Bladder Urothelial Carcinoma: Mutation Analysis (MutSig)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v1.5 was used to generate the results found in this report.

Working with individual set: BLCA.

Number of patients in set: 28

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

Significantly mutated genes (q ≤ 0.1): 25

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 0

Significantly mutated genesets: 6

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

Results
Breakdown of Mutations by Type

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

type count
In_Frame_Del 1
Missense_Mutation 79
Nonsense_Mutation 6
Silent 33
Total 119
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
Tp*C->(T/G) 44 684404 0.000064 64 4.1 2.6
Tp*C->A 4 684404 5.8e-06 5.8 0.37 3.3
(A/C/G)p*C->mut 20 2423008 8.3e-06 8.3 0.52 2.6
A->mut 11 2353008 4.7e-06 4.7 0.3 4.2
indel+null 7 5460420 1.3e-06 1.3 0.081 NaN
Total 86 5460420 0.000016 16 1 3.2
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. 

Significantly Mutated Genes

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 25. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 p_ns_s p q
1 MXRA5 matrix-remodelling associated 5 60480 2 2 2 0 0 0 1 1 0 0.57 8.2e-06 0.0032
2 B3GALT4 UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4 9324 2 2 2 0 1 0 0 0 1 0.48 0.000033 0.0065
3 CLUAP1 clusterin associated protein 1 10388 2 2 2 0 1 0 1 0 0 0.66 0.000055 0.0071
4 NISCH nischarin 34496 3 3 3 0 1 0 1 0 1 0.35 0.000095 0.0084
5 NRBP1 nuclear receptor binding protein 1 19180 2 2 2 0 0 0 1 1 0 0.63 0.00011 0.0084
6 CRYBA2 crystallin, beta A2 6524 1 1 1 0 0 0 0 0 1 1 0.00022 0.015
7 OR6C70 olfactory receptor, family 6, subfamily C, member 70 7504 1 1 1 1 0 0 1 0 0 0.96 0.00028 0.016
8 C16orf54 chromosome 16 open reading frame 54 5516 1 1 1 0 0 0 1 0 0 0.77 0.00032 0.016
9 CACNG8 calcium channel, voltage-dependent, gamma subunit 8 9212 1 1 1 0 0 0 0 1 0 0.98 0.00036 0.016
10 OR4L1 olfactory receptor, family 4, subfamily L, member 1 9436 1 1 1 0 0 0 0 1 0 0.79 0.00048 0.019
11 CTU1 14336 1 1 1 0 0 0 0 1 0 0.9 0.00083 0.029
12 SYT3 synaptotagmin III 13076 2 2 2 0 1 0 0 1 0 0.54 0.00095 0.031
13 PRR22 16912 1 1 1 0 0 0 1 0 0 0.68 0.0017 0.048
14 KLHL17 kelch-like 17 (Drosophila) 18480 1 1 1 0 0 1 0 0 0 0.79 0.0019 0.048
15 GLYR1 14980 1 1 1 0 0 0 0 0 1 0.75 0.0019 0.048
16 PCDHB10 protocadherin beta 10 18564 1 1 1 1 0 0 1 0 0 0.89 0.0023 0.055
17 ZNF777 zinc finger protein 777 19264 1 1 1 0 0 0 1 0 0 0.71 0.0028 0.059
18 ZNF214 zinc finger protein 214 19964 1 1 1 0 0 1 0 0 0 0.92 0.0029 0.059
19 RBPJL recombination signal binding protein for immunoglobulin kappa J region-like 20748 1 1 1 0 0 0 0 1 0 0.9 0.0029 0.059
20 MSH5 mutS homolog 5 (E. coli) 20804 1 1 1 1 0 0 1 0 0 0.93 0.0032 0.063
21 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 32872 1 1 1 0 0 0 1 0 0 0.68 0.0049 0.086
22 PCDHA4 protocadherin alpha 4 36988 1 1 1 0 0 0 1 0 0 0.67 0.0051 0.086
23 CIC capicua homolog (Drosophila) 40040 1 1 1 1 0 0 0 1 0 0.9 0.0052 0.086
24 C17orf81 chromosome 17 open reading frame 81 13692 3 2 3 1 2 0 1 0 0 0.77 0.0054 0.086
25 PCDHGA5 protocadherin gamma subfamily A, 5 34132 1 1 1 0 0 0 1 0 0 0.72 0.0055 0.086
26 PCDHA10 protocadherin alpha 10 55972 1 1 1 0 0 0 1 0 0 0.68 0.0087 0.13
27 PHRF1 57596 1 1 1 1 0 0 1 0 0 0.92 0.011 0.16
28 SLC35B2 solute carrier family 35, member B2 12096 1 1 1 0 0 0 1 0 0 0.72 0.013 0.18
29 B3GNT1 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1 14504 1 1 1 0 1 0 0 0 0 0.69 0.03 0.38
30 MCOLN1 mucolipin 1 17192 1 1 1 0 0 0 0 0 1 0.69 0.03 0.38
31 MAP4K2 mitogen-activated protein kinase kinase kinase kinase 2 19852 2 2 2 0 2 0 0 0 0 0.4 0.031 0.38
32 ZNF275 zinc finger protein 275 8764 1 1 1 0 1 0 0 0 0 0.68 0.033 0.4
33 TIAF1 TGFB1-induced anti-apoptotic factor 1 2716 1 1 1 0 1 0 0 0 0 0.82 0.034 0.4
34 NPFF neuropeptide FF-amide peptide precursor 2968 1 1 1 0 1 0 0 0 0 0.89 0.036 0.42
35 FBXW12 F-box and WD repeat domain containing 12 12152 1 1 1 0 0 0 0 0 1 0.76 0.038 0.42

Note:

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: Tp*C->(T/G) .

n2 - number of nonsilent mutations of type: Tp*C->A .

n3 - number of nonsilent mutations of type: (A/C/G)p*C->mut .

n4 - number of nonsilent mutations of type: A->mut .

n5 - number of nonsilent mutations of type: indel+null .

null - mutation category that includes nonsense, frameshift, splice-site mutations

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 = p-value (overall)

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

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: 0. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 1 0 0 0 0 1 1
2 BACH2 BTB and CNC homology 1, basic leucine zipper transcription factor 2 1 0 0 0 0 1 1
3 BSN bassoon (presynaptic cytomatrix protein) 1 0 0 0 0 1 1
4 CLIC1 chloride intracellular channel 1 0 0 0 0 0 1 1
5 FAM78B family with sequence similarity 78, member B 0 0 0 0 0 1 1
6 FGF23 fibroblast growth factor 23 0 0 0 0 0 1 1
7 GNAT1 guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1 0 0 0 0 0 1 1
8 KLC4 kinesin light chain 4 0 0 0 0 0 1 1
9 LACRT lacritin 0 0 0 0 0 1 1
10 MSH5 mutS homolog 5 (E. coli) 1 0 0 0 0 1 1

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 npairs3 npairs12
68 ZNF200 zinc finger protein 200 3 7 0 2
37 MXRA5 matrix-remodelling associated 5 2 48 0 0
5 B3GALT4 UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4 2 128 0 0
55 PCDHGB4 protocadherin gamma subfamily B, 4 2 141 0 0
33 MAP4K2 mitogen-activated protein kinase kinase kinase kinase 2 2 292 0 0
38 NISCH nischarin 3 309 0 0
63 SYT3 synaptotagmin III 2 379 0 0
40 NRBP1 nuclear receptor binding protein 1 2 446 0 0
11 C17orf81 chromosome 17 open reading frame 81 3 Inf 0 0
17 CLUAP1 clusterin associated protein 1 2 Inf 0 0

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: 6. Number of genesets displayed: 10

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 p_ns_s p q
1 GANGLIOSIDE_BIOSYNTHESIS B3GALT4, GALGT, SIAT4A, SIAT4B, SIAT7B, SIAT7D, SIAT9, ST3GAL1, ST3GAL2, ST3GAL4, ST3GAL5, ST6GALNAC2, ST6GALNAC4, ST8SIA1 1 B3GALT4(2) 9324 2 2 2 0 1 0 0 0 1 0.48 0.000033 0.0026
2 HSA00604_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIOSERIES Genes involved in glycosphingolipid biosynthesis - ganglioseries B3GALT4, B4GALNT1, GLB1, HEXA, HEXB, LCT, SLC33A1, ST3GAL1, ST3GAL2, ST3GAL5, ST6GALNAC3, ST6GALNAC4, ST6GALNAC5, ST6GALNAC6, ST8SIA1, ST8SIA5 1 B3GALT4(2) 9324 2 2 2 0 1 0 0 0 1 0.48 0.000033 0.0026
3 HSA04010_MAPK_SIGNALING_PATHWAY Genes involved in MAPK signaling pathway ACVR1B, ACVR1C, AKT1, AKT2, AKT3, ARRB1, ARRB2, ATF2, ATF4, BDNF, BRAF, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CACNA2D1, CACNA2D2, CACNA2D3, CACNA2D4, CACNB1, CACNB2, CACNB3, CACNB4, CACNG1, CACNG2, CACNG3, CACNG4, CACNG5, CACNG6, CACNG7, CACNG8, CASP3, CD14, CDC25B, CDC42, CHP, CHUK, CRK, CRKL, DAXX, DDIT3, DUSP1, DUSP10, DUSP14, DUSP16, DUSP2, DUSP3, DUSP4, DUSP5, DUSP6, DUSP7, DUSP8, DUSP9, ECSIT, EGF, EGFR, ELK1, ELK4, EVI1, FAS, FASLG, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FLNA, FLNB, FLNC, FOS, GADD45A, GADD45B, GADD45G, GNA12, GNG12, GRB2, HRAS, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1R2, JUN, JUND, KRAS, LOC653852, MAP2K1, MAP2K1IP1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K12, MAP3K13, MAP3K14, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K8, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPT, MAX, MEF2C, MKNK1, MKNK2, MOS, MRAS, MYC, NF1, NFATC2, NFATC4, NFKB1, NFKB2, NGFB, NLK, NR4A1, NRAS, NTF3, NTF5, NTRK1, NTRK2, PAK1, PAK2, PDGFA, PDGFB, PDGFRA, PDGFRB, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PPM1A, PPM1B, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PPP5C, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTPN5, PTPN7, PTPRR, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF2, RASA1, RASA2, RASGRF1, RASGRF2, RASGRP1, RASGRP2, RASGRP3, RASGRP4, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KA5, RPS6KA6, RRAS, RRAS2, SOS1, SOS2, SRF, STK3, STK4, STMN1, TAOK1, TAOK2, TAOK3, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF1A, TP53, TRAF2, TRAF6, ZAK 6 CACNG8(1), MAP4K2(2) 58240 3 3 3 0 2 0 0 1 0 0.38 0.00046 0.023
4 HSA01031_GLYCAN_STRUCTURES_BIOSYNTHESIS_2 Genes involved in glycan structures - biosynthesis 2 A4GALT, ABO, B3GALNT1, B3GALT1, B3GALT2, B3GALT4, B3GALT5, B3GNT1, B3GNT2, B3GNT3, B3GNT4, B3GNT5, B4GALNT1, B4GALT1, B4GALT2, B4GALT3, B4GALT4, B4GALT6, FUT1, FUT2, FUT3, FUT4, FUT5, FUT6, FUT7, FUT9, GBGT1, GCNT2, PIGA, PIGB, PIGC, PIGF, PIGG, PIGH, PIGK, PIGL, PIGM, PIGN, PIGO, PIGP, PIGQ, PIGS, PIGT, PIGU, PIGV, PIGX, PIGZ, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4, ST3GAL5, ST3GAL6, ST6GALNAC3, ST6GALNAC4, ST6GALNAC5, ST6GALNAC6, ST8SIA1, ST8SIA5, UGCG, UGCGL1, UGCGL2 4 B3GALT4(2), B3GNT1(1) 82572 3 3 3 0 2 0 0 0 1 0.34 0.00059 0.023
5 RIBOSOMAL_PROTEINS ANK2, APG10L, RPS23, B3GALT4, CDR1, DGKI, FAU, IL6ST, KIAA1394, LOC133957, MRPL19, NET_5, PIGK, RPL10, RPL11, RPL12, RPL13, RPL13, LOC388344, RPL13A, RPL13A, LOC283340, LOC387930, RPL14, RPL14, RPL14L, RPL15, RPL15, LOC136321, LOC402694, RPL17, RPL17, dJ612B15.1, RPL18, RPL18A, LOC285053, LOC347544, LOC390354, RPL18A, LOC390354, RPL19, RPL21, RPL21, LOC387753, LOC388143, LOC388532, LOC388621, LOC389156, LOC390488, LOC402336, LOC440487, LOC440575, RPL21, LOC387753, LOC388143, LOC388532, LOC388621, LOC389156, LOC390488, LOC440487, LOC440575, RPL22, RPL23, RPL24, RPL24, SLC36A2, RPL26, LOC391126, LOC392501, LOC400055, LOC441073, LOC441533, RPL27, RPL27A, RPL27A, LOC389435, RPL28, RPL29, RPL29, LOC283412, LOC284064, LOC389655, LOC391738, LOC401911, RPL3, RPL30, RPL31, RPL32, RPL34, LOC342994, RPL35, RPL35A, RPL36, RPL37, RPL38, RPL39, RPL3L, RPL4, RPL41, RPL5, RPL5, LOC388907, RPL5, RNU66, LOC388907, RPL6, RPL7, RPL7, LOC389305, RPL7, LOC90193, LOC388401, LOC389305, LOC392550, LOC439954, RPL7A, RPL7A, LOC133748, LOC388474, RPL7A, RNU36B, LOC133748, LOC388474, RPL8, RPL9, RPLP0, RPLP0, RPLP0_like, RPLP1, RPLP2, RPS10, RPS10, LOC158104, LOC388885, LOC389127, LOC390842, LOC401817, RPS10, LOC388885, RPS11, RPS12, RPS13, RPS14, RPS15, RPS16, RPS16, LOC441876, RPS17, RPS17, LOC402057, RPS18, RPS19, RPS2, RPS2, LOC91561, LOC148430, LOC286444, LOC400963, LOC440589, RPS20, RPS21, RPS23, RPS24, RPS25, RPS26, RPS26L, LOC440440, RPS27, RPS27A, RPS27A, LOC388720, LOC389425, RPS28, RPS29, RPS3, RPS3A, RPS3A, LOC146053, LOC400652, LOC401016, LOC439992, RPS4X, RPS4Y1, RPS5, RPS6, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA6, RPS6KB1, RPS6KB2, RPS7, RPS8, RPS9, RPSA, LOC388524, LOC388654, SCDR10, TBC1D10C, TSPAN9, UBA52, UBB, UBC 7 B3GALT4(2) 46032 2 2 2 0 1 0 0 0 1 0.52 0.0011 0.035
6 OVARIAN_INFERTILITY_GENES ATM, BMPR1B, CCND2, CDK4, CDKN1B, CEBPB, DAZL, DMC1, EGR1, ESR2, FSHR, GJA4, INHA, LHCGR, MLH1, MSH5, NCOR1, NR5A1, NRIP1, PGR, PRLR, PTGER2, SMPD1, VDR, ZP2 1 MSH5(1) 20804 1 1 1 1 0 0 1 0 0 0.93 0.0032 0.085
7 HSA02010_ABC_TRANSPORTERS_GENERAL Genes involved in ABC transporters - general ABCA1, ABCA10, ABCA12, ABCA13, ABCA2, ABCA3, ABCA4, ABCA5, ABCA6, ABCA7, ABCA8, ABCA9, ABCB1, ABCB10, ABCB11, ABCB4, ABCB5, ABCB6, ABCB7, ABCB8, ABCB9, ABCC1, ABCC10, ABCC11, ABCC12, ABCC2, ABCC3, ABCC4, ABCC5, ABCC6, ABCC8, ABCC9, ABCD1, ABCD2, ABCD3, ABCD4, ABCG1, ABCG2, ABCG4, ABCG5, ABCG8, CFTR, TAP1, TAP2 1 ABCC10(1) 32872 1 1 1 0 0 0 1 0 0 0.68 0.0049 0.11
8 HSA04330_NOTCH_SIGNALING_PATHWAY Genes involved in Notch signaling pathway ADAM17, APH1A, CIR, CREBBP, CTBP1, CTBP2, DLL1, DLL3, DLL4, DTX1, DTX2, DTX3, DTX3L, DTX4, DVL1, DVL2, DVL3, EP300, GCN5L2, HDAC1, HDAC2, HES1, JAG1, JAG2, LFNG, LOC652788, MAML1, MAML2, MAML3, MFNG, NCOR2, NCSTN, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NUMB, NUMBL, PCAF, PSEN1, PSEN2, PSENEN, PTCRA, RBPJ, RBPJL, RFNG, SNW1 3 RBPJL(1) 62580 1 1 1 0 0 0 0 1 0 0.84 0.011 0.22
9 HSA00533_KERATAN_SULFATE_BIOSYNTHESIS Genes involved in keratan sulfate biosynthesis B3GNT1, B3GNT2, B3GNT7, B4GALT1, B4GALT2, B4GALT3, B4GALT4, CHST1, CHST2, CHST4, CHST6, FUT8, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4 1 B3GNT1(1) 14504 1 1 1 0 1 0 0 0 0 0.69 0.03 0.4
10 KERATAN_SULFATE_BIOSYNTHESIS B3GNT1, B4GALT1, B4GALT2, B4GALT3, B4GALT5, FUT8, SIAT4A, SIAT4B, SIAT6, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4 1 B3GNT1(1) 14504 1 1 1 0 1 0 0 0 0 0.69 0.03 0.4

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 p_ns_s p q
1 HSA00533_KERATAN_SULFATE_BIOSYNTHESIS Genes involved in keratan sulfate biosynthesis B3GNT1, B3GNT2, B3GNT7, B4GALT1, B4GALT2, B4GALT3, B4GALT4, CHST1, CHST2, CHST4, CHST6, FUT8, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4 1 B3GNT1(1) 14504 1 1 1 0 1 0 0 0 0 0.69 0.03 1
2 KERATAN_SULFATE_BIOSYNTHESIS B3GNT1, B4GALT1, B4GALT2, B4GALT3, B4GALT5, FUT8, SIAT4A, SIAT4B, SIAT6, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4 1 B3GNT1(1) 14504 1 1 1 0 1 0 0 0 0 0.69 0.03 1
3 MAPKPATHWAY The mitogen-activated protein (MAP) kinase pathway is a common signaling mechanism and has four main sub-pathways: Erk, JNK/SAPK, p53, and ERK5. ARAF1, ATF2, BRAF, CEBPA, CHUK, CREB1, DAXX, ELK1, FOS, GRB2, HRAS, IKBKB, JUN, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K11, MAP3K12, MAP3K13, MAP3K14, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K8, MAP3K9, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAP4K5, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK4, MAPK6, MAPK7, MAPK8, MAPK9, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAX, MEF2A, MEF2B, MEF2C, MEF2D, MKNK1, MKNK2, MYC, NFKB1, NFKBIA, PAK1, PAK2, PDZGEF1, RAC1, RAF1, RELA, RIPK1, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KA5, RPS6KB1, RPS6KB2, SHC1, SP1, STAT1, TGFB1, TGFB2, TGFB3, TGFBR1, TRADD, TRAF2 1 MAP4K2(2) 19852 2 2 2 0 2 0 0 0 0 0.4 0.031 1
4 STRESSPATHWAY Tumor necrosis factor receptor TNFR1 promotes apoptosis and activates the pro-inflammatory NF-kB, while TNFR2 activates stress-activated protein kinases (SAPKs). ATF1, CASP2, CHUK, CRADD, IKBKB, IKBKG, JUN, LTA, MAP2K3, MAP2K4, MAP2K6, MAP3K1, MAP3K14, MAP4K2, MAPK14, MAPK8, NFKB1, NFKBIA, RELA, RIPK1, TANK, TNF, TNFRSF1A, TRADD, TRAF2 1 MAP4K2(2) 19852 2 2 2 0 2 0 0 0 0 0.4 0.031 1
5 ST_ADRENERGIC Adrenergic receptors respond to epinephrine and norepinephrine signaling. AKT1, APC, AR, ASAH1, BF, BRAF, CAMP, CCL13, CCL15, CCL16, DAG1, EGFR, GAS, GNA11, GNA15, GNAI1, GNAQ, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, MAPK10, MAPK14, PHKA2, PIK3CA, PIK3CD, PIK3R1, PITX2, PTX1, PTX3, RAF1, SRC 1 CCL15(1) 4732 1 1 1 0 1 0 0 0 0 0.61 0.051 1
6 HSA01030_GLYCAN_STRUCTURES_BIOSYNTHESIS_1 Genes involved in glycan structures - biosynthesis 1 A4GNT, ALG1, ALG10, ALG10B, ALG11, ALG12, ALG13, ALG14, ALG2, ALG3, ALG6, ALG8, ALG9, B3GALT6, B3GNT1, B3GNT2, B3GNT6, B3GNT7, B4GALT1, B4GALT2, B4GALT3, B4GALT4, B4GALT5, B4GALT7, C1GALT1, C1GALT1C1, ChGn, CHPF, CHST1, CHST11, CHST12, CHST13, CHST14, CHST2, CHST3, CHST4, CHST6, CHST7, CHSY-2, CHSY1, CSGlcA-T, DAD1, DDOST, DPAGT1, EXT1, EXT2, EXTL1, EXTL2, EXTL3, FUT11, FUT8, GALNAC4S-6ST, GALNACT-2, GALNT1, GALNT10, GALNT11, GALNT12, GALNT13, GALNT14, GALNT17, GALNT2, GALNT3, GALNT4, GALNT5, GALNT6, GALNT7, GALNT8, GALNT9, GALNTL1, GALNTL2, GALNTL4, GALNTL5, GANAB, GCNT1, GCNT3, GCNT4, GCS1, HS2ST1, HS3ST1, HS3ST2, HS3ST3A1, HS3ST3B1, HS3ST5, HS6ST1, HS6ST2, HS6ST3, LOC728969, MAN1A1, MAN1A2, MAN1B1, MAN1C1, MAN2A1, MGAT1, MGAT2, MGAT3, MGAT4A, MGAT4B, MGAT5, MGAT5B, NDST1, NDST2, NDST3, NDST4, OGT, RPN1, RPN2, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4, ST6GAL1, ST6GALNAC1, STT3B, UST, WBSCR17, XYLT1, XYLT2 2 B3GNT1(1) 22008 1 1 1 0 1 0 0 0 0 0.71 0.062 1
7 GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM ACO1, ACO2, CS, GRHPR, HAO1, HAO2, HYI, MDH1, MDH2, MTHFD1, MTHFD1L, MTHFD2 1 GRHPR(1) 7924 1 1 1 0 1 0 0 0 0 0.61 0.11 1
8 HSA00620_PYRUVATE_METABOLISM Genes involved in pyruvate metabolism ACACA, ACACB, ACAT1, ACAT2, ACOT12, ACSS1, ACSS2, ACYP1, ACYP2, AKR1B1, ALDH1A3, ALDH1B1, ALDH2, ALDH3A1, ALDH3A2, ALDH7A1, ALDH9A1, DLAT, DLD, GLO1, GRHPR, HAGH, HAGHL, LDHA, LDHAL6A, LDHAL6B, LDHB, LDHC, LDHD, MDH1, MDH2, ME1, ME2, ME3, PC, PCK1, PCK2, PDHA1, PDHA2, PDHB, PKLR, PKM2 1 GRHPR(1) 7924 1 1 1 0 1 0 0 0 0 0.61 0.11 1
9 HSA00630_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM Genes involved in glyoxylate and dicarboxylate metabolism ACO1, ACO2, AFMID, CS, GRHPR, HAO1, HAO2, HYI, LOC441996, MDH1, MDH2, MTHFD1, MTHFD1L, MTHFD2 1 GRHPR(1) 7924 1 1 1 0 1 0 0 0 0 0.61 0.11 1
10 PYRUVATE_METABOLISM ACACA, ACAS2, ACAS2L, ACAT1, ACAT2, ACYP1, ACYP2, ADH5, AKR1B1, ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, ALDH2, ALDH3A1, ALDH3A2, ALDH9A1, CACH_1, DLAT, DLD, GLO1, GRHPR, HAGH, HAGHL, LDHA, LDHB, LDHC, LDHD, MDH1, MDH2, ME1, ME2, ME3, PC, PCK1, PDHA1, PDHA2, PDHB, PKLR, PKM2 1 GRHPR(1) 7924 1 1 1 0 1 0 0 0 0 0.61 0.11 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