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 in BLCA-TP. 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: 192 |
Number of samples: 408 |
Original number of Gene Sets: 404 |
Maximum gene set size: 388 |
Table 2. Get Full Table pheno data info
phenotype info |
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pheno.type: 1 - 3 :[ clus1 ] 116 |
pheno.type: 2 - 3 :[ clus2 ] 182 |
pheno.type: 3 - 3 :[ clus3 ] 110 |
For the expression subtypes of 18215 genes in 409 samples, GSEA found enriched gene sets in each cluster using 408 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 BIOCARTA NO1 PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY
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And common core enriched genes are PIK3CG, AKT3, IGF1, PIK3CD, PIK3R5, FGFR1, LEF1, PDGFC, PDGFRA, PDGFRB
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clus2
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Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG TYROSINE METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG ETHER LIPID METABOLISM
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And common core enriched genes are UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A8, UGT1A9, UGT2A3, UGT2B10
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clus3
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Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA MAPK PATHWAY, BIOCARTA P38MAPK PATHWAY, BIOCARTA IL1R PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG PYRIMIDINE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS
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And common core enriched genes are CDK6, CDKN1A, TFDP1, CDK7, PCNA, POLD1, POLD2, POLE2, POLE3, CHUK
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
BIOCARTA NO1 PATHWAY | 27 | genes.ES.table | 0.52 | 1.3 | 0.17 | 0.19 | 0.97 | 0.41 | 0.2 | 0.33 | 0.16 | 0 |
BIOCARTA ALK PATHWAY | 33 | genes.ES.table | 0.48 | 1.4 | 0.09 | 0.16 | 0.96 | 0.33 | 0.22 | 0.26 | 0.13 | 0 |
BIOCARTA AT1R PATHWAY | 32 | genes.ES.table | 0.39 | 1.4 | 0.13 | 0.18 | 0.97 | 0.5 | 0.38 | 0.31 | 0.15 | 0 |
BIOCARTA BCR PATHWAY | 33 | genes.ES.table | 0.61 | 1.7 | 0.01 | 0.067 | 0.49 | 0.3 | 0.2 | 0.24 | 0 | 0.003 |
BIOCARTA BIOPEPTIDES PATHWAY | 39 | genes.ES.table | 0.45 | 1.5 | 0.051 | 0.11 | 0.86 | 0.56 | 0.38 | 0.35 | 0.079 | 0 |
BIOCARTA HDAC PATHWAY | 26 | genes.ES.table | 0.6 | 1.7 | 0.01 | 0.065 | 0.47 | 0.5 | 0.3 | 0.35 | 0 | 0.003 |
BIOCARTA EGF PATHWAY | 30 | genes.ES.table | 0.42 | 1.3 | 0.23 | 0.23 | 0.99 | 0.5 | 0.39 | 0.31 | 0.2 | 0 |
BIOCARTA ERK PATHWAY | 27 | genes.ES.table | 0.43 | 1.4 | 0.12 | 0.16 | 0.95 | 0.11 | 0.074 | 0.1 | 0.13 | 0 |
BIOCARTA FCER1 PATHWAY | 37 | genes.ES.table | 0.59 | 1.7 | 0.018 | 0.068 | 0.57 | 0.27 | 0.2 | 0.22 | 0.034 | 0.002 |
BIOCARTA FMLP PATHWAY | 35 | genes.ES.table | 0.59 | 1.9 | 0 | 0.098 | 0.17 | 0.23 | 0.14 | 0.2 | 0 | 0.022 |
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 | IGF1 | IGF1 | IGF1 | 4 | 0.88 | 0.077 | YES |
2 | FGFR1 | FGFR1 | FGFR1 | 249 | 0.64 | 0.12 | YES |
3 | PIK3R5 | PIK3R5 | PIK3R5 | 353 | 0.61 | 0.17 | YES |
4 | PDGFRA | PDGFRA | PDGFRA | 691 | 0.53 | 0.19 | YES |
5 | AKT3 | AKT3 | AKT3 | 775 | 0.51 | 0.23 | YES |
6 | CREB3L1 | CREB3L1 | CREB3L1 | 837 | 0.5 | 0.27 | YES |
7 | PDGFC | PDGFC | PDGFC | 862 | 0.5 | 0.32 | YES |
8 | LEF1 | LEF1 | LEF1 | 1081 | 0.46 | 0.34 | YES |
9 | PDGFRB | PDGFRB | PDGFRB | 1207 | 0.44 | 0.38 | YES |
10 | PIK3CG | PIK3CG | PIK3CG | 1254 | 0.44 | 0.41 | YES |
11 | INSRR | INSRR | INSRR | 1284 | 0.43 | 0.45 | YES |
12 | CREB5 | CREB5 | CREB5 | 1367 | 0.42 | 0.48 | YES |
13 | PIK3CD | PIK3CD | PIK3CD | 1387 | 0.42 | 0.51 | YES |
14 | TCF7L1 | TCF7L1 | TCF7L1 | 1770 | 0.37 | 0.52 | YES |
15 | BCL2 | BCL2 | BCL2 | 2173 | 0.31 | 0.53 | YES |
16 | TCF7 | TCF7 | TCF7 | 2429 | 0.28 | 0.54 | YES |
17 | PDGFB | PDGFB | PDGFB | 2464 | 0.28 | 0.56 | YES |
18 | PDGFD | PDGFD | PDGFD | 2879 | 0.24 | 0.56 | NO |
19 | CREB3L3 | CREB3L3 | CREB3L3 | 4556 | 0.12 | 0.48 | NO |
20 | NKX3-1 | NKX3-1 | NKX3-1 | 4583 | 0.12 | 0.49 | NO |
21 | PDGFA | PDGFA | PDGFA | 4589 | 0.12 | 0.5 | NO |
22 | CREB3 | CREB3 | CREB3 | 5046 | 0.095 | 0.48 | NO |
23 | E2F1 | E2F1 | E2F1 | 5449 | 0.079 | 0.46 | NO |
24 | CREB3L2 | CREB3L2 | CREB3L2 | 5463 | 0.079 | 0.47 | NO |
25 | MAPK3 | MAPK3 | MAPK3 | 5782 | 0.068 | 0.46 | NO |
26 | E2F2 | E2F2 | E2F2 | 5902 | 0.064 | 0.46 | NO |
27 | GRB2 | GRB2 | GRB2 | 6063 | 0.06 | 0.46 | NO |
28 | FOXO1 | FOXO1 | FOXO1 | 6166 | 0.057 | 0.45 | NO |
29 | ARAF | ARAF | ARAF | 6619 | 0.047 | 0.43 | NO |
30 | CDKN1B | CDKN1B | CDKN1B | 6754 | 0.044 | 0.43 | NO |
31 | PTEN | PTEN | PTEN | 6762 | 0.044 | 0.43 | NO |
32 | BAD | BAD | BAD | 7053 | 0.038 | 0.42 | NO |
33 | TP53 | TP53 | TP53 | 7102 | 0.037 | 0.42 | NO |
34 | CTNNB1 | CTNNB1 | CTNNB1 | 7197 | 0.035 | 0.42 | NO |
35 | HSP90B1 | HSP90B1 | HSP90B1 | 7562 | 0.029 | 0.4 | NO |
36 | IKBKG | IKBKG | IKBKG | 7640 | 0.028 | 0.4 | NO |
37 | EGF | EGF | EGF | 7701 | 0.026 | 0.4 | NO |
38 | PIK3R1 | PIK3R1 | PIK3R1 | 7820 | 0.024 | 0.39 | NO |
39 | CDK2 | CDK2 | CDK2 | 7831 | 0.024 | 0.4 | NO |
40 | ATF4 | ATF4 | ATF4 | 8126 | 0.02 | 0.38 | NO |
41 | CHUK | CHUK | CHUK | 8167 | 0.019 | 0.38 | NO |
42 | NFKB1 | NFKB1 | NFKB1 | 8209 | 0.018 | 0.38 | NO |
43 | MAP2K2 | MAP2K2 | MAP2K2 | 8259 | 0.018 | 0.38 | NO |
44 | CCNE1 | CCNE1 | CCNE1 | 8536 | 0.014 | 0.36 | NO |
45 | PIK3R3 | PIK3R3 | PIK3R3 | 8553 | 0.014 | 0.36 | NO |
46 | AKT2 | AKT2 | AKT2 | 8686 | 0.012 | 0.36 | NO |
47 | PIK3CA | PIK3CA | PIK3CA | 8689 | 0.012 | 0.36 | NO |
48 | MAP2K1 | MAP2K1 | MAP2K1 | 9023 | 0.0074 | 0.34 | NO |
49 | AR | AR | AR | 9054 | 0.007 | 0.34 | NO |
50 | PIK3CB | PIK3CB | PIK3CB | 9188 | 0.0054 | 0.33 | NO |
51 | RELA | RELA | RELA | 9209 | 0.0052 | 0.33 | NO |
52 | MAPK1 | MAPK1 | MAPK1 | 9367 | 0.0035 | 0.32 | NO |
53 | NFKBIA | NFKBIA | NFKBIA | 9532 | 0.0019 | 0.32 | NO |
54 | KLK3 | KLK3 | KLK3 | 9970 | -0.003 | 0.29 | NO |
55 | NRAS | NRAS | NRAS | 10018 | -0.0035 | 0.29 | NO |
56 | AKT1 | AKT1 | AKT1 | 10046 | -0.0038 | 0.29 | NO |
57 | CREBBP | CREBBP | CREBBP | 10060 | -0.004 | 0.29 | NO |
58 | RAF1 | RAF1 | RAF1 | 10280 | -0.0068 | 0.28 | NO |
59 | CREB1 | CREB1 | CREB1 | 10647 | -0.011 | 0.26 | NO |
60 | MTOR | MTOR | MTOR | 10706 | -0.012 | 0.26 | NO |
61 | IGF1R | IGF1R | IGF1R | 11044 | -0.016 | 0.24 | NO |
62 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 11170 | -0.017 | 0.23 | NO |
63 | SOS2 | SOS2 | SOS2 | 11197 | -0.018 | 0.23 | NO |
64 | CCNE2 | CCNE2 | CCNE2 | 11323 | -0.019 | 0.23 | NO |
65 | SOS1 | SOS1 | SOS1 | 12020 | -0.027 | 0.19 | NO |
66 | RB1 | RB1 | RB1 | 12198 | -0.029 | 0.18 | NO |
67 | KRAS | KRAS | KRAS | 12296 | -0.03 | 0.18 | NO |
68 | GSK3B | GSK3B | GSK3B | 12321 | -0.031 | 0.18 | NO |
69 | CDKN1A | CDKN1A | CDKN1A | 12459 | -0.032 | 0.18 | NO |
70 | PDPK1 | PDPK1 | PDPK1 | 13384 | -0.045 | 0.13 | NO |
71 | MDM2 | MDM2 | MDM2 | 13524 | -0.047 | 0.13 | NO |
72 | EGFR | EGFR | EGFR | 13569 | -0.048 | 0.13 | NO |
73 | TCF7L2 | TCF7L2 | TCF7L2 | 13803 | -0.051 | 0.12 | NO |
74 | EP300 | EP300 | EP300 | 13957 | -0.053 | 0.12 | NO |
75 | PIK3R2 | PIK3R2 | PIK3R2 | 14062 | -0.055 | 0.12 | NO |
76 | CASP9 | CASP9 | CASP9 | 14345 | -0.061 | 0.11 | NO |
77 | FGFR2 | FGFR2 | FGFR2 | 14470 | -0.064 | 0.1 | NO |
78 | CREB3L4 | CREB3L4 | CREB3L4 | 14908 | -0.072 | 0.086 | NO |
79 | IKBKB | IKBKB | IKBKB | 14924 | -0.073 | 0.092 | NO |
80 | CCND1 | CCND1 | CCND1 | 15241 | -0.08 | 0.082 | NO |
81 | E2F3 | E2F3 | E2F3 | 15555 | -0.09 | 0.072 | NO |
82 | HRAS | HRAS | HRAS | 15575 | -0.09 | 0.079 | NO |
83 | ERBB2 | ERBB2 | ERBB2 | 16020 | -0.11 | 0.064 | NO |
84 | GSTP1 | GSTP1 | GSTP1 | 16147 | -0.11 | 0.067 | NO |
85 | TGFA | TGFA | TGFA | 16792 | -0.15 | 0.044 | NO |
86 | BRAF | BRAF | BRAF | 17100 | -0.18 | 0.043 | NO |
87 | SRD5A2 | SRD5A2 | SRD5A2 | 17343 | -0.2 | 0.047 | 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: BIOCARTA NO1 PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_NO1_PATHWAY.heatmap_plot.clus1.118.png)
Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_PROSTATE_CANCER.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 |
---|---|---|---|---|---|---|---|
1 | RUNX1T1 | RUNX1T1 | RUNX1T1 | 107 | 0.71 | 0.085 | YES |
2 | PIK3R5 | PIK3R5 | PIK3R5 | 353 | 0.61 | 0.15 | YES |
3 | SPI1 | SPI1 | SPI1 | 570 | 0.55 | 0.21 | YES |
4 | AKT3 | AKT3 | AKT3 | 775 | 0.51 | 0.26 | YES |
5 | FLT3 | FLT3 | FLT3 | 855 | 0.5 | 0.32 | YES |
6 | LEF1 | LEF1 | LEF1 | 1081 | 0.46 | 0.37 | YES |
7 | ZBTB16 | ZBTB16 | ZBTB16 | 1198 | 0.44 | 0.42 | YES |
8 | PIK3CG | PIK3CG | PIK3CG | 1254 | 0.44 | 0.47 | YES |
9 | PIK3CD | PIK3CD | PIK3CD | 1387 | 0.42 | 0.52 | YES |
10 | TCF7L1 | TCF7L1 | TCF7L1 | 1770 | 0.37 | 0.55 | YES |
11 | TCF7 | TCF7 | TCF7 | 2429 | 0.28 | 0.55 | YES |
12 | PIM2 | PIM2 | PIM2 | 2515 | 0.27 | 0.58 | YES |
13 | STAT5A | STAT5A | STAT5A | 3869 | 0.16 | 0.52 | NO |
14 | KIT | KIT | KIT | 3976 | 0.15 | 0.54 | NO |
15 | CCNA1 | CCNA1 | CCNA1 | 4945 | 0.099 | 0.5 | NO |
16 | RARA | RARA | RARA | 5561 | 0.076 | 0.47 | NO |
17 | MAPK3 | MAPK3 | MAPK3 | 5782 | 0.068 | 0.47 | NO |
18 | GRB2 | GRB2 | GRB2 | 6063 | 0.06 | 0.46 | NO |
19 | STAT5B | STAT5B | STAT5B | 6262 | 0.055 | 0.46 | NO |
20 | ARAF | ARAF | ARAF | 6619 | 0.047 | 0.44 | NO |
21 | STAT3 | STAT3 | STAT3 | 6830 | 0.043 | 0.44 | NO |
22 | BAD | BAD | BAD | 7053 | 0.038 | 0.43 | NO |
23 | RUNX1 | RUNX1 | RUNX1 | 7148 | 0.036 | 0.43 | NO |
24 | PML | PML | PML | 7627 | 0.028 | 0.41 | NO |
25 | IKBKG | IKBKG | IKBKG | 7640 | 0.028 | 0.41 | NO |
26 | PIK3R1 | PIK3R1 | PIK3R1 | 7820 | 0.024 | 0.4 | NO |
27 | CHUK | CHUK | CHUK | 8167 | 0.019 | 0.39 | NO |
28 | NFKB1 | NFKB1 | NFKB1 | 8209 | 0.018 | 0.39 | NO |
29 | MYC | MYC | MYC | 8243 | 0.018 | 0.39 | NO |
30 | MAP2K2 | MAP2K2 | MAP2K2 | 8259 | 0.018 | 0.39 | NO |
31 | PIK3R3 | PIK3R3 | PIK3R3 | 8553 | 0.014 | 0.37 | NO |
32 | AKT2 | AKT2 | AKT2 | 8686 | 0.012 | 0.37 | NO |
33 | PIK3CA | PIK3CA | PIK3CA | 8689 | 0.012 | 0.37 | NO |
34 | MAP2K1 | MAP2K1 | MAP2K1 | 9023 | 0.0074 | 0.35 | NO |
35 | PIK3CB | PIK3CB | PIK3CB | 9188 | 0.0054 | 0.34 | NO |
36 | RELA | RELA | RELA | 9209 | 0.0052 | 0.34 | NO |
37 | MAPK1 | MAPK1 | MAPK1 | 9367 | 0.0035 | 0.34 | NO |
38 | NRAS | NRAS | NRAS | 10018 | -0.0035 | 0.3 | NO |
39 | AKT1 | AKT1 | AKT1 | 10046 | -0.0038 | 0.3 | NO |
40 | RAF1 | RAF1 | RAF1 | 10280 | -0.0068 | 0.29 | NO |
41 | MTOR | MTOR | MTOR | 10706 | -0.012 | 0.26 | NO |
42 | SOS2 | SOS2 | SOS2 | 11197 | -0.018 | 0.24 | NO |
43 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 11579 | -0.022 | 0.22 | NO |
44 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 11811 | -0.025 | 0.21 | NO |
45 | SOS1 | SOS1 | SOS1 | 12020 | -0.027 | 0.2 | NO |
46 | PIM1 | PIM1 | PIM1 | 12144 | -0.028 | 0.2 | NO |
47 | KRAS | KRAS | KRAS | 12296 | -0.03 | 0.2 | NO |
48 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 13625 | -0.048 | 0.13 | NO |
49 | TCF7L2 | TCF7L2 | TCF7L2 | 13803 | -0.051 | 0.13 | NO |
50 | PIK3R2 | PIK3R2 | PIK3R2 | 14062 | -0.055 | 0.12 | NO |
51 | IKBKB | IKBKB | IKBKB | 14924 | -0.073 | 0.082 | NO |
52 | CCND1 | CCND1 | CCND1 | 15241 | -0.08 | 0.075 | NO |
53 | HRAS | HRAS | HRAS | 15575 | -0.09 | 0.068 | NO |
54 | BRAF | BRAF | BRAF | 17100 | -0.18 | 0.0072 | NO |
55 | JUP | JUP | JUP | 17334 | -0.2 | 0.02 | NO |
56 | CEBPA | CEBPA | CEBPA | 17464 | -0.21 | 0.04 | 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: BIOCARTA ALK PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_ALK_PATHWAY.heatmap_plot.clus1.106.png)
Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ALK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_ACUTE_MYELOID_LEUKEMIA.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 | IGF1 | IGF1 | IGF1 | 4 | 0.88 | 0.066 | YES |
2 | FGF7 | FGF7 | FGF7 | 37 | 0.77 | 0.12 | YES |
3 | FGF2 | FGF2 | FGF2 | 161 | 0.67 | 0.17 | YES |
4 | HGF | HGF | HGF | 186 | 0.66 | 0.22 | YES |
5 | FGFR1 | FGFR1 | FGFR1 | 249 | 0.64 | 0.26 | YES |
6 | FGF14 | FGF14 | FGF14 | 328 | 0.61 | 0.3 | YES |
7 | PIK3R5 | PIK3R5 | PIK3R5 | 353 | 0.61 | 0.35 | YES |
8 | FGF1 | FGF1 | FGF1 | 580 | 0.55 | 0.38 | YES |
9 | PDGFRA | PDGFRA | PDGFRA | 691 | 0.53 | 0.41 | YES |
10 | AKT3 | AKT3 | AKT3 | 775 | 0.51 | 0.44 | YES |
11 | PDGFC | PDGFC | PDGFC | 862 | 0.5 | 0.48 | YES |
12 | MITF | MITF | MITF | 1021 | 0.47 | 0.5 | YES |
13 | FGF10 | FGF10 | FGF10 | 1125 | 0.46 | 0.53 | YES |
14 | PDGFRB | PDGFRB | PDGFRB | 1207 | 0.44 | 0.56 | YES |
15 | PIK3CG | PIK3CG | PIK3CG | 1254 | 0.44 | 0.59 | YES |
16 | FGF18 | FGF18 | FGF18 | 1296 | 0.43 | 0.62 | YES |
17 | PIK3CD | PIK3CD | PIK3CD | 1387 | 0.42 | 0.65 | YES |
18 | FGF13 | FGF13 | FGF13 | 1829 | 0.36 | 0.65 | YES |
19 | FGF5 | FGF5 | FGF5 | 1848 | 0.36 | 0.68 | YES |
20 | FGF9 | FGF9 | FGF9 | 2071 | 0.33 | 0.69 | YES |
21 | PDGFB | PDGFB | PDGFB | 2464 | 0.28 | 0.69 | NO |
22 | PDGFD | PDGFD | PDGFD | 2879 | 0.24 | 0.68 | NO |
23 | CDK6 | CDK6 | CDK6 | 4112 | 0.14 | 0.62 | NO |
24 | CDKN2A | CDKN2A | CDKN2A | 4248 | 0.14 | 0.63 | NO |
25 | PDGFA | PDGFA | PDGFA | 4589 | 0.12 | 0.62 | NO |
26 | MAPK3 | MAPK3 | MAPK3 | 5782 | 0.068 | 0.56 | NO |
27 | E2F2 | E2F2 | E2F2 | 5902 | 0.064 | 0.56 | NO |
28 | FGF22 | FGF22 | FGF22 | 6456 | 0.05 | 0.53 | NO |
29 | ARAF | ARAF | ARAF | 6619 | 0.047 | 0.52 | NO |
30 | PTEN | PTEN | PTEN | 6762 | 0.044 | 0.52 | NO |
31 | BAD | BAD | BAD | 7053 | 0.038 | 0.51 | NO |
32 | TP53 | TP53 | TP53 | 7102 | 0.037 | 0.51 | NO |
33 | CDK4 | CDK4 | CDK4 | 7258 | 0.034 | 0.5 | NO |
34 | FGF8 | FGF8 | FGF8 | 7343 | 0.033 | 0.5 | NO |
35 | MET | MET | MET | 7535 | 0.029 | 0.49 | NO |
36 | EGF | EGF | EGF | 7701 | 0.026 | 0.48 | NO |
37 | PIK3R1 | PIK3R1 | PIK3R1 | 7820 | 0.024 | 0.48 | NO |
38 | MAP2K2 | MAP2K2 | MAP2K2 | 8259 | 0.018 | 0.46 | NO |
39 | PIK3R3 | PIK3R3 | PIK3R3 | 8553 | 0.014 | 0.44 | NO |
40 | AKT2 | AKT2 | AKT2 | 8686 | 0.012 | 0.43 | NO |
41 | PIK3CA | PIK3CA | PIK3CA | 8689 | 0.012 | 0.43 | NO |
42 | MAP2K1 | MAP2K1 | MAP2K1 | 9023 | 0.0074 | 0.42 | NO |
43 | PIK3CB | PIK3CB | PIK3CB | 9188 | 0.0054 | 0.41 | NO |
44 | MAPK1 | MAPK1 | MAPK1 | 9367 | 0.0035 | 0.4 | NO |
45 | NRAS | NRAS | NRAS | 10018 | -0.0035 | 0.36 | NO |
46 | AKT1 | AKT1 | AKT1 | 10046 | -0.0038 | 0.36 | NO |
47 | FGF19 | FGF19 | FGF19 | 10087 | -0.0042 | 0.36 | NO |
48 | RAF1 | RAF1 | RAF1 | 10280 | -0.0068 | 0.35 | NO |
49 | FGF12 | FGF12 | FGF12 | 10961 | -0.015 | 0.31 | NO |
50 | IGF1R | IGF1R | IGF1R | 11044 | -0.016 | 0.31 | NO |
51 | RB1 | RB1 | RB1 | 12198 | -0.029 | 0.25 | NO |
52 | KRAS | KRAS | KRAS | 12296 | -0.03 | 0.24 | NO |
53 | CDKN1A | CDKN1A | CDKN1A | 12459 | -0.032 | 0.24 | NO |
54 | FGF17 | FGF17 | FGF17 | 13442 | -0.046 | 0.19 | NO |
55 | MDM2 | MDM2 | MDM2 | 13524 | -0.047 | 0.19 | NO |
56 | EGFR | EGFR | EGFR | 13569 | -0.048 | 0.19 | NO |
57 | PIK3R2 | PIK3R2 | PIK3R2 | 14062 | -0.055 | 0.16 | NO |
58 | CCND1 | CCND1 | CCND1 | 15241 | -0.08 | 0.11 | NO |
59 | E2F3 | E2F3 | E2F3 | 15555 | -0.09 | 0.096 | NO |
60 | HRAS | HRAS | HRAS | 15575 | -0.09 | 0.1 | NO |
61 | FGF11 | FGF11 | FGF11 | 16996 | -0.17 | 0.036 | NO |
62 | BRAF | BRAF | BRAF | 17100 | -0.18 | 0.044 | NO |
63 | CDH1 | CDH1 | CDH1 | 17510 | -0.22 | 0.038 | 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: BIOCARTA AT1R PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_AT1R_PATHWAY.heatmap_plot.clus1.110.png)
Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_MELANOMA.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 | IGF1 | IGF1 | IGF1 | 4 | 0.88 | 0.16 | YES |
2 | PIK3R5 | PIK3R5 | PIK3R5 | 353 | 0.61 | 0.25 | YES |
3 | AKT3 | AKT3 | AKT3 | 775 | 0.51 | 0.31 | YES |
4 | PIK3CG | PIK3CG | PIK3CG | 1254 | 0.44 | 0.36 | YES |
5 | PIK3CD | PIK3CD | PIK3CD | 1387 | 0.42 | 0.43 | YES |
6 | VEGFC | VEGFC | VEGFC | 2409 | 0.28 | 0.43 | YES |
7 | PRKAA2 | PRKAA2 | PRKAA2 | 2710 | 0.25 | 0.46 | YES |
8 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3562 | 0.18 | 0.44 | YES |
9 | VEGFB | VEGFB | VEGFB | 3781 | 0.17 | 0.46 | YES |
10 | FIGF | FIGF | FIGF | 4016 | 0.15 | 0.47 | YES |
11 | ULK2 | ULK2 | ULK2 | 4838 | 0.1 | 0.44 | NO |
12 | MAPK3 | MAPK3 | MAPK3 | 5782 | 0.068 | 0.41 | NO |
13 | EIF4E2 | EIF4E2 | EIF4E2 | 6733 | 0.044 | 0.36 | NO |
14 | RHEB | RHEB | RHEB | 7311 | 0.033 | 0.34 | NO |
15 | HIF1A | HIF1A | HIF1A | 7589 | 0.029 | 0.32 | NO |
16 | PIK3R1 | PIK3R1 | PIK3R1 | 7820 | 0.024 | 0.32 | NO |
17 | CAB39 | CAB39 | CAB39 | 8406 | 0.016 | 0.29 | NO |
18 | PIK3R3 | PIK3R3 | PIK3R3 | 8553 | 0.014 | 0.28 | NO |
19 | AKT2 | AKT2 | AKT2 | 8686 | 0.012 | 0.28 | NO |
20 | PIK3CA | PIK3CA | PIK3CA | 8689 | 0.012 | 0.28 | NO |
21 | RPTOR | RPTOR | RPTOR | 8696 | 0.012 | 0.28 | NO |
22 | PIK3CB | PIK3CB | PIK3CB | 9188 | 0.0054 | 0.25 | NO |
23 | MAPK1 | MAPK1 | MAPK1 | 9367 | 0.0035 | 0.24 | NO |
24 | MLST8 | MLST8 | MLST8 | 9877 | -0.002 | 0.22 | NO |
25 | AKT1 | AKT1 | AKT1 | 10046 | -0.0038 | 0.21 | NO |
26 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 10062 | -0.004 | 0.21 | NO |
27 | STRADA | STRADA | STRADA | 10503 | -0.0095 | 0.19 | NO |
28 | EIF4B | EIF4B | EIF4B | 10578 | -0.01 | 0.18 | NO |
29 | MTOR | MTOR | MTOR | 10706 | -0.012 | 0.18 | NO |
30 | TSC2 | TSC2 | TSC2 | 10790 | -0.013 | 0.18 | NO |
31 | ULK1 | ULK1 | ULK1 | 10841 | -0.014 | 0.18 | NO |
32 | STK11 | STK11 | STK11 | 10987 | -0.015 | 0.17 | NO |
33 | DDIT4 | DDIT4 | DDIT4 | 11160 | -0.017 | 0.16 | NO |
34 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 11579 | -0.022 | 0.15 | NO |
35 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 11811 | -0.025 | 0.14 | NO |
36 | TSC1 | TSC1 | TSC1 | 12363 | -0.031 | 0.11 | NO |
37 | PDPK1 | PDPK1 | PDPK1 | 13384 | -0.045 | 0.064 | NO |
38 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 13625 | -0.048 | 0.06 | NO |
39 | EIF4E | EIF4E | EIF4E | 13898 | -0.052 | 0.054 | NO |
40 | PIK3R2 | PIK3R2 | PIK3R2 | 14062 | -0.055 | 0.055 | NO |
41 | RPS6 | RPS6 | RPS6 | 14206 | -0.058 | 0.058 | NO |
42 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 14514 | -0.064 | 0.052 | NO |
43 | PRKAA1 | PRKAA1 | PRKAA1 | 14529 | -0.065 | 0.063 | NO |
44 | RICTOR | RICTOR | RICTOR | 14547 | -0.065 | 0.074 | NO |
45 | ULK3 | ULK3 | ULK3 | 14919 | -0.073 | 0.066 | NO |
46 | RPS6KA6 | RPS6KA6 | RPS6KA6 | 16129 | -0.11 | 0.02 | NO |
47 | CAB39L | CAB39L | CAB39L | 16420 | -0.13 | 0.026 | NO |
48 | BRAF | BRAF | BRAF | 17100 | -0.18 | 0.021 | NO |
49 | VEGFA | VEGFA | VEGFA | 17530 | -0.22 | 0.037 | NO |
Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA BCR PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_BCR_PATHWAY.heatmap_plot.clus1.31.png)
Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BCR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_MTOR_SIGNALING_PATHWAY.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 | IGF1 | IGF1 | IGF1 | 4 | 0.88 | 0.11 | YES |
2 | FGF2 | FGF2 | FGF2 | 161 | 0.67 | 0.18 | YES |
3 | HAND2 | HAND2 | HAND2 | 303 | 0.62 | 0.25 | YES |
4 | HAND1 | HAND1 | HAND1 | 571 | 0.55 | 0.31 | YES |
5 | NFATC1 | NFATC1 | NFATC1 | 1043 | 0.47 | 0.34 | YES |
6 | PIK3CG | PIK3CG | PIK3CG | 1254 | 0.44 | 0.38 | YES |
7 | CAMK1G | CAMK1G | CAMK1G | 1377 | 0.42 | 0.43 | YES |
8 | PRKAR2B | PRKAR2B | PRKAR2B | 1959 | 0.34 | 0.44 | YES |
9 | CAMK4 | CAMK4 | CAMK4 | 1981 | 0.34 | 0.48 | YES |
10 | CAMK1 | CAMK1 | CAMK1 | 2299 | 0.3 | 0.5 | YES |
11 | NFATC4 | NFATC4 | NFATC4 | 2389 | 0.29 | 0.53 | YES |
12 | NFATC2 | NFATC2 | NFATC2 | 2457 | 0.28 | 0.56 | YES |
13 | LIF | LIF | LIF | 2467 | 0.28 | 0.6 | YES |
14 | AGT | AGT | AGT | 2569 | 0.27 | 0.62 | YES |
15 | ACTA1 | ACTA1 | ACTA1 | 3401 | 0.2 | 0.6 | YES |
16 | GATA4 | GATA4 | GATA4 | 3672 | 0.18 | 0.61 | YES |
17 | PPP3CC | PPP3CC | PPP3CC | 3721 | 0.17 | 0.63 | YES |
18 | EDN1 | EDN1 | EDN1 | 3823 | 0.16 | 0.64 | YES |
19 | NKX2-5 | NKX2-5 | NKX2-5 | 4777 | 0.11 | 0.6 | NO |
20 | PRKAR2A | PRKAR2A | PRKAR2A | 5121 | 0.091 | 0.59 | NO |
21 | PPP3CB | PPP3CB | PPP3CB | 5203 | 0.088 | 0.6 | NO |
22 | CALM2 | CALM2 | CALM2 | 5414 | 0.08 | 0.6 | NO |
23 | MAPK3 | MAPK3 | MAPK3 | 5782 | 0.068 | 0.59 | NO |
24 | PRKACB | PRKACB | PRKACB | 6671 | 0.046 | 0.54 | NO |
25 | MAPK14 | MAPK14 | MAPK14 | 6794 | 0.043 | 0.54 | NO |
26 | NFATC3 | NFATC3 | NFATC3 | 6862 | 0.042 | 0.54 | NO |
27 | PPP3CA | PPP3CA | PPP3CA | 6911 | 0.041 | 0.55 | NO |
28 | CALM3 | CALM3 | CALM3 | 6917 | 0.041 | 0.55 | NO |
29 | FKBP1A | FKBP1A | FKBP1A | 7093 | 0.037 | 0.55 | NO |
30 | CALR | CALR | CALR | 7481 | 0.03 | 0.53 | NO |
31 | CALM1 | CALM1 | CALM1 | 7534 | 0.03 | 0.53 | NO |
32 | PIK3R1 | PIK3R1 | PIK3R1 | 7820 | 0.024 | 0.52 | NO |
33 | PRKAR1A | PRKAR1A | PRKAR1A | 8430 | 0.015 | 0.49 | NO |
34 | PIK3CA | PIK3CA | PIK3CA | 8689 | 0.012 | 0.47 | NO |
35 | PRKAR1B | PRKAR1B | PRKAR1B | 8843 | 0.0099 | 0.47 | NO |
36 | MAP2K1 | MAP2K1 | MAP2K1 | 9023 | 0.0074 | 0.46 | NO |
37 | MAPK1 | MAPK1 | MAPK1 | 9367 | 0.0035 | 0.44 | NO |
38 | HBEGF | HBEGF | HBEGF | 9502 | 0.0021 | 0.43 | NO |
39 | AKT1 | AKT1 | AKT1 | 10046 | -0.0038 | 0.4 | NO |
40 | CREBBP | CREBBP | CREBBP | 10060 | -0.004 | 0.4 | NO |
41 | CTF1 | CTF1 | CTF1 | 10162 | -0.0053 | 0.4 | NO |
42 | RAF1 | RAF1 | RAF1 | 10280 | -0.0068 | 0.39 | NO |
43 | MAPK8 | MAPK8 | MAPK8 | 11676 | -0.023 | 0.32 | NO |
44 | GSK3B | GSK3B | GSK3B | 12321 | -0.031 | 0.28 | NO |
45 | F2 | F2 | F2 | 13010 | -0.04 | 0.25 | NO |
46 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 13625 | -0.048 | 0.22 | NO |
47 | NPPA | NPPA | NPPA | 14243 | -0.059 | 0.2 | NO |
48 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 14779 | -0.07 | 0.18 | NO |
49 | HRAS | HRAS | HRAS | 15575 | -0.09 | 0.14 | 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: BIOCARTA BIOPEPTIDES PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_BIOPEPTIDES_PATHWAY.heatmap_plot.clus1.79.png)
Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BIOPEPTIDES PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_NFAT_PATHWAY.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 | FPR1 | FPR1 | FPR1 | 141 | 0.68 | 0.14 | YES |
2 | NCF1C | NCF1C | NCF1C | 382 | 0.6 | 0.25 | YES |
3 | NFATC1 | NFATC1 | NFATC1 | 1043 | 0.47 | 0.31 | YES |
4 | NCF2 | NCF2 | NCF2 | 1154 | 0.45 | 0.4 | YES |
5 | CAMK1G | CAMK1G | CAMK1G | 1377 | 0.42 | 0.47 | YES |
6 | CAMK1 | CAMK1 | CAMK1 | 2299 | 0.3 | 0.48 | YES |
7 | NFATC4 | NFATC4 | NFATC4 | 2389 | 0.29 | 0.54 | YES |
8 | NFATC2 | NFATC2 | NFATC2 | 2457 | 0.28 | 0.59 | YES |
9 | PPP3CC | PPP3CC | PPP3CC | 3721 | 0.17 | 0.56 | NO |
10 | PPP3CB | PPP3CB | PPP3CB | 5203 | 0.088 | 0.5 | NO |
11 | CALM2 | CALM2 | CALM2 | 5414 | 0.08 | 0.5 | NO |
12 | MAPK3 | MAPK3 | MAPK3 | 5782 | 0.068 | 0.5 | NO |
13 | MAPK14 | MAPK14 | MAPK14 | 6794 | 0.043 | 0.45 | NO |
14 | NFATC3 | NFATC3 | NFATC3 | 6862 | 0.042 | 0.46 | NO |
15 | ELK1 | ELK1 | ELK1 | 6879 | 0.042 | 0.46 | NO |
16 | PPP3CA | PPP3CA | PPP3CA | 6911 | 0.041 | 0.47 | NO |
17 | CALM3 | CALM3 | CALM3 | 6917 | 0.041 | 0.48 | NO |
18 | CALM1 | CALM1 | CALM1 | 7534 | 0.03 | 0.45 | NO |
19 | GNB1 | GNB1 | GNB1 | 7543 | 0.029 | 0.46 | NO |
20 | NFKB1 | NFKB1 | NFKB1 | 8209 | 0.018 | 0.42 | NO |
21 | MAP2K2 | MAP2K2 | MAP2K2 | 8259 | 0.018 | 0.42 | NO |
22 | MAP2K3 | MAP2K3 | MAP2K3 | 8324 | 0.017 | 0.42 | NO |
23 | MAP3K1 | MAP3K1 | MAP3K1 | 8370 | 0.016 | 0.42 | NO |
24 | MAP2K1 | MAP2K1 | MAP2K1 | 9023 | 0.0074 | 0.39 | NO |
25 | RELA | RELA | RELA | 9209 | 0.0052 | 0.38 | NO |
26 | MAPK1 | MAPK1 | MAPK1 | 9367 | 0.0035 | 0.37 | NO |
27 | NFKBIA | NFKBIA | NFKBIA | 9532 | 0.0019 | 0.36 | NO |
28 | RAF1 | RAF1 | RAF1 | 10280 | -0.0068 | 0.32 | NO |
29 | RAC1 | RAC1 | RAC1 | 11993 | -0.027 | 0.24 | NO |
30 | PLCB1 | PLCB1 | PLCB1 | 12386 | -0.032 | 0.22 | NO |
31 | MAP2K6 | MAP2K6 | MAP2K6 | 12653 | -0.035 | 0.21 | NO |
32 | PIK3C2G | PIK3C2G | PIK3C2G | 14757 | -0.069 | 0.11 | NO |
33 | PAK1 | PAK1 | PAK1 | 14825 | -0.071 | 0.12 | NO |
34 | HRAS | HRAS | HRAS | 15575 | -0.09 | 0.1 | NO |
35 | GNGT1 | GNGT1 | GNGT1 | 17369 | -0.2 | 0.046 | NO |
Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA HDAC PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_HDAC_PATHWAY.heatmap_plot.clus1.30.png)
Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HDAC PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_FMLP_PATHWAY.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 | ENPP1 | ENPP1 | ENPP1 | 43 | 0.76 | 0.038 | YES |
2 | PDE1A | PDE1A | PDE1A | 103 | 0.71 | 0.072 | YES |
3 | PDE4B | PDE4B | PDE4B | 434 | 0.59 | 0.084 | YES |
4 | NPR1 | NPR1 | NPR1 | 615 | 0.54 | 0.1 | YES |
5 | ADCY5 | ADCY5 | ADCY5 | 695 | 0.53 | 0.13 | YES |
6 | PDE1B | PDE1B | PDE1B | 728 | 0.52 | 0.15 | YES |
7 | PDE2A | PDE2A | PDE2A | 987 | 0.47 | 0.16 | YES |
8 | ADCY2 | ADCY2 | ADCY2 | 1009 | 0.47 | 0.19 | YES |
9 | ENPP3 | ENPP3 | ENPP3 | 1055 | 0.46 | 0.21 | YES |
10 | PAPSS2 | PAPSS2 | PAPSS2 | 1268 | 0.44 | 0.22 | YES |
11 | PDE6G | PDE6G | PDE6G | 1313 | 0.43 | 0.24 | YES |
12 | GUCY1B3 | GUCY1B3 | GUCY1B3 | 1372 | 0.42 | 0.26 | YES |
13 | GUCY1A3 | GUCY1A3 | GUCY1A3 | 1382 | 0.42 | 0.28 | YES |
14 | ADCY4 | ADCY4 | ADCY4 | 1678 | 0.38 | 0.28 | YES |
15 | NT5M | NT5M | NT5M | 1710 | 0.38 | 0.3 | YES |
16 | PDE5A | PDE5A | PDE5A | 1760 | 0.37 | 0.32 | YES |
17 | PDE3A | PDE3A | PDE3A | 1784 | 0.37 | 0.34 | YES |
18 | AMPD1 | AMPD1 | AMPD1 | 1809 | 0.36 | 0.35 | YES |
19 | NPR2 | NPR2 | NPR2 | 1827 | 0.36 | 0.37 | YES |
20 | GMPR | GMPR | GMPR | 2046 | 0.33 | 0.38 | YES |
21 | NT5E | NT5E | NT5E | 2060 | 0.33 | 0.39 | YES |
22 | PDE1C | PDE1C | PDE1C | 2137 | 0.32 | 0.4 | YES |
23 | PDE6B | PDE6B | PDE6B | 2169 | 0.31 | 0.42 | YES |
24 | AK5 | AK5 | AK5 | 2428 | 0.28 | 0.42 | YES |
25 | GUCY1A2 | GUCY1A2 | GUCY1A2 | 2530 | 0.27 | 0.43 | YES |
26 | ADCY7 | ADCY7 | ADCY7 | 2761 | 0.25 | 0.43 | YES |
27 | ENTPD1 | ENTPD1 | ENTPD1 | 2782 | 0.25 | 0.44 | YES |
28 | PDE11A | PDE11A | PDE11A | 2833 | 0.24 | 0.45 | YES |
29 | ADCY9 | ADCY9 | ADCY9 | 3050 | 0.22 | 0.45 | YES |
30 | NME5 | NME5 | NME5 | 3229 | 0.21 | 0.45 | YES |
31 | PDE3B | PDE3B | PDE3B | 3391 | 0.2 | 0.45 | YES |
32 | PDE4A | PDE4A | PDE4A | 3486 | 0.19 | 0.46 | YES |
33 | ADA | ADA | ADA | 3637 | 0.18 | 0.46 | YES |
34 | AK1 | AK1 | AK1 | 4001 | 0.15 | 0.45 | NO |
35 | POLR3GL | POLR3GL | POLR3GL | 4069 | 0.15 | 0.45 | NO |
36 | PDE4D | PDE4D | PDE4D | 4652 | 0.11 | 0.42 | NO |
37 | PDE9A | PDE9A | PDE9A | 4698 | 0.11 | 0.43 | NO |
38 | NME7 | NME7 | NME7 | 4725 | 0.11 | 0.43 | NO |
39 | IMPDH1 | IMPDH1 | IMPDH1 | 4742 | 0.11 | 0.44 | NO |
40 | AK7 | AK7 | AK7 | 4831 | 0.1 | 0.44 | NO |
41 | PRIM1 | PRIM1 | PRIM1 | 5018 | 0.096 | 0.43 | NO |
42 | AK3L1 | AK3L1 | AK3L1 | 5553 | 0.076 | 0.41 | NO |
43 | POLR1E | POLR1E | POLR1E | 5595 | 0.075 | 0.41 | NO |
44 | ENTPD8 | ENTPD8 | ENTPD8 | 5624 | 0.074 | 0.41 | NO |
45 | PDE7B | PDE7B | PDE7B | 5645 | 0.073 | 0.41 | NO |
46 | PRPS1 | PRPS1 | PRPS1 | 5646 | 0.073 | 0.42 | NO |
47 | AMPD3 | AMPD3 | AMPD3 | 5696 | 0.071 | 0.42 | NO |
48 | POLR3C | POLR3C | POLR3C | 5901 | 0.064 | 0.41 | NO |
49 | POLR3D | POLR3D | POLR3D | 5909 | 0.064 | 0.41 | NO |
50 | PRPS1L1 | PRPS1L1 | PRPS1L1 | 6037 | 0.061 | 0.41 | NO |
51 | POLD4 | POLD4 | POLD4 | 6553 | 0.048 | 0.38 | NO |
52 | POLA2 | POLA2 | POLA2 | 6555 | 0.048 | 0.39 | NO |
53 | AMPD2 | AMPD2 | AMPD2 | 6605 | 0.047 | 0.39 | NO |
54 | POLE4 | POLE4 | POLE4 | 7013 | 0.039 | 0.37 | NO |
55 | GUK1 | GUK1 | GUK1 | 7066 | 0.038 | 0.36 | NO |
56 | PDE6D | PDE6D | PDE6D | 7069 | 0.038 | 0.37 | NO |
57 | CANT1 | CANT1 | CANT1 | 7126 | 0.036 | 0.37 | NO |
58 | GUCY2C | GUCY2C | GUCY2C | 7147 | 0.036 | 0.37 | NO |
59 | POLR3G | POLR3G | POLR3G | 7209 | 0.035 | 0.36 | NO |
60 | POLR2L | POLR2L | POLR2L | 7286 | 0.034 | 0.36 | NO |
61 | ADSL | ADSL | ADSL | 7291 | 0.034 | 0.36 | NO |
62 | ATIC | ATIC | ATIC | 7626 | 0.028 | 0.35 | NO |
63 | POLD1 | POLD1 | POLD1 | 7733 | 0.026 | 0.34 | NO |
64 | POLD3 | POLD3 | POLD3 | 7851 | 0.024 | 0.34 | NO |
65 | DCK | DCK | DCK | 7877 | 0.023 | 0.34 | NO |
66 | GUCY2D | GUCY2D | GUCY2D | 7997 | 0.022 | 0.33 | NO |
67 | PRIM2 | PRIM2 | PRIM2 | 8011 | 0.021 | 0.33 | NO |
68 | PAPSS1 | PAPSS1 | PAPSS1 | 8022 | 0.021 | 0.33 | NO |
69 | ADCY6 | ADCY6 | ADCY6 | 8046 | 0.021 | 0.33 | NO |
70 | POLR2I | POLR2I | POLR2I | 8072 | 0.02 | 0.33 | NO |
71 | NME4 | NME4 | NME4 | 8188 | 0.019 | 0.33 | NO |
72 | PDE6A | PDE6A | PDE6A | 8207 | 0.018 | 0.33 | NO |
73 | NME6 | NME6 | NME6 | 8237 | 0.018 | 0.33 | NO |
74 | RRM1 | RRM1 | RRM1 | 8293 | 0.017 | 0.32 | NO |
75 | POLR2D | POLR2D | POLR2D | 8305 | 0.017 | 0.32 | NO |
76 | POLA1 | POLA1 | POLA1 | 8312 | 0.017 | 0.32 | NO |
77 | POLR2E | POLR2E | POLR2E | 8321 | 0.017 | 0.32 | NO |
78 | PDE8B | PDE8B | PDE8B | 8322 | 0.017 | 0.33 | NO |
79 | PNP | PNP | PNP | 8393 | 0.016 | 0.32 | NO |
80 | NUDT5 | NUDT5 | NUDT5 | 8521 | 0.014 | 0.32 | NO |
81 | GMPS | GMPS | GMPS | 8579 | 0.013 | 0.31 | NO |
82 | POLR2G | POLR2G | POLR2G | 8932 | 0.0085 | 0.3 | NO |
83 | POLE3 | POLE3 | POLE3 | 8937 | 0.0085 | 0.3 | NO |
84 | POLR3F | POLR3F | POLR3F | 9095 | 0.0064 | 0.29 | NO |
85 | NME3 | NME3 | NME3 | 9319 | 0.004 | 0.28 | NO |
86 | POLR2C | POLR2C | POLR2C | 9430 | 0.0029 | 0.27 | NO |
87 | NUDT2 | NUDT2 | NUDT2 | 9639 | 0.00063 | 0.26 | NO |
88 | ITPA | ITPA | ITPA | 9778 | -0.00096 | 0.25 | NO |
89 | ADCY1 | ADCY1 | ADCY1 | 9854 | -0.0018 | 0.25 | NO |
90 | RRM2 | RRM2 | RRM2 | 9915 | -0.0024 | 0.24 | NO |
91 | RRM2B | RRM2B | RRM2B | 10032 | -0.0036 | 0.24 | NO |
92 | POLD2 | POLD2 | POLD2 | 10141 | -0.0051 | 0.23 | NO |
93 | ADCY10 | ADCY10 | ADCY10 | 10344 | -0.0076 | 0.22 | NO |
94 | POLR3A | POLR3A | POLR3A | 10468 | -0.0092 | 0.21 | NO |
95 | PKM2 | PKM2 | PKM2 | 10677 | -0.011 | 0.2 | NO |
96 | IMPDH2 | IMPDH2 | IMPDH2 | 10725 | -0.012 | 0.2 | NO |
97 | POLR1A | POLR1A | POLR1A | 10772 | -0.012 | 0.2 | NO |
98 | GMPR2 | GMPR2 | GMPR2 | 10958 | -0.015 | 0.19 | NO |
99 | POLR2J2 | POLR2J2 | POLR2J2 | 10978 | -0.015 | 0.19 | NO |
100 | PFAS | PFAS | PFAS | 11141 | -0.017 | 0.18 | NO |
101 | NME1-NME2 | NME1-NME2 | NME1-NME2 | 11161 | -0.017 | 0.18 | NO |
102 | GART | GART | GART | 11193 | -0.018 | 0.18 | NO |
103 | AK2 | AK2 | AK2 | 11218 | -0.018 | 0.18 | NO |
104 | ADK | ADK | ADK | 11240 | -0.018 | 0.18 | NO |
105 | POLE2 | POLE2 | POLE2 | 11422 | -0.02 | 0.17 | NO |
106 | POLR2F | POLR2F | POLR2F | 11531 | -0.021 | 0.16 | NO |
107 | ENTPD2 | ENTPD2 | ENTPD2 | 12019 | -0.027 | 0.14 | NO |
108 | DGUOK | DGUOK | DGUOK | 12063 | -0.028 | 0.14 | NO |
109 | POLR2A | POLR2A | POLR2A | 12172 | -0.029 | 0.13 | NO |
110 | POLR3H | POLR3H | POLR3H | 12180 | -0.029 | 0.14 | NO |
111 | POLE | POLE | POLE | 12219 | -0.03 | 0.14 | NO |
112 | PRUNE | PRUNE | PRUNE | 12234 | -0.03 | 0.14 | NO |
113 | POLR2B | POLR2B | POLR2B | 12346 | -0.031 | 0.13 | NO |
114 | FHIT | FHIT | FHIT | 12375 | -0.031 | 0.13 | NO |
115 | POLR3K | POLR3K | POLR3K | 12449 | -0.032 | 0.13 | NO |
116 | APRT | APRT | APRT | 12729 | -0.036 | 0.12 | NO |
117 | POLR2J | POLR2J | POLR2J | 12987 | -0.04 | 0.1 | NO |
118 | PNPT1 | PNPT1 | PNPT1 | 13154 | -0.042 | 0.096 | NO |
119 | ENTPD6 | ENTPD6 | ENTPD6 | 13316 | -0.044 | 0.09 | NO |
120 | HPRT1 | HPRT1 | HPRT1 | 13544 | -0.047 | 0.08 | NO |
121 | ADSS | ADSS | ADSS | 13554 | -0.048 | 0.082 | NO |
122 | PDE7A | PDE7A | PDE7A | 13584 | -0.048 | 0.082 | NO |
123 | PKLR | PKLR | PKLR | 13620 | -0.048 | 0.083 | NO |
124 | NUDT9 | NUDT9 | NUDT9 | 13749 | -0.05 | 0.079 | NO |
125 | PRPS2 | PRPS2 | PRPS2 | 13785 | -0.051 | 0.079 | NO |
126 | PPAT | PPAT | PPAT | 13875 | -0.052 | 0.077 | NO |
127 | POLR2K | POLR2K | POLR2K | 14014 | -0.054 | 0.072 | NO |
128 | POLR1D | POLR1D | POLR1D | 14024 | -0.055 | 0.075 | NO |
129 | POLR2H | POLR2H | POLR2H | 14026 | -0.055 | 0.078 | NO |
130 | NME2 | NME2 | NME2 | 14047 | -0.055 | 0.079 | NO |
131 | ENTPD4 | ENTPD4 | ENTPD4 | 14130 | -0.057 | 0.078 | NO |
132 | NME1 | NME1 | NME1 | 14191 | -0.058 | 0.078 | NO |
133 | POLR3B | POLR3B | POLR3B | 14204 | -0.058 | 0.08 | NO |
134 | ZNRD1 | ZNRD1 | ZNRD1 | 14394 | -0.062 | 0.073 | NO |
135 | PDE4C | PDE4C | PDE4C | 14554 | -0.065 | 0.067 | NO |
136 | PAICS | PAICS | PAICS | 14699 | -0.068 | 0.063 | NO |
137 | NT5C3 | NT5C3 | NT5C3 | 14743 | -0.069 | 0.064 | NO |
138 | NT5C | NT5C | NT5C | 14928 | -0.073 | 0.058 | NO |
139 | PDE8A | PDE8A | PDE8A | 15449 | -0.086 | 0.034 | NO |
140 | NT5C2 | NT5C2 | NT5C2 | 15469 | -0.087 | 0.037 | NO |
141 | POLR1B | POLR1B | POLR1B | 15512 | -0.088 | 0.039 | NO |
142 | POLR1C | POLR1C | POLR1C | 15740 | -0.096 | 0.032 | NO |
143 | POLR2J3 | POLR2J3 | POLR2J3 | 16501 | -0.13 | -0.0032 | NO |
144 | ENTPD5 | ENTPD5 | ENTPD5 | 16647 | -0.14 | -0.0038 | NO |
145 | PDE10A | PDE10A | PDE10A | 17355 | -0.2 | -0.032 | NO |
146 | ADSSL1 | ADSSL1 | ADSSL1 | 17536 | -0.22 | -0.031 | NO |
147 | GDA | GDA | GDA | 17826 | -0.27 | -0.032 | NO |
148 | XDH | XDH | XDH | 17988 | -0.32 | -0.024 | NO |
149 | ENTPD3 | ENTPD3 | ENTPD3 | 18016 | -0.32 | -0.009 | NO |
150 | NT5C1B | NT5C1B | NT5C1B | 18087 | -0.36 | 0.0061 | NO |
Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA EGF PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_EGF_PATHWAY.heatmap_plot.clus1.125.png)
Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EGF PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_PURINE_METABOLISM.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 | FGF7 | FGF7 | FGF7 | 37 | 0.77 | 0.02 | YES |
2 | FGF2 | FGF2 | FGF2 | 161 | 0.67 | 0.032 | YES |
3 | ITGAM | ITGAM | ITGAM | 171 | 0.67 | 0.05 | YES |
4 | ITGA11 | ITGA11 | ITGA11 | 188 | 0.66 | 0.068 | YES |
5 | NCKAP1L | NCKAP1L | NCKAP1L | 210 | 0.65 | 0.085 | YES |
6 | FGFR1 | FGFR1 | FGFR1 | 249 | 0.64 | 0.1 | YES |
7 | ITGA7 | ITGA7 | ITGA7 | 267 | 0.63 | 0.12 | YES |
8 | FGF14 | FGF14 | FGF14 | 328 | 0.61 | 0.13 | YES |
9 | PIK3R5 | PIK3R5 | PIK3R5 | 353 | 0.61 | 0.15 | YES |
10 | WAS | WAS | WAS | 449 | 0.58 | 0.16 | YES |
11 | IQGAP2 | IQGAP2 | IQGAP2 | 462 | 0.58 | 0.18 | YES |
12 | ITGB2 | ITGB2 | ITGB2 | 551 | 0.56 | 0.19 | YES |
13 | FGF1 | FGF1 | FGF1 | 580 | 0.55 | 0.2 | YES |
14 | ITGB3 | ITGB3 | ITGB3 | 600 | 0.54 | 0.21 | YES |
15 | MYLK | MYLK | MYLK | 612 | 0.54 | 0.23 | YES |
16 | PDGFRA | PDGFRA | PDGFRA | 691 | 0.53 | 0.24 | YES |
17 | ITGAX | ITGAX | ITGAX | 756 | 0.52 | 0.25 | YES |
18 | CD14 | CD14 | CD14 | 763 | 0.51 | 0.26 | YES |
19 | ACTN2 | ACTN2 | ACTN2 | 805 | 0.51 | 0.28 | YES |
20 | PDGFC | PDGFC | PDGFC | 862 | 0.5 | 0.29 | YES |
21 | ITGAL | ITGAL | ITGAL | 884 | 0.49 | 0.3 | YES |
22 | FN1 | FN1 | FN1 | 965 | 0.48 | 0.31 | YES |
23 | MYL9 | MYL9 | MYL9 | 989 | 0.47 | 0.32 | YES |
24 | ITGA4 | ITGA4 | ITGA4 | 994 | 0.47 | 0.33 | YES |
25 | TIAM2 | TIAM2 | TIAM2 | 1007 | 0.47 | 0.35 | YES |
26 | VAV1 | VAV1 | VAV1 | 1049 | 0.47 | 0.36 | YES |
27 | MRAS | MRAS | MRAS | 1116 | 0.46 | 0.37 | YES |
28 | FGF10 | FGF10 | FGF10 | 1125 | 0.46 | 0.38 | YES |
29 | CHRM2 | CHRM2 | CHRM2 | 1143 | 0.45 | 0.39 | YES |
30 | PDGFRB | PDGFRB | PDGFRB | 1207 | 0.44 | 0.4 | YES |
31 | ITGA9 | ITGA9 | ITGA9 | 1237 | 0.44 | 0.41 | YES |
32 | PIK3CG | PIK3CG | PIK3CG | 1254 | 0.44 | 0.42 | YES |
33 | INSRR | INSRR | INSRR | 1284 | 0.43 | 0.43 | YES |
34 | ITGAD | ITGAD | ITGAD | 1286 | 0.43 | 0.44 | YES |
35 | FGF18 | FGF18 | FGF18 | 1296 | 0.43 | 0.46 | YES |
36 | PIK3CD | PIK3CD | PIK3CD | 1387 | 0.42 | 0.46 | YES |
37 | CFL2 | CFL2 | CFL2 | 1413 | 0.41 | 0.47 | YES |
38 | CHRM4 | CHRM4 | CHRM4 | 1591 | 0.39 | 0.48 | YES |
39 | ITGA5 | ITGA5 | ITGA5 | 1780 | 0.37 | 0.48 | YES |
40 | FGF13 | FGF13 | FGF13 | 1829 | 0.36 | 0.48 | YES |
41 | FGF5 | FGF5 | FGF5 | 1848 | 0.36 | 0.49 | YES |
42 | ACTN3 | ACTN3 | ACTN3 | 1928 | 0.34 | 0.5 | YES |
43 | ITGA10 | ITGA10 | ITGA10 | 1961 | 0.34 | 0.5 | YES |
44 | FGF9 | FGF9 | FGF9 | 2071 | 0.33 | 0.51 | YES |
45 | ITGA1 | ITGA1 | ITGA1 | 2136 | 0.32 | 0.51 | YES |
46 | PIP4K2A | PIP4K2A | PIP4K2A | 2327 | 0.3 | 0.51 | YES |
47 | F2R | F2R | F2R | 2412 | 0.28 | 0.52 | YES |
48 | PDGFB | PDGFB | PDGFB | 2464 | 0.28 | 0.52 | YES |
49 | PIP5K1B | PIP5K1B | PIP5K1B | 2480 | 0.28 | 0.53 | YES |
50 | PAK3 | PAK3 | PAK3 | 2503 | 0.27 | 0.53 | YES |
51 | BDKRB1 | BDKRB1 | BDKRB1 | 2845 | 0.24 | 0.52 | YES |
52 | PDGFD | PDGFD | PDGFD | 2879 | 0.24 | 0.53 | YES |
53 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 3020 | 0.22 | 0.52 | YES |
54 | ACTN1 | ACTN1 | ACTN1 | 3152 | 0.21 | 0.52 | YES |
55 | ITGA8 | ITGA8 | ITGA8 | 3241 | 0.21 | 0.52 | YES |
56 | RRAS | RRAS | RRAS | 3256 | 0.21 | 0.53 | YES |
57 | MYH10 | MYH10 | MYH10 | 3377 | 0.2 | 0.53 | YES |
58 | MSN | MSN | MSN | 3431 | 0.19 | 0.53 | YES |
59 | GSN | GSN | GSN | 3441 | 0.19 | 0.54 | YES |
60 | CHRM5 | CHRM5 | CHRM5 | 3485 | 0.19 | 0.54 | YES |
61 | ITGB5 | ITGB5 | ITGB5 | 3553 | 0.18 | 0.54 | YES |
62 | BDKRB2 | BDKRB2 | BDKRB2 | 3647 | 0.18 | 0.54 | NO |
63 | RAC2 | RAC2 | RAC2 | 3743 | 0.17 | 0.54 | NO |
64 | GNA12 | GNA12 | GNA12 | 3883 | 0.16 | 0.54 | NO |
65 | DIAPH3 | DIAPH3 | DIAPH3 | 3967 | 0.15 | 0.54 | NO |
66 | PFN4 | PFN4 | PFN4 | 4042 | 0.15 | 0.54 | NO |
67 | RDX | RDX | RDX | 4229 | 0.14 | 0.53 | NO |
68 | FGD1 | FGD1 | FGD1 | 4232 | 0.14 | 0.53 | NO |
69 | ITGB7 | ITGB7 | ITGB7 | 4298 | 0.13 | 0.53 | NO |
70 | RAC3 | RAC3 | RAC3 | 4332 | 0.13 | 0.54 | NO |
71 | TMSB4Y | TMSB4Y | TMSB4Y | 4426 | 0.12 | 0.53 | NO |
72 | CHRM3 | CHRM3 | CHRM3 | 4481 | 0.12 | 0.53 | NO |
73 | CYFIP2 | CYFIP2 | CYFIP2 | 4567 | 0.12 | 0.53 | NO |
74 | ITGAV | ITGAV | ITGAV | 4587 | 0.12 | 0.54 | NO |
75 | PDGFA | PDGFA | PDGFA | 4589 | 0.12 | 0.54 | NO |
76 | ARPC1B | ARPC1B | ARPC1B | 4712 | 0.11 | 0.54 | NO |
77 | CHRM1 | CHRM1 | CHRM1 | 4781 | 0.11 | 0.53 | NO |
78 | VCL | VCL | VCL | 4999 | 0.097 | 0.52 | NO |
79 | ITGB1 | ITGB1 | ITGB1 | 5148 | 0.09 | 0.52 | NO |
80 | ENAH | ENAH | ENAH | 5185 | 0.088 | 0.52 | NO |
81 | LIMK1 | LIMK1 | LIMK1 | 5280 | 0.085 | 0.52 | NO |
82 | ACTB | ACTB | ACTB | 5294 | 0.084 | 0.52 | NO |
83 | ITGAE | ITGAE | ITGAE | 5363 | 0.082 | 0.52 | NO |
84 | ITGA2B | ITGA2B | ITGA2B | 5389 | 0.081 | 0.52 | NO |
85 | RHOA | RHOA | RHOA | 5572 | 0.075 | 0.51 | NO |
86 | MYLK3 | MYLK3 | MYLK3 | 5619 | 0.074 | 0.51 | NO |
87 | MAPK3 | MAPK3 | MAPK3 | 5782 | 0.068 | 0.5 | NO |
88 | PIP5K1C | PIP5K1C | PIP5K1C | 5798 | 0.068 | 0.5 | NO |
89 | MYL12A | MYL12A | MYL12A | 5923 | 0.064 | 0.5 | NO |
90 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 5972 | 0.063 | 0.5 | NO |
91 | BCAR1 | BCAR1 | BCAR1 | 5984 | 0.062 | 0.5 | NO |
92 | ABI2 | ABI2 | ABI2 | 5998 | 0.062 | 0.5 | NO |
93 | TMSL3 | TMSL3 | TMSL3 | 6074 | 0.06 | 0.5 | NO |
94 | FGD3 | FGD3 | FGD3 | 6115 | 0.059 | 0.5 | NO |
95 | PFN1 | PFN1 | PFN1 | 6212 | 0.056 | 0.49 | NO |
96 | ROCK1 | ROCK1 | ROCK1 | 6236 | 0.055 | 0.49 | NO |
97 | MYH9 | MYH9 | MYH9 | 6251 | 0.055 | 0.49 | NO |
98 | ROCK2 | ROCK2 | ROCK2 | 6446 | 0.05 | 0.48 | NO |
99 | FGF22 | FGF22 | FGF22 | 6456 | 0.05 | 0.48 | NO |
100 | PPP1R12A | PPP1R12A | PPP1R12A | 6469 | 0.05 | 0.49 | NO |
101 | GNG12 | GNG12 | GNG12 | 6571 | 0.048 | 0.48 | NO |
102 | ARAF | ARAF | ARAF | 6619 | 0.047 | 0.48 | NO |
103 | ARPC4 | ARPC4 | ARPC4 | 6687 | 0.045 | 0.48 | NO |
104 | DIAPH2 | DIAPH2 | DIAPH2 | 7022 | 0.039 | 0.46 | NO |
105 | SSH1 | SSH1 | SSH1 | 7076 | 0.037 | 0.46 | NO |
106 | RRAS2 | RRAS2 | RRAS2 | 7290 | 0.034 | 0.45 | NO |
107 | FGF8 | FGF8 | FGF8 | 7343 | 0.033 | 0.45 | NO |
108 | DOCK1 | DOCK1 | DOCK1 | 7376 | 0.032 | 0.44 | NO |
109 | GNA13 | GNA13 | GNA13 | 7397 | 0.032 | 0.44 | NO |
110 | SSH2 | SSH2 | SSH2 | 7412 | 0.032 | 0.44 | NO |
111 | IQGAP1 | IQGAP1 | IQGAP1 | 7438 | 0.031 | 0.44 | NO |
112 | VAV2 | VAV2 | VAV2 | 7477 | 0.031 | 0.44 | NO |
113 | WASF1 | WASF1 | WASF1 | 7499 | 0.03 | 0.44 | NO |
114 | CSK | CSK | CSK | 7561 | 0.029 | 0.44 | NO |
115 | ARPC5 | ARPC5 | ARPC5 | 7572 | 0.029 | 0.44 | NO |
116 | CFL1 | CFL1 | CFL1 | 7694 | 0.027 | 0.44 | NO |
117 | EGF | EGF | EGF | 7701 | 0.026 | 0.44 | NO |
118 | PIK3R1 | PIK3R1 | PIK3R1 | 7820 | 0.024 | 0.43 | NO |
119 | ACTN4 | ACTN4 | ACTN4 | 7857 | 0.024 | 0.43 | NO |
120 | PIP5K1A | PIP5K1A | PIP5K1A | 8073 | 0.02 | 0.42 | NO |
121 | PIP4K2B | PIP4K2B | PIP4K2B | 8186 | 0.019 | 0.41 | NO |
122 | MAP2K2 | MAP2K2 | MAP2K2 | 8259 | 0.018 | 0.41 | NO |
123 | ARPC5L | ARPC5L | ARPC5L | 8288 | 0.017 | 0.41 | NO |
124 | PIK3R3 | PIK3R3 | PIK3R3 | 8553 | 0.014 | 0.39 | NO |
125 | PIK3CA | PIK3CA | PIK3CA | 8689 | 0.012 | 0.38 | NO |
126 | MAP2K1 | MAP2K1 | MAP2K1 | 9023 | 0.0074 | 0.37 | NO |
127 | BAIAP2 | BAIAP2 | BAIAP2 | 9089 | 0.0065 | 0.36 | NO |
128 | CYFIP1 | CYFIP1 | CYFIP1 | 9145 | 0.0058 | 0.36 | NO |
129 | PIK3CB | PIK3CB | PIK3CB | 9188 | 0.0054 | 0.36 | NO |
130 | ARPC2 | ARPC2 | ARPC2 | 9212 | 0.0052 | 0.36 | NO |
131 | MAPK1 | MAPK1 | MAPK1 | 9367 | 0.0035 | 0.35 | NO |
132 | APC2 | APC2 | APC2 | 9412 | 0.0031 | 0.35 | NO |
133 | WASF2 | WASF2 | WASF2 | 9413 | 0.003 | 0.35 | NO |
134 | PAK2 | PAK2 | PAK2 | 9472 | 0.0025 | 0.34 | NO |
135 | PPP1CB | PPP1CB | PPP1CB | 9500 | 0.0021 | 0.34 | NO |
136 | GRLF1 | GRLF1 | GRLF1 | 9636 | 0.00072 | 0.33 | NO |
137 | NRAS | NRAS | NRAS | 10018 | -0.0035 | 0.31 | NO |
138 | ACTG1 | ACTG1 | ACTG1 | 10082 | -0.0042 | 0.31 | NO |
139 | FGF19 | FGF19 | FGF19 | 10087 | -0.0042 | 0.31 | NO |
140 | CRK | CRK | CRK | 10227 | -0.0061 | 0.3 | NO |
141 | PPP1CC | PPP1CC | PPP1CC | 10256 | -0.0066 | 0.3 | NO |
142 | RAF1 | RAF1 | RAF1 | 10280 | -0.0068 | 0.3 | NO |
143 | PXN | PXN | PXN | 10763 | -0.012 | 0.27 | NO |
144 | PPP1CA | PPP1CA | PPP1CA | 10765 | -0.012 | 0.27 | NO |
145 | CDC42 | CDC42 | CDC42 | 10923 | -0.015 | 0.26 | NO |
146 | FGF12 | FGF12 | FGF12 | 10961 | -0.015 | 0.26 | NO |
147 | GIT1 | GIT1 | GIT1 | 10967 | -0.015 | 0.26 | NO |
148 | DIAPH1 | DIAPH1 | DIAPH1 | 10988 | -0.015 | 0.26 | NO |
149 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 11142 | -0.017 | 0.26 | NO |
150 | PIKFYVE | PIKFYVE | PIKFYVE | 11172 | -0.017 | 0.25 | NO |
151 | SOS2 | SOS2 | SOS2 | 11197 | -0.018 | 0.25 | NO |
152 | MYL12B | MYL12B | MYL12B | 11621 | -0.022 | 0.23 | NO |
153 | APC | APC | APC | 11907 | -0.026 | 0.22 | NO |
154 | RAC1 | RAC1 | RAC1 | 11993 | -0.027 | 0.21 | NO |
155 | SOS1 | SOS1 | SOS1 | 12020 | -0.027 | 0.21 | NO |
156 | KRAS | KRAS | KRAS | 12296 | -0.03 | 0.2 | NO |
157 | LIMK2 | LIMK2 | LIMK2 | 12585 | -0.034 | 0.18 | NO |
158 | ARPC3 | ARPC3 | ARPC3 | 12616 | -0.034 | 0.18 | NO |
159 | F2 | F2 | F2 | 13010 | -0.04 | 0.16 | NO |
160 | NCKAP1 | NCKAP1 | NCKAP1 | 13096 | -0.041 | 0.16 | NO |
161 | ITGA2 | ITGA2 | ITGA2 | 13114 | -0.041 | 0.16 | NO |
162 | FGF17 | FGF17 | FGF17 | 13442 | -0.046 | 0.14 | NO |
163 | PAK4 | PAK4 | PAK4 | 13464 | -0.046 | 0.14 | NO |
164 | EGFR | EGFR | EGFR | 13569 | -0.048 | 0.14 | NO |
165 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 13672 | -0.049 | 0.13 | NO |
166 | EZR | EZR | EZR | 13769 | -0.05 | 0.13 | NO |
167 | ARPC1A | ARPC1A | ARPC1A | 13784 | -0.051 | 0.13 | NO |
168 | MYLPF | MYLPF | MYLPF | 13867 | -0.052 | 0.12 | NO |
169 | PIP4K2C | PIP4K2C | PIP4K2C | 13873 | -0.052 | 0.12 | NO |
170 | PIK3R2 | PIK3R2 | PIK3R2 | 14062 | -0.055 | 0.12 | NO |
171 | ARHGEF4 | ARHGEF4 | ARHGEF4 | 14121 | -0.057 | 0.12 | NO |
172 | CRKL | CRKL | CRKL | 14128 | -0.057 | 0.12 | NO |
173 | FGFR2 | FGFR2 | FGFR2 | 14470 | -0.064 | 0.099 | NO |
174 | IQGAP3 | IQGAP3 | IQGAP3 | 14478 | -0.064 | 0.1 | NO |
175 | FGFR4 | FGFR4 | FGFR4 | 14602 | -0.066 | 0.096 | NO |
176 | ITGB8 | ITGB8 | ITGB8 | 14759 | -0.069 | 0.089 | NO |
177 | PAK1 | PAK1 | PAK1 | 14825 | -0.071 | 0.087 | NO |
178 | PFN2 | PFN2 | PFN2 | 14932 | -0.073 | 0.083 | NO |
179 | WASL | WASL | WASL | 15303 | -0.082 | 0.065 | NO |
180 | PTK2 | PTK2 | PTK2 | 15586 | -0.091 | 0.052 | NO |
181 | SLC9A1 | SLC9A1 | SLC9A1 | 15777 | -0.098 | 0.044 | NO |
182 | MYLK2 | MYLK2 | MYLK2 | 16024 | -0.11 | 0.034 | NO |
183 | MYL5 | MYL5 | MYL5 | 16071 | -0.11 | 0.034 | NO |
184 | TIAM1 | TIAM1 | TIAM1 | 16257 | -0.12 | 0.027 | NO |
185 | ITGA3 | ITGA3 | ITGA3 | 16325 | -0.12 | 0.027 | NO |
186 | ITGA6 | ITGA6 | ITGA6 | 16326 | -0.12 | 0.03 | NO |
187 | PAK7 | PAK7 | PAK7 | 16857 | -0.16 | 0.0056 | NO |
188 | ITGB4 | ITGB4 | ITGB4 | 16978 | -0.17 | 0.0036 | NO |
189 | FGF11 | FGF11 | FGF11 | 16996 | -0.17 | 0.0074 | NO |
190 | SCIN | SCIN | SCIN | 17015 | -0.17 | 0.011 | NO |
191 | BRAF | BRAF | BRAF | 17100 | -0.18 | 0.012 | NO |
192 | MYH14 | MYH14 | MYH14 | 17159 | -0.18 | 0.014 | NO |
193 | ITGB6 | ITGB6 | ITGB6 | 17349 | -0.2 | 0.0088 | NO |
194 | SSH3 | SSH3 | SSH3 | 17700 | -0.25 | -0.0036 | NO |
195 | PAK6 | PAK6 | PAK6 | 17935 | -0.3 | -0.0082 | NO |
196 | VAV3 | VAV3 | VAV3 | 18026 | -0.33 | -0.0039 | NO |
197 | FGFR3 | FGFR3 | FGFR3 | 18190 | -0.47 | 0.00039 | NO |
Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA ERK PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_ERK_PATHWAY.heatmap_plot.clus1.105.png)
Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ERK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.KEGG_REGULATION_OF_ACTIN_CYTOSKELETON.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 | LY96 | LY96 | LY96 | 158 | 0.67 | 0.18 | YES |
2 | CD14 | CD14 | CD14 | 763 | 0.51 | 0.3 | YES |
3 | LEF1 | LEF1 | LEF1 | 1081 | 0.46 | 0.41 | YES |
4 | LBP | LBP | LBP | 1791 | 0.37 | 0.48 | YES |
5 | TLR4 | TLR4 | TLR4 | 2272 | 0.3 | 0.54 | YES |
6 | WNT1 | WNT1 | WNT1 | 2623 | 0.26 | 0.59 | YES |
7 | FZD1 | FZD1 | FZD1 | 2980 | 0.23 | 0.64 | YES |
8 | GJA1 | GJA1 | GJA1 | 7024 | 0.038 | 0.43 | NO |
9 | IRAK1 | IRAK1 | IRAK1 | 7058 | 0.038 | 0.44 | NO |
10 | CTNNB1 | CTNNB1 | CTNNB1 | 7197 | 0.035 | 0.44 | NO |
11 | PIK3R1 | PIK3R1 | PIK3R1 | 7820 | 0.024 | 0.41 | NO |
12 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 8017 | 0.021 | 0.41 | NO |
13 | NFKB1 | NFKB1 | NFKB1 | 8209 | 0.018 | 0.4 | NO |
14 | PIK3CA | PIK3CA | PIK3CA | 8689 | 0.012 | 0.38 | NO |
15 | RELA | RELA | RELA | 9209 | 0.0052 | 0.35 | NO |
16 | AKT1 | AKT1 | AKT1 | 10046 | -0.0038 | 0.31 | NO |
17 | TIRAP | TIRAP | TIRAP | 10495 | -0.0095 | 0.28 | NO |
18 | MYD88 | MYD88 | MYD88 | 11236 | -0.018 | 0.25 | NO |
19 | APC | APC | APC | 11907 | -0.026 | 0.22 | NO |
20 | PPP2CA | PPP2CA | PPP2CA | 12290 | -0.03 | 0.21 | NO |
21 | GSK3B | GSK3B | GSK3B | 12321 | -0.031 | 0.21 | NO |
22 | AXIN1 | AXIN1 | AXIN1 | 12813 | -0.037 | 0.2 | NO |
23 | PDPK1 | PDPK1 | PDPK1 | 13384 | -0.045 | 0.18 | NO |
24 | DVL1 | DVL1 | DVL1 | 14040 | -0.055 | 0.16 | NO |
25 | CCND1 | CCND1 | CCND1 | 15241 | -0.08 | 0.12 | NO |
26 | GNAI1 | GNAI1 | GNAI1 | 16917 | -0.16 | 0.07 | NO |
Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_FCER1_PATHWAY.heatmap_plot.clus1.40.png)
Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_GSK3_PATHWAY.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 | PTPN7 | PTPN7 | PTPN7 | 752 | 0.52 | 0.03 | YES |
2 | ZAP70 | ZAP70 | ZAP70 | 1001 | 0.47 | 0.081 | YES |
3 | NFATC1 | NFATC1 | NFATC1 | 1043 | 0.47 | 0.14 | YES |
4 | VAV1 | VAV1 | VAV1 | 1049 | 0.47 | 0.21 | YES |
5 | CD3E | CD3E | CD3E | 1118 | 0.46 | 0.26 | YES |
6 | PIK3CG | PIK3CG | PIK3CG | 1254 | 0.44 | 0.32 | YES |
7 | CD247 | CD247 | CD247 | 1275 | 0.43 | 0.38 | YES |
8 | LCK | LCK | LCK | 1304 | 0.43 | 0.43 | YES |
9 | PRKCB | PRKCB | PRKCB | 1308 | 0.43 | 0.49 | YES |
10 | CD3D | CD3D | CD3D | 1487 | 0.4 | 0.54 | YES |
11 | CD3G | CD3G | CD3G | 1630 | 0.39 | 0.58 | YES |
12 | FYN | FYN | FYN | 1685 | 0.38 | 0.63 | YES |
13 | LAT | LAT | LAT | 2375 | 0.29 | 0.63 | YES |
14 | NFATC4 | NFATC4 | NFATC4 | 2389 | 0.29 | 0.67 | YES |
15 | NFATC2 | NFATC2 | NFATC2 | 2457 | 0.28 | 0.71 | YES |
16 | PPP3CC | PPP3CC | PPP3CC | 3721 | 0.17 | 0.66 | NO |
17 | PPP3CB | PPP3CB | PPP3CB | 5203 | 0.088 | 0.59 | NO |
18 | CALM2 | CALM2 | CALM2 | 5414 | 0.08 | 0.59 | NO |
19 | JUN | JUN | JUN | 5425 | 0.08 | 0.6 | NO |
20 | MAPK3 | MAPK3 | MAPK3 | 5782 | 0.068 | 0.59 | NO |
21 | PRKCA | PRKCA | PRKCA | 5833 | 0.067 | 0.6 | NO |
22 | GRB2 | GRB2 | GRB2 | 6063 | 0.06 | 0.59 | NO |
23 | SHC1 | SHC1 | SHC1 | 6708 | 0.045 | 0.56 | NO |
24 | NFATC3 | NFATC3 | NFATC3 | 6862 | 0.042 | 0.56 | NO |
25 | ELK1 | ELK1 | ELK1 | 6879 | 0.042 | 0.57 | NO |
26 | PPP3CA | PPP3CA | PPP3CA | 6911 | 0.041 | 0.57 | NO |
27 | CALM3 | CALM3 | CALM3 | 6917 | 0.041 | 0.58 | NO |
28 | RASA1 | RASA1 | RASA1 | 7028 | 0.038 | 0.57 | NO |
29 | CALM1 | CALM1 | CALM1 | 7534 | 0.03 | 0.55 | NO |
30 | PIK3R1 | PIK3R1 | PIK3R1 | 7820 | 0.024 | 0.54 | NO |
31 | NFKB1 | NFKB1 | NFKB1 | 8209 | 0.018 | 0.52 | NO |
32 | PLCG1 | PLCG1 | PLCG1 | 8217 | 0.018 | 0.52 | NO |
33 | MAP3K1 | MAP3K1 | MAP3K1 | 8370 | 0.016 | 0.52 | NO |
34 | PIK3CA | PIK3CA | PIK3CA | 8689 | 0.012 | 0.5 | NO |
35 | MAP2K1 | MAP2K1 | MAP2K1 | 9023 | 0.0074 | 0.48 | NO |
36 | RELA | RELA | RELA | 9209 | 0.0052 | 0.47 | NO |
37 | NFKBIA | NFKBIA | NFKBIA | 9532 | 0.0019 | 0.46 | NO |
38 | RAF1 | RAF1 | RAF1 | 10280 | -0.0068 | 0.42 | NO |
39 | MAPK8 | MAPK8 | MAPK8 | 11676 | -0.023 | 0.34 | NO |
40 | RAC1 | RAC1 | RAC1 | 11993 | -0.027 | 0.33 | NO |
41 | SOS1 | SOS1 | SOS1 | 12020 | -0.027 | 0.33 | NO |
42 | FOS | FOS | FOS | 12182 | -0.029 | 0.32 | NO |
43 | MAP2K4 | MAP2K4 | MAP2K4 | 13229 | -0.043 | 0.27 | NO |
Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FMLP PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_FMLP_PATHWAY.heatmap_plot.clus1.6.png)
Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FMLP PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus1___Class2-CanonicalPathway.BIOCARTA_TCR_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 GLYCOLYSIS GLUCONEOGENESIS | 59 | genes.ES.table | 0.3 | 1 | 0.46 | 0.82 | 1 | 0.22 | 0.13 | 0.19 | 0.8 | 0.24 |
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS | 26 | genes.ES.table | 0.79 | 1.7 | 0.015 | 0.29 | 0.54 | 0.62 | 0.12 | 0.55 | 0.14 | 0.068 |
KEGG FATTY ACID METABOLISM | 41 | genes.ES.table | 0.42 | 1.3 | 0.19 | 0.69 | 0.99 | 0.46 | 0.24 | 0.35 | 0.59 | 0.19 |
KEGG STEROID HORMONE BIOSYNTHESIS | 51 | genes.ES.table | 0.63 | 1.5 | 0.047 | 0.29 | 0.85 | 0.57 | 0.12 | 0.5 | 0.2 | 0.041 |
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION | 43 | genes.ES.table | 0.36 | 1.2 | 0.23 | 0.68 | 0.99 | 0.42 | 0.23 | 0.32 | 0.59 | 0.18 |
KEGG TYROSINE METABOLISM | 39 | genes.ES.table | 0.4 | 1.1 | 0.34 | 0.69 | 1 | 0.23 | 0.11 | 0.2 | 0.64 | 0.16 |
KEGG GLUTATHIONE METABOLISM | 45 | genes.ES.table | 0.38 | 1.1 | 0.32 | 0.73 | 1 | 0.33 | 0.17 | 0.28 | 0.67 | 0.2 |
KEGG STARCH AND SUCROSE METABOLISM | 46 | genes.ES.table | 0.55 | 1.4 | 0.061 | 0.42 | 0.93 | 0.44 | 0.13 | 0.38 | 0.32 | 0.086 |
KEGG GLYCEROPHOSPHOLIPID METABOLISM | 70 | genes.ES.table | 0.27 | 1 | 0.41 | 0.8 | 1 | 0.51 | 0.3 | 0.36 | 0.77 | 0.24 |
KEGG ETHER LIPID METABOLISM | 28 | genes.ES.table | 0.4 | 1.2 | 0.23 | 0.67 | 1 | 0.39 | 0.15 | 0.33 | 0.6 | 0.17 |
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 | UGT1A1 | UGT1A1 | UGT1A1 | 63 | 0.69 | 0.086 | YES |
2 | UGT2B28 | UGT2B28 | UGT2B28 | 101 | 0.62 | 0.16 | YES |
3 | UGT1A9 | UGT1A9 | UGT1A9 | 228 | 0.53 | 0.23 | YES |
4 | UGT2B15 | UGT2B15 | UGT2B15 | 292 | 0.49 | 0.29 | YES |
5 | UGT1A6 | UGT1A6 | UGT1A6 | 328 | 0.47 | 0.34 | YES |
6 | UGT2B11 | UGT2B11 | UGT2B11 | 386 | 0.45 | 0.4 | YES |
7 | UGT1A3 | UGT1A3 | UGT1A3 | 484 | 0.42 | 0.45 | YES |
8 | UGT2B7 | UGT2B7 | UGT2B7 | 650 | 0.38 | 0.49 | YES |
9 | UGT1A4 | UGT1A4 | UGT1A4 | 871 | 0.34 | 0.52 | YES |
10 | UGT2A3 | UGT2A3 | UGT2A3 | 899 | 0.33 | 0.56 | YES |
11 | UGT2B10 | UGT2B10 | UGT2B10 | 923 | 0.33 | 0.6 | YES |
12 | UGT1A5 | UGT1A5 | UGT1A5 | 1105 | 0.3 | 0.63 | YES |
13 | UGT1A10 | UGT1A10 | UGT1A10 | 1438 | 0.26 | 0.65 | YES |
14 | UGT2B4 | UGT2B4 | UGT2B4 | 1597 | 0.24 | 0.67 | YES |
15 | ALAS1 | ALAS1 | ALAS1 | 1634 | 0.24 | 0.7 | YES |
16 | UGT1A8 | UGT1A8 | UGT1A8 | 1917 | 0.21 | 0.71 | YES |
17 | PPOX | PPOX | PPOX | 2828 | 0.15 | 0.68 | NO |
18 | MMAB | MMAB | MMAB | 6242 | 0.045 | 0.5 | NO |
19 | EARS2 | EARS2 | EARS2 | 6533 | 0.04 | 0.49 | NO |
20 | UGT1A7 | UGT1A7 | UGT1A7 | 6763 | 0.035 | 0.48 | NO |
21 | UGT2A1 | UGT2A1 | UGT2A1 | 7310 | 0.025 | 0.45 | NO |
22 | COX15 | COX15 | COX15 | 8174 | 0.0087 | 0.41 | NO |
23 | GUSB | GUSB | GUSB | 8231 | 0.0079 | 0.4 | NO |
24 | HMOX2 | HMOX2 | HMOX2 | 8492 | 0.0031 | 0.39 | NO |
25 | ALAD | ALAD | ALAD | 8684 | -0.00044 | 0.38 | NO |
26 | COX10 | COX10 | COX10 | 9744 | -0.018 | 0.32 | NO |
27 | ALAS2 | ALAS2 | ALAS2 | 9880 | -0.021 | 0.32 | NO |
28 | FTH1 | FTH1 | FTH1 | 10848 | -0.04 | 0.27 | NO |
29 | HMBS | HMBS | HMBS | 11034 | -0.045 | 0.27 | NO |
30 | UROD | UROD | UROD | 11281 | -0.05 | 0.26 | NO |
31 | CP | CP | CP | 11534 | -0.055 | 0.25 | NO |
32 | CPOX | CPOX | CPOX | 11837 | -0.063 | 0.24 | NO |
33 | EPRS | EPRS | EPRS | 12718 | -0.087 | 0.21 | NO |
34 | BLVRB | BLVRB | BLVRB | 12739 | -0.088 | 0.22 | NO |
35 | FECH | FECH | FECH | 12936 | -0.095 | 0.22 | NO |
36 | HMOX1 | HMOX1 | HMOX1 | 13858 | -0.13 | 0.19 | NO |
37 | UROS | UROS | UROS | 13937 | -0.14 | 0.2 | NO |
38 | BLVRA | BLVRA | BLVRA | 15856 | -0.27 | 0.13 | 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 GLYCOLYSIS GLUCONEOGENESIS.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_GLYCOLYSIS_GLUCONEOGENESIS.heatmap_plot.clus2.20.png)
Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM.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 | UGT1A1 | UGT1A1 | UGT1A1 | 63 | 0.69 | 0.096 | YES |
2 | UGT2B28 | UGT2B28 | UGT2B28 | 101 | 0.62 | 0.18 | YES |
3 | UGT1A9 | UGT1A9 | UGT1A9 | 228 | 0.53 | 0.25 | YES |
4 | UGT2B15 | UGT2B15 | UGT2B15 | 292 | 0.49 | 0.32 | YES |
5 | UGT1A6 | UGT1A6 | UGT1A6 | 328 | 0.47 | 0.38 | YES |
6 | UGT2B11 | UGT2B11 | UGT2B11 | 386 | 0.45 | 0.45 | YES |
7 | UGT1A3 | UGT1A3 | UGT1A3 | 484 | 0.42 | 0.5 | YES |
8 | UGT2B7 | UGT2B7 | UGT2B7 | 650 | 0.38 | 0.55 | YES |
9 | UGT1A4 | UGT1A4 | UGT1A4 | 871 | 0.34 | 0.58 | YES |
10 | UGT2A3 | UGT2A3 | UGT2A3 | 899 | 0.33 | 0.63 | YES |
11 | UGT2B10 | UGT2B10 | UGT2B10 | 923 | 0.33 | 0.68 | YES |
12 | UGT1A5 | UGT1A5 | UGT1A5 | 1105 | 0.3 | 0.71 | YES |
13 | UGT1A10 | UGT1A10 | UGT1A10 | 1438 | 0.26 | 0.73 | YES |
14 | UGT2B4 | UGT2B4 | UGT2B4 | 1597 | 0.24 | 0.75 | YES |
15 | UGT1A8 | UGT1A8 | UGT1A8 | 1917 | 0.21 | 0.77 | YES |
16 | XYLB | XYLB | XYLB | 2104 | 0.2 | 0.79 | YES |
17 | DCXR | DCXR | DCXR | 3334 | 0.13 | 0.74 | NO |
18 | CRYL1 | CRYL1 | CRYL1 | 3353 | 0.13 | 0.75 | NO |
19 | UGT1A7 | UGT1A7 | UGT1A7 | 6763 | 0.035 | 0.57 | NO |
20 | UGT2A1 | UGT2A1 | UGT2A1 | 7310 | 0.025 | 0.55 | NO |
21 | GUSB | GUSB | GUSB | 8231 | 0.0079 | 0.5 | NO |
22 | DHDH | DHDH | DHDH | 8241 | 0.0078 | 0.5 | NO |
23 | AKR1B1 | AKR1B1 | AKR1B1 | 9340 | -0.012 | 0.44 | NO |
24 | RPE | RPE | RPE | 11689 | -0.059 | 0.32 | NO |
25 | UGP2 | UGP2 | UGP2 | 12190 | -0.072 | 0.3 | NO |
26 | LOC729020 | LOC729020 | LOC729020 | 15183 | -0.22 | 0.17 | 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS.heatmap_plot.clus2.2.png)
Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS.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 | UGT1A1 | UGT1A1 | UGT1A1 | 63 | 0.69 | 0.04 | YES |
2 | UGT2B28 | UGT2B28 | UGT2B28 | 101 | 0.62 | 0.077 | YES |
3 | CYP3A5 | CYP3A5 | CYP3A5 | 103 | 0.62 | 0.12 | YES |
4 | CYP2C8 | CYP2C8 | CYP2C8 | 215 | 0.54 | 0.14 | YES |
5 | ADH6 | ADH6 | ADH6 | 216 | 0.54 | 0.18 | YES |
6 | UGT1A9 | UGT1A9 | UGT1A9 | 228 | 0.53 | 0.21 | YES |
7 | UGT2B15 | UGT2B15 | UGT2B15 | 292 | 0.49 | 0.24 | YES |
8 | UGT1A6 | UGT1A6 | UGT1A6 | 328 | 0.47 | 0.26 | YES |
9 | UGT2B11 | UGT2B11 | UGT2B11 | 386 | 0.45 | 0.29 | YES |
10 | UGT1A3 | UGT1A3 | UGT1A3 | 484 | 0.42 | 0.31 | YES |
11 | CYP2C9 | CYP2C9 | CYP2C9 | 485 | 0.42 | 0.34 | YES |
12 | AKR1C2 | AKR1C2 | AKR1C2 | 514 | 0.41 | 0.36 | YES |
13 | UGT2B7 | UGT2B7 | UGT2B7 | 650 | 0.38 | 0.38 | YES |
14 | CYP3A7 | CYP3A7 | CYP3A7 | 732 | 0.36 | 0.4 | YES |
15 | GSTM4 | GSTM4 | GSTM4 | 767 | 0.36 | 0.42 | YES |
16 | AKR1C3 | AKR1C3 | AKR1C3 | 780 | 0.35 | 0.44 | YES |
17 | CYP1A1 | CYP1A1 | CYP1A1 | 844 | 0.34 | 0.45 | YES |
18 | UGT1A4 | UGT1A4 | UGT1A4 | 871 | 0.34 | 0.47 | YES |
19 | GSTM2 | GSTM2 | GSTM2 | 894 | 0.33 | 0.49 | YES |
20 | UGT2A3 | UGT2A3 | UGT2A3 | 899 | 0.33 | 0.51 | YES |
21 | UGT2B10 | UGT2B10 | UGT2B10 | 923 | 0.33 | 0.53 | YES |
22 | UGT1A5 | UGT1A5 | UGT1A5 | 1105 | 0.3 | 0.54 | YES |
23 | GSTA1 | GSTA1 | GSTA1 | 1108 | 0.3 | 0.56 | YES |
24 | CYP3A43 | CYP3A43 | CYP3A43 | 1123 | 0.3 | 0.58 | YES |
25 | ADH1C | ADH1C | ADH1C | 1174 | 0.29 | 0.59 | YES |
26 | CYP2C19 | CYP2C19 | CYP2C19 | 1245 | 0.28 | 0.61 | YES |
27 | CYP1A2 | CYP1A2 | CYP1A2 | 1252 | 0.28 | 0.62 | YES |
28 | GSTM3 | GSTM3 | GSTM3 | 1268 | 0.28 | 0.64 | YES |
29 | UGT1A10 | UGT1A10 | UGT1A10 | 1438 | 0.26 | 0.65 | YES |
30 | AKR1C1 | AKR1C1 | AKR1C1 | 1475 | 0.26 | 0.66 | YES |
31 | MGST2 | MGST2 | MGST2 | 1549 | 0.25 | 0.67 | YES |
32 | CYP2C18 | CYP2C18 | CYP2C18 | 1564 | 0.25 | 0.69 | YES |
33 | GSTA2 | GSTA2 | GSTA2 | 1592 | 0.24 | 0.7 | YES |
34 | UGT2B4 | UGT2B4 | UGT2B4 | 1597 | 0.24 | 0.72 | YES |
35 | ADH4 | ADH4 | ADH4 | 1713 | 0.23 | 0.72 | YES |
36 | UGT1A8 | UGT1A8 | UGT1A8 | 1917 | 0.21 | 0.73 | YES |
37 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 1995 | 0.21 | 0.74 | YES |
38 | MGST1 | MGST1 | MGST1 | 2409 | 0.18 | 0.72 | NO |
39 | AKR1C4 | AKR1C4 | AKR1C4 | 2512 | 0.17 | 0.73 | NO |
40 | GSTM1 | GSTM1 | GSTM1 | 2894 | 0.15 | 0.72 | NO |
41 | GSTO2 | GSTO2 | GSTO2 | 3026 | 0.14 | 0.72 | NO |
42 | ADH1A | ADH1A | ADH1A | 3706 | 0.11 | 0.69 | NO |
43 | CYP2B6 | CYP2B6 | CYP2B6 | 4695 | 0.082 | 0.64 | NO |
44 | GSTK1 | GSTK1 | GSTK1 | 5580 | 0.06 | 0.59 | NO |
45 | GSTZ1 | GSTZ1 | GSTZ1 | 5772 | 0.056 | 0.59 | NO |
46 | GSTT1 | GSTT1 | GSTT1 | 6385 | 0.043 | 0.56 | NO |
47 | ADH7 | ADH7 | ADH7 | 6742 | 0.036 | 0.54 | NO |
48 | UGT1A7 | UGT1A7 | UGT1A7 | 6763 | 0.035 | 0.54 | NO |
49 | MGST3 | MGST3 | MGST3 | 6837 | 0.034 | 0.54 | NO |
50 | UGT2A1 | UGT2A1 | UGT2A1 | 7310 | 0.025 | 0.51 | NO |
51 | CYP2E1 | CYP2E1 | CYP2E1 | 7502 | 0.021 | 0.5 | NO |
52 | ADH5 | ADH5 | ADH5 | 7534 | 0.021 | 0.5 | NO |
53 | DHDH | DHDH | DHDH | 8241 | 0.0078 | 0.46 | NO |
54 | ADH1B | ADH1B | ADH1B | 8596 | 0.0015 | 0.44 | NO |
55 | GSTT2 | GSTT2 | GSTT2 | 9094 | -0.0074 | 0.42 | NO |
56 | CYP2F1 | CYP2F1 | CYP2F1 | 9228 | -0.0098 | 0.41 | NO |
57 | GSTP1 | GSTP1 | GSTP1 | 9623 | -0.017 | 0.39 | NO |
58 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 10050 | -0.024 | 0.37 | NO |
59 | EPHX1 | EPHX1 | EPHX1 | 11774 | -0.061 | 0.28 | NO |
60 | GSTO1 | GSTO1 | GSTO1 | 12133 | -0.071 | 0.26 | NO |
61 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 12363 | -0.077 | 0.26 | NO |
62 | GSTA4 | GSTA4 | GSTA4 | 13952 | -0.14 | 0.18 | NO |
63 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 14609 | -0.17 | 0.15 | NO |
64 | GSTM5 | GSTM5 | GSTM5 | 14772 | -0.18 | 0.15 | NO |
65 | CYP2S1 | CYP2S1 | CYP2S1 | 15434 | -0.24 | 0.13 | NO |
66 | CYP1B1 | CYP1B1 | CYP1B1 | 16545 | -0.34 | 0.091 | 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 FATTY ACID METABOLISM.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_FATTY_ACID_METABOLISM.heatmap_plot.clus2.10.png)
Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FATTY ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450.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 | UGT1A1 | UGT1A1 | UGT1A1 | 63 | 0.69 | 0.042 | YES |
2 | UGT2B28 | UGT2B28 | UGT2B28 | 101 | 0.62 | 0.081 | YES |
3 | CYP3A5 | CYP3A5 | CYP3A5 | 103 | 0.62 | 0.12 | YES |
4 | CYP2C8 | CYP2C8 | CYP2C8 | 215 | 0.54 | 0.15 | YES |
5 | ADH6 | ADH6 | ADH6 | 216 | 0.54 | 0.19 | YES |
6 | UGT1A9 | UGT1A9 | UGT1A9 | 228 | 0.53 | 0.22 | YES |
7 | UGT2B15 | UGT2B15 | UGT2B15 | 292 | 0.49 | 0.25 | YES |
8 | UGT1A6 | UGT1A6 | UGT1A6 | 328 | 0.47 | 0.28 | YES |
9 | UGT2B11 | UGT2B11 | UGT2B11 | 386 | 0.45 | 0.3 | YES |
10 | DGAT2 | DGAT2 | DGAT2 | 461 | 0.43 | 0.33 | YES |
11 | UGT1A3 | UGT1A3 | UGT1A3 | 484 | 0.42 | 0.36 | YES |
12 | CYP2C9 | CYP2C9 | CYP2C9 | 485 | 0.42 | 0.38 | YES |
13 | UGT2B7 | UGT2B7 | UGT2B7 | 650 | 0.38 | 0.4 | YES |
14 | CYP3A7 | CYP3A7 | CYP3A7 | 732 | 0.36 | 0.42 | YES |
15 | CYP4A11 | CYP4A11 | CYP4A11 | 816 | 0.35 | 0.44 | YES |
16 | CYP1A1 | CYP1A1 | CYP1A1 | 844 | 0.34 | 0.46 | YES |
17 | UGT1A4 | UGT1A4 | UGT1A4 | 871 | 0.34 | 0.48 | YES |
18 | UGT2A3 | UGT2A3 | UGT2A3 | 899 | 0.33 | 0.5 | YES |
19 | UGT2B10 | UGT2B10 | UGT2B10 | 923 | 0.33 | 0.52 | YES |
20 | ALDH1A2 | ALDH1A2 | ALDH1A2 | 937 | 0.33 | 0.54 | YES |
21 | UGT1A5 | UGT1A5 | UGT1A5 | 1105 | 0.3 | 0.55 | YES |
22 | CYP3A43 | CYP3A43 | CYP3A43 | 1123 | 0.3 | 0.57 | YES |
23 | ADH1C | ADH1C | ADH1C | 1174 | 0.29 | 0.58 | YES |
24 | CYP2C19 | CYP2C19 | CYP2C19 | 1245 | 0.28 | 0.6 | YES |
25 | CYP1A2 | CYP1A2 | CYP1A2 | 1252 | 0.28 | 0.62 | YES |
26 | UGT1A10 | UGT1A10 | UGT1A10 | 1438 | 0.26 | 0.62 | YES |
27 | BCMO1 | BCMO1 | BCMO1 | 1546 | 0.25 | 0.64 | YES |
28 | CYP2C18 | CYP2C18 | CYP2C18 | 1564 | 0.25 | 0.65 | YES |
29 | UGT2B4 | UGT2B4 | UGT2B4 | 1597 | 0.24 | 0.66 | YES |
30 | CYP4A22 | CYP4A22 | CYP4A22 | 1602 | 0.24 | 0.68 | YES |
31 | ADH4 | ADH4 | ADH4 | 1713 | 0.23 | 0.69 | YES |
32 | UGT1A8 | UGT1A8 | UGT1A8 | 1917 | 0.21 | 0.69 | YES |
33 | DHRS3 | DHRS3 | DHRS3 | 2931 | 0.15 | 0.65 | NO |
34 | DGAT1 | DGAT1 | DGAT1 | 3007 | 0.14 | 0.65 | NO |
35 | ADH1A | ADH1A | ADH1A | 3706 | 0.11 | 0.62 | NO |
36 | CYP2B6 | CYP2B6 | CYP2B6 | 4695 | 0.082 | 0.57 | NO |
37 | LRAT | LRAT | LRAT | 5094 | 0.072 | 0.55 | NO |
38 | RDH16 | RDH16 | RDH16 | 5929 | 0.052 | 0.51 | NO |
39 | RDH10 | RDH10 | RDH10 | 6057 | 0.049 | 0.51 | NO |
40 | RDH12 | RDH12 | RDH12 | 6532 | 0.04 | 0.48 | NO |
41 | ADH7 | ADH7 | ADH7 | 6742 | 0.036 | 0.48 | NO |
42 | UGT1A7 | UGT1A7 | UGT1A7 | 6763 | 0.035 | 0.48 | NO |
43 | RDH11 | RDH11 | RDH11 | 6767 | 0.035 | 0.48 | NO |
44 | UGT2A1 | UGT2A1 | UGT2A1 | 7310 | 0.025 | 0.45 | NO |
45 | ADH5 | ADH5 | ADH5 | 7534 | 0.021 | 0.44 | NO |
46 | ADH1B | ADH1B | ADH1B | 8596 | 0.0015 | 0.38 | NO |
47 | CYP2A6 | CYP2A6 | CYP2A6 | 8619 | 0.00096 | 0.38 | NO |
48 | CYP26A1 | CYP26A1 | CYP26A1 | 8698 | -0.0006 | 0.38 | NO |
49 | PNPLA4 | PNPLA4 | PNPLA4 | 9793 | -0.019 | 0.32 | NO |
50 | RDH5 | RDH5 | RDH5 | 10060 | -0.024 | 0.3 | NO |
51 | DHRS4 | DHRS4 | DHRS4 | 10413 | -0.031 | 0.29 | NO |
52 | DHRS4L2 | DHRS4L2 | DHRS4L2 | 10705 | -0.037 | 0.27 | NO |
53 | RETSAT | RETSAT | RETSAT | 10816 | -0.039 | 0.27 | NO |
54 | CYP26C1 | CYP26C1 | CYP26C1 | 10985 | -0.044 | 0.26 | NO |
55 | AWAT2 | AWAT2 | AWAT2 | 12807 | -0.09 | 0.17 | NO |
56 | RPE65 | RPE65 | RPE65 | 15256 | -0.22 | 0.048 | NO |
57 | RDH8 | RDH8 | RDH8 | 15595 | -0.25 | 0.046 | NO |
58 | ALDH1A1 | ALDH1A1 | ALDH1A1 | 16757 | -0.37 | 0.0063 | NO |
59 | DHRS9 | DHRS9 | DHRS9 | 17382 | -0.47 | 0.0027 | NO |
60 | CYP26B1 | CYP26B1 | CYP26B1 | 17962 | -0.64 | 0.013 | 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 STEROID HORMONE BIOSYNTHESIS.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_STEROID_HORMONE_BIOSYNTHESIS.heatmap_plot.clus2.6.png)
Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_RETINOL_METABOLISM.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 | UGT1A1 | UGT1A1 | UGT1A1 | 63 | 0.69 | 0.036 | YES |
2 | UGT2B28 | UGT2B28 | UGT2B28 | 101 | 0.62 | 0.068 | YES |
3 | CYP3A5 | CYP3A5 | CYP3A5 | 103 | 0.62 | 0.1 | YES |
4 | FMO5 | FMO5 | FMO5 | 188 | 0.55 | 0.13 | YES |
5 | CYP2C8 | CYP2C8 | CYP2C8 | 215 | 0.54 | 0.16 | YES |
6 | ADH6 | ADH6 | ADH6 | 216 | 0.54 | 0.19 | YES |
7 | UGT1A9 | UGT1A9 | UGT1A9 | 228 | 0.53 | 0.22 | YES |
8 | UGT2B15 | UGT2B15 | UGT2B15 | 292 | 0.49 | 0.24 | YES |
9 | MAOA | MAOA | MAOA | 311 | 0.48 | 0.27 | YES |
10 | UGT1A6 | UGT1A6 | UGT1A6 | 328 | 0.47 | 0.29 | YES |
11 | UGT2B11 | UGT2B11 | UGT2B11 | 386 | 0.45 | 0.32 | YES |
12 | UGT1A3 | UGT1A3 | UGT1A3 | 484 | 0.42 | 0.33 | YES |
13 | CYP2C9 | CYP2C9 | CYP2C9 | 485 | 0.42 | 0.36 | YES |
14 | UGT2B7 | UGT2B7 | UGT2B7 | 650 | 0.38 | 0.37 | YES |
15 | CYP3A7 | CYP3A7 | CYP3A7 | 732 | 0.36 | 0.39 | YES |
16 | GSTM4 | GSTM4 | GSTM4 | 767 | 0.36 | 0.4 | YES |
17 | CYP2D6 | CYP2D6 | CYP2D6 | 788 | 0.35 | 0.42 | YES |
18 | UGT1A4 | UGT1A4 | UGT1A4 | 871 | 0.34 | 0.44 | YES |
19 | GSTM2 | GSTM2 | GSTM2 | 894 | 0.33 | 0.46 | YES |
20 | UGT2A3 | UGT2A3 | UGT2A3 | 899 | 0.33 | 0.47 | YES |
21 | UGT2B10 | UGT2B10 | UGT2B10 | 923 | 0.33 | 0.49 | YES |
22 | UGT1A5 | UGT1A5 | UGT1A5 | 1105 | 0.3 | 0.5 | YES |
23 | GSTA1 | GSTA1 | GSTA1 | 1108 | 0.3 | 0.51 | YES |
24 | CYP3A43 | CYP3A43 | CYP3A43 | 1123 | 0.3 | 0.53 | YES |
25 | ADH1C | ADH1C | ADH1C | 1174 | 0.29 | 0.54 | YES |
26 | CYP2C19 | CYP2C19 | CYP2C19 | 1245 | 0.28 | 0.56 | YES |
27 | CYP1A2 | CYP1A2 | CYP1A2 | 1252 | 0.28 | 0.57 | YES |
28 | GSTM3 | GSTM3 | GSTM3 | 1268 | 0.28 | 0.58 | YES |
29 | UGT1A10 | UGT1A10 | UGT1A10 | 1438 | 0.26 | 0.59 | YES |
30 | MGST2 | MGST2 | MGST2 | 1549 | 0.25 | 0.6 | YES |
31 | CYP2C18 | CYP2C18 | CYP2C18 | 1564 | 0.25 | 0.61 | YES |
32 | GSTA2 | GSTA2 | GSTA2 | 1592 | 0.24 | 0.62 | YES |
33 | UGT2B4 | UGT2B4 | UGT2B4 | 1597 | 0.24 | 0.64 | YES |
34 | ADH4 | ADH4 | ADH4 | 1713 | 0.23 | 0.64 | YES |
35 | UGT1A8 | UGT1A8 | UGT1A8 | 1917 | 0.21 | 0.64 | YES |
36 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 1995 | 0.21 | 0.65 | YES |
37 | MGST1 | MGST1 | MGST1 | 2409 | 0.18 | 0.64 | NO |
38 | GSTM1 | GSTM1 | GSTM1 | 2894 | 0.15 | 0.62 | NO |
39 | GSTO2 | GSTO2 | GSTO2 | 3026 | 0.14 | 0.62 | NO |
40 | ADH1A | ADH1A | ADH1A | 3706 | 0.11 | 0.59 | NO |
41 | CYP2B6 | CYP2B6 | CYP2B6 | 4695 | 0.082 | 0.54 | NO |
42 | GSTK1 | GSTK1 | GSTK1 | 5580 | 0.06 | 0.5 | NO |
43 | GSTZ1 | GSTZ1 | GSTZ1 | 5772 | 0.056 | 0.49 | NO |
44 | GSTT1 | GSTT1 | GSTT1 | 6385 | 0.043 | 0.46 | NO |
45 | ADH7 | ADH7 | ADH7 | 6742 | 0.036 | 0.44 | NO |
46 | UGT1A7 | UGT1A7 | UGT1A7 | 6763 | 0.035 | 0.44 | NO |
47 | MGST3 | MGST3 | MGST3 | 6837 | 0.034 | 0.44 | NO |
48 | UGT2A1 | UGT2A1 | UGT2A1 | 7310 | 0.025 | 0.41 | NO |
49 | CYP2E1 | CYP2E1 | CYP2E1 | 7502 | 0.021 | 0.4 | NO |
50 | ADH5 | ADH5 | ADH5 | 7534 | 0.021 | 0.4 | NO |
51 | FMO4 | FMO4 | FMO4 | 8578 | 0.0018 | 0.34 | NO |
52 | ADH1B | ADH1B | ADH1B | 8596 | 0.0015 | 0.34 | NO |
53 | CYP2A6 | CYP2A6 | CYP2A6 | 8619 | 0.00096 | 0.34 | NO |
54 | GSTT2 | GSTT2 | GSTT2 | 9094 | -0.0074 | 0.32 | NO |
55 | GSTP1 | GSTP1 | GSTP1 | 9623 | -0.017 | 0.29 | NO |
56 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 10050 | -0.024 | 0.27 | NO |
57 | GSTO1 | GSTO1 | GSTO1 | 12133 | -0.071 | 0.16 | NO |
58 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 12363 | -0.077 | 0.15 | NO |
59 | GSTA4 | GSTA4 | GSTA4 | 13952 | -0.14 | 0.068 | NO |
60 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 14609 | -0.17 | 0.042 | NO |
61 | GSTM5 | GSTM5 | GSTM5 | 14772 | -0.18 | 0.043 | NO |
62 | FMO3 | FMO3 | FMO3 | 15097 | -0.21 | 0.037 | NO |
63 | AOX1 | AOX1 | AOX1 | 17492 | -0.49 | -0.067 | NO |
64 | MAOB | MAOB | MAOB | 17604 | -0.52 | -0.044 | NO |
65 | FMO2 | FMO2 | FMO2 | 17868 | -0.6 | -0.025 | NO |
66 | FMO1 | FMO1 | FMO1 | 18153 | -0.77 | 0.0024 | NO |
Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION.heatmap_plot.clus2.12.png)
Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_DRUG_METABOLISM_CYTOCHROME_P450.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 | HSD17B2 | HSD17B2 | HSD17B2 | 47 | 0.74 | 0.048 | YES |
2 | UGT1A1 | UGT1A1 | UGT1A1 | 63 | 0.69 | 0.095 | YES |
3 | UGT2B28 | UGT2B28 | UGT2B28 | 101 | 0.62 | 0.14 | YES |
4 | CYP3A5 | CYP3A5 | CYP3A5 | 103 | 0.62 | 0.18 | YES |
5 | UGT1A9 | UGT1A9 | UGT1A9 | 228 | 0.53 | 0.21 | YES |
6 | UGT2B15 | UGT2B15 | UGT2B15 | 292 | 0.49 | 0.24 | YES |
7 | UGT1A6 | UGT1A6 | UGT1A6 | 328 | 0.47 | 0.27 | YES |
8 | UGT2B11 | UGT2B11 | UGT2B11 | 386 | 0.45 | 0.3 | YES |
9 | UGT1A3 | UGT1A3 | UGT1A3 | 484 | 0.42 | 0.32 | YES |
10 | AKR1C2 | AKR1C2 | AKR1C2 | 514 | 0.41 | 0.35 | YES |
11 | UGT2B7 | UGT2B7 | UGT2B7 | 650 | 0.38 | 0.37 | YES |
12 | CYP3A7 | CYP3A7 | CYP3A7 | 732 | 0.36 | 0.39 | YES |
13 | AKR1C3 | AKR1C3 | AKR1C3 | 780 | 0.35 | 0.41 | YES |
14 | CYP1A1 | CYP1A1 | CYP1A1 | 844 | 0.34 | 0.43 | YES |
15 | UGT1A4 | UGT1A4 | UGT1A4 | 871 | 0.34 | 0.45 | YES |
16 | UGT2A3 | UGT2A3 | UGT2A3 | 899 | 0.33 | 0.48 | YES |
17 | UGT2B10 | UGT2B10 | UGT2B10 | 923 | 0.33 | 0.5 | YES |
18 | UGT1A5 | UGT1A5 | UGT1A5 | 1105 | 0.3 | 0.51 | YES |
19 | CYP3A43 | CYP3A43 | CYP3A43 | 1123 | 0.3 | 0.53 | YES |
20 | HSD11B2 | HSD11B2 | HSD11B2 | 1159 | 0.29 | 0.54 | YES |
21 | SULT1E1 | SULT1E1 | SULT1E1 | 1191 | 0.29 | 0.56 | YES |
22 | UGT1A10 | UGT1A10 | UGT1A10 | 1438 | 0.26 | 0.57 | YES |
23 | AKR1C1 | AKR1C1 | AKR1C1 | 1475 | 0.26 | 0.58 | YES |
24 | SRD5A2 | SRD5A2 | SRD5A2 | 1499 | 0.25 | 0.6 | YES |
25 | UGT2B4 | UGT2B4 | UGT2B4 | 1597 | 0.24 | 0.61 | YES |
26 | UGT1A8 | UGT1A8 | UGT1A8 | 1917 | 0.21 | 0.61 | YES |
27 | COMT | COMT | COMT | 2052 | 0.2 | 0.61 | YES |
28 | HSD3B1 | HSD3B1 | HSD3B1 | 2163 | 0.2 | 0.62 | YES |
29 | AKR1D1 | AKR1D1 | AKR1D1 | 2249 | 0.19 | 0.63 | YES |
30 | AKR1C4 | AKR1C4 | AKR1C4 | 2512 | 0.17 | 0.63 | NO |
31 | HSD17B7 | HSD17B7 | HSD17B7 | 2801 | 0.16 | 0.62 | NO |
32 | STS | STS | STS | 3160 | 0.14 | 0.61 | NO |
33 | HSD3B2 | HSD3B2 | HSD3B2 | 4411 | 0.091 | 0.55 | NO |
34 | SRD5A3 | SRD5A3 | SRD5A3 | 5544 | 0.061 | 0.49 | NO |
35 | HSD17B8 | HSD17B8 | HSD17B8 | 6153 | 0.047 | 0.46 | NO |
36 | UGT1A7 | UGT1A7 | UGT1A7 | 6763 | 0.035 | 0.43 | NO |
37 | UGT2A1 | UGT2A1 | UGT2A1 | 7310 | 0.025 | 0.4 | NO |
38 | HSD17B1 | HSD17B1 | HSD17B1 | 7396 | 0.023 | 0.4 | NO |
39 | CYP11A1 | CYP11A1 | CYP11A1 | 8956 | -0.0049 | 0.31 | NO |
40 | CYP7A1 | CYP7A1 | CYP7A1 | 9287 | -0.011 | 0.3 | NO |
41 | CYP17A1 | CYP17A1 | CYP17A1 | 12075 | -0.069 | 0.15 | NO |
42 | HSD17B12 | HSD17B12 | HSD17B12 | 12735 | -0.088 | 0.12 | NO |
43 | HSD17B3 | HSD17B3 | HSD17B3 | 14109 | -0.15 | 0.051 | NO |
44 | CYP21A2 | CYP21A2 | CYP21A2 | 15696 | -0.26 | -0.019 | NO |
45 | SRD5A1 | SRD5A1 | SRD5A1 | 15753 | -0.26 | -0.0039 | NO |
46 | SULT2B1 | SULT2B1 | SULT2B1 | 15873 | -0.27 | 0.0085 | NO |
47 | CYP7B1 | CYP7B1 | CYP7B1 | 16154 | -0.3 | 0.014 | NO |
48 | CYP19A1 | CYP19A1 | CYP19A1 | 16281 | -0.31 | 0.029 | NO |
49 | CYP1B1 | CYP1B1 | CYP1B1 | 16545 | -0.34 | 0.038 | NO |
50 | HSD11B1 | HSD11B1 | HSD11B1 | 16812 | -0.38 | 0.05 | NO |
51 | HSD17B6 | HSD17B6 | HSD17B6 | 16847 | -0.38 | 0.074 | NO |
Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TYROSINE METABOLISM.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_TYROSINE_METABOLISM.heatmap_plot.clus2.18.png)
Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TYROSINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_STEROID_HORMONE_BIOSYNTHESIS.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 | UGT1A1 | UGT1A1 | UGT1A1 | 63 | 0.69 | 0.061 | YES |
2 | UGT2B28 | UGT2B28 | UGT2B28 | 101 | 0.62 | 0.12 | YES |
3 | UGT1A9 | UGT1A9 | UGT1A9 | 228 | 0.53 | 0.16 | YES |
4 | UGT2B15 | UGT2B15 | UGT2B15 | 292 | 0.49 | 0.2 | YES |
5 | UGT1A6 | UGT1A6 | UGT1A6 | 328 | 0.47 | 0.24 | YES |
6 | UGT2B11 | UGT2B11 | UGT2B11 | 386 | 0.45 | 0.28 | YES |
7 | UGT1A3 | UGT1A3 | UGT1A3 | 484 | 0.42 | 0.32 | YES |
8 | UGT2B7 | UGT2B7 | UGT2B7 | 650 | 0.38 | 0.34 | YES |
9 | AMY2B | AMY2B | AMY2B | 832 | 0.34 | 0.36 | YES |
10 | UGT1A4 | UGT1A4 | UGT1A4 | 871 | 0.34 | 0.39 | YES |
11 | UGT2A3 | UGT2A3 | UGT2A3 | 899 | 0.33 | 0.42 | YES |
12 | UGT2B10 | UGT2B10 | UGT2B10 | 923 | 0.33 | 0.45 | YES |
13 | UGT1A5 | UGT1A5 | UGT1A5 | 1105 | 0.3 | 0.47 | YES |
14 | G6PC | G6PC | G6PC | 1218 | 0.28 | 0.49 | YES |
15 | TREH | TREH | TREH | 1226 | 0.28 | 0.52 | YES |
16 | UGT1A10 | UGT1A10 | UGT1A10 | 1438 | 0.26 | 0.53 | YES |
17 | UGT2B4 | UGT2B4 | UGT2B4 | 1597 | 0.24 | 0.54 | YES |
18 | UGT1A8 | UGT1A8 | UGT1A8 | 1917 | 0.21 | 0.54 | YES |
19 | AMY2A | AMY2A | AMY2A | 2327 | 0.18 | 0.54 | YES |
20 | GYS2 | GYS2 | GYS2 | 2400 | 0.18 | 0.55 | YES |
21 | AGL | AGL | AGL | 5292 | 0.067 | 0.4 | NO |
22 | PGM2 | PGM2 | PGM2 | 6183 | 0.046 | 0.35 | NO |
23 | GYS1 | GYS1 | GYS1 | 6347 | 0.043 | 0.35 | NO |
24 | UGT1A7 | UGT1A7 | UGT1A7 | 6763 | 0.035 | 0.33 | NO |
25 | HK2 | HK2 | HK2 | 6836 | 0.034 | 0.33 | NO |
26 | GBA3 | GBA3 | GBA3 | 6838 | 0.034 | 0.33 | NO |
27 | UGT2A1 | UGT2A1 | UGT2A1 | 7310 | 0.025 | 0.31 | NO |
28 | UGDH | UGDH | UGDH | 8023 | 0.012 | 0.27 | NO |
29 | GUSB | GUSB | GUSB | 8231 | 0.0079 | 0.26 | NO |
30 | GAA | GAA | GAA | 9685 | -0.018 | 0.18 | NO |
31 | GPI | GPI | GPI | 10095 | -0.025 | 0.16 | NO |
32 | GCK | GCK | GCK | 10971 | -0.043 | 0.12 | NO |
33 | AMY1A | AMY1A | AMY1A | 11269 | -0.05 | 0.1 | NO |
34 | HK1 | HK1 | HK1 | 11431 | -0.053 | 0.1 | NO |
35 | UGP2 | UGP2 | UGP2 | 12190 | -0.072 | 0.065 | NO |
36 | GANC | GANC | GANC | 12690 | -0.086 | 0.046 | NO |
37 | MGAM | MGAM | MGAM | 13566 | -0.12 | 0.0084 | NO |
38 | PYGL | PYGL | PYGL | 13898 | -0.13 | 0.0026 | NO |
39 | PYGM | PYGM | PYGM | 14055 | -0.14 | 0.0072 | NO |
40 | GBE1 | GBE1 | GBE1 | 14131 | -0.15 | 0.017 | NO |
41 | PYGB | PYGB | PYGB | 14462 | -0.16 | 0.014 | NO |
42 | PGM1 | PGM1 | PGM1 | 15840 | -0.27 | -0.037 | NO |
43 | ENPP3 | ENPP3 | ENPP3 | 16187 | -0.3 | -0.028 | NO |
44 | PGM2L1 | PGM2L1 | PGM2L1 | 16333 | -0.32 | -0.006 | NO |
45 | ENPP1 | ENPP1 | ENPP1 | 16945 | -0.4 | -0.0028 | NO |
46 | HK3 | HK3 | HK3 | 18159 | -0.77 | 0.0021 | NO |
Figure S33. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLUTATHIONE METABOLISM.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_GLUTATHIONE_METABOLISM.heatmap_plot.clus2.16.png)
Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLUTATHIONE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_STARCH_AND_SUCROSE_METABOLISM.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 | UGT1A1 | UGT1A1 | UGT1A1 | 63 | 0.69 | 0.057 | YES |
2 | UGT2B28 | UGT2B28 | UGT2B28 | 101 | 0.62 | 0.11 | YES |
3 | CYP3A5 | CYP3A5 | CYP3A5 | 103 | 0.62 | 0.16 | YES |
4 | UGT1A9 | UGT1A9 | UGT1A9 | 228 | 0.53 | 0.2 | YES |
5 | UGT2B15 | UGT2B15 | UGT2B15 | 292 | 0.49 | 0.24 | YES |
6 | UGT1A6 | UGT1A6 | UGT1A6 | 328 | 0.47 | 0.28 | YES |
7 | UGT2B11 | UGT2B11 | UGT2B11 | 386 | 0.45 | 0.32 | YES |
8 | UGT1A3 | UGT1A3 | UGT1A3 | 484 | 0.42 | 0.35 | YES |
9 | UGT2B7 | UGT2B7 | UGT2B7 | 650 | 0.38 | 0.38 | YES |
10 | CYP3A7 | CYP3A7 | CYP3A7 | 732 | 0.36 | 0.4 | YES |
11 | UGT1A4 | UGT1A4 | UGT1A4 | 871 | 0.34 | 0.42 | YES |
12 | UGT2A3 | UGT2A3 | UGT2A3 | 899 | 0.33 | 0.45 | YES |
13 | UGT2B10 | UGT2B10 | UGT2B10 | 923 | 0.33 | 0.48 | YES |
14 | UGT1A5 | UGT1A5 | UGT1A5 | 1105 | 0.3 | 0.5 | YES |
15 | CYP3A43 | CYP3A43 | CYP3A43 | 1123 | 0.3 | 0.52 | YES |
16 | UGT1A10 | UGT1A10 | UGT1A10 | 1438 | 0.26 | 0.53 | YES |
17 | UGT2B4 | UGT2B4 | UGT2B4 | 1597 | 0.24 | 0.54 | YES |
18 | UGT1A8 | UGT1A8 | UGT1A8 | 1917 | 0.21 | 0.54 | YES |
19 | NAT1 | NAT1 | NAT1 | 2347 | 0.18 | 0.53 | NO |
20 | UPP2 | UPP2 | UPP2 | 4408 | 0.091 | 0.43 | NO |
21 | UCKL1 | UCKL1 | UCKL1 | 5095 | 0.072 | 0.39 | NO |
22 | NAT2 | NAT2 | NAT2 | 6093 | 0.048 | 0.34 | NO |
23 | UGT1A7 | UGT1A7 | UGT1A7 | 6763 | 0.035 | 0.31 | NO |
24 | UGT2A1 | UGT2A1 | UGT2A1 | 7310 | 0.025 | 0.28 | NO |
25 | IMPDH2 | IMPDH2 | IMPDH2 | 7598 | 0.02 | 0.27 | NO |
26 | ITPA | ITPA | ITPA | 8157 | 0.0092 | 0.24 | NO |
27 | GUSB | GUSB | GUSB | 8231 | 0.0079 | 0.24 | NO |
28 | CYP2A6 | CYP2A6 | CYP2A6 | 8619 | 0.00096 | 0.21 | NO |
29 | TK2 | TK2 | TK2 | 9381 | -0.012 | 0.17 | NO |
30 | UMPS | UMPS | UMPS | 9409 | -0.013 | 0.17 | NO |
31 | TPMT | TPMT | TPMT | 10558 | -0.034 | 0.11 | NO |
32 | UCK1 | UCK1 | UCK1 | 11295 | -0.05 | 0.076 | NO |
33 | UPB1 | UPB1 | UPB1 | 11850 | -0.063 | 0.051 | NO |
34 | CES2 | CES2 | CES2 | 11870 | -0.064 | 0.055 | NO |
35 | HPRT1 | HPRT1 | HPRT1 | 12298 | -0.075 | 0.038 | NO |
36 | UCK2 | UCK2 | UCK2 | 12446 | -0.079 | 0.037 | NO |
37 | XDH | XDH | XDH | 13344 | -0.11 | -0.0026 | NO |
38 | UPP1 | UPP1 | UPP1 | 13809 | -0.13 | -0.017 | NO |
39 | GMPS | GMPS | GMPS | 13959 | -0.14 | -0.013 | NO |
40 | TK1 | TK1 | TK1 | 14077 | -0.14 | -0.0068 | NO |
41 | IMPDH1 | IMPDH1 | IMPDH1 | 15010 | -0.2 | -0.041 | NO |
42 | DPYS | DPYS | DPYS | 15760 | -0.26 | -0.059 | NO |
43 | CES1 | CES1 | CES1 | 16818 | -0.38 | -0.084 | NO |
44 | TYMP | TYMP | TYMP | 17638 | -0.53 | -0.083 | NO |
45 | CDA | CDA | CDA | 17903 | -0.61 | -0.043 | NO |
46 | DPYD | DPYD | DPYD | 18053 | -0.68 | 0.0079 | NO |
Figure S35. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG STARCH AND SUCROSE METABOLISM.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_STARCH_AND_SUCROSE_METABOLISM.heatmap_plot.clus2.7.png)
Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STARCH AND SUCROSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_DRUG_METABOLISM_OTHER_ENZYMES.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 | SLC27A2 | SLC27A2 | SLC27A2 | 419 | 0.44 | 0.023 | YES |
2 | ACSL5 | ACSL5 | ACSL5 | 682 | 0.37 | 0.047 | YES |
3 | CROT | CROT | CROT | 783 | 0.35 | 0.078 | YES |
4 | PEX11G | PEX11G | PEX11G | 946 | 0.32 | 0.1 | YES |
5 | AMACR | AMACR | AMACR | 1101 | 0.3 | 0.13 | YES |
6 | IDH1 | IDH1 | IDH1 | 1156 | 0.29 | 0.15 | YES |
7 | PEX11A | PEX11A | PEX11A | 1310 | 0.27 | 0.17 | YES |
8 | ACOX1 | ACOX1 | ACOX1 | 1316 | 0.27 | 0.2 | YES |
9 | ABCD3 | ABCD3 | ABCD3 | 1588 | 0.24 | 0.21 | YES |
10 | BAAT | BAAT | BAAT | 1614 | 0.24 | 0.24 | YES |
11 | ACAA1 | ACAA1 | ACAA1 | 1659 | 0.24 | 0.26 | YES |
12 | NUDT12 | NUDT12 | NUDT12 | 2068 | 0.2 | 0.26 | YES |
13 | DECR2 | DECR2 | DECR2 | 2641 | 0.16 | 0.24 | YES |
14 | FAR2 | FAR2 | FAR2 | 2689 | 0.16 | 0.26 | YES |
15 | PHYH | PHYH | PHYH | 2854 | 0.15 | 0.26 | YES |
16 | ACOX3 | ACOX3 | ACOX3 | 2917 | 0.15 | 0.27 | YES |
17 | AGXT | AGXT | AGXT | 3008 | 0.14 | 0.28 | YES |
18 | MVK | MVK | MVK | 3014 | 0.14 | 0.3 | YES |
19 | ACSL1 | ACSL1 | ACSL1 | 3278 | 0.13 | 0.3 | YES |
20 | HSD17B4 | HSD17B4 | HSD17B4 | 3424 | 0.12 | 0.3 | YES |
21 | HMGCL | HMGCL | HMGCL | 3475 | 0.12 | 0.31 | YES |
22 | PEX7 | PEX7 | PEX7 | 3559 | 0.12 | 0.32 | YES |
23 | CAT | CAT | CAT | 3959 | 0.11 | 0.31 | YES |
24 | PEX13 | PEX13 | PEX13 | 4175 | 0.098 | 0.31 | YES |
25 | PEX19 | PEX19 | PEX19 | 4266 | 0.096 | 0.31 | YES |
26 | SCP2 | SCP2 | SCP2 | 4355 | 0.092 | 0.32 | YES |
27 | NUDT19 | NUDT19 | NUDT19 | 4416 | 0.091 | 0.32 | YES |
28 | PXMP4 | PXMP4 | PXMP4 | 4418 | 0.09 | 0.33 | YES |
29 | EPHX2 | EPHX2 | EPHX2 | 4528 | 0.087 | 0.34 | YES |
30 | PEX1 | PEX1 | PEX1 | 4599 | 0.084 | 0.34 | YES |
31 | PEX2 | PEX2 | PEX2 | 4630 | 0.083 | 0.35 | YES |
32 | HAO2 | HAO2 | HAO2 | 4775 | 0.08 | 0.35 | YES |
33 | MLYCD | MLYCD | MLYCD | 4813 | 0.078 | 0.35 | YES |
34 | MPV17L | MPV17L | MPV17L | 4874 | 0.077 | 0.36 | YES |
35 | PEX14 | PEX14 | PEX14 | 4902 | 0.076 | 0.36 | YES |
36 | PAOX | PAOX | PAOX | 5031 | 0.073 | 0.37 | YES |
37 | PEX10 | PEX10 | PEX10 | 5097 | 0.071 | 0.37 | YES |
38 | GSTK1 | GSTK1 | GSTK1 | 5580 | 0.06 | 0.35 | NO |
39 | PEX12 | PEX12 | PEX12 | 5615 | 0.059 | 0.35 | NO |
40 | ECH1 | ECH1 | ECH1 | 5632 | 0.059 | 0.36 | NO |
41 | CRAT | CRAT | CRAT | 5727 | 0.056 | 0.36 | NO |
42 | FAR1 | FAR1 | FAR1 | 5732 | 0.056 | 0.36 | NO |
43 | ACOT8 | ACOT8 | ACOT8 | 5862 | 0.053 | 0.36 | NO |
44 | PRDX5 | PRDX5 | PRDX5 | 6018 | 0.05 | 0.36 | NO |
45 | PMVK | PMVK | PMVK | 6265 | 0.045 | 0.35 | NO |
46 | PEX6 | PEX6 | PEX6 | 6295 | 0.044 | 0.35 | NO |
47 | MPV17 | MPV17 | MPV17 | 6508 | 0.04 | 0.35 | NO |
48 | ABCD4 | ABCD4 | ABCD4 | 6692 | 0.037 | 0.34 | NO |
49 | SOD1 | SOD1 | SOD1 | 6786 | 0.035 | 0.34 | NO |
50 | EHHADH | EHHADH | EHHADH | 6951 | 0.032 | 0.33 | NO |
51 | PEX11B | PEX11B | PEX11B | 7442 | 0.022 | 0.31 | NO |
52 | SLC25A17 | SLC25A17 | SLC25A17 | 7602 | 0.019 | 0.3 | NO |
53 | HACL1 | HACL1 | HACL1 | 7957 | 0.013 | 0.28 | NO |
54 | PEX16 | PEX16 | PEX16 | 8184 | 0.0086 | 0.27 | NO |
55 | ABCD1 | ABCD1 | ABCD1 | 8405 | 0.0048 | 0.26 | NO |
56 | ACSL3 | ACSL3 | ACSL3 | 8878 | -0.0038 | 0.24 | NO |
57 | IDH2 | IDH2 | IDH2 | 9441 | -0.013 | 0.2 | NO |
58 | GNPAT | GNPAT | GNPAT | 9911 | -0.022 | 0.18 | NO |
59 | ACSL4 | ACSL4 | ACSL4 | 10149 | -0.026 | 0.17 | NO |
60 | DHRS4 | DHRS4 | DHRS4 | 10413 | -0.031 | 0.16 | NO |
61 | PEX5 | PEX5 | PEX5 | 10483 | -0.032 | 0.16 | NO |
62 | PRDX1 | PRDX1 | PRDX1 | 10614 | -0.035 | 0.16 | NO |
63 | PEX26 | PEX26 | PEX26 | 11622 | -0.057 | 0.11 | NO |
64 | DAO | DAO | DAO | 12330 | -0.076 | 0.075 | NO |
65 | PEX3 | PEX3 | PEX3 | 12596 | -0.084 | 0.069 | NO |
66 | DDO | DDO | DDO | 12774 | -0.089 | 0.069 | NO |
67 | NOS2 | NOS2 | NOS2 | 12880 | -0.093 | 0.072 | NO |
68 | AGPS | AGPS | AGPS | 13268 | -0.11 | 0.062 | NO |
69 | XDH | XDH | XDH | 13344 | -0.11 | 0.069 | NO |
70 | PXMP2 | PXMP2 | PXMP2 | 14636 | -0.18 | 0.016 | NO |
71 | PECI | PECI | PECI | 14986 | -0.2 | 0.018 | NO |
72 | PECR | PECR | PECR | 15278 | -0.22 | 0.025 | NO |
73 | ACSL6 | ACSL6 | ACSL6 | 15437 | -0.24 | 0.041 | NO |
74 | SOD2 | SOD2 | SOD2 | 15714 | -0.26 | 0.052 | NO |
75 | PIPOX | PIPOX | PIPOX | 16654 | -0.36 | 0.038 | NO |
76 | ABCD2 | ABCD2 | ABCD2 | 17292 | -0.46 | 0.05 | NO |
Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_GLYCEROPHOSPHOLIPID_METABOLISM.heatmap_plot.clus2.19.png)
Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_PEROXISOME.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 | ADH6 | ADH6 | ADH6 | 216 | 0.54 | 0.077 | YES |
2 | ACSL5 | ACSL5 | ACSL5 | 682 | 0.37 | 0.11 | YES |
3 | CYP4A11 | CYP4A11 | CYP4A11 | 816 | 0.35 | 0.16 | YES |
4 | ACADSB | ACADSB | ACADSB | 1086 | 0.3 | 0.2 | YES |
5 | ADH1C | ADH1C | ADH1C | 1174 | 0.29 | 0.24 | YES |
6 | CYP4A22 | CYP4A22 | CYP4A22 | 1602 | 0.24 | 0.26 | YES |
7 | ACAA1 | ACAA1 | ACAA1 | 1659 | 0.24 | 0.29 | YES |
8 | CPT1B | CPT1B | CPT1B | 1712 | 0.23 | 0.33 | YES |
9 | ADH4 | ADH4 | ADH4 | 1713 | 0.23 | 0.37 | YES |
10 | ACADL | ACADL | ACADL | 2376 | 0.18 | 0.36 | YES |
11 | ACOX3 | ACOX3 | ACOX3 | 2917 | 0.15 | 0.36 | YES |
12 | HADH | HADH | HADH | 2978 | 0.15 | 0.38 | YES |
13 | ACSL1 | ACSL1 | ACSL1 | 3278 | 0.13 | 0.38 | YES |
14 | DCI | DCI | DCI | 3641 | 0.12 | 0.38 | YES |
15 | ADH1A | ADH1A | ADH1A | 3706 | 0.11 | 0.4 | YES |
16 | ACADVL | ACADVL | ACADVL | 3850 | 0.11 | 0.41 | YES |
17 | ACADS | ACADS | ACADS | 3968 | 0.1 | 0.42 | YES |
18 | ECHS1 | ECHS1 | ECHS1 | 4174 | 0.098 | 0.42 | YES |
19 | HADHB | HADHB | HADHB | 4409 | 0.091 | 0.42 | YES |
20 | GCDH | GCDH | GCDH | 5406 | 0.064 | 0.38 | NO |
21 | CPT2 | CPT2 | CPT2 | 5657 | 0.058 | 0.38 | NO |
22 | ACADM | ACADM | ACADM | 6011 | 0.05 | 0.36 | NO |
23 | ADH7 | ADH7 | ADH7 | 6742 | 0.036 | 0.33 | NO |
24 | EHHADH | EHHADH | EHHADH | 6951 | 0.032 | 0.32 | NO |
25 | ADH5 | ADH5 | ADH5 | 7534 | 0.021 | 0.3 | NO |
26 | ACAT2 | ACAT2 | ACAT2 | 7612 | 0.019 | 0.3 | NO |
27 | HADHA | HADHA | HADHA | 8445 | 0.0041 | 0.25 | NO |
28 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 8452 | 0.0038 | 0.25 | NO |
29 | ADH1B | ADH1B | ADH1B | 8596 | 0.0015 | 0.24 | NO |
30 | ACSL3 | ACSL3 | ACSL3 | 8878 | -0.0038 | 0.23 | NO |
31 | CPT1A | CPT1A | CPT1A | 9865 | -0.02 | 0.18 | NO |
32 | ACSL4 | ACSL4 | ACSL4 | 10149 | -0.026 | 0.16 | NO |
33 | ACAA2 | ACAA2 | ACAA2 | 12662 | -0.086 | 0.041 | NO |
34 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 13256 | -0.11 | 0.026 | NO |
35 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 13591 | -0.12 | 0.027 | NO |
36 | CPT1C | CPT1C | CPT1C | 14087 | -0.14 | 0.024 | NO |
37 | PECI | PECI | PECI | 14986 | -0.2 | 0.0075 | NO |
38 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 15220 | -0.22 | 0.031 | NO |
39 | ACAT1 | ACAT1 | ACAT1 | 15414 | -0.23 | 0.059 | NO |
40 | ACSL6 | ACSL6 | ACSL6 | 15437 | -0.24 | 0.097 | NO |
41 | ALDH2 | ALDH2 | ALDH2 | 16477 | -0.34 | 0.095 | NO |
Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ETHER LIPID METABOLISM.
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_ETHER_LIPID_METABOLISM.heatmap_plot.clus2.14.png)
Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ETHER LIPID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus2___Class2-CanonicalPathway.KEGG_FATTY_ACID_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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
BIOCARTA G1 PATHWAY | 27 | genes.ES.table | 0.58 | 1.7 | 0.0096 | 0.17 | 0.44 | 0.41 | 0.19 | 0.33 | 0 | 0.031 |
BIOCARTA EGF PATHWAY | 30 | genes.ES.table | 0.49 | 1.5 | 0.084 | 0.29 | 0.85 | 0.3 | 0.16 | 0.25 | 0.19 | 0.037 |
BIOCARTA FAS PATHWAY | 29 | genes.ES.table | 0.49 | 1.6 | 0.062 | 0.23 | 0.68 | 0.45 | 0.21 | 0.36 | 0.13 | 0.035 |
BIOCARTA RACCYCD PATHWAY | 25 | genes.ES.table | 0.49 | 1.8 | 0.019 | 0.52 | 0.25 | 0.32 | 0.2 | 0.26 | 0 | 0.17 |
BIOCARTA MAPK PATHWAY | 86 | genes.ES.table | 0.35 | 1.6 | 0.046 | 0.23 | 0.76 | 0.37 | 0.23 | 0.29 | 0.14 | 0.029 |
BIOCARTA P38MAPK PATHWAY | 39 | genes.ES.table | 0.47 | 1.6 | 0.029 | 0.22 | 0.69 | 0.64 | 0.33 | 0.43 | 0.13 | 0.029 |
BIOCARTA IL1R PATHWAY | 32 | genes.ES.table | 0.57 | 1.6 | 0.045 | 0.24 | 0.76 | 0.53 | 0.2 | 0.43 | 0.15 | 0.034 |
BIOCARTA TNFR1 PATHWAY | 28 | genes.ES.table | 0.47 | 1.7 | 0.026 | 0.15 | 0.46 | 0.43 | 0.21 | 0.34 | 0 | 0.022 |
KEGG PYRIMIDINE METABOLISM | 96 | genes.ES.table | 0.4 | 1.8 | 0.0057 | 0.17 | 0.35 | 0.3 | 0.2 | 0.24 | 0 | 0.036 |
KEGG AMINOACYL TRNA BIOSYNTHESIS | 40 | genes.ES.table | 0.45 | 1.8 | 0.039 | 0.15 | 0.36 | 0.57 | 0.35 | 0.38 | 0 | 0.032 |
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 | CDK6 | CDK6 | CDK6 | 104 | 0.59 | 0.3 | YES |
2 | TFDP1 | TFDP1 | TFDP1 | 2831 | 0.11 | 0.21 | YES |
3 | HRAS | HRAS | HRAS | 2833 | 0.11 | 0.27 | YES |
4 | PIK3CA | PIK3CA | PIK3CA | 2896 | 0.11 | 0.32 | YES |
5 | PAK1 | PAK1 | PAK1 | 3075 | 0.1 | 0.36 | YES |
6 | CDKN1A | CDKN1A | CDKN1A | 3142 | 0.1 | 0.41 | YES |
7 | NFKB1 | NFKB1 | NFKB1 | 3262 | 0.096 | 0.46 | YES |
8 | CHUK | CHUK | CHUK | 3546 | 0.087 | 0.49 | YES |
9 | MAPK1 | MAPK1 | MAPK1 | 4964 | 0.053 | 0.44 | NO |
10 | IKBKG | IKBKG | IKBKG | 5015 | 0.052 | 0.46 | NO |
11 | RAC1 | RAC1 | RAC1 | 5759 | 0.038 | 0.44 | NO |
12 | RB1 | RB1 | RB1 | 6335 | 0.027 | 0.42 | NO |
13 | CDK4 | CDK4 | CDK4 | 6378 | 0.026 | 0.43 | NO |
14 | CCND1 | CCND1 | CCND1 | 7008 | 0.016 | 0.41 | NO |
15 | AKT1 | AKT1 | AKT1 | 7737 | 0.0045 | 0.37 | NO |
16 | CDK2 | CDK2 | CDK2 | 8228 | -0.0032 | 0.34 | NO |
17 | RHOA | RHOA | RHOA | 8234 | -0.0033 | 0.35 | NO |
18 | NFKBIA | NFKBIA | NFKBIA | 8271 | -0.004 | 0.35 | NO |
19 | RELA | RELA | RELA | 8584 | -0.009 | 0.33 | NO |
20 | MAPK3 | MAPK3 | MAPK3 | 8962 | -0.015 | 0.32 | NO |
21 | CDKN1B | CDKN1B | CDKN1B | 10608 | -0.044 | 0.25 | NO |
22 | CCNE1 | CCNE1 | CCNE1 | 10902 | -0.05 | 0.26 | NO |
23 | PIK3R1 | PIK3R1 | PIK3R1 | 11962 | -0.073 | 0.24 | NO |
24 | RAF1 | RAF1 | RAF1 | 11996 | -0.074 | 0.28 | NO |
25 | IKBKB | IKBKB | IKBKB | 13436 | -0.12 | 0.26 | 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: BIOCARTA G1 PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_G1_PATHWAY.heatmap_plot.clus3.7.png)
Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_RACCYCD_PATHWAY.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 | CDK6 | CDK6 | CDK6 | 104 | 0.59 | 0.041 | YES |
2 | MYC | MYC | MYC | 327 | 0.4 | 0.061 | YES |
3 | SFN | SFN | SFN | 377 | 0.38 | 0.088 | YES |
4 | ORC1L | ORC1L | ORC1L | 539 | 0.33 | 0.11 | YES |
5 | CCNA1 | CCNA1 | CCNA1 | 558 | 0.32 | 0.13 | YES |
6 | CDC25B | CDC25B | CDC25B | 674 | 0.3 | 0.15 | YES |
7 | CCNE2 | CCNE2 | CCNE2 | 713 | 0.29 | 0.17 | YES |
8 | PTTG1 | PTTG1 | PTTG1 | 927 | 0.25 | 0.18 | YES |
9 | TGFB2 | TGFB2 | TGFB2 | 931 | 0.25 | 0.2 | YES |
10 | PKMYT1 | PKMYT1 | PKMYT1 | 945 | 0.25 | 0.22 | YES |
11 | CCNA2 | CCNA2 | CCNA2 | 995 | 0.24 | 0.23 | YES |
12 | PLK1 | PLK1 | PLK1 | 1041 | 0.24 | 0.25 | YES |
13 | E2F2 | E2F2 | E2F2 | 1139 | 0.23 | 0.26 | YES |
14 | CCNB1 | CCNB1 | CCNB1 | 1216 | 0.22 | 0.28 | YES |
15 | MAD2L1 | MAD2L1 | MAD2L1 | 1231 | 0.22 | 0.29 | YES |
16 | CDC20 | CDC20 | CDC20 | 1260 | 0.21 | 0.31 | YES |
17 | TTK | TTK | TTK | 1379 | 0.2 | 0.32 | YES |
18 | CCNB2 | CCNB2 | CCNB2 | 1393 | 0.2 | 0.33 | YES |
19 | BUB1B | BUB1B | BUB1B | 1482 | 0.19 | 0.34 | YES |
20 | RBL1 | RBL1 | RBL1 | 1556 | 0.18 | 0.35 | YES |
21 | CDC45 | CDC45 | CDC45 | 1775 | 0.17 | 0.35 | YES |
22 | MCM4 | MCM4 | MCM4 | 1997 | 0.15 | 0.35 | YES |
23 | CDK1 | CDK1 | CDK1 | 2000 | 0.15 | 0.37 | YES |
24 | BUB1 | BUB1 | BUB1 | 2134 | 0.15 | 0.37 | YES |
25 | CHEK1 | CHEK1 | CHEK1 | 2170 | 0.14 | 0.38 | YES |
26 | MCM2 | MCM2 | MCM2 | 2295 | 0.14 | 0.38 | YES |
27 | CDC25C | CDC25C | CDC25C | 2297 | 0.14 | 0.4 | YES |
28 | YWHAQ | YWHAQ | YWHAQ | 2538 | 0.12 | 0.39 | YES |
29 | PRKDC | PRKDC | PRKDC | 2587 | 0.12 | 0.4 | YES |
30 | TGFB1 | TGFB1 | TGFB1 | 2610 | 0.12 | 0.41 | YES |
31 | STAG1 | STAG1 | STAG1 | 2740 | 0.12 | 0.41 | YES |
32 | MCM6 | MCM6 | MCM6 | 2777 | 0.12 | 0.42 | YES |
33 | TFDP1 | TFDP1 | TFDP1 | 2831 | 0.11 | 0.42 | YES |
34 | ESPL1 | ESPL1 | ESPL1 | 3005 | 0.11 | 0.42 | YES |
35 | CDC7 | CDC7 | CDC7 | 3054 | 0.1 | 0.43 | YES |
36 | YWHAG | YWHAG | YWHAG | 3140 | 0.1 | 0.43 | YES |
37 | CDKN1A | CDKN1A | CDKN1A | 3142 | 0.1 | 0.44 | YES |
38 | TGFB3 | TGFB3 | TGFB3 | 3207 | 0.098 | 0.44 | YES |
39 | SMC3 | SMC3 | SMC3 | 3208 | 0.098 | 0.45 | YES |
40 | CDC25A | CDC25A | CDC25A | 3216 | 0.098 | 0.46 | YES |
41 | SMC1A | SMC1A | SMC1A | 3275 | 0.096 | 0.46 | YES |
42 | CDKN2B | CDKN2B | CDKN2B | 3341 | 0.093 | 0.47 | YES |
43 | GADD45A | GADD45A | GADD45A | 3364 | 0.092 | 0.47 | YES |
44 | SKP2 | SKP2 | SKP2 | 3391 | 0.092 | 0.48 | YES |
45 | ANAPC10 | ANAPC10 | ANAPC10 | 3575 | 0.086 | 0.48 | YES |
46 | CDK7 | CDK7 | CDK7 | 3585 | 0.086 | 0.48 | YES |
47 | CDC6 | CDC6 | CDC6 | 3604 | 0.085 | 0.49 | YES |
48 | ORC5L | ORC5L | ORC5L | 3636 | 0.084 | 0.49 | YES |
49 | MAD2L2 | MAD2L2 | MAD2L2 | 3670 | 0.083 | 0.5 | YES |
50 | ORC6L | ORC6L | ORC6L | 3732 | 0.082 | 0.5 | YES |
51 | ANAPC1 | ANAPC1 | ANAPC1 | 3980 | 0.075 | 0.49 | YES |
52 | PCNA | PCNA | PCNA | 4013 | 0.074 | 0.5 | YES |
53 | CDC27 | CDC27 | CDC27 | 4091 | 0.072 | 0.5 | YES |
54 | YWHAH | YWHAH | YWHAH | 4152 | 0.071 | 0.5 | YES |
55 | STAG2 | STAG2 | STAG2 | 4272 | 0.068 | 0.5 | YES |
56 | CDKN2A | CDKN2A | CDKN2A | 4414 | 0.064 | 0.5 | YES |
57 | ORC2L | ORC2L | ORC2L | 4497 | 0.062 | 0.5 | YES |
58 | CDC23 | CDC23 | CDC23 | 4606 | 0.06 | 0.5 | YES |
59 | MCM5 | MCM5 | MCM5 | 4627 | 0.059 | 0.5 | YES |
60 | TFDP2 | TFDP2 | TFDP2 | 4650 | 0.059 | 0.5 | YES |
61 | YWHAZ | YWHAZ | YWHAZ | 4990 | 0.052 | 0.49 | NO |
62 | RAD21 | RAD21 | RAD21 | 5239 | 0.047 | 0.48 | NO |
63 | MCM7 | MCM7 | MCM7 | 5264 | 0.046 | 0.48 | NO |
64 | ATR | ATR | ATR | 5524 | 0.042 | 0.47 | NO |
65 | ORC3L | ORC3L | ORC3L | 5796 | 0.037 | 0.46 | NO |
66 | BUB3 | BUB3 | BUB3 | 5843 | 0.036 | 0.46 | NO |
67 | CDKN2D | CDKN2D | CDKN2D | 5861 | 0.035 | 0.46 | NO |
68 | GSK3B | GSK3B | GSK3B | 5885 | 0.035 | 0.46 | NO |
69 | E2F1 | E2F1 | E2F1 | 5923 | 0.034 | 0.46 | NO |
70 | CUL1 | CUL1 | CUL1 | 5958 | 0.034 | 0.46 | NO |
71 | CDC26 | CDC26 | CDC26 | 6044 | 0.032 | 0.46 | NO |
72 | CDKN2C | CDKN2C | CDKN2C | 6086 | 0.032 | 0.46 | NO |
73 | CCND3 | CCND3 | CCND3 | 6179 | 0.03 | 0.46 | NO |
74 | RB1 | RB1 | RB1 | 6335 | 0.027 | 0.45 | NO |
75 | CDK4 | CDK4 | CDK4 | 6378 | 0.026 | 0.45 | NO |
76 | ORC4L | ORC4L | ORC4L | 6380 | 0.026 | 0.45 | NO |
77 | SMAD2 | SMAD2 | SMAD2 | 6912 | 0.018 | 0.42 | NO |
78 | ABL1 | ABL1 | ABL1 | 6917 | 0.017 | 0.43 | NO |
79 | CCND1 | CCND1 | CCND1 | 7008 | 0.016 | 0.42 | NO |
80 | E2F4 | E2F4 | E2F4 | 7080 | 0.015 | 0.42 | NO |
81 | YWHAE | YWHAE | YWHAE | 7193 | 0.013 | 0.42 | NO |
82 | FZR1 | FZR1 | FZR1 | 7236 | 0.012 | 0.41 | NO |
83 | CCNH | CCNH | CCNH | 7412 | 0.0094 | 0.4 | NO |
84 | HDAC2 | HDAC2 | HDAC2 | 7480 | 0.0084 | 0.4 | NO |
85 | SMAD3 | SMAD3 | SMAD3 | 7593 | 0.0067 | 0.4 | NO |
86 | HDAC1 | HDAC1 | HDAC1 | 7625 | 0.0063 | 0.4 | NO |
87 | WEE2 | WEE2 | WEE2 | 7657 | 0.0058 | 0.39 | NO |
88 | ANAPC5 | ANAPC5 | ANAPC5 | 7684 | 0.0054 | 0.39 | NO |
89 | CCND2 | CCND2 | CCND2 | 7792 | 0.0038 | 0.39 | NO |
90 | SKP1 | SKP1 | SKP1 | 7803 | 0.0036 | 0.39 | NO |
91 | MAD1L1 | MAD1L1 | MAD1L1 | 7827 | 0.0032 | 0.39 | NO |
92 | YWHAB | YWHAB | YWHAB | 7858 | 0.0027 | 0.38 | NO |
93 | WEE1 | WEE1 | WEE1 | 8036 | -0.000071 | 0.37 | NO |
94 | ANAPC7 | ANAPC7 | ANAPC7 | 8077 | -0.001 | 0.37 | NO |
95 | CREBBP | CREBBP | CREBBP | 8147 | -0.002 | 0.37 | NO |
96 | CDK2 | CDK2 | CDK2 | 8228 | -0.0032 | 0.36 | NO |
97 | MCM3 | MCM3 | MCM3 | 8246 | -0.0035 | 0.36 | NO |
98 | E2F3 | E2F3 | E2F3 | 8638 | -0.0097 | 0.34 | NO |
99 | CHEK2 | CHEK2 | CHEK2 | 8658 | -0.01 | 0.34 | NO |
100 | ANAPC2 | ANAPC2 | ANAPC2 | 8802 | -0.012 | 0.34 | NO |
101 | ANAPC13 | ANAPC13 | ANAPC13 | 8869 | -0.013 | 0.33 | NO |
102 | RBX1 | RBX1 | RBX1 | 9083 | -0.017 | 0.32 | NO |
103 | SMAD4 | SMAD4 | SMAD4 | 9756 | -0.028 | 0.29 | NO |
104 | SMC1B | SMC1B | SMC1B | 10153 | -0.035 | 0.27 | NO |
105 | ANAPC11 | ANAPC11 | ANAPC11 | 10240 | -0.037 | 0.27 | NO |
106 | CDKN1B | CDKN1B | CDKN1B | 10608 | -0.044 | 0.25 | NO |
107 | ZBTB17 | ZBTB17 | ZBTB17 | 10612 | -0.044 | 0.25 | NO |
108 | RBL2 | RBL2 | RBL2 | 10760 | -0.048 | 0.25 | NO |
109 | MDM2 | MDM2 | MDM2 | 10836 | -0.049 | 0.25 | NO |
110 | CCNE1 | CCNE1 | CCNE1 | 10902 | -0.05 | 0.25 | NO |
111 | CDC16 | CDC16 | CDC16 | 11061 | -0.054 | 0.24 | NO |
112 | EP300 | EP300 | EP300 | 11112 | -0.055 | 0.25 | NO |
113 | GADD45B | GADD45B | GADD45B | 11725 | -0.068 | 0.22 | NO |
114 | ATM | ATM | ATM | 12614 | -0.09 | 0.18 | NO |
115 | TP53 | TP53 | TP53 | 12743 | -0.094 | 0.18 | NO |
116 | ANAPC4 | ANAPC4 | ANAPC4 | 12977 | -0.1 | 0.17 | NO |
117 | CDC14B | CDC14B | CDC14B | 13469 | -0.12 | 0.15 | NO |
118 | CCNB3 | CCNB3 | CCNB3 | 14531 | -0.16 | 0.11 | NO |
119 | GADD45G | GADD45G | GADD45G | 14920 | -0.17 | 0.1 | NO |
120 | CDKN1C | CDKN1C | CDKN1C | 16085 | -0.24 | 0.055 | NO |
121 | PTTG2 | PTTG2 | PTTG2 | 16244 | -0.25 | 0.066 | NO |
122 | E2F5 | E2F5 | E2F5 | 16284 | -0.26 | 0.084 | NO |
123 | CDC14A | CDC14A | CDC14A | 16413 | -0.27 | 0.099 | 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: BIOCARTA EGF PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_EGF_PATHWAY.heatmap_plot.clus3.18.png)
Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EGF PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_CELL_CYCLE.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 | POLE2 | POLE2 | POLE2 | 723 | 0.28 | 0.055 | YES |
2 | GTF2H3 | GTF2H3 | GTF2H3 | 1050 | 0.24 | 0.12 | YES |
3 | RFC4 | RFC4 | RFC4 | 1942 | 0.16 | 0.12 | YES |
4 | POLE3 | POLE3 | POLE3 | 2195 | 0.14 | 0.15 | YES |
5 | MNAT1 | MNAT1 | MNAT1 | 2300 | 0.14 | 0.19 | YES |
6 | POLD2 | POLD2 | POLD2 | 2305 | 0.14 | 0.24 | YES |
7 | RFC3 | RFC3 | RFC3 | 2496 | 0.13 | 0.27 | YES |
8 | GTF2H1 | GTF2H1 | GTF2H1 | 2876 | 0.11 | 0.29 | YES |
9 | POLD1 | POLD1 | POLD1 | 3007 | 0.1 | 0.32 | YES |
10 | ERCC6 | ERCC6 | ERCC6 | 3012 | 0.1 | 0.35 | YES |
11 | RPA3 | RPA3 | RPA3 | 3167 | 0.1 | 0.37 | YES |
12 | ERCC8 | ERCC8 | ERCC8 | 3393 | 0.092 | 0.39 | YES |
13 | CDK7 | CDK7 | CDK7 | 3585 | 0.086 | 0.41 | YES |
14 | ERCC4 | ERCC4 | ERCC4 | 3852 | 0.079 | 0.42 | YES |
15 | PCNA | PCNA | PCNA | 4013 | 0.074 | 0.44 | YES |
16 | POLD3 | POLD3 | POLD3 | 4025 | 0.074 | 0.46 | YES |
17 | RFC2 | RFC2 | RFC2 | 4193 | 0.07 | 0.48 | YES |
18 | RPA1 | RPA1 | RPA1 | 4567 | 0.061 | 0.48 | YES |
19 | RFC1 | RFC1 | RFC1 | 4659 | 0.058 | 0.49 | YES |
20 | ERCC1 | ERCC1 | ERCC1 | 4705 | 0.058 | 0.51 | YES |
21 | CUL4A | CUL4A | CUL4A | 5666 | 0.039 | 0.47 | NO |
22 | GTF2H4 | GTF2H4 | GTF2H4 | 5751 | 0.038 | 0.48 | NO |
23 | RPA4 | RPA4 | RPA4 | 5752 | 0.038 | 0.49 | NO |
24 | RFC5 | RFC5 | RFC5 | 5777 | 0.037 | 0.5 | NO |
25 | POLE | POLE | POLE | 6313 | 0.028 | 0.48 | NO |
26 | DDB2 | DDB2 | DDB2 | 6336 | 0.027 | 0.49 | NO |
27 | ERCC3 | ERCC3 | ERCC3 | 6564 | 0.023 | 0.48 | NO |
28 | CUL4B | CUL4B | CUL4B | 6595 | 0.023 | 0.49 | NO |
29 | XPA | XPA | XPA | 6671 | 0.021 | 0.49 | NO |
30 | RAD23A | RAD23A | RAD23A | 6691 | 0.021 | 0.5 | NO |
31 | POLE4 | POLE4 | POLE4 | 6828 | 0.019 | 0.5 | NO |
32 | CETN2 | CETN2 | CETN2 | 7315 | 0.011 | 0.47 | NO |
33 | CCNH | CCNH | CCNH | 7412 | 0.0094 | 0.47 | NO |
34 | DDB1 | DDB1 | DDB1 | 7536 | 0.0075 | 0.46 | NO |
35 | POLD4 | POLD4 | POLD4 | 8245 | -0.0035 | 0.43 | NO |
36 | LIG1 | LIG1 | LIG1 | 8452 | -0.0066 | 0.42 | NO |
37 | RPA2 | RPA2 | RPA2 | 8468 | -0.0069 | 0.42 | NO |
38 | RBX1 | RBX1 | RBX1 | 9083 | -0.017 | 0.39 | NO |
39 | GTF2H2 | GTF2H2 | GTF2H2 | 9190 | -0.019 | 0.39 | NO |
40 | GTF2H5 | GTF2H5 | GTF2H5 | 10761 | -0.048 | 0.32 | NO |
41 | ERCC2 | ERCC2 | ERCC2 | 11033 | -0.053 | 0.32 | NO |
42 | ERCC5 | ERCC5 | ERCC5 | 11783 | -0.069 | 0.3 | NO |
43 | XPC | XPC | XPC | 14215 | -0.14 | 0.22 | NO |
Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FAS PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_FAS_PATHWAY.heatmap_plot.clus3.12.png)
Figure S46. 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
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_NUCLEOTIDE_EXCISION_REPAIR.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 | PSMB9 | PSMB9 | PSMB9 | 535 | 0.33 | 0.085 | YES |
2 | IFNG | IFNG | IFNG | 751 | 0.28 | 0.17 | YES |
3 | PSMB8 | PSMB8 | PSMB8 | 2401 | 0.13 | 0.13 | YES |
4 | PSMD1 | PSMD1 | PSMD1 | 2955 | 0.11 | 0.13 | YES |
5 | PSMD2 | PSMD2 | PSMD2 | 2958 | 0.11 | 0.17 | YES |
6 | PSMD12 | PSMD12 | PSMD12 | 3076 | 0.1 | 0.2 | YES |
7 | PSMD14 | PSMD14 | PSMD14 | 3096 | 0.1 | 0.24 | YES |
8 | PSMB7 | PSMB7 | PSMB7 | 3231 | 0.097 | 0.26 | YES |
9 | PSMD11 | PSMD11 | PSMD11 | 3233 | 0.097 | 0.3 | YES |
10 | PSMA6 | PSMA6 | PSMA6 | 3302 | 0.094 | 0.32 | YES |
11 | PSMB2 | PSMB2 | PSMB2 | 3428 | 0.09 | 0.35 | YES |
12 | PSME2 | PSME2 | PSME2 | 3542 | 0.087 | 0.37 | YES |
13 | PSMA1 | PSMA1 | PSMA1 | 3826 | 0.079 | 0.38 | YES |
14 | PSMA2 | PSMA2 | PSMA2 | 3941 | 0.076 | 0.41 | YES |
15 | PSMC3 | PSMC3 | PSMC3 | 4129 | 0.071 | 0.42 | YES |
16 | PSMA3 | PSMA3 | PSMA3 | 4212 | 0.07 | 0.44 | YES |
17 | PSMA5 | PSMA5 | PSMA5 | 4283 | 0.068 | 0.46 | YES |
18 | PSMB5 | PSMB5 | PSMB5 | 4416 | 0.064 | 0.48 | YES |
19 | PSMC2 | PSMC2 | PSMC2 | 4454 | 0.063 | 0.5 | YES |
20 | PSME3 | PSME3 | PSME3 | 4613 | 0.059 | 0.51 | YES |
21 | POMP | POMP | POMP | 4667 | 0.058 | 0.52 | YES |
22 | PSMB1 | PSMB1 | PSMB1 | 4744 | 0.057 | 0.54 | YES |
23 | PSMC1 | PSMC1 | PSMC1 | 4883 | 0.054 | 0.55 | YES |
24 | PSMA7 | PSMA7 | PSMA7 | 4918 | 0.054 | 0.57 | YES |
25 | PSMD13 | PSMD13 | PSMD13 | 5023 | 0.052 | 0.58 | YES |
26 | PSMA4 | PSMA4 | PSMA4 | 5256 | 0.047 | 0.58 | YES |
27 | PSMB6 | PSMB6 | PSMB6 | 5494 | 0.042 | 0.59 | YES |
28 | PSME4 | PSME4 | PSME4 | 5546 | 0.041 | 0.6 | YES |
29 | PSME1 | PSME1 | PSME1 | 5862 | 0.035 | 0.59 | YES |
30 | PSMC6 | PSMC6 | PSMC6 | 5913 | 0.034 | 0.6 | YES |
31 | PSMD7 | PSMD7 | PSMD7 | 6374 | 0.026 | 0.59 | NO |
32 | PSMF1 | PSMF1 | PSMF1 | 6402 | 0.026 | 0.59 | NO |
33 | PSMD8 | PSMD8 | PSMD8 | 6478 | 0.025 | 0.6 | NO |
34 | PSMB3 | PSMB3 | PSMB3 | 6867 | 0.018 | 0.58 | NO |
35 | PSMD3 | PSMD3 | PSMD3 | 7045 | 0.015 | 0.58 | NO |
36 | PSMC5 | PSMC5 | PSMC5 | 7178 | 0.013 | 0.57 | NO |
37 | PSMD6 | PSMD6 | PSMD6 | 8058 | -0.00049 | 0.53 | NO |
38 | PSMB4 | PSMB4 | PSMB4 | 8470 | -0.0069 | 0.51 | NO |
39 | SHFM1 | SHFM1 | SHFM1 | 8770 | -0.012 | 0.5 | NO |
40 | PSMD4 | PSMD4 | PSMD4 | 8857 | -0.013 | 0.49 | NO |
41 | PSMC4 | PSMC4 | PSMC4 | 9693 | -0.027 | 0.46 | NO |
42 | PSMA8 | PSMA8 | PSMA8 | 9903 | -0.03 | 0.46 | NO |
Figure S47. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA RACCYCD PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_RACCYCD_PATHWAY.heatmap_plot.clus3.1.png)
Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA RACCYCD PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_PROTEASOME.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 | POLR3G | POLR3G | POLR3G | 88 | 0.61 | 0.062 | YES |
2 | DPYD | DPYD | DPYD | 145 | 0.52 | 0.12 | YES |
3 | TYMP | TYMP | TYMP | 298 | 0.41 | 0.15 | YES |
4 | CDA | CDA | CDA | 372 | 0.38 | 0.19 | YES |
5 | POLE2 | POLE2 | POLE2 | 723 | 0.28 | 0.2 | YES |
6 | NT5E | NT5E | NT5E | 872 | 0.26 | 0.22 | YES |
7 | RRM2 | RRM2 | RRM2 | 1037 | 0.24 | 0.24 | YES |
8 | PNP | PNP | PNP | 1622 | 0.18 | 0.23 | YES |
9 | RRM1 | RRM1 | RRM1 | 1626 | 0.18 | 0.25 | YES |
10 | CMPK2 | CMPK2 | CMPK2 | 1845 | 0.16 | 0.25 | YES |
11 | TXNRD1 | TXNRD1 | TXNRD1 | 1881 | 0.16 | 0.27 | YES |
12 | TK1 | TK1 | TK1 | 2077 | 0.15 | 0.27 | YES |
13 | PRIM1 | PRIM1 | PRIM1 | 2140 | 0.15 | 0.28 | YES |
14 | POLE3 | POLE3 | POLE3 | 2195 | 0.14 | 0.3 | YES |
15 | POLD2 | POLD2 | POLD2 | 2305 | 0.14 | 0.31 | YES |
16 | POLR1A | POLR1A | POLR1A | 2386 | 0.13 | 0.32 | YES |
17 | NT5M | NT5M | NT5M | 2444 | 0.13 | 0.33 | YES |
18 | TYMS | TYMS | TYMS | 2493 | 0.13 | 0.34 | YES |
19 | UPP1 | UPP1 | UPP1 | 2564 | 0.12 | 0.35 | YES |
20 | NT5C1B | NT5C1B | NT5C1B | 2727 | 0.12 | 0.35 | YES |
21 | PRIM2 | PRIM2 | PRIM2 | 2868 | 0.11 | 0.36 | YES |
22 | POLA1 | POLA1 | POLA1 | 2889 | 0.11 | 0.37 | YES |
23 | POLD1 | POLD1 | POLD1 | 3007 | 0.1 | 0.37 | YES |
24 | POLR1E | POLR1E | POLR1E | 3238 | 0.097 | 0.37 | YES |
25 | CAD | CAD | CAD | 3261 | 0.096 | 0.38 | YES |
26 | UCK2 | UCK2 | UCK2 | 3264 | 0.096 | 0.39 | YES |
27 | POLR2D | POLR2D | POLR2D | 3285 | 0.095 | 0.4 | YES |
28 | POLR1B | POLR1B | POLR1B | 3440 | 0.09 | 0.4 | YES |
29 | POLR3D | POLR3D | POLR3D | 3582 | 0.086 | 0.4 | YES |
30 | POLA2 | POLA2 | POLA2 | 3829 | 0.079 | 0.4 | NO |
31 | POLD3 | POLD3 | POLD3 | 4025 | 0.074 | 0.4 | NO |
32 | PNPT1 | PNPT1 | PNPT1 | 4228 | 0.069 | 0.39 | NO |
33 | UMPS | UMPS | UMPS | 4255 | 0.068 | 0.4 | NO |
34 | POLR3A | POLR3A | POLR3A | 4317 | 0.066 | 0.4 | NO |
35 | DTYMK | DTYMK | DTYMK | 4769 | 0.056 | 0.38 | NO |
36 | POLR3F | POLR3F | POLR3F | 4813 | 0.056 | 0.39 | NO |
37 | CANT1 | CANT1 | CANT1 | 4856 | 0.055 | 0.39 | NO |
38 | DCK | DCK | DCK | 4959 | 0.053 | 0.39 | NO |
39 | NT5C3 | NT5C3 | NT5C3 | 5190 | 0.048 | 0.38 | NO |
40 | CMPK1 | CMPK1 | CMPK1 | 5356 | 0.045 | 0.38 | NO |
41 | DUT | DUT | DUT | 5534 | 0.042 | 0.37 | NO |
42 | NME1 | NME1 | NME1 | 5972 | 0.034 | 0.35 | NO |
43 | POLR3B | POLR3B | POLR3B | 6032 | 0.032 | 0.35 | NO |
44 | NME2 | NME2 | NME2 | 6068 | 0.032 | 0.35 | NO |
45 | POLE | POLE | POLE | 6313 | 0.028 | 0.34 | NO |
46 | POLR2L | POLR2L | POLR2L | 6323 | 0.027 | 0.35 | NO |
47 | DCTD | DCTD | DCTD | 6428 | 0.025 | 0.34 | NO |
48 | UCK1 | UCK1 | UCK1 | 6676 | 0.021 | 0.33 | NO |
49 | NME1-NME2 | NME1-NME2 | NME1-NME2 | 6755 | 0.02 | 0.33 | NO |
50 | POLE4 | POLE4 | POLE4 | 6828 | 0.019 | 0.33 | NO |
51 | POLR3H | POLR3H | POLR3H | 6872 | 0.018 | 0.33 | NO |
52 | POLR2A | POLR2A | POLR2A | 6973 | 0.016 | 0.32 | NO |
53 | POLR2B | POLR2B | POLR2B | 7752 | 0.0043 | 0.28 | NO |
54 | DHODH | DHODH | DHODH | 7794 | 0.0037 | 0.28 | NO |
55 | POLR3C | POLR3C | POLR3C | 7915 | 0.0016 | 0.27 | NO |
56 | POLR2C | POLR2C | POLR2C | 7953 | 0.0011 | 0.27 | NO |
57 | POLR2G | POLR2G | POLR2G | 7958 | 0.00099 | 0.27 | NO |
58 | POLR2H | POLR2H | POLR2H | 8207 | -0.0029 | 0.26 | NO |
59 | POLD4 | POLD4 | POLD4 | 8245 | -0.0035 | 0.26 | NO |
60 | AK3 | AK3 | AK3 | 8300 | -0.0045 | 0.25 | NO |
61 | NT5C | NT5C | NT5C | 8383 | -0.0057 | 0.25 | NO |
62 | RRM2B | RRM2B | RRM2B | 8429 | -0.0063 | 0.25 | NO |
63 | POLR1D | POLR1D | POLR1D | 8481 | -0.0071 | 0.24 | NO |
64 | ITPA | ITPA | ITPA | 8688 | -0.01 | 0.24 | NO |
65 | POLR3K | POLR3K | POLR3K | 9185 | -0.019 | 0.21 | NO |
66 | POLR2F | POLR2F | POLR2F | 9196 | -0.019 | 0.21 | NO |
67 | POLR2E | POLR2E | POLR2E | 9284 | -0.02 | 0.21 | NO |
68 | NUDT2 | NUDT2 | NUDT2 | 9299 | -0.021 | 0.21 | NO |
69 | NME6 | NME6 | NME6 | 9430 | -0.023 | 0.2 | NO |
70 | POLR2K | POLR2K | POLR2K | 9559 | -0.025 | 0.2 | NO |
71 | NME7 | NME7 | NME7 | 9564 | -0.025 | 0.2 | NO |
72 | TXNRD2 | TXNRD2 | TXNRD2 | 9621 | -0.026 | 0.2 | NO |
73 | ENTPD6 | ENTPD6 | ENTPD6 | 9860 | -0.03 | 0.19 | NO |
74 | POLR1C | POLR1C | POLR1C | 9956 | -0.031 | 0.19 | NO |
75 | ZNRD1 | ZNRD1 | ZNRD1 | 10057 | -0.033 | 0.19 | NO |
76 | POLR3GL | POLR3GL | POLR3GL | 10339 | -0.039 | 0.18 | NO |
77 | UCKL1 | UCKL1 | UCKL1 | 10458 | -0.041 | 0.18 | NO |
78 | POLR2I | POLR2I | POLR2I | 10617 | -0.045 | 0.17 | NO |
79 | UPRT | UPRT | UPRT | 10691 | -0.046 | 0.17 | NO |
80 | ENTPD4 | ENTPD4 | ENTPD4 | 10966 | -0.052 | 0.16 | NO |
81 | ENTPD1 | ENTPD1 | ENTPD1 | 11636 | -0.066 | 0.13 | NO |
82 | POLR2J | POLR2J | POLR2J | 11666 | -0.066 | 0.14 | NO |
83 | ENTPD8 | ENTPD8 | ENTPD8 | 11874 | -0.071 | 0.14 | NO |
84 | TK2 | TK2 | TK2 | 12382 | -0.084 | 0.12 | NO |
85 | UPP2 | UPP2 | UPP2 | 12813 | -0.096 | 0.1 | NO |
86 | UPB1 | UPB1 | UPB1 | 13055 | -0.1 | 0.1 | NO |
87 | NME3 | NME3 | NME3 | 13189 | -0.11 | 0.11 | NO |
88 | POLR2J3 | POLR2J3 | POLR2J3 | 13447 | -0.12 | 0.1 | NO |
89 | CTPS2 | CTPS2 | CTPS2 | 13508 | -0.12 | 0.11 | NO |
90 | DPYS | DPYS | DPYS | 13609 | -0.12 | 0.12 | NO |
91 | ENTPD5 | ENTPD5 | ENTPD5 | 13970 | -0.13 | 0.12 | NO |
92 | POLR2J2 | POLR2J2 | POLR2J2 | 14124 | -0.14 | 0.12 | NO |
93 | NME4 | NME4 | NME4 | 14694 | -0.16 | 0.11 | NO |
94 | NT5C2 | NT5C2 | NT5C2 | 14713 | -0.16 | 0.13 | NO |
95 | ENTPD3 | ENTPD3 | ENTPD3 | 16316 | -0.26 | 0.066 | NO |
96 | NME5 | NME5 | NME5 | 17139 | -0.34 | 0.058 | 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: BIOCARTA MAPK PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_MAPK_PATHWAY.heatmap_plot.clus3.16.png)
Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MAPK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_PYRIMIDINE_METABOLISM.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 | WARS | WARS | WARS | 565 | 0.32 | 0.11 | YES |
2 | TARS | TARS | TARS | 1850 | 0.16 | 0.11 | YES |
3 | IARS | IARS | IARS | 2457 | 0.13 | 0.13 | YES |
4 | YARS | YARS | YARS | 2850 | 0.11 | 0.16 | YES |
5 | FARSB | FARSB | FARSB | 3146 | 0.1 | 0.19 | YES |
6 | IARS2 | IARS2 | IARS2 | 3306 | 0.094 | 0.22 | YES |
7 | DARS | DARS | DARS | 3632 | 0.084 | 0.24 | YES |
8 | MARS2 | MARS2 | MARS2 | 3864 | 0.078 | 0.26 | YES |
9 | EPRS | EPRS | EPRS | 3993 | 0.075 | 0.29 | YES |
10 | RARS | RARS | RARS | 4104 | 0.072 | 0.31 | YES |
11 | YARS2 | YARS2 | YARS2 | 4153 | 0.071 | 0.34 | YES |
12 | GARS | GARS | GARS | 4190 | 0.07 | 0.37 | YES |
13 | SARS | SARS | SARS | 4354 | 0.066 | 0.39 | YES |
14 | TARSL2 | TARSL2 | TARSL2 | 4480 | 0.063 | 0.41 | YES |
15 | FARS2 | FARS2 | FARS2 | 5075 | 0.051 | 0.4 | YES |
16 | DARS2 | DARS2 | DARS2 | 5285 | 0.046 | 0.41 | YES |
17 | KARS | KARS | KARS | 5365 | 0.045 | 0.42 | YES |
18 | AARS | AARS | AARS | 5693 | 0.039 | 0.42 | YES |
19 | MARS | MARS | MARS | 5886 | 0.035 | 0.43 | YES |
20 | CARS | CARS | CARS | 5929 | 0.034 | 0.44 | YES |
21 | HARS | HARS | HARS | 6163 | 0.03 | 0.44 | YES |
22 | FARSA | FARSA | FARSA | 6209 | 0.029 | 0.45 | YES |
23 | VARS | VARS | VARS | 6348 | 0.027 | 0.45 | YES |
24 | LARS | LARS | LARS | 7012 | 0.016 | 0.42 | NO |
25 | PSTK | PSTK | PSTK | 7148 | 0.014 | 0.42 | NO |
26 | WARS2 | WARS2 | WARS2 | 7523 | 0.0076 | 0.41 | NO |
27 | RARS2 | RARS2 | RARS2 | 7621 | 0.0063 | 0.4 | NO |
28 | PARS2 | PARS2 | PARS2 | 7835 | 0.0031 | 0.39 | NO |
29 | HARS2 | HARS2 | HARS2 | 8134 | -0.0018 | 0.38 | NO |
30 | LARS2 | LARS2 | LARS2 | 8186 | -0.0026 | 0.38 | NO |
31 | EARS2 | EARS2 | EARS2 | 8219 | -0.0031 | 0.38 | NO |
32 | NARS | NARS | NARS | 8396 | -0.0058 | 0.37 | NO |
33 | CARS2 | CARS2 | CARS2 | 9493 | -0.024 | 0.32 | NO |
34 | MTFMT | MTFMT | MTFMT | 9639 | -0.026 | 0.32 | NO |
35 | NARS2 | NARS2 | NARS2 | 9655 | -0.026 | 0.33 | NO |
36 | AARS2 | AARS2 | AARS2 | 9947 | -0.031 | 0.33 | NO |
37 | VARS2 | VARS2 | VARS2 | 11003 | -0.052 | 0.29 | NO |
38 | SARS2 | SARS2 | SARS2 | 11706 | -0.067 | 0.28 | NO |
39 | SEPSECS | SEPSECS | SEPSECS | 12129 | -0.077 | 0.3 | NO |
40 | QARS | QARS | QARS | 12534 | -0.088 | 0.31 | 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: BIOCARTA P38MAPK PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_P38MAPK_PATHWAY.heatmap_plot.clus3.13.png)
Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA P38MAPK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.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 | CDK6 | CDK6 | CDK6 | 104 | 0.59 | 0.22 | YES |
2 | CCNA1 | CCNA1 | CCNA1 | 558 | 0.32 | 0.31 | YES |
3 | TGFB2 | TGFB2 | TGFB2 | 931 | 0.25 | 0.39 | YES |
4 | CDK1 | CDK1 | CDK1 | 2000 | 0.15 | 0.39 | YES |
5 | TGFB1 | TGFB1 | TGFB1 | 2610 | 0.12 | 0.4 | YES |
6 | TFDP1 | TFDP1 | TFDP1 | 2831 | 0.11 | 0.43 | YES |
7 | CDKN1A | CDKN1A | CDKN1A | 3142 | 0.1 | 0.45 | YES |
8 | TGFB3 | TGFB3 | TGFB3 | 3207 | 0.098 | 0.49 | YES |
9 | CDC25A | CDC25A | CDC25A | 3216 | 0.098 | 0.52 | YES |
10 | CDKN2B | CDKN2B | CDKN2B | 3341 | 0.093 | 0.55 | YES |
11 | SKP2 | SKP2 | SKP2 | 3391 | 0.092 | 0.58 | YES |
12 | CDKN2A | CDKN2A | CDKN2A | 4414 | 0.064 | 0.55 | NO |
13 | DHFR | DHFR | DHFR | 4584 | 0.06 | 0.56 | NO |
14 | ATR | ATR | ATR | 5524 | 0.042 | 0.53 | NO |
15 | GSK3B | GSK3B | GSK3B | 5885 | 0.035 | 0.52 | NO |
16 | RB1 | RB1 | RB1 | 6335 | 0.027 | 0.51 | NO |
17 | CDK4 | CDK4 | CDK4 | 6378 | 0.026 | 0.52 | NO |
18 | ABL1 | ABL1 | ABL1 | 6917 | 0.017 | 0.49 | NO |
19 | CCND1 | CCND1 | CCND1 | 7008 | 0.016 | 0.49 | NO |
20 | SMAD3 | SMAD3 | SMAD3 | 7593 | 0.0067 | 0.46 | NO |
21 | HDAC1 | HDAC1 | HDAC1 | 7625 | 0.0063 | 0.46 | NO |
22 | CDK2 | CDK2 | CDK2 | 8228 | -0.0032 | 0.43 | NO |
23 | SMAD4 | SMAD4 | SMAD4 | 9756 | -0.028 | 0.36 | NO |
24 | CDKN1B | CDKN1B | CDKN1B | 10608 | -0.044 | 0.33 | NO |
25 | CCNE1 | CCNE1 | CCNE1 | 10902 | -0.05 | 0.33 | NO |
26 | ATM | ATM | ATM | 12614 | -0.09 | 0.27 | NO |
27 | TP53 | TP53 | TP53 | 12743 | -0.094 | 0.3 | 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: BIOCARTA IL1R PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_IL1R_PATHWAY.heatmap_plot.clus3.15.png)
Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_G1_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 | TNF | TNF | TNF | 1145 | 0.23 | 0.038 | YES |
2 | BAG4 | BAG4 | BAG4 | 2015 | 0.15 | 0.058 | YES |
3 | MAPK8 | MAPK8 | MAPK8 | 2016 | 0.15 | 0.13 | YES |
4 | MAP3K1 | MAP3K1 | MAP3K1 | 2186 | 0.14 | 0.18 | YES |
5 | LMNB2 | LMNB2 | LMNB2 | 2267 | 0.14 | 0.24 | YES |
6 | PRKDC | PRKDC | PRKDC | 2587 | 0.12 | 0.28 | YES |
7 | LMNB1 | LMNB1 | LMNB1 | 2780 | 0.11 | 0.32 | YES |
8 | JUN | JUN | JUN | 2824 | 0.11 | 0.37 | YES |
9 | PAK1 | PAK1 | PAK1 | 3075 | 0.1 | 0.4 | YES |
10 | MAP3K7 | MAP3K7 | MAP3K7 | 3423 | 0.09 | 0.42 | YES |
11 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 3711 | 0.082 | 0.44 | YES |
12 | FADD | FADD | FADD | 3781 | 0.08 | 0.47 | YES |
13 | PAK2 | PAK2 | PAK2 | 5268 | 0.046 | 0.41 | NO |
14 | DFFA | DFFA | DFFA | 5953 | 0.034 | 0.39 | NO |
15 | LMNA | LMNA | LMNA | 6093 | 0.031 | 0.4 | NO |
16 | PARP1 | PARP1 | PARP1 | 6118 | 0.031 | 0.41 | NO |
17 | CASP8 | CASP8 | CASP8 | 6195 | 0.03 | 0.42 | NO |
18 | MAP2K4 | MAP2K4 | MAP2K4 | 6217 | 0.029 | 0.43 | NO |
19 | RB1 | RB1 | RB1 | 6335 | 0.027 | 0.43 | NO |
20 | SPTAN1 | SPTAN1 | SPTAN1 | 6798 | 0.019 | 0.42 | NO |
21 | RIPK1 | RIPK1 | RIPK1 | 6958 | 0.017 | 0.42 | NO |
22 | TRADD | TRADD | TRADD | 7329 | 0.011 | 0.4 | NO |
23 | CRADD | CRADD | CRADD | 7790 | 0.0038 | 0.38 | NO |
24 | CASP2 | CASP2 | CASP2 | 7849 | 0.0029 | 0.38 | NO |
25 | CASP3 | CASP3 | CASP3 | 10019 | -0.033 | 0.27 | NO |
26 | MADD | MADD | MADD | 12769 | -0.094 | 0.16 | NO |
27 | DFFB | DFFB | DFFB | 14139 | -0.14 | 0.15 | NO |
28 | ARHGDIB | ARHGDIB | ARHGDIB | 14788 | -0.17 | 0.19 | 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: BIOCARTA TNFR1 PATHWAY.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_TNFR1_PATHWAY.heatmap_plot.clus3.8.png)
Figure S56. 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
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.BIOCARTA_TNFR1_PATHWAY.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 | POLR3G | POLR3G | POLR3G | 88 | 0.61 | 0.097 | YES |
2 | AIM2 | AIM2 | AIM2 | 92 | 0.61 | 0.2 | YES |
3 | CASP1 | CASP1 | CASP1 | 185 | 0.48 | 0.27 | YES |
4 | CXCL10 | CXCL10 | CXCL10 | 337 | 0.4 | 0.33 | YES |
5 | CCL4 | CCL4 | CCL4 | 510 | 0.34 | 0.38 | YES |
6 | IL18 | IL18 | IL18 | 700 | 0.29 | 0.42 | YES |
7 | CCL4L2 | CCL4L2 | CCL4L2 | 715 | 0.29 | 0.46 | YES |
8 | DDX58 | DDX58 | DDX58 | 970 | 0.25 | 0.49 | YES |
9 | IL1B | IL1B | IL1B | 1086 | 0.23 | 0.52 | YES |
10 | IFNA13 | IFNA13 | IFNA13 | 1572 | 0.18 | 0.53 | YES |
11 | IFNA1 | IFNA1 | IFNA1 | 1587 | 0.18 | 0.56 | YES |
12 | TMEM173 | TMEM173 | TMEM173 | 1671 | 0.18 | 0.58 | YES |
13 | ZBP1 | ZBP1 | ZBP1 | 2003 | 0.15 | 0.59 | YES |
14 | CCL5 | CCL5 | CCL5 | 2159 | 0.14 | 0.6 | YES |
15 | IRF7 | IRF7 | IRF7 | 2318 | 0.14 | 0.62 | YES |
16 | IL6 | IL6 | IL6 | 2372 | 0.13 | 0.64 | YES |
17 | NFKB1 | NFKB1 | NFKB1 | 3262 | 0.096 | 0.6 | NO |
18 | CHUK | CHUK | CHUK | 3546 | 0.087 | 0.6 | NO |
19 | POLR3D | POLR3D | POLR3D | 3582 | 0.086 | 0.62 | NO |
20 | PYCARD | PYCARD | PYCARD | 4171 | 0.07 | 0.6 | NO |
21 | POLR3A | POLR3A | POLR3A | 4317 | 0.066 | 0.6 | NO |
22 | ADAR | ADAR | ADAR | 4510 | 0.062 | 0.6 | NO |
23 | IFNB1 | IFNB1 | IFNB1 | 4760 | 0.057 | 0.6 | NO |
24 | POLR3F | POLR3F | POLR3F | 4813 | 0.056 | 0.6 | NO |
25 | IKBKG | IKBKG | IKBKG | 5015 | 0.052 | 0.6 | NO |
26 | IL33 | IL33 | IL33 | 5064 | 0.051 | 0.6 | NO |
27 | POLR3B | POLR3B | POLR3B | 6032 | 0.032 | 0.56 | NO |
28 | POLR3H | POLR3H | POLR3H | 6872 | 0.018 | 0.51 | NO |
29 | RIPK1 | RIPK1 | RIPK1 | 6958 | 0.017 | 0.51 | NO |
30 | POLR3C | POLR3C | POLR3C | 7915 | 0.0016 | 0.46 | NO |
31 | IKBKE | IKBKE | IKBKE | 7990 | 0.00064 | 0.46 | NO |
32 | NFKBIA | NFKBIA | NFKBIA | 8271 | -0.004 | 0.44 | NO |
33 | POLR1D | POLR1D | POLR1D | 8481 | -0.0071 | 0.43 | NO |
34 | RELA | RELA | RELA | 8584 | -0.009 | 0.43 | NO |
35 | TBK1 | TBK1 | TBK1 | 8758 | -0.012 | 0.42 | NO |
36 | MAVS | MAVS | MAVS | 9165 | -0.018 | 0.4 | NO |
37 | POLR3K | POLR3K | POLR3K | 9185 | -0.019 | 0.4 | NO |
38 | POLR1C | POLR1C | POLR1C | 9956 | -0.031 | 0.36 | NO |
39 | IRF3 | IRF3 | IRF3 | 10095 | -0.034 | 0.36 | NO |
40 | NFKBIB | NFKBIB | NFKBIB | 10286 | -0.038 | 0.36 | NO |
41 | POLR3GL | POLR3GL | POLR3GL | 10339 | -0.039 | 0.36 | NO |
42 | IKBKB | IKBKB | IKBKB | 13436 | -0.12 | 0.21 | NO |
43 | RIPK3 | RIPK3 | RIPK3 | 14284 | -0.15 | 0.19 | NO |
44 | TREX1 | TREX1 | TREX1 | 14702 | -0.16 | 0.19 | 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 PYRIMIDINE METABOLISM.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_PYRIMIDINE_METABOLISM.heatmap_plot.clus3.5.png)
Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRIMIDINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY.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 | POLE2 | POLE2 | POLE2 | 723 | 0.28 | 0.059 | YES |
2 | RFC4 | RFC4 | RFC4 | 1942 | 0.16 | 0.046 | YES |
3 | MCM4 | MCM4 | MCM4 | 1997 | 0.15 | 0.097 | YES |
4 | PRIM1 | PRIM1 | PRIM1 | 2140 | 0.15 | 0.14 | YES |
5 | POLE3 | POLE3 | POLE3 | 2195 | 0.14 | 0.19 | YES |
6 | MCM2 | MCM2 | MCM2 | 2295 | 0.14 | 0.23 | YES |
7 | POLD2 | POLD2 | POLD2 | 2305 | 0.14 | 0.28 | YES |
8 | RFC3 | RFC3 | RFC3 | 2496 | 0.13 | 0.31 | YES |
9 | FEN1 | FEN1 | FEN1 | 2688 | 0.12 | 0.34 | YES |
10 | RNASEH1 | RNASEH1 | RNASEH1 | 2693 | 0.12 | 0.38 | YES |
11 | MCM6 | MCM6 | MCM6 | 2777 | 0.12 | 0.42 | YES |
12 | PRIM2 | PRIM2 | PRIM2 | 2868 | 0.11 | 0.45 | YES |
13 | POLD1 | POLD1 | POLD1 | 3007 | 0.1 | 0.48 | YES |
14 | RPA3 | RPA3 | RPA3 | 3167 | 0.1 | 0.5 | YES |
15 | POLA2 | POLA2 | POLA2 | 3829 | 0.079 | 0.5 | YES |
16 | DNA2 | DNA2 | DNA2 | 3975 | 0.075 | 0.51 | YES |
17 | PCNA | PCNA | PCNA | 4013 | 0.074 | 0.54 | YES |
18 | POLD3 | POLD3 | POLD3 | 4025 | 0.074 | 0.56 | YES |
19 | RFC2 | RFC2 | RFC2 | 4193 | 0.07 | 0.58 | YES |
20 | RPA1 | RPA1 | RPA1 | 4567 | 0.061 | 0.58 | YES |
21 | MCM5 | MCM5 | MCM5 | 4627 | 0.059 | 0.6 | YES |
22 | RFC1 | RFC1 | RFC1 | 4659 | 0.058 | 0.61 | YES |
23 | RNASEH2A | RNASEH2A | RNASEH2A | 5096 | 0.05 | 0.61 | YES |
24 | MCM7 | MCM7 | MCM7 | 5264 | 0.046 | 0.61 | YES |
25 | SSBP1 | SSBP1 | SSBP1 | 5501 | 0.042 | 0.62 | YES |
26 | RPA4 | RPA4 | RPA4 | 5752 | 0.038 | 0.62 | YES |
27 | RFC5 | RFC5 | RFC5 | 5777 | 0.037 | 0.63 | YES |
28 | POLE | POLE | POLE | 6313 | 0.028 | 0.61 | NO |
29 | POLE4 | POLE4 | POLE4 | 6828 | 0.019 | 0.58 | NO |
30 | RNASEH2B | RNASEH2B | RNASEH2B | 8216 | -0.0031 | 0.51 | NO |
31 | POLD4 | POLD4 | POLD4 | 8245 | -0.0035 | 0.51 | NO |
32 | MCM3 | MCM3 | MCM3 | 8246 | -0.0035 | 0.51 | NO |
33 | LIG1 | LIG1 | LIG1 | 8452 | -0.0066 | 0.5 | NO |
34 | RPA2 | RPA2 | RPA2 | 8468 | -0.0069 | 0.5 | NO |
35 | RNASEH2C | RNASEH2C | RNASEH2C | 12717 | -0.093 | 0.3 | 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 AMINOACYL TRNA BIOSYNTHESIS.
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.heatmap_plot.clus3.6.png)
Figure S60. 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
![](BLCA-TP-mRNAseq_cNMF-clus3___Class2-CanonicalPathway.KEGG_DNA_REPLICATION.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
-
Gene set database = c2.cp.v3.0-2.symbols.gmt
-
Expression data file = BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Phenotype data file = BLCA-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.