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.
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Working with individual set: STAD-TP
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Number of patients in set: 289
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:STAD-TP.final_analysis_set.maf
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Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt
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Significantly mutated genes (q ≤ 0.1): 97
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Mutations seen in COSMIC: 695
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Significantly mutated genes in COSMIC territory: 49
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Significantly mutated genesets: 17
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Significantly mutated genesets: (excluding sig. mutated genes):0
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Read 289 MAFs of type "Broad"
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Total number of mutations in input MAFs: 148520
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After removing 95 noncoding mutations: 148425
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After collapsing adjacent/redundant mutations: 147583
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Number of mutations before filtering: 147583
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After removing 239 mutations outside gene set: 147344
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After removing 1042 mutations outside category set: 146302
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After removing 4 "impossible" mutations in
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gene-patient-category bins of zero coverage: 145017
type | count |
---|---|
Frame_Shift_Del | 10745 |
Frame_Shift_Ins | 3490 |
In_Frame_Del | 1019 |
In_Frame_Ins | 114 |
Missense_Mutation | 86947 |
Nonsense_Mutation | 4363 |
Nonstop_Mutation | 93 |
Silent | 36328 |
Splice_Site | 2963 |
Translation_Start_Site | 240 |
Total | 146302 |
category | n | N | rate | rate_per_mb | relative_rate | exp_ns_s_ratio |
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*CpG->T | 31893 | 468903824 | 0.000068 | 68 | 5.2 | 2.1 |
*Np(A/C/T)->transit | 26998 | 6698174757 | 4e-06 | 4 | 0.31 | 2 |
*ApG->G | 4463 | 1298784747 | 3.4e-06 | 3.4 | 0.26 | 2.1 |
transver | 23822 | 8465863328 | 2.8e-06 | 2.8 | 0.22 | 5 |
indel+null | 21801 | 8465863328 | 2.6e-06 | 2.6 | 0.2 | NaN |
double_null | 994 | 8465863328 | 1.2e-07 | 0.12 | 0.009 | NaN |
Total | 109971 | 8465863328 | 0.000013 | 13 | 1 | 3.5 |
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). If the figure is unpopulated, then full coverage is assumed (e.g. MutSig CV doesn't use WIGs and assumes full coverage).
The mutation spectrum is depicted in the lego plots below in which the 96 possible mutation types are subdivided into six large blocks, color-coded to reflect the base substitution type. Each large block is further subdivided into the 16 possible pairs of 5' and 3' neighbors, as listed in the 4x4 trinucleotide context legend. The height of each block corresponds to the mutation frequency for that kind of mutation (counts of mutations normalized by the base coverage in a given bin). The shape of the spectrum is a signature for dominant mutational mechanisms in different tumor types.
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_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
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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_ns_s | p | q |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | TP53 | tumor protein p53 | 354913 | 142 | 137 | 86 | 1 | 38 | 26 | 2 | 22 | 48 | 6 | 7.6e-15 | <1.00e-15 | <9.05e-12 |
2 | ARID1A | AT rich interactive domain 1A (SWI-like) | 1686335 | 98 | 90 | 80 | 4 | 6 | 7 | 1 | 4 | 60 | 20 | 0.00083 | <1.00e-15 | <9.05e-12 |
3 | RNF43 | ring finger protein 43 | 627712 | 56 | 49 | 17 | 2 | 2 | 4 | 0 | 0 | 43 | 7 | 0.29 | 1.78e-15 | 1.07e-11 |
4 | RHOA | ras homolog gene family, member A | 172822 | 17 | 16 | 13 | 0 | 1 | 8 | 0 | 8 | 0 | 0 | 0.0086 | 5.22e-15 | 1.84e-11 |
5 | SMAD4 | SMAD family member 4 | 488947 | 26 | 24 | 21 | 1 | 5 | 6 | 0 | 8 | 5 | 2 | 0.017 | 5.55e-15 | 1.84e-11 |
6 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 197544 | 28 | 28 | 6 | 0 | 0 | 22 | 0 | 6 | 0 | 0 | 0.00011 | 6.22e-15 | 1.84e-11 |
7 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 945337 | 72 | 57 | 34 | 2 | 11 | 46 | 4 | 9 | 2 | 0 | 2.2e-08 | 7.11e-15 | 1.84e-11 |
8 | B2M | beta-2-microglobulin | 107442 | 22 | 17 | 15 | 1 | 0 | 3 | 0 | 2 | 10 | 7 | 0.25 | 1.20e-14 | 2.71e-11 |
9 | CDH1 | cadherin 1, type 1, E-cadherin (epithelial) | 733965 | 30 | 29 | 27 | 4 | 2 | 9 | 2 | 10 | 7 | 0 | 0.041 | 2.28e-14 | 4.58e-11 |
10 | BZRAP1 | benzodiazapine receptor (peripheral) associated protein 1 | 1434697 | 47 | 46 | 17 | 5 | 6 | 4 | 1 | 2 | 34 | 0 | 0.51 | 3.14e-13 | 5.68e-10 |
11 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 345472 | 29 | 23 | 21 | 4 | 1 | 4 | 0 | 6 | 14 | 4 | 0.46 | 1.81e-11 | 2.97e-08 |
12 | PGM5 | phosphoglucomutase 5 | 395150 | 29 | 25 | 7 | 0 | 4 | 19 | 0 | 1 | 5 | 0 | 0.000019 | 3.50e-10 | 5.28e-07 |
13 | SLITRK6 | SLIT and NTRK-like family, member 6 | 730918 | 24 | 24 | 24 | 1 | 5 | 7 | 1 | 9 | 2 | 0 | 0.0075 | 7.60e-10 | 1.06e-06 |
14 | TUSC3 | tumor suppressor candidate 3 | 311216 | 18 | 17 | 16 | 1 | 6 | 0 | 3 | 7 | 2 | 0 | 0.059 | 6.51e-09 | 8.42e-06 |
15 | ZNF43 | zinc finger protein 43 | 702369 | 37 | 34 | 17 | 3 | 0 | 6 | 1 | 8 | 18 | 4 | 0.35 | 1.02e-08 | 1.24e-05 |
16 | EDNRB | endothelin receptor type B | 395127 | 29 | 27 | 22 | 5 | 8 | 3 | 1 | 7 | 9 | 1 | 0.21 | 1.38e-08 | 1.56e-05 |
17 | OR5M3 | olfactory receptor, family 5, subfamily M, member 3 | 265275 | 16 | 15 | 9 | 1 | 2 | 1 | 3 | 3 | 7 | 0 | 0.2 | 2.24e-08 | 2.38e-05 |
18 | FBXW7 | F-box and WD repeat domain containing 7 | 715336 | 28 | 27 | 18 | 1 | 14 | 4 | 0 | 1 | 9 | 0 | 0.01 | 4.66e-08 | 4.69e-05 |
19 | ZNF804B | zinc finger protein 804B | 1172130 | 45 | 34 | 44 | 4 | 4 | 10 | 1 | 26 | 4 | 0 | 0.013 | 6.20e-08 | 5.58e-05 |
20 | KLF3 | Kruppel-like factor 3 (basic) | 305648 | 20 | 19 | 13 | 2 | 6 | 1 | 0 | 1 | 10 | 2 | 0.25 | 6.23e-08 | 5.58e-05 |
21 | CNBD1 | cyclic nucleotide binding domain containing 1 | 276093 | 13 | 13 | 8 | 1 | 1 | 1 | 3 | 7 | 1 | 0 | 0.083 | 6.47e-08 | 5.58e-05 |
22 | GNG12 | guanine nucleotide binding protein (G protein), gamma 12 | 65589 | 11 | 11 | 3 | 2 | 0 | 2 | 0 | 0 | 9 | 0 | 0.81 | 1.25e-07 | 0.000103 |
23 | GPSM3 | G-protein signaling modulator 3 (AGS3-like, C. elegans) | 133004 | 12 | 12 | 10 | 0 | 3 | 1 | 0 | 2 | 5 | 1 | 0.31 | 1.49e-07 | 0.000118 |
24 | TRIML2 | tripartite motif family-like 2 | 343734 | 16 | 16 | 16 | 0 | 1 | 4 | 1 | 10 | 0 | 0 | 0.015 | 1.78e-07 | 0.000134 |
25 | ZWINT | ZW10 interactor | 249621 | 13 | 12 | 13 | 1 | 1 | 4 | 0 | 5 | 3 | 0 | 0.13 | 4.74e-07 | 0.000343 |
26 | XYLT2 | xylosyltransferase II | 650967 | 35 | 32 | 10 | 3 | 6 | 2 | 0 | 0 | 27 | 0 | 0.52 | 5.95e-07 | 0.000414 |
27 | SOHLH2 | spermatogenesis and oogenesis specific basic helix-loop-helix 2 | 379246 | 14 | 14 | 12 | 1 | 2 | 2 | 4 | 5 | 1 | 0 | 0.042 | 8.08e-07 | 0.000542 |
28 | OR2L8 | olfactory receptor, family 2, subfamily L, member 8 | 272407 | 12 | 12 | 12 | 1 | 0 | 2 | 3 | 6 | 1 | 0 | 0.15 | 1.33e-06 | 0.000862 |
29 | DCLK1 | doublecortin-like kinase 1 | 629325 | 33 | 31 | 33 | 5 | 9 | 6 | 2 | 9 | 7 | 0 | 0.06 | 1.71e-06 | 0.00104 |
30 | CYP7B1 | cytochrome P450, family 7, subfamily B, polypeptide 1 | 399747 | 17 | 16 | 14 | 1 | 1 | 1 | 0 | 11 | 4 | 0 | 0.26 | 1.73e-06 | 0.00104 |
31 | CASP8 | caspase 8, apoptosis-related cysteine peptidase | 503877 | 18 | 18 | 15 | 1 | 1 | 1 | 3 | 4 | 9 | 0 | 0.33 | 3.98e-06 | 0.00232 |
32 | RPL10L | ribosomal protein L10-like | 187560 | 12 | 11 | 12 | 0 | 3 | 3 | 1 | 5 | 0 | 0 | 0.047 | 4.70e-06 | 0.00266 |
33 | LARP4B | La ribonucleoprotein domain family, member 4B | 645702 | 29 | 27 | 8 | 2 | 2 | 3 | 0 | 1 | 23 | 0 | 0.4 | 5.22e-06 | 0.00279 |
34 | OR4C16 | olfactory receptor, family 4, subfamily C, member 16 | 267669 | 13 | 13 | 9 | 2 | 1 | 3 | 0 | 7 | 2 | 0 | 0.38 | 5.25e-06 | 0.00279 |
35 | LMAN1 | lectin, mannose-binding, 1 | 449568 | 22 | 22 | 5 | 2 | 0 | 1 | 0 | 0 | 21 | 0 | 0.83 | 6.35e-06 | 0.00328 |
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 | TP53 | tumor protein p53 | 142 | 356 | 132 | 102884 | 35093 | 0 | 0 |
2 | ERBB3 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) | 37 | 6 | 8 | 1734 | 8 | 6e-15 | 1.4e-11 |
3 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 28 | 52 | 27 | 15028 | 197519 | 4.4e-14 | 5e-11 |
4 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 29 | 767 | 29 | 221663 | 785 | 4.4e-14 | 5e-11 |
5 | FBXW7 | F-box and WD repeat domain containing 7 | 28 | 91 | 18 | 26299 | 892 | 6.6e-14 | 5.6e-11 |
6 | SMAD4 | SMAD family member 4 | 26 | 159 | 21 | 45951 | 73 | 9e-14 | 5.6e-11 |
7 | CDH1 | cadherin 1, type 1, E-cadherin (epithelial) | 30 | 185 | 15 | 53465 | 42 | 9.6e-14 | 5.6e-11 |
8 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 72 | 220 | 62 | 63580 | 22978 | 9.9e-14 | 5.6e-11 |
9 | APC | adenomatous polyposis coli | 43 | 839 | 22 | 242471 | 474 | 4.1e-12 | 2e-09 |
10 | ERBB2 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) | 15 | 42 | 8 | 12138 | 80 | 8.3e-12 | 3.7e-09 |
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_ns_s | p | q |
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1 | ARFPATHWAY | Cyclin-dependent kinase inhibitor 2A is a tumor suppressor that induces G1 arrest and can activate the p53 pathway, leading to G2/M arrest. | ABL1, CDKN2A, E2F1, MDM2, MYC, PIK3CA, PIK3R1, POLR1A, POLR1B, POLR1C, POLR1D, RAC1, RB1, TBX2, TP53, TWIST1 | 16 | ABL1(7), CDKN2A(13), E2F1(3), MDM2(5), MYC(5), PIK3CA(72), PIK3R1(11), POLR1A(15), POLR1B(7), POLR1C(3), POLR1D(4), RB1(13), TBX2(6), TP53(142), TWIST1(2) | 8710873 | 308 | 200 | 210 | 37 | 74 | 95 | 7 | 43 | 81 | 8 | 4.5e-12 | <1.00e-15 | <2.58e-13 |
2 | RNAPATHWAY | dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation. | CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53 | 9 | CHUK(4), DNAJC3(3), EIF2S1(2), EIF2S2(2), MAP3K14(5), NFKB1(7), NFKBIA(1), RELA(5), TP53(142) | 4197551 | 171 | 146 | 115 | 8 | 45 | 34 | 2 | 30 | 54 | 6 | 9.3e-12 | 1.67e-15 | 2.58e-13 |
3 | SA_G1_AND_S_PHASES | Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. | ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53 | 15 | ARF1(5), CCND1(1), CDK2(3), CDKN1A(3), CDKN2A(13), CFL1(1), E2F1(3), E2F2(4), MDM2(5), NXT1(2), PRB1(6), TP53(142) | 3621793 | 188 | 157 | 131 | 12 | 50 | 39 | 3 | 27 | 61 | 8 | 1e-11 | 1.89e-15 | 2.58e-13 |
4 | RBPATHWAY | The ATM protein kinase recognizes DNA damage and blocks cell cycle progression by phosphorylating chk1 and p53, which normally inhibits Rb to allow G1/S transitions. | ATM, CDC2, CDC25A, CDC25B, CDC25C, CDK2, CDK4, CHEK1, MYT1, RB1, TP53, WEE1, YWHAH | 12 | ATM(38), CDC25A(6), CDC25B(4), CDC25C(13), CDK2(3), CHEK1(4), MYT1(19), RB1(13), TP53(142), WEE1(4), YWHAH(3) | 7559184 | 249 | 176 | 182 | 22 | 59 | 52 | 6 | 44 | 78 | 10 | 1.3e-09 | 2.55e-15 | 2.58e-13 |
5 | PLK3PATHWAY | Active Plk3 phosphorylates CDC25c, blocking the G2/M transition, and phosphorylates p53 to induce apoptosis. | ATM, ATR, CDC25C, CHEK1, CHEK2, CNK, TP53, YWHAH | 7 | ATM(38), ATR(18), CDC25C(13), CHEK1(4), CHEK2(8), TP53(142), YWHAH(3) | 6857303 | 226 | 171 | 161 | 20 | 56 | 41 | 5 | 39 | 75 | 10 | 4.1e-07 | 2.78e-15 | 2.58e-13 |
6 | TERTPATHWAY | hTERC, the RNA subunit of telomerase, and hTERT, the catalytic protein subunit, are required for telomerase activity and are overexpressed in many cancers. | HDAC1, MAX, MYC, SP1, SP3, TP53, WT1, ZNF42 | 7 | HDAC1(5), MAX(3), MYC(5), SP1(6), SP3(3), TP53(142), WT1(3) | 3032684 | 167 | 151 | 111 | 15 | 44 | 34 | 2 | 28 | 53 | 6 | 1.5e-09 | 3.00e-15 | 2.58e-13 |
7 | P53PATHWAY | p53 induces cell cycle arrest or apoptosis under conditions of DNA damage. | APAF1, ATM, BAX, BCL2, CCND1, CCNE1, CDK2, CDK4, CDKN1A, E2F1, GADD45A, MDM2, PCNA, RB1, TIMP3, TP53 | 16 | APAF1(8), ATM(38), BAX(6), BCL2(3), CCND1(1), CCNE1(5), CDK2(3), CDKN1A(3), E2F1(3), MDM2(5), PCNA(2), RB1(13), TIMP3(6), TP53(142) | 7778948 | 238 | 174 | 169 | 23 | 56 | 51 | 5 | 39 | 77 | 10 | 6.1e-09 | 3.33e-15 | 2.58e-13 |
8 | P53HYPOXIAPATHWAY | Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage. | ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53 | 19 | ABCB1(26), AKT1(3), ATM(38), BAX(6), CDKN1A(3), CPB2(10), CSNK1A1(3), CSNK1D(2), FHL2(4), HIC1(6), HIF1A(7), HSPA1A(2), IGFBP3(6), MAPK8(6), MDM2(5), NFKBIB(6), NQO1(3), TP53(142) | 8909084 | 278 | 182 | 210 | 28 | 69 | 56 | 7 | 45 | 90 | 11 | 8.4e-11 | 3.66e-15 | 2.58e-13 |
9 | CHEMICALPATHWAY | DNA damage promotes Bid cleavage, which stimulates mitochondrial cytochrome c release and consequent caspase activation, resulting in apoptosis. | ADPRT, AKT1, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, CASP3, CASP6, CASP7, CASP9, CYCS, EIF2S1, PRKCA, PRKCB1, PTK2, PXN, STAT1, TLN1, TP53 | 20 | AKT1(3), APAF1(8), ATM(38), BAD(3), BAX(6), BCL2(3), BID(2), CASP3(2), CASP6(1), CASP7(3), CASP9(3), EIF2S1(2), PRKCA(5), PTK2(11), PXN(4), STAT1(10), TLN1(22), TP53(142) | 11749843 | 268 | 178 | 201 | 29 | 73 | 58 | 11 | 39 | 78 | 9 | 3.8e-10 | 3.77e-15 | 2.58e-13 |
10 | PMLPATHWAY | Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis. | CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1 | 13 | CREBBP(40), DAXX(10), PAX3(11), PML(12), RARA(3), RB1(13), SIRT1(6), SP100(15), TNF(3), TNFRSF1A(6), TNFRSF1B(3), TP53(142) | 8160663 | 264 | 173 | 205 | 32 | 80 | 60 | 4 | 39 | 75 | 6 | 1.9e-10 | 6.11e-15 | 3.76e-13 |
rank | geneset | description | genes | N_genes | mut_tally | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p_ns_s | p | q |
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1 | SLRPPATHWAY | Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. | BGN, DCN, DSPG3, FMOD, KERA, LUM | 5 | BGN(1), DCN(8), FMOD(10), KERA(1), LUM(7) | 1561475 | 27 | 24 | 27 | 4 | 12 | 4 | 1 | 7 | 3 | 0 | 0.07 | 0.4 | 1 |
2 | BBCELLPATHWAY | Fas ligand expression by T cells induces apoptosis in Fas-expressing, inactive B cells. | CD28, CD4, HLA-DRA, HLA-DRB1, TNFRSF5, TNFRSF6, TNFSF5, TNFSF6 | 4 | CD28(2), CD4(15), HLA-DRA(8) | 1021938 | 25 | 23 | 16 | 5 | 6 | 4 | 0 | 3 | 12 | 0 | 0.57 | 0.42 | 1 |
3 | ALKALOID_BIOSYNTHESIS_II | ABP1, AOC2, AOC3, CES1, ESD | 5 | ABP1(16), AOC2(6), AOC3(15), CES1(7), ESD(1) | 2594728 | 45 | 32 | 38 | 8 | 10 | 11 | 1 | 7 | 15 | 1 | 0.21 | 0.45 | 1 | |
4 | HSA00643_STYRENE_DEGRADATION | Genes involved in styrene degradation | FAH, GSTZ1, HGD | 3 | FAH(8), GSTZ1(3), HGD(4) | 953469 | 15 | 13 | 14 | 3 | 4 | 3 | 0 | 4 | 4 | 0 | 0.38 | 0.54 | 1 |
5 | HSA00031_INOSITOL_METABOLISM | Genes involved in inositol metabolism | ALDH6A1, TPI1 | 2 | ALDH6A1(6), TPI1(1) | 706305 | 7 | 7 | 7 | 1 | 2 | 2 | 1 | 1 | 1 | 0 | 0.31 | 0.66 | 1 |
6 | FOSBPATHWAY | FOSB gene expression and drug abuse | CDK5, FOSB, GRIA2, JUND, PPP1R1B | 5 | CDK5(2), FOSB(5), GRIA2(23), JUND(2), PPP1R1B(1) | 1603188 | 33 | 27 | 33 | 6 | 7 | 10 | 1 | 10 | 5 | 0 | 0.064 | 0.72 | 1 |
7 | TCRMOLECULE | T Cell Receptor and CD3 Complex | CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@ | 3 | CD3E(2), CD3G(1) | 488715 | 3 | 3 | 3 | 1 | 0 | 1 | 1 | 0 | 1 | 0 | 0.82 | 0.74 | 1 |
8 | TCAPOPTOSISPATHWAY | HIV infection upregulates Fas ligand in macrophages and CD4 in helper T cells, leading to widespread Fas-induced T cell apoptosis. | CCR5, CD28, CD3D, CD3E, CD3G, CD3Z, CD4, TNFRSF6, TNFSF6, TRA@, TRB@ | 6 | CCR5(4), CD28(2), CD3E(2), CD3G(1), CD4(15) | 1381325 | 24 | 22 | 15 | 5 | 2 | 5 | 1 | 3 | 13 | 0 | 0.74 | 0.75 | 1 |
9 | ASBCELLPATHWAY | B cells require interaction with helper T cells to produce antigen-specific immunoglobulins as a key element of the human immune response. | CD28, CD4, CD80, HLA-DRA, HLA-DRB1, IL10, IL2, IL4, TNFRSF5, TNFRSF6, TNFSF5, TNFSF6 | 8 | CD28(2), CD4(15), CD80(4), HLA-DRA(8), IL10(2), IL4(1) | 1707909 | 32 | 28 | 23 | 6 | 10 | 4 | 0 | 5 | 13 | 0 | 0.37 | 0.77 | 1 |
10 | STEMPATHWAY | In the absence of infection, bone marrow stromal cells release hematopoietic cytokines; activated macrophages and Th cells induce hematopoiesis during infection. | CD4, CD8A, CSF1, CSF2, CSF3, EPO, IL11, IL2, IL3, IL4, IL5, IL6, IL7, IL8, IL9 | 15 | CD4(15), CD8A(4), CSF1(2), CSF3(2), EPO(1), IL11(3), IL3(1), IL4(1), IL7(1), IL8(2) | 2609601 | 32 | 28 | 23 | 4 | 6 | 6 | 1 | 6 | 13 | 0 | 0.15 | 0.78 | 1 |
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]
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.