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 "ACC-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: 703 |
Number of samples: 79 |
Original number of Gene Sets: 1320 |
Maximum gene set size: 933 |
Table 2. Get Full Table pheno data info
phenotype info |
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pheno.type: 1 - 4 :[ clus1 ] 24 |
pheno.type: 2 - 4 :[ clus2 ] 15 |
pheno.type: 3 - 4 :[ clus3 ] 17 |
pheno.type: 4 - 4 :[ clus4 ] 23 |
For the expression subtypes of 17733 genes in 80 samples, GSEA found enriched gene sets in each cluster using 79 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 RIBOSOME, KEGG SPLICEOSOME, KEGG PROTEASOME, KEGG BASE EXCISION REPAIR, KEGG CELL CYCLE, PID MYC ACTIVPATHWAY, PID ILK PATHWAY, PID ATM PATHWAY, PID MYC PATHWAY, PID FOXM1PATHWAY
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And common core enriched genes are PSMA1, PSMA4, PSMA5, PSMA8, PSMB3, PSMB4, PSMB5, PSMB9, PSMC1, PSMC3
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clus2
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Top enriched gene sets are KEGG WNT SIGNALING PATHWAY, KEGG HEDGEHOG SIGNALING PATHWAY, KEGG TASTE TRANSDUCTION, KEGG BASAL CELL CARCINOMA, BIOCARTA NO1 PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA WNT PATHWAY, ST WNT BETA CATENIN PATHWAY, PID REELINPATHWAY, PID NECTIN PATHWAY
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And common core enriched genes are MYC, CTNNB1, FRAT1, WIF1, CREBBP, CSNK1A1, GLI1, GLI2, GLI3, GNAO1
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clus3
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Top enriched gene sets are KEGG PENTOSE PHOSPHATE PATHWAY, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG BUTANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG BASAL TRANSCRIPTION FACTORS, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG UBIQUITIN MEDIATED PROTEOLYSIS, BIOCARTA GH PATHWAY, BIOCARTA CREB PATHWAY, ST ERK1 ERK2 MAPK PATHWAY
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And common core enriched genes are CCNH, CDK7, CUL4A, CUL4B, ERCC2, ERCC8, GTF2H2, GTF2H3, MNAT1, BRAF
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clus4
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Top enriched gene sets are KEGG STARCH AND SUCROSE METABOLISM, BIOCARTA HDAC PATHWAY, BIOCARTA IL2RB PATHWAY, SIG BCR SIGNALING PATHWAY, PID FCER1PATHWAY, PID BCR 5PATHWAY, PID GMCSF PATHWAY, PID TCR PATHWAY, PID CD8TCRPATHWAY, PID TCPTP PATHWAY
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And common core enriched genes are PIK3R1, SYK, FAS, FASLG, PIK3CG, MAP2K6, MEF2C, BCL2, IKZF3, IL2RA
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 RIBOSOME | 85 | genes.ES.table | 0.57 | 1.6 | 0.077 | 0.17 | 0.9 | 0.8 | 0.33 | 0.54 | 0.098 | 0.014 |
KEGG SPLICEOSOME | 114 | genes.ES.table | 0.35 | 1.5 | 0.12 | 0.22 | 0.96 | 0.54 | 0.34 | 0.36 | 0.14 | 0.016 |
KEGG PROTEASOME | 44 | genes.ES.table | 0.56 | 1.9 | 0.0083 | 0.18 | 0.26 | 0.77 | 0.36 | 0.5 | 0 | 0.041 |
KEGG BASE EXCISION REPAIR | 33 | genes.ES.table | 0.47 | 1.7 | 0.047 | 0.13 | 0.84 | 0.55 | 0.3 | 0.38 | 0.072 | 0.01 |
KEGG CELL CYCLE | 118 | genes.ES.table | 0.53 | 1.6 | 0.078 | 0.17 | 0.92 | 0.42 | 0.19 | 0.34 | 0.1 | 0.011 |
PID MYC ACTIVPATHWAY | 78 | genes.ES.table | 0.45 | 1.7 | 0.027 | 0.1 | 0.73 | 0.45 | 0.22 | 0.35 | 0.047 | 0.008 |
PID ILK PATHWAY | 45 | genes.ES.table | 0.37 | 1.5 | 0.096 | 0.23 | 0.97 | 0.24 | 0.18 | 0.2 | 0.15 | 0.015 |
PID ATM PATHWAY | 34 | genes.ES.table | 0.51 | 1.6 | 0.081 | 0.17 | 0.92 | 0.41 | 0.2 | 0.33 | 0.1 | 0.01 |
PID MYC PATHWAY | 25 | genes.ES.table | 0.42 | 1.6 | 0.059 | 0.18 | 0.92 | 0.52 | 0.31 | 0.36 | 0.11 | 0.015 |
PID FOXM1PATHWAY | 38 | genes.ES.table | 0.73 | 1.6 | 0.008 | 0.14 | 0.87 | 0.47 | 0.088 | 0.43 | 0.077 | 0.012 |
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 | CCNE2 | CCNE2 | CCNE2 | 779 | 0.3 | 0.027 | YES |
2 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | 0.045 | YES |
3 | RPS27A | RPS27A | RPS27A | 1532 | 0.21 | 0.085 | YES |
4 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.12 | YES |
5 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.15 | YES |
6 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.16 | YES |
7 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.19 | YES |
8 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.21 | YES |
9 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.24 | YES |
10 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.27 | YES |
11 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.29 | YES |
12 | RFWD2 | RFWD2 | RFWD2 | 3192 | 0.12 | 0.3 | YES |
13 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.32 | YES |
14 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.35 | YES |
15 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.36 | YES |
16 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.39 | YES |
17 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.41 | YES |
18 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.42 | YES |
19 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.43 | YES |
20 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.44 | YES |
21 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.46 | YES |
22 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.47 | YES |
23 | UBA52 | UBA52 | UBA52 | 4612 | 0.072 | 0.47 | YES |
24 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.47 | YES |
25 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.47 | YES |
26 | CDK2 | CDK2 | CDK2 | 5385 | 0.053 | 0.47 | YES |
27 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.48 | YES |
28 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.49 | YES |
29 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.48 | YES |
30 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.49 | YES |
31 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.48 | YES |
32 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.48 | YES |
33 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.49 | YES |
34 | CCNE1 | CCNE1 | CCNE1 | 6213 | 0.032 | 0.5 | YES |
35 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.5 | YES |
36 | CDKN1A | CDKN1A | CDKN1A | 6292 | 0.03 | 0.51 | YES |
37 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.51 | YES |
38 | MDM2 | MDM2 | MDM2 | 6349 | 0.029 | 0.52 | YES |
39 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.49 | NO |
40 | TP53 | TP53 | TP53 | 7338 | 0.0068 | 0.47 | NO |
41 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.46 | NO |
42 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.46 | NO |
43 | PSMD9 | PSMD9 | PSMD9 | 7828 | -0.0041 | 0.44 | NO |
44 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.41 | NO |
45 | ATM | ATM | ATM | 8503 | -0.019 | 0.41 | NO |
46 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.41 | NO |
47 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.41 | NO |
48 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.4 | NO |
49 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.39 | NO |
50 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.38 | NO |
51 | PSMD5 | PSMD5 | PSMD5 | 10267 | -0.062 | 0.36 | NO |
52 | CDKN1B | CDKN1B | CDKN1B | 10878 | -0.077 | 0.35 | NO |
53 | PSMD10 | PSMD10 | PSMD10 | 13784 | -0.17 | 0.22 | 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 RIBOSOME.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIBOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table 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 | CDC20 | CDC20 | CDC20 | 83 | 0.57 | 0.073 | YES |
2 | AURKB | AURKB | AURKB | 84 | 0.57 | 0.15 | YES |
3 | UBE2C | UBE2C | UBE2C | 247 | 0.45 | 0.2 | YES |
4 | PLK1 | PLK1 | PLK1 | 285 | 0.43 | 0.26 | YES |
5 | PTTG1 | PTTG1 | PTTG1 | 470 | 0.37 | 0.3 | YES |
6 | AURKA | AURKA | AURKA | 598 | 0.34 | 0.34 | YES |
7 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | 0.32 | YES |
8 | SKP2 | SKP2 | SKP2 | 1495 | 0.21 | 0.35 | YES |
9 | RPS27A | RPS27A | RPS27A | 1532 | 0.21 | 0.37 | YES |
10 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.39 | YES |
11 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.4 | YES |
12 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.4 | YES |
13 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.41 | YES |
14 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.42 | YES |
15 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.44 | YES |
16 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.45 | YES |
17 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.46 | YES |
18 | ANAPC1 | ANAPC1 | ANAPC1 | 3099 | 0.12 | 0.47 | YES |
19 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.47 | YES |
20 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.49 | YES |
21 | ANAPC11 | ANAPC11 | ANAPC11 | 3430 | 0.11 | 0.49 | YES |
22 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.51 | YES |
23 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.52 | YES |
24 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.53 | YES |
25 | CDC26 | CDC26 | CDC26 | 3732 | 0.099 | 0.53 | YES |
26 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.54 | YES |
27 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.55 | YES |
28 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.55 | YES |
29 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.56 | YES |
30 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.56 | YES |
31 | UBA52 | UBA52 | UBA52 | 4612 | 0.072 | 0.55 | NO |
32 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.55 | NO |
33 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.55 | NO |
34 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.53 | NO |
35 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.54 | NO |
36 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.53 | NO |
37 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.53 | NO |
38 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.52 | NO |
39 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.52 | NO |
40 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.52 | NO |
41 | UBE2E1 | UBE2E1 | UBE2E1 | 6224 | 0.032 | 0.52 | NO |
42 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.53 | NO |
43 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.53 | NO |
44 | CDC16 | CDC16 | CDC16 | 6455 | 0.026 | 0.52 | NO |
45 | ANAPC7 | ANAPC7 | ANAPC7 | 6541 | 0.024 | 0.52 | NO |
46 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.5 | NO |
47 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.47 | NO |
48 | CDC27 | CDC27 | CDC27 | 7522 | 0.0029 | 0.47 | NO |
49 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.47 | NO |
50 | PSMD9 | PSMD9 | PSMD9 | 7828 | -0.0041 | 0.45 | NO |
51 | ANAPC2 | ANAPC2 | ANAPC2 | 8293 | -0.014 | 0.43 | NO |
52 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.42 | NO |
53 | ANAPC5 | ANAPC5 | ANAPC5 | 8543 | -0.02 | 0.42 | NO |
54 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.42 | NO |
55 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.42 | NO |
56 | ANAPC10 | ANAPC10 | ANAPC10 | 8944 | -0.028 | 0.41 | NO |
57 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.41 | NO |
58 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.4 | NO |
59 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.38 | NO |
60 | PSMD5 | PSMD5 | PSMD5 | 10267 | -0.062 | 0.36 | NO |
61 | UBE2D1 | UBE2D1 | UBE2D1 | 11121 | -0.083 | 0.32 | NO |
62 | CDC23 | CDC23 | CDC23 | 11409 | -0.091 | 0.32 | NO |
63 | ANAPC4 | ANAPC4 | ANAPC4 | 12869 | -0.14 | 0.25 | NO |
64 | PSMD10 | PSMD10 | PSMD10 | 13784 | -0.17 | 0.22 | 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 SPLICEOSOME.

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

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | -0.011 | YES |
2 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.033 | YES |
3 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.066 | YES |
4 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.093 | YES |
5 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.13 | YES |
6 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.16 | YES |
7 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.2 | YES |
8 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.23 | YES |
9 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.26 | YES |
10 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.28 | YES |
11 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.31 | YES |
12 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.33 | YES |
13 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.36 | YES |
14 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.39 | YES |
15 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.4 | YES |
16 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.42 | YES |
17 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.44 | YES |
18 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.46 | YES |
19 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.48 | YES |
20 | PSMB11 | PSMB11 | PSMB11 | 4623 | 0.072 | 0.48 | YES |
21 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.49 | YES |
22 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.49 | YES |
23 | POMP | POMP | POMP | 5259 | 0.056 | 0.5 | YES |
24 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.51 | YES |
25 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.52 | YES |
26 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.52 | YES |
27 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.52 | YES |
28 | PSME3 | PSME3 | PSME3 | 6028 | 0.036 | 0.52 | YES |
29 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.53 | YES |
30 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.54 | YES |
31 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.55 | YES |
32 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.55 | YES |
33 | IFNG | IFNG | IFNG | 6322 | 0.029 | 0.56 | YES |
34 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.56 | YES |
35 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.54 | NO |
36 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.51 | NO |
37 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.5 | NO |
38 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.46 | NO |
39 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.45 | NO |
40 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.46 | NO |
41 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.45 | NO |
42 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.44 | NO |
43 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.43 | NO |
44 | SHFM1 | SHFM1 | SHFM1 | 10522 | -0.068 | 0.41 | 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 PROTEASOME.

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

Table 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 | E2F2 | E2F2 | E2F2 | 135 | 0.52 | 0.072 | YES |
2 | CDT1 | CDT1 | CDT1 | 150 | 0.51 | 0.15 | YES |
3 | CDC6 | CDC6 | CDC6 | 1019 | 0.27 | 0.14 | YES |
4 | MCM6 | MCM6 | MCM6 | 1046 | 0.26 | 0.18 | YES |
5 | MCM2 | MCM2 | MCM2 | 1182 | 0.25 | 0.21 | YES |
6 | MCM5 | MCM5 | MCM5 | 1270 | 0.24 | 0.24 | YES |
7 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | 0.27 | YES |
8 | RPS27A | RPS27A | RPS27A | 1532 | 0.21 | 0.29 | YES |
9 | MCM7 | MCM7 | MCM7 | 1634 | 0.2 | 0.32 | YES |
10 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.34 | YES |
11 | GMNN | GMNN | GMNN | 1794 | 0.19 | 0.36 | YES |
12 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.38 | YES |
13 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.38 | YES |
14 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.4 | YES |
15 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.41 | YES |
16 | MCM4 | MCM4 | MCM4 | 2694 | 0.14 | 0.43 | YES |
17 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.45 | YES |
18 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.47 | YES |
19 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.48 | YES |
20 | MCM3 | MCM3 | MCM3 | 3110 | 0.12 | 0.48 | YES |
21 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.49 | YES |
22 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.51 | YES |
23 | E2F1 | E2F1 | E2F1 | 3398 | 0.11 | 0.52 | YES |
24 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.53 | YES |
25 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.55 | YES |
26 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.56 | YES |
27 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.56 | YES |
28 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.57 | YES |
29 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.57 | YES |
30 | MCM8 | MCM8 | MCM8 | 4123 | 0.087 | 0.58 | YES |
31 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.59 | YES |
32 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.6 | YES |
33 | UBA52 | UBA52 | UBA52 | 4612 | 0.072 | 0.59 | NO |
34 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.59 | NO |
35 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.58 | NO |
36 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.57 | NO |
37 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.58 | NO |
38 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.57 | NO |
39 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.57 | NO |
40 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.56 | NO |
41 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.56 | NO |
42 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.57 | NO |
43 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.57 | NO |
44 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.57 | NO |
45 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.54 | NO |
46 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.51 | NO |
47 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.5 | NO |
48 | PSMD9 | PSMD9 | PSMD9 | 7828 | -0.0041 | 0.49 | NO |
49 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.45 | NO |
50 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.45 | NO |
51 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.45 | NO |
52 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.44 | NO |
53 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.42 | NO |
54 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.4 | NO |
55 | PSMD5 | PSMD5 | PSMD5 | 10267 | -0.062 | 0.38 | NO |
56 | E2F3 | E2F3 | E2F3 | 10696 | -0.072 | 0.37 | NO |
57 | PSMD10 | PSMD10 | PSMD10 | 13784 | -0.17 | 0.22 | 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 BASE EXCISION REPAIR.

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

Table 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 | CDT1 | CDT1 | CDT1 | 150 | 0.51 | 0.071 | YES |
2 | CCNA2 | CCNA2 | CCNA2 | 505 | 0.36 | 0.11 | YES |
3 | CDC6 | CDC6 | CDC6 | 1019 | 0.27 | 0.12 | YES |
4 | MCM6 | MCM6 | MCM6 | 1046 | 0.26 | 0.16 | YES |
5 | MCM2 | MCM2 | MCM2 | 1182 | 0.25 | 0.19 | YES |
6 | MCM5 | MCM5 | MCM5 | 1270 | 0.24 | 0.22 | YES |
7 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | 0.25 | YES |
8 | RPS27A | RPS27A | RPS27A | 1532 | 0.21 | 0.28 | YES |
9 | MCM7 | MCM7 | MCM7 | 1634 | 0.2 | 0.3 | YES |
10 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.33 | YES |
11 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.34 | YES |
12 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.35 | YES |
13 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.36 | YES |
14 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.37 | YES |
15 | MCM4 | MCM4 | MCM4 | 2694 | 0.14 | 0.39 | YES |
16 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.41 | YES |
17 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.43 | YES |
18 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.44 | YES |
19 | MCM3 | MCM3 | MCM3 | 3110 | 0.12 | 0.45 | YES |
20 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.46 | YES |
21 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.48 | YES |
22 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.48 | YES |
23 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.5 | YES |
24 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.51 | YES |
25 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.51 | YES |
26 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.52 | YES |
27 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.53 | YES |
28 | MCM8 | MCM8 | MCM8 | 4123 | 0.087 | 0.54 | YES |
29 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.55 | YES |
30 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.55 | YES |
31 | UBA52 | UBA52 | UBA52 | 4612 | 0.072 | 0.55 | NO |
32 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.54 | NO |
33 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.54 | NO |
34 | CDK2 | CDK2 | CDK2 | 5385 | 0.053 | 0.53 | NO |
35 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.54 | NO |
36 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.55 | NO |
37 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.53 | NO |
38 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.54 | NO |
39 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.53 | NO |
40 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.53 | NO |
41 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.53 | NO |
42 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.53 | NO |
43 | CDKN1A | CDKN1A | CDKN1A | 6292 | 0.03 | 0.54 | NO |
44 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.54 | NO |
45 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.51 | NO |
46 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.48 | NO |
47 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.47 | NO |
48 | PSMD9 | PSMD9 | PSMD9 | 7828 | -0.0041 | 0.46 | NO |
49 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.42 | NO |
50 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.42 | NO |
51 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.42 | NO |
52 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.41 | NO |
53 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.4 | NO |
54 | CCNA1 | CCNA1 | CCNA1 | 9427 | -0.041 | 0.4 | NO |
55 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.38 | NO |
56 | PSMD5 | PSMD5 | PSMD5 | 10267 | -0.062 | 0.36 | NO |
57 | CDKN1B | CDKN1B | CDKN1B | 10878 | -0.077 | 0.34 | NO |
58 | RB1 | RB1 | RB1 | 12214 | -0.11 | 0.28 | NO |
59 | PSMD10 | PSMD10 | PSMD10 | 13784 | -0.17 | 0.22 | NO |
Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CELL CYCLE.

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

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 | CDC20 | CDC20 | CDC20 | 83 | 0.57 | 0.077 | YES |
2 | UBE2C | UBE2C | UBE2C | 247 | 0.45 | 0.13 | YES |
3 | BUB1B | BUB1B | BUB1B | 351 | 0.4 | 0.18 | YES |
4 | CDK1 | CDK1 | CDK1 | 365 | 0.4 | 0.24 | YES |
5 | PTTG1 | PTTG1 | PTTG1 | 470 | 0.37 | 0.29 | YES |
6 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | 0.27 | YES |
7 | RPS27A | RPS27A | RPS27A | 1532 | 0.21 | 0.29 | YES |
8 | CCNB1 | CCNB1 | CCNB1 | 1566 | 0.21 | 0.32 | YES |
9 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.34 | YES |
10 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.35 | YES |
11 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.35 | YES |
12 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.36 | YES |
13 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.37 | YES |
14 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.39 | YES |
15 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.4 | YES |
16 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.41 | YES |
17 | ANAPC1 | ANAPC1 | ANAPC1 | 3099 | 0.12 | 0.42 | YES |
18 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.43 | YES |
19 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.44 | YES |
20 | BUB3 | BUB3 | BUB3 | 3379 | 0.11 | 0.45 | YES |
21 | ANAPC11 | ANAPC11 | ANAPC11 | 3430 | 0.11 | 0.47 | YES |
22 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.48 | YES |
23 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.5 | YES |
24 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.51 | YES |
25 | CDC26 | CDC26 | CDC26 | 3732 | 0.099 | 0.51 | YES |
26 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.52 | YES |
27 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.52 | YES |
28 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.53 | YES |
29 | MAD2L1 | MAD2L1 | MAD2L1 | 4086 | 0.088 | 0.54 | YES |
30 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.55 | YES |
31 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.55 | YES |
32 | UBA52 | UBA52 | UBA52 | 4612 | 0.072 | 0.55 | NO |
33 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.54 | NO |
34 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.54 | NO |
35 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.52 | NO |
36 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.53 | NO |
37 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.52 | NO |
38 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.52 | NO |
39 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.51 | NO |
40 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.51 | NO |
41 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.52 | NO |
42 | UBE2E1 | UBE2E1 | UBE2E1 | 6224 | 0.032 | 0.52 | NO |
43 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.52 | NO |
44 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.52 | NO |
45 | CDC16 | CDC16 | CDC16 | 6455 | 0.026 | 0.52 | NO |
46 | ANAPC7 | ANAPC7 | ANAPC7 | 6541 | 0.024 | 0.52 | NO |
47 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.5 | NO |
48 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.47 | NO |
49 | CDC27 | CDC27 | CDC27 | 7522 | 0.0029 | 0.46 | NO |
50 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.46 | NO |
51 | PSMD9 | PSMD9 | PSMD9 | 7828 | -0.0041 | 0.45 | NO |
52 | ANAPC2 | ANAPC2 | ANAPC2 | 8293 | -0.014 | 0.42 | NO |
53 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.42 | NO |
54 | ANAPC5 | ANAPC5 | ANAPC5 | 8543 | -0.02 | 0.42 | NO |
55 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.41 | NO |
56 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.41 | NO |
57 | ANAPC10 | ANAPC10 | ANAPC10 | 8944 | -0.028 | 0.4 | NO |
58 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.41 | NO |
59 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.39 | NO |
60 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.37 | NO |
61 | PSMD5 | PSMD5 | PSMD5 | 10267 | -0.062 | 0.35 | NO |
62 | UBE2D1 | UBE2D1 | UBE2D1 | 11121 | -0.083 | 0.32 | NO |
63 | CDC23 | CDC23 | CDC23 | 11409 | -0.091 | 0.31 | NO |
64 | ANAPC4 | ANAPC4 | ANAPC4 | 12869 | -0.14 | 0.25 | NO |
65 | PSMD10 | PSMD10 | PSMD10 | 13784 | -0.17 | 0.22 | NO |
Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MYC ACTIVPATHWAY.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: PID MYC ACTIVPATHWAY, 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 | CDC20 | CDC20 | CDC20 | 83 | 0.57 | 0.038 | YES |
2 | CDC25A | CDC25A | CDC25A | 109 | 0.54 | 0.077 | YES |
3 | CDC45 | CDC45 | CDC45 | 130 | 0.52 | 0.12 | YES |
4 | UBE2C | UBE2C | UBE2C | 247 | 0.45 | 0.14 | YES |
5 | CCNB2 | CCNB2 | CCNB2 | 298 | 0.42 | 0.17 | YES |
6 | MCM10 | MCM10 | MCM10 | 327 | 0.41 | 0.2 | YES |
7 | BUB1B | BUB1B | BUB1B | 351 | 0.4 | 0.23 | YES |
8 | CDK1 | CDK1 | CDK1 | 365 | 0.4 | 0.26 | YES |
9 | CDC7 | CDC7 | CDC7 | 469 | 0.37 | 0.28 | YES |
10 | CDC25C | CDC25C | CDC25C | 751 | 0.31 | 0.29 | YES |
11 | CCNE2 | CCNE2 | CCNE2 | 779 | 0.3 | 0.31 | YES |
12 | CHEK2 | CHEK2 | CHEK2 | 920 | 0.28 | 0.32 | YES |
13 | CHEK1 | CHEK1 | CHEK1 | 959 | 0.28 | 0.34 | YES |
14 | CDC6 | CDC6 | CDC6 | 1019 | 0.27 | 0.36 | YES |
15 | MCM6 | MCM6 | MCM6 | 1046 | 0.26 | 0.37 | YES |
16 | MCM2 | MCM2 | MCM2 | 1182 | 0.25 | 0.38 | YES |
17 | MCM5 | MCM5 | MCM5 | 1270 | 0.24 | 0.4 | YES |
18 | DBF4 | DBF4 | DBF4 | 1326 | 0.23 | 0.41 | YES |
19 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | 0.42 | YES |
20 | RPS27A | RPS27A | RPS27A | 1532 | 0.21 | 0.43 | YES |
21 | CCNB1 | CCNB1 | CCNB1 | 1566 | 0.21 | 0.44 | YES |
22 | MCM7 | MCM7 | MCM7 | 1634 | 0.2 | 0.46 | YES |
23 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.47 | YES |
24 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.46 | YES |
25 | RAD9A | RAD9A | RAD9A | 2242 | 0.16 | 0.46 | YES |
26 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.47 | YES |
27 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.47 | YES |
28 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.47 | YES |
29 | MCM4 | MCM4 | MCM4 | 2694 | 0.14 | 0.48 | YES |
30 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.49 | YES |
31 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.5 | YES |
32 | RFC4 | RFC4 | RFC4 | 2777 | 0.13 | 0.5 | YES |
33 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.51 | YES |
34 | ANAPC1 | ANAPC1 | ANAPC1 | 3099 | 0.12 | 0.5 | YES |
35 | MCM3 | MCM3 | MCM3 | 3110 | 0.12 | 0.51 | YES |
36 | MAD1L1 | MAD1L1 | MAD1L1 | 3189 | 0.12 | 0.52 | YES |
37 | RFWD2 | RFWD2 | RFWD2 | 3192 | 0.12 | 0.53 | YES |
38 | WEE1 | WEE1 | WEE1 | 3241 | 0.12 | 0.53 | YES |
39 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.54 | YES |
40 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.55 | YES |
41 | RFC2 | RFC2 | RFC2 | 3302 | 0.11 | 0.56 | YES |
42 | BUB3 | BUB3 | BUB3 | 3379 | 0.11 | 0.56 | YES |
43 | ANAPC11 | ANAPC11 | ANAPC11 | 3430 | 0.11 | 0.56 | YES |
44 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.57 | YES |
45 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.58 | YES |
46 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.58 | YES |
47 | CDC26 | CDC26 | CDC26 | 3732 | 0.099 | 0.58 | YES |
48 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.58 | YES |
49 | RAD1 | RAD1 | RAD1 | 3901 | 0.093 | 0.58 | YES |
50 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.59 | YES |
51 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.59 | YES |
52 | MAD2L1 | MAD2L1 | MAD2L1 | 4086 | 0.088 | 0.59 | YES |
53 | MCM8 | MCM8 | MCM8 | 4123 | 0.087 | 0.6 | YES |
54 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.6 | YES |
55 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.6 | YES |
56 | UBA52 | UBA52 | UBA52 | 4612 | 0.072 | 0.59 | NO |
57 | RFC3 | RFC3 | RFC3 | 4738 | 0.069 | 0.58 | NO |
58 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.58 | NO |
59 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.57 | NO |
60 | CDK2 | CDK2 | CDK2 | 5385 | 0.053 | 0.56 | NO |
61 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.56 | NO |
62 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.57 | NO |
63 | ATRIP | ATRIP | ATRIP | 5715 | 0.044 | 0.55 | NO |
64 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.55 | NO |
65 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.55 | NO |
66 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.54 | NO |
67 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.54 | NO |
68 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.54 | NO |
69 | CCNE1 | CCNE1 | CCNE1 | 6213 | 0.032 | 0.54 | NO |
70 | UBE2E1 | UBE2E1 | UBE2E1 | 6224 | 0.032 | 0.54 | NO |
71 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.55 | NO |
72 | CDKN1A | CDKN1A | CDKN1A | 6292 | 0.03 | 0.55 | NO |
73 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.55 | NO |
74 | MDM2 | MDM2 | MDM2 | 6349 | 0.029 | 0.55 | NO |
75 | CDC16 | CDC16 | CDC16 | 6455 | 0.026 | 0.54 | NO |
76 | ANAPC7 | ANAPC7 | ANAPC7 | 6541 | 0.024 | 0.54 | NO |
77 | RFC5 | RFC5 | RFC5 | 6738 | 0.02 | 0.53 | NO |
78 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.52 | NO |
79 | TP53 | TP53 | TP53 | 7338 | 0.0068 | 0.5 | NO |
80 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.49 | NO |
81 | CDC27 | CDC27 | CDC27 | 7522 | 0.0029 | 0.49 | NO |
82 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.49 | NO |
83 | PSMD9 | PSMD9 | PSMD9 | 7828 | -0.0041 | 0.47 | NO |
84 | RPA3 | RPA3 | RPA3 | 8119 | -0.011 | 0.46 | NO |
85 | ANAPC2 | ANAPC2 | ANAPC2 | 8293 | -0.014 | 0.45 | NO |
86 | RPA1 | RPA1 | RPA1 | 8295 | -0.014 | 0.45 | NO |
87 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.44 | NO |
88 | ATM | ATM | ATM | 8503 | -0.019 | 0.44 | NO |
89 | ANAPC5 | ANAPC5 | ANAPC5 | 8543 | -0.02 | 0.44 | NO |
90 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.44 | NO |
91 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.43 | NO |
92 | RPA2 | RPA2 | RPA2 | 8717 | -0.023 | 0.43 | NO |
93 | ANAPC10 | ANAPC10 | ANAPC10 | 8944 | -0.028 | 0.42 | NO |
94 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.42 | NO |
95 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.41 | NO |
96 | ATR | ATR | ATR | 9603 | -0.045 | 0.39 | NO |
97 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.39 | NO |
98 | PSMD5 | PSMD5 | PSMD5 | 10267 | -0.062 | 0.36 | NO |
99 | HUS1 | HUS1 | HUS1 | 10675 | -0.072 | 0.35 | NO |
100 | CDKN1B | CDKN1B | CDKN1B | 10878 | -0.077 | 0.34 | NO |
101 | UBE2D1 | UBE2D1 | UBE2D1 | 11121 | -0.083 | 0.33 | NO |
102 | CDC23 | CDC23 | CDC23 | 11409 | -0.091 | 0.32 | NO |
103 | ANAPC4 | ANAPC4 | ANAPC4 | 12869 | -0.14 | 0.25 | NO |
104 | RAD17 | RAD17 | RAD17 | 13568 | -0.16 | 0.22 | NO |
105 | PSMD10 | PSMD10 | PSMD10 | 13784 | -0.17 | 0.22 | 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 ILK PATHWAY.

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

Table S8. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CDC25A | CDC25A | CDC25A | 109 | 0.54 | 0.11 | YES |
2 | CHEK2 | CHEK2 | CHEK2 | 920 | 0.28 | 0.12 | YES |
3 | CHEK1 | CHEK1 | CHEK1 | 959 | 0.28 | 0.18 | YES |
4 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | 0.2 | YES |
5 | RPS27A | RPS27A | RPS27A | 1532 | 0.21 | 0.24 | YES |
6 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.27 | YES |
7 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.29 | YES |
8 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.3 | YES |
9 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.33 | YES |
10 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.35 | YES |
11 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.37 | YES |
12 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.4 | YES |
13 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.42 | YES |
14 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.42 | YES |
15 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.44 | YES |
16 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.46 | YES |
17 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.48 | YES |
18 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.5 | YES |
19 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.5 | YES |
20 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.51 | YES |
21 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.52 | YES |
22 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.53 | YES |
23 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.55 | YES |
24 | UBA52 | UBA52 | UBA52 | 4612 | 0.072 | 0.54 | YES |
25 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.54 | YES |
26 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.54 | YES |
27 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.54 | YES |
28 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.55 | YES |
29 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.54 | YES |
30 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.54 | YES |
31 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.54 | YES |
32 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.54 | YES |
33 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.54 | YES |
34 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.55 | YES |
35 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.55 | YES |
36 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.52 | NO |
37 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.49 | NO |
38 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.48 | NO |
39 | PSMD9 | PSMD9 | PSMD9 | 7828 | -0.0041 | 0.47 | NO |
40 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.44 | NO |
41 | ATM | ATM | ATM | 8503 | -0.019 | 0.44 | NO |
42 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.44 | NO |
43 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.44 | NO |
44 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.43 | NO |
45 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.42 | NO |
46 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.4 | NO |
47 | PSMD5 | PSMD5 | PSMD5 | 10267 | -0.062 | 0.39 | NO |
48 | PSMD10 | PSMD10 | PSMD10 | 13784 | -0.17 | 0.22 | 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: PID ATM PATHWAY.

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

Table S9. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | RPL21 | RPL21 | RPL21 | 446 | 0.38 | -0.0087 | YES |
2 | MAPK11 | MAPK11 | MAPK11 | 1025 | 0.27 | -0.03 | YES |
3 | EXOSC8 | EXOSC8 | EXOSC8 | 1030 | 0.27 | -0.018 | YES |
4 | WDR77 | WDR77 | WDR77 | 1232 | 0.24 | -0.019 | YES |
5 | PSME4 | PSME4 | PSME4 | 1376 | 0.22 | -0.018 | YES |
6 | RQCD1 | RQCD1 | RQCD1 | 1468 | 0.21 | -0.013 | YES |
7 | RPSAP9 | RPSAP9 | RPSAP9 | 1471 | 0.21 | -0.0037 | YES |
8 | RPS27A | RPS27A | RPS27A | 1532 | 0.21 | 0.0021 | YES |
9 | SNRPG | SNRPG | SNRPG | 1608 | 0.2 | 0.0068 | YES |
10 | EIF4A3 | EIF4A3 | EIF4A3 | 1627 | 0.2 | 0.015 | YES |
11 | PSMD4 | PSMD4 | PSMD4 | 1650 | 0.2 | 0.022 | YES |
12 | RPS7 | RPS7 | RPS7 | 1694 | 0.2 | 0.029 | YES |
13 | RPL37A | RPL37A | RPL37A | 1726 | 0.19 | 0.035 | YES |
14 | RPL27A | RPL27A | RPL27A | 1760 | 0.19 | 0.042 | YES |
15 | SNRPD1 | SNRPD1 | SNRPD1 | 1835 | 0.18 | 0.046 | YES |
16 | RPL27 | RPL27 | RPL27 | 1891 | 0.18 | 0.051 | YES |
17 | DCPS | DCPS | DCPS | 1964 | 0.18 | 0.054 | YES |
18 | PSMB9 | PSMB9 | PSMB9 | 1983 | 0.18 | 0.061 | YES |
19 | ANP32A | ANP32A | ANP32A | 2040 | 0.17 | 0.066 | YES |
20 | RPL23A | RPL23A | RPL23A | 2104 | 0.17 | 0.07 | YES |
21 | RPS3 | RPS3 | RPS3 | 2214 | 0.16 | 0.071 | YES |
22 | RPL31 | RPL31 | RPL31 | 2312 | 0.16 | 0.072 | YES |
23 | PSMD13 | PSMD13 | PSMD13 | 2328 | 0.16 | 0.078 | YES |
24 | RPS25 | RPS25 | RPS25 | 2368 | 0.15 | 0.082 | YES |
25 | RPS18 | RPS18 | RPS18 | 2411 | 0.15 | 0.087 | YES |
26 | GEMIN6 | GEMIN6 | GEMIN6 | 2415 | 0.15 | 0.093 | YES |
27 | RPL17 | RPL17 | RPL17 | 2456 | 0.15 | 0.098 | YES |
28 | PSMC3 | PSMC3 | PSMC3 | 2489 | 0.15 | 0.1 | YES |
29 | SNRPE | SNRPE | SNRPE | 2531 | 0.14 | 0.11 | YES |
30 | RPLP2 | RPLP2 | RPLP2 | 2540 | 0.14 | 0.11 | YES |
31 | EXOSC4 | EXOSC4 | EXOSC4 | 2570 | 0.14 | 0.12 | YES |
32 | RBM8A | RBM8A | RBM8A | 2650 | 0.14 | 0.12 | YES |
33 | PSMD1 | PSMD1 | PSMD1 | 2660 | 0.14 | 0.12 | YES |
34 | NUP35 | NUP35 | NUP35 | 2697 | 0.14 | 0.13 | YES |
35 | RPS29 | RPS29 | RPS29 | 2715 | 0.14 | 0.13 | YES |
36 | PSMA8 | PSMA8 | PSMA8 | 2734 | 0.14 | 0.14 | YES |
37 | PSMB4 | PSMB4 | PSMB4 | 2757 | 0.13 | 0.14 | YES |
38 | EXOSC1 | EXOSC1 | EXOSC1 | 2798 | 0.13 | 0.15 | YES |
39 | PRMT5 | PRMT5 | PRMT5 | 2825 | 0.13 | 0.15 | YES |
40 | RPSA | RPSA | RPSA | 2849 | 0.13 | 0.16 | YES |
41 | RPS13 | RPS13 | RPS13 | 2859 | 0.13 | 0.16 | YES |
42 | RPS19 | RPS19 | RPS19 | 2868 | 0.13 | 0.17 | YES |
43 | PSMD14 | PSMD14 | PSMD14 | 2916 | 0.13 | 0.17 | YES |
44 | HSPA1B | HSPA1B | HSPA1B | 2922 | 0.13 | 0.17 | YES |
45 | RPS12 | RPS12 | RPS12 | 2925 | 0.13 | 0.18 | YES |
46 | RPS24 | RPS24 | RPS24 | 2954 | 0.13 | 0.18 | YES |
47 | C2orf29 | C2orf29 | C2orf29 | 2969 | 0.12 | 0.19 | YES |
48 | RPL36 | RPL36 | RPL36 | 2974 | 0.12 | 0.19 | YES |
49 | RPLP1 | RPLP1 | RPLP1 | 2990 | 0.12 | 0.2 | YES |
50 | RPS17 | RPS17 | RPS17 | 3027 | 0.12 | 0.2 | YES |
51 | EXOSC2 | EXOSC2 | EXOSC2 | 3037 | 0.12 | 0.21 | YES |
52 | NUP88 | NUP88 | NUP88 | 3051 | 0.12 | 0.21 | YES |
53 | SNRPD3 | SNRPD3 | SNRPD3 | 3125 | 0.12 | 0.21 | YES |
54 | PATL1 | PATL1 | PATL1 | 3147 | 0.12 | 0.22 | YES |
55 | SMG5 | SMG5 | SMG5 | 3178 | 0.12 | 0.22 | YES |
56 | FAU | FAU | FAU | 3183 | 0.12 | 0.22 | YES |
57 | EDC3 | EDC3 | EDC3 | 3229 | 0.12 | 0.23 | YES |
58 | NUP85 | NUP85 | NUP85 | 3242 | 0.12 | 0.23 | YES |
59 | RPL29 | RPL29 | RPL29 | 3247 | 0.12 | 0.24 | YES |
60 | PSMC1 | PSMC1 | PSMC1 | 3248 | 0.12 | 0.24 | YES |
61 | PSMC5 | PSMC5 | PSMC5 | 3270 | 0.11 | 0.25 | YES |
62 | RPL22 | RPL22 | RPL22 | 3374 | 0.11 | 0.24 | YES |
63 | NUP188 | NUP188 | NUP188 | 3380 | 0.11 | 0.25 | YES |
64 | RPS8 | RPS8 | RPS8 | 3415 | 0.11 | 0.25 | YES |
65 | RPL18A | RPL18A | RPL18A | 3454 | 0.11 | 0.26 | YES |
66 | PSMA4 | PSMA4 | PSMA4 | 3457 | 0.11 | 0.26 | YES |
67 | RPL4 | RPL4 | RPL4 | 3459 | 0.11 | 0.26 | YES |
68 | PSME2 | PSME2 | PSME2 | 3463 | 0.11 | 0.27 | YES |
69 | SNUPN | SNUPN | SNUPN | 3476 | 0.11 | 0.27 | YES |
70 | PSMD11 | PSMD11 | PSMD11 | 3532 | 0.1 | 0.27 | YES |
71 | RPL35 | RPL35 | RPL35 | 3533 | 0.1 | 0.28 | YES |
72 | RPS10 | RPS10 | RPS10 | 3548 | 0.1 | 0.28 | YES |
73 | RPL32 | RPL32 | RPL32 | 3653 | 0.1 | 0.28 | YES |
74 | RPS9 | RPS9 | RPS9 | 3655 | 0.1 | 0.29 | YES |
75 | EXOSC6 | EXOSC6 | EXOSC6 | 3683 | 0.1 | 0.29 | YES |
76 | RPLP0 | RPLP0 | RPLP0 | 3724 | 0.099 | 0.29 | YES |
77 | LSM2 | LSM2 | LSM2 | 3773 | 0.097 | 0.29 | YES |
78 | EIF4A1 | EIF4A1 | EIF4A1 | 3792 | 0.097 | 0.3 | YES |
79 | RPL11 | RPL11 | RPL11 | 3795 | 0.096 | 0.3 | YES |
80 | PSMA1 | PSMA1 | PSMA1 | 3842 | 0.095 | 0.3 | YES |
81 | RPS2 | RPS2 | RPS2 | 3875 | 0.094 | 0.3 | YES |
82 | PSMB5 | PSMB5 | PSMB5 | 3913 | 0.092 | 0.31 | YES |
83 | LSM4 | LSM4 | LSM4 | 3964 | 0.091 | 0.31 | YES |
84 | LSM3 | LSM3 | LSM3 | 3968 | 0.091 | 0.31 | YES |
85 | NUP50 | NUP50 | NUP50 | 3982 | 0.091 | 0.31 | YES |
86 | RPL14 | RPL14 | RPL14 | 3983 | 0.091 | 0.32 | YES |
87 | RPL35A | RPL35A | RPL35A | 3987 | 0.091 | 0.32 | YES |
88 | PSMB3 | PSMB3 | PSMB3 | 4061 | 0.088 | 0.32 | YES |
89 | LSM1 | LSM1 | LSM1 | 4077 | 0.088 | 0.32 | YES |
90 | RPL13A | RPL13A | RPL13A | 4140 | 0.086 | 0.32 | YES |
91 | EXOSC7 | EXOSC7 | EXOSC7 | 4167 | 0.085 | 0.33 | YES |
92 | RPS27 | RPS27 | RPS27 | 4182 | 0.085 | 0.33 | YES |
93 | CLNS1A | CLNS1A | CLNS1A | 4204 | 0.084 | 0.33 | YES |
94 | PSMA5 | PSMA5 | PSMA5 | 4206 | 0.084 | 0.34 | YES |
95 | RPL23 | RPL23 | RPL23 | 4220 | 0.084 | 0.34 | YES |
96 | RPL8 | RPL8 | RPL8 | 4290 | 0.082 | 0.34 | YES |
97 | RPL30 | RPL30 | RPL30 | 4293 | 0.082 | 0.34 | YES |
98 | PSMD2 | PSMD2 | PSMD2 | 4300 | 0.081 | 0.35 | YES |
99 | RPS20 | RPS20 | RPS20 | 4315 | 0.081 | 0.35 | YES |
100 | RPS16 | RPS16 | RPS16 | 4332 | 0.08 | 0.35 | YES |
101 | RPL12 | RPL12 | RPL12 | 4379 | 0.079 | 0.35 | YES |
102 | CNOT3 | CNOT3 | CNOT3 | 4406 | 0.078 | 0.35 | YES |
103 | RPL26 | RPL26 | RPL26 | 4544 | 0.074 | 0.35 | YES |
104 | RPL19 | RPL19 | RPL19 | 4565 | 0.073 | 0.35 | YES |
105 | NUP210 | NUP210 | NUP210 | 4583 | 0.073 | 0.35 | YES |
106 | RPS11 | RPS11 | RPS11 | 4597 | 0.072 | 0.36 | YES |
107 | UBA52 | UBA52 | UBA52 | 4612 | 0.072 | 0.36 | YES |
108 | RPL5 | RPL5 | RPL5 | 4634 | 0.072 | 0.36 | YES |
109 | RPL24 | RPL24 | RPL24 | 4668 | 0.071 | 0.36 | YES |
110 | MAPK14 | MAPK14 | MAPK14 | 4723 | 0.069 | 0.36 | YES |
111 | CASC3 | CASC3 | CASC3 | 4730 | 0.069 | 0.36 | YES |
112 | RPS26 | RPS26 | RPS26 | 4736 | 0.069 | 0.37 | YES |
113 | TPR | TPR | TPR | 4802 | 0.067 | 0.37 | YES |
114 | RPL3 | RPL3 | RPL3 | 4831 | 0.066 | 0.37 | YES |
115 | RPS15 | RPS15 | RPS15 | 4845 | 0.066 | 0.37 | YES |
116 | RPL28 | RPL28 | RPL28 | 4862 | 0.066 | 0.37 | YES |
117 | PSMD12 | PSMD12 | PSMD12 | 4875 | 0.065 | 0.37 | YES |
118 | DCP2 | DCP2 | DCP2 | 4889 | 0.065 | 0.38 | YES |
119 | NUP62 | NUP62 | NUP62 | 4891 | 0.065 | 0.38 | YES |
120 | RPL10A | RPL10A | RPL10A | 4930 | 0.064 | 0.38 | YES |
121 | RAE1 | RAE1 | RAE1 | 4957 | 0.063 | 0.38 | YES |
122 | RPL38 | RPL38 | RPL38 | 4979 | 0.062 | 0.38 | YES |
123 | RPL7 | RPL7 | RPL7 | 5008 | 0.062 | 0.38 | YES |
124 | PSMB7 | PSMB7 | PSMB7 | 5071 | 0.06 | 0.38 | YES |
125 | NCBP1 | NCBP1 | NCBP1 | 5107 | 0.06 | 0.38 | YES |
126 | RPL7A | RPL7A | RPL7A | 5145 | 0.059 | 0.38 | YES |
127 | RPL18 | RPL18 | RPL18 | 5360 | 0.054 | 0.37 | NO |
128 | PSMA6 | PSMA6 | PSMA6 | 5425 | 0.052 | 0.37 | NO |
129 | PSMC6 | PSMC6 | PSMC6 | 5427 | 0.052 | 0.38 | NO |
130 | SEH1L | SEH1L | SEH1L | 5433 | 0.052 | 0.38 | NO |
131 | RPS3A | RPS3A | RPS3A | 5454 | 0.051 | 0.38 | NO |
132 | RPS15A | RPS15A | RPS15A | 5465 | 0.051 | 0.38 | NO |
133 | NUP133 | NUP133 | NUP133 | 5515 | 0.05 | 0.38 | NO |
134 | EXOSC3 | EXOSC3 | EXOSC3 | 5588 | 0.047 | 0.38 | NO |
135 | RPL13 | RPL13 | RPL13 | 5603 | 0.047 | 0.38 | NO |
136 | RPL15 | RPL15 | RPL15 | 5625 | 0.046 | 0.38 | NO |
137 | NCBP2 | NCBP2 | NCBP2 | 5683 | 0.045 | 0.38 | NO |
138 | RPS5 | RPS5 | RPS5 | 5701 | 0.044 | 0.38 | NO |
139 | PSMB1 | PSMB1 | PSMB1 | 5759 | 0.043 | 0.38 | NO |
140 | RPL41 | RPL41 | RPL41 | 5783 | 0.042 | 0.38 | NO |
141 | HNRNPD | HNRNPD | HNRNPD | 5795 | 0.042 | 0.38 | NO |
142 | GEMIN7 | GEMIN7 | GEMIN7 | 5803 | 0.042 | 0.38 | NO |
143 | RANBP2 | RANBP2 | RANBP2 | 5811 | 0.041 | 0.38 | NO |
144 | PSMA3 | PSMA3 | PSMA3 | 5824 | 0.041 | 0.38 | NO |
145 | CNOT10 | CNOT10 | CNOT10 | 5886 | 0.039 | 0.38 | NO |
146 | KHSRP | KHSRP | KHSRP | 5895 | 0.039 | 0.38 | NO |
147 | XPO1 | XPO1 | XPO1 | 5922 | 0.039 | 0.38 | NO |
148 | NUPL1 | NUPL1 | NUPL1 | 5964 | 0.038 | 0.38 | NO |
149 | PSMD3 | PSMD3 | PSMD3 | 6039 | 0.036 | 0.38 | NO |
150 | ZFP36 | ZFP36 | ZFP36 | 6057 | 0.036 | 0.38 | NO |
151 | PSMC4 | PSMC4 | PSMC4 | 6156 | 0.034 | 0.38 | NO |
152 | PSMD6 | PSMD6 | PSMD6 | 6170 | 0.033 | 0.38 | NO |
153 | PSME1 | PSME1 | PSME1 | 6256 | 0.031 | 0.37 | NO |
154 | PSMB6 | PSMB6 | PSMB6 | 6329 | 0.029 | 0.37 | NO |
155 | EDC4 | EDC4 | EDC4 | 6352 | 0.029 | 0.37 | NO |
156 | RPS21 | RPS21 | RPS21 | 6403 | 0.027 | 0.37 | NO |
157 | SNRPD2 | SNRPD2 | SNRPD2 | 6436 | 0.026 | 0.37 | NO |
158 | CNOT2 | CNOT2 | CNOT2 | 6457 | 0.026 | 0.37 | NO |
159 | PABPC1 | PABPC1 | PABPC1 | 6532 | 0.024 | 0.37 | NO |
160 | NUP93 | NUP93 | NUP93 | 6574 | 0.024 | 0.36 | NO |
161 | RPS6 | RPS6 | RPS6 | 6663 | 0.022 | 0.36 | NO |
162 | MAGOH | MAGOH | MAGOH | 6730 | 0.02 | 0.36 | NO |
163 | SNRPB | SNRPB | SNRPB | 6803 | 0.018 | 0.35 | NO |
164 | RPL37 | RPL37 | RPL37 | 6817 | 0.018 | 0.35 | NO |
165 | SNRPF | SNRPF | SNRPF | 6855 | 0.017 | 0.35 | NO |
166 | PSMB2 | PSMB2 | PSMB2 | 6872 | 0.017 | 0.35 | NO |
167 | PPP2R2A | PPP2R2A | PPP2R2A | 6902 | 0.016 | 0.35 | NO |
168 | GEMIN4 | GEMIN4 | GEMIN4 | 7042 | 0.013 | 0.34 | NO |
169 | RPL39 | RPL39 | RPL39 | 7139 | 0.011 | 0.34 | NO |
170 | RPL6 | RPL6 | RPL6 | 7234 | 0.0091 | 0.34 | NO |
171 | LSM6 | LSM6 | LSM6 | 7273 | 0.0082 | 0.33 | NO |
172 | SMG7 | SMG7 | SMG7 | 7347 | 0.0066 | 0.33 | NO |
173 | HSPA8 | HSPA8 | HSPA8 | 7364 | 0.0062 | 0.33 | NO |
174 | YWHAZ | YWHAZ | YWHAZ | 7370 | 0.0061 | 0.33 | NO |
175 | DDX20 | DDX20 | DDX20 | 7397 | 0.0055 | 0.33 | NO |
176 | LSM5 | LSM5 | LSM5 | 7406 | 0.0051 | 0.33 | NO |
177 | PSMA7 | PSMA7 | PSMA7 | 7461 | 0.0041 | 0.32 | NO |
178 | PPP2R1A | PPP2R1A | PPP2R1A | 7485 | 0.0035 | 0.32 | NO |
179 | UPF2 | UPF2 | UPF2 | 7545 | 0.0024 | 0.32 | NO |
180 | PSMA2 | PSMA2 | PSMA2 | 7554 | 0.0021 | 0.32 | NO |
181 | EXOSC9 | EXOSC9 | EXOSC9 | 7576 | 0.0017 | 0.32 | NO |
182 | NUP214 | NUP214 | NUP214 | 7608 | 0.001 | 0.32 | NO |
183 | RPS4X | RPS4X | RPS4X | 7716 | -0.0016 | 0.31 | NO |
184 | PSMD9 | PSMD9 | PSMD9 | 7828 | -0.0041 | 0.3 | NO |
185 | DCP1A | DCP1A | DCP1A | 7847 | -0.0045 | 0.3 | NO |
186 | CNOT7 | CNOT7 | CNOT7 | 7882 | -0.0053 | 0.3 | NO |
187 | NUP43 | NUP43 | NUP43 | 7925 | -0.0061 | 0.3 | NO |
188 | EXOSC5 | EXOSC5 | EXOSC5 | 7999 | -0.0077 | 0.3 | NO |
189 | ELAVL1 | ELAVL1 | ELAVL1 | 8034 | -0.0084 | 0.29 | NO |
190 | NUP107 | NUP107 | NUP107 | 8036 | -0.0084 | 0.29 | NO |
191 | RPL34 | RPL34 | RPL34 | 8102 | -0.01 | 0.29 | NO |
192 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 8202 | -0.012 | 0.29 | NO |
193 | RPL10 | RPL10 | RPL10 | 8258 | -0.014 | 0.28 | NO |
194 | EIF4G1 | EIF4G1 | EIF4G1 | 8332 | -0.015 | 0.28 | NO |
195 | AAAS | AAAS | AAAS | 8379 | -0.016 | 0.28 | NO |
196 | AKT1 | AKT1 | AKT1 | 8423 | -0.017 | 0.28 | NO |
197 | PSMF1 | PSMF1 | PSMF1 | 8465 | -0.018 | 0.28 | NO |
198 | RPS14 | RPS14 | RPS14 | 8594 | -0.021 | 0.27 | NO |
199 | PSMB8 | PSMB8 | PSMB8 | 8609 | -0.021 | 0.27 | NO |
200 | SMN2 | SMN2 | SMN2 | 8679 | -0.022 | 0.26 | NO |
201 | PSMD7 | PSMD7 | PSMD7 | 8689 | -0.023 | 0.27 | NO |
202 | RPS23 | RPS23 | RPS23 | 8692 | -0.023 | 0.27 | NO |
203 | DIS3 | DIS3 | DIS3 | 8726 | -0.024 | 0.27 | NO |
204 | EIF4B | EIF4B | EIF4B | 8811 | -0.025 | 0.26 | NO |
205 | SMG6 | SMG6 | SMG6 | 8919 | -0.028 | 0.26 | NO |
206 | RNPS1 | RNPS1 | RNPS1 | 8958 | -0.029 | 0.26 | NO |
207 | PSMD8 | PSMD8 | PSMD8 | 8968 | -0.029 | 0.26 | NO |
208 | PSMB10 | PSMB10 | PSMB10 | 9282 | -0.037 | 0.24 | NO |
209 | DDX6 | DDX6 | DDX6 | 9368 | -0.039 | 0.24 | NO |
210 | EIF4A2 | EIF4A2 | EIF4A2 | 9543 | -0.044 | 0.23 | NO |
211 | PRKCD | PRKCD | PRKCD | 9550 | -0.044 | 0.23 | NO |
212 | PSMC2 | PSMC2 | PSMC2 | 9757 | -0.049 | 0.22 | NO |
213 | YWHAB | YWHAB | YWHAB | 9778 | -0.05 | 0.22 | NO |
214 | NUP54 | NUP54 | NUP54 | 9811 | -0.05 | 0.22 | NO |
215 | CNOT6 | CNOT6 | CNOT6 | 10018 | -0.055 | 0.21 | NO |
216 | TNKS1BP1 | TNKS1BP1 | TNKS1BP1 | 10172 | -0.059 | 0.21 | NO |
217 | PSMD5 | PSMD5 | PSMD5 | 10267 | -0.062 | 0.2 | NO |
218 | UPF3A | UPF3A | UPF3A | 10334 | -0.063 | 0.2 | NO |
219 | XRN1 | XRN1 | XRN1 | 10457 | -0.066 | 0.2 | NO |
220 | POM121 | POM121 | POM121 | 10639 | -0.071 | 0.19 | NO |
221 | RPS28 | RPS28 | RPS28 | 10647 | -0.071 | 0.2 | NO |
222 | RPL26L1 | RPL26L1 | RPL26L1 | 10697 | -0.072 | 0.2 | NO |
223 | NUP153 | NUP153 | NUP153 | 10758 | -0.074 | 0.2 | NO |
224 | TGS1 | TGS1 | TGS1 | 10781 | -0.074 | 0.2 | NO |
225 | ETF1 | ETF1 | ETF1 | 10817 | -0.075 | 0.2 | NO |
226 | PPP2CA | PPP2CA | PPP2CA | 10835 | -0.076 | 0.2 | NO |
227 | NUP37 | NUP37 | NUP37 | 10866 | -0.077 | 0.2 | NO |
228 | PAIP1 | PAIP1 | PAIP1 | 10885 | -0.077 | 0.21 | NO |
229 | PARN | PARN | PARN | 11123 | -0.083 | 0.2 | NO |
230 | TNFSF13 | TNFSF13 | TNFSF13 | 11141 | -0.084 | 0.2 | NO |
231 | CNOT8 | CNOT8 | CNOT8 | 11152 | -0.084 | 0.2 | NO |
232 | NUP155 | NUP155 | NUP155 | 11198 | -0.085 | 0.2 | NO |
233 | NUP205 | NUP205 | NUP205 | 11211 | -0.085 | 0.21 | NO |
234 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 11213 | -0.085 | 0.21 | NO |
235 | NUPL2 | NUPL2 | NUPL2 | 11340 | -0.089 | 0.21 | NO |
236 | SMN1 | SMN1 | SMN1 | 11361 | -0.089 | 0.21 | NO |
237 | ZFP36L1 | ZFP36L1 | ZFP36L1 | 11494 | -0.093 | 0.21 | NO |
238 | SMG1 | SMG1 | SMG1 | 11622 | -0.097 | 0.2 | NO |
239 | UPF3B | UPF3B | UPF3B | 12251 | -0.12 | 0.17 | NO |
240 | EIF4E | EIF4E | EIF4E | 12357 | -0.12 | 0.17 | NO |
241 | TNPO1 | TNPO1 | TNPO1 | 13032 | -0.14 | 0.14 | NO |
242 | GEMIN5 | GEMIN5 | GEMIN5 | 13105 | -0.14 | 0.14 | NO |
243 | PSMD10 | PSMD10 | PSMD10 | 13784 | -0.17 | 0.11 | NO |
244 | DCP1B | DCP1B | DCP1B | 13910 | -0.18 | 0.11 | NO |
245 | RPL9 | RPL9 | RPL9 | 13932 | -0.18 | 0.12 | NO |
246 | CNOT4 | CNOT4 | CNOT4 | 14389 | -0.2 | 0.1 | NO |
247 | HSPB1 | HSPB1 | HSPB1 | 14686 | -0.21 | 0.092 | NO |
248 | PHAX | PHAX | PHAX | 15156 | -0.24 | 0.076 | NO |
249 | RPL36A | RPL36A | RPL36A | 15622 | -0.28 | 0.062 | NO |
250 | GSPT2 | GSPT2 | GSPT2 | 15678 | -0.28 | 0.071 | NO |
251 | PRKCA | PRKCA | PRKCA | 16794 | -0.42 | 0.026 | NO |
252 | FAM153A | FAM153A | FAM153A | 17452 | -0.6 | 0.015 | 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: PID MYC PATHWAY.

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

Table S10. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | POLR2D | POLR2D | POLR2D | 1127 | 0.25 | 0.013 | YES |
2 | SF3B4 | SF3B4 | SF3B4 | 1350 | 0.23 | 0.07 | YES |
3 | POLR2G | POLR2G | POLR2G | 1368 | 0.22 | 0.14 | YES |
4 | SNRPG | SNRPG | SNRPG | 1608 | 0.2 | 0.19 | YES |
5 | SNRPD1 | SNRPD1 | SNRPD1 | 1835 | 0.18 | 0.23 | YES |
6 | POLR2L | POLR2L | POLR2L | 1914 | 0.18 | 0.28 | YES |
7 | POLR2H | POLR2H | POLR2H | 2527 | 0.14 | 0.29 | YES |
8 | SNRPE | SNRPE | SNRPE | 2531 | 0.14 | 0.33 | YES |
9 | SF3B14 | SF3B14 | SF3B14 | 2551 | 0.14 | 0.38 | YES |
10 | GTF2F2 | GTF2F2 | GTF2F2 | 3003 | 0.12 | 0.39 | YES |
11 | SNRPD3 | SNRPD3 | SNRPD3 | 3125 | 0.12 | 0.42 | YES |
12 | SNRNP40 | SNRNP40 | SNRNP40 | 3196 | 0.12 | 0.45 | YES |
13 | SF3B2 | SF3B2 | SF3B2 | 3549 | 0.1 | 0.46 | YES |
14 | LSM2 | LSM2 | LSM2 | 3773 | 0.097 | 0.48 | YES |
15 | NHP2L1 | NHP2L1 | NHP2L1 | 4024 | 0.089 | 0.49 | YES |
16 | TXNL4A | TXNL4A | TXNL4A | 4466 | 0.076 | 0.49 | YES |
17 | POLR2F | POLR2F | POLR2F | 4520 | 0.074 | 0.51 | YES |
18 | SF3B5 | SF3B5 | SF3B5 | 4834 | 0.066 | 0.51 | YES |
19 | SF3B1 | SF3B1 | SF3B1 | 4906 | 0.064 | 0.53 | YES |
20 | NCBP1 | NCBP1 | NCBP1 | 5107 | 0.06 | 0.53 | YES |
21 | NCBP2 | NCBP2 | NCBP2 | 5683 | 0.045 | 0.51 | NO |
22 | EFTUD2 | EFTUD2 | EFTUD2 | 5693 | 0.044 | 0.53 | NO |
23 | SNRNP200 | SNRNP200 | SNRNP200 | 6090 | 0.035 | 0.52 | NO |
24 | SNRPD2 | SNRPD2 | SNRPD2 | 6436 | 0.026 | 0.5 | NO |
25 | POLR2E | POLR2E | POLR2E | 6494 | 0.025 | 0.51 | NO |
26 | SNRPB | SNRPB | SNRPB | 6803 | 0.018 | 0.5 | NO |
27 | SNRPF | SNRPF | SNRPF | 6855 | 0.017 | 0.5 | NO |
28 | POLR2A | POLR2A | POLR2A | 7066 | 0.013 | 0.49 | NO |
29 | GTF2F1 | GTF2F1 | GTF2F1 | 8299 | -0.014 | 0.43 | NO |
30 | POLR2K | POLR2K | POLR2K | 8522 | -0.019 | 0.42 | NO |
31 | SF3B3 | SF3B3 | SF3B3 | 8548 | -0.02 | 0.42 | NO |
32 | PRPF8 | PRPF8 | PRPF8 | 8649 | -0.022 | 0.42 | NO |
33 | POLR2J | POLR2J | POLR2J | 8809 | -0.025 | 0.42 | NO |
34 | POLR2I | POLR2I | POLR2I | 8916 | -0.028 | 0.43 | NO |
35 | PRPF6 | PRPF6 | PRPF6 | 8984 | -0.029 | 0.43 | NO |
36 | DDX23 | DDX23 | DDX23 | 9246 | -0.036 | 0.43 | NO |
37 | POLR2B | POLR2B | POLR2B | 10993 | -0.08 | 0.35 | NO |
38 | POLR2C | POLR2C | POLR2C | 11422 | -0.091 | 0.36 | 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: PID FOXM1PATHWAY.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: PID FOXM1PATHWAY, 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 WNT SIGNALING PATHWAY | 145 | genes.ES.table | 0.4 | 1.5 | 0.031 | 0.95 | 0.99 | 0.37 | 0.27 | 0.28 | 0.69 | 0.32 |
KEGG HEDGEHOG SIGNALING PATHWAY | 54 | genes.ES.table | 0.56 | 1.5 | 0.013 | 1 | 0.96 | 0.44 | 0.17 | 0.37 | 0.73 | 0.38 |
KEGG TASTE TRANSDUCTION | 38 | genes.ES.table | 0.57 | 1.5 | 0.013 | 1 | 0.98 | 0.4 | 0.099 | 0.36 | 0.77 | 0.4 |
KEGG BASAL CELL CARCINOMA | 54 | genes.ES.table | 0.6 | 1.6 | 0.01 | 0.93 | 0.91 | 0.46 | 0.17 | 0.39 | 0.54 | 0.29 |
BIOCARTA NO1 PATHWAY | 28 | genes.ES.table | 0.53 | 1.5 | 0.056 | 1 | 0.99 | 0.29 | 0.15 | 0.24 | 0.83 | 0.42 |
BIOCARTA CHREBP2 PATHWAY | 41 | genes.ES.table | 0.4 | 1.5 | 0.091 | 1 | 0.99 | 0.12 | 0.1 | 0.11 | 0.73 | 0.35 |
BIOCARTA WNT PATHWAY | 26 | genes.ES.table | 0.48 | 1.7 | 0.036 | 1 | 0.84 | 0.58 | 0.38 | 0.36 | 0.52 | 0.3 |
ST WNT BETA CATENIN PATHWAY | 31 | genes.ES.table | 0.58 | 1.7 | 0.028 | 1 | 0.84 | 0.42 | 0.24 | 0.32 | 0.64 | 0.36 |
PID REELINPATHWAY | 28 | genes.ES.table | 0.48 | 1.6 | 0.029 | 1 | 0.94 | 0.21 | 0.12 | 0.19 | 0.7 | 0.37 |
PID NECTIN PATHWAY | 30 | genes.ES.table | 0.42 | 1.5 | 0.07 | 1 | 0.99 | 0.3 | 0.23 | 0.23 | 0.75 | 0.37 |
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 | SSPO | SSPO | SSPO | 41 | 0.79 | 0.12 | YES |
2 | GLI1 | GLI1 | GLI1 | 235 | 0.57 | 0.2 | YES |
3 | SHH | SHH | SHH | 352 | 0.52 | 0.28 | YES |
4 | SMO | SMO | SMO | 505 | 0.46 | 0.34 | YES |
5 | GNAO1 | GNAO1 | GNAO1 | 927 | 0.38 | 0.38 | YES |
6 | GNAZ | GNAZ | GNAZ | 1027 | 0.36 | 0.43 | YES |
7 | PTCH1 | PTCH1 | PTCH1 | 1572 | 0.29 | 0.44 | YES |
8 | GLI3 | GLI3 | GLI3 | 1726 | 0.28 | 0.48 | YES |
9 | KIF3A | KIF3A | KIF3A | 2413 | 0.22 | 0.48 | YES |
10 | GLI2 | GLI2 | GLI2 | 2584 | 0.21 | 0.5 | YES |
11 | FBXW11 | FBXW11 | FBXW11 | 4698 | 0.11 | 0.4 | NO |
12 | CSNK1G3 | CSNK1G3 | CSNK1G3 | 4724 | 0.11 | 0.41 | NO |
13 | SIN3B | SIN3B | SIN3B | 5523 | 0.089 | 0.38 | NO |
14 | SUFU | SUFU | SUFU | 5603 | 0.087 | 0.39 | NO |
15 | GNAI1 | GNAI1 | GNAI1 | 5614 | 0.086 | 0.4 | NO |
16 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 6021 | 0.076 | 0.39 | NO |
17 | MTSS1 | MTSS1 | MTSS1 | 6065 | 0.076 | 0.4 | NO |
18 | CREBBP | CREBBP | CREBBP | 6359 | 0.069 | 0.4 | NO |
19 | CSNK1E | CSNK1E | CSNK1E | 6413 | 0.068 | 0.41 | NO |
20 | GSK3B | GSK3B | GSK3B | 6428 | 0.068 | 0.42 | NO |
21 | PRKACA | PRKACA | PRKACA | 6541 | 0.065 | 0.42 | NO |
22 | LGALS3 | LGALS3 | LGALS3 | 7181 | 0.052 | 0.39 | NO |
23 | IFT88 | IFT88 | IFT88 | 7667 | 0.042 | 0.37 | NO |
24 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 8115 | 0.033 | 0.35 | NO |
25 | AKT1 | AKT1 | AKT1 | 8174 | 0.032 | 0.35 | NO |
26 | GNAI3 | GNAI3 | GNAI3 | 8750 | 0.022 | 0.32 | NO |
27 | CSNK1G1 | CSNK1G1 | CSNK1G1 | 9052 | 0.016 | 0.31 | NO |
28 | CSNK1D | CSNK1D | CSNK1D | 9298 | 0.011 | 0.3 | NO |
29 | XPO1 | XPO1 | XPO1 | 9360 | 0.0095 | 0.3 | NO |
30 | GNAI2 | GNAI2 | GNAI2 | 9433 | 0.0083 | 0.29 | NO |
31 | PIAS1 | PIAS1 | PIAS1 | 9486 | 0.0074 | 0.29 | NO |
32 | SAP30 | SAP30 | SAP30 | 9673 | 0.0037 | 0.28 | NO |
33 | SIN3A | SIN3A | SIN3A | 9878 | 0.00029 | 0.27 | NO |
34 | RBBP4 | RBBP4 | RBBP4 | 9926 | -0.00053 | 0.27 | NO |
35 | MAP2K1 | MAP2K1 | MAP2K1 | 9967 | -0.0014 | 0.26 | NO |
36 | SPOP | SPOP | SPOP | 11179 | -0.024 | 0.2 | NO |
37 | STK36 | STK36 | STK36 | 11558 | -0.032 | 0.18 | NO |
38 | HDAC2 | HDAC2 | HDAC2 | 11626 | -0.033 | 0.18 | NO |
39 | GNG2 | GNG2 | GNG2 | 11840 | -0.038 | 0.18 | NO |
40 | SAP18 | SAP18 | SAP18 | 11974 | -0.04 | 0.18 | NO |
41 | RBBP7 | RBBP7 | RBBP7 | 13133 | -0.067 | 0.12 | NO |
42 | PRKCD | PRKCD | PRKCD | 13362 | -0.073 | 0.12 | NO |
43 | GNB1 | GNB1 | GNB1 | 13491 | -0.077 | 0.13 | NO |
44 | IFT172 | IFT172 | IFT172 | 13504 | -0.077 | 0.14 | NO |
45 | HDAC1 | HDAC1 | HDAC1 | 14125 | -0.096 | 0.12 | NO |
46 | RAB23 | RAB23 | RAB23 | 14821 | -0.12 | 0.098 | NO |
47 | FOXA2 | FOXA2 | FOXA2 | 15085 | -0.14 | 0.1 | NO |
48 | ARRB2 | ARRB2 | ARRB2 | 16737 | -0.28 | 0.056 | 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 WNT SIGNALING PATHWAY.

Figure S22. 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 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 | RORB | RORB | RORB | 10 | 0.97 | 0.018 | YES |
2 | ZNF114 | ZNF114 | ZNF114 | 37 | 0.82 | 0.032 | YES |
3 | TBX5 | TBX5 | TBX5 | 278 | 0.55 | 0.029 | YES |
4 | ZFP37 | ZFP37 | ZFP37 | 476 | 0.48 | 0.027 | YES |
5 | ZNF483 | ZNF483 | ZNF483 | 572 | 0.45 | 0.03 | YES |
6 | ZNF215 | ZNF215 | ZNF215 | 582 | 0.44 | 0.038 | YES |
7 | ZNF426 | ZNF426 | ZNF426 | 640 | 0.43 | 0.043 | YES |
8 | CCNT1 | CCNT1 | CCNT1 | 847 | 0.39 | 0.038 | YES |
9 | ZNF418 | ZNF418 | ZNF418 | 941 | 0.37 | 0.04 | YES |
10 | ZNF485 | ZNF485 | ZNF485 | 953 | 0.37 | 0.046 | YES |
11 | AR | AR | AR | 972 | 0.37 | 0.052 | YES |
12 | ZNF354C | ZNF354C | ZNF354C | 973 | 0.37 | 0.06 | YES |
13 | ZNF442 | ZNF442 | ZNF442 | 1054 | 0.36 | 0.062 | YES |
14 | ZNF540 | ZNF540 | ZNF540 | 1096 | 0.35 | 0.066 | YES |
15 | ZNF582 | ZNF582 | ZNF582 | 1110 | 0.35 | 0.072 | YES |
16 | ZNF221 | ZNF221 | ZNF221 | 1118 | 0.35 | 0.078 | YES |
17 | MAML3 | MAML3 | MAML3 | 1165 | 0.34 | 0.082 | YES |
18 | NR3C2 | NR3C2 | NR3C2 | 1200 | 0.34 | 0.087 | YES |
19 | ZIK1 | ZIK1 | ZIK1 | 1219 | 0.33 | 0.092 | YES |
20 | ZNF454 | ZNF454 | ZNF454 | 1229 | 0.33 | 0.098 | YES |
21 | ZNF382 | ZNF382 | ZNF382 | 1254 | 0.33 | 0.1 | YES |
22 | ZNF441 | ZNF441 | ZNF441 | 1275 | 0.33 | 0.11 | YES |
23 | ZNF658 | ZNF658 | ZNF658 | 1298 | 0.32 | 0.11 | YES |
24 | NR2E1 | NR2E1 | NR2E1 | 1368 | 0.32 | 0.12 | YES |
25 | PGR | PGR | PGR | 1370 | 0.32 | 0.12 | YES |
26 | ZNF30 | ZNF30 | ZNF30 | 1406 | 0.31 | 0.12 | YES |
27 | ZIM2 | ZIM2 | ZIM2 | 1425 | 0.31 | 0.13 | YES |
28 | ZFP2 | ZFP2 | ZFP2 | 1438 | 0.31 | 0.14 | YES |
29 | NR4A3 | NR4A3 | NR4A3 | 1523 | 0.3 | 0.14 | YES |
30 | ZNF596 | ZNF596 | ZNF596 | 1551 | 0.29 | 0.14 | YES |
31 | ZNF551 | ZNF551 | ZNF551 | 1557 | 0.29 | 0.14 | YES |
32 | ZNF417 | ZNF417 | ZNF417 | 1576 | 0.29 | 0.15 | YES |
33 | ZNF625 | ZNF625 | ZNF625 | 1613 | 0.28 | 0.15 | YES |
34 | ZNF324 | ZNF324 | ZNF324 | 1630 | 0.28 | 0.16 | YES |
35 | ZNF273 | ZNF273 | ZNF273 | 1675 | 0.28 | 0.16 | YES |
36 | ZNF157 | ZNF157 | ZNF157 | 1701 | 0.28 | 0.16 | YES |
37 | TEAD2 | TEAD2 | TEAD2 | 1711 | 0.28 | 0.17 | YES |
38 | ZNF17 | ZNF17 | ZNF17 | 1801 | 0.27 | 0.17 | YES |
39 | ZNF565 | ZNF565 | ZNF565 | 1815 | 0.26 | 0.17 | YES |
40 | ZNF471 | ZNF471 | ZNF471 | 1822 | 0.26 | 0.18 | YES |
41 | ZNF333 | ZNF333 | ZNF333 | 1830 | 0.26 | 0.18 | YES |
42 | RORA | RORA | RORA | 1851 | 0.26 | 0.19 | YES |
43 | ZNF585B | ZNF585B | ZNF585B | 1856 | 0.26 | 0.19 | YES |
44 | ZNF443 | ZNF443 | ZNF443 | 1866 | 0.26 | 0.2 | YES |
45 | RARG | RARG | RARG | 1868 | 0.26 | 0.2 | YES |
46 | ZNF560 | ZNF560 | ZNF560 | 1884 | 0.26 | 0.2 | YES |
47 | ZNF530 | ZNF530 | ZNF530 | 1905 | 0.26 | 0.21 | YES |
48 | ZNF14 | ZNF14 | ZNF14 | 1915 | 0.26 | 0.21 | YES |
49 | ZNF354B | ZNF354B | ZNF354B | 1924 | 0.26 | 0.22 | YES |
50 | ZNF25 | ZNF25 | ZNF25 | 1934 | 0.26 | 0.22 | YES |
51 | ZNF222 | ZNF222 | ZNF222 | 1974 | 0.25 | 0.22 | YES |
52 | ZNF595 | ZNF595 | ZNF595 | 1999 | 0.25 | 0.23 | YES |
53 | ZNF33B | ZNF33B | ZNF33B | 2015 | 0.25 | 0.23 | YES |
54 | ZNF627 | ZNF627 | ZNF627 | 2023 | 0.25 | 0.24 | YES |
55 | ZNF432 | ZNF432 | ZNF432 | 2039 | 0.25 | 0.24 | YES |
56 | ZNF37A | ZNF37A | ZNF37A | 2043 | 0.25 | 0.24 | YES |
57 | ZNF547 | ZNF547 | ZNF547 | 2057 | 0.25 | 0.25 | YES |
58 | TBL1X | TBL1X | TBL1X | 2065 | 0.25 | 0.25 | YES |
59 | ZNF230 | ZNF230 | ZNF230 | 2080 | 0.24 | 0.26 | YES |
60 | ZFP28 | ZFP28 | ZFP28 | 2086 | 0.24 | 0.26 | YES |
61 | ZNF425 | ZNF425 | ZNF425 | 2114 | 0.24 | 0.26 | YES |
62 | ZNF566 | ZNF566 | ZNF566 | 2121 | 0.24 | 0.27 | YES |
63 | NCOA2 | NCOA2 | NCOA2 | 2136 | 0.24 | 0.27 | YES |
64 | ZNF510 | ZNF510 | ZNF510 | 2154 | 0.24 | 0.28 | YES |
65 | ZNF570 | ZNF570 | ZNF570 | 2177 | 0.24 | 0.28 | YES |
66 | ZNF616 | ZNF616 | ZNF616 | 2184 | 0.24 | 0.28 | YES |
67 | ZNF420 | ZNF420 | ZNF420 | 2213 | 0.24 | 0.29 | YES |
68 | ZNF556 | ZNF556 | ZNF556 | 2247 | 0.23 | 0.29 | YES |
69 | ZNF304 | ZNF304 | ZNF304 | 2254 | 0.23 | 0.29 | YES |
70 | ZNF331 | ZNF331 | ZNF331 | 2257 | 0.23 | 0.3 | YES |
71 | ZNF416 | ZNF416 | ZNF416 | 2262 | 0.23 | 0.3 | YES |
72 | ZNF211 | ZNF211 | ZNF211 | 2265 | 0.23 | 0.31 | YES |
73 | ZNF354A | ZNF354A | ZNF354A | 2297 | 0.23 | 0.31 | YES |
74 | ZNF440 | ZNF440 | ZNF440 | 2349 | 0.22 | 0.31 | YES |
75 | ZNF419 | ZNF419 | ZNF419 | 2377 | 0.22 | 0.31 | YES |
76 | ZNF460 | ZNF460 | ZNF460 | 2386 | 0.22 | 0.32 | YES |
77 | ZNF192 | ZNF192 | ZNF192 | 2402 | 0.22 | 0.32 | YES |
78 | ZNF773 | ZNF773 | ZNF773 | 2441 | 0.22 | 0.32 | YES |
79 | ZNF383 | ZNF383 | ZNF383 | 2444 | 0.22 | 0.33 | YES |
80 | TEAD3 | TEAD3 | TEAD3 | 2448 | 0.22 | 0.33 | YES |
81 | THRB | THRB | THRB | 2483 | 0.21 | 0.33 | YES |
82 | ZNF189 | ZNF189 | ZNF189 | 2508 | 0.21 | 0.33 | YES |
83 | ZNF558 | ZNF558 | ZNF558 | 2515 | 0.21 | 0.34 | YES |
84 | ZNF180 | ZNF180 | ZNF180 | 2523 | 0.21 | 0.34 | YES |
85 | ZKSCAN1 | ZKSCAN1 | ZKSCAN1 | 2526 | 0.21 | 0.35 | YES |
86 | NR1D2 | NR1D2 | NR1D2 | 2545 | 0.21 | 0.35 | YES |
87 | ZNF138 | ZNF138 | ZNF138 | 2557 | 0.21 | 0.35 | YES |
88 | ZNF587 | ZNF587 | ZNF587 | 2572 | 0.21 | 0.36 | YES |
89 | ZNF234 | ZNF234 | ZNF234 | 2588 | 0.21 | 0.36 | YES |
90 | ZNF225 | ZNF225 | ZNF225 | 2622 | 0.2 | 0.36 | YES |
91 | ZNF175 | ZNF175 | ZNF175 | 2628 | 0.2 | 0.36 | YES |
92 | ESRRB | ESRRB | ESRRB | 2655 | 0.2 | 0.37 | YES |
93 | ZNF169 | ZNF169 | ZNF169 | 2665 | 0.2 | 0.37 | YES |
94 | ZNF473 | ZNF473 | ZNF473 | 2666 | 0.2 | 0.37 | YES |
95 | ZNF274 | ZNF274 | ZNF274 | 2676 | 0.2 | 0.38 | YES |
96 | ZNF254 | ZNF254 | ZNF254 | 2721 | 0.2 | 0.38 | YES |
97 | ZNF583 | ZNF583 | ZNF583 | 2745 | 0.2 | 0.38 | YES |
98 | ZNF484 | ZNF484 | ZNF484 | 2782 | 0.19 | 0.38 | YES |
99 | ZNF248 | ZNF248 | ZNF248 | 2803 | 0.19 | 0.38 | YES |
100 | ZNF557 | ZNF557 | ZNF557 | 2844 | 0.19 | 0.39 | YES |
101 | ZNF223 | ZNF223 | ZNF223 | 2847 | 0.19 | 0.39 | YES |
102 | ZNF256 | ZNF256 | ZNF256 | 2853 | 0.19 | 0.39 | YES |
103 | ZNF45 | ZNF45 | ZNF45 | 2861 | 0.19 | 0.4 | YES |
104 | ESRRG | ESRRG | ESRRG | 2868 | 0.19 | 0.4 | YES |
105 | ZNF92 | ZNF92 | ZNF92 | 2906 | 0.19 | 0.4 | YES |
106 | ZFP112 | ZFP112 | ZFP112 | 2920 | 0.19 | 0.4 | YES |
107 | ZNF33A | ZNF33A | ZNF33A | 2921 | 0.19 | 0.41 | YES |
108 | ZNF264 | ZNF264 | ZNF264 | 2930 | 0.18 | 0.41 | YES |
109 | ZNF334 | ZNF334 | ZNF334 | 2958 | 0.18 | 0.41 | YES |
110 | ZNF430 | ZNF430 | ZNF430 | 2977 | 0.18 | 0.42 | YES |
111 | ZNF607 | ZNF607 | ZNF607 | 2997 | 0.18 | 0.42 | YES |
112 | ZNF10 | ZNF10 | ZNF10 | 3002 | 0.18 | 0.42 | YES |
113 | ZNF544 | ZNF544 | ZNF544 | 3013 | 0.18 | 0.42 | YES |
114 | HNF4G | HNF4G | HNF4G | 3033 | 0.18 | 0.43 | YES |
115 | ZNF496 | ZNF496 | ZNF496 | 3063 | 0.18 | 0.43 | YES |
116 | ZNF615 | ZNF615 | ZNF615 | 3083 | 0.18 | 0.43 | YES |
117 | ZFP1 | ZFP1 | ZFP1 | 3084 | 0.18 | 0.43 | YES |
118 | ZNF606 | ZNF606 | ZNF606 | 3097 | 0.18 | 0.44 | YES |
119 | ZNF235 | ZNF235 | ZNF235 | 3113 | 0.18 | 0.44 | YES |
120 | ZNF569 | ZNF569 | ZNF569 | 3133 | 0.17 | 0.44 | YES |
121 | ZNF614 | ZNF614 | ZNF614 | 3140 | 0.17 | 0.44 | YES |
122 | MED27 | MED27 | MED27 | 3148 | 0.17 | 0.45 | YES |
123 | ZNF584 | ZNF584 | ZNF584 | 3185 | 0.17 | 0.45 | YES |
124 | ZNF227 | ZNF227 | ZNF227 | 3192 | 0.17 | 0.45 | YES |
125 | ZNF155 | ZNF155 | ZNF155 | 3194 | 0.17 | 0.45 | YES |
126 | ZNF214 | ZNF214 | ZNF214 | 3201 | 0.17 | 0.46 | YES |
127 | ZNF224 | ZNF224 | ZNF224 | 3284 | 0.17 | 0.46 | YES |
128 | ZNF564 | ZNF564 | ZNF564 | 3290 | 0.17 | 0.46 | YES |
129 | ZNF561 | ZNF561 | ZNF561 | 3292 | 0.17 | 0.46 | YES |
130 | ZNF559 | ZNF559 | ZNF559 | 3317 | 0.16 | 0.46 | YES |
131 | ZNF567 | ZNF567 | ZNF567 | 3329 | 0.16 | 0.46 | YES |
132 | ZNF20 | ZNF20 | ZNF20 | 3334 | 0.16 | 0.47 | YES |
133 | ZNF546 | ZNF546 | ZNF546 | 3341 | 0.16 | 0.47 | YES |
134 | ZNF226 | ZNF226 | ZNF226 | 3346 | 0.16 | 0.47 | YES |
135 | MYC | MYC | MYC | 3359 | 0.16 | 0.48 | YES |
136 | RXRA | RXRA | RXRA | 3387 | 0.16 | 0.48 | YES |
137 | ZNF543 | ZNF543 | ZNF543 | 3451 | 0.16 | 0.48 | YES |
138 | ZNF611 | ZNF611 | ZNF611 | 3504 | 0.16 | 0.48 | YES |
139 | WWTR1 | WWTR1 | WWTR1 | 3507 | 0.16 | 0.48 | YES |
140 | ZNF141 | ZNF141 | ZNF141 | 3526 | 0.16 | 0.48 | YES |
141 | SKIL | SKIL | SKIL | 3637 | 0.15 | 0.48 | YES |
142 | ZNF599 | ZNF599 | ZNF599 | 3651 | 0.15 | 0.48 | YES |
143 | ZNF287 | ZNF287 | ZNF287 | 3715 | 0.15 | 0.48 | YES |
144 | ZNF498 | ZNF498 | ZNF498 | 3761 | 0.15 | 0.48 | YES |
145 | PPM1A | PPM1A | PPM1A | 3805 | 0.14 | 0.48 | YES |
146 | ZNF613 | ZNF613 | ZNF613 | 3815 | 0.14 | 0.48 | YES |
147 | ZNF43 | ZNF43 | ZNF43 | 3845 | 0.14 | 0.48 | YES |
148 | ZNF320 | ZNF320 | ZNF320 | 3865 | 0.14 | 0.48 | YES |
149 | SMAD7 | SMAD7 | SMAD7 | 3873 | 0.14 | 0.49 | YES |
150 | MAML1 | MAML1 | MAML1 | 3897 | 0.14 | 0.49 | YES |
151 | ZNF136 | ZNF136 | ZNF136 | 3916 | 0.14 | 0.49 | YES |
152 | ZNF655 | ZNF655 | ZNF655 | 3924 | 0.14 | 0.49 | YES |
153 | ZNF285 | ZNF285 | ZNF285 | 3933 | 0.14 | 0.5 | YES |
154 | ZNF548 | ZNF548 | ZNF548 | 3934 | 0.14 | 0.5 | YES |
155 | ZNF446 | ZNF446 | ZNF446 | 3979 | 0.14 | 0.5 | YES |
156 | ZNF250 | ZNF250 | ZNF250 | 4071 | 0.13 | 0.5 | YES |
157 | ZNF490 | ZNF490 | ZNF490 | 4085 | 0.13 | 0.5 | YES |
158 | ZNF641 | ZNF641 | ZNF641 | 4090 | 0.13 | 0.5 | YES |
159 | ZNF708 | ZNF708 | ZNF708 | 4114 | 0.13 | 0.5 | YES |
160 | ZNF154 | ZNF154 | ZNF154 | 4124 | 0.13 | 0.5 | YES |
161 | SMAD3 | SMAD3 | SMAD3 | 4130 | 0.13 | 0.5 | YES |
162 | ZNF350 | ZNF350 | ZNF350 | 4162 | 0.13 | 0.5 | YES |
163 | ZNF266 | ZNF266 | ZNF266 | 4168 | 0.13 | 0.51 | YES |
164 | ZNF514 | ZNF514 | ZNF514 | 4182 | 0.13 | 0.51 | YES |
165 | ZNF577 | ZNF577 | ZNF577 | 4279 | 0.13 | 0.51 | YES |
166 | ZNF212 | ZNF212 | ZNF212 | 4281 | 0.12 | 0.51 | YES |
167 | CDKN2B | CDKN2B | CDKN2B | 4302 | 0.12 | 0.51 | YES |
168 | TFDP1 | TFDP1 | TFDP1 | 4332 | 0.12 | 0.51 | YES |
169 | SMURF2 | SMURF2 | SMURF2 | 4422 | 0.12 | 0.51 | YES |
170 | NR1D1 | NR1D1 | NR1D1 | 4527 | 0.12 | 0.5 | YES |
171 | NR1H2 | NR1H2 | NR1H2 | 4572 | 0.12 | 0.5 | YES |
172 | MED26 | MED26 | MED26 | 4576 | 0.12 | 0.51 | YES |
173 | ZNF610 | ZNF610 | ZNF610 | 4582 | 0.12 | 0.51 | YES |
174 | ZNF317 | ZNF317 | ZNF317 | 4590 | 0.12 | 0.51 | YES |
175 | ZNF140 | ZNF140 | ZNF140 | 4649 | 0.11 | 0.51 | YES |
176 | ZNF529 | ZNF529 | ZNF529 | 4654 | 0.11 | 0.51 | YES |
177 | ZNF347 | ZNF347 | ZNF347 | 4664 | 0.11 | 0.51 | YES |
178 | NOTCH2 | NOTCH2 | NOTCH2 | 4746 | 0.11 | 0.51 | YES |
179 | ZFP90 | ZFP90 | ZFP90 | 4767 | 0.11 | 0.51 | YES |
180 | ZNF506 | ZNF506 | ZNF506 | 4805 | 0.11 | 0.51 | YES |
181 | ZNF585A | ZNF585A | ZNF585A | 4832 | 0.11 | 0.51 | YES |
182 | ZNF12 | ZNF12 | ZNF12 | 4879 | 0.11 | 0.51 | YES |
183 | ZKSCAN5 | ZKSCAN5 | ZKSCAN5 | 4905 | 0.1 | 0.51 | YES |
184 | CDK9 | CDK9 | CDK9 | 4924 | 0.1 | 0.51 | YES |
185 | ZNF600 | ZNF600 | ZNF600 | 4944 | 0.1 | 0.51 | YES |
186 | NR2F1 | NR2F1 | NR2F1 | 4986 | 0.1 | 0.51 | NO |
187 | SMARCD3 | SMARCD3 | SMARCD3 | 5031 | 0.1 | 0.51 | NO |
188 | ZNF282 | ZNF282 | ZNF282 | 5144 | 0.1 | 0.51 | NO |
189 | PPARA | PPARA | PPARA | 5166 | 0.099 | 0.51 | NO |
190 | THRA | THRA | THRA | 5189 | 0.098 | 0.51 | NO |
191 | VDR | VDR | VDR | 5228 | 0.097 | 0.51 | NO |
192 | ZNF167 | ZNF167 | ZNF167 | 5306 | 0.095 | 0.5 | NO |
193 | ZNF563 | ZNF563 | ZNF563 | 5308 | 0.095 | 0.51 | NO |
194 | NR5A1 | NR5A1 | NR5A1 | 5385 | 0.093 | 0.5 | NO |
195 | ZNF398 | ZNF398 | ZNF398 | 5410 | 0.092 | 0.5 | NO |
196 | ZNF23 | ZNF23 | ZNF23 | 5503 | 0.09 | 0.5 | NO |
197 | ZNF434 | ZNF434 | ZNF434 | 5589 | 0.087 | 0.5 | NO |
198 | ZNF343 | ZNF343 | ZNF343 | 5619 | 0.086 | 0.5 | NO |
199 | E2F5 | E2F5 | E2F5 | 5635 | 0.086 | 0.5 | NO |
200 | ZNF3 | ZNF3 | ZNF3 | 5682 | 0.084 | 0.5 | NO |
201 | TGIF2 | TGIF2 | TGIF2 | 5734 | 0.083 | 0.5 | NO |
202 | MED6 | MED6 | MED6 | 5775 | 0.082 | 0.5 | NO |
203 | MED12 | MED12 | MED12 | 5779 | 0.082 | 0.5 | NO |
204 | TRIM28 | TRIM28 | TRIM28 | 5812 | 0.082 | 0.5 | NO |
205 | NR1I2 | NR1I2 | NR1I2 | 5817 | 0.082 | 0.5 | NO |
206 | ZNF500 | ZNF500 | ZNF500 | 5845 | 0.081 | 0.5 | NO |
207 | ZNF620 | ZNF620 | ZNF620 | 5924 | 0.079 | 0.5 | NO |
208 | NR2C2AP | NR2C2AP | NR2C2AP | 5935 | 0.079 | 0.5 | NO |
209 | ZNF101 | ZNF101 | ZNF101 | 5939 | 0.079 | 0.5 | NO |
210 | ZNF571 | ZNF571 | ZNF571 | 5973 | 0.078 | 0.5 | NO |
211 | ZNF197 | ZNF197 | ZNF197 | 6003 | 0.077 | 0.5 | NO |
212 | ZNF619 | ZNF619 | ZNF619 | 6005 | 0.077 | 0.5 | NO |
213 | ZNF519 | ZNF519 | ZNF519 | 6022 | 0.076 | 0.5 | NO |
214 | ZNF433 | ZNF433 | ZNF433 | 6034 | 0.076 | 0.5 | NO |
215 | UBE2D1 | UBE2D1 | UBE2D1 | 6158 | 0.073 | 0.49 | NO |
216 | ZNF263 | ZNF263 | ZNF263 | 6226 | 0.072 | 0.49 | NO |
217 | CREBBP | CREBBP | CREBBP | 6359 | 0.069 | 0.48 | NO |
218 | ZNF394 | ZNF394 | ZNF394 | 6397 | 0.068 | 0.48 | NO |
219 | MED10 | MED10 | MED10 | 6418 | 0.068 | 0.48 | NO |
220 | ZNF480 | ZNF480 | ZNF480 | 6431 | 0.068 | 0.48 | NO |
221 | ZNF597 | ZNF597 | ZNF597 | 6515 | 0.066 | 0.48 | NO |
222 | ZNF337 | ZNF337 | ZNF337 | 6600 | 0.064 | 0.48 | NO |
223 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 6607 | 0.064 | 0.48 | NO |
224 | ZNF200 | ZNF200 | ZNF200 | 6639 | 0.063 | 0.48 | NO |
225 | ZNF286A | ZNF286A | ZNF286A | 6658 | 0.063 | 0.48 | NO |
226 | ZNF19 | ZNF19 | ZNF19 | 6686 | 0.062 | 0.48 | NO |
227 | ZNF621 | ZNF621 | ZNF621 | 6707 | 0.062 | 0.48 | NO |
228 | ZNF589 | ZNF589 | ZNF589 | 6723 | 0.061 | 0.48 | NO |
229 | ZNF555 | ZNF555 | ZNF555 | 6859 | 0.058 | 0.47 | NO |
230 | TRIM33 | TRIM33 | TRIM33 | 6875 | 0.058 | 0.47 | NO |
231 | NR4A1 | NR4A1 | NR4A1 | 7104 | 0.054 | 0.46 | NO |
232 | ZNF205 | ZNF205 | ZNF205 | 7169 | 0.052 | 0.46 | NO |
233 | NR3C1 | NR3C1 | NR3C1 | 7182 | 0.052 | 0.46 | NO |
234 | SP1 | SP1 | SP1 | 7467 | 0.046 | 0.44 | NO |
235 | ZNF493 | ZNF493 | ZNF493 | 7512 | 0.045 | 0.44 | NO |
236 | CCNT2 | CCNT2 | CCNT2 | 7569 | 0.044 | 0.44 | NO |
237 | CDK8 | CDK8 | CDK8 | 7595 | 0.043 | 0.44 | NO |
238 | SMAD2 | SMAD2 | SMAD2 | 7626 | 0.043 | 0.44 | NO |
239 | NR5A2 | NR5A2 | NR5A2 | 7677 | 0.042 | 0.43 | NO |
240 | ZNF202 | ZNF202 | ZNF202 | 7767 | 0.04 | 0.43 | NO |
241 | NCOR2 | NCOR2 | NCOR2 | 7975 | 0.036 | 0.42 | NO |
242 | YAP1 | YAP1 | YAP1 | 8051 | 0.034 | 0.42 | NO |
243 | SNW1 | SNW1 | SNW1 | 8065 | 0.034 | 0.42 | NO |
244 | TEAD1 | TEAD1 | TEAD1 | 8082 | 0.034 | 0.42 | NO |
245 | ZNF605 | ZNF605 | ZNF605 | 8087 | 0.034 | 0.42 | NO |
246 | ESR2 | ESR2 | ESR2 | 8119 | 0.033 | 0.41 | NO |
247 | UBE2D3 | UBE2D3 | UBE2D3 | 8177 | 0.032 | 0.41 | NO |
248 | ZNF184 | ZNF184 | ZNF184 | 8191 | 0.032 | 0.41 | NO |
249 | ZNF28 | ZNF28 | ZNF28 | 8276 | 0.03 | 0.41 | NO |
250 | RXRG | RXRG | RXRG | 8365 | 0.029 | 0.4 | NO |
251 | ZNF468 | ZNF468 | ZNF468 | 8681 | 0.023 | 0.38 | NO |
252 | ZNF311 | ZNF311 | ZNF311 | 8722 | 0.022 | 0.38 | NO |
253 | UBA52 | UBA52 | UBA52 | 8799 | 0.021 | 0.38 | NO |
254 | ZNF100 | ZNF100 | ZNF100 | 8839 | 0.02 | 0.38 | NO |
255 | ZNF160 | ZNF160 | ZNF160 | 8876 | 0.019 | 0.38 | NO |
256 | NCOA6 | NCOA6 | NCOA6 | 9113 | 0.014 | 0.36 | NO |
257 | ZNF208 | ZNF208 | ZNF208 | 9136 | 0.014 | 0.36 | NO |
258 | ZNF528 | ZNF528 | ZNF528 | 9189 | 0.013 | 0.36 | NO |
259 | ZNF439 | ZNF439 | ZNF439 | 9190 | 0.013 | 0.36 | NO |
260 | NCOR1 | NCOR1 | NCOR1 | 9278 | 0.011 | 0.35 | NO |
261 | ZNF552 | ZNF552 | ZNF552 | 9320 | 0.01 | 0.35 | NO |
262 | MED31 | MED31 | MED31 | 9354 | 0.0097 | 0.35 | NO |
263 | PRIC285 | PRIC285 | PRIC285 | 9390 | 0.0089 | 0.35 | NO |
264 | ZNF445 | ZNF445 | ZNF445 | 9441 | 0.008 | 0.34 | NO |
265 | NOTCH4 | NOTCH4 | NOTCH4 | 9453 | 0.0079 | 0.34 | NO |
266 | MED7 | MED7 | MED7 | 9608 | 0.0048 | 0.34 | NO |
267 | MED25 | MED25 | MED25 | 9642 | 0.0043 | 0.33 | NO |
268 | NRBF2 | NRBF2 | NRBF2 | 9655 | 0.004 | 0.33 | NO |
269 | ZNF2 | ZNF2 | ZNF2 | 9657 | 0.004 | 0.33 | NO |
270 | ZNF436 | ZNF436 | ZNF436 | 9687 | 0.0035 | 0.33 | NO |
271 | MEN1 | MEN1 | MEN1 | 9752 | 0.0026 | 0.33 | NO |
272 | ZNF26 | ZNF26 | ZNF26 | 9905 | -0.000059 | 0.32 | NO |
273 | ZNF213 | ZNF213 | ZNF213 | 9911 | -0.00018 | 0.32 | NO |
274 | TGS1 | TGS1 | TGS1 | 10010 | -0.0022 | 0.31 | NO |
275 | ZNF431 | ZNF431 | ZNF431 | 10072 | -0.0032 | 0.31 | NO |
276 | SKI | SKI | SKI | 10111 | -0.0041 | 0.31 | NO |
277 | MED14 | MED14 | MED14 | 10255 | -0.0069 | 0.3 | NO |
278 | ZNF18 | ZNF18 | ZNF18 | 10462 | -0.011 | 0.29 | NO |
279 | E2F4 | E2F4 | E2F4 | 10515 | -0.012 | 0.29 | NO |
280 | USP9X | USP9X | USP9X | 10561 | -0.012 | 0.28 | NO |
281 | MED23 | MED23 | MED23 | 10635 | -0.014 | 0.28 | NO |
282 | NCOA1 | NCOA1 | NCOA1 | 10657 | -0.014 | 0.28 | NO |
283 | MED8 | MED8 | MED8 | 10682 | -0.014 | 0.28 | NO |
284 | MED15 | MED15 | MED15 | 11008 | -0.021 | 0.26 | NO |
285 | SMAD4 | SMAD4 | SMAD4 | 11033 | -0.021 | 0.26 | NO |
286 | ZNF517 | ZNF517 | ZNF517 | 11093 | -0.022 | 0.26 | NO |
287 | JUNB | JUNB | JUNB | 11167 | -0.024 | 0.25 | NO |
288 | KAT2A | KAT2A | KAT2A | 11248 | -0.026 | 0.25 | NO |
289 | NR6A1 | NR6A1 | NR6A1 | 11315 | -0.027 | 0.24 | NO |
290 | MED17 | MED17 | MED17 | 11366 | -0.028 | 0.24 | NO |
291 | ZNF649 | ZNF649 | ZNF649 | 11393 | -0.028 | 0.24 | NO |
292 | RBL1 | RBL1 | RBL1 | 11525 | -0.031 | 0.23 | NO |
293 | NR2F6 | NR2F6 | NR2F6 | 11621 | -0.033 | 0.23 | NO |
294 | MED16 | MED16 | MED16 | 11742 | -0.035 | 0.22 | NO |
295 | NR4A2 | NR4A2 | NR4A2 | 11996 | -0.041 | 0.21 | NO |
296 | RBPJ | RBPJ | RBPJ | 12062 | -0.042 | 0.21 | NO |
297 | NCOA3 | NCOA3 | NCOA3 | 12365 | -0.049 | 0.19 | NO |
298 | MED4 | MED4 | MED4 | 12378 | -0.049 | 0.19 | NO |
299 | ZNF643 | ZNF643 | ZNF643 | 12457 | -0.051 | 0.19 | NO |
300 | HNF4A | HNF4A | HNF4A | 12815 | -0.059 | 0.17 | NO |
301 | MED30 | MED30 | MED30 | 12840 | -0.06 | 0.17 | NO |
302 | ZNF98 | ZNF98 | ZNF98 | 12983 | -0.063 | 0.16 | NO |
303 | CTGF | CTGF | CTGF | 13038 | -0.065 | 0.16 | NO |
304 | ZNF300 | ZNF300 | ZNF300 | 13055 | -0.065 | 0.16 | NO |
305 | MED1 | MED1 | MED1 | 13078 | -0.066 | 0.16 | NO |
306 | NR2E3 | NR2E3 | NR2E3 | 13138 | -0.068 | 0.16 | NO |
307 | RXRB | RXRB | RXRB | 13278 | -0.071 | 0.15 | NO |
308 | MAMLD1 | MAMLD1 | MAMLD1 | 13358 | -0.073 | 0.15 | NO |
309 | ZKSCAN4 | ZKSCAN4 | ZKSCAN4 | 13416 | -0.075 | 0.14 | NO |
310 | ZKSCAN3 | ZKSCAN3 | ZKSCAN3 | 13815 | -0.086 | 0.12 | NO |
311 | CCNC | CCNC | CCNC | 13829 | -0.086 | 0.12 | NO |
312 | NOTCH3 | NOTCH3 | NOTCH3 | 14004 | -0.092 | 0.12 | NO |
313 | HDAC1 | HDAC1 | HDAC1 | 14125 | -0.096 | 0.11 | NO |
314 | NRBP1 | NRBP1 | NRBP1 | 14201 | -0.098 | 0.11 | NO |
315 | NR1I3 | NR1I3 | NR1I3 | 14245 | -0.1 | 0.11 | NO |
316 | RARA | RARA | RARA | 14526 | -0.11 | 0.094 | NO |
317 | RPS27A | RPS27A | RPS27A | 14536 | -0.11 | 0.095 | NO |
318 | PARP1 | PARP1 | PARP1 | 14731 | -0.12 | 0.086 | NO |
319 | ZNF267 | ZNF267 | ZNF267 | 14774 | -0.12 | 0.086 | NO |
320 | ESRRA | ESRRA | ESRRA | 14797 | -0.12 | 0.087 | NO |
321 | ESR1 | ESR1 | ESR1 | 14836 | -0.12 | 0.087 | NO |
322 | ZNF492 | ZNF492 | ZNF492 | 14916 | -0.13 | 0.085 | NO |
323 | NR0B1 | NR0B1 | NR0B1 | 15174 | -0.14 | 0.073 | NO |
324 | MED24 | MED24 | MED24 | 15240 | -0.14 | 0.072 | NO |
325 | NPPA | NPPA | NPPA | 15278 | -0.15 | 0.073 | NO |
326 | KAT2B | KAT2B | KAT2B | 15316 | -0.15 | 0.074 | NO |
327 | NR1H3 | NR1H3 | NR1H3 | 15401 | -0.15 | 0.072 | NO |
328 | ZNF415 | ZNF415 | ZNF415 | 15434 | -0.16 | 0.073 | NO |
329 | RUNX2 | RUNX2 | RUNX2 | 15493 | -0.16 | 0.073 | NO |
330 | ZNF624 | ZNF624 | ZNF624 | 15506 | -0.16 | 0.075 | NO |
331 | TGIF1 | TGIF1 | TGIF1 | 15560 | -0.16 | 0.075 | NO |
332 | PPARG | PPARG | PPARG | 15567 | -0.16 | 0.078 | NO |
333 | SERPINE1 | SERPINE1 | SERPINE1 | 15671 | -0.17 | 0.075 | NO |
334 | MAML2 | MAML2 | MAML2 | 15685 | -0.17 | 0.078 | NO |
335 | TEAD4 | TEAD4 | TEAD4 | 15736 | -0.18 | 0.078 | NO |
336 | PPARD | PPARD | PPARD | 16122 | -0.21 | 0.06 | NO |
337 | MED20 | MED20 | MED20 | 16234 | -0.22 | 0.058 | NO |
338 | ZNF642 | ZNF642 | ZNF642 | 17021 | -0.32 | 0.019 | NO |
339 | RORC | RORC | RORC | 17443 | -0.42 | 0.0026 | NO |
340 | NR0B2 | NR0B2 | NR0B2 | 17701 | -0.68 | 0.00092 | 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 HEDGEHOG SIGNALING PATHWAY.

Figure S24. 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 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 | FGF9 | FGF9 | FGF9 | 556 | 0.45 | 0.071 | YES |
2 | FGF2 | FGF2 | FGF2 | 905 | 0.38 | 0.14 | YES |
3 | FGF8 | FGF8 | FGF8 | 1036 | 0.36 | 0.21 | YES |
4 | FGF22 | FGF22 | FGF22 | 1131 | 0.35 | 0.29 | YES |
5 | FGF18 | FGF18 | FGF18 | 1157 | 0.34 | 0.36 | YES |
6 | GAB2 | GAB2 | GAB2 | 2654 | 0.2 | 0.32 | YES |
7 | FGFR3 | FGFR3 | FGFR3 | 2757 | 0.2 | 0.36 | YES |
8 | ZMYM2 | ZMYM2 | ZMYM2 | 3307 | 0.16 | 0.37 | YES |
9 | KRAS | KRAS | KRAS | 3807 | 0.14 | 0.37 | YES |
10 | FGF20 | FGF20 | FGF20 | 3828 | 0.14 | 0.41 | YES |
11 | FGFR1 | FGFR1 | FGFR1 | 3904 | 0.14 | 0.43 | YES |
12 | FRS2 | FRS2 | FRS2 | 3948 | 0.14 | 0.46 | YES |
13 | FGFR2 | FGFR2 | FGFR2 | 4135 | 0.13 | 0.48 | YES |
14 | TRIM24 | TRIM24 | TRIM24 | 4211 | 0.13 | 0.51 | YES |
15 | PLCG1 | PLCG1 | PLCG1 | 4888 | 0.11 | 0.49 | NO |
16 | CUX1 | CUX1 | CUX1 | 6576 | 0.064 | 0.41 | NO |
17 | FGFR1OP2 | FGFR1OP2 | FGFR1OP2 | 6742 | 0.061 | 0.42 | NO |
18 | PIK3CA | PIK3CA | PIK3CA | 6863 | 0.058 | 0.42 | NO |
19 | CPSF6 | CPSF6 | CPSF6 | 6894 | 0.057 | 0.43 | NO |
20 | FGFR1OP | FGFR1OP | FGFR1OP | 7599 | 0.043 | 0.4 | NO |
21 | BCR | BCR | BCR | 7895 | 0.038 | 0.4 | NO |
22 | SOS1 | SOS1 | SOS1 | 8256 | 0.03 | 0.38 | NO |
23 | PIK3R1 | PIK3R1 | PIK3R1 | 8934 | 0.018 | 0.35 | NO |
24 | GAB1 | GAB1 | GAB1 | 8968 | 0.017 | 0.35 | NO |
25 | FGF1 | FGF1 | FGF1 | 9002 | 0.016 | 0.35 | NO |
26 | MYO18A | MYO18A | MYO18A | 9344 | 0.0099 | 0.34 | NO |
27 | FGFR4 | FGFR4 | FGFR4 | 10404 | -0.0094 | 0.28 | NO |
28 | FGF17 | FGF17 | FGF17 | 10770 | -0.016 | 0.26 | NO |
29 | STAT1 | STAT1 | STAT1 | 11096 | -0.022 | 0.25 | NO |
30 | FGF7 | FGF7 | FGF7 | 12314 | -0.048 | 0.19 | NO |
31 | GRB2 | GRB2 | GRB2 | 12320 | -0.048 | 0.2 | NO |
32 | HRAS | HRAS | HRAS | 13072 | -0.066 | 0.17 | NO |
33 | STAT3 | STAT3 | STAT3 | 13177 | -0.068 | 0.18 | NO |
34 | STAT5B | STAT5B | STAT5B | 13552 | -0.079 | 0.18 | NO |
35 | STAT5A | STAT5A | STAT5A | 14755 | -0.12 | 0.14 | NO |
36 | NRAS | NRAS | NRAS | 14911 | -0.13 | 0.16 | 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 TASTE TRANSDUCTION.

Figure S26. 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 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 | NKD1 | NKD1 | NKD1 | 50 | 0.76 | 0.14 | YES |
2 | WIF1 | WIF1 | WIF1 | 141 | 0.64 | 0.26 | YES |
3 | DACT1 | DACT1 | DACT1 | 181 | 0.6 | 0.37 | YES |
4 | AXIN2 | AXIN2 | AXIN2 | 451 | 0.48 | 0.45 | YES |
5 | DKK3 | DKK3 | DKK3 | 934 | 0.38 | 0.5 | YES |
6 | AKT3 | AKT3 | AKT3 | 2072 | 0.25 | 0.48 | YES |
7 | SFRP1 | SFRP1 | SFRP1 | 2599 | 0.21 | 0.49 | YES |
8 | NKD2 | NKD2 | NKD2 | 2726 | 0.2 | 0.52 | YES |
9 | ANKRD6 | ANKRD6 | ANKRD6 | 2742 | 0.2 | 0.56 | YES |
10 | CXXC4 | CXXC4 | CXXC4 | 3499 | 0.16 | 0.54 | YES |
11 | AKT2 | AKT2 | AKT2 | 3774 | 0.14 | 0.56 | YES |
12 | CTNNB1 | CTNNB1 | CTNNB1 | 3968 | 0.14 | 0.57 | YES |
13 | FRAT1 | FRAT1 | FRAT1 | 4293 | 0.12 | 0.58 | YES |
14 | APC | APC | APC | 4952 | 0.1 | 0.56 | NO |
15 | DKK1 | DKK1 | DKK1 | 5883 | 0.08 | 0.52 | NO |
16 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 6021 | 0.076 | 0.53 | NO |
17 | GSK3A | GSK3A | GSK3A | 6082 | 0.075 | 0.54 | NO |
18 | GSK3B | GSK3B | GSK3B | 6428 | 0.068 | 0.54 | NO |
19 | PIN1 | PIN1 | PIN1 | 7351 | 0.048 | 0.49 | NO |
20 | PTPRA | PTPRA | PTPRA | 7648 | 0.042 | 0.48 | NO |
21 | SENP2 | SENP2 | SENP2 | 7916 | 0.037 | 0.48 | NO |
22 | AXIN1 | AXIN1 | AXIN1 | 7987 | 0.036 | 0.48 | NO |
23 | AKT1 | AKT1 | AKT1 | 8174 | 0.032 | 0.47 | NO |
24 | CBY1 | CBY1 | CBY1 | 9077 | 0.015 | 0.43 | NO |
25 | PSEN1 | PSEN1 | PSEN1 | 9505 | 0.007 | 0.4 | NO |
26 | LRP1 | LRP1 | LRP1 | 10065 | -0.0031 | 0.37 | NO |
27 | DVL1 | DVL1 | DVL1 | 10092 | -0.0037 | 0.37 | NO |
28 | FSTL1 | FSTL1 | FSTL1 | 10709 | -0.015 | 0.34 | NO |
29 | MVP | MVP | MVP | 11240 | -0.025 | 0.31 | NO |
30 | RPSA | RPSA | RPSA | 11705 | -0.035 | 0.29 | NO |
31 | DKK2 | DKK2 | DKK2 | 16361 | -0.24 | 0.077 | 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 BASAL CELL CARCINOMA.

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

Table S15. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | WIF1 | WIF1 | WIF1 | 141 | 0.64 | 0.2 | YES |
2 | LEF1 | LEF1 | LEF1 | 228 | 0.57 | 0.38 | YES |
3 | TLE1 | TLE1 | TLE1 | 2318 | 0.23 | 0.34 | YES |
4 | MYC | MYC | MYC | 3359 | 0.16 | 0.33 | YES |
5 | CTNNB1 | CTNNB1 | CTNNB1 | 3968 | 0.14 | 0.34 | YES |
6 | CCND1 | CCND1 | CCND1 | 4244 | 0.13 | 0.37 | YES |
7 | FRAT1 | FRAT1 | FRAT1 | 4293 | 0.12 | 0.4 | YES |
8 | BTRC | BTRC | BTRC | 4606 | 0.11 | 0.42 | YES |
9 | APC | APC | APC | 4952 | 0.1 | 0.44 | YES |
10 | FZD1 | FZD1 | FZD1 | 5136 | 0.1 | 0.46 | YES |
11 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 6021 | 0.076 | 0.44 | YES |
12 | CREBBP | CREBBP | CREBBP | 6359 | 0.069 | 0.44 | YES |
13 | GSK3B | GSK3B | GSK3B | 6428 | 0.068 | 0.46 | YES |
14 | NLK | NLK | NLK | 6460 | 0.067 | 0.48 | YES |
15 | WNT1 | WNT1 | WNT1 | 6759 | 0.061 | 0.48 | YES |
16 | AXIN1 | AXIN1 | AXIN1 | 7987 | 0.036 | 0.42 | NO |
17 | MAP3K7 | MAP3K7 | MAP3K7 | 9207 | 0.012 | 0.36 | NO |
18 | PPP2CA | PPP2CA | PPP2CA | 9266 | 0.011 | 0.36 | NO |
19 | CSNK1D | CSNK1D | CSNK1D | 9298 | 0.011 | 0.36 | NO |
20 | CTBP1 | CTBP1 | CTBP1 | 9559 | 0.0058 | 0.35 | NO |
21 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 9690 | 0.0035 | 0.34 | NO |
22 | DVL1 | DVL1 | DVL1 | 10092 | -0.0037 | 0.32 | NO |
23 | TAB1 | TAB1 | TAB1 | 10752 | -0.016 | 0.29 | NO |
24 | SMAD4 | SMAD4 | SMAD4 | 11033 | -0.021 | 0.28 | NO |
25 | HDAC1 | HDAC1 | HDAC1 | 14125 | -0.096 | 0.14 | NO |
26 | PPARD | PPARD | PPARD | 16122 | -0.21 | 0.09 | 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: BIOCARTA NO1 PATHWAY.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 | ETV4 | ETV4 | ETV4 | 46 | 0.78 | 0.16 | YES |
2 | BRSK2 | BRSK2 | BRSK2 | 565 | 0.45 | 0.22 | YES |
3 | BRSK1 | BRSK1 | BRSK1 | 600 | 0.44 | 0.31 | YES |
4 | MAPT | MAPT | MAPT | 760 | 0.41 | 0.39 | YES |
5 | MYC | MYC | MYC | 3359 | 0.16 | 0.28 | NO |
6 | MST4 | MST4 | MST4 | 3503 | 0.16 | 0.3 | NO |
7 | MARK4 | MARK4 | MARK4 | 4592 | 0.12 | 0.26 | NO |
8 | SMARCD3 | SMARCD3 | SMARCD3 | 5031 | 0.1 | 0.26 | NO |
9 | TP53 | TP53 | TP53 | 5328 | 0.094 | 0.26 | NO |
10 | TSC1 | TSC1 | TSC1 | 5857 | 0.08 | 0.25 | NO |
11 | GSK3B | GSK3B | GSK3B | 6428 | 0.068 | 0.23 | NO |
12 | PRKACA | PRKACA | PRKACA | 6541 | 0.065 | 0.24 | NO |
13 | CDC37 | CDC37 | CDC37 | 6562 | 0.065 | 0.25 | NO |
14 | PRKAG1 | PRKAG1 | PRKAG1 | 6771 | 0.06 | 0.25 | NO |
15 | PRKAB1 | PRKAB1 | PRKAB1 | 6800 | 0.06 | 0.26 | NO |
16 | AKT1S1 | AKT1S1 | AKT1S1 | 7054 | 0.054 | 0.26 | NO |
17 | SIK1 | SIK1 | SIK1 | 7065 | 0.054 | 0.27 | NO |
18 | STK11IP | STK11IP | STK11IP | 7275 | 0.05 | 0.27 | NO |
19 | MTOR | MTOR | MTOR | 7668 | 0.042 | 0.25 | NO |
20 | STK11 | STK11 | STK11 | 8302 | 0.03 | 0.22 | NO |
21 | YWHAG | YWHAG | YWHAG | 8349 | 0.029 | 0.23 | NO |
22 | TSC2 | TSC2 | TSC2 | 8865 | 0.019 | 0.2 | NO |
23 | SIK3 | SIK3 | SIK3 | 9237 | 0.012 | 0.18 | NO |
24 | YWHAB | YWHAB | YWHAB | 9651 | 0.004 | 0.16 | NO |
25 | SIK2 | SIK2 | SIK2 | 10562 | -0.012 | 0.11 | NO |
26 | RPTOR | RPTOR | RPTOR | 10582 | -0.013 | 0.11 | NO |
27 | MARK2 | MARK2 | MARK2 | 10827 | -0.018 | 0.1 | NO |
28 | YWHAE | YWHAE | YWHAE | 10875 | -0.018 | 0.1 | NO |
29 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 10908 | -0.019 | 0.11 | NO |
30 | YWHAZ | YWHAZ | YWHAZ | 10951 | -0.02 | 0.11 | NO |
31 | PRKAA1 | PRKAA1 | PRKAA1 | 10984 | -0.02 | 0.11 | NO |
32 | SMAD4 | SMAD4 | SMAD4 | 11033 | -0.021 | 0.11 | NO |
33 | MAP2 | MAP2 | MAP2 | 11502 | -0.03 | 0.093 | NO |
34 | YWHAQ | YWHAQ | YWHAQ | 11688 | -0.034 | 0.09 | NO |
35 | CRTC2 | CRTC2 | CRTC2 | 11800 | -0.037 | 0.091 | NO |
36 | CAB39 | CAB39 | CAB39 | 11882 | -0.038 | 0.094 | NO |
37 | PSEN2 | PSEN2 | PSEN2 | 13057 | -0.066 | 0.042 | NO |
38 | MLST8 | MLST8 | MLST8 | 13289 | -0.071 | 0.043 | NO |
39 | YWHAH | YWHAH | YWHAH | 13419 | -0.075 | 0.052 | NO |
40 | CREB1 | CREB1 | CREB1 | 13547 | -0.078 | 0.061 | NO |
41 | SFN | SFN | SFN | 13700 | -0.083 | 0.069 | NO |
42 | EZR | EZR | EZR | 13755 | -0.084 | 0.084 | NO |
43 | STRADA | STRADA | STRADA | 13957 | -0.09 | 0.091 | NO |
44 | PRKAA2 | PRKAA2 | PRKAA2 | 14706 | -0.12 | 0.074 | NO |
45 | ESR1 | ESR1 | ESR1 | 14836 | -0.12 | 0.092 | NO |
46 | CTSD | CTSD | CTSD | 15256 | -0.14 | 0.099 | NO |
47 | STRADB | STRADB | STRADB | 15975 | -0.2 | 0.099 | 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: BIOCARTA CHREBP2 PATHWAY.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S17. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FGF9 | FGF9 | FGF9 | 556 | 0.45 | 0.095 | YES |
2 | FGF2 | FGF2 | FGF2 | 905 | 0.38 | 0.18 | YES |
3 | FGF8 | FGF8 | FGF8 | 1036 | 0.36 | 0.28 | YES |
4 | FGF22 | FGF22 | FGF22 | 1131 | 0.35 | 0.37 | YES |
5 | FGF18 | FGF18 | FGF18 | 1157 | 0.34 | 0.46 | YES |
6 | FGFR3 | FGFR3 | FGFR3 | 2757 | 0.2 | 0.43 | YES |
7 | KRAS | KRAS | KRAS | 3807 | 0.14 | 0.41 | YES |
8 | FGF20 | FGF20 | FGF20 | 3828 | 0.14 | 0.45 | YES |
9 | FGFR1 | FGFR1 | FGFR1 | 3904 | 0.14 | 0.48 | YES |
10 | FRS2 | FRS2 | FRS2 | 3948 | 0.14 | 0.52 | YES |
11 | FGFR2 | FGFR2 | FGFR2 | 4135 | 0.13 | 0.55 | YES |
12 | SOS1 | SOS1 | SOS1 | 8256 | 0.03 | 0.32 | NO |
13 | MAPK1 | MAPK1 | MAPK1 | 8430 | 0.027 | 0.32 | NO |
14 | FGF1 | FGF1 | FGF1 | 9002 | 0.016 | 0.29 | NO |
15 | YWHAB | YWHAB | YWHAB | 9651 | 0.004 | 0.26 | NO |
16 | KL | KL | KL | 9677 | 0.0037 | 0.26 | NO |
17 | MAP2K2 | MAP2K2 | MAP2K2 | 9851 | 0.0009 | 0.25 | NO |
18 | RAF1 | RAF1 | RAF1 | 9938 | -0.0008 | 0.24 | NO |
19 | MAP2K1 | MAP2K1 | MAP2K1 | 9967 | -0.0014 | 0.24 | NO |
20 | CDK1 | CDK1 | CDK1 | 10143 | -0.0046 | 0.23 | NO |
21 | FGFR4 | FGFR4 | FGFR4 | 10404 | -0.0094 | 0.22 | NO |
22 | FGF17 | FGF17 | FGF17 | 10770 | -0.016 | 0.2 | NO |
23 | FGF7 | FGF7 | FGF7 | 12314 | -0.048 | 0.13 | NO |
24 | GRB2 | GRB2 | GRB2 | 12320 | -0.048 | 0.14 | NO |
25 | MAPK3 | MAPK3 | MAPK3 | 12350 | -0.048 | 0.16 | NO |
26 | HRAS | HRAS | HRAS | 13072 | -0.066 | 0.13 | NO |
27 | FRS3 | FRS3 | FRS3 | 14456 | -0.11 | 0.086 | NO |
28 | NRAS | NRAS | NRAS | 14911 | -0.13 | 0.096 | NO |
29 | KLB | KLB | KLB | 16228 | -0.22 | 0.084 | 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: BIOCARTA WNT PATHWAY.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA WNT 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 | WNT4 | WNT4 | WNT4 | 158 | 0.62 | 0.048 | YES |
2 | LEF1 | LEF1 | LEF1 | 228 | 0.57 | 0.096 | YES |
3 | GLI1 | GLI1 | GLI1 | 235 | 0.57 | 0.15 | YES |
4 | SHH | SHH | SHH | 352 | 0.52 | 0.19 | YES |
5 | AXIN2 | AXIN2 | AXIN2 | 451 | 0.48 | 0.23 | YES |
6 | SMO | SMO | SMO | 505 | 0.46 | 0.27 | YES |
7 | BMP4 | BMP4 | BMP4 | 748 | 0.41 | 0.29 | YES |
8 | FZD10 | FZD10 | FZD10 | 858 | 0.39 | 0.32 | YES |
9 | PTCH2 | PTCH2 | PTCH2 | 937 | 0.38 | 0.35 | YES |
10 | TCF7 | TCF7 | TCF7 | 1326 | 0.32 | 0.36 | YES |
11 | FZD9 | FZD9 | FZD9 | 1344 | 0.32 | 0.38 | YES |
12 | WNT10B | WNT10B | WNT10B | 1420 | 0.31 | 0.41 | YES |
13 | APC2 | APC2 | APC2 | 1448 | 0.3 | 0.43 | YES |
14 | PTCH1 | PTCH1 | PTCH1 | 1572 | 0.29 | 0.45 | YES |
15 | WNT9A | WNT9A | WNT9A | 1586 | 0.29 | 0.48 | YES |
16 | FZD7 | FZD7 | FZD7 | 1713 | 0.28 | 0.5 | YES |
17 | GLI3 | GLI3 | GLI3 | 1726 | 0.28 | 0.52 | YES |
18 | FZD6 | FZD6 | FZD6 | 1740 | 0.27 | 0.55 | YES |
19 | GLI2 | GLI2 | GLI2 | 2584 | 0.21 | 0.52 | YES |
20 | WNT5A | WNT5A | WNT5A | 2650 | 0.2 | 0.53 | YES |
21 | WNT3 | WNT3 | WNT3 | 2669 | 0.2 | 0.55 | YES |
22 | FZD8 | FZD8 | FZD8 | 2696 | 0.2 | 0.56 | YES |
23 | HHIP | HHIP | HHIP | 2902 | 0.19 | 0.57 | YES |
24 | TCF7L2 | TCF7L2 | TCF7L2 | 2961 | 0.18 | 0.58 | YES |
25 | WNT16 | WNT16 | WNT16 | 2964 | 0.18 | 0.6 | YES |
26 | TCF7L1 | TCF7L1 | TCF7L1 | 3474 | 0.16 | 0.59 | NO |
27 | CTNNB1 | CTNNB1 | CTNNB1 | 3968 | 0.14 | 0.57 | NO |
28 | WNT2 | WNT2 | WNT2 | 4289 | 0.12 | 0.56 | NO |
29 | WNT6 | WNT6 | WNT6 | 4568 | 0.12 | 0.56 | NO |
30 | APC | APC | APC | 4952 | 0.1 | 0.55 | NO |
31 | FZD1 | FZD1 | FZD1 | 5136 | 0.1 | 0.55 | NO |
32 | TP53 | TP53 | TP53 | 5328 | 0.094 | 0.54 | NO |
33 | DVL3 | DVL3 | DVL3 | 5579 | 0.087 | 0.54 | NO |
34 | SUFU | SUFU | SUFU | 5603 | 0.087 | 0.54 | NO |
35 | WNT3A | WNT3A | WNT3A | 5652 | 0.085 | 0.55 | NO |
36 | WNT11 | WNT11 | WNT11 | 5767 | 0.083 | 0.55 | NO |
37 | WNT7B | WNT7B | WNT7B | 5999 | 0.077 | 0.54 | NO |
38 | FZD3 | FZD3 | FZD3 | 6198 | 0.072 | 0.54 | NO |
39 | GSK3B | GSK3B | GSK3B | 6428 | 0.068 | 0.53 | NO |
40 | WNT1 | WNT1 | WNT1 | 6759 | 0.061 | 0.52 | NO |
41 | AXIN1 | AXIN1 | AXIN1 | 7987 | 0.036 | 0.45 | NO |
42 | FZD5 | FZD5 | FZD5 | 8214 | 0.031 | 0.44 | NO |
43 | BMP2 | BMP2 | BMP2 | 9587 | 0.0051 | 0.36 | NO |
44 | DVL1 | DVL1 | DVL1 | 10092 | -0.0037 | 0.34 | NO |
45 | WNT8B | WNT8B | WNT8B | 10660 | -0.014 | 0.31 | NO |
46 | FZD2 | FZD2 | FZD2 | 10815 | -0.017 | 0.3 | NO |
47 | STK36 | STK36 | STK36 | 11558 | -0.032 | 0.26 | NO |
48 | WNT10A | WNT10A | WNT10A | 11773 | -0.036 | 0.25 | NO |
49 | DVL2 | DVL2 | DVL2 | 11799 | -0.037 | 0.25 | NO |
50 | WNT2B | WNT2B | WNT2B | 13273 | -0.071 | 0.18 | NO |
51 | FZD4 | FZD4 | FZD4 | 14102 | -0.095 | 0.14 | NO |
52 | WNT7A | WNT7A | WNT7A | 14968 | -0.13 | 0.1 | NO |
53 | WNT9B | WNT9B | WNT9B | 15913 | -0.19 | 0.065 | NO |
54 | WNT5B | WNT5B | WNT5B | 17411 | -0.41 | 0.017 | 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: ST WNT BETA CATENIN PATHWAY.

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

Table 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 | RELN | RELN | RELN | 291 | 0.54 | 0.14 | YES |
2 | MAPT | MAPT | MAPT | 760 | 0.41 | 0.23 | YES |
3 | VLDLR | VLDLR | VLDLR | 1129 | 0.35 | 0.31 | YES |
4 | MAPK8 | MAPK8 | MAPK8 | 1690 | 0.28 | 0.35 | YES |
5 | MAP1B | MAP1B | MAP1B | 1859 | 0.26 | 0.42 | YES |
6 | LRP8 | LRP8 | LRP8 | 2078 | 0.24 | 0.48 | YES |
7 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 4103 | 0.13 | 0.4 | NO |
8 | MAPK8IP1 | MAPK8IP1 | MAPK8IP1 | 4625 | 0.11 | 0.4 | NO |
9 | MAP2K7 | MAP2K7 | MAP2K7 | 5273 | 0.096 | 0.39 | NO |
10 | CBL | CBL | CBL | 6312 | 0.07 | 0.36 | NO |
11 | GSK3B | GSK3B | GSK3B | 6428 | 0.068 | 0.37 | NO |
12 | PIK3CA | PIK3CA | PIK3CA | 6863 | 0.058 | 0.36 | NO |
13 | PAFAH1B1 | PAFAH1B1 | PAFAH1B1 | 7305 | 0.049 | 0.35 | NO |
14 | CRKL | CRKL | CRKL | 7678 | 0.041 | 0.34 | NO |
15 | ITGB1 | ITGB1 | ITGB1 | 8136 | 0.032 | 0.32 | NO |
16 | AKT1 | AKT1 | AKT1 | 8174 | 0.032 | 0.33 | NO |
17 | CDK5 | CDK5 | CDK5 | 8761 | 0.021 | 0.3 | NO |
18 | PIK3R1 | PIK3R1 | PIK3R1 | 8934 | 0.018 | 0.3 | NO |
19 | CDK5R1 | CDK5R1 | CDK5R1 | 9893 | 0.0001 | 0.24 | NO |
20 | RAP1A | RAP1A | RAP1A | 11031 | -0.021 | 0.19 | NO |
21 | NCK2 | NCK2 | NCK2 | 11036 | -0.021 | 0.19 | NO |
22 | FYN | FYN | FYN | 11960 | -0.04 | 0.15 | NO |
23 | LRPAP1 | LRPAP1 | LRPAP1 | 11988 | -0.04 | 0.16 | NO |
24 | DAB1 | DAB1 | DAB1 | 12843 | -0.06 | 0.13 | NO |
25 | MAP3K11 | MAP3K11 | MAP3K11 | 13095 | -0.066 | 0.14 | NO |
26 | GRIN2A | GRIN2A | GRIN2A | 15178 | -0.14 | 0.058 | NO |
27 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 15265 | -0.15 | 0.094 | NO |
28 | ITGA3 | ITGA3 | ITGA3 | 15438 | -0.16 | 0.13 | 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: PID REELINPATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: PID REELINPATHWAY, 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 | FGF9 | FGF9 | FGF9 | 556 | 0.45 | 0.08 | YES |
2 | FGF2 | FGF2 | FGF2 | 905 | 0.38 | 0.16 | YES |
3 | FGF8 | FGF8 | FGF8 | 1036 | 0.36 | 0.24 | YES |
4 | FGF22 | FGF22 | FGF22 | 1131 | 0.35 | 0.32 | YES |
5 | FGF18 | FGF18 | FGF18 | 1157 | 0.34 | 0.4 | YES |
6 | BRAF | BRAF | BRAF | 2132 | 0.24 | 0.41 | YES |
7 | SRC | SRC | SRC | 2529 | 0.21 | 0.44 | YES |
8 | FGFR3 | FGFR3 | FGFR3 | 2757 | 0.2 | 0.47 | YES |
9 | FGF20 | FGF20 | FGF20 | 3828 | 0.14 | 0.45 | YES |
10 | FGFR1 | FGFR1 | FGFR1 | 3904 | 0.14 | 0.48 | YES |
11 | FRS2 | FRS2 | FRS2 | 3948 | 0.14 | 0.51 | YES |
12 | FGFR2 | FGFR2 | FGFR2 | 4135 | 0.13 | 0.53 | YES |
13 | SPRY2 | SPRY2 | SPRY2 | 6147 | 0.074 | 0.44 | NO |
14 | CBL | CBL | CBL | 6312 | 0.07 | 0.44 | NO |
15 | PPP2R1A | PPP2R1A | PPP2R1A | 7309 | 0.049 | 0.4 | NO |
16 | MAPK1 | MAPK1 | MAPK1 | 8430 | 0.027 | 0.34 | NO |
17 | UBA52 | UBA52 | UBA52 | 8799 | 0.021 | 0.33 | NO |
18 | FGF1 | FGF1 | FGF1 | 9002 | 0.016 | 0.32 | NO |
19 | PPP2CA | PPP2CA | PPP2CA | 9266 | 0.011 | 0.31 | NO |
20 | KL | KL | KL | 9677 | 0.0037 | 0.28 | NO |
21 | FGFR4 | FGFR4 | FGFR4 | 10404 | -0.0094 | 0.25 | NO |
22 | FGF17 | FGF17 | FGF17 | 10770 | -0.016 | 0.23 | NO |
23 | PPP2CB | PPP2CB | PPP2CB | 12152 | -0.044 | 0.16 | NO |
24 | FGF7 | FGF7 | FGF7 | 12314 | -0.048 | 0.17 | NO |
25 | GRB2 | GRB2 | GRB2 | 12320 | -0.048 | 0.18 | NO |
26 | MAPK3 | MAPK3 | MAPK3 | 12350 | -0.048 | 0.19 | NO |
27 | RPS27A | RPS27A | RPS27A | 14536 | -0.11 | 0.092 | NO |
28 | MKNK1 | MKNK1 | MKNK1 | 15028 | -0.13 | 0.097 | NO |
29 | KLB | KLB | KLB | 16228 | -0.22 | 0.084 | 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: PID NECTIN PATHWAY.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: PID NECTIN 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 PENTOSE PHOSPHATE PATHWAY | 26 | genes.ES.table | 0.51 | 1.6 | 0.034 | 1 | 0.94 | 0.35 | 0.18 | 0.28 | 0.77 | 0.42 |
KEGG STEROID HORMONE BIOSYNTHESIS | 42 | genes.ES.table | 0.59 | 1.5 | 0.044 | 1 | 0.98 | 0.55 | 0.15 | 0.47 | 0.91 | 0.45 |
KEGG BUTANOATE METABOLISM | 31 | genes.ES.table | 0.57 | 1.6 | 0.033 | 1 | 0.94 | 0.45 | 0.19 | 0.37 | 0.85 | 0.44 |
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.44 | 1.6 | 0.078 | 1 | 0.91 | 0.58 | 0.41 | 0.35 | 0.86 | 0.45 |
KEGG BASAL TRANSCRIPTION FACTORS | 34 | genes.ES.table | 0.42 | 1.5 | 0.094 | 1 | 0.97 | 0.5 | 0.36 | 0.32 | 0.83 | 0.42 |
KEGG NUCLEOTIDE EXCISION REPAIR | 44 | genes.ES.table | 0.43 | 1.7 | 0.057 | 1 | 0.85 | 0.46 | 0.34 | 0.3 | 1 | 0.81 |
KEGG UBIQUITIN MEDIATED PROTEOLYSIS | 132 | genes.ES.table | 0.26 | 1.6 | 0.04 | 1 | 0.9 | 0.38 | 0.34 | 0.25 | 1 | 0.5 |
BIOCARTA GH PATHWAY | 27 | genes.ES.table | 0.42 | 1.4 | 0.053 | 1 | 0.99 | 0.22 | 0.14 | 0.19 | 1 | 0.58 |
BIOCARTA CREB PATHWAY | 27 | genes.ES.table | 0.51 | 1.6 | 0.028 | 1 | 0.94 | 0.22 | 0.12 | 0.2 | 0.89 | 0.46 |
ST ERK1 ERK2 MAPK PATHWAY | 31 | genes.ES.table | 0.43 | 1.6 | 0.037 | 1 | 0.9 | 0.29 | 0.23 | 0.22 | 1 | 0.57 |
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 | RPA4 | RPA4 | RPA4 | 152 | 0.45 | 0.13 | YES |
2 | ERCC4 | ERCC4 | ERCC4 | 1050 | 0.25 | 0.16 | YES |
3 | GTF2H3 | GTF2H3 | GTF2H3 | 1867 | 0.18 | 0.17 | YES |
4 | ERCC8 | ERCC8 | ERCC8 | 2105 | 0.16 | 0.2 | YES |
5 | GTF2H2 | GTF2H2 | GTF2H2 | 2874 | 0.13 | 0.2 | YES |
6 | RPA3 | RPA3 | RPA3 | 3019 | 0.13 | 0.23 | YES |
7 | ERCC2 | ERCC2 | ERCC2 | 3079 | 0.12 | 0.27 | YES |
8 | CDK7 | CDK7 | CDK7 | 3173 | 0.12 | 0.3 | YES |
9 | RPA2 | RPA2 | RPA2 | 3337 | 0.12 | 0.32 | YES |
10 | LIG1 | LIG1 | LIG1 | 3916 | 0.1 | 0.32 | YES |
11 | CUL4B | CUL4B | CUL4B | 3933 | 0.1 | 0.35 | YES |
12 | CCNH | CCNH | CCNH | 4055 | 0.097 | 0.38 | YES |
13 | ERCC5 | ERCC5 | ERCC5 | 4492 | 0.086 | 0.38 | YES |
14 | GTF2H5 | GTF2H5 | GTF2H5 | 4771 | 0.08 | 0.39 | YES |
15 | CUL4A | CUL4A | CUL4A | 5069 | 0.074 | 0.39 | YES |
16 | RFC2 | RFC2 | RFC2 | 5509 | 0.066 | 0.39 | YES |
17 | POLE2 | POLE2 | POLE2 | 5590 | 0.064 | 0.4 | YES |
18 | CETN2 | CETN2 | CETN2 | 5768 | 0.06 | 0.41 | YES |
19 | RFC1 | RFC1 | RFC1 | 6049 | 0.055 | 0.42 | YES |
20 | MNAT1 | MNAT1 | MNAT1 | 6114 | 0.054 | 0.43 | YES |
21 | RFC3 | RFC3 | RFC3 | 6608 | 0.046 | 0.41 | NO |
22 | POLD2 | POLD2 | POLD2 | 6911 | 0.04 | 0.41 | NO |
23 | POLE4 | POLE4 | POLE4 | 6970 | 0.039 | 0.42 | NO |
24 | PCNA | PCNA | PCNA | 7536 | 0.029 | 0.4 | NO |
25 | RFC5 | RFC5 | RFC5 | 7665 | 0.027 | 0.4 | NO |
26 | POLD3 | POLD3 | POLD3 | 7790 | 0.024 | 0.4 | NO |
27 | GTF2H4 | GTF2H4 | GTF2H4 | 8105 | 0.019 | 0.38 | NO |
28 | POLE3 | POLE3 | POLE3 | 8203 | 0.017 | 0.38 | NO |
29 | POLD1 | POLD1 | POLD1 | 8355 | 0.015 | 0.38 | NO |
30 | DDB1 | DDB1 | DDB1 | 8929 | 0.0054 | 0.35 | NO |
31 | RAD23B | RAD23B | RAD23B | 9006 | 0.0041 | 0.35 | NO |
32 | GTF2H1 | GTF2H1 | GTF2H1 | 9481 | -0.0032 | 0.32 | NO |
33 | RAD23A | RAD23A | RAD23A | 9878 | -0.0099 | 0.3 | NO |
34 | XPC | XPC | XPC | 9917 | -0.01 | 0.3 | NO |
35 | POLE | POLE | POLE | 9999 | -0.012 | 0.3 | NO |
36 | ERCC1 | ERCC1 | ERCC1 | 10554 | -0.021 | 0.28 | NO |
37 | ERCC3 | ERCC3 | ERCC3 | 10612 | -0.022 | 0.28 | NO |
38 | ERCC6 | ERCC6 | ERCC6 | 11432 | -0.038 | 0.25 | NO |
39 | POLD4 | POLD4 | POLD4 | 11951 | -0.048 | 0.23 | NO |
40 | RPA1 | RPA1 | RPA1 | 12059 | -0.051 | 0.24 | NO |
41 | DDB2 | DDB2 | DDB2 | 12122 | -0.052 | 0.25 | NO |
42 | RBX1 | RBX1 | RBX1 | 12435 | -0.059 | 0.26 | NO |
43 | RFC4 | RFC4 | RFC4 | 12603 | -0.063 | 0.26 | NO |
44 | XPA | XPA | XPA | 13291 | -0.08 | 0.25 | 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 PENTOSE PHOSPHATE PATHWAY.

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

Table S22. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | BRAF | BRAF | BRAF | 695 | 0.3 | 0.018 | YES |
2 | SGK1 | SGK1 | SGK1 | 1089 | 0.24 | 0.042 | YES |
3 | PXN | PXN | PXN | 2038 | 0.17 | 0.02 | YES |
4 | PRKCA | PRKCA | PRKCA | 2051 | 0.17 | 0.051 | YES |
5 | EEF2K | EEF2K | EEF2K | 2094 | 0.16 | 0.081 | YES |
6 | CCNE1 | CCNE1 | CCNE1 | 2298 | 0.16 | 0.099 | YES |
7 | EIF4E | EIF4E | EIF4E | 2681 | 0.14 | 0.1 | YES |
8 | RRAGC | RRAGC | RRAGC | 2757 | 0.14 | 0.12 | YES |
9 | PDPK1 | PDPK1 | PDPK1 | 3024 | 0.13 | 0.13 | YES |
10 | RRAGB | RRAGB | RRAGB | 3165 | 0.12 | 0.15 | YES |
11 | BNIP3 | BNIP3 | BNIP3 | 3306 | 0.12 | 0.16 | YES |
12 | CYCS | CYCS | CYCS | 3362 | 0.12 | 0.18 | YES |
13 | CLIP1 | CLIP1 | CLIP1 | 3367 | 0.12 | 0.2 | YES |
14 | SFN | SFN | SFN | 3657 | 0.11 | 0.21 | YES |
15 | RRN3 | RRN3 | RRN3 | 3902 | 0.1 | 0.22 | YES |
16 | PDCD4 | PDCD4 | PDCD4 | 3904 | 0.1 | 0.23 | YES |
17 | MAP2K1 | MAP2K1 | MAP2K1 | 3952 | 0.099 | 0.25 | YES |
18 | PPARGC1A | PPARGC1A | PPARGC1A | 3977 | 0.099 | 0.27 | YES |
19 | DDIT4 | DDIT4 | DDIT4 | 4350 | 0.09 | 0.26 | YES |
20 | FBXW11 | FBXW11 | FBXW11 | 4621 | 0.084 | 0.26 | YES |
21 | YWHAG | YWHAG | YWHAG | 4641 | 0.083 | 0.28 | YES |
22 | YY1 | YY1 | YY1 | 4678 | 0.082 | 0.29 | YES |
23 | RHEB | RHEB | RHEB | 4707 | 0.082 | 0.31 | YES |
24 | ULK1 | ULK1 | ULK1 | 5078 | 0.074 | 0.3 | NO |
25 | RRAGA | RRAGA | RRAGA | 5458 | 0.067 | 0.29 | NO |
26 | RRAGD | RRAGD | RRAGD | 5517 | 0.066 | 0.3 | NO |
27 | MLST8 | MLST8 | MLST8 | 5693 | 0.062 | 0.3 | NO |
28 | TSC2 | TSC2 | TSC2 | 6452 | 0.048 | 0.27 | NO |
29 | RICTOR | RICTOR | RICTOR | 6819 | 0.042 | 0.26 | NO |
30 | EEF2 | EEF2 | EEF2 | 6985 | 0.039 | 0.25 | NO |
31 | YWHAB | YWHAB | YWHAB | 8259 | 0.016 | 0.18 | NO |
32 | NRAS | NRAS | NRAS | 8471 | 0.013 | 0.18 | NO |
33 | MTOR | MTOR | MTOR | 8579 | 0.011 | 0.17 | NO |
34 | RAC1 | RAC1 | RAC1 | 8704 | 0.009 | 0.17 | NO |
35 | EIF4B | EIF4B | EIF4B | 9117 | 0.0024 | 0.14 | NO |
36 | MAP2K2 | MAP2K2 | MAP2K2 | 9266 | -0.000032 | 0.14 | NO |
37 | YWHAQ | YWHAQ | YWHAQ | 9393 | -0.0018 | 0.13 | NO |
38 | AKT1 | AKT1 | AKT1 | 9408 | -0.0022 | 0.13 | NO |
39 | YWHAZ | YWHAZ | YWHAZ | 9455 | -0.0029 | 0.13 | NO |
40 | MAPK3 | MAPK3 | MAPK3 | 9483 | -0.0032 | 0.12 | NO |
41 | IRS1 | IRS1 | IRS1 | 9609 | -0.0053 | 0.12 | NO |
42 | CDK2 | CDK2 | CDK2 | 9716 | -0.0069 | 0.11 | NO |
43 | RB1CC1 | RB1CC1 | RB1CC1 | 9900 | -0.01 | 0.11 | NO |
44 | AKT1S1 | AKT1S1 | AKT1S1 | 9987 | -0.012 | 0.1 | NO |
45 | MAPK1 | MAPK1 | MAPK1 | 10010 | -0.012 | 0.1 | NO |
46 | POLDIP3 | POLDIP3 | POLDIP3 | 10173 | -0.015 | 0.098 | NO |
47 | YWHAH | YWHAH | YWHAH | 10503 | -0.02 | 0.083 | NO |
48 | YWHAE | YWHAE | YWHAE | 10698 | -0.024 | 0.077 | NO |
49 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 10708 | -0.024 | 0.081 | NO |
50 | KRAS | KRAS | KRAS | 10924 | -0.028 | 0.074 | NO |
51 | PML | PML | PML | 11230 | -0.034 | 0.063 | NO |
52 | RAF1 | RAF1 | RAF1 | 11242 | -0.034 | 0.069 | NO |
53 | EIF4A1 | EIF4A1 | EIF4A1 | 11297 | -0.035 | 0.073 | NO |
54 | RHOA | RHOA | RHOA | 11562 | -0.04 | 0.066 | NO |
55 | TSC1 | TSC1 | TSC1 | 11624 | -0.042 | 0.07 | NO |
56 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 11946 | -0.048 | 0.061 | NO |
57 | IKBKB | IKBKB | IKBKB | 11974 | -0.049 | 0.069 | NO |
58 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 12559 | -0.062 | 0.048 | NO |
59 | SREBF1 | SREBF1 | SREBF1 | 12817 | -0.068 | 0.046 | NO |
60 | PLD1 | PLD1 | PLD1 | 12820 | -0.068 | 0.059 | NO |
61 | PLD2 | PLD2 | PLD2 | 13364 | -0.082 | 0.044 | NO |
62 | RPTOR | RPTOR | RPTOR | 13628 | -0.089 | 0.046 | NO |
63 | ULK2 | ULK2 | ULK2 | 14420 | -0.12 | 0.024 | NO |
64 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 14475 | -0.12 | 0.043 | NO |
65 | HRAS | HRAS | HRAS | 14854 | -0.13 | 0.047 | NO |
66 | SSPO | SSPO | SSPO | 16447 | -0.24 | 0.0029 | NO |
67 | PRR5 | PRR5 | PRR5 | 17269 | -0.36 | 0.025 | 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 STEROID HORMONE BIOSYNTHESIS.

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

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 | GTF2A1 | GTF2A1 | GTF2A1 | 580 | 0.32 | 0.026 | YES |
2 | TAF13 | TAF13 | TAF13 | 613 | 0.31 | 0.081 | YES |
3 | CCNT1 | CCNT1 | CCNT1 | 1210 | 0.23 | 0.09 | YES |
4 | GTF2H3 | GTF2H3 | GTF2H3 | 1867 | 0.18 | 0.085 | YES |
5 | LSM11 | LSM11 | LSM11 | 2269 | 0.16 | 0.091 | YES |
6 | ZNF473 | ZNF473 | ZNF473 | 2492 | 0.15 | 0.11 | YES |
7 | RNGTT | RNGTT | RNGTT | 2591 | 0.14 | 0.13 | YES |
8 | GTF2H2 | GTF2H2 | GTF2H2 | 2874 | 0.13 | 0.14 | YES |
9 | UPF3B | UPF3B | UPF3B | 3073 | 0.12 | 0.15 | YES |
10 | ERCC2 | ERCC2 | ERCC2 | 3079 | 0.12 | 0.17 | YES |
11 | TAF1 | TAF1 | TAF1 | 3167 | 0.12 | 0.19 | YES |
12 | CDK7 | CDK7 | CDK7 | 3173 | 0.12 | 0.21 | YES |
13 | TBP | TBP | TBP | 3789 | 0.1 | 0.19 | YES |
14 | CDC40 | CDC40 | CDC40 | 3896 | 0.1 | 0.2 | YES |
15 | CCNH | CCNH | CCNH | 4055 | 0.097 | 0.21 | YES |
16 | PAPOLA | PAPOLA | PAPOLA | 4240 | 0.093 | 0.22 | YES |
17 | TAF9 | TAF9 | TAF9 | 4344 | 0.09 | 0.23 | YES |
18 | CSTF2 | CSTF2 | CSTF2 | 4564 | 0.085 | 0.24 | YES |
19 | POLR2B | POLR2B | POLR2B | 4582 | 0.084 | 0.25 | YES |
20 | GTF2A2 | GTF2A2 | GTF2A2 | 5337 | 0.069 | 0.22 | YES |
21 | LSM10 | LSM10 | LSM10 | 5344 | 0.069 | 0.23 | YES |
22 | RNMT | RNMT | RNMT | 5546 | 0.065 | 0.23 | YES |
23 | RNPS1 | RNPS1 | RNPS1 | 5580 | 0.064 | 0.24 | YES |
24 | SLBP | SLBP | SLBP | 5604 | 0.064 | 0.25 | YES |
25 | TAF12 | TAF12 | TAF12 | 5628 | 0.063 | 0.26 | YES |
26 | SUPT16H | SUPT16H | SUPT16H | 5663 | 0.062 | 0.27 | YES |
27 | POLR2C | POLR2C | POLR2C | 5865 | 0.059 | 0.27 | YES |
28 | DHX38 | DHX38 | DHX38 | 5942 | 0.057 | 0.28 | YES |
29 | WHSC2 | WHSC2 | WHSC2 | 5983 | 0.056 | 0.29 | YES |
30 | MNAT1 | MNAT1 | MNAT1 | 6114 | 0.054 | 0.29 | YES |
31 | GTF2F1 | GTF2F1 | GTF2F1 | 6201 | 0.052 | 0.29 | YES |
32 | U2AF2 | U2AF2 | U2AF2 | 6225 | 0.052 | 0.3 | YES |
33 | SNRPF | SNRPF | SNRPF | 6284 | 0.051 | 0.31 | YES |
34 | MAGOH | MAGOH | MAGOH | 6353 | 0.05 | 0.31 | YES |
35 | CPSF2 | CPSF2 | CPSF2 | 6391 | 0.049 | 0.32 | YES |
36 | NFX1 | NFX1 | NFX1 | 6466 | 0.048 | 0.32 | YES |
37 | POLR2J | POLR2J | POLR2J | 6488 | 0.047 | 0.33 | YES |
38 | NCBP1 | NCBP1 | NCBP1 | 6564 | 0.046 | 0.34 | YES |
39 | TAF5 | TAF5 | TAF5 | 6792 | 0.042 | 0.33 | NO |
40 | TCEB2 | TCEB2 | TCEB2 | 7002 | 0.038 | 0.33 | NO |
41 | NUDT21 | NUDT21 | NUDT21 | 7019 | 0.038 | 0.33 | NO |
42 | CTDP1 | CTDP1 | CTDP1 | 7266 | 0.034 | 0.32 | NO |
43 | SUPT5H | SUPT5H | SUPT5H | 7464 | 0.03 | 0.32 | NO |
44 | POLR2I | POLR2I | POLR2I | 7565 | 0.028 | 0.32 | NO |
45 | POLR2F | POLR2F | POLR2F | 7618 | 0.027 | 0.32 | NO |
46 | TAF11 | TAF11 | TAF11 | 7856 | 0.023 | 0.31 | NO |
47 | GTF2B | GTF2B | GTF2B | 8001 | 0.021 | 0.31 | NO |
48 | GTF2H4 | GTF2H4 | GTF2H4 | 8105 | 0.019 | 0.3 | NO |
49 | SRRM1 | SRRM1 | SRRM1 | 8230 | 0.017 | 0.3 | NO |
50 | ELL | ELL | ELL | 8338 | 0.015 | 0.3 | NO |
51 | SNRPB | SNRPB | SNRPB | 8430 | 0.014 | 0.3 | NO |
52 | POLR2D | POLR2D | POLR2D | 8562 | 0.011 | 0.29 | NO |
53 | TAF4 | TAF4 | TAF4 | 8629 | 0.01 | 0.29 | NO |
54 | GTF2H2B | GTF2H2B | GTF2H2B | 8875 | 0.0062 | 0.28 | NO |
55 | POLR2E | POLR2E | POLR2E | 8925 | 0.0055 | 0.27 | NO |
56 | TCEB1 | TCEB1 | TCEB1 | 9038 | 0.0036 | 0.27 | NO |
57 | POLR2A | POLR2A | POLR2A | 9187 | 0.0013 | 0.26 | NO |
58 | POLR2K | POLR2K | POLR2K | 9436 | -0.0026 | 0.25 | NO |
59 | GTF2H1 | GTF2H1 | GTF2H1 | 9481 | -0.0032 | 0.24 | NO |
60 | CCNT2 | CCNT2 | CCNT2 | 9539 | -0.0041 | 0.24 | NO |
61 | RDBP | RDBP | RDBP | 9655 | -0.006 | 0.24 | NO |
62 | CPSF3 | CPSF3 | CPSF3 | 9712 | -0.0069 | 0.23 | NO |
63 | CDK9 | CDK9 | CDK9 | 9797 | -0.0084 | 0.23 | NO |
64 | SNRPG | SNRPG | SNRPG | 9845 | -0.0092 | 0.23 | NO |
65 | TCEB3 | TCEB3 | TCEB3 | 9850 | -0.0093 | 0.23 | NO |
66 | TAF6 | TAF6 | TAF6 | 9933 | -0.011 | 0.23 | NO |
67 | COBRA1 | COBRA1 | COBRA1 | 9983 | -0.012 | 0.23 | NO |
68 | CLP1 | CLP1 | CLP1 | 10085 | -0.014 | 0.22 | NO |
69 | RBM8A | RBM8A | RBM8A | 10214 | -0.016 | 0.22 | NO |
70 | GTF2F2 | GTF2F2 | GTF2F2 | 10282 | -0.017 | 0.22 | NO |
71 | CSTF1 | CSTF1 | CSTF1 | 10323 | -0.017 | 0.22 | NO |
72 | U2AF1 | U2AF1 | U2AF1 | 10357 | -0.018 | 0.22 | NO |
73 | PABPN1 | PABPN1 | PABPN1 | 10501 | -0.02 | 0.22 | NO |
74 | ERCC3 | ERCC3 | ERCC3 | 10612 | -0.022 | 0.22 | NO |
75 | SNRPE | SNRPE | SNRPE | 10648 | -0.022 | 0.22 | NO |
76 | POLR2L | POLR2L | POLR2L | 10778 | -0.025 | 0.22 | NO |
77 | CPSF1 | CPSF1 | CPSF1 | 10789 | -0.026 | 0.22 | NO |
78 | GTF2E1 | GTF2E1 | GTF2E1 | 11211 | -0.033 | 0.2 | NO |
79 | CSTF3 | CSTF3 | CSTF3 | 11302 | -0.035 | 0.2 | NO |
80 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 11421 | -0.038 | 0.2 | NO |
81 | TCEA1 | TCEA1 | TCEA1 | 11448 | -0.038 | 0.21 | NO |
82 | SSRP1 | SSRP1 | SSRP1 | 11457 | -0.038 | 0.22 | NO |
83 | GTF2E2 | GTF2E2 | GTF2E2 | 11459 | -0.038 | 0.22 | NO |
84 | TAF4B | TAF4B | TAF4B | 11586 | -0.041 | 0.22 | NO |
85 | SNRPD3 | SNRPD3 | SNRPD3 | 11746 | -0.044 | 0.22 | NO |
86 | PCF11 | PCF11 | PCF11 | 12113 | -0.052 | 0.21 | NO |
87 | CPSF7 | CPSF7 | CPSF7 | 12210 | -0.054 | 0.22 | NO |
88 | TH1L | TH1L | TH1L | 12746 | -0.066 | 0.2 | NO |
89 | NCBP2 | NCBP2 | NCBP2 | 12870 | -0.069 | 0.2 | NO |
90 | POLR2G | POLR2G | POLR2G | 13040 | -0.073 | 0.21 | NO |
91 | THOC4 | THOC4 | THOC4 | 13639 | -0.09 | 0.19 | NO |
92 | TAF10 | TAF10 | TAF10 | 14210 | -0.11 | 0.18 | NO |
93 | POLR2H | POLR2H | POLR2H | 14479 | -0.12 | 0.18 | 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 BUTANOATE METABOLISM.

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

Table 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 | CREB5 | CREB5 | CREB5 | 446 | 0.35 | 0.11 | YES |
2 | BRAF | BRAF | BRAF | 695 | 0.3 | 0.2 | YES |
3 | DUSP9 | DUSP9 | DUSP9 | 763 | 0.29 | 0.31 | YES |
4 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 1572 | 0.2 | 0.34 | YES |
5 | EEF2K | EEF2K | EEF2K | 2094 | 0.16 | 0.37 | YES |
6 | EIF4E | EIF4E | EIF4E | 2681 | 0.14 | 0.39 | YES |
7 | RAP1A | RAP1A | RAP1A | 3356 | 0.12 | 0.4 | YES |
8 | MAP2K1 | MAP2K1 | MAP2K1 | 3952 | 0.099 | 0.4 | YES |
9 | SOS2 | SOS2 | SOS2 | 4101 | 0.096 | 0.43 | YES |
10 | ARAF | ARAF | ARAF | 5270 | 0.07 | 0.39 | NO |
11 | ATF1 | ATF1 | ATF1 | 5842 | 0.059 | 0.38 | NO |
12 | CREB3 | CREB3 | CREB3 | 6270 | 0.051 | 0.37 | NO |
13 | NFKB1 | NFKB1 | NFKB1 | 8556 | 0.012 | 0.25 | NO |
14 | KLF6 | KLF6 | KLF6 | 8776 | 0.0076 | 0.24 | NO |
15 | MKNK2 | MKNK2 | MKNK2 | 8872 | 0.0062 | 0.24 | NO |
16 | MAP2K2 | MAP2K2 | MAP2K2 | 9266 | -0.000032 | 0.21 | NO |
17 | MAPK3 | MAPK3 | MAPK3 | 9483 | -0.0032 | 0.2 | NO |
18 | DUSP4 | DUSP4 | DUSP4 | 9618 | -0.0054 | 0.2 | NO |
19 | GRB2 | GRB2 | GRB2 | 9634 | -0.0055 | 0.2 | NO |
20 | SOS1 | SOS1 | SOS1 | 9679 | -0.0063 | 0.2 | NO |
21 | MAPK1 | MAPK1 | MAPK1 | 10010 | -0.012 | 0.18 | NO |
22 | MKNK1 | MKNK1 | MKNK1 | 10877 | -0.027 | 0.14 | NO |
23 | CREB1 | CREB1 | CREB1 | 11489 | -0.039 | 0.13 | NO |
24 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 11946 | -0.048 | 0.12 | NO |
25 | KAT5 | KAT5 | KAT5 | 12085 | -0.051 | 0.13 | NO |
26 | SHC1 | SHC1 | SHC1 | 12156 | -0.053 | 0.15 | NO |
27 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 12590 | -0.062 | 0.14 | NO |
28 | TRAF3 | TRAF3 | TRAF3 | 12794 | -0.068 | 0.16 | NO |
29 | BAD | BAD | BAD | 13029 | -0.073 | 0.17 | NO |
30 | DUSP6 | DUSP6 | DUSP6 | 13055 | -0.074 | 0.2 | NO |
31 | MAP3K8 | MAP3K8 | MAP3K8 | 15535 | -0.17 | 0.12 | 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 AMINOACYL TRNA BIOSYNTHESIS.

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

Table 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 | SOCS1 | SOCS1 | SOCS1 | 244 | 0.41 | 0.03 | YES |
2 | PARK2 | PARK2 | PARK2 | 371 | 0.37 | 0.062 | YES |
3 | NHLRC1 | NHLRC1 | NHLRC1 | 551 | 0.32 | 0.086 | YES |
4 | UBE2NL | UBE2NL | UBE2NL | 648 | 0.3 | 0.11 | YES |
5 | HERC3 | HERC3 | HERC3 | 808 | 0.28 | 0.13 | YES |
6 | UBE2QL1 | UBE2QL1 | UBE2QL1 | 1532 | 0.2 | 0.11 | YES |
7 | UBE2D4 | UBE2D4 | UBE2D4 | 2070 | 0.17 | 0.1 | YES |
8 | ERCC8 | ERCC8 | ERCC8 | 2105 | 0.16 | 0.12 | YES |
9 | NEDD4 | NEDD4 | NEDD4 | 2762 | 0.14 | 0.094 | YES |
10 | XIAP | XIAP | XIAP | 2945 | 0.13 | 0.097 | YES |
11 | FBXO4 | FBXO4 | FBXO4 | 3168 | 0.12 | 0.097 | YES |
12 | CDC23 | CDC23 | CDC23 | 3183 | 0.12 | 0.11 | YES |
13 | NEDD4L | NEDD4L | NEDD4L | 3388 | 0.12 | 0.11 | YES |
14 | SAE1 | SAE1 | SAE1 | 3420 | 0.11 | 0.12 | YES |
15 | ANAPC10 | ANAPC10 | ANAPC10 | 3729 | 0.1 | 0.11 | YES |
16 | UBE2B | UBE2B | UBE2B | 3791 | 0.1 | 0.12 | YES |
17 | UBE3C | UBE3C | UBE3C | 3899 | 0.1 | 0.13 | YES |
18 | UBE2A | UBE2A | UBE2A | 3918 | 0.1 | 0.14 | YES |
19 | CUL4B | CUL4B | CUL4B | 3933 | 0.1 | 0.14 | YES |
20 | RCHY1 | RCHY1 | RCHY1 | 4056 | 0.097 | 0.15 | YES |
21 | KLHL9 | KLHL9 | KLHL9 | 4165 | 0.094 | 0.15 | YES |
22 | UBE2H | UBE2H | UBE2H | 4352 | 0.09 | 0.15 | YES |
23 | UBA6 | UBA6 | UBA6 | 4436 | 0.088 | 0.16 | YES |
24 | UBE2K | UBE2K | UBE2K | 4454 | 0.087 | 0.16 | YES |
25 | BIRC3 | BIRC3 | BIRC3 | 4487 | 0.086 | 0.17 | YES |
26 | FBXW11 | FBXW11 | FBXW11 | 4621 | 0.084 | 0.17 | YES |
27 | SKP1 | SKP1 | SKP1 | 4658 | 0.083 | 0.18 | YES |
28 | UBE2D2 | UBE2D2 | UBE2D2 | 4663 | 0.083 | 0.19 | YES |
29 | UBOX5 | UBOX5 | UBOX5 | 4694 | 0.082 | 0.2 | YES |
30 | HUWE1 | HUWE1 | HUWE1 | 4865 | 0.079 | 0.19 | YES |
31 | UBE2C | UBE2C | UBE2C | 4890 | 0.078 | 0.2 | YES |
32 | UBE2D3 | UBE2D3 | UBE2D3 | 4956 | 0.077 | 0.21 | YES |
33 | MGRN1 | MGRN1 | MGRN1 | 5044 | 0.074 | 0.21 | YES |
34 | CUL4A | CUL4A | CUL4A | 5069 | 0.074 | 0.22 | YES |
35 | SMURF1 | SMURF1 | SMURF1 | 5082 | 0.074 | 0.22 | YES |
36 | SKP2 | SKP2 | SKP2 | 5219 | 0.071 | 0.22 | YES |
37 | FZR1 | FZR1 | FZR1 | 5232 | 0.071 | 0.23 | YES |
38 | FBXW8 | FBXW8 | FBXW8 | 5390 | 0.068 | 0.23 | YES |
39 | UBE2E2 | UBE2E2 | UBE2E2 | 5611 | 0.064 | 0.22 | YES |
40 | UBE2I | UBE2I | UBE2I | 5648 | 0.063 | 0.23 | YES |
41 | BTRC | BTRC | BTRC | 5706 | 0.062 | 0.23 | YES |
42 | RHOBTB2 | RHOBTB2 | RHOBTB2 | 5729 | 0.061 | 0.24 | YES |
43 | ANAPC4 | ANAPC4 | ANAPC4 | 5741 | 0.061 | 0.24 | YES |
44 | UBA1 | UBA1 | UBA1 | 5810 | 0.06 | 0.24 | YES |
45 | UBE3B | UBE3B | UBE3B | 5853 | 0.059 | 0.25 | YES |
46 | FANCL | FANCL | FANCL | 5917 | 0.057 | 0.25 | YES |
47 | UBE2N | UBE2N | UBE2N | 5951 | 0.056 | 0.25 | YES |
48 | CUL1 | CUL1 | CUL1 | 6028 | 0.055 | 0.26 | YES |
49 | UBE3A | UBE3A | UBE3A | 6039 | 0.055 | 0.26 | YES |
50 | ANAPC5 | ANAPC5 | ANAPC5 | 6113 | 0.054 | 0.26 | YES |
51 | UBE2M | UBE2M | UBE2M | 6359 | 0.049 | 0.25 | NO |
52 | PIAS4 | PIAS4 | PIAS4 | 6390 | 0.049 | 0.26 | NO |
53 | SIAH1 | SIAH1 | SIAH1 | 6615 | 0.046 | 0.25 | NO |
54 | CDC20 | CDC20 | CDC20 | 6856 | 0.041 | 0.24 | NO |
55 | WWP2 | WWP2 | WWP2 | 6917 | 0.04 | 0.24 | NO |
56 | TCEB2 | TCEB2 | TCEB2 | 7002 | 0.038 | 0.24 | NO |
57 | SYVN1 | SYVN1 | SYVN1 | 7048 | 0.038 | 0.24 | NO |
58 | KEAP1 | KEAP1 | KEAP1 | 7169 | 0.035 | 0.24 | NO |
59 | ANAPC13 | ANAPC13 | ANAPC13 | 7175 | 0.035 | 0.24 | NO |
60 | MID1 | MID1 | MID1 | 7244 | 0.034 | 0.24 | NO |
61 | UBE2G2 | UBE2G2 | UBE2G2 | 7296 | 0.033 | 0.24 | NO |
62 | BIRC6 | BIRC6 | BIRC6 | 7552 | 0.029 | 0.23 | NO |
63 | CUL3 | CUL3 | CUL3 | 7593 | 0.028 | 0.23 | NO |
64 | UBA2 | UBA2 | UBA2 | 7631 | 0.027 | 0.23 | NO |
65 | UBE2J1 | UBE2J1 | UBE2J1 | 7656 | 0.027 | 0.23 | NO |
66 | ANAPC7 | ANAPC7 | ANAPC7 | 7736 | 0.025 | 0.23 | NO |
67 | HERC2 | HERC2 | HERC2 | 7850 | 0.024 | 0.23 | NO |
68 | STUB1 | STUB1 | STUB1 | 7866 | 0.023 | 0.23 | NO |
69 | UBE4A | UBE4A | UBE4A | 7911 | 0.022 | 0.23 | NO |
70 | MAP3K1 | MAP3K1 | MAP3K1 | 7941 | 0.022 | 0.23 | NO |
71 | PPIL2 | PPIL2 | PPIL2 | 7973 | 0.021 | 0.23 | NO |
72 | UBE2S | UBE2S | UBE2S | 8103 | 0.019 | 0.22 | NO |
73 | CUL7 | CUL7 | CUL7 | 8180 | 0.018 | 0.22 | NO |
74 | KLHL13 | KLHL13 | KLHL13 | 8205 | 0.017 | 0.22 | NO |
75 | HERC1 | HERC1 | HERC1 | 8268 | 0.016 | 0.22 | NO |
76 | DET1 | DET1 | DET1 | 8462 | 0.013 | 0.21 | NO |
77 | CDC16 | CDC16 | CDC16 | 8469 | 0.013 | 0.21 | NO |
78 | CDC26 | CDC26 | CDC26 | 8520 | 0.012 | 0.21 | NO |
79 | CUL2 | CUL2 | CUL2 | 8581 | 0.011 | 0.21 | NO |
80 | UBE2R2 | UBE2R2 | UBE2R2 | 8659 | 0.0097 | 0.2 | NO |
81 | DDB1 | DDB1 | DDB1 | 8929 | 0.0054 | 0.19 | NO |
82 | UBE2W | UBE2W | UBE2W | 9000 | 0.0042 | 0.19 | NO |
83 | TCEB1 | TCEB1 | TCEB1 | 9038 | 0.0036 | 0.18 | NO |
84 | FBXW7 | FBXW7 | FBXW7 | 9337 | -0.0011 | 0.17 | NO |
85 | SOCS3 | SOCS3 | SOCS3 | 9463 | -0.003 | 0.16 | NO |
86 | TRIP12 | TRIP12 | TRIP12 | 9816 | -0.0087 | 0.14 | NO |
87 | PIAS2 | PIAS2 | PIAS2 | 9890 | -0.01 | 0.14 | NO |
88 | BRCA1 | BRCA1 | BRCA1 | 9914 | -0.01 | 0.14 | NO |
89 | RNF7 | RNF7 | RNF7 | 9978 | -0.012 | 0.14 | NO |
90 | ANAPC2 | ANAPC2 | ANAPC2 | 10106 | -0.014 | 0.13 | NO |
91 | PIAS1 | PIAS1 | PIAS1 | 10178 | -0.015 | 0.13 | NO |
92 | CDC34 | CDC34 | CDC34 | 10260 | -0.016 | 0.13 | NO |
93 | ITCH | ITCH | ITCH | 10291 | -0.017 | 0.13 | NO |
94 | CUL5 | CUL5 | CUL5 | 10383 | -0.018 | 0.12 | NO |
95 | UBE2F | UBE2F | UBE2F | 10391 | -0.018 | 0.12 | NO |
96 | UBE2O | UBE2O | UBE2O | 10502 | -0.02 | 0.12 | NO |
97 | UBE2Z | UBE2Z | UBE2Z | 10791 | -0.026 | 0.11 | NO |
98 | UBE2G1 | UBE2G1 | UBE2G1 | 10894 | -0.027 | 0.1 | NO |
99 | CDC27 | CDC27 | CDC27 | 10911 | -0.028 | 0.11 | NO |
100 | UBE2Q2 | UBE2Q2 | UBE2Q2 | 11207 | -0.033 | 0.092 | NO |
101 | PML | PML | PML | 11230 | -0.034 | 0.095 | NO |
102 | UBA3 | UBA3 | UBA3 | 11273 | -0.035 | 0.096 | NO |
103 | ANAPC11 | ANAPC11 | ANAPC11 | 11348 | -0.036 | 0.096 | NO |
104 | UBE2J2 | UBE2J2 | UBE2J2 | 11393 | -0.037 | 0.097 | NO |
105 | UBE2L3 | UBE2L3 | UBE2L3 | 11504 | -0.039 | 0.095 | NO |
106 | TRIM37 | TRIM37 | TRIM37 | 11615 | -0.042 | 0.093 | NO |
107 | UBE2Q1 | UBE2Q1 | UBE2Q1 | 11679 | -0.043 | 0.094 | NO |
108 | ANAPC1 | ANAPC1 | ANAPC1 | 11794 | -0.045 | 0.092 | NO |
109 | UBE2L6 | UBE2L6 | UBE2L6 | 12016 | -0.05 | 0.085 | NO |
110 | DDB2 | DDB2 | DDB2 | 12122 | -0.052 | 0.085 | NO |
111 | TRAF6 | TRAF6 | TRAF6 | 12131 | -0.052 | 0.09 | NO |
112 | CBL | CBL | CBL | 12163 | -0.053 | 0.094 | NO |
113 | RFWD2 | RFWD2 | RFWD2 | 12278 | -0.056 | 0.093 | NO |
114 | UBR5 | UBR5 | UBR5 | 12392 | -0.058 | 0.093 | NO |
115 | RBX1 | RBX1 | RBX1 | 12435 | -0.059 | 0.097 | NO |
116 | WWP1 | WWP1 | WWP1 | 12469 | -0.06 | 0.1 | NO |
117 | UBE4B | UBE4B | UBE4B | 12491 | -0.06 | 0.11 | NO |
118 | UBE2D1 | UBE2D1 | UBE2D1 | 12698 | -0.065 | 0.1 | NO |
119 | TRIM32 | TRIM32 | TRIM32 | 12821 | -0.068 | 0.1 | NO |
120 | HERC4 | HERC4 | HERC4 | 12891 | -0.07 | 0.11 | NO |
121 | PRPF19 | PRPF19 | PRPF19 | 12920 | -0.07 | 0.11 | NO |
122 | UBE2E3 | UBE2E3 | UBE2E3 | 13307 | -0.08 | 0.098 | NO |
123 | BIRC2 | BIRC2 | BIRC2 | 13409 | -0.083 | 0.1 | NO |
124 | PIAS3 | PIAS3 | PIAS3 | 13779 | -0.093 | 0.09 | NO |
125 | UBE2E1 | UBE2E1 | UBE2E1 | 13784 | -0.093 | 0.1 | NO |
126 | VHL | VHL | VHL | 13910 | -0.097 | 0.1 | NO |
127 | MDM2 | MDM2 | MDM2 | 14121 | -0.1 | 0.1 | NO |
128 | UBA7 | UBA7 | UBA7 | 14502 | -0.12 | 0.093 | NO |
129 | CBLB | CBLB | CBLB | 14563 | -0.12 | 0.1 | NO |
130 | FBXO2 | FBXO2 | FBXO2 | 16100 | -0.21 | 0.038 | NO |
131 | SMURF2 | SMURF2 | SMURF2 | 16492 | -0.24 | 0.042 | NO |
132 | AIRE | AIRE | AIRE | 16682 | -0.26 | 0.059 | 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 BASAL TRANSCRIPTION FACTORS.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASAL TRANSCRIPTION FACTORS, 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 | MARS2 | MARS2 | MARS2 | 1354 | 0.22 | 0.017 | YES |
2 | TARSL2 | TARSL2 | TARSL2 | 2227 | 0.16 | 0.036 | YES |
3 | RARS | RARS | RARS | 3344 | 0.12 | 0.023 | YES |
4 | HARS2 | HARS2 | HARS2 | 3467 | 0.11 | 0.064 | YES |
5 | MTFMT | MTFMT | MTFMT | 3596 | 0.11 | 0.1 | YES |
6 | HARS | HARS | HARS | 3751 | 0.1 | 0.14 | YES |
7 | GARS | GARS | GARS | 3877 | 0.1 | 0.18 | YES |
8 | FARS2 | FARS2 | FARS2 | 4121 | 0.096 | 0.2 | YES |
9 | LARS | LARS | LARS | 4157 | 0.095 | 0.24 | YES |
10 | EARS2 | EARS2 | EARS2 | 4283 | 0.092 | 0.28 | YES |
11 | VARS2 | VARS2 | VARS2 | 4616 | 0.084 | 0.29 | YES |
12 | PSTK | PSTK | PSTK | 5187 | 0.072 | 0.29 | YES |
13 | YARS2 | YARS2 | YARS2 | 5366 | 0.068 | 0.31 | YES |
14 | VARS | VARS | VARS | 5705 | 0.062 | 0.32 | YES |
15 | AARS2 | AARS2 | AARS2 | 5795 | 0.06 | 0.34 | YES |
16 | MARS | MARS | MARS | 5888 | 0.058 | 0.36 | YES |
17 | SEPSECS | SEPSECS | SEPSECS | 5991 | 0.056 | 0.38 | YES |
18 | SARS | SARS | SARS | 6063 | 0.055 | 0.4 | YES |
19 | SARS2 | SARS2 | SARS2 | 6133 | 0.053 | 0.42 | YES |
20 | TARS2 | TARS2 | TARS2 | 6575 | 0.046 | 0.41 | YES |
21 | IARS2 | IARS2 | IARS2 | 7032 | 0.038 | 0.4 | YES |
22 | FARSA | FARSA | FARSA | 7061 | 0.037 | 0.41 | YES |
23 | LARS2 | LARS2 | LARS2 | 7201 | 0.035 | 0.42 | YES |
24 | KARS | KARS | KARS | 7212 | 0.035 | 0.44 | YES |
25 | PARS2 | PARS2 | PARS2 | 7455 | 0.031 | 0.44 | NO |
26 | TARS | TARS | TARS | 7870 | 0.023 | 0.42 | NO |
27 | IARS | IARS | IARS | 8024 | 0.02 | 0.42 | NO |
28 | FARSB | FARSB | FARSB | 8067 | 0.019 | 0.43 | NO |
29 | WARS | WARS | WARS | 8172 | 0.018 | 0.43 | NO |
30 | NARS | NARS | NARS | 8458 | 0.013 | 0.42 | NO |
31 | EPRS | EPRS | EPRS | 8645 | 0.01 | 0.41 | NO |
32 | NARS2 | NARS2 | NARS2 | 8810 | 0.0072 | 0.41 | NO |
33 | WARS2 | WARS2 | WARS2 | 9126 | 0.0022 | 0.39 | NO |
34 | DARS2 | DARS2 | DARS2 | 9708 | -0.0068 | 0.36 | NO |
35 | DARS | DARS | DARS | 9897 | -0.01 | 0.35 | NO |
36 | YARS | YARS | YARS | 10125 | -0.014 | 0.35 | NO |
37 | RARS2 | RARS2 | RARS2 | 10336 | -0.017 | 0.34 | NO |
38 | CARS2 | CARS2 | CARS2 | 11084 | -0.031 | 0.31 | NO |
39 | AARS | AARS | AARS | 11128 | -0.032 | 0.32 | NO |
40 | CARS | CARS | CARS | 11594 | -0.041 | 0.32 | NO |
41 | QARS | QARS | QARS | 12900 | -0.07 | 0.27 | 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 NUCLEOTIDE EXCISION REPAIR.

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

Table 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 | ERCC4 | ERCC4 | ERCC4 | 1050 | 0.25 | 0.072 | YES |
2 | GTF2H3 | GTF2H3 | GTF2H3 | 1867 | 0.18 | 0.12 | YES |
3 | ERCC8 | ERCC8 | ERCC8 | 2105 | 0.16 | 0.19 | YES |
4 | GTF2H2 | GTF2H2 | GTF2H2 | 2874 | 0.13 | 0.22 | YES |
5 | ERCC2 | ERCC2 | ERCC2 | 3079 | 0.12 | 0.28 | YES |
6 | CDK7 | CDK7 | CDK7 | 3173 | 0.12 | 0.34 | YES |
7 | CCNH | CCNH | CCNH | 4055 | 0.097 | 0.34 | YES |
8 | ERCC5 | ERCC5 | ERCC5 | 4492 | 0.086 | 0.36 | YES |
9 | POLR2B | POLR2B | POLR2B | 4582 | 0.084 | 0.4 | YES |
10 | POLR2C | POLR2C | POLR2C | 5865 | 0.059 | 0.36 | NO |
11 | MNAT1 | MNAT1 | MNAT1 | 6114 | 0.054 | 0.37 | NO |
12 | POLR2J | POLR2J | POLR2J | 6488 | 0.047 | 0.38 | NO |
13 | XAB2 | XAB2 | XAB2 | 6666 | 0.044 | 0.39 | NO |
14 | POLR2I | POLR2I | POLR2I | 7565 | 0.028 | 0.35 | NO |
15 | POLR2F | POLR2F | POLR2F | 7618 | 0.027 | 0.36 | NO |
16 | GTF2H4 | GTF2H4 | GTF2H4 | 8105 | 0.019 | 0.35 | NO |
17 | POLR2D | POLR2D | POLR2D | 8562 | 0.011 | 0.33 | NO |
18 | GTF2H2B | GTF2H2B | GTF2H2B | 8875 | 0.0062 | 0.31 | NO |
19 | POLR2E | POLR2E | POLR2E | 8925 | 0.0055 | 0.31 | NO |
20 | POLR2A | POLR2A | POLR2A | 9187 | 0.0013 | 0.3 | NO |
21 | POLR2K | POLR2K | POLR2K | 9436 | -0.0026 | 0.29 | NO |
22 | GTF2H1 | GTF2H1 | GTF2H1 | 9481 | -0.0032 | 0.29 | NO |
23 | ERCC1 | ERCC1 | ERCC1 | 10554 | -0.021 | 0.24 | NO |
24 | ERCC3 | ERCC3 | ERCC3 | 10612 | -0.022 | 0.24 | NO |
25 | POLR2L | POLR2L | POLR2L | 10778 | -0.025 | 0.25 | NO |
26 | ERCC6 | ERCC6 | ERCC6 | 11432 | -0.038 | 0.23 | NO |
27 | TCEA1 | TCEA1 | TCEA1 | 11448 | -0.038 | 0.25 | NO |
28 | POLR2G | POLR2G | POLR2G | 13040 | -0.073 | 0.2 | NO |
29 | POLR2H | POLR2H | POLR2H | 14479 | -0.12 | 0.18 | 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 UBIQUITIN MEDIATED PROTEOLYSIS.

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

Table 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 | PRKCB | PRKCB | PRKCB | 117 | 0.48 | 0.18 | YES |
2 | PIK3R1 | PIK3R1 | PIK3R1 | 796 | 0.28 | 0.26 | YES |
3 | CAMK2B | CAMK2B | CAMK2B | 1070 | 0.24 | 0.34 | YES |
4 | PRKAR2B | PRKAR2B | PRKAR2B | 1204 | 0.23 | 0.43 | YES |
5 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 1957 | 0.17 | 0.45 | YES |
6 | PRKCA | PRKCA | PRKCA | 2051 | 0.17 | 0.51 | YES |
7 | CAMK2D | CAMK2D | CAMK2D | 4239 | 0.093 | 0.43 | NO |
8 | PRKACG | PRKACG | PRKACG | 4386 | 0.089 | 0.46 | NO |
9 | PRKAR2A | PRKAR2A | PRKAR2A | 4473 | 0.087 | 0.48 | NO |
10 | PRKAR1B | PRKAR1B | PRKAR1B | 5667 | 0.062 | 0.44 | NO |
11 | PRKACB | PRKACB | PRKACB | 8136 | 0.018 | 0.31 | NO |
12 | GNAS | GNAS | GNAS | 8439 | 0.014 | 0.3 | NO |
13 | RAC1 | RAC1 | RAC1 | 8704 | 0.009 | 0.29 | NO |
14 | MAPK14 | MAPK14 | MAPK14 | 8841 | 0.0067 | 0.28 | NO |
15 | AKT1 | AKT1 | AKT1 | 9408 | -0.0022 | 0.25 | NO |
16 | MAPK3 | MAPK3 | MAPK3 | 9483 | -0.0032 | 0.25 | NO |
17 | GRB2 | GRB2 | GRB2 | 9634 | -0.0055 | 0.24 | NO |
18 | SOS1 | SOS1 | SOS1 | 9679 | -0.0063 | 0.24 | NO |
19 | MAPK1 | MAPK1 | MAPK1 | 10010 | -0.012 | 0.23 | NO |
20 | ADCY1 | ADCY1 | ADCY1 | 10564 | -0.021 | 0.21 | NO |
21 | CAMK2G | CAMK2G | CAMK2G | 10983 | -0.029 | 0.19 | NO |
22 | CREB1 | CREB1 | CREB1 | 11489 | -0.039 | 0.18 | NO |
23 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 11946 | -0.048 | 0.18 | NO |
24 | PRKAR1A | PRKAR1A | PRKAR1A | 12311 | -0.056 | 0.18 | NO |
25 | PIK3CA | PIK3CA | PIK3CA | 13093 | -0.074 | 0.16 | NO |
26 | CAMK2A | CAMK2A | CAMK2A | 14344 | -0.11 | 0.14 | NO |
27 | HRAS | HRAS | HRAS | 14854 | -0.13 | 0.16 | NO |
Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GH PATHWAY.
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Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GH PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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Table 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 | ACSM1 | ACSM1 | ACSM1 | 14 | 0.67 | 0.14 | YES |
2 | ACSM3 | ACSM3 | ACSM3 | 84 | 0.51 | 0.24 | YES |
3 | GAD1 | GAD1 | GAD1 | 308 | 0.39 | 0.3 | YES |
4 | ABAT | ABAT | ABAT | 434 | 0.35 | 0.37 | YES |
5 | L2HGDH | L2HGDH | L2HGDH | 976 | 0.26 | 0.39 | YES |
6 | HMGCS1 | HMGCS1 | HMGCS1 | 977 | 0.26 | 0.44 | YES |
7 | ACSM2A | ACSM2A | ACSM2A | 1232 | 0.23 | 0.47 | YES |
8 | ACSM5 | ACSM5 | ACSM5 | 1235 | 0.23 | 0.52 | YES |
9 | ALDH5A1 | ALDH5A1 | ALDH5A1 | 2130 | 0.16 | 0.5 | YES |
10 | ACAT2 | ACAT2 | ACAT2 | 2263 | 0.16 | 0.52 | YES |
11 | HMGCS2 | HMGCS2 | HMGCS2 | 2626 | 0.14 | 0.53 | YES |
12 | AACS | AACS | AACS | 2862 | 0.13 | 0.55 | YES |
13 | OXCT1 | OXCT1 | OXCT1 | 3107 | 0.12 | 0.56 | YES |
14 | HADH | HADH | HADH | 3313 | 0.12 | 0.57 | YES |
15 | AKR1B10 | AKR1B10 | AKR1B10 | 3762 | 0.1 | 0.56 | NO |
16 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 4294 | 0.091 | 0.55 | NO |
17 | ACADS | ACADS | ACADS | 4819 | 0.079 | 0.54 | NO |
18 | PDHA1 | PDHA1 | PDHA1 | 5063 | 0.074 | 0.54 | NO |
19 | BDH2 | BDH2 | BDH2 | 5518 | 0.065 | 0.53 | NO |
20 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 5552 | 0.065 | 0.54 | NO |
21 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 6002 | 0.056 | 0.53 | NO |
22 | HMGCL | HMGCL | HMGCL | 6975 | 0.039 | 0.48 | NO |
23 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 8293 | 0.016 | 0.41 | NO |
24 | ALDH2 | ALDH2 | ALDH2 | 8397 | 0.014 | 0.4 | NO |
25 | ECHS1 | ECHS1 | ECHS1 | 8543 | 0.012 | 0.4 | NO |
26 | HADHA | HADHA | HADHA | 10064 | -0.013 | 0.32 | NO |
27 | ACAT1 | ACAT1 | ACAT1 | 11704 | -0.043 | 0.23 | NO |
28 | OXCT2 | OXCT2 | OXCT2 | 12743 | -0.066 | 0.19 | NO |
29 | PDHB | PDHB | PDHB | 13552 | -0.087 | 0.16 | NO |
30 | BDH1 | BDH1 | BDH1 | 15577 | -0.17 | 0.078 | NO |
31 | EHHADH | EHHADH | EHHADH | 16105 | -0.21 | 0.091 | 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: BIOCARTA CREB PATHWAY.
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Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CREB 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 | PRPS2 | PRPS2 | PRPS2 | 38 | 0.6 | 0.22 | YES |
2 | ALDOB | ALDOB | ALDOB | 443 | 0.35 | 0.32 | YES |
3 | TKTL1 | TKTL1 | TKTL1 | 2302 | 0.16 | 0.27 | YES |
4 | PRPS1 | PRPS1 | PRPS1 | 2651 | 0.14 | 0.3 | YES |
5 | LOC729020 | LOC729020 | LOC729020 | 2659 | 0.14 | 0.35 | YES |
6 | GPI | GPI | GPI | 2869 | 0.13 | 0.39 | YES |
7 | PGM2 | PGM2 | PGM2 | 2968 | 0.13 | 0.43 | YES |
8 | PGM1 | PGM1 | PGM1 | 2988 | 0.13 | 0.47 | YES |
9 | ALDOC | ALDOC | ALDOC | 3142 | 0.12 | 0.51 | YES |
10 | FBP2 | FBP2 | FBP2 | 4257 | 0.092 | 0.48 | NO |
11 | PFKM | PFKM | PFKM | 5051 | 0.074 | 0.46 | NO |
12 | ALDOA | ALDOA | ALDOA | 5188 | 0.072 | 0.48 | NO |
13 | PFKL | PFKL | PFKL | 5901 | 0.057 | 0.46 | NO |
14 | PGLS | PGLS | PGLS | 5925 | 0.057 | 0.48 | NO |
15 | DERA | DERA | DERA | 6961 | 0.039 | 0.44 | NO |
16 | RPE | RPE | RPE | 7178 | 0.035 | 0.44 | NO |
17 | PGD | PGD | PGD | 8916 | 0.0056 | 0.34 | NO |
18 | RBKS | RBKS | RBKS | 9659 | -0.006 | 0.3 | NO |
19 | PFKP | PFKP | PFKP | 9879 | -0.0099 | 0.29 | NO |
20 | G6PD | G6PD | G6PD | 10188 | -0.015 | 0.28 | NO |
21 | H6PD | H6PD | H6PD | 10426 | -0.019 | 0.27 | NO |
22 | TALDO1 | TALDO1 | TALDO1 | 12267 | -0.055 | 0.19 | NO |
23 | RPIA | RPIA | RPIA | 12494 | -0.06 | 0.2 | NO |
24 | TKT | TKT | TKT | 12647 | -0.064 | 0.21 | NO |
25 | PRPS1L1 | PRPS1L1 | PRPS1L1 | 12996 | -0.072 | 0.22 | NO |
26 | FBP1 | FBP1 | FBP1 | 14708 | -0.13 | 0.17 | 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: ST ERK1 ERK2 MAPK PATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: ST ERK1 ERK2 MAPK 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 STARCH AND SUCROSE METABOLISM | 35 | genes.ES.table | 0.65 | 1.7 | 0.0042 | 0.39 | 0.75 | 0.29 | 0.061 | 0.27 | 0.18 | 0.1 |
BIOCARTA HDAC PATHWAY | 26 | genes.ES.table | 0.59 | 1.8 | 0 | 1 | 0.52 | 0.31 | 0.18 | 0.25 | 0.42 | 0.3 |
BIOCARTA IL2RB PATHWAY | 38 | genes.ES.table | 0.71 | 1.9 | 0.002 | 0.95 | 0.28 | 0.34 | 0.097 | 0.31 | 0 | 0.24 |
SIG BCR SIGNALING PATHWAY | 46 | genes.ES.table | 0.6 | 1.7 | 0.014 | 0.52 | 0.73 | 0.3 | 0.12 | 0.27 | 0.24 | 0.14 |
PID FCER1PATHWAY | 61 | genes.ES.table | 0.63 | 1.7 | 0.006 | 0.63 | 0.69 | 0.3 | 0.095 | 0.27 | 0.28 | 0.18 |
PID BCR 5PATHWAY | 65 | genes.ES.table | 0.56 | 1.7 | 0.04 | 0.38 | 0.81 | 0.31 | 0.16 | 0.26 | 0.19 | 0.095 |
PID GMCSF PATHWAY | 37 | genes.ES.table | 0.64 | 1.7 | 0.01 | 0.41 | 0.75 | 0.35 | 0.16 | 0.3 | 0.19 | 0.11 |
PID TCR PATHWAY | 66 | genes.ES.table | 0.73 | 1.7 | 0.012 | 0.49 | 0.73 | 0.44 | 0.12 | 0.39 | 0.23 | 0.13 |
PID CD8TCRPATHWAY | 53 | genes.ES.table | 0.73 | 1.7 | 0.0081 | 0.39 | 0.77 | 0.47 | 0.15 | 0.4 | 0.18 | 0.099 |
PID TCPTP PATHWAY | 42 | genes.ES.table | 0.53 | 1.7 | 0.018 | 0.38 | 0.8 | 0.36 | 0.2 | 0.28 | 0.19 | 0.097 |
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 | IL2RB | IL2RB | IL2RB | 31 | 0.88 | 0.11 | YES |
2 | FASLG | FASLG | FASLG | 138 | 0.68 | 0.18 | YES |
3 | PIK3CG | PIK3CG | PIK3CG | 163 | 0.66 | 0.27 | YES |
4 | IL2RG | IL2RG | IL2RG | 202 | 0.64 | 0.34 | YES |
5 | IL2RA | IL2RA | IL2RA | 336 | 0.58 | 0.41 | YES |
6 | IKZF3 | IKZF3 | IKZF3 | 395 | 0.55 | 0.47 | YES |
7 | SYK | SYK | SYK | 545 | 0.5 | 0.53 | YES |
8 | JAK3 | JAK3 | JAK3 | 794 | 0.44 | 0.57 | YES |
9 | BCL2 | BCL2 | BCL2 | 1394 | 0.33 | 0.57 | YES |
10 | PTPN6 | PTPN6 | PTPN6 | 1559 | 0.31 | 0.6 | YES |
11 | STAT5A | STAT5A | STAT5A | 1627 | 0.3 | 0.64 | YES |
12 | PIK3R1 | PIK3R1 | PIK3R1 | 1657 | 0.3 | 0.67 | YES |
13 | FAS | FAS | FAS | 1721 | 0.29 | 0.71 | YES |
14 | STAT5B | STAT5B | STAT5B | 2744 | 0.2 | 0.67 | NO |
15 | MAPK3 | MAPK3 | MAPK3 | 4472 | 0.11 | 0.59 | NO |
16 | JAK1 | JAK1 | JAK1 | 4779 | 0.097 | 0.58 | NO |
17 | FOS | FOS | FOS | 6045 | 0.06 | 0.52 | NO |
18 | CFLAR | CFLAR | CFLAR | 6344 | 0.052 | 0.51 | NO |
19 | SOS1 | SOS1 | SOS1 | 6990 | 0.037 | 0.48 | NO |
20 | BAD | BAD | BAD | 7089 | 0.034 | 0.48 | NO |
21 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 7186 | 0.032 | 0.48 | NO |
22 | BCL2L1 | BCL2L1 | BCL2L1 | 7288 | 0.03 | 0.47 | NO |
23 | SOCS3 | SOCS3 | SOCS3 | 7444 | 0.027 | 0.47 | NO |
24 | GRB2 | GRB2 | GRB2 | 8173 | 0.012 | 0.43 | NO |
25 | RAF1 | RAF1 | RAF1 | 8205 | 0.012 | 0.43 | NO |
26 | PIK3CA | PIK3CA | PIK3CA | 8369 | 0.0084 | 0.42 | NO |
27 | SHC1 | SHC1 | SHC1 | 8921 | -0.0026 | 0.39 | NO |
28 | NMI | NMI | NMI | 8928 | -0.0029 | 0.39 | NO |
29 | AKT1 | AKT1 | AKT1 | 9017 | -0.0045 | 0.38 | NO |
30 | IRS1 | IRS1 | IRS1 | 10772 | -0.038 | 0.29 | NO |
31 | CBL | CBL | CBL | 11295 | -0.049 | 0.27 | NO |
32 | MAPK1 | MAPK1 | MAPK1 | 11645 | -0.056 | 0.25 | NO |
33 | CRKL | CRKL | CRKL | 11706 | -0.058 | 0.26 | NO |
34 | SOCS1 | SOCS1 | SOCS1 | 12933 | -0.088 | 0.2 | NO |
35 | E2F1 | E2F1 | E2F1 | 13396 | -0.1 | 0.18 | NO |
36 | PPIA | PPIA | PPIA | 13454 | -0.1 | 0.2 | NO |
37 | HRAS | HRAS | HRAS | 13470 | -0.1 | 0.21 | NO |
38 | MYC | MYC | MYC | 16006 | -0.27 | 0.097 | 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 STARCH AND SUCROSE METABOLISM.

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

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 | IGF1 | IGF1 | IGF1 | 95 | 0.72 | 0.18 | YES |
2 | PIK3CG | PIK3CG | PIK3CG | 163 | 0.66 | 0.35 | YES |
3 | MAP2K6 | MAP2K6 | MAP2K6 | 1006 | 0.4 | 0.41 | YES |
4 | PIK3R1 | PIK3R1 | PIK3R1 | 1657 | 0.3 | 0.45 | YES |
5 | MEF2C | MEF2C | MEF2C | 2003 | 0.26 | 0.5 | YES |
6 | NFATC2 | NFATC2 | NFATC2 | 2108 | 0.25 | 0.56 | YES |
7 | HDAC5 | HDAC5 | HDAC5 | 2984 | 0.18 | 0.56 | YES |
8 | CAMK1G | CAMK1G | CAMK1G | 3168 | 0.17 | 0.59 | YES |
9 | NFATC1 | NFATC1 | NFATC1 | 4772 | 0.097 | 0.53 | NO |
10 | IGF1R | IGF1R | IGF1R | 6025 | 0.06 | 0.47 | NO |
11 | PPP3CA | PPP3CA | PPP3CA | 6175 | 0.056 | 0.48 | NO |
12 | PPP3CC | PPP3CC | PPP3CC | 7429 | 0.027 | 0.41 | NO |
13 | MEF2A | MEF2A | MEF2A | 7868 | 0.018 | 0.39 | NO |
14 | PIK3CA | PIK3CA | PIK3CA | 8369 | 0.0084 | 0.37 | NO |
15 | MAPK7 | MAPK7 | MAPK7 | 8375 | 0.0082 | 0.37 | NO |
16 | AKT1 | AKT1 | AKT1 | 9017 | -0.0045 | 0.33 | NO |
17 | CABIN1 | CABIN1 | CABIN1 | 9655 | -0.016 | 0.3 | NO |
18 | PPP3CB | PPP3CB | PPP3CB | 10164 | -0.026 | 0.28 | NO |
19 | CALM1 | CALM1 | CALM1 | 10276 | -0.029 | 0.28 | NO |
20 | MEF2D | MEF2D | MEF2D | 10534 | -0.034 | 0.28 | NO |
21 | CAMK1 | CAMK1 | CAMK1 | 11781 | -0.06 | 0.22 | NO |
22 | INSR | INSR | INSR | 12175 | -0.069 | 0.22 | NO |
23 | YWHAH | YWHAH | YWHAH | 12597 | -0.079 | 0.21 | NO |
24 | CALM3 | CALM3 | CALM3 | 12638 | -0.08 | 0.23 | NO |
25 | CALM2 | CALM2 | CALM2 | 12956 | -0.089 | 0.24 | NO |
26 | MAPK14 | MAPK14 | MAPK14 | 13897 | -0.12 | 0.22 | 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: BIOCARTA HDAC PATHWAY.

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

Table 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 | FASLG | FASLG | FASLG | 138 | 0.68 | 0.1 | YES |
2 | PIK3CD | PIK3CD | PIK3CD | 513 | 0.51 | 0.16 | YES |
3 | SYK | SYK | SYK | 545 | 0.5 | 0.24 | YES |
4 | BTK | BTK | BTK | 610 | 0.48 | 0.32 | YES |
5 | MAP2K6 | MAP2K6 | MAP2K6 | 1006 | 0.4 | 0.36 | YES |
6 | FAIM2 | FAIM2 | FAIM2 | 1308 | 0.35 | 0.4 | YES |
7 | BIRC3 | BIRC3 | BIRC3 | 1313 | 0.35 | 0.45 | YES |
8 | PIK3R1 | PIK3R1 | PIK3R1 | 1657 | 0.3 | 0.48 | YES |
9 | FAS | FAS | FAS | 1721 | 0.29 | 0.53 | YES |
10 | CASP10 | CASP10 | CASP10 | 2105 | 0.25 | 0.55 | YES |
11 | SMPD1 | SMPD1 | SMPD1 | 2437 | 0.22 | 0.56 | YES |
12 | IKBKB | IKBKB | IKBKB | 2693 | 0.21 | 0.58 | YES |
13 | PIK3CB | PIK3CB | PIK3CB | 3429 | 0.16 | 0.57 | NO |
14 | PIK3R2 | PIK3R2 | PIK3R2 | 4715 | 0.099 | 0.51 | NO |
15 | MAP3K1 | MAP3K1 | MAP3K1 | 4767 | 0.097 | 0.52 | NO |
16 | MAPK9 | MAPK9 | MAPK9 | 5210 | 0.083 | 0.51 | NO |
17 | SRC | SRC | SRC | 5993 | 0.061 | 0.48 | NO |
18 | MAPK10 | MAPK10 | MAPK10 | 6087 | 0.058 | 0.48 | NO |
19 | CASP8 | CASP8 | CASP8 | 6103 | 0.058 | 0.49 | NO |
20 | FADD | FADD | FADD | 6136 | 0.057 | 0.5 | NO |
21 | CFLAR | CFLAR | CFLAR | 6344 | 0.052 | 0.49 | NO |
22 | PDPK1 | PDPK1 | PDPK1 | 7074 | 0.035 | 0.46 | NO |
23 | IKBKG | IKBKG | IKBKG | 7452 | 0.026 | 0.44 | NO |
24 | EZR | EZR | EZR | 7760 | 0.02 | 0.43 | NO |
25 | RIPK1 | RIPK1 | RIPK1 | 7939 | 0.017 | 0.42 | NO |
26 | CLTC | CLTC | CLTC | 8069 | 0.014 | 0.41 | NO |
27 | PIK3R3 | PIK3R3 | PIK3R3 | 8181 | 0.012 | 0.41 | NO |
28 | PIK3CA | PIK3CA | PIK3CA | 8369 | 0.0084 | 0.4 | NO |
29 | AKT1 | AKT1 | AKT1 | 9017 | -0.0045 | 0.36 | NO |
30 | BID | BID | BID | 9843 | -0.021 | 0.32 | NO |
31 | MAP2K7 | MAP2K7 | MAP2K7 | 11117 | -0.045 | 0.26 | NO |
32 | RFC1 | RFC1 | RFC1 | 11608 | -0.056 | 0.24 | NO |
33 | CHUK | CHUK | CHUK | 12387 | -0.074 | 0.2 | NO |
34 | MAPK11 | MAPK11 | MAPK11 | 13383 | -0.1 | 0.17 | NO |
35 | BIRC2 | BIRC2 | BIRC2 | 13518 | -0.11 | 0.18 | NO |
36 | MAPK14 | MAPK14 | MAPK14 | 13897 | -0.12 | 0.17 | NO |
37 | CASP3 | CASP3 | CASP3 | 13926 | -0.12 | 0.19 | NO |
38 | MAPK8 | MAPK8 | MAPK8 | 14381 | -0.14 | 0.19 | NO |
Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL2RB PATHWAY.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB 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 | PPARGC1A | PPARGC1A | PPARGC1A | 68 | 0.77 | 0.13 | YES |
2 | KRT8 | KRT8 | KRT8 | 73 | 0.77 | 0.26 | YES |
3 | MITF | MITF | MITF | 373 | 0.56 | 0.34 | YES |
4 | KRT19 | KRT19 | KRT19 | 541 | 0.5 | 0.41 | YES |
5 | PLA2G4A | PLA2G4A | PLA2G4A | 936 | 0.41 | 0.46 | YES |
6 | NOS2 | NOS2 | NOS2 | 1786 | 0.28 | 0.46 | YES |
7 | MEF2C | MEF2C | MEF2C | 2003 | 0.26 | 0.49 | YES |
8 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 2024 | 0.26 | 0.53 | YES |
9 | HSPB1 | HSPB1 | HSPB1 | 2238 | 0.24 | 0.56 | YES |
10 | ESR1 | ESR1 | ESR1 | 4290 | 0.12 | 0.47 | NO |
11 | MAPKAPK5 | MAPKAPK5 | MAPKAPK5 | 4733 | 0.098 | 0.46 | NO |
12 | JUN | JUN | JUN | 4911 | 0.093 | 0.46 | NO |
13 | CEBPB | CEBPB | CEBPB | 4972 | 0.09 | 0.48 | NO |
14 | CSNK2A2 | CSNK2A2 | CSNK2A2 | 5400 | 0.077 | 0.46 | NO |
15 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5544 | 0.072 | 0.47 | NO |
16 | DDIT3 | DDIT3 | DDIT3 | 5609 | 0.071 | 0.48 | NO |
17 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 5932 | 0.062 | 0.47 | NO |
18 | CREB1 | CREB1 | CREB1 | 6212 | 0.055 | 0.46 | NO |
19 | PTGS2 | PTGS2 | PTGS2 | 6302 | 0.053 | 0.47 | NO |
20 | MKNK1 | MKNK1 | MKNK1 | 6472 | 0.049 | 0.47 | NO |
21 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 6764 | 0.042 | 0.46 | NO |
22 | SLC9A1 | SLC9A1 | SLC9A1 | 6831 | 0.041 | 0.46 | NO |
23 | MEF2A | MEF2A | MEF2A | 7868 | 0.018 | 0.4 | NO |
24 | RAB5A | RAB5A | RAB5A | 7912 | 0.017 | 0.4 | NO |
25 | GDI1 | GDI1 | GDI1 | 8188 | 0.012 | 0.39 | NO |
26 | ATF6 | ATF6 | ATF6 | 8691 | 0.0019 | 0.36 | NO |
27 | USF1 | USF1 | USF1 | 9539 | -0.014 | 0.32 | NO |
28 | EIF4E | EIF4E | EIF4E | 9856 | -0.021 | 0.3 | NO |
29 | TP53 | TP53 | TP53 | 9995 | -0.023 | 0.3 | NO |
30 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 10341 | -0.03 | 0.29 | NO |
31 | RPS6KA4 | RPS6KA4 | RPS6KA4 | 11563 | -0.054 | 0.23 | NO |
32 | HBP1 | HBP1 | HBP1 | 11612 | -0.056 | 0.23 | NO |
33 | CSNK2B | CSNK2B | CSNK2B | 12182 | -0.069 | 0.21 | NO |
34 | ATF2 | ATF2 | ATF2 | 12189 | -0.069 | 0.22 | NO |
35 | ATF1 | ATF1 | ATF1 | 12200 | -0.07 | 0.24 | NO |
36 | MAPK11 | MAPK11 | MAPK11 | 13383 | -0.1 | 0.18 | NO |
37 | MAPK14 | MAPK14 | MAPK14 | 13897 | -0.12 | 0.18 | NO |
38 | ELK4 | ELK4 | ELK4 | 15666 | -0.23 | 0.12 | 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: SIG BCR SIGNALING PATHWAY.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: SIG BCR SIGNALING 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 | SNCAIP | SNCAIP | SNCAIP | 126 | 0.7 | 0.11 | YES |
2 | LCK | LCK | LCK | 342 | 0.57 | 0.19 | YES |
3 | SNCA | SNCA | SNCA | 519 | 0.51 | 0.26 | YES |
4 | SYK | SYK | SYK | 545 | 0.5 | 0.34 | YES |
5 | PLCB2 | PLCB2 | PLCB2 | 553 | 0.5 | 0.42 | YES |
6 | HCK | HCK | HCK | 977 | 0.41 | 0.47 | YES |
7 | MAOB | MAOB | MAOB | 1184 | 0.37 | 0.51 | YES |
8 | LYN | LYN | LYN | 1350 | 0.34 | 0.56 | YES |
9 | SLC6A3 | SLC6A3 | SLC6A3 | 1518 | 0.32 | 0.6 | YES |
10 | BLK | BLK | BLK | 2486 | 0.22 | 0.58 | YES |
11 | FGR | FGR | FGR | 2503 | 0.22 | 0.62 | YES |
12 | PARK2 | PARK2 | PARK2 | 2751 | 0.2 | 0.64 | YES |
13 | PTK2B | PTK2B | PTK2B | 2950 | 0.19 | 0.66 | YES |
14 | FYN | FYN | FYN | 4175 | 0.12 | 0.61 | NO |
15 | MAPK3 | MAPK3 | MAPK3 | 4472 | 0.11 | 0.61 | NO |
16 | PLD1 | PLD1 | PLD1 | 5100 | 0.086 | 0.59 | NO |
17 | PLD2 | PLD2 | PLD2 | 5115 | 0.086 | 0.6 | NO |
18 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 5932 | 0.062 | 0.56 | NO |
19 | SRC | SRC | SRC | 5993 | 0.061 | 0.57 | NO |
20 | PRKCD | PRKCD | PRKCD | 6400 | 0.05 | 0.56 | NO |
21 | BAD | BAD | BAD | 7089 | 0.034 | 0.52 | NO |
22 | STUB1 | STUB1 | STUB1 | 7516 | 0.025 | 0.5 | NO |
23 | YES1 | YES1 | YES1 | 7984 | 0.016 | 0.48 | NO |
24 | PARK7 | PARK7 | PARK7 | 8295 | 0.0099 | 0.46 | NO |
25 | GRK5 | GRK5 | GRK5 | 8613 | 0.0037 | 0.45 | NO |
26 | FKBP1A | FKBP1A | FKBP1A | 10031 | -0.024 | 0.37 | NO |
27 | PPP2R5D | PPP2R5D | PPP2R5D | 10807 | -0.039 | 0.33 | NO |
28 | UBE2L3 | UBE2L3 | UBE2L3 | 11144 | -0.046 | 0.32 | NO |
29 | MAPK1 | MAPK1 | MAPK1 | 11645 | -0.056 | 0.3 | NO |
30 | UCHL1 | UCHL1 | UCHL1 | 11842 | -0.061 | 0.3 | NO |
31 | TOR1A | TOR1A | TOR1A | 12674 | -0.081 | 0.27 | NO |
32 | TH | TH | TH | 13575 | -0.11 | 0.23 | 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 FCER1PATHWAY.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: PID FCER1PATHWAY, 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 | ITK | ITK | ITK | 27 | 0.89 | 0.057 | YES |
2 | CD247 | CD247 | CD247 | 62 | 0.78 | 0.1 | YES |
3 | CD3E | CD3E | CD3E | 64 | 0.78 | 0.16 | YES |
4 | PTPRC | PTPRC | PTPRC | 116 | 0.7 | 0.2 | YES |
5 | GRAP2 | GRAP2 | GRAP2 | 158 | 0.67 | 0.24 | YES |
6 | HLA-DRB5 | HLA-DRB5 | HLA-DRB5 | 174 | 0.66 | 0.28 | YES |
7 | HLA-DQA1 | HLA-DQA1 | HLA-DQA1 | 206 | 0.64 | 0.32 | YES |
8 | CD3G | CD3G | CD3G | 213 | 0.64 | 0.36 | YES |
9 | TRAT1 | TRAT1 | TRAT1 | 225 | 0.63 | 0.4 | YES |
10 | CD3D | CD3D | CD3D | 265 | 0.6 | 0.44 | YES |
11 | HLA-DQA2 | HLA-DQA2 | HLA-DQA2 | 284 | 0.6 | 0.48 | YES |
12 | ZAP70 | ZAP70 | ZAP70 | 308 | 0.59 | 0.52 | YES |
13 | FYB | FYB | FYB | 317 | 0.58 | 0.56 | YES |
14 | CD4 | CD4 | CD4 | 328 | 0.58 | 0.59 | YES |
15 | LCK | LCK | LCK | 342 | 0.57 | 0.63 | YES |
16 | LCP2 | LCP2 | LCP2 | 360 | 0.56 | 0.66 | YES |
17 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 584 | 0.49 | 0.68 | YES |
18 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 666 | 0.47 | 0.71 | YES |
19 | WAS | WAS | WAS | 702 | 0.46 | 0.74 | YES |
20 | PAG1 | PAG1 | PAG1 | 744 | 0.45 | 0.77 | YES |
21 | HLA-DPB1 | HLA-DPB1 | HLA-DPB1 | 865 | 0.43 | 0.79 | YES |
22 | LAT | LAT | LAT | 1652 | 0.3 | 0.76 | NO |
23 | PIK3R1 | PIK3R1 | PIK3R1 | 1657 | 0.3 | 0.78 | NO |
24 | CARD11 | CARD11 | CARD11 | 2060 | 0.25 | 0.78 | NO |
25 | IKBKB | IKBKB | IKBKB | 2693 | 0.21 | 0.75 | NO |
26 | PIK3CB | PIK3CB | PIK3CB | 3429 | 0.16 | 0.72 | NO |
27 | RIPK2 | RIPK2 | RIPK2 | 4431 | 0.11 | 0.67 | NO |
28 | PIK3R2 | PIK3R2 | PIK3R2 | 4715 | 0.099 | 0.66 | NO |
29 | NFKBIA | NFKBIA | NFKBIA | 4886 | 0.094 | 0.66 | NO |
30 | NCK1 | NCK1 | NCK1 | 5107 | 0.086 | 0.65 | NO |
31 | MALT1 | MALT1 | MALT1 | 5924 | 0.062 | 0.61 | NO |
32 | PAK1 | PAK1 | PAK1 | 6317 | 0.053 | 0.59 | NO |
33 | TRAF6 | TRAF6 | TRAF6 | 6412 | 0.05 | 0.59 | NO |
34 | TAB2 | TAB2 | TAB2 | 7068 | 0.035 | 0.56 | NO |
35 | PDPK1 | PDPK1 | PDPK1 | 7074 | 0.035 | 0.56 | NO |
36 | IKBKG | IKBKG | IKBKG | 7452 | 0.026 | 0.54 | NO |
37 | PAK2 | PAK2 | PAK2 | 7769 | 0.02 | 0.52 | NO |
38 | PLCG1 | PLCG1 | PLCG1 | 8085 | 0.014 | 0.5 | NO |
39 | PIK3CA | PIK3CA | PIK3CA | 8369 | 0.0084 | 0.49 | NO |
40 | RELA | RELA | RELA | 8802 | -0.00044 | 0.46 | NO |
41 | VASP | VASP | VASP | 9469 | -0.013 | 0.43 | NO |
42 | UBE2N | UBE2N | UBE2N | 9511 | -0.014 | 0.42 | NO |
43 | CSK | CSK | CSK | 9698 | -0.018 | 0.42 | NO |
44 | MAP3K7 | MAP3K7 | MAP3K7 | 9753 | -0.019 | 0.41 | NO |
45 | ENAH | ENAH | ENAH | 9897 | -0.022 | 0.41 | NO |
46 | PTEN | PTEN | PTEN | 9998 | -0.023 | 0.4 | NO |
47 | BCL10 | BCL10 | BCL10 | 10492 | -0.033 | 0.38 | NO |
48 | PRKCQ | PRKCQ | PRKCQ | 10545 | -0.034 | 0.38 | NO |
49 | EVL | EVL | EVL | 11459 | -0.052 | 0.33 | NO |
50 | CHUK | CHUK | CHUK | 12387 | -0.074 | 0.28 | NO |
51 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 16414 | -0.32 | 0.074 | 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 BCR 5PATHWAY.

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

Table 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 | PIK3CG | PIK3CG | PIK3CG | 163 | 0.66 | 0.15 | YES |
2 | PIK3CD | PIK3CD | PIK3CD | 513 | 0.51 | 0.25 | YES |
3 | PIK3R6 | PIK3R6 | PIK3R6 | 1148 | 0.37 | 0.3 | YES |
4 | PIK3C2B | PIK3C2B | PIK3C2B | 1630 | 0.3 | 0.34 | YES |
5 | PIK3R1 | PIK3R1 | PIK3R1 | 1657 | 0.3 | 0.41 | YES |
6 | PIP4K2A | PIP4K2A | PIP4K2A | 1915 | 0.27 | 0.46 | YES |
7 | INPP4B | INPP4B | INPP4B | 1943 | 0.26 | 0.52 | YES |
8 | PIK3R5 | PIK3R5 | PIK3R5 | 1998 | 0.26 | 0.58 | YES |
9 | MTM1 | MTM1 | MTM1 | 2655 | 0.21 | 0.59 | YES |
10 | PIK3CB | PIK3CB | PIK3CB | 3429 | 0.16 | 0.58 | NO |
11 | MTMR1 | MTMR1 | MTMR1 | 4208 | 0.12 | 0.57 | NO |
12 | PIK3C2G | PIK3C2G | PIK3C2G | 4380 | 0.11 | 0.58 | NO |
13 | PIK3R2 | PIK3R2 | PIK3R2 | 4715 | 0.099 | 0.59 | NO |
14 | PIP5K1B | PIP5K1B | PIP5K1B | 5112 | 0.086 | 0.59 | NO |
15 | INPP5K | INPP5K | INPP5K | 6220 | 0.055 | 0.54 | NO |
16 | MTMR14 | MTMR14 | MTMR14 | 6748 | 0.043 | 0.52 | NO |
17 | INPP5J | INPP5J | INPP5J | 7067 | 0.035 | 0.51 | NO |
18 | PIK3R3 | PIK3R3 | PIK3R3 | 8181 | 0.012 | 0.45 | NO |
19 | PIP4K2B | PIP4K2B | PIP4K2B | 8210 | 0.012 | 0.45 | NO |
20 | PIK3CA | PIK3CA | PIK3CA | 8369 | 0.0084 | 0.44 | NO |
21 | PIK3C2A | PIK3C2A | PIK3C2A | 8590 | 0.0042 | 0.43 | NO |
22 | SYNJ2 | SYNJ2 | SYNJ2 | 8833 | -0.0011 | 0.42 | NO |
23 | PI4K2B | PI4K2B | PI4K2B | 9891 | -0.022 | 0.36 | NO |
24 | PIP5K1C | PIP5K1C | PIP5K1C | 9909 | -0.022 | 0.37 | NO |
25 | PTEN | PTEN | PTEN | 9998 | -0.023 | 0.37 | NO |
26 | MTMR6 | MTMR6 | MTMR6 | 10226 | -0.028 | 0.36 | NO |
27 | PI4K2A | PI4K2A | PI4K2A | 10347 | -0.03 | 0.36 | NO |
28 | INPPL1 | INPPL1 | INPPL1 | 11723 | -0.058 | 0.3 | NO |
29 | SYNJ1 | SYNJ1 | SYNJ1 | 12527 | -0.077 | 0.27 | NO |
30 | MTMR3 | MTMR3 | MTMR3 | 13409 | -0.1 | 0.24 | 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: PID GMCSF PATHWAY.

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

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MS4A2 | MS4A2 | MS4A2 | 24 | 0.9 | 0.076 | YES |
2 | ITK | ITK | ITK | 27 | 0.89 | 0.15 | YES |
3 | FCER1A | FCER1A | FCER1A | 358 | 0.56 | 0.18 | YES |
4 | LCP2 | LCP2 | LCP2 | 360 | 0.56 | 0.23 | YES |
5 | SYK | SYK | SYK | 545 | 0.5 | 0.26 | YES |
6 | BTK | BTK | BTK | 610 | 0.48 | 0.3 | YES |
7 | INPP5D | INPP5D | INPP5D | 643 | 0.48 | 0.34 | YES |
8 | KLRG1 | KLRG1 | KLRG1 | 737 | 0.46 | 0.38 | YES |
9 | FCGR2B | FCGR2B | FCGR2B | 754 | 0.45 | 0.41 | YES |
10 | VAV1 | VAV1 | VAV1 | 889 | 0.42 | 0.44 | YES |
11 | FCER1G | FCER1G | FCER1G | 935 | 0.41 | 0.48 | YES |
12 | PLA2G4A | PLA2G4A | PLA2G4A | 936 | 0.41 | 0.51 | YES |
13 | LAT2 | LAT2 | LAT2 | 1176 | 0.37 | 0.53 | YES |
14 | LYN | LYN | LYN | 1350 | 0.34 | 0.55 | YES |
15 | LAT | LAT | LAT | 1652 | 0.3 | 0.56 | YES |
16 | PIK3R1 | PIK3R1 | PIK3R1 | 1657 | 0.3 | 0.58 | YES |
17 | HCLS1 | HCLS1 | HCLS1 | 1673 | 0.3 | 0.61 | YES |
18 | DOK1 | DOK1 | DOK1 | 1686 | 0.3 | 0.63 | YES |
19 | NFATC2 | NFATC2 | NFATC2 | 2108 | 0.25 | 0.63 | NO |
20 | IKBKB | IKBKB | IKBKB | 2693 | 0.21 | 0.61 | NO |
21 | WIPF1 | WIPF1 | WIPF1 | 2858 | 0.2 | 0.62 | NO |
22 | PXN | PXN | PXN | 3957 | 0.13 | 0.57 | NO |
23 | FYN | FYN | FYN | 4175 | 0.12 | 0.57 | NO |
24 | MAPK3 | MAPK3 | MAPK3 | 4472 | 0.11 | 0.56 | NO |
25 | DUSP1 | DUSP1 | DUSP1 | 4637 | 0.1 | 0.56 | NO |
26 | MAP3K1 | MAP3K1 | MAP3K1 | 4767 | 0.097 | 0.56 | NO |
27 | MAP2K4 | MAP2K4 | MAP2K4 | 4774 | 0.097 | 0.57 | NO |
28 | JUN | JUN | JUN | 4911 | 0.093 | 0.57 | NO |
29 | NFKB1 | NFKB1 | NFKB1 | 4945 | 0.091 | 0.58 | NO |
30 | PLD2 | PLD2 | PLD2 | 5115 | 0.086 | 0.57 | NO |
31 | FER | FER | FER | 5432 | 0.076 | 0.56 | NO |
32 | RASA1 | RASA1 | RASA1 | 5938 | 0.062 | 0.54 | NO |
33 | FOS | FOS | FOS | 6045 | 0.06 | 0.54 | NO |
34 | S1PR1 | S1PR1 | S1PR1 | 6083 | 0.058 | 0.54 | NO |
35 | PTPN13 | PTPN13 | PTPN13 | 6392 | 0.051 | 0.53 | NO |
36 | PTPN11 | PTPN11 | PTPN11 | 6523 | 0.048 | 0.52 | NO |
37 | CBLB | CBLB | CBLB | 6956 | 0.038 | 0.5 | NO |
38 | PRKCB | PRKCB | PRKCB | 6978 | 0.037 | 0.51 | NO |
39 | SOS1 | SOS1 | SOS1 | 6990 | 0.037 | 0.51 | NO |
40 | PTK2 | PTK2 | PTK2 | 7287 | 0.03 | 0.5 | NO |
41 | IKBKG | IKBKG | IKBKG | 7452 | 0.026 | 0.49 | NO |
42 | PAK2 | PAK2 | PAK2 | 7769 | 0.02 | 0.47 | NO |
43 | PLCG1 | PLCG1 | PLCG1 | 8085 | 0.014 | 0.46 | NO |
44 | GRB2 | GRB2 | GRB2 | 8173 | 0.012 | 0.45 | NO |
45 | RAF1 | RAF1 | RAF1 | 8205 | 0.012 | 0.45 | NO |
46 | PIK3CA | PIK3CA | PIK3CA | 8369 | 0.0084 | 0.44 | NO |
47 | PPAP2A | PPAP2A | PPAP2A | 8660 | 0.0027 | 0.43 | NO |
48 | RELA | RELA | RELA | 8802 | -0.00044 | 0.42 | NO |
49 | SHC1 | SHC1 | SHC1 | 8921 | -0.0026 | 0.41 | NO |
50 | AKT1 | AKT1 | AKT1 | 9017 | -0.0045 | 0.41 | NO |
51 | MAP2K2 | MAP2K2 | MAP2K2 | 10117 | -0.026 | 0.35 | NO |
52 | MAP2K7 | MAP2K7 | MAP2K7 | 11117 | -0.045 | 0.29 | NO |
53 | CBL | CBL | CBL | 11295 | -0.049 | 0.29 | NO |
54 | MAPK1 | MAPK1 | MAPK1 | 11645 | -0.056 | 0.27 | NO |
55 | CHUK | CHUK | CHUK | 12387 | -0.074 | 0.24 | NO |
56 | MAP2K1 | MAP2K1 | MAP2K1 | 12405 | -0.074 | 0.24 | NO |
57 | GAB2 | GAB2 | GAB2 | 13183 | -0.095 | 0.21 | NO |
58 | HRAS | HRAS | HRAS | 13470 | -0.1 | 0.2 | NO |
59 | PLA2G1B | PLA2G1B | PLA2G1B | 13562 | -0.11 | 0.2 | NO |
60 | MAPK8 | MAPK8 | MAPK8 | 14381 | -0.14 | 0.17 | NO |
61 | SPHK1 | SPHK1 | SPHK1 | 15596 | -0.22 | 0.12 | NO |
Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TCR PATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: PID TCR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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Table 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 | CISH | CISH | CISH | 10 | 0.98 | 0.022 | YES |
2 | IL2RB | IL2RB | IL2RB | 31 | 0.88 | 0.041 | YES |
3 | CASP1 | CASP1 | CASP1 | 152 | 0.67 | 0.049 | YES |
4 | IRF6 | IRF6 | IRF6 | 164 | 0.66 | 0.064 | YES |
5 | GBP7 | GBP7 | GBP7 | 166 | 0.66 | 0.078 | YES |
6 | GBP5 | GBP5 | GBP5 | 172 | 0.66 | 0.093 | YES |
7 | HLA-DRB5 | HLA-DRB5 | HLA-DRB5 | 174 | 0.66 | 0.11 | YES |
8 | CSF2RB | CSF2RB | CSF2RB | 175 | 0.66 | 0.12 | YES |
9 | GBP2 | GBP2 | GBP2 | 186 | 0.65 | 0.14 | YES |
10 | IL2RG | IL2RG | IL2RG | 202 | 0.64 | 0.15 | YES |
11 | HLA-DQA1 | HLA-DQA1 | HLA-DQA1 | 206 | 0.64 | 0.17 | YES |
12 | PRLR | PRLR | PRLR | 218 | 0.63 | 0.18 | YES |
13 | PTAFR | PTAFR | PTAFR | 241 | 0.62 | 0.19 | YES |
14 | HLA-DQA2 | HLA-DQA2 | HLA-DQA2 | 284 | 0.6 | 0.2 | YES |
15 | HGF | HGF | HGF | 295 | 0.59 | 0.22 | YES |
16 | IL2RA | IL2RA | IL2RA | 336 | 0.58 | 0.23 | YES |
17 | LCK | LCK | LCK | 342 | 0.57 | 0.24 | YES |
18 | CAMK2A | CAMK2A | CAMK2A | 349 | 0.57 | 0.25 | YES |
19 | IL7 | IL7 | IL7 | 370 | 0.56 | 0.26 | YES |
20 | IRF5 | IRF5 | IRF5 | 496 | 0.52 | 0.27 | YES |
21 | PIK3CD | PIK3CD | PIK3CD | 513 | 0.51 | 0.28 | YES |
22 | PELI2 | PELI2 | PELI2 | 532 | 0.51 | 0.29 | YES |
23 | SYK | SYK | SYK | 545 | 0.5 | 0.3 | YES |
24 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 584 | 0.49 | 0.31 | YES |
25 | CIITA | CIITA | CIITA | 598 | 0.49 | 0.32 | YES |
26 | CSF2RA | CSF2RA | CSF2RA | 647 | 0.47 | 0.33 | YES |
27 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 666 | 0.47 | 0.34 | YES |
28 | JAK3 | JAK3 | JAK3 | 794 | 0.44 | 0.34 | YES |
29 | IRF4 | IRF4 | IRF4 | 803 | 0.44 | 0.35 | YES |
30 | HLA-DPB1 | HLA-DPB1 | HLA-DPB1 | 865 | 0.43 | 0.36 | YES |
31 | VAV1 | VAV1 | VAV1 | 889 | 0.42 | 0.36 | YES |
32 | CD44 | CD44 | CD44 | 894 | 0.42 | 0.37 | YES |
33 | IRF8 | IRF8 | IRF8 | 913 | 0.42 | 0.38 | YES |
34 | HCK | HCK | HCK | 977 | 0.41 | 0.39 | YES |
35 | MX2 | MX2 | MX2 | 986 | 0.4 | 0.4 | YES |
36 | MAP2K6 | MAP2K6 | MAP2K6 | 1006 | 0.4 | 0.4 | YES |
37 | IRAK2 | IRAK2 | IRAK2 | 1029 | 0.4 | 0.41 | YES |
38 | GBP4 | GBP4 | GBP4 | 1160 | 0.37 | 0.41 | YES |
39 | HLA-F | HLA-F | HLA-F | 1179 | 0.37 | 0.42 | YES |
40 | IRF1 | IRF1 | IRF1 | 1271 | 0.35 | 0.42 | YES |
41 | LYN | LYN | LYN | 1350 | 0.34 | 0.43 | YES |
42 | MAP3K8 | MAP3K8 | MAP3K8 | 1551 | 0.31 | 0.42 | YES |
43 | PTPN6 | PTPN6 | PTPN6 | 1559 | 0.31 | 0.43 | YES |
44 | FCGR1A | FCGR1A | FCGR1A | 1591 | 0.3 | 0.44 | YES |
45 | IL6R | IL6R | IL6R | 1597 | 0.3 | 0.44 | YES |
46 | STAT5A | STAT5A | STAT5A | 1627 | 0.3 | 0.45 | YES |
47 | PIK3R1 | PIK3R1 | PIK3R1 | 1657 | 0.3 | 0.45 | YES |
48 | EIF4E3 | EIF4E3 | EIF4E3 | 1682 | 0.3 | 0.46 | YES |
49 | IL18 | IL18 | IL18 | 1807 | 0.28 | 0.46 | YES |
50 | FCGR1B | FCGR1B | FCGR1B | 1921 | 0.27 | 0.46 | YES |
51 | IFI35 | IFI35 | IFI35 | 1931 | 0.27 | 0.46 | YES |
52 | SOCS2 | SOCS2 | SOCS2 | 2089 | 0.25 | 0.46 | YES |
53 | PELI3 | PELI3 | PELI3 | 2284 | 0.24 | 0.45 | YES |
54 | HLA-B | HLA-B | HLA-B | 2307 | 0.24 | 0.46 | YES |
55 | OAS2 | OAS2 | OAS2 | 2313 | 0.24 | 0.46 | YES |
56 | HLA-A | HLA-A | HLA-A | 2371 | 0.23 | 0.46 | YES |
57 | IL1B | IL1B | IL1B | 2463 | 0.22 | 0.46 | YES |
58 | GBP1 | GBP1 | GBP1 | 2519 | 0.22 | 0.47 | YES |
59 | CSF2 | CSF2 | CSF2 | 2535 | 0.22 | 0.47 | YES |
60 | IL6ST | IL6ST | IL6ST | 2563 | 0.22 | 0.47 | YES |
61 | SQSTM1 | SQSTM1 | SQSTM1 | 2620 | 0.21 | 0.48 | YES |
62 | IRF7 | IRF7 | IRF7 | 2641 | 0.21 | 0.48 | YES |
63 | BLNK | BLNK | BLNK | 2674 | 0.21 | 0.48 | YES |
64 | IRAK3 | IRAK3 | IRAK3 | 2687 | 0.21 | 0.48 | YES |
65 | IKBKB | IKBKB | IKBKB | 2693 | 0.21 | 0.49 | YES |
66 | STAT5B | STAT5B | STAT5B | 2744 | 0.2 | 0.49 | YES |
67 | PSMB8 | PSMB8 | PSMB8 | 2748 | 0.2 | 0.5 | YES |
68 | UBA7 | UBA7 | UBA7 | 2764 | 0.2 | 0.5 | YES |
69 | IL1RN | IL1RN | IL1RN | 2876 | 0.19 | 0.5 | YES |
70 | PELI1 | PELI1 | PELI1 | 2941 | 0.19 | 0.5 | YES |
71 | PTK2B | PTK2B | PTK2B | 2950 | 0.19 | 0.5 | YES |
72 | HERC5 | HERC5 | HERC5 | 3004 | 0.18 | 0.5 | YES |
73 | HLA-C | HLA-C | HLA-C | 3011 | 0.18 | 0.51 | YES |
74 | IL1A | IL1A | IL1A | 3025 | 0.18 | 0.51 | YES |
75 | NOD1 | NOD1 | NOD1 | 3061 | 0.18 | 0.51 | YES |
76 | B2M | B2M | B2M | 3070 | 0.18 | 0.52 | YES |
77 | IL7R | IL7R | IL7R | 3411 | 0.16 | 0.5 | NO |
78 | HLA-G | HLA-G | HLA-G | 3427 | 0.16 | 0.5 | NO |
79 | PIK3CB | PIK3CB | PIK3CB | 3429 | 0.16 | 0.51 | NO |
80 | IFITM1 | IFITM1 | IFITM1 | 3436 | 0.16 | 0.51 | NO |
81 | IFIT3 | IFIT3 | IFIT3 | 3487 | 0.15 | 0.51 | NO |
82 | IFNG | IFNG | IFNG | 3532 | 0.15 | 0.51 | NO |
83 | IRAK4 | IRAK4 | IRAK4 | 3672 | 0.14 | 0.51 | NO |
84 | GBP6 | GBP6 | GBP6 | 3930 | 0.13 | 0.5 | NO |
85 | IFIT2 | IFIT2 | IFIT2 | 3982 | 0.13 | 0.5 | NO |
86 | MYD88 | MYD88 | MYD88 | 4115 | 0.12 | 0.49 | NO |
87 | FYN | FYN | FYN | 4175 | 0.12 | 0.49 | NO |
88 | DDX58 | DDX58 | DDX58 | 4224 | 0.12 | 0.49 | NO |
89 | PML | PML | PML | 4244 | 0.12 | 0.49 | NO |
90 | RIPK2 | RIPK2 | RIPK2 | 4431 | 0.11 | 0.48 | NO |
91 | MAPK3 | MAPK3 | MAPK3 | 4472 | 0.11 | 0.48 | NO |
92 | ICAM1 | ICAM1 | ICAM1 | 4597 | 0.1 | 0.48 | NO |
93 | IL3RA | IL3RA | IL3RA | 4638 | 0.1 | 0.48 | NO |
94 | NOD2 | NOD2 | NOD2 | 4699 | 0.1 | 0.48 | NO |
95 | PIK3R2 | PIK3R2 | PIK3R2 | 4715 | 0.099 | 0.48 | NO |
96 | SP100 | SP100 | SP100 | 4743 | 0.098 | 0.48 | NO |
97 | IFITM2 | IFITM2 | IFITM2 | 4766 | 0.097 | 0.48 | NO |
98 | MAP2K4 | MAP2K4 | MAP2K4 | 4774 | 0.097 | 0.48 | NO |
99 | JAK1 | JAK1 | JAK1 | 4779 | 0.097 | 0.48 | NO |
100 | CAMK2D | CAMK2D | CAMK2D | 4842 | 0.095 | 0.48 | NO |
101 | MAP3K3 | MAP3K3 | MAP3K3 | 4931 | 0.092 | 0.48 | NO |
102 | STAT2 | STAT2 | STAT2 | 4938 | 0.091 | 0.48 | NO |
103 | RNASEL | RNASEL | RNASEL | 5012 | 0.088 | 0.48 | NO |
104 | IRS2 | IRS2 | IRS2 | 5066 | 0.087 | 0.48 | NO |
105 | STAT3 | STAT3 | STAT3 | 5143 | 0.085 | 0.48 | NO |
106 | XAF1 | XAF1 | XAF1 | 5156 | 0.084 | 0.48 | NO |
107 | IFNAR2 | IFNAR2 | IFNAR2 | 5191 | 0.084 | 0.48 | NO |
108 | GHR | GHR | GHR | 5268 | 0.081 | 0.48 | NO |
109 | UBE2L6 | UBE2L6 | UBE2L6 | 5281 | 0.081 | 0.48 | NO |
110 | PRKACB | PRKACB | PRKACB | 5535 | 0.073 | 0.46 | NO |
111 | TAB3 | TAB3 | TAB3 | 5554 | 0.072 | 0.46 | NO |
112 | JAK2 | JAK2 | JAK2 | 5762 | 0.067 | 0.45 | NO |
113 | IL6 | IL6 | IL6 | 5982 | 0.061 | 0.44 | NO |
114 | TNIP2 | TNIP2 | TNIP2 | 6173 | 0.056 | 0.43 | NO |
115 | PTPN1 | PTPN1 | PTPN1 | 6347 | 0.052 | 0.42 | NO |
116 | PRKCD | PRKCD | PRKCD | 6400 | 0.05 | 0.42 | NO |
117 | TRAF6 | TRAF6 | TRAF6 | 6412 | 0.05 | 0.42 | NO |
118 | KPNA4 | KPNA4 | KPNA4 | 6536 | 0.047 | 0.42 | NO |
119 | UBE2E1 | UBE2E1 | UBE2E1 | 6562 | 0.047 | 0.42 | NO |
120 | FLNB | FLNB | FLNB | 6669 | 0.044 | 0.41 | NO |
121 | TOLLIP | TOLLIP | TOLLIP | 6772 | 0.042 | 0.41 | NO |
122 | KPNA1 | KPNA1 | KPNA1 | 6819 | 0.041 | 0.4 | NO |
123 | SOS1 | SOS1 | SOS1 | 6990 | 0.037 | 0.4 | NO |
124 | NCAM1 | NCAM1 | NCAM1 | 7061 | 0.035 | 0.39 | NO |
125 | TAB2 | TAB2 | TAB2 | 7068 | 0.035 | 0.39 | NO |
126 | NFKB2 | NFKB2 | NFKB2 | 7094 | 0.034 | 0.39 | NO |
127 | YWHAB | YWHAB | YWHAB | 7106 | 0.034 | 0.39 | NO |
128 | PPM1B | PPM1B | PPM1B | 7167 | 0.033 | 0.39 | NO |
129 | IFITM3 | IFITM3 | IFITM3 | 7402 | 0.028 | 0.38 | NO |
130 | SOCS3 | SOCS3 | SOCS3 | 7444 | 0.027 | 0.38 | NO |
131 | IKBKG | IKBKG | IKBKG | 7452 | 0.026 | 0.38 | NO |
132 | NUP43 | NUP43 | NUP43 | 7527 | 0.025 | 0.37 | NO |
133 | TEC | TEC | TEC | 7695 | 0.022 | 0.36 | NO |
134 | OASL | OASL | OASL | 7765 | 0.02 | 0.36 | NO |
135 | EIF4G2 | EIF4G2 | EIF4G2 | 7850 | 0.018 | 0.36 | NO |
136 | IFIT1 | IFIT1 | IFIT1 | 7852 | 0.018 | 0.36 | NO |
137 | YES1 | YES1 | YES1 | 7984 | 0.016 | 0.35 | NO |
138 | IP6K2 | IP6K2 | IP6K2 | 7993 | 0.016 | 0.35 | NO |
139 | OAS1 | OAS1 | OAS1 | 8004 | 0.015 | 0.35 | NO |
140 | IRF3 | IRF3 | IRF3 | 8027 | 0.015 | 0.35 | NO |
141 | PLCG1 | PLCG1 | PLCG1 | 8085 | 0.014 | 0.34 | NO |
142 | EIF4G1 | EIF4G1 | EIF4G1 | 8155 | 0.013 | 0.34 | NO |
143 | GRB2 | GRB2 | GRB2 | 8173 | 0.012 | 0.34 | NO |
144 | PIK3R3 | PIK3R3 | PIK3R3 | 8181 | 0.012 | 0.34 | NO |
145 | RAF1 | RAF1 | RAF1 | 8205 | 0.012 | 0.34 | NO |
146 | YWHAZ | YWHAZ | YWHAZ | 8261 | 0.011 | 0.34 | NO |
147 | CRK | CRK | CRK | 8267 | 0.01 | 0.34 | NO |
148 | NUP88 | NUP88 | NUP88 | 8269 | 0.01 | 0.34 | NO |
149 | PIK3CA | PIK3CA | PIK3CA | 8369 | 0.0084 | 0.33 | NO |
150 | EIF4G3 | EIF4G3 | EIF4G3 | 8412 | 0.0075 | 0.33 | NO |
151 | AAAS | AAAS | AAAS | 8454 | 0.0066 | 0.33 | NO |
152 | PIAS1 | PIAS1 | PIAS1 | 8469 | 0.0063 | 0.32 | NO |
153 | SH2B1 | SH2B1 | SH2B1 | 8756 | 0.0007 | 0.31 | NO |
154 | RELA | RELA | RELA | 8802 | -0.00044 | 0.31 | NO |
155 | EIF4A2 | EIF4A2 | EIF4A2 | 8826 | -0.001 | 0.3 | NO |
156 | ISG15 | ISG15 | ISG15 | 8828 | -0.001 | 0.3 | NO |
157 | SHC1 | SHC1 | SHC1 | 8921 | -0.0026 | 0.3 | NO |
158 | SKP1 | SKP1 | SKP1 | 8931 | -0.0029 | 0.3 | NO |
159 | ADAR | ADAR | ADAR | 8997 | -0.0042 | 0.3 | NO |
160 | NUP153 | NUP153 | NUP153 | 9061 | -0.0052 | 0.29 | NO |
161 | SEH1L | SEH1L | SEH1L | 9238 | -0.0083 | 0.28 | NO |
162 | IFNGR1 | IFNGR1 | IFNGR1 | 9400 | -0.012 | 0.27 | NO |
163 | RANBP2 | RANBP2 | RANBP2 | 9411 | -0.012 | 0.27 | NO |
164 | POM121 | POM121 | POM121 | 9416 | -0.012 | 0.27 | NO |
165 | IL1R1 | IL1R1 | IL1R1 | 9422 | -0.012 | 0.27 | NO |
166 | UBE2N | UBE2N | UBE2N | 9511 | -0.014 | 0.27 | NO |
167 | IRF2 | IRF2 | IRF2 | 9569 | -0.015 | 0.26 | NO |
168 | TAB1 | TAB1 | TAB1 | 9712 | -0.018 | 0.26 | NO |
169 | MAP3K7 | MAP3K7 | MAP3K7 | 9753 | -0.019 | 0.26 | NO |
170 | EIF4E | EIF4E | EIF4E | 9856 | -0.021 | 0.25 | NO |
171 | STAT1 | STAT1 | STAT1 | 9907 | -0.022 | 0.25 | NO |
172 | NUP85 | NUP85 | NUP85 | 9932 | -0.022 | 0.25 | NO |
173 | EGR1 | EGR1 | EGR1 | 10042 | -0.024 | 0.24 | NO |
174 | ARIH1 | ARIH1 | ARIH1 | 10047 | -0.024 | 0.24 | NO |
175 | CUL1 | CUL1 | CUL1 | 10077 | -0.025 | 0.24 | NO |
176 | MAP2K2 | MAP2K2 | MAP2K2 | 10117 | -0.026 | 0.24 | NO |
177 | NUP37 | NUP37 | NUP37 | 10476 | -0.033 | 0.22 | NO |
178 | NUP50 | NUP50 | NUP50 | 10517 | -0.033 | 0.22 | NO |
179 | IL1RAP | IL1RAP | IL1RAP | 10551 | -0.034 | 0.22 | NO |
180 | IRS1 | IRS1 | IRS1 | 10772 | -0.038 | 0.2 | NO |
181 | NUP107 | NUP107 | NUP107 | 11063 | -0.044 | 0.19 | NO |
182 | CBL | CBL | CBL | 11295 | -0.049 | 0.18 | NO |
183 | NUP214 | NUP214 | NUP214 | 11303 | -0.049 | 0.18 | NO |
184 | NEDD4 | NEDD4 | NEDD4 | 11353 | -0.05 | 0.18 | NO |
185 | NUP54 | NUP54 | NUP54 | 11372 | -0.05 | 0.18 | NO |
186 | RAE1 | RAE1 | RAE1 | 11381 | -0.05 | 0.18 | NO |
187 | NUP93 | NUP93 | NUP93 | 11412 | -0.051 | 0.18 | NO |
188 | NUP155 | NUP155 | NUP155 | 11456 | -0.052 | 0.18 | NO |
189 | NUP133 | NUP133 | NUP133 | 11519 | -0.053 | 0.17 | NO |
190 | KPNA3 | KPNA3 | KPNA3 | 11548 | -0.054 | 0.17 | NO |
191 | TPR | TPR | TPR | 11598 | -0.055 | 0.17 | NO |
192 | NUPL2 | NUPL2 | NUPL2 | 11605 | -0.055 | 0.17 | NO |
193 | MAPK1 | MAPK1 | MAPK1 | 11645 | -0.056 | 0.17 | NO |
194 | CRKL | CRKL | CRKL | 11706 | -0.058 | 0.17 | NO |
195 | PTPN2 | PTPN2 | PTPN2 | 11708 | -0.058 | 0.17 | NO |
196 | INPPL1 | INPPL1 | INPPL1 | 11723 | -0.058 | 0.17 | NO |
197 | IFNGR2 | IFNGR2 | IFNGR2 | 11808 | -0.06 | 0.17 | NO |
198 | MT2A | MT2A | MT2A | 11944 | -0.064 | 0.16 | NO |
199 | BTRC | BTRC | BTRC | 11984 | -0.064 | 0.16 | NO |
200 | MX1 | MX1 | MX1 | 12070 | -0.066 | 0.16 | NO |
201 | IRAK1 | IRAK1 | IRAK1 | 12302 | -0.072 | 0.14 | NO |
202 | CHUK | CHUK | CHUK | 12387 | -0.074 | 0.14 | NO |
203 | MAP2K1 | MAP2K1 | MAP2K1 | 12405 | -0.074 | 0.14 | NO |
204 | KPNB1 | KPNB1 | KPNB1 | 12412 | -0.074 | 0.14 | NO |
205 | IFI6 | IFI6 | IFI6 | 12464 | -0.076 | 0.14 | NO |
206 | NRAS | NRAS | NRAS | 12488 | -0.076 | 0.14 | NO |
207 | TYK2 | TYK2 | TYK2 | 12507 | -0.077 | 0.14 | NO |
208 | SUMO1 | SUMO1 | SUMO1 | 12639 | -0.08 | 0.14 | NO |
209 | IFNAR1 | IFNAR1 | IFNAR1 | 12668 | -0.081 | 0.14 | NO |
210 | NUP205 | NUP205 | NUP205 | 12725 | -0.082 | 0.14 | NO |
211 | OAS3 | OAS3 | OAS3 | 12773 | -0.084 | 0.14 | NO |
212 | UBA52 | UBA52 | UBA52 | 12879 | -0.087 | 0.13 | NO |
213 | SOCS1 | SOCS1 | SOCS1 | 12933 | -0.088 | 0.13 | NO |
214 | RBX1 | RBX1 | RBX1 | 12962 | -0.089 | 0.13 | NO |
215 | EIF4A1 | EIF4A1 | EIF4A1 | 13026 | -0.091 | 0.13 | NO |
216 | KRAS | KRAS | KRAS | 13044 | -0.091 | 0.13 | NO |
217 | RPS27A | RPS27A | RPS27A | 13117 | -0.093 | 0.13 | NO |
218 | GAB2 | GAB2 | GAB2 | 13183 | -0.095 | 0.13 | NO |
219 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 13215 | -0.096 | 0.13 | NO |
220 | NUPL1 | NUPL1 | NUPL1 | 13317 | -0.1 | 0.12 | NO |
221 | HRAS | HRAS | HRAS | 13470 | -0.1 | 0.12 | NO |
222 | EIF4E2 | EIF4E2 | EIF4E2 | 13658 | -0.11 | 0.11 | NO |
223 | TRIM25 | TRIM25 | TRIM25 | 13740 | -0.12 | 0.11 | NO |
224 | EIF4A3 | EIF4A3 | EIF4A3 | 13990 | -0.12 | 0.097 | NO |
225 | PIN1 | PIN1 | PIN1 | 14053 | -0.13 | 0.096 | NO |
226 | NUP62 | NUP62 | NUP62 | 14096 | -0.13 | 0.097 | NO |
227 | KPNA5 | KPNA5 | KPNA5 | 14125 | -0.13 | 0.098 | NO |
228 | USP18 | USP18 | USP18 | 14157 | -0.13 | 0.099 | NO |
229 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 14367 | -0.14 | 0.091 | NO |
230 | NUP188 | NUP188 | NUP188 | 14616 | -0.16 | 0.08 | NO |
231 | VCAM1 | VCAM1 | VCAM1 | 14723 | -0.16 | 0.078 | NO |
232 | NUP35 | NUP35 | NUP35 | 14755 | -0.16 | 0.08 | NO |
233 | ADAM17 | ADAM17 | ADAM17 | 14780 | -0.16 | 0.082 | NO |
234 | NUP210 | NUP210 | NUP210 | 14896 | -0.17 | 0.079 | NO |
235 | IRF9 | IRF9 | IRF9 | 15081 | -0.18 | 0.073 | NO |
236 | CAMK2B | CAMK2B | CAMK2B | 15516 | -0.22 | 0.053 | NO |
237 | GH1 | GH1 | GH1 | 15775 | -0.24 | 0.044 | NO |
238 | KPNA2 | KPNA2 | KPNA2 | 15901 | -0.26 | 0.042 | NO |
239 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 16414 | -0.32 | 0.02 | NO |
240 | IFI27 | IFI27 | IFI27 | 16685 | -0.36 | 0.013 | NO |
241 | ISG20 | ISG20 | ISG20 | 17112 | -0.46 | -0.00083 | NO |
242 | PRL | PRL | PRL | 17254 | -0.5 | 0.0025 | NO |
243 | IL1R2 | IL1R2 | IL1R2 | 17301 | -0.52 | 0.012 | NO |
244 | CDK1 | CDK1 | CDK1 | 17336 | -0.53 | 0.022 | NO |
Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID CD8TCRPATHWAY.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: PID CD8TCRPATHWAY, 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 | CD247 | CD247 | CD247 | 62 | 0.78 | 0.044 | YES |
2 | CD3E | CD3E | CD3E | 64 | 0.78 | 0.092 | YES |
3 | PDCD1LG2 | PDCD1LG2 | PDCD1LG2 | 153 | 0.67 | 0.13 | YES |
4 | GRAP2 | GRAP2 | GRAP2 | 158 | 0.67 | 0.17 | YES |
5 | HLA-DRB5 | HLA-DRB5 | HLA-DRB5 | 174 | 0.66 | 0.21 | YES |
6 | CD28 | CD28 | CD28 | 183 | 0.65 | 0.25 | YES |
7 | HLA-DQA1 | HLA-DQA1 | HLA-DQA1 | 206 | 0.64 | 0.28 | YES |
8 | CD3G | CD3G | CD3G | 213 | 0.64 | 0.32 | YES |
9 | CD3D | CD3D | CD3D | 265 | 0.6 | 0.36 | YES |
10 | HLA-DQA2 | HLA-DQA2 | HLA-DQA2 | 284 | 0.6 | 0.39 | YES |
11 | ICOS | ICOS | ICOS | 306 | 0.59 | 0.43 | YES |
12 | CD4 | CD4 | CD4 | 328 | 0.58 | 0.46 | YES |
13 | LCK | LCK | LCK | 342 | 0.57 | 0.5 | YES |
14 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 584 | 0.49 | 0.51 | YES |
15 | ICOSLG | ICOSLG | ICOSLG | 629 | 0.48 | 0.54 | YES |
16 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 666 | 0.47 | 0.57 | YES |
17 | HLA-DPB1 | HLA-DPB1 | HLA-DPB1 | 865 | 0.43 | 0.58 | YES |
18 | VAV1 | VAV1 | VAV1 | 889 | 0.42 | 0.61 | YES |
19 | CTLA4 | CTLA4 | CTLA4 | 961 | 0.41 | 0.63 | YES |
20 | CD274 | CD274 | CD274 | 964 | 0.41 | 0.65 | YES |
21 | PDCD1 | PDCD1 | PDCD1 | 1042 | 0.39 | 0.67 | YES |
22 | CD86 | CD86 | CD86 | 1348 | 0.34 | 0.68 | YES |
23 | LYN | LYN | LYN | 1350 | 0.34 | 0.7 | YES |
24 | MAP3K8 | MAP3K8 | MAP3K8 | 1551 | 0.31 | 0.7 | YES |
25 | PTPN6 | PTPN6 | PTPN6 | 1559 | 0.31 | 0.72 | YES |
26 | PIK3R1 | PIK3R1 | PIK3R1 | 1657 | 0.3 | 0.74 | YES |
27 | CD80 | CD80 | CD80 | 2487 | 0.22 | 0.7 | NO |
28 | AKT3 | AKT3 | AKT3 | 3103 | 0.18 | 0.68 | NO |
29 | BTLA | BTLA | BTLA | 3281 | 0.17 | 0.68 | NO |
30 | TNFRSF14 | TNFRSF14 | TNFRSF14 | 3750 | 0.14 | 0.66 | NO |
31 | MAP3K14 | MAP3K14 | MAP3K14 | 3921 | 0.13 | 0.66 | NO |
32 | FYN | FYN | FYN | 4175 | 0.12 | 0.65 | NO |
33 | RICTOR | RICTOR | RICTOR | 4606 | 0.1 | 0.63 | NO |
34 | PIK3R2 | PIK3R2 | PIK3R2 | 4715 | 0.099 | 0.63 | NO |
35 | MLST8 | MLST8 | MLST8 | 5744 | 0.067 | 0.58 | NO |
36 | PPP2CB | PPP2CB | PPP2CB | 5913 | 0.063 | 0.57 | NO |
37 | SRC | SRC | SRC | 5993 | 0.061 | 0.57 | NO |
38 | PAK1 | PAK1 | PAK1 | 6317 | 0.053 | 0.56 | NO |
39 | PDPK1 | PDPK1 | PDPK1 | 7074 | 0.035 | 0.52 | NO |
40 | THEM4 | THEM4 | THEM4 | 7159 | 0.033 | 0.52 | NO |
41 | PAK2 | PAK2 | PAK2 | 7769 | 0.02 | 0.48 | NO |
42 | YES1 | YES1 | YES1 | 7984 | 0.016 | 0.47 | NO |
43 | GRB2 | GRB2 | GRB2 | 8173 | 0.012 | 0.46 | NO |
44 | PIK3R3 | PIK3R3 | PIK3R3 | 8181 | 0.012 | 0.46 | NO |
45 | PIK3CA | PIK3CA | PIK3CA | 8369 | 0.0084 | 0.45 | NO |
46 | PPP2CA | PPP2CA | PPP2CA | 8919 | -0.0026 | 0.42 | NO |
47 | AKT1 | AKT1 | AKT1 | 9017 | -0.0045 | 0.42 | NO |
48 | RAC1 | RAC1 | RAC1 | 9616 | -0.016 | 0.38 | NO |
49 | CSK | CSK | CSK | 9698 | -0.018 | 0.38 | NO |
50 | TRIB3 | TRIB3 | TRIB3 | 9871 | -0.021 | 0.37 | NO |
51 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 10184 | -0.027 | 0.35 | NO |
52 | CDC42 | CDC42 | CDC42 | 10489 | -0.033 | 0.34 | NO |
53 | PPP2R5D | PPP2R5D | PPP2R5D | 10807 | -0.039 | 0.32 | NO |
54 | PPP2R1B | PPP2R1B | PPP2R1B | 11547 | -0.054 | 0.28 | NO |
55 | PPP2R5A | PPP2R5A | PPP2R5A | 12314 | -0.072 | 0.24 | NO |
56 | MTOR | MTOR | MTOR | 13637 | -0.11 | 0.18 | NO |
57 | PPP2R1A | PPP2R1A | PPP2R1A | 14403 | -0.14 | 0.14 | NO |
58 | AKT2 | AKT2 | AKT2 | 14564 | -0.15 | 0.14 | NO |
59 | PPP2R5C | PPP2R5C | PPP2R5C | 15083 | -0.18 | 0.12 | NO |
60 | PPP2R5E | PPP2R5E | PPP2R5E | 15272 | -0.2 | 0.13 | NO |
61 | PPP2R5B | PPP2R5B | PPP2R5B | 15306 | -0.2 | 0.14 | NO |
Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TCPTP PATHWAY.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: PID TCPTP 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
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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 = ACC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Phenotype data file = ACC-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.