Mutation Analysis (MutSig)
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): 9

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

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

Significantly mutated genesets: 33

Significantly mutated genesets: (excluding sig. mutated genes): 2

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 103
Frame_Shift_Ins 48
In_Frame_Del 29
In_Frame_Ins 5
Missense_Mutation 3424
Nonsense_Mutation 305
Nonstop_Mutation 6
Silent 1300
Splice_Site 84
Translation_Start_Site 7
Total 5311
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
A->T 743 415320976 1.8e-06 1.8 0.38
*Np(A/T)->nonflip 1427 459226432 3.1e-06 3.1 0.66
*Np(C/G)->nonflip 838 392937804 2.1e-06 2.1 0.45
C->G 423 436843260 9.7e-07 0.97 0.21
indel+null 566 852164264 6.6e-07 0.66 0.14
double_null 14 852164264 1.6e-08 0.016 0.0035
Total 4011 852164264 4.7e-06 4.7 1
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: 9. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 TP53 tumor protein p53 35896 12 9 12 0 4 4 1 0 3 0 3.5e-14 6.4e-10
2 KDM6A 117040 6 6 6 2 0 0 0 0 6 0 2.8e-07 0.0025
3 HLA-A major histocompatibility complex, class I, A 31640 3 3 3 0 0 0 1 0 2 0 0.000012 0.053
4 ELF3 E74-like factor 3 (ets domain transcription factor, epithelial-specific ) 32144 3 3 3 0 0 0 0 1 2 0 0.000013 0.053
5 XPR1 xenotropic and polytropic retrovirus receptor 60228 4 4 4 1 0 0 1 1 2 0 0.000015 0.053
6 ARID1A AT rich interactive domain 1A (SWI-like) 164864 6 5 6 1 1 0 0 0 5 0 0.000024 0.071
7 OR2T35 olfactory receptor, family 2, subfamily T, member 35 12964 2 2 1 0 0 0 0 0 2 0 0.000038 0.097
8 ERCC2 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) 61460 4 4 4 0 0 1 1 2 0 0 0.000045 0.1
9 FBXW7 F-box and WD repeat domain containing 7 72352 5 4 4 0 0 4 0 0 1 0 0.000097 0.19
10 C20orf20 chromosome 20 open reading frame 20 13524 2 2 2 1 0 0 0 2 0 0 0.00016 0.3
11 NAA25 82684 4 4 4 0 1 0 1 1 1 0 0.00019 0.31
12 LETMD1 LETM1 domain containing 1 31332 3 3 3 0 1 0 1 1 0 0 0.00022 0.33
13 CREBBP CREB binding protein (Rubinstein-Taybi syndrome) 201964 5 5 5 1 1 0 1 0 3 0 0.00024 0.33
14 HCRT hypocretin (orexin) neuropeptide precursor 4060 1 1 1 0 0 0 0 0 1 0 0.00027 0.35
15 FAM57A family with sequence similarity 57, member A 17388 2 2 2 0 0 0 2 0 0 0 0.00036 0.4
16 CUL1 cullin 1 67620 3 3 2 0 1 0 2 0 0 0 0.00038 0.4
17 RIMS3 regulating synaptic membrane exocytosis 3 26572 2 2 2 0 0 0 2 0 0 0 0.00039 0.4
18 MTERFD2 MTERF domain containing 2 31836 3 3 3 0 0 3 0 0 0 0 0.0004 0.4
19 GTF3C3 general transcription factor IIIC, polypeptide 3, 102kDa 76524 3 3 3 0 0 1 0 1 1 0 0.00043 0.41
20 ACN9 ACN9 homolog (S. cerevisiae) 10808 2 2 2 1 0 2 0 0 0 0 0.00046 0.42
21 IL34 20188 2 2 2 0 1 0 1 0 0 0 0.00052 0.43
22 OTUD7A OTU domain containing 7A 57260 3 3 3 0 0 2 0 1 0 0 0.00054 0.43
23 CSNK1E casein kinase 1, epsilon 33992 2 2 2 0 0 0 1 0 1 0 0.00058 0.43
24 C7orf36 chromosome 7 open reading frame 36 19404 2 2 2 0 0 1 1 0 0 0 0.00058 0.43
25 BCLAF1 BCL2-associated transcription factor 1 78596 4 3 4 0 0 1 0 2 1 0 0.00067 0.46
26 ORC3L origin recognition complex, subunit 3-like (yeast) 62132 3 3 3 0 0 1 1 1 0 0 0.00068 0.46
27 CAT catalase 45780 3 3 3 0 0 1 2 0 0 0 0.00071 0.46
28 GPS2 G protein pathway suppressor 2 27468 2 2 2 0 0 1 0 0 1 0 0.00073 0.46
29 CDH22 cadherin-like 22 55244 3 3 3 0 2 1 0 0 0 0 0.00076 0.46
30 NFE2L2 nuclear factor (erythroid-derived 2)-like 2 50092 3 3 3 0 1 1 1 0 0 0 0.0008 0.46
31 TMCO2 transmembrane and coiled-coil domains 2 15596 2 2 1 0 0 0 0 0 2 0 0.00083 0.46
32 PAK3 p21 (CDKN1A)-activated kinase 3 48692 3 3 3 0 0 2 0 1 0 0 0.00085 0.46
33 LASP1 LIM and SH3 protein 1 19656 2 2 2 0 0 0 0 1 1 0 0.00087 0.46
34 CD200 CD200 molecule 25116 2 2 2 0 0 1 1 0 0 0 0.0009 0.46
35 HOXB4 homeobox B4 18256 2 2 2 0 1 1 0 0 0 0 0.00094 0.46

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: A->T .

n2 - number of nonsilent mutations of type: *Np(A/T)->nonflip .

n3 - number of nonsilent mutations of type: *Np(C/G)->nonflip .

n4 - number of nonsilent mutations of type: C->G .

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 A4GNT alpha-1,4-N-acetylglucosaminyltransferase 0 0 0 0 0 1 1
2 AACS acetoacetyl-CoA synthetase 0 0 0 0 0 1 1
3 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 1 0 0 0 0 1 1
4 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 1 0 0 0 0 1 1
5 ABCF2 ATP-binding cassette, sub-family F (GCN20), member 2 0 0 0 0 0 1 1
6 ABHD2 abhydrolase domain containing 2 0 0 0 0 0 1 1
7 ABHD4 abhydrolase domain containing 4 0 0 0 0 0 1 1
8 ACADS acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain 0 0 0 0 0 1 1
9 ACOT11 acyl-CoA thioesterase 11 0 0 0 0 0 1 1
10 ACRBP acrosin binding protein 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
1762 MXRA5 matrix-remodelling associated 5 2 48 0 0
1 A2M alpha-2-macroglobulin 2 Inf 0 0
4 ABCA10 ATP-binding cassette, sub-family A (ABC1), member 10 3 Inf 0 0
6 ABCA13 ATP-binding cassette, sub-family A (ABC1), member 13 2 Inf 0 0
10 ABCA8 ATP-binding cassette, sub-family A (ABC1), member 8 3 Inf 0 0
17 ABCC9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 2 Inf 0 0
32 ACN9 ACN9 homolog (S. cerevisiae) 2 Inf 0 0
38 ACTA2 actin, alpha 2, smooth muscle, aorta 2 Inf 0 0
41 ACTN4 actinin, alpha 4 3 Inf 0 0
50 ADAMTS12 ADAM metallopeptidase with thrombospondin type 1 motif, 12 4 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: 33. 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 q
1 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(5), DAXX(1), PML(2), RARA(1), RB1(1), SP100(1), TNFRSF1B(1), TP53(12) 823508 24 15 24 1 6 7 3 1 7 0 1.7e-08 1e-05
2 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(1), CDKN1A(2), E2F2(1), TP53(12) 343280 16 11 16 0 5 5 2 1 3 0 3.9e-08 0.000012
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 ATM(3), BAX(1), CCND1(1), CDKN1A(2), RB1(1), TP53(12) 778904 20 14 20 2 6 6 2 1 5 0 1.4e-07 0.000024
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 SP3(1), TP53(12) 298060 13 10 13 1 5 4 1 0 3 0 1.6e-07 0.000024
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(3), RB1(1), TP53(12), WEE1(1) 748720 17 13 17 1 5 5 2 0 5 0 3.9e-07 0.000048
6 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 55 ASH1L(3), CARM1(1), CTCFL(1), DOT1L(5), EZH1(2), HCFC1(1), KDM6A(6), MLL(6), MLL2(5), MLL3(7), MLL4(2), NSD1(1), OGT(1), PPP1CA(3), PRDM2(1), PRMT6(1), SETD1A(1), SETD2(3), SETD8(1), STK38(1), SUV420H1(2), WHSC1(2) 5165860 56 24 55 8 9 13 12 4 14 4 2.2e-06 0.00022
7 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 ATM(3), BAX(1), CDKN1A(2), MAPK8(2), TP53(12) 892864 20 13 20 1 6 6 2 2 4 0 6.8e-06 0.0006
8 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 ABL1(1), ATM(3), ATR(2), CCND1(1), CDK6(1), CDKN1A(2), RB1(1), TP53(12) 1271004 23 15 23 0 7 7 4 1 4 0 0.000011 0.00088
9 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 IFNGR2(1), JAK2(1), RB1(1), RELA(1), TNFRSF1B(1), TP53(12), USH1C(1) 798532 18 12 18 0 5 6 2 1 4 0 0.000015 0.001
10 RNAPATHWAY dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation. CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53 9 RELA(1), TP53(12) 430948 13 9 13 0 4 5 1 0 3 0 2e-05 0.0011

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). 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 q
1 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 54 ASH1L(3), CARM1(1), CTCFL(1), DOT1L(5), EZH1(2), HCFC1(1), MLL(6), MLL2(5), MLL3(7), MLL4(2), NSD1(1), OGT(1), PPP1CA(3), PRDM2(1), PRMT6(1), SETD1A(1), SETD2(3), SETD8(1), STK38(1), SUV420H1(2), WHSC1(2) 5048820 50 23 49 6 9 13 12 4 8 4 0.000049 0.018
2 FBW7PATHWAY Cyclin E interacts with cell cycle checkpoint kinase cdk2 to allow transcription of genes required for S phase, including transcription of additional cyclin E. CCNE1, CDC34, CDK2, CUL1, E2F1, FBXW7, RB1, SKP1A, TFDP1 8 CUL1(3), FBXW7(5), RB1(1) 361480 9 7 7 0 1 4 2 0 2 0 0.000058 0.018
3 HSA00680_METHANE_METABOLISM Genes involved in methane metabolism ADH5, CAT, EPX, LPO, MPO, MTHFR, PRDX6, SHMT1, SHMT2, TPO 10 CAT(3), MPO(1), MTHFR(1), PRDX6(1), TPO(2) 496552 8 8 8 1 1 4 2 0 1 0 0.00065 0.13
4 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 12 CREBBP(5), DAXX(1), PML(2), RARA(1), RB1(1), SP100(1), TNFRSF1B(1) 787612 12 9 12 1 2 3 2 1 4 0 0.00094 0.15
5 SODDPATHWAY Some members of the tumor necrosis factor receptor family have cytoplasmic death domains that promote apoptosis when active and are repressed by silencers called SODDs. BAG4, BIRC3, CASP8, FADD, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TRADD, TRAF2 10 BAG4(1), CASP8(2), FADD(1), RIPK1(1), TNFRSF1B(1), TRAF2(1) 369068 7 6 7 1 0 5 0 2 0 0 0.0014 0.15
6 CERAMIDEPATHWAY Ceramide is a lipid signaling molecule that can activate proliferative or apoptotic pathways, depending on signaling context, localization, and cell type. BAD, BAX, BCL2, CASP8, CYCS, FADD, MAP2K1, MAP2K4, MAP3K1, MAPK1, MAPK3, MAPK8, NFKB1, NSMAF, PDCD8, RAF1, RELA, RIPK1, SMPD1, TNFRSF1A, TRADD, TRAF2 21 BAX(1), CASP8(2), FADD(1), MAP2K1(1), MAP3K1(1), MAPK8(2), NSMAF(1), RELA(1), RIPK1(1), SMPD1(1), TRAF2(1) 885640 13 10 13 3 3 6 1 2 1 0 0.0015 0.15
7 SETPATHWAY Cytotoxic T cells release perforin, which to allow entry into target cells of granzyme B, which activates caspases, and granzyme A, which induces caspase-independent apoptosis. ANP32A, APEX1, CREBBP, DFFA, DFFB, GZMA, GZMB, HMGB2, NME1, PRF1, SET 11 CREBBP(5), GZMB(1), PRF1(1) 449904 7 6 7 3 1 1 2 0 3 0 0.0019 0.17
8 HSA00940_PHENYLPROPANOID_BIOSYNTHESIS Genes involved in phenylpropanoid biosynthesis EPX, GBA, GBA3, LPO, MPO, PRDX6, TPO 7 GBA(1), GBA3(1), MPO(1), PRDX6(1), TPO(2) 362236 6 6 6 2 2 2 0 1 1 0 0.0023 0.18
9 METHANE_METABOLISM ADH5, ATP6V0C, SHMT1, CAT, EPX, LPO, MPO, PRDX1, PRDX2, PRDX5, PRDX6, SHMT1, SHMT2, TPO 13 CAT(3), MPO(1), PRDX6(1), TPO(2) 505624 7 7 7 1 1 3 2 0 1 0 0.0032 0.19
10 RELAPATHWAY Acetylated NF-kB proteins are immune to IkB regulation and promote transcription until the histone deacetylase HDAC3 deacetylates the RelA subunit of NF-kB. CHUK, CREBBP, EP300, FADD, HDAC3, IKBKB, IKBKG, NFKB1, NFKBIA, RELA, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TRADD, TRAF6 15 CREBBP(5), EP300(1), FADD(1), RELA(1), RIPK1(1), TNFRSF1B(1) 962360 10 9 10 2 1 4 1 1 3 0 0.0033 0.19
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]

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 Ð 615 (2011)
Made with Nozzle