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 v2.0 and MutSigCV v0.9 merged result was used to generate the results found in this report.
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Working with individual set: COAD-TP
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Number of patients in set: 155
The input for this pipeline is a set of individuals with the following files associated for each:
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An annotated .maf file describing the mutations called for the respective individual, and their properties.
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A .wig file that contains information about the coverage of the sample.
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MAF used for this analysis:COAD-TP.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 14
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Mutations seen in COSMIC: 517
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Significantly mutated genes in COSMIC territory: 23
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Significantly mutated genesets: 156
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Read 102 MAFs of type "Broad"
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Read 53 MAFs of type "Baylor-SOLiD"
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Total number of mutations in input MAFs: 62560
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After removing 1112 invalidated mutations: 61448
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After removing 976 noncoding mutations: 60472
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After collapsing adjacent/redundant mutations: 60470
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Number of mutations before filtering: 60470
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After removing 665 mutations outside gene set: 59805
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After removing 171 mutations outside category set: 59634
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After removing 9 "impossible" mutations in
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gene-patient-category bins of zero coverage: 58789
type | count |
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De_novo_Start_InFrame | 16 |
De_novo_Start_OutOfFrame | 126 |
Frame_Shift_Del | 1137 |
Frame_Shift_Ins | 655 |
In_Frame_Del | 139 |
In_Frame_Ins | 19 |
Missense_Mutation | 39601 |
Nonsense_Mutation | 3274 |
Nonstop_Mutation | 30 |
Silent | 14487 |
Splice_Site | 148 |
Translation_Start_Site | 2 |
Total | 59634 |
category | n | N | rate | rate_per_mb | relative_rate |
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*CpG->T | 15461 | 235764747 | 0.000066 | 66 | 6.2 |
*Np(A/C/T)->transit | 10142 | 3394090912 | 3e-06 | 3 | 0.28 |
*ApG->G | 966 | 657627616 | 1.5e-06 | 1.5 | 0.14 |
transver | 13028 | 4287483275 | 3e-06 | 3 | 0.29 |
indel+null | 5396 | 4287483377 | 1.3e-06 | 1.3 | 0.12 |
double_null | 147 | 4287483377 | 3.4e-08 | 0.034 | 0.0033 |
Total | 45140 | 4287483377 | 0.000011 | 11 | 1 |
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).
Column Descriptions:
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N = number of sequenced bases in this gene across the individual set
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n = number of (nonsilent) mutations in this gene across the individual set
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npat = number of patients (individuals) with at least one nonsilent mutation
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nsite = number of unique sites having a non-silent mutation
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nsil = number of silent mutations in this gene across the individual set
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n1 = number of nonsilent mutations of type: *CpG->T
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n2 = number of nonsilent mutations of type: *Np(A/C/T)->transit
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n3 = number of nonsilent mutations of type: *ApG->G
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n4 = number of nonsilent mutations of type: transver
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n5 = number of nonsilent mutations of type: indel+null
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n6 = number of nonsilent mutations of type: double_null
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p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene
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p_joint = p-value for clustering + conservation
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p = p-value (overall)
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q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
rank | gene | description | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p_cons | p_joint | p_cv | p | q |
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1 | APC | adenomatous polyposis coli | 1314776 | 121 | 103 | 85 | 4 | 5 | 6 | 1 | 11 | 64 | 34 | 0.85 | 0 | 2.9e-15 | 0 | 0 |
2 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 423914 | 33 | 26 | 18 | 1 | 5 | 19 | 1 | 8 | 0 | 0 | 0.000021 | 0 | 1.2e-06 | 0 | 0 |
3 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 342233 | 21 | 20 | 3 | 0 | 0 | 0 | 0 | 21 | 0 | 0 | 0.00017 | 0 | 0.000013 | 0 | 0 |
4 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 109406 | 58 | 58 | 8 | 0 | 0 | 31 | 0 | 27 | 0 | 0 | 9e-06 | 0 | 7.1e-15 | 0 | 0 |
5 | TP53 | tumor protein p53 | 188069 | 77 | 75 | 50 | 1 | 29 | 11 | 0 | 11 | 26 | 0 | 2e-07 | 0 | 1.9e-15 | 0 | 0 |
6 | FBXW7 | F-box and WD repeat domain containing 7 | 400174 | 33 | 29 | 21 | 2 | 17 | 1 | 0 | 8 | 7 | 0 | 0.12 | 0.00077 | 1.9e-13 | 5.4e-15 | 1.6e-11 |
7 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 90830 | 15 | 15 | 7 | 0 | 2 | 2 | 0 | 11 | 0 | 0 | 0.033 | 0.0012 | 5.4e-11 | 2e-12 | 5.1e-09 |
8 | SMAD4 | SMAD family member 4 | 262233 | 21 | 18 | 17 | 0 | 8 | 7 | 0 | 2 | 3 | 1 | 0.01 | 0.016 | 1.5e-08 | 5.7e-09 | 0.000013 |
9 | FAM123B | family with sequence similarity 123B | 451470 | 19 | 19 | 17 | 1 | 1 | 2 | 0 | 2 | 14 | 0 | 0.72 | 0.088 | 1.1e-08 | 2.1e-08 | 0.000042 |
10 | SOX9 | SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) | 180663 | 9 | 9 | 9 | 0 | 0 | 1 | 0 | 0 | 8 | 0 | 0.62 | 0.2 | 5.2e-07 | 1.8e-06 | 0.0032 |
11 | ACVR2A | activin A receptor, type IIA | 245516 | 9 | 8 | 8 | 1 | 0 | 1 | 0 | 3 | 5 | 0 | 0.037 | 0.0089 | 0.000022 | 3.2e-06 | 0.0053 |
12 | TNFRSF10C | tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain | 116831 | 6 | 6 | 2 | 0 | 0 | 0 | 0 | 6 | 0 | 0 | 1 | 0.000036 | 0.0071 | 4.2e-06 | 0.0062 |
13 | SMAD2 | SMAD family member 2 | 223461 | 11 | 10 | 8 | 1 | 3 | 0 | 0 | 4 | 4 | 0 | 0.096 | 0.025 | 0.0001 | 0.000035 | 0.049 |
14 | ACOT4 | acyl-CoA thioesterase 4 | 151821 | 3 | 3 | 2 | 1 | 0 | 0 | 0 | 0 | 2 | 1 | 0.026 | 0.00038 | 0.0077 | 4e-05 | 0.051 |
15 | PCBP1 | poly(rC) binding protein 1 | 127765 | 4 | 4 | 2 | 0 | 0 | 0 | 2 | 2 | 0 | 0 | 0.043 | 5e-05 | 0.21 | 0.00013 | 0.15 |
16 | CRTC1 | CREB regulated transcription coactivator 1 | 244087 | 5 | 5 | 3 | 1 | 1 | 0 | 0 | 0 | 4 | 0 | 0.081 | 0.0095 | 0.0017 | 0.0002 | 0.22 |
17 | SAT1 | spermidine/spermine N1-acetyltransferase 1 | 78557 | 4 | 4 | 2 | 0 | 0 | 0 | 0 | 1 | 3 | 0 | NaN | NaN | 0.00037 | 0.00037 | 0.39 |
18 | TCF7L2 | transcription factor 7-like 2 (T-cell specific, HMG-box) | 281477 | 13 | 11 | 13 | 3 | 3 | 2 | 0 | 3 | 5 | 0 | 0.51 | 0.11 | 0.00033 | 0.0004 | 0.4 |
19 | WBSCR17 | Williams-Beuren syndrome chromosome region 17 | 278161 | 17 | 17 | 16 | 2 | 10 | 2 | 1 | 1 | 3 | 0 | 0.63 | 0.1 | 0.00043 | 0.00048 | 0.45 |
20 | GGT1 | gamma-glutamyltransferase 1 | 178906 | 3 | 3 | 1 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 0.000017 | 0.000052 | 0.84 | 0.00048 | 0.45 |
21 | TXNDC3 | thioredoxin domain containing 3 (spermatozoa) | 283045 | 13 | 10 | 13 | 2 | 3 | 1 | 1 | 3 | 5 | 0 | 0.84 | 0.79 | 0.000061 | 0.00053 | 0.45 |
22 | MGC26647 | chromosome 7 open reading frame 62 | 117898 | 7 | 7 | 7 | 0 | 1 | 1 | 0 | 2 | 3 | 0 | 0.82 | 0.21 | 0.00035 | 0.00078 | 0.64 |
23 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 180955 | 6 | 4 | 5 | 1 | 2 | 0 | 0 | 1 | 2 | 1 | 0.0046 | 0.0051 | 0.017 | 0.00088 | 0.69 |
24 | CASP8 | caspase 8, apoptosis-related cysteine peptidase | 266056 | 11 | 10 | 10 | 0 | 1 | 3 | 1 | 2 | 4 | 0 | 0.6 | 0.81 | 0.00013 | 0.0011 | 0.8 |
25 | ACVR1B | activin A receptor, type IB | 235764 | 13 | 13 | 13 | 0 | 4 | 6 | 0 | 2 | 1 | 0 | 0.0019 | 0.0059 | 0.027 | 0.0015 | 1 |
26 | OR6A2 | olfactory receptor, family 6, subfamily A, member 2 | 153139 | 2 | 2 | 2 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0.0045 | 0.00039 | 0.42 | 0.0016 | 1 |
27 | KLK2 | kallikrein-related peptidase 2 | 127435 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0.2 | 0.00044 | 0.42 | 0.0018 | 1 |
28 | MAP2K4 | mitogen-activated protein kinase kinase 4 | 171130 | 9 | 9 | 8 | 0 | 2 | 3 | 1 | 2 | 1 | 0 | 0.0021 | 0.0042 | 0.046 | 0.0019 | 1 |
29 | ELF3 | E74-like factor 3 (ets domain transcription factor, epithelial-specific ) | 167304 | 3 | 3 | 3 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 0.47 | 0.11 | 0.0019 | 0.0021 | 1 |
30 | MIER3 | mesoderm induction early response 1, family member 3 | 259908 | 10 | 10 | 10 | 0 | 2 | 2 | 0 | 2 | 4 | 0 | 0.64 | 0.64 | 0.00047 | 0.0027 | 1 |
31 | SULT1C4 | sulfotransferase family, cytosolic, 1C, member 4 | 145166 | 3 | 3 | 1 | 0 | 2 | 0 | 0 | 1 | 0 | 0 | 0.2 | 0.0014 | 0.26 | 0.0033 | 1 |
32 | FAM22F | family with sequence similarity 22, member F | 194820 | 8 | 8 | 4 | 1 | 1 | 0 | 0 | 6 | 1 | 0 | 0.4 | 0.07 | 0.0052 | 0.0033 | 1 |
33 | TBC1D10C | TBC1 domain family, member 10C | 134780 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.97 | 0.29 | 0.0013 | 0.0035 | 1 |
34 | MUC20 | mucin 20, cell surface associated | 124950 | 2 | 2 | 1 | 1 | 0 | 0 | 0 | 0 | 2 | 0 | 0.0025 | 0.0036 | 0.12 | 0.0038 | 1 |
35 | OR2M4 | olfactory receptor, family 2, subfamily M, member 4 | 145654 | 8 | 8 | 8 | 0 | 3 | 2 | 1 | 0 | 2 | 0 | 0.044 | 0.17 | 0.0026 | 0.0039 | 1 |
In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.
rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q |
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1 | APC | adenomatous polyposis coli | 121 | 839 | 87 | 130045 | 1536 | 0 | 0 |
2 | TP53 | tumor protein p53 | 77 | 824 | 77 | 127720 | 27419 | 0 | 0 |
3 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 15 | 33 | 13 | 5115 | 12243 | 6.7e-14 | 1e-10 |
4 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 58 | 52 | 58 | 8060 | 650714 | 1e-13 | 1.2e-10 |
5 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 21 | 89 | 19 | 13795 | 273106 | 1.6e-13 | 1.3e-10 |
6 | FBXW7 | F-box and WD repeat domain containing 7 | 33 | 91 | 25 | 14105 | 899 | 1.7e-13 | 1.3e-10 |
7 | SMAD4 | SMAD family member 4 | 21 | 159 | 13 | 24645 | 51 | 2.6e-13 | 1.7e-10 |
8 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 33 | 220 | 30 | 34100 | 11874 | 3.3e-13 | 1.9e-10 |
9 | ERBB3 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) | 11 | 6 | 5 | 930 | 5 | 7.5e-13 | 3.8e-10 |
10 | CDC27 | cell division cycle 27 homolog (S. cerevisiae) | 9 | 3 | 4 | 465 | 4 | 2.4e-11 | 1.1e-08 |
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)
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 | 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 | 144 | APC(121), APC2(1), AXIN1(1), AXIN2(7), BTRC(2), CACYBP(1), CAMK2A(1), CAMK2B(2), CAMK2D(2), CAMK2G(2), CCND2(1), CCND3(1), CER1(3), CHD8(4), CREBBP(21), CSNK1A1(2), CSNK1A1L(5), CSNK2A1(4), CSNK2A2(2), CSNK2B(2), CTBP1(1), CTBP2(2), CTNNB1(8), CTNNBIP1(1), CUL1(7), CXXC4(1), DAAM1(1), DAAM2(5), DKK1(3), DKK2(5), DKK4(4), DVL2(8), DVL3(2), EP300(13), FBXW11(7), FZD10(4), FZD2(2), FZD3(10), FZD4(1), FZD6(3), FZD7(3), FZD8(1), GSK3B(7), LEF1(4), LRP5(5), LRP6(10), MAP3K7(2), MAPK10(4), MAPK8(2), MAPK9(3), MMP7(3), NFAT5(5), NFATC1(1), NFATC2(3), NFATC3(4), NFATC4(4), NKD1(3), NKD2(1), NLK(1), PLCB1(8), PLCB2(3), PLCB3(3), PLCB4(9), PORCN(2), PPARD(1), PPP2CA(1), PPP2R1A(4), PPP2R1B(1), PPP2R2A(1), PPP2R2B(1), PPP2R2C(3), PPP3CA(1), PPP3CB(4), PPP3CC(3), PPP3R1(1), PPP3R2(1), PRICKLE1(8), PRICKLE2(5), PRKACB(1), PRKACG(2), PRKCA(2), PRKCG(8), PRKX(2), PSEN1(3), RHOA(4), ROCK1(8), ROCK2(2), RUVBL1(6), SENP2(2), SFRP1(2), SFRP2(1), SFRP4(3), SFRP5(1), SIAH1(1), SKP1(1), SMAD2(11), SMAD3(6), SMAD4(21), SOX17(2), TBL1X(5), TBL1XR1(6), TCF7(3), TCF7L1(3), TCF7L2(13), TP53(77), VANGL1(2), VANGL2(5), WIF1(2), WNT1(1), WNT10B(3), WNT11(3), WNT16(2), WNT2B(1), WNT3(4), WNT3A(1), WNT4(1), WNT5A(3), WNT7A(2), WNT7B(2), WNT8A(1), WNT9A(2), WNT9B(1) | 35522515 | 631 | 150 | 557 | 121 | 207 | 110 | 8 | 124 | 147 | 35 | <1.00e-15 | <3.24e-14 |
2 | WNT_SIGNALING | Wnt signaling genes | APC, ARHA, AXIN1, C2orf31, CCND1, CCND2, CCND3, CSNK1E, CSNK1E, LOC400927, CTNNB1, DIPA, DVL1, DVL2, DVL3, FBXW2, FOSL1, FRAT1, FZD1, FZD10, FZD2, FZD3, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LDLR, MAPK10, MAPK9, MYC, PAFAH1B1, PLAU, PPP2R5C, PPP2R5E, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCM, PRKCQ, PRKCZ, PRKD1, RAC1, RHOA, SFRP4, TCF7, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B | 58 | APC(121), AXIN1(1), CCND2(1), CCND3(1), CTNNB1(8), DVL2(8), DVL3(2), FBXW2(2), FZD10(4), FZD2(2), FZD3(10), FZD6(3), FZD7(3), FZD8(1), GSK3B(7), LDLR(4), MAPK10(4), MAPK9(3), PAFAH1B1(3), PLAU(2), PPP2R5C(2), PPP2R5E(2), PRKCA(2), PRKCD(3), PRKCE(4), PRKCG(8), PRKCH(2), PRKCI(4), PRKCQ(4), PRKD1(10), RHOA(4), SFRP4(3), TCF7(3), WNT1(1), WNT10B(3), WNT11(3), WNT16(2), WNT2B(1), WNT3(4), WNT4(1), WNT5A(3), WNT7A(2), WNT7B(2) | 13007053 | 263 | 129 | 225 | 48 | 68 | 34 | 3 | 45 | 79 | 34 | <1.00e-15 | <3.24e-14 |
3 | 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 | 108 | ABL1(4), ANAPC1(3), ANAPC10(2), ANAPC2(1), ANAPC4(1), ANAPC5(2), ANAPC7(4), ATM(27), ATR(13), BUB1(4), BUB1B(3), BUB3(2), CCNA1(4), CCNA2(3), CCNB1(2), CCNB2(2), CCNB3(4), CCND2(1), CCND3(1), CCNE1(3), CCNE2(1), CCNH(2), CDC14A(1), CDC14B(3), CDC16(3), CDC20(3), CDC23(6), CDC25A(2), CDC25B(5), CDC25C(3), CDC27(9), CDC7(2), CDK2(2), CDK4(2), CDK6(1), CDK7(1), CDKN1A(1), CDKN1B(1), CDKN2A(1), CDKN2C(1), CHEK1(1), CHEK2(1), CREBBP(21), CUL1(7), DBF4(2), E2F2(1), E2F3(1), EP300(13), ESPL1(8), GSK3B(7), HDAC1(2), HDAC2(2), MAD1L1(1), MAD2L1(1), MAD2L2(1), MCM3(1), MCM4(4), MCM5(3), MCM6(3), MCM7(2), MDM2(4), ORC1L(1), ORC3L(1), ORC4L(1), ORC5L(1), PCNA(2), PKMYT1(1), PLK1(6), PRKDC(13), PTTG1(1), RB1(4), RBL1(3), RBL2(8), SKP1(1), SKP2(1), SMAD2(11), SMAD3(6), SMAD4(21), SMC1A(10), SMC1B(4), TFDP1(4), TGFB1(1), TGFB2(5), TP53(77), WEE1(3), YWHAB(2), YWHAE(3), YWHAQ(1) | 30252673 | 414 | 127 | 377 | 73 | 128 | 89 | 8 | 105 | 81 | 3 | <1.00e-15 | <3.24e-14 |
4 | 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 | 80 | AIFM1(1), AKT1(2), AKT2(5), APAF1(7), ATM(27), BAD(1), BAX(1), BCL2(1), BCL2L1(1), BID(1), BIRC2(2), BIRC3(2), CAPN1(2), CAPN2(5), CASP10(2), CASP3(1), CASP6(1), CASP7(1), CASP8(11), CASP9(2), CFLAR(2), CHUK(4), CSF2RB(7), DFFA(2), DFFB(2), FASLG(1), IKBKB(2), IL1A(1), IL1R1(3), IL3(3), IRAK1(1), IRAK2(8), IRAK3(1), IRAK4(2), MAP3K14(2), MYD88(1), NFKB1(3), NFKB2(2), NTRK1(6), PIK3CA(33), PIK3CB(2), PIK3CD(2), PIK3CG(12), PIK3R1(5), PIK3R2(1), PIK3R5(1), PPP3CA(1), PPP3CB(4), PPP3CC(3), PPP3R1(1), PPP3R2(1), PRKACB(1), PRKACG(2), PRKAR1A(1), PRKAR1B(1), PRKAR2B(2), RELA(2), RIPK1(2), TNFRSF10A(3), TNFRSF10B(2), TNFRSF10C(6), TNFRSF1A(1), TNFSF10(1), TP53(77), TRADD(1), TRAF2(1) | 18529387 | 298 | 127 | 250 | 48 | 91 | 71 | 6 | 74 | 55 | 1 | <1.00e-15 | <3.24e-14 |
5 | ALKPATHWAY | Activin receptor-like kinase 3 (ALK3) is required during gestation for cardiac muscle development. | ACVR1, APC, ATF2, AXIN1, BMP10, BMP2, BMP4, BMP5, BMP7, BMPR1A, BMPR2, CHRD, CTNNB1, DVL1, FZD1, GATA4, GSK3B, MADH1, MADH4, MADH5, MADH6, MAP3K7, MEF2C, MYL2, NKX2-5, NOG, NPPA, NPPB, RFC1, TCF1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TGFBR3, WNT1 | 32 | ACVR1(3), APC(121), AXIN1(1), BMP10(2), BMP4(1), BMP5(4), BMP7(5), BMPR1A(4), BMPR2(7), CHRD(5), CTNNB1(8), GATA4(1), GSK3B(7), MAP3K7(2), MEF2C(7), MYL2(1), NKX2-5(1), NPPA(1), RFC1(10), TGFB1(1), TGFB2(5), TGFBR1(6), TGFBR2(7), TGFBR3(5), WNT1(1) | 7996440 | 216 | 126 | 179 | 31 | 37 | 23 | 2 | 37 | 83 | 34 | <1.00e-15 | <3.24e-14 |
6 | ST_WNT_BETA_CATENIN_PATHWAY | Beta-catenin is degraded in the absence of Wnt signaling; when extracellular Wnt binds Frizzled receptors, beta-catenin accumulates in the nucleus and may promote cell survival. | AKT1, AKT2, AKT3, ANKRD6, APC, AXIN1, AXIN2, C22orf2, CER1, CSNK1A1, CTNNB1, DACT1, DKK1, DKK2, DKK3, DKK4, DVL1, FRAT1, FSTL1, GSK3A, GSK3B, IDAX, LAMR1, LRP1, MVP, NKD1, NKD2, PIN1, PSEN1, PTPRA, SENP2, SFRP1, TSHB, WIF1 | 30 | AKT1(2), AKT2(5), ANKRD6(5), APC(121), AXIN1(1), AXIN2(7), CER1(3), CSNK1A1(2), CTNNB1(8), DACT1(5), DKK1(3), DKK2(5), DKK3(2), DKK4(4), FSTL1(5), GSK3A(2), GSK3B(7), LRP1(14), MVP(4), NKD1(3), NKD2(1), PIN1(1), PSEN1(3), PTPRA(2), SENP2(2), SFRP1(2), WIF1(2) | 8848505 | 221 | 126 | 184 | 33 | 52 | 22 | 4 | 32 | 77 | 34 | <1.00e-15 | <3.24e-14 |
7 | GSK3PATHWAY | Bacterial lipopolysaccharide activates AKT to promote the survival and activation of macrophages and inhibits Gsk3-beta to promote beta-catenin accumulation in the nucleus. | AKT1, APC, AXIN1, CCND1, CD14, CTNNB1, DVL1, FZD1, GJA1, GNAI1, GSK3B, IRAK1, LBP, LEF1, LY96, MYD88, NFKB1, PDPK1, PIK3CA, PIK3R1, PPP2CA, PRKR, RELA, TIRAP, TLR4, TOLLIP, WNT1 | 26 | AKT1(2), APC(121), AXIN1(1), CD14(1), CTNNB1(8), GJA1(3), GNAI1(3), GSK3B(7), IRAK1(1), LBP(1), LEF1(4), LY96(2), MYD88(1), NFKB1(3), PDPK1(1), PIK3CA(33), PIK3R1(5), PPP2CA(1), RELA(2), TIRAP(1), TLR4(7), TOLLIP(1), WNT1(1) | 6608775 | 210 | 123 | 159 | 24 | 32 | 36 | 4 | 29 | 75 | 34 | <1.00e-15 | <3.24e-14 |
8 | HSA04540_GAP_JUNCTION | Genes involved in gap junction | ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADRB1, CDC2, CSNK1D, DRD1, DRD2, EDG2, EGF, EGFR, GJA1, GJD2, GNA11, GNAI1, GNAI2, GNAI3, GNAQ, GNAS, GRB2, GRM1, GRM5, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, HRAS, HTR2A, HTR2B, HTR2C, ITPR1, ITPR2, ITPR3, KRAS, LOC643224, LOC654264, MAP2K1, MAP2K2, MAP2K5, MAP3K2, MAPK1, MAPK3, MAPK7, NPR1, NPR2, NRAS, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PLCB1, PLCB2, PLCB3, PLCB4, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKG1, PRKG2, PRKX, PRKY, RAF1, SOS1, SOS2, SRC, TJP1, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8 | 92 | ADCY1(4), ADCY2(12), ADCY3(1), ADCY4(9), ADCY5(8), ADCY6(1), ADCY7(3), ADCY8(11), ADCY9(4), ADRB1(2), CSNK1D(3), DRD1(1), DRD2(3), EGF(3), EGFR(10), GJA1(3), GNA11(1), GNAI1(3), GNAQ(3), GNAS(6), GRB2(2), GRM1(9), GRM5(8), GUCY1A2(8), GUCY1A3(12), GUCY1B3(7), GUCY2C(7), GUCY2D(4), GUCY2F(7), HTR2A(2), HTR2B(1), HTR2C(6), ITPR1(11), ITPR2(12), ITPR3(11), KRAS(58), MAP2K1(3), MAP2K5(2), MAP3K2(2), MAPK1(2), MAPK3(2), MAPK7(3), NPR1(6), NPR2(9), NRAS(15), PDGFA(1), PDGFC(2), PDGFD(3), PDGFRA(13), PDGFRB(5), PLCB1(8), PLCB2(3), PLCB3(3), PLCB4(9), PRKACB(1), PRKACG(2), PRKCA(2), PRKCG(8), PRKG1(4), PRKG2(3), PRKX(2), RAF1(4), SOS1(5), SOS2(9), SRC(3), TJP1(5), TUBA3C(9), TUBA3D(2), TUBA3E(4), TUBA4A(1), TUBA8(1), TUBAL3(3), TUBB(1), TUBB1(2), TUBB2A(1), TUBB2B(3), TUBB3(1), TUBB4(2), TUBB4Q(2), TUBB6(3), TUBB8(2) | 28826153 | 432 | 123 | 372 | 142 | 154 | 105 | 11 | 133 | 28 | 1 | <1.00e-15 | <3.24e-14 |
9 | ST_MYOCYTE_AD_PATHWAY | Cardiac myocytes have a variety of adrenergic receptors that induce subtype-specific signaling effects. | ADRB1, AKT1, APC, ASAH1, BF, CAMP, CAV3, DAG1, DLG4, EPHB2, GAS, GNAI1, GNAQ, HTATIP, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, PITX2, PLB, PTX1, PTX3, RAC1, RHO, RYR1 | 23 | ADRB1(2), AKT1(2), APC(121), ASAH1(3), CAV3(2), DAG1(4), DLG4(2), EPHB2(7), GNAI1(3), GNAQ(3), ITPR1(11), ITPR2(12), ITPR3(11), KCNJ3(6), KCNJ5(3), KCNJ9(2), MAPK1(2), PITX2(2), PTX3(2), RHO(2), RYR1(19) | 9853585 | 221 | 123 | 184 | 49 | 55 | 22 | 5 | 33 | 72 | 34 | <1.00e-15 | <3.24e-14 |
10 | 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 | 22 | APC(121), AXIN1(1), BTRC(2), CREBBP(21), CSNK1A1(2), CSNK1D(3), CSNK2A1(4), CTBP1(1), CTNNB1(8), GSK3B(7), HDAC1(2), MAP3K7(2), NLK(1), PPARD(1), PPP2CA(1), TLE1(1), WIF1(2), WNT1(1) | 6371845 | 181 | 120 | 145 | 22 | 26 | 21 | 2 | 24 | 74 | 34 | <1.00e-15 | <3.24e-14 |
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]
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.