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 "KICH-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:
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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.
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Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).
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Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).
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Checks if the top core genes are up-regulated or down-regulated.
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Checks if the top core genes are high expressed or low expressed.
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Checks if the top core genes are significantly differently expressed genes.
Table 1. Get Full Table basic data info
basic data info |
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Number of Gene Sets: 701 |
Number of samples: 66 |
Original number of Gene Sets: 1320 |
Maximum gene set size: 933 |
Table 2. Get Full Table pheno data info
phenotype info |
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pheno.type: 1 - 7 :[ clus1 ] 17 |
pheno.type: 2 - 7 :[ clus2 ] 15 |
pheno.type: 3 - 7 :[ clus3 ] 5 |
pheno.type: 4 - 7 :[ clus4 ] 6 |
pheno.type: 5 - 7 :[ clus5 ] 14 |
pheno.type: 6 - 7 :[ clus6 ] 4 |
pheno.type: 7 - 7 :[ clus7 ] 5 |
For the expression subtypes of 17843 genes in 67 samples, GSEA found enriched gene sets in each cluster using 66 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.
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clus1
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Top enriched gene sets are ST WNT BETA CATENIN PATHWAY, PID P38 MKK3 6PATHWAY, PID REELINPATHWAY, REACTOME MEIOSIS, REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS, REACTOME GENERIC TRANSCRIPTION PATHWAY, REACTOME RNA POL I TRANSCRIPTION, REACTOME GLUCONEOGENESIS, REACTOME OLFACTORY SIGNALING PATHWAY, REACTOME TRANSCRIPTION
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And common core enriched genes are HIST1H2AC, HIST1H2AD, HIST1H2AE, HIST1H2BC, HIST1H2BD, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BJ, HIST1H2BK
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clus2
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Top enriched gene sets are KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY, KEGG PATHOGENIC ESCHERICHIA COLI INFECTION, KEGG NON SMALL CELL LUNG CANCER, KEGG GRAFT VERSUS HOST DISEASE, BIOCARTA DEATH PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA MYOSIN PATHWAY
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And common core enriched genes are BIRC3, CASP3, CASP6, CASP7, CFLAR, CYCS, FADD, MAP3K14, NFKB1, NFKBIA
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clus3
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Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG TYROSINE METABOLISM, BIOCARTA RACCYCD PATHWAY, BIOCARTA INTEGRIN PATHWAY, PID WNT NONCANONICAL PATHWAY, PID NECTIN PATHWAY, PID HNF3BPATHWAY, PID IGF1 PATHWAY, PID AR TF PATHWAY, PID ECADHERIN STABILIZATION PATHWAY
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And common core enriched genes are CDKN1A, AKT2, AKT3, BAD, CASP9, FOXO1, FOXO3, FOXO4, GSK3A, PDPK1
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clus4
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Top enriched gene sets are KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG PROPANOATE METABOLISM, KEGG ADHERENS JUNCTION, BIOCARTA AT1R PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA PPARA PATHWAY, BIOCARTA PDGF PATHWAY, BIOCARTA VEGF PATHWAY, PID S1P S1P3 PATHWAY, PID AVB3 OPN PATHWAY
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And common core enriched genes are AGTR1, ITGA5, MAPK8, PIK3CA, PLD2, STAT5A, STAT5B, EGFR, SOS1, ITGA1
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clus5
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Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG RNA DEGRADATION, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG NUCLEOTIDE EXCISION REPAIR, PID FANCONI PATHWAY, REACTOME TRANSLATION, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME MITOCHONDRIAL PROTEIN IMPORT, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S
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And common core enriched genes are FAM153A, RPL10, RPL10A, RPL11, RPL12, RPL13A, RPL14, RPL15, RPL17, RPL18
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clus6
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Top enriched gene sets are KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG GLYCEROLIPID METABOLISM, KEGG PROPANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, SIG CD40PATHWAYMAP, PID TRAIL PATHWAY, PID RET PATHWAY
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And common core enriched genes are ALDH1B1, ALDH2, AHCYL1, CBS, CTH, GGT1, GGT5, GGT6, MARS2, MAT1A
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clus7
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Top enriched gene sets are BIOCARTA RACCYCD PATHWAY, PID ILK PATHWAY, REACTOME TRIF MEDIATED TLR3 SIGNALING, REACTOME ORC1 REMOVAL FROM CHROMATIN, REACTOME ACTIVATION OF NF KAPPAB IN B CELLS, REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT, REACTOME CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6, REACTOME REGULATION OF APOPTOSIS, REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION , REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE
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And common core enriched genes are PSMA1, PSMA4, PSMA5, PSMA6, PSMA7, PSMB1, PSMB10, PSMB2, PSMB3, PSMB4
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ST WNT BETA CATENIN PATHWAY | 33 | genes.ES.table | 0.47 | 1.4 | 0.1 | 1 | 1 | 0.18 | 0.086 | 0.17 | 1 | 0.8 |
PID P38 MKK3 6PATHWAY | 26 | genes.ES.table | 0.54 | 2.1 | 0 | 0.11 | 0.043 | 0.12 | 0.041 | 0.11 | 0 | 0.028 |
PID REELINPATHWAY | 28 | genes.ES.table | 0.44 | 1.4 | 0.14 | 1 | 1 | 0.14 | 0.049 | 0.14 | 1 | 0.78 |
REACTOME MEIOSIS | 92 | genes.ES.table | 0.6 | 1.4 | 0.16 | 1 | 1 | 0.36 | 0.14 | 0.31 | 1 | 0.83 |
REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS | 25 | genes.ES.table | 0.5 | 1.3 | 0.14 | 1 | 1 | 0.24 | 0.052 | 0.23 | 1 | 0.83 |
REACTOME GENERIC TRANSCRIPTION PATHWAY | 337 | genes.ES.table | 0.37 | 1.4 | 0.16 | 1 | 0.99 | 0.42 | 0.27 | 0.31 | 1 | 0.87 |
REACTOME RNA POL I TRANSCRIPTION | 71 | genes.ES.table | 0.61 | 1.4 | 0.16 | 1 | 1 | 0.38 | 0.14 | 0.33 | 1 | 0.81 |
REACTOME GLUCONEOGENESIS | 30 | genes.ES.table | 0.45 | 1.3 | 0.12 | 1 | 1 | 0.27 | 0.11 | 0.24 | 1 | 0.73 |
REACTOME OLFACTORY SIGNALING PATHWAY | 32 | genes.ES.table | 0.59 | 1.4 | 0.047 | 1 | 0.99 | 0.5 | 0.2 | 0.4 | 1 | 0.84 |
REACTOME TRANSCRIPTION | 181 | genes.ES.table | 0.37 | 1.3 | 0.27 | 1 | 1 | 0.2 | 0.19 | 0.17 | 1 | 0.83 |
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 | CAMK2B | CAMK2B | CAMK2B | 244 | 0.46 | 0.24 | YES |
2 | MAP2K6 | MAP2K6 | MAP2K6 | 720 | 0.3 | 0.38 | YES |
3 | GADD45G | GADD45G | GADD45G | 738 | 0.3 | 0.54 | YES |
4 | TAB1 | TAB1 | TAB1 | 5096 | 0.06 | 0.33 | NO |
5 | TXN | TXN | TXN | 5148 | 0.058 | 0.36 | NO |
6 | TAOK2 | TAOK2 | TAOK2 | 6791 | 0.031 | 0.29 | NO |
7 | TAOK3 | TAOK3 | TAOK3 | 7302 | 0.023 | 0.27 | NO |
8 | TAB2 | TAB2 | TAB2 | 8013 | 0.012 | 0.24 | NO |
9 | MAP3K1 | MAP3K1 | MAP3K1 | 8534 | 0.0039 | 0.21 | NO |
10 | MAP3K7 | MAP3K7 | MAP3K7 | 8743 | 0.00081 | 0.2 | NO |
11 | TRAF2 | TRAF2 | TRAF2 | 8829 | -0.00049 | 0.19 | NO |
12 | MAP3K4 | MAP3K4 | MAP3K4 | 8877 | -0.00098 | 0.19 | NO |
13 | RAC1 | RAC1 | RAC1 | 9342 | -0.0076 | 0.17 | NO |
14 | GADD45B | GADD45B | GADD45B | 9372 | -0.0081 | 0.17 | NO |
15 | MAP3K3 | MAP3K3 | MAP3K3 | 10111 | -0.02 | 0.14 | NO |
16 | CCM2 | CCM2 | CCM2 | 10112 | -0.02 | 0.15 | NO |
17 | MAPK14 | MAPK14 | MAPK14 | 10115 | -0.02 | 0.16 | NO |
18 | MAP3K10 | MAP3K10 | MAP3K10 | 10873 | -0.031 | 0.14 | NO |
19 | TAOK1 | TAOK1 | TAOK1 | 11018 | -0.034 | 0.15 | NO |
20 | TRAF6 | TRAF6 | TRAF6 | 11036 | -0.034 | 0.17 | NO |
21 | ATM | ATM | ATM | 11637 | -0.045 | 0.16 | NO |
22 | GADD45A | GADD45A | GADD45A | 11924 | -0.05 | 0.17 | NO |
23 | MAP3K5 | MAP3K5 | MAP3K5 | 12025 | -0.052 | 0.19 | NO |
24 | MAP2K3 | MAP2K3 | MAP2K3 | 12074 | -0.052 | 0.22 | NO |
25 | MAP3K6 | MAP3K6 | MAP3K6 | 12894 | -0.07 | 0.21 | NO |
26 | MAPK11 | MAPK11 | MAPK11 | 14495 | -0.12 | 0.19 | 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: ST WNT BETA CATENIN PATHWAY.

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

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 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 87 | 0.58 | 0.085 | YES |
2 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 276 | 0.44 | 0.14 | YES |
3 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 316 | 0.42 | 0.2 | YES |
4 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 408 | 0.38 | 0.26 | YES |
5 | HIST4H4 | HIST4H4 | HIST4H4 | 472 | 0.35 | 0.31 | YES |
6 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 509 | 0.34 | 0.36 | YES |
7 | HIST1H4E | HIST1H4E | HIST1H4E | 567 | 0.33 | 0.41 | YES |
8 | HIST1H4H | HIST1H4H | HIST1H4H | 653 | 0.31 | 0.45 | YES |
9 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 769 | 0.29 | 0.49 | YES |
10 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 973 | 0.26 | 0.52 | YES |
11 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 1208 | 0.23 | 0.54 | YES |
12 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 1281 | 0.22 | 0.57 | YES |
13 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 1359 | 0.22 | 0.6 | YES |
14 | HIST1H4D | HIST1H4D | HIST1H4D | 1379 | 0.21 | 0.63 | YES |
15 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 1386 | 0.21 | 0.66 | YES |
16 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 1490 | 0.2 | 0.69 | YES |
17 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1552 | 0.2 | 0.72 | YES |
18 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 1923 | 0.17 | 0.72 | YES |
19 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 1942 | 0.17 | 0.75 | YES |
20 | HIST1H4B | HIST1H4B | HIST1H4B | 2312 | 0.14 | 0.75 | YES |
21 | HIST1H4I | HIST1H4I | HIST1H4I | 2488 | 0.14 | 0.76 | YES |
22 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 5233 | 0.057 | 0.61 | NO |
23 | HIST1H4C | HIST1H4C | HIST1H4C | 5429 | 0.053 | 0.61 | NO |
24 | HIST1H4A | HIST1H4A | HIST1H4A | 5492 | 0.052 | 0.62 | NO |
25 | HIST1H4J | HIST1H4J | HIST1H4J | 5871 | 0.046 | 0.6 | NO |
26 | HIST2H4A | HIST2H4A | HIST2H4A | 6074 | 0.043 | 0.6 | NO |
27 | H2AFX | H2AFX | H2AFX | 6177 | 0.041 | 0.6 | NO |
28 | TERF2IP | TERF2IP | TERF2IP | 6561 | 0.035 | 0.58 | NO |
29 | TERF2 | TERF2 | TERF2 | 7733 | 0.016 | 0.52 | NO |
30 | H2AFZ | H2AFZ | H2AFZ | 7926 | 0.013 | 0.51 | NO |
31 | POT1 | POT1 | POT1 | 8565 | 0.0034 | 0.47 | NO |
32 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 9110 | -0.0042 | 0.44 | NO |
33 | TINF2 | TINF2 | TINF2 | 9134 | -0.0046 | 0.44 | NO |
34 | ACD | ACD | ACD | 9509 | -0.01 | 0.42 | NO |
35 | TERF1 | TERF1 | TERF1 | 10934 | -0.032 | 0.35 | NO |
36 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 14284 | -0.11 | 0.18 | NO |
37 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 15117 | -0.15 | 0.15 | NO |
Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID P38 MKK3 6PATHWAY.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: PID P38 MKK3 6PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 87 | 0.58 | 0.064 | YES |
2 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 276 | 0.44 | 0.11 | YES |
3 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 316 | 0.42 | 0.15 | YES |
4 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 408 | 0.38 | 0.19 | YES |
5 | TEX12 | TEX12 | TEX12 | 422 | 0.37 | 0.24 | YES |
6 | HIST4H4 | HIST4H4 | HIST4H4 | 472 | 0.35 | 0.28 | YES |
7 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 509 | 0.34 | 0.32 | YES |
8 | HIST1H4E | HIST1H4E | HIST1H4E | 567 | 0.33 | 0.35 | YES |
9 | HIST1H4H | HIST1H4H | HIST1H4H | 653 | 0.31 | 0.38 | YES |
10 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 769 | 0.29 | 0.41 | YES |
11 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 973 | 0.26 | 0.43 | YES |
12 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 1208 | 0.23 | 0.45 | YES |
13 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 1281 | 0.22 | 0.47 | YES |
14 | SYNE1 | SYNE1 | SYNE1 | 1358 | 0.22 | 0.49 | YES |
15 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 1359 | 0.22 | 0.52 | YES |
16 | HIST1H4D | HIST1H4D | HIST1H4D | 1379 | 0.21 | 0.54 | YES |
17 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 1386 | 0.21 | 0.57 | YES |
18 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 1490 | 0.2 | 0.58 | YES |
19 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1552 | 0.2 | 0.6 | YES |
20 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 1923 | 0.17 | 0.6 | YES |
21 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 1942 | 0.17 | 0.62 | YES |
22 | LMNB1 | LMNB1 | LMNB1 | 2242 | 0.15 | 0.62 | YES |
23 | HIST1H4B | HIST1H4B | HIST1H4B | 2312 | 0.14 | 0.64 | YES |
24 | HIST1H4I | HIST1H4I | HIST1H4I | 2488 | 0.14 | 0.64 | YES |
25 | SMC1B | SMC1B | SMC1B | 3201 | 0.11 | 0.62 | NO |
26 | ATR | ATR | ATR | 3285 | 0.1 | 0.62 | NO |
27 | SUN2 | SUN2 | SUN2 | 4014 | 0.083 | 0.59 | NO |
28 | SYNE2 | SYNE2 | SYNE2 | 4438 | 0.073 | 0.58 | NO |
29 | STAG2 | STAG2 | STAG2 | 5127 | 0.059 | 0.55 | NO |
30 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 5233 | 0.057 | 0.55 | NO |
31 | DIDO1 | DIDO1 | DIDO1 | 5386 | 0.054 | 0.55 | NO |
32 | HIST1H4C | HIST1H4C | HIST1H4C | 5429 | 0.053 | 0.55 | NO |
33 | HIST1H4A | HIST1H4A | HIST1H4A | 5492 | 0.052 | 0.55 | NO |
34 | HIST1H4J | HIST1H4J | HIST1H4J | 5871 | 0.046 | 0.54 | NO |
35 | HIST2H4A | HIST2H4A | HIST2H4A | 6074 | 0.043 | 0.53 | NO |
36 | H2AFX | H2AFX | H2AFX | 6177 | 0.041 | 0.53 | NO |
37 | SYCP2 | SYCP2 | SYCP2 | 6443 | 0.037 | 0.52 | NO |
38 | UBE2I | UBE2I | UBE2I | 6496 | 0.036 | 0.52 | NO |
39 | TERF2IP | TERF2IP | TERF2IP | 6561 | 0.035 | 0.52 | NO |
40 | STAG1 | STAG1 | STAG1 | 6663 | 0.033 | 0.52 | NO |
41 | TERF2 | TERF2 | TERF2 | 7733 | 0.016 | 0.46 | NO |
42 | H2AFZ | H2AFZ | H2AFZ | 7926 | 0.013 | 0.45 | NO |
43 | SMC1A | SMC1A | SMC1A | 7978 | 0.012 | 0.45 | NO |
44 | POT1 | POT1 | POT1 | 8565 | 0.0034 | 0.42 | NO |
45 | BRCA1 | BRCA1 | BRCA1 | 8613 | 0.0028 | 0.42 | NO |
46 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 9110 | -0.0042 | 0.39 | NO |
47 | TINF2 | TINF2 | TINF2 | 9134 | -0.0046 | 0.39 | NO |
48 | ACD | ACD | ACD | 9509 | -0.01 | 0.37 | NO |
49 | REC8 | REC8 | REC8 | 10081 | -0.019 | 0.34 | NO |
50 | TERF1 | TERF1 | TERF1 | 10934 | -0.032 | 0.29 | NO |
51 | RAD21 | RAD21 | RAD21 | 11252 | -0.038 | 0.28 | NO |
52 | LMNA | LMNA | LMNA | 11958 | -0.05 | 0.25 | NO |
53 | SMC3 | SMC3 | SMC3 | 12439 | -0.06 | 0.23 | NO |
54 | HSPA2 | HSPA2 | HSPA2 | 13462 | -0.084 | 0.18 | NO |
55 | STAG3 | STAG3 | STAG3 | 13723 | -0.091 | 0.18 | NO |
56 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 14284 | -0.11 | 0.16 | NO |
57 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 15117 | -0.15 | 0.13 | NO |
58 | FKBP6 | FKBP6 | FKBP6 | 16130 | -0.21 | 0.095 | NO |
Figure S5. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID REELINPATHWAY.

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

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 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 87 | 0.58 | 0.065 | YES |
2 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 276 | 0.44 | 0.11 | YES |
3 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 316 | 0.42 | 0.16 | YES |
4 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 408 | 0.38 | 0.2 | YES |
5 | HIST4H4 | HIST4H4 | HIST4H4 | 472 | 0.35 | 0.23 | YES |
6 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 509 | 0.34 | 0.27 | YES |
7 | HIST1H4E | HIST1H4E | HIST1H4E | 567 | 0.33 | 0.31 | YES |
8 | CENPP | CENPP | CENPP | 640 | 0.32 | 0.34 | YES |
9 | HIST1H4H | HIST1H4H | HIST1H4H | 653 | 0.31 | 0.38 | YES |
10 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 769 | 0.29 | 0.41 | YES |
11 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 973 | 0.26 | 0.43 | YES |
12 | MLF1IP | MLF1IP | MLF1IP | 995 | 0.26 | 0.46 | YES |
13 | CENPH | CENPH | CENPH | 997 | 0.26 | 0.49 | YES |
14 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 1208 | 0.23 | 0.5 | YES |
15 | HJURP | HJURP | HJURP | 1262 | 0.23 | 0.53 | YES |
16 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 1281 | 0.22 | 0.56 | YES |
17 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 1359 | 0.22 | 0.58 | YES |
18 | HIST1H4D | HIST1H4D | HIST1H4D | 1379 | 0.21 | 0.6 | YES |
19 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 1386 | 0.21 | 0.63 | YES |
20 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 1490 | 0.2 | 0.64 | YES |
21 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1552 | 0.2 | 0.66 | YES |
22 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 1923 | 0.17 | 0.66 | YES |
23 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 1942 | 0.17 | 0.68 | YES |
24 | HIST1H4B | HIST1H4B | HIST1H4B | 2312 | 0.14 | 0.68 | YES |
25 | HIST1H4I | HIST1H4I | HIST1H4I | 2488 | 0.14 | 0.69 | YES |
26 | CENPK | CENPK | CENPK | 2622 | 0.13 | 0.7 | YES |
27 | CENPI | CENPI | CENPI | 3327 | 0.1 | 0.67 | NO |
28 | NPM1 | NPM1 | NPM1 | 3734 | 0.091 | 0.66 | NO |
29 | RUVBL1 | RUVBL1 | RUVBL1 | 3847 | 0.087 | 0.66 | NO |
30 | CENPA | CENPA | CENPA | 4035 | 0.083 | 0.66 | NO |
31 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 5233 | 0.057 | 0.6 | NO |
32 | CENPN | CENPN | CENPN | 5345 | 0.055 | 0.6 | NO |
33 | HIST1H4C | HIST1H4C | HIST1H4C | 5429 | 0.053 | 0.6 | NO |
34 | HIST1H4A | HIST1H4A | HIST1H4A | 5492 | 0.052 | 0.6 | NO |
35 | HIST1H4J | HIST1H4J | HIST1H4J | 5871 | 0.046 | 0.59 | NO |
36 | HIST2H4A | HIST2H4A | HIST2H4A | 6074 | 0.043 | 0.58 | NO |
37 | H2AFX | H2AFX | H2AFX | 6177 | 0.041 | 0.58 | NO |
38 | RSF1 | RSF1 | RSF1 | 6838 | 0.03 | 0.55 | NO |
39 | OIP5 | OIP5 | OIP5 | 7391 | 0.022 | 0.52 | NO |
40 | ITGB3BP | ITGB3BP | ITGB3BP | 7611 | 0.018 | 0.51 | NO |
41 | H2AFZ | H2AFZ | H2AFZ | 7926 | 0.013 | 0.49 | NO |
42 | CENPQ | CENPQ | CENPQ | 7988 | 0.012 | 0.49 | NO |
43 | RBBP7 | RBBP7 | RBBP7 | 8769 | 0.00034 | 0.45 | NO |
44 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 9110 | -0.0042 | 0.43 | NO |
45 | SMARCA5 | SMARCA5 | SMARCA5 | 9357 | -0.0079 | 0.42 | NO |
46 | RBBP4 | RBBP4 | RBBP4 | 11171 | -0.036 | 0.32 | NO |
47 | CASC5 | CASC5 | CASC5 | 11923 | -0.05 | 0.28 | NO |
48 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 14284 | -0.11 | 0.16 | NO |
49 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 15117 | -0.15 | 0.13 | NO |
50 | CENPO | CENPO | CENPO | 15337 | -0.16 | 0.14 | NO |
Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME MEIOSIS.

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

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 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 87 | 0.58 | 0.07 | YES |
2 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 276 | 0.44 | 0.12 | YES |
3 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 316 | 0.42 | 0.17 | YES |
4 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 408 | 0.38 | 0.21 | YES |
5 | HIST4H4 | HIST4H4 | HIST4H4 | 472 | 0.35 | 0.25 | YES |
6 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 509 | 0.34 | 0.3 | YES |
7 | HIST1H4E | HIST1H4E | HIST1H4E | 567 | 0.33 | 0.34 | YES |
8 | HIST1H4H | HIST1H4H | HIST1H4H | 653 | 0.31 | 0.37 | YES |
9 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 769 | 0.29 | 0.4 | YES |
10 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 973 | 0.26 | 0.42 | YES |
11 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 1208 | 0.23 | 0.44 | YES |
12 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 1281 | 0.22 | 0.46 | YES |
13 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 1359 | 0.22 | 0.49 | YES |
14 | HIST1H4D | HIST1H4D | HIST1H4D | 1379 | 0.21 | 0.51 | YES |
15 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 1386 | 0.21 | 0.54 | YES |
16 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 1490 | 0.2 | 0.56 | YES |
17 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1552 | 0.2 | 0.58 | YES |
18 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 1923 | 0.17 | 0.58 | YES |
19 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 1942 | 0.17 | 0.61 | YES |
20 | HIST1H4B | HIST1H4B | HIST1H4B | 2312 | 0.14 | 0.6 | YES |
21 | HIST1H4I | HIST1H4I | HIST1H4I | 2488 | 0.14 | 0.61 | YES |
22 | POLD4 | POLD4 | POLD4 | 2815 | 0.12 | 0.61 | NO |
23 | POLA1 | POLA1 | POLA1 | 3495 | 0.097 | 0.58 | NO |
24 | RPA3 | RPA3 | RPA3 | 3822 | 0.088 | 0.58 | NO |
25 | RUVBL1 | RUVBL1 | RUVBL1 | 3847 | 0.087 | 0.59 | NO |
26 | NHP2 | NHP2 | NHP2 | 3916 | 0.086 | 0.59 | NO |
27 | RFC4 | RFC4 | RFC4 | 4125 | 0.08 | 0.59 | NO |
28 | LIG1 | LIG1 | LIG1 | 5097 | 0.06 | 0.54 | NO |
29 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 5233 | 0.057 | 0.54 | NO |
30 | HIST1H4C | HIST1H4C | HIST1H4C | 5429 | 0.053 | 0.54 | NO |
31 | HIST1H4A | HIST1H4A | HIST1H4A | 5492 | 0.052 | 0.54 | NO |
32 | POLE2 | POLE2 | POLE2 | 5588 | 0.051 | 0.55 | NO |
33 | RFC3 | RFC3 | RFC3 | 5731 | 0.048 | 0.54 | NO |
34 | HIST1H4J | HIST1H4J | HIST1H4J | 5871 | 0.046 | 0.54 | NO |
35 | HIST2H4A | HIST2H4A | HIST2H4A | 6074 | 0.043 | 0.54 | NO |
36 | H2AFX | H2AFX | H2AFX | 6177 | 0.041 | 0.54 | NO |
37 | RUVBL2 | RUVBL2 | RUVBL2 | 6499 | 0.036 | 0.52 | NO |
38 | POLD1 | POLD1 | POLD1 | 6501 | 0.036 | 0.53 | NO |
39 | TERF2IP | TERF2IP | TERF2IP | 6561 | 0.035 | 0.53 | NO |
40 | POLA2 | POLA2 | POLA2 | 7005 | 0.028 | 0.51 | NO |
41 | DKC1 | DKC1 | DKC1 | 7250 | 0.024 | 0.5 | NO |
42 | RFC5 | RFC5 | RFC5 | 7494 | 0.02 | 0.48 | NO |
43 | FEN1 | FEN1 | FEN1 | 7581 | 0.018 | 0.48 | NO |
44 | PCNA | PCNA | PCNA | 7710 | 0.017 | 0.48 | NO |
45 | TERF2 | TERF2 | TERF2 | 7733 | 0.016 | 0.48 | NO |
46 | DNA2 | DNA2 | DNA2 | 7917 | 0.013 | 0.47 | NO |
47 | H2AFZ | H2AFZ | H2AFZ | 7926 | 0.013 | 0.47 | NO |
48 | POLE | POLE | POLE | 8117 | 0.01 | 0.46 | NO |
49 | RPA2 | RPA2 | RPA2 | 8171 | 0.0092 | 0.46 | NO |
50 | POT1 | POT1 | POT1 | 8565 | 0.0034 | 0.44 | NO |
51 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 9110 | -0.0042 | 0.41 | NO |
52 | TINF2 | TINF2 | TINF2 | 9134 | -0.0046 | 0.41 | NO |
53 | ACD | ACD | ACD | 9509 | -0.01 | 0.39 | NO |
54 | RFC2 | RFC2 | RFC2 | 10565 | -0.026 | 0.33 | NO |
55 | RPA1 | RPA1 | RPA1 | 10805 | -0.03 | 0.32 | NO |
56 | TERF1 | TERF1 | TERF1 | 10934 | -0.032 | 0.32 | NO |
57 | PRIM2 | PRIM2 | PRIM2 | 11336 | -0.039 | 0.3 | NO |
58 | POLD2 | POLD2 | POLD2 | 11384 | -0.04 | 0.3 | NO |
59 | POLD3 | POLD3 | POLD3 | 11642 | -0.045 | 0.29 | NO |
60 | PRIM1 | PRIM1 | PRIM1 | 13188 | -0.077 | 0.22 | NO |
61 | WRAP53 | WRAP53 | WRAP53 | 13507 | -0.085 | 0.21 | NO |
62 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 14284 | -0.11 | 0.18 | NO |
63 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 15117 | -0.15 | 0.15 | NO |
Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | HIST1H3G | HIST1H3G | HIST1H3G | 79 | 0.59 | 0.049 | YES |
2 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 87 | 0.58 | 0.1 | YES |
3 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 276 | 0.44 | 0.13 | YES |
4 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 316 | 0.42 | 0.16 | YES |
5 | TTR | TTR | TTR | 351 | 0.4 | 0.2 | YES |
6 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 408 | 0.38 | 0.23 | YES |
7 | HIST4H4 | HIST4H4 | HIST4H4 | 472 | 0.35 | 0.26 | YES |
8 | ODAM | ODAM | ODAM | 494 | 0.35 | 0.29 | YES |
9 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 509 | 0.34 | 0.32 | YES |
10 | HIST1H3H | HIST1H3H | HIST1H3H | 564 | 0.33 | 0.34 | YES |
11 | HIST1H4E | HIST1H4E | HIST1H4E | 567 | 0.33 | 0.38 | YES |
12 | HIST1H3E | HIST1H3E | HIST1H3E | 624 | 0.32 | 0.4 | YES |
13 | HIST1H4H | HIST1H4H | HIST1H4H | 653 | 0.31 | 0.43 | YES |
14 | LTF | LTF | LTF | 681 | 0.31 | 0.45 | YES |
15 | HIST1H3D | HIST1H3D | HIST1H3D | 748 | 0.29 | 0.48 | YES |
16 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 769 | 0.29 | 0.5 | YES |
17 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 973 | 0.26 | 0.51 | YES |
18 | HIST2H3D | HIST2H3D | HIST2H3D | 1037 | 0.25 | 0.53 | YES |
19 | NPPA | NPPA | NPPA | 1153 | 0.24 | 0.55 | YES |
20 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 1208 | 0.23 | 0.56 | YES |
21 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 1281 | 0.22 | 0.58 | YES |
22 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 1359 | 0.22 | 0.59 | YES |
23 | HIST1H4D | HIST1H4D | HIST1H4D | 1379 | 0.21 | 0.61 | YES |
24 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 1386 | 0.21 | 0.63 | YES |
25 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 1490 | 0.2 | 0.64 | YES |
26 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1552 | 0.2 | 0.66 | YES |
27 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 1923 | 0.17 | 0.65 | YES |
28 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 1942 | 0.17 | 0.67 | YES |
29 | HIST1H4B | HIST1H4B | HIST1H4B | 2312 | 0.14 | 0.66 | NO |
30 | HIST1H4I | HIST1H4I | HIST1H4I | 2488 | 0.14 | 0.66 | NO |
31 | GSN | GSN | GSN | 2981 | 0.11 | 0.64 | NO |
32 | HIST2H3C | HIST2H3C | HIST2H3C | 3400 | 0.1 | 0.63 | NO |
33 | HIST1H3A | HIST1H3A | HIST1H3A | 5149 | 0.058 | 0.54 | NO |
34 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 5233 | 0.057 | 0.54 | NO |
35 | HIST1H4C | HIST1H4C | HIST1H4C | 5429 | 0.053 | 0.53 | NO |
36 | HIST1H4A | HIST1H4A | HIST1H4A | 5492 | 0.052 | 0.53 | NO |
37 | HIST1H4J | HIST1H4J | HIST1H4J | 5871 | 0.046 | 0.52 | NO |
38 | HIST2H4A | HIST2H4A | HIST2H4A | 6074 | 0.043 | 0.51 | NO |
39 | H2AFX | H2AFX | H2AFX | 6177 | 0.041 | 0.5 | NO |
40 | HSPG2 | HSPG2 | HSPG2 | 7331 | 0.022 | 0.44 | NO |
41 | SNCA | SNCA | SNCA | 7476 | 0.02 | 0.44 | NO |
42 | H2AFZ | H2AFZ | H2AFZ | 7926 | 0.013 | 0.41 | NO |
43 | B2M | B2M | B2M | 8627 | 0.0026 | 0.37 | NO |
44 | CST3 | CST3 | CST3 | 8970 | -0.0023 | 0.35 | NO |
45 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 9110 | -0.0042 | 0.35 | NO |
46 | H3F3A | H3F3A | H3F3A | 9617 | -0.012 | 0.32 | NO |
47 | APOA1 | APOA1 | APOA1 | 10848 | -0.031 | 0.25 | NO |
48 | ITM2B | ITM2B | ITM2B | 11185 | -0.037 | 0.24 | NO |
49 | LYZ | LYZ | LYZ | 11673 | -0.045 | 0.21 | NO |
50 | H3F3B | H3F3B | H3F3B | 12513 | -0.062 | 0.17 | NO |
51 | HIST1H3B | HIST1H3B | HIST1H3B | 12723 | -0.066 | 0.17 | NO |
52 | HIST1H3C | HIST1H3C | HIST1H3C | 13286 | -0.08 | 0.14 | NO |
53 | MFGE8 | MFGE8 | MFGE8 | 13561 | -0.087 | 0.13 | NO |
54 | FGA | FGA | FGA | 14211 | -0.11 | 0.11 | NO |
55 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 14284 | -0.11 | 0.11 | NO |
56 | APP | APP | APP | 14537 | -0.12 | 0.11 | NO |
57 | TGFBI | TGFBI | TGFBI | 14580 | -0.12 | 0.12 | NO |
58 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 15117 | -0.15 | 0.1 | NO |
59 | SAA1 | SAA1 | SAA1 | 15487 | -0.17 | 0.095 | NO |
60 | CALCA | CALCA | CALCA | 16023 | -0.2 | 0.082 | NO |
61 | HIST1H3J | HIST1H3J | HIST1H3J | 16167 | -0.21 | 0.093 | NO |
Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME GENERIC TRANSCRIPTION PATHWAY.

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

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 | HIST1H3G | HIST1H3G | HIST1H3G | 79 | 0.59 | 0.051 | YES |
2 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 87 | 0.58 | 0.1 | YES |
3 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 276 | 0.44 | 0.13 | YES |
4 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 316 | 0.42 | 0.17 | YES |
5 | MND1 | MND1 | MND1 | 350 | 0.4 | 0.21 | YES |
6 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 408 | 0.38 | 0.24 | YES |
7 | HIST4H4 | HIST4H4 | HIST4H4 | 472 | 0.35 | 0.27 | YES |
8 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 509 | 0.34 | 0.3 | YES |
9 | HIST1H3H | HIST1H3H | HIST1H3H | 564 | 0.33 | 0.32 | YES |
10 | HIST1H4E | HIST1H4E | HIST1H4E | 567 | 0.33 | 0.36 | YES |
11 | MSH4 | MSH4 | MSH4 | 599 | 0.32 | 0.38 | YES |
12 | HIST1H3E | HIST1H3E | HIST1H3E | 624 | 0.32 | 0.41 | YES |
13 | HIST1H4H | HIST1H4H | HIST1H4H | 653 | 0.31 | 0.44 | YES |
14 | HIST1H3D | HIST1H3D | HIST1H3D | 748 | 0.29 | 0.46 | YES |
15 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 769 | 0.29 | 0.49 | YES |
16 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 973 | 0.26 | 0.5 | YES |
17 | HIST2H3D | HIST2H3D | HIST2H3D | 1037 | 0.25 | 0.52 | YES |
18 | TEX15 | TEX15 | TEX15 | 1160 | 0.24 | 0.53 | YES |
19 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 1208 | 0.23 | 0.55 | YES |
20 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 1281 | 0.22 | 0.57 | YES |
21 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 1359 | 0.22 | 0.58 | YES |
22 | HIST1H4D | HIST1H4D | HIST1H4D | 1379 | 0.21 | 0.6 | YES |
23 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 1386 | 0.21 | 0.62 | YES |
24 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 1490 | 0.2 | 0.64 | YES |
25 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1552 | 0.2 | 0.65 | YES |
26 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 1923 | 0.17 | 0.64 | YES |
27 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 1942 | 0.17 | 0.66 | YES |
28 | HIST1H4B | HIST1H4B | HIST1H4B | 2312 | 0.14 | 0.65 | YES |
29 | HIST1H4I | HIST1H4I | HIST1H4I | 2488 | 0.14 | 0.66 | YES |
30 | RBBP8 | RBBP8 | RBBP8 | 2516 | 0.14 | 0.67 | YES |
31 | HIST2H3C | HIST2H3C | HIST2H3C | 3400 | 0.1 | 0.63 | NO |
32 | RAD50 | RAD50 | RAD50 | 3430 | 0.099 | 0.63 | NO |
33 | RPA3 | RPA3 | RPA3 | 3822 | 0.088 | 0.62 | NO |
34 | DMC1 | DMC1 | DMC1 | 4715 | 0.067 | 0.57 | NO |
35 | HIST1H3A | HIST1H3A | HIST1H3A | 5149 | 0.058 | 0.56 | NO |
36 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 5233 | 0.057 | 0.56 | NO |
37 | HIST1H4C | HIST1H4C | HIST1H4C | 5429 | 0.053 | 0.55 | NO |
38 | HIST1H4A | HIST1H4A | HIST1H4A | 5492 | 0.052 | 0.55 | NO |
39 | RAD51 | RAD51 | RAD51 | 5778 | 0.048 | 0.54 | NO |
40 | HIST1H4J | HIST1H4J | HIST1H4J | 5871 | 0.046 | 0.54 | NO |
41 | BRCA2 | BRCA2 | BRCA2 | 5918 | 0.045 | 0.54 | NO |
42 | BLM | BLM | BLM | 6051 | 0.043 | 0.54 | NO |
43 | HIST2H4A | HIST2H4A | HIST2H4A | 6074 | 0.043 | 0.54 | NO |
44 | H2AFX | H2AFX | H2AFX | 6177 | 0.041 | 0.54 | NO |
45 | MLH1 | MLH1 | MLH1 | 7129 | 0.026 | 0.49 | NO |
46 | H2AFZ | H2AFZ | H2AFZ | 7926 | 0.013 | 0.44 | NO |
47 | RPA2 | RPA2 | RPA2 | 8171 | 0.0092 | 0.43 | NO |
48 | MRE11A | MRE11A | MRE11A | 8381 | 0.0064 | 0.42 | NO |
49 | BRCA1 | BRCA1 | BRCA1 | 8613 | 0.0028 | 0.41 | NO |
50 | MLH3 | MLH3 | MLH3 | 9031 | -0.0032 | 0.38 | NO |
51 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 9110 | -0.0042 | 0.38 | NO |
52 | CDK4 | CDK4 | CDK4 | 9260 | -0.0063 | 0.37 | NO |
53 | H3F3A | H3F3A | H3F3A | 9617 | -0.012 | 0.35 | NO |
54 | NBN | NBN | NBN | 10415 | -0.024 | 0.31 | NO |
55 | RPA1 | RPA1 | RPA1 | 10805 | -0.03 | 0.29 | NO |
56 | TOP3A | TOP3A | TOP3A | 11524 | -0.043 | 0.26 | NO |
57 | ATM | ATM | ATM | 11637 | -0.045 | 0.25 | NO |
58 | CDK2 | CDK2 | CDK2 | 11937 | -0.05 | 0.24 | NO |
59 | H3F3B | H3F3B | H3F3B | 12513 | -0.062 | 0.21 | NO |
60 | HIST1H3B | HIST1H3B | HIST1H3B | 12723 | -0.066 | 0.21 | NO |
61 | HIST1H3C | HIST1H3C | HIST1H3C | 13286 | -0.08 | 0.18 | NO |
62 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 14284 | -0.11 | 0.14 | NO |
63 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 15117 | -0.15 | 0.1 | NO |
64 | RAD51C | RAD51C | RAD51C | 15118 | -0.15 | 0.12 | NO |
65 | MSH5 | MSH5 | MSH5 | 15370 | -0.16 | 0.12 | NO |
66 | HIST1H3J | HIST1H3J | HIST1H3J | 16167 | -0.21 | 0.093 | NO |
Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME RNA POL I TRANSCRIPTION.

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

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 | AR | AR | AR | 119 | 0.54 | 0.0088 | YES |
2 | ZNF483 | ZNF483 | ZNF483 | 151 | 0.51 | 0.022 | YES |
3 | RORB | RORB | RORB | 249 | 0.46 | 0.029 | YES |
4 | ZNF221 | ZNF221 | ZNF221 | 251 | 0.45 | 0.042 | YES |
5 | NR4A2 | NR4A2 | NR4A2 | 255 | 0.45 | 0.055 | YES |
6 | ZNF154 | ZNF154 | ZNF154 | 362 | 0.4 | 0.06 | YES |
7 | ZNF540 | ZNF540 | ZNF540 | 388 | 0.39 | 0.07 | YES |
8 | NR4A3 | NR4A3 | NR4A3 | 389 | 0.39 | 0.081 | YES |
9 | ZNF439 | ZNF439 | ZNF439 | 523 | 0.34 | 0.083 | YES |
10 | ZNF418 | ZNF418 | ZNF418 | 538 | 0.34 | 0.092 | YES |
11 | NR4A1 | NR4A1 | NR4A1 | 586 | 0.33 | 0.099 | YES |
12 | ZNF208 | ZNF208 | ZNF208 | 637 | 0.32 | 0.1 | YES |
13 | ZNF311 | ZNF311 | ZNF311 | 686 | 0.3 | 0.11 | YES |
14 | MAMLD1 | MAMLD1 | MAMLD1 | 698 | 0.3 | 0.12 | YES |
15 | ZIM2 | ZIM2 | ZIM2 | 813 | 0.28 | 0.12 | YES |
16 | ZNF492 | ZNF492 | ZNF492 | 814 | 0.28 | 0.13 | YES |
17 | ZNF331 | ZNF331 | ZNF331 | 833 | 0.28 | 0.14 | YES |
18 | NR2E3 | NR2E3 | NR2E3 | 836 | 0.28 | 0.14 | YES |
19 | ZNF620 | ZNF620 | ZNF620 | 957 | 0.26 | 0.14 | YES |
20 | ZNF285 | ZNF285 | ZNF285 | 1006 | 0.26 | 0.15 | YES |
21 | ZNF334 | ZNF334 | ZNF334 | 1011 | 0.25 | 0.16 | YES |
22 | ZNF167 | ZNF167 | ZNF167 | 1033 | 0.25 | 0.16 | YES |
23 | NR5A2 | NR5A2 | NR5A2 | 1038 | 0.25 | 0.17 | YES |
24 | VDR | VDR | VDR | 1045 | 0.25 | 0.18 | YES |
25 | ZNF547 | ZNF547 | ZNF547 | 1090 | 0.24 | 0.18 | YES |
26 | ZNF563 | ZNF563 | ZNF563 | 1105 | 0.24 | 0.19 | YES |
27 | NPPA | NPPA | NPPA | 1153 | 0.24 | 0.19 | YES |
28 | ZNF98 | ZNF98 | ZNF98 | 1241 | 0.23 | 0.19 | YES |
29 | ZNF10 | ZNF10 | ZNF10 | 1283 | 0.22 | 0.2 | YES |
30 | ZNF610 | ZNF610 | ZNF610 | 1327 | 0.22 | 0.2 | YES |
31 | ZNF19 | ZNF19 | ZNF19 | 1343 | 0.22 | 0.2 | YES |
32 | ZIK1 | ZIK1 | ZIK1 | 1451 | 0.21 | 0.2 | YES |
33 | ZNF442 | ZNF442 | ZNF442 | 1462 | 0.21 | 0.21 | YES |
34 | ZNF493 | ZNF493 | ZNF493 | 1531 | 0.2 | 0.21 | YES |
35 | ZNF546 | ZNF546 | ZNF546 | 1540 | 0.2 | 0.22 | YES |
36 | ZNF658 | ZNF658 | ZNF658 | 1546 | 0.2 | 0.22 | YES |
37 | ZNF256 | ZNF256 | ZNF256 | 1587 | 0.2 | 0.22 | YES |
38 | ZNF169 | ZNF169 | ZNF169 | 1730 | 0.18 | 0.22 | YES |
39 | ESRRB | ESRRB | ESRRB | 1746 | 0.18 | 0.23 | YES |
40 | ZNF530 | ZNF530 | ZNF530 | 1810 | 0.18 | 0.23 | YES |
41 | ZNF582 | ZNF582 | ZNF582 | 1818 | 0.18 | 0.23 | YES |
42 | MAML3 | MAML3 | MAML3 | 1831 | 0.18 | 0.24 | YES |
43 | ZNF597 | ZNF597 | ZNF597 | 1839 | 0.18 | 0.24 | YES |
44 | ZNF619 | ZNF619 | ZNF619 | 1937 | 0.17 | 0.24 | YES |
45 | ZNF274 | ZNF274 | ZNF274 | 1943 | 0.17 | 0.25 | YES |
46 | ZNF226 | ZNF226 | ZNF226 | 2020 | 0.16 | 0.25 | YES |
47 | ZNF551 | ZNF551 | ZNF551 | 2057 | 0.16 | 0.25 | YES |
48 | ZNF141 | ZNF141 | ZNF141 | 2067 | 0.16 | 0.25 | YES |
49 | ZNF43 | ZNF43 | ZNF43 | 2164 | 0.15 | 0.25 | YES |
50 | ZNF510 | ZNF510 | ZNF510 | 2265 | 0.15 | 0.25 | YES |
51 | ZNF431 | ZNF431 | ZNF431 | 2280 | 0.15 | 0.25 | YES |
52 | ZNF354B | ZNF354B | ZNF354B | 2346 | 0.14 | 0.25 | YES |
53 | ZNF23 | ZNF23 | ZNF23 | 2367 | 0.14 | 0.26 | YES |
54 | ZNF585B | ZNF585B | ZNF585B | 2378 | 0.14 | 0.26 | YES |
55 | ZNF528 | ZNF528 | ZNF528 | 2405 | 0.14 | 0.26 | YES |
56 | ZNF224 | ZNF224 | ZNF224 | 2413 | 0.14 | 0.27 | YES |
57 | THRB | THRB | THRB | 2419 | 0.14 | 0.27 | YES |
58 | ZNF417 | ZNF417 | ZNF417 | 2430 | 0.14 | 0.27 | YES |
59 | ZNF571 | ZNF571 | ZNF571 | 2443 | 0.14 | 0.28 | YES |
60 | ZNF197 | ZNF197 | ZNF197 | 2455 | 0.14 | 0.28 | YES |
61 | ZNF304 | ZNF304 | ZNF304 | 2501 | 0.14 | 0.28 | YES |
62 | ZNF441 | ZNF441 | ZNF441 | 2536 | 0.13 | 0.28 | YES |
63 | ZNF223 | ZNF223 | ZNF223 | 2539 | 0.13 | 0.29 | YES |
64 | ZNF101 | ZNF101 | ZNF101 | 2617 | 0.13 | 0.29 | YES |
65 | SKIL | SKIL | SKIL | 2644 | 0.13 | 0.29 | YES |
66 | ZNF138 | ZNF138 | ZNF138 | 2711 | 0.13 | 0.29 | YES |
67 | PPARG | PPARG | PPARG | 2717 | 0.13 | 0.29 | YES |
68 | ZNF157 | ZNF157 | ZNF157 | 2744 | 0.12 | 0.29 | YES |
69 | NR3C1 | NR3C1 | NR3C1 | 2747 | 0.12 | 0.3 | YES |
70 | NR1D2 | NR1D2 | NR1D2 | 2752 | 0.12 | 0.3 | YES |
71 | ZNF440 | ZNF440 | ZNF440 | 2785 | 0.12 | 0.3 | YES |
72 | CDK9 | CDK9 | CDK9 | 2786 | 0.12 | 0.31 | YES |
73 | SMAD3 | SMAD3 | SMAD3 | 2810 | 0.12 | 0.31 | YES |
74 | ZNF155 | ZNF155 | ZNF155 | 2848 | 0.12 | 0.31 | YES |
75 | ZNF14 | ZNF14 | ZNF14 | 2861 | 0.12 | 0.31 | YES |
76 | ZNF548 | ZNF548 | ZNF548 | 2988 | 0.11 | 0.31 | YES |
77 | CCNT1 | CCNT1 | CCNT1 | 2990 | 0.11 | 0.31 | YES |
78 | ZNF606 | ZNF606 | ZNF606 | 2991 | 0.11 | 0.32 | YES |
79 | MED7 | MED7 | MED7 | 3003 | 0.11 | 0.32 | YES |
80 | ZNF426 | ZNF426 | ZNF426 | 3024 | 0.11 | 0.32 | YES |
81 | ZNF471 | ZNF471 | ZNF471 | 3051 | 0.11 | 0.32 | YES |
82 | ZNF708 | ZNF708 | ZNF708 | 3055 | 0.11 | 0.32 | YES |
83 | ZNF566 | ZNF566 | ZNF566 | 3119 | 0.11 | 0.32 | YES |
84 | ZNF394 | ZNF394 | ZNF394 | 3142 | 0.11 | 0.33 | YES |
85 | ZNF420 | ZNF420 | ZNF420 | 3166 | 0.11 | 0.33 | YES |
86 | ZNF595 | ZNF595 | ZNF595 | 3196 | 0.11 | 0.33 | YES |
87 | PPM1A | PPM1A | PPM1A | 3234 | 0.1 | 0.33 | YES |
88 | ZNF627 | ZNF627 | ZNF627 | 3244 | 0.1 | 0.33 | YES |
89 | ZNF589 | ZNF589 | ZNF589 | 3251 | 0.1 | 0.34 | YES |
90 | PPARD | PPARD | PPARD | 3262 | 0.1 | 0.34 | YES |
91 | ZNF136 | ZNF136 | ZNF136 | 3365 | 0.1 | 0.33 | YES |
92 | ZNF773 | ZNF773 | ZNF773 | 3432 | 0.099 | 0.33 | YES |
93 | ZNF230 | ZNF230 | ZNF230 | 3442 | 0.099 | 0.34 | YES |
94 | ZNF227 | ZNF227 | ZNF227 | 3464 | 0.098 | 0.34 | YES |
95 | ZNF354A | ZNF354A | ZNF354A | 3500 | 0.097 | 0.34 | YES |
96 | NR3C2 | NR3C2 | NR3C2 | 3542 | 0.096 | 0.34 | YES |
97 | ZNF484 | ZNF484 | ZNF484 | 3550 | 0.096 | 0.34 | YES |
98 | ZNF184 | ZNF184 | ZNF184 | 3579 | 0.095 | 0.34 | YES |
99 | MED27 | MED27 | MED27 | 3617 | 0.094 | 0.34 | YES |
100 | ZNF189 | ZNF189 | ZNF189 | 3629 | 0.094 | 0.34 | YES |
101 | ZNF100 | ZNF100 | ZNF100 | 3659 | 0.093 | 0.34 | YES |
102 | ZNF266 | ZNF266 | ZNF266 | 3681 | 0.092 | 0.35 | YES |
103 | ZNF506 | ZNF506 | ZNF506 | 3683 | 0.092 | 0.35 | YES |
104 | NR6A1 | NR6A1 | NR6A1 | 3692 | 0.092 | 0.35 | YES |
105 | ZNF92 | ZNF92 | ZNF92 | 3774 | 0.09 | 0.35 | YES |
106 | ZNF544 | ZNF544 | ZNF544 | 3801 | 0.089 | 0.35 | YES |
107 | ZNF621 | ZNF621 | ZNF621 | 3938 | 0.085 | 0.34 | YES |
108 | ZNF587 | ZNF587 | ZNF587 | 3976 | 0.084 | 0.35 | YES |
109 | RORA | RORA | RORA | 3982 | 0.084 | 0.35 | YES |
110 | ZNF45 | ZNF45 | ZNF45 | 4010 | 0.083 | 0.35 | YES |
111 | ZNF570 | ZNF570 | ZNF570 | 4021 | 0.083 | 0.35 | YES |
112 | ZNF596 | ZNF596 | ZNF596 | 4040 | 0.082 | 0.35 | YES |
113 | ZNF254 | ZNF254 | ZNF254 | 4108 | 0.08 | 0.35 | YES |
114 | ZNF616 | ZNF616 | ZNF616 | 4196 | 0.078 | 0.35 | YES |
115 | ZNF543 | ZNF543 | ZNF543 | 4214 | 0.078 | 0.35 | YES |
116 | ZNF607 | ZNF607 | ZNF607 | 4242 | 0.077 | 0.35 | YES |
117 | RBPJ | RBPJ | RBPJ | 4251 | 0.077 | 0.35 | YES |
118 | ZNF234 | ZNF234 | ZNF234 | 4254 | 0.077 | 0.35 | YES |
119 | ZNF500 | ZNF500 | ZNF500 | 4260 | 0.077 | 0.36 | YES |
120 | NR1H2 | NR1H2 | NR1H2 | 4310 | 0.076 | 0.36 | YES |
121 | ZNF443 | ZNF443 | ZNF443 | 4331 | 0.075 | 0.36 | YES |
122 | ZNF557 | ZNF557 | ZNF557 | 4332 | 0.075 | 0.36 | YES |
123 | ZNF350 | ZNF350 | ZNF350 | 4347 | 0.075 | 0.36 | YES |
124 | ZNF211 | ZNF211 | ZNF211 | 4363 | 0.075 | 0.36 | YES |
125 | TGIF1 | TGIF1 | TGIF1 | 4412 | 0.074 | 0.36 | YES |
126 | ZNF212 | ZNF212 | ZNF212 | 4425 | 0.074 | 0.36 | YES |
127 | ZNF485 | ZNF485 | ZNF485 | 4444 | 0.073 | 0.36 | YES |
128 | ZNF446 | ZNF446 | ZNF446 | 4471 | 0.072 | 0.36 | YES |
129 | MED10 | MED10 | MED10 | 4522 | 0.071 | 0.36 | YES |
130 | ZNF564 | ZNF564 | ZNF564 | 4535 | 0.071 | 0.36 | YES |
131 | ZNF419 | ZNF419 | ZNF419 | 4576 | 0.07 | 0.36 | YES |
132 | KAT2B | KAT2B | KAT2B | 4611 | 0.069 | 0.36 | YES |
133 | ZNF287 | ZNF287 | ZNF287 | 4616 | 0.069 | 0.36 | YES |
134 | ZNF565 | ZNF565 | ZNF565 | 4740 | 0.066 | 0.36 | YES |
135 | ZNF17 | ZNF17 | ZNF17 | 4782 | 0.066 | 0.36 | YES |
136 | NOTCH4 | NOTCH4 | NOTCH4 | 4797 | 0.066 | 0.36 | YES |
137 | MED6 | MED6 | MED6 | 4811 | 0.066 | 0.36 | YES |
138 | ZNF561 | ZNF561 | ZNF561 | 4831 | 0.065 | 0.36 | YES |
139 | ZNF445 | ZNF445 | ZNF445 | 4843 | 0.065 | 0.36 | YES |
140 | ZNF347 | ZNF347 | ZNF347 | 4862 | 0.064 | 0.36 | YES |
141 | NCOR2 | NCOR2 | NCOR2 | 4871 | 0.064 | 0.37 | YES |
142 | ZNF416 | ZNF416 | ZNF416 | 4907 | 0.064 | 0.36 | NO |
143 | ZNF613 | ZNF613 | ZNF613 | 4987 | 0.062 | 0.36 | NO |
144 | ZNF641 | ZNF641 | ZNF641 | 5038 | 0.061 | 0.36 | NO |
145 | RARG | RARG | RARG | 5043 | 0.061 | 0.36 | NO |
146 | ZNF317 | ZNF317 | ZNF317 | 5117 | 0.059 | 0.36 | NO |
147 | ZNF490 | ZNF490 | ZNF490 | 5135 | 0.059 | 0.36 | NO |
148 | MAML1 | MAML1 | MAML1 | 5191 | 0.058 | 0.36 | NO |
149 | RORC | RORC | RORC | 5315 | 0.056 | 0.35 | NO |
150 | TEAD1 | TEAD1 | TEAD1 | 5352 | 0.055 | 0.35 | NO |
151 | ZFP2 | ZFP2 | ZFP2 | 5359 | 0.055 | 0.36 | NO |
152 | TRIM28 | TRIM28 | TRIM28 | 5394 | 0.054 | 0.36 | NO |
153 | ZNF37A | ZNF37A | ZNF37A | 5407 | 0.054 | 0.36 | NO |
154 | ZNF337 | ZNF337 | ZNF337 | 5415 | 0.054 | 0.36 | NO |
155 | ZNF222 | ZNF222 | ZNF222 | 5428 | 0.053 | 0.36 | NO |
156 | ZNF320 | ZNF320 | ZNF320 | 5495 | 0.052 | 0.36 | NO |
157 | ZNF175 | ZNF175 | ZNF175 | 5553 | 0.051 | 0.35 | NO |
158 | ZNF3 | ZNF3 | ZNF3 | 5671 | 0.049 | 0.35 | NO |
159 | ZNF263 | ZNF263 | ZNF263 | 5718 | 0.048 | 0.35 | NO |
160 | ZKSCAN1 | ZKSCAN1 | ZKSCAN1 | 5735 | 0.048 | 0.35 | NO |
161 | ZNF577 | ZNF577 | ZNF577 | 5748 | 0.048 | 0.35 | NO |
162 | NR2C2AP | NR2C2AP | NR2C2AP | 5766 | 0.048 | 0.35 | NO |
163 | ZNF433 | ZNF433 | ZNF433 | 5792 | 0.048 | 0.35 | NO |
164 | NR1D1 | NR1D1 | NR1D1 | 5801 | 0.047 | 0.35 | NO |
165 | ZNF585A | ZNF585A | ZNF585A | 5843 | 0.047 | 0.35 | NO |
166 | ZFP28 | ZFP28 | ZFP28 | 5875 | 0.046 | 0.35 | NO |
167 | NR1I2 | NR1I2 | NR1I2 | 5963 | 0.045 | 0.34 | NO |
168 | ZFP112 | ZFP112 | ZFP112 | 6027 | 0.044 | 0.34 | NO |
169 | E2F4 | E2F4 | E2F4 | 6029 | 0.044 | 0.34 | NO |
170 | ZFP1 | ZFP1 | ZFP1 | 6044 | 0.043 | 0.34 | NO |
171 | ZNF213 | ZNF213 | ZNF213 | 6065 | 0.043 | 0.34 | NO |
172 | ZNF225 | ZNF225 | ZNF225 | 6119 | 0.042 | 0.34 | NO |
173 | ZNF192 | ZNF192 | ZNF192 | 6131 | 0.042 | 0.34 | NO |
174 | ZNF605 | ZNF605 | ZNF605 | 6141 | 0.042 | 0.34 | NO |
175 | ZNF583 | ZNF583 | ZNF583 | 6181 | 0.041 | 0.34 | NO |
176 | ZNF558 | ZNF558 | ZNF558 | 6209 | 0.04 | 0.34 | NO |
177 | ZNF614 | ZNF614 | ZNF614 | 6272 | 0.039 | 0.34 | NO |
178 | ZNF430 | ZNF430 | ZNF430 | 6388 | 0.038 | 0.33 | NO |
179 | ZNF415 | ZNF415 | ZNF415 | 6398 | 0.037 | 0.33 | NO |
180 | ZNF559 | ZNF559 | ZNF559 | 6399 | 0.037 | 0.34 | NO |
181 | RXRA | RXRA | RXRA | 6419 | 0.037 | 0.34 | NO |
182 | ZNF552 | ZNF552 | ZNF552 | 6538 | 0.035 | 0.33 | NO |
183 | ZNF160 | ZNF160 | ZNF160 | 6550 | 0.035 | 0.33 | NO |
184 | ZKSCAN5 | ZKSCAN5 | ZKSCAN5 | 6596 | 0.034 | 0.33 | NO |
185 | ZNF611 | ZNF611 | ZNF611 | 6701 | 0.032 | 0.32 | NO |
186 | UBE2D3 | UBE2D3 | UBE2D3 | 6759 | 0.032 | 0.32 | NO |
187 | ZNF398 | ZNF398 | ZNF398 | 6865 | 0.03 | 0.32 | NO |
188 | TBL1X | TBL1X | TBL1X | 6937 | 0.029 | 0.31 | NO |
189 | ZNF333 | ZNF333 | ZNF333 | 6946 | 0.029 | 0.31 | NO |
190 | HNF4A | HNF4A | HNF4A | 6992 | 0.028 | 0.31 | NO |
191 | ZNF33A | ZNF33A | ZNF33A | 7025 | 0.027 | 0.31 | NO |
192 | THRA | THRA | THRA | 7143 | 0.025 | 0.3 | NO |
193 | ZNF20 | ZNF20 | ZNF20 | 7158 | 0.025 | 0.3 | NO |
194 | ZNF600 | ZNF600 | ZNF600 | 7216 | 0.024 | 0.3 | NO |
195 | ZNF514 | ZNF514 | ZNF514 | 7226 | 0.024 | 0.3 | NO |
196 | SMAD2 | SMAD2 | SMAD2 | 7237 | 0.024 | 0.3 | NO |
197 | CDKN2B | CDKN2B | CDKN2B | 7283 | 0.023 | 0.3 | NO |
198 | UBA52 | UBA52 | UBA52 | 7294 | 0.023 | 0.3 | NO |
199 | ZNF140 | ZNF140 | ZNF140 | 7333 | 0.022 | 0.3 | NO |
200 | ZNF273 | ZNF273 | ZNF273 | 7422 | 0.021 | 0.29 | NO |
201 | CCNT2 | CCNT2 | CCNT2 | 7438 | 0.021 | 0.29 | NO |
202 | ZNF480 | ZNF480 | ZNF480 | 7474 | 0.02 | 0.29 | NO |
203 | ZNF26 | ZNF26 | ZNF26 | 7512 | 0.02 | 0.29 | NO |
204 | ZKSCAN4 | ZKSCAN4 | ZKSCAN4 | 7542 | 0.019 | 0.29 | NO |
205 | ZNF382 | ZNF382 | ZNF382 | 7567 | 0.019 | 0.29 | NO |
206 | ZNF180 | ZNF180 | ZNF180 | 7591 | 0.018 | 0.29 | NO |
207 | ZNF569 | ZNF569 | ZNF569 | 7600 | 0.018 | 0.29 | NO |
208 | SMAD4 | SMAD4 | SMAD4 | 7605 | 0.018 | 0.29 | NO |
209 | JUNB | JUNB | JUNB | 7635 | 0.018 | 0.29 | NO |
210 | ZNF12 | ZNF12 | ZNF12 | 7667 | 0.017 | 0.29 | NO |
211 | NR2F6 | NR2F6 | NR2F6 | 7738 | 0.016 | 0.28 | NO |
212 | ZNF460 | ZNF460 | ZNF460 | 7761 | 0.016 | 0.28 | NO |
213 | ZNF567 | ZNF567 | ZNF567 | 7844 | 0.014 | 0.28 | NO |
214 | CREBBP | CREBBP | CREBBP | 7907 | 0.013 | 0.27 | NO |
215 | ZNF205 | ZNF205 | ZNF205 | 7909 | 0.013 | 0.27 | NO |
216 | ZNF28 | ZNF28 | ZNF28 | 7955 | 0.013 | 0.27 | NO |
217 | MED16 | MED16 | MED16 | 7987 | 0.012 | 0.27 | NO |
218 | PPARA | PPARA | PPARA | 8018 | 0.012 | 0.27 | NO |
219 | ZNF529 | ZNF529 | ZNF529 | 8083 | 0.01 | 0.27 | NO |
220 | MED15 | MED15 | MED15 | 8107 | 0.01 | 0.26 | NO |
221 | ZNF383 | ZNF383 | ZNF383 | 8115 | 0.01 | 0.26 | NO |
222 | ZNF324 | ZNF324 | ZNF324 | 8192 | 0.0089 | 0.26 | NO |
223 | ZNF434 | ZNF434 | ZNF434 | 8229 | 0.0084 | 0.26 | NO |
224 | ZNF498 | ZNF498 | ZNF498 | 8384 | 0.0064 | 0.25 | NO |
225 | ZNF649 | ZNF649 | ZNF649 | 8414 | 0.0058 | 0.25 | NO |
226 | ZNF432 | ZNF432 | ZNF432 | 8431 | 0.0056 | 0.25 | NO |
227 | MED12 | MED12 | MED12 | 8541 | 0.0038 | 0.24 | NO |
228 | MED25 | MED25 | MED25 | 8629 | 0.0025 | 0.24 | NO |
229 | MED14 | MED14 | MED14 | 8672 | 0.0018 | 0.24 | NO |
230 | ZNF615 | ZNF615 | ZNF615 | 8819 | -0.00038 | 0.23 | NO |
231 | WWTR1 | WWTR1 | WWTR1 | 8870 | -0.00094 | 0.22 | NO |
232 | USP9X | USP9X | USP9X | 8922 | -0.0017 | 0.22 | NO |
233 | ZNF584 | ZNF584 | ZNF584 | 8992 | -0.0027 | 0.22 | NO |
234 | MEN1 | MEN1 | MEN1 | 9003 | -0.0029 | 0.22 | NO |
235 | ZNF655 | ZNF655 | ZNF655 | 9013 | -0.003 | 0.22 | NO |
236 | ZNF282 | ZNF282 | ZNF282 | 9045 | -0.0033 | 0.21 | NO |
237 | NCOA3 | NCOA3 | NCOA3 | 9118 | -0.0044 | 0.21 | NO |
238 | ZNF468 | ZNF468 | ZNF468 | 9135 | -0.0046 | 0.21 | NO |
239 | MED23 | MED23 | MED23 | 9195 | -0.0053 | 0.21 | NO |
240 | ZNF235 | ZNF235 | ZNF235 | 9206 | -0.0055 | 0.21 | NO |
241 | NOTCH3 | NOTCH3 | NOTCH3 | 9264 | -0.0064 | 0.2 | NO |
242 | ZNF264 | ZNF264 | ZNF264 | 9341 | -0.0076 | 0.2 | NO |
243 | TRIM33 | TRIM33 | TRIM33 | 9502 | -0.01 | 0.19 | NO |
244 | MED4 | MED4 | MED4 | 9583 | -0.011 | 0.18 | NO |
245 | SP1 | SP1 | SP1 | 9635 | -0.012 | 0.18 | NO |
246 | SNW1 | SNW1 | SNW1 | 9783 | -0.014 | 0.18 | NO |
247 | E2F5 | E2F5 | E2F5 | 9886 | -0.016 | 0.17 | NO |
248 | ZNF425 | ZNF425 | ZNF425 | 9934 | -0.016 | 0.17 | NO |
249 | NCOA6 | NCOA6 | NCOA6 | 9964 | -0.017 | 0.17 | NO |
250 | CCNC | CCNC | CCNC | 9984 | -0.017 | 0.16 | NO |
251 | ZNF599 | ZNF599 | ZNF599 | 9996 | -0.017 | 0.16 | NO |
252 | ZNF200 | ZNF200 | ZNF200 | 10042 | -0.018 | 0.16 | NO |
253 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 10049 | -0.018 | 0.16 | NO |
254 | NCOA2 | NCOA2 | NCOA2 | 10104 | -0.019 | 0.16 | NO |
255 | KAT2A | KAT2A | KAT2A | 10121 | -0.02 | 0.16 | NO |
256 | YAP1 | YAP1 | YAP1 | 10179 | -0.02 | 0.16 | NO |
257 | MED26 | MED26 | MED26 | 10190 | -0.021 | 0.16 | NO |
258 | ZNF250 | ZNF250 | ZNF250 | 10191 | -0.021 | 0.16 | NO |
259 | ESRRA | ESRRA | ESRRA | 10292 | -0.022 | 0.15 | NO |
260 | HDAC1 | HDAC1 | HDAC1 | 10502 | -0.025 | 0.14 | NO |
261 | ZFP90 | ZFP90 | ZFP90 | 10601 | -0.027 | 0.14 | NO |
262 | TGS1 | TGS1 | TGS1 | 10750 | -0.029 | 0.13 | NO |
263 | MED31 | MED31 | MED31 | 10761 | -0.03 | 0.13 | NO |
264 | TFDP1 | TFDP1 | TFDP1 | 10764 | -0.03 | 0.13 | NO |
265 | RXRB | RXRB | RXRB | 10959 | -0.032 | 0.12 | NO |
266 | ZNF33B | ZNF33B | ZNF33B | 11015 | -0.034 | 0.12 | NO |
267 | ZNF114 | ZNF114 | ZNF114 | 11184 | -0.037 | 0.11 | NO |
268 | NRBF2 | NRBF2 | NRBF2 | 11214 | -0.037 | 0.11 | NO |
269 | ZNF248 | ZNF248 | ZNF248 | 11235 | -0.038 | 0.11 | NO |
270 | ZNF18 | ZNF18 | ZNF18 | 11350 | -0.04 | 0.1 | NO |
271 | ZNF343 | ZNF343 | ZNF343 | 11373 | -0.04 | 0.1 | NO |
272 | ZNF624 | ZNF624 | ZNF624 | 11378 | -0.04 | 0.1 | NO |
273 | NR1H3 | NR1H3 | NR1H3 | 11418 | -0.041 | 0.1 | NO |
274 | MED24 | MED24 | MED24 | 11439 | -0.041 | 0.1 | NO |
275 | SMARCD3 | SMARCD3 | SMARCD3 | 11564 | -0.043 | 0.098 | NO |
276 | MED1 | MED1 | MED1 | 11692 | -0.046 | 0.092 | NO |
277 | ESR1 | ESR1 | ESR1 | 11851 | -0.048 | 0.084 | NO |
278 | ZNF202 | ZNF202 | ZNF202 | 11882 | -0.049 | 0.084 | NO |
279 | ZNF496 | ZNF496 | ZNF496 | 11891 | -0.049 | 0.085 | NO |
280 | SKI | SKI | SKI | 11978 | -0.051 | 0.081 | NO |
281 | MED17 | MED17 | MED17 | 12012 | -0.051 | 0.081 | NO |
282 | ZNF267 | ZNF267 | ZNF267 | 12100 | -0.053 | 0.077 | NO |
283 | NCOR1 | NCOR1 | NCOR1 | 12174 | -0.054 | 0.075 | NO |
284 | NCOA1 | NCOA1 | NCOA1 | 12346 | -0.058 | 0.067 | NO |
285 | RPS27A | RPS27A | RPS27A | 12398 | -0.059 | 0.065 | NO |
286 | ZNF560 | ZNF560 | ZNF560 | 12591 | -0.063 | 0.056 | NO |
287 | RARA | RARA | RARA | 12675 | -0.065 | 0.053 | NO |
288 | PRIC285 | PRIC285 | PRIC285 | 12786 | -0.068 | 0.049 | NO |
289 | MED8 | MED8 | MED8 | 13077 | -0.075 | 0.035 | NO |
290 | ZNF555 | ZNF555 | ZNF555 | 13100 | -0.076 | 0.036 | NO |
291 | NRBP1 | NRBP1 | NRBP1 | 13161 | -0.077 | 0.034 | NO |
292 | RBL1 | RBL1 | RBL1 | 13274 | -0.08 | 0.03 | NO |
293 | ZNF454 | ZNF454 | ZNF454 | 13287 | -0.08 | 0.032 | NO |
294 | ZNF354C | ZNF354C | ZNF354C | 13322 | -0.081 | 0.032 | NO |
295 | ZNF436 | ZNF436 | ZNF436 | 13392 | -0.082 | 0.03 | NO |
296 | ZNF214 | ZNF214 | ZNF214 | 13478 | -0.085 | 0.028 | NO |
297 | MYC | MYC | MYC | 13518 | -0.086 | 0.028 | NO |
298 | ZNF473 | ZNF473 | ZNF473 | 13539 | -0.086 | 0.03 | NO |
299 | ZNF556 | ZNF556 | ZNF556 | 13579 | -0.087 | 0.03 | NO |
300 | SMAD7 | SMAD7 | SMAD7 | 13709 | -0.091 | 0.025 | NO |
301 | MED30 | MED30 | MED30 | 13727 | -0.091 | 0.027 | NO |
302 | MED20 | MED20 | MED20 | 13867 | -0.096 | 0.022 | NO |
303 | PARP1 | PARP1 | PARP1 | 13955 | -0.098 | 0.019 | NO |
304 | ZNF625 | ZNF625 | ZNF625 | 13962 | -0.098 | 0.022 | NO |
305 | ZNF517 | ZNF517 | ZNF517 | 13989 | -0.099 | 0.023 | NO |
306 | CTGF | CTGF | CTGF | 14004 | -0.099 | 0.025 | NO |
307 | CDK8 | CDK8 | CDK8 | 14031 | -0.1 | 0.027 | NO |
308 | MAML2 | MAML2 | MAML2 | 14107 | -0.1 | 0.025 | NO |
309 | NR0B2 | NR0B2 | NR0B2 | 14179 | -0.1 | 0.024 | NO |
310 | TGIF2 | TGIF2 | TGIF2 | 14501 | -0.12 | 0.0092 | NO |
311 | ZKSCAN3 | ZKSCAN3 | ZKSCAN3 | 14530 | -0.12 | 0.011 | NO |
312 | ZNF2 | ZNF2 | ZNF2 | 14585 | -0.12 | 0.011 | NO |
313 | ZNF286A | ZNF286A | ZNF286A | 14781 | -0.13 | 0.0039 | NO |
314 | ZFP37 | ZFP37 | ZFP37 | 14867 | -0.13 | 0.0029 | NO |
315 | SMURF2 | SMURF2 | SMURF2 | 14884 | -0.14 | 0.0058 | NO |
316 | ESR2 | ESR2 | ESR2 | 14913 | -0.14 | 0.0081 | NO |
317 | ZNF25 | ZNF25 | ZNF25 | 15044 | -0.14 | 0.0048 | NO |
318 | TEAD2 | TEAD2 | TEAD2 | 15144 | -0.15 | 0.0033 | NO |
319 | ZNF642 | ZNF642 | ZNF642 | 15164 | -0.15 | 0.0065 | NO |
320 | UBE2D1 | UBE2D1 | UBE2D1 | 15291 | -0.16 | 0.0038 | NO |
321 | ESRRG | ESRRG | ESRRG | 15418 | -0.16 | 0.0012 | NO |
322 | NR2F1 | NR2F1 | NR2F1 | 15668 | -0.18 | -0.008 | NO |
323 | TEAD3 | TEAD3 | TEAD3 | 15889 | -0.19 | -0.015 | NO |
324 | ZNF300 | ZNF300 | ZNF300 | 15986 | -0.2 | -0.015 | NO |
325 | ZNF519 | ZNF519 | ZNF519 | 16150 | -0.21 | -0.018 | NO |
326 | ZNF215 | ZNF215 | ZNF215 | 16156 | -0.21 | -0.013 | NO |
327 | TEAD4 | TEAD4 | TEAD4 | 16483 | -0.24 | -0.024 | NO |
328 | ZNF30 | ZNF30 | ZNF30 | 16519 | -0.24 | -0.02 | NO |
329 | ZNF643 | ZNF643 | ZNF643 | 16788 | -0.26 | -0.027 | NO |
330 | SERPINE1 | SERPINE1 | SERPINE1 | 16978 | -0.29 | -0.03 | NO |
331 | NR1I3 | NR1I3 | NR1I3 | 17001 | -0.29 | -0.023 | NO |
332 | RUNX2 | RUNX2 | RUNX2 | 17072 | -0.3 | -0.018 | NO |
333 | NOTCH2 | NOTCH2 | NOTCH2 | 17290 | -0.34 | -0.021 | NO |
334 | HNF4G | HNF4G | HNF4G | 17362 | -0.36 | -0.014 | NO |
335 | NR0B1 | NR0B1 | NR0B1 | 17559 | -0.42 | -0.013 | NO |
336 | RXRG | RXRG | RXRG | 17627 | -0.46 | -0.0042 | NO |
337 | PGR | PGR | PGR | 17729 | -0.54 | 0.0054 | NO |
Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME GLUCONEOGENESIS.

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

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 | OR1N1 | OR1N1 | OR1N1 | 7 | 1 | 0.16 | YES |
2 | OR1L8 | OR1L8 | OR1L8 | 37 | 0.76 | 0.27 | YES |
3 | OR1N2 | OR1N2 | OR1N2 | 73 | 0.62 | 0.37 | YES |
4 | OR5B12 | OR5B12 | OR5B12 | 77 | 0.6 | 0.46 | YES |
5 | OR1B1 | OR1B1 | OR1B1 | 105 | 0.56 | 0.54 | YES |
6 | OR2A1 | OR2A1 | OR2A1 | 1159 | 0.24 | 0.52 | YES |
7 | OR1J1 | OR1J1 | OR1J1 | 1606 | 0.2 | 0.53 | YES |
8 | OR51E1 | OR51E1 | OR51E1 | 1842 | 0.18 | 0.54 | YES |
9 | OR2A5 | OR2A5 | OR2A5 | 2313 | 0.14 | 0.54 | YES |
10 | OR1J2 | OR1J2 | OR1J2 | 2438 | 0.14 | 0.55 | YES |
11 | GNGT1 | GNGT1 | GNGT1 | 2467 | 0.14 | 0.57 | YES |
12 | OR2A25 | OR2A25 | OR2A25 | 2529 | 0.13 | 0.59 | YES |
13 | OR7D2 | OR7D2 | OR7D2 | 2946 | 0.12 | 0.58 | YES |
14 | OR6T1 | OR6T1 | OR6T1 | 3222 | 0.11 | 0.58 | YES |
15 | OR2A4 | OR2A4 | OR2A4 | 3592 | 0.094 | 0.58 | YES |
16 | OR1Q1 | OR1Q1 | OR1Q1 | 3644 | 0.093 | 0.59 | YES |
17 | OR2A7 | OR2A7 | OR2A7 | 4156 | 0.079 | 0.57 | NO |
18 | OR2W3 | OR2W3 | OR2W3 | 4850 | 0.065 | 0.54 | NO |
19 | OR56B4 | OR56B4 | OR56B4 | 5956 | 0.045 | 0.49 | NO |
20 | OR3A2 | OR3A2 | OR3A2 | 7187 | 0.025 | 0.42 | NO |
21 | OR51E2 | OR51E2 | OR51E2 | 8167 | 0.0093 | 0.37 | NO |
22 | OR5K2 | OR5K2 | OR5K2 | 8869 | -0.00093 | 0.33 | NO |
23 | OR2A14 | OR2A14 | OR2A14 | 10457 | -0.024 | 0.24 | NO |
24 | OR10AD1 | OR10AD1 | OR10AD1 | 10523 | -0.026 | 0.24 | NO |
25 | OR2A2 | OR2A2 | OR2A2 | 10703 | -0.028 | 0.24 | NO |
26 | OR4F29 | OR4F29 | OR4F29 | 12210 | -0.055 | 0.16 | NO |
27 | OR2C1 | OR2C1 | OR2C1 | 12242 | -0.056 | 0.17 | NO |
28 | GNB1 | GNB1 | GNB1 | 13489 | -0.085 | 0.11 | NO |
29 | GNAL | GNAL | GNAL | 14479 | -0.12 | 0.074 | NO |
30 | OR52R1 | OR52R1 | OR52R1 | 15778 | -0.18 | 0.029 | NO |
31 | OR52N4 | OR52N4 | OR52N4 | 16650 | -0.25 | 0.019 | NO |
32 | OR51T1 | OR51T1 | OR51T1 | 17094 | -0.31 | 0.041 | NO |
Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME OLFACTORY SIGNALING PATHWAY.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME OLFACTORY SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | HIST1H3G | HIST1H3G | HIST1H3G | 79 | 0.59 | 0.042 | YES |
2 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 87 | 0.58 | 0.087 | YES |
3 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 276 | 0.44 | 0.11 | YES |
4 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 316 | 0.42 | 0.14 | YES |
5 | MND1 | MND1 | MND1 | 350 | 0.4 | 0.17 | YES |
6 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 408 | 0.38 | 0.2 | YES |
7 | TEX12 | TEX12 | TEX12 | 422 | 0.37 | 0.22 | YES |
8 | HIST4H4 | HIST4H4 | HIST4H4 | 472 | 0.35 | 0.25 | YES |
9 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 509 | 0.34 | 0.28 | YES |
10 | HIST1H3H | HIST1H3H | HIST1H3H | 564 | 0.33 | 0.3 | YES |
11 | HIST1H4E | HIST1H4E | HIST1H4E | 567 | 0.33 | 0.32 | YES |
12 | MSH4 | MSH4 | MSH4 | 599 | 0.32 | 0.35 | YES |
13 | HIST1H3E | HIST1H3E | HIST1H3E | 624 | 0.32 | 0.37 | YES |
14 | HIST1H4H | HIST1H4H | HIST1H4H | 653 | 0.31 | 0.39 | YES |
15 | HIST1H3D | HIST1H3D | HIST1H3D | 748 | 0.29 | 0.41 | YES |
16 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 769 | 0.29 | 0.43 | YES |
17 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 973 | 0.26 | 0.44 | YES |
18 | HIST2H3D | HIST2H3D | HIST2H3D | 1037 | 0.25 | 0.46 | YES |
19 | TEX15 | TEX15 | TEX15 | 1160 | 0.24 | 0.47 | YES |
20 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 1208 | 0.23 | 0.48 | YES |
21 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 1281 | 0.22 | 0.5 | YES |
22 | SYNE1 | SYNE1 | SYNE1 | 1358 | 0.22 | 0.51 | YES |
23 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 1359 | 0.22 | 0.53 | YES |
24 | HIST1H4D | HIST1H4D | HIST1H4D | 1379 | 0.21 | 0.54 | YES |
25 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 1386 | 0.21 | 0.56 | YES |
26 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 1490 | 0.2 | 0.57 | YES |
27 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1552 | 0.2 | 0.58 | YES |
28 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 1923 | 0.17 | 0.57 | YES |
29 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 1942 | 0.17 | 0.59 | YES |
30 | LMNB1 | LMNB1 | LMNB1 | 2242 | 0.15 | 0.58 | YES |
31 | HIST1H4B | HIST1H4B | HIST1H4B | 2312 | 0.14 | 0.59 | YES |
32 | HIST1H4I | HIST1H4I | HIST1H4I | 2488 | 0.14 | 0.59 | YES |
33 | RBBP8 | RBBP8 | RBBP8 | 2516 | 0.14 | 0.6 | YES |
34 | SMC1B | SMC1B | SMC1B | 3201 | 0.11 | 0.57 | NO |
35 | ATR | ATR | ATR | 3285 | 0.1 | 0.57 | NO |
36 | HIST2H3C | HIST2H3C | HIST2H3C | 3400 | 0.1 | 0.57 | NO |
37 | RAD50 | RAD50 | RAD50 | 3430 | 0.099 | 0.58 | NO |
38 | RPA3 | RPA3 | RPA3 | 3822 | 0.088 | 0.56 | NO |
39 | SUN2 | SUN2 | SUN2 | 4014 | 0.083 | 0.56 | NO |
40 | SYNE2 | SYNE2 | SYNE2 | 4438 | 0.073 | 0.54 | NO |
41 | DMC1 | DMC1 | DMC1 | 4715 | 0.067 | 0.53 | NO |
42 | STAG2 | STAG2 | STAG2 | 5127 | 0.059 | 0.51 | NO |
43 | HIST1H3A | HIST1H3A | HIST1H3A | 5149 | 0.058 | 0.52 | NO |
44 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 5233 | 0.057 | 0.52 | NO |
45 | DIDO1 | DIDO1 | DIDO1 | 5386 | 0.054 | 0.51 | NO |
46 | HIST1H4C | HIST1H4C | HIST1H4C | 5429 | 0.053 | 0.51 | NO |
47 | HIST1H4A | HIST1H4A | HIST1H4A | 5492 | 0.052 | 0.51 | NO |
48 | RAD51 | RAD51 | RAD51 | 5778 | 0.048 | 0.5 | NO |
49 | HIST1H4J | HIST1H4J | HIST1H4J | 5871 | 0.046 | 0.5 | NO |
50 | BRCA2 | BRCA2 | BRCA2 | 5918 | 0.045 | 0.5 | NO |
51 | BLM | BLM | BLM | 6051 | 0.043 | 0.5 | NO |
52 | HIST2H4A | HIST2H4A | HIST2H4A | 6074 | 0.043 | 0.5 | NO |
53 | H2AFX | H2AFX | H2AFX | 6177 | 0.041 | 0.5 | NO |
54 | SYCP2 | SYCP2 | SYCP2 | 6443 | 0.037 | 0.48 | NO |
55 | UBE2I | UBE2I | UBE2I | 6496 | 0.036 | 0.48 | NO |
56 | TERF2IP | TERF2IP | TERF2IP | 6561 | 0.035 | 0.48 | NO |
57 | STAG1 | STAG1 | STAG1 | 6663 | 0.033 | 0.48 | NO |
58 | MLH1 | MLH1 | MLH1 | 7129 | 0.026 | 0.46 | NO |
59 | TERF2 | TERF2 | TERF2 | 7733 | 0.016 | 0.42 | NO |
60 | H2AFZ | H2AFZ | H2AFZ | 7926 | 0.013 | 0.41 | NO |
61 | SMC1A | SMC1A | SMC1A | 7978 | 0.012 | 0.41 | NO |
62 | RPA2 | RPA2 | RPA2 | 8171 | 0.0092 | 0.4 | NO |
63 | MRE11A | MRE11A | MRE11A | 8381 | 0.0064 | 0.39 | NO |
64 | POT1 | POT1 | POT1 | 8565 | 0.0034 | 0.38 | NO |
65 | BRCA1 | BRCA1 | BRCA1 | 8613 | 0.0028 | 0.38 | NO |
66 | MLH3 | MLH3 | MLH3 | 9031 | -0.0032 | 0.35 | NO |
67 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 9110 | -0.0042 | 0.35 | NO |
68 | TINF2 | TINF2 | TINF2 | 9134 | -0.0046 | 0.35 | NO |
69 | CDK4 | CDK4 | CDK4 | 9260 | -0.0063 | 0.34 | NO |
70 | ACD | ACD | ACD | 9509 | -0.01 | 0.33 | NO |
71 | H3F3A | H3F3A | H3F3A | 9617 | -0.012 | 0.32 | NO |
72 | REC8 | REC8 | REC8 | 10081 | -0.019 | 0.3 | NO |
73 | NBN | NBN | NBN | 10415 | -0.024 | 0.28 | NO |
74 | RPA1 | RPA1 | RPA1 | 10805 | -0.03 | 0.26 | NO |
75 | TERF1 | TERF1 | TERF1 | 10934 | -0.032 | 0.26 | NO |
76 | RAD21 | RAD21 | RAD21 | 11252 | -0.038 | 0.24 | NO |
77 | TOP3A | TOP3A | TOP3A | 11524 | -0.043 | 0.23 | NO |
78 | ATM | ATM | ATM | 11637 | -0.045 | 0.23 | NO |
79 | CDK2 | CDK2 | CDK2 | 11937 | -0.05 | 0.22 | NO |
80 | LMNA | LMNA | LMNA | 11958 | -0.05 | 0.22 | NO |
81 | SMC3 | SMC3 | SMC3 | 12439 | -0.06 | 0.2 | NO |
82 | H3F3B | H3F3B | H3F3B | 12513 | -0.062 | 0.2 | NO |
83 | HIST1H3B | HIST1H3B | HIST1H3B | 12723 | -0.066 | 0.19 | NO |
84 | HIST1H3C | HIST1H3C | HIST1H3C | 13286 | -0.08 | 0.16 | NO |
85 | HSPA2 | HSPA2 | HSPA2 | 13462 | -0.084 | 0.16 | NO |
86 | STAG3 | STAG3 | STAG3 | 13723 | -0.091 | 0.15 | NO |
87 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 14284 | -0.11 | 0.13 | NO |
88 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 15117 | -0.15 | 0.096 | NO |
89 | RAD51C | RAD51C | RAD51C | 15118 | -0.15 | 0.11 | NO |
90 | MSH5 | MSH5 | MSH5 | 15370 | -0.16 | 0.11 | NO |
91 | FKBP6 | FKBP6 | FKBP6 | 16130 | -0.21 | 0.079 | NO |
92 | HIST1H3J | HIST1H3J | HIST1H3J | 16167 | -0.21 | 0.093 | NO |
Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANSCRIPTION.

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

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES | 26 | genes.ES.table | 0.52 | 1.4 | 0.03 | 1 | 0.99 | 0.31 | 0.1 | 0.28 | 1 | 0.92 |
KEGG ANTIGEN PROCESSING AND PRESENTATION | 67 | genes.ES.table | 0.56 | 1.4 | 0.16 | 1 | 1 | 0.4 | 0.19 | 0.33 | 1 | 0.89 |
KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY | 116 | genes.ES.table | 0.54 | 1.4 | 0.14 | 1 | 1 | 0.4 | 0.19 | 0.33 | 1 | 0.91 |
KEGG PATHOGENIC ESCHERICHIA COLI INFECTION | 50 | genes.ES.table | 0.39 | 1.3 | 0.13 | 1 | 1 | 0.14 | 0.11 | 0.12 | 1 | 0.86 |
KEGG NON SMALL CELL LUNG CANCER | 54 | genes.ES.table | 0.35 | 1.3 | 0.13 | 1 | 1 | 0.39 | 0.28 | 0.28 | 1 | 0.88 |
KEGG GRAFT VERSUS HOST DISEASE | 36 | genes.ES.table | 0.71 | 1.3 | 0.16 | 1 | 1 | 0.64 | 0.19 | 0.52 | 1 | 0.89 |
BIOCARTA DEATH PATHWAY | 33 | genes.ES.table | 0.51 | 1.6 | 0.024 | 1 | 0.85 | 0.58 | 0.34 | 0.38 | 1 | 0.8 |
BIOCARTA KERATINOCYTE PATHWAY | 46 | genes.ES.table | 0.42 | 1.4 | 0.12 | 1 | 1 | 0.48 | 0.29 | 0.34 | 1 | 0.93 |
BIOCARTA PYK2 PATHWAY | 28 | genes.ES.table | 0.31 | 1.3 | 0.13 | 1 | 1 | 0.32 | 0.28 | 0.23 | 1 | 0.9 |
BIOCARTA MYOSIN PATHWAY | 29 | genes.ES.table | 0.42 | 1.4 | 0.075 | 1 | 0.99 | 0.31 | 0.21 | 0.25 | 1 | 0.93 |
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 | GAS2 | GAS2 | GAS2 | 618 | 0.32 | 0.095 | YES |
2 | BIRC3 | BIRC3 | BIRC3 | 1020 | 0.26 | 0.18 | YES |
3 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 1812 | 0.18 | 0.21 | YES |
4 | CASP3 | CASP3 | CASP3 | 2087 | 0.17 | 0.26 | YES |
5 | CASP6 | CASP6 | CASP6 | 2257 | 0.16 | 0.32 | YES |
6 | TNFSF12 | TNFSF12 | TNFSF12 | 2768 | 0.13 | 0.34 | YES |
7 | NFKBIA | NFKBIA | NFKBIA | 3839 | 0.094 | 0.32 | YES |
8 | TRADD | TRADD | TRADD | 3983 | 0.09 | 0.35 | YES |
9 | CASP7 | CASP7 | CASP7 | 4119 | 0.086 | 0.38 | YES |
10 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 4479 | 0.076 | 0.39 | YES |
11 | RELA | RELA | RELA | 4607 | 0.074 | 0.41 | YES |
12 | NFKB1 | NFKB1 | NFKB1 | 4850 | 0.068 | 0.43 | YES |
13 | TRAF2 | TRAF2 | TRAF2 | 5248 | 0.06 | 0.43 | YES |
14 | FADD | FADD | FADD | 5544 | 0.054 | 0.43 | YES |
15 | CFLAR | CFLAR | CFLAR | 5632 | 0.052 | 0.45 | YES |
16 | SPTAN1 | SPTAN1 | SPTAN1 | 5658 | 0.052 | 0.47 | YES |
17 | BIRC2 | BIRC2 | BIRC2 | 5780 | 0.049 | 0.48 | YES |
18 | CYCS | CYCS | CYCS | 5997 | 0.045 | 0.49 | YES |
19 | MAP3K14 | MAP3K14 | MAP3K14 | 6034 | 0.044 | 0.51 | YES |
20 | TNFRSF25 | TNFRSF25 | TNFRSF25 | 6477 | 0.036 | 0.5 | NO |
21 | XIAP | XIAP | XIAP | 7613 | 0.017 | 0.44 | NO |
22 | RIPK1 | RIPK1 | RIPK1 | 7748 | 0.016 | 0.44 | NO |
23 | APAF1 | APAF1 | APAF1 | 8392 | 0.0058 | 0.4 | NO |
24 | CHUK | CHUK | CHUK | 8682 | 0.0018 | 0.39 | NO |
25 | BCL2 | BCL2 | BCL2 | 8698 | 0.0016 | 0.39 | NO |
26 | TNFSF10 | TNFSF10 | TNFSF10 | 9639 | -0.012 | 0.34 | NO |
27 | CASP10 | CASP10 | CASP10 | 10076 | -0.019 | 0.32 | NO |
28 | LMNA | LMNA | LMNA | 10212 | -0.021 | 0.32 | NO |
29 | DFFA | DFFA | DFFA | 10297 | -0.022 | 0.33 | NO |
30 | CASP9 | CASP9 | CASP9 | 11394 | -0.041 | 0.28 | NO |
31 | BID | BID | BID | 11439 | -0.042 | 0.3 | NO |
32 | DFFB | DFFB | DFFB | 11798 | -0.049 | 0.3 | NO |
33 | CASP8 | CASP8 | CASP8 | 13773 | -0.097 | 0.23 | 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

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 | FASLG | FASLG | FASLG | 191 | 0.46 | 0.15 | YES |
2 | CD247 | CD247 | CD247 | 479 | 0.35 | 0.25 | YES |
3 | BIRC3 | BIRC3 | BIRC3 | 1020 | 0.26 | 0.31 | YES |
4 | CASP3 | CASP3 | CASP3 | 2087 | 0.17 | 0.31 | YES |
5 | CASP6 | CASP6 | CASP6 | 2257 | 0.16 | 0.35 | YES |
6 | FAS | FAS | FAS | 2971 | 0.12 | 0.36 | YES |
7 | NFKBIA | NFKBIA | NFKBIA | 3839 | 0.094 | 0.34 | YES |
8 | TRADD | TRADD | TRADD | 3983 | 0.09 | 0.36 | YES |
9 | CASP7 | CASP7 | CASP7 | 4119 | 0.086 | 0.38 | YES |
10 | TRAF1 | TRAF1 | TRAF1 | 4495 | 0.076 | 0.39 | YES |
11 | RELA | RELA | RELA | 4607 | 0.074 | 0.41 | YES |
12 | TNF | TNF | TNF | 4741 | 0.07 | 0.43 | YES |
13 | NFKB1 | NFKB1 | NFKB1 | 4850 | 0.068 | 0.44 | YES |
14 | MAPK8 | MAPK8 | MAPK8 | 5041 | 0.064 | 0.46 | YES |
15 | MAP2K7 | MAP2K7 | MAP2K7 | 5076 | 0.064 | 0.48 | YES |
16 | TRAF2 | TRAF2 | TRAF2 | 5248 | 0.06 | 0.49 | YES |
17 | FADD | FADD | FADD | 5544 | 0.054 | 0.49 | YES |
18 | CFLAR | CFLAR | CFLAR | 5632 | 0.052 | 0.5 | YES |
19 | CYCS | CYCS | CYCS | 5997 | 0.045 | 0.5 | YES |
20 | MAP3K14 | MAP3K14 | MAP3K14 | 6034 | 0.044 | 0.51 | YES |
21 | CRADD | CRADD | CRADD | 7541 | 0.018 | 0.43 | NO |
22 | MAP3K5 | MAP3K5 | MAP3K5 | 7628 | 0.017 | 0.43 | NO |
23 | DAXX | DAXX | DAXX | 7721 | 0.016 | 0.43 | NO |
24 | RIPK1 | RIPK1 | RIPK1 | 7748 | 0.016 | 0.44 | NO |
25 | APAF1 | APAF1 | APAF1 | 8392 | 0.0058 | 0.4 | NO |
26 | CHUK | CHUK | CHUK | 8682 | 0.0018 | 0.39 | NO |
27 | BCL2 | BCL2 | BCL2 | 8698 | 0.0016 | 0.39 | NO |
28 | CASP2 | CASP2 | CASP2 | 9189 | -0.0056 | 0.36 | NO |
29 | DFFA | DFFA | DFFA | 10297 | -0.022 | 0.31 | NO |
30 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 10598 | -0.027 | 0.3 | NO |
31 | CASP9 | CASP9 | CASP9 | 11394 | -0.041 | 0.27 | NO |
32 | BID | BID | BID | 11439 | -0.042 | 0.28 | NO |
33 | DFFB | DFFB | DFFB | 11798 | -0.049 | 0.28 | NO |
34 | BAG4 | BAG4 | BAG4 | 12987 | -0.075 | 0.24 | NO |
35 | CASP8 | CASP8 | CASP8 | 13773 | -0.097 | 0.23 | 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 ANTIGEN PROCESSING AND PRESENTATION.

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

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 | ITGA2B | ITGA2B | ITGA2B | 710 | 0.3 | 0.084 | YES |
2 | APBB1IP | APBB1IP | APBB1IP | 993 | 0.26 | 0.18 | YES |
3 | FGB | FGB | FGB | 1833 | 0.18 | 0.2 | YES |
4 | RAPGEF3 | RAPGEF3 | RAPGEF3 | 1947 | 0.18 | 0.27 | YES |
5 | RASGRP2 | RASGRP2 | RASGRP2 | 2016 | 0.17 | 0.34 | YES |
6 | SYK | SYK | SYK | 2455 | 0.15 | 0.37 | YES |
7 | AKT1 | AKT1 | AKT1 | 2514 | 0.14 | 0.43 | YES |
8 | BCAR1 | BCAR1 | BCAR1 | 3508 | 0.1 | 0.42 | YES |
9 | SRC | SRC | SRC | 3808 | 0.095 | 0.44 | YES |
10 | CSK | CSK | CSK | 4065 | 0.087 | 0.46 | YES |
11 | PDPK1 | PDPK1 | PDPK1 | 4713 | 0.071 | 0.45 | YES |
12 | RAPGEF4 | RAPGEF4 | RAPGEF4 | 4727 | 0.071 | 0.48 | YES |
13 | FGG | FGG | FGG | 4839 | 0.068 | 0.5 | YES |
14 | VWF | VWF | VWF | 5109 | 0.063 | 0.52 | YES |
15 | FGA | FGA | FGA | 5303 | 0.059 | 0.53 | YES |
16 | RASGRP1 | RASGRP1 | RASGRP1 | 5732 | 0.05 | 0.52 | NO |
17 | PTK2 | PTK2 | PTK2 | 6348 | 0.038 | 0.51 | NO |
18 | ITGB3 | ITGB3 | ITGB3 | 6934 | 0.028 | 0.48 | NO |
19 | SHC1 | SHC1 | SHC1 | 8444 | 0.0052 | 0.4 | NO |
20 | SOS1 | SOS1 | SOS1 | 9833 | -0.015 | 0.33 | NO |
21 | PTPN1 | PTPN1 | PTPN1 | 9892 | -0.016 | 0.33 | NO |
22 | RAP1B | RAP1B | RAP1B | 10117 | -0.019 | 0.33 | NO |
23 | RAP1A | RAP1A | RAP1A | 10469 | -0.025 | 0.32 | NO |
24 | GRB2 | GRB2 | GRB2 | 10636 | -0.028 | 0.32 | NO |
25 | TLN1 | TLN1 | TLN1 | 11153 | -0.036 | 0.31 | NO |
26 | CRK | CRK | CRK | 12788 | -0.07 | 0.24 | NO |
27 | FN1 | FN1 | FN1 | 13603 | -0.092 | 0.24 | NO |
Figure S25. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY.

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

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 | KIR2DL3 | KIR2DL3 | KIR2DL3 | 133 | 0.5 | 0.036 | YES |
2 | ULBP3 | ULBP3 | ULBP3 | 156 | 0.47 | 0.076 | YES |
3 | ICAM4 | ICAM4 | ICAM4 | 204 | 0.45 | 0.11 | YES |
4 | CD160 | CD160 | CD160 | 238 | 0.43 | 0.15 | YES |
5 | KLRK1 | KLRK1 | KLRK1 | 246 | 0.43 | 0.18 | YES |
6 | KIR2DL4 | KIR2DL4 | KIR2DL4 | 337 | 0.39 | 0.21 | YES |
7 | CD247 | CD247 | CD247 | 479 | 0.35 | 0.24 | YES |
8 | KIR3DL1 | KIR3DL1 | KIR3DL1 | 494 | 0.34 | 0.26 | YES |
9 | ITGB7 | ITGB7 | ITGB7 | 573 | 0.33 | 0.29 | YES |
10 | CD3D | CD3D | CD3D | 607 | 0.32 | 0.32 | YES |
11 | ITGAL | ITGAL | ITGAL | 640 | 0.31 | 0.34 | YES |
12 | CD96 | CD96 | CD96 | 652 | 0.31 | 0.37 | YES |
13 | CD40LG | CD40LG | CD40LG | 685 | 0.3 | 0.39 | YES |
14 | CD3E | CD3E | CD3E | 689 | 0.3 | 0.42 | YES |
15 | KLRC1 | KLRC1 | KLRC1 | 700 | 0.3 | 0.44 | YES |
16 | ULBP1 | ULBP1 | ULBP1 | 725 | 0.3 | 0.47 | YES |
17 | CD8A | CD8A | CD8A | 860 | 0.28 | 0.48 | YES |
18 | KIR2DL1 | KIR2DL1 | KIR2DL1 | 888 | 0.27 | 0.51 | YES |
19 | C3 | C3 | C3 | 979 | 0.26 | 0.52 | YES |
20 | KIR3DL2 | KIR3DL2 | KIR3DL2 | 1142 | 0.24 | 0.54 | YES |
21 | CRTAM | CRTAM | CRTAM | 1210 | 0.23 | 0.55 | YES |
22 | CD19 | CD19 | CD19 | 1307 | 0.22 | 0.57 | YES |
23 | AMICA1 | AMICA1 | AMICA1 | 1328 | 0.22 | 0.59 | YES |
24 | FCGR3A | FCGR3A | FCGR3A | 1350 | 0.22 | 0.6 | YES |
25 | FCGR2B | FCGR2B | FCGR2B | 1393 | 0.22 | 0.62 | YES |
26 | LILRA1 | LILRA1 | LILRA1 | 1592 | 0.2 | 0.63 | YES |
27 | LILRB2 | LILRB2 | LILRB2 | 1627 | 0.2 | 0.64 | YES |
28 | ICAM3 | ICAM3 | ICAM3 | 1665 | 0.2 | 0.66 | YES |
29 | CD3G | CD3G | CD3G | 1732 | 0.19 | 0.67 | YES |
30 | CDH1 | CDH1 | CDH1 | 2008 | 0.17 | 0.67 | YES |
31 | LILRB1 | LILRB1 | LILRB1 | 2378 | 0.15 | 0.66 | YES |
32 | VCAM1 | VCAM1 | VCAM1 | 2649 | 0.14 | 0.66 | YES |
33 | ITGB2 | ITGB2 | ITGB2 | 2660 | 0.14 | 0.67 | YES |
34 | TYROBP | TYROBP | TYROBP | 2672 | 0.14 | 0.68 | YES |
35 | HCST | HCST | HCST | 2706 | 0.14 | 0.69 | YES |
36 | SELL | SELL | SELL | 2782 | 0.13 | 0.7 | YES |
37 | CD8B | CD8B | CD8B | 2942 | 0.12 | 0.7 | YES |
38 | HLA-F | HLA-F | HLA-F | 3183 | 0.12 | 0.7 | YES |
39 | LILRB4 | LILRB4 | LILRB4 | 3215 | 0.11 | 0.71 | YES |
40 | IFITM1 | IFITM1 | IFITM1 | 3281 | 0.11 | 0.71 | YES |
41 | PVRL2 | PVRL2 | PVRL2 | 3328 | 0.11 | 0.72 | YES |
42 | CD34 | CD34 | CD34 | 3779 | 0.096 | 0.7 | NO |
43 | ICAM2 | ICAM2 | ICAM2 | 3826 | 0.094 | 0.71 | NO |
44 | CD226 | CD226 | CD226 | 4301 | 0.081 | 0.69 | NO |
45 | CD81 | CD81 | CD81 | 4323 | 0.08 | 0.69 | NO |
46 | ICAM1 | ICAM1 | ICAM1 | 4716 | 0.071 | 0.68 | NO |
47 | ULBP2 | ULBP2 | ULBP2 | 4941 | 0.066 | 0.67 | NO |
48 | HLA-C | HLA-C | HLA-C | 5004 | 0.065 | 0.67 | NO |
49 | PVR | PVR | PVR | 5383 | 0.057 | 0.66 | NO |
50 | HLA-B | HLA-B | HLA-B | 5458 | 0.056 | 0.66 | NO |
51 | CD200R1 | CD200R1 | CD200R1 | 5785 | 0.049 | 0.64 | NO |
52 | HLA-A | HLA-A | HLA-A | 6203 | 0.041 | 0.62 | NO |
53 | B2M | B2M | B2M | 7908 | 0.013 | 0.53 | NO |
54 | RAET1E | RAET1E | RAET1E | 8420 | 0.0055 | 0.5 | NO |
55 | LILRB3 | LILRB3 | LILRB3 | 8425 | 0.0054 | 0.5 | NO |
56 | KLRD1 | KLRD1 | KLRD1 | 8491 | 0.0046 | 0.5 | NO |
57 | LILRB5 | LILRB5 | LILRB5 | 8848 | -0.00054 | 0.48 | NO |
58 | ITGB1 | ITGB1 | ITGB1 | 9668 | -0.013 | 0.43 | NO |
59 | HLA-G | HLA-G | HLA-G | 11435 | -0.042 | 0.34 | NO |
60 | CD40 | CD40 | CD40 | 12023 | -0.053 | 0.31 | NO |
61 | CXADR | CXADR | CXADR | 15994 | -0.2 | 0.1 | NO |
Figure S27. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PATHOGENIC ESCHERICHIA COLI INFECTION.

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

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 | ARHGEF19 | ARHGEF19 | ARHGEF19 | 115 | 0.52 | 0.19 | YES |
2 | ARHGEF16 | ARHGEF16 | ARHGEF16 | 1310 | 0.22 | 0.21 | YES |
3 | PLCB1 | PLCB1 | PLCB1 | 1445 | 0.21 | 0.29 | YES |
4 | ARHGEF15 | ARHGEF15 | ARHGEF15 | 2626 | 0.14 | 0.28 | YES |
5 | PRKCB | PRKCB | PRKCB | 3235 | 0.11 | 0.29 | YES |
6 | ARHGEF18 | ARHGEF18 | ARHGEF18 | 3341 | 0.11 | 0.32 | YES |
7 | MYLK | MYLK | MYLK | 3410 | 0.11 | 0.36 | YES |
8 | PKN1 | PKN1 | PKN1 | 3603 | 0.1 | 0.39 | YES |
9 | GNGT1 | GNGT1 | GNGT1 | 3720 | 0.097 | 0.42 | YES |
10 | ARHGEF9 | ARHGEF9 | ARHGEF9 | 5550 | 0.054 | 0.34 | NO |
11 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 5846 | 0.048 | 0.34 | NO |
12 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 5871 | 0.047 | 0.36 | NO |
13 | ARHGEF5 | ARHGEF5 | ARHGEF5 | 5935 | 0.046 | 0.37 | NO |
14 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 6776 | 0.031 | 0.34 | NO |
15 | ARHGEF17 | ARHGEF17 | ARHGEF17 | 7077 | 0.025 | 0.33 | NO |
16 | GNB1 | GNB1 | GNB1 | 7089 | 0.025 | 0.34 | NO |
17 | PRKCA | PRKCA | PRKCA | 7164 | 0.024 | 0.34 | NO |
18 | PPP1R12B | PPP1R12B | PPP1R12B | 7388 | 0.02 | 0.34 | NO |
19 | GNA12 | GNA12 | GNA12 | 7652 | 0.017 | 0.33 | NO |
20 | ARHGAP5 | ARHGAP5 | ARHGAP5 | 7964 | 0.012 | 0.32 | NO |
21 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 9232 | -0.0062 | 0.25 | NO |
22 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 9556 | -0.011 | 0.24 | NO |
23 | ROCK1 | ROCK1 | ROCK1 | 11258 | -0.038 | 0.16 | NO |
24 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 11358 | -0.04 | 0.16 | NO |
25 | ARHGEF10 | ARHGEF10 | ARHGEF10 | 12167 | -0.056 | 0.14 | NO |
26 | GNA13 | GNA13 | GNA13 | 13592 | -0.092 | 0.096 | NO |
27 | ARHGEF3 | ARHGEF3 | ARHGEF3 | 14226 | -0.11 | 0.1 | NO |
28 | GNAQ | GNAQ | GNAQ | 14506 | -0.12 | 0.14 | NO |
29 | ARHGEF4 | ARHGEF4 | ARHGEF4 | 14571 | -0.13 | 0.18 | NO |
Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NON SMALL CELL LUNG CANCER.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NON SMALL CELL LUNG CANCER, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | FUT2 | FUT2 | FUT2 | 140 | 0.48 | 0.11 | YES |
2 | FUT1 | FUT1 | FUT1 | 176 | 0.46 | 0.21 | YES |
3 | FUT5 | FUT5 | FUT5 | 366 | 0.38 | 0.29 | YES |
4 | ABO | ABO | ABO | 390 | 0.37 | 0.37 | YES |
5 | B3GNT4 | B3GNT4 | B3GNT4 | 737 | 0.3 | 0.42 | YES |
6 | FUT3 | FUT3 | FUT3 | 853 | 0.28 | 0.48 | YES |
7 | FUT7 | FUT7 | FUT7 | 1729 | 0.19 | 0.48 | YES |
8 | GCNT2 | GCNT2 | GCNT2 | 1814 | 0.18 | 0.52 | YES |
9 | FUT4 | FUT4 | FUT4 | 2883 | 0.13 | 0.48 | NO |
10 | FUT6 | FUT6 | FUT6 | 3519 | 0.1 | 0.47 | NO |
11 | B4GALT2 | B4GALT2 | B4GALT2 | 5601 | 0.053 | 0.37 | NO |
12 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 6811 | 0.03 | 0.31 | NO |
13 | B3GNT3 | B3GNT3 | B3GNT3 | 7293 | 0.022 | 0.29 | NO |
14 | B3GALT1 | B3GALT1 | B3GALT1 | 9324 | -0.0076 | 0.17 | NO |
15 | B3GALT5 | B3GALT5 | B3GALT5 | 9679 | -0.013 | 0.16 | NO |
16 | B3GNT1 | B3GNT1 | B3GNT1 | 10007 | -0.018 | 0.14 | NO |
17 | B4GALT3 | B4GALT3 | B4GALT3 | 10201 | -0.021 | 0.14 | NO |
18 | B3GNT5 | B3GNT5 | B3GNT5 | 10266 | -0.022 | 0.14 | NO |
19 | FUT9 | FUT9 | FUT9 | 12910 | -0.073 | 0.0068 | NO |
20 | B3GNT2 | B3GNT2 | B3GNT2 | 13088 | -0.077 | 0.015 | NO |
21 | B3GALT2 | B3GALT2 | B3GALT2 | 13767 | -0.097 | -0.00041 | NO |
22 | B4GALT1 | B4GALT1 | B4GALT1 | 14053 | -0.11 | 0.0086 | NO |
23 | ST3GAL6 | ST3GAL6 | ST3GAL6 | 15622 | -0.18 | -0.038 | NO |
24 | B4GALT4 | B4GALT4 | B4GALT4 | 16213 | -0.22 | -0.019 | NO |
25 | ST8SIA1 | ST8SIA1 | ST8SIA1 | 16252 | -0.23 | 0.032 | NO |
26 | ST3GAL4 | ST3GAL4 | ST3GAL4 | 16380 | -0.24 | 0.081 | NO |
Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GRAFT VERSUS HOST DISEASE.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GRAFT VERSUS HOST DISEASE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | FASLG | FASLG | FASLG | 191 | 0.46 | 0.093 | YES |
2 | PRKCG | PRKCG | PRKCG | 262 | 0.42 | 0.18 | YES |
3 | JUN | JUN | JUN | 901 | 0.27 | 0.21 | YES |
4 | CEBPA | CEBPA | CEBPA | 1242 | 0.23 | 0.24 | YES |
5 | HOXA7 | HOXA7 | HOXA7 | 1371 | 0.22 | 0.29 | YES |
6 | EGF | EGF | EGF | 1728 | 0.19 | 0.31 | YES |
7 | FAS | FAS | FAS | 2971 | 0.12 | 0.27 | YES |
8 | MAPK13 | MAPK13 | MAPK13 | 3220 | 0.11 | 0.28 | YES |
9 | PRKCB | PRKCB | PRKCB | 3235 | 0.11 | 0.3 | YES |
10 | MAP2K1 | MAP2K1 | MAP2K1 | 3579 | 0.1 | 0.31 | YES |
11 | EGFR | EGFR | EGFR | 3728 | 0.097 | 0.32 | YES |
12 | NFKBIA | NFKBIA | NFKBIA | 3839 | 0.094 | 0.34 | YES |
13 | TNFRSF1B | TNFRSF1B | TNFRSF1B | 4025 | 0.088 | 0.35 | YES |
14 | HRAS | HRAS | HRAS | 4452 | 0.077 | 0.34 | YES |
15 | RELA | RELA | RELA | 4607 | 0.074 | 0.35 | YES |
16 | TNF | TNF | TNF | 4741 | 0.07 | 0.36 | YES |
17 | MAPK3 | MAPK3 | MAPK3 | 4805 | 0.069 | 0.37 | YES |
18 | NFKB1 | NFKB1 | NFKB1 | 4850 | 0.068 | 0.38 | YES |
19 | PRKCE | PRKCE | PRKCE | 4929 | 0.066 | 0.39 | YES |
20 | MAPK8 | MAPK8 | MAPK8 | 5041 | 0.064 | 0.4 | YES |
21 | MAP2K7 | MAP2K7 | MAP2K7 | 5076 | 0.064 | 0.41 | YES |
22 | TRAF2 | TRAF2 | TRAF2 | 5248 | 0.06 | 0.42 | YES |
23 | ETS1 | ETS1 | ETS1 | 5648 | 0.052 | 0.41 | NO |
24 | MAP3K14 | MAP3K14 | MAP3K14 | 6034 | 0.044 | 0.39 | NO |
25 | SP1 | SP1 | SP1 | 6406 | 0.037 | 0.38 | NO |
26 | PRKCA | PRKCA | PRKCA | 7164 | 0.024 | 0.34 | NO |
27 | PRKCD | PRKCD | PRKCD | 7482 | 0.019 | 0.33 | NO |
28 | MAP3K5 | MAP3K5 | MAP3K5 | 7628 | 0.017 | 0.33 | NO |
29 | DAXX | DAXX | DAXX | 7721 | 0.016 | 0.32 | NO |
30 | RIPK1 | RIPK1 | RIPK1 | 7748 | 0.016 | 0.33 | NO |
31 | MAPK1 | MAPK1 | MAPK1 | 8530 | 0.004 | 0.28 | NO |
32 | CHUK | CHUK | CHUK | 8682 | 0.0018 | 0.28 | NO |
33 | BCL2 | BCL2 | BCL2 | 8698 | 0.0016 | 0.28 | NO |
34 | IKBKB | IKBKB | IKBKB | 9005 | -0.0029 | 0.26 | NO |
35 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 10598 | -0.027 | 0.18 | NO |
36 | MAPK14 | MAPK14 | MAPK14 | 11005 | -0.033 | 0.16 | NO |
37 | MAP2K3 | MAP2K3 | MAP2K3 | 11150 | -0.036 | 0.16 | NO |
38 | MAP2K4 | MAP2K4 | MAP2K4 | 11956 | -0.052 | 0.13 | NO |
39 | MAP3K1 | MAP3K1 | MAP3K1 | 12198 | -0.057 | 0.13 | NO |
40 | PRKCH | PRKCH | PRKCH | 12694 | -0.068 | 0.11 | NO |
41 | RAF1 | RAF1 | RAF1 | 13287 | -0.083 | 0.1 | NO |
42 | FOS | FOS | FOS | 13683 | -0.094 | 0.099 | NO |
43 | ETS2 | ETS2 | ETS2 | 13800 | -0.098 | 0.12 | NO |
44 | PPP2CA | PPP2CA | PPP2CA | 14644 | -0.13 | 0.097 | NO |
45 | PRKCQ | PRKCQ | PRKCQ | 15517 | -0.17 | 0.086 | NO |
46 | MAP2K6 | MAP2K6 | MAP2K6 | 15845 | -0.19 | 0.11 | 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: BIOCARTA DEATH PATHWAY.

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

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 | NCR1 | NCR1 | NCR1 | 123 | 0.5 | 0.024 | YES |
2 | KIR2DL3 | KIR2DL3 | KIR2DL3 | 133 | 0.5 | 0.053 | YES |
3 | ULBP3 | ULBP3 | ULBP3 | 156 | 0.47 | 0.081 | YES |
4 | FASLG | FASLG | FASLG | 191 | 0.46 | 0.11 | YES |
5 | KLRK1 | KLRK1 | KLRK1 | 246 | 0.43 | 0.13 | YES |
6 | PRKCG | PRKCG | PRKCG | 262 | 0.42 | 0.15 | YES |
7 | KLRC3 | KLRC3 | KLRC3 | 329 | 0.39 | 0.17 | YES |
8 | KIR2DL4 | KIR2DL4 | KIR2DL4 | 337 | 0.39 | 0.2 | YES |
9 | KIR2DS4 | KIR2DS4 | KIR2DS4 | 362 | 0.38 | 0.22 | YES |
10 | CD244 | CD244 | CD244 | 437 | 0.36 | 0.24 | YES |
11 | LCK | LCK | LCK | 446 | 0.36 | 0.26 | YES |
12 | ZAP70 | ZAP70 | ZAP70 | 463 | 0.35 | 0.28 | YES |
13 | CD247 | CD247 | CD247 | 479 | 0.35 | 0.3 | YES |
14 | KIR3DL1 | KIR3DL1 | KIR3DL1 | 494 | 0.34 | 0.32 | YES |
15 | NCR3 | NCR3 | NCR3 | 555 | 0.33 | 0.33 | YES |
16 | ITGAL | ITGAL | ITGAL | 640 | 0.31 | 0.35 | YES |
17 | KLRC1 | KLRC1 | KLRC1 | 700 | 0.3 | 0.36 | YES |
18 | ULBP1 | ULBP1 | ULBP1 | 725 | 0.3 | 0.38 | YES |
19 | PRF1 | PRF1 | PRF1 | 789 | 0.29 | 0.39 | YES |
20 | SH2D1A | SH2D1A | SH2D1A | 814 | 0.28 | 0.41 | YES |
21 | KIR2DL1 | KIR2DL1 | KIR2DL1 | 888 | 0.27 | 0.42 | YES |
22 | CD48 | CD48 | CD48 | 1119 | 0.24 | 0.42 | YES |
23 | KIR3DL2 | KIR3DL2 | KIR3DL2 | 1142 | 0.24 | 0.44 | YES |
24 | FCGR3B | FCGR3B | FCGR3B | 1192 | 0.24 | 0.45 | YES |
25 | PIK3R5 | PIK3R5 | PIK3R5 | 1222 | 0.23 | 0.46 | YES |
26 | FCGR3A | FCGR3A | FCGR3A | 1350 | 0.22 | 0.47 | YES |
27 | GZMB | GZMB | GZMB | 1421 | 0.22 | 0.48 | YES |
28 | VAV1 | VAV1 | VAV1 | 1468 | 0.21 | 0.49 | YES |
29 | KLRC2 | KLRC2 | KLRC2 | 1552 | 0.2 | 0.5 | YES |
30 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 1812 | 0.18 | 0.49 | YES |
31 | CASP3 | CASP3 | CASP3 | 2087 | 0.17 | 0.49 | YES |
32 | PIK3CG | PIK3CG | PIK3CG | 2098 | 0.17 | 0.5 | YES |
33 | RAET1G | RAET1G | RAET1G | 2185 | 0.16 | 0.5 | YES |
34 | SYK | SYK | SYK | 2455 | 0.15 | 0.49 | YES |
35 | RAC2 | RAC2 | RAC2 | 2590 | 0.14 | 0.5 | YES |
36 | ITGB2 | ITGB2 | ITGB2 | 2660 | 0.14 | 0.5 | YES |
37 | TYROBP | TYROBP | TYROBP | 2672 | 0.14 | 0.51 | YES |
38 | IFNG | IFNG | IFNG | 2684 | 0.14 | 0.52 | YES |
39 | HCST | HCST | HCST | 2706 | 0.14 | 0.52 | YES |
40 | TNFRSF10C | TNFRSF10C | TNFRSF10C | 2757 | 0.13 | 0.53 | YES |
41 | RAC3 | RAC3 | RAC3 | 2801 | 0.13 | 0.53 | YES |
42 | FAS | FAS | FAS | 2971 | 0.12 | 0.53 | YES |
43 | RAET1L | RAET1L | RAET1L | 3058 | 0.12 | 0.53 | YES |
44 | PRKCB | PRKCB | PRKCB | 3235 | 0.11 | 0.53 | YES |
45 | PAK1 | PAK1 | PAK1 | 3247 | 0.11 | 0.54 | YES |
46 | PIK3CD | PIK3CD | PIK3CD | 3346 | 0.11 | 0.54 | YES |
47 | FCER1G | FCER1G | FCER1G | 3353 | 0.11 | 0.54 | YES |
48 | MAP2K1 | MAP2K1 | MAP2K1 | 3579 | 0.1 | 0.54 | NO |
49 | ICAM2 | ICAM2 | ICAM2 | 3826 | 0.094 | 0.53 | NO |
50 | SHC2 | SHC2 | SHC2 | 3993 | 0.089 | 0.52 | NO |
51 | NFAT5 | NFAT5 | NFAT5 | 4001 | 0.089 | 0.53 | NO |
52 | LCP2 | LCP2 | LCP2 | 4051 | 0.088 | 0.53 | NO |
53 | SH2D1B | SH2D1B | SH2D1B | 4394 | 0.079 | 0.52 | NO |
54 | PPP3CC | PPP3CC | PPP3CC | 4420 | 0.078 | 0.52 | NO |
55 | HRAS | HRAS | HRAS | 4452 | 0.077 | 0.52 | NO |
56 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 4479 | 0.076 | 0.53 | NO |
57 | LAT | LAT | LAT | 4518 | 0.076 | 0.53 | NO |
58 | HLA-E | HLA-E | HLA-E | 4714 | 0.071 | 0.52 | NO |
59 | ICAM1 | ICAM1 | ICAM1 | 4716 | 0.071 | 0.53 | NO |
60 | TNF | TNF | TNF | 4741 | 0.07 | 0.53 | NO |
61 | MAPK3 | MAPK3 | MAPK3 | 4805 | 0.069 | 0.53 | NO |
62 | VAV3 | VAV3 | VAV3 | 4834 | 0.068 | 0.53 | NO |
63 | ULBP2 | ULBP2 | ULBP2 | 4941 | 0.066 | 0.53 | NO |
64 | HLA-C | HLA-C | HLA-C | 5004 | 0.065 | 0.53 | NO |
65 | NFATC3 | NFATC3 | NFATC3 | 5254 | 0.06 | 0.52 | NO |
66 | NCR2 | NCR2 | NCR2 | 5366 | 0.058 | 0.52 | NO |
67 | HLA-B | HLA-B | HLA-B | 5458 | 0.056 | 0.52 | NO |
68 | MAP2K2 | MAP2K2 | MAP2K2 | 5799 | 0.049 | 0.5 | NO |
69 | FYN | FYN | FYN | 5807 | 0.048 | 0.5 | NO |
70 | HLA-A | HLA-A | HLA-A | 6203 | 0.041 | 0.48 | NO |
71 | PTPN6 | PTPN6 | PTPN6 | 6208 | 0.041 | 0.49 | NO |
72 | PTK2B | PTK2B | PTK2B | 6210 | 0.041 | 0.49 | NO |
73 | KRAS | KRAS | KRAS | 6233 | 0.041 | 0.49 | NO |
74 | SH3BP2 | SH3BP2 | SH3BP2 | 6514 | 0.035 | 0.48 | NO |
75 | PLCG1 | PLCG1 | PLCG1 | 6727 | 0.031 | 0.46 | NO |
76 | ARAF | ARAF | ARAF | 6732 | 0.031 | 0.47 | NO |
77 | SOS2 | SOS2 | SOS2 | 6817 | 0.03 | 0.46 | NO |
78 | PRKCA | PRKCA | PRKCA | 7164 | 0.024 | 0.45 | NO |
79 | VAV2 | VAV2 | VAV2 | 7817 | 0.014 | 0.41 | NO |
80 | RAET1E | RAET1E | RAET1E | 8420 | 0.0055 | 0.38 | NO |
81 | PIK3R3 | PIK3R3 | PIK3R3 | 8442 | 0.0052 | 0.38 | NO |
82 | SHC1 | SHC1 | SHC1 | 8444 | 0.0052 | 0.38 | NO |
83 | KLRD1 | KLRD1 | KLRD1 | 8491 | 0.0046 | 0.37 | NO |
84 | MAPK1 | MAPK1 | MAPK1 | 8530 | 0.004 | 0.37 | NO |
85 | PPP3CB | PPP3CB | PPP3CB | 8599 | 0.0031 | 0.37 | NO |
86 | RAC1 | RAC1 | RAC1 | 8732 | 0.0011 | 0.36 | NO |
87 | PTPN11 | PTPN11 | PTPN11 | 8957 | -0.0023 | 0.35 | NO |
88 | NRAS | NRAS | NRAS | 9274 | -0.0068 | 0.33 | NO |
89 | PLCG2 | PLCG2 | PLCG2 | 9317 | -0.0075 | 0.33 | NO |
90 | TNFSF10 | TNFSF10 | TNFSF10 | 9639 | -0.012 | 0.31 | NO |
91 | SOS1 | SOS1 | SOS1 | 9833 | -0.015 | 0.3 | NO |
92 | PIK3R2 | PIK3R2 | PIK3R2 | 9949 | -0.017 | 0.3 | NO |
93 | IFNAR2 | IFNAR2 | IFNAR2 | 10013 | -0.018 | 0.29 | NO |
94 | IFNGR1 | IFNGR1 | IFNGR1 | 10291 | -0.022 | 0.28 | NO |
95 | PPP3CA | PPP3CA | PPP3CA | 10398 | -0.024 | 0.28 | NO |
96 | GRB2 | GRB2 | GRB2 | 10636 | -0.028 | 0.26 | NO |
97 | CHP | CHP | CHP | 11423 | -0.041 | 0.22 | NO |
98 | HLA-G | HLA-G | HLA-G | 11435 | -0.042 | 0.22 | NO |
99 | BID | BID | BID | 11439 | -0.042 | 0.22 | NO |
100 | IFNAR1 | IFNAR1 | IFNAR1 | 12086 | -0.054 | 0.19 | NO |
101 | MICA | MICA | MICA | 12491 | -0.063 | 0.17 | NO |
102 | IFNGR2 | IFNGR2 | IFNGR2 | 12642 | -0.067 | 0.17 | NO |
103 | MICB | MICB | MICB | 12758 | -0.07 | 0.17 | NO |
104 | PPP3R1 | PPP3R1 | PPP3R1 | 13122 | -0.078 | 0.15 | NO |
105 | PPP3R2 | PPP3R2 | PPP3R2 | 13200 | -0.081 | 0.15 | NO |
106 | RAF1 | RAF1 | RAF1 | 13287 | -0.083 | 0.15 | NO |
107 | PIK3R1 | PIK3R1 | PIK3R1 | 13471 | -0.088 | 0.15 | NO |
108 | BRAF | BRAF | BRAF | 14082 | -0.11 | 0.12 | NO |
109 | NFATC1 | NFATC1 | NFATC1 | 14264 | -0.12 | 0.12 | NO |
110 | TNFRSF10D | TNFRSF10D | TNFRSF10D | 14511 | -0.12 | 0.11 | NO |
111 | PIK3CB | PIK3CB | PIK3CB | 14975 | -0.14 | 0.091 | NO |
112 | NFATC4 | NFATC4 | NFATC4 | 15202 | -0.15 | 0.088 | NO |
113 | SHC4 | SHC4 | SHC4 | 15519 | -0.17 | 0.08 | NO |
114 | SHC3 | SHC3 | SHC3 | 16171 | -0.22 | 0.057 | NO |
115 | PIK3CA | PIK3CA | PIK3CA | 16354 | -0.24 | 0.061 | NO |
116 | NFATC2 | NFATC2 | NFATC2 | 17224 | -0.36 | 0.034 | 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: BIOCARTA KERATINOCYTE PATHWAY.

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

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 | KIR2DL3 | KIR2DL3 | KIR2DL3 | 133 | 0.5 | 0.049 | YES |
2 | HLA-DOB | HLA-DOB | HLA-DOB | 242 | 0.43 | 0.092 | YES |
3 | KLRC3 | KLRC3 | KLRC3 | 329 | 0.39 | 0.13 | YES |
4 | KIR2DL4 | KIR2DL4 | KIR2DL4 | 337 | 0.39 | 0.18 | YES |
5 | KIR2DS4 | KIR2DS4 | KIR2DS4 | 362 | 0.38 | 0.22 | YES |
6 | KIR3DL1 | KIR3DL1 | KIR3DL1 | 494 | 0.34 | 0.25 | YES |
7 | KLRC4 | KLRC4 | KLRC4 | 620 | 0.32 | 0.28 | YES |
8 | KLRC1 | KLRC1 | KLRC1 | 700 | 0.3 | 0.31 | YES |
9 | HLA-DQA2 | HLA-DQA2 | HLA-DQA2 | 774 | 0.29 | 0.34 | YES |
10 | CD8A | CD8A | CD8A | 860 | 0.28 | 0.37 | YES |
11 | KIR2DL1 | KIR2DL1 | KIR2DL1 | 888 | 0.27 | 0.4 | YES |
12 | HLA-DOA | HLA-DOA | HLA-DOA | 984 | 0.26 | 0.42 | YES |
13 | KIR3DL2 | KIR3DL2 | KIR3DL2 | 1142 | 0.24 | 0.44 | YES |
14 | HLA-DQA1 | HLA-DQA1 | HLA-DQA1 | 1407 | 0.22 | 0.45 | YES |
15 | HSPA6 | HSPA6 | HSPA6 | 1408 | 0.22 | 0.47 | YES |
16 | KLRC2 | KLRC2 | KLRC2 | 1552 | 0.2 | 0.49 | YES |
17 | CIITA | CIITA | CIITA | 1698 | 0.19 | 0.5 | YES |
18 | HSPA2 | HSPA2 | HSPA2 | 2314 | 0.16 | 0.49 | YES |
19 | HLA-DPB1 | HLA-DPB1 | HLA-DPB1 | 2384 | 0.15 | 0.5 | YES |
20 | HLA-DMA | HLA-DMA | HLA-DMA | 2441 | 0.15 | 0.51 | YES |
21 | HLA-DMB | HLA-DMB | HLA-DMB | 2659 | 0.14 | 0.52 | YES |
22 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 2787 | 0.13 | 0.52 | YES |
23 | HLA-DRA | HLA-DRA | HLA-DRA | 2851 | 0.13 | 0.54 | YES |
24 | CD8B | CD8B | CD8B | 2942 | 0.12 | 0.55 | YES |
25 | HLA-DRB5 | HLA-DRB5 | HLA-DRB5 | 3005 | 0.12 | 0.56 | YES |
26 | HLA-F | HLA-F | HLA-F | 3183 | 0.12 | 0.56 | YES |
27 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 3396 | 0.11 | 0.56 | YES |
28 | CD4 | CD4 | CD4 | 4587 | 0.074 | 0.5 | NO |
29 | LTA | LTA | LTA | 4600 | 0.074 | 0.51 | NO |
30 | HLA-E | HLA-E | HLA-E | 4714 | 0.071 | 0.51 | NO |
31 | HLA-C | HLA-C | HLA-C | 5004 | 0.065 | 0.5 | NO |
32 | HLA-DQB1 | HLA-DQB1 | HLA-DQB1 | 5073 | 0.064 | 0.5 | NO |
33 | CD74 | CD74 | CD74 | 5321 | 0.058 | 0.5 | NO |
34 | HLA-B | HLA-B | HLA-B | 5458 | 0.056 | 0.5 | NO |
35 | LGMN | LGMN | LGMN | 5517 | 0.054 | 0.5 | NO |
36 | NFYC | NFYC | NFYC | 5584 | 0.053 | 0.5 | NO |
37 | PSME1 | PSME1 | PSME1 | 5664 | 0.052 | 0.5 | NO |
38 | HLA-A | HLA-A | HLA-A | 6203 | 0.041 | 0.48 | NO |
39 | NFYB | NFYB | NFYB | 6434 | 0.037 | 0.47 | NO |
40 | CTSS | CTSS | CTSS | 6546 | 0.035 | 0.47 | NO |
41 | TAP2 | TAP2 | TAP2 | 6766 | 0.031 | 0.46 | NO |
42 | TAP1 | TAP1 | TAP1 | 6891 | 0.029 | 0.45 | NO |
43 | TAPBP | TAPBP | TAPBP | 6896 | 0.028 | 0.46 | NO |
44 | PSME2 | PSME2 | PSME2 | 7213 | 0.023 | 0.44 | NO |
45 | HSPA8 | HSPA8 | HSPA8 | 7449 | 0.02 | 0.43 | NO |
46 | B2M | B2M | B2M | 7908 | 0.013 | 0.41 | NO |
47 | RFXANK | RFXANK | RFXANK | 8066 | 0.01 | 0.4 | NO |
48 | PSME3 | PSME3 | PSME3 | 8208 | 0.0083 | 0.39 | NO |
49 | KLRD1 | KLRD1 | KLRD1 | 8491 | 0.0046 | 0.38 | NO |
50 | CALR | CALR | CALR | 8569 | 0.0036 | 0.37 | NO |
51 | CREB1 | CREB1 | CREB1 | 9432 | -0.0091 | 0.32 | NO |
52 | RFX5 | RFX5 | RFX5 | 10190 | -0.02 | 0.28 | NO |
53 | NFYA | NFYA | NFYA | 10280 | -0.022 | 0.28 | NO |
54 | HLA-G | HLA-G | HLA-G | 11435 | -0.042 | 0.22 | NO |
55 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 11735 | -0.048 | 0.21 | NO |
56 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 11874 | -0.05 | 0.21 | NO |
57 | PDIA3 | PDIA3 | PDIA3 | 11949 | -0.052 | 0.21 | NO |
58 | CTSL1 | CTSL1 | CTSL1 | 12282 | -0.059 | 0.2 | NO |
59 | HSPA1A | HSPA1A | HSPA1A | 12458 | -0.062 | 0.2 | NO |
60 | HSPA5 | HSPA5 | HSPA5 | 13179 | -0.08 | 0.16 | NO |
61 | HSPA1B | HSPA1B | HSPA1B | 13369 | -0.085 | 0.16 | NO |
62 | CTSB | CTSB | CTSB | 13827 | -0.099 | 0.15 | NO |
63 | HSPA1L | HSPA1L | HSPA1L | 13905 | -0.1 | 0.16 | NO |
64 | CANX | CANX | CANX | 13918 | -0.1 | 0.17 | NO |
65 | IFI30 | IFI30 | IFI30 | 14836 | -0.14 | 0.13 | NO |
66 | HSPA4 | HSPA4 | HSPA4 | 15203 | -0.15 | 0.13 | NO |
67 | RFXAP | RFXAP | RFXAP | 15442 | -0.17 | 0.13 | 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: BIOCARTA PYK2 PATHWAY.

Figure S38. 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

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 | SPON2 | SPON2 | SPON2 | 80 | 0.55 | 0.12 | YES |
2 | ICAM4 | ICAM4 | ICAM4 | 204 | 0.45 | 0.21 | YES |
3 | ITGAL | ITGAL | ITGAL | 640 | 0.31 | 0.26 | YES |
4 | CD40LG | CD40LG | CD40LG | 685 | 0.3 | 0.32 | YES |
5 | PROC | PROC | PROC | 818 | 0.28 | 0.38 | YES |
6 | C3 | C3 | C3 | 979 | 0.26 | 0.43 | YES |
7 | ICAM3 | ICAM3 | ICAM3 | 1665 | 0.2 | 0.43 | YES |
8 | FGB | FGB | FGB | 1833 | 0.18 | 0.46 | YES |
9 | PLAT | PLAT | PLAT | 2029 | 0.17 | 0.49 | YES |
10 | ITGAD | ITGAD | ITGAD | 2312 | 0.16 | 0.51 | YES |
11 | KNG1 | KNG1 | KNG1 | 2373 | 0.15 | 0.54 | YES |
12 | ITGAM | ITGAM | ITGAM | 2410 | 0.15 | 0.57 | YES |
13 | F10 | F10 | F10 | 2604 | 0.14 | 0.59 | YES |
14 | VCAM1 | VCAM1 | VCAM1 | 2649 | 0.14 | 0.62 | YES |
15 | ITGB2 | ITGB2 | ITGB2 | 2660 | 0.14 | 0.65 | YES |
16 | ITGAX | ITGAX | ITGAX | 3254 | 0.11 | 0.64 | YES |
17 | GP1BA | GP1BA | GP1BA | 3674 | 0.099 | 0.64 | YES |
18 | ICAM2 | ICAM2 | ICAM2 | 3826 | 0.094 | 0.66 | YES |
19 | ICAM1 | ICAM1 | ICAM1 | 4716 | 0.071 | 0.62 | NO |
20 | FGG | FGG | FGG | 4839 | 0.068 | 0.63 | NO |
21 | FGA | FGA | FGA | 5303 | 0.059 | 0.62 | NO |
22 | FCGR2A | FCGR2A | FCGR2A | 5467 | 0.055 | 0.62 | NO |
23 | F11R | F11R | F11R | 6457 | 0.036 | 0.57 | NO |
24 | JAM3 | JAM3 | JAM3 | 7705 | 0.016 | 0.5 | NO |
25 | THY1 | THY1 | THY1 | 9644 | -0.012 | 0.4 | NO |
26 | CYR61 | CYR61 | CYR61 | 10135 | -0.02 | 0.38 | NO |
27 | PLAUR | PLAUR | PLAUR | 12203 | -0.057 | 0.27 | NO |
28 | PLAU | PLAU | PLAU | 12769 | -0.07 | 0.26 | NO |
29 | TGFBI | TGFBI | TGFBI | 14484 | -0.12 | 0.19 | 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: BIOCARTA MYOSIN PATHWAY.

Figure S40. 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

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 5. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG GLYCOLYSIS GLUCONEOGENESIS | 59 | genes.ES.table | 0.52 | 1.6 | 0.017 | 0.75 | 0.88 | 0.25 | 0.096 | 0.23 | 0.4 | 0.21 |
KEGG TYROSINE METABOLISM | 41 | genes.ES.table | 0.65 | 1.8 | 0.0074 | 0.27 | 0.59 | 0.37 | 0.089 | 0.33 | 0.095 | 0.062 |
BIOCARTA RACCYCD PATHWAY | 26 | genes.ES.table | 0.59 | 2.3 | 0 | 0.0062 | 0.006 | 0.5 | 0.23 | 0.38 | 0 | 0.003 |
BIOCARTA INTEGRIN PATHWAY | 38 | genes.ES.table | 0.37 | 1.5 | 0.086 | 0.98 | 0.96 | 0.34 | 0.25 | 0.26 | 0.64 | 0.32 |
PID WNT NONCANONICAL PATHWAY | 32 | genes.ES.table | 0.44 | 1.5 | 0.041 | 0.95 | 0.97 | 0.34 | 0.22 | 0.27 | 0.62 | 0.31 |
PID NECTIN PATHWAY | 30 | genes.ES.table | 0.56 | 1.9 | 0.0039 | 0.07 | 0.22 | 0.47 | 0.25 | 0.35 | 0 | 0.011 |
PID HNF3BPATHWAY | 41 | genes.ES.table | 0.57 | 1.6 | 0.011 | 0.68 | 0.9 | 0.39 | 0.1 | 0.35 | 0.38 | 0.19 |
PID IGF1 PATHWAY | 30 | genes.ES.table | 0.48 | 2 | 0.0062 | 0.06 | 0.18 | 0.57 | 0.32 | 0.38 | 0 | 0.011 |
PID AR TF PATHWAY | 51 | genes.ES.table | 0.42 | 1.5 | 0.06 | 0.88 | 0.95 | 0.22 | 0.15 | 0.18 | 0.56 | 0.28 |
PID ECADHERIN STABILIZATION PATHWAY | 40 | genes.ES.table | 0.44 | 1.5 | 0.093 | 0.99 | 0.97 | 0.4 | 0.25 | 0.3 | 0.65 | 0.33 |
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 | PHLPP1 | PHLPP1 | PHLPP1 | 1540 | 0.19 | 0.026 | YES |
2 | FOXO1 | FOXO1 | FOXO1 | 2165 | 0.14 | 0.074 | YES |
3 | AKT2 | AKT2 | AKT2 | 2199 | 0.14 | 0.15 | YES |
4 | AKT3 | AKT3 | AKT3 | 2426 | 0.13 | 0.21 | YES |
5 | CDKN1A | CDKN1A | CDKN1A | 2644 | 0.12 | 0.27 | YES |
6 | NR4A1 | NR4A1 | NR4A1 | 3112 | 0.094 | 0.3 | YES |
7 | THEM4 | THEM4 | THEM4 | 3153 | 0.093 | 0.35 | YES |
8 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 3535 | 0.081 | 0.37 | YES |
9 | TRIB3 | TRIB3 | TRIB3 | 3751 | 0.074 | 0.4 | YES |
10 | BAD | BAD | BAD | 3783 | 0.073 | 0.44 | YES |
11 | FOXO3 | FOXO3 | FOXO3 | 3908 | 0.07 | 0.48 | YES |
12 | GSK3A | GSK3A | GSK3A | 4236 | 0.062 | 0.5 | YES |
13 | FOXO4 | FOXO4 | FOXO4 | 4364 | 0.059 | 0.52 | YES |
14 | MDM2 | MDM2 | MDM2 | 4381 | 0.059 | 0.56 | YES |
15 | CASP9 | CASP9 | CASP9 | 4393 | 0.058 | 0.59 | YES |
16 | PDPK1 | PDPK1 | PDPK1 | 4556 | 0.054 | 0.61 | YES |
17 | TSC2 | TSC2 | TSC2 | 5497 | 0.035 | 0.58 | NO |
18 | PTEN | PTEN | PTEN | 5556 | 0.034 | 0.6 | NO |
19 | AKT1 | AKT1 | AKT1 | 5795 | 0.03 | 0.6 | NO |
20 | CREB1 | CREB1 | CREB1 | 6225 | 0.023 | 0.59 | NO |
21 | AKT1S1 | AKT1S1 | AKT1S1 | 6427 | 0.019 | 0.59 | NO |
22 | MTOR | MTOR | MTOR | 6458 | 0.019 | 0.6 | NO |
23 | RICTOR | RICTOR | RICTOR | 7205 | 0.0066 | 0.56 | NO |
24 | CHUK | CHUK | CHUK | 7834 | -0.0029 | 0.53 | NO |
25 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 8359 | -0.011 | 0.5 | NO |
26 | CDKN1B | CDKN1B | CDKN1B | 8790 | -0.017 | 0.49 | NO |
27 | MLST8 | MLST8 | MLST8 | 9650 | -0.031 | 0.46 | NO |
Figure S41. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS.

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

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 | CCNE1 | CCNE1 | CCNE1 | 864 | 0.29 | 0.1 | YES |
2 | RAF1 | RAF1 | RAF1 | 1440 | 0.2 | 0.18 | YES |
3 | PIK3CA | PIK3CA | PIK3CA | 1702 | 0.18 | 0.26 | YES |
4 | IKBKB | IKBKB | IKBKB | 2548 | 0.12 | 0.28 | YES |
5 | NFKB1 | NFKB1 | NFKB1 | 2602 | 0.12 | 0.34 | YES |
6 | CDKN1A | CDKN1A | CDKN1A | 2644 | 0.12 | 0.4 | YES |
7 | PAK1 | PAK1 | PAK1 | 3073 | 0.096 | 0.42 | YES |
8 | CCND1 | CCND1 | CCND1 | 3619 | 0.078 | 0.44 | YES |
9 | NFKBIA | NFKBIA | NFKBIA | 3634 | 0.078 | 0.48 | YES |
10 | RELA | RELA | RELA | 3807 | 0.073 | 0.5 | YES |
11 | CDK2 | CDK2 | CDK2 | 4092 | 0.066 | 0.52 | YES |
12 | E2F1 | E2F1 | E2F1 | 4106 | 0.065 | 0.56 | YES |
13 | MAPK1 | MAPK1 | MAPK1 | 4117 | 0.065 | 0.59 | YES |
14 | PIK3R1 | PIK3R1 | PIK3R1 | 5107 | 0.043 | 0.56 | NO |
15 | RHOA | RHOA | RHOA | 5411 | 0.036 | 0.56 | NO |
16 | AKT1 | AKT1 | AKT1 | 5795 | 0.03 | 0.56 | NO |
17 | CDK6 | CDK6 | CDK6 | 7279 | 0.0054 | 0.48 | NO |
18 | MAPK3 | MAPK3 | MAPK3 | 7402 | 0.0036 | 0.47 | NO |
19 | CHUK | CHUK | CHUK | 7834 | -0.0029 | 0.45 | NO |
20 | CDK4 | CDK4 | CDK4 | 7868 | -0.0033 | 0.45 | NO |
21 | RAC1 | RAC1 | RAC1 | 7880 | -0.0035 | 0.45 | NO |
22 | CDKN1B | CDKN1B | CDKN1B | 8790 | -0.017 | 0.41 | NO |
23 | HRAS | HRAS | HRAS | 9542 | -0.03 | 0.38 | NO |
24 | IKBKG | IKBKG | IKBKG | 10660 | -0.048 | 0.34 | NO |
25 | RB1 | RB1 | RB1 | 10703 | -0.049 | 0.37 | NO |
26 | TFDP1 | TFDP1 | TFDP1 | 11395 | -0.062 | 0.36 | 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 TYROSINE METABOLISM.

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

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 | EGFR | EGFR | EGFR | 776 | 0.31 | 0.07 | YES |
2 | PHLPP1 | PHLPP1 | PHLPP1 | 1540 | 0.19 | 0.1 | YES |
3 | SRC | SRC | SRC | 1612 | 0.19 | 0.17 | YES |
4 | PIK3CA | PIK3CA | PIK3CA | 1702 | 0.18 | 0.23 | YES |
5 | FOXO1 | FOXO1 | FOXO1 | 2165 | 0.14 | 0.26 | YES |
6 | AKT2 | AKT2 | AKT2 | 2199 | 0.14 | 0.3 | YES |
7 | AKT3 | AKT3 | AKT3 | 2426 | 0.13 | 0.34 | YES |
8 | CDKN1A | CDKN1A | CDKN1A | 2644 | 0.12 | 0.37 | YES |
9 | NR4A1 | NR4A1 | NR4A1 | 3112 | 0.094 | 0.38 | YES |
10 | THEM4 | THEM4 | THEM4 | 3153 | 0.093 | 0.41 | YES |
11 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 3535 | 0.081 | 0.42 | YES |
12 | TRIB3 | TRIB3 | TRIB3 | 3751 | 0.074 | 0.44 | YES |
13 | BAD | BAD | BAD | 3783 | 0.073 | 0.46 | YES |
14 | FOXO3 | FOXO3 | FOXO3 | 3908 | 0.07 | 0.48 | YES |
15 | GSK3A | GSK3A | GSK3A | 4236 | 0.062 | 0.48 | YES |
16 | FOXO4 | FOXO4 | FOXO4 | 4364 | 0.059 | 0.5 | YES |
17 | MDM2 | MDM2 | MDM2 | 4381 | 0.059 | 0.52 | YES |
18 | CASP9 | CASP9 | CASP9 | 4393 | 0.058 | 0.54 | YES |
19 | PDPK1 | PDPK1 | PDPK1 | 4556 | 0.054 | 0.55 | YES |
20 | PIK3R1 | PIK3R1 | PIK3R1 | 5107 | 0.043 | 0.54 | NO |
21 | TSC2 | TSC2 | TSC2 | 5497 | 0.035 | 0.53 | NO |
22 | PTEN | PTEN | PTEN | 5556 | 0.034 | 0.54 | NO |
23 | AKT1 | AKT1 | AKT1 | 5795 | 0.03 | 0.54 | NO |
24 | CSK | CSK | CSK | 6185 | 0.024 | 0.52 | NO |
25 | CREB1 | CREB1 | CREB1 | 6225 | 0.023 | 0.53 | NO |
26 | AKT1S1 | AKT1S1 | AKT1S1 | 6427 | 0.019 | 0.53 | NO |
27 | MTOR | MTOR | MTOR | 6458 | 0.019 | 0.53 | NO |
28 | RICTOR | RICTOR | RICTOR | 7205 | 0.0066 | 0.49 | NO |
29 | EGF | EGF | EGF | 7468 | 0.0023 | 0.48 | NO |
30 | CHUK | CHUK | CHUK | 7834 | -0.0029 | 0.46 | NO |
31 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 8359 | -0.011 | 0.43 | NO |
32 | GRB2 | GRB2 | GRB2 | 8736 | -0.016 | 0.42 | NO |
33 | CDKN1B | CDKN1B | CDKN1B | 8790 | -0.017 | 0.42 | NO |
34 | MLST8 | MLST8 | MLST8 | 9650 | -0.031 | 0.38 | NO |
35 | GAB1 | GAB1 | GAB1 | 10145 | -0.04 | 0.37 | NO |
36 | PAG1 | PAG1 | PAG1 | 14521 | -0.16 | 0.19 | NO |
Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA RACCYCD PATHWAY.

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

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 | NTRK1 | NTRK1 | NTRK1 | 755 | 0.31 | 0.069 | YES |
2 | PHLPP1 | PHLPP1 | PHLPP1 | 1540 | 0.19 | 0.094 | YES |
3 | PIK3CA | PIK3CA | PIK3CA | 1702 | 0.18 | 0.15 | YES |
4 | FOXO1 | FOXO1 | FOXO1 | 2165 | 0.14 | 0.17 | YES |
5 | AKT2 | AKT2 | AKT2 | 2199 | 0.14 | 0.22 | YES |
6 | AKT3 | AKT3 | AKT3 | 2426 | 0.13 | 0.26 | YES |
7 | CDKN1A | CDKN1A | CDKN1A | 2644 | 0.12 | 0.28 | YES |
8 | PIK3CB | PIK3CB | PIK3CB | 2837 | 0.11 | 0.31 | YES |
9 | NR4A1 | NR4A1 | NR4A1 | 3112 | 0.094 | 0.33 | YES |
10 | THEM4 | THEM4 | THEM4 | 3153 | 0.093 | 0.36 | YES |
11 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 3535 | 0.081 | 0.37 | YES |
12 | TRIB3 | TRIB3 | TRIB3 | 3751 | 0.074 | 0.38 | YES |
13 | BAD | BAD | BAD | 3783 | 0.073 | 0.41 | YES |
14 | FOXO3 | FOXO3 | FOXO3 | 3908 | 0.07 | 0.42 | YES |
15 | GSK3A | GSK3A | GSK3A | 4236 | 0.062 | 0.43 | YES |
16 | FOXO4 | FOXO4 | FOXO4 | 4364 | 0.059 | 0.44 | YES |
17 | MDM2 | MDM2 | MDM2 | 4381 | 0.059 | 0.46 | YES |
18 | CASP9 | CASP9 | CASP9 | 4393 | 0.058 | 0.48 | YES |
19 | IRS1 | IRS1 | IRS1 | 4411 | 0.058 | 0.5 | YES |
20 | PDPK1 | PDPK1 | PDPK1 | 4556 | 0.054 | 0.51 | YES |
21 | IRS2 | IRS2 | IRS2 | 5094 | 0.043 | 0.5 | YES |
22 | PIK3R1 | PIK3R1 | PIK3R1 | 5107 | 0.043 | 0.51 | YES |
23 | RHOA | RHOA | RHOA | 5411 | 0.036 | 0.51 | YES |
24 | TSC2 | TSC2 | TSC2 | 5497 | 0.035 | 0.52 | YES |
25 | PTEN | PTEN | PTEN | 5556 | 0.034 | 0.53 | YES |
26 | AKT1 | AKT1 | AKT1 | 5795 | 0.03 | 0.52 | NO |
27 | CREB1 | CREB1 | CREB1 | 6225 | 0.023 | 0.51 | NO |
28 | AKT1S1 | AKT1S1 | AKT1S1 | 6427 | 0.019 | 0.5 | NO |
29 | MTOR | MTOR | MTOR | 6458 | 0.019 | 0.51 | NO |
30 | RICTOR | RICTOR | RICTOR | 7205 | 0.0066 | 0.47 | NO |
31 | PIK3R2 | PIK3R2 | PIK3R2 | 7497 | 0.002 | 0.45 | NO |
32 | CHUK | CHUK | CHUK | 7834 | -0.0029 | 0.44 | NO |
33 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 8359 | -0.011 | 0.41 | NO |
34 | CDKN1B | CDKN1B | CDKN1B | 8790 | -0.017 | 0.39 | NO |
35 | MLST8 | MLST8 | MLST8 | 9650 | -0.031 | 0.36 | NO |
36 | NGF | NGF | NGF | 16337 | -0.29 | 0.084 | NO |
Figure S47. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA INTEGRIN PATHWAY.

Figure S48. 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

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 | RAF1 | RAF1 | RAF1 | 1440 | 0.2 | 0.0097 | YES |
2 | SRC | SRC | SRC | 1612 | 0.19 | 0.083 | YES |
3 | FOXO1 | FOXO1 | FOXO1 | 2165 | 0.14 | 0.12 | YES |
4 | AKT2 | AKT2 | AKT2 | 2199 | 0.14 | 0.18 | YES |
5 | AKT3 | AKT3 | AKT3 | 2426 | 0.13 | 0.22 | YES |
6 | CDKN1A | CDKN1A | CDKN1A | 2644 | 0.12 | 0.26 | YES |
7 | SFN | SFN | SFN | 2674 | 0.11 | 0.31 | YES |
8 | YWHAH | YWHAH | YWHAH | 3610 | 0.079 | 0.29 | YES |
9 | BAD | BAD | BAD | 3783 | 0.073 | 0.31 | YES |
10 | FOXO3 | FOXO3 | FOXO3 | 3908 | 0.07 | 0.34 | YES |
11 | KPNA1 | KPNA1 | KPNA1 | 3984 | 0.068 | 0.36 | YES |
12 | GSK3A | GSK3A | GSK3A | 4236 | 0.062 | 0.38 | YES |
13 | FOXO4 | FOXO4 | FOXO4 | 4364 | 0.059 | 0.39 | YES |
14 | CASP9 | CASP9 | CASP9 | 4393 | 0.058 | 0.42 | YES |
15 | PDPK1 | PDPK1 | PDPK1 | 4556 | 0.054 | 0.43 | YES |
16 | GSK3B | GSK3B | GSK3B | 4790 | 0.05 | 0.44 | YES |
17 | BCL2L1 | BCL2L1 | BCL2L1 | 5117 | 0.042 | 0.44 | YES |
18 | YWHAB | YWHAB | YWHAB | 5205 | 0.04 | 0.46 | YES |
19 | PRKDC | PRKDC | PRKDC | 5464 | 0.036 | 0.46 | YES |
20 | AKT1 | AKT1 | AKT1 | 5795 | 0.03 | 0.45 | NO |
21 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 6073 | 0.025 | 0.45 | NO |
22 | MAP3K5 | MAP3K5 | MAP3K5 | 6131 | 0.024 | 0.46 | NO |
23 | MTOR | MTOR | MTOR | 6458 | 0.019 | 0.44 | NO |
24 | PRKACA | PRKACA | PRKACA | 6580 | 0.017 | 0.45 | NO |
25 | RICTOR | RICTOR | RICTOR | 7205 | 0.0066 | 0.41 | NO |
26 | YWHAG | YWHAG | YWHAG | 7769 | -0.002 | 0.38 | NO |
27 | CHUK | CHUK | CHUK | 7834 | -0.0029 | 0.38 | NO |
28 | YWHAZ | YWHAZ | YWHAZ | 7967 | -0.0049 | 0.38 | NO |
29 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 8359 | -0.011 | 0.36 | NO |
30 | CDKN1B | CDKN1B | CDKN1B | 8790 | -0.017 | 0.34 | NO |
31 | MLST8 | MLST8 | MLST8 | 9650 | -0.031 | 0.31 | NO |
32 | YWHAE | YWHAE | YWHAE | 10444 | -0.045 | 0.28 | NO |
33 | TBC1D4 | TBC1D4 | TBC1D4 | 10612 | -0.047 | 0.29 | NO |
34 | YWHAQ | YWHAQ | YWHAQ | 10900 | -0.052 | 0.3 | NO |
35 | SLC2A4 | SLC2A4 | SLC2A4 | 15191 | -0.2 | 0.15 | 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: PID WNT NONCANONICAL PATHWAY.

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

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 | IGF1 | IGF1 | IGF1 | 64 | 0.69 | 0.28 | YES |
2 | RAF1 | RAF1 | RAF1 | 1440 | 0.2 | 0.29 | YES |
3 | PIK3CA | PIK3CA | PIK3CA | 1702 | 0.18 | 0.35 | YES |
4 | PRKD1 | PRKD1 | PRKD1 | 2259 | 0.14 | 0.38 | YES |
5 | PRKCD | PRKCD | PRKCD | 3311 | 0.087 | 0.36 | YES |
6 | GRB10 | GRB10 | GRB10 | 3719 | 0.075 | 0.36 | YES |
7 | BAD | BAD | BAD | 3783 | 0.073 | 0.39 | YES |
8 | PXN | PXN | PXN | 4039 | 0.067 | 0.4 | YES |
9 | CRKL | CRKL | CRKL | 4069 | 0.066 | 0.43 | YES |
10 | IGF1R | IGF1R | IGF1R | 4404 | 0.058 | 0.44 | YES |
11 | IRS1 | IRS1 | IRS1 | 4411 | 0.058 | 0.46 | YES |
12 | PDPK1 | PDPK1 | PDPK1 | 4556 | 0.054 | 0.47 | YES |
13 | IRS2 | IRS2 | IRS2 | 5094 | 0.043 | 0.46 | YES |
14 | PIK3R1 | PIK3R1 | PIK3R1 | 5107 | 0.043 | 0.48 | YES |
15 | PTPN11 | PTPN11 | PTPN11 | 5355 | 0.038 | 0.48 | YES |
16 | BCAR1 | BCAR1 | BCAR1 | 5608 | 0.033 | 0.48 | YES |
17 | AKT1 | AKT1 | AKT1 | 5795 | 0.03 | 0.48 | YES |
18 | PTPN1 | PTPN1 | PTPN1 | 6234 | 0.023 | 0.47 | NO |
19 | PTK2 | PTK2 | PTK2 | 6299 | 0.022 | 0.47 | NO |
20 | PRKCZ | PRKCZ | PRKCZ | 6347 | 0.021 | 0.48 | NO |
21 | YWHAZ | YWHAZ | YWHAZ | 7967 | -0.0049 | 0.39 | NO |
22 | CRK | CRK | CRK | 8318 | -0.01 | 0.38 | NO |
23 | SOS1 | SOS1 | SOS1 | 8339 | -0.01 | 0.38 | NO |
24 | GRB2 | GRB2 | GRB2 | 8736 | -0.016 | 0.36 | NO |
25 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 9032 | -0.021 | 0.36 | NO |
26 | HRAS | HRAS | HRAS | 9542 | -0.03 | 0.34 | NO |
27 | SHC1 | SHC1 | SHC1 | 10200 | -0.04 | 0.32 | NO |
28 | YWHAE | YWHAE | YWHAE | 10444 | -0.045 | 0.32 | NO |
29 | GNB2L1 | GNB2L1 | GNB2L1 | 11270 | -0.06 | 0.3 | NO |
30 | NCK2 | NCK2 | NCK2 | 14438 | -0.16 | 0.19 | 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: PID NECTIN PATHWAY.

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

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 | CLDN1 | CLDN1 | CLDN1 | 457 | 0.39 | 0.14 | YES |
2 | SRC | SRC | SRC | 1612 | 0.19 | 0.16 | YES |
3 | PIK3CA | PIK3CA | PIK3CA | 1702 | 0.18 | 0.23 | YES |
4 | CDH1 | CDH1 | CDH1 | 1775 | 0.17 | 0.3 | YES |
5 | PVRL1 | PVRL1 | PVRL1 | 1961 | 0.16 | 0.36 | YES |
6 | ITGAV | ITGAV | ITGAV | 2533 | 0.12 | 0.38 | YES |
7 | PVRL2 | PVRL2 | PVRL2 | 2694 | 0.11 | 0.42 | YES |
8 | PVR | PVR | PVR | 2929 | 0.1 | 0.45 | YES |
9 | FARP2 | FARP2 | FARP2 | 3040 | 0.098 | 0.49 | YES |
10 | ITGB3 | ITGB3 | ITGB3 | 3136 | 0.094 | 0.52 | YES |
11 | MLLT4 | MLLT4 | MLLT4 | 3646 | 0.077 | 0.53 | YES |
12 | CTNNB1 | CTNNB1 | CTNNB1 | 3792 | 0.073 | 0.55 | YES |
13 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 4406 | 0.058 | 0.54 | YES |
14 | PIP5K1C | PIP5K1C | PIP5K1C | 4508 | 0.055 | 0.56 | YES |
15 | PIK3R1 | PIK3R1 | PIK3R1 | 5107 | 0.043 | 0.55 | NO |
16 | RAP1B | RAP1B | RAP1B | 6176 | 0.024 | 0.5 | NO |
17 | PTK2 | PTK2 | PTK2 | 6299 | 0.022 | 0.5 | NO |
18 | CDC42 | CDC42 | CDC42 | 6967 | 0.011 | 0.47 | NO |
19 | CTNNA1 | CTNNA1 | CTNNA1 | 7168 | 0.0071 | 0.46 | NO |
20 | F11R | F11R | F11R | 7466 | 0.0023 | 0.44 | NO |
21 | PTPRM | PTPRM | PTPRM | 7491 | 0.0021 | 0.44 | NO |
22 | IQGAP1 | IQGAP1 | IQGAP1 | 7666 | -0.00048 | 0.43 | NO |
23 | RAC1 | RAC1 | RAC1 | 7880 | -0.0035 | 0.42 | NO |
24 | CRK | CRK | CRK | 8318 | -0.01 | 0.4 | NO |
25 | RAP1A | RAP1A | RAP1A | 8609 | -0.014 | 0.39 | NO |
26 | PVRL3 | PVRL3 | PVRL3 | 9645 | -0.031 | 0.35 | NO |
27 | PDGFB | PDGFB | PDGFB | 9853 | -0.034 | 0.35 | NO |
28 | VAV2 | VAV2 | VAV2 | 10197 | -0.04 | 0.35 | NO |
29 | TLN1 | TLN1 | TLN1 | 11253 | -0.059 | 0.31 | NO |
30 | PDGFRB | PDGFRB | PDGFRB | 13692 | -0.13 | 0.23 | 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: PID HNF3BPATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: PID HNF3BPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | DDC | DDC | DDC | 62 | 0.69 | 0.098 | YES |
2 | TAT | TAT | TAT | 109 | 0.62 | 0.19 | YES |
3 | ADH6 | ADH6 | ADH6 | 191 | 0.53 | 0.26 | YES |
4 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 385 | 0.43 | 0.31 | YES |
5 | ADH1C | ADH1C | ADH1C | 400 | 0.42 | 0.37 | YES |
6 | TH | TH | TH | 629 | 0.34 | 0.41 | YES |
7 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 927 | 0.28 | 0.43 | YES |
8 | MAOA | MAOA | MAOA | 939 | 0.28 | 0.47 | YES |
9 | TYR | TYR | TYR | 1051 | 0.26 | 0.5 | YES |
10 | ADH1A | ADH1A | ADH1A | 1294 | 0.22 | 0.52 | YES |
11 | ADH4 | ADH4 | ADH4 | 1314 | 0.22 | 0.55 | YES |
12 | MAOB | MAOB | MAOB | 1433 | 0.21 | 0.58 | YES |
13 | ADH7 | ADH7 | ADH7 | 1491 | 0.2 | 0.6 | YES |
14 | PNMT | PNMT | PNMT | 1564 | 0.19 | 0.63 | YES |
15 | DBH | DBH | DBH | 1585 | 0.19 | 0.65 | YES |
16 | AOC2 | AOC2 | AOC2 | 1999 | 0.15 | 0.65 | NO |
17 | METTL6 | METTL6 | METTL6 | 3316 | 0.087 | 0.59 | NO |
18 | HPD | HPD | HPD | 3980 | 0.068 | 0.56 | NO |
19 | HGD | HGD | HGD | 3992 | 0.068 | 0.57 | NO |
20 | COMT | COMT | COMT | 5452 | 0.036 | 0.5 | NO |
21 | LCMT2 | LCMT2 | LCMT2 | 5807 | 0.03 | 0.48 | NO |
22 | NAT6 | NAT6 | NAT6 | 6326 | 0.021 | 0.46 | NO |
23 | HEMK1 | HEMK1 | HEMK1 | 6392 | 0.02 | 0.45 | NO |
24 | ADH5 | ADH5 | ADH5 | 6657 | 0.016 | 0.44 | NO |
25 | AOX1 | AOX1 | AOX1 | 7039 | 0.0093 | 0.42 | NO |
26 | GSTZ1 | GSTZ1 | GSTZ1 | 7519 | 0.0016 | 0.4 | NO |
27 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 7652 | -0.00023 | 0.39 | NO |
28 | LCMT1 | LCMT1 | LCMT1 | 7723 | -0.0014 | 0.38 | NO |
29 | GOT2 | GOT2 | GOT2 | 7827 | -0.0028 | 0.38 | NO |
30 | FAH | FAH | FAH | 8147 | -0.0076 | 0.36 | NO |
31 | GOT1 | GOT1 | GOT1 | 8759 | -0.016 | 0.33 | NO |
32 | MIF | MIF | MIF | 8808 | -0.017 | 0.33 | NO |
33 | WBSCR22 | WBSCR22 | WBSCR22 | 10456 | -0.045 | 0.24 | NO |
34 | AOC3 | AOC3 | AOC3 | 11335 | -0.061 | 0.2 | NO |
35 | METTL2B | METTL2B | METTL2B | 12628 | -0.091 | 0.14 | NO |
36 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 12745 | -0.095 | 0.15 | NO |
37 | IL4I1 | IL4I1 | IL4I1 | 13512 | -0.12 | 0.13 | NO |
38 | TRMT11 | TRMT11 | TRMT11 | 14283 | -0.15 | 0.1 | NO |
39 | DCT | DCT | DCT | 14585 | -0.16 | 0.11 | NO |
40 | TYRP1 | TYRP1 | TYRP1 | 14738 | -0.17 | 0.13 | NO |
41 | ADH1B | ADH1B | ADH1B | 16508 | -0.31 | 0.074 | 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: PID IGF1 PATHWAY.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: PID IGF1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | EGFR | EGFR | EGFR | 776 | 0.31 | 0.052 | YES |
2 | ERBB4 | ERBB4 | ERBB4 | 1285 | 0.22 | 0.093 | YES |
3 | ERBB3 | ERBB3 | ERBB3 | 1536 | 0.2 | 0.14 | YES |
4 | PHLPP1 | PHLPP1 | PHLPP1 | 1540 | 0.19 | 0.2 | YES |
5 | PIK3CA | PIK3CA | PIK3CA | 1702 | 0.18 | 0.25 | YES |
6 | FOXO1 | FOXO1 | FOXO1 | 2165 | 0.14 | 0.26 | YES |
7 | AKT2 | AKT2 | AKT2 | 2199 | 0.14 | 0.31 | YES |
8 | AKT3 | AKT3 | AKT3 | 2426 | 0.13 | 0.33 | YES |
9 | CDKN1A | CDKN1A | CDKN1A | 2644 | 0.12 | 0.36 | YES |
10 | NR4A1 | NR4A1 | NR4A1 | 3112 | 0.094 | 0.36 | YES |
11 | THEM4 | THEM4 | THEM4 | 3153 | 0.093 | 0.39 | YES |
12 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 3535 | 0.081 | 0.39 | YES |
13 | TRIB3 | TRIB3 | TRIB3 | 3751 | 0.074 | 0.4 | YES |
14 | BAD | BAD | BAD | 3783 | 0.073 | 0.42 | YES |
15 | FOXO3 | FOXO3 | FOXO3 | 3908 | 0.07 | 0.44 | YES |
16 | ERBB2 | ERBB2 | ERBB2 | 3942 | 0.069 | 0.46 | YES |
17 | GSK3A | GSK3A | GSK3A | 4236 | 0.062 | 0.46 | YES |
18 | FOXO4 | FOXO4 | FOXO4 | 4364 | 0.059 | 0.47 | YES |
19 | MDM2 | MDM2 | MDM2 | 4381 | 0.059 | 0.49 | YES |
20 | CASP9 | CASP9 | CASP9 | 4393 | 0.058 | 0.51 | YES |
21 | PDPK1 | PDPK1 | PDPK1 | 4556 | 0.054 | 0.51 | YES |
22 | PIK3R1 | PIK3R1 | PIK3R1 | 5107 | 0.043 | 0.5 | NO |
23 | NRG2 | NRG2 | NRG2 | 5156 | 0.042 | 0.51 | NO |
24 | TSC2 | TSC2 | TSC2 | 5497 | 0.035 | 0.5 | NO |
25 | PTEN | PTEN | PTEN | 5556 | 0.034 | 0.5 | NO |
26 | AKT1 | AKT1 | AKT1 | 5795 | 0.03 | 0.5 | NO |
27 | CREB1 | CREB1 | CREB1 | 6225 | 0.023 | 0.48 | NO |
28 | AKT1S1 | AKT1S1 | AKT1S1 | 6427 | 0.019 | 0.48 | NO |
29 | MTOR | MTOR | MTOR | 6458 | 0.019 | 0.48 | NO |
30 | EREG | EREG | EREG | 6935 | 0.011 | 0.46 | NO |
31 | RICTOR | RICTOR | RICTOR | 7205 | 0.0066 | 0.45 | NO |
32 | HBEGF | HBEGF | HBEGF | 7265 | 0.0057 | 0.44 | NO |
33 | EGF | EGF | EGF | 7468 | 0.0023 | 0.44 | NO |
34 | CHUK | CHUK | CHUK | 7834 | -0.0029 | 0.42 | NO |
35 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 8359 | -0.011 | 0.39 | NO |
36 | GRB2 | GRB2 | GRB2 | 8736 | -0.016 | 0.37 | NO |
37 | CDKN1B | CDKN1B | CDKN1B | 8790 | -0.017 | 0.38 | NO |
38 | MLST8 | MLST8 | MLST8 | 9650 | -0.031 | 0.34 | NO |
39 | GAB1 | GAB1 | GAB1 | 10145 | -0.04 | 0.32 | NO |
40 | NRG4 | NRG4 | NRG4 | 10399 | -0.044 | 0.32 | NO |
41 | NRG1 | NRG1 | NRG1 | 11906 | -0.074 | 0.26 | NO |
42 | BTC | BTC | BTC | 15722 | -0.24 | 0.12 | 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: PID AR TF PATHWAY.

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

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 | G6PC | G6PC | G6PC | 171 | 0.54 | 0.056 | YES |
2 | ADH6 | ADH6 | ADH6 | 191 | 0.53 | 0.12 | YES |
3 | PKLR | PKLR | PKLR | 230 | 0.5 | 0.18 | YES |
4 | ALDOB | ALDOB | ALDOB | 247 | 0.5 | 0.24 | YES |
5 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 385 | 0.43 | 0.28 | YES |
6 | ADH1C | ADH1C | ADH1C | 400 | 0.42 | 0.33 | YES |
7 | ALDOC | ALDOC | ALDOC | 484 | 0.38 | 0.37 | YES |
8 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 927 | 0.28 | 0.38 | YES |
9 | PCK1 | PCK1 | PCK1 | 967 | 0.27 | 0.41 | YES |
10 | G6PC2 | G6PC2 | G6PC2 | 1130 | 0.24 | 0.43 | YES |
11 | ADH1A | ADH1A | ADH1A | 1294 | 0.22 | 0.45 | YES |
12 | ADH4 | ADH4 | ADH4 | 1314 | 0.22 | 0.48 | YES |
13 | ADH7 | ADH7 | ADH7 | 1491 | 0.2 | 0.49 | YES |
14 | GCK | GCK | GCK | 1556 | 0.19 | 0.51 | YES |
15 | FBP1 | FBP1 | FBP1 | 1715 | 0.18 | 0.52 | YES |
16 | GALM | GALM | GALM | 2380 | 0.13 | 0.5 | NO |
17 | LDHAL6A | LDHAL6A | LDHAL6A | 2716 | 0.11 | 0.5 | NO |
18 | ENO2 | ENO2 | ENO2 | 2777 | 0.11 | 0.51 | NO |
19 | PGM2 | PGM2 | PGM2 | 4174 | 0.063 | 0.44 | NO |
20 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4488 | 0.056 | 0.42 | NO |
21 | HK2 | HK2 | HK2 | 4761 | 0.05 | 0.42 | NO |
22 | HK1 | HK1 | HK1 | 5108 | 0.043 | 0.4 | NO |
23 | PKM2 | PKM2 | PKM2 | 5111 | 0.043 | 0.41 | NO |
24 | PGK1 | PGK1 | PGK1 | 5914 | 0.028 | 0.36 | NO |
25 | PDHB | PDHB | PDHB | 5917 | 0.028 | 0.37 | NO |
26 | LDHB | LDHB | LDHB | 5919 | 0.028 | 0.37 | NO |
27 | TPI1 | TPI1 | TPI1 | 5980 | 0.027 | 0.37 | NO |
28 | PFKL | PFKL | PFKL | 6320 | 0.022 | 0.36 | NO |
29 | GAPDH | GAPDH | GAPDH | 6529 | 0.018 | 0.34 | NO |
30 | ADH5 | ADH5 | ADH5 | 6657 | 0.016 | 0.34 | NO |
31 | LDHA | LDHA | LDHA | 6718 | 0.015 | 0.34 | NO |
32 | PGM1 | PGM1 | PGM1 | 6983 | 0.01 | 0.32 | NO |
33 | ALDOA | ALDOA | ALDOA | 7394 | 0.0037 | 0.3 | NO |
34 | AKR1A1 | AKR1A1 | AKR1A1 | 7503 | 0.0018 | 0.3 | NO |
35 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 7652 | -0.00023 | 0.29 | NO |
36 | GPI | GPI | GPI | 8019 | -0.0056 | 0.27 | NO |
37 | BPGM | BPGM | BPGM | 8063 | -0.0063 | 0.27 | NO |
38 | ENO1 | ENO1 | ENO1 | 8302 | -0.0099 | 0.25 | NO |
39 | PGAM1 | PGAM1 | PGAM1 | 8314 | -0.01 | 0.26 | NO |
40 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 8892 | -0.019 | 0.22 | NO |
41 | PFKM | PFKM | PFKM | 8899 | -0.019 | 0.23 | NO |
42 | LDHC | LDHC | LDHC | 9456 | -0.028 | 0.2 | NO |
43 | DLD | DLD | DLD | 9726 | -0.032 | 0.19 | NO |
44 | PGAM4 | PGAM4 | PGAM4 | 9922 | -0.036 | 0.18 | NO |
45 | ACSS1 | ACSS1 | ACSS1 | 10501 | -0.046 | 0.15 | NO |
46 | PFKP | PFKP | PFKP | 10507 | -0.046 | 0.16 | NO |
47 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 10528 | -0.046 | 0.16 | NO |
48 | ACSS2 | ACSS2 | ACSS2 | 10783 | -0.05 | 0.16 | NO |
49 | DLAT | DLAT | DLAT | 11829 | -0.072 | 0.1 | NO |
50 | PDHA1 | PDHA1 | PDHA1 | 12356 | -0.084 | 0.086 | NO |
51 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 12745 | -0.095 | 0.075 | NO |
52 | PCK2 | PCK2 | PCK2 | 13119 | -0.11 | 0.067 | NO |
53 | PGAM2 | PGAM2 | PGAM2 | 14264 | -0.15 | 0.021 | NO |
54 | ALDH2 | ALDH2 | ALDH2 | 14278 | -0.15 | 0.039 | NO |
55 | LDHAL6B | LDHAL6B | LDHAL6B | 14289 | -0.15 | 0.057 | NO |
56 | ENO3 | ENO3 | ENO3 | 15030 | -0.19 | 0.038 | NO |
57 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 15055 | -0.19 | 0.06 | NO |
58 | ADH1B | ADH1B | ADH1B | 16508 | -0.31 | 0.016 | NO |
59 | HK3 | HK3 | HK3 | 17461 | -0.48 | 0.02 | NO |
Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ECADHERIN STABILIZATION PATHWAY.

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

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION | 44 | genes.ES.table | 0.48 | 1.5 | 0.071 | 1 | 0.93 | 0.52 | 0.26 | 0.39 | 0.88 | 0.44 |
KEGG PROPANOATE METABOLISM | 32 | genes.ES.table | 0.59 | 1.7 | 0.039 | 1 | 0.83 | 0.59 | 0.27 | 0.43 | 0.8 | 0.42 |
KEGG ADHERENS JUNCTION | 73 | genes.ES.table | 0.36 | 1.5 | 0.041 | 1 | 0.96 | 0.29 | 0.2 | 0.23 | 0.87 | 0.44 |
BIOCARTA AT1R PATHWAY | 32 | genes.ES.table | 0.45 | 1.8 | 0.016 | 1 | 0.55 | 0.31 | 0.17 | 0.26 | 0.49 | 0.34 |
BIOCARTA EGF PATHWAY | 31 | genes.ES.table | 0.47 | 1.6 | 0.024 | 1 | 0.86 | 0.39 | 0.22 | 0.3 | 0.62 | 0.34 |
BIOCARTA PPARA PATHWAY | 55 | genes.ES.table | 0.44 | 1.5 | 0.04 | 1 | 0.96 | 0.42 | 0.22 | 0.33 | 0.85 | 0.43 |
BIOCARTA PDGF PATHWAY | 32 | genes.ES.table | 0.54 | 1.6 | 0.01 | 1 | 0.84 | 0.44 | 0.22 | 0.34 | 0.76 | 0.41 |
BIOCARTA VEGF PATHWAY | 29 | genes.ES.table | 0.46 | 1.5 | 0.063 | 1 | 0.94 | 0.34 | 0.23 | 0.27 | 0.86 | 0.42 |
PID S1P S1P3 PATHWAY | 29 | genes.ES.table | 0.53 | 1.6 | 0.023 | 1 | 0.85 | 0.45 | 0.26 | 0.33 | 0.67 | 0.37 |
PID AVB3 OPN PATHWAY | 31 | genes.ES.table | 0.49 | 1.5 | 0.055 | 1 | 0.94 | 0.29 | 0.17 | 0.24 | 0.84 | 0.42 |
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 | NOS3 | NOS3 | NOS3 | 661 | 0.36 | 0.019 | YES |
2 | PLD2 | PLD2 | PLD2 | 783 | 0.34 | 0.064 | YES |
3 | TEK | TEK | TEK | 798 | 0.34 | 0.12 | YES |
4 | GRB14 | GRB14 | GRB14 | 917 | 0.32 | 0.16 | YES |
5 | ANGPT2 | ANGPT2 | ANGPT2 | 1235 | 0.27 | 0.18 | YES |
6 | AGTR1 | AGTR1 | AGTR1 | 1501 | 0.25 | 0.21 | YES |
7 | ETS1 | ETS1 | ETS1 | 1713 | 0.23 | 0.23 | YES |
8 | ANGPT4 | ANGPT4 | ANGPT4 | 1885 | 0.22 | 0.25 | YES |
9 | TNF | TNF | TNF | 1901 | 0.22 | 0.29 | YES |
10 | ELF1 | ELF1 | ELF1 | 1959 | 0.21 | 0.32 | YES |
11 | MAPK8 | MAPK8 | MAPK8 | 2252 | 0.19 | 0.33 | YES |
12 | CRK | CRK | CRK | 2258 | 0.19 | 0.36 | YES |
13 | FES | FES | FES | 2454 | 0.18 | 0.38 | YES |
14 | PIK3CA | PIK3CA | PIK3CA | 2559 | 0.18 | 0.4 | YES |
15 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 2627 | 0.18 | 0.42 | YES |
16 | STAT5B | STAT5B | STAT5B | 2658 | 0.17 | 0.45 | YES |
17 | BMX | BMX | BMX | 2766 | 0.17 | 0.47 | YES |
18 | FGF2 | FGF2 | FGF2 | 2860 | 0.16 | 0.49 | YES |
19 | FOXO1 | FOXO1 | FOXO1 | 2923 | 0.16 | 0.51 | YES |
20 | GRB7 | GRB7 | GRB7 | 3149 | 0.15 | 0.52 | YES |
21 | PLG | PLG | PLG | 3295 | 0.14 | 0.53 | YES |
22 | ITGA5 | ITGA5 | ITGA5 | 3545 | 0.13 | 0.54 | YES |
23 | FYN | FYN | FYN | 3590 | 0.13 | 0.56 | YES |
24 | CDKN1A | CDKN1A | CDKN1A | 3792 | 0.12 | 0.57 | YES |
25 | STAT5A | STAT5A | STAT5A | 3928 | 0.12 | 0.58 | YES |
26 | FN1 | FN1 | FN1 | 4308 | 0.1 | 0.57 | NO |
27 | ITGB1 | ITGB1 | ITGB1 | 4833 | 0.088 | 0.56 | NO |
28 | PTK2 | PTK2 | PTK2 | 5146 | 0.078 | 0.55 | NO |
29 | PTPN11 | PTPN11 | PTPN11 | 5284 | 0.074 | 0.55 | NO |
30 | MMP2 | MMP2 | MMP2 | 5497 | 0.068 | 0.55 | NO |
31 | GRB2 | GRB2 | GRB2 | 5671 | 0.062 | 0.55 | NO |
32 | MAPK14 | MAPK14 | MAPK14 | 6505 | 0.041 | 0.51 | NO |
33 | MAPK1 | MAPK1 | MAPK1 | 6728 | 0.036 | 0.5 | NO |
34 | RAC1 | RAC1 | RAC1 | 6796 | 0.034 | 0.51 | NO |
35 | MAPK3 | MAPK3 | MAPK3 | 6903 | 0.032 | 0.5 | NO |
36 | SHC1 | SHC1 | SHC1 | 7427 | 0.019 | 0.48 | NO |
37 | RASA1 | RASA1 | RASA1 | 7450 | 0.019 | 0.48 | NO |
38 | PXN | PXN | PXN | 7485 | 0.018 | 0.48 | NO |
39 | PIK3R1 | PIK3R1 | PIK3R1 | 8099 | 0.0029 | 0.45 | NO |
40 | TNIP2 | TNIP2 | TNIP2 | 8243 | -0.00061 | 0.44 | NO |
41 | NFKB1 | NFKB1 | NFKB1 | 8782 | -0.014 | 0.41 | NO |
42 | ELF2 | ELF2 | ELF2 | 9149 | -0.022 | 0.39 | NO |
43 | RELA | RELA | RELA | 9780 | -0.037 | 0.36 | NO |
44 | PAK1 | PAK1 | PAK1 | 9861 | -0.039 | 0.37 | NO |
45 | NCK1 | NCK1 | NCK1 | 10543 | -0.055 | 0.34 | NO |
46 | ELK1 | ELK1 | ELK1 | 11836 | -0.09 | 0.28 | NO |
47 | DOK2 | DOK2 | DOK2 | 11953 | -0.093 | 0.28 | NO |
48 | AKT1 | AKT1 | AKT1 | 11975 | -0.094 | 0.3 | NO |
49 | ANGPT1 | ANGPT1 | ANGPT1 | 14613 | -0.2 | 0.18 | 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S62. 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

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 | AGT | AGT | AGT | 458 | 0.42 | 0.091 | YES |
2 | ATF2 | ATF2 | ATF2 | 815 | 0.33 | 0.16 | YES |
3 | AGTR1 | AGTR1 | AGTR1 | 1501 | 0.25 | 0.2 | YES |
4 | MAP2K4 | MAP2K4 | MAP2K4 | 2035 | 0.21 | 0.22 | YES |
5 | MAPK8 | MAPK8 | MAPK8 | 2252 | 0.19 | 0.27 | YES |
6 | PRKCA | PRKCA | PRKCA | 2439 | 0.18 | 0.31 | YES |
7 | SOS1 | SOS1 | SOS1 | 2646 | 0.17 | 0.34 | YES |
8 | MEF2C | MEF2C | MEF2C | 2777 | 0.17 | 0.38 | YES |
9 | MEF2D | MEF2D | MEF2D | 3008 | 0.16 | 0.42 | YES |
10 | EGFR | EGFR | EGFR | 3098 | 0.15 | 0.45 | YES |
11 | PTK2 | PTK2 | PTK2 | 5146 | 0.078 | 0.36 | NO |
12 | CALM2 | CALM2 | CALM2 | 5626 | 0.064 | 0.35 | NO |
13 | GRB2 | GRB2 | GRB2 | 5671 | 0.062 | 0.36 | NO |
14 | JUN | JUN | JUN | 5906 | 0.056 | 0.37 | NO |
15 | PRKCB | PRKCB | PRKCB | 6098 | 0.051 | 0.37 | NO |
16 | MAPK1 | MAPK1 | MAPK1 | 6728 | 0.036 | 0.35 | NO |
17 | RAC1 | RAC1 | RAC1 | 6796 | 0.034 | 0.35 | NO |
18 | MAPK3 | MAPK3 | MAPK3 | 6903 | 0.032 | 0.36 | NO |
19 | MEF2A | MEF2A | MEF2A | 7266 | 0.023 | 0.34 | NO |
20 | GNAQ | GNAQ | GNAQ | 7331 | 0.021 | 0.34 | NO |
21 | SHC1 | SHC1 | SHC1 | 7427 | 0.019 | 0.34 | NO |
22 | MAP2K1 | MAP2K1 | MAP2K1 | 8196 | 0.00046 | 0.3 | NO |
23 | SRC | SRC | SRC | 8213 | 0.000058 | 0.3 | NO |
24 | MAP3K1 | MAP3K1 | MAP3K1 | 8592 | -0.0086 | 0.28 | NO |
25 | PAK1 | PAK1 | PAK1 | 9861 | -0.039 | 0.22 | NO |
26 | CALM1 | CALM1 | CALM1 | 11136 | -0.071 | 0.17 | NO |
27 | ELK1 | ELK1 | ELK1 | 11836 | -0.09 | 0.15 | NO |
28 | PTK2B | PTK2B | PTK2B | 11881 | -0.091 | 0.18 | NO |
29 | HRAS | HRAS | HRAS | 13120 | -0.13 | 0.14 | NO |
30 | RAF1 | RAF1 | RAF1 | 13125 | -0.13 | 0.18 | NO |
31 | MAP2K2 | MAP2K2 | MAP2K2 | 13425 | -0.14 | 0.2 | NO |
32 | CALM3 | CALM3 | CALM3 | 13813 | -0.16 | 0.22 | 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 PROPANOATE METABOLISM.

Figure S64. 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

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 | EDNRB | EDNRB | EDNRB | 242 | 0.5 | 0.053 | YES |
2 | TSHR | TSHR | TSHR | 308 | 0.47 | 0.11 | YES |
3 | ITGA11 | ITGA11 | ITGA11 | 398 | 0.44 | 0.16 | YES |
4 | ITGA8 | ITGA8 | ITGA8 | 552 | 0.39 | 0.21 | YES |
5 | PLD2 | PLD2 | PLD2 | 783 | 0.34 | 0.24 | YES |
6 | SPAG9 | SPAG9 | SPAG9 | 893 | 0.32 | 0.28 | YES |
7 | IL2RA | IL2RA | IL2RA | 1131 | 0.28 | 0.3 | YES |
8 | ITGA4 | ITGA4 | ITGA4 | 1148 | 0.28 | 0.34 | YES |
9 | ITGA10 | ITGA10 | ITGA10 | 1284 | 0.27 | 0.36 | YES |
10 | CPE | CPE | CPE | 1390 | 0.26 | 0.39 | YES |
11 | AGTR1 | AGTR1 | AGTR1 | 1501 | 0.25 | 0.42 | YES |
12 | ITGA2 | ITGA2 | ITGA2 | 1853 | 0.22 | 0.43 | YES |
13 | CLTC | CLTC | CLTC | 2078 | 0.21 | 0.44 | YES |
14 | ITGA1 | ITGA1 | ITGA1 | 2095 | 0.2 | 0.47 | YES |
15 | EXOC6 | EXOC6 | EXOC6 | 2688 | 0.17 | 0.46 | YES |
16 | ITGA6 | ITGA6 | ITGA6 | 2927 | 0.16 | 0.47 | YES |
17 | ITGAV | ITGAV | ITGAV | 3086 | 0.15 | 0.48 | YES |
18 | ASAP2 | ASAP2 | ASAP2 | 3088 | 0.15 | 0.5 | YES |
19 | EXOC2 | EXOC2 | EXOC2 | 3442 | 0.14 | 0.5 | YES |
20 | ITGA5 | ITGA5 | ITGA5 | 3545 | 0.13 | 0.51 | YES |
21 | PLD1 | PLD1 | PLD1 | 3602 | 0.13 | 0.52 | YES |
22 | ITGB1 | ITGB1 | ITGB1 | 4833 | 0.088 | 0.47 | NO |
23 | NME1 | NME1 | NME1 | 5209 | 0.076 | 0.46 | NO |
24 | EXOC5 | EXOC5 | EXOC5 | 6112 | 0.051 | 0.41 | NO |
25 | EXOC1 | EXOC1 | EXOC1 | 6182 | 0.049 | 0.41 | NO |
26 | ITGA9 | ITGA9 | ITGA9 | 6329 | 0.045 | 0.41 | NO |
27 | EXOC7 | EXOC7 | EXOC7 | 6672 | 0.037 | 0.4 | NO |
28 | ITGA7 | ITGA7 | ITGA7 | 6673 | 0.037 | 0.4 | NO |
29 | VAMP3 | VAMP3 | VAMP3 | 6729 | 0.036 | 0.4 | NO |
30 | ITGA3 | ITGA3 | ITGA3 | 6759 | 0.035 | 0.41 | NO |
31 | EXOC4 | EXOC4 | EXOC4 | 7162 | 0.025 | 0.39 | NO |
32 | CTNNB1 | CTNNB1 | CTNNB1 | 7629 | 0.014 | 0.36 | NO |
33 | CTNNA1 | CTNNA1 | CTNNA1 | 7672 | 0.013 | 0.36 | NO |
34 | CTNND1 | CTNND1 | CTNND1 | 7757 | 0.011 | 0.36 | NO |
35 | RALA | RALA | RALA | 8033 | 0.0045 | 0.34 | NO |
36 | ADRB2 | ADRB2 | ADRB2 | 8690 | -0.011 | 0.31 | NO |
37 | EXOC3 | EXOC3 | EXOC3 | 8828 | -0.015 | 0.3 | NO |
38 | KLC1 | KLC1 | KLC1 | 10175 | -0.046 | 0.23 | NO |
39 | CDH1 | CDH1 | CDH1 | 10832 | -0.063 | 0.21 | NO |
40 | DNM2 | DNM2 | DNM2 | 11748 | -0.088 | 0.17 | NO |
41 | ARF6 | ARF6 | ARF6 | 12004 | -0.094 | 0.16 | NO |
42 | SCAMP2 | SCAMP2 | SCAMP2 | 12037 | -0.095 | 0.18 | NO |
43 | BIN1 | BIN1 | BIN1 | 12422 | -0.11 | 0.17 | NO |
44 | PIP5K1C | PIP5K1C | PIP5K1C | 12870 | -0.12 | 0.16 | NO |
45 | SLC2A4 | SLC2A4 | SLC2A4 | 14180 | -0.17 | 0.11 | NO |
46 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 14408 | -0.18 | 0.12 | NO |
47 | AVPR2 | AVPR2 | AVPR2 | 15498 | -0.26 | 0.092 | NO |
48 | ACAP1 | ACAP1 | ACAP1 | 15857 | -0.29 | 0.11 | 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 ADHERENS JUNCTION.

Figure S66. 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

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 | PDGFB | PDGFB | PDGFB | 1286 | 0.27 | -0.0081 | YES |
2 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 1370 | 0.26 | 0.05 | YES |
3 | PDGFRB | PDGFRB | PDGFRB | 1429 | 0.26 | 0.11 | YES |
4 | KDR | KDR | KDR | 1470 | 0.25 | 0.16 | YES |
5 | ITGA1 | ITGA1 | ITGA1 | 2095 | 0.2 | 0.18 | YES |
6 | CSF1 | CSF1 | CSF1 | 2150 | 0.2 | 0.22 | YES |
7 | PIK3CA | PIK3CA | PIK3CA | 2559 | 0.18 | 0.24 | YES |
8 | SOS1 | SOS1 | SOS1 | 2646 | 0.17 | 0.28 | YES |
9 | STAT5B | STAT5B | STAT5B | 2658 | 0.17 | 0.32 | YES |
10 | EGFR | EGFR | EGFR | 3098 | 0.15 | 0.33 | YES |
11 | STAT1 | STAT1 | STAT1 | 3105 | 0.15 | 0.37 | YES |
12 | JAK1 | JAK1 | JAK1 | 3249 | 0.15 | 0.4 | YES |
13 | VEGFA | VEGFA | VEGFA | 3425 | 0.14 | 0.42 | YES |
14 | STAT3 | STAT3 | STAT3 | 3717 | 0.13 | 0.43 | YES |
15 | STAT5A | STAT5A | STAT5A | 3928 | 0.12 | 0.45 | YES |
16 | KPNB1 | KPNB1 | KPNB1 | 3976 | 0.12 | 0.48 | YES |
17 | EIF2A | EIF2A | EIF2A | 4004 | 0.12 | 0.5 | YES |
18 | HGF | HGF | HGF | 4649 | 0.094 | 0.49 | NO |
19 | ITGB1 | ITGB1 | ITGB1 | 4833 | 0.088 | 0.5 | NO |
20 | RAB4A | RAB4A | RAB4A | 5298 | 0.073 | 0.49 | NO |
21 | GRB2 | GRB2 | GRB2 | 5671 | 0.062 | 0.48 | NO |
22 | PIK3CB | PIK3CB | PIK3CB | 5674 | 0.062 | 0.5 | NO |
23 | MET | MET | MET | 5953 | 0.055 | 0.5 | NO |
24 | PTPN2 | PTPN2 | PTPN2 | 6317 | 0.046 | 0.49 | NO |
25 | PIAS1 | PIAS1 | PIAS1 | 6410 | 0.043 | 0.49 | NO |
26 | SHC1 | SHC1 | SHC1 | 7427 | 0.019 | 0.44 | NO |
27 | STAT6 | STAT6 | STAT6 | 7804 | 0.0098 | 0.42 | NO |
28 | GAB1 | GAB1 | GAB1 | 7862 | 0.0086 | 0.42 | NO |
29 | KPNA2 | KPNA2 | KPNA2 | 8002 | 0.005 | 0.41 | NO |
30 | CSF1R | CSF1R | CSF1R | 8039 | 0.0044 | 0.41 | NO |
31 | PIK3R1 | PIK3R1 | PIK3R1 | 8099 | 0.0029 | 0.41 | NO |
32 | SRC | SRC | SRC | 8213 | 0.000058 | 0.4 | NO |
33 | EGF | EGF | EGF | 8422 | -0.0048 | 0.39 | NO |
34 | INSR | INSR | INSR | 8601 | -0.0088 | 0.38 | NO |
35 | LMAN1 | LMAN1 | LMAN1 | 8733 | -0.012 | 0.38 | NO |
36 | PIK3CD | PIK3CD | PIK3CD | 8893 | -0.016 | 0.37 | NO |
37 | ATR | ATR | ATR | 8974 | -0.018 | 0.37 | NO |
38 | CREBBP | CREBBP | CREBBP | 10520 | -0.055 | 0.3 | NO |
39 | PIK3R3 | PIK3R3 | PIK3R3 | 11135 | -0.071 | 0.28 | NO |
40 | PTPN1 | PTPN1 | PTPN1 | 11520 | -0.082 | 0.28 | NO |
41 | PIK3R2 | PIK3R2 | PIK3R2 | 13241 | -0.13 | 0.22 | NO |
42 | JAK3 | JAK3 | JAK3 | 14228 | -0.18 | 0.2 | NO |
Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AT1R PATHWAY.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | ALDH2 | ALDH2 | ALDH2 | 655 | 0.36 | 0.06 | YES |
2 | HIBCH | HIBCH | HIBCH | 983 | 0.3 | 0.12 | YES |
3 | ACADM | ACADM | ACADM | 1674 | 0.24 | 0.14 | YES |
4 | SUCLA2 | SUCLA2 | SUCLA2 | 1681 | 0.24 | 0.21 | YES |
5 | MUT | MUT | MUT | 1774 | 0.23 | 0.26 | YES |
6 | PCCA | PCCA | PCCA | 1800 | 0.22 | 0.32 | YES |
7 | MCEE | MCEE | MCEE | 1829 | 0.22 | 0.38 | YES |
8 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 2650 | 0.17 | 0.38 | YES |
9 | SUCLG1 | SUCLG1 | SUCLG1 | 2770 | 0.17 | 0.41 | YES |
10 | HADHA | HADHA | HADHA | 3342 | 0.14 | 0.42 | YES |
11 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 3684 | 0.13 | 0.43 | YES |
12 | EHHADH | EHHADH | EHHADH | 3788 | 0.12 | 0.46 | YES |
13 | PCCB | PCCB | PCCB | 3859 | 0.12 | 0.49 | YES |
14 | ECHS1 | ECHS1 | ECHS1 | 4162 | 0.11 | 0.5 | YES |
15 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4287 | 0.11 | 0.52 | YES |
16 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 4474 | 0.099 | 0.54 | YES |
17 | LDHA | LDHA | LDHA | 4500 | 0.098 | 0.56 | YES |
18 | ACAT1 | ACAT1 | ACAT1 | 4616 | 0.095 | 0.58 | YES |
19 | LDHAL6B | LDHAL6B | LDHAL6B | 4838 | 0.088 | 0.59 | YES |
20 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 6206 | 0.048 | 0.53 | NO |
21 | SUCLG2 | SUCLG2 | SUCLG2 | 6533 | 0.04 | 0.52 | NO |
22 | ACSS3 | ACSS3 | ACSS3 | 7274 | 0.022 | 0.48 | NO |
23 | ACACB | ACACB | ACACB | 7277 | 0.022 | 0.49 | NO |
24 | ACAT2 | ACAT2 | ACAT2 | 7559 | 0.016 | 0.48 | NO |
25 | ACACA | ACACA | ACACA | 7630 | 0.014 | 0.48 | NO |
26 | LDHB | LDHB | LDHB | 8491 | -0.0059 | 0.43 | NO |
27 | ACSS1 | ACSS1 | ACSS1 | 9452 | -0.03 | 0.39 | NO |
28 | MLYCD | MLYCD | MLYCD | 9966 | -0.042 | 0.37 | NO |
29 | ABAT | ABAT | ABAT | 10085 | -0.044 | 0.37 | NO |
30 | LDHAL6A | LDHAL6A | LDHAL6A | 10649 | -0.058 | 0.36 | NO |
31 | ACSS2 | ACSS2 | ACSS2 | 10676 | -0.059 | 0.37 | NO |
32 | LDHC | LDHC | LDHC | 12676 | -0.12 | 0.29 | NO |
Figure S69. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA EGF PATHWAY.

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

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PDGFRA | PDGFRA | PDGFRA | 58 | 0.76 | 0.19 | YES |
2 | FOS | FOS | FOS | 1154 | 0.28 | 0.2 | YES |
3 | MAP2K4 | MAP2K4 | MAP2K4 | 2035 | 0.21 | 0.21 | YES |
4 | MAPK8 | MAPK8 | MAPK8 | 2252 | 0.19 | 0.25 | YES |
5 | PRKCA | PRKCA | PRKCA | 2439 | 0.18 | 0.28 | YES |
6 | PIK3CA | PIK3CA | PIK3CA | 2559 | 0.18 | 0.32 | YES |
7 | SOS1 | SOS1 | SOS1 | 2646 | 0.17 | 0.36 | YES |
8 | STAT5B | STAT5B | STAT5B | 2658 | 0.17 | 0.41 | YES |
9 | STAT1 | STAT1 | STAT1 | 3105 | 0.15 | 0.42 | YES |
10 | JAK1 | JAK1 | JAK1 | 3249 | 0.15 | 0.45 | YES |
11 | PDGFA | PDGFA | PDGFA | 3610 | 0.13 | 0.46 | YES |
12 | STAT3 | STAT3 | STAT3 | 3717 | 0.13 | 0.49 | YES |
13 | PIK3CG | PIK3CG | PIK3CG | 3728 | 0.13 | 0.52 | YES |
14 | STAT5A | STAT5A | STAT5A | 3928 | 0.12 | 0.54 | YES |
15 | STAT4 | STAT4 | STAT4 | 4942 | 0.085 | 0.51 | NO |
16 | GRB2 | GRB2 | GRB2 | 5671 | 0.062 | 0.48 | NO |
17 | SRF | SRF | SRF | 5852 | 0.057 | 0.48 | NO |
18 | JUN | JUN | JUN | 5906 | 0.056 | 0.5 | NO |
19 | PRKCB | PRKCB | PRKCB | 6098 | 0.051 | 0.5 | NO |
20 | MAPK3 | MAPK3 | MAPK3 | 6903 | 0.032 | 0.46 | NO |
21 | SHC1 | SHC1 | SHC1 | 7427 | 0.019 | 0.44 | NO |
22 | RASA1 | RASA1 | RASA1 | 7450 | 0.019 | 0.44 | NO |
23 | STAT6 | STAT6 | STAT6 | 7804 | 0.0098 | 0.42 | NO |
24 | PIK3R1 | PIK3R1 | PIK3R1 | 8099 | 0.0029 | 0.41 | NO |
25 | MAP2K1 | MAP2K1 | MAP2K1 | 8196 | 0.00046 | 0.4 | NO |
26 | MAP3K1 | MAP3K1 | MAP3K1 | 8592 | -0.0086 | 0.38 | NO |
27 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 8707 | -0.011 | 0.38 | NO |
28 | PLCG1 | PLCG1 | PLCG1 | 11345 | -0.077 | 0.25 | NO |
29 | STAT2 | STAT2 | STAT2 | 11707 | -0.087 | 0.25 | NO |
30 | ELK1 | ELK1 | ELK1 | 11836 | -0.09 | 0.27 | NO |
31 | HRAS | HRAS | HRAS | 13120 | -0.13 | 0.23 | NO |
32 | RAF1 | RAF1 | RAF1 | 13125 | -0.13 | 0.26 | NO |
Figure S71. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PPARA PATHWAY.

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

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 | ITGB3 | ITGB3 | ITGB3 | 116 | 0.62 | 0.15 | YES |
2 | S1PR3 | S1PR3 | S1PR3 | 345 | 0.45 | 0.24 | YES |
3 | FLT1 | FLT1 | FLT1 | 903 | 0.32 | 0.29 | YES |
4 | PDGFB | PDGFB | PDGFB | 1286 | 0.27 | 0.34 | YES |
5 | GNA13 | GNA13 | GNA13 | 1368 | 0.26 | 0.4 | YES |
6 | PDGFRB | PDGFRB | PDGFRB | 1429 | 0.26 | 0.46 | YES |
7 | S1PR1 | S1PR1 | S1PR1 | 1791 | 0.23 | 0.49 | YES |
8 | CXCR4 | CXCR4 | CXCR4 | 2489 | 0.18 | 0.5 | YES |
9 | ITGAV | ITGAV | ITGAV | 3086 | 0.15 | 0.5 | YES |
10 | VEGFA | VEGFA | VEGFA | 3425 | 0.14 | 0.52 | YES |
11 | GNA14 | GNA14 | GNA14 | 3971 | 0.12 | 0.51 | YES |
12 | GNAI3 | GNAI3 | GNAI3 | 4574 | 0.096 | 0.5 | YES |
13 | GNA15 | GNA15 | GNA15 | 4576 | 0.096 | 0.53 | YES |
14 | GNAI1 | GNAI1 | GNAI1 | 5173 | 0.077 | 0.51 | NO |
15 | JAK2 | JAK2 | JAK2 | 5672 | 0.062 | 0.5 | NO |
16 | AKT3 | AKT3 | AKT3 | 6584 | 0.039 | 0.46 | NO |
17 | MAPK1 | MAPK1 | MAPK1 | 6728 | 0.036 | 0.46 | NO |
18 | RAC1 | RAC1 | RAC1 | 6796 | 0.034 | 0.46 | NO |
19 | MAPK3 | MAPK3 | MAPK3 | 6903 | 0.032 | 0.47 | NO |
20 | GNAZ | GNAZ | GNAZ | 6950 | 0.03 | 0.47 | NO |
21 | GNAQ | GNAQ | GNAQ | 7331 | 0.021 | 0.46 | NO |
22 | GNAI2 | GNAI2 | GNAI2 | 7699 | 0.012 | 0.44 | NO |
23 | RHOA | RHOA | RHOA | 7875 | 0.0082 | 0.43 | NO |
24 | SRC | SRC | SRC | 8213 | 0.000058 | 0.41 | NO |
25 | GNA12 | GNA12 | GNA12 | 9025 | -0.019 | 0.37 | NO |
26 | GNA11 | GNA11 | GNA11 | 9599 | -0.033 | 0.34 | NO |
27 | AKT1 | AKT1 | AKT1 | 11975 | -0.094 | 0.24 | NO |
28 | GNAO1 | GNAO1 | GNAO1 | 13706 | -0.15 | 0.18 | NO |
29 | S1PR2 | S1PR2 | S1PR2 | 15107 | -0.23 | 0.15 | NO |
Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PDGF PATHWAY.

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

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 | FOS | FOS | FOS | 1154 | 0.28 | 0.028 | YES |
2 | MAP2K4 | MAP2K4 | MAP2K4 | 2035 | 0.21 | 0.048 | YES |
3 | MAPK8 | MAPK8 | MAPK8 | 2252 | 0.19 | 0.1 | YES |
4 | PRKCA | PRKCA | PRKCA | 2439 | 0.18 | 0.15 | YES |
5 | PIK3CA | PIK3CA | PIK3CA | 2559 | 0.18 | 0.2 | YES |
6 | SOS1 | SOS1 | SOS1 | 2646 | 0.17 | 0.26 | YES |
7 | STAT5B | STAT5B | STAT5B | 2658 | 0.17 | 0.31 | YES |
8 | EGFR | EGFR | EGFR | 3098 | 0.15 | 0.34 | YES |
9 | STAT1 | STAT1 | STAT1 | 3105 | 0.15 | 0.39 | YES |
10 | JAK1 | JAK1 | JAK1 | 3249 | 0.15 | 0.43 | YES |
11 | STAT3 | STAT3 | STAT3 | 3717 | 0.13 | 0.44 | YES |
12 | STAT5A | STAT5A | STAT5A | 3928 | 0.12 | 0.47 | YES |
13 | STAT4 | STAT4 | STAT4 | 4942 | 0.085 | 0.44 | NO |
14 | GRB2 | GRB2 | GRB2 | 5671 | 0.062 | 0.42 | NO |
15 | SRF | SRF | SRF | 5852 | 0.057 | 0.43 | NO |
16 | JUN | JUN | JUN | 5906 | 0.056 | 0.45 | NO |
17 | PRKCB | PRKCB | PRKCB | 6098 | 0.051 | 0.45 | NO |
18 | MAPK3 | MAPK3 | MAPK3 | 6903 | 0.032 | 0.42 | NO |
19 | SHC1 | SHC1 | SHC1 | 7427 | 0.019 | 0.4 | NO |
20 | RASA1 | RASA1 | RASA1 | 7450 | 0.019 | 0.4 | NO |
21 | STAT6 | STAT6 | STAT6 | 7804 | 0.0098 | 0.38 | NO |
22 | PIK3R1 | PIK3R1 | PIK3R1 | 8099 | 0.0029 | 0.37 | NO |
23 | MAP2K1 | MAP2K1 | MAP2K1 | 8196 | 0.00046 | 0.36 | NO |
24 | EGF | EGF | EGF | 8422 | -0.0048 | 0.35 | NO |
25 | MAP3K1 | MAP3K1 | MAP3K1 | 8592 | -0.0086 | 0.34 | NO |
26 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 8707 | -0.011 | 0.34 | NO |
27 | PLCG1 | PLCG1 | PLCG1 | 11345 | -0.077 | 0.22 | NO |
28 | STAT2 | STAT2 | STAT2 | 11707 | -0.087 | 0.23 | NO |
29 | ELK1 | ELK1 | ELK1 | 11836 | -0.09 | 0.25 | NO |
30 | HRAS | HRAS | HRAS | 13120 | -0.13 | 0.22 | NO |
31 | RAF1 | RAF1 | RAF1 | 13125 | -0.13 | 0.26 | NO |
Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA VEGF PATHWAY.

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

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 | COL9A2 | COL9A2 | COL9A2 | 16 | 0.95 | 0.052 | YES |
2 | PDGFRA | PDGFRA | PDGFRA | 58 | 0.76 | 0.091 | YES |
3 | ADCY5 | ADCY5 | ADCY5 | 224 | 0.52 | 0.11 | YES |
4 | ITPR3 | ITPR3 | ITPR3 | 469 | 0.41 | 0.12 | YES |
5 | PDGFD | PDGFD | PDGFD | 733 | 0.35 | 0.12 | YES |
6 | THBS2 | THBS2 | THBS2 | 830 | 0.33 | 0.14 | YES |
7 | CAMK4 | CAMK4 | CAMK4 | 867 | 0.32 | 0.15 | YES |
8 | COL4A3 | COL4A3 | COL4A3 | 887 | 0.32 | 0.17 | YES |
9 | THBS4 | THBS4 | THBS4 | 1032 | 0.3 | 0.18 | YES |
10 | COL6A3 | COL6A3 | COL6A3 | 1074 | 0.29 | 0.19 | YES |
11 | PDGFB | PDGFB | PDGFB | 1286 | 0.27 | 0.19 | YES |
12 | ADCY3 | ADCY3 | ADCY3 | 1342 | 0.26 | 0.2 | YES |
13 | ADCY4 | ADCY4 | ADCY4 | 1383 | 0.26 | 0.22 | YES |
14 | PDGFRB | PDGFRB | PDGFRB | 1429 | 0.26 | 0.23 | YES |
15 | PLAT | PLAT | PLAT | 1525 | 0.25 | 0.24 | YES |
16 | COL5A1 | COL5A1 | COL5A1 | 1601 | 0.24 | 0.24 | YES |
17 | PDE1B | PDE1B | PDE1B | 1751 | 0.23 | 0.25 | YES |
18 | ADCY2 | ADCY2 | ADCY2 | 1793 | 0.23 | 0.26 | YES |
19 | COL4A4 | COL4A4 | COL4A4 | 1869 | 0.22 | 0.27 | YES |
20 | CHUK | CHUK | CHUK | 1880 | 0.22 | 0.28 | YES |
21 | COL9A3 | COL9A3 | COL9A3 | 2160 | 0.2 | 0.27 | YES |
22 | COL4A1 | COL4A1 | COL4A1 | 2206 | 0.2 | 0.28 | YES |
23 | CRK | CRK | CRK | 2258 | 0.19 | 0.29 | YES |
24 | PRKAR1A | PRKAR1A | PRKAR1A | 2300 | 0.19 | 0.3 | YES |
25 | COL3A1 | COL3A1 | COL3A1 | 2380 | 0.19 | 0.3 | YES |
26 | COL5A2 | COL5A2 | COL5A2 | 2387 | 0.19 | 0.31 | YES |
27 | PRKCA | PRKCA | PRKCA | 2439 | 0.18 | 0.32 | YES |
28 | PIK3CA | PIK3CA | PIK3CA | 2559 | 0.18 | 0.32 | YES |
29 | SOS1 | SOS1 | SOS1 | 2646 | 0.17 | 0.33 | YES |
30 | STAT5B | STAT5B | STAT5B | 2658 | 0.17 | 0.34 | YES |
31 | COL6A2 | COL6A2 | COL6A2 | 2673 | 0.17 | 0.35 | YES |
32 | COL4A2 | COL4A2 | COL4A2 | 2678 | 0.17 | 0.36 | YES |
33 | FOXO1 | FOXO1 | FOXO1 | 2923 | 0.16 | 0.35 | YES |
34 | SPP1 | SPP1 | SPP1 | 2932 | 0.16 | 0.36 | YES |
35 | THEM4 | THEM4 | THEM4 | 2979 | 0.16 | 0.36 | YES |
36 | PDE1A | PDE1A | PDE1A | 3064 | 0.15 | 0.37 | YES |
37 | STAT1 | STAT1 | STAT1 | 3105 | 0.15 | 0.38 | YES |
38 | GRB7 | GRB7 | GRB7 | 3149 | 0.15 | 0.38 | YES |
39 | PLG | PLG | PLG | 3295 | 0.14 | 0.38 | YES |
40 | COL1A2 | COL1A2 | COL1A2 | 3521 | 0.13 | 0.38 | YES |
41 | PDGFA | PDGFA | PDGFA | 3610 | 0.13 | 0.38 | YES |
42 | COL1A1 | COL1A1 | COL1A1 | 3708 | 0.13 | 0.38 | YES |
43 | STAT3 | STAT3 | STAT3 | 3717 | 0.13 | 0.39 | YES |
44 | CDKN1A | CDKN1A | CDKN1A | 3792 | 0.12 | 0.39 | YES |
45 | CREB1 | CREB1 | CREB1 | 3794 | 0.12 | 0.4 | YES |
46 | STAT5A | STAT5A | STAT5A | 3928 | 0.12 | 0.39 | NO |
47 | THBS1 | THBS1 | THBS1 | 4344 | 0.1 | 0.38 | NO |
48 | COL4A5 | COL4A5 | COL4A5 | 4350 | 0.1 | 0.38 | NO |
49 | FOXO3 | FOXO3 | FOXO3 | 4689 | 0.093 | 0.37 | NO |
50 | NRAS | NRAS | NRAS | 4714 | 0.092 | 0.37 | NO |
51 | PTEN | PTEN | PTEN | 4801 | 0.09 | 0.37 | NO |
52 | ITPR2 | ITPR2 | ITPR2 | 4884 | 0.086 | 0.37 | NO |
53 | ADCY9 | ADCY9 | ADCY9 | 5272 | 0.074 | 0.35 | NO |
54 | FOXO4 | FOXO4 | FOXO4 | 5485 | 0.068 | 0.34 | NO |
55 | MDM2 | MDM2 | MDM2 | 5512 | 0.067 | 0.35 | NO |
56 | COL9A1 | COL9A1 | COL9A1 | 5524 | 0.066 | 0.35 | NO |
57 | CALM2 | CALM2 | CALM2 | 5626 | 0.064 | 0.35 | NO |
58 | GRB2 | GRB2 | GRB2 | 5671 | 0.062 | 0.35 | NO |
59 | PIK3CB | PIK3CB | PIK3CB | 5674 | 0.062 | 0.35 | NO |
60 | NCK2 | NCK2 | NCK2 | 5821 | 0.058 | 0.35 | NO |
61 | AKT3 | AKT3 | AKT3 | 6584 | 0.039 | 0.31 | NO |
62 | MAPK1 | MAPK1 | MAPK1 | 6728 | 0.036 | 0.3 | NO |
63 | MAPK3 | MAPK3 | MAPK3 | 6903 | 0.032 | 0.29 | NO |
64 | PRKAR2A | PRKAR2A | PRKAR2A | 7029 | 0.029 | 0.29 | NO |
65 | KRAS | KRAS | KRAS | 7072 | 0.028 | 0.29 | NO |
66 | RICTOR | RICTOR | RICTOR | 7232 | 0.024 | 0.28 | NO |
67 | RASA1 | RASA1 | RASA1 | 7450 | 0.019 | 0.27 | NO |
68 | MTOR | MTOR | MTOR | 7462 | 0.018 | 0.27 | NO |
69 | YWHAB | YWHAB | YWHAB | 7651 | 0.014 | 0.26 | NO |
70 | CDKN1B | CDKN1B | CDKN1B | 7724 | 0.012 | 0.25 | NO |
71 | PRKACB | PRKACB | PRKACB | 7789 | 0.01 | 0.25 | NO |
72 | STAT6 | STAT6 | STAT6 | 7804 | 0.0098 | 0.25 | NO |
73 | NR4A1 | NR4A1 | NR4A1 | 7868 | 0.0085 | 0.25 | NO |
74 | PIK3R1 | PIK3R1 | PIK3R1 | 8099 | 0.0029 | 0.24 | NO |
75 | MAP2K1 | MAP2K1 | MAP2K1 | 8196 | 0.00046 | 0.23 | NO |
76 | SRC | SRC | SRC | 8213 | 0.000058 | 0.23 | NO |
77 | PRKAR2B | PRKAR2B | PRKAR2B | 8581 | -0.0083 | 0.21 | NO |
78 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 8655 | -0.01 | 0.2 | NO |
79 | PRKCE | PRKCE | PRKCE | 8831 | -0.015 | 0.2 | NO |
80 | COL6A1 | COL6A1 | COL6A1 | 8902 | -0.016 | 0.19 | NO |
81 | CASP9 | CASP9 | CASP9 | 9889 | -0.04 | 0.14 | NO |
82 | THBS3 | THBS3 | THBS3 | 9963 | -0.042 | 0.14 | NO |
83 | PHLPP1 | PHLPP1 | PHLPP1 | 10053 | -0.044 | 0.14 | NO |
84 | PDPK1 | PDPK1 | PDPK1 | 10065 | -0.044 | 0.14 | NO |
85 | PDGFC | PDGFC | PDGFC | 10078 | -0.044 | 0.14 | NO |
86 | CRKL | CRKL | CRKL | 10161 | -0.046 | 0.14 | NO |
87 | FURIN | FURIN | FURIN | 10300 | -0.05 | 0.13 | NO |
88 | NCK1 | NCK1 | NCK1 | 10543 | -0.055 | 0.12 | NO |
89 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 11052 | -0.069 | 0.096 | NO |
90 | CALM1 | CALM1 | CALM1 | 11136 | -0.071 | 0.095 | NO |
91 | PRKCD | PRKCD | PRKCD | 11230 | -0.074 | 0.094 | NO |
92 | ADCY1 | ADCY1 | ADCY1 | 11267 | -0.075 | 0.096 | NO |
93 | PLCG1 | PLCG1 | PLCG1 | 11345 | -0.077 | 0.096 | NO |
94 | PRKAR1B | PRKAR1B | PRKAR1B | 11384 | -0.078 | 0.098 | NO |
95 | TSC2 | TSC2 | TSC2 | 11575 | -0.083 | 0.092 | NO |
96 | GSK3A | GSK3A | GSK3A | 11917 | -0.092 | 0.078 | NO |
97 | AKT1 | AKT1 | AKT1 | 11975 | -0.094 | 0.08 | NO |
98 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 12205 | -0.1 | 0.072 | NO |
99 | ADCY6 | ADCY6 | ADCY6 | 12207 | -0.1 | 0.078 | NO |
100 | BCAR1 | BCAR1 | BCAR1 | 12587 | -0.11 | 0.062 | NO |
101 | BAD | BAD | BAD | 12624 | -0.11 | 0.067 | NO |
102 | HRAS | HRAS | HRAS | 13120 | -0.13 | 0.046 | NO |
103 | RAF1 | RAF1 | RAF1 | 13125 | -0.13 | 0.053 | NO |
104 | PIK3R2 | PIK3R2 | PIK3R2 | 13241 | -0.13 | 0.054 | NO |
105 | AKT2 | AKT2 | AKT2 | 13301 | -0.14 | 0.058 | NO |
106 | MLST8 | MLST8 | MLST8 | 13406 | -0.14 | 0.06 | NO |
107 | MAP2K2 | MAP2K2 | MAP2K2 | 13425 | -0.14 | 0.066 | NO |
108 | ADRBK1 | ADRBK1 | ADRBK1 | 13717 | -0.15 | 0.058 | NO |
109 | CALM3 | CALM3 | CALM3 | 13813 | -0.16 | 0.062 | NO |
110 | AKT1S1 | AKT1S1 | AKT1S1 | 14032 | -0.16 | 0.058 | NO |
111 | PRKACA | PRKACA | PRKACA | 14048 | -0.17 | 0.067 | NO |
112 | ADCY7 | ADCY7 | ADCY7 | 14634 | -0.2 | 0.044 | NO |
113 | CDK1 | CDK1 | CDK1 | 15268 | -0.24 | 0.022 | NO |
114 | PRKACG | PRKACG | PRKACG | 15839 | -0.29 | 0.0056 | NO |
115 | COL2A1 | COL2A1 | COL2A1 | 16283 | -0.34 | -0.00058 | NO |
116 | PRKCG | PRKCG | PRKCG | 16890 | -0.45 | -0.01 | NO |
117 | TRIB3 | TRIB3 | TRIB3 | 17116 | -0.52 | 0.0057 | NO |
118 | ADCY8 | ADCY8 | ADCY8 | 17403 | -0.62 | 0.024 | NO |
Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID S1P S1P3 PATHWAY.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: PID S1P S1P3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | DOCK1 | DOCK1 | DOCK1 | 1072 | 0.29 | -0.0093 | YES |
2 | ROCK2 | ROCK2 | ROCK2 | 1276 | 0.27 | 0.026 | YES |
3 | ETS1 | ETS1 | ETS1 | 1713 | 0.23 | 0.042 | YES |
4 | RGNEF | RGNEF | RGNEF | 1747 | 0.23 | 0.081 | YES |
5 | MAP2K4 | MAP2K4 | MAP2K4 | 2035 | 0.21 | 0.1 | YES |
6 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 2127 | 0.2 | 0.13 | YES |
7 | MAPK8 | MAPK8 | MAPK8 | 2252 | 0.19 | 0.16 | YES |
8 | CRK | CRK | CRK | 2258 | 0.19 | 0.19 | YES |
9 | ELMO1 | ELMO1 | ELMO1 | 2285 | 0.19 | 0.22 | YES |
10 | WASL | WASL | WASL | 2552 | 0.18 | 0.24 | YES |
11 | PIK3CA | PIK3CA | PIK3CA | 2559 | 0.18 | 0.27 | YES |
12 | SOS1 | SOS1 | SOS1 | 2646 | 0.17 | 0.3 | YES |
13 | BMX | BMX | BMX | 2766 | 0.17 | 0.32 | YES |
14 | ITGAV | ITGAV | ITGAV | 3086 | 0.15 | 0.33 | YES |
15 | GRB7 | GRB7 | GRB7 | 3149 | 0.15 | 0.35 | YES |
16 | BRAF | BRAF | BRAF | 3373 | 0.14 | 0.36 | YES |
17 | ITGA5 | ITGA5 | ITGA5 | 3545 | 0.13 | 0.38 | YES |
18 | FYN | FYN | FYN | 3590 | 0.13 | 0.4 | YES |
19 | ASAP1 | ASAP1 | ASAP1 | 4036 | 0.12 | 0.39 | YES |
20 | ARHGAP26 | ARHGAP26 | ARHGAP26 | 4551 | 0.097 | 0.38 | YES |
21 | ITGB5 | ITGB5 | ITGB5 | 4809 | 0.089 | 0.38 | YES |
22 | ITGB1 | ITGB1 | ITGB1 | 4833 | 0.088 | 0.4 | YES |
23 | CAPN2 | CAPN2 | CAPN2 | 4888 | 0.086 | 0.41 | YES |
24 | PTK2 | PTK2 | PTK2 | 5146 | 0.078 | 0.41 | YES |
25 | YES1 | YES1 | YES1 | 5317 | 0.072 | 0.41 | YES |
26 | KLF8 | KLF8 | KLF8 | 5469 | 0.068 | 0.41 | YES |
27 | VCL | VCL | VCL | 5552 | 0.066 | 0.42 | YES |
28 | GRB2 | GRB2 | GRB2 | 5671 | 0.062 | 0.42 | YES |
29 | RAP1B | RAP1B | RAP1B | 5709 | 0.061 | 0.43 | YES |
30 | NCK2 | NCK2 | NCK2 | 5821 | 0.058 | 0.44 | YES |
31 | JUN | JUN | JUN | 5906 | 0.056 | 0.44 | YES |
32 | ACTN1 | ACTN1 | ACTN1 | 6163 | 0.05 | 0.44 | NO |
33 | RAP1A | RAP1A | RAP1A | 6242 | 0.048 | 0.44 | NO |
34 | MMP14 | MMP14 | MMP14 | 6670 | 0.037 | 0.42 | NO |
35 | MAPK1 | MAPK1 | MAPK1 | 6728 | 0.036 | 0.42 | NO |
36 | RAC1 | RAC1 | RAC1 | 6796 | 0.034 | 0.43 | NO |
37 | MAPK9 | MAPK9 | MAPK9 | 7413 | 0.019 | 0.4 | NO |
38 | RASA1 | RASA1 | RASA1 | 7450 | 0.019 | 0.4 | NO |
39 | PXN | PXN | PXN | 7485 | 0.018 | 0.4 | NO |
40 | GIT2 | GIT2 | GIT2 | 7719 | 0.012 | 0.39 | NO |
41 | RRAS | RRAS | RRAS | 7801 | 0.0099 | 0.38 | NO |
42 | RHOA | RHOA | RHOA | 7875 | 0.0082 | 0.38 | NO |
43 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 7953 | 0.0063 | 0.38 | NO |
44 | TLN1 | TLN1 | TLN1 | 8081 | 0.0035 | 0.37 | NO |
45 | PIK3R1 | PIK3R1 | PIK3R1 | 8099 | 0.0029 | 0.37 | NO |
46 | MAP2K1 | MAP2K1 | MAP2K1 | 8196 | 0.00046 | 0.37 | NO |
47 | SRC | SRC | SRC | 8213 | 0.000058 | 0.36 | NO |
48 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 8655 | -0.01 | 0.34 | NO |
49 | CCND1 | CCND1 | CCND1 | 9670 | -0.035 | 0.29 | NO |
50 | PAK1 | PAK1 | PAK1 | 9861 | -0.039 | 0.29 | NO |
51 | PTPN21 | PTPN21 | PTPN21 | 10267 | -0.049 | 0.27 | NO |
52 | NCK1 | NCK1 | NCK1 | 10543 | -0.055 | 0.27 | NO |
53 | PLCG1 | PLCG1 | PLCG1 | 11345 | -0.077 | 0.24 | NO |
54 | SH3GL1 | SH3GL1 | SH3GL1 | 12482 | -0.11 | 0.19 | NO |
55 | BCAR1 | BCAR1 | BCAR1 | 12587 | -0.11 | 0.2 | NO |
56 | RAF1 | RAF1 | RAF1 | 13125 | -0.13 | 0.2 | NO |
57 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 14408 | -0.18 | 0.16 | NO |
58 | ACTA1 | ACTA1 | ACTA1 | 14698 | -0.2 | 0.18 | NO |
Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AVB3 OPN PATHWAY.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: PID AVB3 OPN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.5 | 1.5 | 0.13 | 0.25 | 0.98 | 0.83 | 0.46 | 0.45 | 0.17 | 0.024 |
KEGG RNA DEGRADATION | 57 | genes.ES.table | 0.37 | 1.7 | 0.058 | 0.25 | 0.82 | 0.4 | 0.26 | 0.3 | 0.12 | 0.052 |
KEGG DNA REPLICATION | 36 | genes.ES.table | 0.64 | 1.8 | 0.029 | 0.39 | 0.63 | 0.67 | 0.24 | 0.51 | 0.13 | 0.087 |
KEGG SPLICEOSOME | 114 | genes.ES.table | 0.35 | 1.5 | 0.13 | 0.25 | 0.97 | 0.6 | 0.42 | 0.35 | 0.16 | 0.027 |
KEGG NUCLEOTIDE EXCISION REPAIR | 44 | genes.ES.table | 0.45 | 1.6 | 0.059 | 0.28 | 0.85 | 0.52 | 0.3 | 0.37 | 0.14 | 0.06 |
PID FANCONI PATHWAY | 46 | genes.ES.table | 0.64 | 1.7 | 0.018 | 0.26 | 0.76 | 0.63 | 0.23 | 0.48 | 0.11 | 0.058 |
REACTOME TRANSLATION | 146 | genes.ES.table | 0.54 | 1.9 | 0.041 | 0.87 | 0.33 | 0.73 | 0.35 | 0.48 | 0 | 0.17 |
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE | 109 | genes.ES.table | 0.56 | 1.7 | 0.069 | 0.31 | 0.71 | 0.78 | 0.35 | 0.51 | 0.12 | 0.075 |
REACTOME MITOCHONDRIAL PROTEIN IMPORT | 49 | genes.ES.table | 0.52 | 1.8 | 0.039 | 0.34 | 0.64 | 0.71 | 0.35 | 0.47 | 0.12 | 0.084 |
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S | 57 | genes.ES.table | 0.57 | 1.7 | 0.057 | 0.33 | 0.7 | 0.74 | 0.31 | 0.51 | 0.12 | 0.08 |
Table S41. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FAM153A | FAM153A | FAM153A | 296 | 0.38 | 0.021 | YES |
2 | RPSAP9 | RPSAP9 | RPSAP9 | 1115 | 0.23 | -0.0026 | YES |
3 | RPL9 | RPL9 | RPL9 | 1677 | 0.17 | -0.018 | YES |
4 | RPS26 | RPS26 | RPS26 | 1725 | 0.17 | -0.0037 | YES |
5 | RPL7 | RPL7 | RPL7 | 1751 | 0.16 | 0.011 | YES |
6 | RPL36A | RPL36A | RPL36A | 1800 | 0.16 | 0.024 | YES |
7 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 1930 | 0.15 | 0.032 | YES |
8 | RPSA | RPSA | RPSA | 1975 | 0.15 | 0.044 | YES |
9 | RPS17 | RPS17 | RPS17 | 2327 | 0.13 | 0.037 | YES |
10 | RPL24 | RPL24 | RPL24 | 2336 | 0.13 | 0.05 | YES |
11 | RPS27 | RPS27 | RPS27 | 2342 | 0.13 | 0.062 | YES |
12 | RPL15 | RPL15 | RPL15 | 2568 | 0.12 | 0.061 | YES |
13 | RPS5 | RPS5 | RPS5 | 2600 | 0.12 | 0.071 | YES |
14 | RPS14 | RPS14 | RPS14 | 2637 | 0.12 | 0.08 | YES |
15 | RPL32 | RPL32 | RPL32 | 2666 | 0.12 | 0.09 | YES |
16 | RPL7A | RPL7A | RPL7A | 2770 | 0.11 | 0.095 | YES |
17 | RPS23 | RPS23 | RPS23 | 2791 | 0.11 | 0.1 | YES |
18 | RPL41 | RPL41 | RPL41 | 2880 | 0.11 | 0.11 | YES |
19 | RPS6 | RPS6 | RPS6 | 2885 | 0.11 | 0.12 | YES |
20 | RPS3A | RPS3A | RPS3A | 2945 | 0.1 | 0.13 | YES |
21 | RPL18A | RPL18A | RPL18A | 2949 | 0.1 | 0.14 | YES |
22 | RPL17 | RPL17 | RPL17 | 3057 | 0.1 | 0.14 | YES |
23 | RPL35A | RPL35A | RPL35A | 3066 | 0.1 | 0.15 | YES |
24 | RPL35 | RPL35 | RPL35 | 3075 | 0.1 | 0.16 | YES |
25 | RPL14 | RPL14 | RPL14 | 3078 | 0.1 | 0.17 | YES |
26 | RPS15 | RPS15 | RPS15 | 3084 | 0.1 | 0.18 | YES |
27 | RPL6 | RPL6 | RPL6 | 3095 | 0.1 | 0.19 | YES |
28 | RPL29 | RPL29 | RPL29 | 3150 | 0.098 | 0.2 | YES |
29 | EIF4A2 | EIF4A2 | EIF4A2 | 3178 | 0.097 | 0.2 | YES |
30 | SEC61G | SEC61G | SEC61G | 3309 | 0.093 | 0.21 | YES |
31 | RPL37 | RPL37 | RPL37 | 3390 | 0.091 | 0.21 | YES |
32 | RPLP0 | RPLP0 | RPLP0 | 3439 | 0.09 | 0.22 | YES |
33 | SPCS1 | SPCS1 | SPCS1 | 3495 | 0.088 | 0.22 | YES |
34 | RPS16 | RPS16 | RPS16 | 3497 | 0.088 | 0.23 | YES |
35 | EIF3K | EIF3K | EIF3K | 3504 | 0.088 | 0.24 | YES |
36 | RPL38 | RPL38 | RPL38 | 3522 | 0.087 | 0.25 | YES |
37 | EIF3E | EIF3E | EIF3E | 3570 | 0.086 | 0.25 | YES |
38 | RPS29 | RPS29 | RPS29 | 3572 | 0.085 | 0.26 | YES |
39 | UBA52 | UBA52 | UBA52 | 3677 | 0.083 | 0.26 | YES |
40 | RPL8 | RPL8 | RPL8 | 3707 | 0.082 | 0.27 | YES |
41 | EEF1B2 | EEF1B2 | EEF1B2 | 3716 | 0.082 | 0.28 | YES |
42 | RPL18 | RPL18 | RPL18 | 3747 | 0.081 | 0.28 | YES |
43 | EIF3G | EIF3G | EIF3G | 3806 | 0.08 | 0.29 | YES |
44 | RPL3 | RPL3 | RPL3 | 3819 | 0.08 | 0.3 | YES |
45 | EEF2 | EEF2 | EEF2 | 3820 | 0.08 | 0.3 | YES |
46 | RPS8 | RPS8 | RPS8 | 3844 | 0.079 | 0.31 | YES |
47 | SRPRB | SRPRB | SRPRB | 3872 | 0.078 | 0.32 | YES |
48 | RPS10 | RPS10 | RPS10 | 3960 | 0.076 | 0.32 | YES |
49 | RPS9 | RPS9 | RPS9 | 3971 | 0.076 | 0.33 | YES |
50 | EIF4B | EIF4B | EIF4B | 3995 | 0.076 | 0.33 | YES |
51 | RPL28 | RPL28 | RPL28 | 4029 | 0.075 | 0.34 | YES |
52 | EEF1G | EEF1G | EEF1G | 4095 | 0.074 | 0.34 | YES |
53 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 4122 | 0.073 | 0.35 | YES |
54 | RPL4 | RPL4 | RPL4 | 4127 | 0.073 | 0.35 | YES |
55 | RPL39 | RPL39 | RPL39 | 4144 | 0.072 | 0.36 | YES |
56 | RPL10 | RPL10 | RPL10 | 4189 | 0.072 | 0.36 | YES |
57 | RPL5 | RPL5 | RPL5 | 4233 | 0.071 | 0.37 | YES |
58 | RPS3 | RPS3 | RPS3 | 4244 | 0.07 | 0.38 | YES |
59 | EIF3H | EIF3H | EIF3H | 4308 | 0.069 | 0.38 | YES |
60 | ETF1 | ETF1 | ETF1 | 4324 | 0.069 | 0.38 | YES |
61 | EIF3D | EIF3D | EIF3D | 4334 | 0.068 | 0.39 | YES |
62 | PABPC1 | PABPC1 | PABPC1 | 4344 | 0.068 | 0.4 | YES |
63 | RPS11 | RPS11 | RPS11 | 4361 | 0.068 | 0.4 | YES |
64 | RPS25 | RPS25 | RPS25 | 4404 | 0.067 | 0.41 | YES |
65 | RPL36 | RPL36 | RPL36 | 4410 | 0.067 | 0.41 | YES |
66 | SEC61B | SEC61B | SEC61B | 4430 | 0.067 | 0.42 | YES |
67 | RPL34 | RPL34 | RPL34 | 4431 | 0.067 | 0.43 | YES |
68 | RPL30 | RPL30 | RPL30 | 4433 | 0.067 | 0.43 | YES |
69 | RPS18 | RPS18 | RPS18 | 4439 | 0.067 | 0.44 | YES |
70 | RPL13A | RPL13A | RPL13A | 4450 | 0.066 | 0.44 | YES |
71 | EIF5 | EIF5 | EIF5 | 4451 | 0.066 | 0.45 | YES |
72 | RPS4X | RPS4X | RPS4X | 4468 | 0.066 | 0.46 | YES |
73 | RPL22 | RPL22 | RPL22 | 4521 | 0.065 | 0.46 | YES |
74 | RPL10A | RPL10A | RPL10A | 4581 | 0.064 | 0.46 | YES |
75 | RPS2 | RPS2 | RPS2 | 4614 | 0.063 | 0.47 | YES |
76 | RPL26 | RPL26 | RPL26 | 4625 | 0.063 | 0.47 | YES |
77 | RPL11 | RPL11 | RPL11 | 4651 | 0.063 | 0.48 | YES |
78 | RPN1 | RPN1 | RPN1 | 4783 | 0.06 | 0.48 | YES |
79 | SPCS3 | SPCS3 | SPCS3 | 4910 | 0.058 | 0.48 | YES |
80 | EIF1AX | EIF1AX | EIF1AX | 4914 | 0.058 | 0.48 | YES |
81 | RPL26L1 | RPL26L1 | RPL26L1 | 5000 | 0.057 | 0.48 | YES |
82 | RPL12 | RPL12 | RPL12 | 5003 | 0.057 | 0.49 | YES |
83 | EIF2B5 | EIF2B5 | EIF2B5 | 5004 | 0.057 | 0.49 | YES |
84 | RPS15A | RPS15A | RPS15A | 5021 | 0.056 | 0.5 | YES |
85 | SEC11A | SEC11A | SEC11A | 5041 | 0.056 | 0.5 | YES |
86 | RPS21 | RPS21 | RPS21 | 5098 | 0.055 | 0.5 | YES |
87 | EIF2S1 | EIF2S1 | EIF2S1 | 5108 | 0.055 | 0.51 | YES |
88 | RPLP1 | RPLP1 | RPLP1 | 5146 | 0.054 | 0.51 | YES |
89 | RPL27 | RPL27 | RPL27 | 5166 | 0.054 | 0.52 | YES |
90 | EIF4H | EIF4H | EIF4H | 5209 | 0.053 | 0.52 | YES |
91 | EIF3B | EIF3B | EIF3B | 5228 | 0.053 | 0.52 | YES |
92 | EIF2S3 | EIF2S3 | EIF2S3 | 5356 | 0.051 | 0.52 | YES |
93 | SRP54 | SRP54 | SRP54 | 5421 | 0.05 | 0.52 | YES |
94 | SEC11C | SEC11C | SEC11C | 5527 | 0.048 | 0.52 | YES |
95 | RPS13 | RPS13 | RPS13 | 5587 | 0.047 | 0.52 | YES |
96 | RPS19 | RPS19 | RPS19 | 5593 | 0.047 | 0.53 | YES |
97 | RPS20 | RPS20 | RPS20 | 5601 | 0.047 | 0.53 | YES |
98 | RPL23 | RPL23 | RPL23 | 5675 | 0.046 | 0.53 | YES |
99 | EIF2B3 | EIF2B3 | EIF2B3 | 5699 | 0.045 | 0.54 | YES |
100 | SRP14 | SRP14 | SRP14 | 5872 | 0.043 | 0.53 | YES |
101 | RPL37A | RPL37A | RPL37A | 5882 | 0.042 | 0.53 | YES |
102 | TRAM1 | TRAM1 | TRAM1 | 5945 | 0.042 | 0.54 | YES |
103 | RPS24 | RPS24 | RPS24 | 5985 | 0.041 | 0.54 | YES |
104 | EEF1D | EEF1D | EEF1D | 6113 | 0.039 | 0.53 | YES |
105 | SSR4 | SSR4 | SSR4 | 6116 | 0.039 | 0.54 | YES |
106 | RPL31 | RPL31 | RPL31 | 6158 | 0.038 | 0.54 | YES |
107 | FAU | FAU | FAU | 6177 | 0.038 | 0.54 | YES |
108 | EEF1A1 | EEF1A1 | EEF1A1 | 6320 | 0.036 | 0.54 | NO |
109 | RPS12 | RPS12 | RPS12 | 6360 | 0.036 | 0.54 | NO |
110 | RPS7 | RPS7 | RPS7 | 6372 | 0.035 | 0.54 | NO |
111 | SEC61A1 | SEC61A1 | SEC61A1 | 6437 | 0.034 | 0.54 | NO |
112 | RPN2 | RPN2 | RPN2 | 6512 | 0.033 | 0.54 | NO |
113 | SRP68 | SRP68 | SRP68 | 6709 | 0.03 | 0.53 | NO |
114 | RPL27A | RPL27A | RPL27A | 6741 | 0.03 | 0.53 | NO |
115 | RPL13 | RPL13 | RPL13 | 6809 | 0.029 | 0.53 | NO |
116 | RPS27A | RPS27A | RPS27A | 6817 | 0.029 | 0.54 | NO |
117 | SRP19 | SRP19 | SRP19 | 6857 | 0.029 | 0.54 | NO |
118 | RPLP2 | RPLP2 | RPLP2 | 7042 | 0.026 | 0.53 | NO |
119 | DDOST | DDOST | DDOST | 7090 | 0.025 | 0.53 | NO |
120 | EIF3J | EIF3J | EIF3J | 7255 | 0.023 | 0.52 | NO |
121 | EIF3I | EIF3I | EIF3I | 7331 | 0.022 | 0.52 | NO |
122 | RPL23A | RPL23A | RPL23A | 7349 | 0.022 | 0.52 | NO |
123 | SRP9 | SRP9 | SRP9 | 7359 | 0.022 | 0.52 | NO |
124 | EIF3F | EIF3F | EIF3F | 7628 | 0.018 | 0.51 | NO |
125 | RPL19 | RPL19 | RPL19 | 7648 | 0.018 | 0.51 | NO |
126 | SRP72 | SRP72 | SRP72 | 7680 | 0.018 | 0.51 | NO |
127 | LOC653566 | LOC653566 | LOC653566 | 7778 | 0.016 | 0.5 | NO |
128 | SPCS2 | SPCS2 | SPCS2 | 7899 | 0.014 | 0.5 | NO |
129 | EIF4E | EIF4E | EIF4E | 8157 | 0.011 | 0.49 | NO |
130 | SSR2 | SSR2 | SSR2 | 8393 | 0.0077 | 0.47 | NO |
131 | EIF2S2 | EIF2S2 | EIF2S2 | 8475 | 0.0067 | 0.47 | NO |
132 | EIF2B1 | EIF2B1 | EIF2B1 | 8626 | 0.0046 | 0.46 | NO |
133 | SSR3 | SSR3 | SSR3 | 8693 | 0.0037 | 0.46 | NO |
134 | EIF4G1 | EIF4G1 | EIF4G1 | 8749 | 0.003 | 0.46 | NO |
135 | EIF2B2 | EIF2B2 | EIF2B2 | 9421 | -0.0068 | 0.42 | NO |
136 | EIF3A | EIF3A | EIF3A | 10022 | -0.016 | 0.39 | NO |
137 | SRPR | SRPR | SRPR | 10807 | -0.028 | 0.34 | NO |
138 | RPL21 | RPL21 | RPL21 | 11119 | -0.033 | 0.33 | NO |
139 | GSPT2 | GSPT2 | GSPT2 | 11167 | -0.034 | 0.33 | NO |
140 | SSR1 | SSR1 | SSR1 | 11189 | -0.035 | 0.33 | NO |
141 | EIF3C | EIF3C | EIF3C | 11377 | -0.038 | 0.33 | NO |
142 | EIF4A1 | EIF4A1 | EIF4A1 | 11387 | -0.038 | 0.33 | NO |
143 | EIF5B | EIF5B | EIF5B | 12085 | -0.052 | 0.3 | NO |
144 | EIF2B4 | EIF2B4 | EIF2B4 | 12217 | -0.055 | 0.29 | NO |
145 | SEC61A2 | SEC61A2 | SEC61A2 | 13952 | -0.1 | 0.2 | NO |
146 | RPS28 | RPS28 | RPS28 | 14788 | -0.14 | 0.17 | NO |
Figure S81. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE.

Figure S82. 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

Table S42. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | GTF2H2B | GTF2H2B | GTF2H2B | 1048 | 0.24 | 0.087 | YES |
2 | GTF2H2 | GTF2H2 | GTF2H2 | 1085 | 0.23 | 0.23 | YES |
3 | POLR2I | POLR2I | POLR2I | 3605 | 0.085 | 0.14 | YES |
4 | NCBP1 | NCBP1 | NCBP1 | 3885 | 0.078 | 0.17 | YES |
5 | ERCC2 | ERCC2 | ERCC2 | 4646 | 0.063 | 0.17 | YES |
6 | MNAT1 | MNAT1 | MNAT1 | 4659 | 0.063 | 0.2 | YES |
7 | POLR2K | POLR2K | POLR2K | 4749 | 0.061 | 0.24 | YES |
8 | GTF2H3 | GTF2H3 | GTF2H3 | 4983 | 0.057 | 0.26 | YES |
9 | POLR2L | POLR2L | POLR2L | 5026 | 0.056 | 0.29 | YES |
10 | POLR2F | POLR2F | POLR2F | 5103 | 0.055 | 0.32 | YES |
11 | POLR2E | POLR2E | POLR2E | 5297 | 0.052 | 0.34 | YES |
12 | GTF2F1 | GTF2F1 | GTF2F1 | 5417 | 0.05 | 0.37 | YES |
13 | POLR2J | POLR2J | POLR2J | 5621 | 0.047 | 0.38 | YES |
14 | CDK7 | CDK7 | CDK7 | 5742 | 0.044 | 0.41 | YES |
15 | POLR2H | POLR2H | POLR2H | 5774 | 0.044 | 0.43 | YES |
16 | RNGTT | RNGTT | RNGTT | 5839 | 0.043 | 0.45 | YES |
17 | POLR2B | POLR2B | POLR2B | 6052 | 0.04 | 0.47 | YES |
18 | SUPT5H | SUPT5H | SUPT5H | 6252 | 0.037 | 0.48 | YES |
19 | NCBP2 | NCBP2 | NCBP2 | 7028 | 0.026 | 0.45 | NO |
20 | POLR2C | POLR2C | POLR2C | 7355 | 0.022 | 0.45 | NO |
21 | CCNH | CCNH | CCNH | 7584 | 0.019 | 0.44 | NO |
22 | RNMT | RNMT | RNMT | 8199 | 0.01 | 0.42 | NO |
23 | POLR2G | POLR2G | POLR2G | 8620 | 0.0047 | 0.4 | NO |
24 | GTF2F2 | GTF2F2 | GTF2F2 | 9458 | -0.0074 | 0.35 | NO |
25 | ERCC3 | ERCC3 | ERCC3 | 9516 | -0.0082 | 0.36 | NO |
26 | POLR2A | POLR2A | POLR2A | 10858 | -0.029 | 0.3 | NO |
27 | POLR2D | POLR2D | POLR2D | 11662 | -0.043 | 0.28 | NO |
28 | GTF2H1 | GTF2H1 | GTF2H1 | 11807 | -0.046 | 0.3 | NO |
29 | GTF2H4 | GTF2H4 | GTF2H4 | 12481 | -0.061 | 0.3 | NO |
Figure S83. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA DEGRADATION.

Figure S84. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S43. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FAM153A | FAM153A | FAM153A | 296 | 0.38 | 0.024 | YES |
2 | RPSAP9 | RPSAP9 | RPSAP9 | 1115 | 0.23 | 0.0023 | YES |
3 | NUP155 | NUP155 | NUP155 | 1373 | 0.2 | 0.0091 | YES |
4 | RPL9 | RPL9 | RPL9 | 1677 | 0.17 | 0.01 | YES |
5 | NUP210 | NUP210 | NUP210 | 1697 | 0.17 | 0.027 | YES |
6 | RPS26 | RPS26 | RPS26 | 1725 | 0.17 | 0.043 | YES |
7 | RPL7 | RPL7 | RPL7 | 1751 | 0.16 | 0.06 | YES |
8 | RPL36A | RPL36A | RPL36A | 1800 | 0.16 | 0.074 | YES |
9 | RPSA | RPSA | RPSA | 1975 | 0.15 | 0.08 | YES |
10 | RPS17 | RPS17 | RPS17 | 2327 | 0.13 | 0.074 | YES |
11 | RPL24 | RPL24 | RPL24 | 2336 | 0.13 | 0.087 | YES |
12 | RPS27 | RPS27 | RPS27 | 2342 | 0.13 | 0.1 | YES |
13 | RPL15 | RPL15 | RPL15 | 2568 | 0.12 | 0.1 | YES |
14 | RPS5 | RPS5 | RPS5 | 2600 | 0.12 | 0.11 | YES |
15 | RPS14 | RPS14 | RPS14 | 2637 | 0.12 | 0.12 | YES |
16 | RPL32 | RPL32 | RPL32 | 2666 | 0.12 | 0.13 | YES |
17 | RPL7A | RPL7A | RPL7A | 2770 | 0.11 | 0.14 | YES |
18 | RPS23 | RPS23 | RPS23 | 2791 | 0.11 | 0.15 | YES |
19 | RPL41 | RPL41 | RPL41 | 2880 | 0.11 | 0.16 | YES |
20 | RPS6 | RPS6 | RPS6 | 2885 | 0.11 | 0.17 | YES |
21 | RPS3A | RPS3A | RPS3A | 2945 | 0.1 | 0.18 | YES |
22 | RPL18A | RPL18A | RPL18A | 2949 | 0.1 | 0.19 | YES |
23 | RPL17 | RPL17 | RPL17 | 3057 | 0.1 | 0.19 | YES |
24 | RPL35A | RPL35A | RPL35A | 3066 | 0.1 | 0.2 | YES |
25 | RPL35 | RPL35 | RPL35 | 3075 | 0.1 | 0.21 | YES |
26 | RPL14 | RPL14 | RPL14 | 3078 | 0.1 | 0.22 | YES |
27 | RPS15 | RPS15 | RPS15 | 3084 | 0.1 | 0.23 | YES |
28 | RPL6 | RPL6 | RPL6 | 3095 | 0.1 | 0.24 | YES |
29 | RPL29 | RPL29 | RPL29 | 3150 | 0.098 | 0.25 | YES |
30 | RPL37 | RPL37 | RPL37 | 3390 | 0.091 | 0.25 | YES |
31 | RPLP0 | RPLP0 | RPLP0 | 3439 | 0.09 | 0.25 | YES |
32 | RPS16 | RPS16 | RPS16 | 3497 | 0.088 | 0.26 | YES |
33 | RPL38 | RPL38 | RPL38 | 3522 | 0.087 | 0.27 | YES |
34 | RPS29 | RPS29 | RPS29 | 3572 | 0.085 | 0.27 | YES |
35 | NUP205 | NUP205 | NUP205 | 3603 | 0.085 | 0.28 | YES |
36 | POLR2I | POLR2I | POLR2I | 3605 | 0.085 | 0.29 | YES |
37 | CANX | CANX | CANX | 3606 | 0.085 | 0.3 | YES |
38 | NUP37 | NUP37 | NUP37 | 3623 | 0.084 | 0.31 | YES |
39 | UBA52 | UBA52 | UBA52 | 3677 | 0.083 | 0.31 | YES |
40 | RPL8 | RPL8 | RPL8 | 3707 | 0.082 | 0.32 | YES |
41 | NUP107 | NUP107 | NUP107 | 3743 | 0.081 | 0.33 | YES |
42 | RPL18 | RPL18 | RPL18 | 3747 | 0.081 | 0.34 | YES |
43 | RPL3 | RPL3 | RPL3 | 3819 | 0.08 | 0.34 | YES |
44 | RPS8 | RPS8 | RPS8 | 3844 | 0.079 | 0.35 | YES |
45 | AAAS | AAAS | AAAS | 3877 | 0.078 | 0.35 | YES |
46 | RPS10 | RPS10 | RPS10 | 3960 | 0.076 | 0.36 | YES |
47 | RPS9 | RPS9 | RPS9 | 3971 | 0.076 | 0.36 | YES |
48 | RPL28 | RPL28 | RPL28 | 4029 | 0.075 | 0.37 | YES |
49 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 4122 | 0.073 | 0.37 | YES |
50 | RPL4 | RPL4 | RPL4 | 4127 | 0.073 | 0.38 | YES |
51 | RPL39 | RPL39 | RPL39 | 4144 | 0.072 | 0.39 | YES |
52 | RPL10 | RPL10 | RPL10 | 4189 | 0.072 | 0.39 | YES |
53 | RPL5 | RPL5 | RPL5 | 4233 | 0.071 | 0.4 | YES |
54 | RPS3 | RPS3 | RPS3 | 4244 | 0.07 | 0.4 | YES |
55 | RPS11 | RPS11 | RPS11 | 4361 | 0.068 | 0.4 | YES |
56 | RPS25 | RPS25 | RPS25 | 4404 | 0.067 | 0.41 | YES |
57 | RPL36 | RPL36 | RPL36 | 4410 | 0.067 | 0.42 | YES |
58 | RPL34 | RPL34 | RPL34 | 4431 | 0.067 | 0.42 | YES |
59 | RPL30 | RPL30 | RPL30 | 4433 | 0.067 | 0.43 | YES |
60 | RPS18 | RPS18 | RPS18 | 4439 | 0.067 | 0.44 | YES |
61 | RPL13A | RPL13A | RPL13A | 4450 | 0.066 | 0.44 | YES |
62 | RPS4X | RPS4X | RPS4X | 4468 | 0.066 | 0.45 | YES |
63 | NUP35 | NUP35 | NUP35 | 4478 | 0.066 | 0.46 | YES |
64 | CLTA | CLTA | CLTA | 4509 | 0.065 | 0.46 | YES |
65 | RPL22 | RPL22 | RPL22 | 4521 | 0.065 | 0.47 | YES |
66 | RPL10A | RPL10A | RPL10A | 4581 | 0.064 | 0.47 | YES |
67 | RPS2 | RPS2 | RPS2 | 4614 | 0.063 | 0.48 | YES |
68 | RPL26 | RPL26 | RPL26 | 4625 | 0.063 | 0.48 | YES |
69 | RPL11 | RPL11 | RPL11 | 4651 | 0.063 | 0.49 | YES |
70 | POLR2K | POLR2K | POLR2K | 4749 | 0.061 | 0.49 | YES |
71 | POM121 | POM121 | POM121 | 4973 | 0.057 | 0.48 | YES |
72 | RPL26L1 | RPL26L1 | RPL26L1 | 5000 | 0.057 | 0.49 | YES |
73 | RPL12 | RPL12 | RPL12 | 5003 | 0.057 | 0.49 | YES |
74 | RPS15A | RPS15A | RPS15A | 5021 | 0.056 | 0.5 | YES |
75 | POLR2L | POLR2L | POLR2L | 5026 | 0.056 | 0.5 | YES |
76 | RPS21 | RPS21 | RPS21 | 5098 | 0.055 | 0.5 | YES |
77 | POLR2F | POLR2F | POLR2F | 5103 | 0.055 | 0.51 | YES |
78 | RPLP1 | RPLP1 | RPLP1 | 5146 | 0.054 | 0.51 | YES |
79 | RPL27 | RPL27 | RPL27 | 5166 | 0.054 | 0.52 | YES |
80 | POLR2E | POLR2E | POLR2E | 5297 | 0.052 | 0.52 | YES |
81 | GTF2F1 | GTF2F1 | GTF2F1 | 5417 | 0.05 | 0.52 | YES |
82 | RPS13 | RPS13 | RPS13 | 5587 | 0.047 | 0.51 | YES |
83 | RPS19 | RPS19 | RPS19 | 5593 | 0.047 | 0.52 | YES |
84 | RPS20 | RPS20 | RPS20 | 5601 | 0.047 | 0.52 | YES |
85 | POLR2J | POLR2J | POLR2J | 5621 | 0.047 | 0.52 | YES |
86 | RPL23 | RPL23 | RPL23 | 5675 | 0.046 | 0.53 | YES |
87 | POLR2H | POLR2H | POLR2H | 5774 | 0.044 | 0.52 | YES |
88 | IPO5 | IPO5 | IPO5 | 5781 | 0.044 | 0.53 | YES |
89 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 5827 | 0.043 | 0.53 | YES |
90 | RPL37A | RPL37A | RPL37A | 5882 | 0.042 | 0.53 | YES |
91 | RPS24 | RPS24 | RPS24 | 5985 | 0.041 | 0.53 | YES |
92 | POLR2B | POLR2B | POLR2B | 6052 | 0.04 | 0.53 | YES |
93 | RPL31 | RPL31 | RPL31 | 6158 | 0.038 | 0.53 | YES |
94 | NUP54 | NUP54 | NUP54 | 6163 | 0.038 | 0.53 | YES |
95 | FAU | FAU | FAU | 6177 | 0.038 | 0.54 | YES |
96 | RAE1 | RAE1 | RAE1 | 6272 | 0.037 | 0.54 | YES |
97 | NUP214 | NUP214 | NUP214 | 6348 | 0.036 | 0.54 | YES |
98 | RPS12 | RPS12 | RPS12 | 6360 | 0.036 | 0.54 | YES |
99 | RPS7 | RPS7 | RPS7 | 6372 | 0.035 | 0.54 | YES |
100 | XPO1 | XPO1 | XPO1 | 6438 | 0.034 | 0.54 | NO |
101 | NUP133 | NUP133 | NUP133 | 6586 | 0.032 | 0.54 | NO |
102 | NUPL2 | NUPL2 | NUPL2 | 6591 | 0.032 | 0.54 | NO |
103 | GRSF1 | GRSF1 | GRSF1 | 6658 | 0.031 | 0.54 | NO |
104 | RPL27A | RPL27A | RPL27A | 6741 | 0.03 | 0.54 | NO |
105 | RPL13 | RPL13 | RPL13 | 6809 | 0.029 | 0.54 | NO |
106 | RPS27A | RPS27A | RPS27A | 6817 | 0.029 | 0.54 | NO |
107 | RPLP2 | RPLP2 | RPLP2 | 7042 | 0.026 | 0.53 | NO |
108 | NUP62 | NUP62 | NUP62 | 7167 | 0.024 | 0.53 | NO |
109 | RPL23A | RPL23A | RPL23A | 7349 | 0.022 | 0.52 | NO |
110 | POLR2C | POLR2C | POLR2C | 7355 | 0.022 | 0.52 | NO |
111 | TPR | TPR | TPR | 7544 | 0.019 | 0.51 | NO |
112 | RPL19 | RPL19 | RPL19 | 7648 | 0.018 | 0.51 | NO |
113 | RAN | RAN | RAN | 7723 | 0.017 | 0.51 | NO |
114 | NUP188 | NUP188 | NUP188 | 7785 | 0.016 | 0.5 | NO |
115 | CALR | CALR | CALR | 7895 | 0.014 | 0.5 | NO |
116 | POLR2G | POLR2G | POLR2G | 8620 | 0.0047 | 0.46 | NO |
117 | KPNA1 | KPNA1 | KPNA1 | 8666 | 0.0041 | 0.46 | NO |
118 | DNAJC3 | DNAJC3 | DNAJC3 | 8874 | 0.0011 | 0.44 | NO |
119 | NUP85 | NUP85 | NUP85 | 9040 | -0.0014 | 0.44 | NO |
120 | SEH1L | SEH1L | SEH1L | 9202 | -0.0037 | 0.43 | NO |
121 | RANBP2 | RANBP2 | RANBP2 | 9220 | -0.004 | 0.43 | NO |
122 | GTF2F2 | GTF2F2 | GTF2F2 | 9458 | -0.0074 | 0.41 | NO |
123 | NUPL1 | NUPL1 | NUPL1 | 9477 | -0.0077 | 0.41 | NO |
124 | KPNB1 | KPNB1 | KPNB1 | 10197 | -0.018 | 0.38 | NO |
125 | NUP50 | NUP50 | NUP50 | 10381 | -0.021 | 0.37 | NO |
126 | CLTC | CLTC | CLTC | 10463 | -0.023 | 0.36 | NO |
127 | NUP93 | NUP93 | NUP93 | 10715 | -0.027 | 0.35 | NO |
128 | POLR2A | POLR2A | POLR2A | 10858 | -0.029 | 0.35 | NO |
129 | NUP43 | NUP43 | NUP43 | 10877 | -0.029 | 0.35 | NO |
130 | NUP153 | NUP153 | NUP153 | 11036 | -0.032 | 0.34 | NO |
131 | RPL21 | RPL21 | RPL21 | 11119 | -0.033 | 0.34 | NO |
132 | POLR2D | POLR2D | POLR2D | 11662 | -0.043 | 0.32 | NO |
133 | NUP88 | NUP88 | NUP88 | 12612 | -0.065 | 0.27 | NO |
134 | HSPA1B | HSPA1B | HSPA1B | 13008 | -0.074 | 0.26 | NO |
135 | RPS28 | RPS28 | RPS28 | 14788 | -0.14 | 0.17 | NO |
Figure S85. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DNA REPLICATION.

Figure S86. 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

Table S44. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | GTF2H2B | GTF2H2B | GTF2H2B | 1048 | 0.24 | 0.043 | YES |
2 | GTF2H2 | GTF2H2 | GTF2H2 | 1085 | 0.23 | 0.14 | YES |
3 | CCNT1 | CCNT1 | CCNT1 | 1694 | 0.17 | 0.18 | YES |
4 | POLR2I | POLR2I | POLR2I | 3605 | 0.085 | 0.11 | YES |
5 | NCBP1 | NCBP1 | NCBP1 | 3885 | 0.078 | 0.13 | YES |
6 | TCEB1 | TCEB1 | TCEB1 | 4290 | 0.069 | 0.14 | YES |
7 | ERCC2 | ERCC2 | ERCC2 | 4646 | 0.063 | 0.14 | YES |
8 | MNAT1 | MNAT1 | MNAT1 | 4659 | 0.063 | 0.17 | YES |
9 | SUPT16H | SUPT16H | SUPT16H | 4669 | 0.062 | 0.2 | YES |
10 | POLR2K | POLR2K | POLR2K | 4749 | 0.061 | 0.22 | YES |
11 | GTF2H3 | GTF2H3 | GTF2H3 | 4983 | 0.057 | 0.23 | YES |
12 | POLR2L | POLR2L | POLR2L | 5026 | 0.056 | 0.25 | YES |
13 | SSRP1 | SSRP1 | SSRP1 | 5089 | 0.055 | 0.27 | YES |
14 | POLR2F | POLR2F | POLR2F | 5103 | 0.055 | 0.3 | YES |
15 | POLR2E | POLR2E | POLR2E | 5297 | 0.052 | 0.31 | YES |
16 | GTF2F1 | GTF2F1 | GTF2F1 | 5417 | 0.05 | 0.32 | YES |
17 | POLR2J | POLR2J | POLR2J | 5621 | 0.047 | 0.33 | YES |
18 | CDK7 | CDK7 | CDK7 | 5742 | 0.044 | 0.34 | YES |
19 | POLR2H | POLR2H | POLR2H | 5774 | 0.044 | 0.36 | YES |
20 | TCEB2 | TCEB2 | TCEB2 | 5907 | 0.042 | 0.37 | YES |
21 | COBRA1 | COBRA1 | COBRA1 | 6043 | 0.04 | 0.38 | YES |
22 | POLR2B | POLR2B | POLR2B | 6052 | 0.04 | 0.4 | YES |
23 | SUPT5H | SUPT5H | SUPT5H | 6252 | 0.037 | 0.4 | YES |
24 | TCEA1 | TCEA1 | TCEA1 | 6355 | 0.036 | 0.41 | YES |
25 | NCBP2 | NCBP2 | NCBP2 | 7028 | 0.026 | 0.39 | NO |
26 | POLR2C | POLR2C | POLR2C | 7355 | 0.022 | 0.38 | NO |
27 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 7357 | 0.022 | 0.39 | NO |
28 | CCNH | CCNH | CCNH | 7584 | 0.019 | 0.38 | NO |
29 | ELL | ELL | ELL | 8531 | 0.0058 | 0.33 | NO |
30 | POLR2G | POLR2G | POLR2G | 8620 | 0.0047 | 0.33 | NO |
31 | GTF2F2 | GTF2F2 | GTF2F2 | 9458 | -0.0074 | 0.28 | NO |
32 | ERCC3 | ERCC3 | ERCC3 | 9516 | -0.0082 | 0.28 | NO |
33 | CCNT2 | CCNT2 | CCNT2 | 10134 | -0.017 | 0.26 | NO |
34 | WHSC2 | WHSC2 | WHSC2 | 10323 | -0.02 | 0.26 | NO |
35 | TH1L | TH1L | TH1L | 10328 | -0.02 | 0.26 | NO |
36 | RDBP | RDBP | RDBP | 10443 | -0.022 | 0.27 | NO |
37 | CDK9 | CDK9 | CDK9 | 10700 | -0.026 | 0.26 | NO |
38 | POLR2A | POLR2A | POLR2A | 10858 | -0.029 | 0.27 | NO |
39 | POLR2D | POLR2D | POLR2D | 11662 | -0.043 | 0.24 | NO |
40 | GTF2H1 | GTF2H1 | GTF2H1 | 11807 | -0.046 | 0.25 | NO |
41 | GTF2H4 | GTF2H4 | GTF2H4 | 12481 | -0.061 | 0.24 | NO |
42 | TCEB3 | TCEB3 | TCEB3 | 12698 | -0.067 | 0.26 | NO |
43 | CTDP1 | CTDP1 | CTDP1 | 12744 | -0.068 | 0.29 | NO |
Figure S87. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SPLICEOSOME.

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPLICEOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S45. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FAM153A | FAM153A | FAM153A | 296 | 0.38 | 0.033 | YES |
2 | RPSAP9 | RPSAP9 | RPSAP9 | 1115 | 0.23 | 0.016 | YES |
3 | RPL9 | RPL9 | RPL9 | 1677 | 0.17 | 0.0069 | YES |
4 | RPS26 | RPS26 | RPS26 | 1725 | 0.17 | 0.026 | YES |
5 | RPL7 | RPL7 | RPL7 | 1751 | 0.16 | 0.046 | YES |
6 | RPL36A | RPL36A | RPL36A | 1800 | 0.16 | 0.064 | YES |
7 | RPSA | RPSA | RPSA | 1975 | 0.15 | 0.074 | YES |
8 | RPS17 | RPS17 | RPS17 | 2327 | 0.13 | 0.071 | YES |
9 | RPL24 | RPL24 | RPL24 | 2336 | 0.13 | 0.087 | YES |
10 | RPS27 | RPS27 | RPS27 | 2342 | 0.13 | 0.1 | YES |
11 | RPL15 | RPL15 | RPL15 | 2568 | 0.12 | 0.11 | YES |
12 | RPS5 | RPS5 | RPS5 | 2600 | 0.12 | 0.12 | YES |
13 | RPS14 | RPS14 | RPS14 | 2637 | 0.12 | 0.13 | YES |
14 | RPL32 | RPL32 | RPL32 | 2666 | 0.12 | 0.15 | YES |
15 | RPL7A | RPL7A | RPL7A | 2770 | 0.11 | 0.16 | YES |
16 | RPS23 | RPS23 | RPS23 | 2791 | 0.11 | 0.17 | YES |
17 | RPL41 | RPL41 | RPL41 | 2880 | 0.11 | 0.18 | YES |
18 | RPS6 | RPS6 | RPS6 | 2885 | 0.11 | 0.19 | YES |
19 | RPS3A | RPS3A | RPS3A | 2945 | 0.1 | 0.2 | YES |
20 | RPL18A | RPL18A | RPL18A | 2949 | 0.1 | 0.21 | YES |
21 | RPL17 | RPL17 | RPL17 | 3057 | 0.1 | 0.22 | YES |
22 | RPL35A | RPL35A | RPL35A | 3066 | 0.1 | 0.23 | YES |
23 | RPL35 | RPL35 | RPL35 | 3075 | 0.1 | 0.25 | YES |
24 | RPL14 | RPL14 | RPL14 | 3078 | 0.1 | 0.26 | YES |
25 | RPS15 | RPS15 | RPS15 | 3084 | 0.1 | 0.27 | YES |
26 | RPL6 | RPL6 | RPL6 | 3095 | 0.1 | 0.28 | YES |
27 | RPL29 | RPL29 | RPL29 | 3150 | 0.098 | 0.29 | YES |
28 | RPL37 | RPL37 | RPL37 | 3390 | 0.091 | 0.29 | YES |
29 | RPLP0 | RPLP0 | RPLP0 | 3439 | 0.09 | 0.3 | YES |
30 | RPS16 | RPS16 | RPS16 | 3497 | 0.088 | 0.31 | YES |
31 | RPL38 | RPL38 | RPL38 | 3522 | 0.087 | 0.32 | YES |
32 | RPS29 | RPS29 | RPS29 | 3572 | 0.085 | 0.33 | YES |
33 | PPP2R2A | PPP2R2A | PPP2R2A | 3593 | 0.085 | 0.34 | YES |
34 | UBA52 | UBA52 | UBA52 | 3677 | 0.083 | 0.34 | YES |
35 | RPL8 | RPL8 | RPL8 | 3707 | 0.082 | 0.35 | YES |
36 | RPL18 | RPL18 | RPL18 | 3747 | 0.081 | 0.36 | YES |
37 | RPL3 | RPL3 | RPL3 | 3819 | 0.08 | 0.37 | YES |
38 | RPS8 | RPS8 | RPS8 | 3844 | 0.079 | 0.38 | YES |
39 | NCBP1 | NCBP1 | NCBP1 | 3885 | 0.078 | 0.38 | YES |
40 | RPS10 | RPS10 | RPS10 | 3960 | 0.076 | 0.39 | YES |
41 | RPS9 | RPS9 | RPS9 | 3971 | 0.076 | 0.4 | YES |
42 | RPL28 | RPL28 | RPL28 | 4029 | 0.075 | 0.41 | YES |
43 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 4122 | 0.073 | 0.41 | YES |
44 | RPL4 | RPL4 | RPL4 | 4127 | 0.073 | 0.42 | YES |
45 | RPL39 | RPL39 | RPL39 | 4144 | 0.072 | 0.43 | YES |
46 | RPL10 | RPL10 | RPL10 | 4189 | 0.072 | 0.44 | YES |
47 | RPL5 | RPL5 | RPL5 | 4233 | 0.071 | 0.44 | YES |
48 | RPS3 | RPS3 | RPS3 | 4244 | 0.07 | 0.45 | YES |
49 | ETF1 | ETF1 | ETF1 | 4324 | 0.069 | 0.46 | YES |
50 | PABPC1 | PABPC1 | PABPC1 | 4344 | 0.068 | 0.46 | YES |
51 | RPS11 | RPS11 | RPS11 | 4361 | 0.068 | 0.47 | YES |
52 | RPS25 | RPS25 | RPS25 | 4404 | 0.067 | 0.48 | YES |
53 | RPL36 | RPL36 | RPL36 | 4410 | 0.067 | 0.48 | YES |
54 | RPL34 | RPL34 | RPL34 | 4431 | 0.067 | 0.49 | YES |
55 | RPL30 | RPL30 | RPL30 | 4433 | 0.067 | 0.5 | YES |
56 | RPS18 | RPS18 | RPS18 | 4439 | 0.067 | 0.51 | YES |
57 | RPL13A | RPL13A | RPL13A | 4450 | 0.066 | 0.52 | YES |
58 | RPS4X | RPS4X | RPS4X | 4468 | 0.066 | 0.52 | YES |
59 | RPL22 | RPL22 | RPL22 | 4521 | 0.065 | 0.53 | YES |
60 | RPL10A | RPL10A | RPL10A | 4581 | 0.064 | 0.54 | YES |
61 | RPS2 | RPS2 | RPS2 | 4614 | 0.063 | 0.54 | YES |
62 | RPL26 | RPL26 | RPL26 | 4625 | 0.063 | 0.55 | YES |
63 | RPL11 | RPL11 | RPL11 | 4651 | 0.063 | 0.56 | YES |
64 | RPL26L1 | RPL26L1 | RPL26L1 | 5000 | 0.057 | 0.55 | YES |
65 | RPL12 | RPL12 | RPL12 | 5003 | 0.057 | 0.55 | YES |
66 | RPS15A | RPS15A | RPS15A | 5021 | 0.056 | 0.56 | YES |
67 | RPS21 | RPS21 | RPS21 | 5098 | 0.055 | 0.56 | YES |
68 | UPF3B | UPF3B | UPF3B | 5132 | 0.055 | 0.57 | YES |
69 | RPLP1 | RPLP1 | RPLP1 | 5146 | 0.054 | 0.57 | YES |
70 | RPL27 | RPL27 | RPL27 | 5166 | 0.054 | 0.58 | YES |
71 | RPS13 | RPS13 | RPS13 | 5587 | 0.047 | 0.56 | NO |
72 | RPS19 | RPS19 | RPS19 | 5593 | 0.047 | 0.57 | NO |
73 | RPS20 | RPS20 | RPS20 | 5601 | 0.047 | 0.57 | NO |
74 | RPL23 | RPL23 | RPL23 | 5675 | 0.046 | 0.57 | NO |
75 | PPP2CA | PPP2CA | PPP2CA | 5881 | 0.042 | 0.57 | NO |
76 | RPL37A | RPL37A | RPL37A | 5882 | 0.042 | 0.57 | NO |
77 | RPS24 | RPS24 | RPS24 | 5985 | 0.041 | 0.57 | NO |
78 | RPL31 | RPL31 | RPL31 | 6158 | 0.038 | 0.57 | NO |
79 | FAU | FAU | FAU | 6177 | 0.038 | 0.57 | NO |
80 | RPS12 | RPS12 | RPS12 | 6360 | 0.036 | 0.57 | NO |
81 | RPS7 | RPS7 | RPS7 | 6372 | 0.035 | 0.57 | NO |
82 | RPL27A | RPL27A | RPL27A | 6741 | 0.03 | 0.55 | NO |
83 | RPL13 | RPL13 | RPL13 | 6809 | 0.029 | 0.55 | NO |
84 | RPS27A | RPS27A | RPS27A | 6817 | 0.029 | 0.56 | NO |
85 | SMG7 | SMG7 | SMG7 | 6882 | 0.028 | 0.56 | NO |
86 | NCBP2 | NCBP2 | NCBP2 | 7028 | 0.026 | 0.55 | NO |
87 | RPLP2 | RPLP2 | RPLP2 | 7042 | 0.026 | 0.56 | NO |
88 | RPL23A | RPL23A | RPL23A | 7349 | 0.022 | 0.54 | NO |
89 | RNPS1 | RNPS1 | RNPS1 | 7386 | 0.021 | 0.54 | NO |
90 | SMG5 | SMG5 | SMG5 | 7421 | 0.021 | 0.54 | NO |
91 | EIF4A3 | EIF4A3 | EIF4A3 | 7460 | 0.021 | 0.54 | NO |
92 | RPL19 | RPL19 | RPL19 | 7648 | 0.018 | 0.54 | NO |
93 | EIF4G1 | EIF4G1 | EIF4G1 | 8749 | 0.003 | 0.47 | NO |
94 | SMG1 | SMG1 | SMG1 | 8822 | 0.0019 | 0.47 | NO |
95 | MAGOH | MAGOH | MAGOH | 8832 | 0.0018 | 0.47 | NO |
96 | RBM8A | RBM8A | RBM8A | 8866 | 0.0012 | 0.47 | NO |
97 | UPF3A | UPF3A | UPF3A | 9649 | -0.01 | 0.42 | NO |
98 | SMG6 | SMG6 | SMG6 | 9951 | -0.015 | 0.41 | NO |
99 | PPP2R1A | PPP2R1A | PPP2R1A | 9980 | -0.015 | 0.41 | NO |
100 | CASC3 | CASC3 | CASC3 | 10271 | -0.02 | 0.4 | NO |
101 | UPF2 | UPF2 | UPF2 | 10380 | -0.021 | 0.39 | NO |
102 | RPL21 | RPL21 | RPL21 | 11119 | -0.033 | 0.36 | NO |
103 | GSPT2 | GSPT2 | GSPT2 | 11167 | -0.034 | 0.36 | NO |
104 | RPS28 | RPS28 | RPS28 | 14788 | -0.14 | 0.17 | NO |
Figure S89. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NUCLEOTIDE EXCISION REPAIR.

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

Table S46. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | POLE2 | POLE2 | POLE2 | 1042 | 0.24 | 0.007 | YES |
2 | PRIM1 | PRIM1 | PRIM1 | 1165 | 0.22 | 0.061 | YES |
3 | MCM2 | MCM2 | MCM2 | 1240 | 0.21 | 0.12 | YES |
4 | RFC4 | RFC4 | RFC4 | 1427 | 0.19 | 0.16 | YES |
5 | RNASEH2A | RNASEH2A | RNASEH2A | 1507 | 0.18 | 0.21 | YES |
6 | FEN1 | FEN1 | FEN1 | 2015 | 0.15 | 0.22 | YES |
7 | LIG1 | LIG1 | LIG1 | 2101 | 0.14 | 0.25 | YES |
8 | POLA1 | POLA1 | POLA1 | 2145 | 0.14 | 0.29 | YES |
9 | RPA3 | RPA3 | RPA3 | 2165 | 0.14 | 0.32 | YES |
10 | MCM4 | MCM4 | MCM4 | 2220 | 0.13 | 0.36 | YES |
11 | RFC5 | RFC5 | RFC5 | 2341 | 0.13 | 0.39 | YES |
12 | POLE3 | POLE3 | POLE3 | 2456 | 0.12 | 0.42 | YES |
13 | POLD2 | POLD2 | POLD2 | 2559 | 0.12 | 0.44 | YES |
14 | MCM7 | MCM7 | MCM7 | 2592 | 0.12 | 0.47 | YES |
15 | POLA2 | POLA2 | POLA2 | 2650 | 0.12 | 0.5 | YES |
16 | POLD1 | POLD1 | POLD1 | 2658 | 0.12 | 0.54 | YES |
17 | PRIM2 | PRIM2 | PRIM2 | 2776 | 0.11 | 0.56 | YES |
18 | RFC1 | RFC1 | RFC1 | 2886 | 0.11 | 0.58 | YES |
19 | RFC2 | RFC2 | RFC2 | 3360 | 0.092 | 0.58 | YES |
20 | POLE4 | POLE4 | POLE4 | 3420 | 0.09 | 0.6 | YES |
21 | RNASEH2C | RNASEH2C | RNASEH2C | 3713 | 0.082 | 0.61 | YES |
22 | SSBP1 | SSBP1 | SSBP1 | 3917 | 0.077 | 0.62 | YES |
23 | RFC3 | RFC3 | RFC3 | 4175 | 0.072 | 0.62 | YES |
24 | MCM6 | MCM6 | MCM6 | 4187 | 0.072 | 0.64 | YES |
25 | PCNA | PCNA | PCNA | 4546 | 0.065 | 0.64 | NO |
26 | MCM5 | MCM5 | MCM5 | 5629 | 0.047 | 0.59 | NO |
27 | RPA1 | RPA1 | RPA1 | 6739 | 0.03 | 0.54 | NO |
28 | POLD3 | POLD3 | POLD3 | 6947 | 0.028 | 0.54 | NO |
29 | MCM3 | MCM3 | MCM3 | 7012 | 0.026 | 0.54 | NO |
30 | POLE | POLE | POLE | 7690 | 0.017 | 0.51 | NO |
31 | RPA2 | RPA2 | RPA2 | 7759 | 0.016 | 0.51 | NO |
32 | RNASEH1 | RNASEH1 | RNASEH1 | 8032 | 0.012 | 0.5 | NO |
33 | DNA2 | DNA2 | DNA2 | 8038 | 0.012 | 0.5 | NO |
34 | RPA4 | RPA4 | RPA4 | 10611 | -0.025 | 0.36 | NO |
35 | RNASEH2B | RNASEH2B | RNASEH2B | 10999 | -0.031 | 0.35 | NO |
36 | POLD4 | POLD4 | POLD4 | 14539 | -0.13 | 0.18 | NO |
Figure S91. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FANCONI PATHWAY.

Figure S92. Get High-res Image For the top 5 core enriched genes in the pathway: PID FANCONI PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S47. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | TIMM10 | TIMM10 | TIMM10 | 1983 | 0.15 | -0.062 | YES |
2 | CHCHD4 | CHCHD4 | CHCHD4 | 2352 | 0.13 | -0.04 | YES |
3 | GRPEL2 | GRPEL2 | GRPEL2 | 2433 | 0.12 | -0.0029 | YES |
4 | HSPA9 | HSPA9 | HSPA9 | 2491 | 0.12 | 0.035 | YES |
5 | TOMM7 | TOMM7 | TOMM7 | 2741 | 0.11 | 0.058 | YES |
6 | COX17 | COX17 | COX17 | 2973 | 0.1 | 0.08 | YES |
7 | SLC25A4 | SLC25A4 | SLC25A4 | 2998 | 0.1 | 0.11 | YES |
8 | COQ2 | COQ2 | COQ2 | 3272 | 0.094 | 0.13 | YES |
9 | PMPCB | PMPCB | PMPCB | 3274 | 0.094 | 0.16 | YES |
10 | DNAJC19 | DNAJC19 | DNAJC19 | 3400 | 0.091 | 0.18 | YES |
11 | TOMM20 | TOMM20 | TOMM20 | 3624 | 0.084 | 0.2 | YES |
12 | HSCB | HSCB | HSCB | 3694 | 0.082 | 0.22 | YES |
13 | TIMM8A | TIMM8A | TIMM8A | 3712 | 0.082 | 0.25 | YES |
14 | VDAC1 | VDAC1 | VDAC1 | 3777 | 0.081 | 0.27 | YES |
15 | GRPEL1 | GRPEL1 | GRPEL1 | 4058 | 0.074 | 0.28 | YES |
16 | SAMM50 | SAMM50 | SAMM50 | 4138 | 0.073 | 0.3 | YES |
17 | TOMM70A | TOMM70A | TOMM70A | 4190 | 0.072 | 0.32 | YES |
18 | TOMM5 | TOMM5 | TOMM5 | 4212 | 0.071 | 0.34 | YES |
19 | TIMM9 | TIMM9 | TIMM9 | 4214 | 0.071 | 0.37 | YES |
20 | TIMM17B | TIMM17B | TIMM17B | 4675 | 0.062 | 0.36 | YES |
21 | TIMM50 | TIMM50 | TIMM50 | 4709 | 0.062 | 0.38 | YES |
22 | ATP5G1 | ATP5G1 | ATP5G1 | 4780 | 0.06 | 0.4 | YES |
23 | HSPD1 | HSPD1 | HSPD1 | 4906 | 0.058 | 0.41 | YES |
24 | TOMM40 | TOMM40 | TOMM40 | 4932 | 0.058 | 0.43 | YES |
25 | PMPCA | PMPCA | PMPCA | 5280 | 0.052 | 0.43 | YES |
26 | CYC1 | CYC1 | CYC1 | 5285 | 0.052 | 0.44 | YES |
27 | C18orf55 | C18orf55 | C18orf55 | 5287 | 0.052 | 0.46 | YES |
28 | ATP5B | ATP5B | ATP5B | 5563 | 0.048 | 0.46 | YES |
29 | CS | CS | CS | 5663 | 0.046 | 0.47 | YES |
30 | TOMM22 | TOMM22 | TOMM22 | 5764 | 0.044 | 0.48 | YES |
31 | TIMM13 | TIMM13 | TIMM13 | 5995 | 0.041 | 0.48 | YES |
32 | SLC25A12 | SLC25A12 | SLC25A12 | 6053 | 0.04 | 0.49 | YES |
33 | ACO2 | ACO2 | ACO2 | 6071 | 0.039 | 0.5 | YES |
34 | FXC1 | FXC1 | FXC1 | 6099 | 0.039 | 0.51 | YES |
35 | FXN | FXN | FXN | 6202 | 0.038 | 0.52 | YES |
36 | ATP5A1 | ATP5A1 | ATP5A1 | 6903 | 0.028 | 0.49 | NO |
37 | TIMM17A | TIMM17A | TIMM17A | 7044 | 0.026 | 0.49 | NO |
38 | SLC25A6 | SLC25A6 | SLC25A6 | 7985 | 0.013 | 0.44 | NO |
39 | TIMM44 | TIMM44 | TIMM44 | 8384 | 0.0077 | 0.42 | NO |
40 | GFER | GFER | GFER | 8497 | 0.0064 | 0.42 | NO |
41 | MTX2 | MTX2 | MTX2 | 9427 | -0.0069 | 0.37 | NO |
42 | SLC25A13 | SLC25A13 | SLC25A13 | 9521 | -0.0083 | 0.37 | NO |
43 | TIMM8B | TIMM8B | TIMM8B | 10050 | -0.016 | 0.34 | NO |
44 | TAZ | TAZ | TAZ | 10292 | -0.02 | 0.34 | NO |
45 | IDH3G | IDH3G | IDH3G | 10820 | -0.028 | 0.32 | NO |
46 | MTX1 | MTX1 | MTX1 | 11861 | -0.047 | 0.27 | NO |
47 | LDHD | LDHD | LDHD | 12482 | -0.061 | 0.26 | NO |
48 | TIMM22 | TIMM22 | TIMM22 | 12508 | -0.062 | 0.28 | NO |
49 | BCS1L | BCS1L | BCS1L | 12717 | -0.067 | 0.29 | NO |
Figure S93. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANSLATION.

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

Table S48. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FAM153A | FAM153A | FAM153A | 296 | 0.38 | 0.03 | YES |
2 | RPSAP9 | RPSAP9 | RPSAP9 | 1115 | 0.23 | 0.012 | YES |
3 | RPL9 | RPL9 | RPL9 | 1677 | 0.17 | 0.0014 | YES |
4 | RPS26 | RPS26 | RPS26 | 1725 | 0.17 | 0.019 | YES |
5 | RPL7 | RPL7 | RPL7 | 1751 | 0.16 | 0.038 | YES |
6 | RPL36A | RPL36A | RPL36A | 1800 | 0.16 | 0.055 | YES |
7 | RPSA | RPSA | RPSA | 1975 | 0.15 | 0.064 | YES |
8 | RPS17 | RPS17 | RPS17 | 2327 | 0.13 | 0.06 | YES |
9 | RPL24 | RPL24 | RPL24 | 2336 | 0.13 | 0.075 | YES |
10 | RPS27 | RPS27 | RPS27 | 2342 | 0.13 | 0.091 | YES |
11 | RPL15 | RPL15 | RPL15 | 2568 | 0.12 | 0.093 | YES |
12 | RPS5 | RPS5 | RPS5 | 2600 | 0.12 | 0.1 | YES |
13 | RPS14 | RPS14 | RPS14 | 2637 | 0.12 | 0.12 | YES |
14 | RPL32 | RPL32 | RPL32 | 2666 | 0.12 | 0.13 | YES |
15 | RPL7A | RPL7A | RPL7A | 2770 | 0.11 | 0.14 | YES |
16 | RPS23 | RPS23 | RPS23 | 2791 | 0.11 | 0.15 | YES |
17 | RPL41 | RPL41 | RPL41 | 2880 | 0.11 | 0.16 | YES |
18 | RPS6 | RPS6 | RPS6 | 2885 | 0.11 | 0.17 | YES |
19 | RPS3A | RPS3A | RPS3A | 2945 | 0.1 | 0.18 | YES |
20 | RPL18A | RPL18A | RPL18A | 2949 | 0.1 | 0.19 | YES |
21 | RPL17 | RPL17 | RPL17 | 3057 | 0.1 | 0.2 | YES |
22 | RPL35A | RPL35A | RPL35A | 3066 | 0.1 | 0.21 | YES |
23 | RPL35 | RPL35 | RPL35 | 3075 | 0.1 | 0.22 | YES |
24 | RPL14 | RPL14 | RPL14 | 3078 | 0.1 | 0.24 | YES |
25 | RPS15 | RPS15 | RPS15 | 3084 | 0.1 | 0.25 | YES |
26 | RPL6 | RPL6 | RPL6 | 3095 | 0.1 | 0.26 | YES |
27 | RPL29 | RPL29 | RPL29 | 3150 | 0.098 | 0.27 | YES |
28 | EIF4A2 | EIF4A2 | EIF4A2 | 3178 | 0.097 | 0.28 | YES |
29 | RPL37 | RPL37 | RPL37 | 3390 | 0.091 | 0.28 | YES |
30 | RPLP0 | RPLP0 | RPLP0 | 3439 | 0.09 | 0.29 | YES |
31 | RPS16 | RPS16 | RPS16 | 3497 | 0.088 | 0.29 | YES |
32 | EIF3K | EIF3K | EIF3K | 3504 | 0.088 | 0.3 | YES |
33 | RPL38 | RPL38 | RPL38 | 3522 | 0.087 | 0.31 | YES |
34 | EIF3E | EIF3E | EIF3E | 3570 | 0.086 | 0.32 | YES |
35 | RPS29 | RPS29 | RPS29 | 3572 | 0.085 | 0.33 | YES |
36 | UBA52 | UBA52 | UBA52 | 3677 | 0.083 | 0.34 | YES |
37 | RPL8 | RPL8 | RPL8 | 3707 | 0.082 | 0.35 | YES |
38 | RPL18 | RPL18 | RPL18 | 3747 | 0.081 | 0.35 | YES |
39 | EIF3G | EIF3G | EIF3G | 3806 | 0.08 | 0.36 | YES |
40 | RPL3 | RPL3 | RPL3 | 3819 | 0.08 | 0.37 | YES |
41 | RPS8 | RPS8 | RPS8 | 3844 | 0.079 | 0.38 | YES |
42 | RPS10 | RPS10 | RPS10 | 3960 | 0.076 | 0.38 | YES |
43 | RPS9 | RPS9 | RPS9 | 3971 | 0.076 | 0.39 | YES |
44 | EIF4B | EIF4B | EIF4B | 3995 | 0.076 | 0.4 | YES |
45 | RPL28 | RPL28 | RPL28 | 4029 | 0.075 | 0.4 | YES |
46 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 4122 | 0.073 | 0.41 | YES |
47 | RPL4 | RPL4 | RPL4 | 4127 | 0.073 | 0.42 | YES |
48 | RPL39 | RPL39 | RPL39 | 4144 | 0.072 | 0.42 | YES |
49 | RPL10 | RPL10 | RPL10 | 4189 | 0.072 | 0.43 | YES |
50 | RPL5 | RPL5 | RPL5 | 4233 | 0.071 | 0.44 | YES |
51 | RPS3 | RPS3 | RPS3 | 4244 | 0.07 | 0.44 | YES |
52 | EIF3H | EIF3H | EIF3H | 4308 | 0.069 | 0.45 | YES |
53 | EIF3D | EIF3D | EIF3D | 4334 | 0.068 | 0.46 | YES |
54 | PABPC1 | PABPC1 | PABPC1 | 4344 | 0.068 | 0.46 | YES |
55 | RPS11 | RPS11 | RPS11 | 4361 | 0.068 | 0.47 | YES |
56 | RPS25 | RPS25 | RPS25 | 4404 | 0.067 | 0.48 | YES |
57 | RPL36 | RPL36 | RPL36 | 4410 | 0.067 | 0.49 | YES |
58 | RPL34 | RPL34 | RPL34 | 4431 | 0.067 | 0.49 | YES |
59 | RPL30 | RPL30 | RPL30 | 4433 | 0.067 | 0.5 | YES |
60 | RPS18 | RPS18 | RPS18 | 4439 | 0.067 | 0.51 | YES |
61 | RPL13A | RPL13A | RPL13A | 4450 | 0.066 | 0.52 | YES |
62 | RPS4X | RPS4X | RPS4X | 4468 | 0.066 | 0.52 | YES |
63 | RPL22 | RPL22 | RPL22 | 4521 | 0.065 | 0.53 | YES |
64 | RPL10A | RPL10A | RPL10A | 4581 | 0.064 | 0.53 | YES |
65 | RPS2 | RPS2 | RPS2 | 4614 | 0.063 | 0.54 | YES |
66 | RPL26 | RPL26 | RPL26 | 4625 | 0.063 | 0.55 | YES |
67 | RPL11 | RPL11 | RPL11 | 4651 | 0.063 | 0.55 | YES |
68 | EIF1AX | EIF1AX | EIF1AX | 4914 | 0.058 | 0.55 | YES |
69 | RPL26L1 | RPL26L1 | RPL26L1 | 5000 | 0.057 | 0.55 | YES |
70 | RPL12 | RPL12 | RPL12 | 5003 | 0.057 | 0.56 | YES |
71 | RPS15A | RPS15A | RPS15A | 5021 | 0.056 | 0.56 | YES |
72 | RPS21 | RPS21 | RPS21 | 5098 | 0.055 | 0.56 | YES |
73 | EIF2S1 | EIF2S1 | EIF2S1 | 5108 | 0.055 | 0.57 | YES |
74 | RPLP1 | RPLP1 | RPLP1 | 5146 | 0.054 | 0.57 | YES |
75 | RPL27 | RPL27 | RPL27 | 5166 | 0.054 | 0.58 | YES |
76 | EIF4H | EIF4H | EIF4H | 5209 | 0.053 | 0.58 | YES |
77 | EIF3B | EIF3B | EIF3B | 5228 | 0.053 | 0.59 | YES |
78 | EIF2S3 | EIF2S3 | EIF2S3 | 5356 | 0.051 | 0.59 | YES |
79 | RPS13 | RPS13 | RPS13 | 5587 | 0.047 | 0.58 | YES |
80 | RPS19 | RPS19 | RPS19 | 5593 | 0.047 | 0.59 | YES |
81 | RPS20 | RPS20 | RPS20 | 5601 | 0.047 | 0.59 | YES |
82 | RPL23 | RPL23 | RPL23 | 5675 | 0.046 | 0.59 | YES |
83 | RPL37A | RPL37A | RPL37A | 5882 | 0.042 | 0.59 | NO |
84 | RPS24 | RPS24 | RPS24 | 5985 | 0.041 | 0.59 | NO |
85 | RPL31 | RPL31 | RPL31 | 6158 | 0.038 | 0.58 | NO |
86 | FAU | FAU | FAU | 6177 | 0.038 | 0.58 | NO |
87 | RPS12 | RPS12 | RPS12 | 6360 | 0.036 | 0.58 | NO |
88 | RPS7 | RPS7 | RPS7 | 6372 | 0.035 | 0.58 | NO |
89 | RPL27A | RPL27A | RPL27A | 6741 | 0.03 | 0.57 | NO |
90 | RPL13 | RPL13 | RPL13 | 6809 | 0.029 | 0.57 | NO |
91 | RPS27A | RPS27A | RPS27A | 6817 | 0.029 | 0.57 | NO |
92 | RPLP2 | RPLP2 | RPLP2 | 7042 | 0.026 | 0.56 | NO |
93 | EIF3J | EIF3J | EIF3J | 7255 | 0.023 | 0.55 | NO |
94 | EIF3I | EIF3I | EIF3I | 7331 | 0.022 | 0.55 | NO |
95 | RPL23A | RPL23A | RPL23A | 7349 | 0.022 | 0.55 | NO |
96 | EIF3F | EIF3F | EIF3F | 7628 | 0.018 | 0.54 | NO |
97 | RPL19 | RPL19 | RPL19 | 7648 | 0.018 | 0.54 | NO |
98 | EIF4E | EIF4E | EIF4E | 8157 | 0.011 | 0.51 | NO |
99 | EIF2S2 | EIF2S2 | EIF2S2 | 8475 | 0.0067 | 0.49 | NO |
100 | EIF4G1 | EIF4G1 | EIF4G1 | 8749 | 0.003 | 0.48 | NO |
101 | EIF3A | EIF3A | EIF3A | 10022 | -0.016 | 0.41 | NO |
102 | RPL21 | RPL21 | RPL21 | 11119 | -0.033 | 0.35 | NO |
103 | EIF3C | EIF3C | EIF3C | 11377 | -0.038 | 0.34 | NO |
104 | EIF4A1 | EIF4A1 | EIF4A1 | 11387 | -0.038 | 0.35 | NO |
105 | RPS28 | RPS28 | RPS28 | 14788 | -0.14 | 0.17 | NO |
Figure S95. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S49. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | RPSAP9 | RPSAP9 | RPSAP9 | 1115 | 0.23 | -0.0078 | YES |
2 | RPS26 | RPS26 | RPS26 | 1725 | 0.17 | -0.0019 | YES |
3 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 1930 | 0.15 | 0.023 | YES |
4 | RPSA | RPSA | RPSA | 1975 | 0.15 | 0.057 | YES |
5 | RPS17 | RPS17 | RPS17 | 2327 | 0.13 | 0.068 | YES |
6 | RPS27 | RPS27 | RPS27 | 2342 | 0.13 | 0.099 | YES |
7 | RPS5 | RPS5 | RPS5 | 2600 | 0.12 | 0.11 | YES |
8 | RPS14 | RPS14 | RPS14 | 2637 | 0.12 | 0.14 | YES |
9 | RPS23 | RPS23 | RPS23 | 2791 | 0.11 | 0.16 | YES |
10 | RPS6 | RPS6 | RPS6 | 2885 | 0.11 | 0.18 | YES |
11 | RPS3A | RPS3A | RPS3A | 2945 | 0.1 | 0.2 | YES |
12 | RPS15 | RPS15 | RPS15 | 3084 | 0.1 | 0.22 | YES |
13 | EIF4A2 | EIF4A2 | EIF4A2 | 3178 | 0.097 | 0.23 | YES |
14 | RPS16 | RPS16 | RPS16 | 3497 | 0.088 | 0.24 | YES |
15 | EIF3K | EIF3K | EIF3K | 3504 | 0.088 | 0.26 | YES |
16 | EIF3E | EIF3E | EIF3E | 3570 | 0.086 | 0.28 | YES |
17 | RPS29 | RPS29 | RPS29 | 3572 | 0.085 | 0.3 | YES |
18 | EIF3G | EIF3G | EIF3G | 3806 | 0.08 | 0.3 | YES |
19 | RPS8 | RPS8 | RPS8 | 3844 | 0.079 | 0.32 | YES |
20 | RPS10 | RPS10 | RPS10 | 3960 | 0.076 | 0.33 | YES |
21 | RPS9 | RPS9 | RPS9 | 3971 | 0.076 | 0.35 | YES |
22 | EIF4B | EIF4B | EIF4B | 3995 | 0.076 | 0.37 | YES |
23 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 4122 | 0.073 | 0.38 | YES |
24 | RPS3 | RPS3 | RPS3 | 4244 | 0.07 | 0.39 | YES |
25 | EIF3H | EIF3H | EIF3H | 4308 | 0.069 | 0.4 | YES |
26 | EIF3D | EIF3D | EIF3D | 4334 | 0.068 | 0.42 | YES |
27 | PABPC1 | PABPC1 | PABPC1 | 4344 | 0.068 | 0.43 | YES |
28 | RPS11 | RPS11 | RPS11 | 4361 | 0.068 | 0.45 | YES |
29 | RPS25 | RPS25 | RPS25 | 4404 | 0.067 | 0.46 | YES |
30 | RPS18 | RPS18 | RPS18 | 4439 | 0.067 | 0.47 | YES |
31 | RPS4X | RPS4X | RPS4X | 4468 | 0.066 | 0.49 | YES |
32 | RPS2 | RPS2 | RPS2 | 4614 | 0.063 | 0.5 | YES |
33 | EIF1AX | EIF1AX | EIF1AX | 4914 | 0.058 | 0.49 | YES |
34 | RPS15A | RPS15A | RPS15A | 5021 | 0.056 | 0.5 | YES |
35 | RPS21 | RPS21 | RPS21 | 5098 | 0.055 | 0.51 | YES |
36 | EIF2S1 | EIF2S1 | EIF2S1 | 5108 | 0.055 | 0.52 | YES |
37 | EIF4H | EIF4H | EIF4H | 5209 | 0.053 | 0.53 | YES |
38 | EIF3B | EIF3B | EIF3B | 5228 | 0.053 | 0.54 | YES |
39 | EIF2S3 | EIF2S3 | EIF2S3 | 5356 | 0.051 | 0.55 | YES |
40 | RPS13 | RPS13 | RPS13 | 5587 | 0.047 | 0.55 | YES |
41 | RPS19 | RPS19 | RPS19 | 5593 | 0.047 | 0.56 | YES |
42 | RPS20 | RPS20 | RPS20 | 5601 | 0.047 | 0.57 | YES |
43 | RPS24 | RPS24 | RPS24 | 5985 | 0.041 | 0.56 | NO |
44 | FAU | FAU | FAU | 6177 | 0.038 | 0.55 | NO |
45 | RPS12 | RPS12 | RPS12 | 6360 | 0.036 | 0.55 | NO |
46 | RPS7 | RPS7 | RPS7 | 6372 | 0.035 | 0.56 | NO |
47 | RPS27A | RPS27A | RPS27A | 6817 | 0.029 | 0.54 | NO |
48 | EIF3J | EIF3J | EIF3J | 7255 | 0.023 | 0.52 | NO |
49 | EIF3I | EIF3I | EIF3I | 7331 | 0.022 | 0.52 | NO |
50 | EIF3F | EIF3F | EIF3F | 7628 | 0.018 | 0.51 | NO |
51 | EIF4E | EIF4E | EIF4E | 8157 | 0.011 | 0.48 | NO |
52 | EIF2S2 | EIF2S2 | EIF2S2 | 8475 | 0.0067 | 0.47 | NO |
53 | EIF4G1 | EIF4G1 | EIF4G1 | 8749 | 0.003 | 0.45 | NO |
54 | EIF3A | EIF3A | EIF3A | 10022 | -0.016 | 0.39 | NO |
55 | EIF3C | EIF3C | EIF3C | 11377 | -0.038 | 0.32 | NO |
56 | EIF4A1 | EIF4A1 | EIF4A1 | 11387 | -0.038 | 0.33 | NO |
57 | RPS28 | RPS28 | RPS28 | 14788 | -0.14 | 0.17 | NO |
Figure S97. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME MITOCHONDRIAL PROTEIN IMPORT.

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

Table S50. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FAM153A | FAM153A | FAM153A | 296 | 0.38 | 0.03 | YES |
2 | RPSAP9 | RPSAP9 | RPSAP9 | 1115 | 0.23 | 0.012 | YES |
3 | RPL9 | RPL9 | RPL9 | 1677 | 0.17 | 0.00087 | YES |
4 | RPS26 | RPS26 | RPS26 | 1725 | 0.17 | 0.019 | YES |
5 | RPL7 | RPL7 | RPL7 | 1751 | 0.16 | 0.037 | YES |
6 | RPL36A | RPL36A | RPL36A | 1800 | 0.16 | 0.054 | YES |
7 | RPSA | RPSA | RPSA | 1975 | 0.15 | 0.063 | YES |
8 | RPS17 | RPS17 | RPS17 | 2327 | 0.13 | 0.059 | YES |
9 | RPL24 | RPL24 | RPL24 | 2336 | 0.13 | 0.074 | YES |
10 | RPS27 | RPS27 | RPS27 | 2342 | 0.13 | 0.089 | YES |
11 | RPL15 | RPL15 | RPL15 | 2568 | 0.12 | 0.091 | YES |
12 | RPS5 | RPS5 | RPS5 | 2600 | 0.12 | 0.1 | YES |
13 | RPS14 | RPS14 | RPS14 | 2637 | 0.12 | 0.12 | YES |
14 | RPL32 | RPL32 | RPL32 | 2666 | 0.12 | 0.13 | YES |
15 | RPL7A | RPL7A | RPL7A | 2770 | 0.11 | 0.14 | YES |
16 | RPS23 | RPS23 | RPS23 | 2791 | 0.11 | 0.15 | YES |
17 | RPL41 | RPL41 | RPL41 | 2880 | 0.11 | 0.16 | YES |
18 | RPS6 | RPS6 | RPS6 | 2885 | 0.11 | 0.17 | YES |
19 | RPS3A | RPS3A | RPS3A | 2945 | 0.1 | 0.18 | YES |
20 | RPL18A | RPL18A | RPL18A | 2949 | 0.1 | 0.19 | YES |
21 | RPL17 | RPL17 | RPL17 | 3057 | 0.1 | 0.2 | YES |
22 | RPL35A | RPL35A | RPL35A | 3066 | 0.1 | 0.21 | YES |
23 | RPL35 | RPL35 | RPL35 | 3075 | 0.1 | 0.22 | YES |
24 | RPL14 | RPL14 | RPL14 | 3078 | 0.1 | 0.23 | YES |
25 | RPS15 | RPS15 | RPS15 | 3084 | 0.1 | 0.25 | YES |
26 | RPL6 | RPL6 | RPL6 | 3095 | 0.1 | 0.26 | YES |
27 | RPL29 | RPL29 | RPL29 | 3150 | 0.098 | 0.27 | YES |
28 | SEC61G | SEC61G | SEC61G | 3309 | 0.093 | 0.27 | YES |
29 | RPL37 | RPL37 | RPL37 | 3390 | 0.091 | 0.28 | YES |
30 | RPLP0 | RPLP0 | RPLP0 | 3439 | 0.09 | 0.28 | YES |
31 | SPCS1 | SPCS1 | SPCS1 | 3495 | 0.088 | 0.29 | YES |
32 | RPS16 | RPS16 | RPS16 | 3497 | 0.088 | 0.3 | YES |
33 | RPL38 | RPL38 | RPL38 | 3522 | 0.087 | 0.31 | YES |
34 | RPS29 | RPS29 | RPS29 | 3572 | 0.085 | 0.32 | YES |
35 | UBA52 | UBA52 | UBA52 | 3677 | 0.083 | 0.32 | YES |
36 | RPL8 | RPL8 | RPL8 | 3707 | 0.082 | 0.33 | YES |
37 | RPL18 | RPL18 | RPL18 | 3747 | 0.081 | 0.34 | YES |
38 | RPL3 | RPL3 | RPL3 | 3819 | 0.08 | 0.34 | YES |
39 | RPS8 | RPS8 | RPS8 | 3844 | 0.079 | 0.35 | YES |
40 | SRPRB | SRPRB | SRPRB | 3872 | 0.078 | 0.36 | YES |
41 | RPS10 | RPS10 | RPS10 | 3960 | 0.076 | 0.37 | YES |
42 | RPS9 | RPS9 | RPS9 | 3971 | 0.076 | 0.38 | YES |
43 | RPL28 | RPL28 | RPL28 | 4029 | 0.075 | 0.38 | YES |
44 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 4122 | 0.073 | 0.38 | YES |
45 | RPL4 | RPL4 | RPL4 | 4127 | 0.073 | 0.39 | YES |
46 | RPL39 | RPL39 | RPL39 | 4144 | 0.072 | 0.4 | YES |
47 | RPL10 | RPL10 | RPL10 | 4189 | 0.072 | 0.41 | YES |
48 | RPL5 | RPL5 | RPL5 | 4233 | 0.071 | 0.41 | YES |
49 | RPS3 | RPS3 | RPS3 | 4244 | 0.07 | 0.42 | YES |
50 | RPS11 | RPS11 | RPS11 | 4361 | 0.068 | 0.42 | YES |
51 | RPS25 | RPS25 | RPS25 | 4404 | 0.067 | 0.43 | YES |
52 | RPL36 | RPL36 | RPL36 | 4410 | 0.067 | 0.44 | YES |
53 | SEC61B | SEC61B | SEC61B | 4430 | 0.067 | 0.44 | YES |
54 | RPL34 | RPL34 | RPL34 | 4431 | 0.067 | 0.45 | YES |
55 | RPL30 | RPL30 | RPL30 | 4433 | 0.067 | 0.46 | YES |
56 | RPS18 | RPS18 | RPS18 | 4439 | 0.067 | 0.47 | YES |
57 | RPL13A | RPL13A | RPL13A | 4450 | 0.066 | 0.48 | YES |
58 | RPS4X | RPS4X | RPS4X | 4468 | 0.066 | 0.48 | YES |
59 | RPL22 | RPL22 | RPL22 | 4521 | 0.065 | 0.49 | YES |
60 | RPL10A | RPL10A | RPL10A | 4581 | 0.064 | 0.49 | YES |
61 | RPS2 | RPS2 | RPS2 | 4614 | 0.063 | 0.5 | YES |
62 | RPL26 | RPL26 | RPL26 | 4625 | 0.063 | 0.5 | YES |
63 | RPL11 | RPL11 | RPL11 | 4651 | 0.063 | 0.51 | YES |
64 | RPN1 | RPN1 | RPN1 | 4783 | 0.06 | 0.51 | YES |
65 | SPCS3 | SPCS3 | SPCS3 | 4910 | 0.058 | 0.51 | YES |
66 | RPL26L1 | RPL26L1 | RPL26L1 | 5000 | 0.057 | 0.51 | YES |
67 | RPL12 | RPL12 | RPL12 | 5003 | 0.057 | 0.52 | YES |
68 | RPS15A | RPS15A | RPS15A | 5021 | 0.056 | 0.53 | YES |
69 | SEC11A | SEC11A | SEC11A | 5041 | 0.056 | 0.53 | YES |
70 | RPS21 | RPS21 | RPS21 | 5098 | 0.055 | 0.54 | YES |
71 | RPLP1 | RPLP1 | RPLP1 | 5146 | 0.054 | 0.54 | YES |
72 | RPL27 | RPL27 | RPL27 | 5166 | 0.054 | 0.55 | YES |
73 | SRP54 | SRP54 | SRP54 | 5421 | 0.05 | 0.54 | YES |
74 | SEC11C | SEC11C | SEC11C | 5527 | 0.048 | 0.54 | YES |
75 | RPS13 | RPS13 | RPS13 | 5587 | 0.047 | 0.54 | YES |
76 | RPS19 | RPS19 | RPS19 | 5593 | 0.047 | 0.55 | YES |
77 | RPS20 | RPS20 | RPS20 | 5601 | 0.047 | 0.55 | YES |
78 | RPL23 | RPL23 | RPL23 | 5675 | 0.046 | 0.55 | YES |
79 | SRP14 | SRP14 | SRP14 | 5872 | 0.043 | 0.55 | YES |
80 | RPL37A | RPL37A | RPL37A | 5882 | 0.042 | 0.55 | YES |
81 | TRAM1 | TRAM1 | TRAM1 | 5945 | 0.042 | 0.55 | YES |
82 | RPS24 | RPS24 | RPS24 | 5985 | 0.041 | 0.56 | YES |
83 | SSR4 | SSR4 | SSR4 | 6116 | 0.039 | 0.55 | YES |
84 | RPL31 | RPL31 | RPL31 | 6158 | 0.038 | 0.56 | YES |
85 | FAU | FAU | FAU | 6177 | 0.038 | 0.56 | YES |
86 | RPS12 | RPS12 | RPS12 | 6360 | 0.036 | 0.55 | NO |
87 | RPS7 | RPS7 | RPS7 | 6372 | 0.035 | 0.56 | NO |
88 | SEC61A1 | SEC61A1 | SEC61A1 | 6437 | 0.034 | 0.56 | NO |
89 | RPN2 | RPN2 | RPN2 | 6512 | 0.033 | 0.56 | NO |
90 | SRP68 | SRP68 | SRP68 | 6709 | 0.03 | 0.55 | NO |
91 | RPL27A | RPL27A | RPL27A | 6741 | 0.03 | 0.55 | NO |
92 | RPL13 | RPL13 | RPL13 | 6809 | 0.029 | 0.55 | NO |
93 | RPS27A | RPS27A | RPS27A | 6817 | 0.029 | 0.55 | NO |
94 | SRP19 | SRP19 | SRP19 | 6857 | 0.029 | 0.56 | NO |
95 | RPLP2 | RPLP2 | RPLP2 | 7042 | 0.026 | 0.55 | NO |
96 | DDOST | DDOST | DDOST | 7090 | 0.025 | 0.55 | NO |
97 | RPL23A | RPL23A | RPL23A | 7349 | 0.022 | 0.54 | NO |
98 | SRP9 | SRP9 | SRP9 | 7359 | 0.022 | 0.54 | NO |
99 | RPL19 | RPL19 | RPL19 | 7648 | 0.018 | 0.52 | NO |
100 | SRP72 | SRP72 | SRP72 | 7680 | 0.018 | 0.52 | NO |
101 | LOC653566 | LOC653566 | LOC653566 | 7778 | 0.016 | 0.52 | NO |
102 | SPCS2 | SPCS2 | SPCS2 | 7899 | 0.014 | 0.52 | NO |
103 | SSR2 | SSR2 | SSR2 | 8393 | 0.0077 | 0.49 | NO |
104 | SSR3 | SSR3 | SSR3 | 8693 | 0.0037 | 0.47 | NO |
105 | SRPR | SRPR | SRPR | 10807 | -0.028 | 0.36 | NO |
106 | RPL21 | RPL21 | RPL21 | 11119 | -0.033 | 0.34 | NO |
107 | SSR1 | SSR1 | SSR1 | 11189 | -0.035 | 0.34 | NO |
108 | SEC61A2 | SEC61A2 | SEC61A2 | 13952 | -0.1 | 0.2 | NO |
109 | RPS28 | RPS28 | RPS28 | 14788 | -0.14 | 0.17 | NO |
Figure S99. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S100. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 8. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus6. 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 ARGININE AND PROLINE METABOLISM | 54 | genes.ES.table | 0.44 | 1.5 | 0.029 | 1 | 0.98 | 0.39 | 0.22 | 0.31 | 0.93 | 0.46 |
KEGG HISTIDINE METABOLISM | 29 | genes.ES.table | 0.64 | 1.6 | 0.016 | 1 | 0.91 | 0.41 | 0.076 | 0.38 | 1 | 0.68 |
KEGG SELENOAMINO ACID METABOLISM | 26 | genes.ES.table | 0.59 | 1.7 | 0.024 | 1 | 0.73 | 0.42 | 0.2 | 0.34 | 1 | 0.64 |
KEGG GLUTATHIONE METABOLISM | 47 | genes.ES.table | 0.52 | 1.5 | 0.062 | 1 | 0.96 | 0.32 | 0.13 | 0.28 | 0.91 | 0.46 |
KEGG GLYCEROLIPID METABOLISM | 44 | genes.ES.table | 0.51 | 1.5 | 0.03 | 1 | 0.95 | 0.36 | 0.15 | 0.31 | 1 | 0.66 |
KEGG PROPANOATE METABOLISM | 32 | genes.ES.table | 0.51 | 1.4 | 0.11 | 1 | 0.98 | 0.47 | 0.18 | 0.39 | 0.91 | 0.46 |
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.41 | 1.4 | 0.12 | 1 | 0.98 | 0.58 | 0.37 | 0.37 | 0.87 | 0.44 |
SIG CD40PATHWAYMAP | 33 | genes.ES.table | 0.49 | 1.6 | 0.018 | 1 | 0.89 | 0.18 | 0.062 | 0.17 | 1 | 0.72 |
PID TRAIL PATHWAY | 28 | genes.ES.table | 0.49 | 1.5 | 0.056 | 1 | 0.96 | 0.5 | 0.33 | 0.34 | 1 | 0.65 |
PID RET PATHWAY | 38 | genes.ES.table | 0.45 | 1.5 | 0.062 | 1 | 0.96 | 0.1 | 0.052 | 0.1 | 1 | 0.6 |
Table S51. 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 | MAT1A | MAT1A | MAT1A | 308 | 1.1 | 0.13 | YES |
2 | CBS | CBS | CBS | 646 | 0.8 | 0.22 | YES |
3 | CTH | CTH | CTH | 827 | 0.71 | 0.3 | YES |
4 | GGT1 | GGT1 | GGT1 | 930 | 0.67 | 0.38 | YES |
5 | GGT5 | GGT5 | GGT5 | 1241 | 0.56 | 0.44 | YES |
6 | SCLY | SCLY | SCLY | 1350 | 0.53 | 0.5 | YES |
7 | GGT6 | GGT6 | GGT6 | 1549 | 0.48 | 0.55 | YES |
8 | SEPHS2 | SEPHS2 | SEPHS2 | 1844 | 0.42 | 0.59 | YES |
9 | PAPSS2 | PAPSS2 | PAPSS2 | 2584 | 0.32 | 0.59 | YES |
10 | MARS2 | MARS2 | MARS2 | 3520 | 0.24 | 0.57 | YES |
11 | AHCYL1 | AHCYL1 | AHCYL1 | 3650 | 0.23 | 0.59 | YES |
12 | PAPSS1 | PAPSS1 | PAPSS1 | 5446 | 0.13 | 0.51 | NO |
13 | TRMT11 | TRMT11 | TRMT11 | 5496 | 0.13 | 0.52 | NO |
14 | MAT2A | MAT2A | MAT2A | 5546 | 0.12 | 0.54 | NO |
15 | SEPHS1 | SEPHS1 | SEPHS1 | 5552 | 0.12 | 0.55 | NO |
16 | METTL6 | METTL6 | METTL6 | 5678 | 0.12 | 0.56 | NO |
17 | LCMT2 | LCMT2 | LCMT2 | 7138 | 0.055 | 0.48 | NO |
18 | HEMK1 | HEMK1 | HEMK1 | 7603 | 0.038 | 0.46 | NO |
19 | GGT7 | GGT7 | GGT7 | 8517 | 0.0026 | 0.41 | NO |
20 | MARS | MARS | MARS | 10022 | -0.051 | 0.34 | NO |
21 | MAT2B | MAT2B | MAT2B | 10802 | -0.078 | 0.3 | NO |
22 | LCMT1 | LCMT1 | LCMT1 | 10844 | -0.08 | 0.31 | NO |
23 | METTL2B | METTL2B | METTL2B | 10980 | -0.085 | 0.31 | NO |
24 | WBSCR22 | WBSCR22 | WBSCR22 | 12568 | -0.15 | 0.24 | NO |
25 | AHCY | AHCY | AHCY | 13024 | -0.17 | 0.24 | NO |
26 | AHCYL2 | AHCYL2 | AHCYL2 | 13731 | -0.22 | 0.23 | NO |
Figure S101. 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 S102. 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

Table S52. 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 | SYT1 | SYT1 | SYT1 | 63 | 1.7 | 0.18 | YES |
2 | MAPK10 | MAPK10 | MAPK10 | 579 | 0.85 | 0.24 | YES |
3 | PIK3R1 | PIK3R1 | PIK3R1 | 894 | 0.68 | 0.3 | YES |
4 | PIK3CD | PIK3CD | PIK3CD | 971 | 0.66 | 0.37 | YES |
5 | TRAF5 | TRAF5 | TRAF5 | 1080 | 0.61 | 0.43 | YES |
6 | MAPK12 | MAPK12 | MAPK12 | 1112 | 0.6 | 0.49 | YES |
7 | NFKBIE | NFKBIE | NFKBIE | 2643 | 0.32 | 0.44 | NO |
8 | MAPK11 | MAPK11 | MAPK11 | 2888 | 0.29 | 0.46 | NO |
9 | NFKBIL1 | NFKBIL1 | NFKBIL1 | 3978 | 0.2 | 0.42 | NO |
10 | MAP2K4 | MAP2K4 | MAP2K4 | 4989 | 0.15 | 0.38 | NO |
11 | MAPK14 | MAPK14 | MAPK14 | 5153 | 0.14 | 0.39 | NO |
12 | MAPK8 | MAPK8 | MAPK8 | 5477 | 0.13 | 0.38 | NO |
13 | MAPK8IP2 | MAPK8IP2 | MAPK8IP2 | 5663 | 0.12 | 0.39 | NO |
14 | NFKB2 | NFKB2 | NFKB2 | 5772 | 0.11 | 0.39 | NO |
15 | NFKBIB | NFKBIB | NFKBIB | 6109 | 0.099 | 0.38 | NO |
16 | TRAF6 | TRAF6 | TRAF6 | 6246 | 0.093 | 0.39 | NO |
17 | MAPK9 | MAPK9 | MAPK9 | 8430 | 0.0059 | 0.26 | NO |
18 | NFKBIA | NFKBIA | NFKBIA | 8592 | -0.00021 | 0.26 | NO |
19 | MAPK1 | MAPK1 | MAPK1 | 9469 | -0.033 | 0.21 | NO |
20 | NFKB1 | NFKB1 | NFKB1 | 9756 | -0.042 | 0.2 | NO |
21 | TRAF2 | TRAF2 | TRAF2 | 10126 | -0.054 | 0.18 | NO |
22 | MAP2K7 | MAP2K7 | MAP2K7 | 10402 | -0.064 | 0.18 | NO |
23 | PIK3CA | PIK3CA | PIK3CA | 10811 | -0.079 | 0.16 | NO |
24 | MAPK8IP1 | MAPK8IP1 | MAPK8IP1 | 10820 | -0.079 | 0.17 | NO |
25 | MAPK3 | MAPK3 | MAPK3 | 11036 | -0.087 | 0.17 | NO |
26 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 11298 | -0.097 | 0.16 | NO |
27 | IKBKG | IKBKG | IKBKG | 11577 | -0.11 | 0.16 | NO |
28 | MAPK13 | MAPK13 | MAPK13 | 12496 | -0.15 | 0.12 | NO |
29 | MAPKAPK5 | MAPKAPK5 | MAPKAPK5 | 12923 | -0.17 | 0.12 | NO |
30 | GORASP1 | GORASP1 | GORASP1 | 13134 | -0.18 | 0.12 | NO |
31 | TRAF3 | TRAF3 | TRAF3 | 13871 | -0.23 | 0.11 | NO |
32 | DUSP1 | DUSP1 | DUSP1 | 14670 | -0.3 | 0.096 | NO |
33 | CD40 | CD40 | CD40 | 16823 | -0.74 | 0.056 | NO |
Figure S103. 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 S104. 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

Table S53. 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 | ABP1 | ABP1 | ABP1 | 82 | 1.6 | 0.11 | YES |
2 | UROC1 | UROC1 | UROC1 | 298 | 1.1 | 0.18 | YES |
3 | MAOB | MAOB | MAOB | 304 | 1.1 | 0.26 | YES |
4 | CNDP1 | CNDP1 | CNDP1 | 431 | 0.98 | 0.33 | YES |
5 | HDC | HDC | HDC | 564 | 0.86 | 0.38 | YES |
6 | HAL | HAL | HAL | 834 | 0.71 | 0.42 | YES |
7 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 1091 | 0.61 | 0.45 | YES |
8 | ALDH2 | ALDH2 | ALDH2 | 1097 | 0.61 | 0.49 | YES |
9 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 1196 | 0.57 | 0.53 | YES |
10 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 1221 | 0.57 | 0.57 | YES |
11 | ASPA | ASPA | ASPA | 1238 | 0.56 | 0.61 | YES |
12 | ACY3 | ACY3 | ACY3 | 1348 | 0.53 | 0.64 | YES |
13 | AMDHD1 | AMDHD1 | AMDHD1 | 2603 | 0.32 | 0.59 | NO |
14 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 2677 | 0.31 | 0.61 | NO |
15 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 4739 | 0.16 | 0.51 | NO |
16 | TRMT11 | TRMT11 | TRMT11 | 5496 | 0.13 | 0.48 | NO |
17 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 5662 | 0.12 | 0.48 | NO |
18 | METTL6 | METTL6 | METTL6 | 5678 | 0.12 | 0.48 | NO |
19 | HNMT | HNMT | HNMT | 6918 | 0.065 | 0.42 | NO |
20 | LCMT2 | LCMT2 | LCMT2 | 7138 | 0.055 | 0.41 | NO |
21 | HEMK1 | HEMK1 | HEMK1 | 7603 | 0.038 | 0.39 | NO |
22 | LCMT1 | LCMT1 | LCMT1 | 10844 | -0.08 | 0.21 | NO |
23 | METTL2B | METTL2B | METTL2B | 10980 | -0.085 | 0.21 | NO |
24 | WBSCR22 | WBSCR22 | WBSCR22 | 12568 | -0.15 | 0.13 | NO |
25 | MAOA | MAOA | MAOA | 13198 | -0.18 | 0.11 | NO |
26 | DDC | DDC | DDC | 14498 | -0.28 | 0.056 | NO |
27 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 16054 | -0.53 | 0.0073 | NO |
28 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 16306 | -0.59 | 0.036 | NO |
29 | FTCD | FTCD | FTCD | 16624 | -0.67 | 0.067 | NO |
Figure S105. 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 S106. 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

Table S54. 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 | SLC19A3 | SLC19A3 | SLC19A3 | 62 | 1.7 | 0.13 | YES |
2 | SHMT1 | SHMT1 | SHMT1 | 667 | 0.79 | 0.16 | YES |
3 | TPK1 | TPK1 | TPK1 | 748 | 0.75 | 0.21 | YES |
4 | QPRT | QPRT | QPRT | 1086 | 0.61 | 0.24 | YES |
5 | SLC25A16 | SLC25A16 | SLC25A16 | 1417 | 0.51 | 0.26 | YES |
6 | MOCS1 | MOCS1 | MOCS1 | 1528 | 0.49 | 0.29 | YES |
7 | SLC2A1 | SLC2A1 | SLC2A1 | 1532 | 0.48 | 0.33 | YES |
8 | GSTO2 | GSTO2 | GSTO2 | 1655 | 0.46 | 0.36 | YES |
9 | PANK1 | PANK1 | PANK1 | 2066 | 0.39 | 0.36 | YES |
10 | DHFR | DHFR | DHFR | 2341 | 0.35 | 0.38 | YES |
11 | MOCOS | MOCOS | MOCOS | 2374 | 0.35 | 0.4 | YES |
12 | GPHN | GPHN | GPHN | 3018 | 0.28 | 0.39 | NO |
13 | NMNAT1 | NMNAT1 | NMNAT1 | 3166 | 0.27 | 0.4 | NO |
14 | COASY | COASY | COASY | 4043 | 0.2 | 0.36 | NO |
15 | PPCS | PPCS | PPCS | 4786 | 0.16 | 0.34 | NO |
16 | PNPO | PNPO | PNPO | 4855 | 0.16 | 0.34 | NO |
17 | MTHFR | MTHFR | MTHFR | 5039 | 0.15 | 0.34 | NO |
18 | SLC2A3 | SLC2A3 | SLC2A3 | 5540 | 0.12 | 0.33 | NO |
19 | MOCS2 | MOCS2 | MOCS2 | 5682 | 0.12 | 0.33 | NO |
20 | MTHFD1 | MTHFD1 | MTHFD1 | 5809 | 0.11 | 0.33 | NO |
21 | FLAD1 | FLAD1 | FLAD1 | 6237 | 0.093 | 0.31 | NO |
22 | THTPA | THTPA | THTPA | 6603 | 0.078 | 0.3 | NO |
23 | SLC5A6 | SLC5A6 | SLC5A6 | 6795 | 0.07 | 0.29 | NO |
24 | SLC19A1 | SLC19A1 | SLC19A1 | 6915 | 0.065 | 0.29 | NO |
25 | AASDHPPT | AASDHPPT | AASDHPPT | 7013 | 0.061 | 0.29 | NO |
26 | NADK | NADK | NADK | 7128 | 0.056 | 0.29 | NO |
27 | PANK3 | PANK3 | PANK3 | 7154 | 0.055 | 0.29 | NO |
28 | PDXK | PDXK | PDXK | 7166 | 0.054 | 0.3 | NO |
29 | CYB5A | CYB5A | CYB5A | 7560 | 0.039 | 0.28 | NO |
30 | PANK4 | PANK4 | PANK4 | 8219 | 0.014 | 0.24 | NO |
31 | SLC46A1 | SLC46A1 | SLC46A1 | 8248 | 0.012 | 0.24 | NO |
32 | NMNAT3 | NMNAT3 | NMNAT3 | 8263 | 0.012 | 0.24 | NO |
33 | PANK2 | PANK2 | PANK2 | 8576 | 0.00036 | 0.22 | NO |
34 | PPCDC | PPCDC | PPCDC | 8585 | 0.000016 | 0.22 | NO |
35 | GSTO1 | GSTO1 | GSTO1 | 9354 | -0.028 | 0.18 | NO |
36 | NFS1 | NFS1 | NFS1 | 9384 | -0.03 | 0.18 | NO |
37 | SLC19A2 | SLC19A2 | SLC19A2 | 10341 | -0.062 | 0.13 | NO |
38 | SLC23A2 | SLC23A2 | SLC23A2 | 10384 | -0.063 | 0.14 | NO |
39 | FPGS | FPGS | FPGS | 11817 | -0.12 | 0.063 | NO |
40 | CYB5R3 | CYB5R3 | CYB5R3 | 12838 | -0.16 | 0.018 | NO |
41 | MOCS3 | MOCS3 | MOCS3 | 13073 | -0.18 | 0.019 | NO |
42 | NAMPT | NAMPT | NAMPT | 13451 | -0.2 | 0.013 | NO |
43 | FASN | FASN | FASN | 13596 | -0.21 | 0.021 | NO |
44 | SLC25A32 | SLC25A32 | SLC25A32 | 13682 | -0.22 | 0.033 | NO |
45 | SLC23A1 | SLC23A1 | SLC23A1 | 14605 | -0.29 | 0.0038 | NO |
46 | NADSYN1 | NADSYN1 | NADSYN1 | 14941 | -0.33 | 0.011 | NO |
47 | RFK | RFK | RFK | 14964 | -0.34 | 0.035 | NO |
48 | ENPP1 | ENPP1 | ENPP1 | 15111 | -0.36 | 0.055 | NO |
49 | NMNAT2 | NMNAT2 | NMNAT2 | 15487 | -0.42 | 0.066 | NO |
50 | ACP5 | ACP5 | ACP5 | 17052 | -0.85 | 0.043 | NO |
Figure S107. 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 S108. 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

Table S55. 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 | LIPF | LIPF | LIPF | 80 | 1.6 | 0.09 | YES |
2 | DGAT2 | DGAT2 | DGAT2 | 176 | 1.3 | 0.16 | YES |
3 | CEL | CEL | CEL | 474 | 0.93 | 0.2 | YES |
4 | AGPAT4 | AGPAT4 | AGPAT4 | 480 | 0.93 | 0.25 | YES |
5 | LPL | LPL | LPL | 573 | 0.85 | 0.3 | YES |
6 | PPAP2C | PPAP2C | PPAP2C | 608 | 0.83 | 0.35 | YES |
7 | PNPLA3 | PNPLA3 | PNPLA3 | 677 | 0.79 | 0.39 | YES |
8 | ALDH2 | ALDH2 | ALDH2 | 1097 | 0.61 | 0.4 | YES |
9 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 1196 | 0.57 | 0.43 | YES |
10 | MBOAT2 | MBOAT2 | MBOAT2 | 1304 | 0.54 | 0.45 | YES |
11 | LIPC | LIPC | LIPC | 1380 | 0.52 | 0.48 | YES |
12 | GPAM | GPAM | GPAM | 1707 | 0.45 | 0.49 | YES |
13 | DGKA | DGKA | DGKA | 2437 | 0.34 | 0.47 | YES |
14 | LIPG | LIPG | LIPG | 2600 | 0.32 | 0.48 | YES |
15 | DGKG | DGKG | DGKG | 2622 | 0.32 | 0.49 | YES |
16 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 2677 | 0.31 | 0.51 | YES |
17 | DAK | DAK | DAK | 4152 | 0.2 | 0.44 | NO |
18 | PPAP2B | PPAP2B | PPAP2B | 4467 | 0.18 | 0.43 | NO |
19 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 4739 | 0.16 | 0.42 | NO |
20 | DGKE | DGKE | DGKE | 5255 | 0.14 | 0.4 | NO |
21 | DGKQ | DGKQ | DGKQ | 5300 | 0.14 | 0.41 | NO |
22 | AGPAT6 | AGPAT6 | AGPAT6 | 5337 | 0.13 | 0.41 | NO |
23 | GPAT2 | GPAT2 | GPAT2 | 5466 | 0.13 | 0.42 | NO |
24 | AGPAT1 | AGPAT1 | AGPAT1 | 5491 | 0.13 | 0.42 | NO |
25 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 5662 | 0.12 | 0.42 | NO |
26 | AGPAT3 | AGPAT3 | AGPAT3 | 7210 | 0.053 | 0.33 | NO |
27 | AKR1A1 | AKR1A1 | AKR1A1 | 7553 | 0.039 | 0.32 | NO |
28 | AGK | AGK | AGK | 7630 | 0.036 | 0.32 | NO |
29 | DGKD | DGKD | DGKD | 8884 | -0.011 | 0.24 | NO |
30 | GLYCTK | GLYCTK | GLYCTK | 8927 | -0.013 | 0.24 | NO |
31 | LCLAT1 | LCLAT1 | LCLAT1 | 8982 | -0.015 | 0.24 | NO |
32 | DGKH | DGKH | DGKH | 9448 | -0.032 | 0.22 | NO |
33 | MBOAT1 | MBOAT1 | MBOAT1 | 9561 | -0.036 | 0.21 | NO |
34 | PPAP2A | PPAP2A | PPAP2A | 9732 | -0.041 | 0.21 | NO |
35 | AKR1B1 | AKR1B1 | AKR1B1 | 10026 | -0.051 | 0.19 | NO |
36 | DGAT1 | DGAT1 | DGAT1 | 11012 | -0.086 | 0.14 | NO |
37 | GLA | GLA | GLA | 13029 | -0.17 | 0.039 | NO |
38 | GK | GK | GK | 13916 | -0.23 | 0.0026 | NO |
39 | AGPAT9 | AGPAT9 | AGPAT9 | 14143 | -0.25 | 0.0044 | NO |
40 | DGKZ | DGKZ | DGKZ | 14349 | -0.27 | 0.0085 | NO |
41 | AGPAT2 | AGPAT2 | AGPAT2 | 14381 | -0.27 | 0.023 | NO |
42 | MGLL | MGLL | MGLL | 15608 | -0.44 | -0.021 | NO |
43 | DGKB | DGKB | DGKB | 16848 | -0.75 | -0.046 | NO |
44 | DGKI | DGKI | DGKI | 17717 | -1.7 | 0.006 | NO |
Figure S109. 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 S110. 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

Table S56. 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 | PIK3R1 | PIK3R1 | PIK3R1 | 894 | 0.68 | 0.084 | YES |
2 | PIK3CD | PIK3CD | PIK3CD | 971 | 0.66 | 0.21 | YES |
3 | CASP10 | CASP10 | CASP10 | 1266 | 0.55 | 0.3 | YES |
4 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 1623 | 0.47 | 0.37 | YES |
5 | TNFRSF10C | TNFRSF10C | TNFRSF10C | 2190 | 0.37 | 0.41 | YES |
6 | PIK3R3 | PIK3R3 | PIK3R3 | 2851 | 0.3 | 0.43 | YES |
7 | TNFRSF10D | TNFRSF10D | TNFRSF10D | 4379 | 0.18 | 0.38 | YES |
8 | CHUK | CHUK | CHUK | 4431 | 0.18 | 0.41 | YES |
9 | DAP3 | DAP3 | DAP3 | 4587 | 0.17 | 0.44 | YES |
10 | PIK3R2 | PIK3R2 | PIK3R2 | 4752 | 0.16 | 0.46 | YES |
11 | MAP2K4 | MAP2K4 | MAP2K4 | 4989 | 0.15 | 0.48 | YES |
12 | MAPK8 | MAPK8 | MAPK8 | 5477 | 0.13 | 0.48 | YES |
13 | CASP8 | CASP8 | CASP8 | 5764 | 0.11 | 0.48 | YES |
14 | RIPK1 | RIPK1 | RIPK1 | 5905 | 0.11 | 0.5 | YES |
15 | PIK3CB | PIK3CB | PIK3CB | 7005 | 0.062 | 0.44 | NO |
16 | CFLAR | CFLAR | CFLAR | 7242 | 0.051 | 0.44 | NO |
17 | SMPD1 | SMPD1 | SMPD1 | 7629 | 0.036 | 0.43 | NO |
18 | MAP3K1 | MAP3K1 | MAP3K1 | 7684 | 0.034 | 0.43 | NO |
19 | FADD | FADD | FADD | 8330 | 0.0095 | 0.4 | NO |
20 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 9423 | -0.031 | 0.34 | NO |
21 | MAPK1 | MAPK1 | MAPK1 | 9469 | -0.033 | 0.34 | NO |
22 | TNFSF10 | TNFSF10 | TNFSF10 | 9560 | -0.036 | 0.35 | NO |
23 | TRAF2 | TRAF2 | TRAF2 | 10126 | -0.054 | 0.33 | NO |
24 | PIK3CA | PIK3CA | PIK3CA | 10811 | -0.079 | 0.3 | NO |
25 | MAPK3 | MAPK3 | MAPK3 | 11036 | -0.087 | 0.31 | NO |
26 | IKBKB | IKBKB | IKBKB | 11387 | -0.1 | 0.31 | NO |
27 | IKBKG | IKBKG | IKBKG | 11577 | -0.11 | 0.32 | NO |
28 | TRADD | TRADD | TRADD | 12907 | -0.17 | 0.28 | NO |
Figure S111. 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 S112. 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

Table S57. 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 | DOK5 | DOK5 | DOK5 | 107 | 1.5 | 0.21 | YES |
2 | GFRA1 | GFRA1 | GFRA1 | 859 | 0.7 | 0.26 | YES |
3 | PIK3R1 | PIK3R1 | PIK3R1 | 894 | 0.68 | 0.36 | YES |
4 | DOK6 | DOK6 | DOK6 | 933 | 0.67 | 0.45 | YES |
5 | GAB1 | GAB1 | GAB1 | 2306 | 0.36 | 0.42 | NO |
6 | CRK | CRK | CRK | 3923 | 0.21 | 0.36 | NO |
7 | MAPK8 | MAPK8 | MAPK8 | 5477 | 0.13 | 0.29 | NO |
8 | FRS2 | FRS2 | FRS2 | 5865 | 0.11 | 0.28 | NO |
9 | DOK1 | DOK1 | DOK1 | 5906 | 0.11 | 0.3 | NO |
10 | GRB2 | GRB2 | GRB2 | 5908 | 0.11 | 0.31 | NO |
11 | SRC | SRC | SRC | 6192 | 0.095 | 0.31 | NO |
12 | PRKCA | PRKCA | PRKCA | 6768 | 0.071 | 0.29 | NO |
13 | RAP1A | RAP1A | RAP1A | 7369 | 0.046 | 0.26 | NO |
14 | HRAS | HRAS | HRAS | 7821 | 0.03 | 0.24 | NO |
15 | SHC1 | SHC1 | SHC1 | 7925 | 0.026 | 0.24 | NO |
16 | SOS1 | SOS1 | SOS1 | 8191 | 0.015 | 0.22 | NO |
17 | NCK1 | NCK1 | NCK1 | 8297 | 0.011 | 0.22 | NO |
18 | RHOA | RHOA | RHOA | 8460 | 0.0049 | 0.21 | NO |
19 | PRKACA | PRKACA | PRKACA | 8493 | 0.0037 | 0.21 | NO |
20 | PTPN11 | PTPN11 | PTPN11 | 9049 | -0.017 | 0.18 | NO |
21 | MAPK1 | MAPK1 | MAPK1 | 9469 | -0.033 | 0.16 | NO |
22 | PDLIM7 | PDLIM7 | PDLIM7 | 9480 | -0.033 | 0.17 | NO |
23 | CREB1 | CREB1 | CREB1 | 9510 | -0.034 | 0.17 | NO |
24 | RASA1 | RASA1 | RASA1 | 9611 | -0.038 | 0.17 | NO |
25 | SHANK3 | SHANK3 | SHANK3 | 9852 | -0.045 | 0.16 | NO |
26 | RAC1 | RAC1 | RAC1 | 10523 | -0.068 | 0.13 | NO |
27 | DOK4 | DOK4 | DOK4 | 10780 | -0.078 | 0.13 | NO |
28 | PIK3CA | PIK3CA | PIK3CA | 10811 | -0.079 | 0.14 | NO |
29 | PTK2 | PTK2 | PTK2 | 10841 | -0.08 | 0.15 | NO |
30 | BCAR1 | BCAR1 | BCAR1 | 11023 | -0.087 | 0.15 | NO |
31 | MAPK3 | MAPK3 | MAPK3 | 11036 | -0.087 | 0.16 | NO |
32 | JUN | JUN | JUN | 11189 | -0.093 | 0.17 | NO |
33 | RET | RET | RET | 11398 | -0.1 | 0.17 | NO |
34 | GRB7 | GRB7 | GRB7 | 13003 | -0.17 | 0.1 | NO |
35 | PXN | PXN | PXN | 13264 | -0.19 | 0.12 | NO |
36 | GRB10 | GRB10 | GRB10 | 13322 | -0.19 | 0.14 | NO |
37 | IRS1 | IRS1 | IRS1 | 14800 | -0.31 | 0.1 | NO |
38 | IRS2 | IRS2 | IRS2 | 15877 | -0.49 | 0.11 | NO |
Figure S113. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS.

Figure S114. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S58. 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 | KCNJ16 | KCNJ16 | KCNJ16 | 10 | 2.4 | 0.14 | YES |
2 | KCNJ10 | KCNJ10 | KCNJ10 | 39 | 1.8 | 0.24 | YES |
3 | KCNJ3 | KCNJ3 | KCNJ3 | 202 | 1.3 | 0.31 | YES |
4 | GABRB3 | GABRB3 | GABRB3 | 248 | 1.2 | 0.37 | YES |
5 | GABRB1 | GABRB1 | GABRB1 | 544 | 0.87 | 0.4 | YES |
6 | KCNJ5 | KCNJ5 | KCNJ5 | 845 | 0.7 | 0.43 | YES |
7 | KCNJ9 | KCNJ9 | KCNJ9 | 957 | 0.66 | 0.46 | YES |
8 | KCNJ15 | KCNJ15 | KCNJ15 | 1370 | 0.52 | 0.47 | YES |
9 | GNAL | GNAL | GNAL | 1562 | 0.48 | 0.48 | YES |
10 | GABBR1 | GABBR1 | GABBR1 | 1855 | 0.42 | 0.49 | YES |
11 | GABRR2 | GABRR2 | GABRR2 | 1987 | 0.4 | 0.51 | YES |
12 | GNG7 | GNG7 | GNG7 | 2428 | 0.34 | 0.5 | YES |
13 | GNAI3 | GNAI3 | GNAI3 | 2450 | 0.34 | 0.52 | YES |
14 | KCNJ2 | KCNJ2 | KCNJ2 | 2563 | 0.33 | 0.53 | YES |
15 | ADCY5 | ADCY5 | ADCY5 | 2613 | 0.32 | 0.55 | YES |
16 | GABBR2 | GABBR2 | GABBR2 | 3689 | 0.23 | 0.5 | NO |
17 | ARHGEF9 | ARHGEF9 | ARHGEF9 | 4642 | 0.17 | 0.46 | NO |
18 | ADCY9 | ADCY9 | ADCY9 | 4848 | 0.16 | 0.45 | NO |
19 | GNG5 | GNG5 | GNG5 | 5484 | 0.13 | 0.42 | NO |
20 | GNB1 | GNB1 | GNB1 | 6171 | 0.096 | 0.39 | NO |
21 | GNAI2 | GNAI2 | GNAI2 | 7515 | 0.04 | 0.32 | NO |
22 | ADCY2 | ADCY2 | ADCY2 | 7541 | 0.04 | 0.32 | NO |
23 | KCNJ12 | KCNJ12 | KCNJ12 | 7775 | 0.031 | 0.31 | NO |
24 | GNAI1 | GNAI1 | GNAI1 | 8101 | 0.018 | 0.29 | NO |
25 | GNG2 | GNG2 | GNG2 | 8117 | 0.018 | 0.29 | NO |
26 | ADCY6 | ADCY6 | ADCY6 | 8185 | 0.015 | 0.29 | NO |
27 | GABRB2 | GABRB2 | GABRB2 | 8662 | -0.0029 | 0.26 | NO |
28 | GNGT2 | GNGT2 | GNGT2 | 10236 | -0.058 | 0.18 | NO |
29 | GNG12 | GNG12 | GNG12 | 10823 | -0.079 | 0.15 | NO |
30 | GNG10 | GNG10 | GNG10 | 10918 | -0.082 | 0.15 | NO |
31 | GNB3 | GNB3 | GNB3 | 11046 | -0.088 | 0.14 | NO |
32 | ADCY1 | ADCY1 | ADCY1 | 11911 | -0.12 | 0.1 | NO |
33 | ADCY4 | ADCY4 | ADCY4 | 12047 | -0.13 | 0.1 | NO |
34 | GNB2 | GNB2 | GNB2 | 12066 | -0.13 | 0.11 | NO |
35 | ADCY7 | ADCY7 | ADCY7 | 12204 | -0.14 | 0.11 | NO |
36 | ADCY3 | ADCY3 | ADCY3 | 13078 | -0.18 | 0.07 | NO |
37 | GABRR1 | GABRR1 | GABRR1 | 15083 | -0.35 | -0.023 | NO |
38 | GNG4 | GNG4 | GNG4 | 16110 | -0.54 | -0.05 | NO |
39 | KCNJ6 | KCNJ6 | KCNJ6 | 16149 | -0.56 | -0.02 | NO |
40 | ADCY8 | ADCY8 | ADCY8 | 16385 | -0.61 | 0.0015 | NO |
41 | GNG3 | GNG3 | GNG3 | 16572 | -0.65 | 0.028 | NO |
42 | GNGT1 | GNGT1 | GNGT1 | 16816 | -0.74 | 0.057 | NO |
Figure S115. 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: SIG CD40PATHWAYMAP.

Figure S116. Get High-res Image For the top 5 core enriched genes in the pathway: SIG CD40PATHWAYMAP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S59. 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 | PARS2 | PARS2 | PARS2 | 1529 | 0.49 | 0.0034 | YES |
2 | EEF1E1 | EEF1E1 | EEF1E1 | 2366 | 0.35 | 0.021 | YES |
3 | WARS2 | WARS2 | WARS2 | 2792 | 0.3 | 0.052 | YES |
4 | DARS2 | DARS2 | DARS2 | 3038 | 0.28 | 0.089 | YES |
5 | MARS2 | MARS2 | MARS2 | 3520 | 0.24 | 0.11 | YES |
6 | FARSB | FARSB | FARSB | 3904 | 0.21 | 0.12 | YES |
7 | NARS | NARS | NARS | 4364 | 0.18 | 0.13 | YES |
8 | WARS | WARS | WARS | 4470 | 0.18 | 0.16 | YES |
9 | RARS2 | RARS2 | RARS2 | 4503 | 0.18 | 0.19 | YES |
10 | YARS | YARS | YARS | 4524 | 0.17 | 0.22 | YES |
11 | GARS | GARS | GARS | 4593 | 0.17 | 0.25 | YES |
12 | SARS | SARS | SARS | 4753 | 0.16 | 0.27 | YES |
13 | EPRS | EPRS | EPRS | 4771 | 0.16 | 0.3 | YES |
14 | SARS2 | SARS2 | SARS2 | 5056 | 0.15 | 0.31 | YES |
15 | AARS2 | AARS2 | AARS2 | 5155 | 0.14 | 0.33 | YES |
16 | IARS2 | IARS2 | IARS2 | 5181 | 0.14 | 0.35 | YES |
17 | PPA1 | PPA1 | PPA1 | 5660 | 0.12 | 0.35 | YES |
18 | NARS2 | NARS2 | NARS2 | 5688 | 0.12 | 0.37 | YES |
19 | IARS | IARS | IARS | 5847 | 0.11 | 0.38 | YES |
20 | HARS2 | HARS2 | HARS2 | 5863 | 0.11 | 0.4 | YES |
21 | TARS2 | TARS2 | TARS2 | 5965 | 0.1 | 0.41 | YES |
22 | TARS | TARS | TARS | 6406 | 0.086 | 0.4 | YES |
23 | VARS2 | VARS2 | VARS2 | 6530 | 0.082 | 0.41 | YES |
24 | VARS | VARS | VARS | 6615 | 0.078 | 0.42 | YES |
25 | DARS | DARS | DARS | 6620 | 0.078 | 0.44 | YES |
26 | FARS2 | FARS2 | FARS2 | 7232 | 0.052 | 0.41 | NO |
27 | AIMP2 | AIMP2 | AIMP2 | 7529 | 0.04 | 0.4 | NO |
28 | LARS2 | LARS2 | LARS2 | 7590 | 0.038 | 0.4 | NO |
29 | AARS | AARS | AARS | 8406 | 0.0067 | 0.36 | NO |
30 | YARS2 | YARS2 | YARS2 | 8894 | -0.011 | 0.34 | NO |
31 | CARS2 | CARS2 | CARS2 | 9424 | -0.031 | 0.31 | NO |
32 | HARS | HARS | HARS | 9991 | -0.05 | 0.29 | NO |
33 | MARS | MARS | MARS | 10022 | -0.051 | 0.3 | NO |
34 | AIMP1 | AIMP1 | AIMP1 | 10164 | -0.055 | 0.3 | NO |
35 | PPA2 | PPA2 | PPA2 | 10194 | -0.056 | 0.31 | NO |
36 | CARS | CARS | CARS | 10207 | -0.057 | 0.32 | NO |
37 | QARS | QARS | QARS | 10454 | -0.066 | 0.32 | NO |
38 | LARS | LARS | LARS | 10583 | -0.071 | 0.32 | NO |
39 | KARS | KARS | KARS | 10744 | -0.076 | 0.33 | NO |
40 | RARS | RARS | RARS | 11659 | -0.11 | 0.3 | NO |
41 | FARSA | FARSA | FARSA | 11975 | -0.12 | 0.3 | NO |
42 | EARS2 | EARS2 | EARS2 | 12723 | -0.16 | 0.29 | NO |
Figure S117. 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 TRAIL PATHWAY.

Figure S118. Get High-res Image For the top 5 core enriched genes in the pathway: PID TRAIL PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S60. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MAPK10 | MAPK10 | MAPK10 | 579 | 0.85 | 0.069 | YES |
2 | PIK3R1 | PIK3R1 | PIK3R1 | 894 | 0.68 | 0.13 | YES |
3 | FAIM2 | FAIM2 | FAIM2 | 941 | 0.67 | 0.21 | YES |
4 | MAP2K6 | MAP2K6 | MAP2K6 | 952 | 0.67 | 0.29 | YES |
5 | PIK3CD | PIK3CD | PIK3CD | 971 | 0.66 | 0.37 | YES |
6 | FAS | FAS | FAS | 1034 | 0.63 | 0.44 | YES |
7 | CASP10 | CASP10 | CASP10 | 1266 | 0.55 | 0.49 | YES |
8 | PIK3R3 | PIK3R3 | PIK3R3 | 2851 | 0.3 | 0.44 | NO |
9 | MAPK11 | MAPK11 | MAPK11 | 2888 | 0.29 | 0.47 | NO |
10 | BTK | BTK | BTK | 3945 | 0.21 | 0.44 | NO |
11 | CLTC | CLTC | CLTC | 4262 | 0.19 | 0.44 | NO |
12 | EZR | EZR | EZR | 4354 | 0.18 | 0.46 | NO |
13 | CHUK | CHUK | CHUK | 4431 | 0.18 | 0.48 | NO |
14 | PIK3R2 | PIK3R2 | PIK3R2 | 4752 | 0.16 | 0.48 | NO |
15 | MAPK14 | MAPK14 | MAPK14 | 5153 | 0.14 | 0.47 | NO |
16 | MAPK8 | MAPK8 | MAPK8 | 5477 | 0.13 | 0.47 | NO |
17 | CASP8 | CASP8 | CASP8 | 5764 | 0.11 | 0.47 | NO |
18 | RIPK1 | RIPK1 | RIPK1 | 5905 | 0.11 | 0.47 | NO |
19 | SRC | SRC | SRC | 6192 | 0.095 | 0.47 | NO |
20 | BIRC2 | BIRC2 | BIRC2 | 6989 | 0.062 | 0.43 | NO |
21 | PIK3CB | PIK3CB | PIK3CB | 7005 | 0.062 | 0.44 | NO |
22 | CFLAR | CFLAR | CFLAR | 7242 | 0.051 | 0.43 | NO |
23 | FASLG | FASLG | FASLG | 7532 | 0.04 | 0.42 | NO |
24 | SMPD1 | SMPD1 | SMPD1 | 7629 | 0.036 | 0.42 | NO |
25 | MAP3K1 | MAP3K1 | MAP3K1 | 7684 | 0.034 | 0.42 | NO |
26 | BIRC3 | BIRC3 | BIRC3 | 8070 | 0.02 | 0.4 | NO |
27 | FADD | FADD | FADD | 8330 | 0.0095 | 0.38 | NO |
28 | MAPK9 | MAPK9 | MAPK9 | 8430 | 0.0059 | 0.38 | NO |
29 | MAP2K7 | MAP2K7 | MAP2K7 | 10402 | -0.064 | 0.28 | NO |
30 | PIK3CA | PIK3CA | PIK3CA | 10811 | -0.079 | 0.26 | NO |
31 | IKBKB | IKBKB | IKBKB | 11387 | -0.1 | 0.24 | NO |
32 | IKBKG | IKBKG | IKBKG | 11577 | -0.11 | 0.25 | NO |
33 | RFC1 | RFC1 | RFC1 | 11751 | -0.12 | 0.25 | NO |
34 | SYK | SYK | SYK | 11774 | -0.12 | 0.26 | NO |
35 | CASP3 | CASP3 | CASP3 | 12232 | -0.14 | 0.25 | NO |
36 | PDPK1 | PDPK1 | PDPK1 | 12284 | -0.14 | 0.27 | NO |
37 | AKT1 | AKT1 | AKT1 | 12861 | -0.16 | 0.25 | NO |
38 | BID | BID | BID | 13620 | -0.21 | 0.24 | NO |
Figure S119. 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 RET PATHWAY.

Figure S120. Get High-res Image For the top 5 core enriched genes in the pathway: PID RET PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 9. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus7. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
BIOCARTA RACCYCD PATHWAY | 26 | genes.ES.table | 0.47 | 1.8 | 0.011 | 0.35 | 0.5 | 0.46 | 0.32 | 0.31 | 0.089 | 0.082 |
PID ILK PATHWAY | 45 | genes.ES.table | 0.47 | 1.9 | 0.0041 | 0.33 | 0.39 | 0.44 | 0.37 | 0.28 | 0 | 0.073 |
REACTOME TRIF MEDIATED TLR3 SIGNALING | 72 | genes.ES.table | 0.5 | 1.8 | 0.0061 | 0.35 | 0.59 | 0.26 | 0.22 | 0.21 | 0.11 | 0.084 |
REACTOME ORC1 REMOVAL FROM CHROMATIN | 58 | genes.ES.table | 0.48 | 1.9 | 0.015 | 0.47 | 0.29 | 0.78 | 0.45 | 0.42 | 0 | 0.11 |
REACTOME ACTIVATION OF NF KAPPAB IN B CELLS | 60 | genes.ES.table | 0.44 | 1.9 | 0 | 0.73 | 0.23 | 0.67 | 0.45 | 0.36 | 0 | 0.14 |
REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT | 47 | genes.ES.table | 0.47 | 1.9 | 0.011 | 0.41 | 0.32 | 0.74 | 0.45 | 0.41 | 0 | 0.096 |
REACTOME CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6 | 45 | genes.ES.table | 0.46 | 1.7 | 0.024 | 0.34 | 0.63 | 0.78 | 0.46 | 0.42 | 0.12 | 0.079 |
REACTOME REGULATION OF APOPTOSIS | 55 | genes.ES.table | 0.44 | 1.9 | 0.011 | 0.34 | 0.36 | 0.73 | 0.45 | 0.4 | 0 | 0.075 |
REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION | 62 | genes.ES.table | 0.47 | 1.7 | 0.019 | 0.37 | 0.69 | 0.74 | 0.45 | 0.41 | 0.15 | 0.086 |
REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE | 52 | genes.ES.table | 0.46 | 1.9 | 0.014 | 0.62 | 0.29 | 0.75 | 0.46 | 0.4 | 0 | 0.14 |
Table S61. 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 | CCR5 | CCR5 | CCR5 | 379 | 0.75 | 0.015 | YES |
2 | DOCK2 | DOCK2 | DOCK2 | 792 | 0.62 | 0.021 | YES |
3 | APOBEC3G | APOBEC3G | APOBEC3G | 925 | 0.59 | 0.042 | YES |
4 | CD28 | CD28 | CD28 | 1182 | 0.53 | 0.053 | YES |
5 | LCK | LCK | LCK | 1186 | 0.53 | 0.078 | YES |
6 | CD4 | CD4 | CD4 | 1361 | 0.5 | 0.092 | YES |
7 | CD247 | CD247 | CD247 | 1408 | 0.49 | 0.11 | YES |
8 | CD8B | CD8B | CD8B | 1917 | 0.41 | 0.1 | YES |
9 | HCK | HCK | HCK | 2222 | 0.37 | 0.1 | YES |
10 | CXCR4 | CXCR4 | CXCR4 | 2414 | 0.34 | 0.11 | YES |
11 | HMGA1 | HMGA1 | HMGA1 | 2596 | 0.32 | 0.12 | YES |
12 | RCC1 | RCC1 | RCC1 | 2767 | 0.3 | 0.12 | YES |
13 | TAF5 | TAF5 | TAF5 | 3007 | 0.28 | 0.12 | YES |
14 | FYN | FYN | FYN | 3155 | 0.27 | 0.12 | YES |
15 | AP1S2 | AP1S2 | AP1S2 | 3163 | 0.26 | 0.14 | YES |
16 | TAF12 | TAF12 | TAF12 | 3285 | 0.25 | 0.14 | YES |
17 | PSMB9 | PSMB9 | PSMB9 | 3583 | 0.23 | 0.14 | YES |
18 | GTF2E2 | GTF2E2 | GTF2E2 | 3592 | 0.23 | 0.15 | YES |
19 | ELMO1 | ELMO1 | ELMO1 | 3841 | 0.21 | 0.14 | YES |
20 | GTF2F2 | GTF2F2 | GTF2F2 | 3976 | 0.2 | 0.14 | YES |
21 | NUP85 | NUP85 | NUP85 | 4054 | 0.19 | 0.15 | YES |
22 | POLR2D | POLR2D | POLR2D | 4060 | 0.19 | 0.16 | YES |
23 | GTF2E1 | GTF2E1 | GTF2E1 | 4213 | 0.18 | 0.16 | YES |
24 | CDK7 | CDK7 | CDK7 | 4244 | 0.18 | 0.16 | YES |
25 | RPS27A | RPS27A | RPS27A | 4385 | 0.17 | 0.16 | YES |
26 | PSMD4 | PSMD4 | PSMD4 | 4433 | 0.17 | 0.17 | YES |
27 | PSMB10 | PSMB10 | PSMB10 | 4455 | 0.17 | 0.18 | YES |
28 | TAF10 | TAF10 | TAF10 | 4695 | 0.16 | 0.17 | YES |
29 | RANGAP1 | RANGAP1 | RANGAP1 | 4727 | 0.15 | 0.18 | YES |
30 | RDBP | RDBP | RDBP | 4887 | 0.15 | 0.18 | YES |
31 | PSMB3 | PSMB3 | PSMB3 | 4974 | 0.14 | 0.18 | YES |
32 | PSMD14 | PSMD14 | PSMD14 | 5003 | 0.14 | 0.18 | YES |
33 | PSMB2 | PSMB2 | PSMB2 | 5045 | 0.14 | 0.19 | YES |
34 | GTF2H4 | GTF2H4 | GTF2H4 | 5056 | 0.14 | 0.19 | YES |
35 | GTF2H1 | GTF2H1 | GTF2H1 | 5078 | 0.14 | 0.2 | YES |
36 | PSMA5 | PSMA5 | PSMA5 | 5096 | 0.14 | 0.2 | YES |
37 | XRCC4 | XRCC4 | XRCC4 | 5109 | 0.14 | 0.21 | YES |
38 | RANBP1 | RANBP1 | RANBP1 | 5122 | 0.14 | 0.22 | YES |
39 | PSMD13 | PSMD13 | PSMD13 | 5319 | 0.13 | 0.21 | YES |
40 | NUP62 | NUP62 | NUP62 | 5334 | 0.12 | 0.22 | YES |
41 | AP2A1 | AP2A1 | AP2A1 | 5357 | 0.12 | 0.22 | YES |
42 | AP1M1 | AP1M1 | AP1M1 | 5441 | 0.12 | 0.22 | YES |
43 | LIG1 | LIG1 | LIG1 | 5461 | 0.12 | 0.23 | YES |
44 | NUPL1 | NUPL1 | NUPL1 | 5490 | 0.12 | 0.23 | YES |
45 | AP2S1 | AP2S1 | AP2S1 | 5526 | 0.12 | 0.23 | YES |
46 | TCEB1 | TCEB1 | TCEB1 | 5591 | 0.12 | 0.24 | YES |
47 | KPNB1 | KPNB1 | KPNB1 | 5684 | 0.11 | 0.24 | YES |
48 | PSME4 | PSME4 | PSME4 | 5697 | 0.11 | 0.24 | YES |
49 | PSMD12 | PSMD12 | PSMD12 | 5708 | 0.11 | 0.24 | YES |
50 | TCEA1 | TCEA1 | TCEA1 | 5852 | 0.1 | 0.24 | YES |
51 | PSMB4 | PSMB4 | PSMB4 | 5929 | 0.1 | 0.24 | YES |
52 | NUP93 | NUP93 | NUP93 | 5963 | 0.1 | 0.24 | YES |
53 | BANF1 | BANF1 | BANF1 | 6018 | 0.099 | 0.25 | YES |
54 | CCNH | CCNH | CCNH | 6021 | 0.098 | 0.25 | YES |
55 | AP2M1 | AP2M1 | AP2M1 | 6075 | 0.096 | 0.25 | YES |
56 | AP1S1 | AP1S1 | AP1S1 | 6103 | 0.095 | 0.26 | YES |
57 | PSMB6 | PSMB6 | PSMB6 | 6126 | 0.094 | 0.26 | YES |
58 | XPO1 | XPO1 | XPO1 | 6155 | 0.093 | 0.26 | YES |
59 | PSMC1 | PSMC1 | PSMC1 | 6166 | 0.093 | 0.27 | YES |
60 | PSMC3 | PSMC3 | PSMC3 | 6255 | 0.09 | 0.27 | YES |
61 | RAN | RAN | RAN | 6278 | 0.089 | 0.27 | YES |
62 | PSMC5 | PSMC5 | PSMC5 | 6287 | 0.089 | 0.27 | YES |
63 | GTF2B | GTF2B | GTF2B | 6376 | 0.086 | 0.27 | YES |
64 | NPM1 | NPM1 | NPM1 | 6393 | 0.085 | 0.28 | YES |
65 | PAK2 | PAK2 | PAK2 | 6423 | 0.084 | 0.28 | YES |
66 | RAC1 | RAC1 | RAC1 | 6566 | 0.081 | 0.27 | YES |
67 | TAF9 | TAF9 | TAF9 | 6593 | 0.08 | 0.28 | YES |
68 | PSMD11 | PSMD11 | PSMD11 | 6652 | 0.078 | 0.28 | YES |
69 | UBA52 | UBA52 | UBA52 | 6667 | 0.078 | 0.28 | YES |
70 | PSMD3 | PSMD3 | PSMD3 | 6694 | 0.077 | 0.28 | YES |
71 | ELL | ELL | ELL | 6705 | 0.076 | 0.28 | YES |
72 | NUP107 | NUP107 | NUP107 | 6773 | 0.074 | 0.28 | YES |
73 | PSMB1 | PSMB1 | PSMB1 | 6784 | 0.074 | 0.29 | YES |
74 | POLR2L | POLR2L | POLR2L | 6805 | 0.073 | 0.29 | YES |
75 | SEH1L | SEH1L | SEH1L | 6816 | 0.073 | 0.29 | YES |
76 | GTF2H2 | GTF2H2 | GTF2H2 | 6890 | 0.071 | 0.29 | YES |
77 | NUP188 | NUP188 | NUP188 | 6995 | 0.068 | 0.29 | YES |
78 | POLR2J | POLR2J | POLR2J | 7049 | 0.066 | 0.29 | YES |
79 | PSMA4 | PSMA4 | PSMA4 | 7102 | 0.064 | 0.29 | YES |
80 | POLR2H | POLR2H | POLR2H | 7155 | 0.063 | 0.29 | YES |
81 | HLA-A | HLA-A | HLA-A | 7191 | 0.062 | 0.29 | YES |
82 | PSME2 | PSME2 | PSME2 | 7203 | 0.062 | 0.29 | YES |
83 | PSMD2 | PSMD2 | PSMD2 | 7217 | 0.062 | 0.3 | YES |
84 | VPS28 | VPS28 | VPS28 | 7282 | 0.06 | 0.29 | YES |
85 | NMT2 | NMT2 | NMT2 | 7311 | 0.059 | 0.3 | YES |
86 | ERCC2 | ERCC2 | ERCC2 | 7312 | 0.059 | 0.3 | YES |
87 | TCEB2 | TCEB2 | TCEB2 | 7313 | 0.059 | 0.3 | YES |
88 | NUP35 | NUP35 | NUP35 | 7328 | 0.058 | 0.3 | YES |
89 | FEN1 | FEN1 | FEN1 | 7333 | 0.058 | 0.3 | YES |
90 | NUP43 | NUP43 | NUP43 | 7369 | 0.057 | 0.31 | YES |
91 | POLR2G | POLR2G | POLR2G | 7378 | 0.057 | 0.31 | YES |
92 | TAF6 | TAF6 | TAF6 | 7381 | 0.057 | 0.31 | YES |
93 | TH1L | TH1L | TH1L | 7419 | 0.056 | 0.31 | YES |
94 | PPIA | PPIA | PPIA | 7461 | 0.055 | 0.31 | YES |
95 | NUP88 | NUP88 | NUP88 | 7499 | 0.054 | 0.31 | YES |
96 | PSMD7 | PSMD7 | PSMD7 | 7536 | 0.052 | 0.31 | YES |
97 | PSMA1 | PSMA1 | PSMA1 | 7543 | 0.052 | 0.32 | YES |
98 | PSMC2 | PSMC2 | PSMC2 | 7551 | 0.052 | 0.32 | YES |
99 | AP2A2 | AP2A2 | AP2A2 | 7603 | 0.051 | 0.32 | YES |
100 | PSMB8 | PSMB8 | PSMB8 | 7623 | 0.05 | 0.32 | YES |
101 | TCEB3 | TCEB3 | TCEB3 | 7688 | 0.048 | 0.32 | YES |
102 | PSMA6 | PSMA6 | PSMA6 | 7727 | 0.048 | 0.32 | YES |
103 | TAF11 | TAF11 | TAF11 | 7764 | 0.046 | 0.32 | YES |
104 | TAF4 | TAF4 | TAF4 | 7803 | 0.046 | 0.32 | YES |
105 | NUP153 | NUP153 | NUP153 | 7867 | 0.044 | 0.32 | YES |
106 | POLR2F | POLR2F | POLR2F | 7885 | 0.043 | 0.32 | YES |
107 | RAE1 | RAE1 | RAE1 | 7938 | 0.042 | 0.32 | YES |
108 | TAF4B | TAF4B | TAF4B | 7969 | 0.041 | 0.32 | YES |
109 | PSMB7 | PSMB7 | PSMB7 | 7970 | 0.041 | 0.32 | YES |
110 | RBX1 | RBX1 | RBX1 | 7976 | 0.041 | 0.32 | YES |
111 | XRCC6 | XRCC6 | XRCC6 | 7995 | 0.04 | 0.32 | YES |
112 | PSMF1 | PSMF1 | PSMF1 | 8065 | 0.038 | 0.32 | YES |
113 | PSMA7 | PSMA7 | PSMA7 | 8086 | 0.038 | 0.32 | YES |
114 | PSMD5 | PSMD5 | PSMD5 | 8091 | 0.038 | 0.32 | YES |
115 | NCBP2 | NCBP2 | NCBP2 | 8109 | 0.037 | 0.32 | YES |
116 | LIG4 | LIG4 | LIG4 | 8210 | 0.035 | 0.32 | NO |
117 | PSMB5 | PSMB5 | PSMB5 | 8246 | 0.034 | 0.32 | NO |
118 | XRCC5 | XRCC5 | XRCC5 | 8269 | 0.033 | 0.32 | NO |
119 | ARF1 | ARF1 | ARF1 | 8290 | 0.033 | 0.32 | NO |
120 | NMT1 | NMT1 | NMT1 | 8336 | 0.031 | 0.32 | NO |
121 | VPS37B | VPS37B | VPS37B | 8377 | 0.03 | 0.32 | NO |
122 | SSRP1 | SSRP1 | SSRP1 | 8390 | 0.03 | 0.32 | NO |
123 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 8455 | 0.028 | 0.32 | NO |
124 | PSMA3 | PSMA3 | PSMA3 | 8564 | 0.025 | 0.31 | NO |
125 | PSMC4 | PSMC4 | PSMC4 | 8613 | 0.024 | 0.31 | NO |
126 | BTRC | BTRC | BTRC | 8756 | 0.02 | 0.3 | NO |
127 | POLR2E | POLR2E | POLR2E | 8785 | 0.02 | 0.3 | NO |
128 | VPS37A | VPS37A | VPS37A | 8822 | 0.019 | 0.3 | NO |
129 | PSMD9 | PSMD9 | PSMD9 | 8908 | 0.016 | 0.3 | NO |
130 | PSMA2 | PSMA2 | PSMA2 | 8985 | 0.014 | 0.29 | NO |
131 | RNMT | RNMT | RNMT | 8986 | 0.014 | 0.29 | NO |
132 | GTF2F1 | GTF2F1 | GTF2F1 | 8997 | 0.014 | 0.29 | NO |
133 | ERCC3 | ERCC3 | ERCC3 | 9040 | 0.013 | 0.29 | NO |
134 | PACS1 | PACS1 | PACS1 | 9057 | 0.012 | 0.29 | NO |
135 | CDK9 | CDK9 | CDK9 | 9064 | 0.012 | 0.29 | NO |
136 | TAF13 | TAF13 | TAF13 | 9106 | 0.011 | 0.29 | NO |
137 | NUP37 | NUP37 | NUP37 | 9183 | 0.0091 | 0.28 | NO |
138 | NUP54 | NUP54 | NUP54 | 9188 | 0.009 | 0.28 | NO |
139 | PSMD1 | PSMD1 | PSMD1 | 9306 | 0.0062 | 0.28 | NO |
140 | NUP50 | NUP50 | NUP50 | 9312 | 0.006 | 0.28 | NO |
141 | TBP | TBP | TBP | 9335 | 0.0053 | 0.28 | NO |
142 | SUPT16H | SUPT16H | SUPT16H | 9379 | 0.004 | 0.28 | NO |
143 | SLC25A6 | SLC25A6 | SLC25A6 | 9497 | 0.00083 | 0.27 | NO |
144 | KPNA1 | KPNA1 | KPNA1 | 9550 | -0.0002 | 0.27 | NO |
145 | POLR2B | POLR2B | POLR2B | 9668 | -0.0033 | 0.26 | NO |
146 | TSG101 | TSG101 | TSG101 | 9706 | -0.004 | 0.26 | NO |
147 | NUP155 | NUP155 | NUP155 | 9708 | -0.0041 | 0.26 | NO |
148 | POLR2K | POLR2K | POLR2K | 9743 | -0.0049 | 0.26 | NO |
149 | AP1B1 | AP1B1 | AP1B1 | 9782 | -0.0058 | 0.25 | NO |
150 | CTDP1 | CTDP1 | CTDP1 | 9795 | -0.0062 | 0.25 | NO |
151 | NUP133 | NUP133 | NUP133 | 9846 | -0.0073 | 0.25 | NO |
152 | RANBP2 | RANBP2 | RANBP2 | 9922 | -0.0091 | 0.25 | NO |
153 | GTF2A2 | GTF2A2 | GTF2A2 | 9971 | -0.01 | 0.24 | NO |
154 | B2M | B2M | B2M | 10039 | -0.012 | 0.24 | NO |
155 | AAAS | AAAS | AAAS | 10081 | -0.014 | 0.24 | NO |
156 | TPR | TPR | TPR | 10114 | -0.014 | 0.24 | NO |
157 | AP2B1 | AP2B1 | AP2B1 | 10278 | -0.019 | 0.23 | NO |
158 | POLR2I | POLR2I | POLR2I | 10360 | -0.021 | 0.23 | NO |
159 | RNGTT | RNGTT | RNGTT | 10363 | -0.021 | 0.23 | NO |
160 | CCNT2 | CCNT2 | CCNT2 | 10492 | -0.025 | 0.22 | NO |
161 | NCBP1 | NCBP1 | NCBP1 | 10503 | -0.025 | 0.22 | NO |
162 | PSMC6 | PSMC6 | PSMC6 | 10607 | -0.028 | 0.22 | NO |
163 | COBRA1 | COBRA1 | COBRA1 | 10682 | -0.03 | 0.22 | NO |
164 | PSMD6 | PSMD6 | PSMD6 | 10711 | -0.03 | 0.22 | NO |
165 | POM121 | POM121 | POM121 | 10760 | -0.032 | 0.21 | NO |
166 | PSME1 | PSME1 | PSME1 | 10788 | -0.032 | 0.21 | NO |
167 | TAF1 | TAF1 | TAF1 | 10830 | -0.033 | 0.21 | NO |
168 | WHSC2 | WHSC2 | WHSC2 | 10918 | -0.036 | 0.21 | NO |
169 | MNAT1 | MNAT1 | MNAT1 | 11050 | -0.04 | 0.2 | NO |
170 | SUPT5H | SUPT5H | SUPT5H | 11248 | -0.045 | 0.2 | NO |
171 | PSMD8 | PSMD8 | PSMD8 | 11299 | -0.046 | 0.2 | NO |
172 | GTF2H3 | GTF2H3 | GTF2H3 | 11339 | -0.047 | 0.2 | NO |
173 | NUPL2 | NUPL2 | NUPL2 | 11394 | -0.048 | 0.19 | NO |
174 | VPS37C | VPS37C | VPS37C | 11502 | -0.051 | 0.19 | NO |
175 | PSMD10 | PSMD10 | PSMD10 | 11913 | -0.064 | 0.17 | NO |
176 | NUP205 | NUP205 | NUP205 | 12122 | -0.069 | 0.16 | NO |
177 | SKP1 | SKP1 | SKP1 | 12367 | -0.078 | 0.15 | NO |
178 | POLR2C | POLR2C | POLR2C | 12506 | -0.083 | 0.15 | NO |
179 | POLR2A | POLR2A | POLR2A | 13317 | -0.11 | 0.11 | NO |
180 | NUP214 | NUP214 | NUP214 | 13322 | -0.11 | 0.11 | NO |
181 | AP1G1 | AP1G1 | AP1G1 | 13566 | -0.12 | 0.1 | NO |
182 | PSIP1 | PSIP1 | PSIP1 | 13654 | -0.13 | 0.11 | NO |
183 | ATP6V1H | ATP6V1H | ATP6V1H | 14441 | -0.16 | 0.069 | NO |
184 | GTF2A1 | GTF2A1 | GTF2A1 | 14681 | -0.18 | 0.064 | NO |
185 | CUL5 | CUL5 | CUL5 | 15244 | -0.21 | 0.042 | NO |
186 | SLC25A5 | SLC25A5 | SLC25A5 | 15457 | -0.23 | 0.042 | NO |
187 | VPS37D | VPS37D | VPS37D | 15499 | -0.24 | 0.05 | NO |
188 | GTF2H2B | GTF2H2B | GTF2H2B | 15751 | -0.26 | 0.049 | NO |
189 | CCNT1 | CCNT1 | CCNT1 | 15879 | -0.27 | 0.054 | NO |
190 | AP1M2 | AP1M2 | AP1M2 | 16542 | -0.35 | 0.033 | NO |
191 | SLC25A4 | SLC25A4 | SLC25A4 | 16839 | -0.39 | 0.035 | NO |
192 | NUP210 | NUP210 | NUP210 | 17097 | -0.43 | 0.041 | NO |
Figure S121. 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 RACCYCD PATHWAY.

Figure S122. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA RACCYCD PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S62. 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 | 571 | 0.68 | 0.091 | YES |
2 | CARD11 | CARD11 | CARD11 | 1849 | 0.42 | 0.095 | YES |
3 | NFKBIE | NFKBIE | NFKBIE | 3141 | 0.27 | 0.07 | YES |
4 | PSMB9 | PSMB9 | PSMB9 | 3583 | 0.23 | 0.087 | YES |
5 | MALT1 | MALT1 | MALT1 | 4326 | 0.18 | 0.077 | YES |
6 | RPS27A | RPS27A | RPS27A | 4385 | 0.17 | 0.1 | YES |
7 | PSMD4 | PSMD4 | PSMD4 | 4433 | 0.17 | 0.13 | YES |
8 | PSMB10 | PSMB10 | PSMB10 | 4455 | 0.17 | 0.16 | YES |
9 | PSMB3 | PSMB3 | PSMB3 | 4974 | 0.14 | 0.16 | YES |
10 | PSMD14 | PSMD14 | PSMD14 | 5003 | 0.14 | 0.18 | YES |
11 | PSMB2 | PSMB2 | PSMB2 | 5045 | 0.14 | 0.2 | YES |
12 | PSMA5 | PSMA5 | PSMA5 | 5096 | 0.14 | 0.23 | YES |
13 | PSMD13 | PSMD13 | PSMD13 | 5319 | 0.13 | 0.24 | YES |
14 | IKBKB | IKBKB | IKBKB | 5648 | 0.11 | 0.24 | YES |
15 | NFKBIA | NFKBIA | NFKBIA | 5672 | 0.11 | 0.26 | YES |
16 | PSME4 | PSME4 | PSME4 | 5697 | 0.11 | 0.28 | YES |
17 | PSMD12 | PSMD12 | PSMD12 | 5708 | 0.11 | 0.3 | YES |
18 | BCL10 | BCL10 | BCL10 | 5747 | 0.11 | 0.31 | YES |
19 | PSMB4 | PSMB4 | PSMB4 | 5929 | 0.1 | 0.32 | YES |
20 | PSMB6 | PSMB6 | PSMB6 | 6126 | 0.094 | 0.33 | YES |
21 | PSMC1 | PSMC1 | PSMC1 | 6166 | 0.093 | 0.34 | YES |
22 | PSMC3 | PSMC3 | PSMC3 | 6255 | 0.09 | 0.35 | YES |
23 | PSMC5 | PSMC5 | PSMC5 | 6287 | 0.089 | 0.37 | YES |
24 | PSMD11 | PSMD11 | PSMD11 | 6652 | 0.078 | 0.36 | YES |
25 | UBA52 | UBA52 | UBA52 | 6667 | 0.078 | 0.38 | YES |
26 | PSMD3 | PSMD3 | PSMD3 | 6694 | 0.077 | 0.39 | YES |
27 | PSMB1 | PSMB1 | PSMB1 | 6784 | 0.074 | 0.4 | YES |
28 | REL | REL | REL | 6990 | 0.068 | 0.4 | YES |
29 | PSMA4 | PSMA4 | PSMA4 | 7102 | 0.064 | 0.4 | YES |
30 | PSME2 | PSME2 | PSME2 | 7203 | 0.062 | 0.41 | YES |
31 | PSMD2 | PSMD2 | PSMD2 | 7217 | 0.062 | 0.42 | YES |
32 | PSMD7 | PSMD7 | PSMD7 | 7536 | 0.052 | 0.41 | YES |
33 | PSMA1 | PSMA1 | PSMA1 | 7543 | 0.052 | 0.42 | YES |
34 | PSMC2 | PSMC2 | PSMC2 | 7551 | 0.052 | 0.43 | YES |
35 | PSMB8 | PSMB8 | PSMB8 | 7623 | 0.05 | 0.43 | YES |
36 | PSMA6 | PSMA6 | PSMA6 | 7727 | 0.048 | 0.44 | YES |
37 | PSMB7 | PSMB7 | PSMB7 | 7970 | 0.041 | 0.43 | YES |
38 | PSMF1 | PSMF1 | PSMF1 | 8065 | 0.038 | 0.43 | YES |
39 | PSMA7 | PSMA7 | PSMA7 | 8086 | 0.038 | 0.44 | YES |
40 | PSMD5 | PSMD5 | PSMD5 | 8091 | 0.038 | 0.44 | YES |
41 | PSMB5 | PSMB5 | PSMB5 | 8246 | 0.034 | 0.44 | NO |
42 | PSMA3 | PSMA3 | PSMA3 | 8564 | 0.025 | 0.43 | NO |
43 | PSMC4 | PSMC4 | PSMC4 | 8613 | 0.024 | 0.43 | NO |
44 | BTRC | BTRC | BTRC | 8756 | 0.02 | 0.42 | NO |
45 | PSMD9 | PSMD9 | PSMD9 | 8908 | 0.016 | 0.42 | NO |
46 | RELA | RELA | RELA | 8914 | 0.016 | 0.42 | NO |
47 | PSMA2 | PSMA2 | PSMA2 | 8985 | 0.014 | 0.42 | NO |
48 | PSMD1 | PSMD1 | PSMD1 | 9306 | 0.0062 | 0.4 | NO |
49 | IKBKG | IKBKG | IKBKG | 9634 | -0.0024 | 0.39 | NO |
50 | MAP3K7 | MAP3K7 | MAP3K7 | 9876 | -0.0078 | 0.37 | NO |
51 | NFKBIB | NFKBIB | NFKBIB | 10545 | -0.026 | 0.34 | NO |
52 | PSMC6 | PSMC6 | PSMC6 | 10607 | -0.028 | 0.34 | NO |
53 | CUL1 | CUL1 | CUL1 | 10653 | -0.029 | 0.34 | NO |
54 | PSMD6 | PSMD6 | PSMD6 | 10711 | -0.03 | 0.35 | NO |
55 | FBXW11 | FBXW11 | FBXW11 | 10747 | -0.031 | 0.35 | NO |
56 | PSME1 | PSME1 | PSME1 | 10788 | -0.032 | 0.36 | NO |
57 | CHUK | CHUK | CHUK | 11084 | -0.04 | 0.34 | NO |
58 | PSMD8 | PSMD8 | PSMD8 | 11299 | -0.046 | 0.34 | NO |
59 | PSMD10 | PSMD10 | PSMD10 | 11913 | -0.064 | 0.32 | NO |
60 | SKP1 | SKP1 | SKP1 | 12367 | -0.078 | 0.31 | NO |
Figure S123. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ILK PATHWAY.

Figure S124. Get High-res Image For the top 5 core enriched genes in the pathway: PID ILK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S63. 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 | CCNE1 | CCNE1 | CCNE1 | 1091 | 0.55 | 0.057 | YES |
2 | CCNE2 | CCNE2 | CCNE2 | 2912 | 0.29 | 0.016 | YES |
3 | PSMB9 | PSMB9 | PSMB9 | 3583 | 0.23 | 0.028 | YES |
4 | CDKN1A | CDKN1A | CDKN1A | 4114 | 0.19 | 0.039 | YES |
5 | RPS27A | RPS27A | RPS27A | 4385 | 0.17 | 0.061 | YES |
6 | PSMD4 | PSMD4 | PSMD4 | 4433 | 0.17 | 0.095 | YES |
7 | PSMB10 | PSMB10 | PSMB10 | 4455 | 0.17 | 0.13 | YES |
8 | PSMB3 | PSMB3 | PSMB3 | 4974 | 0.14 | 0.13 | YES |
9 | PSMD14 | PSMD14 | PSMD14 | 5003 | 0.14 | 0.16 | YES |
10 | PSMB2 | PSMB2 | PSMB2 | 5045 | 0.14 | 0.19 | YES |
11 | PSMA5 | PSMA5 | PSMA5 | 5096 | 0.14 | 0.21 | YES |
12 | PSMD13 | PSMD13 | PSMD13 | 5319 | 0.13 | 0.23 | YES |
13 | PSME4 | PSME4 | PSME4 | 5697 | 0.11 | 0.23 | YES |
14 | PSMD12 | PSMD12 | PSMD12 | 5708 | 0.11 | 0.25 | YES |
15 | CDK2 | CDK2 | CDK2 | 5719 | 0.11 | 0.28 | YES |
16 | PSMB4 | PSMB4 | PSMB4 | 5929 | 0.1 | 0.29 | YES |
17 | PSMB6 | PSMB6 | PSMB6 | 6126 | 0.094 | 0.3 | YES |
18 | PSMC1 | PSMC1 | PSMC1 | 6166 | 0.093 | 0.31 | YES |
19 | PSMC3 | PSMC3 | PSMC3 | 6255 | 0.09 | 0.33 | YES |
20 | PSMC5 | PSMC5 | PSMC5 | 6287 | 0.089 | 0.35 | YES |
21 | PSMD11 | PSMD11 | PSMD11 | 6652 | 0.078 | 0.34 | YES |
22 | UBA52 | UBA52 | UBA52 | 6667 | 0.078 | 0.36 | YES |
23 | PSMD3 | PSMD3 | PSMD3 | 6694 | 0.077 | 0.37 | YES |
24 | PSMB1 | PSMB1 | PSMB1 | 6784 | 0.074 | 0.38 | YES |
25 | PSMA4 | PSMA4 | PSMA4 | 7102 | 0.064 | 0.38 | YES |
26 | PSME2 | PSME2 | PSME2 | 7203 | 0.062 | 0.39 | YES |
27 | PSMD2 | PSMD2 | PSMD2 | 7217 | 0.062 | 0.4 | YES |
28 | RFWD2 | RFWD2 | RFWD2 | 7436 | 0.055 | 0.4 | YES |
29 | PSMD7 | PSMD7 | PSMD7 | 7536 | 0.052 | 0.41 | YES |
30 | PSMA1 | PSMA1 | PSMA1 | 7543 | 0.052 | 0.42 | YES |
31 | PSMC2 | PSMC2 | PSMC2 | 7551 | 0.052 | 0.43 | YES |
32 | PSMB8 | PSMB8 | PSMB8 | 7623 | 0.05 | 0.44 | YES |
33 | PSMA6 | PSMA6 | PSMA6 | 7727 | 0.048 | 0.44 | YES |
34 | PSMB7 | PSMB7 | PSMB7 | 7970 | 0.041 | 0.43 | YES |
35 | PSMF1 | PSMF1 | PSMF1 | 8065 | 0.038 | 0.44 | YES |
36 | PSMA7 | PSMA7 | PSMA7 | 8086 | 0.038 | 0.44 | YES |
37 | PSMD5 | PSMD5 | PSMD5 | 8091 | 0.038 | 0.45 | YES |
38 | TP53 | TP53 | TP53 | 8191 | 0.035 | 0.45 | YES |
39 | PSMB5 | PSMB5 | PSMB5 | 8246 | 0.034 | 0.46 | YES |
40 | PSMA3 | PSMA3 | PSMA3 | 8564 | 0.025 | 0.45 | NO |
41 | PSMC4 | PSMC4 | PSMC4 | 8613 | 0.024 | 0.45 | NO |
42 | PSMD9 | PSMD9 | PSMD9 | 8908 | 0.016 | 0.44 | NO |
43 | PSMA2 | PSMA2 | PSMA2 | 8985 | 0.014 | 0.43 | NO |
44 | PSMD1 | PSMD1 | PSMD1 | 9306 | 0.0062 | 0.42 | NO |
45 | ATM | ATM | ATM | 9751 | -0.0051 | 0.39 | NO |
46 | MDM2 | MDM2 | MDM2 | 10294 | -0.02 | 0.37 | NO |
47 | PSMC6 | PSMC6 | PSMC6 | 10607 | -0.028 | 0.36 | NO |
48 | PSMD6 | PSMD6 | PSMD6 | 10711 | -0.03 | 0.36 | NO |
49 | PSME1 | PSME1 | PSME1 | 10788 | -0.032 | 0.36 | NO |
50 | PSMD8 | PSMD8 | PSMD8 | 11299 | -0.046 | 0.34 | NO |
51 | CDKN1B | CDKN1B | CDKN1B | 11800 | -0.06 | 0.32 | NO |
52 | PSMD10 | PSMD10 | PSMD10 | 11913 | -0.064 | 0.33 | NO |
Figure S125. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING.

Figure S126. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S64. 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 | CDC6 | CDC6 | CDC6 | 1639 | 0.45 | -0.018 | YES |
2 | CDT1 | CDT1 | CDT1 | 1897 | 0.41 | 0.035 | YES |
3 | CCNA2 | CCNA2 | CCNA2 | 2176 | 0.37 | 0.08 | YES |
4 | PSMB9 | PSMB9 | PSMB9 | 3583 | 0.23 | 0.038 | YES |
5 | CCNA1 | CCNA1 | CCNA1 | 3632 | 0.22 | 0.072 | YES |
6 | MCM5 | MCM5 | MCM5 | 3703 | 0.22 | 0.1 | YES |
7 | MCM6 | MCM6 | MCM6 | 3775 | 0.21 | 0.13 | YES |
8 | CDKN1A | CDKN1A | CDKN1A | 4114 | 0.19 | 0.15 | YES |
9 | RPS27A | RPS27A | RPS27A | 4385 | 0.17 | 0.16 | YES |
10 | PSMD4 | PSMD4 | PSMD4 | 4433 | 0.17 | 0.18 | YES |
11 | PSMB10 | PSMB10 | PSMB10 | 4455 | 0.17 | 0.21 | YES |
12 | RB1 | RB1 | RB1 | 4501 | 0.17 | 0.24 | YES |
13 | MCM7 | MCM7 | MCM7 | 4908 | 0.14 | 0.24 | YES |
14 | PSMB3 | PSMB3 | PSMB3 | 4974 | 0.14 | 0.26 | YES |
15 | PSMD14 | PSMD14 | PSMD14 | 5003 | 0.14 | 0.28 | YES |
16 | PSMB2 | PSMB2 | PSMB2 | 5045 | 0.14 | 0.3 | YES |
17 | PSMA5 | PSMA5 | PSMA5 | 5096 | 0.14 | 0.32 | YES |
18 | PSMD13 | PSMD13 | PSMD13 | 5319 | 0.13 | 0.32 | YES |
19 | PSME4 | PSME4 | PSME4 | 5697 | 0.11 | 0.32 | YES |
20 | PSMD12 | PSMD12 | PSMD12 | 5708 | 0.11 | 0.34 | YES |
21 | CDK2 | CDK2 | CDK2 | 5719 | 0.11 | 0.36 | YES |
22 | PSMB4 | PSMB4 | PSMB4 | 5929 | 0.1 | 0.36 | YES |
23 | PSMB6 | PSMB6 | PSMB6 | 6126 | 0.094 | 0.37 | YES |
24 | PSMC1 | PSMC1 | PSMC1 | 6166 | 0.093 | 0.38 | YES |
25 | MCM2 | MCM2 | MCM2 | 6176 | 0.093 | 0.39 | YES |
26 | PSMC3 | PSMC3 | PSMC3 | 6255 | 0.09 | 0.4 | YES |
27 | PSMC5 | PSMC5 | PSMC5 | 6287 | 0.089 | 0.42 | YES |
28 | PSMD11 | PSMD11 | PSMD11 | 6652 | 0.078 | 0.41 | YES |
29 | UBA52 | UBA52 | UBA52 | 6667 | 0.078 | 0.42 | YES |
30 | PSMD3 | PSMD3 | PSMD3 | 6694 | 0.077 | 0.43 | YES |
31 | PSMB1 | PSMB1 | PSMB1 | 6784 | 0.074 | 0.44 | YES |
32 | MCM4 | MCM4 | MCM4 | 7029 | 0.067 | 0.44 | YES |
33 | PSMA4 | PSMA4 | PSMA4 | 7102 | 0.064 | 0.44 | YES |
34 | PSME2 | PSME2 | PSME2 | 7203 | 0.062 | 0.45 | YES |
35 | PSMD2 | PSMD2 | PSMD2 | 7217 | 0.062 | 0.46 | YES |
36 | PSMD7 | PSMD7 | PSMD7 | 7536 | 0.052 | 0.45 | YES |
37 | PSMA1 | PSMA1 | PSMA1 | 7543 | 0.052 | 0.46 | YES |
38 | PSMC2 | PSMC2 | PSMC2 | 7551 | 0.052 | 0.46 | YES |
39 | PSMB8 | PSMB8 | PSMB8 | 7623 | 0.05 | 0.47 | YES |
40 | PSMA6 | PSMA6 | PSMA6 | 7727 | 0.048 | 0.47 | YES |
41 | PSMB7 | PSMB7 | PSMB7 | 7970 | 0.041 | 0.46 | YES |
42 | PSMF1 | PSMF1 | PSMF1 | 8065 | 0.038 | 0.46 | YES |
43 | MCM3 | MCM3 | MCM3 | 8067 | 0.038 | 0.47 | YES |
44 | PSMA7 | PSMA7 | PSMA7 | 8086 | 0.038 | 0.48 | YES |
45 | PSMD5 | PSMD5 | PSMD5 | 8091 | 0.038 | 0.48 | YES |
46 | PSMB5 | PSMB5 | PSMB5 | 8246 | 0.034 | 0.48 | NO |
47 | PSMA3 | PSMA3 | PSMA3 | 8564 | 0.025 | 0.46 | NO |
48 | PSMC4 | PSMC4 | PSMC4 | 8613 | 0.024 | 0.47 | NO |
49 | MCM8 | MCM8 | MCM8 | 8774 | 0.02 | 0.46 | NO |
50 | PSMD9 | PSMD9 | PSMD9 | 8908 | 0.016 | 0.46 | NO |
51 | PSMA2 | PSMA2 | PSMA2 | 8985 | 0.014 | 0.45 | NO |
52 | PSMD1 | PSMD1 | PSMD1 | 9306 | 0.0062 | 0.44 | NO |
53 | PSMC6 | PSMC6 | PSMC6 | 10607 | -0.028 | 0.37 | NO |
54 | PSMD6 | PSMD6 | PSMD6 | 10711 | -0.03 | 0.37 | NO |
55 | PSME1 | PSME1 | PSME1 | 10788 | -0.032 | 0.37 | NO |
56 | PSMD8 | PSMD8 | PSMD8 | 11299 | -0.046 | 0.35 | NO |
57 | CDKN1B | CDKN1B | CDKN1B | 11800 | -0.06 | 0.33 | NO |
58 | PSMD10 | PSMD10 | PSMD10 | 11913 | -0.064 | 0.33 | NO |
Figure S127. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ORC1 REMOVAL FROM CHROMATIN.

Figure S128. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ORC1 REMOVAL FROM CHROMATIN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S65. 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 | CHEK2 | CHEK2 | CHEK2 | 1287 | 0.51 | 0.054 | YES |
2 | PSMB9 | PSMB9 | PSMB9 | 3583 | 0.23 | -0.019 | YES |
3 | RPS27A | RPS27A | RPS27A | 4385 | 0.17 | -0.021 | YES |
4 | PSMD4 | PSMD4 | PSMD4 | 4433 | 0.17 | 0.018 | YES |
5 | PSMB10 | PSMB10 | PSMB10 | 4455 | 0.17 | 0.059 | YES |
6 | CDC25A | CDC25A | CDC25A | 4815 | 0.15 | 0.075 | YES |
7 | PSMB3 | PSMB3 | PSMB3 | 4974 | 0.14 | 0.1 | YES |
8 | PSMD14 | PSMD14 | PSMD14 | 5003 | 0.14 | 0.14 | YES |
9 | PSMB2 | PSMB2 | PSMB2 | 5045 | 0.14 | 0.17 | YES |
10 | PSMA5 | PSMA5 | PSMA5 | 5096 | 0.14 | 0.2 | YES |
11 | PSMD13 | PSMD13 | PSMD13 | 5319 | 0.13 | 0.22 | YES |
12 | PSME4 | PSME4 | PSME4 | 5697 | 0.11 | 0.22 | YES |
13 | PSMD12 | PSMD12 | PSMD12 | 5708 | 0.11 | 0.25 | YES |
14 | PSMB4 | PSMB4 | PSMB4 | 5929 | 0.1 | 0.26 | YES |
15 | PSMB6 | PSMB6 | PSMB6 | 6126 | 0.094 | 0.27 | YES |
16 | PSMC1 | PSMC1 | PSMC1 | 6166 | 0.093 | 0.3 | YES |
17 | PSMC3 | PSMC3 | PSMC3 | 6255 | 0.09 | 0.31 | YES |
18 | PSMC5 | PSMC5 | PSMC5 | 6287 | 0.089 | 0.33 | YES |
19 | PSMD11 | PSMD11 | PSMD11 | 6652 | 0.078 | 0.33 | YES |
20 | UBA52 | UBA52 | UBA52 | 6667 | 0.078 | 0.35 | YES |
21 | PSMD3 | PSMD3 | PSMD3 | 6694 | 0.077 | 0.37 | YES |
22 | PSMB1 | PSMB1 | PSMB1 | 6784 | 0.074 | 0.38 | YES |
23 | PSMA4 | PSMA4 | PSMA4 | 7102 | 0.064 | 0.38 | YES |
24 | PSME2 | PSME2 | PSME2 | 7203 | 0.062 | 0.39 | YES |
25 | PSMD2 | PSMD2 | PSMD2 | 7217 | 0.062 | 0.4 | YES |
26 | PSMD7 | PSMD7 | PSMD7 | 7536 | 0.052 | 0.4 | YES |
27 | PSMA1 | PSMA1 | PSMA1 | 7543 | 0.052 | 0.41 | YES |
28 | PSMC2 | PSMC2 | PSMC2 | 7551 | 0.052 | 0.42 | YES |
29 | PSMB8 | PSMB8 | PSMB8 | 7623 | 0.05 | 0.43 | YES |
30 | PSMA6 | PSMA6 | PSMA6 | 7727 | 0.048 | 0.44 | YES |
31 | CHEK1 | CHEK1 | CHEK1 | 7853 | 0.044 | 0.44 | YES |
32 | PSMB7 | PSMB7 | PSMB7 | 7970 | 0.041 | 0.44 | YES |
33 | PSMF1 | PSMF1 | PSMF1 | 8065 | 0.038 | 0.45 | YES |
34 | PSMA7 | PSMA7 | PSMA7 | 8086 | 0.038 | 0.46 | YES |
35 | PSMD5 | PSMD5 | PSMD5 | 8091 | 0.038 | 0.47 | YES |
36 | PSMB5 | PSMB5 | PSMB5 | 8246 | 0.034 | 0.47 | NO |
37 | PSMA3 | PSMA3 | PSMA3 | 8564 | 0.025 | 0.46 | NO |
38 | PSMC4 | PSMC4 | PSMC4 | 8613 | 0.024 | 0.46 | NO |
39 | PSMD9 | PSMD9 | PSMD9 | 8908 | 0.016 | 0.44 | NO |
40 | PSMA2 | PSMA2 | PSMA2 | 8985 | 0.014 | 0.44 | NO |
41 | PSMD1 | PSMD1 | PSMD1 | 9306 | 0.0062 | 0.43 | NO |
42 | ATM | ATM | ATM | 9751 | -0.0051 | 0.4 | NO |
43 | PSMC6 | PSMC6 | PSMC6 | 10607 | -0.028 | 0.36 | NO |
44 | PSMD6 | PSMD6 | PSMD6 | 10711 | -0.03 | 0.36 | NO |
45 | PSME1 | PSME1 | PSME1 | 10788 | -0.032 | 0.37 | NO |
46 | PSMD8 | PSMD8 | PSMD8 | 11299 | -0.046 | 0.35 | NO |
47 | PSMD10 | PSMD10 | PSMD10 | 11913 | -0.064 | 0.33 | NO |
Figure S129. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS.

Figure S130. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S66. 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 | CDC6 | CDC6 | CDC6 | 1639 | 0.45 | 0.013 | YES |
2 | CDT1 | CDT1 | CDT1 | 1897 | 0.41 | 0.094 | YES |
3 | PSMB9 | PSMB9 | PSMB9 | 3583 | 0.23 | 0.052 | YES |
4 | RPS27A | RPS27A | RPS27A | 4385 | 0.17 | 0.048 | YES |
5 | PSMD4 | PSMD4 | PSMD4 | 4433 | 0.17 | 0.084 | YES |
6 | PSMB10 | PSMB10 | PSMB10 | 4455 | 0.17 | 0.12 | YES |
7 | PSMB3 | PSMB3 | PSMB3 | 4974 | 0.14 | 0.13 | YES |
8 | PSMD14 | PSMD14 | PSMD14 | 5003 | 0.14 | 0.16 | YES |
9 | PSMB2 | PSMB2 | PSMB2 | 5045 | 0.14 | 0.19 | YES |
10 | PSMA5 | PSMA5 | PSMA5 | 5096 | 0.14 | 0.22 | YES |
11 | PSMD13 | PSMD13 | PSMD13 | 5319 | 0.13 | 0.23 | YES |
12 | PSME4 | PSME4 | PSME4 | 5697 | 0.11 | 0.24 | YES |
13 | PSMD12 | PSMD12 | PSMD12 | 5708 | 0.11 | 0.26 | YES |
14 | PSMB4 | PSMB4 | PSMB4 | 5929 | 0.1 | 0.27 | YES |
15 | PSMB6 | PSMB6 | PSMB6 | 6126 | 0.094 | 0.28 | YES |
16 | PSMC1 | PSMC1 | PSMC1 | 6166 | 0.093 | 0.3 | YES |
17 | PSMC3 | PSMC3 | PSMC3 | 6255 | 0.09 | 0.32 | YES |
18 | PSMC5 | PSMC5 | PSMC5 | 6287 | 0.089 | 0.34 | YES |
19 | GMNN | GMNN | GMNN | 6291 | 0.089 | 0.36 | YES |
20 | PSMD11 | PSMD11 | PSMD11 | 6652 | 0.078 | 0.36 | YES |
21 | UBA52 | UBA52 | UBA52 | 6667 | 0.078 | 0.37 | YES |
22 | PSMD3 | PSMD3 | PSMD3 | 6694 | 0.077 | 0.39 | YES |
23 | PSMB1 | PSMB1 | PSMB1 | 6784 | 0.074 | 0.4 | YES |
24 | PSMA4 | PSMA4 | PSMA4 | 7102 | 0.064 | 0.4 | YES |
25 | PSME2 | PSME2 | PSME2 | 7203 | 0.062 | 0.41 | YES |
26 | PSMD2 | PSMD2 | PSMD2 | 7217 | 0.062 | 0.42 | YES |
27 | PSMD7 | PSMD7 | PSMD7 | 7536 | 0.052 | 0.42 | YES |
28 | PSMA1 | PSMA1 | PSMA1 | 7543 | 0.052 | 0.43 | YES |
29 | PSMC2 | PSMC2 | PSMC2 | 7551 | 0.052 | 0.44 | YES |
30 | PSMB8 | PSMB8 | PSMB8 | 7623 | 0.05 | 0.45 | YES |
31 | PSMA6 | PSMA6 | PSMA6 | 7727 | 0.048 | 0.45 | YES |
32 | PSMB7 | PSMB7 | PSMB7 | 7970 | 0.041 | 0.45 | YES |
33 | PSMF1 | PSMF1 | PSMF1 | 8065 | 0.038 | 0.45 | YES |
34 | PSMA7 | PSMA7 | PSMA7 | 8086 | 0.038 | 0.46 | YES |
35 | PSMD5 | PSMD5 | PSMD5 | 8091 | 0.038 | 0.47 | YES |
36 | PSMB5 | PSMB5 | PSMB5 | 8246 | 0.034 | 0.47 | NO |
37 | PSMA3 | PSMA3 | PSMA3 | 8564 | 0.025 | 0.46 | NO |
38 | PSMC4 | PSMC4 | PSMC4 | 8613 | 0.024 | 0.46 | NO |
39 | MCM8 | MCM8 | MCM8 | 8774 | 0.02 | 0.45 | NO |
40 | PSMD9 | PSMD9 | PSMD9 | 8908 | 0.016 | 0.45 | NO |
41 | PSMA2 | PSMA2 | PSMA2 | 8985 | 0.014 | 0.45 | NO |
42 | PSMD1 | PSMD1 | PSMD1 | 9306 | 0.0062 | 0.43 | NO |
43 | PSMC6 | PSMC6 | PSMC6 | 10607 | -0.028 | 0.37 | NO |
44 | PSMD6 | PSMD6 | PSMD6 | 10711 | -0.03 | 0.37 | NO |
45 | PSME1 | PSME1 | PSME1 | 10788 | -0.032 | 0.37 | NO |
46 | PSMD8 | PSMD8 | PSMD8 | 11299 | -0.046 | 0.35 | NO |
47 | PSMD10 | PSMD10 | PSMD10 | 11913 | -0.064 | 0.33 | NO |
Figure S131. 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 P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT.

Figure S132. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S67. 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 | ARHGAP10 | ARHGAP10 | ARHGAP10 | 212 | 0.84 | 0.14 | YES |
2 | UNC5A | UNC5A | UNC5A | 2763 | 0.3 | 0.045 | YES |
3 | DAPK1 | DAPK1 | DAPK1 | 2864 | 0.29 | 0.091 | YES |
4 | PSMB9 | PSMB9 | PSMB9 | 3583 | 0.23 | 0.091 | YES |
5 | RPS27A | RPS27A | RPS27A | 4385 | 0.17 | 0.076 | YES |
6 | PSMD4 | PSMD4 | PSMD4 | 4433 | 0.17 | 0.1 | YES |
7 | PSMB10 | PSMB10 | PSMB10 | 4455 | 0.17 | 0.13 | YES |
8 | DCC | DCC | DCC | 4530 | 0.16 | 0.16 | YES |
9 | UNC5B | UNC5B | UNC5B | 4875 | 0.15 | 0.16 | YES |
10 | CASP3 | CASP3 | CASP3 | 4888 | 0.15 | 0.19 | YES |
11 | PSMB3 | PSMB3 | PSMB3 | 4974 | 0.14 | 0.21 | YES |
12 | PSMD14 | PSMD14 | PSMD14 | 5003 | 0.14 | 0.23 | YES |
13 | PSMB2 | PSMB2 | PSMB2 | 5045 | 0.14 | 0.25 | YES |
14 | PSMA5 | PSMA5 | PSMA5 | 5096 | 0.14 | 0.28 | YES |
15 | PSMD13 | PSMD13 | PSMD13 | 5319 | 0.13 | 0.28 | YES |
16 | PSME4 | PSME4 | PSME4 | 5697 | 0.11 | 0.28 | YES |
17 | PSMD12 | PSMD12 | PSMD12 | 5708 | 0.11 | 0.3 | YES |
18 | PSMB4 | PSMB4 | PSMB4 | 5929 | 0.1 | 0.31 | YES |
19 | PSMB6 | PSMB6 | PSMB6 | 6126 | 0.094 | 0.31 | YES |
20 | PSMC1 | PSMC1 | PSMC1 | 6166 | 0.093 | 0.33 | YES |
21 | PSMC3 | PSMC3 | PSMC3 | 6255 | 0.09 | 0.34 | YES |
22 | PSMC5 | PSMC5 | PSMC5 | 6287 | 0.089 | 0.35 | YES |
23 | DAPK3 | DAPK3 | DAPK3 | 6340 | 0.087 | 0.36 | YES |
24 | PAK2 | PAK2 | PAK2 | 6423 | 0.084 | 0.38 | YES |
25 | PSMD11 | PSMD11 | PSMD11 | 6652 | 0.078 | 0.38 | YES |
26 | UBA52 | UBA52 | UBA52 | 6667 | 0.078 | 0.39 | YES |
27 | PSMD3 | PSMD3 | PSMD3 | 6694 | 0.077 | 0.4 | YES |
28 | PSMB1 | PSMB1 | PSMB1 | 6784 | 0.074 | 0.41 | YES |
29 | PSMA4 | PSMA4 | PSMA4 | 7102 | 0.064 | 0.4 | YES |
30 | PSME2 | PSME2 | PSME2 | 7203 | 0.062 | 0.41 | YES |
31 | PSMD2 | PSMD2 | PSMD2 | 7217 | 0.062 | 0.42 | YES |
32 | PSMD7 | PSMD7 | PSMD7 | 7536 | 0.052 | 0.41 | YES |
33 | PSMA1 | PSMA1 | PSMA1 | 7543 | 0.052 | 0.42 | YES |
34 | PSMC2 | PSMC2 | PSMC2 | 7551 | 0.052 | 0.43 | YES |
35 | PSMB8 | PSMB8 | PSMB8 | 7623 | 0.05 | 0.43 | YES |
36 | PSMA6 | PSMA6 | PSMA6 | 7727 | 0.048 | 0.43 | YES |
37 | PSMB7 | PSMB7 | PSMB7 | 7970 | 0.041 | 0.43 | YES |
38 | PSMF1 | PSMF1 | PSMF1 | 8065 | 0.038 | 0.43 | YES |
39 | PSMA7 | PSMA7 | PSMA7 | 8086 | 0.038 | 0.44 | YES |
40 | PSMD5 | PSMD5 | PSMD5 | 8091 | 0.038 | 0.44 | YES |
41 | PSMB5 | PSMB5 | PSMB5 | 8246 | 0.034 | 0.44 | NO |
42 | PSMA3 | PSMA3 | PSMA3 | 8564 | 0.025 | 0.42 | NO |
43 | PSMC4 | PSMC4 | PSMC4 | 8613 | 0.024 | 0.43 | NO |
44 | MAGED1 | MAGED1 | MAGED1 | 8619 | 0.024 | 0.43 | NO |
45 | PSMD9 | PSMD9 | PSMD9 | 8908 | 0.016 | 0.42 | NO |
46 | PSMA2 | PSMA2 | PSMA2 | 8985 | 0.014 | 0.42 | NO |
47 | CASP9 | CASP9 | CASP9 | 9154 | 0.0099 | 0.41 | NO |
48 | PSMD1 | PSMD1 | PSMD1 | 9306 | 0.0062 | 0.4 | NO |
49 | PSMC6 | PSMC6 | PSMC6 | 10607 | -0.028 | 0.33 | NO |
50 | PSMD6 | PSMD6 | PSMD6 | 10711 | -0.03 | 0.33 | NO |
51 | PSME1 | PSME1 | PSME1 | 10788 | -0.032 | 0.33 | NO |
52 | PSMD8 | PSMD8 | PSMD8 | 11299 | -0.046 | 0.31 | NO |
53 | PSMD10 | PSMD10 | PSMD10 | 11913 | -0.064 | 0.29 | NO |
54 | APPL1 | APPL1 | APPL1 | 12571 | -0.085 | 0.27 | NO |
55 | DAPK2 | DAPK2 | DAPK2 | 14413 | -0.16 | 0.19 | NO |
Figure S133. 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 CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6.

Figure S134. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S68. 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 | PARVG | PARVG | PARVG | 254 | 0.82 | 0.11 | YES |
2 | SNAI1 | SNAI1 | SNAI1 | 459 | 0.72 | 0.2 | YES |
3 | PPP1R14C | PPP1R14C | PPP1R14C | 843 | 0.61 | 0.28 | YES |
4 | ACTN1 | ACTN1 | ACTN1 | 1597 | 0.46 | 0.3 | YES |
5 | ZYX | ZYX | ZYX | 1720 | 0.44 | 0.36 | YES |
6 | MYL9 | MYL9 | MYL9 | 1828 | 0.42 | 0.42 | YES |
7 | TACC3 | TACC3 | TACC3 | 2531 | 0.33 | 0.43 | YES |
8 | RHOG | RHOG | RHOG | 3270 | 0.26 | 0.43 | YES |
9 | PPP1R14B | PPP1R14B | PPP1R14B | 3843 | 0.21 | 0.43 | YES |
10 | AURKA | AURKA | AURKA | 4263 | 0.18 | 0.43 | YES |
11 | ZEB1 | ZEB1 | ZEB1 | 4324 | 0.18 | 0.45 | YES |
12 | NCK2 | NCK2 | NCK2 | 4793 | 0.15 | 0.45 | YES |
13 | PARVA | PARVA | PARVA | 5352 | 0.12 | 0.44 | YES |
14 | ILK | ILK | ILK | 5400 | 0.12 | 0.45 | YES |
15 | PPP1R14A | PPP1R14A | PPP1R14A | 5722 | 0.11 | 0.45 | YES |
16 | JUN | JUN | JUN | 6043 | 0.098 | 0.45 | YES |
17 | XPO1 | XPO1 | XPO1 | 6155 | 0.093 | 0.46 | YES |
18 | ILKAP | ILKAP | ILKAP | 6228 | 0.091 | 0.46 | YES |
19 | RUVBL2 | RUVBL2 | RUVBL2 | 6482 | 0.083 | 0.46 | YES |
20 | RAC1 | RAC1 | RAC1 | 6566 | 0.081 | 0.47 | YES |
21 | ELMO2 | ELMO2 | ELMO2 | 6868 | 0.072 | 0.46 | NO |
22 | CDC37 | CDC37 | CDC37 | 7288 | 0.06 | 0.45 | NO |
23 | CDC42 | CDC42 | CDC42 | 7685 | 0.048 | 0.44 | NO |
24 | PARP1 | PARP1 | PARP1 | 8214 | 0.035 | 0.41 | NO |
25 | IQGAP1 | IQGAP1 | IQGAP1 | 8389 | 0.03 | 0.4 | NO |
26 | NACA | NACA | NACA | 8498 | 0.027 | 0.4 | NO |
27 | RUVBL1 | RUVBL1 | RUVBL1 | 8541 | 0.026 | 0.4 | NO |
28 | CREB1 | CREB1 | CREB1 | 8797 | 0.019 | 0.39 | NO |
29 | LIMS2 | LIMS2 | LIMS2 | 9107 | 0.011 | 0.38 | NO |
30 | CKAP5 | CKAP5 | CKAP5 | 9124 | 0.01 | 0.38 | NO |
31 | PPP1R12A | PPP1R12A | PPP1R12A | 9509 | 0.00056 | 0.36 | NO |
32 | GIT2 | GIT2 | GIT2 | 9516 | 0.00045 | 0.36 | NO |
33 | CTNNB1 | CTNNB1 | CTNNB1 | 9851 | -0.0074 | 0.34 | NO |
34 | PXN | PXN | PXN | 10032 | -0.012 | 0.33 | NO |
35 | LIMS1 | LIMS1 | LIMS1 | 10206 | -0.017 | 0.32 | NO |
36 | CCND1 | CCND1 | CCND1 | 10392 | -0.022 | 0.32 | NO |
37 | AKT1 | AKT1 | AKT1 | 10438 | -0.023 | 0.32 | NO |
38 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 10852 | -0.034 | 0.3 | NO |
39 | DIAPH1 | DIAPH1 | DIAPH1 | 11220 | -0.044 | 0.28 | NO |
40 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 11423 | -0.049 | 0.28 | NO |
41 | GSK3B | GSK3B | GSK3B | 11561 | -0.053 | 0.28 | NO |
42 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 11945 | -0.065 | 0.27 | NO |
43 | PARVB | PARVB | PARVB | 12626 | -0.087 | 0.24 | NO |
44 | RICTOR | RICTOR | RICTOR | 12708 | -0.09 | 0.25 | NO |
45 | TNS1 | TNS1 | TNS1 | 15419 | -0.23 | 0.14 | NO |
Figure S135. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME REGULATION OF APOPTOSIS.

Figure S136. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME REGULATION OF APOPTOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S69. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | KDELR3 | KDELR3 | KDELR3 | 439 | 0.72 | 0.15 | YES |
2 | PDIA5 | PDIA5 | PDIA5 | 3147 | 0.27 | 0.058 | YES |
3 | SHC1 | SHC1 | SHC1 | 3268 | 0.26 | 0.11 | YES |
4 | WIPI1 | WIPI1 | WIPI1 | 3565 | 0.23 | 0.15 | YES |
5 | HDGF | HDGF | HDGF | 3599 | 0.23 | 0.2 | YES |
6 | LMNA | LMNA | LMNA | 3657 | 0.22 | 0.25 | YES |
7 | FKBP14 | FKBP14 | FKBP14 | 4542 | 0.16 | 0.24 | YES |
8 | ARFGAP1 | ARFGAP1 | ARFGAP1 | 4645 | 0.16 | 0.27 | YES |
9 | DDX11 | DDX11 | DDX11 | 4902 | 0.14 | 0.29 | YES |
10 | SULT1A3 | SULT1A3 | SULT1A3 | 5161 | 0.13 | 0.31 | YES |
11 | TPP1 | TPP1 | TPP1 | 5662 | 0.11 | 0.31 | YES |
12 | C19orf10 | C19orf10 | C19orf10 | 5830 | 0.11 | 0.32 | YES |
13 | PDIA6 | PDIA6 | PDIA6 | 6063 | 0.097 | 0.33 | YES |
14 | SSR1 | SSR1 | SSR1 | 6073 | 0.096 | 0.35 | YES |
15 | PREB | PREB | PREB | 6288 | 0.089 | 0.36 | YES |
16 | DNAJB11 | DNAJB11 | DNAJB11 | 6559 | 0.081 | 0.37 | YES |
17 | ZBTB17 | ZBTB17 | ZBTB17 | 6621 | 0.079 | 0.38 | YES |
18 | YIF1A | YIF1A | YIF1A | 6677 | 0.077 | 0.4 | YES |
19 | EXTL3 | EXTL3 | EXTL3 | 6722 | 0.076 | 0.41 | YES |
20 | SEC31A | SEC31A | SEC31A | 6937 | 0.07 | 0.42 | YES |
21 | KLHDC3 | KLHDC3 | KLHDC3 | 7272 | 0.06 | 0.41 | YES |
22 | DCTN1 | DCTN1 | DCTN1 | 7350 | 0.058 | 0.42 | YES |
23 | EDEM1 | EDEM1 | EDEM1 | 7384 | 0.057 | 0.43 | YES |
24 | SRPRB | SRPRB | SRPRB | 8001 | 0.04 | 0.41 | NO |
25 | GOSR2 | GOSR2 | GOSR2 | 8598 | 0.025 | 0.38 | NO |
26 | PPP2R5B | PPP2R5B | PPP2R5B | 8793 | 0.02 | 0.38 | NO |
27 | TATDN2 | TATDN2 | TATDN2 | 8837 | 0.018 | 0.38 | NO |
28 | TLN1 | TLN1 | TLN1 | 8875 | 0.017 | 0.38 | NO |
29 | CXXC1 | CXXC1 | CXXC1 | 9140 | 0.01 | 0.37 | NO |
30 | ACADVL | ACADVL | ACADVL | 9579 | -0.0011 | 0.34 | NO |
31 | XBP1 | XBP1 | XBP1 | 9632 | -0.0024 | 0.34 | NO |
32 | HYOU1 | HYOU1 | HYOU1 | 9802 | -0.0063 | 0.33 | NO |
33 | CUL7 | CUL7 | CUL7 | 9947 | -0.0098 | 0.33 | NO |
34 | ADD1 | ADD1 | ADD1 | 9980 | -0.011 | 0.33 | NO |
35 | DNAJC3 | DNAJC3 | DNAJC3 | 10052 | -0.013 | 0.33 | NO |
36 | WFS1 | WFS1 | WFS1 | 10073 | -0.013 | 0.33 | NO |
37 | SRPR | SRPR | SRPR | 10171 | -0.016 | 0.33 | NO |
38 | SERP1 | SERP1 | SERP1 | 10271 | -0.018 | 0.32 | NO |
39 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 10326 | -0.02 | 0.33 | NO |
40 | TSPYL2 | TSPYL2 | TSPYL2 | 10919 | -0.036 | 0.3 | NO |
41 | CTDSP2 | CTDSP2 | CTDSP2 | 11603 | -0.054 | 0.28 | NO |
42 | GSK3A | GSK3A | GSK3A | 11854 | -0.062 | 0.28 | NO |
43 | SYVN1 | SYVN1 | SYVN1 | 12031 | -0.067 | 0.28 | NO |
44 | DNAJB9 | DNAJB9 | DNAJB9 | 14786 | -0.18 | 0.17 | NO |
Figure S137. 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 CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION .

Figure S138. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION , this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S70. 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 | CDC6 | CDC6 | CDC6 | 1639 | 0.45 | -0.013 | YES |
2 | CDT1 | CDT1 | CDT1 | 1897 | 0.41 | 0.044 | YES |
3 | E2F2 | E2F2 | E2F2 | 2552 | 0.33 | 0.064 | YES |
4 | PSMB9 | PSMB9 | PSMB9 | 3583 | 0.23 | 0.046 | YES |
5 | MCM5 | MCM5 | MCM5 | 3703 | 0.22 | 0.077 | YES |
6 | MCM6 | MCM6 | MCM6 | 3775 | 0.21 | 0.11 | YES |
7 | E2F1 | E2F1 | E2F1 | 3827 | 0.21 | 0.14 | YES |
8 | RPS27A | RPS27A | RPS27A | 4385 | 0.17 | 0.14 | YES |
9 | PSMD4 | PSMD4 | PSMD4 | 4433 | 0.17 | 0.17 | YES |
10 | PSMB10 | PSMB10 | PSMB10 | 4455 | 0.17 | 0.2 | YES |
11 | MCM7 | MCM7 | MCM7 | 4908 | 0.14 | 0.2 | YES |
12 | PSMB3 | PSMB3 | PSMB3 | 4974 | 0.14 | 0.22 | YES |
13 | PSMD14 | PSMD14 | PSMD14 | 5003 | 0.14 | 0.24 | YES |
14 | PSMB2 | PSMB2 | PSMB2 | 5045 | 0.14 | 0.26 | YES |
15 | PSMA5 | PSMA5 | PSMA5 | 5096 | 0.14 | 0.28 | YES |
16 | E2F3 | E2F3 | E2F3 | 5259 | 0.13 | 0.3 | YES |
17 | PSMD13 | PSMD13 | PSMD13 | 5319 | 0.13 | 0.32 | YES |
18 | PSME4 | PSME4 | PSME4 | 5697 | 0.11 | 0.31 | YES |
19 | PSMD12 | PSMD12 | PSMD12 | 5708 | 0.11 | 0.33 | YES |
20 | PSMB4 | PSMB4 | PSMB4 | 5929 | 0.1 | 0.34 | YES |
21 | PSMB6 | PSMB6 | PSMB6 | 6126 | 0.094 | 0.34 | YES |
22 | PSMC1 | PSMC1 | PSMC1 | 6166 | 0.093 | 0.36 | YES |
23 | MCM2 | MCM2 | MCM2 | 6176 | 0.093 | 0.37 | YES |
24 | PSMC3 | PSMC3 | PSMC3 | 6255 | 0.09 | 0.38 | YES |
25 | PSMC5 | PSMC5 | PSMC5 | 6287 | 0.089 | 0.4 | YES |
26 | GMNN | GMNN | GMNN | 6291 | 0.089 | 0.41 | YES |
27 | PSMD11 | PSMD11 | PSMD11 | 6652 | 0.078 | 0.41 | YES |
28 | UBA52 | UBA52 | UBA52 | 6667 | 0.078 | 0.42 | YES |
29 | PSMD3 | PSMD3 | PSMD3 | 6694 | 0.077 | 0.43 | YES |
30 | PSMB1 | PSMB1 | PSMB1 | 6784 | 0.074 | 0.44 | YES |
31 | MCM4 | MCM4 | MCM4 | 7029 | 0.067 | 0.44 | YES |
32 | PSMA4 | PSMA4 | PSMA4 | 7102 | 0.064 | 0.44 | YES |
33 | PSME2 | PSME2 | PSME2 | 7203 | 0.062 | 0.45 | YES |
34 | PSMD2 | PSMD2 | PSMD2 | 7217 | 0.062 | 0.46 | YES |
35 | PSMD7 | PSMD7 | PSMD7 | 7536 | 0.052 | 0.45 | YES |
36 | PSMA1 | PSMA1 | PSMA1 | 7543 | 0.052 | 0.46 | YES |
37 | PSMC2 | PSMC2 | PSMC2 | 7551 | 0.052 | 0.47 | YES |
38 | PSMB8 | PSMB8 | PSMB8 | 7623 | 0.05 | 0.47 | YES |
39 | PSMA6 | PSMA6 | PSMA6 | 7727 | 0.048 | 0.48 | YES |
40 | PSMB7 | PSMB7 | PSMB7 | 7970 | 0.041 | 0.47 | YES |
41 | PSMF1 | PSMF1 | PSMF1 | 8065 | 0.038 | 0.47 | YES |
42 | MCM3 | MCM3 | MCM3 | 8067 | 0.038 | 0.48 | YES |
43 | PSMA7 | PSMA7 | PSMA7 | 8086 | 0.038 | 0.48 | YES |
44 | PSMD5 | PSMD5 | PSMD5 | 8091 | 0.038 | 0.49 | YES |
45 | PSMB5 | PSMB5 | PSMB5 | 8246 | 0.034 | 0.48 | NO |
46 | PSMA3 | PSMA3 | PSMA3 | 8564 | 0.025 | 0.47 | NO |
47 | PSMC4 | PSMC4 | PSMC4 | 8613 | 0.024 | 0.47 | NO |
48 | MCM8 | MCM8 | MCM8 | 8774 | 0.02 | 0.47 | NO |
49 | PSMD9 | PSMD9 | PSMD9 | 8908 | 0.016 | 0.46 | NO |
50 | PSMA2 | PSMA2 | PSMA2 | 8985 | 0.014 | 0.46 | NO |
51 | PSMD1 | PSMD1 | PSMD1 | 9306 | 0.0062 | 0.44 | NO |
52 | PSMC6 | PSMC6 | PSMC6 | 10607 | -0.028 | 0.38 | NO |
53 | PSMD6 | PSMD6 | PSMD6 | 10711 | -0.03 | 0.38 | NO |
54 | PSME1 | PSME1 | PSME1 | 10788 | -0.032 | 0.38 | NO |
55 | PSMD8 | PSMD8 | PSMD8 | 11299 | -0.046 | 0.36 | NO |
56 | PSMD10 | PSMD10 | PSMD10 | 11913 | -0.064 | 0.33 | NO |
Figure S139. 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 P53 DEPENDENT G1 DNA DAMAGE RESPONSE.

Figure S140. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
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Gene set database = c2.cp.v4.0.symbols.gmt
-
Expression data file = KICH-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Phenotype data file = KICH-TP.mergedcluster.txt
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.
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.