Kidney Renal Clear Cell 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 v2.0 was used to generate the results found in this report.

Working with individual set: KIRC.

Number of patients in set: 293

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): 53

Mutations seen in COSMIC: 344

Significantly mutated genes in COSMIC territory: 85

Genes with clustered mutations (&le 3 aa apart): 203

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
Frame_Shift_Del 533
Frame_Shift_Ins 143
In_Frame_Del 135
In_Frame_Ins 44
Missense_Mutation 16015
Nonsense_Mutation 1090
Nonstop_Mutation 21
Silent 6671
Splice_Site 529
Translation_Start_Site 42
Total 25223
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 1765 484078369 3.6e-06 3.6 1.7 2.1
*ApG->G 1224 1342141277 9.1e-07 0.91 0.43 2.1
*Np(A/C/T)->transit 5291 6921093572 7.6e-07 0.76 0.36 2
transver 7772 8747313218 8.9e-07 0.89 0.42 5
indel+null 2491 8747313218 2.8e-07 0.28 0.13 NaN
double_null 9 8747313218 1e-09 0.001 0.00049 NaN
Total 18552 8747313218 2.1e-06 2.1 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).

Figure 1. 

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

Figure 2. 

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

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 53. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p_classic p_ns_s p_ks p_cons p_joint p q
1 VHL von Hippel-Lindau tumor suppressor 123072 149 145 95 4 2 14 15 31 87 0 <1.00e-15 4.8e-09 0.021 0.00038 0.00033 <0.00 <0.00
2 PBRM1 polybromo 1 1470408 112 110 109 2 0 1 6 15 90 0 <1.00e-15 0.000015 0.038 0.029 0.0096 <3.33e-16 <2.59e-12
3 KDM5C 1253863 19 18 19 1 0 0 2 5 12 0 1.22e-15 0.1 0.0079 0.31 0.02 9.99e-16 2.59e-12
4 RRAD Ras-related associated with diabetes 202274 4 4 1 0 0 0 0 4 0 0 0.00026 0.43 4e-07 0.001 0 <1.00e-15 <2.59e-12
5 SV2C synaptic vesicle glycoprotein 2C 653960 3 3 3 0 0 1 1 0 1 0 0.080 0.3 0.14 0.0017 0 <1.00e-15 <2.59e-12
6 TOR1A torsin family 1, member A (torsin A) 280456 3 3 1 0 0 0 3 0 0 0 0.011 0.27 4.8e-06 0.0012 0 <1.00e-15 <2.59e-12
7 TPST1 tyrosylprotein sulfotransferase 1 330797 2 2 2 0 0 0 0 1 1 0 0.031 0.74 0.08 0.00085 0 <1.00e-15 <2.59e-12
8 SETD2 SET domain containing 2 1866089 36 35 36 1 2 2 2 7 22 1 <1.00e-15 0.0045 0.36 0.044 0.1 <3.89e-15 <8.80e-12
9 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 365609 16 15 16 2 0 1 5 3 7 0 1.11e-15 0.11 0.11 0.91 0.18 7.55e-15 1.52e-11
10 BAP1 BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) 589189 29 28 26 1 0 2 6 5 15 1 2.33e-15 0.0024 0.13 0.38 0.18 1.54e-14 2.80e-11
11 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 963086 14 14 13 1 0 2 6 5 1 0 4.46e-10 0.061 0.0014 0.21 0.0014 1.86e-11 3.07e-08
12 MTOR 2294678 26 24 22 2 1 2 4 19 0 0 8.61e-11 0.043 0.0045 0.45 0.0088 2.20e-11 3.31e-08
13 STAG3L2 stromal antigen 3-like 2 83876 6 6 2 0 0 0 0 0 6 0 3.49e-10 1 0.0051 0.16 0.0068 6.55e-11 9.13e-08
14 EBPL emopamil binding protein-like 139558 7 6 3 0 1 0 0 6 0 0 5.51e-08 0.2 0.0019 1 0.004 5.16e-09 6.68e-06
15 KANK3 KN motif and ankyrin repeat domains 3 301372 6 6 2 0 0 0 0 0 6 0 5.35e-09 1 0.043 0.64 0.098 1.17e-08 0.000014
16 NUDT11 nudix (nucleoside diphosphate linked moiety X)-type motif 11 127356 3 3 1 0 0 0 0 0 3 0 0.00021 1 3.8e-06 0.96 6.2e-06 2.81e-08 0.000032
17 ZCCHC3 zinc finger, CCHC domain containing 3 208403 3 3 1 0 0 0 0 0 3 0 0.00022 1 2.2e-06 1 0.000012 5.70e-08 0.000061
18 FAM174B 72325 3 3 1 0 0 0 0 0 3 0 0.00021 1 0.000018 0.97 2e-05 8.42e-08 0.000085
19 ANKRD36 ankyrin repeat domain 36 752950 11 10 6 2 1 0 0 9 1 0 1.61e-06 0.52 0.0011 0.83 0.003 9.84e-08 0.000094
20 TSPAN19 tetraspanin 19 144817 4 4 4 0 0 0 1 1 2 0 6.50e-07 0.6 0.016 0.25 0.033 4.01e-07 0.00036
21 DACH2 dachshund homolog 2 (Drosophila) 506733 7 7 3 0 0 0 0 7 0 0 9.33e-06 0.27 0.0014 0.2 0.0032 5.53e-07 0.00048
22 KRTAP1-1 keratin associated protein 1-1 157631 3 3 1 0 0 0 0 3 0 0 0.0024 0.62 6e-06 0.8 0.000021 9.02e-07 0.00072
23 UQCRFS1 ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 180195 3 3 1 0 0 0 3 0 0 0 0.0042 0.31 8.8e-06 1 0.000012 9.19e-07 0.00072
24 CR1 complement component (3b/4b) receptor 1 (Knops blood group) 1444581 11 11 8 0 1 0 0 4 6 0 2.78e-06 0.095 0.073 0.059 0.039 1.87e-06 0.0014
25 VCX2 variable charge, X-linked 2 46999 4 3 4 0 0 1 0 1 2 0 9.26e-06 0.67 0.0071 0.82 0.021 3.16e-06 0.0023
26 KRT1 keratin 1 (epidermolytic hyperkeratosis) 500192 5 5 2 0 1 0 0 0 4 0 0.00012 0.72 0.0008 0.98 0.0026 4.83e-06 0.0034
27 ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 1157641 9 8 9 0 0 0 4 3 2 0 0.00011 0.084 0.0039 0.15 0.0047 7.75e-06 0.0052
28 MADCAM1 mucosal vascular addressin cell adhesion molecule 1 158333 4 4 2 0 0 0 0 4 0 0 0.00041 0.35 0.00028 0.99 0.002 0.000012 0.0081
29 POLDIP2 polymerase (DNA-directed), delta interacting protein 2 257573 4 4 3 0 0 0 1 0 3 0 0.000014 0.66 0.073 0.99 0.11 0.000021 0.013
30 PCDHGA8 protocadherin gamma subfamily A, 8 835388 4 4 2 1 1 0 0 3 0 0 0.059 0.61 0.000026 0.084 3e-05 0.000025 0.015
31 WDR52 WD repeat domain 52 887493 10 9 6 1 1 1 0 8 0 0 0.000012 0.35 1 0.077 0.16 0.000027 0.016
32 DNAH9 dynein, axonemal, heavy chain 9 3901910 19 18 19 0 2 1 4 9 3 0 4.77e-06 0.0079 0.26 0.55 0.42 0.000028 0.016
33 TPTE2 transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 483148 8 7 8 1 1 0 0 6 1 0 3.24e-06 0.49 0.44 0.57 0.63 0.000029 0.016
34 CCNB2 cyclin B2 353170 5 5 5 0 0 0 2 1 2 0 0.000015 0.22 0.23 0.15 0.15 0.000031 0.016
35 OR5H1 olfactory receptor, family 5, subfamily H, member 1 276592 5 4 3 1 0 2 1 2 0 0 0.00070 0.38 0.00091 0.51 0.0032 0.000031 0.016

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: *CpG->T .

n2 - number of nonsilent mutations of type: *ApG->G .

n3 - number of nonsilent mutations of type: *Np(A/C/T)->transit .

n4 - number of nonsilent mutations of type: transver .

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: 85. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 VHL von Hippel-Lindau tumor suppressor 149 537 149 157341 3739 0 0
2 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 14 184 12 53912 3014 0 0
3 TP53 tumor protein p53 13 308 12 90244 1649 0 0
4 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 16 728 16 213304 120 0 0
5 CHEK2 CHK2 checkpoint homolog (S. pombe) 7 2 4 586 4 7.6e-14 6.8e-11
6 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 11 285 6 83505 8 3.7e-08 0.000026
7 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 4 51 4 14943 14813 4.1e-08 0.000026
8 ARHGAP20 Rho GTPase activating protein 20 4 2 2 586 2 7.7e-07 0.00044
9 NF2 neurofibromin 2 (merlin) 6 543 6 159099 36 1.5e-06 0.00077
10 SBNO1 strawberry notch homolog 1 (Drosophila) 3 4 2 1172 4 3.1e-06 0.0014

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
8819 VHL von Hippel-Lindau tumor suppressor 149 0 134 429 1068 134 429 1068
5061 MUC4 mucin 4, cell surface associated 108 0 41 68 169 41 68 169
415 ANKRD36 ankyrin repeat domain 36 11 0 15 15 16 15 15 16
4764 MED12L mediator complex subunit 12-like 9 0 15 15 15 15 15 15
2477 EBPL emopamil binding protein-like 7 0 10 10 15 10 10 15
2116 DACH2 dachshund homolog 2 (Drosophila) 7 0 10 10 10 10 10 10
8893 WDR52 WD repeat domain 52 10 0 10 10 10 10 10 10
5195 NBPF10 neuroblastoma breakpoint family, member 10 26 0 7 11 11 7 11 11
6285 POTEC 10 0 7 7 8 7 7 8
751 BAP1 BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) 29 0 6 11 22 6 11 22

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 n6 p_ns_s p q
1 HSA04120_UBIQUITIN_MEDIATED_PROTEOLYSIS Genes involved in ubiquitin mediated proteolysis ANAPC1, ANAPC10, ANAPC11, ANAPC2, ANAPC4, ANAPC5, ANAPC7, BTRC, CDC16, CDC20, CDC23, CDC26, CDC27, CUL1, CUL2, CUL3, FBXW11, FBXW7, FZR1, ITCH, LOC728919, RBX1, SKP1, SKP2, SMURF1, SMURF2, TCEB1, TCEB2, UBA1, UBE2C, UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE2E1, UBE2E2, UBE2E3, VHL, WWP1, WWP2 39 ANAPC1(4), ANAPC11(1), ANAPC2(1), ANAPC4(2), ANAPC5(2), ANAPC7(1), CDC16(2), CDC20(1), CDC23(2), CDC27(5), CUL1(3), CUL2(1), CUL3(2), FBXW11(1), FBXW7(4), FZR1(1), SKP2(1), SMURF1(1), SMURF2(2), TCEB1(2), UBA1(1), UBE2D1(2), UBE2D2(1), UBE2D3(1), UBE2E2(1), VHL(149), WWP1(1), WWP2(1) 17820449 196 165 142 23 4 19 31 46 96 0 0.00022 <1.00e-15 <2.05e-13
2 VEGFPATHWAY Vascular endothelial growth factor (VEGF) is upregulated by hypoxic conditions and promotes normal blood vessel formation and angiogenesis related to tumor growth or cardiac disease. ARNT, EIF1, EIF1A, EIF2B1, EIF2B2, EIF2B3, EIF2B4, EIF2B5, EIF2S1, EIF2S2, EIF2S3, ELAVL1, FLT1, FLT4, HIF1A, HRAS, KDR, NOS3, PIK3CA, PIK3R1, PLCG1, PRKCA, PRKCB1, PTK2, PXN, SHC1, VEGF, VHL 25 EIF1(1), EIF2B1(2), EIF2B2(1), EIF2B5(2), EIF2S1(1), EIF2S2(1), ELAVL1(1), FLT1(3), FLT4(4), HIF1A(3), KDR(5), NOS3(1), PIK3CA(14), PIK3R1(1), PTK2(1), PXN(2), SHC1(2), VHL(149) 14983008 194 165 139 19 7 18 26 51 92 0 0.000033 <1.00e-15 <2.05e-13
3 HIFPATHWAY Under normal conditions, hypoxia inducible factor HIF-1 is degraded; under hypoxic conditions, it activates transcription of genes controlled by hpoxic response elements (HREs). ARNT, ASPH, COPS5, CREB1, EDN1, EP300, EPO, HIF1A, HSPCA, JUN, LDHA, NOS3, P4HB, VEGF, VHL 13 ASPH(1), EP300(6), HIF1A(3), JUN(1), NOS3(1), VHL(149) 7504580 161 150 107 10 2 15 18 37 89 0 2.9e-06 <1.00e-15 <2.05e-13
4 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), AKT2(2), AKT3(2), MAPK1(1), MAPK3(1), PDK1(1), PIK3CA(14), PIK3CD(1), PTEN(16), PTK2B(2), RBL2(3), SHC1(2), SOS1(4) 8973555 50 45 49 5 3 5 19 14 9 0 0.0012 3.27e-06 0.00050
5 SA_TRKA_RECEPTOR The TrkA receptor binds nerve growth factor to activate MAP kinase pathways and promote cell growth. AKT1, AKT2, AKT3, ARHA, CDKN1A, ELK1, GRB2, HRAS, MAP2K1, MAP2K2, NGFB, NGFR, NTRK1, PIK3CA, PIK3CD, SHC1, SOS1 15 AKT1(1), AKT2(2), AKT3(2), CDKN1A(1), ELK1(1), MAP2K1(1), NGFR(1), NTRK1(2), PIK3CA(14), PIK3CD(1), SHC1(2), SOS1(4) 7184719 32 31 31 2 2 3 13 13 1 0 0.0029 0.00014 0.017
6 HSA00950_ALKALOID_BIOSYNTHESIS_I Genes involved in alkaloid biosynthesis I DDC, GOT1, GOT2, TAT, TYR 5 DDC(3), GOT1(2), GOT2(3), TAT(1), TYR(1) 2063429 10 10 10 1 1 0 5 1 3 0 0.21 0.00085 0.088
7 BLYMPHOCYTEPATHWAY B cells express the major histocompatibility complex (class II MHC), immunoglobulins, adhesion proteins, and other factors on their cell surface. CD80, CR1, CR2, FCGR2B, HLA-DRA, HLA-DRB1, ICAM1, ITGAL, ITGB2, PTPRC, TNFRSF5 10 CD80(1), CR1(11), CR2(1), HLA-DRA(1), ITGAL(3), ITGB2(1), PTPRC(6) 6737962 24 23 21 2 2 0 2 12 8 0 0.08 0.0025 0.22
8 CYSTEINE_METABOLISM CARS, CTH, GOT1, GOT2, LDHA, LDHB, LDHC, MPST 8 CARS(2), CTH(1), GOT1(2), GOT2(3), LDHB(1), LDHC(2), MPST(2) 3003190 13 13 13 2 2 0 4 3 4 0 0.33 0.0049 0.38
9 HSA00272_CYSTEINE_METABOLISM Genes involved in cysteine metabolism CARS, CARS2, CDO1, CTH, GOT1, GOT2, LDHA, LDHAL6A, LDHAL6B, LDHB, LDHC, MPST, SDS, SULT1B1, SULT1C2, SULT1C4, SULT4A1 17 CARS(2), CARS2(3), CTH(1), GOT1(2), GOT2(3), LDHAL6B(1), LDHB(1), LDHC(2), MPST(2), SULT1C2(1), SULT4A1(1) 5521164 19 19 19 2 2 1 5 5 6 0 0.14 0.0067 0.41
10 ACETAMINOPHENPATHWAY Acetaminophen selectively inhibits Cox-3, which is localized to the brain, and yields the toxic metabolite NAPQI when processed by CAR in the liver. CYP1A2, CYP2E1, CYP3A, NR1I3, PTGS1, PTGS2 5 CYP1A2(2), CYP2E1(2), NR1I3(1), PTGS2(4) 2332448 9 9 9 1 1 0 1 5 2 0 0.35 0.0072 0.41

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 HSA00950_ALKALOID_BIOSYNTHESIS_I Genes involved in alkaloid biosynthesis I DDC, GOT1, GOT2, TAT, TYR 5 DDC(3), GOT1(2), GOT2(3), TAT(1), TYR(1) 2063429 10 10 10 1 1 0 5 1 3 0 0.21 0.00085 0.53
2 CYSTEINE_METABOLISM CARS, CTH, GOT1, GOT2, LDHA, LDHB, LDHC, MPST 8 CARS(2), CTH(1), GOT1(2), GOT2(3), LDHB(1), LDHC(2), MPST(2) 3003190 13 13 13 2 2 0 4 3 4 0 0.33 0.0049 0.76
3 HSA00272_CYSTEINE_METABOLISM Genes involved in cysteine metabolism CARS, CARS2, CDO1, CTH, GOT1, GOT2, LDHA, LDHAL6A, LDHAL6B, LDHB, LDHC, MPST, SDS, SULT1B1, SULT1C2, SULT1C4, SULT4A1 17 CARS(2), CARS2(3), CTH(1), GOT1(2), GOT2(3), LDHAL6B(1), LDHB(1), LDHC(2), MPST(2), SULT1C2(1), SULT4A1(1) 5521164 19 19 19 2 2 1 5 5 6 0 0.14 0.0067 0.76
4 ACETAMINOPHENPATHWAY Acetaminophen selectively inhibits Cox-3, which is localized to the brain, and yields the toxic metabolite NAPQI when processed by CAR in the liver. CYP1A2, CYP2E1, CYP3A, NR1I3, PTGS1, PTGS2 5 CYP1A2(2), CYP2E1(2), NR1I3(1), PTGS2(4) 2332448 9 9 9 1 1 0 1 5 2 0 0.35 0.0072 0.76
5 HSA04140_REGULATION_OF_AUTOPHAGY Genes involved in regulation of autophagy ATG12, ATG3, ATG5, ATG7, BECN1, GABARAP, GABARAPL1, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNG, INS, LOC441925, PIK3C3, PIK3R4, PRKAA1, PRKAA2, ULK1, ULK2, ULK3 29 ATG12(1), ATG3(3), ATG7(4), BECN1(1), IFNA1(1), IFNA14(1), IFNA16(1), IFNA21(1), IFNA5(1), IFNA7(1), IFNA8(1), PIK3C3(4), PIK3R4(7), PRKAA1(1), ULK1(1), ULK2(2), ULK3(2) 9349525 33 32 33 4 3 1 5 17 7 0 0.077 0.0073 0.76
6 UREACYCLEPATHWAY Ammonia released from amino acid deamination is used to produce carbamoyl phosphate, which is used to convert ornithine to citrulline, from which urea is eventually formed. ARG1, ASL, ASS, CPS1, GLS, GLUD1, GOT1 6 ARG1(1), CPS1(5), GLS(1), GLUD1(2), GOT1(2) 3418789 11 11 11 1 0 0 6 2 3 0 0.16 0.008 0.76
7 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(2), GOT2(3), TAT(1) 1153972 6 6 6 1 1 0 3 0 2 0 0.42 0.0086 0.76
8 HSA00400_PHENYLALANINE_TYROSINE_AND_TRYPTOPHAN_BIOSYNTHESIS Genes involved in phenylalanine, tyrosine and tryptophan biosynthesis FARS2, FARSA, FARSB, GOT1, GOT2, PAH, TAT, YARS, YARS2 9 FARSA(1), FARSB(1), GOT1(2), GOT2(3), PAH(3), TAT(1), YARS(1) 3828103 12 12 12 1 1 0 3 5 3 0 0.18 0.013 1
9 PHENYLALANINE_TYROSINE_AND_TRYPTOPHAN_BIOSYNTHESIS ENO1, ENO2, ENO3, FARS2, FARSLB, GOT1, GOT2, PAH, TAT, YARS 9 ENO1(1), GOT1(2), GOT2(3), PAH(3), TAT(1), YARS(1) 3637448 11 11 11 1 1 0 3 4 3 0 0.21 0.02 1
10 HSA00130_UBIQUINONE_BIOSYNTHESIS Genes involved in ubiquinone biosynthesis COQ2, COQ3, COQ5, COQ6, COQ7, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, NDUFA12, NDUFA13, NDUFB11 8 COQ5(2), COQ6(1), NDUFA13(3), NDUFB11(1) 1778759 7 7 7 0 2 0 1 3 1 0 0.15 0.024 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)