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 "COAD-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: 711 |
Number of samples: 457 |
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 - 4 :[ clus1 ] 129 |
pheno.type: 2 - 4 :[ clus2 ] 95 |
pheno.type: 3 - 4 :[ clus3 ] 98 |
pheno.type: 4 - 4 :[ clus4 ] 135 |
For the expression subtypes of 18012 genes in 458 samples, GSEA found enriched gene sets in each cluster using 457 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 KEGG LYSINE DEGRADATION, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RNA DEGRADATION, KEGG SPLICEOSOME, PID ATM PATHWAY, PID BARD1PATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME METABOLISM OF VITAMINS AND COFACTORS, REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM
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And common core enriched genes are CDC40, CPSF1, CPSF3, MAGOH, NCBP1, NCBP2, UPF3B, CLP1, CPSF2, CPSF7
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clus2
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Top enriched gene sets are KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG BASE EXCISION REPAIR, BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA TNFR1 PATHWAY, PID TRAIL PATHWAY
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And common core enriched genes are MAPK8, CASP8, MDM2, CASP3, CASP7, FAS, LMNA, LMNB1, PARP1, RIPK1
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clus3
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Top enriched gene sets are KEGG TRYPTOPHAN METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG ABC TRANSPORTERS, KEGG MAPK SIGNALING PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION
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And common core enriched genes are PIK3CA, AKT3, PIK3CD, PIK3R5, IRS1, MAPK11, PIK3R1, PREX1, RAPGEF1, RPS6KA2
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clus4
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Top enriched gene sets are KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG PARKINSONS DISEASE, KEGG PATHOGENIC ESCHERICHIA COLI INFECTION, KEGG SYSTEMIC LUPUS ERYTHEMATOSUS, REACTOME TRANSLATION, REACTOME MEIOSIS, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME RNA POL I TRANSCRIPTION, REACTOME PROTEIN FOLDING, REACTOME METABOLISM OF PROTEINS
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And common core enriched genes are HIST1H2AB, HIST1H2AJ, HIST1H2BC, HIST1H2BE, HIST1H2BG, HIST1H2BH, HIST1H2BI, HIST1H2BJ, HIST1H2BL, HIST1H2BN
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 |
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KEGG LYSINE DEGRADATION | 44 | genes.ES.table | 0.48 | 1.9 | 0.0085 | 0.57 | 0.26 | 0.46 | 0.29 | 0.32 | 0 | 0.099 |
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.4 | 1.5 | 0.12 | 0.61 | 0.97 | 0.66 | 0.38 | 0.41 | 0.39 | 0.18 |
KEGG RNA DEGRADATION | 56 | genes.ES.table | 0.37 | 1.5 | 0.12 | 0.61 | 0.97 | 0.71 | 0.41 | 0.42 | 0.38 | 0.18 |
KEGG SPLICEOSOME | 114 | genes.ES.table | 0.36 | 1.6 | 0.084 | 0.49 | 0.89 | 0.57 | 0.36 | 0.37 | 0.22 | 0.13 |
PID ATM PATHWAY | 34 | genes.ES.table | 0.5 | 1.6 | 0.062 | 0.49 | 0.88 | 0.71 | 0.35 | 0.46 | 0.2 | 0.12 |
PID BARD1PATHWAY | 29 | genes.ES.table | 0.52 | 1.6 | 0.081 | 0.53 | 0.93 | 0.41 | 0.21 | 0.33 | 0.28 | 0.15 |
REACTOME METABOLISM OF NON CODING RNA | 47 | genes.ES.table | 0.45 | 1.6 | 0.088 | 0.5 | 0.93 | 0.72 | 0.36 | 0.47 | 0.26 | 0.13 |
REACTOME METABOLISM OF VITAMINS AND COFACTORS | 50 | genes.ES.table | 0.41 | 1.5 | 0.05 | 0.5 | 0.94 | 0.22 | 0.11 | 0.2 | 0.27 | 0.14 |
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA | 126 | genes.ES.table | 0.42 | 1.7 | 0.062 | 0.46 | 0.78 | 0.59 | 0.39 | 0.36 | 0.15 | 0.11 |
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM | 44 | genes.ES.table | 0.5 | 1.7 | 0.026 | 0.47 | 0.67 | 0.64 | 0.37 | 0.4 | 0.12 | 0.11 |
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 | PIPOX | PIPOX | PIPOX | 100 | 0.37 | 0.14 | YES |
2 | OGDHL | OGDHL | OGDHL | 238 | 0.29 | 0.25 | YES |
3 | SETDB2 | SETDB2 | SETDB2 | 993 | 0.17 | 0.27 | YES |
4 | SETMAR | SETMAR | SETMAR | 1950 | 0.11 | 0.26 | YES |
5 | TMLHE | TMLHE | TMLHE | 2171 | 0.1 | 0.29 | YES |
6 | AASDHPPT | AASDHPPT | AASDHPPT | 2416 | 0.095 | 0.31 | YES |
7 | AADAT | AADAT | AADAT | 2658 | 0.089 | 0.33 | YES |
8 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 3423 | 0.071 | 0.32 | YES |
9 | SETD2 | SETD2 | SETD2 | 3480 | 0.069 | 0.34 | YES |
10 | SUV39H2 | SUV39H2 | SUV39H2 | 3540 | 0.068 | 0.36 | YES |
11 | ASH1L | ASH1L | ASH1L | 3541 | 0.068 | 0.39 | YES |
12 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 4112 | 0.057 | 0.38 | YES |
13 | AASS | AASS | AASS | 4145 | 0.057 | 0.4 | YES |
14 | ACAT1 | ACAT1 | ACAT1 | 4254 | 0.055 | 0.42 | YES |
15 | ACAT2 | ACAT2 | ACAT2 | 4373 | 0.054 | 0.43 | YES |
16 | WHSC1L1 | WHSC1L1 | WHSC1L1 | 4549 | 0.05 | 0.44 | YES |
17 | SUV39H1 | SUV39H1 | SUV39H1 | 4577 | 0.05 | 0.46 | YES |
18 | SUV420H1 | SUV420H1 | SUV420H1 | 4703 | 0.048 | 0.47 | YES |
19 | PLOD2 | PLOD2 | PLOD2 | 5117 | 0.042 | 0.46 | YES |
20 | AASDH | AASDH | AASDH | 5164 | 0.041 | 0.48 | YES |
21 | SETDB1 | SETDB1 | SETDB1 | 5661 | 0.034 | 0.46 | NO |
22 | SETD1A | SETD1A | SETD1A | 6204 | 0.027 | 0.44 | NO |
23 | EHMT2 | EHMT2 | EHMT2 | 6691 | 0.021 | 0.43 | NO |
24 | ALDH2 | ALDH2 | ALDH2 | 6738 | 0.021 | 0.43 | NO |
25 | PLOD3 | PLOD3 | PLOD3 | 6912 | 0.018 | 0.43 | NO |
26 | HADHA | HADHA | HADHA | 7421 | 0.012 | 0.41 | NO |
27 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 7529 | 0.011 | 0.4 | NO |
28 | WHSC1 | WHSC1 | WHSC1 | 7684 | 0.0092 | 0.4 | NO |
29 | GCDH | GCDH | GCDH | 7698 | 0.009 | 0.4 | NO |
30 | HADH | HADH | HADH | 7757 | 0.0082 | 0.4 | NO |
31 | SUV420H2 | SUV420H2 | SUV420H2 | 7953 | 0.0057 | 0.39 | NO |
32 | SETD1B | SETD1B | SETD1B | 8596 | -0.0025 | 0.36 | NO |
33 | NSD1 | NSD1 | NSD1 | 8799 | -0.0052 | 0.35 | NO |
34 | EHHADH | EHHADH | EHHADH | 9061 | -0.0086 | 0.34 | NO |
35 | BBOX1 | BBOX1 | BBOX1 | 9227 | -0.011 | 0.33 | NO |
36 | OGDH | OGDH | OGDH | 9394 | -0.014 | 0.33 | NO |
37 | SETD8 | SETD8 | SETD8 | 9509 | -0.015 | 0.33 | NO |
38 | EHMT1 | EHMT1 | EHMT1 | 10089 | -0.023 | 0.3 | NO |
39 | SETD7 | SETD7 | SETD7 | 10874 | -0.037 | 0.28 | NO |
40 | ECHS1 | ECHS1 | ECHS1 | 11028 | -0.04 | 0.28 | NO |
41 | DOT1L | DOT1L | DOT1L | 11685 | -0.053 | 0.27 | NO |
42 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 11981 | -0.06 | 0.27 | NO |
43 | DLST | DLST | DLST | 12569 | -0.075 | 0.27 | NO |
44 | PLOD1 | PLOD1 | PLOD1 | 12741 | -0.08 | 0.29 | NO |
Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG LYSINE DEGRADATION.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_LYSINE_DEGRADATION.heatmap_plot.clus1.1.png)
Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_LYSINE_DEGRADATION.volcano_plot.clus1.1.png)
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 |
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1 | CAB39L | CAB39L | CAB39L | 86 | 0.38 | 0.27 | YES |
2 | PRKAA2 | PRKAA2 | PRKAA2 | 1176 | 0.15 | 0.32 | YES |
3 | STRADB | STRADB | STRADB | 1729 | 0.12 | 0.38 | YES |
4 | RHEB | RHEB | RHEB | 2124 | 0.1 | 0.43 | YES |
5 | PDE3B | PDE3B | PDE3B | 2317 | 0.098 | 0.49 | YES |
6 | PRKAB1 | PRKAB1 | PRKAB1 | 3671 | 0.066 | 0.46 | NO |
7 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 4631 | 0.049 | 0.44 | NO |
8 | PRKAA1 | PRKAA1 | PRKAA1 | 5150 | 0.041 | 0.44 | NO |
9 | TSC1 | TSC1 | TSC1 | 5213 | 0.04 | 0.47 | NO |
10 | RPS6 | RPS6 | RPS6 | 5510 | 0.036 | 0.48 | NO |
11 | EEF2K | EEF2K | EEF2K | 6037 | 0.03 | 0.47 | NO |
12 | PRKAB2 | PRKAB2 | PRKAB2 | 6462 | 0.024 | 0.47 | NO |
13 | CAB39 | CAB39 | CAB39 | 6967 | 0.018 | 0.45 | NO |
14 | RPTOR | RPTOR | RPTOR | 7378 | 0.013 | 0.44 | NO |
15 | TSC2 | TSC2 | TSC2 | 7461 | 0.012 | 0.44 | NO |
16 | EIF4B | EIF4B | EIF4B | 7650 | 0.0096 | 0.44 | NO |
17 | AKT2 | AKT2 | AKT2 | 8144 | 0.0031 | 0.41 | NO |
18 | PRKAG2 | PRKAG2 | PRKAG2 | 8350 | 0.00061 | 0.4 | NO |
19 | EIF4G1 | EIF4G1 | EIF4G1 | 8545 | -0.002 | 0.39 | NO |
20 | PRKAG1 | PRKAG1 | PRKAG1 | 8710 | -0.004 | 0.38 | NO |
21 | EIF4E | EIF4E | EIF4E | 8948 | -0.0071 | 0.38 | NO |
22 | STK11 | STK11 | STK11 | 9615 | -0.016 | 0.35 | NO |
23 | MLST8 | MLST8 | MLST8 | 10168 | -0.024 | 0.34 | NO |
24 | PPM1A | PPM1A | PPM1A | 10314 | -0.026 | 0.35 | NO |
25 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 10346 | -0.027 | 0.37 | NO |
26 | MTOR | MTOR | MTOR | 10708 | -0.034 | 0.37 | NO |
27 | STRADA | STRADA | STRADA | 11366 | -0.046 | 0.37 | NO |
Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.heatmap_plot.clus1.20.png)
Figure S4. 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
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_PKB_MEDIATED_EVENTS.volcano_plot.clus1.2.png)
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 | UPF3B | UPF3B | UPF3B | 1365 | 0.14 | 0.023 | YES |
2 | NCBP2 | NCBP2 | NCBP2 | 2076 | 0.11 | 0.059 | YES |
3 | CSTF3 | CSTF3 | CSTF3 | 2962 | 0.081 | 0.067 | YES |
4 | PCF11 | PCF11 | PCF11 | 3149 | 0.077 | 0.11 | YES |
5 | SNRPE | SNRPE | SNRPE | 3183 | 0.076 | 0.16 | YES |
6 | CSTF1 | CSTF1 | CSTF1 | 3388 | 0.071 | 0.2 | YES |
7 | MAGOH | MAGOH | MAGOH | 3950 | 0.06 | 0.22 | YES |
8 | ZNF473 | ZNF473 | ZNF473 | 3991 | 0.06 | 0.26 | YES |
9 | CPSF3 | CPSF3 | CPSF3 | 3999 | 0.059 | 0.3 | YES |
10 | SNRPG | SNRPG | SNRPG | 4015 | 0.059 | 0.34 | YES |
11 | NUDT21 | NUDT21 | NUDT21 | 4247 | 0.056 | 0.36 | YES |
12 | CSTF2 | CSTF2 | CSTF2 | 4525 | 0.051 | 0.38 | YES |
13 | LSM11 | LSM11 | LSM11 | 4653 | 0.048 | 0.41 | YES |
14 | CDC40 | CDC40 | CDC40 | 4800 | 0.046 | 0.44 | YES |
15 | PAPOLA | PAPOLA | PAPOLA | 4918 | 0.044 | 0.46 | YES |
16 | NCBP1 | NCBP1 | NCBP1 | 4932 | 0.044 | 0.49 | YES |
17 | CPSF1 | CPSF1 | CPSF1 | 5456 | 0.037 | 0.49 | YES |
18 | SNRPF | SNRPF | SNRPF | 5954 | 0.031 | 0.48 | YES |
19 | SNRPD3 | SNRPD3 | SNRPD3 | 6100 | 0.029 | 0.5 | YES |
20 | SNRPB | SNRPB | SNRPB | 6420 | 0.024 | 0.5 | YES |
21 | CPSF7 | CPSF7 | CPSF7 | 6434 | 0.024 | 0.51 | YES |
22 | SLBP | SLBP | SLBP | 6561 | 0.023 | 0.52 | YES |
23 | NFX1 | NFX1 | NFX1 | 6904 | 0.018 | 0.52 | YES |
24 | CPSF2 | CPSF2 | CPSF2 | 7078 | 0.016 | 0.52 | YES |
25 | RNPS1 | RNPS1 | RNPS1 | 7259 | 0.014 | 0.52 | YES |
26 | PABPN1 | PABPN1 | PABPN1 | 7291 | 0.014 | 0.52 | YES |
27 | U2AF2 | U2AF2 | U2AF2 | 7456 | 0.012 | 0.52 | YES |
28 | THOC4 | THOC4 | THOC4 | 7488 | 0.011 | 0.53 | YES |
29 | CLP1 | CLP1 | CLP1 | 7541 | 0.011 | 0.54 | YES |
30 | DHX38 | DHX38 | DHX38 | 7758 | 0.0082 | 0.53 | NO |
31 | U2AF1 | U2AF1 | U2AF1 | 7933 | 0.006 | 0.52 | NO |
32 | SRRM1 | SRRM1 | SRRM1 | 8564 | -0.0022 | 0.49 | NO |
33 | RBM8A | RBM8A | RBM8A | 8834 | -0.0056 | 0.48 | NO |
34 | LSM10 | LSM10 | LSM10 | 11223 | -0.043 | 0.38 | NO |
Figure S5. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA DEGRADATION.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_RNA_DEGRADATION.heatmap_plot.clus1.19.png)
Figure S6. 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
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATION_REGION_.volcano_plot.clus1.3.png)
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 | UPF3B | UPF3B | UPF3B | 1365 | 0.14 | 0.061 | YES |
2 | NCBP2 | NCBP2 | NCBP2 | 2076 | 0.11 | 0.13 | YES |
3 | CSTF3 | CSTF3 | CSTF3 | 2962 | 0.081 | 0.16 | YES |
4 | PCF11 | PCF11 | PCF11 | 3149 | 0.077 | 0.22 | YES |
5 | CSTF1 | CSTF1 | CSTF1 | 3388 | 0.071 | 0.28 | YES |
6 | MAGOH | MAGOH | MAGOH | 3950 | 0.06 | 0.31 | YES |
7 | CPSF3 | CPSF3 | CPSF3 | 3999 | 0.059 | 0.36 | YES |
8 | NUDT21 | NUDT21 | NUDT21 | 4247 | 0.056 | 0.4 | YES |
9 | CSTF2 | CSTF2 | CSTF2 | 4525 | 0.051 | 0.44 | YES |
10 | CDC40 | CDC40 | CDC40 | 4800 | 0.046 | 0.47 | YES |
11 | PAPOLA | PAPOLA | PAPOLA | 4918 | 0.044 | 0.51 | YES |
12 | NCBP1 | NCBP1 | NCBP1 | 4932 | 0.044 | 0.55 | YES |
13 | CPSF1 | CPSF1 | CPSF1 | 5456 | 0.037 | 0.56 | YES |
14 | CPSF7 | CPSF7 | CPSF7 | 6434 | 0.024 | 0.53 | YES |
15 | NFX1 | NFX1 | NFX1 | 6904 | 0.018 | 0.52 | YES |
16 | CPSF2 | CPSF2 | CPSF2 | 7078 | 0.016 | 0.52 | YES |
17 | RNPS1 | RNPS1 | RNPS1 | 7259 | 0.014 | 0.53 | YES |
18 | PABPN1 | PABPN1 | PABPN1 | 7291 | 0.014 | 0.54 | YES |
19 | U2AF2 | U2AF2 | U2AF2 | 7456 | 0.012 | 0.54 | YES |
20 | THOC4 | THOC4 | THOC4 | 7488 | 0.011 | 0.55 | YES |
21 | CLP1 | CLP1 | CLP1 | 7541 | 0.011 | 0.56 | YES |
22 | DHX38 | DHX38 | DHX38 | 7758 | 0.0082 | 0.56 | NO |
23 | U2AF1 | U2AF1 | U2AF1 | 7933 | 0.006 | 0.55 | NO |
24 | SRRM1 | SRRM1 | SRRM1 | 8564 | -0.0022 | 0.52 | NO |
25 | RBM8A | RBM8A | RBM8A | 8834 | -0.0056 | 0.51 | NO |
Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SPLICEOSOME.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_SPLICEOSOME.heatmap_plot.clus1.11.png)
Figure S8. 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
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_MRNA_3_END_PROCESSING.volcano_plot.clus1.4.png)
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 | RAE1 | RAE1 | RAE1 | 1357 | 0.14 | -0.00012 | YES |
2 | UPF3B | UPF3B | UPF3B | 1365 | 0.14 | 0.075 | YES |
3 | NUPL2 | NUPL2 | NUPL2 | 1542 | 0.13 | 0.14 | YES |
4 | NCBP2 | NCBP2 | NCBP2 | 2076 | 0.11 | 0.16 | YES |
5 | NUP35 | NUP35 | NUP35 | 2511 | 0.093 | 0.19 | YES |
6 | NUPL1 | NUPL1 | NUPL1 | 3230 | 0.075 | 0.19 | YES |
7 | NUP107 | NUP107 | NUP107 | 3525 | 0.069 | 0.21 | YES |
8 | NUP155 | NUP155 | NUP155 | 3758 | 0.064 | 0.23 | YES |
9 | MAGOH | MAGOH | MAGOH | 3950 | 0.06 | 0.25 | YES |
10 | CPSF3 | CPSF3 | CPSF3 | 3999 | 0.059 | 0.28 | YES |
11 | NUP43 | NUP43 | NUP43 | 4280 | 0.055 | 0.3 | YES |
12 | NUP153 | NUP153 | NUP153 | 4501 | 0.051 | 0.31 | YES |
13 | NUP205 | NUP205 | NUP205 | 4664 | 0.048 | 0.33 | YES |
14 | NUP54 | NUP54 | NUP54 | 4668 | 0.048 | 0.36 | YES |
15 | CDC40 | CDC40 | CDC40 | 4800 | 0.046 | 0.37 | YES |
16 | NUP133 | NUP133 | NUP133 | 4903 | 0.044 | 0.39 | YES |
17 | NCBP1 | NCBP1 | NCBP1 | 4932 | 0.044 | 0.41 | YES |
18 | NUP210 | NUP210 | NUP210 | 5057 | 0.042 | 0.43 | YES |
19 | TPR | TPR | TPR | 5282 | 0.039 | 0.44 | YES |
20 | NUP85 | NUP85 | NUP85 | 5364 | 0.038 | 0.46 | YES |
21 | CPSF1 | CPSF1 | CPSF1 | 5456 | 0.037 | 0.47 | YES |
22 | RANBP2 | RANBP2 | RANBP2 | 5521 | 0.036 | 0.49 | YES |
23 | NUP37 | NUP37 | NUP37 | 5788 | 0.033 | 0.49 | YES |
24 | NUP214 | NUP214 | NUP214 | 6043 | 0.03 | 0.49 | YES |
25 | POM121 | POM121 | POM121 | 6409 | 0.024 | 0.48 | YES |
26 | SLBP | SLBP | SLBP | 6561 | 0.023 | 0.49 | YES |
27 | NXF1 | NXF1 | NXF1 | 6614 | 0.022 | 0.5 | YES |
28 | NUP93 | NUP93 | NUP93 | 6716 | 0.021 | 0.5 | YES |
29 | NFX1 | NFX1 | NFX1 | 6904 | 0.018 | 0.5 | NO |
30 | CPSF2 | CPSF2 | CPSF2 | 7078 | 0.016 | 0.5 | NO |
31 | RNPS1 | RNPS1 | RNPS1 | 7259 | 0.014 | 0.5 | NO |
32 | U2AF2 | U2AF2 | U2AF2 | 7456 | 0.012 | 0.49 | NO |
33 | THOC4 | THOC4 | THOC4 | 7488 | 0.011 | 0.5 | NO |
34 | DHX38 | DHX38 | DHX38 | 7758 | 0.0082 | 0.49 | NO |
35 | U2AF1 | U2AF1 | U2AF1 | 7933 | 0.006 | 0.48 | NO |
36 | NUP88 | NUP88 | NUP88 | 8482 | -0.0011 | 0.45 | NO |
37 | SRRM1 | SRRM1 | SRRM1 | 8564 | -0.0022 | 0.45 | NO |
38 | NUP50 | NUP50 | NUP50 | 8610 | -0.0027 | 0.45 | NO |
39 | RBM8A | RBM8A | RBM8A | 8834 | -0.0056 | 0.44 | NO |
40 | EIF4E | EIF4E | EIF4E | 8948 | -0.0071 | 0.44 | NO |
41 | AAAS | AAAS | AAAS | 9214 | -0.011 | 0.43 | NO |
42 | NUP62 | NUP62 | NUP62 | 9934 | -0.021 | 0.4 | NO |
43 | NUP188 | NUP188 | NUP188 | 11002 | -0.039 | 0.36 | NO |
44 | SEH1L | SEH1L | SEH1L | 11799 | -0.056 | 0.34 | 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: PID ATM PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.PID_ATM_PATHWAY.heatmap_plot.clus1.10.png)
Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: PID ATM PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM.volcano_plot.clus1.5.png)
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 | A1CF | A1CF | A1CF | 190 | 0.31 | 0.042 | YES |
2 | GTF2F2 | GTF2F2 | GTF2F2 | 1053 | 0.16 | 0.02 | YES |
3 | RAE1 | RAE1 | RAE1 | 1357 | 0.14 | 0.027 | YES |
4 | UPF3B | UPF3B | UPF3B | 1365 | 0.14 | 0.05 | YES |
5 | NUPL2 | NUPL2 | NUPL2 | 1542 | 0.13 | 0.062 | YES |
6 | POLR2K | POLR2K | POLR2K | 1800 | 0.12 | 0.067 | YES |
7 | PRPF6 | PRPF6 | PRPF6 | 1959 | 0.11 | 0.077 | YES |
8 | NCBP2 | NCBP2 | NCBP2 | 2076 | 0.11 | 0.088 | YES |
9 | CCAR1 | CCAR1 | CCAR1 | 2395 | 0.096 | 0.087 | YES |
10 | SNRPB2 | SNRPB2 | SNRPB2 | 2470 | 0.094 | 0.098 | YES |
11 | NUP35 | NUP35 | NUP35 | 2511 | 0.093 | 0.11 | YES |
12 | CSTF3 | CSTF3 | CSTF3 | 2962 | 0.081 | 0.1 | YES |
13 | CCNH | CCNH | CCNH | 3007 | 0.08 | 0.11 | YES |
14 | PCF11 | PCF11 | PCF11 | 3149 | 0.077 | 0.12 | YES |
15 | SNRPE | SNRPE | SNRPE | 3183 | 0.076 | 0.13 | YES |
16 | SNRPA1 | SNRPA1 | SNRPA1 | 3214 | 0.075 | 0.14 | YES |
17 | NUPL1 | NUPL1 | NUPL1 | 3230 | 0.075 | 0.15 | YES |
18 | CDK7 | CDK7 | CDK7 | 3253 | 0.074 | 0.16 | YES |
19 | SF3B14 | SF3B14 | SF3B14 | 3355 | 0.072 | 0.17 | YES |
20 | CSTF1 | CSTF1 | CSTF1 | 3388 | 0.071 | 0.18 | YES |
21 | NUP107 | NUP107 | NUP107 | 3525 | 0.069 | 0.18 | YES |
22 | NUP155 | NUP155 | NUP155 | 3758 | 0.064 | 0.18 | YES |
23 | MAGOH | MAGOH | MAGOH | 3950 | 0.06 | 0.18 | YES |
24 | ZNF473 | ZNF473 | ZNF473 | 3991 | 0.06 | 0.19 | YES |
25 | CPSF3 | CPSF3 | CPSF3 | 3999 | 0.059 | 0.2 | YES |
26 | SNRPG | SNRPG | SNRPG | 4015 | 0.059 | 0.2 | YES |
27 | GTF2H1 | GTF2H1 | GTF2H1 | 4087 | 0.058 | 0.21 | YES |
28 | NUDT21 | NUDT21 | NUDT21 | 4247 | 0.056 | 0.21 | YES |
29 | NUP43 | NUP43 | NUP43 | 4280 | 0.055 | 0.22 | YES |
30 | NUP153 | NUP153 | NUP153 | 4501 | 0.051 | 0.22 | YES |
31 | CSTF2 | CSTF2 | CSTF2 | 4525 | 0.051 | 0.22 | YES |
32 | LSM11 | LSM11 | LSM11 | 4653 | 0.048 | 0.22 | YES |
33 | POLR2D | POLR2D | POLR2D | 4656 | 0.048 | 0.23 | YES |
34 | NUP205 | NUP205 | NUP205 | 4664 | 0.048 | 0.24 | YES |
35 | NUP54 | NUP54 | NUP54 | 4668 | 0.048 | 0.25 | YES |
36 | POLR2J | POLR2J | POLR2J | 4680 | 0.048 | 0.25 | YES |
37 | RBMX | RBMX | RBMX | 4733 | 0.047 | 0.26 | YES |
38 | ERCC3 | ERCC3 | ERCC3 | 4792 | 0.046 | 0.26 | YES |
39 | CDC40 | CDC40 | CDC40 | 4800 | 0.046 | 0.27 | YES |
40 | NUP133 | NUP133 | NUP133 | 4903 | 0.044 | 0.27 | YES |
41 | PAPOLA | PAPOLA | PAPOLA | 4918 | 0.044 | 0.28 | YES |
42 | NCBP1 | NCBP1 | NCBP1 | 4932 | 0.044 | 0.29 | YES |
43 | NUP210 | NUP210 | NUP210 | 5057 | 0.042 | 0.29 | YES |
44 | POLR2F | POLR2F | POLR2F | 5244 | 0.04 | 0.28 | YES |
45 | HNRNPK | HNRNPK | HNRNPK | 5260 | 0.039 | 0.29 | YES |
46 | TPR | TPR | TPR | 5282 | 0.039 | 0.29 | YES |
47 | HNRNPH2 | HNRNPH2 | HNRNPH2 | 5325 | 0.039 | 0.3 | YES |
48 | SF3B1 | SF3B1 | SF3B1 | 5354 | 0.038 | 0.3 | YES |
49 | NUP85 | NUP85 | NUP85 | 5364 | 0.038 | 0.31 | YES |
50 | HNRNPA2B1 | HNRNPA2B1 | HNRNPA2B1 | 5419 | 0.037 | 0.31 | YES |
51 | CPSF1 | CPSF1 | CPSF1 | 5456 | 0.037 | 0.32 | YES |
52 | HNRNPU | HNRNPU | HNRNPU | 5470 | 0.037 | 0.32 | YES |
53 | RANBP2 | RANBP2 | RANBP2 | 5521 | 0.036 | 0.32 | YES |
54 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 5581 | 0.036 | 0.33 | YES |
55 | SNRNP200 | SNRNP200 | SNRNP200 | 5599 | 0.035 | 0.33 | YES |
56 | POLR2C | POLR2C | POLR2C | 5689 | 0.034 | 0.33 | YES |
57 | NUP37 | NUP37 | NUP37 | 5788 | 0.033 | 0.33 | YES |
58 | SF3B3 | SF3B3 | SF3B3 | 5809 | 0.032 | 0.34 | YES |
59 | SMC1A | SMC1A | SMC1A | 5861 | 0.032 | 0.34 | YES |
60 | SNRPF | SNRPF | SNRPF | 5954 | 0.031 | 0.34 | YES |
61 | NUP214 | NUP214 | NUP214 | 6043 | 0.03 | 0.34 | YES |
62 | SF3B2 | SF3B2 | SF3B2 | 6070 | 0.029 | 0.34 | YES |
63 | SNRPD3 | SNRPD3 | SNRPD3 | 6100 | 0.029 | 0.35 | YES |
64 | HNRNPD | HNRNPD | HNRNPD | 6103 | 0.029 | 0.35 | YES |
65 | CD2BP2 | CD2BP2 | CD2BP2 | 6267 | 0.026 | 0.35 | YES |
66 | SNRPD2 | SNRPD2 | SNRPD2 | 6320 | 0.026 | 0.35 | YES |
67 | MNAT1 | MNAT1 | MNAT1 | 6332 | 0.026 | 0.35 | YES |
68 | POM121 | POM121 | POM121 | 6409 | 0.024 | 0.35 | YES |
69 | SNRPB | SNRPB | SNRPB | 6420 | 0.024 | 0.36 | YES |
70 | SNRPA | SNRPA | SNRPA | 6425 | 0.024 | 0.36 | YES |
71 | CPSF7 | CPSF7 | CPSF7 | 6434 | 0.024 | 0.36 | YES |
72 | SLBP | SLBP | SLBP | 6561 | 0.023 | 0.36 | YES |
73 | NXF1 | NXF1 | NXF1 | 6614 | 0.022 | 0.36 | YES |
74 | HNRNPUL1 | HNRNPUL1 | HNRNPUL1 | 6670 | 0.022 | 0.36 | YES |
75 | RBM5 | RBM5 | RBM5 | 6698 | 0.021 | 0.36 | YES |
76 | HNRNPL | HNRNPL | HNRNPL | 6711 | 0.021 | 0.36 | YES |
77 | NUP93 | NUP93 | NUP93 | 6716 | 0.021 | 0.37 | YES |
78 | HNRNPR | HNRNPR | HNRNPR | 6737 | 0.021 | 0.37 | YES |
79 | EFTUD2 | EFTUD2 | EFTUD2 | 6764 | 0.02 | 0.37 | YES |
80 | HNRNPH1 | HNRNPH1 | HNRNPH1 | 6895 | 0.018 | 0.37 | NO |
81 | NFX1 | NFX1 | NFX1 | 6904 | 0.018 | 0.37 | NO |
82 | DHX9 | DHX9 | DHX9 | 6940 | 0.018 | 0.37 | NO |
83 | CPSF2 | CPSF2 | CPSF2 | 7078 | 0.016 | 0.37 | NO |
84 | APOBEC1 | APOBEC1 | APOBEC1 | 7142 | 0.016 | 0.37 | NO |
85 | FUS | FUS | FUS | 7198 | 0.015 | 0.37 | NO |
86 | SF3A3 | SF3A3 | SF3A3 | 7212 | 0.015 | 0.37 | NO |
87 | YBX1 | YBX1 | YBX1 | 7248 | 0.014 | 0.37 | NO |
88 | RNPS1 | RNPS1 | RNPS1 | 7259 | 0.014 | 0.37 | NO |
89 | PABPN1 | PABPN1 | PABPN1 | 7291 | 0.014 | 0.37 | NO |
90 | GTF2H3 | GTF2H3 | GTF2H3 | 7411 | 0.012 | 0.37 | NO |
91 | U2AF2 | U2AF2 | U2AF2 | 7456 | 0.012 | 0.37 | NO |
92 | THOC4 | THOC4 | THOC4 | 7488 | 0.011 | 0.37 | NO |
93 | POLR2H | POLR2H | POLR2H | 7501 | 0.011 | 0.37 | NO |
94 | CLP1 | CLP1 | CLP1 | 7541 | 0.011 | 0.37 | NO |
95 | HNRNPF | HNRNPF | HNRNPF | 7626 | 0.0098 | 0.36 | NO |
96 | PTBP1 | PTBP1 | PTBP1 | 7638 | 0.0097 | 0.36 | NO |
97 | RNGTT | RNGTT | RNGTT | 7652 | 0.0095 | 0.37 | NO |
98 | NHP2L1 | NHP2L1 | NHP2L1 | 7668 | 0.0094 | 0.37 | NO |
99 | SNRNP70 | SNRNP70 | SNRNP70 | 7724 | 0.0086 | 0.36 | NO |
100 | DHX38 | DHX38 | DHX38 | 7758 | 0.0082 | 0.36 | NO |
101 | SF3A2 | SF3A2 | SF3A2 | 7778 | 0.0079 | 0.36 | NO |
102 | POLR2B | POLR2B | POLR2B | 7828 | 0.0073 | 0.36 | NO |
103 | SF3B4 | SF3B4 | SF3B4 | 7850 | 0.007 | 0.36 | NO |
104 | U2AF1 | U2AF1 | U2AF1 | 7933 | 0.006 | 0.36 | NO |
105 | HNRNPC | HNRNPC | HNRNPC | 7981 | 0.0053 | 0.36 | NO |
106 | HNRNPA0 | HNRNPA0 | HNRNPA0 | 7986 | 0.0052 | 0.36 | NO |
107 | GTF2F1 | GTF2F1 | GTF2F1 | 8007 | 0.005 | 0.36 | NO |
108 | DNAJC8 | DNAJC8 | DNAJC8 | 8048 | 0.0045 | 0.36 | NO |
109 | DDX23 | DDX23 | DDX23 | 8107 | 0.0036 | 0.35 | NO |
110 | PRPF4 | PRPF4 | PRPF4 | 8362 | 0.00039 | 0.34 | NO |
111 | PCBP1 | PCBP1 | PCBP1 | 8476 | -0.001 | 0.33 | NO |
112 | NUP88 | NUP88 | NUP88 | 8482 | -0.0011 | 0.33 | NO |
113 | SRRM1 | SRRM1 | SRRM1 | 8564 | -0.0022 | 0.33 | NO |
114 | METTL3 | METTL3 | METTL3 | 8580 | -0.0024 | 0.33 | NO |
115 | NUP50 | NUP50 | NUP50 | 8610 | -0.0027 | 0.33 | NO |
116 | POLR2G | POLR2G | POLR2G | 8691 | -0.0037 | 0.32 | NO |
117 | RBM8A | RBM8A | RBM8A | 8834 | -0.0056 | 0.32 | NO |
118 | HNRNPM | HNRNPM | HNRNPM | 8851 | -0.0058 | 0.32 | NO |
119 | EIF4E | EIF4E | EIF4E | 8948 | -0.0071 | 0.31 | NO |
120 | PCBP2 | PCBP2 | PCBP2 | 9165 | -0.01 | 0.3 | NO |
121 | AAAS | AAAS | AAAS | 9214 | -0.011 | 0.3 | NO |
122 | LSM2 | LSM2 | LSM2 | 9319 | -0.012 | 0.3 | NO |
123 | GTF2H4 | GTF2H4 | GTF2H4 | 9395 | -0.014 | 0.3 | NO |
124 | ERCC2 | ERCC2 | ERCC2 | 9411 | -0.014 | 0.3 | NO |
125 | SUPT5H | SUPT5H | SUPT5H | 9490 | -0.015 | 0.3 | NO |
126 | PHF5A | PHF5A | PHF5A | 9784 | -0.019 | 0.28 | NO |
127 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 9834 | -0.02 | 0.28 | NO |
128 | POLR2E | POLR2E | POLR2E | 9929 | -0.021 | 0.28 | NO |
129 | NUP62 | NUP62 | NUP62 | 9934 | -0.021 | 0.28 | NO |
130 | SF3A1 | SF3A1 | SF3A1 | 10217 | -0.025 | 0.27 | NO |
131 | SNRPD1 | SNRPD1 | SNRPD1 | 10219 | -0.025 | 0.28 | NO |
132 | POLR2I | POLR2I | POLR2I | 10256 | -0.026 | 0.28 | NO |
133 | SNRNP40 | SNRNP40 | SNRNP40 | 10540 | -0.031 | 0.27 | NO |
134 | SF3B5 | SF3B5 | SF3B5 | 10626 | -0.032 | 0.27 | NO |
135 | ADAR | ADAR | ADAR | 10750 | -0.034 | 0.27 | NO |
136 | NUP188 | NUP188 | NUP188 | 11002 | -0.039 | 0.26 | NO |
137 | LSM10 | LSM10 | LSM10 | 11223 | -0.043 | 0.26 | NO |
138 | RNMT | RNMT | RNMT | 11512 | -0.05 | 0.25 | NO |
139 | GTF2H2 | GTF2H2 | GTF2H2 | 11613 | -0.052 | 0.25 | NO |
140 | PRPF8 | PRPF8 | PRPF8 | 11733 | -0.054 | 0.25 | NO |
141 | SEH1L | SEH1L | SEH1L | 11799 | -0.056 | 0.26 | NO |
142 | POLR2A | POLR2A | POLR2A | 12857 | -0.084 | 0.21 | NO |
143 | TXNL4A | TXNL4A | TXNL4A | 12983 | -0.087 | 0.22 | NO |
144 | POLR2L | POLR2L | POLR2L | 13158 | -0.094 | 0.23 | NO |
145 | ADARB1 | ADARB1 | ADARB1 | 13734 | -0.12 | 0.21 | NO |
146 | GTF2H2B | GTF2H2B | GTF2H2B | 14430 | -0.14 | 0.2 | NO |
Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID BARD1PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.PID_BARD1PATHWAY.heatmap_plot.clus1.14.png)
Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: PID BARD1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_MRNA_PROCESSING.volcano_plot.clus1.6.png)
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 | GTF2F2 | GTF2F2 | GTF2F2 | 1053 | 0.16 | -0.025 | YES |
2 | RAE1 | RAE1 | RAE1 | 1357 | 0.14 | -0.012 | YES |
3 | UPF3B | UPF3B | UPF3B | 1365 | 0.14 | 0.017 | YES |
4 | NUPL2 | NUPL2 | NUPL2 | 1542 | 0.13 | 0.034 | YES |
5 | POLR2K | POLR2K | POLR2K | 1800 | 0.12 | 0.045 | YES |
6 | PRPF6 | PRPF6 | PRPF6 | 1959 | 0.11 | 0.059 | YES |
7 | NCBP2 | NCBP2 | NCBP2 | 2076 | 0.11 | 0.075 | YES |
8 | CCAR1 | CCAR1 | CCAR1 | 2395 | 0.096 | 0.078 | YES |
9 | SNRPB2 | SNRPB2 | SNRPB2 | 2470 | 0.094 | 0.094 | YES |
10 | NUP35 | NUP35 | NUP35 | 2511 | 0.093 | 0.11 | YES |
11 | CSTF3 | CSTF3 | CSTF3 | 2962 | 0.081 | 0.1 | YES |
12 | PCF11 | PCF11 | PCF11 | 3149 | 0.077 | 0.11 | YES |
13 | SNRPE | SNRPE | SNRPE | 3183 | 0.076 | 0.12 | YES |
14 | SNRPA1 | SNRPA1 | SNRPA1 | 3214 | 0.075 | 0.14 | YES |
15 | NUPL1 | NUPL1 | NUPL1 | 3230 | 0.075 | 0.15 | YES |
16 | SF3B14 | SF3B14 | SF3B14 | 3355 | 0.072 | 0.16 | YES |
17 | CSTF1 | CSTF1 | CSTF1 | 3388 | 0.071 | 0.17 | YES |
18 | NUP107 | NUP107 | NUP107 | 3525 | 0.069 | 0.18 | YES |
19 | NUP155 | NUP155 | NUP155 | 3758 | 0.064 | 0.18 | YES |
20 | MAGOH | MAGOH | MAGOH | 3950 | 0.06 | 0.18 | YES |
21 | CPSF3 | CPSF3 | CPSF3 | 3999 | 0.059 | 0.19 | YES |
22 | SNRPG | SNRPG | SNRPG | 4015 | 0.059 | 0.2 | YES |
23 | NUDT21 | NUDT21 | NUDT21 | 4247 | 0.056 | 0.2 | YES |
24 | NUP43 | NUP43 | NUP43 | 4280 | 0.055 | 0.21 | YES |
25 | NUP153 | NUP153 | NUP153 | 4501 | 0.051 | 0.21 | YES |
26 | CSTF2 | CSTF2 | CSTF2 | 4525 | 0.051 | 0.22 | YES |
27 | POLR2D | POLR2D | POLR2D | 4656 | 0.048 | 0.22 | YES |
28 | NUP205 | NUP205 | NUP205 | 4664 | 0.048 | 0.23 | YES |
29 | NUP54 | NUP54 | NUP54 | 4668 | 0.048 | 0.24 | YES |
30 | POLR2J | POLR2J | POLR2J | 4680 | 0.048 | 0.25 | YES |
31 | RBMX | RBMX | RBMX | 4733 | 0.047 | 0.26 | YES |
32 | CDC40 | CDC40 | CDC40 | 4800 | 0.046 | 0.27 | YES |
33 | NUP133 | NUP133 | NUP133 | 4903 | 0.044 | 0.27 | YES |
34 | PAPOLA | PAPOLA | PAPOLA | 4918 | 0.044 | 0.28 | YES |
35 | NCBP1 | NCBP1 | NCBP1 | 4932 | 0.044 | 0.29 | YES |
36 | NUP210 | NUP210 | NUP210 | 5057 | 0.042 | 0.29 | YES |
37 | POLR2F | POLR2F | POLR2F | 5244 | 0.04 | 0.29 | YES |
38 | HNRNPK | HNRNPK | HNRNPK | 5260 | 0.039 | 0.3 | YES |
39 | TPR | TPR | TPR | 5282 | 0.039 | 0.3 | YES |
40 | HNRNPH2 | HNRNPH2 | HNRNPH2 | 5325 | 0.039 | 0.31 | YES |
41 | SF3B1 | SF3B1 | SF3B1 | 5354 | 0.038 | 0.31 | YES |
42 | NUP85 | NUP85 | NUP85 | 5364 | 0.038 | 0.32 | YES |
43 | HNRNPA2B1 | HNRNPA2B1 | HNRNPA2B1 | 5419 | 0.037 | 0.33 | YES |
44 | CPSF1 | CPSF1 | CPSF1 | 5456 | 0.037 | 0.33 | YES |
45 | HNRNPU | HNRNPU | HNRNPU | 5470 | 0.037 | 0.34 | YES |
46 | RANBP2 | RANBP2 | RANBP2 | 5521 | 0.036 | 0.34 | YES |
47 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 5581 | 0.036 | 0.35 | YES |
48 | SNRNP200 | SNRNP200 | SNRNP200 | 5599 | 0.035 | 0.36 | YES |
49 | POLR2C | POLR2C | POLR2C | 5689 | 0.034 | 0.36 | YES |
50 | NUP37 | NUP37 | NUP37 | 5788 | 0.033 | 0.36 | YES |
51 | SF3B3 | SF3B3 | SF3B3 | 5809 | 0.032 | 0.36 | YES |
52 | SMC1A | SMC1A | SMC1A | 5861 | 0.032 | 0.37 | YES |
53 | SNRPF | SNRPF | SNRPF | 5954 | 0.031 | 0.37 | YES |
54 | NUP214 | NUP214 | NUP214 | 6043 | 0.03 | 0.37 | YES |
55 | SF3B2 | SF3B2 | SF3B2 | 6070 | 0.029 | 0.38 | YES |
56 | SNRPD3 | SNRPD3 | SNRPD3 | 6100 | 0.029 | 0.38 | YES |
57 | HNRNPD | HNRNPD | HNRNPD | 6103 | 0.029 | 0.39 | YES |
58 | CD2BP2 | CD2BP2 | CD2BP2 | 6267 | 0.026 | 0.38 | YES |
59 | SNRPD2 | SNRPD2 | SNRPD2 | 6320 | 0.026 | 0.38 | YES |
60 | POM121 | POM121 | POM121 | 6409 | 0.024 | 0.38 | YES |
61 | SNRPB | SNRPB | SNRPB | 6420 | 0.024 | 0.39 | YES |
62 | SNRPA | SNRPA | SNRPA | 6425 | 0.024 | 0.4 | YES |
63 | CPSF7 | CPSF7 | CPSF7 | 6434 | 0.024 | 0.4 | YES |
64 | SLBP | SLBP | SLBP | 6561 | 0.023 | 0.4 | YES |
65 | NXF1 | NXF1 | NXF1 | 6614 | 0.022 | 0.4 | YES |
66 | HNRNPUL1 | HNRNPUL1 | HNRNPUL1 | 6670 | 0.022 | 0.4 | YES |
67 | RBM5 | RBM5 | RBM5 | 6698 | 0.021 | 0.4 | YES |
68 | HNRNPL | HNRNPL | HNRNPL | 6711 | 0.021 | 0.41 | YES |
69 | NUP93 | NUP93 | NUP93 | 6716 | 0.021 | 0.41 | YES |
70 | HNRNPR | HNRNPR | HNRNPR | 6737 | 0.021 | 0.41 | YES |
71 | EFTUD2 | EFTUD2 | EFTUD2 | 6764 | 0.02 | 0.42 | YES |
72 | HNRNPH1 | HNRNPH1 | HNRNPH1 | 6895 | 0.018 | 0.41 | YES |
73 | NFX1 | NFX1 | NFX1 | 6904 | 0.018 | 0.42 | YES |
74 | DHX9 | DHX9 | DHX9 | 6940 | 0.018 | 0.42 | YES |
75 | CPSF2 | CPSF2 | CPSF2 | 7078 | 0.016 | 0.42 | NO |
76 | FUS | FUS | FUS | 7198 | 0.015 | 0.41 | NO |
77 | SF3A3 | SF3A3 | SF3A3 | 7212 | 0.015 | 0.41 | NO |
78 | YBX1 | YBX1 | YBX1 | 7248 | 0.014 | 0.42 | NO |
79 | RNPS1 | RNPS1 | RNPS1 | 7259 | 0.014 | 0.42 | NO |
80 | PABPN1 | PABPN1 | PABPN1 | 7291 | 0.014 | 0.42 | NO |
81 | U2AF2 | U2AF2 | U2AF2 | 7456 | 0.012 | 0.41 | NO |
82 | THOC4 | THOC4 | THOC4 | 7488 | 0.011 | 0.41 | NO |
83 | POLR2H | POLR2H | POLR2H | 7501 | 0.011 | 0.41 | NO |
84 | CLP1 | CLP1 | CLP1 | 7541 | 0.011 | 0.41 | NO |
85 | HNRNPF | HNRNPF | HNRNPF | 7626 | 0.0098 | 0.41 | NO |
86 | PTBP1 | PTBP1 | PTBP1 | 7638 | 0.0097 | 0.41 | NO |
87 | NHP2L1 | NHP2L1 | NHP2L1 | 7668 | 0.0094 | 0.41 | NO |
88 | SNRNP70 | SNRNP70 | SNRNP70 | 7724 | 0.0086 | 0.41 | NO |
89 | DHX38 | DHX38 | DHX38 | 7758 | 0.0082 | 0.41 | NO |
90 | SF3A2 | SF3A2 | SF3A2 | 7778 | 0.0079 | 0.41 | NO |
91 | POLR2B | POLR2B | POLR2B | 7828 | 0.0073 | 0.41 | NO |
92 | SF3B4 | SF3B4 | SF3B4 | 7850 | 0.007 | 0.41 | NO |
93 | U2AF1 | U2AF1 | U2AF1 | 7933 | 0.006 | 0.41 | NO |
94 | HNRNPC | HNRNPC | HNRNPC | 7981 | 0.0053 | 0.41 | NO |
95 | HNRNPA0 | HNRNPA0 | HNRNPA0 | 7986 | 0.0052 | 0.41 | NO |
96 | GTF2F1 | GTF2F1 | GTF2F1 | 8007 | 0.005 | 0.41 | NO |
97 | DNAJC8 | DNAJC8 | DNAJC8 | 8048 | 0.0045 | 0.41 | NO |
98 | DDX23 | DDX23 | DDX23 | 8107 | 0.0036 | 0.4 | NO |
99 | PRPF4 | PRPF4 | PRPF4 | 8362 | 0.00039 | 0.39 | NO |
100 | PCBP1 | PCBP1 | PCBP1 | 8476 | -0.001 | 0.38 | NO |
101 | NUP88 | NUP88 | NUP88 | 8482 | -0.0011 | 0.38 | NO |
102 | SRRM1 | SRRM1 | SRRM1 | 8564 | -0.0022 | 0.38 | NO |
103 | METTL3 | METTL3 | METTL3 | 8580 | -0.0024 | 0.38 | NO |
104 | NUP50 | NUP50 | NUP50 | 8610 | -0.0027 | 0.38 | NO |
105 | POLR2G | POLR2G | POLR2G | 8691 | -0.0037 | 0.38 | NO |
106 | RBM8A | RBM8A | RBM8A | 8834 | -0.0056 | 0.37 | NO |
107 | HNRNPM | HNRNPM | HNRNPM | 8851 | -0.0058 | 0.37 | NO |
108 | EIF4E | EIF4E | EIF4E | 8948 | -0.0071 | 0.36 | NO |
109 | PCBP2 | PCBP2 | PCBP2 | 9165 | -0.01 | 0.35 | NO |
110 | AAAS | AAAS | AAAS | 9214 | -0.011 | 0.35 | NO |
111 | LSM2 | LSM2 | LSM2 | 9319 | -0.012 | 0.35 | NO |
112 | PHF5A | PHF5A | PHF5A | 9784 | -0.019 | 0.33 | NO |
113 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 9834 | -0.02 | 0.33 | NO |
114 | POLR2E | POLR2E | POLR2E | 9929 | -0.021 | 0.33 | NO |
115 | NUP62 | NUP62 | NUP62 | 9934 | -0.021 | 0.33 | NO |
116 | SF3A1 | SF3A1 | SF3A1 | 10217 | -0.025 | 0.32 | NO |
117 | SNRPD1 | SNRPD1 | SNRPD1 | 10219 | -0.025 | 0.33 | NO |
118 | POLR2I | POLR2I | POLR2I | 10256 | -0.026 | 0.33 | NO |
119 | SNRNP40 | SNRNP40 | SNRNP40 | 10540 | -0.031 | 0.32 | NO |
120 | SF3B5 | SF3B5 | SF3B5 | 10626 | -0.032 | 0.32 | NO |
121 | NUP188 | NUP188 | NUP188 | 11002 | -0.039 | 0.31 | NO |
122 | PRPF8 | PRPF8 | PRPF8 | 11733 | -0.054 | 0.28 | NO |
123 | SEH1L | SEH1L | SEH1L | 11799 | -0.056 | 0.29 | NO |
124 | POLR2A | POLR2A | POLR2A | 12857 | -0.084 | 0.25 | NO |
125 | TXNL4A | TXNL4A | TXNL4A | 12983 | -0.087 | 0.26 | NO |
126 | POLR2L | POLR2L | POLR2L | 13158 | -0.094 | 0.27 | 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 METABOLISM OF NON CODING RNA.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_METABOLISM_OF_NON_CODING_RNA.heatmap_plot.clus1.15.png)
Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF NON CODING RNA, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA.volcano_plot.clus1.7.png)
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 | RAE1 | RAE1 | RAE1 | 1357 | 0.14 | 0.017 | YES |
2 | NUPL2 | NUPL2 | NUPL2 | 1542 | 0.13 | 0.092 | YES |
3 | NCBP2 | NCBP2 | NCBP2 | 2076 | 0.11 | 0.13 | YES |
4 | NUP35 | NUP35 | NUP35 | 2511 | 0.093 | 0.17 | YES |
5 | NUPL1 | NUPL1 | NUPL1 | 3230 | 0.075 | 0.18 | YES |
6 | NUP107 | NUP107 | NUP107 | 3525 | 0.069 | 0.21 | YES |
7 | NUP155 | NUP155 | NUP155 | 3758 | 0.064 | 0.24 | YES |
8 | CPSF3 | CPSF3 | CPSF3 | 3999 | 0.059 | 0.26 | YES |
9 | NUP43 | NUP43 | NUP43 | 4280 | 0.055 | 0.28 | YES |
10 | NUP153 | NUP153 | NUP153 | 4501 | 0.051 | 0.31 | YES |
11 | NUP205 | NUP205 | NUP205 | 4664 | 0.048 | 0.33 | YES |
12 | NUP54 | NUP54 | NUP54 | 4668 | 0.048 | 0.36 | YES |
13 | NUP133 | NUP133 | NUP133 | 4903 | 0.044 | 0.38 | YES |
14 | NCBP1 | NCBP1 | NCBP1 | 4932 | 0.044 | 0.4 | YES |
15 | NUP210 | NUP210 | NUP210 | 5057 | 0.042 | 0.42 | YES |
16 | TPR | TPR | TPR | 5282 | 0.039 | 0.44 | YES |
17 | NUP85 | NUP85 | NUP85 | 5364 | 0.038 | 0.46 | YES |
18 | CPSF1 | CPSF1 | CPSF1 | 5456 | 0.037 | 0.48 | YES |
19 | RANBP2 | RANBP2 | RANBP2 | 5521 | 0.036 | 0.5 | YES |
20 | NUP37 | NUP37 | NUP37 | 5788 | 0.033 | 0.51 | YES |
21 | NUP214 | NUP214 | NUP214 | 6043 | 0.03 | 0.51 | YES |
22 | POM121 | POM121 | POM121 | 6409 | 0.024 | 0.51 | YES |
23 | NXF1 | NXF1 | NXF1 | 6614 | 0.022 | 0.51 | YES |
24 | NUP93 | NUP93 | NUP93 | 6716 | 0.021 | 0.52 | YES |
25 | CPSF2 | CPSF2 | CPSF2 | 7078 | 0.016 | 0.51 | NO |
26 | THOC4 | THOC4 | THOC4 | 7488 | 0.011 | 0.49 | NO |
27 | NUP88 | NUP88 | NUP88 | 8482 | -0.0011 | 0.44 | NO |
28 | NUP50 | NUP50 | NUP50 | 8610 | -0.0027 | 0.43 | NO |
29 | EIF4E | EIF4E | EIF4E | 8948 | -0.0071 | 0.42 | NO |
30 | AAAS | AAAS | AAAS | 9214 | -0.011 | 0.41 | NO |
31 | NUP62 | NUP62 | NUP62 | 9934 | -0.021 | 0.39 | NO |
32 | NUP188 | NUP188 | NUP188 | 11002 | -0.039 | 0.35 | NO |
33 | SEH1L | SEH1L | SEH1L | 11799 | -0.056 | 0.34 | 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 METABOLISM OF VITAMINS AND COFACTORS.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS.heatmap_plot.clus1.16.png)
Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF VITAMINS AND COFACTORS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT.volcano_plot.clus1.8.png)
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 | RAE1 | RAE1 | RAE1 | 1357 | 0.14 | 0.02 | YES |
2 | NUPL2 | NUPL2 | NUPL2 | 1542 | 0.13 | 0.099 | YES |
3 | NUP35 | NUP35 | NUP35 | 2511 | 0.093 | 0.11 | YES |
4 | PSIP1 | PSIP1 | PSIP1 | 2945 | 0.081 | 0.14 | YES |
5 | NUPL1 | NUPL1 | NUPL1 | 3230 | 0.075 | 0.18 | YES |
6 | NUP107 | NUP107 | NUP107 | 3525 | 0.069 | 0.21 | YES |
7 | NUP155 | NUP155 | NUP155 | 3758 | 0.064 | 0.24 | YES |
8 | NUP43 | NUP43 | NUP43 | 4280 | 0.055 | 0.24 | YES |
9 | NUP153 | NUP153 | NUP153 | 4501 | 0.051 | 0.27 | YES |
10 | NUP205 | NUP205 | NUP205 | 4664 | 0.048 | 0.29 | YES |
11 | NUP54 | NUP54 | NUP54 | 4668 | 0.048 | 0.32 | YES |
12 | NUP133 | NUP133 | NUP133 | 4903 | 0.044 | 0.34 | YES |
13 | NUP210 | NUP210 | NUP210 | 5057 | 0.042 | 0.36 | YES |
14 | TPR | TPR | TPR | 5282 | 0.039 | 0.38 | YES |
15 | SLC25A6 | SLC25A6 | SLC25A6 | 5319 | 0.039 | 0.4 | YES |
16 | NUP85 | NUP85 | NUP85 | 5364 | 0.038 | 0.42 | YES |
17 | BANF1 | BANF1 | BANF1 | 5451 | 0.037 | 0.44 | YES |
18 | RANBP2 | RANBP2 | RANBP2 | 5521 | 0.036 | 0.47 | YES |
19 | NUP37 | NUP37 | NUP37 | 5788 | 0.033 | 0.47 | YES |
20 | NUP214 | NUP214 | NUP214 | 6043 | 0.03 | 0.48 | YES |
21 | POM121 | POM121 | POM121 | 6409 | 0.024 | 0.48 | NO |
22 | NUP93 | NUP93 | NUP93 | 6716 | 0.021 | 0.47 | NO |
23 | KPNA1 | KPNA1 | KPNA1 | 6864 | 0.019 | 0.48 | NO |
24 | HMGA1 | HMGA1 | HMGA1 | 8086 | 0.004 | 0.41 | NO |
25 | NUP88 | NUP88 | NUP88 | 8482 | -0.0011 | 0.39 | NO |
26 | NUP50 | NUP50 | NUP50 | 8610 | -0.0027 | 0.39 | NO |
27 | AAAS | AAAS | AAAS | 9214 | -0.011 | 0.36 | NO |
28 | SLC25A5 | SLC25A5 | SLC25A5 | 9724 | -0.018 | 0.34 | NO |
29 | NUP62 | NUP62 | NUP62 | 9934 | -0.021 | 0.35 | NO |
30 | NUP188 | NUP188 | NUP188 | 11002 | -0.039 | 0.31 | NO |
31 | SLC25A4 | SLC25A4 | SLC25A4 | 11706 | -0.054 | 0.31 | NO |
32 | SEH1L | SEH1L | SEH1L | 11799 | -0.056 | 0.34 | 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 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA.heatmap_plot.clus1.7.png)
Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS.volcano_plot.clus1.9.png)
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 | MRE11A | MRE11A | MRE11A | 918 | 0.17 | 0.04 | YES |
2 | RAD50 | RAD50 | RAD50 | 2055 | 0.11 | 0.033 | YES |
3 | CHEK2 | CHEK2 | CHEK2 | 2282 | 0.1 | 0.072 | YES |
4 | BRCA1 | BRCA1 | BRCA1 | 2498 | 0.093 | 0.11 | YES |
5 | CDC25A | CDC25A | CDC25A | 2520 | 0.092 | 0.16 | YES |
6 | YWHAB | YWHAB | YWHAB | 2609 | 0.09 | 0.2 | YES |
7 | ATM | ATM | ATM | 2749 | 0.086 | 0.24 | YES |
8 | BLM | BLM | BLM | 3043 | 0.079 | 0.26 | YES |
9 | XRCC4 | XRCC4 | XRCC4 | 3250 | 0.074 | 0.29 | YES |
10 | SMC3 | SMC3 | SMC3 | 3524 | 0.069 | 0.31 | YES |
11 | MDC1 | MDC1 | MDC1 | 3713 | 0.065 | 0.33 | YES |
12 | CDC25C | CDC25C | CDC25C | 3750 | 0.064 | 0.36 | YES |
13 | DCLRE1C | DCLRE1C | DCLRE1C | 4061 | 0.058 | 0.38 | YES |
14 | RAD17 | RAD17 | RAD17 | 4096 | 0.058 | 0.41 | YES |
15 | RNF8 | RNF8 | RNF8 | 4161 | 0.057 | 0.43 | YES |
16 | FAM175A | FAM175A | FAM175A | 4237 | 0.056 | 0.46 | YES |
17 | RFWD2 | RFWD2 | RFWD2 | 4652 | 0.048 | 0.46 | YES |
18 | TP53BP1 | TP53BP1 | TP53BP1 | 4852 | 0.045 | 0.47 | YES |
19 | UIMC1 | UIMC1 | UIMC1 | 4980 | 0.043 | 0.49 | YES |
20 | NBN | NBN | NBN | 5436 | 0.037 | 0.48 | YES |
21 | UBE2N | UBE2N | UBE2N | 5715 | 0.034 | 0.48 | YES |
22 | SMC1A | SMC1A | SMC1A | 5861 | 0.032 | 0.49 | YES |
23 | FANCD2 | FANCD2 | FANCD2 | 6176 | 0.028 | 0.49 | YES |
24 | TERF2 | TERF2 | TERF2 | 6231 | 0.027 | 0.5 | YES |
25 | ABL1 | ABL1 | ABL1 | 7270 | 0.014 | 0.45 | NO |
26 | BID | BID | BID | 7525 | 0.011 | 0.44 | NO |
27 | RAD9A | RAD9A | RAD9A | 7700 | 0.009 | 0.44 | NO |
28 | KAT5 | KAT5 | KAT5 | 9123 | -0.0095 | 0.36 | NO |
29 | CTBP1 | CTBP1 | CTBP1 | 9168 | -0.01 | 0.37 | NO |
30 | TRIM28 | TRIM28 | TRIM28 | 9335 | -0.013 | 0.36 | NO |
31 | H2AFX | H2AFX | H2AFX | 10150 | -0.024 | 0.33 | NO |
32 | RBBP8 | RBBP8 | RBBP8 | 11019 | -0.04 | 0.3 | NO |
33 | MDM2 | MDM2 | MDM2 | 12611 | -0.077 | 0.26 | NO |
34 | TOP3A | TOP3A | TOP3A | 12917 | -0.086 | 0.28 | 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 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM.
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM.heatmap_plot.clus1.5.png)
Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.PID_ATM_PATHWAY.volcano_plot.clus1.10.png)
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 FRUCTOSE AND MANNOSE METABOLISM | 34 | genes.ES.table | 0.38 | 1.3 | 0.19 | 1 | 1 | 0.32 | 0.12 | 0.28 | 1 | 0.8 |
KEGG BUTANOATE METABOLISM | 30 | genes.ES.table | 0.43 | 1.3 | 0.21 | 1 | 1 | 0.57 | 0.2 | 0.45 | 1 | 0.8 |
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM | 34 | genes.ES.table | 0.53 | 1.4 | 0.15 | 1 | 0.99 | 0.35 | 0.1 | 0.32 | 1 | 0.73 |
KEGG BASE EXCISION REPAIR | 33 | genes.ES.table | 0.38 | 1.3 | 0.19 | 1 | 1 | 1 | 0.62 | 0.38 | 1 | 0.73 |
BIOCARTA FAS PATHWAY | 30 | genes.ES.table | 0.46 | 1.6 | 0.055 | 1 | 0.92 | 0.37 | 0.22 | 0.29 | 1 | 0.62 |
BIOCARTA HIVNEF PATHWAY | 58 | genes.ES.table | 0.4 | 1.7 | 0.044 | 1 | 0.79 | 0.4 | 0.26 | 0.3 | 0.83 | 0.45 |
BIOCARTA DEATH PATHWAY | 33 | genes.ES.table | 0.36 | 1.5 | 0.086 | 1 | 0.98 | 0.46 | 0.21 | 0.36 | 1 | 0.7 |
BIOCARTA PYK2 PATHWAY | 28 | genes.ES.table | 0.32 | 1.3 | 0.15 | 1 | 1 | 0.36 | 0.21 | 0.28 | 1 | 0.73 |
BIOCARTA TNFR1 PATHWAY | 29 | genes.ES.table | 0.35 | 1.4 | 0.1 | 1 | 0.99 | 0.48 | 0.3 | 0.34 | 1 | 0.73 |
PID TRAIL PATHWAY | 28 | genes.ES.table | 0.42 | 1.5 | 0.087 | 1 | 0.97 | 0.43 | 0.21 | 0.34 | 1 | 0.68 |
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 | TP53AIP1 | TP53AIP1 | TP53AIP1 | 251 | 0.26 | 0.1 | YES |
2 | KAT2B | KAT2B | KAT2B | 1221 | 0.12 | 0.1 | YES |
3 | MDM2 | MDM2 | MDM2 | 1320 | 0.11 | 0.15 | YES |
4 | HIPK2 | HIPK2 | HIPK2 | 1409 | 0.1 | 0.19 | YES |
5 | CSNK1G1 | CSNK1G1 | CSNK1G1 | 2298 | 0.07 | 0.17 | YES |
6 | CSNK1G3 | CSNK1G3 | CSNK1G3 | 2385 | 0.067 | 0.2 | YES |
7 | PPP1R13L | PPP1R13L | PPP1R13L | 2392 | 0.067 | 0.22 | YES |
8 | TP53 | TP53 | TP53 | 2574 | 0.063 | 0.24 | YES |
9 | DYRK2 | DYRK2 | DYRK2 | 2652 | 0.06 | 0.27 | YES |
10 | CCNG1 | CCNG1 | CCNG1 | 2697 | 0.059 | 0.29 | YES |
11 | PPM1D | PPM1D | PPM1D | 2940 | 0.055 | 0.3 | YES |
12 | SETD7 | SETD7 | SETD7 | 2972 | 0.054 | 0.32 | YES |
13 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 3187 | 0.05 | 0.33 | YES |
14 | SETD8 | SETD8 | SETD8 | 3375 | 0.046 | 0.34 | YES |
15 | CCNA2 | CCNA2 | CCNA2 | 3426 | 0.046 | 0.36 | YES |
16 | EP300 | EP300 | EP300 | 3463 | 0.045 | 0.38 | YES |
17 | PPP2R4 | PPP2R4 | PPP2R4 | 3709 | 0.041 | 0.38 | YES |
18 | MAPK8 | MAPK8 | MAPK8 | 3718 | 0.041 | 0.4 | YES |
19 | PRMT5 | PRMT5 | PRMT5 | 4138 | 0.035 | 0.39 | YES |
20 | AKT1 | AKT1 | AKT1 | 4289 | 0.032 | 0.4 | YES |
21 | RASSF1 | RASSF1 | RASSF1 | 4600 | 0.028 | 0.4 | YES |
22 | RPL11 | RPL11 | RPL11 | 4671 | 0.027 | 0.4 | YES |
23 | PPP2CA | PPP2CA | PPP2CA | 5791 | 0.014 | 0.35 | NO |
24 | MAPK9 | MAPK9 | MAPK9 | 6114 | 0.011 | 0.34 | NO |
25 | PRKCD | PRKCD | PRKCD | 6270 | 0.0093 | 0.33 | NO |
26 | RPL5 | RPL5 | RPL5 | 6353 | 0.0084 | 0.33 | NO |
27 | CSNK1E | CSNK1E | CSNK1E | 6380 | 0.008 | 0.33 | NO |
28 | CDK2 | CDK2 | CDK2 | 6456 | 0.0071 | 0.33 | NO |
29 | CHEK2 | CHEK2 | CHEK2 | 6489 | 0.0067 | 0.33 | NO |
30 | FBXO11 | FBXO11 | FBXO11 | 6579 | 0.0056 | 0.33 | NO |
31 | DAXX | DAXX | DAXX | 6686 | 0.0044 | 0.33 | NO |
32 | YY1 | YY1 | YY1 | 6735 | 0.0039 | 0.32 | NO |
33 | PIN1 | PIN1 | PIN1 | 7099 | 0.00022 | 0.3 | NO |
34 | KAT5 | KAT5 | KAT5 | 7352 | -0.0027 | 0.29 | NO |
35 | RFWD2 | RFWD2 | RFWD2 | 7617 | -0.0057 | 0.28 | NO |
36 | GSK3B | GSK3B | GSK3B | 7625 | -0.0058 | 0.28 | NO |
37 | UBE2D1 | UBE2D1 | UBE2D1 | 7676 | -0.0064 | 0.28 | NO |
38 | SMYD2 | SMYD2 | SMYD2 | 7842 | -0.0082 | 0.28 | NO |
39 | RCHY1 | RCHY1 | RCHY1 | 7863 | -0.0084 | 0.28 | NO |
40 | CSNK1D | CSNK1D | CSNK1D | 7908 | -0.0089 | 0.28 | NO |
41 | NEDD8 | NEDD8 | NEDD8 | 7942 | -0.0093 | 0.28 | NO |
42 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 7947 | -0.0093 | 0.29 | NO |
43 | CREBBP | CREBBP | CREBBP | 8274 | -0.013 | 0.28 | NO |
44 | TTC5 | TTC5 | TTC5 | 8317 | -0.013 | 0.28 | NO |
45 | HUWE1 | HUWE1 | HUWE1 | 8478 | -0.015 | 0.28 | NO |
46 | CHEK1 | CHEK1 | CHEK1 | 8552 | -0.016 | 0.28 | NO |
47 | ABL1 | ABL1 | ABL1 | 8625 | -0.017 | 0.28 | NO |
48 | ATM | ATM | ATM | 8776 | -0.019 | 0.28 | NO |
49 | TRIM28 | TRIM28 | TRIM28 | 8992 | -0.022 | 0.28 | NO |
50 | ATR | ATR | ATR | 9210 | -0.025 | 0.28 | NO |
51 | USP7 | USP7 | USP7 | 9245 | -0.025 | 0.29 | NO |
52 | RPL23 | RPL23 | RPL23 | 9336 | -0.026 | 0.3 | NO |
53 | SKP2 | SKP2 | SKP2 | 9758 | -0.032 | 0.29 | NO |
54 | MDM4 | MDM4 | MDM4 | 9963 | -0.035 | 0.29 | NO |
55 | E4F1 | E4F1 | E4F1 | 10085 | -0.037 | 0.3 | NO |
56 | MAPK14 | MAPK14 | MAPK14 | 11295 | -0.06 | 0.26 | NO |
57 | CSE1L | CSE1L | CSE1L | 12302 | -0.085 | 0.24 | NO |
58 | CDKN2A | CDKN2A | CDKN2A | 14380 | -0.17 | 0.2 | 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 FRUCTOSE AND MANNOSE METABOLISM.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM.heatmap_plot.clus2.18.png)
Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.PID_P53REGULATIONPATHWAY.volcano_plot.clus2.1.png)
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 | MAP3K5 | MAP3K5 | MAP3K5 | 525 | 0.19 | 0.045 | YES |
2 | CASP7 | CASP7 | CASP7 | 703 | 0.16 | 0.099 | YES |
3 | FAS | FAS | FAS | 820 | 0.15 | 0.15 | YES |
4 | BCL2 | BCL2 | BCL2 | 888 | 0.14 | 0.2 | YES |
5 | BIRC3 | BIRC3 | BIRC3 | 1131 | 0.12 | 0.24 | YES |
6 | MDM2 | MDM2 | MDM2 | 1320 | 0.11 | 0.27 | YES |
7 | APAF1 | APAF1 | APAF1 | 1598 | 0.094 | 0.29 | YES |
8 | LMNA | LMNA | LMNA | 2238 | 0.071 | 0.28 | YES |
9 | CASP3 | CASP3 | CASP3 | 2326 | 0.069 | 0.3 | YES |
10 | RIPK1 | RIPK1 | RIPK1 | 2398 | 0.067 | 0.32 | YES |
11 | GSN | GSN | GSN | 2755 | 0.058 | 0.33 | YES |
12 | PSEN1 | PSEN1 | PSEN1 | 2859 | 0.056 | 0.34 | YES |
13 | CASP9 | CASP9 | CASP9 | 3274 | 0.048 | 0.34 | YES |
14 | CASP8 | CASP8 | CASP8 | 3555 | 0.044 | 0.34 | YES |
15 | CYCS | CYCS | CYCS | 3607 | 0.043 | 0.35 | YES |
16 | MAPK8 | MAPK8 | MAPK8 | 3718 | 0.041 | 0.36 | YES |
17 | BIRC2 | BIRC2 | BIRC2 | 3787 | 0.04 | 0.38 | YES |
18 | PARP1 | PARP1 | PARP1 | 3989 | 0.037 | 0.38 | YES |
19 | LMNB1 | LMNB1 | LMNB1 | 3998 | 0.036 | 0.39 | YES |
20 | BAG4 | BAG4 | BAG4 | 4147 | 0.034 | 0.4 | YES |
21 | CDK11B | CDK11B | CDK11B | 4504 | 0.03 | 0.39 | YES |
22 | MAP2K7 | MAP2K7 | MAP2K7 | 4658 | 0.027 | 0.39 | YES |
23 | SPTAN1 | SPTAN1 | SPTAN1 | 4665 | 0.027 | 0.4 | YES |
24 | CHUK | CHUK | CHUK | 5282 | 0.02 | 0.37 | NO |
25 | PAK2 | PAK2 | PAK2 | 5373 | 0.019 | 0.38 | NO |
26 | NFKB1 | NFKB1 | NFKB1 | 5384 | 0.019 | 0.38 | NO |
27 | CRADD | CRADD | CRADD | 5451 | 0.018 | 0.39 | NO |
28 | FASLG | FASLG | FASLG | 5595 | 0.017 | 0.38 | NO |
29 | ACTG1 | ACTG1 | ACTG1 | 5815 | 0.014 | 0.38 | NO |
30 | PRKCD | PRKCD | PRKCD | 6270 | 0.0093 | 0.36 | NO |
31 | NFKBIA | NFKBIA | NFKBIA | 6371 | 0.0081 | 0.35 | NO |
32 | RB1 | RB1 | RB1 | 6417 | 0.0075 | 0.36 | NO |
33 | CASP2 | CASP2 | CASP2 | 6623 | 0.0051 | 0.34 | NO |
34 | DAXX | DAXX | DAXX | 6686 | 0.0044 | 0.34 | NO |
35 | CASP6 | CASP6 | CASP6 | 6753 | 0.0038 | 0.34 | NO |
36 | LMNB2 | LMNB2 | LMNB2 | 6770 | 0.0036 | 0.34 | NO |
37 | RASA1 | RASA1 | RASA1 | 6779 | 0.0035 | 0.34 | NO |
38 | TRAF2 | TRAF2 | TRAF2 | 6999 | 0.0013 | 0.33 | NO |
39 | MAP3K1 | MAP3K1 | MAP3K1 | 7176 | -0.00061 | 0.32 | NO |
40 | DFFB | DFFB | DFFB | 7598 | -0.0055 | 0.3 | NO |
41 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 7613 | -0.0057 | 0.3 | NO |
42 | TRADD | TRADD | TRADD | 7776 | -0.0075 | 0.3 | NO |
43 | NUMA1 | NUMA1 | NUMA1 | 7893 | -0.0087 | 0.29 | NO |
44 | XIAP | XIAP | XIAP | 8230 | -0.013 | 0.28 | NO |
45 | RELA | RELA | RELA | 8267 | -0.013 | 0.28 | NO |
46 | ARHGDIB | ARHGDIB | ARHGDIB | 8494 | -0.016 | 0.28 | NO |
47 | CDK11A | CDK11A | CDK11A | 8825 | -0.02 | 0.26 | NO |
48 | DFFA | DFFA | DFFA | 9419 | -0.027 | 0.24 | NO |
49 | PTK2 | PTK2 | PTK2 | 9477 | -0.028 | 0.25 | NO |
50 | FADD | FADD | FADD | 9587 | -0.03 | 0.25 | NO |
51 | MAP3K14 | MAP3K14 | MAP3K14 | 10347 | -0.041 | 0.23 | NO |
52 | TNFRSF1B | TNFRSF1B | TNFRSF1B | 10475 | -0.043 | 0.24 | NO |
53 | PRKDC | PRKDC | PRKDC | 10506 | -0.044 | 0.25 | NO |
54 | PSEN2 | PSEN2 | PSEN2 | 10839 | -0.05 | 0.25 | NO |
55 | BID | BID | BID | 11041 | -0.054 | 0.26 | NO |
56 | CFLAR | CFLAR | CFLAR | 11091 | -0.055 | 0.28 | NO |
57 | TNF | TNF | TNF | 12983 | -0.11 | 0.22 | NO |
58 | TRAF1 | TRAF1 | TRAF1 | 14144 | -0.16 | 0.22 | NO |
Figure S23. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BUTANOATE METABOLISM.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_BUTANOATE_METABOLISM.heatmap_plot.clus2.17.png)
Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BUTANOATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_HIVNEF_PATHWAY.volcano_plot.clus2.2.png)
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 | PTPN13 | PTPN13 | PTPN13 | 457 | 0.21 | 0.12 | YES |
2 | CASP7 | CASP7 | CASP7 | 703 | 0.16 | 0.22 | YES |
3 | FAS | FAS | FAS | 820 | 0.15 | 0.31 | YES |
4 | MAP2K4 | MAP2K4 | MAP2K4 | 1887 | 0.083 | 0.31 | YES |
5 | CASP10 | CASP10 | CASP10 | 1955 | 0.08 | 0.36 | YES |
6 | LMNA | LMNA | LMNA | 2238 | 0.071 | 0.4 | YES |
7 | CASP3 | CASP3 | CASP3 | 2326 | 0.069 | 0.44 | YES |
8 | CASP8 | CASP8 | CASP8 | 3555 | 0.044 | 0.4 | YES |
9 | MAPK8 | MAPK8 | MAPK8 | 3718 | 0.041 | 0.42 | YES |
10 | PARP1 | PARP1 | PARP1 | 3989 | 0.037 | 0.43 | YES |
11 | LMNB1 | LMNB1 | LMNB1 | 3998 | 0.036 | 0.46 | YES |
12 | SPTAN1 | SPTAN1 | SPTAN1 | 4665 | 0.027 | 0.44 | NO |
13 | PAK1 | PAK1 | PAK1 | 5047 | 0.022 | 0.43 | NO |
14 | PAK2 | PAK2 | PAK2 | 5373 | 0.019 | 0.43 | NO |
15 | FASLG | FASLG | FASLG | 5595 | 0.017 | 0.42 | NO |
16 | RB1 | RB1 | RB1 | 6417 | 0.0075 | 0.38 | NO |
17 | DAXX | DAXX | DAXX | 6686 | 0.0044 | 0.37 | NO |
18 | CASP6 | CASP6 | CASP6 | 6753 | 0.0038 | 0.37 | NO |
19 | LMNB2 | LMNB2 | LMNB2 | 6770 | 0.0036 | 0.37 | NO |
20 | MAP3K1 | MAP3K1 | MAP3K1 | 7176 | -0.00061 | 0.35 | NO |
21 | DFFB | DFFB | DFFB | 7598 | -0.0055 | 0.33 | NO |
22 | ARHGDIB | ARHGDIB | ARHGDIB | 8494 | -0.016 | 0.29 | NO |
23 | JUN | JUN | JUN | 9085 | -0.023 | 0.28 | NO |
24 | DFFA | DFFA | DFFA | 9419 | -0.027 | 0.28 | NO |
25 | FADD | FADD | FADD | 9587 | -0.03 | 0.29 | NO |
26 | FAF1 | FAF1 | FAF1 | 9648 | -0.03 | 0.3 | NO |
27 | MAP3K7 | MAP3K7 | MAP3K7 | 9896 | -0.034 | 0.31 | NO |
28 | PRKDC | PRKDC | PRKDC | 10506 | -0.044 | 0.31 | NO |
29 | CFLAR | CFLAR | CFLAR | 11091 | -0.055 | 0.32 | NO |
30 | RIPK2 | RIPK2 | RIPK2 | 12732 | -0.1 | 0.29 | 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM.heatmap_plot.clus2.12.png)
Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_FAS_PATHWAY.volcano_plot.clus2.3.png)
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 | PLA2G4D | PLA2G4D | PLA2G4D | 124 | 0.33 | 0.1 | YES |
2 | PLA2G4A | PLA2G4A | PLA2G4A | 160 | 0.32 | 0.21 | YES |
3 | PLA2G2A | PLA2G2A | PLA2G2A | 274 | 0.26 | 0.29 | YES |
4 | PLA2G10 | PLA2G10 | PLA2G10 | 388 | 0.22 | 0.36 | YES |
5 | AGPAT9 | AGPAT9 | AGPAT9 | 544 | 0.19 | 0.41 | YES |
6 | LPCAT4 | LPCAT4 | LPCAT4 | 645 | 0.17 | 0.46 | YES |
7 | AGPAT4 | AGPAT4 | AGPAT4 | 802 | 0.15 | 0.51 | YES |
8 | PLD1 | PLD1 | PLD1 | 974 | 0.14 | 0.54 | YES |
9 | PLA2G2F | PLA2G2F | PLA2G2F | 1200 | 0.12 | 0.57 | YES |
10 | LPCAT1 | LPCAT1 | LPCAT1 | 2042 | 0.077 | 0.55 | NO |
11 | AGPAT5 | AGPAT5 | AGPAT5 | 2736 | 0.058 | 0.53 | NO |
12 | PLD2 | PLD2 | PLD2 | 2851 | 0.056 | 0.54 | NO |
13 | PLA2G1B | PLA2G1B | PLA2G1B | 3282 | 0.048 | 0.54 | NO |
14 | GPD1L | GPD1L | GPD1L | 3591 | 0.043 | 0.53 | NO |
15 | GNPAT | GNPAT | GNPAT | 4407 | 0.031 | 0.5 | NO |
16 | AGPAT2 | AGPAT2 | AGPAT2 | 4905 | 0.024 | 0.48 | NO |
17 | PLA2G12A | PLA2G12A | PLA2G12A | 5476 | 0.018 | 0.45 | NO |
18 | AGPAT6 | AGPAT6 | AGPAT6 | 6602 | 0.0053 | 0.39 | NO |
19 | LCLAT1 | LCLAT1 | LCLAT1 | 7084 | 0.00034 | 0.36 | NO |
20 | GPD1 | GPD1 | GPD1 | 7524 | -0.0046 | 0.34 | NO |
21 | AGPAT3 | AGPAT3 | AGPAT3 | 8147 | -0.012 | 0.31 | NO |
22 | AGPAT1 | AGPAT1 | AGPAT1 | 8679 | -0.018 | 0.29 | NO |
23 | GPAM | GPAM | GPAM | 9299 | -0.026 | 0.26 | NO |
24 | PLA2G2D | PLA2G2D | PLA2G2D | 13905 | -0.15 | 0.054 | NO |
25 | GPAT2 | GPAT2 | GPAT2 | 14035 | -0.15 | 0.098 | NO |
26 | PLA2G5 | PLA2G5 | PLA2G5 | 17222 | -0.36 | 0.043 | 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 BASE EXCISION REPAIR.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_BASE_EXCISION_REPAIR.heatmap_plot.clus2.14.png)
Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASE EXCISION REPAIR, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.REACTOME_SYNTHESIS_OF_PA.volcano_plot.clus2.4.png)
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 | TNFRSF10D | TNFRSF10D | TNFRSF10D | 1726 | 0.089 | -0.026 | YES |
2 | MAP2K4 | MAP2K4 | MAP2K4 | 1887 | 0.083 | 0.03 | YES |
3 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 1928 | 0.081 | 0.092 | YES |
4 | CASP10 | CASP10 | CASP10 | 1955 | 0.08 | 0.15 | YES |
5 | TNFSF10 | TNFSF10 | TNFSF10 | 2104 | 0.075 | 0.2 | YES |
6 | PIK3R3 | PIK3R3 | PIK3R3 | 2261 | 0.071 | 0.25 | YES |
7 | RIPK1 | RIPK1 | RIPK1 | 2398 | 0.067 | 0.3 | YES |
8 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 2472 | 0.065 | 0.34 | YES |
9 | PIK3CB | PIK3CB | PIK3CB | 2999 | 0.053 | 0.36 | YES |
10 | MAPK3 | MAPK3 | MAPK3 | 3506 | 0.044 | 0.36 | YES |
11 | CASP8 | CASP8 | CASP8 | 3555 | 0.044 | 0.4 | YES |
12 | MAPK8 | MAPK8 | MAPK8 | 3718 | 0.041 | 0.42 | YES |
13 | CHUK | CHUK | CHUK | 5282 | 0.02 | 0.35 | NO |
14 | MAPK1 | MAPK1 | MAPK1 | 5571 | 0.017 | 0.34 | NO |
15 | TRAF2 | TRAF2 | TRAF2 | 6999 | 0.0013 | 0.26 | NO |
16 | MAP3K1 | MAP3K1 | MAP3K1 | 7176 | -0.00061 | 0.26 | NO |
17 | TNFRSF10C | TNFRSF10C | TNFRSF10C | 7264 | -0.0017 | 0.25 | NO |
18 | DAP3 | DAP3 | DAP3 | 7369 | -0.0029 | 0.25 | NO |
19 | PIK3CA | PIK3CA | PIK3CA | 7612 | -0.0056 | 0.24 | NO |
20 | TRADD | TRADD | TRADD | 7776 | -0.0075 | 0.24 | NO |
21 | PIK3R2 | PIK3R2 | PIK3R2 | 8607 | -0.017 | 0.2 | NO |
22 | FADD | FADD | FADD | 9587 | -0.03 | 0.17 | NO |
23 | IKBKB | IKBKB | IKBKB | 9741 | -0.032 | 0.19 | NO |
24 | PIK3R1 | PIK3R1 | PIK3R1 | 10005 | -0.036 | 0.2 | NO |
25 | CFLAR | CFLAR | CFLAR | 11091 | -0.055 | 0.19 | NO |
26 | PIK3CD | PIK3CD | PIK3CD | 11430 | -0.063 | 0.22 | NO |
27 | IKBKG | IKBKG | IKBKG | 12531 | -0.093 | 0.23 | NO |
28 | SMPD1 | SMPD1 | SMPD1 | 12632 | -0.096 | 0.3 | 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: BIOCARTA FAS PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_FAS_PATHWAY.heatmap_plot.clus2.3.png)
Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FAS PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.PID_TRAIL_PATHWAY.volcano_plot.clus2.5.png)
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 | CASP7 | CASP7 | CASP7 | 703 | 0.16 | 0.039 | YES |
2 | BCL2 | BCL2 | BCL2 | 888 | 0.14 | 0.096 | YES |
3 | BIRC3 | BIRC3 | BIRC3 | 1131 | 0.12 | 0.14 | YES |
4 | APAF1 | APAF1 | APAF1 | 1598 | 0.094 | 0.16 | YES |
5 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 1928 | 0.081 | 0.18 | YES |
6 | CASP10 | CASP10 | CASP10 | 1955 | 0.08 | 0.21 | YES |
7 | TNFSF10 | TNFSF10 | TNFSF10 | 2104 | 0.075 | 0.24 | YES |
8 | LMNA | LMNA | LMNA | 2238 | 0.071 | 0.27 | YES |
9 | CASP3 | CASP3 | CASP3 | 2326 | 0.069 | 0.3 | YES |
10 | RIPK1 | RIPK1 | RIPK1 | 2398 | 0.067 | 0.32 | YES |
11 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 2472 | 0.065 | 0.35 | YES |
12 | CASP9 | CASP9 | CASP9 | 3274 | 0.048 | 0.33 | YES |
13 | CASP8 | CASP8 | CASP8 | 3555 | 0.044 | 0.33 | YES |
14 | CYCS | CYCS | CYCS | 3607 | 0.043 | 0.35 | YES |
15 | BIRC2 | BIRC2 | BIRC2 | 3787 | 0.04 | 0.36 | YES |
16 | SPTAN1 | SPTAN1 | SPTAN1 | 4665 | 0.027 | 0.32 | NO |
17 | CHUK | CHUK | CHUK | 5282 | 0.02 | 0.3 | NO |
18 | NFKB1 | NFKB1 | NFKB1 | 5384 | 0.019 | 0.3 | NO |
19 | NFKBIA | NFKBIA | NFKBIA | 6371 | 0.0081 | 0.25 | NO |
20 | CASP6 | CASP6 | CASP6 | 6753 | 0.0038 | 0.23 | NO |
21 | TRAF2 | TRAF2 | TRAF2 | 6999 | 0.0013 | 0.22 | NO |
22 | DFFB | DFFB | DFFB | 7598 | -0.0055 | 0.18 | NO |
23 | TRADD | TRADD | TRADD | 7776 | -0.0075 | 0.18 | NO |
24 | XIAP | XIAP | XIAP | 8230 | -0.013 | 0.16 | NO |
25 | RELA | RELA | RELA | 8267 | -0.013 | 0.16 | NO |
26 | DFFA | DFFA | DFFA | 9419 | -0.027 | 0.11 | NO |
27 | FADD | FADD | FADD | 9587 | -0.03 | 0.12 | NO |
28 | MAP3K14 | MAP3K14 | MAP3K14 | 10347 | -0.041 | 0.094 | NO |
29 | BID | BID | BID | 11041 | -0.054 | 0.081 | NO |
30 | CFLAR | CFLAR | CFLAR | 11091 | -0.055 | 0.1 | NO |
31 | TNFSF12 | TNFSF12 | TNFSF12 | 12375 | -0.088 | 0.074 | NO |
32 | TNFRSF25 | TNFRSF25 | TNFRSF25 | 15804 | -0.25 | -0.0012 | NO |
33 | GAS2 | GAS2 | GAS2 | 16037 | -0.26 | 0.11 | 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: BIOCARTA HIVNEF PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_HIVNEF_PATHWAY.heatmap_plot.clus2.2.png)
Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HIVNEF PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_DEATH_PATHWAY.volcano_plot.clus2.6.png)
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 | TFF1 | TFF1 | TFF1 | 13 | 0.48 | 0.096 | YES |
2 | C4BPB | C4BPB | C4BPB | 17 | 0.47 | 0.19 | YES |
3 | KLK3 | KLK3 | KLK3 | 93 | 0.36 | 0.26 | YES |
4 | CYP2C18 | CYP2C18 | CYP2C18 | 128 | 0.33 | 0.32 | YES |
5 | FOXA1 | FOXA1 | FOXA1 | 211 | 0.29 | 0.38 | YES |
6 | SERPINA1 | SERPINA1 | SERPINA1 | 261 | 0.26 | 0.42 | YES |
7 | FOXA3 | FOXA3 | FOXA3 | 587 | 0.18 | 0.44 | YES |
8 | FOS | FOS | FOS | 767 | 0.16 | 0.46 | YES |
9 | SFTPA2 | SFTPA2 | SFTPA2 | 877 | 0.14 | 0.49 | YES |
10 | NKX3-1 | NKX3-1 | NKX3-1 | 1553 | 0.097 | 0.47 | NO |
11 | XBP1 | XBP1 | XBP1 | 1678 | 0.091 | 0.48 | NO |
12 | ATP5J | ATP5J | ATP5J | 2874 | 0.056 | 0.43 | NO |
13 | SOD1 | SOD1 | SOD1 | 3076 | 0.052 | 0.42 | NO |
14 | SP1 | SP1 | SP1 | 3159 | 0.05 | 0.43 | NO |
15 | EP300 | EP300 | EP300 | 3463 | 0.045 | 0.42 | NO |
16 | NDUFV3 | NDUFV3 | NDUFV3 | 3618 | 0.042 | 0.42 | NO |
17 | NRIP1 | NRIP1 | NRIP1 | 3914 | 0.038 | 0.41 | NO |
18 | NFIA | NFIA | NFIA | 4019 | 0.036 | 0.42 | NO |
19 | BRCA1 | BRCA1 | BRCA1 | 4603 | 0.028 | 0.39 | NO |
20 | NFIB | NFIB | NFIB | 4699 | 0.027 | 0.39 | NO |
21 | VTN | VTN | VTN | 5103 | 0.022 | 0.37 | NO |
22 | FOXA2 | FOXA2 | FOXA2 | 5677 | 0.016 | 0.34 | NO |
23 | NFIC | NFIC | NFIC | 5726 | 0.015 | 0.34 | NO |
24 | POU2F1 | POU2F1 | POU2F1 | 6257 | 0.0094 | 0.32 | NO |
25 | AP1B1 | AP1B1 | AP1B1 | 6261 | 0.0094 | 0.32 | NO |
26 | NR2F2 | NR2F2 | NR2F2 | 7371 | -0.0029 | 0.26 | NO |
27 | CREBBP | CREBBP | CREBBP | 8274 | -0.013 | 0.21 | NO |
28 | JUN | JUN | JUN | 9085 | -0.023 | 0.17 | NO |
29 | CDKN1B | CDKN1B | CDKN1B | 9547 | -0.029 | 0.15 | NO |
30 | PISD | PISD | PISD | 9999 | -0.036 | 0.13 | NO |
31 | PRDM15 | PRDM15 | PRDM15 | 10049 | -0.036 | 0.13 | NO |
32 | NCOA3 | NCOA3 | NCOA3 | 11978 | -0.077 | 0.042 | NO |
33 | DSCAM | DSCAM | DSCAM | 11979 | -0.077 | 0.057 | NO |
34 | GCG | GCG | GCG | 12082 | -0.079 | 0.067 | NO |
35 | SFTPD | SFTPD | SFTPD | 12728 | -0.099 | 0.051 | NO |
36 | SHH | SHH | SHH | 12941 | -0.11 | 0.061 | NO |
37 | AR | AR | AR | 13387 | -0.12 | 0.061 | NO |
38 | SFTPA1 | SFTPA1 | SFTPA1 | 13495 | -0.13 | 0.081 | NO |
39 | COL18A1 | COL18A1 | COL18A1 | 14033 | -0.15 | 0.081 | NO |
40 | ESR1 | ESR1 | ESR1 | 14876 | -0.19 | 0.073 | NO |
41 | CEBPB | CEBPB | CEBPB | 15001 | -0.2 | 0.11 | NO |
42 | APOB | APOB | APOB | 16574 | -0.3 | 0.079 | 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.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_DEATH_PATHWAY.heatmap_plot.clus2.6.png)
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
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.PID_HNF3APATHWAY.volcano_plot.clus2.7.png)
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 | MAP2K4 | MAP2K4 | MAP2K4 | 1887 | 0.083 | -0.015 | YES |
2 | LMNA | LMNA | LMNA | 2238 | 0.071 | 0.044 | YES |
3 | CASP3 | CASP3 | CASP3 | 2326 | 0.069 | 0.11 | YES |
4 | RIPK1 | RIPK1 | RIPK1 | 2398 | 0.067 | 0.18 | YES |
5 | CASP8 | CASP8 | CASP8 | 3555 | 0.044 | 0.17 | YES |
6 | MAPK8 | MAPK8 | MAPK8 | 3718 | 0.041 | 0.2 | YES |
7 | PARP1 | PARP1 | PARP1 | 3989 | 0.037 | 0.23 | YES |
8 | LMNB1 | LMNB1 | LMNB1 | 3998 | 0.036 | 0.27 | YES |
9 | BAG4 | BAG4 | BAG4 | 4147 | 0.034 | 0.3 | YES |
10 | MADD | MADD | MADD | 4629 | 0.028 | 0.3 | YES |
11 | SPTAN1 | SPTAN1 | SPTAN1 | 4665 | 0.027 | 0.33 | YES |
12 | PAK1 | PAK1 | PAK1 | 5047 | 0.022 | 0.33 | YES |
13 | PAK2 | PAK2 | PAK2 | 5373 | 0.019 | 0.33 | YES |
14 | CRADD | CRADD | CRADD | 5451 | 0.018 | 0.35 | YES |
15 | RB1 | RB1 | RB1 | 6417 | 0.0075 | 0.3 | NO |
16 | CASP2 | CASP2 | CASP2 | 6623 | 0.0051 | 0.3 | NO |
17 | LMNB2 | LMNB2 | LMNB2 | 6770 | 0.0036 | 0.29 | NO |
18 | TRAF2 | TRAF2 | TRAF2 | 6999 | 0.0013 | 0.28 | NO |
19 | MAP3K1 | MAP3K1 | MAP3K1 | 7176 | -0.00061 | 0.27 | NO |
20 | DFFB | DFFB | DFFB | 7598 | -0.0055 | 0.26 | NO |
21 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 7613 | -0.0057 | 0.26 | NO |
22 | TRADD | TRADD | TRADD | 7776 | -0.0075 | 0.26 | NO |
23 | ARHGDIB | ARHGDIB | ARHGDIB | 8494 | -0.016 | 0.24 | NO |
24 | JUN | JUN | JUN | 9085 | -0.023 | 0.23 | NO |
25 | DFFA | DFFA | DFFA | 9419 | -0.027 | 0.24 | NO |
26 | FADD | FADD | FADD | 9587 | -0.03 | 0.26 | NO |
27 | MAP3K7 | MAP3K7 | MAP3K7 | 9896 | -0.034 | 0.28 | NO |
28 | PRKDC | PRKDC | PRKDC | 10506 | -0.044 | 0.3 | NO |
29 | TNF | TNF | TNF | 12983 | -0.11 | 0.28 | 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 PYK2 PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_PYK2_PATHWAY.heatmap_plot.clus2.15.png)
Figure S36. 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
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_TNFR1_PATHWAY.volcano_plot.clus2.8.png)
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 | SPDEF | SPDEF | SPDEF | 4 | 0.55 | 0.14 | YES |
2 | KLK3 | KLK3 | KLK3 | 93 | 0.36 | 0.24 | YES |
3 | PDE9A | PDE9A | PDE9A | 972 | 0.14 | 0.22 | YES |
4 | HOXB13 | HOXB13 | HOXB13 | 1051 | 0.13 | 0.25 | YES |
5 | KLK2 | KLK2 | KLK2 | 1157 | 0.12 | 0.28 | YES |
6 | KAT2B | KAT2B | KAT2B | 1221 | 0.12 | 0.3 | YES |
7 | MDM2 | MDM2 | MDM2 | 1320 | 0.11 | 0.33 | YES |
8 | TMPRSS2 | TMPRSS2 | TMPRSS2 | 1862 | 0.084 | 0.32 | YES |
9 | MAP2K4 | MAP2K4 | MAP2K4 | 1887 | 0.083 | 0.34 | YES |
10 | GATA2 | GATA2 | GATA2 | 2347 | 0.069 | 0.33 | YES |
11 | MAP2K6 | MAP2K6 | MAP2K6 | 2618 | 0.061 | 0.34 | YES |
12 | REL | REL | REL | 2967 | 0.054 | 0.33 | YES |
13 | HDAC1 | HDAC1 | HDAC1 | 3011 | 0.053 | 0.34 | YES |
14 | SMARCA2 | SMARCA2 | SMARCA2 | 3146 | 0.05 | 0.35 | YES |
15 | SIRT1 | SIRT1 | SIRT1 | 3349 | 0.047 | 0.35 | YES |
16 | EP300 | EP300 | EP300 | 3463 | 0.045 | 0.36 | YES |
17 | NR2C1 | NR2C1 | NR2C1 | 3508 | 0.044 | 0.36 | YES |
18 | MAPK8 | MAPK8 | MAPK8 | 3718 | 0.041 | 0.36 | YES |
19 | NCOA1 | NCOA1 | NCOA1 | 3838 | 0.039 | 0.37 | YES |
20 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 4237 | 0.033 | 0.35 | NO |
21 | APPBP2 | APPBP2 | APPBP2 | 5039 | 0.023 | 0.32 | NO |
22 | RXRA | RXRA | RXRA | 5757 | 0.015 | 0.28 | NO |
23 | POU2F1 | POU2F1 | POU2F1 | 6257 | 0.0094 | 0.25 | NO |
24 | GNB2L1 | GNB2L1 | GNB2L1 | 7308 | -0.0022 | 0.2 | NO |
25 | KAT5 | KAT5 | KAT5 | 7352 | -0.0027 | 0.19 | NO |
26 | GSK3B | GSK3B | GSK3B | 7625 | -0.0058 | 0.18 | NO |
27 | SMARCE1 | SMARCE1 | SMARCE1 | 7650 | -0.006 | 0.18 | NO |
28 | RCHY1 | RCHY1 | RCHY1 | 7863 | -0.0084 | 0.17 | NO |
29 | NR2C2 | NR2C2 | NR2C2 | 7925 | -0.0091 | 0.17 | NO |
30 | CREBBP | CREBBP | CREBBP | 8274 | -0.013 | 0.16 | NO |
31 | RXRB | RXRB | RXRB | 8302 | -0.013 | 0.16 | NO |
32 | DNAJA1 | DNAJA1 | DNAJA1 | 8346 | -0.014 | 0.16 | NO |
33 | HDAC7 | HDAC7 | HDAC7 | 8452 | -0.015 | 0.16 | NO |
34 | SENP1 | SENP1 | SENP1 | 8479 | -0.015 | 0.16 | NO |
35 | SMARCC1 | SMARCC1 | SMARCC1 | 8561 | -0.016 | 0.16 | NO |
36 | SRC | SRC | SRC | 9083 | -0.023 | 0.14 | NO |
37 | JUN | JUN | JUN | 9085 | -0.023 | 0.14 | NO |
38 | NCOA2 | NCOA2 | NCOA2 | 9447 | -0.028 | 0.13 | NO |
39 | TRIM24 | TRIM24 | TRIM24 | 9939 | -0.035 | 0.11 | NO |
40 | CARM1 | CARM1 | CARM1 | 10243 | -0.039 | 0.1 | NO |
41 | EGR1 | EGR1 | EGR1 | 10383 | -0.042 | 0.11 | NO |
42 | EHMT2 | EHMT2 | EHMT2 | 10717 | -0.047 | 0.1 | NO |
43 | ZMIZ2 | ZMIZ2 | ZMIZ2 | 10960 | -0.052 | 0.1 | NO |
44 | MAPK14 | MAPK14 | MAPK14 | 11295 | -0.06 | 0.099 | NO |
45 | PKN1 | PKN1 | PKN1 | 12028 | -0.078 | 0.079 | NO |
46 | CEBPA | CEBPA | CEBPA | 12303 | -0.085 | 0.087 | NO |
47 | FOXO1 | FOXO1 | FOXO1 | 12947 | -0.11 | 0.08 | NO |
48 | AR | AR | AR | 13387 | -0.12 | 0.088 | NO |
49 | NR3C1 | NR3C1 | NR3C1 | 14358 | -0.17 | 0.078 | NO |
50 | NR0B1 | NR0B1 | NR0B1 | 14932 | -0.19 | 0.098 | NO |
51 | RXRG | RXRG | RXRG | 16219 | -0.28 | 0.099 | 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 TNFR1 PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.BIOCARTA_TNFR1_PATHWAY.heatmap_plot.clus2.8.png)
Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.PID_AR_TF_PATHWAY.volcano_plot.clus2.9.png)
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 | XDH | XDH | XDH | 375 | 0.23 | 0.085 | YES |
2 | GDA | GDA | GDA | 505 | 0.2 | 0.17 | YES |
3 | NT5E | NT5E | NT5E | 637 | 0.18 | 0.24 | YES |
4 | GMPR | GMPR | GMPR | 682 | 0.17 | 0.32 | YES |
5 | ADSSL1 | ADSSL1 | ADSSL1 | 696 | 0.17 | 0.4 | YES |
6 | PNP | PNP | PNP | 2954 | 0.054 | 0.3 | NO |
7 | NT5C2 | NT5C2 | NT5C2 | 3865 | 0.039 | 0.26 | NO |
8 | DCK | DCK | DCK | 4009 | 0.036 | 0.27 | NO |
9 | PFAS | PFAS | PFAS | 4206 | 0.034 | 0.28 | NO |
10 | ADSS | ADSS | ADSS | 4663 | 0.027 | 0.26 | NO |
11 | PAICS | PAICS | PAICS | 5239 | 0.02 | 0.24 | NO |
12 | PPAT | PPAT | PPAT | 5591 | 0.017 | 0.23 | NO |
13 | GMPR2 | GMPR2 | GMPR2 | 5685 | 0.016 | 0.23 | NO |
14 | IMPDH2 | IMPDH2 | IMPDH2 | 5734 | 0.015 | 0.24 | NO |
15 | HPRT1 | HPRT1 | HPRT1 | 5804 | 0.014 | 0.24 | NO |
16 | GART | GART | GART | 6599 | 0.0053 | 0.2 | NO |
17 | NT5C | NT5C | NT5C | 7186 | -0.00074 | 0.16 | NO |
18 | GMPS | GMPS | GMPS | 7435 | -0.0037 | 0.15 | NO |
19 | APRT | APRT | APRT | 7522 | -0.0046 | 0.15 | NO |
20 | AMPD3 | AMPD3 | AMPD3 | 8942 | -0.021 | 0.081 | NO |
21 | CAT | CAT | CAT | 9158 | -0.024 | 0.081 | NO |
22 | AMPD2 | AMPD2 | AMPD2 | 9257 | -0.025 | 0.087 | NO |
23 | DGUOK | DGUOK | DGUOK | 9346 | -0.026 | 0.094 | NO |
24 | IMPDH1 | IMPDH1 | IMPDH1 | 10935 | -0.052 | 0.03 | NO |
25 | GPX1 | GPX1 | GPX1 | 11070 | -0.055 | 0.048 | NO |
26 | ADSL | ADSL | ADSL | 11126 | -0.056 | 0.071 | NO |
27 | ATIC | ATIC | ATIC | 11216 | -0.058 | 0.093 | NO |
28 | AMPD1 | AMPD1 | AMPD1 | 11572 | -0.067 | 0.1 | NO |
29 | ADAL | ADAL | ADAL | 12425 | -0.089 | 0.099 | NO |
30 | ADK | ADK | ADK | 13869 | -0.14 | 0.086 | NO |
31 | NT5C1B | NT5C1B | NT5C1B | 13911 | -0.15 | 0.15 | NO |
32 | ADA | ADA | ADA | 14245 | -0.16 | 0.21 | NO |
Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TRAIL PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.PID_TRAIL_PATHWAY.heatmap_plot.clus2.5.png)
Figure S40. 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
![](COAD-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.REACTOME_PURINE_METABOLISM.volcano_plot.clus2.10.png)
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 TRYPTOPHAN METABOLISM | 37 | genes.ES.table | 0.55 | 1.6 | 0.017 | 0.09 | 0.91 | 0.24 | 0.12 | 0.22 | 0.045 | 0 |
KEGG O GLYCAN BIOSYNTHESIS | 29 | genes.ES.table | 0.49 | 1.3 | 0.13 | 0.19 | 0.99 | 0.28 | 0.18 | 0.23 | 0.14 | 0 |
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM | 43 | genes.ES.table | 0.39 | 1.5 | 0.094 | 0.12 | 0.97 | 0.07 | 0.038 | 0.067 | 0.074 | 0 |
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE | 25 | genes.ES.table | 0.57 | 1.5 | 0.032 | 0.1 | 0.94 | 0.4 | 0.23 | 0.31 | 0.059 | 0 |
KEGG INOSITOL PHOSPHATE METABOLISM | 52 | genes.ES.table | 0.35 | 1.3 | 0.13 | 0.19 | 0.99 | 0.33 | 0.31 | 0.22 | 0.14 | 0 |
KEGG ABC TRANSPORTERS | 43 | genes.ES.table | 0.49 | 1.4 | 0.067 | 0.16 | 0.98 | 0.21 | 0.12 | 0.18 | 0.11 | 0 |
KEGG MAPK SIGNALING PATHWAY | 250 | genes.ES.table | 0.5 | 1.7 | 0 | 0.076 | 0.66 | 0.37 | 0.28 | 0.27 | 0.021 | 0.008 |
KEGG ERBB SIGNALING PATHWAY | 86 | genes.ES.table | 0.46 | 1.7 | 0.013 | 0.077 | 0.66 | 0.13 | 0.076 | 0.12 | 0.021 | 0.009 |
KEGG CALCIUM SIGNALING PATHWAY | 164 | genes.ES.table | 0.61 | 1.6 | 0.0021 | 0.084 | 0.85 | 0.52 | 0.25 | 0.4 | 0.035 | 0.002 |
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION | 236 | genes.ES.table | 0.62 | 1.5 | 0.026 | 0.1 | 0.95 | 0.49 | 0.19 | 0.4 | 0.059 | 0 |
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 | PDE1B | PDE1B | PDE1B | 237 | 0.68 | 0.018 | YES |
2 | PDE1A | PDE1A | PDE1A | 337 | 0.63 | 0.042 | YES |
3 | NGFR | NGFR | NGFR | 343 | 0.63 | 0.07 | YES |
4 | AKT3 | AKT3 | AKT3 | 521 | 0.57 | 0.087 | YES |
5 | TIAM1 | TIAM1 | TIAM1 | 649 | 0.55 | 0.1 | YES |
6 | ADCYAP1 | ADCYAP1 | ADCYAP1 | 743 | 0.52 | 0.12 | YES |
7 | ADCY2 | ADCY2 | ADCY2 | 786 | 0.52 | 0.14 | YES |
8 | NGF | NGF | NGF | 1066 | 0.46 | 0.15 | YES |
9 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 1106 | 0.46 | 0.17 | YES |
10 | NTRK1 | NTRK1 | NTRK1 | 1180 | 0.45 | 0.19 | YES |
11 | MEF2C | MEF2C | MEF2C | 1461 | 0.41 | 0.19 | YES |
12 | PCSK5 | PCSK5 | PCSK5 | 1466 | 0.4 | 0.21 | YES |
13 | MAPK11 | MAPK11 | MAPK11 | 1533 | 0.4 | 0.22 | YES |
14 | ADCY5 | ADCY5 | ADCY5 | 1655 | 0.38 | 0.23 | YES |
15 | FGD2 | FGD2 | FGD2 | 1767 | 0.37 | 0.24 | YES |
16 | RASGRF2 | RASGRF2 | RASGRF2 | 1843 | 0.36 | 0.26 | YES |
17 | ARHGEF17 | ARHGEF17 | ARHGEF17 | 1881 | 0.35 | 0.27 | YES |
18 | CAMK4 | CAMK4 | CAMK4 | 1898 | 0.35 | 0.28 | YES |
19 | SORCS3 | SORCS3 | SORCS3 | 1902 | 0.35 | 0.3 | YES |
20 | PRKAR2B | PRKAR2B | PRKAR2B | 1976 | 0.34 | 0.31 | YES |
21 | ADCY1 | ADCY1 | ADCY1 | 2094 | 0.33 | 0.32 | YES |
22 | VAV1 | VAV1 | VAV1 | 2198 | 0.32 | 0.33 | YES |
23 | MCF2 | MCF2 | MCF2 | 2401 | 0.29 | 0.33 | YES |
24 | ADORA2A | ADORA2A | ADORA2A | 2524 | 0.28 | 0.34 | YES |
25 | PLEKHG2 | PLEKHG2 | PLEKHG2 | 2646 | 0.27 | 0.34 | YES |
26 | ADCY4 | ADCY4 | ADCY4 | 2693 | 0.26 | 0.35 | YES |
27 | PREX1 | PREX1 | PREX1 | 2787 | 0.25 | 0.36 | YES |
28 | TIAM2 | TIAM2 | TIAM2 | 2973 | 0.23 | 0.36 | YES |
29 | NTRK2 | NTRK2 | NTRK2 | 3000 | 0.23 | 0.37 | YES |
30 | ARHGEF4 | ARHGEF4 | ARHGEF4 | 3052 | 0.22 | 0.38 | YES |
31 | DNM1 | DNM1 | DNM1 | 3058 | 0.22 | 0.39 | YES |
32 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3120 | 0.22 | 0.39 | YES |
33 | IRS1 | IRS1 | IRS1 | 3240 | 0.2 | 0.4 | YES |
34 | ADCY7 | ADCY7 | ADCY7 | 3504 | 0.18 | 0.39 | YES |
35 | FGD1 | FGD1 | FGD1 | 3508 | 0.18 | 0.4 | YES |
36 | ITPR2 | ITPR2 | ITPR2 | 3553 | 0.18 | 0.4 | YES |
37 | PIK3CA | PIK3CA | PIK3CA | 3573 | 0.18 | 0.41 | YES |
38 | MAPK12 | MAPK12 | MAPK12 | 3642 | 0.17 | 0.41 | YES |
39 | FOXO1 | FOXO1 | FOXO1 | 3696 | 0.17 | 0.42 | YES |
40 | MAG | MAG | MAG | 3858 | 0.16 | 0.42 | YES |
41 | ITSN1 | ITSN1 | ITSN1 | 3873 | 0.16 | 0.42 | YES |
42 | AKAP13 | AKAP13 | AKAP13 | 3962 | 0.15 | 0.42 | YES |
43 | DUSP4 | DUSP4 | DUSP4 | 4116 | 0.14 | 0.42 | YES |
44 | MEF2A | MEF2A | MEF2A | 4201 | 0.14 | 0.42 | YES |
45 | ADCY9 | ADCY9 | ADCY9 | 4351 | 0.13 | 0.42 | YES |
46 | BCL2L11 | BCL2L11 | BCL2L11 | 4392 | 0.13 | 0.43 | YES |
47 | KIDINS220 | KIDINS220 | KIDINS220 | 4396 | 0.13 | 0.43 | YES |
48 | ARHGEF3 | ARHGEF3 | ARHGEF3 | 4564 | 0.12 | 0.43 | YES |
49 | LINGO1 | LINGO1 | LINGO1 | 4599 | 0.12 | 0.43 | YES |
50 | RICTOR | RICTOR | RICTOR | 4620 | 0.12 | 0.44 | YES |
51 | SHC2 | SHC2 | SHC2 | 4712 | 0.11 | 0.44 | YES |
52 | APH1B | APH1B | APH1B | 4717 | 0.11 | 0.44 | YES |
53 | ARHGAP4 | ARHGAP4 | ARHGAP4 | 4770 | 0.11 | 0.44 | YES |
54 | TRIO | TRIO | TRIO | 4785 | 0.11 | 0.45 | YES |
55 | NGFRAP1 | NGFRAP1 | NGFRAP1 | 5008 | 0.1 | 0.44 | YES |
56 | SOS1 | SOS1 | SOS1 | 5044 | 0.099 | 0.44 | YES |
57 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5055 | 0.098 | 0.45 | YES |
58 | FOXO4 | FOXO4 | FOXO4 | 5069 | 0.098 | 0.45 | YES |
59 | FGD3 | FGD3 | FGD3 | 5086 | 0.097 | 0.45 | YES |
60 | PRKAR1A | PRKAR1A | PRKAR1A | 5136 | 0.096 | 0.46 | YES |
61 | DUSP7 | DUSP7 | DUSP7 | 5197 | 0.093 | 0.46 | YES |
62 | RASGRF1 | RASGRF1 | RASGRF1 | 5285 | 0.09 | 0.46 | YES |
63 | CREB1 | CREB1 | CREB1 | 5330 | 0.088 | 0.46 | YES |
64 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 5398 | 0.086 | 0.46 | YES |
65 | ADAM17 | ADAM17 | ADAM17 | 5450 | 0.085 | 0.46 | YES |
66 | PIK3R1 | PIK3R1 | PIK3R1 | 5759 | 0.077 | 0.44 | NO |
67 | PRKCE | PRKCE | PRKCE | 5921 | 0.073 | 0.44 | NO |
68 | RAP1A | RAP1A | RAP1A | 5925 | 0.072 | 0.44 | NO |
69 | FRS2 | FRS2 | FRS2 | 5939 | 0.072 | 0.44 | NO |
70 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 6042 | 0.07 | 0.44 | NO |
71 | SOS2 | SOS2 | SOS2 | 6080 | 0.069 | 0.44 | NO |
72 | NFKBIA | NFKBIA | NFKBIA | 6124 | 0.068 | 0.44 | NO |
73 | SHC1 | SHC1 | SHC1 | 6210 | 0.066 | 0.44 | NO |
74 | DUSP3 | DUSP3 | DUSP3 | 6226 | 0.066 | 0.44 | NO |
75 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 6251 | 0.065 | 0.44 | NO |
76 | MTOR | MTOR | MTOR | 6358 | 0.063 | 0.44 | NO |
77 | PTEN | PTEN | PTEN | 6576 | 0.058 | 0.43 | NO |
78 | GRB2 | GRB2 | GRB2 | 6785 | 0.054 | 0.42 | NO |
79 | PRKACA | PRKACA | PRKACA | 6809 | 0.054 | 0.42 | NO |
80 | PLCG1 | PLCG1 | PLCG1 | 6814 | 0.053 | 0.43 | NO |
81 | BRAF | BRAF | BRAF | 6874 | 0.052 | 0.43 | NO |
82 | TRAF6 | TRAF6 | TRAF6 | 6889 | 0.052 | 0.43 | NO |
83 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 6918 | 0.051 | 0.43 | NO |
84 | RIT1 | RIT1 | RIT1 | 6967 | 0.05 | 0.43 | NO |
85 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 7015 | 0.049 | 0.43 | NO |
86 | MAPK7 | MAPK7 | MAPK7 | 7017 | 0.049 | 0.43 | NO |
87 | SH3GL2 | SH3GL2 | SH3GL2 | 7024 | 0.049 | 0.43 | NO |
88 | NR4A1 | NR4A1 | NR4A1 | 7094 | 0.048 | 0.43 | NO |
89 | STAT3 | STAT3 | STAT3 | 7190 | 0.046 | 0.43 | NO |
90 | PRKCA | PRKCA | PRKCA | 7209 | 0.045 | 0.43 | NO |
91 | ARHGEF18 | ARHGEF18 | ARHGEF18 | 7235 | 0.045 | 0.43 | NO |
92 | PIK3CB | PIK3CB | PIK3CB | 7239 | 0.045 | 0.43 | NO |
93 | PRKCG | PRKCG | PRKCG | 7292 | 0.044 | 0.43 | NO |
94 | CRK | CRK | CRK | 7369 | 0.043 | 0.43 | NO |
95 | CHUK | CHUK | CHUK | 7389 | 0.043 | 0.43 | NO |
96 | KRAS | KRAS | KRAS | 7479 | 0.041 | 0.42 | NO |
97 | FURIN | FURIN | FURIN | 7499 | 0.041 | 0.43 | NO |
98 | ATF1 | ATF1 | ATF1 | 7520 | 0.04 | 0.43 | NO |
99 | RIPK2 | RIPK2 | RIPK2 | 7533 | 0.04 | 0.43 | NO |
100 | ELK1 | ELK1 | ELK1 | 7595 | 0.039 | 0.43 | NO |
101 | MAP2K1 | MAP2K1 | MAP2K1 | 7607 | 0.039 | 0.43 | NO |
102 | RALB | RALB | RALB | 7608 | 0.039 | 0.43 | NO |
103 | PDPK1 | PDPK1 | PDPK1 | 7609 | 0.039 | 0.43 | NO |
104 | MAPK8 | MAPK8 | MAPK8 | 7660 | 0.038 | 0.43 | NO |
105 | NET1 | NET1 | NET1 | 7690 | 0.037 | 0.43 | NO |
106 | FGD4 | FGD4 | FGD4 | 7694 | 0.037 | 0.43 | NO |
107 | PRKACB | PRKACB | PRKACB | 7719 | 0.037 | 0.43 | NO |
108 | RPS27A | RPS27A | RPS27A | 7772 | 0.036 | 0.43 | NO |
109 | CDKN1B | CDKN1B | CDKN1B | 7821 | 0.035 | 0.43 | NO |
110 | IKBKB | IKBKB | IKBKB | 7884 | 0.034 | 0.43 | NO |
111 | ARHGEF9 | ARHGEF9 | ARHGEF9 | 7911 | 0.034 | 0.43 | NO |
112 | IRS2 | IRS2 | IRS2 | 8010 | 0.032 | 0.42 | NO |
113 | PRKCI | PRKCI | PRKCI | 8086 | 0.031 | 0.42 | NO |
114 | RALGDS | RALGDS | RALGDS | 8087 | 0.031 | 0.42 | NO |
115 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 8168 | 0.03 | 0.42 | NO |
116 | MAGED1 | MAGED1 | MAGED1 | 8188 | 0.029 | 0.42 | NO |
117 | RELA | RELA | RELA | 8255 | 0.028 | 0.42 | NO |
118 | ECT2 | ECT2 | ECT2 | 8364 | 0.027 | 0.41 | NO |
119 | AP2M1 | AP2M1 | AP2M1 | 8422 | 0.026 | 0.41 | NO |
120 | AP2A1 | AP2A1 | AP2A1 | 8508 | 0.024 | 0.41 | NO |
121 | MYD88 | MYD88 | MYD88 | 8616 | 0.023 | 0.4 | NO |
122 | NCSTN | NCSTN | NCSTN | 8819 | 0.02 | 0.39 | NO |
123 | FOXO3 | FOXO3 | FOXO3 | 8826 | 0.02 | 0.39 | NO |
124 | MAPK1 | MAPK1 | MAPK1 | 8927 | 0.018 | 0.39 | NO |
125 | NRAS | NRAS | NRAS | 8928 | 0.018 | 0.39 | NO |
126 | CLTC | CLTC | CLTC | 9003 | 0.018 | 0.38 | NO |
127 | MDM2 | MDM2 | MDM2 | 9123 | 0.016 | 0.38 | NO |
128 | ABR | ABR | ABR | 9138 | 0.016 | 0.38 | NO |
129 | PSEN1 | PSEN1 | PSEN1 | 9153 | 0.016 | 0.38 | NO |
130 | RHOA | RHOA | RHOA | 9156 | 0.016 | 0.38 | NO |
131 | PPP2CB | PPP2CB | PPP2CB | 9165 | 0.015 | 0.38 | NO |
132 | ADCY3 | ADCY3 | ADCY3 | 9240 | 0.014 | 0.38 | NO |
133 | RTN4 | RTN4 | RTN4 | 9278 | 0.013 | 0.37 | NO |
134 | AATF | AATF | AATF | 9318 | 0.013 | 0.37 | NO |
135 | PHLPP1 | PHLPP1 | PHLPP1 | 9513 | 0.0099 | 0.36 | NO |
136 | IRAK1 | IRAK1 | IRAK1 | 9514 | 0.0098 | 0.36 | NO |
137 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 9533 | 0.0095 | 0.36 | NO |
138 | AP2B1 | AP2B1 | AP2B1 | 9647 | 0.0081 | 0.36 | NO |
139 | CALM3 | CALM3 | CALM3 | 9751 | 0.0064 | 0.35 | NO |
140 | CASP2 | CASP2 | CASP2 | 9767 | 0.0062 | 0.35 | NO |
141 | YWHAB | YWHAB | YWHAB | 9789 | 0.0059 | 0.35 | NO |
142 | AKT1 | AKT1 | AKT1 | 9834 | 0.0053 | 0.35 | NO |
143 | GSK3A | GSK3A | GSK3A | 9855 | 0.0051 | 0.35 | NO |
144 | SQSTM1 | SQSTM1 | SQSTM1 | 9871 | 0.0048 | 0.34 | NO |
145 | PRDM4 | PRDM4 | PRDM4 | 9877 | 0.0048 | 0.34 | NO |
146 | CALM1 | CALM1 | CALM1 | 9912 | 0.0044 | 0.34 | NO |
147 | MAPK14 | MAPK14 | MAPK14 | 10276 | -0.00059 | 0.32 | NO |
148 | CALM2 | CALM2 | CALM2 | 10364 | -0.0018 | 0.32 | NO |
149 | OMG | OMG | OMG | 10368 | -0.0018 | 0.32 | NO |
150 | CASP9 | CASP9 | CASP9 | 10375 | -0.0019 | 0.32 | NO |
151 | DUSP6 | DUSP6 | DUSP6 | 10401 | -0.0024 | 0.32 | NO |
152 | AP2A2 | AP2A2 | AP2A2 | 10409 | -0.0025 | 0.32 | NO |
153 | DNAL4 | DNAL4 | DNAL4 | 10480 | -0.0035 | 0.31 | NO |
154 | RALA | RALA | RALA | 10515 | -0.0041 | 0.31 | NO |
155 | PRKAR2A | PRKAR2A | PRKAR2A | 10560 | -0.0047 | 0.31 | NO |
156 | TSC2 | TSC2 | TSC2 | 10581 | -0.005 | 0.31 | NO |
157 | ITPR3 | ITPR3 | ITPR3 | 10607 | -0.0054 | 0.31 | NO |
158 | RAF1 | RAF1 | RAF1 | 10611 | -0.0054 | 0.31 | NO |
159 | CASP3 | CASP3 | CASP3 | 10677 | -0.0064 | 0.3 | NO |
160 | SHC3 | SHC3 | SHC3 | 10720 | -0.0071 | 0.3 | NO |
161 | ARHGDIA | ARHGDIA | ARHGDIA | 10763 | -0.0078 | 0.3 | NO |
162 | HDAC2 | HDAC2 | HDAC2 | 10875 | -0.0096 | 0.29 | NO |
163 | PPP2R1B | PPP2R1B | PPP2R1B | 10912 | -0.01 | 0.29 | NO |
164 | AKT2 | AKT2 | AKT2 | 11018 | -0.012 | 0.29 | NO |
165 | PPP2R5D | PPP2R5D | PPP2R5D | 11060 | -0.012 | 0.28 | NO |
166 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 11109 | -0.013 | 0.28 | NO |
167 | HDAC3 | HDAC3 | HDAC3 | 11242 | -0.015 | 0.28 | NO |
168 | PSENEN | PSENEN | PSENEN | 11247 | -0.015 | 0.28 | NO |
169 | PRKCD | PRKCD | PRKCD | 11331 | -0.016 | 0.27 | NO |
170 | CDKN1A | CDKN1A | CDKN1A | 11383 | -0.017 | 0.27 | NO |
171 | OBSCN | OBSCN | OBSCN | 11397 | -0.017 | 0.27 | NO |
172 | APH1A | APH1A | APH1A | 11426 | -0.017 | 0.27 | NO |
173 | YWHAE | YWHAE | YWHAE | 11432 | -0.018 | 0.27 | NO |
174 | PSEN2 | PSEN2 | PSEN2 | 11497 | -0.018 | 0.27 | NO |
175 | RAC1 | RAC1 | RAC1 | 11915 | -0.025 | 0.24 | NO |
176 | PPP2R1A | PPP2R1A | PPP2R1A | 11975 | -0.026 | 0.24 | NO |
177 | PPP2CA | PPP2CA | PPP2CA | 11986 | -0.026 | 0.24 | NO |
178 | SRC | SRC | SRC | 12005 | -0.027 | 0.24 | NO |
179 | HDAC1 | HDAC1 | HDAC1 | 12079 | -0.028 | 0.24 | NO |
180 | AKT1S1 | AKT1S1 | AKT1S1 | 12220 | -0.03 | 0.24 | NO |
181 | MAP2K5 | MAP2K5 | MAP2K5 | 12249 | -0.031 | 0.24 | NO |
182 | ADCY6 | ADCY6 | ADCY6 | 12296 | -0.031 | 0.23 | NO |
183 | ADRBK1 | ADRBK1 | ADRBK1 | 12321 | -0.032 | 0.23 | NO |
184 | PIK3R2 | PIK3R2 | PIK3R2 | 12407 | -0.033 | 0.23 | NO |
185 | THEM4 | THEM4 | THEM4 | 12626 | -0.036 | 0.22 | NO |
186 | KALRN | KALRN | KALRN | 12729 | -0.038 | 0.22 | NO |
187 | CDK1 | CDK1 | CDK1 | 12971 | -0.042 | 0.2 | NO |
188 | DNM2 | DNM2 | DNM2 | 13045 | -0.044 | 0.2 | NO |
189 | AP2S1 | AP2S1 | AP2S1 | 13096 | -0.044 | 0.2 | NO |
190 | HRAS | HRAS | HRAS | 13243 | -0.047 | 0.2 | NO |
191 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 13398 | -0.05 | 0.19 | NO |
192 | BAD | BAD | BAD | 13679 | -0.055 | 0.18 | NO |
193 | ITGB3BP | ITGB3BP | ITGB3BP | 13715 | -0.056 | 0.18 | NO |
194 | MAP2K2 | MAP2K2 | MAP2K2 | 13800 | -0.058 | 0.17 | NO |
195 | MAPK3 | MAPK3 | MAPK3 | 13966 | -0.061 | 0.17 | NO |
196 | UBA52 | UBA52 | UBA52 | 14153 | -0.065 | 0.16 | NO |
197 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 14408 | -0.071 | 0.15 | NO |
198 | TRIB3 | TRIB3 | TRIB3 | 14604 | -0.076 | 0.14 | NO |
199 | CLTA | CLTA | CLTA | 14605 | -0.076 | 0.14 | NO |
200 | MAPK13 | MAPK13 | MAPK13 | 14662 | -0.077 | 0.15 | NO |
201 | PCSK6 | PCSK6 | PCSK6 | 14831 | -0.082 | 0.14 | NO |
202 | PRKAR1B | PRKAR1B | PRKAR1B | 15053 | -0.088 | 0.13 | NO |
203 | MLST8 | MLST8 | MLST8 | 15125 | -0.09 | 0.13 | NO |
204 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 15463 | -0.1 | 0.12 | NO |
205 | ARHGEF16 | ARHGEF16 | ARHGEF16 | 15473 | -0.1 | 0.12 | NO |
206 | NGEF | NGEF | NGEF | 15930 | -0.12 | 0.1 | NO |
207 | SMPD2 | SMPD2 | SMPD2 | 16522 | -0.15 | 0.075 | NO |
208 | VAV3 | VAV3 | VAV3 | 16601 | -0.16 | 0.078 | 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 TRYPTOPHAN METABOLISM.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_TRYPTOPHAN_METABOLISM.heatmap_plot.clus3.279.png)
Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TRYPTOPHAN METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.REACTOME_SIGNALLING_BY_NGF.volcano_plot.clus3.1.png)
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 | TGFB3 | TGFB3 | TGFB3 | 115 | 0.74 | 0.072 | YES |
2 | VEGFC | VEGFC | VEGFC | 211 | 0.69 | 0.14 | YES |
3 | AKT3 | AKT3 | AKT3 | 521 | 0.57 | 0.18 | YES |
4 | PIK3R5 | PIK3R5 | PIK3R5 | 562 | 0.56 | 0.24 | YES |
5 | HGF | HGF | HGF | 597 | 0.56 | 0.3 | YES |
6 | PIK3CG | PIK3CG | PIK3CG | 611 | 0.55 | 0.35 | YES |
7 | TGFB2 | TGFB2 | TGFB2 | 937 | 0.49 | 0.39 | YES |
8 | PAK3 | PAK3 | PAK3 | 1116 | 0.46 | 0.42 | YES |
9 | PIK3CD | PIK3CD | PIK3CD | 1218 | 0.44 | 0.46 | YES |
10 | ARNT2 | ARNT2 | ARNT2 | 1392 | 0.42 | 0.5 | YES |
11 | ETS1 | ETS1 | ETS1 | 2187 | 0.32 | 0.49 | YES |
12 | PDGFB | PDGFB | PDGFB | 2332 | 0.3 | 0.51 | YES |
13 | FIGF | FIGF | FIGF | 2494 | 0.28 | 0.53 | YES |
14 | TGFB1 | TGFB1 | TGFB1 | 2752 | 0.26 | 0.55 | YES |
15 | PGF | PGF | PGF | 2985 | 0.23 | 0.56 | YES |
16 | PIK3CA | PIK3CA | PIK3CA | 3573 | 0.18 | 0.54 | NO |
17 | HIF1A | HIF1A | HIF1A | 3840 | 0.16 | 0.54 | NO |
18 | EPAS1 | EPAS1 | EPAS1 | 4773 | 0.11 | 0.5 | NO |
19 | EP300 | EP300 | EP300 | 5040 | 0.099 | 0.5 | NO |
20 | SOS1 | SOS1 | SOS1 | 5044 | 0.099 | 0.51 | NO |
21 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5055 | 0.098 | 0.52 | NO |
22 | PIK3R3 | PIK3R3 | PIK3R3 | 5205 | 0.093 | 0.52 | NO |
23 | CREBBP | CREBBP | CREBBP | 5352 | 0.088 | 0.52 | NO |
24 | ARNT | ARNT | ARNT | 5435 | 0.085 | 0.53 | NO |
25 | PIK3R1 | PIK3R1 | PIK3R1 | 5759 | 0.077 | 0.52 | NO |
26 | RAP1A | RAP1A | RAP1A | 5925 | 0.072 | 0.52 | NO |
27 | SOS2 | SOS2 | SOS2 | 6080 | 0.069 | 0.51 | NO |
28 | PTPN11 | PTPN11 | PTPN11 | 6089 | 0.069 | 0.52 | NO |
29 | GRB2 | GRB2 | GRB2 | 6785 | 0.054 | 0.49 | NO |
30 | FLCN | FLCN | FLCN | 6864 | 0.052 | 0.49 | NO |
31 | BRAF | BRAF | BRAF | 6874 | 0.052 | 0.49 | NO |
32 | PAK2 | PAK2 | PAK2 | 7107 | 0.047 | 0.48 | NO |
33 | PIK3CB | PIK3CB | PIK3CB | 7239 | 0.045 | 0.48 | NO |
34 | VEGFB | VEGFB | VEGFB | 7348 | 0.043 | 0.48 | NO |
35 | CRK | CRK | CRK | 7369 | 0.043 | 0.48 | NO |
36 | KRAS | KRAS | KRAS | 7479 | 0.041 | 0.48 | NO |
37 | MAP2K1 | MAP2K1 | MAP2K1 | 7607 | 0.039 | 0.48 | NO |
38 | CDC42 | CDC42 | CDC42 | 8075 | 0.031 | 0.46 | NO |
39 | GAB1 | GAB1 | GAB1 | 8625 | 0.023 | 0.43 | NO |
40 | CRKL | CRKL | CRKL | 8665 | 0.022 | 0.43 | NO |
41 | TGFA | TGFA | TGFA | 8831 | 0.02 | 0.42 | NO |
42 | MAPK1 | MAPK1 | MAPK1 | 8927 | 0.018 | 0.42 | NO |
43 | NRAS | NRAS | NRAS | 8928 | 0.018 | 0.42 | NO |
44 | MET | MET | MET | 9092 | 0.016 | 0.41 | NO |
45 | AKT1 | AKT1 | AKT1 | 9834 | 0.0053 | 0.37 | NO |
46 | CUL2 | CUL2 | CUL2 | 9939 | 0.004 | 0.37 | NO |
47 | EGLN2 | EGLN2 | EGLN2 | 10045 | 0.0026 | 0.36 | NO |
48 | JUN | JUN | JUN | 10052 | 0.0025 | 0.36 | NO |
49 | EGLN3 | EGLN3 | EGLN3 | 10255 | -0.00018 | 0.35 | NO |
50 | RAF1 | RAF1 | RAF1 | 10611 | -0.0054 | 0.33 | NO |
51 | EGLN1 | EGLN1 | EGLN1 | 10712 | -0.007 | 0.33 | NO |
52 | SLC2A1 | SLC2A1 | SLC2A1 | 10832 | -0.0089 | 0.32 | NO |
53 | VHL | VHL | VHL | 10997 | -0.011 | 0.31 | NO |
54 | AKT2 | AKT2 | AKT2 | 11018 | -0.012 | 0.31 | NO |
55 | VEGFA | VEGFA | VEGFA | 11198 | -0.014 | 0.3 | NO |
56 | TCEB1 | TCEB1 | TCEB1 | 11877 | -0.024 | 0.27 | NO |
57 | ARAF | ARAF | ARAF | 11885 | -0.025 | 0.27 | NO |
58 | RAC1 | RAC1 | RAC1 | 11915 | -0.025 | 0.27 | NO |
59 | PAK1 | PAK1 | PAK1 | 12117 | -0.028 | 0.26 | NO |
60 | PIK3R2 | PIK3R2 | PIK3R2 | 12407 | -0.033 | 0.25 | NO |
61 | RAP1B | RAP1B | RAP1B | 12423 | -0.033 | 0.25 | NO |
62 | HRAS | HRAS | HRAS | 13243 | -0.047 | 0.21 | NO |
63 | RBX1 | RBX1 | RBX1 | 13347 | -0.049 | 0.21 | NO |
64 | PAK4 | PAK4 | PAK4 | 13574 | -0.053 | 0.21 | NO |
65 | MAP2K2 | MAP2K2 | MAP2K2 | 13800 | -0.058 | 0.2 | NO |
66 | MAPK3 | MAPK3 | MAPK3 | 13966 | -0.061 | 0.2 | NO |
67 | FH | FH | FH | 14970 | -0.085 | 0.15 | NO |
68 | PAK6 | PAK6 | PAK6 | 15098 | -0.089 | 0.15 | NO |
69 | TCEB2 | TCEB2 | TCEB2 | 15236 | -0.093 | 0.15 | 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 O GLYCAN BIOSYNTHESIS.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_O_GLYCAN_BIOSYNTHESIS.heatmap_plot.clus3.444.png)
Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG O GLYCAN BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_RENAL_CELL_CARCINOMA.volcano_plot.clus3.2.png)
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 | IGF1 | IGF1 | IGF1 | 220 | 0.68 | 0.092 | YES |
2 | AKT3 | AKT3 | AKT3 | 521 | 0.57 | 0.16 | YES |
3 | PIK3R5 | PIK3R5 | PIK3R5 | 562 | 0.56 | 0.25 | YES |
4 | PAK3 | PAK3 | PAK3 | 1116 | 0.46 | 0.29 | YES |
5 | PIK3CD | PIK3CD | PIK3CD | 1218 | 0.44 | 0.35 | YES |
6 | CREB5 | CREB5 | CREB5 | 2596 | 0.27 | 0.31 | YES |
7 | PREX1 | PREX1 | PREX1 | 2787 | 0.25 | 0.34 | YES |
8 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3120 | 0.22 | 0.36 | YES |
9 | ERBB4 | ERBB4 | ERBB4 | 3161 | 0.21 | 0.39 | YES |
10 | IRS1 | IRS1 | IRS1 | 3240 | 0.2 | 0.41 | YES |
11 | F2RL2 | F2RL2 | F2RL2 | 3495 | 0.18 | 0.43 | YES |
12 | PIK3CA | PIK3CA | PIK3CA | 3573 | 0.18 | 0.45 | YES |
13 | CYTH3 | CYTH3 | CYTH3 | 3584 | 0.18 | 0.48 | YES |
14 | SLC2A4 | SLC2A4 | SLC2A4 | 4134 | 0.14 | 0.47 | NO |
15 | SOS1 | SOS1 | SOS1 | 5044 | 0.099 | 0.43 | NO |
16 | CREB1 | CREB1 | CREB1 | 5330 | 0.088 | 0.43 | NO |
17 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 5884 | 0.074 | 0.41 | NO |
18 | SOS2 | SOS2 | SOS2 | 6080 | 0.069 | 0.41 | NO |
19 | SHC1 | SHC1 | SHC1 | 6210 | 0.066 | 0.41 | NO |
20 | MTOR | MTOR | MTOR | 6358 | 0.063 | 0.41 | NO |
21 | PTEN | PTEN | PTEN | 6576 | 0.058 | 0.41 | NO |
22 | GRB2 | GRB2 | GRB2 | 6785 | 0.054 | 0.41 | NO |
23 | GADD45A | GADD45A | GADD45A | 6843 | 0.053 | 0.41 | NO |
24 | YWHAG | YWHAG | YWHAG | 7059 | 0.048 | 0.41 | NO |
25 | PAK2 | PAK2 | PAK2 | 7107 | 0.047 | 0.41 | NO |
26 | YWHAH | YWHAH | YWHAH | 7517 | 0.04 | 0.4 | NO |
27 | CDKN1B | CDKN1B | CDKN1B | 7821 | 0.035 | 0.38 | NO |
28 | BCL2L1 | BCL2L1 | BCL2L1 | 7975 | 0.033 | 0.38 | NO |
29 | IRS2 | IRS2 | IRS2 | 8010 | 0.032 | 0.38 | NO |
30 | NOLC1 | NOLC1 | NOLC1 | 8040 | 0.032 | 0.39 | NO |
31 | CDC42 | CDC42 | CDC42 | 8075 | 0.031 | 0.39 | NO |
32 | PTPN1 | PTPN1 | PTPN1 | 8121 | 0.03 | 0.39 | NO |
33 | PARD3 | PARD3 | PARD3 | 8241 | 0.028 | 0.39 | NO |
34 | CDKN2A | CDKN2A | CDKN2A | 8362 | 0.027 | 0.39 | NO |
35 | PTK2 | PTK2 | PTK2 | 8371 | 0.027 | 0.39 | NO |
36 | TSC1 | TSC1 | TSC1 | 8485 | 0.025 | 0.39 | NO |
37 | GAB1 | GAB1 | GAB1 | 8625 | 0.023 | 0.38 | NO |
38 | INPPL1 | INPPL1 | INPPL1 | 8814 | 0.02 | 0.38 | NO |
39 | FOXO3 | FOXO3 | FOXO3 | 8826 | 0.02 | 0.38 | NO |
40 | GSK3B | GSK3B | GSK3B | 8853 | 0.02 | 0.38 | NO |
41 | MET | MET | MET | 9092 | 0.016 | 0.37 | NO |
42 | YWHAZ | YWHAZ | YWHAZ | 9749 | 0.0064 | 0.34 | NO |
43 | YWHAB | YWHAB | YWHAB | 9789 | 0.0059 | 0.33 | NO |
44 | CDK2 | CDK2 | CDK2 | 9809 | 0.0056 | 0.33 | NO |
45 | AKT1 | AKT1 | AKT1 | 9834 | 0.0053 | 0.33 | NO |
46 | GSK3A | GSK3A | GSK3A | 9855 | 0.0051 | 0.33 | NO |
47 | CREB3 | CREB3 | CREB3 | 9862 | 0.005 | 0.33 | NO |
48 | TSC2 | TSC2 | TSC2 | 10581 | -0.005 | 0.29 | NO |
49 | PPP1R13B | PPP1R13B | PPP1R13B | 10690 | -0.0066 | 0.29 | NO |
50 | AKT2 | AKT2 | AKT2 | 11018 | -0.012 | 0.27 | NO |
51 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 11109 | -0.013 | 0.27 | NO |
52 | YWHAE | YWHAE | YWHAE | 11432 | -0.018 | 0.25 | NO |
53 | IFI27 | IFI27 | IFI27 | 11603 | -0.02 | 0.25 | NO |
54 | YWHAQ | YWHAQ | YWHAQ | 11648 | -0.021 | 0.25 | NO |
55 | PAK1 | PAK1 | PAK1 | 12117 | -0.028 | 0.23 | NO |
56 | MYC | MYC | MYC | 12212 | -0.03 | 0.23 | NO |
57 | PDK1 | PDK1 | PDK1 | 12817 | -0.04 | 0.2 | NO |
58 | IGFBP1 | IGFBP1 | IGFBP1 | 12954 | -0.042 | 0.2 | NO |
59 | SFN | SFN | SFN | 13083 | -0.044 | 0.2 | NO |
60 | PAK4 | PAK4 | PAK4 | 13574 | -0.053 | 0.18 | NO |
61 | BAD | BAD | BAD | 13679 | -0.055 | 0.18 | NO |
62 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 14408 | -0.071 | 0.15 | NO |
63 | PAK6 | PAK6 | PAK6 | 15098 | -0.089 | 0.13 | NO |
64 | PARD6A | PARD6A | PARD6A | 15742 | -0.11 | 0.11 | NO |
65 | EBP | EBP | EBP | 16031 | -0.12 | 0.11 | NO |
Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM.heatmap_plot.clus3.362.png)
Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.SIG_PIP3_SIGNALING_IN_CARDIAC_MYOCTES.volcano_plot.clus3.3.png)
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 | PPP2R2B | PPP2R2B | PPP2R2B | 127 | 0.73 | 0.043 | YES |
2 | PIK3R5 | PIK3R5 | PIK3R5 | 562 | 0.56 | 0.058 | YES |
3 | PIK3CG | PIK3CG | PIK3CG | 611 | 0.55 | 0.093 | YES |
4 | FGR | FGR | FGR | 616 | 0.55 | 0.13 | YES |
5 | PIK3R6 | PIK3R6 | PIK3R6 | 664 | 0.54 | 0.17 | YES |
6 | SPHK1 | SPHK1 | SPHK1 | 913 | 0.49 | 0.19 | YES |
7 | SLA | SLA | SLA | 939 | 0.49 | 0.22 | YES |
8 | ITGB3 | ITGB3 | ITGB3 | 1077 | 0.46 | 0.24 | YES |
9 | MYOCD | MYOCD | MYOCD | 1205 | 0.44 | 0.26 | YES |
10 | PIK3CD | PIK3CD | PIK3CD | 1218 | 0.44 | 0.3 | YES |
11 | DOCK4 | DOCK4 | DOCK4 | 1341 | 0.42 | 0.32 | YES |
12 | HCK | HCK | HCK | 1347 | 0.42 | 0.35 | YES |
13 | MAPK10 | MAPK10 | MAPK10 | 1365 | 0.42 | 0.37 | YES |
14 | S1PR1 | S1PR1 | S1PR1 | 1455 | 0.41 | 0.4 | YES |
15 | TAGLN | TAGLN | TAGLN | 1620 | 0.38 | 0.41 | YES |
16 | PDGFRB | PDGFRB | PDGFRB | 1827 | 0.36 | 0.43 | YES |
17 | FYN | FYN | FYN | 2193 | 0.32 | 0.43 | YES |
18 | ACTA2 | ACTA2 | ACTA2 | 2237 | 0.31 | 0.45 | YES |
19 | PDGFB | PDGFB | PDGFB | 2332 | 0.3 | 0.46 | YES |
20 | JAK2 | JAK2 | JAK2 | 3053 | 0.22 | 0.44 | YES |
21 | ITGAV | ITGAV | ITGAV | 3070 | 0.22 | 0.45 | YES |
22 | LCK | LCK | LCK | 3127 | 0.22 | 0.46 | YES |
23 | BLK | BLK | BLK | 3169 | 0.21 | 0.48 | YES |
24 | PIK3CA | PIK3CA | PIK3CA | 3573 | 0.18 | 0.47 | YES |
25 | STAT1 | STAT1 | STAT1 | 3797 | 0.16 | 0.46 | YES |
26 | LRP1 | LRP1 | LRP1 | 3875 | 0.16 | 0.47 | YES |
27 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 4112 | 0.14 | 0.47 | YES |
28 | CBL | CBL | CBL | 4160 | 0.14 | 0.48 | YES |
29 | PLA2G4A | PLA2G4A | PLA2G4A | 4321 | 0.13 | 0.48 | YES |
30 | SOS1 | SOS1 | SOS1 | 5044 | 0.099 | 0.44 | YES |
31 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5055 | 0.098 | 0.45 | YES |
32 | PTPRJ | PTPRJ | PTPRJ | 5191 | 0.093 | 0.45 | YES |
33 | PIK3R3 | PIK3R3 | PIK3R3 | 5205 | 0.093 | 0.45 | YES |
34 | KSR1 | KSR1 | KSR1 | 5253 | 0.091 | 0.46 | YES |
35 | PAG1 | PAG1 | PAG1 | 5426 | 0.086 | 0.45 | YES |
36 | SIPA1 | SIPA1 | SIPA1 | 5458 | 0.084 | 0.46 | YES |
37 | STAT5A | STAT5A | STAT5A | 5529 | 0.082 | 0.46 | YES |
38 | GRB10 | GRB10 | GRB10 | 5537 | 0.082 | 0.46 | YES |
39 | BAIAP2 | BAIAP2 | BAIAP2 | 5685 | 0.079 | 0.46 | YES |
40 | PIK3R1 | PIK3R1 | PIK3R1 | 5759 | 0.077 | 0.46 | YES |
41 | VAV2 | VAV2 | VAV2 | 5824 | 0.075 | 0.46 | YES |
42 | ARAP1 | ARAP1 | ARAP1 | 5830 | 0.075 | 0.47 | YES |
43 | STAT5B | STAT5B | STAT5B | 5892 | 0.073 | 0.47 | YES |
44 | PRKCE | PRKCE | PRKCE | 5921 | 0.073 | 0.47 | YES |
45 | RAP1A | RAP1A | RAP1A | 5925 | 0.072 | 0.48 | YES |
46 | LYN | LYN | LYN | 5970 | 0.072 | 0.48 | YES |
47 | NCK1 | NCK1 | NCK1 | 6008 | 0.07 | 0.48 | YES |
48 | SRF | SRF | SRF | 6066 | 0.069 | 0.48 | YES |
49 | PTPN11 | PTPN11 | PTPN11 | 6089 | 0.069 | 0.49 | YES |
50 | RASA1 | RASA1 | RASA1 | 6134 | 0.068 | 0.49 | YES |
51 | SHC1 | SHC1 | SHC1 | 6210 | 0.066 | 0.49 | YES |
52 | SLC9A3R2 | SLC9A3R2 | SLC9A3R2 | 6326 | 0.063 | 0.49 | YES |
53 | ABL1 | ABL1 | ABL1 | 6374 | 0.062 | 0.49 | YES |
54 | WASF2 | WASF2 | WASF2 | 6379 | 0.062 | 0.49 | YES |
55 | ACTR2 | ACTR2 | ACTR2 | 6408 | 0.062 | 0.5 | YES |
56 | PTEN | PTEN | PTEN | 6576 | 0.058 | 0.49 | NO |
57 | IQGAP1 | IQGAP1 | IQGAP1 | 6705 | 0.056 | 0.49 | NO |
58 | GRB2 | GRB2 | GRB2 | 6785 | 0.054 | 0.49 | NO |
59 | PLCG1 | PLCG1 | PLCG1 | 6814 | 0.053 | 0.49 | NO |
60 | BRAF | BRAF | BRAF | 6874 | 0.052 | 0.49 | NO |
61 | YWHAG | YWHAG | YWHAG | 7059 | 0.048 | 0.48 | NO |
62 | MAP2K7 | MAP2K7 | MAP2K7 | 7082 | 0.048 | 0.48 | NO |
63 | PTPN2 | PTPN2 | PTPN2 | 7101 | 0.048 | 0.49 | NO |
64 | STAT3 | STAT3 | STAT3 | 7190 | 0.046 | 0.49 | NO |
65 | FOS | FOS | FOS | 7194 | 0.046 | 0.49 | NO |
66 | PRKCA | PRKCA | PRKCA | 7209 | 0.045 | 0.49 | NO |
67 | PIK3CB | PIK3CB | PIK3CB | 7239 | 0.045 | 0.49 | NO |
68 | CRK | CRK | CRK | 7369 | 0.043 | 0.49 | NO |
69 | RAB5A | RAB5A | RAB5A | 7410 | 0.042 | 0.49 | NO |
70 | KRAS | KRAS | KRAS | 7479 | 0.041 | 0.49 | NO |
71 | YWHAH | YWHAH | YWHAH | 7517 | 0.04 | 0.49 | NO |
72 | MAP2K4 | MAP2K4 | MAP2K4 | 7559 | 0.04 | 0.49 | NO |
73 | ELK1 | ELK1 | ELK1 | 7595 | 0.039 | 0.49 | NO |
74 | MAP2K1 | MAP2K1 | MAP2K1 | 7607 | 0.039 | 0.49 | NO |
75 | MAPK8 | MAPK8 | MAPK8 | 7660 | 0.038 | 0.49 | NO |
76 | DOK1 | DOK1 | DOK1 | 7876 | 0.034 | 0.48 | NO |
77 | NCKAP1 | NCKAP1 | NCKAP1 | 7889 | 0.034 | 0.48 | NO |
78 | ARPC3 | ARPC3 | ARPC3 | 8117 | 0.03 | 0.47 | NO |
79 | PTPN1 | PTPN1 | PTPN1 | 8121 | 0.03 | 0.48 | NO |
80 | GAB1 | GAB1 | GAB1 | 8625 | 0.023 | 0.45 | NO |
81 | ACTR3 | ACTR3 | ACTR3 | 8754 | 0.021 | 0.44 | NO |
82 | MLLT4 | MLLT4 | MLLT4 | 8894 | 0.019 | 0.44 | NO |
83 | MAPK1 | MAPK1 | MAPK1 | 8927 | 0.018 | 0.44 | NO |
84 | NRAS | NRAS | NRAS | 8928 | 0.018 | 0.44 | NO |
85 | BCAR1 | BCAR1 | BCAR1 | 8976 | 0.018 | 0.44 | NO |
86 | ARPC1B | ARPC1B | ARPC1B | 9012 | 0.017 | 0.44 | NO |
87 | ARPC2 | ARPC2 | ARPC2 | 9061 | 0.017 | 0.43 | NO |
88 | RHOA | RHOA | RHOA | 9156 | 0.016 | 0.43 | NO |
89 | ACTN4 | ACTN4 | ACTN4 | 9182 | 0.015 | 0.43 | NO |
90 | YES1 | YES1 | YES1 | 9183 | 0.015 | 0.43 | NO |
91 | ABI1 | ABI1 | ABI1 | 9298 | 0.013 | 0.42 | NO |
92 | EPS8 | EPS8 | EPS8 | 9568 | 0.009 | 0.41 | NO |
93 | YWHAZ | YWHAZ | YWHAZ | 9749 | 0.0064 | 0.4 | NO |
94 | WASL | WASL | WASL | 9785 | 0.0059 | 0.4 | NO |
95 | YWHAB | YWHAB | YWHAB | 9789 | 0.0059 | 0.4 | NO |
96 | JUN | JUN | JUN | 10052 | 0.0025 | 0.38 | NO |
97 | NCK2 | NCK2 | NCK2 | 10123 | 0.0015 | 0.38 | NO |
98 | CSK | CSK | CSK | 10196 | 0.00053 | 0.38 | NO |
99 | ARPC5 | ARPC5 | ARPC5 | 10281 | -0.00066 | 0.37 | NO |
100 | USP6NL | USP6NL | USP6NL | 10376 | -0.0019 | 0.37 | NO |
101 | RAF1 | RAF1 | RAF1 | 10611 | -0.0054 | 0.35 | NO |
102 | ARHGDIA | ARHGDIA | ARHGDIA | 10763 | -0.0078 | 0.35 | NO |
103 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 11109 | -0.013 | 0.33 | NO |
104 | PRKCD | PRKCD | PRKCD | 11331 | -0.016 | 0.32 | NO |
105 | YWHAE | YWHAE | YWHAE | 11432 | -0.018 | 0.31 | NO |
106 | ARPC4 | ARPC4 | ARPC4 | 11495 | -0.018 | 0.31 | NO |
107 | CTTN | CTTN | CTTN | 11556 | -0.019 | 0.31 | NO |
108 | MAPK9 | MAPK9 | MAPK9 | 11622 | -0.02 | 0.3 | NO |
109 | YWHAQ | YWHAQ | YWHAQ | 11648 | -0.021 | 0.3 | NO |
110 | CYFIP2 | CYFIP2 | CYFIP2 | 11705 | -0.022 | 0.3 | NO |
111 | RAC1 | RAC1 | RAC1 | 11915 | -0.025 | 0.29 | NO |
112 | PPP2R1A | PPP2R1A | PPP2R1A | 11975 | -0.026 | 0.29 | NO |
113 | PPP2CA | PPP2CA | PPP2CA | 11986 | -0.026 | 0.29 | NO |
114 | SRC | SRC | SRC | 12005 | -0.027 | 0.29 | NO |
115 | PAK1 | PAK1 | PAK1 | 12117 | -0.028 | 0.29 | NO |
116 | MYC | MYC | MYC | 12212 | -0.03 | 0.29 | NO |
117 | PIK3R2 | PIK3R2 | PIK3R2 | 12407 | -0.033 | 0.28 | NO |
118 | RAP1B | RAP1B | RAP1B | 12423 | -0.033 | 0.28 | NO |
119 | PIN1 | PIN1 | PIN1 | 12661 | -0.037 | 0.27 | NO |
120 | JUND | JUND | JUND | 12919 | -0.041 | 0.26 | NO |
121 | DNM2 | DNM2 | DNM2 | 13045 | -0.044 | 0.25 | NO |
122 | SFN | SFN | SFN | 13083 | -0.044 | 0.26 | NO |
123 | RAB4A | RAB4A | RAB4A | 13211 | -0.047 | 0.25 | NO |
124 | HRAS | HRAS | HRAS | 13243 | -0.047 | 0.25 | NO |
125 | MAP2K2 | MAP2K2 | MAP2K2 | 13800 | -0.058 | 0.22 | NO |
126 | MAPK3 | MAPK3 | MAPK3 | 13966 | -0.061 | 0.22 | NO |
127 | SLC9A3R1 | SLC9A3R1 | SLC9A3R1 | 14773 | -0.08 | 0.18 | NO |
Figure S47. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE.heatmap_plot.clus3.322.png)
Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.PID_PDGFRBPATHWAY.volcano_plot.clus3.4.png)
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 | PRKCB | PRKCB | PRKCB | 683 | 0.54 | 0.039 | YES |
2 | ITGB3 | ITGB3 | ITGB3 | 1077 | 0.46 | 0.084 | YES |
3 | MAPK11 | MAPK11 | MAPK11 | 1533 | 0.4 | 0.12 | YES |
4 | FYN | FYN | FYN | 2193 | 0.32 | 0.12 | YES |
5 | CDH5 | CDH5 | CDH5 | 2208 | 0.31 | 0.17 | YES |
6 | VTN | VTN | VTN | 2255 | 0.31 | 0.21 | YES |
7 | KDR | KDR | KDR | 2287 | 0.31 | 0.25 | YES |
8 | CAV1 | CAV1 | CAV1 | 2406 | 0.29 | 0.29 | YES |
9 | FES | FES | FES | 2486 | 0.28 | 0.32 | YES |
10 | FLT1 | FLT1 | FLT1 | 2523 | 0.28 | 0.36 | YES |
11 | PRKAA2 | PRKAA2 | PRKAA2 | 2768 | 0.26 | 0.39 | YES |
12 | ITGAV | ITGAV | ITGAV | 3070 | 0.22 | 0.4 | YES |
13 | MYOF | MYOF | MYOF | 3518 | 0.18 | 0.4 | YES |
14 | PIK3CA | PIK3CA | PIK3CA | 3573 | 0.18 | 0.42 | YES |
15 | ROCK1 | ROCK1 | ROCK1 | 3707 | 0.17 | 0.44 | YES |
16 | VCL | VCL | VCL | 4110 | 0.14 | 0.44 | YES |
17 | CBL | CBL | CBL | 4160 | 0.14 | 0.46 | YES |
18 | NOS3 | NOS3 | NOS3 | 4486 | 0.12 | 0.46 | YES |
19 | NEDD4 | NEDD4 | NEDD4 | 5178 | 0.094 | 0.43 | YES |
20 | PTPRJ | PTPRJ | PTPRJ | 5191 | 0.093 | 0.44 | YES |
21 | GRB10 | GRB10 | GRB10 | 5537 | 0.082 | 0.44 | YES |
22 | PIK3R1 | PIK3R1 | PIK3R1 | 5759 | 0.077 | 0.43 | YES |
23 | NCK1 | NCK1 | NCK1 | 6008 | 0.07 | 0.43 | YES |
24 | PTPN11 | PTPN11 | PTPN11 | 6089 | 0.069 | 0.44 | YES |
25 | FBXW11 | FBXW11 | FBXW11 | 6198 | 0.066 | 0.44 | YES |
26 | IQGAP1 | IQGAP1 | IQGAP1 | 6705 | 0.056 | 0.42 | YES |
27 | GRB2 | GRB2 | GRB2 | 6785 | 0.054 | 0.42 | YES |
28 | PRKACA | PRKACA | PRKACA | 6809 | 0.054 | 0.43 | YES |
29 | PLCG1 | PLCG1 | PLCG1 | 6814 | 0.053 | 0.44 | YES |
30 | BRAF | BRAF | BRAF | 6874 | 0.052 | 0.44 | YES |
31 | PTPN6 | PTPN6 | PTPN6 | 6962 | 0.05 | 0.44 | YES |
32 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 7015 | 0.049 | 0.45 | YES |
33 | PTPN2 | PTPN2 | PTPN2 | 7101 | 0.048 | 0.45 | YES |
34 | PAK2 | PAK2 | PAK2 | 7107 | 0.047 | 0.46 | YES |
35 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 7164 | 0.046 | 0.46 | YES |
36 | SH2D2A | SH2D2A | SH2D2A | 7181 | 0.046 | 0.46 | YES |
37 | PRKCA | PRKCA | PRKCA | 7209 | 0.045 | 0.47 | YES |
38 | MAP2K1 | MAP2K1 | MAP2K1 | 7607 | 0.039 | 0.45 | NO |
39 | PDPK1 | PDPK1 | PDPK1 | 7609 | 0.039 | 0.46 | NO |
40 | PRKAA1 | PRKAA1 | PRKAA1 | 7894 | 0.034 | 0.45 | NO |
41 | PTK2B | PTK2B | PTK2B | 7906 | 0.034 | 0.45 | NO |
42 | CDC42 | CDC42 | CDC42 | 8075 | 0.031 | 0.45 | NO |
43 | PTK2 | PTK2 | PTK2 | 8371 | 0.027 | 0.44 | NO |
44 | CAMKK2 | CAMKK2 | CAMKK2 | 8514 | 0.024 | 0.43 | NO |
45 | GAB1 | GAB1 | GAB1 | 8625 | 0.023 | 0.43 | NO |
46 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 8713 | 0.022 | 0.43 | NO |
47 | MAPK1 | MAPK1 | MAPK1 | 8927 | 0.018 | 0.42 | NO |
48 | PXN | PXN | PXN | 8958 | 0.018 | 0.42 | NO |
49 | RHOA | RHOA | RHOA | 9156 | 0.016 | 0.41 | NO |
50 | AKT1 | AKT1 | AKT1 | 9834 | 0.0053 | 0.37 | NO |
51 | MAP2K3 | MAP2K3 | MAP2K3 | 9933 | 0.0042 | 0.37 | NO |
52 | NCK2 | NCK2 | NCK2 | 10123 | 0.0015 | 0.36 | NO |
53 | MAPK14 | MAPK14 | MAPK14 | 10276 | -0.00059 | 0.35 | NO |
54 | CTNNB1 | CTNNB1 | CTNNB1 | 10504 | -0.004 | 0.34 | NO |
55 | CTNNA1 | CTNNA1 | CTNNA1 | 10529 | -0.0044 | 0.34 | NO |
56 | RAF1 | RAF1 | RAF1 | 10611 | -0.0054 | 0.33 | NO |
57 | VEGFA | VEGFA | VEGFA | 11198 | -0.014 | 0.3 | NO |
58 | PRKCD | PRKCD | PRKCD | 11331 | -0.016 | 0.3 | NO |
59 | HGS | HGS | HGS | 11509 | -0.019 | 0.29 | NO |
60 | PRKAG1 | PRKAG1 | PRKAG1 | 11694 | -0.021 | 0.28 | NO |
61 | SHB | SHB | SHB | 11814 | -0.024 | 0.28 | NO |
62 | SRC | SRC | SRC | 12005 | -0.027 | 0.27 | NO |
63 | AKAP1 | AKAP1 | AKAP1 | 12129 | -0.029 | 0.27 | NO |
64 | DNM2 | DNM2 | DNM2 | 13045 | -0.044 | 0.22 | NO |
65 | ARF1 | ARF1 | ARF1 | 13308 | -0.048 | 0.22 | NO |
66 | MAP2K2 | MAP2K2 | MAP2K2 | 13800 | -0.058 | 0.2 | NO |
67 | MAPK3 | MAPK3 | MAPK3 | 13966 | -0.061 | 0.2 | NO |
68 | PRKAB1 | PRKAB1 | PRKAB1 | 15006 | -0.086 | 0.15 | NO |
69 | MAP2K6 | MAP2K6 | MAP2K6 | 15551 | -0.1 | 0.14 | NO |
Figure S49. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG INOSITOL PHOSPHATE METABOLISM.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_INOSITOL_PHOSPHATE_METABOLISM.heatmap_plot.clus3.438.png)
Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG INOSITOL PHOSPHATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.PID_VEGFR1_2_PATHWAY.volcano_plot.clus3.5.png)
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 | ESR1 | ESR1 | ESR1 | 171 | 0.71 | 0.065 | YES |
2 | AR | AR | AR | 670 | 0.54 | 0.094 | YES |
3 | IL10 | IL10 | IL10 | 1042 | 0.47 | 0.12 | YES |
4 | NR3C1 | NR3C1 | NR3C1 | 1069 | 0.46 | 0.17 | YES |
5 | GATA3 | GATA3 | GATA3 | 1160 | 0.45 | 0.21 | YES |
6 | SERPINE1 | SERPINE1 | SERPINE1 | 1289 | 0.43 | 0.25 | YES |
7 | RUNX2 | RUNX2 | RUNX2 | 1376 | 0.42 | 0.29 | YES |
8 | MEF2C | MEF2C | MEF2C | 1461 | 0.41 | 0.33 | YES |
9 | GSC | GSC | GSC | 1578 | 0.39 | 0.36 | YES |
10 | RUNX3 | RUNX3 | RUNX3 | 1952 | 0.34 | 0.38 | YES |
11 | COL1A2 | COL1A2 | COL1A2 | 2072 | 0.33 | 0.4 | YES |
12 | CDKN2B | CDKN2B | CDKN2B | 2367 | 0.3 | 0.42 | YES |
13 | KAT2B | KAT2B | KAT2B | 3056 | 0.22 | 0.4 | YES |
14 | LAMC1 | LAMC1 | LAMC1 | 3450 | 0.18 | 0.4 | YES |
15 | RUNX1 | RUNX1 | RUNX1 | 3514 | 0.18 | 0.42 | YES |
16 | FOXO1 | FOXO1 | FOXO1 | 3696 | 0.17 | 0.42 | YES |
17 | PIAS3 | PIAS3 | PIAS3 | 3759 | 0.16 | 0.44 | YES |
18 | NCOA2 | NCOA2 | NCOA2 | 3993 | 0.15 | 0.44 | YES |
19 | DLX1 | DLX1 | DLX1 | 4135 | 0.14 | 0.45 | YES |
20 | SMAD7 | SMAD7 | SMAD7 | 4251 | 0.13 | 0.46 | YES |
21 | NCOA1 | NCOA1 | NCOA1 | 4622 | 0.12 | 0.45 | YES |
22 | ATF2 | ATF2 | ATF2 | 4753 | 0.11 | 0.45 | YES |
23 | ITGB5 | ITGB5 | ITGB5 | 4958 | 0.1 | 0.45 | YES |
24 | EP300 | EP300 | EP300 | 5040 | 0.099 | 0.46 | YES |
25 | FOXO4 | FOXO4 | FOXO4 | 5069 | 0.098 | 0.46 | YES |
26 | IRF7 | IRF7 | IRF7 | 5078 | 0.097 | 0.47 | YES |
27 | TFE3 | TFE3 | TFE3 | 5220 | 0.092 | 0.48 | YES |
28 | CREB1 | CREB1 | CREB1 | 5330 | 0.088 | 0.48 | YES |
29 | SKI | SKI | SKI | 5336 | 0.088 | 0.49 | YES |
30 | CREBBP | CREBBP | CREBBP | 5352 | 0.088 | 0.5 | YES |
31 | TGIF2 | TGIF2 | TGIF2 | 5355 | 0.088 | 0.51 | YES |
32 | SKIL | SKIL | SKIL | 5385 | 0.087 | 0.51 | YES |
33 | NCOR1 | NCOR1 | NCOR1 | 5960 | 0.072 | 0.49 | NO |
34 | SAP30 | SAP30 | SAP30 | 6068 | 0.069 | 0.49 | NO |
35 | SMAD2 | SMAD2 | SMAD2 | 6308 | 0.064 | 0.48 | NO |
36 | SMAD3 | SMAD3 | SMAD3 | 6426 | 0.061 | 0.48 | NO |
37 | MAX | MAX | MAX | 6546 | 0.059 | 0.48 | NO |
38 | SIN3A | SIN3A | SIN3A | 6571 | 0.058 | 0.49 | NO |
39 | SP3 | SP3 | SP3 | 6715 | 0.055 | 0.48 | NO |
40 | IL5 | IL5 | IL5 | 6775 | 0.054 | 0.49 | NO |
41 | SNIP1 | SNIP1 | SNIP1 | 6834 | 0.053 | 0.49 | NO |
42 | SIN3B | SIN3B | SIN3B | 7067 | 0.048 | 0.48 | NO |
43 | FOS | FOS | FOS | 7194 | 0.046 | 0.48 | NO |
44 | SP1 | SP1 | SP1 | 7275 | 0.044 | 0.48 | NO |
45 | ATF3 | ATF3 | ATF3 | 7420 | 0.042 | 0.48 | NO |
46 | RBL1 | RBL1 | RBL1 | 7536 | 0.04 | 0.47 | NO |
47 | MED15 | MED15 | MED15 | 7622 | 0.039 | 0.47 | NO |
48 | ZBTB17 | ZBTB17 | ZBTB17 | 7676 | 0.038 | 0.48 | NO |
49 | SMAD4 | SMAD4 | SMAD4 | 7951 | 0.033 | 0.46 | NO |
50 | CBFB | CBFB | CBFB | 8000 | 0.032 | 0.46 | NO |
51 | DCP1A | DCP1A | DCP1A | 8441 | 0.025 | 0.44 | NO |
52 | FOXO3 | FOXO3 | FOXO3 | 8826 | 0.02 | 0.42 | NO |
53 | CEBPB | CEBPB | CEBPB | 9030 | 0.017 | 0.41 | NO |
54 | VDR | VDR | VDR | 9380 | 0.012 | 0.4 | NO |
55 | CDK2 | CDK2 | CDK2 | 9809 | 0.0056 | 0.37 | NO |
56 | AKT1 | AKT1 | AKT1 | 9834 | 0.0053 | 0.37 | NO |
57 | RBBP4 | RBBP4 | RBBP4 | 9845 | 0.0052 | 0.37 | NO |
58 | JUN | JUN | JUN | 10052 | 0.0025 | 0.36 | NO |
59 | HSPA8 | HSPA8 | HSPA8 | 10306 | -0.001 | 0.34 | NO |
60 | PIAS4 | PIAS4 | PIAS4 | 10573 | -0.0048 | 0.33 | NO |
61 | TGIF1 | TGIF1 | TGIF1 | 10839 | -0.009 | 0.32 | NO |
62 | HDAC2 | HDAC2 | HDAC2 | 10875 | -0.0096 | 0.32 | NO |
63 | CDKN1A | CDKN1A | CDKN1A | 11383 | -0.017 | 0.29 | NO |
64 | TCF3 | TCF3 | TCF3 | 11473 | -0.018 | 0.29 | NO |
65 | E2F5 | E2F5 | E2F5 | 11631 | -0.02 | 0.28 | NO |
66 | CTBP1 | CTBP1 | CTBP1 | 11871 | -0.024 | 0.27 | NO |
67 | HDAC1 | HDAC1 | HDAC1 | 12079 | -0.028 | 0.26 | NO |
68 | MYC | MYC | MYC | 12212 | -0.03 | 0.26 | NO |
69 | HNF4A | HNF4A | HNF4A | 12223 | -0.03 | 0.26 | NO |
70 | TFDP1 | TFDP1 | TFDP1 | 12432 | -0.034 | 0.25 | NO |
71 | E2F4 | E2F4 | E2F4 | 12506 | -0.035 | 0.25 | NO |
72 | SAP18 | SAP18 | SAP18 | 12959 | -0.042 | 0.23 | NO |
73 | CDK4 | CDK4 | CDK4 | 13519 | -0.052 | 0.2 | NO |
74 | RBBP7 | RBBP7 | RBBP7 | 13548 | -0.053 | 0.21 | NO |
75 | KAT2A | KAT2A | KAT2A | 13603 | -0.054 | 0.21 | NO |
76 | CITED1 | CITED1 | CITED1 | 13960 | -0.061 | 0.2 | NO |
77 | FOXG1 | FOXG1 | FOXG1 | 14461 | -0.072 | 0.18 | NO |
78 | FOXH1 | FOXH1 | FOXH1 | 16954 | -0.2 | 0.058 | NO |
Figure S51. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ABC TRANSPORTERS.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_ABC_TRANSPORTERS.heatmap_plot.clus3.422.png)
Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ABC TRANSPORTERS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.PID_SMAD2_3NUCLEARPATHWAY.volcano_plot.clus3.6.png)
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 | KLF8 | KLF8 | KLF8 | 1137 | 0.45 | 0.019 | YES |
2 | ITGA5 | ITGA5 | ITGA5 | 1640 | 0.38 | 0.061 | YES |
3 | ELMO1 | ELMO1 | ELMO1 | 2108 | 0.33 | 0.094 | YES |
4 | ETS1 | ETS1 | ETS1 | 2187 | 0.32 | 0.15 | YES |
5 | FYN | FYN | FYN | 2193 | 0.32 | 0.2 | YES |
6 | BMX | BMX | BMX | 2369 | 0.3 | 0.25 | YES |
7 | MMP14 | MMP14 | MMP14 | 2528 | 0.28 | 0.29 | YES |
8 | ITGAV | ITGAV | ITGAV | 3070 | 0.22 | 0.3 | YES |
9 | ASAP1 | ASAP1 | ASAP1 | 3467 | 0.18 | 0.31 | YES |
10 | PIK3CA | PIK3CA | PIK3CA | 3573 | 0.18 | 0.34 | YES |
11 | TLN1 | TLN1 | TLN1 | 3986 | 0.15 | 0.34 | YES |
12 | VCL | VCL | VCL | 4110 | 0.14 | 0.36 | YES |
13 | PTPN21 | PTPN21 | PTPN21 | 4204 | 0.14 | 0.38 | YES |
14 | ACTN1 | ACTN1 | ACTN1 | 4480 | 0.12 | 0.39 | YES |
15 | GIT2 | GIT2 | GIT2 | 4499 | 0.12 | 0.41 | YES |
16 | ACTA1 | ACTA1 | ACTA1 | 4856 | 0.11 | 0.41 | YES |
17 | DOCK1 | DOCK1 | DOCK1 | 4928 | 0.1 | 0.42 | YES |
18 | ITGB5 | ITGB5 | ITGB5 | 4958 | 0.1 | 0.44 | YES |
19 | ITGB1 | ITGB1 | ITGB1 | 5005 | 0.1 | 0.46 | YES |
20 | SOS1 | SOS1 | SOS1 | 5044 | 0.099 | 0.47 | YES |
21 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5055 | 0.098 | 0.49 | YES |
22 | PIK3R1 | PIK3R1 | PIK3R1 | 5759 | 0.077 | 0.47 | YES |
23 | RAP1A | RAP1A | RAP1A | 5925 | 0.072 | 0.47 | YES |
24 | NCK1 | NCK1 | NCK1 | 6008 | 0.07 | 0.48 | YES |
25 | RASA1 | RASA1 | RASA1 | 6134 | 0.068 | 0.48 | YES |
26 | CCND1 | CCND1 | CCND1 | 6209 | 0.066 | 0.49 | YES |
27 | ROCK2 | ROCK2 | ROCK2 | 6608 | 0.058 | 0.48 | YES |
28 | GRB2 | GRB2 | GRB2 | 6785 | 0.054 | 0.48 | YES |
29 | PLCG1 | PLCG1 | PLCG1 | 6814 | 0.053 | 0.49 | YES |
30 | BRAF | BRAF | BRAF | 6874 | 0.052 | 0.49 | YES |
31 | CAPN2 | CAPN2 | CAPN2 | 7272 | 0.044 | 0.48 | YES |
32 | CRK | CRK | CRK | 7369 | 0.043 | 0.48 | YES |
33 | MAP2K4 | MAP2K4 | MAP2K4 | 7559 | 0.04 | 0.48 | YES |
34 | RGNEF | RGNEF | RGNEF | 7566 | 0.039 | 0.49 | YES |
35 | MAP2K1 | MAP2K1 | MAP2K1 | 7607 | 0.039 | 0.49 | YES |
36 | MAPK8 | MAPK8 | MAPK8 | 7660 | 0.038 | 0.5 | YES |
37 | RRAS | RRAS | RRAS | 7999 | 0.032 | 0.48 | NO |
38 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 8168 | 0.03 | 0.48 | NO |
39 | PTK2 | PTK2 | PTK2 | 8371 | 0.027 | 0.47 | NO |
40 | MAPK1 | MAPK1 | MAPK1 | 8927 | 0.018 | 0.44 | NO |
41 | PXN | PXN | PXN | 8958 | 0.018 | 0.45 | NO |
42 | BCAR1 | BCAR1 | BCAR1 | 8976 | 0.018 | 0.45 | NO |
43 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 9054 | 0.017 | 0.45 | NO |
44 | RHOA | RHOA | RHOA | 9156 | 0.016 | 0.44 | NO |
45 | SH3GL1 | SH3GL1 | SH3GL1 | 9163 | 0.015 | 0.45 | NO |
46 | YES1 | YES1 | YES1 | 9183 | 0.015 | 0.45 | NO |
47 | ARHGAP26 | ARHGAP26 | ARHGAP26 | 9723 | 0.0068 | 0.42 | NO |
48 | WASL | WASL | WASL | 9785 | 0.0059 | 0.42 | NO |
49 | JUN | JUN | JUN | 10052 | 0.0025 | 0.4 | NO |
50 | NCK2 | NCK2 | NCK2 | 10123 | 0.0015 | 0.4 | NO |
51 | RAF1 | RAF1 | RAF1 | 10611 | -0.0054 | 0.37 | NO |
52 | MAPK9 | MAPK9 | MAPK9 | 11622 | -0.02 | 0.32 | NO |
53 | RAC1 | RAC1 | RAC1 | 11915 | -0.025 | 0.31 | NO |
54 | SRC | SRC | SRC | 12005 | -0.027 | 0.31 | NO |
55 | PAK1 | PAK1 | PAK1 | 12117 | -0.028 | 0.31 | NO |
56 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 12418 | -0.033 | 0.3 | NO |
57 | RAP1B | RAP1B | RAP1B | 12423 | -0.033 | 0.3 | NO |
58 | GRB7 | GRB7 | GRB7 | 13041 | -0.044 | 0.28 | NO |
Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG MAPK SIGNALING PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_MAPK_SIGNALING_PATHWAY.heatmap_plot.clus3.110.png)
Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MAPK SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.PID_FAK_PATHWAY.volcano_plot.clus3.7.png)
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 | WAS | WAS | WAS | 950 | 0.48 | 0.011 | YES |
2 | SNAI2 | SNAI2 | SNAI2 | 1048 | 0.47 | 0.068 | YES |
3 | FGFR1 | FGFR1 | FGFR1 | 1381 | 0.42 | 0.1 | YES |
4 | PTPRM | PTPRM | PTPRM | 1656 | 0.38 | 0.14 | YES |
5 | WASF3 | WASF3 | WASF3 | 2007 | 0.34 | 0.16 | YES |
6 | FYN | FYN | FYN | 2193 | 0.32 | 0.2 | YES |
7 | SORBS1 | SORBS1 | SORBS1 | 2253 | 0.31 | 0.23 | YES |
8 | WASF1 | WASF1 | WASF1 | 2436 | 0.29 | 0.26 | YES |
9 | TCF7L1 | TCF7L1 | TCF7L1 | 2437 | 0.29 | 0.3 | YES |
10 | ACTN3 | ACTN3 | ACTN3 | 2609 | 0.27 | 0.33 | YES |
11 | SNAI1 | SNAI1 | SNAI1 | 2636 | 0.27 | 0.36 | YES |
12 | ACTN2 | ACTN2 | ACTN2 | 2649 | 0.27 | 0.4 | YES |
13 | LEF1 | LEF1 | LEF1 | 2672 | 0.26 | 0.43 | YES |
14 | CTNNA3 | CTNNA3 | CTNNA3 | 2793 | 0.25 | 0.46 | YES |
15 | FER | FER | FER | 3171 | 0.21 | 0.46 | YES |
16 | TGFBR1 | TGFBR1 | TGFBR1 | 4060 | 0.14 | 0.43 | YES |
17 | VCL | VCL | VCL | 4110 | 0.14 | 0.45 | YES |
18 | RAC2 | RAC2 | RAC2 | 4406 | 0.13 | 0.45 | YES |
19 | ACTN1 | ACTN1 | ACTN1 | 4480 | 0.12 | 0.46 | YES |
20 | EGFR | EGFR | EGFR | 4745 | 0.11 | 0.46 | YES |
21 | TGFBR2 | TGFBR2 | TGFBR2 | 4879 | 0.11 | 0.47 | YES |
22 | EP300 | EP300 | EP300 | 5040 | 0.099 | 0.47 | YES |
23 | PTPRJ | PTPRJ | PTPRJ | 5191 | 0.093 | 0.48 | YES |
24 | IGF1R | IGF1R | IGF1R | 5232 | 0.092 | 0.49 | YES |
25 | CREBBP | CREBBP | CREBBP | 5352 | 0.088 | 0.49 | YES |
26 | TJP1 | TJP1 | TJP1 | 5673 | 0.079 | 0.48 | YES |
27 | BAIAP2 | BAIAP2 | BAIAP2 | 5685 | 0.079 | 0.49 | YES |
28 | CTNNA2 | CTNNA2 | CTNNA2 | 6297 | 0.064 | 0.47 | YES |
29 | PTPRB | PTPRB | PTPRB | 6299 | 0.064 | 0.48 | YES |
30 | SMAD2 | SMAD2 | SMAD2 | 6308 | 0.064 | 0.48 | YES |
31 | WASF2 | WASF2 | WASF2 | 6379 | 0.062 | 0.49 | YES |
32 | SMAD3 | SMAD3 | SMAD3 | 6426 | 0.061 | 0.49 | YES |
33 | LMO7 | LMO7 | LMO7 | 6569 | 0.058 | 0.49 | NO |
34 | IQGAP1 | IQGAP1 | IQGAP1 | 6705 | 0.056 | 0.49 | NO |
35 | MAP3K7 | MAP3K7 | MAP3K7 | 6852 | 0.053 | 0.49 | NO |
36 | PTPN6 | PTPN6 | PTPN6 | 6962 | 0.05 | 0.49 | NO |
37 | INSR | INSR | INSR | 7433 | 0.042 | 0.47 | NO |
38 | SMAD4 | SMAD4 | SMAD4 | 7951 | 0.033 | 0.45 | NO |
39 | CDC42 | CDC42 | CDC42 | 8075 | 0.031 | 0.44 | NO |
40 | PTPN1 | PTPN1 | PTPN1 | 8121 | 0.03 | 0.45 | NO |
41 | SSX2IP | SSX2IP | SSX2IP | 8156 | 0.03 | 0.45 | NO |
42 | CTNND1 | CTNND1 | CTNND1 | 8191 | 0.029 | 0.45 | NO |
43 | PARD3 | PARD3 | PARD3 | 8241 | 0.028 | 0.45 | NO |
44 | MLLT4 | MLLT4 | MLLT4 | 8894 | 0.019 | 0.42 | NO |
45 | MAPK1 | MAPK1 | MAPK1 | 8927 | 0.018 | 0.42 | NO |
46 | MET | MET | MET | 9092 | 0.016 | 0.41 | NO |
47 | PVRL2 | PVRL2 | PVRL2 | 9136 | 0.016 | 0.41 | NO |
48 | RHOA | RHOA | RHOA | 9156 | 0.016 | 0.41 | NO |
49 | ACTN4 | ACTN4 | ACTN4 | 9182 | 0.015 | 0.41 | NO |
50 | YES1 | YES1 | YES1 | 9183 | 0.015 | 0.42 | NO |
51 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 9208 | 0.015 | 0.42 | NO |
52 | ACTB | ACTB | ACTB | 9644 | 0.0081 | 0.39 | NO |
53 | WASL | WASL | WASL | 9785 | 0.0059 | 0.38 | NO |
54 | RAC3 | RAC3 | RAC3 | 10214 | 0.00033 | 0.36 | NO |
55 | CTNNB1 | CTNNB1 | CTNNB1 | 10504 | -0.004 | 0.34 | NO |
56 | CTNNA1 | CTNNA1 | CTNNA1 | 10529 | -0.0044 | 0.34 | NO |
57 | PTPRF | PTPRF | PTPRF | 10824 | -0.0088 | 0.33 | NO |
58 | PVRL1 | PVRL1 | PVRL1 | 11067 | -0.012 | 0.32 | NO |
59 | TCF7L2 | TCF7L2 | TCF7L2 | 11310 | -0.016 | 0.31 | NO |
60 | PVRL3 | PVRL3 | PVRL3 | 11342 | -0.016 | 0.31 | NO |
61 | CDH1 | CDH1 | CDH1 | 11586 | -0.02 | 0.3 | NO |
62 | NLK | NLK | NLK | 11593 | -0.02 | 0.3 | NO |
63 | TCF7 | TCF7 | TCF7 | 11709 | -0.022 | 0.29 | NO |
64 | ACTG1 | ACTG1 | ACTG1 | 11875 | -0.024 | 0.29 | NO |
65 | ERBB2 | ERBB2 | ERBB2 | 11894 | -0.025 | 0.29 | NO |
66 | RAC1 | RAC1 | RAC1 | 11915 | -0.025 | 0.29 | NO |
67 | SRC | SRC | SRC | 12005 | -0.027 | 0.29 | NO |
68 | FARP2 | FARP2 | FARP2 | 12262 | -0.031 | 0.28 | NO |
69 | ACP1 | ACP1 | ACP1 | 13047 | -0.044 | 0.24 | NO |
70 | PVRL4 | PVRL4 | PVRL4 | 13745 | -0.057 | 0.21 | NO |
71 | CSNK2B | CSNK2B | CSNK2B | 13889 | -0.059 | 0.21 | NO |
72 | MAPK3 | MAPK3 | MAPK3 | 13966 | -0.061 | 0.22 | NO |
73 | CSNK2A2 | CSNK2A2 | CSNK2A2 | 14335 | -0.069 | 0.2 | NO |
Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ERBB SIGNALING PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_ERBB_SIGNALING_PATHWAY.heatmap_plot.clus3.108.png)
Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ERBB SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_ADHERENS_JUNCTION.volcano_plot.clus3.8.png)
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 | PDE1B | PDE1B | PDE1B | 237 | 0.68 | 0.039 | YES |
2 | PDE1A | PDE1A | PDE1A | 337 | 0.63 | 0.082 | YES |
3 | AKT3 | AKT3 | AKT3 | 521 | 0.57 | 0.12 | YES |
4 | ADCYAP1 | ADCYAP1 | ADCYAP1 | 743 | 0.52 | 0.14 | YES |
5 | ADCY2 | ADCY2 | ADCY2 | 786 | 0.52 | 0.18 | YES |
6 | NGF | NGF | NGF | 1066 | 0.46 | 0.2 | YES |
7 | NTRK1 | NTRK1 | NTRK1 | 1180 | 0.45 | 0.23 | YES |
8 | MEF2C | MEF2C | MEF2C | 1461 | 0.41 | 0.25 | YES |
9 | MAPK11 | MAPK11 | MAPK11 | 1533 | 0.4 | 0.27 | YES |
10 | ADCY5 | ADCY5 | ADCY5 | 1655 | 0.38 | 0.3 | YES |
11 | CAMK4 | CAMK4 | CAMK4 | 1898 | 0.35 | 0.31 | YES |
12 | PRKAR2B | PRKAR2B | PRKAR2B | 1976 | 0.34 | 0.33 | YES |
13 | ADCY1 | ADCY1 | ADCY1 | 2094 | 0.33 | 0.35 | YES |
14 | ADORA2A | ADORA2A | ADORA2A | 2524 | 0.28 | 0.35 | YES |
15 | ADCY4 | ADCY4 | ADCY4 | 2693 | 0.26 | 0.36 | YES |
16 | NTRK2 | NTRK2 | NTRK2 | 3000 | 0.23 | 0.36 | YES |
17 | DNM1 | DNM1 | DNM1 | 3058 | 0.22 | 0.37 | YES |
18 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3120 | 0.22 | 0.38 | YES |
19 | IRS1 | IRS1 | IRS1 | 3240 | 0.2 | 0.39 | YES |
20 | ADCY7 | ADCY7 | ADCY7 | 3504 | 0.18 | 0.39 | YES |
21 | ITPR2 | ITPR2 | ITPR2 | 3553 | 0.18 | 0.4 | YES |
22 | PIK3CA | PIK3CA | PIK3CA | 3573 | 0.18 | 0.42 | YES |
23 | MAPK12 | MAPK12 | MAPK12 | 3642 | 0.17 | 0.43 | YES |
24 | FOXO1 | FOXO1 | FOXO1 | 3696 | 0.17 | 0.44 | YES |
25 | DUSP4 | DUSP4 | DUSP4 | 4116 | 0.14 | 0.42 | YES |
26 | MEF2A | MEF2A | MEF2A | 4201 | 0.14 | 0.43 | YES |
27 | ADCY9 | ADCY9 | ADCY9 | 4351 | 0.13 | 0.43 | YES |
28 | KIDINS220 | KIDINS220 | KIDINS220 | 4396 | 0.13 | 0.44 | YES |
29 | RICTOR | RICTOR | RICTOR | 4620 | 0.12 | 0.44 | YES |
30 | SHC2 | SHC2 | SHC2 | 4712 | 0.11 | 0.44 | YES |
31 | SOS1 | SOS1 | SOS1 | 5044 | 0.099 | 0.43 | YES |
32 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5055 | 0.098 | 0.44 | YES |
33 | FOXO4 | FOXO4 | FOXO4 | 5069 | 0.098 | 0.44 | YES |
34 | PRKAR1A | PRKAR1A | PRKAR1A | 5136 | 0.096 | 0.44 | YES |
35 | DUSP7 | DUSP7 | DUSP7 | 5197 | 0.093 | 0.45 | YES |
36 | CREB1 | CREB1 | CREB1 | 5330 | 0.088 | 0.45 | NO |
37 | PIK3R1 | PIK3R1 | PIK3R1 | 5759 | 0.077 | 0.43 | NO |
38 | PRKCE | PRKCE | PRKCE | 5921 | 0.073 | 0.43 | NO |
39 | RAP1A | RAP1A | RAP1A | 5925 | 0.072 | 0.43 | NO |
40 | FRS2 | FRS2 | FRS2 | 5939 | 0.072 | 0.44 | NO |
41 | SHC1 | SHC1 | SHC1 | 6210 | 0.066 | 0.43 | NO |
42 | DUSP3 | DUSP3 | DUSP3 | 6226 | 0.066 | 0.43 | NO |
43 | MTOR | MTOR | MTOR | 6358 | 0.063 | 0.43 | NO |
44 | PTEN | PTEN | PTEN | 6576 | 0.058 | 0.42 | NO |
45 | GRB2 | GRB2 | GRB2 | 6785 | 0.054 | 0.41 | NO |
46 | PRKACA | PRKACA | PRKACA | 6809 | 0.054 | 0.42 | NO |
47 | PLCG1 | PLCG1 | PLCG1 | 6814 | 0.053 | 0.42 | NO |
48 | BRAF | BRAF | BRAF | 6874 | 0.052 | 0.42 | NO |
49 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 6918 | 0.051 | 0.42 | NO |
50 | RIT1 | RIT1 | RIT1 | 6967 | 0.05 | 0.42 | NO |
51 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 7015 | 0.049 | 0.42 | NO |
52 | MAPK7 | MAPK7 | MAPK7 | 7017 | 0.049 | 0.43 | NO |
53 | SH3GL2 | SH3GL2 | SH3GL2 | 7024 | 0.049 | 0.43 | NO |
54 | NR4A1 | NR4A1 | NR4A1 | 7094 | 0.048 | 0.43 | NO |
55 | STAT3 | STAT3 | STAT3 | 7190 | 0.046 | 0.43 | NO |
56 | PRKCA | PRKCA | PRKCA | 7209 | 0.045 | 0.43 | NO |
57 | PIK3CB | PIK3CB | PIK3CB | 7239 | 0.045 | 0.44 | NO |
58 | PRKCG | PRKCG | PRKCG | 7292 | 0.044 | 0.44 | NO |
59 | CRK | CRK | CRK | 7369 | 0.043 | 0.43 | NO |
60 | CHUK | CHUK | CHUK | 7389 | 0.043 | 0.44 | NO |
61 | KRAS | KRAS | KRAS | 7479 | 0.041 | 0.44 | NO |
62 | ATF1 | ATF1 | ATF1 | 7520 | 0.04 | 0.44 | NO |
63 | ELK1 | ELK1 | ELK1 | 7595 | 0.039 | 0.43 | NO |
64 | MAP2K1 | MAP2K1 | MAP2K1 | 7607 | 0.039 | 0.44 | NO |
65 | RALB | RALB | RALB | 7608 | 0.039 | 0.44 | NO |
66 | PDPK1 | PDPK1 | PDPK1 | 7609 | 0.039 | 0.44 | NO |
67 | PRKACB | PRKACB | PRKACB | 7719 | 0.037 | 0.44 | NO |
68 | CDKN1B | CDKN1B | CDKN1B | 7821 | 0.035 | 0.44 | NO |
69 | IRS2 | IRS2 | IRS2 | 8010 | 0.032 | 0.43 | NO |
70 | RALGDS | RALGDS | RALGDS | 8087 | 0.031 | 0.43 | NO |
71 | AP2M1 | AP2M1 | AP2M1 | 8422 | 0.026 | 0.41 | NO |
72 | AP2A1 | AP2A1 | AP2A1 | 8508 | 0.024 | 0.41 | NO |
73 | FOXO3 | FOXO3 | FOXO3 | 8826 | 0.02 | 0.39 | NO |
74 | MAPK1 | MAPK1 | MAPK1 | 8927 | 0.018 | 0.39 | NO |
75 | NRAS | NRAS | NRAS | 8928 | 0.018 | 0.39 | NO |
76 | CLTC | CLTC | CLTC | 9003 | 0.018 | 0.38 | NO |
77 | MDM2 | MDM2 | MDM2 | 9123 | 0.016 | 0.38 | NO |
78 | RHOA | RHOA | RHOA | 9156 | 0.016 | 0.38 | NO |
79 | PPP2CB | PPP2CB | PPP2CB | 9165 | 0.015 | 0.38 | NO |
80 | ADCY3 | ADCY3 | ADCY3 | 9240 | 0.014 | 0.38 | NO |
81 | PHLPP1 | PHLPP1 | PHLPP1 | 9513 | 0.0099 | 0.36 | NO |
82 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 9533 | 0.0095 | 0.36 | NO |
83 | AP2B1 | AP2B1 | AP2B1 | 9647 | 0.0081 | 0.36 | NO |
84 | CALM3 | CALM3 | CALM3 | 9751 | 0.0064 | 0.35 | NO |
85 | YWHAB | YWHAB | YWHAB | 9789 | 0.0059 | 0.35 | NO |
86 | AKT1 | AKT1 | AKT1 | 9834 | 0.0053 | 0.35 | NO |
87 | GSK3A | GSK3A | GSK3A | 9855 | 0.0051 | 0.35 | NO |
88 | CALM1 | CALM1 | CALM1 | 9912 | 0.0044 | 0.34 | NO |
89 | MAPK14 | MAPK14 | MAPK14 | 10276 | -0.00059 | 0.32 | NO |
90 | CALM2 | CALM2 | CALM2 | 10364 | -0.0018 | 0.32 | NO |
91 | CASP9 | CASP9 | CASP9 | 10375 | -0.0019 | 0.32 | NO |
92 | DUSP6 | DUSP6 | DUSP6 | 10401 | -0.0024 | 0.32 | NO |
93 | AP2A2 | AP2A2 | AP2A2 | 10409 | -0.0025 | 0.32 | NO |
94 | DNAL4 | DNAL4 | DNAL4 | 10480 | -0.0035 | 0.31 | NO |
95 | RALA | RALA | RALA | 10515 | -0.0041 | 0.31 | NO |
96 | PRKAR2A | PRKAR2A | PRKAR2A | 10560 | -0.0047 | 0.31 | NO |
97 | TSC2 | TSC2 | TSC2 | 10581 | -0.005 | 0.31 | NO |
98 | ITPR3 | ITPR3 | ITPR3 | 10607 | -0.0054 | 0.31 | NO |
99 | RAF1 | RAF1 | RAF1 | 10611 | -0.0054 | 0.31 | NO |
100 | SHC3 | SHC3 | SHC3 | 10720 | -0.0071 | 0.3 | NO |
101 | PPP2R1B | PPP2R1B | PPP2R1B | 10912 | -0.01 | 0.29 | NO |
102 | AKT2 | AKT2 | AKT2 | 11018 | -0.012 | 0.29 | NO |
103 | PPP2R5D | PPP2R5D | PPP2R5D | 11060 | -0.012 | 0.29 | NO |
104 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 11109 | -0.013 | 0.28 | NO |
105 | PRKCD | PRKCD | PRKCD | 11331 | -0.016 | 0.27 | NO |
106 | CDKN1A | CDKN1A | CDKN1A | 11383 | -0.017 | 0.27 | NO |
107 | PPP2R1A | PPP2R1A | PPP2R1A | 11975 | -0.026 | 0.24 | NO |
108 | PPP2CA | PPP2CA | PPP2CA | 11986 | -0.026 | 0.24 | NO |
109 | SRC | SRC | SRC | 12005 | -0.027 | 0.24 | NO |
110 | AKT1S1 | AKT1S1 | AKT1S1 | 12220 | -0.03 | 0.23 | NO |
111 | MAP2K5 | MAP2K5 | MAP2K5 | 12249 | -0.031 | 0.24 | NO |
112 | ADCY6 | ADCY6 | ADCY6 | 12296 | -0.031 | 0.24 | NO |
113 | ADRBK1 | ADRBK1 | ADRBK1 | 12321 | -0.032 | 0.24 | NO |
114 | PIK3R2 | PIK3R2 | PIK3R2 | 12407 | -0.033 | 0.23 | NO |
115 | THEM4 | THEM4 | THEM4 | 12626 | -0.036 | 0.22 | NO |
116 | CDK1 | CDK1 | CDK1 | 12971 | -0.042 | 0.21 | NO |
117 | DNM2 | DNM2 | DNM2 | 13045 | -0.044 | 0.21 | NO |
118 | AP2S1 | AP2S1 | AP2S1 | 13096 | -0.044 | 0.21 | NO |
119 | HRAS | HRAS | HRAS | 13243 | -0.047 | 0.2 | NO |
120 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 13398 | -0.05 | 0.2 | NO |
121 | BAD | BAD | BAD | 13679 | -0.055 | 0.19 | NO |
122 | MAP2K2 | MAP2K2 | MAP2K2 | 13800 | -0.058 | 0.18 | NO |
123 | MAPK3 | MAPK3 | MAPK3 | 13966 | -0.061 | 0.18 | NO |
124 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 14408 | -0.071 | 0.16 | NO |
125 | TRIB3 | TRIB3 | TRIB3 | 14604 | -0.076 | 0.16 | NO |
126 | CLTA | CLTA | CLTA | 14605 | -0.076 | 0.16 | NO |
127 | MAPK13 | MAPK13 | MAPK13 | 14662 | -0.077 | 0.16 | NO |
128 | PRKAR1B | PRKAR1B | PRKAR1B | 15053 | -0.088 | 0.15 | NO |
129 | MLST8 | MLST8 | MLST8 | 15125 | -0.09 | 0.15 | NO |
130 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 15463 | -0.1 | 0.14 | NO |
Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CALCIUM SIGNALING PATHWAY.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_CALCIUM_SIGNALING_PATHWAY.heatmap_plot.clus3.208.png)
Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CALCIUM SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.REACTOME_NGF_SIGNALLING_VIA_TRKA_FROM_THE_PLASMA_MEMBRANE.volcano_plot.clus3.9.png)
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 | THBS4 | THBS4 | THBS4 | 72 | 0.78 | 0.042 | YES |
2 | PDE1B | PDE1B | PDE1B | 237 | 0.68 | 0.072 | YES |
3 | PDE1A | PDE1A | PDE1A | 337 | 0.63 | 0.1 | YES |
4 | THBS2 | THBS2 | THBS2 | 464 | 0.59 | 0.13 | YES |
5 | AKT3 | AKT3 | AKT3 | 521 | 0.57 | 0.16 | YES |
6 | SPP1 | SPP1 | SPP1 | 783 | 0.52 | 0.18 | YES |
7 | ADCY2 | ADCY2 | ADCY2 | 786 | 0.52 | 0.21 | YES |
8 | PDGFC | PDGFC | PDGFC | 1027 | 0.47 | 0.22 | YES |
9 | COL5A2 | COL5A2 | COL5A2 | 1515 | 0.4 | 0.22 | YES |
10 | COL6A3 | COL6A3 | COL6A3 | 1610 | 0.39 | 0.24 | YES |
11 | ADCY5 | ADCY5 | ADCY5 | 1655 | 0.38 | 0.25 | YES |
12 | PDGFRB | PDGFRB | PDGFRB | 1827 | 0.36 | 0.27 | YES |
13 | COL5A1 | COL5A1 | COL5A1 | 1869 | 0.36 | 0.28 | YES |
14 | CAMK4 | CAMK4 | CAMK4 | 1898 | 0.35 | 0.3 | YES |
15 | COL4A4 | COL4A4 | COL4A4 | 1915 | 0.35 | 0.32 | YES |
16 | PRKAR2B | PRKAR2B | PRKAR2B | 1976 | 0.34 | 0.34 | YES |
17 | COL1A1 | COL1A1 | COL1A1 | 2056 | 0.33 | 0.36 | YES |
18 | COL1A2 | COL1A2 | COL1A2 | 2072 | 0.33 | 0.37 | YES |
19 | ADCY1 | ADCY1 | ADCY1 | 2094 | 0.33 | 0.39 | YES |
20 | COL3A1 | COL3A1 | COL3A1 | 2096 | 0.33 | 0.41 | YES |
21 | PDGFB | PDGFB | PDGFB | 2332 | 0.3 | 0.42 | YES |
22 | COL6A2 | COL6A2 | COL6A2 | 2351 | 0.3 | 0.43 | YES |
23 | COL6A1 | COL6A1 | COL6A1 | 2445 | 0.29 | 0.44 | YES |
24 | PDGFRA | PDGFRA | PDGFRA | 2467 | 0.29 | 0.46 | YES |
25 | ADCY4 | ADCY4 | ADCY4 | 2693 | 0.26 | 0.46 | YES |
26 | PDGFD | PDGFD | PDGFD | 2747 | 0.26 | 0.47 | YES |
27 | THBS1 | THBS1 | THBS1 | 2820 | 0.25 | 0.48 | YES |
28 | COL4A2 | COL4A2 | COL4A2 | 2950 | 0.23 | 0.49 | YES |
29 | COL4A3 | COL4A3 | COL4A3 | 3036 | 0.22 | 0.5 | YES |
30 | COL4A1 | COL4A1 | COL4A1 | 3083 | 0.22 | 0.51 | YES |
31 | THBS3 | THBS3 | THBS3 | 3135 | 0.22 | 0.52 | YES |
32 | PLAT | PLAT | PLAT | 3258 | 0.2 | 0.52 | YES |
33 | ADCY7 | ADCY7 | ADCY7 | 3504 | 0.18 | 0.52 | YES |
34 | ITPR2 | ITPR2 | ITPR2 | 3553 | 0.18 | 0.53 | YES |
35 | PIK3CA | PIK3CA | PIK3CA | 3573 | 0.18 | 0.54 | YES |
36 | FOXO1 | FOXO1 | FOXO1 | 3696 | 0.17 | 0.54 | YES |
37 | STAT1 | STAT1 | STAT1 | 3797 | 0.16 | 0.54 | YES |
38 | ADCY9 | ADCY9 | ADCY9 | 4351 | 0.13 | 0.52 | NO |
39 | RICTOR | RICTOR | RICTOR | 4620 | 0.12 | 0.51 | NO |
40 | SOS1 | SOS1 | SOS1 | 5044 | 0.099 | 0.49 | NO |
41 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5055 | 0.098 | 0.5 | NO |
42 | FOXO4 | FOXO4 | FOXO4 | 5069 | 0.098 | 0.5 | NO |
43 | PRKAR1A | PRKAR1A | PRKAR1A | 5136 | 0.096 | 0.51 | NO |
44 | CREB1 | CREB1 | CREB1 | 5330 | 0.088 | 0.5 | NO |
45 | STAT5A | STAT5A | STAT5A | 5529 | 0.082 | 0.49 | NO |
46 | PIK3R1 | PIK3R1 | PIK3R1 | 5759 | 0.077 | 0.49 | NO |
47 | STAT5B | STAT5B | STAT5B | 5892 | 0.073 | 0.48 | NO |
48 | PRKCE | PRKCE | PRKCE | 5921 | 0.073 | 0.49 | NO |
49 | NCK1 | NCK1 | NCK1 | 6008 | 0.07 | 0.48 | NO |
50 | PDGFA | PDGFA | PDGFA | 6122 | 0.068 | 0.48 | NO |
51 | RASA1 | RASA1 | RASA1 | 6134 | 0.068 | 0.49 | NO |
52 | MTOR | MTOR | MTOR | 6358 | 0.063 | 0.48 | NO |
53 | PTEN | PTEN | PTEN | 6576 | 0.058 | 0.47 | NO |
54 | GRB2 | GRB2 | GRB2 | 6785 | 0.054 | 0.46 | NO |
55 | PRKACA | PRKACA | PRKACA | 6809 | 0.054 | 0.46 | NO |
56 | PLCG1 | PLCG1 | PLCG1 | 6814 | 0.053 | 0.46 | NO |
57 | NR4A1 | NR4A1 | NR4A1 | 7094 | 0.048 | 0.45 | NO |
58 | STAT3 | STAT3 | STAT3 | 7190 | 0.046 | 0.45 | NO |
59 | PRKCA | PRKCA | PRKCA | 7209 | 0.045 | 0.45 | NO |
60 | PIK3CB | PIK3CB | PIK3CB | 7239 | 0.045 | 0.45 | NO |
61 | PRKCG | PRKCG | PRKCG | 7292 | 0.044 | 0.45 | NO |
62 | CRK | CRK | CRK | 7369 | 0.043 | 0.45 | NO |
63 | CHUK | CHUK | CHUK | 7389 | 0.043 | 0.45 | NO |
64 | KRAS | KRAS | KRAS | 7479 | 0.041 | 0.45 | NO |
65 | FURIN | FURIN | FURIN | 7499 | 0.041 | 0.45 | NO |
66 | MAP2K1 | MAP2K1 | MAP2K1 | 7607 | 0.039 | 0.45 | NO |
67 | PDPK1 | PDPK1 | PDPK1 | 7609 | 0.039 | 0.45 | NO |
68 | PRKACB | PRKACB | PRKACB | 7719 | 0.037 | 0.44 | NO |
69 | CDKN1B | CDKN1B | CDKN1B | 7821 | 0.035 | 0.44 | NO |
70 | CRKL | CRKL | CRKL | 8665 | 0.022 | 0.4 | NO |
71 | FOXO3 | FOXO3 | FOXO3 | 8826 | 0.02 | 0.39 | NO |
72 | MAPK1 | MAPK1 | MAPK1 | 8927 | 0.018 | 0.38 | NO |
73 | NRAS | NRAS | NRAS | 8928 | 0.018 | 0.38 | NO |
74 | BCAR1 | BCAR1 | BCAR1 | 8976 | 0.018 | 0.38 | NO |
75 | MDM2 | MDM2 | MDM2 | 9123 | 0.016 | 0.38 | NO |
76 | ADCY3 | ADCY3 | ADCY3 | 9240 | 0.014 | 0.37 | NO |
77 | COL9A3 | COL9A3 | COL9A3 | 9365 | 0.012 | 0.36 | NO |
78 | PHLPP1 | PHLPP1 | PHLPP1 | 9513 | 0.0099 | 0.36 | NO |
79 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 9533 | 0.0095 | 0.36 | NO |
80 | CALM3 | CALM3 | CALM3 | 9751 | 0.0064 | 0.34 | NO |
81 | YWHAB | YWHAB | YWHAB | 9789 | 0.0059 | 0.34 | NO |
82 | AKT1 | AKT1 | AKT1 | 9834 | 0.0053 | 0.34 | NO |
83 | GSK3A | GSK3A | GSK3A | 9855 | 0.0051 | 0.34 | NO |
84 | CALM1 | CALM1 | CALM1 | 9912 | 0.0044 | 0.34 | NO |
85 | NCK2 | NCK2 | NCK2 | 10123 | 0.0015 | 0.32 | NO |
86 | CALM2 | CALM2 | CALM2 | 10364 | -0.0018 | 0.31 | NO |
87 | CASP9 | CASP9 | CASP9 | 10375 | -0.0019 | 0.31 | NO |
88 | STAT6 | STAT6 | STAT6 | 10446 | -0.0031 | 0.31 | NO |
89 | PRKAR2A | PRKAR2A | PRKAR2A | 10560 | -0.0047 | 0.3 | NO |
90 | TSC2 | TSC2 | TSC2 | 10581 | -0.005 | 0.3 | NO |
91 | ITPR3 | ITPR3 | ITPR3 | 10607 | -0.0054 | 0.3 | NO |
92 | RAF1 | RAF1 | RAF1 | 10611 | -0.0054 | 0.3 | NO |
93 | AKT2 | AKT2 | AKT2 | 11018 | -0.012 | 0.28 | NO |
94 | PRKCD | PRKCD | PRKCD | 11331 | -0.016 | 0.26 | NO |
95 | CDKN1A | CDKN1A | CDKN1A | 11383 | -0.017 | 0.26 | NO |
96 | COL4A5 | COL4A5 | COL4A5 | 11699 | -0.021 | 0.24 | NO |
97 | SRC | SRC | SRC | 12005 | -0.027 | 0.23 | NO |
98 | AKT1S1 | AKT1S1 | AKT1S1 | 12220 | -0.03 | 0.22 | NO |
99 | ADCY6 | ADCY6 | ADCY6 | 12296 | -0.031 | 0.21 | NO |
100 | ADRBK1 | ADRBK1 | ADRBK1 | 12321 | -0.032 | 0.22 | NO |
101 | PIK3R2 | PIK3R2 | PIK3R2 | 12407 | -0.033 | 0.21 | NO |
102 | THEM4 | THEM4 | THEM4 | 12626 | -0.036 | 0.2 | NO |
103 | CDK1 | CDK1 | CDK1 | 12971 | -0.042 | 0.18 | NO |
104 | GRB7 | GRB7 | GRB7 | 13041 | -0.044 | 0.18 | NO |
105 | HRAS | HRAS | HRAS | 13243 | -0.047 | 0.18 | NO |
106 | COL2A1 | COL2A1 | COL2A1 | 13315 | -0.048 | 0.17 | NO |
107 | BAD | BAD | BAD | 13679 | -0.055 | 0.16 | NO |
108 | MAP2K2 | MAP2K2 | MAP2K2 | 13800 | -0.058 | 0.15 | NO |
109 | MAPK3 | MAPK3 | MAPK3 | 13966 | -0.061 | 0.15 | NO |
110 | TRIB3 | TRIB3 | TRIB3 | 14604 | -0.076 | 0.12 | NO |
111 | PRKAR1B | PRKAR1B | PRKAR1B | 15053 | -0.088 | 0.097 | NO |
112 | MLST8 | MLST8 | MLST8 | 15125 | -0.09 | 0.098 | NO |
113 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 15463 | -0.1 | 0.085 | NO |
114 | COL9A1 | COL9A1 | COL9A1 | 17094 | -0.21 | 0.0063 | NO |
115 | COL9A2 | COL9A2 | COL9A2 | 17242 | -0.24 | 0.012 | NO |
116 | PLG | PLG | PLG | 17921 | -0.52 | 0.0042 | NO |
Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION.heatmap_plot.clus3.323.png)
Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.REACTOME_SIGNALING_BY_PDGF.volcano_plot.clus3.10.png)
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 FRUCTOSE AND MANNOSE METABOLISM | 34 | genes.ES.table | 0.5 | 1.7 | 0.016 | 0.94 | 0.82 | 0.62 | 0.3 | 0.44 | 0.32 | 0.23 |
KEGG PARKINSONS DISEASE | 109 | genes.ES.table | 0.42 | 1.6 | 0.064 | 0.76 | 0.86 | 0.55 | 0.34 | 0.36 | 0.29 | 0.2 |
KEGG PATHOGENIC ESCHERICHIA COLI INFECTION | 52 | genes.ES.table | 0.49 | 1.8 | 0.0021 | 1 | 0.53 | 0.19 | 0.12 | 0.17 | 0.8 | 0.44 |
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS | 116 | genes.ES.table | 0.76 | 1.7 | 0.0022 | 1 | 0.78 | 0.65 | 0.15 | 0.55 | 0.34 | 0.24 |
REACTOME TRANSLATION | 146 | genes.ES.table | 0.49 | 1.6 | 0.1 | 0.76 | 0.89 | 0.13 | 0.12 | 0.12 | 0.34 | 0.21 |
REACTOME MEIOSIS | 97 | genes.ES.table | 0.67 | 1.7 | 0.012 | 1 | 0.78 | 0.41 | 0.12 | 0.37 | 0.38 | 0.26 |
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE | 109 | genes.ES.table | 0.55 | 1.6 | 0.083 | 0.72 | 0.86 | 0.16 | 0.12 | 0.14 | 0.27 | 0.19 |
REACTOME RNA POL I TRANSCRIPTION | 77 | genes.ES.table | 0.73 | 1.7 | 0.016 | 0.75 | 0.82 | 0.51 | 0.12 | 0.45 | 0.25 | 0.19 |
REACTOME PROTEIN FOLDING | 48 | genes.ES.table | 0.38 | 1.7 | 0.027 | 0.86 | 0.82 | 0.21 | 0.18 | 0.17 | 0.29 | 0.22 |
REACTOME METABOLISM OF PROTEINS | 415 | genes.ES.table | 0.31 | 1.7 | 0.027 | 1 | 0.75 | 0.26 | 0.28 | 0.19 | 0.43 | 0.29 |
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 | TUBB8 | TUBB8 | TUBB8 | 54 | 1.2 | 0.19 | YES |
2 | TUBA1A | TUBA1A | TUBA1A | 439 | 0.5 | 0.24 | YES |
3 | TUBB2A | TUBB2A | TUBB2A | 489 | 0.46 | 0.31 | YES |
4 | TUBA3D | TUBA3D | TUBA3D | 640 | 0.38 | 0.37 | YES |
5 | TUBB3 | TUBB3 | TUBB3 | 699 | 0.36 | 0.42 | YES |
6 | TUBA3E | TUBA3E | TUBA3E | 1258 | 0.25 | 0.43 | YES |
7 | TUBAL3 | TUBAL3 | TUBAL3 | 1544 | 0.22 | 0.44 | YES |
8 | TUBB2B | TUBB2B | TUBB2B | 1858 | 0.19 | 0.46 | YES |
9 | CD14 | CD14 | CD14 | 2067 | 0.17 | 0.47 | YES |
10 | TUBA1C | TUBA1C | TUBA1C | 2168 | 0.16 | 0.49 | YES |
11 | WAS | WAS | WAS | 2740 | 0.13 | 0.48 | NO |
12 | TUBB6 | TUBB6 | TUBB6 | 3286 | 0.11 | 0.47 | NO |
13 | TUBA8 | TUBA8 | TUBA8 | 3754 | 0.095 | 0.46 | NO |
14 | ARPC5L | ARPC5L | ARPC5L | 4395 | 0.078 | 0.43 | NO |
15 | TUBA4A | TUBA4A | TUBA4A | 4833 | 0.068 | 0.42 | NO |
16 | TUBA1B | TUBA1B | TUBA1B | 4843 | 0.068 | 0.43 | NO |
17 | OCLN | OCLN | OCLN | 5496 | 0.054 | 0.4 | NO |
18 | ARPC1B | ARPC1B | ARPC1B | 5625 | 0.052 | 0.4 | NO |
19 | ACTB | ACTB | ACTB | 5716 | 0.05 | 0.41 | NO |
20 | ACTG1 | ACTG1 | ACTG1 | 6495 | 0.037 | 0.37 | NO |
21 | HCLS1 | HCLS1 | HCLS1 | 6693 | 0.033 | 0.36 | NO |
22 | ARPC1A | ARPC1A | ARPC1A | 6950 | 0.029 | 0.35 | NO |
23 | KRT18 | KRT18 | KRT18 | 7120 | 0.026 | 0.35 | NO |
24 | YWHAQ | YWHAQ | YWHAQ | 7278 | 0.024 | 0.34 | NO |
25 | TUBB | TUBB | TUBB | 7490 | 0.02 | 0.33 | NO |
26 | LY96 | LY96 | LY96 | 7648 | 0.018 | 0.33 | NO |
27 | CTNNB1 | CTNNB1 | CTNNB1 | 7721 | 0.017 | 0.33 | NO |
28 | ARPC2 | ARPC2 | ARPC2 | 7767 | 0.016 | 0.33 | NO |
29 | CTTN | CTTN | CTTN | 7800 | 0.016 | 0.33 | NO |
30 | ARPC4 | ARPC4 | ARPC4 | 8177 | 0.01 | 0.31 | NO |
31 | RHOA | RHOA | RHOA | 8429 | 0.0065 | 0.3 | NO |
32 | ARPC5 | ARPC5 | ARPC5 | 9063 | -0.0026 | 0.26 | NO |
33 | EZR | EZR | EZR | 9246 | -0.0052 | 0.25 | NO |
34 | NCK2 | NCK2 | NCK2 | 9291 | -0.0057 | 0.25 | NO |
35 | FYN | FYN | FYN | 11312 | -0.034 | 0.14 | NO |
36 | ITGB1 | ITGB1 | ITGB1 | 11612 | -0.039 | 0.13 | NO |
37 | TLR4 | TLR4 | TLR4 | 11816 | -0.042 | 0.13 | NO |
38 | YWHAZ | YWHAZ | YWHAZ | 11934 | -0.043 | 0.13 | NO |
39 | ABL1 | ABL1 | ABL1 | 12430 | -0.051 | 0.11 | NO |
40 | CLDN1 | CLDN1 | CLDN1 | 12947 | -0.059 | 0.088 | NO |
41 | NCK1 | NCK1 | NCK1 | 12961 | -0.059 | 0.096 | NO |
42 | CDC42 | CDC42 | CDC42 | 13006 | -0.06 | 0.1 | NO |
43 | CDH1 | CDH1 | CDH1 | 13044 | -0.061 | 0.11 | NO |
44 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 13476 | -0.068 | 0.098 | NO |
45 | WASL | WASL | WASL | 13602 | -0.07 | 0.1 | NO |
46 | TUBB1 | TUBB1 | TUBB1 | 13785 | -0.073 | 0.1 | NO |
47 | PRKCA | PRKCA | PRKCA | 15178 | -0.1 | 0.041 | NO |
48 | NCL | NCL | NCL | 15559 | -0.11 | 0.037 | NO |
49 | ROCK1 | ROCK1 | ROCK1 | 16396 | -0.13 | 0.011 | NO |
50 | ARPC3 | ARPC3 | ARPC3 | 16440 | -0.14 | 0.03 | NO |
51 | TLR5 | TLR5 | TLR5 | 17321 | -0.18 | 0.0093 | NO |
52 | ROCK2 | ROCK2 | ROCK2 | 17334 | -0.18 | 0.037 | 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 FRUCTOSE AND MANNOSE METABOLISM.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM.heatmap_plot.clus4.11.png)
Figure S62. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION.volcano_plot.clus4.1.png)
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 | HIST1H4K | HIST1H4K | HIST1H4K | 3 | 1.7 | 0.063 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 47 | 1.2 | 0.11 | YES |
3 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 80 | 1.1 | 0.14 | YES |
4 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 150 | 0.88 | 0.17 | YES |
5 | HIST2H3C | HIST2H3C | HIST2H3C | 195 | 0.78 | 0.2 | YES |
6 | HIST2H3D | HIST2H3D | HIST2H3D | 250 | 0.71 | 0.22 | YES |
7 | GTF2H2B | GTF2H2B | GTF2H2B | 299 | 0.64 | 0.24 | YES |
8 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 344 | 0.6 | 0.26 | YES |
9 | HIST1H4J | HIST1H4J | HIST1H4J | 408 | 0.53 | 0.28 | YES |
10 | HIST1H4I | HIST1H4I | HIST1H4I | 503 | 0.46 | 0.29 | YES |
11 | GTF2H2 | GTF2H2 | GTF2H2 | 511 | 0.45 | 0.31 | YES |
12 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 529 | 0.44 | 0.32 | YES |
13 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 566 | 0.42 | 0.34 | YES |
14 | HIST1H4A | HIST1H4A | HIST1H4A | 569 | 0.42 | 0.35 | YES |
15 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 583 | 0.41 | 0.37 | YES |
16 | HIST2H4A | HIST2H4A | HIST2H4A | 586 | 0.41 | 0.38 | YES |
17 | HIST1H3H | HIST1H3H | HIST1H3H | 828 | 0.32 | 0.38 | YES |
18 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 845 | 0.32 | 0.39 | YES |
19 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 858 | 0.32 | 0.4 | YES |
20 | HIST1H4B | HIST1H4B | HIST1H4B | 873 | 0.31 | 0.41 | YES |
21 | HIST1H4D | HIST1H4D | HIST1H4D | 925 | 0.3 | 0.42 | YES |
22 | HIST1H3D | HIST1H3D | HIST1H3D | 927 | 0.3 | 0.43 | YES |
23 | HIST1H4E | HIST1H4E | HIST1H4E | 949 | 0.29 | 0.44 | YES |
24 | HIST1H3B | HIST1H3B | HIST1H3B | 960 | 0.29 | 0.45 | YES |
25 | HIST1H4C | HIST1H4C | HIST1H4C | 966 | 0.29 | 0.46 | YES |
26 | HIST1H3F | HIST1H3F | HIST1H3F | 1080 | 0.27 | 0.47 | YES |
27 | HIST1H3J | HIST1H3J | HIST1H3J | 1221 | 0.25 | 0.47 | YES |
28 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 1359 | 0.23 | 0.47 | YES |
29 | HIST1H3I | HIST1H3I | HIST1H3I | 1413 | 0.23 | 0.48 | YES |
30 | HIST1H4H | HIST1H4H | HIST1H4H | 1474 | 0.22 | 0.48 | YES |
31 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 1634 | 0.21 | 0.48 | YES |
32 | POLR2I | POLR2I | POLR2I | 1638 | 0.21 | 0.49 | YES |
33 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 1699 | 0.2 | 0.49 | YES |
34 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1706 | 0.2 | 0.5 | YES |
35 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 1738 | 0.2 | 0.5 | YES |
36 | HIST1H3C | HIST1H3C | HIST1H3C | 1745 | 0.2 | 0.51 | YES |
37 | HIST1H3G | HIST1H3G | HIST1H3G | 1950 | 0.18 | 0.51 | YES |
38 | HIST1H3A | HIST1H3A | HIST1H3A | 2045 | 0.17 | 0.51 | YES |
39 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2066 | 0.17 | 0.51 | YES |
40 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2121 | 0.17 | 0.52 | YES |
41 | POLR2L | POLR2L | POLR2L | 2179 | 0.16 | 0.52 | YES |
42 | TAF10 | TAF10 | TAF10 | 2450 | 0.15 | 0.51 | NO |
43 | H3F3A | H3F3A | H3F3A | 2480 | 0.14 | 0.51 | NO |
44 | POLR2G | POLR2G | POLR2G | 2585 | 0.14 | 0.51 | NO |
45 | H2AFX | H2AFX | H2AFX | 2653 | 0.14 | 0.51 | NO |
46 | POLR3K | POLR3K | POLR3K | 3258 | 0.11 | 0.48 | NO |
47 | TCEB2 | TCEB2 | TCEB2 | 3368 | 0.11 | 0.48 | NO |
48 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3383 | 0.11 | 0.48 | NO |
49 | LSM10 | LSM10 | LSM10 | 3445 | 0.1 | 0.48 | NO |
50 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 3638 | 0.098 | 0.48 | NO |
51 | SNAPC5 | SNAPC5 | SNAPC5 | 4039 | 0.087 | 0.46 | NO |
52 | POLR2H | POLR2H | POLR2H | 4058 | 0.086 | 0.46 | NO |
53 | COBRA1 | COBRA1 | COBRA1 | 4475 | 0.076 | 0.44 | NO |
54 | POLR1C | POLR1C | POLR1C | 4567 | 0.074 | 0.44 | NO |
55 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 4874 | 0.067 | 0.42 | NO |
56 | MAPK3 | MAPK3 | MAPK3 | 5061 | 0.063 | 0.41 | NO |
57 | CSTF1 | CSTF1 | CSTF1 | 5154 | 0.061 | 0.41 | NO |
58 | POLR2F | POLR2F | POLR2F | 5192 | 0.06 | 0.41 | NO |
59 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 5411 | 0.056 | 0.4 | NO |
60 | POLR3H | POLR3H | POLR3H | 5423 | 0.056 | 0.4 | NO |
61 | THOC4 | THOC4 | THOC4 | 5453 | 0.055 | 0.4 | NO |
62 | POLR2C | POLR2C | POLR2C | 5632 | 0.052 | 0.4 | NO |
63 | POLR2J | POLR2J | POLR2J | 5656 | 0.052 | 0.4 | NO |
64 | SNRPB | SNRPB | SNRPB | 5838 | 0.049 | 0.39 | NO |
65 | POLR2D | POLR2D | POLR2D | 6098 | 0.044 | 0.38 | NO |
66 | SNRPF | SNRPF | SNRPF | 6124 | 0.043 | 0.38 | NO |
67 | CTDP1 | CTDP1 | CTDP1 | 6159 | 0.042 | 0.37 | NO |
68 | U2AF1 | U2AF1 | U2AF1 | 6433 | 0.038 | 0.36 | NO |
69 | ERCC2 | ERCC2 | ERCC2 | 6471 | 0.037 | 0.36 | NO |
70 | BRF2 | BRF2 | BRF2 | 6489 | 0.037 | 0.36 | NO |
71 | CDK9 | CDK9 | CDK9 | 6514 | 0.036 | 0.36 | NO |
72 | POLR2E | POLR2E | POLR2E | 6525 | 0.036 | 0.36 | NO |
73 | CLP1 | CLP1 | CLP1 | 6575 | 0.035 | 0.36 | NO |
74 | POLRMT | POLRMT | POLRMT | 6651 | 0.034 | 0.36 | NO |
75 | GTF3C5 | GTF3C5 | GTF3C5 | 6759 | 0.032 | 0.35 | NO |
76 | RNPS1 | RNPS1 | RNPS1 | 6825 | 0.031 | 0.35 | NO |
77 | POLR3E | POLR3E | POLR3E | 6853 | 0.031 | 0.35 | NO |
78 | RDBP | RDBP | RDBP | 6867 | 0.03 | 0.35 | NO |
79 | POLR3D | POLR3D | POLR3D | 6925 | 0.03 | 0.35 | NO |
80 | ZNF143 | ZNF143 | ZNF143 | 6969 | 0.029 | 0.35 | NO |
81 | POLR3C | POLR3C | POLR3C | 7034 | 0.028 | 0.34 | NO |
82 | TH1L | TH1L | TH1L | 7351 | 0.023 | 0.33 | NO |
83 | CPSF1 | CPSF1 | CPSF1 | 7392 | 0.022 | 0.32 | NO |
84 | H2AFZ | H2AFZ | H2AFZ | 7459 | 0.021 | 0.32 | NO |
85 | POLR3B | POLR3B | POLR3B | 7745 | 0.016 | 0.31 | NO |
86 | TBP | TBP | TBP | 7825 | 0.015 | 0.3 | NO |
87 | EHMT2 | EHMT2 | EHMT2 | 7964 | 0.014 | 0.3 | NO |
88 | GTF2H4 | GTF2H4 | GTF2H4 | 8021 | 0.013 | 0.29 | NO |
89 | WHSC2 | WHSC2 | WHSC2 | 8068 | 0.012 | 0.29 | NO |
90 | SLBP | SLBP | SLBP | 8321 | 0.0084 | 0.28 | NO |
91 | TAF6 | TAF6 | TAF6 | 8522 | 0.005 | 0.27 | NO |
92 | TAF9 | TAF9 | TAF9 | 8588 | 0.0039 | 0.26 | NO |
93 | GTF2E2 | GTF2E2 | GTF2E2 | 8600 | 0.0037 | 0.26 | NO |
94 | SNRPG | SNRPG | SNRPG | 8646 | 0.0032 | 0.26 | NO |
95 | BRF1 | BRF1 | BRF1 | 8790 | 0.00098 | 0.25 | NO |
96 | CPSF3 | CPSF3 | CPSF3 | 8854 | 0.00011 | 0.25 | NO |
97 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 9002 | -0.0019 | 0.24 | NO |
98 | SNAPC2 | SNAPC2 | SNAPC2 | 9015 | -0.002 | 0.24 | NO |
99 | ELL | ELL | ELL | 9157 | -0.0038 | 0.23 | NO |
100 | MNAT1 | MNAT1 | MNAT1 | 9325 | -0.0062 | 0.22 | NO |
101 | TCEA1 | TCEA1 | TCEA1 | 9356 | -0.0068 | 0.22 | NO |
102 | DHX38 | DHX38 | DHX38 | 9407 | -0.0075 | 0.22 | NO |
103 | TAF1C | TAF1C | TAF1C | 9415 | -0.0076 | 0.22 | NO |
104 | U2AF2 | U2AF2 | U2AF2 | 9637 | -0.011 | 0.21 | NO |
105 | ERCC3 | ERCC3 | ERCC3 | 9895 | -0.014 | 0.19 | NO |
106 | POLR1B | POLR1B | POLR1B | 10021 | -0.016 | 0.19 | NO |
107 | GTF2E1 | GTF2E1 | GTF2E1 | 10060 | -0.016 | 0.18 | NO |
108 | MAGOH | MAGOH | MAGOH | 10154 | -0.018 | 0.18 | NO |
109 | GTF2F1 | GTF2F1 | GTF2F1 | 10547 | -0.023 | 0.16 | NO |
110 | TCEB1 | TCEB1 | TCEB1 | 10581 | -0.024 | 0.16 | NO |
111 | POLR1D | POLR1D | POLR1D | 10597 | -0.024 | 0.16 | NO |
112 | POLR2B | POLR2B | POLR2B | 10850 | -0.028 | 0.14 | NO |
113 | SNAPC4 | SNAPC4 | SNAPC4 | 10912 | -0.028 | 0.14 | NO |
114 | SUPT5H | SUPT5H | SUPT5H | 10998 | -0.03 | 0.14 | NO |
115 | POLR3A | POLR3A | POLR3A | 11016 | -0.03 | 0.14 | NO |
116 | GTF2H3 | GTF2H3 | GTF2H3 | 11145 | -0.032 | 0.13 | NO |
117 | CCNH | CCNH | CCNH | 11147 | -0.032 | 0.13 | NO |
118 | GTF3C2 | GTF3C2 | GTF3C2 | 11183 | -0.032 | 0.13 | NO |
119 | NCBP1 | NCBP1 | NCBP1 | 11309 | -0.034 | 0.13 | NO |
120 | GTF3C3 | GTF3C3 | GTF3C3 | 11324 | -0.034 | 0.13 | NO |
121 | TAF5 | TAF5 | TAF5 | 11406 | -0.036 | 0.12 | NO |
122 | NFX1 | NFX1 | NFX1 | 11587 | -0.038 | 0.12 | NO |
123 | SNRPE | SNRPE | SNRPE | 11591 | -0.038 | 0.12 | NO |
124 | SNRPD3 | SNRPD3 | SNRPD3 | 11718 | -0.04 | 0.11 | NO |
125 | PABPN1 | PABPN1 | PABPN1 | 11785 | -0.041 | 0.11 | NO |
126 | CSTF2 | CSTF2 | CSTF2 | 11825 | -0.042 | 0.11 | NO |
127 | TAF4 | TAF4 | TAF4 | 11922 | -0.043 | 0.1 | NO |
128 | RBM8A | RBM8A | RBM8A | 11931 | -0.043 | 0.11 | NO |
129 | POLR3F | POLR3F | POLR3F | 12224 | -0.048 | 0.091 | NO |
130 | CPSF7 | CPSF7 | CPSF7 | 12261 | -0.048 | 0.091 | NO |
131 | NUDT21 | NUDT21 | NUDT21 | 12310 | -0.049 | 0.09 | NO |
132 | SSRP1 | SSRP1 | SSRP1 | 12359 | -0.05 | 0.089 | NO |
133 | GTF2A2 | GTF2A2 | GTF2A2 | 12493 | -0.052 | 0.084 | NO |
134 | GTF2H1 | GTF2H1 | GTF2H1 | 12545 | -0.053 | 0.083 | NO |
135 | ZNF473 | ZNF473 | ZNF473 | 12813 | -0.057 | 0.07 | NO |
136 | RNMT | RNMT | RNMT | 12883 | -0.058 | 0.068 | NO |
137 | GTF3C4 | GTF3C4 | GTF3C4 | 12897 | -0.058 | 0.07 | NO |
138 | GTF2B | GTF2B | GTF2B | 12905 | -0.058 | 0.072 | NO |
139 | NFIB | NFIB | NFIB | 12928 | -0.059 | 0.072 | NO |
140 | H3F3B | H3F3B | H3F3B | 13149 | -0.062 | 0.062 | NO |
141 | TAF11 | TAF11 | TAF11 | 13188 | -0.063 | 0.063 | NO |
142 | TAF12 | TAF12 | TAF12 | 13367 | -0.066 | 0.055 | NO |
143 | PTRF | PTRF | PTRF | 13646 | -0.071 | 0.042 | NO |
144 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 13878 | -0.075 | 0.032 | NO |
145 | SUPT16H | SUPT16H | SUPT16H | 13888 | -0.075 | 0.034 | NO |
146 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 13897 | -0.075 | 0.036 | NO |
147 | SNAPC3 | SNAPC3 | SNAPC3 | 13925 | -0.075 | 0.038 | NO |
148 | NCBP2 | NCBP2 | NCBP2 | 13939 | -0.076 | 0.04 | NO |
149 | MBD2 | MBD2 | MBD2 | 14074 | -0.078 | 0.035 | NO |
150 | POLR2A | POLR2A | POLR2A | 14271 | -0.082 | 0.027 | NO |
151 | TCEB3 | TCEB3 | TCEB3 | 14412 | -0.084 | 0.023 | NO |
152 | POLR1A | POLR1A | POLR1A | 14554 | -0.087 | 0.018 | NO |
153 | LSM11 | LSM11 | LSM11 | 14627 | -0.089 | 0.017 | NO |
154 | CPSF2 | CPSF2 | CPSF2 | 14733 | -0.091 | 0.015 | NO |
155 | SRRM1 | SRRM1 | SRRM1 | 14749 | -0.091 | 0.017 | NO |
156 | UBTF | UBTF | UBTF | 14756 | -0.092 | 0.02 | NO |
157 | RNGTT | RNGTT | RNGTT | 14824 | -0.093 | 0.02 | NO |
158 | CDC40 | CDC40 | CDC40 | 15070 | -0.098 | 0.0098 | NO |
159 | GTF2F2 | GTF2F2 | GTF2F2 | 15083 | -0.099 | 0.013 | NO |
160 | HIST4H4 | HIST4H4 | HIST4H4 | 15165 | -0.1 | 0.012 | NO |
161 | POLR2K | POLR2K | POLR2K | 15179 | -0.1 | 0.015 | NO |
162 | CCNT2 | CCNT2 | CCNT2 | 15265 | -0.1 | 0.014 | NO |
163 | LZTS1 | LZTS1 | LZTS1 | 15299 | -0.1 | 0.016 | NO |
164 | PAPOLA | PAPOLA | PAPOLA | 15332 | -0.1 | 0.018 | NO |
165 | TFB2M | TFB2M | TFB2M | 15336 | -0.1 | 0.022 | NO |
166 | TFAM | TFAM | TFAM | 15541 | -0.11 | 0.014 | NO |
167 | RRN3 | RRN3 | RRN3 | 15588 | -0.11 | 0.016 | NO |
168 | CCNT1 | CCNT1 | CCNT1 | 15695 | -0.11 | 0.014 | NO |
169 | CDK7 | CDK7 | CDK7 | 15725 | -0.11 | 0.016 | NO |
170 | HIST1H3E | HIST1H3E | HIST1H3E | 15748 | -0.11 | 0.02 | NO |
171 | CSTF3 | CSTF3 | CSTF3 | 15812 | -0.12 | 0.02 | NO |
172 | GTF2A1 | GTF2A1 | GTF2A1 | 16021 | -0.12 | 0.013 | NO |
173 | PCF11 | PCF11 | PCF11 | 16520 | -0.14 | -0.0098 | NO |
174 | ERCC6 | ERCC6 | ERCC6 | 16548 | -0.14 | -0.0062 | NO |
175 | TAF4B | TAF4B | TAF4B | 16864 | -0.15 | -0.018 | NO |
176 | TAF13 | TAF13 | TAF13 | 16901 | -0.16 | -0.014 | NO |
177 | CBX3 | CBX3 | CBX3 | 16917 | -0.16 | -0.0095 | NO |
178 | MTERF | MTERF | MTERF | 17009 | -0.16 | -0.0086 | NO |
179 | POU2F1 | POU2F1 | POU2F1 | 17060 | -0.16 | -0.0054 | NO |
180 | KAT2B | KAT2B | KAT2B | 17096 | -0.16 | -0.0013 | NO |
181 | POLR3GL | POLR3GL | POLR3GL | 17103 | -0.16 | 0.0045 | NO |
182 | UPF3B | UPF3B | UPF3B | 17332 | -0.18 | -0.0016 | NO |
183 | TAF1B | TAF1B | TAF1B | 17394 | -0.18 | 0.0018 | NO |
184 | TAF1 | TAF1 | TAF1 | 17417 | -0.19 | 0.0076 | NO |
185 | TAF1A | TAF1A | TAF1A | 17489 | -0.2 | 0.011 | NO |
186 | SNAPC1 | SNAPC1 | SNAPC1 | 17656 | -0.22 | 0.0095 | NO |
187 | SSB | SSB | SSB | 17847 | -0.26 | 0.0084 | 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 PARKINSONS DISEASE.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.KEGG_PARKINSONS_DISEASE.heatmap_plot.clus4.16.png)
Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PARKINSONS DISEASE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_TRANSCRIPTION.volcano_plot.clus4.2.png)
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 | HIST1H4K | HIST1H4K | HIST1H4K | 3 | 1.7 | 0.076 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 47 | 1.2 | 0.13 | YES |
3 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 80 | 1.1 | 0.18 | YES |
4 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 150 | 0.88 | 0.21 | YES |
5 | HIST2H3C | HIST2H3C | HIST2H3C | 195 | 0.78 | 0.25 | YES |
6 | HIST2H3D | HIST2H3D | HIST2H3D | 250 | 0.71 | 0.28 | YES |
7 | GTF2H2B | GTF2H2B | GTF2H2B | 299 | 0.64 | 0.3 | YES |
8 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 344 | 0.6 | 0.33 | YES |
9 | HIST1H4J | HIST1H4J | HIST1H4J | 408 | 0.53 | 0.35 | YES |
10 | HIST1H4I | HIST1H4I | HIST1H4I | 503 | 0.46 | 0.36 | YES |
11 | GTF2H2 | GTF2H2 | GTF2H2 | 511 | 0.45 | 0.38 | YES |
12 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 529 | 0.44 | 0.4 | YES |
13 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 566 | 0.42 | 0.42 | YES |
14 | HIST1H4A | HIST1H4A | HIST1H4A | 569 | 0.42 | 0.44 | YES |
15 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 583 | 0.41 | 0.45 | YES |
16 | HIST2H4A | HIST2H4A | HIST2H4A | 586 | 0.41 | 0.47 | YES |
17 | HIST1H3H | HIST1H3H | HIST1H3H | 828 | 0.32 | 0.47 | YES |
18 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 845 | 0.32 | 0.49 | YES |
19 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 858 | 0.32 | 0.5 | YES |
20 | HIST1H4B | HIST1H4B | HIST1H4B | 873 | 0.31 | 0.51 | YES |
21 | HIST1H4D | HIST1H4D | HIST1H4D | 925 | 0.3 | 0.52 | YES |
22 | HIST1H3D | HIST1H3D | HIST1H3D | 927 | 0.3 | 0.54 | YES |
23 | HIST1H4E | HIST1H4E | HIST1H4E | 949 | 0.29 | 0.55 | YES |
24 | HIST1H3B | HIST1H3B | HIST1H3B | 960 | 0.29 | 0.56 | YES |
25 | HIST1H4C | HIST1H4C | HIST1H4C | 966 | 0.29 | 0.57 | YES |
26 | HIST1H3F | HIST1H3F | HIST1H3F | 1080 | 0.27 | 0.58 | YES |
27 | HIST1H3J | HIST1H3J | HIST1H3J | 1221 | 0.25 | 0.58 | YES |
28 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 1359 | 0.23 | 0.59 | YES |
29 | HIST1H3I | HIST1H3I | HIST1H3I | 1413 | 0.23 | 0.6 | YES |
30 | HIST1H4H | HIST1H4H | HIST1H4H | 1474 | 0.22 | 0.6 | YES |
31 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 1634 | 0.21 | 0.6 | YES |
32 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 1699 | 0.2 | 0.61 | YES |
33 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1706 | 0.2 | 0.62 | YES |
34 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 1738 | 0.2 | 0.62 | YES |
35 | HIST1H3C | HIST1H3C | HIST1H3C | 1745 | 0.2 | 0.63 | YES |
36 | HIST1H3G | HIST1H3G | HIST1H3G | 1950 | 0.18 | 0.63 | YES |
37 | HIST1H3A | HIST1H3A | HIST1H3A | 2045 | 0.17 | 0.63 | YES |
38 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2066 | 0.17 | 0.64 | YES |
39 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2121 | 0.17 | 0.64 | YES |
40 | POLR2L | POLR2L | POLR2L | 2179 | 0.16 | 0.65 | YES |
41 | H3F3A | H3F3A | H3F3A | 2480 | 0.14 | 0.64 | NO |
42 | H2AFX | H2AFX | H2AFX | 2653 | 0.14 | 0.63 | NO |
43 | POLR3K | POLR3K | POLR3K | 3258 | 0.11 | 0.6 | NO |
44 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3383 | 0.11 | 0.6 | NO |
45 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 3638 | 0.098 | 0.59 | NO |
46 | SNAPC5 | SNAPC5 | SNAPC5 | 4039 | 0.087 | 0.57 | NO |
47 | POLR2H | POLR2H | POLR2H | 4058 | 0.086 | 0.58 | NO |
48 | POLR1C | POLR1C | POLR1C | 4567 | 0.074 | 0.55 | NO |
49 | MAPK3 | MAPK3 | MAPK3 | 5061 | 0.063 | 0.53 | NO |
50 | POLR2F | POLR2F | POLR2F | 5192 | 0.06 | 0.52 | NO |
51 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 5411 | 0.056 | 0.51 | NO |
52 | POLR3H | POLR3H | POLR3H | 5423 | 0.056 | 0.51 | NO |
53 | ERCC2 | ERCC2 | ERCC2 | 6471 | 0.037 | 0.46 | NO |
54 | BRF2 | BRF2 | BRF2 | 6489 | 0.037 | 0.46 | NO |
55 | POLR2E | POLR2E | POLR2E | 6525 | 0.036 | 0.46 | NO |
56 | POLRMT | POLRMT | POLRMT | 6651 | 0.034 | 0.45 | NO |
57 | GTF3C5 | GTF3C5 | GTF3C5 | 6759 | 0.032 | 0.45 | NO |
58 | POLR3E | POLR3E | POLR3E | 6853 | 0.031 | 0.44 | NO |
59 | POLR3D | POLR3D | POLR3D | 6925 | 0.03 | 0.44 | NO |
60 | ZNF143 | ZNF143 | ZNF143 | 6969 | 0.029 | 0.44 | NO |
61 | POLR3C | POLR3C | POLR3C | 7034 | 0.028 | 0.44 | NO |
62 | H2AFZ | H2AFZ | H2AFZ | 7459 | 0.021 | 0.42 | NO |
63 | POLR3B | POLR3B | POLR3B | 7745 | 0.016 | 0.4 | NO |
64 | TBP | TBP | TBP | 7825 | 0.015 | 0.4 | NO |
65 | EHMT2 | EHMT2 | EHMT2 | 7964 | 0.014 | 0.39 | NO |
66 | GTF2H4 | GTF2H4 | GTF2H4 | 8021 | 0.013 | 0.39 | NO |
67 | BRF1 | BRF1 | BRF1 | 8790 | 0.00098 | 0.34 | NO |
68 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 9002 | -0.0019 | 0.33 | NO |
69 | SNAPC2 | SNAPC2 | SNAPC2 | 9015 | -0.002 | 0.33 | NO |
70 | MNAT1 | MNAT1 | MNAT1 | 9325 | -0.0062 | 0.31 | NO |
71 | TAF1C | TAF1C | TAF1C | 9415 | -0.0076 | 0.31 | NO |
72 | ERCC3 | ERCC3 | ERCC3 | 9895 | -0.014 | 0.28 | NO |
73 | POLR1B | POLR1B | POLR1B | 10021 | -0.016 | 0.28 | NO |
74 | POLR1D | POLR1D | POLR1D | 10597 | -0.024 | 0.25 | NO |
75 | SNAPC4 | SNAPC4 | SNAPC4 | 10912 | -0.028 | 0.23 | NO |
76 | POLR3A | POLR3A | POLR3A | 11016 | -0.03 | 0.22 | NO |
77 | GTF2H3 | GTF2H3 | GTF2H3 | 11145 | -0.032 | 0.22 | NO |
78 | CCNH | CCNH | CCNH | 11147 | -0.032 | 0.22 | NO |
79 | GTF3C2 | GTF3C2 | GTF3C2 | 11183 | -0.032 | 0.22 | NO |
80 | GTF3C3 | GTF3C3 | GTF3C3 | 11324 | -0.034 | 0.21 | NO |
81 | POLR3F | POLR3F | POLR3F | 12224 | -0.048 | 0.17 | NO |
82 | GTF2H1 | GTF2H1 | GTF2H1 | 12545 | -0.053 | 0.15 | NO |
83 | GTF3C4 | GTF3C4 | GTF3C4 | 12897 | -0.058 | 0.13 | NO |
84 | NFIB | NFIB | NFIB | 12928 | -0.059 | 0.14 | NO |
85 | H3F3B | H3F3B | H3F3B | 13149 | -0.062 | 0.12 | NO |
86 | PTRF | PTRF | PTRF | 13646 | -0.071 | 0.1 | NO |
87 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 13878 | -0.075 | 0.091 | NO |
88 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 13897 | -0.075 | 0.093 | NO |
89 | SNAPC3 | SNAPC3 | SNAPC3 | 13925 | -0.075 | 0.095 | NO |
90 | MBD2 | MBD2 | MBD2 | 14074 | -0.078 | 0.09 | NO |
91 | POLR1A | POLR1A | POLR1A | 14554 | -0.087 | 0.068 | NO |
92 | UBTF | UBTF | UBTF | 14756 | -0.092 | 0.06 | NO |
93 | HIST4H4 | HIST4H4 | HIST4H4 | 15165 | -0.1 | 0.042 | NO |
94 | POLR2K | POLR2K | POLR2K | 15179 | -0.1 | 0.046 | NO |
95 | LZTS1 | LZTS1 | LZTS1 | 15299 | -0.1 | 0.044 | NO |
96 | TFB2M | TFB2M | TFB2M | 15336 | -0.1 | 0.047 | NO |
97 | TFAM | TFAM | TFAM | 15541 | -0.11 | 0.04 | NO |
98 | RRN3 | RRN3 | RRN3 | 15588 | -0.11 | 0.043 | NO |
99 | CDK7 | CDK7 | CDK7 | 15725 | -0.11 | 0.04 | NO |
100 | HIST1H3E | HIST1H3E | HIST1H3E | 15748 | -0.11 | 0.044 | NO |
101 | ERCC6 | ERCC6 | ERCC6 | 16548 | -0.14 | 0.0055 | NO |
102 | CBX3 | CBX3 | CBX3 | 16917 | -0.16 | -0.008 | NO |
103 | MTERF | MTERF | MTERF | 17009 | -0.16 | -0.0059 | NO |
104 | POU2F1 | POU2F1 | POU2F1 | 17060 | -0.16 | -0.0013 | NO |
105 | KAT2B | KAT2B | KAT2B | 17096 | -0.16 | 0.0042 | NO |
106 | POLR3GL | POLR3GL | POLR3GL | 17103 | -0.16 | 0.011 | NO |
107 | TAF1B | TAF1B | TAF1B | 17394 | -0.18 | 0.0034 | NO |
108 | TAF1A | TAF1A | TAF1A | 17489 | -0.2 | 0.0069 | NO |
109 | SNAPC1 | SNAPC1 | SNAPC1 | 17656 | -0.22 | 0.0074 | NO |
110 | SSB | SSB | SSB | 17847 | -0.26 | 0.0083 | 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 PATHOGENIC ESCHERICHIA COLI INFECTION.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION.heatmap_plot.clus4.1.png)
Figure S66. 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
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION.volcano_plot.clus4.3.png)
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 | HIST1H4K | HIST1H4K | HIST1H4K | 3 | 1.7 | 0.089 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 47 | 1.2 | 0.15 | YES |
3 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 80 | 1.1 | 0.21 | YES |
4 | FKBP6 | FKBP6 | FKBP6 | 134 | 0.93 | 0.25 | YES |
5 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 150 | 0.88 | 0.3 | YES |
6 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 344 | 0.6 | 0.32 | YES |
7 | HIST1H4J | HIST1H4J | HIST1H4J | 408 | 0.53 | 0.34 | YES |
8 | STAG3 | STAG3 | STAG3 | 448 | 0.49 | 0.37 | YES |
9 | HIST1H4I | HIST1H4I | HIST1H4I | 503 | 0.46 | 0.39 | YES |
10 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 529 | 0.44 | 0.41 | YES |
11 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 566 | 0.42 | 0.43 | YES |
12 | HIST1H4A | HIST1H4A | HIST1H4A | 569 | 0.42 | 0.45 | YES |
13 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 583 | 0.41 | 0.47 | YES |
14 | HIST2H4A | HIST2H4A | HIST2H4A | 586 | 0.41 | 0.49 | YES |
15 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 845 | 0.32 | 0.5 | YES |
16 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 858 | 0.32 | 0.51 | YES |
17 | HIST1H4B | HIST1H4B | HIST1H4B | 873 | 0.31 | 0.53 | YES |
18 | HIST1H4D | HIST1H4D | HIST1H4D | 925 | 0.3 | 0.54 | YES |
19 | HIST1H4E | HIST1H4E | HIST1H4E | 949 | 0.29 | 0.56 | YES |
20 | HIST1H4C | HIST1H4C | HIST1H4C | 966 | 0.29 | 0.57 | YES |
21 | TERT | TERT | TERT | 1177 | 0.26 | 0.57 | YES |
22 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 1359 | 0.23 | 0.57 | YES |
23 | HIST1H4H | HIST1H4H | HIST1H4H | 1474 | 0.22 | 0.58 | YES |
24 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 1634 | 0.21 | 0.58 | YES |
25 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 1699 | 0.2 | 0.59 | YES |
26 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1706 | 0.2 | 0.6 | YES |
27 | REC8 | REC8 | REC8 | 1710 | 0.2 | 0.61 | YES |
28 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 1738 | 0.2 | 0.62 | YES |
29 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2066 | 0.17 | 0.61 | NO |
30 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2121 | 0.17 | 0.61 | NO |
31 | H2AFX | H2AFX | H2AFX | 2653 | 0.14 | 0.59 | NO |
32 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3383 | 0.11 | 0.56 | NO |
33 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 3638 | 0.098 | 0.55 | NO |
34 | POLD1 | POLD1 | POLD1 | 3930 | 0.09 | 0.54 | NO |
35 | RUVBL2 | RUVBL2 | RUVBL2 | 4079 | 0.086 | 0.53 | NO |
36 | PCNA | PCNA | PCNA | 4483 | 0.076 | 0.51 | NO |
37 | ACD | ACD | ACD | 4657 | 0.071 | 0.51 | NO |
38 | SMC1B | SMC1B | SMC1B | 4679 | 0.071 | 0.51 | NO |
39 | OIP5 | OIP5 | OIP5 | 5130 | 0.062 | 0.49 | NO |
40 | POLA2 | POLA2 | POLA2 | 5204 | 0.06 | 0.49 | NO |
41 | NHP2 | NHP2 | NHP2 | 5248 | 0.059 | 0.49 | NO |
42 | WRAP53 | WRAP53 | WRAP53 | 5332 | 0.057 | 0.49 | NO |
43 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 5411 | 0.056 | 0.48 | NO |
44 | PRIM2 | PRIM2 | PRIM2 | 5437 | 0.055 | 0.49 | NO |
45 | POLE2 | POLE2 | POLE2 | 5903 | 0.047 | 0.46 | NO |
46 | RFC2 | RFC2 | RFC2 | 5972 | 0.046 | 0.46 | NO |
47 | POLD2 | POLD2 | POLD2 | 6370 | 0.039 | 0.44 | NO |
48 | POLD4 | POLD4 | POLD4 | 6429 | 0.038 | 0.44 | NO |
49 | CENPN | CENPN | CENPN | 6430 | 0.038 | 0.44 | NO |
50 | UBE2I | UBE2I | UBE2I | 6715 | 0.033 | 0.43 | NO |
51 | RFC5 | RFC5 | RFC5 | 6728 | 0.033 | 0.43 | NO |
52 | H2AFZ | H2AFZ | H2AFZ | 7459 | 0.021 | 0.39 | NO |
53 | RPA2 | RPA2 | RPA2 | 7520 | 0.02 | 0.39 | NO |
54 | RPA3 | RPA3 | RPA3 | 7935 | 0.014 | 0.36 | NO |
55 | CENPP | CENPP | CENPP | 7944 | 0.014 | 0.36 | NO |
56 | RPA1 | RPA1 | RPA1 | 8220 | 0.0097 | 0.35 | NO |
57 | PRIM1 | PRIM1 | PRIM1 | 8281 | 0.0088 | 0.35 | NO |
58 | RUVBL1 | RUVBL1 | RUVBL1 | 8432 | 0.0064 | 0.34 | NO |
59 | LMNA | LMNA | LMNA | 8487 | 0.0056 | 0.34 | NO |
60 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 9002 | -0.0019 | 0.31 | NO |
61 | FEN1 | FEN1 | FEN1 | 9084 | -0.0028 | 0.3 | NO |
62 | CENPO | CENPO | CENPO | 9267 | -0.0054 | 0.29 | NO |
63 | TINF2 | TINF2 | TINF2 | 9273 | -0.0055 | 0.29 | NO |
64 | RBBP7 | RBBP7 | RBBP7 | 9448 | -0.0081 | 0.28 | NO |
65 | RFC3 | RFC3 | RFC3 | 9450 | -0.0081 | 0.28 | NO |
66 | CENPH | CENPH | CENPH | 9487 | -0.0087 | 0.28 | NO |
67 | LMNB1 | LMNB1 | LMNB1 | 9673 | -0.011 | 0.27 | NO |
68 | CENPA | CENPA | CENPA | 9736 | -0.012 | 0.27 | NO |
69 | LIG1 | LIG1 | LIG1 | 10123 | -0.017 | 0.25 | NO |
70 | POLE | POLE | POLE | 10147 | -0.018 | 0.25 | NO |
71 | TERF2 | TERF2 | TERF2 | 10274 | -0.019 | 0.24 | NO |
72 | RBBP4 | RBBP4 | RBBP4 | 10298 | -0.02 | 0.24 | NO |
73 | HJURP | HJURP | HJURP | 10988 | -0.03 | 0.2 | NO |
74 | RFC4 | RFC4 | RFC4 | 11007 | -0.03 | 0.21 | NO |
75 | HSPA2 | HSPA2 | HSPA2 | 11291 | -0.034 | 0.19 | NO |
76 | DIDO1 | DIDO1 | DIDO1 | 13072 | -0.061 | 0.096 | NO |
77 | SUN2 | SUN2 | SUN2 | 13151 | -0.062 | 0.094 | NO |
78 | POLD3 | POLD3 | POLD3 | 13194 | -0.063 | 0.095 | NO |
79 | MLF1IP | MLF1IP | MLF1IP | 13366 | -0.066 | 0.089 | NO |
80 | DKC1 | DKC1 | DKC1 | 13480 | -0.068 | 0.087 | NO |
81 | POT1 | POT1 | POT1 | 13585 | -0.07 | 0.084 | NO |
82 | ATR | ATR | ATR | 13592 | -0.07 | 0.088 | NO |
83 | RAD21 | RAD21 | RAD21 | 13733 | -0.072 | 0.084 | NO |
84 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 13878 | -0.075 | 0.08 | NO |
85 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 13897 | -0.075 | 0.082 | NO |
86 | SMC1A | SMC1A | SMC1A | 13898 | -0.075 | 0.086 | NO |
87 | CENPI | CENPI | CENPI | 14004 | -0.076 | 0.085 | NO |
88 | TERF2IP | TERF2IP | TERF2IP | 14105 | -0.078 | 0.083 | NO |
89 | POLA1 | POLA1 | POLA1 | 14257 | -0.081 | 0.079 | NO |
90 | BRCA1 | BRCA1 | BRCA1 | 15061 | -0.098 | 0.039 | NO |
91 | HIST4H4 | HIST4H4 | HIST4H4 | 15165 | -0.1 | 0.039 | NO |
92 | ITGB3BP | ITGB3BP | ITGB3BP | 15170 | -0.1 | 0.044 | NO |
93 | SYCP2 | SYCP2 | SYCP2 | 15473 | -0.11 | 0.032 | NO |
94 | DNA2 | DNA2 | DNA2 | 15653 | -0.11 | 0.028 | NO |
95 | STAG2 | STAG2 | STAG2 | 15692 | -0.11 | 0.032 | NO |
96 | SMARCA5 | SMARCA5 | SMARCA5 | 15966 | -0.12 | 0.023 | NO |
97 | STAG1 | STAG1 | STAG1 | 16010 | -0.12 | 0.027 | NO |
98 | CASC5 | CASC5 | CASC5 | 16120 | -0.12 | 0.027 | NO |
99 | TERF1 | TERF1 | TERF1 | 16180 | -0.13 | 0.031 | NO |
100 | TEX12 | TEX12 | TEX12 | 16561 | -0.14 | 0.017 | NO |
101 | SYNE2 | SYNE2 | SYNE2 | 16759 | -0.15 | 0.013 | NO |
102 | SMC3 | SMC3 | SMC3 | 16787 | -0.15 | 0.02 | NO |
103 | CENPK | CENPK | CENPK | 16801 | -0.15 | 0.027 | NO |
104 | NPM1 | NPM1 | NPM1 | 16809 | -0.15 | 0.034 | NO |
105 | SYNE1 | SYNE1 | SYNE1 | 17355 | -0.18 | 0.013 | NO |
106 | CENPQ | CENPQ | CENPQ | 17377 | -0.18 | 0.022 | NO |
107 | RSF1 | RSF1 | RSF1 | 17795 | -0.24 | 0.011 | NO |
Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SYSTEMIC LUPUS ERYTHEMATOSUS.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS.heatmap_plot.clus4.9.png)
Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SYSTEMIC LUPUS ERYTHEMATOSUS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_CHROMOSOME_MAINTENANCE.volcano_plot.clus4.4.png)
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 | HIST1H4K | HIST1H4K | HIST1H4K | 3 | 1.7 | 0.12 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 47 | 1.2 | 0.2 | YES |
3 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 80 | 1.1 | 0.28 | YES |
4 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 150 | 0.88 | 0.33 | YES |
5 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 344 | 0.6 | 0.36 | YES |
6 | HIST1H4J | HIST1H4J | HIST1H4J | 408 | 0.53 | 0.4 | YES |
7 | HIST1H4I | HIST1H4I | HIST1H4I | 503 | 0.46 | 0.42 | YES |
8 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 529 | 0.44 | 0.45 | YES |
9 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 566 | 0.42 | 0.48 | YES |
10 | HIST1H4A | HIST1H4A | HIST1H4A | 569 | 0.42 | 0.51 | YES |
11 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 583 | 0.41 | 0.53 | YES |
12 | HIST2H4A | HIST2H4A | HIST2H4A | 586 | 0.41 | 0.56 | YES |
13 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 845 | 0.32 | 0.57 | YES |
14 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 858 | 0.32 | 0.59 | YES |
15 | HIST1H4B | HIST1H4B | HIST1H4B | 873 | 0.31 | 0.61 | YES |
16 | HIST1H4D | HIST1H4D | HIST1H4D | 925 | 0.3 | 0.63 | YES |
17 | HIST1H4E | HIST1H4E | HIST1H4E | 949 | 0.29 | 0.65 | YES |
18 | HIST1H4C | HIST1H4C | HIST1H4C | 966 | 0.29 | 0.67 | YES |
19 | TERT | TERT | TERT | 1177 | 0.26 | 0.67 | YES |
20 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 1359 | 0.23 | 0.68 | YES |
21 | HIST1H4H | HIST1H4H | HIST1H4H | 1474 | 0.22 | 0.69 | YES |
22 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 1634 | 0.21 | 0.7 | YES |
23 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 1699 | 0.2 | 0.7 | YES |
24 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1706 | 0.2 | 0.72 | YES |
25 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 1738 | 0.2 | 0.73 | YES |
26 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2066 | 0.17 | 0.72 | YES |
27 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2121 | 0.17 | 0.73 | YES |
28 | H2AFX | H2AFX | H2AFX | 2653 | 0.14 | 0.71 | NO |
29 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3383 | 0.11 | 0.68 | NO |
30 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 3638 | 0.098 | 0.67 | NO |
31 | POLD1 | POLD1 | POLD1 | 3930 | 0.09 | 0.66 | NO |
32 | RUVBL2 | RUVBL2 | RUVBL2 | 4079 | 0.086 | 0.66 | NO |
33 | PCNA | PCNA | PCNA | 4483 | 0.076 | 0.64 | NO |
34 | ACD | ACD | ACD | 4657 | 0.071 | 0.64 | NO |
35 | POLA2 | POLA2 | POLA2 | 5204 | 0.06 | 0.61 | NO |
36 | NHP2 | NHP2 | NHP2 | 5248 | 0.059 | 0.61 | NO |
37 | WRAP53 | WRAP53 | WRAP53 | 5332 | 0.057 | 0.61 | NO |
38 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 5411 | 0.056 | 0.61 | NO |
39 | PRIM2 | PRIM2 | PRIM2 | 5437 | 0.055 | 0.61 | NO |
40 | POLE2 | POLE2 | POLE2 | 5903 | 0.047 | 0.59 | NO |
41 | RFC2 | RFC2 | RFC2 | 5972 | 0.046 | 0.59 | NO |
42 | POLD2 | POLD2 | POLD2 | 6370 | 0.039 | 0.57 | NO |
43 | POLD4 | POLD4 | POLD4 | 6429 | 0.038 | 0.57 | NO |
44 | RFC5 | RFC5 | RFC5 | 6728 | 0.033 | 0.56 | NO |
45 | H2AFZ | H2AFZ | H2AFZ | 7459 | 0.021 | 0.52 | NO |
46 | RPA2 | RPA2 | RPA2 | 7520 | 0.02 | 0.52 | NO |
47 | RPA3 | RPA3 | RPA3 | 7935 | 0.014 | 0.49 | NO |
48 | RPA1 | RPA1 | RPA1 | 8220 | 0.0097 | 0.48 | NO |
49 | PRIM1 | PRIM1 | PRIM1 | 8281 | 0.0088 | 0.48 | NO |
50 | RUVBL1 | RUVBL1 | RUVBL1 | 8432 | 0.0064 | 0.47 | NO |
51 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 9002 | -0.0019 | 0.44 | NO |
52 | FEN1 | FEN1 | FEN1 | 9084 | -0.0028 | 0.43 | NO |
53 | TINF2 | TINF2 | TINF2 | 9273 | -0.0055 | 0.42 | NO |
54 | RFC3 | RFC3 | RFC3 | 9450 | -0.0081 | 0.41 | NO |
55 | LIG1 | LIG1 | LIG1 | 10123 | -0.017 | 0.38 | NO |
56 | POLE | POLE | POLE | 10147 | -0.018 | 0.38 | NO |
57 | TERF2 | TERF2 | TERF2 | 10274 | -0.019 | 0.37 | NO |
58 | RFC4 | RFC4 | RFC4 | 11007 | -0.03 | 0.33 | NO |
59 | POLD3 | POLD3 | POLD3 | 13194 | -0.063 | 0.21 | NO |
60 | DKC1 | DKC1 | DKC1 | 13480 | -0.068 | 0.2 | NO |
61 | POT1 | POT1 | POT1 | 13585 | -0.07 | 0.2 | NO |
62 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 13878 | -0.075 | 0.19 | NO |
63 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 13897 | -0.075 | 0.19 | NO |
64 | TERF2IP | TERF2IP | TERF2IP | 14105 | -0.078 | 0.19 | NO |
65 | POLA1 | POLA1 | POLA1 | 14257 | -0.081 | 0.18 | NO |
66 | HIST4H4 | HIST4H4 | HIST4H4 | 15165 | -0.1 | 0.14 | NO |
67 | DNA2 | DNA2 | DNA2 | 15653 | -0.11 | 0.12 | NO |
68 | TERF1 | TERF1 | TERF1 | 16180 | -0.13 | 0.1 | 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: REACTOME TRANSLATION.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_TRANSLATION.heatmap_plot.clus4.20.png)
Figure S70. 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
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_TELOMERE_MAINTENANCE.volcano_plot.clus4.5.png)
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 | RPL21 | RPL21 | RPL21 | 21 | 1.4 | 0.038 | YES |
2 | RPSAP9 | RPSAP9 | RPSAP9 | 30 | 1.3 | 0.074 | YES |
3 | RPL36A | RPL36A | RPL36A | 143 | 0.91 | 0.092 | YES |
4 | RPL39 | RPL39 | RPL39 | 212 | 0.76 | 0.11 | YES |
5 | RPS28 | RPS28 | RPS28 | 251 | 0.71 | 0.13 | YES |
6 | RPS27 | RPS27 | RPS27 | 345 | 0.59 | 0.14 | YES |
7 | RPL9 | RPL9 | RPL9 | 392 | 0.54 | 0.15 | YES |
8 | RPS26 | RPS26 | RPS26 | 426 | 0.51 | 0.16 | YES |
9 | TUBA1A | TUBA1A | TUBA1A | 439 | 0.5 | 0.17 | YES |
10 | RPL7 | RPL7 | RPL7 | 455 | 0.49 | 0.19 | YES |
11 | TUBB2A | TUBB2A | TUBB2A | 489 | 0.46 | 0.2 | YES |
12 | RPL18A | RPL18A | RPL18A | 550 | 0.43 | 0.2 | YES |
13 | TUBA3D | TUBA3D | TUBA3D | 640 | 0.38 | 0.21 | YES |
14 | EIF3C | EIF3C | EIF3C | 693 | 0.37 | 0.22 | YES |
15 | TUBB3 | TUBB3 | TUBB3 | 699 | 0.36 | 0.23 | YES |
16 | MUC4 | MUC4 | MUC4 | 833 | 0.32 | 0.23 | YES |
17 | RPS3A | RPS3A | RPS3A | 855 | 0.32 | 0.24 | YES |
18 | MUC2 | MUC2 | MUC2 | 872 | 0.31 | 0.24 | YES |
19 | FAM153A | FAM153A | FAM153A | 886 | 0.31 | 0.25 | YES |
20 | MUC16 | MUC16 | MUC16 | 1092 | 0.27 | 0.25 | YES |
21 | B3GNT7 | B3GNT7 | B3GNT7 | 1226 | 0.25 | 0.25 | YES |
22 | DPM3 | DPM3 | DPM3 | 1285 | 0.24 | 0.25 | YES |
23 | MUC6 | MUC6 | MUC6 | 1331 | 0.24 | 0.25 | YES |
24 | RPSA | RPSA | RPSA | 1395 | 0.23 | 0.26 | YES |
25 | B3GNT4 | B3GNT4 | B3GNT4 | 1430 | 0.22 | 0.26 | YES |
26 | GALNT9 | GALNT9 | GALNT9 | 1442 | 0.22 | 0.27 | YES |
27 | RPL23A | RPL23A | RPL23A | 1453 | 0.22 | 0.27 | YES |
28 | LDHD | LDHD | LDHD | 1508 | 0.22 | 0.27 | YES |
29 | MUC5B | MUC5B | MUC5B | 1742 | 0.2 | 0.27 | YES |
30 | TUBB2B | TUBB2B | TUBB2B | 1858 | 0.19 | 0.26 | YES |
31 | TIMM8B | TIMM8B | TIMM8B | 1978 | 0.18 | 0.26 | YES |
32 | B3GNT6 | B3GNT6 | B3GNT6 | 1979 | 0.18 | 0.27 | YES |
33 | GMPPB | GMPPB | GMPPB | 2004 | 0.17 | 0.27 | YES |
34 | RPS15 | RPS15 | RPS15 | 2018 | 0.17 | 0.28 | YES |
35 | RPS2 | RPS2 | RPS2 | 2060 | 0.17 | 0.28 | YES |
36 | EEF1A1 | EEF1A1 | EEF1A1 | 2072 | 0.17 | 0.28 | YES |
37 | SPCS2 | SPCS2 | SPCS2 | 2073 | 0.17 | 0.29 | YES |
38 | FBXO6 | FBXO6 | FBXO6 | 2105 | 0.17 | 0.29 | YES |
39 | CYC1 | CYC1 | CYC1 | 2120 | 0.17 | 0.29 | YES |
40 | PIGL | PIGL | PIGL | 2138 | 0.16 | 0.3 | YES |
41 | TUBA1C | TUBA1C | TUBA1C | 2168 | 0.16 | 0.3 | YES |
42 | GCNT3 | GCNT3 | GCNT3 | 2330 | 0.15 | 0.29 | YES |
43 | ARSE | ARSE | ARSE | 2371 | 0.15 | 0.3 | YES |
44 | F2 | F2 | F2 | 2390 | 0.15 | 0.3 | YES |
45 | SPHK1 | SPHK1 | SPHK1 | 2454 | 0.15 | 0.3 | YES |
46 | ARSG | ARSG | ARSG | 2659 | 0.14 | 0.29 | YES |
47 | RPL41 | RPL41 | RPL41 | 2713 | 0.13 | 0.29 | YES |
48 | RPL13 | RPL13 | RPL13 | 2858 | 0.13 | 0.29 | YES |
49 | ST6GALNAC4 | ST6GALNAC4 | ST6GALNAC4 | 2909 | 0.12 | 0.29 | YES |
50 | FBXW5 | FBXW5 | FBXW5 | 2985 | 0.12 | 0.29 | YES |
51 | GALNT14 | GALNT14 | GALNT14 | 3067 | 0.12 | 0.28 | YES |
52 | RPLP0 | RPLP0 | RPLP0 | 3082 | 0.12 | 0.29 | YES |
53 | MTX1 | MTX1 | MTX1 | 3111 | 0.12 | 0.29 | YES |
54 | RPS5 | RPS5 | RPS5 | 3123 | 0.12 | 0.29 | YES |
55 | GALNTL6 | GALNTL6 | GALNTL6 | 3186 | 0.11 | 0.29 | YES |
56 | IDH3G | IDH3G | IDH3G | 3227 | 0.11 | 0.29 | YES |
57 | EIF4E | EIF4E | EIF4E | 3277 | 0.11 | 0.29 | YES |
58 | TUBB6 | TUBB6 | TUBB6 | 3286 | 0.11 | 0.3 | YES |
59 | TUSC3 | TUSC3 | TUSC3 | 3310 | 0.11 | 0.3 | YES |
60 | GPAA1 | GPAA1 | GPAA1 | 3331 | 0.11 | 0.3 | YES |
61 | TIMM13 | TIMM13 | TIMM13 | 3394 | 0.11 | 0.3 | YES |
62 | B3GNTL1 | B3GNTL1 | B3GNTL1 | 3451 | 0.1 | 0.3 | YES |
63 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 3503 | 0.1 | 0.3 | YES |
64 | RPL29 | RPL29 | RPL29 | 3523 | 0.1 | 0.3 | YES |
65 | RPL28 | RPL28 | RPL28 | 3529 | 0.1 | 0.3 | YES |
66 | TIMM50 | TIMM50 | TIMM50 | 3544 | 0.1 | 0.3 | YES |
67 | WBSCR17 | WBSCR17 | WBSCR17 | 3563 | 0.1 | 0.3 | YES |
68 | SSR4 | SSR4 | SSR4 | 3600 | 0.1 | 0.31 | YES |
69 | GALNT8 | GALNT8 | GALNT8 | 3609 | 0.099 | 0.31 | YES |
70 | TIMM10 | TIMM10 | TIMM10 | 3652 | 0.098 | 0.31 | YES |
71 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 3799 | 0.093 | 0.3 | YES |
72 | UBA52 | UBA52 | UBA52 | 3845 | 0.092 | 0.3 | YES |
73 | VKORC1 | VKORC1 | VKORC1 | 3868 | 0.091 | 0.3 | YES |
74 | RPL10 | RPL10 | RPL10 | 3877 | 0.091 | 0.31 | YES |
75 | RPS14 | RPS14 | RPS14 | 3923 | 0.09 | 0.31 | YES |
76 | ALG3 | ALG3 | ALG3 | 3973 | 0.088 | 0.3 | YES |
77 | RPL15 | RPL15 | RPL15 | 3997 | 0.088 | 0.31 | YES |
78 | BCS1L | BCS1L | BCS1L | 4003 | 0.088 | 0.31 | YES |
79 | TBCB | TBCB | TBCB | 4035 | 0.087 | 0.31 | YES |
80 | DOHH | DOHH | DOHH | 4062 | 0.086 | 0.31 | YES |
81 | RPLP2 | RPLP2 | RPLP2 | 4167 | 0.083 | 0.31 | YES |
82 | TIMM17B | TIMM17B | TIMM17B | 4178 | 0.083 | 0.31 | YES |
83 | TIMM44 | TIMM44 | TIMM44 | 4197 | 0.082 | 0.31 | YES |
84 | GFER | GFER | GFER | 4234 | 0.081 | 0.31 | YES |
85 | B3GNT8 | B3GNT8 | B3GNT8 | 4271 | 0.081 | 0.31 | YES |
86 | MGAT4B | MGAT4B | MGAT4B | 4283 | 0.08 | 0.31 | YES |
87 | PMM1 | PMM1 | PMM1 | 4303 | 0.08 | 0.31 | YES |
88 | EEF1G | EEF1G | EEF1G | 4392 | 0.078 | 0.31 | YES |
89 | GFPT2 | GFPT2 | GFPT2 | 4447 | 0.076 | 0.31 | YES |
90 | ARSH | ARSH | ARSH | 4453 | 0.076 | 0.31 | YES |
91 | SLC25A4 | SLC25A4 | SLC25A4 | 4564 | 0.074 | 0.31 | YES |
92 | SEC13 | SEC13 | SEC13 | 4581 | 0.073 | 0.31 | YES |
93 | DHPS | DHPS | DHPS | 4612 | 0.073 | 0.31 | YES |
94 | RPS21 | RPS21 | RPS21 | 4617 | 0.073 | 0.31 | YES |
95 | MUC17 | MUC17 | MUC17 | 4647 | 0.072 | 0.31 | YES |
96 | ARSI | ARSI | ARSI | 4669 | 0.071 | 0.31 | YES |
97 | RPS10 | RPS10 | RPS10 | 4756 | 0.069 | 0.31 | YES |
98 | EIF4H | EIF4H | EIF4H | 4763 | 0.069 | 0.31 | YES |
99 | ST8SIA6 | ST8SIA6 | ST8SIA6 | 4788 | 0.069 | 0.31 | YES |
100 | RPL18 | RPL18 | RPL18 | 4815 | 0.068 | 0.31 | YES |
101 | TUBA4A | TUBA4A | TUBA4A | 4833 | 0.068 | 0.31 | YES |
102 | TUBA1B | TUBA1B | TUBA1B | 4843 | 0.068 | 0.31 | YES |
103 | PROZ | PROZ | PROZ | 4876 | 0.067 | 0.31 | YES |
104 | PMPCA | PMPCA | PMPCA | 4882 | 0.067 | 0.31 | YES |
105 | RPS3 | RPS3 | RPS3 | 4904 | 0.066 | 0.31 | YES |
106 | EIF3K | EIF3K | EIF3K | 4953 | 0.065 | 0.31 | YES |
107 | ATP5B | ATP5B | ATP5B | 4988 | 0.064 | 0.31 | YES |
108 | MGAT1 | MGAT1 | MGAT1 | 5008 | 0.064 | 0.31 | YES |
109 | RPL8 | RPL8 | RPL8 | 5027 | 0.064 | 0.31 | YES |
110 | EDEM2 | EDEM2 | EDEM2 | 5079 | 0.063 | 0.31 | NO |
111 | RPS9 | RPS9 | RPS9 | 5108 | 0.062 | 0.31 | NO |
112 | RPL27 | RPL27 | RPL27 | 5149 | 0.061 | 0.31 | NO |
113 | PFDN5 | PFDN5 | PFDN5 | 5198 | 0.06 | 0.31 | NO |
114 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 5244 | 0.059 | 0.31 | NO |
115 | PIGQ | PIGQ | PIGQ | 5249 | 0.059 | 0.31 | NO |
116 | DOLPP1 | DOLPP1 | DOLPP1 | 5256 | 0.059 | 0.31 | NO |
117 | PLAUR | PLAUR | PLAUR | 5284 | 0.058 | 0.31 | NO |
118 | ST6GALNAC3 | ST6GALNAC3 | ST6GALNAC3 | 5336 | 0.057 | 0.31 | NO |
119 | ALG12 | ALG12 | ALG12 | 5385 | 0.056 | 0.31 | NO |
120 | EIF5A | EIF5A | EIF5A | 5446 | 0.055 | 0.31 | NO |
121 | EIF3F | EIF3F | EIF3F | 5471 | 0.055 | 0.31 | NO |
122 | RPL36 | RPL36 | RPL36 | 5485 | 0.055 | 0.31 | NO |
123 | RPL26L1 | RPL26L1 | RPL26L1 | 5539 | 0.054 | 0.31 | NO |
124 | TBCD | TBCD | TBCD | 5682 | 0.051 | 0.3 | NO |
125 | ACTB | ACTB | ACTB | 5716 | 0.05 | 0.3 | NO |
126 | RPS16 | RPS16 | RPS16 | 5831 | 0.049 | 0.3 | NO |
127 | TOMM5 | TOMM5 | TOMM5 | 5857 | 0.048 | 0.3 | NO |
128 | GMPPA | GMPPA | GMPPA | 5949 | 0.046 | 0.29 | NO |
129 | ATP5A1 | ATP5A1 | ATP5A1 | 5962 | 0.046 | 0.29 | NO |
130 | SAMM50 | SAMM50 | SAMM50 | 5984 | 0.046 | 0.29 | NO |
131 | RPN1 | RPN1 | RPN1 | 6039 | 0.045 | 0.29 | NO |
132 | ARSA | ARSA | ARSA | 6050 | 0.044 | 0.29 | NO |
133 | RPL35 | RPL35 | RPL35 | 6078 | 0.044 | 0.29 | NO |
134 | DDOST | DDOST | DDOST | 6127 | 0.043 | 0.29 | NO |
135 | TIMM22 | TIMM22 | TIMM22 | 6146 | 0.043 | 0.29 | NO |
136 | F7 | F7 | F7 | 6191 | 0.042 | 0.29 | NO |
137 | TOMM7 | TOMM7 | TOMM7 | 6195 | 0.042 | 0.29 | NO |
138 | CCT2 | CCT2 | CCT2 | 6233 | 0.041 | 0.29 | NO |
139 | DOLK | DOLK | DOLK | 6343 | 0.039 | 0.28 | NO |
140 | B4GALT3 | B4GALT3 | B4GALT3 | 6362 | 0.039 | 0.28 | NO |
141 | TAZ | TAZ | TAZ | 6382 | 0.039 | 0.28 | NO |
142 | FAU | FAU | FAU | 6404 | 0.038 | 0.28 | NO |
143 | RPS6 | RPS6 | RPS6 | 6427 | 0.038 | 0.28 | NO |
144 | MAN1B1 | MAN1B1 | MAN1B1 | 6469 | 0.037 | 0.28 | NO |
145 | ALG14 | ALG14 | ALG14 | 6517 | 0.036 | 0.28 | NO |
146 | EIF2B3 | EIF2B3 | EIF2B3 | 6552 | 0.036 | 0.28 | NO |
147 | RPLP1 | RPLP1 | RPLP1 | 6581 | 0.035 | 0.28 | NO |
148 | ALG1 | ALG1 | ALG1 | 6587 | 0.035 | 0.28 | NO |
149 | CCT7 | CCT7 | CCT7 | 6618 | 0.034 | 0.28 | NO |
150 | EEF2 | EEF2 | EEF2 | 6660 | 0.034 | 0.28 | NO |
151 | PREB | PREB | PREB | 6663 | 0.034 | 0.28 | NO |
152 | SPCS1 | SPCS1 | SPCS1 | 6697 | 0.033 | 0.28 | NO |
153 | RPL17 | RPL17 | RPL17 | 6706 | 0.033 | 0.28 | NO |
154 | DPM2 | DPM2 | DPM2 | 6748 | 0.032 | 0.28 | NO |
155 | RPS13 | RPS13 | RPS13 | 6751 | 0.032 | 0.28 | NO |
156 | PIGH | PIGH | PIGH | 6797 | 0.032 | 0.27 | NO |
157 | RPS8 | RPS8 | RPS8 | 6828 | 0.031 | 0.27 | NO |
158 | SAR1B | SAR1B | SAR1B | 6830 | 0.031 | 0.27 | NO |
159 | SEMA6D | SEMA6D | SEMA6D | 6836 | 0.031 | 0.28 | NO |
160 | COQ2 | COQ2 | COQ2 | 6848 | 0.031 | 0.28 | NO |
161 | MPI | MPI | MPI | 6870 | 0.03 | 0.28 | NO |
162 | EIF4A1 | EIF4A1 | EIF4A1 | 6876 | 0.03 | 0.28 | NO |
163 | SLC25A6 | SLC25A6 | SLC25A6 | 6877 | 0.03 | 0.28 | NO |
164 | EEF1D | EEF1D | EEF1D | 6900 | 0.03 | 0.28 | NO |
165 | CS | CS | CS | 6901 | 0.03 | 0.28 | NO |
166 | ATP5G1 | ATP5G1 | ATP5G1 | 6968 | 0.029 | 0.27 | NO |
167 | EIF1AX | EIF1AX | EIF1AX | 7021 | 0.028 | 0.27 | NO |
168 | C18orf55 | C18orf55 | C18orf55 | 7022 | 0.028 | 0.27 | NO |
169 | LOC653566 | LOC653566 | LOC653566 | 7064 | 0.027 | 0.27 | NO |
170 | EIF2B1 | EIF2B1 | EIF2B1 | 7070 | 0.027 | 0.27 | NO |
171 | SSR2 | SSR2 | SSR2 | 7151 | 0.026 | 0.27 | NO |
172 | ALG2 | ALG2 | ALG2 | 7165 | 0.026 | 0.27 | NO |
173 | FBXW4 | FBXW4 | FBXW4 | 7200 | 0.025 | 0.27 | NO |
174 | TBCC | TBCC | TBCC | 7212 | 0.025 | 0.27 | NO |
175 | SEC61B | SEC61B | SEC61B | 7213 | 0.025 | 0.27 | NO |
176 | KIFC3 | KIFC3 | KIFC3 | 7242 | 0.024 | 0.26 | NO |
177 | EIF3G | EIF3G | EIF3G | 7284 | 0.024 | 0.26 | NO |
178 | FXN | FXN | FXN | 7303 | 0.024 | 0.26 | NO |
179 | PMPCB | PMPCB | PMPCB | 7333 | 0.023 | 0.26 | NO |
180 | F10 | F10 | F10 | 7344 | 0.023 | 0.26 | NO |
181 | B4GALT2 | B4GALT2 | B4GALT2 | 7358 | 0.023 | 0.26 | NO |
182 | RFT1 | RFT1 | RFT1 | 7380 | 0.022 | 0.26 | NO |
183 | ACO2 | ACO2 | ACO2 | 7415 | 0.022 | 0.26 | NO |
184 | ARSB | ARSB | ARSB | 7500 | 0.02 | 0.26 | NO |
185 | PIGF | PIGF | PIGF | 7580 | 0.019 | 0.25 | NO |
186 | B3GNT9 | B3GNT9 | B3GNT9 | 7584 | 0.019 | 0.25 | NO |
187 | RPS11 | RPS11 | RPS11 | 7637 | 0.018 | 0.25 | NO |
188 | EIF3I | EIF3I | EIF3I | 7672 | 0.018 | 0.25 | NO |
189 | MUCL1 | MUCL1 | MUCL1 | 7679 | 0.018 | 0.25 | NO |
190 | MGAT3 | MGAT3 | MGAT3 | 7738 | 0.016 | 0.25 | NO |
191 | RPL35A | RPL35A | RPL35A | 7755 | 0.016 | 0.24 | NO |
192 | B3GNT3 | B3GNT3 | B3GNT3 | 7777 | 0.016 | 0.24 | NO |
193 | CHCHD4 | CHCHD4 | CHCHD4 | 7810 | 0.016 | 0.24 | NO |
194 | CCT4 | CCT4 | CCT4 | 7813 | 0.016 | 0.24 | NO |
195 | SUMF2 | SUMF2 | SUMF2 | 7816 | 0.016 | 0.24 | NO |
196 | CALR | CALR | CALR | 7850 | 0.015 | 0.24 | NO |
197 | RPS29 | RPS29 | RPS29 | 7857 | 0.015 | 0.24 | NO |
198 | RPL6 | RPL6 | RPL6 | 7861 | 0.015 | 0.24 | NO |
199 | EIF2B2 | EIF2B2 | EIF2B2 | 7910 | 0.014 | 0.24 | NO |
200 | PIGT | PIGT | PIGT | 7967 | 0.014 | 0.24 | NO |
201 | CCT5 | CCT5 | CCT5 | 8024 | 0.013 | 0.24 | NO |
202 | RPS19 | RPS19 | RPS19 | 8061 | 0.012 | 0.23 | NO |
203 | RPL3 | RPL3 | RPL3 | 8099 | 0.012 | 0.23 | NO |
204 | EIF2B4 | EIF2B4 | EIF2B4 | 8100 | 0.012 | 0.23 | NO |
205 | DPAGT1 | DPAGT1 | DPAGT1 | 8116 | 0.011 | 0.23 | NO |
206 | FKBP9 | FKBP9 | FKBP9 | 8120 | 0.011 | 0.23 | NO |
207 | RPS15A | RPS15A | RPS15A | 8121 | 0.011 | 0.23 | NO |
208 | EEF1B2 | EEF1B2 | EEF1B2 | 8175 | 0.01 | 0.23 | NO |
209 | SUMF1 | SUMF1 | SUMF1 | 8197 | 0.01 | 0.23 | NO |
210 | ALG5 | ALG5 | ALG5 | 8221 | 0.0097 | 0.23 | NO |
211 | PMM2 | PMM2 | PMM2 | 8246 | 0.0094 | 0.22 | NO |
212 | PIGO | PIGO | PIGO | 8262 | 0.0092 | 0.22 | NO |
213 | SEC61A2 | SEC61A2 | SEC61A2 | 8326 | 0.0083 | 0.22 | NO |
214 | EIF2B5 | EIF2B5 | EIF2B5 | 8332 | 0.0081 | 0.22 | NO |
215 | FXC1 | FXC1 | FXC1 | 8363 | 0.0076 | 0.22 | NO |
216 | RPL10A | RPL10A | RPL10A | 8389 | 0.0071 | 0.22 | NO |
217 | TCP1 | TCP1 | TCP1 | 8407 | 0.0068 | 0.22 | NO |
218 | SRP9 | SRP9 | SRP9 | 8444 | 0.0062 | 0.22 | NO |
219 | PIGG | PIGG | PIGG | 8516 | 0.0051 | 0.21 | NO |
220 | RPL7A | RPL7A | RPL7A | 8566 | 0.0043 | 0.21 | NO |
221 | DAD1 | DAD1 | DAD1 | 8569 | 0.0042 | 0.21 | NO |
222 | ST6GAL1 | ST6GAL1 | ST6GAL1 | 8597 | 0.0038 | 0.21 | NO |
223 | GALNTL4 | GALNTL4 | GALNTL4 | 8661 | 0.0029 | 0.2 | NO |
224 | RPS4X | RPS4X | RPS4X | 8775 | 0.0012 | 0.2 | NO |
225 | SEC61A1 | SEC61A1 | SEC61A1 | 8794 | 0.00092 | 0.2 | NO |
226 | PIGS | PIGS | PIGS | 8798 | 0.00087 | 0.2 | NO |
227 | RPL38 | RPL38 | RPL38 | 8824 | 0.00045 | 0.2 | NO |
228 | FUT8 | FUT8 | FUT8 | 8836 | 0.0003 | 0.2 | NO |
229 | GGCX | GGCX | GGCX | 8864 | -3e-05 | 0.19 | NO |
230 | MOGS | MOGS | MOGS | 8865 | -0.000044 | 0.19 | NO |
231 | EIF3B | EIF3B | EIF3B | 8868 | -0.000096 | 0.19 | NO |
232 | PIGV | PIGV | PIGV | 8916 | -0.00074 | 0.19 | NO |
233 | ALG13 | ALG13 | ALG13 | 8930 | -0.00088 | 0.19 | NO |
234 | RPS17 | RPS17 | RPS17 | 8937 | -0.00099 | 0.19 | NO |
235 | TOMM22 | TOMM22 | TOMM22 | 8948 | -0.0012 | 0.19 | NO |
236 | RPL37A | RPL37A | RPL37A | 8999 | -0.0018 | 0.19 | NO |
237 | ST6GALNAC2 | ST6GALNAC2 | ST6GALNAC2 | 9014 | -0.002 | 0.19 | NO |
238 | EIF3D | EIF3D | EIF3D | 9067 | -0.0027 | 0.18 | NO |
239 | MUC12 | MUC12 | MUC12 | 9260 | -0.0053 | 0.17 | NO |
240 | CCT3 | CCT3 | CCT3 | 9464 | -0.0083 | 0.16 | NO |
241 | SSR3 | SSR3 | SSR3 | 9467 | -0.0084 | 0.16 | NO |
242 | FBXO4 | FBXO4 | FBXO4 | 9554 | -0.0096 | 0.16 | NO |
243 | GALNT12 | GALNT12 | GALNT12 | 9565 | -0.0098 | 0.16 | NO |
244 | GNPNAT1 | GNPNAT1 | GNPNAT1 | 9608 | -0.01 | 0.15 | NO |
245 | EIF4A2 | EIF4A2 | EIF4A2 | 9617 | -0.01 | 0.15 | NO |
246 | NOP56 | NOP56 | NOP56 | 9627 | -0.011 | 0.15 | NO |
247 | SEC24D | SEC24D | SEC24D | 9638 | -0.011 | 0.15 | NO |
248 | PIGU | PIGU | PIGU | 9640 | -0.011 | 0.15 | NO |
249 | SRPRB | SRPRB | SRPRB | 9651 | -0.011 | 0.15 | NO |
250 | FBXL5 | FBXL5 | FBXL5 | 9657 | -0.011 | 0.15 | NO |
251 | RPL31 | RPL31 | RPL31 | 9733 | -0.012 | 0.15 | NO |
252 | MUC15 | MUC15 | MUC15 | 9745 | -0.012 | 0.15 | NO |
253 | MLEC | MLEC | MLEC | 9759 | -0.012 | 0.15 | NO |
254 | FURIN | FURIN | FURIN | 9798 | -0.013 | 0.15 | NO |
255 | EIF3H | EIF3H | EIF3H | 9805 | -0.013 | 0.15 | NO |
256 | PIGC | PIGC | PIGC | 9806 | -0.013 | 0.15 | NO |
257 | ST3GAL2 | ST3GAL2 | ST3GAL2 | 9822 | -0.013 | 0.15 | NO |
258 | RPN2 | RPN2 | RPN2 | 9877 | -0.014 | 0.14 | NO |
259 | SEC24C | SEC24C | SEC24C | 9904 | -0.014 | 0.14 | NO |
260 | EIF2S2 | EIF2S2 | EIF2S2 | 9913 | -0.014 | 0.14 | NO |
261 | RPL32 | RPL32 | RPL32 | 9941 | -0.015 | 0.14 | NO |
262 | SLC25A13 | SLC25A13 | SLC25A13 | 9963 | -0.015 | 0.14 | NO |
263 | VDAC1 | VDAC1 | VDAC1 | 9981 | -0.015 | 0.14 | NO |
264 | LONP2 | LONP2 | LONP2 | 9997 | -0.016 | 0.14 | NO |
265 | MGAT2 | MGAT2 | MGAT2 | 10050 | -0.016 | 0.14 | NO |
266 | RPS23 | RPS23 | RPS23 | 10057 | -0.016 | 0.14 | NO |
267 | USP11 | USP11 | USP11 | 10089 | -0.017 | 0.14 | NO |
268 | RPL27A | RPL27A | RPL27A | 10095 | -0.017 | 0.14 | NO |
269 | STT3A | STT3A | STT3A | 10134 | -0.018 | 0.13 | NO |
270 | RPL34 | RPL34 | RPL34 | 10156 | -0.018 | 0.13 | NO |
271 | GRPEL1 | GRPEL1 | GRPEL1 | 10235 | -0.019 | 0.13 | NO |
272 | RPL37 | RPL37 | RPL37 | 10245 | -0.019 | 0.13 | NO |
273 | SRPR | SRPR | SRPR | 10284 | -0.02 | 0.13 | NO |
274 | GALNT2 | GALNT2 | GALNT2 | 10285 | -0.02 | 0.13 | NO |
275 | RPL22 | RPL22 | RPL22 | 10340 | -0.02 | 0.13 | NO |
276 | TOMM20 | TOMM20 | TOMM20 | 10343 | -0.02 | 0.13 | NO |
277 | B4GALT1 | B4GALT1 | B4GALT1 | 10433 | -0.022 | 0.12 | NO |
278 | GANAB | GANAB | GANAB | 10443 | -0.022 | 0.12 | NO |
279 | GALNT11 | GALNT11 | GALNT11 | 10498 | -0.023 | 0.12 | NO |
280 | EIF4B | EIF4B | EIF4B | 10523 | -0.023 | 0.12 | NO |
281 | ALG9 | ALG9 | ALG9 | 10563 | -0.023 | 0.12 | NO |
282 | RPL5 | RPL5 | RPL5 | 10583 | -0.024 | 0.12 | NO |
283 | SSR1 | SSR1 | SSR1 | 10677 | -0.025 | 0.11 | NO |
284 | EIF5 | EIF5 | EIF5 | 10756 | -0.026 | 0.11 | NO |
285 | EDEM1 | EDEM1 | EDEM1 | 10763 | -0.026 | 0.11 | NO |
286 | SRP14 | SRP14 | SRP14 | 10767 | -0.026 | 0.11 | NO |
287 | PFDN2 | PFDN2 | PFDN2 | 10907 | -0.028 | 0.1 | NO |
288 | PGM3 | PGM3 | PGM3 | 10981 | -0.029 | 0.099 | NO |
289 | ETF1 | ETF1 | ETF1 | 11015 | -0.03 | 0.098 | NO |
290 | SPCS3 | SPCS3 | SPCS3 | 11050 | -0.03 | 0.097 | NO |
291 | RPL11 | RPL11 | RPL11 | 11053 | -0.031 | 0.098 | NO |
292 | TOMM40 | TOMM40 | TOMM40 | 11148 | -0.032 | 0.093 | NO |
293 | RPL30 | RPL30 | RPL30 | 11196 | -0.033 | 0.091 | NO |
294 | RPL19 | RPL19 | RPL19 | 11282 | -0.034 | 0.088 | NO |
295 | SEC11A | SEC11A | SEC11A | 11387 | -0.036 | 0.083 | NO |
296 | PRKCSH | PRKCSH | PRKCSH | 11418 | -0.036 | 0.082 | NO |
297 | RPL23 | RPL23 | RPL23 | 11447 | -0.036 | 0.081 | NO |
298 | SLC25A12 | SLC25A12 | SLC25A12 | 11486 | -0.037 | 0.08 | NO |
299 | EIF4G1 | EIF4G1 | EIF4G1 | 11554 | -0.038 | 0.077 | NO |
300 | MTX2 | MTX2 | MTX2 | 11600 | -0.039 | 0.076 | NO |
301 | GALNT13 | GALNT13 | GALNT13 | 11605 | -0.039 | 0.077 | NO |
302 | HSPA9 | HSPA9 | HSPA9 | 11606 | -0.039 | 0.078 | NO |
303 | PABPC1 | PABPC1 | PABPC1 | 11650 | -0.039 | 0.076 | NO |
304 | TBCA | TBCA | TBCA | 11653 | -0.039 | 0.077 | NO |
305 | SRP68 | SRP68 | SRP68 | 11725 | -0.04 | 0.074 | NO |
306 | STS | STS | STS | 11737 | -0.04 | 0.075 | NO |
307 | CCT6A | CCT6A | CCT6A | 11741 | -0.04 | 0.076 | NO |
308 | MAN1C1 | MAN1C1 | MAN1C1 | 11779 | -0.041 | 0.075 | NO |
309 | MUC13 | MUC13 | MUC13 | 11801 | -0.042 | 0.075 | NO |
310 | EIF2S1 | EIF2S1 | EIF2S1 | 11876 | -0.043 | 0.072 | NO |
311 | HSCB | HSCB | HSCB | 11960 | -0.044 | 0.068 | NO |
312 | RPL4 | RPL4 | RPL4 | 11962 | -0.044 | 0.069 | NO |
313 | PIGN | PIGN | PIGN | 11964 | -0.044 | 0.07 | NO |
314 | FBXW2 | FBXW2 | FBXW2 | 11972 | -0.044 | 0.071 | NO |
315 | SEC11C | SEC11C | SEC11C | 12013 | -0.045 | 0.07 | NO |
316 | RPL13A | RPL13A | RPL13A | 12014 | -0.045 | 0.071 | NO |
317 | SEC24B | SEC24B | SEC24B | 12027 | -0.045 | 0.072 | NO |
318 | PFDN1 | PFDN1 | PFDN1 | 12055 | -0.045 | 0.072 | NO |
319 | B4GALT4 | B4GALT4 | B4GALT4 | 12217 | -0.048 | 0.064 | NO |
320 | RPL14 | RPL14 | RPL14 | 12247 | -0.048 | 0.063 | NO |
321 | GRPEL2 | GRPEL2 | GRPEL2 | 12253 | -0.048 | 0.064 | NO |
322 | GALNTL1 | GALNTL1 | GALNTL1 | 12360 | -0.05 | 0.06 | NO |
323 | XRN2 | XRN2 | XRN2 | 12361 | -0.05 | 0.061 | NO |
324 | TOMM70A | TOMM70A | TOMM70A | 12385 | -0.05 | 0.061 | NO |
325 | CANX | CANX | CANX | 12496 | -0.052 | 0.056 | NO |
326 | TIMM17A | TIMM17A | TIMM17A | 12497 | -0.052 | 0.058 | NO |
327 | B4GALT5 | B4GALT5 | B4GALT5 | 12522 | -0.052 | 0.058 | NO |
328 | GALNTL2 | GALNTL2 | GALNTL2 | 12523 | -0.052 | 0.059 | NO |
329 | PDIA3 | PDIA3 | PDIA3 | 12583 | -0.053 | 0.057 | NO |
330 | C1GALT1C1 | C1GALT1C1 | C1GALT1C1 | 12659 | -0.055 | 0.054 | NO |
331 | MAN2A1 | MAN2A1 | MAN2A1 | 12728 | -0.056 | 0.052 | NO |
332 | GALNT10 | GALNT10 | GALNT10 | 12779 | -0.057 | 0.051 | NO |
333 | UGGT1 | UGGT1 | UGGT1 | 12791 | -0.057 | 0.052 | NO |
334 | EIF2S3 | EIF2S3 | EIF2S3 | 12824 | -0.057 | 0.052 | NO |
335 | SEC31A | SEC31A | SEC31A | 12835 | -0.057 | 0.052 | NO |
336 | RPS20 | RPS20 | RPS20 | 12944 | -0.059 | 0.048 | NO |
337 | SEC23A | SEC23A | SEC23A | 13121 | -0.062 | 0.04 | NO |
338 | MUC21 | MUC21 | MUC21 | 13138 | -0.062 | 0.04 | NO |
339 | PIGP | PIGP | PIGP | 13166 | -0.062 | 0.041 | NO |
340 | HSPD1 | HSPD1 | HSPD1 | 13216 | -0.063 | 0.04 | NO |
341 | RPL26 | RPL26 | RPL26 | 13273 | -0.064 | 0.038 | NO |
342 | SRP54 | SRP54 | SRP54 | 13311 | -0.065 | 0.038 | NO |
343 | DPM1 | DPM1 | DPM1 | 13352 | -0.066 | 0.037 | NO |
344 | AP3M1 | AP3M1 | AP3M1 | 13407 | -0.067 | 0.036 | NO |
345 | TIMM9 | TIMM9 | TIMM9 | 13415 | -0.067 | 0.037 | NO |
346 | SRP72 | SRP72 | SRP72 | 13498 | -0.068 | 0.035 | NO |
347 | PROC | PROC | PROC | 13567 | -0.069 | 0.033 | NO |
348 | SEC61G | SEC61G | SEC61G | 13594 | -0.07 | 0.033 | NO |
349 | MCFD2 | MCFD2 | MCFD2 | 13604 | -0.07 | 0.034 | NO |
350 | ALG8 | ALG8 | ALG8 | 13633 | -0.07 | 0.035 | NO |
351 | ST3GAL1 | ST3GAL1 | ST3GAL1 | 13688 | -0.072 | 0.034 | NO |
352 | TIMM8A | TIMM8A | TIMM8A | 13706 | -0.072 | 0.035 | NO |
353 | ARFGEF2 | ARFGEF2 | ARFGEF2 | 13731 | -0.072 | 0.035 | NO |
354 | CCT8 | CCT8 | CCT8 | 13732 | -0.072 | 0.037 | NO |
355 | TUBB1 | TUBB1 | TUBB1 | 13785 | -0.073 | 0.036 | NO |
356 | RPS7 | RPS7 | RPS7 | 13819 | -0.074 | 0.036 | NO |
357 | ARSJ | ARSJ | ARSJ | 13825 | -0.074 | 0.038 | NO |
358 | FBXL3 | FBXL3 | FBXL3 | 13922 | -0.075 | 0.035 | NO |
359 | LMAN1 | LMAN1 | LMAN1 | 14172 | -0.08 | 0.023 | NO |
360 | MAN1A1 | MAN1A1 | MAN1A1 | 14224 | -0.08 | 0.022 | NO |
361 | GALNT3 | GALNT3 | GALNT3 | 14251 | -0.081 | 0.023 | NO |
362 | TRAM1 | TRAM1 | TRAM1 | 14272 | -0.082 | 0.024 | NO |
363 | EIF5A2 | EIF5A2 | EIF5A2 | 14287 | -0.082 | 0.025 | NO |
364 | PFDN6 | PFDN6 | PFDN6 | 14382 | -0.084 | 0.022 | NO |
365 | TBCE | TBCE | TBCE | 14414 | -0.084 | 0.023 | NO |
366 | MGAT4A | MGAT4A | MGAT4A | 14421 | -0.084 | 0.025 | NO |
367 | PIGX | PIGX | PIGX | 14478 | -0.086 | 0.024 | NO |
368 | FBXW7 | FBXW7 | FBXW7 | 14724 | -0.091 | 0.012 | NO |
369 | GCNT4 | GCNT4 | GCNT4 | 14765 | -0.092 | 0.013 | NO |
370 | GCNT1 | GCNT1 | GCNT1 | 14801 | -0.092 | 0.013 | NO |
371 | VBP1 | VBP1 | VBP1 | 14821 | -0.093 | 0.015 | NO |
372 | PIGW | PIGW | PIGW | 14851 | -0.094 | 0.016 | NO |
373 | PIGB | PIGB | PIGB | 14890 | -0.094 | 0.016 | NO |
374 | B3GNT2 | B3GNT2 | B3GNT2 | 15097 | -0.099 | 0.0068 | NO |
375 | PROS1 | PROS1 | PROS1 | 15276 | -0.1 | -0.00048 | NO |
376 | PIGK | PIGK | PIGK | 15293 | -0.1 | 0.0014 | NO |
377 | GALNT6 | GALNT6 | GALNT6 | 15370 | -0.1 | -7e-05 | NO |
378 | ALG10B | ALG10B | ALG10B | 15390 | -0.1 | 0.0017 | NO |
379 | PIGM | PIGM | PIGM | 15452 | -0.11 | 0.0011 | NO |
380 | GALNT1 | GALNT1 | GALNT1 | 15537 | -0.11 | -0.0007 | NO |
381 | SRP19 | SRP19 | SRP19 | 15563 | -0.11 | 0.00084 | NO |
382 | ALG11 | ALG11 | ALG11 | 15738 | -0.11 | -0.006 | NO |
383 | KIF13A | KIF13A | KIF13A | 15744 | -0.11 | -0.0032 | NO |
384 | EIF3E | EIF3E | EIF3E | 15796 | -0.12 | -0.0029 | NO |
385 | GALNT7 | GALNT7 | GALNT7 | 15830 | -0.12 | -0.0017 | NO |
386 | EIF3J | EIF3J | EIF3J | 15858 | -0.12 | -3e-05 | NO |
387 | RPS12 | RPS12 | RPS12 | 15909 | -0.12 | 0.00033 | NO |
388 | RPS24 | RPS24 | RPS24 | 15920 | -0.12 | 0.003 | NO |
389 | GALNT5 | GALNT5 | GALNT5 | 15967 | -0.12 | 0.0036 | NO |
390 | RPS25 | RPS25 | RPS25 | 16000 | -0.12 | 0.005 | NO |
391 | RPL24 | RPL24 | RPL24 | 16028 | -0.12 | 0.0068 | NO |
392 | RPL12 | RPL12 | RPL12 | 16147 | -0.12 | 0.0035 | NO |
393 | RPS18 | RPS18 | RPS18 | 16152 | -0.12 | 0.0067 | NO |
394 | DNAJC19 | DNAJC19 | DNAJC19 | 16250 | -0.13 | 0.0046 | NO |
395 | ALG6 | ALG6 | ALG6 | 16252 | -0.13 | 0.0081 | NO |
396 | PIGA | PIGA | PIGA | 16357 | -0.13 | 0.0058 | NO |
397 | EIF3A | EIF3A | EIF3A | 16385 | -0.13 | 0.0078 | NO |
398 | ARSK | ARSK | ARSK | 16444 | -0.14 | 0.0082 | NO |
399 | ST8SIA3 | ST8SIA3 | ST8SIA3 | 16470 | -0.14 | 0.01 | NO |
400 | GSPT2 | GSPT2 | GSPT2 | 16474 | -0.14 | 0.014 | NO |
401 | UGGT2 | UGGT2 | UGGT2 | 16559 | -0.14 | 0.013 | NO |
402 | B3GNT5 | B3GNT5 | B3GNT5 | 16741 | -0.15 | 0.0068 | NO |
403 | COX17 | COX17 | COX17 | 16816 | -0.15 | 0.0067 | NO |
404 | ALG10 | ALG10 | ALG10 | 16876 | -0.15 | 0.0075 | NO |
405 | EDEM3 | EDEM3 | EDEM3 | 16966 | -0.16 | 0.0068 | NO |
406 | RPS27A | RPS27A | RPS27A | 16977 | -0.16 | 0.01 | NO |
407 | ST8SIA2 | ST8SIA2 | ST8SIA2 | 17002 | -0.16 | 0.014 | NO |
408 | C1GALT1 | C1GALT1 | C1GALT1 | 17158 | -0.17 | 0.0093 | NO |
409 | MAN1A2 | MAN1A2 | MAN1A2 | 17192 | -0.17 | 0.012 | NO |
410 | MGAT5 | MGAT5 | MGAT5 | 17267 | -0.18 | 0.013 | NO |
411 | EIF5B | EIF5B | EIF5B | 17384 | -0.18 | 0.011 | NO |
412 | PGAP1 | PGAP1 | PGAP1 | 17420 | -0.19 | 0.014 | NO |
413 | MANEA | MANEA | MANEA | 17559 | -0.2 | 0.012 | NO |
414 | B4GALT6 | B4GALT6 | B4GALT6 | 17606 | -0.21 | 0.015 | NO |
415 | PFDN4 | PFDN4 | PFDN4 | 17880 | -0.27 | 0.0066 | 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: REACTOME MEIOSIS.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_MEIOSIS.heatmap_plot.clus4.8.png)
Figure S72. 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
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_METABOLISM_OF_PROTEINS.volcano_plot.clus4.6.png)
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 | HIST1H4K | HIST1H4K | HIST1H4K | 3 | 1.7 | 0.1 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 47 | 1.2 | 0.18 | YES |
3 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 80 | 1.1 | 0.24 | YES |
4 | FKBP6 | FKBP6 | FKBP6 | 134 | 0.93 | 0.3 | YES |
5 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 150 | 0.88 | 0.35 | YES |
6 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 344 | 0.6 | 0.38 | YES |
7 | HIST1H4J | HIST1H4J | HIST1H4J | 408 | 0.53 | 0.41 | YES |
8 | STAG3 | STAG3 | STAG3 | 448 | 0.49 | 0.44 | YES |
9 | HIST1H4I | HIST1H4I | HIST1H4I | 503 | 0.46 | 0.46 | YES |
10 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 529 | 0.44 | 0.49 | YES |
11 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 566 | 0.42 | 0.51 | YES |
12 | HIST1H4A | HIST1H4A | HIST1H4A | 569 | 0.42 | 0.54 | YES |
13 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 583 | 0.41 | 0.56 | YES |
14 | HIST2H4A | HIST2H4A | HIST2H4A | 586 | 0.41 | 0.58 | YES |
15 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 845 | 0.32 | 0.59 | YES |
16 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 858 | 0.32 | 0.61 | YES |
17 | HIST1H4B | HIST1H4B | HIST1H4B | 873 | 0.31 | 0.63 | YES |
18 | HIST1H4D | HIST1H4D | HIST1H4D | 925 | 0.3 | 0.64 | YES |
19 | HIST1H4E | HIST1H4E | HIST1H4E | 949 | 0.29 | 0.66 | YES |
20 | HIST1H4C | HIST1H4C | HIST1H4C | 966 | 0.29 | 0.68 | YES |
21 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 1359 | 0.23 | 0.67 | YES |
22 | HIST1H4H | HIST1H4H | HIST1H4H | 1474 | 0.22 | 0.68 | YES |
23 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 1634 | 0.21 | 0.68 | YES |
24 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 1699 | 0.2 | 0.69 | YES |
25 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1706 | 0.2 | 0.7 | YES |
26 | REC8 | REC8 | REC8 | 1710 | 0.2 | 0.71 | YES |
27 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 1738 | 0.2 | 0.72 | YES |
28 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2066 | 0.17 | 0.72 | NO |
29 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2121 | 0.17 | 0.72 | NO |
30 | H2AFX | H2AFX | H2AFX | 2653 | 0.14 | 0.7 | NO |
31 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3383 | 0.11 | 0.67 | NO |
32 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 3638 | 0.098 | 0.66 | NO |
33 | ACD | ACD | ACD | 4657 | 0.071 | 0.61 | NO |
34 | SMC1B | SMC1B | SMC1B | 4679 | 0.071 | 0.61 | NO |
35 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 5411 | 0.056 | 0.57 | NO |
36 | UBE2I | UBE2I | UBE2I | 6715 | 0.033 | 0.5 | NO |
37 | H2AFZ | H2AFZ | H2AFZ | 7459 | 0.021 | 0.46 | NO |
38 | LMNA | LMNA | LMNA | 8487 | 0.0056 | 0.41 | NO |
39 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 9002 | -0.0019 | 0.38 | NO |
40 | TINF2 | TINF2 | TINF2 | 9273 | -0.0055 | 0.36 | NO |
41 | LMNB1 | LMNB1 | LMNB1 | 9673 | -0.011 | 0.34 | NO |
42 | TERF2 | TERF2 | TERF2 | 10274 | -0.019 | 0.31 | NO |
43 | HSPA2 | HSPA2 | HSPA2 | 11291 | -0.034 | 0.26 | NO |
44 | DIDO1 | DIDO1 | DIDO1 | 13072 | -0.061 | 0.16 | NO |
45 | SUN2 | SUN2 | SUN2 | 13151 | -0.062 | 0.16 | NO |
46 | POT1 | POT1 | POT1 | 13585 | -0.07 | 0.14 | NO |
47 | ATR | ATR | ATR | 13592 | -0.07 | 0.14 | NO |
48 | RAD21 | RAD21 | RAD21 | 13733 | -0.072 | 0.14 | NO |
49 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 13878 | -0.075 | 0.14 | NO |
50 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 13897 | -0.075 | 0.14 | NO |
51 | SMC1A | SMC1A | SMC1A | 13898 | -0.075 | 0.14 | NO |
52 | TERF2IP | TERF2IP | TERF2IP | 14105 | -0.078 | 0.14 | NO |
53 | BRCA1 | BRCA1 | BRCA1 | 15061 | -0.098 | 0.09 | NO |
54 | HIST4H4 | HIST4H4 | HIST4H4 | 15165 | -0.1 | 0.091 | NO |
55 | SYCP2 | SYCP2 | SYCP2 | 15473 | -0.11 | 0.08 | NO |
56 | STAG2 | STAG2 | STAG2 | 15692 | -0.11 | 0.075 | NO |
57 | STAG1 | STAG1 | STAG1 | 16010 | -0.12 | 0.065 | NO |
58 | TERF1 | TERF1 | TERF1 | 16180 | -0.13 | 0.063 | NO |
59 | TEX12 | TEX12 | TEX12 | 16561 | -0.14 | 0.05 | NO |
60 | SYNE2 | SYNE2 | SYNE2 | 16759 | -0.15 | 0.048 | NO |
61 | SMC3 | SMC3 | SMC3 | 16787 | -0.15 | 0.056 | NO |
62 | SYNE1 | SYNE1 | SYNE1 | 17355 | -0.18 | 0.036 | 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: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE.heatmap_plot.clus4.17.png)
Figure S74. 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
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_MEIOTIC_SYNAPSIS.volcano_plot.clus4.7.png)
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 | HIST1H4K | HIST1H4K | HIST1H4K | 3 | 1.7 | 0.077 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 47 | 1.2 | 0.13 | YES |
3 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 80 | 1.1 | 0.18 | YES |
4 | FKBP6 | FKBP6 | FKBP6 | 134 | 0.93 | 0.22 | YES |
5 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 150 | 0.88 | 0.26 | YES |
6 | HIST2H3C | HIST2H3C | HIST2H3C | 195 | 0.78 | 0.29 | YES |
7 | HIST2H3D | HIST2H3D | HIST2H3D | 250 | 0.71 | 0.32 | YES |
8 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 344 | 0.6 | 0.34 | YES |
9 | HIST1H4J | HIST1H4J | HIST1H4J | 408 | 0.53 | 0.36 | YES |
10 | STAG3 | STAG3 | STAG3 | 448 | 0.49 | 0.38 | YES |
11 | HIST1H4I | HIST1H4I | HIST1H4I | 503 | 0.46 | 0.4 | YES |
12 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 529 | 0.44 | 0.42 | YES |
13 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 566 | 0.42 | 0.44 | YES |
14 | HIST1H4A | HIST1H4A | HIST1H4A | 569 | 0.42 | 0.45 | YES |
15 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 583 | 0.41 | 0.47 | YES |
16 | HIST2H4A | HIST2H4A | HIST2H4A | 586 | 0.41 | 0.49 | YES |
17 | HIST1H3H | HIST1H3H | HIST1H3H | 828 | 0.32 | 0.49 | YES |
18 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 845 | 0.32 | 0.5 | YES |
19 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 858 | 0.32 | 0.52 | YES |
20 | HIST1H4B | HIST1H4B | HIST1H4B | 873 | 0.31 | 0.53 | YES |
21 | HIST1H4D | HIST1H4D | HIST1H4D | 925 | 0.3 | 0.54 | YES |
22 | HIST1H3D | HIST1H3D | HIST1H3D | 927 | 0.3 | 0.56 | YES |
23 | HIST1H4E | HIST1H4E | HIST1H4E | 949 | 0.29 | 0.57 | YES |
24 | HIST1H3B | HIST1H3B | HIST1H3B | 960 | 0.29 | 0.58 | YES |
25 | HIST1H4C | HIST1H4C | HIST1H4C | 966 | 0.29 | 0.6 | YES |
26 | HIST1H3F | HIST1H3F | HIST1H3F | 1080 | 0.27 | 0.6 | YES |
27 | HIST1H3J | HIST1H3J | HIST1H3J | 1221 | 0.25 | 0.6 | YES |
28 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 1359 | 0.23 | 0.61 | YES |
29 | HIST1H3I | HIST1H3I | HIST1H3I | 1413 | 0.23 | 0.61 | YES |
30 | HIST1H4H | HIST1H4H | HIST1H4H | 1474 | 0.22 | 0.62 | YES |
31 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 1634 | 0.21 | 0.62 | YES |
32 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 1699 | 0.2 | 0.63 | YES |
33 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1706 | 0.2 | 0.64 | YES |
34 | REC8 | REC8 | REC8 | 1710 | 0.2 | 0.64 | YES |
35 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 1738 | 0.2 | 0.65 | YES |
36 | HIST1H3C | HIST1H3C | HIST1H3C | 1745 | 0.2 | 0.66 | YES |
37 | HIST1H3G | HIST1H3G | HIST1H3G | 1950 | 0.18 | 0.66 | YES |
38 | HIST1H3A | HIST1H3A | HIST1H3A | 2045 | 0.17 | 0.66 | YES |
39 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2066 | 0.17 | 0.67 | YES |
40 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2121 | 0.17 | 0.67 | YES |
41 | H3F3A | H3F3A | H3F3A | 2480 | 0.14 | 0.66 | NO |
42 | MSH4 | MSH4 | MSH4 | 2487 | 0.14 | 0.66 | NO |
43 | H2AFX | H2AFX | H2AFX | 2653 | 0.14 | 0.66 | NO |
44 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3383 | 0.11 | 0.62 | NO |
45 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 3638 | 0.098 | 0.62 | NO |
46 | ACD | ACD | ACD | 4657 | 0.071 | 0.56 | NO |
47 | SMC1B | SMC1B | SMC1B | 4679 | 0.071 | 0.56 | NO |
48 | MSH5 | MSH5 | MSH5 | 5259 | 0.059 | 0.53 | NO |
49 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 5411 | 0.056 | 0.53 | NO |
50 | RAD51 | RAD51 | RAD51 | 5431 | 0.056 | 0.53 | NO |
51 | CDK4 | CDK4 | CDK4 | 6474 | 0.037 | 0.47 | NO |
52 | UBE2I | UBE2I | UBE2I | 6715 | 0.033 | 0.46 | NO |
53 | DMC1 | DMC1 | DMC1 | 7407 | 0.022 | 0.42 | NO |
54 | H2AFZ | H2AFZ | H2AFZ | 7459 | 0.021 | 0.42 | NO |
55 | RPA2 | RPA2 | RPA2 | 7520 | 0.02 | 0.42 | NO |
56 | RPA3 | RPA3 | RPA3 | 7935 | 0.014 | 0.4 | NO |
57 | RPA1 | RPA1 | RPA1 | 8220 | 0.0097 | 0.38 | NO |
58 | LMNA | LMNA | LMNA | 8487 | 0.0056 | 0.37 | NO |
59 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 9002 | -0.0019 | 0.34 | NO |
60 | TINF2 | TINF2 | TINF2 | 9273 | -0.0055 | 0.32 | NO |
61 | LMNB1 | LMNB1 | LMNB1 | 9673 | -0.011 | 0.3 | NO |
62 | TERF2 | TERF2 | TERF2 | 10274 | -0.019 | 0.27 | NO |
63 | TOP3A | TOP3A | TOP3A | 10348 | -0.02 | 0.26 | NO |
64 | RAD51C | RAD51C | RAD51C | 11004 | -0.03 | 0.23 | NO |
65 | HSPA2 | HSPA2 | HSPA2 | 11291 | -0.034 | 0.22 | NO |
66 | CDK2 | CDK2 | CDK2 | 11580 | -0.038 | 0.2 | NO |
67 | MLH1 | MLH1 | MLH1 | 12345 | -0.05 | 0.16 | NO |
68 | DIDO1 | DIDO1 | DIDO1 | 13072 | -0.061 | 0.12 | NO |
69 | H3F3B | H3F3B | H3F3B | 13149 | -0.062 | 0.12 | NO |
70 | SUN2 | SUN2 | SUN2 | 13151 | -0.062 | 0.12 | NO |
71 | POT1 | POT1 | POT1 | 13585 | -0.07 | 0.1 | NO |
72 | ATR | ATR | ATR | 13592 | -0.07 | 0.11 | NO |
73 | RAD21 | RAD21 | RAD21 | 13733 | -0.072 | 0.1 | NO |
74 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 13878 | -0.075 | 0.097 | NO |
75 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 13897 | -0.075 | 0.099 | NO |
76 | SMC1A | SMC1A | SMC1A | 13898 | -0.075 | 0.1 | NO |
77 | TERF2IP | TERF2IP | TERF2IP | 14105 | -0.078 | 0.095 | NO |
78 | BRCA1 | BRCA1 | BRCA1 | 15061 | -0.098 | 0.046 | NO |
79 | HIST4H4 | HIST4H4 | HIST4H4 | 15165 | -0.1 | 0.045 | NO |
80 | SYCP2 | SYCP2 | SYCP2 | 15473 | -0.11 | 0.032 | NO |
81 | NBN | NBN | NBN | 15656 | -0.11 | 0.027 | NO |
82 | STAG2 | STAG2 | STAG2 | 15692 | -0.11 | 0.03 | NO |
83 | BLM | BLM | BLM | 15706 | -0.11 | 0.035 | NO |
84 | HIST1H3E | HIST1H3E | HIST1H3E | 15748 | -0.11 | 0.038 | NO |
85 | MLH3 | MLH3 | MLH3 | 15785 | -0.12 | 0.041 | NO |
86 | STAG1 | STAG1 | STAG1 | 16010 | -0.12 | 0.034 | NO |
87 | RAD50 | RAD50 | RAD50 | 16151 | -0.12 | 0.032 | NO |
88 | TERF1 | TERF1 | TERF1 | 16180 | -0.13 | 0.036 | NO |
89 | TEX12 | TEX12 | TEX12 | 16561 | -0.14 | 0.021 | NO |
90 | SYNE2 | SYNE2 | SYNE2 | 16759 | -0.15 | 0.016 | NO |
91 | RBBP8 | RBBP8 | RBBP8 | 16780 | -0.15 | 0.022 | NO |
92 | SMC3 | SMC3 | SMC3 | 16787 | -0.15 | 0.028 | NO |
93 | BRCA2 | BRCA2 | BRCA2 | 16792 | -0.15 | 0.035 | NO |
94 | MRE11A | MRE11A | MRE11A | 17130 | -0.17 | 0.024 | NO |
95 | MND1 | MND1 | MND1 | 17183 | -0.17 | 0.029 | NO |
96 | SYNE1 | SYNE1 | SYNE1 | 17355 | -0.18 | 0.027 | NO |
97 | ATM | ATM | ATM | 17403 | -0.19 | 0.033 | NO |
Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME RNA POL I TRANSCRIPTION.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_RNA_POL_I_TRANSCRIPTION.heatmap_plot.clus4.14.png)
Figure S76. 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
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_MEIOSIS.volcano_plot.clus4.8.png)
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 | HIST1H4K | HIST1H4K | HIST1H4K | 3 | 1.7 | 0.057 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 47 | 1.2 | 0.097 | YES |
3 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 80 | 1.1 | 0.13 | YES |
4 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 150 | 0.88 | 0.16 | YES |
5 | FCGR2C | FCGR2C | FCGR2C | 188 | 0.8 | 0.18 | YES |
6 | HIST2H3C | HIST2H3C | HIST2H3C | 195 | 0.78 | 0.21 | YES |
7 | HIST2H3D | HIST2H3D | HIST2H3D | 250 | 0.71 | 0.23 | YES |
8 | FCGR3B | FCGR3B | FCGR3B | 272 | 0.68 | 0.25 | YES |
9 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 344 | 0.6 | 0.27 | YES |
10 | FCGR1A | FCGR1A | FCGR1A | 367 | 0.57 | 0.29 | YES |
11 | HIST2H2BF | HIST2H2BF | HIST2H2BF | 381 | 0.55 | 0.3 | YES |
12 | HIST1H4J | HIST1H4J | HIST1H4J | 408 | 0.53 | 0.32 | YES |
13 | HLA-DQA2 | HLA-DQA2 | HLA-DQA2 | 414 | 0.52 | 0.34 | YES |
14 | HIST3H2A | HIST3H2A | HIST3H2A | 422 | 0.52 | 0.36 | YES |
15 | HIST1H4I | HIST1H4I | HIST1H4I | 503 | 0.46 | 0.37 | YES |
16 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 529 | 0.44 | 0.38 | YES |
17 | H3F3C | H3F3C | H3F3C | 552 | 0.43 | 0.39 | YES |
18 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 566 | 0.42 | 0.41 | YES |
19 | HIST1H4A | HIST1H4A | HIST1H4A | 569 | 0.42 | 0.42 | YES |
20 | HLA-DRB5 | HLA-DRB5 | HLA-DRB5 | 572 | 0.42 | 0.44 | YES |
21 | FCGR2B | FCGR2B | FCGR2B | 577 | 0.42 | 0.45 | YES |
22 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 583 | 0.41 | 0.46 | YES |
23 | HIST2H4A | HIST2H4A | HIST2H4A | 586 | 0.41 | 0.48 | YES |
24 | C8G | C8G | C8G | 766 | 0.34 | 0.48 | YES |
25 | HIST1H3H | HIST1H3H | HIST1H3H | 828 | 0.32 | 0.48 | YES |
26 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 845 | 0.32 | 0.5 | YES |
27 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 858 | 0.32 | 0.5 | YES |
28 | HIST1H4B | HIST1H4B | HIST1H4B | 873 | 0.31 | 0.52 | YES |
29 | HIST1H2AG | HIST1H2AG | HIST1H2AG | 887 | 0.31 | 0.52 | YES |
30 | H2AFB1 | H2AFB1 | H2AFB1 | 889 | 0.31 | 0.54 | YES |
31 | HIST1H2AL | HIST1H2AL | HIST1H2AL | 901 | 0.31 | 0.55 | YES |
32 | HIST1H4D | HIST1H4D | HIST1H4D | 925 | 0.3 | 0.55 | YES |
33 | HIST1H3D | HIST1H3D | HIST1H3D | 927 | 0.3 | 0.56 | YES |
34 | HIST1H4E | HIST1H4E | HIST1H4E | 949 | 0.29 | 0.57 | YES |
35 | HIST1H3B | HIST1H3B | HIST1H3B | 960 | 0.29 | 0.58 | YES |
36 | HIST1H4C | HIST1H4C | HIST1H4C | 966 | 0.29 | 0.59 | YES |
37 | HLA-DQA1 | HLA-DQA1 | HLA-DQA1 | 1005 | 0.28 | 0.6 | YES |
38 | IL10 | IL10 | IL10 | 1027 | 0.28 | 0.61 | YES |
39 | HIST1H3F | HIST1H3F | HIST1H3F | 1080 | 0.27 | 0.61 | YES |
40 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 1123 | 0.26 | 0.62 | YES |
41 | HIST1H3J | HIST1H3J | HIST1H3J | 1221 | 0.25 | 0.62 | YES |
42 | HIST1H2AH | HIST1H2AH | HIST1H2AH | 1265 | 0.24 | 0.63 | YES |
43 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 1359 | 0.23 | 0.63 | YES |
44 | HIST2H2AB | HIST2H2AB | HIST2H2AB | 1370 | 0.23 | 0.64 | YES |
45 | HLA-DQB1 | HLA-DQB1 | HLA-DQB1 | 1376 | 0.23 | 0.65 | YES |
46 | C1QB | C1QB | C1QB | 1409 | 0.23 | 0.65 | YES |
47 | HIST1H3I | HIST1H3I | HIST1H3I | 1413 | 0.23 | 0.66 | YES |
48 | HIST1H4H | HIST1H4H | HIST1H4H | 1474 | 0.22 | 0.66 | YES |
49 | C1QC | C1QC | C1QC | 1542 | 0.22 | 0.67 | YES |
50 | HLA-DPB1 | HLA-DPB1 | HLA-DPB1 | 1554 | 0.21 | 0.68 | YES |
51 | HIST1H2AK | HIST1H2AK | HIST1H2AK | 1576 | 0.21 | 0.68 | YES |
52 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 1634 | 0.21 | 0.68 | YES |
53 | HLA-DMB | HLA-DMB | HLA-DMB | 1686 | 0.2 | 0.69 | YES |
54 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 1699 | 0.2 | 0.7 | YES |
55 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1706 | 0.2 | 0.7 | YES |
56 | TNF | TNF | TNF | 1711 | 0.2 | 0.71 | YES |
57 | HIST1H2AM | HIST1H2AM | HIST1H2AM | 1715 | 0.2 | 0.71 | YES |
58 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 1738 | 0.2 | 0.72 | YES |
59 | HIST1H3C | HIST1H3C | HIST1H3C | 1745 | 0.2 | 0.73 | YES |
60 | CD80 | CD80 | CD80 | 1761 | 0.2 | 0.73 | YES |
61 | HIST1H3G | HIST1H3G | HIST1H3G | 1950 | 0.18 | 0.73 | YES |
62 | HIST1H3A | HIST1H3A | HIST1H3A | 2045 | 0.17 | 0.73 | YES |
63 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2066 | 0.17 | 0.73 | YES |
64 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2121 | 0.17 | 0.74 | YES |
65 | IFNG | IFNG | IFNG | 2142 | 0.16 | 0.74 | YES |
66 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 2235 | 0.16 | 0.74 | YES |
67 | ELANE | ELANE | ELANE | 2341 | 0.15 | 0.74 | YES |
68 | HLA-DOA | HLA-DOA | HLA-DOA | 2471 | 0.14 | 0.74 | YES |
69 | H3F3A | H3F3A | H3F3A | 2480 | 0.14 | 0.74 | YES |
70 | C1QA | C1QA | C1QA | 2509 | 0.14 | 0.74 | YES |
71 | CD86 | CD86 | CD86 | 2515 | 0.14 | 0.75 | YES |
72 | CTSG | CTSG | CTSG | 2600 | 0.14 | 0.75 | YES |
73 | H2AFX | H2AFX | H2AFX | 2653 | 0.14 | 0.75 | YES |
74 | HLA-DRA | HLA-DRA | HLA-DRA | 2662 | 0.14 | 0.76 | YES |
75 | FCGR2A | FCGR2A | FCGR2A | 2665 | 0.14 | 0.76 | YES |
76 | CD40 | CD40 | CD40 | 2800 | 0.13 | 0.76 | NO |
77 | FCGR3A | FCGR3A | FCGR3A | 2887 | 0.13 | 0.76 | NO |
78 | HLA-DMA | HLA-DMA | HLA-DMA | 3036 | 0.12 | 0.75 | NO |
79 | C4A | C4A | C4A | 3114 | 0.12 | 0.75 | NO |
80 | HLA-DOB | HLA-DOB | HLA-DOB | 3361 | 0.11 | 0.74 | NO |
81 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3383 | 0.11 | 0.74 | NO |
82 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 3638 | 0.098 | 0.73 | NO |
83 | CD40LG | CD40LG | CD40LG | 3712 | 0.096 | 0.73 | NO |
84 | CD28 | CD28 | CD28 | 4476 | 0.076 | 0.69 | NO |
85 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 5411 | 0.056 | 0.64 | NO |
86 | H2AFJ | H2AFJ | H2AFJ | 5760 | 0.05 | 0.62 | NO |
87 | C2 | C2 | C2 | 5808 | 0.049 | 0.62 | NO |
88 | SNRPB | SNRPB | SNRPB | 5838 | 0.049 | 0.62 | NO |
89 | ACTN2 | ACTN2 | ACTN2 | 6309 | 0.04 | 0.6 | NO |
90 | C3 | C3 | C3 | 6698 | 0.033 | 0.58 | NO |
91 | H2AFZ | H2AFZ | H2AFZ | 7459 | 0.021 | 0.54 | NO |
92 | TRIM21 | TRIM21 | TRIM21 | 7676 | 0.018 | 0.52 | NO |
93 | C1R | C1R | C1R | 7720 | 0.017 | 0.52 | NO |
94 | H2AFY | H2AFY | H2AFY | 8323 | 0.0083 | 0.49 | NO |
95 | H2AFV | H2AFV | H2AFV | 8376 | 0.0073 | 0.49 | NO |
96 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 9002 | -0.0019 | 0.45 | NO |
97 | C9 | C9 | C9 | 9849 | -0.014 | 0.4 | NO |
98 | C1S | C1S | C1S | 10114 | -0.017 | 0.39 | NO |
99 | C6 | C6 | C6 | 10702 | -0.025 | 0.36 | NO |
100 | ACTN1 | ACTN1 | ACTN1 | 10914 | -0.028 | 0.35 | NO |
101 | SNRPD1 | SNRPD1 | SNRPD1 | 11073 | -0.031 | 0.34 | NO |
102 | ACTN4 | ACTN4 | ACTN4 | 11248 | -0.034 | 0.33 | NO |
103 | SNRPD3 | SNRPD3 | SNRPD3 | 11718 | -0.04 | 0.31 | NO |
104 | H3F3B | H3F3B | H3F3B | 13149 | -0.062 | 0.23 | NO |
105 | H2AFY2 | H2AFY2 | H2AFY2 | 13344 | -0.065 | 0.22 | NO |
106 | GRIN2A | GRIN2A | GRIN2A | 13698 | -0.072 | 0.2 | NO |
107 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 13878 | -0.075 | 0.19 | NO |
108 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 13897 | -0.075 | 0.2 | NO |
109 | GRIN2B | GRIN2B | GRIN2B | 14111 | -0.079 | 0.19 | NO |
110 | C5 | C5 | C5 | 14852 | -0.094 | 0.15 | NO |
111 | ACTN3 | ACTN3 | ACTN3 | 15029 | -0.097 | 0.14 | NO |
112 | HIST4H4 | HIST4H4 | HIST4H4 | 15165 | -0.1 | 0.14 | NO |
113 | TROVE2 | TROVE2 | TROVE2 | 15475 | -0.11 | 0.12 | NO |
114 | HIST1H3E | HIST1H3E | HIST1H3E | 15748 | -0.11 | 0.11 | NO |
115 | C7 | C7 | C7 | 16089 | -0.12 | 0.098 | NO |
116 | SSB | SSB | SSB | 17847 | -0.26 | 0.0083 | NO |
Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PROTEIN FOLDING.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_PROTEIN_FOLDING.heatmap_plot.clus4.12.png)
Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PROTEIN FOLDING, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS.volcano_plot.clus4.9.png)
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 | HIST1H4K | HIST1H4K | HIST1H4K | 3 | 1.7 | 0.09 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 47 | 1.2 | 0.15 | YES |
3 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 80 | 1.1 | 0.21 | YES |
4 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 150 | 0.88 | 0.25 | YES |
5 | HIST2H3C | HIST2H3C | HIST2H3C | 195 | 0.78 | 0.29 | YES |
6 | HIST2H3D | HIST2H3D | HIST2H3D | 250 | 0.71 | 0.33 | YES |
7 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 344 | 0.6 | 0.35 | YES |
8 | HIST1H4J | HIST1H4J | HIST1H4J | 408 | 0.53 | 0.38 | YES |
9 | NPPA | NPPA | NPPA | 445 | 0.5 | 0.4 | YES |
10 | HIST1H4I | HIST1H4I | HIST1H4I | 503 | 0.46 | 0.42 | YES |
11 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 529 | 0.44 | 0.45 | YES |
12 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 566 | 0.42 | 0.47 | YES |
13 | HIST1H4A | HIST1H4A | HIST1H4A | 569 | 0.42 | 0.49 | YES |
14 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 583 | 0.41 | 0.51 | YES |
15 | HIST2H4A | HIST2H4A | HIST2H4A | 586 | 0.41 | 0.53 | YES |
16 | HIST1H3H | HIST1H3H | HIST1H3H | 828 | 0.32 | 0.54 | YES |
17 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 845 | 0.32 | 0.55 | YES |
18 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 858 | 0.32 | 0.57 | YES |
19 | HIST1H4B | HIST1H4B | HIST1H4B | 873 | 0.31 | 0.58 | YES |
20 | APOA1 | APOA1 | APOA1 | 910 | 0.3 | 0.6 | YES |
21 | HIST1H4D | HIST1H4D | HIST1H4D | 925 | 0.3 | 0.61 | YES |
22 | HIST1H3D | HIST1H3D | HIST1H3D | 927 | 0.3 | 0.63 | YES |
23 | HIST1H4E | HIST1H4E | HIST1H4E | 949 | 0.29 | 0.64 | YES |
24 | HIST1H3B | HIST1H3B | HIST1H3B | 960 | 0.29 | 0.66 | YES |
25 | HIST1H4C | HIST1H4C | HIST1H4C | 966 | 0.29 | 0.67 | YES |
26 | HIST1H3F | HIST1H3F | HIST1H3F | 1080 | 0.27 | 0.68 | YES |
27 | SAA1 | SAA1 | SAA1 | 1214 | 0.25 | 0.69 | YES |
28 | HIST1H3J | HIST1H3J | HIST1H3J | 1221 | 0.25 | 0.7 | YES |
29 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 1359 | 0.23 | 0.7 | YES |
30 | HIST1H3I | HIST1H3I | HIST1H3I | 1413 | 0.23 | 0.71 | YES |
31 | HIST1H4H | HIST1H4H | HIST1H4H | 1474 | 0.22 | 0.72 | YES |
32 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 1634 | 0.21 | 0.72 | YES |
33 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 1699 | 0.2 | 0.73 | YES |
34 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1706 | 0.2 | 0.74 | YES |
35 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 1738 | 0.2 | 0.75 | YES |
36 | HIST1H3C | HIST1H3C | HIST1H3C | 1745 | 0.2 | 0.76 | YES |
37 | HIST1H3G | HIST1H3G | HIST1H3G | 1950 | 0.18 | 0.76 | YES |
38 | HIST1H3A | HIST1H3A | HIST1H3A | 2045 | 0.17 | 0.76 | YES |
39 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2066 | 0.17 | 0.77 | YES |
40 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2121 | 0.17 | 0.78 | YES |
41 | H3F3A | H3F3A | H3F3A | 2480 | 0.14 | 0.76 | NO |
42 | CST3 | CST3 | CST3 | 2615 | 0.14 | 0.76 | NO |
43 | H2AFX | H2AFX | H2AFX | 2653 | 0.14 | 0.77 | NO |
44 | SNCA | SNCA | SNCA | 2722 | 0.13 | 0.77 | NO |
45 | TTR | TTR | TTR | 3062 | 0.12 | 0.76 | NO |
46 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3383 | 0.11 | 0.75 | NO |
47 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 3638 | 0.098 | 0.74 | NO |
48 | SEMG1 | SEMG1 | SEMG1 | 5114 | 0.062 | 0.66 | NO |
49 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 5411 | 0.056 | 0.65 | NO |
50 | FGA | FGA | FGA | 5507 | 0.054 | 0.64 | NO |
51 | CALCA | CALCA | CALCA | 5601 | 0.052 | 0.64 | NO |
52 | LYZ | LYZ | LYZ | 5707 | 0.051 | 0.64 | NO |
53 | B2M | B2M | B2M | 6745 | 0.032 | 0.58 | NO |
54 | MFGE8 | MFGE8 | MFGE8 | 7121 | 0.026 | 0.56 | NO |
55 | H2AFZ | H2AFZ | H2AFZ | 7459 | 0.021 | 0.55 | NO |
56 | GSN | GSN | GSN | 7725 | 0.017 | 0.53 | NO |
57 | TGFBI | TGFBI | TGFBI | 7751 | 0.016 | 0.53 | NO |
58 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 9002 | -0.0019 | 0.46 | NO |
59 | LTF | LTF | LTF | 10573 | -0.024 | 0.38 | NO |
60 | ITM2B | ITM2B | ITM2B | 10871 | -0.028 | 0.36 | NO |
61 | APP | APP | APP | 11192 | -0.032 | 0.34 | NO |
62 | ODAM | ODAM | ODAM | 11522 | -0.037 | 0.33 | NO |
63 | H3F3B | H3F3B | H3F3B | 13149 | -0.062 | 0.24 | NO |
64 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 13878 | -0.075 | 0.2 | NO |
65 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 13897 | -0.075 | 0.21 | NO |
66 | PRL | PRL | PRL | 15021 | -0.097 | 0.15 | NO |
67 | HIST4H4 | HIST4H4 | HIST4H4 | 15165 | -0.1 | 0.15 | NO |
68 | HSPG2 | HSPG2 | HSPG2 | 15349 | -0.1 | 0.14 | NO |
69 | HIST1H3E | HIST1H3E | HIST1H3E | 15748 | -0.11 | 0.12 | NO |
Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME METABOLISM OF PROTEINS.
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_METABOLISM_OF_PROTEINS.heatmap_plot.clus4.6.png)
Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF PROTEINS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](COAD-TP-mRNAseq_cNMF-clus4___Class2-CanonicalPathway.REACTOME_AMYLOIDS.volcano_plot.clus4.10.png)
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
-
Gene set database = c2.cp.v4.0.symbols.gmt
-
Expression data file = COAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
-
Phenotype data file = COAD-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.