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 v1.5 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): 102

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

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

Significantly mutated genesets: 44

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 3
In_Frame_Del 2
In_Frame_Ins 1
Missense_Mutation 203
Nonsense_Mutation 10
Silent 97
Splice_Site 2
Translation_Start_Site 2
Total 320
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 22 5077983 4.3e-06 4.3 1.1 1.8
*ApG->G 15 8662545 1.7e-06 1.7 0.44 2.6
*Np(A/C/T)->transit 63 43398867 1.5e-06 1.5 0.37 1.8
transver 105 57139395 1.8e-06 1.8 0.47 4.4
indel+null 18 57139395 3.2e-07 0.32 0.081 NaN
Total 223 57139395 3.9e-06 3.9 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: 102. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 p_ns_s p q
1 PCDHA10 protocadherin alpha 10 585707 5 5 5 0 1 0 2 2 0 0.15 1.5e-07 0.000042
2 CT47B1 93467 3 3 3 1 0 0 1 2 0 0.8 2.2e-07 0.000042
3 WDR46 WD repeat domain 46 146500 3 3 3 0 0 0 2 1 0 0.33 7.6e-07 0.000098
4 PCDHGA1 protocadherin gamma subfamily A, 1 645772 4 4 4 1 0 0 0 4 0 0.67 1.4e-06 0.00014
5 USP48 ubiquitin specific peptidase 48 292121 3 3 3 0 0 0 1 2 0 0.54 6.2e-06 0.00048
6 TNFSF14 tumor necrosis factor (ligand) superfamily, member 14 68855 2 2 2 0 0 0 0 2 0 0.61 0.000012 0.00066
7 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 343982 3 3 3 1 0 0 1 2 0 0.63 0.000012 0.00066
8 HOXC6 homeobox C6 70027 2 2 2 0 0 0 2 0 0 0.41 0.000017 0.00077
9 LACRT lacritin 34281 2 2 2 0 0 0 1 0 1 0.58 0.000018 0.00077
10 PCDHGA8 protocadherin gamma subfamily A, 8 565197 4 4 2 1 1 0 0 3 0 0.6 0.000021 0.00083
11 KRTAP4-8 keratin associated protein 4-8 55084 2 2 2 1 0 0 0 1 1 0.84 3e-05 0.001
12 CRYGB crystallin, gamma B 50396 2 2 2 0 0 0 0 2 0 0.76 0.000031 0.001
13 KHK ketohexokinase (fructokinase) 89951 3 3 3 1 0 1 1 1 0 0.73 0.000042 0.0012
14 ZNF200 zinc finger protein 200 96397 2 2 2 0 0 0 0 2 0 0.75 0.000044 0.0012
15 UBE2Q1 ubiquitin-conjugating enzyme E2Q (putative) 1 97862 2 2 2 0 0 0 0 1 1 0.48 0.000066 0.0017
16 CLUAP1 clusterin associated protein 1 108703 2 2 2 0 0 0 0 2 0 0.8 0.000075 0.0018
17 C2orf62 chromosome 2 open reading frame 62 108410 2 2 2 0 0 0 0 2 0 0.71 0.000077 0.0018
18 PARS2 prolyl-tRNA synthetase 2, mitochondrial (putative) 109582 2 2 2 0 0 0 1 1 0 0.51 0.000086 0.0018
19 KIAA1147 KIAA1147 106066 2 2 2 0 0 0 1 1 0 0.55 0.000087 0.0018
20 SLC35B2 solute carrier family 35, member B2 126576 2 2 2 1 0 0 2 0 0 0.71 0.00015 0.0028
21 FCRL1 Fc receptor-like 1 161736 2 2 2 0 0 0 1 1 0 0.53 0.00035 0.0065
22 ZNF20 zinc finger protein 20 173163 2 2 2 0 0 0 0 1 1 0.75 0.00037 0.0065
23 LIMA1 LIM domain and actin binding 1 180195 2 2 2 1 0 0 0 1 1 0.81 0.00041 0.0069
24 MAML1 mastermind-like 1 (Drosophila) 236158 2 2 2 1 0 0 0 2 0 0.92 0.00044 0.0071
25 TMEM102 transmembrane protein 102 160857 2 2 2 0 0 0 1 0 1 0.64 0.00047 0.0071
26 ZNF214 zinc finger protein 214 208909 2 2 2 0 0 0 0 2 0 0.77 0.00047 0.0071
27 PCDHB9 protocadherin beta 9 186348 2 2 2 0 0 0 1 1 0 0.52 0.00056 0.0078
28 BACH2 BTB and CNC homology 1, basic leucine zipper transcription factor 2 201291 2 2 2 1 0 0 1 1 0 0.85 0.00057 0.0078
29 ZDHHC8 zinc finger, DHHC-type containing 8 225024 2 2 2 1 0 0 0 2 0 0.87 0.00059 0.0078
30 KLHL17 kelch-like 17 (Drosophila) 193380 2 2 2 0 0 0 1 1 0 0.5 0.0006 0.0078
31 KRT36 keratin 36 199826 2 2 2 0 0 0 0 2 0 0.72 0.00062 0.0078
32 SLC12A9 solute carrier family 12 (potassium/chloride transporters), member 9 261063 2 2 2 0 0 0 0 2 0 0.59 0.00077 0.0093
33 ZNF284 zinc finger protein 284 287433 2 2 2 0 0 0 1 0 1 0.43 0.00094 0.011
34 SEMA4G sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G 303255 2 2 2 0 0 0 1 1 0 0.52 0.0013 0.015
35 PCDHB10 protocadherin beta 10 194259 4 3 4 1 2 0 0 1 1 0.61 0.0014 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: 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 3 0 0 0 0 1 1
2 BACH2 BTB and CNC homology 1, basic leucine zipper transcription factor 2 2 0 0 0 0 1 1
3 BSN bassoon (presynaptic cytomatrix protein) 3 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 1 0 0 0 0 1 1
7 GNAT1 guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1 1 0 0 0 0 1 1
8 KLC4 kinesin light chain 4 0 0 0 0 0 1 1
9 LACRT lacritin 2 0 0 0 0 1 1
10 MSH5 mutS homolog 5 (E. coli) 0 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
94 PCDHGA8 protocadherin gamma subfamily A, 8 4 0 3 3
84 PCDHB10 protocadherin beta 10 4 1 1 1
55 KHK ketohexokinase (fructokinase) 3 2 1 1
58 KRT36 keratin 36 2 7 0 1
133 USP48 ubiquitin specific peptidase 48 3 7 0 1
82 PCDHA6 protocadherin alpha 6 4 13 0 0
9 BSN bassoon (presynaptic cytomatrix protein) 3 22 0 0
86 PCDHB7 protocadherin beta 7 4 22 0 0
144 ZNF284 zinc finger protein 284 2 31 0 0
60 LACRT lacritin 2 32 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: 44. 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 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(3) 343982 3 3 3 1 0 0 1 2 0 0.63 0.000012 0.0019
2 FEEDERPATHWAY Sugars such as mannose, galactose, and fructose are enzymatically converted to glucose via feeder pathways that lead to glycolysis. HK1, KHK, LCT, MPI, PGM1, PYGL, PYGM, TPI1, TREH 1 KHK(3) 89951 3 3 3 1 0 1 1 1 0 0.73 0.000042 0.002
3 FRUCTOSE_AND_MANNOSE_METABOLISM AKR1B1, ALDOA, ALDOB, ALDOC, FBP1, FBP2, FPGT, GCK, GMDS, GMPPA, GMPPB, HK1, HK2, HK3, KHK, MPI, PFKFB1, PFKFB3, PFKFB4, PFKM, PFKP, PMM1, PMM2, SORD, TPI1 1 KHK(3) 89951 3 3 3 1 0 1 1 1 0 0.73 0.000042 0.002
4 HSA04060_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION Genes involved in cytokine-cytokine receptor interaction ACVR1, ACVR1B, ACVR2A, ACVR2B, AMH, AMHR2, BMP2, BMP7, BMPR1A, BMPR1B, BMPR2, CCL1, CCL11, CCL13, CCL14, CCL15, CCL16, CCL17, CCL18, CCL19, CCL2, CCL20, CCL21, CCL22, CCL23, CCL24, CCL25, CCL26, CCL27, CCL28, CCL3, CCL4, CCL5, CCL7, CCL8, CCR1, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CD27, CD40, CD40LG, CD70, CLCF1, CNTF, CNTFR, CRLF2, CSF1, CSF1R, CSF2, CSF2RA, CSF2RB, CSF3, CSF3R, CTF1, CX3CL1, CX3CR1, CXCL1, CXCL10, CXCL11, CXCL12, CXCL13, CXCL14, CXCL16, CXCL2, CXCL3, CXCL5, CXCL6, CXCL9, CXCR3, CXCR4, CXCR6, EDA, EDA2R, EDAR, EGF, EGFR, EPO, EPOR, FAS, FASLG, FLJ78302, FLT1, FLT3, FLT3LG, FLT4, GDF5, GH1, GH2, GHR, HGF, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNE1, IFNG, IFNGR1, IFNGR2, IFNK, IFNW1, IL10, IL10RA, IL10RB, IL11, IL11RA, IL12A, IL12B, IL12RB1, IL12RB2, IL13, IL13RA1, IL15, IL15RA, IL17A, IL17B, IL17RA, IL17RB, IL18, IL18R1, IL18RAP, IL19, IL1A, IL1B, IL1R1, IL1R2, IL1RAP, IL2, IL20, IL20RA, IL21, IL21R, IL22, IL22RA1, IL22RA2, IL23A, IL23R, IL24, IL25, IL26, IL28A, IL28B, IL28RA, IL29, IL2RA, IL2RB, IL2RG, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL6ST, IL7, IL7R, IL8, IL8RA, IL8RB, IL9, IL9R, INHBA, INHBB, INHBC, INHBE, KDR, KIT, KITLG, LEP, LEPR, LIF, LIFR, LOC728045, LTA, LTB, LTBR, MET, MPL, NGFR, OSM, OSMR, PDGFB, PDGFC, PDGFRA, PDGFRB, PF4, PF4V1, PLEKHO2, PPBP, PRL, PRLR, RELT, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF11A, TNFRSF11B, TNFRSF12A, TNFRSF13B, TNFRSF13C, TNFRSF14, TNFRSF17, TNFRSF18, TNFRSF19, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF4, TNFRSF6B, TNFRSF8, TNFRSF9, TNFSF10, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF15, TNFSF18, TNFSF4, TNFSF8, TNFSF9, TPO, TSLP, VEGFA, VEGFB, VEGFC, XCL1, XCL2, XCR1 8 CCL2(1), TNFSF14(2) 458252 3 3 3 0 0 0 0 3 0 0.55 0.000051 0.002
5 HSA00970_AMINOACYL_TRNA_BIOSYNTHESIS Genes involved in aminoacyl-tRNA biosynthesis AARS, AARS2, CARS, CARS2, DARS, DARS2, EARS2, EPRS, FARS2, FARSA, FARSB, GARS, HARS, HARS2, IARS, IARS2, KARS, LARS, LARS2, MARS, MARS2, MTFMT, NARS, NARS2, PARS2, QARS, RARS, RARS2, SARS, SARS2, TARS, TARS2, VARS, VARS2, WARS, WARS2, YARS, YARS2 2 PARS2(2), QARS(1) 477297 3 3 3 1 0 0 2 1 0 0.62 0.000076 0.0023
6 HSA00330_ARGININE_AND_PROLINE_METABOLISM Genes involved in arginine and proline metabolism ALDH4A1, ARG1, ARG2, ASL, ASS1, CKB, CKM, CKMT1A, CKMT1B, CKMT2, CPS1, DAO, EPRS, GAMT, GATM, GLUD1, GLUD2, GOT1, GOT2, LAP3, NOS1, NOS2A, NOS3, OAT, OTC, P4HA1, P4HA2, P4HA3, PARS2, PRODH, PYCR1, PYCR2, PYCRL, RARS, RARS2 1 PARS2(2) 109582 2 2 2 0 0 0 1 1 0 0.51 0.000086 0.0023
7 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 MAML1(2), RBPJL(1) 654855 3 3 3 1 0 0 1 2 0 0.79 0.00027 0.006
8 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(1), B3GNT1(1), PIGO(1) 864057 3 3 3 1 0 0 1 2 0 0.68 0.0007 0.014
9 HSA00920_SULFUR_METABOLISM Genes involved in sulfur metabolism BPNT1, CHST11, CHST12, CHST13, PAPSS1, PAPSS2, SULT1A1, SULT1A2, SULT1A3, SULT1A4, SULT1E1, SULT2A1, SULT2B1, SUOX 1 SUOX(2) 135952 2 2 2 0 0 1 1 0 0 0.38 0.0022 0.035
10 SULFUR_METABOLISM BPNT1, PAPSS1, PAPSS2, SULT1A2, SULT1A3, SULT1A3, SULT1A4, SULT1E1, SULT2A1, SUOX 1 SUOX(2) 135952 2 2 2 0 0 1 1 0 0 0.38 0.0022 0.035

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) 151774 1 1 1 0 0 0 1 0 0 0.59 0.027 0.68
2 KERATAN_SULFATE_BIOSYNTHESIS B3GNT1, B4GALT1, B4GALT2, B4GALT3, B4GALT5, FUT8, SIAT4A, SIAT4B, SIAT6, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4 1 B3GNT1(1) 151774 1 1 1 0 0 0 1 0 0 0.59 0.027 0.68
3 HISTONE_METHYLTRANSFERASE Genes with HMT activity AOF2, KDM6A, ASH1L, ASH2L, C17orf79, CARM1, CTCFL, DOT1L, EED, EHMT1, EHMT2, EZH1, EZH2, FBXL10, FBXL11, FBXO11, HCFC1, HSF4, JMJD1A, JMJD1B, JMJD2A, JMJD2B, JMJD2C, JMJD2D, JMJD3, JMJD4, JMJD6, MEN1, MLL, MLL2, MLL3, MLL4, MLL5, NSD1, OGT, PAXIP1, PPP1CA, PPP1CB, PPP1CC, PRDM2, PRDM6, PRDM7, PRDM9, PRMT1, PRMT5, PRMT6, PRMT7, PRMT8, RBBP5, SATB1, SETD1A, SETD1B, SETD2, SETD7, SETD8, SETDB1, SETDB2, SETMAR, SMYD3, STK38, SUV39H1, SUV39H2, SUV420H1, SUV420H2, SUZ12, WHSC1, WHSC1L1 1 EHMT2(2) 293879 2 2 2 0 1 1 0 0 0 0.52 0.027 0.68
4 LYSINE_DEGRADATION AADAT, AASDH, AASDHPPT, AASS, ACAT1, ACAT2, ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, ALDH2, ALDH3A1, ALDH3A2, ALDH9A1, ATP6V0C, SHMT1, BAT8, BBOX1, DLST, DLSTP, DOT1L, ECHS1, EHHADH, EHMT1, EHMT2, GCDH, HADHA, PLOD1, PLOD2, PLOD3, SDS, SHMT1, SHMT2, TMLHE 1 EHMT2(2) 293879 2 2 2 0 1 1 0 0 0 0.52 0.027 0.68
5 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 3 B3GNT1(1), PIGO(1) 766488 2 2 2 1 0 0 1 1 0 0.77 0.029 0.68
6 HSA00100_BIOSYNTHESIS_OF_STEROIDS Genes involved in biosynthesis of steroids CYP27B1, CYP51A1, DHCR24, DHCR7, EBP, FDFT1, FDPS, GGCX, GGPS1, HMGCR, HSD17B7, IDI1, IDI2, LSS, MVD, MVK, NQO1, NSDHL, PMVK, SC4MOL, SC5DL, SQLE, TM7SF2, VKORC1 1 TM7SF2(1) 166131 1 1 1 0 0 0 0 0 1 1 0.031 0.68
7 PARKINPATHWAY In Parkinson's disease, dopaminergic neurons contain Lewy bodies consisting of alpha-synuclein and parkin, an E3 ubiquitin ligase that targets glycosylated alpha-synuclein. GPR37, PARK2, PNUTL1, SNCA, SNCAIP, UBE2E2, UBE2F, UBE2G1, UBE2G2, UBE2L3, UBE2L6, UBL1 1 SNCAIP(1) 248757 1 1 1 1 0 0 1 0 0 0.88 0.067 1
8 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) 230298 1 1 1 0 0 0 1 0 0 0.59 0.076 1
9 HSA03030_DNA_POLYMERASE Genes involved in DNA polymerase POLA1, POLA2, POLB, POLD1, POLD2, POLD3, POLD4, POLE, POLE2, POLE3, POLE4, POLG, POLG2, POLH, POLI, POLK, POLL, POLM, POLQ, POLS, PRIM1, PRIM2, REV1, REV3L, RFC5 1 POLM(1) 256668 1 1 1 1 0 0 0 1 0 0.95 0.082 1
10 HSA00563_GLYCOSYLPHOSPHATIDYLINOSITOL_ANCHOR_BIOSYNTHESIS Genes involved in glycosylphosphatidylinositol(GPI)-anchor biosynthesis GPAA1, GPLD1, PGAP1, PIGA, PIGB, PIGC, PIGF, PIGG, PIGH, PIGK, PIGL, PIGM, PIGN, PIGO, PIGP, PIGQ, PIGS, PIGT, PIGU, PIGV, PIGW, PIGX, PIGZ 1 PIGO(1) 322007 1 1 1 1 0 0 0 1 0 0.92 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

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