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 "PRAD-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: 717 |
Number of samples: 497 |
Original number of Gene Sets: 1320 |
Maximum gene set size: 933 |
Table 2. Get Full Table pheno data info
phenotype info |
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pheno.type: 1 - 4 :[ clus1 ] 96 |
pheno.type: 2 - 4 :[ clus2 ] 142 |
pheno.type: 3 - 4 :[ clus3 ] 151 |
pheno.type: 4 - 4 :[ clus4 ] 108 |
For the expression subtypes of 18274 genes in 498 samples, GSEA found enriched gene sets in each cluster using 497 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG PROPANOATE METABOLISM, KEGG ADHERENS JUNCTION, KEGG INSULIN SIGNALING PATHWAY, KEGG THYROID CANCER, BIOCARTA AGR PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA MYOSIN PATHWAY
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And common core enriched genes are ACTN1, ACTN2, ACTN3, MAPK1, VCL, ABAT, ACACB, ACAT2, ACSS2, ACSS3
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clus2
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Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG N GLYCAN BIOSYNTHESIS, KEGG UBIQUITIN MEDIATED PROTEOLYSIS, PID ECADHERIN NASCENTAJ PATHWAY, PID LIS1PATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER, REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, REACTOME RNA POL II TRANSCRIPTION, REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES
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And common core enriched genes are NCBP1, NUP107, NUP133, NUP153, NUP155, NUP188, NUP205, NUP210, NUP214, NUP37
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clus3
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Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG RIBOSOME, KEGG DNA REPLICATION, KEGG PROTEASOME, KEGG BASE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG CELL CYCLE, KEGG PARKINSONS DISEASE
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And common core enriched genes are MCM7, POLE2, PRIM2, RPA3, CDC45, CDC6, CDT1, DNA2, FEN1, MCM5
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clus4
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Top enriched gene sets are KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG LYSINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG GLYCEROLIPID METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM
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And common core enriched genes are BDNF, BEX1, BIRC3, MMP7, NGFR, NTF3, NTF4, NTRK1, BBOX1, PIPOX
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION | 44 | genes.ES.table | 0.55 | 1.7 | 0.025 | 0.46 | 0.66 | 0.5 | 0.26 | 0.37 | 0.13 | 0.11 |
KEGG PROPANOATE METABOLISM | 32 | genes.ES.table | 0.63 | 1.9 | 0.004 | 1 | 0.22 | 0.59 | 0.26 | 0.44 | 0 | 0.19 |
KEGG ADHERENS JUNCTION | 73 | genes.ES.table | 0.51 | 1.8 | 0.002 | 0.64 | 0.47 | 0.33 | 0.24 | 0.25 | 0 | 0.14 |
KEGG INSULIN SIGNALING PATHWAY | 133 | genes.ES.table | 0.42 | 1.7 | 0.0041 | 0.45 | 0.8 | 0.33 | 0.24 | 0.25 | 0.16 | 0.12 |
KEGG THYROID CANCER | 29 | genes.ES.table | 0.54 | 1.7 | 0.014 | 0.41 | 0.75 | 0.17 | 0.11 | 0.15 | 0.14 | 0.11 |
BIOCARTA AGR PATHWAY | 36 | genes.ES.table | 0.69 | 1.8 | 0 | 0.54 | 0.61 | 0.36 | 0.14 | 0.31 | 0.13 | 0.13 |
BIOCARTA HDAC PATHWAY | 26 | genes.ES.table | 0.64 | 1.8 | 0 | 0.76 | 0.44 | 0.46 | 0.26 | 0.34 | 0 | 0.16 |
BIOCARTA INTEGRIN PATHWAY | 38 | genes.ES.table | 0.59 | 1.9 | 0 | 0.64 | 0.33 | 0.37 | 0.24 | 0.28 | 0 | 0.14 |
BIOCARTA PYK2 PATHWAY | 28 | genes.ES.table | 0.46 | 1.7 | 0.0078 | 0.51 | 0.62 | 0.29 | 0.26 | 0.21 | 0.12 | 0.13 |
BIOCARTA MYOSIN PATHWAY | 29 | genes.ES.table | 0.61 | 1.8 | 0 | 0.57 | 0.58 | 0.45 | 0.19 | 0.36 | 0.13 | 0.14 |
Table S1. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ACSS3 | ACSS3 | ACSS3 | 181 | 0.44 | 0.14 | YES |
2 | EHHADH | EHHADH | EHHADH | 530 | 0.33 | 0.24 | YES |
3 | LDHAL6A | LDHAL6A | LDHAL6A | 1128 | 0.23 | 0.28 | YES |
4 | ABAT | ABAT | ABAT | 1442 | 0.2 | 0.34 | YES |
5 | ACACB | ACACB | ACACB | 2119 | 0.15 | 0.35 | YES |
6 | ALDH2 | ALDH2 | ALDH2 | 2276 | 0.14 | 0.39 | YES |
7 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 2584 | 0.13 | 0.42 | YES |
8 | LDHC | LDHC | LDHC | 2901 | 0.11 | 0.44 | YES |
9 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 2986 | 0.11 | 0.47 | YES |
10 | MLYCD | MLYCD | MLYCD | 3265 | 0.095 | 0.49 | YES |
11 | SUCLA2 | SUCLA2 | SUCLA2 | 3413 | 0.089 | 0.51 | YES |
12 | LDHB | LDHB | LDHB | 3498 | 0.086 | 0.54 | YES |
13 | PCCA | PCCA | PCCA | 3575 | 0.084 | 0.56 | YES |
14 | ACAT2 | ACAT2 | ACAT2 | 3629 | 0.082 | 0.58 | YES |
15 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3877 | 0.074 | 0.6 | YES |
16 | MCEE | MCEE | MCEE | 4352 | 0.062 | 0.59 | YES |
17 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 4437 | 0.06 | 0.61 | YES |
18 | ACSS2 | ACSS2 | ACSS2 | 4528 | 0.058 | 0.62 | YES |
19 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4797 | 0.052 | 0.62 | YES |
20 | ACADM | ACADM | ACADM | 5495 | 0.04 | 0.6 | NO |
21 | SUCLG2 | SUCLG2 | SUCLG2 | 6439 | 0.027 | 0.56 | NO |
22 | LDHAL6B | LDHAL6B | LDHAL6B | 6950 | 0.02 | 0.54 | NO |
23 | HIBCH | HIBCH | HIBCH | 8274 | 0.0052 | 0.47 | NO |
24 | MUT | MUT | MUT | 9393 | -0.0064 | 0.41 | NO |
25 | HADHA | HADHA | HADHA | 9777 | -0.01 | 0.39 | NO |
26 | ACACA | ACACA | ACACA | 10658 | -0.02 | 0.35 | NO |
27 | PCCB | PCCB | PCCB | 11114 | -0.025 | 0.33 | NO |
28 | ECHS1 | ECHS1 | ECHS1 | 11160 | -0.025 | 0.34 | NO |
29 | SUCLG1 | SUCLG1 | SUCLG1 | 11218 | -0.026 | 0.34 | NO |
30 | ACSS1 | ACSS1 | ACSS1 | 11326 | -0.027 | 0.35 | NO |
31 | ACAT1 | ACAT1 | ACAT1 | 12444 | -0.04 | 0.3 | NO |
32 | LDHA | LDHA | LDHA | 13675 | -0.056 | 0.25 | 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S2. 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 S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
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1 | PAK3 | PAK3 | PAK3 | 5 | 0.73 | 0.2 | YES |
2 | FLNC | FLNC | FLNC | 477 | 0.34 | 0.27 | YES |
3 | MYLK | MYLK | MYLK | 800 | 0.28 | 0.33 | YES |
4 | MYH2 | MYH2 | MYH2 | 839 | 0.27 | 0.4 | YES |
5 | ACTG2 | ACTG2 | ACTG2 | 1011 | 0.25 | 0.46 | YES |
6 | PAK7 | PAK7 | PAK7 | 1189 | 0.23 | 0.51 | YES |
7 | FLNA | FLNA | FLNA | 1304 | 0.22 | 0.57 | YES |
8 | ROCK2 | ROCK2 | ROCK2 | 1370 | 0.21 | 0.62 | YES |
9 | CFL2 | CFL2 | CFL2 | 1528 | 0.2 | 0.67 | YES |
10 | MYLK2 | MYLK2 | MYLK2 | 2881 | 0.11 | 0.62 | NO |
11 | ROCK1 | ROCK1 | ROCK1 | 4263 | 0.064 | 0.56 | NO |
12 | ANGPTL2 | ANGPTL2 | ANGPTL2 | 5020 | 0.049 | 0.54 | NO |
13 | PAK1 | PAK1 | PAK1 | 6748 | 0.023 | 0.45 | NO |
14 | ACTR2 | ACTR2 | ACTR2 | 7092 | 0.019 | 0.43 | NO |
15 | PAK2 | PAK2 | PAK2 | 7954 | 0.0086 | 0.39 | NO |
16 | ACTR3 | ACTR3 | ACTR3 | 8415 | 0.0039 | 0.36 | NO |
17 | WASL | WASL | WASL | 8438 | 0.0036 | 0.36 | NO |
18 | VASP | VASP | VASP | 8568 | 0.0023 | 0.36 | NO |
19 | PFN2 | PFN2 | PFN2 | 8616 | 0.0018 | 0.36 | NO |
20 | AKT1 | AKT1 | AKT1 | 8881 | -0.0011 | 0.34 | NO |
21 | CDC42 | CDC42 | CDC42 | 9838 | -0.011 | 0.29 | NO |
22 | PFN1 | PFN1 | PFN1 | 10331 | -0.016 | 0.27 | NO |
23 | FSCN3 | FSCN3 | FSCN3 | 10526 | -0.018 | 0.26 | NO |
24 | GDI2 | GDI2 | GDI2 | 10920 | -0.022 | 0.25 | NO |
25 | PAK4 | PAK4 | PAK4 | 10973 | -0.023 | 0.25 | NO |
26 | CFL1 | CFL1 | CFL1 | 11779 | -0.032 | 0.22 | NO |
27 | ACTG1 | ACTG1 | ACTG1 | 11852 | -0.033 | 0.22 | NO |
28 | GDI1 | GDI1 | GDI1 | 11911 | -0.034 | 0.23 | NO |
29 | RPS4X | RPS4X | RPS4X | 12167 | -0.036 | 0.22 | NO |
30 | RHO | RHO | RHO | 12182 | -0.037 | 0.23 | NO |
31 | FSCN1 | FSCN1 | FSCN1 | 12200 | -0.037 | 0.24 | NO |
32 | PAK6 | PAK6 | PAK6 | 13444 | -0.053 | 0.19 | NO |
33 | LIMK1 | LIMK1 | LIMK1 | 13799 | -0.058 | 0.19 | NO |
34 | WASF1 | WASF1 | WASF1 | 14340 | -0.068 | 0.18 | NO |
35 | FSCN2 | FSCN2 | FSCN2 | 16592 | -0.15 | 0.091 | 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 PROPANOATE METABOLISM.

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

Table 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 | ACTA1 | ACTA1 | ACTA1 | 204 | 0.43 | 0.12 | YES |
2 | ACTN2 | ACTN2 | ACTN2 | 523 | 0.33 | 0.21 | YES |
3 | CAV1 | CAV1 | CAV1 | 988 | 0.25 | 0.27 | YES |
4 | ITGA1 | ITGA1 | ITGA1 | 1022 | 0.25 | 0.34 | YES |
5 | VCL | VCL | VCL | 1215 | 0.22 | 0.41 | YES |
6 | ACTN3 | ACTN3 | ACTN3 | 1331 | 0.21 | 0.47 | YES |
7 | PPP1R12B | PPP1R12B | PPP1R12B | 1444 | 0.2 | 0.53 | YES |
8 | TNS1 | TNS1 | TNS1 | 1505 | 0.2 | 0.59 | YES |
9 | ACTN1 | ACTN1 | ACTN1 | 2592 | 0.12 | 0.57 | YES |
10 | TLN1 | TLN1 | TLN1 | 3154 | 0.1 | 0.57 | YES |
11 | JUN | JUN | JUN | 3467 | 0.087 | 0.58 | YES |
12 | SOS1 | SOS1 | SOS1 | 4197 | 0.066 | 0.56 | YES |
13 | ROCK1 | ROCK1 | ROCK1 | 4263 | 0.064 | 0.57 | YES |
14 | MAPK1 | MAPK1 | MAPK1 | 4310 | 0.063 | 0.59 | YES |
15 | ITGB1 | ITGB1 | ITGB1 | 5128 | 0.047 | 0.56 | NO |
16 | ZYX | ZYX | ZYX | 5487 | 0.041 | 0.56 | NO |
17 | RAP1A | RAP1A | RAP1A | 5716 | 0.037 | 0.56 | NO |
18 | MAPK8 | MAPK8 | MAPK8 | 6660 | 0.024 | 0.51 | NO |
19 | MAP2K1 | MAP2K1 | MAP2K1 | 7035 | 0.019 | 0.5 | NO |
20 | CRKL | CRKL | CRKL | 7072 | 0.019 | 0.5 | NO |
21 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 7131 | 0.018 | 0.5 | NO |
22 | GRB2 | GRB2 | GRB2 | 7569 | 0.013 | 0.48 | NO |
23 | BCAR1 | BCAR1 | BCAR1 | 7759 | 0.011 | 0.48 | NO |
24 | PXN | PXN | PXN | 8011 | 0.008 | 0.46 | NO |
25 | CAPNS2 | CAPNS2 | CAPNS2 | 8217 | 0.006 | 0.46 | NO |
26 | FYN | FYN | FYN | 8432 | 0.0037 | 0.44 | NO |
27 | RHOA | RHOA | RHOA | 8975 | -0.0021 | 0.42 | NO |
28 | RAF1 | RAF1 | RAF1 | 9259 | -0.0051 | 0.4 | NO |
29 | MAPK3 | MAPK3 | MAPK3 | 9285 | -0.0054 | 0.4 | NO |
30 | SHC1 | SHC1 | SHC1 | 9297 | -0.0055 | 0.4 | NO |
31 | CAPN1 | CAPN1 | CAPN1 | 9939 | -0.012 | 0.37 | NO |
32 | SRC | SRC | SRC | 10220 | -0.015 | 0.36 | NO |
33 | CAPNS1 | CAPNS1 | CAPNS1 | 10615 | -0.019 | 0.35 | NO |
34 | MAP2K2 | MAP2K2 | MAP2K2 | 11396 | -0.028 | 0.31 | NO |
35 | PTK2 | PTK2 | PTK2 | 11585 | -0.03 | 0.31 | NO |
36 | CSK | CSK | CSK | 12196 | -0.037 | 0.29 | NO |
37 | BCR | BCR | BCR | 13098 | -0.048 | 0.26 | NO |
38 | HRAS | HRAS | HRAS | 15206 | -0.086 | 0.17 | 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 ADHERENS JUNCTION.

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

Table 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 | CAMK1G | CAMK1G | CAMK1G | 201 | 0.43 | 0.2 | YES |
2 | NFATC2 | NFATC2 | NFATC2 | 845 | 0.27 | 0.3 | YES |
3 | IGF1 | IGF1 | IGF1 | 886 | 0.27 | 0.43 | YES |
4 | MEF2C | MEF2C | MEF2C | 1683 | 0.18 | 0.47 | YES |
5 | PIK3CG | PIK3CG | PIK3CG | 2292 | 0.14 | 0.51 | YES |
6 | PIK3R1 | PIK3R1 | PIK3R1 | 2618 | 0.12 | 0.55 | YES |
7 | CALM1 | CALM1 | CALM1 | 3402 | 0.089 | 0.55 | YES |
8 | MEF2A | MEF2A | MEF2A | 3535 | 0.085 | 0.59 | YES |
9 | PIK3CA | PIK3CA | PIK3CA | 3567 | 0.084 | 0.63 | YES |
10 | MEF2D | MEF2D | MEF2D | 4323 | 0.063 | 0.62 | YES |
11 | PPP3CC | PPP3CC | PPP3CC | 4350 | 0.062 | 0.64 | YES |
12 | PPP3CB | PPP3CB | PPP3CB | 4802 | 0.052 | 0.64 | YES |
13 | MAPK7 | MAPK7 | MAPK7 | 5849 | 0.035 | 0.6 | NO |
14 | INSR | INSR | INSR | 6550 | 0.025 | 0.58 | NO |
15 | IGF1R | IGF1R | IGF1R | 6955 | 0.02 | 0.57 | NO |
16 | NFATC1 | NFATC1 | NFATC1 | 7051 | 0.019 | 0.57 | NO |
17 | CABIN1 | CABIN1 | CABIN1 | 7410 | 0.015 | 0.56 | NO |
18 | CAMK1 | CAMK1 | CAMK1 | 7573 | 0.013 | 0.56 | NO |
19 | HDAC5 | HDAC5 | HDAC5 | 8103 | 0.0069 | 0.53 | NO |
20 | YWHAH | YWHAH | YWHAH | 8264 | 0.0054 | 0.52 | NO |
21 | CALM2 | CALM2 | CALM2 | 8591 | 0.0021 | 0.51 | NO |
22 | AKT1 | AKT1 | AKT1 | 8881 | -0.0011 | 0.49 | NO |
23 | CALM3 | CALM3 | CALM3 | 8915 | -0.0016 | 0.49 | NO |
24 | MAPK14 | MAPK14 | MAPK14 | 9149 | -0.004 | 0.48 | NO |
25 | MAP2K6 | MAP2K6 | MAP2K6 | 9517 | -0.0077 | 0.46 | NO |
26 | PPP3CA | PPP3CA | PPP3CA | 11885 | -0.034 | 0.35 | NO |
Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG INSULIN SIGNALING PATHWAY.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG INSULIN SIGNALING 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 | ACTN2 | ACTN2 | ACTN2 | 523 | 0.33 | 0.041 | YES |
2 | SNAI2 | SNAI2 | SNAI2 | 685 | 0.3 | 0.094 | YES |
3 | SORBS1 | SORBS1 | SORBS1 | 794 | 0.28 | 0.15 | YES |
4 | VCL | VCL | VCL | 1215 | 0.22 | 0.17 | YES |
5 | ACTN3 | ACTN3 | ACTN3 | 1331 | 0.21 | 0.21 | YES |
6 | FER | FER | FER | 1571 | 0.19 | 0.24 | YES |
7 | CTNNA3 | CTNNA3 | CTNNA3 | 1834 | 0.17 | 0.26 | YES |
8 | PTPRM | PTPRM | PTPRM | 1972 | 0.16 | 0.28 | YES |
9 | TCF7 | TCF7 | TCF7 | 2000 | 0.16 | 0.32 | YES |
10 | TCF7L1 | TCF7L1 | TCF7L1 | 2070 | 0.16 | 0.35 | YES |
11 | LMO7 | LMO7 | LMO7 | 2182 | 0.15 | 0.37 | YES |
12 | FGFR1 | FGFR1 | FGFR1 | 2200 | 0.15 | 0.4 | YES |
13 | TGFBR2 | TGFBR2 | TGFBR2 | 2386 | 0.14 | 0.42 | YES |
14 | EGFR | EGFR | EGFR | 2471 | 0.13 | 0.44 | YES |
15 | ACTN1 | ACTN1 | ACTN1 | 2592 | 0.12 | 0.46 | YES |
16 | PTPRB | PTPRB | PTPRB | 3429 | 0.088 | 0.44 | YES |
17 | CTNNA2 | CTNNA2 | CTNNA2 | 3475 | 0.087 | 0.45 | YES |
18 | SMAD4 | SMAD4 | SMAD4 | 3667 | 0.081 | 0.46 | YES |
19 | SSX2IP | SSX2IP | SSX2IP | 3705 | 0.079 | 0.47 | YES |
20 | IQGAP1 | IQGAP1 | IQGAP1 | 3987 | 0.07 | 0.47 | YES |
21 | TGFBR1 | TGFBR1 | TGFBR1 | 4126 | 0.067 | 0.48 | YES |
22 | SNAI1 | SNAI1 | SNAI1 | 4182 | 0.066 | 0.49 | YES |
23 | MAPK1 | MAPK1 | MAPK1 | 4310 | 0.063 | 0.5 | YES |
24 | EP300 | EP300 | EP300 | 4311 | 0.063 | 0.51 | YES |
25 | PVRL3 | PVRL3 | PVRL3 | 4775 | 0.053 | 0.49 | NO |
26 | PTPN1 | PTPN1 | PTPN1 | 4921 | 0.05 | 0.5 | NO |
27 | MET | MET | MET | 5095 | 0.047 | 0.5 | NO |
28 | SMAD3 | SMAD3 | SMAD3 | 5297 | 0.044 | 0.5 | NO |
29 | BAIAP2 | BAIAP2 | BAIAP2 | 5544 | 0.04 | 0.49 | NO |
30 | TCF7L2 | TCF7L2 | TCF7L2 | 5771 | 0.036 | 0.48 | NO |
31 | CREBBP | CREBBP | CREBBP | 5796 | 0.036 | 0.49 | NO |
32 | CDH1 | CDH1 | CDH1 | 6263 | 0.029 | 0.47 | NO |
33 | CTNNB1 | CTNNB1 | CTNNB1 | 6338 | 0.028 | 0.47 | NO |
34 | WASF3 | WASF3 | WASF3 | 6392 | 0.028 | 0.48 | NO |
35 | INSR | INSR | INSR | 6550 | 0.025 | 0.47 | NO |
36 | MAP3K7 | MAP3K7 | MAP3K7 | 6595 | 0.025 | 0.48 | NO |
37 | ACTB | ACTB | ACTB | 6663 | 0.024 | 0.48 | NO |
38 | PARD3 | PARD3 | PARD3 | 6736 | 0.023 | 0.48 | NO |
39 | CTNND1 | CTNND1 | CTNND1 | 6833 | 0.022 | 0.48 | NO |
40 | IGF1R | IGF1R | IGF1R | 6955 | 0.02 | 0.48 | NO |
41 | MLLT4 | MLLT4 | MLLT4 | 7362 | 0.015 | 0.46 | NO |
42 | ACTN4 | ACTN4 | ACTN4 | 7443 | 0.014 | 0.45 | NO |
43 | TJP1 | TJP1 | TJP1 | 7533 | 0.013 | 0.45 | NO |
44 | PTPRF | PTPRF | PTPRF | 7577 | 0.013 | 0.45 | NO |
45 | ERBB2 | ERBB2 | ERBB2 | 7804 | 0.01 | 0.44 | NO |
46 | PVRL4 | PVRL4 | PVRL4 | 7846 | 0.0098 | 0.44 | NO |
47 | WASF2 | WASF2 | WASF2 | 7854 | 0.0097 | 0.44 | NO |
48 | CTNNA1 | CTNNA1 | CTNNA1 | 8219 | 0.006 | 0.42 | NO |
49 | SMAD2 | SMAD2 | SMAD2 | 8250 | 0.0055 | 0.42 | NO |
50 | FYN | FYN | FYN | 8432 | 0.0037 | 0.42 | NO |
51 | WASL | WASL | WASL | 8438 | 0.0036 | 0.42 | NO |
52 | CSNK2A2 | CSNK2A2 | CSNK2A2 | 8759 | 0.000045 | 0.4 | NO |
53 | RHOA | RHOA | RHOA | 8975 | -0.0021 | 0.39 | NO |
54 | NLK | NLK | NLK | 9125 | -0.0038 | 0.38 | NO |
55 | PTPRJ | PTPRJ | PTPRJ | 9267 | -0.0052 | 0.37 | NO |
56 | MAPK3 | MAPK3 | MAPK3 | 9285 | -0.0054 | 0.37 | NO |
57 | YES1 | YES1 | YES1 | 9462 | -0.0073 | 0.36 | NO |
58 | PTPN6 | PTPN6 | PTPN6 | 9756 | -0.01 | 0.35 | NO |
59 | PVRL2 | PVRL2 | PVRL2 | 9802 | -0.01 | 0.35 | NO |
60 | CDC42 | CDC42 | CDC42 | 9838 | -0.011 | 0.35 | NO |
61 | PVRL1 | PVRL1 | PVRL1 | 10036 | -0.013 | 0.34 | NO |
62 | SRC | SRC | SRC | 10220 | -0.015 | 0.34 | NO |
63 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 10443 | -0.017 | 0.33 | NO |
64 | RAC1 | RAC1 | RAC1 | 10867 | -0.022 | 0.31 | NO |
65 | RAC2 | RAC2 | RAC2 | 11154 | -0.025 | 0.3 | NO |
66 | ACP1 | ACP1 | ACP1 | 11562 | -0.03 | 0.28 | NO |
67 | LEF1 | LEF1 | LEF1 | 11583 | -0.03 | 0.29 | NO |
68 | ACTG1 | ACTG1 | ACTG1 | 11852 | -0.033 | 0.28 | NO |
69 | CSNK2B | CSNK2B | CSNK2B | 12664 | -0.042 | 0.24 | NO |
70 | FARP2 | FARP2 | FARP2 | 13572 | -0.055 | 0.2 | NO |
71 | WAS | WAS | WAS | 13892 | -0.06 | 0.2 | NO |
72 | WASF1 | WASF1 | WASF1 | 14340 | -0.068 | 0.19 | NO |
73 | RAC3 | RAC3 | RAC3 | 16208 | -0.12 | 0.11 | 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: KEGG THYROID CANCER.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID CANCER, 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 | PRKCB | PRKCB | PRKCB | 152 | 0.46 | 0.099 | YES |
2 | ITGB3 | ITGB3 | ITGB3 | 195 | 0.44 | 0.2 | YES |
3 | CAV1 | CAV1 | CAV1 | 988 | 0.25 | 0.22 | YES |
4 | VCL | VCL | VCL | 1215 | 0.22 | 0.26 | YES |
5 | PRKCA | PRKCA | PRKCA | 1470 | 0.2 | 0.29 | YES |
6 | KDR | KDR | KDR | 1480 | 0.2 | 0.34 | YES |
7 | NEDD4 | NEDD4 | NEDD4 | 1796 | 0.18 | 0.36 | YES |
8 | MYOF | MYOF | MYOF | 2017 | 0.16 | 0.39 | YES |
9 | PRKAA2 | PRKAA2 | PRKAA2 | 2469 | 0.13 | 0.39 | YES |
10 | PIK3R1 | PIK3R1 | PIK3R1 | 2618 | 0.12 | 0.41 | YES |
11 | FLT1 | FLT1 | FLT1 | 2653 | 0.12 | 0.44 | YES |
12 | PIK3CA | PIK3CA | PIK3CA | 3567 | 0.084 | 0.41 | YES |
13 | CDH5 | CDH5 | CDH5 | 3944 | 0.072 | 0.41 | YES |
14 | IQGAP1 | IQGAP1 | IQGAP1 | 3987 | 0.07 | 0.42 | YES |
15 | ITGAV | ITGAV | ITGAV | 4029 | 0.069 | 0.44 | YES |
16 | PTPN11 | PTPN11 | PTPN11 | 4205 | 0.065 | 0.44 | YES |
17 | ROCK1 | ROCK1 | ROCK1 | 4263 | 0.064 | 0.45 | YES |
18 | CBL | CBL | CBL | 4265 | 0.064 | 0.47 | YES |
19 | MAPK1 | MAPK1 | MAPK1 | 4310 | 0.063 | 0.48 | YES |
20 | PTK2B | PTK2B | PTK2B | 4747 | 0.054 | 0.47 | NO |
21 | AKAP1 | AKAP1 | AKAP1 | 4835 | 0.052 | 0.48 | NO |
22 | GAB1 | GAB1 | GAB1 | 5615 | 0.038 | 0.44 | NO |
23 | FBXW11 | FBXW11 | FBXW11 | 5873 | 0.034 | 0.44 | NO |
24 | GRB10 | GRB10 | GRB10 | 5994 | 0.033 | 0.44 | NO |
25 | VEGFA | VEGFA | VEGFA | 6160 | 0.03 | 0.44 | NO |
26 | SHB | SHB | SHB | 6186 | 0.03 | 0.44 | NO |
27 | PDPK1 | PDPK1 | PDPK1 | 6296 | 0.029 | 0.44 | NO |
28 | CTNNB1 | CTNNB1 | CTNNB1 | 6338 | 0.028 | 0.45 | NO |
29 | NOS3 | NOS3 | NOS3 | 6518 | 0.026 | 0.44 | NO |
30 | MAP2K1 | MAP2K1 | MAP2K1 | 7035 | 0.019 | 0.42 | NO |
31 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 7402 | 0.015 | 0.4 | NO |
32 | PRKACA | PRKACA | PRKACA | 7495 | 0.014 | 0.4 | NO |
33 | GRB2 | GRB2 | GRB2 | 7569 | 0.013 | 0.4 | NO |
34 | PAK2 | PAK2 | PAK2 | 7954 | 0.0086 | 0.38 | NO |
35 | PXN | PXN | PXN | 8011 | 0.008 | 0.38 | NO |
36 | CTNNA1 | CTNNA1 | CTNNA1 | 8219 | 0.006 | 0.37 | NO |
37 | CAMKK2 | CAMKK2 | CAMKK2 | 8411 | 0.0039 | 0.36 | NO |
38 | FYN | FYN | FYN | 8432 | 0.0037 | 0.36 | NO |
39 | PRKAA1 | PRKAA1 | PRKAA1 | 8599 | 0.002 | 0.35 | NO |
40 | DNM2 | DNM2 | DNM2 | 8717 | 0.00053 | 0.34 | NO |
41 | AKT1 | AKT1 | AKT1 | 8881 | -0.0011 | 0.34 | NO |
42 | PRKAB1 | PRKAB1 | PRKAB1 | 8890 | -0.0012 | 0.34 | NO |
43 | RHOA | RHOA | RHOA | 8975 | -0.0021 | 0.33 | NO |
44 | ARF1 | ARF1 | ARF1 | 9113 | -0.0037 | 0.32 | NO |
45 | MAPK14 | MAPK14 | MAPK14 | 9149 | -0.004 | 0.32 | NO |
46 | RAF1 | RAF1 | RAF1 | 9259 | -0.0051 | 0.32 | NO |
47 | PTPRJ | PTPRJ | PTPRJ | 9267 | -0.0052 | 0.32 | NO |
48 | MAPK3 | MAPK3 | MAPK3 | 9285 | -0.0054 | 0.32 | NO |
49 | PRKAG1 | PRKAG1 | PRKAG1 | 9415 | -0.0067 | 0.31 | NO |
50 | MAP2K6 | MAP2K6 | MAP2K6 | 9517 | -0.0077 | 0.31 | NO |
51 | NCK2 | NCK2 | NCK2 | 9660 | -0.0092 | 0.3 | NO |
52 | PTPN6 | PTPN6 | PTPN6 | 9756 | -0.01 | 0.3 | NO |
53 | CDC42 | CDC42 | CDC42 | 9838 | -0.011 | 0.3 | NO |
54 | SRC | SRC | SRC | 10220 | -0.015 | 0.28 | NO |
55 | HGS | HGS | HGS | 10404 | -0.017 | 0.28 | NO |
56 | MAPK11 | MAPK11 | MAPK11 | 10414 | -0.017 | 0.28 | NO |
57 | FES | FES | FES | 10497 | -0.018 | 0.28 | NO |
58 | MAP2K2 | MAP2K2 | MAP2K2 | 11396 | -0.028 | 0.24 | NO |
59 | PTK2 | PTK2 | PTK2 | 11585 | -0.03 | 0.23 | NO |
60 | MAP2K3 | MAP2K3 | MAP2K3 | 11737 | -0.032 | 0.23 | NO |
61 | NCK1 | NCK1 | NCK1 | 11856 | -0.033 | 0.23 | NO |
62 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 11941 | -0.034 | 0.24 | NO |
63 | PLCG1 | PLCG1 | PLCG1 | 12034 | -0.035 | 0.24 | NO |
64 | BRAF | BRAF | BRAF | 12356 | -0.039 | 0.23 | NO |
65 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 12818 | -0.044 | 0.22 | NO |
66 | PTPN2 | PTPN2 | PTPN2 | 14011 | -0.062 | 0.17 | NO |
67 | SH2D2A | SH2D2A | SH2D2A | 14495 | -0.07 | 0.16 | NO |
68 | PRKCD | PRKCD | PRKCD | 14667 | -0.074 | 0.16 | NO |
69 | VTN | VTN | VTN | 16531 | -0.14 | 0.095 | NO |
Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AGR PATHWAY.

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

Table S7. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PRKCB | PRKCB | PRKCB | 152 | 0.46 | 0.2 | YES |
2 | CAMK2A | CAMK2A | CAMK2A | 164 | 0.45 | 0.4 | YES |
3 | PRKCA | PRKCA | PRKCA | 1470 | 0.2 | 0.42 | YES |
4 | PRKAR2A | PRKAR2A | PRKAR2A | 1486 | 0.2 | 0.51 | YES |
5 | CAMK2G | CAMK2G | CAMK2G | 2549 | 0.13 | 0.51 | YES |
6 | PIK3R1 | PIK3R1 | PIK3R1 | 2618 | 0.12 | 0.56 | YES |
7 | PIK3CA | PIK3CA | PIK3CA | 3567 | 0.084 | 0.55 | YES |
8 | SOS1 | SOS1 | SOS1 | 4197 | 0.066 | 0.54 | YES |
9 | PRKAR2B | PRKAR2B | PRKAR2B | 4273 | 0.064 | 0.56 | YES |
10 | MAPK1 | MAPK1 | MAPK1 | 4310 | 0.063 | 0.59 | YES |
11 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5482 | 0.041 | 0.55 | NO |
12 | PRKACB | PRKACB | PRKACB | 5519 | 0.04 | 0.56 | NO |
13 | PRKAR1A | PRKAR1A | PRKAR1A | 6282 | 0.029 | 0.53 | NO |
14 | CREB1 | CREB1 | CREB1 | 7163 | 0.018 | 0.49 | NO |
15 | GRB2 | GRB2 | GRB2 | 7569 | 0.013 | 0.48 | NO |
16 | CAMK2D | CAMK2D | CAMK2D | 8838 | -0.00074 | 0.41 | NO |
17 | AKT1 | AKT1 | AKT1 | 8881 | -0.0011 | 0.4 | NO |
18 | MAPK14 | MAPK14 | MAPK14 | 9149 | -0.004 | 0.39 | NO |
19 | MAPK3 | MAPK3 | MAPK3 | 9285 | -0.0054 | 0.39 | NO |
20 | CAMK2B | CAMK2B | CAMK2B | 9476 | -0.0074 | 0.38 | NO |
21 | ADCY1 | ADCY1 | ADCY1 | 10231 | -0.015 | 0.34 | NO |
22 | RAC1 | RAC1 | RAC1 | 10867 | -0.022 | 0.32 | NO |
23 | GNAS | GNAS | GNAS | 11117 | -0.025 | 0.32 | NO |
24 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 11294 | -0.027 | 0.32 | NO |
25 | PRKAR1B | PRKAR1B | PRKAR1B | 13330 | -0.052 | 0.23 | NO |
26 | HRAS | HRAS | HRAS | 15206 | -0.086 | 0.17 | NO |
Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA HDAC PATHWAY.

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

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 | PRKCB | PRKCB | PRKCB | 152 | 0.46 | 0.15 | YES |
2 | MYL2 | MYL2 | MYL2 | 647 | 0.3 | 0.23 | YES |
3 | MYLK | MYLK | MYLK | 800 | 0.28 | 0.32 | YES |
4 | PPP1R12B | PPP1R12B | PPP1R12B | 1444 | 0.2 | 0.35 | YES |
5 | PRKCA | PRKCA | PRKCA | 1470 | 0.2 | 0.42 | YES |
6 | ARHGEF4 | ARHGEF4 | ARHGEF4 | 2152 | 0.15 | 0.44 | YES |
7 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 2833 | 0.11 | 0.44 | YES |
8 | ARHGEF17 | ARHGEF17 | ARHGEF17 | 2962 | 0.11 | 0.47 | YES |
9 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 3099 | 0.1 | 0.5 | YES |
10 | ARHGEF9 | ARHGEF9 | ARHGEF9 | 3119 | 0.1 | 0.53 | YES |
11 | ARHGEF10 | ARHGEF10 | ARHGEF10 | 3137 | 0.1 | 0.57 | YES |
12 | PLCB1 | PLCB1 | PLCB1 | 3235 | 0.096 | 0.6 | YES |
13 | ARHGEF15 | ARHGEF15 | ARHGEF15 | 3502 | 0.086 | 0.61 | YES |
14 | ROCK1 | ROCK1 | ROCK1 | 4263 | 0.064 | 0.59 | NO |
15 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 5686 | 0.037 | 0.53 | NO |
16 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 5818 | 0.035 | 0.53 | NO |
17 | GNAQ | GNAQ | GNAQ | 5836 | 0.035 | 0.54 | NO |
18 | GNA12 | GNA12 | GNA12 | 6515 | 0.026 | 0.52 | NO |
19 | ARHGEF18 | ARHGEF18 | ARHGEF18 | 6644 | 0.024 | 0.52 | NO |
20 | ARHGAP5 | ARHGAP5 | ARHGAP5 | 6675 | 0.024 | 0.52 | NO |
21 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 6677 | 0.024 | 0.53 | NO |
22 | ARHGEF5 | ARHGEF5 | ARHGEF5 | 6996 | 0.02 | 0.52 | NO |
23 | GNA13 | GNA13 | GNA13 | 8311 | 0.0049 | 0.45 | NO |
24 | GNB1 | GNB1 | GNB1 | 8425 | 0.0038 | 0.44 | NO |
25 | ARHGEF3 | ARHGEF3 | ARHGEF3 | 12361 | -0.039 | 0.24 | NO |
26 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 12509 | -0.04 | 0.25 | NO |
27 | ARHGEF19 | ARHGEF19 | ARHGEF19 | 13032 | -0.048 | 0.24 | NO |
28 | ARHGEF16 | ARHGEF16 | ARHGEF16 | 13204 | -0.05 | 0.24 | NO |
29 | PKN1 | PKN1 | PKN1 | 15439 | -0.093 | 0.16 | NO |
Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA INTEGRIN PATHWAY.

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

Table 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 | PAK3 | PAK3 | PAK3 | 5 | 0.73 | 0.17 | YES |
2 | ACTA1 | ACTA1 | ACTA1 | 204 | 0.43 | 0.26 | YES |
3 | NRG2 | NRG2 | NRG2 | 239 | 0.42 | 0.35 | YES |
4 | NRG1 | NRG1 | NRG1 | 498 | 0.34 | 0.41 | YES |
5 | DMD | DMD | DMD | 775 | 0.28 | 0.46 | YES |
6 | ITGA1 | ITGA1 | ITGA1 | 1022 | 0.25 | 0.5 | YES |
7 | PAK7 | PAK7 | PAK7 | 1189 | 0.23 | 0.55 | YES |
8 | MUSK | MUSK | MUSK | 1340 | 0.21 | 0.59 | YES |
9 | CHRM1 | CHRM1 | CHRM1 | 1544 | 0.19 | 0.62 | YES |
10 | LAMA2 | LAMA2 | LAMA2 | 2010 | 0.16 | 0.63 | YES |
11 | EGFR | EGFR | EGFR | 2471 | 0.13 | 0.64 | YES |
12 | LAMA4 | LAMA4 | LAMA4 | 2526 | 0.13 | 0.67 | YES |
13 | CHRNA1 | CHRNA1 | CHRNA1 | 2598 | 0.12 | 0.69 | YES |
14 | JUN | JUN | JUN | 3467 | 0.087 | 0.66 | NO |
15 | MAPK1 | MAPK1 | MAPK1 | 4310 | 0.063 | 0.63 | NO |
16 | RAPSN | RAPSN | RAPSN | 4534 | 0.058 | 0.63 | NO |
17 | ITGB1 | ITGB1 | ITGB1 | 5128 | 0.047 | 0.61 | NO |
18 | MAPK8 | MAPK8 | MAPK8 | 6660 | 0.024 | 0.53 | NO |
19 | SP1 | SP1 | SP1 | 6700 | 0.024 | 0.54 | NO |
20 | PAK1 | PAK1 | PAK1 | 6748 | 0.023 | 0.54 | NO |
21 | DAG1 | DAG1 | DAG1 | 7036 | 0.019 | 0.53 | NO |
22 | LAMA3 | LAMA3 | LAMA3 | 7428 | 0.014 | 0.51 | NO |
23 | PAK2 | PAK2 | PAK2 | 7954 | 0.0086 | 0.48 | NO |
24 | PXN | PXN | PXN | 8011 | 0.008 | 0.48 | NO |
25 | UTRN | UTRN | UTRN | 8112 | 0.0069 | 0.48 | NO |
26 | GIT2 | GIT2 | GIT2 | 8287 | 0.0051 | 0.47 | NO |
27 | MAPK3 | MAPK3 | MAPK3 | 9285 | -0.0054 | 0.42 | NO |
28 | CTTN | CTTN | CTTN | 9436 | -0.0069 | 0.41 | NO |
29 | CDC42 | CDC42 | CDC42 | 9838 | -0.011 | 0.39 | NO |
30 | SRC | SRC | SRC | 10220 | -0.015 | 0.37 | NO |
31 | RAC1 | RAC1 | RAC1 | 10867 | -0.022 | 0.34 | NO |
32 | PAK4 | PAK4 | PAK4 | 10973 | -0.023 | 0.34 | NO |
33 | PTK2 | PTK2 | PTK2 | 11585 | -0.03 | 0.31 | NO |
34 | PAK6 | PAK6 | PAK6 | 13444 | -0.053 | 0.22 | NO |
35 | DVL1 | DVL1 | DVL1 | 14683 | -0.074 | 0.17 | NO |
36 | NRG3 | NRG3 | NRG3 | 15645 | -0.1 | 0.14 | NO |
Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PYK2 PATHWAY.
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Figure S18. 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 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 | PRKCB | PRKCB | PRKCB | 152 | 0.46 | 0.3 | YES |
2 | PRKCA | PRKCA | PRKCA | 1470 | 0.2 | 0.36 | YES |
3 | CALM1 | CALM1 | CALM1 | 3402 | 0.089 | 0.31 | YES |
4 | JUN | JUN | JUN | 3467 | 0.087 | 0.37 | YES |
5 | MAP2K4 | MAP2K4 | MAP2K4 | 4056 | 0.069 | 0.38 | YES |
6 | SOS1 | SOS1 | SOS1 | 4197 | 0.066 | 0.42 | YES |
7 | MAPK1 | MAPK1 | MAPK1 | 4310 | 0.063 | 0.45 | YES |
8 | PTK2B | PTK2B | PTK2B | 4747 | 0.054 | 0.46 | YES |
9 | GNAQ | GNAQ | GNAQ | 5836 | 0.035 | 0.43 | NO |
10 | MAP3K1 | MAP3K1 | MAP3K1 | 6134 | 0.031 | 0.43 | NO |
11 | MAPK8 | MAPK8 | MAPK8 | 6660 | 0.024 | 0.42 | NO |
12 | PAK1 | PAK1 | PAK1 | 6748 | 0.023 | 0.43 | NO |
13 | MAP2K1 | MAP2K1 | MAP2K1 | 7035 | 0.019 | 0.43 | NO |
14 | CRKL | CRKL | CRKL | 7072 | 0.019 | 0.44 | NO |
15 | GRB2 | GRB2 | GRB2 | 7569 | 0.013 | 0.42 | NO |
16 | BCAR1 | BCAR1 | BCAR1 | 7759 | 0.011 | 0.41 | NO |
17 | CALM2 | CALM2 | CALM2 | 8591 | 0.0021 | 0.37 | NO |
18 | CALM3 | CALM3 | CALM3 | 8915 | -0.0016 | 0.35 | NO |
19 | MAPK14 | MAPK14 | MAPK14 | 9149 | -0.004 | 0.34 | NO |
20 | RAF1 | RAF1 | RAF1 | 9259 | -0.0051 | 0.34 | NO |
21 | MAPK3 | MAPK3 | MAPK3 | 9285 | -0.0054 | 0.34 | NO |
22 | SHC1 | SHC1 | SHC1 | 9297 | -0.0055 | 0.35 | NO |
23 | SRC | SRC | SRC | 10220 | -0.015 | 0.3 | NO |
24 | RAC1 | RAC1 | RAC1 | 10867 | -0.022 | 0.28 | NO |
25 | MAP2K2 | MAP2K2 | MAP2K2 | 11396 | -0.028 | 0.27 | NO |
26 | MAP2K3 | MAP2K3 | MAP2K3 | 11737 | -0.032 | 0.28 | NO |
27 | PLCG1 | PLCG1 | PLCG1 | 12034 | -0.035 | 0.28 | NO |
28 | HRAS | HRAS | HRAS | 15206 | -0.086 | 0.17 | NO |
Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA MYOSIN PATHWAY.

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

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 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 CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.51 | 1.7 | 0.029 | 0.44 | 0.75 | 0.034 | 0.00038 | 0.034 | 0.17 | 0.12 |
KEGG N GLYCAN BIOSYNTHESIS | 46 | genes.ES.table | 0.49 | 1.6 | 0.031 | 0.55 | 0.9 | 0.46 | 0.29 | 0.32 | 0.26 | 0.15 |
KEGG UBIQUITIN MEDIATED PROTEOLYSIS | 133 | genes.ES.table | 0.31 | 1.8 | 0.0019 | 0.71 | 0.56 | 0.44 | 0.3 | 0.32 | 0.17 | 0.16 |
PID ECADHERIN NASCENTAJ PATHWAY | 39 | genes.ES.table | 0.38 | 1.6 | 0.032 | 0.54 | 0.9 | 0.33 | 0.24 | 0.25 | 0.27 | 0.16 |
PID LIS1PATHWAY | 28 | genes.ES.table | 0.58 | 1.8 | 0.0063 | 0.43 | 0.62 | 0.21 | 0.087 | 0.2 | 0.12 | 0.1 |
REACTOME METABOLISM OF NON CODING RNA | 47 | genes.ES.table | 0.5 | 1.8 | 0.042 | 0.55 | 0.57 | 0.68 | 0.37 | 0.43 | 0.14 | 0.14 |
REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER | 36 | genes.ES.table | 0.55 | 1.6 | 0.016 | 0.57 | 0.89 | 0.5 | 0.25 | 0.38 | 0.27 | 0.16 |
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM | 44 | genes.ES.table | 0.53 | 1.9 | 0.004 | 0.55 | 0.36 | 0.61 | 0.33 | 0.41 | 0 | 0.12 |
REACTOME RNA POL II TRANSCRIPTION | 93 | genes.ES.table | 0.34 | 1.6 | 0.066 | 0.6 | 0.94 | 0.38 | 0.32 | 0.26 | 0.33 | 0.18 |
REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES | 59 | genes.ES.table | 0.41 | 1.6 | 0.089 | 0.62 | 0.95 | 0.32 | 0.22 | 0.25 | 0.37 | 0.18 |
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 | CCNT1 | CCNT1 | CCNT1 | 534 | 0.23 | 0.023 | YES |
2 | TAF4B | TAF4B | TAF4B | 808 | 0.18 | 0.05 | YES |
3 | GTF2A1 | GTF2A1 | GTF2A1 | 845 | 0.18 | 0.088 | YES |
4 | GTF2H2 | GTF2H2 | GTF2H2 | 1117 | 0.15 | 0.11 | YES |
5 | NUP210 | NUP210 | NUP210 | 1167 | 0.15 | 0.14 | YES |
6 | GTF2H3 | GTF2H3 | GTF2H3 | 1408 | 0.13 | 0.16 | YES |
7 | RCC1 | RCC1 | RCC1 | 1622 | 0.12 | 0.17 | YES |
8 | TAF1 | TAF1 | TAF1 | 1789 | 0.11 | 0.18 | YES |
9 | GTF2E1 | GTF2E1 | GTF2E1 | 1841 | 0.11 | 0.21 | YES |
10 | NUP155 | NUP155 | NUP155 | 2195 | 0.092 | 0.21 | YES |
11 | RANBP2 | RANBP2 | RANBP2 | 2435 | 0.086 | 0.22 | YES |
12 | CCNT2 | CCNT2 | CCNT2 | 2543 | 0.083 | 0.23 | YES |
13 | TAF4 | TAF4 | TAF4 | 2743 | 0.077 | 0.23 | YES |
14 | NUP54 | NUP54 | NUP54 | 2756 | 0.077 | 0.25 | YES |
15 | TPR | TPR | TPR | 2985 | 0.071 | 0.26 | YES |
16 | NUPL1 | NUPL1 | NUPL1 | 3073 | 0.069 | 0.27 | YES |
17 | CDK7 | CDK7 | CDK7 | 3142 | 0.068 | 0.28 | YES |
18 | POM121 | POM121 | POM121 | 3241 | 0.065 | 0.29 | YES |
19 | NUP133 | NUP133 | NUP133 | 3284 | 0.064 | 0.3 | YES |
20 | NUP153 | NUP153 | NUP153 | 3387 | 0.062 | 0.31 | YES |
21 | POLR2B | POLR2B | POLR2B | 3577 | 0.059 | 0.31 | YES |
22 | TAF9 | TAF9 | TAF9 | 3631 | 0.058 | 0.32 | YES |
23 | XPO1 | XPO1 | XPO1 | 3662 | 0.057 | 0.33 | YES |
24 | POLR2D | POLR2D | POLR2D | 3706 | 0.056 | 0.34 | YES |
25 | NUP205 | NUP205 | NUP205 | 3924 | 0.052 | 0.34 | YES |
26 | SEH1L | SEH1L | SEH1L | 3927 | 0.052 | 0.35 | YES |
27 | RNGTT | RNGTT | RNGTT | 4072 | 0.05 | 0.36 | YES |
28 | TAF13 | TAF13 | TAF13 | 4226 | 0.048 | 0.36 | YES |
29 | NCBP1 | NCBP1 | NCBP1 | 4246 | 0.048 | 0.37 | YES |
30 | NUP188 | NUP188 | NUP188 | 4343 | 0.046 | 0.38 | YES |
31 | NUP50 | NUP50 | NUP50 | 4709 | 0.041 | 0.36 | YES |
32 | RNMT | RNMT | RNMT | 4763 | 0.04 | 0.37 | YES |
33 | GTF2H2B | GTF2H2B | GTF2H2B | 4963 | 0.036 | 0.37 | YES |
34 | SSRP1 | SSRP1 | SSRP1 | 5029 | 0.036 | 0.37 | YES |
35 | ERCC3 | ERCC3 | ERCC3 | 5072 | 0.035 | 0.38 | YES |
36 | TSG101 | TSG101 | TSG101 | 5236 | 0.033 | 0.38 | YES |
37 | SUPT16H | SUPT16H | SUPT16H | 5336 | 0.032 | 0.38 | YES |
38 | NUP43 | NUP43 | NUP43 | 5341 | 0.032 | 0.38 | YES |
39 | RANBP1 | RANBP1 | RANBP1 | 5423 | 0.03 | 0.39 | YES |
40 | GTF2H1 | GTF2H1 | GTF2H1 | 5431 | 0.03 | 0.39 | YES |
41 | NUP107 | NUP107 | NUP107 | 5505 | 0.029 | 0.4 | YES |
42 | NUPL2 | NUPL2 | NUPL2 | 5570 | 0.028 | 0.4 | YES |
43 | GTF2A2 | GTF2A2 | GTF2A2 | 5800 | 0.025 | 0.39 | YES |
44 | NUP37 | NUP37 | NUP37 | 5914 | 0.023 | 0.39 | YES |
45 | MNAT1 | MNAT1 | MNAT1 | 5965 | 0.022 | 0.39 | YES |
46 | NUP214 | NUP214 | NUP214 | 6006 | 0.022 | 0.4 | YES |
47 | VPS37A | VPS37A | VPS37A | 6018 | 0.022 | 0.4 | YES |
48 | RAN | RAN | RAN | 6225 | 0.019 | 0.39 | NO |
49 | RAE1 | RAE1 | RAE1 | 6332 | 0.018 | 0.39 | NO |
50 | CCNH | CCNH | CCNH | 6509 | 0.016 | 0.39 | NO |
51 | NCBP2 | NCBP2 | NCBP2 | 6679 | 0.014 | 0.38 | NO |
52 | NUP62 | NUP62 | NUP62 | 6823 | 0.012 | 0.38 | NO |
53 | POLR2A | POLR2A | POLR2A | 6936 | 0.01 | 0.37 | NO |
54 | TCEA1 | TCEA1 | TCEA1 | 6953 | 0.0099 | 0.37 | NO |
55 | TCEB3 | TCEB3 | TCEB3 | 7236 | 0.0065 | 0.36 | NO |
56 | POLR2C | POLR2C | POLR2C | 7468 | 0.0038 | 0.35 | NO |
57 | GTF2E2 | GTF2E2 | GTF2E2 | 7543 | 0.0027 | 0.34 | NO |
58 | WHSC2 | WHSC2 | WHSC2 | 7621 | 0.0017 | 0.34 | NO |
59 | CTDP1 | CTDP1 | CTDP1 | 7891 | -0.0016 | 0.32 | NO |
60 | NMT1 | NMT1 | NMT1 | 7934 | -0.0023 | 0.32 | NO |
61 | COBRA1 | COBRA1 | COBRA1 | 7989 | -0.0028 | 0.32 | NO |
62 | TBP | TBP | TBP | 8031 | -0.0032 | 0.32 | NO |
63 | ERCC2 | ERCC2 | ERCC2 | 8157 | -0.005 | 0.31 | NO |
64 | RANGAP1 | RANGAP1 | RANGAP1 | 8191 | -0.0053 | 0.31 | NO |
65 | NUP88 | NUP88 | NUP88 | 8218 | -0.0057 | 0.31 | NO |
66 | RPS27A | RPS27A | RPS27A | 8342 | -0.0071 | 0.31 | NO |
67 | AAAS | AAAS | AAAS | 8506 | -0.0094 | 0.3 | NO |
68 | VPS37D | VPS37D | VPS37D | 8535 | -0.0099 | 0.3 | NO |
69 | TH1L | TH1L | TH1L | 8562 | -0.01 | 0.3 | NO |
70 | POLR2H | POLR2H | POLR2H | 8577 | -0.01 | 0.3 | NO |
71 | NMT2 | NMT2 | NMT2 | 8684 | -0.012 | 0.3 | NO |
72 | TAF5 | TAF5 | TAF5 | 8709 | -0.012 | 0.3 | NO |
73 | NUP35 | NUP35 | NUP35 | 8846 | -0.014 | 0.3 | NO |
74 | TAF12 | TAF12 | TAF12 | 8897 | -0.014 | 0.3 | NO |
75 | NUP93 | NUP93 | NUP93 | 9030 | -0.016 | 0.3 | NO |
76 | TCEB1 | TCEB1 | TCEB1 | 9057 | -0.016 | 0.3 | NO |
77 | TAF11 | TAF11 | TAF11 | 9111 | -0.017 | 0.3 | NO |
78 | NUP85 | NUP85 | NUP85 | 9155 | -0.018 | 0.3 | NO |
79 | GTF2F2 | GTF2F2 | GTF2F2 | 9403 | -0.021 | 0.29 | NO |
80 | GTF2F1 | GTF2F1 | GTF2F1 | 9438 | -0.021 | 0.29 | NO |
81 | POLR2K | POLR2K | POLR2K | 9532 | -0.022 | 0.29 | NO |
82 | CDK9 | CDK9 | CDK9 | 9572 | -0.023 | 0.3 | NO |
83 | UBA52 | UBA52 | UBA52 | 9623 | -0.024 | 0.3 | NO |
84 | TAF6 | TAF6 | TAF6 | 9660 | -0.024 | 0.3 | NO |
85 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 9920 | -0.028 | 0.3 | NO |
86 | GTF2H4 | GTF2H4 | GTF2H4 | 9932 | -0.028 | 0.3 | NO |
87 | ELL | ELL | ELL | 9970 | -0.029 | 0.3 | NO |
88 | SUPT5H | SUPT5H | SUPT5H | 9981 | -0.029 | 0.31 | NO |
89 | VPS37C | VPS37C | VPS37C | 10056 | -0.03 | 0.31 | NO |
90 | POLR2F | POLR2F | POLR2F | 10472 | -0.036 | 0.3 | NO |
91 | VPS37B | VPS37B | VPS37B | 10562 | -0.037 | 0.3 | NO |
92 | RDBP | RDBP | RDBP | 10609 | -0.038 | 0.31 | NO |
93 | POLR2E | POLR2E | POLR2E | 10610 | -0.038 | 0.32 | NO |
94 | TAF10 | TAF10 | TAF10 | 10632 | -0.039 | 0.33 | NO |
95 | VPS28 | VPS28 | VPS28 | 11012 | -0.044 | 0.32 | NO |
96 | POLR2G | POLR2G | POLR2G | 11172 | -0.047 | 0.32 | NO |
97 | GTF2B | GTF2B | GTF2B | 11558 | -0.054 | 0.31 | NO |
98 | POLR2L | POLR2L | POLR2L | 11891 | -0.06 | 0.3 | NO |
99 | POLR2I | POLR2I | POLR2I | 12011 | -0.063 | 0.31 | NO |
100 | POLR2J | POLR2J | POLR2J | 12325 | -0.069 | 0.31 | NO |
101 | TCEB2 | TCEB2 | TCEB2 | 12641 | -0.076 | 0.31 | 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 CITRATE CYCLE TCA CYCLE.

Figure S22. 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 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 | NUP210 | NUP210 | NUP210 | 1167 | 0.15 | 0.022 | YES |
2 | CDC40 | CDC40 | CDC40 | 1643 | 0.12 | 0.064 | YES |
3 | NUP155 | NUP155 | NUP155 | 2195 | 0.092 | 0.088 | YES |
4 | RANBP2 | RANBP2 | RANBP2 | 2435 | 0.086 | 0.12 | YES |
5 | NUP54 | NUP54 | NUP54 | 2756 | 0.077 | 0.15 | YES |
6 | TPR | TPR | TPR | 2985 | 0.071 | 0.18 | YES |
7 | NUPL1 | NUPL1 | NUPL1 | 3073 | 0.069 | 0.22 | YES |
8 | POM121 | POM121 | POM121 | 3241 | 0.065 | 0.25 | YES |
9 | NUP133 | NUP133 | NUP133 | 3284 | 0.064 | 0.28 | YES |
10 | NUP153 | NUP153 | NUP153 | 3387 | 0.062 | 0.31 | YES |
11 | NUP205 | NUP205 | NUP205 | 3924 | 0.052 | 0.31 | YES |
12 | SEH1L | SEH1L | SEH1L | 3927 | 0.052 | 0.34 | YES |
13 | CPSF2 | CPSF2 | CPSF2 | 4117 | 0.049 | 0.36 | YES |
14 | NCBP1 | NCBP1 | NCBP1 | 4246 | 0.048 | 0.38 | YES |
15 | NUP188 | NUP188 | NUP188 | 4343 | 0.046 | 0.41 | YES |
16 | EIF4E | EIF4E | EIF4E | 4414 | 0.045 | 0.43 | YES |
17 | NUP50 | NUP50 | NUP50 | 4709 | 0.041 | 0.44 | YES |
18 | CPSF3 | CPSF3 | CPSF3 | 5144 | 0.034 | 0.43 | YES |
19 | NFX1 | NFX1 | NFX1 | 5163 | 0.034 | 0.45 | YES |
20 | NUP43 | NUP43 | NUP43 | 5341 | 0.032 | 0.46 | YES |
21 | NUP107 | NUP107 | NUP107 | 5505 | 0.029 | 0.47 | YES |
22 | RBM8A | RBM8A | RBM8A | 5565 | 0.028 | 0.48 | YES |
23 | NUPL2 | NUPL2 | NUPL2 | 5570 | 0.028 | 0.5 | YES |
24 | UPF3B | UPF3B | UPF3B | 5751 | 0.026 | 0.5 | YES |
25 | NUP37 | NUP37 | NUP37 | 5914 | 0.023 | 0.51 | YES |
26 | NUP214 | NUP214 | NUP214 | 6006 | 0.022 | 0.52 | YES |
27 | U2AF2 | U2AF2 | U2AF2 | 6014 | 0.022 | 0.53 | YES |
28 | RAE1 | RAE1 | RAE1 | 6332 | 0.018 | 0.52 | NO |
29 | NCBP2 | NCBP2 | NCBP2 | 6679 | 0.014 | 0.51 | NO |
30 | NUP62 | NUP62 | NUP62 | 6823 | 0.012 | 0.51 | NO |
31 | THOC4 | THOC4 | THOC4 | 7518 | 0.0031 | 0.47 | NO |
32 | SLBP | SLBP | SLBP | 7547 | 0.0027 | 0.47 | NO |
33 | U2AF1 | U2AF1 | U2AF1 | 8180 | -0.0052 | 0.44 | NO |
34 | NUP88 | NUP88 | NUP88 | 8218 | -0.0057 | 0.44 | NO |
35 | MAGOH | MAGOH | MAGOH | 8457 | -0.0086 | 0.43 | NO |
36 | AAAS | AAAS | AAAS | 8506 | -0.0094 | 0.44 | NO |
37 | NUP35 | NUP35 | NUP35 | 8846 | -0.014 | 0.43 | NO |
38 | RNPS1 | RNPS1 | RNPS1 | 8939 | -0.015 | 0.43 | NO |
39 | NUP93 | NUP93 | NUP93 | 9030 | -0.016 | 0.44 | NO |
40 | NUP85 | NUP85 | NUP85 | 9155 | -0.018 | 0.44 | NO |
41 | SRRM1 | SRRM1 | SRRM1 | 9259 | -0.019 | 0.44 | NO |
42 | DHX38 | DHX38 | DHX38 | 9535 | -0.023 | 0.44 | NO |
43 | CPSF1 | CPSF1 | CPSF1 | 9996 | -0.029 | 0.43 | NO |
44 | NXF1 | NXF1 | NXF1 | 10311 | -0.034 | 0.44 | 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 N GLYCAN BIOSYNTHESIS.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG N GLYCAN BIOSYNTHESIS, 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 | CBLC | CBLC | CBLC | 558 | 0.23 | 0.0016 | YES |
2 | UBE2NL | UBE2NL | UBE2NL | 826 | 0.18 | 0.012 | YES |
3 | SKP2 | SKP2 | SKP2 | 852 | 0.18 | 0.036 | YES |
4 | UBE2E3 | UBE2E3 | UBE2E3 | 884 | 0.17 | 0.06 | YES |
5 | ANAPC1 | ANAPC1 | ANAPC1 | 1258 | 0.14 | 0.059 | YES |
6 | NHLRC1 | NHLRC1 | NHLRC1 | 1270 | 0.14 | 0.078 | YES |
7 | MID1 | MID1 | MID1 | 1860 | 0.11 | 0.061 | YES |
8 | ERCC8 | ERCC8 | ERCC8 | 2067 | 0.098 | 0.063 | YES |
9 | PARK2 | PARK2 | PARK2 | 2087 | 0.097 | 0.076 | YES |
10 | TRIM37 | TRIM37 | TRIM37 | 2127 | 0.095 | 0.087 | YES |
11 | WWP2 | WWP2 | WWP2 | 2320 | 0.089 | 0.09 | YES |
12 | XIAP | XIAP | XIAP | 2472 | 0.085 | 0.093 | YES |
13 | CDC20 | CDC20 | CDC20 | 2547 | 0.083 | 0.1 | YES |
14 | BIRC6 | BIRC6 | BIRC6 | 2578 | 0.082 | 0.11 | YES |
15 | HERC2 | HERC2 | HERC2 | 2725 | 0.078 | 0.11 | YES |
16 | HERC1 | HERC1 | HERC1 | 2770 | 0.077 | 0.12 | YES |
17 | VHL | VHL | VHL | 2777 | 0.076 | 0.13 | YES |
18 | CUL7 | CUL7 | CUL7 | 2878 | 0.074 | 0.14 | YES |
19 | ITCH | ITCH | ITCH | 2905 | 0.073 | 0.15 | YES |
20 | UBE2C | UBE2C | UBE2C | 2975 | 0.072 | 0.15 | YES |
21 | HERC3 | HERC3 | HERC3 | 2980 | 0.071 | 0.16 | YES |
22 | CUL4B | CUL4B | CUL4B | 3046 | 0.07 | 0.17 | YES |
23 | UBE3C | UBE3C | UBE3C | 3063 | 0.07 | 0.18 | YES |
24 | RCHY1 | RCHY1 | RCHY1 | 3097 | 0.069 | 0.19 | YES |
25 | UBE2J1 | UBE2J1 | UBE2J1 | 3170 | 0.067 | 0.19 | YES |
26 | UBA2 | UBA2 | UBA2 | 3186 | 0.066 | 0.2 | YES |
27 | PIAS2 | PIAS2 | PIAS2 | 3204 | 0.066 | 0.21 | YES |
28 | KLHL9 | KLHL9 | KLHL9 | 3215 | 0.066 | 0.22 | YES |
29 | UBE2G1 | UBE2G1 | UBE2G1 | 3255 | 0.065 | 0.22 | YES |
30 | UBE2H | UBE2H | UBE2H | 3314 | 0.064 | 0.23 | YES |
31 | CBLB | CBLB | CBLB | 3334 | 0.063 | 0.24 | YES |
32 | SIAH1 | SIAH1 | SIAH1 | 3380 | 0.063 | 0.25 | YES |
33 | UBE2W | UBE2W | UBE2W | 3425 | 0.062 | 0.25 | YES |
34 | BRCA1 | BRCA1 | BRCA1 | 3447 | 0.062 | 0.26 | YES |
35 | PIAS3 | PIAS3 | PIAS3 | 3583 | 0.059 | 0.26 | YES |
36 | TRIM32 | TRIM32 | TRIM32 | 3621 | 0.058 | 0.27 | YES |
37 | UBR5 | UBR5 | UBR5 | 3931 | 0.052 | 0.26 | YES |
38 | UBE2K | UBE2K | UBE2K | 3952 | 0.052 | 0.26 | YES |
39 | FBXW11 | FBXW11 | FBXW11 | 4042 | 0.05 | 0.27 | YES |
40 | CUL5 | CUL5 | CUL5 | 4075 | 0.05 | 0.27 | YES |
41 | UBE3A | UBE3A | UBE3A | 4080 | 0.05 | 0.28 | YES |
42 | NEDD4L | NEDD4L | NEDD4L | 4218 | 0.048 | 0.28 | YES |
43 | HUWE1 | HUWE1 | HUWE1 | 4249 | 0.048 | 0.28 | YES |
44 | RFWD2 | RFWD2 | RFWD2 | 4555 | 0.043 | 0.27 | YES |
45 | BIRC2 | BIRC2 | BIRC2 | 4594 | 0.043 | 0.28 | YES |
46 | UBE2I | UBE2I | UBE2I | 4608 | 0.042 | 0.28 | YES |
47 | UBA3 | UBA3 | UBA3 | 4638 | 0.042 | 0.28 | YES |
48 | UBE2Q2 | UBE2Q2 | UBE2Q2 | 4654 | 0.042 | 0.29 | YES |
49 | TRIP12 | TRIP12 | TRIP12 | 4663 | 0.041 | 0.3 | YES |
50 | UBE2N | UBE2N | UBE2N | 4795 | 0.039 | 0.29 | YES |
51 | PIAS1 | PIAS1 | PIAS1 | 4943 | 0.037 | 0.29 | YES |
52 | MAP3K1 | MAP3K1 | MAP3K1 | 4967 | 0.036 | 0.3 | YES |
53 | UBE2R2 | UBE2R2 | UBE2R2 | 5044 | 0.035 | 0.3 | YES |
54 | DET1 | DET1 | DET1 | 5107 | 0.035 | 0.3 | YES |
55 | TRAF6 | TRAF6 | TRAF6 | 5140 | 0.034 | 0.3 | YES |
56 | UBE4B | UBE4B | UBE4B | 5277 | 0.032 | 0.3 | YES |
57 | FBXO4 | FBXO4 | FBXO4 | 5294 | 0.032 | 0.3 | YES |
58 | HERC4 | HERC4 | HERC4 | 5360 | 0.031 | 0.3 | YES |
59 | CDC27 | CDC27 | CDC27 | 5390 | 0.031 | 0.3 | YES |
60 | UBE2Q1 | UBE2Q1 | UBE2Q1 | 5634 | 0.027 | 0.3 | NO |
61 | ANAPC10 | ANAPC10 | ANAPC10 | 5668 | 0.027 | 0.3 | NO |
62 | DDB1 | DDB1 | DDB1 | 5764 | 0.026 | 0.3 | NO |
63 | CUL2 | CUL2 | CUL2 | 5831 | 0.025 | 0.3 | NO |
64 | FBXW8 | FBXW8 | FBXW8 | 5855 | 0.024 | 0.3 | NO |
65 | UBA6 | UBA6 | UBA6 | 5983 | 0.022 | 0.29 | NO |
66 | CUL3 | CUL3 | CUL3 | 6239 | 0.019 | 0.28 | NO |
67 | UBE2O | UBE2O | UBE2O | 6255 | 0.019 | 0.28 | NO |
68 | UBE2A | UBE2A | UBE2A | 6258 | 0.019 | 0.29 | NO |
69 | PIAS4 | PIAS4 | PIAS4 | 6262 | 0.019 | 0.29 | NO |
70 | UBE2Z | UBE2Z | UBE2Z | 6294 | 0.018 | 0.29 | NO |
71 | SYVN1 | SYVN1 | SYVN1 | 6326 | 0.018 | 0.29 | NO |
72 | UBE2E2 | UBE2E2 | UBE2E2 | 6508 | 0.016 | 0.28 | NO |
73 | CUL4A | CUL4A | CUL4A | 6575 | 0.015 | 0.28 | NO |
74 | KEAP1 | KEAP1 | KEAP1 | 6625 | 0.014 | 0.28 | NO |
75 | UBE2D3 | UBE2D3 | UBE2D3 | 6642 | 0.014 | 0.28 | NO |
76 | CBL | CBL | CBL | 6690 | 0.013 | 0.28 | NO |
77 | MGRN1 | MGRN1 | MGRN1 | 6768 | 0.012 | 0.28 | NO |
78 | UBE2E1 | UBE2E1 | UBE2E1 | 6876 | 0.011 | 0.28 | NO |
79 | MDM2 | MDM2 | MDM2 | 6951 | 0.0099 | 0.27 | NO |
80 | SMURF2 | SMURF2 | SMURF2 | 7018 | 0.0091 | 0.27 | NO |
81 | UBE2J2 | UBE2J2 | UBE2J2 | 7092 | 0.0083 | 0.27 | NO |
82 | UBE2D2 | UBE2D2 | UBE2D2 | 7171 | 0.0073 | 0.26 | NO |
83 | FANCL | FANCL | FANCL | 7210 | 0.0068 | 0.26 | NO |
84 | UBE4A | UBE4A | UBE4A | 7280 | 0.006 | 0.26 | NO |
85 | CDC26 | CDC26 | CDC26 | 7302 | 0.0058 | 0.26 | NO |
86 | WWP1 | WWP1 | WWP1 | 7322 | 0.0055 | 0.26 | NO |
87 | SKP1 | SKP1 | SKP1 | 7451 | 0.0039 | 0.25 | NO |
88 | BTRC | BTRC | BTRC | 7719 | 0.00054 | 0.24 | NO |
89 | CDC16 | CDC16 | CDC16 | 7966 | -0.0026 | 0.22 | NO |
90 | UBE2D1 | UBE2D1 | UBE2D1 | 7996 | -0.0028 | 0.22 | NO |
91 | PRPF19 | PRPF19 | PRPF19 | 8521 | -0.0097 | 0.2 | NO |
92 | UBE3B | UBE3B | UBE3B | 8546 | -0.01 | 0.2 | NO |
93 | BIRC3 | BIRC3 | BIRC3 | 8609 | -0.011 | 0.2 | NO |
94 | ANAPC7 | ANAPC7 | ANAPC7 | 8617 | -0.011 | 0.2 | NO |
95 | PML | PML | PML | 8764 | -0.013 | 0.19 | NO |
96 | UBA1 | UBA1 | UBA1 | 8784 | -0.013 | 0.19 | NO |
97 | FBXW7 | FBXW7 | FBXW7 | 8913 | -0.015 | 0.18 | NO |
98 | ANAPC5 | ANAPC5 | ANAPC5 | 8984 | -0.016 | 0.18 | NO |
99 | TCEB1 | TCEB1 | TCEB1 | 9057 | -0.016 | 0.18 | NO |
100 | UBE2B | UBE2B | UBE2B | 9120 | -0.017 | 0.18 | NO |
101 | CUL1 | CUL1 | CUL1 | 9236 | -0.019 | 0.18 | NO |
102 | CDC23 | CDC23 | CDC23 | 9412 | -0.021 | 0.17 | NO |
103 | NEDD4 | NEDD4 | NEDD4 | 9875 | -0.028 | 0.15 | NO |
104 | RBX1 | RBX1 | RBX1 | 9961 | -0.029 | 0.15 | NO |
105 | RNF7 | RNF7 | RNF7 | 10044 | -0.03 | 0.15 | NO |
106 | PPIL2 | PPIL2 | PPIL2 | 10122 | -0.031 | 0.15 | NO |
107 | UBE2F | UBE2F | UBE2F | 10212 | -0.032 | 0.15 | NO |
108 | UBE2L3 | UBE2L3 | UBE2L3 | 10504 | -0.036 | 0.14 | NO |
109 | ANAPC2 | ANAPC2 | ANAPC2 | 10747 | -0.04 | 0.13 | NO |
110 | UBE2M | UBE2M | UBE2M | 10802 | -0.041 | 0.13 | NO |
111 | SAE1 | SAE1 | SAE1 | 10873 | -0.042 | 0.14 | NO |
112 | UBE2L6 | UBE2L6 | UBE2L6 | 11022 | -0.044 | 0.13 | NO |
113 | UBE2G2 | UBE2G2 | UBE2G2 | 11128 | -0.047 | 0.13 | NO |
114 | ANAPC13 | ANAPC13 | ANAPC13 | 11151 | -0.047 | 0.14 | NO |
115 | FZR1 | FZR1 | FZR1 | 11422 | -0.051 | 0.13 | NO |
116 | UBOX5 | UBOX5 | UBOX5 | 11439 | -0.052 | 0.14 | NO |
117 | UBE2S | UBE2S | UBE2S | 11453 | -0.052 | 0.14 | NO |
118 | AIRE | AIRE | AIRE | 11572 | -0.054 | 0.15 | NO |
119 | ANAPC4 | ANAPC4 | ANAPC4 | 11608 | -0.055 | 0.15 | NO |
120 | UBE2D4 | UBE2D4 | UBE2D4 | 11618 | -0.055 | 0.16 | NO |
121 | STUB1 | STUB1 | STUB1 | 12019 | -0.063 | 0.15 | NO |
122 | ANAPC11 | ANAPC11 | ANAPC11 | 12278 | -0.068 | 0.14 | NO |
123 | TCEB2 | TCEB2 | TCEB2 | 12641 | -0.076 | 0.13 | NO |
124 | SMURF1 | SMURF1 | SMURF1 | 12661 | -0.076 | 0.14 | NO |
125 | UBE2QL1 | UBE2QL1 | UBE2QL1 | 13276 | -0.091 | 0.12 | NO |
126 | CDC34 | CDC34 | CDC34 | 13327 | -0.092 | 0.13 | NO |
127 | RHOBTB2 | RHOBTB2 | RHOBTB2 | 13543 | -0.098 | 0.13 | NO |
128 | FBXO2 | FBXO2 | FBXO2 | 13998 | -0.11 | 0.12 | NO |
129 | KLHL13 | KLHL13 | KLHL13 | 14154 | -0.12 | 0.13 | NO |
130 | DDB2 | DDB2 | DDB2 | 14444 | -0.13 | 0.14 | NO |
131 | SOCS3 | SOCS3 | SOCS3 | 15311 | -0.16 | 0.11 | NO |
132 | UBA7 | UBA7 | UBA7 | 15887 | -0.18 | 0.1 | NO |
133 | SOCS1 | SOCS1 | SOCS1 | 15982 | -0.19 | 0.12 | 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 UBIQUITIN MEDIATED PROTEOLYSIS.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS, 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 | SMN1 | SMN1 | SMN1 | 501 | 0.24 | 0.093 | YES |
2 | NUP210 | NUP210 | NUP210 | 1167 | 0.15 | 0.13 | YES |
3 | NUP155 | NUP155 | NUP155 | 2195 | 0.092 | 0.12 | YES |
4 | RANBP2 | RANBP2 | RANBP2 | 2435 | 0.086 | 0.15 | YES |
5 | NUP54 | NUP54 | NUP54 | 2756 | 0.077 | 0.17 | YES |
6 | TPR | TPR | TPR | 2985 | 0.071 | 0.2 | YES |
7 | NUPL1 | NUPL1 | NUPL1 | 3073 | 0.069 | 0.23 | YES |
8 | POM121 | POM121 | POM121 | 3241 | 0.065 | 0.25 | YES |
9 | NUP133 | NUP133 | NUP133 | 3284 | 0.064 | 0.28 | YES |
10 | NUP153 | NUP153 | NUP153 | 3387 | 0.062 | 0.31 | YES |
11 | SMN2 | SMN2 | SMN2 | 3840 | 0.054 | 0.31 | YES |
12 | NUP205 | NUP205 | NUP205 | 3924 | 0.052 | 0.33 | YES |
13 | SEH1L | SEH1L | SEH1L | 3927 | 0.052 | 0.36 | YES |
14 | NCBP1 | NCBP1 | NCBP1 | 4246 | 0.048 | 0.36 | YES |
15 | PHAX | PHAX | PHAX | 4260 | 0.047 | 0.39 | YES |
16 | GEMIN5 | GEMIN5 | GEMIN5 | 4327 | 0.046 | 0.41 | YES |
17 | NUP188 | NUP188 | NUP188 | 4343 | 0.046 | 0.43 | YES |
18 | CLNS1A | CLNS1A | CLNS1A | 4481 | 0.044 | 0.44 | YES |
19 | NUP50 | NUP50 | NUP50 | 4709 | 0.041 | 0.45 | YES |
20 | NUP43 | NUP43 | NUP43 | 5341 | 0.032 | 0.43 | YES |
21 | NUP107 | NUP107 | NUP107 | 5505 | 0.029 | 0.44 | YES |
22 | SNRPD3 | SNRPD3 | SNRPD3 | 5547 | 0.029 | 0.45 | YES |
23 | PRMT5 | PRMT5 | PRMT5 | 5561 | 0.028 | 0.47 | YES |
24 | NUPL2 | NUPL2 | NUPL2 | 5570 | 0.028 | 0.48 | YES |
25 | TGS1 | TGS1 | TGS1 | 5582 | 0.028 | 0.49 | YES |
26 | NUP37 | NUP37 | NUP37 | 5914 | 0.023 | 0.49 | YES |
27 | NUP214 | NUP214 | NUP214 | 6006 | 0.022 | 0.49 | YES |
28 | RAE1 | RAE1 | RAE1 | 6332 | 0.018 | 0.48 | YES |
29 | SNRPE | SNRPE | SNRPE | 6357 | 0.017 | 0.49 | YES |
30 | SNRPG | SNRPG | SNRPG | 6462 | 0.016 | 0.49 | YES |
31 | GEMIN4 | GEMIN4 | GEMIN4 | 6669 | 0.014 | 0.49 | YES |
32 | NCBP2 | NCBP2 | NCBP2 | 6679 | 0.014 | 0.5 | YES |
33 | NUP62 | NUP62 | NUP62 | 6823 | 0.012 | 0.49 | NO |
34 | SNRPD1 | SNRPD1 | SNRPD1 | 7272 | 0.0061 | 0.47 | NO |
35 | SNRPF | SNRPF | SNRPF | 7644 | 0.0014 | 0.45 | NO |
36 | SNRPB | SNRPB | SNRPB | 7963 | -0.0026 | 0.44 | NO |
37 | NUP88 | NUP88 | NUP88 | 8218 | -0.0057 | 0.43 | NO |
38 | DDX20 | DDX20 | DDX20 | 8490 | -0.0092 | 0.42 | NO |
39 | AAAS | AAAS | AAAS | 8506 | -0.0094 | 0.42 | NO |
40 | NUP35 | NUP35 | NUP35 | 8846 | -0.014 | 0.41 | NO |
41 | SNRPD2 | SNRPD2 | SNRPD2 | 8965 | -0.015 | 0.41 | NO |
42 | NUP93 | NUP93 | NUP93 | 9030 | -0.016 | 0.41 | NO |
43 | NUP85 | NUP85 | NUP85 | 9155 | -0.018 | 0.42 | NO |
44 | SNUPN | SNUPN | SNUPN | 9322 | -0.02 | 0.42 | NO |
45 | WDR77 | WDR77 | WDR77 | 9988 | -0.029 | 0.4 | NO |
46 | GEMIN6 | GEMIN6 | GEMIN6 | 10120 | -0.031 | 0.4 | NO |
47 | GEMIN7 | GEMIN7 | GEMIN7 | 13065 | -0.086 | 0.28 | 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: PID ECADHERIN NASCENTAJ PATHWAY.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: PID ECADHERIN NASCENTAJ PATHWAY, 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 | NUP210 | NUP210 | NUP210 | 1167 | 0.15 | 0.04 | YES |
2 | NUP155 | NUP155 | NUP155 | 2195 | 0.092 | 0.049 | YES |
3 | RANBP2 | RANBP2 | RANBP2 | 2435 | 0.086 | 0.097 | YES |
4 | NUP54 | NUP54 | NUP54 | 2756 | 0.077 | 0.13 | YES |
5 | TPR | TPR | TPR | 2985 | 0.071 | 0.17 | YES |
6 | NUPL1 | NUPL1 | NUPL1 | 3073 | 0.069 | 0.22 | YES |
7 | POM121 | POM121 | POM121 | 3241 | 0.065 | 0.25 | YES |
8 | NUP133 | NUP133 | NUP133 | 3284 | 0.064 | 0.3 | YES |
9 | NUP153 | NUP153 | NUP153 | 3387 | 0.062 | 0.34 | YES |
10 | NUP205 | NUP205 | NUP205 | 3924 | 0.052 | 0.34 | YES |
11 | SEH1L | SEH1L | SEH1L | 3927 | 0.052 | 0.38 | YES |
12 | CPSF2 | CPSF2 | CPSF2 | 4117 | 0.049 | 0.41 | YES |
13 | NCBP1 | NCBP1 | NCBP1 | 4246 | 0.048 | 0.43 | YES |
14 | NUP188 | NUP188 | NUP188 | 4343 | 0.046 | 0.46 | YES |
15 | EIF4E | EIF4E | EIF4E | 4414 | 0.045 | 0.49 | YES |
16 | NUP50 | NUP50 | NUP50 | 4709 | 0.041 | 0.5 | YES |
17 | CPSF3 | CPSF3 | CPSF3 | 5144 | 0.034 | 0.5 | YES |
18 | NUP43 | NUP43 | NUP43 | 5341 | 0.032 | 0.51 | YES |
19 | NUP107 | NUP107 | NUP107 | 5505 | 0.029 | 0.52 | YES |
20 | NUPL2 | NUPL2 | NUPL2 | 5570 | 0.028 | 0.54 | YES |
21 | NUP37 | NUP37 | NUP37 | 5914 | 0.023 | 0.54 | YES |
22 | NUP214 | NUP214 | NUP214 | 6006 | 0.022 | 0.55 | YES |
23 | RAE1 | RAE1 | RAE1 | 6332 | 0.018 | 0.54 | NO |
24 | NCBP2 | NCBP2 | NCBP2 | 6679 | 0.014 | 0.54 | NO |
25 | NUP62 | NUP62 | NUP62 | 6823 | 0.012 | 0.54 | NO |
26 | THOC4 | THOC4 | THOC4 | 7518 | 0.0031 | 0.5 | NO |
27 | NUP88 | NUP88 | NUP88 | 8218 | -0.0057 | 0.46 | NO |
28 | AAAS | AAAS | AAAS | 8506 | -0.0094 | 0.46 | NO |
29 | NUP35 | NUP35 | NUP35 | 8846 | -0.014 | 0.45 | NO |
30 | NUP93 | NUP93 | NUP93 | 9030 | -0.016 | 0.45 | NO |
31 | NUP85 | NUP85 | NUP85 | 9155 | -0.018 | 0.46 | NO |
32 | CPSF1 | CPSF1 | CPSF1 | 9996 | -0.029 | 0.43 | NO |
33 | NXF1 | NXF1 | NXF1 | 10311 | -0.034 | 0.44 | 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: PID LIS1PATHWAY.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: PID LIS1PATHWAY, 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 | PLA2G7 | PLA2G7 | PLA2G7 | 102 | 0.47 | 0.21 | YES |
2 | CDK5R2 | CDK5R2 | CDK5R2 | 364 | 0.27 | 0.32 | YES |
3 | VLDLR | VLDLR | VLDLR | 385 | 0.27 | 0.45 | YES |
4 | LRP8 | LRP8 | LRP8 | 877 | 0.17 | 0.5 | YES |
5 | DAB1 | DAB1 | DAB1 | 1516 | 0.12 | 0.53 | YES |
6 | PAFAH1B2 | PAFAH1B2 | PAFAH1B2 | 1590 | 0.12 | 0.58 | YES |
7 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 2648 | 0.08 | 0.56 | NO |
8 | CDK5R1 | CDK5R1 | CDK5R1 | 3917 | 0.052 | 0.51 | NO |
9 | DYNC1H1 | DYNC1H1 | DYNC1H1 | 5222 | 0.033 | 0.46 | NO |
10 | KATNA1 | KATNA1 | KATNA1 | 5609 | 0.028 | 0.45 | NO |
11 | ABL1 | ABL1 | ABL1 | 5611 | 0.028 | 0.46 | NO |
12 | YWHAE | YWHAE | YWHAE | 6543 | 0.015 | 0.42 | NO |
13 | CDC42 | CDC42 | CDC42 | 6822 | 0.012 | 0.41 | NO |
14 | RHOA | RHOA | RHOA | 6939 | 0.01 | 0.4 | NO |
15 | CLIP1 | CLIP1 | CLIP1 | 7066 | 0.0086 | 0.4 | NO |
16 | IQGAP1 | IQGAP1 | IQGAP1 | 7593 | 0.002 | 0.37 | NO |
17 | CDK5 | CDK5 | CDK5 | 7739 | 0.00029 | 0.37 | NO |
18 | PAFAH1B1 | PAFAH1B1 | PAFAH1B1 | 8042 | -0.0034 | 0.35 | NO |
19 | PPP2R5D | PPP2R5D | PPP2R5D | 8214 | -0.0056 | 0.34 | NO |
20 | RAC1 | RAC1 | RAC1 | 8754 | -0.013 | 0.32 | NO |
21 | DYNLT1 | DYNLT1 | DYNLT1 | 9729 | -0.025 | 0.28 | NO |
22 | LRPAP1 | LRPAP1 | LRPAP1 | 9788 | -0.026 | 0.29 | NO |
23 | MAP1B | MAP1B | MAP1B | 10426 | -0.035 | 0.27 | NO |
24 | NUDC | NUDC | NUDC | 10698 | -0.04 | 0.27 | NO |
25 | NDEL1 | NDEL1 | NDEL1 | 10752 | -0.04 | 0.29 | NO |
26 | PAFAH1B3 | PAFAH1B3 | PAFAH1B3 | 12142 | -0.066 | 0.24 | NO |
27 | DCX | DCX | DCX | 12301 | -0.068 | 0.27 | NO |
28 | RELN | RELN | RELN | 14501 | -0.13 | 0.21 | 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: REACTOME METABOLISM OF NON CODING RNA.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF NON CODING RNA, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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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 | NUP210 | NUP210 | NUP210 | 1167 | 0.15 | 0.056 | YES |
2 | NUP155 | NUP155 | NUP155 | 2195 | 0.092 | 0.076 | YES |
3 | RANBP2 | RANBP2 | RANBP2 | 2435 | 0.086 | 0.13 | YES |
4 | NUP54 | NUP54 | NUP54 | 2756 | 0.077 | 0.18 | YES |
5 | TPR | TPR | TPR | 2985 | 0.071 | 0.22 | YES |
6 | NUPL1 | NUPL1 | NUPL1 | 3073 | 0.069 | 0.28 | YES |
7 | POM121 | POM121 | POM121 | 3241 | 0.065 | 0.32 | YES |
8 | NUP133 | NUP133 | NUP133 | 3284 | 0.064 | 0.37 | YES |
9 | NUP153 | NUP153 | NUP153 | 3387 | 0.062 | 0.42 | YES |
10 | KPNB1 | KPNB1 | KPNB1 | 3464 | 0.061 | 0.46 | YES |
11 | NUP205 | NUP205 | NUP205 | 3924 | 0.052 | 0.48 | YES |
12 | SEH1L | SEH1L | SEH1L | 3927 | 0.052 | 0.52 | YES |
13 | NUP188 | NUP188 | NUP188 | 4343 | 0.046 | 0.54 | YES |
14 | NUP50 | NUP50 | NUP50 | 4709 | 0.041 | 0.55 | YES |
15 | NUP43 | NUP43 | NUP43 | 5341 | 0.032 | 0.54 | YES |
16 | NUP107 | NUP107 | NUP107 | 5505 | 0.029 | 0.56 | YES |
17 | NUPL2 | NUPL2 | NUPL2 | 5570 | 0.028 | 0.58 | YES |
18 | NUP37 | NUP37 | NUP37 | 5914 | 0.023 | 0.58 | YES |
19 | NUP214 | NUP214 | NUP214 | 6006 | 0.022 | 0.59 | YES |
20 | RAE1 | RAE1 | RAE1 | 6332 | 0.018 | 0.59 | NO |
21 | NUP62 | NUP62 | NUP62 | 6823 | 0.012 | 0.57 | NO |
22 | KPNA1 | KPNA1 | KPNA1 | 7412 | 0.0044 | 0.54 | NO |
23 | NUP88 | NUP88 | NUP88 | 8218 | -0.0057 | 0.5 | NO |
24 | AAAS | AAAS | AAAS | 8506 | -0.0094 | 0.5 | NO |
25 | NUP35 | NUP35 | NUP35 | 8846 | -0.014 | 0.49 | NO |
26 | NUP93 | NUP93 | NUP93 | 9030 | -0.016 | 0.49 | NO |
27 | NUP85 | NUP85 | NUP85 | 9155 | -0.018 | 0.5 | 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: REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER, 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 | NUP210 | NUP210 | NUP210 | 1167 | 0.15 | 0.055 | YES |
2 | NUP155 | NUP155 | NUP155 | 2195 | 0.092 | 0.074 | YES |
3 | RANBP2 | RANBP2 | RANBP2 | 2435 | 0.086 | 0.13 | YES |
4 | NUP54 | NUP54 | NUP54 | 2756 | 0.077 | 0.18 | YES |
5 | TPR | TPR | TPR | 2985 | 0.071 | 0.22 | YES |
6 | NUPL1 | NUPL1 | NUPL1 | 3073 | 0.069 | 0.27 | YES |
7 | POM121 | POM121 | POM121 | 3241 | 0.065 | 0.32 | YES |
8 | NUP133 | NUP133 | NUP133 | 3284 | 0.064 | 0.37 | YES |
9 | NUP153 | NUP153 | NUP153 | 3387 | 0.062 | 0.41 | YES |
10 | XPO1 | XPO1 | XPO1 | 3662 | 0.057 | 0.44 | YES |
11 | NUP205 | NUP205 | NUP205 | 3924 | 0.052 | 0.47 | YES |
12 | SEH1L | SEH1L | SEH1L | 3927 | 0.052 | 0.52 | YES |
13 | NUP188 | NUP188 | NUP188 | 4343 | 0.046 | 0.53 | YES |
14 | NUP50 | NUP50 | NUP50 | 4709 | 0.041 | 0.54 | YES |
15 | NUP43 | NUP43 | NUP43 | 5341 | 0.032 | 0.53 | YES |
16 | NUP107 | NUP107 | NUP107 | 5505 | 0.029 | 0.55 | YES |
17 | NUPL2 | NUPL2 | NUPL2 | 5570 | 0.028 | 0.57 | YES |
18 | NUP37 | NUP37 | NUP37 | 5914 | 0.023 | 0.57 | YES |
19 | NUP214 | NUP214 | NUP214 | 6006 | 0.022 | 0.58 | YES |
20 | RAN | RAN | RAN | 6225 | 0.019 | 0.58 | YES |
21 | RAE1 | RAE1 | RAE1 | 6332 | 0.018 | 0.59 | YES |
22 | NUP62 | NUP62 | NUP62 | 6823 | 0.012 | 0.58 | NO |
23 | NUP88 | NUP88 | NUP88 | 8218 | -0.0057 | 0.5 | NO |
24 | AAAS | AAAS | AAAS | 8506 | -0.0094 | 0.5 | NO |
25 | NUP35 | NUP35 | NUP35 | 8846 | -0.014 | 0.49 | NO |
26 | NUP93 | NUP93 | NUP93 | 9030 | -0.016 | 0.49 | NO |
27 | NUP85 | NUP85 | NUP85 | 9155 | -0.018 | 0.5 | 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: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM.

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

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 | OGDHL | OGDHL | OGDHL | 7 | 0.82 | 0.51 | YES |
2 | DLAT | DLAT | DLAT | 1966 | 0.1 | 0.47 | NO |
3 | CS | CS | CS | 4658 | 0.042 | 0.35 | NO |
4 | SDHD | SDHD | SDHD | 5496 | 0.029 | 0.32 | NO |
5 | ACLY | ACLY | ACLY | 5839 | 0.024 | 0.32 | NO |
6 | FH | FH | FH | 6009 | 0.022 | 0.32 | NO |
7 | DLD | DLD | DLD | 6099 | 0.021 | 0.33 | NO |
8 | MDH2 | MDH2 | MDH2 | 6129 | 0.021 | 0.34 | NO |
9 | OGDH | OGDH | OGDH | 6137 | 0.02 | 0.35 | NO |
10 | SUCLG1 | SUCLG1 | SUCLG1 | 6351 | 0.018 | 0.35 | NO |
11 | IDH1 | IDH1 | IDH1 | 6549 | 0.015 | 0.35 | NO |
12 | PDHB | PDHB | PDHB | 6709 | 0.013 | 0.35 | NO |
13 | SDHC | SDHC | SDHC | 6716 | 0.013 | 0.36 | NO |
14 | SDHB | SDHB | SDHB | 6725 | 0.013 | 0.37 | NO |
15 | SUCLG2 | SUCLG2 | SUCLG2 | 6820 | 0.012 | 0.37 | NO |
16 | PDHA1 | PDHA1 | PDHA1 | 6848 | 0.011 | 0.37 | NO |
17 | ACO1 | ACO1 | ACO1 | 6976 | 0.0096 | 0.37 | NO |
18 | ACO2 | ACO2 | ACO2 | 6988 | 0.0095 | 0.38 | NO |
19 | SUCLA2 | SUCLA2 | SUCLA2 | 7439 | 0.0041 | 0.36 | NO |
20 | MDH1 | MDH1 | MDH1 | 7680 | 0.0009 | 0.34 | NO |
21 | SDHA | SDHA | SDHA | 8712 | -0.012 | 0.29 | NO |
22 | DLST | DLST | DLST | 9434 | -0.021 | 0.27 | NO |
23 | IDH3A | IDH3A | IDH3A | 9488 | -0.022 | 0.28 | NO |
24 | IDH3G | IDH3G | IDH3G | 9947 | -0.028 | 0.27 | NO |
25 | PCK2 | PCK2 | PCK2 | 10253 | -0.033 | 0.28 | NO |
26 | IDH2 | IDH2 | IDH2 | 10532 | -0.037 | 0.28 | NO |
27 | IDH3B | IDH3B | IDH3B | 10880 | -0.042 | 0.29 | NO |
28 | PCK1 | PCK1 | PCK1 | 11708 | -0.057 | 0.28 | NO |
29 | PC | PC | PC | 14460 | -0.13 | 0.21 | 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: REACTOME RNA POL II TRANSCRIPTION.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RNA POL II TRANSCRIPTION, 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 | GTF2H2 | GTF2H2 | GTF2H2 | 1117 | 0.15 | -0.033 | YES |
2 | NUP210 | NUP210 | NUP210 | 1167 | 0.15 | -0.0076 | YES |
3 | SNRNP40 | SNRNP40 | SNRNP40 | 1388 | 0.13 | 0.0053 | YES |
4 | GTF2H3 | GTF2H3 | GTF2H3 | 1408 | 0.13 | 0.029 | YES |
5 | CDC40 | CDC40 | CDC40 | 1643 | 0.12 | 0.038 | YES |
6 | NUP155 | NUP155 | NUP155 | 2195 | 0.092 | 0.026 | YES |
7 | ZNF473 | ZNF473 | ZNF473 | 2380 | 0.087 | 0.032 | YES |
8 | RANBP2 | RANBP2 | RANBP2 | 2435 | 0.086 | 0.046 | YES |
9 | NUP54 | NUP54 | NUP54 | 2756 | 0.077 | 0.043 | YES |
10 | TPR | TPR | TPR | 2985 | 0.071 | 0.044 | YES |
11 | NUPL1 | NUPL1 | NUPL1 | 3073 | 0.069 | 0.052 | YES |
12 | CDK7 | CDK7 | CDK7 | 3142 | 0.068 | 0.061 | YES |
13 | CCAR1 | CCAR1 | CCAR1 | 3222 | 0.066 | 0.07 | YES |
14 | POM121 | POM121 | POM121 | 3241 | 0.065 | 0.081 | YES |
15 | NUP133 | NUP133 | NUP133 | 3284 | 0.064 | 0.091 | YES |
16 | HNRNPR | HNRNPR | HNRNPR | 3351 | 0.063 | 0.099 | YES |
17 | NUP153 | NUP153 | NUP153 | 3387 | 0.062 | 0.11 | YES |
18 | HNRNPUL1 | HNRNPUL1 | HNRNPUL1 | 3395 | 0.062 | 0.12 | YES |
19 | NUDT21 | NUDT21 | NUDT21 | 3398 | 0.062 | 0.13 | YES |
20 | POLR2B | POLR2B | POLR2B | 3577 | 0.059 | 0.13 | YES |
21 | CPSF7 | CPSF7 | CPSF7 | 3586 | 0.059 | 0.14 | YES |
22 | DHX9 | DHX9 | DHX9 | 3634 | 0.058 | 0.15 | YES |
23 | SNRPB2 | SNRPB2 | SNRPB2 | 3700 | 0.056 | 0.16 | YES |
24 | POLR2D | POLR2D | POLR2D | 3706 | 0.056 | 0.17 | YES |
25 | HNRNPF | HNRNPF | HNRNPF | 3842 | 0.054 | 0.17 | YES |
26 | NUP205 | NUP205 | NUP205 | 3924 | 0.052 | 0.18 | YES |
27 | SEH1L | SEH1L | SEH1L | 3927 | 0.052 | 0.19 | YES |
28 | PCF11 | PCF11 | PCF11 | 3947 | 0.052 | 0.2 | YES |
29 | SNRNP200 | SNRNP200 | SNRNP200 | 4025 | 0.051 | 0.2 | YES |
30 | RNGTT | RNGTT | RNGTT | 4072 | 0.05 | 0.21 | YES |
31 | CPSF2 | CPSF2 | CPSF2 | 4117 | 0.049 | 0.22 | YES |
32 | NCBP1 | NCBP1 | NCBP1 | 4246 | 0.048 | 0.22 | YES |
33 | NUP188 | NUP188 | NUP188 | 4343 | 0.046 | 0.22 | YES |
34 | RBMX | RBMX | RBMX | 4385 | 0.046 | 0.23 | YES |
35 | EIF4E | EIF4E | EIF4E | 4414 | 0.045 | 0.24 | YES |
36 | HNRNPA0 | HNRNPA0 | HNRNPA0 | 4447 | 0.045 | 0.24 | YES |
37 | HNRNPK | HNRNPK | HNRNPK | 4513 | 0.044 | 0.25 | YES |
38 | PAPOLA | PAPOLA | PAPOLA | 4686 | 0.041 | 0.25 | YES |
39 | NUP50 | NUP50 | NUP50 | 4709 | 0.041 | 0.25 | YES |
40 | ADAR | ADAR | ADAR | 4725 | 0.04 | 0.26 | YES |
41 | RNMT | RNMT | RNMT | 4763 | 0.04 | 0.27 | YES |
42 | SF3B3 | SF3B3 | SF3B3 | 4824 | 0.039 | 0.27 | YES |
43 | SF3A1 | SF3A1 | SF3A1 | 4849 | 0.038 | 0.28 | YES |
44 | SMC1A | SMC1A | SMC1A | 4859 | 0.038 | 0.28 | YES |
45 | SF3B1 | SF3B1 | SF3B1 | 4879 | 0.038 | 0.29 | YES |
46 | HNRNPL | HNRNPL | HNRNPL | 4884 | 0.038 | 0.3 | YES |
47 | PRPF8 | PRPF8 | PRPF8 | 4922 | 0.037 | 0.3 | YES |
48 | GTF2H2B | GTF2H2B | GTF2H2B | 4963 | 0.036 | 0.31 | YES |
49 | PCBP2 | PCBP2 | PCBP2 | 4986 | 0.036 | 0.31 | YES |
50 | ERCC3 | ERCC3 | ERCC3 | 5072 | 0.035 | 0.31 | YES |
51 | CPSF3 | CPSF3 | CPSF3 | 5144 | 0.034 | 0.32 | YES |
52 | NFX1 | NFX1 | NFX1 | 5163 | 0.034 | 0.32 | YES |
53 | HNRNPU | HNRNPU | HNRNPU | 5197 | 0.033 | 0.33 | YES |
54 | NUP43 | NUP43 | NUP43 | 5341 | 0.032 | 0.32 | YES |
55 | HNRNPH2 | HNRNPH2 | HNRNPH2 | 5370 | 0.031 | 0.33 | YES |
56 | GTF2H1 | GTF2H1 | GTF2H1 | 5431 | 0.03 | 0.33 | YES |
57 | HNRNPC | HNRNPC | HNRNPC | 5468 | 0.03 | 0.34 | YES |
58 | NUP107 | NUP107 | NUP107 | 5505 | 0.029 | 0.34 | YES |
59 | SNRPD3 | SNRPD3 | SNRPD3 | 5547 | 0.029 | 0.34 | YES |
60 | RBM8A | RBM8A | RBM8A | 5565 | 0.028 | 0.35 | YES |
61 | NUPL2 | NUPL2 | NUPL2 | 5570 | 0.028 | 0.35 | YES |
62 | UPF3B | UPF3B | UPF3B | 5751 | 0.026 | 0.35 | YES |
63 | SNRPA1 | SNRPA1 | SNRPA1 | 5842 | 0.024 | 0.35 | YES |
64 | NUP37 | NUP37 | NUP37 | 5914 | 0.023 | 0.35 | YES |
65 | PCBP1 | PCBP1 | PCBP1 | 5917 | 0.023 | 0.35 | YES |
66 | PTBP1 | PTBP1 | PTBP1 | 5926 | 0.023 | 0.36 | YES |
67 | MNAT1 | MNAT1 | MNAT1 | 5965 | 0.022 | 0.36 | YES |
68 | NUP214 | NUP214 | NUP214 | 6006 | 0.022 | 0.36 | YES |
69 | U2AF2 | U2AF2 | U2AF2 | 6014 | 0.022 | 0.36 | YES |
70 | HNRNPA2B1 | HNRNPA2B1 | HNRNPA2B1 | 6260 | 0.019 | 0.35 | NO |
71 | SF3B14 | SF3B14 | SF3B14 | 6329 | 0.018 | 0.35 | NO |
72 | RAE1 | RAE1 | RAE1 | 6332 | 0.018 | 0.36 | NO |
73 | SNRPE | SNRPE | SNRPE | 6357 | 0.017 | 0.36 | NO |
74 | HNRNPD | HNRNPD | HNRNPD | 6440 | 0.016 | 0.36 | NO |
75 | SNRPG | SNRPG | SNRPG | 6462 | 0.016 | 0.36 | NO |
76 | CCNH | CCNH | CCNH | 6509 | 0.016 | 0.36 | NO |
77 | SF3B4 | SF3B4 | SF3B4 | 6581 | 0.015 | 0.36 | NO |
78 | PRPF4 | PRPF4 | PRPF4 | 6649 | 0.014 | 0.36 | NO |
79 | NCBP2 | NCBP2 | NCBP2 | 6679 | 0.014 | 0.36 | NO |
80 | SF3A3 | SF3A3 | SF3A3 | 6781 | 0.012 | 0.35 | NO |
81 | NUP62 | NUP62 | NUP62 | 6823 | 0.012 | 0.35 | NO |
82 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 6860 | 0.011 | 0.36 | NO |
83 | CSTF3 | CSTF3 | CSTF3 | 6866 | 0.011 | 0.36 | NO |
84 | POLR2A | POLR2A | POLR2A | 6936 | 0.01 | 0.36 | NO |
85 | DDX23 | DDX23 | DDX23 | 7051 | 0.0087 | 0.35 | NO |
86 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 7071 | 0.0085 | 0.35 | NO |
87 | SF3B2 | SF3B2 | SF3B2 | 7248 | 0.0064 | 0.34 | NO |
88 | SNRPD1 | SNRPD1 | SNRPD1 | 7272 | 0.0061 | 0.34 | NO |
89 | FUS | FUS | FUS | 7321 | 0.0055 | 0.34 | NO |
90 | HNRNPH1 | HNRNPH1 | HNRNPH1 | 7403 | 0.0045 | 0.34 | NO |
91 | PHF5A | PHF5A | PHF5A | 7408 | 0.0044 | 0.34 | NO |
92 | POLR2C | POLR2C | POLR2C | 7468 | 0.0038 | 0.34 | NO |
93 | THOC4 | THOC4 | THOC4 | 7518 | 0.0031 | 0.33 | NO |
94 | SLBP | SLBP | SLBP | 7547 | 0.0027 | 0.33 | NO |
95 | YBX1 | YBX1 | YBX1 | 7557 | 0.0026 | 0.33 | NO |
96 | CSTF1 | CSTF1 | CSTF1 | 7636 | 0.0015 | 0.33 | NO |
97 | SNRPF | SNRPF | SNRPF | 7644 | 0.0014 | 0.33 | NO |
98 | SNRPB | SNRPB | SNRPB | 7963 | -0.0026 | 0.31 | NO |
99 | PRPF6 | PRPF6 | PRPF6 | 7978 | -0.0027 | 0.31 | NO |
100 | ERCC2 | ERCC2 | ERCC2 | 8157 | -0.005 | 0.3 | NO |
101 | SF3A2 | SF3A2 | SF3A2 | 8178 | -0.0052 | 0.3 | NO |
102 | U2AF1 | U2AF1 | U2AF1 | 8180 | -0.0052 | 0.3 | NO |
103 | NUP88 | NUP88 | NUP88 | 8218 | -0.0057 | 0.3 | NO |
104 | CLP1 | CLP1 | CLP1 | 8224 | -0.0058 | 0.3 | NO |
105 | METTL3 | METTL3 | METTL3 | 8388 | -0.0077 | 0.29 | NO |
106 | MAGOH | MAGOH | MAGOH | 8457 | -0.0086 | 0.29 | NO |
107 | AAAS | AAAS | AAAS | 8506 | -0.0094 | 0.29 | NO |
108 | POLR2H | POLR2H | POLR2H | 8577 | -0.01 | 0.29 | NO |
109 | HNRNPM | HNRNPM | HNRNPM | 8666 | -0.012 | 0.29 | NO |
110 | EFTUD2 | EFTUD2 | EFTUD2 | 8708 | -0.012 | 0.29 | NO |
111 | DNAJC8 | DNAJC8 | DNAJC8 | 8820 | -0.014 | 0.28 | NO |
112 | NUP35 | NUP35 | NUP35 | 8846 | -0.014 | 0.28 | NO |
113 | PABPN1 | PABPN1 | PABPN1 | 8925 | -0.015 | 0.28 | NO |
114 | RNPS1 | RNPS1 | RNPS1 | 8939 | -0.015 | 0.29 | NO |
115 | SNRPD2 | SNRPD2 | SNRPD2 | 8965 | -0.015 | 0.29 | NO |
116 | LSM2 | LSM2 | LSM2 | 8999 | -0.016 | 0.29 | NO |
117 | NUP93 | NUP93 | NUP93 | 9030 | -0.016 | 0.29 | NO |
118 | NUP85 | NUP85 | NUP85 | 9155 | -0.018 | 0.29 | NO |
119 | SRRM1 | SRRM1 | SRRM1 | 9259 | -0.019 | 0.28 | NO |
120 | GTF2F2 | GTF2F2 | GTF2F2 | 9403 | -0.021 | 0.28 | NO |
121 | GTF2F1 | GTF2F1 | GTF2F1 | 9438 | -0.021 | 0.28 | NO |
122 | POLR2K | POLR2K | POLR2K | 9532 | -0.022 | 0.28 | NO |
123 | DHX38 | DHX38 | DHX38 | 9535 | -0.023 | 0.29 | NO |
124 | RBM5 | RBM5 | RBM5 | 9545 | -0.023 | 0.29 | NO |
125 | TXNL4A | TXNL4A | TXNL4A | 9885 | -0.028 | 0.28 | NO |
126 | GTF2H4 | GTF2H4 | GTF2H4 | 9932 | -0.028 | 0.28 | NO |
127 | A1CF | A1CF | A1CF | 9948 | -0.028 | 0.28 | NO |
128 | SUPT5H | SUPT5H | SUPT5H | 9981 | -0.029 | 0.29 | NO |
129 | CPSF1 | CPSF1 | CPSF1 | 9996 | -0.029 | 0.29 | NO |
130 | NHP2L1 | NHP2L1 | NHP2L1 | 10052 | -0.03 | 0.3 | NO |
131 | CSTF2 | CSTF2 | CSTF2 | 10089 | -0.031 | 0.3 | NO |
132 | NXF1 | NXF1 | NXF1 | 10311 | -0.034 | 0.29 | NO |
133 | SNRNP70 | SNRNP70 | SNRNP70 | 10372 | -0.035 | 0.3 | NO |
134 | POLR2F | POLR2F | POLR2F | 10472 | -0.036 | 0.3 | NO |
135 | SNRPA | SNRPA | SNRPA | 10526 | -0.037 | 0.3 | NO |
136 | POLR2E | POLR2E | POLR2E | 10610 | -0.038 | 0.3 | NO |
137 | CD2BP2 | CD2BP2 | CD2BP2 | 11087 | -0.046 | 0.29 | NO |
138 | POLR2G | POLR2G | POLR2G | 11172 | -0.047 | 0.29 | NO |
139 | POLR2L | POLR2L | POLR2L | 11891 | -0.06 | 0.26 | NO |
140 | POLR2I | POLR2I | POLR2I | 12011 | -0.063 | 0.27 | NO |
141 | POLR2J | POLR2J | POLR2J | 12325 | -0.069 | 0.26 | NO |
142 | SF3B5 | SF3B5 | SF3B5 | 12331 | -0.069 | 0.28 | NO |
143 | LSM11 | LSM11 | LSM11 | 12433 | -0.071 | 0.29 | NO |
144 | LSM10 | LSM10 | LSM10 | 13311 | -0.092 | 0.26 | NO |
145 | ADARB1 | ADARB1 | ADARB1 | 13370 | -0.094 | 0.27 | 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: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES, 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 OXIDATIVE PHOSPHORYLATION | 114 | genes.ES.table | 0.52 | 1.6 | 0.036 | 0.21 | 0.88 | 0.64 | 0.28 | 0.46 | 0.11 | 0.031 |
KEGG PYRIMIDINE METABOLISM | 98 | genes.ES.table | 0.38 | 1.7 | 0.013 | 0.18 | 0.78 | 0.44 | 0.27 | 0.32 | 0.078 | 0.034 |
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM | 33 | genes.ES.table | 0.63 | 1.5 | 0.047 | 0.22 | 0.98 | 0.52 | 0.2 | 0.41 | 0.14 | 0.017 |
KEGG RIBOSOME | 86 | genes.ES.table | 0.64 | 1.5 | 0.098 | 0.21 | 0.96 | 0.85 | 0.32 | 0.58 | 0.13 | 0.019 |
KEGG DNA REPLICATION | 36 | genes.ES.table | 0.6 | 1.8 | 0.022 | 0.47 | 0.41 | 0.5 | 0.22 | 0.39 | 0 | 0.1 |
KEGG PROTEASOME | 43 | genes.ES.table | 0.56 | 1.7 | 0.036 | 0.28 | 0.68 | 0.74 | 0.37 | 0.47 | 0.096 | 0.069 |
KEGG BASE EXCISION REPAIR | 33 | genes.ES.table | 0.52 | 1.7 | 0.045 | 0.19 | 0.73 | 0.7 | 0.35 | 0.45 | 0.073 | 0.034 |
KEGG HOMOLOGOUS RECOMBINATION | 26 | genes.ES.table | 0.64 | 1.5 | 0.074 | 0.21 | 0.98 | 0.58 | 0.22 | 0.45 | 0.14 | 0.014 |
KEGG CELL CYCLE | 118 | genes.ES.table | 0.51 | 1.6 | 0.063 | 0.21 | 0.93 | 0.26 | 0.13 | 0.23 | 0.12 | 0.023 |
KEGG PARKINSONS DISEASE | 111 | genes.ES.table | 0.42 | 1.5 | 0.12 | 0.23 | 0.98 | 0.63 | 0.28 | 0.45 | 0.16 | 0.012 |
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 | CDT1 | CDT1 | CDT1 | 59 | 0.43 | 0.067 | YES |
2 | GINS2 | GINS2 | GINS2 | 248 | 0.32 | 0.11 | YES |
3 | CDC6 | CDC6 | CDC6 | 376 | 0.29 | 0.15 | YES |
4 | CCNA2 | CCNA2 | CCNA2 | 506 | 0.26 | 0.18 | YES |
5 | CDC45 | CDC45 | CDC45 | 551 | 0.26 | 0.22 | YES |
6 | POLE2 | POLE2 | POLE2 | 597 | 0.25 | 0.26 | YES |
7 | GINS1 | GINS1 | GINS1 | 829 | 0.21 | 0.28 | YES |
8 | DNA2 | DNA2 | DNA2 | 998 | 0.19 | 0.3 | YES |
9 | PRIM2 | PRIM2 | PRIM2 | 1064 | 0.18 | 0.33 | YES |
10 | RFC4 | RFC4 | RFC4 | 1169 | 0.17 | 0.35 | YES |
11 | GINS4 | GINS4 | GINS4 | 1212 | 0.17 | 0.38 | YES |
12 | RFC3 | RFC3 | RFC3 | 1654 | 0.14 | 0.38 | YES |
13 | POLD4 | POLD4 | POLD4 | 1834 | 0.13 | 0.39 | YES |
14 | RPA3 | RPA3 | RPA3 | 2175 | 0.11 | 0.39 | YES |
15 | RFC2 | RFC2 | RFC2 | 2242 | 0.11 | 0.4 | YES |
16 | PSMC1 | PSMC1 | PSMC1 | 2564 | 0.097 | 0.4 | YES |
17 | PSME2 | PSME2 | PSME2 | 2596 | 0.096 | 0.41 | YES |
18 | FEN1 | FEN1 | FEN1 | 2686 | 0.094 | 0.42 | YES |
19 | PSMB7 | PSMB7 | PSMB7 | 2861 | 0.089 | 0.43 | YES |
20 | PSMB3 | PSMB3 | PSMB3 | 2925 | 0.087 | 0.44 | YES |
21 | POLD2 | POLD2 | POLD2 | 3118 | 0.082 | 0.44 | YES |
22 | MCM7 | MCM7 | MCM7 | 3337 | 0.078 | 0.44 | YES |
23 | PSMD9 | PSMD9 | PSMD9 | 3516 | 0.074 | 0.44 | YES |
24 | PSMB4 | PSMB4 | PSMB4 | 3775 | 0.068 | 0.44 | YES |
25 | UBA52 | UBA52 | UBA52 | 3903 | 0.065 | 0.44 | YES |
26 | PCNA | PCNA | PCNA | 3917 | 0.065 | 0.45 | YES |
27 | PSMD4 | PSMD4 | PSMD4 | 3919 | 0.065 | 0.46 | YES |
28 | PSMA3 | PSMA3 | PSMA3 | 3929 | 0.065 | 0.48 | YES |
29 | POLD1 | POLD1 | POLD1 | 3948 | 0.064 | 0.48 | YES |
30 | PSMB1 | PSMB1 | PSMB1 | 4032 | 0.063 | 0.49 | YES |
31 | PSMB6 | PSMB6 | PSMB6 | 4124 | 0.061 | 0.5 | YES |
32 | PSMA4 | PSMA4 | PSMA4 | 4132 | 0.06 | 0.5 | YES |
33 | PSMA6 | PSMA6 | PSMA6 | 4173 | 0.06 | 0.51 | YES |
34 | PSMB5 | PSMB5 | PSMB5 | 4332 | 0.057 | 0.51 | YES |
35 | PSMA7 | PSMA7 | PSMA7 | 4443 | 0.055 | 0.52 | YES |
36 | PSMA5 | PSMA5 | PSMA5 | 4474 | 0.054 | 0.52 | YES |
37 | PSMA2 | PSMA2 | PSMA2 | 4513 | 0.053 | 0.53 | YES |
38 | PSMD13 | PSMD13 | PSMD13 | 4563 | 0.052 | 0.54 | YES |
39 | LIG1 | LIG1 | LIG1 | 4702 | 0.05 | 0.54 | YES |
40 | CDKN1A | CDKN1A | CDKN1A | 4721 | 0.05 | 0.54 | YES |
41 | PSMC2 | PSMC2 | PSMC2 | 4913 | 0.046 | 0.54 | YES |
42 | PSMB2 | PSMB2 | PSMB2 | 5057 | 0.044 | 0.54 | YES |
43 | POLA2 | POLA2 | POLA2 | 5084 | 0.044 | 0.55 | YES |
44 | RPS27A | RPS27A | RPS27A | 5181 | 0.042 | 0.55 | YES |
45 | PSMC3 | PSMC3 | PSMC3 | 5230 | 0.041 | 0.55 | YES |
46 | MCM5 | MCM5 | MCM5 | 5318 | 0.04 | 0.55 | YES |
47 | PSMC5 | PSMC5 | PSMC5 | 5584 | 0.036 | 0.54 | NO |
48 | MCM2 | MCM2 | MCM2 | 5820 | 0.032 | 0.54 | NO |
49 | PSME1 | PSME1 | PSME1 | 5831 | 0.032 | 0.54 | NO |
50 | PSMC6 | PSMC6 | PSMC6 | 5960 | 0.031 | 0.54 | NO |
51 | PSMD3 | PSMD3 | PSMD3 | 6167 | 0.027 | 0.53 | NO |
52 | POLE | POLE | POLE | 6400 | 0.024 | 0.52 | NO |
53 | MCM4 | MCM4 | MCM4 | 6480 | 0.023 | 0.52 | NO |
54 | RPA2 | RPA2 | RPA2 | 6548 | 0.022 | 0.52 | NO |
55 | PSMD14 | PSMD14 | PSMD14 | 6592 | 0.021 | 0.52 | NO |
56 | PSMC4 | PSMC4 | PSMC4 | 6606 | 0.021 | 0.52 | NO |
57 | PSMD6 | PSMD6 | PSMD6 | 6652 | 0.02 | 0.53 | NO |
58 | MCM3 | MCM3 | MCM3 | 6679 | 0.02 | 0.53 | NO |
59 | PSMA1 | PSMA1 | PSMA1 | 6765 | 0.019 | 0.53 | NO |
60 | RFC5 | RFC5 | RFC5 | 6768 | 0.019 | 0.53 | NO |
61 | PSMD8 | PSMD8 | PSMD8 | 6780 | 0.019 | 0.53 | NO |
62 | PSMD11 | PSMD11 | PSMD11 | 7003 | 0.016 | 0.52 | NO |
63 | PSMB10 | PSMB10 | PSMB10 | 7416 | 0.0097 | 0.5 | NO |
64 | PSMD12 | PSMD12 | PSMD12 | 7542 | 0.0078 | 0.5 | NO |
65 | CDK2 | CDK2 | CDK2 | 7776 | 0.0047 | 0.48 | NO |
66 | PSMF1 | PSMF1 | PSMF1 | 7778 | 0.0046 | 0.48 | NO |
67 | PSMD2 | PSMD2 | PSMD2 | 8193 | -0.0013 | 0.46 | NO |
68 | PSME4 | PSME4 | PSME4 | 8241 | -0.0018 | 0.46 | NO |
69 | PSMB9 | PSMB9 | PSMB9 | 8664 | -0.0073 | 0.44 | NO |
70 | CCNA1 | CCNA1 | CCNA1 | 8702 | -0.0077 | 0.44 | NO |
71 | PSMD7 | PSMD7 | PSMD7 | 8770 | -0.0086 | 0.43 | NO |
72 | PSMD1 | PSMD1 | PSMD1 | 8998 | -0.012 | 0.42 | NO |
73 | POLD3 | POLD3 | POLD3 | 9619 | -0.02 | 0.39 | NO |
74 | PSMD10 | PSMD10 | PSMD10 | 9843 | -0.023 | 0.38 | NO |
75 | CDKN1B | CDKN1B | CDKN1B | 10343 | -0.031 | 0.36 | NO |
76 | MCM6 | MCM6 | MCM6 | 10350 | -0.031 | 0.37 | NO |
77 | POLA1 | POLA1 | POLA1 | 10639 | -0.035 | 0.36 | NO |
78 | RPA1 | RPA1 | RPA1 | 10860 | -0.039 | 0.35 | NO |
79 | PRIM1 | PRIM1 | PRIM1 | 10904 | -0.04 | 0.36 | NO |
80 | PSMB8 | PSMB8 | PSMB8 | 11588 | -0.05 | 0.32 | NO |
81 | MCM8 | MCM8 | MCM8 | 11995 | -0.057 | 0.31 | NO |
82 | PSMD5 | PSMD5 | PSMD5 | 13662 | -0.094 | 0.24 | NO |
83 | RB1 | RB1 | RB1 | 14004 | -0.1 | 0.23 | 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 OXIDATIVE PHOSPHORYLATION.

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

Table 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 | POLE2 | POLE2 | POLE2 | 597 | 0.25 | 0.058 | YES |
2 | DNA2 | DNA2 | DNA2 | 998 | 0.19 | 0.1 | YES |
3 | PRIM2 | PRIM2 | PRIM2 | 1064 | 0.18 | 0.17 | YES |
4 | RFC4 | RFC4 | RFC4 | 1169 | 0.17 | 0.22 | YES |
5 | RNASEH2A | RNASEH2A | RNASEH2A | 1356 | 0.16 | 0.27 | YES |
6 | RPA4 | RPA4 | RPA4 | 1444 | 0.15 | 0.32 | YES |
7 | RFC3 | RFC3 | RFC3 | 1654 | 0.14 | 0.36 | YES |
8 | POLE4 | POLE4 | POLE4 | 1741 | 0.13 | 0.4 | YES |
9 | POLD4 | POLD4 | POLD4 | 1834 | 0.13 | 0.44 | YES |
10 | RPA3 | RPA3 | RPA3 | 2175 | 0.11 | 0.47 | YES |
11 | RFC2 | RFC2 | RFC2 | 2242 | 0.11 | 0.5 | YES |
12 | FEN1 | FEN1 | FEN1 | 2686 | 0.094 | 0.51 | YES |
13 | POLD2 | POLD2 | POLD2 | 3118 | 0.082 | 0.52 | YES |
14 | MCM7 | MCM7 | MCM7 | 3337 | 0.078 | 0.54 | YES |
15 | SSBP1 | SSBP1 | SSBP1 | 3395 | 0.076 | 0.56 | YES |
16 | RNASEH2C | RNASEH2C | RNASEH2C | 3652 | 0.071 | 0.57 | YES |
17 | PCNA | PCNA | PCNA | 3917 | 0.065 | 0.58 | YES |
18 | POLD1 | POLD1 | POLD1 | 3948 | 0.064 | 0.6 | YES |
19 | LIG1 | LIG1 | LIG1 | 4702 | 0.05 | 0.58 | NO |
20 | POLA2 | POLA2 | POLA2 | 5084 | 0.044 | 0.57 | NO |
21 | MCM5 | MCM5 | MCM5 | 5318 | 0.04 | 0.58 | NO |
22 | MCM2 | MCM2 | MCM2 | 5820 | 0.032 | 0.56 | NO |
23 | POLE | POLE | POLE | 6400 | 0.024 | 0.54 | NO |
24 | MCM4 | MCM4 | MCM4 | 6480 | 0.023 | 0.54 | NO |
25 | RPA2 | RPA2 | RPA2 | 6548 | 0.022 | 0.55 | NO |
26 | MCM3 | MCM3 | MCM3 | 6679 | 0.02 | 0.55 | NO |
27 | RFC5 | RFC5 | RFC5 | 6768 | 0.019 | 0.55 | NO |
28 | POLE3 | POLE3 | POLE3 | 7804 | 0.0042 | 0.49 | NO |
29 | RNASEH1 | RNASEH1 | RNASEH1 | 8463 | -0.0048 | 0.46 | NO |
30 | RNASEH2B | RNASEH2B | RNASEH2B | 9600 | -0.02 | 0.4 | NO |
31 | POLD3 | POLD3 | POLD3 | 9619 | -0.02 | 0.41 | NO |
32 | RFC1 | RFC1 | RFC1 | 10184 | -0.028 | 0.39 | NO |
33 | MCM6 | MCM6 | MCM6 | 10350 | -0.031 | 0.39 | NO |
34 | POLA1 | POLA1 | POLA1 | 10639 | -0.035 | 0.39 | NO |
35 | RPA1 | RPA1 | RPA1 | 10860 | -0.039 | 0.39 | NO |
36 | PRIM1 | PRIM1 | PRIM1 | 10904 | -0.04 | 0.4 | 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 PYRIMIDINE METABOLISM.

Figure S44. 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 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 | CDT1 | CDT1 | CDT1 | 59 | 0.43 | 0.056 | YES |
2 | GINS2 | GINS2 | GINS2 | 248 | 0.32 | 0.09 | YES |
3 | CDC6 | CDC6 | CDC6 | 376 | 0.29 | 0.12 | YES |
4 | CCNA2 | CCNA2 | CCNA2 | 506 | 0.26 | 0.15 | YES |
5 | CDC45 | CDC45 | CDC45 | 551 | 0.26 | 0.18 | YES |
6 | POLE2 | POLE2 | POLE2 | 597 | 0.25 | 0.22 | YES |
7 | CCNE1 | CCNE1 | CCNE1 | 772 | 0.22 | 0.24 | YES |
8 | GINS1 | GINS1 | GINS1 | 829 | 0.21 | 0.26 | YES |
9 | CDC25A | CDC25A | CDC25A | 872 | 0.21 | 0.29 | YES |
10 | CCNE2 | CCNE2 | CCNE2 | 920 | 0.2 | 0.31 | YES |
11 | DNA2 | DNA2 | DNA2 | 998 | 0.19 | 0.33 | YES |
12 | PRIM2 | PRIM2 | PRIM2 | 1064 | 0.18 | 0.36 | YES |
13 | RFC4 | RFC4 | RFC4 | 1169 | 0.17 | 0.37 | YES |
14 | GINS4 | GINS4 | GINS4 | 1212 | 0.17 | 0.39 | YES |
15 | RFC3 | RFC3 | RFC3 | 1654 | 0.14 | 0.39 | YES |
16 | POLD4 | POLD4 | POLD4 | 1834 | 0.13 | 0.4 | YES |
17 | RPA3 | RPA3 | RPA3 | 2175 | 0.11 | 0.39 | YES |
18 | RFC2 | RFC2 | RFC2 | 2242 | 0.11 | 0.4 | YES |
19 | PSMC1 | PSMC1 | PSMC1 | 2564 | 0.097 | 0.4 | YES |
20 | PSME2 | PSME2 | PSME2 | 2596 | 0.096 | 0.41 | YES |
21 | FEN1 | FEN1 | FEN1 | 2686 | 0.094 | 0.42 | YES |
22 | PSMB7 | PSMB7 | PSMB7 | 2861 | 0.089 | 0.42 | YES |
23 | PSMB3 | PSMB3 | PSMB3 | 2925 | 0.087 | 0.43 | YES |
24 | POLD2 | POLD2 | POLD2 | 3118 | 0.082 | 0.43 | YES |
25 | CKS1B | CKS1B | CKS1B | 3330 | 0.078 | 0.43 | YES |
26 | MCM7 | MCM7 | MCM7 | 3337 | 0.078 | 0.44 | YES |
27 | PSMD9 | PSMD9 | PSMD9 | 3516 | 0.074 | 0.44 | YES |
28 | PSMB4 | PSMB4 | PSMB4 | 3775 | 0.068 | 0.44 | YES |
29 | UBA52 | UBA52 | UBA52 | 3903 | 0.065 | 0.44 | YES |
30 | PCNA | PCNA | PCNA | 3917 | 0.065 | 0.45 | YES |
31 | PSMD4 | PSMD4 | PSMD4 | 3919 | 0.065 | 0.46 | YES |
32 | PSMA3 | PSMA3 | PSMA3 | 3929 | 0.065 | 0.46 | YES |
33 | CDC25B | CDC25B | CDC25B | 3945 | 0.064 | 0.47 | YES |
34 | POLD1 | POLD1 | POLD1 | 3948 | 0.064 | 0.48 | YES |
35 | PSMB1 | PSMB1 | PSMB1 | 4032 | 0.063 | 0.48 | YES |
36 | PSMB6 | PSMB6 | PSMB6 | 4124 | 0.061 | 0.49 | YES |
37 | PSMA4 | PSMA4 | PSMA4 | 4132 | 0.06 | 0.5 | YES |
38 | PSMA6 | PSMA6 | PSMA6 | 4173 | 0.06 | 0.5 | YES |
39 | PSMB5 | PSMB5 | PSMB5 | 4332 | 0.057 | 0.5 | YES |
40 | PSMA7 | PSMA7 | PSMA7 | 4443 | 0.055 | 0.5 | YES |
41 | PSMA5 | PSMA5 | PSMA5 | 4474 | 0.054 | 0.51 | YES |
42 | PSMA2 | PSMA2 | PSMA2 | 4513 | 0.053 | 0.51 | YES |
43 | PSMD13 | PSMD13 | PSMD13 | 4563 | 0.052 | 0.52 | YES |
44 | LIG1 | LIG1 | LIG1 | 4702 | 0.05 | 0.52 | YES |
45 | CDKN1A | CDKN1A | CDKN1A | 4721 | 0.05 | 0.52 | YES |
46 | MNAT1 | MNAT1 | MNAT1 | 4796 | 0.048 | 0.52 | YES |
47 | PSMC2 | PSMC2 | PSMC2 | 4913 | 0.046 | 0.52 | YES |
48 | PSMB2 | PSMB2 | PSMB2 | 5057 | 0.044 | 0.52 | YES |
49 | POLA2 | POLA2 | POLA2 | 5084 | 0.044 | 0.53 | YES |
50 | RPS27A | RPS27A | RPS27A | 5181 | 0.042 | 0.53 | YES |
51 | PSMC3 | PSMC3 | PSMC3 | 5230 | 0.041 | 0.53 | YES |
52 | MCM5 | MCM5 | MCM5 | 5318 | 0.04 | 0.53 | YES |
53 | PSMC5 | PSMC5 | PSMC5 | 5584 | 0.036 | 0.52 | NO |
54 | CCND1 | CCND1 | CCND1 | 5735 | 0.034 | 0.52 | NO |
55 | MCM2 | MCM2 | MCM2 | 5820 | 0.032 | 0.52 | NO |
56 | PSME1 | PSME1 | PSME1 | 5831 | 0.032 | 0.52 | NO |
57 | CDK4 | CDK4 | CDK4 | 5865 | 0.032 | 0.52 | NO |
58 | PSMC6 | PSMC6 | PSMC6 | 5960 | 0.031 | 0.52 | NO |
59 | PSMD3 | PSMD3 | PSMD3 | 6167 | 0.027 | 0.52 | NO |
60 | POLE | POLE | POLE | 6400 | 0.024 | 0.51 | NO |
61 | MCM4 | MCM4 | MCM4 | 6480 | 0.023 | 0.5 | NO |
62 | RPA2 | RPA2 | RPA2 | 6548 | 0.022 | 0.5 | NO |
63 | PSMD14 | PSMD14 | PSMD14 | 6592 | 0.021 | 0.5 | NO |
64 | PSMC4 | PSMC4 | PSMC4 | 6606 | 0.021 | 0.51 | NO |
65 | PSMD6 | PSMD6 | PSMD6 | 6652 | 0.02 | 0.51 | NO |
66 | MCM3 | MCM3 | MCM3 | 6679 | 0.02 | 0.51 | NO |
67 | PSMA1 | PSMA1 | PSMA1 | 6765 | 0.019 | 0.51 | NO |
68 | RFC5 | RFC5 | RFC5 | 6768 | 0.019 | 0.51 | NO |
69 | PSMD8 | PSMD8 | PSMD8 | 6780 | 0.019 | 0.51 | NO |
70 | PSMD11 | PSMD11 | PSMD11 | 7003 | 0.016 | 0.5 | NO |
71 | PSMB10 | PSMB10 | PSMB10 | 7416 | 0.0097 | 0.48 | NO |
72 | CCNH | CCNH | CCNH | 7441 | 0.0094 | 0.48 | NO |
73 | MAX | MAX | MAX | 7448 | 0.0093 | 0.48 | NO |
74 | PSMD12 | PSMD12 | PSMD12 | 7542 | 0.0078 | 0.48 | NO |
75 | CDK2 | CDK2 | CDK2 | 7776 | 0.0047 | 0.46 | NO |
76 | PSMF1 | PSMF1 | PSMF1 | 7778 | 0.0046 | 0.46 | NO |
77 | CUL1 | CUL1 | CUL1 | 7921 | 0.0026 | 0.46 | NO |
78 | SKP1 | SKP1 | SKP1 | 7936 | 0.0023 | 0.46 | NO |
79 | PSMD2 | PSMD2 | PSMD2 | 8193 | -0.0013 | 0.44 | NO |
80 | PSME4 | PSME4 | PSME4 | 8241 | -0.0018 | 0.44 | NO |
81 | CDK7 | CDK7 | CDK7 | 8495 | -0.0054 | 0.43 | NO |
82 | PSMB9 | PSMB9 | PSMB9 | 8664 | -0.0073 | 0.42 | NO |
83 | CCNA1 | CCNA1 | CCNA1 | 8702 | -0.0077 | 0.42 | NO |
84 | PSMD7 | PSMD7 | PSMD7 | 8770 | -0.0086 | 0.42 | NO |
85 | PSMD1 | PSMD1 | PSMD1 | 8998 | -0.012 | 0.4 | NO |
86 | MYC | MYC | MYC | 9306 | -0.016 | 0.39 | NO |
87 | POLD3 | POLD3 | POLD3 | 9619 | -0.02 | 0.38 | NO |
88 | PSMD10 | PSMD10 | PSMD10 | 9843 | -0.023 | 0.37 | NO |
89 | CDKN1B | CDKN1B | CDKN1B | 10343 | -0.031 | 0.34 | NO |
90 | MCM6 | MCM6 | MCM6 | 10350 | -0.031 | 0.35 | NO |
91 | POLA1 | POLA1 | POLA1 | 10639 | -0.035 | 0.34 | NO |
92 | RPA1 | RPA1 | RPA1 | 10860 | -0.039 | 0.33 | NO |
93 | PRIM1 | PRIM1 | PRIM1 | 10904 | -0.04 | 0.33 | NO |
94 | PSMB8 | PSMB8 | PSMB8 | 11588 | -0.05 | 0.3 | NO |
95 | MCM8 | MCM8 | MCM8 | 11995 | -0.057 | 0.29 | NO |
96 | PSMD5 | PSMD5 | PSMD5 | 13662 | -0.094 | 0.21 | NO |
97 | WEE1 | WEE1 | WEE1 | 13681 | -0.094 | 0.22 | NO |
98 | RB1 | RB1 | RB1 | 14004 | -0.1 | 0.22 | NO |
99 | SKP2 | SKP2 | SKP2 | 14650 | -0.12 | 0.2 | 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

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

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 | COX17 | COX17 | COX17 | 1351 | 0.16 | -0.023 | YES |
2 | LDHD | LDHD | LDHD | 1381 | 0.15 | 0.026 | YES |
3 | TAZ | TAZ | TAZ | 1886 | 0.12 | 0.039 | YES |
4 | MTX1 | MTX1 | MTX1 | 1887 | 0.12 | 0.079 | YES |
5 | TIMM10 | TIMM10 | TIMM10 | 1888 | 0.12 | 0.12 | YES |
6 | BCS1L | BCS1L | BCS1L | 2150 | 0.11 | 0.14 | YES |
7 | TIMM8B | TIMM8B | TIMM8B | 2160 | 0.11 | 0.18 | YES |
8 | TIMM13 | TIMM13 | TIMM13 | 2227 | 0.11 | 0.21 | YES |
9 | GFER | GFER | GFER | 2237 | 0.11 | 0.25 | YES |
10 | TIMM8A | TIMM8A | TIMM8A | 2295 | 0.11 | 0.28 | YES |
11 | ATP5G1 | ATP5G1 | ATP5G1 | 2382 | 0.1 | 0.31 | YES |
12 | TOMM7 | TOMM7 | TOMM7 | 2696 | 0.093 | 0.32 | YES |
13 | TOMM5 | TOMM5 | TOMM5 | 2798 | 0.091 | 0.35 | YES |
14 | TIMM50 | TIMM50 | TIMM50 | 2974 | 0.086 | 0.36 | YES |
15 | DNAJC19 | DNAJC19 | DNAJC19 | 2982 | 0.086 | 0.39 | YES |
16 | TIMM17B | TIMM17B | TIMM17B | 3091 | 0.083 | 0.41 | YES |
17 | TOMM40 | TOMM40 | TOMM40 | 3513 | 0.074 | 0.42 | YES |
18 | CYC1 | CYC1 | CYC1 | 3728 | 0.069 | 0.43 | YES |
19 | TIMM44 | TIMM44 | TIMM44 | 3729 | 0.069 | 0.45 | YES |
20 | PMPCB | PMPCB | PMPCB | 4063 | 0.062 | 0.45 | YES |
21 | PMPCA | PMPCA | PMPCA | 4076 | 0.062 | 0.47 | YES |
22 | GRPEL1 | GRPEL1 | GRPEL1 | 4097 | 0.061 | 0.49 | YES |
23 | TIMM9 | TIMM9 | TIMM9 | 4264 | 0.058 | 0.5 | YES |
24 | HSPD1 | HSPD1 | HSPD1 | 4270 | 0.058 | 0.52 | YES |
25 | CHCHD4 | CHCHD4 | CHCHD4 | 4295 | 0.057 | 0.54 | YES |
26 | MTX2 | MTX2 | MTX2 | 4564 | 0.052 | 0.54 | YES |
27 | IDH3G | IDH3G | IDH3G | 4642 | 0.051 | 0.55 | YES |
28 | COQ2 | COQ2 | COQ2 | 4704 | 0.05 | 0.56 | YES |
29 | TIMM17A | TIMM17A | TIMM17A | 4844 | 0.048 | 0.57 | YES |
30 | HSCB | HSCB | HSCB | 4881 | 0.047 | 0.58 | YES |
31 | TOMM70A | TOMM70A | TOMM70A | 5149 | 0.042 | 0.58 | YES |
32 | GRPEL2 | GRPEL2 | GRPEL2 | 5415 | 0.038 | 0.58 | YES |
33 | VDAC1 | VDAC1 | VDAC1 | 5485 | 0.037 | 0.59 | YES |
34 | FXN | FXN | FXN | 5673 | 0.035 | 0.59 | YES |
35 | TOMM22 | TOMM22 | TOMM22 | 5697 | 0.034 | 0.6 | YES |
36 | TIMM22 | TIMM22 | TIMM22 | 5904 | 0.032 | 0.6 | NO |
37 | HSPA9 | HSPA9 | HSPA9 | 7104 | 0.014 | 0.54 | NO |
38 | ATP5B | ATP5B | ATP5B | 7312 | 0.011 | 0.53 | NO |
39 | SLC25A13 | SLC25A13 | SLC25A13 | 7588 | 0.0072 | 0.52 | NO |
40 | SLC25A6 | SLC25A6 | SLC25A6 | 7790 | 0.0045 | 0.51 | NO |
41 | CS | CS | CS | 8126 | -0.00031 | 0.49 | NO |
42 | SLC25A4 | SLC25A4 | SLC25A4 | 8247 | -0.0019 | 0.49 | NO |
43 | TOMM20 | TOMM20 | TOMM20 | 8290 | -0.0024 | 0.48 | NO |
44 | ATP5A1 | ATP5A1 | ATP5A1 | 8296 | -0.0024 | 0.48 | NO |
45 | ACO2 | ACO2 | ACO2 | 8473 | -0.005 | 0.48 | NO |
46 | SAMM50 | SAMM50 | SAMM50 | 8903 | -0.01 | 0.46 | NO |
47 | C18orf55 | C18orf55 | C18orf55 | 9386 | -0.017 | 0.44 | NO |
48 | FXC1 | FXC1 | FXC1 | 12117 | -0.06 | 0.31 | NO |
49 | SLC25A12 | SLC25A12 | SLC25A12 | 13750 | -0.096 | 0.25 | 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 RIBOSOME.

Figure S48. 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 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 | CDT1 | CDT1 | CDT1 | 59 | 0.43 | 0.082 | YES |
2 | E2F1 | E2F1 | E2F1 | 274 | 0.32 | 0.13 | YES |
3 | E2F2 | E2F2 | E2F2 | 313 | 0.3 | 0.19 | YES |
4 | CDC6 | CDC6 | CDC6 | 376 | 0.29 | 0.24 | YES |
5 | CDC45 | CDC45 | CDC45 | 551 | 0.26 | 0.28 | YES |
6 | POLE2 | POLE2 | POLE2 | 597 | 0.25 | 0.33 | YES |
7 | MCM10 | MCM10 | MCM10 | 648 | 0.24 | 0.37 | YES |
8 | PRIM2 | PRIM2 | PRIM2 | 1064 | 0.18 | 0.39 | YES |
9 | RPA4 | RPA4 | RPA4 | 1444 | 0.15 | 0.4 | YES |
10 | RPA3 | RPA3 | RPA3 | 2175 | 0.11 | 0.38 | YES |
11 | PSMC1 | PSMC1 | PSMC1 | 2564 | 0.097 | 0.38 | YES |
12 | PSME2 | PSME2 | PSME2 | 2596 | 0.096 | 0.39 | YES |
13 | DBF4 | DBF4 | DBF4 | 2852 | 0.089 | 0.4 | YES |
14 | PSMB7 | PSMB7 | PSMB7 | 2861 | 0.089 | 0.41 | YES |
15 | PSMB3 | PSMB3 | PSMB3 | 2925 | 0.087 | 0.43 | YES |
16 | MCM7 | MCM7 | MCM7 | 3337 | 0.078 | 0.42 | YES |
17 | CDC7 | CDC7 | CDC7 | 3448 | 0.075 | 0.43 | YES |
18 | PSMD9 | PSMD9 | PSMD9 | 3516 | 0.074 | 0.44 | YES |
19 | PSMB4 | PSMB4 | PSMB4 | 3775 | 0.068 | 0.44 | YES |
20 | UBA52 | UBA52 | UBA52 | 3903 | 0.065 | 0.44 | YES |
21 | PSMD4 | PSMD4 | PSMD4 | 3919 | 0.065 | 0.46 | YES |
22 | PSMA3 | PSMA3 | PSMA3 | 3929 | 0.065 | 0.47 | YES |
23 | PSMB1 | PSMB1 | PSMB1 | 4032 | 0.063 | 0.48 | YES |
24 | PSMB6 | PSMB6 | PSMB6 | 4124 | 0.061 | 0.48 | YES |
25 | PSMA4 | PSMA4 | PSMA4 | 4132 | 0.06 | 0.49 | YES |
26 | PSMA6 | PSMA6 | PSMA6 | 4173 | 0.06 | 0.5 | YES |
27 | PSMB5 | PSMB5 | PSMB5 | 4332 | 0.057 | 0.5 | YES |
28 | PSMA7 | PSMA7 | PSMA7 | 4443 | 0.055 | 0.51 | YES |
29 | PSMA5 | PSMA5 | PSMA5 | 4474 | 0.054 | 0.52 | YES |
30 | PSMA2 | PSMA2 | PSMA2 | 4513 | 0.053 | 0.53 | YES |
31 | PSMD13 | PSMD13 | PSMD13 | 4563 | 0.052 | 0.54 | YES |
32 | PSMC2 | PSMC2 | PSMC2 | 4913 | 0.046 | 0.52 | YES |
33 | PSMB2 | PSMB2 | PSMB2 | 5057 | 0.044 | 0.53 | YES |
34 | POLA2 | POLA2 | POLA2 | 5084 | 0.044 | 0.53 | YES |
35 | RPS27A | RPS27A | RPS27A | 5181 | 0.042 | 0.54 | YES |
36 | PSMC3 | PSMC3 | PSMC3 | 5230 | 0.041 | 0.54 | YES |
37 | MCM5 | MCM5 | MCM5 | 5318 | 0.04 | 0.54 | YES |
38 | GMNN | GMNN | GMNN | 5386 | 0.039 | 0.55 | YES |
39 | PSMC5 | PSMC5 | PSMC5 | 5584 | 0.036 | 0.54 | NO |
40 | MCM2 | MCM2 | MCM2 | 5820 | 0.032 | 0.54 | NO |
41 | PSME1 | PSME1 | PSME1 | 5831 | 0.032 | 0.54 | NO |
42 | PSMC6 | PSMC6 | PSMC6 | 5960 | 0.031 | 0.54 | NO |
43 | PSMD3 | PSMD3 | PSMD3 | 6167 | 0.027 | 0.54 | NO |
44 | POLE | POLE | POLE | 6400 | 0.024 | 0.53 | NO |
45 | MCM4 | MCM4 | MCM4 | 6480 | 0.023 | 0.53 | NO |
46 | RPA2 | RPA2 | RPA2 | 6548 | 0.022 | 0.53 | NO |
47 | PSMD14 | PSMD14 | PSMD14 | 6592 | 0.021 | 0.53 | NO |
48 | PSMC4 | PSMC4 | PSMC4 | 6606 | 0.021 | 0.54 | NO |
49 | PSMD6 | PSMD6 | PSMD6 | 6652 | 0.02 | 0.54 | NO |
50 | MCM3 | MCM3 | MCM3 | 6679 | 0.02 | 0.54 | NO |
51 | PSMA1 | PSMA1 | PSMA1 | 6765 | 0.019 | 0.54 | NO |
52 | PSMD8 | PSMD8 | PSMD8 | 6780 | 0.019 | 0.54 | NO |
53 | PSMD11 | PSMD11 | PSMD11 | 7003 | 0.016 | 0.53 | NO |
54 | PSMB10 | PSMB10 | PSMB10 | 7416 | 0.0097 | 0.51 | NO |
55 | PSMD12 | PSMD12 | PSMD12 | 7542 | 0.0078 | 0.5 | NO |
56 | CDK2 | CDK2 | CDK2 | 7776 | 0.0047 | 0.49 | NO |
57 | PSMF1 | PSMF1 | PSMF1 | 7778 | 0.0046 | 0.49 | NO |
58 | PSMD2 | PSMD2 | PSMD2 | 8193 | -0.0013 | 0.47 | NO |
59 | PSME4 | PSME4 | PSME4 | 8241 | -0.0018 | 0.47 | NO |
60 | PSMB9 | PSMB9 | PSMB9 | 8664 | -0.0073 | 0.45 | NO |
61 | PSMD7 | PSMD7 | PSMD7 | 8770 | -0.0086 | 0.44 | NO |
62 | E2F3 | E2F3 | E2F3 | 8991 | -0.012 | 0.43 | NO |
63 | PSMD1 | PSMD1 | PSMD1 | 8998 | -0.012 | 0.44 | NO |
64 | PSMD10 | PSMD10 | PSMD10 | 9843 | -0.023 | 0.39 | NO |
65 | MCM6 | MCM6 | MCM6 | 10350 | -0.031 | 0.37 | NO |
66 | POLA1 | POLA1 | POLA1 | 10639 | -0.035 | 0.36 | NO |
67 | RPA1 | RPA1 | RPA1 | 10860 | -0.039 | 0.36 | NO |
68 | PRIM1 | PRIM1 | PRIM1 | 10904 | -0.04 | 0.36 | NO |
69 | PSMB8 | PSMB8 | PSMB8 | 11588 | -0.05 | 0.34 | NO |
70 | MCM8 | MCM8 | MCM8 | 11995 | -0.057 | 0.33 | NO |
71 | PSMD5 | PSMD5 | PSMD5 | 13662 | -0.094 | 0.25 | 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 DNA REPLICATION.

Figure S50. 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 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 | CDT1 | CDT1 | CDT1 | 59 | 0.43 | 0.13 | YES |
2 | CDC6 | CDC6 | CDC6 | 376 | 0.29 | 0.2 | YES |
3 | CCNA2 | CCNA2 | CCNA2 | 506 | 0.26 | 0.27 | YES |
4 | PSMC1 | PSMC1 | PSMC1 | 2564 | 0.097 | 0.19 | YES |
5 | PSME2 | PSME2 | PSME2 | 2596 | 0.096 | 0.21 | YES |
6 | PSMB7 | PSMB7 | PSMB7 | 2861 | 0.089 | 0.22 | YES |
7 | PSMB3 | PSMB3 | PSMB3 | 2925 | 0.087 | 0.25 | YES |
8 | MCM7 | MCM7 | MCM7 | 3337 | 0.078 | 0.25 | YES |
9 | PSMD9 | PSMD9 | PSMD9 | 3516 | 0.074 | 0.26 | YES |
10 | PSMB4 | PSMB4 | PSMB4 | 3775 | 0.068 | 0.27 | YES |
11 | UBA52 | UBA52 | UBA52 | 3903 | 0.065 | 0.28 | YES |
12 | PSMD4 | PSMD4 | PSMD4 | 3919 | 0.065 | 0.3 | YES |
13 | PSMA3 | PSMA3 | PSMA3 | 3929 | 0.065 | 0.32 | YES |
14 | PSMB1 | PSMB1 | PSMB1 | 4032 | 0.063 | 0.33 | YES |
15 | PSMB6 | PSMB6 | PSMB6 | 4124 | 0.061 | 0.34 | YES |
16 | PSMA4 | PSMA4 | PSMA4 | 4132 | 0.06 | 0.36 | YES |
17 | PSMA6 | PSMA6 | PSMA6 | 4173 | 0.06 | 0.38 | YES |
18 | PSMB5 | PSMB5 | PSMB5 | 4332 | 0.057 | 0.39 | YES |
19 | PSMA7 | PSMA7 | PSMA7 | 4443 | 0.055 | 0.4 | YES |
20 | PSMA5 | PSMA5 | PSMA5 | 4474 | 0.054 | 0.41 | YES |
21 | PSMA2 | PSMA2 | PSMA2 | 4513 | 0.053 | 0.42 | YES |
22 | PSMD13 | PSMD13 | PSMD13 | 4563 | 0.052 | 0.44 | YES |
23 | CDKN1A | CDKN1A | CDKN1A | 4721 | 0.05 | 0.44 | YES |
24 | PSMC2 | PSMC2 | PSMC2 | 4913 | 0.046 | 0.45 | YES |
25 | PSMB2 | PSMB2 | PSMB2 | 5057 | 0.044 | 0.45 | YES |
26 | RPS27A | RPS27A | RPS27A | 5181 | 0.042 | 0.46 | YES |
27 | PSMC3 | PSMC3 | PSMC3 | 5230 | 0.041 | 0.47 | YES |
28 | MCM5 | MCM5 | MCM5 | 5318 | 0.04 | 0.48 | YES |
29 | PSMC5 | PSMC5 | PSMC5 | 5584 | 0.036 | 0.47 | YES |
30 | MCM2 | MCM2 | MCM2 | 5820 | 0.032 | 0.47 | YES |
31 | PSME1 | PSME1 | PSME1 | 5831 | 0.032 | 0.48 | YES |
32 | PSMC6 | PSMC6 | PSMC6 | 5960 | 0.031 | 0.48 | YES |
33 | PSMD3 | PSMD3 | PSMD3 | 6167 | 0.027 | 0.48 | YES |
34 | MCM4 | MCM4 | MCM4 | 6480 | 0.023 | 0.47 | YES |
35 | PSMD14 | PSMD14 | PSMD14 | 6592 | 0.021 | 0.47 | YES |
36 | PSMC4 | PSMC4 | PSMC4 | 6606 | 0.021 | 0.47 | YES |
37 | PSMD6 | PSMD6 | PSMD6 | 6652 | 0.02 | 0.48 | YES |
38 | MCM3 | MCM3 | MCM3 | 6679 | 0.02 | 0.48 | YES |
39 | PSMA1 | PSMA1 | PSMA1 | 6765 | 0.019 | 0.48 | YES |
40 | PSMD8 | PSMD8 | PSMD8 | 6780 | 0.019 | 0.49 | YES |
41 | PSMD11 | PSMD11 | PSMD11 | 7003 | 0.016 | 0.48 | NO |
42 | PSMB10 | PSMB10 | PSMB10 | 7416 | 0.0097 | 0.46 | NO |
43 | PSMD12 | PSMD12 | PSMD12 | 7542 | 0.0078 | 0.46 | NO |
44 | CDK2 | CDK2 | CDK2 | 7776 | 0.0047 | 0.44 | NO |
45 | PSMF1 | PSMF1 | PSMF1 | 7778 | 0.0046 | 0.45 | NO |
46 | PSMD2 | PSMD2 | PSMD2 | 8193 | -0.0013 | 0.42 | NO |
47 | PSME4 | PSME4 | PSME4 | 8241 | -0.0018 | 0.42 | NO |
48 | PSMB9 | PSMB9 | PSMB9 | 8664 | -0.0073 | 0.4 | NO |
49 | CCNA1 | CCNA1 | CCNA1 | 8702 | -0.0077 | 0.4 | NO |
50 | PSMD7 | PSMD7 | PSMD7 | 8770 | -0.0086 | 0.4 | NO |
51 | PSMD1 | PSMD1 | PSMD1 | 8998 | -0.012 | 0.39 | NO |
52 | PSMD10 | PSMD10 | PSMD10 | 9843 | -0.023 | 0.35 | NO |
53 | CDKN1B | CDKN1B | CDKN1B | 10343 | -0.031 | 0.33 | NO |
54 | MCM6 | MCM6 | MCM6 | 10350 | -0.031 | 0.34 | NO |
55 | PSMB8 | PSMB8 | PSMB8 | 11588 | -0.05 | 0.29 | NO |
56 | MCM8 | MCM8 | MCM8 | 11995 | -0.057 | 0.28 | NO |
57 | PSMD5 | PSMD5 | PSMD5 | 13662 | -0.094 | 0.22 | NO |
58 | RB1 | RB1 | RB1 | 14004 | -0.1 | 0.23 | 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 PROTEASOME.

Figure S52. 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 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 | UBE2C | UBE2C | UBE2C | 22 | 0.5 | 0.057 | YES |
2 | CDC25C | CDC25C | CDC25C | 36 | 0.46 | 0.11 | YES |
3 | CDC20 | CDC20 | CDC20 | 97 | 0.4 | 0.15 | YES |
4 | CDK1 | CDK1 | CDK1 | 139 | 0.37 | 0.2 | YES |
5 | CDC6 | CDC6 | CDC6 | 376 | 0.29 | 0.22 | YES |
6 | BUB1B | BUB1B | BUB1B | 522 | 0.26 | 0.24 | YES |
7 | CDC45 | CDC45 | CDC45 | 551 | 0.26 | 0.27 | YES |
8 | MCM10 | MCM10 | MCM10 | 648 | 0.24 | 0.29 | YES |
9 | CCNE1 | CCNE1 | CCNE1 | 772 | 0.22 | 0.31 | YES |
10 | CCNB2 | CCNB2 | CCNB2 | 852 | 0.21 | 0.33 | YES |
11 | CDC25A | CDC25A | CDC25A | 872 | 0.21 | 0.35 | YES |
12 | CCNE2 | CCNE2 | CCNE2 | 920 | 0.2 | 0.37 | YES |
13 | CHEK1 | CHEK1 | CHEK1 | 1041 | 0.18 | 0.39 | YES |
14 | RFC4 | RFC4 | RFC4 | 1169 | 0.17 | 0.4 | YES |
15 | CCNB1 | CCNB1 | CCNB1 | 1228 | 0.16 | 0.42 | YES |
16 | MAD1L1 | MAD1L1 | MAD1L1 | 1409 | 0.15 | 0.42 | YES |
17 | RAD9A | RAD9A | RAD9A | 1545 | 0.14 | 0.43 | YES |
18 | RFC3 | RFC3 | RFC3 | 1654 | 0.14 | 0.44 | YES |
19 | ANAPC11 | ANAPC11 | ANAPC11 | 1776 | 0.13 | 0.45 | YES |
20 | RPA3 | RPA3 | RPA3 | 2175 | 0.11 | 0.44 | YES |
21 | RFC2 | RFC2 | RFC2 | 2242 | 0.11 | 0.45 | YES |
22 | MAD2L1 | MAD2L1 | MAD2L1 | 2404 | 0.1 | 0.46 | YES |
23 | PSMC1 | PSMC1 | PSMC1 | 2564 | 0.097 | 0.46 | YES |
24 | PSME2 | PSME2 | PSME2 | 2596 | 0.096 | 0.47 | YES |
25 | DBF4 | DBF4 | DBF4 | 2852 | 0.089 | 0.46 | YES |
26 | PSMB7 | PSMB7 | PSMB7 | 2861 | 0.089 | 0.48 | YES |
27 | CHEK2 | CHEK2 | CHEK2 | 2893 | 0.088 | 0.48 | YES |
28 | PSMB3 | PSMB3 | PSMB3 | 2925 | 0.087 | 0.49 | YES |
29 | MCM7 | MCM7 | MCM7 | 3337 | 0.078 | 0.48 | YES |
30 | CDC7 | CDC7 | CDC7 | 3448 | 0.075 | 0.48 | YES |
31 | PSMD9 | PSMD9 | PSMD9 | 3516 | 0.074 | 0.49 | YES |
32 | ATRIP | ATRIP | ATRIP | 3595 | 0.072 | 0.49 | YES |
33 | ANAPC5 | ANAPC5 | ANAPC5 | 3622 | 0.072 | 0.5 | YES |
34 | PSMB4 | PSMB4 | PSMB4 | 3775 | 0.068 | 0.5 | YES |
35 | UBA52 | UBA52 | UBA52 | 3903 | 0.065 | 0.5 | YES |
36 | PSMD4 | PSMD4 | PSMD4 | 3919 | 0.065 | 0.5 | YES |
37 | PSMA3 | PSMA3 | PSMA3 | 3929 | 0.065 | 0.51 | YES |
38 | PSMB1 | PSMB1 | PSMB1 | 4032 | 0.063 | 0.51 | YES |
39 | PSMB6 | PSMB6 | PSMB6 | 4124 | 0.061 | 0.52 | YES |
40 | PSMA4 | PSMA4 | PSMA4 | 4132 | 0.06 | 0.52 | YES |
41 | PSMA6 | PSMA6 | PSMA6 | 4173 | 0.06 | 0.53 | YES |
42 | PSMB5 | PSMB5 | PSMB5 | 4332 | 0.057 | 0.52 | YES |
43 | PSMA7 | PSMA7 | PSMA7 | 4443 | 0.055 | 0.52 | YES |
44 | PSMA5 | PSMA5 | PSMA5 | 4474 | 0.054 | 0.53 | YES |
45 | HUS1 | HUS1 | HUS1 | 4506 | 0.054 | 0.53 | YES |
46 | PSMA2 | PSMA2 | PSMA2 | 4513 | 0.053 | 0.54 | YES |
47 | PSMD13 | PSMD13 | PSMD13 | 4563 | 0.052 | 0.54 | YES |
48 | CDKN1A | CDKN1A | CDKN1A | 4721 | 0.05 | 0.54 | YES |
49 | UBE2E1 | UBE2E1 | UBE2E1 | 4842 | 0.048 | 0.54 | YES |
50 | PSMC2 | PSMC2 | PSMC2 | 4913 | 0.046 | 0.54 | YES |
51 | ANAPC2 | ANAPC2 | ANAPC2 | 4945 | 0.046 | 0.55 | YES |
52 | PSMB2 | PSMB2 | PSMB2 | 5057 | 0.044 | 0.54 | YES |
53 | UBE2D1 | UBE2D1 | UBE2D1 | 5112 | 0.043 | 0.55 | YES |
54 | RPS27A | RPS27A | RPS27A | 5181 | 0.042 | 0.55 | YES |
55 | PSMC3 | PSMC3 | PSMC3 | 5230 | 0.041 | 0.55 | YES |
56 | MCM5 | MCM5 | MCM5 | 5318 | 0.04 | 0.55 | NO |
57 | PSMC5 | PSMC5 | PSMC5 | 5584 | 0.036 | 0.54 | NO |
58 | MCM2 | MCM2 | MCM2 | 5820 | 0.032 | 0.53 | NO |
59 | PSME1 | PSME1 | PSME1 | 5831 | 0.032 | 0.53 | NO |
60 | CDC26 | CDC26 | CDC26 | 5946 | 0.031 | 0.53 | NO |
61 | PSMC6 | PSMC6 | PSMC6 | 5960 | 0.031 | 0.53 | NO |
62 | PSMD3 | PSMD3 | PSMD3 | 6167 | 0.027 | 0.52 | NO |
63 | ANAPC7 | ANAPC7 | ANAPC7 | 6221 | 0.027 | 0.52 | NO |
64 | MCM4 | MCM4 | MCM4 | 6480 | 0.023 | 0.51 | NO |
65 | RPA2 | RPA2 | RPA2 | 6548 | 0.022 | 0.51 | NO |
66 | PSMD14 | PSMD14 | PSMD14 | 6592 | 0.021 | 0.51 | NO |
67 | PSMC4 | PSMC4 | PSMC4 | 6606 | 0.021 | 0.52 | NO |
68 | PSMD6 | PSMD6 | PSMD6 | 6652 | 0.02 | 0.51 | NO |
69 | MCM3 | MCM3 | MCM3 | 6679 | 0.02 | 0.52 | NO |
70 | PSMA1 | PSMA1 | PSMA1 | 6765 | 0.019 | 0.51 | NO |
71 | RFC5 | RFC5 | RFC5 | 6768 | 0.019 | 0.52 | NO |
72 | PSMD8 | PSMD8 | PSMD8 | 6780 | 0.019 | 0.52 | NO |
73 | PSMD11 | PSMD11 | PSMD11 | 7003 | 0.016 | 0.51 | NO |
74 | BUB3 | BUB3 | BUB3 | 7267 | 0.012 | 0.49 | NO |
75 | PSMB10 | PSMB10 | PSMB10 | 7416 | 0.0097 | 0.49 | NO |
76 | PSMD12 | PSMD12 | PSMD12 | 7542 | 0.0078 | 0.48 | NO |
77 | RAD1 | RAD1 | RAD1 | 7607 | 0.007 | 0.48 | NO |
78 | CDK2 | CDK2 | CDK2 | 7776 | 0.0047 | 0.47 | NO |
79 | PSMF1 | PSMF1 | PSMF1 | 7778 | 0.0046 | 0.47 | NO |
80 | CDC16 | CDC16 | CDC16 | 7795 | 0.0044 | 0.47 | NO |
81 | CDC23 | CDC23 | CDC23 | 8158 | -0.00084 | 0.45 | NO |
82 | PSMD2 | PSMD2 | PSMD2 | 8193 | -0.0013 | 0.45 | NO |
83 | PSME4 | PSME4 | PSME4 | 8241 | -0.0018 | 0.44 | NO |
84 | RFWD2 | RFWD2 | RFWD2 | 8568 | -0.0062 | 0.43 | NO |
85 | PSMB9 | PSMB9 | PSMB9 | 8664 | -0.0073 | 0.42 | NO |
86 | ANAPC4 | ANAPC4 | ANAPC4 | 8740 | -0.0082 | 0.42 | NO |
87 | ANAPC10 | ANAPC10 | ANAPC10 | 8767 | -0.0086 | 0.42 | NO |
88 | PSMD7 | PSMD7 | PSMD7 | 8770 | -0.0086 | 0.42 | NO |
89 | PSMD1 | PSMD1 | PSMD1 | 8998 | -0.012 | 0.41 | NO |
90 | MDM2 | MDM2 | MDM2 | 9104 | -0.013 | 0.4 | NO |
91 | TP53 | TP53 | TP53 | 9333 | -0.016 | 0.4 | NO |
92 | PSMD10 | PSMD10 | PSMD10 | 9843 | -0.023 | 0.37 | NO |
93 | CDKN1B | CDKN1B | CDKN1B | 10343 | -0.031 | 0.34 | NO |
94 | MCM6 | MCM6 | MCM6 | 10350 | -0.031 | 0.35 | NO |
95 | RPA1 | RPA1 | RPA1 | 10860 | -0.039 | 0.32 | NO |
96 | CDC27 | CDC27 | CDC27 | 11105 | -0.042 | 0.32 | NO |
97 | PSMB8 | PSMB8 | PSMB8 | 11588 | -0.05 | 0.3 | NO |
98 | RAD17 | RAD17 | RAD17 | 11702 | -0.052 | 0.3 | NO |
99 | MCM8 | MCM8 | MCM8 | 11995 | -0.057 | 0.29 | NO |
100 | ATR | ATR | ATR | 12371 | -0.064 | 0.27 | NO |
101 | PSMD5 | PSMD5 | PSMD5 | 13662 | -0.094 | 0.21 | NO |
102 | WEE1 | WEE1 | WEE1 | 13681 | -0.094 | 0.22 | NO |
103 | ATM | ATM | ATM | 14535 | -0.12 | 0.19 | NO |
104 | ANAPC1 | ANAPC1 | ANAPC1 | 14683 | -0.12 | 0.2 | 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 BASE EXCISION REPAIR.

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

Table 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 | SHFM1 | SHFM1 | SHFM1 | 1315 | 0.16 | 0.008 | YES |
2 | PSMB11 | PSMB11 | PSMB11 | 1687 | 0.14 | 0.056 | YES |
3 | PSMC1 | PSMC1 | PSMC1 | 2564 | 0.097 | 0.057 | YES |
4 | PSME2 | PSME2 | PSME2 | 2596 | 0.096 | 0.1 | YES |
5 | PSMB7 | PSMB7 | PSMB7 | 2861 | 0.089 | 0.13 | YES |
6 | PSMB3 | PSMB3 | PSMB3 | 2925 | 0.087 | 0.18 | YES |
7 | PSMB4 | PSMB4 | PSMB4 | 3775 | 0.068 | 0.16 | YES |
8 | PSMD4 | PSMD4 | PSMD4 | 3919 | 0.065 | 0.19 | YES |
9 | PSMA3 | PSMA3 | PSMA3 | 3929 | 0.065 | 0.22 | YES |
10 | PSMB1 | PSMB1 | PSMB1 | 4032 | 0.063 | 0.25 | YES |
11 | POMP | POMP | POMP | 4114 | 0.061 | 0.27 | YES |
12 | PSMB6 | PSMB6 | PSMB6 | 4124 | 0.061 | 0.3 | YES |
13 | PSMA4 | PSMA4 | PSMA4 | 4132 | 0.06 | 0.33 | YES |
14 | PSMA6 | PSMA6 | PSMA6 | 4173 | 0.06 | 0.36 | YES |
15 | PSMB5 | PSMB5 | PSMB5 | 4332 | 0.057 | 0.38 | YES |
16 | IFNG | IFNG | IFNG | 4423 | 0.055 | 0.4 | YES |
17 | PSMA7 | PSMA7 | PSMA7 | 4443 | 0.055 | 0.43 | YES |
18 | PSMA5 | PSMA5 | PSMA5 | 4474 | 0.054 | 0.46 | YES |
19 | PSMA2 | PSMA2 | PSMA2 | 4513 | 0.053 | 0.48 | YES |
20 | PSMD13 | PSMD13 | PSMD13 | 4563 | 0.052 | 0.5 | YES |
21 | PSMC2 | PSMC2 | PSMC2 | 4913 | 0.046 | 0.51 | YES |
22 | PSMB2 | PSMB2 | PSMB2 | 5057 | 0.044 | 0.52 | YES |
23 | PSMC3 | PSMC3 | PSMC3 | 5230 | 0.041 | 0.54 | YES |
24 | PSMC5 | PSMC5 | PSMC5 | 5584 | 0.036 | 0.53 | YES |
25 | PSME1 | PSME1 | PSME1 | 5831 | 0.032 | 0.54 | YES |
26 | PSMC6 | PSMC6 | PSMC6 | 5960 | 0.031 | 0.55 | YES |
27 | PSMD3 | PSMD3 | PSMD3 | 6167 | 0.027 | 0.55 | YES |
28 | PSMD14 | PSMD14 | PSMD14 | 6592 | 0.021 | 0.54 | YES |
29 | PSMC4 | PSMC4 | PSMC4 | 6606 | 0.021 | 0.55 | YES |
30 | PSMD6 | PSMD6 | PSMD6 | 6652 | 0.02 | 0.55 | YES |
31 | PSMA1 | PSMA1 | PSMA1 | 6765 | 0.019 | 0.56 | YES |
32 | PSMD8 | PSMD8 | PSMD8 | 6780 | 0.019 | 0.56 | YES |
33 | PSMD11 | PSMD11 | PSMD11 | 7003 | 0.016 | 0.56 | NO |
34 | PSMB10 | PSMB10 | PSMB10 | 7416 | 0.0097 | 0.54 | NO |
35 | PSMD12 | PSMD12 | PSMD12 | 7542 | 0.0078 | 0.54 | NO |
36 | PSMF1 | PSMF1 | PSMF1 | 7778 | 0.0046 | 0.53 | NO |
37 | PSMD2 | PSMD2 | PSMD2 | 8193 | -0.0013 | 0.51 | NO |
38 | PSME4 | PSME4 | PSME4 | 8241 | -0.0018 | 0.5 | NO |
39 | PSMB9 | PSMB9 | PSMB9 | 8664 | -0.0073 | 0.49 | NO |
40 | PSMD7 | PSMD7 | PSMD7 | 8770 | -0.0086 | 0.48 | NO |
41 | PSME3 | PSME3 | PSME3 | 8840 | -0.0097 | 0.48 | NO |
42 | PSMD1 | PSMD1 | PSMD1 | 8998 | -0.012 | 0.48 | NO |
43 | PSMB8 | PSMB8 | PSMB8 | 11588 | -0.05 | 0.37 | 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 HOMOLOGOUS RECOMBINATION.

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

Table 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 | AURKB | AURKB | AURKB | 3 | 0.58 | 0.09 | YES |
2 | UBE2C | UBE2C | UBE2C | 22 | 0.5 | 0.17 | YES |
3 | PTTG1 | PTTG1 | PTTG1 | 39 | 0.46 | 0.24 | YES |
4 | CDC20 | CDC20 | CDC20 | 97 | 0.4 | 0.29 | YES |
5 | CDK1 | CDK1 | CDK1 | 139 | 0.37 | 0.35 | YES |
6 | PLK1 | PLK1 | PLK1 | 165 | 0.36 | 0.4 | YES |
7 | AURKA | AURKA | AURKA | 309 | 0.3 | 0.44 | YES |
8 | CCNA2 | CCNA2 | CCNA2 | 506 | 0.26 | 0.47 | YES |
9 | BUB1B | BUB1B | BUB1B | 522 | 0.26 | 0.51 | YES |
10 | CCNB1 | CCNB1 | CCNB1 | 1228 | 0.16 | 0.5 | YES |
11 | ANAPC11 | ANAPC11 | ANAPC11 | 1776 | 0.13 | 0.49 | YES |
12 | MAD2L1 | MAD2L1 | MAD2L1 | 2404 | 0.1 | 0.47 | YES |
13 | PSMC1 | PSMC1 | PSMC1 | 2564 | 0.097 | 0.48 | YES |
14 | PSME2 | PSME2 | PSME2 | 2596 | 0.096 | 0.49 | YES |
15 | PSMB7 | PSMB7 | PSMB7 | 2861 | 0.089 | 0.49 | YES |
16 | PSMB3 | PSMB3 | PSMB3 | 2925 | 0.087 | 0.5 | YES |
17 | PSMD9 | PSMD9 | PSMD9 | 3516 | 0.074 | 0.48 | YES |
18 | ANAPC5 | ANAPC5 | ANAPC5 | 3622 | 0.072 | 0.48 | YES |
19 | PSMB4 | PSMB4 | PSMB4 | 3775 | 0.068 | 0.48 | YES |
20 | UBA52 | UBA52 | UBA52 | 3903 | 0.065 | 0.49 | YES |
21 | PSMD4 | PSMD4 | PSMD4 | 3919 | 0.065 | 0.5 | YES |
22 | PSMA3 | PSMA3 | PSMA3 | 3929 | 0.065 | 0.51 | YES |
23 | PSMB1 | PSMB1 | PSMB1 | 4032 | 0.063 | 0.51 | YES |
24 | PSMB6 | PSMB6 | PSMB6 | 4124 | 0.061 | 0.52 | YES |
25 | PSMA4 | PSMA4 | PSMA4 | 4132 | 0.06 | 0.52 | YES |
26 | PSMA6 | PSMA6 | PSMA6 | 4173 | 0.06 | 0.53 | YES |
27 | PSMB5 | PSMB5 | PSMB5 | 4332 | 0.057 | 0.53 | YES |
28 | PSMA7 | PSMA7 | PSMA7 | 4443 | 0.055 | 0.53 | YES |
29 | PSMA5 | PSMA5 | PSMA5 | 4474 | 0.054 | 0.54 | YES |
30 | PSMA2 | PSMA2 | PSMA2 | 4513 | 0.053 | 0.55 | YES |
31 | PSMD13 | PSMD13 | PSMD13 | 4563 | 0.052 | 0.55 | YES |
32 | UBE2E1 | UBE2E1 | UBE2E1 | 4842 | 0.048 | 0.54 | YES |
33 | PSMC2 | PSMC2 | PSMC2 | 4913 | 0.046 | 0.55 | YES |
34 | ANAPC2 | ANAPC2 | ANAPC2 | 4945 | 0.046 | 0.55 | YES |
35 | PSMB2 | PSMB2 | PSMB2 | 5057 | 0.044 | 0.55 | YES |
36 | UBE2D1 | UBE2D1 | UBE2D1 | 5112 | 0.043 | 0.56 | YES |
37 | RPS27A | RPS27A | RPS27A | 5181 | 0.042 | 0.56 | YES |
38 | PSMC3 | PSMC3 | PSMC3 | 5230 | 0.041 | 0.56 | YES |
39 | PSMC5 | PSMC5 | PSMC5 | 5584 | 0.036 | 0.55 | NO |
40 | PSME1 | PSME1 | PSME1 | 5831 | 0.032 | 0.54 | NO |
41 | CDC26 | CDC26 | CDC26 | 5946 | 0.031 | 0.54 | NO |
42 | PSMC6 | PSMC6 | PSMC6 | 5960 | 0.031 | 0.54 | NO |
43 | PSMD3 | PSMD3 | PSMD3 | 6167 | 0.027 | 0.54 | NO |
44 | ANAPC7 | ANAPC7 | ANAPC7 | 6221 | 0.027 | 0.54 | NO |
45 | PSMD14 | PSMD14 | PSMD14 | 6592 | 0.021 | 0.52 | NO |
46 | PSMC4 | PSMC4 | PSMC4 | 6606 | 0.021 | 0.52 | NO |
47 | PSMD6 | PSMD6 | PSMD6 | 6652 | 0.02 | 0.52 | NO |
48 | PSMA1 | PSMA1 | PSMA1 | 6765 | 0.019 | 0.52 | NO |
49 | PSMD8 | PSMD8 | PSMD8 | 6780 | 0.019 | 0.52 | NO |
50 | PSMD11 | PSMD11 | PSMD11 | 7003 | 0.016 | 0.51 | NO |
51 | BUB3 | BUB3 | BUB3 | 7267 | 0.012 | 0.5 | NO |
52 | FBXO5 | FBXO5 | FBXO5 | 7322 | 0.011 | 0.5 | NO |
53 | PSMB10 | PSMB10 | PSMB10 | 7416 | 0.0097 | 0.5 | NO |
54 | PSMD12 | PSMD12 | PSMD12 | 7542 | 0.0078 | 0.49 | NO |
55 | CDK2 | CDK2 | CDK2 | 7776 | 0.0047 | 0.48 | NO |
56 | PSMF1 | PSMF1 | PSMF1 | 7778 | 0.0046 | 0.48 | NO |
57 | CDC16 | CDC16 | CDC16 | 7795 | 0.0044 | 0.48 | NO |
58 | CUL1 | CUL1 | CUL1 | 7921 | 0.0026 | 0.47 | NO |
59 | SKP1 | SKP1 | SKP1 | 7936 | 0.0023 | 0.47 | NO |
60 | CDC23 | CDC23 | CDC23 | 8158 | -0.00084 | 0.46 | NO |
61 | PSMD2 | PSMD2 | PSMD2 | 8193 | -0.0013 | 0.46 | NO |
62 | PSME4 | PSME4 | PSME4 | 8241 | -0.0018 | 0.46 | NO |
63 | PSMB9 | PSMB9 | PSMB9 | 8664 | -0.0073 | 0.43 | NO |
64 | CCNA1 | CCNA1 | CCNA1 | 8702 | -0.0077 | 0.43 | NO |
65 | ANAPC4 | ANAPC4 | ANAPC4 | 8740 | -0.0082 | 0.43 | NO |
66 | ANAPC10 | ANAPC10 | ANAPC10 | 8767 | -0.0086 | 0.43 | NO |
67 | PSMD7 | PSMD7 | PSMD7 | 8770 | -0.0086 | 0.43 | NO |
68 | PSMD1 | PSMD1 | PSMD1 | 8998 | -0.012 | 0.42 | NO |
69 | PSMD10 | PSMD10 | PSMD10 | 9843 | -0.023 | 0.38 | NO |
70 | BTRC | BTRC | BTRC | 10644 | -0.036 | 0.34 | NO |
71 | CDC27 | CDC27 | CDC27 | 11105 | -0.042 | 0.32 | NO |
72 | PSMB8 | PSMB8 | PSMB8 | 11588 | -0.05 | 0.3 | NO |
73 | CDC14A | CDC14A | CDC14A | 12656 | -0.07 | 0.26 | NO |
74 | PSMD5 | PSMD5 | PSMD5 | 13662 | -0.094 | 0.21 | NO |
75 | SKP2 | SKP2 | SKP2 | 14650 | -0.12 | 0.18 | NO |
76 | ANAPC1 | ANAPC1 | ANAPC1 | 14683 | -0.12 | 0.2 | 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 CELL CYCLE.
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Figure S58. 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
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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 | UCP3 | UCP3 | UCP3 | 889 | 0.2 | -0.025 | YES |
2 | COX6C | COX6C | COX6C | 1303 | 0.16 | -0.028 | YES |
3 | ATP5I | ATP5I | ATP5I | 1515 | 0.14 | -0.023 | YES |
4 | NDUFA3 | NDUFA3 | NDUFA3 | 1523 | 0.14 | -0.0061 | YES |
5 | NDUFB9 | NDUFB9 | NDUFB9 | 1671 | 0.14 | 0.002 | YES |
6 | ATP5J2 | ATP5J2 | ATP5J2 | 1701 | 0.13 | 0.016 | YES |
7 | NDUFB1 | NDUFB1 | NDUFB1 | 1712 | 0.13 | 0.032 | YES |
8 | COX6A1 | COX6A1 | COX6A1 | 1757 | 0.13 | 0.045 | YES |
9 | UQCRHL | UQCRHL | UQCRHL | 1774 | 0.13 | 0.06 | YES |
10 | ATP5D | ATP5D | ATP5D | 1786 | 0.13 | 0.074 | YES |
11 | NDUFB7 | NDUFB7 | NDUFB7 | 1839 | 0.13 | 0.087 | YES |
12 | COX5B | COX5B | COX5B | 1854 | 0.12 | 0.1 | YES |
13 | UQCR11 | UQCR11 | UQCR11 | 1969 | 0.12 | 0.11 | YES |
14 | NDUFA2 | NDUFA2 | NDUFA2 | 1978 | 0.12 | 0.12 | YES |
15 | NDUFB10 | NDUFB10 | NDUFB10 | 2082 | 0.12 | 0.13 | YES |
16 | UQCRB | UQCRB | UQCRB | 2091 | 0.12 | 0.14 | YES |
17 | NDUFA13 | NDUFA13 | NDUFA13 | 2095 | 0.12 | 0.16 | YES |
18 | NDUFS8 | NDUFS8 | NDUFS8 | 2134 | 0.11 | 0.17 | YES |
19 | UQCRQ | UQCRQ | UQCRQ | 2165 | 0.11 | 0.18 | YES |
20 | NDUFA7 | NDUFA7 | NDUFA7 | 2185 | 0.11 | 0.19 | YES |
21 | COX7B | COX7B | COX7B | 2217 | 0.11 | 0.21 | YES |
22 | NDUFA1 | NDUFA1 | NDUFA1 | 2361 | 0.1 | 0.21 | YES |
23 | D2HGDH | D2HGDH | D2HGDH | 2379 | 0.1 | 0.22 | YES |
24 | ATP5G1 | ATP5G1 | ATP5G1 | 2382 | 0.1 | 0.23 | YES |
25 | SLC16A1 | SLC16A1 | SLC16A1 | 2394 | 0.1 | 0.25 | YES |
26 | NDUFS6 | NDUFS6 | NDUFS6 | 2409 | 0.1 | 0.26 | YES |
27 | ADHFE1 | ADHFE1 | ADHFE1 | 2468 | 0.1 | 0.27 | YES |
28 | NDUFC2 | NDUFC2 | NDUFC2 | 2577 | 0.097 | 0.27 | YES |
29 | ATP5E | ATP5E | ATP5E | 2667 | 0.094 | 0.28 | YES |
30 | COX6B1 | COX6B1 | COX6B1 | 2672 | 0.094 | 0.29 | YES |
31 | UQCRH | UQCRH | UQCRH | 2744 | 0.092 | 0.3 | YES |
32 | COX8A | COX8A | COX8A | 2764 | 0.092 | 0.31 | YES |
33 | NDUFV3 | NDUFV3 | NDUFV3 | 2766 | 0.091 | 0.32 | YES |
34 | NDUFV1 | NDUFV1 | NDUFV1 | 2838 | 0.09 | 0.32 | YES |
35 | NDUFA11 | NDUFA11 | NDUFA11 | 2946 | 0.086 | 0.33 | YES |
36 | NDUFB2 | NDUFB2 | NDUFB2 | 2954 | 0.086 | 0.34 | YES |
37 | NDUFV2 | NDUFV2 | NDUFV2 | 2958 | 0.086 | 0.35 | YES |
38 | NDUFA8 | NDUFA8 | NDUFA8 | 2986 | 0.085 | 0.36 | YES |
39 | NDUFB3 | NDUFB3 | NDUFB3 | 3038 | 0.084 | 0.36 | YES |
40 | NDUFB6 | NDUFB6 | NDUFB6 | 3060 | 0.084 | 0.37 | YES |
41 | NDUFS7 | NDUFS7 | NDUFS7 | 3074 | 0.083 | 0.38 | YES |
42 | COX5A | COX5A | COX5A | 3143 | 0.082 | 0.39 | YES |
43 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 3509 | 0.074 | 0.38 | YES |
44 | UCP2 | UCP2 | UCP2 | 3533 | 0.073 | 0.38 | YES |
45 | CYC1 | CYC1 | CYC1 | 3728 | 0.069 | 0.38 | YES |
46 | NDUFC1 | NDUFC1 | NDUFC1 | 3763 | 0.068 | 0.39 | YES |
47 | NDUFB8 | NDUFB8 | NDUFB8 | 3856 | 0.066 | 0.39 | YES |
48 | NDUFA12 | NDUFA12 | NDUFA12 | 3865 | 0.066 | 0.4 | YES |
49 | BSG | BSG | BSG | 3958 | 0.064 | 0.4 | YES |
50 | NDUFS5 | NDUFS5 | NDUFS5 | 4059 | 0.062 | 0.4 | YES |
51 | NDUFB4 | NDUFB4 | NDUFB4 | 4123 | 0.061 | 0.41 | YES |
52 | COX4I1 | COX4I1 | COX4I1 | 4178 | 0.06 | 0.41 | YES |
53 | ATP5H | ATP5H | ATP5H | 4182 | 0.06 | 0.42 | YES |
54 | ATP5L | ATP5L | ATP5L | 4319 | 0.057 | 0.42 | YES |
55 | NDUFA10 | NDUFA10 | NDUFA10 | 4487 | 0.054 | 0.42 | YES |
56 | ATP5O | ATP5O | ATP5O | 4511 | 0.053 | 0.42 | YES |
57 | UQCRC1 | UQCRC1 | UQCRC1 | 4523 | 0.053 | 0.43 | YES |
58 | SLC16A8 | SLC16A8 | SLC16A8 | 4546 | 0.053 | 0.43 | YES |
59 | NDUFA6 | NDUFA6 | NDUFA6 | 4560 | 0.052 | 0.44 | YES |
60 | IDH3B | IDH3B | IDH3B | 4629 | 0.051 | 0.44 | YES |
61 | IDH3G | IDH3G | IDH3G | 4642 | 0.051 | 0.44 | YES |
62 | IDH2 | IDH2 | IDH2 | 4771 | 0.049 | 0.44 | YES |
63 | NDUFA4 | NDUFA4 | NDUFA4 | 4831 | 0.048 | 0.45 | YES |
64 | NDUFS3 | NDUFS3 | NDUFS3 | 4903 | 0.047 | 0.45 | YES |
65 | COX7C | COX7C | COX7C | 4952 | 0.046 | 0.45 | YES |
66 | NDUFA9 | NDUFA9 | NDUFA9 | 5016 | 0.044 | 0.45 | YES |
67 | MDH2 | MDH2 | MDH2 | 5054 | 0.044 | 0.46 | YES |
68 | ATP5J | ATP5J | ATP5J | 5091 | 0.043 | 0.46 | YES |
69 | CYCS | CYCS | CYCS | 5196 | 0.042 | 0.46 | YES |
70 | ATP5C1 | ATP5C1 | ATP5C1 | 5197 | 0.042 | 0.46 | YES |
71 | FH | FH | FH | 5227 | 0.041 | 0.47 | YES |
72 | NDUFB5 | NDUFB5 | NDUFB5 | 5436 | 0.038 | 0.46 | NO |
73 | SDHB | SDHB | SDHB | 5896 | 0.032 | 0.44 | NO |
74 | PDHX | PDHX | PDHX | 5981 | 0.03 | 0.44 | NO |
75 | NDUFA5 | NDUFA5 | NDUFA5 | 6139 | 0.028 | 0.43 | NO |
76 | COX7A2L | COX7A2L | COX7A2L | 6258 | 0.026 | 0.43 | NO |
77 | PDHA1 | PDHA1 | PDHA1 | 6466 | 0.023 | 0.42 | NO |
78 | ETFB | ETFB | ETFB | 6671 | 0.02 | 0.41 | NO |
79 | ETFA | ETFA | ETFA | 6681 | 0.02 | 0.41 | NO |
80 | SDHA | SDHA | SDHA | 6718 | 0.02 | 0.41 | NO |
81 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 6745 | 0.019 | 0.41 | NO |
82 | NDUFS2 | NDUFS2 | NDUFS2 | 7008 | 0.015 | 0.4 | NO |
83 | DLST | DLST | DLST | 7208 | 0.013 | 0.39 | NO |
84 | L2HGDH | L2HGDH | L2HGDH | 7214 | 0.013 | 0.39 | NO |
85 | SDHC | SDHC | SDHC | 7220 | 0.013 | 0.4 | NO |
86 | ATP5B | ATP5B | ATP5B | 7312 | 0.011 | 0.39 | NO |
87 | NDUFS4 | NDUFS4 | NDUFS4 | 7614 | 0.0069 | 0.38 | NO |
88 | SUCLG1 | SUCLG1 | SUCLG1 | 7620 | 0.0069 | 0.38 | NO |
89 | PDHB | PDHB | PDHB | 7869 | 0.0033 | 0.36 | NO |
90 | ATP5F1 | ATP5F1 | ATP5F1 | 7890 | 0.003 | 0.36 | NO |
91 | IDH1 | IDH1 | IDH1 | 8077 | 0.00017 | 0.35 | NO |
92 | CS | CS | CS | 8126 | -0.00031 | 0.35 | NO |
93 | PDK1 | PDK1 | PDK1 | 8176 | -0.0011 | 0.35 | NO |
94 | DLD | DLD | DLD | 8206 | -0.0014 | 0.34 | NO |
95 | ETFDH | ETFDH | ETFDH | 8223 | -0.0016 | 0.34 | NO |
96 | SUCLG2 | SUCLG2 | SUCLG2 | 8257 | -0.002 | 0.34 | NO |
97 | SLC16A3 | SLC16A3 | SLC16A3 | 8279 | -0.0023 | 0.34 | NO |
98 | ATP5A1 | ATP5A1 | ATP5A1 | 8296 | -0.0024 | 0.34 | NO |
99 | LDHA | LDHA | LDHA | 8332 | -0.0029 | 0.34 | NO |
100 | ACO2 | ACO2 | ACO2 | 8473 | -0.005 | 0.33 | NO |
101 | IDH3A | IDH3A | IDH3A | 9758 | -0.022 | 0.26 | NO |
102 | UQCRC2 | UQCRC2 | UQCRC2 | 10390 | -0.031 | 0.23 | NO |
103 | OGDH | OGDH | OGDH | 11054 | -0.042 | 0.2 | NO |
104 | DLAT | DLAT | DLAT | 11814 | -0.054 | 0.17 | NO |
105 | SDHD | SDHD | SDHD | 12065 | -0.059 | 0.16 | NO |
106 | PDP1 | PDP1 | PDP1 | 12402 | -0.065 | 0.15 | NO |
107 | NDUFS1 | NDUFS1 | NDUFS1 | 12526 | -0.067 | 0.15 | NO |
108 | PDK2 | PDK2 | PDK2 | 12617 | -0.069 | 0.15 | NO |
109 | SUCLA2 | SUCLA2 | SUCLA2 | 13068 | -0.078 | 0.14 | NO |
110 | PDK3 | PDK3 | PDK3 | 14597 | -0.12 | 0.068 | NO |
111 | PDP2 | PDP2 | PDP2 | 15888 | -0.18 | 0.019 | NO |
112 | LDHB | LDHB | LDHB | 16386 | -0.21 | 0.017 | NO |
113 | NNT | NNT | NNT | 16414 | -0.21 | 0.041 | NO |
114 | PDPR | PDPR | PDPR | 16526 | -0.22 | 0.061 | NO |
115 | PDK4 | PDK4 | PDK4 | 17262 | -0.28 | 0.055 | 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 PARKINSONS DISEASE.

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

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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM | 30 | genes.ES.table | 0.52 | 1.6 | 0.024 | 0.2 | 0.93 | 0.43 | 0.29 | 0.31 | 0.11 | 0.015 |
KEGG LYSINE DEGRADATION | 44 | genes.ES.table | 0.46 | 1.9 | 0.0061 | 0.91 | 0.32 | 0.068 | 0.059 | 0.064 | 0 | 0.19 |
KEGG ARGININE AND PROLINE METABOLISM | 51 | genes.ES.table | 0.44 | 1.4 | 0.11 | 0.22 | 1 | 0.2 | 0.13 | 0.17 | 0.16 | 0.001 |
KEGG HISTIDINE METABOLISM | 29 | genes.ES.table | 0.58 | 1.5 | 0.029 | 0.19 | 0.98 | 0.34 | 0.2 | 0.28 | 0.13 | 0.004 |
KEGG TRYPTOPHAN METABOLISM | 38 | genes.ES.table | 0.59 | 1.6 | 0.0021 | 0.21 | 0.82 | 0.34 | 0.19 | 0.28 | 0.097 | 0.033 |
KEGG SELENOAMINO ACID METABOLISM | 26 | genes.ES.table | 0.47 | 1.6 | 0.04 | 0.21 | 0.86 | 0.077 | 0.019 | 0.076 | 0.1 | 0.031 |
KEGG GLUTATHIONE METABOLISM | 48 | genes.ES.table | 0.55 | 1.6 | 0.037 | 0.2 | 0.93 | 0.31 | 0.21 | 0.25 | 0.11 | 0.014 |
KEGG O GLYCAN BIOSYNTHESIS | 29 | genes.ES.table | 0.57 | 1.4 | 0.06 | 0.19 | 0.99 | 0.21 | 0.08 | 0.19 | 0.13 | 0.002 |
KEGG GLYCEROLIPID METABOLISM | 44 | genes.ES.table | 0.44 | 1.4 | 0.098 | 0.22 | 1 | 0.41 | 0.29 | 0.29 | 0.17 | 0.001 |
KEGG INOSITOL PHOSPHATE METABOLISM | 53 | genes.ES.table | 0.46 | 1.6 | 0.022 | 0.2 | 0.93 | 0.26 | 0.23 | 0.2 | 0.11 | 0.014 |
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 | NTF4 | NTF4 | NTF4 | 23 | 0.81 | 0.14 | YES |
2 | NTF3 | NTF3 | NTF3 | 436 | 0.46 | 0.2 | YES |
3 | MMP7 | MMP7 | MMP7 | 616 | 0.42 | 0.26 | YES |
4 | NGFR | NGFR | NGFR | 633 | 0.41 | 0.34 | YES |
5 | BEX1 | BEX1 | BEX1 | 718 | 0.4 | 0.4 | YES |
6 | BDNF | BDNF | BDNF | 905 | 0.37 | 0.46 | YES |
7 | NTRK1 | NTRK1 | NTRK1 | 1592 | 0.28 | 0.47 | YES |
8 | BIRC3 | BIRC3 | BIRC3 | 1715 | 0.28 | 0.51 | YES |
9 | OMG | OMG | OMG | 3031 | 0.18 | 0.47 | NO |
10 | RHOB | RHOB | RHOB | 4168 | 0.13 | 0.43 | NO |
11 | NGF | NGF | NGF | 4673 | 0.1 | 0.42 | NO |
12 | NDN | NDN | NDN | 4904 | 0.097 | 0.42 | NO |
13 | MAG | MAG | MAG | 5279 | 0.085 | 0.42 | NO |
14 | PIK3R1 | PIK3R1 | PIK3R1 | 5289 | 0.085 | 0.43 | NO |
15 | IKBKB | IKBKB | IKBKB | 5888 | 0.067 | 0.41 | NO |
16 | TRAF6 | TRAF6 | TRAF6 | 5933 | 0.065 | 0.42 | NO |
17 | PLG | PLG | PLG | 6634 | 0.049 | 0.39 | NO |
18 | SQSTM1 | SQSTM1 | SQSTM1 | 7190 | 0.038 | 0.37 | NO |
19 | IKBKG | IKBKG | IKBKG | 7285 | 0.037 | 0.37 | NO |
20 | SHC1 | SHC1 | SHC1 | 7466 | 0.034 | 0.36 | NO |
21 | NDNL2 | NDNL2 | NDNL2 | 7564 | 0.032 | 0.36 | NO |
22 | CASP9 | CASP9 | CASP9 | 7837 | 0.029 | 0.36 | NO |
23 | FURIN | FURIN | FURIN | 7914 | 0.028 | 0.36 | NO |
24 | ZNF274 | ZNF274 | ZNF274 | 8071 | 0.026 | 0.35 | NO |
25 | APP | APP | APP | 8575 | 0.019 | 0.33 | NO |
26 | TP53 | TP53 | TP53 | 8592 | 0.019 | 0.33 | NO |
27 | MYD88 | MYD88 | MYD88 | 8650 | 0.018 | 0.33 | NO |
28 | ADAM17 | ADAM17 | ADAM17 | 8674 | 0.018 | 0.33 | NO |
29 | CASP3 | CASP3 | CASP3 | 8703 | 0.018 | 0.33 | NO |
30 | MAPK10 | MAPK10 | MAPK10 | 8765 | 0.017 | 0.33 | NO |
31 | BIRC2 | BIRC2 | BIRC2 | 8806 | 0.016 | 0.33 | NO |
32 | RTN4R | RTN4R | RTN4R | 8863 | 0.016 | 0.33 | NO |
33 | RTN4 | RTN4 | RTN4 | 9098 | 0.013 | 0.32 | NO |
34 | DIABLO | DIABLO | DIABLO | 9538 | 0.0092 | 0.3 | NO |
35 | BCL2L11 | BCL2L11 | BCL2L11 | 9762 | 0.0069 | 0.29 | NO |
36 | PRDM4 | PRDM4 | PRDM4 | 9767 | 0.0069 | 0.29 | NO |
37 | RHOC | RHOC | RHOC | 10018 | 0.0044 | 0.28 | NO |
38 | RHOA | RHOA | RHOA | 10188 | 0.0027 | 0.27 | NO |
39 | CASP6 | CASP6 | CASP6 | 10357 | 0.0013 | 0.26 | NO |
40 | NGFRAP1 | NGFRAP1 | NGFRAP1 | 10549 | -0.00028 | 0.25 | NO |
41 | APH1A | APH1A | APH1A | 10643 | -0.0011 | 0.24 | NO |
42 | SORT1 | SORT1 | SORT1 | 10677 | -0.0014 | 0.24 | NO |
43 | PRKCZ | PRKCZ | PRKCZ | 10679 | -0.0014 | 0.24 | NO |
44 | RAC1 | RAC1 | RAC1 | 10712 | -0.0017 | 0.24 | NO |
45 | APAF1 | APAF1 | APAF1 | 10827 | -0.0028 | 0.24 | NO |
46 | PIK3CA | PIK3CA | PIK3CA | 10930 | -0.0038 | 0.23 | NO |
47 | PSENEN | PSENEN | PSENEN | 11199 | -0.0059 | 0.22 | NO |
48 | PSEN1 | PSEN1 | PSEN1 | 11543 | -0.0086 | 0.2 | NO |
49 | CHUK | CHUK | CHUK | 11656 | -0.0095 | 0.2 | NO |
50 | MAGEH1 | MAGEH1 | MAGEH1 | 11701 | -0.0099 | 0.2 | NO |
51 | SMPD2 | SMPD2 | SMPD2 | 11832 | -0.011 | 0.19 | NO |
52 | BAD | BAD | BAD | 12165 | -0.014 | 0.17 | NO |
53 | ARHGDIA | ARHGDIA | ARHGDIA | 12922 | -0.02 | 0.14 | NO |
54 | APH1B | APH1B | APH1B | 12943 | -0.02 | 0.14 | NO |
55 | NCSTN | NCSTN | NCSTN | 13585 | -0.026 | 0.11 | NO |
56 | AKT1 | AKT1 | AKT1 | 13643 | -0.027 | 0.11 | NO |
57 | MMP3 | MMP3 | MMP3 | 13790 | -0.028 | 0.11 | NO |
58 | YWHAE | YWHAE | YWHAE | 13820 | -0.029 | 0.11 | NO |
59 | PRKCI | PRKCI | PRKCI | 14097 | -0.032 | 0.1 | NO |
60 | IRAK1 | IRAK1 | IRAK1 | 14719 | -0.038 | 0.072 | NO |
61 | MAPK8 | MAPK8 | MAPK8 | 14780 | -0.039 | 0.076 | NO |
62 | XIAP | XIAP | XIAP | 15262 | -0.045 | 0.057 | NO |
63 | MAPK9 | MAPK9 | MAPK9 | 15445 | -0.049 | 0.056 | NO |
64 | CYCS | CYCS | CYCS | 15484 | -0.05 | 0.063 | NO |
65 | PRKACB | PRKACB | PRKACB | 15832 | -0.056 | 0.053 | NO |
66 | MAGED1 | MAGED1 | MAGED1 | 15984 | -0.06 | 0.056 | NO |
67 | RIPK2 | RIPK2 | RIPK2 | 17175 | -0.1 | 0.0083 | NO |
68 | E2F1 | E2F1 | E2F1 | 17486 | -0.12 | 0.013 | NO |
69 | LINGO1 | LINGO1 | LINGO1 | 17827 | -0.16 | 0.024 | 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S62. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE 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 | TMLHE | TMLHE | TMLHE | 401 | 0.47 | 0.18 | YES |
2 | PIPOX | PIPOX | PIPOX | 737 | 0.39 | 0.33 | YES |
3 | BBOX1 | BBOX1 | BBOX1 | 1070 | 0.34 | 0.46 | YES |
4 | ALDH2 | ALDH2 | ALDH2 | 3386 | 0.16 | 0.4 | NO |
5 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 5278 | 0.085 | 0.33 | NO |
6 | SUV420H2 | SUV420H2 | SUV420H2 | 7311 | 0.036 | 0.23 | NO |
7 | WHSC1L1 | WHSC1L1 | WHSC1L1 | 7611 | 0.032 | 0.23 | NO |
8 | SETDB2 | SETDB2 | SETDB2 | 7694 | 0.031 | 0.24 | NO |
9 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 8327 | 0.022 | 0.22 | NO |
10 | SETD1A | SETD1A | SETD1A | 8356 | 0.022 | 0.22 | NO |
11 | AASS | AASS | AASS | 8377 | 0.022 | 0.23 | NO |
12 | EHMT2 | EHMT2 | EHMT2 | 8565 | 0.019 | 0.23 | NO |
13 | AASDH | AASDH | AASDH | 9722 | 0.0073 | 0.17 | NO |
14 | SUV39H1 | SUV39H1 | SUV39H1 | 10183 | 0.0027 | 0.14 | NO |
15 | HADHA | HADHA | HADHA | 10219 | 0.0024 | 0.14 | NO |
16 | DOT1L | DOT1L | DOT1L | 10235 | 0.0022 | 0.14 | NO |
17 | SETD1B | SETD1B | SETD1B | 10653 | -0.0012 | 0.12 | NO |
18 | SETDB1 | SETDB1 | SETDB1 | 10965 | -0.004 | 0.11 | NO |
19 | SETMAR | SETMAR | SETMAR | 11132 | -0.0053 | 0.099 | NO |
20 | DLST | DLST | DLST | 11273 | -0.0064 | 0.094 | NO |
21 | OGDH | OGDH | OGDH | 11493 | -0.0082 | 0.085 | NO |
22 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 11576 | -0.0089 | 0.085 | NO |
23 | GCDH | GCDH | GCDH | 11719 | -0.01 | 0.081 | NO |
24 | EHMT1 | EHMT1 | EHMT1 | 12044 | -0.013 | 0.069 | NO |
25 | SETD8 | SETD8 | SETD8 | 12220 | -0.014 | 0.065 | NO |
26 | PLOD1 | PLOD1 | PLOD1 | 12251 | -0.014 | 0.07 | NO |
27 | ASH1L | ASH1L | ASH1L | 12336 | -0.015 | 0.072 | NO |
28 | SUV420H1 | SUV420H1 | SUV420H1 | 12352 | -0.015 | 0.077 | NO |
29 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 12358 | -0.015 | 0.083 | NO |
30 | SETD2 | SETD2 | SETD2 | 12361 | -0.015 | 0.09 | NO |
31 | OGDHL | OGDHL | OGDHL | 12417 | -0.016 | 0.094 | NO |
32 | HADH | HADH | HADH | 12793 | -0.019 | 0.081 | NO |
33 | NSD1 | NSD1 | NSD1 | 12907 | -0.02 | 0.083 | NO |
34 | PLOD3 | PLOD3 | PLOD3 | 13717 | -0.028 | 0.051 | NO |
35 | AASDHPPT | AASDHPPT | AASDHPPT | 14000 | -0.03 | 0.048 | NO |
36 | ECHS1 | ECHS1 | ECHS1 | 14050 | -0.031 | 0.059 | NO |
37 | ACAT2 | ACAT2 | ACAT2 | 14226 | -0.033 | 0.063 | NO |
38 | PLOD2 | PLOD2 | PLOD2 | 14648 | -0.038 | 0.056 | NO |
39 | SUV39H2 | SUV39H2 | SUV39H2 | 15417 | -0.048 | 0.034 | NO |
40 | ACAT1 | ACAT1 | ACAT1 | 15682 | -0.053 | 0.042 | NO |
41 | SETD7 | SETD7 | SETD7 | 15807 | -0.055 | 0.059 | NO |
42 | EHHADH | EHHADH | EHHADH | 15856 | -0.056 | 0.08 | NO |
43 | AADAT | AADAT | AADAT | 15949 | -0.059 | 0.1 | NO |
44 | WHSC1 | WHSC1 | WHSC1 | 16147 | -0.063 | 0.12 | 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 LYSINE DEGRADATION.
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Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | MUC4 | MUC4 | MUC4 | 8 | 0.88 | 0.047 | YES |
2 | B3GNT8 | B3GNT8 | B3GNT8 | 87 | 0.69 | 0.08 | YES |
3 | MUC15 | MUC15 | MUC15 | 121 | 0.65 | 0.11 | YES |
4 | ST6GALNAC2 | ST6GALNAC2 | ST6GALNAC2 | 133 | 0.64 | 0.15 | YES |
5 | B3GNT3 | B3GNT3 | B3GNT3 | 139 | 0.64 | 0.18 | YES |
6 | MUC16 | MUC16 | MUC16 | 158 | 0.62 | 0.21 | YES |
7 | GALNT5 | GALNT5 | GALNT5 | 238 | 0.55 | 0.24 | YES |
8 | GCNT3 | GCNT3 | GCNT3 | 272 | 0.53 | 0.26 | YES |
9 | GALNT14 | GALNT14 | GALNT14 | 284 | 0.52 | 0.29 | YES |
10 | GALNT6 | GALNT6 | GALNT6 | 479 | 0.45 | 0.31 | YES |
11 | SEMA6D | SEMA6D | SEMA6D | 634 | 0.41 | 0.32 | YES |
12 | ST8SIA3 | ST8SIA3 | ST8SIA3 | 710 | 0.4 | 0.34 | YES |
13 | MUC21 | MUC21 | MUC21 | 772 | 0.39 | 0.36 | YES |
14 | MGAT3 | MGAT3 | MGAT3 | 827 | 0.38 | 0.37 | YES |
15 | GALNT9 | GALNT9 | GALNT9 | 1008 | 0.35 | 0.38 | YES |
16 | MUC12 | MUC12 | MUC12 | 1030 | 0.35 | 0.4 | YES |
17 | MUC5B | MUC5B | MUC5B | 1034 | 0.35 | 0.42 | YES |
18 | ST6GALNAC4 | ST6GALNAC4 | ST6GALNAC4 | 1190 | 0.33 | 0.43 | YES |
19 | ARSE | ARSE | ARSE | 1212 | 0.32 | 0.44 | YES |
20 | GCNT4 | GCNT4 | GCNT4 | 1469 | 0.3 | 0.44 | YES |
21 | MUC13 | MUC13 | MUC13 | 1623 | 0.28 | 0.45 | YES |
22 | MGAT4C | MGAT4C | MGAT4C | 1892 | 0.26 | 0.45 | YES |
23 | ARSJ | ARSJ | ARSJ | 1959 | 0.26 | 0.46 | YES |
24 | B3GNT9 | B3GNT9 | B3GNT9 | 2067 | 0.25 | 0.47 | YES |
25 | B3GNT7 | B3GNT7 | B3GNT7 | 2274 | 0.23 | 0.47 | YES |
26 | ARSF | ARSF | ARSF | 2357 | 0.22 | 0.48 | YES |
27 | B3GNT5 | B3GNT5 | B3GNT5 | 2434 | 0.22 | 0.48 | YES |
28 | PLAUR | PLAUR | PLAUR | 2553 | 0.21 | 0.49 | YES |
29 | F10 | F10 | F10 | 2715 | 0.2 | 0.49 | YES |
30 | F7 | F7 | F7 | 2739 | 0.2 | 0.5 | YES |
31 | GALNT8 | GALNT8 | GALNT8 | 2745 | 0.2 | 0.51 | YES |
32 | MUC17 | MUC17 | MUC17 | 3037 | 0.18 | 0.5 | YES |
33 | GFPT2 | GFPT2 | GFPT2 | 3042 | 0.18 | 0.51 | YES |
34 | ST6GALNAC3 | ST6GALNAC3 | ST6GALNAC3 | 3201 | 0.17 | 0.51 | YES |
35 | PGAP1 | PGAP1 | PGAP1 | 3492 | 0.16 | 0.51 | NO |
36 | ARSI | ARSI | ARSI | 3971 | 0.14 | 0.49 | NO |
37 | ST3GAL2 | ST3GAL2 | ST3GAL2 | 4438 | 0.12 | 0.47 | NO |
38 | ST6GAL1 | ST6GAL1 | ST6GAL1 | 5397 | 0.082 | 0.42 | NO |
39 | MAN1A1 | MAN1A1 | MAN1A1 | 5489 | 0.078 | 0.42 | NO |
40 | SEC23A | SEC23A | SEC23A | 5601 | 0.074 | 0.42 | NO |
41 | B4GALT1 | B4GALT1 | B4GALT1 | 5816 | 0.068 | 0.41 | NO |
42 | GALNTL1 | GALNTL1 | GALNTL1 | 5853 | 0.068 | 0.41 | NO |
43 | WBSCR17 | WBSCR17 | WBSCR17 | 6039 | 0.062 | 0.4 | NO |
44 | B3GNT2 | B3GNT2 | B3GNT2 | 6074 | 0.062 | 0.4 | NO |
45 | PROS1 | PROS1 | PROS1 | 6083 | 0.061 | 0.41 | NO |
46 | GALNTL4 | GALNTL4 | GALNTL4 | 6347 | 0.055 | 0.4 | NO |
47 | GALNT12 | GALNT12 | GALNT12 | 6605 | 0.049 | 0.38 | NO |
48 | B4GALT5 | B4GALT5 | B4GALT5 | 6683 | 0.048 | 0.38 | NO |
49 | STS | STS | STS | 6830 | 0.045 | 0.38 | NO |
50 | EIF5A2 | EIF5A2 | EIF5A2 | 6998 | 0.042 | 0.37 | NO |
51 | MGAT1 | MGAT1 | MGAT1 | 7055 | 0.041 | 0.37 | NO |
52 | ST3GAL1 | ST3GAL1 | ST3GAL1 | 7145 | 0.039 | 0.37 | NO |
53 | FUT8 | FUT8 | FUT8 | 7250 | 0.037 | 0.36 | NO |
54 | C1GALT1 | C1GALT1 | C1GALT1 | 7499 | 0.034 | 0.35 | NO |
55 | FURIN | FURIN | FURIN | 7914 | 0.028 | 0.33 | NO |
56 | PROC | PROC | PROC | 7953 | 0.027 | 0.33 | NO |
57 | MAN1C1 | MAN1C1 | MAN1C1 | 8166 | 0.024 | 0.32 | NO |
58 | B4GALT4 | B4GALT4 | B4GALT4 | 8211 | 0.024 | 0.32 | NO |
59 | PIGB | PIGB | PIGB | 8258 | 0.023 | 0.32 | NO |
60 | ARSK | ARSK | ARSK | 8264 | 0.023 | 0.32 | NO |
61 | PIGC | PIGC | PIGC | 8595 | 0.019 | 0.3 | NO |
62 | DOHH | DOHH | DOHH | 8759 | 0.017 | 0.29 | NO |
63 | B4GALT6 | B4GALT6 | B4GALT6 | 8924 | 0.015 | 0.28 | NO |
64 | PIGS | PIGS | PIGS | 8985 | 0.015 | 0.28 | NO |
65 | ARSB | ARSB | ARSB | 9029 | 0.014 | 0.28 | NO |
66 | GALNT2 | GALNT2 | GALNT2 | 9195 | 0.012 | 0.27 | NO |
67 | DPM1 | DPM1 | DPM1 | 9519 | 0.0093 | 0.25 | NO |
68 | GALNTL2 | GALNTL2 | GALNTL2 | 9572 | 0.0088 | 0.25 | NO |
69 | PIGQ | PIGQ | PIGQ | 9591 | 0.0085 | 0.25 | NO |
70 | B3GNT4 | B3GNT4 | B3GNT4 | 9797 | 0.0066 | 0.24 | NO |
71 | GMPPA | GMPPA | GMPPA | 9959 | 0.0049 | 0.23 | NO |
72 | PIGA | PIGA | PIGA | 10016 | 0.0044 | 0.23 | NO |
73 | ALG5 | ALG5 | ALG5 | 10055 | 0.004 | 0.23 | NO |
74 | EDEM2 | EDEM2 | EDEM2 | 10498 | 0.00026 | 0.2 | NO |
75 | VKORC1 | VKORC1 | VKORC1 | 10620 | -0.00091 | 0.2 | NO |
76 | SUMF2 | SUMF2 | SUMF2 | 10666 | -0.0013 | 0.19 | NO |
77 | F2 | F2 | F2 | 10700 | -0.0016 | 0.19 | NO |
78 | DPM3 | DPM3 | DPM3 | 10715 | -0.0017 | 0.19 | NO |
79 | PIGT | PIGT | PIGT | 11070 | -0.0048 | 0.17 | NO |
80 | RFT1 | RFT1 | RFT1 | 11171 | -0.0056 | 0.16 | NO |
81 | PIGL | PIGL | PIGL | 11335 | -0.0068 | 0.16 | NO |
82 | MAN1B1 | MAN1B1 | MAN1B1 | 11427 | -0.0076 | 0.15 | NO |
83 | ALG12 | ALG12 | ALG12 | 11510 | -0.0083 | 0.15 | NO |
84 | DAD1 | DAD1 | DAD1 | 11511 | -0.0083 | 0.15 | NO |
85 | PRKCSH | PRKCSH | PRKCSH | 11895 | -0.012 | 0.13 | NO |
86 | ALG1 | ALG1 | ALG1 | 11995 | -0.012 | 0.12 | NO |
87 | B4GALT2 | B4GALT2 | B4GALT2 | 12101 | -0.013 | 0.12 | NO |
88 | PIGG | PIGG | PIGG | 12110 | -0.013 | 0.12 | NO |
89 | ALG13 | ALG13 | ALG13 | 12155 | -0.014 | 0.12 | NO |
90 | UGGT1 | UGGT1 | UGGT1 | 12234 | -0.014 | 0.11 | NO |
91 | SEC13 | SEC13 | SEC13 | 12403 | -0.016 | 0.1 | NO |
92 | EIF5A | EIF5A | EIF5A | 12422 | -0.016 | 0.1 | NO |
93 | GALNT10 | GALNT10 | GALNT10 | 12428 | -0.016 | 0.1 | NO |
94 | DOLK | DOLK | DOLK | 12587 | -0.017 | 0.097 | NO |
95 | ARSA | ARSA | ARSA | 12596 | -0.017 | 0.097 | NO |
96 | GMPPB | GMPPB | GMPPB | 12629 | -0.018 | 0.097 | NO |
97 | PIGF | PIGF | PIGF | 12655 | -0.018 | 0.096 | NO |
98 | GPAA1 | GPAA1 | GPAA1 | 12713 | -0.018 | 0.094 | NO |
99 | PREB | PREB | PREB | 12729 | -0.018 | 0.094 | NO |
100 | ALG2 | ALG2 | ALG2 | 12741 | -0.019 | 0.095 | NO |
101 | PROZ | PROZ | PROZ | 12850 | -0.02 | 0.09 | NO |
102 | MOGS | MOGS | MOGS | 12859 | -0.02 | 0.09 | NO |
103 | MCFD2 | MCFD2 | MCFD2 | 12888 | -0.02 | 0.09 | NO |
104 | PIGV | PIGV | PIGV | 12906 | -0.02 | 0.09 | NO |
105 | RPN1 | RPN1 | RPN1 | 12916 | -0.02 | 0.09 | NO |
106 | DPM2 | DPM2 | DPM2 | 12926 | -0.02 | 0.091 | NO |
107 | PIGU | PIGU | PIGU | 13023 | -0.021 | 0.087 | NO |
108 | SEC24B | SEC24B | SEC24B | 13029 | -0.021 | 0.088 | NO |
109 | PIGN | PIGN | PIGN | 13228 | -0.023 | 0.078 | NO |
110 | GGCX | GGCX | GGCX | 13312 | -0.024 | 0.075 | NO |
111 | LMAN1 | LMAN1 | LMAN1 | 13333 | -0.024 | 0.075 | NO |
112 | EDEM1 | EDEM1 | EDEM1 | 13359 | -0.024 | 0.075 | NO |
113 | RPN2 | RPN2 | RPN2 | 13404 | -0.025 | 0.074 | NO |
114 | GALNT1 | GALNT1 | GALNT1 | 13436 | -0.025 | 0.073 | NO |
115 | MUCL1 | MUCL1 | MUCL1 | 13486 | -0.025 | 0.072 | NO |
116 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 13513 | -0.026 | 0.072 | NO |
117 | PIGO | PIGO | PIGO | 13543 | -0.026 | 0.072 | NO |
118 | GANAB | GANAB | GANAB | 13598 | -0.026 | 0.07 | NO |
119 | DPAGT1 | DPAGT1 | DPAGT1 | 13674 | -0.027 | 0.068 | NO |
120 | SEC24C | SEC24C | SEC24C | 13840 | -0.029 | 0.06 | NO |
121 | SEC24D | SEC24D | SEC24D | 13875 | -0.029 | 0.06 | NO |
122 | UGGT2 | UGGT2 | UGGT2 | 14058 | -0.031 | 0.051 | NO |
123 | ALG9 | ALG9 | ALG9 | 14090 | -0.031 | 0.051 | NO |
124 | SEC31A | SEC31A | SEC31A | 14122 | -0.032 | 0.051 | NO |
125 | DHPS | DHPS | DHPS | 14153 | -0.032 | 0.051 | NO |
126 | MAN2A1 | MAN2A1 | MAN2A1 | 14222 | -0.033 | 0.049 | NO |
127 | SUMF1 | SUMF1 | SUMF1 | 14350 | -0.034 | 0.044 | NO |
128 | C1GALT1C1 | C1GALT1C1 | C1GALT1C1 | 14357 | -0.034 | 0.046 | NO |
129 | ALG3 | ALG3 | ALG3 | 14378 | -0.034 | 0.046 | NO |
130 | MGAT5 | MGAT5 | MGAT5 | 14400 | -0.035 | 0.047 | NO |
131 | DDOST | DDOST | DDOST | 14532 | -0.036 | 0.042 | NO |
132 | DOLPP1 | DOLPP1 | DOLPP1 | 14574 | -0.037 | 0.041 | NO |
133 | MLEC | MLEC | MLEC | 14622 | -0.037 | 0.041 | NO |
134 | PMM1 | PMM1 | PMM1 | 14742 | -0.039 | 0.036 | NO |
135 | B3GNTL1 | B3GNTL1 | B3GNTL1 | 14743 | -0.039 | 0.038 | NO |
136 | MPI | MPI | MPI | 14758 | -0.039 | 0.04 | NO |
137 | MGAT4B | MGAT4B | MGAT4B | 14829 | -0.04 | 0.038 | NO |
138 | PMM2 | PMM2 | PMM2 | 14874 | -0.04 | 0.038 | NO |
139 | PDIA3 | PDIA3 | PDIA3 | 14892 | -0.04 | 0.039 | NO |
140 | CALR | CALR | CALR | 14930 | -0.041 | 0.039 | NO |
141 | ALG11 | ALG11 | ALG11 | 14934 | -0.041 | 0.041 | NO |
142 | MGAT2 | MGAT2 | MGAT2 | 14993 | -0.042 | 0.04 | NO |
143 | STT3A | STT3A | STT3A | 15111 | -0.043 | 0.036 | NO |
144 | MUC6 | MUC6 | MUC6 | 15132 | -0.043 | 0.037 | NO |
145 | CANX | CANX | CANX | 15133 | -0.043 | 0.039 | NO |
146 | MUC2 | MUC2 | MUC2 | 15206 | -0.044 | 0.038 | NO |
147 | MAN1A2 | MAN1A2 | MAN1A2 | 15212 | -0.044 | 0.04 | NO |
148 | PIGK | PIGK | PIGK | 15502 | -0.05 | 0.027 | NO |
149 | ST8SIA6 | ST8SIA6 | ST8SIA6 | 15511 | -0.05 | 0.029 | NO |
150 | B4GALT3 | B4GALT3 | B4GALT3 | 15532 | -0.051 | 0.03 | NO |
151 | GALNT11 | GALNT11 | GALNT11 | 15599 | -0.052 | 0.03 | NO |
152 | PIGX | PIGX | PIGX | 15689 | -0.053 | 0.028 | NO |
153 | PIGH | PIGH | PIGH | 15744 | -0.054 | 0.028 | NO |
154 | MANEA | MANEA | MANEA | 15803 | -0.055 | 0.027 | NO |
155 | PIGM | PIGM | PIGM | 15847 | -0.056 | 0.028 | NO |
156 | PIGP | PIGP | PIGP | 15887 | -0.057 | 0.029 | NO |
157 | ALG8 | ALG8 | ALG8 | 15983 | -0.059 | 0.027 | NO |
158 | ARSG | ARSG | ARSG | 16018 | -0.06 | 0.028 | NO |
159 | ALG14 | ALG14 | ALG14 | 16104 | -0.062 | 0.027 | NO |
160 | PGM3 | PGM3 | PGM3 | 16224 | -0.065 | 0.024 | NO |
161 | ALG10B | ALG10B | ALG10B | 16299 | -0.067 | 0.023 | NO |
162 | ALG10 | ALG10 | ALG10 | 16367 | -0.069 | 0.023 | NO |
163 | MGAT4A | MGAT4A | MGAT4A | 16383 | -0.07 | 0.026 | NO |
164 | ALG6 | ALG6 | ALG6 | 16519 | -0.074 | 0.023 | NO |
165 | TUSC3 | TUSC3 | TUSC3 | 16671 | -0.08 | 0.018 | NO |
166 | GALNTL6 | GALNTL6 | GALNTL6 | 16719 | -0.082 | 0.02 | NO |
167 | SAR1B | SAR1B | SAR1B | 16732 | -0.082 | 0.024 | NO |
168 | GCNT1 | GCNT1 | GCNT1 | 16786 | -0.084 | 0.026 | NO |
169 | GNPNAT1 | GNPNAT1 | GNPNAT1 | 17066 | -0.098 | 0.016 | NO |
170 | GALNT13 | GALNT13 | GALNT13 | 17084 | -0.099 | 0.02 | NO |
171 | PIGW | PIGW | PIGW | 17123 | -0.1 | 0.023 | NO |
172 | GALNT7 | GALNT7 | GALNT7 | 17125 | -0.1 | 0.029 | NO |
173 | GALNT3 | GALNT3 | GALNT3 | 17130 | -0.1 | 0.034 | NO |
174 | ST8SIA2 | ST8SIA2 | ST8SIA2 | 17230 | -0.11 | 0.034 | NO |
175 | EDEM3 | EDEM3 | EDEM3 | 17448 | -0.12 | 0.029 | NO |
176 | B3GNT6 | B3GNT6 | B3GNT6 | 17531 | -0.13 | 0.031 | NO |
177 | ARSH | ARSH | ARSH | 17836 | -0.17 | 0.023 | NO |
Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ARGININE AND PROLINE METABOLISM.

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

Table 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 | CXCL1 | CXCL1 | CXCL1 | 106 | 0.67 | 0.085 | YES |
2 | CXCR2 | CXCR2 | CXCR2 | 118 | 0.66 | 0.17 | YES |
3 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 293 | 0.52 | 0.23 | YES |
4 | PTPRZ1 | PTPRZ1 | PTPRZ1 | 375 | 0.48 | 0.29 | YES |
5 | MET | MET | MET | 636 | 0.41 | 0.33 | YES |
6 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 692 | 0.4 | 0.38 | YES |
7 | ATP6V1G3 | ATP6V1G3 | ATP6V1G3 | 856 | 0.38 | 0.43 | YES |
8 | CCL5 | CCL5 | CCL5 | 1260 | 0.32 | 0.45 | YES |
9 | IL8 | IL8 | IL8 | 1498 | 0.3 | 0.47 | YES |
10 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 1542 | 0.29 | 0.51 | YES |
11 | PLCG2 | PLCG2 | PLCG2 | 2173 | 0.24 | 0.51 | YES |
12 | MAP3K14 | MAP3K14 | MAP3K14 | 2348 | 0.22 | 0.53 | YES |
13 | TCIRG1 | TCIRG1 | TCIRG1 | 3061 | 0.18 | 0.51 | YES |
14 | HBEGF | HBEGF | HBEGF | 3229 | 0.17 | 0.53 | YES |
15 | JAM2 | JAM2 | JAM2 | 3631 | 0.15 | 0.53 | YES |
16 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 4407 | 0.12 | 0.5 | YES |
17 | PAK1 | PAK1 | PAK1 | 4428 | 0.12 | 0.51 | YES |
18 | JAM3 | JAM3 | JAM3 | 4504 | 0.11 | 0.52 | YES |
19 | NOD1 | NOD1 | NOD1 | 4755 | 0.1 | 0.52 | YES |
20 | EGFR | EGFR | EGFR | 4956 | 0.095 | 0.53 | YES |
21 | NFKBIA | NFKBIA | NFKBIA | 5062 | 0.092 | 0.53 | YES |
22 | CXCR1 | CXCR1 | CXCR1 | 5203 | 0.088 | 0.54 | YES |
23 | NFKB1 | NFKB1 | NFKB1 | 5246 | 0.086 | 0.55 | YES |
24 | F11R | F11R | F11R | 5538 | 0.077 | 0.54 | NO |
25 | JUN | JUN | JUN | 5829 | 0.068 | 0.53 | NO |
26 | IKBKB | IKBKB | IKBKB | 5888 | 0.067 | 0.54 | NO |
27 | MAPK11 | MAPK11 | MAPK11 | 6844 | 0.045 | 0.49 | NO |
28 | MAPK13 | MAPK13 | MAPK13 | 7133 | 0.039 | 0.48 | NO |
29 | IKBKG | IKBKG | IKBKG | 7285 | 0.037 | 0.48 | NO |
30 | LYN | LYN | LYN | 7496 | 0.034 | 0.47 | NO |
31 | SRC | SRC | SRC | 7608 | 0.032 | 0.47 | NO |
32 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 7803 | 0.029 | 0.46 | NO |
33 | ADAM17 | ADAM17 | ADAM17 | 8674 | 0.018 | 0.42 | NO |
34 | CASP3 | CASP3 | CASP3 | 8703 | 0.018 | 0.42 | NO |
35 | MAPK10 | MAPK10 | MAPK10 | 8765 | 0.017 | 0.42 | NO |
36 | MAPK14 | MAPK14 | MAPK14 | 9039 | 0.014 | 0.4 | NO |
37 | RELA | RELA | RELA | 9076 | 0.014 | 0.4 | NO |
38 | PLCG1 | PLCG1 | PLCG1 | 9371 | 0.011 | 0.39 | NO |
39 | GIT1 | GIT1 | GIT1 | 9760 | 0.0069 | 0.37 | NO |
40 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 9814 | 0.0063 | 0.37 | NO |
41 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 10216 | 0.0024 | 0.35 | NO |
42 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 10245 | 0.0022 | 0.34 | NO |
43 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 10254 | 0.0021 | 0.34 | NO |
44 | CSK | CSK | CSK | 10302 | 0.0017 | 0.34 | NO |
45 | RAC1 | RAC1 | RAC1 | 10712 | -0.0017 | 0.32 | NO |
46 | CDC42 | CDC42 | CDC42 | 10947 | -0.0039 | 0.31 | NO |
47 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 11183 | -0.0058 | 0.3 | NO |
48 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 11635 | -0.0094 | 0.27 | NO |
49 | CHUK | CHUK | CHUK | 11656 | -0.0095 | 0.27 | NO |
50 | ATP6V0C | ATP6V0C | ATP6V0C | 11972 | -0.012 | 0.26 | NO |
51 | MAP2K4 | MAP2K4 | MAP2K4 | 12025 | -0.013 | 0.26 | NO |
52 | IGSF5 | IGSF5 | IGSF5 | 12320 | -0.015 | 0.24 | NO |
53 | ATP6V1H | ATP6V1H | ATP6V1H | 12383 | -0.016 | 0.24 | NO |
54 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 12592 | -0.017 | 0.23 | NO |
55 | ATP6V1F | ATP6V1F | ATP6V1F | 12933 | -0.02 | 0.21 | NO |
56 | ATP6V0B | ATP6V0B | ATP6V0B | 13174 | -0.022 | 0.2 | NO |
57 | ATP6V1D | ATP6V1D | ATP6V1D | 13366 | -0.024 | 0.2 | NO |
58 | PTPN11 | PTPN11 | PTPN11 | 13442 | -0.025 | 0.2 | NO |
59 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 14343 | -0.034 | 0.15 | NO |
60 | ADAM10 | ADAM10 | ADAM10 | 14715 | -0.038 | 0.14 | NO |
61 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 14746 | -0.039 | 0.14 | NO |
62 | MAPK8 | MAPK8 | MAPK8 | 14780 | -0.039 | 0.14 | NO |
63 | MAPK9 | MAPK9 | MAPK9 | 15445 | -0.049 | 0.11 | NO |
64 | MAPK12 | MAPK12 | MAPK12 | 15636 | -0.052 | 0.11 | NO |
65 | ATP6V1A | ATP6V1A | ATP6V1A | 15991 | -0.06 | 0.098 | NO |
66 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 16050 | -0.061 | 0.1 | NO |
67 | TJP1 | TJP1 | TJP1 | 16055 | -0.061 | 0.11 | NO |
68 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 16504 | -0.073 | 0.096 | NO |
Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HISTIDINE METABOLISM.

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

Table 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 | PPARGC1A | PPARGC1A | PPARGC1A | 489 | 0.45 | 0.055 | YES |
2 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 984 | 0.36 | 0.092 | YES |
3 | SLC2A4 | SLC2A4 | SLC2A4 | 1037 | 0.35 | 0.15 | YES |
4 | TNF | TNF | TNF | 1148 | 0.33 | 0.21 | YES |
5 | WNT1 | WNT1 | WNT1 | 1172 | 0.33 | 0.27 | YES |
6 | FABP4 | FABP4 | FABP4 | 1237 | 0.32 | 0.32 | YES |
7 | SMARCD3 | SMARCD3 | SMARCD3 | 1303 | 0.32 | 0.37 | YES |
8 | KLF5 | KLF5 | KLF5 | 1405 | 0.3 | 0.42 | YES |
9 | PCK1 | PCK1 | PCK1 | 2062 | 0.25 | 0.43 | YES |
10 | CEBPB | CEBPB | CEBPB | 2225 | 0.23 | 0.47 | YES |
11 | CEBPD | CEBPD | CEBPD | 2501 | 0.21 | 0.49 | YES |
12 | TGFB1 | TGFB1 | TGFB1 | 3672 | 0.15 | 0.45 | YES |
13 | PPARG | PPARG | PPARG | 3768 | 0.15 | 0.47 | YES |
14 | KLF4 | KLF4 | KLF4 | 4637 | 0.11 | 0.44 | YES |
15 | EBF1 | EBF1 | EBF1 | 4644 | 0.11 | 0.46 | YES |
16 | EGR2 | EGR2 | EGR2 | 4657 | 0.11 | 0.48 | YES |
17 | CCND3 | CCND3 | CCND3 | 4822 | 0.1 | 0.49 | YES |
18 | WNT10B | WNT10B | WNT10B | 4835 | 0.1 | 0.51 | YES |
19 | MED30 | MED30 | MED30 | 6260 | 0.057 | 0.44 | NO |
20 | RXRA | RXRA | RXRA | 6438 | 0.053 | 0.44 | NO |
21 | MED21 | MED21 | MED21 | 6571 | 0.05 | 0.44 | NO |
22 | MED4 | MED4 | MED4 | 7002 | 0.042 | 0.43 | NO |
23 | MED15 | MED15 | MED15 | 7131 | 0.039 | 0.43 | NO |
24 | MED11 | MED11 | MED11 | 7942 | 0.027 | 0.39 | NO |
25 | NCOR2 | NCOR2 | NCOR2 | 8370 | 0.022 | 0.37 | NO |
26 | MED9 | MED9 | MED9 | 8395 | 0.021 | 0.37 | NO |
27 | MED24 | MED24 | MED24 | 8409 | 0.021 | 0.37 | NO |
28 | MED10 | MED10 | MED10 | 8427 | 0.021 | 0.38 | NO |
29 | MED12 | MED12 | MED12 | 8544 | 0.02 | 0.37 | NO |
30 | MED6 | MED6 | MED6 | 8562 | 0.019 | 0.38 | NO |
31 | TBL1X | TBL1X | TBL1X | 8582 | 0.019 | 0.38 | NO |
32 | MED16 | MED16 | MED16 | 8725 | 0.017 | 0.37 | NO |
33 | MED7 | MED7 | MED7 | 8873 | 0.016 | 0.37 | NO |
34 | MED20 | MED20 | MED20 | 8887 | 0.016 | 0.37 | NO |
35 | RELA | RELA | RELA | 9076 | 0.014 | 0.36 | NO |
36 | CREBBP | CREBBP | CREBBP | 9162 | 0.013 | 0.36 | NO |
37 | TGS1 | TGS1 | TGS1 | 9199 | 0.012 | 0.36 | NO |
38 | MED31 | MED31 | MED31 | 9446 | 0.01 | 0.35 | NO |
39 | MED25 | MED25 | MED25 | 9492 | 0.0095 | 0.35 | NO |
40 | PRIC285 | PRIC285 | PRIC285 | 9632 | 0.0081 | 0.34 | NO |
41 | MED18 | MED18 | MED18 | 10068 | 0.0039 | 0.32 | NO |
42 | HDAC3 | HDAC3 | HDAC3 | 10105 | 0.0035 | 0.32 | NO |
43 | PPARA | PPARA | PPARA | 10226 | 0.0023 | 0.31 | NO |
44 | MED26 | MED26 | MED26 | 10488 | 0.00031 | 0.3 | NO |
45 | MED22 | MED22 | MED22 | 10556 | -0.00034 | 0.29 | NO |
46 | NR2F2 | NR2F2 | NR2F2 | 10698 | -0.0016 | 0.29 | NO |
47 | MED13L | MED13L | MED13L | 10958 | -0.004 | 0.27 | NO |
48 | LEP | LEP | LEP | 10977 | -0.0041 | 0.27 | NO |
49 | MED27 | MED27 | MED27 | 11133 | -0.0053 | 0.26 | NO |
50 | MED8 | MED8 | MED8 | 11860 | -0.011 | 0.23 | NO |
51 | NCOA3 | NCOA3 | NCOA3 | 11962 | -0.012 | 0.22 | NO |
52 | MED29 | MED29 | MED29 | 12126 | -0.014 | 0.22 | NO |
53 | MED17 | MED17 | MED17 | 12235 | -0.014 | 0.21 | NO |
54 | MED19 | MED19 | MED19 | 12307 | -0.015 | 0.21 | NO |
55 | CDK8 | CDK8 | CDK8 | 12348 | -0.015 | 0.21 | NO |
56 | LPL | LPL | LPL | 12366 | -0.016 | 0.22 | NO |
57 | NCOA1 | NCOA1 | NCOA1 | 12491 | -0.017 | 0.21 | NO |
58 | NCOR1 | NCOR1 | NCOR1 | 12647 | -0.018 | 0.21 | NO |
59 | CCNC | CCNC | CCNC | 12773 | -0.019 | 0.2 | NO |
60 | CDK4 | CDK4 | CDK4 | 12785 | -0.019 | 0.2 | NO |
61 | MED23 | MED23 | MED23 | 12885 | -0.02 | 0.2 | NO |
62 | CDK19 | CDK19 | CDK19 | 13209 | -0.023 | 0.19 | NO |
63 | MED1 | MED1 | MED1 | 13886 | -0.029 | 0.16 | NO |
64 | MED14 | MED14 | MED14 | 14168 | -0.032 | 0.15 | NO |
65 | EP300 | EP300 | EP300 | 14397 | -0.034 | 0.14 | NO |
66 | NCOA6 | NCOA6 | NCOA6 | 14709 | -0.038 | 0.13 | NO |
67 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 15247 | -0.045 | 0.11 | NO |
68 | PLIN1 | PLIN1 | PLIN1 | 15882 | -0.057 | 0.086 | NO |
69 | CD36 | CD36 | CD36 | 16031 | -0.061 | 0.089 | NO |
70 | SREBF1 | SREBF1 | SREBF1 | 16518 | -0.074 | 0.076 | NO |
71 | NCOA2 | NCOA2 | NCOA2 | 17278 | -0.11 | 0.054 | NO |
Figure S69. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TRYPTOPHAN METABOLISM.

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

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 | MUC4 | MUC4 | MUC4 | 8 | 0.88 | 0.034 | YES |
2 | B3GNT8 | B3GNT8 | B3GNT8 | 87 | 0.69 | 0.056 | YES |
3 | MUC15 | MUC15 | MUC15 | 121 | 0.65 | 0.079 | YES |
4 | ST6GALNAC2 | ST6GALNAC2 | ST6GALNAC2 | 133 | 0.64 | 0.1 | YES |
5 | B3GNT3 | B3GNT3 | B3GNT3 | 139 | 0.64 | 0.13 | YES |
6 | MUC16 | MUC16 | MUC16 | 158 | 0.62 | 0.15 | YES |
7 | GALNT5 | GALNT5 | GALNT5 | 238 | 0.55 | 0.17 | YES |
8 | GCNT3 | GCNT3 | GCNT3 | 272 | 0.53 | 0.18 | YES |
9 | GALNT14 | GALNT14 | GALNT14 | 284 | 0.52 | 0.2 | YES |
10 | FAM153A | FAM153A | FAM153A | 473 | 0.45 | 0.21 | YES |
11 | GALNT6 | GALNT6 | GALNT6 | 479 | 0.45 | 0.23 | YES |
12 | SEMA6D | SEMA6D | SEMA6D | 634 | 0.41 | 0.24 | YES |
13 | ST8SIA3 | ST8SIA3 | ST8SIA3 | 710 | 0.4 | 0.25 | YES |
14 | MUC21 | MUC21 | MUC21 | 772 | 0.39 | 0.26 | YES |
15 | MGAT3 | MGAT3 | MGAT3 | 827 | 0.38 | 0.27 | YES |
16 | GALNT9 | GALNT9 | GALNT9 | 1008 | 0.35 | 0.27 | YES |
17 | MUC12 | MUC12 | MUC12 | 1030 | 0.35 | 0.28 | YES |
18 | MUC5B | MUC5B | MUC5B | 1034 | 0.35 | 0.3 | YES |
19 | ST6GALNAC4 | ST6GALNAC4 | ST6GALNAC4 | 1190 | 0.33 | 0.3 | YES |
20 | ARSE | ARSE | ARSE | 1212 | 0.32 | 0.31 | YES |
21 | GCNT4 | GCNT4 | GCNT4 | 1469 | 0.3 | 0.31 | YES |
22 | MUC13 | MUC13 | MUC13 | 1623 | 0.28 | 0.31 | YES |
23 | KIFC3 | KIFC3 | KIFC3 | 1678 | 0.28 | 0.32 | YES |
24 | MGAT4C | MGAT4C | MGAT4C | 1892 | 0.26 | 0.32 | YES |
25 | ARSJ | ARSJ | ARSJ | 1959 | 0.26 | 0.32 | YES |
26 | TUBA4A | TUBA4A | TUBA4A | 1963 | 0.26 | 0.33 | YES |
27 | B3GNT9 | B3GNT9 | B3GNT9 | 2067 | 0.25 | 0.34 | YES |
28 | B3GNT7 | B3GNT7 | B3GNT7 | 2274 | 0.23 | 0.34 | YES |
29 | ARSF | ARSF | ARSF | 2357 | 0.22 | 0.34 | YES |
30 | B3GNT5 | B3GNT5 | B3GNT5 | 2434 | 0.22 | 0.34 | YES |
31 | PLAUR | PLAUR | PLAUR | 2553 | 0.21 | 0.34 | YES |
32 | SPHK1 | SPHK1 | SPHK1 | 2676 | 0.2 | 0.35 | YES |
33 | F10 | F10 | F10 | 2715 | 0.2 | 0.35 | YES |
34 | F7 | F7 | F7 | 2739 | 0.2 | 0.36 | YES |
35 | GALNT8 | GALNT8 | GALNT8 | 2745 | 0.2 | 0.36 | YES |
36 | MUC17 | MUC17 | MUC17 | 3037 | 0.18 | 0.36 | NO |
37 | GFPT2 | GFPT2 | GFPT2 | 3042 | 0.18 | 0.36 | NO |
38 | ST6GALNAC3 | ST6GALNAC3 | ST6GALNAC3 | 3201 | 0.17 | 0.36 | NO |
39 | TUBB2B | TUBB2B | TUBB2B | 3434 | 0.16 | 0.35 | NO |
40 | PGAP1 | PGAP1 | PGAP1 | 3492 | 0.16 | 0.36 | NO |
41 | ARSI | ARSI | ARSI | 3971 | 0.14 | 0.33 | NO |
42 | ST3GAL2 | ST3GAL2 | ST3GAL2 | 4438 | 0.12 | 0.31 | NO |
43 | RPL21 | RPL21 | RPL21 | 4589 | 0.11 | 0.31 | NO |
44 | SLC25A12 | SLC25A12 | SLC25A12 | 4728 | 0.1 | 0.3 | NO |
45 | TUBB6 | TUBB6 | TUBB6 | 4794 | 0.1 | 0.3 | NO |
46 | TUBA1A | TUBA1A | TUBA1A | 5119 | 0.09 | 0.29 | NO |
47 | ST6GAL1 | ST6GAL1 | ST6GAL1 | 5397 | 0.082 | 0.28 | NO |
48 | MAN1A1 | MAN1A1 | MAN1A1 | 5489 | 0.078 | 0.28 | NO |
49 | SEC23A | SEC23A | SEC23A | 5601 | 0.074 | 0.27 | NO |
50 | B4GALT1 | B4GALT1 | B4GALT1 | 5816 | 0.068 | 0.26 | NO |
51 | GALNTL1 | GALNTL1 | GALNTL1 | 5853 | 0.068 | 0.26 | NO |
52 | RPS27 | RPS27 | RPS27 | 5951 | 0.065 | 0.26 | NO |
53 | WBSCR17 | WBSCR17 | WBSCR17 | 6039 | 0.062 | 0.26 | NO |
54 | B3GNT2 | B3GNT2 | B3GNT2 | 6074 | 0.062 | 0.26 | NO |
55 | PROS1 | PROS1 | PROS1 | 6083 | 0.061 | 0.26 | NO |
56 | USP11 | USP11 | USP11 | 6106 | 0.061 | 0.26 | NO |
57 | TAZ | TAZ | TAZ | 6114 | 0.06 | 0.26 | NO |
58 | GALNTL4 | GALNTL4 | GALNTL4 | 6347 | 0.055 | 0.25 | NO |
59 | GSPT2 | GSPT2 | GSPT2 | 6452 | 0.052 | 0.25 | NO |
60 | GALNT12 | GALNT12 | GALNT12 | 6605 | 0.049 | 0.24 | NO |
61 | B4GALT5 | B4GALT5 | B4GALT5 | 6683 | 0.048 | 0.24 | NO |
62 | STS | STS | STS | 6830 | 0.045 | 0.23 | NO |
63 | ACTB | ACTB | ACTB | 6909 | 0.043 | 0.23 | NO |
64 | LDHD | LDHD | LDHD | 6949 | 0.042 | 0.23 | NO |
65 | EIF5A2 | EIF5A2 | EIF5A2 | 6998 | 0.042 | 0.23 | NO |
66 | MGAT1 | MGAT1 | MGAT1 | 7055 | 0.041 | 0.23 | NO |
67 | ST3GAL1 | ST3GAL1 | ST3GAL1 | 7145 | 0.039 | 0.22 | NO |
68 | PFDN5 | PFDN5 | PFDN5 | 7183 | 0.038 | 0.22 | NO |
69 | TUBB1 | TUBB1 | TUBB1 | 7215 | 0.038 | 0.22 | NO |
70 | FUT8 | FUT8 | FUT8 | 7250 | 0.037 | 0.22 | NO |
71 | FBXW7 | FBXW7 | FBXW7 | 7320 | 0.036 | 0.22 | NO |
72 | C1GALT1 | C1GALT1 | C1GALT1 | 7499 | 0.034 | 0.21 | NO |
73 | FBXW4 | FBXW4 | FBXW4 | 7638 | 0.032 | 0.2 | NO |
74 | TUBA3D | TUBA3D | TUBA3D | 7862 | 0.028 | 0.19 | NO |
75 | FURIN | FURIN | FURIN | 7914 | 0.028 | 0.19 | NO |
76 | PROC | PROC | PROC | 7953 | 0.027 | 0.19 | NO |
77 | EIF3G | EIF3G | EIF3G | 7972 | 0.027 | 0.19 | NO |
78 | RPS28 | RPS28 | RPS28 | 8002 | 0.027 | 0.19 | NO |
79 | MAN1C1 | MAN1C1 | MAN1C1 | 8166 | 0.024 | 0.18 | NO |
80 | B4GALT4 | B4GALT4 | B4GALT4 | 8211 | 0.024 | 0.18 | NO |
81 | PIGB | PIGB | PIGB | 8258 | 0.023 | 0.18 | NO |
82 | ARSK | ARSK | ARSK | 8264 | 0.023 | 0.18 | NO |
83 | HSCB | HSCB | HSCB | 8316 | 0.022 | 0.18 | NO |
84 | RPS12 | RPS12 | RPS12 | 8385 | 0.021 | 0.17 | NO |
85 | PIGC | PIGC | PIGC | 8595 | 0.019 | 0.16 | NO |
86 | RPL13 | RPL13 | RPL13 | 8601 | 0.019 | 0.16 | NO |
87 | EIF3K | EIF3K | EIF3K | 8606 | 0.019 | 0.16 | NO |
88 | TUBA3C | TUBA3C | TUBA3C | 8633 | 0.018 | 0.16 | NO |
89 | EEF1B2 | EEF1B2 | EEF1B2 | 8649 | 0.018 | 0.16 | NO |
90 | DOHH | DOHH | DOHH | 8759 | 0.017 | 0.16 | NO |
91 | RPS9 | RPS9 | RPS9 | 8767 | 0.017 | 0.16 | NO |
92 | ETF1 | ETF1 | ETF1 | 8832 | 0.016 | 0.16 | NO |
93 | B4GALT6 | B4GALT6 | B4GALT6 | 8924 | 0.015 | 0.15 | NO |
94 | RPL34 | RPL34 | RPL34 | 8977 | 0.015 | 0.15 | NO |
95 | PIGS | PIGS | PIGS | 8985 | 0.015 | 0.15 | NO |
96 | FAU | FAU | FAU | 9025 | 0.014 | 0.15 | NO |
97 | ARSB | ARSB | ARSB | 9029 | 0.014 | 0.15 | NO |
98 | EIF3F | EIF3F | EIF3F | 9070 | 0.014 | 0.14 | NO |
99 | EEF1D | EEF1D | EEF1D | 9131 | 0.013 | 0.14 | NO |
100 | SLC25A4 | SLC25A4 | SLC25A4 | 9137 | 0.013 | 0.14 | NO |
101 | GALNT2 | GALNT2 | GALNT2 | 9195 | 0.012 | 0.14 | NO |
102 | FXC1 | FXC1 | FXC1 | 9204 | 0.012 | 0.14 | NO |
103 | EEF1A1 | EEF1A1 | EEF1A1 | 9227 | 0.012 | 0.14 | NO |
104 | RPL11 | RPL11 | RPL11 | 9236 | 0.012 | 0.14 | NO |
105 | TBCC | TBCC | TBCC | 9269 | 0.012 | 0.14 | NO |
106 | FBXL3 | FBXL3 | FBXL3 | 9273 | 0.012 | 0.14 | NO |
107 | FKBP9 | FKBP9 | FKBP9 | 9303 | 0.011 | 0.14 | NO |
108 | RPL10A | RPL10A | RPL10A | 9456 | 0.0099 | 0.13 | NO |
109 | RPS20 | RPS20 | RPS20 | 9461 | 0.0098 | 0.13 | NO |
110 | DPM1 | DPM1 | DPM1 | 9519 | 0.0093 | 0.13 | NO |
111 | GALNTL2 | GALNTL2 | GALNTL2 | 9572 | 0.0088 | 0.12 | NO |
112 | PIGQ | PIGQ | PIGQ | 9591 | 0.0085 | 0.12 | NO |
113 | RPS19 | RPS19 | RPS19 | 9640 | 0.008 | 0.12 | NO |
114 | RPL17 | RPL17 | RPL17 | 9667 | 0.0078 | 0.12 | NO |
115 | RPL10 | RPL10 | RPL10 | 9748 | 0.007 | 0.12 | NO |
116 | RPLP1 | RPLP1 | RPLP1 | 9750 | 0.007 | 0.12 | NO |
117 | C18orf55 | C18orf55 | C18orf55 | 9751 | 0.007 | 0.12 | NO |
118 | B3GNT4 | B3GNT4 | B3GNT4 | 9797 | 0.0066 | 0.11 | NO |
119 | RPLP2 | RPLP2 | RPLP2 | 9850 | 0.006 | 0.11 | NO |
120 | RPS27A | RPS27A | RPS27A | 9873 | 0.0058 | 0.11 | NO |
121 | TOMM7 | TOMM7 | TOMM7 | 9899 | 0.0055 | 0.11 | NO |
122 | GMPPA | GMPPA | GMPPA | 9959 | 0.0049 | 0.1 | NO |
123 | PIGA | PIGA | PIGA | 10016 | 0.0044 | 0.1 | NO |
124 | ALG5 | ALG5 | ALG5 | 10055 | 0.004 | 0.1 | NO |
125 | SEC61A2 | SEC61A2 | SEC61A2 | 10062 | 0.004 | 0.1 | NO |
126 | TIMM22 | TIMM22 | TIMM22 | 10117 | 0.0034 | 0.097 | NO |
127 | FBXW5 | FBXW5 | FBXW5 | 10236 | 0.0022 | 0.091 | NO |
128 | TIMM44 | TIMM44 | TIMM44 | 10249 | 0.0021 | 0.09 | NO |
129 | UBA52 | UBA52 | UBA52 | 10270 | 0.002 | 0.089 | NO |
130 | RPS3 | RPS3 | RPS3 | 10282 | 0.0019 | 0.088 | NO |
131 | RPS14 | RPS14 | RPS14 | 10352 | 0.0014 | 0.085 | NO |
132 | RPL5 | RPL5 | RPL5 | 10366 | 0.0012 | 0.084 | NO |
133 | EIF3D | EIF3D | EIF3D | 10387 | 0.0011 | 0.083 | NO |
134 | EIF5 | EIF5 | EIF5 | 10423 | 0.00084 | 0.081 | NO |
135 | SRP68 | SRP68 | SRP68 | 10431 | 0.00078 | 0.08 | NO |
136 | RPS21 | RPS21 | RPS21 | 10465 | 0.00048 | 0.079 | NO |
137 | RPS23 | RPS23 | RPS23 | 10485 | 0.00033 | 0.078 | NO |
138 | GFER | GFER | GFER | 10496 | 0.00028 | 0.077 | NO |
139 | EDEM2 | EDEM2 | EDEM2 | 10498 | 0.00026 | 0.077 | NO |
140 | RPS4X | RPS4X | RPS4X | 10519 | 0.000026 | 0.076 | NO |
141 | RPL35 | RPL35 | RPL35 | 10531 | -0.00014 | 0.075 | NO |
142 | RPS11 | RPS11 | RPS11 | 10613 | -0.00085 | 0.071 | NO |
143 | VKORC1 | VKORC1 | VKORC1 | 10620 | -0.00091 | 0.07 | NO |
144 | RPL22 | RPL22 | RPL22 | 10665 | -0.0013 | 0.068 | NO |
145 | SUMF2 | SUMF2 | SUMF2 | 10666 | -0.0013 | 0.068 | NO |
146 | RPL27A | RPL27A | RPL27A | 10669 | -0.0013 | 0.068 | NO |
147 | EEF1G | EEF1G | EEF1G | 10693 | -0.0016 | 0.067 | NO |
148 | F2 | F2 | F2 | 10700 | -0.0016 | 0.067 | NO |
149 | DPM3 | DPM3 | DPM3 | 10715 | -0.0017 | 0.066 | NO |
150 | ATP5A1 | ATP5A1 | ATP5A1 | 10722 | -0.0018 | 0.066 | NO |
151 | RPL18 | RPL18 | RPL18 | 10741 | -0.002 | 0.065 | NO |
152 | RPL18A | RPL18A | RPL18A | 10773 | -0.0023 | 0.063 | NO |
153 | RPS3A | RPS3A | RPS3A | 10832 | -0.0029 | 0.06 | NO |
154 | RPS29 | RPS29 | RPS29 | 10848 | -0.003 | 0.059 | NO |
155 | SRP14 | SRP14 | SRP14 | 10873 | -0.0033 | 0.058 | NO |
156 | RPL23A | RPL23A | RPL23A | 10931 | -0.0038 | 0.055 | NO |
157 | RPL3 | RPL3 | RPL3 | 10991 | -0.0042 | 0.052 | NO |
158 | RPS16 | RPS16 | RPS16 | 10993 | -0.0042 | 0.052 | NO |
159 | RPL26 | RPL26 | RPL26 | 10997 | -0.0043 | 0.052 | NO |
160 | RPS5 | RPS5 | RPS5 | 11010 | -0.0044 | 0.051 | NO |
161 | RPL41 | RPL41 | RPL41 | 11046 | -0.0046 | 0.05 | NO |
162 | TBCB | TBCB | TBCB | 11050 | -0.0046 | 0.05 | NO |
163 | PIGT | PIGT | PIGT | 11070 | -0.0048 | 0.049 | NO |
164 | EIF2B2 | EIF2B2 | EIF2B2 | 11114 | -0.0051 | 0.046 | NO |
165 | RPS10 | RPS10 | RPS10 | 11131 | -0.0052 | 0.046 | NO |
166 | EIF4A2 | EIF4A2 | EIF4A2 | 11163 | -0.0056 | 0.044 | NO |
167 | RPS25 | RPS25 | RPS25 | 11170 | -0.0056 | 0.044 | NO |
168 | RFT1 | RFT1 | RFT1 | 11171 | -0.0056 | 0.044 | NO |
169 | RPS24 | RPS24 | RPS24 | 11247 | -0.0062 | 0.04 | NO |
170 | RPS17 | RPS17 | RPS17 | 11249 | -0.0063 | 0.04 | NO |
171 | PIGL | PIGL | PIGL | 11335 | -0.0068 | 0.036 | NO |
172 | RPL13A | RPL13A | RPL13A | 11370 | -0.0072 | 0.034 | NO |
173 | SEC11C | SEC11C | SEC11C | 11408 | -0.0075 | 0.033 | NO |
174 | RPS8 | RPS8 | RPS8 | 11412 | -0.0075 | 0.033 | NO |
175 | EIF4H | EIF4H | EIF4H | 11414 | -0.0076 | 0.033 | NO |
176 | MAN1B1 | MAN1B1 | MAN1B1 | 11427 | -0.0076 | 0.033 | NO |
177 | RPL15 | RPL15 | RPL15 | 11450 | -0.0078 | 0.032 | NO |
178 | RPL4 | RPL4 | RPL4 | 11484 | -0.0081 | 0.03 | NO |
179 | RPL19 | RPL19 | RPL19 | 11487 | -0.0081 | 0.03 | NO |
180 | TUBA1B | TUBA1B | TUBA1B | 11497 | -0.0082 | 0.03 | NO |
181 | RPL35A | RPL35A | RPL35A | 11505 | -0.0082 | 0.03 | NO |
182 | ALG12 | ALG12 | ALG12 | 11510 | -0.0083 | 0.03 | NO |
183 | DAD1 | DAD1 | DAD1 | 11511 | -0.0083 | 0.03 | NO |
184 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 11518 | -0.0084 | 0.03 | NO |
185 | RPL38 | RPL38 | RPL38 | 11540 | -0.0086 | 0.03 | NO |
186 | RPL8 | RPL8 | RPL8 | 11599 | -0.0091 | 0.027 | NO |
187 | PMPCA | PMPCA | PMPCA | 11620 | -0.0093 | 0.026 | NO |
188 | RPS15 | RPS15 | RPS15 | 11651 | -0.0095 | 0.025 | NO |
189 | FXN | FXN | FXN | 11675 | -0.0097 | 0.024 | NO |
190 | RPL32 | RPL32 | RPL32 | 11678 | -0.0097 | 0.024 | NO |
191 | SRP19 | SRP19 | SRP19 | 11681 | -0.0097 | 0.024 | NO |
192 | EIF2B1 | EIF2B1 | EIF2B1 | 11687 | -0.0098 | 0.024 | NO |
193 | IDH3G | IDH3G | IDH3G | 11756 | -0.01 | 0.021 | NO |
194 | SAMM50 | SAMM50 | SAMM50 | 11802 | -0.011 | 0.019 | NO |
195 | RPL36 | RPL36 | RPL36 | 11842 | -0.011 | 0.017 | NO |
196 | RPL28 | RPL28 | RPL28 | 11863 | -0.011 | 0.016 | NO |
197 | RPL24 | RPL24 | RPL24 | 11879 | -0.012 | 0.016 | NO |
198 | EIF2B5 | EIF2B5 | EIF2B5 | 11892 | -0.012 | 0.016 | NO |
199 | PRKCSH | PRKCSH | PRKCSH | 11895 | -0.012 | 0.016 | NO |
200 | RPSAP9 | RPSAP9 | RPSAP9 | 11929 | -0.012 | 0.015 | NO |
201 | RPS13 | RPS13 | RPS13 | 11956 | -0.012 | 0.014 | NO |
202 | RPS6 | RPS6 | RPS6 | 11974 | -0.012 | 0.013 | NO |
203 | RPS15A | RPS15A | RPS15A | 11991 | -0.012 | 0.013 | NO |
204 | RPL31 | RPL31 | RPL31 | 11993 | -0.012 | 0.013 | NO |
205 | ALG1 | ALG1 | ALG1 | 11995 | -0.012 | 0.014 | NO |
206 | SPCS2 | SPCS2 | SPCS2 | 12039 | -0.013 | 0.012 | NO |
207 | B4GALT2 | B4GALT2 | B4GALT2 | 12101 | -0.013 | 0.0087 | NO |
208 | PIGG | PIGG | PIGG | 12110 | -0.013 | 0.0088 | NO |
209 | ALG13 | ALG13 | ALG13 | 12155 | -0.014 | 0.0069 | NO |
210 | RPL6 | RPL6 | RPL6 | 12216 | -0.014 | 0.004 | NO |
211 | RPL14 | RPL14 | RPL14 | 12222 | -0.014 | 0.0043 | NO |
212 | UGGT1 | UGGT1 | UGGT1 | 12234 | -0.014 | 0.0042 | NO |
213 | LOC653566 | LOC653566 | LOC653566 | 12299 | -0.015 | 0.0012 | NO |
214 | RPSA | RPSA | RPSA | 12329 | -0.015 | 0.00018 | NO |
215 | TOMM22 | TOMM22 | TOMM22 | 12330 | -0.015 | 0.00076 | NO |
216 | TIMM9 | TIMM9 | TIMM9 | 12335 | -0.015 | 0.0011 | NO |
217 | RPL37 | RPL37 | RPL37 | 12365 | -0.016 | 0.000082 | NO |
218 | SEC13 | SEC13 | SEC13 | 12403 | -0.016 | -0.0014 | NO |
219 | SEC11A | SEC11A | SEC11A | 12420 | -0.016 | -0.0017 | NO |
220 | EIF5A | EIF5A | EIF5A | 12422 | -0.016 | -0.0011 | NO |
221 | GALNT10 | GALNT10 | GALNT10 | 12428 | -0.016 | -0.00079 | NO |
222 | TIMM17A | TIMM17A | TIMM17A | 12447 | -0.016 | -0.0012 | NO |
223 | TIMM50 | TIMM50 | TIMM50 | 12463 | -0.016 | -0.0014 | NO |
224 | EIF4B | EIF4B | EIF4B | 12474 | -0.016 | -0.0013 | NO |
225 | RPL37A | RPL37A | RPL37A | 12485 | -0.016 | -0.0012 | NO |
226 | BCS1L | BCS1L | BCS1L | 12529 | -0.017 | -0.003 | NO |
227 | PFDN1 | PFDN1 | PFDN1 | 12544 | -0.017 | -0.0032 | NO |
228 | DOLK | DOLK | DOLK | 12587 | -0.017 | -0.0048 | NO |
229 | ARSA | ARSA | ARSA | 12596 | -0.017 | -0.0046 | NO |
230 | RPL12 | RPL12 | RPL12 | 12610 | -0.018 | -0.0047 | NO |
231 | RPL27 | RPL27 | RPL27 | 12627 | -0.018 | -0.0049 | NO |
232 | GMPPB | GMPPB | GMPPB | 12629 | -0.018 | -0.0043 | NO |
233 | TBCD | TBCD | TBCD | 12646 | -0.018 | -0.0045 | NO |
234 | PIGF | PIGF | PIGF | 12655 | -0.018 | -0.0043 | NO |
235 | RPL39 | RPL39 | RPL39 | 12666 | -0.018 | -0.0041 | NO |
236 | SPCS3 | SPCS3 | SPCS3 | 12694 | -0.018 | -0.005 | NO |
237 | MTX1 | MTX1 | MTX1 | 12698 | -0.018 | -0.0044 | NO |
238 | SSR4 | SSR4 | SSR4 | 12703 | -0.018 | -0.004 | NO |
239 | GPAA1 | GPAA1 | GPAA1 | 12713 | -0.018 | -0.0038 | NO |
240 | RPS2 | RPS2 | RPS2 | 12721 | -0.018 | -0.0034 | NO |
241 | PREB | PREB | PREB | 12729 | -0.018 | -0.0031 | NO |
242 | RPLP0 | RPLP0 | RPLP0 | 12732 | -0.018 | -0.0025 | NO |
243 | ALG2 | ALG2 | ALG2 | 12741 | -0.019 | -0.0022 | NO |
244 | COQ2 | COQ2 | COQ2 | 12775 | -0.019 | -0.0034 | NO |
245 | RPL23 | RPL23 | RPL23 | 12783 | -0.019 | -0.003 | NO |
246 | CHCHD4 | CHCHD4 | CHCHD4 | 12795 | -0.019 | -0.0029 | NO |
247 | ARFGEF2 | ARFGEF2 | ARFGEF2 | 12799 | -0.019 | -0.0024 | NO |
248 | EIF2S2 | EIF2S2 | EIF2S2 | 12829 | -0.019 | -0.0033 | NO |
249 | PROZ | PROZ | PROZ | 12850 | -0.02 | -0.0036 | NO |
250 | MOGS | MOGS | MOGS | 12859 | -0.02 | -0.0033 | NO |
251 | MCFD2 | MCFD2 | MCFD2 | 12888 | -0.02 | -0.0041 | NO |
252 | PIGV | PIGV | PIGV | 12906 | -0.02 | -0.0043 | NO |
253 | RPN1 | RPN1 | RPN1 | 12916 | -0.02 | -0.0041 | NO |
254 | PFDN2 | PFDN2 | PFDN2 | 12918 | -0.02 | -0.0034 | NO |
255 | DPM2 | DPM2 | DPM2 | 12926 | -0.02 | -0.003 | NO |
256 | FBXO6 | FBXO6 | FBXO6 | 12977 | -0.021 | -0.005 | NO |
257 | RPL30 | RPL30 | RPL30 | 13017 | -0.021 | -0.0064 | NO |
258 | PIGU | PIGU | PIGU | 13023 | -0.021 | -0.0058 | NO |
259 | SEC24B | SEC24B | SEC24B | 13029 | -0.021 | -0.0053 | NO |
260 | TIMM17B | TIMM17B | TIMM17B | 13041 | -0.021 | -0.0051 | NO |
261 | ACO2 | ACO2 | ACO2 | 13049 | -0.021 | -0.0047 | NO |
262 | RPL29 | RPL29 | RPL29 | 13063 | -0.021 | -0.0046 | NO |
263 | TUBA1C | TUBA1C | TUBA1C | 13064 | -0.021 | -0.0038 | NO |
264 | FBXL5 | FBXL5 | FBXL5 | 13096 | -0.022 | -0.0047 | NO |
265 | FBXW2 | FBXW2 | FBXW2 | 13105 | -0.022 | -0.0043 | NO |
266 | EIF2B3 | EIF2B3 | EIF2B3 | 13143 | -0.022 | -0.0055 | NO |
267 | EIF3E | EIF3E | EIF3E | 13156 | -0.022 | -0.0054 | NO |
268 | XRN2 | XRN2 | XRN2 | 13168 | -0.022 | -0.0051 | NO |
269 | RPL7 | RPL7 | RPL7 | 13170 | -0.022 | -0.0043 | NO |
270 | PIGN | PIGN | PIGN | 13228 | -0.023 | -0.0066 | NO |
271 | EIF2S1 | EIF2S1 | EIF2S1 | 13279 | -0.023 | -0.0086 | NO |
272 | RPS18 | RPS18 | RPS18 | 13301 | -0.024 | -0.0088 | NO |
273 | SSR1 | SSR1 | SSR1 | 13311 | -0.024 | -0.0084 | NO |
274 | GGCX | GGCX | GGCX | 13312 | -0.024 | -0.0075 | NO |
275 | LMAN1 | LMAN1 | LMAN1 | 13333 | -0.024 | -0.0077 | NO |
276 | EDEM1 | EDEM1 | EDEM1 | 13359 | -0.024 | -0.0082 | NO |
277 | EIF3H | EIF3H | EIF3H | 13391 | -0.024 | -0.009 | NO |
278 | GRPEL1 | GRPEL1 | GRPEL1 | 13402 | -0.025 | -0.0086 | NO |
279 | TRAM1 | TRAM1 | TRAM1 | 13403 | -0.025 | -0.0077 | NO |
280 | RPN2 | RPN2 | RPN2 | 13404 | -0.025 | -0.0067 | NO |
281 | EIF2S3 | EIF2S3 | EIF2S3 | 13420 | -0.025 | -0.0066 | NO |
282 | RPS7 | RPS7 | RPS7 | 13428 | -0.025 | -0.0061 | NO |
283 | GALNT1 | GALNT1 | GALNT1 | 13436 | -0.025 | -0.0055 | NO |
284 | MUCL1 | MUCL1 | MUCL1 | 13486 | -0.025 | -0.0073 | NO |
285 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 13513 | -0.026 | -0.0078 | NO |
286 | PIGO | PIGO | PIGO | 13543 | -0.026 | -0.0084 | NO |
287 | SEC61A1 | SEC61A1 | SEC61A1 | 13575 | -0.026 | -0.0091 | NO |
288 | GANAB | GANAB | GANAB | 13598 | -0.026 | -0.0093 | NO |
289 | KIF13A | KIF13A | KIF13A | 13601 | -0.026 | -0.0084 | NO |
290 | SSR2 | SSR2 | SSR2 | 13606 | -0.027 | -0.0076 | NO |
291 | FBXO4 | FBXO4 | FBXO4 | 13641 | -0.027 | -0.0085 | NO |
292 | DPAGT1 | DPAGT1 | DPAGT1 | 13674 | -0.027 | -0.0092 | NO |
293 | EIF2B4 | EIF2B4 | EIF2B4 | 13676 | -0.027 | -0.0083 | NO |
294 | SRPR | SRPR | SRPR | 13687 | -0.028 | -0.0078 | NO |
295 | CS | CS | CS | 13703 | -0.028 | -0.0076 | NO |
296 | NOP56 | NOP56 | NOP56 | 13718 | -0.028 | -0.0073 | NO |
297 | SPCS1 | SPCS1 | SPCS1 | 13733 | -0.028 | -0.007 | NO |
298 | EIF1AX | EIF1AX | EIF1AX | 13757 | -0.028 | -0.0072 | NO |
299 | EIF3A | EIF3A | EIF3A | 13764 | -0.028 | -0.0065 | NO |
300 | EIF4A1 | EIF4A1 | EIF4A1 | 13768 | -0.028 | -0.0056 | NO |
301 | CCT4 | CCT4 | CCT4 | 13777 | -0.028 | -0.0049 | NO |
302 | TIMM13 | TIMM13 | TIMM13 | 13782 | -0.028 | -0.004 | NO |
303 | SEC24C | SEC24C | SEC24C | 13840 | -0.029 | -0.0062 | NO |
304 | SRP9 | SRP9 | SRP9 | 13854 | -0.029 | -0.0058 | NO |
305 | SEC24D | SEC24D | SEC24D | 13875 | -0.029 | -0.0058 | NO |
306 | RPS26 | RPS26 | RPS26 | 13891 | -0.029 | -0.0055 | NO |
307 | TOMM5 | TOMM5 | TOMM5 | 13928 | -0.03 | -0.0064 | NO |
308 | TBCA | TBCA | TBCA | 13962 | -0.03 | -0.0071 | NO |
309 | EIF5B | EIF5B | EIF5B | 13965 | -0.03 | -0.006 | NO |
310 | RPL7A | RPL7A | RPL7A | 13970 | -0.03 | -0.0051 | NO |
311 | EIF3B | EIF3B | EIF3B | 13983 | -0.03 | -0.0046 | NO |
312 | SLC25A6 | SLC25A6 | SLC25A6 | 14006 | -0.031 | -0.0047 | NO |
313 | VDAC1 | VDAC1 | VDAC1 | 14007 | -0.031 | -0.0035 | NO |
314 | TOMM40 | TOMM40 | TOMM40 | 14038 | -0.031 | -0.004 | NO |
315 | PFDN6 | PFDN6 | PFDN6 | 14054 | -0.031 | -0.0036 | NO |
316 | UGGT2 | UGGT2 | UGGT2 | 14058 | -0.031 | -0.0026 | NO |
317 | ALG9 | ALG9 | ALG9 | 14090 | -0.031 | -0.0032 | NO |
318 | CCT7 | CCT7 | CCT7 | 14099 | -0.032 | -0.0024 | NO |
319 | PFDN4 | PFDN4 | PFDN4 | 14113 | -0.032 | -0.0019 | NO |
320 | SEC31A | SEC31A | SEC31A | 14122 | -0.032 | -0.0011 | NO |
321 | DHPS | DHPS | DHPS | 14153 | -0.032 | -0.0016 | NO |
322 | EIF3I | EIF3I | EIF3I | 14181 | -0.032 | -0.0019 | NO |
323 | AP3M1 | AP3M1 | AP3M1 | 14183 | -0.032 | -0.00069 | NO |
324 | MAN2A1 | MAN2A1 | MAN2A1 | 14222 | -0.033 | -0.0016 | NO |
325 | EEF2 | EEF2 | EEF2 | 14263 | -0.033 | -0.0025 | NO |
326 | SEC61B | SEC61B | SEC61B | 14286 | -0.033 | -0.0025 | NO |
327 | ATP5B | ATP5B | ATP5B | 14298 | -0.034 | -0.0018 | NO |
328 | SUMF1 | SUMF1 | SUMF1 | 14350 | -0.034 | -0.0034 | NO |
329 | C1GALT1C1 | C1GALT1C1 | C1GALT1C1 | 14357 | -0.034 | -0.0024 | NO |
330 | ALG3 | ALG3 | ALG3 | 14378 | -0.034 | -0.0022 | NO |
331 | MGAT5 | MGAT5 | MGAT5 | 14400 | -0.035 | -0.002 | NO |
332 | EIF4G1 | EIF4G1 | EIF4G1 | 14404 | -0.035 | -0.00089 | NO |
333 | TOMM20 | TOMM20 | TOMM20 | 14415 | -0.035 | -0.00012 | NO |
334 | DDOST | DDOST | DDOST | 14532 | -0.036 | -0.0052 | NO |
335 | DOLPP1 | DOLPP1 | DOLPP1 | 14574 | -0.037 | -0.0061 | NO |
336 | CYC1 | CYC1 | CYC1 | 14581 | -0.037 | -0.0051 | NO |
337 | MLEC | MLEC | MLEC | 14622 | -0.037 | -0.0059 | NO |
338 | ATP5G1 | ATP5G1 | ATP5G1 | 14736 | -0.038 | -0.011 | NO |
339 | PMM1 | PMM1 | PMM1 | 14742 | -0.039 | -0.0095 | NO |
340 | B3GNTL1 | B3GNTL1 | B3GNTL1 | 14743 | -0.039 | -0.0081 | NO |
341 | MPI | MPI | MPI | 14758 | -0.039 | -0.0074 | NO |
342 | MGAT4B | MGAT4B | MGAT4B | 14829 | -0.04 | -0.0098 | NO |
343 | TIMM10 | TIMM10 | TIMM10 | 14847 | -0.04 | -0.0092 | NO |
344 | PMM2 | PMM2 | PMM2 | 14874 | -0.04 | -0.0091 | NO |
345 | PDIA3 | PDIA3 | PDIA3 | 14892 | -0.04 | -0.0085 | NO |
346 | CALR | CALR | CALR | 14930 | -0.041 | -0.009 | NO |
347 | ALG11 | ALG11 | ALG11 | 14934 | -0.041 | -0.0076 | NO |
348 | HSPA9 | HSPA9 | HSPA9 | 14982 | -0.041 | -0.0087 | NO |
349 | MGAT2 | MGAT2 | MGAT2 | 14993 | -0.042 | -0.0076 | NO |
350 | EIF4E | EIF4E | EIF4E | 15074 | -0.043 | -0.01 | NO |
351 | STT3A | STT3A | STT3A | 15111 | -0.043 | -0.011 | NO |
352 | DNAJC19 | DNAJC19 | DNAJC19 | 15121 | -0.043 | -0.0097 | NO |
353 | MUC6 | MUC6 | MUC6 | 15132 | -0.043 | -0.0086 | NO |
354 | CANX | CANX | CANX | 15133 | -0.043 | -0.007 | NO |
355 | PMPCB | PMPCB | PMPCB | 15137 | -0.043 | -0.0055 | NO |
356 | SSR3 | SSR3 | SSR3 | 15165 | -0.044 | -0.0053 | NO |
357 | SRP72 | SRP72 | SRP72 | 15171 | -0.044 | -0.0039 | NO |
358 | CCT3 | CCT3 | CCT3 | 15182 | -0.044 | -0.0028 | NO |
359 | MUC2 | MUC2 | MUC2 | 15206 | -0.044 | -0.0024 | NO |
360 | MAN1A2 | MAN1A2 | MAN1A2 | 15212 | -0.044 | -0.00092 | NO |
361 | TIMM8A | TIMM8A | TIMM8A | 15307 | -0.046 | -0.0044 | NO |
362 | VBP1 | VBP1 | VBP1 | 15337 | -0.046 | -0.0043 | NO |
363 | SEC61G | SEC61G | SEC61G | 15351 | -0.047 | -0.0032 | NO |
364 | TCP1 | TCP1 | TCP1 | 15390 | -0.048 | -0.0035 | NO |
365 | CCT6A | CCT6A | CCT6A | 15403 | -0.048 | -0.0024 | NO |
366 | TBCE | TBCE | TBCE | 15457 | -0.049 | -0.0034 | NO |
367 | TIMM8B | TIMM8B | TIMM8B | 15492 | -0.05 | -0.0034 | NO |
368 | PIGK | PIGK | PIGK | 15502 | -0.05 | -0.002 | NO |
369 | ST8SIA6 | ST8SIA6 | ST8SIA6 | 15511 | -0.05 | -0.00055 | NO |
370 | B4GALT3 | B4GALT3 | B4GALT3 | 15532 | -0.051 | 0.00027 | NO |
371 | SRPRB | SRPRB | SRPRB | 15533 | -0.051 | 0.0022 | NO |
372 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 15543 | -0.051 | 0.0036 | NO |
373 | SRP54 | SRP54 | SRP54 | 15575 | -0.051 | 0.0039 | NO |
374 | CCT5 | CCT5 | CCT5 | 15582 | -0.051 | 0.0055 | NO |
375 | GALNT11 | GALNT11 | GALNT11 | 15599 | -0.052 | 0.0066 | NO |
376 | RPL26L1 | RPL26L1 | RPL26L1 | 15623 | -0.052 | 0.0073 | NO |
377 | RPL9 | RPL9 | RPL9 | 15651 | -0.052 | 0.0078 | NO |
378 | CCT8 | CCT8 | CCT8 | 15660 | -0.053 | 0.0094 | NO |
379 | PIGX | PIGX | PIGX | 15689 | -0.053 | 0.0098 | NO |
380 | PIGH | PIGH | PIGH | 15744 | -0.054 | 0.0089 | NO |
381 | PABPC1 | PABPC1 | PABPC1 | 15745 | -0.054 | 0.011 | NO |
382 | EIF3J | EIF3J | EIF3J | 15766 | -0.054 | 0.012 | NO |
383 | MANEA | MANEA | MANEA | 15803 | -0.055 | 0.012 | NO |
384 | PIGM | PIGM | PIGM | 15847 | -0.056 | 0.012 | NO |
385 | PIGP | PIGP | PIGP | 15887 | -0.057 | 0.012 | NO |
386 | CCT2 | CCT2 | CCT2 | 15905 | -0.057 | 0.013 | NO |
387 | ALG8 | ALG8 | ALG8 | 15983 | -0.059 | 0.011 | NO |
388 | ARSG | ARSG | ARSG | 16018 | -0.06 | 0.011 | NO |
389 | LONP2 | LONP2 | LONP2 | 16075 | -0.062 | 0.011 | NO |
390 | ALG14 | ALG14 | ALG14 | 16104 | -0.062 | 0.011 | NO |
391 | TOMM70A | TOMM70A | TOMM70A | 16149 | -0.063 | 0.011 | NO |
392 | PGM3 | PGM3 | PGM3 | 16224 | -0.065 | 0.0097 | NO |
393 | GRPEL2 | GRPEL2 | GRPEL2 | 16268 | -0.066 | 0.0098 | NO |
394 | COX17 | COX17 | COX17 | 16278 | -0.066 | 0.012 | NO |
395 | ALG10B | ALG10B | ALG10B | 16299 | -0.067 | 0.013 | NO |
396 | MTX2 | MTX2 | MTX2 | 16308 | -0.068 | 0.015 | NO |
397 | ALG10 | ALG10 | ALG10 | 16367 | -0.069 | 0.015 | NO |
398 | MGAT4A | MGAT4A | MGAT4A | 16383 | -0.07 | 0.017 | NO |
399 | SLC25A13 | SLC25A13 | SLC25A13 | 16465 | -0.072 | 0.015 | NO |
400 | ALG6 | ALG6 | ALG6 | 16519 | -0.074 | 0.015 | NO |
401 | HSPD1 | HSPD1 | HSPD1 | 16528 | -0.074 | 0.017 | NO |
402 | TUSC3 | TUSC3 | TUSC3 | 16671 | -0.08 | 0.012 | NO |
403 | GALNTL6 | GALNTL6 | GALNTL6 | 16719 | -0.082 | 0.013 | NO |
404 | SAR1B | SAR1B | SAR1B | 16732 | -0.082 | 0.015 | NO |
405 | GCNT1 | GCNT1 | GCNT1 | 16786 | -0.084 | 0.016 | NO |
406 | EIF3C | EIF3C | EIF3C | 17052 | -0.097 | 0.0044 | NO |
407 | GNPNAT1 | GNPNAT1 | GNPNAT1 | 17066 | -0.098 | 0.0074 | NO |
408 | GALNT13 | GALNT13 | GALNT13 | 17084 | -0.099 | 0.01 | NO |
409 | PIGW | PIGW | PIGW | 17123 | -0.1 | 0.012 | NO |
410 | GALNT7 | GALNT7 | GALNT7 | 17125 | -0.1 | 0.016 | NO |
411 | GALNT3 | GALNT3 | GALNT3 | 17130 | -0.1 | 0.02 | NO |
412 | ST8SIA2 | ST8SIA2 | ST8SIA2 | 17230 | -0.11 | 0.018 | NO |
413 | RPL36A | RPL36A | RPL36A | 17239 | -0.11 | 0.022 | NO |
414 | TUBB3 | TUBB3 | TUBB3 | 17259 | -0.11 | 0.025 | NO |
415 | EDEM3 | EDEM3 | EDEM3 | 17448 | -0.12 | 0.019 | NO |
416 | B3GNT6 | B3GNT6 | B3GNT6 | 17531 | -0.13 | 0.019 | NO |
417 | TUBB2A | TUBB2A | TUBB2A | 17662 | -0.14 | 0.018 | NO |
418 | ARSH | ARSH | ARSH | 17836 | -0.17 | 0.014 | NO |
419 | RPL3L | RPL3L | RPL3L | 18160 | -0.24 | 0.0054 | NO |
Figure S71. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SELENOAMINO ACID METABOLISM.

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

Table 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 | GJB4 | GJB4 | GJB4 | 5 | 0.93 | 0.11 | YES |
2 | GJB5 | GJB5 | GJB5 | 10 | 0.87 | 0.22 | YES |
3 | GJB3 | GJB3 | GJB3 | 25 | 0.81 | 0.32 | YES |
4 | GJC2 | GJC2 | GJC2 | 381 | 0.48 | 0.36 | YES |
5 | GJA1 | GJA1 | GJA1 | 1672 | 0.28 | 0.32 | NO |
6 | GJA9 | GJA9 | GJA9 | 2597 | 0.21 | 0.3 | NO |
7 | DNM1 | DNM1 | DNM1 | 3307 | 0.17 | 0.28 | NO |
8 | GJB6 | GJB6 | GJB6 | 3515 | 0.16 | 0.29 | NO |
9 | CLTCL1 | CLTCL1 | CLTCL1 | 3829 | 0.14 | 0.29 | NO |
10 | GJC1 | GJC1 | GJC1 | 4216 | 0.12 | 0.28 | NO |
11 | VPS37D | VPS37D | VPS37D | 4585 | 0.11 | 0.27 | NO |
12 | TFRC | TFRC | TFRC | 4608 | 0.11 | 0.28 | NO |
13 | DNASE2 | DNASE2 | DNASE2 | 5104 | 0.091 | 0.27 | NO |
14 | GJB2 | GJB2 | GJB2 | 5191 | 0.088 | 0.28 | NO |
15 | SH3GL2 | SH3GL2 | SH3GL2 | 5368 | 0.082 | 0.28 | NO |
16 | GJB7 | GJB7 | GJB7 | 5544 | 0.077 | 0.28 | NO |
17 | SEC23A | SEC23A | SEC23A | 5601 | 0.074 | 0.28 | NO |
18 | AP1S2 | AP1S2 | AP1S2 | 5721 | 0.071 | 0.28 | NO |
19 | STX4 | STX4 | STX4 | 6036 | 0.063 | 0.27 | NO |
20 | ARRB1 | ARRB1 | ARRB1 | 6109 | 0.061 | 0.28 | NO |
21 | M6PR | M6PR | M6PR | 6149 | 0.06 | 0.28 | NO |
22 | CHMP4A | CHMP4A | CHMP4A | 6263 | 0.057 | 0.28 | NO |
23 | HIP1R | HIP1R | HIP1R | 6390 | 0.054 | 0.28 | NO |
24 | VAMP8 | VAMP8 | VAMP8 | 6632 | 0.049 | 0.28 | NO |
25 | CHMP7 | CHMP7 | CHMP7 | 6798 | 0.046 | 0.27 | NO |
26 | VPS36 | VPS36 | VPS36 | 6922 | 0.043 | 0.27 | NO |
27 | CHMP6 | CHMP6 | CHMP6 | 6939 | 0.043 | 0.28 | NO |
28 | GJA4 | GJA4 | GJA4 | 6970 | 0.042 | 0.28 | NO |
29 | FTH1 | FTH1 | FTH1 | 7136 | 0.039 | 0.27 | NO |
30 | AP4B1 | AP4B1 | AP4B1 | 7256 | 0.037 | 0.27 | NO |
31 | VAMP2 | VAMP2 | VAMP2 | 7459 | 0.034 | 0.26 | NO |
32 | SRC | SRC | SRC | 7608 | 0.032 | 0.26 | NO |
33 | CLTB | CLTB | CLTB | 7640 | 0.032 | 0.26 | NO |
34 | AP4E1 | AP4E1 | AP4E1 | 7648 | 0.031 | 0.27 | NO |
35 | DTNBP1 | DTNBP1 | DTNBP1 | 7825 | 0.029 | 0.26 | NO |
36 | GJA5 | GJA5 | GJA5 | 8215 | 0.024 | 0.24 | NO |
37 | ARFGAP1 | ARFGAP1 | ARFGAP1 | 8216 | 0.024 | 0.24 | NO |
38 | CTSZ | CTSZ | CTSZ | 8230 | 0.024 | 0.25 | NO |
39 | AP1B1 | AP1B1 | AP1B1 | 8357 | 0.022 | 0.24 | NO |
40 | BLOC1S1 | BLOC1S1 | BLOC1S1 | 8400 | 0.021 | 0.24 | NO |
41 | CHMP4B | CHMP4B | CHMP4B | 8438 | 0.021 | 0.24 | NO |
42 | VPS4B | VPS4B | VPS4B | 9033 | 0.014 | 0.21 | NO |
43 | VPS37B | VPS37B | VPS37B | 9144 | 0.013 | 0.21 | NO |
44 | GJA3 | GJA3 | GJA3 | 9237 | 0.012 | 0.2 | NO |
45 | TGOLN2 | TGOLN2 | TGOLN2 | 9284 | 0.012 | 0.2 | NO |
46 | VPS4A | VPS4A | VPS4A | 9414 | 0.01 | 0.2 | NO |
47 | FTL | FTL | FTL | 9520 | 0.0093 | 0.19 | NO |
48 | TPD52L1 | TPD52L1 | TPD52L1 | 9593 | 0.0085 | 0.19 | NO |
49 | AP2M1 | AP2M1 | AP2M1 | 9612 | 0.0082 | 0.19 | NO |
50 | AP1M1 | AP1M1 | AP1M1 | 9793 | 0.0066 | 0.18 | NO |
51 | RPS27A | RPS27A | RPS27A | 9873 | 0.0058 | 0.18 | NO |
52 | SNF8 | SNF8 | SNF8 | 10044 | 0.0041 | 0.17 | NO |
53 | SNX2 | SNX2 | SNX2 | 10174 | 0.0028 | 0.16 | NO |
54 | UBA52 | UBA52 | UBA52 | 10270 | 0.002 | 0.16 | NO |
55 | CHMP2A | CHMP2A | CHMP2A | 10367 | 0.0012 | 0.15 | NO |
56 | RAB5C | RAB5C | RAB5C | 10462 | 0.0005 | 0.15 | NO |
57 | DNM2 | DNM2 | DNM2 | 10508 | 0.00016 | 0.14 | NO |
58 | VPS28 | VPS28 | VPS28 | 10560 | -0.00038 | 0.14 | NO |
59 | SORT1 | SORT1 | SORT1 | 10677 | -0.0014 | 0.14 | NO |
60 | VPS37A | VPS37A | VPS37A | 10707 | -0.0017 | 0.13 | NO |
61 | HGS | HGS | HGS | 10726 | -0.0018 | 0.13 | NO |
62 | GAK | GAK | GAK | 10764 | -0.0022 | 0.13 | NO |
63 | CHMP2B | CHMP2B | CHMP2B | 10839 | -0.0029 | 0.13 | NO |
64 | CLTA | CLTA | CLTA | 10849 | -0.003 | 0.13 | NO |
65 | VPS25 | VPS25 | VPS25 | 10872 | -0.0033 | 0.13 | NO |
66 | SNX5 | SNX5 | SNX5 | 11032 | -0.0045 | 0.12 | NO |
67 | AP1G1 | AP1G1 | AP1G1 | 11091 | -0.005 | 0.12 | NO |
68 | CNO | CNO | CNO | 11292 | -0.0065 | 0.1 | NO |
69 | NAPA | NAPA | NAPA | 11564 | -0.0088 | 0.091 | NO |
70 | SH3D19 | SH3D19 | SH3D19 | 11566 | -0.0089 | 0.092 | NO |
71 | SNX9 | SNX9 | SNX9 | 11586 | -0.009 | 0.092 | NO |
72 | CHMP5 | CHMP5 | CHMP5 | 11696 | -0.0098 | 0.087 | NO |
73 | AP3B1 | AP3B1 | AP3B1 | 12199 | -0.014 | 0.061 | NO |
74 | SNAPIN | SNAPIN | SNAPIN | 12267 | -0.015 | 0.06 | NO |
75 | GNS | GNS | GNS | 12392 | -0.016 | 0.055 | NO |
76 | SEC13 | SEC13 | SEC13 | 12403 | -0.016 | 0.056 | NO |
77 | VTA1 | VTA1 | VTA1 | 12446 | -0.016 | 0.056 | NO |
78 | PUM1 | PUM1 | PUM1 | 12489 | -0.016 | 0.055 | NO |
79 | BLOC1S3 | BLOC1S3 | BLOC1S3 | 12499 | -0.017 | 0.057 | NO |
80 | PLDN | PLDN | PLDN | 12550 | -0.017 | 0.056 | NO |
81 | DAB2 | DAB2 | DAB2 | 12569 | -0.017 | 0.057 | NO |
82 | GBF1 | GBF1 | GBF1 | 12599 | -0.017 | 0.058 | NO |
83 | STAM2 | STAM2 | STAM2 | 12611 | -0.018 | 0.059 | NO |
84 | PREB | PREB | PREB | 12729 | -0.018 | 0.055 | NO |
85 | CPD | CPD | CPD | 12764 | -0.019 | 0.056 | NO |
86 | SEC24B | SEC24B | SEC24B | 13029 | -0.021 | 0.044 | NO |
87 | COPE | COPE | COPE | 13073 | -0.022 | 0.044 | NO |
88 | COPZ1 | COPZ1 | COPZ1 | 13079 | -0.022 | 0.046 | NO |
89 | IGF2R | IGF2R | IGF2R | 13120 | -0.022 | 0.047 | NO |
90 | AP3S1 | AP3S1 | AP3S1 | 13189 | -0.022 | 0.046 | NO |
91 | NECAP1 | NECAP1 | NECAP1 | 13356 | -0.024 | 0.04 | NO |
92 | SNAP23 | SNAP23 | SNAP23 | 13500 | -0.026 | 0.035 | NO |
93 | PIK3C2A | PIK3C2A | PIK3C2A | 13627 | -0.027 | 0.031 | NO |
94 | SEC24C | SEC24C | SEC24C | 13840 | -0.029 | 0.023 | NO |
95 | SEC24D | SEC24D | SEC24D | 13875 | -0.029 | 0.025 | NO |
96 | PICALM | PICALM | PICALM | 14010 | -0.031 | 0.021 | NO |
97 | TSG101 | TSG101 | TSG101 | 14053 | -0.031 | 0.023 | NO |
98 | SEC31A | SEC31A | SEC31A | 14122 | -0.032 | 0.023 | NO |
99 | ARF1 | ARF1 | ARF1 | 14179 | -0.032 | 0.024 | NO |
100 | ARCN1 | ARCN1 | ARCN1 | 14708 | -0.038 | -0.00082 | NO |
101 | STAM | STAM | STAM | 14790 | -0.039 | -0.00048 | NO |
102 | TBC1D8B | TBC1D8B | TBC1D8B | 14793 | -0.039 | 0.0042 | NO |
103 | GJD4 | GJD4 | GJD4 | 14990 | -0.042 | -0.0015 | NO |
104 | COPB1 | COPB1 | COPB1 | 15048 | -0.042 | 0.00053 | NO |
105 | TXNDC5 | TXNDC5 | TXNDC5 | 15119 | -0.043 | 0.002 | NO |
106 | AP1S1 | AP1S1 | AP1S1 | 15145 | -0.044 | 0.0059 | NO |
107 | HSPA8 | HSPA8 | HSPA8 | 15207 | -0.044 | 0.008 | NO |
108 | COPA | COPA | COPA | 15223 | -0.045 | 0.013 | NO |
109 | CLTC | CLTC | CLTC | 15447 | -0.049 | 0.0064 | NO |
110 | COPG | COPG | COPG | 15693 | -0.053 | -0.00062 | NO |
111 | COPB2 | COPB2 | COPB2 | 15844 | -0.056 | -0.002 | NO |
112 | VAMP7 | VAMP7 | VAMP7 | 16021 | -0.06 | -0.0043 | NO |
113 | TJP1 | TJP1 | TJP1 | 16055 | -0.061 | 0.0013 | NO |
114 | AP1M2 | AP1M2 | AP1M2 | 16195 | -0.064 | 0.0015 | NO |
115 | VPS37C | VPS37C | VPS37C | 16441 | -0.071 | -0.0032 | NO |
116 | OCRL | OCRL | OCRL | 16570 | -0.076 | -0.00099 | NO |
117 | SAR1B | SAR1B | SAR1B | 16732 | -0.082 | 0.00021 | NO |
118 | TPD52 | TPD52 | TPD52 | 16910 | -0.09 | 0.0015 | NO |
119 | MYO6 | MYO6 | MYO6 | 16995 | -0.094 | 0.0085 | NO |
120 | YIPF6 | YIPF6 | YIPF6 | 17269 | -0.11 | 0.007 | NO |
121 | CHMP4C | CHMP4C | CHMP4C | 17297 | -0.11 | 0.019 | NO |
122 | DNAJC6 | DNAJC6 | DNAJC6 | 17502 | -0.13 | 0.024 | NO |
123 | GJB1 | GJB1 | GJB1 | 17704 | -0.15 | 0.03 | NO |
Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLUTATHIONE METABOLISM.

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

Table 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 | CFTR | CFTR | CFTR | 39 | 0.77 | 0.16 | YES |
2 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 293 | 0.52 | 0.26 | YES |
3 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 692 | 0.4 | 0.32 | YES |
4 | ATP6V1G3 | ATP6V1G3 | ATP6V1G3 | 856 | 0.38 | 0.39 | YES |
5 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 1542 | 0.29 | 0.42 | YES |
6 | PRKCB | PRKCB | PRKCB | 1561 | 0.29 | 0.48 | YES |
7 | PLCG2 | PLCG2 | PLCG2 | 2173 | 0.24 | 0.49 | YES |
8 | TCIRG1 | TCIRG1 | TCIRG1 | 3061 | 0.18 | 0.48 | YES |
9 | ADCY3 | ADCY3 | ADCY3 | 3484 | 0.16 | 0.49 | YES |
10 | KCNQ1 | KCNQ1 | KCNQ1 | 4048 | 0.13 | 0.49 | YES |
11 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 4407 | 0.12 | 0.5 | YES |
12 | PRKCA | PRKCA | PRKCA | 5217 | 0.087 | 0.47 | NO |
13 | ADCY9 | ADCY9 | ADCY9 | 5813 | 0.068 | 0.45 | NO |
14 | ACTB | ACTB | ACTB | 6909 | 0.043 | 0.4 | NO |
15 | PRKX | PRKX | PRKX | 7390 | 0.035 | 0.38 | NO |
16 | PRKCG | PRKCG | PRKCG | 7416 | 0.035 | 0.39 | NO |
17 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 7803 | 0.029 | 0.37 | NO |
18 | ERO1L | ERO1L | ERO1L | 8317 | 0.022 | 0.35 | NO |
19 | PLCG1 | PLCG1 | PLCG1 | 9371 | 0.011 | 0.3 | NO |
20 | TJP2 | TJP2 | TJP2 | 9487 | 0.0096 | 0.29 | NO |
21 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 9814 | 0.0063 | 0.27 | NO |
22 | SEC61A2 | SEC61A2 | SEC61A2 | 10062 | 0.004 | 0.26 | NO |
23 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 10216 | 0.0024 | 0.25 | NO |
24 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 10245 | 0.0022 | 0.25 | NO |
25 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 10254 | 0.0021 | 0.25 | NO |
26 | PRKACA | PRKACA | PRKACA | 10454 | 0.00057 | 0.24 | NO |
27 | KDELR3 | KDELR3 | KDELR3 | 10631 | -0.00099 | 0.23 | NO |
28 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 11183 | -0.0058 | 0.2 | NO |
29 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 11635 | -0.0094 | 0.18 | NO |
30 | KDELR1 | KDELR1 | KDELR1 | 11875 | -0.011 | 0.17 | NO |
31 | ATP6V0C | ATP6V0C | ATP6V0C | 11972 | -0.012 | 0.17 | NO |
32 | ACTG1 | ACTG1 | ACTG1 | 12237 | -0.014 | 0.16 | NO |
33 | ATP6V1H | ATP6V1H | ATP6V1H | 12383 | -0.016 | 0.15 | NO |
34 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 12592 | -0.017 | 0.14 | NO |
35 | ATP6V1F | ATP6V1F | ATP6V1F | 12933 | -0.02 | 0.13 | NO |
36 | ATP6V0B | ATP6V0B | ATP6V0B | 13174 | -0.022 | 0.12 | NO |
37 | ATP6V1D | ATP6V1D | ATP6V1D | 13366 | -0.024 | 0.12 | NO |
38 | SEC61A1 | SEC61A1 | SEC61A1 | 13575 | -0.026 | 0.11 | NO |
39 | SLC12A2 | SLC12A2 | SLC12A2 | 13623 | -0.027 | 0.11 | NO |
40 | ARF1 | ARF1 | ARF1 | 14179 | -0.032 | 0.088 | NO |
41 | GNAS | GNAS | GNAS | 14260 | -0.033 | 0.091 | NO |
42 | SEC61B | SEC61B | SEC61B | 14286 | -0.033 | 0.097 | NO |
43 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 14343 | -0.034 | 0.1 | NO |
44 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 14746 | -0.039 | 0.087 | NO |
45 | MUC2 | MUC2 | MUC2 | 15206 | -0.044 | 0.071 | NO |
46 | PDIA4 | PDIA4 | PDIA4 | 15322 | -0.046 | 0.075 | NO |
47 | SEC61G | SEC61G | SEC61G | 15351 | -0.047 | 0.083 | NO |
48 | KDELR2 | KDELR2 | KDELR2 | 15361 | -0.047 | 0.093 | NO |
49 | PRKACB | PRKACB | PRKACB | 15832 | -0.056 | 0.079 | NO |
50 | ATP6V1A | ATP6V1A | ATP6V1A | 15991 | -0.06 | 0.083 | NO |
51 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 16050 | -0.061 | 0.092 | NO |
52 | TJP1 | TJP1 | TJP1 | 16055 | -0.061 | 0.1 | NO |
53 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 16504 | -0.073 | 0.096 | NO |
Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG O GLYCAN BIOSYNTHESIS.

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

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 | SAA1 | SAA1 | SAA1 | 285 | 0.52 | 0.1 | YES |
2 | S100B | S100B | S100B | 615 | 0.42 | 0.18 | YES |
3 | IKBKE | IKBKE | IKBKE | 960 | 0.36 | 0.24 | YES |
4 | AGER | AGER | AGER | 1310 | 0.31 | 0.29 | YES |
5 | UBA7 | UBA7 | UBA7 | 2009 | 0.25 | 0.31 | YES |
6 | CASP10 | CASP10 | CASP10 | 2344 | 0.22 | 0.34 | YES |
7 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 2444 | 0.22 | 0.38 | YES |
8 | NLRC5 | NLRC5 | NLRC5 | 2511 | 0.21 | 0.43 | YES |
9 | IRF1 | IRF1 | IRF1 | 2747 | 0.2 | 0.46 | YES |
10 | UBE2L6 | UBE2L6 | UBE2L6 | 4057 | 0.13 | 0.42 | YES |
11 | IRF3 | IRF3 | IRF3 | 4945 | 0.096 | 0.39 | YES |
12 | NFKBIA | NFKBIA | NFKBIA | 5062 | 0.092 | 0.4 | YES |
13 | MAP3K1 | MAP3K1 | MAP3K1 | 5110 | 0.091 | 0.42 | YES |
14 | S100A12 | S100A12 | S100A12 | 5515 | 0.078 | 0.42 | YES |
15 | HERC5 | HERC5 | HERC5 | 5626 | 0.074 | 0.43 | YES |
16 | IKBKB | IKBKB | IKBKB | 5888 | 0.067 | 0.43 | YES |
17 | DHX58 | DHX58 | DHX58 | 5893 | 0.066 | 0.44 | YES |
18 | TRAF6 | TRAF6 | TRAF6 | 5933 | 0.065 | 0.45 | YES |
19 | NFKB2 | NFKB2 | NFKB2 | 6151 | 0.06 | 0.46 | YES |
20 | TRAF3 | TRAF3 | TRAF3 | 6471 | 0.052 | 0.45 | YES |
21 | CYLD | CYLD | CYLD | 6476 | 0.052 | 0.46 | YES |
22 | IRF2 | IRF2 | IRF2 | 6682 | 0.048 | 0.46 | YES |
23 | ATG5 | ATG5 | ATG5 | 6721 | 0.047 | 0.47 | YES |
24 | DDX58 | DDX58 | DDX58 | 6750 | 0.046 | 0.48 | YES |
25 | NFKBIB | NFKBIB | NFKBIB | 6898 | 0.044 | 0.48 | YES |
26 | ISG15 | ISG15 | ISG15 | 6929 | 0.043 | 0.49 | YES |
27 | IRF7 | IRF7 | IRF7 | 7219 | 0.038 | 0.48 | YES |
28 | RIPK1 | RIPK1 | RIPK1 | 7223 | 0.038 | 0.49 | YES |
29 | IKBKG | IKBKG | IKBKG | 7285 | 0.037 | 0.49 | YES |
30 | TRAF2 | TRAF2 | TRAF2 | 7510 | 0.033 | 0.49 | NO |
31 | FADD | FADD | FADD | 8190 | 0.024 | 0.46 | NO |
32 | APP | APP | APP | 8575 | 0.019 | 0.44 | NO |
33 | TANK | TANK | TANK | 8687 | 0.018 | 0.44 | NO |
34 | RELA | RELA | RELA | 9076 | 0.014 | 0.42 | NO |
35 | NLRX1 | NLRX1 | NLRX1 | 9103 | 0.013 | 0.42 | NO |
36 | OTUD5 | OTUD5 | OTUD5 | 9106 | 0.013 | 0.42 | NO |
37 | CREBBP | CREBBP | CREBBP | 9162 | 0.013 | 0.42 | NO |
38 | HMGB1 | HMGB1 | HMGB1 | 9344 | 0.011 | 0.42 | NO |
39 | RPS27A | RPS27A | RPS27A | 9873 | 0.0058 | 0.39 | NO |
40 | IFIH1 | IFIH1 | IFIH1 | 10091 | 0.0036 | 0.38 | NO |
41 | UBE2D3 | UBE2D3 | UBE2D3 | 10100 | 0.0035 | 0.38 | NO |
42 | ATG12 | ATG12 | ATG12 | 10239 | 0.0022 | 0.37 | NO |
43 | UBA52 | UBA52 | UBA52 | 10270 | 0.002 | 0.37 | NO |
44 | RNF125 | RNF125 | RNF125 | 10763 | -0.0022 | 0.34 | NO |
45 | PIN1 | PIN1 | PIN1 | 11118 | -0.0051 | 0.32 | NO |
46 | CASP8 | CASP8 | CASP8 | 11160 | -0.0056 | 0.32 | NO |
47 | TBK1 | TBK1 | TBK1 | 11306 | -0.0067 | 0.32 | NO |
48 | RNF135 | RNF135 | RNF135 | 11405 | -0.0075 | 0.31 | NO |
49 | TRIM25 | TRIM25 | TRIM25 | 11437 | -0.0077 | 0.31 | NO |
50 | PCBP2 | PCBP2 | PCBP2 | 11580 | -0.0089 | 0.31 | NO |
51 | CHUK | CHUK | CHUK | 11656 | -0.0095 | 0.3 | NO |
52 | UBE2D2 | UBE2D2 | UBE2D2 | 12532 | -0.017 | 0.26 | NO |
53 | MAVS | MAVS | MAVS | 13485 | -0.025 | 0.21 | NO |
54 | UBE2D1 | UBE2D1 | UBE2D1 | 13911 | -0.03 | 0.2 | NO |
55 | DAK | DAK | DAK | 14270 | -0.033 | 0.18 | NO |
56 | EP300 | EP300 | EP300 | 14397 | -0.034 | 0.19 | NO |
57 | SIKE1 | SIKE1 | SIKE1 | 14606 | -0.037 | 0.18 | NO |
58 | UBE2K | UBE2K | UBE2K | 14660 | -0.038 | 0.19 | NO |
59 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 15034 | -0.042 | 0.18 | NO |
Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCEROLIPID METABOLISM.
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Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROLIPID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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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 | CD7 | CD7 | CD7 | 392 | 0.48 | 0.07 | YES |
2 | MET | MET | MET | 636 | 0.41 | 0.14 | YES |
3 | NR0B2 | NR0B2 | NR0B2 | 1165 | 0.33 | 0.17 | YES |
4 | TNFRSF6B | TNFRSF6B | TNFRSF6B | 1340 | 0.31 | 0.22 | YES |
5 | IL8 | IL8 | IL8 | 1498 | 0.3 | 0.27 | YES |
6 | BTK | BTK | BTK | 1624 | 0.28 | 0.31 | YES |
7 | FAIM2 | FAIM2 | FAIM2 | 1845 | 0.26 | 0.35 | YES |
8 | CASP10 | CASP10 | CASP10 | 2344 | 0.22 | 0.37 | YES |
9 | IL1A | IL1A | IL1A | 2421 | 0.22 | 0.41 | YES |
10 | FAS | FAS | FAS | 3385 | 0.16 | 0.38 | YES |
11 | NCS1 | NCS1 | NCS1 | 3795 | 0.14 | 0.39 | YES |
12 | NFKBIE | NFKBIE | NFKBIE | 4052 | 0.13 | 0.4 | YES |
13 | HSPB1 | HSPB1 | HSPB1 | 4645 | 0.11 | 0.39 | YES |
14 | EGFR | EGFR | EGFR | 4956 | 0.095 | 0.39 | YES |
15 | NFKBIA | NFKBIA | NFKBIA | 5062 | 0.092 | 0.4 | YES |
16 | MAP3K1 | MAP3K1 | MAP3K1 | 5110 | 0.091 | 0.42 | YES |
17 | NFKB1 | NFKB1 | NFKB1 | 5246 | 0.086 | 0.42 | YES |
18 | EPHB2 | EPHB2 | EPHB2 | 5255 | 0.086 | 0.44 | YES |
19 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 5340 | 0.083 | 0.45 | YES |
20 | NFKB2 | NFKB2 | NFKB2 | 6151 | 0.06 | 0.42 | NO |
21 | MAP3K5 | MAP3K5 | MAP3K5 | 6454 | 0.052 | 0.41 | NO |
22 | NFKBIB | NFKBIB | NFKBIB | 6898 | 0.044 | 0.4 | NO |
23 | NFAT5 | NFAT5 | NFAT5 | 6993 | 0.042 | 0.4 | NO |
24 | RIPK1 | RIPK1 | RIPK1 | 7223 | 0.038 | 0.39 | NO |
25 | TRAF2 | TRAF2 | TRAF2 | 7510 | 0.033 | 0.38 | NO |
26 | DEDD2 | DEDD2 | DEDD2 | 7673 | 0.031 | 0.38 | NO |
27 | BAK1 | BAK1 | BAK1 | 7801 | 0.03 | 0.38 | NO |
28 | FADD | FADD | FADD | 8190 | 0.024 | 0.36 | NO |
29 | MAP2K7 | MAP2K7 | MAP2K7 | 8366 | 0.022 | 0.36 | NO |
30 | PFN1 | PFN1 | PFN1 | 8458 | 0.021 | 0.36 | NO |
31 | TP53 | TP53 | TP53 | 8592 | 0.019 | 0.35 | NO |
32 | CASP3 | CASP3 | CASP3 | 8703 | 0.018 | 0.35 | NO |
33 | MAPK10 | MAPK10 | MAPK10 | 8765 | 0.017 | 0.35 | NO |
34 | DAXX | DAXX | DAXX | 9209 | 0.012 | 0.33 | NO |
35 | DIABLO | DIABLO | DIABLO | 9538 | 0.0092 | 0.31 | NO |
36 | CASP8AP2 | CASP8AP2 | CASP8AP2 | 9556 | 0.0089 | 0.31 | NO |
37 | EZR | EZR | EZR | 9836 | 0.0061 | 0.3 | NO |
38 | CAD | CAD | CAD | 10421 | 0.00087 | 0.27 | NO |
39 | DFFA | DFFA | DFFA | 10923 | -0.0038 | 0.24 | NO |
40 | BAX | BAX | BAX | 11043 | -0.0046 | 0.23 | NO |
41 | SMPD1 | SMPD1 | SMPD1 | 11121 | -0.0051 | 0.23 | NO |
42 | CASP8 | CASP8 | CASP8 | 11160 | -0.0056 | 0.23 | NO |
43 | TUFM | TUFM | TUFM | 11456 | -0.0079 | 0.22 | NO |
44 | DEDD | DEDD | DEDD | 11579 | -0.0089 | 0.21 | NO |
45 | NFKBIL1 | NFKBIL1 | NFKBIL1 | 11986 | -0.012 | 0.19 | NO |
46 | MAP2K4 | MAP2K4 | MAP2K4 | 12025 | -0.013 | 0.19 | NO |
47 | PARP1 | PARP1 | PARP1 | 12305 | -0.015 | 0.18 | NO |
48 | FAF1 | FAF1 | FAF1 | 12332 | -0.015 | 0.18 | NO |
49 | BFAR | BFAR | BFAR | 12350 | -0.015 | 0.18 | NO |
50 | AGFG1 | AGFG1 | AGFG1 | 12395 | -0.016 | 0.18 | NO |
51 | ROCK1 | ROCK1 | ROCK1 | 12623 | -0.018 | 0.17 | NO |
52 | ALG2 | ALG2 | ALG2 | 12741 | -0.019 | 0.17 | NO |
53 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 13225 | -0.023 | 0.15 | NO |
54 | CDK2AP1 | CDK2AP1 | CDK2AP1 | 13444 | -0.025 | 0.14 | NO |
55 | RALBP1 | RALBP1 | RALBP1 | 13753 | -0.028 | 0.13 | NO |
56 | MAPK1 | MAPK1 | MAPK1 | 13960 | -0.03 | 0.12 | NO |
57 | MAPK8IP1 | MAPK8IP1 | MAPK8IP1 | 14288 | -0.034 | 0.11 | NO |
58 | MAPK8 | MAPK8 | MAPK8 | 14780 | -0.039 | 0.093 | NO |
59 | PFN2 | PFN2 | PFN2 | 15076 | -0.043 | 0.085 | NO |
60 | XIAP | XIAP | XIAP | 15262 | -0.045 | 0.083 | NO |
61 | MAPK9 | MAPK9 | MAPK9 | 15445 | -0.049 | 0.082 | NO |
62 | PTPN13 | PTPN13 | PTPN13 | 15585 | -0.052 | 0.085 | NO |
63 | MAPK8IP2 | MAPK8IP2 | MAPK8IP2 | 16406 | -0.07 | 0.053 | NO |
64 | TPX2 | TPX2 | TPX2 | 18189 | -0.26 | 0.0037 | NO |
Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG INOSITOL PHOSPHATE METABOLISM.
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Figure S80. 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
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For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
-
Gene set database = c2.cp.v4.0.symbols.gmt
-
Expression data file = PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
-
Phenotype data file = PRAD-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.