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 "STAD-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: 726 |
Number of samples: 415 |
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 - 5 :[ clus1 ] 94 |
pheno.type: 2 - 5 :[ clus2 ] 95 |
pheno.type: 3 - 5 :[ clus3 ] 94 |
pheno.type: 4 - 5 :[ clus4 ] 82 |
pheno.type: 5 - 5 :[ clus5 ] 50 |
For the expression subtypes of 18694 genes in 416 samples, GSEA found enriched gene sets in each cluster using 415 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 GLYCINE SERINE AND THREONINE METABOLISM, KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG SPLICEOSOME, ST WNT BETA CATENIN PATHWAY, PID HNF3BPATHWAY, REACTOME PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION, REACTOME METABOLISM OF STEROID HORMONES AND VITAMINS A AND D, REACTOME METABOLISM OF VITAMINS AND COFACTORS, REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE
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And common core enriched genes are F2, F10, F7, PROC, ENPP1, FASN, FLAD1, MOCS1, MOCS3, NFS1
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clus2
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Top enriched gene sets are KEGG PURINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG ABC TRANSPORTERS, KEGG MAPK SIGNALING PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION
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And common core enriched genes are AKT3, ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY7, ADCY8, ADCY9, CAMK4
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clus3
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Top enriched gene sets are KEGG PYRIMIDINE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA DEGRADATION, KEGG RNA POLYMERASE, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG PROTEASOME, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG CELL CYCLE
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And common core enriched genes are CCNH, CDK7, MNAT1, CCNA2, CCNE2, CDK2, CDKN1A, CKS1B, PSMA1, PSMA2
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clus4
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Top enriched gene sets are KEGG INOSITOL PHOSPHATE METABOLISM, KEGG APOPTOSIS, BIOCARTA HIVNEF PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA STRESS PATHWAY, ST TUMOR NECROSIS FACTOR PATHWAY, ST INTERLEUKIN 4 PATHWAY, PID BCR 5PATHWAY, PID TRAIL PATHWAY, PID CDC42 PATHWAY
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And common core enriched genes are MAP3K1, CHUK, CRADD, MAP3K14, NFKB1, TNF, TRADD, AP1B1, AP1G1, AP1M2
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clus5
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Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG PYRUVATE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG PEROXISOME, BIOCARTA DEATH PATHWAY, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT
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And common core enriched genes are AARS2, CARS2, DARS, DARS2, EPRS, FARSA, FARSB, GARS, HARS2, IARS
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 GLYCINE SERINE AND THREONINE METABOLISM | 31 | genes.ES.table | 0.63 | 1.6 | 0.0079 | 1 | 0.94 | 0.39 | 0.11 | 0.35 | 0.93 | 0.47 |
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS | 25 | genes.ES.table | 0.45 | 1.6 | 0.06 | 1 | 0.94 | 0.52 | 0.39 | 0.32 | 1 | 0.51 |
KEGG SPLICEOSOME | 114 | genes.ES.table | 0.41 | 1.6 | 0.086 | 1 | 0.94 | 0.68 | 0.5 | 0.34 | 1 | 0.55 |
ST WNT BETA CATENIN PATHWAY | 32 | genes.ES.table | 0.55 | 1.5 | 0.057 | 1 | 0.99 | 0.19 | 0.075 | 0.17 | 0.69 | 0.37 |
PID HNF3BPATHWAY | 44 | genes.ES.table | 0.66 | 1.7 | 0.0079 | 1 | 0.87 | 0.48 | 0.19 | 0.39 | 1 | 0.55 |
REACTOME PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION | 25 | genes.ES.table | 0.6 | 1.7 | 0.0019 | 1 | 0.86 | 0.16 | 0.0064 | 0.16 | 1 | 0.67 |
REACTOME METABOLISM OF STEROID HORMONES AND VITAMINS A AND D | 31 | genes.ES.table | 0.61 | 1.5 | 0.014 | 1 | 0.98 | 0.48 | 0.16 | 0.41 | 0.77 | 0.42 |
REACTOME METABOLISM OF VITAMINS AND COFACTORS | 50 | genes.ES.table | 0.43 | 1.7 | 0.02 | 1 | 0.86 | 0.36 | 0.26 | 0.27 | 1 | 0.78 |
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA | 126 | genes.ES.table | 0.44 | 1.6 | 0.095 | 1 | 0.97 | 0.73 | 0.51 | 0.36 | 1 | 0.53 |
REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE | 31 | genes.ES.table | 0.6 | 1.6 | 0.023 | 1 | 0.97 | 0.48 | 0.23 | 0.38 | 0.95 | 0.48 |
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 | QPRT | QPRT | QPRT | 38 | 0.66 | 0.14 | YES |
2 | SLC23A1 | SLC23A1 | SLC23A1 | 502 | 0.4 | 0.19 | YES |
3 | MOCS3 | MOCS3 | MOCS3 | 1491 | 0.25 | 0.19 | YES |
4 | SLC46A1 | SLC46A1 | SLC46A1 | 2070 | 0.21 | 0.2 | YES |
5 | NMNAT2 | NMNAT2 | NMNAT2 | 2466 | 0.18 | 0.22 | YES |
6 | SLC19A3 | SLC19A3 | SLC19A3 | 2586 | 0.18 | 0.25 | YES |
7 | MOCS1 | MOCS1 | MOCS1 | 2630 | 0.17 | 0.28 | YES |
8 | NMNAT3 | NMNAT3 | NMNAT3 | 2863 | 0.16 | 0.3 | YES |
9 | NFS1 | NFS1 | NFS1 | 3108 | 0.15 | 0.32 | YES |
10 | SLC5A6 | SLC5A6 | SLC5A6 | 3359 | 0.14 | 0.34 | YES |
11 | SLC19A2 | SLC19A2 | SLC19A2 | 3949 | 0.12 | 0.33 | YES |
12 | PPCDC | PPCDC | PPCDC | 4013 | 0.12 | 0.35 | YES |
13 | FLAD1 | FLAD1 | FLAD1 | 4066 | 0.12 | 0.37 | YES |
14 | ENPP1 | ENPP1 | ENPP1 | 4392 | 0.11 | 0.38 | YES |
15 | SLC19A1 | SLC19A1 | SLC19A1 | 4513 | 0.1 | 0.39 | YES |
16 | FASN | FASN | FASN | 4583 | 0.1 | 0.41 | YES |
17 | SLC23A2 | SLC23A2 | SLC23A2 | 4759 | 0.096 | 0.42 | YES |
18 | SLC2A1 | SLC2A1 | SLC2A1 | 4919 | 0.093 | 0.43 | YES |
19 | PANK2 | PANK2 | PANK2 | 6257 | 0.066 | 0.37 | NO |
20 | THTPA | THTPA | THTPA | 6355 | 0.064 | 0.38 | NO |
21 | AASDHPPT | AASDHPPT | AASDHPPT | 6367 | 0.064 | 0.39 | NO |
22 | PANK1 | PANK1 | PANK1 | 6381 | 0.064 | 0.4 | NO |
23 | COASY | COASY | COASY | 6425 | 0.063 | 0.42 | NO |
24 | RFK | RFK | RFK | 7338 | 0.048 | 0.38 | NO |
25 | GSTO2 | GSTO2 | GSTO2 | 7551 | 0.045 | 0.37 | NO |
26 | SLC25A32 | SLC25A32 | SLC25A32 | 8117 | 0.037 | 0.35 | NO |
27 | PNPO | PNPO | PNPO | 8605 | 0.03 | 0.33 | NO |
28 | SHMT1 | SHMT1 | SHMT1 | 9873 | 0.014 | 0.27 | NO |
29 | PANK4 | PANK4 | PANK4 | 10372 | 0.0075 | 0.24 | NO |
30 | SLC25A16 | SLC25A16 | SLC25A16 | 10524 | 0.0055 | 0.23 | NO |
31 | CYB5R3 | CYB5R3 | CYB5R3 | 10822 | 0.0014 | 0.22 | NO |
32 | NAMPT | NAMPT | NAMPT | 11040 | -0.0017 | 0.21 | NO |
33 | PDXK | PDXK | PDXK | 11353 | -0.0057 | 0.19 | NO |
34 | CYB5A | CYB5A | CYB5A | 11575 | -0.0088 | 0.18 | NO |
35 | NADK | NADK | NADK | 11776 | -0.011 | 0.17 | NO |
36 | PPCS | PPCS | PPCS | 11804 | -0.012 | 0.17 | NO |
37 | SLC2A3 | SLC2A3 | SLC2A3 | 12112 | -0.016 | 0.16 | NO |
38 | GSTO1 | GSTO1 | GSTO1 | 12412 | -0.021 | 0.15 | NO |
39 | MTHFD1 | MTHFD1 | MTHFD1 | 13558 | -0.039 | 0.096 | NO |
40 | GPHN | GPHN | GPHN | 13582 | -0.039 | 0.1 | NO |
41 | MTHFR | MTHFR | MTHFR | 13693 | -0.041 | 0.1 | NO |
42 | ACP5 | ACP5 | ACP5 | 13942 | -0.046 | 0.1 | NO |
43 | FPGS | FPGS | FPGS | 14086 | -0.049 | 0.1 | NO |
44 | PANK3 | PANK3 | PANK3 | 14260 | -0.053 | 0.1 | NO |
45 | DHFR | DHFR | DHFR | 14321 | -0.054 | 0.11 | NO |
46 | MOCS2 | MOCS2 | MOCS2 | 14325 | -0.054 | 0.12 | NO |
47 | NADSYN1 | NADSYN1 | NADSYN1 | 15671 | -0.089 | 0.07 | NO |
48 | NMNAT1 | NMNAT1 | NMNAT1 | 15847 | -0.094 | 0.08 | NO |
49 | MOCOS | MOCOS | MOCOS | 15853 | -0.094 | 0.1 | NO |
50 | TPK1 | TPK1 | TPK1 | 18088 | -0.25 | 0.032 | 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 GLYCINE SERINE AND THREONINE METABOLISM.

Figure S2. 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 S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | F7 | F7 | F7 | 22 | 0.71 | 0.17 | YES |
2 | F2 | F2 | F2 | 33 | 0.67 | 0.33 | YES |
3 | F10 | F10 | F10 | 101 | 0.57 | 0.47 | YES |
4 | PROC | PROC | PROC | 120 | 0.55 | 0.6 | YES |
5 | PROZ | PROZ | PROZ | 1795 | 0.23 | 0.56 | NO |
6 | PROS1 | PROS1 | PROS1 | 3319 | 0.14 | 0.51 | NO |
7 | ARSE | ARSE | ARSE | 3502 | 0.13 | 0.54 | NO |
8 | GGCX | GGCX | GGCX | 3962 | 0.12 | 0.54 | NO |
9 | EIF5A2 | EIF5A2 | EIF5A2 | 4431 | 0.11 | 0.54 | NO |
10 | FURIN | FURIN | FURIN | 5973 | 0.071 | 0.48 | NO |
11 | SUMF2 | SUMF2 | SUMF2 | 6460 | 0.062 | 0.46 | NO |
12 | DOHH | DOHH | DOHH | 7923 | 0.039 | 0.4 | NO |
13 | VKORC1 | VKORC1 | VKORC1 | 8454 | 0.032 | 0.38 | NO |
14 | SUMF1 | SUMF1 | SUMF1 | 9379 | 0.02 | 0.33 | NO |
15 | EIF5A | EIF5A | EIF5A | 10246 | 0.009 | 0.29 | NO |
16 | DHPS | DHPS | DHPS | 11579 | -0.0089 | 0.22 | NO |
17 | ARSI | ARSI | ARSI | 11600 | -0.0092 | 0.22 | NO |
18 | ARSK | ARSK | ARSK | 12881 | -0.028 | 0.16 | NO |
19 | ARSA | ARSA | ARSA | 13318 | -0.035 | 0.14 | NO |
20 | ARSH | ARSH | ARSH | 13394 | -0.036 | 0.14 | NO |
21 | ARSB | ARSB | ARSB | 13682 | -0.041 | 0.14 | NO |
22 | ARSG | ARSG | ARSG | 15220 | -0.076 | 0.076 | NO |
23 | ARSF | ARSF | ARSF | 15533 | -0.085 | 0.079 | NO |
24 | ARSJ | ARSJ | ARSJ | 16907 | -0.14 | 0.04 | NO |
25 | STS | STS | STS | 17935 | -0.23 | 0.04 | NO |
Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, 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 | F2 | F2 | F2 | 33 | 0.67 | 0.085 | YES |
2 | APOA1 | APOA1 | APOA1 | 59 | 0.62 | 0.16 | YES |
3 | TTR | TTR | TTR | 215 | 0.5 | 0.22 | YES |
4 | NKX2-1 | NKX2-1 | NKX2-1 | 286 | 0.47 | 0.28 | YES |
5 | FOXA2 | FOXA2 | FOXA2 | 369 | 0.44 | 0.33 | YES |
6 | AFP | AFP | AFP | 565 | 0.38 | 0.37 | YES |
7 | PKLR | PKLR | PKLR | 719 | 0.35 | 0.41 | YES |
8 | IGFBP1 | IGFBP1 | IGFBP1 | 1008 | 0.31 | 0.43 | YES |
9 | TAT | TAT | TAT | 1127 | 0.29 | 0.46 | YES |
10 | ALB | ALB | ALB | 1156 | 0.29 | 0.5 | YES |
11 | ABCC8 | ABCC8 | ABCC8 | 1312 | 0.27 | 0.52 | YES |
12 | KCNJ11 | KCNJ11 | KCNJ11 | 1366 | 0.26 | 0.56 | YES |
13 | GCK | GCK | GCK | 1397 | 0.26 | 0.59 | YES |
14 | G6PC | G6PC | G6PC | 1568 | 0.25 | 0.61 | YES |
15 | CPT1C | CPT1C | CPT1C | 1758 | 0.23 | 0.63 | YES |
16 | SLC2A2 | SLC2A2 | SLC2A2 | 1904 | 0.22 | 0.65 | YES |
17 | CPT1B | CPT1B | CPT1B | 2677 | 0.17 | 0.63 | YES |
18 | HMGCS1 | HMGCS1 | HMGCS1 | 3015 | 0.16 | 0.63 | YES |
19 | HNF1A | HNF1A | HNF1A | 3252 | 0.14 | 0.64 | YES |
20 | CEBPA | CEBPA | CEBPA | 3460 | 0.14 | 0.65 | YES |
21 | CEBPB | CEBPB | CEBPB | 3524 | 0.13 | 0.66 | YES |
22 | HNF4A | HNF4A | HNF4A | 4053 | 0.12 | 0.65 | NO |
23 | DLK1 | DLK1 | DLK1 | 4658 | 0.1 | 0.63 | NO |
24 | NF1 | NF1 | NF1 | 7744 | 0.042 | 0.47 | NO |
25 | HNF1B | HNF1B | HNF1B | 7922 | 0.039 | 0.46 | NO |
26 | FOXA1 | FOXA1 | FOXA1 | 8383 | 0.033 | 0.44 | NO |
27 | PDX1 | PDX1 | PDX1 | 8621 | 0.03 | 0.43 | NO |
28 | PCK1 | PCK1 | PCK1 | 9352 | 0.02 | 0.4 | NO |
29 | TFRC | TFRC | TFRC | 9471 | 0.018 | 0.39 | NO |
30 | ACADM | ACADM | ACADM | 10149 | 0.01 | 0.36 | NO |
31 | AKT1 | AKT1 | AKT1 | 11005 | -0.0012 | 0.31 | NO |
32 | CREB1 | CREB1 | CREB1 | 11398 | -0.0064 | 0.29 | NO |
33 | UCP2 | UCP2 | UCP2 | 11430 | -0.0069 | 0.29 | NO |
34 | CEBPD | CEBPD | CEBPD | 11875 | -0.013 | 0.27 | NO |
35 | ALAS1 | ALAS1 | ALAS1 | 11963 | -0.014 | 0.27 | NO |
36 | ACADVL | ACADVL | ACADVL | 12448 | -0.021 | 0.24 | NO |
37 | BDH1 | BDH1 | BDH1 | 12777 | -0.026 | 0.23 | NO |
38 | SP1 | SP1 | SP1 | 13943 | -0.046 | 0.17 | NO |
39 | FOXA3 | FOXA3 | FOXA3 | 14214 | -0.052 | 0.16 | NO |
40 | CPT1A | CPT1A | CPT1A | 14900 | -0.067 | 0.14 | NO |
41 | NR3C1 | NR3C1 | NR3C1 | 15241 | -0.076 | 0.13 | NO |
42 | HADH | HADH | HADH | 16096 | -0.1 | 0.095 | NO |
43 | FOXF1 | FOXF1 | FOXF1 | 16816 | -0.14 | 0.074 | NO |
44 | ALDOB | ALDOB | ALDOB | 17714 | -0.2 | 0.052 | 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 SPLICEOSOME.

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

Table 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 | F7 | F7 | F7 | 22 | 0.71 | 0.1 | YES |
2 | F2 | F2 | F2 | 33 | 0.67 | 0.2 | YES |
3 | F10 | F10 | F10 | 101 | 0.57 | 0.28 | YES |
4 | FGG | FGG | FGG | 119 | 0.55 | 0.36 | YES |
5 | PROC | PROC | PROC | 120 | 0.55 | 0.44 | YES |
6 | FGA | FGA | FGA | 124 | 0.55 | 0.51 | YES |
7 | FGB | FGB | FGB | 189 | 0.51 | 0.58 | YES |
8 | KNG1 | KNG1 | KNG1 | 263 | 0.47 | 0.65 | YES |
9 | SERPINC1 | SERPINC1 | SERPINC1 | 790 | 0.34 | 0.67 | YES |
10 | F11 | F11 | F11 | 1649 | 0.24 | 0.66 | YES |
11 | F5 | F5 | F5 | 1728 | 0.23 | 0.69 | YES |
12 | GP5 | GP5 | GP5 | 2608 | 0.18 | 0.67 | NO |
13 | PROS1 | PROS1 | PROS1 | 3319 | 0.14 | 0.65 | NO |
14 | GP9 | GP9 | GP9 | 4831 | 0.095 | 0.58 | NO |
15 | PF4 | PF4 | PF4 | 10231 | 0.0092 | 0.29 | NO |
16 | KLKB1 | KLKB1 | KLKB1 | 10286 | 0.0085 | 0.29 | NO |
17 | PRCP | PRCP | PRCP | 11160 | -0.0032 | 0.24 | NO |
18 | PF4V1 | PF4V1 | PF4V1 | 11474 | -0.0075 | 0.23 | NO |
19 | C1QBP | C1QBP | C1QBP | 11865 | -0.013 | 0.21 | NO |
20 | F12 | F12 | F12 | 12165 | -0.017 | 0.2 | NO |
21 | TFPI | TFPI | TFPI | 12244 | -0.018 | 0.19 | NO |
22 | THBD | THBD | THBD | 12306 | -0.019 | 0.19 | NO |
23 | GP1BA | GP1BA | GP1BA | 15881 | -0.095 | 0.016 | NO |
24 | A2M | A2M | A2M | 16297 | -0.11 | 0.0095 | NO |
25 | SERPING1 | SERPING1 | SERPING1 | 16539 | -0.12 | 0.014 | NO |
26 | VWF | VWF | VWF | 16645 | -0.13 | 0.027 | NO |
27 | F8 | F8 | F8 | 16730 | -0.13 | 0.041 | NO |
28 | F3 | F3 | F3 | 17607 | -0.19 | 0.022 | NO |
29 | F13A1 | F13A1 | F13A1 | 18012 | -0.24 | 0.036 | 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: ST WNT BETA CATENIN PATHWAY.

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

Table 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 | PRPF40B | PRPF40B | PRPF40B | 1128 | 0.29 | -0.0038 | YES |
2 | SNRPA1 | SNRPA1 | SNRPA1 | 3807 | 0.12 | -0.12 | YES |
3 | SNRPB2 | SNRPB2 | SNRPB2 | 3857 | 0.12 | -0.1 | YES |
4 | HSPA1L | HSPA1L | HSPA1L | 3904 | 0.12 | -0.082 | YES |
5 | PPIE | PPIE | PPIE | 4007 | 0.12 | -0.065 | YES |
6 | PRPF6 | PRPF6 | PRPF6 | 4497 | 0.1 | -0.071 | YES |
7 | CTNNBL1 | CTNNBL1 | CTNNBL1 | 4548 | 0.1 | -0.054 | YES |
8 | SNRPC | SNRPC | SNRPC | 4559 | 0.1 | -0.034 | YES |
9 | SNRPE | SNRPE | SNRPE | 4600 | 0.1 | -0.017 | YES |
10 | SNRPB | SNRPB | SNRPB | 4657 | 0.1 | -0.00035 | YES |
11 | SF3B4 | SF3B4 | SF3B4 | 4726 | 0.098 | 0.015 | YES |
12 | SNRPD1 | SNRPD1 | SNRPD1 | 4743 | 0.097 | 0.033 | YES |
13 | PPIL1 | PPIL1 | PPIL1 | 4866 | 0.094 | 0.044 | YES |
14 | SNRPG | SNRPG | SNRPG | 4949 | 0.092 | 0.058 | YES |
15 | THOC1 | THOC1 | THOC1 | 4954 | 0.092 | 0.076 | YES |
16 | LSM5 | LSM5 | LSM5 | 4979 | 0.091 | 0.092 | YES |
17 | HSPA1A | HSPA1A | HSPA1A | 5175 | 0.086 | 0.098 | YES |
18 | PRPF3 | PRPF3 | PRPF3 | 5221 | 0.086 | 0.11 | YES |
19 | PQBP1 | PQBP1 | PQBP1 | 5284 | 0.084 | 0.12 | YES |
20 | CRNKL1 | CRNKL1 | CRNKL1 | 5427 | 0.081 | 0.13 | YES |
21 | SNRPD3 | SNRPD3 | SNRPD3 | 5785 | 0.074 | 0.13 | YES |
22 | MAGOH | MAGOH | MAGOH | 5835 | 0.074 | 0.14 | YES |
23 | PPIH | PPIH | PPIH | 5849 | 0.073 | 0.15 | YES |
24 | SNRPF | SNRPF | SNRPF | 5930 | 0.072 | 0.16 | YES |
25 | USP39 | USP39 | USP39 | 6039 | 0.07 | 0.17 | YES |
26 | CWC15 | CWC15 | CWC15 | 6165 | 0.068 | 0.18 | YES |
27 | RBM17 | RBM17 | RBM17 | 6219 | 0.067 | 0.19 | YES |
28 | NCBP2 | NCBP2 | NCBP2 | 6285 | 0.066 | 0.2 | YES |
29 | CCDC12 | CCDC12 | CCDC12 | 6551 | 0.061 | 0.19 | YES |
30 | PUF60 | PUF60 | PUF60 | 6562 | 0.06 | 0.2 | YES |
31 | BUD31 | BUD31 | BUD31 | 6592 | 0.06 | 0.22 | YES |
32 | PRPF19 | PRPF19 | PRPF19 | 6806 | 0.056 | 0.22 | YES |
33 | MAGOHB | MAGOHB | MAGOHB | 7032 | 0.053 | 0.21 | YES |
34 | RBM8A | RBM8A | RBM8A | 7060 | 0.052 | 0.22 | YES |
35 | PHF5A | PHF5A | PHF5A | 7072 | 0.052 | 0.23 | YES |
36 | EIF4A3 | EIF4A3 | EIF4A3 | 7167 | 0.051 | 0.24 | YES |
37 | NHP2L1 | NHP2L1 | NHP2L1 | 7202 | 0.05 | 0.24 | YES |
38 | SART1 | SART1 | SART1 | 7214 | 0.05 | 0.25 | YES |
39 | LSM2 | LSM2 | LSM2 | 7219 | 0.05 | 0.26 | YES |
40 | U2AF1 | U2AF1 | U2AF1 | 7332 | 0.048 | 0.27 | YES |
41 | DHX16 | DHX16 | DHX16 | 7465 | 0.046 | 0.27 | YES |
42 | LSM4 | LSM4 | LSM4 | 7502 | 0.046 | 0.28 | YES |
43 | PRPF4 | PRPF4 | PRPF4 | 7539 | 0.045 | 0.28 | YES |
44 | PRPF38A | PRPF38A | PRPF38A | 7549 | 0.045 | 0.29 | YES |
45 | THOC4 | THOC4 | THOC4 | 7589 | 0.044 | 0.3 | YES |
46 | EFTUD2 | EFTUD2 | EFTUD2 | 7616 | 0.044 | 0.3 | YES |
47 | PRPF31 | PRPF31 | PRPF31 | 7660 | 0.043 | 0.31 | YES |
48 | SNRNP27 | SNRNP27 | SNRNP27 | 7663 | 0.043 | 0.32 | YES |
49 | SMNDC1 | SMNDC1 | SMNDC1 | 7745 | 0.042 | 0.32 | YES |
50 | TXNL4A | TXNL4A | TXNL4A | 7755 | 0.042 | 0.33 | YES |
51 | SNRNP200 | SNRNP200 | SNRNP200 | 7863 | 0.041 | 0.33 | YES |
52 | HSPA1B | HSPA1B | HSPA1B | 7880 | 0.04 | 0.34 | YES |
53 | SF3B14 | SF3B14 | SF3B14 | 7883 | 0.04 | 0.35 | YES |
54 | SF3B3 | SF3B3 | SF3B3 | 7889 | 0.04 | 0.35 | YES |
55 | TRA2A | TRA2A | TRA2A | 7907 | 0.04 | 0.36 | YES |
56 | LSM6 | LSM6 | LSM6 | 7976 | 0.039 | 0.36 | YES |
57 | SNRPA | SNRPA | SNRPA | 7981 | 0.038 | 0.37 | YES |
58 | SNRNP40 | SNRNP40 | SNRNP40 | 8127 | 0.037 | 0.37 | YES |
59 | U2AF2 | U2AF2 | U2AF2 | 8138 | 0.036 | 0.38 | YES |
60 | RBMX | RBMX | RBMX | 8257 | 0.035 | 0.38 | YES |
61 | RBM25 | RBM25 | RBM25 | 8542 | 0.031 | 0.37 | YES |
62 | HSPA6 | HSPA6 | HSPA6 | 8610 | 0.03 | 0.37 | YES |
63 | SNRPD2 | SNRPD2 | SNRPD2 | 8625 | 0.029 | 0.38 | YES |
64 | SF3B2 | SF3B2 | SF3B2 | 8636 | 0.029 | 0.38 | YES |
65 | CDC5L | CDC5L | CDC5L | 8652 | 0.029 | 0.38 | YES |
66 | HNRNPU | HNRNPU | HNRNPU | 8654 | 0.029 | 0.39 | YES |
67 | SNW1 | SNW1 | SNW1 | 8706 | 0.028 | 0.39 | YES |
68 | PCBP1 | PCBP1 | PCBP1 | 8742 | 0.028 | 0.4 | YES |
69 | HNRNPC | HNRNPC | HNRNPC | 8783 | 0.027 | 0.4 | YES |
70 | SNRNP70 | SNRNP70 | SNRNP70 | 8798 | 0.027 | 0.4 | YES |
71 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 8855 | 0.026 | 0.41 | YES |
72 | THOC2 | THOC2 | THOC2 | 9087 | 0.023 | 0.4 | YES |
73 | TRA2B | TRA2B | TRA2B | 9100 | 0.023 | 0.4 | YES |
74 | LSM3 | LSM3 | LSM3 | 9145 | 0.022 | 0.4 | YES |
75 | ACIN1 | ACIN1 | ACIN1 | 9188 | 0.022 | 0.41 | YES |
76 | PRPF40A | PRPF40A | PRPF40A | 9207 | 0.022 | 0.41 | YES |
77 | SF3A3 | SF3A3 | SF3A3 | 9254 | 0.021 | 0.41 | YES |
78 | DDX23 | DDX23 | DDX23 | 9482 | 0.018 | 0.4 | NO |
79 | PRPF38B | PRPF38B | PRPF38B | 9794 | 0.015 | 0.39 | NO |
80 | PRPF18 | PRPF18 | PRPF18 | 9803 | 0.015 | 0.39 | NO |
81 | SF3A2 | SF3A2 | SF3A2 | 9806 | 0.014 | 0.39 | NO |
82 | THOC3 | THOC3 | THOC3 | 9809 | 0.014 | 0.4 | NO |
83 | CHERP | CHERP | CHERP | 9851 | 0.014 | 0.4 | NO |
84 | DDX46 | DDX46 | DDX46 | 9866 | 0.014 | 0.4 | NO |
85 | ISY1 | ISY1 | ISY1 | 9932 | 0.013 | 0.4 | NO |
86 | TCERG1 | TCERG1 | TCERG1 | 10211 | 0.0094 | 0.38 | NO |
87 | WBP11 | WBP11 | WBP11 | 10228 | 0.0092 | 0.39 | NO |
88 | HNRNPK | HNRNPK | HNRNPK | 10329 | 0.008 | 0.38 | NO |
89 | HNRNPA1L2 | HNRNPA1L2 | HNRNPA1L2 | 10333 | 0.008 | 0.38 | NO |
90 | DDX42 | DDX42 | DDX42 | 10443 | 0.0064 | 0.38 | NO |
91 | HNRNPM | HNRNPM | HNRNPM | 10477 | 0.006 | 0.38 | NO |
92 | SF3B5 | SF3B5 | SF3B5 | 10561 | 0.005 | 0.38 | NO |
93 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 10581 | 0.0048 | 0.38 | NO |
94 | SF3B1 | SF3B1 | SF3B1 | 10724 | 0.0026 | 0.37 | NO |
95 | LSM7 | LSM7 | LSM7 | 10867 | 0.00074 | 0.36 | NO |
96 | DDX5 | DDX5 | DDX5 | 10875 | 0.00065 | 0.36 | NO |
97 | DHX8 | DHX8 | DHX8 | 10968 | -0.00072 | 0.36 | NO |
98 | SYF2 | SYF2 | SYF2 | 11042 | -0.0017 | 0.35 | NO |
99 | BCAS2 | BCAS2 | BCAS2 | 11183 | -0.0035 | 0.34 | NO |
100 | PLRG1 | PLRG1 | PLRG1 | 11222 | -0.004 | 0.34 | NO |
101 | CDC40 | CDC40 | CDC40 | 11571 | -0.0088 | 0.33 | NO |
102 | NCBP1 | NCBP1 | NCBP1 | 11671 | -0.01 | 0.32 | NO |
103 | DHX15 | DHX15 | DHX15 | 11699 | -0.01 | 0.32 | NO |
104 | DHX38 | DHX38 | DHX38 | 11790 | -0.012 | 0.32 | NO |
105 | XAB2 | XAB2 | XAB2 | 11855 | -0.012 | 0.32 | NO |
106 | PRPF8 | PRPF8 | PRPF8 | 12145 | -0.016 | 0.31 | NO |
107 | SF3A1 | SF3A1 | SF3A1 | 12215 | -0.017 | 0.31 | NO |
108 | ZMAT2 | ZMAT2 | ZMAT2 | 12275 | -0.018 | 0.31 | NO |
109 | AQR | AQR | AQR | 12623 | -0.024 | 0.29 | NO |
110 | NAA38 | NAA38 | NAA38 | 12644 | -0.024 | 0.3 | NO |
111 | SLU7 | SLU7 | SLU7 | 12825 | -0.027 | 0.29 | NO |
112 | RBM22 | RBM22 | RBM22 | 12899 | -0.028 | 0.29 | NO |
113 | HSPA8 | HSPA8 | HSPA8 | 12924 | -0.029 | 0.3 | NO |
114 | HSPA2 | HSPA2 | HSPA2 | 14594 | -0.06 | 0.22 | 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 HNF3BPATHWAY.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: PID HNF3BPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table 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 | GPLD1 | GPLD1 | GPLD1 | 1142 | 0.29 | 0.088 | YES |
2 | PIGZ | PIGZ | PIGZ | 1637 | 0.24 | 0.18 | YES |
3 | PIGM | PIGM | PIGM | 2312 | 0.19 | 0.24 | YES |
4 | PIGU | PIGU | PIGU | 2997 | 0.16 | 0.29 | YES |
5 | PIGT | PIGT | PIGT | 3116 | 0.15 | 0.36 | YES |
6 | PIGW | PIGW | PIGW | 3845 | 0.12 | 0.38 | YES |
7 | PIGC | PIGC | PIGC | 4932 | 0.092 | 0.37 | YES |
8 | GPAA1 | GPAA1 | GPAA1 | 5089 | 0.088 | 0.41 | YES |
9 | PIGH | PIGH | PIGH | 5518 | 0.08 | 0.43 | YES |
10 | DPM2 | DPM2 | DPM2 | 6057 | 0.069 | 0.43 | YES |
11 | PIGO | PIGO | PIGO | 6805 | 0.056 | 0.42 | YES |
12 | PIGX | PIGX | PIGX | 6886 | 0.055 | 0.44 | YES |
13 | PIGA | PIGA | PIGA | 7279 | 0.049 | 0.45 | YES |
14 | PIGP | PIGP | PIGP | 8736 | 0.028 | 0.38 | NO |
15 | PIGS | PIGS | PIGS | 9177 | 0.022 | 0.37 | NO |
16 | PIGG | PIGG | PIGG | 10180 | 0.0098 | 0.32 | NO |
17 | PIGK | PIGK | PIGK | 10836 | 0.0012 | 0.29 | NO |
18 | PGAP1 | PGAP1 | PGAP1 | 11006 | -0.0012 | 0.28 | NO |
19 | PIGV | PIGV | PIGV | 12027 | -0.014 | 0.23 | NO |
20 | PIGF | PIGF | PIGF | 12160 | -0.016 | 0.24 | NO |
21 | PIGQ | PIGQ | PIGQ | 12257 | -0.018 | 0.24 | NO |
22 | PIGN | PIGN | PIGN | 12801 | -0.027 | 0.22 | NO |
23 | PIGY | PIGY | PIGY | 13008 | -0.03 | 0.23 | NO |
24 | PIGL | PIGL | PIGL | 14562 | -0.06 | 0.18 | NO |
25 | PIGB | PIGB | PIGB | 15667 | -0.089 | 0.16 | NO |
Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION, 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 | GLDC | GLDC | GLDC | 5 | 0.77 | 0.12 | YES |
2 | CBS | CBS | CBS | 98 | 0.57 | 0.21 | YES |
3 | AGXT | AGXT | AGXT | 415 | 0.42 | 0.26 | YES |
4 | AGXT2 | AGXT2 | AGXT2 | 451 | 0.41 | 0.33 | YES |
5 | PIPOX | PIPOX | PIPOX | 461 | 0.41 | 0.39 | YES |
6 | GAMT | GAMT | GAMT | 509 | 0.4 | 0.45 | YES |
7 | PHGDH | PHGDH | PHGDH | 520 | 0.39 | 0.52 | YES |
8 | DAO | DAO | DAO | 1148 | 0.29 | 0.53 | YES |
9 | PSPH | PSPH | PSPH | 1669 | 0.24 | 0.54 | YES |
10 | AMT | AMT | AMT | 1860 | 0.22 | 0.56 | YES |
11 | GLYCTK | GLYCTK | GLYCTK | 1953 | 0.21 | 0.6 | YES |
12 | GNMT | GNMT | GNMT | 2013 | 0.21 | 0.62 | YES |
13 | BHMT | BHMT | BHMT | 2834 | 0.16 | 0.61 | NO |
14 | ALAS2 | ALAS2 | ALAS2 | 3566 | 0.13 | 0.59 | NO |
15 | SARDH | SARDH | SARDH | 4430 | 0.11 | 0.56 | NO |
16 | PSAT1 | PSAT1 | PSAT1 | 4442 | 0.11 | 0.58 | NO |
17 | CHDH | CHDH | CHDH | 5073 | 0.089 | 0.56 | NO |
18 | AOC2 | AOC2 | AOC2 | 5963 | 0.071 | 0.52 | NO |
19 | GCAT | GCAT | GCAT | 7215 | 0.05 | 0.46 | NO |
20 | CTH | CTH | CTH | 8123 | 0.037 | 0.42 | NO |
21 | SHMT2 | SHMT2 | SHMT2 | 9849 | 0.014 | 0.33 | NO |
22 | SHMT1 | SHMT1 | SHMT1 | 9873 | 0.014 | 0.33 | NO |
23 | ALAS1 | ALAS1 | ALAS1 | 11963 | -0.014 | 0.22 | NO |
24 | MAOB | MAOB | MAOB | 12039 | -0.015 | 0.22 | NO |
25 | DLD | DLD | DLD | 12889 | -0.028 | 0.18 | NO |
26 | GATM | GATM | GATM | 13494 | -0.038 | 0.15 | NO |
27 | SRR | SRR | SRR | 15771 | -0.092 | 0.044 | NO |
28 | MAOA | MAOA | MAOA | 16893 | -0.14 | 0.0063 | NO |
29 | SDS | SDS | SDS | 17387 | -0.17 | 0.0078 | NO |
30 | DMGDH | DMGDH | DMGDH | 17512 | -0.18 | 0.031 | NO |
31 | AOC3 | AOC3 | AOC3 | 17642 | -0.2 | 0.055 | NO |
Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME METABOLISM OF STEROID HORMONES AND VITAMINS A AND D.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF STEROID HORMONES AND VITAMINS A AND D, 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 | NUP210 | NUP210 | NUP210 | 1723 | 0.23 | -0.052 | YES |
2 | RAE1 | RAE1 | RAE1 | 2111 | 0.2 | -0.038 | YES |
3 | UPF3B | UPF3B | UPF3B | 2981 | 0.16 | -0.057 | YES |
4 | SNRPA1 | SNRPA1 | SNRPA1 | 3807 | 0.12 | -0.08 | YES |
5 | SNRPB2 | SNRPB2 | SNRPB2 | 3857 | 0.12 | -0.061 | YES |
6 | NUP155 | NUP155 | NUP155 | 3971 | 0.12 | -0.046 | YES |
7 | CSTF1 | CSTF1 | CSTF1 | 4078 | 0.12 | -0.032 | YES |
8 | POLR2I | POLR2I | POLR2I | 4108 | 0.12 | -0.013 | YES |
9 | GTF2F2 | GTF2F2 | GTF2F2 | 4436 | 0.11 | -0.012 | YES |
10 | PRPF6 | PRPF6 | PRPF6 | 4497 | 0.1 | 0.0026 | YES |
11 | SNRPE | SNRPE | SNRPE | 4600 | 0.1 | 0.015 | YES |
12 | SNRPB | SNRPB | SNRPB | 4657 | 0.1 | 0.029 | YES |
13 | SF3B4 | SF3B4 | SF3B4 | 4726 | 0.098 | 0.043 | YES |
14 | SNRPD1 | SNRPD1 | SNRPD1 | 4743 | 0.097 | 0.059 | YES |
15 | POLR2K | POLR2K | POLR2K | 4806 | 0.095 | 0.072 | YES |
16 | POLR2D | POLR2D | POLR2D | 4835 | 0.095 | 0.087 | YES |
17 | SNRPG | SNRPG | SNRPG | 4949 | 0.092 | 0.097 | YES |
18 | AAAS | AAAS | AAAS | 5286 | 0.084 | 0.094 | YES |
19 | POLR2F | POLR2F | POLR2F | 5288 | 0.084 | 0.11 | YES |
20 | PABPN1 | PABPN1 | PABPN1 | 5562 | 0.079 | 0.11 | YES |
21 | NUPL2 | NUPL2 | NUPL2 | 5654 | 0.077 | 0.12 | YES |
22 | NUP43 | NUP43 | NUP43 | 5655 | 0.077 | 0.13 | YES |
23 | POLR2J | POLR2J | POLR2J | 5664 | 0.077 | 0.14 | YES |
24 | SNRPD3 | SNRPD3 | SNRPD3 | 5785 | 0.074 | 0.15 | YES |
25 | MAGOH | MAGOH | MAGOH | 5835 | 0.074 | 0.16 | YES |
26 | POLR2G | POLR2G | POLR2G | 5888 | 0.073 | 0.17 | YES |
27 | SNRPF | SNRPF | SNRPF | 5930 | 0.072 | 0.18 | YES |
28 | NUP107 | NUP107 | NUP107 | 6025 | 0.07 | 0.19 | YES |
29 | NCBP2 | NCBP2 | NCBP2 | 6285 | 0.066 | 0.18 | YES |
30 | POLR2C | POLR2C | POLR2C | 6338 | 0.064 | 0.19 | YES |
31 | CSTF3 | CSTF3 | CSTF3 | 6373 | 0.064 | 0.2 | YES |
32 | METTL3 | METTL3 | METTL3 | 6394 | 0.064 | 0.21 | YES |
33 | CCAR1 | CCAR1 | CCAR1 | 6414 | 0.063 | 0.22 | YES |
34 | POLR2H | POLR2H | POLR2H | 6422 | 0.063 | 0.23 | YES |
35 | FUS | FUS | FUS | 6734 | 0.058 | 0.23 | YES |
36 | NUP35 | NUP35 | NUP35 | 6927 | 0.054 | 0.22 | YES |
37 | CPSF1 | CPSF1 | CPSF1 | 7011 | 0.053 | 0.23 | YES |
38 | RBM8A | RBM8A | RBM8A | 7060 | 0.052 | 0.24 | YES |
39 | PHF5A | PHF5A | PHF5A | 7072 | 0.052 | 0.24 | YES |
40 | CLP1 | CLP1 | CLP1 | 7198 | 0.05 | 0.25 | YES |
41 | NHP2L1 | NHP2L1 | NHP2L1 | 7202 | 0.05 | 0.26 | YES |
42 | LSM2 | LSM2 | LSM2 | 7219 | 0.05 | 0.26 | YES |
43 | CPSF3 | CPSF3 | CPSF3 | 7257 | 0.049 | 0.27 | YES |
44 | U2AF1 | U2AF1 | U2AF1 | 7332 | 0.048 | 0.28 | YES |
45 | CPSF7 | CPSF7 | CPSF7 | 7348 | 0.048 | 0.28 | YES |
46 | DNAJC8 | DNAJC8 | DNAJC8 | 7476 | 0.046 | 0.28 | YES |
47 | HNRNPL | HNRNPL | HNRNPL | 7479 | 0.046 | 0.29 | YES |
48 | PAPOLA | PAPOLA | PAPOLA | 7501 | 0.046 | 0.3 | YES |
49 | PRPF4 | PRPF4 | PRPF4 | 7539 | 0.045 | 0.3 | YES |
50 | NUP133 | NUP133 | NUP133 | 7554 | 0.045 | 0.31 | YES |
51 | THOC4 | THOC4 | THOC4 | 7589 | 0.044 | 0.32 | YES |
52 | EFTUD2 | EFTUD2 | EFTUD2 | 7616 | 0.044 | 0.32 | YES |
53 | HNRNPA2B1 | HNRNPA2B1 | HNRNPA2B1 | 7642 | 0.044 | 0.33 | YES |
54 | HNRNPD | HNRNPD | HNRNPD | 7681 | 0.043 | 0.34 | YES |
55 | TXNL4A | TXNL4A | TXNL4A | 7755 | 0.042 | 0.34 | YES |
56 | NUP153 | NUP153 | NUP153 | 7806 | 0.041 | 0.34 | YES |
57 | NUP93 | NUP93 | NUP93 | 7845 | 0.041 | 0.35 | YES |
58 | SNRNP200 | SNRNP200 | SNRNP200 | 7863 | 0.041 | 0.36 | YES |
59 | SF3B14 | SF3B14 | SF3B14 | 7883 | 0.04 | 0.36 | YES |
60 | SF3B3 | SF3B3 | SF3B3 | 7889 | 0.04 | 0.37 | YES |
61 | SNRPA | SNRPA | SNRPA | 7981 | 0.038 | 0.37 | YES |
62 | NUP37 | NUP37 | NUP37 | 8035 | 0.038 | 0.37 | YES |
63 | NUP85 | NUP85 | NUP85 | 8100 | 0.037 | 0.38 | YES |
64 | CSTF2 | CSTF2 | CSTF2 | 8104 | 0.037 | 0.38 | YES |
65 | SNRNP40 | SNRNP40 | SNRNP40 | 8127 | 0.037 | 0.39 | YES |
66 | U2AF2 | U2AF2 | U2AF2 | 8138 | 0.036 | 0.39 | YES |
67 | PCBP2 | PCBP2 | PCBP2 | 8229 | 0.035 | 0.4 | YES |
68 | SLBP | SLBP | SLBP | 8254 | 0.035 | 0.4 | YES |
69 | RBMX | RBMX | RBMX | 8257 | 0.035 | 0.4 | YES |
70 | SEH1L | SEH1L | SEH1L | 8474 | 0.032 | 0.4 | YES |
71 | DHX9 | DHX9 | DHX9 | 8561 | 0.03 | 0.4 | YES |
72 | SNRPD2 | SNRPD2 | SNRPD2 | 8625 | 0.029 | 0.4 | YES |
73 | SF3B2 | SF3B2 | SF3B2 | 8636 | 0.029 | 0.41 | YES |
74 | HNRNPU | HNRNPU | HNRNPU | 8654 | 0.029 | 0.41 | YES |
75 | NUP62 | NUP62 | NUP62 | 8715 | 0.028 | 0.41 | YES |
76 | PCBP1 | PCBP1 | PCBP1 | 8742 | 0.028 | 0.42 | YES |
77 | HNRNPC | HNRNPC | HNRNPC | 8783 | 0.027 | 0.42 | YES |
78 | TPR | TPR | TPR | 8793 | 0.027 | 0.42 | YES |
79 | SNRNP70 | SNRNP70 | SNRNP70 | 8798 | 0.027 | 0.43 | YES |
80 | NUP50 | NUP50 | NUP50 | 8838 | 0.027 | 0.43 | YES |
81 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 8855 | 0.026 | 0.43 | YES |
82 | NXF1 | NXF1 | NXF1 | 8978 | 0.024 | 0.43 | YES |
83 | NUPL1 | NUPL1 | NUPL1 | 9033 | 0.024 | 0.43 | YES |
84 | PTBP1 | PTBP1 | PTBP1 | 9084 | 0.023 | 0.43 | YES |
85 | HNRNPR | HNRNPR | HNRNPR | 9140 | 0.022 | 0.43 | YES |
86 | SF3A3 | SF3A3 | SF3A3 | 9254 | 0.021 | 0.43 | YES |
87 | POM121 | POM121 | POM121 | 9264 | 0.021 | 0.44 | YES |
88 | SMC1A | SMC1A | SMC1A | 9446 | 0.019 | 0.43 | YES |
89 | DDX23 | DDX23 | DDX23 | 9482 | 0.018 | 0.43 | YES |
90 | POLR2L | POLR2L | POLR2L | 9511 | 0.018 | 0.43 | YES |
91 | NUP88 | NUP88 | NUP88 | 9530 | 0.018 | 0.43 | YES |
92 | HNRNPUL1 | HNRNPUL1 | HNRNPUL1 | 9556 | 0.018 | 0.44 | YES |
93 | SF3A2 | SF3A2 | SF3A2 | 9806 | 0.014 | 0.42 | NO |
94 | CPSF2 | CPSF2 | CPSF2 | 10187 | 0.0097 | 0.41 | NO |
95 | RNPS1 | RNPS1 | RNPS1 | 10196 | 0.0096 | 0.41 | NO |
96 | YBX1 | YBX1 | YBX1 | 10214 | 0.0094 | 0.41 | NO |
97 | HNRNPK | HNRNPK | HNRNPK | 10329 | 0.008 | 0.4 | NO |
98 | CD2BP2 | CD2BP2 | CD2BP2 | 10462 | 0.0062 | 0.4 | NO |
99 | HNRNPM | HNRNPM | HNRNPM | 10477 | 0.006 | 0.4 | NO |
100 | NUP188 | NUP188 | NUP188 | 10553 | 0.0051 | 0.39 | NO |
101 | SF3B5 | SF3B5 | SF3B5 | 10561 | 0.005 | 0.4 | NO |
102 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 10581 | 0.0048 | 0.4 | NO |
103 | NFX1 | NFX1 | NFX1 | 10600 | 0.0046 | 0.39 | NO |
104 | EIF4E | EIF4E | EIF4E | 10616 | 0.0044 | 0.39 | NO |
105 | HNRNPH2 | HNRNPH2 | HNRNPH2 | 10693 | 0.0031 | 0.39 | NO |
106 | SF3B1 | SF3B1 | SF3B1 | 10724 | 0.0026 | 0.39 | NO |
107 | POLR2E | POLR2E | POLR2E | 10761 | 0.0021 | 0.39 | NO |
108 | HNRNPH1 | HNRNPH1 | HNRNPH1 | 10778 | 0.0019 | 0.39 | NO |
109 | NUP214 | NUP214 | NUP214 | 10816 | 0.0015 | 0.39 | NO |
110 | HNRNPA0 | HNRNPA0 | HNRNPA0 | 10833 | 0.0013 | 0.38 | NO |
111 | NUP54 | NUP54 | NUP54 | 11009 | -0.0013 | 0.38 | NO |
112 | NUP205 | NUP205 | NUP205 | 11198 | -0.0037 | 0.37 | NO |
113 | SRRM1 | SRRM1 | SRRM1 | 11477 | -0.0075 | 0.35 | NO |
114 | CDC40 | CDC40 | CDC40 | 11571 | -0.0088 | 0.35 | NO |
115 | NUDT21 | NUDT21 | NUDT21 | 11649 | -0.0099 | 0.35 | NO |
116 | NCBP1 | NCBP1 | NCBP1 | 11671 | -0.01 | 0.35 | NO |
117 | RANBP2 | RANBP2 | RANBP2 | 11716 | -0.011 | 0.35 | NO |
118 | HNRNPF | HNRNPF | HNRNPF | 11777 | -0.011 | 0.35 | NO |
119 | DHX38 | DHX38 | DHX38 | 11790 | -0.012 | 0.35 | NO |
120 | RBM5 | RBM5 | RBM5 | 11808 | -0.012 | 0.35 | NO |
121 | POLR2A | POLR2A | POLR2A | 11899 | -0.013 | 0.35 | NO |
122 | PRPF8 | PRPF8 | PRPF8 | 12145 | -0.016 | 0.34 | NO |
123 | SF3A1 | SF3A1 | SF3A1 | 12215 | -0.017 | 0.34 | NO |
124 | PCF11 | PCF11 | PCF11 | 12400 | -0.02 | 0.33 | NO |
125 | POLR2B | POLR2B | POLR2B | 12555 | -0.022 | 0.32 | NO |
126 | GTF2F1 | GTF2F1 | GTF2F1 | 13269 | -0.034 | 0.29 | NO |
Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME METABOLISM OF VITAMINS AND COFACTORS.

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

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 | APOA1 | APOA1 | APOA1 | 59 | 0.62 | 0.12 | YES |
2 | APOC3 | APOC3 | APOC3 | 60 | 0.62 | 0.25 | YES |
3 | APOA2 | APOA2 | APOA2 | 211 | 0.5 | 0.35 | YES |
4 | APOA5 | APOA5 | APOA5 | 270 | 0.47 | 0.44 | YES |
5 | APOB | APOB | APOB | 526 | 0.39 | 0.51 | YES |
6 | LIPC | LIPC | LIPC | 1015 | 0.31 | 0.54 | YES |
7 | ALB | ALB | ALB | 1156 | 0.29 | 0.6 | YES |
8 | SCARB1 | SCARB1 | SCARB1 | 1673 | 0.24 | 0.62 | YES |
9 | LPA | LPA | LPA | 1960 | 0.21 | 0.64 | YES |
10 | APOC2 | APOC2 | APOC2 | 3056 | 0.15 | 0.62 | NO |
11 | MTTP | MTTP | MTTP | 3202 | 0.15 | 0.64 | NO |
12 | PLTP | PLTP | PLTP | 4156 | 0.11 | 0.61 | NO |
13 | LPL | LPL | LPL | 7966 | 0.039 | 0.42 | NO |
14 | P4HB | P4HB | P4HB | 8401 | 0.033 | 0.4 | NO |
15 | LCAT | LCAT | LCAT | 10024 | 0.012 | 0.31 | NO |
16 | LDLRAP1 | LDLRAP1 | LDLRAP1 | 10807 | 0.0016 | 0.27 | NO |
17 | CUBN | CUBN | CUBN | 10926 | -0.000095 | 0.27 | NO |
18 | BMP1 | BMP1 | BMP1 | 10949 | -0.00044 | 0.26 | NO |
19 | AMN | AMN | AMN | 12893 | -0.028 | 0.17 | NO |
20 | SAR1B | SAR1B | SAR1B | 13521 | -0.038 | 0.14 | NO |
21 | ABCA1 | ABCA1 | ABCA1 | 13716 | -0.041 | 0.14 | NO |
22 | APOE | APOE | APOE | 14069 | -0.049 | 0.13 | NO |
23 | HSPG2 | HSPG2 | HSPG2 | 14596 | -0.06 | 0.11 | NO |
24 | SDC1 | SDC1 | SDC1 | 14745 | -0.064 | 0.12 | NO |
25 | ABCG1 | ABCG1 | ABCG1 | 15212 | -0.075 | 0.11 | NO |
26 | A2M | A2M | A2M | 16297 | -0.11 | 0.074 | NO |
27 | CETP | CETP | CETP | 16614 | -0.12 | 0.083 | NO |
28 | LDLR | LDLR | LDLR | 16800 | -0.13 | 0.1 | NO |
Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA.

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

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 | SLC38A3 | SLC38A3 | SLC38A3 | 57 | 0.62 | 0.14 | YES |
2 | SLC7A10 | SLC7A10 | SLC7A10 | 131 | 0.54 | 0.26 | YES |
3 | SLC16A10 | SLC16A10 | SLC16A10 | 174 | 0.52 | 0.38 | YES |
4 | SLC7A2 | SLC7A2 | SLC7A2 | 1477 | 0.26 | 0.36 | YES |
5 | SLC6A12 | SLC6A12 | SLC6A12 | 1528 | 0.25 | 0.42 | YES |
6 | SLC7A9 | SLC7A9 | SLC7A9 | 1791 | 0.23 | 0.46 | YES |
7 | SLC6A15 | SLC6A15 | SLC6A15 | 2142 | 0.2 | 0.48 | YES |
8 | SLC7A5 | SLC7A5 | SLC7A5 | 3220 | 0.14 | 0.46 | YES |
9 | SLC36A2 | SLC36A2 | SLC36A2 | 3517 | 0.13 | 0.47 | YES |
10 | SLC43A2 | SLC43A2 | SLC43A2 | 3623 | 0.13 | 0.5 | YES |
11 | SLC38A4 | SLC38A4 | SLC38A4 | 3658 | 0.13 | 0.52 | YES |
12 | SLC1A5 | SLC1A5 | SLC1A5 | 3763 | 0.13 | 0.55 | YES |
13 | SLC6A19 | SLC6A19 | SLC6A19 | 3777 | 0.13 | 0.58 | YES |
14 | SLC3A2 | SLC3A2 | SLC3A2 | 4160 | 0.11 | 0.58 | YES |
15 | SLC43A1 | SLC43A1 | SLC43A1 | 4217 | 0.11 | 0.6 | YES |
16 | SLC3A1 | SLC3A1 | SLC3A1 | 5879 | 0.073 | 0.53 | NO |
17 | SLC7A3 | SLC7A3 | SLC7A3 | 6354 | 0.064 | 0.52 | NO |
18 | SLC7A7 | SLC7A7 | SLC7A7 | 6732 | 0.058 | 0.51 | NO |
19 | SLC6A18 | SLC6A18 | SLC6A18 | 7579 | 0.045 | 0.48 | NO |
20 | SLC7A6 | SLC7A6 | SLC7A6 | 9235 | 0.021 | 0.4 | NO |
21 | SLC38A5 | SLC38A5 | SLC38A5 | 9493 | 0.018 | 0.38 | NO |
22 | SLC1A4 | SLC1A4 | SLC1A4 | 10137 | 0.01 | 0.35 | NO |
23 | SLC6A6 | SLC6A6 | SLC6A6 | 10421 | 0.0067 | 0.34 | NO |
24 | SLC38A1 | SLC38A1 | SLC38A1 | 10554 | 0.0051 | 0.33 | NO |
25 | SLC7A8 | SLC7A8 | SLC7A8 | 11789 | -0.012 | 0.27 | NO |
26 | SLC38A2 | SLC38A2 | SLC38A2 | 12549 | -0.022 | 0.23 | NO |
27 | SLC36A1 | SLC36A1 | SLC36A1 | 12967 | -0.029 | 0.22 | NO |
28 | SLC7A1 | SLC7A1 | SLC7A1 | 13379 | -0.036 | 0.2 | NO |
29 | SLC6A20 | SLC6A20 | SLC6A20 | 15530 | -0.085 | 0.11 | NO |
30 | SLC7A11 | SLC7A11 | SLC7A11 | 16228 | -0.11 | 0.096 | NO |
31 | SLC6A14 | SLC6A14 | SLC6A14 | 17115 | -0.15 | 0.084 | 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 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE, 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 PURINE METABOLISM | 155 | genes.ES.table | 0.39 | 1.6 | 0.01 | 0.18 | 0.97 | 0.17 | 0.13 | 0.15 | 0.095 | 0.015 |
KEGG TYROSINE METABOLISM | 41 | genes.ES.table | 0.49 | 1.3 | 0.098 | 0.25 | 1 | 0.22 | 0.1 | 0.2 | 0.19 | 0.001 |
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE | 26 | genes.ES.table | 0.52 | 1.4 | 0.09 | 0.22 | 1 | 0.42 | 0.27 | 0.31 | 0.17 | 0.003 |
KEGG ABC TRANSPORTERS | 44 | genes.ES.table | 0.59 | 1.6 | 0.015 | 0.18 | 0.97 | 0.25 | 0.12 | 0.22 | 0.1 | 0.015 |
KEGG MAPK SIGNALING PATHWAY | 257 | genes.ES.table | 0.45 | 1.7 | 0 | 0.18 | 0.86 | 0.38 | 0.3 | 0.28 | 0.073 | 0.036 |
KEGG ERBB SIGNALING PATHWAY | 87 | genes.ES.table | 0.4 | 1.5 | 0.023 | 0.17 | 0.98 | 0.22 | 0.19 | 0.18 | 0.097 | 0.009 |
KEGG CALCIUM SIGNALING PATHWAY | 175 | genes.ES.table | 0.63 | 1.7 | 0 | 0.18 | 0.86 | 0.46 | 0.19 | 0.37 | 0.073 | 0.037 |
KEGG CHEMOKINE SIGNALING PATHWAY | 185 | genes.ES.table | 0.48 | 1.4 | 0.13 | 0.22 | 1 | 0.38 | 0.23 | 0.3 | 0.17 | 0.002 |
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM | 76 | genes.ES.table | 0.41 | 1.5 | 0.052 | 0.18 | 1 | 0.47 | 0.32 | 0.32 | 0.12 | 0.005 |
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION | 245 | genes.ES.table | 0.58 | 1.5 | 0.0041 | 0.19 | 1 | 0.51 | 0.24 | 0.4 | 0.13 | 0.004 |
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 | ADCY5 | ADCY5 | ADCY5 | 160 | 0.85 | 0.037 | YES |
2 | ADCY2 | ADCY2 | ADCY2 | 261 | 0.78 | 0.074 | YES |
3 | ADCYAP1R1 | ADCYAP1R1 | ADCYAP1R1 | 314 | 0.74 | 0.11 | YES |
4 | ADCYAP1 | ADCYAP1 | ADCYAP1 | 320 | 0.74 | 0.15 | YES |
5 | PDE1A | PDE1A | PDE1A | 342 | 0.72 | 0.19 | YES |
6 | PDE1B | PDE1B | PDE1B | 515 | 0.66 | 0.21 | YES |
7 | NGF | NGF | NGF | 624 | 0.62 | 0.24 | YES |
8 | PRKAR2B | PRKAR2B | PRKAR2B | 828 | 0.55 | 0.26 | YES |
9 | NTRK1 | NTRK1 | NTRK1 | 953 | 0.52 | 0.28 | YES |
10 | NTRK2 | NTRK2 | NTRK2 | 994 | 0.52 | 0.31 | YES |
11 | AKT3 | AKT3 | AKT3 | 1032 | 0.51 | 0.33 | YES |
12 | CAMK4 | CAMK4 | CAMK4 | 1118 | 0.49 | 0.35 | YES |
13 | MEF2C | MEF2C | MEF2C | 1496 | 0.42 | 0.36 | YES |
14 | ADCY4 | ADCY4 | ADCY4 | 1577 | 0.41 | 0.37 | YES |
15 | SHC2 | SHC2 | SHC2 | 2257 | 0.32 | 0.35 | YES |
16 | MAPK11 | MAPK11 | MAPK11 | 2763 | 0.26 | 0.34 | YES |
17 | PRKACB | PRKACB | PRKACB | 2792 | 0.26 | 0.35 | YES |
18 | SHC3 | SHC3 | SHC3 | 2952 | 0.25 | 0.36 | YES |
19 | ADORA2A | ADORA2A | ADORA2A | 3000 | 0.24 | 0.37 | YES |
20 | ADCY9 | ADCY9 | ADCY9 | 3153 | 0.23 | 0.37 | YES |
21 | SH3GL2 | SH3GL2 | SH3GL2 | 3411 | 0.21 | 0.37 | YES |
22 | PIK3R1 | PIK3R1 | PIK3R1 | 3462 | 0.21 | 0.38 | YES |
23 | ITPR2 | ITPR2 | ITPR2 | 3504 | 0.21 | 0.39 | YES |
24 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 3585 | 0.2 | 0.4 | YES |
25 | MEF2A | MEF2A | MEF2A | 3620 | 0.2 | 0.4 | YES |
26 | IRS2 | IRS2 | IRS2 | 3649 | 0.2 | 0.41 | YES |
27 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3709 | 0.19 | 0.42 | YES |
28 | IRS1 | IRS1 | IRS1 | 3781 | 0.19 | 0.43 | YES |
29 | DNM1 | DNM1 | DNM1 | 3847 | 0.18 | 0.43 | YES |
30 | PRKCE | PRKCE | PRKCE | 4134 | 0.16 | 0.43 | YES |
31 | FOXO4 | FOXO4 | FOXO4 | 4292 | 0.15 | 0.43 | YES |
32 | DUSP3 | DUSP3 | DUSP3 | 4358 | 0.15 | 0.43 | YES |
33 | ADCY8 | ADCY8 | ADCY8 | 4557 | 0.14 | 0.43 | YES |
34 | FOXO1 | FOXO1 | FOXO1 | 4563 | 0.14 | 0.44 | YES |
35 | ADCY1 | ADCY1 | ADCY1 | 4693 | 0.13 | 0.44 | YES |
36 | RAP1A | RAP1A | RAP1A | 5026 | 0.12 | 0.42 | YES |
37 | PIK3CA | PIK3CA | PIK3CA | 5049 | 0.12 | 0.43 | YES |
38 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5155 | 0.11 | 0.43 | YES |
39 | MAP2K5 | MAP2K5 | MAP2K5 | 5197 | 0.11 | 0.43 | YES |
40 | PRKCG | PRKCG | PRKCG | 5226 | 0.11 | 0.44 | YES |
41 | PTEN | PTEN | PTEN | 5404 | 0.1 | 0.43 | YES |
42 | PRKCA | PRKCA | PRKCA | 5442 | 0.099 | 0.44 | YES |
43 | ADCY7 | ADCY7 | ADCY7 | 5533 | 0.095 | 0.44 | YES |
44 | NR4A1 | NR4A1 | NR4A1 | 5545 | 0.095 | 0.44 | YES |
45 | KIDINS220 | KIDINS220 | KIDINS220 | 5553 | 0.094 | 0.44 | YES |
46 | CDKN1B | CDKN1B | CDKN1B | 5721 | 0.088 | 0.44 | YES |
47 | ADCY3 | ADCY3 | ADCY3 | 5752 | 0.087 | 0.44 | YES |
48 | PRKACA | PRKACA | PRKACA | 5809 | 0.085 | 0.44 | YES |
49 | MAPK12 | MAPK12 | MAPK12 | 5814 | 0.085 | 0.45 | YES |
50 | PLCG1 | PLCG1 | PLCG1 | 5848 | 0.084 | 0.45 | YES |
51 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 6033 | 0.077 | 0.45 | NO |
52 | SOS1 | SOS1 | SOS1 | 6105 | 0.075 | 0.45 | NO |
53 | PRKAR2A | PRKAR2A | PRKAR2A | 6208 | 0.072 | 0.44 | NO |
54 | TSC2 | TSC2 | TSC2 | 6211 | 0.072 | 0.45 | NO |
55 | BRAF | BRAF | BRAF | 6609 | 0.06 | 0.43 | NO |
56 | STAT3 | STAT3 | STAT3 | 6623 | 0.06 | 0.43 | NO |
57 | PRKAR1A | PRKAR1A | PRKAR1A | 6674 | 0.058 | 0.43 | NO |
58 | CREB1 | CREB1 | CREB1 | 6736 | 0.057 | 0.43 | NO |
59 | PDPK1 | PDPK1 | PDPK1 | 7090 | 0.047 | 0.42 | NO |
60 | CALM1 | CALM1 | CALM1 | 7097 | 0.047 | 0.42 | NO |
61 | RICTOR | RICTOR | RICTOR | 7155 | 0.046 | 0.42 | NO |
62 | MAPK7 | MAPK7 | MAPK7 | 7205 | 0.045 | 0.42 | NO |
63 | AKT2 | AKT2 | AKT2 | 7332 | 0.042 | 0.41 | NO |
64 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 7337 | 0.041 | 0.42 | NO |
65 | ELK1 | ELK1 | ELK1 | 7440 | 0.039 | 0.41 | NO |
66 | AP2A2 | AP2A2 | AP2A2 | 7473 | 0.038 | 0.41 | NO |
67 | FOXO3 | FOXO3 | FOXO3 | 7485 | 0.038 | 0.41 | NO |
68 | MAPK14 | MAPK14 | MAPK14 | 7542 | 0.037 | 0.41 | NO |
69 | FRS2 | FRS2 | FRS2 | 7782 | 0.032 | 0.4 | NO |
70 | MAPK1 | MAPK1 | MAPK1 | 8166 | 0.024 | 0.38 | NO |
71 | AP2A1 | AP2A1 | AP2A1 | 8328 | 0.021 | 0.38 | NO |
72 | SHC1 | SHC1 | SHC1 | 8385 | 0.019 | 0.37 | NO |
73 | DUSP6 | DUSP6 | DUSP6 | 8625 | 0.015 | 0.36 | NO |
74 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 8859 | 0.011 | 0.35 | NO |
75 | CRK | CRK | CRK | 8934 | 0.0094 | 0.35 | NO |
76 | RAF1 | RAF1 | RAF1 | 9003 | 0.0082 | 0.34 | NO |
77 | RALGDS | RALGDS | RALGDS | 9090 | 0.0066 | 0.34 | NO |
78 | AP2M1 | AP2M1 | AP2M1 | 9180 | 0.0051 | 0.33 | NO |
79 | RIT1 | RIT1 | RIT1 | 9248 | 0.0037 | 0.33 | NO |
80 | PPP2CB | PPP2CB | PPP2CB | 9249 | 0.0036 | 0.33 | NO |
81 | AKT1 | AKT1 | AKT1 | 9288 | 0.0029 | 0.33 | NO |
82 | MTOR | MTOR | MTOR | 9314 | 0.0024 | 0.33 | NO |
83 | RHOA | RHOA | RHOA | 9354 | 0.0015 | 0.32 | NO |
84 | PRKAR1B | PRKAR1B | PRKAR1B | 9587 | -0.0024 | 0.31 | NO |
85 | MDM2 | MDM2 | MDM2 | 9639 | -0.0032 | 0.31 | NO |
86 | CALM3 | CALM3 | CALM3 | 9767 | -0.0058 | 0.3 | NO |
87 | BAD | BAD | BAD | 9784 | -0.0062 | 0.3 | NO |
88 | ADCY6 | ADCY6 | ADCY6 | 9896 | -0.0082 | 0.3 | NO |
89 | CDKN1A | CDKN1A | CDKN1A | 9949 | -0.0091 | 0.3 | NO |
90 | CALM2 | CALM2 | CALM2 | 9971 | -0.0096 | 0.3 | NO |
91 | CASP9 | CASP9 | CASP9 | 9989 | -0.0099 | 0.29 | NO |
92 | GRB2 | GRB2 | GRB2 | 10085 | -0.011 | 0.29 | NO |
93 | ATF1 | ATF1 | ATF1 | 10465 | -0.018 | 0.27 | NO |
94 | PPP2R1A | PPP2R1A | PPP2R1A | 10580 | -0.019 | 0.26 | NO |
95 | AP2B1 | AP2B1 | AP2B1 | 10648 | -0.02 | 0.26 | NO |
96 | DUSP7 | DUSP7 | DUSP7 | 10697 | -0.021 | 0.26 | NO |
97 | THEM4 | THEM4 | THEM4 | 10796 | -0.023 | 0.26 | NO |
98 | MAP2K1 | MAP2K1 | MAP2K1 | 10906 | -0.025 | 0.25 | NO |
99 | PPP2R5D | PPP2R5D | PPP2R5D | 10979 | -0.026 | 0.25 | NO |
100 | KRAS | KRAS | KRAS | 10994 | -0.027 | 0.25 | NO |
101 | AKT1S1 | AKT1S1 | AKT1S1 | 11074 | -0.028 | 0.25 | NO |
102 | PIK3R2 | PIK3R2 | PIK3R2 | 11116 | -0.029 | 0.25 | NO |
103 | MAP2K2 | MAP2K2 | MAP2K2 | 11283 | -0.031 | 0.24 | NO |
104 | ADRBK1 | ADRBK1 | ADRBK1 | 11340 | -0.032 | 0.24 | NO |
105 | PPP2CA | PPP2CA | PPP2CA | 11572 | -0.036 | 0.23 | NO |
106 | CLTC | CLTC | CLTC | 11636 | -0.036 | 0.23 | NO |
107 | GSK3A | GSK3A | GSK3A | 11704 | -0.038 | 0.22 | NO |
108 | MAPK3 | MAPK3 | MAPK3 | 11852 | -0.04 | 0.22 | NO |
109 | PHLPP1 | PHLPP1 | PHLPP1 | 12525 | -0.051 | 0.19 | NO |
110 | CHUK | CHUK | CHUK | 12593 | -0.052 | 0.18 | NO |
111 | MLST8 | MLST8 | MLST8 | 12618 | -0.053 | 0.19 | NO |
112 | RALB | RALB | RALB | 12673 | -0.054 | 0.19 | NO |
113 | YWHAB | YWHAB | YWHAB | 12844 | -0.057 | 0.18 | NO |
114 | PIK3CB | PIK3CB | PIK3CB | 13345 | -0.066 | 0.16 | NO |
115 | AP2S1 | AP2S1 | AP2S1 | 13564 | -0.07 | 0.15 | NO |
116 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 13598 | -0.071 | 0.15 | NO |
117 | DNAL4 | DNAL4 | DNAL4 | 13635 | -0.071 | 0.15 | NO |
118 | DNM2 | DNM2 | DNM2 | 13653 | -0.072 | 0.16 | NO |
119 | CLTA | CLTA | CLTA | 13722 | -0.073 | 0.16 | NO |
120 | NRAS | NRAS | NRAS | 14079 | -0.08 | 0.14 | NO |
121 | PRKACG | PRKACG | PRKACG | 14345 | -0.086 | 0.13 | NO |
122 | HRAS | HRAS | HRAS | 14495 | -0.089 | 0.13 | NO |
123 | DUSP4 | DUSP4 | DUSP4 | 14625 | -0.092 | 0.13 | NO |
124 | RALA | RALA | RALA | 15022 | -0.1 | 0.11 | NO |
125 | PPP2R1B | PPP2R1B | PPP2R1B | 15172 | -0.11 | 0.11 | NO |
126 | SRC | SRC | SRC | 15271 | -0.11 | 0.11 | NO |
127 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 15545 | -0.12 | 0.1 | NO |
128 | PRKCD | PRKCD | PRKCD | 15704 | -0.12 | 0.099 | NO |
129 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 15741 | -0.12 | 0.1 | NO |
130 | ITPR3 | ITPR3 | ITPR3 | 15966 | -0.13 | 0.099 | NO |
131 | MAPK13 | MAPK13 | MAPK13 | 17652 | -0.23 | 0.02 | NO |
132 | CDK1 | CDK1 | CDK1 | 18076 | -0.27 | 0.012 | NO |
133 | TRIB3 | TRIB3 | TRIB3 | 18564 | -0.38 | 0.0059 | 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 PURINE METABOLISM.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE 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 | IGF1 | IGF1 | IGF1 | 205 | 0.82 | 0.094 | YES |
2 | FIGF | FIGF | FIGF | 420 | 0.68 | 0.17 | YES |
3 | PRKAA2 | PRKAA2 | PRKAA2 | 923 | 0.53 | 0.21 | YES |
4 | AKT3 | AKT3 | AKT3 | 1032 | 0.51 | 0.27 | YES |
5 | RPS6KA6 | RPS6KA6 | RPS6KA6 | 1132 | 0.49 | 0.33 | YES |
6 | PIK3CG | PIK3CG | PIK3CG | 1485 | 0.42 | 0.36 | YES |
7 | VEGFC | VEGFC | VEGFC | 1671 | 0.39 | 0.4 | YES |
8 | CAB39L | CAB39L | CAB39L | 1767 | 0.38 | 0.45 | YES |
9 | ULK2 | ULK2 | ULK2 | 2169 | 0.33 | 0.47 | YES |
10 | PIK3R5 | PIK3R5 | PIK3R5 | 2199 | 0.33 | 0.51 | YES |
11 | PIK3CD | PIK3CD | PIK3CD | 2647 | 0.28 | 0.52 | YES |
12 | PIK3R1 | PIK3R1 | PIK3R1 | 3462 | 0.21 | 0.51 | NO |
13 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3709 | 0.19 | 0.52 | NO |
14 | VEGFB | VEGFB | VEGFB | 4164 | 0.16 | 0.51 | NO |
15 | PIK3R3 | PIK3R3 | PIK3R3 | 4598 | 0.14 | 0.51 | NO |
16 | PIK3CA | PIK3CA | PIK3CA | 5049 | 0.12 | 0.5 | NO |
17 | PGF | PGF | PGF | 5515 | 0.096 | 0.49 | NO |
18 | ULK1 | ULK1 | ULK1 | 5849 | 0.084 | 0.48 | NO |
19 | TSC2 | TSC2 | TSC2 | 6211 | 0.072 | 0.47 | NO |
20 | BRAF | BRAF | BRAF | 6609 | 0.06 | 0.46 | NO |
21 | PDPK1 | PDPK1 | PDPK1 | 7090 | 0.047 | 0.44 | NO |
22 | RICTOR | RICTOR | RICTOR | 7155 | 0.046 | 0.44 | NO |
23 | RPTOR | RPTOR | RPTOR | 7321 | 0.042 | 0.44 | NO |
24 | AKT2 | AKT2 | AKT2 | 7332 | 0.042 | 0.44 | NO |
25 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 7337 | 0.041 | 0.44 | NO |
26 | EIF4B | EIF4B | EIF4B | 7701 | 0.033 | 0.43 | NO |
27 | TSC1 | TSC1 | TSC1 | 7717 | 0.033 | 0.43 | NO |
28 | MAPK1 | MAPK1 | MAPK1 | 8166 | 0.024 | 0.41 | NO |
29 | STRADA | STRADA | STRADA | 8271 | 0.022 | 0.41 | NO |
30 | AKT1 | AKT1 | AKT1 | 9288 | 0.0029 | 0.36 | NO |
31 | MTOR | MTOR | MTOR | 9314 | 0.0024 | 0.35 | NO |
32 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 9510 | -0.0011 | 0.34 | NO |
33 | HIF1A | HIF1A | HIF1A | 9991 | -0.0099 | 0.32 | NO |
34 | STK11 | STK11 | STK11 | 10167 | -0.013 | 0.31 | NO |
35 | CAB39 | CAB39 | CAB39 | 10226 | -0.014 | 0.31 | NO |
36 | RPS6 | RPS6 | RPS6 | 10364 | -0.016 | 0.3 | NO |
37 | DDIT4 | DDIT4 | DDIT4 | 10863 | -0.024 | 0.28 | NO |
38 | PRKAA1 | PRKAA1 | PRKAA1 | 11051 | -0.028 | 0.27 | NO |
39 | PIK3R2 | PIK3R2 | PIK3R2 | 11116 | -0.029 | 0.28 | NO |
40 | RHEB | RHEB | RHEB | 11433 | -0.033 | 0.26 | NO |
41 | MAPK3 | MAPK3 | MAPK3 | 11852 | -0.04 | 0.24 | NO |
42 | MLST8 | MLST8 | MLST8 | 12618 | -0.053 | 0.21 | NO |
43 | ULK3 | ULK3 | ULK3 | 12985 | -0.059 | 0.2 | NO |
44 | EIF4E2 | EIF4E2 | EIF4E2 | 13125 | -0.062 | 0.2 | NO |
45 | PIK3CB | PIK3CB | PIK3CB | 13345 | -0.066 | 0.2 | NO |
46 | EIF4E | EIF4E | EIF4E | 14870 | -0.098 | 0.13 | NO |
47 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 15545 | -0.12 | 0.11 | NO |
48 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 15741 | -0.12 | 0.11 | NO |
49 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 16432 | -0.15 | 0.094 | NO |
50 | VEGFA | VEGFA | VEGFA | 17374 | -0.2 | 0.07 | 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 TYROSINE METABOLISM.

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

Table 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 | ADCY5 | ADCY5 | ADCY5 | 160 | 0.85 | 0.061 | YES |
2 | ADCY2 | ADCY2 | ADCY2 | 261 | 0.78 | 0.12 | YES |
3 | PDE1A | PDE1A | PDE1A | 342 | 0.72 | 0.17 | YES |
4 | PDE1B | PDE1B | PDE1B | 515 | 0.66 | 0.22 | YES |
5 | PRKAR2B | PRKAR2B | PRKAR2B | 828 | 0.55 | 0.25 | YES |
6 | AKT3 | AKT3 | AKT3 | 1032 | 0.51 | 0.28 | YES |
7 | CAMK4 | CAMK4 | CAMK4 | 1118 | 0.49 | 0.31 | YES |
8 | ADCY4 | ADCY4 | ADCY4 | 1577 | 0.41 | 0.32 | YES |
9 | PRKACB | PRKACB | PRKACB | 2792 | 0.26 | 0.28 | YES |
10 | LRIG1 | LRIG1 | LRIG1 | 3031 | 0.24 | 0.28 | YES |
11 | ADCY9 | ADCY9 | ADCY9 | 3153 | 0.23 | 0.3 | YES |
12 | SH3GL2 | SH3GL2 | SH3GL2 | 3411 | 0.21 | 0.3 | YES |
13 | PIK3R1 | PIK3R1 | PIK3R1 | 3462 | 0.21 | 0.31 | YES |
14 | ITPR2 | ITPR2 | ITPR2 | 3504 | 0.21 | 0.33 | YES |
15 | GAB1 | GAB1 | GAB1 | 3561 | 0.2 | 0.34 | YES |
16 | PRKCE | PRKCE | PRKCE | 4134 | 0.16 | 0.32 | YES |
17 | FOXO4 | FOXO4 | FOXO4 | 4292 | 0.15 | 0.33 | YES |
18 | ADAM12 | ADAM12 | ADAM12 | 4303 | 0.15 | 0.34 | YES |
19 | ADCY8 | ADCY8 | ADCY8 | 4557 | 0.14 | 0.34 | YES |
20 | FOXO1 | FOXO1 | FOXO1 | 4563 | 0.14 | 0.35 | YES |
21 | SPRY1 | SPRY1 | SPRY1 | 4588 | 0.14 | 0.36 | YES |
22 | ADCY1 | ADCY1 | ADCY1 | 4693 | 0.13 | 0.36 | YES |
23 | PIK3CA | PIK3CA | PIK3CA | 5049 | 0.12 | 0.36 | YES |
24 | PRKCG | PRKCG | PRKCG | 5226 | 0.11 | 0.35 | YES |
25 | CBL | CBL | CBL | 5320 | 0.1 | 0.36 | YES |
26 | PTEN | PTEN | PTEN | 5404 | 0.1 | 0.36 | YES |
27 | PRKCA | PRKCA | PRKCA | 5442 | 0.099 | 0.37 | YES |
28 | EGFR | EGFR | EGFR | 5456 | 0.098 | 0.38 | YES |
29 | ADCY7 | ADCY7 | ADCY7 | 5533 | 0.095 | 0.38 | YES |
30 | NR4A1 | NR4A1 | NR4A1 | 5545 | 0.095 | 0.39 | YES |
31 | CDKN1B | CDKN1B | CDKN1B | 5721 | 0.088 | 0.38 | YES |
32 | ADCY3 | ADCY3 | ADCY3 | 5752 | 0.087 | 0.39 | YES |
33 | PRKACA | PRKACA | PRKACA | 5809 | 0.085 | 0.39 | YES |
34 | PLCG1 | PLCG1 | PLCG1 | 5848 | 0.084 | 0.4 | YES |
35 | EPS15 | EPS15 | EPS15 | 5905 | 0.081 | 0.4 | YES |
36 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 6033 | 0.077 | 0.4 | YES |
37 | SOS1 | SOS1 | SOS1 | 6105 | 0.075 | 0.4 | YES |
38 | PRKAR2A | PRKAR2A | PRKAR2A | 6208 | 0.072 | 0.4 | YES |
39 | TSC2 | TSC2 | TSC2 | 6211 | 0.072 | 0.41 | YES |
40 | PRKAR1A | PRKAR1A | PRKAR1A | 6674 | 0.058 | 0.39 | NO |
41 | CREB1 | CREB1 | CREB1 | 6736 | 0.057 | 0.39 | NO |
42 | PAG1 | PAG1 | PAG1 | 6844 | 0.054 | 0.39 | NO |
43 | PDPK1 | PDPK1 | PDPK1 | 7090 | 0.047 | 0.38 | NO |
44 | CALM1 | CALM1 | CALM1 | 7097 | 0.047 | 0.38 | NO |
45 | RICTOR | RICTOR | RICTOR | 7155 | 0.046 | 0.38 | NO |
46 | AKT2 | AKT2 | AKT2 | 7332 | 0.042 | 0.38 | NO |
47 | AP2A2 | AP2A2 | AP2A2 | 7473 | 0.038 | 0.37 | NO |
48 | FOXO3 | FOXO3 | FOXO3 | 7485 | 0.038 | 0.38 | NO |
49 | SPRY2 | SPRY2 | SPRY2 | 7946 | 0.028 | 0.35 | NO |
50 | MAPK1 | MAPK1 | MAPK1 | 8166 | 0.024 | 0.34 | NO |
51 | STAM2 | STAM2 | STAM2 | 8295 | 0.021 | 0.34 | NO |
52 | AP2A1 | AP2A1 | AP2A1 | 8328 | 0.021 | 0.34 | NO |
53 | SHC1 | SHC1 | SHC1 | 8385 | 0.019 | 0.34 | NO |
54 | EPS15L1 | EPS15L1 | EPS15L1 | 8634 | 0.015 | 0.32 | NO |
55 | SH3KBP1 | SH3KBP1 | SH3KBP1 | 8798 | 0.012 | 0.32 | NO |
56 | RAF1 | RAF1 | RAF1 | 9003 | 0.0082 | 0.31 | NO |
57 | AP2M1 | AP2M1 | AP2M1 | 9180 | 0.0051 | 0.3 | NO |
58 | AKT1 | AKT1 | AKT1 | 9288 | 0.0029 | 0.29 | NO |
59 | MTOR | MTOR | MTOR | 9314 | 0.0024 | 0.29 | NO |
60 | PRKAR1B | PRKAR1B | PRKAR1B | 9587 | -0.0024 | 0.28 | NO |
61 | MDM2 | MDM2 | MDM2 | 9639 | -0.0032 | 0.27 | NO |
62 | CALM3 | CALM3 | CALM3 | 9767 | -0.0058 | 0.27 | NO |
63 | BAD | BAD | BAD | 9784 | -0.0062 | 0.27 | NO |
64 | CDC42 | CDC42 | CDC42 | 9840 | -0.0072 | 0.26 | NO |
65 | ADCY6 | ADCY6 | ADCY6 | 9896 | -0.0082 | 0.26 | NO |
66 | CDKN1A | CDKN1A | CDKN1A | 9949 | -0.0091 | 0.26 | NO |
67 | CALM2 | CALM2 | CALM2 | 9971 | -0.0096 | 0.26 | NO |
68 | CASP9 | CASP9 | CASP9 | 9989 | -0.0099 | 0.26 | NO |
69 | ADAM17 | ADAM17 | ADAM17 | 10054 | -0.011 | 0.26 | NO |
70 | RPS27A | RPS27A | RPS27A | 10077 | -0.011 | 0.26 | NO |
71 | GRB2 | GRB2 | GRB2 | 10085 | -0.011 | 0.26 | NO |
72 | UBA52 | UBA52 | UBA52 | 10288 | -0.015 | 0.25 | NO |
73 | AP2B1 | AP2B1 | AP2B1 | 10648 | -0.02 | 0.23 | NO |
74 | THEM4 | THEM4 | THEM4 | 10796 | -0.023 | 0.22 | NO |
75 | MAP2K1 | MAP2K1 | MAP2K1 | 10906 | -0.025 | 0.22 | NO |
76 | KRAS | KRAS | KRAS | 10994 | -0.027 | 0.22 | NO |
77 | AKT1S1 | AKT1S1 | AKT1S1 | 11074 | -0.028 | 0.22 | NO |
78 | STAM | STAM | STAM | 11187 | -0.03 | 0.21 | NO |
79 | MAP2K2 | MAP2K2 | MAP2K2 | 11283 | -0.031 | 0.21 | NO |
80 | ADRBK1 | ADRBK1 | ADRBK1 | 11340 | -0.032 | 0.21 | NO |
81 | CLTC | CLTC | CLTC | 11636 | -0.036 | 0.2 | NO |
82 | CSK | CSK | CSK | 11637 | -0.036 | 0.2 | NO |
83 | GSK3A | GSK3A | GSK3A | 11704 | -0.038 | 0.2 | NO |
84 | MAPK3 | MAPK3 | MAPK3 | 11852 | -0.04 | 0.19 | NO |
85 | CDC37 | CDC37 | CDC37 | 12060 | -0.044 | 0.19 | NO |
86 | EGF | EGF | EGF | 12353 | -0.049 | 0.18 | NO |
87 | PHLPP1 | PHLPP1 | PHLPP1 | 12525 | -0.051 | 0.17 | NO |
88 | CHUK | CHUK | CHUK | 12593 | -0.052 | 0.17 | NO |
89 | MLST8 | MLST8 | MLST8 | 12618 | -0.053 | 0.17 | NO |
90 | ADAM10 | ADAM10 | ADAM10 | 12723 | -0.055 | 0.17 | NO |
91 | EPN1 | EPN1 | EPN1 | 12725 | -0.055 | 0.18 | NO |
92 | YWHAB | YWHAB | YWHAB | 12844 | -0.057 | 0.18 | NO |
93 | HGS | HGS | HGS | 13279 | -0.064 | 0.16 | NO |
94 | AP2S1 | AP2S1 | AP2S1 | 13564 | -0.07 | 0.15 | NO |
95 | CLTA | CLTA | CLTA | 13722 | -0.073 | 0.14 | NO |
96 | NRAS | NRAS | NRAS | 14079 | -0.08 | 0.13 | NO |
97 | PRKACG | PRKACG | PRKACG | 14345 | -0.086 | 0.12 | NO |
98 | HRAS | HRAS | HRAS | 14495 | -0.089 | 0.12 | NO |
99 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 14530 | -0.09 | 0.13 | NO |
100 | SRC | SRC | SRC | 15271 | -0.11 | 0.099 | NO |
101 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 15545 | -0.12 | 0.094 | NO |
102 | PRKCD | PRKCD | PRKCD | 15704 | -0.12 | 0.096 | NO |
103 | ITPR3 | ITPR3 | ITPR3 | 15966 | -0.13 | 0.093 | NO |
104 | CDK1 | CDK1 | CDK1 | 18076 | -0.27 | 0.0013 | NO |
105 | TRIB3 | TRIB3 | TRIB3 | 18564 | -0.38 | 0.0059 | 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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.
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Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | ESR1 | ESR1 | ESR1 | 393 | 0.7 | 0.1 | YES |
2 | MAPT | MAPT | MAPT | 541 | 0.65 | 0.21 | YES |
3 | PRKAA2 | PRKAA2 | PRKAA2 | 923 | 0.53 | 0.28 | YES |
4 | MAP2 | MAP2 | MAP2 | 1378 | 0.44 | 0.34 | YES |
5 | SMARCD3 | SMARCD3 | SMARCD3 | 1380 | 0.44 | 0.41 | YES |
6 | BRSK1 | BRSK1 | BRSK1 | 1866 | 0.36 | 0.45 | YES |
7 | SIK3 | SIK3 | SIK3 | 4512 | 0.14 | 0.34 | NO |
8 | SMAD4 | SMAD4 | SMAD4 | 5154 | 0.11 | 0.32 | NO |
9 | SIK2 | SIK2 | SIK2 | 5339 | 0.1 | 0.33 | NO |
10 | SIK1 | SIK1 | SIK1 | 5653 | 0.091 | 0.33 | NO |
11 | PRKACA | PRKACA | PRKACA | 5809 | 0.085 | 0.34 | NO |
12 | TSC2 | TSC2 | TSC2 | 6211 | 0.072 | 0.33 | NO |
13 | CREB1 | CREB1 | CREB1 | 6736 | 0.057 | 0.31 | NO |
14 | RPTOR | RPTOR | RPTOR | 7321 | 0.042 | 0.28 | NO |
15 | TSC1 | TSC1 | TSC1 | 7717 | 0.033 | 0.27 | NO |
16 | BRSK2 | BRSK2 | BRSK2 | 7944 | 0.028 | 0.26 | NO |
17 | TP53 | TP53 | TP53 | 8022 | 0.027 | 0.26 | NO |
18 | STRADA | STRADA | STRADA | 8271 | 0.022 | 0.25 | NO |
19 | MARK4 | MARK4 | MARK4 | 8468 | 0.018 | 0.24 | NO |
20 | PRKAB1 | PRKAB1 | PRKAB1 | 9095 | 0.0065 | 0.21 | NO |
21 | YWHAH | YWHAH | YWHAH | 9245 | 0.0037 | 0.2 | NO |
22 | MTOR | MTOR | MTOR | 9314 | 0.0024 | 0.2 | NO |
23 | YWHAQ | YWHAQ | YWHAQ | 9697 | -0.0044 | 0.18 | NO |
24 | MYC | MYC | MYC | 9862 | -0.0077 | 0.18 | NO |
25 | STK11 | STK11 | STK11 | 10167 | -0.013 | 0.16 | NO |
26 | CAB39 | CAB39 | CAB39 | 10226 | -0.014 | 0.16 | NO |
27 | GSK3B | GSK3B | GSK3B | 10374 | -0.016 | 0.16 | NO |
28 | PRKAG1 | PRKAG1 | PRKAG1 | 10780 | -0.023 | 0.14 | NO |
29 | PRKAA1 | PRKAA1 | PRKAA1 | 11051 | -0.028 | 0.13 | NO |
30 | AKT1S1 | AKT1S1 | AKT1S1 | 11074 | -0.028 | 0.13 | NO |
31 | CTSD | CTSD | CTSD | 11322 | -0.031 | 0.12 | NO |
32 | CRTC2 | CRTC2 | CRTC2 | 11357 | -0.032 | 0.13 | NO |
33 | YWHAG | YWHAG | YWHAG | 11423 | -0.033 | 0.13 | NO |
34 | PSEN2 | PSEN2 | PSEN2 | 11459 | -0.034 | 0.13 | NO |
35 | CDC37 | CDC37 | CDC37 | 12060 | -0.044 | 0.11 | NO |
36 | MLST8 | MLST8 | MLST8 | 12618 | -0.053 | 0.089 | NO |
37 | YWHAB | YWHAB | YWHAB | 12844 | -0.057 | 0.087 | NO |
38 | STK11IP | STK11IP | STK11IP | 12964 | -0.059 | 0.091 | NO |
39 | YWHAZ | YWHAZ | YWHAZ | 14238 | -0.084 | 0.038 | NO |
40 | MARK2 | MARK2 | MARK2 | 14389 | -0.086 | 0.045 | NO |
41 | YWHAE | YWHAE | YWHAE | 14434 | -0.088 | 0.058 | NO |
42 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 14530 | -0.09 | 0.069 | NO |
43 | STRADB | STRADB | STRADB | 14741 | -0.095 | 0.074 | NO |
44 | MST4 | MST4 | MST4 | 15098 | -0.1 | 0.074 | NO |
45 | EZR | EZR | EZR | 15431 | -0.12 | 0.076 | NO |
46 | ETV4 | ETV4 | ETV4 | 17874 | -0.25 | -0.011 | NO |
47 | SFN | SFN | SFN | 18304 | -0.3 | 0.02 | 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 ABC TRANSPORTERS.

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

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 | ACTG2 | ACTG2 | ACTG2 | 114 | 0.87 | 0.13 | YES |
2 | FLNC | FLNC | FLNC | 117 | 0.87 | 0.27 | YES |
3 | MYLK | MYLK | MYLK | 564 | 0.64 | 0.35 | YES |
4 | PAK3 | PAK3 | PAK3 | 676 | 0.6 | 0.44 | YES |
5 | CFL2 | CFL2 | CFL2 | 846 | 0.55 | 0.52 | YES |
6 | FLNA | FLNA | FLNA | 1499 | 0.42 | 0.55 | YES |
7 | ANGPTL2 | ANGPTL2 | ANGPTL2 | 1818 | 0.37 | 0.59 | YES |
8 | WASF1 | WASF1 | WASF1 | 1974 | 0.35 | 0.64 | YES |
9 | PFN2 | PFN2 | PFN2 | 4902 | 0.12 | 0.5 | NO |
10 | ROCK1 | ROCK1 | ROCK1 | 6056 | 0.076 | 0.45 | NO |
11 | PAK7 | PAK7 | PAK7 | 6362 | 0.067 | 0.45 | NO |
12 | ROCK2 | ROCK2 | ROCK2 | 6777 | 0.055 | 0.44 | NO |
13 | FSCN1 | FSCN1 | FSCN1 | 7185 | 0.045 | 0.42 | NO |
14 | RPS4X | RPS4X | RPS4X | 8992 | 0.0084 | 0.32 | NO |
15 | GDI1 | GDI1 | GDI1 | 9027 | 0.0077 | 0.32 | NO |
16 | RHO | RHO | RHO | 9160 | 0.0054 | 0.32 | NO |
17 | AKT1 | AKT1 | AKT1 | 9288 | 0.0029 | 0.31 | NO |
18 | PFN1 | PFN1 | PFN1 | 9699 | -0.0044 | 0.29 | NO |
19 | CDC42 | CDC42 | CDC42 | 9840 | -0.0072 | 0.28 | NO |
20 | PAK2 | PAK2 | PAK2 | 10131 | -0.012 | 0.27 | NO |
21 | ACTR2 | ACTR2 | ACTR2 | 10159 | -0.012 | 0.27 | NO |
22 | WASL | WASL | WASL | 10191 | -0.013 | 0.27 | NO |
23 | VASP | VASP | VASP | 10233 | -0.014 | 0.27 | NO |
24 | LIMK1 | LIMK1 | LIMK1 | 11178 | -0.03 | 0.23 | NO |
25 | GDI2 | GDI2 | GDI2 | 11230 | -0.03 | 0.23 | NO |
26 | ACTG1 | ACTG1 | ACTG1 | 11592 | -0.036 | 0.21 | NO |
27 | ACTR3 | ACTR3 | ACTR3 | 11617 | -0.036 | 0.22 | NO |
28 | FSCN2 | FSCN2 | FSCN2 | 11689 | -0.037 | 0.22 | NO |
29 | CFL1 | CFL1 | CFL1 | 12664 | -0.054 | 0.18 | NO |
30 | PAK1 | PAK1 | PAK1 | 14234 | -0.084 | 0.11 | NO |
31 | PAK4 | PAK4 | PAK4 | 16207 | -0.14 | 0.023 | NO |
32 | MYLK2 | MYLK2 | MYLK2 | 16229 | -0.14 | 0.045 | NO |
33 | FSCN3 | FSCN3 | FSCN3 | 17262 | -0.2 | 0.021 | NO |
34 | PAK6 | PAK6 | PAK6 | 18474 | -0.34 | 0.011 | 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 | MYOCD | MYOCD | MYOCD | 83 | 0.91 | 0.058 | YES |
2 | MAPK10 | MAPK10 | MAPK10 | 149 | 0.85 | 0.11 | YES |
3 | PPP2R2B | PPP2R2B | PPP2R2B | 652 | 0.61 | 0.13 | YES |
4 | TAGLN | TAGLN | TAGLN | 855 | 0.55 | 0.15 | YES |
5 | BLK | BLK | BLK | 1192 | 0.47 | 0.17 | YES |
6 | ACTA2 | ACTA2 | ACTA2 | 1287 | 0.46 | 0.19 | YES |
7 | ITGB3 | ITGB3 | ITGB3 | 1388 | 0.44 | 0.22 | YES |
8 | PIK3CG | PIK3CG | PIK3CG | 1485 | 0.42 | 0.24 | YES |
9 | PIK3R6 | PIK3R6 | PIK3R6 | 1634 | 0.4 | 0.26 | YES |
10 | S1PR1 | S1PR1 | S1PR1 | 1652 | 0.4 | 0.28 | YES |
11 | PIK3R5 | PIK3R5 | PIK3R5 | 2199 | 0.33 | 0.28 | YES |
12 | SLA | SLA | SLA | 2548 | 0.29 | 0.28 | YES |
13 | PIK3CD | PIK3CD | PIK3CD | 2647 | 0.28 | 0.29 | YES |
14 | CYFIP2 | CYFIP2 | CYFIP2 | 2750 | 0.27 | 0.3 | YES |
15 | PDGFRB | PDGFRB | PDGFRB | 2885 | 0.25 | 0.32 | YES |
16 | DOCK4 | DOCK4 | DOCK4 | 3092 | 0.24 | 0.32 | YES |
17 | PIK3R1 | PIK3R1 | PIK3R1 | 3462 | 0.21 | 0.31 | YES |
18 | GAB1 | GAB1 | GAB1 | 3561 | 0.2 | 0.32 | YES |
19 | STAT5B | STAT5B | STAT5B | 3566 | 0.2 | 0.34 | YES |
20 | FYN | FYN | FYN | 3593 | 0.2 | 0.35 | YES |
21 | FGR | FGR | FGR | 3602 | 0.2 | 0.36 | YES |
22 | STAT5A | STAT5A | STAT5A | 3922 | 0.18 | 0.36 | YES |
23 | LRP1 | LRP1 | LRP1 | 3983 | 0.17 | 0.36 | YES |
24 | HCK | HCK | HCK | 4063 | 0.17 | 0.37 | YES |
25 | ABL1 | ABL1 | ABL1 | 4088 | 0.17 | 0.38 | YES |
26 | PRKCE | PRKCE | PRKCE | 4134 | 0.16 | 0.39 | YES |
27 | SRF | SRF | SRF | 4262 | 0.16 | 0.39 | YES |
28 | LCK | LCK | LCK | 4427 | 0.15 | 0.4 | YES |
29 | PIK3R3 | PIK3R3 | PIK3R3 | 4598 | 0.14 | 0.4 | YES |
30 | SIPA1 | SIPA1 | SIPA1 | 4774 | 0.13 | 0.4 | YES |
31 | KSR1 | KSR1 | KSR1 | 4841 | 0.12 | 0.4 | YES |
32 | RAP1A | RAP1A | RAP1A | 5026 | 0.12 | 0.4 | YES |
33 | ITGAV | ITGAV | ITGAV | 5029 | 0.12 | 0.4 | YES |
34 | PIK3CA | PIK3CA | PIK3CA | 5049 | 0.12 | 0.41 | YES |
35 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5155 | 0.11 | 0.41 | YES |
36 | CBL | CBL | CBL | 5320 | 0.1 | 0.41 | YES |
37 | JAK2 | JAK2 | JAK2 | 5361 | 0.1 | 0.42 | YES |
38 | PTEN | PTEN | PTEN | 5404 | 0.1 | 0.42 | YES |
39 | PRKCA | PRKCA | PRKCA | 5442 | 0.099 | 0.43 | YES |
40 | WASF2 | WASF2 | WASF2 | 5525 | 0.096 | 0.43 | YES |
41 | JUN | JUN | JUN | 5808 | 0.085 | 0.42 | NO |
42 | PLCG1 | PLCG1 | PLCG1 | 5848 | 0.084 | 0.42 | NO |
43 | PLA2G4A | PLA2G4A | PLA2G4A | 5945 | 0.079 | 0.42 | NO |
44 | SOS1 | SOS1 | SOS1 | 6105 | 0.075 | 0.42 | NO |
45 | MAP2K7 | MAP2K7 | MAP2K7 | 6294 | 0.069 | 0.41 | NO |
46 | BRAF | BRAF | BRAF | 6609 | 0.06 | 0.4 | NO |
47 | STAT3 | STAT3 | STAT3 | 6623 | 0.06 | 0.4 | NO |
48 | SLC9A3R2 | SLC9A3R2 | SLC9A3R2 | 6641 | 0.059 | 0.41 | NO |
49 | RASA1 | RASA1 | RASA1 | 6682 | 0.058 | 0.41 | NO |
50 | PDGFB | PDGFB | PDGFB | 6695 | 0.058 | 0.41 | NO |
51 | ARAP1 | ARAP1 | ARAP1 | 6788 | 0.055 | 0.41 | NO |
52 | PAG1 | PAG1 | PAG1 | 6844 | 0.054 | 0.41 | NO |
53 | NCK1 | NCK1 | NCK1 | 6871 | 0.053 | 0.41 | NO |
54 | SPHK1 | SPHK1 | SPHK1 | 7139 | 0.046 | 0.4 | NO |
55 | PIN1 | PIN1 | PIN1 | 7219 | 0.044 | 0.4 | NO |
56 | DOK1 | DOK1 | DOK1 | 7292 | 0.043 | 0.4 | NO |
57 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 7337 | 0.041 | 0.4 | NO |
58 | PTPN11 | PTPN11 | PTPN11 | 7377 | 0.041 | 0.4 | NO |
59 | ELK1 | ELK1 | ELK1 | 7440 | 0.039 | 0.4 | NO |
60 | GRB10 | GRB10 | GRB10 | 7655 | 0.034 | 0.39 | NO |
61 | FOS | FOS | FOS | 7690 | 0.033 | 0.39 | NO |
62 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 8049 | 0.026 | 0.37 | NO |
63 | MAPK1 | MAPK1 | MAPK1 | 8166 | 0.024 | 0.37 | NO |
64 | JUND | JUND | JUND | 8207 | 0.023 | 0.37 | NO |
65 | IQGAP1 | IQGAP1 | IQGAP1 | 8370 | 0.02 | 0.36 | NO |
66 | SHC1 | SHC1 | SHC1 | 8385 | 0.019 | 0.36 | NO |
67 | PTPRJ | PTPRJ | PTPRJ | 8568 | 0.016 | 0.35 | NO |
68 | PTPN1 | PTPN1 | PTPN1 | 8659 | 0.014 | 0.35 | NO |
69 | MAP2K4 | MAP2K4 | MAP2K4 | 8745 | 0.013 | 0.35 | NO |
70 | CRK | CRK | CRK | 8934 | 0.0094 | 0.34 | NO |
71 | RAF1 | RAF1 | RAF1 | 9003 | 0.0082 | 0.33 | NO |
72 | NCK2 | NCK2 | NCK2 | 9172 | 0.0052 | 0.32 | NO |
73 | YWHAH | YWHAH | YWHAH | 9245 | 0.0037 | 0.32 | NO |
74 | RHOA | RHOA | RHOA | 9354 | 0.0015 | 0.32 | NO |
75 | RAP1B | RAP1B | RAP1B | 9438 | 0.0002 | 0.31 | NO |
76 | EPS8 | EPS8 | EPS8 | 9612 | -0.0029 | 0.3 | NO |
77 | MAPK8 | MAPK8 | MAPK8 | 9647 | -0.0034 | 0.3 | NO |
78 | MAPK9 | MAPK9 | MAPK9 | 9668 | -0.0038 | 0.3 | NO |
79 | YWHAQ | YWHAQ | YWHAQ | 9697 | -0.0044 | 0.3 | NO |
80 | RAB4A | RAB4A | RAB4A | 9707 | -0.0046 | 0.3 | NO |
81 | MYC | MYC | MYC | 9862 | -0.0077 | 0.29 | NO |
82 | ACTN4 | ACTN4 | ACTN4 | 9988 | -0.0099 | 0.28 | NO |
83 | GRB2 | GRB2 | GRB2 | 10085 | -0.011 | 0.28 | NO |
84 | ACTR2 | ACTR2 | ACTR2 | 10159 | -0.012 | 0.28 | NO |
85 | STAT1 | STAT1 | STAT1 | 10181 | -0.013 | 0.28 | NO |
86 | WASL | WASL | WASL | 10191 | -0.013 | 0.28 | NO |
87 | NCKAP1 | NCKAP1 | NCKAP1 | 10366 | -0.016 | 0.27 | NO |
88 | PPP2R1A | PPP2R1A | PPP2R1A | 10580 | -0.019 | 0.26 | NO |
89 | BAIAP2 | BAIAP2 | BAIAP2 | 10622 | -0.02 | 0.26 | NO |
90 | MAP2K1 | MAP2K1 | MAP2K1 | 10906 | -0.025 | 0.24 | NO |
91 | RAB5A | RAB5A | RAB5A | 10991 | -0.026 | 0.24 | NO |
92 | KRAS | KRAS | KRAS | 10994 | -0.027 | 0.24 | NO |
93 | ABI1 | ABI1 | ABI1 | 11056 | -0.028 | 0.24 | NO |
94 | USP6NL | USP6NL | USP6NL | 11068 | -0.028 | 0.24 | NO |
95 | ARPC2 | ARPC2 | ARPC2 | 11102 | -0.028 | 0.24 | NO |
96 | PIK3R2 | PIK3R2 | PIK3R2 | 11116 | -0.029 | 0.24 | NO |
97 | ARPC1B | ARPC1B | ARPC1B | 11209 | -0.03 | 0.24 | NO |
98 | MAP2K2 | MAP2K2 | MAP2K2 | 11283 | -0.031 | 0.24 | NO |
99 | YWHAG | YWHAG | YWHAG | 11423 | -0.033 | 0.23 | NO |
100 | PPP2CA | PPP2CA | PPP2CA | 11572 | -0.036 | 0.23 | NO |
101 | ACTR3 | ACTR3 | ACTR3 | 11617 | -0.036 | 0.23 | NO |
102 | CSK | CSK | CSK | 11637 | -0.036 | 0.23 | NO |
103 | ARPC5 | ARPC5 | ARPC5 | 11780 | -0.039 | 0.22 | NO |
104 | MAPK3 | MAPK3 | MAPK3 | 11852 | -0.04 | 0.22 | NO |
105 | ARHGDIA | ARHGDIA | ARHGDIA | 11854 | -0.04 | 0.23 | NO |
106 | ARPC4 | ARPC4 | ARPC4 | 12247 | -0.046 | 0.21 | NO |
107 | LYN | LYN | LYN | 12568 | -0.052 | 0.2 | NO |
108 | RAC1 | RAC1 | RAC1 | 12692 | -0.054 | 0.19 | NO |
109 | YWHAB | YWHAB | YWHAB | 12844 | -0.057 | 0.19 | NO |
110 | PIK3CB | PIK3CB | PIK3CB | 13345 | -0.066 | 0.16 | NO |
111 | ARPC3 | ARPC3 | ARPC3 | 13376 | -0.066 | 0.17 | NO |
112 | MLLT4 | MLLT4 | MLLT4 | 13640 | -0.071 | 0.16 | NO |
113 | DNM2 | DNM2 | DNM2 | 13653 | -0.072 | 0.16 | NO |
114 | PTPN2 | PTPN2 | PTPN2 | 13830 | -0.076 | 0.16 | NO |
115 | CTTN | CTTN | CTTN | 14029 | -0.079 | 0.15 | NO |
116 | NRAS | NRAS | NRAS | 14079 | -0.08 | 0.16 | NO |
117 | BCAR1 | BCAR1 | BCAR1 | 14134 | -0.082 | 0.16 | NO |
118 | PAK1 | PAK1 | PAK1 | 14234 | -0.084 | 0.16 | NO |
119 | YWHAZ | YWHAZ | YWHAZ | 14238 | -0.084 | 0.16 | NO |
120 | YWHAE | YWHAE | YWHAE | 14434 | -0.088 | 0.16 | NO |
121 | YES1 | YES1 | YES1 | 14468 | -0.088 | 0.16 | NO |
122 | HRAS | HRAS | HRAS | 14495 | -0.089 | 0.17 | NO |
123 | VAV2 | VAV2 | VAV2 | 15267 | -0.11 | 0.14 | NO |
124 | SRC | SRC | SRC | 15271 | -0.11 | 0.14 | NO |
125 | PRKCD | PRKCD | PRKCD | 15704 | -0.12 | 0.13 | NO |
126 | SLC9A3R1 | SLC9A3R1 | SLC9A3R1 | 17013 | -0.18 | 0.069 | NO |
127 | SFN | SFN | SFN | 18304 | -0.3 | 0.02 | 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 ERBB SIGNALING PATHWAY.

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

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 | IGF1 | IGF1 | IGF1 | 205 | 0.82 | 0.19 | YES |
2 | PIK3CG | PIK3CG | PIK3CG | 1485 | 0.42 | 0.22 | YES |
3 | MEF2C | MEF2C | MEF2C | 1496 | 0.42 | 0.32 | YES |
4 | NFATC1 | NFATC1 | NFATC1 | 2546 | 0.29 | 0.34 | YES |
5 | CAMK1 | CAMK1 | CAMK1 | 3263 | 0.22 | 0.35 | YES |
6 | CAMK1G | CAMK1G | CAMK1G | 3337 | 0.22 | 0.4 | YES |
7 | PIK3R1 | PIK3R1 | PIK3R1 | 3462 | 0.21 | 0.44 | YES |
8 | MEF2A | MEF2A | MEF2A | 3620 | 0.2 | 0.48 | YES |
9 | IGF1R | IGF1R | IGF1R | 3880 | 0.18 | 0.51 | YES |
10 | NFATC2 | NFATC2 | NFATC2 | 4324 | 0.15 | 0.53 | YES |
11 | HDAC5 | HDAC5 | HDAC5 | 4356 | 0.15 | 0.56 | YES |
12 | PPP3CC | PPP3CC | PPP3CC | 4501 | 0.14 | 0.59 | YES |
13 | PPP3CB | PPP3CB | PPP3CB | 4635 | 0.14 | 0.61 | YES |
14 | MEF2D | MEF2D | MEF2D | 4661 | 0.13 | 0.64 | YES |
15 | PIK3CA | PIK3CA | PIK3CA | 5049 | 0.12 | 0.65 | YES |
16 | INSR | INSR | INSR | 6303 | 0.069 | 0.6 | NO |
17 | CALM1 | CALM1 | CALM1 | 7097 | 0.047 | 0.57 | NO |
18 | MAPK7 | MAPK7 | MAPK7 | 7205 | 0.045 | 0.57 | NO |
19 | CABIN1 | CABIN1 | CABIN1 | 7418 | 0.04 | 0.57 | NO |
20 | MAPK14 | MAPK14 | MAPK14 | 7542 | 0.037 | 0.58 | NO |
21 | PPP3CA | PPP3CA | PPP3CA | 7708 | 0.033 | 0.57 | NO |
22 | YWHAH | YWHAH | YWHAH | 9245 | 0.0037 | 0.49 | NO |
23 | AKT1 | AKT1 | AKT1 | 9288 | 0.0029 | 0.49 | NO |
24 | CALM3 | CALM3 | CALM3 | 9767 | -0.0058 | 0.47 | NO |
25 | CALM2 | CALM2 | CALM2 | 9971 | -0.0096 | 0.46 | NO |
26 | MAP2K6 | MAP2K6 | MAP2K6 | 11353 | -0.032 | 0.39 | 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 CALCIUM SIGNALING PATHWAY.

Figure S34. 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 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 | NGFR | NGFR | NGFR | 61 | 0.94 | 0.03 | YES |
2 | ADCY5 | ADCY5 | ADCY5 | 160 | 0.85 | 0.054 | YES |
3 | ADCY2 | ADCY2 | ADCY2 | 261 | 0.78 | 0.076 | YES |
4 | ADCYAP1R1 | ADCYAP1R1 | ADCYAP1R1 | 314 | 0.74 | 0.099 | YES |
5 | ADCYAP1 | ADCYAP1 | ADCYAP1 | 320 | 0.74 | 0.12 | YES |
6 | PDE1A | PDE1A | PDE1A | 342 | 0.72 | 0.15 | YES |
7 | PDE1B | PDE1B | PDE1B | 515 | 0.66 | 0.16 | YES |
8 | NGF | NGF | NGF | 624 | 0.62 | 0.18 | YES |
9 | PRKAR2B | PRKAR2B | PRKAR2B | 828 | 0.55 | 0.19 | YES |
10 | NTRK1 | NTRK1 | NTRK1 | 953 | 0.52 | 0.2 | YES |
11 | NTRK2 | NTRK2 | NTRK2 | 994 | 0.52 | 0.21 | YES |
12 | AKT3 | AKT3 | AKT3 | 1032 | 0.51 | 0.23 | YES |
13 | CAMK4 | CAMK4 | CAMK4 | 1118 | 0.49 | 0.24 | YES |
14 | MEF2C | MEF2C | MEF2C | 1496 | 0.42 | 0.24 | YES |
15 | ADCY4 | ADCY4 | ADCY4 | 1577 | 0.41 | 0.25 | YES |
16 | RASGRF2 | RASGRF2 | RASGRF2 | 1659 | 0.4 | 0.26 | YES |
17 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 1702 | 0.39 | 0.27 | YES |
18 | SORCS3 | SORCS3 | SORCS3 | 1783 | 0.38 | 0.28 | YES |
19 | MCF2 | MCF2 | MCF2 | 1814 | 0.37 | 0.29 | YES |
20 | FGD2 | FGD2 | FGD2 | 1925 | 0.36 | 0.29 | YES |
21 | ARHGEF4 | ARHGEF4 | ARHGEF4 | 2109 | 0.34 | 0.3 | YES |
22 | SHC2 | SHC2 | SHC2 | 2257 | 0.32 | 0.3 | YES |
23 | TIAM1 | TIAM1 | TIAM1 | 2288 | 0.32 | 0.31 | YES |
24 | ARHGEF17 | ARHGEF17 | ARHGEF17 | 2380 | 0.3 | 0.31 | YES |
25 | FGD1 | FGD1 | FGD1 | 2387 | 0.3 | 0.32 | YES |
26 | VAV1 | VAV1 | VAV1 | 2681 | 0.27 | 0.32 | YES |
27 | MAPK11 | MAPK11 | MAPK11 | 2763 | 0.26 | 0.32 | YES |
28 | PRKACB | PRKACB | PRKACB | 2792 | 0.26 | 0.33 | YES |
29 | SHC3 | SHC3 | SHC3 | 2952 | 0.25 | 0.33 | YES |
30 | ADORA2A | ADORA2A | ADORA2A | 3000 | 0.24 | 0.34 | YES |
31 | ADCY9 | ADCY9 | ADCY9 | 3153 | 0.23 | 0.34 | YES |
32 | NGFRAP1 | NGFRAP1 | NGFRAP1 | 3281 | 0.22 | 0.34 | YES |
33 | SH3GL2 | SH3GL2 | SH3GL2 | 3411 | 0.21 | 0.34 | YES |
34 | PIK3R1 | PIK3R1 | PIK3R1 | 3462 | 0.21 | 0.34 | YES |
35 | ITPR2 | ITPR2 | ITPR2 | 3504 | 0.21 | 0.35 | YES |
36 | FGD3 | FGD3 | FGD3 | 3581 | 0.2 | 0.35 | YES |
37 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 3585 | 0.2 | 0.36 | YES |
38 | MEF2A | MEF2A | MEF2A | 3620 | 0.2 | 0.36 | YES |
39 | MAG | MAG | MAG | 3647 | 0.2 | 0.37 | YES |
40 | IRS2 | IRS2 | IRS2 | 3649 | 0.2 | 0.38 | YES |
41 | ARHGEF9 | ARHGEF9 | ARHGEF9 | 3655 | 0.2 | 0.38 | YES |
42 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3709 | 0.19 | 0.38 | YES |
43 | IRS1 | IRS1 | IRS1 | 3781 | 0.19 | 0.39 | YES |
44 | DNM1 | DNM1 | DNM1 | 3847 | 0.18 | 0.39 | YES |
45 | PREX1 | PREX1 | PREX1 | 3857 | 0.18 | 0.4 | YES |
46 | PRKCE | PRKCE | PRKCE | 4134 | 0.16 | 0.39 | YES |
47 | OMG | OMG | OMG | 4201 | 0.16 | 0.39 | YES |
48 | FOXO4 | FOXO4 | FOXO4 | 4292 | 0.15 | 0.39 | YES |
49 | APH1B | APH1B | APH1B | 4327 | 0.15 | 0.39 | YES |
50 | DUSP3 | DUSP3 | DUSP3 | 4358 | 0.15 | 0.4 | YES |
51 | TRIO | TRIO | TRIO | 4421 | 0.15 | 0.4 | YES |
52 | ADCY8 | ADCY8 | ADCY8 | 4557 | 0.14 | 0.4 | YES |
53 | FOXO1 | FOXO1 | FOXO1 | 4563 | 0.14 | 0.4 | YES |
54 | PLEKHG2 | PLEKHG2 | PLEKHG2 | 4656 | 0.13 | 0.4 | YES |
55 | ADCY1 | ADCY1 | ADCY1 | 4693 | 0.13 | 0.4 | YES |
56 | RAP1A | RAP1A | RAP1A | 5026 | 0.12 | 0.39 | YES |
57 | PIK3CA | PIK3CA | PIK3CA | 5049 | 0.12 | 0.39 | YES |
58 | ITSN1 | ITSN1 | ITSN1 | 5055 | 0.12 | 0.4 | YES |
59 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5155 | 0.11 | 0.4 | YES |
60 | MAP2K5 | MAP2K5 | MAP2K5 | 5197 | 0.11 | 0.4 | YES |
61 | ARHGEF3 | ARHGEF3 | ARHGEF3 | 5211 | 0.11 | 0.4 | YES |
62 | PRKCG | PRKCG | PRKCG | 5226 | 0.11 | 0.4 | YES |
63 | TRAF6 | TRAF6 | TRAF6 | 5311 | 0.1 | 0.4 | YES |
64 | PTEN | PTEN | PTEN | 5404 | 0.1 | 0.4 | YES |
65 | PCSK5 | PCSK5 | PCSK5 | 5414 | 0.1 | 0.4 | YES |
66 | PRKCA | PRKCA | PRKCA | 5442 | 0.099 | 0.4 | YES |
67 | ADCY7 | ADCY7 | ADCY7 | 5533 | 0.095 | 0.4 | YES |
68 | NR4A1 | NR4A1 | NR4A1 | 5545 | 0.095 | 0.41 | YES |
69 | KIDINS220 | KIDINS220 | KIDINS220 | 5553 | 0.094 | 0.41 | YES |
70 | CDKN1B | CDKN1B | CDKN1B | 5721 | 0.088 | 0.4 | YES |
71 | ADCY3 | ADCY3 | ADCY3 | 5752 | 0.087 | 0.4 | YES |
72 | RTN4 | RTN4 | RTN4 | 5800 | 0.085 | 0.4 | YES |
73 | PRKACA | PRKACA | PRKACA | 5809 | 0.085 | 0.41 | YES |
74 | MAPK12 | MAPK12 | MAPK12 | 5814 | 0.085 | 0.41 | YES |
75 | PLCG1 | PLCG1 | PLCG1 | 5848 | 0.084 | 0.41 | YES |
76 | ARHGAP4 | ARHGAP4 | ARHGAP4 | 5936 | 0.08 | 0.41 | YES |
77 | SOS2 | SOS2 | SOS2 | 5938 | 0.08 | 0.41 | YES |
78 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 6033 | 0.077 | 0.41 | YES |
79 | SOS1 | SOS1 | SOS1 | 6105 | 0.075 | 0.41 | YES |
80 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 6145 | 0.074 | 0.41 | YES |
81 | PRKAR2A | PRKAR2A | PRKAR2A | 6208 | 0.072 | 0.41 | YES |
82 | TSC2 | TSC2 | TSC2 | 6211 | 0.072 | 0.41 | YES |
83 | KALRN | KALRN | KALRN | 6218 | 0.072 | 0.41 | YES |
84 | RASGRF1 | RASGRF1 | RASGRF1 | 6248 | 0.071 | 0.41 | YES |
85 | AKAP13 | AKAP13 | AKAP13 | 6414 | 0.066 | 0.41 | NO |
86 | OBSCN | OBSCN | OBSCN | 6583 | 0.061 | 0.4 | NO |
87 | BRAF | BRAF | BRAF | 6609 | 0.06 | 0.4 | NO |
88 | STAT3 | STAT3 | STAT3 | 6623 | 0.06 | 0.4 | NO |
89 | PRKAR1A | PRKAR1A | PRKAR1A | 6674 | 0.058 | 0.4 | NO |
90 | CREB1 | CREB1 | CREB1 | 6736 | 0.057 | 0.4 | NO |
91 | NFKBIA | NFKBIA | NFKBIA | 6744 | 0.056 | 0.4 | NO |
92 | ARHGEF18 | ARHGEF18 | ARHGEF18 | 6874 | 0.052 | 0.4 | NO |
93 | PDPK1 | PDPK1 | PDPK1 | 7090 | 0.047 | 0.39 | NO |
94 | CALM1 | CALM1 | CALM1 | 7097 | 0.047 | 0.39 | NO |
95 | IKBKB | IKBKB | IKBKB | 7146 | 0.046 | 0.39 | NO |
96 | RICTOR | RICTOR | RICTOR | 7155 | 0.046 | 0.39 | NO |
97 | MAPK7 | MAPK7 | MAPK7 | 7205 | 0.045 | 0.39 | NO |
98 | AKT2 | AKT2 | AKT2 | 7332 | 0.042 | 0.38 | NO |
99 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 7337 | 0.041 | 0.38 | NO |
100 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 7396 | 0.04 | 0.38 | NO |
101 | ELK1 | ELK1 | ELK1 | 7440 | 0.039 | 0.38 | NO |
102 | AP2A2 | AP2A2 | AP2A2 | 7473 | 0.038 | 0.38 | NO |
103 | FOXO3 | FOXO3 | FOXO3 | 7485 | 0.038 | 0.38 | NO |
104 | MAPK14 | MAPK14 | MAPK14 | 7542 | 0.037 | 0.38 | NO |
105 | FRS2 | FRS2 | FRS2 | 7782 | 0.032 | 0.37 | NO |
106 | ABR | ABR | ABR | 7791 | 0.031 | 0.37 | NO |
107 | MAPK1 | MAPK1 | MAPK1 | 8166 | 0.024 | 0.35 | NO |
108 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 8189 | 0.023 | 0.35 | NO |
109 | AP2A1 | AP2A1 | AP2A1 | 8328 | 0.021 | 0.34 | NO |
110 | MAGED1 | MAGED1 | MAGED1 | 8376 | 0.02 | 0.34 | NO |
111 | SHC1 | SHC1 | SHC1 | 8385 | 0.019 | 0.34 | NO |
112 | VAV3 | VAV3 | VAV3 | 8623 | 0.015 | 0.33 | NO |
113 | DUSP6 | DUSP6 | DUSP6 | 8625 | 0.015 | 0.33 | NO |
114 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 8859 | 0.011 | 0.32 | NO |
115 | CRK | CRK | CRK | 8934 | 0.0094 | 0.31 | NO |
116 | BCL2L11 | BCL2L11 | BCL2L11 | 8939 | 0.0092 | 0.31 | NO |
117 | RAF1 | RAF1 | RAF1 | 9003 | 0.0082 | 0.31 | NO |
118 | RELA | RELA | RELA | 9063 | 0.0069 | 0.31 | NO |
119 | RALGDS | RALGDS | RALGDS | 9090 | 0.0066 | 0.3 | NO |
120 | AP2M1 | AP2M1 | AP2M1 | 9180 | 0.0051 | 0.3 | NO |
121 | RIT1 | RIT1 | RIT1 | 9248 | 0.0037 | 0.3 | NO |
122 | PPP2CB | PPP2CB | PPP2CB | 9249 | 0.0036 | 0.3 | NO |
123 | AKT1 | AKT1 | AKT1 | 9288 | 0.0029 | 0.3 | NO |
124 | MTOR | MTOR | MTOR | 9314 | 0.0024 | 0.29 | NO |
125 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 9319 | 0.0023 | 0.29 | NO |
126 | RHOA | RHOA | RHOA | 9354 | 0.0015 | 0.29 | NO |
127 | HDAC3 | HDAC3 | HDAC3 | 9560 | -0.0018 | 0.28 | NO |
128 | PRKAR1B | PRKAR1B | PRKAR1B | 9587 | -0.0024 | 0.28 | NO |
129 | MDM2 | MDM2 | MDM2 | 9639 | -0.0032 | 0.28 | NO |
130 | MAPK8 | MAPK8 | MAPK8 | 9647 | -0.0034 | 0.28 | NO |
131 | CALM3 | CALM3 | CALM3 | 9767 | -0.0058 | 0.27 | NO |
132 | BAD | BAD | BAD | 9784 | -0.0062 | 0.27 | NO |
133 | ADCY6 | ADCY6 | ADCY6 | 9896 | -0.0082 | 0.26 | NO |
134 | CDKN1A | CDKN1A | CDKN1A | 9949 | -0.0091 | 0.26 | NO |
135 | CALM2 | CALM2 | CALM2 | 9971 | -0.0096 | 0.26 | NO |
136 | CASP9 | CASP9 | CASP9 | 9989 | -0.0099 | 0.26 | NO |
137 | ADAM17 | ADAM17 | ADAM17 | 10054 | -0.011 | 0.26 | NO |
138 | RPS27A | RPS27A | RPS27A | 10077 | -0.011 | 0.26 | NO |
139 | GRB2 | GRB2 | GRB2 | 10085 | -0.011 | 0.26 | NO |
140 | FGD4 | FGD4 | FGD4 | 10248 | -0.014 | 0.25 | NO |
141 | SQSTM1 | SQSTM1 | SQSTM1 | 10263 | -0.014 | 0.25 | NO |
142 | UBA52 | UBA52 | UBA52 | 10288 | -0.015 | 0.25 | NO |
143 | ATF1 | ATF1 | ATF1 | 10465 | -0.018 | 0.24 | NO |
144 | PPP2R1A | PPP2R1A | PPP2R1A | 10580 | -0.019 | 0.23 | NO |
145 | AP2B1 | AP2B1 | AP2B1 | 10648 | -0.02 | 0.23 | NO |
146 | DUSP7 | DUSP7 | DUSP7 | 10697 | -0.021 | 0.23 | NO |
147 | THEM4 | THEM4 | THEM4 | 10796 | -0.023 | 0.22 | NO |
148 | MAP2K1 | MAP2K1 | MAP2K1 | 10906 | -0.025 | 0.22 | NO |
149 | PPP2R5D | PPP2R5D | PPP2R5D | 10979 | -0.026 | 0.22 | NO |
150 | KRAS | KRAS | KRAS | 10994 | -0.027 | 0.22 | NO |
151 | MYD88 | MYD88 | MYD88 | 11003 | -0.027 | 0.22 | NO |
152 | AKT1S1 | AKT1S1 | AKT1S1 | 11074 | -0.028 | 0.21 | NO |
153 | PIK3R2 | PIK3R2 | PIK3R2 | 11116 | -0.029 | 0.21 | NO |
154 | MAP2K2 | MAP2K2 | MAP2K2 | 11283 | -0.031 | 0.2 | NO |
155 | PRDM4 | PRDM4 | PRDM4 | 11305 | -0.031 | 0.2 | NO |
156 | ADRBK1 | ADRBK1 | ADRBK1 | 11340 | -0.032 | 0.2 | NO |
157 | CASP2 | CASP2 | CASP2 | 11381 | -0.032 | 0.2 | NO |
158 | PSEN2 | PSEN2 | PSEN2 | 11459 | -0.034 | 0.2 | NO |
159 | PPP2CA | PPP2CA | PPP2CA | 11572 | -0.036 | 0.19 | NO |
160 | CLTC | CLTC | CLTC | 11636 | -0.036 | 0.19 | NO |
161 | GSK3A | GSK3A | GSK3A | 11704 | -0.038 | 0.19 | NO |
162 | MAPK3 | MAPK3 | MAPK3 | 11852 | -0.04 | 0.18 | NO |
163 | ARHGDIA | ARHGDIA | ARHGDIA | 11854 | -0.04 | 0.18 | NO |
164 | IRAK1 | IRAK1 | IRAK1 | 12231 | -0.046 | 0.16 | NO |
165 | TIAM2 | TIAM2 | TIAM2 | 12381 | -0.049 | 0.16 | NO |
166 | PHLPP1 | PHLPP1 | PHLPP1 | 12525 | -0.051 | 0.15 | NO |
167 | CHUK | CHUK | CHUK | 12593 | -0.052 | 0.15 | NO |
168 | MLST8 | MLST8 | MLST8 | 12618 | -0.053 | 0.15 | NO |
169 | RALB | RALB | RALB | 12673 | -0.054 | 0.15 | NO |
170 | RAC1 | RAC1 | RAC1 | 12692 | -0.054 | 0.15 | NO |
171 | NET1 | NET1 | NET1 | 12709 | -0.054 | 0.15 | NO |
172 | LINGO1 | LINGO1 | LINGO1 | 12795 | -0.056 | 0.15 | NO |
173 | YWHAB | YWHAB | YWHAB | 12844 | -0.057 | 0.15 | NO |
174 | FURIN | FURIN | FURIN | 12860 | -0.057 | 0.15 | NO |
175 | PSEN1 | PSEN1 | PSEN1 | 12918 | -0.058 | 0.15 | NO |
176 | APH1A | APH1A | APH1A | 13001 | -0.06 | 0.15 | NO |
177 | PIK3CB | PIK3CB | PIK3CB | 13345 | -0.066 | 0.13 | NO |
178 | AATF | AATF | AATF | 13388 | -0.067 | 0.13 | NO |
179 | NCSTN | NCSTN | NCSTN | 13490 | -0.069 | 0.13 | NO |
180 | AP2S1 | AP2S1 | AP2S1 | 13564 | -0.07 | 0.13 | NO |
181 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 13598 | -0.071 | 0.13 | NO |
182 | DNAL4 | DNAL4 | DNAL4 | 13635 | -0.071 | 0.13 | NO |
183 | DNM2 | DNM2 | DNM2 | 13653 | -0.072 | 0.13 | NO |
184 | CLTA | CLTA | CLTA | 13722 | -0.073 | 0.13 | NO |
185 | HDAC2 | HDAC2 | HDAC2 | 13896 | -0.077 | 0.12 | NO |
186 | NRAS | NRAS | NRAS | 14079 | -0.08 | 0.12 | NO |
187 | PSENEN | PSENEN | PSENEN | 14287 | -0.084 | 0.11 | NO |
188 | PRKACG | PRKACG | PRKACG | 14345 | -0.086 | 0.11 | NO |
189 | YWHAE | YWHAE | YWHAE | 14434 | -0.088 | 0.1 | NO |
190 | HRAS | HRAS | HRAS | 14495 | -0.089 | 0.1 | NO |
191 | PRKCI | PRKCI | PRKCI | 14591 | -0.091 | 0.1 | NO |
192 | DUSP4 | DUSP4 | DUSP4 | 14625 | -0.092 | 0.1 | NO |
193 | HDAC1 | HDAC1 | HDAC1 | 14631 | -0.092 | 0.11 | NO |
194 | RIPK2 | RIPK2 | RIPK2 | 14667 | -0.093 | 0.11 | NO |
195 | RALA | RALA | RALA | 15022 | -0.1 | 0.092 | NO |
196 | PPP2R1B | PPP2R1B | PPP2R1B | 15172 | -0.11 | 0.088 | NO |
197 | SRC | SRC | SRC | 15271 | -0.11 | 0.087 | NO |
198 | ITGB3BP | ITGB3BP | ITGB3BP | 15414 | -0.11 | 0.083 | NO |
199 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 15545 | -0.12 | 0.08 | NO |
200 | CASP3 | CASP3 | CASP3 | 15637 | -0.12 | 0.08 | NO |
201 | PRKCD | PRKCD | PRKCD | 15704 | -0.12 | 0.08 | NO |
202 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 15741 | -0.12 | 0.083 | NO |
203 | ITPR3 | ITPR3 | ITPR3 | 15966 | -0.13 | 0.075 | NO |
204 | SMPD2 | SMPD2 | SMPD2 | 16415 | -0.15 | 0.056 | NO |
205 | NGEF | NGEF | NGEF | 17283 | -0.2 | 0.016 | NO |
206 | ECT2 | ECT2 | ECT2 | 17594 | -0.22 | 0.0072 | NO |
207 | MAPK13 | MAPK13 | MAPK13 | 17652 | -0.23 | 0.012 | NO |
208 | PCSK6 | PCSK6 | PCSK6 | 17906 | -0.25 | 0.0072 | NO |
209 | CDK1 | CDK1 | CDK1 | 18076 | -0.27 | 0.0075 | NO |
210 | ARHGEF16 | ARHGEF16 | ARHGEF16 | 18425 | -0.33 | 0.00023 | NO |
211 | TRIB3 | TRIB3 | TRIB3 | 18564 | -0.38 | 0.006 | 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 | BMX | BMX | BMX | 605 | 0.62 | 0.063 | YES |
2 | KLF8 | KLF8 | KLF8 | 733 | 0.58 | 0.15 | YES |
3 | ACTA1 | ACTA1 | ACTA1 | 1547 | 0.41 | 0.16 | YES |
4 | ELMO1 | ELMO1 | ELMO1 | 2395 | 0.3 | 0.17 | YES |
5 | ITGA5 | ITGA5 | ITGA5 | 2697 | 0.27 | 0.19 | YES |
6 | ACTN1 | ACTN1 | ACTN1 | 3225 | 0.23 | 0.2 | YES |
7 | TLN1 | TLN1 | TLN1 | 3228 | 0.23 | 0.23 | YES |
8 | PIK3R1 | PIK3R1 | PIK3R1 | 3462 | 0.21 | 0.25 | YES |
9 | FYN | FYN | FYN | 3593 | 0.2 | 0.28 | YES |
10 | VCL | VCL | VCL | 3628 | 0.2 | 0.3 | YES |
11 | PTPN21 | PTPN21 | PTPN21 | 3777 | 0.19 | 0.32 | YES |
12 | GIT2 | GIT2 | GIT2 | 3915 | 0.18 | 0.34 | YES |
13 | ETS1 | ETS1 | ETS1 | 3924 | 0.18 | 0.37 | YES |
14 | RRAS | RRAS | RRAS | 3959 | 0.17 | 0.4 | YES |
15 | RAP1A | RAP1A | RAP1A | 5026 | 0.12 | 0.36 | YES |
16 | ITGAV | ITGAV | ITGAV | 5029 | 0.12 | 0.38 | YES |
17 | PIK3CA | PIK3CA | PIK3CA | 5049 | 0.12 | 0.39 | YES |
18 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5155 | 0.11 | 0.4 | YES |
19 | DOCK1 | DOCK1 | DOCK1 | 5496 | 0.096 | 0.4 | YES |
20 | ASAP1 | ASAP1 | ASAP1 | 5588 | 0.093 | 0.41 | YES |
21 | ITGB1 | ITGB1 | ITGB1 | 5781 | 0.086 | 0.41 | YES |
22 | JUN | JUN | JUN | 5808 | 0.085 | 0.42 | YES |
23 | PLCG1 | PLCG1 | PLCG1 | 5848 | 0.084 | 0.43 | YES |
24 | SOS1 | SOS1 | SOS1 | 6105 | 0.075 | 0.43 | YES |
25 | MMP14 | MMP14 | MMP14 | 6407 | 0.066 | 0.42 | YES |
26 | ITGB5 | ITGB5 | ITGB5 | 6531 | 0.063 | 0.43 | YES |
27 | BRAF | BRAF | BRAF | 6609 | 0.06 | 0.43 | YES |
28 | RASA1 | RASA1 | RASA1 | 6682 | 0.058 | 0.44 | YES |
29 | ROCK2 | ROCK2 | ROCK2 | 6777 | 0.055 | 0.44 | YES |
30 | NCK1 | NCK1 | NCK1 | 6871 | 0.053 | 0.44 | YES |
31 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 8162 | 0.024 | 0.38 | NO |
32 | MAPK1 | MAPK1 | MAPK1 | 8166 | 0.024 | 0.38 | NO |
33 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 8220 | 0.023 | 0.38 | NO |
34 | RGNEF | RGNEF | RGNEF | 8351 | 0.02 | 0.38 | NO |
35 | MAP2K4 | MAP2K4 | MAP2K4 | 8745 | 0.013 | 0.36 | NO |
36 | CRK | CRK | CRK | 8934 | 0.0094 | 0.35 | NO |
37 | RAF1 | RAF1 | RAF1 | 9003 | 0.0082 | 0.35 | NO |
38 | ARHGAP26 | ARHGAP26 | ARHGAP26 | 9154 | 0.0055 | 0.34 | NO |
39 | NCK2 | NCK2 | NCK2 | 9172 | 0.0052 | 0.34 | NO |
40 | PXN | PXN | PXN | 9205 | 0.0044 | 0.34 | NO |
41 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 9319 | 0.0023 | 0.34 | NO |
42 | CAPN2 | CAPN2 | CAPN2 | 9330 | 0.0021 | 0.34 | NO |
43 | RHOA | RHOA | RHOA | 9354 | 0.0015 | 0.33 | NO |
44 | RAP1B | RAP1B | RAP1B | 9438 | 0.0002 | 0.33 | NO |
45 | MAPK8 | MAPK8 | MAPK8 | 9647 | -0.0034 | 0.32 | NO |
46 | MAPK9 | MAPK9 | MAPK9 | 9668 | -0.0038 | 0.32 | NO |
47 | GRB2 | GRB2 | GRB2 | 10085 | -0.011 | 0.3 | NO |
48 | WASL | WASL | WASL | 10191 | -0.013 | 0.29 | NO |
49 | MAP2K1 | MAP2K1 | MAP2K1 | 10906 | -0.025 | 0.26 | NO |
50 | PTK2 | PTK2 | PTK2 | 11957 | -0.042 | 0.21 | NO |
51 | SH3GL1 | SH3GL1 | SH3GL1 | 11968 | -0.042 | 0.22 | NO |
52 | RAC1 | RAC1 | RAC1 | 12692 | -0.054 | 0.18 | NO |
53 | BCAR1 | BCAR1 | BCAR1 | 14134 | -0.082 | 0.12 | NO |
54 | PAK1 | PAK1 | PAK1 | 14234 | -0.084 | 0.13 | NO |
55 | YES1 | YES1 | YES1 | 14468 | -0.088 | 0.13 | NO |
56 | SRC | SRC | SRC | 15271 | -0.11 | 0.1 | NO |
57 | CCND1 | CCND1 | CCND1 | 15715 | -0.12 | 0.098 | NO |
58 | GRB7 | GRB7 | GRB7 | 18603 | -0.4 | 0.0038 | 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 PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, 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 | CNR1 | CNR1 | CNR1 | 201 | 0.82 | 0.15 | YES |
2 | GAP43 | GAP43 | GAP43 | 459 | 0.67 | 0.27 | YES |
3 | FGFR1 | FGFR1 | FGFR1 | 1271 | 0.46 | 0.32 | YES |
4 | CDH2 | CDH2 | CDH2 | 1556 | 0.41 | 0.38 | YES |
5 | FER | FER | FER | 2222 | 0.32 | 0.41 | YES |
6 | GRIA2 | GRIA2 | GRIA2 | 2807 | 0.26 | 0.43 | YES |
7 | GJA1 | GJA1 | GJA1 | 2844 | 0.26 | 0.48 | YES |
8 | GSN | GSN | GSN | 3066 | 0.24 | 0.52 | YES |
9 | PIK3R1 | PIK3R1 | PIK3R1 | 3462 | 0.21 | 0.54 | YES |
10 | PIP5K1C | PIP5K1C | PIP5K1C | 3654 | 0.2 | 0.57 | YES |
11 | CAMK2G | CAMK2G | CAMK2G | 4747 | 0.13 | 0.54 | NO |
12 | PIK3CA | PIK3CA | PIK3CA | 5049 | 0.12 | 0.54 | NO |
13 | PLCG1 | PLCG1 | PLCG1 | 5848 | 0.084 | 0.52 | NO |
14 | ROCK1 | ROCK1 | ROCK1 | 6056 | 0.076 | 0.52 | NO |
15 | PTPN11 | PTPN11 | PTPN11 | 7377 | 0.041 | 0.46 | NO |
16 | DCTN1 | DCTN1 | DCTN1 | 7496 | 0.038 | 0.46 | NO |
17 | PTPN1 | PTPN1 | PTPN1 | 8659 | 0.014 | 0.4 | NO |
18 | MYL2 | MYL2 | MYL2 | 8757 | 0.013 | 0.4 | NO |
19 | RHOA | RHOA | RHOA | 9354 | 0.0015 | 0.36 | NO |
20 | MAPK8 | MAPK8 | MAPK8 | 9647 | -0.0034 | 0.35 | NO |
21 | KIF5B | KIF5B | KIF5B | 9746 | -0.0053 | 0.34 | NO |
22 | CTNNB1 | CTNNB1 | CTNNB1 | 9763 | -0.0057 | 0.34 | NO |
23 | CDC42 | CDC42 | CDC42 | 9840 | -0.0072 | 0.34 | NO |
24 | CTNNA1 | CTNNA1 | CTNNA1 | 10375 | -0.016 | 0.32 | NO |
25 | AXIN1 | AXIN1 | AXIN1 | 10457 | -0.018 | 0.32 | NO |
26 | MAPRE1 | MAPRE1 | MAPRE1 | 10544 | -0.019 | 0.32 | NO |
27 | RAC1 | RAC1 | RAC1 | 12692 | -0.054 | 0.21 | NO |
28 | CTNND1 | CTNND1 | CTNND1 | 12802 | -0.056 | 0.22 | NO |
29 | LRP5 | LRP5 | LRP5 | 12937 | -0.058 | 0.22 | NO |
30 | DAGLB | DAGLB | DAGLB | 13006 | -0.06 | 0.23 | NO |
31 | CTTN | CTTN | CTTN | 14029 | -0.079 | 0.19 | NO |
32 | DAGLA | DAGLA | DAGLA | 14385 | -0.086 | 0.19 | NO |
33 | JUP | JUP | JUP | 17483 | -0.21 | 0.064 | 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 NEUROACTIVE LIGAND RECEPTOR INTERACTION.

Figure S40. 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

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 PYRIMIDINE METABOLISM | 98 | genes.ES.table | 0.35 | 1.5 | 0.065 | 0.16 | 0.99 | 0.36 | 0.16 | 0.3 | 0.1 | 0.003 |
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.48 | 1.6 | 0.11 | 0.13 | 0.98 | 0.54 | 0.26 | 0.4 | 0.071 | 0.003 |
KEGG RIBOSOME | 86 | genes.ES.table | 0.61 | 1.7 | 0.051 | 0.08 | 0.87 | 0.79 | 0.26 | 0.59 | 0.035 | 0.004 |
KEGG RNA DEGRADATION | 57 | genes.ES.table | 0.36 | 1.4 | 0.15 | 0.22 | 1 | 0.47 | 0.24 | 0.36 | 0.15 | 0.004 |
KEGG RNA POLYMERASE | 29 | genes.ES.table | 0.59 | 2 | 0.016 | 0.038 | 0.29 | 0.62 | 0.28 | 0.45 | 0 | 0.005 |
KEGG DNA REPLICATION | 36 | genes.ES.table | 0.62 | 1.6 | 0.063 | 0.12 | 0.97 | 0.64 | 0.19 | 0.52 | 0.06 | 0.003 |
KEGG SPLICEOSOME | 114 | genes.ES.table | 0.42 | 1.7 | 0.084 | 0.089 | 0.91 | 0.6 | 0.3 | 0.42 | 0.041 | 0.004 |
KEGG PROTEASOME | 43 | genes.ES.table | 0.61 | 1.7 | 0.032 | 0.064 | 0.74 | 0.81 | 0.28 | 0.59 | 0.024 | 0.004 |
KEGG NUCLEOTIDE EXCISION REPAIR | 44 | genes.ES.table | 0.57 | 2.1 | 0.004 | 0.036 | 0.13 | 0.5 | 0.19 | 0.4 | 0 | 0.009 |
KEGG CELL CYCLE | 118 | genes.ES.table | 0.46 | 1.7 | 0.054 | 0.079 | 0.87 | 0.42 | 0.16 | 0.36 | 0.034 | 0.004 |
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 | CDC25A | CDC25A | CDC25A | 603 | 0.14 | 0.016 | YES |
2 | PKMYT1 | PKMYT1 | PKMYT1 | 740 | 0.12 | 0.052 | YES |
3 | CDK7 | CDK7 | CDK7 | 801 | 0.12 | 0.089 | YES |
4 | CCNA2 | CCNA2 | CCNA2 | 839 | 0.12 | 0.13 | YES |
5 | PSMB10 | PSMB10 | PSMB10 | 905 | 0.11 | 0.16 | YES |
6 | PSMB9 | PSMB9 | PSMB9 | 1005 | 0.1 | 0.19 | YES |
7 | PSME2 | PSME2 | PSME2 | 1091 | 0.098 | 0.22 | YES |
8 | CKS1B | CKS1B | CKS1B | 1436 | 0.081 | 0.23 | YES |
9 | CDKN1A | CDKN1A | CDKN1A | 1526 | 0.078 | 0.25 | YES |
10 | PSMB7 | PSMB7 | PSMB7 | 1757 | 0.07 | 0.26 | YES |
11 | PSMD9 | PSMD9 | PSMD9 | 1788 | 0.07 | 0.28 | YES |
12 | MYC | MYC | MYC | 1919 | 0.066 | 0.3 | YES |
13 | PSMA5 | PSMA5 | PSMA5 | 1935 | 0.065 | 0.32 | YES |
14 | PSME1 | PSME1 | PSME1 | 1943 | 0.065 | 0.34 | YES |
15 | CCNE2 | CCNE2 | CCNE2 | 1978 | 0.064 | 0.36 | YES |
16 | PSMA6 | PSMA6 | PSMA6 | 1979 | 0.064 | 0.39 | YES |
17 | PSMD12 | PSMD12 | PSMD12 | 2014 | 0.063 | 0.41 | YES |
18 | MNAT1 | MNAT1 | MNAT1 | 2020 | 0.062 | 0.43 | YES |
19 | PSMB6 | PSMB6 | PSMB6 | 2194 | 0.058 | 0.44 | YES |
20 | PSMA4 | PSMA4 | PSMA4 | 2261 | 0.056 | 0.45 | YES |
21 | PSMA1 | PSMA1 | PSMA1 | 2335 | 0.055 | 0.47 | YES |
22 | RB1 | RB1 | RB1 | 2501 | 0.052 | 0.48 | YES |
23 | PSMB8 | PSMB8 | PSMB8 | 2625 | 0.05 | 0.49 | YES |
24 | PSMD14 | PSMD14 | PSMD14 | 2631 | 0.049 | 0.5 | YES |
25 | PSMB2 | PSMB2 | PSMB2 | 2641 | 0.049 | 0.52 | YES |
26 | PSMD8 | PSMD8 | PSMD8 | 2684 | 0.048 | 0.54 | YES |
27 | PSMD6 | PSMD6 | PSMD6 | 2692 | 0.048 | 0.55 | YES |
28 | CCNH | CCNH | CCNH | 2843 | 0.046 | 0.56 | YES |
29 | PSMD2 | PSMD2 | PSMD2 | 2875 | 0.045 | 0.57 | YES |
30 | SKP2 | SKP2 | SKP2 | 2907 | 0.045 | 0.59 | YES |
31 | PSMD13 | PSMD13 | PSMD13 | 2997 | 0.044 | 0.6 | YES |
32 | PSMA3 | PSMA3 | PSMA3 | 3111 | 0.042 | 0.61 | YES |
33 | PSMA2 | PSMA2 | PSMA2 | 3158 | 0.041 | 0.62 | YES |
34 | MAX | MAX | MAX | 3346 | 0.038 | 0.62 | YES |
35 | PSMB5 | PSMB5 | PSMB5 | 3503 | 0.036 | 0.62 | YES |
36 | CDK2 | CDK2 | CDK2 | 3747 | 0.033 | 0.62 | YES |
37 | PSMD11 | PSMD11 | PSMD11 | 3768 | 0.033 | 0.63 | YES |
38 | PSMC4 | PSMC4 | PSMC4 | 3879 | 0.032 | 0.64 | YES |
39 | PSMC1 | PSMC1 | PSMC1 | 3907 | 0.031 | 0.65 | YES |
40 | PSMC5 | PSMC5 | PSMC5 | 3966 | 0.03 | 0.65 | YES |
41 | SKP1 | SKP1 | SKP1 | 3981 | 0.03 | 0.66 | YES |
42 | UBA52 | UBA52 | UBA52 | 4047 | 0.029 | 0.67 | YES |
43 | PSMC6 | PSMC6 | PSMC6 | 4057 | 0.029 | 0.68 | YES |
44 | PSMB3 | PSMB3 | PSMB3 | 4323 | 0.026 | 0.68 | YES |
45 | PSMD5 | PSMD5 | PSMD5 | 4340 | 0.026 | 0.68 | YES |
46 | PSMB1 | PSMB1 | PSMB1 | 4378 | 0.026 | 0.69 | YES |
47 | PSMD3 | PSMD3 | PSMD3 | 4720 | 0.022 | 0.68 | NO |
48 | PSMD10 | PSMD10 | PSMD10 | 4863 | 0.02 | 0.68 | NO |
49 | PSMD7 | PSMD7 | PSMD7 | 4938 | 0.02 | 0.68 | NO |
50 | PSMC2 | PSMC2 | PSMC2 | 5159 | 0.018 | 0.68 | NO |
51 | PSMD1 | PSMD1 | PSMD1 | 5333 | 0.016 | 0.67 | NO |
52 | RPS27A | RPS27A | RPS27A | 5355 | 0.015 | 0.68 | NO |
53 | PSMC3 | PSMC3 | PSMC3 | 5963 | 0.0089 | 0.65 | NO |
54 | CUL1 | CUL1 | CUL1 | 6448 | 0.0041 | 0.62 | NO |
55 | PSMB4 | PSMB4 | PSMB4 | 6659 | 0.0021 | 0.61 | NO |
56 | CDKN1B | CDKN1B | CDKN1B | 6673 | 0.002 | 0.61 | NO |
57 | PSMD4 | PSMD4 | PSMD4 | 7513 | -0.0065 | 0.57 | NO |
58 | PSMA7 | PSMA7 | PSMA7 | 7576 | -0.0071 | 0.57 | NO |
59 | WEE1 | WEE1 | WEE1 | 7821 | -0.0098 | 0.56 | NO |
60 | CCNE1 | CCNE1 | CCNE1 | 8211 | -0.014 | 0.54 | NO |
61 | PSMF1 | PSMF1 | PSMF1 | 8235 | -0.015 | 0.55 | NO |
62 | CCNA1 | CCNA1 | CCNA1 | 10570 | -0.045 | 0.44 | 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 PYRIMIDINE METABOLISM.

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

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 | CCNA2 | CCNA2 | CCNA2 | 839 | 0.12 | 0.006 | YES |
2 | PSMB10 | PSMB10 | PSMB10 | 905 | 0.11 | 0.051 | YES |
3 | PSMB9 | PSMB9 | PSMB9 | 1005 | 0.1 | 0.091 | YES |
4 | PSME2 | PSME2 | PSME2 | 1091 | 0.098 | 0.13 | YES |
5 | CKS1B | CKS1B | CKS1B | 1436 | 0.081 | 0.15 | YES |
6 | CDKN1A | CDKN1A | CDKN1A | 1526 | 0.078 | 0.18 | YES |
7 | PSMB7 | PSMB7 | PSMB7 | 1757 | 0.07 | 0.2 | YES |
8 | PSMD9 | PSMD9 | PSMD9 | 1788 | 0.07 | 0.22 | YES |
9 | PSMA5 | PSMA5 | PSMA5 | 1935 | 0.065 | 0.25 | YES |
10 | PSME1 | PSME1 | PSME1 | 1943 | 0.065 | 0.28 | YES |
11 | CCNE2 | CCNE2 | CCNE2 | 1978 | 0.064 | 0.3 | YES |
12 | PSMA6 | PSMA6 | PSMA6 | 1979 | 0.064 | 0.33 | YES |
13 | PSMD12 | PSMD12 | PSMD12 | 2014 | 0.063 | 0.36 | YES |
14 | PSMB6 | PSMB6 | PSMB6 | 2194 | 0.058 | 0.37 | YES |
15 | PSMA4 | PSMA4 | PSMA4 | 2261 | 0.056 | 0.39 | YES |
16 | PSMA1 | PSMA1 | PSMA1 | 2335 | 0.055 | 0.41 | YES |
17 | PSMB8 | PSMB8 | PSMB8 | 2625 | 0.05 | 0.42 | YES |
18 | PSMD14 | PSMD14 | PSMD14 | 2631 | 0.049 | 0.44 | YES |
19 | PSMB2 | PSMB2 | PSMB2 | 2641 | 0.049 | 0.46 | YES |
20 | PSMD8 | PSMD8 | PSMD8 | 2684 | 0.048 | 0.48 | YES |
21 | PSMD6 | PSMD6 | PSMD6 | 2692 | 0.048 | 0.5 | YES |
22 | PSMD2 | PSMD2 | PSMD2 | 2875 | 0.045 | 0.52 | YES |
23 | SKP2 | SKP2 | SKP2 | 2907 | 0.045 | 0.53 | YES |
24 | PSMD13 | PSMD13 | PSMD13 | 2997 | 0.044 | 0.55 | YES |
25 | PSMA3 | PSMA3 | PSMA3 | 3111 | 0.042 | 0.56 | YES |
26 | PSMA2 | PSMA2 | PSMA2 | 3158 | 0.041 | 0.58 | YES |
27 | PSMB5 | PSMB5 | PSMB5 | 3503 | 0.036 | 0.57 | YES |
28 | CDK2 | CDK2 | CDK2 | 3747 | 0.033 | 0.57 | YES |
29 | PSMD11 | PSMD11 | PSMD11 | 3768 | 0.033 | 0.59 | YES |
30 | PSMC4 | PSMC4 | PSMC4 | 3879 | 0.032 | 0.6 | YES |
31 | PSMC1 | PSMC1 | PSMC1 | 3907 | 0.031 | 0.61 | YES |
32 | PSMC5 | PSMC5 | PSMC5 | 3966 | 0.03 | 0.62 | YES |
33 | SKP1 | SKP1 | SKP1 | 3981 | 0.03 | 0.63 | YES |
34 | UBA52 | UBA52 | UBA52 | 4047 | 0.029 | 0.64 | YES |
35 | PSMC6 | PSMC6 | PSMC6 | 4057 | 0.029 | 0.65 | YES |
36 | PSMB3 | PSMB3 | PSMB3 | 4323 | 0.026 | 0.65 | YES |
37 | PSMD5 | PSMD5 | PSMD5 | 4340 | 0.026 | 0.66 | YES |
38 | PSMB1 | PSMB1 | PSMB1 | 4378 | 0.026 | 0.67 | YES |
39 | PSMD3 | PSMD3 | PSMD3 | 4720 | 0.022 | 0.66 | NO |
40 | PSMD10 | PSMD10 | PSMD10 | 4863 | 0.02 | 0.66 | NO |
41 | PSMD7 | PSMD7 | PSMD7 | 4938 | 0.02 | 0.67 | NO |
42 | PSMC2 | PSMC2 | PSMC2 | 5159 | 0.018 | 0.66 | NO |
43 | PSMD1 | PSMD1 | PSMD1 | 5333 | 0.016 | 0.66 | NO |
44 | RPS27A | RPS27A | RPS27A | 5355 | 0.015 | 0.67 | NO |
45 | PSMC3 | PSMC3 | PSMC3 | 5963 | 0.0089 | 0.64 | NO |
46 | CUL1 | CUL1 | CUL1 | 6448 | 0.0041 | 0.62 | NO |
47 | PSMB4 | PSMB4 | PSMB4 | 6659 | 0.0021 | 0.6 | NO |
48 | CDKN1B | CDKN1B | CDKN1B | 6673 | 0.002 | 0.6 | NO |
49 | PSMD4 | PSMD4 | PSMD4 | 7513 | -0.0065 | 0.56 | NO |
50 | PSMA7 | PSMA7 | PSMA7 | 7576 | -0.0071 | 0.56 | NO |
51 | CCNE1 | CCNE1 | CCNE1 | 8211 | -0.014 | 0.54 | NO |
52 | PSMF1 | PSMF1 | PSMF1 | 8235 | -0.015 | 0.54 | NO |
53 | CCNA1 | CCNA1 | CCNA1 | 10570 | -0.045 | 0.44 | 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 AMINOACYL TRNA BIOSYNTHESIS.

Figure S44. 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 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 | CDK7 | CDK7 | CDK7 | 801 | 0.12 | 0.02 | YES |
2 | DDB2 | DDB2 | DDB2 | 1025 | 0.1 | 0.062 | YES |
3 | POLE2 | POLE2 | POLE2 | 1170 | 0.094 | 0.1 | YES |
4 | RFC2 | RFC2 | RFC2 | 1314 | 0.086 | 0.14 | YES |
5 | RFC4 | RFC4 | RFC4 | 1385 | 0.083 | 0.18 | YES |
6 | PCNA | PCNA | PCNA | 1395 | 0.083 | 0.22 | YES |
7 | POLD2 | POLD2 | POLD2 | 1607 | 0.075 | 0.25 | YES |
8 | RFC5 | RFC5 | RFC5 | 1669 | 0.073 | 0.29 | YES |
9 | GTF2H3 | GTF2H3 | GTF2H3 | 1742 | 0.071 | 0.32 | YES |
10 | LIG1 | LIG1 | LIG1 | 1886 | 0.066 | 0.35 | YES |
11 | MNAT1 | MNAT1 | MNAT1 | 2020 | 0.062 | 0.38 | YES |
12 | POLR2L | POLR2L | POLR2L | 2044 | 0.062 | 0.41 | YES |
13 | GTF2H2 | GTF2H2 | GTF2H2 | 2366 | 0.054 | 0.42 | YES |
14 | POLD1 | POLD1 | POLD1 | 2377 | 0.054 | 0.45 | YES |
15 | POLR2H | POLR2H | POLR2H | 2435 | 0.053 | 0.47 | YES |
16 | POLR2F | POLR2F | POLR2F | 2591 | 0.05 | 0.49 | YES |
17 | RPA3 | RPA3 | RPA3 | 2759 | 0.047 | 0.51 | YES |
18 | CCNH | CCNH | CCNH | 2843 | 0.046 | 0.53 | YES |
19 | POLR2E | POLR2E | POLR2E | 3008 | 0.043 | 0.54 | YES |
20 | ERCC8 | ERCC8 | ERCC8 | 3147 | 0.041 | 0.55 | YES |
21 | RAD23B | RAD23B | RAD23B | 3456 | 0.037 | 0.56 | YES |
22 | POLR2I | POLR2I | POLR2I | 3508 | 0.036 | 0.57 | YES |
23 | GTF2H4 | GTF2H4 | GTF2H4 | 3591 | 0.035 | 0.59 | YES |
24 | RFC3 | RFC3 | RFC3 | 3954 | 0.03 | 0.58 | YES |
25 | GTF2H2B | GTF2H2B | GTF2H2B | 4269 | 0.027 | 0.58 | YES |
26 | RPA2 | RPA2 | RPA2 | 4349 | 0.026 | 0.59 | YES |
27 | POLR2A | POLR2A | POLR2A | 4371 | 0.026 | 0.6 | YES |
28 | TCEA1 | TCEA1 | TCEA1 | 4476 | 0.025 | 0.61 | YES |
29 | POLR2D | POLR2D | POLR2D | 4780 | 0.022 | 0.61 | YES |
30 | POLR2G | POLR2G | POLR2G | 4845 | 0.021 | 0.61 | YES |
31 | RPA1 | RPA1 | RPA1 | 5209 | 0.017 | 0.6 | YES |
32 | ERCC1 | ERCC1 | ERCC1 | 5217 | 0.017 | 0.61 | YES |
33 | POLD4 | POLD4 | POLD4 | 5325 | 0.016 | 0.62 | YES |
34 | POLE | POLE | POLE | 5582 | 0.013 | 0.61 | NO |
35 | XAB2 | XAB2 | XAB2 | 5590 | 0.013 | 0.61 | NO |
36 | ERCC3 | ERCC3 | ERCC3 | 6172 | 0.0067 | 0.59 | NO |
37 | GTF2H1 | GTF2H1 | GTF2H1 | 6254 | 0.0058 | 0.58 | NO |
38 | ERCC2 | ERCC2 | ERCC2 | 6338 | 0.0052 | 0.58 | NO |
39 | POLR2B | POLR2B | POLR2B | 6464 | 0.0038 | 0.58 | NO |
40 | POLR2C | POLR2C | POLR2C | 6533 | 0.0031 | 0.58 | NO |
41 | POLR2J | POLR2J | POLR2J | 6646 | 0.0022 | 0.57 | NO |
42 | XPC | XPC | XPC | 6956 | -0.00085 | 0.56 | NO |
43 | XPA | XPA | XPA | 6980 | -0.0011 | 0.56 | NO |
44 | DDB1 | DDB1 | DDB1 | 7498 | -0.0063 | 0.53 | NO |
45 | POLR2K | POLR2K | POLR2K | 7791 | -0.0093 | 0.52 | NO |
46 | ERCC5 | ERCC5 | ERCC5 | 7894 | -0.011 | 0.52 | NO |
47 | POLD3 | POLD3 | POLD3 | 8301 | -0.015 | 0.51 | NO |
48 | ERCC6 | ERCC6 | ERCC6 | 9543 | -0.03 | 0.46 | NO |
49 | ERCC4 | ERCC4 | ERCC4 | 11705 | -0.065 | 0.37 | 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 RIBOSOME.

Figure S46. 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 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 | CDC45 | CDC45 | CDC45 | 460 | 0.16 | 0.0043 | YES |
2 | CDT1 | CDT1 | CDT1 | 520 | 0.15 | 0.029 | YES |
3 | CDC25A | CDC25A | CDC25A | 603 | 0.14 | 0.05 | YES |
4 | MCM10 | MCM10 | MCM10 | 605 | 0.14 | 0.075 | YES |
5 | CCNB1 | CCNB1 | CCNB1 | 620 | 0.14 | 0.1 | YES |
6 | RRM2 | RRM2 | RRM2 | 644 | 0.14 | 0.12 | YES |
7 | PKMYT1 | PKMYT1 | PKMYT1 | 740 | 0.12 | 0.14 | YES |
8 | CDK7 | CDK7 | CDK7 | 801 | 0.12 | 0.16 | YES |
9 | CCNA2 | CCNA2 | CCNA2 | 839 | 0.12 | 0.18 | YES |
10 | TYMS | TYMS | TYMS | 840 | 0.12 | 0.2 | YES |
11 | CDC6 | CDC6 | CDC6 | 901 | 0.11 | 0.21 | YES |
12 | PSMB10 | PSMB10 | PSMB10 | 905 | 0.11 | 0.23 | YES |
13 | CDK1 | CDK1 | CDK1 | 943 | 0.11 | 0.25 | YES |
14 | PSMB9 | PSMB9 | PSMB9 | 1005 | 0.1 | 0.26 | YES |
15 | PSME2 | PSME2 | PSME2 | 1091 | 0.098 | 0.28 | YES |
16 | POLE2 | POLE2 | POLE2 | 1170 | 0.094 | 0.29 | YES |
17 | DHFR | DHFR | DHFR | 1188 | 0.092 | 0.31 | YES |
18 | TK2 | TK2 | TK2 | 1215 | 0.091 | 0.32 | YES |
19 | MCM2 | MCM2 | MCM2 | 1219 | 0.09 | 0.34 | YES |
20 | MCM4 | MCM4 | MCM4 | 1329 | 0.085 | 0.35 | YES |
21 | PCNA | PCNA | PCNA | 1395 | 0.083 | 0.36 | YES |
22 | CKS1B | CKS1B | CKS1B | 1436 | 0.081 | 0.37 | YES |
23 | CDC7 | CDC7 | CDC7 | 1490 | 0.079 | 0.38 | YES |
24 | MCM5 | MCM5 | MCM5 | 1523 | 0.078 | 0.39 | YES |
25 | CDKN1A | CDKN1A | CDKN1A | 1526 | 0.078 | 0.41 | YES |
26 | PSMB7 | PSMB7 | PSMB7 | 1757 | 0.07 | 0.41 | YES |
27 | FBXO5 | FBXO5 | FBXO5 | 1759 | 0.07 | 0.42 | YES |
28 | PSMD9 | PSMD9 | PSMD9 | 1788 | 0.07 | 0.43 | YES |
29 | MYC | MYC | MYC | 1919 | 0.066 | 0.44 | YES |
30 | PSMA5 | PSMA5 | PSMA5 | 1935 | 0.065 | 0.45 | YES |
31 | PSME1 | PSME1 | PSME1 | 1943 | 0.065 | 0.46 | YES |
32 | PRIM1 | PRIM1 | PRIM1 | 1954 | 0.064 | 0.47 | YES |
33 | CCNE2 | CCNE2 | CCNE2 | 1978 | 0.064 | 0.48 | YES |
34 | PSMA6 | PSMA6 | PSMA6 | 1979 | 0.064 | 0.49 | YES |
35 | PSMD12 | PSMD12 | PSMD12 | 2014 | 0.063 | 0.5 | YES |
36 | MNAT1 | MNAT1 | MNAT1 | 2020 | 0.062 | 0.51 | YES |
37 | PSMB6 | PSMB6 | PSMB6 | 2194 | 0.058 | 0.51 | YES |
38 | DBF4 | DBF4 | DBF4 | 2247 | 0.057 | 0.52 | YES |
39 | PSMA4 | PSMA4 | PSMA4 | 2261 | 0.056 | 0.53 | YES |
40 | TFDP1 | TFDP1 | TFDP1 | 2271 | 0.056 | 0.54 | YES |
41 | PSMA1 | PSMA1 | PSMA1 | 2335 | 0.055 | 0.55 | YES |
42 | RB1 | RB1 | RB1 | 2501 | 0.052 | 0.55 | YES |
43 | PPP2CB | PPP2CB | PPP2CB | 2504 | 0.052 | 0.56 | YES |
44 | PSMB8 | PSMB8 | PSMB8 | 2625 | 0.05 | 0.56 | YES |
45 | PSMD14 | PSMD14 | PSMD14 | 2631 | 0.049 | 0.57 | YES |
46 | PSMB2 | PSMB2 | PSMB2 | 2641 | 0.049 | 0.57 | YES |
47 | PSMD8 | PSMD8 | PSMD8 | 2684 | 0.048 | 0.58 | YES |
48 | PSMD6 | PSMD6 | PSMD6 | 2692 | 0.048 | 0.59 | YES |
49 | PRIM2 | PRIM2 | PRIM2 | 2707 | 0.048 | 0.6 | YES |
50 | RPA3 | RPA3 | RPA3 | 2759 | 0.047 | 0.6 | YES |
51 | MCM6 | MCM6 | MCM6 | 2820 | 0.046 | 0.61 | YES |
52 | PPP2CA | PPP2CA | PPP2CA | 2838 | 0.046 | 0.62 | YES |
53 | CCNH | CCNH | CCNH | 2843 | 0.046 | 0.62 | YES |
54 | PSMD2 | PSMD2 | PSMD2 | 2875 | 0.045 | 0.63 | YES |
55 | MCM3 | MCM3 | MCM3 | 2904 | 0.045 | 0.64 | YES |
56 | SKP2 | SKP2 | SKP2 | 2907 | 0.045 | 0.64 | YES |
57 | PSMD13 | PSMD13 | PSMD13 | 2997 | 0.044 | 0.65 | YES |
58 | PSMA3 | PSMA3 | PSMA3 | 3111 | 0.042 | 0.65 | YES |
59 | PSMA2 | PSMA2 | PSMA2 | 3158 | 0.041 | 0.65 | YES |
60 | E2F1 | E2F1 | E2F1 | 3299 | 0.039 | 0.65 | YES |
61 | MAX | MAX | MAX | 3346 | 0.038 | 0.66 | YES |
62 | MCM7 | MCM7 | MCM7 | 3418 | 0.037 | 0.66 | YES |
63 | PPP2R3B | PPP2R3B | PPP2R3B | 3436 | 0.037 | 0.67 | YES |
64 | PSMB5 | PSMB5 | PSMB5 | 3503 | 0.036 | 0.67 | YES |
65 | POLA2 | POLA2 | POLA2 | 3563 | 0.035 | 0.67 | YES |
66 | CDK2 | CDK2 | CDK2 | 3747 | 0.033 | 0.67 | YES |
67 | PSMD11 | PSMD11 | PSMD11 | 3768 | 0.033 | 0.67 | YES |
68 | PSMC4 | PSMC4 | PSMC4 | 3879 | 0.032 | 0.67 | YES |
69 | PSMC1 | PSMC1 | PSMC1 | 3907 | 0.031 | 0.68 | YES |
70 | PSMC5 | PSMC5 | PSMC5 | 3966 | 0.03 | 0.68 | YES |
71 | SKP1 | SKP1 | SKP1 | 3981 | 0.03 | 0.68 | YES |
72 | UBA52 | UBA52 | UBA52 | 4047 | 0.029 | 0.69 | YES |
73 | PSMC6 | PSMC6 | PSMC6 | 4057 | 0.029 | 0.69 | YES |
74 | PSMB3 | PSMB3 | PSMB3 | 4323 | 0.026 | 0.68 | YES |
75 | PSMD5 | PSMD5 | PSMD5 | 4340 | 0.026 | 0.68 | YES |
76 | RPA2 | RPA2 | RPA2 | 4349 | 0.026 | 0.69 | YES |
77 | PSMB1 | PSMB1 | PSMB1 | 4378 | 0.026 | 0.69 | YES |
78 | PSMD3 | PSMD3 | PSMD3 | 4720 | 0.022 | 0.68 | NO |
79 | PSMD10 | PSMD10 | PSMD10 | 4863 | 0.02 | 0.67 | NO |
80 | PSMD7 | PSMD7 | PSMD7 | 4938 | 0.02 | 0.67 | NO |
81 | PSMC2 | PSMC2 | PSMC2 | 5159 | 0.018 | 0.66 | NO |
82 | RPA1 | RPA1 | RPA1 | 5209 | 0.017 | 0.67 | NO |
83 | PSMD1 | PSMD1 | PSMD1 | 5333 | 0.016 | 0.66 | NO |
84 | RPS27A | RPS27A | RPS27A | 5355 | 0.015 | 0.66 | NO |
85 | POLE | POLE | POLE | 5582 | 0.013 | 0.65 | NO |
86 | PPP2R1B | PPP2R1B | PPP2R1B | 5813 | 0.01 | 0.64 | NO |
87 | PSMC3 | PSMC3 | PSMC3 | 5963 | 0.0089 | 0.64 | NO |
88 | PPP2R1A | PPP2R1A | PPP2R1A | 6146 | 0.007 | 0.63 | NO |
89 | CUL1 | CUL1 | CUL1 | 6448 | 0.0041 | 0.61 | NO |
90 | POLA1 | POLA1 | POLA1 | 6594 | 0.0026 | 0.6 | NO |
91 | PSMB4 | PSMB4 | PSMB4 | 6659 | 0.0021 | 0.6 | NO |
92 | CDKN1B | CDKN1B | CDKN1B | 6673 | 0.002 | 0.6 | NO |
93 | PSMD4 | PSMD4 | PSMD4 | 7513 | -0.0065 | 0.56 | NO |
94 | PSMA7 | PSMA7 | PSMA7 | 7576 | -0.0071 | 0.56 | NO |
95 | WEE1 | WEE1 | WEE1 | 7821 | -0.0098 | 0.54 | NO |
96 | CCNE1 | CCNE1 | CCNE1 | 8211 | -0.014 | 0.53 | NO |
97 | PSMF1 | PSMF1 | PSMF1 | 8235 | -0.015 | 0.53 | NO |
98 | MCM8 | MCM8 | MCM8 | 9519 | -0.03 | 0.46 | NO |
99 | CCNA1 | CCNA1 | CCNA1 | 10570 | -0.045 | 0.42 | NO |
100 | RPA4 | RPA4 | RPA4 | 13774 | -0.12 | 0.26 | NO |
Figure S47. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA DEGRADATION.

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

Table 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 | CDK7 | CDK7 | CDK7 | 801 | 0.12 | 0.056 | YES |
2 | GTF2H3 | GTF2H3 | GTF2H3 | 1742 | 0.071 | 0.065 | YES |
3 | MNAT1 | MNAT1 | MNAT1 | 2020 | 0.062 | 0.1 | YES |
4 | POLR2L | POLR2L | POLR2L | 2044 | 0.062 | 0.15 | YES |
5 | GTF2H2 | GTF2H2 | GTF2H2 | 2366 | 0.054 | 0.18 | YES |
6 | POLR2H | POLR2H | POLR2H | 2435 | 0.053 | 0.22 | YES |
7 | POLR2F | POLR2F | POLR2F | 2591 | 0.05 | 0.26 | YES |
8 | CCNH | CCNH | CCNH | 2843 | 0.046 | 0.28 | YES |
9 | WHSC2 | WHSC2 | WHSC2 | 2912 | 0.045 | 0.32 | YES |
10 | POLR2E | POLR2E | POLR2E | 3008 | 0.043 | 0.35 | YES |
11 | GTF2F1 | GTF2F1 | GTF2F1 | 3437 | 0.037 | 0.35 | YES |
12 | POLR2I | POLR2I | POLR2I | 3508 | 0.036 | 0.38 | YES |
13 | GTF2H4 | GTF2H4 | GTF2H4 | 3591 | 0.035 | 0.4 | YES |
14 | TCEB2 | TCEB2 | TCEB2 | 3696 | 0.034 | 0.43 | YES |
15 | TCEB1 | TCEB1 | TCEB1 | 3937 | 0.031 | 0.44 | YES |
16 | COBRA1 | COBRA1 | COBRA1 | 4116 | 0.029 | 0.46 | YES |
17 | GTF2H2B | GTF2H2B | GTF2H2B | 4269 | 0.027 | 0.47 | YES |
18 | POLR2A | POLR2A | POLR2A | 4371 | 0.026 | 0.49 | YES |
19 | TCEA1 | TCEA1 | TCEA1 | 4476 | 0.025 | 0.5 | YES |
20 | SSRP1 | SSRP1 | SSRP1 | 4492 | 0.024 | 0.52 | YES |
21 | POLR2D | POLR2D | POLR2D | 4780 | 0.022 | 0.52 | YES |
22 | POLR2G | POLR2G | POLR2G | 4845 | 0.021 | 0.54 | YES |
23 | NCBP2 | NCBP2 | NCBP2 | 5080 | 0.018 | 0.54 | YES |
24 | RDBP | RDBP | RDBP | 5279 | 0.016 | 0.54 | YES |
25 | GTF2F2 | GTF2F2 | GTF2F2 | 5318 | 0.016 | 0.55 | YES |
26 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 5383 | 0.015 | 0.56 | YES |
27 | CDK9 | CDK9 | CDK9 | 5555 | 0.013 | 0.56 | YES |
28 | ERCC3 | ERCC3 | ERCC3 | 6172 | 0.0067 | 0.54 | NO |
29 | NCBP1 | NCBP1 | NCBP1 | 6173 | 0.0067 | 0.54 | NO |
30 | ELL | ELL | ELL | 6244 | 0.006 | 0.55 | NO |
31 | GTF2H1 | GTF2H1 | GTF2H1 | 6254 | 0.0058 | 0.55 | NO |
32 | ERCC2 | ERCC2 | ERCC2 | 6338 | 0.0052 | 0.55 | NO |
33 | SUPT16H | SUPT16H | SUPT16H | 6400 | 0.0046 | 0.55 | NO |
34 | POLR2B | POLR2B | POLR2B | 6464 | 0.0038 | 0.55 | NO |
35 | POLR2C | POLR2C | POLR2C | 6533 | 0.0031 | 0.55 | NO |
36 | POLR2J | POLR2J | POLR2J | 6646 | 0.0022 | 0.54 | NO |
37 | SUPT5H | SUPT5H | SUPT5H | 7210 | -0.0036 | 0.52 | NO |
38 | CCNT1 | CCNT1 | CCNT1 | 7243 | -0.0039 | 0.52 | NO |
39 | POLR2K | POLR2K | POLR2K | 7791 | -0.0093 | 0.5 | NO |
40 | CTDP1 | CTDP1 | CTDP1 | 7900 | -0.011 | 0.5 | NO |
41 | TCEB3 | TCEB3 | TCEB3 | 8281 | -0.015 | 0.49 | NO |
42 | TH1L | TH1L | TH1L | 9964 | -0.036 | 0.43 | NO |
43 | CCNT2 | CCNT2 | CCNT2 | 10391 | -0.042 | 0.44 | NO |
Figure S49. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA POLYMERASE.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA POLYMERASE, 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 | CDK7 | CDK7 | CDK7 | 801 | 0.12 | 0.076 | YES |
2 | GTF2H3 | GTF2H3 | GTF2H3 | 1742 | 0.071 | 0.097 | YES |
3 | MNAT1 | MNAT1 | MNAT1 | 2020 | 0.062 | 0.14 | YES |
4 | POLR2L | POLR2L | POLR2L | 2044 | 0.062 | 0.21 | YES |
5 | GTF2H2 | GTF2H2 | GTF2H2 | 2366 | 0.054 | 0.24 | YES |
6 | POLR2H | POLR2H | POLR2H | 2435 | 0.053 | 0.29 | YES |
7 | POLR2F | POLR2F | POLR2F | 2591 | 0.05 | 0.34 | YES |
8 | CCNH | CCNH | CCNH | 2843 | 0.046 | 0.37 | YES |
9 | WHSC2 | WHSC2 | WHSC2 | 2912 | 0.045 | 0.41 | YES |
10 | POLR2E | POLR2E | POLR2E | 3008 | 0.043 | 0.45 | YES |
11 | GTF2F1 | GTF2F1 | GTF2F1 | 3437 | 0.037 | 0.46 | YES |
12 | POLR2I | POLR2I | POLR2I | 3508 | 0.036 | 0.49 | YES |
13 | GTF2H4 | GTF2H4 | GTF2H4 | 3591 | 0.035 | 0.52 | YES |
14 | COBRA1 | COBRA1 | COBRA1 | 4116 | 0.029 | 0.52 | YES |
15 | GTF2H2B | GTF2H2B | GTF2H2B | 4269 | 0.027 | 0.54 | YES |
16 | POLR2A | POLR2A | POLR2A | 4371 | 0.026 | 0.56 | YES |
17 | POLR2D | POLR2D | POLR2D | 4780 | 0.022 | 0.56 | YES |
18 | POLR2G | POLR2G | POLR2G | 4845 | 0.021 | 0.58 | YES |
19 | NCBP2 | NCBP2 | NCBP2 | 5080 | 0.018 | 0.59 | YES |
20 | RDBP | RDBP | RDBP | 5279 | 0.016 | 0.59 | YES |
21 | GTF2F2 | GTF2F2 | GTF2F2 | 5318 | 0.016 | 0.61 | YES |
22 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 5383 | 0.015 | 0.62 | YES |
23 | ERCC3 | ERCC3 | ERCC3 | 6172 | 0.0067 | 0.58 | NO |
24 | NCBP1 | NCBP1 | NCBP1 | 6173 | 0.0067 | 0.59 | NO |
25 | GTF2H1 | GTF2H1 | GTF2H1 | 6254 | 0.0058 | 0.59 | NO |
26 | ERCC2 | ERCC2 | ERCC2 | 6338 | 0.0052 | 0.59 | NO |
27 | POLR2B | POLR2B | POLR2B | 6464 | 0.0038 | 0.59 | NO |
28 | POLR2C | POLR2C | POLR2C | 6533 | 0.0031 | 0.59 | NO |
29 | POLR2J | POLR2J | POLR2J | 6646 | 0.0022 | 0.58 | NO |
30 | SUPT5H | SUPT5H | SUPT5H | 7210 | -0.0036 | 0.56 | NO |
31 | POLR2K | POLR2K | POLR2K | 7791 | -0.0093 | 0.54 | NO |
32 | CTDP1 | CTDP1 | CTDP1 | 7900 | -0.011 | 0.54 | NO |
33 | TH1L | TH1L | TH1L | 9964 | -0.036 | 0.47 | NO |
Figure S51. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DNA REPLICATION.

Figure S52. 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 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 | CDC45 | CDC45 | CDC45 | 460 | 0.16 | -0.00056 | YES |
2 | CDT1 | CDT1 | CDT1 | 520 | 0.15 | 0.019 | YES |
3 | CDC25A | CDC25A | CDC25A | 603 | 0.14 | 0.036 | YES |
4 | MCM10 | MCM10 | MCM10 | 605 | 0.14 | 0.057 | YES |
5 | CCNB1 | CCNB1 | CCNB1 | 620 | 0.14 | 0.078 | YES |
6 | RRM2 | RRM2 | RRM2 | 644 | 0.14 | 0.097 | YES |
7 | PKMYT1 | PKMYT1 | PKMYT1 | 740 | 0.12 | 0.11 | YES |
8 | CCND1 | CCND1 | CCND1 | 746 | 0.12 | 0.13 | YES |
9 | CDK7 | CDK7 | CDK7 | 801 | 0.12 | 0.14 | YES |
10 | CCNA2 | CCNA2 | CCNA2 | 839 | 0.12 | 0.16 | YES |
11 | TYMS | TYMS | TYMS | 840 | 0.12 | 0.18 | YES |
12 | CDC6 | CDC6 | CDC6 | 901 | 0.11 | 0.19 | YES |
13 | PSMB10 | PSMB10 | PSMB10 | 905 | 0.11 | 0.2 | YES |
14 | CDK1 | CDK1 | CDK1 | 943 | 0.11 | 0.22 | YES |
15 | E2F2 | E2F2 | E2F2 | 989 | 0.1 | 0.23 | YES |
16 | PSMB9 | PSMB9 | PSMB9 | 1005 | 0.1 | 0.25 | YES |
17 | PSME2 | PSME2 | PSME2 | 1091 | 0.098 | 0.26 | YES |
18 | POLE2 | POLE2 | POLE2 | 1170 | 0.094 | 0.27 | YES |
19 | DHFR | DHFR | DHFR | 1188 | 0.092 | 0.28 | YES |
20 | TK2 | TK2 | TK2 | 1215 | 0.091 | 0.29 | YES |
21 | MCM2 | MCM2 | MCM2 | 1219 | 0.09 | 0.3 | YES |
22 | PPP2R2A | PPP2R2A | PPP2R2A | 1230 | 0.09 | 0.32 | YES |
23 | MCM4 | MCM4 | MCM4 | 1329 | 0.085 | 0.32 | YES |
24 | PCNA | PCNA | PCNA | 1395 | 0.083 | 0.33 | YES |
25 | CKS1B | CKS1B | CKS1B | 1436 | 0.081 | 0.34 | YES |
26 | CDC7 | CDC7 | CDC7 | 1490 | 0.079 | 0.35 | YES |
27 | MCM5 | MCM5 | MCM5 | 1523 | 0.078 | 0.36 | YES |
28 | CDKN1A | CDKN1A | CDKN1A | 1526 | 0.078 | 0.38 | YES |
29 | CDKN2D | CDKN2D | CDKN2D | 1739 | 0.071 | 0.37 | YES |
30 | PSMB7 | PSMB7 | PSMB7 | 1757 | 0.07 | 0.38 | YES |
31 | FBXO5 | FBXO5 | FBXO5 | 1759 | 0.07 | 0.39 | YES |
32 | PSMD9 | PSMD9 | PSMD9 | 1788 | 0.07 | 0.4 | YES |
33 | MYC | MYC | MYC | 1919 | 0.066 | 0.41 | YES |
34 | PSMA5 | PSMA5 | PSMA5 | 1935 | 0.065 | 0.42 | YES |
35 | PSME1 | PSME1 | PSME1 | 1943 | 0.065 | 0.42 | YES |
36 | PRIM1 | PRIM1 | PRIM1 | 1954 | 0.064 | 0.43 | YES |
37 | CCNE2 | CCNE2 | CCNE2 | 1978 | 0.064 | 0.44 | YES |
38 | PSMA6 | PSMA6 | PSMA6 | 1979 | 0.064 | 0.45 | YES |
39 | PSMD12 | PSMD12 | PSMD12 | 2014 | 0.063 | 0.46 | YES |
40 | MNAT1 | MNAT1 | MNAT1 | 2020 | 0.062 | 0.47 | YES |
41 | LIN54 | LIN54 | LIN54 | 2153 | 0.059 | 0.47 | YES |
42 | PSMB6 | PSMB6 | PSMB6 | 2194 | 0.058 | 0.48 | YES |
43 | DBF4 | DBF4 | DBF4 | 2247 | 0.057 | 0.48 | YES |
44 | PSMA4 | PSMA4 | PSMA4 | 2261 | 0.056 | 0.49 | YES |
45 | TFDP1 | TFDP1 | TFDP1 | 2271 | 0.056 | 0.5 | YES |
46 | PSMA1 | PSMA1 | PSMA1 | 2335 | 0.055 | 0.5 | YES |
47 | RB1 | RB1 | RB1 | 2501 | 0.052 | 0.5 | YES |
48 | PPP2CB | PPP2CB | PPP2CB | 2504 | 0.052 | 0.51 | YES |
49 | LIN9 | LIN9 | LIN9 | 2619 | 0.05 | 0.51 | YES |
50 | PSMB8 | PSMB8 | PSMB8 | 2625 | 0.05 | 0.52 | YES |
51 | PSMD14 | PSMD14 | PSMD14 | 2631 | 0.049 | 0.52 | YES |
52 | PSMB2 | PSMB2 | PSMB2 | 2641 | 0.049 | 0.53 | YES |
53 | PSMD8 | PSMD8 | PSMD8 | 2684 | 0.048 | 0.54 | YES |
54 | PSMD6 | PSMD6 | PSMD6 | 2692 | 0.048 | 0.54 | YES |
55 | PRIM2 | PRIM2 | PRIM2 | 2707 | 0.048 | 0.55 | YES |
56 | E2F5 | E2F5 | E2F5 | 2724 | 0.048 | 0.56 | YES |
57 | RPA3 | RPA3 | RPA3 | 2759 | 0.047 | 0.56 | YES |
58 | HDAC1 | HDAC1 | HDAC1 | 2760 | 0.047 | 0.57 | YES |
59 | MCM6 | MCM6 | MCM6 | 2820 | 0.046 | 0.57 | YES |
60 | PPP2CA | PPP2CA | PPP2CA | 2838 | 0.046 | 0.58 | YES |
61 | CCNH | CCNH | CCNH | 2843 | 0.046 | 0.58 | YES |
62 | PSMD2 | PSMD2 | PSMD2 | 2875 | 0.045 | 0.59 | YES |
63 | MCM3 | MCM3 | MCM3 | 2904 | 0.045 | 0.6 | YES |
64 | SKP2 | SKP2 | SKP2 | 2907 | 0.045 | 0.6 | YES |
65 | PSMD13 | PSMD13 | PSMD13 | 2997 | 0.044 | 0.6 | YES |
66 | PSMA3 | PSMA3 | PSMA3 | 3111 | 0.042 | 0.6 | YES |
67 | PSMA2 | PSMA2 | PSMA2 | 3158 | 0.041 | 0.61 | YES |
68 | E2F1 | E2F1 | E2F1 | 3299 | 0.039 | 0.6 | YES |
69 | MAX | MAX | MAX | 3346 | 0.038 | 0.61 | YES |
70 | MCM7 | MCM7 | MCM7 | 3418 | 0.037 | 0.61 | YES |
71 | PPP2R3B | PPP2R3B | PPP2R3B | 3436 | 0.037 | 0.62 | YES |
72 | PSMB5 | PSMB5 | PSMB5 | 3503 | 0.036 | 0.62 | YES |
73 | POLA2 | POLA2 | POLA2 | 3563 | 0.035 | 0.62 | YES |
74 | CDK2 | CDK2 | CDK2 | 3747 | 0.033 | 0.61 | YES |
75 | PSMD11 | PSMD11 | PSMD11 | 3768 | 0.033 | 0.62 | YES |
76 | PSMC4 | PSMC4 | PSMC4 | 3879 | 0.032 | 0.62 | YES |
77 | PSMC1 | PSMC1 | PSMC1 | 3907 | 0.031 | 0.62 | YES |
78 | PSMC5 | PSMC5 | PSMC5 | 3966 | 0.03 | 0.62 | YES |
79 | SKP1 | SKP1 | SKP1 | 3981 | 0.03 | 0.62 | YES |
80 | UBA52 | UBA52 | UBA52 | 4047 | 0.029 | 0.63 | YES |
81 | PSMC6 | PSMC6 | PSMC6 | 4057 | 0.029 | 0.63 | YES |
82 | CDK4 | CDK4 | CDK4 | 4210 | 0.028 | 0.63 | YES |
83 | RBBP4 | RBBP4 | RBBP4 | 4217 | 0.028 | 0.63 | YES |
84 | PSMB3 | PSMB3 | PSMB3 | 4323 | 0.026 | 0.63 | YES |
85 | PSMD5 | PSMD5 | PSMD5 | 4340 | 0.026 | 0.63 | YES |
86 | RPA2 | RPA2 | RPA2 | 4349 | 0.026 | 0.63 | YES |
87 | PSMB1 | PSMB1 | PSMB1 | 4378 | 0.026 | 0.64 | YES |
88 | CDKN2B | CDKN2B | CDKN2B | 4474 | 0.025 | 0.64 | NO |
89 | PSMD3 | PSMD3 | PSMD3 | 4720 | 0.022 | 0.62 | NO |
90 | CDKN2C | CDKN2C | CDKN2C | 4748 | 0.022 | 0.63 | NO |
91 | E2F4 | E2F4 | E2F4 | 4835 | 0.021 | 0.63 | NO |
92 | PSMD10 | PSMD10 | PSMD10 | 4863 | 0.02 | 0.63 | NO |
93 | PSMD7 | PSMD7 | PSMD7 | 4938 | 0.02 | 0.63 | NO |
94 | LIN37 | LIN37 | LIN37 | 4984 | 0.019 | 0.63 | NO |
95 | PSMC2 | PSMC2 | PSMC2 | 5159 | 0.018 | 0.62 | NO |
96 | RPA1 | RPA1 | RPA1 | 5209 | 0.017 | 0.62 | NO |
97 | PSMD1 | PSMD1 | PSMD1 | 5333 | 0.016 | 0.62 | NO |
98 | RPS27A | RPS27A | RPS27A | 5355 | 0.015 | 0.62 | NO |
99 | POLE | POLE | POLE | 5582 | 0.013 | 0.61 | NO |
100 | PPP2R1B | PPP2R1B | PPP2R1B | 5813 | 0.01 | 0.6 | NO |
101 | PSMC3 | PSMC3 | PSMC3 | 5963 | 0.0089 | 0.59 | NO |
102 | PPP2R1A | PPP2R1A | PPP2R1A | 6146 | 0.007 | 0.58 | NO |
103 | CUL1 | CUL1 | CUL1 | 6448 | 0.0041 | 0.56 | NO |
104 | POLA1 | POLA1 | POLA1 | 6594 | 0.0026 | 0.56 | NO |
105 | PSMB4 | PSMB4 | PSMB4 | 6659 | 0.0021 | 0.55 | NO |
106 | CDKN1B | CDKN1B | CDKN1B | 6673 | 0.002 | 0.55 | NO |
107 | MYBL2 | MYBL2 | MYBL2 | 6880 | -0.000032 | 0.54 | NO |
108 | RBL1 | RBL1 | RBL1 | 7465 | -0.006 | 0.51 | NO |
109 | PSMD4 | PSMD4 | PSMD4 | 7513 | -0.0065 | 0.51 | NO |
110 | PSMA7 | PSMA7 | PSMA7 | 7576 | -0.0071 | 0.51 | NO |
111 | WEE1 | WEE1 | WEE1 | 7821 | -0.0098 | 0.5 | NO |
112 | CCNE1 | CCNE1 | CCNE1 | 8211 | -0.014 | 0.48 | NO |
113 | PSMF1 | PSMF1 | PSMF1 | 8235 | -0.015 | 0.48 | NO |
114 | E2F3 | E2F3 | E2F3 | 8385 | -0.016 | 0.47 | NO |
115 | RBL2 | RBL2 | RBL2 | 8989 | -0.023 | 0.44 | NO |
116 | MCM8 | MCM8 | MCM8 | 9519 | -0.03 | 0.42 | NO |
117 | LIN52 | LIN52 | LIN52 | 9612 | -0.031 | 0.42 | NO |
118 | CDK6 | CDK6 | CDK6 | 10359 | -0.042 | 0.38 | NO |
119 | CCNA1 | CCNA1 | CCNA1 | 10570 | -0.045 | 0.38 | NO |
120 | CCND3 | CCND3 | CCND3 | 10575 | -0.045 | 0.39 | NO |
121 | DYRK1A | DYRK1A | DYRK1A | 11239 | -0.056 | 0.36 | NO |
122 | CCND2 | CCND2 | CCND2 | 11965 | -0.07 | 0.33 | NO |
123 | CDKN2A | CDKN2A | CDKN2A | 12616 | -0.084 | 0.31 | NO |
124 | RPA4 | RPA4 | RPA4 | 13774 | -0.12 | 0.26 | NO |
Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SPLICEOSOME.

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

Table 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 | CDK7 | CDK7 | CDK7 | 801 | 0.12 | 0.02 | YES |
2 | DDB2 | DDB2 | DDB2 | 1025 | 0.1 | 0.063 | YES |
3 | POLE2 | POLE2 | POLE2 | 1170 | 0.094 | 0.1 | YES |
4 | RFC2 | RFC2 | RFC2 | 1314 | 0.086 | 0.14 | YES |
5 | RFC4 | RFC4 | RFC4 | 1385 | 0.083 | 0.18 | YES |
6 | PCNA | PCNA | PCNA | 1395 | 0.083 | 0.23 | YES |
7 | POLD2 | POLD2 | POLD2 | 1607 | 0.075 | 0.26 | YES |
8 | RFC5 | RFC5 | RFC5 | 1669 | 0.073 | 0.29 | YES |
9 | GTF2H3 | GTF2H3 | GTF2H3 | 1742 | 0.071 | 0.33 | YES |
10 | LIG1 | LIG1 | LIG1 | 1886 | 0.066 | 0.35 | YES |
11 | MNAT1 | MNAT1 | MNAT1 | 2020 | 0.062 | 0.38 | YES |
12 | POLE3 | POLE3 | POLE3 | 2193 | 0.058 | 0.4 | YES |
13 | RBX1 | RBX1 | RBX1 | 2313 | 0.056 | 0.42 | YES |
14 | GTF2H2 | GTF2H2 | GTF2H2 | 2366 | 0.054 | 0.45 | YES |
15 | POLD1 | POLD1 | POLD1 | 2377 | 0.054 | 0.48 | YES |
16 | RPA3 | RPA3 | RPA3 | 2759 | 0.047 | 0.48 | YES |
17 | CCNH | CCNH | CCNH | 2843 | 0.046 | 0.5 | YES |
18 | RAD23A | RAD23A | RAD23A | 2845 | 0.046 | 0.53 | YES |
19 | CETN2 | CETN2 | CETN2 | 3119 | 0.042 | 0.54 | YES |
20 | ERCC8 | ERCC8 | ERCC8 | 3147 | 0.041 | 0.56 | YES |
21 | RAD23B | RAD23B | RAD23B | 3456 | 0.037 | 0.56 | YES |
22 | GTF2H4 | GTF2H4 | GTF2H4 | 3591 | 0.035 | 0.57 | YES |
23 | RFC3 | RFC3 | RFC3 | 3954 | 0.03 | 0.57 | NO |
24 | RPA2 | RPA2 | RPA2 | 4349 | 0.026 | 0.56 | NO |
25 | RPA1 | RPA1 | RPA1 | 5209 | 0.017 | 0.52 | NO |
26 | ERCC1 | ERCC1 | ERCC1 | 5217 | 0.017 | 0.53 | NO |
27 | POLD4 | POLD4 | POLD4 | 5325 | 0.016 | 0.54 | NO |
28 | POLE | POLE | POLE | 5582 | 0.013 | 0.53 | NO |
29 | ERCC3 | ERCC3 | ERCC3 | 6172 | 0.0067 | 0.5 | NO |
30 | RFC1 | RFC1 | RFC1 | 6201 | 0.0063 | 0.5 | NO |
31 | GTF2H1 | GTF2H1 | GTF2H1 | 6254 | 0.0058 | 0.5 | NO |
32 | ERCC2 | ERCC2 | ERCC2 | 6338 | 0.0052 | 0.5 | NO |
33 | CUL4A | CUL4A | CUL4A | 6851 | 0.00025 | 0.47 | NO |
34 | XPC | XPC | XPC | 6956 | -0.00085 | 0.47 | NO |
35 | XPA | XPA | XPA | 6980 | -0.0011 | 0.47 | NO |
36 | DDB1 | DDB1 | DDB1 | 7498 | -0.0063 | 0.44 | NO |
37 | GTF2H5 | GTF2H5 | GTF2H5 | 7773 | -0.0092 | 0.43 | NO |
38 | ERCC5 | ERCC5 | ERCC5 | 7894 | -0.011 | 0.43 | NO |
39 | POLD3 | POLD3 | POLD3 | 8301 | -0.015 | 0.42 | NO |
40 | CUL4B | CUL4B | CUL4B | 8457 | -0.017 | 0.42 | NO |
41 | POLE4 | POLE4 | POLE4 | 9287 | -0.026 | 0.39 | NO |
42 | ERCC6 | ERCC6 | ERCC6 | 9543 | -0.03 | 0.39 | NO |
43 | ERCC4 | ERCC4 | ERCC4 | 11705 | -0.065 | 0.31 | NO |
44 | RPA4 | RPA4 | RPA4 | 13774 | -0.12 | 0.26 | NO |
Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PROTEASOME.

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

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 | EIF4E | EIF4E | EIF4E | 1417 | 0.082 | -0.018 | YES |
2 | EXOSC7 | EXOSC7 | EXOSC7 | 1685 | 0.073 | 0.019 | YES |
3 | EIF4A1 | EIF4A1 | EIF4A1 | 1876 | 0.067 | 0.056 | YES |
4 | EIF4A3 | EIF4A3 | EIF4A3 | 1976 | 0.064 | 0.096 | YES |
5 | RQCD1 | RQCD1 | RQCD1 | 2299 | 0.056 | 0.12 | YES |
6 | LSM4 | LSM4 | LSM4 | 2569 | 0.05 | 0.14 | YES |
7 | EXOSC8 | EXOSC8 | EXOSC8 | 2614 | 0.05 | 0.17 | YES |
8 | LSM6 | LSM6 | LSM6 | 2745 | 0.047 | 0.2 | YES |
9 | EXOSC9 | EXOSC9 | EXOSC9 | 2756 | 0.047 | 0.23 | YES |
10 | EXOSC2 | EXOSC2 | EXOSC2 | 2835 | 0.046 | 0.26 | YES |
11 | CNOT6 | CNOT6 | CNOT6 | 2925 | 0.044 | 0.29 | YES |
12 | LSM1 | LSM1 | LSM1 | 3090 | 0.042 | 0.31 | YES |
13 | LSM3 | LSM3 | LSM3 | 3128 | 0.041 | 0.34 | YES |
14 | LSM2 | LSM2 | LSM2 | 3174 | 0.041 | 0.36 | YES |
15 | EXOSC3 | EXOSC3 | EXOSC3 | 3459 | 0.037 | 0.37 | YES |
16 | CNOT8 | CNOT8 | CNOT8 | 3507 | 0.036 | 0.4 | YES |
17 | CNOT7 | CNOT7 | CNOT7 | 3676 | 0.034 | 0.41 | YES |
18 | LSM5 | LSM5 | LSM5 | 3845 | 0.032 | 0.42 | YES |
19 | XRN1 | XRN1 | XRN1 | 4017 | 0.03 | 0.44 | YES |
20 | EXOSC4 | EXOSC4 | EXOSC4 | 4167 | 0.028 | 0.45 | YES |
21 | CNOT10 | CNOT10 | CNOT10 | 4258 | 0.027 | 0.46 | YES |
22 | EXOSC5 | EXOSC5 | EXOSC5 | 4395 | 0.026 | 0.47 | YES |
23 | EIF4A2 | EIF4A2 | EIF4A2 | 4488 | 0.024 | 0.48 | YES |
24 | PATL1 | PATL1 | PATL1 | 4505 | 0.024 | 0.5 | YES |
25 | C2orf29 | C2orf29 | C2orf29 | 4650 | 0.023 | 0.51 | YES |
26 | DCPS | DCPS | DCPS | 4786 | 0.021 | 0.52 | YES |
27 | TNKS1BP1 | TNKS1BP1 | TNKS1BP1 | 4909 | 0.02 | 0.52 | YES |
28 | PAIP1 | PAIP1 | PAIP1 | 5052 | 0.018 | 0.53 | YES |
29 | EXOSC1 | EXOSC1 | EXOSC1 | 5091 | 0.018 | 0.54 | YES |
30 | EIF4G1 | EIF4G1 | EIF4G1 | 5334 | 0.016 | 0.54 | YES |
31 | DIS3 | DIS3 | DIS3 | 5415 | 0.015 | 0.55 | YES |
32 | PABPC1 | PABPC1 | PABPC1 | 5617 | 0.013 | 0.54 | NO |
33 | EIF4B | EIF4B | EIF4B | 6373 | 0.0048 | 0.51 | NO |
34 | DCP2 | DCP2 | DCP2 | 6417 | 0.0044 | 0.51 | NO |
35 | EXOSC6 | EXOSC6 | EXOSC6 | 6861 | 0.00015 | 0.48 | NO |
36 | DDX6 | DDX6 | DDX6 | 6946 | -0.00072 | 0.48 | NO |
37 | EDC4 | EDC4 | EDC4 | 7450 | -0.0058 | 0.46 | NO |
38 | CNOT2 | CNOT2 | CNOT2 | 7559 | -0.007 | 0.46 | NO |
39 | PARN | PARN | PARN | 7562 | -0.007 | 0.46 | NO |
40 | CNOT4 | CNOT4 | CNOT4 | 8054 | -0.012 | 0.44 | NO |
41 | CNOT3 | CNOT3 | CNOT3 | 9410 | -0.028 | 0.39 | NO |
42 | DCP1A | DCP1A | DCP1A | 9671 | -0.032 | 0.4 | NO |
43 | DCP1B | DCP1B | DCP1B | 10260 | -0.04 | 0.4 | NO |
44 | EDC3 | EDC3 | EDC3 | 12368 | -0.078 | 0.34 | NO |
Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NUCLEOTIDE EXCISION REPAIR.

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

Table 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 | CDK7 | CDK7 | CDK7 | 801 | 0.12 | 0.025 | YES |
2 | POLE2 | POLE2 | POLE2 | 1170 | 0.094 | 0.059 | YES |
3 | RFC2 | RFC2 | RFC2 | 1314 | 0.086 | 0.1 | YES |
4 | RFC4 | RFC4 | RFC4 | 1385 | 0.083 | 0.14 | YES |
5 | PCNA | PCNA | PCNA | 1395 | 0.083 | 0.19 | YES |
6 | POLD2 | POLD2 | POLD2 | 1607 | 0.075 | 0.22 | YES |
7 | RFC5 | RFC5 | RFC5 | 1669 | 0.073 | 0.26 | YES |
8 | GTF2H3 | GTF2H3 | GTF2H3 | 1742 | 0.071 | 0.3 | YES |
9 | LIG1 | LIG1 | LIG1 | 1886 | 0.066 | 0.33 | YES |
10 | MNAT1 | MNAT1 | MNAT1 | 2020 | 0.062 | 0.36 | YES |
11 | POLR2L | POLR2L | POLR2L | 2044 | 0.062 | 0.39 | YES |
12 | GTF2H2 | GTF2H2 | GTF2H2 | 2366 | 0.054 | 0.41 | YES |
13 | POLD1 | POLD1 | POLD1 | 2377 | 0.054 | 0.44 | YES |
14 | POLR2H | POLR2H | POLR2H | 2435 | 0.053 | 0.46 | YES |
15 | POLR2F | POLR2F | POLR2F | 2591 | 0.05 | 0.48 | YES |
16 | RPA3 | RPA3 | RPA3 | 2759 | 0.047 | 0.5 | YES |
17 | CCNH | CCNH | CCNH | 2843 | 0.046 | 0.52 | YES |
18 | POLR2E | POLR2E | POLR2E | 3008 | 0.043 | 0.54 | YES |
19 | ERCC8 | ERCC8 | ERCC8 | 3147 | 0.041 | 0.56 | YES |
20 | POLR2I | POLR2I | POLR2I | 3508 | 0.036 | 0.56 | YES |
21 | GTF2H4 | GTF2H4 | GTF2H4 | 3591 | 0.035 | 0.57 | YES |
22 | RFC3 | RFC3 | RFC3 | 3954 | 0.03 | 0.57 | YES |
23 | GTF2H2B | GTF2H2B | GTF2H2B | 4269 | 0.027 | 0.57 | YES |
24 | RPA2 | RPA2 | RPA2 | 4349 | 0.026 | 0.58 | YES |
25 | POLR2A | POLR2A | POLR2A | 4371 | 0.026 | 0.6 | YES |
26 | TCEA1 | TCEA1 | TCEA1 | 4476 | 0.025 | 0.6 | YES |
27 | POLR2D | POLR2D | POLR2D | 4780 | 0.022 | 0.6 | YES |
28 | POLR2G | POLR2G | POLR2G | 4845 | 0.021 | 0.61 | YES |
29 | RPA1 | RPA1 | RPA1 | 5209 | 0.017 | 0.6 | YES |
30 | ERCC1 | ERCC1 | ERCC1 | 5217 | 0.017 | 0.61 | YES |
31 | POLD4 | POLD4 | POLD4 | 5325 | 0.016 | 0.61 | YES |
32 | POLE | POLE | POLE | 5582 | 0.013 | 0.6 | YES |
33 | XAB2 | XAB2 | XAB2 | 5590 | 0.013 | 0.61 | YES |
34 | ERCC3 | ERCC3 | ERCC3 | 6172 | 0.0067 | 0.58 | NO |
35 | GTF2H1 | GTF2H1 | GTF2H1 | 6254 | 0.0058 | 0.58 | NO |
36 | ERCC2 | ERCC2 | ERCC2 | 6338 | 0.0052 | 0.58 | NO |
37 | POLR2B | POLR2B | POLR2B | 6464 | 0.0038 | 0.58 | NO |
38 | POLR2C | POLR2C | POLR2C | 6533 | 0.0031 | 0.57 | NO |
39 | POLR2J | POLR2J | POLR2J | 6646 | 0.0022 | 0.57 | NO |
40 | POLR2K | POLR2K | POLR2K | 7791 | -0.0093 | 0.52 | NO |
41 | ERCC5 | ERCC5 | ERCC5 | 7894 | -0.011 | 0.52 | NO |
42 | POLD3 | POLD3 | POLD3 | 8301 | -0.015 | 0.5 | NO |
43 | ERCC6 | ERCC6 | ERCC6 | 9543 | -0.03 | 0.45 | NO |
44 | ERCC4 | ERCC4 | ERCC4 | 11705 | -0.065 | 0.37 | NO |
Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CELL CYCLE.

Figure S60. 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 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 INOSITOL PHOSPHATE METABOLISM | 54 | genes.ES.table | 0.48 | 1.8 | 0.006 | 0.3 | 0.58 | 0.33 | 0.18 | 0.27 | 0.08 | 0.069 |
KEGG APOPTOSIS | 86 | genes.ES.table | 0.46 | 1.7 | 0.028 | 0.39 | 0.78 | 0.57 | 0.32 | 0.39 | 0.15 | 0.086 |
BIOCARTA HIVNEF PATHWAY | 58 | genes.ES.table | 0.5 | 2.1 | 0.0061 | 0.42 | 0.14 | 0.48 | 0.33 | 0.32 | 0 | 0.099 |
BIOCARTA PYK2 PATHWAY | 28 | genes.ES.table | 0.42 | 1.8 | 0.0099 | 0.28 | 0.59 | 0.36 | 0.24 | 0.27 | 0.075 | 0.064 |
BIOCARTA STRESS PATHWAY | 25 | genes.ES.table | 0.57 | 2 | 0.0019 | 0.21 | 0.18 | 0.44 | 0.24 | 0.34 | 0 | 0.041 |
ST TUMOR NECROSIS FACTOR PATHWAY | 28 | genes.ES.table | 0.55 | 1.8 | 0.01 | 0.31 | 0.53 | 0.54 | 0.28 | 0.39 | 0.078 | 0.07 |
ST INTERLEUKIN 4 PATHWAY | 25 | genes.ES.table | 0.59 | 1.9 | 0.0079 | 0.36 | 0.47 | 0.36 | 0.19 | 0.29 | 0 | 0.078 |
PID BCR 5PATHWAY | 65 | genes.ES.table | 0.58 | 1.8 | 0.03 | 0.37 | 0.72 | 0.48 | 0.24 | 0.36 | 0.12 | 0.078 |
PID TRAIL PATHWAY | 28 | genes.ES.table | 0.56 | 1.9 | 0.012 | 0.32 | 0.48 | 0.57 | 0.31 | 0.4 | 0 | 0.073 |
PID CDC42 PATHWAY | 70 | genes.ES.table | 0.39 | 2 | 0.004 | 0.18 | 0.24 | 0.53 | 0.34 | 0.35 | 0 | 0.037 |
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 | BIRC3 | BIRC3 | BIRC3 | 627 | 0.22 | 0.069 | YES |
2 | TNF | TNF | TNF | 981 | 0.18 | 0.13 | YES |
3 | CASP7 | CASP7 | CASP7 | 1424 | 0.14 | 0.17 | YES |
4 | PRKCD | PRKCD | PRKCD | 2192 | 0.098 | 0.18 | YES |
5 | CFLAR | CFLAR | CFLAR | 2200 | 0.098 | 0.22 | YES |
6 | APAF1 | APAF1 | APAF1 | 2583 | 0.083 | 0.24 | YES |
7 | FAS | FAS | FAS | 2622 | 0.082 | 0.27 | YES |
8 | TRADD | TRADD | TRADD | 2725 | 0.079 | 0.3 | YES |
9 | MAP3K14 | MAP3K14 | MAP3K14 | 3161 | 0.067 | 0.31 | YES |
10 | FASLG | FASLG | FASLG | 3264 | 0.064 | 0.33 | YES |
11 | ARHGDIB | ARHGDIB | ARHGDIB | 3629 | 0.056 | 0.34 | YES |
12 | NFKB1 | NFKB1 | NFKB1 | 3658 | 0.056 | 0.36 | YES |
13 | MDM2 | MDM2 | MDM2 | 3671 | 0.056 | 0.39 | YES |
14 | TNFRSF1B | TNFRSF1B | TNFRSF1B | 3713 | 0.055 | 0.41 | YES |
15 | CRADD | CRADD | CRADD | 3865 | 0.052 | 0.43 | YES |
16 | MAP3K5 | MAP3K5 | MAP3K5 | 4011 | 0.049 | 0.44 | YES |
17 | MAP3K1 | MAP3K1 | MAP3K1 | 4297 | 0.044 | 0.45 | YES |
18 | CASP3 | CASP3 | CASP3 | 4353 | 0.043 | 0.46 | YES |
19 | CHUK | CHUK | CHUK | 4441 | 0.042 | 0.48 | YES |
20 | CASP8 | CASP8 | CASP8 | 4717 | 0.038 | 0.48 | YES |
21 | CASP9 | CASP9 | CASP9 | 5033 | 0.033 | 0.48 | YES |
22 | FADD | FADD | FADD | 5183 | 0.031 | 0.48 | YES |
23 | NFKBIA | NFKBIA | NFKBIA | 5559 | 0.027 | 0.48 | YES |
24 | RB1 | RB1 | RB1 | 5616 | 0.026 | 0.49 | YES |
25 | PSEN1 | PSEN1 | PSEN1 | 5780 | 0.024 | 0.49 | YES |
26 | CYCS | CYCS | CYCS | 5873 | 0.023 | 0.49 | YES |
27 | RELA | RELA | RELA | 6090 | 0.021 | 0.49 | YES |
28 | TRAF1 | TRAF1 | TRAF1 | 6160 | 0.02 | 0.5 | YES |
29 | ACTG1 | ACTG1 | ACTG1 | 6403 | 0.017 | 0.49 | NO |
30 | PAK2 | PAK2 | PAK2 | 6470 | 0.017 | 0.5 | NO |
31 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 6900 | 0.012 | 0.48 | NO |
32 | BIRC2 | BIRC2 | BIRC2 | 7079 | 0.01 | 0.47 | NO |
33 | RASA1 | RASA1 | RASA1 | 7097 | 0.01 | 0.48 | NO |
34 | RIPK1 | RIPK1 | RIPK1 | 7350 | 0.0082 | 0.47 | NO |
35 | CDK11A | CDK11A | CDK11A | 7722 | 0.0044 | 0.45 | NO |
36 | XIAP | XIAP | XIAP | 7893 | 0.003 | 0.44 | NO |
37 | MAPK8 | MAPK8 | MAPK8 | 7894 | 0.003 | 0.44 | NO |
38 | DFFB | DFFB | DFFB | 7898 | 0.003 | 0.44 | NO |
39 | PRKDC | PRKDC | PRKDC | 8286 | -0.00034 | 0.42 | NO |
40 | BAG4 | BAG4 | BAG4 | 8401 | -0.0014 | 0.42 | NO |
41 | LMNA | LMNA | LMNA | 8592 | -0.003 | 0.41 | NO |
42 | NUMA1 | NUMA1 | NUMA1 | 8837 | -0.0051 | 0.4 | NO |
43 | TRAF2 | TRAF2 | TRAF2 | 8937 | -0.006 | 0.4 | NO |
44 | CDK11B | CDK11B | CDK11B | 8977 | -0.0063 | 0.4 | NO |
45 | SPTAN1 | SPTAN1 | SPTAN1 | 9180 | -0.0081 | 0.39 | NO |
46 | BID | BID | BID | 9225 | -0.0085 | 0.39 | NO |
47 | PSEN2 | PSEN2 | PSEN2 | 9295 | -0.0091 | 0.39 | NO |
48 | PARP1 | PARP1 | PARP1 | 9356 | -0.0096 | 0.39 | NO |
49 | CASP6 | CASP6 | CASP6 | 9373 | -0.0098 | 0.4 | NO |
50 | GSN | GSN | GSN | 9476 | -0.011 | 0.4 | NO |
51 | PTK2 | PTK2 | PTK2 | 9654 | -0.012 | 0.39 | NO |
52 | MAP2K7 | MAP2K7 | MAP2K7 | 9850 | -0.014 | 0.39 | NO |
53 | DAXX | DAXX | DAXX | 10532 | -0.02 | 0.36 | NO |
54 | LMNB1 | LMNB1 | LMNB1 | 10706 | -0.022 | 0.36 | NO |
55 | LMNB2 | LMNB2 | LMNB2 | 10768 | -0.022 | 0.37 | NO |
56 | CASP2 | CASP2 | CASP2 | 11180 | -0.026 | 0.36 | NO |
57 | DFFA | DFFA | DFFA | 11894 | -0.034 | 0.34 | NO |
58 | BCL2 | BCL2 | BCL2 | 14047 | -0.064 | 0.25 | 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 INOSITOL PHOSPHATE METABOLISM.

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

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 | HIP1R | HIP1R | HIP1R | 1259 | 0.15 | -0.0095 | YES |
2 | TBC1D8B | TBC1D8B | TBC1D8B | 1344 | 0.15 | 0.042 | YES |
3 | CPD | CPD | CPD | 1434 | 0.14 | 0.091 | YES |
4 | AP4B1 | AP4B1 | AP4B1 | 1976 | 0.11 | 0.1 | YES |
5 | AP1M2 | AP1M2 | AP1M2 | 2255 | 0.096 | 0.13 | YES |
6 | VAMP8 | VAMP8 | VAMP8 | 2376 | 0.091 | 0.15 | YES |
7 | GAK | GAK | GAK | 2569 | 0.084 | 0.18 | YES |
8 | DNM2 | DNM2 | DNM2 | 2712 | 0.079 | 0.2 | YES |
9 | SH3GL2 | SH3GL2 | SH3GL2 | 2966 | 0.072 | 0.21 | YES |
10 | AP1G1 | AP1G1 | AP1G1 | 2980 | 0.072 | 0.24 | YES |
11 | TFRC | TFRC | TFRC | 3079 | 0.069 | 0.26 | YES |
12 | TPD52 | TPD52 | TPD52 | 3103 | 0.068 | 0.28 | YES |
13 | AP3B1 | AP3B1 | AP3B1 | 3554 | 0.058 | 0.28 | YES |
14 | TXNDC5 | TXNDC5 | TXNDC5 | 3753 | 0.054 | 0.29 | YES |
15 | NECAP1 | NECAP1 | NECAP1 | 3912 | 0.051 | 0.3 | YES |
16 | TGOLN2 | TGOLN2 | TGOLN2 | 3931 | 0.051 | 0.32 | YES |
17 | ARRB1 | ARRB1 | ARRB1 | 4236 | 0.045 | 0.32 | YES |
18 | SNX2 | SNX2 | SNX2 | 4333 | 0.044 | 0.34 | YES |
19 | AP1B1 | AP1B1 | AP1B1 | 4426 | 0.042 | 0.35 | YES |
20 | CLTC | CLTC | CLTC | 4579 | 0.04 | 0.35 | YES |
21 | AP4E1 | AP4E1 | AP4E1 | 4769 | 0.037 | 0.36 | YES |
22 | DNASE2 | DNASE2 | DNASE2 | 4833 | 0.036 | 0.37 | YES |
23 | PIK3C2A | PIK3C2A | PIK3C2A | 4918 | 0.035 | 0.38 | YES |
24 | YIPF6 | YIPF6 | YIPF6 | 4980 | 0.034 | 0.39 | YES |
25 | GBF1 | GBF1 | GBF1 | 5196 | 0.031 | 0.39 | YES |
26 | NAPA | NAPA | NAPA | 5272 | 0.03 | 0.39 | YES |
27 | BLOC1S1 | BLOC1S1 | BLOC1S1 | 5484 | 0.027 | 0.39 | YES |
28 | STX4 | STX4 | STX4 | 5611 | 0.026 | 0.4 | YES |
29 | SNAP23 | SNAP23 | SNAP23 | 6158 | 0.02 | 0.38 | NO |
30 | TPD52L1 | TPD52L1 | TPD52L1 | 6445 | 0.017 | 0.37 | NO |
31 | CNO | CNO | CNO | 6553 | 0.016 | 0.37 | NO |
32 | ARF1 | ARF1 | ARF1 | 6960 | 0.012 | 0.35 | NO |
33 | RAB5C | RAB5C | RAB5C | 7072 | 0.011 | 0.35 | NO |
34 | AP1S1 | AP1S1 | AP1S1 | 7344 | 0.0082 | 0.34 | NO |
35 | PICALM | PICALM | PICALM | 7348 | 0.0082 | 0.34 | NO |
36 | BLOC1S3 | BLOC1S3 | BLOC1S3 | 7598 | 0.006 | 0.33 | NO |
37 | VAMP7 | VAMP7 | VAMP7 | 8032 | 0.0019 | 0.3 | NO |
38 | M6PR | M6PR | M6PR | 8062 | 0.0017 | 0.3 | NO |
39 | HSPA8 | HSPA8 | HSPA8 | 8361 | -0.0011 | 0.29 | NO |
40 | IGF2R | IGF2R | IGF2R | 8483 | -0.002 | 0.28 | NO |
41 | GNS | GNS | GNS | 8550 | -0.0027 | 0.28 | NO |
42 | OCRL | OCRL | OCRL | 8716 | -0.004 | 0.27 | NO |
43 | CLTA | CLTA | CLTA | 8783 | -0.0046 | 0.27 | NO |
44 | FTL | FTL | FTL | 8942 | -0.006 | 0.26 | NO |
45 | SNX5 | SNX5 | SNX5 | 9349 | -0.0095 | 0.25 | NO |
46 | PUM1 | PUM1 | PUM1 | 9531 | -0.011 | 0.24 | NO |
47 | PLDN | PLDN | PLDN | 9605 | -0.012 | 0.24 | NO |
48 | CTSZ | CTSZ | CTSZ | 9828 | -0.014 | 0.24 | NO |
49 | SNX9 | SNX9 | SNX9 | 10503 | -0.02 | 0.21 | NO |
50 | SNAPIN | SNAPIN | SNAPIN | 10783 | -0.022 | 0.2 | NO |
51 | AP3S1 | AP3S1 | AP3S1 | 12208 | -0.037 | 0.14 | NO |
52 | AP1M1 | AP1M1 | AP1M1 | 12221 | -0.037 | 0.15 | NO |
53 | SORT1 | SORT1 | SORT1 | 12332 | -0.038 | 0.16 | NO |
54 | FTH1 | FTH1 | FTH1 | 12893 | -0.046 | 0.15 | NO |
55 | DTNBP1 | DTNBP1 | DTNBP1 | 13037 | -0.048 | 0.16 | NO |
56 | VAMP2 | VAMP2 | VAMP2 | 13072 | -0.048 | 0.18 | NO |
57 | DNAJC6 | DNAJC6 | DNAJC6 | 14040 | -0.064 | 0.15 | NO |
58 | SH3D19 | SH3D19 | SH3D19 | 14400 | -0.072 | 0.16 | NO |
59 | AP1S2 | AP1S2 | AP1S2 | 17438 | -0.19 | 0.066 | 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 APOPTOSIS.

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG APOPTOSIS, 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 | TNF | TNF | TNF | 981 | 0.18 | 0.13 | YES |
2 | LTA | LTA | LTA | 2181 | 0.099 | 0.17 | YES |
3 | TRADD | TRADD | TRADD | 2725 | 0.079 | 0.22 | YES |
4 | MAP2K3 | MAP2K3 | MAP2K3 | 2848 | 0.075 | 0.29 | YES |
5 | MAP3K14 | MAP3K14 | MAP3K14 | 3161 | 0.067 | 0.35 | YES |
6 | NFKB1 | NFKB1 | NFKB1 | 3658 | 0.056 | 0.38 | YES |
7 | CRADD | CRADD | CRADD | 3865 | 0.052 | 0.42 | YES |
8 | MAP2K6 | MAP2K6 | MAP2K6 | 4288 | 0.044 | 0.44 | YES |
9 | MAP3K1 | MAP3K1 | MAP3K1 | 4297 | 0.044 | 0.49 | YES |
10 | IKBKB | IKBKB | IKBKB | 4430 | 0.042 | 0.52 | YES |
11 | CHUK | CHUK | CHUK | 4441 | 0.042 | 0.57 | YES |
12 | NFKBIA | NFKBIA | NFKBIA | 5559 | 0.027 | 0.53 | NO |
13 | RELA | RELA | RELA | 6090 | 0.021 | 0.53 | NO |
14 | TANK | TANK | TANK | 6262 | 0.019 | 0.54 | NO |
15 | IKBKG | IKBKG | IKBKG | 6840 | 0.013 | 0.52 | NO |
16 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 6900 | 0.012 | 0.53 | NO |
17 | RIPK1 | RIPK1 | RIPK1 | 7350 | 0.0082 | 0.51 | NO |
18 | MAPK8 | MAPK8 | MAPK8 | 7894 | 0.003 | 0.49 | NO |
19 | MAP2K4 | MAP2K4 | MAP2K4 | 8605 | -0.0031 | 0.45 | NO |
20 | JUN | JUN | JUN | 8713 | -0.004 | 0.45 | NO |
21 | TRAF2 | TRAF2 | TRAF2 | 8937 | -0.006 | 0.45 | NO |
22 | MAP4K2 | MAP4K2 | MAP4K2 | 9022 | -0.0067 | 0.45 | NO |
23 | MAPK14 | MAPK14 | MAPK14 | 10041 | -0.016 | 0.41 | NO |
24 | ATF1 | ATF1 | ATF1 | 11043 | -0.025 | 0.38 | NO |
25 | CASP2 | CASP2 | CASP2 | 11180 | -0.026 | 0.4 | 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: BIOCARTA HIVNEF PATHWAY.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HIVNEF PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | HIP1R | HIP1R | HIP1R | 1259 | 0.15 | -0.0064 | YES |
2 | TBC1D8B | TBC1D8B | TBC1D8B | 1344 | 0.15 | 0.048 | YES |
3 | CPD | CPD | CPD | 1434 | 0.14 | 0.1 | YES |
4 | AP4B1 | AP4B1 | AP4B1 | 1976 | 0.11 | 0.12 | YES |
5 | AP1M2 | AP1M2 | AP1M2 | 2255 | 0.096 | 0.14 | YES |
6 | VAMP8 | VAMP8 | VAMP8 | 2376 | 0.091 | 0.17 | YES |
7 | GAK | GAK | GAK | 2569 | 0.084 | 0.19 | YES |
8 | DNM2 | DNM2 | DNM2 | 2712 | 0.079 | 0.22 | YES |
9 | SH3GL2 | SH3GL2 | SH3GL2 | 2966 | 0.072 | 0.23 | YES |
10 | AP1G1 | AP1G1 | AP1G1 | 2980 | 0.072 | 0.26 | YES |
11 | TFRC | TFRC | TFRC | 3079 | 0.069 | 0.28 | YES |
12 | TPD52 | TPD52 | TPD52 | 3103 | 0.068 | 0.31 | YES |
13 | AP3B1 | AP3B1 | AP3B1 | 3554 | 0.058 | 0.31 | YES |
14 | TXNDC5 | TXNDC5 | TXNDC5 | 3753 | 0.054 | 0.32 | YES |
15 | NECAP1 | NECAP1 | NECAP1 | 3912 | 0.051 | 0.33 | YES |
16 | TGOLN2 | TGOLN2 | TGOLN2 | 3931 | 0.051 | 0.35 | YES |
17 | ARRB1 | ARRB1 | ARRB1 | 4236 | 0.045 | 0.35 | YES |
18 | SNX2 | SNX2 | SNX2 | 4333 | 0.044 | 0.36 | YES |
19 | AP1B1 | AP1B1 | AP1B1 | 4426 | 0.042 | 0.38 | YES |
20 | CLTC | CLTC | CLTC | 4579 | 0.04 | 0.38 | YES |
21 | AP4E1 | AP4E1 | AP4E1 | 4769 | 0.037 | 0.39 | YES |
22 | PIK3C2A | PIK3C2A | PIK3C2A | 4918 | 0.035 | 0.4 | YES |
23 | YIPF6 | YIPF6 | YIPF6 | 4980 | 0.034 | 0.41 | YES |
24 | NAPA | NAPA | NAPA | 5272 | 0.03 | 0.4 | NO |
25 | BLOC1S1 | BLOC1S1 | BLOC1S1 | 5484 | 0.027 | 0.4 | NO |
26 | TPD52L1 | TPD52L1 | TPD52L1 | 6445 | 0.017 | 0.36 | NO |
27 | CNO | CNO | CNO | 6553 | 0.016 | 0.36 | NO |
28 | ARF1 | ARF1 | ARF1 | 6960 | 0.012 | 0.34 | NO |
29 | RAB5C | RAB5C | RAB5C | 7072 | 0.011 | 0.34 | NO |
30 | AP1S1 | AP1S1 | AP1S1 | 7344 | 0.0082 | 0.33 | NO |
31 | PICALM | PICALM | PICALM | 7348 | 0.0082 | 0.33 | NO |
32 | BLOC1S3 | BLOC1S3 | BLOC1S3 | 7598 | 0.006 | 0.32 | NO |
33 | VAMP7 | VAMP7 | VAMP7 | 8032 | 0.0019 | 0.3 | NO |
34 | HSPA8 | HSPA8 | HSPA8 | 8361 | -0.0011 | 0.28 | NO |
35 | IGF2R | IGF2R | IGF2R | 8483 | -0.002 | 0.28 | NO |
36 | OCRL | OCRL | OCRL | 8716 | -0.004 | 0.26 | NO |
37 | CLTA | CLTA | CLTA | 8783 | -0.0046 | 0.26 | NO |
38 | FTL | FTL | FTL | 8942 | -0.006 | 0.26 | NO |
39 | SNX5 | SNX5 | SNX5 | 9349 | -0.0095 | 0.24 | NO |
40 | PUM1 | PUM1 | PUM1 | 9531 | -0.011 | 0.23 | NO |
41 | PLDN | PLDN | PLDN | 9605 | -0.012 | 0.23 | NO |
42 | SNX9 | SNX9 | SNX9 | 10503 | -0.02 | 0.19 | NO |
43 | SNAPIN | SNAPIN | SNAPIN | 10783 | -0.022 | 0.19 | NO |
44 | AP3S1 | AP3S1 | AP3S1 | 12208 | -0.037 | 0.13 | NO |
45 | AP1M1 | AP1M1 | AP1M1 | 12221 | -0.037 | 0.14 | NO |
46 | SORT1 | SORT1 | SORT1 | 12332 | -0.038 | 0.15 | NO |
47 | FTH1 | FTH1 | FTH1 | 12893 | -0.046 | 0.14 | NO |
48 | DTNBP1 | DTNBP1 | DTNBP1 | 13037 | -0.048 | 0.15 | NO |
49 | VAMP2 | VAMP2 | VAMP2 | 13072 | -0.048 | 0.17 | NO |
50 | DNAJC6 | DNAJC6 | DNAJC6 | 14040 | -0.064 | 0.14 | NO |
51 | SH3D19 | SH3D19 | SH3D19 | 14400 | -0.072 | 0.15 | NO |
52 | AP1S2 | AP1S2 | AP1S2 | 17438 | -0.19 | 0.066 | NO |
Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PYK2 PATHWAY.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table 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 | MYL2 | MYL2 | MYL2 | 1553 | 0.13 | -0.035 | YES |
2 | CDH1 | CDH1 | CDH1 | 1870 | 0.11 | -0.011 | YES |
3 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 1985 | 0.11 | 0.022 | YES |
4 | CDC42BPA | CDC42BPA | CDC42BPA | 2067 | 0.1 | 0.055 | YES |
5 | LIMK2 | LIMK2 | LIMK2 | 2307 | 0.094 | 0.076 | YES |
6 | F2RL2 | F2RL2 | F2RL2 | 2434 | 0.089 | 0.1 | YES |
7 | PLD1 | PLD1 | PLD1 | 2568 | 0.084 | 0.12 | YES |
8 | MAP2K3 | MAP2K3 | MAP2K3 | 2848 | 0.075 | 0.14 | YES |
9 | DLG1 | DLG1 | DLG1 | 2883 | 0.074 | 0.16 | YES |
10 | SRC | SRC | SRC | 2915 | 0.073 | 0.19 | YES |
11 | CTNNA1 | CTNNA1 | CTNNA1 | 3155 | 0.067 | 0.2 | YES |
12 | ARPC1B | ARPC1B | ARPC1B | 3330 | 0.063 | 0.21 | YES |
13 | BCAR1 | BCAR1 | BCAR1 | 3437 | 0.06 | 0.23 | YES |
14 | MAP3K11 | MAP3K11 | MAP3K11 | 3605 | 0.057 | 0.24 | YES |
15 | TIAM1 | TIAM1 | TIAM1 | 3667 | 0.056 | 0.26 | YES |
16 | EPS8 | EPS8 | EPS8 | 3831 | 0.052 | 0.26 | YES |
17 | TNK2 | TNK2 | TNK2 | 4000 | 0.05 | 0.27 | YES |
18 | IQGAP3 | IQGAP3 | IQGAP3 | 4085 | 0.048 | 0.29 | YES |
19 | PAK1 | PAK1 | PAK1 | 4147 | 0.047 | 0.3 | YES |
20 | MAP2K6 | MAP2K6 | MAP2K6 | 4288 | 0.044 | 0.31 | YES |
21 | MAP3K1 | MAP3K1 | MAP3K1 | 4297 | 0.044 | 0.32 | YES |
22 | PRKCE | PRKCE | PRKCE | 4385 | 0.043 | 0.34 | YES |
23 | RAF1 | RAF1 | RAF1 | 4396 | 0.042 | 0.35 | YES |
24 | ARPC4 | ARPC4 | ARPC4 | 4488 | 0.041 | 0.36 | YES |
25 | APC | APC | APC | 4610 | 0.039 | 0.37 | YES |
26 | MAPK9 | MAPK9 | MAPK9 | 4744 | 0.037 | 0.37 | YES |
27 | IQGAP1 | IQGAP1 | IQGAP1 | 4857 | 0.035 | 0.38 | YES |
28 | ATF2 | ATF2 | ATF2 | 5199 | 0.031 | 0.37 | YES |
29 | WASL | WASL | WASL | 5302 | 0.03 | 0.38 | YES |
30 | YES1 | YES1 | YES1 | 5465 | 0.028 | 0.38 | YES |
31 | PAX6 | PAX6 | PAX6 | 5477 | 0.028 | 0.39 | YES |
32 | MAPK3 | MAPK3 | MAPK3 | 5794 | 0.024 | 0.38 | YES |
33 | ACTR3 | ACTR3 | ACTR3 | 6009 | 0.022 | 0.38 | YES |
34 | ACTR2 | ACTR2 | ACTR2 | 6075 | 0.021 | 0.38 | YES |
35 | MTOR | MTOR | MTOR | 6110 | 0.02 | 0.39 | YES |
36 | ARPC3 | ARPC3 | ARPC3 | 6233 | 0.019 | 0.39 | YES |
37 | BRAF | BRAF | BRAF | 6257 | 0.019 | 0.39 | YES |
38 | PAK2 | PAK2 | PAK2 | 6470 | 0.017 | 0.39 | NO |
39 | ARPC2 | ARPC2 | ARPC2 | 6496 | 0.016 | 0.39 | NO |
40 | ARHGDIA | ARHGDIA | ARHGDIA | 6646 | 0.015 | 0.39 | NO |
41 | PRKCZ | PRKCZ | PRKCZ | 6750 | 0.014 | 0.39 | NO |
42 | CFL1 | CFL1 | CFL1 | 6787 | 0.013 | 0.39 | NO |
43 | ARPC5 | ARPC5 | ARPC5 | 6867 | 0.013 | 0.39 | NO |
44 | RAC1 | RAC1 | RAC1 | 7207 | 0.0094 | 0.38 | NO |
45 | PIK3CA | PIK3CA | PIK3CA | 7464 | 0.0073 | 0.37 | NO |
46 | PAK4 | PAK4 | PAK4 | 7666 | 0.0051 | 0.36 | NO |
47 | MAPK8 | MAPK8 | MAPK8 | 7894 | 0.003 | 0.35 | NO |
48 | GSK3B | GSK3B | GSK3B | 8204 | 0.00037 | 0.33 | NO |
49 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 8514 | -0.0023 | 0.31 | NO |
50 | MAP2K4 | MAP2K4 | MAP2K4 | 8605 | -0.0031 | 0.31 | NO |
51 | CDC42 | CDC42 | CDC42 | 8654 | -0.0035 | 0.31 | NO |
52 | JUN | JUN | JUN | 8713 | -0.004 | 0.31 | NO |
53 | EXOC7 | EXOC7 | EXOC7 | 8801 | -0.0048 | 0.3 | NO |
54 | MAPK1 | MAPK1 | MAPK1 | 8979 | -0.0063 | 0.3 | NO |
55 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 9800 | -0.013 | 0.26 | NO |
56 | MAP2K7 | MAP2K7 | MAP2K7 | 9850 | -0.014 | 0.26 | NO |
57 | MAPK14 | MAPK14 | MAPK14 | 10041 | -0.016 | 0.26 | NO |
58 | PARD6A | PARD6A | PARD6A | 10961 | -0.024 | 0.22 | NO |
59 | CBL | CBL | CBL | 11066 | -0.025 | 0.22 | NO |
60 | VAV2 | VAV2 | VAV2 | 11469 | -0.029 | 0.21 | NO |
61 | SEPT2 | SEPT2 | SEPT2 | 11779 | -0.032 | 0.2 | NO |
62 | RASGRF1 | RASGRF1 | RASGRF1 | 11811 | -0.033 | 0.21 | NO |
63 | BAIAP2 | BAIAP2 | BAIAP2 | 11821 | -0.033 | 0.22 | NO |
64 | DIAPH3 | DIAPH3 | DIAPH3 | 12464 | -0.04 | 0.2 | NO |
65 | LIMK1 | LIMK1 | LIMK1 | 12563 | -0.041 | 0.21 | NO |
66 | CTNNB1 | CTNNB1 | CTNNB1 | 12935 | -0.046 | 0.21 | NO |
67 | HRAS | HRAS | HRAS | 13778 | -0.059 | 0.19 | NO |
68 | PIK3R1 | PIK3R1 | PIK3R1 | 14200 | -0.068 | 0.19 | NO |
69 | ENAH | ENAH | ENAH | 14301 | -0.07 | 0.21 | NO |
70 | HES5 | HES5 | HES5 | 14539 | -0.075 | 0.22 | NO |
Figure S69. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA STRESS PATHWAY.

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

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | HDAC9 | HDAC9 | HDAC9 | 371 | 0.28 | 0.079 | YES |
2 | PPARG | PPARG | PPARG | 891 | 0.19 | 0.12 | YES |
3 | TNF | TNF | TNF | 981 | 0.18 | 0.17 | YES |
4 | ZFPM1 | ZFPM1 | ZFPM1 | 1273 | 0.15 | 0.21 | YES |
5 | KAT2B | KAT2B | KAT2B | 1693 | 0.12 | 0.23 | YES |
6 | GATA1 | GATA1 | GATA1 | 2126 | 0.1 | 0.24 | YES |
7 | MXD1 | MXD1 | MXD1 | 2141 | 0.1 | 0.28 | YES |
8 | SIRT7 | SIRT7 | SIRT7 | 2258 | 0.096 | 0.31 | YES |
9 | SMURF1 | SMURF1 | SMURF1 | 2304 | 0.094 | 0.34 | YES |
10 | GATA2 | GATA2 | GATA2 | 2634 | 0.082 | 0.35 | YES |
11 | NFKB1 | NFKB1 | NFKB1 | 3658 | 0.056 | 0.31 | NO |
12 | SIRT6 | SIRT6 | SIRT6 | 5325 | 0.03 | 0.23 | NO |
13 | NFKBIA | NFKBIA | NFKBIA | 5559 | 0.027 | 0.23 | NO |
14 | MBD2 | MBD2 | MBD2 | 5876 | 0.023 | 0.22 | NO |
15 | RELA | RELA | RELA | 6090 | 0.021 | 0.22 | NO |
16 | NCOR1 | NCOR1 | NCOR1 | 6253 | 0.019 | 0.22 | NO |
17 | RANBP2 | RANBP2 | RANBP2 | 6260 | 0.019 | 0.22 | NO |
18 | WDR77 | WDR77 | WDR77 | 6602 | 0.015 | 0.21 | NO |
19 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 6900 | 0.012 | 0.2 | NO |
20 | HDAC10 | HDAC10 | HDAC10 | 7060 | 0.011 | 0.19 | NO |
21 | SIRT2 | SIRT2 | SIRT2 | 7159 | 0.0097 | 0.19 | NO |
22 | TFCP2 | TFCP2 | TFCP2 | 7377 | 0.008 | 0.18 | NO |
23 | GATAD2A | GATAD2A | GATAD2A | 7454 | 0.0074 | 0.18 | NO |
24 | STAT3 | STAT3 | STAT3 | 7498 | 0.0071 | 0.18 | NO |
25 | CREBBP | CREBBP | CREBBP | 7609 | 0.0058 | 0.18 | NO |
26 | EP300 | EP300 | EP300 | 7820 | 0.0036 | 0.17 | NO |
27 | SMG5 | SMG5 | SMG5 | 8022 | 0.002 | 0.16 | NO |
28 | CHD3 | CHD3 | CHD3 | 8322 | -0.00075 | 0.14 | NO |
29 | HDAC1 | HDAC1 | HDAC1 | 8721 | -0.0041 | 0.12 | NO |
30 | HDAC3 | HDAC3 | HDAC3 | 8945 | -0.006 | 0.11 | NO |
31 | NCOR2 | NCOR2 | NCOR2 | 8971 | -0.0062 | 0.11 | NO |
32 | SIRT1 | SIRT1 | SIRT1 | 9024 | -0.0067 | 0.11 | NO |
33 | XPO1 | XPO1 | XPO1 | 9036 | -0.0068 | 0.11 | NO |
34 | SIN3A | SIN3A | SIN3A | 9122 | -0.0076 | 0.11 | NO |
35 | RANGAP1 | RANGAP1 | RANGAP1 | 9192 | -0.0083 | 0.11 | NO |
36 | HDAC6 | HDAC6 | HDAC6 | 9326 | -0.0094 | 0.11 | NO |
37 | MTA2 | MTA2 | MTA2 | 9359 | -0.0096 | 0.11 | NO |
38 | HDAC7 | HDAC7 | HDAC7 | 9538 | -0.011 | 0.1 | NO |
39 | YY1 | YY1 | YY1 | 9545 | -0.011 | 0.1 | NO |
40 | RBBP7 | RBBP7 | RBBP7 | 9739 | -0.013 | 0.1 | NO |
41 | HDAC8 | HDAC8 | HDAC8 | 10044 | -0.016 | 0.089 | NO |
42 | SUMO1 | SUMO1 | SUMO1 | 10075 | -0.016 | 0.092 | NO |
43 | GATAD2B | GATAD2B | GATAD2B | 10130 | -0.016 | 0.095 | NO |
44 | SIRT5 | SIRT5 | SIRT5 | 10179 | -0.017 | 0.099 | NO |
45 | SAP30 | SAP30 | SAP30 | 10182 | -0.017 | 0.1 | NO |
46 | RAN | RAN | RAN | 10295 | -0.018 | 0.1 | NO |
47 | SIN3B | SIN3B | SIN3B | 11433 | -0.029 | 0.054 | NO |
48 | CHD4 | CHD4 | CHD4 | 11458 | -0.029 | 0.062 | NO |
49 | RBBP4 | RBBP4 | RBBP4 | 11734 | -0.032 | 0.059 | NO |
50 | MAX | MAX | MAX | 11736 | -0.032 | 0.07 | NO |
51 | MBD3 | MBD3 | MBD3 | 11909 | -0.034 | 0.073 | NO |
52 | PRKACA | PRKACA | PRKACA | 11925 | -0.034 | 0.084 | NO |
53 | NR2C1 | NR2C1 | NR2C1 | 12028 | -0.035 | 0.09 | NO |
54 | UBE2I | UBE2I | UBE2I | 12326 | -0.038 | 0.088 | NO |
55 | PRMT5 | PRMT5 | PRMT5 | 12378 | -0.039 | 0.099 | NO |
56 | SSPO | SSPO | SSPO | 12401 | -0.039 | 0.11 | NO |
57 | SAP18 | SAP18 | SAP18 | 12715 | -0.043 | 0.11 | NO |
58 | FKBP3 | FKBP3 | FKBP3 | 12887 | -0.046 | 0.12 | NO |
59 | SMAD7 | SMAD7 | SMAD7 | 12902 | -0.046 | 0.13 | NO |
60 | SIRT3 | SIRT3 | SIRT3 | 13283 | -0.051 | 0.13 | NO |
61 | HDAC2 | HDAC2 | HDAC2 | 14141 | -0.066 | 0.11 | NO |
62 | HDAC5 | HDAC5 | HDAC5 | 14808 | -0.082 | 0.099 | NO |
63 | HDAC11 | HDAC11 | HDAC11 | 14922 | -0.085 | 0.12 | NO |
64 | SIRT4 | SIRT4 | SIRT4 | 15679 | -0.11 | 0.12 | NO |
65 | HDAC4 | HDAC4 | HDAC4 | 15921 | -0.12 | 0.15 | 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: ST TUMOR NECROSIS FACTOR PATHWAY.

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

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NR0B2 | NR0B2 | NR0B2 | 146 | 0.38 | 0.2 | YES |
2 | SERPINA4 | SERPINA4 | SERPINA4 | 159 | 0.37 | 0.4 | YES |
3 | JAK2 | JAK2 | JAK2 | 977 | 0.18 | 0.45 | YES |
4 | IL2RG | IL2RG | IL2RG | 1667 | 0.13 | 0.49 | YES |
5 | PI3 | PI3 | PI3 | 2101 | 0.1 | 0.52 | YES |
6 | INPP5D | INPP5D | INPP5D | 2746 | 0.078 | 0.53 | YES |
7 | SRC | SRC | SRC | 2915 | 0.073 | 0.56 | YES |
8 | TYK2 | TYK2 | TYK2 | 3313 | 0.063 | 0.57 | YES |
9 | PPP1R13B | PPP1R13B | PPP1R13B | 3575 | 0.058 | 0.59 | YES |
10 | JAK3 | JAK3 | JAK3 | 4372 | 0.043 | 0.57 | NO |
11 | JAK1 | JAK1 | JAK1 | 4556 | 0.04 | 0.58 | NO |
12 | IL4R | IL4R | IL4R | 5872 | 0.023 | 0.52 | NO |
13 | STAT6 | STAT6 | STAT6 | 5981 | 0.022 | 0.53 | NO |
14 | GRB2 | GRB2 | GRB2 | 6193 | 0.02 | 0.53 | NO |
15 | SOS2 | SOS2 | SOS2 | 7365 | 0.0081 | 0.47 | NO |
16 | PIK3CA | PIK3CA | PIK3CA | 7464 | 0.0073 | 0.47 | NO |
17 | AKT1 | AKT1 | AKT1 | 7547 | 0.0066 | 0.47 | NO |
18 | IARS | IARS | IARS | 7569 | 0.0062 | 0.47 | NO |
19 | SOS1 | SOS1 | SOS1 | 7962 | 0.0025 | 0.45 | NO |
20 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 8514 | -0.0023 | 0.42 | NO |
21 | IL13RA1 | IL13RA1 | IL13RA1 | 9579 | -0.012 | 0.37 | NO |
22 | SHC1 | SHC1 | SHC1 | 9901 | -0.014 | 0.36 | NO |
23 | CISH | CISH | CISH | 11653 | -0.031 | 0.28 | NO |
24 | AKT2 | AKT2 | AKT2 | 12096 | -0.036 | 0.28 | NO |
25 | AKT3 | AKT3 | AKT3 | 16419 | -0.14 | 0.12 | 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: ST INTERLEUKIN 4 PATHWAY.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: ST INTERLEUKIN 4 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | TNFRSF10C | TNFRSF10C | TNFRSF10C | 1206 | 0.16 | 0.064 | YES |
2 | CASP10 | CASP10 | CASP10 | 1363 | 0.14 | 0.17 | YES |
3 | TNFSF10 | TNFSF10 | TNFSF10 | 1919 | 0.11 | 0.24 | YES |
4 | CFLAR | CFLAR | CFLAR | 2200 | 0.098 | 0.3 | YES |
5 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 2373 | 0.091 | 0.37 | YES |
6 | TRADD | TRADD | TRADD | 2725 | 0.079 | 0.41 | YES |
7 | PIK3CB | PIK3CB | PIK3CB | 3365 | 0.062 | 0.43 | YES |
8 | MAP3K1 | MAP3K1 | MAP3K1 | 4297 | 0.044 | 0.42 | YES |
9 | IKBKB | IKBKB | IKBKB | 4430 | 0.042 | 0.44 | YES |
10 | PIK3CD | PIK3CD | PIK3CD | 4439 | 0.042 | 0.48 | YES |
11 | CHUK | CHUK | CHUK | 4441 | 0.042 | 0.51 | YES |
12 | CASP8 | CASP8 | CASP8 | 4717 | 0.038 | 0.53 | YES |
13 | FADD | FADD | FADD | 5183 | 0.031 | 0.53 | YES |
14 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 5467 | 0.028 | 0.54 | YES |
15 | PIK3R3 | PIK3R3 | PIK3R3 | 5613 | 0.026 | 0.55 | YES |
16 | MAPK3 | MAPK3 | MAPK3 | 5794 | 0.024 | 0.56 | YES |
17 | IKBKG | IKBKG | IKBKG | 6840 | 0.013 | 0.51 | NO |
18 | RIPK1 | RIPK1 | RIPK1 | 7350 | 0.0082 | 0.49 | NO |
19 | PIK3CA | PIK3CA | PIK3CA | 7464 | 0.0073 | 0.49 | NO |
20 | MAPK8 | MAPK8 | MAPK8 | 7894 | 0.003 | 0.47 | NO |
21 | SMPD1 | SMPD1 | SMPD1 | 8177 | 0.0006 | 0.46 | NO |
22 | TNFRSF10D | TNFRSF10D | TNFRSF10D | 8272 | -0.00024 | 0.45 | NO |
23 | MAP2K4 | MAP2K4 | MAP2K4 | 8605 | -0.0031 | 0.44 | NO |
24 | TRAF2 | TRAF2 | TRAF2 | 8937 | -0.006 | 0.42 | NO |
25 | MAPK1 | MAPK1 | MAPK1 | 8979 | -0.0063 | 0.43 | NO |
26 | DAP3 | DAP3 | DAP3 | 10191 | -0.017 | 0.38 | NO |
27 | PIK3R2 | PIK3R2 | PIK3R2 | 11309 | -0.028 | 0.34 | NO |
28 | PIK3R1 | PIK3R1 | PIK3R1 | 14200 | -0.068 | 0.24 | 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: PID BCR 5PATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: PID BCR 5PATHWAY, 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 | BLNK | BLNK | BLNK | 243 | 0.33 | 0.046 | YES |
2 | BLK | BLK | BLK | 277 | 0.31 | 0.099 | YES |
3 | CD79A | CD79A | CD79A | 316 | 0.3 | 0.15 | YES |
4 | CD19 | CD19 | CD19 | 702 | 0.22 | 0.17 | YES |
5 | CD79B | CD79B | CD79B | 864 | 0.19 | 0.19 | YES |
6 | CARD11 | CARD11 | CARD11 | 942 | 0.18 | 0.22 | YES |
7 | BTK | BTK | BTK | 1163 | 0.16 | 0.24 | YES |
8 | RASGRP1 | RASGRP1 | RASGRP1 | 1673 | 0.13 | 0.23 | YES |
9 | CBLB | CBLB | CBLB | 1927 | 0.11 | 0.24 | YES |
10 | VAV1 | VAV1 | VAV1 | 1943 | 0.11 | 0.26 | YES |
11 | REL | REL | REL | 1979 | 0.11 | 0.28 | YES |
12 | PRKCB | PRKCB | PRKCB | 2025 | 0.11 | 0.29 | YES |
13 | BCL10 | BCL10 | BCL10 | 2124 | 0.1 | 0.3 | YES |
14 | RASGRP3 | RASGRP3 | RASGRP3 | 2136 | 0.1 | 0.32 | YES |
15 | ITPR3 | ITPR3 | ITPR3 | 2357 | 0.092 | 0.33 | YES |
16 | LYN | LYN | LYN | 2428 | 0.089 | 0.34 | YES |
17 | SYK | SYK | SYK | 2670 | 0.08 | 0.34 | YES |
18 | NFKBIE | NFKBIE | NFKBIE | 2671 | 0.08 | 0.36 | YES |
19 | PSME4 | PSME4 | PSME4 | 2867 | 0.075 | 0.36 | YES |
20 | NR4A1 | NR4A1 | NR4A1 | 2904 | 0.074 | 0.37 | YES |
21 | PLCG2 | PLCG2 | PLCG2 | 3015 | 0.071 | 0.38 | YES |
22 | SH3KBP1 | SH3KBP1 | SH3KBP1 | 3084 | 0.069 | 0.38 | YES |
23 | PHLPP1 | PHLPP1 | PHLPP1 | 3174 | 0.066 | 0.39 | YES |
24 | MDM2 | MDM2 | MDM2 | 3671 | 0.056 | 0.37 | YES |
25 | PSMB10 | PSMB10 | PSMB10 | 3840 | 0.052 | 0.37 | YES |
26 | KRAS | KRAS | KRAS | 3883 | 0.052 | 0.38 | YES |
27 | NRAS | NRAS | NRAS | 3930 | 0.051 | 0.39 | YES |
28 | IKBKB | IKBKB | IKBKB | 4430 | 0.042 | 0.37 | YES |
29 | NFKBIB | NFKBIB | NFKBIB | 4434 | 0.042 | 0.38 | YES |
30 | PIK3CD | PIK3CD | PIK3CD | 4439 | 0.042 | 0.38 | YES |
31 | CHUK | CHUK | CHUK | 4441 | 0.042 | 0.39 | YES |
32 | FBXW11 | FBXW11 | FBXW11 | 4493 | 0.041 | 0.4 | YES |
33 | PSMC2 | PSMC2 | PSMC2 | 4890 | 0.035 | 0.38 | NO |
34 | PIK3AP1 | PIK3AP1 | PIK3AP1 | 4924 | 0.034 | 0.38 | NO |
35 | CASP9 | CASP9 | CASP9 | 5033 | 0.033 | 0.38 | NO |
36 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 5072 | 0.033 | 0.39 | NO |
37 | PDPK1 | PDPK1 | PDPK1 | 5284 | 0.03 | 0.38 | NO |
38 | PSMB8 | PSMB8 | PSMB8 | 5401 | 0.028 | 0.38 | NO |
39 | PSMA5 | PSMA5 | PSMA5 | 5441 | 0.028 | 0.38 | NO |
40 | NFKBIA | NFKBIA | NFKBIA | 5559 | 0.027 | 0.38 | NO |
41 | BAD | BAD | BAD | 5652 | 0.026 | 0.38 | NO |
42 | ORAI1 | ORAI1 | ORAI1 | 5992 | 0.022 | 0.37 | NO |
43 | RELA | RELA | RELA | 6090 | 0.021 | 0.37 | NO |
44 | MTOR | MTOR | MTOR | 6110 | 0.02 | 0.37 | NO |
45 | PSME2 | PSME2 | PSME2 | 6128 | 0.02 | 0.37 | NO |
46 | PSMD2 | PSMD2 | PSMD2 | 6134 | 0.02 | 0.38 | NO |
47 | GRB2 | GRB2 | GRB2 | 6193 | 0.02 | 0.38 | NO |
48 | PSMC4 | PSMC4 | PSMC4 | 6201 | 0.019 | 0.38 | NO |
49 | PSMD9 | PSMD9 | PSMD9 | 6204 | 0.019 | 0.38 | NO |
50 | TSC2 | TSC2 | TSC2 | 6592 | 0.015 | 0.36 | NO |
51 | CDKN1A | CDKN1A | CDKN1A | 6731 | 0.014 | 0.36 | NO |
52 | IKBKG | IKBKG | IKBKG | 6840 | 0.013 | 0.36 | NO |
53 | PTEN | PTEN | PTEN | 6995 | 0.011 | 0.35 | NO |
54 | CALM3 | CALM3 | CALM3 | 7321 | 0.0083 | 0.33 | NO |
55 | ITPR2 | ITPR2 | ITPR2 | 7458 | 0.0074 | 0.33 | NO |
56 | PSMA4 | PSMA4 | PSMA4 | 7493 | 0.0071 | 0.33 | NO |
57 | AKT1 | AKT1 | AKT1 | 7547 | 0.0066 | 0.32 | NO |
58 | PSMB9 | PSMB9 | PSMB9 | 7676 | 0.0049 | 0.32 | NO |
59 | GSK3A | GSK3A | GSK3A | 7684 | 0.0048 | 0.32 | NO |
60 | PSMA8 | PSMA8 | PSMA8 | 7688 | 0.0048 | 0.32 | NO |
61 | PSMC5 | PSMC5 | PSMC5 | 7922 | 0.0028 | 0.31 | NO |
62 | PSME1 | PSME1 | PSME1 | 7946 | 0.0026 | 0.31 | NO |
63 | SOS1 | SOS1 | SOS1 | 7962 | 0.0025 | 0.31 | NO |
64 | PSMB2 | PSMB2 | PSMB2 | 8045 | 0.0018 | 0.3 | NO |
65 | PSMD11 | PSMD11 | PSMD11 | 8048 | 0.0018 | 0.3 | NO |
66 | AKT1S1 | AKT1S1 | AKT1S1 | 8138 | 0.0011 | 0.3 | NO |
67 | STIM1 | STIM1 | STIM1 | 8225 | 0.00017 | 0.29 | NO |
68 | RICTOR | RICTOR | RICTOR | 8337 | -0.00087 | 0.29 | NO |
69 | PSMA3 | PSMA3 | PSMA3 | 8373 | -0.0012 | 0.29 | NO |
70 | MLST8 | MLST8 | MLST8 | 8422 | -0.0016 | 0.28 | NO |
71 | PSMD8 | PSMD8 | PSMD8 | 8578 | -0.0029 | 0.28 | NO |
72 | PSMC6 | PSMC6 | PSMC6 | 8726 | -0.0041 | 0.27 | NO |
73 | PSMD12 | PSMD12 | PSMD12 | 8774 | -0.0046 | 0.27 | NO |
74 | NCK1 | NCK1 | NCK1 | 8829 | -0.005 | 0.26 | NO |
75 | RPS27A | RPS27A | RPS27A | 8902 | -0.0056 | 0.26 | NO |
76 | PSMD6 | PSMD6 | PSMD6 | 8929 | -0.0059 | 0.26 | NO |
77 | PSMD10 | PSMD10 | PSMD10 | 9065 | -0.0071 | 0.26 | NO |
78 | PSMD1 | PSMD1 | PSMD1 | 9090 | -0.0073 | 0.26 | NO |
79 | PSMA2 | PSMA2 | PSMA2 | 9113 | -0.0075 | 0.26 | NO |
80 | PSMC1 | PSMC1 | PSMC1 | 9173 | -0.0081 | 0.25 | NO |
81 | UBA52 | UBA52 | UBA52 | 9280 | -0.009 | 0.25 | NO |
82 | PSMC3 | PSMC3 | PSMC3 | 9315 | -0.0093 | 0.25 | NO |
83 | PSMD14 | PSMD14 | PSMD14 | 9319 | -0.0094 | 0.25 | NO |
84 | CALM2 | CALM2 | CALM2 | 9333 | -0.0094 | 0.25 | NO |
85 | PSMB3 | PSMB3 | PSMB3 | 9393 | -0.01 | 0.25 | NO |
86 | FOXO1 | FOXO1 | FOXO1 | 9397 | -0.01 | 0.25 | NO |
87 | PSMD13 | PSMD13 | PSMD13 | 9398 | -0.01 | 0.25 | NO |
88 | PSMD7 | PSMD7 | PSMD7 | 9627 | -0.012 | 0.24 | NO |
89 | PSMA1 | PSMA1 | PSMA1 | 9761 | -0.013 | 0.24 | NO |
90 | PSMD3 | PSMD3 | PSMD3 | 9894 | -0.014 | 0.23 | NO |
91 | SHC1 | SHC1 | SHC1 | 9901 | -0.014 | 0.24 | NO |
92 | FYN | FYN | FYN | 9933 | -0.014 | 0.24 | NO |
93 | PSMA7 | PSMA7 | PSMA7 | 9983 | -0.015 | 0.24 | NO |
94 | PSMB4 | PSMB4 | PSMB4 | 10262 | -0.017 | 0.23 | NO |
95 | CALM1 | CALM1 | CALM1 | 10275 | -0.018 | 0.23 | NO |
96 | FOXO4 | FOXO4 | FOXO4 | 10353 | -0.018 | 0.23 | NO |
97 | BTRC | BTRC | BTRC | 10451 | -0.019 | 0.22 | NO |
98 | PSMD5 | PSMD5 | PSMD5 | 10488 | -0.02 | 0.23 | NO |
99 | PSMA6 | PSMA6 | PSMA6 | 10501 | -0.02 | 0.23 | NO |
100 | CUL1 | CUL1 | CUL1 | 10507 | -0.02 | 0.23 | NO |
101 | CREB1 | CREB1 | CREB1 | 10572 | -0.02 | 0.23 | NO |
102 | PSMD4 | PSMD4 | PSMD4 | 10752 | -0.022 | 0.23 | NO |
103 | SKP1 | SKP1 | SKP1 | 10926 | -0.024 | 0.22 | NO |
104 | PSMB5 | PSMB5 | PSMB5 | 10992 | -0.024 | 0.22 | NO |
105 | PSMB1 | PSMB1 | PSMB1 | 11023 | -0.025 | 0.23 | NO |
106 | CBL | CBL | CBL | 11066 | -0.025 | 0.23 | NO |
107 | PSMB6 | PSMB6 | PSMB6 | 11558 | -0.03 | 0.21 | NO |
108 | PSMF1 | PSMF1 | PSMF1 | 11844 | -0.033 | 0.2 | NO |
109 | PSMB7 | PSMB7 | PSMB7 | 12044 | -0.035 | 0.19 | NO |
110 | AKT2 | AKT2 | AKT2 | 12096 | -0.036 | 0.2 | NO |
111 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 12305 | -0.038 | 0.19 | NO |
112 | MAP3K7 | MAP3K7 | MAP3K7 | 12345 | -0.039 | 0.2 | NO |
113 | MALT1 | MALT1 | MALT1 | 12835 | -0.045 | 0.18 | NO |
114 | FOXO3 | FOXO3 | FOXO3 | 12988 | -0.047 | 0.18 | NO |
115 | HRAS | HRAS | HRAS | 13778 | -0.059 | 0.15 | NO |
116 | THEM4 | THEM4 | THEM4 | 14138 | -0.066 | 0.14 | NO |
117 | PIK3R1 | PIK3R1 | PIK3R1 | 14200 | -0.068 | 0.15 | NO |
118 | CDKN1B | CDKN1B | CDKN1B | 14326 | -0.07 | 0.15 | NO |
119 | PLCG1 | PLCG1 | PLCG1 | 15006 | -0.087 | 0.13 | NO |
120 | AKT3 | AKT3 | AKT3 | 16419 | -0.14 | 0.081 | NO |
121 | TRIB3 | TRIB3 | TRIB3 | 17804 | -0.22 | 0.047 | NO |
Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TRAIL PATHWAY.

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

Table 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 | BIRC3 | BIRC3 | BIRC3 | 627 | 0.22 | 0.14 | YES |
2 | TNF | TNF | TNF | 981 | 0.18 | 0.25 | YES |
3 | CFLAR | CFLAR | CFLAR | 2200 | 0.098 | 0.26 | YES |
4 | NFKBIE | NFKBIE | NFKBIE | 2671 | 0.08 | 0.29 | YES |
5 | TRADD | TRADD | TRADD | 2725 | 0.079 | 0.35 | YES |
6 | NFKB1 | NFKB1 | NFKB1 | 3658 | 0.056 | 0.34 | YES |
7 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 3699 | 0.055 | 0.38 | YES |
8 | TNFRSF1B | TNFRSF1B | TNFRSF1B | 3713 | 0.055 | 0.42 | YES |
9 | NFKB2 | NFKB2 | NFKB2 | 3889 | 0.051 | 0.45 | YES |
10 | CASP3 | CASP3 | CASP3 | 4353 | 0.043 | 0.46 | YES |
11 | NFKBIB | NFKBIB | NFKBIB | 4434 | 0.042 | 0.48 | YES |
12 | AGFG1 | AGFG1 | AGFG1 | 4634 | 0.039 | 0.5 | YES |
13 | CASP8 | CASP8 | CASP8 | 4717 | 0.038 | 0.53 | YES |
14 | RALBP1 | RALBP1 | RALBP1 | 5172 | 0.031 | 0.53 | YES |
15 | FADD | FADD | FADD | 5183 | 0.031 | 0.55 | YES |
16 | NFKBIA | NFKBIA | NFKBIA | 5559 | 0.027 | 0.55 | NO |
17 | NR2C2 | NR2C2 | NR2C2 | 6432 | 0.017 | 0.52 | NO |
18 | IKBKG | IKBKG | IKBKG | 6840 | 0.013 | 0.5 | NO |
19 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 6900 | 0.012 | 0.51 | NO |
20 | BIRC2 | BIRC2 | BIRC2 | 7079 | 0.01 | 0.51 | NO |
21 | RIPK1 | RIPK1 | RIPK1 | 7350 | 0.0082 | 0.5 | NO |
22 | BAG4 | BAG4 | BAG4 | 8401 | -0.0014 | 0.44 | NO |
23 | MAP2K4 | MAP2K4 | MAP2K4 | 8605 | -0.0031 | 0.44 | NO |
24 | JUN | JUN | JUN | 8713 | -0.004 | 0.43 | NO |
25 | TRAF2 | TRAF2 | TRAF2 | 8937 | -0.006 | 0.43 | NO |
26 | NFKBIL1 | NFKBIL1 | NFKBIL1 | 11303 | -0.028 | 0.32 | NO |
27 | MAP3K7 | MAP3K7 | MAP3K7 | 12345 | -0.039 | 0.29 | NO |
28 | MAP3K3 | MAP3K3 | MAP3K3 | 13925 | -0.062 | 0.26 | NO |
Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID CDC42 PATHWAY.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: PID CDC42 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.65 | 2 | 0.0041 | 0.13 | 0.26 | 0.69 | 0.21 | 0.55 | 0 | 0.025 |
KEGG FRUCTOSE AND MANNOSE METABOLISM | 34 | genes.ES.table | 0.66 | 2.1 | 0.002 | 0.19 | 0.11 | 0.44 | 0.13 | 0.38 | 0 | 0.055 |
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION | 44 | genes.ES.table | 0.51 | 1.8 | 0.024 | 0.41 | 0.62 | 0.57 | 0.22 | 0.44 | 0.12 | 0.099 |
KEGG PYRUVATE METABOLISM | 38 | genes.ES.table | 0.53 | 1.8 | 0.006 | 0.37 | 0.63 | 0.47 | 0.18 | 0.39 | 0.11 | 0.095 |
KEGG BUTANOATE METABOLISM | 31 | genes.ES.table | 0.57 | 1.7 | 0.012 | 0.53 | 0.92 | 0.52 | 0.18 | 0.42 | 0.26 | 0.14 |
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.61 | 2 | 0.0041 | 0.24 | 0.21 | 0.68 | 0.26 | 0.51 | 0 | 0.06 |
KEGG PEROXISOME | 76 | genes.ES.table | 0.54 | 2 | 0 | 0.15 | 0.25 | 0.34 | 0.14 | 0.3 | 0 | 0.035 |
BIOCARTA DEATH PATHWAY | 33 | genes.ES.table | 0.47 | 1.7 | 0.049 | 0.44 | 0.78 | 0.39 | 0.22 | 0.31 | 0.17 | 0.11 |
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX | 49 | genes.ES.table | 0.58 | 1.7 | 0.074 | 0.54 | 0.91 | 0.86 | 0.31 | 0.59 | 0.26 | 0.15 |
REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT | 115 | genes.ES.table | 0.47 | 1.7 | 0.09 | 0.55 | 0.87 | 0.61 | 0.25 | 0.46 | 0.24 | 0.15 |
Table S41. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ALDOB | ALDOB | ALDOB | 66 | 0.53 | 0.16 | YES |
2 | KHK | KHK | KHK | 183 | 0.39 | 0.27 | YES |
3 | PFKFB4 | PFKFB4 | PFKFB4 | 309 | 0.31 | 0.36 | YES |
4 | SORD | SORD | SORD | 759 | 0.19 | 0.39 | YES |
5 | AKR1B10 | AKR1B10 | AKR1B10 | 850 | 0.18 | 0.44 | YES |
6 | PFKFB2 | PFKFB2 | PFKFB2 | 1030 | 0.15 | 0.48 | YES |
7 | FUK | FUK | FUK | 1122 | 0.14 | 0.51 | YES |
8 | FBP1 | FBP1 | FBP1 | 1405 | 0.12 | 0.54 | YES |
9 | GMDS | GMDS | GMDS | 1726 | 0.1 | 0.55 | YES |
10 | TSTA3 | TSTA3 | TSTA3 | 2080 | 0.089 | 0.56 | YES |
11 | PFKL | PFKL | PFKL | 2185 | 0.085 | 0.58 | YES |
12 | PMM1 | PMM1 | PMM1 | 2300 | 0.082 | 0.6 | YES |
13 | TPI1 | TPI1 | TPI1 | 2372 | 0.08 | 0.62 | YES |
14 | PMM2 | PMM2 | PMM2 | 2383 | 0.079 | 0.64 | YES |
15 | ALDOC | ALDOC | ALDOC | 2484 | 0.076 | 0.66 | YES |
16 | MPI | MPI | MPI | 5009 | 0.03 | 0.53 | NO |
17 | PFKP | PFKP | PFKP | 5176 | 0.027 | 0.53 | NO |
18 | ALDOA | ALDOA | ALDOA | 5364 | 0.025 | 0.53 | NO |
19 | FPGT | FPGT | FPGT | 5437 | 0.024 | 0.53 | NO |
20 | MTMR6 | MTMR6 | MTMR6 | 5523 | 0.023 | 0.53 | NO |
21 | GMPPA | GMPPA | GMPPA | 5654 | 0.021 | 0.53 | NO |
22 | PHPT1 | PHPT1 | PHPT1 | 6012 | 0.018 | 0.52 | NO |
23 | MTMR1 | MTMR1 | MTMR1 | 6482 | 0.011 | 0.5 | NO |
24 | FBP2 | FBP2 | FBP2 | 7293 | 0.0021 | 0.46 | NO |
25 | PFKFB3 | PFKFB3 | PFKFB3 | 7809 | -0.0036 | 0.43 | NO |
26 | GMPPB | GMPPB | GMPPB | 8075 | -0.0067 | 0.42 | NO |
27 | HK2 | HK2 | HK2 | 8125 | -0.0073 | 0.42 | NO |
28 | MTMR7 | MTMR7 | MTMR7 | 8459 | -0.011 | 0.4 | NO |
29 | PFKM | PFKM | PFKM | 8781 | -0.014 | 0.39 | NO |
30 | HK3 | HK3 | HK3 | 9508 | -0.024 | 0.36 | NO |
31 | PFKFB1 | PFKFB1 | PFKFB1 | 9527 | -0.024 | 0.36 | NO |
32 | MTMR2 | MTMR2 | MTMR2 | 11048 | -0.048 | 0.3 | NO |
33 | HK1 | HK1 | HK1 | 14540 | -0.14 | 0.15 | NO |
34 | AKR1B1 | AKR1B1 | AKR1B1 | 16486 | -0.23 | 0.12 | NO |
Figure S81. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE.

Figure S82. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S42. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MARS2 | MARS2 | MARS2 | 1221 | 0.14 | -0.0051 | YES |
2 | NARS2 | NARS2 | NARS2 | 1261 | 0.13 | 0.052 | YES |
3 | SEPSECS | SEPSECS | SEPSECS | 1360 | 0.12 | 0.1 | YES |
4 | FARSB | FARSB | FARSB | 1440 | 0.12 | 0.15 | YES |
5 | PARS2 | PARS2 | PARS2 | 1494 | 0.12 | 0.2 | YES |
6 | AARS2 | AARS2 | AARS2 | 1718 | 0.1 | 0.24 | YES |
7 | DARS2 | DARS2 | DARS2 | 1857 | 0.098 | 0.27 | YES |
8 | WARS2 | WARS2 | WARS2 | 2404 | 0.078 | 0.28 | YES |
9 | NARS | NARS | NARS | 2436 | 0.077 | 0.31 | YES |
10 | QARS | QARS | QARS | 2577 | 0.074 | 0.34 | YES |
11 | CARS2 | CARS2 | CARS2 | 2713 | 0.07 | 0.36 | YES |
12 | LARS2 | LARS2 | LARS2 | 2742 | 0.07 | 0.39 | YES |
13 | KARS | KARS | KARS | 2772 | 0.069 | 0.42 | YES |
14 | EPRS | EPRS | EPRS | 2844 | 0.067 | 0.45 | YES |
15 | YARS2 | YARS2 | YARS2 | 3242 | 0.059 | 0.45 | YES |
16 | IARS2 | IARS2 | IARS2 | 3617 | 0.052 | 0.46 | YES |
17 | IARS | IARS | IARS | 3735 | 0.049 | 0.47 | YES |
18 | FARSA | FARSA | FARSA | 3743 | 0.049 | 0.49 | YES |
19 | MTFMT | MTFMT | MTFMT | 3972 | 0.045 | 0.5 | YES |
20 | RARS2 | RARS2 | RARS2 | 4022 | 0.044 | 0.52 | YES |
21 | LARS | LARS | LARS | 4273 | 0.04 | 0.52 | YES |
22 | HARS2 | HARS2 | HARS2 | 4301 | 0.04 | 0.54 | YES |
23 | PSTK | PSTK | PSTK | 4388 | 0.038 | 0.55 | YES |
24 | RARS | RARS | RARS | 4394 | 0.038 | 0.57 | YES |
25 | GARS | GARS | GARS | 4407 | 0.038 | 0.58 | YES |
26 | VARS | VARS | VARS | 4770 | 0.033 | 0.58 | YES |
27 | SARS | SARS | SARS | 4773 | 0.033 | 0.6 | YES |
28 | DARS | DARS | DARS | 4836 | 0.032 | 0.61 | YES |
29 | TARS | TARS | TARS | 5754 | 0.02 | 0.57 | NO |
30 | YARS | YARS | YARS | 6076 | 0.016 | 0.56 | NO |
31 | FARS2 | FARS2 | FARS2 | 6293 | 0.013 | 0.55 | NO |
32 | SARS2 | SARS2 | SARS2 | 6354 | 0.013 | 0.55 | NO |
33 | CARS | CARS | CARS | 6356 | 0.013 | 0.56 | NO |
34 | TARS2 | TARS2 | TARS2 | 6370 | 0.012 | 0.56 | NO |
35 | EARS2 | EARS2 | EARS2 | 6429 | 0.012 | 0.56 | NO |
36 | VARS2 | VARS2 | VARS2 | 6510 | 0.011 | 0.57 | NO |
37 | HARS | HARS | HARS | 7509 | -0.0003 | 0.51 | NO |
38 | AARS | AARS | AARS | 8431 | -0.011 | 0.47 | NO |
39 | MARS | MARS | MARS | 10272 | -0.035 | 0.38 | NO |
40 | TARSL2 | TARSL2 | TARSL2 | 12038 | -0.068 | 0.32 | NO |
41 | WARS | WARS | WARS | 12576 | -0.08 | 0.33 | NO |
Figure S83. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM.

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

Table S43. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MARS2 | MARS2 | MARS2 | 1221 | 0.14 | -0.0039 | YES |
2 | NARS2 | NARS2 | NARS2 | 1261 | 0.13 | 0.054 | YES |
3 | FARSB | FARSB | FARSB | 1440 | 0.12 | 0.099 | YES |
4 | PARS2 | PARS2 | PARS2 | 1494 | 0.12 | 0.15 | YES |
5 | AARS2 | AARS2 | AARS2 | 1718 | 0.1 | 0.19 | YES |
6 | DARS2 | DARS2 | DARS2 | 1857 | 0.098 | 0.22 | YES |
7 | WARS2 | WARS2 | WARS2 | 2404 | 0.078 | 0.23 | YES |
8 | NARS | NARS | NARS | 2436 | 0.077 | 0.26 | YES |
9 | AIMP2 | AIMP2 | AIMP2 | 2508 | 0.076 | 0.29 | YES |
10 | QARS | QARS | QARS | 2577 | 0.074 | 0.32 | YES |
11 | CARS2 | CARS2 | CARS2 | 2713 | 0.07 | 0.35 | YES |
12 | LARS2 | LARS2 | LARS2 | 2742 | 0.07 | 0.38 | YES |
13 | KARS | KARS | KARS | 2772 | 0.069 | 0.41 | YES |
14 | EPRS | EPRS | EPRS | 2844 | 0.067 | 0.44 | YES |
15 | YARS2 | YARS2 | YARS2 | 3242 | 0.059 | 0.44 | YES |
16 | PPA2 | PPA2 | PPA2 | 3256 | 0.059 | 0.47 | YES |
17 | IARS2 | IARS2 | IARS2 | 3617 | 0.052 | 0.47 | YES |
18 | PPA1 | PPA1 | PPA1 | 3733 | 0.05 | 0.49 | YES |
19 | IARS | IARS | IARS | 3735 | 0.049 | 0.51 | YES |
20 | FARSA | FARSA | FARSA | 3743 | 0.049 | 0.53 | YES |
21 | RARS2 | RARS2 | RARS2 | 4022 | 0.044 | 0.54 | YES |
22 | AIMP1 | AIMP1 | AIMP1 | 4098 | 0.043 | 0.56 | YES |
23 | LARS | LARS | LARS | 4273 | 0.04 | 0.56 | YES |
24 | HARS2 | HARS2 | HARS2 | 4301 | 0.04 | 0.58 | YES |
25 | RARS | RARS | RARS | 4394 | 0.038 | 0.59 | YES |
26 | GARS | GARS | GARS | 4407 | 0.038 | 0.61 | YES |
27 | VARS | VARS | VARS | 4770 | 0.033 | 0.6 | YES |
28 | SARS | SARS | SARS | 4773 | 0.033 | 0.62 | YES |
29 | DARS | DARS | DARS | 4836 | 0.032 | 0.63 | YES |
30 | TARS | TARS | TARS | 5754 | 0.02 | 0.59 | NO |
31 | YARS | YARS | YARS | 6076 | 0.016 | 0.58 | NO |
32 | FARS2 | FARS2 | FARS2 | 6293 | 0.013 | 0.58 | NO |
33 | SARS2 | SARS2 | SARS2 | 6354 | 0.013 | 0.58 | NO |
34 | CARS | CARS | CARS | 6356 | 0.013 | 0.58 | NO |
35 | TARS2 | TARS2 | TARS2 | 6370 | 0.012 | 0.59 | NO |
36 | EARS2 | EARS2 | EARS2 | 6429 | 0.012 | 0.59 | NO |
37 | VARS2 | VARS2 | VARS2 | 6510 | 0.011 | 0.59 | NO |
38 | EEF1E1 | EEF1E1 | EEF1E1 | 6955 | 0.0057 | 0.57 | NO |
39 | HARS | HARS | HARS | 7509 | -0.0003 | 0.54 | NO |
40 | AARS | AARS | AARS | 8431 | -0.011 | 0.5 | NO |
41 | MARS | MARS | MARS | 10272 | -0.035 | 0.41 | NO |
42 | WARS | WARS | WARS | 12576 | -0.08 | 0.33 | NO |
Figure S85. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S86. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S44. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NOS2 | NOS2 | NOS2 | 7 | 0.8 | 0.11 | YES |
2 | XDH | XDH | XDH | 100 | 0.46 | 0.16 | YES |
3 | ACSL6 | ACSL6 | ACSL6 | 213 | 0.37 | 0.21 | YES |
4 | FAR2 | FAR2 | FAR2 | 218 | 0.37 | 0.25 | YES |
5 | ACOX2 | ACOX2 | ACOX2 | 271 | 0.34 | 0.3 | YES |
6 | EPHX2 | EPHX2 | EPHX2 | 322 | 0.31 | 0.34 | YES |
7 | SLC27A2 | SLC27A2 | SLC27A2 | 567 | 0.23 | 0.35 | YES |
8 | AMACR | AMACR | AMACR | 696 | 0.2 | 0.37 | YES |
9 | ACSL5 | ACSL5 | ACSL5 | 753 | 0.19 | 0.39 | YES |
10 | AGXT | AGXT | AGXT | 937 | 0.16 | 0.41 | YES |
11 | PEX7 | PEX7 | PEX7 | 939 | 0.16 | 0.43 | YES |
12 | IDH2 | IDH2 | IDH2 | 1017 | 0.15 | 0.44 | YES |
13 | PEX6 | PEX6 | PEX6 | 1123 | 0.14 | 0.46 | YES |
14 | DECR2 | DECR2 | DECR2 | 1198 | 0.14 | 0.47 | YES |
15 | PXMP2 | PXMP2 | PXMP2 | 1482 | 0.12 | 0.47 | YES |
16 | NUDT12 | NUDT12 | NUDT12 | 1530 | 0.11 | 0.48 | YES |
17 | PEX11G | PEX11G | PEX11G | 1679 | 0.11 | 0.49 | YES |
18 | GSTK1 | GSTK1 | GSTK1 | 1803 | 0.1 | 0.5 | YES |
19 | PEX1 | PEX1 | PEX1 | 1863 | 0.098 | 0.51 | YES |
20 | PEX11A | PEX11A | PEX11A | 1895 | 0.096 | 0.52 | YES |
21 | HSD17B4 | HSD17B4 | HSD17B4 | 2196 | 0.085 | 0.51 | YES |
22 | CRAT | CRAT | CRAT | 2198 | 0.085 | 0.52 | YES |
23 | DHRS4 | DHRS4 | DHRS4 | 2257 | 0.083 | 0.53 | YES |
24 | SOD1 | SOD1 | SOD1 | 2378 | 0.079 | 0.54 | YES |
25 | HMGCL | HMGCL | HMGCL | 2534 | 0.075 | 0.54 | YES |
26 | MLYCD | MLYCD | MLYCD | 2618 | 0.073 | 0.54 | YES |
27 | EHHADH | EHHADH | EHHADH | 3354 | 0.056 | 0.51 | NO |
28 | PEX11B | PEX11B | PEX11B | 3419 | 0.055 | 0.52 | NO |
29 | ABCD1 | ABCD1 | ABCD1 | 3481 | 0.054 | 0.52 | NO |
30 | PEX2 | PEX2 | PEX2 | 3504 | 0.054 | 0.52 | NO |
31 | IDH1 | IDH1 | IDH1 | 3636 | 0.051 | 0.52 | NO |
32 | ABCD3 | ABCD3 | ABCD3 | 3681 | 0.05 | 0.53 | NO |
33 | SCP2 | SCP2 | SCP2 | 3746 | 0.049 | 0.53 | NO |
34 | PIPOX | PIPOX | PIPOX | 3853 | 0.047 | 0.53 | NO |
35 | NUDT19 | NUDT19 | NUDT19 | 3924 | 0.046 | 0.54 | NO |
36 | MVK | MVK | MVK | 3985 | 0.045 | 0.54 | NO |
37 | PAOX | PAOX | PAOX | 4100 | 0.043 | 0.54 | NO |
38 | PRDX5 | PRDX5 | PRDX5 | 4140 | 0.043 | 0.54 | NO |
39 | PEX5 | PEX5 | PEX5 | 4302 | 0.04 | 0.54 | NO |
40 | ACOT8 | ACOT8 | ACOT8 | 4612 | 0.035 | 0.53 | NO |
41 | HAO2 | HAO2 | HAO2 | 4725 | 0.033 | 0.52 | NO |
42 | GNPAT | GNPAT | GNPAT | 4756 | 0.033 | 0.53 | NO |
43 | ABCD4 | ABCD4 | ABCD4 | 4828 | 0.032 | 0.53 | NO |
44 | PEX16 | PEX16 | PEX16 | 4858 | 0.032 | 0.53 | NO |
45 | PECR | PECR | PECR | 5283 | 0.026 | 0.51 | NO |
46 | PEX14 | PEX14 | PEX14 | 5475 | 0.023 | 0.5 | NO |
47 | HACL1 | HACL1 | HACL1 | 5559 | 0.022 | 0.5 | NO |
48 | ACAA1 | ACAA1 | ACAA1 | 5571 | 0.022 | 0.5 | NO |
49 | PEX13 | PEX13 | PEX13 | 5873 | 0.019 | 0.49 | NO |
50 | PHYH | PHYH | PHYH | 6577 | 0.0099 | 0.46 | NO |
51 | PEX10 | PEX10 | PEX10 | 6580 | 0.0098 | 0.46 | NO |
52 | AGPS | AGPS | AGPS | 6645 | 0.0091 | 0.45 | NO |
53 | CAT | CAT | CAT | 6921 | 0.006 | 0.44 | NO |
54 | PEX26 | PEX26 | PEX26 | 7150 | 0.0035 | 0.43 | NO |
55 | PRDX1 | PRDX1 | PRDX1 | 7681 | -0.002 | 0.4 | NO |
56 | PEX3 | PEX3 | PEX3 | 8005 | -0.0059 | 0.38 | NO |
57 | ACOX3 | ACOX3 | ACOX3 | 8112 | -0.0071 | 0.38 | NO |
58 | SOD2 | SOD2 | SOD2 | 8153 | -0.0076 | 0.38 | NO |
59 | PXMP4 | PXMP4 | PXMP4 | 8492 | -0.011 | 0.36 | NO |
60 | MPV17 | MPV17 | MPV17 | 8624 | -0.013 | 0.36 | NO |
61 | FAR1 | FAR1 | FAR1 | 8693 | -0.013 | 0.35 | NO |
62 | SLC25A17 | SLC25A17 | SLC25A17 | 9029 | -0.017 | 0.34 | NO |
63 | PEX19 | PEX19 | PEX19 | 9305 | -0.021 | 0.32 | NO |
64 | CROT | CROT | CROT | 9496 | -0.024 | 0.32 | NO |
65 | BAAT | BAAT | BAAT | 10221 | -0.034 | 0.28 | NO |
66 | ACOX1 | ACOX1 | ACOX1 | 10562 | -0.04 | 0.27 | NO |
67 | PMVK | PMVK | PMVK | 11225 | -0.051 | 0.24 | NO |
68 | ACSL3 | ACSL3 | ACSL3 | 11706 | -0.06 | 0.22 | NO |
69 | PEX12 | PEX12 | PEX12 | 12090 | -0.069 | 0.21 | NO |
70 | ACSL4 | ACSL4 | ACSL4 | 12481 | -0.078 | 0.2 | NO |
71 | DAO | DAO | DAO | 13475 | -0.11 | 0.16 | NO |
72 | MPV17L | MPV17L | MPV17L | 13608 | -0.11 | 0.17 | NO |
73 | ECH1 | ECH1 | ECH1 | 14238 | -0.13 | 0.15 | NO |
74 | ACSL1 | ACSL1 | ACSL1 | 14331 | -0.14 | 0.17 | NO |
75 | DDO | DDO | DDO | 16674 | -0.24 | 0.074 | NO |
76 | ABCD2 | ABCD2 | ABCD2 | 16885 | -0.26 | 0.096 | NO |
Figure S87. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PYRUVATE METABOLISM.

Figure S88. 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 S45. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PCK1 | PCK1 | PCK1 | 70 | 0.52 | 0.2 | YES |
2 | PCK2 | PCK2 | PCK2 | 657 | 0.21 | 0.25 | YES |
3 | IDH2 | IDH2 | IDH2 | 1017 | 0.15 | 0.29 | YES |
4 | SUCLG1 | SUCLG1 | SUCLG1 | 1161 | 0.14 | 0.34 | YES |
5 | IDH3A | IDH3A | IDH3A | 1313 | 0.13 | 0.38 | YES |
6 | DLD | DLD | DLD | 1740 | 0.1 | 0.4 | YES |
7 | PDHA1 | PDHA1 | PDHA1 | 2106 | 0.088 | 0.41 | YES |
8 | SUCLG2 | SUCLG2 | SUCLG2 | 2116 | 0.088 | 0.45 | YES |
9 | SDHB | SDHB | SDHB | 2266 | 0.082 | 0.47 | YES |
10 | IDH3G | IDH3G | IDH3G | 2278 | 0.082 | 0.5 | YES |
11 | IDH3B | IDH3B | IDH3B | 2287 | 0.082 | 0.54 | YES |
12 | SUCLA2 | SUCLA2 | SUCLA2 | 2629 | 0.072 | 0.55 | YES |
13 | SDHD | SDHD | SDHD | 2952 | 0.065 | 0.55 | YES |
14 | CS | CS | CS | 2985 | 0.064 | 0.58 | YES |
15 | MDH2 | MDH2 | MDH2 | 3041 | 0.063 | 0.6 | YES |
16 | DLAT | DLAT | DLAT | 3264 | 0.058 | 0.61 | YES |
17 | DLST | DLST | DLST | 3472 | 0.054 | 0.62 | YES |
18 | FH | FH | FH | 3586 | 0.052 | 0.63 | YES |
19 | IDH1 | IDH1 | IDH1 | 3636 | 0.051 | 0.65 | YES |
20 | SDHA | SDHA | SDHA | 3951 | 0.046 | 0.65 | YES |
21 | ACO2 | ACO2 | ACO2 | 4472 | 0.037 | 0.64 | NO |
22 | OGDH | OGDH | OGDH | 4727 | 0.033 | 0.64 | NO |
23 | MDH1 | MDH1 | MDH1 | 4954 | 0.03 | 0.64 | NO |
24 | ACO1 | ACO1 | ACO1 | 5220 | 0.027 | 0.63 | NO |
25 | SDHC | SDHC | SDHC | 5645 | 0.021 | 0.62 | NO |
26 | ACLY | ACLY | ACLY | 6083 | 0.016 | 0.6 | NO |
27 | PDHB | PDHB | PDHB | 6828 | 0.007 | 0.57 | NO |
28 | PC | PC | PC | 11469 | -0.055 | 0.34 | NO |
29 | OGDHL | OGDHL | OGDHL | 13950 | -0.12 | 0.25 | NO |
Figure S89. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BUTANOATE METABOLISM.

Figure S90. 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 S46. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | HMGCS2 | HMGCS2 | HMGCS2 | 588 | 0.23 | 0.042 | YES |
2 | ACAA2 | ACAA2 | ACAA2 | 752 | 0.19 | 0.094 | YES |
3 | ACADS | ACADS | ACADS | 831 | 0.18 | 0.15 | YES |
4 | HADH | HADH | HADH | 1277 | 0.13 | 0.17 | YES |
5 | BCKDHB | BCKDHB | BCKDHB | 1337 | 0.13 | 0.2 | YES |
6 | AUH | AUH | AUH | 1579 | 0.11 | 0.23 | YES |
7 | DLD | DLD | DLD | 1740 | 0.1 | 0.25 | YES |
8 | HIBCH | HIBCH | HIBCH | 2032 | 0.091 | 0.27 | YES |
9 | HADHA | HADHA | HADHA | 2142 | 0.087 | 0.29 | YES |
10 | ACAT2 | ACAT2 | ACAT2 | 2419 | 0.078 | 0.3 | YES |
11 | HADHB | HADHB | HADHB | 2449 | 0.077 | 0.32 | YES |
12 | PCCA | PCCA | PCCA | 2450 | 0.077 | 0.35 | YES |
13 | HMGCL | HMGCL | HMGCL | 2534 | 0.075 | 0.37 | YES |
14 | ECHS1 | ECHS1 | ECHS1 | 2572 | 0.074 | 0.39 | YES |
15 | HIBADH | HIBADH | HIBADH | 2611 | 0.073 | 0.41 | YES |
16 | MCCC1 | MCCC1 | MCCC1 | 2839 | 0.067 | 0.42 | YES |
17 | MCCC2 | MCCC2 | MCCC2 | 3072 | 0.062 | 0.43 | YES |
18 | ALDH2 | ALDH2 | ALDH2 | 3192 | 0.06 | 0.44 | YES |
19 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3221 | 0.059 | 0.46 | YES |
20 | MCEE | MCEE | MCEE | 3278 | 0.058 | 0.47 | YES |
21 | ABAT | ABAT | ABAT | 3346 | 0.057 | 0.49 | YES |
22 | EHHADH | EHHADH | EHHADH | 3354 | 0.056 | 0.51 | YES |
23 | MUT | MUT | MUT | 3832 | 0.048 | 0.5 | YES |
24 | PCCB | PCCB | PCCB | 3941 | 0.046 | 0.5 | YES |
25 | ACADSB | ACADSB | ACADSB | 4114 | 0.043 | 0.51 | YES |
26 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4430 | 0.038 | 0.51 | NO |
27 | HSD17B10 | HSD17B10 | HSD17B10 | 5260 | 0.026 | 0.47 | NO |
28 | ACAA1 | ACAA1 | ACAA1 | 5571 | 0.022 | 0.46 | NO |
29 | ACADM | ACADM | ACADM | 5947 | 0.018 | 0.45 | NO |
30 | HMGCS1 | HMGCS1 | HMGCS1 | 7228 | 0.0028 | 0.38 | NO |
31 | IVD | IVD | IVD | 7386 | 0.0011 | 0.37 | NO |
32 | ACAT1 | ACAT1 | ACAT1 | 7411 | 0.00079 | 0.37 | NO |
33 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 8485 | -0.011 | 0.32 | NO |
34 | BCAT2 | BCAT2 | BCAT2 | 8664 | -0.013 | 0.31 | NO |
35 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 9036 | -0.018 | 0.3 | NO |
36 | ACAD8 | ACAD8 | ACAD8 | 9258 | -0.021 | 0.29 | NO |
37 | OXCT2 | OXCT2 | OXCT2 | 9453 | -0.023 | 0.29 | NO |
38 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 10008 | -0.03 | 0.27 | NO |
39 | BCKDHA | BCKDHA | BCKDHA | 10306 | -0.035 | 0.26 | NO |
40 | IL4I1 | IL4I1 | IL4I1 | 10754 | -0.043 | 0.25 | NO |
41 | DBT | DBT | DBT | 11802 | -0.062 | 0.22 | NO |
42 | OXCT1 | OXCT1 | OXCT1 | 13776 | -0.12 | 0.15 | NO |
43 | BCAT1 | BCAT1 | BCAT1 | 15088 | -0.17 | 0.13 | NO |
44 | AOX1 | AOX1 | AOX1 | 15582 | -0.19 | 0.17 | NO |
Figure S91. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS.

Figure S92. 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 S47. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PCK1 | PCK1 | PCK1 | 70 | 0.52 | 0.14 | YES |
2 | PKLR | PKLR | PKLR | 278 | 0.33 | 0.22 | YES |
3 | ACSS2 | ACSS2 | ACSS2 | 424 | 0.28 | 0.29 | YES |
4 | PCK2 | PCK2 | PCK2 | 657 | 0.21 | 0.34 | YES |
5 | ME1 | ME1 | ME1 | 1062 | 0.15 | 0.36 | YES |
6 | ACSS1 | ACSS1 | ACSS1 | 1555 | 0.11 | 0.37 | YES |
7 | LDHC | LDHC | LDHC | 1652 | 0.11 | 0.39 | YES |
8 | DLD | DLD | DLD | 1740 | 0.1 | 0.42 | YES |
9 | ME2 | ME2 | ME2 | 1766 | 0.1 | 0.44 | YES |
10 | ACYP1 | ACYP1 | ACYP1 | 1862 | 0.098 | 0.46 | YES |
11 | PDHA1 | PDHA1 | PDHA1 | 2106 | 0.088 | 0.48 | YES |
12 | ACAT2 | ACAT2 | ACAT2 | 2419 | 0.078 | 0.48 | YES |
13 | LDHD | LDHD | LDHD | 2969 | 0.064 | 0.47 | YES |
14 | MDH2 | MDH2 | MDH2 | 3041 | 0.063 | 0.48 | YES |
15 | ALDH2 | ALDH2 | ALDH2 | 3192 | 0.06 | 0.49 | YES |
16 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3221 | 0.059 | 0.51 | YES |
17 | DLAT | DLAT | DLAT | 3264 | 0.058 | 0.52 | YES |
18 | HAGHL | HAGHL | HAGHL | 3444 | 0.055 | 0.53 | YES |
19 | LDHA | LDHA | LDHA | 3928 | 0.046 | 0.52 | NO |
20 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4430 | 0.038 | 0.5 | NO |
21 | MDH1 | MDH1 | MDH1 | 4954 | 0.03 | 0.48 | NO |
22 | GLO1 | GLO1 | GLO1 | 5799 | 0.02 | 0.44 | NO |
23 | GRHPR | GRHPR | GRHPR | 6460 | 0.011 | 0.41 | NO |
24 | PDHB | PDHB | PDHB | 6828 | 0.007 | 0.39 | NO |
25 | ACACA | ACACA | ACACA | 7254 | 0.0026 | 0.37 | NO |
26 | ACAT1 | ACAT1 | ACAT1 | 7411 | 0.00079 | 0.36 | NO |
27 | PKM2 | PKM2 | PKM2 | 8291 | -0.0089 | 0.31 | NO |
28 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 8485 | -0.011 | 0.31 | NO |
29 | LDHAL6B | LDHAL6B | LDHAL6B | 9713 | -0.026 | 0.25 | NO |
30 | HAGH | HAGH | HAGH | 9927 | -0.029 | 0.24 | NO |
31 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 10008 | -0.03 | 0.25 | NO |
32 | ME3 | ME3 | ME3 | 10029 | -0.031 | 0.26 | NO |
33 | ACYP2 | ACYP2 | ACYP2 | 11117 | -0.049 | 0.21 | NO |
34 | PC | PC | PC | 11469 | -0.055 | 0.21 | NO |
35 | LDHAL6A | LDHAL6A | LDHAL6A | 12311 | -0.074 | 0.18 | NO |
36 | ACACB | ACACB | ACACB | 12694 | -0.083 | 0.19 | NO |
37 | AKR1B1 | AKR1B1 | AKR1B1 | 16486 | -0.23 | 0.049 | NO |
38 | LDHB | LDHB | LDHB | 16696 | -0.24 | 0.11 | NO |
Figure S93. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PEROXISOME.

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

Table S48. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | A1CF | A1CF | A1CF | 18 | 0.71 | 0.14 | YES |
2 | APOBEC1 | APOBEC1 | APOBEC1 | 71 | 0.52 | 0.24 | YES |
3 | GTF2F2 | GTF2F2 | GTF2F2 | 1985 | 0.093 | 0.16 | YES |
4 | SEH1L | SEH1L | SEH1L | 2258 | 0.083 | 0.16 | YES |
5 | NCBP1 | NCBP1 | NCBP1 | 2414 | 0.078 | 0.16 | YES |
6 | NUP37 | NUP37 | NUP37 | 2420 | 0.078 | 0.18 | YES |
7 | NUPL1 | NUPL1 | NUPL1 | 2503 | 0.076 | 0.19 | YES |
8 | METTL3 | METTL3 | METTL3 | 2585 | 0.073 | 0.2 | YES |
9 | UPF3B | UPF3B | UPF3B | 2622 | 0.072 | 0.21 | YES |
10 | CPSF1 | CPSF1 | CPSF1 | 2838 | 0.067 | 0.22 | YES |
11 | CSTF2 | CSTF2 | CSTF2 | 2936 | 0.065 | 0.22 | YES |
12 | NUP88 | NUP88 | NUP88 | 2996 | 0.064 | 0.23 | YES |
13 | CPSF3 | CPSF3 | CPSF3 | 3115 | 0.061 | 0.24 | YES |
14 | NUP35 | NUP35 | NUP35 | 3123 | 0.061 | 0.25 | YES |
15 | GTF2H2 | GTF2H2 | GTF2H2 | 3265 | 0.058 | 0.25 | YES |
16 | SF3B14 | SF3B14 | SF3B14 | 3433 | 0.055 | 0.26 | YES |
17 | SNRPA1 | SNRPA1 | SNRPA1 | 3574 | 0.052 | 0.26 | YES |
18 | SNRPE | SNRPE | SNRPE | 3710 | 0.05 | 0.26 | YES |
19 | NUP54 | NUP54 | NUP54 | 3718 | 0.05 | 0.27 | YES |
20 | CDK7 | CDK7 | CDK7 | 3806 | 0.048 | 0.28 | YES |
21 | LSM2 | LSM2 | LSM2 | 3884 | 0.047 | 0.28 | YES |
22 | PRPF4 | PRPF4 | PRPF4 | 3975 | 0.045 | 0.28 | YES |
23 | CLP1 | CLP1 | CLP1 | 4064 | 0.044 | 0.29 | YES |
24 | RBMX | RBMX | RBMX | 4119 | 0.043 | 0.3 | YES |
25 | GTF2H2B | GTF2H2B | GTF2H2B | 4146 | 0.042 | 0.3 | YES |
26 | SNRPF | SNRPF | SNRPF | 4151 | 0.042 | 0.31 | YES |
27 | EIF4E | EIF4E | EIF4E | 4162 | 0.042 | 0.32 | YES |
28 | RAE1 | RAE1 | RAE1 | 4179 | 0.042 | 0.32 | YES |
29 | HNRNPF | HNRNPF | HNRNPF | 4356 | 0.039 | 0.32 | YES |
30 | NUP205 | NUP205 | NUP205 | 4365 | 0.039 | 0.33 | YES |
31 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 4370 | 0.039 | 0.34 | YES |
32 | GTF2H3 | GTF2H3 | GTF2H3 | 4441 | 0.038 | 0.34 | YES |
33 | SNRPB | SNRPB | SNRPB | 4556 | 0.036 | 0.34 | YES |
34 | NFX1 | NFX1 | NFX1 | 4566 | 0.036 | 0.35 | YES |
35 | POLR2H | POLR2H | POLR2H | 4567 | 0.036 | 0.36 | YES |
36 | SNRPA | SNRPA | SNRPA | 4580 | 0.036 | 0.36 | YES |
37 | MAGOH | MAGOH | MAGOH | 4795 | 0.032 | 0.36 | YES |
38 | PAPOLA | PAPOLA | PAPOLA | 4808 | 0.032 | 0.36 | YES |
39 | SNRPB2 | SNRPB2 | SNRPB2 | 4824 | 0.032 | 0.37 | YES |
40 | SNRPD3 | SNRPD3 | SNRPD3 | 4852 | 0.032 | 0.37 | YES |
41 | SF3B3 | SF3B3 | SF3B3 | 4856 | 0.032 | 0.38 | YES |
42 | NUPL2 | NUPL2 | NUPL2 | 4877 | 0.031 | 0.39 | YES |
43 | SF3A2 | SF3A2 | SF3A2 | 5044 | 0.029 | 0.38 | YES |
44 | POM121 | POM121 | POM121 | 5207 | 0.027 | 0.38 | YES |
45 | PHF5A | PHF5A | PHF5A | 5226 | 0.027 | 0.38 | YES |
46 | CCAR1 | CCAR1 | CCAR1 | 5291 | 0.026 | 0.38 | YES |
47 | EFTUD2 | EFTUD2 | EFTUD2 | 5328 | 0.026 | 0.39 | YES |
48 | HNRNPC | HNRNPC | HNRNPC | 5340 | 0.025 | 0.39 | YES |
49 | RNMT | RNMT | RNMT | 5409 | 0.024 | 0.39 | YES |
50 | SNRPD2 | SNRPD2 | SNRPD2 | 5467 | 0.024 | 0.4 | YES |
51 | NUDT21 | NUDT21 | NUDT21 | 5504 | 0.023 | 0.4 | YES |
52 | CSTF3 | CSTF3 | CSTF3 | 5681 | 0.021 | 0.39 | YES |
53 | DHX9 | DHX9 | DHX9 | 5696 | 0.021 | 0.4 | YES |
54 | NHP2L1 | NHP2L1 | NHP2L1 | 5730 | 0.02 | 0.4 | YES |
55 | SMC1A | SMC1A | SMC1A | 5755 | 0.02 | 0.4 | YES |
56 | RNPS1 | RNPS1 | RNPS1 | 5819 | 0.019 | 0.4 | YES |
57 | U2AF1 | U2AF1 | U2AF1 | 5821 | 0.019 | 0.4 | YES |
58 | NUP85 | NUP85 | NUP85 | 5853 | 0.019 | 0.41 | YES |
59 | HNRNPR | HNRNPR | HNRNPR | 5974 | 0.018 | 0.4 | YES |
60 | HNRNPL | HNRNPL | HNRNPL | 5976 | 0.018 | 0.41 | YES |
61 | CDC40 | CDC40 | CDC40 | 5989 | 0.018 | 0.41 | YES |
62 | NUP43 | NUP43 | NUP43 | 6065 | 0.017 | 0.41 | YES |
63 | POLR2K | POLR2K | POLR2K | 6075 | 0.016 | 0.41 | YES |
64 | SF3A3 | SF3A3 | SF3A3 | 6103 | 0.016 | 0.42 | YES |
65 | GTF2H1 | GTF2H1 | GTF2H1 | 6122 | 0.016 | 0.42 | YES |
66 | NUP107 | NUP107 | NUP107 | 6136 | 0.016 | 0.42 | YES |
67 | POLR2B | POLR2B | POLR2B | 6140 | 0.016 | 0.42 | YES |
68 | NUP214 | NUP214 | NUP214 | 6221 | 0.014 | 0.42 | YES |
69 | NUP133 | NUP133 | NUP133 | 6248 | 0.014 | 0.42 | YES |
70 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 6255 | 0.014 | 0.42 | YES |
71 | SLBP | SLBP | SLBP | 6273 | 0.014 | 0.43 | YES |
72 | SNRNP40 | SNRNP40 | SNRNP40 | 6292 | 0.013 | 0.43 | YES |
73 | SF3B5 | SF3B5 | SF3B5 | 6302 | 0.013 | 0.43 | YES |
74 | HNRNPA2B1 | HNRNPA2B1 | HNRNPA2B1 | 6333 | 0.013 | 0.43 | YES |
75 | PTBP1 | PTBP1 | PTBP1 | 6355 | 0.013 | 0.43 | YES |
76 | RNGTT | RNGTT | RNGTT | 6385 | 0.012 | 0.43 | YES |
77 | CPSF2 | CPSF2 | CPSF2 | 6407 | 0.012 | 0.44 | YES |
78 | DHX38 | DHX38 | DHX38 | 6411 | 0.012 | 0.44 | YES |
79 | HNRNPH1 | HNRNPH1 | HNRNPH1 | 6415 | 0.012 | 0.44 | YES |
80 | HNRNPH2 | HNRNPH2 | HNRNPH2 | 6499 | 0.011 | 0.44 | NO |
81 | NUP93 | NUP93 | NUP93 | 6504 | 0.011 | 0.44 | NO |
82 | HNRNPK | HNRNPK | HNRNPK | 6565 | 0.01 | 0.44 | NO |
83 | CSTF1 | CSTF1 | CSTF1 | 6589 | 0.0097 | 0.44 | NO |
84 | DNAJC8 | DNAJC8 | DNAJC8 | 6626 | 0.0094 | 0.44 | NO |
85 | SNRPD1 | SNRPD1 | SNRPD1 | 6691 | 0.0086 | 0.44 | NO |
86 | SF3B2 | SF3B2 | SF3B2 | 6710 | 0.0084 | 0.44 | NO |
87 | HNRNPM | HNRNPM | HNRNPM | 6780 | 0.0077 | 0.44 | NO |
88 | PRPF6 | PRPF6 | PRPF6 | 6804 | 0.0074 | 0.44 | NO |
89 | THOC4 | THOC4 | THOC4 | 6825 | 0.0071 | 0.44 | NO |
90 | POLR2C | POLR2C | POLR2C | 6842 | 0.0069 | 0.44 | NO |
91 | SF3A1 | SF3A1 | SF3A1 | 6864 | 0.0067 | 0.44 | NO |
92 | PCBP1 | PCBP1 | PCBP1 | 6896 | 0.0063 | 0.44 | NO |
93 | POLR2D | POLR2D | POLR2D | 6917 | 0.0061 | 0.44 | NO |
94 | NXF1 | NXF1 | NXF1 | 6928 | 0.006 | 0.44 | NO |
95 | CCNH | CCNH | CCNH | 6977 | 0.0054 | 0.44 | NO |
96 | YBX1 | YBX1 | YBX1 | 7072 | 0.0042 | 0.43 | NO |
97 | SNRNP70 | SNRNP70 | SNRNP70 | 7088 | 0.0041 | 0.43 | NO |
98 | SNRPG | SNRPG | SNRPG | 7155 | 0.0035 | 0.43 | NO |
99 | PCF11 | PCF11 | PCF11 | 7165 | 0.0034 | 0.43 | NO |
100 | RANBP2 | RANBP2 | RANBP2 | 7200 | 0.0031 | 0.43 | NO |
101 | SF3B1 | SF3B1 | SF3B1 | 7216 | 0.0029 | 0.43 | NO |
102 | NUP188 | NUP188 | NUP188 | 7246 | 0.0027 | 0.43 | NO |
103 | PABPN1 | PABPN1 | PABPN1 | 7270 | 0.0024 | 0.42 | NO |
104 | POLR2E | POLR2E | POLR2E | 7373 | 0.0012 | 0.42 | NO |
105 | RBM5 | RBM5 | RBM5 | 7423 | 0.00067 | 0.42 | NO |
106 | TXNL4A | TXNL4A | TXNL4A | 7467 | 0.0002 | 0.42 | NO |
107 | POLR2J | POLR2J | POLR2J | 7470 | 0.00015 | 0.42 | NO |
108 | GTF2F1 | GTF2F1 | GTF2F1 | 7555 | -0.0008 | 0.41 | NO |
109 | POLR2L | POLR2L | POLR2L | 7607 | -0.0012 | 0.41 | NO |
110 | HNRNPD | HNRNPD | HNRNPD | 7685 | -0.0021 | 0.4 | NO |
111 | NUP50 | NUP50 | NUP50 | 7759 | -0.003 | 0.4 | NO |
112 | SF3B4 | SF3B4 | SF3B4 | 7783 | -0.0032 | 0.4 | NO |
113 | ZNF473 | ZNF473 | ZNF473 | 7829 | -0.0038 | 0.4 | NO |
114 | TPR | TPR | TPR | 7848 | -0.004 | 0.4 | NO |
115 | POLR2G | POLR2G | POLR2G | 7897 | -0.0046 | 0.4 | NO |
116 | ERCC2 | ERCC2 | ERCC2 | 7925 | -0.005 | 0.4 | NO |
117 | HNRNPU | HNRNPU | HNRNPU | 7974 | -0.0055 | 0.4 | NO |
118 | HNRNPUL1 | HNRNPUL1 | HNRNPUL1 | 8014 | -0.006 | 0.39 | NO |
119 | POLR2F | POLR2F | POLR2F | 8036 | -0.0062 | 0.39 | NO |
120 | AAAS | AAAS | AAAS | 8085 | -0.0068 | 0.39 | NO |
121 | CPSF7 | CPSF7 | CPSF7 | 8095 | -0.0069 | 0.39 | NO |
122 | DDX23 | DDX23 | DDX23 | 8138 | -0.0074 | 0.39 | NO |
123 | PRPF8 | PRPF8 | PRPF8 | 8252 | -0.0085 | 0.39 | NO |
124 | NUP62 | NUP62 | NUP62 | 8288 | -0.0089 | 0.39 | NO |
125 | NUP155 | NUP155 | NUP155 | 8312 | -0.0092 | 0.39 | NO |
126 | SNRNP200 | SNRNP200 | SNRNP200 | 8462 | -0.011 | 0.38 | NO |
127 | PCBP2 | PCBP2 | PCBP2 | 8498 | -0.011 | 0.38 | NO |
128 | ADAR | ADAR | ADAR | 8618 | -0.012 | 0.38 | NO |
129 | HNRNPA0 | HNRNPA0 | HNRNPA0 | 8667 | -0.013 | 0.38 | NO |
130 | U2AF2 | U2AF2 | U2AF2 | 8904 | -0.016 | 0.37 | NO |
131 | LSM11 | LSM11 | LSM11 | 8960 | -0.017 | 0.37 | NO |
132 | POLR2I | POLR2I | POLR2I | 8980 | -0.017 | 0.37 | NO |
133 | NUP153 | NUP153 | NUP153 | 9101 | -0.018 | 0.37 | NO |
134 | RBM8A | RBM8A | RBM8A | 9140 | -0.019 | 0.37 | NO |
135 | GTF2H4 | GTF2H4 | GTF2H4 | 9301 | -0.021 | 0.37 | NO |
136 | ERCC3 | ERCC3 | ERCC3 | 9340 | -0.022 | 0.37 | NO |
137 | SUPT5H | SUPT5H | SUPT5H | 9462 | -0.023 | 0.37 | NO |
138 | SRRM1 | SRRM1 | SRRM1 | 9546 | -0.024 | 0.37 | NO |
139 | CD2BP2 | CD2BP2 | CD2BP2 | 9741 | -0.027 | 0.36 | NO |
140 | FUS | FUS | FUS | 10113 | -0.032 | 0.35 | NO |
141 | NCBP2 | NCBP2 | NCBP2 | 10173 | -0.033 | 0.35 | NO |
142 | POLR2A | POLR2A | POLR2A | 10275 | -0.035 | 0.35 | NO |
143 | LSM10 | LSM10 | LSM10 | 12310 | -0.074 | 0.26 | NO |
144 | MNAT1 | MNAT1 | MNAT1 | 12647 | -0.082 | 0.26 | NO |
145 | ADARB1 | ADARB1 | ADARB1 | 14693 | -0.15 | 0.18 | NO |
146 | NUP210 | NUP210 | NUP210 | 15762 | -0.2 | 0.16 | NO |
Figure S95. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA DEATH PATHWAY.
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Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA DEATH PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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Table S49. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CYC1 | CYC1 | CYC1 | 1375 | 0.12 | -0.024 | YES |
2 | ATP5G1 | ATP5G1 | ATP5G1 | 1935 | 0.095 | -0.017 | YES |
3 | COQ2 | COQ2 | COQ2 | 2133 | 0.087 | 0.0074 | YES |
4 | CHCHD4 | CHCHD4 | CHCHD4 | 2217 | 0.084 | 0.036 | YES |
5 | IDH3G | IDH3G | IDH3G | 2278 | 0.082 | 0.066 | YES |
6 | GRPEL1 | GRPEL1 | GRPEL1 | 2359 | 0.08 | 0.094 | YES |
7 | PMPCA | PMPCA | PMPCA | 2500 | 0.076 | 0.12 | YES |
8 | C18orf55 | C18orf55 | C18orf55 | 2561 | 0.074 | 0.14 | YES |
9 | VDAC1 | VDAC1 | VDAC1 | 2699 | 0.071 | 0.16 | YES |
10 | PMPCB | PMPCB | PMPCB | 2729 | 0.07 | 0.19 | YES |
11 | TIMM8A | TIMM8A | TIMM8A | 2835 | 0.067 | 0.21 | YES |
12 | HSPD1 | HSPD1 | HSPD1 | 2903 | 0.066 | 0.23 | YES |
13 | LDHD | LDHD | LDHD | 2969 | 0.064 | 0.26 | YES |
14 | ATP5B | ATP5B | ATP5B | 2976 | 0.064 | 0.28 | YES |
15 | CS | CS | CS | 2985 | 0.064 | 0.31 | YES |
16 | FXN | FXN | FXN | 3005 | 0.064 | 0.33 | YES |
17 | TOMM40 | TOMM40 | TOMM40 | 3065 | 0.062 | 0.35 | YES |
18 | BCS1L | BCS1L | BCS1L | 3140 | 0.061 | 0.37 | YES |
19 | TOMM22 | TOMM22 | TOMM22 | 3199 | 0.06 | 0.39 | YES |
20 | ATP5A1 | ATP5A1 | ATP5A1 | 3280 | 0.058 | 0.41 | YES |
21 | TAZ | TAZ | TAZ | 3310 | 0.058 | 0.43 | YES |
22 | TIMM9 | TIMM9 | TIMM9 | 3635 | 0.051 | 0.44 | YES |
23 | TIMM13 | TIMM13 | TIMM13 | 3989 | 0.045 | 0.44 | YES |
24 | TIMM44 | TIMM44 | TIMM44 | 4143 | 0.042 | 0.44 | YES |
25 | SLC25A13 | SLC25A13 | SLC25A13 | 4170 | 0.042 | 0.46 | YES |
26 | GFER | GFER | GFER | 4182 | 0.042 | 0.48 | YES |
27 | GRPEL2 | GRPEL2 | GRPEL2 | 4245 | 0.041 | 0.49 | YES |
28 | SLC25A6 | SLC25A6 | SLC25A6 | 4260 | 0.041 | 0.5 | YES |
29 | TIMM10 | TIMM10 | TIMM10 | 4321 | 0.04 | 0.52 | YES |
30 | ACO2 | ACO2 | ACO2 | 4472 | 0.037 | 0.52 | YES |
31 | MTX2 | MTX2 | MTX2 | 4502 | 0.037 | 0.54 | YES |
32 | TOMM5 | TOMM5 | TOMM5 | 4628 | 0.035 | 0.54 | YES |
33 | HSPA9 | HSPA9 | HSPA9 | 4720 | 0.033 | 0.55 | YES |
34 | TOMM20 | TOMM20 | TOMM20 | 4838 | 0.032 | 0.56 | YES |
35 | TOMM70A | TOMM70A | TOMM70A | 4991 | 0.03 | 0.56 | YES |
36 | TIMM17A | TIMM17A | TIMM17A | 5614 | 0.022 | 0.54 | NO |
37 | SLC25A4 | SLC25A4 | SLC25A4 | 6150 | 0.016 | 0.52 | NO |
38 | TIMM50 | TIMM50 | TIMM50 | 6176 | 0.015 | 0.52 | NO |
39 | FXC1 | FXC1 | FXC1 | 6604 | 0.0096 | 0.5 | NO |
40 | HSCB | HSCB | HSCB | 6634 | 0.0092 | 0.5 | NO |
41 | TIMM8B | TIMM8B | TIMM8B | 6826 | 0.0071 | 0.5 | NO |
42 | SAMM50 | SAMM50 | SAMM50 | 6868 | 0.0066 | 0.5 | NO |
43 | TIMM17B | TIMM17B | TIMM17B | 7720 | -0.0025 | 0.45 | NO |
44 | TOMM7 | TOMM7 | TOMM7 | 7877 | -0.0044 | 0.44 | NO |
45 | TIMM22 | TIMM22 | TIMM22 | 10044 | -0.031 | 0.34 | NO |
46 | DNAJC19 | DNAJC19 | DNAJC19 | 10245 | -0.034 | 0.34 | NO |
47 | MTX1 | MTX1 | MTX1 | 10258 | -0.034 | 0.36 | NO |
48 | COX17 | COX17 | COX17 | 12825 | -0.087 | 0.25 | NO |
49 | SLC25A12 | SLC25A12 | SLC25A12 | 14765 | -0.15 | 0.21 | NO |
Figure S97. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.
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Figure S98. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S50. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CASP6 | CASP6 | CASP6 | 484 | 0.26 | 0.096 | YES |
2 | TNFRSF25 | TNFRSF25 | TNFRSF25 | 610 | 0.22 | 0.19 | YES |
3 | GAS2 | GAS2 | GAS2 | 718 | 0.2 | 0.28 | YES |
4 | DFFB | DFFB | DFFB | 771 | 0.19 | 0.37 | YES |
5 | CASP10 | CASP10 | CASP10 | 1076 | 0.15 | 0.42 | YES |
6 | CYCS | CYCS | CYCS | 2507 | 0.076 | 0.38 | YES |
7 | CASP3 | CASP3 | CASP3 | 2540 | 0.075 | 0.42 | YES |
8 | CASP7 | CASP7 | CASP7 | 3090 | 0.062 | 0.42 | YES |
9 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 3406 | 0.056 | 0.42 | YES |
10 | CASP8 | CASP8 | CASP8 | 3876 | 0.047 | 0.42 | YES |
11 | APAF1 | APAF1 | APAF1 | 3969 | 0.045 | 0.44 | YES |
12 | BID | BID | BID | 3981 | 0.045 | 0.46 | YES |
13 | TNFSF10 | TNFSF10 | TNFSF10 | 4159 | 0.042 | 0.47 | YES |
14 | FADD | FADD | FADD | 5119 | 0.028 | 0.43 | NO |
15 | TRAF2 | TRAF2 | TRAF2 | 5381 | 0.025 | 0.43 | NO |
16 | XIAP | XIAP | XIAP | 5725 | 0.02 | 0.42 | NO |
17 | RIPK1 | RIPK1 | RIPK1 | 6907 | 0.0062 | 0.36 | NO |
18 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 7314 | 0.0019 | 0.34 | NO |
19 | CHUK | CHUK | CHUK | 7713 | -0.0024 | 0.32 | NO |
20 | NFKB1 | NFKB1 | NFKB1 | 7981 | -0.0056 | 0.31 | NO |
21 | SPTAN1 | SPTAN1 | SPTAN1 | 8171 | -0.0078 | 0.3 | NO |
22 | CASP9 | CASP9 | CASP9 | 8443 | -0.011 | 0.29 | NO |
23 | BIRC2 | BIRC2 | BIRC2 | 8962 | -0.017 | 0.27 | NO |
24 | RELA | RELA | RELA | 9084 | -0.018 | 0.28 | NO |
25 | DFFA | DFFA | DFFA | 9649 | -0.026 | 0.26 | NO |
26 | BCL2 | BCL2 | BCL2 | 9985 | -0.03 | 0.25 | NO |
27 | MAP3K14 | MAP3K14 | MAP3K14 | 10072 | -0.031 | 0.26 | NO |
28 | NFKBIA | NFKBIA | NFKBIA | 10159 | -0.033 | 0.28 | NO |
29 | LMNA | LMNA | LMNA | 10224 | -0.034 | 0.29 | NO |
30 | BIRC3 | BIRC3 | BIRC3 | 10620 | -0.041 | 0.29 | NO |
31 | TRADD | TRADD | TRADD | 10914 | -0.046 | 0.29 | NO |
32 | CFLAR | CFLAR | CFLAR | 12159 | -0.07 | 0.26 | NO |
33 | TNFSF12 | TNFSF12 | TNFSF12 | 15654 | -0.19 | 0.16 | NO |
Figure S99. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT.

Figure S100. 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

For the top enriched genes, if you want to check whether they are
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up-regulated, please check the list of up-regulated genes
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down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
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highly expressed genes, please check the list of high (top 30%) expressed genes
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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
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significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
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Gene set database = c2.cp.v4.0.symbols.gmt
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Expression data file = STAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Phenotype data file = STAD-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.