Mutation Analysis (MutSig v2.0)
Prostate Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1QZ27X0
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Prostate Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C1QZ27X0
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: PRAD-TP

  • Number of patients in set: 83

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:PRAD-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 11

  • Mutations seen in COSMIC: 26

  • Significantly mutated genes in COSMIC territory: 6

  • Genes with clustered mutations (≤ 3 aa apart): 11

  • Significantly mutated genesets: 2

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

Mutation Preprocessing

  • Read 83 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 5917

  • After removing 18 mutations outside chr1-24: 5899

  • After removing 602 blacklisted mutations: 5297

  • After removing 219 noncoding mutations: 5078

Mutation Filtering

  • Number of mutations before filtering: 5078

  • After removing 135 mutations outside gene set: 4943

  • After removing 4 mutations outside category set: 4939

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 145
Frame_Shift_Ins 65
In_Frame_Del 42
In_Frame_Ins 7
Missense_Mutation 3041
Nonsense_Mutation 173
Nonstop_Mutation 2
Silent 1368
Splice_Site 88
Translation_Start_Site 8
Total 4939
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 816 138713067 5.9e-06 5.9 4.1 2.1
*Np(A/C/T)->transit 829 1965699488 4.2e-07 0.42 0.29 2
*ApG->G 94 381313535 2.5e-07 0.25 0.17 2.1
transver 1310 2485726090 5.3e-07 0.53 0.37 5
indel+null 519 2485726090 2.1e-07 0.21 0.15 NaN
double_null 3 2485726090 1.2e-09 0.0012 0.00084 NaN
Total 3571 2485726090 1.4e-06 1.4 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).

Figure 1. 

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

Figure 2.  Patients counts and rates file used to generate this plot: PRAD-TP.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: *Np(A/C/T)->transit

  • n3 = number of nonsilent mutations of type: *ApG->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_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: 11. 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_cons p_joint p q
1 NKX3-1 NK3 homeobox 1 43527 5 5 5 0 0 2 0 2 1 0 2.1e-09 0.26 0.013 0.034 1.8e-09 0.000032
2 TP53 tumor protein p53 105521 5 5 5 0 3 0 0 1 1 0 5.5e-07 0.34 0.002 0.0071 8e-08 0.00072
3 SPOP speckle-type POZ protein 96345 4 4 3 0 0 0 1 3 0 0 3.8e-06 0.39 0.32 0.0097 6.6e-07 0.0035
4 FRG1 FSHD region gene 1 67208 4 4 2 0 0 0 0 3 1 0 2.9e-07 0.65 1 0.15 7.7e-07 0.0035
5 YBX1 Y box binding protein 1 68945 4 3 2 0 0 2 0 2 0 0 0.00012 0.32 0.0093 0.0026 5e-06 0.018
6 CLSTN1 calsyntenin 1 242387 3 3 1 0 0 0 0 3 0 0 0.0056 0.6 0.083 0.00012 1e-05 0.03
7 CCNF cyclin F 199411 3 3 1 1 0 0 0 3 0 0 0.0024 0.79 0.034 0.00032 0.000012 0.03
8 PRR21 proline rich 21 58941 4 4 4 0 1 1 0 2 0 0 2.3e-06 0.26 0.95 0.42 0.000014 0.032
9 AGT angiotensinogen (serpin peptidase inhibitor, clade A, member 8) 122342 3 3 1 0 0 0 0 3 0 0 0.00053 0.53 1 0.0021 0.000016 0.033
10 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 199245 3 3 3 0 0 1 0 2 0 0 0.0011 0.46 0.3 0.0021 0.000033 0.059
11 DUSP27 dual specificity phosphatase 27 (putative) 264959 3 3 1 1 0 0 0 3 0 0 0.0014 0.82 0.94 0.0023 0.000044 0.073
12 OR4D5 olfactory receptor, family 4, subfamily D, member 5 79763 3 3 3 0 2 0 0 1 0 0 0.000012 0.46 0.32 0.56 0.000083 0.13
13 OR6N1 olfactory receptor, family 6, subfamily N, member 1 78146 3 3 2 0 0 0 2 1 0 0 0.000012 0.46 0.55 0.62 0.000097 0.14
14 MLL3 myeloid/lymphoid or mixed-lineage leukemia 3 1228308 8 7 7 0 0 1 0 2 4 1 0.00012 0.23 0.78 0.15 0.00022 0.28
15 C1orf116 chromosome 1 open reading frame 116 150780 2 2 2 0 0 1 0 1 0 0 0.015 0.52 0.0025 0.002 0.00036 0.43
16 CNTNAP5 contactin associated protein-like 5 309961 5 5 5 0 2 0 0 2 1 0 5e-05 0.2 0.85 0.71 0.0004 0.45
17 BCL6 B-cell CLL/lymphoma 6 (zinc finger protein 51) 178187 3 3 3 1 1 2 0 0 0 0 0.00051 0.6 0.94 0.074 0.00042 0.45
18 ATM ataxia telangiectasia mutated 780236 5 5 5 0 0 4 0 1 0 0 0.0018 0.18 0.017 0.023 0.00047 0.45
19 SLITRK4 SLIT and NTRK-like family, member 4 208728 3 3 2 0 0 0 0 0 3 0 0.00034 0.72 1 0.13 0.00047 0.45
20 OR5L2 olfactory receptor, family 5, subfamily L, member 2 78017 3 3 3 0 0 0 0 3 0 0 0.0001 0.55 0.2 0.46 0.00051 0.47
21 OR2AE1 olfactory receptor, family 2, subfamily AE, member 1 81008 2 2 2 0 1 0 0 0 1 0 0.00098 0.62 0.0093 0.051 0.00055 0.47
22 AIM2 absent in melanoma 2 87306 3 3 3 0 0 1 0 1 1 0 0.00011 0.57 0.82 0.81 0.00094 0.75
23 GPATCH4 G patch domain containing 4 97579 2 2 1 0 0 0 0 0 2 0 0.0013 1 0.3 0.075 0.00099 0.75
24 PCDHB14 protocadherin beta 14 199174 3 3 3 0 1 0 0 1 1 0 0.00047 0.27 0.59 0.22 0.0011 0.75
25 ZMYM3 zinc finger, MYM-type 3 288038 5 4 5 0 0 0 0 2 3 0 0.00026 0.48 0.21 0.4 0.0011 0.75
26 LPHN3 latrophilin 3 311602 4 4 4 1 2 1 0 1 0 0 0.00034 0.61 0.57 0.31 0.0011 0.75
27 CROCC ciliary rootlet coiled-coil, rootletin 295882 4 4 2 1 3 0 0 1 0 0 0.00063 0.59 0.76 0.18 0.0011 0.75
28 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 102374 3 3 3 0 0 1 0 1 1 0 0.00016 0.4 0.14 0.74 0.0012 0.75
29 SETD5 SET domain containing 5 345156 4 1 4 1 0 3 0 1 0 0 0.27 0.54 0.46 0.00047 0.0013 0.75
30 OR5B12 olfactory receptor, family 5, subfamily B, member 12 78709 2 2 2 0 1 0 0 1 0 0 0.00063 0.83 0.11 0.2 0.0013 0.75
31 OR52A1 olfactory receptor, family 52, subfamily A, member 1 78103 2 2 2 0 2 0 0 0 0 0 0.00017 0.84 0.64 0.78 0.0013 0.75
32 GGTLC2 gamma-glutamyltransferase light chain 2 47824 2 2 2 1 0 0 1 1 0 0 0.00013 0.81 0.16 1 0.0013 0.75
33 LHX3 LIM homeobox 3 74497 2 2 2 0 0 1 0 1 0 0 0.0026 0.52 0.055 0.058 0.0015 0.8
34 TAF1L TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like 455255 3 3 3 0 1 2 0 0 0 0 0.013 0.38 0.022 0.012 0.0015 0.8
35 CRIPAK cysteine-rich PAK1 inhibitor 110493 3 3 3 1 0 1 0 2 0 0 0.00026 0.7 1 0.62 0.0016 0.8
NKX3-1

Figure S1.  This figure depicts the distribution of mutations and mutation types across the NKX3-1 significant gene.

TP53

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

SPOP

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

FRG1

Figure S4.  This figure depicts the distribution of mutations and mutation types across the FRG1 significant gene.

YBX1

Figure S5.  This figure depicts the distribution of mutations and mutation types across the YBX1 significant gene.

CLSTN1

Figure S6.  This figure depicts the distribution of mutations and mutation types across the CLSTN1 significant gene.

CCNF

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

PRR21

Figure S8.  This figure depicts the distribution of mutations and mutation types across the PRR21 significant gene.

AGT

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

CTNNB1

Figure S10.  This figure depicts the distribution of mutations and mutation types across the CTNNB1 significant gene.

DUSP27

Figure S11.  This figure depicts the distribution of mutations and mutation types across the DUSP27 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: 6. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 TP53 tumor protein p53 5 356 5 29548 1608 1.1e-09 5e-06
2 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 3 138 3 11454 1229 7.3e-07 0.0017
3 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 3 767 3 63661 15 0.00012 0.09
4 ACSM2B acyl-CoA synthetase medium-chain family member 2B 1 1 1 83 1 0.00012 0.09
5 BRE brain and reproductive organ-expressed (TNFRSF1A modulator) 1 1 1 83 1 0.00012 0.09
6 KCNH1 potassium voltage-gated channel, subfamily H (eag-related), member 1 1 1 1 83 1 0.00012 0.09
7 CHAT choline acetyltransferase 2 2 1 166 1 0.00024 0.13
8 CYP4F2 cytochrome P450, family 4, subfamily F, polypeptide 2 1 2 1 166 2 0.00024 0.13
9 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 2 220 2 18260 355 0.00034 0.16
10 ACVR2A activin A receptor, type IIA 1 3 1 249 1 0.00036 0.16

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
89 AGT angiotensinogen (serpin peptidase inhibitor, clade A, member 8) 3 0 3 3 3 3 3 3
451 CCNF cyclin F 3 0 3 3 3 3 3 3
544 CLSTN1 calsyntenin 1 3 0 3 3 3 3 3 3
600 CROCC ciliary rootlet coiled-coil, rootletin 4 0 3 3 3 3 3 3
749 DUSP27 dual specificity phosphatase 27 (putative) 3 0 3 3 3 3 3 3
939 FRG1 FSHD region gene 1 4 0 3 3 3 3 3 3
2737 YBX1 Y box binding protein 1 4 0 2 2 2 2 2 2
2363 SPOP speckle-type POZ protein 4 0 1 3 3 1 3 3
1527 MLL3 myeloid/lymphoid or mixed-lineage leukemia 3 8 0 1 1 3 1 1 3
85 AGK acylglycerol kinase 2 0 1 1 1 1 1 1

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: 2. 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 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 CDKN1B(2), PRB1(2), TP53(5) 1062488 9 9 9 0 3 1 0 2 3 0 0.15 2e-05 0.013
2 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(2), AKT1(1), ATM(5), TP53(5) 2602579 13 12 13 0 4 6 0 2 1 0 0.015 0.00016 0.048
3 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), TP53(5) 2266716 11 10 11 0 3 5 0 2 1 0 0.034 0.0008 0.16
4 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 SP1(1), TP53(5) 879118 6 6 6 0 3 1 0 1 1 0 0.16 0.0015 0.23
5 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(5), TP53(5) 2195302 10 9 10 0 3 4 0 2 1 0 0.058 0.0019 0.23
6 SA_REG_CASCADE_OF_CYCLIN_EXPR Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1 13 CCNA1(1), CCNE2(1), CDKN1B(2), PRB1(2) 1130432 6 6 6 0 0 2 0 2 2 0 0.3 0.0026 0.25
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 ATM(5), CCNA1(1), CDKN1B(2), DHFR(1), TP53(5) 3787641 14 12 14 0 3 5 0 2 4 0 0.032 0.003 0.25
8 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(1), APAF1(1), ATM(5), TLN1(1), TP53(5) 3433242 13 12 13 0 3 6 0 3 1 0 0.019 0.0032 0.25
9 SMALL_LIGAND_GPCRS C9orf47, CNR1, CNR2, DNMT1, EDG1, EDG2, EDG5, EDG6, MTNR1A, MTNR1B, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, TBXA2R 13 DNMT1(3), MTNR1A(1), PTGER2(1), TBXA2R(2) 1410721 7 7 7 1 3 2 0 1 1 0 0.19 0.0076 0.44
10 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(2), PIK3CA(2), PTEN(3) 2419782 8 8 8 1 0 3 1 1 3 0 0.36 0.0076 0.44

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_ns_s p q
1 SA_REG_CASCADE_OF_CYCLIN_EXPR Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1 13 CCNA1(1), CCNE2(1), CDKN1B(2), PRB1(2) 1130432 6 6 6 0 0 2 0 2 2 0 0.3 0.0026 1
2 SMALL_LIGAND_GPCRS C9orf47, CNR1, CNR2, DNMT1, EDG1, EDG2, EDG5, EDG6, MTNR1A, MTNR1B, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, TBXA2R 13 DNMT1(3), MTNR1A(1), PTGER2(1), TBXA2R(2) 1410721 7 7 7 1 3 2 0 1 1 0 0.19 0.0076 1
3 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(2), PIK3CA(2), PTEN(3) 2419782 8 8 8 1 0 3 1 1 3 0 0.36 0.0076 1
4 HSA00830_RETINOL_METABOLISM Genes involved in retinol metabolism ALDH1A1, ALDH1A2, BCMO1, RDH5 4 ALDH1A2(1), BCMO1(2) 483292 3 3 2 0 0 2 0 1 0 0 0.37 0.008 1
5 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 18 ABCB1(2), AKT1(1), ATM(5) 2497058 8 8 8 0 1 6 0 1 0 0 0.053 0.012 1
6 HSA00564_GLYCEROPHOSPHOLIPID_METABOLISM Genes involved in glycerophospholipid metabolism ACHE, AGPAT1, AGPAT2, AGPAT3, AGPAT4, AGPAT6, ARD1A, CDIPT, CDS1, CDS2, CHAT, CHKA, CHKB, CHPT1, CRLS1, DGKA, DGKB, DGKD, DGKE, DGKG, DGKH, DGKI, DGKQ, DGKZ, ESCO1, ESCO2, ETNK1, ETNK2, GNPAT, GPAM, GPD1, GPD1L, GPD2, LCAT, LYCAT, LYPLA1, LYPLA2, LYPLA3, MYST3, MYST4, NAT5, NAT6, PCYT1A, PCYT1B, PEMT, PHOSPHO1, PISD, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLD1, PLD2, PNPLA3, PPAP2A, PPAP2B, PPAP2C, PTDSS1, PTDSS2, SH3GLB1 64 AGPAT2(1), AGPAT3(1), CHAT(2), DGKD(1), DGKH(1), DGKI(1), DGKQ(2), ESCO1(3), GNPAT(1), MYST3(1), PEMT(1), PLA2G2A(1), PLA2G4A(1), PLA2G5(1), PLD1(1), PTDSS1(1) 8241571 20 19 20 2 2 4 1 9 4 0 0.11 0.014 1
7 LONGEVITYPATHWAY Caloric restriction in animals often increases lifespan, which may occur via decreased IGF receptor expression and consequent expression of stress-resistance proteins. AKT1, CAT, FOXO3A, GH1, GHR, HRAS, IGF1, IGF1R, PIK3CA, PIK3R1, SHC1, SOD1, SOD2, SOD3 13 AKT1(1), GHR(1), IGF1R(1), PIK3CA(2), SOD3(1) 1657357 6 6 6 0 0 4 1 1 0 0 0.12 0.016 1
8 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 14 CDKN1B(2), PRB1(2) 956967 4 4 4 0 0 1 0 1 2 0 0.54 0.02 1
9 TRKAPATHWAY Nerve growth factor (NGF) promotes neuronal survival and proliferation by binding its receptor TrkA, which activates PI3K/AKT, Ras, and the MAP kinase pathway. AKT1, DPM2, GRB2, HRAS, KLK2, NGFB, NTRK1, PIK3CA, PIK3R1, PLCG1, PRKCA, PRKCB1, SHC1, SOS1 12 AKT1(1), KLK2(1), NTRK1(2), PIK3CA(2) 1940556 6 6 6 0 0 4 1 0 1 0 0.13 0.021 1
10 ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY The phosphoinositide-3 kinase pathway produces the lipid second messenger PIP3 and regulates cell growth, survival, and movement. A1BG, AKT1, AKT2, AKT3, BAD, BTK, CDKN2A, CSL4, DAF, DAPP1, FOXO1A, GRB2, GSK3A, GSK3B, IARS, IGFBP1, INPP5D, P14, PDK1, PIK3CA, PPP1R13B, PSCD3, PTEN, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SFN, SHC1, SOS1, SOS2, TEC, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ 33 A1BG(1), AKT1(1), BTK(1), GSK3A(1), PDK1(1), PIK3CA(2), PPP1R13B(1), PTEN(3) 4518736 11 11 11 1 1 3 1 4 2 0 0.16 0.022 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

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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