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 "KIRC-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: 533 |
Original number of Gene Sets: 1320 |
Maximum gene set size: 933 |
Table 2. Get Full Table pheno data info
phenotype info |
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pheno.type: 1 - 5 :[ clus1 ] 85 |
pheno.type: 2 - 5 :[ clus2 ] 172 |
pheno.type: 3 - 5 :[ clus3 ] 82 |
pheno.type: 4 - 5 :[ clus4 ] 154 |
pheno.type: 5 - 5 :[ clus5 ] 40 |
For the expression subtypes of 18278 genes in 534 samples, GSEA found enriched gene sets in each cluster using 533 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.
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clus1
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Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, KEGG ALZHEIMERS DISEASE, KEGG PARKINSONS DISEASE, KEGG VIBRIO CHOLERAE INFECTION, KEGG EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI INFECTION, SIG PIP3 SIGNALING IN CARDIAC MYOCTES, PID PI3KCIAKTPATHWAY, REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT, REACTOME TRANS GOLGI NETWORK VESICLE BUDDING, REACTOME MITOCHONDRIAL PROTEIN IMPORT
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And common core enriched genes are ATP6V0A2, ATP6V0A4, ATP6V0B, ATP6V0C, ATP6V0D1, ATP6V0D2, ATP6V1A, ATP6V1B1, ATP6V1C2, ATP6V1D
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clus2
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Top enriched gene sets are KEGG FATTY ACID METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG PROPANOATE METABOLISM, KEGG PPAR SIGNALING PATHWAY, KEGG PEROXISOME, KEGG ADIPOCYTOKINE SIGNALING PATHWAY, BIOCARTA AT1R PATHWAY
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And common core enriched genes are EHHADH, ACAT1, ALDH1B1, ALDH2, ALDH3A2, ALDH7A1, ALDH9A1, HADHA, MLYCD, ABAT
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clus3
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Top enriched gene sets are KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG MAPK SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, KEGG MTOR SIGNALING PATHWAY, KEGG VASCULAR SMOOTH MUSCLE CONTRACTION, KEGG WNT SIGNALING PATHWAY, KEGG NOTCH SIGNALING PATHWAY, KEGG HEDGEHOG SIGNALING PATHWAY, KEGG TGF BETA SIGNALING PATHWAY
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And common core enriched genes are PIK3CA, PIK3R1, PLCG1, SHC1, ADCY1, ADCY3, ADCY4, ADCY8, AKT3, CALM1
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clus4
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Top enriched gene sets are KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG P53 SIGNALING PATHWAY, KEGG CYTOSOLIC DNA SENSING PATHWAY, PID AURORA B PATHWAY, PID E2F PATHWAY, PID INTEGRIN2 PATHWAY, REACTOME ANTIGEN PROCESSING CROSS PRESENTATION, REACTOME ORC1 REMOVAL FROM CHROMATIN, REACTOME ACTIVATION OF NF KAPPAB IN B CELLS, REACTOME MHC CLASS II ANTIGEN PRESENTATION
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And common core enriched genes are CD4, PSMA1, PSMA2, PSMA4, PSMA5, PSMA7, PSMA8, PSMB10, PSMB2, PSMB3
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clus5
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Top enriched gene sets are KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, KEGG NOTCH SIGNALING PATHWAY, KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY, KEGG OLFACTORY TRANSDUCTION, KEGG TASTE TRANSDUCTION, SIG CD40PATHWAYMAP, PID RHOA REG PATHWAY, PID HDAC CLASSI PATHWAY, REACTOME MEIOSIS, REACTOME SIGNALING BY FGFR1 MUTANTS
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And common core enriched genes are ACD, HIST1H2AD, HIST1H2AE, HIST1H2BD, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BH, HIST1H2BJ, HIST1H2BL
Table 3. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
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KEGG OXIDATIVE PHOSPHORYLATION | 113 | genes.ES.table | 0.66 | 1.9 | 0.0093 | 0.26 | 0.39 | 0.78 | 0.23 | 0.61 | 0 | 0.07 |
KEGG ALZHEIMERS DISEASE | 155 | genes.ES.table | 0.37 | 1.6 | 0.052 | 0.5 | 0.92 | 0.52 | 0.23 | 0.4 | 0.33 | 0.15 |
KEGG PARKINSONS DISEASE | 110 | genes.ES.table | 0.5 | 1.7 | 0.091 | 0.46 | 0.84 | 0.64 | 0.23 | 0.5 | 0.25 | 0.14 |
KEGG VIBRIO CHOLERAE INFECTION | 52 | genes.ES.table | 0.6 | 2 | 0 | 0.1 | 0.14 | 0.36 | 0.17 | 0.3 | 0 | 0.032 |
KEGG EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI INFECTION | 67 | genes.ES.table | 0.42 | 1.6 | 0.019 | 0.51 | 0.9 | 0.25 | 0.17 | 0.21 | 0.32 | 0.16 |
SIG PIP3 SIGNALING IN CARDIAC MYOCTES | 66 | genes.ES.table | 0.4 | 1.7 | 0.01 | 0.46 | 0.78 | 0.14 | 0.1 | 0.12 | 0.22 | 0.15 |
PID PI3KCIAKTPATHWAY | 35 | genes.ES.table | 0.49 | 2.1 | 0.0021 | 0.14 | 0.1 | 0.43 | 0.27 | 0.31 | 0 | 0.051 |
REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT | 115 | genes.ES.table | 0.61 | 1.8 | 0.03 | 0.49 | 0.62 | 0.75 | 0.23 | 0.58 | 0.18 | 0.15 |
REACTOME TRANS GOLGI NETWORK VESICLE BUDDING | 59 | genes.ES.table | 0.36 | 1.6 | 0.054 | 0.47 | 0.87 | 0.051 | 0.041 | 0.049 | 0.28 | 0.14 |
REACTOME MITOCHONDRIAL PROTEIN IMPORT | 49 | genes.ES.table | 0.62 | 1.8 | 0.034 | 0.46 | 0.64 | 0.71 | 0.3 | 0.5 | 0.18 | 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 |
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1 | SLC2A4 | SLC2A4 | SLC2A4 | 500 | 0.37 | 0.17 | YES |
2 | SFN | SFN | SFN | 1823 | 0.16 | 0.18 | YES |
3 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 2236 | 0.13 | 0.23 | YES |
4 | TBC1D4 | TBC1D4 | TBC1D4 | 2771 | 0.1 | 0.26 | YES |
5 | GSK3B | GSK3B | GSK3B | 3344 | 0.085 | 0.27 | YES |
6 | FOXO1 | FOXO1 | FOXO1 | 3368 | 0.084 | 0.32 | YES |
7 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 3462 | 0.081 | 0.35 | YES |
8 | RAF1 | RAF1 | RAF1 | 3832 | 0.071 | 0.37 | YES |
9 | CHUK | CHUK | CHUK | 4540 | 0.053 | 0.36 | YES |
10 | AKT2 | AKT2 | AKT2 | 4662 | 0.051 | 0.38 | YES |
11 | KPNA1 | KPNA1 | KPNA1 | 4723 | 0.05 | 0.4 | YES |
12 | YWHAB | YWHAB | YWHAB | 4825 | 0.048 | 0.42 | YES |
13 | BCL2L1 | BCL2L1 | BCL2L1 | 4891 | 0.047 | 0.45 | YES |
14 | MLST8 | MLST8 | MLST8 | 4902 | 0.046 | 0.47 | YES |
15 | MTOR | MTOR | MTOR | 4903 | 0.046 | 0.5 | YES |
16 | AKT1 | AKT1 | AKT1 | 5567 | 0.035 | 0.48 | NO |
17 | PRKDC | PRKDC | PRKDC | 6184 | 0.026 | 0.46 | NO |
18 | YWHAE | YWHAE | YWHAE | 6617 | 0.019 | 0.44 | NO |
19 | PRKACA | PRKACA | PRKACA | 6788 | 0.016 | 0.44 | NO |
20 | GSK3A | GSK3A | GSK3A | 6934 | 0.014 | 0.44 | NO |
21 | RICTOR | RICTOR | RICTOR | 6961 | 0.014 | 0.45 | NO |
22 | FOXO4 | FOXO4 | FOXO4 | 6988 | 0.014 | 0.45 | NO |
23 | CDKN1A | CDKN1A | CDKN1A | 7351 | 0.0086 | 0.44 | NO |
24 | BAD | BAD | BAD | 7761 | 0.0033 | 0.42 | NO |
25 | PDPK1 | PDPK1 | PDPK1 | 7787 | 0.003 | 0.42 | NO |
26 | SRC | SRC | SRC | 7993 | 0.0002 | 0.41 | NO |
27 | YWHAQ | YWHAQ | YWHAQ | 8143 | -0.0018 | 0.4 | NO |
28 | YWHAZ | YWHAZ | YWHAZ | 8882 | -0.011 | 0.36 | NO |
29 | CASP9 | CASP9 | CASP9 | 9173 | -0.015 | 0.36 | NO |
30 | YWHAG | YWHAG | YWHAG | 9234 | -0.016 | 0.36 | NO |
31 | YWHAH | YWHAH | YWHAH | 9910 | -0.025 | 0.34 | NO |
32 | AKT3 | AKT3 | AKT3 | 10601 | -0.036 | 0.32 | NO |
33 | MAP3K5 | MAP3K5 | MAP3K5 | 10677 | -0.037 | 0.34 | NO |
34 | FOXO3 | FOXO3 | FOXO3 | 11288 | -0.047 | 0.33 | NO |
35 | CDKN1B | CDKN1B | CDKN1B | 13638 | -0.1 | 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 OXIDATIVE PHOSPHORYLATION.
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Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
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1 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 5 | 0.99 | 0.13 | YES |
2 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 42 | 0.8 | 0.24 | YES |
3 | CFTR | CFTR | CFTR | 63 | 0.72 | 0.34 | YES |
4 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 108 | 0.64 | 0.42 | YES |
5 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 515 | 0.37 | 0.45 | YES |
6 | PLCG2 | PLCG2 | PLCG2 | 948 | 0.27 | 0.46 | YES |
7 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 1116 | 0.24 | 0.48 | YES |
8 | ATP6V1A | ATP6V1A | ATP6V1A | 1369 | 0.2 | 0.5 | YES |
9 | KCNQ1 | KCNQ1 | KCNQ1 | 1549 | 0.18 | 0.51 | YES |
10 | ATP6V1H | ATP6V1H | ATP6V1H | 1647 | 0.18 | 0.53 | YES |
11 | ATP6V1D | ATP6V1D | ATP6V1D | 1732 | 0.17 | 0.55 | YES |
12 | ATP6V0B | ATP6V0B | ATP6V0B | 1852 | 0.16 | 0.56 | YES |
13 | PRKCA | PRKCA | PRKCA | 2098 | 0.14 | 0.57 | YES |
14 | ATP6V0C | ATP6V0C | ATP6V0C | 2103 | 0.14 | 0.59 | YES |
15 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 2607 | 0.11 | 0.57 | YES |
16 | ATP6V1F | ATP6V1F | ATP6V1F | 2832 | 0.1 | 0.58 | YES |
17 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 2974 | 0.097 | 0.58 | YES |
18 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 3004 | 0.096 | 0.59 | YES |
19 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 3065 | 0.094 | 0.6 | YES |
20 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 3586 | 0.078 | 0.58 | NO |
21 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 3655 | 0.076 | 0.59 | NO |
22 | GNAS | GNAS | GNAS | 4260 | 0.059 | 0.56 | NO |
23 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 4410 | 0.056 | 0.56 | NO |
24 | SLC12A2 | SLC12A2 | SLC12A2 | 4421 | 0.056 | 0.57 | NO |
25 | PRKCG | PRKCG | PRKCG | 4456 | 0.055 | 0.58 | NO |
26 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 5410 | 0.038 | 0.53 | NO |
27 | TJP2 | TJP2 | TJP2 | 5561 | 0.035 | 0.53 | NO |
28 | ACTG1 | ACTG1 | ACTG1 | 5655 | 0.034 | 0.53 | NO |
29 | TJP1 | TJP1 | TJP1 | 5793 | 0.032 | 0.52 | NO |
30 | KDELR1 | KDELR1 | KDELR1 | 5881 | 0.031 | 0.52 | NO |
31 | PRKACB | PRKACB | PRKACB | 6482 | 0.021 | 0.49 | NO |
32 | PRKACA | PRKACA | PRKACA | 6788 | 0.016 | 0.48 | NO |
33 | MUC2 | MUC2 | MUC2 | 6953 | 0.014 | 0.47 | NO |
34 | SEC61B | SEC61B | SEC61B | 7112 | 0.012 | 0.46 | NO |
35 | ACTB | ACTB | ACTB | 7293 | 0.0094 | 0.46 | NO |
36 | SEC61A1 | SEC61A1 | SEC61A1 | 7988 | 0.00027 | 0.42 | NO |
37 | PRKX | PRKX | PRKX | 8112 | -0.0013 | 0.41 | NO |
38 | ARF1 | ARF1 | ARF1 | 8367 | -0.0044 | 0.4 | NO |
39 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 9258 | -0.016 | 0.35 | NO |
40 | KDELR2 | KDELR2 | KDELR2 | 10074 | -0.027 | 0.31 | NO |
41 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 10647 | -0.037 | 0.28 | NO |
42 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 10728 | -0.038 | 0.28 | NO |
43 | PLCG1 | PLCG1 | PLCG1 | 11134 | -0.044 | 0.27 | NO |
44 | PDIA4 | PDIA4 | PDIA4 | 12076 | -0.064 | 0.22 | NO |
45 | ADCY9 | ADCY9 | ADCY9 | 12153 | -0.065 | 0.23 | NO |
46 | KDELR3 | KDELR3 | KDELR3 | 12187 | -0.066 | 0.24 | NO |
47 | SEC61G | SEC61G | SEC61G | 12578 | -0.075 | 0.22 | NO |
48 | ERO1L | ERO1L | ERO1L | 12702 | -0.078 | 0.23 | NO |
49 | ADCY3 | ADCY3 | ADCY3 | 13439 | -0.097 | 0.2 | NO |
50 | TCIRG1 | TCIRG1 | TCIRG1 | 13457 | -0.098 | 0.21 | NO |
51 | SEC61A2 | SEC61A2 | SEC61A2 | 13662 | -0.1 | 0.22 | NO |
52 | PRKCB | PRKCB | PRKCB | 16904 | -0.27 | 0.074 | 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 ALZHEIMERS DISEASE.

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

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
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1 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 5 | 0.99 | 0.088 | YES |
2 | FGF9 | FGF9 | FGF9 | 7 | 0.96 | 0.17 | YES |
3 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 42 | 0.8 | 0.24 | YES |
4 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 108 | 0.64 | 0.3 | YES |
5 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 515 | 0.37 | 0.3 | YES |
6 | FGF7 | FGF7 | FGF7 | 706 | 0.32 | 0.32 | YES |
7 | CAB39L | CAB39L | CAB39L | 965 | 0.26 | 0.33 | YES |
8 | FGF1 | FGF1 | FGF1 | 1002 | 0.26 | 0.35 | YES |
9 | IRS1 | IRS1 | IRS1 | 1203 | 0.22 | 0.36 | YES |
10 | ATP6V1A | ATP6V1A | ATP6V1A | 1369 | 0.2 | 0.37 | YES |
11 | ATP6V1H | ATP6V1H | ATP6V1H | 1647 | 0.18 | 0.37 | YES |
12 | ATP6V1D | ATP6V1D | ATP6V1D | 1732 | 0.17 | 0.38 | YES |
13 | PDE3B | PDE3B | PDE3B | 1800 | 0.16 | 0.39 | YES |
14 | IRS2 | IRS2 | IRS2 | 1820 | 0.16 | 0.4 | YES |
15 | ATP6V0B | ATP6V0B | ATP6V0B | 1852 | 0.16 | 0.42 | YES |
16 | FGF18 | FGF18 | FGF18 | 1916 | 0.15 | 0.43 | YES |
17 | ATP6V0C | ATP6V0C | ATP6V0C | 2103 | 0.14 | 0.43 | YES |
18 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 2607 | 0.11 | 0.41 | YES |
19 | EIF4E | EIF4E | EIF4E | 2703 | 0.11 | 0.42 | YES |
20 | ATP6V1F | ATP6V1F | ATP6V1F | 2832 | 0.1 | 0.42 | YES |
21 | PRKAG2 | PRKAG2 | PRKAG2 | 2939 | 0.098 | 0.42 | YES |
22 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 2974 | 0.097 | 0.43 | YES |
23 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 3004 | 0.096 | 0.43 | YES |
24 | PPM1A | PPM1A | PPM1A | 3005 | 0.096 | 0.44 | YES |
25 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 3065 | 0.094 | 0.45 | YES |
26 | PRKAB1 | PRKAB1 | PRKAB1 | 3133 | 0.091 | 0.45 | YES |
27 | RHEB | RHEB | RHEB | 3185 | 0.09 | 0.46 | YES |
28 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 3586 | 0.078 | 0.44 | NO |
29 | FGF23 | FGF23 | FGF23 | 3607 | 0.077 | 0.45 | NO |
30 | RAF1 | RAF1 | RAF1 | 3832 | 0.071 | 0.44 | NO |
31 | SHC3 | SHC3 | SHC3 | 4246 | 0.06 | 0.42 | NO |
32 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 4410 | 0.056 | 0.42 | NO |
33 | AKT2 | AKT2 | AKT2 | 4662 | 0.051 | 0.41 | NO |
34 | PRKAG1 | PRKAG1 | PRKAG1 | 4664 | 0.051 | 0.42 | NO |
35 | CAB39 | CAB39 | CAB39 | 4732 | 0.05 | 0.42 | NO |
36 | FGFR1 | FGFR1 | FGFR1 | 4790 | 0.049 | 0.42 | NO |
37 | YWHAB | YWHAB | YWHAB | 4825 | 0.048 | 0.42 | NO |
38 | MLST8 | MLST8 | MLST8 | 4902 | 0.046 | 0.42 | NO |
39 | MTOR | MTOR | MTOR | 4903 | 0.046 | 0.42 | NO |
40 | THEM4 | THEM4 | THEM4 | 5176 | 0.042 | 0.41 | NO |
41 | PIK3R4 | PIK3R4 | PIK3R4 | 5253 | 0.04 | 0.41 | NO |
42 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 5410 | 0.038 | 0.41 | NO |
43 | RPTOR | RPTOR | RPTOR | 5417 | 0.037 | 0.41 | NO |
44 | KRAS | KRAS | KRAS | 5767 | 0.032 | 0.39 | NO |
45 | PIK3R2 | PIK3R2 | PIK3R2 | 6052 | 0.028 | 0.38 | NO |
46 | FGFR2 | FGFR2 | FGFR2 | 6266 | 0.024 | 0.37 | NO |
47 | PRKAB2 | PRKAB2 | PRKAB2 | 6520 | 0.02 | 0.36 | NO |
48 | PIK3CA | PIK3CA | PIK3CA | 6546 | 0.02 | 0.36 | NO |
49 | KLB | KLB | KLB | 6550 | 0.02 | 0.36 | NO |
50 | MAP2K2 | MAP2K2 | MAP2K2 | 7025 | 0.013 | 0.34 | NO |
51 | FRS2 | FRS2 | FRS2 | 7057 | 0.013 | 0.34 | NO |
52 | EIF4G1 | EIF4G1 | EIF4G1 | 7184 | 0.011 | 0.33 | NO |
53 | PIK3C3 | PIK3C3 | PIK3C3 | 7380 | 0.0082 | 0.32 | NO |
54 | TSC1 | TSC1 | TSC1 | 7550 | 0.0061 | 0.31 | NO |
55 | TSC2 | TSC2 | TSC2 | 7595 | 0.0054 | 0.31 | NO |
56 | MAP2K1 | MAP2K1 | MAP2K1 | 7598 | 0.0054 | 0.31 | NO |
57 | STK11 | STK11 | STK11 | 7601 | 0.0054 | 0.31 | NO |
58 | RPS6 | RPS6 | RPS6 | 7633 | 0.005 | 0.31 | NO |
59 | PDPK1 | PDPK1 | PDPK1 | 7787 | 0.003 | 0.3 | NO |
60 | FGF8 | FGF8 | FGF8 | 7824 | 0.0025 | 0.3 | NO |
61 | CRK | CRK | CRK | 7984 | 0.00034 | 0.29 | NO |
62 | STRADA | STRADA | STRADA | 8250 | -0.0031 | 0.27 | NO |
63 | SHC2 | SHC2 | SHC2 | 8699 | -0.0087 | 0.25 | NO |
64 | PRKAA1 | PRKAA1 | PRKAA1 | 9230 | -0.016 | 0.22 | NO |
65 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 9258 | -0.016 | 0.22 | NO |
66 | EIF4B | EIF4B | EIF4B | 9555 | -0.02 | 0.21 | NO |
67 | GRB2 | GRB2 | GRB2 | 9568 | -0.02 | 0.21 | NO |
68 | HRAS | HRAS | HRAS | 9804 | -0.023 | 0.2 | NO |
69 | MAPK3 | MAPK3 | MAPK3 | 10607 | -0.036 | 0.16 | NO |
70 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 10624 | -0.036 | 0.16 | NO |
71 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 10647 | -0.037 | 0.16 | NO |
72 | FGF17 | FGF17 | FGF17 | 10843 | -0.04 | 0.15 | NO |
73 | PIK3CB | PIK3CB | PIK3CB | 10847 | -0.04 | 0.16 | NO |
74 | KL | KL | KL | 11242 | -0.046 | 0.14 | NO |
75 | GAB1 | GAB1 | GAB1 | 11253 | -0.046 | 0.14 | NO |
76 | PRKAA2 | PRKAA2 | PRKAA2 | 11719 | -0.056 | 0.12 | NO |
77 | SOS1 | SOS1 | SOS1 | 11807 | -0.058 | 0.12 | NO |
78 | EEF2K | EEF2K | EEF2K | 11833 | -0.058 | 0.13 | NO |
79 | FGF2 | FGF2 | FGF2 | 12158 | -0.065 | 0.12 | NO |
80 | MAPK1 | MAPK1 | MAPK1 | 12274 | -0.068 | 0.12 | NO |
81 | NRAS | NRAS | NRAS | 12572 | -0.075 | 0.1 | NO |
82 | GRB10 | GRB10 | GRB10 | 12676 | -0.078 | 0.11 | NO |
83 | STRADB | STRADB | STRADB | 13377 | -0.096 | 0.076 | NO |
84 | TCIRG1 | TCIRG1 | TCIRG1 | 13457 | -0.098 | 0.081 | NO |
85 | PIK3R1 | PIK3R1 | PIK3R1 | 13813 | -0.11 | 0.071 | NO |
86 | DOK1 | DOK1 | DOK1 | 13947 | -0.11 | 0.074 | NO |
87 | SHC1 | SHC1 | SHC1 | 14166 | -0.12 | 0.072 | NO |
88 | INSR | INSR | INSR | 14480 | -0.13 | 0.067 | NO |
89 | CDK1 | CDK1 | CDK1 | 14630 | -0.14 | 0.071 | NO |
90 | FGF20 | FGF20 | FGF20 | 14660 | -0.14 | 0.082 | NO |
91 | FGF5 | FGF5 | FGF5 | 15583 | -0.18 | 0.047 | NO |
92 | TRIB3 | TRIB3 | TRIB3 | 16045 | -0.2 | 0.04 | NO |
93 | FGFR4 | FGFR4 | FGFR4 | 16260 | -0.22 | 0.047 | NO |
94 | FGFR3 | FGFR3 | FGFR3 | 16420 | -0.23 | 0.059 | NO |
95 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 16496 | -0.23 | 0.075 | NO |
96 | TLR9 | TLR9 | TLR9 | 16658 | -0.24 | 0.088 | 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 PARKINSONS DISEASE.

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

Table 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 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 5 | 0.99 | 0.065 | YES |
2 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 42 | 0.8 | 0.12 | YES |
3 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 108 | 0.64 | 0.15 | YES |
4 | ATP12A | ATP12A | ATP12A | 208 | 0.54 | 0.18 | YES |
5 | ATP4B | ATP4B | ATP4B | 505 | 0.37 | 0.19 | YES |
6 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 515 | 0.37 | 0.21 | YES |
7 | COX7A1 | COX7A1 | COX7A1 | 1027 | 0.25 | 0.2 | YES |
8 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 1116 | 0.24 | 0.21 | YES |
9 | COX6B2 | COX6B2 | COX6B2 | 1234 | 0.22 | 0.22 | YES |
10 | UQCRHL | UQCRHL | UQCRHL | 1265 | 0.22 | 0.23 | YES |
11 | NDUFA4 | NDUFA4 | NDUFA4 | 1308 | 0.21 | 0.24 | YES |
12 | ATP6V1A | ATP6V1A | ATP6V1A | 1369 | 0.2 | 0.26 | YES |
13 | UQCRC1 | UQCRC1 | UQCRC1 | 1378 | 0.2 | 0.27 | YES |
14 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 1395 | 0.2 | 0.28 | YES |
15 | UQCRH | UQCRH | UQCRH | 1435 | 0.2 | 0.29 | YES |
16 | COX5A | COX5A | COX5A | 1584 | 0.18 | 0.29 | YES |
17 | NDUFS8 | NDUFS8 | NDUFS8 | 1616 | 0.18 | 0.3 | YES |
18 | ATP6V1H | ATP6V1H | ATP6V1H | 1647 | 0.18 | 0.31 | YES |
19 | COX7B | COX7B | COX7B | 1693 | 0.17 | 0.32 | YES |
20 | ATP6V1D | ATP6V1D | ATP6V1D | 1732 | 0.17 | 0.33 | YES |
21 | PPA2 | PPA2 | PPA2 | 1848 | 0.16 | 0.34 | YES |
22 | ATP6V0B | ATP6V0B | ATP6V0B | 1852 | 0.16 | 0.34 | YES |
23 | NDUFA6 | NDUFA6 | NDUFA6 | 1892 | 0.16 | 0.35 | YES |
24 | ATP5G1 | ATP5G1 | ATP5G1 | 1896 | 0.15 | 0.36 | YES |
25 | NDUFB1 | NDUFB1 | NDUFB1 | 1953 | 0.15 | 0.37 | YES |
26 | NDUFA3 | NDUFA3 | NDUFA3 | 1962 | 0.15 | 0.38 | YES |
27 | ATP5A1 | ATP5A1 | ATP5A1 | 2016 | 0.14 | 0.39 | YES |
28 | ATP6V0C | ATP6V0C | ATP6V0C | 2103 | 0.14 | 0.39 | YES |
29 | NDUFB2 | NDUFB2 | NDUFB2 | 2115 | 0.14 | 0.4 | YES |
30 | COX10 | COX10 | COX10 | 2161 | 0.14 | 0.4 | YES |
31 | COX6A1 | COX6A1 | COX6A1 | 2186 | 0.13 | 0.41 | YES |
32 | COX7A2 | COX7A2 | COX7A2 | 2195 | 0.13 | 0.42 | YES |
33 | COX6C | COX6C | COX6C | 2197 | 0.13 | 0.43 | YES |
34 | NDUFB9 | NDUFB9 | NDUFB9 | 2235 | 0.13 | 0.44 | YES |
35 | NDUFA9 | NDUFA9 | NDUFA9 | 2286 | 0.13 | 0.44 | YES |
36 | NDUFB5 | NDUFB5 | NDUFB5 | 2295 | 0.13 | 0.45 | YES |
37 | ATP5B | ATP5B | ATP5B | 2317 | 0.13 | 0.46 | YES |
38 | UQCRC2 | UQCRC2 | UQCRC2 | 2356 | 0.12 | 0.46 | YES |
39 | COX8A | COX8A | COX8A | 2436 | 0.12 | 0.47 | YES |
40 | UQCR10 | UQCR10 | UQCR10 | 2440 | 0.12 | 0.47 | YES |
41 | NDUFA8 | NDUFA8 | NDUFA8 | 2454 | 0.12 | 0.48 | YES |
42 | ATP5L | ATP5L | ATP5L | 2481 | 0.12 | 0.49 | YES |
43 | UQCR11 | UQCR11 | UQCR11 | 2565 | 0.12 | 0.49 | YES |
44 | NDUFC2 | NDUFC2 | NDUFC2 | 2586 | 0.11 | 0.5 | YES |
45 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 2607 | 0.11 | 0.5 | YES |
46 | ATP5J2 | ATP5J2 | ATP5J2 | 2633 | 0.11 | 0.51 | YES |
47 | COX4I1 | COX4I1 | COX4I1 | 2694 | 0.11 | 0.51 | YES |
48 | NDUFS1 | NDUFS1 | NDUFS1 | 2702 | 0.11 | 0.52 | YES |
49 | COX5B | COX5B | COX5B | 2761 | 0.11 | 0.52 | YES |
50 | NDUFS3 | NDUFS3 | NDUFS3 | 2821 | 0.1 | 0.53 | YES |
51 | ATP6V1F | ATP6V1F | ATP6V1F | 2832 | 0.1 | 0.53 | YES |
52 | COX17 | COX17 | COX17 | 2833 | 0.1 | 0.54 | YES |
53 | COX6B1 | COX6B1 | COX6B1 | 2847 | 0.1 | 0.55 | YES |
54 | NDUFV1 | NDUFV1 | NDUFV1 | 2900 | 0.1 | 0.55 | YES |
55 | SDHD | SDHD | SDHD | 2914 | 0.099 | 0.56 | YES |
56 | ATP5E | ATP5E | ATP5E | 2950 | 0.098 | 0.56 | YES |
57 | NDUFB7 | NDUFB7 | NDUFB7 | 2955 | 0.098 | 0.57 | YES |
58 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 2974 | 0.097 | 0.57 | YES |
59 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 3004 | 0.096 | 0.58 | YES |
60 | ATP5I | ATP5I | ATP5I | 3056 | 0.094 | 0.58 | YES |
61 | NDUFS6 | NDUFS6 | NDUFS6 | 3059 | 0.094 | 0.58 | YES |
62 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 3065 | 0.094 | 0.59 | YES |
63 | NDUFS7 | NDUFS7 | NDUFS7 | 3077 | 0.094 | 0.6 | YES |
64 | ATP5D | ATP5D | ATP5D | 3144 | 0.091 | 0.6 | YES |
65 | COX7C | COX7C | COX7C | 3165 | 0.09 | 0.6 | YES |
66 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 3187 | 0.09 | 0.61 | YES |
67 | NDUFA5 | NDUFA5 | NDUFA5 | 3201 | 0.089 | 0.61 | YES |
68 | NDUFA1 | NDUFA1 | NDUFA1 | 3385 | 0.083 | 0.61 | YES |
69 | ATP5G3 | ATP5G3 | ATP5G3 | 3421 | 0.082 | 0.61 | YES |
70 | NDUFB6 | NDUFB6 | NDUFB6 | 3542 | 0.079 | 0.61 | YES |
71 | ATP5H | ATP5H | ATP5H | 3546 | 0.079 | 0.62 | YES |
72 | ATP5J | ATP5J | ATP5J | 3553 | 0.079 | 0.62 | YES |
73 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 3586 | 0.078 | 0.62 | YES |
74 | NDUFA7 | NDUFA7 | NDUFA7 | 3613 | 0.077 | 0.63 | YES |
75 | NDUFB8 | NDUFB8 | NDUFB8 | 3616 | 0.077 | 0.63 | YES |
76 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 3655 | 0.076 | 0.64 | YES |
77 | UQCRQ | UQCRQ | UQCRQ | 3657 | 0.076 | 0.64 | YES |
78 | CYC1 | CYC1 | CYC1 | 3699 | 0.074 | 0.64 | YES |
79 | NDUFB3 | NDUFB3 | NDUFB3 | 3729 | 0.074 | 0.65 | YES |
80 | NDUFA11 | NDUFA11 | NDUFA11 | 3769 | 0.073 | 0.65 | YES |
81 | UQCRB | UQCRB | UQCRB | 3791 | 0.072 | 0.65 | YES |
82 | NDUFS2 | NDUFS2 | NDUFS2 | 3820 | 0.071 | 0.66 | YES |
83 | NDUFB10 | NDUFB10 | NDUFB10 | 3921 | 0.069 | 0.65 | YES |
84 | NDUFA10 | NDUFA10 | NDUFA10 | 4059 | 0.065 | 0.65 | YES |
85 | ATP5O | ATP5O | ATP5O | 4080 | 0.064 | 0.65 | YES |
86 | SDHA | SDHA | SDHA | 4100 | 0.064 | 0.66 | YES |
87 | COX7A2L | COX7A2L | COX7A2L | 4134 | 0.063 | 0.66 | YES |
88 | ATP5F1 | ATP5F1 | ATP5F1 | 4149 | 0.062 | 0.66 | YES |
89 | ATP5C1 | ATP5C1 | ATP5C1 | 4248 | 0.06 | 0.66 | NO |
90 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 4410 | 0.056 | 0.66 | NO |
91 | SDHC | SDHC | SDHC | 4442 | 0.055 | 0.66 | NO |
92 | NDUFB4 | NDUFB4 | NDUFB4 | 4720 | 0.05 | 0.65 | NO |
93 | NDUFS4 | NDUFS4 | NDUFS4 | 4835 | 0.048 | 0.64 | NO |
94 | LHPP | LHPP | LHPP | 4847 | 0.047 | 0.64 | NO |
95 | NDUFV2 | NDUFV2 | NDUFV2 | 5035 | 0.044 | 0.64 | NO |
96 | NDUFS5 | NDUFS5 | NDUFS5 | 5188 | 0.041 | 0.63 | NO |
97 | NDUFA2 | NDUFA2 | NDUFA2 | 5369 | 0.038 | 0.62 | NO |
98 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 5410 | 0.038 | 0.62 | NO |
99 | COX11 | COX11 | COX11 | 5637 | 0.034 | 0.62 | NO |
100 | SDHB | SDHB | SDHB | 6002 | 0.028 | 0.6 | NO |
101 | COX15 | COX15 | COX15 | 7385 | 0.0081 | 0.52 | NO |
102 | ATP5G2 | ATP5G2 | ATP5G2 | 7409 | 0.0078 | 0.52 | NO |
103 | PPA1 | PPA1 | PPA1 | 7758 | 0.0034 | 0.5 | NO |
104 | NDUFV3 | NDUFV3 | NDUFV3 | 8072 | -0.00086 | 0.48 | NO |
105 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 9258 | -0.016 | 0.42 | NO |
106 | NDUFC1 | NDUFC1 | NDUFC1 | 9449 | -0.018 | 0.41 | NO |
107 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 10647 | -0.037 | 0.35 | NO |
108 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 10728 | -0.038 | 0.34 | NO |
109 | TCIRG1 | TCIRG1 | TCIRG1 | 13457 | -0.098 | 0.2 | NO |
110 | COX4I2 | COX4I2 | COX4I2 | 13556 | -0.1 | 0.2 | NO |
111 | COX8C | COX8C | COX8C | 14869 | -0.15 | 0.14 | NO |
112 | COX6A2 | COX6A2 | COX6A2 | 16926 | -0.27 | 0.044 | NO |
113 | NDUFA4L2 | NDUFA4L2 | NDUFA4L2 | 18072 | -0.45 | 0.01 | 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 VIBRIO CHOLERAE INFECTION.

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

Table 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 | NNT | NNT | NNT | 1126 | 0.23 | -0.043 | YES |
2 | PDP2 | PDP2 | PDP2 | 1154 | 0.23 | -0.026 | YES |
3 | UQCRHL | UQCRHL | UQCRHL | 1265 | 0.22 | -0.014 | YES |
4 | NDUFA4 | NDUFA4 | NDUFA4 | 1308 | 0.21 | 0.00094 | YES |
5 | UQCRC1 | UQCRC1 | UQCRC1 | 1378 | 0.2 | 0.014 | YES |
6 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 1395 | 0.2 | 0.029 | YES |
7 | PDP1 | PDP1 | PDP1 | 1402 | 0.2 | 0.045 | YES |
8 | CYCS | CYCS | CYCS | 1432 | 0.2 | 0.06 | YES |
9 | UQCRH | UQCRH | UQCRH | 1435 | 0.2 | 0.075 | YES |
10 | COX5A | COX5A | COX5A | 1584 | 0.18 | 0.082 | YES |
11 | NDUFS8 | NDUFS8 | NDUFS8 | 1616 | 0.18 | 0.095 | YES |
12 | IDH3A | IDH3A | IDH3A | 1619 | 0.18 | 0.11 | YES |
13 | PDHB | PDHB | PDHB | 1683 | 0.17 | 0.12 | YES |
14 | COX7B | COX7B | COX7B | 1693 | 0.17 | 0.13 | YES |
15 | PDHA1 | PDHA1 | PDHA1 | 1843 | 0.16 | 0.14 | YES |
16 | SUCLG1 | SUCLG1 | SUCLG1 | 1875 | 0.16 | 0.15 | YES |
17 | NDUFA6 | NDUFA6 | NDUFA6 | 1892 | 0.16 | 0.16 | YES |
18 | ATP5G1 | ATP5G1 | ATP5G1 | 1896 | 0.15 | 0.17 | YES |
19 | NDUFB1 | NDUFB1 | NDUFB1 | 1953 | 0.15 | 0.18 | YES |
20 | NDUFA3 | NDUFA3 | NDUFA3 | 1962 | 0.15 | 0.19 | YES |
21 | ATP5A1 | ATP5A1 | ATP5A1 | 2016 | 0.14 | 0.2 | YES |
22 | NDUFB2 | NDUFB2 | NDUFB2 | 2115 | 0.14 | 0.21 | YES |
23 | LDHB | LDHB | LDHB | 2157 | 0.14 | 0.22 | YES |
24 | COX6A1 | COX6A1 | COX6A1 | 2186 | 0.13 | 0.23 | YES |
25 | PDHX | PDHX | PDHX | 2188 | 0.13 | 0.24 | YES |
26 | COX6C | COX6C | COX6C | 2197 | 0.13 | 0.25 | YES |
27 | NDUFB9 | NDUFB9 | NDUFB9 | 2235 | 0.13 | 0.26 | YES |
28 | NDUFA9 | NDUFA9 | NDUFA9 | 2286 | 0.13 | 0.26 | YES |
29 | NDUFB5 | NDUFB5 | NDUFB5 | 2295 | 0.13 | 0.27 | YES |
30 | ATP5B | ATP5B | ATP5B | 2317 | 0.13 | 0.28 | YES |
31 | UQCRC2 | UQCRC2 | UQCRC2 | 2356 | 0.12 | 0.29 | YES |
32 | DLD | DLD | DLD | 2373 | 0.12 | 0.3 | YES |
33 | SUCLG2 | SUCLG2 | SUCLG2 | 2374 | 0.12 | 0.31 | YES |
34 | COX8A | COX8A | COX8A | 2436 | 0.12 | 0.32 | YES |
35 | NDUFA8 | NDUFA8 | NDUFA8 | 2454 | 0.12 | 0.33 | YES |
36 | ATP5L | ATP5L | ATP5L | 2481 | 0.12 | 0.33 | YES |
37 | UQCR11 | UQCR11 | UQCR11 | 2565 | 0.12 | 0.34 | YES |
38 | FH | FH | FH | 2567 | 0.12 | 0.35 | YES |
39 | NDUFC2 | NDUFC2 | NDUFC2 | 2586 | 0.11 | 0.36 | YES |
40 | L2HGDH | L2HGDH | L2HGDH | 2611 | 0.11 | 0.36 | YES |
41 | ATP5J2 | ATP5J2 | ATP5J2 | 2633 | 0.11 | 0.37 | YES |
42 | COX4I1 | COX4I1 | COX4I1 | 2694 | 0.11 | 0.38 | YES |
43 | NDUFS1 | NDUFS1 | NDUFS1 | 2702 | 0.11 | 0.39 | YES |
44 | COX5B | COX5B | COX5B | 2761 | 0.11 | 0.39 | YES |
45 | DLAT | DLAT | DLAT | 2807 | 0.1 | 0.4 | YES |
46 | NDUFS3 | NDUFS3 | NDUFS3 | 2821 | 0.1 | 0.41 | YES |
47 | COX6B1 | COX6B1 | COX6B1 | 2847 | 0.1 | 0.41 | YES |
48 | NDUFA13 | NDUFA13 | NDUFA13 | 2863 | 0.1 | 0.42 | YES |
49 | ADHFE1 | ADHFE1 | ADHFE1 | 2878 | 0.1 | 0.43 | YES |
50 | NDUFV1 | NDUFV1 | NDUFV1 | 2900 | 0.1 | 0.44 | YES |
51 | SDHD | SDHD | SDHD | 2914 | 0.099 | 0.44 | YES |
52 | ATP5E | ATP5E | ATP5E | 2950 | 0.098 | 0.45 | YES |
53 | NDUFB7 | NDUFB7 | NDUFB7 | 2955 | 0.098 | 0.46 | YES |
54 | DLST | DLST | DLST | 2961 | 0.098 | 0.46 | YES |
55 | SUCLA2 | SUCLA2 | SUCLA2 | 2973 | 0.097 | 0.47 | YES |
56 | ATP5I | ATP5I | ATP5I | 3056 | 0.094 | 0.47 | YES |
57 | NDUFS6 | NDUFS6 | NDUFS6 | 3059 | 0.094 | 0.48 | YES |
58 | NDUFS7 | NDUFS7 | NDUFS7 | 3077 | 0.094 | 0.49 | YES |
59 | ATP5D | ATP5D | ATP5D | 3144 | 0.091 | 0.49 | YES |
60 | COX7C | COX7C | COX7C | 3165 | 0.09 | 0.5 | YES |
61 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 3187 | 0.09 | 0.5 | YES |
62 | NDUFA5 | NDUFA5 | NDUFA5 | 3201 | 0.089 | 0.51 | YES |
63 | CS | CS | CS | 3266 | 0.087 | 0.52 | YES |
64 | IDH2 | IDH2 | IDH2 | 3284 | 0.086 | 0.52 | YES |
65 | NDUFA12 | NDUFA12 | NDUFA12 | 3294 | 0.086 | 0.53 | YES |
66 | OGDH | OGDH | OGDH | 3365 | 0.084 | 0.53 | YES |
67 | NDUFA1 | NDUFA1 | NDUFA1 | 3385 | 0.083 | 0.54 | YES |
68 | BSG | BSG | BSG | 3471 | 0.081 | 0.54 | YES |
69 | MDH2 | MDH2 | MDH2 | 3490 | 0.08 | 0.54 | YES |
70 | NDUFB6 | NDUFB6 | NDUFB6 | 3542 | 0.079 | 0.55 | YES |
71 | ATP5H | ATP5H | ATP5H | 3546 | 0.079 | 0.55 | YES |
72 | ATP5J | ATP5J | ATP5J | 3553 | 0.079 | 0.56 | YES |
73 | NDUFA7 | NDUFA7 | NDUFA7 | 3613 | 0.077 | 0.56 | YES |
74 | NDUFB8 | NDUFB8 | NDUFB8 | 3616 | 0.077 | 0.57 | YES |
75 | UQCRQ | UQCRQ | UQCRQ | 3657 | 0.076 | 0.57 | YES |
76 | CYC1 | CYC1 | CYC1 | 3699 | 0.074 | 0.58 | YES |
77 | NDUFB3 | NDUFB3 | NDUFB3 | 3729 | 0.074 | 0.58 | YES |
78 | NDUFA11 | NDUFA11 | NDUFA11 | 3769 | 0.073 | 0.58 | YES |
79 | UQCRB | UQCRB | UQCRB | 3791 | 0.072 | 0.59 | YES |
80 | NDUFS2 | NDUFS2 | NDUFS2 | 3820 | 0.071 | 0.59 | YES |
81 | NDUFB10 | NDUFB10 | NDUFB10 | 3921 | 0.069 | 0.59 | YES |
82 | NDUFA10 | NDUFA10 | NDUFA10 | 4059 | 0.065 | 0.59 | YES |
83 | ATP5O | ATP5O | ATP5O | 4080 | 0.064 | 0.6 | YES |
84 | SDHA | SDHA | SDHA | 4100 | 0.064 | 0.6 | YES |
85 | COX7A2L | COX7A2L | COX7A2L | 4134 | 0.063 | 0.6 | YES |
86 | ATP5F1 | ATP5F1 | ATP5F1 | 4149 | 0.062 | 0.61 | YES |
87 | ATP5C1 | ATP5C1 | ATP5C1 | 4248 | 0.06 | 0.61 | NO |
88 | IDH3G | IDH3G | IDH3G | 4348 | 0.057 | 0.61 | NO |
89 | SDHC | SDHC | SDHC | 4442 | 0.055 | 0.6 | NO |
90 | NDUFB4 | NDUFB4 | NDUFB4 | 4720 | 0.05 | 0.59 | NO |
91 | NDUFS4 | NDUFS4 | NDUFS4 | 4835 | 0.048 | 0.59 | NO |
92 | ACO2 | ACO2 | ACO2 | 4885 | 0.047 | 0.59 | NO |
93 | NDUFV2 | NDUFV2 | NDUFV2 | 5035 | 0.044 | 0.59 | NO |
94 | ETFA | ETFA | ETFA | 5078 | 0.043 | 0.59 | NO |
95 | IDH3B | IDH3B | IDH3B | 5115 | 0.043 | 0.59 | NO |
96 | NDUFS5 | NDUFS5 | NDUFS5 | 5188 | 0.041 | 0.59 | NO |
97 | NDUFA2 | NDUFA2 | NDUFA2 | 5369 | 0.038 | 0.58 | NO |
98 | ETFDH | ETFDH | ETFDH | 5883 | 0.031 | 0.56 | NO |
99 | SDHB | SDHB | SDHB | 6002 | 0.028 | 0.55 | NO |
100 | SLC16A8 | SLC16A8 | SLC16A8 | 7086 | 0.012 | 0.5 | NO |
101 | ETFB | ETFB | ETFB | 7194 | 0.011 | 0.49 | NO |
102 | NDUFV3 | NDUFV3 | NDUFV3 | 8072 | -0.00086 | 0.44 | NO |
103 | PDPR | PDPR | PDPR | 9390 | -0.018 | 0.37 | NO |
104 | NDUFC1 | NDUFC1 | NDUFC1 | 9449 | -0.018 | 0.37 | NO |
105 | IDH1 | IDH1 | IDH1 | 10102 | -0.028 | 0.34 | NO |
106 | UCP2 | UCP2 | UCP2 | 10258 | -0.03 | 0.33 | NO |
107 | PDK2 | PDK2 | PDK2 | 10654 | -0.037 | 0.31 | NO |
108 | PDK3 | PDK3 | PDK3 | 11780 | -0.057 | 0.25 | NO |
109 | D2HGDH | D2HGDH | D2HGDH | 13066 | -0.088 | 0.19 | NO |
110 | SLC16A1 | SLC16A1 | SLC16A1 | 14597 | -0.14 | 0.12 | NO |
111 | LDHA | LDHA | LDHA | 14783 | -0.15 | 0.12 | NO |
112 | UCP3 | UCP3 | UCP3 | 15739 | -0.19 | 0.081 | NO |
113 | PDK1 | PDK1 | PDK1 | 16088 | -0.21 | 0.078 | NO |
114 | PDK4 | PDK4 | PDK4 | 16462 | -0.23 | 0.077 | NO |
115 | SLC16A3 | SLC16A3 | SLC16A3 | 16990 | -0.27 | 0.07 | 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 EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI INFECTION.
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Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG EPITHELIAL CELL SIGNALING IN HELICOBACTER PYLORI INFECTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S6. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | LDHD | LDHD | LDHD | 416 | 0.41 | 0.087 | YES |
2 | COQ2 | COQ2 | COQ2 | 1095 | 0.24 | 0.12 | YES |
3 | SLC25A4 | SLC25A4 | SLC25A4 | 1660 | 0.17 | 0.13 | YES |
4 | FXC1 | FXC1 | FXC1 | 1748 | 0.17 | 0.17 | YES |
5 | TIMM8A | TIMM8A | TIMM8A | 1880 | 0.16 | 0.2 | YES |
6 | ATP5G1 | ATP5G1 | ATP5G1 | 1896 | 0.15 | 0.25 | YES |
7 | FXN | FXN | FXN | 2008 | 0.14 | 0.28 | YES |
8 | ATP5A1 | ATP5A1 | ATP5A1 | 2016 | 0.14 | 0.32 | YES |
9 | CHCHD4 | CHCHD4 | CHCHD4 | 2249 | 0.13 | 0.34 | YES |
10 | ATP5B | ATP5B | ATP5B | 2317 | 0.13 | 0.37 | YES |
11 | SLC25A12 | SLC25A12 | SLC25A12 | 2339 | 0.12 | 0.4 | YES |
12 | COX17 | COX17 | COX17 | 2833 | 0.1 | 0.4 | YES |
13 | CS | CS | CS | 3266 | 0.087 | 0.4 | YES |
14 | TIMM17B | TIMM17B | TIMM17B | 3428 | 0.082 | 0.42 | YES |
15 | PMPCB | PMPCB | PMPCB | 3448 | 0.082 | 0.44 | YES |
16 | TIMM50 | TIMM50 | TIMM50 | 3503 | 0.08 | 0.46 | YES |
17 | PMPCA | PMPCA | PMPCA | 3559 | 0.078 | 0.48 | YES |
18 | CYC1 | CYC1 | CYC1 | 3699 | 0.074 | 0.49 | YES |
19 | GFER | GFER | GFER | 3991 | 0.067 | 0.49 | YES |
20 | TIMM10 | TIMM10 | TIMM10 | 4152 | 0.062 | 0.5 | YES |
21 | TIMM13 | TIMM13 | TIMM13 | 4192 | 0.061 | 0.51 | YES |
22 | IDH3G | IDH3G | IDH3G | 4348 | 0.057 | 0.52 | YES |
23 | TIMM17A | TIMM17A | TIMM17A | 4370 | 0.057 | 0.53 | YES |
24 | DNAJC19 | DNAJC19 | DNAJC19 | 4472 | 0.055 | 0.54 | YES |
25 | TOMM40 | TOMM40 | TOMM40 | 4688 | 0.05 | 0.54 | YES |
26 | MTX2 | MTX2 | MTX2 | 4713 | 0.05 | 0.56 | YES |
27 | C18orf55 | C18orf55 | C18orf55 | 4737 | 0.049 | 0.57 | YES |
28 | TIMM22 | TIMM22 | TIMM22 | 4853 | 0.047 | 0.57 | YES |
29 | ACO2 | ACO2 | ACO2 | 4885 | 0.047 | 0.59 | YES |
30 | TOMM22 | TOMM22 | TOMM22 | 5021 | 0.044 | 0.59 | YES |
31 | TIMM8B | TIMM8B | TIMM8B | 5045 | 0.044 | 0.6 | YES |
32 | TIMM9 | TIMM9 | TIMM9 | 5094 | 0.043 | 0.61 | YES |
33 | SLC25A6 | SLC25A6 | SLC25A6 | 5381 | 0.038 | 0.6 | YES |
34 | TOMM5 | TOMM5 | TOMM5 | 5428 | 0.037 | 0.61 | YES |
35 | TIMM44 | TIMM44 | TIMM44 | 5463 | 0.037 | 0.62 | YES |
36 | SAMM50 | SAMM50 | SAMM50 | 5702 | 0.033 | 0.62 | NO |
37 | HSPA9 | HSPA9 | HSPA9 | 5886 | 0.03 | 0.61 | NO |
38 | GRPEL1 | GRPEL1 | GRPEL1 | 7406 | 0.0079 | 0.53 | NO |
39 | HSPD1 | HSPD1 | HSPD1 | 7727 | 0.0038 | 0.52 | NO |
40 | SLC25A13 | SLC25A13 | SLC25A13 | 7766 | 0.0033 | 0.52 | NO |
41 | GRPEL2 | GRPEL2 | GRPEL2 | 8282 | -0.0034 | 0.49 | NO |
42 | VDAC1 | VDAC1 | VDAC1 | 8313 | -0.0038 | 0.49 | NO |
43 | MTX1 | MTX1 | MTX1 | 8493 | -0.0062 | 0.48 | NO |
44 | TOMM70A | TOMM70A | TOMM70A | 8758 | -0.0095 | 0.47 | NO |
45 | TOMM7 | TOMM7 | TOMM7 | 9482 | -0.019 | 0.43 | NO |
46 | TOMM20 | TOMM20 | TOMM20 | 9562 | -0.02 | 0.43 | NO |
47 | BCS1L | BCS1L | BCS1L | 11014 | -0.042 | 0.36 | NO |
48 | HSCB | HSCB | HSCB | 11692 | -0.055 | 0.34 | NO |
49 | TAZ | TAZ | TAZ | 12204 | -0.066 | 0.33 | 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: SIG PIP3 SIGNALING IN CARDIAC MYOCTES.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: SIG PIP3 SIGNALING IN CARDIAC MYOCTES, 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 | SH3GL2 | SH3GL2 | SH3GL2 | 65 | 0.72 | 0.21 | YES |
2 | L1CAM | L1CAM | L1CAM | 148 | 0.59 | 0.37 | YES |
3 | RPS6KA6 | RPS6KA6 | RPS6KA6 | 203 | 0.54 | 0.53 | YES |
4 | AP2B1 | AP2B1 | AP2B1 | 4200 | 0.061 | 0.33 | NO |
5 | CLTA | CLTA | CLTA | 4487 | 0.054 | 0.33 | NO |
6 | FGFR1 | FGFR1 | FGFR1 | 4790 | 0.049 | 0.32 | NO |
7 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 5217 | 0.041 | 0.31 | NO |
8 | CLTC | CLTC | CLTC | 5593 | 0.035 | 0.3 | NO |
9 | CSNK2A2 | CSNK2A2 | CSNK2A2 | 5801 | 0.032 | 0.3 | NO |
10 | ITGB3 | ITGB3 | ITGB3 | 6339 | 0.023 | 0.28 | NO |
11 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 6556 | 0.02 | 0.27 | NO |
12 | AP2S1 | AP2S1 | AP2S1 | 6951 | 0.014 | 0.25 | NO |
13 | MAP2K2 | MAP2K2 | MAP2K2 | 7025 | 0.013 | 0.25 | NO |
14 | MAP2K1 | MAP2K1 | MAP2K1 | 7598 | 0.0054 | 0.22 | NO |
15 | AP2A2 | AP2A2 | AP2A2 | 7618 | 0.0052 | 0.22 | NO |
16 | RAC1 | RAC1 | RAC1 | 7792 | 0.0029 | 0.22 | NO |
17 | AP2M1 | AP2M1 | AP2M1 | 8099 | -0.0012 | 0.2 | NO |
18 | RPS6KA4 | RPS6KA4 | RPS6KA4 | 8648 | -0.0081 | 0.17 | NO |
19 | ITGAV | ITGAV | ITGAV | 9431 | -0.018 | 0.13 | NO |
20 | CSNK2B | CSNK2B | CSNK2B | 9626 | -0.02 | 0.13 | NO |
21 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 9929 | -0.025 | 0.12 | NO |
22 | NCAM1 | NCAM1 | NCAM1 | 9938 | -0.025 | 0.13 | NO |
23 | PAK1 | PAK1 | PAK1 | 10181 | -0.029 | 0.12 | NO |
24 | MAPK3 | MAPK3 | MAPK3 | 10607 | -0.036 | 0.11 | NO |
25 | ITGA2B | ITGA2B | ITGA2B | 11501 | -0.051 | 0.075 | NO |
26 | ITGB1 | ITGB1 | ITGB1 | 11533 | -0.052 | 0.089 | NO |
27 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 11551 | -0.052 | 0.1 | NO |
28 | AP2A1 | AP2A1 | AP2A1 | 12148 | -0.065 | 0.089 | NO |
29 | MAPK1 | MAPK1 | MAPK1 | 12274 | -0.068 | 0.1 | NO |
30 | ITGA9 | ITGA9 | ITGA9 | 12872 | -0.082 | 0.094 | NO |
31 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 15137 | -0.16 | 0.016 | NO |
32 | EGFR | EGFR | EGFR | 15370 | -0.17 | 0.053 | NO |
33 | NRP1 | NRP1 | NRP1 | 15450 | -0.18 | 0.1 | NO |
34 | ITGA5 | ITGA5 | ITGA5 | 15680 | -0.19 | 0.14 | NO |
Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID PI3KCIAKTPATHWAY.

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

Table S8. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SH3GL2 | SH3GL2 | SH3GL2 | 65 | 0.72 | 0.21 | YES |
2 | TPD52L1 | TPD52L1 | TPD52L1 | 326 | 0.46 | 0.32 | YES |
3 | AP1M2 | AP1M2 | AP1M2 | 743 | 0.31 | 0.39 | YES |
4 | SORT1 | SORT1 | SORT1 | 2764 | 0.11 | 0.31 | YES |
5 | CPD | CPD | CPD | 3342 | 0.085 | 0.31 | YES |
6 | NAPA | NAPA | NAPA | 3998 | 0.067 | 0.29 | YES |
7 | GAK | GAK | GAK | 4023 | 0.066 | 0.31 | YES |
8 | HSPA8 | HSPA8 | HSPA8 | 4107 | 0.063 | 0.32 | YES |
9 | OCRL | OCRL | OCRL | 4275 | 0.059 | 0.33 | YES |
10 | DNAJC6 | DNAJC6 | DNAJC6 | 4394 | 0.056 | 0.34 | YES |
11 | YIPF6 | YIPF6 | YIPF6 | 4398 | 0.056 | 0.36 | YES |
12 | CLTA | CLTA | CLTA | 4487 | 0.054 | 0.37 | YES |
13 | RAB5C | RAB5C | RAB5C | 4603 | 0.052 | 0.38 | YES |
14 | VAMP7 | VAMP7 | VAMP7 | 4616 | 0.052 | 0.39 | YES |
15 | VAMP2 | VAMP2 | VAMP2 | 5005 | 0.044 | 0.38 | YES |
16 | BLOC1S1 | BLOC1S1 | BLOC1S1 | 5022 | 0.044 | 0.39 | YES |
17 | CLTC | CLTC | CLTC | 5593 | 0.035 | 0.37 | NO |
18 | HIP1R | HIP1R | HIP1R | 5848 | 0.031 | 0.37 | NO |
19 | PICALM | PICALM | PICALM | 6003 | 0.028 | 0.37 | NO |
20 | AP1B1 | AP1B1 | AP1B1 | 6354 | 0.023 | 0.35 | NO |
21 | AP1G1 | AP1G1 | AP1G1 | 6399 | 0.022 | 0.36 | NO |
22 | PIK3C2A | PIK3C2A | PIK3C2A | 6657 | 0.018 | 0.35 | NO |
23 | TFRC | TFRC | TFRC | 6708 | 0.018 | 0.35 | NO |
24 | AP3B1 | AP3B1 | AP3B1 | 6730 | 0.017 | 0.36 | NO |
25 | TPD52 | TPD52 | TPD52 | 7300 | 0.0093 | 0.33 | NO |
26 | IGF2R | IGF2R | IGF2R | 7325 | 0.009 | 0.33 | NO |
27 | AP1S1 | AP1S1 | AP1S1 | 7465 | 0.007 | 0.32 | NO |
28 | VAMP8 | VAMP8 | VAMP8 | 7566 | 0.0058 | 0.32 | NO |
29 | SNX2 | SNX2 | SNX2 | 7657 | 0.0047 | 0.32 | NO |
30 | SH3D19 | SH3D19 | SH3D19 | 7708 | 0.0041 | 0.31 | NO |
31 | AP4E1 | AP4E1 | AP4E1 | 7838 | 0.0023 | 0.31 | NO |
32 | BLOC1S3 | BLOC1S3 | BLOC1S3 | 7891 | 0.0017 | 0.3 | NO |
33 | SNAPIN | SNAPIN | SNAPIN | 8151 | -0.0019 | 0.29 | NO |
34 | SNX5 | SNX5 | SNX5 | 8183 | -0.0023 | 0.29 | NO |
35 | SNX9 | SNX9 | SNX9 | 8184 | -0.0023 | 0.29 | NO |
36 | PUM1 | PUM1 | PUM1 | 8223 | -0.0028 | 0.29 | NO |
37 | ARF1 | ARF1 | ARF1 | 8367 | -0.0044 | 0.28 | NO |
38 | FTL | FTL | FTL | 8852 | -0.011 | 0.26 | NO |
39 | TGOLN2 | TGOLN2 | TGOLN2 | 9076 | -0.013 | 0.25 | NO |
40 | CNO | CNO | CNO | 9079 | -0.014 | 0.26 | NO |
41 | NECAP1 | NECAP1 | NECAP1 | 9377 | -0.017 | 0.24 | NO |
42 | PLDN | PLDN | PLDN | 9521 | -0.019 | 0.24 | NO |
43 | FTH1 | FTH1 | FTH1 | 10434 | -0.033 | 0.2 | NO |
44 | AP1S2 | AP1S2 | AP1S2 | 11146 | -0.045 | 0.18 | NO |
45 | AP1M1 | AP1M1 | AP1M1 | 11570 | -0.052 | 0.17 | NO |
46 | DNM2 | DNM2 | DNM2 | 11632 | -0.054 | 0.18 | NO |
47 | ARRB1 | ARRB1 | ARRB1 | 12015 | -0.062 | 0.18 | NO |
48 | TXNDC5 | TXNDC5 | TXNDC5 | 12424 | -0.072 | 0.18 | NO |
49 | AP4B1 | AP4B1 | AP4B1 | 12478 | -0.073 | 0.19 | NO |
50 | DTNBP1 | DTNBP1 | DTNBP1 | 12685 | -0.078 | 0.2 | NO |
51 | AP3S1 | AP3S1 | AP3S1 | 14687 | -0.14 | 0.14 | NO |
52 | TBC1D8B | TBC1D8B | TBC1D8B | 16033 | -0.2 | 0.12 | NO |
Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT.

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

Table 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 | SH3GL2 | SH3GL2 | SH3GL2 | 65 | 0.72 | 0.2 | YES |
2 | L1CAM | L1CAM | L1CAM | 148 | 0.59 | 0.37 | YES |
3 | RPS6KA6 | RPS6KA6 | RPS6KA6 | 203 | 0.54 | 0.52 | YES |
4 | AP2B1 | AP2B1 | AP2B1 | 4200 | 0.061 | 0.32 | NO |
5 | CLTA | CLTA | CLTA | 4487 | 0.054 | 0.32 | NO |
6 | KIAA1598 | KIAA1598 | KIAA1598 | 5270 | 0.04 | 0.29 | NO |
7 | CLTC | CLTC | CLTC | 5593 | 0.035 | 0.28 | NO |
8 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 6556 | 0.02 | 0.24 | NO |
9 | AP2S1 | AP2S1 | AP2S1 | 6951 | 0.014 | 0.22 | NO |
10 | EZR | EZR | EZR | 7433 | 0.0075 | 0.2 | NO |
11 | AP2A2 | AP2A2 | AP2A2 | 7618 | 0.0052 | 0.19 | NO |
12 | SRC | SRC | SRC | 7993 | 0.0002 | 0.17 | NO |
13 | AP2M1 | AP2M1 | AP2M1 | 8099 | -0.0012 | 0.16 | NO |
14 | RPS6KA4 | RPS6KA4 | RPS6KA4 | 8648 | -0.0081 | 0.13 | NO |
15 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 9929 | -0.025 | 0.071 | NO |
16 | NUMB | NUMB | NUMB | 10032 | -0.026 | 0.073 | NO |
17 | RDX | RDX | RDX | 10379 | -0.032 | 0.063 | NO |
18 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 11551 | -0.052 | 0.014 | NO |
19 | DNM2 | DNM2 | DNM2 | 11632 | -0.054 | 0.025 | NO |
20 | AP2A1 | AP2A1 | AP2A1 | 12148 | -0.065 | 0.016 | NO |
21 | MAPK1 | MAPK1 | MAPK1 | 12274 | -0.068 | 0.029 | NO |
22 | MSN | MSN | MSN | 12348 | -0.07 | 0.045 | NO |
23 | DNM1 | DNM1 | DNM1 | 13501 | -0.099 | 0.011 | NO |
24 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 15137 | -0.16 | -0.032 | NO |
25 | DPYSL2 | DPYSL2 | DPYSL2 | 15186 | -0.16 | 0.012 | NO |
26 | KIF4A | KIF4A | KIF4A | 15940 | -0.2 | 0.028 | NO |
27 | KIF4B | KIF4B | KIF4B | 17575 | -0.34 | 0.038 | NO |
Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANS GOLGI NETWORK VESICLE BUDDING.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANS GOLGI NETWORK VESICLE BUDDING, 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 | PAK6 | PAK6 | PAK6 | 31 | 0.83 | 0.12 | YES |
2 | ERBB4 | ERBB4 | ERBB4 | 49 | 0.77 | 0.23 | YES |
3 | PAK7 | PAK7 | PAK7 | 243 | 0.5 | 0.3 | YES |
4 | SLC2A4 | SLC2A4 | SLC2A4 | 500 | 0.37 | 0.34 | YES |
5 | PARD6A | PARD6A | PARD6A | 1066 | 0.25 | 0.34 | YES |
6 | IRS1 | IRS1 | IRS1 | 1203 | 0.22 | 0.37 | YES |
7 | IGF1 | IGF1 | IGF1 | 1721 | 0.17 | 0.36 | YES |
8 | IRS2 | IRS2 | IRS2 | 1820 | 0.16 | 0.38 | YES |
9 | SFN | SFN | SFN | 1823 | 0.16 | 0.4 | YES |
10 | SOS2 | SOS2 | SOS2 | 3158 | 0.09 | 0.34 | NO |
11 | GSK3B | GSK3B | GSK3B | 3344 | 0.085 | 0.35 | NO |
12 | EBP | EBP | EBP | 3509 | 0.08 | 0.35 | NO |
13 | PAK4 | PAK4 | PAK4 | 3898 | 0.069 | 0.34 | NO |
14 | PPP1R13B | PPP1R13B | PPP1R13B | 4123 | 0.063 | 0.33 | NO |
15 | CYTH3 | CYTH3 | CYTH3 | 4446 | 0.055 | 0.32 | NO |
16 | AKT2 | AKT2 | AKT2 | 4662 | 0.051 | 0.32 | NO |
17 | YWHAB | YWHAB | YWHAB | 4825 | 0.048 | 0.32 | NO |
18 | BCL2L1 | BCL2L1 | BCL2L1 | 4891 | 0.047 | 0.32 | NO |
19 | MTOR | MTOR | MTOR | 4903 | 0.046 | 0.33 | NO |
20 | AKT1 | AKT1 | AKT1 | 5567 | 0.035 | 0.3 | NO |
21 | GADD45A | GADD45A | GADD45A | 5724 | 0.033 | 0.29 | NO |
22 | PIK3CA | PIK3CA | PIK3CA | 6546 | 0.02 | 0.25 | NO |
23 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 6556 | 0.02 | 0.25 | NO |
24 | YWHAE | YWHAE | YWHAE | 6617 | 0.019 | 0.25 | NO |
25 | GSK3A | GSK3A | GSK3A | 6934 | 0.014 | 0.24 | NO |
26 | TSC1 | TSC1 | TSC1 | 7550 | 0.0061 | 0.2 | NO |
27 | TSC2 | TSC2 | TSC2 | 7595 | 0.0054 | 0.2 | NO |
28 | INPPL1 | INPPL1 | INPPL1 | 7621 | 0.0052 | 0.2 | NO |
29 | BAD | BAD | BAD | 7761 | 0.0033 | 0.2 | NO |
30 | CREB3 | CREB3 | CREB3 | 7854 | 0.0022 | 0.19 | NO |
31 | CDC42 | CDC42 | CDC42 | 7983 | 0.00039 | 0.18 | NO |
32 | YWHAQ | YWHAQ | YWHAQ | 8143 | -0.0018 | 0.17 | NO |
33 | PTPN1 | PTPN1 | PTPN1 | 8383 | -0.0048 | 0.16 | NO |
34 | MET | MET | MET | 8516 | -0.0065 | 0.16 | NO |
35 | PTEN | PTEN | PTEN | 8564 | -0.007 | 0.15 | NO |
36 | PTK2 | PTK2 | PTK2 | 8569 | -0.0071 | 0.16 | NO |
37 | PAK2 | PAK2 | PAK2 | 8814 | -0.01 | 0.14 | NO |
38 | YWHAZ | YWHAZ | YWHAZ | 8882 | -0.011 | 0.14 | NO |
39 | NOLC1 | NOLC1 | NOLC1 | 9077 | -0.013 | 0.13 | NO |
40 | YWHAG | YWHAG | YWHAG | 9234 | -0.016 | 0.13 | NO |
41 | GRB2 | GRB2 | GRB2 | 9568 | -0.02 | 0.11 | NO |
42 | PARD3 | PARD3 | PARD3 | 9843 | -0.024 | 0.099 | NO |
43 | CDK2 | CDK2 | CDK2 | 9880 | -0.024 | 0.1 | NO |
44 | YWHAH | YWHAH | YWHAH | 9910 | -0.025 | 0.1 | NO |
45 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 9929 | -0.025 | 0.1 | NO |
46 | PAK1 | PAK1 | PAK1 | 10181 | -0.029 | 0.096 | NO |
47 | AKT3 | AKT3 | AKT3 | 10601 | -0.036 | 0.078 | NO |
48 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 10624 | -0.036 | 0.082 | NO |
49 | CREB1 | CREB1 | CREB1 | 11007 | -0.042 | 0.067 | NO |
50 | GAB1 | GAB1 | GAB1 | 11253 | -0.046 | 0.061 | NO |
51 | FOXO3 | FOXO3 | FOXO3 | 11288 | -0.047 | 0.066 | NO |
52 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 11551 | -0.052 | 0.059 | NO |
53 | F2RL2 | F2RL2 | F2RL2 | 11598 | -0.053 | 0.064 | NO |
54 | SOS1 | SOS1 | SOS1 | 11807 | -0.058 | 0.061 | NO |
55 | IFI27 | IFI27 | IFI27 | 11919 | -0.06 | 0.064 | NO |
56 | IGFBP1 | IGFBP1 | IGFBP1 | 12926 | -0.084 | 0.021 | NO |
57 | PAK3 | PAK3 | PAK3 | 13613 | -0.1 | -0.0018 | NO |
58 | CDKN1B | CDKN1B | CDKN1B | 13638 | -0.1 | 0.012 | NO |
59 | SHC1 | SHC1 | SHC1 | 14166 | -0.12 | 0.00094 | NO |
60 | PIK3CD | PIK3CD | PIK3CD | 14632 | -0.14 | -0.0042 | NO |
61 | PREX1 | PREX1 | PREX1 | 15073 | -0.16 | -0.0053 | NO |
62 | PDK1 | PDK1 | PDK1 | 16088 | -0.21 | -0.031 | NO |
63 | MYC | MYC | MYC | 16451 | -0.23 | -0.017 | NO |
64 | CDKN2A | CDKN2A | CDKN2A | 16617 | -0.24 | 0.0092 | NO |
65 | CREB5 | CREB5 | CREB5 | 16831 | -0.26 | 0.036 | NO |
66 | PIK3R5 | PIK3R5 | PIK3R5 | 17195 | -0.29 | 0.058 | NO |
Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME MITOCHONDRIAL PROTEIN IMPORT.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MITOCHONDRIAL PROTEIN IMPORT, 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 FATTY ACID METABOLISM | 39 | genes.ES.table | 0.55 | 1.5 | 0.071 | 1 | 0.97 | 0.44 | 0.16 | 0.37 | 1 | 0.55 |
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION | 44 | genes.ES.table | 0.59 | 1.6 | 0.061 | 1 | 0.89 | 0.73 | 0.24 | 0.56 | 0.76 | 0.43 |
KEGG LYSINE DEGRADATION | 44 | genes.ES.table | 0.42 | 1.6 | 0.049 | 1 | 0.88 | 0.34 | 0.2 | 0.27 | 0.91 | 0.48 |
KEGG HISTIDINE METABOLISM | 29 | genes.ES.table | 0.62 | 1.5 | 0.049 | 1 | 0.97 | 0.48 | 0.14 | 0.42 | 1 | 0.56 |
KEGG TRYPTOPHAN METABOLISM | 39 | genes.ES.table | 0.49 | 1.3 | 0.1 | 1 | 1 | 0.56 | 0.2 | 0.45 | 1 | 0.6 |
KEGG PROPANOATE METABOLISM | 32 | genes.ES.table | 0.61 | 1.7 | 0.045 | 1 | 0.8 | 0.62 | 0.21 | 0.49 | 0.71 | 0.4 |
KEGG PPAR SIGNALING PATHWAY | 65 | genes.ES.table | 0.58 | 1.6 | 0.023 | 1 | 0.95 | 0.34 | 0.099 | 0.31 | 0.96 | 0.49 |
KEGG PEROXISOME | 76 | genes.ES.table | 0.54 | 1.7 | 0.033 | 1 | 0.77 | 0.41 | 0.16 | 0.35 | 0.97 | 0.49 |
KEGG ADIPOCYTOKINE SIGNALING PATHWAY | 64 | genes.ES.table | 0.38 | 1.4 | 0.079 | 1 | 0.99 | 0.25 | 0.15 | 0.21 | 1 | 0.6 |
BIOCARTA AT1R PATHWAY | 32 | genes.ES.table | 0.38 | 1.5 | 0.079 | 1 | 0.98 | 0.22 | 0.18 | 0.18 | 1 | 0.52 |
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 | RXRG | RXRG | RXRG | 663 | 0.24 | 0.1 | YES |
2 | NR4A1 | NR4A1 | NR4A1 | 840 | 0.2 | 0.21 | YES |
3 | BCL2 | BCL2 | BCL2 | 1148 | 0.16 | 0.29 | YES |
4 | NR1H4 | NR1H4 | NR1H4 | 1505 | 0.13 | 0.35 | YES |
5 | THRA | THRA | THRA | 1560 | 0.13 | 0.42 | YES |
6 | RARB | RARB | RARB | 1773 | 0.12 | 0.48 | YES |
7 | THRB | THRB | THRB | 1982 | 0.11 | 0.53 | YES |
8 | PPARG | PPARG | PPARG | 2253 | 0.096 | 0.57 | YES |
9 | PPARA | PPARA | PPARA | 2346 | 0.093 | 0.62 | YES |
10 | RARA | RARA | RARA | 3914 | 0.052 | 0.56 | NO |
11 | FAM120B | FAM120B | FAM120B | 4363 | 0.043 | 0.56 | NO |
12 | NCOA1 | NCOA1 | NCOA1 | 4372 | 0.043 | 0.59 | NO |
13 | MED1 | MED1 | MED1 | 6161 | 0.018 | 0.5 | NO |
14 | ABCA1 | ABCA1 | ABCA1 | 6296 | 0.017 | 0.5 | NO |
15 | SREBF1 | SREBF1 | SREBF1 | 6632 | 0.012 | 0.49 | NO |
16 | RXRB | RXRB | RXRB | 6927 | 0.0089 | 0.48 | NO |
17 | VDR | VDR | VDR | 7034 | 0.0077 | 0.48 | NO |
18 | RARG | RARG | RARG | 7198 | 0.006 | 0.48 | NO |
19 | RXRA | RXRA | RXRA | 7546 | 0.0022 | 0.46 | NO |
20 | NR1H3 | NR1H3 | NR1H3 | 8662 | -0.012 | 0.4 | NO |
21 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 8880 | -0.014 | 0.4 | NO |
22 | NCOR2 | NCOR2 | NCOR2 | 9377 | -0.02 | 0.38 | NO |
23 | PPARD | PPARD | PPARD | 9476 | -0.022 | 0.39 | NO |
24 | NR1H2 | NR1H2 | NR1H2 | 10752 | -0.038 | 0.34 | NO |
25 | TNF | TNF | TNF | 11542 | -0.049 | 0.33 | NO |
26 | TGFB1 | TGFB1 | TGFB1 | 12447 | -0.065 | 0.32 | 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 FATTY ACID METABOLISM.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FATTY ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | HAO2 | HAO2 | HAO2 | 14 | 0.7 | 0.089 | YES |
2 | SLC27A2 | SLC27A2 | SLC27A2 | 43 | 0.55 | 0.16 | YES |
3 | DAO | DAO | DAO | 163 | 0.41 | 0.2 | YES |
4 | EHHADH | EHHADH | EHHADH | 466 | 0.28 | 0.22 | YES |
5 | AGXT | AGXT | AGXT | 571 | 0.26 | 0.25 | YES |
6 | PXMP2 | PXMP2 | PXMP2 | 620 | 0.24 | 0.28 | YES |
7 | EPHX2 | EPHX2 | EPHX2 | 757 | 0.22 | 0.3 | YES |
8 | DDO | DDO | DDO | 846 | 0.2 | 0.32 | YES |
9 | FAR2 | FAR2 | FAR2 | 855 | 0.2 | 0.34 | YES |
10 | PEX11A | PEX11A | PEX11A | 1061 | 0.18 | 0.36 | YES |
11 | PECR | PECR | PECR | 1107 | 0.17 | 0.37 | YES |
12 | NOS2 | NOS2 | NOS2 | 1223 | 0.16 | 0.39 | YES |
13 | ACOX2 | ACOX2 | ACOX2 | 1262 | 0.15 | 0.4 | YES |
14 | NUDT12 | NUDT12 | NUDT12 | 1442 | 0.14 | 0.41 | YES |
15 | ACSL1 | ACSL1 | ACSL1 | 1484 | 0.14 | 0.43 | YES |
16 | MLYCD | MLYCD | MLYCD | 1811 | 0.12 | 0.42 | YES |
17 | CAT | CAT | CAT | 1955 | 0.11 | 0.43 | YES |
18 | PHYH | PHYH | PHYH | 2021 | 0.11 | 0.44 | YES |
19 | AGPS | AGPS | AGPS | 2092 | 0.1 | 0.45 | YES |
20 | ABCD3 | ABCD3 | ABCD3 | 2097 | 0.1 | 0.46 | YES |
21 | CRAT | CRAT | CRAT | 2136 | 0.1 | 0.47 | YES |
22 | PEX11G | PEX11G | PEX11G | 2364 | 0.092 | 0.47 | YES |
23 | MPV17L | MPV17L | MPV17L | 2392 | 0.092 | 0.48 | YES |
24 | PAOX | PAOX | PAOX | 2470 | 0.089 | 0.49 | YES |
25 | PEX1 | PEX1 | PEX1 | 2472 | 0.089 | 0.5 | YES |
26 | DHRS4 | DHRS4 | DHRS4 | 2506 | 0.088 | 0.51 | YES |
27 | PEX3 | PEX3 | PEX3 | 2756 | 0.08 | 0.51 | YES |
28 | AMACR | AMACR | AMACR | 2769 | 0.079 | 0.52 | YES |
29 | ABCD2 | ABCD2 | ABCD2 | 2815 | 0.078 | 0.52 | YES |
30 | ECH1 | ECH1 | ECH1 | 2825 | 0.078 | 0.53 | YES |
31 | DECR2 | DECR2 | DECR2 | 2829 | 0.078 | 0.54 | YES |
32 | ACOX1 | ACOX1 | ACOX1 | 3359 | 0.063 | 0.52 | NO |
33 | PEX7 | PEX7 | PEX7 | 3361 | 0.063 | 0.53 | NO |
34 | PIPOX | PIPOX | PIPOX | 3551 | 0.059 | 0.53 | NO |
35 | ACSL6 | ACSL6 | ACSL6 | 3953 | 0.051 | 0.51 | NO |
36 | HMGCL | HMGCL | HMGCL | 4061 | 0.049 | 0.51 | NO |
37 | ABCD4 | ABCD4 | ABCD4 | 4153 | 0.048 | 0.51 | NO |
38 | SCP2 | SCP2 | SCP2 | 4159 | 0.047 | 0.52 | NO |
39 | PEX11B | PEX11B | PEX11B | 4268 | 0.045 | 0.52 | NO |
40 | PEX26 | PEX26 | PEX26 | 4332 | 0.044 | 0.52 | NO |
41 | PEX10 | PEX10 | PEX10 | 4495 | 0.041 | 0.52 | NO |
42 | PMVK | PMVK | PMVK | 4527 | 0.041 | 0.52 | NO |
43 | PEX19 | PEX19 | PEX19 | 4641 | 0.039 | 0.52 | NO |
44 | PEX5 | PEX5 | PEX5 | 4676 | 0.038 | 0.52 | NO |
45 | PEX12 | PEX12 | PEX12 | 4764 | 0.037 | 0.52 | NO |
46 | PEX13 | PEX13 | PEX13 | 5800 | 0.023 | 0.47 | NO |
47 | SLC25A17 | SLC25A17 | SLC25A17 | 6386 | 0.016 | 0.44 | NO |
48 | HSD17B4 | HSD17B4 | HSD17B4 | 6623 | 0.013 | 0.43 | NO |
49 | ACAA1 | ACAA1 | ACAA1 | 6706 | 0.012 | 0.42 | NO |
50 | CROT | CROT | CROT | 7270 | 0.0051 | 0.39 | NO |
51 | GNPAT | GNPAT | GNPAT | 7719 | 0.00032 | 0.37 | NO |
52 | ACSL3 | ACSL3 | ACSL3 | 7836 | -0.0012 | 0.36 | NO |
53 | SOD1 | SOD1 | SOD1 | 7880 | -0.0018 | 0.36 | NO |
54 | IDH2 | IDH2 | IDH2 | 8840 | -0.014 | 0.31 | NO |
55 | PEX2 | PEX2 | PEX2 | 9335 | -0.02 | 0.28 | NO |
56 | GSTK1 | GSTK1 | GSTK1 | 9833 | -0.026 | 0.26 | NO |
57 | PEX14 | PEX14 | PEX14 | 10177 | -0.03 | 0.24 | NO |
58 | HACL1 | HACL1 | HACL1 | 10368 | -0.033 | 0.24 | NO |
59 | ABCD1 | ABCD1 | ABCD1 | 10547 | -0.035 | 0.23 | NO |
60 | PEX6 | PEX6 | PEX6 | 10664 | -0.037 | 0.23 | NO |
61 | FAR1 | FAR1 | FAR1 | 11214 | -0.044 | 0.21 | NO |
62 | MPV17 | MPV17 | MPV17 | 11428 | -0.047 | 0.2 | NO |
63 | PRDX1 | PRDX1 | PRDX1 | 11661 | -0.051 | 0.2 | NO |
64 | PRDX5 | PRDX5 | PRDX5 | 11821 | -0.054 | 0.19 | NO |
65 | ACSL5 | ACSL5 | ACSL5 | 11838 | -0.054 | 0.2 | NO |
66 | PXMP4 | PXMP4 | PXMP4 | 12118 | -0.059 | 0.19 | NO |
67 | MVK | MVK | MVK | 12483 | -0.066 | 0.18 | NO |
68 | PEX16 | PEX16 | PEX16 | 12544 | -0.067 | 0.18 | NO |
69 | NUDT19 | NUDT19 | NUDT19 | 12565 | -0.068 | 0.19 | NO |
70 | ACSL4 | ACSL4 | ACSL4 | 12951 | -0.076 | 0.18 | NO |
71 | SOD2 | SOD2 | SOD2 | 13040 | -0.078 | 0.19 | NO |
72 | IDH1 | IDH1 | IDH1 | 13743 | -0.096 | 0.16 | NO |
73 | ACOT8 | ACOT8 | ACOT8 | 13857 | -0.1 | 0.17 | NO |
74 | ACOX3 | ACOX3 | ACOX3 | 13946 | -0.1 | 0.18 | NO |
75 | BAAT | BAAT | BAAT | 14741 | -0.13 | 0.15 | NO |
76 | XDH | XDH | XDH | 17450 | -0.35 | 0.044 | 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S24. 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 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 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 241 | 0.37 | 0.093 | YES |
2 | EHHADH | EHHADH | EHHADH | 466 | 0.28 | 0.16 | YES |
3 | ABAT | ABAT | ABAT | 730 | 0.22 | 0.21 | YES |
4 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 797 | 0.21 | 0.27 | YES |
5 | HIBCH | HIBCH | HIBCH | 803 | 0.21 | 0.33 | YES |
6 | ACAT1 | ACAT1 | ACAT1 | 956 | 0.19 | 0.38 | YES |
7 | ACADM | ACADM | ACADM | 1125 | 0.17 | 0.42 | YES |
8 | PCCA | PCCA | PCCA | 1279 | 0.15 | 0.45 | YES |
9 | MUT | MUT | MUT | 1547 | 0.13 | 0.48 | YES |
10 | ACSS3 | ACSS3 | ACSS3 | 1599 | 0.13 | 0.51 | YES |
11 | MLYCD | MLYCD | MLYCD | 1811 | 0.12 | 0.53 | YES |
12 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 2098 | 0.1 | 0.55 | YES |
13 | LDHAL6A | LDHAL6A | LDHAL6A | 2403 | 0.091 | 0.56 | YES |
14 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2499 | 0.088 | 0.58 | YES |
15 | SUCLA2 | SUCLA2 | SUCLA2 | 2617 | 0.084 | 0.6 | YES |
16 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 2837 | 0.078 | 0.61 | YES |
17 | ALDH2 | ALDH2 | ALDH2 | 3504 | 0.06 | 0.59 | YES |
18 | HADHA | HADHA | HADHA | 3729 | 0.055 | 0.59 | YES |
19 | ACSS1 | ACSS1 | ACSS1 | 3793 | 0.054 | 0.6 | YES |
20 | MCEE | MCEE | MCEE | 3894 | 0.052 | 0.61 | YES |
21 | LDHA | LDHA | LDHA | 4775 | 0.037 | 0.57 | NO |
22 | ECHS1 | ECHS1 | ECHS1 | 5476 | 0.027 | 0.55 | NO |
23 | SUCLG1 | SUCLG1 | SUCLG1 | 7405 | 0.0039 | 0.44 | NO |
24 | ACACB | ACACB | ACACB | 7417 | 0.0038 | 0.44 | NO |
25 | SUCLG2 | SUCLG2 | SUCLG2 | 8207 | -0.0059 | 0.4 | NO |
26 | LDHC | LDHC | LDHC | 8870 | -0.014 | 0.37 | NO |
27 | ACSS2 | ACSS2 | ACSS2 | 9556 | -0.023 | 0.34 | NO |
28 | LDHB | LDHB | LDHB | 10552 | -0.035 | 0.29 | NO |
29 | PCCB | PCCB | PCCB | 11847 | -0.054 | 0.24 | NO |
30 | ACAT2 | ACAT2 | ACAT2 | 12031 | -0.057 | 0.24 | NO |
31 | ACACA | ACACA | ACACA | 13498 | -0.09 | 0.19 | NO |
32 | LDHAL6B | LDHAL6B | LDHAL6B | 16530 | -0.25 | 0.095 | 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 LYSINE DEGRADATION.

Figure S26. 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
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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 | BBOX1 | BBOX1 | BBOX1 | 164 | 0.41 | 0.12 | YES |
2 | EHHADH | EHHADH | EHHADH | 466 | 0.28 | 0.2 | YES |
3 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 797 | 0.21 | 0.24 | YES |
4 | ACAT1 | ACAT1 | ACAT1 | 956 | 0.19 | 0.3 | YES |
5 | OGDHL | OGDHL | OGDHL | 1613 | 0.13 | 0.3 | YES |
6 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 2098 | 0.1 | 0.31 | YES |
7 | AASS | AASS | AASS | 2369 | 0.092 | 0.32 | YES |
8 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2499 | 0.088 | 0.34 | YES |
9 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 2837 | 0.078 | 0.35 | YES |
10 | TMLHE | TMLHE | TMLHE | 2973 | 0.073 | 0.36 | YES |
11 | ASH1L | ASH1L | ASH1L | 3208 | 0.067 | 0.37 | YES |
12 | ALDH2 | ALDH2 | ALDH2 | 3504 | 0.06 | 0.38 | YES |
13 | PIPOX | PIPOX | PIPOX | 3551 | 0.059 | 0.39 | YES |
14 | HADHA | HADHA | HADHA | 3729 | 0.055 | 0.4 | YES |
15 | AASDH | AASDH | AASDH | 3752 | 0.055 | 0.42 | YES |
16 | SUV420H1 | SUV420H1 | SUV420H1 | 4113 | 0.048 | 0.41 | NO |
17 | AASDHPPT | AASDHPPT | AASDHPPT | 4403 | 0.043 | 0.41 | NO |
18 | DLST | DLST | DLST | 5109 | 0.032 | 0.38 | NO |
19 | ECHS1 | ECHS1 | ECHS1 | 5476 | 0.027 | 0.37 | NO |
20 | OGDH | OGDH | OGDH | 5488 | 0.027 | 0.38 | NO |
21 | SETD7 | SETD7 | SETD7 | 5703 | 0.024 | 0.38 | NO |
22 | HADH | HADH | HADH | 5781 | 0.023 | 0.38 | NO |
23 | AADAT | AADAT | AADAT | 7096 | 0.0069 | 0.31 | NO |
24 | SETDB1 | SETDB1 | SETDB1 | 7301 | 0.0048 | 0.3 | NO |
25 | NSD1 | NSD1 | NSD1 | 7335 | 0.0045 | 0.3 | NO |
26 | DOT1L | DOT1L | DOT1L | 7510 | 0.0026 | 0.29 | NO |
27 | SUV39H2 | SUV39H2 | SUV39H2 | 7690 | 0.00068 | 0.28 | NO |
28 | EHMT1 | EHMT1 | EHMT1 | 7884 | -0.0018 | 0.27 | NO |
29 | WHSC1L1 | WHSC1L1 | WHSC1L1 | 8059 | -0.0042 | 0.26 | NO |
30 | SETD1B | SETD1B | SETD1B | 8560 | -0.01 | 0.24 | NO |
31 | SETDB2 | SETDB2 | SETDB2 | 8857 | -0.014 | 0.23 | NO |
32 | SETD2 | SETD2 | SETD2 | 8894 | -0.015 | 0.23 | NO |
33 | SETD1A | SETD1A | SETD1A | 9062 | -0.016 | 0.22 | NO |
34 | EHMT2 | EHMT2 | EHMT2 | 9727 | -0.025 | 0.2 | NO |
35 | WHSC1 | WHSC1 | WHSC1 | 10382 | -0.033 | 0.17 | NO |
36 | PLOD3 | PLOD3 | PLOD3 | 10481 | -0.034 | 0.18 | NO |
37 | SUV39H1 | SUV39H1 | SUV39H1 | 10689 | -0.037 | 0.18 | NO |
38 | PLOD1 | PLOD1 | PLOD1 | 11247 | -0.044 | 0.16 | NO |
39 | GCDH | GCDH | GCDH | 11299 | -0.045 | 0.17 | NO |
40 | ACAT2 | ACAT2 | ACAT2 | 12031 | -0.057 | 0.15 | NO |
41 | SETD8 | SETD8 | SETD8 | 13163 | -0.081 | 0.11 | NO |
42 | PLOD2 | PLOD2 | PLOD2 | 14019 | -0.11 | 0.1 | NO |
43 | SUV420H2 | SUV420H2 | SUV420H2 | 15766 | -0.19 | 0.067 | NO |
44 | SETMAR | SETMAR | SETMAR | 16154 | -0.22 | 0.12 | NO |
Figure S27. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HISTIDINE METABOLISM.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HISTIDINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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Table 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 | HMGCS2 | HMGCS2 | HMGCS2 | 107 | 0.46 | 0.082 | YES |
2 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 241 | 0.37 | 0.14 | YES |
3 | AOX1 | AOX1 | AOX1 | 403 | 0.3 | 0.19 | YES |
4 | EHHADH | EHHADH | EHHADH | 466 | 0.28 | 0.24 | YES |
5 | ABAT | ABAT | ABAT | 730 | 0.22 | 0.27 | YES |
6 | ACAA2 | ACAA2 | ACAA2 | 733 | 0.22 | 0.32 | YES |
7 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 797 | 0.21 | 0.35 | YES |
8 | HIBCH | HIBCH | HIBCH | 803 | 0.21 | 0.39 | YES |
9 | ACAT1 | ACAT1 | ACAT1 | 956 | 0.19 | 0.42 | YES |
10 | ACADM | ACADM | ACADM | 1125 | 0.17 | 0.44 | YES |
11 | PCCA | PCCA | PCCA | 1279 | 0.15 | 0.46 | YES |
12 | ACADSB | ACADSB | ACADSB | 1405 | 0.14 | 0.48 | YES |
13 | AUH | AUH | AUH | 1409 | 0.14 | 0.51 | YES |
14 | MUT | MUT | MUT | 1547 | 0.13 | 0.53 | YES |
15 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 2098 | 0.1 | 0.52 | YES |
16 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2499 | 0.088 | 0.51 | YES |
17 | IVD | IVD | IVD | 2709 | 0.081 | 0.52 | YES |
18 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 2837 | 0.078 | 0.52 | YES |
19 | BCKDHB | BCKDHB | BCKDHB | 3341 | 0.064 | 0.51 | YES |
20 | DBT | DBT | DBT | 3488 | 0.06 | 0.51 | YES |
21 | ALDH2 | ALDH2 | ALDH2 | 3504 | 0.06 | 0.52 | YES |
22 | HMGCS1 | HMGCS1 | HMGCS1 | 3521 | 0.06 | 0.53 | YES |
23 | HIBADH | HIBADH | HIBADH | 3619 | 0.057 | 0.54 | YES |
24 | HADHB | HADHB | HADHB | 3620 | 0.057 | 0.55 | YES |
25 | MCCC1 | MCCC1 | MCCC1 | 3677 | 0.056 | 0.56 | YES |
26 | HADHA | HADHA | HADHA | 3729 | 0.055 | 0.57 | YES |
27 | MCEE | MCEE | MCEE | 3894 | 0.052 | 0.57 | YES |
28 | ACADS | ACADS | ACADS | 3959 | 0.05 | 0.57 | YES |
29 | HMGCL | HMGCL | HMGCL | 4061 | 0.049 | 0.58 | YES |
30 | OXCT1 | OXCT1 | OXCT1 | 4216 | 0.046 | 0.58 | YES |
31 | BCKDHA | BCKDHA | BCKDHA | 4312 | 0.045 | 0.58 | YES |
32 | ACAD8 | ACAD8 | ACAD8 | 4344 | 0.044 | 0.59 | YES |
33 | MCCC2 | MCCC2 | MCCC2 | 4822 | 0.036 | 0.57 | NO |
34 | ECHS1 | ECHS1 | ECHS1 | 5476 | 0.027 | 0.54 | NO |
35 | HADH | HADH | HADH | 5781 | 0.023 | 0.53 | NO |
36 | DLD | DLD | DLD | 5916 | 0.022 | 0.52 | NO |
37 | ACAA1 | ACAA1 | ACAA1 | 6706 | 0.012 | 0.48 | NO |
38 | IL4I1 | IL4I1 | IL4I1 | 8905 | -0.015 | 0.36 | NO |
39 | BCAT2 | BCAT2 | BCAT2 | 9890 | -0.027 | 0.32 | NO |
40 | HSD17B10 | HSD17B10 | HSD17B10 | 11503 | -0.048 | 0.24 | NO |
41 | PCCB | PCCB | PCCB | 11847 | -0.054 | 0.23 | NO |
42 | ACAT2 | ACAT2 | ACAT2 | 12031 | -0.057 | 0.23 | NO |
43 | BCAT1 | BCAT1 | BCAT1 | 16293 | -0.23 | 0.038 | NO |
44 | OXCT2 | OXCT2 | OXCT2 | 17505 | -0.36 | 0.041 | NO |
Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TRYPTOPHAN METABOLISM.
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Figure S30. 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 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 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 997 | 0.18 | 0.072 | YES |
2 | MAPK8 | MAPK8 | MAPK8 | 1271 | 0.15 | 0.16 | YES |
3 | MAPK1 | MAPK1 | MAPK1 | 2487 | 0.088 | 0.16 | YES |
4 | MAPK10 | MAPK10 | MAPK10 | 2507 | 0.088 | 0.22 | YES |
5 | ATF2 | ATF2 | ATF2 | 2616 | 0.084 | 0.27 | YES |
6 | DUSP6 | DUSP6 | DUSP6 | 2828 | 0.078 | 0.32 | YES |
7 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 2948 | 0.074 | 0.36 | YES |
8 | MEF2C | MEF2C | MEF2C | 3187 | 0.067 | 0.4 | YES |
9 | PPP2R1B | PPP2R1B | PPP2R1B | 3469 | 0.061 | 0.42 | YES |
10 | MEF2A | MEF2A | MEF2A | 4154 | 0.048 | 0.42 | YES |
11 | DUSP3 | DUSP3 | DUSP3 | 4630 | 0.039 | 0.42 | YES |
12 | DUSP7 | DUSP7 | DUSP7 | 4666 | 0.038 | 0.44 | YES |
13 | FOS | FOS | FOS | 4765 | 0.037 | 0.46 | YES |
14 | PPP2CB | PPP2CB | PPP2CB | 5394 | 0.028 | 0.45 | YES |
15 | CREB1 | CREB1 | CREB1 | 5395 | 0.028 | 0.47 | YES |
16 | MAPK3 | MAPK3 | MAPK3 | 5559 | 0.026 | 0.48 | YES |
17 | MAPK14 | MAPK14 | MAPK14 | 6416 | 0.016 | 0.44 | NO |
18 | PPP2CA | PPP2CA | PPP2CA | 6654 | 0.012 | 0.44 | NO |
19 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 6819 | 0.01 | 0.44 | NO |
20 | JUN | JUN | JUN | 7060 | 0.0074 | 0.43 | NO |
21 | MAPK9 | MAPK9 | MAPK9 | 7120 | 0.0066 | 0.43 | NO |
22 | PPP2R5D | PPP2R5D | PPP2R5D | 7226 | 0.0057 | 0.43 | NO |
23 | ATF1 | ATF1 | ATF1 | 7236 | 0.0056 | 0.43 | NO |
24 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 7834 | -0.0012 | 0.4 | NO |
25 | PPP2R1A | PPP2R1A | PPP2R1A | 9438 | -0.021 | 0.33 | NO |
26 | MAPK7 | MAPK7 | MAPK7 | 9875 | -0.026 | 0.32 | NO |
27 | DUSP4 | DUSP4 | DUSP4 | 10238 | -0.031 | 0.32 | NO |
28 | MAPK11 | MAPK11 | MAPK11 | 10417 | -0.034 | 0.34 | NO |
29 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 11667 | -0.051 | 0.3 | NO |
30 | ELK1 | ELK1 | ELK1 | 13212 | -0.082 | 0.28 | NO |
Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PROPANOATE METABOLISM.

Figure S32. 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 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 | CYP4A11 | CYP4A11 | CYP4A11 | 2 | 0.79 | 0.08 | YES |
2 | CYP4A22 | CYP4A22 | CYP4A22 | 26 | 0.63 | 0.14 | YES |
3 | PCK1 | PCK1 | PCK1 | 39 | 0.56 | 0.2 | YES |
4 | SLC27A2 | SLC27A2 | SLC27A2 | 43 | 0.55 | 0.25 | YES |
5 | HMGCS2 | HMGCS2 | HMGCS2 | 107 | 0.46 | 0.3 | YES |
6 | AQP7 | AQP7 | AQP7 | 124 | 0.44 | 0.34 | YES |
7 | ACADL | ACADL | ACADL | 196 | 0.39 | 0.38 | YES |
8 | FABP4 | FABP4 | FABP4 | 246 | 0.36 | 0.41 | YES |
9 | EHHADH | EHHADH | EHHADH | 466 | 0.28 | 0.43 | YES |
10 | CD36 | CD36 | CD36 | 512 | 0.27 | 0.45 | YES |
11 | RXRG | RXRG | RXRG | 663 | 0.24 | 0.47 | YES |
12 | FABP1 | FABP1 | FABP1 | 758 | 0.22 | 0.48 | YES |
13 | GK | GK | GK | 812 | 0.21 | 0.5 | YES |
14 | CYP27A1 | CYP27A1 | CYP27A1 | 924 | 0.19 | 0.52 | YES |
15 | ACADM | ACADM | ACADM | 1125 | 0.17 | 0.52 | YES |
16 | CPT2 | CPT2 | CPT2 | 1149 | 0.16 | 0.54 | YES |
17 | ACOX2 | ACOX2 | ACOX2 | 1262 | 0.15 | 0.55 | YES |
18 | ACSL1 | ACSL1 | ACSL1 | 1484 | 0.14 | 0.55 | YES |
19 | PCK2 | PCK2 | PCK2 | 1487 | 0.14 | 0.56 | YES |
20 | LPL | LPL | LPL | 1548 | 0.13 | 0.57 | YES |
21 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 1760 | 0.12 | 0.57 | YES |
22 | CPT1A | CPT1A | CPT1A | 1810 | 0.12 | 0.58 | YES |
23 | PPARG | PPARG | PPARG | 2253 | 0.096 | 0.57 | NO |
24 | PPARA | PPARA | PPARA | 2346 | 0.093 | 0.57 | NO |
25 | FABP2 | FABP2 | FABP2 | 3104 | 0.069 | 0.54 | NO |
26 | FABP7 | FABP7 | FABP7 | 3138 | 0.068 | 0.54 | NO |
27 | PLIN1 | PLIN1 | PLIN1 | 3226 | 0.066 | 0.54 | NO |
28 | ACOX1 | ACOX1 | ACOX1 | 3359 | 0.063 | 0.54 | NO |
29 | FABP3 | FABP3 | FABP3 | 3646 | 0.057 | 0.53 | NO |
30 | ACSL6 | ACSL6 | ACSL6 | 3953 | 0.051 | 0.52 | NO |
31 | PDPK1 | PDPK1 | PDPK1 | 4127 | 0.048 | 0.52 | NO |
32 | SCP2 | SCP2 | SCP2 | 4159 | 0.047 | 0.52 | NO |
33 | SCD | SCD | SCD | 6244 | 0.018 | 0.41 | NO |
34 | ILK | ILK | ILK | 6541 | 0.014 | 0.39 | NO |
35 | ACAA1 | ACAA1 | ACAA1 | 6706 | 0.012 | 0.38 | NO |
36 | SORBS1 | SORBS1 | SORBS1 | 6893 | 0.0093 | 0.37 | NO |
37 | RXRB | RXRB | RXRB | 6927 | 0.0089 | 0.37 | NO |
38 | RXRA | RXRA | RXRA | 7546 | 0.0022 | 0.34 | NO |
39 | SCD5 | SCD5 | SCD5 | 7676 | 0.00081 | 0.33 | NO |
40 | ACSL3 | ACSL3 | ACSL3 | 7836 | -0.0012 | 0.32 | NO |
41 | NR1H3 | NR1H3 | NR1H3 | 8662 | -0.012 | 0.28 | NO |
42 | APOA2 | APOA2 | APOA2 | 8835 | -0.014 | 0.27 | NO |
43 | UBC | UBC | UBC | 8846 | -0.014 | 0.27 | NO |
44 | FADS2 | FADS2 | FADS2 | 9190 | -0.018 | 0.26 | NO |
45 | PPARD | PPARD | PPARD | 9476 | -0.022 | 0.24 | NO |
46 | OLR1 | OLR1 | OLR1 | 9821 | -0.026 | 0.23 | NO |
47 | CYP8B1 | CYP8B1 | CYP8B1 | 10076 | -0.029 | 0.22 | NO |
48 | SLC27A1 | SLC27A1 | SLC27A1 | 10759 | -0.038 | 0.18 | NO |
49 | ACSL5 | ACSL5 | ACSL5 | 11838 | -0.054 | 0.13 | NO |
50 | CPT1B | CPT1B | CPT1B | 12266 | -0.062 | 0.11 | NO |
51 | SLC27A4 | SLC27A4 | SLC27A4 | 12698 | -0.07 | 0.094 | NO |
52 | FABP6 | FABP6 | FABP6 | 12878 | -0.074 | 0.091 | NO |
53 | CYP7A1 | CYP7A1 | CYP7A1 | 12888 | -0.074 | 0.098 | NO |
54 | ACSL4 | ACSL4 | ACSL4 | 12951 | -0.076 | 0.1 | NO |
55 | DBI | DBI | DBI | 13155 | -0.081 | 0.1 | NO |
56 | CPT1C | CPT1C | CPT1C | 13257 | -0.084 | 0.1 | NO |
57 | ACOX3 | ACOX3 | ACOX3 | 13946 | -0.1 | 0.075 | NO |
58 | FABP5 | FABP5 | FABP5 | 14508 | -0.12 | 0.057 | NO |
59 | MMP1 | MMP1 | MMP1 | 14557 | -0.13 | 0.067 | NO |
60 | ADIPOQ | ADIPOQ | ADIPOQ | 14580 | -0.13 | 0.079 | NO |
61 | APOA1 | APOA1 | APOA1 | 15303 | -0.16 | 0.056 | NO |
62 | APOC3 | APOC3 | APOC3 | 15682 | -0.18 | 0.054 | NO |
63 | SLC27A5 | SLC27A5 | SLC27A5 | 15868 | -0.2 | 0.064 | NO |
64 | ME1 | ME1 | ME1 | 16422 | -0.24 | 0.057 | NO |
65 | PLTP | PLTP | PLTP | 17812 | -0.43 | 0.024 | NO |
Figure S33. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PPAR SIGNALING PATHWAY.

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

Table 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 | AMDHD1 | AMDHD1 | AMDHD1 | 36 | 0.58 | 0.12 | YES |
2 | DDC | DDC | DDC | 73 | 0.49 | 0.22 | YES |
3 | FTCD | FTCD | FTCD | 109 | 0.46 | 0.31 | YES |
4 | ASPA | ASPA | ASPA | 199 | 0.39 | 0.38 | YES |
5 | ABP1 | ABP1 | ABP1 | 399 | 0.3 | 0.43 | YES |
6 | CNDP1 | CNDP1 | CNDP1 | 446 | 0.29 | 0.49 | YES |
7 | ACY3 | ACY3 | ACY3 | 580 | 0.25 | 0.53 | YES |
8 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 797 | 0.21 | 0.56 | YES |
9 | MAOB | MAOB | MAOB | 1008 | 0.18 | 0.59 | YES |
10 | HDC | HDC | HDC | 1294 | 0.15 | 0.61 | YES |
11 | HNMT | HNMT | HNMT | 1558 | 0.13 | 0.62 | YES |
12 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 2098 | 0.1 | 0.61 | YES |
13 | LCMT2 | LCMT2 | LCMT2 | 2486 | 0.088 | 0.61 | YES |
14 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2499 | 0.088 | 0.62 | YES |
15 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 2837 | 0.078 | 0.62 | NO |
16 | ALDH2 | ALDH2 | ALDH2 | 3504 | 0.06 | 0.6 | NO |
17 | METTL2B | METTL2B | METTL2B | 6867 | 0.0096 | 0.41 | NO |
18 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 6961 | 0.0085 | 0.41 | NO |
19 | TRMT11 | TRMT11 | TRMT11 | 7126 | 0.0066 | 0.4 | NO |
20 | HEMK1 | HEMK1 | HEMK1 | 8079 | -0.0044 | 0.35 | NO |
21 | HAL | HAL | HAL | 8261 | -0.0067 | 0.34 | NO |
22 | MAOA | MAOA | MAOA | 9675 | -0.024 | 0.27 | NO |
23 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 9852 | -0.026 | 0.27 | NO |
24 | LCMT1 | LCMT1 | LCMT1 | 10915 | -0.04 | 0.22 | NO |
25 | WBSCR22 | WBSCR22 | WBSCR22 | 12730 | -0.071 | 0.13 | NO |
26 | UROC1 | UROC1 | UROC1 | 13341 | -0.086 | 0.12 | NO |
27 | METTL6 | METTL6 | METTL6 | 13568 | -0.091 | 0.12 | NO |
28 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 16042 | -0.21 | 0.03 | NO |
29 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 17880 | -0.45 | 0.021 | NO |
Figure S35. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PEROXISOME.

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

Table 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 | CYP4A11 | CYP4A11 | CYP4A11 | 2 | 0.79 | 0.13 | YES |
2 | CYP4A22 | CYP4A22 | CYP4A22 | 26 | 0.63 | 0.23 | YES |
3 | ADH6 | ADH6 | ADH6 | 54 | 0.53 | 0.32 | YES |
4 | ACADL | ACADL | ACADL | 196 | 0.39 | 0.37 | YES |
5 | EHHADH | EHHADH | EHHADH | 466 | 0.28 | 0.4 | YES |
6 | ACAA2 | ACAA2 | ACAA2 | 733 | 0.22 | 0.43 | YES |
7 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 797 | 0.21 | 0.46 | YES |
8 | ACAT1 | ACAT1 | ACAT1 | 956 | 0.19 | 0.48 | YES |
9 | ACADM | ACADM | ACADM | 1125 | 0.17 | 0.5 | YES |
10 | CPT2 | CPT2 | CPT2 | 1149 | 0.16 | 0.52 | YES |
11 | ACADSB | ACADSB | ACADSB | 1405 | 0.14 | 0.53 | YES |
12 | ACSL1 | ACSL1 | ACSL1 | 1484 | 0.14 | 0.55 | YES |
13 | CPT1A | CPT1A | CPT1A | 1810 | 0.12 | 0.55 | YES |
14 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 2098 | 0.1 | 0.55 | YES |
15 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2499 | 0.088 | 0.55 | YES |
16 | ADH5 | ADH5 | ADH5 | 2657 | 0.083 | 0.55 | YES |
17 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 2837 | 0.078 | 0.55 | YES |
18 | ACOX1 | ACOX1 | ACOX1 | 3359 | 0.063 | 0.54 | NO |
19 | ALDH2 | ALDH2 | ALDH2 | 3504 | 0.06 | 0.54 | NO |
20 | HADHB | HADHB | HADHB | 3620 | 0.057 | 0.54 | NO |
21 | HADHA | HADHA | HADHA | 3729 | 0.055 | 0.54 | NO |
22 | ACSL6 | ACSL6 | ACSL6 | 3953 | 0.051 | 0.54 | NO |
23 | ACADS | ACADS | ACADS | 3959 | 0.05 | 0.55 | NO |
24 | ACADVL | ACADVL | ACADVL | 5216 | 0.031 | 0.48 | NO |
25 | ECHS1 | ECHS1 | ECHS1 | 5476 | 0.027 | 0.48 | NO |
26 | HADH | HADH | HADH | 5781 | 0.023 | 0.46 | NO |
27 | ACAA1 | ACAA1 | ACAA1 | 6706 | 0.012 | 0.41 | NO |
28 | ACSL3 | ACSL3 | ACSL3 | 7836 | -0.0012 | 0.35 | NO |
29 | GCDH | GCDH | GCDH | 11299 | -0.045 | 0.17 | NO |
30 | ACSL5 | ACSL5 | ACSL5 | 11838 | -0.054 | 0.15 | NO |
31 | ACAT2 | ACAT2 | ACAT2 | 12031 | -0.057 | 0.15 | NO |
32 | CPT1B | CPT1B | CPT1B | 12266 | -0.062 | 0.14 | NO |
33 | ACSL4 | ACSL4 | ACSL4 | 12951 | -0.076 | 0.12 | NO |
34 | CPT1C | CPT1C | CPT1C | 13257 | -0.084 | 0.12 | NO |
35 | ACOX3 | ACOX3 | ACOX3 | 13946 | -0.1 | 0.096 | NO |
36 | ADH1B | ADH1B | ADH1B | 14917 | -0.14 | 0.066 | NO |
37 | ADH1A | ADH1A | ADH1A | 16008 | -0.21 | 0.04 | NO |
38 | ADH4 | ADH4 | ADH4 | 16014 | -0.21 | 0.074 | NO |
39 | ADH1C | ADH1C | ADH1C | 17029 | -0.3 | 0.068 | NO |
Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ADIPOCYTOKINE SIGNALING PATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ADIPOCYTOKINE SIGNALING PATHWAY, 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 | AGTR1 | AGTR1 | AGTR1 | 53 | 0.54 | 0.25 | YES |
2 | AGT | AGT | AGT | 914 | 0.19 | 0.29 | YES |
3 | MAPK8 | MAPK8 | MAPK8 | 1271 | 0.15 | 0.34 | YES |
4 | MAPK1 | MAPK1 | MAPK1 | 2487 | 0.088 | 0.32 | YES |
5 | ATF2 | ATF2 | ATF2 | 2616 | 0.084 | 0.35 | YES |
6 | EGFR | EGFR | EGFR | 2705 | 0.081 | 0.38 | YES |
7 | MEF2C | MEF2C | MEF2C | 3187 | 0.067 | 0.38 | YES |
8 | MEF2A | MEF2A | MEF2A | 4154 | 0.048 | 0.35 | NO |
9 | SOS1 | SOS1 | SOS1 | 4818 | 0.036 | 0.33 | NO |
10 | CALM1 | CALM1 | CALM1 | 4857 | 0.036 | 0.35 | NO |
11 | CALM3 | CALM3 | CALM3 | 5266 | 0.03 | 0.34 | NO |
12 | PAK1 | PAK1 | PAK1 | 5464 | 0.027 | 0.34 | NO |
13 | MAPK3 | MAPK3 | MAPK3 | 5559 | 0.026 | 0.35 | NO |
14 | GNAQ | GNAQ | GNAQ | 5562 | 0.026 | 0.36 | NO |
15 | MAP2K4 | MAP2K4 | MAP2K4 | 5686 | 0.024 | 0.37 | NO |
16 | MAP3K1 | MAP3K1 | MAP3K1 | 5777 | 0.023 | 0.37 | NO |
17 | PTK2 | PTK2 | PTK2 | 6113 | 0.019 | 0.36 | NO |
18 | MEF2D | MEF2D | MEF2D | 6543 | 0.014 | 0.34 | NO |
19 | JUN | JUN | JUN | 7060 | 0.0074 | 0.32 | NO |
20 | PRKCB | PRKCB | PRKCB | 7381 | 0.0041 | 0.3 | NO |
21 | MAP2K1 | MAP2K1 | MAP2K1 | 9463 | -0.022 | 0.2 | NO |
22 | GRB2 | GRB2 | GRB2 | 9661 | -0.024 | 0.2 | NO |
23 | RAC1 | RAC1 | RAC1 | 10519 | -0.035 | 0.17 | NO |
24 | HRAS | HRAS | HRAS | 10851 | -0.04 | 0.17 | NO |
25 | RAF1 | RAF1 | RAF1 | 11192 | -0.044 | 0.17 | NO |
26 | SRC | SRC | SRC | 11296 | -0.045 | 0.19 | NO |
27 | CALM2 | CALM2 | CALM2 | 11823 | -0.054 | 0.18 | NO |
28 | PTK2B | PTK2B | PTK2B | 12625 | -0.069 | 0.17 | NO |
29 | MAP2K2 | MAP2K2 | MAP2K2 | 12631 | -0.069 | 0.2 | NO |
30 | PRKCA | PRKCA | PRKCA | 12718 | -0.071 | 0.23 | NO |
31 | SHC1 | SHC1 | SHC1 | 12923 | -0.075 | 0.25 | NO |
32 | ELK1 | ELK1 | ELK1 | 13212 | -0.082 | 0.28 | 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: BIOCARTA AT1R PATHWAY.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE | 25 | genes.ES.table | 0.54 | 1.4 | 0.083 | 0.22 | 0.99 | 0.56 | 0.24 | 0.42 | 0.16 | 0.003 |
KEGG MAPK SIGNALING PATHWAY | 247 | genes.ES.table | 0.43 | 1.6 | 0.0041 | 0.15 | 0.87 | 0.33 | 0.21 | 0.26 | 0.083 | 0.004 |
KEGG CALCIUM SIGNALING PATHWAY | 168 | genes.ES.table | 0.58 | 1.7 | 0 | 0.14 | 0.84 | 0.47 | 0.19 | 0.38 | 0.069 | 0.006 |
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION | 223 | genes.ES.table | 0.56 | 1.5 | 0.0021 | 0.19 | 0.97 | 0.5 | 0.2 | 0.41 | 0.13 | 0.003 |
KEGG MTOR SIGNALING PATHWAY | 50 | genes.ES.table | 0.38 | 1.6 | 0.02 | 0.14 | 0.89 | 0.38 | 0.34 | 0.25 | 0.083 | 0.003 |
KEGG VASCULAR SMOOTH MUSCLE CONTRACTION | 107 | genes.ES.table | 0.56 | 1.7 | 0.002 | 0.15 | 0.78 | 0.43 | 0.19 | 0.35 | 0.067 | 0.013 |
KEGG WNT SIGNALING PATHWAY | 146 | genes.ES.table | 0.5 | 1.7 | 0.0082 | 0.14 | 0.81 | 0.42 | 0.27 | 0.31 | 0.066 | 0.01 |
KEGG NOTCH SIGNALING PATHWAY | 46 | genes.ES.table | 0.5 | 1.7 | 0.018 | 0.14 | 0.81 | 0.37 | 0.2 | 0.3 | 0.067 | 0.01 |
KEGG HEDGEHOG SIGNALING PATHWAY | 54 | genes.ES.table | 0.57 | 1.5 | 0.033 | 0.21 | 0.98 | 0.39 | 0.13 | 0.34 | 0.15 | 0.003 |
KEGG TGF BETA SIGNALING PATHWAY | 85 | genes.ES.table | 0.59 | 1.8 | 0 | 0.13 | 0.64 | 0.44 | 0.18 | 0.36 | 0.051 | 0.017 |
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 | PIK3CG | PIK3CG | PIK3CG | 1306 | 0.21 | 0.036 | YES |
2 | NOS3 | NOS3 | NOS3 | 1421 | 0.2 | 0.13 | YES |
3 | FLT4 | FLT4 | FLT4 | 1787 | 0.17 | 0.2 | YES |
4 | KDR | KDR | KDR | 1890 | 0.16 | 0.28 | YES |
5 | FLT1 | FLT1 | FLT1 | 2421 | 0.13 | 0.32 | YES |
6 | PIK3CA | PIK3CA | PIK3CA | 2892 | 0.12 | 0.36 | YES |
7 | HIF1A | HIF1A | HIF1A | 3251 | 0.1 | 0.39 | YES |
8 | SHC1 | SHC1 | SHC1 | 3962 | 0.083 | 0.39 | YES |
9 | VHL | VHL | VHL | 4099 | 0.079 | 0.43 | YES |
10 | PTK2 | PTK2 | PTK2 | 4536 | 0.07 | 0.44 | YES |
11 | EIF2B2 | EIF2B2 | EIF2B2 | 4576 | 0.069 | 0.47 | YES |
12 | PLCG1 | PLCG1 | PLCG1 | 4753 | 0.065 | 0.5 | YES |
13 | PRKCB | PRKCB | PRKCB | 4838 | 0.063 | 0.52 | YES |
14 | VEGFA | VEGFA | VEGFA | 5041 | 0.059 | 0.54 | YES |
15 | EIF2S1 | EIF2S1 | EIF2S1 | 5144 | 0.057 | 0.57 | YES |
16 | ARNT | ARNT | ARNT | 5345 | 0.054 | 0.58 | YES |
17 | PIK3R1 | PIK3R1 | PIK3R1 | 5512 | 0.051 | 0.6 | YES |
18 | PXN | PXN | PXN | 5520 | 0.051 | 0.63 | YES |
19 | EIF2S3 | EIF2S3 | EIF2S3 | 8630 | 0.013 | 0.47 | NO |
20 | EIF2B4 | EIF2B4 | EIF2B4 | 8712 | 0.012 | 0.47 | NO |
21 | EIF2B3 | EIF2B3 | EIF2B3 | 8716 | 0.012 | 0.47 | NO |
22 | EIF2S2 | EIF2S2 | EIF2S2 | 9371 | 0.0051 | 0.44 | NO |
23 | EIF1 | EIF1 | EIF1 | 10102 | -0.0026 | 0.4 | NO |
24 | EIF1AX | EIF1AX | EIF1AX | 10446 | -0.0064 | 0.39 | NO |
25 | PRKCA | PRKCA | PRKCA | 10479 | -0.0067 | 0.39 | NO |
26 | EIF2B1 | EIF2B1 | EIF2B1 | 10557 | -0.0075 | 0.39 | NO |
27 | ELAVL1 | ELAVL1 | ELAVL1 | 10728 | -0.0096 | 0.38 | NO |
28 | EIF2B5 | EIF2B5 | EIF2B5 | 11916 | -0.024 | 0.33 | NO |
29 | HRAS | HRAS | HRAS | 12579 | -0.033 | 0.31 | 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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

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

Table 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 | SERPINE1 | SERPINE1 | SERPINE1 | 988 | 0.24 | 0.053 | YES |
2 | CDKN2B | CDKN2B | CDKN2B | 1277 | 0.21 | 0.13 | YES |
3 | CCNT1 | CCNT1 | CCNT1 | 1871 | 0.16 | 0.17 | YES |
4 | SKIL | SKIL | SKIL | 1960 | 0.16 | 0.24 | YES |
5 | JUNB | JUNB | JUNB | 2089 | 0.15 | 0.3 | YES |
6 | SMAD7 | SMAD7 | SMAD7 | 2847 | 0.12 | 0.31 | YES |
7 | SMURF2 | SMURF2 | SMURF2 | 2930 | 0.11 | 0.36 | YES |
8 | MYC | MYC | MYC | 2969 | 0.11 | 0.4 | YES |
9 | CDK8 | CDK8 | CDK8 | 3012 | 0.11 | 0.45 | YES |
10 | SKI | SKI | SKI | 3085 | 0.11 | 0.5 | YES |
11 | WWTR1 | WWTR1 | WWTR1 | 3140 | 0.11 | 0.54 | YES |
12 | RBL1 | RBL1 | RBL1 | 3328 | 0.1 | 0.58 | YES |
13 | HDAC1 | HDAC1 | HDAC1 | 4937 | 0.061 | 0.52 | NO |
14 | SMAD2 | SMAD2 | SMAD2 | 6024 | 0.044 | 0.48 | NO |
15 | TGIF2 | TGIF2 | TGIF2 | 6261 | 0.04 | 0.48 | NO |
16 | SMAD4 | SMAD4 | SMAD4 | 6527 | 0.037 | 0.48 | NO |
17 | TFDP1 | TFDP1 | TFDP1 | 7164 | 0.029 | 0.46 | NO |
18 | USP9X | USP9X | USP9X | 7316 | 0.028 | 0.46 | NO |
19 | TRIM33 | TRIM33 | TRIM33 | 7582 | 0.025 | 0.46 | NO |
20 | NCOR2 | NCOR2 | NCOR2 | 7891 | 0.021 | 0.46 | NO |
21 | SP1 | SP1 | SP1 | 8065 | 0.019 | 0.45 | NO |
22 | NCOR1 | NCOR1 | NCOR1 | 8069 | 0.019 | 0.46 | NO |
23 | RPS27A | RPS27A | RPS27A | 8353 | 0.016 | 0.45 | NO |
24 | CCNT2 | CCNT2 | CCNT2 | 8372 | 0.016 | 0.46 | NO |
25 | PPM1A | PPM1A | PPM1A | 8735 | 0.012 | 0.44 | NO |
26 | UBE2D1 | UBE2D1 | UBE2D1 | 8938 | 0.0098 | 0.44 | NO |
27 | PARP1 | PARP1 | PARP1 | 8967 | 0.0095 | 0.44 | NO |
28 | UBA52 | UBA52 | UBA52 | 9038 | 0.0086 | 0.44 | NO |
29 | CDK9 | CDK9 | CDK9 | 9545 | 0.0033 | 0.42 | NO |
30 | CCNC | CCNC | CCNC | 10193 | -0.0037 | 0.38 | NO |
31 | UBE2D3 | UBE2D3 | UBE2D3 | 10717 | -0.0094 | 0.36 | NO |
32 | E2F4 | E2F4 | E2F4 | 11098 | -0.014 | 0.34 | NO |
33 | MEN1 | MEN1 | MEN1 | 11157 | -0.014 | 0.34 | NO |
34 | SMAD3 | SMAD3 | SMAD3 | 11205 | -0.015 | 0.35 | NO |
35 | TGIF1 | TGIF1 | TGIF1 | 11379 | -0.017 | 0.35 | NO |
36 | E2F5 | E2F5 | E2F5 | 14579 | -0.066 | 0.2 | 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 MAPK SIGNALING PATHWAY.

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

Table 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 | ADCY1 | ADCY1 | ADCY1 | 240 | 0.38 | 0.029 | YES |
2 | CAMK4 | CAMK4 | CAMK4 | 389 | 0.34 | 0.058 | YES |
3 | NTRK2 | NTRK2 | NTRK2 | 484 | 0.31 | 0.088 | YES |
4 | NGF | NGF | NGF | 599 | 0.29 | 0.11 | YES |
5 | ADCYAP1R1 | ADCYAP1R1 | ADCYAP1R1 | 671 | 0.28 | 0.14 | YES |
6 | PDE1A | PDE1A | PDE1A | 685 | 0.28 | 0.17 | YES |
7 | SHC3 | SHC3 | SHC3 | 883 | 0.25 | 0.19 | YES |
8 | ADCY4 | ADCY4 | ADCY4 | 1031 | 0.23 | 0.2 | YES |
9 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 1484 | 0.19 | 0.2 | YES |
10 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 1567 | 0.19 | 0.22 | YES |
11 | ADCYAP1 | ADCYAP1 | ADCYAP1 | 1735 | 0.17 | 0.23 | YES |
12 | DUSP7 | DUSP7 | DUSP7 | 1758 | 0.17 | 0.25 | YES |
13 | MEF2C | MEF2C | MEF2C | 1808 | 0.17 | 0.26 | YES |
14 | PRKAR2A | PRKAR2A | PRKAR2A | 1818 | 0.17 | 0.28 | YES |
15 | PDE1B | PDE1B | PDE1B | 2259 | 0.14 | 0.27 | YES |
16 | ADCY3 | ADCY3 | ADCY3 | 2295 | 0.14 | 0.28 | YES |
17 | NTRK1 | NTRK1 | NTRK1 | 2514 | 0.13 | 0.29 | YES |
18 | DUSP6 | DUSP6 | DUSP6 | 2543 | 0.13 | 0.3 | YES |
19 | AKT3 | AKT3 | AKT3 | 2621 | 0.13 | 0.31 | YES |
20 | FOXO1 | FOXO1 | FOXO1 | 2667 | 0.12 | 0.32 | YES |
21 | IRS1 | IRS1 | IRS1 | 2769 | 0.12 | 0.33 | YES |
22 | PIK3CA | PIK3CA | PIK3CA | 2892 | 0.12 | 0.34 | YES |
23 | PHLPP1 | PHLPP1 | PHLPP1 | 3117 | 0.11 | 0.34 | YES |
24 | PRKAR2B | PRKAR2B | PRKAR2B | 3130 | 0.11 | 0.35 | YES |
25 | ADORA2A | ADORA2A | ADORA2A | 3367 | 0.099 | 0.34 | YES |
26 | MAPK11 | MAPK11 | MAPK11 | 3478 | 0.096 | 0.35 | YES |
27 | SHC2 | SHC2 | SHC2 | 3501 | 0.096 | 0.36 | YES |
28 | DUSP4 | DUSP4 | DUSP4 | 3570 | 0.094 | 0.36 | YES |
29 | IRS2 | IRS2 | IRS2 | 3586 | 0.093 | 0.37 | YES |
30 | FOXO4 | FOXO4 | FOXO4 | 3928 | 0.083 | 0.36 | YES |
31 | SHC1 | SHC1 | SHC1 | 3962 | 0.083 | 0.37 | YES |
32 | CREB1 | CREB1 | CREB1 | 4132 | 0.079 | 0.37 | YES |
33 | BRAF | BRAF | BRAF | 4148 | 0.078 | 0.38 | YES |
34 | NR4A1 | NR4A1 | NR4A1 | 4337 | 0.074 | 0.38 | YES |
35 | CRK | CRK | CRK | 4422 | 0.072 | 0.38 | YES |
36 | CALM1 | CALM1 | CALM1 | 4493 | 0.071 | 0.38 | YES |
37 | ADCY8 | ADCY8 | ADCY8 | 4687 | 0.066 | 0.38 | YES |
38 | FOXO3 | FOXO3 | FOXO3 | 4703 | 0.066 | 0.39 | YES |
39 | RALA | RALA | RALA | 4710 | 0.066 | 0.4 | YES |
40 | PTEN | PTEN | PTEN | 4734 | 0.065 | 0.4 | YES |
41 | PLCG1 | PLCG1 | PLCG1 | 4753 | 0.065 | 0.41 | YES |
42 | ITPR2 | ITPR2 | ITPR2 | 4986 | 0.06 | 0.4 | YES |
43 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5102 | 0.058 | 0.4 | YES |
44 | RALGDS | RALGDS | RALGDS | 5259 | 0.055 | 0.4 | YES |
45 | SOS1 | SOS1 | SOS1 | 5299 | 0.055 | 0.4 | YES |
46 | TRIB3 | TRIB3 | TRIB3 | 5381 | 0.054 | 0.4 | YES |
47 | MAPK3 | MAPK3 | MAPK3 | 5425 | 0.053 | 0.41 | YES |
48 | ELK1 | ELK1 | ELK1 | 5474 | 0.052 | 0.41 | YES |
49 | MEF2A | MEF2A | MEF2A | 5477 | 0.052 | 0.42 | YES |
50 | PIK3R1 | PIK3R1 | PIK3R1 | 5512 | 0.051 | 0.42 | YES |
51 | STAT3 | STAT3 | STAT3 | 5566 | 0.05 | 0.42 | YES |
52 | CDKN1B | CDKN1B | CDKN1B | 5697 | 0.048 | 0.42 | YES |
53 | PRKACB | PRKACB | PRKACB | 5713 | 0.048 | 0.43 | YES |
54 | MTOR | MTOR | MTOR | 5788 | 0.047 | 0.43 | YES |
55 | NRAS | NRAS | NRAS | 5791 | 0.047 | 0.43 | YES |
56 | RHOA | RHOA | RHOA | 5836 | 0.046 | 0.44 | YES |
57 | KIDINS220 | KIDINS220 | KIDINS220 | 5918 | 0.045 | 0.44 | YES |
58 | ATF1 | ATF1 | ATF1 | 6002 | 0.044 | 0.44 | YES |
59 | AKT1 | AKT1 | AKT1 | 6015 | 0.044 | 0.44 | YES |
60 | MAP2K5 | MAP2K5 | MAP2K5 | 6250 | 0.041 | 0.43 | NO |
61 | CDK1 | CDK1 | CDK1 | 6265 | 0.04 | 0.44 | NO |
62 | RAP1A | RAP1A | RAP1A | 6395 | 0.038 | 0.43 | NO |
63 | ADCY2 | ADCY2 | ADCY2 | 6581 | 0.036 | 0.43 | NO |
64 | PPP2R5D | PPP2R5D | PPP2R5D | 6829 | 0.033 | 0.42 | NO |
65 | MAP2K1 | MAP2K1 | MAP2K1 | 6871 | 0.033 | 0.42 | NO |
66 | AP2A1 | AP2A1 | AP2A1 | 6927 | 0.032 | 0.42 | NO |
67 | ADCY7 | ADCY7 | ADCY7 | 6977 | 0.031 | 0.42 | NO |
68 | PRKAR1A | PRKAR1A | PRKAR1A | 7006 | 0.031 | 0.42 | NO |
69 | FRS2 | FRS2 | FRS2 | 7028 | 0.031 | 0.42 | NO |
70 | PRKACA | PRKACA | PRKACA | 7491 | 0.026 | 0.4 | NO |
71 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 7510 | 0.025 | 0.4 | NO |
72 | YWHAB | YWHAB | YWHAB | 7583 | 0.025 | 0.4 | NO |
73 | RALB | RALB | RALB | 7665 | 0.024 | 0.4 | NO |
74 | MAPK14 | MAPK14 | MAPK14 | 7700 | 0.023 | 0.4 | NO |
75 | ADCY5 | ADCY5 | ADCY5 | 7709 | 0.023 | 0.4 | NO |
76 | TSC2 | TSC2 | TSC2 | 7845 | 0.022 | 0.4 | NO |
77 | CLTC | CLTC | CLTC | 7882 | 0.021 | 0.4 | NO |
78 | CDKN1A | CDKN1A | CDKN1A | 7965 | 0.02 | 0.4 | NO |
79 | RAF1 | RAF1 | RAF1 | 8310 | 0.016 | 0.38 | NO |
80 | ADRBK1 | ADRBK1 | ADRBK1 | 8337 | 0.016 | 0.38 | NO |
81 | KRAS | KRAS | KRAS | 8394 | 0.016 | 0.38 | NO |
82 | ADCY6 | ADCY6 | ADCY6 | 8463 | 0.015 | 0.38 | NO |
83 | AP2A2 | AP2A2 | AP2A2 | 8487 | 0.014 | 0.38 | NO |
84 | MAPK12 | MAPK12 | MAPK12 | 8545 | 0.014 | 0.37 | NO |
85 | MAPK1 | MAPK1 | MAPK1 | 8689 | 0.012 | 0.37 | NO |
86 | MAPK7 | MAPK7 | MAPK7 | 8747 | 0.012 | 0.36 | NO |
87 | PRKCE | PRKCE | PRKCE | 9094 | 0.0079 | 0.35 | NO |
88 | AP2S1 | AP2S1 | AP2S1 | 9224 | 0.0066 | 0.34 | NO |
89 | AP2M1 | AP2M1 | AP2M1 | 9232 | 0.0065 | 0.34 | NO |
90 | CASP9 | CASP9 | CASP9 | 9260 | 0.0062 | 0.34 | NO |
91 | ADCY9 | ADCY9 | ADCY9 | 9308 | 0.0058 | 0.34 | NO |
92 | MDM2 | MDM2 | MDM2 | 9493 | 0.0038 | 0.33 | NO |
93 | DNM1 | DNM1 | DNM1 | 9556 | 0.0032 | 0.32 | NO |
94 | PPP2CB | PPP2CB | PPP2CB | 9873 | -0.0003 | 0.31 | NO |
95 | AP2B1 | AP2B1 | AP2B1 | 9931 | -0.00097 | 0.3 | NO |
96 | CHUK | CHUK | CHUK | 10007 | -0.0017 | 0.3 | NO |
97 | ITPR3 | ITPR3 | ITPR3 | 10077 | -0.0024 | 0.3 | NO |
98 | PDPK1 | PDPK1 | PDPK1 | 10122 | -0.0028 | 0.3 | NO |
99 | RICTOR | RICTOR | RICTOR | 10181 | -0.0036 | 0.29 | NO |
100 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 10351 | -0.0054 | 0.28 | NO |
101 | RIT1 | RIT1 | RIT1 | 10406 | -0.006 | 0.28 | NO |
102 | PRKCA | PRKCA | PRKCA | 10479 | -0.0067 | 0.28 | NO |
103 | CALM2 | CALM2 | CALM2 | 10491 | -0.0069 | 0.28 | NO |
104 | GRB2 | GRB2 | GRB2 | 10764 | -0.0099 | 0.26 | NO |
105 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 10782 | -0.01 | 0.26 | NO |
106 | CALM3 | CALM3 | CALM3 | 10872 | -0.011 | 0.26 | NO |
107 | PPP2R1A | PPP2R1A | PPP2R1A | 11050 | -0.013 | 0.25 | NO |
108 | GSK3A | GSK3A | GSK3A | 11174 | -0.015 | 0.25 | NO |
109 | PRKAR1B | PRKAR1B | PRKAR1B | 11253 | -0.016 | 0.24 | NO |
110 | DNM2 | DNM2 | DNM2 | 11304 | -0.016 | 0.24 | NO |
111 | PPP2R1B | PPP2R1B | PPP2R1B | 11660 | -0.021 | 0.23 | NO |
112 | MAP2K2 | MAP2K2 | MAP2K2 | 11728 | -0.022 | 0.22 | NO |
113 | PIK3R2 | PIK3R2 | PIK3R2 | 11871 | -0.024 | 0.22 | NO |
114 | DNAL4 | DNAL4 | DNAL4 | 12299 | -0.029 | 0.2 | NO |
115 | CLTA | CLTA | CLTA | 12530 | -0.033 | 0.19 | NO |
116 | PIK3CB | PIK3CB | PIK3CB | 12549 | -0.033 | 0.19 | NO |
117 | HRAS | HRAS | HRAS | 12579 | -0.033 | 0.2 | NO |
118 | DUSP3 | DUSP3 | DUSP3 | 12958 | -0.038 | 0.18 | NO |
119 | AKT2 | AKT2 | AKT2 | 13029 | -0.039 | 0.18 | NO |
120 | AKT1S1 | AKT1S1 | AKT1S1 | 13138 | -0.041 | 0.18 | NO |
121 | PPP2CA | PPP2CA | PPP2CA | 13186 | -0.042 | 0.18 | NO |
122 | PRKCG | PRKCG | PRKCG | 13502 | -0.047 | 0.17 | NO |
123 | MAPK13 | MAPK13 | MAPK13 | 13574 | -0.048 | 0.17 | NO |
124 | MLST8 | MLST8 | MLST8 | 13643 | -0.049 | 0.17 | NO |
125 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 13896 | -0.053 | 0.16 | NO |
126 | BAD | BAD | BAD | 14073 | -0.056 | 0.16 | NO |
127 | SRC | SRC | SRC | 14810 | -0.071 | 0.13 | NO |
128 | PRKCD | PRKCD | PRKCD | 14855 | -0.072 | 0.13 | NO |
129 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 14930 | -0.074 | 0.14 | NO |
130 | THEM4 | THEM4 | THEM4 | 15546 | -0.088 | 0.11 | NO |
131 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 16155 | -0.11 | 0.09 | NO |
132 | SH3GL2 | SH3GL2 | SH3GL2 | 17814 | -0.23 | 0.024 | 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 CALCIUM SIGNALING PATHWAY.

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

Table 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 | ADAM12 | ADAM12 | ADAM12 | 30 | 0.54 | 0.077 | YES |
2 | ADCY1 | ADCY1 | ADCY1 | 240 | 0.38 | 0.12 | YES |
3 | CAMK4 | CAMK4 | CAMK4 | 389 | 0.34 | 0.16 | YES |
4 | PDE1A | PDE1A | PDE1A | 685 | 0.28 | 0.19 | YES |
5 | ADCY4 | ADCY4 | ADCY4 | 1031 | 0.23 | 0.2 | YES |
6 | SPRY1 | SPRY1 | SPRY1 | 1492 | 0.19 | 0.21 | YES |
7 | PRKAR2A | PRKAR2A | PRKAR2A | 1818 | 0.17 | 0.21 | YES |
8 | PDE1B | PDE1B | PDE1B | 2259 | 0.14 | 0.21 | YES |
9 | ADCY3 | ADCY3 | ADCY3 | 2295 | 0.14 | 0.23 | YES |
10 | AKT3 | AKT3 | AKT3 | 2621 | 0.13 | 0.23 | YES |
11 | FOXO1 | FOXO1 | FOXO1 | 2667 | 0.12 | 0.24 | YES |
12 | LRIG1 | LRIG1 | LRIG1 | 2743 | 0.12 | 0.26 | YES |
13 | ADAM17 | ADAM17 | ADAM17 | 2867 | 0.12 | 0.27 | YES |
14 | CBL | CBL | CBL | 2887 | 0.12 | 0.28 | YES |
15 | PIK3CA | PIK3CA | PIK3CA | 2892 | 0.12 | 0.3 | YES |
16 | SPRY2 | SPRY2 | SPRY2 | 2903 | 0.12 | 0.32 | YES |
17 | PHLPP1 | PHLPP1 | PHLPP1 | 3117 | 0.11 | 0.32 | YES |
18 | PRKAR2B | PRKAR2B | PRKAR2B | 3130 | 0.11 | 0.34 | YES |
19 | SH3KBP1 | SH3KBP1 | SH3KBP1 | 3712 | 0.089 | 0.32 | YES |
20 | GAB1 | GAB1 | GAB1 | 3823 | 0.086 | 0.32 | YES |
21 | FOXO4 | FOXO4 | FOXO4 | 3928 | 0.083 | 0.33 | YES |
22 | SHC1 | SHC1 | SHC1 | 3962 | 0.083 | 0.34 | YES |
23 | ADAM10 | ADAM10 | ADAM10 | 3987 | 0.082 | 0.35 | YES |
24 | EGFR | EGFR | EGFR | 4058 | 0.08 | 0.36 | YES |
25 | CREB1 | CREB1 | CREB1 | 4132 | 0.079 | 0.37 | YES |
26 | NR4A1 | NR4A1 | NR4A1 | 4337 | 0.074 | 0.37 | YES |
27 | PAG1 | PAG1 | PAG1 | 4363 | 0.073 | 0.38 | YES |
28 | CALM1 | CALM1 | CALM1 | 4493 | 0.071 | 0.38 | YES |
29 | ADCY8 | ADCY8 | ADCY8 | 4687 | 0.066 | 0.38 | YES |
30 | FOXO3 | FOXO3 | FOXO3 | 4703 | 0.066 | 0.39 | YES |
31 | PTEN | PTEN | PTEN | 4734 | 0.065 | 0.4 | YES |
32 | PLCG1 | PLCG1 | PLCG1 | 4753 | 0.065 | 0.4 | YES |
33 | ITPR2 | ITPR2 | ITPR2 | 4986 | 0.06 | 0.4 | YES |
34 | SOS1 | SOS1 | SOS1 | 5299 | 0.055 | 0.39 | YES |
35 | TRIB3 | TRIB3 | TRIB3 | 5381 | 0.054 | 0.4 | YES |
36 | MAPK3 | MAPK3 | MAPK3 | 5425 | 0.053 | 0.4 | YES |
37 | PIK3R1 | PIK3R1 | PIK3R1 | 5512 | 0.051 | 0.4 | YES |
38 | CDKN1B | CDKN1B | CDKN1B | 5697 | 0.048 | 0.4 | YES |
39 | PRKACB | PRKACB | PRKACB | 5713 | 0.048 | 0.41 | YES |
40 | MTOR | MTOR | MTOR | 5788 | 0.047 | 0.41 | YES |
41 | NRAS | NRAS | NRAS | 5791 | 0.047 | 0.42 | YES |
42 | AKT1 | AKT1 | AKT1 | 6015 | 0.044 | 0.41 | NO |
43 | CDK1 | CDK1 | CDK1 | 6265 | 0.04 | 0.4 | NO |
44 | ADCY2 | ADCY2 | ADCY2 | 6581 | 0.036 | 0.39 | NO |
45 | MAP2K1 | MAP2K1 | MAP2K1 | 6871 | 0.033 | 0.38 | NO |
46 | AP2A1 | AP2A1 | AP2A1 | 6927 | 0.032 | 0.38 | NO |
47 | ADCY7 | ADCY7 | ADCY7 | 6977 | 0.031 | 0.38 | NO |
48 | PRKAR1A | PRKAR1A | PRKAR1A | 7006 | 0.031 | 0.39 | NO |
49 | CDC42 | CDC42 | CDC42 | 7113 | 0.03 | 0.38 | NO |
50 | PRKACA | PRKACA | PRKACA | 7491 | 0.026 | 0.37 | NO |
51 | YWHAB | YWHAB | YWHAB | 7583 | 0.025 | 0.37 | NO |
52 | ADCY5 | ADCY5 | ADCY5 | 7709 | 0.023 | 0.36 | NO |
53 | TSC2 | TSC2 | TSC2 | 7845 | 0.022 | 0.36 | NO |
54 | EPS15 | EPS15 | EPS15 | 7861 | 0.022 | 0.36 | NO |
55 | CLTC | CLTC | CLTC | 7882 | 0.021 | 0.36 | NO |
56 | CDKN1A | CDKN1A | CDKN1A | 7965 | 0.02 | 0.36 | NO |
57 | RAF1 | RAF1 | RAF1 | 8310 | 0.016 | 0.34 | NO |
58 | CDC37 | CDC37 | CDC37 | 8315 | 0.016 | 0.35 | NO |
59 | ADRBK1 | ADRBK1 | ADRBK1 | 8337 | 0.016 | 0.35 | NO |
60 | RPS27A | RPS27A | RPS27A | 8353 | 0.016 | 0.35 | NO |
61 | KRAS | KRAS | KRAS | 8394 | 0.016 | 0.35 | NO |
62 | ADCY6 | ADCY6 | ADCY6 | 8463 | 0.015 | 0.35 | NO |
63 | AP2A2 | AP2A2 | AP2A2 | 8487 | 0.014 | 0.35 | NO |
64 | MAPK1 | MAPK1 | MAPK1 | 8689 | 0.012 | 0.34 | NO |
65 | UBA52 | UBA52 | UBA52 | 9038 | 0.0086 | 0.32 | NO |
66 | PRKCE | PRKCE | PRKCE | 9094 | 0.0079 | 0.32 | NO |
67 | AP2S1 | AP2S1 | AP2S1 | 9224 | 0.0066 | 0.31 | NO |
68 | AP2M1 | AP2M1 | AP2M1 | 9232 | 0.0065 | 0.32 | NO |
69 | STAM2 | STAM2 | STAM2 | 9245 | 0.0064 | 0.32 | NO |
70 | CASP9 | CASP9 | CASP9 | 9260 | 0.0062 | 0.32 | NO |
71 | ADCY9 | ADCY9 | ADCY9 | 9308 | 0.0058 | 0.31 | NO |
72 | EPS15L1 | EPS15L1 | EPS15L1 | 9340 | 0.0056 | 0.31 | NO |
73 | CSK | CSK | CSK | 9465 | 0.0042 | 0.31 | NO |
74 | MDM2 | MDM2 | MDM2 | 9493 | 0.0038 | 0.3 | NO |
75 | STAM | STAM | STAM | 9869 | -0.00026 | 0.28 | NO |
76 | AP2B1 | AP2B1 | AP2B1 | 9931 | -0.00097 | 0.28 | NO |
77 | CHUK | CHUK | CHUK | 10007 | -0.0017 | 0.28 | NO |
78 | ITPR3 | ITPR3 | ITPR3 | 10077 | -0.0024 | 0.27 | NO |
79 | PDPK1 | PDPK1 | PDPK1 | 10122 | -0.0028 | 0.27 | NO |
80 | RICTOR | RICTOR | RICTOR | 10181 | -0.0036 | 0.27 | NO |
81 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 10351 | -0.0054 | 0.26 | NO |
82 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 10395 | -0.0058 | 0.26 | NO |
83 | PRKCA | PRKCA | PRKCA | 10479 | -0.0067 | 0.26 | NO |
84 | CALM2 | CALM2 | CALM2 | 10491 | -0.0069 | 0.26 | NO |
85 | GRB2 | GRB2 | GRB2 | 10764 | -0.0099 | 0.24 | NO |
86 | CALM3 | CALM3 | CALM3 | 10872 | -0.011 | 0.24 | NO |
87 | GSK3A | GSK3A | GSK3A | 11174 | -0.015 | 0.22 | NO |
88 | PRKAR1B | PRKAR1B | PRKAR1B | 11253 | -0.016 | 0.22 | NO |
89 | MAP2K2 | MAP2K2 | MAP2K2 | 11728 | -0.022 | 0.2 | NO |
90 | HGS | HGS | HGS | 12071 | -0.026 | 0.18 | NO |
91 | CLTA | CLTA | CLTA | 12530 | -0.033 | 0.16 | NO |
92 | HRAS | HRAS | HRAS | 12579 | -0.033 | 0.17 | NO |
93 | EPN1 | EPN1 | EPN1 | 12743 | -0.035 | 0.16 | NO |
94 | AKT2 | AKT2 | AKT2 | 13029 | -0.039 | 0.15 | NO |
95 | AKT1S1 | AKT1S1 | AKT1S1 | 13138 | -0.041 | 0.15 | NO |
96 | PRKCG | PRKCG | PRKCG | 13502 | -0.047 | 0.14 | NO |
97 | MLST8 | MLST8 | MLST8 | 13643 | -0.049 | 0.14 | NO |
98 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 13896 | -0.053 | 0.13 | NO |
99 | BAD | BAD | BAD | 14073 | -0.056 | 0.13 | NO |
100 | SRC | SRC | SRC | 14810 | -0.071 | 0.1 | NO |
101 | PRKCD | PRKCD | PRKCD | 14855 | -0.072 | 0.11 | NO |
102 | THEM4 | THEM4 | THEM4 | 15546 | -0.088 | 0.084 | NO |
103 | EGF | EGF | EGF | 17688 | -0.21 | -0.0024 | NO |
104 | SH3GL2 | SH3GL2 | SH3GL2 | 17814 | -0.23 | 0.024 | 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 NEUROACTIVE LIGAND RECEPTOR INTERACTION.

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

Table 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 | PDGFRA | PDGFRA | PDGFRA | 9 | 0.57 | 0.051 | YES |
2 | COL5A1 | COL5A1 | COL5A1 | 145 | 0.42 | 0.082 | YES |
3 | THBS2 | THBS2 | THBS2 | 154 | 0.42 | 0.12 | YES |
4 | COL1A1 | COL1A1 | COL1A1 | 227 | 0.38 | 0.15 | YES |
5 | COL6A3 | COL6A3 | COL6A3 | 237 | 0.38 | 0.18 | YES |
6 | ADCY1 | ADCY1 | ADCY1 | 240 | 0.38 | 0.22 | YES |
7 | CAMK4 | CAMK4 | CAMK4 | 389 | 0.34 | 0.24 | YES |
8 | COL3A1 | COL3A1 | COL3A1 | 432 | 0.33 | 0.27 | YES |
9 | COL1A2 | COL1A2 | COL1A2 | 454 | 0.32 | 0.3 | YES |
10 | COL5A2 | COL5A2 | COL5A2 | 531 | 0.3 | 0.32 | YES |
11 | PDE1A | PDE1A | PDE1A | 685 | 0.28 | 0.34 | YES |
12 | ADCY4 | ADCY4 | ADCY4 | 1031 | 0.23 | 0.34 | YES |
13 | PDGFRB | PDGFRB | PDGFRB | 1035 | 0.23 | 0.36 | YES |
14 | COL4A5 | COL4A5 | COL4A5 | 1134 | 0.22 | 0.37 | YES |
15 | COL6A2 | COL6A2 | COL6A2 | 1290 | 0.21 | 0.38 | YES |
16 | COL4A1 | COL4A1 | COL4A1 | 1514 | 0.19 | 0.39 | YES |
17 | PLAT | PLAT | PLAT | 1706 | 0.18 | 0.39 | YES |
18 | COL4A2 | COL4A2 | COL4A2 | 1732 | 0.17 | 0.41 | YES |
19 | PRKAR2A | PRKAR2A | PRKAR2A | 1818 | 0.17 | 0.42 | YES |
20 | COL6A1 | COL6A1 | COL6A1 | 1891 | 0.16 | 0.43 | YES |
21 | THBS4 | THBS4 | THBS4 | 1985 | 0.16 | 0.44 | YES |
22 | PDGFB | PDGFB | PDGFB | 1989 | 0.16 | 0.45 | YES |
23 | PDGFD | PDGFD | PDGFD | 2135 | 0.15 | 0.46 | YES |
24 | PDE1B | PDE1B | PDE1B | 2259 | 0.14 | 0.46 | YES |
25 | ADCY3 | ADCY3 | ADCY3 | 2295 | 0.14 | 0.47 | YES |
26 | AKT3 | AKT3 | AKT3 | 2621 | 0.13 | 0.47 | YES |
27 | THBS1 | THBS1 | THBS1 | 2644 | 0.13 | 0.48 | YES |
28 | FOXO1 | FOXO1 | FOXO1 | 2667 | 0.12 | 0.49 | YES |
29 | PIK3CA | PIK3CA | PIK3CA | 2892 | 0.12 | 0.49 | YES |
30 | PHLPP1 | PHLPP1 | PHLPP1 | 3117 | 0.11 | 0.48 | YES |
31 | PRKAR2B | PRKAR2B | PRKAR2B | 3130 | 0.11 | 0.49 | YES |
32 | PDGFA | PDGFA | PDGFA | 3539 | 0.095 | 0.48 | YES |
33 | COL2A1 | COL2A1 | COL2A1 | 3554 | 0.094 | 0.49 | YES |
34 | FOXO4 | FOXO4 | FOXO4 | 3928 | 0.083 | 0.47 | YES |
35 | CREB1 | CREB1 | CREB1 | 4132 | 0.079 | 0.47 | YES |
36 | NR4A1 | NR4A1 | NR4A1 | 4337 | 0.074 | 0.46 | YES |
37 | CRK | CRK | CRK | 4422 | 0.072 | 0.47 | YES |
38 | CALM1 | CALM1 | CALM1 | 4493 | 0.071 | 0.47 | YES |
39 | PDGFC | PDGFC | PDGFC | 4679 | 0.066 | 0.46 | YES |
40 | ADCY8 | ADCY8 | ADCY8 | 4687 | 0.066 | 0.47 | YES |
41 | FOXO3 | FOXO3 | FOXO3 | 4703 | 0.066 | 0.48 | YES |
42 | PTEN | PTEN | PTEN | 4734 | 0.065 | 0.48 | YES |
43 | PLCG1 | PLCG1 | PLCG1 | 4753 | 0.065 | 0.48 | YES |
44 | COL9A1 | COL9A1 | COL9A1 | 4929 | 0.061 | 0.48 | YES |
45 | COL9A3 | COL9A3 | COL9A3 | 4963 | 0.061 | 0.48 | YES |
46 | ITPR2 | ITPR2 | ITPR2 | 4986 | 0.06 | 0.49 | YES |
47 | NCK2 | NCK2 | NCK2 | 4991 | 0.06 | 0.49 | YES |
48 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5102 | 0.058 | 0.49 | YES |
49 | SOS1 | SOS1 | SOS1 | 5299 | 0.055 | 0.49 | YES |
50 | TRIB3 | TRIB3 | TRIB3 | 5381 | 0.054 | 0.49 | YES |
51 | MAPK3 | MAPK3 | MAPK3 | 5425 | 0.053 | 0.49 | YES |
52 | PIK3R1 | PIK3R1 | PIK3R1 | 5512 | 0.051 | 0.49 | YES |
53 | STAT3 | STAT3 | STAT3 | 5566 | 0.05 | 0.49 | YES |
54 | CDKN1B | CDKN1B | CDKN1B | 5697 | 0.048 | 0.49 | YES |
55 | PRKACB | PRKACB | PRKACB | 5713 | 0.048 | 0.49 | YES |
56 | MTOR | MTOR | MTOR | 5788 | 0.047 | 0.49 | YES |
57 | NRAS | NRAS | NRAS | 5791 | 0.047 | 0.5 | YES |
58 | AKT1 | AKT1 | AKT1 | 6015 | 0.044 | 0.49 | NO |
59 | COL9A2 | COL9A2 | COL9A2 | 6166 | 0.042 | 0.48 | NO |
60 | CDK1 | CDK1 | CDK1 | 6265 | 0.04 | 0.48 | NO |
61 | ADCY2 | ADCY2 | ADCY2 | 6581 | 0.036 | 0.47 | NO |
62 | FURIN | FURIN | FURIN | 6799 | 0.034 | 0.46 | NO |
63 | MAP2K1 | MAP2K1 | MAP2K1 | 6871 | 0.033 | 0.46 | NO |
64 | ADCY7 | ADCY7 | ADCY7 | 6977 | 0.031 | 0.46 | NO |
65 | PRKAR1A | PRKAR1A | PRKAR1A | 7006 | 0.031 | 0.46 | NO |
66 | RASA1 | RASA1 | RASA1 | 7022 | 0.031 | 0.46 | NO |
67 | THBS3 | THBS3 | THBS3 | 7121 | 0.03 | 0.46 | NO |
68 | CRKL | CRKL | CRKL | 7456 | 0.026 | 0.44 | NO |
69 | PRKACA | PRKACA | PRKACA | 7491 | 0.026 | 0.44 | NO |
70 | YWHAB | YWHAB | YWHAB | 7583 | 0.025 | 0.44 | NO |
71 | STAT5B | STAT5B | STAT5B | 7690 | 0.024 | 0.43 | NO |
72 | ADCY5 | ADCY5 | ADCY5 | 7709 | 0.023 | 0.43 | NO |
73 | NCK1 | NCK1 | NCK1 | 7715 | 0.023 | 0.44 | NO |
74 | TSC2 | TSC2 | TSC2 | 7845 | 0.022 | 0.43 | NO |
75 | CDKN1A | CDKN1A | CDKN1A | 7965 | 0.02 | 0.43 | NO |
76 | RAF1 | RAF1 | RAF1 | 8310 | 0.016 | 0.41 | NO |
77 | ADRBK1 | ADRBK1 | ADRBK1 | 8337 | 0.016 | 0.41 | NO |
78 | KRAS | KRAS | KRAS | 8394 | 0.016 | 0.41 | NO |
79 | ADCY6 | ADCY6 | ADCY6 | 8463 | 0.015 | 0.4 | NO |
80 | MAPK1 | MAPK1 | MAPK1 | 8689 | 0.012 | 0.39 | NO |
81 | PRKCE | PRKCE | PRKCE | 9094 | 0.0079 | 0.37 | NO |
82 | CASP9 | CASP9 | CASP9 | 9260 | 0.0062 | 0.36 | NO |
83 | BCAR1 | BCAR1 | BCAR1 | 9303 | 0.0059 | 0.36 | NO |
84 | ADCY9 | ADCY9 | ADCY9 | 9308 | 0.0058 | 0.36 | NO |
85 | MDM2 | MDM2 | MDM2 | 9493 | 0.0038 | 0.35 | NO |
86 | CHUK | CHUK | CHUK | 10007 | -0.0017 | 0.32 | NO |
87 | ITPR3 | ITPR3 | ITPR3 | 10077 | -0.0024 | 0.32 | NO |
88 | PDPK1 | PDPK1 | PDPK1 | 10122 | -0.0028 | 0.32 | NO |
89 | RICTOR | RICTOR | RICTOR | 10181 | -0.0036 | 0.32 | NO |
90 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 10351 | -0.0054 | 0.31 | NO |
91 | PRKCA | PRKCA | PRKCA | 10479 | -0.0067 | 0.3 | NO |
92 | CALM2 | CALM2 | CALM2 | 10491 | -0.0069 | 0.3 | NO |
93 | GRB2 | GRB2 | GRB2 | 10764 | -0.0099 | 0.29 | NO |
94 | CALM3 | CALM3 | CALM3 | 10872 | -0.011 | 0.28 | NO |
95 | GSK3A | GSK3A | GSK3A | 11174 | -0.015 | 0.27 | NO |
96 | PRKAR1B | PRKAR1B | PRKAR1B | 11253 | -0.016 | 0.26 | NO |
97 | STAT5A | STAT5A | STAT5A | 11355 | -0.017 | 0.26 | NO |
98 | STAT1 | STAT1 | STAT1 | 11641 | -0.02 | 0.24 | NO |
99 | MAP2K2 | MAP2K2 | MAP2K2 | 11728 | -0.022 | 0.24 | NO |
100 | PIK3R2 | PIK3R2 | PIK3R2 | 11871 | -0.024 | 0.24 | NO |
101 | SPP1 | SPP1 | SPP1 | 11997 | -0.025 | 0.23 | NO |
102 | STAT6 | STAT6 | STAT6 | 12013 | -0.025 | 0.23 | NO |
103 | PIK3CB | PIK3CB | PIK3CB | 12549 | -0.033 | 0.21 | NO |
104 | HRAS | HRAS | HRAS | 12579 | -0.033 | 0.21 | NO |
105 | PLG | PLG | PLG | 12952 | -0.038 | 0.19 | NO |
106 | AKT2 | AKT2 | AKT2 | 13029 | -0.039 | 0.19 | NO |
107 | AKT1S1 | AKT1S1 | AKT1S1 | 13138 | -0.041 | 0.19 | NO |
108 | PRKCG | PRKCG | PRKCG | 13502 | -0.047 | 0.17 | NO |
109 | MLST8 | MLST8 | MLST8 | 13643 | -0.049 | 0.17 | NO |
110 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 13896 | -0.053 | 0.16 | NO |
111 | BAD | BAD | BAD | 14073 | -0.056 | 0.16 | NO |
112 | SRC | SRC | SRC | 14810 | -0.071 | 0.12 | NO |
113 | PRKCD | PRKCD | PRKCD | 14855 | -0.072 | 0.12 | NO |
114 | THEM4 | THEM4 | THEM4 | 15546 | -0.088 | 0.095 | NO |
115 | COL4A4 | COL4A4 | COL4A4 | 17099 | -0.16 | 0.024 | NO |
116 | COL4A3 | COL4A3 | COL4A3 | 17656 | -0.21 | 0.012 | NO |
117 | GRB7 | GRB7 | GRB7 | 17820 | -0.23 | 0.024 | 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 MTOR SIGNALING PATHWAY.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S26. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PDGFRA | PDGFRA | PDGFRA | 9 | 0.57 | 0.024 | YES |
2 | ITGA11 | ITGA11 | ITGA11 | 17 | 0.55 | 0.047 | YES |
3 | LAMA2 | LAMA2 | LAMA2 | 52 | 0.5 | 0.066 | YES |
4 | COL11A1 | COL11A1 | COL11A1 | 64 | 0.49 | 0.086 | YES |
5 | COMP | COMP | COMP | 109 | 0.45 | 0.1 | YES |
6 | COL5A1 | COL5A1 | COL5A1 | 145 | 0.42 | 0.12 | YES |
7 | THBS2 | THBS2 | THBS2 | 154 | 0.42 | 0.14 | YES |
8 | ITGA9 | ITGA9 | ITGA9 | 222 | 0.38 | 0.15 | YES |
9 | COL1A1 | COL1A1 | COL1A1 | 227 | 0.38 | 0.16 | YES |
10 | COL6A3 | COL6A3 | COL6A3 | 237 | 0.38 | 0.18 | YES |
11 | ITGA10 | ITGA10 | ITGA10 | 365 | 0.34 | 0.19 | YES |
12 | SHC4 | SHC4 | SHC4 | 367 | 0.34 | 0.2 | YES |
13 | HGF | HGF | HGF | 424 | 0.33 | 0.21 | YES |
14 | COL3A1 | COL3A1 | COL3A1 | 432 | 0.33 | 0.23 | YES |
15 | ITGA8 | ITGA8 | ITGA8 | 434 | 0.33 | 0.24 | YES |
16 | COL1A2 | COL1A2 | COL1A2 | 454 | 0.32 | 0.25 | YES |
17 | FLNC | FLNC | FLNC | 494 | 0.31 | 0.26 | YES |
18 | PGF | PGF | PGF | 506 | 0.31 | 0.28 | YES |
19 | COL5A2 | COL5A2 | COL5A2 | 531 | 0.3 | 0.29 | YES |
20 | COL5A3 | COL5A3 | COL5A3 | 540 | 0.3 | 0.3 | YES |
21 | LAMC3 | LAMC3 | LAMC3 | 545 | 0.3 | 0.31 | YES |
22 | TNC | TNC | TNC | 569 | 0.3 | 0.32 | YES |
23 | TNXB | TNXB | TNXB | 632 | 0.28 | 0.33 | YES |
24 | SHC3 | SHC3 | SHC3 | 883 | 0.25 | 0.33 | YES |
25 | VEGFC | VEGFC | VEGFC | 1017 | 0.23 | 0.33 | YES |
26 | PDGFRB | PDGFRB | PDGFRB | 1035 | 0.23 | 0.34 | YES |
27 | MYLK2 | MYLK2 | MYLK2 | 1038 | 0.23 | 0.35 | YES |
28 | IGF1 | IGF1 | IGF1 | 1050 | 0.23 | 0.36 | YES |
29 | FN1 | FN1 | FN1 | 1153 | 0.22 | 0.36 | YES |
30 | LAMB4 | LAMB4 | LAMB4 | 1171 | 0.22 | 0.37 | YES |
31 | COL6A2 | COL6A2 | COL6A2 | 1290 | 0.21 | 0.38 | YES |
32 | PIK3CG | PIK3CG | PIK3CG | 1306 | 0.21 | 0.38 | YES |
33 | LAMA4 | LAMA4 | LAMA4 | 1311 | 0.21 | 0.39 | YES |
34 | ITGB3 | ITGB3 | ITGB3 | 1429 | 0.2 | 0.39 | YES |
35 | ITGA5 | ITGA5 | ITGA5 | 1467 | 0.19 | 0.4 | YES |
36 | RELN | RELN | RELN | 1501 | 0.19 | 0.41 | YES |
37 | COL4A1 | COL4A1 | COL4A1 | 1514 | 0.19 | 0.41 | YES |
38 | TNR | TNR | TNR | 1545 | 0.19 | 0.42 | YES |
39 | ITGA7 | ITGA7 | ITGA7 | 1585 | 0.18 | 0.42 | YES |
40 | ITGA1 | ITGA1 | ITGA1 | 1612 | 0.18 | 0.43 | YES |
41 | IBSP | IBSP | IBSP | 1633 | 0.18 | 0.44 | YES |
42 | COL4A2 | COL4A2 | COL4A2 | 1732 | 0.17 | 0.44 | YES |
43 | FLT4 | FLT4 | FLT4 | 1787 | 0.17 | 0.44 | YES |
44 | VWF | VWF | VWF | 1819 | 0.17 | 0.45 | YES |
45 | ITGA2 | ITGA2 | ITGA2 | 1840 | 0.17 | 0.46 | YES |
46 | KDR | KDR | KDR | 1890 | 0.16 | 0.46 | YES |
47 | COL6A1 | COL6A1 | COL6A1 | 1891 | 0.16 | 0.47 | YES |
48 | THBS4 | THBS4 | THBS4 | 1985 | 0.16 | 0.47 | YES |
49 | PDGFB | PDGFB | PDGFB | 1989 | 0.16 | 0.48 | YES |
50 | ROCK2 | ROCK2 | ROCK2 | 2072 | 0.15 | 0.48 | YES |
51 | ITGA4 | ITGA4 | ITGA4 | 2121 | 0.15 | 0.48 | YES |
52 | PDGFD | PDGFD | PDGFD | 2135 | 0.15 | 0.49 | YES |
53 | CAV1 | CAV1 | CAV1 | 2155 | 0.15 | 0.49 | YES |
54 | FYN | FYN | FYN | 2170 | 0.15 | 0.5 | YES |
55 | VCL | VCL | VCL | 2234 | 0.14 | 0.5 | YES |
56 | ACTN1 | ACTN1 | ACTN1 | 2236 | 0.14 | 0.5 | YES |
57 | LAMC1 | LAMC1 | LAMC1 | 2305 | 0.14 | 0.51 | YES |
58 | FLT1 | FLT1 | FLT1 | 2421 | 0.13 | 0.51 | YES |
59 | ACTN3 | ACTN3 | ACTN3 | 2422 | 0.13 | 0.51 | YES |
60 | FLNA | FLNA | FLNA | 2541 | 0.13 | 0.51 | YES |
61 | CCND2 | CCND2 | CCND2 | 2563 | 0.13 | 0.52 | YES |
62 | MYL9 | MYL9 | MYL9 | 2572 | 0.13 | 0.52 | YES |
63 | COL6A6 | COL6A6 | COL6A6 | 2597 | 0.13 | 0.52 | YES |
64 | AKT3 | AKT3 | AKT3 | 2621 | 0.13 | 0.53 | YES |
65 | THBS1 | THBS1 | THBS1 | 2644 | 0.13 | 0.53 | YES |
66 | PIK3R3 | PIK3R3 | PIK3R3 | 2738 | 0.12 | 0.53 | YES |
67 | ACTN2 | ACTN2 | ACTN2 | 2800 | 0.12 | 0.54 | YES |
68 | LAMB1 | LAMB1 | LAMB1 | 2864 | 0.12 | 0.54 | YES |
69 | PIK3CA | PIK3CA | PIK3CA | 2892 | 0.12 | 0.54 | YES |
70 | ITGB1 | ITGB1 | ITGB1 | 2994 | 0.11 | 0.54 | YES |
71 | ITGA2B | ITGA2B | ITGA2B | 3003 | 0.11 | 0.54 | YES |
72 | PARVA | PARVA | PARVA | 3010 | 0.11 | 0.55 | YES |
73 | VTN | VTN | VTN | 3165 | 0.11 | 0.54 | YES |
74 | MYLK | MYLK | MYLK | 3224 | 0.1 | 0.55 | YES |
75 | CTNNB1 | CTNNB1 | CTNNB1 | 3232 | 0.1 | 0.55 | YES |
76 | TNN | TNN | TNN | 3321 | 0.1 | 0.55 | YES |
77 | ROCK1 | ROCK1 | ROCK1 | 3381 | 0.099 | 0.55 | YES |
78 | DOCK1 | DOCK1 | DOCK1 | 3414 | 0.098 | 0.55 | YES |
79 | ITGB5 | ITGB5 | ITGB5 | 3448 | 0.097 | 0.55 | YES |
80 | SHC2 | SHC2 | SHC2 | 3501 | 0.096 | 0.56 | YES |
81 | PDGFA | PDGFA | PDGFA | 3539 | 0.095 | 0.56 | YES |
82 | COL2A1 | COL2A1 | COL2A1 | 3554 | 0.094 | 0.56 | YES |
83 | MAPK8 | MAPK8 | MAPK8 | 3701 | 0.09 | 0.56 | NO |
84 | COL4A6 | COL4A6 | COL4A6 | 3916 | 0.084 | 0.55 | NO |
85 | SHC1 | SHC1 | SHC1 | 3962 | 0.083 | 0.55 | NO |
86 | EGFR | EGFR | EGFR | 4058 | 0.08 | 0.55 | NO |
87 | BRAF | BRAF | BRAF | 4148 | 0.078 | 0.55 | NO |
88 | PPP1R12A | PPP1R12A | PPP1R12A | 4282 | 0.075 | 0.54 | NO |
89 | LAMB2 | LAMB2 | LAMB2 | 4320 | 0.074 | 0.54 | NO |
90 | CRK | CRK | CRK | 4422 | 0.072 | 0.54 | NO |
91 | TLN1 | TLN1 | TLN1 | 4452 | 0.072 | 0.54 | NO |
92 | PTK2 | PTK2 | PTK2 | 4536 | 0.07 | 0.54 | NO |
93 | PDGFC | PDGFC | PDGFC | 4679 | 0.066 | 0.53 | NO |
94 | PTEN | PTEN | PTEN | 4734 | 0.065 | 0.53 | NO |
95 | PIK3R5 | PIK3R5 | PIK3R5 | 4794 | 0.064 | 0.53 | NO |
96 | PIP5K1C | PIP5K1C | PIP5K1C | 4835 | 0.063 | 0.53 | NO |
97 | PRKCB | PRKCB | PRKCB | 4838 | 0.063 | 0.54 | NO |
98 | ITGA6 | ITGA6 | ITGA6 | 4881 | 0.062 | 0.54 | NO |
99 | MYL2 | MYL2 | MYL2 | 4941 | 0.061 | 0.54 | NO |
100 | VEGFA | VEGFA | VEGFA | 5041 | 0.059 | 0.53 | NO |
101 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5102 | 0.058 | 0.53 | NO |
102 | SOS1 | SOS1 | SOS1 | 5299 | 0.055 | 0.52 | NO |
103 | SOS2 | SOS2 | SOS2 | 5334 | 0.054 | 0.52 | NO |
104 | ARHGAP5 | ARHGAP5 | ARHGAP5 | 5353 | 0.054 | 0.52 | NO |
105 | FLNB | FLNB | FLNB | 5397 | 0.053 | 0.52 | NO |
106 | MAPK3 | MAPK3 | MAPK3 | 5425 | 0.053 | 0.53 | NO |
107 | ELK1 | ELK1 | ELK1 | 5474 | 0.052 | 0.53 | NO |
108 | PIK3R1 | PIK3R1 | PIK3R1 | 5512 | 0.051 | 0.53 | NO |
109 | PXN | PXN | PXN | 5520 | 0.051 | 0.53 | NO |
110 | VASP | VASP | VASP | 5740 | 0.048 | 0.52 | NO |
111 | RHOA | RHOA | RHOA | 5836 | 0.046 | 0.51 | NO |
112 | ZYX | ZYX | ZYX | 5886 | 0.045 | 0.51 | NO |
113 | VAV1 | VAV1 | VAV1 | 5912 | 0.045 | 0.51 | NO |
114 | AKT1 | AKT1 | AKT1 | 6015 | 0.044 | 0.51 | NO |
115 | ITGAV | ITGAV | ITGAV | 6093 | 0.043 | 0.51 | NO |
116 | LAMB3 | LAMB3 | LAMB3 | 6160 | 0.042 | 0.51 | NO |
117 | JUN | JUN | JUN | 6320 | 0.04 | 0.5 | NO |
118 | RAP1A | RAP1A | RAP1A | 6395 | 0.038 | 0.5 | NO |
119 | IGF1R | IGF1R | IGF1R | 6660 | 0.035 | 0.48 | NO |
120 | CAV2 | CAV2 | CAV2 | 6720 | 0.034 | 0.48 | NO |
121 | PARVB | PARVB | PARVB | 6745 | 0.034 | 0.48 | NO |
122 | COL11A2 | COL11A2 | COL11A2 | 6772 | 0.034 | 0.48 | NO |
123 | MAP2K1 | MAP2K1 | MAP2K1 | 6871 | 0.033 | 0.48 | NO |
124 | MYL12A | MYL12A | MYL12A | 6881 | 0.032 | 0.48 | NO |
125 | MAPK10 | MAPK10 | MAPK10 | 6965 | 0.031 | 0.48 | NO |
126 | CDC42 | CDC42 | CDC42 | 7113 | 0.03 | 0.47 | NO |
127 | THBS3 | THBS3 | THBS3 | 7121 | 0.03 | 0.47 | NO |
128 | FIGF | FIGF | FIGF | 7283 | 0.028 | 0.46 | NO |
129 | ACTN4 | ACTN4 | ACTN4 | 7362 | 0.027 | 0.46 | NO |
130 | CRKL | CRKL | CRKL | 7456 | 0.026 | 0.45 | NO |
131 | ACTG1 | ACTG1 | ACTG1 | 7717 | 0.023 | 0.44 | NO |
132 | PPP1CC | PPP1CC | PPP1CC | 7765 | 0.023 | 0.44 | NO |
133 | CCND3 | CCND3 | CCND3 | 7779 | 0.022 | 0.44 | NO |
134 | PAK2 | PAK2 | PAK2 | 7803 | 0.022 | 0.44 | NO |
135 | GSK3B | GSK3B | GSK3B | 7819 | 0.022 | 0.44 | NO |
136 | ILK | ILK | ILK | 8037 | 0.019 | 0.43 | NO |
137 | PPP1CB | PPP1CB | PPP1CB | 8144 | 0.018 | 0.42 | NO |
138 | LAMA5 | LAMA5 | LAMA5 | 8154 | 0.018 | 0.42 | NO |
139 | RAF1 | RAF1 | RAF1 | 8310 | 0.016 | 0.42 | NO |
140 | PIK3CD | PIK3CD | PIK3CD | 8314 | 0.016 | 0.42 | NO |
141 | RAC2 | RAC2 | RAC2 | 8438 | 0.015 | 0.41 | NO |
142 | RAP1B | RAP1B | RAP1B | 8634 | 0.013 | 0.4 | NO |
143 | ACTB | ACTB | ACTB | 8675 | 0.013 | 0.4 | NO |
144 | MAPK1 | MAPK1 | MAPK1 | 8689 | 0.012 | 0.4 | NO |
145 | LAMA3 | LAMA3 | LAMA3 | 8853 | 0.011 | 0.39 | NO |
146 | XIAP | XIAP | XIAP | 8962 | 0.0096 | 0.38 | NO |
147 | RAC1 | RAC1 | RAC1 | 9015 | 0.0089 | 0.38 | NO |
148 | ITGB4 | ITGB4 | ITGB4 | 9204 | 0.0068 | 0.37 | NO |
149 | CAPN2 | CAPN2 | CAPN2 | 9210 | 0.0067 | 0.37 | NO |
150 | BCAR1 | BCAR1 | BCAR1 | 9303 | 0.0059 | 0.37 | NO |
151 | BCL2 | BCL2 | BCL2 | 9338 | 0.0056 | 0.36 | NO |
152 | CCND1 | CCND1 | CCND1 | 9649 | 0.0023 | 0.35 | NO |
153 | PAK3 | PAK3 | PAK3 | 9685 | 0.0018 | 0.34 | NO |
154 | BIRC2 | BIRC2 | BIRC2 | 9707 | 0.0016 | 0.34 | NO |
155 | PDPK1 | PDPK1 | PDPK1 | 10122 | -0.0028 | 0.32 | NO |
156 | PRKCA | PRKCA | PRKCA | 10479 | -0.0067 | 0.3 | NO |
157 | PARVG | PARVG | PARVG | 10593 | -0.008 | 0.3 | NO |
158 | GRB2 | GRB2 | GRB2 | 10764 | -0.0099 | 0.29 | NO |
159 | MYL12B | MYL12B | MYL12B | 11264 | -0.016 | 0.26 | NO |
160 | MAPK9 | MAPK9 | MAPK9 | 11463 | -0.018 | 0.25 | NO |
161 | PIK3R2 | PIK3R2 | PIK3R2 | 11871 | -0.024 | 0.23 | NO |
162 | SPP1 | SPP1 | SPP1 | 11997 | -0.025 | 0.22 | NO |
163 | PIK3CB | PIK3CB | PIK3CB | 12549 | -0.033 | 0.19 | NO |
164 | HRAS | HRAS | HRAS | 12579 | -0.033 | 0.19 | NO |
165 | LAMC2 | LAMC2 | LAMC2 | 12992 | -0.039 | 0.17 | NO |
166 | AKT2 | AKT2 | AKT2 | 13029 | -0.039 | 0.17 | NO |
167 | VAV2 | VAV2 | VAV2 | 13057 | -0.04 | 0.17 | NO |
168 | ITGA3 | ITGA3 | ITGA3 | 13111 | -0.04 | 0.17 | NO |
169 | PPP1CA | PPP1CA | PPP1CA | 13148 | -0.041 | 0.17 | NO |
170 | RASGRF1 | RASGRF1 | RASGRF1 | 13245 | -0.043 | 0.17 | NO |
171 | DIAPH1 | DIAPH1 | DIAPH1 | 13322 | -0.044 | 0.16 | NO |
172 | VEGFB | VEGFB | VEGFB | 13387 | -0.045 | 0.16 | NO |
173 | PAK1 | PAK1 | PAK1 | 13413 | -0.045 | 0.16 | NO |
174 | PRKCG | PRKCG | PRKCG | 13502 | -0.047 | 0.16 | NO |
175 | TLN2 | TLN2 | TLN2 | 13521 | -0.047 | 0.16 | NO |
176 | BAD | BAD | BAD | 14073 | -0.056 | 0.13 | NO |
177 | BIRC3 | BIRC3 | BIRC3 | 14251 | -0.06 | 0.13 | NO |
178 | MYLK3 | MYLK3 | MYLK3 | 14307 | -0.061 | 0.13 | NO |
179 | LAMA1 | LAMA1 | LAMA1 | 14658 | -0.068 | 0.11 | NO |
180 | PAK4 | PAK4 | PAK4 | 14744 | -0.07 | 0.11 | NO |
181 | SRC | SRC | SRC | 14810 | -0.071 | 0.11 | NO |
182 | ITGB6 | ITGB6 | ITGB6 | 14979 | -0.075 | 0.1 | NO |
183 | MYLPF | MYLPF | MYLPF | 15551 | -0.088 | 0.073 | NO |
184 | MET | MET | MET | 15592 | -0.089 | 0.074 | NO |
185 | VAV3 | VAV3 | VAV3 | 15699 | -0.093 | 0.072 | NO |
186 | ITGB8 | ITGB8 | ITGB8 | 15735 | -0.094 | 0.075 | NO |
187 | ERBB2 | ERBB2 | ERBB2 | 16189 | -0.11 | 0.054 | NO |
188 | RAC3 | RAC3 | RAC3 | 16228 | -0.11 | 0.057 | NO |
189 | MYL5 | MYL5 | MYL5 | 16679 | -0.13 | 0.037 | NO |
190 | PAK6 | PAK6 | PAK6 | 16958 | -0.15 | 0.028 | NO |
191 | ITGB7 | ITGB7 | ITGB7 | 17084 | -0.16 | 0.028 | NO |
192 | COL4A4 | COL4A4 | COL4A4 | 17099 | -0.16 | 0.034 | NO |
193 | PAK7 | PAK7 | PAK7 | 17505 | -0.19 | 0.02 | NO |
194 | EGF | EGF | EGF | 17688 | -0.21 | 0.018 | NO |
195 | CHAD | CHAD | CHAD | 18103 | -0.31 | 0.0086 | 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 VASCULAR SMOOTH MUSCLE CONTRACTION.

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

Table 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 | CNTN1 | CNTN1 | CNTN1 | 203 | 0.39 | 0.037 | YES |
2 | HEYL | HEYL | HEYL | 859 | 0.25 | 0.032 | YES |
3 | TLE2 | TLE2 | TLE2 | 918 | 0.24 | 0.058 | YES |
4 | NOTCH3 | NOTCH3 | NOTCH3 | 1156 | 0.22 | 0.072 | YES |
5 | DLL4 | DLL4 | DLL4 | 1183 | 0.22 | 0.098 | YES |
6 | HEY1 | HEY1 | HEY1 | 1192 | 0.22 | 0.12 | YES |
7 | HES5 | HES5 | HES5 | 1235 | 0.21 | 0.15 | YES |
8 | HEY2 | HEY2 | HEY2 | 1318 | 0.2 | 0.17 | YES |
9 | MAMLD1 | MAMLD1 | MAMLD1 | 1496 | 0.19 | 0.18 | YES |
10 | EIF2C2 | EIF2C2 | EIF2C2 | 1536 | 0.19 | 0.2 | YES |
11 | MAML3 | MAML3 | MAML3 | 1702 | 0.18 | 0.22 | YES |
12 | DLL1 | DLL1 | DLL1 | 1768 | 0.17 | 0.23 | YES |
13 | NOTCH4 | NOTCH4 | NOTCH4 | 1793 | 0.17 | 0.25 | YES |
14 | JAG2 | JAG2 | JAG2 | 1911 | 0.16 | 0.26 | YES |
15 | ARRB1 | ARRB1 | ARRB1 | 1978 | 0.16 | 0.28 | YES |
16 | HDAC9 | HDAC9 | HDAC9 | 2156 | 0.15 | 0.29 | YES |
17 | HES1 | HES1 | HES1 | 2312 | 0.14 | 0.3 | YES |
18 | MAML2 | MAML2 | MAML2 | 2343 | 0.14 | 0.31 | YES |
19 | TLE4 | TLE4 | TLE4 | 2468 | 0.13 | 0.32 | YES |
20 | JAG1 | JAG1 | JAG1 | 2527 | 0.13 | 0.34 | YES |
21 | MIB1 | MIB1 | MIB1 | 2708 | 0.12 | 0.34 | YES |
22 | ADAM17 | ADAM17 | ADAM17 | 2867 | 0.12 | 0.34 | YES |
23 | HDAC4 | HDAC4 | HDAC4 | 2893 | 0.12 | 0.36 | YES |
24 | LFNG | LFNG | LFNG | 2895 | 0.12 | 0.37 | YES |
25 | MYC | MYC | MYC | 2969 | 0.11 | 0.38 | YES |
26 | ATP2A3 | ATP2A3 | ATP2A3 | 2987 | 0.11 | 0.39 | YES |
27 | CDK8 | CDK8 | CDK8 | 3012 | 0.11 | 0.41 | YES |
28 | NOTCH2 | NOTCH2 | NOTCH2 | 3083 | 0.11 | 0.42 | YES |
29 | HIF1A | HIF1A | HIF1A | 3251 | 0.1 | 0.42 | YES |
30 | MFNG | MFNG | MFNG | 3330 | 0.1 | 0.43 | YES |
31 | TNRC6C | TNRC6C | TNRC6C | 3657 | 0.091 | 0.42 | YES |
32 | DTX1 | DTX1 | DTX1 | 3724 | 0.089 | 0.43 | YES |
33 | TLE1 | TLE1 | TLE1 | 3789 | 0.087 | 0.44 | YES |
34 | ADAM10 | ADAM10 | ADAM10 | 3987 | 0.082 | 0.43 | YES |
35 | ST3GAL6 | ST3GAL6 | ST3GAL6 | 4256 | 0.076 | 0.43 | YES |
36 | HDAC7 | HDAC7 | HDAC7 | 4293 | 0.075 | 0.44 | YES |
37 | EIF2C4 | EIF2C4 | EIF2C4 | 4371 | 0.073 | 0.44 | YES |
38 | EIF2C1 | EIF2C1 | EIF2C1 | 4412 | 0.072 | 0.45 | YES |
39 | HDAC2 | HDAC2 | HDAC2 | 4531 | 0.07 | 0.45 | YES |
40 | EIF2C3 | EIF2C3 | EIF2C3 | 4609 | 0.068 | 0.45 | YES |
41 | MAML1 | MAML1 | MAML1 | 4723 | 0.066 | 0.46 | YES |
42 | HDAC1 | HDAC1 | HDAC1 | 4937 | 0.061 | 0.45 | NO |
43 | TNRC6B | TNRC6B | TNRC6B | 5248 | 0.056 | 0.44 | NO |
44 | HDAC5 | HDAC5 | HDAC5 | 5307 | 0.055 | 0.44 | NO |
45 | SNW1 | SNW1 | SNW1 | 5382 | 0.054 | 0.45 | NO |
46 | CREBBP | CREBBP | CREBBP | 5671 | 0.049 | 0.44 | NO |
47 | EP300 | EP300 | EP300 | 5807 | 0.046 | 0.44 | NO |
48 | SEL1L | SEL1L | SEL1L | 6107 | 0.042 | 0.42 | NO |
49 | FBXW7 | FBXW7 | FBXW7 | 6216 | 0.041 | 0.42 | NO |
50 | JUN | JUN | JUN | 6320 | 0.04 | 0.42 | NO |
51 | RAB6A | RAB6A | RAB6A | 6641 | 0.035 | 0.41 | NO |
52 | FURIN | FURIN | FURIN | 6799 | 0.034 | 0.4 | NO |
53 | NEURL | NEURL | NEURL | 6835 | 0.033 | 0.41 | NO |
54 | B4GALT1 | B4GALT1 | B4GALT1 | 6905 | 0.032 | 0.41 | NO |
55 | TP53 | TP53 | TP53 | 6994 | 0.031 | 0.4 | NO |
56 | ATP2A2 | ATP2A2 | ATP2A2 | 7047 | 0.03 | 0.41 | NO |
57 | APH1B | APH1B | APH1B | 7155 | 0.029 | 0.4 | NO |
58 | TFDP1 | TFDP1 | TFDP1 | 7164 | 0.029 | 0.41 | NO |
59 | TLE3 | TLE3 | TLE3 | 7350 | 0.027 | 0.4 | NO |
60 | PSEN1 | PSEN1 | PSEN1 | 7534 | 0.025 | 0.39 | NO |
61 | RBPJ | RBPJ | RBPJ | 7723 | 0.023 | 0.38 | NO |
62 | NCOR2 | NCOR2 | NCOR2 | 7891 | 0.021 | 0.38 | NO |
63 | KAT2B | KAT2B | KAT2B | 8029 | 0.02 | 0.37 | NO |
64 | NCOR1 | NCOR1 | NCOR1 | 8069 | 0.019 | 0.37 | NO |
65 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 8080 | 0.019 | 0.38 | NO |
66 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 8147 | 0.018 | 0.37 | NO |
67 | E2F3 | E2F3 | E2F3 | 8255 | 0.017 | 0.37 | NO |
68 | TBL1X | TBL1X | TBL1X | 8281 | 0.017 | 0.37 | NO |
69 | RPS27A | RPS27A | RPS27A | 8353 | 0.016 | 0.37 | NO |
70 | NUMB | NUMB | NUMB | 8524 | 0.014 | 0.36 | NO |
71 | NCSTN | NCSTN | NCSTN | 8734 | 0.012 | 0.35 | NO |
72 | TMED2 | TMED2 | TMED2 | 8906 | 0.01 | 0.34 | NO |
73 | DTX4 | DTX4 | DTX4 | 8919 | 0.01 | 0.34 | NO |
74 | UBA52 | UBA52 | UBA52 | 9038 | 0.0086 | 0.34 | NO |
75 | CUL1 | CUL1 | CUL1 | 9172 | 0.007 | 0.33 | NO |
76 | POFUT1 | POFUT1 | POFUT1 | 9514 | 0.0036 | 0.31 | NO |
77 | ARRB2 | ARRB2 | ARRB2 | 9588 | 0.0029 | 0.31 | NO |
78 | CCND1 | CCND1 | CCND1 | 9649 | 0.0023 | 0.31 | NO |
79 | APH1A | APH1A | APH1A | 9839 | 0.00016 | 0.3 | NO |
80 | MIB2 | MIB2 | MIB2 | 10022 | -0.0019 | 0.29 | NO |
81 | CCNC | CCNC | CCNC | 10193 | -0.0037 | 0.28 | NO |
82 | HDAC3 | HDAC3 | HDAC3 | 10271 | -0.0047 | 0.27 | NO |
83 | TNRC6A | TNRC6A | TNRC6A | 10466 | -0.0066 | 0.26 | NO |
84 | DTX2 | DTX2 | DTX2 | 11770 | -0.022 | 0.2 | NO |
85 | SKP1 | SKP1 | SKP1 | 12319 | -0.029 | 0.17 | NO |
86 | MOV10 | MOV10 | MOV10 | 12420 | -0.031 | 0.17 | NO |
87 | HDAC8 | HDAC8 | HDAC8 | 12464 | -0.032 | 0.17 | NO |
88 | PSEN2 | PSEN2 | PSEN2 | 13248 | -0.043 | 0.13 | NO |
89 | KAT2A | KAT2A | KAT2A | 13988 | -0.055 | 0.096 | NO |
90 | RFNG | RFNG | RFNG | 14135 | -0.058 | 0.095 | NO |
91 | RBX1 | RBX1 | RBX1 | 14373 | -0.062 | 0.09 | NO |
92 | HDAC6 | HDAC6 | HDAC6 | 14639 | -0.067 | 0.084 | NO |
93 | E2F1 | E2F1 | E2F1 | 15325 | -0.083 | 0.056 | NO |
94 | HDAC10 | HDAC10 | HDAC10 | 15998 | -0.1 | 0.032 | NO |
95 | PSENEN | PSENEN | PSENEN | 16327 | -0.12 | 0.028 | NO |
96 | DLK1 | DLK1 | DLK1 | 16441 | -0.12 | 0.036 | NO |
97 | HDAC11 | HDAC11 | HDAC11 | 16615 | -0.13 | 0.042 | NO |
98 | ATP2A1 | ATP2A1 | ATP2A1 | 17355 | -0.18 | 0.023 | NO |
99 | DNER | DNER | DNER | 17740 | -0.22 | 0.028 | 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 WNT SIGNALING PATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG WNT SIGNALING PATHWAY, 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 | ITGA1 | ITGA1 | ITGA1 | 1612 | 0.18 | -0.019 | YES |
2 | ACTA1 | ACTA1 | ACTA1 | 1983 | 0.16 | 0.02 | YES |
3 | CAV1 | CAV1 | CAV1 | 2155 | 0.15 | 0.066 | YES |
4 | FYN | FYN | FYN | 2170 | 0.15 | 0.12 | YES |
5 | VCL | VCL | VCL | 2234 | 0.14 | 0.17 | YES |
6 | ACTN1 | ACTN1 | ACTN1 | 2236 | 0.14 | 0.22 | YES |
7 | PPP1R12B | PPP1R12B | PPP1R12B | 2378 | 0.14 | 0.27 | YES |
8 | ACTN3 | ACTN3 | ACTN3 | 2422 | 0.13 | 0.32 | YES |
9 | ACTN2 | ACTN2 | ACTN2 | 2800 | 0.12 | 0.34 | YES |
10 | ITGB1 | ITGB1 | ITGB1 | 2994 | 0.11 | 0.37 | YES |
11 | ROCK1 | ROCK1 | ROCK1 | 3381 | 0.099 | 0.39 | YES |
12 | MAPK8 | MAPK8 | MAPK8 | 3701 | 0.09 | 0.41 | YES |
13 | SHC1 | SHC1 | SHC1 | 3962 | 0.083 | 0.42 | YES |
14 | TLN1 | TLN1 | TLN1 | 4452 | 0.072 | 0.42 | YES |
15 | PTK2 | PTK2 | PTK2 | 4536 | 0.07 | 0.44 | YES |
16 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5102 | 0.058 | 0.44 | YES |
17 | SOS1 | SOS1 | SOS1 | 5299 | 0.055 | 0.45 | YES |
18 | MAPK3 | MAPK3 | MAPK3 | 5425 | 0.053 | 0.46 | YES |
19 | PXN | PXN | PXN | 5520 | 0.051 | 0.47 | YES |
20 | RHOA | RHOA | RHOA | 5836 | 0.046 | 0.47 | YES |
21 | ZYX | ZYX | ZYX | 5886 | 0.045 | 0.49 | YES |
22 | TNS1 | TNS1 | TNS1 | 5905 | 0.045 | 0.5 | YES |
23 | JUN | JUN | JUN | 6320 | 0.04 | 0.5 | YES |
24 | RAP1A | RAP1A | RAP1A | 6395 | 0.038 | 0.51 | YES |
25 | MAP2K1 | MAP2K1 | MAP2K1 | 6871 | 0.033 | 0.49 | NO |
26 | CRKL | CRKL | CRKL | 7456 | 0.026 | 0.47 | NO |
27 | RAF1 | RAF1 | RAF1 | 8310 | 0.016 | 0.43 | NO |
28 | MAPK1 | MAPK1 | MAPK1 | 8689 | 0.012 | 0.41 | NO |
29 | BCAR1 | BCAR1 | BCAR1 | 9303 | 0.0059 | 0.38 | NO |
30 | CSK | CSK | CSK | 9465 | 0.0042 | 0.38 | NO |
31 | BCR | BCR | BCR | 9813 | 0.00045 | 0.36 | NO |
32 | GRB2 | GRB2 | GRB2 | 10764 | -0.0099 | 0.31 | NO |
33 | CAPN1 | CAPN1 | CAPN1 | 11435 | -0.018 | 0.28 | NO |
34 | MAP2K2 | MAP2K2 | MAP2K2 | 11728 | -0.022 | 0.27 | NO |
35 | CAPNS1 | CAPNS1 | CAPNS1 | 11943 | -0.024 | 0.27 | NO |
36 | HRAS | HRAS | HRAS | 12579 | -0.033 | 0.24 | NO |
37 | SRC | SRC | SRC | 14810 | -0.071 | 0.15 | NO |
38 | CAPNS2 | CAPNS2 | CAPNS2 | 16071 | -0.1 | 0.12 | 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 NOTCH SIGNALING PATHWAY.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH SIGNALING PATHWAY, 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 | PDGFRA | PDGFRA | PDGFRA | 9 | 0.57 | 0.093 | YES |
2 | ADCY1 | ADCY1 | ADCY1 | 240 | 0.38 | 0.14 | YES |
3 | CAMK4 | CAMK4 | CAMK4 | 389 | 0.34 | 0.19 | YES |
4 | PDE1A | PDE1A | PDE1A | 685 | 0.28 | 0.22 | YES |
5 | ADCY4 | ADCY4 | ADCY4 | 1031 | 0.23 | 0.24 | YES |
6 | PDGFRB | PDGFRB | PDGFRB | 1035 | 0.23 | 0.28 | YES |
7 | PRKAR2A | PRKAR2A | PRKAR2A | 1818 | 0.17 | 0.26 | YES |
8 | PDGFB | PDGFB | PDGFB | 1989 | 0.16 | 0.28 | YES |
9 | PDE1B | PDE1B | PDE1B | 2259 | 0.14 | 0.28 | YES |
10 | ADCY3 | ADCY3 | ADCY3 | 2295 | 0.14 | 0.3 | YES |
11 | AKT3 | AKT3 | AKT3 | 2621 | 0.13 | 0.31 | YES |
12 | FOXO1 | FOXO1 | FOXO1 | 2667 | 0.12 | 0.32 | YES |
13 | PIK3CA | PIK3CA | PIK3CA | 2892 | 0.12 | 0.33 | YES |
14 | PHLPP1 | PHLPP1 | PHLPP1 | 3117 | 0.11 | 0.34 | YES |
15 | PRKAR2B | PRKAR2B | PRKAR2B | 3130 | 0.11 | 0.35 | YES |
16 | PDGFA | PDGFA | PDGFA | 3539 | 0.095 | 0.35 | YES |
17 | FOXO4 | FOXO4 | FOXO4 | 3928 | 0.083 | 0.34 | YES |
18 | CREB1 | CREB1 | CREB1 | 4132 | 0.079 | 0.34 | YES |
19 | NR4A1 | NR4A1 | NR4A1 | 4337 | 0.074 | 0.34 | YES |
20 | CRK | CRK | CRK | 4422 | 0.072 | 0.35 | YES |
21 | CALM1 | CALM1 | CALM1 | 4493 | 0.071 | 0.36 | YES |
22 | ADCY8 | ADCY8 | ADCY8 | 4687 | 0.066 | 0.36 | YES |
23 | FOXO3 | FOXO3 | FOXO3 | 4703 | 0.066 | 0.37 | YES |
24 | PTEN | PTEN | PTEN | 4734 | 0.065 | 0.38 | YES |
25 | PLCG1 | PLCG1 | PLCG1 | 4753 | 0.065 | 0.38 | YES |
26 | ITPR2 | ITPR2 | ITPR2 | 4986 | 0.06 | 0.38 | YES |
27 | NCK2 | NCK2 | NCK2 | 4991 | 0.06 | 0.39 | YES |
28 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 5102 | 0.058 | 0.4 | YES |
29 | SOS1 | SOS1 | SOS1 | 5299 | 0.055 | 0.39 | YES |
30 | TRIB3 | TRIB3 | TRIB3 | 5381 | 0.054 | 0.4 | YES |
31 | MAPK3 | MAPK3 | MAPK3 | 5425 | 0.053 | 0.4 | YES |
32 | PIK3R1 | PIK3R1 | PIK3R1 | 5512 | 0.051 | 0.41 | YES |
33 | STAT3 | STAT3 | STAT3 | 5566 | 0.05 | 0.41 | YES |
34 | CDKN1B | CDKN1B | CDKN1B | 5697 | 0.048 | 0.41 | YES |
35 | PRKACB | PRKACB | PRKACB | 5713 | 0.048 | 0.42 | YES |
36 | MTOR | MTOR | MTOR | 5788 | 0.047 | 0.42 | YES |
37 | NRAS | NRAS | NRAS | 5791 | 0.047 | 0.43 | YES |
38 | AKT1 | AKT1 | AKT1 | 6015 | 0.044 | 0.43 | NO |
39 | CDK1 | CDK1 | CDK1 | 6265 | 0.04 | 0.42 | NO |
40 | ADCY2 | ADCY2 | ADCY2 | 6581 | 0.036 | 0.41 | NO |
41 | MAP2K1 | MAP2K1 | MAP2K1 | 6871 | 0.033 | 0.4 | NO |
42 | ADCY7 | ADCY7 | ADCY7 | 6977 | 0.031 | 0.4 | NO |
43 | PRKAR1A | PRKAR1A | PRKAR1A | 7006 | 0.031 | 0.4 | NO |
44 | RASA1 | RASA1 | RASA1 | 7022 | 0.031 | 0.4 | NO |
45 | CRKL | CRKL | CRKL | 7456 | 0.026 | 0.38 | NO |
46 | PRKACA | PRKACA | PRKACA | 7491 | 0.026 | 0.39 | NO |
47 | YWHAB | YWHAB | YWHAB | 7583 | 0.025 | 0.39 | NO |
48 | STAT5B | STAT5B | STAT5B | 7690 | 0.024 | 0.38 | NO |
49 | ADCY5 | ADCY5 | ADCY5 | 7709 | 0.023 | 0.39 | NO |
50 | NCK1 | NCK1 | NCK1 | 7715 | 0.023 | 0.39 | NO |
51 | TSC2 | TSC2 | TSC2 | 7845 | 0.022 | 0.39 | NO |
52 | CDKN1A | CDKN1A | CDKN1A | 7965 | 0.02 | 0.38 | NO |
53 | RAF1 | RAF1 | RAF1 | 8310 | 0.016 | 0.37 | NO |
54 | ADRBK1 | ADRBK1 | ADRBK1 | 8337 | 0.016 | 0.37 | NO |
55 | KRAS | KRAS | KRAS | 8394 | 0.016 | 0.37 | NO |
56 | ADCY6 | ADCY6 | ADCY6 | 8463 | 0.015 | 0.37 | NO |
57 | MAPK1 | MAPK1 | MAPK1 | 8689 | 0.012 | 0.36 | NO |
58 | PRKCE | PRKCE | PRKCE | 9094 | 0.0079 | 0.34 | NO |
59 | CASP9 | CASP9 | CASP9 | 9260 | 0.0062 | 0.33 | NO |
60 | BCAR1 | BCAR1 | BCAR1 | 9303 | 0.0059 | 0.33 | NO |
61 | ADCY9 | ADCY9 | ADCY9 | 9308 | 0.0058 | 0.33 | NO |
62 | MDM2 | MDM2 | MDM2 | 9493 | 0.0038 | 0.32 | NO |
63 | CHUK | CHUK | CHUK | 10007 | -0.0017 | 0.29 | NO |
64 | ITPR3 | ITPR3 | ITPR3 | 10077 | -0.0024 | 0.29 | NO |
65 | PDPK1 | PDPK1 | PDPK1 | 10122 | -0.0028 | 0.28 | NO |
66 | RICTOR | RICTOR | RICTOR | 10181 | -0.0036 | 0.28 | NO |
67 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 10351 | -0.0054 | 0.27 | NO |
68 | PRKCA | PRKCA | PRKCA | 10479 | -0.0067 | 0.27 | NO |
69 | CALM2 | CALM2 | CALM2 | 10491 | -0.0069 | 0.27 | NO |
70 | GRB2 | GRB2 | GRB2 | 10764 | -0.0099 | 0.25 | NO |
71 | CALM3 | CALM3 | CALM3 | 10872 | -0.011 | 0.25 | NO |
72 | GSK3A | GSK3A | GSK3A | 11174 | -0.015 | 0.24 | NO |
73 | PRKAR1B | PRKAR1B | PRKAR1B | 11253 | -0.016 | 0.23 | NO |
74 | STAT5A | STAT5A | STAT5A | 11355 | -0.017 | 0.23 | NO |
75 | STAT1 | STAT1 | STAT1 | 11641 | -0.02 | 0.22 | NO |
76 | MAP2K2 | MAP2K2 | MAP2K2 | 11728 | -0.022 | 0.22 | NO |
77 | PIK3R2 | PIK3R2 | PIK3R2 | 11871 | -0.024 | 0.21 | NO |
78 | STAT6 | STAT6 | STAT6 | 12013 | -0.025 | 0.21 | NO |
79 | PIK3CB | PIK3CB | PIK3CB | 12549 | -0.033 | 0.19 | NO |
80 | HRAS | HRAS | HRAS | 12579 | -0.033 | 0.19 | NO |
81 | AKT2 | AKT2 | AKT2 | 13029 | -0.039 | 0.17 | NO |
82 | AKT1S1 | AKT1S1 | AKT1S1 | 13138 | -0.041 | 0.17 | NO |
83 | PRKCG | PRKCG | PRKCG | 13502 | -0.047 | 0.16 | NO |
84 | MLST8 | MLST8 | MLST8 | 13643 | -0.049 | 0.16 | NO |
85 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 13896 | -0.053 | 0.16 | NO |
86 | BAD | BAD | BAD | 14073 | -0.056 | 0.16 | NO |
87 | SRC | SRC | SRC | 14810 | -0.071 | 0.13 | NO |
88 | PRKCD | PRKCD | PRKCD | 14855 | -0.072 | 0.14 | NO |
89 | THEM4 | THEM4 | THEM4 | 15546 | -0.088 | 0.11 | NO |
90 | GRB7 | GRB7 | GRB7 | 17820 | -0.23 | 0.024 | 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 HEDGEHOG SIGNALING PATHWAY.

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

Table S30. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ADCY1 | ADCY1 | ADCY1 | 240 | 0.38 | 0.13 | YES |
2 | NFATC2 | NFATC2 | NFATC2 | 722 | 0.27 | 0.21 | YES |
3 | NFATC4 | NFATC4 | NFATC4 | 773 | 0.26 | 0.31 | YES |
4 | PRKAR2A | PRKAR2A | PRKAR2A | 1818 | 0.17 | 0.32 | YES |
5 | FOS | FOS | FOS | 1909 | 0.16 | 0.38 | YES |
6 | GNAI1 | GNAI1 | GNAI1 | 2838 | 0.12 | 0.37 | YES |
7 | PRKAR2B | PRKAR2B | PRKAR2B | 3130 | 0.11 | 0.39 | YES |
8 | PPP3CA | PPP3CA | PPP3CA | 3162 | 0.11 | 0.43 | YES |
9 | CREB1 | CREB1 | CREB1 | 4132 | 0.079 | 0.41 | YES |
10 | NFATC1 | NFATC1 | NFATC1 | 4195 | 0.077 | 0.44 | YES |
11 | CALM1 | CALM1 | CALM1 | 4493 | 0.071 | 0.45 | YES |
12 | PLCG1 | PLCG1 | PLCG1 | 4753 | 0.065 | 0.46 | YES |
13 | PRKCB | PRKCB | PRKCB | 4838 | 0.063 | 0.48 | YES |
14 | PPP3CC | PPP3CC | PPP3CC | 4860 | 0.063 | 0.5 | YES |
15 | GNB1 | GNB1 | GNB1 | 5220 | 0.056 | 0.5 | YES |
16 | PPP3CB | PPP3CB | PPP3CB | 5250 | 0.056 | 0.52 | YES |
17 | MAPK3 | MAPK3 | MAPK3 | 5425 | 0.053 | 0.53 | YES |
18 | ELK1 | ELK1 | ELK1 | 5474 | 0.052 | 0.55 | YES |
19 | PRKACB | PRKACB | PRKACB | 5713 | 0.048 | 0.56 | YES |
20 | GNAQ | GNAQ | GNAQ | 5921 | 0.045 | 0.56 | YES |
21 | NFATC3 | NFATC3 | NFATC3 | 6218 | 0.041 | 0.56 | YES |
22 | JUN | JUN | JUN | 6320 | 0.04 | 0.57 | YES |
23 | MAP2K1 | MAP2K1 | MAP2K1 | 6871 | 0.033 | 0.55 | NO |
24 | PRKAR1A | PRKAR1A | PRKAR1A | 7006 | 0.031 | 0.56 | NO |
25 | GNGT1 | GNGT1 | GNGT1 | 7409 | 0.026 | 0.55 | NO |
26 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 7510 | 0.025 | 0.55 | NO |
27 | RAF1 | RAF1 | RAF1 | 8310 | 0.016 | 0.51 | NO |
28 | GNAS | GNAS | GNAS | 8944 | 0.0098 | 0.48 | NO |
29 | PRKCA | PRKCA | PRKCA | 10479 | -0.0067 | 0.4 | NO |
30 | CALM2 | CALM2 | CALM2 | 10491 | -0.0069 | 0.4 | NO |
31 | CALM3 | CALM3 | CALM3 | 10872 | -0.011 | 0.39 | NO |
32 | PRKAR1B | PRKAR1B | PRKAR1B | 11253 | -0.016 | 0.37 | NO |
33 | HRAS | HRAS | HRAS | 12579 | -0.033 | 0.31 | 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 TGF BETA SIGNALING PATHWAY.

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

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 6. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus4. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM | 44 | genes.ES.table | 0.53 | 1.8 | 0.026 | 1 | 0.64 | 0.52 | 0.3 | 0.37 | 0.84 | 0.47 |
KEGG P53 SIGNALING PATHWAY | 67 | genes.ES.table | 0.53 | 1.7 | 0.016 | 0.78 | 0.83 | 0.25 | 0.13 | 0.22 | 0.41 | 0.25 |
KEGG CYTOSOLIC DNA SENSING PATHWAY | 45 | genes.ES.table | 0.58 | 1.7 | 0.018 | 0.91 | 0.83 | 0.33 | 0.16 | 0.28 | 0.48 | 0.28 |
PID AURORA B PATHWAY | 39 | genes.ES.table | 0.74 | 1.7 | 0.004 | 1 | 0.76 | 0.38 | 0.083 | 0.35 | 0.61 | 0.36 |
PID E2F PATHWAY | 69 | genes.ES.table | 0.54 | 1.7 | 0.025 | 0.84 | 0.83 | 0.25 | 0.14 | 0.21 | 0.44 | 0.26 |
PID INTEGRIN2 PATHWAY | 29 | genes.ES.table | 0.69 | 1.6 | 0.014 | 0.74 | 0.87 | 0.62 | 0.16 | 0.52 | 0.41 | 0.24 |
REACTOME ANTIGEN PROCESSING CROSS PRESENTATION | 72 | genes.ES.table | 0.47 | 1.7 | 0.049 | 0.77 | 0.85 | 0.6 | 0.36 | 0.38 | 0.42 | 0.25 |
REACTOME ORC1 REMOVAL FROM CHROMATIN | 59 | genes.ES.table | 0.51 | 1.7 | 0.062 | 0.95 | 0.79 | 0.58 | 0.36 | 0.37 | 0.46 | 0.29 |
REACTOME ACTIVATION OF NF KAPPAB IN B CELLS | 61 | genes.ES.table | 0.42 | 1.7 | 0.055 | 0.76 | 0.84 | 0.51 | 0.36 | 0.33 | 0.39 | 0.24 |
REACTOME MHC CLASS II ANTIGEN PRESENTATION | 89 | genes.ES.table | 0.45 | 1.6 | 0.034 | 0.7 | 0.88 | 0.39 | 0.25 | 0.3 | 0.39 | 0.23 |
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 | CD8B | CD8B | CD8B | 552 | 0.34 | 0.013 | YES |
2 | CD28 | CD28 | CD28 | 712 | 0.32 | 0.044 | YES |
3 | RCC1 | RCC1 | RCC1 | 943 | 0.28 | 0.067 | YES |
4 | LCK | LCK | LCK | 1147 | 0.25 | 0.088 | YES |
5 | APOBEC3G | APOBEC3G | APOBEC3G | 1332 | 0.24 | 0.11 | YES |
6 | PSMA8 | PSMA8 | PSMA8 | 1581 | 0.22 | 0.12 | YES |
7 | DOCK2 | DOCK2 | DOCK2 | 1662 | 0.21 | 0.14 | YES |
8 | CD247 | CD247 | CD247 | 1773 | 0.2 | 0.16 | YES |
9 | HCK | HCK | HCK | 1818 | 0.2 | 0.19 | YES |
10 | PSMB10 | PSMB10 | PSMB10 | 1945 | 0.19 | 0.2 | YES |
11 | NUP210 | NUP210 | NUP210 | 1998 | 0.18 | 0.22 | YES |
12 | HMGA1 | HMGA1 | HMGA1 | 2035 | 0.18 | 0.24 | YES |
13 | CD4 | CD4 | CD4 | 2645 | 0.14 | 0.23 | YES |
14 | AP1M2 | AP1M2 | AP1M2 | 3089 | 0.13 | 0.22 | YES |
15 | PSMB9 | PSMB9 | PSMB9 | 3151 | 0.12 | 0.23 | YES |
16 | PSMD14 | PSMD14 | PSMD14 | 3340 | 0.12 | 0.24 | YES |
17 | PSMA5 | PSMA5 | PSMA5 | 3406 | 0.11 | 0.25 | YES |
18 | PSME2 | PSME2 | PSME2 | 3498 | 0.11 | 0.26 | YES |
19 | AP1M1 | AP1M1 | AP1M1 | 3798 | 0.1 | 0.25 | YES |
20 | PSMB3 | PSMB3 | PSMB3 | 3979 | 0.094 | 0.26 | YES |
21 | TCEB1 | TCEB1 | TCEB1 | 4086 | 0.091 | 0.26 | YES |
22 | BANF1 | BANF1 | BANF1 | 4211 | 0.088 | 0.26 | YES |
23 | TCEB2 | TCEB2 | TCEB2 | 4283 | 0.086 | 0.27 | YES |
24 | AP2S1 | AP2S1 | AP2S1 | 4469 | 0.081 | 0.27 | YES |
25 | AP2A1 | AP2A1 | AP2A1 | 4519 | 0.08 | 0.28 | YES |
26 | PSMB4 | PSMB4 | PSMB4 | 4606 | 0.078 | 0.28 | YES |
27 | RAN | RAN | RAN | 4634 | 0.077 | 0.29 | YES |
28 | PSMB2 | PSMB2 | PSMB2 | 4675 | 0.076 | 0.3 | YES |
29 | RBX1 | RBX1 | RBX1 | 4740 | 0.075 | 0.31 | YES |
30 | NUP37 | NUP37 | NUP37 | 4747 | 0.075 | 0.32 | YES |
31 | PSMC4 | PSMC4 | PSMC4 | 4886 | 0.072 | 0.32 | YES |
32 | NUPL2 | NUPL2 | NUPL2 | 4919 | 0.071 | 0.32 | YES |
33 | PSMA7 | PSMA7 | PSMA7 | 5338 | 0.062 | 0.31 | YES |
34 | NUP62 | NUP62 | NUP62 | 5447 | 0.06 | 0.31 | YES |
35 | PSMB8 | PSMB8 | PSMB8 | 5451 | 0.06 | 0.32 | YES |
36 | PPIA | PPIA | PPIA | 5506 | 0.059 | 0.32 | YES |
37 | PSMC2 | PSMC2 | PSMC2 | 5508 | 0.059 | 0.33 | YES |
38 | RANGAP1 | RANGAP1 | RANGAP1 | 5520 | 0.059 | 0.34 | YES |
39 | PSMD4 | PSMD4 | PSMD4 | 5525 | 0.058 | 0.34 | YES |
40 | PSMD7 | PSMD7 | PSMD7 | 5570 | 0.058 | 0.35 | YES |
41 | PSMD13 | PSMD13 | PSMD13 | 5641 | 0.057 | 0.35 | YES |
42 | PSMA4 | PSMA4 | PSMA4 | 5646 | 0.056 | 0.36 | YES |
43 | PSME4 | PSME4 | PSME4 | 5663 | 0.056 | 0.36 | YES |
44 | RAE1 | RAE1 | RAE1 | 5682 | 0.056 | 0.37 | YES |
45 | PSMA1 | PSMA1 | PSMA1 | 5693 | 0.056 | 0.38 | YES |
46 | AAAS | AAAS | AAAS | 5906 | 0.052 | 0.37 | YES |
47 | HLA-A | HLA-A | HLA-A | 5912 | 0.052 | 0.38 | YES |
48 | PSMD8 | PSMD8 | PSMD8 | 5933 | 0.051 | 0.38 | YES |
49 | AP1B1 | AP1B1 | AP1B1 | 5935 | 0.051 | 0.39 | YES |
50 | PSMA2 | PSMA2 | PSMA2 | 6013 | 0.05 | 0.39 | YES |
51 | PSMB6 | PSMB6 | PSMB6 | 6090 | 0.049 | 0.4 | YES |
52 | NUP93 | NUP93 | NUP93 | 6177 | 0.047 | 0.4 | YES |
53 | AP1S1 | AP1S1 | AP1S1 | 6212 | 0.047 | 0.4 | YES |
54 | AP2M1 | AP2M1 | AP2M1 | 6279 | 0.046 | 0.4 | YES |
55 | PSMD9 | PSMD9 | PSMD9 | 6286 | 0.046 | 0.41 | YES |
56 | RANBP1 | RANBP1 | RANBP1 | 6379 | 0.044 | 0.41 | YES |
57 | PSMD2 | PSMD2 | PSMD2 | 6527 | 0.042 | 0.4 | NO |
58 | UBA52 | UBA52 | UBA52 | 6586 | 0.041 | 0.41 | NO |
59 | NUP107 | NUP107 | NUP107 | 6783 | 0.037 | 0.4 | NO |
60 | RAC1 | RAC1 | RAC1 | 7167 | 0.032 | 0.38 | NO |
61 | PSMC5 | PSMC5 | PSMC5 | 7226 | 0.031 | 0.38 | NO |
62 | PSMD1 | PSMD1 | PSMD1 | 7275 | 0.03 | 0.39 | NO |
63 | ARF1 | ARF1 | ARF1 | 7317 | 0.03 | 0.39 | NO |
64 | PSMD3 | PSMD3 | PSMD3 | 7330 | 0.03 | 0.39 | NO |
65 | PSMC3 | PSMC3 | PSMC3 | 7444 | 0.028 | 0.39 | NO |
66 | PACS1 | PACS1 | PACS1 | 7608 | 0.026 | 0.38 | NO |
67 | RPS27A | RPS27A | RPS27A | 7637 | 0.025 | 0.38 | NO |
68 | PSMF1 | PSMF1 | PSMF1 | 7677 | 0.025 | 0.38 | NO |
69 | PSMB1 | PSMB1 | PSMB1 | 7946 | 0.021 | 0.37 | NO |
70 | PSMD10 | PSMD10 | PSMD10 | 8053 | 0.02 | 0.37 | NO |
71 | PAK2 | PAK2 | PAK2 | 8079 | 0.02 | 0.37 | NO |
72 | PSMD11 | PSMD11 | PSMD11 | 8085 | 0.02 | 0.37 | NO |
73 | POM121 | POM121 | POM121 | 8196 | 0.018 | 0.37 | NO |
74 | SLC25A6 | SLC25A6 | SLC25A6 | 8205 | 0.018 | 0.37 | NO |
75 | B2M | B2M | B2M | 8691 | 0.011 | 0.35 | NO |
76 | ELMO1 | ELMO1 | ELMO1 | 8833 | 0.0095 | 0.34 | NO |
77 | PSMC1 | PSMC1 | PSMC1 | 8857 | 0.0092 | 0.34 | NO |
78 | PSMD12 | PSMD12 | PSMD12 | 8951 | 0.0081 | 0.34 | NO |
79 | NPM1 | NPM1 | NPM1 | 9060 | 0.0069 | 0.33 | NO |
80 | KPNB1 | KPNB1 | KPNB1 | 9082 | 0.0067 | 0.33 | NO |
81 | ATP6V1H | ATP6V1H | ATP6V1H | 9094 | 0.0065 | 0.33 | NO |
82 | PSMA6 | PSMA6 | PSMA6 | 9098 | 0.0065 | 0.33 | NO |
83 | XPO1 | XPO1 | XPO1 | 9102 | 0.0064 | 0.33 | NO |
84 | PSME1 | PSME1 | PSME1 | 9110 | 0.0063 | 0.33 | NO |
85 | NUP50 | NUP50 | NUP50 | 9117 | 0.0062 | 0.33 | NO |
86 | PSMA3 | PSMA3 | PSMA3 | 9175 | 0.0055 | 0.33 | NO |
87 | NUP85 | NUP85 | NUP85 | 9193 | 0.0052 | 0.33 | NO |
88 | PSMB5 | PSMB5 | PSMB5 | 9342 | 0.0032 | 0.32 | NO |
89 | PSMD6 | PSMD6 | PSMD6 | 9575 | 0.00057 | 0.31 | NO |
90 | NUP88 | NUP88 | NUP88 | 9761 | -0.0016 | 0.3 | NO |
91 | SLC25A5 | SLC25A5 | SLC25A5 | 9879 | -0.003 | 0.29 | NO |
92 | SKP1 | SKP1 | SKP1 | 10040 | -0.0051 | 0.28 | NO |
93 | TPR | TPR | TPR | 10250 | -0.0074 | 0.27 | NO |
94 | NUP43 | NUP43 | NUP43 | 10259 | -0.0075 | 0.27 | NO |
95 | PSMB7 | PSMB7 | PSMB7 | 10453 | -0.0096 | 0.26 | NO |
96 | CDK9 | CDK9 | CDK9 | 10706 | -0.013 | 0.25 | NO |
97 | NUP205 | NUP205 | NUP205 | 10765 | -0.013 | 0.25 | NO |
98 | KPNA1 | KPNA1 | KPNA1 | 10948 | -0.016 | 0.24 | NO |
99 | NUPL1 | NUPL1 | NUPL1 | 11223 | -0.02 | 0.23 | NO |
100 | AP1S2 | AP1S2 | AP1S2 | 11407 | -0.022 | 0.22 | NO |
101 | NUP155 | NUP155 | NUP155 | 11494 | -0.023 | 0.22 | NO |
102 | AP2B1 | AP2B1 | AP2B1 | 11575 | -0.024 | 0.22 | NO |
103 | AP1G1 | AP1G1 | AP1G1 | 11774 | -0.027 | 0.21 | NO |
104 | AP2A2 | AP2A2 | AP2A2 | 12434 | -0.037 | 0.18 | NO |
105 | NUP35 | NUP35 | NUP35 | 12509 | -0.038 | 0.18 | NO |
106 | NUP54 | NUP54 | NUP54 | 12806 | -0.043 | 0.17 | NO |
107 | NUP133 | NUP133 | NUP133 | 12835 | -0.043 | 0.18 | NO |
108 | RANBP2 | RANBP2 | RANBP2 | 13016 | -0.046 | 0.17 | NO |
109 | PSMD5 | PSMD5 | PSMD5 | 13285 | -0.05 | 0.16 | NO |
110 | NUP188 | NUP188 | NUP188 | 13394 | -0.052 | 0.16 | NO |
111 | NUP214 | NUP214 | NUP214 | 13454 | -0.053 | 0.17 | NO |
112 | PSMC6 | PSMC6 | PSMC6 | 13553 | -0.055 | 0.17 | NO |
113 | NUP153 | NUP153 | NUP153 | 13741 | -0.058 | 0.16 | NO |
114 | SEH1L | SEH1L | SEH1L | 13788 | -0.059 | 0.17 | NO |
115 | BTRC | BTRC | BTRC | 13803 | -0.059 | 0.18 | NO |
116 | CUL5 | CUL5 | CUL5 | 14724 | -0.078 | 0.14 | NO |
117 | SLC25A4 | SLC25A4 | SLC25A4 | 15502 | -0.1 | 0.1 | NO |
118 | PSIP1 | PSIP1 | PSIP1 | 15548 | -0.1 | 0.12 | NO |
119 | FYN | FYN | FYN | 15712 | -0.11 | 0.12 | NO |
120 | CCNT1 | CCNT1 | CCNT1 | 16636 | -0.16 | 0.089 | 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

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

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 | GFPT2 | GFPT2 | GFPT2 | 9 | 0.74 | 0.17 | YES |
2 | HK3 | HK3 | HK3 | 754 | 0.31 | 0.2 | YES |
3 | NPL | NPL | NPL | 906 | 0.29 | 0.26 | YES |
4 | CHIT1 | CHIT1 | CHIT1 | 987 | 0.27 | 0.31 | YES |
5 | GALK1 | GALK1 | GALK1 | 1830 | 0.2 | 0.31 | YES |
6 | HK2 | HK2 | HK2 | 1938 | 0.19 | 0.35 | YES |
7 | PMM2 | PMM2 | PMM2 | 2516 | 0.15 | 0.35 | YES |
8 | GALE | GALE | GALE | 2597 | 0.15 | 0.38 | YES |
9 | GMPPB | GMPPB | GMPPB | 2778 | 0.14 | 0.4 | YES |
10 | GCK | GCK | GCK | 2889 | 0.13 | 0.43 | YES |
11 | TSTA3 | TSTA3 | TSTA3 | 2912 | 0.13 | 0.46 | YES |
12 | GMPPA | GMPPA | GMPPA | 3361 | 0.12 | 0.46 | YES |
13 | CMAS | CMAS | CMAS | 4160 | 0.089 | 0.44 | YES |
14 | PGM1 | PGM1 | PGM1 | 4203 | 0.088 | 0.45 | YES |
15 | NAGK | NAGK | NAGK | 4525 | 0.08 | 0.45 | YES |
16 | UGDH | UGDH | UGDH | 4636 | 0.077 | 0.47 | YES |
17 | GMDS | GMDS | GMDS | 4681 | 0.076 | 0.48 | YES |
18 | GNPDA1 | GNPDA1 | GNPDA1 | 4943 | 0.07 | 0.48 | YES |
19 | UGP2 | UGP2 | UGP2 | 5200 | 0.065 | 0.48 | YES |
20 | NANS | NANS | NANS | 5318 | 0.063 | 0.49 | YES |
21 | HEXA | HEXA | HEXA | 5412 | 0.061 | 0.5 | YES |
22 | HK1 | HK1 | HK1 | 5421 | 0.061 | 0.51 | YES |
23 | CYB5R3 | CYB5R3 | CYB5R3 | 5431 | 0.06 | 0.53 | YES |
24 | AMDHD2 | AMDHD2 | AMDHD2 | 6368 | 0.044 | 0.48 | NO |
25 | HEXB | HEXB | HEXB | 6652 | 0.04 | 0.48 | NO |
26 | UAP1 | UAP1 | UAP1 | 6705 | 0.039 | 0.48 | NO |
27 | GPI | GPI | GPI | 6764 | 0.038 | 0.49 | NO |
28 | PGM3 | PGM3 | PGM3 | 6921 | 0.035 | 0.49 | NO |
29 | RENBP | RENBP | RENBP | 8121 | 0.019 | 0.43 | NO |
30 | GFPT1 | GFPT1 | GFPT1 | 8125 | 0.019 | 0.43 | NO |
31 | FUK | FUK | FUK | 8270 | 0.017 | 0.43 | NO |
32 | CYB5R1 | CYB5R1 | CYB5R1 | 10476 | -0.0099 | 0.31 | NO |
33 | MPI | MPI | MPI | 10763 | -0.013 | 0.3 | NO |
34 | NANP | NANP | NANP | 11164 | -0.019 | 0.28 | NO |
35 | CHIA | CHIA | CHIA | 11211 | -0.02 | 0.28 | NO |
36 | UXS1 | UXS1 | UXS1 | 11253 | -0.02 | 0.28 | NO |
37 | PGM2 | PGM2 | PGM2 | 11521 | -0.024 | 0.27 | NO |
38 | GALK2 | GALK2 | GALK2 | 11722 | -0.026 | 0.27 | NO |
39 | FPGT | FPGT | FPGT | 12138 | -0.032 | 0.25 | NO |
40 | GNPDA2 | GNPDA2 | GNPDA2 | 12186 | -0.033 | 0.26 | NO |
41 | GALT | GALT | GALT | 13947 | -0.062 | 0.18 | NO |
42 | GNPNAT1 | GNPNAT1 | GNPNAT1 | 14143 | -0.066 | 0.18 | NO |
43 | PMM1 | PMM1 | PMM1 | 14474 | -0.073 | 0.18 | NO |
44 | GNE | GNE | GNE | 16081 | -0.12 | 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 P53 SIGNALING PATHWAY.

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG P53 SIGNALING PATHWAY, 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 | SAA1 | SAA1 | SAA1 | 2 | 0.93 | 0.035 | YES |
2 | LBP | LBP | LBP | 14 | 0.67 | 0.06 | YES |
3 | AIM2 | AIM2 | AIM2 | 47 | 0.57 | 0.08 | YES |
4 | CRP | CRP | CRP | 121 | 0.48 | 0.094 | YES |
5 | MBL2 | MBL2 | MBL2 | 189 | 0.44 | 0.11 | YES |
6 | C2 | C2 | C2 | 231 | 0.42 | 0.12 | YES |
7 | ZBP1 | ZBP1 | ZBP1 | 240 | 0.42 | 0.14 | YES |
8 | NOD2 | NOD2 | NOD2 | 263 | 0.42 | 0.15 | YES |
9 | C1S | C1S | C1S | 279 | 0.41 | 0.17 | YES |
10 | C8G | C8G | C8G | 305 | 0.4 | 0.18 | YES |
11 | LY96 | LY96 | LY96 | 346 | 0.39 | 0.19 | YES |
12 | CFHR3 | CFHR3 | CFHR3 | 356 | 0.39 | 0.21 | YES |
13 | IKBKE | IKBKE | IKBKE | 442 | 0.37 | 0.22 | YES |
14 | TLR6 | TLR6 | TLR6 | 563 | 0.34 | 0.22 | YES |
15 | CCR6 | CCR6 | CCR6 | 586 | 0.34 | 0.23 | YES |
16 | CARD9 | CARD9 | CARD9 | 597 | 0.34 | 0.25 | YES |
17 | PYCARD | PYCARD | PYCARD | 612 | 0.33 | 0.26 | YES |
18 | MEFV | MEFV | MEFV | 629 | 0.33 | 0.27 | YES |
19 | TLR10 | TLR10 | TLR10 | 684 | 0.32 | 0.28 | YES |
20 | PSTPIP1 | PSTPIP1 | PSTPIP1 | 695 | 0.32 | 0.29 | YES |
21 | IFNB1 | IFNB1 | IFNB1 | 728 | 0.31 | 0.3 | YES |
22 | C9 | C9 | C9 | 792 | 0.3 | 0.31 | YES |
23 | C3 | C3 | C3 | 858 | 0.29 | 0.32 | YES |
24 | S100B | S100B | S100B | 887 | 0.29 | 0.33 | YES |
25 | CFB | CFB | CFB | 931 | 0.28 | 0.33 | YES |
26 | TLR8 | TLR8 | TLR8 | 974 | 0.28 | 0.34 | YES |
27 | CFD | CFD | CFD | 1006 | 0.27 | 0.35 | YES |
28 | NLRC4 | NLRC4 | NLRC4 | 1041 | 0.27 | 0.36 | YES |
29 | TLR9 | TLR9 | TLR9 | 1046 | 0.27 | 0.37 | YES |
30 | C4BPA | C4BPA | C4BPA | 1062 | 0.26 | 0.38 | YES |
31 | CD180 | CD180 | CD180 | 1083 | 0.26 | 0.39 | YES |
32 | BIRC3 | BIRC3 | BIRC3 | 1092 | 0.26 | 0.4 | YES |
33 | CR1 | CR1 | CR1 | 1127 | 0.26 | 0.4 | YES |
34 | TICAM2 | TICAM2 | TICAM2 | 1166 | 0.25 | 0.41 | YES |
35 | CFH | CFH | CFH | 1189 | 0.25 | 0.42 | YES |
36 | LY86 | LY86 | LY86 | 1256 | 0.25 | 0.43 | YES |
37 | TLR7 | TLR7 | TLR7 | 1341 | 0.24 | 0.43 | YES |
38 | TLR2 | TLR2 | TLR2 | 1363 | 0.24 | 0.44 | YES |
39 | CDK1 | CDK1 | CDK1 | 1537 | 0.22 | 0.44 | YES |
40 | CCR2 | CCR2 | CCR2 | 1553 | 0.22 | 0.44 | YES |
41 | C1QB | C1QB | C1QB | 1598 | 0.22 | 0.45 | YES |
42 | TLR5 | TLR5 | TLR5 | 1600 | 0.22 | 0.46 | YES |
43 | BTK | BTK | BTK | 1708 | 0.21 | 0.46 | YES |
44 | C1QC | C1QC | C1QC | 1748 | 0.2 | 0.46 | YES |
45 | IRF7 | IRF7 | IRF7 | 1851 | 0.2 | 0.47 | YES |
46 | C1QA | C1QA | C1QA | 1882 | 0.19 | 0.47 | YES |
47 | CD14 | CD14 | CD14 | 2028 | 0.18 | 0.47 | YES |
48 | RIPK2 | RIPK2 | RIPK2 | 2271 | 0.17 | 0.46 | YES |
49 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 2285 | 0.17 | 0.47 | YES |
50 | CASP4 | CASP4 | CASP4 | 2356 | 0.16 | 0.47 | YES |
51 | UNC93B1 | UNC93B1 | UNC93B1 | 2481 | 0.15 | 0.47 | YES |
52 | CFI | CFI | CFI | 2486 | 0.15 | 0.48 | YES |
53 | CD4 | CD4 | CD4 | 2645 | 0.14 | 0.47 | YES |
54 | CTSS | CTSS | CTSS | 2646 | 0.14 | 0.48 | YES |
55 | NLRP3 | NLRP3 | NLRP3 | 2666 | 0.14 | 0.48 | YES |
56 | CASP1 | CASP1 | CASP1 | 2682 | 0.14 | 0.49 | YES |
57 | TLR1 | TLR1 | TLR1 | 2695 | 0.14 | 0.49 | YES |
58 | P2RX7 | P2RX7 | P2RX7 | 2930 | 0.13 | 0.48 | NO |
59 | CASP8 | CASP8 | CASP8 | 3317 | 0.12 | 0.47 | NO |
60 | RIPK3 | RIPK3 | RIPK3 | 3389 | 0.11 | 0.47 | NO |
61 | IRAK1 | IRAK1 | IRAK1 | 3463 | 0.11 | 0.47 | NO |
62 | ISG15 | ISG15 | ISG15 | 3604 | 0.11 | 0.46 | NO |
63 | PROS1 | PROS1 | PROS1 | 3855 | 0.098 | 0.46 | NO |
64 | HSP90B1 | HSP90B1 | HSP90B1 | 3883 | 0.097 | 0.46 | NO |
65 | CAPZA1 | CAPZA1 | CAPZA1 | 3898 | 0.097 | 0.46 | NO |
66 | LGALS3 | LGALS3 | LGALS3 | 3978 | 0.094 | 0.46 | NO |
67 | PANX1 | PANX1 | PANX1 | 3982 | 0.094 | 0.46 | NO |
68 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 4018 | 0.093 | 0.46 | NO |
69 | DHX58 | DHX58 | DHX58 | 4130 | 0.09 | 0.46 | NO |
70 | IRF1 | IRF1 | IRF1 | 4146 | 0.09 | 0.46 | NO |
71 | CTSB | CTSB | CTSB | 4172 | 0.089 | 0.47 | NO |
72 | CTSK | CTSK | CTSK | 4217 | 0.088 | 0.47 | NO |
73 | DUSP4 | DUSP4 | DUSP4 | 4243 | 0.087 | 0.47 | NO |
74 | C4A | C4A | C4A | 4454 | 0.082 | 0.46 | NO |
75 | RNF135 | RNF135 | RNF135 | 4478 | 0.081 | 0.46 | NO |
76 | MYD88 | MYD88 | MYD88 | 4538 | 0.08 | 0.46 | NO |
77 | UBA7 | UBA7 | UBA7 | 4574 | 0.079 | 0.46 | NO |
78 | CNPY3 | CNPY3 | CNPY3 | 4624 | 0.078 | 0.46 | NO |
79 | UBE2L6 | UBE2L6 | UBE2L6 | 4641 | 0.077 | 0.46 | NO |
80 | FADD | FADD | FADD | 4730 | 0.075 | 0.46 | NO |
81 | EEA1 | EEA1 | EEA1 | 4738 | 0.075 | 0.46 | NO |
82 | MAPK13 | MAPK13 | MAPK13 | 4744 | 0.075 | 0.47 | NO |
83 | ART1 | ART1 | ART1 | 4878 | 0.072 | 0.46 | NO |
84 | IKBKG | IKBKG | IKBKG | 4911 | 0.071 | 0.46 | NO |
85 | NFKB2 | NFKB2 | NFKB2 | 4926 | 0.071 | 0.47 | NO |
86 | DDOST | DDOST | DDOST | 5165 | 0.066 | 0.46 | NO |
87 | ELK1 | ELK1 | ELK1 | 5187 | 0.065 | 0.46 | NO |
88 | IRF3 | IRF3 | IRF3 | 5213 | 0.065 | 0.46 | NO |
89 | BCL2L1 | BCL2L1 | BCL2L1 | 5289 | 0.063 | 0.46 | NO |
90 | UBE2D1 | UBE2D1 | UBE2D1 | 5319 | 0.063 | 0.46 | NO |
91 | MAP2K2 | MAP2K2 | MAP2K2 | 5601 | 0.057 | 0.44 | NO |
92 | DNM2 | DNM2 | DNM2 | 5668 | 0.056 | 0.44 | NO |
93 | ATG12 | ATG12 | ATG12 | 5706 | 0.055 | 0.44 | NO |
94 | CYLD | CYLD | CYLD | 5807 | 0.053 | 0.44 | NO |
95 | TICAM1 | TICAM1 | TICAM1 | 5970 | 0.051 | 0.43 | NO |
96 | DEFB1 | DEFB1 | DEFB1 | 6033 | 0.05 | 0.43 | NO |
97 | PRKCSH | PRKCSH | PRKCSH | 6080 | 0.049 | 0.43 | NO |
98 | IRF2 | IRF2 | IRF2 | 6228 | 0.046 | 0.42 | NO |
99 | TBK1 | TBK1 | TBK1 | 6255 | 0.046 | 0.42 | NO |
100 | NLRC5 | NLRC5 | NLRC5 | 6321 | 0.045 | 0.42 | NO |
101 | MAPK9 | MAPK9 | MAPK9 | 6482 | 0.042 | 0.41 | NO |
102 | JUN | JUN | JUN | 6495 | 0.042 | 0.42 | NO |
103 | UBA52 | UBA52 | UBA52 | 6586 | 0.041 | 0.41 | NO |
104 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 6617 | 0.04 | 0.41 | NO |
105 | TRAF3 | TRAF3 | TRAF3 | 6702 | 0.039 | 0.41 | NO |
106 | TRAF2 | TRAF2 | TRAF2 | 6789 | 0.037 | 0.4 | NO |
107 | UBE2D2 | UBE2D2 | UBE2D2 | 6950 | 0.035 | 0.4 | NO |
108 | NFKBIB | NFKBIB | NFKBIB | 7112 | 0.032 | 0.39 | NO |
109 | MAPK7 | MAPK7 | MAPK7 | 7124 | 0.032 | 0.39 | NO |
110 | IRAK4 | IRAK4 | IRAK4 | 7359 | 0.029 | 0.38 | NO |
111 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 7421 | 0.028 | 0.38 | NO |
112 | TLR3 | TLR3 | TLR3 | 7434 | 0.028 | 0.38 | NO |
113 | DDX58 | DDX58 | DDX58 | 7445 | 0.028 | 0.38 | NO |
114 | CASP9 | CASP9 | CASP9 | 7498 | 0.027 | 0.38 | NO |
115 | CTSL1 | CTSL1 | CTSL1 | 7521 | 0.027 | 0.38 | NO |
116 | CASP2 | CASP2 | CASP2 | 7562 | 0.026 | 0.37 | NO |
117 | OTUD5 | OTUD5 | OTUD5 | 7626 | 0.026 | 0.37 | NO |
118 | RPS27A | RPS27A | RPS27A | 7637 | 0.025 | 0.37 | NO |
119 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 7856 | 0.022 | 0.36 | NO |
120 | TANK | TANK | TANK | 7883 | 0.022 | 0.36 | NO |
121 | BIRC2 | BIRC2 | BIRC2 | 7909 | 0.022 | 0.36 | NO |
122 | TXN | TXN | TXN | 7954 | 0.021 | 0.36 | NO |
123 | CASP10 | CASP10 | CASP10 | 8006 | 0.02 | 0.36 | NO |
124 | MAPK11 | MAPK11 | MAPK11 | 8347 | 0.016 | 0.34 | NO |
125 | MAP2K1 | MAP2K1 | MAP2K1 | 8389 | 0.016 | 0.34 | NO |
126 | PPP2R1A | PPP2R1A | PPP2R1A | 8408 | 0.016 | 0.34 | NO |
127 | MAPK14 | MAPK14 | MAPK14 | 8425 | 0.015 | 0.34 | NO |
128 | AGER | AGER | AGER | 8569 | 0.013 | 0.33 | NO |
129 | NLRX1 | NLRX1 | NLRX1 | 8969 | 0.0079 | 0.31 | NO |
130 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 9038 | 0.0072 | 0.3 | NO |
131 | LGMN | LGMN | LGMN | 9112 | 0.0062 | 0.3 | NO |
132 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 9123 | 0.0061 | 0.3 | NO |
133 | NLRP1 | NLRP1 | NLRP1 | 9158 | 0.0057 | 0.3 | NO |
134 | PPP2CA | PPP2CA | PPP2CA | 9292 | 0.0038 | 0.29 | NO |
135 | UBE2N | UBE2N | UBE2N | 9481 | 0.0016 | 0.28 | NO |
136 | TAB3 | TAB3 | TAB3 | 9716 | -0.00095 | 0.27 | NO |
137 | TAB1 | TAB1 | TAB1 | 9903 | -0.0033 | 0.26 | NO |
138 | RELA | RELA | RELA | 9920 | -0.0036 | 0.26 | NO |
139 | RIPK1 | RIPK1 | RIPK1 | 10186 | -0.0068 | 0.24 | NO |
140 | PIN1 | PIN1 | PIN1 | 10206 | -0.007 | 0.24 | NO |
141 | DAK | DAK | DAK | 10236 | -0.0072 | 0.24 | NO |
142 | ATG5 | ATG5 | ATG5 | 10286 | -0.0078 | 0.24 | NO |
143 | CD55 | CD55 | CD55 | 10391 | -0.0089 | 0.23 | NO |
144 | UBE2K | UBE2K | UBE2K | 10461 | -0.0098 | 0.23 | NO |
145 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 10556 | -0.011 | 0.22 | NO |
146 | MAP2K4 | MAP2K4 | MAP2K4 | 10557 | -0.011 | 0.22 | NO |
147 | MAP2K7 | MAP2K7 | MAP2K7 | 10806 | -0.014 | 0.21 | NO |
148 | TAB2 | TAB2 | TAB2 | 10820 | -0.014 | 0.21 | NO |
149 | IKBKB | IKBKB | IKBKB | 10857 | -0.014 | 0.21 | NO |
150 | NOD1 | NOD1 | NOD1 | 10950 | -0.016 | 0.2 | NO |
151 | CAPZA2 | CAPZA2 | CAPZA2 | 11020 | -0.017 | 0.2 | NO |
152 | ATF1 | ATF1 | ATF1 | 11086 | -0.018 | 0.2 | NO |
153 | PCBP2 | PCBP2 | PCBP2 | 11089 | -0.018 | 0.2 | NO |
154 | MAVS | MAVS | MAVS | 11116 | -0.018 | 0.2 | NO |
155 | DUSP3 | DUSP3 | DUSP3 | 11133 | -0.018 | 0.2 | NO |
156 | IFIH1 | IFIH1 | IFIH1 | 11146 | -0.019 | 0.2 | NO |
157 | UBE2D3 | UBE2D3 | UBE2D3 | 11190 | -0.02 | 0.2 | NO |
158 | HMGB1 | HMGB1 | HMGB1 | 11317 | -0.021 | 0.19 | NO |
159 | MAP3K7 | MAP3K7 | MAP3K7 | 11379 | -0.022 | 0.19 | NO |
160 | SIKE1 | SIKE1 | SIKE1 | 11682 | -0.026 | 0.17 | NO |
161 | C5 | C5 | C5 | 11703 | -0.026 | 0.17 | NO |
162 | MAP2K3 | MAP2K3 | MAP2K3 | 11877 | -0.029 | 0.16 | NO |
163 | PPP2R5D | PPP2R5D | PPP2R5D | 11969 | -0.03 | 0.16 | NO |
164 | PELI1 | PELI1 | PELI1 | 12115 | -0.032 | 0.15 | NO |
165 | MAPK1 | MAPK1 | MAPK1 | 12294 | -0.035 | 0.14 | NO |
166 | ECSIT | ECSIT | ECSIT | 12350 | -0.036 | 0.14 | NO |
167 | MAP3K1 | MAP3K1 | MAP3K1 | 12363 | -0.036 | 0.14 | NO |
168 | TXNIP | TXNIP | TXNIP | 12417 | -0.037 | 0.14 | NO |
169 | PPP2CB | PPP2CB | PPP2CB | 12693 | -0.041 | 0.13 | NO |
170 | RNF125 | RNF125 | RNF125 | 12765 | -0.042 | 0.12 | NO |
171 | MAPK3 | MAPK3 | MAPK3 | 12864 | -0.044 | 0.12 | NO |
172 | TRIM25 | TRIM25 | TRIM25 | 12899 | -0.044 | 0.12 | NO |
173 | CREB1 | CREB1 | CREB1 | 12976 | -0.045 | 0.12 | NO |
174 | CD46 | CD46 | CD46 | 13012 | -0.046 | 0.12 | NO |
175 | CREBBP | CREBBP | CREBBP | 13021 | -0.046 | 0.12 | NO |
176 | S100A12 | S100A12 | S100A12 | 13063 | -0.046 | 0.12 | NO |
177 | SIGIRR | SIGIRR | SIGIRR | 13075 | -0.046 | 0.12 | NO |
178 | PELI3 | PELI3 | PELI3 | 13169 | -0.048 | 0.12 | NO |
179 | HERC5 | HERC5 | HERC5 | 13171 | -0.048 | 0.12 | NO |
180 | APP | APP | APP | 13199 | -0.049 | 0.12 | NO |
181 | CHUK | CHUK | CHUK | 13258 | -0.05 | 0.12 | NO |
182 | ATF2 | ATF2 | ATF2 | 13443 | -0.053 | 0.11 | NO |
183 | MAP2K6 | MAP2K6 | MAP2K6 | 13519 | -0.054 | 0.11 | NO |
184 | EP300 | EP300 | EP300 | 13575 | -0.055 | 0.11 | NO |
185 | TLR4 | TLR4 | TLR4 | 13780 | -0.059 | 0.096 | NO |
186 | PIK3R4 | PIK3R4 | PIK3R4 | 13827 | -0.06 | 0.096 | NO |
187 | DEFA1B | DEFA1B | DEFA1B | 14018 | -0.064 | 0.088 | NO |
188 | MEF2A | MEF2A | MEF2A | 14194 | -0.068 | 0.081 | NO |
189 | TIRAP | TIRAP | TIRAP | 14507 | -0.074 | 0.066 | NO |
190 | MEF2C | MEF2C | MEF2C | 14708 | -0.078 | 0.058 | NO |
191 | NFKBIA | NFKBIA | NFKBIA | 14800 | -0.08 | 0.056 | NO |
192 | FOS | FOS | FOS | 14891 | -0.082 | 0.054 | NO |
193 | IRAK2 | IRAK2 | IRAK2 | 15006 | -0.085 | 0.051 | NO |
194 | PIK3C3 | PIK3C3 | PIK3C3 | 15008 | -0.085 | 0.055 | NO |
195 | PPP2R1B | PPP2R1B | PPP2R1B | 15015 | -0.086 | 0.058 | NO |
196 | DUSP7 | DUSP7 | DUSP7 | 15079 | -0.088 | 0.057 | NO |
197 | PLCG2 | PLCG2 | PLCG2 | 15091 | -0.088 | 0.06 | NO |
198 | IRAK3 | IRAK3 | IRAK3 | 15220 | -0.092 | 0.056 | NO |
199 | ZFYVE20 | ZFYVE20 | ZFYVE20 | 15301 | -0.095 | 0.056 | NO |
200 | C4BPB | C4BPB | C4BPB | 15445 | -0.099 | 0.051 | NO |
201 | IFNA21 | IFNA21 | IFNA21 | 15487 | -0.1 | 0.053 | NO |
202 | DUSP6 | DUSP6 | DUSP6 | 16097 | -0.12 | 0.024 | NO |
203 | C7 | C7 | C7 | 16149 | -0.13 | 0.026 | NO |
204 | MAPK12 | MAPK12 | MAPK12 | 16308 | -0.14 | 0.022 | NO |
205 | C6 | C6 | C6 | 16529 | -0.15 | 0.016 | NO |
206 | BCL2 | BCL2 | BCL2 | 16550 | -0.15 | 0.02 | NO |
207 | PELI2 | PELI2 | PELI2 | 16762 | -0.16 | 0.015 | NO |
208 | TRAF6 | TRAF6 | TRAF6 | 16785 | -0.17 | 0.02 | NO |
209 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 16802 | -0.17 | 0.026 | NO |
210 | MAPK10 | MAPK10 | MAPK10 | 16805 | -0.17 | 0.032 | NO |
211 | MAPK8 | MAPK8 | MAPK8 | 16891 | -0.17 | 0.034 | NO |
212 | IFNA5 | IFNA5 | IFNA5 | 17138 | -0.19 | 0.027 | NO |
213 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 17195 | -0.2 | 0.032 | NO |
214 | DNM1 | DNM1 | DNM1 | 17287 | -0.21 | 0.034 | NO |
215 | MASP2 | MASP2 | MASP2 | 17471 | -0.23 | 0.033 | NO |
216 | MASP1 | MASP1 | MASP1 | 17760 | -0.28 | 0.028 | 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 CYTOSOLIC DNA SENSING PATHWAY.

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

Table S34. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CDC45 | CDC45 | CDC45 | 984 | 0.28 | -0.0062 | YES |
2 | CCNA2 | CCNA2 | CCNA2 | 1393 | 0.23 | 0.012 | YES |
3 | CDC6 | CDC6 | CDC6 | 1515 | 0.22 | 0.044 | YES |
4 | PSMA8 | PSMA8 | PSMA8 | 1581 | 0.22 | 0.078 | YES |
5 | CDT1 | CDT1 | CDT1 | 1601 | 0.22 | 0.11 | YES |
6 | CCNA1 | CCNA1 | CCNA1 | 1733 | 0.2 | 0.14 | YES |
7 | PSMB10 | PSMB10 | PSMB10 | 1945 | 0.19 | 0.16 | YES |
8 | DNA2 | DNA2 | DNA2 | 2143 | 0.18 | 0.18 | YES |
9 | GINS2 | GINS2 | GINS2 | 2418 | 0.16 | 0.2 | YES |
10 | POLD4 | POLD4 | POLD4 | 2428 | 0.16 | 0.22 | YES |
11 | GINS1 | GINS1 | GINS1 | 2773 | 0.14 | 0.23 | YES |
12 | PSMB9 | PSMB9 | PSMB9 | 3151 | 0.12 | 0.23 | YES |
13 | PSMD14 | PSMD14 | PSMD14 | 3340 | 0.12 | 0.24 | YES |
14 | PSMA5 | PSMA5 | PSMA5 | 3406 | 0.11 | 0.26 | YES |
15 | PSME2 | PSME2 | PSME2 | 3498 | 0.11 | 0.27 | YES |
16 | RFC4 | RFC4 | RFC4 | 3795 | 0.1 | 0.27 | YES |
17 | GINS4 | GINS4 | GINS4 | 3862 | 0.098 | 0.28 | YES |
18 | POLA2 | POLA2 | POLA2 | 3894 | 0.097 | 0.3 | YES |
19 | POLD1 | POLD1 | POLD1 | 3902 | 0.096 | 0.32 | YES |
20 | PSMB3 | PSMB3 | PSMB3 | 3979 | 0.094 | 0.33 | YES |
21 | RFC2 | RFC2 | RFC2 | 4319 | 0.085 | 0.32 | YES |
22 | MCM6 | MCM6 | MCM6 | 4328 | 0.085 | 0.34 | YES |
23 | MCM2 | MCM2 | MCM2 | 4371 | 0.084 | 0.35 | YES |
24 | PSMB4 | PSMB4 | PSMB4 | 4606 | 0.078 | 0.35 | YES |
25 | PSMB2 | PSMB2 | PSMB2 | 4675 | 0.076 | 0.36 | YES |
26 | RPA3 | RPA3 | RPA3 | 4761 | 0.074 | 0.37 | YES |
27 | PSMC4 | PSMC4 | PSMC4 | 4886 | 0.072 | 0.38 | YES |
28 | MCM8 | MCM8 | MCM8 | 4987 | 0.069 | 0.38 | YES |
29 | LIG1 | LIG1 | LIG1 | 5068 | 0.068 | 0.39 | YES |
30 | PCNA | PCNA | PCNA | 5081 | 0.068 | 0.4 | YES |
31 | POLE | POLE | POLE | 5140 | 0.066 | 0.41 | YES |
32 | RFC5 | RFC5 | RFC5 | 5284 | 0.063 | 0.41 | YES |
33 | PSMA7 | PSMA7 | PSMA7 | 5338 | 0.062 | 0.42 | YES |
34 | MCM4 | MCM4 | MCM4 | 5418 | 0.061 | 0.42 | YES |
35 | PSMB8 | PSMB8 | PSMB8 | 5451 | 0.06 | 0.43 | YES |
36 | PSMC2 | PSMC2 | PSMC2 | 5508 | 0.059 | 0.44 | YES |
37 | PSMD4 | PSMD4 | PSMD4 | 5525 | 0.058 | 0.45 | YES |
38 | PSMD7 | PSMD7 | PSMD7 | 5570 | 0.058 | 0.46 | YES |
39 | MCM5 | MCM5 | MCM5 | 5598 | 0.057 | 0.47 | YES |
40 | POLD2 | POLD2 | POLD2 | 5620 | 0.057 | 0.48 | YES |
41 | PSMD13 | PSMD13 | PSMD13 | 5641 | 0.057 | 0.48 | YES |
42 | PSMA4 | PSMA4 | PSMA4 | 5646 | 0.056 | 0.49 | YES |
43 | PSME4 | PSME4 | PSME4 | 5663 | 0.056 | 0.5 | YES |
44 | PSMA1 | PSMA1 | PSMA1 | 5693 | 0.056 | 0.51 | YES |
45 | PSMD8 | PSMD8 | PSMD8 | 5933 | 0.051 | 0.51 | YES |
46 | PSMA2 | PSMA2 | PSMA2 | 6013 | 0.05 | 0.51 | YES |
47 | PSMB6 | PSMB6 | PSMB6 | 6090 | 0.049 | 0.52 | YES |
48 | PSMD9 | PSMD9 | PSMD9 | 6286 | 0.046 | 0.51 | YES |
49 | FEN1 | FEN1 | FEN1 | 6406 | 0.044 | 0.51 | YES |
50 | POLD3 | POLD3 | POLD3 | 6418 | 0.043 | 0.52 | YES |
51 | PSMD2 | PSMD2 | PSMD2 | 6527 | 0.042 | 0.52 | YES |
52 | UBA52 | UBA52 | UBA52 | 6586 | 0.041 | 0.53 | YES |
53 | PSMC5 | PSMC5 | PSMC5 | 7226 | 0.031 | 0.5 | NO |
54 | PSMD1 | PSMD1 | PSMD1 | 7275 | 0.03 | 0.5 | NO |
55 | PSMD3 | PSMD3 | PSMD3 | 7330 | 0.03 | 0.5 | NO |
56 | PSMC3 | PSMC3 | PSMC3 | 7444 | 0.028 | 0.5 | NO |
57 | PRIM2 | PRIM2 | PRIM2 | 7485 | 0.028 | 0.5 | NO |
58 | RPS27A | RPS27A | RPS27A | 7637 | 0.025 | 0.5 | NO |
59 | PSMF1 | PSMF1 | PSMF1 | 7677 | 0.025 | 0.5 | NO |
60 | PSMB1 | PSMB1 | PSMB1 | 7946 | 0.021 | 0.49 | NO |
61 | CDK2 | CDK2 | CDK2 | 7980 | 0.021 | 0.49 | NO |
62 | PSMD10 | PSMD10 | PSMD10 | 8053 | 0.02 | 0.49 | NO |
63 | PSMD11 | PSMD11 | PSMD11 | 8085 | 0.02 | 0.49 | NO |
64 | PSMC1 | PSMC1 | PSMC1 | 8857 | 0.0092 | 0.45 | NO |
65 | PSMD12 | PSMD12 | PSMD12 | 8951 | 0.0081 | 0.45 | NO |
66 | RPA2 | RPA2 | RPA2 | 9063 | 0.0069 | 0.44 | NO |
67 | PSMA6 | PSMA6 | PSMA6 | 9098 | 0.0065 | 0.44 | NO |
68 | PSME1 | PSME1 | PSME1 | 9110 | 0.0063 | 0.44 | NO |
69 | PSMA3 | PSMA3 | PSMA3 | 9175 | 0.0055 | 0.44 | NO |
70 | PSMB5 | PSMB5 | PSMB5 | 9342 | 0.0032 | 0.43 | NO |
71 | PSMD6 | PSMD6 | PSMD6 | 9575 | 0.00057 | 0.42 | NO |
72 | RB1 | RB1 | RB1 | 9824 | -0.0022 | 0.41 | NO |
73 | PRIM1 | PRIM1 | PRIM1 | 9925 | -0.0036 | 0.4 | NO |
74 | PSMB7 | PSMB7 | PSMB7 | 10453 | -0.0096 | 0.37 | NO |
75 | POLA1 | POLA1 | POLA1 | 10488 | -0.01 | 0.37 | NO |
76 | MCM7 | MCM7 | MCM7 | 10511 | -0.01 | 0.37 | NO |
77 | RPA1 | RPA1 | RPA1 | 10623 | -0.012 | 0.37 | NO |
78 | CDKN1A | CDKN1A | CDKN1A | 10846 | -0.014 | 0.36 | NO |
79 | MCM3 | MCM3 | MCM3 | 11124 | -0.018 | 0.35 | NO |
80 | CDKN1B | CDKN1B | CDKN1B | 12291 | -0.035 | 0.29 | NO |
81 | PSMD5 | PSMD5 | PSMD5 | 13285 | -0.05 | 0.24 | NO |
82 | POLE2 | POLE2 | POLE2 | 13426 | -0.053 | 0.25 | NO |
83 | PSMC6 | PSMC6 | PSMC6 | 13553 | -0.055 | 0.25 | NO |
84 | RFC3 | RFC3 | RFC3 | 13881 | -0.061 | 0.24 | 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: PID AURORA B PATHWAY.

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

Table S35. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | XDH | XDH | XDH | 316 | 0.4 | 0.046 | YES |
2 | RRM2 | RRM2 | RRM2 | 611 | 0.33 | 0.082 | YES |
3 | AMPD1 | AMPD1 | AMPD1 | 867 | 0.29 | 0.11 | YES |
4 | ADA | ADA | ADA | 959 | 0.28 | 0.15 | YES |
5 | TK1 | TK1 | TK1 | 1261 | 0.24 | 0.18 | YES |
6 | NME1-NME2 | NME1-NME2 | NME1-NME2 | 1293 | 0.24 | 0.21 | YES |
7 | IMPDH1 | IMPDH1 | IMPDH1 | 1710 | 0.21 | 0.22 | YES |
8 | TYMP | TYMP | TYMP | 1753 | 0.2 | 0.25 | YES |
9 | NME1 | NME1 | NME1 | 2194 | 0.17 | 0.25 | YES |
10 | GPX1 | GPX1 | GPX1 | 2434 | 0.16 | 0.26 | YES |
11 | NME4 | NME4 | NME4 | 2492 | 0.15 | 0.29 | YES |
12 | NT5M | NT5M | NT5M | 2726 | 0.14 | 0.3 | YES |
13 | AMPD3 | AMPD3 | AMPD3 | 2898 | 0.13 | 0.31 | YES |
14 | GLRX | GLRX | GLRX | 2904 | 0.13 | 0.33 | YES |
15 | DTYMK | DTYMK | DTYMK | 3002 | 0.13 | 0.34 | YES |
16 | CDA | CDA | CDA | 3114 | 0.12 | 0.36 | YES |
17 | APRT | APRT | APRT | 3383 | 0.11 | 0.36 | YES |
18 | ATIC | ATIC | ATIC | 3438 | 0.11 | 0.37 | YES |
19 | NME2 | NME2 | NME2 | 3709 | 0.1 | 0.38 | YES |
20 | UCK2 | UCK2 | UCK2 | 3725 | 0.1 | 0.39 | YES |
21 | AMPD2 | AMPD2 | AMPD2 | 3769 | 0.1 | 0.4 | YES |
22 | NT5C3 | NT5C3 | NT5C3 | 3871 | 0.097 | 0.41 | YES |
23 | DPYS | DPYS | DPYS | 3975 | 0.094 | 0.42 | YES |
24 | DGUOK | DGUOK | DGUOK | 3976 | 0.094 | 0.44 | YES |
25 | UPP2 | UPP2 | UPP2 | 4065 | 0.092 | 0.45 | YES |
26 | AK5 | AK5 | AK5 | 4187 | 0.089 | 0.46 | YES |
27 | NT5C1B | NT5C1B | NT5C1B | 4304 | 0.085 | 0.46 | YES |
28 | CAD | CAD | CAD | 4398 | 0.083 | 0.47 | YES |
29 | TXNRD1 | TXNRD1 | TXNRD1 | 4456 | 0.082 | 0.48 | YES |
30 | GUK1 | GUK1 | GUK1 | 4651 | 0.077 | 0.48 | YES |
31 | TK2 | TK2 | TK2 | 4964 | 0.07 | 0.48 | NO |
32 | DHODH | DHODH | DHODH | 5090 | 0.067 | 0.48 | NO |
33 | DPYD | DPYD | DPYD | 5597 | 0.057 | 0.46 | NO |
34 | HPRT1 | HPRT1 | HPRT1 | 5609 | 0.057 | 0.47 | NO |
35 | AK2 | AK2 | AK2 | 5671 | 0.056 | 0.47 | NO |
36 | NT5C | NT5C | NT5C | 5826 | 0.053 | 0.47 | NO |
37 | PAICS | PAICS | PAICS | 5901 | 0.052 | 0.48 | NO |
38 | UPP1 | UPP1 | UPP1 | 6306 | 0.045 | 0.46 | NO |
39 | CMPK1 | CMPK1 | CMPK1 | 6544 | 0.041 | 0.46 | NO |
40 | RRM2B | RRM2B | RRM2B | 6616 | 0.04 | 0.46 | NO |
41 | GMPS | GMPS | GMPS | 7020 | 0.034 | 0.44 | NO |
42 | AGXT2 | AGXT2 | AGXT2 | 7106 | 0.032 | 0.44 | NO |
43 | DCTD | DCTD | DCTD | 7528 | 0.027 | 0.42 | NO |
44 | GDA | GDA | GDA | 7629 | 0.025 | 0.42 | NO |
45 | TXN | TXN | TXN | 7954 | 0.021 | 0.41 | NO |
46 | GART | GART | GART | 7975 | 0.021 | 0.41 | NO |
47 | CTPS | CTPS | CTPS | 8189 | 0.018 | 0.4 | NO |
48 | CTPS2 | CTPS2 | CTPS2 | 8381 | 0.016 | 0.39 | NO |
49 | PPAT | PPAT | PPAT | 8520 | 0.014 | 0.39 | NO |
50 | DUT | DUT | DUT | 8536 | 0.014 | 0.39 | NO |
51 | RRM1 | RRM1 | RRM1 | 8712 | 0.011 | 0.38 | NO |
52 | UMPS | UMPS | UMPS | 8866 | 0.0091 | 0.37 | NO |
53 | IMPDH2 | IMPDH2 | IMPDH2 | 8986 | 0.0077 | 0.37 | NO |
54 | UPB1 | UPB1 | UPB1 | 9023 | 0.0074 | 0.37 | NO |
55 | GSR | GSR | GSR | 9126 | 0.0061 | 0.36 | NO |
56 | NT5C2 | NT5C2 | NT5C2 | 9297 | 0.0037 | 0.35 | NO |
57 | GMPR | GMPR | GMPR | 9411 | 0.0024 | 0.35 | NO |
58 | PFAS | PFAS | PFAS | 9439 | 0.0022 | 0.35 | NO |
59 | TYMS | TYMS | TYMS | 9443 | 0.0021 | 0.35 | NO |
60 | ADSS | ADSS | ADSS | 10128 | -0.0061 | 0.31 | NO |
61 | ADK | ADK | ADK | 10345 | -0.0084 | 0.3 | NO |
62 | DCK | DCK | DCK | 10433 | -0.0094 | 0.3 | NO |
63 | ADSL | ADSL | ADSL | 10830 | -0.014 | 0.28 | NO |
64 | UCK1 | UCK1 | UCK1 | 13849 | -0.06 | 0.12 | NO |
65 | ADAL | ADAL | ADAL | 13883 | -0.061 | 0.13 | NO |
66 | NT5C1A | NT5C1A | NT5C1A | 14071 | -0.065 | 0.13 | NO |
67 | CAT | CAT | CAT | 14450 | -0.072 | 0.12 | NO |
68 | PNP | PNP | PNP | 14455 | -0.073 | 0.13 | NO |
69 | GMPR2 | GMPR2 | GMPR2 | 14731 | -0.079 | 0.13 | NO |
70 | NT5E | NT5E | NT5E | 14818 | -0.08 | 0.14 | NO |
71 | AK1 | AK1 | AK1 | 16324 | -0.14 | 0.074 | NO |
72 | ADSSL1 | ADSSL1 | ADSSL1 | 17277 | -0.21 | 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: PID E2F PATHWAY.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: PID E2F PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CENPA | CENPA | CENPA | 127 | 0.48 | 0.072 | YES |
2 | AURKB | AURKB | AURKB | 183 | 0.45 | 0.14 | YES |
3 | KIF20A | KIF20A | KIF20A | 210 | 0.43 | 0.21 | YES |
4 | BUB1 | BUB1 | BUB1 | 211 | 0.43 | 0.28 | YES |
5 | BIRC5 | BIRC5 | BIRC5 | 217 | 0.43 | 0.36 | YES |
6 | KIF2C | KIF2C | KIF2C | 555 | 0.34 | 0.39 | YES |
7 | CDCA8 | CDCA8 | CDCA8 | 679 | 0.32 | 0.44 | YES |
8 | SGOL1 | SGOL1 | SGOL1 | 777 | 0.3 | 0.49 | YES |
9 | NCAPG | NCAPG | NCAPG | 893 | 0.29 | 0.53 | YES |
10 | NCAPH | NCAPH | NCAPH | 898 | 0.29 | 0.57 | YES |
11 | AURKA | AURKA | AURKA | 1044 | 0.27 | 0.61 | YES |
12 | KIF23 | KIF23 | KIF23 | 1207 | 0.25 | 0.64 | YES |
13 | SEPT1 | SEPT1 | SEPT1 | 1247 | 0.25 | 0.68 | YES |
14 | NDC80 | NDC80 | NDC80 | 1334 | 0.24 | 0.72 | YES |
15 | AURKC | AURKC | AURKC | 1516 | 0.22 | 0.74 | YES |
16 | RACGAP1 | RACGAP1 | RACGAP1 | 3826 | 0.098 | 0.63 | NO |
17 | NCAPD2 | NCAPD2 | NCAPD2 | 4812 | 0.073 | 0.59 | NO |
18 | VIM | VIM | VIM | 4945 | 0.07 | 0.6 | NO |
19 | SMC4 | SMC4 | SMC4 | 5817 | 0.053 | 0.56 | NO |
20 | CBX5 | CBX5 | CBX5 | 6810 | 0.037 | 0.51 | NO |
21 | STMN1 | STMN1 | STMN1 | 7048 | 0.033 | 0.5 | NO |
22 | PPP1CC | PPP1CC | PPP1CC | 7249 | 0.031 | 0.49 | NO |
23 | NSUN2 | NSUN2 | NSUN2 | 7898 | 0.022 | 0.46 | NO |
24 | INCENP | INCENP | INCENP | 8138 | 0.019 | 0.45 | NO |
25 | NPM1 | NPM1 | NPM1 | 9060 | 0.0069 | 0.4 | NO |
26 | PSMA3 | PSMA3 | PSMA3 | 9175 | 0.0055 | 0.4 | NO |
27 | DES | DES | DES | 10037 | -0.005 | 0.35 | NO |
28 | NCL | NCL | NCL | 10091 | -0.0057 | 0.35 | NO |
29 | RASA1 | RASA1 | RASA1 | 10144 | -0.0062 | 0.35 | NO |
30 | EVI5 | EVI5 | EVI5 | 11096 | -0.018 | 0.3 | NO |
31 | MYLK | MYLK | MYLK | 11278 | -0.02 | 0.29 | NO |
32 | PPP2R5D | PPP2R5D | PPP2R5D | 11969 | -0.03 | 0.26 | NO |
33 | RHOA | RHOA | RHOA | 12368 | -0.036 | 0.24 | NO |
34 | PEBP1 | PEBP1 | PEBP1 | 12441 | -0.037 | 0.24 | NO |
35 | KLHL13 | KLHL13 | KLHL13 | 13013 | -0.046 | 0.22 | NO |
36 | CUL3 | CUL3 | CUL3 | 13080 | -0.047 | 0.22 | NO |
37 | SMC2 | SMC2 | SMC2 | 13306 | -0.05 | 0.22 | NO |
38 | KLHL9 | KLHL9 | KLHL9 | 16306 | -0.14 | 0.079 | NO |
39 | TACC1 | TACC1 | TACC1 | 16876 | -0.17 | 0.076 | 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: PID INTEGRIN2 PATHWAY.

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: PID INTEGRIN2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CD8B | CD8B | CD8B | 552 | 0.34 | 0.000085 | YES |
2 | CD28 | CD28 | CD28 | 712 | 0.32 | 0.019 | YES |
3 | CCR5 | CCR5 | CCR5 | 847 | 0.29 | 0.038 | YES |
4 | RCC1 | RCC1 | RCC1 | 943 | 0.28 | 0.058 | YES |
5 | LCK | LCK | LCK | 1147 | 0.25 | 0.069 | YES |
6 | APOBEC3G | APOBEC3G | APOBEC3G | 1332 | 0.24 | 0.08 | YES |
7 | PSMA8 | PSMA8 | PSMA8 | 1581 | 0.22 | 0.086 | YES |
8 | DOCK2 | DOCK2 | DOCK2 | 1662 | 0.21 | 0.1 | YES |
9 | TAF10 | TAF10 | TAF10 | 1663 | 0.21 | 0.12 | YES |
10 | CD247 | CD247 | CD247 | 1773 | 0.2 | 0.13 | YES |
11 | HCK | HCK | HCK | 1818 | 0.2 | 0.15 | YES |
12 | PSMB10 | PSMB10 | PSMB10 | 1945 | 0.19 | 0.16 | YES |
13 | NUP210 | NUP210 | NUP210 | 1998 | 0.18 | 0.17 | YES |
14 | HMGA1 | HMGA1 | HMGA1 | 2035 | 0.18 | 0.18 | YES |
15 | CD4 | CD4 | CD4 | 2645 | 0.14 | 0.16 | YES |
16 | AP1M2 | AP1M2 | AP1M2 | 3089 | 0.13 | 0.15 | YES |
17 | POLR2J | POLR2J | POLR2J | 3113 | 0.12 | 0.16 | YES |
18 | PSMB9 | PSMB9 | PSMB9 | 3151 | 0.12 | 0.17 | YES |
19 | PSMD14 | PSMD14 | PSMD14 | 3340 | 0.12 | 0.17 | YES |
20 | PSMA5 | PSMA5 | PSMA5 | 3406 | 0.11 | 0.18 | YES |
21 | PSME2 | PSME2 | PSME2 | 3498 | 0.11 | 0.18 | YES |
22 | POLR2L | POLR2L | POLR2L | 3739 | 0.1 | 0.18 | YES |
23 | AP1M1 | AP1M1 | AP1M1 | 3798 | 0.1 | 0.18 | YES |
24 | CXCR4 | CXCR4 | CXCR4 | 3888 | 0.097 | 0.18 | YES |
25 | POLR2H | POLR2H | POLR2H | 3969 | 0.094 | 0.19 | YES |
26 | PSMB3 | PSMB3 | PSMB3 | 3979 | 0.094 | 0.2 | YES |
27 | TCEB1 | TCEB1 | TCEB1 | 4086 | 0.091 | 0.2 | YES |
28 | BANF1 | BANF1 | BANF1 | 4211 | 0.088 | 0.2 | YES |
29 | CDK7 | CDK7 | CDK7 | 4242 | 0.087 | 0.21 | YES |
30 | TCEB2 | TCEB2 | TCEB2 | 4283 | 0.086 | 0.21 | YES |
31 | AP2S1 | AP2S1 | AP2S1 | 4469 | 0.081 | 0.21 | YES |
32 | AP2A1 | AP2A1 | AP2A1 | 4519 | 0.08 | 0.21 | YES |
33 | GTF2H2B | GTF2H2B | GTF2H2B | 4547 | 0.079 | 0.22 | YES |
34 | PSMB4 | PSMB4 | PSMB4 | 4606 | 0.078 | 0.22 | YES |
35 | RAN | RAN | RAN | 4634 | 0.077 | 0.23 | YES |
36 | PSMB2 | PSMB2 | PSMB2 | 4675 | 0.076 | 0.23 | YES |
37 | RBX1 | RBX1 | RBX1 | 4740 | 0.075 | 0.24 | YES |
38 | NUP37 | NUP37 | NUP37 | 4747 | 0.075 | 0.24 | YES |
39 | PSMC4 | PSMC4 | PSMC4 | 4886 | 0.072 | 0.24 | YES |
40 | NUPL2 | NUPL2 | NUPL2 | 4919 | 0.071 | 0.24 | YES |
41 | LIG1 | LIG1 | LIG1 | 5068 | 0.068 | 0.24 | YES |
42 | PSMA7 | PSMA7 | PSMA7 | 5338 | 0.062 | 0.23 | YES |
43 | NUP62 | NUP62 | NUP62 | 5447 | 0.06 | 0.23 | YES |
44 | PSMB8 | PSMB8 | PSMB8 | 5451 | 0.06 | 0.24 | YES |
45 | XRCC4 | XRCC4 | XRCC4 | 5487 | 0.059 | 0.24 | YES |
46 | PPIA | PPIA | PPIA | 5506 | 0.059 | 0.24 | YES |
47 | PSMC2 | PSMC2 | PSMC2 | 5508 | 0.059 | 0.25 | YES |
48 | RANGAP1 | RANGAP1 | RANGAP1 | 5520 | 0.059 | 0.26 | YES |
49 | VPS28 | VPS28 | VPS28 | 5522 | 0.059 | 0.26 | YES |
50 | PSMD4 | PSMD4 | PSMD4 | 5525 | 0.058 | 0.26 | YES |
51 | PSMD7 | PSMD7 | PSMD7 | 5570 | 0.058 | 0.27 | YES |
52 | PSMD13 | PSMD13 | PSMD13 | 5641 | 0.057 | 0.27 | YES |
53 | PSMA4 | PSMA4 | PSMA4 | 5646 | 0.056 | 0.27 | YES |
54 | PSME4 | PSME4 | PSME4 | 5663 | 0.056 | 0.28 | YES |
55 | RAE1 | RAE1 | RAE1 | 5682 | 0.056 | 0.28 | YES |
56 | PSMA1 | PSMA1 | PSMA1 | 5693 | 0.056 | 0.29 | YES |
57 | AAAS | AAAS | AAAS | 5906 | 0.052 | 0.28 | YES |
58 | HLA-A | HLA-A | HLA-A | 5912 | 0.052 | 0.28 | YES |
59 | POLR2G | POLR2G | POLR2G | 5932 | 0.052 | 0.29 | YES |
60 | PSMD8 | PSMD8 | PSMD8 | 5933 | 0.051 | 0.29 | YES |
61 | AP1B1 | AP1B1 | AP1B1 | 5935 | 0.051 | 0.3 | YES |
62 | GTF2E2 | GTF2E2 | GTF2E2 | 5948 | 0.051 | 0.3 | YES |
63 | PSMA2 | PSMA2 | PSMA2 | 6013 | 0.05 | 0.3 | YES |
64 | PSMB6 | PSMB6 | PSMB6 | 6090 | 0.049 | 0.3 | YES |
65 | TAF12 | TAF12 | TAF12 | 6172 | 0.048 | 0.3 | YES |
66 | NUP93 | NUP93 | NUP93 | 6177 | 0.047 | 0.3 | YES |
67 | AP1S1 | AP1S1 | AP1S1 | 6212 | 0.047 | 0.31 | YES |
68 | AP2M1 | AP2M1 | AP2M1 | 6279 | 0.046 | 0.31 | YES |
69 | PSMD9 | PSMD9 | PSMD9 | 6286 | 0.046 | 0.31 | YES |
70 | POLR2I | POLR2I | POLR2I | 6300 | 0.045 | 0.32 | YES |
71 | RANBP1 | RANBP1 | RANBP1 | 6379 | 0.044 | 0.31 | YES |
72 | FEN1 | FEN1 | FEN1 | 6406 | 0.044 | 0.32 | YES |
73 | PSMD2 | PSMD2 | PSMD2 | 6527 | 0.042 | 0.31 | YES |
74 | NMT1 | NMT1 | NMT1 | 6543 | 0.041 | 0.32 | YES |
75 | UBA52 | UBA52 | UBA52 | 6586 | 0.041 | 0.32 | YES |
76 | CCNH | CCNH | CCNH | 6589 | 0.041 | 0.32 | YES |
77 | NUP107 | NUP107 | NUP107 | 6783 | 0.037 | 0.31 | NO |
78 | RAC1 | RAC1 | RAC1 | 7167 | 0.032 | 0.3 | NO |
79 | PSMC5 | PSMC5 | PSMC5 | 7226 | 0.031 | 0.3 | NO |
80 | PSMD1 | PSMD1 | PSMD1 | 7275 | 0.03 | 0.3 | NO |
81 | ARF1 | ARF1 | ARF1 | 7317 | 0.03 | 0.3 | NO |
82 | PSMD3 | PSMD3 | PSMD3 | 7330 | 0.03 | 0.3 | NO |
83 | POLR2F | POLR2F | POLR2F | 7340 | 0.03 | 0.3 | NO |
84 | POLR2K | POLR2K | POLR2K | 7370 | 0.029 | 0.3 | NO |
85 | PSMC3 | PSMC3 | PSMC3 | 7444 | 0.028 | 0.3 | NO |
86 | PACS1 | PACS1 | PACS1 | 7608 | 0.026 | 0.29 | NO |
87 | RPS27A | RPS27A | RPS27A | 7637 | 0.025 | 0.29 | NO |
88 | PSMF1 | PSMF1 | PSMF1 | 7677 | 0.025 | 0.29 | NO |
89 | TCEA1 | TCEA1 | TCEA1 | 7768 | 0.024 | 0.29 | NO |
90 | POLR2E | POLR2E | POLR2E | 7836 | 0.022 | 0.29 | NO |
91 | PSMB1 | PSMB1 | PSMB1 | 7946 | 0.021 | 0.28 | NO |
92 | WHSC2 | WHSC2 | WHSC2 | 8002 | 0.02 | 0.28 | NO |
93 | PSMD10 | PSMD10 | PSMD10 | 8053 | 0.02 | 0.28 | NO |
94 | PAK2 | PAK2 | PAK2 | 8079 | 0.02 | 0.28 | NO |
95 | PSMD11 | PSMD11 | PSMD11 | 8085 | 0.02 | 0.28 | NO |
96 | TAF6 | TAF6 | TAF6 | 8088 | 0.019 | 0.29 | NO |
97 | POM121 | POM121 | POM121 | 8196 | 0.018 | 0.28 | NO |
98 | SLC25A6 | SLC25A6 | SLC25A6 | 8205 | 0.018 | 0.28 | NO |
99 | TAF4 | TAF4 | TAF4 | 8322 | 0.016 | 0.28 | NO |
100 | NCBP2 | NCBP2 | NCBP2 | 8419 | 0.015 | 0.27 | NO |
101 | POLR2D | POLR2D | POLR2D | 8545 | 0.014 | 0.27 | NO |
102 | TH1L | TH1L | TH1L | 8597 | 0.013 | 0.27 | NO |
103 | GTF2A2 | GTF2A2 | GTF2A2 | 8661 | 0.012 | 0.26 | NO |
104 | B2M | B2M | B2M | 8691 | 0.011 | 0.26 | NO |
105 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 8813 | 0.0097 | 0.26 | NO |
106 | ELMO1 | ELMO1 | ELMO1 | 8833 | 0.0095 | 0.26 | NO |
107 | GTF2E1 | GTF2E1 | GTF2E1 | 8851 | 0.0093 | 0.26 | NO |
108 | PSMC1 | PSMC1 | PSMC1 | 8857 | 0.0092 | 0.26 | NO |
109 | GTF2H2 | GTF2H2 | GTF2H2 | 8910 | 0.0086 | 0.26 | NO |
110 | PSMD12 | PSMD12 | PSMD12 | 8951 | 0.0081 | 0.25 | NO |
111 | SUPT5H | SUPT5H | SUPT5H | 8966 | 0.0079 | 0.25 | NO |
112 | ELL | ELL | ELL | 8987 | 0.0077 | 0.25 | NO |
113 | NPM1 | NPM1 | NPM1 | 9060 | 0.0069 | 0.25 | NO |
114 | KPNB1 | KPNB1 | KPNB1 | 9082 | 0.0067 | 0.25 | NO |
115 | ATP6V1H | ATP6V1H | ATP6V1H | 9094 | 0.0065 | 0.25 | NO |
116 | PSMA6 | PSMA6 | PSMA6 | 9098 | 0.0065 | 0.25 | NO |
117 | XPO1 | XPO1 | XPO1 | 9102 | 0.0064 | 0.25 | NO |
118 | PSME1 | PSME1 | PSME1 | 9110 | 0.0063 | 0.25 | NO |
119 | SSRP1 | SSRP1 | SSRP1 | 9115 | 0.0062 | 0.25 | NO |
120 | NUP50 | NUP50 | NUP50 | 9117 | 0.0062 | 0.25 | NO |
121 | PSMA3 | PSMA3 | PSMA3 | 9175 | 0.0055 | 0.25 | NO |
122 | NUP85 | NUP85 | NUP85 | 9193 | 0.0052 | 0.25 | NO |
123 | CTDP1 | CTDP1 | CTDP1 | 9199 | 0.0051 | 0.25 | NO |
124 | PSMB5 | PSMB5 | PSMB5 | 9342 | 0.0032 | 0.24 | NO |
125 | VPS37A | VPS37A | VPS37A | 9395 | 0.0027 | 0.24 | NO |
126 | GTF2F1 | GTF2F1 | GTF2F1 | 9430 | 0.0023 | 0.24 | NO |
127 | PSMD6 | PSMD6 | PSMD6 | 9575 | 0.00057 | 0.23 | NO |
128 | XRCC5 | XRCC5 | XRCC5 | 9652 | -0.00029 | 0.22 | NO |
129 | RDBP | RDBP | RDBP | 9691 | -0.00066 | 0.22 | NO |
130 | GTF2H1 | GTF2H1 | GTF2H1 | 9709 | -0.00086 | 0.22 | NO |
131 | NUP88 | NUP88 | NUP88 | 9761 | -0.0016 | 0.22 | NO |
132 | TAF9 | TAF9 | TAF9 | 9776 | -0.0018 | 0.22 | NO |
133 | SLC25A5 | SLC25A5 | SLC25A5 | 9879 | -0.003 | 0.21 | NO |
134 | XRCC6 | XRCC6 | XRCC6 | 9975 | -0.0041 | 0.21 | NO |
135 | SKP1 | SKP1 | SKP1 | 10040 | -0.0051 | 0.2 | NO |
136 | TPR | TPR | TPR | 10250 | -0.0074 | 0.19 | NO |
137 | NUP43 | NUP43 | NUP43 | 10259 | -0.0075 | 0.19 | NO |
138 | PSMB7 | PSMB7 | PSMB7 | 10453 | -0.0096 | 0.18 | NO |
139 | CDK9 | CDK9 | CDK9 | 10706 | -0.013 | 0.17 | NO |
140 | NUP205 | NUP205 | NUP205 | 10765 | -0.013 | 0.17 | NO |
141 | ERCC3 | ERCC3 | ERCC3 | 10836 | -0.014 | 0.17 | NO |
142 | POLR2C | POLR2C | POLR2C | 10870 | -0.015 | 0.17 | NO |
143 | KPNA1 | KPNA1 | KPNA1 | 10948 | -0.016 | 0.16 | NO |
144 | GTF2F2 | GTF2F2 | GTF2F2 | 10965 | -0.016 | 0.16 | NO |
145 | TSG101 | TSG101 | TSG101 | 10982 | -0.016 | 0.16 | NO |
146 | VPS37C | VPS37C | VPS37C | 11128 | -0.018 | 0.16 | NO |
147 | NUPL1 | NUPL1 | NUPL1 | 11223 | -0.02 | 0.16 | NO |
148 | GTF2B | GTF2B | GTF2B | 11402 | -0.022 | 0.15 | NO |
149 | AP1S2 | AP1S2 | AP1S2 | 11407 | -0.022 | 0.15 | NO |
150 | NUP155 | NUP155 | NUP155 | 11494 | -0.023 | 0.15 | NO |
151 | POLR2B | POLR2B | POLR2B | 11515 | -0.024 | 0.15 | NO |
152 | ERCC2 | ERCC2 | ERCC2 | 11555 | -0.024 | 0.15 | NO |
153 | AP2B1 | AP2B1 | AP2B1 | 11575 | -0.024 | 0.15 | NO |
154 | AP1G1 | AP1G1 | AP1G1 | 11774 | -0.027 | 0.14 | NO |
155 | LIG4 | LIG4 | LIG4 | 11917 | -0.029 | 0.13 | NO |
156 | TAF1 | TAF1 | TAF1 | 11997 | -0.03 | 0.13 | NO |
157 | RNGTT | RNGTT | RNGTT | 12026 | -0.031 | 0.13 | NO |
158 | CCNT2 | CCNT2 | CCNT2 | 12146 | -0.033 | 0.13 | NO |
159 | GTF2H4 | GTF2H4 | GTF2H4 | 12366 | -0.036 | 0.12 | NO |
160 | NMT2 | NMT2 | NMT2 | 12394 | -0.036 | 0.12 | NO |
161 | AP2A2 | AP2A2 | AP2A2 | 12434 | -0.037 | 0.12 | NO |
162 | NUP35 | NUP35 | NUP35 | 12509 | -0.038 | 0.12 | NO |
163 | TCEB3 | TCEB3 | TCEB3 | 12556 | -0.039 | 0.12 | NO |
164 | RNMT | RNMT | RNMT | 12710 | -0.041 | 0.12 | NO |
165 | POLR2A | POLR2A | POLR2A | 12752 | -0.042 | 0.12 | NO |
166 | TBP | TBP | TBP | 12760 | -0.042 | 0.12 | NO |
167 | NUP54 | NUP54 | NUP54 | 12806 | -0.043 | 0.12 | NO |
168 | NUP133 | NUP133 | NUP133 | 12835 | -0.043 | 0.13 | NO |
169 | RANBP2 | RANBP2 | RANBP2 | 13016 | -0.046 | 0.12 | NO |
170 | TAF11 | TAF11 | TAF11 | 13212 | -0.049 | 0.12 | NO |
171 | GTF2H3 | GTF2H3 | GTF2H3 | 13245 | -0.049 | 0.12 | NO |
172 | PSMD5 | PSMD5 | PSMD5 | 13285 | -0.05 | 0.12 | NO |
173 | TAF13 | TAF13 | TAF13 | 13352 | -0.051 | 0.12 | NO |
174 | NUP188 | NUP188 | NUP188 | 13394 | -0.052 | 0.12 | NO |
175 | NUP214 | NUP214 | NUP214 | 13454 | -0.053 | 0.12 | NO |
176 | PSMC6 | PSMC6 | PSMC6 | 13553 | -0.055 | 0.12 | NO |
177 | NCBP1 | NCBP1 | NCBP1 | 13611 | -0.056 | 0.13 | NO |
178 | NUP153 | NUP153 | NUP153 | 13741 | -0.058 | 0.12 | NO |
179 | SUPT16H | SUPT16H | SUPT16H | 13772 | -0.059 | 0.13 | NO |
180 | SEH1L | SEH1L | SEH1L | 13788 | -0.059 | 0.13 | NO |
181 | BTRC | BTRC | BTRC | 13803 | -0.059 | 0.14 | NO |
182 | TAF4B | TAF4B | TAF4B | 13850 | -0.06 | 0.14 | NO |
183 | TAF5 | TAF5 | TAF5 | 13952 | -0.062 | 0.14 | NO |
184 | COBRA1 | COBRA1 | COBRA1 | 14117 | -0.066 | 0.14 | NO |
185 | CUL5 | CUL5 | CUL5 | 14724 | -0.078 | 0.11 | NO |
186 | VPS37B | VPS37B | VPS37B | 14896 | -0.082 | 0.11 | NO |
187 | MNAT1 | MNAT1 | MNAT1 | 15348 | -0.096 | 0.091 | NO |
188 | SLC25A4 | SLC25A4 | SLC25A4 | 15502 | -0.1 | 0.092 | NO |
189 | PSIP1 | PSIP1 | PSIP1 | 15548 | -0.1 | 0.098 | NO |
190 | FYN | FYN | FYN | 15712 | -0.11 | 0.099 | NO |
191 | CCNT1 | CCNT1 | CCNT1 | 16636 | -0.16 | 0.062 | NO |
192 | GTF2A1 | GTF2A1 | GTF2A1 | 16673 | -0.16 | 0.074 | NO |
193 | VPS37D | VPS37D | VPS37D | 16683 | -0.16 | 0.087 | NO |
Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION, 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 | CCNE1 | CCNE1 | CCNE1 | 409 | 0.38 | 0.03 | YES |
2 | CDC45 | CDC45 | CDC45 | 984 | 0.28 | 0.037 | YES |
3 | CCNA2 | CCNA2 | CCNA2 | 1393 | 0.23 | 0.047 | YES |
4 | CDC6 | CDC6 | CDC6 | 1515 | 0.22 | 0.072 | YES |
5 | PSMA8 | PSMA8 | PSMA8 | 1581 | 0.22 | 0.098 | YES |
6 | CDT1 | CDT1 | CDT1 | 1601 | 0.22 | 0.13 | YES |
7 | CCNA1 | CCNA1 | CCNA1 | 1733 | 0.2 | 0.15 | YES |
8 | PSMB10 | PSMB10 | PSMB10 | 1945 | 0.19 | 0.16 | YES |
9 | DNA2 | DNA2 | DNA2 | 2143 | 0.18 | 0.18 | YES |
10 | CDC25A | CDC25A | CDC25A | 2305 | 0.16 | 0.19 | YES |
11 | CCNE2 | CCNE2 | CCNE2 | 2379 | 0.16 | 0.21 | YES |
12 | GINS2 | GINS2 | GINS2 | 2418 | 0.16 | 0.23 | YES |
13 | POLD4 | POLD4 | POLD4 | 2428 | 0.16 | 0.25 | YES |
14 | GINS1 | GINS1 | GINS1 | 2773 | 0.14 | 0.25 | YES |
15 | CDC25B | CDC25B | CDC25B | 3118 | 0.12 | 0.25 | YES |
16 | PSMB9 | PSMB9 | PSMB9 | 3151 | 0.12 | 0.27 | YES |
17 | PSMD14 | PSMD14 | PSMD14 | 3340 | 0.12 | 0.27 | YES |
18 | PSMA5 | PSMA5 | PSMA5 | 3406 | 0.11 | 0.28 | YES |
19 | PSME2 | PSME2 | PSME2 | 3498 | 0.11 | 0.3 | YES |
20 | RFC4 | RFC4 | RFC4 | 3795 | 0.1 | 0.29 | YES |
21 | GINS4 | GINS4 | GINS4 | 3862 | 0.098 | 0.3 | YES |
22 | POLA2 | POLA2 | POLA2 | 3894 | 0.097 | 0.31 | YES |
23 | POLD1 | POLD1 | POLD1 | 3902 | 0.096 | 0.33 | YES |
24 | PSMB3 | PSMB3 | PSMB3 | 3979 | 0.094 | 0.34 | YES |
25 | CDK7 | CDK7 | CDK7 | 4242 | 0.087 | 0.33 | YES |
26 | RFC2 | RFC2 | RFC2 | 4319 | 0.085 | 0.34 | YES |
27 | MCM6 | MCM6 | MCM6 | 4328 | 0.085 | 0.35 | YES |
28 | MCM2 | MCM2 | MCM2 | 4371 | 0.084 | 0.36 | YES |
29 | PSMB4 | PSMB4 | PSMB4 | 4606 | 0.078 | 0.36 | YES |
30 | PSMB2 | PSMB2 | PSMB2 | 4675 | 0.076 | 0.37 | YES |
31 | RPA3 | RPA3 | RPA3 | 4761 | 0.074 | 0.37 | YES |
32 | PSMC4 | PSMC4 | PSMC4 | 4886 | 0.072 | 0.38 | YES |
33 | MCM8 | MCM8 | MCM8 | 4987 | 0.069 | 0.38 | YES |
34 | LIG1 | LIG1 | LIG1 | 5068 | 0.068 | 0.39 | YES |
35 | PCNA | PCNA | PCNA | 5081 | 0.068 | 0.4 | YES |
36 | POLE | POLE | POLE | 5140 | 0.066 | 0.4 | YES |
37 | RFC5 | RFC5 | RFC5 | 5284 | 0.063 | 0.4 | YES |
38 | PSMA7 | PSMA7 | PSMA7 | 5338 | 0.062 | 0.41 | YES |
39 | MCM4 | MCM4 | MCM4 | 5418 | 0.061 | 0.41 | YES |
40 | PSMB8 | PSMB8 | PSMB8 | 5451 | 0.06 | 0.42 | YES |
41 | PSMC2 | PSMC2 | PSMC2 | 5508 | 0.059 | 0.42 | YES |
42 | PSMD4 | PSMD4 | PSMD4 | 5525 | 0.058 | 0.43 | YES |
43 | PSMD7 | PSMD7 | PSMD7 | 5570 | 0.058 | 0.44 | YES |
44 | MCM5 | MCM5 | MCM5 | 5598 | 0.057 | 0.44 | YES |
45 | POLD2 | POLD2 | POLD2 | 5620 | 0.057 | 0.45 | YES |
46 | PSMD13 | PSMD13 | PSMD13 | 5641 | 0.057 | 0.46 | YES |
47 | PSMA4 | PSMA4 | PSMA4 | 5646 | 0.056 | 0.46 | YES |
48 | PSME4 | PSME4 | PSME4 | 5663 | 0.056 | 0.47 | YES |
49 | PSMA1 | PSMA1 | PSMA1 | 5693 | 0.056 | 0.48 | YES |
50 | CDK4 | CDK4 | CDK4 | 5734 | 0.055 | 0.48 | YES |
51 | CKS1B | CKS1B | CKS1B | 5815 | 0.053 | 0.49 | YES |
52 | PSMD8 | PSMD8 | PSMD8 | 5933 | 0.051 | 0.49 | YES |
53 | PSMA2 | PSMA2 | PSMA2 | 6013 | 0.05 | 0.49 | YES |
54 | PSMB6 | PSMB6 | PSMB6 | 6090 | 0.049 | 0.49 | YES |
55 | CUL1 | CUL1 | CUL1 | 6261 | 0.046 | 0.49 | YES |
56 | PSMD9 | PSMD9 | PSMD9 | 6286 | 0.046 | 0.49 | YES |
57 | FEN1 | FEN1 | FEN1 | 6406 | 0.044 | 0.49 | YES |
58 | POLD3 | POLD3 | POLD3 | 6418 | 0.043 | 0.5 | YES |
59 | PSMD2 | PSMD2 | PSMD2 | 6527 | 0.042 | 0.5 | YES |
60 | UBA52 | UBA52 | UBA52 | 6586 | 0.041 | 0.5 | YES |
61 | CCNH | CCNH | CCNH | 6589 | 0.041 | 0.51 | YES |
62 | PSMC5 | PSMC5 | PSMC5 | 7226 | 0.031 | 0.48 | NO |
63 | PSMD1 | PSMD1 | PSMD1 | 7275 | 0.03 | 0.48 | NO |
64 | PSMD3 | PSMD3 | PSMD3 | 7330 | 0.03 | 0.48 | NO |
65 | PSMC3 | PSMC3 | PSMC3 | 7444 | 0.028 | 0.48 | NO |
66 | PRIM2 | PRIM2 | PRIM2 | 7485 | 0.028 | 0.48 | NO |
67 | RPS27A | RPS27A | RPS27A | 7637 | 0.025 | 0.47 | NO |
68 | PSMF1 | PSMF1 | PSMF1 | 7677 | 0.025 | 0.48 | NO |
69 | PSMB1 | PSMB1 | PSMB1 | 7946 | 0.021 | 0.46 | NO |
70 | CDK2 | CDK2 | CDK2 | 7980 | 0.021 | 0.46 | NO |
71 | PSMD10 | PSMD10 | PSMD10 | 8053 | 0.02 | 0.46 | NO |
72 | PSMD11 | PSMD11 | PSMD11 | 8085 | 0.02 | 0.46 | NO |
73 | MYC | MYC | MYC | 8710 | 0.011 | 0.43 | NO |
74 | PSMC1 | PSMC1 | PSMC1 | 8857 | 0.0092 | 0.42 | NO |
75 | PSMD12 | PSMD12 | PSMD12 | 8951 | 0.0081 | 0.42 | NO |
76 | RPA2 | RPA2 | RPA2 | 9063 | 0.0069 | 0.42 | NO |
77 | PSMA6 | PSMA6 | PSMA6 | 9098 | 0.0065 | 0.42 | NO |
78 | PSME1 | PSME1 | PSME1 | 9110 | 0.0063 | 0.42 | NO |
79 | PSMA3 | PSMA3 | PSMA3 | 9175 | 0.0055 | 0.41 | NO |
80 | MAX | MAX | MAX | 9176 | 0.0055 | 0.41 | NO |
81 | PSMB5 | PSMB5 | PSMB5 | 9342 | 0.0032 | 0.4 | NO |
82 | PSMD6 | PSMD6 | PSMD6 | 9575 | 0.00057 | 0.39 | NO |
83 | RB1 | RB1 | RB1 | 9824 | -0.0022 | 0.38 | NO |
84 | PRIM1 | PRIM1 | PRIM1 | 9925 | -0.0036 | 0.37 | NO |
85 | SKP1 | SKP1 | SKP1 | 10040 | -0.0051 | 0.37 | NO |
86 | PSMB7 | PSMB7 | PSMB7 | 10453 | -0.0096 | 0.35 | NO |
87 | SKP2 | SKP2 | SKP2 | 10468 | -0.0098 | 0.35 | NO |
88 | POLA1 | POLA1 | POLA1 | 10488 | -0.01 | 0.35 | NO |
89 | MCM7 | MCM7 | MCM7 | 10511 | -0.01 | 0.35 | NO |
90 | RPA1 | RPA1 | RPA1 | 10623 | -0.012 | 0.34 | NO |
91 | CDKN1A | CDKN1A | CDKN1A | 10846 | -0.014 | 0.33 | NO |
92 | MCM3 | MCM3 | MCM3 | 11124 | -0.018 | 0.32 | NO |
93 | CDKN1B | CDKN1B | CDKN1B | 12291 | -0.035 | 0.26 | NO |
94 | PSMD5 | PSMD5 | PSMD5 | 13285 | -0.05 | 0.21 | NO |
95 | POLE2 | POLE2 | POLE2 | 13426 | -0.053 | 0.21 | NO |
96 | PSMC6 | PSMC6 | PSMC6 | 13553 | -0.055 | 0.21 | NO |
97 | RFC3 | RFC3 | RFC3 | 13881 | -0.061 | 0.2 | NO |
98 | CCND1 | CCND1 | CCND1 | 14808 | -0.08 | 0.16 | NO |
99 | WEE1 | WEE1 | WEE1 | 15023 | -0.086 | 0.16 | NO |
100 | MNAT1 | MNAT1 | MNAT1 | 15348 | -0.096 | 0.16 | NO |
Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ORC1 REMOVAL FROM CHROMATIN.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ORC1 REMOVAL FROM CHROMATIN, 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 | CCNA2 | CCNA2 | CCNA2 | 1393 | 0.23 | -0.014 | YES |
2 | CDC6 | CDC6 | CDC6 | 1515 | 0.22 | 0.04 | YES |
3 | PSMA8 | PSMA8 | PSMA8 | 1581 | 0.22 | 0.094 | YES |
4 | CDT1 | CDT1 | CDT1 | 1601 | 0.22 | 0.15 | YES |
5 | CCNA1 | CCNA1 | CCNA1 | 1733 | 0.2 | 0.2 | YES |
6 | PSMB10 | PSMB10 | PSMB10 | 1945 | 0.19 | 0.24 | YES |
7 | PSMB9 | PSMB9 | PSMB9 | 3151 | 0.12 | 0.21 | YES |
8 | PSMD14 | PSMD14 | PSMD14 | 3340 | 0.12 | 0.23 | YES |
9 | PSMA5 | PSMA5 | PSMA5 | 3406 | 0.11 | 0.25 | YES |
10 | PSME2 | PSME2 | PSME2 | 3498 | 0.11 | 0.28 | YES |
11 | PSMB3 | PSMB3 | PSMB3 | 3979 | 0.094 | 0.28 | YES |
12 | MCM6 | MCM6 | MCM6 | 4328 | 0.085 | 0.28 | YES |
13 | MCM2 | MCM2 | MCM2 | 4371 | 0.084 | 0.3 | YES |
14 | PSMB4 | PSMB4 | PSMB4 | 4606 | 0.078 | 0.31 | YES |
15 | PSMB2 | PSMB2 | PSMB2 | 4675 | 0.076 | 0.33 | YES |
16 | PSMC4 | PSMC4 | PSMC4 | 4886 | 0.072 | 0.34 | YES |
17 | MCM8 | MCM8 | MCM8 | 4987 | 0.069 | 0.35 | YES |
18 | PSMA7 | PSMA7 | PSMA7 | 5338 | 0.062 | 0.35 | YES |
19 | MCM4 | MCM4 | MCM4 | 5418 | 0.061 | 0.36 | YES |
20 | PSMB8 | PSMB8 | PSMB8 | 5451 | 0.06 | 0.37 | YES |
21 | PSMC2 | PSMC2 | PSMC2 | 5508 | 0.059 | 0.38 | YES |
22 | PSMD4 | PSMD4 | PSMD4 | 5525 | 0.058 | 0.4 | YES |
23 | PSMD7 | PSMD7 | PSMD7 | 5570 | 0.058 | 0.41 | YES |
24 | MCM5 | MCM5 | MCM5 | 5598 | 0.057 | 0.43 | YES |
25 | PSMD13 | PSMD13 | PSMD13 | 5641 | 0.057 | 0.44 | YES |
26 | PSMA4 | PSMA4 | PSMA4 | 5646 | 0.056 | 0.46 | YES |
27 | PSME4 | PSME4 | PSME4 | 5663 | 0.056 | 0.47 | YES |
28 | PSMA1 | PSMA1 | PSMA1 | 5693 | 0.056 | 0.48 | YES |
29 | PSMD8 | PSMD8 | PSMD8 | 5933 | 0.051 | 0.48 | YES |
30 | PSMA2 | PSMA2 | PSMA2 | 6013 | 0.05 | 0.49 | YES |
31 | PSMB6 | PSMB6 | PSMB6 | 6090 | 0.049 | 0.5 | YES |
32 | PSMD9 | PSMD9 | PSMD9 | 6286 | 0.046 | 0.5 | YES |
33 | PSMD2 | PSMD2 | PSMD2 | 6527 | 0.042 | 0.5 | YES |
34 | UBA52 | UBA52 | UBA52 | 6586 | 0.041 | 0.51 | YES |
35 | PSMC5 | PSMC5 | PSMC5 | 7226 | 0.031 | 0.48 | NO |
36 | PSMD1 | PSMD1 | PSMD1 | 7275 | 0.03 | 0.49 | NO |
37 | PSMD3 | PSMD3 | PSMD3 | 7330 | 0.03 | 0.49 | NO |
38 | PSMC3 | PSMC3 | PSMC3 | 7444 | 0.028 | 0.5 | NO |
39 | RPS27A | RPS27A | RPS27A | 7637 | 0.025 | 0.49 | NO |
40 | PSMF1 | PSMF1 | PSMF1 | 7677 | 0.025 | 0.5 | NO |
41 | PSMB1 | PSMB1 | PSMB1 | 7946 | 0.021 | 0.49 | NO |
42 | CDK2 | CDK2 | CDK2 | 7980 | 0.021 | 0.49 | NO |
43 | PSMD10 | PSMD10 | PSMD10 | 8053 | 0.02 | 0.49 | NO |
44 | PSMD11 | PSMD11 | PSMD11 | 8085 | 0.02 | 0.5 | NO |
45 | PSMC1 | PSMC1 | PSMC1 | 8857 | 0.0092 | 0.46 | NO |
46 | PSMD12 | PSMD12 | PSMD12 | 8951 | 0.0081 | 0.45 | NO |
47 | PSMA6 | PSMA6 | PSMA6 | 9098 | 0.0065 | 0.45 | NO |
48 | PSME1 | PSME1 | PSME1 | 9110 | 0.0063 | 0.45 | NO |
49 | PSMA3 | PSMA3 | PSMA3 | 9175 | 0.0055 | 0.44 | NO |
50 | PSMB5 | PSMB5 | PSMB5 | 9342 | 0.0032 | 0.44 | NO |
51 | PSMD6 | PSMD6 | PSMD6 | 9575 | 0.00057 | 0.42 | NO |
52 | RB1 | RB1 | RB1 | 9824 | -0.0022 | 0.41 | NO |
53 | PSMB7 | PSMB7 | PSMB7 | 10453 | -0.0096 | 0.38 | NO |
54 | MCM7 | MCM7 | MCM7 | 10511 | -0.01 | 0.38 | NO |
55 | CDKN1A | CDKN1A | CDKN1A | 10846 | -0.014 | 0.36 | NO |
56 | MCM3 | MCM3 | MCM3 | 11124 | -0.018 | 0.35 | NO |
57 | CDKN1B | CDKN1B | CDKN1B | 12291 | -0.035 | 0.3 | NO |
58 | PSMD5 | PSMD5 | PSMD5 | 13285 | -0.05 | 0.26 | NO |
59 | PSMC6 | PSMC6 | PSMC6 | 13553 | -0.055 | 0.26 | NO |
Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS.

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

Table S40. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | UNC5A | UNC5A | UNC5A | 879 | 0.29 | 0.036 | YES |
2 | PSMA8 | PSMA8 | PSMA8 | 1581 | 0.22 | 0.061 | YES |
3 | PSMB10 | PSMB10 | PSMB10 | 1945 | 0.19 | 0.096 | YES |
4 | DCC | DCC | DCC | 2161 | 0.17 | 0.14 | YES |
5 | DAPK2 | DAPK2 | DAPK2 | 2231 | 0.17 | 0.18 | YES |
6 | PSMB9 | PSMB9 | PSMB9 | 3151 | 0.12 | 0.17 | YES |
7 | PSMD14 | PSMD14 | PSMD14 | 3340 | 0.12 | 0.19 | YES |
8 | PSMA5 | PSMA5 | PSMA5 | 3406 | 0.11 | 0.22 | YES |
9 | PSME2 | PSME2 | PSME2 | 3498 | 0.11 | 0.25 | YES |
10 | CASP3 | CASP3 | CASP3 | 3885 | 0.097 | 0.25 | YES |
11 | PSMB3 | PSMB3 | PSMB3 | 3979 | 0.094 | 0.28 | YES |
12 | PSMB4 | PSMB4 | PSMB4 | 4606 | 0.078 | 0.26 | YES |
13 | PSMB2 | PSMB2 | PSMB2 | 4675 | 0.076 | 0.28 | YES |
14 | PSMC4 | PSMC4 | PSMC4 | 4886 | 0.072 | 0.29 | YES |
15 | MAGED1 | MAGED1 | MAGED1 | 5109 | 0.067 | 0.3 | YES |
16 | PSMA7 | PSMA7 | PSMA7 | 5338 | 0.062 | 0.3 | YES |
17 | PSMB8 | PSMB8 | PSMB8 | 5451 | 0.06 | 0.32 | YES |
18 | PSMC2 | PSMC2 | PSMC2 | 5508 | 0.059 | 0.33 | YES |
19 | PSMD4 | PSMD4 | PSMD4 | 5525 | 0.058 | 0.34 | YES |
20 | PSMD7 | PSMD7 | PSMD7 | 5570 | 0.058 | 0.36 | YES |
21 | PSMD13 | PSMD13 | PSMD13 | 5641 | 0.057 | 0.37 | YES |
22 | PSMA4 | PSMA4 | PSMA4 | 5646 | 0.056 | 0.39 | YES |
23 | PSME4 | PSME4 | PSME4 | 5663 | 0.056 | 0.4 | YES |
24 | PSMA1 | PSMA1 | PSMA1 | 5693 | 0.056 | 0.42 | YES |
25 | PSMD8 | PSMD8 | PSMD8 | 5933 | 0.051 | 0.42 | YES |
26 | PSMA2 | PSMA2 | PSMA2 | 6013 | 0.05 | 0.43 | YES |
27 | PSMB6 | PSMB6 | PSMB6 | 6090 | 0.049 | 0.44 | YES |
28 | PSMD9 | PSMD9 | PSMD9 | 6286 | 0.046 | 0.44 | YES |
29 | PSMD2 | PSMD2 | PSMD2 | 6527 | 0.042 | 0.44 | YES |
30 | UBA52 | UBA52 | UBA52 | 6586 | 0.041 | 0.45 | YES |
31 | PSMC5 | PSMC5 | PSMC5 | 7226 | 0.031 | 0.42 | NO |
32 | PSMD1 | PSMD1 | PSMD1 | 7275 | 0.03 | 0.43 | NO |
33 | PSMD3 | PSMD3 | PSMD3 | 7330 | 0.03 | 0.44 | NO |
34 | PSMC3 | PSMC3 | PSMC3 | 7444 | 0.028 | 0.44 | NO |
35 | CASP9 | CASP9 | CASP9 | 7498 | 0.027 | 0.44 | NO |
36 | RPS27A | RPS27A | RPS27A | 7637 | 0.025 | 0.44 | NO |
37 | PSMF1 | PSMF1 | PSMF1 | 7677 | 0.025 | 0.45 | NO |
38 | PSMB1 | PSMB1 | PSMB1 | 7946 | 0.021 | 0.44 | NO |
39 | PSMD10 | PSMD10 | PSMD10 | 8053 | 0.02 | 0.44 | NO |
40 | PAK2 | PAK2 | PAK2 | 8079 | 0.02 | 0.44 | NO |
41 | PSMD11 | PSMD11 | PSMD11 | 8085 | 0.02 | 0.45 | NO |
42 | DAPK3 | DAPK3 | DAPK3 | 8379 | 0.016 | 0.44 | NO |
43 | PSMC1 | PSMC1 | PSMC1 | 8857 | 0.0092 | 0.42 | NO |
44 | PSMD12 | PSMD12 | PSMD12 | 8951 | 0.0081 | 0.41 | NO |
45 | PSMA6 | PSMA6 | PSMA6 | 9098 | 0.0065 | 0.41 | NO |
46 | PSME1 | PSME1 | PSME1 | 9110 | 0.0063 | 0.41 | NO |
47 | PSMA3 | PSMA3 | PSMA3 | 9175 | 0.0055 | 0.41 | NO |
48 | PSMB5 | PSMB5 | PSMB5 | 9342 | 0.0032 | 0.4 | NO |
49 | PSMD6 | PSMD6 | PSMD6 | 9575 | 0.00057 | 0.38 | NO |
50 | PSMB7 | PSMB7 | PSMB7 | 10453 | -0.0096 | 0.34 | NO |
51 | DAPK1 | DAPK1 | DAPK1 | 11052 | -0.017 | 0.31 | NO |
52 | ARHGAP10 | ARHGAP10 | ARHGAP10 | 12028 | -0.031 | 0.27 | NO |
53 | PSMD5 | PSMD5 | PSMD5 | 13285 | -0.05 | 0.21 | NO |
54 | PSMC6 | PSMC6 | PSMC6 | 13553 | -0.055 | 0.21 | NO |
55 | UNC5B | UNC5B | UNC5B | 14509 | -0.074 | 0.18 | NO |
56 | APPL1 | APPL1 | APPL1 | 14756 | -0.079 | 0.19 | NO |
Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME MHC CLASS II ANTIGEN PRESENTATION.

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

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT | 38 | genes.ES.table | 0.42 | 1.6 | 0.037 | 1 | 0.91 | 0.32 | 0.3 | 0.22 | 1 | 0.74 |
KEGG NOTCH SIGNALING PATHWAY | 46 | genes.ES.table | 0.39 | 1.3 | 0.17 | 1 | 1 | 0.28 | 0.25 | 0.21 | 1 | 0.82 |
KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY | 61 | genes.ES.table | 0.36 | 1.3 | 0.16 | 1 | 1 | 0.28 | 0.26 | 0.21 | 1 | 0.8 |
KEGG OLFACTORY TRANSDUCTION | 72 | genes.ES.table | 0.56 | 1.4 | 0.04 | 1 | 0.99 | 0.39 | 0.17 | 0.32 | 1 | 0.74 |
KEGG TASTE TRANSDUCTION | 37 | genes.ES.table | 0.66 | 1.5 | 0.017 | 1 | 0.97 | 0.49 | 0.14 | 0.42 | 1 | 0.8 |
SIG CD40PATHWAYMAP | 33 | genes.ES.table | 0.36 | 1.3 | 0.17 | 1 | 1 | 0.46 | 0.32 | 0.31 | 1 | 0.85 |
PID RHOA REG PATHWAY | 44 | genes.ES.table | 0.38 | 1.3 | 0.16 | 1 | 1 | 0.3 | 0.27 | 0.22 | 1 | 0.85 |
PID HDAC CLASSI PATHWAY | 65 | genes.ES.table | 0.33 | 1.6 | 0.03 | 1 | 0.86 | 0.31 | 0.37 | 0.2 | 1 | 0.79 |
REACTOME MEIOSIS | 96 | genes.ES.table | 0.59 | 1.5 | 0.075 | 1 | 0.98 | 0.42 | 0.2 | 0.33 | 1 | 0.78 |
REACTOME SIGNALING BY FGFR1 MUTANTS | 26 | genes.ES.table | 0.47 | 1.5 | 0.055 | 1 | 0.99 | 0.12 | 0.04 | 0.11 | 1 | 0.74 |
Table S41. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SSPO | SSPO | SSPO | 101 | 0.66 | 0.15 | YES |
2 | GATA1 | GATA1 | GATA1 | 2252 | 0.22 | 0.079 | YES |
3 | SIRT4 | SIRT4 | SIRT4 | 2473 | 0.21 | 0.12 | YES |
4 | HDAC10 | HDAC10 | HDAC10 | 2649 | 0.2 | 0.15 | YES |
5 | SIN3B | SIN3B | SIN3B | 2848 | 0.18 | 0.18 | YES |
6 | ZFPM1 | ZFPM1 | ZFPM1 | 3205 | 0.17 | 0.2 | YES |
7 | SIRT7 | SIRT7 | SIRT7 | 3324 | 0.16 | 0.23 | YES |
8 | SMAD7 | SMAD7 | SMAD7 | 3474 | 0.15 | 0.26 | YES |
9 | GATA2 | GATA2 | GATA2 | 3916 | 0.14 | 0.27 | YES |
10 | SIRT6 | SIRT6 | SIRT6 | 3954 | 0.14 | 0.3 | YES |
11 | HDAC7 | HDAC7 | HDAC7 | 4121 | 0.13 | 0.32 | YES |
12 | NR2C1 | NR2C1 | NR2C1 | 4301 | 0.12 | 0.33 | YES |
13 | NFKBIA | NFKBIA | NFKBIA | 4747 | 0.11 | 0.33 | YES |
14 | HDAC5 | HDAC5 | HDAC5 | 5943 | 0.075 | 0.29 | YES |
15 | SIRT3 | SIRT3 | SIRT3 | 6025 | 0.074 | 0.3 | YES |
16 | FKBP3 | FKBP3 | FKBP3 | 6135 | 0.071 | 0.31 | YES |
17 | PPARG | PPARG | PPARG | 6335 | 0.066 | 0.31 | YES |
18 | SAP30 | SAP30 | SAP30 | 6529 | 0.062 | 0.32 | YES |
19 | HDAC6 | HDAC6 | HDAC6 | 6558 | 0.062 | 0.33 | YES |
20 | MBD3 | MBD3 | MBD3 | 6704 | 0.059 | 0.34 | YES |
21 | SIRT2 | SIRT2 | SIRT2 | 7508 | 0.044 | 0.3 | NO |
22 | HDAC1 | HDAC1 | HDAC1 | 7589 | 0.043 | 0.31 | NO |
23 | GATAD2B | GATAD2B | GATAD2B | 7640 | 0.042 | 0.31 | NO |
24 | MBD2 | MBD2 | MBD2 | 7660 | 0.042 | 0.32 | NO |
25 | RELA | RELA | RELA | 8092 | 0.034 | 0.31 | NO |
26 | MTA2 | MTA2 | MTA2 | 8127 | 0.034 | 0.31 | NO |
27 | XPO1 | XPO1 | XPO1 | 8211 | 0.032 | 0.31 | NO |
28 | HDAC8 | HDAC8 | HDAC8 | 8231 | 0.032 | 0.32 | NO |
29 | SAP18 | SAP18 | SAP18 | 8425 | 0.029 | 0.32 | NO |
30 | SIRT5 | SIRT5 | SIRT5 | 8432 | 0.028 | 0.32 | NO |
31 | MXD1 | MXD1 | MXD1 | 8514 | 0.027 | 0.32 | NO |
32 | MAX | MAX | MAX | 9065 | 0.019 | 0.3 | NO |
33 | UBE2I | UBE2I | UBE2I | 9435 | 0.013 | 0.28 | NO |
34 | SMURF1 | SMURF1 | SMURF1 | 9547 | 0.011 | 0.28 | NO |
35 | RANGAP1 | RANGAP1 | RANGAP1 | 9560 | 0.011 | 0.28 | NO |
36 | SIRT1 | SIRT1 | SIRT1 | 9572 | 0.011 | 0.28 | NO |
37 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 9583 | 0.011 | 0.28 | NO |
38 | HDAC4 | HDAC4 | HDAC4 | 9778 | 0.0076 | 0.28 | NO |
39 | PRKACA | PRKACA | PRKACA | 9899 | 0.0056 | 0.27 | NO |
40 | NCOR2 | NCOR2 | NCOR2 | 9924 | 0.0054 | 0.27 | NO |
41 | SUMO1 | SUMO1 | SUMO1 | 9989 | 0.0045 | 0.27 | NO |
42 | WDR77 | WDR77 | WDR77 | 10078 | 0.0027 | 0.26 | NO |
43 | CHD3 | CHD3 | CHD3 | 10088 | 0.0026 | 0.26 | NO |
44 | YY1 | YY1 | YY1 | 10150 | 0.0017 | 0.26 | NO |
45 | CREBBP | CREBBP | CREBBP | 10483 | -0.0036 | 0.24 | NO |
46 | SMG5 | SMG5 | SMG5 | 10490 | -0.0037 | 0.24 | NO |
47 | HDAC11 | HDAC11 | HDAC11 | 10546 | -0.0049 | 0.24 | NO |
48 | GATAD2A | GATAD2A | GATAD2A | 10620 | -0.006 | 0.24 | NO |
49 | RBBP7 | RBBP7 | RBBP7 | 11074 | -0.012 | 0.22 | NO |
50 | HDAC9 | HDAC9 | HDAC9 | 11121 | -0.013 | 0.22 | NO |
51 | HDAC3 | HDAC3 | HDAC3 | 12027 | -0.026 | 0.17 | NO |
52 | TNF | TNF | TNF | 12140 | -0.028 | 0.17 | NO |
53 | KAT2B | KAT2B | KAT2B | 12507 | -0.033 | 0.16 | NO |
54 | SIN3A | SIN3A | SIN3A | 12564 | -0.034 | 0.17 | NO |
55 | RBBP4 | RBBP4 | RBBP4 | 12620 | -0.035 | 0.17 | NO |
56 | HDAC2 | HDAC2 | HDAC2 | 12794 | -0.038 | 0.17 | NO |
57 | STAT3 | STAT3 | STAT3 | 13106 | -0.042 | 0.16 | NO |
58 | CHD4 | CHD4 | CHD4 | 13137 | -0.042 | 0.17 | NO |
59 | EP300 | EP300 | EP300 | 13387 | -0.047 | 0.17 | NO |
60 | PRMT5 | PRMT5 | PRMT5 | 13615 | -0.051 | 0.17 | NO |
61 | TFCP2 | TFCP2 | TFCP2 | 14046 | -0.059 | 0.16 | NO |
62 | NFKB1 | NFKB1 | NFKB1 | 14460 | -0.066 | 0.15 | NO |
63 | RAN | RAN | RAN | 14781 | -0.072 | 0.15 | NO |
64 | RANBP2 | RANBP2 | RANBP2 | 15391 | -0.087 | 0.14 | NO |
65 | NCOR1 | NCOR1 | NCOR1 | 15781 | -0.098 | 0.14 | NO |
Figure S81. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT.

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

Table S42. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | STX1B | STX1B | STX1B | 569 | 0.46 | 0.089 | YES |
2 | VAMP1 | VAMP1 | VAMP1 | 833 | 0.39 | 0.18 | YES |
3 | STX1A | STX1A | STX1A | 1024 | 0.36 | 0.26 | YES |
4 | SNAP25 | SNAP25 | SNAP25 | 1089 | 0.35 | 0.35 | YES |
5 | STX19 | STX19 | STX19 | 1661 | 0.27 | 0.39 | YES |
6 | TSNARE1 | TSNARE1 | TSNARE1 | 2442 | 0.21 | 0.4 | YES |
7 | USE1 | USE1 | USE1 | 3453 | 0.16 | 0.39 | YES |
8 | STX16 | STX16 | STX16 | 3789 | 0.14 | 0.4 | YES |
9 | STX10 | STX10 | STX10 | 4578 | 0.11 | 0.39 | YES |
10 | STX2 | STX2 | STX2 | 4665 | 0.11 | 0.42 | YES |
11 | STX4 | STX4 | STX4 | 5055 | 0.098 | 0.42 | YES |
12 | VAMP5 | VAMP5 | VAMP5 | 5427 | 0.088 | 0.42 | YES |
13 | VAMP4 | VAMP4 | VAMP4 | 5896 | 0.077 | 0.42 | NO |
14 | VAMP2 | VAMP2 | VAMP2 | 6589 | 0.061 | 0.4 | NO |
15 | STX8 | STX8 | STX8 | 6850 | 0.056 | 0.4 | NO |
16 | STX3 | STX3 | STX3 | 8604 | 0.026 | 0.31 | NO |
17 | BNIP1 | BNIP1 | BNIP1 | 8695 | 0.024 | 0.31 | NO |
18 | STX17 | STX17 | STX17 | 9038 | 0.019 | 0.29 | NO |
19 | BET1L | BET1L | BET1L | 9483 | 0.012 | 0.27 | NO |
20 | STX7 | STX7 | STX7 | 10430 | -0.0028 | 0.22 | NO |
21 | STX5 | STX5 | STX5 | 10468 | -0.0035 | 0.22 | NO |
22 | BET1 | BET1 | BET1 | 10767 | -0.0083 | 0.21 | NO |
23 | VTI1B | VTI1B | VTI1B | 11581 | -0.019 | 0.17 | NO |
24 | VAMP8 | VAMP8 | VAMP8 | 11665 | -0.02 | 0.17 | NO |
25 | STX11 | STX11 | STX11 | 11942 | -0.025 | 0.16 | NO |
26 | STX18 | STX18 | STX18 | 11972 | -0.025 | 0.16 | NO |
27 | SNAP29 | SNAP29 | SNAP29 | 12402 | -0.032 | 0.15 | NO |
28 | STX12 | STX12 | STX12 | 12426 | -0.032 | 0.16 | NO |
29 | STX6 | STX6 | STX6 | 12467 | -0.033 | 0.16 | NO |
30 | GOSR1 | GOSR1 | GOSR1 | 12729 | -0.037 | 0.16 | NO |
31 | SNAP23 | SNAP23 | SNAP23 | 12736 | -0.037 | 0.17 | NO |
32 | VTI1A | VTI1A | VTI1A | 13801 | -0.054 | 0.12 | NO |
33 | VAMP3 | VAMP3 | VAMP3 | 14414 | -0.065 | 0.11 | NO |
34 | YKT6 | YKT6 | YKT6 | 14436 | -0.065 | 0.12 | NO |
35 | SNAP47 | SNAP47 | SNAP47 | 14493 | -0.066 | 0.14 | NO |
36 | SEC22B | SEC22B | SEC22B | 14911 | -0.076 | 0.13 | NO |
37 | VAMP7 | VAMP7 | VAMP7 | 15639 | -0.094 | 0.12 | NO |
38 | GOSR2 | GOSR2 | GOSR2 | 15706 | -0.096 | 0.14 | NO |
Figure S83. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NOTCH SIGNALING PATHWAY.

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

Table S43. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | REC8 | REC8 | REC8 | 547 | 0.47 | 0.021 | YES |
2 | TEX12 | TEX12 | TEX12 | 627 | 0.44 | 0.065 | YES |
3 | HIST4H4 | HIST4H4 | HIST4H4 | 865 | 0.39 | 0.094 | YES |
4 | SYCP2 | SYCP2 | SYCP2 | 917 | 0.38 | 0.13 | YES |
5 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 1094 | 0.34 | 0.16 | YES |
6 | HIST1H4E | HIST1H4E | HIST1H4E | 1192 | 0.33 | 0.19 | YES |
7 | HIST1H4B | HIST1H4B | HIST1H4B | 1217 | 0.33 | 0.22 | YES |
8 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1263 | 0.32 | 0.26 | YES |
9 | HIST1H4I | HIST1H4I | HIST1H4I | 1344 | 0.31 | 0.29 | YES |
10 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 1422 | 0.3 | 0.32 | YES |
11 | HIST1H4C | HIST1H4C | HIST1H4C | 1519 | 0.29 | 0.34 | YES |
12 | STAG3 | STAG3 | STAG3 | 1761 | 0.26 | 0.36 | YES |
13 | HIST1H4J | HIST1H4J | HIST1H4J | 1764 | 0.26 | 0.39 | YES |
14 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1978 | 0.25 | 0.4 | YES |
15 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2033 | 0.24 | 0.42 | YES |
16 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 2074 | 0.24 | 0.45 | YES |
17 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2180 | 0.23 | 0.47 | YES |
18 | SMC1B | SMC1B | SMC1B | 2300 | 0.22 | 0.48 | YES |
19 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 2340 | 0.22 | 0.51 | YES |
20 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 2495 | 0.21 | 0.52 | YES |
21 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 2547 | 0.2 | 0.54 | YES |
22 | SYCP3 | SYCP3 | SYCP3 | 2671 | 0.2 | 0.55 | YES |
23 | HIST3H3 | HIST3H3 | HIST3H3 | 2871 | 0.18 | 0.56 | YES |
24 | HIST1H4A | HIST1H4A | HIST1H4A | 2942 | 0.18 | 0.58 | YES |
25 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 3067 | 0.17 | 0.59 | YES |
26 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 3073 | 0.17 | 0.61 | YES |
27 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 3226 | 0.16 | 0.62 | YES |
28 | HIST1H4D | HIST1H4D | HIST1H4D | 3329 | 0.16 | 0.63 | YES |
29 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 3596 | 0.15 | 0.63 | YES |
30 | ACD | ACD | ACD | 3696 | 0.14 | 0.64 | YES |
31 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 3710 | 0.14 | 0.66 | YES |
32 | FKBP6 | FKBP6 | FKBP6 | 4064 | 0.13 | 0.65 | NO |
33 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 5337 | 0.091 | 0.59 | NO |
34 | HIST1H4H | HIST1H4H | HIST1H4H | 6250 | 0.068 | 0.55 | NO |
35 | LMNA | LMNA | LMNA | 6356 | 0.066 | 0.55 | NO |
36 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 6736 | 0.058 | 0.54 | NO |
37 | H2AFX | H2AFX | H2AFX | 7902 | 0.037 | 0.48 | NO |
38 | HIST2H4A | HIST2H4A | HIST2H4A | 8210 | 0.032 | 0.46 | NO |
39 | DIDO1 | DIDO1 | DIDO1 | 8301 | 0.031 | 0.46 | NO |
40 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 8562 | 0.026 | 0.45 | NO |
41 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 8564 | 0.026 | 0.45 | NO |
42 | SYNE1 | SYNE1 | SYNE1 | 9030 | 0.019 | 0.43 | NO |
43 | UBE2I | UBE2I | UBE2I | 9435 | 0.013 | 0.41 | NO |
44 | TERF2IP | TERF2IP | TERF2IP | 9479 | 0.012 | 0.41 | NO |
45 | SYNE2 | SYNE2 | SYNE2 | 9855 | 0.0064 | 0.39 | NO |
46 | TINF2 | TINF2 | TINF2 | 10053 | 0.0034 | 0.38 | NO |
47 | ATR | ATR | ATR | 10206 | 0.0008 | 0.37 | NO |
48 | SUN2 | SUN2 | SUN2 | 10314 | -0.00085 | 0.36 | NO |
49 | H2AFZ | H2AFZ | H2AFZ | 11927 | -0.025 | 0.28 | NO |
50 | SMC3 | SMC3 | SMC3 | 12490 | -0.033 | 0.25 | NO |
51 | LMNB1 | LMNB1 | LMNB1 | 12840 | -0.038 | 0.24 | NO |
52 | TERF2 | TERF2 | TERF2 | 13025 | -0.041 | 0.23 | NO |
53 | TERF1 | TERF1 | TERF1 | 13142 | -0.043 | 0.23 | NO |
54 | POT1 | POT1 | POT1 | 13367 | -0.047 | 0.22 | NO |
55 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 13493 | -0.049 | 0.22 | NO |
56 | STAG2 | STAG2 | STAG2 | 13516 | -0.049 | 0.22 | NO |
57 | RAD21 | RAD21 | RAD21 | 13620 | -0.051 | 0.22 | NO |
58 | HSPA2 | HSPA2 | HSPA2 | 14021 | -0.058 | 0.21 | NO |
59 | BRCA1 | BRCA1 | BRCA1 | 14261 | -0.062 | 0.2 | NO |
60 | STAG1 | STAG1 | STAG1 | 15323 | -0.085 | 0.15 | NO |
61 | SMC1A | SMC1A | SMC1A | 15387 | -0.087 | 0.16 | NO |
Figure S85. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY.

Figure S86. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S44. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | TAS2R5 | TAS2R5 | TAS2R5 | 139 | 0.63 | 0.065 | YES |
2 | TAS2R20 | TAS2R20 | TAS2R20 | 233 | 0.57 | 0.13 | YES |
3 | TAS2R10 | TAS2R10 | TAS2R10 | 335 | 0.54 | 0.18 | YES |
4 | TAS2R14 | TAS2R14 | TAS2R14 | 392 | 0.51 | 0.24 | YES |
5 | CACNA1A | CACNA1A | CACNA1A | 496 | 0.48 | 0.29 | YES |
6 | GNG3 | GNG3 | GNG3 | 571 | 0.46 | 0.34 | YES |
7 | TAS2R19 | TAS2R19 | TAS2R19 | 661 | 0.43 | 0.38 | YES |
8 | GNB3 | GNB3 | GNB3 | 770 | 0.41 | 0.42 | YES |
9 | TAS2R4 | TAS2R4 | TAS2R4 | 780 | 0.4 | 0.47 | YES |
10 | TRPM5 | TRPM5 | TRPM5 | 829 | 0.39 | 0.51 | YES |
11 | TAS2R31 | TAS2R31 | TAS2R31 | 1157 | 0.34 | 0.53 | YES |
12 | TAS2R1 | TAS2R1 | TAS2R1 | 1236 | 0.33 | 0.57 | YES |
13 | TAS2R13 | TAS2R13 | TAS2R13 | 1359 | 0.31 | 0.6 | YES |
14 | ADCY4 | ADCY4 | ADCY4 | 1823 | 0.26 | 0.6 | YES |
15 | TAS2R50 | TAS2R50 | TAS2R50 | 1881 | 0.26 | 0.63 | YES |
16 | TAS1R1 | TAS1R1 | TAS1R1 | 2049 | 0.24 | 0.64 | YES |
17 | TAS2R43 | TAS2R43 | TAS2R43 | 2437 | 0.21 | 0.65 | YES |
18 | PLCB2 | PLCB2 | PLCB2 | 2599 | 0.2 | 0.66 | YES |
19 | TAS2R46 | TAS2R46 | TAS2R46 | 3628 | 0.15 | 0.62 | NO |
20 | TAS1R3 | TAS1R3 | TAS1R3 | 4371 | 0.12 | 0.6 | NO |
21 | SCNN1B | SCNN1B | SCNN1B | 5701 | 0.082 | 0.53 | NO |
22 | TAS2R3 | TAS2R3 | TAS2R3 | 6950 | 0.054 | 0.47 | NO |
23 | GRM4 | GRM4 | GRM4 | 7529 | 0.044 | 0.44 | NO |
24 | ADCY6 | ADCY6 | ADCY6 | 7977 | 0.036 | 0.42 | NO |
25 | ITPR3 | ITPR3 | ITPR3 | 8342 | 0.03 | 0.41 | NO |
26 | GNAS | GNAS | GNAS | 8406 | 0.029 | 0.41 | NO |
27 | CACNA1B | CACNA1B | CACNA1B | 9231 | 0.016 | 0.36 | NO |
28 | PRKACA | PRKACA | PRKACA | 9899 | 0.0056 | 0.33 | NO |
29 | PRKX | PRKX | PRKX | 10498 | -0.0038 | 0.3 | NO |
30 | GNB1 | GNB1 | GNB1 | 13459 | -0.048 | 0.14 | NO |
31 | SCNN1G | SCNN1G | SCNN1G | 13788 | -0.054 | 0.13 | NO |
32 | PRKACB | PRKACB | PRKACB | 15529 | -0.091 | 0.041 | NO |
33 | ADCY8 | ADCY8 | ADCY8 | 16150 | -0.11 | 0.02 | NO |
34 | PDE1A | PDE1A | PDE1A | 16723 | -0.14 | 0.0044 | NO |
35 | KCNB1 | KCNB1 | KCNB1 | 17034 | -0.16 | 0.0058 | NO |
36 | SCNN1A | SCNN1A | SCNN1A | 17577 | -0.21 | 0.00054 | NO |
37 | ACCN1 | ACCN1 | ACCN1 | 18094 | -0.32 | 0.009 | NO |
Figure S87. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OLFACTORY TRANSDUCTION.

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OLFACTORY TRANSDUCTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S45. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MSH4 | MSH4 | MSH4 | 269 | 0.56 | 0.028 | YES |
2 | MSH5 | MSH5 | MSH5 | 494 | 0.48 | 0.052 | YES |
3 | REC8 | REC8 | REC8 | 547 | 0.47 | 0.085 | YES |
4 | TEX12 | TEX12 | TEX12 | 627 | 0.44 | 0.12 | YES |
5 | HIST4H4 | HIST4H4 | HIST4H4 | 865 | 0.39 | 0.13 | YES |
6 | SYCP2 | SYCP2 | SYCP2 | 917 | 0.38 | 0.16 | YES |
7 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 1094 | 0.34 | 0.17 | YES |
8 | HIST1H4E | HIST1H4E | HIST1H4E | 1192 | 0.33 | 0.19 | YES |
9 | HIST1H4B | HIST1H4B | HIST1H4B | 1217 | 0.33 | 0.22 | YES |
10 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1263 | 0.32 | 0.24 | YES |
11 | HIST1H4I | HIST1H4I | HIST1H4I | 1344 | 0.31 | 0.26 | YES |
12 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 1422 | 0.3 | 0.28 | YES |
13 | TEX15 | TEX15 | TEX15 | 1469 | 0.29 | 0.3 | YES |
14 | HIST1H4C | HIST1H4C | HIST1H4C | 1519 | 0.29 | 0.32 | YES |
15 | STAG3 | STAG3 | STAG3 | 1761 | 0.26 | 0.32 | YES |
16 | HIST1H4J | HIST1H4J | HIST1H4J | 1764 | 0.26 | 0.34 | YES |
17 | DMC1 | DMC1 | DMC1 | 1887 | 0.25 | 0.36 | YES |
18 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1978 | 0.25 | 0.37 | YES |
19 | HIST1H3J | HIST1H3J | HIST1H3J | 2023 | 0.24 | 0.39 | YES |
20 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2033 | 0.24 | 0.41 | YES |
21 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 2074 | 0.24 | 0.42 | YES |
22 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2180 | 0.23 | 0.43 | YES |
23 | SMC1B | SMC1B | SMC1B | 2300 | 0.22 | 0.44 | YES |
24 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 2340 | 0.22 | 0.46 | YES |
25 | HIST1H3H | HIST1H3H | HIST1H3H | 2392 | 0.21 | 0.47 | YES |
26 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 2495 | 0.21 | 0.48 | YES |
27 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 2547 | 0.2 | 0.49 | YES |
28 | SYCP3 | SYCP3 | SYCP3 | 2671 | 0.2 | 0.5 | YES |
29 | HIST2H3C | HIST2H3C | HIST2H3C | 2721 | 0.19 | 0.52 | YES |
30 | HIST3H3 | HIST3H3 | HIST3H3 | 2871 | 0.18 | 0.52 | YES |
31 | HIST1H4A | HIST1H4A | HIST1H4A | 2942 | 0.18 | 0.53 | YES |
32 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 3067 | 0.17 | 0.54 | YES |
33 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 3073 | 0.17 | 0.55 | YES |
34 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 3226 | 0.16 | 0.55 | YES |
35 | HIST1H4D | HIST1H4D | HIST1H4D | 3329 | 0.16 | 0.56 | YES |
36 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 3596 | 0.15 | 0.56 | YES |
37 | MLH3 | MLH3 | MLH3 | 3672 | 0.15 | 0.56 | YES |
38 | ACD | ACD | ACD | 3696 | 0.14 | 0.57 | YES |
39 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 3710 | 0.14 | 0.58 | YES |
40 | HIST1H3D | HIST1H3D | HIST1H3D | 3726 | 0.14 | 0.6 | YES |
41 | FKBP6 | FKBP6 | FKBP6 | 4064 | 0.13 | 0.59 | NO |
42 | ATM | ATM | ATM | 4284 | 0.12 | 0.58 | NO |
43 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 5337 | 0.091 | 0.53 | NO |
44 | HIST1H3C | HIST1H3C | HIST1H3C | 5597 | 0.084 | 0.52 | NO |
45 | H3F3A | H3F3A | H3F3A | 5939 | 0.075 | 0.51 | NO |
46 | HIST1H4H | HIST1H4H | HIST1H4H | 6250 | 0.068 | 0.5 | NO |
47 | LMNA | LMNA | LMNA | 6356 | 0.066 | 0.5 | NO |
48 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 6736 | 0.058 | 0.48 | NO |
49 | HIST1H3B | HIST1H3B | HIST1H3B | 7409 | 0.046 | 0.45 | NO |
50 | HIST1H3F | HIST1H3F | HIST1H3F | 7548 | 0.044 | 0.44 | NO |
51 | H2AFX | H2AFX | H2AFX | 7902 | 0.037 | 0.43 | NO |
52 | HIST1H3A | HIST1H3A | HIST1H3A | 8066 | 0.035 | 0.42 | NO |
53 | HIST2H4A | HIST2H4A | HIST2H4A | 8210 | 0.032 | 0.42 | NO |
54 | DIDO1 | DIDO1 | DIDO1 | 8301 | 0.031 | 0.41 | NO |
55 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 8562 | 0.026 | 0.4 | NO |
56 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 8564 | 0.026 | 0.4 | NO |
57 | CDK2 | CDK2 | CDK2 | 8947 | 0.021 | 0.38 | NO |
58 | HIST1H3E | HIST1H3E | HIST1H3E | 8978 | 0.02 | 0.38 | NO |
59 | SYNE1 | SYNE1 | SYNE1 | 9030 | 0.019 | 0.38 | NO |
60 | H3F3B | H3F3B | H3F3B | 9179 | 0.017 | 0.38 | NO |
61 | UBE2I | UBE2I | UBE2I | 9435 | 0.013 | 0.36 | NO |
62 | HIST2H3D | HIST2H3D | HIST2H3D | 9436 | 0.013 | 0.36 | NO |
63 | TERF2IP | TERF2IP | TERF2IP | 9479 | 0.012 | 0.36 | NO |
64 | TOP3A | TOP3A | TOP3A | 9609 | 0.01 | 0.36 | NO |
65 | RPA2 | RPA2 | RPA2 | 9663 | 0.0094 | 0.35 | NO |
66 | MRE11A | MRE11A | MRE11A | 9676 | 0.0091 | 0.35 | NO |
67 | SYNE2 | SYNE2 | SYNE2 | 9855 | 0.0064 | 0.34 | NO |
68 | TINF2 | TINF2 | TINF2 | 10053 | 0.0034 | 0.34 | NO |
69 | ATR | ATR | ATR | 10206 | 0.0008 | 0.33 | NO |
70 | SUN2 | SUN2 | SUN2 | 10314 | -0.00085 | 0.32 | NO |
71 | MND1 | MND1 | MND1 | 11787 | -0.022 | 0.24 | NO |
72 | H2AFZ | H2AFZ | H2AFZ | 11927 | -0.025 | 0.24 | NO |
73 | SMC3 | SMC3 | SMC3 | 12490 | -0.033 | 0.21 | NO |
74 | LMNB1 | LMNB1 | LMNB1 | 12840 | -0.038 | 0.19 | NO |
75 | TERF2 | TERF2 | TERF2 | 13025 | -0.041 | 0.18 | NO |
76 | RBBP8 | RBBP8 | RBBP8 | 13051 | -0.041 | 0.18 | NO |
77 | TERF1 | TERF1 | TERF1 | 13142 | -0.043 | 0.18 | NO |
78 | MLH1 | MLH1 | MLH1 | 13205 | -0.044 | 0.18 | NO |
79 | BLM | BLM | BLM | 13215 | -0.044 | 0.19 | NO |
80 | CDK4 | CDK4 | CDK4 | 13303 | -0.046 | 0.18 | NO |
81 | POT1 | POT1 | POT1 | 13367 | -0.047 | 0.18 | NO |
82 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 13493 | -0.049 | 0.18 | NO |
83 | STAG2 | STAG2 | STAG2 | 13516 | -0.049 | 0.18 | NO |
84 | RAD51C | RAD51C | RAD51C | 13572 | -0.05 | 0.18 | NO |
85 | RAD21 | RAD21 | RAD21 | 13620 | -0.051 | 0.19 | NO |
86 | HSPA2 | HSPA2 | HSPA2 | 14021 | -0.058 | 0.17 | NO |
87 | HIST1H3G | HIST1H3G | HIST1H3G | 14198 | -0.061 | 0.16 | NO |
88 | BRCA1 | BRCA1 | BRCA1 | 14261 | -0.062 | 0.16 | NO |
89 | RAD50 | RAD50 | RAD50 | 14505 | -0.067 | 0.16 | NO |
90 | RPA1 | RPA1 | RPA1 | 14710 | -0.071 | 0.15 | NO |
91 | RPA3 | RPA3 | RPA3 | 14745 | -0.071 | 0.16 | NO |
92 | NBN | NBN | NBN | 15276 | -0.084 | 0.13 | NO |
93 | STAG1 | STAG1 | STAG1 | 15323 | -0.085 | 0.14 | NO |
94 | SMC1A | SMC1A | SMC1A | 15387 | -0.087 | 0.14 | NO |
95 | RAD51 | RAD51 | RAD51 | 16397 | -0.12 | 0.093 | NO |
96 | BRCA2 | BRCA2 | BRCA2 | 16407 | -0.12 | 0.1 | NO |
Figure S89. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TASTE TRANSDUCTION.

Figure S90. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TASTE TRANSDUCTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S46. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | HIST4H4 | HIST4H4 | HIST4H4 | 865 | 0.39 | 0.012 | YES |
2 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 1094 | 0.34 | 0.053 | YES |
3 | HIST1H4E | HIST1H4E | HIST1H4E | 1192 | 0.33 | 0.098 | YES |
4 | HIST1H4B | HIST1H4B | HIST1H4B | 1217 | 0.33 | 0.15 | YES |
5 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1263 | 0.32 | 0.2 | YES |
6 | HIST1H4I | HIST1H4I | HIST1H4I | 1344 | 0.31 | 0.24 | YES |
7 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 1422 | 0.3 | 0.28 | YES |
8 | HIST1H4C | HIST1H4C | HIST1H4C | 1519 | 0.29 | 0.32 | YES |
9 | HIST1H4J | HIST1H4J | HIST1H4J | 1764 | 0.26 | 0.35 | YES |
10 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1978 | 0.25 | 0.37 | YES |
11 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2033 | 0.24 | 0.41 | YES |
12 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 2074 | 0.24 | 0.44 | YES |
13 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2180 | 0.23 | 0.47 | YES |
14 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 2340 | 0.22 | 0.5 | YES |
15 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 2495 | 0.21 | 0.52 | YES |
16 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 2547 | 0.2 | 0.55 | YES |
17 | HIST3H3 | HIST3H3 | HIST3H3 | 2871 | 0.18 | 0.56 | YES |
18 | HIST1H4A | HIST1H4A | HIST1H4A | 2942 | 0.18 | 0.58 | YES |
19 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 3067 | 0.17 | 0.6 | YES |
20 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 3073 | 0.17 | 0.63 | YES |
21 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 3226 | 0.16 | 0.65 | YES |
22 | HIST1H4D | HIST1H4D | HIST1H4D | 3329 | 0.16 | 0.66 | YES |
23 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 3596 | 0.15 | 0.67 | YES |
24 | ACD | ACD | ACD | 3696 | 0.14 | 0.69 | YES |
25 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 3710 | 0.14 | 0.71 | YES |
26 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 5337 | 0.091 | 0.64 | NO |
27 | HIST1H4H | HIST1H4H | HIST1H4H | 6250 | 0.068 | 0.6 | NO |
28 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 6736 | 0.058 | 0.58 | NO |
29 | H2AFX | H2AFX | H2AFX | 7902 | 0.037 | 0.52 | NO |
30 | HIST2H4A | HIST2H4A | HIST2H4A | 8210 | 0.032 | 0.51 | NO |
31 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 8562 | 0.026 | 0.49 | NO |
32 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 8564 | 0.026 | 0.5 | NO |
33 | TERF2IP | TERF2IP | TERF2IP | 9479 | 0.012 | 0.45 | NO |
34 | TINF2 | TINF2 | TINF2 | 10053 | 0.0034 | 0.42 | NO |
35 | H2AFZ | H2AFZ | H2AFZ | 11927 | -0.025 | 0.32 | NO |
36 | TERF2 | TERF2 | TERF2 | 13025 | -0.041 | 0.27 | NO |
37 | TERF1 | TERF1 | TERF1 | 13142 | -0.043 | 0.27 | NO |
38 | POT1 | POT1 | POT1 | 13367 | -0.047 | 0.26 | NO |
39 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 13493 | -0.049 | 0.26 | NO |
Figure S91. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: SIG CD40PATHWAYMAP.

Figure S92. Get High-res Image For the top 5 core enriched genes in the pathway: SIG CD40PATHWAYMAP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S47. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FGF17 | FGF17 | FGF17 | 38 | 0.73 | 0.23 | YES |
2 | FGF23 | FGF23 | FGF23 | 554 | 0.46 | 0.35 | YES |
3 | FGF8 | FGF8 | FGF8 | 740 | 0.41 | 0.47 | YES |
4 | FGFR1OP | FGFR1OP | FGFR1OP | 2780 | 0.19 | 0.42 | NO |
5 | FGF20 | FGF20 | FGF20 | 3154 | 0.17 | 0.45 | NO |
6 | ZMYM2 | ZMYM2 | ZMYM2 | 5145 | 0.096 | 0.37 | NO |
7 | PLCG1 | PLCG1 | PLCG1 | 5503 | 0.087 | 0.38 | NO |
8 | CPSF6 | CPSF6 | CPSF6 | 7053 | 0.052 | 0.31 | NO |
9 | FGFR1 | FGFR1 | FGFR1 | 8074 | 0.034 | 0.27 | NO |
10 | FGF2 | FGF2 | FGF2 | 8761 | 0.023 | 0.24 | NO |
11 | STAT5B | STAT5B | STAT5B | 9249 | 0.016 | 0.22 | NO |
12 | FGFR1OP2 | FGFR1OP2 | FGFR1OP2 | 9441 | 0.013 | 0.21 | NO |
13 | FGF1 | FGF1 | FGF1 | 10634 | -0.0063 | 0.14 | NO |
14 | STAT5A | STAT5A | STAT5A | 11195 | -0.014 | 0.12 | NO |
15 | MYO18A | MYO18A | MYO18A | 11940 | -0.025 | 0.086 | NO |
16 | TRIM24 | TRIM24 | TRIM24 | 12376 | -0.031 | 0.072 | NO |
17 | BCR | BCR | BCR | 12390 | -0.032 | 0.082 | NO |
18 | STAT3 | STAT3 | STAT3 | 13106 | -0.042 | 0.056 | NO |
19 | GAB2 | GAB2 | GAB2 | 13680 | -0.052 | 0.041 | NO |
20 | GRB2 | GRB2 | GRB2 | 13869 | -0.055 | 0.048 | NO |
21 | CUX1 | CUX1 | CUX1 | 14653 | -0.07 | 0.027 | NO |
22 | FGF5 | FGF5 | FGF5 | 14773 | -0.072 | 0.043 | NO |
23 | PIK3R1 | PIK3R1 | PIK3R1 | 14782 | -0.072 | 0.066 | NO |
24 | STAT1 | STAT1 | STAT1 | 15826 | -0.1 | 0.04 | NO |
25 | FGF9 | FGF9 | FGF9 | 16839 | -0.14 | 0.031 | NO |
26 | PIK3CA | PIK3CA | PIK3CA | 16867 | -0.15 | 0.076 | NO |
Figure S93. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID RHOA REG PATHWAY.

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

Table S48. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | DNA2 | DNA2 | DNA2 | 480 | 0.49 | 0.03 | YES |
2 | HIST4H4 | HIST4H4 | HIST4H4 | 865 | 0.39 | 0.053 | YES |
3 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 1094 | 0.34 | 0.081 | YES |
4 | HIST1H4E | HIST1H4E | HIST1H4E | 1192 | 0.33 | 0.11 | YES |
5 | HIST1H4B | HIST1H4B | HIST1H4B | 1217 | 0.33 | 0.15 | YES |
6 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1263 | 0.32 | 0.18 | YES |
7 | HIST1H4I | HIST1H4I | HIST1H4I | 1344 | 0.31 | 0.22 | YES |
8 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 1422 | 0.3 | 0.25 | YES |
9 | HIST1H4C | HIST1H4C | HIST1H4C | 1519 | 0.29 | 0.28 | YES |
10 | TERT | TERT | TERT | 1682 | 0.27 | 0.3 | YES |
11 | HIST1H4J | HIST1H4J | HIST1H4J | 1764 | 0.26 | 0.32 | YES |
12 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1978 | 0.25 | 0.34 | YES |
13 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2033 | 0.24 | 0.36 | YES |
14 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 2074 | 0.24 | 0.39 | YES |
15 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2180 | 0.23 | 0.41 | YES |
16 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 2340 | 0.22 | 0.43 | YES |
17 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 2495 | 0.21 | 0.44 | YES |
18 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 2547 | 0.2 | 0.46 | YES |
19 | HIST3H3 | HIST3H3 | HIST3H3 | 2871 | 0.18 | 0.47 | YES |
20 | HIST1H4A | HIST1H4A | HIST1H4A | 2942 | 0.18 | 0.48 | YES |
21 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 3067 | 0.17 | 0.5 | YES |
22 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 3073 | 0.17 | 0.52 | YES |
23 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 3226 | 0.16 | 0.53 | YES |
24 | HIST1H4D | HIST1H4D | HIST1H4D | 3329 | 0.16 | 0.54 | YES |
25 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 3596 | 0.15 | 0.54 | YES |
26 | ACD | ACD | ACD | 3696 | 0.14 | 0.55 | YES |
27 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 3710 | 0.14 | 0.57 | YES |
28 | POLE | POLE | POLE | 3816 | 0.14 | 0.58 | YES |
29 | LIG1 | LIG1 | LIG1 | 4286 | 0.12 | 0.57 | NO |
30 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 5337 | 0.091 | 0.52 | NO |
31 | POLD1 | POLD1 | POLD1 | 5343 | 0.09 | 0.53 | NO |
32 | WRAP53 | WRAP53 | WRAP53 | 5971 | 0.075 | 0.5 | NO |
33 | HIST1H4H | HIST1H4H | HIST1H4H | 6250 | 0.068 | 0.5 | NO |
34 | RFC4 | RFC4 | RFC4 | 6679 | 0.06 | 0.48 | NO |
35 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 6736 | 0.058 | 0.48 | NO |
36 | RFC2 | RFC2 | RFC2 | 7601 | 0.043 | 0.44 | NO |
37 | POLE2 | POLE2 | POLE2 | 7827 | 0.039 | 0.43 | NO |
38 | H2AFX | H2AFX | H2AFX | 7902 | 0.037 | 0.43 | NO |
39 | RUVBL2 | RUVBL2 | RUVBL2 | 8007 | 0.036 | 0.43 | NO |
40 | POLD4 | POLD4 | POLD4 | 8097 | 0.034 | 0.43 | NO |
41 | HIST2H4A | HIST2H4A | HIST2H4A | 8210 | 0.032 | 0.43 | NO |
42 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 8562 | 0.026 | 0.41 | NO |
43 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 8564 | 0.026 | 0.42 | NO |
44 | NHP2 | NHP2 | NHP2 | 9263 | 0.016 | 0.38 | NO |
45 | TERF2IP | TERF2IP | TERF2IP | 9479 | 0.012 | 0.37 | NO |
46 | RPA2 | RPA2 | RPA2 | 9663 | 0.0094 | 0.36 | NO |
47 | TINF2 | TINF2 | TINF2 | 10053 | 0.0034 | 0.34 | NO |
48 | POLD3 | POLD3 | POLD3 | 10741 | -0.0078 | 0.3 | NO |
49 | POLD2 | POLD2 | POLD2 | 11177 | -0.014 | 0.28 | NO |
50 | DKC1 | DKC1 | DKC1 | 11909 | -0.024 | 0.24 | NO |
51 | POLA2 | POLA2 | POLA2 | 11925 | -0.024 | 0.24 | NO |
52 | H2AFZ | H2AFZ | H2AFZ | 11927 | -0.025 | 0.25 | NO |
53 | RFC3 | RFC3 | RFC3 | 12243 | -0.03 | 0.23 | NO |
54 | TERF2 | TERF2 | TERF2 | 13025 | -0.041 | 0.2 | NO |
55 | RFC5 | RFC5 | RFC5 | 13088 | -0.042 | 0.2 | NO |
56 | TERF1 | TERF1 | TERF1 | 13142 | -0.043 | 0.2 | NO |
57 | RUVBL1 | RUVBL1 | RUVBL1 | 13243 | -0.044 | 0.2 | NO |
58 | POT1 | POT1 | POT1 | 13367 | -0.047 | 0.2 | NO |
59 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 13493 | -0.049 | 0.2 | NO |
60 | PCNA | PCNA | PCNA | 14197 | -0.061 | 0.16 | NO |
61 | PRIM2 | PRIM2 | PRIM2 | 14631 | -0.069 | 0.15 | NO |
62 | RPA1 | RPA1 | RPA1 | 14710 | -0.071 | 0.15 | NO |
63 | RPA3 | RPA3 | RPA3 | 14745 | -0.071 | 0.16 | NO |
64 | FEN1 | FEN1 | FEN1 | 14858 | -0.074 | 0.16 | NO |
65 | POLA1 | POLA1 | POLA1 | 15977 | -0.1 | 0.11 | NO |
66 | PRIM1 | PRIM1 | PRIM1 | 16434 | -0.12 | 0.1 | NO |
Figure S95. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID HDAC CLASSI PATHWAY.

Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: PID HDAC CLASSI PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S49. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | AGER | AGER | AGER | 88 | 0.66 | 0.12 | YES |
2 | IFNA5 | IFNA5 | IFNA5 | 785 | 0.4 | 0.17 | YES |
3 | IFNA21 | IFNA21 | IFNA21 | 844 | 0.39 | 0.24 | YES |
4 | IRF7 | IRF7 | IRF7 | 1746 | 0.26 | 0.24 | YES |
5 | S100A12 | S100A12 | S100A12 | 2145 | 0.23 | 0.26 | YES |
6 | IRF3 | IRF3 | IRF3 | 2581 | 0.2 | 0.28 | YES |
7 | ISG15 | ISG15 | ISG15 | 2933 | 0.18 | 0.3 | YES |
8 | NFKB2 | NFKB2 | NFKB2 | 3307 | 0.16 | 0.31 | YES |
9 | IKBKB | IKBKB | IKBKB | 3982 | 0.13 | 0.3 | YES |
10 | NLRC5 | NLRC5 | NLRC5 | 4101 | 0.13 | 0.31 | YES |
11 | DHX58 | DHX58 | DHX58 | 4506 | 0.12 | 0.32 | YES |
12 | TRAF2 | TRAF2 | TRAF2 | 4521 | 0.12 | 0.34 | YES |
13 | NFKBIA | NFKBIA | NFKBIA | 4747 | 0.11 | 0.34 | YES |
14 | UBA7 | UBA7 | UBA7 | 4875 | 0.1 | 0.36 | YES |
15 | NFKBIB | NFKBIB | NFKBIB | 5891 | 0.077 | 0.32 | NO |
16 | CASP10 | CASP10 | CASP10 | 6379 | 0.065 | 0.3 | NO |
17 | IKBKG | IKBKG | IKBKG | 6392 | 0.065 | 0.32 | NO |
18 | HMGB1 | HMGB1 | HMGB1 | 6807 | 0.057 | 0.3 | NO |
19 | PIN1 | PIN1 | PIN1 | 7531 | 0.044 | 0.27 | NO |
20 | TANK | TANK | TANK | 7670 | 0.041 | 0.27 | NO |
21 | IRF1 | IRF1 | IRF1 | 7901 | 0.037 | 0.27 | NO |
22 | RNF135 | RNF135 | RNF135 | 8059 | 0.035 | 0.27 | NO |
23 | RELA | RELA | RELA | 8092 | 0.034 | 0.27 | NO |
24 | DAK | DAK | DAK | 8248 | 0.032 | 0.27 | NO |
25 | RPS27A | RPS27A | RPS27A | 8269 | 0.031 | 0.27 | NO |
26 | RNF125 | RNF125 | RNF125 | 8297 | 0.031 | 0.28 | NO |
27 | MAVS | MAVS | MAVS | 8543 | 0.027 | 0.27 | NO |
28 | OTUD5 | OTUD5 | OTUD5 | 8557 | 0.027 | 0.27 | NO |
29 | UBE2D2 | UBE2D2 | UBE2D2 | 8739 | 0.024 | 0.27 | NO |
30 | ATG12 | ATG12 | ATG12 | 8900 | 0.021 | 0.26 | NO |
31 | UBA52 | UBA52 | UBA52 | 9080 | 0.019 | 0.26 | NO |
32 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 9403 | 0.014 | 0.24 | NO |
33 | SIKE1 | SIKE1 | SIKE1 | 9406 | 0.014 | 0.24 | NO |
34 | RIPK1 | RIPK1 | RIPK1 | 9465 | 0.012 | 0.24 | NO |
35 | TRIM25 | TRIM25 | TRIM25 | 9704 | 0.0087 | 0.23 | NO |
36 | IFNB1 | IFNB1 | IFNB1 | 9732 | 0.0083 | 0.23 | NO |
37 | CREBBP | CREBBP | CREBBP | 10483 | -0.0036 | 0.19 | NO |
38 | HERC5 | HERC5 | HERC5 | 10617 | -0.006 | 0.19 | NO |
39 | MAP3K1 | MAP3K1 | MAP3K1 | 10821 | -0.0089 | 0.18 | NO |
40 | PCBP2 | PCBP2 | PCBP2 | 10864 | -0.0095 | 0.18 | NO |
41 | IRF2 | IRF2 | IRF2 | 11013 | -0.012 | 0.17 | NO |
42 | CASP8 | CASP8 | CASP8 | 11031 | -0.012 | 0.17 | NO |
43 | TBK1 | TBK1 | TBK1 | 12006 | -0.026 | 0.12 | NO |
44 | DDX58 | DDX58 | DDX58 | 12156 | -0.028 | 0.12 | NO |
45 | UBE2D3 | UBE2D3 | UBE2D3 | 12619 | -0.035 | 0.1 | NO |
46 | CYLD | CYLD | CYLD | 12807 | -0.038 | 0.1 | NO |
47 | UBE2K | UBE2K | UBE2K | 12839 | -0.038 | 0.11 | NO |
48 | APP | APP | APP | 12930 | -0.039 | 0.11 | NO |
49 | ATG5 | ATG5 | ATG5 | 13068 | -0.041 | 0.11 | NO |
50 | UBE2D1 | UBE2D1 | UBE2D1 | 13379 | -0.047 | 0.1 | NO |
51 | EP300 | EP300 | EP300 | 13387 | -0.047 | 0.11 | NO |
52 | FADD | FADD | FADD | 13401 | -0.047 | 0.12 | NO |
53 | NLRX1 | NLRX1 | NLRX1 | 13446 | -0.048 | 0.12 | NO |
54 | TRAF3 | TRAF3 | TRAF3 | 13506 | -0.049 | 0.13 | NO |
55 | S100B | S100B | S100B | 13561 | -0.05 | 0.14 | NO |
56 | UBE2L6 | UBE2L6 | UBE2L6 | 13649 | -0.051 | 0.14 | NO |
57 | TRAF6 | TRAF6 | TRAF6 | 13840 | -0.055 | 0.14 | NO |
58 | IFIH1 | IFIH1 | IFIH1 | 14395 | -0.064 | 0.13 | NO |
59 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 14670 | -0.07 | 0.12 | NO |
60 | CHUK | CHUK | CHUK | 15341 | -0.086 | 0.1 | NO |
61 | IKBKE | IKBKE | IKBKE | 15782 | -0.098 | 0.099 | NO |
62 | SAA1 | SAA1 | SAA1 | 17371 | -0.19 | 0.049 | NO |
Figure S97. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME MEIOSIS.
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Figure S98. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MEIOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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Table S50. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MSH4 | MSH4 | MSH4 | 269 | 0.56 | 0.04 | YES |
2 | MSH5 | MSH5 | MSH5 | 494 | 0.48 | 0.076 | YES |
3 | HIST4H4 | HIST4H4 | HIST4H4 | 865 | 0.39 | 0.093 | YES |
4 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 1094 | 0.34 | 0.12 | YES |
5 | HIST1H4E | HIST1H4E | HIST1H4E | 1192 | 0.33 | 0.14 | YES |
6 | HIST1H4B | HIST1H4B | HIST1H4B | 1217 | 0.33 | 0.17 | YES |
7 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 1263 | 0.32 | 0.2 | YES |
8 | HIST1H4I | HIST1H4I | HIST1H4I | 1344 | 0.31 | 0.23 | YES |
9 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 1422 | 0.3 | 0.25 | YES |
10 | TEX15 | TEX15 | TEX15 | 1469 | 0.29 | 0.28 | YES |
11 | HIST1H4C | HIST1H4C | HIST1H4C | 1519 | 0.29 | 0.31 | YES |
12 | HIST1H4J | HIST1H4J | HIST1H4J | 1764 | 0.26 | 0.32 | YES |
13 | DMC1 | DMC1 | DMC1 | 1887 | 0.25 | 0.34 | YES |
14 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 1978 | 0.25 | 0.36 | YES |
15 | HIST1H3J | HIST1H3J | HIST1H3J | 2023 | 0.24 | 0.38 | YES |
16 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 2033 | 0.24 | 0.4 | YES |
17 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 2074 | 0.24 | 0.42 | YES |
18 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 2180 | 0.23 | 0.44 | YES |
19 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 2340 | 0.22 | 0.45 | YES |
20 | HIST1H3H | HIST1H3H | HIST1H3H | 2392 | 0.21 | 0.47 | YES |
21 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 2495 | 0.21 | 0.48 | YES |
22 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 2547 | 0.2 | 0.5 | YES |
23 | HIST2H3C | HIST2H3C | HIST2H3C | 2721 | 0.19 | 0.51 | YES |
24 | HIST3H3 | HIST3H3 | HIST3H3 | 2871 | 0.18 | 0.52 | YES |
25 | HIST1H4A | HIST1H4A | HIST1H4A | 2942 | 0.18 | 0.54 | YES |
26 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 3067 | 0.17 | 0.55 | YES |
27 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 3073 | 0.17 | 0.56 | YES |
28 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 3226 | 0.16 | 0.57 | YES |
29 | HIST1H4D | HIST1H4D | HIST1H4D | 3329 | 0.16 | 0.58 | YES |
30 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 3596 | 0.15 | 0.58 | YES |
31 | MLH3 | MLH3 | MLH3 | 3672 | 0.15 | 0.59 | YES |
32 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 3710 | 0.14 | 0.6 | YES |
33 | HIST1H3D | HIST1H3D | HIST1H3D | 3726 | 0.14 | 0.62 | YES |
34 | ATM | ATM | ATM | 4284 | 0.12 | 0.6 | NO |
35 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 5337 | 0.091 | 0.55 | NO |
36 | HIST1H3C | HIST1H3C | HIST1H3C | 5597 | 0.084 | 0.54 | NO |
37 | H3F3A | H3F3A | H3F3A | 5939 | 0.075 | 0.53 | NO |
38 | HIST1H4H | HIST1H4H | HIST1H4H | 6250 | 0.068 | 0.52 | NO |
39 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 6736 | 0.058 | 0.5 | NO |
40 | HIST1H3B | HIST1H3B | HIST1H3B | 7409 | 0.046 | 0.47 | NO |
41 | HIST1H3F | HIST1H3F | HIST1H3F | 7548 | 0.044 | 0.46 | NO |
42 | H2AFX | H2AFX | H2AFX | 7902 | 0.037 | 0.45 | NO |
43 | HIST1H3A | HIST1H3A | HIST1H3A | 8066 | 0.035 | 0.44 | NO |
44 | HIST2H4A | HIST2H4A | HIST2H4A | 8210 | 0.032 | 0.44 | NO |
45 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 8562 | 0.026 | 0.42 | NO |
46 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 8564 | 0.026 | 0.42 | NO |
47 | CDK2 | CDK2 | CDK2 | 8947 | 0.021 | 0.41 | NO |
48 | HIST1H3E | HIST1H3E | HIST1H3E | 8978 | 0.02 | 0.41 | NO |
49 | H3F3B | H3F3B | H3F3B | 9179 | 0.017 | 0.4 | NO |
50 | HIST2H3D | HIST2H3D | HIST2H3D | 9436 | 0.013 | 0.38 | NO |
51 | TOP3A | TOP3A | TOP3A | 9609 | 0.01 | 0.38 | NO |
52 | RPA2 | RPA2 | RPA2 | 9663 | 0.0094 | 0.37 | NO |
53 | MRE11A | MRE11A | MRE11A | 9676 | 0.0091 | 0.37 | NO |
54 | MND1 | MND1 | MND1 | 11787 | -0.022 | 0.26 | NO |
55 | H2AFZ | H2AFZ | H2AFZ | 11927 | -0.025 | 0.26 | NO |
56 | RBBP8 | RBBP8 | RBBP8 | 13051 | -0.041 | 0.2 | NO |
57 | MLH1 | MLH1 | MLH1 | 13205 | -0.044 | 0.19 | NO |
58 | BLM | BLM | BLM | 13215 | -0.044 | 0.2 | NO |
59 | CDK4 | CDK4 | CDK4 | 13303 | -0.046 | 0.2 | NO |
60 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 13493 | -0.049 | 0.19 | NO |
61 | RAD51C | RAD51C | RAD51C | 13572 | -0.05 | 0.19 | NO |
62 | HIST1H3G | HIST1H3G | HIST1H3G | 14198 | -0.061 | 0.16 | NO |
63 | BRCA1 | BRCA1 | BRCA1 | 14261 | -0.062 | 0.17 | NO |
64 | RAD50 | RAD50 | RAD50 | 14505 | -0.067 | 0.16 | NO |
65 | RPA1 | RPA1 | RPA1 | 14710 | -0.071 | 0.16 | NO |
66 | RPA3 | RPA3 | RPA3 | 14745 | -0.071 | 0.16 | NO |
67 | NBN | NBN | NBN | 15276 | -0.084 | 0.14 | NO |
68 | RAD51 | RAD51 | RAD51 | 16397 | -0.12 | 0.09 | NO |
69 | BRCA2 | BRCA2 | BRCA2 | 16407 | -0.12 | 0.1 | NO |
Figure S99. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME SIGNALING BY FGFR1 MUTANTS.
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Figure S100. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SIGNALING BY FGFR1 MUTANTS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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