Mutation Analysis (MutSig v2.0)
Adrenocortical Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C19S1QCS
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C19S1QCS
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: ACC-TP

  • Number of patients in set: 90

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:ACC-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 208

  • Mutations seen in COSMIC: 61

  • Significantly mutated genes in COSMIC territory: 3

  • Significantly mutated genesets: 21

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

Mutation Preprocessing

  • Read 90 MAFs of type "maf1"

  • Total number of mutations in input MAFs: 20147

  • After removing 1222 blacklisted mutations: 18925

  • After removing 579 noncoding mutations: 18346

  • After collapsing adjacent/redundant mutations: 18337

Mutation Filtering

  • Number of mutations before filtering: 18337

  • After removing 1275 mutations outside gene set: 17062

  • After removing 65 mutations outside category set: 16997

  • After removing 1 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 15656

Results
Breakdown of Mutations by Type

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

type count
De_novo_Start_InFrame 3
De_novo_Start_OutOfFrame 2
Frame_Shift_Del 465
Frame_Shift_Ins 174
In_Frame_Del 236
In_Frame_Ins 80
Missense_Mutation 9572
Nonsense_Mutation 534
Nonstop_Mutation 6
Silent 5441
Splice_Site 459
Start_Codon_Del 5
Start_Codon_SNP 11
Stop_Codon_Del 7
Stop_Codon_Ins 2
Total 16997
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 1918 159474080 0.000012 12 2.9 2.1
*CpG->(G/A) 658 159474080 4.1e-06 4.1 1 2.7
*Cp(A/C/T)->mut 4622 1285484037 3.6e-06 3.6 0.88 3.3
A->mut 2385 1372092527 1.7e-06 1.7 0.42 3.9
indel+null 1913 2817050644 6.8e-07 0.68 0.17 NaN
double_null 60 2817050644 2.1e-08 0.021 0.0052 NaN
Total 11556 2817050644 4.1e-06 4.1 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: ACC-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: *CpG->(G/A)

  • n3 = number of nonsilent mutations of type: *Cp(A/C/T)->mut

  • 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_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene

  • 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: 208. 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_ns_s p_clust p_cons p_joint p q
1 RNF222 ring finger protein 222 30166 7 7 1 0 7 0 0 0 0 0 2.6e-12 0.061 2.6e-06 1 9.6e-06 9.99e-16 2.40e-13
2 ZFPM1 zinc finger protein, multitype 1 133160 91 47 5 0 0 0 4 0 66 21 1.3e-15 0.16 0 1 0 <1.00e-15 <2.40e-13
3 GARS glycyl-tRNA synthetase 184616 35 34 3 6 1 0 33 1 0 0 5.4e-15 0.27 0 1 0 <1.00e-15 <2.40e-13
4 ZNF517 zinc finger protein 517 112718 34 33 2 0 0 0 0 34 0 0 2.8e-15 0.0076 0 1 0 <1.00e-15 <2.40e-13
5 LRIG1 leucine-rich repeats and immunoglobulin-like domains 1 282211 54 31 2 0 0 0 54 0 0 0 2.9e-15 6e-08 0 1 0 <1.00e-15 <2.40e-13
6 LACTB lactamase, beta 116298 27 27 3 0 0 0 1 25 1 0 8.1e-15 0.0012 0 1 0 <1.00e-15 <2.40e-13
7 OBSCN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 2164618 32 27 14 12 23 1 6 1 1 0 1 0.28 0 0.98 0 <1.00e-15 <2.40e-13
8 CCDC102A coiled-coil domain containing 102A 83550 26 26 1 0 26 0 0 0 0 0 2.9e-15 0.00033 0 0.96 0 <1.00e-15 <2.40e-13
9 OPRD1 opioid receptor, delta 1 70226 26 26 1 1 0 0 26 0 0 0 1.1e-15 0.000065 0 1 0 <1.00e-15 <2.40e-13
10 MUC5B mucin 5B, oligomeric mucus/gel-forming 1541207 29 25 13 8 3 0 5 21 0 0 0.00054 0.47 1e-06 0.022 0 <1.00e-15 <2.40e-13
11 TOR3A torsin family 3, member A 96841 25 25 1 0 0 0 0 25 0 0 4.1e-15 0.03 0 1 0 <1.00e-15 <2.40e-13
12 TRIOBP TRIO and F-actin binding protein 620852 24 23 4 0 0 0 2 21 1 0 9.8e-15 0.002 0 0.98 0 <1.00e-15 <2.40e-13
13 MAL2 mal, T-cell differentiation protein 2 37122 22 22 1 1 0 0 0 0 21 1 1.9e-15 1 0 0.84 0 <1.00e-15 <2.40e-13
14 IRX3 iroquois homeobox 3 75820 21 21 1 0 0 0 0 21 0 0 2.1e-15 0.056 0 1 0 <1.00e-15 <2.40e-13
15 TPO thyroid peroxidase 229899 22 21 3 0 1 0 21 0 0 0 6.8e-15 0.001 0 0.56 0 <1.00e-15 <2.40e-13
16 ASPDH aspartate dehydrogenase domain containing 74718 19 19 2 0 0 0 1 18 0 0 5.7e-15 0.0084 0 1 0 <1.00e-15 <2.40e-13
17 ERCC2 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) 196253 19 19 1 0 19 0 0 0 0 0 7.7e-15 0.0012 0 0 0 <1.00e-15 <2.40e-13
18 GLTPD2 glycolipid transfer protein domain containing 2 42201 19 19 1 2 0 19 0 0 0 0 4.4e-15 0.017 0 0.16 0 <1.00e-15 <2.40e-13
19 KCNK17 potassium channel, subfamily K, member 17 88332 19 19 2 0 0 0 1 18 0 0 3.9e-15 0.044 0 0.96 0 <1.00e-15 <2.40e-13
20 RINL Ras and Rab interactor-like 102936 19 19 1 0 0 0 19 0 0 0 3.2e-15 0.003 0 0.53 0 <1.00e-15 <2.40e-13
21 ZNF598 zinc finger protein 598 183308 20 19 5 2 0 1 3 16 0 0 4.6e-15 0.23 0 1 0 <1.00e-15 <2.40e-13
22 AMDHD1 amidohydrolase domain containing 1 103268 18 18 1 15 0 0 0 18 0 0 1 1 0 1 0 <1.00e-15 <2.40e-13
23 FAM184B family with sequence similarity 184, member B 276441 18 18 3 1 17 0 1 0 0 0 7.6e-15 0.0074 0 1 0 <1.00e-15 <2.40e-13
24 MUC2 mucin 2, oligomeric mucus/gel-forming 755805 21 18 15 8 3 0 16 1 1 0 0.1 0.5 0 0.99 0 <1.00e-15 <2.40e-13
25 C1orf106 chromosome 1 open reading frame 106 159139 16 16 2 0 15 0 0 1 0 0 5.6e-15 0.0062 0 1 0 <1.00e-15 <2.40e-13
26 SEMA5B sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B 275306 17 16 2 0 0 0 1 16 0 0 3.3e-15 0.043 0 0.99 0 <1.00e-15 <2.40e-13
27 ADAD2 adenosine deaminase domain containing 2 153125 15 15 1 0 0 0 15 0 0 0 1.1e-14 0.005 0 1 0 <1.00e-15 <2.40e-13
28 KNDC1 kinase non-catalytic C-lobe domain (KIND) containing 1 407586 17 15 5 10 0 0 2 15 0 0 1 1 0 1 0 <1.00e-15 <2.40e-13
29 PANK2 pantothenate kinase 2 (Hallervorden-Spatz syndrome) 122370 15 15 2 0 0 0 15 0 0 0 6.3e-15 0.024 0 1 0 <1.00e-15 <2.40e-13
30 ATXN1 ataxin 1 201752 15 14 9 1 0 1 4 0 10 0 8.8e-15 0.4 0 1 0 <1.00e-15 <2.40e-13
31 C2orf81 chromosome 2 open reading frame 81 152558 15 14 3 0 0 0 0 15 0 0 7.7e-15 0.029 0 1 0 <1.00e-15 <2.40e-13
32 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 216091 14 14 9 0 0 0 4 6 4 0 9.6e-15 0.063 0 0.28 0 <1.00e-15 <2.40e-13
33 FPGS folylpolyglutamate synthase 136084 14 14 2 0 0 0 1 13 0 0 3.9e-15 0.086 0 1 0 <1.00e-15 <2.40e-13
34 IDUA iduronidase, alpha-L- 116170 14 14 4 1 2 0 0 12 0 0 1.1e-14 0.27 4e-07 0.0032 0 <1.00e-15 <2.40e-13
35 SYT8 synaptotagmin VIII 99744 14 14 3 0 14 0 0 0 0 0 1.8e-15 0.0034 0 0.00066 0 <1.00e-15 <2.40e-13
RNF222

Figure S1.  This figure depicts the distribution of mutations and mutation types across the RNF222 significant gene.

ZFPM1

Figure S2.  This figure depicts the distribution of mutations and mutation types across the ZFPM1 significant gene.

GARS

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

ZNF517

Figure S4.  This figure depicts the distribution of mutations and mutation types across the ZNF517 significant gene.

LRIG1

Figure S5.  This figure depicts the distribution of mutations and mutation types across the LRIG1 significant gene.

LACTB

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

OBSCN

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

CCDC102A

Figure S8.  This figure depicts the distribution of mutations and mutation types across the CCDC102A significant gene.

OPRD1

Figure S9.  This figure depicts the distribution of mutations and mutation types across the OPRD1 significant gene.

MUC5B

Figure S10.  This figure depicts the distribution of mutations and mutation types across the MUC5B significant gene.

TOR3A

Figure S11.  This figure depicts the distribution of mutations and mutation types across the TOR3A significant gene.

TRIOBP

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

MAL2

Figure S13.  This figure depicts the distribution of mutations and mutation types across the MAL2 significant gene.

IRX3

Figure S14.  This figure depicts the distribution of mutations and mutation types across the IRX3 significant gene.

TPO

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

ASPDH

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

ERCC2

Figure S17.  This figure depicts the distribution of mutations and mutation types across the ERCC2 significant gene.

GLTPD2

Figure S18.  This figure depicts the distribution of mutations and mutation types across the GLTPD2 significant gene.

KCNK17

Figure S19.  This figure depicts the distribution of mutations and mutation types across the KCNK17 significant gene.

RINL

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

ZNF598

Figure S21.  This figure depicts the distribution of mutations and mutation types across the ZNF598 significant gene.

AMDHD1

Figure S22.  This figure depicts the distribution of mutations and mutation types across the AMDHD1 significant gene.

FAM184B

Figure S23.  This figure depicts the distribution of mutations and mutation types across the FAM184B significant gene.

MUC2

Figure S24.  This figure depicts the distribution of mutations and mutation types across the MUC2 significant gene.

C1orf106

Figure S25.  This figure depicts the distribution of mutations and mutation types across the C1orf106 significant gene.

SEMA5B

Figure S26.  This figure depicts the distribution of mutations and mutation types across the SEMA5B significant gene.

ADAD2

Figure S27.  This figure depicts the distribution of mutations and mutation types across the ADAD2 significant gene.

KNDC1

Figure S28.  This figure depicts the distribution of mutations and mutation types across the KNDC1 significant gene.

PANK2

Figure S29.  This figure depicts the distribution of mutations and mutation types across the PANK2 significant gene.

ATXN1

Figure S30.  This figure depicts the distribution of mutations and mutation types across the ATXN1 significant gene.

C2orf81

Figure S31.  This figure depicts the distribution of mutations and mutation types across the C2orf81 significant gene.

CTNNB1

Figure S32.  This figure depicts the distribution of mutations and mutation types across the CTNNB1 significant gene.

FPGS

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

IDUA

Figure S34.  This figure depicts the distribution of mutations and mutation types across the IDUA 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: 3. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 14 138 14 12420 6397 2.4e-13 1.1e-09
2 TP53 tumor protein p53 19 356 18 32040 1630 5.8e-13 1.3e-09
3 MEN1 multiple endocrine neoplasia I 8 208 5 18720 25 2.1e-08 0.000032
4 ABCA12 ATP-binding cassette, sub-family A (ABC1), member 12 3 1 1 90 1 0.00037 0.21
5 ANKRD30A ankyrin repeat domain 30A 6 1 1 90 1 0.00037 0.21
6 CCND2 cyclin D2 1 1 1 90 1 0.00037 0.21
7 KRTAP5-5 keratin associated protein 5-5 6 1 1 90 0 0.00037 0.21
8 LACE1 lactation elevated 1 1 1 1 90 1 0.00037 0.21
9 GRM3 glutamate receptor, metabotropic 3 3 2 1 180 1 0.00074 0.33
10 IGFBP3 insulin-like growth factor binding protein 3 1 2 1 180 1 0.00074 0.33

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: 21. 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 FOLATE_BIOSYNTHESIS ALPI, ALPL, ALPP, ALPP, ALPPL2, ALPPL2, DHFR, FPGS, GCH1, GGH, SPR 9 ALPI(1), ALPP(1), ALPPL2(8), FPGS(14), SPR(1) 921600 25 23 7 2 0 9 3 13 0 0 0.041 7e-14 4.3e-11
2 STILBENE_COUMARINE_AND_LIGNIN_BIOSYNTHESIS EPX, GBA3, LPO, MPO, PRDX1, PRDX2, PRDX5, PRDX6, TPO, TYR 10 EPX(1), PRDX1(1), PRDX2(2), TPO(22) 1336570 26 25 7 2 3 0 21 0 2 0 0.016 1.6e-09 4.8e-07
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 ARF3(1), CDKN2A(2), MDM2(2), TP53(19) 1124314 24 19 24 1 2 0 7 1 13 1 0.028 5.7e-09 1.2e-06
4 HSA00940_PHENYLPROPANOID_BIOSYNTHESIS Genes involved in phenylpropanoid biosynthesis EPX, GBA, GBA3, LPO, MPO, PRDX6, TPO 7 EPX(1), TPO(22) 1154920 23 22 4 2 2 0 21 0 0 0 0.018 2e-08 3.1e-06
5 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(1), DAXX(4), PML(2), RARA(1), RB1(2), SIRT1(1), TNFRSF1A(1), TP53(19) 2553179 31 25 31 1 3 1 7 1 18 1 0.011 8.6e-08 0.000011
6 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(1), ATM(5), MDM2(2), RB1(2), TIMP3(1), TP53(19) 2416850 30 24 30 2 2 0 6 1 20 1 0.086 2.2e-07 0.000021
7 METHANE_METABOLISM ADH5, ATP6V0C, SHMT1, CAT, EPX, LPO, MPO, PRDX1, PRDX2, PRDX5, PRDX6, SHMT1, SHMT2, TPO 13 ATP6V0C(1), EPX(1), PRDX1(1), PRDX2(2), SHMT2(1), TPO(22) 1628686 28 27 9 3 4 0 22 0 2 0 0.025 2.4e-07 0.000021
8 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 NFKB1(1), TP53(19) 1391271 20 18 20 0 2 0 5 1 11 1 0.023 4.6e-07 0.000034
9 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(5), ATR(3), CHEK2(2), TP53(19) 2105624 29 25 29 3 3 0 6 3 16 1 0.28 5e-07 0.000034
10 GSPATHWAY Activated G-protein coupled receptors stimulate cAMP production and thus activate protein kinase A, involved in a number of signal transduction pathways. ADCY1, GNAS, GNB1, GNGT1, PRKACA, PRKAR1A 6 ADCY1(1), GNAS(5), GNB1(3), PRKACA(1), PRKAR1A(7) 921215 17 15 16 1 1 0 3 2 11 0 0.24 5.4e-07 0.000034

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 GSPATHWAY Activated G-protein coupled receptors stimulate cAMP production and thus activate protein kinase A, involved in a number of signal transduction pathways. ADCY1, GNAS, GNB1, GNGT1, PRKACA, PRKAR1A 5 ADCY1(1), GNAS(5), GNB1(3), PRKACA(1) 814601 10 8 10 1 1 0 3 2 4 0 0.42 0.017 1
2 TERPENOID_BIOSYNTHESIS FDFT1, FDPS, FDPS, LOC402397, IDI1, SQLE 4 FDFT1(1), IDI1(1), SQLE(2) 449336 4 4 4 0 0 1 3 0 0 0 0.34 0.056 1
3 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 HLA-DRB1(3) 328912 3 3 3 1 0 0 2 1 0 0 0.74 0.058 1
4 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 CCL11(1), CCR3(1), HLA-DRB1(3), IL3(1) 407360 6 5 6 2 0 0 4 2 0 0 0.68 0.078 1
5 CAPROLACTAM_DEGRADATION AKR1A1, ECHS1, EHHADH, HADHA, SDS 5 AKR1A1(1), ECHS1(2), EHHADH(1), HADHA(1), SDS(1) 665589 6 5 6 0 1 0 2 1 2 0 0.24 0.085 1
6 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(1) 97560 1 1 1 0 0 0 0 0 1 0 0.72 0.098 1
7 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(1), GOT2(2) 356738 3 3 3 0 2 0 1 0 0 0 0.4 0.1 1
8 SULFUR_METABOLISM BPNT1, PAPSS1, PAPSS2, SULT1A2, SULT1A3, SULT1A3, SULT1A4, SULT1E1, SULT2A1, SUOX 7 BPNT1(3), PAPSS2(1), SUOX(2) 815298 6 5 6 1 0 0 3 0 2 1 0.78 0.11 1
9 HSA00900_TERPENOID_BIOSYNTHESIS Genes involved in terpenoid biosynthesis FDFT1, FDPS, GGPS1, IDI1, IDI2, SQLE 6 FDFT1(1), IDI1(1), SQLE(2) 590510 4 4 4 0 0 1 3 0 0 0 0.34 0.12 1
10 UBIQUINONE_BIOSYNTHESIS NDUFA1, NDUFA10, NDUFA11, NDUFA4, NDUFA5, NDUFA8, NDUFB2, NDUFB4, NDUFB5, NDUFB6, NDUFB7, NDUFS1, NDUFS2, NDUFV1, NDUFV2 15 NDUFA1(1), NDUFA10(2), NDUFB5(2), NDUFB7(1), NDUFS2(1) 964591 7 6 7 0 1 0 4 0 2 0 0.22 0.12 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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