Glioblastoma Multiforme: Mutation Analysis (MutSig v2.0)
Maintained by Dan DiCara (Broad Institute)
Overview
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 v2.0 was used to generate the results found in this report.

  • Working with individual set: GBM

  • Number of patients in set: 276

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.

Summary

  • MAF used for this analysis:GBM.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 257

  • Mutations seen in COSMIC: 446

  • Significantly mutated genes in COSMIC territory: 55

  • Genes with clustered mutations (≤ 3 aa apart): 393

  • Significantly mutated genesets: 164

  • Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

  • Read 276 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 36691

Mutation Filtering

  • Number of mutations before filtering: 36691

  • After removing 139 mutations outside gene set: 36552

  • After removing 81 mutations outside category set: 36471

  • After removing 233 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 36238

Results
Breakdown of Mutations by Type

Table 1.  Get Full Table Table representing breakdown of mutations by type.

type count
De_novo_Start_InFrame 6
De_novo_Start_OutOfFrame 10
Frame_Shift_Del 814
Frame_Shift_Ins 363
In_Frame_Del 329
In_Frame_Ins 38
Indel 1
Missense_Mutation 23575
Nonsense_Mutation 1747
Nonstop_Mutation 17
Silent 8955
Splice_Site_DNP 11
Splice_Site_Del 102
Splice_Site_Ins 28
Splice_Site_ONP 1
Splice_Site_SNP 469
Start_Codon_Del 2
Start_Codon_Ins 1
Stop_Codon_Del 2
Total 36471
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 8794 406970401 0.000022 22 6
*Cp(A/C/T)->T 3993 3448378213 1.2e-06 1.2 0.32
C->(G/A) 5881 3855348614 1.5e-06 1.5 0.43
A->mut 4753 3770634164 1.3e-06 1.3 0.35
indel+null 3857 7625982864 5.1e-07 0.51 0.14
double_null 79 7625982864 1e-08 0.01 0.0029
Total 27357 7625982864 3.6e-06 3.6 1
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. 

Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

Figure 2.  Patients counts and rates file used to generate this plot: GBM.patients.counts_and_rates.txt

CoMut Plot

Figure 3.  Get High-res Image The matrix in the center of the figure represents individual mutations in patient samples, color-coded by type of mutation, for the significantly mutated genes. The rate of synonymous and non-synonymous mutations is displayed at the top of the matrix. The barplot on the left of the matrix shows the number of mutations in each gene. The percentages represent the fraction of tumors with at least one mutation in the specified gene. The barplot to the right of the matrix displays the q-values for the most significantly mutated genes. The purple boxplots below the matrix (only displayed if required columns are present in the provided MAF) represent the distributions of allelic fractions observed in each sample. The plot at the bottom represents the base substitution distribution of individual samples, using the same categories that were used to calculate significance.

Significantly Mutated Genes

Column Descriptions:

  • 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

  • n6 = number of nonsilent mutations of type: double_null

  • p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene

  • p_ks = p-value for clustering of mutations (Kolmogorov-Smirnoff test)

  • p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene

  • p_joint = p-value for clustering + conservation

  • p = p-value (overall)

  • q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 257. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p_classic p_ks p_cons p_joint p q
1 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 642722 17 17 14 0 0 3 2 4 8 0 1.90e-14 0.000013 0.0045 0.000014 0.000 0.000
2 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 349470 15 15 2 0 14 0 1 0 0 0 6.11e-15 2e-07 0.97 0.000012 0.000 0.000
3 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 885302 19 19 17 1 3 5 2 7 2 0 5.33e-15 0.018 0.0053 0.0028 5.55e-16 8.92e-13
4 KRTAP5-5 keratin associated protein 5-5 181491 18 16 7 0 0 0 3 1 14 0 4.22e-15 0.0012 1 0.0039 6.66e-16 8.92e-13
5 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 314597 80 79 65 0 7 19 8 11 35 0 <1.00e-15 0.0098 0.48 0.02 <7.77e-16 <8.92e-13
6 TP53 tumor protein p53 344937 89 80 63 1 23 15 12 13 24 2 1.89e-15 2e-07 2e-07 0 <1.00e-15 <8.92e-13
7 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 1089173 58 54 26 5 9 21 23 5 0 0 2.55e-15 2e-07 2e-07 0 <1.00e-15 <8.92e-13
8 MICALCL MICAL C-terminal like 537385 13 13 3 0 0 0 0 1 12 0 3.66e-12 2e-07 0.63 0 <1.00e-15 <8.92e-13
9 C7orf52 chromosome 7 open reading frame 52 247344 6 6 2 1 1 5 0 0 0 0 0.000105 0.00082 2e-07 0 <1.00e-15 <8.92e-13
10 CRYBA2 crystallin, beta A2 136089 6 6 3 1 0 0 5 1 0 0 2.72e-07 2e-07 0.86 0 <1.00e-15 <8.92e-13
11 BID BH3 interacting domain death agonist 174925 4 4 1 0 0 0 0 4 0 0 0.000365 2e-07 0.89 0 <1.00e-15 <8.92e-13
12 FOXC1 forkhead box C1 130178 4 4 3 1 0 0 3 1 0 0 0.000199 2e-07 0.57 0 <1.00e-15 <8.92e-13
13 MRM1 mitochondrial rRNA methyltransferase 1 homolog (S. cerevisiae) 284558 4 4 1 0 0 0 0 4 0 0 0.00203 2e-07 0.42 0 <1.00e-15 <8.92e-13
14 PUF60 poly-U binding splicing factor 60KDa 249059 4 4 1 2 0 0 4 0 0 0 0.00106 2e-07 0.21 0 <1.00e-15 <8.92e-13
15 SALL2 sal-like 2 (Drosophila) 820150 4 4 2 2 0 0 4 0 0 0 0.0675 2e-07 0.76 0 <1.00e-15 <8.92e-13
16 SPHK2 sphingosine kinase 2 414038 2 3 1 0 0 0 2 0 0 0 0.188 1e-06 0.000026 0 <1.00e-15 <8.92e-13
17 ACSM2B acyl-CoA synthetase medium-chain family member 2B 454814 2 2 2 2 0 0 0 1 1 0 0.131 0.00023 0.68 0 <1.00e-15 <8.92e-13
18 C1orf100 chromosome 1 open reading frame 100 126907 2 2 2 0 0 0 0 0 2 0 0.0386 0.013 0.75 0 <1.00e-15 <8.92e-13
19 TAPBPL TAP binding protein-like 353808 2 2 2 1 0 1 0 0 1 0 0.206 0.00049 0.66 0 <1.00e-15 <8.92e-13
20 ABCA3 ATP-binding cassette, sub-family A (ABC1), member 3 1218196 3 1 3 1 0 0 2 1 0 0 0.945 2e-07 0.011 0 <1.00e-15 <8.92e-13
21 RB1 retinoblastoma 1 (including osteosarcoma) 722445 21 21 19 1 1 1 1 0 18 0 1.15e-14 0.045 0.28 0.059 2.44e-14 2.08e-11
22 SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2) 2040988 30 26 28 5 12 4 6 1 7 0 1.82e-14 0.27 0.3 0.49 2.99e-13 2.42e-10
23 FOXRED1 FAD-dependent oxidoreductase domain containing 1 345284 9 9 1 0 0 0 0 9 0 0 4.46e-09 2e-07 0.93 0.000015 2.15e-12 1.67e-09
24 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 2380799 31 25 30 1 2 5 3 4 14 3 8.69e-13 0.43 0.66 0.59 1.50e-11 1.12e-08
25 COMMD4 COMM domain containing 4 147026 6 6 1 0 0 0 6 0 0 0 1.79e-07 2e-07 1 0.000019 9.21e-11 6.58e-08
26 RYR2 ryanodine receptor 2 (cardiac) 3381004 36 28 35 7 21 3 6 6 0 0 1.10e-10 0.11 0.38 0.13 3.78e-10 2.59e-07
27 PLA2G2A phospholipase A2, group IIA (platelets, synovial fluid) 123007 5 5 1 0 0 0 5 0 0 0 1.62e-06 4e-07 0.27 1e-05 4.27e-10 2.82e-07
28 NRBP2 nuclear receptor binding protein 2 119779 4 4 1 0 0 4 0 0 0 0 2.33e-05 4e-07 0.99 1.6e-06 9.33e-10 5.95e-07
29 FUT7 fucosyltransferase 7 (alpha (1,3) fucosyltransferase) 113313 5 5 1 0 0 0 5 0 0 0 5.18e-06 2e-07 0.95 0.000017 2.10e-09 1.29e-06
30 FLG filaggrin 3183335 30 28 30 13 12 6 6 3 3 0 8.10e-10 0.63 0.038 0.15 2.84e-09 1.69e-06
31 HMP19 143577 5 5 1 0 0 0 5 0 0 0 1.30e-05 2e-07 0.92 1e-05 3.15e-09 1.81e-06
32 DNASE1L1 deoxyribonuclease I-like 1 189681 6 6 2 1 1 0 5 0 0 0 1.43e-06 0.000065 0.07 0.0001 3.51e-09 1.96e-06
33 KDSR 3-ketodihydrosphingosine reductase 270146 5 5 1 0 0 0 5 0 0 0 6.51e-05 2e-07 0.62 4e-06 6.00e-09 3.25e-06
34 TMEM45A transmembrane protein 45A 233464 5 5 1 0 0 0 0 5 0 0 5.02e-05 2e-07 0.08 8.8e-06 9.96e-09 5.23e-06
35 MUC2 mucin 2, oligomeric mucus/gel-forming 1046521 22 15 19 4 9 1 7 4 1 0 4.09e-09 0.19 0.94 0.29 2.57e-08 1.31e-05
PIK3R1

Figure S1.  This figure depicts the distribution of mutations and mutation types across the PIK3R1 significant gene.

IDH1

Figure S2.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

PIK3CA

Figure S3.  This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

KRTAP5-5

Figure S4.  This figure depicts the distribution of mutations and mutation types across the KRTAP5-5 significant gene.

PTEN

Figure S5.  This figure depicts the distribution of mutations and mutation types across the PTEN significant gene.

TP53

Figure S6.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

EGFR

Figure S7.  This figure depicts the distribution of mutations and mutation types across the EGFR significant gene.

MICALCL

Figure S8.  This figure depicts the distribution of mutations and mutation types across the MICALCL significant gene.

C7orf52

Figure S9.  This figure depicts the distribution of mutations and mutation types across the C7orf52 significant gene.

CRYBA2

Figure S10.  This figure depicts the distribution of mutations and mutation types across the CRYBA2 significant gene.

BID

Figure S11.  This figure depicts the distribution of mutations and mutation types across the BID significant gene.

FOXC1

Figure S12.  This figure depicts the distribution of mutations and mutation types across the FOXC1 significant gene.

MRM1

Figure S13.  This figure depicts the distribution of mutations and mutation types across the MRM1 significant gene.

PUF60

Figure S14.  This figure depicts the distribution of mutations and mutation types across the PUF60 significant gene.

SALL2

Figure S15.  This figure depicts the distribution of mutations and mutation types across the SALL2 significant gene.

SPHK2

Figure S16.  This figure depicts the distribution of mutations and mutation types across the SPHK2 significant gene.

ACSM2B

Figure S17.  This figure depicts the distribution of mutations and mutation types across the ACSM2B significant gene.

C1orf100

Figure S18.  This figure depicts the distribution of mutations and mutation types across the C1orf100 significant gene.

TAPBPL

Figure S19.  This figure depicts the distribution of mutations and mutation types across the TAPBPL significant gene.

ABCA3

Figure S20.  This figure depicts the distribution of mutations and mutation types across the ABCA3 significant gene.

RB1

Figure S21.  This figure depicts the distribution of mutations and mutation types across the RB1 significant gene.

SPTA1

Figure S22.  This figure depicts the distribution of mutations and mutation types across the SPTA1 significant gene.

FOXRED1

Figure S23.  This figure depicts the distribution of mutations and mutation types across the FOXRED1 significant gene.

NF1

Figure S24.  This figure depicts the distribution of mutations and mutation types across the NF1 significant gene.

COMMD4

Figure S25.  This figure depicts the distribution of mutations and mutation types across the COMMD4 significant gene.

RYR2

Figure S26.  This figure depicts the distribution of mutations and mutation types across the RYR2 significant gene.

PLA2G2A

Figure S27.  This figure depicts the distribution of mutations and mutation types across the PLA2G2A significant gene.

NRBP2

Figure S28.  This figure depicts the distribution of mutations and mutation types across the NRBP2 significant gene.

FUT7

Figure S29.  This figure depicts the distribution of mutations and mutation types across the FUT7 significant gene.

FLG

Figure S30.  This figure depicts the distribution of mutations and mutation types across the FLG significant gene.

HMP19

Figure S31.  This figure depicts the distribution of mutations and mutation types across the HMP19 significant gene.

DNASE1L1

Figure S32.  This figure depicts the distribution of mutations and mutation types across the DNASE1L1 significant gene.

KDSR

Figure S33.  This figure depicts the distribution of mutations and mutation types across the KDSR significant gene.

TMEM45A

Figure S34.  This figure depicts the distribution of mutations and mutation types across the TMEM45A significant gene.

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: 55. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 15 3 15 828 22380 0 0
2 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 17 33 9 9108 20 0 0
3 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 58 218 46 60168 640 0 0
4 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 80 728 79 200928 2714 0 0
5 TP53 tumor protein p53 89 823 89 227148 26312 0 0
6 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 19 184 15 50784 3911 0 0
7 RB1 retinoblastoma 1 (including osteosarcoma) 21 267 11 73692 30 0 0
8 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 31 285 10 78660 18 0 0
9 PTPN11 protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) 6 31 4 8556 16 3.6e-08 0.000018
10 BRAF v-raf murine sarcoma viral oncogene homolog B1 6 88 5 24288 42058 3.9e-08 0.000018

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)

Clustered Mutations

Table 5.  Get Full Table Genes with Clustered Mutations

num gene desc n mindist nmuts0 nmuts3 nmuts12 npairs0 npairs3 npairs12
2969 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 58 0 158 172 199 158 172 199
4509 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 15 0 105 105 105 105 105 105
10131 TP53 tumor protein p53 89 0 69 161 418 69 161 418
3613 FOXRED1 FAD-dependent oxidoreductase domain containing 1 9 0 36 36 36 36 36 36
7921 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 80 0 25 74 157 25 74 157
5448 LPHN1 latrophilin 1 10 0 16 16 18 16 16 18
879 BBS1 Bardet-Biedl syndrome 1 8 0 15 15 15 15 15 15
2208 COL5A3 collagen, type V, alpha 3 11 0 15 15 15 15 15 15
2221 COMMD4 COMM domain containing 4 6 0 15 15 15 15 15 15
2851 DSCAM Down syndrome cell adhesion molecule 10 0 15 15 15 15 15 15

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.

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: 164. 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 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 246 ACVR1C(2), AKT1(1), AKT2(1), AKT3(1), ATF2(1), ATF4(1), BDNF(1), BRAF(6), CACNA1A(4), CACNA1B(7), CACNA1C(5), CACNA1D(9), CACNA1E(9), CACNA1F(10), CACNA1G(6), CACNA1H(9), CACNA1I(5), CACNA1S(12), CACNA2D1(8), CACNA2D2(1), CACNA2D3(3), CACNA2D4(1), CACNB2(1), CACNB3(1), CACNG1(1), CACNG2(1), CACNG3(4), CACNG6(1), CACNG7(1), CACNG8(1), CD14(2), CDC25B(1), CHUK(4), DAXX(4), DDIT3(1), DUSP10(1), DUSP14(1), DUSP16(1), DUSP2(2), DUSP4(3), DUSP8(1), DUSP9(1), EGF(3), EGFR(58), ELK1(1), ELK4(1), FGF10(1), FGF13(1), FGF14(2), FGF18(1), FGF2(1), FGF20(2), FGF21(1), FGF23(3), FGF3(1), FGF6(3), FGF9(1), FGFR1(3), FGFR2(3), FGFR3(2), FGFR4(3), FLNA(14), FLNB(4), FLNC(6), FOS(1), GADD45B(1), GNA12(2), IKBKB(2), IL1R1(2), KRAS(1), MAP2K1(1), MAP2K2(1), MAP2K3(1), MAP2K5(1), MAP2K7(1), MAP3K1(5), MAP3K10(3), MAP3K12(5), MAP3K13(2), MAP3K14(2), MAP3K2(1), MAP3K3(4), MAP3K4(2), MAP3K5(1), MAP3K6(5), MAP3K7(2), MAP4K1(1), MAP4K2(1), MAP4K3(1), MAP4K4(5), MAPK1(3), MAPK13(1), MAPK14(1), MAPK3(2), MAPK7(3), MAPK8IP1(3), MAPK8IP2(3), MAPK8IP3(5), MAPK9(2), MAPKAPK2(1), MAPKAPK3(1), MAPT(1), MAX(2), MEF2C(1), MKNK1(1), NF1(31), NFATC2(1), NFATC4(2), NFKB1(1), NFKB2(1), NR4A1(3), NRAS(1), NTF3(1), NTRK1(4), NTRK2(1), PAK1(2), PDGFRA(10), PDGFRB(5), PLA2G12A(3), PLA2G2A(5), PLA2G2F(2), PLA2G3(2), PLA2G4A(4), PLA2G5(1), PLA2G6(3), PPM1B(1), PPP3CB(1), PPP3R1(1), PPP3R2(1), PPP5C(1), PRKACG(1), PRKCA(3), PRKCG(1), PRKX(2), PTPRR(2), RAP1B(2), RAPGEF2(4), RASA2(1), RASGRF1(5), RASGRF2(6), RASGRP1(1), RASGRP2(2), RASGRP3(2), RASGRP4(3), RPS6KA2(2), RPS6KA3(5), RRAS2(3), SOS1(1), SOS2(4), SRF(2), STK3(2), STK4(1), STMN1(1), TAOK1(1), TAOK2(2), TAOK3(2), TGFB1(1), TGFB2(1), TGFBR1(1), TGFBR2(5), TNFRSF1A(2), TP53(89), TRAF2(2), ZAK(1) 111569559 586 213 518 148 184 87 111 98 100 6 <1.00e-15 <5.60e-14
2 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 AKT1(1), BCL2(3), EGFR(58), IGF1R(2), POLR2A(2), PPP2CA(1), PRKCA(3), RB1(21), TEP1(4), TERT(8), TNKS(4), TP53(89), XRCC5(1) 11328048 197 139 135 11 45 40 42 22 46 2 <1.00e-15 <5.60e-14
3 SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES Genes related to the insulin receptor pathway AKT1, AKT2, AKT3, BRD4, CAP1, CBL, CDC42, CDKN2A, F2RL2, FLOT1, FLOT2, FOXO1A, GRB2, GSK3A, GSK3B, IGFBP1, INPPL1, IRS1, IRS2, IRS4, LNPEP, MAPK1, MAPK3, PARD3, PARD6A, PDK1, PIK3CA, PIK3CD, PIK3R1, PPYR1, PSCD3, PTEN, PTPN1, RAF1, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SERPINB6, SFN, SHC1, SLC2A4, SORBS1, SOS1, SOS2, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ 48 AKT1(1), AKT2(1), AKT3(1), BRD4(7), CBL(1), CDKN2A(3), FLOT1(2), GSK3B(1), IGFBP1(1), INPPL1(4), IRS1(4), IRS4(3), LNPEP(2), MAPK1(3), MAPK3(2), PARD3(2), PARD6A(1), PIK3CA(19), PIK3CD(2), PIK3R1(17), PPYR1(2), PTEN(80), PTPN1(1), RPS6KA2(2), RPS6KA3(5), RPS6KB1(1), SERPINB6(1), SLC2A4(3), SORBS1(2), SOS1(1), SOS2(4), YWHAB(1), YWHAE(2) 23158627 182 128 162 32 30 35 21 36 60 0 <1.00e-15 <5.60e-14
4 MTORPATHWAY Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation. AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2 21 AKT1(1), EIF4A1(4), EIF4B(3), EIF4E(2), EIF4G1(2), EIF4G2(2), EIF4G3(1), FKBP1A(1), MKNK1(1), PIK3CA(19), PIK3R1(17), PPP2CA(1), PTEN(80), RPS6KB1(1), TSC1(4), TSC2(2) 10941579 141 117 121 5 15 30 17 25 54 0 <1.00e-15 <5.60e-14
5 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(1), CDKN2A(3), MDM2(1), PIK3CA(19), PIK3R1(17), POLR1A(3), POLR1B(1), POLR1C(1), RB1(21), TBX2(1), TP53(89) 8040458 157 113 124 13 28 28 20 25 54 2 <1.00e-15 <5.60e-14
6 SA_PTEN_PATHWAY PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate. AKT1, AKT2, AKT3, BPNT1, GRB2, ILK, MAPK1, MAPK3, PDK1, PIK3CA, PIK3CD, PIP3-E, PTEN, PTK2B, RBL2, SHC1, SOS1 16 AKT1(1), AKT2(1), AKT3(1), BPNT1(1), ILK(2), MAPK1(3), MAPK3(2), PIK3CA(19), PIK3CD(2), PTEN(80), PTK2B(1), RBL2(1), SOS1(1) 8079012 115 104 98 7 14 26 13 24 38 0 <1.00e-15 <5.60e-14
7 G1PATHWAY CDK4/6-cyclin D and CDK2-cyclin E phosphorylate Rb, which allows the transcription of genes needed for the G1/S cell cycle transition. ABL1, ATM, ATR, CCNA1, CCND1, CCNE1, CDC2, CDC25A, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, DHFR, E2F1, GSK3B, HDAC1, MADH3, MADH4, RB1, SKP2, TFDP1, TGFB1, TGFB2, TGFB3, TP53 25 ABL1(1), ATM(7), ATR(9), CCNA1(1), CCNE1(1), CDKN1A(1), CDKN1B(3), CDKN2A(3), CDKN2B(1), DHFR(1), GSK3B(1), HDAC1(1), RB1(21), TGFB1(1), TGFB2(1), TP53(89) 12112046 142 96 114 11 30 24 19 17 50 2 <1.00e-15 <5.60e-14
8 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(1), MAX(2), SP1(6), SP3(1), TP53(89), WT1(3) 2849491 102 86 76 2 27 17 14 14 28 2 <1.00e-15 <5.60e-14
9 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 17 ABCB1(4), AKT1(1), ATM(7), CDKN1A(1), CPB2(1), FHL2(1), HIF1A(1), IGFBP3(1), MDM2(1), NFKBIB(1), TP53(89) 8064819 108 83 82 5 29 22 13 16 26 2 <1.00e-15 <5.60e-14
10 EGFR_SMRTEPATHWAY EGF receptor activation inhibits SMRT, a transcriptional co-repressor that interacts with transcription factor complexes and gene silencers. EGF, EGFR, MAP2K1, MAP3K1, MAPK14, NCOR2, RARA, RXRA, THRA, THRB, ZNF145 10 EGF(3), EGFR(58), MAP2K1(1), MAP3K1(5), MAPK14(1), NCOR2(5), RARA(5), RXRA(3), THRA(1) 6703510 82 66 48 13 14 24 25 14 5 0 <1.00e-15 <5.60e-14

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. 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 HSA00040_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS Genes involved in pentose and glucuronate interconversions AKR1B1, DCXR, GUSB, RPE, UGDH, UGP2, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT2A1, UGT2A3, UGT2B10, UGT2B11, UGT2B15, UGT2B17, UGT2B28, UGT2B4, UGT2B7, XYLB 24 GUSB(3), RPE(1), UGP2(1), UGT1A1(1), UGT1A10(1), UGT1A3(1), UGT1A5(2), UGT1A6(2), UGT1A9(1), UGT2A1(5), UGT2A3(3), UGT2B10(1), UGT2B11(3), UGT2B17(1), UGT2B28(5), UGT2B4(5), UGT2B7(3), XYLB(4) 9832004 43 32 42 16 12 6 11 10 4 0 0.0013 0.32
2 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(4), NR0B2(3), NR1H3(1), NR1H4(3), RXRA(3) 2161711 14 15 15 3 3 2 4 3 2 0 0.002 0.32
3 HSA04640_HEMATOPOIETIC_CELL_LINEAGE Genes involved in hematopoietic cell lineage ANPEP, CD14, CD19, CD1A, CD1B, CD1C, CD1D, CD1E, CD2, CD22, CD24, CD33, CD34, CD36, CD37, CD38, CD3D, CD3E, CD3G, CD4, CD44, CD5, CD55, CD59, CD7, CD8A, CD8B, CD9, CR1, CR2, CSF1, CSF1R, CSF2, CSF2RA, CSF3, CSF3R, DNTT, EPO, EPOR, FCER2, FCGR1A, FLT3, FLT3LG, GP1BA, GP1BB, GP5, GP9, GYPA, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, IL11, IL11RA, IL1A, IL1B, IL1R1, IL1R2, IL2RA, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL7, IL7R, IL9R, ITGA1, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGAM, ITGB3, KIT, KITLG, MME, MS4A1, TFRC, THPO, TNF, TPO 79 ANPEP(3), CD14(2), CD19(2), CD1B(1), CD1D(2), CD1E(1), CD22(5), CD33(3), CD34(2), CD36(2), CD38(2), CD3E(1), CD3G(1), CD44(4), CD5(2), CD55(2), CD7(2), CD8A(1), CD8B(1), CD9(2), CR1(5), CR2(6), CSF1R(3), CSF3R(2), DNTT(2), EPO(1), EPOR(1), FLT3(7), FLT3LG(1), GP9(1), GYPA(1), HLA-DRA(1), HLA-DRB1(2), HLA-DRB5(2), IL1R1(2), IL2RA(3), IL4(1), IL4R(6), IL5RA(1), IL6(2), IL6R(2), IL7(1), IL7R(1), ITGA1(1), ITGA2(4), ITGA2B(2), ITGA3(2), ITGA4(7), ITGA5(1), ITGA6(2), ITGAM(8), ITGB3(1), KIT(3), KITLG(2), MS4A1(2), TFRC(2), THPO(1), TPO(4) 31351365 137 76 135 51 54 23 28 20 12 0 0.002 0.32
4 TYROSINE_METABOLISM ABP1, ADH1A, ADH1A, ADH1B, ADH1C, ADH1B, ADH1C, ADH4, ADH6, ADH7, ADHFE1, ALDH1A3, ALDH3A1, ALDH3B1, ALDH3B2, AOC2, AOC3, AOX1, COMT, DBH, DCT, DDC, FAH, GOT1, GOT2, GSTZ1, HGD, HPD, MAOA, MAOB, PNMT, TAT, TH, TPO, TYR 31 ABP1(9), ADH1A(4), ADH1B(3), ADH1C(3), ADH6(2), ADH7(1), ALDH1A3(1), ALDH3A1(3), ALDH3B1(2), ALDH3B2(1), AOC2(2), AOC3(2), AOX1(7), COMT(2), DBH(6), DDC(1), FAH(1), GOT1(1), HPD(1), MAOB(1), PNMT(1), TAT(3), TPO(4), TYR(5) 12332970 66 42 65 14 35 9 9 13 0 0 0.0021 0.32
5 HSA00980_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 Genes involved in metabolism of xenobiotics by cytochrome P450 ADH1A, ADH1B, ADH1C, ADH4, ADH5, ADH6, ADH7, ADHFE1, AKR1C1, AKR1C2, AKR1C3, AKR1C4, ALDH1A3, ALDH3A1, ALDH3B1, ALDH3B2, CYP1A1, CYP1A2, CYP1B1, CYP2B6, CYP2C18, CYP2C19, CYP2C8, CYP2C9, CYP2E1, CYP2F1, CYP2S1, CYP3A4, CYP3A43, CYP3A5, CYP3A7, DHDH, EPHX1, GSTA1, GSTA2, GSTA3, GSTA4, GSTA5, GSTK1, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, MGST1, MGST2, MGST3, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT2A1, UGT2A3, UGT2B10, UGT2B11, UGT2B15, UGT2B17, UGT2B28, UGT2B4, UGT2B7 68 ADH1A(4), ADH1B(3), ADH1C(3), ADH6(2), ADH7(1), AKR1C1(3), AKR1C4(2), ALDH1A3(1), ALDH3A1(3), ALDH3B1(2), ALDH3B2(1), CYP1A1(1), CYP1B1(4), CYP2B6(2), CYP2C18(1), CYP2C8(2), CYP2C9(2), CYP2E1(4), CYP2S1(1), CYP3A4(3), CYP3A43(2), CYP3A7(3), DHDH(1), GSTA1(2), GSTA4(2), GSTA5(1), GSTK1(2), GSTM1(1), GSTM3(1), GSTP1(1), GSTT1(1), MGST1(1), MGST3(1), UGT1A1(1), UGT1A10(1), UGT1A3(1), UGT1A5(2), UGT1A6(2), UGT1A9(1), UGT2A1(5), UGT2A3(3), UGT2B10(1), UGT2B11(3), UGT2B17(1), UGT2B28(5), UGT2B4(5), UGT2B7(3) 21984496 98 57 98 32 38 8 24 25 3 0 0.0043 0.51
6 BLOOD_CLOTTING_CASCADE F10, F11, F12, F13B, F2, F5, F7, F8, F8A1, F9, FGA, FGB, FGG, LPA, PLG, PLAT, PLAU, PLG, SERPINB2, SERPINE1, SERPINF2, VWF 19 F10(1), F13B(2), F2(1), F5(9), F7(1), F8(8), FGA(3), FGB(1), FGG(4), LPA(6), PLAU(2), PLG(2), SERPINB2(2), SERPINE1(1), SERPINF2(1), VWF(10) 13638969 54 40 54 22 19 9 11 5 10 0 0.0053 0.51
7 HSA01430_CELL_COMMUNICATION Genes involved in cell communication ACTB, ACTG1, CHAD, COL11A1, COL11A2, COL17A1, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, DES, DSC1, DSC2, DSC3, DSG1, DSG2, DSG3, DSG4, FN1, GJA1, GJA10, GJA3, GJA4, GJA5, GJA8, GJA9, GJB1, GJB2, GJB3, GJB4, GJB5, GJB6, GJB7, GJC1, GJC2, GJC3, GJD2, GJD3, GJD4, IBSP, INA, ITGA6, ITGB4, KRT1, KRT10, KRT12, KRT13, KRT14, KRT15, KRT16, KRT17, KRT18, KRT19, KRT2, KRT20, KRT23, KRT24, KRT25, KRT27, KRT28, KRT3, KRT31, KRT32, KRT33A, KRT33B, KRT34, KRT35, KRT36, KRT37, KRT38, KRT39, KRT4, KRT40, KRT5, KRT6A, KRT6B, KRT6C, KRT7, KRT71, KRT72, KRT73, KRT74, KRT75, KRT76, KRT77, KRT78, KRT79, KRT8, KRT81, KRT82, KRT83, KRT84, KRT85, KRT86, KRT9, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LMNA, LMNB1, LMNB2, LOC728760, NES, PRPH, RELN, SPP1, THBS1, THBS2, THBS3, THBS4, TNC, TNN, TNR, TNXB, VIM, VTN, VWF 129 ACTB(1), CHAD(1), COL11A1(8), COL11A2(9), COL17A1(3), COL1A1(4), COL1A2(9), COL2A1(2), COL3A1(5), COL4A1(4), COL4A2(8), COL4A4(4), COL4A6(5), COL5A1(3), COL5A2(5), COL6A1(5), COL6A2(3), COL6A6(7), COMP(1), DES(3), DSC1(5), DSC2(2), DSC3(2), DSG1(4), DSG2(1), DSG3(8), DSG4(10), FN1(3), GJA1(1), GJA10(1), GJA8(1), GJA9(1), GJB3(2), GJB5(2), GJB6(1), GJB7(1), GJC1(1), GJC2(1), GJC3(1), INA(2), ITGA6(2), ITGB4(5), KRT1(2), KRT10(1), KRT12(3), KRT14(3), KRT15(1), KRT16(4), KRT17(3), KRT18(3), KRT19(5), KRT2(3), KRT20(1), KRT23(8), KRT24(1), KRT25(3), KRT28(3), KRT3(1), KRT31(3), KRT32(2), KRT33A(3), KRT33B(2), KRT34(3), KRT36(4), KRT37(2), KRT38(2), KRT4(2), KRT5(1), KRT6A(1), KRT6B(2), KRT6C(1), KRT7(3), KRT72(1), KRT73(1), KRT74(3), KRT75(2), KRT76(2), KRT77(2), KRT78(1), KRT79(2), KRT8(3), KRT81(1), KRT82(1), KRT83(2), KRT84(2), KRT85(2), KRT9(3), LAMA1(17), LAMA2(12), LAMA3(7), LAMA4(4), LAMA5(9), LAMB1(4), LAMB2(3), LAMB3(4), LAMB4(10), LAMC1(2), LAMC2(6), LAMC3(5), LMNB1(1), LMNB2(3), NES(3), RELN(20), SPP1(1), THBS1(3), THBS2(5), THBS3(1), THBS4(2), TNC(7), TNN(5), TNR(2), TNXB(6), VIM(1), VWF(10) 91828164 404 152 402 167 153 79 71 45 55 1 0.0058 0.51
8 NEUROTRANSMITTERSPATHWAY Biosynthesis of neurotransmitters DBH, GAD1, HDC, PNMT, TH, TPH1 6 DBH(6), GAD1(4), HDC(3), PNMT(1), TPH1(3) 2333567 17 13 17 6 10 4 2 1 0 0 0.0066 0.51
9 CTLPATHWAY Cytotoxic T lymphocytes induce apoptosis in infected cells presenting antigen-MHC-I complexes via the perforin and Fas/Fas ligand pathways. B2M, CD3D, CD3E, CD3G, CD3Z, GZMB, HLA-A, ICAM1, ITGAL, ITGB2, PRF1, TNFRSF6, TNFSF6, TRA@, TRB@ 10 B2M(2), CD3E(1), CD3G(1), GZMB(3), HLA-A(1), ITGAL(4), ITGB2(5), PRF1(3) 3417489 20 15 20 14 6 1 4 1 8 0 0.0074 0.51
10 PEPTIDE_GPCRS AGTR1, AGTR2, ATP8A1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BLR1, BRS3, C3AR1, C5R1, CCKAR, CCKBR, CCR1, CCR10, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CX3CR1, CXCR3, CXCR4, CXCR6, EDNRA, EDNRB, ELA3A, FPR1, FPRL1, FPRL2, FSHR, FY, GALR1, GALR2, GALR3, GALT, GHSR, GNB2L1, GNRHR, GPR77, GRPR, IL8RA, IL8RB, LHCGR, MC1R, MC2R, MC3R, MC4R, MC5R, NMBR, NPY1R, NPY2R, NPY5R, NPY6R, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, PPYR1, SSTR1, SSTR2, SSTR3, SSTR4, TAC4, TACR1, TACR2, TACR3, TRHR, TSHR 63 AGTR1(2), AGTR2(1), ATP8A1(3), AVPR1A(3), AVPR1B(1), BDKRB1(1), BDKRB2(3), BRS3(2), C3AR1(1), CCKAR(3), CCKBR(2), CCR1(2), CCR10(1), CCR3(2), CCR4(1), CCR6(2), CCR7(2), CCR8(1), CX3CR1(2), CXCR3(2), CXCR6(1), EDNRA(1), EDNRB(1), FPR1(1), FSHR(1), GALR1(3), GALR2(1), GALT(1), GHSR(4), GNB2L1(1), GRPR(1), LHCGR(1), MC2R(1), MC3R(6), MC4R(3), MC5R(2), NPY5R(4), NTSR1(2), OPRK1(1), OPRL1(2), OXTR(2), PPYR1(2), SSTR2(1), SSTR3(2), SSTR4(4), TACR1(1), TACR3(4), TRHR(2), TSHR(1) 19529660 94 54 94 38 39 19 18 14 4 0 0.0097 0.6
Methods & Data
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]

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.

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
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