This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "KIPAN-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:
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For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.
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Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).
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Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).
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Checks if the top core genes are up-regulated or down-regulated.
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Checks if the top core genes are high expressed or low expressed.
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Checks if the top core genes are significantly differently expressed genes.
Table 1. Get Full Table basic data info
basic data info |
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Number of Gene Sets: 715 |
Number of samples: 889 |
Original number of Gene Sets: 1320 |
Maximum gene set size: 933 |
Table 2. Get Full Table pheno data info
phenotype info |
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pheno.type: 1 - 4 :[ clus4 ] 276 |
pheno.type: 2 - 4 :[ clus1 ] 125 |
pheno.type: 3 - 4 :[ clus2 ] 200 |
pheno.type: 4 - 4 :[ clus3 ] 288 |
For the expression subtypes of 18216 genes in 890 samples, GSEA found enriched gene sets in each cluster using 889 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.
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clus1
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Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, KEGG PARKINSONS DISEASE, KEGG VIBRIO CHOLERAE INFECTION, KEGG EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI INFECTION, PID MTOR 4PATHWAY, PID IGF1 PATHWAY, PID PI3KCIAKTPATHWAY, REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE, REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT, REACTOME SIGNALING BY ERBB4
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And common core enriched genes are ATP6V0A4, ATP6V0B, ATP6V0C, ATP6V0D2, ATP6V1A, ATP6V1B1, ATP6V1C2, ATP6V1D, ATP6V1H, FOXO1
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clus2
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Top enriched gene sets are KEGG ETHER LIPID METABOLISM, KEGG RIBOSOME, KEGG DNA REPLICATION, KEGG HOMOLOGOUS RECOMBINATION, KEGG MAPK SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, KEGG CELL CYCLE
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And common core enriched genes are CASP1, IL1B, IL6, AIM2, CCL4, CCL4L2, CCL5, CXCL10, IFNB1, IKBKE
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clus3
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Top enriched gene sets are KEGG PPAR SIGNALING PATHWAY, KEGG VASCULAR SMOOTH MUSCLE CONTRACTION, KEGG VASOPRESSIN REGULATED WATER REABSORPTION, BIOCARTA AT1R PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA VEGF PATHWAY, PID HIF2PATHWAY, PID ARF6 TRAFFICKINGPATHWAY, PID ANGIOPOIETINRECEPTOR PATHWAY, PID SHP2 PATHWAY
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And common core enriched genes are AVPR2, ITGA5, ITGAV, JUN, MAPK1, MAPK8, ADCY3, AQP3, AQP4, ARHGDIB
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clus4
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Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG PYRUVATE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG BASE EXCISION REPAIR, KEGG LYSOSOME, KEGG TIGHT JUNCTION
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And common core enriched genes are HEMK1, LCMT1, TRMT11, WBSCR22, ALDH1B1, ALDH2, APEX2, LIG1, MPG, MUTYH
Table 3. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
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KEGG OXIDATIVE PHOSPHORYLATION | 113 | genes.ES.table | 0.63 | 1.6 | 0.061 | 0.77 | 0.87 | 0.68 | 0.21 | 0.54 | 0.41 | 0.25 |
KEGG PARKINSONS DISEASE | 111 | genes.ES.table | 0.5 | 1.5 | 0.12 | 0.87 | 0.96 | 0.69 | 0.26 | 0.52 | 0.57 | 0.31 |
KEGG VIBRIO CHOLERAE INFECTION | 52 | genes.ES.table | 0.56 | 1.9 | 0.0021 | 1 | 0.38 | 0.27 | 0.089 | 0.25 | 0 | 0.23 |
KEGG EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI INFECTION | 67 | genes.ES.table | 0.37 | 1.4 | 0.07 | 1 | 0.99 | 0.21 | 0.13 | 0.18 | 0.77 | 0.38 |
PID MTOR 4PATHWAY | 67 | genes.ES.table | 0.27 | 1.5 | 0.09 | 1 | 0.99 | 0.43 | 0.26 | 0.32 | 0.78 | 0.39 |
PID IGF1 PATHWAY | 30 | genes.ES.table | 0.37 | 1.4 | 0.11 | 0.97 | 0.99 | 0.13 | 0.048 | 0.13 | 0.76 | 0.37 |
PID PI3KCIAKTPATHWAY | 35 | genes.ES.table | 0.41 | 1.7 | 0.059 | 1 | 0.77 | 0.51 | 0.3 | 0.36 | 0.62 | 0.38 |
REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE | 40 | genes.ES.table | 0.55 | 1.6 | 0.066 | 0.76 | 0.84 | 0.6 | 0.19 | 0.49 | 0.39 | 0.24 |
REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT | 115 | genes.ES.table | 0.63 | 1.7 | 0.048 | 1 | 0.76 | 0.7 | 0.21 | 0.56 | 0.91 | 0.47 |
REACTOME SIGNALING BY ERBB4 | 83 | genes.ES.table | 0.35 | 1.4 | 0.077 | 1 | 0.99 | 0.13 | 0.076 | 0.12 | 0.79 | 0.4 |
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 |
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1 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 18 | 1.4 | 0.09 | YES |
2 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 27 | 1.3 | 0.18 | YES |
3 | CFTR | CFTR | CFTR | 46 | 1.2 | 0.25 | YES |
4 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 64 | 1.1 | 0.32 | YES |
5 | PLCG2 | PLCG2 | PLCG2 | 169 | 0.88 | 0.38 | YES |
6 | KCNQ1 | KCNQ1 | KCNQ1 | 187 | 0.84 | 0.43 | YES |
7 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 214 | 0.8 | 0.48 | YES |
8 | ATP6V1A | ATP6V1A | ATP6V1A | 908 | 0.41 | 0.47 | YES |
9 | ATP6V1H | ATP6V1H | ATP6V1H | 1253 | 0.33 | 0.48 | YES |
10 | SLC12A2 | SLC12A2 | SLC12A2 | 1323 | 0.32 | 0.49 | YES |
11 | ATP6V0B | ATP6V0B | ATP6V0B | 1370 | 0.31 | 0.51 | YES |
12 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 1477 | 0.3 | 0.53 | YES |
13 | ATP6V1D | ATP6V1D | ATP6V1D | 1530 | 0.29 | 0.54 | YES |
14 | ATP6V0C | ATP6V0C | ATP6V0C | 1618 | 0.28 | 0.56 | YES |
15 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 2128 | 0.22 | 0.54 | NO |
16 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 2314 | 0.2 | 0.55 | NO |
17 | ATP6V1F | ATP6V1F | ATP6V1F | 2895 | 0.16 | 0.52 | NO |
18 | GNAS | GNAS | GNAS | 3151 | 0.15 | 0.52 | NO |
19 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 3335 | 0.14 | 0.52 | NO |
20 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 3749 | 0.12 | 0.5 | NO |
21 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 4140 | 0.1 | 0.49 | NO |
22 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 4172 | 0.1 | 0.5 | NO |
23 | ERO1L | ERO1L | ERO1L | 4325 | 0.096 | 0.49 | NO |
24 | PRKACA | PRKACA | PRKACA | 4796 | 0.08 | 0.47 | NO |
25 | MUC2 | MUC2 | MUC2 | 5043 | 0.072 | 0.46 | NO |
26 | PRKCA | PRKCA | PRKCA | 5170 | 0.068 | 0.46 | NO |
27 | TJP2 | TJP2 | TJP2 | 5334 | 0.063 | 0.46 | NO |
28 | KDELR1 | KDELR1 | KDELR1 | 5562 | 0.056 | 0.45 | NO |
29 | PRKACB | PRKACB | PRKACB | 5758 | 0.05 | 0.44 | NO |
30 | SEC61B | SEC61B | SEC61B | 6052 | 0.042 | 0.43 | NO |
31 | SEC61A1 | SEC61A1 | SEC61A1 | 6251 | 0.036 | 0.42 | NO |
32 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 6393 | 0.033 | 0.41 | NO |
33 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 6746 | 0.023 | 0.4 | NO |
34 | TJP1 | TJP1 | TJP1 | 7307 | 0.0082 | 0.36 | NO |
35 | ARF1 | ARF1 | ARF1 | 7812 | -0.0048 | 0.34 | NO |
36 | ACTB | ACTB | ACTB | 8524 | -0.023 | 0.3 | NO |
37 | ACTG1 | ACTG1 | ACTG1 | 8873 | -0.032 | 0.28 | NO |
38 | TCIRG1 | TCIRG1 | TCIRG1 | 9703 | -0.055 | 0.24 | NO |
39 | SEC61G | SEC61G | SEC61G | 10258 | -0.071 | 0.22 | NO |
40 | KDELR2 | KDELR2 | KDELR2 | 10312 | -0.072 | 0.22 | NO |
41 | PLCG1 | PLCG1 | PLCG1 | 11746 | -0.12 | 0.15 | NO |
42 | ADCY3 | ADCY3 | ADCY3 | 12299 | -0.14 | 0.12 | NO |
43 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 12631 | -0.16 | 0.12 | NO |
44 | PDIA4 | PDIA4 | PDIA4 | 13107 | -0.18 | 0.1 | NO |
45 | ADCY9 | ADCY9 | ADCY9 | 13215 | -0.18 | 0.11 | NO |
46 | SEC61A2 | SEC61A2 | SEC61A2 | 14401 | -0.26 | 0.061 | NO |
47 | PRKCG | PRKCG | PRKCG | 14519 | -0.26 | 0.072 | NO |
48 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 14628 | -0.27 | 0.084 | NO |
49 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 14716 | -0.28 | 0.098 | NO |
50 | PRKX | PRKX | PRKX | 14923 | -0.3 | 0.11 | NO |
51 | KDELR3 | KDELR3 | KDELR3 | 16814 | -0.51 | 0.036 | NO |
52 | PRKCB | PRKCB | PRKCB | 17319 | -0.6 | 0.048 | NO |
Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION.
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Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
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1 | PDP2 | PDP2 | PDP2 | 574 | 0.53 | -0.0056 | YES |
2 | NNT | NNT | NNT | 1032 | 0.38 | -0.012 | YES |
3 | PDP1 | PDP1 | PDP1 | 1133 | 0.35 | 0.000082 | YES |
4 | IDH3A | IDH3A | IDH3A | 1167 | 0.35 | 0.016 | YES |
5 | CYCS | CYCS | CYCS | 1216 | 0.34 | 0.03 | YES |
6 | IDH2 | IDH2 | IDH2 | 1218 | 0.34 | 0.046 | YES |
7 | COX5A | COX5A | COX5A | 1275 | 0.33 | 0.06 | YES |
8 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 1389 | 0.31 | 0.069 | YES |
9 | NDUFA4 | NDUFA4 | NDUFA4 | 1463 | 0.3 | 0.08 | YES |
10 | NDUFA6 | NDUFA6 | NDUFA6 | 1485 | 0.29 | 0.093 | YES |
11 | COX7B | COX7B | COX7B | 1568 | 0.28 | 0.1 | YES |
12 | COX8A | COX8A | COX8A | 1580 | 0.28 | 0.12 | YES |
13 | COX6C | COX6C | COX6C | 1590 | 0.28 | 0.13 | YES |
14 | L2HGDH | L2HGDH | L2HGDH | 1664 | 0.27 | 0.14 | YES |
15 | UQCRC1 | UQCRC1 | UQCRC1 | 1668 | 0.27 | 0.15 | YES |
16 | PDHX | PDHX | PDHX | 1756 | 0.26 | 0.16 | YES |
17 | NDUFS7 | NDUFS7 | NDUFS7 | 1835 | 0.25 | 0.17 | YES |
18 | ATP5A1 | ATP5A1 | ATP5A1 | 1838 | 0.25 | 0.18 | YES |
19 | NDUFS8 | NDUFS8 | NDUFS8 | 1917 | 0.24 | 0.19 | YES |
20 | ETFDH | ETFDH | ETFDH | 1936 | 0.24 | 0.2 | YES |
21 | NDUFA3 | NDUFA3 | NDUFA3 | 1955 | 0.24 | 0.21 | YES |
22 | SDHD | SDHD | SDHD | 1969 | 0.24 | 0.22 | YES |
23 | DLAT | DLAT | DLAT | 1983 | 0.23 | 0.23 | YES |
24 | NDUFA8 | NDUFA8 | NDUFA8 | 1994 | 0.23 | 0.24 | YES |
25 | UQCR11 | UQCR11 | UQCR11 | 1998 | 0.23 | 0.25 | YES |
26 | COX6A1 | COX6A1 | COX6A1 | 2068 | 0.22 | 0.26 | YES |
27 | NDUFB1 | NDUFB1 | NDUFB1 | 2101 | 0.22 | 0.27 | YES |
28 | PDHA1 | PDHA1 | PDHA1 | 2107 | 0.22 | 0.28 | YES |
29 | CYC1 | CYC1 | CYC1 | 2114 | 0.22 | 0.29 | YES |
30 | PDHB | PDHB | PDHB | 2176 | 0.22 | 0.3 | YES |
31 | NDUFV1 | NDUFV1 | NDUFV1 | 2252 | 0.21 | 0.31 | YES |
32 | NDUFC2 | NDUFC2 | NDUFC2 | 2260 | 0.21 | 0.32 | YES |
33 | ATP5L | ATP5L | ATP5L | 2261 | 0.21 | 0.33 | YES |
34 | ATP5B | ATP5B | ATP5B | 2268 | 0.21 | 0.34 | YES |
35 | OGDH | OGDH | OGDH | 2293 | 0.2 | 0.34 | YES |
36 | ATP5D | ATP5D | ATP5D | 2316 | 0.2 | 0.35 | YES |
37 | NDUFA12 | NDUFA12 | NDUFA12 | 2363 | 0.2 | 0.36 | YES |
38 | BSG | BSG | BSG | 2384 | 0.2 | 0.37 | YES |
39 | SLC16A8 | SLC16A8 | SLC16A8 | 2394 | 0.2 | 0.38 | YES |
40 | DLD | DLD | DLD | 2415 | 0.2 | 0.39 | YES |
41 | NDUFB7 | NDUFB7 | NDUFB7 | 2432 | 0.19 | 0.4 | YES |
42 | SDHA | SDHA | SDHA | 2468 | 0.19 | 0.4 | YES |
43 | FH | FH | FH | 2496 | 0.19 | 0.41 | YES |
44 | DLST | DLST | DLST | 2525 | 0.19 | 0.42 | YES |
45 | UQCRHL | UQCRHL | UQCRHL | 2536 | 0.19 | 0.43 | YES |
46 | CS | CS | CS | 2598 | 0.18 | 0.43 | YES |
47 | SUCLG2 | SUCLG2 | SUCLG2 | 2609 | 0.18 | 0.44 | YES |
48 | NDUFA9 | NDUFA9 | NDUFA9 | 2614 | 0.18 | 0.45 | YES |
49 | UQCRH | UQCRH | UQCRH | 2621 | 0.18 | 0.46 | YES |
50 | ACO2 | ACO2 | ACO2 | 2675 | 0.18 | 0.46 | YES |
51 | NDUFB2 | NDUFB2 | NDUFB2 | 2681 | 0.18 | 0.47 | YES |
52 | NDUFB9 | NDUFB9 | NDUFB9 | 2721 | 0.17 | 0.48 | YES |
53 | UQCRQ | UQCRQ | UQCRQ | 2765 | 0.17 | 0.49 | YES |
54 | NDUFA7 | NDUFA7 | NDUFA7 | 2789 | 0.17 | 0.49 | YES |
55 | NDUFS3 | NDUFS3 | NDUFS3 | 2821 | 0.17 | 0.5 | YES |
56 | NDUFB6 | NDUFB6 | NDUFB6 | 2858 | 0.16 | 0.51 | YES |
57 | COX6B1 | COX6B1 | COX6B1 | 2859 | 0.16 | 0.51 | YES |
58 | COX7C | COX7C | COX7C | 2871 | 0.16 | 0.52 | YES |
59 | ATP5I | ATP5I | ATP5I | 2928 | 0.16 | 0.53 | YES |
60 | NDUFA5 | NDUFA5 | NDUFA5 | 2948 | 0.16 | 0.53 | YES |
61 | COX4I1 | COX4I1 | COX4I1 | 2983 | 0.16 | 0.54 | YES |
62 | UQCRC2 | UQCRC2 | UQCRC2 | 3015 | 0.16 | 0.55 | YES |
63 | NDUFA13 | NDUFA13 | NDUFA13 | 3073 | 0.15 | 0.55 | YES |
64 | NDUFA1 | NDUFA1 | NDUFA1 | 3099 | 0.15 | 0.56 | YES |
65 | NDUFS6 | NDUFS6 | NDUFS6 | 3118 | 0.15 | 0.56 | YES |
66 | SUCLG1 | SUCLG1 | SUCLG1 | 3222 | 0.14 | 0.56 | YES |
67 | ATP5E | ATP5E | ATP5E | 3263 | 0.14 | 0.57 | YES |
68 | MDH2 | MDH2 | MDH2 | 3271 | 0.14 | 0.57 | YES |
69 | ATP5J | ATP5J | ATP5J | 3281 | 0.14 | 0.58 | YES |
70 | COX5B | COX5B | COX5B | 3298 | 0.14 | 0.59 | YES |
71 | NDUFS1 | NDUFS1 | NDUFS1 | 3302 | 0.14 | 0.59 | YES |
72 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 3337 | 0.14 | 0.6 | YES |
73 | NDUFA11 | NDUFA11 | NDUFA11 | 3382 | 0.14 | 0.6 | YES |
74 | LDHB | LDHB | LDHB | 3436 | 0.13 | 0.61 | YES |
75 | UQCRB | UQCRB | UQCRB | 3445 | 0.13 | 0.61 | YES |
76 | ETFA | ETFA | ETFA | 3474 | 0.13 | 0.62 | YES |
77 | NDUFV2 | NDUFV2 | NDUFV2 | 3483 | 0.13 | 0.62 | YES |
78 | NDUFB5 | NDUFB5 | NDUFB5 | 3525 | 0.13 | 0.63 | YES |
79 | ATP5J2 | ATP5J2 | ATP5J2 | 3753 | 0.12 | 0.62 | YES |
80 | ATP5G1 | ATP5G1 | ATP5G1 | 3820 | 0.12 | 0.62 | YES |
81 | ATP5O | ATP5O | ATP5O | 3822 | 0.12 | 0.63 | YES |
82 | NDUFS2 | NDUFS2 | NDUFS2 | 3993 | 0.11 | 0.63 | NO |
83 | NDUFB8 | NDUFB8 | NDUFB8 | 4141 | 0.1 | 0.62 | NO |
84 | COX7A2L | COX7A2L | COX7A2L | 4254 | 0.098 | 0.62 | NO |
85 | NDUFS4 | NDUFS4 | NDUFS4 | 4371 | 0.094 | 0.62 | NO |
86 | NDUFB10 | NDUFB10 | NDUFB10 | 4377 | 0.094 | 0.62 | NO |
87 | NDUFA10 | NDUFA10 | NDUFA10 | 4452 | 0.091 | 0.62 | NO |
88 | SUCLA2 | SUCLA2 | SUCLA2 | 4630 | 0.085 | 0.62 | NO |
89 | NDUFB4 | NDUFB4 | NDUFB4 | 4664 | 0.084 | 0.62 | NO |
90 | SDHB | SDHB | SDHB | 4870 | 0.077 | 0.61 | NO |
91 | NDUFA2 | NDUFA2 | NDUFA2 | 5009 | 0.073 | 0.61 | NO |
92 | IDH3G | IDH3G | IDH3G | 5081 | 0.07 | 0.61 | NO |
93 | NDUFC1 | NDUFC1 | NDUFC1 | 5187 | 0.067 | 0.61 | NO |
94 | ATP5F1 | ATP5F1 | ATP5F1 | 5291 | 0.064 | 0.6 | NO |
95 | ATP5H | ATP5H | ATP5H | 5384 | 0.061 | 0.6 | NO |
96 | ATP5C1 | ATP5C1 | ATP5C1 | 5387 | 0.061 | 0.61 | NO |
97 | ADHFE1 | ADHFE1 | ADHFE1 | 5408 | 0.061 | 0.61 | NO |
98 | NDUFV3 | NDUFV3 | NDUFV3 | 5492 | 0.058 | 0.61 | NO |
99 | ETFB | ETFB | ETFB | 5504 | 0.058 | 0.61 | NO |
100 | UCP2 | UCP2 | UCP2 | 5801 | 0.049 | 0.59 | NO |
101 | IDH3B | IDH3B | IDH3B | 5847 | 0.047 | 0.59 | NO |
102 | NDUFB3 | NDUFB3 | NDUFB3 | 6023 | 0.043 | 0.59 | NO |
103 | SDHC | SDHC | SDHC | 6336 | 0.034 | 0.57 | NO |
104 | PDK3 | PDK3 | PDK3 | 6717 | 0.024 | 0.55 | NO |
105 | NDUFS5 | NDUFS5 | NDUFS5 | 6865 | 0.02 | 0.54 | NO |
106 | PDPR | PDPR | PDPR | 7828 | -0.0052 | 0.49 | NO |
107 | UCP3 | UCP3 | UCP3 | 8369 | -0.02 | 0.46 | NO |
108 | PDK2 | PDK2 | PDK2 | 10936 | -0.092 | 0.32 | NO |
109 | D2HGDH | D2HGDH | D2HGDH | 11174 | -0.1 | 0.32 | NO |
110 | IDH1 | IDH1 | IDH1 | 11788 | -0.12 | 0.29 | NO |
111 | SLC16A1 | SLC16A1 | SLC16A1 | 11818 | -0.12 | 0.29 | NO |
112 | PDK4 | PDK4 | PDK4 | 13474 | -0.2 | 0.21 | NO |
113 | LDHA | LDHA | LDHA | 13586 | -0.2 | 0.22 | NO |
114 | PDK1 | PDK1 | PDK1 | 14794 | -0.29 | 0.16 | NO |
115 | SLC16A3 | SLC16A3 | SLC16A3 | 16776 | -0.5 | 0.079 | NO |
Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PARKINSONS DISEASE.

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

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 | SLC2A4 | SLC2A4 | SLC2A4 | 318 | 0.7 | 0.16 | YES |
2 | FOXO1 | FOXO1 | FOXO1 | 1339 | 0.32 | 0.19 | YES |
3 | TBC1D4 | TBC1D4 | TBC1D4 | 2020 | 0.23 | 0.21 | YES |
4 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 2813 | 0.17 | 0.21 | YES |
5 | AKT1 | AKT1 | AKT1 | 3207 | 0.14 | 0.23 | YES |
6 | RAF1 | RAF1 | RAF1 | 3209 | 0.14 | 0.27 | YES |
7 | AKT2 | AKT2 | AKT2 | 3383 | 0.14 | 0.29 | YES |
8 | RICTOR | RICTOR | RICTOR | 3581 | 0.13 | 0.31 | YES |
9 | PDPK1 | PDPK1 | PDPK1 | 4080 | 0.1 | 0.31 | YES |
10 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 4374 | 0.094 | 0.32 | YES |
11 | MLST8 | MLST8 | MLST8 | 4591 | 0.086 | 0.33 | YES |
12 | MTOR | MTOR | MTOR | 4740 | 0.081 | 0.35 | YES |
13 | PRKACA | PRKACA | PRKACA | 4796 | 0.08 | 0.36 | YES |
14 | GSK3A | GSK3A | GSK3A | 4985 | 0.074 | 0.37 | YES |
15 | GSK3B | GSK3B | GSK3B | 5008 | 0.073 | 0.39 | YES |
16 | MAP3K5 | MAP3K5 | MAP3K5 | 5235 | 0.066 | 0.4 | YES |
17 | BCL2L1 | BCL2L1 | BCL2L1 | 5429 | 0.06 | 0.4 | YES |
18 | YWHAB | YWHAB | YWHAB | 5440 | 0.06 | 0.42 | YES |
19 | BAD | BAD | BAD | 6190 | 0.038 | 0.38 | NO |
20 | CHUK | CHUK | CHUK | 6454 | 0.031 | 0.38 | NO |
21 | PRKDC | PRKDC | PRKDC | 6842 | 0.02 | 0.36 | NO |
22 | FOXO4 | FOXO4 | FOXO4 | 6847 | 0.02 | 0.37 | NO |
23 | KPNA1 | KPNA1 | KPNA1 | 7058 | 0.014 | 0.36 | NO |
24 | YWHAH | YWHAH | YWHAH | 8120 | -0.013 | 0.3 | NO |
25 | YWHAZ | YWHAZ | YWHAZ | 8782 | -0.03 | 0.28 | NO |
26 | YWHAE | YWHAE | YWHAE | 9412 | -0.047 | 0.25 | NO |
27 | SRC | SRC | SRC | 9654 | -0.054 | 0.25 | NO |
28 | YWHAG | YWHAG | YWHAG | 9831 | -0.059 | 0.26 | NO |
29 | CASP9 | CASP9 | CASP9 | 10428 | -0.076 | 0.25 | NO |
30 | CDKN1B | CDKN1B | CDKN1B | 10906 | -0.091 | 0.24 | NO |
31 | AKT3 | AKT3 | AKT3 | 11294 | -0.1 | 0.25 | NO |
32 | FOXO3 | FOXO3 | FOXO3 | 11315 | -0.1 | 0.28 | NO |
33 | YWHAQ | YWHAQ | YWHAQ | 11537 | -0.11 | 0.29 | NO |
34 | CDKN1A | CDKN1A | CDKN1A | 11645 | -0.12 | 0.32 | NO |
35 | SFN | SFN | SFN | 12889 | -0.17 | 0.29 | NO |
Figure S5. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VIBRIO CHOLERAE INFECTION.

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

Table S4. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FGF9 | FGF9 | FGF9 | 12 | 1.4 | 0.063 | YES |
2 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 18 | 1.4 | 0.12 | YES |
3 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 27 | 1.3 | 0.18 | YES |
4 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 64 | 1.1 | 0.23 | YES |
5 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 214 | 0.8 | 0.26 | YES |
6 | FGF7 | FGF7 | FGF7 | 305 | 0.71 | 0.28 | YES |
7 | IRS2 | IRS2 | IRS2 | 815 | 0.44 | 0.28 | YES |
8 | PRKAG2 | PRKAG2 | PRKAG2 | 851 | 0.43 | 0.29 | YES |
9 | IRS1 | IRS1 | IRS1 | 860 | 0.43 | 0.31 | YES |
10 | ATP6V1A | ATP6V1A | ATP6V1A | 908 | 0.41 | 0.33 | YES |
11 | CAB39L | CAB39L | CAB39L | 1159 | 0.35 | 0.33 | YES |
12 | ATP6V1H | ATP6V1H | ATP6V1H | 1253 | 0.33 | 0.34 | YES |
13 | ATP6V0B | ATP6V0B | ATP6V0B | 1370 | 0.31 | 0.35 | YES |
14 | ATP6V1D | ATP6V1D | ATP6V1D | 1530 | 0.29 | 0.35 | YES |
15 | ATP6V0C | ATP6V0C | ATP6V0C | 1618 | 0.28 | 0.36 | YES |
16 | EIF4E | EIF4E | EIF4E | 1628 | 0.28 | 0.37 | YES |
17 | FGF1 | FGF1 | FGF1 | 2182 | 0.21 | 0.35 | YES |
18 | PRKAB2 | PRKAB2 | PRKAB2 | 2193 | 0.21 | 0.36 | YES |
19 | PPM1A | PPM1A | PPM1A | 2197 | 0.21 | 0.37 | YES |
20 | PDE3B | PDE3B | PDE3B | 2220 | 0.21 | 0.38 | YES |
21 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 2314 | 0.2 | 0.38 | YES |
22 | THEM4 | THEM4 | THEM4 | 2835 | 0.17 | 0.36 | NO |
23 | ATP6V1F | ATP6V1F | ATP6V1F | 2895 | 0.16 | 0.36 | NO |
24 | SHC3 | SHC3 | SHC3 | 2990 | 0.16 | 0.37 | NO |
25 | RAF1 | RAF1 | RAF1 | 3209 | 0.14 | 0.36 | NO |
26 | MAP2K1 | MAP2K1 | MAP2K1 | 3247 | 0.14 | 0.37 | NO |
27 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 3335 | 0.14 | 0.37 | NO |
28 | AKT2 | AKT2 | AKT2 | 3383 | 0.14 | 0.37 | NO |
29 | STK11 | STK11 | STK11 | 3513 | 0.13 | 0.37 | NO |
30 | PRKAB1 | PRKAB1 | PRKAB1 | 3600 | 0.13 | 0.37 | NO |
31 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 3749 | 0.12 | 0.37 | NO |
32 | RHEB | RHEB | RHEB | 3971 | 0.11 | 0.36 | NO |
33 | MAP2K2 | MAP2K2 | MAP2K2 | 4006 | 0.11 | 0.36 | NO |
34 | PRKAG1 | PRKAG1 | PRKAG1 | 4065 | 0.11 | 0.36 | NO |
35 | PDPK1 | PDPK1 | PDPK1 | 4080 | 0.1 | 0.37 | NO |
36 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 4140 | 0.1 | 0.37 | NO |
37 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 4172 | 0.1 | 0.37 | NO |
38 | KLB | KLB | KLB | 4292 | 0.097 | 0.37 | NO |
39 | TSC1 | TSC1 | TSC1 | 4494 | 0.09 | 0.36 | NO |
40 | MLST8 | MLST8 | MLST8 | 4591 | 0.086 | 0.36 | NO |
41 | PIK3R4 | PIK3R4 | PIK3R4 | 4684 | 0.083 | 0.36 | NO |
42 | MTOR | MTOR | MTOR | 4740 | 0.081 | 0.36 | NO |
43 | KRAS | KRAS | KRAS | 4784 | 0.08 | 0.36 | NO |
44 | CAB39 | CAB39 | CAB39 | 4989 | 0.073 | 0.36 | NO |
45 | FGFR1 | FGFR1 | FGFR1 | 5047 | 0.072 | 0.36 | NO |
46 | YWHAB | YWHAB | YWHAB | 5440 | 0.06 | 0.34 | NO |
47 | PRKAA1 | PRKAA1 | PRKAA1 | 5570 | 0.056 | 0.33 | NO |
48 | PIK3C3 | PIK3C3 | PIK3C3 | 5848 | 0.047 | 0.32 | NO |
49 | PIK3CA | PIK3CA | PIK3CA | 5945 | 0.045 | 0.32 | NO |
50 | HRAS | HRAS | HRAS | 6087 | 0.041 | 0.31 | NO |
51 | EIF4G1 | EIF4G1 | EIF4G1 | 6300 | 0.036 | 0.3 | NO |
52 | PIK3R2 | PIK3R2 | PIK3R2 | 6348 | 0.034 | 0.3 | NO |
53 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 6393 | 0.033 | 0.3 | NO |
54 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 6746 | 0.023 | 0.28 | NO |
55 | TSC2 | TSC2 | TSC2 | 6789 | 0.022 | 0.28 | NO |
56 | RPTOR | RPTOR | RPTOR | 6932 | 0.018 | 0.27 | NO |
57 | RPS6 | RPS6 | RPS6 | 7184 | 0.011 | 0.26 | NO |
58 | EIF4B | EIF4B | EIF4B | 7368 | 0.0068 | 0.25 | NO |
59 | FRS2 | FRS2 | FRS2 | 7713 | -0.002 | 0.23 | NO |
60 | PRKAA2 | PRKAA2 | PRKAA2 | 7968 | -0.0093 | 0.22 | NO |
61 | INSR | INSR | INSR | 7977 | -0.0095 | 0.22 | NO |
62 | MAPK1 | MAPK1 | MAPK1 | 8032 | -0.011 | 0.21 | NO |
63 | FGF23 | FGF23 | FGF23 | 8056 | -0.011 | 0.21 | NO |
64 | TRIB3 | TRIB3 | TRIB3 | 8148 | -0.014 | 0.21 | NO |
65 | FGFR2 | FGFR2 | FGFR2 | 8352 | -0.019 | 0.2 | NO |
66 | GRB10 | GRB10 | GRB10 | 8548 | -0.024 | 0.19 | NO |
67 | FGF18 | FGF18 | FGF18 | 8669 | -0.027 | 0.18 | NO |
68 | SOS1 | SOS1 | SOS1 | 9385 | -0.046 | 0.14 | NO |
69 | MAPK3 | MAPK3 | MAPK3 | 9619 | -0.053 | 0.13 | NO |
70 | TCIRG1 | TCIRG1 | TCIRG1 | 9703 | -0.055 | 0.13 | NO |
71 | CRK | CRK | CRK | 11264 | -0.1 | 0.05 | NO |
72 | STRADA | STRADA | STRADA | 11588 | -0.11 | 0.038 | NO |
73 | PIK3CB | PIK3CB | PIK3CB | 11734 | -0.12 | 0.035 | NO |
74 | GRB2 | GRB2 | GRB2 | 11942 | -0.13 | 0.03 | NO |
75 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 12048 | -0.13 | 0.03 | NO |
76 | CDK1 | CDK1 | CDK1 | 12280 | -0.14 | 0.023 | NO |
77 | SHC1 | SHC1 | SHC1 | 12366 | -0.14 | 0.025 | NO |
78 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 12631 | -0.16 | 0.018 | NO |
79 | GAB1 | GAB1 | GAB1 | 12662 | -0.16 | 0.023 | NO |
80 | NRAS | NRAS | NRAS | 13190 | -0.18 | 0.0022 | NO |
81 | STRADB | STRADB | STRADB | 13363 | -0.19 | 0.0014 | NO |
82 | FGF17 | FGF17 | FGF17 | 14210 | -0.24 | -0.034 | NO |
83 | EEF2K | EEF2K | EEF2K | 14347 | -0.25 | -0.031 | NO |
84 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 14628 | -0.27 | -0.034 | NO |
85 | FGF5 | FGF5 | FGF5 | 14688 | -0.28 | -0.024 | NO |
86 | PIK3R1 | PIK3R1 | PIK3R1 | 14710 | -0.28 | -0.013 | NO |
87 | SHC2 | SHC2 | SHC2 | 14721 | -0.28 | -0.00075 | NO |
88 | FGF2 | FGF2 | FGF2 | 15610 | -0.36 | -0.034 | NO |
89 | FGF20 | FGF20 | FGF20 | 15710 | -0.37 | -0.023 | NO |
90 | DOK1 | DOK1 | DOK1 | 16426 | -0.45 | -0.042 | NO |
91 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 16585 | -0.48 | -0.029 | NO |
92 | TLR9 | TLR9 | TLR9 | 16750 | -0.5 | -0.016 | NO |
93 | KL | KL | KL | 17193 | -0.57 | -0.014 | NO |
94 | FGFR3 | FGFR3 | FGFR3 | 17579 | -0.66 | -0.0055 | NO |
95 | FGFR4 | FGFR4 | FGFR4 | 17971 | -0.87 | 0.012 | NO |
Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI INFECTION.

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

Table S5. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ERBB4 | ERBB4 | ERBB4 | 79 | 1.1 | 0.13 | YES |
2 | NRG4 | NRG4 | NRG4 | 147 | 0.91 | 0.25 | YES |
3 | NRG2 | NRG2 | NRG2 | 208 | 0.8 | 0.34 | YES |
4 | BTC | BTC | BTC | 529 | 0.56 | 0.4 | YES |
5 | NR4A1 | NR4A1 | NR4A1 | 1046 | 0.38 | 0.42 | YES |
6 | FOXO1 | FOXO1 | FOXO1 | 1339 | 0.32 | 0.44 | YES |
7 | PHLPP1 | PHLPP1 | PHLPP1 | 1375 | 0.31 | 0.48 | YES |
8 | THEM4 | THEM4 | THEM4 | 2835 | 0.17 | 0.42 | NO |
9 | AKT1 | AKT1 | AKT1 | 3207 | 0.14 | 0.42 | NO |
10 | AKT2 | AKT2 | AKT2 | 3383 | 0.14 | 0.43 | NO |
11 | RICTOR | RICTOR | RICTOR | 3581 | 0.13 | 0.43 | NO |
12 | PDPK1 | PDPK1 | PDPK1 | 4080 | 0.1 | 0.42 | NO |
13 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 4374 | 0.094 | 0.42 | NO |
14 | MLST8 | MLST8 | MLST8 | 4591 | 0.086 | 0.41 | NO |
15 | MTOR | MTOR | MTOR | 4740 | 0.081 | 0.42 | NO |
16 | GSK3A | GSK3A | GSK3A | 4985 | 0.074 | 0.41 | NO |
17 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 5663 | 0.054 | 0.38 | NO |
18 | PIK3CA | PIK3CA | PIK3CA | 5945 | 0.045 | 0.37 | NO |
19 | BAD | BAD | BAD | 6190 | 0.038 | 0.36 | NO |
20 | CHUK | CHUK | CHUK | 6454 | 0.031 | 0.35 | NO |
21 | TSC2 | TSC2 | TSC2 | 6789 | 0.022 | 0.34 | NO |
22 | FOXO4 | FOXO4 | FOXO4 | 6847 | 0.02 | 0.34 | NO |
23 | TRIB3 | TRIB3 | TRIB3 | 8148 | -0.014 | 0.27 | NO |
24 | AKT1S1 | AKT1S1 | AKT1S1 | 8654 | -0.027 | 0.24 | NO |
25 | CASP9 | CASP9 | CASP9 | 10428 | -0.076 | 0.16 | NO |
26 | CDKN1B | CDKN1B | CDKN1B | 10906 | -0.091 | 0.14 | NO |
27 | PTEN | PTEN | PTEN | 11267 | -0.1 | 0.13 | NO |
28 | AKT3 | AKT3 | AKT3 | 11294 | -0.1 | 0.15 | NO |
29 | FOXO3 | FOXO3 | FOXO3 | 11315 | -0.1 | 0.16 | NO |
30 | CREB1 | CREB1 | CREB1 | 11558 | -0.11 | 0.16 | NO |
31 | CDKN1A | CDKN1A | CDKN1A | 11645 | -0.12 | 0.17 | NO |
32 | HBEGF | HBEGF | HBEGF | 12340 | -0.14 | 0.15 | NO |
33 | MDM2 | MDM2 | MDM2 | 12599 | -0.16 | 0.16 | NO |
34 | PIK3R1 | PIK3R1 | PIK3R1 | 14710 | -0.28 | 0.075 | NO |
35 | EREG | EREG | EREG | 16184 | -0.42 | 0.047 | NO |
36 | NRG1 | NRG1 | NRG1 | 16739 | -0.5 | 0.08 | NO |
Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MTOR 4PATHWAY.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: PID MTOR 4PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | LDHD | LDHD | LDHD | 588 | 0.52 | 0.039 | YES |
2 | COQ2 | COQ2 | COQ2 | 854 | 0.43 | 0.084 | YES |
3 | SLC25A4 | SLC25A4 | SLC25A4 | 983 | 0.39 | 0.13 | YES |
4 | TIMM8A | TIMM8A | TIMM8A | 1492 | 0.29 | 0.14 | YES |
5 | FXC1 | FXC1 | FXC1 | 1686 | 0.27 | 0.17 | YES |
6 | ATP5A1 | ATP5A1 | ATP5A1 | 1838 | 0.25 | 0.2 | YES |
7 | CHCHD4 | CHCHD4 | CHCHD4 | 2021 | 0.23 | 0.22 | YES |
8 | CYC1 | CYC1 | CYC1 | 2114 | 0.22 | 0.24 | YES |
9 | FXN | FXN | FXN | 2134 | 0.22 | 0.27 | YES |
10 | ATP5B | ATP5B | ATP5B | 2268 | 0.21 | 0.29 | YES |
11 | COX17 | COX17 | COX17 | 2328 | 0.2 | 0.32 | YES |
12 | GRPEL2 | GRPEL2 | GRPEL2 | 2333 | 0.2 | 0.35 | YES |
13 | TIMM13 | TIMM13 | TIMM13 | 2475 | 0.19 | 0.36 | YES |
14 | SLC25A12 | SLC25A12 | SLC25A12 | 2557 | 0.18 | 0.38 | YES |
15 | CS | CS | CS | 2598 | 0.18 | 0.41 | YES |
16 | PMPCB | PMPCB | PMPCB | 2607 | 0.18 | 0.43 | YES |
17 | ACO2 | ACO2 | ACO2 | 2675 | 0.18 | 0.45 | YES |
18 | DNAJC19 | DNAJC19 | DNAJC19 | 2882 | 0.16 | 0.46 | YES |
19 | TOMM40 | TOMM40 | TOMM40 | 2919 | 0.16 | 0.48 | YES |
20 | TIMM10 | TIMM10 | TIMM10 | 3037 | 0.15 | 0.5 | YES |
21 | HSPA9 | HSPA9 | HSPA9 | 3141 | 0.15 | 0.51 | YES |
22 | C18orf55 | C18orf55 | C18orf55 | 3144 | 0.15 | 0.54 | YES |
23 | TIMM44 | TIMM44 | TIMM44 | 3146 | 0.15 | 0.56 | YES |
24 | GFER | GFER | GFER | 3347 | 0.14 | 0.56 | YES |
25 | SLC25A6 | SLC25A6 | SLC25A6 | 3401 | 0.14 | 0.58 | YES |
26 | MTX2 | MTX2 | MTX2 | 3413 | 0.13 | 0.6 | YES |
27 | TIMM17B | TIMM17B | TIMM17B | 3585 | 0.13 | 0.6 | YES |
28 | TIMM50 | TIMM50 | TIMM50 | 3734 | 0.12 | 0.61 | YES |
29 | ATP5G1 | ATP5G1 | ATP5G1 | 3820 | 0.12 | 0.62 | YES |
30 | PMPCA | PMPCA | PMPCA | 3920 | 0.11 | 0.64 | YES |
31 | GRPEL1 | GRPEL1 | GRPEL1 | 4286 | 0.097 | 0.63 | YES |
32 | VDAC1 | VDAC1 | VDAC1 | 4451 | 0.091 | 0.63 | YES |
33 | TOMM22 | TOMM22 | TOMM22 | 4606 | 0.085 | 0.64 | YES |
34 | IDH3G | IDH3G | IDH3G | 5081 | 0.07 | 0.62 | NO |
35 | SAMM50 | SAMM50 | SAMM50 | 5158 | 0.068 | 0.62 | NO |
36 | TIMM9 | TIMM9 | TIMM9 | 6621 | 0.026 | 0.55 | NO |
37 | TIMM8B | TIMM8B | TIMM8B | 6678 | 0.025 | 0.55 | NO |
38 | TIMM17A | TIMM17A | TIMM17A | 7229 | 0.01 | 0.52 | NO |
39 | TOMM7 | TOMM7 | TOMM7 | 7438 | 0.005 | 0.51 | NO |
40 | HSPD1 | HSPD1 | HSPD1 | 7527 | 0.0028 | 0.5 | NO |
41 | TOMM5 | TOMM5 | TOMM5 | 7907 | -0.0075 | 0.48 | NO |
42 | TIMM22 | TIMM22 | TIMM22 | 8331 | -0.019 | 0.46 | NO |
43 | SLC25A13 | SLC25A13 | SLC25A13 | 9743 | -0.056 | 0.39 | NO |
44 | HSCB | HSCB | HSCB | 9857 | -0.06 | 0.4 | NO |
45 | TOMM20 | TOMM20 | TOMM20 | 10176 | -0.068 | 0.39 | NO |
46 | TAZ | TAZ | TAZ | 10198 | -0.069 | 0.4 | NO |
47 | BCS1L | BCS1L | BCS1L | 11063 | -0.096 | 0.36 | NO |
48 | MTX1 | MTX1 | MTX1 | 11500 | -0.11 | 0.35 | NO |
49 | TOMM70A | TOMM70A | TOMM70A | 11720 | -0.12 | 0.36 | NO |
Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID IGF1 PATHWAY.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: PID IGF1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table 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 | PDP2 | PDP2 | PDP2 | 574 | 0.53 | 0.036 | YES |
2 | NNT | NNT | NNT | 1032 | 0.38 | 0.06 | YES |
3 | PDP1 | PDP1 | PDP1 | 1133 | 0.35 | 0.1 | YES |
4 | IDH3A | IDH3A | IDH3A | 1167 | 0.35 | 0.14 | YES |
5 | IDH2 | IDH2 | IDH2 | 1218 | 0.34 | 0.18 | YES |
6 | L2HGDH | L2HGDH | L2HGDH | 1664 | 0.27 | 0.2 | YES |
7 | PDHX | PDHX | PDHX | 1756 | 0.26 | 0.22 | YES |
8 | SDHD | SDHD | SDHD | 1969 | 0.24 | 0.24 | YES |
9 | DLAT | DLAT | DLAT | 1983 | 0.23 | 0.27 | YES |
10 | PDHA1 | PDHA1 | PDHA1 | 2107 | 0.22 | 0.29 | YES |
11 | PDHB | PDHB | PDHB | 2176 | 0.22 | 0.32 | YES |
12 | OGDH | OGDH | OGDH | 2293 | 0.2 | 0.34 | YES |
13 | BSG | BSG | BSG | 2384 | 0.2 | 0.36 | YES |
14 | SLC16A8 | SLC16A8 | SLC16A8 | 2394 | 0.2 | 0.38 | YES |
15 | DLD | DLD | DLD | 2415 | 0.2 | 0.41 | YES |
16 | SDHA | SDHA | SDHA | 2468 | 0.19 | 0.43 | YES |
17 | FH | FH | FH | 2496 | 0.19 | 0.45 | YES |
18 | DLST | DLST | DLST | 2525 | 0.19 | 0.48 | YES |
19 | CS | CS | CS | 2598 | 0.18 | 0.5 | YES |
20 | SUCLG2 | SUCLG2 | SUCLG2 | 2609 | 0.18 | 0.52 | YES |
21 | ACO2 | ACO2 | ACO2 | 2675 | 0.18 | 0.54 | YES |
22 | SUCLG1 | SUCLG1 | SUCLG1 | 3222 | 0.14 | 0.52 | YES |
23 | MDH2 | MDH2 | MDH2 | 3271 | 0.14 | 0.54 | YES |
24 | LDHB | LDHB | LDHB | 3436 | 0.13 | 0.55 | YES |
25 | SUCLA2 | SUCLA2 | SUCLA2 | 4630 | 0.085 | 0.49 | NO |
26 | SDHB | SDHB | SDHB | 4870 | 0.077 | 0.49 | NO |
27 | IDH3G | IDH3G | IDH3G | 5081 | 0.07 | 0.49 | NO |
28 | ADHFE1 | ADHFE1 | ADHFE1 | 5408 | 0.061 | 0.48 | NO |
29 | IDH3B | IDH3B | IDH3B | 5847 | 0.047 | 0.46 | NO |
30 | SDHC | SDHC | SDHC | 6336 | 0.034 | 0.44 | NO |
31 | PDK3 | PDK3 | PDK3 | 6717 | 0.024 | 0.42 | NO |
32 | PDPR | PDPR | PDPR | 7828 | -0.0052 | 0.36 | NO |
33 | PDK2 | PDK2 | PDK2 | 10936 | -0.092 | 0.2 | NO |
34 | D2HGDH | D2HGDH | D2HGDH | 11174 | -0.1 | 0.2 | NO |
35 | IDH1 | IDH1 | IDH1 | 11788 | -0.12 | 0.18 | NO |
36 | SLC16A1 | SLC16A1 | SLC16A1 | 11818 | -0.12 | 0.2 | NO |
37 | PDK4 | PDK4 | PDK4 | 13474 | -0.2 | 0.13 | NO |
38 | LDHA | LDHA | LDHA | 13586 | -0.2 | 0.15 | NO |
39 | PDK1 | PDK1 | PDK1 | 14794 | -0.29 | 0.12 | NO |
40 | SLC16A3 | SLC16A3 | SLC16A3 | 16776 | -0.5 | 0.078 | 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: PID PI3KCIAKTPATHWAY.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: PID PI3KCIAKTPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S8. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 18 | 1.4 | 0.056 | YES |
2 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 27 | 1.3 | 0.11 | YES |
3 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 64 | 1.1 | 0.15 | YES |
4 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 214 | 0.8 | 0.18 | YES |
5 | ATP4B | ATP4B | ATP4B | 700 | 0.47 | 0.17 | YES |
6 | COX7A1 | COX7A1 | COX7A1 | 736 | 0.46 | 0.19 | YES |
7 | ATP6V1A | ATP6V1A | ATP6V1A | 908 | 0.41 | 0.2 | YES |
8 | ATP6V1H | ATP6V1H | ATP6V1H | 1253 | 0.33 | 0.19 | YES |
9 | COX5A | COX5A | COX5A | 1275 | 0.33 | 0.2 | YES |
10 | ATP12A | ATP12A | ATP12A | 1287 | 0.33 | 0.22 | YES |
11 | ATP6V0B | ATP6V0B | ATP6V0B | 1370 | 0.31 | 0.22 | YES |
12 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 1389 | 0.31 | 0.24 | YES |
13 | NDUFA4 | NDUFA4 | NDUFA4 | 1463 | 0.3 | 0.24 | YES |
14 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 1477 | 0.3 | 0.26 | YES |
15 | NDUFA6 | NDUFA6 | NDUFA6 | 1485 | 0.29 | 0.27 | YES |
16 | ATP6V1D | ATP6V1D | ATP6V1D | 1530 | 0.29 | 0.28 | YES |
17 | COX7B | COX7B | COX7B | 1568 | 0.28 | 0.29 | YES |
18 | COX8A | COX8A | COX8A | 1580 | 0.28 | 0.3 | YES |
19 | COX6C | COX6C | COX6C | 1590 | 0.28 | 0.31 | YES |
20 | ATP6V0C | ATP6V0C | ATP6V0C | 1618 | 0.28 | 0.32 | YES |
21 | UQCRC1 | UQCRC1 | UQCRC1 | 1668 | 0.27 | 0.33 | YES |
22 | NDUFS7 | NDUFS7 | NDUFS7 | 1835 | 0.25 | 0.33 | YES |
23 | ATP5A1 | ATP5A1 | ATP5A1 | 1838 | 0.25 | 0.34 | YES |
24 | NDUFS8 | NDUFS8 | NDUFS8 | 1917 | 0.24 | 0.34 | YES |
25 | UQCR10 | UQCR10 | UQCR10 | 1946 | 0.24 | 0.35 | YES |
26 | NDUFA3 | NDUFA3 | NDUFA3 | 1955 | 0.24 | 0.36 | YES |
27 | SDHD | SDHD | SDHD | 1969 | 0.24 | 0.37 | YES |
28 | NDUFA8 | NDUFA8 | NDUFA8 | 1994 | 0.23 | 0.38 | YES |
29 | UQCR11 | UQCR11 | UQCR11 | 1998 | 0.23 | 0.39 | YES |
30 | PPA2 | PPA2 | PPA2 | 2013 | 0.23 | 0.4 | YES |
31 | COX6A1 | COX6A1 | COX6A1 | 2068 | 0.22 | 0.4 | YES |
32 | NDUFB1 | NDUFB1 | NDUFB1 | 2101 | 0.22 | 0.41 | YES |
33 | CYC1 | CYC1 | CYC1 | 2114 | 0.22 | 0.42 | YES |
34 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 2128 | 0.22 | 0.43 | YES |
35 | NDUFV1 | NDUFV1 | NDUFV1 | 2252 | 0.21 | 0.43 | YES |
36 | NDUFC2 | NDUFC2 | NDUFC2 | 2260 | 0.21 | 0.44 | YES |
37 | ATP5L | ATP5L | ATP5L | 2261 | 0.21 | 0.45 | YES |
38 | ATP5B | ATP5B | ATP5B | 2268 | 0.21 | 0.46 | YES |
39 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 2314 | 0.2 | 0.46 | YES |
40 | ATP5D | ATP5D | ATP5D | 2316 | 0.2 | 0.47 | YES |
41 | COX17 | COX17 | COX17 | 2328 | 0.2 | 0.48 | YES |
42 | NDUFB7 | NDUFB7 | NDUFB7 | 2432 | 0.19 | 0.48 | YES |
43 | SDHA | SDHA | SDHA | 2468 | 0.19 | 0.49 | YES |
44 | COX7A2 | COX7A2 | COX7A2 | 2476 | 0.19 | 0.49 | YES |
45 | UQCRHL | UQCRHL | UQCRHL | 2536 | 0.19 | 0.5 | YES |
46 | NDUFA9 | NDUFA9 | NDUFA9 | 2614 | 0.18 | 0.5 | YES |
47 | UQCRH | UQCRH | UQCRH | 2621 | 0.18 | 0.51 | YES |
48 | NDUFB2 | NDUFB2 | NDUFB2 | 2681 | 0.18 | 0.51 | YES |
49 | NDUFB9 | NDUFB9 | NDUFB9 | 2721 | 0.17 | 0.52 | YES |
50 | UQCRQ | UQCRQ | UQCRQ | 2765 | 0.17 | 0.52 | YES |
51 | NDUFA7 | NDUFA7 | NDUFA7 | 2789 | 0.17 | 0.53 | YES |
52 | NDUFS3 | NDUFS3 | NDUFS3 | 2821 | 0.17 | 0.53 | YES |
53 | NDUFB6 | NDUFB6 | NDUFB6 | 2858 | 0.16 | 0.54 | YES |
54 | COX6B1 | COX6B1 | COX6B1 | 2859 | 0.16 | 0.55 | YES |
55 | COX7C | COX7C | COX7C | 2871 | 0.16 | 0.55 | YES |
56 | ATP6V1F | ATP6V1F | ATP6V1F | 2895 | 0.16 | 0.56 | YES |
57 | ATP5I | ATP5I | ATP5I | 2928 | 0.16 | 0.56 | YES |
58 | NDUFA5 | NDUFA5 | NDUFA5 | 2948 | 0.16 | 0.57 | YES |
59 | COX4I1 | COX4I1 | COX4I1 | 2983 | 0.16 | 0.57 | YES |
60 | UQCRC2 | UQCRC2 | UQCRC2 | 3015 | 0.16 | 0.58 | YES |
61 | NDUFA1 | NDUFA1 | NDUFA1 | 3099 | 0.15 | 0.58 | YES |
62 | NDUFS6 | NDUFS6 | NDUFS6 | 3118 | 0.15 | 0.58 | YES |
63 | ATP5E | ATP5E | ATP5E | 3263 | 0.14 | 0.58 | YES |
64 | ATP5J | ATP5J | ATP5J | 3281 | 0.14 | 0.59 | YES |
65 | COX5B | COX5B | COX5B | 3298 | 0.14 | 0.59 | YES |
66 | NDUFS1 | NDUFS1 | NDUFS1 | 3302 | 0.14 | 0.6 | YES |
67 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 3335 | 0.14 | 0.6 | YES |
68 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 3337 | 0.14 | 0.61 | YES |
69 | NDUFA11 | NDUFA11 | NDUFA11 | 3382 | 0.14 | 0.61 | YES |
70 | UQCRB | UQCRB | UQCRB | 3445 | 0.13 | 0.61 | YES |
71 | NDUFV2 | NDUFV2 | NDUFV2 | 3483 | 0.13 | 0.62 | YES |
72 | NDUFB5 | NDUFB5 | NDUFB5 | 3525 | 0.13 | 0.62 | YES |
73 | ATP5G3 | ATP5G3 | ATP5G3 | 3612 | 0.13 | 0.62 | YES |
74 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 3749 | 0.12 | 0.62 | YES |
75 | ATP5J2 | ATP5J2 | ATP5J2 | 3753 | 0.12 | 0.62 | YES |
76 | ATP5G1 | ATP5G1 | ATP5G1 | 3820 | 0.12 | 0.62 | YES |
77 | ATP5O | ATP5O | ATP5O | 3822 | 0.12 | 0.63 | YES |
78 | NDUFS2 | NDUFS2 | NDUFS2 | 3993 | 0.11 | 0.62 | NO |
79 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 4140 | 0.1 | 0.62 | NO |
80 | NDUFB8 | NDUFB8 | NDUFB8 | 4141 | 0.1 | 0.62 | NO |
81 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 4172 | 0.1 | 0.63 | NO |
82 | COX7A2L | COX7A2L | COX7A2L | 4254 | 0.098 | 0.63 | NO |
83 | NDUFS4 | NDUFS4 | NDUFS4 | 4371 | 0.094 | 0.62 | NO |
84 | NDUFB10 | NDUFB10 | NDUFB10 | 4377 | 0.094 | 0.63 | NO |
85 | NDUFA10 | NDUFA10 | NDUFA10 | 4452 | 0.091 | 0.63 | NO |
86 | NDUFB4 | NDUFB4 | NDUFB4 | 4664 | 0.084 | 0.62 | NO |
87 | SDHB | SDHB | SDHB | 4870 | 0.077 | 0.61 | NO |
88 | NDUFA2 | NDUFA2 | NDUFA2 | 5009 | 0.073 | 0.6 | NO |
89 | NDUFC1 | NDUFC1 | NDUFC1 | 5187 | 0.067 | 0.6 | NO |
90 | ATP5F1 | ATP5F1 | ATP5F1 | 5291 | 0.064 | 0.6 | NO |
91 | ATP5H | ATP5H | ATP5H | 5384 | 0.061 | 0.59 | NO |
92 | ATP5C1 | ATP5C1 | ATP5C1 | 5387 | 0.061 | 0.6 | NO |
93 | NDUFV3 | NDUFV3 | NDUFV3 | 5492 | 0.058 | 0.59 | NO |
94 | COX10 | COX10 | COX10 | 5998 | 0.043 | 0.57 | NO |
95 | NDUFB3 | NDUFB3 | NDUFB3 | 6023 | 0.043 | 0.57 | NO |
96 | COX4I2 | COX4I2 | COX4I2 | 6222 | 0.037 | 0.56 | NO |
97 | SDHC | SDHC | SDHC | 6336 | 0.034 | 0.55 | NO |
98 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 6393 | 0.033 | 0.55 | NO |
99 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 6746 | 0.023 | 0.53 | NO |
100 | NDUFS5 | NDUFS5 | NDUFS5 | 6865 | 0.02 | 0.53 | NO |
101 | ATP5G2 | ATP5G2 | ATP5G2 | 7295 | 0.0086 | 0.5 | NO |
102 | PPA1 | PPA1 | PPA1 | 9674 | -0.054 | 0.37 | NO |
103 | TCIRG1 | TCIRG1 | TCIRG1 | 9703 | -0.055 | 0.37 | NO |
104 | COX11 | COX11 | COX11 | 9730 | -0.055 | 0.38 | NO |
105 | COX15 | COX15 | COX15 | 10430 | -0.077 | 0.34 | NO |
106 | COX6B2 | COX6B2 | COX6B2 | 11082 | -0.097 | 0.31 | NO |
107 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 12631 | -0.16 | 0.23 | NO |
108 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 14628 | -0.27 | 0.13 | NO |
109 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 14716 | -0.28 | 0.14 | NO |
110 | NDUFA4L2 | NDUFA4L2 | NDUFA4L2 | 15125 | -0.31 | 0.13 | NO |
111 | LHPP | LHPP | LHPP | 15201 | -0.32 | 0.14 | NO |
112 | COX6A2 | COX6A2 | COX6A2 | 15416 | -0.34 | 0.14 | NO |
113 | COX8C | COX8C | COX8C | 15716 | -0.37 | 0.14 | NO |
Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE.

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

Table S9. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ERBB4 | ERBB4 | ERBB4 | 79 | 1.1 | 0.11 | YES |
2 | NRG4 | NRG4 | NRG4 | 147 | 0.91 | 0.2 | YES |
3 | NRG2 | NRG2 | NRG2 | 208 | 0.8 | 0.28 | YES |
4 | EGF | EGF | EGF | 320 | 0.7 | 0.35 | YES |
5 | BTC | BTC | BTC | 529 | 0.56 | 0.4 | YES |
6 | NR4A1 | NR4A1 | NR4A1 | 1046 | 0.38 | 0.41 | YES |
7 | FOXO1 | FOXO1 | FOXO1 | 1339 | 0.32 | 0.42 | YES |
8 | PHLPP1 | PHLPP1 | PHLPP1 | 1375 | 0.31 | 0.46 | YES |
9 | THEM4 | THEM4 | THEM4 | 2835 | 0.17 | 0.39 | NO |
10 | AKT1 | AKT1 | AKT1 | 3207 | 0.14 | 0.39 | NO |
11 | AKT2 | AKT2 | AKT2 | 3383 | 0.14 | 0.39 | NO |
12 | RICTOR | RICTOR | RICTOR | 3581 | 0.13 | 0.39 | NO |
13 | PDPK1 | PDPK1 | PDPK1 | 4080 | 0.1 | 0.38 | NO |
14 | ERBB2 | ERBB2 | ERBB2 | 4143 | 0.1 | 0.38 | NO |
15 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 4374 | 0.094 | 0.38 | NO |
16 | MLST8 | MLST8 | MLST8 | 4591 | 0.086 | 0.38 | NO |
17 | MTOR | MTOR | MTOR | 4740 | 0.081 | 0.38 | NO |
18 | GSK3A | GSK3A | GSK3A | 4985 | 0.074 | 0.37 | NO |
19 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 5663 | 0.054 | 0.34 | NO |
20 | PIK3CA | PIK3CA | PIK3CA | 5945 | 0.045 | 0.33 | NO |
21 | BAD | BAD | BAD | 6190 | 0.038 | 0.32 | NO |
22 | CHUK | CHUK | CHUK | 6454 | 0.031 | 0.31 | NO |
23 | TSC2 | TSC2 | TSC2 | 6789 | 0.022 | 0.3 | NO |
24 | FOXO4 | FOXO4 | FOXO4 | 6847 | 0.02 | 0.29 | NO |
25 | TRIB3 | TRIB3 | TRIB3 | 8148 | -0.014 | 0.22 | NO |
26 | AKT1S1 | AKT1S1 | AKT1S1 | 8654 | -0.027 | 0.2 | NO |
27 | CASP9 | CASP9 | CASP9 | 10428 | -0.076 | 0.11 | NO |
28 | CDKN1B | CDKN1B | CDKN1B | 10906 | -0.091 | 0.092 | NO |
29 | PTEN | PTEN | PTEN | 11267 | -0.1 | 0.084 | NO |
30 | AKT3 | AKT3 | AKT3 | 11294 | -0.1 | 0.093 | NO |
31 | FOXO3 | FOXO3 | FOXO3 | 11315 | -0.1 | 0.1 | NO |
32 | CREB1 | CREB1 | CREB1 | 11558 | -0.11 | 0.1 | NO |
33 | CDKN1A | CDKN1A | CDKN1A | 11645 | -0.12 | 0.11 | NO |
34 | GRB2 | GRB2 | GRB2 | 11942 | -0.13 | 0.11 | NO |
35 | HBEGF | HBEGF | HBEGF | 12340 | -0.14 | 0.099 | NO |
36 | MDM2 | MDM2 | MDM2 | 12599 | -0.16 | 0.1 | NO |
37 | GAB1 | GAB1 | GAB1 | 12662 | -0.16 | 0.12 | NO |
38 | EGFR | EGFR | EGFR | 13398 | -0.19 | 0.095 | NO |
39 | PIK3R1 | PIK3R1 | PIK3R1 | 14710 | -0.28 | 0.052 | NO |
40 | ERBB3 | ERBB3 | ERBB3 | 16163 | -0.42 | 0.016 | NO |
41 | EREG | EREG | EREG | 16184 | -0.42 | 0.058 | NO |
42 | NRG1 | NRG1 | NRG1 | 16739 | -0.5 | 0.08 | NO |
Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT.

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

Table S10. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ERBB4 | ERBB4 | ERBB4 | 79 | 1.1 | 0.12 | YES |
2 | NRG4 | NRG4 | NRG4 | 147 | 0.91 | 0.22 | YES |
3 | NRG2 | NRG2 | NRG2 | 208 | 0.8 | 0.3 | YES |
4 | PGR | PGR | PGR | 492 | 0.58 | 0.35 | YES |
5 | PRLR | PRLR | PRLR | 524 | 0.56 | 0.42 | YES |
6 | BTC | BTC | BTC | 529 | 0.56 | 0.48 | YES |
7 | GFAP | GFAP | GFAP | 613 | 0.5 | 0.53 | YES |
8 | APH1B | APH1B | APH1B | 1872 | 0.24 | 0.49 | NO |
9 | SH2B1 | SH2B1 | SH2B1 | 2848 | 0.16 | 0.45 | NO |
10 | PSEN2 | PSEN2 | PSEN2 | 3121 | 0.15 | 0.46 | NO |
11 | GHR | GHR | GHR | 4216 | 0.1 | 0.41 | NO |
12 | PSEN1 | PSEN1 | PSEN1 | 4891 | 0.076 | 0.38 | NO |
13 | SKP1 | SKP1 | SKP1 | 5298 | 0.064 | 0.36 | NO |
14 | CUL1 | CUL1 | CUL1 | 5932 | 0.045 | 0.33 | NO |
15 | YAP1 | YAP1 | YAP1 | 6114 | 0.04 | 0.33 | NO |
16 | TAB2 | TAB2 | TAB2 | 6201 | 0.038 | 0.33 | NO |
17 | RBX1 | RBX1 | RBX1 | 6529 | 0.029 | 0.31 | NO |
18 | APH1A | APH1A | APH1A | 7856 | -0.0059 | 0.24 | NO |
19 | JAK2 | JAK2 | JAK2 | 8340 | -0.019 | 0.22 | NO |
20 | PSENEN | PSENEN | PSENEN | 8853 | -0.031 | 0.19 | NO |
21 | NCOR1 | NCOR1 | NCOR1 | 9460 | -0.048 | 0.16 | NO |
22 | STAT5B | STAT5B | STAT5B | 9815 | -0.059 | 0.15 | NO |
23 | NCSTN | NCSTN | NCSTN | 10320 | -0.073 | 0.13 | NO |
24 | WWOX | WWOX | WWOX | 10668 | -0.083 | 0.12 | NO |
25 | BTRC | BTRC | BTRC | 10972 | -0.093 | 0.12 | NO |
26 | ADAM17 | ADAM17 | ADAM17 | 11945 | -0.13 | 0.076 | NO |
27 | HBEGF | HBEGF | HBEGF | 12340 | -0.14 | 0.07 | NO |
28 | STAT5A | STAT5A | STAT5A | 12373 | -0.14 | 0.085 | NO |
29 | GH1 | GH1 | GH1 | 13191 | -0.18 | 0.06 | NO |
30 | S100B | S100B | S100B | 14963 | -0.3 | -0.0031 | NO |
31 | CXCL12 | CXCL12 | CXCL12 | 15389 | -0.34 | 0.012 | NO |
32 | ESR1 | ESR1 | ESR1 | 15513 | -0.35 | 0.044 | NO |
33 | EREG | EREG | EREG | 16184 | -0.42 | 0.054 | NO |
34 | NRG1 | NRG1 | NRG1 | 16739 | -0.5 | 0.08 | NO |
Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME SIGNALING BY ERBB4.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SIGNALING BY ERBB4, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 4. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus2. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG ETHER LIPID METABOLISM | 27 | genes.ES.table | 0.48 | 1.4 | 0.071 | 0.2 | 1 | 0.26 | 0.17 | 0.22 | 0.15 | 0 |
KEGG RIBOSOME | 85 | genes.ES.table | 0.48 | 1.3 | 0.26 | 0.23 | 1 | 0.86 | 0.48 | 0.45 | 0.18 | 0 |
KEGG DNA REPLICATION | 36 | genes.ES.table | 0.47 | 1.5 | 0.13 | 0.15 | 0.97 | 0.69 | 0.46 | 0.37 | 0.11 | 0.001 |
KEGG HOMOLOGOUS RECOMBINATION | 26 | genes.ES.table | 0.72 | 1.8 | 0.0021 | 0.93 | 0.5 | 0.31 | 0.1 | 0.28 | 0.25 | 0.23 |
KEGG MAPK SIGNALING PATHWAY | 245 | genes.ES.table | 0.43 | 1.6 | 0.011 | 0.16 | 0.91 | 0.44 | 0.31 | 0.31 | 0.1 | 0.002 |
KEGG CALCIUM SIGNALING PATHWAY | 168 | genes.ES.table | 0.54 | 1.6 | 0.0081 | 0.16 | 0.92 | 0.48 | 0.23 | 0.38 | 0.1 | 0.002 |
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION | 238 | genes.ES.table | 0.64 | 1.6 | 0.0042 | 0.18 | 0.89 | 0.54 | 0.18 | 0.44 | 0.11 | 0.009 |
KEGG CHEMOKINE SIGNALING PATHWAY | 183 | genes.ES.table | 0.6 | 1.6 | 0.013 | 0.18 | 0.86 | 0.44 | 0.21 | 0.35 | 0.11 | 0.018 |
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION | 224 | genes.ES.table | 0.57 | 1.5 | 0.0021 | 0.16 | 0.95 | 0.5 | 0.2 | 0.4 | 0.1 | 0.002 |
KEGG CELL CYCLE | 118 | genes.ES.table | 0.5 | 1.6 | 0.055 | 0.18 | 0.88 | 0.3 | 0.22 | 0.23 | 0.11 | 0.012 |
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 | AIM2 | AIM2 | AIM2 | 25 | 0.78 | 0.095 | YES |
2 | IL6 | IL6 | IL6 | 39 | 0.74 | 0.18 | YES |
3 | ZBP1 | ZBP1 | ZBP1 | 456 | 0.51 | 0.22 | YES |
4 | CCL5 | CCL5 | CCL5 | 875 | 0.43 | 0.25 | YES |
5 | CCL4 | CCL4 | CCL4 | 925 | 0.42 | 0.3 | YES |
6 | CXCL10 | CXCL10 | CXCL10 | 1080 | 0.4 | 0.34 | YES |
7 | TMEM173 | TMEM173 | TMEM173 | 1133 | 0.39 | 0.39 | YES |
8 | IL33 | IL33 | IL33 | 1436 | 0.36 | 0.42 | YES |
9 | IL1B | IL1B | IL1B | 1465 | 0.36 | 0.46 | YES |
10 | RIPK3 | RIPK3 | RIPK3 | 1802 | 0.32 | 0.48 | YES |
11 | CASP1 | CASP1 | CASP1 | 2147 | 0.29 | 0.5 | YES |
12 | POLR3G | POLR3G | POLR3G | 2198 | 0.28 | 0.53 | YES |
13 | CCL4L2 | CCL4L2 | CCL4L2 | 2216 | 0.28 | 0.56 | YES |
14 | IFNB1 | IFNB1 | IFNB1 | 2494 | 0.26 | 0.58 | YES |
15 | PYCARD | PYCARD | PYCARD | 2639 | 0.25 | 0.6 | YES |
16 | IKBKE | IKBKE | IKBKE | 2673 | 0.24 | 0.63 | YES |
17 | IRF7 | IRF7 | IRF7 | 2719 | 0.24 | 0.66 | YES |
18 | DDX58 | DDX58 | DDX58 | 4694 | 0.13 | 0.56 | NO |
19 | POLR3C | POLR3C | POLR3C | 5626 | 0.093 | 0.52 | NO |
20 | TBK1 | TBK1 | TBK1 | 6493 | 0.071 | 0.48 | NO |
21 | POLR3D | POLR3D | POLR3D | 6694 | 0.066 | 0.48 | NO |
22 | POLR3GL | POLR3GL | POLR3GL | 6710 | 0.066 | 0.49 | NO |
23 | ADAR | ADAR | ADAR | 6934 | 0.061 | 0.48 | NO |
24 | POLR3A | POLR3A | POLR3A | 7447 | 0.05 | 0.46 | NO |
25 | POLR3H | POLR3H | POLR3H | 7626 | 0.047 | 0.46 | NO |
26 | RIPK1 | RIPK1 | RIPK1 | 7629 | 0.047 | 0.46 | NO |
27 | NFKBIA | NFKBIA | NFKBIA | 8275 | 0.036 | 0.43 | NO |
28 | RELA | RELA | RELA | 8385 | 0.034 | 0.43 | NO |
29 | POLR1D | POLR1D | POLR1D | 9017 | 0.024 | 0.4 | NO |
30 | IRF3 | IRF3 | IRF3 | 9378 | 0.018 | 0.38 | NO |
31 | IKBKG | IKBKG | IKBKG | 9977 | 0.0086 | 0.35 | NO |
32 | NFKB1 | NFKB1 | NFKB1 | 10698 | -0.0022 | 0.31 | NO |
33 | IL18 | IL18 | IL18 | 11272 | -0.011 | 0.28 | NO |
34 | POLR3F | POLR3F | POLR3F | 11540 | -0.015 | 0.27 | NO |
35 | IKBKB | IKBKB | IKBKB | 11716 | -0.018 | 0.26 | NO |
36 | POLR1C | POLR1C | POLR1C | 12381 | -0.029 | 0.23 | NO |
37 | MAVS | MAVS | MAVS | 13274 | -0.047 | 0.18 | NO |
38 | TREX1 | TREX1 | TREX1 | 13848 | -0.059 | 0.16 | NO |
39 | POLR3K | POLR3K | POLR3K | 13985 | -0.061 | 0.16 | NO |
40 | CHUK | CHUK | CHUK | 14184 | -0.066 | 0.16 | NO |
41 | NFKBIB | NFKBIB | NFKBIB | 14833 | -0.084 | 0.13 | NO |
42 | POLR3B | POLR3B | POLR3B | 15130 | -0.093 | 0.13 | NO |
43 | IFNA13 | IFNA13 | IFNA13 | 16309 | -0.14 | 0.079 | NO |
44 | IFNA1 | IFNA1 | IFNA1 | 17098 | -0.21 | 0.06 | 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 ETHER LIPID METABOLISM.

Figure S22. 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

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 | ACAN | ACAN | ACAN | 156 | 0.6 | 0.088 | YES |
2 | LUM | LUM | LUM | 195 | 0.59 | 0.18 | YES |
3 | B3GNT4 | B3GNT4 | B3GNT4 | 255 | 0.56 | 0.27 | YES |
4 | CHST1 | CHST1 | CHST1 | 259 | 0.56 | 0.36 | YES |
5 | FMOD | FMOD | FMOD | 323 | 0.55 | 0.44 | YES |
6 | PRELP | PRELP | PRELP | 458 | 0.51 | 0.51 | YES |
7 | OMD | OMD | OMD | 1157 | 0.39 | 0.54 | YES |
8 | OGN | OGN | OGN | 1410 | 0.36 | 0.58 | YES |
9 | KERA | KERA | KERA | 1550 | 0.35 | 0.63 | YES |
10 | CHST2 | CHST2 | CHST2 | 1867 | 0.31 | 0.66 | YES |
11 | CHST6 | CHST6 | CHST6 | 2177 | 0.28 | 0.69 | YES |
12 | ST3GAL2 | ST3GAL2 | ST3GAL2 | 4076 | 0.16 | 0.61 | NO |
13 | B3GNT7 | B3GNT7 | B3GNT7 | 4198 | 0.15 | 0.63 | NO |
14 | B4GALT1 | B4GALT1 | B4GALT1 | 6308 | 0.075 | 0.52 | NO |
15 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 6728 | 0.065 | 0.51 | NO |
16 | B4GALT3 | B4GALT3 | B4GALT3 | 6955 | 0.06 | 0.51 | NO |
17 | B4GALT2 | B4GALT2 | B4GALT2 | 7198 | 0.055 | 0.5 | NO |
18 | B3GNT2 | B3GNT2 | B3GNT2 | 7261 | 0.054 | 0.51 | NO |
19 | HEXB | HEXB | HEXB | 9106 | 0.022 | 0.41 | NO |
20 | HEXA | HEXA | HEXA | 9385 | 0.018 | 0.4 | NO |
21 | ST3GAL1 | ST3GAL1 | ST3GAL1 | 9408 | 0.018 | 0.4 | NO |
22 | B4GALT4 | B4GALT4 | B4GALT4 | 9820 | 0.011 | 0.38 | NO |
23 | GNS | GNS | GNS | 10285 | 0.0041 | 0.35 | NO |
24 | B3GNT1 | B3GNT1 | B3GNT1 | 11060 | -0.0077 | 0.31 | NO |
25 | ST3GAL6 | ST3GAL6 | ST3GAL6 | 11672 | -0.017 | 0.28 | NO |
26 | B4GALT5 | B4GALT5 | B4GALT5 | 12627 | -0.034 | 0.23 | NO |
27 | B3GNT3 | B3GNT3 | B3GNT3 | 14365 | -0.07 | 0.15 | NO |
28 | CHST5 | CHST5 | CHST5 | 15153 | -0.094 | 0.12 | NO |
29 | GLB1 | GLB1 | GLB1 | 15256 | -0.098 | 0.13 | NO |
30 | B4GALT6 | B4GALT6 | B4GALT6 | 16991 | -0.2 | 0.066 | 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 RIBOSOME.

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

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 | SNAI1 | SNAI1 | SNAI1 | 272 | 0.56 | 0.099 | YES |
2 | PPP1R14A | PPP1R14A | PPP1R14A | 1077 | 0.4 | 0.14 | YES |
3 | PARVG | PARVG | PARVG | 1891 | 0.31 | 0.16 | YES |
4 | ACTN1 | ACTN1 | ACTN1 | 2652 | 0.25 | 0.16 | YES |
5 | MYL9 | MYL9 | MYL9 | 2732 | 0.24 | 0.21 | YES |
6 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 2810 | 0.24 | 0.25 | YES |
7 | TACC3 | TACC3 | TACC3 | 2936 | 0.23 | 0.29 | YES |
8 | ZEB1 | ZEB1 | ZEB1 | 3120 | 0.21 | 0.32 | YES |
9 | LIMS1 | LIMS1 | LIMS1 | 3203 | 0.21 | 0.36 | YES |
10 | AURKA | AURKA | AURKA | 3760 | 0.17 | 0.37 | YES |
11 | PARVB | PARVB | PARVB | 4210 | 0.15 | 0.37 | YES |
12 | CCND1 | CCND1 | CCND1 | 4707 | 0.13 | 0.37 | YES |
13 | JUN | JUN | JUN | 4804 | 0.12 | 0.39 | YES |
14 | RHOG | RHOG | RHOG | 4949 | 0.12 | 0.41 | YES |
15 | PARVA | PARVA | PARVA | 5201 | 0.11 | 0.42 | YES |
16 | GIT2 | GIT2 | GIT2 | 5242 | 0.1 | 0.43 | YES |
17 | PXN | PXN | PXN | 5350 | 0.1 | 0.45 | YES |
18 | TNS1 | TNS1 | TNS1 | 5494 | 0.097 | 0.46 | YES |
19 | PPP1R12A | PPP1R12A | PPP1R12A | 6019 | 0.083 | 0.45 | YES |
20 | PARP1 | PARP1 | PARP1 | 6073 | 0.082 | 0.46 | YES |
21 | CREB1 | CREB1 | CREB1 | 6311 | 0.075 | 0.46 | YES |
22 | IQGAP1 | IQGAP1 | IQGAP1 | 6422 | 0.072 | 0.47 | YES |
23 | LIMS2 | LIMS2 | LIMS2 | 6490 | 0.071 | 0.48 | YES |
24 | NACA | NACA | NACA | 7269 | 0.054 | 0.45 | NO |
25 | NCK2 | NCK2 | NCK2 | 7304 | 0.053 | 0.46 | NO |
26 | ZYX | ZYX | ZYX | 7359 | 0.052 | 0.47 | NO |
27 | CKAP5 | CKAP5 | CKAP5 | 7366 | 0.052 | 0.48 | NO |
28 | PPP1R14B | PPP1R14B | PPP1R14B | 8256 | 0.036 | 0.44 | NO |
29 | XPO1 | XPO1 | XPO1 | 8321 | 0.035 | 0.44 | NO |
30 | CDC42 | CDC42 | CDC42 | 8943 | 0.025 | 0.41 | NO |
31 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 8948 | 0.025 | 0.42 | NO |
32 | ILK | ILK | ILK | 9077 | 0.023 | 0.42 | NO |
33 | RAC1 | RAC1 | RAC1 | 9290 | 0.02 | 0.41 | NO |
34 | ELMO2 | ELMO2 | ELMO2 | 9567 | 0.015 | 0.4 | NO |
35 | CTNNB1 | CTNNB1 | CTNNB1 | 9644 | 0.014 | 0.39 | NO |
36 | RICTOR | RICTOR | RICTOR | 10230 | 0.0048 | 0.36 | NO |
37 | RUVBL2 | RUVBL2 | RUVBL2 | 10480 | 0.00092 | 0.35 | NO |
38 | CDC37 | CDC37 | CDC37 | 11186 | -0.0093 | 0.31 | NO |
39 | AKT1 | AKT1 | AKT1 | 11800 | -0.02 | 0.28 | NO |
40 | DIAPH1 | DIAPH1 | DIAPH1 | 11864 | -0.021 | 0.28 | NO |
41 | ILKAP | ILKAP | ILKAP | 13282 | -0.047 | 0.22 | NO |
42 | GSK3B | GSK3B | GSK3B | 13818 | -0.058 | 0.2 | NO |
43 | PPP1R14C | PPP1R14C | PPP1R14C | 14072 | -0.063 | 0.2 | NO |
44 | RUVBL1 | RUVBL1 | RUVBL1 | 14571 | -0.076 | 0.18 | NO |
45 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 14586 | -0.077 | 0.2 | NO |
Figure S25. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DNA REPLICATION.

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

Table 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 | BLM | BLM | BLM | 446 | 0.51 | 0.11 | YES |
2 | RAD54B | RAD54B | RAD54B | 966 | 0.42 | 0.19 | YES |
3 | RAD51 | RAD51 | RAD51 | 1058 | 0.4 | 0.29 | YES |
4 | RAD54L | RAD54L | RAD54L | 1100 | 0.4 | 0.39 | YES |
5 | BRCA2 | BRCA2 | BRCA2 | 1199 | 0.39 | 0.49 | YES |
6 | EME1 | EME1 | EME1 | 1232 | 0.38 | 0.59 | YES |
7 | RPA4 | RPA4 | RPA4 | 1823 | 0.32 | 0.64 | YES |
8 | XRCC2 | XRCC2 | XRCC2 | 1895 | 0.31 | 0.72 | YES |
9 | POLD3 | POLD3 | POLD3 | 4689 | 0.13 | 0.6 | NO |
10 | MRE11A | MRE11A | MRE11A | 5601 | 0.094 | 0.57 | NO |
11 | NBN | NBN | NBN | 5609 | 0.093 | 0.6 | NO |
12 | POLD4 | POLD4 | POLD4 | 6553 | 0.069 | 0.56 | NO |
13 | RPA2 | RPA2 | RPA2 | 8111 | 0.038 | 0.49 | NO |
14 | SHFM1 | SHFM1 | SHFM1 | 9047 | 0.023 | 0.44 | NO |
15 | RAD51C | RAD51C | RAD51C | 9174 | 0.021 | 0.44 | NO |
16 | SSBP1 | SSBP1 | SSBP1 | 9684 | 0.013 | 0.41 | NO |
17 | RPA1 | RPA1 | RPA1 | 9811 | 0.011 | 0.41 | NO |
18 | RAD50 | RAD50 | RAD50 | 10165 | 0.0059 | 0.39 | NO |
19 | RAD52 | RAD52 | RAD52 | 10393 | 0.0024 | 0.38 | NO |
20 | TOP3A | TOP3A | TOP3A | 10648 | -0.0015 | 0.37 | NO |
21 | POLD1 | POLD1 | POLD1 | 11171 | -0.0091 | 0.34 | NO |
22 | POLD2 | POLD2 | POLD2 | 11686 | -0.018 | 0.32 | NO |
23 | MUS81 | MUS81 | MUS81 | 12090 | -0.024 | 0.3 | NO |
24 | XRCC3 | XRCC3 | XRCC3 | 12325 | -0.029 | 0.3 | NO |
25 | RPA3 | RPA3 | RPA3 | 12623 | -0.034 | 0.29 | NO |
26 | TOP3B | TOP3B | TOP3B | 14332 | -0.069 | 0.21 | 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 HOMOLOGOUS RECOMBINATION.

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

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 | IL1R2 | IL1R2 | IL1R2 | 5 | 0.89 | 0.055 | YES |
2 | IL6 | IL6 | IL6 | 39 | 0.74 | 0.099 | YES |
3 | IL2RA | IL2RA | IL2RA | 54 | 0.69 | 0.14 | YES |
4 | HGF | HGF | HGF | 409 | 0.52 | 0.15 | YES |
5 | NOD2 | NOD2 | NOD2 | 426 | 0.52 | 0.18 | YES |
6 | IL2RB | IL2RB | IL2RB | 541 | 0.49 | 0.21 | YES |
7 | LCK | LCK | LCK | 580 | 0.48 | 0.24 | YES |
8 | JAK3 | JAK3 | JAK3 | 733 | 0.45 | 0.26 | YES |
9 | IL2RG | IL2RG | IL2RG | 786 | 0.45 | 0.28 | YES |
10 | IL1RAP | IL1RAP | IL1RAP | 862 | 0.43 | 0.3 | YES |
11 | IL7R | IL7R | IL7R | 878 | 0.43 | 0.33 | YES |
12 | IL2 | IL2 | IL2 | 1027 | 0.41 | 0.35 | YES |
13 | CDK1 | CDK1 | CDK1 | 1064 | 0.4 | 0.37 | YES |
14 | CSF2RB | CSF2RB | CSF2RB | 1089 | 0.4 | 0.39 | YES |
15 | IL3RA | IL3RA | IL3RA | 1118 | 0.4 | 0.42 | YES |
16 | VAV1 | VAV1 | VAV1 | 1268 | 0.38 | 0.43 | YES |
17 | IL1RN | IL1RN | IL1RN | 1303 | 0.37 | 0.45 | YES |
18 | IL1B | IL1B | IL1B | 1465 | 0.36 | 0.47 | YES |
19 | IL7 | IL7 | IL7 | 1680 | 0.33 | 0.48 | YES |
20 | CSF2 | CSF2 | CSF2 | 1699 | 0.33 | 0.49 | YES |
21 | IRAK3 | IRAK3 | IRAK3 | 2043 | 0.3 | 0.49 | YES |
22 | CSF2RA | CSF2RA | CSF2RA | 2093 | 0.29 | 0.51 | YES |
23 | CASP1 | CASP1 | CASP1 | 2147 | 0.29 | 0.52 | YES |
24 | HCK | HCK | HCK | 2167 | 0.29 | 0.54 | YES |
25 | SOCS3 | SOCS3 | SOCS3 | 2188 | 0.28 | 0.56 | YES |
26 | MAP3K8 | MAP3K8 | MAP3K8 | 2496 | 0.26 | 0.56 | YES |
27 | RIPK2 | RIPK2 | RIPK2 | 2853 | 0.23 | 0.55 | YES |
28 | LYN | LYN | LYN | 3020 | 0.22 | 0.56 | YES |
29 | IL1R1 | IL1R1 | IL1R1 | 3078 | 0.22 | 0.57 | YES |
30 | SHC1 | SHC1 | SHC1 | 3096 | 0.22 | 0.58 | YES |
31 | IL6ST | IL6ST | IL6ST | 3331 | 0.2 | 0.58 | YES |
32 | PELI1 | PELI1 | PELI1 | 3508 | 0.19 | 0.58 | YES |
33 | FYN | FYN | FYN | 3583 | 0.18 | 0.59 | YES |
34 | IL1A | IL1A | IL1A | 4051 | 0.16 | 0.57 | NO |
35 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 4522 | 0.13 | 0.55 | NO |
36 | PIK3CD | PIK3CD | PIK3CD | 4559 | 0.13 | 0.56 | NO |
37 | STAT1 | STAT1 | STAT1 | 4591 | 0.13 | 0.57 | NO |
38 | JAK2 | JAK2 | JAK2 | 4729 | 0.12 | 0.57 | NO |
39 | MYD88 | MYD88 | MYD88 | 4748 | 0.12 | 0.57 | NO |
40 | PIK3R1 | PIK3R1 | PIK3R1 | 4819 | 0.12 | 0.58 | NO |
41 | NFKB2 | NFKB2 | NFKB2 | 5574 | 0.094 | 0.54 | NO |
42 | CRKL | CRKL | CRKL | 5585 | 0.094 | 0.55 | NO |
43 | NRAS | NRAS | NRAS | 5632 | 0.092 | 0.55 | NO |
44 | NOD1 | NOD1 | NOD1 | 5682 | 0.091 | 0.55 | NO |
45 | IL5RA | IL5RA | IL5RA | 5767 | 0.089 | 0.55 | NO |
46 | IRAK2 | IRAK2 | IRAK2 | 5886 | 0.086 | 0.55 | NO |
47 | CBL | CBL | CBL | 6082 | 0.081 | 0.55 | NO |
48 | MAP2K1 | MAP2K1 | MAP2K1 | 6443 | 0.072 | 0.53 | NO |
49 | SOS1 | SOS1 | SOS1 | 6632 | 0.068 | 0.52 | NO |
50 | PTPN6 | PTPN6 | PTPN6 | 6659 | 0.067 | 0.53 | NO |
51 | STAT5A | STAT5A | STAT5A | 6673 | 0.067 | 0.53 | NO |
52 | YWHAZ | YWHAZ | YWHAZ | 6733 | 0.065 | 0.53 | NO |
53 | STAT3 | STAT3 | STAT3 | 6793 | 0.064 | 0.53 | NO |
54 | SYK | SYK | SYK | 6805 | 0.064 | 0.54 | NO |
55 | PIK3CA | PIK3CA | PIK3CA | 6830 | 0.063 | 0.54 | NO |
56 | PIK3R3 | PIK3R3 | PIK3R3 | 7200 | 0.055 | 0.52 | NO |
57 | CUL1 | CUL1 | CUL1 | 7436 | 0.05 | 0.51 | NO |
58 | TAB2 | TAB2 | TAB2 | 7699 | 0.046 | 0.5 | NO |
59 | MAP2K6 | MAP2K6 | MAP2K6 | 7719 | 0.045 | 0.5 | NO |
60 | MAPK1 | MAPK1 | MAPK1 | 8062 | 0.039 | 0.48 | NO |
61 | RBX1 | RBX1 | RBX1 | 8235 | 0.036 | 0.48 | NO |
62 | RELA | RELA | RELA | 8385 | 0.034 | 0.47 | NO |
63 | IRAK1 | IRAK1 | IRAK1 | 8437 | 0.033 | 0.47 | NO |
64 | TNIP2 | TNIP2 | TNIP2 | 8679 | 0.029 | 0.46 | NO |
65 | PTK2B | PTK2B | PTK2B | 8891 | 0.026 | 0.45 | NO |
66 | IRAK4 | IRAK4 | IRAK4 | 8945 | 0.025 | 0.45 | NO |
67 | IL5 | IL5 | IL5 | 9048 | 0.023 | 0.44 | NO |
68 | MAPK3 | MAPK3 | MAPK3 | 9142 | 0.022 | 0.44 | NO |
69 | UBE2N | UBE2N | UBE2N | 9359 | 0.018 | 0.43 | NO |
70 | TYK2 | TYK2 | TYK2 | 9540 | 0.016 | 0.42 | NO |
71 | JAK1 | JAK1 | JAK1 | 9605 | 0.014 | 0.42 | NO |
72 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 9666 | 0.013 | 0.42 | NO |
73 | CRK | CRK | CRK | 9824 | 0.011 | 0.41 | NO |
74 | MAP3K7 | MAP3K7 | MAP3K7 | 9835 | 0.011 | 0.41 | NO |
75 | IKBKG | IKBKG | IKBKG | 9977 | 0.0086 | 0.4 | NO |
76 | YWHAB | YWHAB | YWHAB | 10047 | 0.0076 | 0.4 | NO |
77 | GRB2 | GRB2 | GRB2 | 10108 | 0.0067 | 0.39 | NO |
78 | PIK3CB | PIK3CB | PIK3CB | 10152 | 0.006 | 0.39 | NO |
79 | BLNK | BLNK | BLNK | 10198 | 0.0054 | 0.39 | NO |
80 | GAB2 | GAB2 | GAB2 | 10254 | 0.0045 | 0.39 | NO |
81 | IL6R | IL6R | IL6R | 10469 | 0.0011 | 0.38 | NO |
82 | MAP3K3 | MAP3K3 | MAP3K3 | 10797 | -0.0038 | 0.36 | NO |
83 | YES1 | YES1 | YES1 | 10870 | -0.0048 | 0.35 | NO |
84 | MAP2K2 | MAP2K2 | MAP2K2 | 10960 | -0.0062 | 0.35 | NO |
85 | SKP1 | SKP1 | SKP1 | 11074 | -0.0079 | 0.34 | NO |
86 | IL18 | IL18 | IL18 | 11272 | -0.011 | 0.33 | NO |
87 | MAP2K4 | MAP2K4 | MAP2K4 | 11518 | -0.015 | 0.32 | NO |
88 | SQSTM1 | SQSTM1 | SQSTM1 | 11521 | -0.015 | 0.32 | NO |
89 | STAT5B | STAT5B | STAT5B | 11568 | -0.016 | 0.32 | NO |
90 | PRKACB | PRKACB | PRKACB | 11569 | -0.016 | 0.32 | NO |
91 | TRAF6 | TRAF6 | TRAF6 | 11607 | -0.016 | 0.32 | NO |
92 | IKBKB | IKBKB | IKBKB | 11716 | -0.018 | 0.32 | NO |
93 | INPPL1 | INPPL1 | INPPL1 | 12149 | -0.026 | 0.29 | NO |
94 | RAF1 | RAF1 | RAF1 | 12262 | -0.027 | 0.29 | NO |
95 | HRAS | HRAS | HRAS | 12430 | -0.03 | 0.28 | NO |
96 | TAB1 | TAB1 | TAB1 | 12859 | -0.038 | 0.26 | NO |
97 | TAB3 | TAB3 | TAB3 | 13096 | -0.043 | 0.25 | NO |
98 | PIK3R2 | PIK3R2 | PIK3R2 | 13129 | -0.044 | 0.25 | NO |
99 | PELI2 | PELI2 | PELI2 | 13223 | -0.046 | 0.25 | NO |
100 | BTRC | BTRC | BTRC | 13309 | -0.047 | 0.25 | NO |
101 | KRAS | KRAS | KRAS | 13554 | -0.052 | 0.24 | NO |
102 | PELI3 | PELI3 | PELI3 | 13792 | -0.058 | 0.23 | NO |
103 | CHUK | CHUK | CHUK | 14184 | -0.066 | 0.21 | NO |
104 | TEC | TEC | TEC | 14827 | -0.084 | 0.18 | NO |
105 | TOLLIP | TOLLIP | TOLLIP | 16067 | -0.13 | 0.12 | 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 MAPK SIGNALING PATHWAY.

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

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 | GZMB | GZMB | GZMB | 341 | 0.54 | 0.076 | YES |
2 | BIRC3 | BIRC3 | BIRC3 | 1081 | 0.4 | 0.1 | YES |
3 | PRF1 | PRF1 | PRF1 | 1359 | 0.37 | 0.16 | YES |
4 | LMNB1 | LMNB1 | LMNB1 | 1480 | 0.35 | 0.21 | YES |
5 | TFAP2A | TFAP2A | TFAP2A | 1744 | 0.32 | 0.25 | YES |
6 | CASP1 | CASP1 | CASP1 | 2147 | 0.29 | 0.28 | YES |
7 | ARHGDIB | ARHGDIB | ARHGDIB | 2950 | 0.22 | 0.28 | YES |
8 | BID | BID | BID | 2955 | 0.22 | 0.32 | YES |
9 | VIM | VIM | VIM | 3207 | 0.21 | 0.34 | YES |
10 | CASP4 | CASP4 | CASP4 | 3309 | 0.2 | 0.37 | YES |
11 | CASP10 | CASP10 | CASP10 | 3569 | 0.18 | 0.38 | YES |
12 | ACTA1 | ACTA1 | ACTA1 | 4298 | 0.14 | 0.37 | YES |
13 | LIMK1 | LIMK1 | LIMK1 | 4633 | 0.13 | 0.37 | YES |
14 | CASP3 | CASP3 | CASP3 | 4877 | 0.12 | 0.38 | YES |
15 | CASP8 | CASP8 | CASP8 | 5005 | 0.11 | 0.4 | YES |
16 | TNF | TNF | TNF | 5070 | 0.11 | 0.41 | YES |
17 | CASP7 | CASP7 | CASP7 | 5287 | 0.1 | 0.42 | YES |
18 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 5388 | 0.1 | 0.43 | YES |
19 | APAF1 | APAF1 | APAF1 | 5417 | 0.099 | 0.44 | YES |
20 | PARP1 | PARP1 | PARP1 | 6073 | 0.082 | 0.42 | NO |
21 | BIRC2 | BIRC2 | BIRC2 | 6415 | 0.072 | 0.42 | NO |
22 | RIPK1 | RIPK1 | RIPK1 | 7629 | 0.047 | 0.36 | NO |
23 | TOP1 | TOP1 | TOP1 | 7665 | 0.046 | 0.36 | NO |
24 | PTK2 | PTK2 | PTK2 | 8165 | 0.038 | 0.34 | NO |
25 | CASP2 | CASP2 | CASP2 | 8175 | 0.037 | 0.35 | NO |
26 | GSN | GSN | GSN | 8354 | 0.034 | 0.35 | NO |
27 | DFFB | DFFB | DFFB | 8594 | 0.03 | 0.34 | NO |
28 | TRADD | TRADD | TRADD | 9398 | 0.018 | 0.3 | NO |
29 | MADD | MADD | MADD | 9523 | 0.016 | 0.29 | NO |
30 | XIAP | XIAP | XIAP | 9576 | 0.015 | 0.29 | NO |
31 | CFL2 | CFL2 | CFL2 | 9689 | 0.013 | 0.29 | NO |
32 | BAX | BAX | BAX | 9825 | 0.011 | 0.28 | NO |
33 | LMNA | LMNA | LMNA | 10086 | 0.007 | 0.27 | NO |
34 | LMNB2 | LMNB2 | LMNB2 | 10325 | 0.0035 | 0.26 | NO |
35 | CASP6 | CASP6 | CASP6 | 10438 | 0.0015 | 0.25 | NO |
36 | NUMA1 | NUMA1 | NUMA1 | 11529 | -0.015 | 0.19 | NO |
37 | DIABLO | DIABLO | DIABLO | 11857 | -0.021 | 0.18 | NO |
38 | CASP9 | CASP9 | CASP9 | 11983 | -0.023 | 0.18 | NO |
39 | APP | APP | APP | 12088 | -0.024 | 0.18 | NO |
40 | CRADD | CRADD | CRADD | 12673 | -0.035 | 0.15 | NO |
41 | SLK | SLK | SLK | 12921 | -0.04 | 0.14 | NO |
42 | DFFA | DFFA | DFFA | 13073 | -0.043 | 0.14 | NO |
43 | TRAF2 | TRAF2 | TRAF2 | 13448 | -0.05 | 0.13 | NO |
44 | SPTAN1 | SPTAN1 | SPTAN1 | 14012 | -0.062 | 0.11 | NO |
45 | KRT18 | KRT18 | KRT18 | 14174 | -0.066 | 0.11 | NO |
46 | SREBF1 | SREBF1 | SREBF1 | 14333 | -0.069 | 0.12 | NO |
47 | SATB1 | SATB1 | SATB1 | 14613 | -0.078 | 0.11 | NO |
48 | MAP3K1 | MAP3K1 | MAP3K1 | 14903 | -0.086 | 0.11 | NO |
49 | GAS2 | GAS2 | GAS2 | 15757 | -0.12 | 0.086 | NO |
50 | BCL2 | BCL2 | BCL2 | 16136 | -0.14 | 0.089 | NO |
51 | CYCS | CYCS | CYCS | 16249 | -0.14 | 0.11 | NO |
Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CALCIUM SIGNALING PATHWAY.

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

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 | ACAN | ACAN | ACAN | 156 | 0.6 | 0.09 | YES |
2 | LUM | LUM | LUM | 195 | 0.59 | 0.18 | YES |
3 | B3GNT4 | B3GNT4 | B3GNT4 | 255 | 0.56 | 0.27 | YES |
4 | CHST1 | CHST1 | CHST1 | 259 | 0.56 | 0.36 | YES |
5 | FMOD | FMOD | FMOD | 323 | 0.55 | 0.45 | YES |
6 | PRELP | PRELP | PRELP | 458 | 0.51 | 0.52 | YES |
7 | OMD | OMD | OMD | 1157 | 0.39 | 0.55 | YES |
8 | OGN | OGN | OGN | 1410 | 0.36 | 0.6 | YES |
9 | KERA | KERA | KERA | 1550 | 0.35 | 0.64 | YES |
10 | CHST2 | CHST2 | CHST2 | 1867 | 0.31 | 0.68 | YES |
11 | CHST6 | CHST6 | CHST6 | 2177 | 0.28 | 0.71 | YES |
12 | ST3GAL2 | ST3GAL2 | ST3GAL2 | 4076 | 0.16 | 0.63 | NO |
13 | B3GNT7 | B3GNT7 | B3GNT7 | 4198 | 0.15 | 0.65 | NO |
14 | B4GALT1 | B4GALT1 | B4GALT1 | 6308 | 0.075 | 0.54 | NO |
15 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 6728 | 0.065 | 0.53 | NO |
16 | B4GALT3 | B4GALT3 | B4GALT3 | 6955 | 0.06 | 0.53 | NO |
17 | B4GALT2 | B4GALT2 | B4GALT2 | 7198 | 0.055 | 0.52 | NO |
18 | B3GNT2 | B3GNT2 | B3GNT2 | 7261 | 0.054 | 0.53 | NO |
19 | ST3GAL1 | ST3GAL1 | ST3GAL1 | 9408 | 0.018 | 0.41 | NO |
20 | B4GALT4 | B4GALT4 | B4GALT4 | 9820 | 0.011 | 0.39 | NO |
21 | B3GNT1 | B3GNT1 | B3GNT1 | 11060 | -0.0077 | 0.32 | NO |
22 | ST3GAL6 | ST3GAL6 | ST3GAL6 | 11672 | -0.017 | 0.3 | NO |
23 | B4GALT5 | B4GALT5 | B4GALT5 | 12627 | -0.034 | 0.25 | NO |
24 | B3GNT3 | B3GNT3 | B3GNT3 | 14365 | -0.07 | 0.16 | NO |
25 | CHST5 | CHST5 | CHST5 | 15153 | -0.094 | 0.14 | NO |
26 | B4GALT6 | B4GALT6 | B4GALT6 | 16991 | -0.2 | 0.066 | 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 CYTOKINE CYTOKINE RECEPTOR INTERACTION.

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

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 | IL2RA | IL2RA | IL2RA | 54 | 0.69 | 0.11 | YES |
2 | IL2RB | IL2RB | IL2RB | 541 | 0.49 | 0.16 | YES |
3 | LCK | LCK | LCK | 580 | 0.48 | 0.23 | YES |
4 | JAK3 | JAK3 | JAK3 | 733 | 0.45 | 0.29 | YES |
5 | IL2RG | IL2RG | IL2RG | 786 | 0.45 | 0.36 | YES |
6 | IL2 | IL2 | IL2 | 1027 | 0.41 | 0.41 | YES |
7 | CDK1 | CDK1 | CDK1 | 1064 | 0.4 | 0.47 | YES |
8 | CSF2RB | CSF2RB | CSF2RB | 1089 | 0.4 | 0.53 | YES |
9 | IL3RA | IL3RA | IL3RA | 1118 | 0.4 | 0.59 | YES |
10 | CSF2 | CSF2 | CSF2 | 1699 | 0.33 | 0.61 | YES |
11 | CSF2RA | CSF2RA | CSF2RA | 2093 | 0.29 | 0.64 | YES |
12 | SHC1 | SHC1 | SHC1 | 3096 | 0.22 | 0.62 | NO |
13 | PIK3CD | PIK3CD | PIK3CD | 4559 | 0.13 | 0.56 | NO |
14 | JAK2 | JAK2 | JAK2 | 4729 | 0.12 | 0.57 | NO |
15 | PIK3R1 | PIK3R1 | PIK3R1 | 4819 | 0.12 | 0.58 | NO |
16 | NRAS | NRAS | NRAS | 5632 | 0.092 | 0.55 | NO |
17 | IL5RA | IL5RA | IL5RA | 5767 | 0.089 | 0.56 | NO |
18 | MAP2K1 | MAP2K1 | MAP2K1 | 6443 | 0.072 | 0.53 | NO |
19 | SOS1 | SOS1 | SOS1 | 6632 | 0.068 | 0.53 | NO |
20 | PTPN6 | PTPN6 | PTPN6 | 6659 | 0.067 | 0.54 | NO |
21 | STAT5A | STAT5A | STAT5A | 6673 | 0.067 | 0.55 | NO |
22 | SYK | SYK | SYK | 6805 | 0.064 | 0.55 | NO |
23 | PIK3CA | PIK3CA | PIK3CA | 6830 | 0.063 | 0.56 | NO |
24 | PIK3R3 | PIK3R3 | PIK3R3 | 7200 | 0.055 | 0.55 | NO |
25 | MAPK1 | MAPK1 | MAPK1 | 8062 | 0.039 | 0.51 | NO |
26 | PTK2B | PTK2B | PTK2B | 8891 | 0.026 | 0.47 | NO |
27 | IL5 | IL5 | IL5 | 9048 | 0.023 | 0.46 | NO |
28 | MAPK3 | MAPK3 | MAPK3 | 9142 | 0.022 | 0.46 | NO |
29 | JAK1 | JAK1 | JAK1 | 9605 | 0.014 | 0.44 | NO |
30 | YWHAB | YWHAB | YWHAB | 10047 | 0.0076 | 0.41 | NO |
31 | GRB2 | GRB2 | GRB2 | 10108 | 0.0067 | 0.41 | NO |
32 | PIK3CB | PIK3CB | PIK3CB | 10152 | 0.006 | 0.41 | NO |
33 | GAB2 | GAB2 | GAB2 | 10254 | 0.0045 | 0.41 | NO |
34 | MAP2K2 | MAP2K2 | MAP2K2 | 10960 | -0.0062 | 0.37 | NO |
35 | STAT5B | STAT5B | STAT5B | 11568 | -0.016 | 0.34 | NO |
36 | INPPL1 | INPPL1 | INPPL1 | 12149 | -0.026 | 0.31 | NO |
37 | RAF1 | RAF1 | RAF1 | 12262 | -0.027 | 0.31 | NO |
38 | HRAS | HRAS | HRAS | 12430 | -0.03 | 0.3 | NO |
39 | PIK3R2 | PIK3R2 | PIK3R2 | 13129 | -0.044 | 0.27 | NO |
40 | KRAS | KRAS | KRAS | 13554 | -0.052 | 0.26 | 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 CHEMOKINE SIGNALING PATHWAY.

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

Table S19. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SERPINE1 | SERPINE1 | SERPINE1 | 63 | 0.68 | 0.062 | YES |
2 | RUNX2 | RUNX2 | RUNX2 | 361 | 0.54 | 0.098 | YES |
3 | IL10 | IL10 | IL10 | 463 | 0.51 | 0.14 | YES |
4 | RUNX1 | RUNX1 | RUNX1 | 597 | 0.48 | 0.18 | YES |
5 | COL1A2 | COL1A2 | COL1A2 | 702 | 0.46 | 0.22 | YES |
6 | DLX1 | DLX1 | DLX1 | 710 | 0.46 | 0.26 | YES |
7 | GSC | GSC | GSC | 808 | 0.44 | 0.3 | YES |
8 | SAP30 | SAP30 | SAP30 | 978 | 0.42 | 0.33 | YES |
9 | RUNX3 | RUNX3 | RUNX3 | 1122 | 0.4 | 0.36 | YES |
10 | CEBPB | CEBPB | CEBPB | 1930 | 0.31 | 0.35 | YES |
11 | MEF2C | MEF2C | MEF2C | 2164 | 0.29 | 0.36 | YES |
12 | CDKN2B | CDKN2B | CDKN2B | 2175 | 0.28 | 0.39 | YES |
13 | IFNB1 | IFNB1 | IFNB1 | 2494 | 0.26 | 0.4 | YES |
14 | NKX2-5 | NKX2-5 | NKX2-5 | 2506 | 0.26 | 0.42 | YES |
15 | IRF7 | IRF7 | IRF7 | 2719 | 0.24 | 0.44 | YES |
16 | SKIL | SKIL | SKIL | 2781 | 0.24 | 0.46 | YES |
17 | FOXG1 | FOXG1 | FOXG1 | 2857 | 0.23 | 0.47 | YES |
18 | RBL1 | RBL1 | RBL1 | 2945 | 0.22 | 0.49 | YES |
19 | GATA3 | GATA3 | GATA3 | 3052 | 0.22 | 0.51 | YES |
20 | NR3C1 | NR3C1 | NR3C1 | 3177 | 0.21 | 0.52 | YES |
21 | FOS | FOS | FOS | 3629 | 0.18 | 0.51 | YES |
22 | MYC | MYC | MYC | 3777 | 0.17 | 0.52 | YES |
23 | ESR1 | ESR1 | ESR1 | 4005 | 0.16 | 0.52 | YES |
24 | PIAS3 | PIAS3 | PIAS3 | 4184 | 0.15 | 0.53 | YES |
25 | JUN | JUN | JUN | 4804 | 0.12 | 0.51 | NO |
26 | ITGB5 | ITGB5 | ITGB5 | 4952 | 0.12 | 0.51 | NO |
27 | CBFB | CBFB | CBFB | 4961 | 0.12 | 0.52 | NO |
28 | ATF3 | ATF3 | ATF3 | 5103 | 0.11 | 0.52 | NO |
29 | SKI | SKI | SKI | 5311 | 0.1 | 0.52 | NO |
30 | SP3 | SP3 | SP3 | 5397 | 0.1 | 0.53 | NO |
31 | CDK2 | CDK2 | CDK2 | 5726 | 0.09 | 0.52 | NO |
32 | KAT2B | KAT2B | KAT2B | 5969 | 0.084 | 0.51 | NO |
33 | HDAC1 | HDAC1 | HDAC1 | 5994 | 0.083 | 0.52 | NO |
34 | LAMC1 | LAMC1 | LAMC1 | 6119 | 0.08 | 0.52 | NO |
35 | CREB1 | CREB1 | CREB1 | 6311 | 0.075 | 0.52 | NO |
36 | ATF2 | ATF2 | ATF2 | 6507 | 0.07 | 0.51 | NO |
37 | TFE3 | TFE3 | TFE3 | 6963 | 0.06 | 0.49 | NO |
38 | HNF4A | HNF4A | HNF4A | 7410 | 0.051 | 0.47 | NO |
39 | FOXH1 | FOXH1 | FOXH1 | 7910 | 0.042 | 0.45 | NO |
40 | CDK4 | CDK4 | CDK4 | 8070 | 0.039 | 0.44 | NO |
41 | TGIF2 | TGIF2 | TGIF2 | 8184 | 0.037 | 0.44 | NO |
42 | MED15 | MED15 | MED15 | 8213 | 0.037 | 0.44 | NO |
43 | RBBP4 | RBBP4 | RBBP4 | 8251 | 0.036 | 0.45 | NO |
44 | TCF3 | TCF3 | TCF3 | 8542 | 0.031 | 0.43 | NO |
45 | NCOA2 | NCOA2 | NCOA2 | 8606 | 0.03 | 0.43 | NO |
46 | MAX | MAX | MAX | 8667 | 0.029 | 0.43 | NO |
47 | FOXO1 | FOXO1 | FOXO1 | 8958 | 0.025 | 0.42 | NO |
48 | FOXO3 | FOXO3 | FOXO3 | 8967 | 0.025 | 0.42 | NO |
49 | IL5 | IL5 | IL5 | 9048 | 0.023 | 0.42 | NO |
50 | EP300 | EP300 | EP300 | 9266 | 0.02 | 0.41 | NO |
51 | HDAC2 | HDAC2 | HDAC2 | 9538 | 0.016 | 0.39 | NO |
52 | SMAD7 | SMAD7 | SMAD7 | 9550 | 0.016 | 0.4 | NO |
53 | SNIP1 | SNIP1 | SNIP1 | 9555 | 0.015 | 0.4 | NO |
54 | SMAD2 | SMAD2 | SMAD2 | 9662 | 0.014 | 0.39 | NO |
55 | SP1 | SP1 | SP1 | 9700 | 0.013 | 0.39 | NO |
56 | NCOA1 | NCOA1 | NCOA1 | 9799 | 0.011 | 0.39 | NO |
57 | SIN3A | SIN3A | SIN3A | 10179 | 0.0056 | 0.37 | NO |
58 | ZBTB17 | ZBTB17 | ZBTB17 | 10210 | 0.0052 | 0.36 | NO |
59 | RBBP7 | RBBP7 | RBBP7 | 10350 | 0.0032 | 0.36 | NO |
60 | HSPA8 | HSPA8 | HSPA8 | 10501 | 0.00064 | 0.35 | NO |
61 | CREBBP | CREBBP | CREBBP | 10880 | -0.005 | 0.33 | NO |
62 | E2F4 | E2F4 | E2F4 | 11009 | -0.0069 | 0.32 | NO |
63 | SIN3B | SIN3B | SIN3B | 11175 | -0.0091 | 0.32 | NO |
64 | DCP1A | DCP1A | DCP1A | 11201 | -0.0097 | 0.31 | NO |
65 | TFDP1 | TFDP1 | TFDP1 | 11292 | -0.011 | 0.31 | NO |
66 | PIAS4 | PIAS4 | PIAS4 | 11714 | -0.018 | 0.29 | NO |
67 | AKT1 | AKT1 | AKT1 | 11800 | -0.02 | 0.29 | NO |
68 | NCOR1 | NCOR1 | NCOR1 | 11847 | -0.02 | 0.29 | NO |
69 | CTBP1 | CTBP1 | CTBP1 | 11936 | -0.022 | 0.28 | NO |
70 | SAP18 | SAP18 | SAP18 | 12057 | -0.024 | 0.28 | NO |
71 | CDKN1A | CDKN1A | CDKN1A | 12156 | -0.026 | 0.28 | NO |
72 | CITED1 | CITED1 | CITED1 | 12167 | -0.026 | 0.28 | NO |
73 | KAT2A | KAT2A | KAT2A | 12930 | -0.04 | 0.24 | NO |
74 | TGIF1 | TGIF1 | TGIF1 | 13229 | -0.046 | 0.23 | NO |
75 | FOXO4 | FOXO4 | FOXO4 | 13270 | -0.047 | 0.23 | NO |
76 | SMAD4 | SMAD4 | SMAD4 | 13443 | -0.05 | 0.22 | NO |
77 | E2F5 | E2F5 | E2F5 | 13820 | -0.058 | 0.21 | NO |
78 | SMAD3 | SMAD3 | SMAD3 | 14319 | -0.069 | 0.19 | NO |
79 | VDR | VDR | VDR | 15146 | -0.094 | 0.15 | NO |
80 | AR | AR | AR | 16541 | -0.16 | 0.091 | 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 NEUROACTIVE LIGAND RECEPTOR INTERACTION.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S20. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SERPINE1 | SERPINE1 | SERPINE1 | 63 | 0.68 | 0.041 | YES |
2 | FGA | FGA | FGA | 142 | 0.61 | 0.077 | YES |
3 | F13A1 | F13A1 | F13A1 | 276 | 0.56 | 0.11 | YES |
4 | HGF | HGF | HGF | 409 | 0.52 | 0.13 | YES |
5 | FGG | FGG | FGG | 430 | 0.52 | 0.17 | YES |
6 | TF | TF | TF | 586 | 0.48 | 0.19 | YES |
7 | MMRN1 | MMRN1 | MMRN1 | 588 | 0.48 | 0.22 | YES |
8 | FGB | FGB | FGB | 688 | 0.46 | 0.25 | YES |
9 | ACTN2 | ACTN2 | ACTN2 | 769 | 0.45 | 0.27 | YES |
10 | FN1 | FN1 | FN1 | 1098 | 0.4 | 0.28 | YES |
11 | TGFB3 | TGFB3 | TGFB3 | 1155 | 0.39 | 0.3 | YES |
12 | PRKCB | PRKCB | PRKCB | 1166 | 0.39 | 0.33 | YES |
13 | PLEK | PLEK | PLEK | 1198 | 0.39 | 0.35 | YES |
14 | VEGFA | VEGFA | VEGFA | 1691 | 0.33 | 0.35 | YES |
15 | SELP | SELP | SELP | 1713 | 0.33 | 0.37 | YES |
16 | TGFB1 | TGFB1 | TGFB1 | 1916 | 0.31 | 0.38 | YES |
17 | VEGFC | VEGFC | VEGFC | 1925 | 0.31 | 0.4 | YES |
18 | TIMP1 | TIMP1 | TIMP1 | 1964 | 0.3 | 0.42 | YES |
19 | TGFB2 | TGFB2 | TGFB2 | 2046 | 0.3 | 0.43 | YES |
20 | SERPINF2 | SERPINF2 | SERPINF2 | 2197 | 0.28 | 0.44 | YES |
21 | SRGN | SRGN | SRGN | 2334 | 0.27 | 0.45 | YES |
22 | SERPINA1 | SERPINA1 | SERPINA1 | 2404 | 0.26 | 0.46 | YES |
23 | CD36 | CD36 | CD36 | 2439 | 0.26 | 0.48 | YES |
24 | PECAM1 | PECAM1 | PECAM1 | 2480 | 0.26 | 0.5 | YES |
25 | SERPING1 | SERPING1 | SERPING1 | 2571 | 0.25 | 0.51 | YES |
26 | ACTN1 | ACTN1 | ACTN1 | 2652 | 0.25 | 0.52 | YES |
27 | PPBP | PPBP | PPBP | 3017 | 0.22 | 0.51 | YES |
28 | CFD | CFD | CFD | 3041 | 0.22 | 0.53 | YES |
29 | ITGA2B | ITGA2B | ITGA2B | 3058 | 0.22 | 0.54 | YES |
30 | PROS1 | PROS1 | PROS1 | 3114 | 0.22 | 0.55 | YES |
31 | SPARC | SPARC | SPARC | 3161 | 0.21 | 0.56 | YES |
32 | LEFTY2 | LEFTY2 | LEFTY2 | 3186 | 0.21 | 0.57 | YES |
33 | THBS1 | THBS1 | THBS1 | 3283 | 0.2 | 0.58 | YES |
34 | VWF | VWF | VWF | 3294 | 0.2 | 0.6 | YES |
35 | F8 | F8 | F8 | 3318 | 0.2 | 0.61 | YES |
36 | PDGFB | PDGFB | PDGFB | 3526 | 0.19 | 0.61 | YES |
37 | A2M | A2M | A2M | 3622 | 0.18 | 0.62 | YES |
38 | ITGB3 | ITGB3 | ITGB3 | 3757 | 0.17 | 0.62 | YES |
39 | F5 | F5 | F5 | 3843 | 0.17 | 0.63 | YES |
40 | CALU | CALU | CALU | 3867 | 0.17 | 0.64 | YES |
41 | APOA1 | APOA1 | APOA1 | 4403 | 0.14 | 0.62 | NO |
42 | PF4 | PF4 | PF4 | 4734 | 0.12 | 0.61 | NO |
43 | VCL | VCL | VCL | 5746 | 0.09 | 0.56 | NO |
44 | CAP1 | CAP1 | CAP1 | 6362 | 0.074 | 0.53 | NO |
45 | HSPA5 | HSPA5 | HSPA5 | 6822 | 0.063 | 0.51 | NO |
46 | STX4 | STX4 | STX4 | 7095 | 0.057 | 0.49 | NO |
47 | TLN1 | TLN1 | TLN1 | 7504 | 0.049 | 0.48 | NO |
48 | PFN1 | PFN1 | PFN1 | 7672 | 0.046 | 0.47 | NO |
49 | ALB | ALB | ALB | 8035 | 0.04 | 0.45 | NO |
50 | CFL1 | CFL1 | CFL1 | 8442 | 0.033 | 0.43 | NO |
51 | TUBA4A | TUBA4A | TUBA4A | 8664 | 0.029 | 0.42 | NO |
52 | CALM3 | CALM3 | CALM3 | 9018 | 0.024 | 0.4 | NO |
53 | PSAP | PSAP | PSAP | 9347 | 0.019 | 0.39 | NO |
54 | LAMP2 | LAMP2 | LAMP2 | 9376 | 0.018 | 0.39 | NO |
55 | PDGFA | PDGFA | PDGFA | 9781 | 0.012 | 0.36 | NO |
56 | CALM1 | CALM1 | CALM1 | 9936 | 0.0092 | 0.36 | NO |
57 | CD63 | CD63 | CD63 | 10256 | 0.0045 | 0.34 | NO |
58 | PRKCG | PRKCG | PRKCG | 10424 | 0.0018 | 0.33 | NO |
59 | ACTN4 | ACTN4 | ACTN4 | 10431 | 0.0017 | 0.33 | NO |
60 | ALDOA | ALDOA | ALDOA | 10509 | 0.00056 | 0.33 | NO |
61 | PPIA | PPIA | PPIA | 10639 | -0.0013 | 0.32 | NO |
62 | CALM2 | CALM2 | CALM2 | 10653 | -0.0015 | 0.32 | NO |
63 | SOD1 | SOD1 | SOD1 | 11047 | -0.0074 | 0.3 | NO |
64 | WDR1 | WDR1 | WDR1 | 11898 | -0.022 | 0.25 | NO |
65 | STXBP3 | STXBP3 | STXBP3 | 11928 | -0.022 | 0.25 | NO |
66 | BRPF3 | BRPF3 | BRPF3 | 11938 | -0.022 | 0.25 | NO |
67 | APP | APP | APP | 12088 | -0.024 | 0.25 | NO |
68 | HRG | HRG | HRG | 12515 | -0.032 | 0.22 | NO |
69 | VEGFB | VEGFB | VEGFB | 12593 | -0.034 | 0.22 | NO |
70 | FIGF | FIGF | FIGF | 13272 | -0.047 | 0.19 | NO |
71 | KNG1 | KNG1 | KNG1 | 13668 | -0.054 | 0.17 | NO |
72 | PRKCA | PRKCA | PRKCA | 14487 | -0.074 | 0.13 | NO |
73 | CLU | CLU | CLU | 14701 | -0.08 | 0.12 | NO |
74 | CD9 | CD9 | CD9 | 14947 | -0.087 | 0.12 | NO |
75 | SCG3 | SCG3 | SCG3 | 15985 | -0.13 | 0.066 | NO |
76 | PLG | PLG | PLG | 16768 | -0.18 | 0.035 | NO |
77 | HABP4 | HABP4 | HABP4 | 17075 | -0.2 | 0.031 | NO |
78 | ABCC4 | ABCC4 | ABCC4 | 17090 | -0.2 | 0.044 | NO |
79 | EGF | EGF | EGF | 17456 | -0.25 | 0.041 | 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 CELL CYCLE.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 5. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG PPAR SIGNALING PATHWAY | 65 | genes.ES.table | 0.6 | 1.6 | 0.018 | 1 | 0.93 | 0.35 | 0.13 | 0.31 | 1 | 0.58 |
KEGG VASCULAR SMOOTH MUSCLE CONTRACTION | 107 | genes.ES.table | 0.58 | 1.6 | 0.0096 | 1 | 0.93 | 0.36 | 0.15 | 0.31 | 1 | 0.62 |
KEGG VASOPRESSIN REGULATED WATER REABSORPTION | 42 | genes.ES.table | 0.47 | 1.8 | 0.0098 | 1 | 0.62 | 0.19 | 0.13 | 0.16 | 1 | 0.57 |
BIOCARTA AT1R PATHWAY | 32 | genes.ES.table | 0.42 | 1.5 | 0.055 | 1 | 0.97 | 0.38 | 0.26 | 0.28 | 0.97 | 0.48 |
BIOCARTA FAS PATHWAY | 30 | genes.ES.table | 0.46 | 1.5 | 0.099 | 1 | 0.97 | 0.33 | 0.25 | 0.25 | 1 | 0.5 |
BIOCARTA VEGF PATHWAY | 29 | genes.ES.table | 0.62 | 1.7 | 0.016 | 1 | 0.85 | 0.21 | 0.046 | 0.2 | 1 | 0.58 |
PID HIF2PATHWAY | 34 | genes.ES.table | 0.63 | 1.6 | 0.02 | 1 | 0.93 | 0.41 | 0.16 | 0.35 | 1 | 0.67 |
PID ARF6 TRAFFICKINGPATHWAY | 48 | genes.ES.table | 0.58 | 1.7 | 0.0077 | 1 | 0.82 | 0.42 | 0.23 | 0.32 | 1 | 0.62 |
PID ANGIOPOIETINRECEPTOR PATHWAY | 50 | genes.ES.table | 0.53 | 1.5 | 0.033 | 1 | 0.97 | 0.24 | 0.11 | 0.22 | 1 | 0.5 |
PID SHP2 PATHWAY | 57 | genes.ES.table | 0.6 | 1.5 | 0.023 | 1 | 0.97 | 0.35 | 0.13 | 0.31 | 1 | 0.56 |
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 | CREB3L3 | CREB3L3 | CREB3L3 | 25 | 0.87 | 0.16 | YES |
2 | AQP4 | AQP4 | AQP4 | 606 | 0.48 | 0.22 | YES |
3 | DYNC1I1 | DYNC1I1 | DYNC1I1 | 774 | 0.44 | 0.28 | YES |
4 | AQP3 | AQP3 | AQP3 | 996 | 0.39 | 0.34 | YES |
5 | AVPR2 | AVPR2 | AVPR2 | 1104 | 0.37 | 0.41 | YES |
6 | ADCY3 | ADCY3 | ADCY3 | 1861 | 0.27 | 0.42 | YES |
7 | DYNC2H1 | DYNC2H1 | DYNC2H1 | 2250 | 0.24 | 0.44 | YES |
8 | ARHGDIB | ARHGDIB | ARHGDIB | 2438 | 0.23 | 0.47 | YES |
9 | DCTN6 | DCTN6 | DCTN6 | 3316 | 0.17 | 0.45 | NO |
10 | CREB1 | CREB1 | CREB1 | 4149 | 0.13 | 0.43 | NO |
11 | CREB3L4 | CREB3L4 | CREB3L4 | 4924 | 0.1 | 0.41 | NO |
12 | ADCY9 | ADCY9 | ADCY9 | 5196 | 0.097 | 0.41 | NO |
13 | DCTN4 | DCTN4 | DCTN4 | 5652 | 0.086 | 0.4 | NO |
14 | DYNC1I2 | DYNC1I2 | DYNC1I2 | 5848 | 0.081 | 0.41 | NO |
15 | VAMP2 | VAMP2 | VAMP2 | 6140 | 0.073 | 0.4 | NO |
16 | CREB5 | CREB5 | CREB5 | 7293 | 0.047 | 0.35 | NO |
17 | DCTN1 | DCTN1 | DCTN1 | 7515 | 0.042 | 0.34 | NO |
18 | CREB3L2 | CREB3L2 | CREB3L2 | 7663 | 0.039 | 0.34 | NO |
19 | CREB3 | CREB3 | CREB3 | 7921 | 0.033 | 0.34 | NO |
20 | PRKACB | PRKACB | PRKACB | 8528 | 0.02 | 0.31 | NO |
21 | DYNC1LI2 | DYNC1LI2 | DYNC1LI2 | 8619 | 0.018 | 0.3 | NO |
22 | RAB11A | RAB11A | RAB11A | 8965 | 0.011 | 0.29 | NO |
23 | STX4 | STX4 | STX4 | 9517 | 0.00019 | 0.26 | NO |
24 | RAB5B | RAB5B | RAB5B | 10070 | -0.012 | 0.23 | NO |
25 | DYNLL1 | DYNLL1 | DYNLL1 | 10207 | -0.014 | 0.22 | NO |
26 | DYNC1H1 | DYNC1H1 | DYNC1H1 | 10701 | -0.025 | 0.2 | NO |
27 | DYNLL2 | DYNLL2 | DYNLL2 | 10802 | -0.027 | 0.2 | NO |
28 | PRKACA | PRKACA | PRKACA | 11069 | -0.033 | 0.19 | NO |
29 | RAB5C | RAB5C | RAB5C | 11298 | -0.038 | 0.19 | NO |
30 | DYNC1LI1 | DYNC1LI1 | DYNC1LI1 | 11316 | -0.038 | 0.19 | NO |
31 | DCTN5 | DCTN5 | DCTN5 | 11460 | -0.042 | 0.19 | NO |
32 | AQP2 | AQP2 | AQP2 | 12089 | -0.056 | 0.17 | NO |
33 | NSF | NSF | NSF | 12094 | -0.056 | 0.18 | NO |
34 | ARHGDIA | ARHGDIA | ARHGDIA | 12159 | -0.058 | 0.19 | NO |
35 | ADCY6 | ADCY6 | ADCY6 | 12230 | -0.059 | 0.19 | NO |
36 | RAB5A | RAB5A | RAB5A | 12468 | -0.065 | 0.19 | NO |
37 | PRKX | PRKX | PRKX | 12570 | -0.067 | 0.2 | NO |
38 | DCTN2 | DCTN2 | DCTN2 | 13298 | -0.088 | 0.17 | NO |
39 | DYNC2LI1 | DYNC2LI1 | DYNC2LI1 | 13350 | -0.089 | 0.19 | NO |
40 | RAB11B | RAB11B | RAB11B | 13545 | -0.095 | 0.2 | NO |
41 | GNAS | GNAS | GNAS | 14050 | -0.11 | 0.19 | NO |
42 | CREB3L1 | CREB3L1 | CREB3L1 | 16160 | -0.22 | 0.11 | NO |
Figure S41. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PPAR SIGNALING PATHWAY.

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

Table S22. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | BMX | BMX | BMX | 269 | 0.6 | 0.065 | YES |
2 | ELMO1 | ELMO1 | ELMO1 | 689 | 0.46 | 0.1 | YES |
3 | ETS1 | ETS1 | ETS1 | 827 | 0.42 | 0.15 | YES |
4 | CCND1 | CCND1 | CCND1 | 934 | 0.4 | 0.2 | YES |
5 | FYN | FYN | FYN | 1309 | 0.34 | 0.22 | YES |
6 | ITGA5 | ITGA5 | ITGA5 | 1956 | 0.26 | 0.22 | YES |
7 | ROCK2 | ROCK2 | ROCK2 | 2140 | 0.25 | 0.25 | YES |
8 | ASAP1 | ASAP1 | ASAP1 | 2350 | 0.23 | 0.27 | YES |
9 | GIT2 | GIT2 | GIT2 | 2507 | 0.22 | 0.29 | YES |
10 | ARHGAP26 | ARHGAP26 | ARHGAP26 | 2539 | 0.22 | 0.32 | YES |
11 | KLF8 | KLF8 | KLF8 | 2656 | 0.21 | 0.34 | YES |
12 | MAPK8 | MAPK8 | MAPK8 | 2968 | 0.19 | 0.34 | YES |
13 | MAPK1 | MAPK1 | MAPK1 | 3599 | 0.16 | 0.33 | YES |
14 | NCK1 | NCK1 | NCK1 | 3643 | 0.15 | 0.35 | YES |
15 | PIK3CA | PIK3CA | PIK3CA | 3863 | 0.14 | 0.36 | YES |
16 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 4107 | 0.13 | 0.36 | YES |
17 | ITGAV | ITGAV | ITGAV | 4189 | 0.13 | 0.37 | YES |
18 | JUN | JUN | JUN | 4537 | 0.12 | 0.37 | YES |
19 | CRK | CRK | CRK | 4564 | 0.12 | 0.38 | YES |
20 | SOS1 | SOS1 | SOS1 | 4688 | 0.11 | 0.39 | YES |
21 | NCK2 | NCK2 | NCK2 | 4751 | 0.11 | 0.4 | YES |
22 | PIK3R1 | PIK3R1 | PIK3R1 | 4885 | 0.11 | 0.41 | YES |
23 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 4900 | 0.11 | 0.42 | YES |
24 | YES1 | YES1 | YES1 | 4983 | 0.1 | 0.43 | YES |
25 | RGNEF | RGNEF | RGNEF | 5185 | 0.098 | 0.44 | YES |
26 | BRAF | BRAF | BRAF | 5208 | 0.097 | 0.45 | YES |
27 | ITGB1 | ITGB1 | ITGB1 | 5253 | 0.096 | 0.46 | YES |
28 | DOCK1 | DOCK1 | DOCK1 | 5271 | 0.095 | 0.47 | YES |
29 | RAP1A | RAP1A | RAP1A | 5552 | 0.088 | 0.47 | NO |
30 | PTK2 | PTK2 | PTK2 | 5727 | 0.084 | 0.47 | NO |
31 | TLN1 | TLN1 | TLN1 | 6637 | 0.061 | 0.42 | NO |
32 | MAPK9 | MAPK9 | MAPK9 | 7035 | 0.052 | 0.41 | NO |
33 | ACTN1 | ACTN1 | ACTN1 | 7080 | 0.051 | 0.42 | NO |
34 | RAP1B | RAP1B | RAP1B | 7122 | 0.05 | 0.42 | NO |
35 | VCL | VCL | VCL | 7166 | 0.049 | 0.42 | NO |
36 | MAP2K1 | MAP2K1 | MAP2K1 | 7286 | 0.047 | 0.42 | NO |
37 | RASA1 | RASA1 | RASA1 | 7315 | 0.046 | 0.43 | NO |
38 | ITGB5 | ITGB5 | ITGB5 | 7806 | 0.035 | 0.4 | NO |
39 | PAK1 | PAK1 | PAK1 | 8467 | 0.022 | 0.37 | NO |
40 | SH3GL1 | SH3GL1 | SH3GL1 | 8555 | 0.02 | 0.37 | NO |
41 | MAP2K4 | MAP2K4 | MAP2K4 | 8919 | 0.012 | 0.35 | NO |
42 | PLCG1 | PLCG1 | PLCG1 | 9566 | -0.00095 | 0.32 | NO |
43 | PXN | PXN | PXN | 9618 | -0.002 | 0.31 | NO |
44 | RRAS | RRAS | RRAS | 10119 | -0.012 | 0.29 | NO |
45 | WASL | WASL | WASL | 10900 | -0.029 | 0.25 | NO |
46 | RHOA | RHOA | RHOA | 10930 | -0.03 | 0.25 | NO |
47 | MMP14 | MMP14 | MMP14 | 11277 | -0.038 | 0.24 | NO |
48 | RAC1 | RAC1 | RAC1 | 11421 | -0.041 | 0.23 | NO |
49 | PTPN21 | PTPN21 | PTPN21 | 11422 | -0.041 | 0.24 | NO |
50 | ACTA1 | ACTA1 | ACTA1 | 12187 | -0.058 | 0.2 | NO |
51 | CAPN2 | CAPN2 | CAPN2 | 12507 | -0.066 | 0.2 | NO |
52 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 12697 | -0.071 | 0.2 | NO |
53 | GRB2 | GRB2 | GRB2 | 12787 | -0.073 | 0.2 | NO |
54 | RAF1 | RAF1 | RAF1 | 13261 | -0.087 | 0.19 | NO |
55 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 13328 | -0.088 | 0.19 | NO |
56 | SRC | SRC | SRC | 14707 | -0.14 | 0.14 | NO |
57 | BCAR1 | BCAR1 | BCAR1 | 15214 | -0.16 | 0.13 | NO |
58 | GRB7 | GRB7 | GRB7 | 16640 | -0.26 | 0.086 | NO |
Figure S43. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VASCULAR SMOOTH MUSCLE CONTRACTION.

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

Table S23. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | AGTR1 | AGTR1 | AGTR1 | 8 | 0.96 | 0.1 | YES |
2 | ITGA8 | ITGA8 | ITGA8 | 94 | 0.71 | 0.18 | YES |
3 | ITGA10 | ITGA10 | ITGA10 | 120 | 0.68 | 0.25 | YES |
4 | TSHR | TSHR | TSHR | 127 | 0.68 | 0.33 | YES |
5 | ITGA9 | ITGA9 | ITGA9 | 426 | 0.53 | 0.37 | YES |
6 | ITGA4 | ITGA4 | ITGA4 | 544 | 0.5 | 0.42 | YES |
7 | ITGA1 | ITGA1 | ITGA1 | 659 | 0.46 | 0.46 | YES |
8 | EDNRB | EDNRB | EDNRB | 682 | 0.46 | 0.51 | YES |
9 | AVPR2 | AVPR2 | AVPR2 | 1104 | 0.37 | 0.53 | YES |
10 | ITGA5 | ITGA5 | ITGA5 | 1956 | 0.26 | 0.51 | YES |
11 | ITGA11 | ITGA11 | ITGA11 | 2404 | 0.23 | 0.51 | YES |
12 | CPE | CPE | CPE | 2409 | 0.23 | 0.54 | YES |
13 | PLD1 | PLD1 | PLD1 | 2929 | 0.19 | 0.53 | YES |
14 | ACAP1 | ACAP1 | ACAP1 | 3017 | 0.19 | 0.55 | YES |
15 | ITGA2 | ITGA2 | ITGA2 | 3411 | 0.17 | 0.54 | YES |
16 | ITGA6 | ITGA6 | ITGA6 | 3586 | 0.16 | 0.55 | YES |
17 | EXOC3 | EXOC3 | EXOC3 | 3694 | 0.15 | 0.56 | YES |
18 | ITGA7 | ITGA7 | ITGA7 | 3800 | 0.15 | 0.57 | YES |
19 | CTNND1 | CTNND1 | CTNND1 | 4122 | 0.13 | 0.57 | YES |
20 | ITGAV | ITGAV | ITGAV | 4189 | 0.13 | 0.58 | YES |
21 | EXOC5 | EXOC5 | EXOC5 | 4929 | 0.1 | 0.55 | NO |
22 | SPAG9 | SPAG9 | SPAG9 | 5109 | 0.1 | 0.55 | NO |
23 | CTNNB1 | CTNNB1 | CTNNB1 | 5136 | 0.099 | 0.56 | NO |
24 | ASAP2 | ASAP2 | ASAP2 | 5200 | 0.097 | 0.57 | NO |
25 | ITGB1 | ITGB1 | ITGB1 | 5253 | 0.096 | 0.57 | NO |
26 | VAMP3 | VAMP3 | VAMP3 | 5473 | 0.09 | 0.57 | NO |
27 | EXOC6 | EXOC6 | EXOC6 | 5726 | 0.084 | 0.57 | NO |
28 | IL2RA | IL2RA | IL2RA | 6503 | 0.064 | 0.53 | NO |
29 | EXOC1 | EXOC1 | EXOC1 | 7294 | 0.046 | 0.49 | NO |
30 | CTNNA1 | CTNNA1 | CTNNA1 | 8284 | 0.025 | 0.44 | NO |
31 | CDH1 | CDH1 | CDH1 | 8901 | 0.012 | 0.41 | NO |
32 | KLC1 | KLC1 | KLC1 | 9032 | 0.01 | 0.4 | NO |
33 | EXOC2 | EXOC2 | EXOC2 | 9141 | 0.0078 | 0.4 | NO |
34 | SLC2A4 | SLC2A4 | SLC2A4 | 9216 | 0.0062 | 0.4 | NO |
35 | CLTC | CLTC | CLTC | 9711 | -0.0041 | 0.37 | NO |
36 | SCAMP2 | SCAMP2 | SCAMP2 | 10121 | -0.012 | 0.35 | NO |
37 | DNM2 | DNM2 | DNM2 | 10259 | -0.015 | 0.34 | NO |
38 | PLD2 | PLD2 | PLD2 | 10407 | -0.018 | 0.34 | NO |
39 | EXOC4 | EXOC4 | EXOC4 | 10596 | -0.023 | 0.33 | NO |
40 | EXOC7 | EXOC7 | EXOC7 | 10657 | -0.024 | 0.33 | NO |
41 | RALA | RALA | RALA | 10931 | -0.03 | 0.31 | NO |
42 | ARF6 | ARF6 | ARF6 | 11724 | -0.048 | 0.28 | NO |
43 | PIP5K1C | PIP5K1C | PIP5K1C | 12417 | -0.064 | 0.24 | NO |
44 | ADRB2 | ADRB2 | ADRB2 | 12525 | -0.066 | 0.25 | NO |
45 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 13328 | -0.088 | 0.21 | NO |
46 | BIN1 | BIN1 | BIN1 | 14923 | -0.15 | 0.14 | NO |
47 | ITGA3 | ITGA3 | ITGA3 | 14950 | -0.15 | 0.16 | NO |
48 | NME1 | NME1 | NME1 | 16124 | -0.22 | 0.11 | NO |
Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VASOPRESSIN REGULATED WATER REABSORPTION.

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

Table S24. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | KDR | KDR | KDR | 108 | 0.69 | 0.13 | YES |
2 | FLT1 | FLT1 | FLT1 | 163 | 0.66 | 0.25 | YES |
3 | FLT4 | FLT4 | FLT4 | 284 | 0.59 | 0.36 | YES |
4 | VEGFA | VEGFA | VEGFA | 335 | 0.57 | 0.47 | YES |
5 | NOS3 | NOS3 | NOS3 | 529 | 0.5 | 0.56 | YES |
6 | PIK3CG | PIK3CG | PIK3CG | 844 | 0.42 | 0.62 | YES |
7 | PRKCB | PRKCB | PRKCB | 2132 | 0.25 | 0.6 | NO |
8 | PIK3CA | PIK3CA | PIK3CA | 3863 | 0.14 | 0.53 | NO |
9 | PIK3R1 | PIK3R1 | PIK3R1 | 4885 | 0.11 | 0.5 | NO |
10 | ARNT | ARNT | ARNT | 5017 | 0.1 | 0.51 | NO |
11 | EIF1AX | EIF1AX | EIF1AX | 5566 | 0.088 | 0.5 | NO |
12 | PTK2 | PTK2 | PTK2 | 5727 | 0.084 | 0.5 | NO |
13 | EIF2S3 | EIF2S3 | EIF2S3 | 5972 | 0.077 | 0.51 | NO |
14 | EIF2S1 | EIF2S1 | EIF2S1 | 6281 | 0.07 | 0.5 | NO |
15 | SHC1 | SHC1 | SHC1 | 6401 | 0.067 | 0.51 | NO |
16 | EIF1 | EIF1 | EIF1 | 8474 | 0.021 | 0.4 | NO |
17 | EIF2B4 | EIF2B4 | EIF2B4 | 8845 | 0.014 | 0.38 | NO |
18 | PLCG1 | PLCG1 | PLCG1 | 9566 | -0.00095 | 0.34 | NO |
19 | PXN | PXN | PXN | 9618 | -0.002 | 0.34 | NO |
20 | EIF2B2 | EIF2B2 | EIF2B2 | 9720 | -0.0042 | 0.34 | NO |
21 | EIF2B3 | EIF2B3 | EIF2B3 | 9793 | -0.0058 | 0.33 | NO |
22 | EIF2B5 | EIF2B5 | EIF2B5 | 10519 | -0.021 | 0.3 | NO |
23 | EIF2B1 | EIF2B1 | EIF2B1 | 10836 | -0.028 | 0.28 | NO |
24 | EIF2S2 | EIF2S2 | EIF2S2 | 11234 | -0.037 | 0.27 | NO |
25 | ELAVL1 | ELAVL1 | ELAVL1 | 11968 | -0.053 | 0.24 | NO |
26 | HRAS | HRAS | HRAS | 12189 | -0.058 | 0.24 | NO |
27 | HIF1A | HIF1A | HIF1A | 13880 | -0.11 | 0.17 | NO |
28 | VHL | VHL | VHL | 14595 | -0.13 | 0.15 | NO |
29 | PRKCA | PRKCA | PRKCA | 16255 | -0.23 | 0.11 | 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 AT1R PATHWAY.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table 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 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 643 | 0.47 | 0.076 | YES |
2 | MEF2C | MEF2C | MEF2C | 756 | 0.44 | 0.18 | YES |
3 | DUSP7 | DUSP7 | DUSP7 | 1749 | 0.28 | 0.19 | YES |
4 | FOS | FOS | FOS | 1979 | 0.26 | 0.24 | YES |
5 | DUSP4 | DUSP4 | DUSP4 | 2407 | 0.23 | 0.27 | YES |
6 | MAPK11 | MAPK11 | MAPK11 | 2531 | 0.22 | 0.32 | YES |
7 | DUSP6 | DUSP6 | DUSP6 | 2563 | 0.22 | 0.37 | YES |
8 | MAPK8 | MAPK8 | MAPK8 | 2968 | 0.19 | 0.39 | YES |
9 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3261 | 0.17 | 0.42 | YES |
10 | ATF2 | ATF2 | ATF2 | 3414 | 0.17 | 0.45 | YES |
11 | MAPK1 | MAPK1 | MAPK1 | 3599 | 0.16 | 0.47 | YES |
12 | MEF2A | MEF2A | MEF2A | 3926 | 0.14 | 0.49 | YES |
13 | CREB1 | CREB1 | CREB1 | 4149 | 0.13 | 0.51 | YES |
14 | MAPK10 | MAPK10 | MAPK10 | 4324 | 0.13 | 0.53 | YES |
15 | JUN | JUN | JUN | 4537 | 0.12 | 0.55 | YES |
16 | MAPK3 | MAPK3 | MAPK3 | 5501 | 0.09 | 0.51 | NO |
17 | PPP2R1B | PPP2R1B | PPP2R1B | 5671 | 0.085 | 0.52 | NO |
18 | ATF1 | ATF1 | ATF1 | 6127 | 0.073 | 0.52 | NO |
19 | MAPK9 | MAPK9 | MAPK9 | 7035 | 0.052 | 0.48 | NO |
20 | MAPK14 | MAPK14 | MAPK14 | 7231 | 0.048 | 0.48 | NO |
21 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 7236 | 0.048 | 0.49 | NO |
22 | PPP2CA | PPP2CA | PPP2CA | 8207 | 0.027 | 0.44 | NO |
23 | PPP2R5D | PPP2R5D | PPP2R5D | 8288 | 0.025 | 0.45 | NO |
24 | PPP2CB | PPP2CB | PPP2CB | 8353 | 0.024 | 0.45 | NO |
25 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 8466 | 0.022 | 0.45 | NO |
26 | DUSP3 | DUSP3 | DUSP3 | 10885 | -0.029 | 0.32 | NO |
27 | ELK1 | ELK1 | ELK1 | 12050 | -0.055 | 0.27 | NO |
28 | MAPK7 | MAPK7 | MAPK7 | 12257 | -0.06 | 0.27 | NO |
29 | PPP2R1A | PPP2R1A | PPP2R1A | 12314 | -0.061 | 0.28 | NO |
30 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 15251 | -0.16 | 0.16 | 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 FAS PATHWAY.

Figure S50. 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

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 | ABCG2 | ABCG2 | ABCG2 | 71 | 0.74 | 0.091 | YES |
2 | KDR | KDR | KDR | 108 | 0.69 | 0.18 | YES |
3 | FLT1 | FLT1 | FLT1 | 163 | 0.66 | 0.26 | YES |
4 | EGLN3 | EGLN3 | EGLN3 | 308 | 0.58 | 0.33 | YES |
5 | VEGFA | VEGFA | VEGFA | 335 | 0.57 | 0.4 | YES |
6 | ADORA2A | ADORA2A | ADORA2A | 568 | 0.49 | 0.45 | YES |
7 | ETS1 | ETS1 | ETS1 | 827 | 0.42 | 0.49 | YES |
8 | EPAS1 | EPAS1 | EPAS1 | 993 | 0.39 | 0.53 | YES |
9 | SERPINE1 | SERPINE1 | SERPINE1 | 1693 | 0.29 | 0.53 | YES |
10 | POU5F1 | POU5F1 | POU5F1 | 1729 | 0.29 | 0.57 | YES |
11 | SLC2A1 | SLC2A1 | SLC2A1 | 1838 | 0.28 | 0.6 | YES |
12 | TWIST1 | TWIST1 | TWIST1 | 1869 | 0.27 | 0.63 | YES |
13 | EPO | EPO | EPO | 2435 | 0.23 | 0.63 | YES |
14 | SIRT1 | SIRT1 | SIRT1 | 2833 | 0.2 | 0.63 | YES |
15 | EFNA1 | EFNA1 | EFNA1 | 3461 | 0.16 | 0.62 | NO |
16 | EGLN1 | EGLN1 | EGLN1 | 3721 | 0.15 | 0.63 | NO |
17 | PGK1 | PGK1 | PGK1 | 4496 | 0.12 | 0.6 | NO |
18 | ARNT | ARNT | ARNT | 5017 | 0.1 | 0.58 | NO |
19 | EP300 | EP300 | EP300 | 5555 | 0.088 | 0.56 | NO |
20 | EIF3E | EIF3E | EIF3E | 6425 | 0.066 | 0.53 | NO |
21 | CREBBP | CREBBP | CREBBP | 7601 | 0.04 | 0.47 | NO |
22 | BHLHE40 | BHLHE40 | BHLHE40 | 7687 | 0.038 | 0.47 | NO |
23 | APEX1 | APEX1 | APEX1 | 7801 | 0.036 | 0.46 | NO |
24 | SP1 | SP1 | SP1 | 8395 | 0.023 | 0.44 | NO |
25 | CITED2 | CITED2 | CITED2 | 9462 | 0.0013 | 0.38 | NO |
26 | HIF1AN | HIF1AN | HIF1AN | 10112 | -0.012 | 0.34 | NO |
27 | MMP14 | MMP14 | MMP14 | 11277 | -0.038 | 0.28 | NO |
28 | ELK1 | ELK1 | ELK1 | 12050 | -0.055 | 0.25 | NO |
29 | TCEB1 | TCEB1 | TCEB1 | 12768 | -0.073 | 0.22 | NO |
30 | EGLN2 | EGLN2 | EGLN2 | 13060 | -0.08 | 0.21 | NO |
31 | SLC11A2 | SLC11A2 | SLC11A2 | 13209 | -0.086 | 0.22 | NO |
32 | VHL | VHL | VHL | 14595 | -0.13 | 0.16 | NO |
33 | FXN | FXN | FXN | 14671 | -0.14 | 0.17 | NO |
34 | TCEB2 | TCEB2 | TCEB2 | 15728 | -0.19 | 0.14 | 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 VEGF PATHWAY.

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

Table 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 | CYP4A11 | CYP4A11 | CYP4A11 | 2 | 1.2 | 0.048 | YES |
2 | AGTR1 | AGTR1 | AGTR1 | 8 | 0.96 | 0.087 | YES |
3 | AVPR1B | AVPR1B | AVPR1B | 11 | 0.95 | 0.13 | YES |
4 | CYP4A22 | CYP4A22 | CYP4A22 | 153 | 0.66 | 0.15 | YES |
5 | RAMP3 | RAMP3 | RAMP3 | 261 | 0.6 | 0.17 | YES |
6 | ADCY4 | ADCY4 | ADCY4 | 266 | 0.6 | 0.19 | YES |
7 | CALCRL | CALCRL | CALCRL | 324 | 0.58 | 0.21 | YES |
8 | PLCB1 | PLCB1 | PLCB1 | 340 | 0.57 | 0.24 | YES |
9 | EDNRA | EDNRA | EDNRA | 368 | 0.56 | 0.26 | YES |
10 | CACNA1C | CACNA1C | CACNA1C | 388 | 0.55 | 0.28 | YES |
11 | ADRA1B | ADRA1B | ADRA1B | 414 | 0.54 | 0.3 | YES |
12 | PLA2G12B | PLA2G12B | PLA2G12B | 433 | 0.53 | 0.32 | YES |
13 | PRKG1 | PRKG1 | PRKG1 | 518 | 0.5 | 0.34 | YES |
14 | KCNMA1 | KCNMA1 | KCNMA1 | 522 | 0.5 | 0.36 | YES |
15 | ADCY5 | ADCY5 | ADCY5 | 523 | 0.5 | 0.38 | YES |
16 | RAMP2 | RAMP2 | RAMP2 | 524 | 0.5 | 0.4 | YES |
17 | ADORA2A | ADORA2A | ADORA2A | 568 | 0.49 | 0.42 | YES |
18 | GUCY1A2 | GUCY1A2 | GUCY1A2 | 647 | 0.47 | 0.43 | YES |
19 | ACTG2 | ACTG2 | ACTG2 | 783 | 0.43 | 0.44 | YES |
20 | PRKCH | PRKCH | PRKCH | 821 | 0.42 | 0.46 | YES |
21 | ADRA1A | ADRA1A | ADRA1A | 941 | 0.4 | 0.47 | YES |
22 | MYH11 | MYH11 | MYH11 | 945 | 0.4 | 0.48 | YES |
23 | MRVI1 | MRVI1 | MRVI1 | 1095 | 0.38 | 0.49 | YES |
24 | PTGIR | PTGIR | PTGIR | 1190 | 0.36 | 0.5 | YES |
25 | AVPR1A | AVPR1A | AVPR1A | 1281 | 0.34 | 0.51 | YES |
26 | ADORA2B | ADORA2B | ADORA2B | 1523 | 0.31 | 0.51 | YES |
27 | KCNMB1 | KCNMB1 | KCNMB1 | 1595 | 0.3 | 0.52 | YES |
28 | GUCY1A3 | GUCY1A3 | GUCY1A3 | 1601 | 0.3 | 0.53 | YES |
29 | MYLK | MYLK | MYLK | 1725 | 0.29 | 0.54 | YES |
30 | ADCY1 | ADCY1 | ADCY1 | 1743 | 0.29 | 0.55 | YES |
31 | ADCY3 | ADCY3 | ADCY3 | 1861 | 0.27 | 0.55 | YES |
32 | ACTA2 | ACTA2 | ACTA2 | 1944 | 0.27 | 0.56 | YES |
33 | PRKCB | PRKCB | PRKCB | 2132 | 0.25 | 0.56 | YES |
34 | ROCK2 | ROCK2 | ROCK2 | 2140 | 0.25 | 0.57 | YES |
35 | PRKCE | PRKCE | PRKCE | 2260 | 0.24 | 0.57 | YES |
36 | GUCY1B3 | GUCY1B3 | GUCY1B3 | 2442 | 0.23 | 0.57 | YES |
37 | CALD1 | CALD1 | CALD1 | 2610 | 0.21 | 0.57 | YES |
38 | CACNA1F | CACNA1F | CACNA1F | 2702 | 0.21 | 0.58 | YES |
39 | PLA2G5 | PLA2G5 | PLA2G5 | 2770 | 0.2 | 0.58 | YES |
40 | ADCY8 | ADCY8 | ADCY8 | 3135 | 0.18 | 0.57 | NO |
41 | CACNA1S | CACNA1S | CACNA1S | 3248 | 0.18 | 0.57 | NO |
42 | PPP1R14A | PPP1R14A | PPP1R14A | 3507 | 0.16 | 0.56 | NO |
43 | MAPK1 | MAPK1 | MAPK1 | 3599 | 0.16 | 0.56 | NO |
44 | ROCK1 | ROCK1 | ROCK1 | 3743 | 0.15 | 0.56 | NO |
45 | PPP1R12B | PPP1R12B | PPP1R12B | 4217 | 0.13 | 0.54 | NO |
46 | GNA13 | GNA13 | GNA13 | 5041 | 0.1 | 0.5 | NO |
47 | ITPR1 | ITPR1 | ITPR1 | 5047 | 0.1 | 0.5 | NO |
48 | ADCY9 | ADCY9 | ADCY9 | 5196 | 0.097 | 0.5 | NO |
49 | BRAF | BRAF | BRAF | 5208 | 0.097 | 0.5 | NO |
50 | KCNMB2 | KCNMB2 | KCNMB2 | 5471 | 0.09 | 0.49 | NO |
51 | MAPK3 | MAPK3 | MAPK3 | 5501 | 0.09 | 0.49 | NO |
52 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 5518 | 0.089 | 0.5 | NO |
53 | MYL9 | MYL9 | MYL9 | 5661 | 0.085 | 0.49 | NO |
54 | PLCB2 | PLCB2 | PLCB2 | 5766 | 0.083 | 0.49 | NO |
55 | PPP1R12A | PPP1R12A | PPP1R12A | 5774 | 0.083 | 0.49 | NO |
56 | CALM1 | CALM1 | CALM1 | 6035 | 0.075 | 0.48 | NO |
57 | PLCB4 | PLCB4 | PLCB4 | 6125 | 0.073 | 0.48 | NO |
58 | CALM3 | CALM3 | CALM3 | 6536 | 0.064 | 0.46 | NO |
59 | NPR1 | NPR1 | NPR1 | 6653 | 0.061 | 0.46 | NO |
60 | GNAQ | GNAQ | GNAQ | 6770 | 0.058 | 0.45 | NO |
61 | GNA11 | GNA11 | GNA11 | 7116 | 0.05 | 0.44 | NO |
62 | PLA2G1B | PLA2G1B | PLA2G1B | 7253 | 0.047 | 0.43 | NO |
63 | MAP2K1 | MAP2K1 | MAP2K1 | 7286 | 0.047 | 0.43 | NO |
64 | MYL6B | MYL6B | MYL6B | 7587 | 0.04 | 0.42 | NO |
65 | PPP1CC | PPP1CC | PPP1CC | 7642 | 0.039 | 0.41 | NO |
66 | PPP1CB | PPP1CB | PPP1CB | 7816 | 0.035 | 0.41 | NO |
67 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 7935 | 0.032 | 0.4 | NO |
68 | PRKACB | PRKACB | PRKACB | 8528 | 0.02 | 0.37 | NO |
69 | ADCY7 | ADCY7 | ADCY7 | 9982 | -0.0097 | 0.29 | NO |
70 | GNA12 | GNA12 | GNA12 | 10067 | -0.011 | 0.28 | NO |
71 | CALML6 | CALML6 | CALML6 | 10837 | -0.028 | 0.24 | NO |
72 | ADCY2 | ADCY2 | ADCY2 | 10848 | -0.028 | 0.24 | NO |
73 | RHOA | RHOA | RHOA | 10930 | -0.03 | 0.24 | NO |
74 | PRKACA | PRKACA | PRKACA | 11069 | -0.033 | 0.23 | NO |
75 | ITPR3 | ITPR3 | ITPR3 | 11297 | -0.038 | 0.22 | NO |
76 | MYL6 | MYL6 | MYL6 | 11313 | -0.038 | 0.22 | NO |
77 | PLA2G12A | PLA2G12A | PLA2G12A | 11325 | -0.038 | 0.22 | NO |
78 | MYLK2 | MYLK2 | MYLK2 | 11528 | -0.043 | 0.22 | NO |
79 | ARAF | ARAF | ARAF | 11857 | -0.051 | 0.2 | NO |
80 | ADRA1D | ADRA1D | ADRA1D | 11961 | -0.053 | 0.2 | NO |
81 | PLCB3 | PLCB3 | PLCB3 | 11971 | -0.053 | 0.2 | NO |
82 | ADCY6 | ADCY6 | ADCY6 | 12230 | -0.059 | 0.19 | NO |
83 | MYLK3 | MYLK3 | MYLK3 | 12535 | -0.066 | 0.17 | NO |
84 | PRKX | PRKX | PRKX | 12570 | -0.067 | 0.17 | NO |
85 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 12697 | -0.071 | 0.17 | NO |
86 | CALML3 | CALML3 | CALML3 | 12714 | -0.072 | 0.17 | NO |
87 | CALM2 | CALM2 | CALM2 | 12773 | -0.073 | 0.17 | NO |
88 | PLA2G4A | PLA2G4A | PLA2G4A | 12836 | -0.074 | 0.17 | NO |
89 | PPP1CA | PPP1CA | PPP1CA | 12898 | -0.076 | 0.17 | NO |
90 | KCNMB3 | KCNMB3 | KCNMB3 | 13069 | -0.081 | 0.16 | NO |
91 | RAMP1 | RAMP1 | RAMP1 | 13146 | -0.083 | 0.16 | NO |
92 | RAF1 | RAF1 | RAF1 | 13261 | -0.087 | 0.16 | NO |
93 | PRKCQ | PRKCQ | PRKCQ | 13308 | -0.088 | 0.16 | NO |
94 | JMJD7-PLA2G4B | JMJD7-PLA2G4B | JMJD7-PLA2G4B | 13376 | -0.09 | 0.16 | NO |
95 | ITPR2 | ITPR2 | ITPR2 | 13832 | -0.11 | 0.14 | NO |
96 | GNAS | GNAS | GNAS | 14050 | -0.11 | 0.13 | NO |
97 | MAP2K2 | MAP2K2 | MAP2K2 | 14176 | -0.12 | 0.13 | NO |
98 | PLA2G10 | PLA2G10 | PLA2G10 | 14194 | -0.12 | 0.14 | NO |
99 | PLA2G6 | PLA2G6 | PLA2G6 | 15426 | -0.17 | 0.075 | NO |
100 | PLA2G2A | PLA2G2A | PLA2G2A | 15528 | -0.18 | 0.077 | NO |
101 | PRKCD | PRKCD | PRKCD | 15666 | -0.18 | 0.077 | NO |
102 | NPR2 | NPR2 | NPR2 | 15742 | -0.19 | 0.081 | NO |
103 | CACNA1D | CACNA1D | CACNA1D | 15744 | -0.19 | 0.089 | NO |
104 | KCNMB4 | KCNMB4 | KCNMB4 | 15745 | -0.19 | 0.097 | NO |
105 | PRKCA | PRKCA | PRKCA | 16255 | -0.23 | 0.078 | NO |
106 | PLA2G2D | PLA2G2D | PLA2G2D | 16841 | -0.28 | 0.058 | NO |
107 | PRKCG | PRKCG | PRKCG | 17558 | -0.42 | 0.035 | NO |
Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID HIF2PATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: PID HIF2PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S28. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CYP4A11 | CYP4A11 | CYP4A11 | 2 | 1.2 | 0.077 | YES |
2 | CD36 | CD36 | CD36 | 68 | 0.74 | 0.12 | YES |
3 | FABP7 | FABP7 | FABP7 | 117 | 0.68 | 0.17 | YES |
4 | CYP4A22 | CYP4A22 | CYP4A22 | 153 | 0.66 | 0.21 | YES |
5 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 158 | 0.66 | 0.25 | YES |
6 | HMGCS2 | HMGCS2 | HMGCS2 | 225 | 0.62 | 0.29 | YES |
7 | FABP4 | FABP4 | FABP4 | 248 | 0.61 | 0.33 | YES |
8 | PCK1 | PCK1 | PCK1 | 454 | 0.52 | 0.35 | YES |
9 | CPT1C | CPT1C | CPT1C | 581 | 0.48 | 0.38 | YES |
10 | FABP6 | FABP6 | FABP6 | 597 | 0.48 | 0.41 | YES |
11 | SLC27A2 | SLC27A2 | SLC27A2 | 628 | 0.47 | 0.44 | YES |
12 | LPL | LPL | LPL | 631 | 0.47 | 0.47 | YES |
13 | PLIN1 | PLIN1 | PLIN1 | 718 | 0.45 | 0.5 | YES |
14 | ACADL | ACADL | ACADL | 869 | 0.42 | 0.52 | YES |
15 | RXRG | RXRG | RXRG | 1437 | 0.32 | 0.51 | YES |
16 | EHHADH | EHHADH | EHHADH | 1446 | 0.32 | 0.53 | YES |
17 | FABP1 | FABP1 | FABP1 | 1471 | 0.32 | 0.55 | YES |
18 | AQP7 | AQP7 | AQP7 | 1679 | 0.29 | 0.56 | YES |
19 | FADS2 | FADS2 | FADS2 | 1809 | 0.28 | 0.57 | YES |
20 | ACSL5 | ACSL5 | ACSL5 | 2230 | 0.24 | 0.56 | YES |
21 | MMP1 | MMP1 | MMP1 | 2253 | 0.24 | 0.58 | YES |
22 | SCD | SCD | SCD | 2256 | 0.24 | 0.59 | YES |
23 | FABP5 | FABP5 | FABP5 | 2428 | 0.23 | 0.6 | YES |
24 | SORBS1 | SORBS1 | SORBS1 | 2891 | 0.2 | 0.59 | NO |
25 | CYP7A1 | CYP7A1 | CYP7A1 | 3464 | 0.16 | 0.56 | NO |
26 | CYP27A1 | CYP27A1 | CYP27A1 | 3548 | 0.16 | 0.57 | NO |
27 | CYP8B1 | CYP8B1 | CYP8B1 | 3802 | 0.15 | 0.57 | NO |
28 | ACADM | ACADM | ACADM | 3922 | 0.14 | 0.57 | NO |
29 | ACSL1 | ACSL1 | ACSL1 | 4154 | 0.13 | 0.57 | NO |
30 | RXRA | RXRA | RXRA | 4402 | 0.12 | 0.56 | NO |
31 | ACOX2 | ACOX2 | ACOX2 | 5101 | 0.1 | 0.53 | NO |
32 | CPT1A | CPT1A | CPT1A | 5118 | 0.1 | 0.54 | NO |
33 | GK | GK | GK | 5462 | 0.091 | 0.52 | NO |
34 | CPT2 | CPT2 | CPT2 | 5540 | 0.089 | 0.52 | NO |
35 | PCK2 | PCK2 | PCK2 | 6212 | 0.071 | 0.49 | NO |
36 | NR1H3 | NR1H3 | NR1H3 | 6470 | 0.065 | 0.48 | NO |
37 | UBC | UBC | UBC | 6821 | 0.056 | 0.47 | NO |
38 | ILK | ILK | ILK | 6926 | 0.054 | 0.46 | NO |
39 | SCP2 | SCP2 | SCP2 | 7060 | 0.051 | 0.46 | NO |
40 | ACSL6 | ACSL6 | ACSL6 | 7162 | 0.049 | 0.46 | NO |
41 | OLR1 | OLR1 | OLR1 | 7498 | 0.042 | 0.44 | NO |
42 | PPARA | PPARA | PPARA | 7598 | 0.04 | 0.44 | NO |
43 | FABP2 | FABP2 | FABP2 | 7666 | 0.038 | 0.44 | NO |
44 | ADIPOQ | ADIPOQ | ADIPOQ | 7679 | 0.038 | 0.44 | NO |
45 | SCD5 | SCD5 | SCD5 | 8063 | 0.03 | 0.42 | NO |
46 | RXRB | RXRB | RXRB | 8556 | 0.02 | 0.4 | NO |
47 | PDPK1 | PDPK1 | PDPK1 | 9014 | 0.01 | 0.37 | NO |
48 | ME1 | ME1 | ME1 | 9202 | 0.0064 | 0.36 | NO |
49 | PPARG | PPARG | PPARG | 9274 | 0.005 | 0.36 | NO |
50 | PPARD | PPARD | PPARD | 9454 | 0.0014 | 0.35 | NO |
51 | ACOX1 | ACOX1 | ACOX1 | 9855 | -0.0072 | 0.33 | NO |
52 | FABP3 | FABP3 | FABP3 | 10141 | -0.013 | 0.31 | NO |
53 | ACSL3 | ACSL3 | ACSL3 | 10174 | -0.013 | 0.31 | NO |
54 | ACSL4 | ACSL4 | ACSL4 | 11488 | -0.042 | 0.24 | NO |
55 | APOC3 | APOC3 | APOC3 | 12010 | -0.054 | 0.22 | NO |
56 | APOA2 | APOA2 | APOA2 | 12407 | -0.063 | 0.2 | NO |
57 | SLC27A1 | SLC27A1 | SLC27A1 | 12969 | -0.078 | 0.17 | NO |
58 | APOA1 | APOA1 | APOA1 | 13286 | -0.087 | 0.16 | NO |
59 | ACAA1 | ACAA1 | ACAA1 | 13870 | -0.11 | 0.14 | NO |
60 | ACOX3 | ACOX3 | ACOX3 | 14034 | -0.11 | 0.13 | NO |
61 | DBI | DBI | DBI | 14180 | -0.12 | 0.13 | NO |
62 | SLC27A4 | SLC27A4 | SLC27A4 | 16569 | -0.25 | 0.019 | NO |
63 | CPT1B | CPT1B | CPT1B | 16807 | -0.28 | 0.025 | NO |
64 | PLTP | PLTP | PLTP | 17416 | -0.38 | 0.017 | NO |
65 | SLC27A5 | SLC27A5 | SLC27A5 | 17437 | -0.39 | 0.042 | NO |
Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ARF6 TRAFFICKINGPATHWAY.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: PID ARF6 TRAFFICKINGPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S29. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ABCG2 | ABCG2 | ABCG2 | 71 | 0.74 | 0.05 | YES |
2 | CA9 | CA9 | CA9 | 74 | 0.73 | 0.1 | YES |
3 | EDN1 | EDN1 | EDN1 | 184 | 0.65 | 0.14 | YES |
4 | NOS2 | NOS2 | NOS2 | 274 | 0.59 | 0.18 | YES |
5 | EGLN3 | EGLN3 | EGLN3 | 308 | 0.58 | 0.22 | YES |
6 | PLIN2 | PLIN2 | PLIN2 | 322 | 0.58 | 0.26 | YES |
7 | VEGFA | VEGFA | VEGFA | 335 | 0.57 | 0.3 | YES |
8 | CP | CP | CP | 497 | 0.51 | 0.33 | YES |
9 | ADM | ADM | ADM | 775 | 0.44 | 0.35 | YES |
10 | ETS1 | ETS1 | ETS1 | 827 | 0.42 | 0.38 | YES |
11 | TFF3 | TFF3 | TFF3 | 949 | 0.4 | 0.4 | YES |
12 | HNF4A | HNF4A | HNF4A | 1195 | 0.36 | 0.41 | YES |
13 | ENG | ENG | ENG | 1423 | 0.32 | 0.42 | YES |
14 | BNIP3 | BNIP3 | BNIP3 | 1666 | 0.29 | 0.43 | YES |
15 | SERPINE1 | SERPINE1 | SERPINE1 | 1693 | 0.29 | 0.45 | YES |
16 | RORA | RORA | RORA | 1760 | 0.28 | 0.47 | YES |
17 | SLC2A1 | SLC2A1 | SLC2A1 | 1838 | 0.28 | 0.48 | YES |
18 | CXCR4 | CXCR4 | CXCR4 | 1947 | 0.26 | 0.5 | YES |
19 | FOS | FOS | FOS | 1979 | 0.26 | 0.51 | YES |
20 | CXCL12 | CXCL12 | CXCL12 | 1996 | 0.26 | 0.53 | YES |
21 | NDRG1 | NDRG1 | NDRG1 | 2066 | 0.26 | 0.55 | YES |
22 | HMOX1 | HMOX1 | HMOX1 | 2170 | 0.25 | 0.56 | YES |
23 | BHLHE41 | BHLHE41 | BHLHE41 | 2235 | 0.24 | 0.57 | YES |
24 | PFKFB3 | PFKFB3 | PFKFB3 | 2354 | 0.23 | 0.58 | YES |
25 | EPO | EPO | EPO | 2435 | 0.23 | 0.6 | YES |
26 | HK2 | HK2 | HK2 | 2705 | 0.21 | 0.6 | YES |
27 | GATA2 | GATA2 | GATA2 | 2719 | 0.21 | 0.61 | YES |
28 | LDHA | LDHA | LDHA | 2997 | 0.19 | 0.61 | YES |
29 | NCOA2 | NCOA2 | NCOA2 | 3685 | 0.15 | 0.58 | YES |
30 | EGLN1 | EGLN1 | EGLN1 | 3721 | 0.15 | 0.59 | YES |
31 | NT5E | NT5E | NT5E | 3949 | 0.14 | 0.59 | YES |
32 | CREB1 | CREB1 | CREB1 | 4149 | 0.13 | 0.59 | YES |
33 | NPM1 | NPM1 | NPM1 | 4211 | 0.13 | 0.59 | YES |
34 | ID2 | ID2 | ID2 | 4439 | 0.12 | 0.59 | YES |
35 | ITGB2 | ITGB2 | ITGB2 | 4441 | 0.12 | 0.6 | YES |
36 | PGK1 | PGK1 | PGK1 | 4496 | 0.12 | 0.6 | YES |
37 | JUN | JUN | JUN | 4537 | 0.12 | 0.61 | YES |
38 | TFRC | TFRC | TFRC | 4921 | 0.1 | 0.6 | NO |
39 | ARNT | ARNT | ARNT | 5017 | 0.1 | 0.6 | NO |
40 | ENO1 | ENO1 | ENO1 | 5295 | 0.095 | 0.59 | NO |
41 | EP300 | EP300 | EP300 | 5555 | 0.088 | 0.58 | NO |
42 | NCOA1 | NCOA1 | NCOA1 | 5657 | 0.085 | 0.58 | NO |
43 | MCL1 | MCL1 | MCL1 | 5747 | 0.083 | 0.59 | NO |
44 | PFKL | PFKL | PFKL | 5862 | 0.08 | 0.58 | NO |
45 | HK1 | HK1 | HK1 | 5941 | 0.078 | 0.59 | NO |
46 | SMAD4 | SMAD4 | SMAD4 | 6294 | 0.069 | 0.57 | NO |
47 | ABCB1 | ABCB1 | ABCB1 | 7408 | 0.044 | 0.51 | NO |
48 | CREBBP | CREBBP | CREBBP | 7601 | 0.04 | 0.51 | NO |
49 | BHLHE40 | BHLHE40 | BHLHE40 | 7687 | 0.038 | 0.5 | NO |
50 | SP1 | SP1 | SP1 | 8395 | 0.023 | 0.47 | NO |
51 | FECH | FECH | FECH | 9204 | 0.0064 | 0.42 | NO |
52 | HDAC7 | HDAC7 | HDAC7 | 9277 | 0.0049 | 0.42 | NO |
53 | CITED2 | CITED2 | CITED2 | 9462 | 0.0013 | 0.41 | NO |
54 | COPS5 | COPS5 | COPS5 | 9522 | 0.00012 | 0.41 | NO |
55 | PKM2 | PKM2 | PKM2 | 9595 | -0.0016 | 0.4 | NO |
56 | PGM1 | PGM1 | PGM1 | 9816 | -0.0063 | 0.39 | NO |
57 | ALDOA | ALDOA | ALDOA | 10156 | -0.013 | 0.37 | NO |
58 | SMAD3 | SMAD3 | SMAD3 | 10634 | -0.024 | 0.35 | NO |
59 | TERT | TERT | TERT | 10705 | -0.025 | 0.35 | NO |
60 | TF | TF | TF | 11251 | -0.037 | 0.32 | NO |
61 | FURIN | FURIN | FURIN | 11597 | -0.045 | 0.3 | NO |
62 | AKT1 | AKT1 | AKT1 | 11992 | -0.054 | 0.28 | NO |
63 | HIF1A | HIF1A | HIF1A | 13880 | -0.11 | 0.19 | NO |
64 | IGFBP1 | IGFBP1 | IGFBP1 | 14955 | -0.15 | 0.14 | NO |
65 | LEP | LEP | LEP | 16156 | -0.22 | 0.09 | NO |
66 | GCK | GCK | GCK | 17013 | -0.31 | 0.065 | NO |
Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ANGIOPOIETINRECEPTOR PATHWAY.

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

Table S30. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | P2RX7 | P2RX7 | P2RX7 | 665 | 0.46 | 0.045 | YES |
2 | NLRP1 | NLRP1 | NLRP1 | 1005 | 0.39 | 0.096 | YES |
3 | MEFV | MEFV | MEFV | 1147 | 0.37 | 0.15 | YES |
4 | NLRC4 | NLRC4 | NLRC4 | 1235 | 0.35 | 0.21 | YES |
5 | MAPK12 | MAPK12 | MAPK12 | 1310 | 0.34 | 0.27 | YES |
6 | BIRC3 | BIRC3 | BIRC3 | 2009 | 0.26 | 0.27 | YES |
7 | CASP1 | CASP1 | CASP1 | 2092 | 0.25 | 0.31 | YES |
8 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 2232 | 0.24 | 0.35 | YES |
9 | MAPK11 | MAPK11 | MAPK11 | 2531 | 0.22 | 0.37 | YES |
10 | NOD2 | NOD2 | NOD2 | 2545 | 0.22 | 0.41 | YES |
11 | NLRP3 | NLRP3 | NLRP3 | 2594 | 0.22 | 0.44 | YES |
12 | PSTPIP1 | PSTPIP1 | PSTPIP1 | 2664 | 0.21 | 0.48 | YES |
13 | IRAK2 | IRAK2 | IRAK2 | 2751 | 0.2 | 0.51 | YES |
14 | BCL2 | BCL2 | BCL2 | 3012 | 0.19 | 0.53 | YES |
15 | TRAF6 | TRAF6 | TRAF6 | 3071 | 0.19 | 0.56 | YES |
16 | AIM2 | AIM2 | AIM2 | 3204 | 0.18 | 0.58 | YES |
17 | BIRC2 | BIRC2 | BIRC2 | 5532 | 0.089 | 0.47 | NO |
18 | TXNIP | TXNIP | TXNIP | 5757 | 0.083 | 0.47 | NO |
19 | CYLD | CYLD | CYLD | 6066 | 0.075 | 0.47 | NO |
20 | PANX1 | PANX1 | PANX1 | 6200 | 0.071 | 0.48 | NO |
21 | NOD1 | NOD1 | NOD1 | 6746 | 0.058 | 0.46 | NO |
22 | CASP8 | CASP8 | CASP8 | 6868 | 0.055 | 0.46 | NO |
23 | MAPK14 | MAPK14 | MAPK14 | 7231 | 0.048 | 0.45 | NO |
24 | TAB2 | TAB2 | TAB2 | 7571 | 0.041 | 0.44 | NO |
25 | APP | APP | APP | 8487 | 0.021 | 0.39 | NO |
26 | CARD9 | CARD9 | CARD9 | 8660 | 0.018 | 0.38 | NO |
27 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 8802 | 0.014 | 0.38 | NO |
28 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 8928 | 0.012 | 0.37 | NO |
29 | MAP2K6 | MAP2K6 | MAP2K6 | 9043 | 0.0097 | 0.37 | NO |
30 | UBE2N | UBE2N | UBE2N | 9107 | 0.0086 | 0.37 | NO |
31 | CASP4 | CASP4 | CASP4 | 9225 | 0.0061 | 0.36 | NO |
32 | CHUK | CHUK | CHUK | 9335 | 0.0037 | 0.36 | NO |
33 | MAP3K7 | MAP3K7 | MAP3K7 | 9723 | -0.0043 | 0.34 | NO |
34 | RIPK2 | RIPK2 | RIPK2 | 9967 | -0.0095 | 0.32 | NO |
35 | TXN | TXN | TXN | 9974 | -0.0096 | 0.32 | NO |
36 | TAB1 | TAB1 | TAB1 | 10455 | -0.019 | 0.3 | NO |
37 | CASP2 | CASP2 | CASP2 | 10542 | -0.021 | 0.3 | NO |
38 | IKBKB | IKBKB | IKBKB | 10769 | -0.027 | 0.29 | NO |
39 | TAB3 | TAB3 | TAB3 | 11107 | -0.034 | 0.28 | NO |
40 | MAPK13 | MAPK13 | MAPK13 | 12683 | -0.071 | 0.21 | NO |
41 | CASP9 | CASP9 | CASP9 | 13484 | -0.093 | 0.18 | NO |
42 | IRAK1 | IRAK1 | IRAK1 | 13931 | -0.11 | 0.17 | NO |
43 | PYCARD | PYCARD | PYCARD | 14015 | -0.11 | 0.19 | NO |
44 | IKBKG | IKBKG | IKBKG | 14132 | -0.12 | 0.2 | NO |
45 | BCL2L1 | BCL2L1 | BCL2L1 | 14224 | -0.12 | 0.22 | NO |
Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID SHP2 PATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: PID SHP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 6. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus4. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.48 | 1.2 | 0.37 | 1 | 1 | 0.69 | 0.39 | 0.42 | 1 | 0.83 |
KEGG GLYCINE SERINE AND THREONINE METABOLISM | 31 | genes.ES.table | 0.52 | 1.2 | 0.25 | 1 | 1 | 0.48 | 0.16 | 0.41 | 1 | 0.84 |
KEGG HISTIDINE METABOLISM | 29 | genes.ES.table | 0.55 | 1.3 | 0.2 | 1 | 1 | 0.52 | 0.22 | 0.4 | 1 | 0.97 |
KEGG SELENOAMINO ACID METABOLISM | 26 | genes.ES.table | 0.44 | 1.4 | 0.1 | 1 | 1 | 0.65 | 0.35 | 0.43 | 1 | 0.9 |
KEGG PYRUVATE METABOLISM | 39 | genes.ES.table | 0.45 | 1.3 | 0.23 | 1 | 1 | 0.41 | 0.24 | 0.31 | 1 | 0.92 |
KEGG BUTANOATE METABOLISM | 31 | genes.ES.table | 0.5 | 1.3 | 0.21 | 1 | 1 | 0.55 | 0.24 | 0.42 | 1 | 0.96 |
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.36 | 1.2 | 0.27 | 1 | 1 | 0.49 | 0.35 | 0.32 | 1 | 0.81 |
KEGG BASE EXCISION REPAIR | 33 | genes.ES.table | 0.48 | 1.6 | 0.065 | 1 | 0.94 | 0.55 | 0.35 | 0.36 | 1 | 0.8 |
KEGG LYSOSOME | 120 | genes.ES.table | 0.36 | 1.4 | 0.14 | 1 | 0.99 | 0.5 | 0.33 | 0.34 | 1 | 0.92 |
KEGG TIGHT JUNCTION | 125 | genes.ES.table | 0.3 | 1.2 | 0.21 | 1 | 1 | 0.2 | 0.12 | 0.18 | 1 | 0.85 |
Table S31. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NEIL1 | NEIL1 | NEIL1 | 981 | 0.39 | 0.051 | YES |
2 | NTHL1 | NTHL1 | NTHL1 | 1300 | 0.33 | 0.12 | YES |
3 | PARP3 | PARP3 | PARP3 | 1329 | 0.33 | 0.21 | YES |
4 | OGG1 | OGG1 | OGG1 | 1353 | 0.33 | 0.3 | YES |
5 | MUTYH | MUTYH | MUTYH | 1848 | 0.27 | 0.34 | YES |
6 | POLD1 | POLD1 | POLD1 | 2513 | 0.22 | 0.36 | YES |
7 | MPG | MPG | MPG | 2954 | 0.19 | 0.39 | YES |
8 | POLD2 | POLD2 | POLD2 | 3346 | 0.16 | 0.41 | YES |
9 | LIG1 | LIG1 | LIG1 | 4451 | 0.12 | 0.38 | YES |
10 | NEIL2 | NEIL2 | NEIL2 | 4662 | 0.11 | 0.4 | YES |
11 | UNG | UNG | UNG | 4829 | 0.1 | 0.42 | YES |
12 | PARP4 | PARP4 | PARP4 | 4950 | 0.099 | 0.44 | YES |
13 | POLE | POLE | POLE | 5167 | 0.091 | 0.45 | YES |
14 | SMUG1 | SMUG1 | SMUG1 | 5348 | 0.085 | 0.46 | YES |
15 | APEX2 | APEX2 | APEX2 | 5572 | 0.078 | 0.47 | YES |
16 | POLD4 | POLD4 | POLD4 | 6049 | 0.064 | 0.46 | YES |
17 | POLL | POLL | POLL | 6199 | 0.06 | 0.47 | YES |
18 | XRCC1 | XRCC1 | XRCC1 | 6328 | 0.056 | 0.48 | YES |
19 | LIG3 | LIG3 | LIG3 | 7089 | 0.035 | 0.45 | NO |
20 | PCNA | PCNA | PCNA | 7702 | 0.018 | 0.42 | NO |
21 | PARP2 | PARP2 | PARP2 | 8694 | -0.0069 | 0.36 | NO |
22 | POLE3 | POLE3 | POLE3 | 8697 | -0.007 | 0.37 | NO |
23 | POLB | POLB | POLB | 9039 | -0.016 | 0.35 | NO |
24 | APEX1 | APEX1 | APEX1 | 9063 | -0.016 | 0.36 | NO |
25 | MBD4 | MBD4 | MBD4 | 9266 | -0.022 | 0.35 | NO |
26 | FEN1 | FEN1 | FEN1 | 9605 | -0.03 | 0.34 | NO |
27 | POLE4 | POLE4 | POLE4 | 9733 | -0.033 | 0.34 | NO |
28 | PARP1 | PARP1 | PARP1 | 9736 | -0.033 | 0.35 | NO |
29 | TDG | TDG | TDG | 10852 | -0.062 | 0.31 | NO |
30 | POLE2 | POLE2 | POLE2 | 11059 | -0.068 | 0.31 | NO |
31 | HMGB1 | HMGB1 | HMGB1 | 11100 | -0.069 | 0.33 | NO |
32 | POLD3 | POLD3 | POLD3 | 12109 | -0.1 | 0.3 | NO |
33 | NEIL3 | NEIL3 | NEIL3 | 12882 | -0.13 | 0.29 | NO |
Figure S61. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE.

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

Table S32. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NAPSA | NAPSA | NAPSA | 188 | 0.7 | 0.033 | YES |
2 | CTSL2 | CTSL2 | CTSL2 | 267 | 0.64 | 0.069 | YES |
3 | AP3B2 | AP3B2 | AP3B2 | 434 | 0.55 | 0.094 | YES |
4 | AP1M2 | AP1M2 | AP1M2 | 940 | 0.4 | 0.091 | YES |
5 | CTSC | CTSC | CTSC | 975 | 0.39 | 0.11 | YES |
6 | IDUA | IDUA | IDUA | 1155 | 0.36 | 0.13 | YES |
7 | DNASE2B | DNASE2B | DNASE2B | 1551 | 0.3 | 0.12 | YES |
8 | NAGLU | NAGLU | NAGLU | 1704 | 0.28 | 0.13 | YES |
9 | GLB1 | GLB1 | GLB1 | 1709 | 0.28 | 0.15 | YES |
10 | AP1S3 | AP1S3 | AP1S3 | 1715 | 0.28 | 0.17 | YES |
11 | NEU1 | NEU1 | NEU1 | 1743 | 0.28 | 0.18 | YES |
12 | ACP5 | ACP5 | ACP5 | 1819 | 0.27 | 0.2 | YES |
13 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 1996 | 0.26 | 0.2 | YES |
14 | SMPD1 | SMPD1 | SMPD1 | 2229 | 0.24 | 0.2 | YES |
15 | NAGPA | NAGPA | NAGPA | 2314 | 0.23 | 0.21 | YES |
16 | SUMF1 | SUMF1 | SUMF1 | 2342 | 0.23 | 0.23 | YES |
17 | ABCB9 | ABCB9 | ABCB9 | 2398 | 0.22 | 0.24 | YES |
18 | PPT2 | PPT2 | PPT2 | 2426 | 0.22 | 0.25 | YES |
19 | LAPTM4B | LAPTM4B | LAPTM4B | 2482 | 0.22 | 0.26 | YES |
20 | GALNS | GALNS | GALNS | 2646 | 0.21 | 0.26 | YES |
21 | PLA2G15 | PLA2G15 | PLA2G15 | 2718 | 0.2 | 0.27 | YES |
22 | GAA | GAA | GAA | 2878 | 0.19 | 0.28 | YES |
23 | GNPTG | GNPTG | GNPTG | 2985 | 0.18 | 0.28 | YES |
24 | SGSH | SGSH | SGSH | 3217 | 0.17 | 0.28 | YES |
25 | CTSH | CTSH | CTSH | 3221 | 0.17 | 0.29 | YES |
26 | ATP6V0C | ATP6V0C | ATP6V0C | 3229 | 0.17 | 0.3 | YES |
27 | AP1S1 | AP1S1 | AP1S1 | 3304 | 0.17 | 0.31 | YES |
28 | AP4M1 | AP4M1 | AP4M1 | 3447 | 0.16 | 0.31 | YES |
29 | CTSA | CTSA | CTSA | 3822 | 0.14 | 0.3 | YES |
30 | CTNS | CTNS | CTNS | 3901 | 0.14 | 0.3 | YES |
31 | ACP2 | ACP2 | ACP2 | 3991 | 0.14 | 0.3 | YES |
32 | GGA3 | GGA3 | GGA3 | 4003 | 0.13 | 0.31 | YES |
33 | GGA1 | GGA1 | GGA1 | 4065 | 0.13 | 0.32 | YES |
34 | GLA | GLA | GLA | 4140 | 0.13 | 0.32 | YES |
35 | CTSF | CTSF | CTSF | 4154 | 0.13 | 0.33 | YES |
36 | ARSA | ARSA | ARSA | 4223 | 0.12 | 0.33 | YES |
37 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 4289 | 0.12 | 0.34 | YES |
38 | CTSG | CTSG | CTSG | 4324 | 0.12 | 0.34 | YES |
39 | CLN3 | CLN3 | CLN3 | 4387 | 0.12 | 0.34 | YES |
40 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 4799 | 0.1 | 0.33 | YES |
41 | CTSK | CTSK | CTSK | 4896 | 0.1 | 0.33 | YES |
42 | CTSB | CTSB | CTSB | 5053 | 0.095 | 0.33 | YES |
43 | CLTA | CLTA | CLTA | 5119 | 0.093 | 0.33 | YES |
44 | CTSZ | CTSZ | CTSZ | 5127 | 0.092 | 0.33 | YES |
45 | CTSD | CTSD | CTSD | 5128 | 0.092 | 0.34 | YES |
46 | MCOLN1 | MCOLN1 | MCOLN1 | 5229 | 0.089 | 0.34 | YES |
47 | ARSG | ARSG | ARSG | 5333 | 0.085 | 0.34 | YES |
48 | AGA | AGA | AGA | 5418 | 0.083 | 0.34 | YES |
49 | GUSB | GUSB | GUSB | 5421 | 0.083 | 0.34 | YES |
50 | CD63 | CD63 | CD63 | 5443 | 0.082 | 0.35 | YES |
51 | CD68 | CD68 | CD68 | 5455 | 0.082 | 0.35 | YES |
52 | GNS | GNS | GNS | 5468 | 0.081 | 0.36 | YES |
53 | CTSL1 | CTSL1 | CTSL1 | 5624 | 0.077 | 0.35 | YES |
54 | LAPTM4A | LAPTM4A | LAPTM4A | 5671 | 0.075 | 0.36 | YES |
55 | PSAP | PSAP | PSAP | 5814 | 0.071 | 0.35 | YES |
56 | LAMP1 | LAMP1 | LAMP1 | 5831 | 0.07 | 0.36 | YES |
57 | SORT1 | SORT1 | SORT1 | 5833 | 0.07 | 0.36 | YES |
58 | SLC11A1 | SLC11A1 | SLC11A1 | 5952 | 0.067 | 0.36 | YES |
59 | ATP6V1H | ATP6V1H | ATP6V1H | 6000 | 0.066 | 0.36 | YES |
60 | NPC2 | NPC2 | NPC2 | 6005 | 0.066 | 0.36 | YES |
61 | AP1M1 | AP1M1 | AP1M1 | 6153 | 0.061 | 0.36 | NO |
62 | MAN2B1 | MAN2B1 | MAN2B1 | 6532 | 0.05 | 0.34 | NO |
63 | ATP6V0B | ATP6V0B | ATP6V0B | 6634 | 0.048 | 0.34 | NO |
64 | AP3S2 | AP3S2 | AP3S2 | 6718 | 0.046 | 0.34 | NO |
65 | AP3D1 | AP3D1 | AP3D1 | 6726 | 0.045 | 0.34 | NO |
66 | AP1G1 | AP1G1 | AP1G1 | 6742 | 0.045 | 0.34 | NO |
67 | CLTB | CLTB | CLTB | 6766 | 0.044 | 0.34 | NO |
68 | HGSNAT | HGSNAT | HGSNAT | 6804 | 0.043 | 0.34 | NO |
69 | SLC11A2 | SLC11A2 | SLC11A2 | 6882 | 0.041 | 0.34 | NO |
70 | FUCA1 | FUCA1 | FUCA1 | 6943 | 0.039 | 0.34 | NO |
71 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 6978 | 0.038 | 0.34 | NO |
72 | CLTC | CLTC | CLTC | 7217 | 0.032 | 0.33 | NO |
73 | ENTPD4 | ENTPD4 | ENTPD4 | 7273 | 0.03 | 0.33 | NO |
74 | GBA | GBA | GBA | 7332 | 0.029 | 0.33 | NO |
75 | HEXA | HEXA | HEXA | 7462 | 0.025 | 0.32 | NO |
76 | AP1B1 | AP1B1 | AP1B1 | 7561 | 0.022 | 0.32 | NO |
77 | GM2A | GM2A | GM2A | 7563 | 0.022 | 0.32 | NO |
78 | HEXB | HEXB | HEXB | 7597 | 0.021 | 0.32 | NO |
79 | HYAL1 | HYAL1 | HYAL1 | 7611 | 0.021 | 0.32 | NO |
80 | ARSB | ARSB | ARSB | 7617 | 0.02 | 0.32 | NO |
81 | NPC1 | NPC1 | NPC1 | 7783 | 0.016 | 0.31 | NO |
82 | GGA2 | GGA2 | GGA2 | 7924 | 0.013 | 0.31 | NO |
83 | AP4S1 | AP4S1 | AP4S1 | 8267 | 0.0038 | 0.29 | NO |
84 | SLC17A5 | SLC17A5 | SLC17A5 | 8361 | 0.0016 | 0.28 | NO |
85 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 8737 | -0.0081 | 0.26 | NO |
86 | NAGA | NAGA | NAGA | 8819 | -0.01 | 0.26 | NO |
87 | M6PR | M6PR | M6PR | 9257 | -0.022 | 0.24 | NO |
88 | CLTCL1 | CLTCL1 | CLTCL1 | 9276 | -0.022 | 0.24 | NO |
89 | ASAH1 | ASAH1 | ASAH1 | 9315 | -0.023 | 0.24 | NO |
90 | CLN5 | CLN5 | CLN5 | 9441 | -0.026 | 0.23 | NO |
91 | DNASE2 | DNASE2 | DNASE2 | 9503 | -0.028 | 0.23 | NO |
92 | AP3B1 | AP3B1 | AP3B1 | 9545 | -0.029 | 0.23 | NO |
93 | IGF2R | IGF2R | IGF2R | 9612 | -0.03 | 0.23 | NO |
94 | ABCA2 | ABCA2 | ABCA2 | 9645 | -0.031 | 0.23 | NO |
95 | CD164 | CD164 | CD164 | 9824 | -0.036 | 0.22 | NO |
96 | LIPA | LIPA | LIPA | 9856 | -0.036 | 0.22 | NO |
97 | AP3M1 | AP3M1 | AP3M1 | 10035 | -0.041 | 0.21 | NO |
98 | TPP1 | TPP1 | TPP1 | 10114 | -0.043 | 0.21 | NO |
99 | TCIRG1 | TCIRG1 | TCIRG1 | 10361 | -0.05 | 0.2 | NO |
100 | LAMP2 | LAMP2 | LAMP2 | 10521 | -0.054 | 0.19 | NO |
101 | AP3M2 | AP3M2 | AP3M2 | 10604 | -0.056 | 0.19 | NO |
102 | AP4B1 | AP4B1 | AP4B1 | 10760 | -0.06 | 0.19 | NO |
103 | PPT1 | PPT1 | PPT1 | 10793 | -0.061 | 0.19 | NO |
104 | SCARB2 | SCARB2 | SCARB2 | 11836 | -0.091 | 0.14 | NO |
105 | AP4E1 | AP4E1 | AP4E1 | 11848 | -0.092 | 0.14 | NO |
106 | LGMN | LGMN | LGMN | 11942 | -0.094 | 0.14 | NO |
107 | MFSD8 | MFSD8 | MFSD8 | 11967 | -0.095 | 0.15 | NO |
108 | MANBA | MANBA | MANBA | 12182 | -0.1 | 0.14 | NO |
109 | LAPTM5 | LAPTM5 | LAPTM5 | 12539 | -0.12 | 0.13 | NO |
110 | GNPTAB | GNPTAB | GNPTAB | 12673 | -0.12 | 0.13 | NO |
111 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 12674 | -0.12 | 0.14 | NO |
112 | CTSS | CTSS | CTSS | 13125 | -0.14 | 0.12 | NO |
113 | CTSE | CTSE | CTSE | 13561 | -0.16 | 0.11 | NO |
114 | CTSO | CTSO | CTSO | 13831 | -0.17 | 0.1 | NO |
115 | AP3S1 | AP3S1 | AP3S1 | 14118 | -0.18 | 0.099 | NO |
116 | GALC | GALC | GALC | 14300 | -0.19 | 0.1 | NO |
117 | IDS | IDS | IDS | 15162 | -0.25 | 0.069 | NO |
118 | AP1S2 | AP1S2 | AP1S2 | 16520 | -0.39 | 0.019 | NO |
119 | CTSW | CTSW | CTSW | 17080 | -0.5 | 0.019 | NO |
120 | LAMP3 | LAMP3 | LAMP3 | 17603 | -0.69 | 0.033 | NO |
Figure S63. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM.

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

Table S33. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CBS | CBS | CBS | 207 | 0.68 | 0.17 | YES |
2 | GGT1 | GGT1 | GGT1 | 1156 | 0.36 | 0.21 | YES |
3 | HEMK1 | HEMK1 | HEMK1 | 1935 | 0.26 | 0.24 | YES |
4 | SCLY | SCLY | SCLY | 2206 | 0.24 | 0.29 | YES |
5 | PAPSS2 | PAPSS2 | PAPSS2 | 2893 | 0.19 | 0.3 | YES |
6 | WBSCR22 | WBSCR22 | WBSCR22 | 3164 | 0.18 | 0.33 | YES |
7 | LCMT1 | LCMT1 | LCMT1 | 3349 | 0.16 | 0.37 | YES |
8 | TRMT11 | TRMT11 | TRMT11 | 3508 | 0.16 | 0.4 | YES |
9 | SEPHS2 | SEPHS2 | SEPHS2 | 3762 | 0.14 | 0.42 | YES |
10 | LCMT2 | LCMT2 | LCMT2 | 4968 | 0.098 | 0.38 | YES |
11 | METTL6 | METTL6 | METTL6 | 5065 | 0.095 | 0.4 | YES |
12 | SEPHS1 | SEPHS1 | SEPHS1 | 5088 | 0.094 | 0.43 | YES |
13 | AHCY | AHCY | AHCY | 5808 | 0.071 | 0.41 | YES |
14 | MARS | MARS | MARS | 5975 | 0.066 | 0.42 | YES |
15 | CTH | CTH | CTH | 6015 | 0.065 | 0.43 | YES |
16 | MARS2 | MARS2 | MARS2 | 6317 | 0.056 | 0.43 | YES |
17 | PAPSS1 | PAPSS1 | PAPSS1 | 6347 | 0.055 | 0.44 | YES |
18 | METTL2B | METTL2B | METTL2B | 6707 | 0.046 | 0.44 | NO |
19 | MAT2A | MAT2A | MAT2A | 7486 | 0.024 | 0.4 | NO |
20 | GGT7 | GGT7 | GGT7 | 7737 | 0.018 | 0.39 | NO |
21 | GGT6 | GGT6 | GGT6 | 8017 | 0.01 | 0.38 | NO |
22 | AHCYL1 | AHCYL1 | AHCYL1 | 8373 | 0.0012 | 0.36 | NO |
23 | AHCYL2 | AHCYL2 | AHCYL2 | 8874 | -0.011 | 0.34 | NO |
24 | MAT2B | MAT2B | MAT2B | 10450 | -0.052 | 0.26 | NO |
25 | MAT1A | MAT1A | MAT1A | 14059 | -0.18 | 0.11 | NO |
26 | GGT5 | GGT5 | GGT5 | 16768 | -0.43 | 0.079 | NO |
Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HISTIDINE METABOLISM.
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Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HISTIDINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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Table S34. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 565 | 0.5 | 0.073 | YES |
2 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 1244 | 0.34 | 0.11 | YES |
3 | ALDH2 | ALDH2 | ALDH2 | 1463 | 0.31 | 0.16 | YES |
4 | FTCD | FTCD | FTCD | 1569 | 0.3 | 0.21 | YES |
5 | UROC1 | UROC1 | UROC1 | 1722 | 0.28 | 0.26 | YES |
6 | ACY3 | ACY3 | ACY3 | 1837 | 0.27 | 0.31 | YES |
7 | CNDP1 | CNDP1 | CNDP1 | 1909 | 0.26 | 0.36 | YES |
8 | HEMK1 | HEMK1 | HEMK1 | 1935 | 0.26 | 0.42 | YES |
9 | DDC | DDC | DDC | 2271 | 0.23 | 0.44 | YES |
10 | AMDHD1 | AMDHD1 | AMDHD1 | 3018 | 0.18 | 0.44 | YES |
11 | WBSCR22 | WBSCR22 | WBSCR22 | 3164 | 0.18 | 0.47 | YES |
12 | LCMT1 | LCMT1 | LCMT1 | 3349 | 0.16 | 0.49 | YES |
13 | TRMT11 | TRMT11 | TRMT11 | 3508 | 0.16 | 0.52 | YES |
14 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 3764 | 0.14 | 0.53 | YES |
15 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3958 | 0.14 | 0.55 | YES |
16 | LCMT2 | LCMT2 | LCMT2 | 4968 | 0.098 | 0.51 | NO |
17 | METTL6 | METTL6 | METTL6 | 5065 | 0.095 | 0.53 | NO |
18 | MAOA | MAOA | MAOA | 5508 | 0.08 | 0.52 | NO |
19 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 5884 | 0.069 | 0.51 | NO |
20 | MAOB | MAOB | MAOB | 6543 | 0.05 | 0.49 | NO |
21 | METTL2B | METTL2B | METTL2B | 6707 | 0.046 | 0.49 | NO |
22 | HDC | HDC | HDC | 6888 | 0.04 | 0.49 | NO |
23 | HAL | HAL | HAL | 8280 | 0.0033 | 0.41 | NO |
24 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 9596 | -0.03 | 0.34 | NO |
25 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 9937 | -0.038 | 0.33 | NO |
26 | ABP1 | ABP1 | ABP1 | 10919 | -0.064 | 0.29 | NO |
27 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 11152 | -0.071 | 0.3 | NO |
28 | ASPA | ASPA | ASPA | 13520 | -0.16 | 0.2 | NO |
29 | HNMT | HNMT | HNMT | 15705 | -0.3 | 0.14 | NO |
Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SELENOAMINO ACID METABOLISM.
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Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SELENOAMINO ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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Table S35. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ACSM1 | ACSM1 | ACSM1 | 23 | 1 | 0.14 | YES |
2 | BDH1 | BDH1 | BDH1 | 325 | 0.6 | 0.2 | YES |
3 | OXCT2 | OXCT2 | OXCT2 | 364 | 0.59 | 0.28 | YES |
4 | AKR1B10 | AKR1B10 | AKR1B10 | 479 | 0.53 | 0.35 | YES |
5 | ABAT | ABAT | ABAT | 803 | 0.44 | 0.39 | YES |
6 | ACSM2A | ACSM2A | ACSM2A | 859 | 0.42 | 0.44 | YES |
7 | ALDH2 | ALDH2 | ALDH2 | 1463 | 0.31 | 0.45 | YES |
8 | PDHA1 | PDHA1 | PDHA1 | 2568 | 0.21 | 0.42 | YES |
9 | ACSM5 | ACSM5 | ACSM5 | 2616 | 0.21 | 0.44 | YES |
10 | ACSM3 | ACSM3 | ACSM3 | 3041 | 0.18 | 0.44 | YES |
11 | AACS | AACS | AACS | 3226 | 0.17 | 0.46 | YES |
12 | HMGCL | HMGCL | HMGCL | 3412 | 0.16 | 0.47 | YES |
13 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3958 | 0.14 | 0.46 | YES |
14 | PDHB | PDHB | PDHB | 3965 | 0.14 | 0.47 | YES |
15 | ECHS1 | ECHS1 | ECHS1 | 4183 | 0.13 | 0.48 | YES |
16 | BDH2 | BDH2 | BDH2 | 4247 | 0.12 | 0.49 | YES |
17 | OXCT1 | OXCT1 | OXCT1 | 4356 | 0.12 | 0.5 | YES |
18 | ALDH5A1 | ALDH5A1 | ALDH5A1 | 4750 | 0.1 | 0.5 | NO |
19 | ACAT1 | ACAT1 | ACAT1 | 5107 | 0.093 | 0.49 | NO |
20 | L2HGDH | L2HGDH | L2HGDH | 5650 | 0.076 | 0.47 | NO |
21 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 5884 | 0.069 | 0.46 | NO |
22 | HADH | HADH | HADH | 6580 | 0.049 | 0.43 | NO |
23 | HMGCS1 | HMGCS1 | HMGCS1 | 6764 | 0.044 | 0.43 | NO |
24 | ACADS | ACADS | ACADS | 6773 | 0.044 | 0.43 | NO |
25 | HADHA | HADHA | HADHA | 7479 | 0.024 | 0.4 | NO |
26 | ACAT2 | ACAT2 | ACAT2 | 7910 | 0.013 | 0.38 | NO |
27 | EHHADH | EHHADH | EHHADH | 9238 | -0.021 | 0.31 | NO |
28 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 9596 | -0.03 | 0.29 | NO |
29 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 9937 | -0.038 | 0.28 | NO |
30 | GAD1 | GAD1 | GAD1 | 17147 | -0.52 | -0.049 | NO |
31 | HMGCS2 | HMGCS2 | HMGCS2 | 17776 | -0.8 | 0.023 | NO |
Figure S69. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PYRUVATE METABOLISM.
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Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRUVATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | GTF2H4 | GTF2H4 | GTF2H4 | 2723 | 0.2 | -0.068 | YES |
2 | POLR2J | POLR2J | POLR2J | 2998 | 0.18 | -0.0079 | YES |
3 | ERCC2 | ERCC2 | ERCC2 | 3032 | 0.18 | 0.065 | YES |
4 | POLR2L | POLR2L | POLR2L | 3394 | 0.16 | 0.11 | YES |
5 | GTF2F2 | GTF2F2 | GTF2F2 | 3972 | 0.14 | 0.13 | YES |
6 | WHSC2 | WHSC2 | WHSC2 | 4660 | 0.11 | 0.14 | YES |
7 | GTF2H2B | GTF2H2B | GTF2H2B | 4708 | 0.11 | 0.18 | YES |
8 | POLR2E | POLR2E | POLR2E | 5383 | 0.084 | 0.18 | YES |
9 | POLR2I | POLR2I | POLR2I | 5394 | 0.084 | 0.21 | YES |
10 | RDBP | RDBP | RDBP | 5417 | 0.083 | 0.24 | YES |
11 | POLR2G | POLR2G | POLR2G | 5481 | 0.081 | 0.27 | YES |
12 | TH1L | TH1L | TH1L | 5936 | 0.068 | 0.28 | YES |
13 | COBRA1 | COBRA1 | COBRA1 | 5946 | 0.067 | 0.3 | YES |
14 | NCBP2 | NCBP2 | NCBP2 | 6081 | 0.063 | 0.32 | YES |
15 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 6177 | 0.06 | 0.34 | YES |
16 | CTDP1 | CTDP1 | CTDP1 | 6488 | 0.051 | 0.34 | YES |
17 | POLR2H | POLR2H | POLR2H | 7104 | 0.035 | 0.32 | NO |
18 | POLR2F | POLR2F | POLR2F | 7252 | 0.031 | 0.33 | NO |
19 | GTF2F1 | GTF2F1 | GTF2F1 | 7365 | 0.028 | 0.34 | NO |
20 | ERCC3 | ERCC3 | ERCC3 | 7738 | 0.018 | 0.32 | NO |
21 | POLR2C | POLR2C | POLR2C | 8264 | 0.004 | 0.3 | NO |
22 | CDK7 | CDK7 | CDK7 | 8957 | -0.014 | 0.26 | NO |
23 | CCNH | CCNH | CCNH | 9458 | -0.026 | 0.24 | NO |
24 | SUPT5H | SUPT5H | SUPT5H | 9463 | -0.027 | 0.26 | NO |
25 | GTF2H2 | GTF2H2 | GTF2H2 | 9789 | -0.035 | 0.25 | NO |
26 | POLR2K | POLR2K | POLR2K | 9851 | -0.036 | 0.26 | NO |
27 | NCBP1 | NCBP1 | NCBP1 | 9875 | -0.037 | 0.28 | NO |
28 | MNAT1 | MNAT1 | MNAT1 | 10038 | -0.041 | 0.28 | NO |
29 | POLR2A | POLR2A | POLR2A | 10354 | -0.05 | 0.29 | NO |
30 | POLR2B | POLR2B | POLR2B | 10391 | -0.051 | 0.31 | NO |
31 | GTF2H1 | GTF2H1 | GTF2H1 | 11375 | -0.077 | 0.28 | NO |
32 | POLR2D | POLR2D | POLR2D | 12131 | -0.1 | 0.28 | NO |
33 | GTF2H3 | GTF2H3 | GTF2H3 | 12726 | -0.12 | 0.3 | NO |
Figure S71. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BUTANOATE METABOLISM.

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

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | LDHD | LDHD | LDHD | 356 | 0.59 | 0.09 | YES |
2 | HAGHL | HAGHL | HAGHL | 464 | 0.54 | 0.18 | YES |
3 | ACSS2 | ACSS2 | ACSS2 | 1232 | 0.34 | 0.2 | YES |
4 | ALDH2 | ALDH2 | ALDH2 | 1463 | 0.31 | 0.25 | YES |
5 | ACYP1 | ACYP1 | ACYP1 | 2556 | 0.21 | 0.23 | YES |
6 | PDHA1 | PDHA1 | PDHA1 | 2568 | 0.21 | 0.27 | YES |
7 | PC | PC | PC | 2580 | 0.21 | 0.3 | YES |
8 | HAGH | HAGH | HAGH | 2993 | 0.18 | 0.32 | YES |
9 | LDHB | LDHB | LDHB | 3055 | 0.18 | 0.35 | YES |
10 | ACACA | ACACA | ACACA | 3586 | 0.15 | 0.34 | YES |
11 | DLD | DLD | DLD | 3753 | 0.14 | 0.36 | YES |
12 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3958 | 0.14 | 0.38 | YES |
13 | PDHB | PDHB | PDHB | 3965 | 0.14 | 0.4 | YES |
14 | AKR1B1 | AKR1B1 | AKR1B1 | 4136 | 0.13 | 0.42 | YES |
15 | MDH1 | MDH1 | MDH1 | 4311 | 0.12 | 0.43 | YES |
16 | MDH2 | MDH2 | MDH2 | 4373 | 0.12 | 0.45 | YES |
17 | ACAT1 | ACAT1 | ACAT1 | 5107 | 0.093 | 0.42 | NO |
18 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 5884 | 0.069 | 0.39 | NO |
19 | PKLR | PKLR | PKLR | 6108 | 0.062 | 0.39 | NO |
20 | GRHPR | GRHPR | GRHPR | 6181 | 0.06 | 0.4 | NO |
21 | PCK2 | PCK2 | PCK2 | 6237 | 0.058 | 0.41 | NO |
22 | ACOT12 | ACOT12 | ACOT12 | 6280 | 0.057 | 0.42 | NO |
23 | ACAT2 | ACAT2 | ACAT2 | 7910 | 0.013 | 0.33 | NO |
24 | PKM2 | PKM2 | PKM2 | 8573 | -0.0037 | 0.29 | NO |
25 | DLAT | DLAT | DLAT | 8822 | -0.01 | 0.28 | NO |
26 | ACSS1 | ACSS1 | ACSS1 | 8871 | -0.011 | 0.28 | NO |
27 | PCK1 | PCK1 | PCK1 | 9059 | -0.016 | 0.27 | NO |
28 | LDHAL6A | LDHAL6A | LDHAL6A | 9422 | -0.025 | 0.26 | NO |
29 | ACACB | ACACB | ACACB | 9440 | -0.026 | 0.26 | NO |
30 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 9596 | -0.03 | 0.26 | NO |
31 | ACYP2 | ACYP2 | ACYP2 | 9806 | -0.035 | 0.25 | NO |
32 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 9937 | -0.038 | 0.25 | NO |
33 | GLO1 | GLO1 | GLO1 | 10941 | -0.065 | 0.21 | NO |
34 | LDHC | LDHC | LDHC | 12101 | -0.1 | 0.16 | NO |
35 | ME2 | ME2 | ME2 | 12507 | -0.12 | 0.16 | NO |
36 | ME3 | ME3 | ME3 | 13274 | -0.14 | 0.15 | NO |
37 | ME1 | ME1 | ME1 | 14580 | -0.21 | 0.12 | NO |
38 | LDHAL6B | LDHAL6B | LDHAL6B | 14878 | -0.23 | 0.14 | NO |
39 | LDHA | LDHA | LDHA | 14907 | -0.23 | 0.18 | NO |
Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS.

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

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NDUFS8 | NDUFS8 | NDUFS8 | 1448 | 0.31 | -0.045 | YES |
2 | ATP5G1 | ATP5G1 | ATP5G1 | 1481 | 0.31 | -0.012 | YES |
3 | NDUFB2 | NDUFB2 | NDUFB2 | 2004 | 0.25 | -0.012 | YES |
4 | UQCRC1 | UQCRC1 | UQCRC1 | 2112 | 0.24 | 0.0091 | YES |
5 | UQCRHL | UQCRHL | UQCRHL | 2393 | 0.22 | 0.019 | YES |
6 | NDUFS7 | NDUFS7 | NDUFS7 | 2435 | 0.22 | 0.041 | YES |
7 | NDUFA4 | NDUFA4 | NDUFA4 | 2612 | 0.21 | 0.054 | YES |
8 | ATP5J2 | ATP5J2 | ATP5J2 | 2662 | 0.2 | 0.075 | YES |
9 | UQCRH | UQCRH | UQCRH | 2757 | 0.2 | 0.092 | YES |
10 | ATP5D | ATP5D | ATP5D | 2809 | 0.2 | 0.11 | YES |
11 | COX6A1 | COX6A1 | COX6A1 | 2819 | 0.2 | 0.13 | YES |
12 | NDUFS6 | NDUFS6 | NDUFS6 | 3048 | 0.18 | 0.14 | YES |
13 | NDUFA3 | NDUFA3 | NDUFA3 | 3190 | 0.17 | 0.15 | YES |
14 | COX4I1 | COX4I1 | COX4I1 | 3233 | 0.17 | 0.17 | YES |
15 | NDUFB9 | NDUFB9 | NDUFB9 | 3262 | 0.17 | 0.19 | YES |
16 | NDUFA7 | NDUFA7 | NDUFA7 | 3281 | 0.17 | 0.2 | YES |
17 | ATP5H | ATP5H | ATP5H | 3340 | 0.16 | 0.22 | YES |
18 | NDUFB10 | NDUFB10 | NDUFB10 | 3422 | 0.16 | 0.23 | YES |
19 | NDUFA11 | NDUFA11 | NDUFA11 | 3485 | 0.16 | 0.25 | YES |
20 | NDUFA9 | NDUFA9 | NDUFA9 | 3631 | 0.15 | 0.26 | YES |
21 | NDUFV1 | NDUFV1 | NDUFV1 | 3813 | 0.14 | 0.26 | YES |
22 | NDUFB8 | NDUFB8 | NDUFB8 | 3889 | 0.14 | 0.27 | YES |
23 | NDUFB3 | NDUFB3 | NDUFB3 | 4013 | 0.13 | 0.28 | YES |
24 | NDUFB7 | NDUFB7 | NDUFB7 | 4050 | 0.13 | 0.29 | YES |
25 | UQCRC2 | UQCRC2 | UQCRC2 | 4084 | 0.13 | 0.31 | YES |
26 | CYCS | CYCS | CYCS | 4147 | 0.13 | 0.32 | YES |
27 | COX5A | COX5A | COX5A | 4174 | 0.13 | 0.33 | YES |
28 | ATP5I | ATP5I | ATP5I | 4185 | 0.12 | 0.34 | YES |
29 | NDUFA13 | NDUFA13 | NDUFA13 | 4210 | 0.12 | 0.36 | YES |
30 | UQCR11 | UQCR11 | UQCR11 | 4220 | 0.12 | 0.37 | YES |
31 | COX5B | COX5B | COX5B | 4288 | 0.12 | 0.38 | YES |
32 | ETFB | ETFB | ETFB | 4294 | 0.12 | 0.39 | YES |
33 | NDUFS5 | NDUFS5 | NDUFS5 | 4395 | 0.12 | 0.4 | YES |
34 | NDUFB1 | NDUFB1 | NDUFB1 | 4481 | 0.11 | 0.41 | YES |
35 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 4607 | 0.11 | 0.41 | YES |
36 | NDUFA8 | NDUFA8 | NDUFA8 | 4875 | 0.1 | 0.41 | YES |
37 | ATP5B | ATP5B | ATP5B | 4879 | 0.1 | 0.42 | YES |
38 | NDUFA2 | NDUFA2 | NDUFA2 | 4881 | 0.1 | 0.43 | YES |
39 | COX6B1 | COX6B1 | COX6B1 | 5000 | 0.097 | 0.44 | YES |
40 | NDUFA10 | NDUFA10 | NDUFA10 | 5052 | 0.095 | 0.44 | YES |
41 | ATP5E | ATP5E | ATP5E | 5138 | 0.092 | 0.45 | YES |
42 | NDUFB5 | NDUFB5 | NDUFB5 | 5147 | 0.092 | 0.46 | YES |
43 | NDUFS1 | NDUFS1 | NDUFS1 | 5155 | 0.091 | 0.47 | YES |
44 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 5198 | 0.09 | 0.48 | YES |
45 | NDUFA5 | NDUFA5 | NDUFA5 | 5281 | 0.087 | 0.48 | YES |
46 | NDUFS2 | NDUFS2 | NDUFS2 | 5294 | 0.087 | 0.49 | YES |
47 | CYC1 | CYC1 | CYC1 | 5296 | 0.087 | 0.5 | YES |
48 | NDUFS3 | NDUFS3 | NDUFS3 | 5302 | 0.087 | 0.51 | YES |
49 | COX8A | COX8A | COX8A | 5334 | 0.085 | 0.52 | YES |
50 | NDUFA1 | NDUFA1 | NDUFA1 | 5370 | 0.084 | 0.52 | YES |
51 | ATP5A1 | ATP5A1 | ATP5A1 | 5441 | 0.082 | 0.53 | YES |
52 | COX7B | COX7B | COX7B | 5465 | 0.081 | 0.54 | YES |
53 | ATP5C1 | ATP5C1 | ATP5C1 | 5548 | 0.079 | 0.54 | YES |
54 | NDUFB4 | NDUFB4 | NDUFB4 | 5598 | 0.077 | 0.55 | YES |
55 | UQCRQ | UQCRQ | UQCRQ | 5738 | 0.073 | 0.55 | YES |
56 | NDUFA6 | NDUFA6 | NDUFA6 | 5818 | 0.071 | 0.55 | YES |
57 | ATP5F1 | ATP5F1 | ATP5F1 | 5917 | 0.068 | 0.56 | YES |
58 | COX6C | COX6C | COX6C | 5957 | 0.067 | 0.56 | YES |
59 | COX7C | COX7C | COX7C | 6164 | 0.061 | 0.56 | NO |
60 | NDUFC2 | NDUFC2 | NDUFC2 | 6398 | 0.054 | 0.55 | NO |
61 | ATP5J | ATP5J | ATP5J | 6407 | 0.054 | 0.55 | NO |
62 | ATP5L | ATP5L | ATP5L | 6746 | 0.045 | 0.54 | NO |
63 | UQCRB | UQCRB | UQCRB | 6827 | 0.042 | 0.54 | NO |
64 | ATP5O | ATP5O | ATP5O | 6851 | 0.042 | 0.54 | NO |
65 | NDUFB6 | NDUFB6 | NDUFB6 | 6870 | 0.041 | 0.55 | NO |
66 | SDHC | SDHC | SDHC | 6909 | 0.04 | 0.55 | NO |
67 | SDHA | SDHA | SDHA | 7116 | 0.034 | 0.54 | NO |
68 | SDHB | SDHB | SDHB | 7153 | 0.033 | 0.55 | NO |
69 | NDUFS4 | NDUFS4 | NDUFS4 | 7302 | 0.029 | 0.54 | NO |
70 | NDUFA12 | NDUFA12 | NDUFA12 | 7692 | 0.018 | 0.52 | NO |
71 | ETFA | ETFA | ETFA | 7857 | 0.014 | 0.51 | NO |
72 | NDUFV3 | NDUFV3 | NDUFV3 | 8015 | 0.01 | 0.5 | NO |
73 | NDUFV2 | NDUFV2 | NDUFV2 | 8699 | -0.0071 | 0.47 | NO |
74 | COX7A2L | COX7A2L | COX7A2L | 8967 | -0.014 | 0.46 | NO |
75 | NDUFC1 | NDUFC1 | NDUFC1 | 8985 | -0.014 | 0.46 | NO |
76 | SDHD | SDHD | SDHD | 9775 | -0.034 | 0.42 | NO |
77 | UCP3 | UCP3 | UCP3 | 11900 | -0.093 | 0.31 | NO |
78 | ETFDH | ETFDH | ETFDH | 12860 | -0.13 | 0.27 | NO |
79 | UCP2 | UCP2 | UCP2 | 14651 | -0.21 | 0.2 | NO |
Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASE EXCISION REPAIR.

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

Table S39. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NDUFS8 | NDUFS8 | NDUFS8 | 1448 | 0.31 | -0.036 | YES |
2 | NDUFB2 | NDUFB2 | NDUFB2 | 2004 | 0.25 | -0.03 | YES |
3 | UQCRC1 | UQCRC1 | UQCRC1 | 2112 | 0.24 | -0.0014 | YES |
4 | UQCRHL | UQCRHL | UQCRHL | 2393 | 0.22 | 0.015 | YES |
5 | NDUFS7 | NDUFS7 | NDUFS7 | 2435 | 0.22 | 0.044 | YES |
6 | NDUFA4 | NDUFA4 | NDUFA4 | 2612 | 0.21 | 0.063 | YES |
7 | UQCRH | UQCRH | UQCRH | 2757 | 0.2 | 0.083 | YES |
8 | COX6A1 | COX6A1 | COX6A1 | 2819 | 0.2 | 0.11 | YES |
9 | NDUFS6 | NDUFS6 | NDUFS6 | 3048 | 0.18 | 0.12 | YES |
10 | NDUFA3 | NDUFA3 | NDUFA3 | 3190 | 0.17 | 0.14 | YES |
11 | COX4I1 | COX4I1 | COX4I1 | 3233 | 0.17 | 0.16 | YES |
12 | NDUFB9 | NDUFB9 | NDUFB9 | 3262 | 0.17 | 0.18 | YES |
13 | NDUFA7 | NDUFA7 | NDUFA7 | 3281 | 0.17 | 0.2 | YES |
14 | NDUFB10 | NDUFB10 | NDUFB10 | 3422 | 0.16 | 0.22 | YES |
15 | NDUFA11 | NDUFA11 | NDUFA11 | 3485 | 0.16 | 0.24 | YES |
16 | NDUFA9 | NDUFA9 | NDUFA9 | 3631 | 0.15 | 0.25 | YES |
17 | NDUFV1 | NDUFV1 | NDUFV1 | 3813 | 0.14 | 0.26 | YES |
18 | NDUFB8 | NDUFB8 | NDUFB8 | 3889 | 0.14 | 0.28 | YES |
19 | NDUFB3 | NDUFB3 | NDUFB3 | 4013 | 0.13 | 0.29 | YES |
20 | NDUFB7 | NDUFB7 | NDUFB7 | 4050 | 0.13 | 0.3 | YES |
21 | UQCRC2 | UQCRC2 | UQCRC2 | 4084 | 0.13 | 0.32 | YES |
22 | CYCS | CYCS | CYCS | 4147 | 0.13 | 0.34 | YES |
23 | COX5A | COX5A | COX5A | 4174 | 0.13 | 0.35 | YES |
24 | NDUFA13 | NDUFA13 | NDUFA13 | 4210 | 0.12 | 0.37 | YES |
25 | UQCR11 | UQCR11 | UQCR11 | 4220 | 0.12 | 0.38 | YES |
26 | COX5B | COX5B | COX5B | 4288 | 0.12 | 0.4 | YES |
27 | ETFB | ETFB | ETFB | 4294 | 0.12 | 0.42 | YES |
28 | NDUFS5 | NDUFS5 | NDUFS5 | 4395 | 0.12 | 0.43 | YES |
29 | NDUFB1 | NDUFB1 | NDUFB1 | 4481 | 0.11 | 0.44 | YES |
30 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 4607 | 0.11 | 0.45 | YES |
31 | NDUFA8 | NDUFA8 | NDUFA8 | 4875 | 0.1 | 0.45 | YES |
32 | NDUFA2 | NDUFA2 | NDUFA2 | 4881 | 0.1 | 0.46 | YES |
33 | COX6B1 | COX6B1 | COX6B1 | 5000 | 0.097 | 0.47 | YES |
34 | NDUFA10 | NDUFA10 | NDUFA10 | 5052 | 0.095 | 0.48 | YES |
35 | NDUFB5 | NDUFB5 | NDUFB5 | 5147 | 0.092 | 0.49 | YES |
36 | NDUFS1 | NDUFS1 | NDUFS1 | 5155 | 0.091 | 0.5 | YES |
37 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 5198 | 0.09 | 0.51 | YES |
38 | NDUFA5 | NDUFA5 | NDUFA5 | 5281 | 0.087 | 0.52 | YES |
39 | NDUFS2 | NDUFS2 | NDUFS2 | 5294 | 0.087 | 0.53 | YES |
40 | CYC1 | CYC1 | CYC1 | 5296 | 0.087 | 0.54 | YES |
41 | NDUFS3 | NDUFS3 | NDUFS3 | 5302 | 0.087 | 0.55 | YES |
42 | COX8A | COX8A | COX8A | 5334 | 0.085 | 0.56 | YES |
43 | NDUFA1 | NDUFA1 | NDUFA1 | 5370 | 0.084 | 0.57 | YES |
44 | COX7B | COX7B | COX7B | 5465 | 0.081 | 0.58 | YES |
45 | NDUFB4 | NDUFB4 | NDUFB4 | 5598 | 0.077 | 0.58 | YES |
46 | UQCRQ | UQCRQ | UQCRQ | 5738 | 0.073 | 0.59 | YES |
47 | NDUFA6 | NDUFA6 | NDUFA6 | 5818 | 0.071 | 0.59 | YES |
48 | COX6C | COX6C | COX6C | 5957 | 0.067 | 0.59 | YES |
49 | COX7C | COX7C | COX7C | 6164 | 0.061 | 0.59 | NO |
50 | NDUFC2 | NDUFC2 | NDUFC2 | 6398 | 0.054 | 0.58 | NO |
51 | UQCRB | UQCRB | UQCRB | 6827 | 0.042 | 0.57 | NO |
52 | NDUFB6 | NDUFB6 | NDUFB6 | 6870 | 0.041 | 0.57 | NO |
53 | SDHC | SDHC | SDHC | 6909 | 0.04 | 0.57 | NO |
54 | SDHA | SDHA | SDHA | 7116 | 0.034 | 0.57 | NO |
55 | SDHB | SDHB | SDHB | 7153 | 0.033 | 0.57 | NO |
56 | NDUFS4 | NDUFS4 | NDUFS4 | 7302 | 0.029 | 0.57 | NO |
57 | NDUFA12 | NDUFA12 | NDUFA12 | 7692 | 0.018 | 0.55 | NO |
58 | ETFA | ETFA | ETFA | 7857 | 0.014 | 0.54 | NO |
59 | NDUFV3 | NDUFV3 | NDUFV3 | 8015 | 0.01 | 0.53 | NO |
60 | NDUFV2 | NDUFV2 | NDUFV2 | 8699 | -0.0071 | 0.5 | NO |
61 | COX7A2L | COX7A2L | COX7A2L | 8967 | -0.014 | 0.48 | NO |
62 | NDUFC1 | NDUFC1 | NDUFC1 | 8985 | -0.014 | 0.48 | NO |
63 | SDHD | SDHD | SDHD | 9775 | -0.034 | 0.45 | NO |
64 | ETFDH | ETFDH | ETFDH | 12860 | -0.13 | 0.29 | NO |
Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG LYSOSOME.

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

Table S40. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | POLR2J | POLR2J | POLR2J | 2998 | 0.18 | -0.13 | YES |
2 | POLR2L | POLR2L | POLR2L | 3394 | 0.16 | -0.12 | YES |
3 | SF3B5 | SF3B5 | SF3B5 | 3675 | 0.15 | -0.11 | YES |
4 | SNRPB | SNRPB | SNRPB | 3802 | 0.14 | -0.088 | YES |
5 | CPSF1 | CPSF1 | CPSF1 | 3970 | 0.14 | -0.071 | YES |
6 | GTF2F2 | GTF2F2 | GTF2F2 | 3972 | 0.14 | -0.045 | YES |
7 | SNRNP70 | SNRNP70 | SNRNP70 | 4413 | 0.12 | -0.047 | YES |
8 | SNRPF | SNRPF | SNRPF | 4736 | 0.11 | -0.044 | YES |
9 | CD2BP2 | CD2BP2 | CD2BP2 | 4752 | 0.1 | -0.025 | YES |
10 | RBM5 | RBM5 | RBM5 | 4768 | 0.1 | -0.0055 | YES |
11 | RNPS1 | RNPS1 | RNPS1 | 4857 | 0.1 | 0.0093 | YES |
12 | THOC4 | THOC4 | THOC4 | 5048 | 0.095 | 0.017 | YES |
13 | SF3B4 | SF3B4 | SF3B4 | 5257 | 0.088 | 0.023 | YES |
14 | POLR2E | POLR2E | POLR2E | 5383 | 0.084 | 0.032 | YES |
15 | POLR2I | POLR2I | POLR2I | 5394 | 0.084 | 0.048 | YES |
16 | EFTUD2 | EFTUD2 | EFTUD2 | 5408 | 0.083 | 0.063 | YES |
17 | POLR2G | POLR2G | POLR2G | 5481 | 0.081 | 0.074 | YES |
18 | PABPN1 | PABPN1 | PABPN1 | 5830 | 0.07 | 0.069 | YES |
19 | NCBP2 | NCBP2 | NCBP2 | 6081 | 0.063 | 0.067 | YES |
20 | SNRPG | SNRPG | SNRPG | 6114 | 0.062 | 0.077 | YES |
21 | SNRPA | SNRPA | SNRPA | 6118 | 0.062 | 0.089 | YES |
22 | CSTF3 | CSTF3 | CSTF3 | 6600 | 0.048 | 0.072 | YES |
23 | U2AF2 | U2AF2 | U2AF2 | 6838 | 0.042 | 0.067 | YES |
24 | SF3A2 | SF3A2 | SF3A2 | 6945 | 0.039 | 0.068 | YES |
25 | TXNL4A | TXNL4A | TXNL4A | 6987 | 0.038 | 0.073 | YES |
26 | HNRNPA2B1 | HNRNPA2B1 | HNRNPA2B1 | 7023 | 0.037 | 0.078 | YES |
27 | CPSF3 | CPSF3 | CPSF3 | 7027 | 0.037 | 0.085 | YES |
28 | POLR2H | POLR2H | POLR2H | 7104 | 0.035 | 0.088 | YES |
29 | DHX38 | DHX38 | DHX38 | 7128 | 0.034 | 0.093 | YES |
30 | POLR2F | POLR2F | POLR2F | 7252 | 0.031 | 0.092 | YES |
31 | MAGOH | MAGOH | MAGOH | 7298 | 0.029 | 0.095 | YES |
32 | U2AF1 | U2AF1 | U2AF1 | 7347 | 0.029 | 0.098 | YES |
33 | NHP2L1 | NHP2L1 | NHP2L1 | 7355 | 0.028 | 0.1 | YES |
34 | GTF2F1 | GTF2F1 | GTF2F1 | 7365 | 0.028 | 0.11 | YES |
35 | PTBP1 | PTBP1 | PTBP1 | 7429 | 0.026 | 0.11 | YES |
36 | PRPF6 | PRPF6 | PRPF6 | 7475 | 0.025 | 0.11 | YES |
37 | SNRPD2 | SNRPD2 | SNRPD2 | 7588 | 0.021 | 0.11 | YES |
38 | SF3B2 | SF3B2 | SF3B2 | 7620 | 0.02 | 0.11 | YES |
39 | DNAJC8 | DNAJC8 | DNAJC8 | 7729 | 0.018 | 0.11 | YES |
40 | LSM2 | LSM2 | LSM2 | 7939 | 0.012 | 0.1 | YES |
41 | PRPF8 | PRPF8 | PRPF8 | 8004 | 0.011 | 0.099 | YES |
42 | SF3B14 | SF3B14 | SF3B14 | 8026 | 0.01 | 0.1 | YES |
43 | DDX23 | DDX23 | DDX23 | 8133 | 0.0074 | 0.095 | YES |
44 | YBX1 | YBX1 | YBX1 | 8202 | 0.0054 | 0.093 | YES |
45 | HNRNPL | HNRNPL | HNRNPL | 8223 | 0.005 | 0.093 | YES |
46 | POLR2C | POLR2C | POLR2C | 8264 | 0.004 | 0.091 | YES |
47 | HNRNPC | HNRNPC | HNRNPC | 8287 | 0.0032 | 0.09 | YES |
48 | SNRNP200 | SNRNP200 | SNRNP200 | 8375 | 0.0011 | 0.086 | YES |
49 | FUS | FUS | FUS | 8572 | -0.0037 | 0.076 | YES |
50 | SF3B1 | SF3B1 | SF3B1 | 8653 | -0.0059 | 0.072 | YES |
51 | HNRNPM | HNRNPM | HNRNPM | 8684 | -0.0066 | 0.072 | YES |
52 | HNRNPU | HNRNPU | HNRNPU | 8686 | -0.0066 | 0.073 | YES |
53 | SRRM1 | SRRM1 | SRRM1 | 8721 | -0.0076 | 0.073 | YES |
54 | SF3B3 | SF3B3 | SF3B3 | 8741 | -0.0083 | 0.074 | YES |
55 | PRPF4 | PRPF4 | PRPF4 | 8783 | -0.009 | 0.073 | YES |
56 | SNRPD3 | SNRPD3 | SNRPD3 | 8789 | -0.0091 | 0.074 | YES |
57 | SNRPA1 | SNRPA1 | SNRPA1 | 9094 | -0.017 | 0.061 | YES |
58 | CCAR1 | CCAR1 | CCAR1 | 9176 | -0.02 | 0.06 | YES |
59 | SNRPE | SNRPE | SNRPE | 9227 | -0.021 | 0.062 | YES |
60 | HNRNPH1 | HNRNPH1 | HNRNPH1 | 9373 | -0.024 | 0.058 | YES |
61 | CPSF2 | CPSF2 | CPSF2 | 9609 | -0.03 | 0.051 | YES |
62 | UPF3B | UPF3B | UPF3B | 9643 | -0.031 | 0.055 | YES |
63 | HNRNPF | HNRNPF | HNRNPF | 9644 | -0.031 | 0.061 | YES |
64 | DHX9 | DHX9 | DHX9 | 9667 | -0.032 | 0.066 | YES |
65 | SNRPB2 | SNRPB2 | SNRPB2 | 9685 | -0.032 | 0.071 | YES |
66 | PCBP1 | PCBP1 | PCBP1 | 9724 | -0.033 | 0.076 | YES |
67 | CSTF2 | CSTF2 | CSTF2 | 9730 | -0.033 | 0.082 | YES |
68 | HNRNPA0 | HNRNPA0 | HNRNPA0 | 9796 | -0.035 | 0.085 | YES |
69 | POLR2K | POLR2K | POLR2K | 9851 | -0.036 | 0.089 | YES |
70 | NCBP1 | NCBP1 | NCBP1 | 9875 | -0.037 | 0.095 | YES |
71 | SF3A3 | SF3A3 | SF3A3 | 10102 | -0.043 | 0.09 | YES |
72 | CDC40 | CDC40 | CDC40 | 10219 | -0.046 | 0.093 | YES |
73 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 10237 | -0.046 | 0.1 | YES |
74 | HNRNPK | HNRNPK | HNRNPK | 10310 | -0.048 | 0.11 | YES |
75 | POLR2A | POLR2A | POLR2A | 10354 | -0.05 | 0.11 | YES |
76 | POLR2B | POLR2B | POLR2B | 10391 | -0.051 | 0.12 | YES |
77 | CSTF1 | CSTF1 | CSTF1 | 10427 | -0.052 | 0.13 | YES |
78 | SF3A1 | SF3A1 | SF3A1 | 10456 | -0.052 | 0.14 | YES |
79 | SNRNP40 | SNRNP40 | SNRNP40 | 10477 | -0.053 | 0.15 | YES |
80 | SNRPD1 | SNRPD1 | SNRPD1 | 10548 | -0.055 | 0.15 | YES |
81 | HNRNPH2 | HNRNPH2 | HNRNPH2 | 10552 | -0.055 | 0.16 | YES |
82 | PCBP2 | PCBP2 | PCBP2 | 10714 | -0.059 | 0.17 | YES |
83 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 10958 | -0.065 | 0.16 | YES |
84 | HNRNPUL1 | HNRNPUL1 | HNRNPUL1 | 11052 | -0.068 | 0.17 | YES |
85 | HNRNPR | HNRNPR | HNRNPR | 11248 | -0.074 | 0.18 | YES |
86 | HNRNPD | HNRNPD | HNRNPD | 11388 | -0.077 | 0.18 | YES |
87 | CLP1 | CLP1 | CLP1 | 11431 | -0.079 | 0.2 | YES |
88 | PAPOLA | PAPOLA | PAPOLA | 11488 | -0.081 | 0.21 | YES |
89 | NFX1 | NFX1 | NFX1 | 11579 | -0.083 | 0.22 | YES |
90 | PHF5A | PHF5A | PHF5A | 11606 | -0.084 | 0.24 | YES |
91 | SMC1A | SMC1A | SMC1A | 11650 | -0.086 | 0.25 | YES |
92 | RBM8A | RBM8A | RBM8A | 11665 | -0.086 | 0.26 | YES |
93 | RBMX | RBMX | RBMX | 11675 | -0.087 | 0.28 | YES |
94 | CPSF7 | CPSF7 | CPSF7 | 11689 | -0.087 | 0.3 | YES |
95 | NUDT21 | NUDT21 | NUDT21 | 12064 | -0.099 | 0.3 | YES |
96 | POLR2D | POLR2D | POLR2D | 12131 | -0.1 | 0.31 | YES |
97 | PCF11 | PCF11 | PCF11 | 12778 | -0.12 | 0.3 | NO |
Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TIGHT JUNCTION.

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

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