8 PSMB8 PSMB8 11588 -0.05 0.29 NO
56 MCM8 MCM8 MCM8 11995 -0.057 0.28 NO
57 PSMD5 PSMD5 PSMD5 13662 -0.094 0.22 NO
58 RB1 RB1 RB1 14004 -0.1 0.23 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 PROTEASOME.

Figure S52.  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 BASE EXCISION REPAIR

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 UBE2C UBE2C UBE2C 22 0.5 0.057 YES
2 CDC25C CDC25C CDC25C 36 0.46 0.11 YES
3 CDC20 CDC20 CDC20 97 0.4 0.15 YES
4 CDK1 CDK1 CDK1 139 0.37 0.2 YES
5 CDC6 CDC6 CDC6 376 0.29 0.22 YES
6 BUB1B BUB1B BUB1B 522 0.26 0.24 YES
7 CDC45 CDC45 CDC45 551 0.26 0.27 YES
8 MCM10 MCM10 MCM10 648 0.24 0.29 YES
9 CCNE1 CCNE1 CCNE1 772 0.22 0.31 YES
10 CCNB2 CCNB2 CCNB2 852 0.21 0.33 YES
11 CDC25A CDC25A CDC25A 872 0.21 0.35 YES
12 CCNE2 CCNE2 CCNE2 920 0.2 0.37 YES
13 CHEK1 CHEK1 CHEK1 1041 0.18 0.39 YES
14 RFC4 RFC4 RFC4 1169 0.17 0.4 YES
15 CCNB1 CCNB1 CCNB1 1228 0.16 0.42 YES
16 MAD1L1 MAD1L1 MAD1L1 1409 0.15 0.42 YES
17 RAD9A RAD9A RAD9A 1545 0.14 0.43 YES
18 RFC3 RFC3 RFC3 1654 0.14 0.44 YES
19 ANAPC11 ANAPC11 ANAPC11 1776 0.13 0.45 YES
20 RPA3 RPA3 RPA3 2175 0.11 0.44 YES
21 RFC2 RFC2 RFC2 2242 0.11 0.45 YES
22 MAD2L1 MAD2L1 MAD2L1 2404 0.1 0.46 YES
23 PSMC1 PSMC1 PSMC1 2564 0.097 0.46 YES
24 PSME2 PSME2 PSME2 2596 0.096 0.47 YES
25 DBF4 DBF4 DBF4 2852 0.089 0.46 YES
26 PSMB7 PSMB7 PSMB7 2861 0.089 0.48 YES
27 CHEK2 CHEK2 CHEK2 2893 0.088 0.48 YES
28 PSMB3 PSMB3 PSMB3 2925 0.087 0.49 YES
29 MCM7 MCM7 MCM7 3337 0.078 0.48 YES
30 CDC7 CDC7 CDC7 3448 0.075 0.48 YES
31 PSMD9 PSMD9 PSMD9 3516 0.074 0.49 YES
32 ATRIP ATRIP ATRIP 3595 0.072 0.49 YES
33 ANAPC5 ANAPC5 ANAPC5 3622 0.072 0.5 YES
34 PSMB4 PSMB4 PSMB4 3775 0.068 0.5 YES
35 UBA52 UBA52 UBA52 3903 0.065 0.5 YES
36 PSMD4 PSMD4 PSMD4 3919 0.065 0.5 YES
37 PSMA3 PSMA3 PSMA3 3929 0.065 0.51 YES
38 PSMB1 PSMB1 PSMB1 4032 0.063 0.51 YES
39 PSMB6 PSMB6 PSMB6 4124 0.061 0.52 YES
40 PSMA4 PSMA4 PSMA4 4132 0.06 0.52 YES
41 PSMA6 PSMA6 PSMA6 4173 0.06 0.53 YES
42 PSMB5 PSMB5 PSMB5 4332 0.057 0.52 YES
43 PSMA7 PSMA7 PSMA7 4443 0.055 0.52 YES
44 PSMA5 PSMA5 PSMA5 4474 0.054 0.53 YES
45 HUS1 HUS1 HUS1 4506 0.054 0.53 YES
46 PSMA2 PSMA2 PSMA2 4513 0.053 0.54 YES
47 PSMD13 PSMD13 PSMD13 4563 0.052 0.54 YES
48 CDKN1A CDKN1A CDKN1A 4721 0.05 0.54 YES
49 UBE2E1 UBE2E1 UBE2E1 4842 0.048 0.54 YES
50 PSMC2 PSMC2 PSMC2 4913 0.046 0.54 YES
51 ANAPC2 ANAPC2 ANAPC2 4945 0.046 0.55 YES
52 PSMB2 PSMB2 PSMB2 5057 0.044 0.54 YES
53 UBE2D1 UBE2D1 UBE2D1 5112 0.043 0.55 YES
54 RPS27A RPS27A RPS27A 5181 0.042 0.55 YES
55 PSMC3 PSMC3 PSMC3 5230 0.041 0.55 YES
56 MCM5 MCM5 MCM5 5318 0.04 0.55 NO
57 PSMC5 PSMC5 PSMC5 5584 0.036 0.54 NO
58 MCM2 MCM2 MCM2 5820 0.032 0.53 NO
59 PSME1 PSME1 PSME1 5831 0.032 0.53 NO
60 CDC26 CDC26 CDC26 5946 0.031 0.53 NO
61 PSMC6 PSMC6 PSMC6 5960 0.031 0.53 NO
62 PSMD3 PSMD3 PSMD3 6167 0.027 0.52 NO
63 ANAPC7 ANAPC7 ANAPC7 6221 0.027 0.52 NO
64 MCM4 MCM4 MCM4 6480 0.023 0.51 NO
65 RPA2 RPA2 RPA2 6548 0.022 0.51 NO
66 PSMD14 PSMD14 PSMD14 6592 0.021 0.51 NO
67 PSMC4 PSMC4 PSMC4 6606 0.021 0.52 NO
68 PSMD6 PSMD6 PSMD6 6652 0.02 0.51 NO
69 MCM3 MCM3 MCM3 6679 0.02 0.52 NO
70 PSMA1 PSMA1 PSMA1 6765 0.019 0.51 NO
71 RFC5 RFC5 RFC5 6768 0.019 0.52 NO
72 PSMD8 PSMD8 PSMD8 6780 0.019 0.52 NO
73 PSMD11 PSMD11 PSMD11 7003 0.016 0.51 NO
74 BUB3 BUB3 BUB3 7267 0.012 0.49 NO
75 PSMB10 PSMB10 PSMB10 7416 0.0097 0.49 NO
76 PSMD12 PSMD12 PSMD12 7542 0.0078 0.48 NO
77 RAD1 RAD1 RAD1 7607 0.007 0.48 NO
78 CDK2 CDK2 CDK2 7776 0.0047 0.47 NO
79 PSMF1 PSMF1 PSMF1 7778 0.0046 0.47 NO
80 CDC16 CDC16 CDC16 7795 0.0044 0.47 NO
81 CDC23 CDC23 CDC23 8158 -0.00084 0.45 NO
82 PSMD2 PSMD2 PSMD2 8193 -0.0013 0.45 NO
83 PSME4 PSME4 PSME4 8241 -0.0018 0.44 NO
84 RFWD2 RFWD2 RFWD2 8568 -0.0062 0.43 NO
85 PSMB9 PSMB9 PSMB9 8664 -0.0073 0.42 NO
86 ANAPC4 ANAPC4 ANAPC4 8740 -0.0082 0.42 NO
87 ANAPC10 ANAPC10 ANAPC10 8767 -0.0086 0.42 NO
88 PSMD7 PSMD7 PSMD7 8770 -0.0086 0.42 NO
89 PSMD1 PSMD1 PSMD1 8998 -0.012 0.41 NO
90 MDM2 MDM2 MDM2 9104 -0.013 0.4 NO
91 TP53 TP53 TP53 9333 -0.016 0.4 NO
92 PSMD10 PSMD10 PSMD10 9843 -0.023 0.37 NO
93 CDKN1B CDKN1B CDKN1B 10343 -0.031 0.34 NO
94 MCM6 MCM6 MCM6 10350 -0.031 0.35 NO
95 RPA1 RPA1 RPA1 10860 -0.039 0.32 NO
96 CDC27 CDC27 CDC27 11105 -0.042 0.32 NO
97 PSMB8 PSMB8 PSMB8 11588 -0.05 0.3 NO
98 RAD17 RAD17 RAD17 11702 -0.052 0.3 NO
99 MCM8 MCM8 MCM8 11995 -0.057 0.29 NO
100 ATR ATR ATR 12371 -0.064 0.27 NO
101 PSMD5 PSMD5 PSMD5 13662 -0.094 0.21 NO
102 WEE1 WEE1 WEE1 13681 -0.094 0.22 NO
103 ATM ATM ATM 14535 -0.12 0.19 NO
104 ANAPC1 ANAPC1 ANAPC1 14683 -0.12 0.2 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 BASE EXCISION REPAIR.

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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 SHFM1 SHFM1 SHFM1 1315 0.16 0.008 YES
2 PSMB11 PSMB11 PSMB11 1687 0.14 0.056 YES
3 PSMC1 PSMC1 PSMC1 2564 0.097 0.057 YES
4 PSME2 PSME2 PSME2 2596 0.096 0.1 YES
5 PSMB7 PSMB7 PSMB7 2861 0.089 0.13 YES
6 PSMB3 PSMB3 PSMB3 2925 0.087 0.18 YES
7 PSMB4 PSMB4 PSMB4 3775 0.068 0.16 YES
8 PSMD4 PSMD4 PSMD4 3919 0.065 0.19 YES
9 PSMA3 PSMA3 PSMA3 3929 0.065 0.22 YES
10 PSMB1 PSMB1 PSMB1 4032 0.063 0.25 YES
11 POMP POMP POMP 4114 0.061 0.27 YES
12 PSMB6 PSMB6 PSMB6 4124 0.061 0.3 YES
13 PSMA4 PSMA4 PSMA4 4132 0.06 0.33 YES
14 PSMA6 PSMA6 PSMA6 4173 0.06 0.36 YES
15 PSMB5 PSMB5 PSMB5 4332 0.057 0.38 YES
16 IFNG IFNG IFNG 4423 0.055 0.4 YES
17 PSMA7 PSMA7 PSMA7 4443 0.055 0.43 YES
18 PSMA5 PSMA5 PSMA5 4474 0.054 0.46 YES
19 PSMA2 PSMA2 PSMA2 4513 0.053 0.48 YES
20 PSMD13 PSMD13 PSMD13 4563 0.052 0.5 YES
21 PSMC2 PSMC2 PSMC2 4913 0.046 0.51 YES
22 PSMB2 PSMB2 PSMB2 5057 0.044 0.52 YES
23 PSMC3 PSMC3 PSMC3 5230 0.041 0.54 YES
24 PSMC5 PSMC5 PSMC5 5584 0.036 0.53 YES
25 PSME1 PSME1 PSME1 5831 0.032 0.54 YES
26 PSMC6 PSMC6 PSMC6 5960 0.031 0.55 YES
27 PSMD3 PSMD3 PSMD3 6167 0.027 0.55 YES
28 PSMD14 PSMD14 PSMD14 6592 0.021 0.54 YES
29 PSMC4 PSMC4 PSMC4 6606 0.021 0.55 YES
30 PSMD6 PSMD6 PSMD6 6652 0.02 0.55 YES
31 PSMA1 PSMA1 PSMA1 6765 0.019 0.56 YES
32 PSMD8 PSMD8 PSMD8 6780 0.019 0.56 YES
33 PSMD11 PSMD11 PSMD11 7003 0.016 0.56 NO
34 PSMB10 PSMB10 PSMB10 7416 0.0097 0.54 NO
35 PSMD12 PSMD12 PSMD12 7542 0.0078 0.54 NO
36 PSMF1 PSMF1 PSMF1 7778 0.0046 0.53 NO
37 PSMD2 PSMD2 PSMD2 8193 -0.0013 0.51 NO
38 PSME4 PSME4 PSME4 8241 -0.0018 0.5 NO
39 PSMB9 PSMB9 PSMB9 8664 -0.0073 0.49 NO
40 PSMD7 PSMD7 PSMD7 8770 -0.0086 0.48 NO
41 PSME3 PSME3 PSME3 8840 -0.0097 0.48 NO
42 PSMD1 PSMD1 PSMD1 8998 -0.012 0.48 NO
43 PSMB8 PSMB8 PSMB8 11588 -0.05 0.37 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 HOMOLOGOUS RECOMBINATION.

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

genes ES table in pathway: KEGG CELL CYCLE

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 AURKB AURKB AURKB 3 0.58 0.09 YES
2 UBE2C UBE2C UBE2C 22 0.5 0.17 YES
3 PTTG1 PTTG1 PTTG1 39 0.46 0.24 YES
4 CDC20 CDC20 CDC20 97 0.4 0.29 YES
5 CDK1 CDK1 CDK1 139 0.37 0.35 YES
6 PLK1 PLK1 PLK1 165 0.36 0.4 YES
7 AURKA AURKA AURKA 309 0.3 0.44 YES
8 CCNA2 CCNA2 CCNA2 506 0.26 0.47 YES
9 BUB1B BUB1B BUB1B 522 0.26 0.51 YES
10 CCNB1 CCNB1 CCNB1 1228 0.16 0.5 YES
11 ANAPC11 ANAPC11 ANAPC11 1776 0.13 0.49 YES
12 MAD2L1 MAD2L1 MAD2L1 2404 0.1 0.47 YES
13 PSMC1 PSMC1 PSMC1 2564 0.097 0.48 YES
14 PSME2 PSME2 PSME2 2596 0.096 0.49 YES
15 PSMB7 PSMB7 PSMB7 2861 0.089 0.49 YES
16 PSMB3 PSMB3 PSMB3 2925 0.087 0.5 YES
17 PSMD9 PSMD9 PSMD9 3516 0.074 0.48 YES
18 ANAPC5 ANAPC5 ANAPC5 3622 0.072 0.48 YES
19 PSMB4 PSMB4 PSMB4 3775 0.068 0.48 YES
20 UBA52 UBA52 UBA52 3903 0.065 0.49 YES
21 PSMD4 PSMD4 PSMD4 3919 0.065 0.5 YES
22 PSMA3 PSMA3 PSMA3 3929 0.065 0.51 YES
23 PSMB1 PSMB1 PSMB1 4032 0.063 0.51 YES
24 PSMB6 PSMB6 PSMB6 4124 0.061 0.52 YES
25 PSMA4 PSMA4 PSMA4 4132 0.06 0.52 YES
26 PSMA6 PSMA6 PSMA6 4173 0.06 0.53 YES
27 PSMB5 PSMB5 PSMB5 4332 0.057 0.53 YES
28 PSMA7 PSMA7 PSMA7 4443 0.055 0.53 YES
29 PSMA5 PSMA5 PSMA5 4474 0.054 0.54 YES
30 PSMA2 PSMA2 PSMA2 4513 0.053 0.55 YES
31 PSMD13 PSMD13 PSMD13 4563 0.052 0.55 YES
32 UBE2E1 UBE2E1 UBE2E1 4842 0.048 0.54 YES
33 PSMC2 PSMC2 PSMC2 4913 0.046 0.55 YES
34 ANAPC2 ANAPC2 ANAPC2 4945 0.046 0.55 YES
35 PSMB2 PSMB2 PSMB2 5057 0.044 0.55 YES
36 UBE2D1 UBE2D1 UBE2D1 5112 0.043 0.56 YES
37 RPS27A RPS27A RPS27A 5181 0.042 0.56 YES
38 PSMC3 PSMC3 PSMC3 5230 0.041 0.56 YES
39 PSMC5 PSMC5 PSMC5 5584 0.036 0.55 NO
40 PSME1 PSME1 PSME1 5831 0.032 0.54 NO
41 CDC26 CDC26 CDC26 5946 0.031 0.54 NO
42 PSMC6 PSMC6 PSMC6 5960 0.031 0.54 NO
43 PSMD3 PSMD3 PSMD3 6167 0.027 0.54 NO
44 ANAPC7 ANAPC7 ANAPC7 6221 0.027 0.54 NO
45 PSMD14 PSMD14 PSMD14 6592 0.021 0.52 NO
46 PSMC4 PSMC4 PSMC4 6606 0.021 0.52 NO
47 PSMD6 PSMD6 PSMD6 6652 0.02 0.52 NO
48 PSMA1 PSMA1 PSMA1 6765 0.019 0.52 NO
49 PSMD8 PSMD8 PSMD8 6780 0.019 0.52 NO
50 PSMD11 PSMD11 PSMD11 7003 0.016 0.51 NO
51 BUB3 BUB3 BUB3 7267 0.012 0.5 NO
52 FBXO5 FBXO5 FBXO5 7322 0.011 0.5 NO
53 PSMB10 PSMB10 PSMB10 7416 0.0097 0.5 NO
54 PSMD12 PSMD12 PSMD12 7542 0.0078 0.49 NO
55 CDK2 CDK2 CDK2 7776 0.0047 0.48 NO
56 PSMF1 PSMF1 PSMF1 7778 0.0046 0.48 NO
57 CDC16 CDC16 CDC16 7795 0.0044 0.48 NO
58 CUL1 CUL1 CUL1 7921 0.0026 0.47 NO
59 SKP1 SKP1 SKP1 7936 0.0023 0.47 NO
60 CDC23 CDC23 CDC23 8158 -0.00084 0.46 NO
61 PSMD2 PSMD2 PSMD2 8193 -0.0013 0.46 NO
62 PSME4 PSME4 PSME4 8241 -0.0018 0.46 NO
63 PSMB9 PSMB9 PSMB9 8664 -0.0073 0.43 NO
64 CCNA1 CCNA1 CCNA1 8702 -0.0077 0.43 NO
65 ANAPC4 ANAPC4 ANAPC4 8740 -0.0082 0.43 NO
66 ANAPC10 ANAPC10 ANAPC10 8767 -0.0086 0.43 NO
67 PSMD7 PSMD7 PSMD7 8770 -0.0086 0.43 NO
68 PSMD1 PSMD1 PSMD1 8998 -0.012 0.42 NO
69 PSMD10 PSMD10 PSMD10 9843 -0.023 0.38 NO
70 BTRC BTRC BTRC 10644 -0.036 0.34 NO
71 CDC27 CDC27 CDC27 11105 -0.042 0.32 NO
72 PSMB8 PSMB8 PSMB8 11588 -0.05 0.3 NO
73 CDC14A CDC14A CDC14A 12656 -0.07 0.26 NO
74 PSMD5 PSMD5 PSMD5 13662 -0.094 0.21 NO
75 SKP2 SKP2 SKP2 14650 -0.12 0.18 NO
76 ANAPC1 ANAPC1 ANAPC1 14683 -0.12 0.2 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 CELL CYCLE.

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

genes ES table in pathway: KEGG PARKINSONS DISEASE

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 UCP3 UCP3 UCP3 889 0.2 -0.025 YES
2 COX6C COX6C COX6C 1303 0.16 -0.028 YES
3 ATP5I ATP5I ATP5I 1515 0.14 -0.023 YES
4 NDUFA3 NDUFA3 NDUFA3 1523 0.14 -0.0061 YES
5 NDUFB9 NDUFB9 NDUFB9 1671 0.14 0.002 YES
6 ATP5J2 ATP5J2 ATP5J2 1701 0.13 0.016 YES
7 NDUFB1 NDUFB1 NDUFB1 1712 0.13 0.032 YES
8 COX6A1 COX6A1 COX6A1 1757 0.13 0.045 YES
9 UQCRHL UQCRHL UQCRHL 1774 0.13 0.06 YES
10 ATP5D ATP5D ATP5D 1786 0.13 0.074 YES
11 NDUFB7 NDUFB7 NDUFB7 1839 0.13 0.087 YES
12 COX5B COX5B COX5B 1854 0.12 0.1 YES
13 UQCR11 UQCR11 UQCR11 1969 0.12 0.11 YES
14 NDUFA2 NDUFA2 NDUFA2 1978 0.12 0.12 YES
15 NDUFB10 NDUFB10 NDUFB10 2082 0.12 0.13 YES
16 UQCRB UQCRB UQCRB 2091 0.12 0.14 YES
17 NDUFA13 NDUFA13 NDUFA13 2095 0.12 0.16 YES
18 NDUFS8 NDUFS8 NDUFS8 2134 0.11 0.17 YES
19 UQCRQ UQCRQ UQCRQ 2165 0.11 0.18 YES
20 NDUFA7 NDUFA7 NDUFA7 2185 0.11 0.19 YES
21 COX7B COX7B COX7B 2217 0.11 0.21 YES
22 NDUFA1 NDUFA1 NDUFA1 2361 0.1 0.21 YES
23 D2HGDH D2HGDH D2HGDH 2379 0.1 0.22 YES
24 ATP5G1 ATP5G1 ATP5G1 2382 0.1 0.23 YES
25 SLC16A1 SLC16A1 SLC16A1 2394 0.1 0.25 YES
26 NDUFS6 NDUFS6 NDUFS6 2409 0.1 0.26 YES
27 ADHFE1 ADHFE1 ADHFE1 2468 0.1 0.27 YES
28 NDUFC2 NDUFC2 NDUFC2 2577 0.097 0.27 YES
29 ATP5E ATP5E ATP5E 2667 0.094 0.28 YES
30 COX6B1 COX6B1 COX6B1 2672 0.094 0.29 YES
31 UQCRH UQCRH UQCRH 2744 0.092 0.3 YES
32 COX8A COX8A COX8A 2764 0.092 0.31 YES
33 NDUFV3 NDUFV3 NDUFV3 2766 0.091 0.32 YES
34 NDUFV1 NDUFV1 NDUFV1 2838 0.09 0.32 YES
35 NDUFA11 NDUFA11 NDUFA11 2946 0.086 0.33 YES
36 NDUFB2 NDUFB2 NDUFB2 2954 0.086 0.34 YES
37 NDUFV2 NDUFV2 NDUFV2 2958 0.086 0.35 YES
38 NDUFA8 NDUFA8 NDUFA8 2986 0.085 0.36 YES
39 NDUFB3 NDUFB3 NDUFB3 3038 0.084 0.36 YES
40 NDUFB6 NDUFB6 NDUFB6 3060 0.084 0.37 YES
41 NDUFS7 NDUFS7 NDUFS7 3074 0.083 0.38 YES
42 COX5A COX5A COX5A 3143 0.082 0.39 YES
43 NDUFAB1 NDUFAB1 NDUFAB1 3509 0.074 0.38 YES
44 UCP2 UCP2 UCP2 3533 0.073 0.38 YES
45 CYC1 CYC1 CYC1 3728 0.069 0.38 YES
46 NDUFC1 NDUFC1 NDUFC1 3763 0.068 0.39 YES
47 NDUFB8 NDUFB8 NDUFB8 3856 0.066 0.39 YES
48 NDUFA12 NDUFA12 NDUFA12 3865 0.066 0.4 YES
49 BSG BSG BSG 3958 0.064 0.4 YES
50 NDUFS5 NDUFS5 NDUFS5 4059 0.062 0.4 YES
51 NDUFB4 NDUFB4 NDUFB4 4123 0.061 0.41 YES
52 COX4I1 COX4I1 COX4I1 4178 0.06 0.41 YES
53 ATP5H ATP5H ATP5H 4182 0.06 0.42 YES
54 ATP5L ATP5L ATP5L 4319 0.057 0.42 YES
55 NDUFA10 NDUFA10 NDUFA10 4487 0.054 0.42 YES
56 ATP5O ATP5O ATP5O 4511 0.053 0.42 YES
57 UQCRC1 UQCRC1 UQCRC1 4523 0.053 0.43 YES
58 SLC16A8 SLC16A8 SLC16A8 4546 0.053 0.43 YES
59 NDUFA6 NDUFA6 NDUFA6 4560 0.052 0.44 YES
60 IDH3B IDH3B IDH3B 4629 0.051 0.44 YES
61 IDH3G IDH3G IDH3G 4642 0.051 0.44 YES
62 IDH2 IDH2 IDH2 4771 0.049 0.44 YES
63 NDUFA4 NDUFA4 NDUFA4 4831 0.048 0.45 YES
64 NDUFS3 NDUFS3 NDUFS3 4903 0.047 0.45 YES
65 COX7C COX7C COX7C 4952 0.046 0.45 YES
66 NDUFA9 NDUFA9 NDUFA9 5016 0.044 0.45 YES
67 MDH2 MDH2 MDH2 5054 0.044 0.46 YES
68 ATP5J ATP5J ATP5J 5091 0.043 0.46 YES
69 CYCS CYCS CYCS 5196 0.042 0.46 YES
70 ATP5C1 ATP5C1 ATP5C1 5197 0.042 0.46 YES
71 FH FH FH 5227 0.041 0.47 YES
72 NDUFB5 NDUFB5 NDUFB5 5436 0.038 0.46 NO
73 SDHB SDHB SDHB 5896 0.032 0.44 NO
74 PDHX PDHX PDHX 5981 0.03 0.44 NO
75 NDUFA5 NDUFA5 NDUFA5 6139 0.028 0.43 NO
76 COX7A2L COX7A2L COX7A2L 6258 0.026 0.43 NO
77 PDHA1 PDHA1 PDHA1 6466 0.023 0.42 NO
78 ETFB ETFB ETFB 6671 0.02 0.41 NO
79 ETFA ETFA ETFA 6681 0.02 0.41 NO
80 SDHA SDHA SDHA 6718 0.02 0.41 NO
81 UQCRFS1 UQCRFS1 UQCRFS1 6745 0.019 0.41 NO
82 NDUFS2 NDUFS2 NDUFS2 7008 0.015 0.4 NO
83 DLST DLST DLST 7208 0.013 0.39 NO
84 L2HGDH L2HGDH L2HGDH 7214 0.013 0.39 NO
85 SDHC SDHC SDHC 7220 0.013 0.4 NO
86 ATP5B ATP5B ATP5B 7312 0.011 0.39 NO
87 NDUFS4 NDUFS4 NDUFS4 7614 0.0069 0.38 NO
88 SUCLG1 SUCLG1 SUCLG1 7620 0.0069 0.38 NO
89 PDHB PDHB PDHB 7869 0.0033 0.36 NO
90 ATP5F1 ATP5F1 ATP5F1 7890 0.003 0.36 NO
91 IDH1 IDH1 IDH1 8077 0.00017 0.35 NO
92 CS CS CS 8126 -0.00031 0.35 NO
93 PDK1 PDK1 PDK1 8176 -0.0011 0.35 NO
94 DLD DLD DLD 8206 -0.0014 0.34 NO
95 ETFDH ETFDH ETFDH 8223 -0.0016 0.34 NO
96 SUCLG2 SUCLG2 SUCLG2 8257 -0.002 0.34 NO
97 SLC16A3 SLC16A3 SLC16A3 8279 -0.0023 0.34 NO
98 ATP5A1 ATP5A1 ATP5A1 8296 -0.0024 0.34 NO
99 LDHA LDHA LDHA 8332 -0.0029 0.34 NO
100 ACO2 ACO2 ACO2 8473 -0.005 0.33 NO
101 IDH3A IDH3A IDH3A 9758 -0.022 0.26 NO
102 UQCRC2 UQCRC2 UQCRC2 10390 -0.031 0.23 NO
103 OGDH OGDH OGDH 11054 -0.042 0.2 NO
104 DLAT DLAT DLAT 11814 -0.054 0.17 NO
105 SDHD SDHD SDHD 12065 -0.059 0.16 NO
106 PDP1 PDP1 PDP1 12402 -0.065 0.15 NO
107 NDUFS1 NDUFS1 NDUFS1 12526 -0.067 0.15 NO
108 PDK2 PDK2 PDK2 12617 -0.069 0.15 NO
109 SUCLA2 SUCLA2 SUCLA2 13068 -0.078 0.14 NO
110 PDK3 PDK3 PDK3 14597 -0.12 0.068 NO
111 PDP2 PDP2 PDP2 15888 -0.18 0.019 NO
112 LDHB LDHB LDHB 16386 -0.21 0.017 NO
113 NNT NNT NNT 16414 -0.21 0.041 NO
114 PDPR PDPR PDPR 16526 -0.22 0.061 NO
115 PDK4 PDK4 PDK4 17262 -0.28 0.055 NO

Figure S59.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PARKINSONS DISEASE.

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

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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM 30 genes.ES.table 0.52 1.6 0.024 0.2 0.93 0.43 0.29 0.31 0.11 0.015
KEGG LYSINE DEGRADATION 44 genes.ES.table 0.46 1.9 0.0061 0.91 0.32 0.068 0.059 0.064 0 0.19
KEGG ARGININE AND PROLINE METABOLISM 51 genes.ES.table 0.44 1.4 0.11 0.22 1 0.2 0.13 0.17 0.16 0.001
KEGG HISTIDINE METABOLISM 29 genes.ES.table 0.58 1.5 0.029 0.19 0.98 0.34 0.2 0.28 0.13 0.004
KEGG TRYPTOPHAN METABOLISM 38 genes.ES.table 0.59 1.6 0.0021 0.21 0.82 0.34 0.19 0.28 0.097 0.033
KEGG SELENOAMINO ACID METABOLISM 26 genes.ES.table 0.47 1.6 0.04 0.21 0.86 0.077 0.019 0.076 0.1 0.031
KEGG GLUTATHIONE METABOLISM 48 genes.ES.table 0.55 1.6 0.037 0.2 0.93 0.31 0.21 0.25 0.11 0.014
KEGG O GLYCAN BIOSYNTHESIS 29 genes.ES.table 0.57 1.4 0.06 0.19 0.99 0.21 0.08 0.19 0.13 0.002
KEGG GLYCEROLIPID METABOLISM 44 genes.ES.table 0.44 1.4 0.098 0.22 1 0.41 0.29 0.29 0.17 0.001
KEGG INOSITOL PHOSPHATE METABOLISM 53 genes.ES.table 0.46 1.6 0.022 0.2 0.93 0.26 0.23 0.2 0.11 0.014
genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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 NTF4 NTF4 NTF4 23 0.81 0.14 YES
2 NTF3 NTF3 NTF3 436 0.46 0.2 YES
3 MMP7 MMP7 MMP7 616 0.42 0.26 YES
4 NGFR NGFR NGFR 633 0.41 0.34 YES
5 BEX1 BEX1 BEX1 718 0.4 0.4 YES
6 BDNF BDNF BDNF 905 0.37 0.46 YES
7 NTRK1 NTRK1 NTRK1 1592 0.28 0.47 YES
8 BIRC3 BIRC3 BIRC3 1715 0.28 0.51 YES
9 OMG OMG OMG 3031 0.18 0.47 NO
10 RHOB RHOB RHOB 4168 0.13 0.43 NO
11 NGF NGF NGF 4673 0.1 0.42 NO
12 NDN NDN NDN 4904 0.097 0.42 NO
13 MAG MAG MAG 5279 0.085 0.42 NO
14 PIK3R1 PIK3R1 PIK3R1 5289 0.085 0.43 NO
15 IKBKB IKBKB IKBKB 5888 0.067 0.41 NO
16 TRAF6 TRAF6 TRAF6 5933 0.065 0.42 NO
17 PLG PLG PLG 6634 0.049 0.39 NO
18 SQSTM1 SQSTM1 SQSTM1 7190 0.038 0.37 NO
19 IKBKG IKBKG IKBKG 7285 0.037 0.37 NO
20 SHC1 SHC1 SHC1 7466 0.034 0.36 NO
21 NDNL2 NDNL2 NDNL2 7564 0.032 0.36 NO
22 CASP9 CASP9 CASP9 7837 0.029 0.36 NO
23 FURIN FURIN FURIN 7914 0.028 0.36 NO
24 ZNF274 ZNF274 ZNF274 8071 0.026 0.35 NO
25 APP APP APP 8575 0.019 0.33 NO
26 TP53 TP53 TP53 8592 0.019 0.33 NO
27 MYD88 MYD88 MYD88 8650 0.018 0.33 NO
28 ADAM17 ADAM17 ADAM17 8674 0.018 0.33 NO
29 CASP3 CASP3 CASP3 8703 0.018 0.33 NO
30 MAPK10 MAPK10 MAPK10 8765 0.017 0.33 NO
31 BIRC2 BIRC2 BIRC2 8806 0.016 0.33 NO
32 RTN4R RTN4R RTN4R 8863 0.016 0.33 NO
33 RTN4 RTN4 RTN4 9098 0.013 0.32 NO
34 DIABLO DIABLO DIABLO 9538 0.0092 0.3 NO
35 BCL2L11 BCL2L11 BCL2L11 9762 0.0069 0.29 NO
36 PRDM4 PRDM4 PRDM4 9767 0.0069 0.29 NO
37 RHOC RHOC RHOC 10018 0.0044 0.28 NO
38 RHOA RHOA RHOA 10188 0.0027 0.27 NO
39 CASP6 CASP6 CASP6 10357 0.0013 0.26 NO
40 NGFRAP1 NGFRAP1 NGFRAP1 10549 -0.00028 0.25 NO
41 APH1A APH1A APH1A 10643 -0.0011 0.24 NO
42 SORT1 SORT1 SORT1 10677 -0.0014 0.24 NO
43 PRKCZ PRKCZ PRKCZ 10679 -0.0014 0.24 NO
44 RAC1 RAC1 RAC1 10712 -0.0017 0.24 NO
45 APAF1 APAF1 APAF1 10827 -0.0028 0.24 NO
46 PIK3CA PIK3CA PIK3CA 10930 -0.0038 0.23 NO
47 PSENEN PSENEN PSENEN 11199 -0.0059 0.22 NO
48 PSEN1 PSEN1 PSEN1 11543 -0.0086 0.2 NO
49 CHUK CHUK CHUK 11656 -0.0095 0.2 NO
50 MAGEH1 MAGEH1 MAGEH1 11701 -0.0099 0.2 NO
51 SMPD2 SMPD2 SMPD2 11832 -0.011 0.19 NO
52 BAD BAD BAD 12165 -0.014 0.17 NO
53 ARHGDIA ARHGDIA ARHGDIA 12922 -0.02 0.14 NO
54 APH1B APH1B APH1B 12943 -0.02 0.14 NO
55 NCSTN NCSTN NCSTN 13585 -0.026 0.11 NO
56 AKT1 AKT1 AKT1 13643 -0.027 0.11 NO
57 MMP3 MMP3 MMP3 13790 -0.028 0.11 NO
58 YWHAE YWHAE YWHAE 13820 -0.029 0.11 NO
59 PRKCI PRKCI PRKCI 14097 -0.032 0.1 NO
60 IRAK1 IRAK1 IRAK1 14719 -0.038 0.072 NO
61 MAPK8 MAPK8 MAPK8 14780 -0.039 0.076 NO
62 XIAP XIAP XIAP 15262 -0.045 0.057 NO
63 MAPK9 MAPK9 MAPK9 15445 -0.049 0.056 NO
64 CYCS CYCS CYCS 15484 -0.05 0.063 NO
65 PRKACB PRKACB PRKACB 15832 -0.056 0.053 NO
66 MAGED1 MAGED1 MAGED1 15984 -0.06 0.056 NO
67 RIPK2 RIPK2 RIPK2 17175 -0.1 0.0083 NO
68 E2F1 E2F1 E2F1 17486 -0.12 0.013 NO
69 LINGO1 LINGO1 LINGO1 17827 -0.16 0.024 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S62.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG LYSINE DEGRADATION

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 TMLHE TMLHE TMLHE 401 0.47 0.18 YES
2 PIPOX PIPOX PIPOX 737 0.39 0.33 YES
3 BBOX1 BBOX1 BBOX1 1070 0.34 0.46 YES
4 ALDH2 ALDH2 ALDH2 3386 0.16 0.4 NO
5 ALDH3A2 ALDH3A2 ALDH3A2 5278 0.085 0.33 NO
6 SUV420H2 SUV420H2 SUV420H2 7311 0.036 0.23 NO
7 WHSC1L1 WHSC1L1 WHSC1L1 7611 0.032 0.23 NO
8 SETDB2 SETDB2 SETDB2 7694 0.031 0.24 NO
9 ALDH1B1 ALDH1B1 ALDH1B1 8327 0.022 0.22 NO
10 SETD1A SETD1A SETD1A 8356 0.022 0.22 NO
11 AASS AASS AASS 8377 0.022 0.23 NO
12 EHMT2 EHMT2 EHMT2 8565 0.019 0.23 NO
13 AASDH AASDH AASDH 9722 0.0073 0.17 NO
14 SUV39H1 SUV39H1 SUV39H1 10183 0.0027 0.14 NO
15 HADHA HADHA HADHA 10219 0.0024 0.14 NO
16 DOT1L DOT1L DOT1L 10235 0.0022 0.14 NO
17 SETD1B SETD1B SETD1B 10653 -0.0012 0.12 NO
18 SETDB1 SETDB1 SETDB1 10965 -0.004 0.11 NO
19 SETMAR SETMAR SETMAR 11132 -0.0053 0.099 NO
20 DLST DLST DLST 11273 -0.0064 0.094 NO
21 OGDH OGDH OGDH 11493 -0.0082 0.085 NO
22 ALDH7A1 ALDH7A1 ALDH7A1 11576 -0.0089 0.085 NO
23 GCDH GCDH GCDH 11719 -0.01 0.081 NO
24 EHMT1 EHMT1 EHMT1 12044 -0.013 0.069 NO
25 SETD8 SETD8 SETD8 12220 -0.014 0.065 NO
26 PLOD1 PLOD1 PLOD1 12251 -0.014 0.07 NO
27 ASH1L ASH1L ASH1L 12336 -0.015 0.072 NO
28 SUV420H1 SUV420H1 SUV420H1 12352 -0.015 0.077 NO
29 ALDH9A1 ALDH9A1 ALDH9A1 12358 -0.015 0.083 NO
30 SETD2 SETD2 SETD2 12361 -0.015 0.09 NO
31 OGDHL OGDHL OGDHL 12417 -0.016 0.094 NO
32 HADH HADH HADH 12793 -0.019 0.081 NO
33 NSD1 NSD1 NSD1 12907 -0.02 0.083 NO
34 PLOD3 PLOD3 PLOD3 13717 -0.028 0.051 NO
35 AASDHPPT AASDHPPT AASDHPPT 14000 -0.03 0.048 NO
36 ECHS1 ECHS1 ECHS1 14050 -0.031 0.059 NO
37 ACAT2 ACAT2 ACAT2 14226 -0.033 0.063 NO
38 PLOD2 PLOD2 PLOD2 14648 -0.038 0.056 NO
39 SUV39H2 SUV39H2 SUV39H2 15417 -0.048 0.034 NO
40 ACAT1 ACAT1 ACAT1 15682 -0.053 0.042 NO
41 SETD7 SETD7 SETD7 15807 -0.055 0.059 NO
42 EHHADH EHHADH EHHADH 15856 -0.056 0.08 NO
43 AADAT AADAT AADAT 15949 -0.059 0.1 NO
44 WHSC1 WHSC1 WHSC1 16147 -0.063 0.12 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 LYSINE DEGRADATION.

Figure S64.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

Table 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 MUC4 MUC4 MUC4 8 0.88 0.047 YES
2 B3GNT8 B3GNT8 B3GNT8 87 0.69 0.08 YES
3 MUC15 MUC15 MUC15 121 0.65 0.11 YES
4 ST6GALNAC2 ST6GALNAC2 ST6GALNAC2 133 0.64 0.15 YES
5 B3GNT3 B3GNT3 B3GNT3 139 0.64 0.18 YES
6 MUC16 MUC16 MUC16 158 0.62 0.21 YES
7 GALNT5 GALNT5 GALNT5 238 0.55 0.24 YES
8 GCNT3 GCNT3 GCNT3 272 0.53 0.26 YES
9 GALNT14 GALNT14 GALNT14 284 0.52 0.29 YES
10 GALNT6 GALNT6 GALNT6 479 0.45 0.31 YES
11 SEMA6D SEMA6D SEMA6D 634 0.41 0.32 YES
12 ST8SIA3 ST8SIA3 ST8SIA3 710 0.4 0.34 YES
13 MUC21 MUC21 MUC21 772 0.39 0.36 YES
14 MGAT3 MGAT3 MGAT3 827 0.38 0.37 YES
15 GALNT9 GALNT9 GALNT9 1008 0.35 0.38 YES
16 MUC12 MUC12 MUC12 1030 0.35 0.4 YES
17 MUC5B MUC5B MUC5B 1034 0.35 0.42 YES
18 ST6GALNAC4 ST6GALNAC4 ST6GALNAC4 1190 0.33 0.43 YES
19 ARSE ARSE ARSE 1212 0.32 0.44 YES
20 GCNT4 GCNT4 GCNT4 1469 0.3 0.44 YES
21 MUC13 MUC13 MUC13 1623 0.28 0.45 YES
22 MGAT4C MGAT4C MGAT4C 1892 0.26 0.45 YES
23 ARSJ ARSJ ARSJ 1959 0.26 0.46 YES
24 B3GNT9 B3GNT9 B3GNT9 2067 0.25 0.47 YES
25 B3GNT7 B3GNT7 B3GNT7 2274 0.23 0.47 YES
26 ARSF ARSF ARSF 2357 0.22 0.48 YES
27 B3GNT5 B3GNT5 B3GNT5 2434 0.22 0.48 YES
28 PLAUR PLAUR PLAUR 2553 0.21 0.49 YES
29 F10 F10 F10 2715 0.2 0.49 YES
30 F7 F7 F7 2739 0.2 0.5 YES
31 GALNT8 GALNT8 GALNT8 2745 0.2 0.51 YES
32 MUC17 MUC17 MUC17 3037 0.18 0.5 YES
33 GFPT2 GFPT2 GFPT2 3042 0.18 0.51 YES
34 ST6GALNAC3 ST6GALNAC3 ST6GALNAC3 3201 0.17 0.51 YES
35 PGAP1 PGAP1 PGAP1 3492 0.16 0.51 NO
36 ARSI ARSI ARSI 3971 0.14 0.49 NO
37 ST3GAL2 ST3GAL2 ST3GAL2 4438 0.12 0.47 NO
38 ST6GAL1 ST6GAL1 ST6GAL1 5397 0.082 0.42 NO
39 MAN1A1 MAN1A1 MAN1A1 5489 0.078 0.42 NO
40 SEC23A SEC23A SEC23A 5601 0.074 0.42 NO
41 B4GALT1 B4GALT1 B4GALT1 5816 0.068 0.41 NO
42 GALNTL1 GALNTL1 GALNTL1 5853 0.068 0.41 NO
43 WBSCR17 WBSCR17 WBSCR17 6039 0.062 0.4 NO
44 B3GNT2 B3GNT2 B3GNT2 6074 0.062 0.4 NO
45 PROS1 PROS1 PROS1 6083 0.061 0.41 NO
46 GALNTL4 GALNTL4 GALNTL4 6347 0.055 0.4 NO
47 GALNT12 GALNT12 GALNT12 6605 0.049 0.38 NO
48 B4GALT5 B4GALT5 B4GALT5 6683 0.048 0.38 NO
49 STS STS STS 6830 0.045 0.38 NO
50 EIF5A2 EIF5A2 EIF5A2 6998 0.042 0.37 NO
51 MGAT1 MGAT1 MGAT1 7055 0.041 0.37 NO
52 ST3GAL1 ST3GAL1 ST3GAL1 7145 0.039 0.37 NO
53 FUT8 FUT8 FUT8 7250 0.037 0.36 NO
54 C1GALT1 C1GALT1 C1GALT1 7499 0.034 0.35 NO
55 FURIN FURIN FURIN 7914 0.028 0.33 NO
56 PROC PROC PROC 7953 0.027 0.33 NO
57 MAN1C1 MAN1C1 MAN1C1 8166 0.024 0.32 NO
58 B4GALT4 B4GALT4 B4GALT4 8211 0.024 0.32 NO
59 PIGB PIGB PIGB 8258 0.023 0.32 NO
60 ARSK ARSK ARSK 8264 0.023 0.32 NO
61 PIGC PIGC PIGC 8595 0.019 0.3 NO
62 DOHH DOHH DOHH 8759 0.017 0.29 NO
63 B4GALT6 B4GALT6 B4GALT6 8924 0.015 0.28 NO
64 PIGS PIGS PIGS 8985 0.015 0.28 NO
65 ARSB ARSB ARSB 9029 0.014 0.28 NO
66 GALNT2 GALNT2 GALNT2 9195 0.012 0.27 NO
67 DPM1 DPM1 DPM1 9519 0.0093 0.25 NO
68 GALNTL2 GALNTL2 GALNTL2 9572 0.0088 0.25 NO
69 PIGQ PIGQ PIGQ 9591 0.0085 0.25 NO
70 B3GNT4 B3GNT4 B3GNT4 9797 0.0066 0.24 NO
71 GMPPA GMPPA GMPPA 9959 0.0049 0.23 NO
72 PIGA PIGA PIGA 10016 0.0044 0.23 NO
73 ALG5 ALG5 ALG5 10055 0.004 0.23 NO
74 EDEM2 EDEM2 EDEM2 10498 0.00026 0.2 NO
75 VKORC1 VKORC1 VKORC1 10620 -0.00091 0.2 NO
76 SUMF2 SUMF2 SUMF2 10666 -0.0013 0.19 NO
77 F2 F2 F2 10700 -0.0016 0.19 NO
78 DPM3 DPM3 DPM3 10715 -0.0017 0.19 NO
79 PIGT PIGT PIGT 11070 -0.0048 0.17 NO
80 RFT1 RFT1 RFT1 11171 -0.0056 0.16 NO
81 PIGL PIGL PIGL 11335 -0.0068 0.16 NO
82 MAN1B1 MAN1B1 MAN1B1 11427 -0.0076 0.15 NO
83 ALG12 ALG12 ALG12 11510 -0.0083 0.15 NO
84 DAD1 DAD1 DAD1 11511 -0.0083 0.15 NO
85 PRKCSH PRKCSH PRKCSH 11895 -0.012 0.13 NO
86 ALG1 ALG1 ALG1 11995 -0.012 0.12 NO
87 B4GALT2 B4GALT2 B4GALT2 12101 -0.013 0.12 NO
88 PIGG PIGG PIGG 12110 -0.013 0.12 NO
89 ALG13 ALG13 ALG13 12155 -0.014 0.12 NO
90 UGGT1 UGGT1 UGGT1 12234 -0.014 0.11 NO
91 SEC13 SEC13 SEC13 12403 -0.016 0.1 NO
92 EIF5A EIF5A EIF5A 12422 -0.016 0.1 NO
93 GALNT10 GALNT10 GALNT10 12428 -0.016 0.1 NO
94 DOLK DOLK DOLK 12587 -0.017 0.097 NO
95 ARSA ARSA ARSA 12596 -0.017 0.097 NO
96 GMPPB GMPPB GMPPB 12629 -0.018 0.097 NO
97 PIGF PIGF PIGF 12655 -0.018 0.096 NO
98 GPAA1 GPAA1 GPAA1 12713 -0.018 0.094 NO
99 PREB PREB PREB 12729 -0.018 0.094 NO
100 ALG2 ALG2 ALG2 12741 -0.019 0.095 NO
101 PROZ PROZ PROZ 12850 -0.02 0.09 NO
102 MOGS MOGS MOGS 12859 -0.02 0.09 NO
103 MCFD2 MCFD2 MCFD2 12888 -0.02 0.09 NO
104 PIGV PIGV PIGV 12906 -0.02 0.09 NO
105 RPN1 RPN1 RPN1 12916 -0.02 0.09 NO
106 DPM2 DPM2 DPM2 12926 -0.02 0.091 NO
107 PIGU PIGU PIGU 13023 -0.021 0.087 NO
108 SEC24B SEC24B SEC24B 13029 -0.021 0.088 NO
109 PIGN PIGN PIGN 13228 -0.023 0.078 NO
110 GGCX GGCX GGCX 13312 -0.024 0.075 NO
111 LMAN1 LMAN1 LMAN1 13333 -0.024 0.075 NO
112 EDEM1 EDEM1 EDEM1 13359 -0.024 0.075 NO
113 RPN2 RPN2 RPN2 13404 -0.025 0.074 NO
114 GALNT1 GALNT1 GALNT1 13436 -0.025 0.073 NO
115 MUCL1 MUCL1 MUCL1 13486 -0.025 0.072 NO
116 ST3GAL3 ST3GAL3 ST3GAL3 13513 -0.026 0.072 NO
117 PIGO PIGO PIGO 13543 -0.026 0.072 NO
118 GANAB GANAB GANAB 13598 -0.026 0.07 NO
119 DPAGT1 DPAGT1 DPAGT1 13674 -0.027 0.068 NO
120 SEC24C SEC24C SEC24C 13840 -0.029 0.06 NO
121 SEC24D SEC24D SEC24D 13875 -0.029 0.06 NO
122 UGGT2 UGGT2 UGGT2 14058 -0.031 0.051 NO
123 ALG9 ALG9 ALG9 14090 -0.031 0.051 NO
124 SEC31A SEC31A SEC31A 14122 -0.032 0.051 NO
125 DHPS DHPS DHPS 14153 -0.032 0.051 NO
126 MAN2A1 MAN2A1 MAN2A1 14222 -0.033 0.049 NO
127 SUMF1 SUMF1 SUMF1 14350 -0.034 0.044 NO
128 C1GALT1C1 C1GALT1C1 C1GALT1C1 14357 -0.034 0.046 NO
129 ALG3 ALG3 ALG3 14378 -0.034 0.046 NO
130 MGAT5 MGAT5 MGAT5 14400 -0.035 0.047 NO
131 DDOST DDOST DDOST 14532 -0.036 0.042 NO
132 DOLPP1 DOLPP1 DOLPP1 14574 -0.037 0.041 NO
133 MLEC MLEC MLEC 14622 -0.037 0.041 NO
134 PMM1 PMM1 PMM1 14742 -0.039 0.036 NO
135 B3GNTL1 B3GNTL1 B3GNTL1 14743 -0.039 0.038 NO
136 MPI MPI MPI 14758 -0.039 0.04 NO
137 MGAT4B MGAT4B MGAT4B 14829 -0.04 0.038 NO
138 PMM2 PMM2 PMM2 14874 -0.04 0.038 NO
139 PDIA3 PDIA3 PDIA3 14892 -0.04 0.039 NO
140 CALR CALR CALR 14930 -0.041 0.039 NO
141 ALG11 ALG11 ALG11 14934 -0.041 0.041 NO
142 MGAT2 MGAT2 MGAT2 14993 -0.042 0.04 NO
143 STT3A STT3A STT3A 15111 -0.043 0.036 NO
144 MUC6 MUC6 MUC6 15132 -0.043 0.037 NO
145 CANX CANX CANX 15133 -0.043 0.039 NO
146 MUC2 MUC2 MUC2 15206 -0.044 0.038 NO
147 MAN1A2 MAN1A2 MAN1A2 15212 -0.044 0.04 NO
148 PIGK PIGK PIGK 15502 -0.05 0.027 NO
149 ST8SIA6 ST8SIA6 ST8SIA6 15511 -0.05 0.029 NO
150 B4GALT3 B4GALT3 B4GALT3 15532 -0.051 0.03 NO
151 GALNT11 GALNT11 GALNT11 15599 -0.052 0.03 NO
152 PIGX PIGX PIGX 15689 -0.053 0.028 NO
153 PIGH PIGH PIGH 15744 -0.054 0.028 NO
154 MANEA MANEA MANEA 15803 -0.055 0.027 NO
155 PIGM PIGM PIGM 15847 -0.056 0.028 NO
156 PIGP PIGP PIGP 15887 -0.057 0.029 NO
157 ALG8 ALG8 ALG8 15983 -0.059 0.027 NO
158 ARSG ARSG ARSG 16018 -0.06 0.028 NO
159 ALG14 ALG14 ALG14 16104 -0.062 0.027 NO
160 PGM3 PGM3 PGM3 16224 -0.065 0.024 NO
161 ALG10B ALG10B ALG10B 16299 -0.067 0.023 NO
162 ALG10 ALG10 ALG10 16367 -0.069 0.023 NO
163 MGAT4A MGAT4A MGAT4A 16383 -0.07 0.026 NO
164 ALG6 ALG6 ALG6 16519 -0.074 0.023 NO
165 TUSC3 TUSC3 TUSC3 16671 -0.08 0.018 NO
166 GALNTL6 GALNTL6 GALNTL6 16719 -0.082 0.02 NO
167 SAR1B SAR1B SAR1B 16732 -0.082 0.024 NO
168 GCNT1 GCNT1 GCNT1 16786 -0.084 0.026 NO
169 GNPNAT1 GNPNAT1 GNPNAT1 17066 -0.098 0.016 NO
170 GALNT13 GALNT13 GALNT13 17084 -0.099 0.02 NO
171 PIGW PIGW PIGW 17123 -0.1 0.023 NO
172 GALNT7 GALNT7 GALNT7 17125 -0.1 0.029 NO
173 GALNT3 GALNT3 GALNT3 17130 -0.1 0.034 NO
174 ST8SIA2 ST8SIA2 ST8SIA2 17230 -0.11 0.034 NO
175 EDEM3 EDEM3 EDEM3 17448 -0.12 0.029 NO
176 B3GNT6 B3GNT6 B3GNT6 17531 -0.13 0.031 NO
177 ARSH ARSH ARSH 17836 -0.17 0.023 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 HISTIDINE 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 CXCL1 CXCL1 CXCL1 106 0.67 0.085 YES
2 CXCR2 CXCR2 CXCR2 118 0.66 0.17 YES
3 ATP6V0A4 ATP6V0A4 ATP6V0A4 293 0.52 0.23 YES
4 PTPRZ1 PTPRZ1 PTPRZ1 375 0.48 0.29 YES
5 MET MET MET 636 0.41 0.33 YES
6 ATP6V0D2 ATP6V0D2 ATP6V0D2 692 0.4 0.38 YES
7 ATP6V1G3 ATP6V1G3 ATP6V1G3 856 0.38 0.43 YES
8 CCL5 CCL5 CCL5 1260 0.32 0.45 YES
9 IL8 IL8 IL8 1498 0.3 0.47 YES
10 ATP6V1B1 ATP6V1B1 ATP6V1B1 1542 0.29 0.51 YES
11 PLCG2 PLCG2 PLCG2 2173 0.24 0.51 YES
12 MAP3K14 MAP3K14 MAP3K14 2348 0.22 0.53 YES
13 TCIRG1 TCIRG1 TCIRG1 3061 0.18 0.51 YES
14 HBEGF HBEGF HBEGF 3229 0.17 0.53 YES
15 JAM2 JAM2 JAM2 3631 0.15 0.53 YES
16 ATP6V1C2 ATP6V1C2 ATP6V1C2 4407 0.12 0.5 YES
17 PAK1 PAK1 PAK1 4428 0.12 0.51 YES
18 JAM3 JAM3 JAM3 4504 0.11 0.52 YES
19 NOD1 NOD1 NOD1 4755 0.1 0.52 YES
20 EGFR EGFR EGFR 4956 0.095 0.53 YES
21 NFKBIA NFKBIA NFKBIA 5062 0.092 0.53 YES
22 CXCR1 CXCR1 CXCR1 5203 0.088 0.54 YES
23 NFKB1 NFKB1 NFKB1 5246 0.086 0.55 YES
24 F11R F11R F11R 5538 0.077 0.54 NO
25 JUN JUN JUN 5829 0.068 0.53 NO
26 IKBKB IKBKB IKBKB 5888 0.067 0.54 NO
27 MAPK11 MAPK11 MAPK11 6844 0.045 0.49 NO
28 MAPK13 MAPK13 MAPK13 7133 0.039 0.48 NO
29 IKBKG IKBKG IKBKG 7285 0.037 0.48 NO
30 LYN LYN LYN 7496 0.034 0.47 NO
31 SRC SRC SRC 7608 0.032 0.47 NO
32 ATP6V0D1 ATP6V0D1 ATP6V0D1 7803 0.029 0.46 NO
33 ADAM17 ADAM17 ADAM17 8674 0.018 0.42 NO
34 CASP3 CASP3 CASP3 8703 0.018 0.42 NO
35 MAPK10 MAPK10 MAPK10 8765 0.017 0.42 NO
36 MAPK14 MAPK14 MAPK14 9039 0.014 0.4 NO
37 RELA RELA RELA 9076 0.014 0.4 NO
38 PLCG1 PLCG1 PLCG1 9371 0.011 0.39 NO
39 GIT1 GIT1 GIT1 9760 0.0069 0.37 NO
40 ATP6V0E1 ATP6V0E1 ATP6V0E1 9814 0.0063 0.37 NO
41 ATP6V1G2 ATP6V1G2 ATP6V1G2 10216 0.0024 0.35 NO
42 ATP6V0A2 ATP6V0A2 ATP6V0A2 10245 0.0022 0.34 NO
43 ATP6V1B2 ATP6V1B2 ATP6V1B2 10254 0.0021 0.34 NO
44 CSK CSK CSK 10302 0.0017 0.34 NO
45 RAC1 RAC1 RAC1 10712 -0.0017 0.32 NO
46 CDC42 CDC42 CDC42 10947 -0.0039 0.31 NO
47 ATP6V1E1 ATP6V1E1 ATP6V1E1 11183 -0.0058 0.3 NO
48 ATP6V0A1 ATP6V0A1 ATP6V0A1 11635 -0.0094 0.27 NO
49 CHUK CHUK CHUK 11656 -0.0095 0.27 NO
50 ATP6V0C ATP6V0C ATP6V0C 11972 -0.012 0.26 NO
51 MAP2K4 MAP2K4 MAP2K4 12025 -0.013 0.26 NO
52 IGSF5 IGSF5 IGSF5 12320 -0.015 0.24 NO
53 ATP6V1H ATP6V1H ATP6V1H 12383 -0.016 0.24 NO
54 ATP6V1E2 ATP6V1E2 ATP6V1E2 12592 -0.017 0.23 NO
55 ATP6V1F ATP6V1F ATP6V1F 12933 -0.02 0.21 NO
56 ATP6V0B ATP6V0B ATP6V0B 13174 -0.022 0.2 NO
57 ATP6V1D ATP6V1D ATP6V1D 13366 -0.024 0.2 NO
58 PTPN11 PTPN11 PTPN11 13442 -0.025 0.2 NO
59 ATP6AP1 ATP6AP1 ATP6AP1 14343 -0.034 0.15 NO
60 ADAM10 ADAM10 ADAM10 14715 -0.038 0.14 NO
61 ATP6V1C1 ATP6V1C1 ATP6V1C1 14746 -0.039 0.14 NO
62 MAPK8 MAPK8 MAPK8 14780 -0.039 0.14 NO
63 MAPK9 MAPK9 MAPK9 15445 -0.049 0.11 NO
64 MAPK12 MAPK12 MAPK12 15636 -0.052 0.11 NO
65 ATP6V1A ATP6V1A ATP6V1A 15991 -0.06 0.098 NO
66 ATP6V1G1 ATP6V1G1 ATP6V1G1 16050 -0.061 0.1 NO
67 TJP1 TJP1 TJP1 16055 -0.061 0.11 NO
68 ATP6V0E2 ATP6V0E2 ATP6V0E2 16504 -0.073 0.096 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 HISTIDINE METABOLISM.

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

genes ES table in pathway: KEGG TRYPTOPHAN 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 PPARGC1A PPARGC1A PPARGC1A 489 0.45 0.055 YES
2 ANGPTL4 ANGPTL4 ANGPTL4 984 0.36 0.092 YES
3 SLC2A4 SLC2A4 SLC2A4 1037 0.35 0.15 YES
4 TNF TNF TNF 1148 0.33 0.21 YES
5 WNT1 WNT1 WNT1 1172 0.33 0.27 YES
6 FABP4 FABP4 FABP4 1237 0.32 0.32 YES
7 SMARCD3 SMARCD3 SMARCD3 1303 0.32 0.37 YES
8 KLF5 KLF5 KLF5 1405 0.3 0.42 YES
9 PCK1 PCK1 PCK1 2062 0.25 0.43 YES
10 CEBPB CEBPB CEBPB 2225 0.23 0.47 YES
11 CEBPD CEBPD CEBPD 2501 0.21 0.49 YES
12 TGFB1 TGFB1 TGFB1 3672 0.15 0.45 YES
13 PPARG PPARG PPARG 3768 0.15 0.47 YES
14 KLF4 KLF4 KLF4 4637 0.11 0.44 YES
15 EBF1 EBF1 EBF1 4644 0.11 0.46 YES
16 EGR2 EGR2 EGR2 4657 0.11 0.48 YES
17 CCND3 CCND3 CCND3 4822 0.1 0.49 YES
18 WNT10B WNT10B WNT10B 4835 0.1 0.51 YES
19 MED30 MED30 MED30 6260 0.057 0.44 NO
20 RXRA RXRA RXRA 6438 0.053 0.44 NO
21 MED21 MED21 MED21 6571 0.05 0.44 NO
22 MED4 MED4 MED4 7002 0.042 0.43 NO
23 MED15 MED15 MED15 7131 0.039 0.43 NO
24 MED11 MED11 MED11 7942 0.027 0.39 NO
25 NCOR2 NCOR2 NCOR2 8370 0.022 0.37 NO
26 MED9 MED9 MED9 8395 0.021 0.37 NO
27 MED24 MED24 MED24 8409 0.021 0.37 NO
28 MED10 MED10 MED10 8427 0.021 0.38 NO
29 MED12 MED12 MED12 8544 0.02 0.37 NO
30 MED6 MED6 MED6 8562 0.019 0.38 NO
31 TBL1X TBL1X TBL1X 8582 0.019 0.38 NO
32 MED16 MED16 MED16 8725 0.017 0.37 NO
33 MED7 MED7 MED7 8873 0.016 0.37 NO
34 MED20 MED20 MED20 8887 0.016 0.37 NO
35 RELA RELA RELA 9076 0.014 0.36 NO
36 CREBBP CREBBP CREBBP 9162 0.013 0.36 NO
37 TGS1 TGS1 TGS1 9199 0.012 0.36 NO
38 MED31 MED31 MED31 9446 0.01 0.35 NO
39 MED25 MED25 MED25 9492 0.0095 0.35 NO
40 PRIC285 PRIC285 PRIC285 9632 0.0081 0.34 NO
41 MED18 MED18 MED18 10068 0.0039 0.32 NO
42 HDAC3 HDAC3 HDAC3 10105 0.0035 0.32 NO
43 PPARA PPARA PPARA 10226 0.0023 0.31 NO
44 MED26 MED26 MED26 10488 0.00031 0.3 NO
45 MED22 MED22 MED22 10556 -0.00034 0.29 NO
46 NR2F2 NR2F2 NR2F2 10698 -0.0016 0.29 NO
47 MED13L MED13L MED13L 10958 -0.004 0.27 NO
48 LEP LEP LEP 10977 -0.0041 0.27 NO
49 MED27 MED27 MED27 11133 -0.0053 0.26 NO
50 MED8 MED8 MED8 11860 -0.011 0.23 NO
51 NCOA3 NCOA3 NCOA3 11962 -0.012 0.22 NO
52 MED29 MED29 MED29 12126 -0.014 0.22 NO
53 MED17 MED17 MED17 12235 -0.014 0.21 NO
54 MED19 MED19 MED19 12307 -0.015 0.21 NO
55 CDK8 CDK8 CDK8 12348 -0.015 0.21 NO
56 LPL LPL LPL 12366 -0.016 0.22 NO
57 NCOA1 NCOA1 NCOA1 12491 -0.017 0.21 NO
58 NCOR1 NCOR1 NCOR1 12647 -0.018 0.21 NO
59 CCNC CCNC CCNC 12773 -0.019 0.2 NO
60 CDK4 CDK4 CDK4 12785 -0.019 0.2 NO
61 MED23 MED23 MED23 12885 -0.02 0.2 NO
62 CDK19 CDK19 CDK19 13209 -0.023 0.19 NO
63 MED1 MED1 MED1 13886 -0.029 0.16 NO
64 MED14 MED14 MED14 14168 -0.032 0.15 NO
65 EP300 EP300 EP300 14397 -0.034 0.14 NO
66 NCOA6 NCOA6 NCOA6 14709 -0.038 0.13 NO
67 TBL1XR1 TBL1XR1 TBL1XR1 15247 -0.045 0.11 NO
68 PLIN1 PLIN1 PLIN1 15882 -0.057 0.086 NO
69 CD36 CD36 CD36 16031 -0.061 0.089 NO
70 SREBF1 SREBF1 SREBF1 16518 -0.074 0.076 NO
71 NCOA2 NCOA2 NCOA2 17278 -0.11 0.054 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 TRYPTOPHAN METABOLISM.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TRYPTOPHAN METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG SELENOAMINO ACID 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 MUC4 MUC4 MUC4 8 0.88 0.034 YES
2 B3GNT8 B3GNT8 B3GNT8 87 0.69 0.056 YES
3 MUC15 MUC15 MUC15 121 0.65 0.079 YES
4 ST6GALNAC2 ST6GALNAC2 ST6GALNAC2 133 0.64 0.1 YES
5 B3GNT3 B3GNT3 B3GNT3 139 0.64 0.13 YES
6 MUC16 MUC16 MUC16 158 0.62 0.15 YES
7 GALNT5 GALNT5 GALNT5 238 0.55 0.17 YES
8 GCNT3 GCNT3 GCNT3 272 0.53 0.18 YES
9 GALNT14 GALNT14 GALNT14 284 0.52 0.2 YES
10 FAM153A FAM153A FAM153A 473 0.45 0.21 YES
11 GALNT6 GALNT6 GALNT6 479 0.45 0.23 YES
12 SEMA6D SEMA6D SEMA6D 634 0.41 0.24 YES
13 ST8SIA3 ST8SIA3 ST8SIA3 710 0.4 0.25 YES
14 MUC21 MUC21 MUC21 772 0.39 0.26 YES
15 MGAT3 MGAT3 MGAT3 827 0.38 0.27 YES
16 GALNT9 GALNT9 GALNT9 1008 0.35 0.27 YES
17 MUC12 MUC12 MUC12 1030 0.35 0.28 YES
18 MUC5B MUC5B MUC5B 1034 0.35 0.3 YES
19 ST6GALNAC4 ST6GALNAC4 ST6GALNAC4 1190 0.33 0.3 YES
20 ARSE ARSE ARSE 1212 0.32 0.31 YES
21 GCNT4 GCNT4 GCNT4 1469 0.3 0.31 YES
22 MUC13 MUC13 MUC13 1623 0.28 0.31 YES
23 KIFC3 KIFC3 KIFC3 1678 0.28 0.32 YES
24 MGAT4C MGAT4C MGAT4C 1892 0.26 0.32 YES
25 ARSJ ARSJ ARSJ 1959 0.26 0.32 YES
26 TUBA4A TUBA4A TUBA4A 1963 0.26 0.33 YES
27 B3GNT9 B3GNT9 B3GNT9 2067 0.25 0.34 YES
28 B3GNT7 B3GNT7 B3GNT7 2274 0.23 0.34 YES
29 ARSF ARSF ARSF 2357 0.22 0.34 YES
30 B3GNT5 B3GNT5 B3GNT5 2434 0.22 0.34 YES
31 PLAUR PLAUR PLAUR 2553 0.21 0.34 YES
32 SPHK1 SPHK1 SPHK1 2676 0.2 0.35 YES
33 F10 F10 F10 2715 0.2 0.35 YES
34 F7 F7 F7 2739 0.2 0.36 YES
35 GALNT8 GALNT8 GALNT8 2745 0.2 0.36 YES
36 MUC17 MUC17 MUC17 3037 0.18 0.36 NO
37 GFPT2 GFPT2 GFPT2 3042 0.18 0.36 NO
38 ST6GALNAC3 ST6GALNAC3 ST6GALNAC3 3201 0.17 0.36 NO
39 TUBB2B TUBB2B TUBB2B 3434 0.16 0.35 NO
40 PGAP1 PGAP1 PGAP1 3492 0.16 0.36 NO
41 ARSI ARSI ARSI 3971 0.14 0.33 NO
42 ST3GAL2 ST3GAL2 ST3GAL2 4438 0.12 0.31 NO
43 RPL21 RPL21 RPL21 4589 0.11 0.31 NO
44 SLC25A12 SLC25A12 SLC25A12 4728 0.1 0.3 NO
45 TUBB6 TUBB6 TUBB6 4794 0.1 0.3 NO
46 TUBA1A TUBA1A TUBA1A 5119 0.09 0.29 NO
47 ST6GAL1 ST6GAL1 ST6GAL1 5397 0.082 0.28 NO
48 MAN1A1 MAN1A1 MAN1A1 5489 0.078 0.28 NO
49 SEC23A SEC23A SEC23A 5601 0.074 0.27 NO
50 B4GALT1 B4GALT1 B4GALT1 5816 0.068 0.26 NO
51 GALNTL1 GALNTL1 GALNTL1 5853 0.068 0.26 NO
52 RPS27 RPS27 RPS27 5951 0.065 0.26 NO
53 WBSCR17 WBSCR17 WBSCR17 6039 0.062 0.26 NO
54 B3GNT2 B3GNT2 B3GNT2 6074 0.062 0.26 NO
55 PROS1 PROS1 PROS1 6083 0.061 0.26 NO
56 USP11 USP11 USP11 6106 0.061 0.26 NO
57 TAZ TAZ TAZ 6114 0.06 0.26 NO
58 GALNTL4 GALNTL4 GALNTL4 6347 0.055 0.25 NO
59 GSPT2 GSPT2 GSPT2 6452 0.052 0.25 NO
60 GALNT12 GALNT12 GALNT12 6605 0.049 0.24 NO
61 B4GALT5 B4GALT5 B4GALT5 6683 0.048 0.24 NO
62 STS STS STS 6830 0.045 0.23 NO
63 ACTB ACTB ACTB 6909 0.043 0.23 NO
64 LDHD LDHD LDHD 6949 0.042 0.23 NO
65 EIF5A2 EIF5A2 EIF5A2 6998 0.042 0.23 NO
66 MGAT1 MGAT1 MGAT1 7055 0.041 0.23 NO
67 ST3GAL1 ST3GAL1 ST3GAL1 7145 0.039 0.22 NO
68 PFDN5 PFDN5 PFDN5 7183 0.038 0.22 NO
69 TUBB1 TUBB1 TUBB1 7215 0.038 0.22 NO
70 FUT8 FUT8 FUT8 7250 0.037 0.22 NO
71 FBXW7 FBXW7 FBXW7 7320 0.036 0.22 NO
72 C1GALT1 C1GALT1 C1GALT1 7499 0.034 0.21 NO
73 FBXW4 FBXW4 FBXW4 7638 0.032 0.2 NO
74 TUBA3D TUBA3D TUBA3D 7862 0.028 0.19 NO
75 FURIN FURIN FURIN 7914 0.028 0.19 NO
76 PROC PROC PROC 7953 0.027 0.19 NO
77 EIF3G EIF3G EIF3G 7972 0.027 0.19 NO
78 RPS28 RPS28 RPS28 8002 0.027 0.19 NO
79 MAN1C1 MAN1C1 MAN1C1 8166 0.024 0.18 NO
80 B4GALT4 B4GALT4 B4GALT4 8211 0.024 0.18 NO
81 PIGB PIGB PIGB 8258 0.023 0.18 NO
82 ARSK ARSK ARSK 8264 0.023 0.18 NO
83 HSCB HSCB HSCB 8316 0.022 0.18 NO
84 RPS12 RPS12 RPS12 8385 0.021 0.17 NO
85 PIGC PIGC PIGC 8595 0.019 0.16 NO
86 RPL13 RPL13 RPL13 8601 0.019 0.16 NO
87 EIF3K EIF3K EIF3K 8606 0.019 0.16 NO
88 TUBA3C TUBA3C TUBA3C 8633 0.018 0.16 NO
89 EEF1B2 EEF1B2 EEF1B2 8649 0.018 0.16 NO
90 DOHH DOHH DOHH 8759 0.017 0.16 NO
91 RPS9 RPS9 RPS9 8767 0.017 0.16 NO
92 ETF1 ETF1 ETF1 8832 0.016 0.16 NO
93 B4GALT6 B4GALT6 B4GALT6 8924 0.015 0.15 NO
94 RPL34 RPL34 RPL34 8977 0.015 0.15 NO
95 PIGS PIGS PIGS 8985 0.015 0.15 NO
96 FAU FAU FAU 9025 0.014 0.15 NO
97 ARSB ARSB ARSB 9029 0.014 0.15 NO
98 EIF3F EIF3F EIF3F 9070 0.014 0.14 NO
99 EEF1D EEF1D EEF1D 9131 0.013 0.14 NO
100 SLC25A4 SLC25A4 SLC25A4 9137 0.013 0.14 NO
101 GALNT2 GALNT2 GALNT2 9195 0.012 0.14 NO
102 FXC1 FXC1 FXC1 9204 0.012 0.14 NO
103 EEF1A1 EEF1A1 EEF1A1 9227 0.012 0.14 NO
104 RPL11 RPL11 RPL11 9236 0.012 0.14 NO
105 TBCC TBCC TBCC 9269 0.012 0.14 NO
106 FBXL3 FBXL3 FBXL3 9273 0.012 0.14 NO
107 FKBP9 FKBP9 FKBP9 9303 0.011 0.14 NO
108 RPL10A RPL10A RPL10A 9456 0.0099 0.13 NO
109 RPS20 RPS20 RPS20 9461 0.0098 0.13 NO
110 DPM1 DPM1 DPM1 9519 0.0093 0.13 NO
111 GALNTL2 GALNTL2 GALNTL2 9572 0.0088 0.12 NO
112 PIGQ PIGQ PIGQ 9591 0.0085 0.12 NO
113 RPS19 RPS19 RPS19 9640 0.008 0.12 NO
114 RPL17 RPL17 RPL17 9667 0.0078 0.12 NO
115 RPL10 RPL10 RPL10 9748 0.007 0.12 NO
116 RPLP1 RPLP1 RPLP1 9750 0.007 0.12 NO
117 C18orf55 C18orf55 C18orf55 9751 0.007 0.12 NO
118 B3GNT4 B3GNT4 B3GNT4 9797 0.0066 0.11 NO
119 RPLP2 RPLP2 RPLP2 9850 0.006 0.11 NO
120 RPS27A RPS27A RPS27A 9873 0.0058 0.11 NO
121 TOMM7 TOMM7 TOMM7 9899 0.0055 0.11 NO
122 GMPPA GMPPA GMPPA 9959 0.0049 0.1 NO
123 PIGA PIGA PIGA 10016 0.0044 0.1 NO
124 ALG5 ALG5 ALG5 10055 0.004 0.1 NO
125 SEC61A2 SEC61A2 SEC61A2 10062 0.004 0.1 NO
126 TIMM22 TIMM22 TIMM22 10117 0.0034 0.097 NO
127 FBXW5 FBXW5 FBXW5 10236 0.0022 0.091 NO
128 TIMM44 TIMM44 TIMM44 10249 0.0021 0.09 NO
129 UBA52 UBA52 UBA52 10270 0.002 0.089 NO
130 RPS3 RPS3 RPS3 10282 0.0019 0.088 NO
131 RPS14 RPS14 RPS14 10352 0.0014 0.085 NO
132 RPL5 RPL5 RPL5 10366 0.0012 0.084 NO
133 EIF3D EIF3D EIF3D 10387 0.0011 0.083 NO
134 EIF5 EIF5 EIF5 10423 0.00084 0.081 NO
135 SRP68 SRP68 SRP68 10431 0.00078 0.08 NO
136 RPS21 RPS21 RPS21 10465 0.00048 0.079 NO
137 RPS23 RPS23 RPS23 10485 0.00033 0.078 NO
138 GFER GFER GFER 10496 0.00028 0.077 NO
139 EDEM2 EDEM2 EDEM2 10498 0.00026 0.077 NO
140 RPS4X RPS4X RPS4X 10519 0.000026 0.076 NO
141 RPL35 RPL35 RPL35 10531 -0.00014 0.075 NO
142 RPS11 RPS11 RPS11 10613 -0.00085 0.071 NO
143 VKORC1 VKORC1 VKORC1 10620 -0.00091 0.07 NO
144 RPL22 RPL22 RPL22 10665 -0.0013 0.068 NO
145 SUMF2 SUMF2 SUMF2 10666 -0.0013 0.068 NO
146 RPL27A RPL27A RPL27A 10669 -0.0013 0.068 NO
147 EEF1G EEF1G EEF1G 10693 -0.0016 0.067 NO
148 F2 F2 F2 10700 -0.0016 0.067 NO
149 DPM3 DPM3 DPM3 10715 -0.0017 0.066 NO
150 ATP5A1 ATP5A1 ATP5A1 10722 -0.0018 0.066 NO
151 RPL18 RPL18 RPL18 10741 -0.002 0.065 NO
152 RPL18A RPL18A RPL18A 10773 -0.0023 0.063 NO
153 RPS3A RPS3A RPS3A 10832 -0.0029 0.06 NO
154 RPS29 RPS29 RPS29 10848 -0.003 0.059 NO
155 SRP14 SRP14 SRP14 10873 -0.0033 0.058 NO
156 RPL23A RPL23A RPL23A 10931 -0.0038 0.055 NO
157 RPL3 RPL3 RPL3 10991 -0.0042 0.052 NO
158 RPS16 RPS16 RPS16 10993 -0.0042 0.052 NO
159 RPL26 RPL26 RPL26 10997 -0.0043 0.052 NO
160 RPS5 RPS5 RPS5 11010 -0.0044 0.051 NO
161 RPL41 RPL41 RPL41 11046 -0.0046 0.05 NO
162 TBCB TBCB TBCB 11050 -0.0046 0.05 NO
163 PIGT PIGT PIGT 11070 -0.0048 0.049 NO
164 EIF2B2 EIF2B2 EIF2B2 11114 -0.0051 0.046 NO
165 RPS10 RPS10 RPS10 11131 -0.0052 0.046 NO
166 EIF4A2 EIF4A2 EIF4A2 11163 -0.0056 0.044 NO
167 RPS25 RPS25 RPS25 11170 -0.0056 0.044 NO
168 RFT1 RFT1 RFT1 11171 -0.0056 0.044 NO
169 RPS24 RPS24 RPS24 11247 -0.0062 0.04 NO
170 RPS17 RPS17 RPS17 11249 -0.0063 0.04 NO
171 PIGL PIGL PIGL 11335 -0.0068 0.036 NO
172 RPL13A RPL13A RPL13A 11370 -0.0072 0.034 NO
173 SEC11C SEC11C SEC11C 11408 -0.0075 0.033 NO
174 RPS8 RPS8 RPS8 11412 -0.0075 0.033 NO
175 EIF4H EIF4H EIF4H 11414 -0.0076 0.033 NO
176 MAN1B1 MAN1B1 MAN1B1 11427 -0.0076 0.033 NO
177 RPL15 RPL15 RPL15 11450 -0.0078 0.032 NO
178 RPL4 RPL4 RPL4 11484 -0.0081 0.03 NO
179 RPL19 RPL19 RPL19 11487 -0.0081 0.03 NO
180 TUBA1B TUBA1B TUBA1B 11497 -0.0082 0.03 NO
181 RPL35A RPL35A RPL35A 11505 -0.0082 0.03 NO
182 ALG12 ALG12 ALG12 11510 -0.0083 0.03 NO
183 DAD1 DAD1 DAD1 11511 -0.0083 0.03 NO
184 RPS4Y1 RPS4Y1 RPS4Y1 11518 -0.0084 0.03 NO
185 RPL38 RPL38 RPL38 11540 -0.0086 0.03 NO
186 RPL8 RPL8 RPL8 11599 -0.0091 0.027 NO
187 PMPCA PMPCA PMPCA 11620 -0.0093 0.026 NO
188 RPS15 RPS15 RPS15 11651 -0.0095 0.025 NO
189 FXN FXN FXN 11675 -0.0097 0.024 NO
190 RPL32 RPL32 RPL32 11678 -0.0097 0.024 NO
191 SRP19 SRP19 SRP19 11681 -0.0097 0.024 NO
192 EIF2B1 EIF2B1 EIF2B1 11687 -0.0098 0.024 NO
193 IDH3G IDH3G IDH3G 11756 -0.01 0.021 NO
194 SAMM50 SAMM50 SAMM50 11802 -0.011 0.019 NO
195 RPL36 RPL36 RPL36 11842 -0.011 0.017 NO
196 RPL28 RPL28 RPL28 11863 -0.011 0.016 NO
197 RPL24 RPL24 RPL24 11879 -0.012 0.016 NO
198 EIF2B5 EIF2B5 EIF2B5 11892 -0.012 0.016 NO
199 PRKCSH PRKCSH PRKCSH 11895 -0.012 0.016 NO
200 RPSAP9 RPSAP9 RPSAP9 11929 -0.012 0.015 NO
201 RPS13 RPS13 RPS13 11956 -0.012 0.014 NO
202 RPS6 RPS6 RPS6 11974 -0.012 0.013 NO
203 RPS15A RPS15A RPS15A 11991 -0.012 0.013 NO
204 RPL31 RPL31 RPL31 11993 -0.012 0.013 NO
205 ALG1 ALG1 ALG1 11995 -0.012 0.014 NO
206 SPCS2 SPCS2 SPCS2 12039 -0.013 0.012 NO
207 B4GALT2 B4GALT2 B4GALT2 12101 -0.013 0.0087 NO
208 PIGG PIGG PIGG 12110 -0.013 0.0088 NO
209 ALG13 ALG13 ALG13 12155 -0.014 0.0069 NO
210 RPL6 RPL6 RPL6 12216 -0.014 0.004 NO
211 RPL14 RPL14 RPL14 12222 -0.014 0.0043 NO
212 UGGT1 UGGT1 UGGT1 12234 -0.014 0.0042 NO
213 LOC653566 LOC653566 LOC653566 12299 -0.015 0.0012 NO
214 RPSA RPSA RPSA 12329 -0.015 0.00018 NO
215 TOMM22 TOMM22 TOMM22 12330 -0.015 0.00076 NO
216 TIMM9 TIMM9 TIMM9 12335 -0.015 0.0011 NO
217 RPL37 RPL37 RPL37 12365 -0.016 0.000082 NO
218 SEC13 SEC13 SEC13 12403 -0.016 -0.0014 NO
219 SEC11A SEC11A SEC11A 12420 -0.016 -0.0017 NO
220 EIF5A EIF5A EIF5A 12422 -0.016 -0.0011 NO
221 GALNT10 GALNT10 GALNT10 12428 -0.016 -0.00079 NO
222 TIMM17A TIMM17A TIMM17A 12447 -0.016 -0.0012 NO
223 TIMM50 TIMM50 TIMM50 12463 -0.016 -0.0014 NO
224 EIF4B EIF4B EIF4B 12474 -0.016 -0.0013 NO
225 RPL37A RPL37A RPL37A 12485 -0.016 -0.0012 NO
226 BCS1L BCS1L BCS1L 12529 -0.017 -0.003 NO
227 PFDN1 PFDN1 PFDN1 12544 -0.017 -0.0032 NO
228 DOLK DOLK DOLK 12587 -0.017 -0.0048 NO
229 ARSA ARSA ARSA 12596 -0.017 -0.0046 NO
230 RPL12 RPL12 RPL12 12610 -0.018 -0.0047 NO
231 RPL27 RPL27 RPL27 12627 -0.018 -0.0049 NO
232 GMPPB GMPPB GMPPB 12629 -0.018 -0.0043 NO
233 TBCD TBCD TBCD 12646 -0.018 -0.0045 NO
234 PIGF PIGF PIGF 12655 -0.018 -0.0043 NO
235 RPL39 RPL39 RPL39 12666 -0.018 -0.0041 NO
236 SPCS3 SPCS3 SPCS3 12694 -0.018 -0.005 NO
237 MTX1 MTX1 MTX1 12698 -0.018 -0.0044 NO
238 SSR4 SSR4 SSR4 12703 -0.018 -0.004 NO
239 GPAA1 GPAA1 GPAA1 12713 -0.018 -0.0038 NO
240 RPS2 RPS2 RPS2 12721 -0.018 -0.0034 NO
241 PREB PREB PREB 12729 -0.018 -0.0031 NO
242 RPLP0 RPLP0 RPLP0 12732 -0.018 -0.0025 NO
243 ALG2 ALG2 ALG2 12741 -0.019 -0.0022 NO
244 COQ2 COQ2 COQ2 12775 -0.019 -0.0034 NO
245 RPL23 RPL23 RPL23 12783 -0.019 -0.003 NO
246 CHCHD4 CHCHD4 CHCHD4 12795 -0.019 -0.0029 NO
247 ARFGEF2 ARFGEF2 ARFGEF2 12799 -0.019 -0.0024 NO
248 EIF2S2 EIF2S2 EIF2S2 12829 -0.019 -0.0033 NO
249 PROZ PROZ PROZ 12850 -0.02 -0.0036 NO
250 MOGS MOGS MOGS 12859 -0.02 -0.0033 NO
251 MCFD2 MCFD2 MCFD2 12888 -0.02 -0.0041 NO
252 PIGV PIGV PIGV 12906 -0.02 -0.0043 NO
253 RPN1 RPN1 RPN1 12916 -0.02 -0.0041 NO
254 PFDN2 PFDN2 PFDN2 12918 -0.02 -0.0034 NO
255 DPM2 DPM2 DPM2 12926 -0.02 -0.003 NO
256 FBXO6 FBXO6 FBXO6 12977 -0.021 -0.005 NO
257 RPL30 RPL30 RPL30 13017 -0.021 -0.0064 NO
258 PIGU PIGU PIGU 13023 -0.021 -0.0058 NO
259 SEC24B SEC24B SEC24B 13029 -0.021 -0.0053 NO
260 TIMM17B TIMM17B TIMM17B 13041 -0.021 -0.0051 NO
261 ACO2 ACO2 ACO2 13049 -0.021 -0.0047 NO
262 RPL29 RPL29 RPL29 13063 -0.021 -0.0046 NO
263 TUBA1C TUBA1C TUBA1C 13064 -0.021 -0.0038 NO
264 FBXL5 FBXL5 FBXL5 13096 -0.022 -0.0047 NO
265 FBXW2 FBXW2 FBXW2 13105 -0.022 -0.0043 NO
266 EIF2B3 EIF2B3 EIF2B3 13143 -0.022 -0.0055 NO
267 EIF3E EIF3E EIF3E 13156 -0.022 -0.0054 NO
268 XRN2 XRN2 XRN2 13168 -0.022 -0.0051 NO
269 RPL7 RPL7 RPL7 13170 -0.022 -0.0043 NO
270 PIGN PIGN PIGN 13228 -0.023 -0.0066 NO
271 EIF2S1 EIF2S1 EIF2S1 13279 -0.023 -0.0086 NO
272 RPS18 RPS18 RPS18 13301 -0.024 -0.0088 NO
273 SSR1 SSR1 SSR1 13311 -0.024 -0.0084 NO
274 GGCX GGCX GGCX 13312 -0.024 -0.0075 NO
275 LMAN1 LMAN1 LMAN1 13333 -0.024 -0.0077 NO
276 EDEM1 EDEM1 EDEM1 13359 -0.024 -0.0082 NO
277 EIF3H EIF3H EIF3H 13391 -0.024 -0.009 NO
278 GRPEL1 GRPEL1 GRPEL1 13402 -0.025 -0.0086 NO
279 TRAM1 TRAM1 TRAM1 13403 -0.025 -0.0077 NO
280 RPN2 RPN2 RPN2 13404 -0.025 -0.0067 NO
281 EIF2S3 EIF2S3 EIF2S3 13420 -0.025 -0.0066 NO
282 RPS7 RPS7 RPS7 13428 -0.025 -0.0061 NO
283 GALNT1 GALNT1 GALNT1 13436 -0.025 -0.0055 NO
284 MUCL1 MUCL1 MUCL1 13486 -0.025 -0.0073 NO
285 ST3GAL3 ST3GAL3 ST3GAL3 13513 -0.026 -0.0078 NO
286 PIGO PIGO PIGO 13543 -0.026 -0.0084 NO
287 SEC61A1 SEC61A1 SEC61A1 13575 -0.026 -0.0091 NO
288 GANAB GANAB GANAB 13598 -0.026 -0.0093 NO
289 KIF13A KIF13A KIF13A 13601 -0.026 -0.0084 NO
290 SSR2 SSR2 SSR2 13606 -0.027 -0.0076 NO
291 FBXO4 FBXO4 FBXO4 13641 -0.027 -0.0085 NO
292 DPAGT1 DPAGT1 DPAGT1 13674 -0.027 -0.0092 NO
293 EIF2B4 EIF2B4 EIF2B4 13676 -0.027 -0.0083 NO
294 SRPR SRPR SRPR 13687 -0.028 -0.0078 NO
295 CS CS CS 13703 -0.028 -0.0076 NO
296 NOP56 NOP56 NOP56 13718 -0.028 -0.0073 NO
297 SPCS1 SPCS1 SPCS1 13733 -0.028 -0.007 NO
298 EIF1AX EIF1AX EIF1AX 13757 -0.028 -0.0072 NO
299 EIF3A EIF3A EIF3A 13764 -0.028 -0.0065 NO
300 EIF4A1 EIF4A1 EIF4A1 13768 -0.028 -0.0056 NO
301 CCT4 CCT4 CCT4 13777 -0.028 -0.0049 NO
302 TIMM13 TIMM13 TIMM13 13782 -0.028 -0.004 NO
303 SEC24C SEC24C SEC24C 13840 -0.029 -0.0062 NO
304 SRP9 SRP9 SRP9 13854 -0.029 -0.0058 NO
305 SEC24D SEC24D SEC24D 13875 -0.029 -0.0058 NO
306 RPS26 RPS26 RPS26 13891 -0.029 -0.0055 NO
307 TOMM5 TOMM5 TOMM5 13928 -0.03 -0.0064 NO
308 TBCA TBCA TBCA 13962 -0.03 -0.0071 NO
309 EIF5B EIF5B EIF5B 13965 -0.03 -0.006 NO
310 RPL7A RPL7A RPL7A 13970 -0.03 -0.0051 NO
311 EIF3B EIF3B EIF3B 13983 -0.03 -0.0046 NO
312 SLC25A6 SLC25A6 SLC25A6 14006 -0.031 -0.0047 NO
313 VDAC1 VDAC1 VDAC1 14007 -0.031 -0.0035 NO
314 TOMM40 TOMM40 TOMM40 14038 -0.031 -0.004 NO
315 PFDN6 PFDN6 PFDN6 14054 -0.031 -0.0036 NO
316 UGGT2 UGGT2 UGGT2 14058 -0.031 -0.0026 NO
317 ALG9 ALG9 ALG9 14090 -0.031 -0.0032 NO
318 CCT7 CCT7 CCT7 14099 -0.032 -0.0024 NO
319 PFDN4 PFDN4 PFDN4 14113 -0.032 -0.0019 NO
320 SEC31A SEC31A SEC31A 14122 -0.032 -0.0011 NO
321 DHPS DHPS DHPS 14153 -0.032 -0.0016 NO
322 EIF3I EIF3I EIF3I 14181 -0.032 -0.0019 NO
323 AP3M1 AP3M1 AP3M1 14183 -0.032 -0.00069 NO
324 MAN2A1 MAN2A1 MAN2A1 14222 -0.033 -0.0016 NO
325 EEF2 EEF2 EEF2 14263 -0.033 -0.0025 NO
326 SEC61B SEC61B SEC61B 14286 -0.033 -0.0025 NO
327 ATP5B ATP5B ATP5B 14298 -0.034 -0.0018 NO
328 SUMF1 SUMF1 SUMF1 14350 -0.034 -0.0034 NO
329 C1GALT1C1 C1GALT1C1 C1GALT1C1 14357 -0.034 -0.0024 NO
330 ALG3 ALG3 ALG3 14378 -0.034 -0.0022 NO
331 MGAT5 MGAT5 MGAT5 14400 -0.035 -0.002 NO
332 EIF4G1 EIF4G1 EIF4G1 14404 -0.035 -0.00089 NO
333 TOMM20 TOMM20 TOMM20 14415 -0.035 -0.00012 NO
334 DDOST DDOST DDOST 14532 -0.036 -0.0052 NO
335 DOLPP1 DOLPP1 DOLPP1 14574 -0.037 -0.0061 NO
336 CYC1 CYC1 CYC1 14581 -0.037 -0.0051 NO
337 MLEC MLEC MLEC 14622 -0.037 -0.0059 NO
338 ATP5G1 ATP5G1 ATP5G1 14736 -0.038 -0.011 NO
339 PMM1 PMM1 PMM1 14742 -0.039 -0.0095 NO
340 B3GNTL1 B3GNTL1 B3GNTL1 14743 -0.039 -0.0081 NO
341 MPI MPI MPI 14758 -0.039 -0.0074 NO
342 MGAT4B MGAT4B MGAT4B 14829 -0.04 -0.0098 NO
343 TIMM10 TIMM10 TIMM10 14847 -0.04 -0.0092 NO
344 PMM2 PMM2 PMM2 14874 -0.04 -0.0091 NO
345 PDIA3 PDIA3 PDIA3 14892 -0.04 -0.0085 NO
346 CALR CALR CALR 14930 -0.041 -0.009 NO
347 ALG11 ALG11 ALG11 14934 -0.041 -0.0076 NO
348 HSPA9 HSPA9 HSPA9 14982 -0.041 -0.0087 NO
349 MGAT2 MGAT2 MGAT2 14993 -0.042 -0.0076 NO
350 EIF4E EIF4E EIF4E 15074 -0.043 -0.01 NO
351 STT3A STT3A STT3A 15111 -0.043 -0.011 NO
352 DNAJC19 DNAJC19 DNAJC19 15121 -0.043 -0.0097 NO
353 MUC6 MUC6 MUC6 15132 -0.043 -0.0086 NO
354 CANX CANX CANX 15133 -0.043 -0.007 NO
355 PMPCB PMPCB PMPCB 15137 -0.043 -0.0055 NO
356 SSR3 SSR3 SSR3 15165 -0.044 -0.0053 NO
357 SRP72 SRP72 SRP72 15171 -0.044 -0.0039 NO
358 CCT3 CCT3 CCT3 15182 -0.044 -0.0028 NO
359 MUC2 MUC2 MUC2 15206 -0.044 -0.0024 NO
360 MAN1A2 MAN1A2 MAN1A2 15212 -0.044 -0.00092 NO
361 TIMM8A TIMM8A TIMM8A 15307 -0.046 -0.0044 NO
362 VBP1 VBP1 VBP1 15337 -0.046 -0.0043 NO
363 SEC61G SEC61G SEC61G 15351 -0.047 -0.0032 NO
364 TCP1 TCP1 TCP1 15390 -0.048 -0.0035 NO
365 CCT6A CCT6A CCT6A 15403 -0.048 -0.0024 NO
366 TBCE TBCE TBCE 15457 -0.049 -0.0034 NO
367 TIMM8B TIMM8B TIMM8B 15492 -0.05 -0.0034 NO
368 PIGK PIGK PIGK 15502 -0.05 -0.002 NO
369 ST8SIA6 ST8SIA6 ST8SIA6 15511 -0.05 -0.00055 NO
370 B4GALT3 B4GALT3 B4GALT3 15532 -0.051 0.00027 NO
371 SRPRB SRPRB SRPRB 15533 -0.051 0.0022 NO
372 EIF4EBP1 EIF4EBP1 EIF4EBP1 15543 -0.051 0.0036 NO
373 SRP54 SRP54 SRP54 15575 -0.051 0.0039 NO
374 CCT5 CCT5 CCT5 15582 -0.051 0.0055 NO
375 GALNT11 GALNT11 GALNT11 15599 -0.052 0.0066 NO
376 RPL26L1 RPL26L1 RPL26L1 15623 -0.052 0.0073 NO
377 RPL9 RPL9 RPL9 15651 -0.052 0.0078 NO
378 CCT8 CCT8 CCT8 15660 -0.053 0.0094 NO
379 PIGX PIGX PIGX 15689 -0.053 0.0098 NO
380 PIGH PIGH PIGH 15744 -0.054 0.0089 NO
381 PABPC1 PABPC1 PABPC1 15745 -0.054 0.011 NO
382 EIF3J EIF3J EIF3J 15766 -0.054 0.012 NO
383 MANEA MANEA MANEA 15803 -0.055 0.012 NO
384 PIGM PIGM PIGM 15847 -0.056 0.012 NO
385 PIGP PIGP PIGP 15887 -0.057 0.012 NO
386 CCT2 CCT2 CCT2 15905 -0.057 0.013 NO
387 ALG8 ALG8 ALG8 15983 -0.059 0.011 NO
388 ARSG ARSG ARSG 16018 -0.06 0.011 NO
389 LONP2 LONP2 LONP2 16075 -0.062 0.011 NO
390 ALG14 ALG14 ALG14 16104 -0.062 0.011 NO
391 TOMM70A TOMM70A TOMM70A 16149 -0.063 0.011 NO
392 PGM3 PGM3 PGM3 16224 -0.065 0.0097 NO
393 GRPEL2 GRPEL2 GRPEL2 16268 -0.066 0.0098 NO
394 COX17 COX17 COX17 16278 -0.066 0.012 NO
395 ALG10B ALG10B ALG10B 16299 -0.067 0.013 NO
396 MTX2 MTX2 MTX2 16308 -0.068 0.015 NO
397 ALG10 ALG10 ALG10 16367 -0.069 0.015 NO
398 MGAT4A MGAT4A MGAT4A 16383 -0.07 0.017 NO
399 SLC25A13 SLC25A13 SLC25A13 16465 -0.072 0.015 NO
400 ALG6 ALG6 ALG6 16519 -0.074 0.015 NO
401 HSPD1 HSPD1 HSPD1 16528 -0.074 0.017 NO
402 TUSC3 TUSC3 TUSC3 16671 -0.08 0.012 NO
403 GALNTL6 GALNTL6 GALNTL6 16719 -0.082 0.013 NO
404 SAR1B SAR1B SAR1B 16732 -0.082 0.015 NO
405 GCNT1 GCNT1 GCNT1 16786 -0.084 0.016 NO
406 EIF3C EIF3C EIF3C 17052 -0.097 0.0044 NO
407 GNPNAT1 GNPNAT1 GNPNAT1 17066 -0.098 0.0074 NO
408 GALNT13 GALNT13 GALNT13 17084 -0.099 0.01 NO
409 PIGW PIGW PIGW 17123 -0.1 0.012 NO
410 GALNT7 GALNT7 GALNT7 17125 -0.1 0.016 NO
411 GALNT3 GALNT3 GALNT3 17130 -0.1 0.02 NO
412 ST8SIA2 ST8SIA2 ST8SIA2 17230 -0.11 0.018 NO
413 RPL36A RPL36A RPL36A 17239 -0.11 0.022 NO
414 TUBB3 TUBB3 TUBB3 17259 -0.11 0.025 NO
415 EDEM3 EDEM3 EDEM3 17448 -0.12 0.019 NO
416 B3GNT6 B3GNT6 B3GNT6 17531 -0.13 0.019 NO
417 TUBB2A TUBB2A TUBB2A 17662 -0.14 0.018 NO
418 ARSH ARSH ARSH 17836 -0.17 0.014 NO
419 RPL3L RPL3L RPL3L 18160 -0.24 0.0054 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 SELENOAMINO ACID METABOLISM.

Figure S72.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SELENOAMINO 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 GLUTATHIONE 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 GJB4 GJB4 GJB4 5 0.93 0.11 YES
2 GJB5 GJB5 GJB5 10 0.87 0.22 YES
3 GJB3 GJB3 GJB3 25 0.81 0.32 YES
4 GJC2 GJC2 GJC2 381 0.48 0.36 YES
5 GJA1 GJA1 GJA1 1672 0.28 0.32 NO
6 GJA9 GJA9 GJA9 2597 0.21 0.3 NO
7 DNM1 DNM1 DNM1 3307 0.17 0.28 NO
8 GJB6 GJB6 GJB6 3515 0.16 0.29 NO
9 CLTCL1 CLTCL1 CLTCL1 3829 0.14 0.29 NO
10 GJC1 GJC1 GJC1 4216 0.12 0.28 NO
11 VPS37D VPS37D VPS37D 4585 0.11 0.27 NO
12 TFRC TFRC TFRC 4608 0.11 0.28 NO
13 DNASE2 DNASE2 DNASE2 5104 0.091 0.27 NO
14 GJB2 GJB2 GJB2 5191 0.088 0.28 NO
15 SH3GL2 SH3GL2 SH3GL2 5368 0.082 0.28 NO
16 GJB7 GJB7 GJB7 5544 0.077 0.28 NO
17 SEC23A SEC23A SEC23A 5601 0.074 0.28 NO
18 AP1S2 AP1S2 AP1S2 5721 0.071 0.28 NO
19 STX4 STX4 STX4 6036 0.063 0.27 NO
20 ARRB1 ARRB1 ARRB1 6109 0.061 0.28 NO
21 M6PR M6PR M6PR 6149 0.06 0.28 NO
22 CHMP4A CHMP4A CHMP4A 6263 0.057 0.28 NO
23 HIP1R HIP1R HIP1R 6390 0.054 0.28 NO
24 VAMP8 VAMP8 VAMP8 6632 0.049 0.28 NO
25 CHMP7 CHMP7 CHMP7 6798 0.046 0.27 NO
26 VPS36 VPS36 VPS36 6922 0.043 0.27 NO
27 CHMP6 CHMP6 CHMP6 6939 0.043 0.28 NO
28 GJA4 GJA4 GJA4 6970 0.042 0.28 NO
29 FTH1 FTH1 FTH1 7136 0.039 0.27 NO
30 AP4B1 AP4B1 AP4B1 7256 0.037 0.27 NO
31 VAMP2 VAMP2 VAMP2 7459 0.034 0.26 NO
32 SRC SRC SRC 7608 0.032 0.26 NO
33 CLTB CLTB CLTB 7640 0.032 0.26 NO
34 AP4E1 AP4E1 AP4E1 7648 0.031 0.27 NO
35 DTNBP1 DTNBP1 DTNBP1 7825 0.029 0.26 NO
36 GJA5 GJA5 GJA5 8215 0.024 0.24 NO
37 ARFGAP1 ARFGAP1 ARFGAP1 8216 0.024 0.24 NO
38 CTSZ CTSZ CTSZ 8230 0.024 0.25 NO
39 AP1B1 AP1B1 AP1B1 8357 0.022 0.24 NO
40 BLOC1S1 BLOC1S1 BLOC1S1 8400 0.021 0.24 NO
41 CHMP4B CHMP4B CHMP4B 8438 0.021 0.24 NO
42 VPS4B VPS4B VPS4B 9033 0.014 0.21 NO
43 VPS37B VPS37B VPS37B 9144 0.013 0.21 NO
44 GJA3 GJA3 GJA3 9237 0.012 0.2 NO
45 TGOLN2 TGOLN2 TGOLN2 9284 0.012 0.2 NO
46 VPS4A VPS4A VPS4A 9414 0.01 0.2 NO
47 FTL FTL FTL 9520 0.0093 0.19 NO
48 TPD52L1 TPD52L1 TPD52L1 9593 0.0085 0.19 NO
49 AP2M1 AP2M1 AP2M1 9612 0.0082 0.19 NO
50 AP1M1 AP1M1 AP1M1 9793 0.0066 0.18 NO
51 RPS27A RPS27A RPS27A 9873 0.0058 0.18 NO
52 SNF8 SNF8 SNF8 10044 0.0041 0.17 NO
53 SNX2 SNX2 SNX2 10174 0.0028 0.16 NO
54 UBA52 UBA52 UBA52 10270 0.002 0.16 NO
55 CHMP2A CHMP2A CHMP2A 10367 0.0012 0.15 NO
56 RAB5C RAB5C RAB5C 10462 0.0005 0.15 NO
57 DNM2 DNM2 DNM2 10508 0.00016 0.14 NO
58 VPS28 VPS28 VPS28 10560 -0.00038 0.14 NO
59 SORT1 SORT1 SORT1 10677 -0.0014 0.14 NO
60 VPS37A VPS37A VPS37A 10707 -0.0017 0.13 NO
61 HGS HGS HGS 10726 -0.0018 0.13 NO
62 GAK GAK GAK 10764 -0.0022 0.13 NO
63 CHMP2B CHMP2B CHMP2B 10839 -0.0029 0.13 NO
64 CLTA CLTA CLTA 10849 -0.003 0.13 NO
65 VPS25 VPS25 VPS25 10872 -0.0033 0.13 NO
66 SNX5 SNX5 SNX5 11032 -0.0045 0.12 NO
67 AP1G1 AP1G1 AP1G1 11091 -0.005 0.12 NO
68 CNO CNO CNO 11292 -0.0065 0.1 NO
69 NAPA NAPA NAPA 11564 -0.0088 0.091 NO
70 SH3D19 SH3D19 SH3D19 11566 -0.0089 0.092 NO
71 SNX9 SNX9 SNX9 11586 -0.009 0.092 NO
72 CHMP5 CHMP5 CHMP5 11696 -0.0098 0.087 NO
73 AP3B1 AP3B1 AP3B1 12199 -0.014 0.061 NO
74 SNAPIN SNAPIN SNAPIN 12267 -0.015 0.06 NO
75 GNS GNS GNS 12392 -0.016 0.055 NO
76 SEC13 SEC13 SEC13 12403 -0.016 0.056 NO
77 VTA1 VTA1 VTA1 12446 -0.016 0.056 NO
78 PUM1 PUM1 PUM1 12489 -0.016 0.055 NO
79 BLOC1S3 BLOC1S3 BLOC1S3 12499 -0.017 0.057 NO
80 PLDN PLDN PLDN 12550 -0.017 0.056 NO
81 DAB2 DAB2 DAB2 12569 -0.017 0.057 NO
82 GBF1 GBF1 GBF1 12599 -0.017 0.058 NO
83 STAM2 STAM2 STAM2 12611 -0.018 0.059 NO
84 PREB PREB PREB 12729 -0.018 0.055 NO
85 CPD CPD CPD 12764 -0.019 0.056 NO
86 SEC24B SEC24B SEC24B 13029 -0.021 0.044 NO
87 COPE COPE COPE 13073 -0.022 0.044 NO
88 COPZ1 COPZ1 COPZ1 13079 -0.022 0.046 NO
89 IGF2R IGF2R IGF2R 13120 -0.022 0.047 NO
90 AP3S1 AP3S1 AP3S1 13189 -0.022 0.046 NO
91 NECAP1 NECAP1 NECAP1 13356 -0.024 0.04 NO
92 SNAP23 SNAP23 SNAP23 13500 -0.026 0.035 NO
93 PIK3C2A PIK3C2A PIK3C2A 13627 -0.027 0.031 NO
94 SEC24C SEC24C SEC24C 13840 -0.029 0.023 NO
95 SEC24D SEC24D SEC24D 13875 -0.029 0.025 NO
96 PICALM PICALM PICALM 14010 -0.031 0.021 NO
97 TSG101 TSG101 TSG101 14053 -0.031 0.023 NO
98 SEC31A SEC31A SEC31A 14122 -0.032 0.023 NO
99 ARF1 ARF1 ARF1 14179 -0.032 0.024 NO
100 ARCN1 ARCN1 ARCN1 14708 -0.038 -0.00082 NO
101 STAM STAM STAM 14790 -0.039 -0.00048 NO
102 TBC1D8B TBC1D8B TBC1D8B 14793 -0.039 0.0042 NO
103 GJD4 GJD4 GJD4 14990 -0.042 -0.0015 NO
104 COPB1 COPB1 COPB1 15048 -0.042 0.00053 NO
105 TXNDC5 TXNDC5 TXNDC5 15119 -0.043 0.002 NO
106 AP1S1 AP1S1 AP1S1 15145 -0.044 0.0059 NO
107 HSPA8 HSPA8 HSPA8 15207 -0.044 0.008 NO
108 COPA COPA COPA 15223 -0.045 0.013 NO
109 CLTC CLTC CLTC 15447 -0.049 0.0064 NO
110 COPG COPG COPG 15693 -0.053 -0.00062 NO
111 COPB2 COPB2 COPB2 15844 -0.056 -0.002 NO
112 VAMP7 VAMP7 VAMP7 16021 -0.06 -0.0043 NO
113 TJP1 TJP1 TJP1 16055 -0.061 0.0013 NO
114 AP1M2 AP1M2 AP1M2 16195 -0.064 0.0015 NO
115 VPS37C VPS37C VPS37C 16441 -0.071 -0.0032 NO
116 OCRL OCRL OCRL 16570 -0.076 -0.00099 NO
117 SAR1B SAR1B SAR1B 16732 -0.082 0.00021 NO
118 TPD52 TPD52 TPD52 16910 -0.09 0.0015 NO
119 MYO6 MYO6 MYO6 16995 -0.094 0.0085 NO
120 YIPF6 YIPF6 YIPF6 17269 -0.11 0.007 NO
121 CHMP4C CHMP4C CHMP4C 17297 -0.11 0.019 NO
122 DNAJC6 DNAJC6 DNAJC6 17502 -0.13 0.024 NO
123 GJB1 GJB1 GJB1 17704 -0.15 0.03 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 GLUTATHIONE METABOLISM.

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

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 CFTR CFTR CFTR 39 0.77 0.16 YES
2 ATP6V0A4 ATP6V0A4 ATP6V0A4 293 0.52 0.26 YES
3 ATP6V0D2 ATP6V0D2 ATP6V0D2 692 0.4 0.32 YES
4 ATP6V1G3 ATP6V1G3 ATP6V1G3 856 0.38 0.39 YES
5 ATP6V1B1 ATP6V1B1 ATP6V1B1 1542 0.29 0.42 YES
6 PRKCB PRKCB PRKCB 1561 0.29 0.48 YES
7 PLCG2 PLCG2 PLCG2 2173 0.24 0.49 YES
8 TCIRG1 TCIRG1 TCIRG1 3061 0.18 0.48 YES
9 ADCY3 ADCY3 ADCY3 3484 0.16 0.49 YES
10 KCNQ1 KCNQ1 KCNQ1 4048 0.13 0.49 YES
11 ATP6V1C2 ATP6V1C2 ATP6V1C2 4407 0.12 0.5 YES
12 PRKCA PRKCA PRKCA 5217 0.087 0.47 NO
13 ADCY9 ADCY9 ADCY9 5813 0.068 0.45 NO
14 ACTB ACTB ACTB 6909 0.043 0.4 NO
15 PRKX PRKX PRKX 7390 0.035 0.38 NO
16 PRKCG PRKCG PRKCG 7416 0.035 0.39 NO
17 ATP6V0D1 ATP6V0D1 ATP6V0D1 7803 0.029 0.37 NO
18 ERO1L ERO1L ERO1L 8317 0.022 0.35 NO
19 PLCG1 PLCG1 PLCG1 9371 0.011 0.3 NO
20 TJP2 TJP2 TJP2 9487 0.0096 0.29 NO
21 ATP6V0E1 ATP6V0E1 ATP6V0E1 9814 0.0063 0.27 NO
22 SEC61A2 SEC61A2 SEC61A2 10062 0.004 0.26 NO
23 ATP6V1G2 ATP6V1G2 ATP6V1G2 10216 0.0024 0.25 NO
24 ATP6V0A2 ATP6V0A2 ATP6V0A2 10245 0.0022 0.25 NO
25 ATP6V1B2 ATP6V1B2 ATP6V1B2 10254 0.0021 0.25 NO
26 PRKACA PRKACA PRKACA 10454 0.00057 0.24 NO
27 KDELR3 KDELR3 KDELR3 10631 -0.00099 0.23 NO
28 ATP6V1E1 ATP6V1E1 ATP6V1E1 11183 -0.0058 0.2 NO
29 ATP6V0A1 ATP6V0A1 ATP6V0A1 11635 -0.0094 0.18 NO
30 KDELR1 KDELR1 KDELR1 11875 -0.011 0.17 NO
31 ATP6V0C ATP6V0C ATP6V0C 11972 -0.012 0.17 NO
32 ACTG1 ACTG1 ACTG1 12237 -0.014 0.16 NO
33 ATP6V1H ATP6V1H ATP6V1H 12383 -0.016 0.15 NO
34 ATP6V1E2 ATP6V1E2 ATP6V1E2 12592 -0.017 0.14 NO
35 ATP6V1F ATP6V1F ATP6V1F 12933 -0.02 0.13 NO
36 ATP6V0B ATP6V0B ATP6V0B 13174 -0.022 0.12 NO
37 ATP6V1D ATP6V1D ATP6V1D 13366 -0.024 0.12 NO
38 SEC61A1 SEC61A1 SEC61A1 13575 -0.026 0.11 NO
39 SLC12A2 SLC12A2 SLC12A2 13623 -0.027 0.11 NO
40 ARF1 ARF1 ARF1 14179 -0.032 0.088 NO
41 GNAS GNAS GNAS 14260 -0.033 0.091 NO
42 SEC61B SEC61B SEC61B 14286 -0.033 0.097 NO
43 ATP6AP1 ATP6AP1 ATP6AP1 14343 -0.034 0.1 NO
44 ATP6V1C1 ATP6V1C1 ATP6V1C1 14746 -0.039 0.087 NO
45 MUC2 MUC2 MUC2 15206 -0.044 0.071 NO
46 PDIA4 PDIA4 PDIA4 15322 -0.046 0.075 NO
47 SEC61G SEC61G SEC61G 15351 -0.047 0.083 NO
48 KDELR2 KDELR2 KDELR2 15361 -0.047 0.093 NO
49 PRKACB PRKACB PRKACB 15832 -0.056 0.079 NO
50 ATP6V1A ATP6V1A ATP6V1A 15991 -0.06 0.083 NO
51 ATP6V1G1 ATP6V1G1 ATP6V1G1 16050 -0.061 0.092 NO
52 TJP1 TJP1 TJP1 16055 -0.061 0.1 NO
53 ATP6V0E2 ATP6V0E2 ATP6V0E2 16504 -0.073 0.096 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 O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG GLYCEROLIPID METABOLISM

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 SAA1 SAA1 SAA1 285 0.52 0.1 YES
2 S100B S100B S100B 615 0.42 0.18 YES
3 IKBKE IKBKE IKBKE 960 0.36 0.24 YES
4 AGER AGER AGER 1310 0.31 0.29 YES
5 UBA7 UBA7 UBA7 2009 0.25 0.31 YES
6 CASP10 CASP10 CASP10 2344 0.22 0.34 YES
7 TNFAIP3 TNFAIP3 TNFAIP3 2444 0.22 0.38 YES
8 NLRC5 NLRC5 NLRC5 2511 0.21 0.43 YES
9 IRF1 IRF1 IRF1 2747 0.2 0.46 YES
10 UBE2L6 UBE2L6 UBE2L6 4057 0.13 0.42 YES
11 IRF3 IRF3 IRF3 4945 0.096 0.39 YES
12 NFKBIA NFKBIA NFKBIA 5062 0.092 0.4 YES
13 MAP3K1 MAP3K1 MAP3K1 5110 0.091 0.42 YES
14 S100A12 S100A12 S100A12 5515 0.078 0.42 YES
15 HERC5 HERC5 HERC5 5626 0.074 0.43 YES
16 IKBKB IKBKB IKBKB 5888 0.067 0.43 YES
17 DHX58 DHX58 DHX58 5893 0.066 0.44 YES
18 TRAF6 TRAF6 TRAF6 5933 0.065 0.45 YES
19 NFKB2 NFKB2 NFKB2 6151 0.06 0.46 YES
20 TRAF3 TRAF3 TRAF3 6471 0.052 0.45 YES
21 CYLD CYLD CYLD 6476 0.052 0.46 YES
22 IRF2 IRF2 IRF2 6682 0.048 0.46 YES
23 ATG5 ATG5 ATG5 6721 0.047 0.47 YES
24 DDX58 DDX58 DDX58 6750 0.046 0.48 YES
25 NFKBIB NFKBIB NFKBIB 6898 0.044 0.48 YES
26 ISG15 ISG15 ISG15 6929 0.043 0.49 YES
27 IRF7 IRF7 IRF7 7219 0.038 0.48 YES
28 RIPK1 RIPK1 RIPK1 7223 0.038 0.49 YES
29 IKBKG IKBKG IKBKG 7285 0.037 0.49 YES
30 TRAF2 TRAF2 TRAF2 7510 0.033 0.49 NO
31 FADD FADD FADD 8190 0.024 0.46 NO
32 APP APP APP 8575 0.019 0.44 NO
33 TANK TANK TANK 8687 0.018 0.44 NO
34 RELA RELA RELA 9076 0.014 0.42 NO
35 NLRX1 NLRX1 NLRX1 9103 0.013 0.42 NO
36 OTUD5 OTUD5 OTUD5 9106 0.013 0.42 NO
37 CREBBP CREBBP CREBBP 9162 0.013 0.42 NO
38 HMGB1 HMGB1 HMGB1 9344 0.011 0.42 NO
39 RPS27A RPS27A RPS27A 9873 0.0058 0.39 NO
40 IFIH1 IFIH1 IFIH1 10091 0.0036 0.38 NO
41 UBE2D3 UBE2D3 UBE2D3 10100 0.0035 0.38 NO
42 ATG12 ATG12 ATG12 10239 0.0022 0.37 NO
43 UBA52 UBA52 UBA52 10270 0.002 0.37 NO
44 RNF125 RNF125 RNF125 10763 -0.0022 0.34 NO
45 PIN1 PIN1 PIN1 11118 -0.0051 0.32 NO
46 CASP8 CASP8 CASP8 11160 -0.0056 0.32 NO
47 TBK1 TBK1 TBK1 11306 -0.0067 0.32 NO
48 RNF135 RNF135 RNF135 11405 -0.0075 0.31 NO
49 TRIM25 TRIM25 TRIM25 11437 -0.0077 0.31 NO
50 PCBP2 PCBP2 PCBP2 11580 -0.0089 0.31 NO
51 CHUK CHUK CHUK 11656 -0.0095 0.3 NO
52 UBE2D2 UBE2D2 UBE2D2 12532 -0.017 0.26 NO
53 MAVS MAVS MAVS 13485 -0.025 0.21 NO
54 UBE2D1 UBE2D1 UBE2D1 13911 -0.03 0.2 NO
55 DAK DAK DAK 14270 -0.033 0.18 NO
56 EP300 EP300 EP300 14397 -0.034 0.19 NO
57 SIKE1 SIKE1 SIKE1 14606 -0.037 0.18 NO
58 UBE2K UBE2K UBE2K 14660 -0.038 0.19 NO
59 TAX1BP1 TAX1BP1 TAX1BP1 15034 -0.042 0.18 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 GLYCEROLIPID METABOLISM.

Figure S78.  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 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 CD7 CD7 CD7 392 0.48 0.07 YES
2 MET MET MET 636 0.41 0.14 YES
3 NR0B2 NR0B2 NR0B2 1165 0.33 0.17 YES
4 TNFRSF6B TNFRSF6B TNFRSF6B 1340 0.31 0.22 YES
5 IL8 IL8 IL8 1498 0.3 0.27 YES
6 BTK BTK BTK 1624 0.28 0.31 YES
7 FAIM2 FAIM2 FAIM2 1845 0.26 0.35 YES
8 CASP10 CASP10 CASP10 2344 0.22 0.37 YES
9 IL1A IL1A IL1A 2421 0.22 0.41 YES
10 FAS FAS FAS 3385 0.16 0.38 YES
11 NCS1 NCS1 NCS1 3795 0.14 0.39 YES
12 NFKBIE NFKBIE NFKBIE 4052 0.13 0.4 YES
13 HSPB1 HSPB1 HSPB1 4645 0.11 0.39 YES
14 EGFR EGFR EGFR 4956 0.095 0.39 YES
15 NFKBIA NFKBIA NFKBIA 5062 0.092 0.4 YES
16 MAP3K1 MAP3K1 MAP3K1 5110 0.091 0.42 YES
17 NFKB1 NFKB1 NFKB1 5246 0.086 0.42 YES
18 EPHB2 EPHB2 EPHB2 5255 0.086 0.44 YES
19 MAPK8IP3 MAPK8IP3 MAPK8IP3 5340 0.083 0.45 YES
20 NFKB2 NFKB2 NFKB2 6151 0.06 0.42 NO
21 MAP3K5 MAP3K5 MAP3K5 6454 0.052 0.41 NO
22 NFKBIB NFKBIB NFKBIB 6898 0.044 0.4 NO
23 NFAT5 NFAT5 NFAT5 6993 0.042 0.4 NO
24 RIPK1 RIPK1 RIPK1 7223 0.038 0.39 NO
25 TRAF2 TRAF2 TRAF2 7510 0.033 0.38 NO
26 DEDD2 DEDD2 DEDD2 7673 0.031 0.38 NO
27 BAK1 BAK1 BAK1 7801 0.03 0.38 NO
28 FADD FADD FADD 8190 0.024 0.36 NO
29 MAP2K7 MAP2K7 MAP2K7 8366 0.022 0.36 NO
30 PFN1 PFN1 PFN1 8458 0.021 0.36 NO
31 TP53 TP53 TP53 8592 0.019 0.35 NO
32 CASP3 CASP3 CASP3 8703 0.018 0.35 NO
33 MAPK10 MAPK10 MAPK10 8765 0.017 0.35 NO
34 DAXX DAXX DAXX 9209 0.012 0.33 NO
35 DIABLO DIABLO DIABLO 9538 0.0092 0.31 NO
36 CASP8AP2 CASP8AP2 CASP8AP2 9556 0.0089 0.31 NO
37 EZR EZR EZR 9836 0.0061 0.3 NO
38 CAD CAD CAD 10421 0.00087 0.27 NO
39 DFFA DFFA DFFA 10923 -0.0038 0.24 NO
40 BAX BAX BAX 11043 -0.0046 0.23 NO
41 SMPD1 SMPD1 SMPD1 11121 -0.0051 0.23 NO
42 CASP8 CASP8 CASP8 11160 -0.0056 0.23 NO
43 TUFM TUFM TUFM 11456 -0.0079 0.22 NO
44 DEDD DEDD DEDD 11579 -0.0089 0.21 NO
45 NFKBIL1 NFKBIL1 NFKBIL1 11986 -0.012 0.19 NO
46 MAP2K4 MAP2K4 MAP2K4 12025 -0.013 0.19 NO
47 PARP1 PARP1 PARP1 12305 -0.015 0.18 NO
48 FAF1 FAF1 FAF1 12332 -0.015 0.18 NO
49 BFAR BFAR BFAR 12350 -0.015 0.18 NO
50 AGFG1 AGFG1 AGFG1 12395 -0.016 0.18 NO
51 ROCK1 ROCK1 ROCK1 12623 -0.018 0.17 NO
52 ALG2 ALG2 ALG2 12741 -0.019 0.17 NO
53 CSNK1A1 CSNK1A1 CSNK1A1 13225 -0.023 0.15 NO
54 CDK2AP1 CDK2AP1 CDK2AP1 13444 -0.025 0.14 NO
55 RALBP1 RALBP1 RALBP1 13753 -0.028 0.13 NO
56 MAPK1 MAPK1 MAPK1 13960 -0.03 0.12 NO
57 MAPK8IP1 MAPK8IP1 MAPK8IP1 14288 -0.034 0.11 NO
58 MAPK8 MAPK8 MAPK8 14780 -0.039 0.093 NO
59 PFN2 PFN2 PFN2 15076 -0.043 0.085 NO
60 XIAP XIAP XIAP 15262 -0.045 0.083 NO
61 MAPK9 MAPK9 MAPK9 15445 -0.049 0.082 NO
62 PTPN13 PTPN13 PTPN13 15585 -0.052 0.085 NO
63 MAPK8IP2 MAPK8IP2 MAPK8IP2 16406 -0.07 0.053 NO
64 TPX2 TPX2 TPX2 18189 -0.26 0.0037 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 INOSITOL PHOSPHATE METABOLISM.

Figure S80.  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

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 = PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = PRAD-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)