Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1QR4V4T
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C1QR4V4T
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 and MutSigCV v0.9 merged result was used to generate the results found in this report.

  • Working with individual set: HNSC-TP

  • Number of patients in set: 306

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:HNSC-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 35

  • Mutations seen in COSMIC: 478

  • Significantly mutated genes in COSMIC territory: 8

  • Significantly mutated genesets: 68

Mutation Preprocessing

  • Read 306 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 74008

  • After removing 10 mutations outside chr1-24: 73998

  • After removing 1938 blacklisted mutations: 72060

  • After removing 4374 noncoding mutations: 67686

  • After collapsing adjacent/redundant mutations: 57613

Mutation Filtering

  • Number of mutations before filtering: 57613

  • After removing 873 mutations outside gene set: 56740

  • After removing 55 mutations outside category set: 56685

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 1339
Frame_Shift_Ins 604
In_Frame_Del 351
In_Frame_Ins 48
Missense_Mutation 36253
Nonsense_Mutation 2885
Nonstop_Mutation 53
Silent 14136
Splice_Site 924
Translation_Start_Site 92
Total 56685
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 5984 498919062 0.000012 12 2.5 2.1
*Cp(A/C/T)->T 9121 4084447193 2.2e-06 2.2 0.47 1.7
C->(G/A) 14182 4583366255 3.1e-06 3.1 0.65 4.8
A->mut 7049 4404728973 1.6e-06 1.6 0.34 3.9
indel+null 6160 8988095228 6.9e-07 0.69 0.14 NaN
double_null 53 8988095228 5.9e-09 0.0059 0.0012 NaN
Total 42549 8988095228 4.7e-06 4.7 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: HNSC-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: *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_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: 35. 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_cons p_joint p_cv p q
1 NSD1 nuclear receptor binding SET domain protein 1 2490988 36 33 36 1 0 2 8 4 20 2 0.069 0.0075 0 0 0
2 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 1003706 65 64 24 0 1 40 6 17 1 0 0.00066 0 5e-15 0 0
3 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 255389 65 65 31 0 2 2 2 6 52 1 0 0 6e-15 0 0
4 HRAS v-Ha-ras Harvey rat sarcoma viral oncogene homolog 198292 11 10 6 0 2 2 6 1 0 0 0.0013 0 5.6e-07 0 0
5 TP53 tumor protein p53 375773 246 214 153 5 41 27 39 40 92 7 0 0 2.4e-15 0 0
6 NFE2L2 nuclear factor (erythroid-derived 2)-like 2 546479 18 17 13 0 0 4 10 4 0 0 1e-06 0 5.3e-08 0 0
7 NOTCH1 Notch homolog 1, translocation-associated (Drosophila) 1904576 62 57 62 5 10 10 10 6 26 0 0.73 0.0011 1.6e-15 1.1e-16 2.9e-13
8 FAT1 FAT tumor suppressor homolog 1 (Drosophila) 4166666 80 72 80 2 1 5 7 6 53 8 0.029 0.14 1e-15 5.2e-15 1.2e-11
9 CASP8 caspase 8, apoptosis-related cysteine peptidase 533487 27 27 24 0 1 4 2 5 15 0 0.028 0.14 3.3e-15 1.6e-14 3.3e-11
10 JUB jub, ajuba homolog (Xenopus laevis) 357659 19 18 19 1 1 2 0 2 14 0 0.38 0.28 7.9e-15 7.5e-14 1.4e-10
11 MLL2 myeloid/lymphoid or mixed-lineage leukemia 2 4343439 58 56 58 3 4 7 7 2 35 3 0.24 0.52 4.8e-15 8.6e-14 1.4e-10
12 FBXW7 F-box and WD repeat domain containing 7 757876 16 15 14 1 2 2 5 3 4 0 0.63 0.000012 1.2e-07 4e-11 6e-08
13 EPHA2 EPH receptor A2 868017 16 14 15 0 3 0 1 1 10 1 0.29 0.11 1.6e-10 4.6e-10 6.3e-07
14 ZNF750 zinc finger protein 750 666533 15 13 14 1 1 2 2 2 8 0 0.016 0.000074 5.5e-07 1e-09 1.3e-06
15 FLG filaggrin 3674091 59 48 59 9 8 12 25 6 7 1 0.45 0.049 1.9e-09 2.2e-09 2.6e-06
16 B2M beta-2-microglobulin 113810 7 7 6 0 0 1 1 1 4 0 0.25 0.46 2e-09 2e-08 0.000023
17 IL32 interleukin 32 162670 4 4 2 0 0 0 0 0 4 0 0.92 0.00026 0.000064 3.2e-07 0.00034
18 EP300 E1A binding protein p300 2248955 25 25 22 1 3 7 4 5 6 0 0.15 0.0053 4.6e-06 4.5e-07 0.00045
19 RHOA ras homolog gene family, member A 182942 4 4 1 0 0 0 4 0 0 0 0.094 6.4e-06 0.025 2.6e-06 0.0025
20 HLA-A major histocompatibility complex, class I, A 335447 9 9 8 2 0 0 0 1 8 0 0.18 0.22 7.7e-07 2.8e-06 0.0025
21 CTCF CCCTC-binding factor (zinc finger protein) 679423 13 11 13 1 1 2 5 0 5 0 0.25 0.067 5.8e-06 6.1e-06 0.0053
22 RB1 retinoblastoma 1 (including osteosarcoma) 790351 10 10 10 2 0 1 1 0 8 0 0.16 0.49 1.3e-06 9.8e-06 0.0081
23 TGFBR2 transforming growth factor, beta receptor II (70/80kDa) 526462 11 10 9 1 1 1 0 2 7 0 0.59 0.54 1.7e-06 0.000014 0.011
24 CSMD3 CUB and Sushi multiple domains 3 3506307 88 70 87 17 6 15 35 18 13 1 0.81 1 1.2e-06 0.000018 0.013
25 NECAB1 N-terminal EF-hand calcium binding protein 1 176105 6 6 6 2 0 0 2 0 3 1 0.9 1 1.3e-06 0.000019 0.014
26 KRTAP1-5 keratin associated protein 1-5 161580 3 3 1 1 0 0 0 0 3 0 0.9 0.00078 0.0019 0.000021 0.014
27 MAPK1 mitogen-activated protein kinase 1 303224 4 4 1 0 3 0 0 0 1 0 0.23 0.00018 0.0095 0.000024 0.016
28 PLSCR1 phospholipid scramblase 1 302255 5 5 4 0 0 0 2 0 3 0 0.98 0.01 0.00031 0.000043 0.028
29 CNPY3 canopy 3 homolog (zebrafish) 204182 3 3 1 0 0 0 0 0 3 0 0.67 0.00076 0.006 6e-05 0.038
30 EPB41L3 erythrocyte membrane protein band 4.1-like 3 1022950 16 16 16 5 3 0 6 4 3 0 0.96 0.03 0.0002 0.000078 0.047
31 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 189570 10 9 8 0 2 3 2 3 0 0 0.33 0.46 0.000015 0.000088 0.051
32 CUL3 cullin 3 703996 10 10 10 1 1 1 3 2 3 0 0.58 0.16 0.000063 0.00013 0.07
33 TRPV4 transient receptor potential cation channel, subfamily V, member 4 780904 7 7 7 4 2 1 1 0 3 0 0.17 0.00054 0.019 0.00013 0.071
34 PRB2 proline-rich protein BstNI subfamily 2 386009 11 10 10 3 0 2 5 1 3 0 0.94 0.078 0.00016 0.00015 0.082
35 PRB1 proline-rich protein BstNI subfamily 1 301974 8 7 7 1 0 1 4 0 3 0 0.28 0.45 0.000035 0.00019 0.099
NSD1

Figure S1.  This figure depicts the distribution of mutations and mutation types across the NSD1 significant gene.

PIK3CA

Figure S2.  This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

CDKN2A

Figure S3.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

HRAS

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

TP53

Figure S5.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

NFE2L2

Figure S6.  This figure depicts the distribution of mutations and mutation types across the NFE2L2 significant gene.

NOTCH1

Figure S7.  This figure depicts the distribution of mutations and mutation types across the NOTCH1 significant gene.

FAT1

Figure S8.  This figure depicts the distribution of mutations and mutation types across the FAT1 significant gene.

JUB

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

MLL2

Figure S10.  This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

FBXW7

Figure S11.  This figure depicts the distribution of mutations and mutation types across the FBXW7 significant gene.

EPHA2

Figure S12.  This figure depicts the distribution of mutations and mutation types across the EPHA2 significant gene.

ZNF750

Figure S13.  This figure depicts the distribution of mutations and mutation types across the ZNF750 significant gene.

FLG

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

B2M

Figure S15.  This figure depicts the distribution of mutations and mutation types across the B2M significant gene.

IL32

Figure S16.  This figure depicts the distribution of mutations and mutation types across the IL32 significant gene.

EP300

Figure S17.  This figure depicts the distribution of mutations and mutation types across the EP300 significant gene.

RHOA

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

HLA-A

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

CTCF

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

RB1

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

TGFBR2

Figure S22.  This figure depicts the distribution of mutations and mutation types across the TGFBR2 significant gene.

CSMD3

Figure S23.  This figure depicts the distribution of mutations and mutation types across the CSMD3 significant gene.

NECAB1

Figure S24.  This figure depicts the distribution of mutations and mutation types across the NECAB1 significant gene.

KRTAP1-5

Figure S25.  This figure depicts the distribution of mutations and mutation types across the KRTAP1-5 significant gene.

MAPK1

Figure S26.  This figure depicts the distribution of mutations and mutation types across the MAPK1 significant gene.

PLSCR1

Figure S27.  This figure depicts the distribution of mutations and mutation types across the PLSCR1 significant gene.

CNPY3

Figure S28.  This figure depicts the distribution of mutations and mutation types across the CNPY3 significant gene.

EPB41L3

Figure S29.  This figure depicts the distribution of mutations and mutation types across the EPB41L3 significant gene.

RAC1

Figure S30.  This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.

CUL3

Figure S31.  This figure depicts the distribution of mutations and mutation types across the CUL3 significant gene.

TRPV4

Figure S32.  This figure depicts the distribution of mutations and mutation types across the TRPV4 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: 8. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 TP53 tumor protein p53 246 356 224 108936 45925 0 0
2 HRAS v-Ha-ras Harvey rat sarcoma viral oncogene homolog 11 19 11 5814 2979 0 0
3 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 65 220 55 67320 26369 0 0
4 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 65 332 63 101592 2920 0 0
5 FBXW7 F-box and WD repeat domain containing 7 16 91 10 27846 183 0 0
6 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 6 33 4 10098 3 2.1e-07 0.00016
7 PTPN14 protein tyrosine phosphatase, non-receptor type 14 13 3 2 918 2 9.4e-06 0.0061
8 SCN9A sodium channel, voltage-gated, type IX, alpha subunit 10 4 2 1224 2 0.000017 0.0094
9 PTCH1 patched homolog 1 (Drosophila) 11 256 4 78336 5 0.00059 0.2
10 RB1 retinoblastoma 1 (including osteosarcoma) 10 267 4 81702 5 0.00069 0.2

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: 68. 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 APOPTOSIS APAF1, BAD, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BCL2L11, BID, BIRC2, BIRC3, BIRC4, BIRC5, BNIP3L, CASP1, CASP10, CASP1, COPl, CASP2, CASP3, CASP4, CASP6, CASP7, CASP8, CASP9, CHUK, CYCS, DFFA, DFFB, FADD, FAS, FASLG, GZMB, HELLS, HRK, IKBKB, IKBKG, IRF1, IRF2, IRF3, IRF4, IRF5, IRF6, IRF7, JUN, LTA, MAP2K4, MAP3K1, MAPK10, MDM2, MYC, NFKB1, NFKBIA, NFKBIB, NFKBIE, PRF1, RELA, RIPK1, TNF, TNFRSF10B, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF25, PLEKHG5, TNFSF10, TP53, TP73, TRADD, TRAF1, TRAF2, TRAF3 66 APAF1(9), BAD(1), BAX(1), BCL2(1), BCL2L1(2), BCL2L11(1), BID(2), BIRC2(1), BIRC3(1), CASP1(2), CASP10(2), CASP3(1), CASP4(1), CASP6(2), CASP7(1), CASP8(27), CHUK(3), FADD(1), FAS(1), FASLG(2), GZMB(1), HELLS(4), IKBKB(5), IRF1(5), IRF2(3), IRF3(1), IRF4(2), IRF5(1), IRF6(4), IRF7(2), LTA(1), MAP2K4(1), MAP3K1(3), MAPK10(3), MDM2(2), MYC(4), NFKB1(2), NFKBIB(1), PLEKHG5(4), PRF1(3), RELA(1), RIPK1(2), TNFRSF10B(1), TNFRSF21(2), TNFRSF25(2), TP53(246), TRAF2(1), TRAF3(3) 26196004 372 243 276 32 61 55 65 61 123 7 <1.00e-15 <1.00e-15 <8.55e-14
2 APOPTOSIS_GENMAPP APAF1, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CASP2, CASP3, CASP6, CASP7, CASP8, CASP9, CYCS, FADD, FAS, FASLG, GZMB, IKBKG, JUN, MAP2K4, MAP3K1, MAP3K14, MAPK10, MCL1, MDM2, MYC, NFKB1, NFKBIA, PARP1, PRF1, RELA, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TNFSF10, TP53, TRADD, TRAF1, TRAF2 41 APAF1(9), BAX(1), BCL2(1), BCL2L1(2), BID(2), BIRC2(1), BIRC3(1), CASP3(1), CASP6(2), CASP7(1), CASP8(27), FADD(1), FAS(1), FASLG(2), GZMB(1), MAP2K4(1), MAP3K1(3), MAP3K14(2), MAPK10(3), MCL1(1), MDM2(2), MYC(4), NFKB1(2), PARP1(3), PRF1(3), RELA(1), RIPK1(2), TP53(246), TRAF2(1) 17088240 327 237 231 21 53 41 56 56 114 7 <1.00e-15 <1.00e-15 <8.55e-14
3 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(2), APAF1(9), ATM(9), BAD(1), BAX(1), BCL2(1), BCL2L1(2), BID(2), CASP3(1), CASP6(2), CASP7(1), EIF2S1(1), PRKCA(2), PTK2(5), PXN(1), STAT1(5), TLN1(13), TP53(246) 12480574 304 233 211 26 48 40 58 51 100 7 9.48e-12 <1.00e-15 <8.55e-14
4 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 DNAJA3(1), IFNG(1), IFNGR1(5), IFNGR2(2), IKBKB(5), JAK2(2), LIN7A(2), NFKB1(2), RB1(10), RELA(1), TP53(246), USH1C(2) 8287879 279 227 185 20 43 33 48 43 105 7 1.09e-13 <1.00e-15 <8.55e-14
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(9), CDC25B(3), CDK4(4), CHEK1(1), MYT1(7), RB1(10), TP53(246), WEE1(1), YWHAH(1) 7991690 282 226 189 12 44 33 49 46 103 7 3.11e-15 <1.00e-15 <8.55e-14
6 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 CCND1(2), CDK4(4), CDKN1B(2), CDKN2A(65), CFL1(2), E2F2(3), MDM2(2), PRB1(8), TP53(246) 3842593 334 223 206 12 44 34 49 50 149 8 <1.00e-15 <1.00e-15 <8.55e-14
7 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 MAX(1), MYC(4), SP1(1), SP3(1), TP53(246) 3219260 253 214 160 7 41 28 42 42 93 7 <1.00e-15 <1.00e-15 <8.55e-14
8 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(15), HRAS(11), PAX3(4), PML(1), RARA(2), RB1(10), SIRT1(1), SP100(2), TP53(246) 8657665 292 234 194 22 44 35 57 44 105 7 2.76e-13 1.11e-15 8.55e-14
9 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(2), BCL2(1), EGFR(14), IGF1R(7), MYC(4), POLR2A(9), PRKCA(2), RB1(10), TEP1(8), TERF1(3), TERT(1), TNKS(4), TP53(246), XRCC5(2) 12869416 313 230 220 29 49 41 60 52 104 7 7.27e-14 1.33e-15 9.12e-14
10 AKTPATHWAY Second messenger PIP3 promotes cell survival by activating the anti-apoptotic kinase AKT. AKT1, BAD, CASP9, CHUK, FOXO1A, FOXO3A, GH1, GHR, HSPCA, MLLT7, NFKB1, NFKBIA, PDPK1, PIK3CA, PIK3R1, PPP2CA, RELA, TNFSF6, YWHAH 14 AKT1(2), BAD(1), CHUK(3), GH1(1), GHR(4), NFKB1(2), PDPK1(2), PIK3CA(65), PIK3R1(6), RELA(1), YWHAH(1) 6437782 88 82 47 4 3 49 8 23 5 0 2.86e-09 1.55e-15 9.57e-14
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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle