Ovarian Serous Cystadenocarcinoma: Mutation Analysis (MutSig)
Maintained by Dan DiCara
(Broad Institute)
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Overview
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Introduction
This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v1.5 was used to generate the results found in this report.
Working with individual set: OV.
Number of patients in set: 316
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Input
The input for this pipeline is a set of individuals with the following files associated for each:
1. An annotated .maf file describing the mutations called for the respective individual, and their properties.
2. A .wig file that contains information about the coverage of the sample.
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Summary
Significantly mutated genes (q ≤ 0.1): 24
Mutations seen in COSMIC: 394
Significantly mutated genes in COSMIC territory: 39
Genes with clustered mutations (&le 3 aa apart): 107
Significantly mutated genesets: 63
Significantly mutated genesets: (excluding sig. mutated genes): 9
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Results
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Breakdown of Mutations by Type
Table 1. Get Full Table Table representing breakdown of mutations by type.
| type | count |
|---|---|
| Frame_Shift_Del | 447 |
| Frame_Shift_Ins | 155 |
| In_Frame_Del | 148 |
| In_Frame_Ins | 37 |
| Indel | 13 |
| Missense_Mutation | 13161 |
| Nonsense_Mutation | 803 |
| Nonstop_Mutation | 16 |
| Silent | 4230 |
| Splice_Site_Del | 33 |
| Splice_Site_Ins | 5 |
| Splice_Site_SNP | 388 |
| Total | 19436 |
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Breakdown of Mutation Rates by Category Type
Table 2. Get Full Table A breakdown of mutation rates per category discovered for this individual set.
| category | n | N | rate | rate_per_mb | relative_rate |
|---|---|---|---|---|---|
| *CpG->T | 1860 | 396729715 | 4.7e-06 | 4.7 | 2.5 |
| *Cp(A/C/T)->T | 2187 | 3661505903 | 6e-07 | 0.6 | 0.32 |
| C->(G/A) | 5212 | 4058235618 | 1.3e-06 | 1.3 | 0.69 |
| A->mut | 3901 | 4115893953 | 9.5e-07 | 0.95 | 0.51 |
| indel+null | 2024 | 8174129610 | 2.5e-07 | 0.25 | 0.13 |
| double_null | 22 | 8174129610 | 2.7e-09 | 0.0027 | 0.0014 |
| Total | 15206 | 8174129610 | 1.9e-06 | 1.9 | 1 |
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Target Coverage for Each Individual
The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).
Figure 1.
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Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples
Figure 2.
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Significantly Mutated Genes
Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 24. Number of genes displayed: 35
| rank | gene | description | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | TP53 | tumor protein p53 | 401524 | 279 | 276 | 143 | 3 | 47 | 31 | 39 | 61 | 101 | 0 | <1.00e-15 | <1.71e-11 |
| 2 | BRCA1 | breast cancer 1, early onset | 1798045 | 12 | 12 | 12 | 0 | 0 | 0 | 1 | 0 | 11 | 0 | 1.76e-08 | 0.00015 |
| 3 | RB1 | retinoblastoma 1 (including osteosarcoma) | 826059 | 9 | 9 | 9 | 0 | 0 | 1 | 3 | 0 | 5 | 0 | 7.52e-07 | 0.0043 |
| 4 | NF1 | neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) | 2619095 | 15 | 14 | 15 | 0 | 1 | 1 | 1 | 3 | 9 | 0 | 1.63e-06 | 0.0057 |
| 5 | CSMD3 | CUB and Sushi multiple domains 3 | 3615081 | 18 | 18 | 18 | 3 | 0 | 2 | 7 | 8 | 1 | 0 | 1.66e-06 | 0.0057 |
| 6 | FAT3 | FAT tumor suppressor homolog 3 (Drosophila) | 3706784 | 20 | 19 | 20 | 1 | 4 | 2 | 3 | 10 | 1 | 0 | 0.000011 | 0.032 |
| 7 | CYP11B1 | cytochrome P450, family 11, subfamily B, polypeptide 1 | 456589 | 7 | 7 | 6 | 0 | 1 | 0 | 3 | 3 | 0 | 0 | 0.000018 | 0.044 |
| 8 | CHST2 | carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2 | 172127 | 5 | 5 | 5 | 1 | 0 | 2 | 2 | 1 | 0 | 0 | 0.000028 | 0.060 |
| 9 | C9orf171 | 251675 | 5 | 5 | 5 | 0 | 2 | 0 | 2 | 0 | 1 | 0 | 0.000038 | 0.066 | |
| 10 | DUSP19 | dual specificity phosphatase 19 | 211393 | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 3 | 0 | 0 | 0.000041 | 0.066 |
| 11 | GABRA6 | gamma-aminobutyric acid (GABA) A receptor, alpha 6 | 440417 | 6 | 6 | 6 | 1 | 1 | 3 | 1 | 1 | 0 | 0 | 0.000043 | 0.066 |
| 12 | TACC3 | transforming, acidic coiled-coil containing protein 3 | 311979 | 5 | 5 | 5 | 0 | 0 | 1 | 0 | 2 | 2 | 0 | 0.000046 | 0.066 |
| 13 | CDK12 | 1351667 | 9 | 9 | 9 | 0 | 0 | 0 | 1 | 3 | 5 | 0 | 0.000056 | 0.071 | |
| 14 | PPP1R3A | protein phosphatase 1, regulatory (inhibitor) subunit 3A | 1053877 | 8 | 8 | 8 | 2 | 1 | 1 | 2 | 4 | 0 | 0 | 0.000060 | 0.071 |
| 15 | EPHA7 | EPH receptor A7 | 941078 | 7 | 7 | 7 | 1 | 0 | 1 | 4 | 2 | 0 | 0 | 0.000062 | 0.071 |
| 16 | USH2A | Usher syndrome 2A (autosomal recessive, mild) | 5014417 | 20 | 20 | 20 | 3 | 2 | 5 | 3 | 7 | 3 | 0 | 0.000068 | 0.073 |
| 17 | GLI2 | GLI-Kruppel family member GLI2 | 947026 | 10 | 9 | 10 | 0 | 2 | 3 | 3 | 1 | 1 | 0 | 0.000075 | 0.075 |
| 18 | FAM171B | 744587 | 7 | 7 | 7 | 0 | 1 | 1 | 2 | 2 | 1 | 0 | 0.000082 | 0.078 | |
| 19 | BRCA2 | breast cancer 2, early onset | 2896444 | 12 | 11 | 12 | 0 | 1 | 0 | 0 | 1 | 8 | 2 | 0.000087 | 0.078 |
| 20 | ZNF479 | zinc finger protein 479 | 365518 | 5 | 5 | 5 | 0 | 0 | 2 | 2 | 1 | 0 | 0 | 0.000091 | 0.078 |
| 21 | SI | sucrase-isomaltase (alpha-glucosidase) | 1778977 | 10 | 10 | 10 | 0 | 1 | 1 | 4 | 4 | 0 | 0 | 0.00011 | 0.086 |
| 22 | SLCO1C1 | solute carrier organic anion transporter family, member 1C1 | 717910 | 6 | 6 | 6 | 0 | 0 | 1 | 4 | 1 | 0 | 0 | 0.00013 | 0.100 |
| 23 | C6orf142 | chromosome 6 open reading frame 142 | 449405 | 5 | 5 | 5 | 3 | 0 | 2 | 1 | 1 | 1 | 0 | 0.00013 | 0.100 |
| 24 | GAS2L1 | growth arrest-specific 2 like 1 | 197396 | 4 | 4 | 4 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0.00017 | 0.12 |
| 25 | C1orf95 | chromosome 1 open reading frame 95 | 81558 | 3 | 3 | 3 | 0 | 0 | 0 | 2 | 0 | 1 | 0 | 0.00020 | 0.14 |
| 26 | KCNJ12 | potassium inwardly-rectifying channel, subfamily J, member 12 | 281754 | 5 | 5 | 3 | 2 | 5 | 0 | 0 | 0 | 0 | 0 | 0.00022 | 0.14 |
| 27 | QSOX2 | quiescin Q6 sulfhydryl oxidase 2 | 422476 | 5 | 5 | 5 | 0 | 0 | 1 | 1 | 2 | 1 | 0 | 0.00022 | 0.14 |
| 28 | TBP | TATA box binding protein | 321652 | 4 | 4 | 2 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0.00023 | 0.14 |
| 29 | ACBD4 | acyl-Coenzyme A binding domain containing 4 | 147905 | 3 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.00024 | 0.14 |
| 30 | C10orf113 | chromosome 10 open reading frame 113 | 154870 | 3 | 3 | 3 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 0.00024 | 0.14 |
| 31 | GPR149 | G protein-coupled receptor 149 | 595318 | 6 | 6 | 6 | 1 | 1 | 2 | 1 | 2 | 0 | 0 | 0.00030 | 0.16 |
| 32 | PXN | paxillin | 321961 | 5 | 5 | 5 | 0 | 1 | 0 | 4 | 0 | 0 | 0 | 0.00031 | 0.16 |
| 33 | PAOX | polyamine oxidase (exo-N4-amino) | 205136 | 4 | 4 | 4 | 0 | 1 | 0 | 0 | 1 | 2 | 0 | 0.00032 | 0.16 |
| 34 | ZNF706 | zinc finger protein 706 | 73696 | 2 | 2 | 2 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0.00033 | 0.17 |
| 35 | SNTG1 | syntrophin, gamma 1 | 505767 | 5 | 5 | 5 | 1 | 0 | 1 | 1 | 0 | 3 | 0 | 0.00034 | 0.17 |
Note:
N - number of sequenced bases in this gene across the individual set.
n - number of (nonsilent) mutations in this gene across the individual set.
npat - number of patients (individuals) with at least one nonsilent mutation.
nsite - number of unique sites having a non-silent mutation.
nsil - number of silent mutations in this gene across the individual set.
n1 - number of nonsilent mutations of type: *CpG->T .
n2 - number of nonsilent mutations of type: *Cp(A/C/T)->T .
n3 - number of nonsilent mutations of type: C->(G/A) .
n4 - number of nonsilent mutations of type: A->mut .
n5 - number of nonsilent mutations of type: indel+null .
null - mutation category that includes nonsense, frameshift, splice-site mutations
p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
p = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
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COSMIC analyses
In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.
Table 4. Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 39. Number of genes displayed: 10
| rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q |
|---|---|---|---|---|---|---|---|---|---|
| 1 | TP53 | tumor protein p53 | 279 | 823 | 278 | 260068 | 70907 | 0 | 0 |
| 2 | RB1 | retinoblastoma 1 (including osteosarcoma) | 9 | 267 | 8 | 84372 | 16 | 5.2e-12 | 1.1e-08 |
| 3 | NF1 | neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) | 15 | 285 | 6 | 90060 | 8 | 2.7e-08 | 0.000039 |
| 4 | MYO3A | myosin IIIA | 7 | 14 | 3 | 4424 | 3 | 9.2e-08 | 0.0001 |
| 5 | KLK10 | kallikrein-related peptidase 10 | 2 | 2 | 2 | 632 | 2 | 6.9e-07 | 0.0006 |
| 6 | CDC27 | cell division cycle 27 homolog (S. cerevisiae) | 4 | 3 | 2 | 948 | 2 | 1.6e-06 | 0.0011 |
| 7 | ERBB2 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) | 4 | 41 | 3 | 12956 | 4 | 2.3e-06 | 0.0014 |
| 8 | MLL4 | 4 | 6 | 2 | 1896 | 2 | 6.2e-06 | 0.0034 | |
| 9 | NIPBL | Nipped-B homolog (Drosophila) | 5 | 7 | 2 | 2212 | 2 | 8.4e-06 | 0.0041 |
| 10 | EGFR | epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) | 7 | 218 | 4 | 68888 | 53 | 1e-05 | 0.0044 |
Note:
n - number of (nonsilent) mutations in this gene across the individual set.
cos = number of unique mutated sites in this gene in COSMIC
n_cos = overlap between n and cos.
N_cos = number of individuals times cos.
cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.
p = p-value for seeing the observed amount of overlap in this gene)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
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Clustered Mutations
Table 5. Get Full Table Genes with Clustered Mutations
| num | gene | desc | n | mindist | npairs3 | npairs12 |
|---|---|---|---|---|---|---|
| 7337 | TP53 | tumor protein p53 | 277 | 0 | 1164 | 3310 |
| 4431 | MTOR | 7 | 0 | 4 | 6 | |
| 2018 | DNAH5 | dynein, axonemal, heavy chain 5 | 15 | 0 | 3 | 6 |
| 6807 | SRC | v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) | 4 | 0 | 3 | 6 |
| 4501 | MYO3A | myosin IIIA | 7 | 0 | 3 | 3 |
| 3564 | KCNJ12 | potassium inwardly-rectifying channel, subfamily J, member 12 | 5 | 0 | 2 | 2 |
| 3474 | ITGB7 | integrin, beta 7 | 4 | 0 | 1 | 3 |
| 5430 | PLA2G4F | phospholipase A2, group IVF | 4 | 0 | 1 | 3 |
| 151 | ADAMTS4 | ADAM metallopeptidase with thrombospondin type 1 motif, 4 | 4 | 0 | 1 | 2 |
| 166 | ADCY2 | adenylate cyclase 2 (brain) | 6 | 0 | 1 | 2 |
Note:
n - number of mutations in this gene in the individual set.
mindist - distance (in aa) between closest pair of mutations in this gene
npairs3 - how many pairs of mutations are within 3 aa of each other.
npairs12 - how many pairs of mutations are within 12 aa of each other.
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Geneset Analyses
Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 63. Number of genesets displayed: 10
| rank | geneset | description | genes | N_genes | mut_tally | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p | q |
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| 1 | HSA04010_MAPK_SIGNALING_PATHWAY | Genes involved in MAPK signaling pathway | ACVR1B, ACVR1C, AKT1, AKT2, AKT3, ARRB1, ARRB2, ATF2, ATF4, BDNF, BRAF, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CACNA2D1, CACNA2D2, CACNA2D3, CACNA2D4, CACNB1, CACNB2, CACNB3, CACNB4, CACNG1, CACNG2, CACNG3, CACNG4, CACNG5, CACNG6, CACNG7, CACNG8, CASP3, CD14, CDC25B, CDC42, CHP, CHUK, CRK, CRKL, DAXX, DDIT3, DUSP1, DUSP10, DUSP14, DUSP16, DUSP2, DUSP3, DUSP4, DUSP5, DUSP6, DUSP7, DUSP8, DUSP9, ECSIT, EGF, EGFR, ELK1, ELK4, EVI1, FAS, FASLG, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FLNA, FLNB, FLNC, FOS, GADD45A, GADD45B, GADD45G, GNA12, GNG12, GRB2, HRAS, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1R2, JUN, JUND, KRAS, LOC653852, MAP2K1, MAP2K1IP1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K12, MAP3K13, MAP3K14, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K8, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPT, MAX, MEF2C, MKNK1, MKNK2, MOS, MRAS, MYC, NF1, NFATC2, NFATC4, NFKB1, NFKB2, NGFB, NLK, NR4A1, NRAS, NTF3, NTF5, NTRK1, NTRK2, PAK1, PAK2, PDGFA, PDGFB, PDGFRA, PDGFRB, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PPM1A, PPM1B, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PPP5C, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTPN5, PTPN7, PTPRR, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF2, RASA1, RASA2, RASGRF1, RASGRF2, RASGRP1, RASGRP2, RASGRP3, RASGRP4, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KA5, RPS6KA6, RRAS, RRAS2, SOS1, SOS2, SRF, STK3, STK4, STMN1, TAOK1, TAOK2, TAOK3, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF1A, TP53, TRAF2, TRAF6, ZAK | 232 | ACVR1B(1), ACVR1C(2), BRAF(2), CACNA1A(5), CACNA1B(1), CACNA1C(9), CACNA1D(6), CACNA1E(4), CACNA1F(4), CACNA1G(3), CACNA1S(5), CACNA2D1(4), CACNA2D2(1), CACNA2D3(1), CACNA2D4(1), CACNB1(1), CACNB2(1), CACNB4(1), CACNG3(1), CACNG6(2), CDC25B(2), CHUK(1), DAXX(1), DDIT3(2), DUSP1(2), DUSP7(1), DUSP9(2), ECSIT(1), EGFR(7), ELK1(2), FGF12(1), FGF2(1), FGF23(2), FGF5(1), FGF6(1), FGFR4(1), FLNA(1), FLNB(3), FLNC(3), FOS(1), GADD45A(1), GADD45B(1), GNA12(1), GRB2(2), IKBKB(1), KRAS(2), MAP2K3(1), MAP2K4(1), MAP2K6(1), MAP3K1(1), MAP3K10(2), MAP3K12(1), MAP3K13(2), MAP3K14(1), MAP3K2(2), MAP3K3(1), MAP3K4(2), MAP3K5(2), MAP3K6(1), MAP3K7(3), MAP4K1(1), MAP4K3(3), MAPK14(1), MAPK8(1), MAPK8IP1(1), MAPK9(1), MAPKAPK3(1), MAPKAPK5(1), MEF2C(1), MKNK1(1), MOS(1), MRAS(1), NF1(15), NFATC2(1), NFATC4(1), NFKB1(1), NLK(1), NRAS(2), NTF3(1), NTRK1(4), NTRK2(1), PAK2(1), PDGFRA(3), PDGFRB(3), PLA2G12A(1), PLA2G12B(1), PLA2G2F(1), PLA2G4A(1), PLA2G6(1), PPP3CC(1), PPP5C(1), PRKACG(1), PRKCA(1), PRKCG(1), PTPN5(3), PTPRR(1), RAPGEF2(1), RASA1(1), RASA2(2), RASGRF1(2), RASGRF2(4), RASGRP1(1), RASGRP2(1), RASGRP3(2), RPS6KA1(1), RPS6KA2(1), RPS6KA4(1), RPS6KA5(1), RRAS(1), SOS1(3), SOS2(1), SRF(1), STK4(1), TAOK1(1), TAOK3(1), TGFBR2(3), TNF(1), TNFRSF1A(1), TP53(279), TRAF2(1), TRAF6(2) | 116594517 | 496 | 293 | 358 | 53 | 79 | 59 | 109 | 115 | 134 | 0 | <1.00e-15 | <2.28e-14 |
| 2 | HSA04110_CELL_CYCLE | Genes involved in cell cycle | ABL1, ANAPC1, ANAPC10, ANAPC11, ANAPC2, ANAPC4, ANAPC5, ANAPC7, ATM, ATR, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDC14A, CDC14B, CDC16, CDC2, CDC20, CDC23, CDC25A, CDC25B, CDC25C, CDC26, CDC27, CDC45L, CDC6, CDC7, CDK2, CDK4, CDK6, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CHEK1, CHEK2, CREBBP, CUL1, DBF4, E2F1, E2F2, E2F3, EP300, ESPL1, FZR1, GADD45A, GADD45B, GADD45G, GSK3B, hCG_1982709, HDAC1, HDAC2, LOC440917, LOC728919, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PKMYT1, PLK1, PRKDC, PTTG1, PTTG2, RB1, RBL1, RBL2, RBX1, SFN, SKP1, SKP2, SMAD2, SMAD3, SMAD4, SMC1A, SMC1B, TFDP1, TGFB1, TGFB2, TGFB3, TP53, WEE1, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ | 106 | ABL1(1), ANAPC1(1), ANAPC2(1), ANAPC4(1), ANAPC5(1), ATM(5), ATR(2), BUB1(1), BUB1B(2), BUB3(1), CCNA1(2), CCNA2(1), CCNB3(3), CCNH(1), CDC20(1), CDC25B(2), CDC27(4), CDC6(1), CDC7(2), CDK2(1), CDKN1A(1), CDKN1B(1), CDKN2C(2), CDKN2D(1), CHEK2(1), CREBBP(7), E2F2(1), EP300(1), GADD45A(1), GADD45B(1), GSK3B(1), HDAC1(1), MAD2L2(1), MCM2(2), MCM3(1), MCM4(2), MCM5(2), ORC1L(1), ORC4L(1), PRKDC(8), RB1(9), RBL1(1), RBL2(3), SKP2(2), SMC1A(5), SMC1B(3), TFDP1(2), TP53(279), YWHAB(1), YWHAE(2), YWHAG(2) | 59044916 | 380 | 287 | 244 | 28 | 60 | 44 | 71 | 84 | 121 | 0 | <1.00e-15 | <2.28e-14 |
| 3 | G1_TO_S_CELL_CYCLE_REACTOME | ATM, CCNA1, CCNB1, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNG2, CCNH, CDC25A, CDC45L, CDK2, CDK4, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CREB3, CREB3L1, CREB3L3, CREB3L4, CREBL1, CREBL1, TNXB, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, FLJ14001, GADD45A, GBA2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, MNAT1, MYC, MYT1, NACA, NACA, FKSG17, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, POLA2, POLE, POLE2, PRIM1, PRIM2A, RB1, RBL1, RPA1, RPA2, RPA3, TFDP1, TFDP2, TP53, WEE1 | 64 | ATM(5), CCNA1(2), CCNG2(1), CCNH(1), CDK2(1), CDKN1A(1), CDKN1B(1), CDKN2C(2), CDKN2D(1), CREB3L1(1), CREB3L4(1), E2F2(1), E2F5(1), GADD45A(1), GBA2(2), MCM2(2), MCM3(1), MCM4(2), MCM5(2), MNAT1(1), MYT1(2), NACA(4), ORC1L(1), ORC4L(1), POLE(2), POLE2(1), RB1(9), RBL1(1), RPA1(2), RPA2(1), TFDP1(2), TNXB(4), TP53(279) | 32487850 | 339 | 286 | 203 | 24 | 56 | 38 | 60 | 70 | 115 | 0 | <1.00e-15 | <2.28e-14 | |
| 4 | HSA04310_WNT_SIGNALING_PATHWAY | Genes involved in Wnt signaling pathway | APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B | 138 | APC(8), AXIN2(1), BTRC(2), CAMK2B(2), CAMK2D(1), CAMK2G(1), CHD8(5), CREBBP(7), CSNK1A1L(1), CSNK1E(1), CSNK2A1(1), CSNK2B(1), CTBP1(1), CTBP2(1), CTNNB1(2), CXXC4(1), DAAM1(2), DAAM2(2), DKK2(2), DVL3(1), EP300(1), FBXW11(1), FOSL1(1), FZD5(2), FZD7(2), GSK3B(1), LRP5(3), LRP6(1), MAP3K7(3), MAPK8(1), MAPK9(1), MMP7(1), NFAT5(1), NFATC1(1), NFATC2(1), NFATC4(1), NLK(1), PLCB1(4), PLCB2(4), PLCB3(2), PLCB4(1), PORCN(2), PPARD(2), PPP2CA(2), PPP2R1A(4), PPP2R2A(1), PPP2R2B(1), PPP3CC(1), PRICKLE1(3), PRICKLE2(2), PRKACG(1), PRKCA(1), PRKCG(1), RHOA(2), SFRP2(1), SFRP5(1), TBL1X(1), TBL1XR1(1), TCF7L2(2), TP53(279), VANGL2(1), WIF1(3), WNT11(2), WNT16(3), WNT2(1), WNT2B(1), WNT4(1), WNT6(2), WNT7A(2), WNT7B(2), WNT8A(1), WNT9A(2), WNT9B(1) | 65706417 | 407 | 284 | 270 | 37 | 65 | 52 | 80 | 90 | 120 | 0 | <1.00e-15 | <2.28e-14 |
| 5 | CELL_CYCLE_KEGG | ABL1, ASK, ATM, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDAN1, CDC14A, CDC14B, CDC14B, CDC14C, CDC2, CDC20, CDC25A, CDC25B, CDC25C, CDC45L, CDC6, CDC7, CDH1, CDK2, CDK4, CDKN1A, CDKN2A, CHEK1, CHEK2, DTX4, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, EP300, ESPL1, FLJ14001, GADD45A, GSK3B, HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7A, HDAC8, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, MPEG1, MPL, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PLK1, PRKDC, PTPRA, PTTG1, PTTG2, PTTG3, RB1, RBL1, SKP2, SMAD4, SMC1L1, TBC1D8, TFDP1, TGFB1, TP53, WEE1 | 82 | ABL1(1), ATM(5), BUB1(1), BUB1B(2), BUB3(1), CCNA1(2), CCNA2(1), CCNB3(3), CCNH(1), CDAN1(2), CDC20(1), CDC25B(2), CDC6(1), CDC7(2), CDH1(2), CDK2(1), CDKN1A(1), CHEK2(1), E2F2(1), E2F5(1), EP300(1), GADD45A(1), GSK3B(1), HDAC1(1), HDAC3(2), HDAC4(2), HDAC5(1), HDAC6(2), MAD2L2(1), MCM2(2), MCM3(1), MCM4(2), MCM5(2), MPEG1(1), ORC1L(1), ORC4L(1), PRKDC(8), RB1(9), RBL1(1), SKP2(2), TBC1D8(3), TFDP1(2), TP53(279) | 48736010 | 358 | 283 | 222 | 27 | 56 | 42 | 65 | 80 | 115 | 0 | <1.00e-15 | <2.28e-14 | |
| 6 | APOPTOSIS | APAF1, BAD, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BCL2L11, BID, BIRC2, BIRC3, BIRC4, BIRC5, BNIP3L, CASP1, CASP10, CASP1, COPl, CASP2, CASP3, CASP4, CASP6, CASP7, CASP8, CASP9, CHUK, CYCS, DFFA, DFFB, FADD, FAS, FASLG, GZMB, HELLS, HRK, IKBKB, IKBKG, IRF1, IRF2, IRF3, IRF4, IRF5, IRF6, IRF7, JUN, LTA, MAP2K4, MAP3K1, MAPK10, MDM2, MYC, NFKB1, NFKBIA, NFKBIB, NFKBIE, PRF1, RELA, RIPK1, TNF, TNFRSF10B, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF25, PLEKHG5, TNFSF10, TP53, TP73, TRADD, TRAF1, TRAF2, TRAF3 | 63 | APAF1(2), BAK1(1), BID(1), BIRC3(2), BNIP3L(1), CASP1(2), CASP2(1), CASP4(1), CASP6(1), CASP7(1), CASP9(1), CHUK(1), FADD(1), IKBKB(1), IRF2(2), IRF3(2), IRF4(1), IRF6(3), MAP2K4(1), MAP3K1(1), NFKB1(1), PRF1(2), RELA(1), TNF(1), TNFRSF1A(1), TNFSF10(1), TP53(279), TRAF1(4), TRAF2(1) | 23644549 | 318 | 282 | 182 | 14 | 51 | 39 | 50 | 73 | 105 | 0 | <1.00e-15 | <2.28e-14 | |
| 7 | HSA04210_APOPTOSIS | Genes involved in apoptosis | AIFM1, AKT1, AKT2, AKT3, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CAPN1, CAPN2, CASP10, CASP3, CASP6, CASP7, CASP8, CASP9, CFLAR, CHP, CHUK, CSF2RB, CYCS, DFFA, DFFB, ENDOG, FADD, FAS, FASLG, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1RAP, IL3, IL3RA, IRAK1, IRAK2, IRAK3, IRAK4, MAP3K14, MYD88, NFKB1, NFKB2, NFKBIA, NGFB, NTRK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, RELA, RIPK1, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF1A, TNFSF10, TP53, TRADD, TRAF2 | 78 | AIFM1(2), APAF1(2), ATM(5), BID(1), BIRC3(2), CASP6(1), CASP7(1), CASP9(1), CHUK(1), CSF2RB(3), FADD(1), IKBKB(1), IRAK1(2), IRAK2(1), IRAK3(2), IRAK4(1), MAP3K14(1), NFKB1(1), NTRK1(4), PIK3CA(2), PIK3CB(1), PIK3CG(3), PIK3R1(1), PIK3R2(2), PIK3R5(1), PPP3CC(1), PRKACG(1), PRKAR2A(1), PRKAR2B(1), RELA(1), TNF(1), TNFRSF10A(2), TNFRSF10D(1), TNFRSF1A(1), TNFSF10(1), TP53(279), TRAF2(1) | 35255671 | 334 | 282 | 198 | 25 | 53 | 42 | 59 | 75 | 105 | 0 | <1.00e-15 | <2.28e-14 |
| 8 | ST_FAS_SIGNALING_PATHWAY | The Fas receptor induces apoptosis and NF-kB activation when bound to Fas ligand. | ADPRT, ALG2, BAK1, BAX, BFAR, BIRC4, BTK, CAD, CASP10, CASP3, CASP8, CASP8AP2, CD7, CDK2AP1, CSNK1A1, DAXX, DEDD, DEDD2, DFFA, DIABLO, EGFR, EPHB2, FADD, FAF1, FAIM2, FREQ, HRB, HSPB1, IL1A, IL8, MAP2K4, MAP2K7, MAP3K1, MAP3K5, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MCP, MET, NFAT5, NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBIE, NFKBIL1, NFKBIL2, NR0B2, PFN1, PFN2, PTPN13, RALBP1, RIPK1, ROCK1, SMPD1, TNFRSF6, TNFRSF6B, TP53, TPX2, TRAF2, TUFM, VIL2 | 53 | ALG2(2), BAK1(1), BFAR(2), BTK(1), CAD(5), CASP8AP2(1), DAXX(1), DEDD2(1), DIABLO(1), EGFR(7), EPHB2(1), FADD(1), IL8(1), MAP2K4(1), MAP3K1(1), MAP3K5(2), MAPK8(1), MAPK8IP1(1), MAPK9(1), MET(4), NFAT5(1), NFKB1(1), PFN2(1), PTPN13(4), TP53(279), TPX2(1), TRAF2(1), TUFM(1) | 29275634 | 325 | 282 | 189 | 18 | 53 | 40 | 52 | 73 | 107 | 0 | <1.00e-15 | <2.28e-14 |
| 9 | TELPATHWAY | Telomerase is a ribonucleotide protein that adds telomeric repeats to the 3' ends of chromosomes. | AKT1, BCL2, EGFR, G22P1, HSPCA, IGF1R, KRAS2, MYC, POLR2A, PPP2CA, PRKCA, RB1, TEP1, TERF1, TERT, TNKS, TP53, XRCC5 | 15 | EGFR(7), IGF1R(1), PPP2CA(2), PRKCA(1), RB1(9), TEP1(5), TERF1(1), TERT(1), TNKS(1), TP53(279) | 12360237 | 307 | 281 | 171 | 10 | 50 | 33 | 49 | 65 | 110 | 0 | <1.00e-15 | <2.28e-14 |
| 10 | APOPTOSIS_GENMAPP | APAF1, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CASP2, CASP3, CASP6, CASP7, CASP8, CASP9, CYCS, FADD, FAS, FASLG, GZMB, IKBKG, JUN, MAP2K4, MAP3K1, MAP3K14, MAPK10, MCL1, MDM2, MYC, NFKB1, NFKBIA, PARP1, PRF1, RELA, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TNFSF10, TP53, TRADD, TRAF1, TRAF2 | 40 | APAF1(2), BAK1(1), BID(1), BIRC3(2), CASP2(1), CASP6(1), CASP7(1), CASP9(1), FADD(1), MAP2K4(1), MAP3K1(1), MAP3K14(1), NFKB1(1), PRF1(2), RELA(1), TNF(1), TNFRSF1A(1), TNFSF10(1), TP53(279), TRAF1(4), TRAF2(1) | 16033981 | 305 | 280 | 169 | 10 | 50 | 36 | 48 | 67 | 104 | 0 | <1.00e-15 | <2.28e-14 |
Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 9. Number of genesets displayed: 10
| rank | geneset | description | genes | N_genes | mut_tally | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION | Genes involved in neuroactive ligand-receptor interaction | ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2 | 220 | ADCYAP1R1(1), ADORA2B(2), ADORA3(2), ADRA1A(1), ADRA2B(3), ADRB2(1), AGTR2(2), AVPR1B(3), AVPR2(1), BDKRB1(4), BDKRB2(3), BRS3(1), C5AR1(2), CALCR(3), CALCRL(1), CCKBR(1), CGA(1), CHRM2(4), CHRM3(3), CHRM5(1), CTSG(1), CYSLTR1(1), DRD1(2), DRD3(1), EDNRA(1), F2(3), F2R(2), F2RL2(1), FPR1(1), FSHB(1), FSHR(4), GABBR1(2), GABBR2(2), GABRA1(2), GABRA2(2), GABRA3(1), GABRA4(1), GABRA5(1), GABRB1(2), GABRB3(1), GABRE(3), GABRG1(2), GABRG2(2), GABRQ(2), GALR1(1), GH2(1), GHR(1), GHRHR(1), GHSR(1), GLP2R(1), GLRA1(1), GLRA2(1), GLRA3(4), GPR156(1), GPR35(1), GPR50(2), GRIA1(1), GRIA2(2), GRIA3(2), GRIA4(3), GRID1(3), GRID2(2), GRIK1(1), GRIK2(2), GRIK3(2), GRIK5(2), GRIN2A(3), GRIN2B(3), GRIN2C(1), GRIN2D(3), GRIN3A(3), GRM1(4), GRM3(1), GRM4(1), GRM5(2), GRM6(1), GRM7(4), GRM8(3), GRPR(1), GZMA(2), HCRTR1(1), HCRTR2(1), HRH1(1), HRH4(2), HTR1A(2), HTR1E(2), HTR1F(3), HTR2A(3), HTR2C(4), HTR4(2), HTR5A(2), HTR6(1), LEPR(1), LHCGR(3), MAS1(1), MC2R(3), MC3R(2), MC4R(1), MC5R(2), MCHR2(2), MLNR(1), MTNR1A(1), NMBR(1), NMUR2(2), NPBWR1(1), NPFFR2(2), NR3C1(2), OPRD1(2), OPRK1(1), P2RX1(1), P2RX5(1), P2RY10(2), P2RY13(4), P2RY2(2), P2RY6(1), PARD3(2), PPYR1(2), PRLHR(1), PRLR(2), PRSS2(1), PRSS3(1), PTGDR(1), PTGFR(3), PTH2R(1), RXFP2(1), SCTR(1), SSTR1(1), TAAR6(2), TACR1(1), TACR2(2), TACR3(1), TRPV1(1), TSHR(4), VIPR2(1) | 92059511 | 241 | 147 | 240 | 74 | 46 | 26 | 84 | 64 | 21 | 0 | 8.8e-06 | 0.0029 |
| 2 | HSA04530_TIGHT_JUNCTION | Genes involved in tight junction | ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK | 128 | ACTG1(2), ACTN2(3), ACTN3(2), AMOTL1(1), ASH1L(3), CASK(2), CGN(2), CLDN10(1), CLDN11(2), CLDN15(1), CLDN16(1), CLDN17(2), CLDN18(2), CLDN2(1), CLDN6(1), CLDN9(1), CSDA(1), CSNK2A1(1), CSNK2B(1), CTNNA1(2), CTNNA3(1), CTNNB1(2), CTTN(1), EPB41(2), EPB41L3(5), EXOC3(1), EXOC4(4), F11R(2), GNAI2(1), INADL(2), JAM3(1), KRAS(2), LLGL2(3), MAGI1(2), MAGI2(4), MAGI3(3), MLLT4(2), MPDZ(4), MPP5(1), MRAS(1), MYH1(9), MYH10(3), MYH11(7), MYH13(6), MYH14(2), MYH15(5), MYH2(5), MYH3(4), MYH4(9), MYH7(3), MYH7B(5), MYH8(3), MYH9(3), MYL2(1), NRAS(2), PARD3(2), PARD6A(1), PPP2CA(2), PPP2R1A(4), PPP2R2A(1), PPP2R2B(1), PPP2R3A(2), PPP2R4(1), PRKCA(1), PRKCE(1), PRKCG(1), PRKCH(1), PRKCI(2), PRKCQ(3), PRKCZ(2), PTEN(2), RAB3B(1), RHOA(2), RRAS(1), SPTAN1(5), SRC(4), TJAP1(1), TJP1(3), TJP3(1), YES1(1) | 82395479 | 189 | 141 | 185 | 38 | 29 | 15 | 68 | 50 | 25 | 2 | 9.3e-06 | 0.0029 |
| 3 | GPCRDB_CLASS_A_RHODOPSIN_LIKE | ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA1D, ADRA2A, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BLR1, BRS3, C3AR1, C5R1, CCBP2, CCKAR, CCKBR, CCR1, CCR10, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CCRL1, CCRL2, CHML, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CMKLR1, CMKOR1, CNR1, CNR2, CX3CR1, CXCR3, CXCR4, DRD1, DRD2, DRD3, DRD4, DRD5, EDNRA, EDNRB, ELA3A, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHR, GALR1, GALR2, GALR3, GALT, GHSR, GNB2L1, GPR10, GPR147, GPR17, GPR173, GPR174, GPR23, GPR24, GPR27, GPR3, GPR30, GPR35, GPR37, GPR37L1, GPR4, GPR44, GPR50, GPR6, GPR63, GPR74, GPR77, GPR83, GPR85, GPR87, GPR92, GRPR, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, HTR7, LOC93164, IL8RA, IL8RB, LHCGR, LTB4R, MAS1, MC1R, MC3R, MC4R, MC5R, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPY1R, NPY2R, NPY5R, NPY6R, NTSR1, NTSR2, OPN1SW, OPN3, OPRD1, OPRK1, OPRL1, OPRM1, OR10A5, OR11A1, OR12D3, OR1C1, OR1F1, OR1Q1, OR2H1, OR5V1, OR5V1, OR12D3, OR7A5, OR7C1, OR8B8, OXTR, P2RY1, P2RY10, P2RY11, P2RY12, P2RY13, P2RY14, P2RY2, P2RY5, P2RY6, PPYR1, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, Rgr, RGR, RHO, RRH, SSTR1, SSTR2, SSTR3, SSTR4, SUCNR1, TBXA2R, TRHR | 151 | ADORA2B(2), ADORA3(2), ADRA1A(1), ADRB2(1), AGTR2(2), AVPR1B(3), AVPR2(1), BDKRB1(4), BDKRB2(3), BRS3(1), CCKBR(1), CCR3(2), CCR6(1), CCR8(1), CCR9(1), CHML(3), CHRM2(4), CHRM3(3), CHRM5(1), CXCR3(2), DRD1(2), DRD3(1), EDNRA(1), F2R(2), F2RL2(1), FPR1(1), FSHR(4), GALR1(1), GHSR(1), GPR173(1), GPR174(1), GPR35(1), GPR37(2), GPR37L1(1), GPR4(2), GPR50(2), GPR77(1), GRPR(1), HCRTR1(1), HCRTR2(1), HRH1(1), HTR1A(2), HTR1E(2), HTR1F(3), HTR2A(3), HTR2C(4), HTR4(2), HTR5A(2), HTR6(1), LHCGR(3), MAS1(1), MC3R(2), MC4R(1), MC5R(2), MLNR(1), MTNR1A(1), NMBR(1), NMUR2(2), OPN1SW(2), OPRD1(2), OPRK1(1), OR10A5(1), OR11A1(1), OR12D3(2), OR5V1(3), OR7C1(2), OR8B8(1), P2RY10(2), P2RY12(1), P2RY13(4), P2RY2(2), P2RY6(1), PPYR1(2), PTGDR(1), PTGFR(3), RRH(1), SSTR1(1), SUCNR1(1) | 48728343 | 135 | 103 | 135 | 30 | 22 | 12 | 52 | 38 | 11 | 0 | 3e-05 | 0.0062 | |
| 4 | AMIPATHWAY | Endogenous anti-thrombosis pathways are overwhelmed in plaque-narrowed blood vessels, resulting in potentially lethal myocardial infarction. | ADCY1, CD3D, CD3E, CD3G, CD3Z, CD4, CREBBP, CSK, GNAS, GNB1, GNGT1, HLA-DRA, HLA-DRB1, LCK, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PTPRC, TRA@, TRB@, ZAP70 | 21 | ADCY1(4), CD3E(2), CD4(1), CREBBP(7), CSK(1), GNAS(3), HLA-DRA(1), HLA-DRB1(1), LCK(1), PRKACG(1), PRKAR2A(1), PRKAR2B(1), PTPRC(3), ZAP70(1) | 9488232 | 28 | 28 | 27 | 3 | 5 | 3 | 6 | 6 | 8 | 0 | 0.00019 | 0.024 |
| 5 | CSKPATHWAY | Csk inhibits T-cell activation by phosphorylating Lck; Csk is regulated by cAMP-dependent kinases and is opposed by the T-cell activator CD45. | ADCY1, CD3D, CD3E, CD3G, CD3Z, CD4, CREBBP, CSK, GNAS, GNB1, GNGT1, HLA-DRA, HLA-DRB1, LCK, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PTPRC, TRA@, TRB@, ZAP70 | 21 | ADCY1(4), CD3E(2), CD4(1), CREBBP(7), CSK(1), GNAS(3), HLA-DRA(1), HLA-DRB1(1), LCK(1), PRKACG(1), PRKAR2A(1), PRKAR2B(1), PTPRC(3), ZAP70(1) | 9488232 | 28 | 28 | 27 | 3 | 5 | 3 | 6 | 6 | 8 | 0 | 0.00019 | 0.024 |
| 6 | GPCRDB_OTHER | ADORA3, ALG6, C5R1, CCKBR, CCR2, CCR3, CCR5, CELSR1, CELSR2, CELSR3, CHRM2, CHRM3, CIDEB, CXCR3, DRD4, EBI2, EDG1, EDNRA, ELA3A, EMR2, EMR3, F2R, FSHR, FY, GHRHR, GNRHR, GPR, GPR116, GPR132, GPR133, GPR135, GPR143, GPR145, GPR17, GPR18, GPR55, GPR56, GPR61, GPR73L1, GPR77, GPR84, GPR88, GRCA, GRM1, GRPR, HRH4, IL8RA, IL8RB, LGR6, LGR7, LPHN2, LPHN3, LTB4R2, MASS1, NTSR1, OR2A9P, OR2M4, OR5E1P, OR7E19P, OR7E47P, OR7E37P, OR7E18P, OR7E35P, LOC441453, OR8G1, LOC442754, OR8G2, P2RY11, P2RY13, PTGFR, RLN3R1, SMO, SSTR2, TAAR5, TSHR, VN1R1 | 50 | ADORA3(2), CCKBR(1), CCR3(2), CELSR1(1), CELSR2(4), CELSR3(6), CHRM2(4), CHRM3(3), CXCR3(2), EDNRA(1), EMR2(1), EMR3(5), F2R(2), FSHR(4), GHRHR(1), GPR116(1), GPR132(2), GPR133(2), GPR55(1), GPR77(1), GRM1(4), GRPR(1), HRH4(2), LGR6(3), LPHN2(1), LPHN3(4), OR8G2(1), P2RY13(4), PTGFR(3), TSHR(4) | 25452491 | 73 | 60 | 73 | 20 | 11 | 10 | 27 | 19 | 6 | 0 | 0.00043 | 0.043 | |
| 7 | FXRPATHWAY | The nuclear receptor transcription factors FXR and LXR are activated by cholesterol metabolites and regulate cholesterol homeostasis. | FABP6, LDLR, NR0B2, NR1H3, NR1H4, RXRA | 6 | LDLR(3), NR1H3(4), NR1H4(3), RXRA(2) | 2264708 | 12 | 12 | 12 | 0 | 2 | 2 | 3 | 2 | 3 | 0 | 0.00049 | 0.043 |
| 8 | HSA04916_MELANOGENESIS | Genes involved in melanogenesis | ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ASIP, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CREB1, CREB3, CREB3L1, CREB3L2, CREB3L3, CREB3L4, CREBBP, CTNNB1, DCT, DVL1, DVL2, DVL3, EDN1, EDNRB, EP300, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNAS, GSK3B, HRAS, KIT, KITLG, KRAS, LEF1, LOC652788, MAP2K1, MAP2K2, MAPK1, MAPK3, MC1R, MITF, NRAS, PLCB1, PLCB2, PLCB3, PLCB4, POMC, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, RAF1, TCF7, TCF7L1, TCF7L2, TYR, TYRP1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B | 96 | ADCY1(4), ADCY2(6), ADCY3(2), ADCY4(1), ADCY5(3), ADCY7(1), ADCY9(5), CALM3(1), CAMK2B(2), CAMK2D(1), CAMK2G(1), CREB3L1(1), CREB3L4(1), CREBBP(7), CTNNB1(2), DCT(2), DVL3(1), EP300(1), FZD5(2), FZD7(2), GNAI2(1), GNAS(3), GSK3B(1), KIT(7), KITLG(1), KRAS(2), MITF(2), NRAS(2), PLCB1(4), PLCB2(4), PLCB3(2), PLCB4(1), POMC(1), PRKACG(1), PRKCA(1), PRKCG(1), TCF7L2(2), TYR(1), WNT11(2), WNT16(3), WNT2(1), WNT2B(1), WNT4(1), WNT6(2), WNT7A(2), WNT7B(2), WNT8A(1), WNT9A(2), WNT9B(1) | 43571057 | 101 | 86 | 96 | 28 | 21 | 14 | 30 | 20 | 16 | 0 | 0.00071 | 0.054 |
| 9 | WNTPATHWAY | The Wnt glycoprotein binds to membrane-bound receptors such as Frizzled to activate a number of signaling pathways, including that of beta-catenin. | APC, AXIN1, BTRC, CCND1, CREBBP, CSNK1A1, CSNK1D, CSNK2A1, CTBP1, CTNNB1, DVL1, FRAT1, FZD1, GSK3B, HDAC1, MADH4, MAP3K7, MAP3K7IP1, MYC, NLK, PPARD, PPP2CA, TCF1, TLE1, WIF1, WNT1 | 21 | APC(8), BTRC(2), CREBBP(7), CSNK2A1(1), CTBP1(1), CTNNB1(2), GSK3B(1), HDAC1(1), MAP3K7(3), NLK(1), PPARD(2), PPP2CA(2), TLE1(1), WIF1(3) | 12038874 | 35 | 30 | 35 | 8 | 0 | 5 | 9 | 12 | 9 | 0 | 0.00098 | 0.067 |
| 10 | HSA03320_PPAR_SIGNALING_PATHWAY | Genes involved in PPAR signaling pathway | ACAA1, ACADL, ACADM, ACOX1, ACOX2, ACOX3, ACSL1, ACSL3, ACSL4, ACSL5, ACSL6, ADIPOQ, ANGPTL4, APOA1, APOA2, APOA5, APOC3, AQP7, CD36, CPT1A, CPT1B, CPT1C, CPT2, CYP27A1, CYP4A11, CYP4A22, CYP7A1, CYP8B1, DBI, EHHADH, FABP1, FABP2, FABP3, FABP4, FABP5, FABP5L1, FABP6, FABP7, FADS2, GK, GK2, HMGCS2, ILK, LOC642956, LPL, ME1, MMP1, NR1H3, OLR1, PCK1, PCK2, PDPK1, PLIN, PLTP, PPARA, PPARD, PPARG, RXRA, RXRB, RXRG, SCD, SCP2, SLC27A1, SLC27A2, SLC27A4, SLC27A5, SLC27A6, SORBS1, UBC, UCP1 | 65 | ACADM(1), ACOX1(2), ACSL1(2), ACSL3(2), ACSL4(1), ACSL6(1), ADIPOQ(1), ANGPTL4(2), CPT1A(2), CPT1B(2), CPT1C(1), CPT2(1), CYP27A1(1), CYP4A11(4), CYP4A22(1), CYP7A1(1), CYP8B1(2), DBI(1), EHHADH(2), FABP2(1), FABP3(2), FABP4(1), FADS2(2), GK2(2), HMGCS2(1), LPL(1), ME1(2), MMP1(1), NR1H3(4), OLR1(1), PDPK1(1), PPARA(1), PPARD(2), RXRA(2), RXRB(2), SCP2(1), SLC27A2(1), SLC27A4(1), SORBS1(2), UBC(3), UCP1(1) | 28493267 | 65 | 60 | 64 | 14 | 6 | 10 | 27 | 11 | 11 | 0 | 0.0022 | 0.13 |
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Methods & Data
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Methods
In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset.[1]
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Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
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References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 Ð 615 (2011)
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Meta
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Maintainer = Dan DiCara
Copyright © 2011
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.