Mutation Analysis (MutSig v1.5)
Glioblastoma Multiforme (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1PZ57JW
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Analysis (MutSig v1.5). Broad Institute of MIT and Harvard. doi:10.7908/C1PZ57JW
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 v1.5 was used to generate the results found in this report.

  • Working with individual set: GBM-TP

  • Number of patients in set: 283

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-TP.final_analysis_set.maf

  • Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt

  • Significantly mutated genes (q ≤ 0.1): 130

  • Mutations seen in COSMIC: 459

  • Significantly mutated genes in COSMIC territory: 71

  • Significantly mutated genesets: 120

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

Mutation Preprocessing

  • Read 283 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 21510

  • After removing 892 blacklisted mutations: 20618

Mutation Filtering

  • Number of mutations before filtering: 20618

  • After removing 325 mutations outside gene set: 20293

  • After removing 12 mutations outside category set: 20281

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 464
Frame_Shift_Ins 150
In_Frame_Del 136
In_Frame_Ins 20
Missense_Mutation 13193
Nonsense_Mutation 803
Nonstop_Mutation 10
Silent 5124
Splice_Site 329
Translation_Start_Site 52
Total 20281
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 exp_ns_s_ratio
*CpG->T 5433 471456280 0.000012 12 6.4 2.1
*Cp(A/C/T)->T 2364 3846173156 6.1e-07 0.61 0.34 1.7
A->G 1639 4141354039 4e-07 0.4 0.22 2.3
transver 3808 8458983475 4.5e-07 0.45 0.25 5
indel+null 1901 8458983475 2.2e-07 0.22 0.13 NaN
double_null 12 8458983475 1.4e-09 0.0014 0.00079 NaN
Total 15157 8458983475 1.8e-06 1.8 1 3.5
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). If the figure is unpopulated, then full coverage is assumed (e.g. MutSig CV doesn't use WIGs and assumes full coverage).

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-TP.patients.counts_and_rates.txt

Lego Plots

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.

Figure 3.  Get High-res Image SNV Mutation rate lego plot for entire set. Each bin is normalized by base coverage for that bin. Colors represent the six SNV types on the upper right. The three-base context for each mutation is labeled in the 4x4 legend on the lower right. The fractional breakdown of SNV counts is shown in the pie chart on the upper left. If this figure is blank, not enough information was provided in the MAF to generate it.

Figure 4.  Get High-res Image SNV Mutation rate lego plots for 4 slices of mutation allele fraction (0<=AF<0.1, 0.1<=AF<0.25, 0.25<=AF<0.5, & 0.5<=AF) . The color code and three-base context legends are the same as the previous figure. If this figure is blank, not enough information was provided in the MAF to generate it.

CoMut Plot

Figure 5.  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: A->G

  • n4 = number of nonsilent mutations of type: transver

  • n5 = number of nonsilent mutations of type: indel+null

  • n6 = number of nonsilent mutations of type: double_null

  • 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)

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 130. 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_ns_s p q
1 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 337830 90 87 73 0 5 20 10 13 42 0 1.9e-09 <1.00e-15 <4.53e-12
2 TP53 tumor protein p53 358092 96 79 59 1 29 15 11 23 18 0 2.8e-11 <1.00e-15 <4.53e-12
3 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 924699 33 30 28 0 5 8 7 6 7 0 0.00033 <1.00e-15 <4.53e-12
4 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 2457594 30 29 30 1 0 2 1 1 21 5 0.011 <1.00e-15 <4.53e-12
5 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 361231 14 14 2 0 13 0 0 1 0 0 0.0076 2.66e-15 9.66e-12
6 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 1131442 92 74 44 7 10 44 2 32 4 0 1.1e-08 3.89e-15 1.17e-11
7 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 668244 33 32 27 0 0 3 4 7 19 0 0.0059 6.00e-15 1.55e-11
8 RB1 retinoblastoma 1 (including osteosarcoma) 752003 24 24 22 1 0 0 0 1 22 1 0.097 7.44e-15 1.69e-11
9 SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2) 2111845 26 24 26 0 11 2 1 9 3 0 0.0044 8.00e-14 1.61e-10
10 GABRA6 gamma-aminobutyric acid (GABA) A receptor, alpha 6 395438 11 11 10 1 4 2 1 4 0 0 0.11 1.83e-11 3.33e-08
11 KEL Kell blood group, metallo-endopeptidase 639794 15 15 12 2 8 0 1 3 3 0 0.19 1.46e-10 2.40e-07
12 SEMA3C sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C 654951 11 11 11 1 3 0 2 5 1 0 0.22 6.66e-09 1.01e-05
13 CDH18 cadherin 18, type 2 682827 11 11 10 0 3 3 0 4 1 0 0.048 9.89e-09 1.38e-05
14 RPL5 ribosomal protein L5 261806 7 7 7 0 0 1 1 0 5 0 0.28 1.52e-08 1.97e-05
15 OR8K3 olfactory receptor, family 8, subfamily K, member 3 265683 7 7 7 1 2 2 0 2 1 0 0.32 1.96e-08 2.37e-05
16 STAG2 stromal antigen 2 1110411 12 12 12 0 0 0 0 2 10 0 0.19 2.57e-08 2.91e-05
17 SEMG1 semenogelin I 395351 8 8 7 0 5 0 2 0 1 0 0.11 5.74e-08 6.13e-05
18 OR5AR1 olfactory receptor, family 5, subfamily AR, member 1 264117 7 7 7 0 3 0 2 2 0 0 0.18 7.04e-08 7.09e-05
19 TPTE2 transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 464692 8 8 6 0 2 1 0 2 3 0 0.1 2.72e-07 0.000259
20 ADAM29 ADAM metallopeptidase domain 29 698127 9 9 8 1 6 0 0 2 1 0 0.34 3.34e-07 0.000303
21 PDGFRA platelet-derived growth factor receptor, alpha polypeptide 950298 13 11 12 1 0 5 2 4 2 0 0.096 4.20e-07 0.000363
22 CALCR calcitonin receptor 424651 8 8 8 0 6 1 1 0 0 0 0.051 8.44e-07 0.000689
23 SULT1B1 sulfotransferase family, cytosolic, 1B, member 1 257699 7 6 7 1 0 2 1 3 1 0 0.36 8.74e-07 0.000689
24 NLRP5 NLR family, pyrin domain containing 5 962338 12 12 11 2 9 0 1 2 0 0 0.11 2.77e-06 0.00207
25 LZTR1 leucine-zipper-like transcription regulator 1 647961 10 10 10 0 4 0 1 4 1 0 0.08 2.85e-06 0.00207
26 OR5D18 olfactory receptor, family 5, subfamily D, member 18 267435 6 6 6 1 0 0 1 5 0 0 0.54 3.55e-06 0.00248
27 ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 1117814 10 10 10 0 5 1 0 3 1 0 0.12 4.32e-06 0.00290
28 ABCC9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 1396433 14 11 14 1 4 0 3 5 2 0 0.1 5.19e-06 0.00336
29 COL1A2 collagen, type I, alpha 2 1162327 11 11 11 1 2 3 0 6 0 0 0.2 6.28e-06 0.00392
30 OR5W2 olfactory receptor, family 5, subfamily W, member 2 264214 5 5 5 1 1 0 2 2 0 0 0.62 6.52e-06 0.00394
31 SEMA3E sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E 674205 8 8 8 0 1 1 0 3 3 0 0.17 7.48e-06 0.00437
32 DCAF12L2 DDB1 and CUL4 associated factor 12-like 2 390549 8 8 7 0 7 0 0 1 0 0 0.034 7.80e-06 0.00442
33 OR5D13 olfactory receptor, family 5, subfamily D, member 13 267731 5 5 4 1 3 0 0 2 0 0 0.54 8.66e-06 0.00476
34 LUM lumican 289227 5 5 4 0 3 0 0 2 0 0 0.37 1.04e-05 0.00552
35 SLC5A7 solute carrier family 5 (choline transporter), member 7 501972 7 7 7 0 3 1 0 2 1 0 0.12 1.12e-05 0.00582
PTEN

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

TP53

Figure S2.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

PIK3CA

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

NF1

Figure S4.  This figure depicts the distribution of mutations and mutation types across the NF1 significant gene.

IDH1

Figure S5.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

EGFR

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

PIK3R1

Figure S7.  This figure depicts the distribution of mutations and mutation types across the PIK3R1 significant gene.

RB1

Figure S8.  This figure depicts the distribution of mutations and mutation types across the RB1 significant gene.

SPTA1

Figure S9.  This figure depicts the distribution of mutations and mutation types across the SPTA1 significant gene.

GABRA6

Figure S10.  This figure depicts the distribution of mutations and mutation types across the GABRA6 significant gene.

KEL

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

SEMA3C

Figure S12.  This figure depicts the distribution of mutations and mutation types across the SEMA3C significant gene.

CDH18

Figure S13.  This figure depicts the distribution of mutations and mutation types across the CDH18 significant gene.

RPL5

Figure S14.  This figure depicts the distribution of mutations and mutation types across the RPL5 significant gene.

OR8K3

Figure S15.  This figure depicts the distribution of mutations and mutation types across the OR8K3 significant gene.

STAG2

Figure S16.  This figure depicts the distribution of mutations and mutation types across the STAG2 significant gene.

SEMG1

Figure S17.  This figure depicts the distribution of mutations and mutation types across the SEMG1 significant gene.

OR5AR1

Figure S18.  This figure depicts the distribution of mutations and mutation types across the OR5AR1 significant gene.

TPTE2

Figure S19.  This figure depicts the distribution of mutations and mutation types across the TPTE2 significant gene.

ADAM29

Figure S20.  This figure depicts the distribution of mutations and mutation types across the ADAM29 significant gene.

PDGFRA

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

CALCR

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

SULT1B1

Figure S23.  This figure depicts the distribution of mutations and mutation types across the SULT1B1 significant gene.

NLRP5

Figure S24.  This figure depicts the distribution of mutations and mutation types across the NLRP5 significant gene.

LZTR1

Figure S25.  This figure depicts the distribution of mutations and mutation types across the LZTR1 significant gene.

OR5D18

Figure S26.  This figure depicts the distribution of mutations and mutation types across the OR5D18 significant gene.

ABCB1

Figure S27.  This figure depicts the distribution of mutations and mutation types across the ABCB1 significant gene.

ABCC9

Figure S28.  This figure depicts the distribution of mutations and mutation types across the ABCC9 significant gene.

COL1A2

Figure S29.  This figure depicts the distribution of mutations and mutation types across the COL1A2 significant gene.

OR5W2

Figure S30.  This figure depicts the distribution of mutations and mutation types across the OR5W2 significant gene.

SEMA3E

Figure S31.  This figure depicts the distribution of mutations and mutation types across the SEMA3E significant gene.

DCAF12L2

Figure S32.  This figure depicts the distribution of mutations and mutation types across the DCAF12L2 significant gene.

OR5D13

Figure S33.  This figure depicts the distribution of mutations and mutation types across the OR5D13 significant gene.

LUM

Figure S34.  This figure depicts the distribution of mutations and mutation types across the LUM 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: 71. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 TP53 tumor protein p53 96 356 92 100748 26305 0 0
2 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 90 767 88 217061 3057 0 0
3 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 14 5 14 1415 20888 3.8e-14 5.7e-11
4 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 33 33 13 9339 25 2.5e-13 2.8e-10
5 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 33 220 25 62260 5654 1.5e-12 1.1e-09
6 RB1 retinoblastoma 1 (including osteosarcoma) 24 267 15 75561 41 1.8e-12 1.1e-09
7 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 30 285 11 80655 23 1.9e-12 1.1e-09
8 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 92 293 70 82919 1144 1.9e-12 1.1e-09
9 BRAF v-raf murine sarcoma viral oncogene homolog B1 6 89 6 25187 71896 1.2e-11 6e-09
10 ADAM29 ADAM metallopeptidase domain 29 9 5 3 1415 3 2.7e-09 1.2e-06

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)

Geneset Analyses

Table 5.  Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 120. 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_ns_s p q
1 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 49 AKT1(1), CBL(1), CDKN2A(2), FLOT1(1), GSK3B(1), INPPL1(3), IRS1(4), IRS4(2), LNPEP(2), MAPK1(2), MAPK3(1), PARD3(1), PIK3CA(33), PIK3R1(33), PPYR1(1), PTEN(90), RAF1(1), RPS6KA1(1), RPS6KA2(2), RPS6KA3(1), SFN(1), SORBS1(2), SOS1(3), YWHAE(2), YWHAH(1) 25218068 192 153 164 10 15 37 27 36 77 0 4.22e-12 <1.00e-15 <3.08e-14
2 METPATHWAY The hepatocyte growth factor receptor c-Met stimulates proliferation and alters cell motility and adhesion on binding the ligand HGF. ACTA1, CRK, CRKL, DOCK1, ELK1, FOS, GAB1, GRB2, GRF2, HGF, HRAS, ITGA1, ITGB1, JUN, MAP2K1, MAP2K2, MAP4K1, MAPK1, MAPK3, MAPK8, MET, PAK1, PIK3CA, PIK3R1, PTEN, PTK2, PTK2B, PTPN11, PXN, RAF1, RAP1A, RAP1B, RASA1, SOS1, SRC, STAT3 35 CRKL(1), DOCK1(2), ELK1(2), FOS(1), HGF(1), ITGA1(2), ITGB1(1), MAP2K1(1), MAP4K1(2), MAPK1(2), MAPK3(1), MET(3), PAK1(1), PIK3CA(33), PIK3R1(33), PTEN(90), PTK2B(3), PTPN11(4), PXN(1), RAF1(1), SOS1(3), SRC(2), STAT3(1) 18829475 191 149 163 5 21 37 25 37 71 0 <1.00e-15 <1.00e-15 <3.08e-14
3 HSA00562_INOSITOL_PHOSPHATE_METABOLISM Genes involved in inositol phosphate metabolism CARKL, FN3K, IMPA1, IMPA2, INPP1, INPP4A, INPP4B, INPP5A, INPP5B, INPP5E, INPPL1, IPMK, ISYNA1, ITGB1BP3, ITPK1, ITPKA, ITPKB, MINPP1, MIOX, OCRL, PI4KA, PI4KB, PIB5PA, PIK3C3, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PTEN, PTPMT1, SKIP, SYNJ1, SYNJ2 47 INPP1(1), INPP4B(1), INPP5A(1), INPP5B(1), INPP5E(1), INPPL1(3), ITGB1BP3(1), MIOX(1), OCRL(2), PI4KA(1), PI4KB(2), PIK3CA(33), PIK3CB(4), PIK3CG(7), PIP4K2C(3), PIP5K1B(2), PIP5K1C(1), PLCB1(1), PLCB2(3), PLCB4(1), PLCD1(3), PLCE1(2), PLCG1(6), PLCG2(3), PLCZ1(1), PTEN(90), SYNJ2(3) 31664122 178 142 156 19 29 35 22 35 57 0 3.22e-08 <1.00e-15 <3.08e-14
4 SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES Genes related to PIP3 signaling in B lymphocytes AKT1, AKT2, AKT3, BCR, BTK, CD19, CDKN2A, DAPP1, FLOT1, FLOT2, FOXO3A, GAB1, ITPR1, ITPR2, ITPR3, LYN, NR0B2, P101-PI3K, PDK1, PHF11, PIK3CA, PITX2, PLCG2, PPP1R13B, PREX1, PSCD3, PTEN, PTPRC, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SAG, SYK, TEC, VAV1 33 AKT1(1), BTK(1), CD19(1), CDKN2A(2), FLOT1(1), ITPR1(5), ITPR2(3), ITPR3(5), LYN(2), NR0B2(1), PIK3CA(33), PITX2(3), PLCG2(3), PREX1(5), PTEN(90), PTPRC(2), RPS6KA1(1), RPS6KA2(2), RPS6KA3(1), TEC(1), VAV1(4) 23616977 167 138 145 16 26 40 21 23 57 0 1.82e-09 <1.00e-15 <3.08e-14
5 PTENPATHWAY PTEN suppresses AKT-induced cell proliferation and antagonizes the action of PI3K. AKT1, BCAR1, CDKN1B, FOXO3A, GRB2, ILK, ITGB1, MAPK1, MAPK3, PDK2, PDPK1, PIK3CA, PIK3R1, PTEN, PTK2, SHC1, SOS1, TNFSF6 16 AKT1(1), CDKN1B(1), ITGB1(1), MAPK1(2), MAPK3(1), PIK3CA(33), PIK3R1(33), PTEN(90), SOS1(3) 8230675 165 137 137 0 11 33 24 29 68 0 <1.00e-15 <1.00e-15 <3.08e-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), MAPK1(2), MAPK3(1), PIK3CA(33), PTEN(90), PTK2B(3), SOS1(3) 8656996 133 118 111 3 13 30 19 21 50 0 2.03e-12 <1.00e-15 <3.08e-14
7 TIDPATHWAY On ligand binding, interferon gamma receptors stimulate JAK2 kinase to phosphorylate STAT transcription factors, which promote expression of interferon responsive genes. DNAJA3, HSPA1A, IFNG, IFNGR1, IFNGR2, IKBKB, JAK2, LIN7A, NFKB1, NFKBIA, RB1, RELA, TIP-1, TNF, TNFRSF1A, TNFRSF1B, TP53, USH1C, WT1 18 IFNG(2), IFNGR1(1), IFNGR2(3), IKBKB(1), JAK2(1), NFKB1(1), NFKBIA(1), RB1(24), TNFRSF1A(1), TNFRSF1B(1), TP53(96), USH1C(1), WT1(2) 7833614 135 98 96 3 31 16 15 30 42 1 3.30e-14 <1.00e-15 <3.08e-14
8 ATMPATHWAY The tumor-suppressing protein kinase ATM responds to radiation-induced DNA damage by blocking cell-cycle progression and activating DNA repair. ABL1, ATM, BRCA1, CDKN1A, CHEK1, CHEK2, GADD45A, JUN, MAPK8, MDM2, MRE11A, NBS1, NFKB1, NFKBIA, RAD50, RAD51, RBBP8, RELA, TP53, TP73 19 ABL1(2), ATM(4), BRCA1(4), CDKN1A(1), CHEK1(3), MDM2(2), MRE11A(1), NFKB1(1), NFKBIA(1), RAD50(1), RBBP8(1), TP53(96) 12680905 117 95 80 6 36 17 14 28 22 0 5.63e-09 <1.00e-15 <3.08e-14
9 PDGFPATHWAY Platelet-derived growth factor (PDGF) receptor is phosphorylated on ligand binding and promotes cell proliferation. CSNK2A1, ELK1, FOS, GRB2, HRAS, JAK1, JUN, MAP2K1, MAP2K4, MAP3K1, MAPK3, MAPK8, PDGFA, PDGFRA, PIK3CA, PIK3R1, PLCG1, PRKCA, PRKCB1, RAF1, RASA1, SHC1, SOS1, SRF, STAT1, STAT3, STAT5A 26 ELK1(2), FOS(1), JAK1(2), MAP2K1(1), MAP3K1(6), MAPK3(1), PDGFRA(13), PIK3CA(33), PIK3R1(33), PLCG1(6), PRKCA(1), RAF1(1), SOS1(3), SRF(1), STAT1(2), STAT3(1) 14833818 107 91 93 6 10 24 17 24 32 0 3.22e-07 <1.00e-15 <3.08e-14
10 CBLPATHWAY Activated EGF receptors undergo endocytosis into clathrin-coated vesicles, where they are recycled to the membrane or ubiquitinated by Cbl. CBL, CSF1R, EGF, EGFR, GRB2, MET, PDGFRA, PRKCA, PRKCB1, SH3GLB1, SH3GLB2, SH3KBP1, SRC 12 CBL(1), CSF1R(1), EGF(3), EGFR(92), MET(3), PDGFRA(13), PRKCA(1), SRC(2) 8244530 116 88 67 12 12 50 5 42 7 0 4.08e-07 <1.00e-15 <3.08e-14

Table 6.  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_ns_s p q
1 IL17PATHWAY Activated T cells secrete IL-17, which stimulates fibroblasts and other cells to secrete inflammatory and hematopoietic cytokines. CD2, CD34, CD3D, CD3E, CD3G, CD3Z, CD4, CD58, CD8A, CSF3, IL17, IL3, IL6, IL8, KITLG, TRA@, TRB@ 13 CD2(1), CD3E(2), CD3G(1), CD4(1), CD58(1), CD8A(1), IL3(1), IL6(1), KITLG(1) 2644975 10 10 10 1 3 1 1 3 2 0 0.15 0.006 1
2 IL18PATHWAY Pro-inflammatory IL-18 is activated in macrophages by caspase-1 cleavage and, in conjunction with IL-12, stimulates Th1 cell differentiation. CASP1, IFNG, IL12A, IL12B, IL18, IL2 6 CASP1(2), IFNG(2), IL12B(2) 1269839 6 6 6 1 2 1 1 0 2 0 0.34 0.0062 1
3 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(1), CD28(1), CD3E(2), CD3G(1), CD4(1) 1364210 6 6 6 1 3 0 1 1 1 0 0.36 0.014 1
4 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(3) 306178 3 3 3 0 2 1 0 0 0 0 0.3 0.015 1
5 TCRMOLECULE T Cell Receptor and CD3 Complex CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@ 3 CD3E(2), CD3G(1) 483380 3 3 3 0 0 0 1 1 1 0 0.42 0.016 1
6 IFNGPATHWAY IFN gamma signaling pathway IFNG, IFNGR1, IFNGR2, JAK1, JAK2, STAT1 6 IFNG(2), IFNGR1(1), IFNGR2(3), JAK1(2), JAK2(1), STAT1(2) 3472100 11 11 11 0 0 0 3 5 3 0 0.067 0.017 1
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 FABP6(1), LDLR(3), NR0B2(1), NR1H4(3), RXRA(3) 2319597 11 11 11 2 4 2 0 4 1 0 0.24 0.018 1
8 EOSINOPHILSPATHWAY Recruitment of eosinophils in the inflammatory response observed in asthma occurs via the chemoattractant eotaxin binding to the CCR3 receptor. CCL11, CCL5, CCR3, CSF2, HLA-DRA, HLA-DRB1, IL3, IL5 8 CCR3(1), CSF2(2), HLA-DRA(1), IL3(1) 1289447 5 5 5 0 2 1 1 0 1 0 0.2 0.028 1
9 NUCLEOTIDE_SUGARS_METABOLISM GALE, GALT, TGDS, UGDH, UXS1 5 GALE(2), GALT(1), TGDS(1), UXS1(2) 1665957 6 6 6 0 1 1 1 2 1 0 0.14 0.03 1
10 FLUMAZENILPATHWAY Flumazenil is a benzodiazepine receptor antagonist that may induce protective preconditioning in ischemic cardiomyocytes. GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GPX1, PRKCE, SOD1 7 GABRA2(1), GABRA3(2), GABRA4(4), GABRA5(3), GPX1(1), PRKCE(1) 2559398 12 12 12 3 2 3 3 4 0 0 0.35 0.034 1
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

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.

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