Skin Cutaneous Melanoma: Mutation Analysis (MutSig v2.0)
(Regional_Metastatic cohort)
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: SKCM-Regional_Metastatic

  • Number of patients in set: 137

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:SKCM-Regional_Metastatic.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 49

  • Mutations seen in COSMIC: 414

  • Significantly mutated genes in COSMIC territory: 30

  • Genes with clustered mutations (≤ 3 aa apart): 1850

  • Significantly mutated genesets: 2

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

Mutation Preprocessing

  • Read 137 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 136253

  • After removing 493 blacklisted mutations: 135760

  • After removing 2491 noncoding mutations: 133269

Mutation Filtering

  • Number of mutations before filtering: 133269

  • After removing 1671 mutations outside gene set: 131598

  • After removing 138 mutations outside category set: 131460

  • After removing 4 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 129647

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 496
Frame_Shift_Ins 179
In_Frame_Del 208
In_Frame_Ins 30
Missense_Mutation 79863
Nonsense_Mutation 4791
Nonstop_Mutation 28
Silent 44640
Splice_Site 1188
Translation_Start_Site 37
Total 131460
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
(C/T)p*C->T 62535 1086024614 0.000058 58 2.6 1.6
(A/G)p*C->T 6722 911139542 7.4e-06 7.4 0.33 1.9
A->G 3074 1930142433 1.6e-06 1.6 0.072 2.3
transver 7563 3927306589 1.9e-06 1.9 0.087 5
indel+null 6803 3927306589 1.7e-06 1.7 0.078 NaN
double_null 120 3927306589 3.1e-08 0.031 0.0014 NaN
Total 86817 3927306589 0.000022 22 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: SKCM-Regional_Metastatic.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: (C/T)p*C->T

  • n2 = number of nonsilent mutations of type: (A/G)p*C->T

  • n3 = number of nonsilent mutations of type: A->G

  • n4 = number of nonsilent mutations of type: transver

  • n5 = number of nonsilent mutations of type: indel+null

  • n6 = number of nonsilent mutations of type: double_null

  • 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_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: 49. 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_classic p_ns_s p_cons p_joint p q
1 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 127245 23 23 13 1 4 0 0 1 18 0 3.3e-15 0.0073 4e-07 8.4e-06 0.000 0.000
2 TP53 tumor protein p53 166589 26 23 23 1 13 0 2 3 8 0 7.1e-15 0.00089 0.18 0.0011 3.33e-16 3.01e-12
3 BRAF v-raf murine sarcoma viral oncogene homolog B1 303705 78 73 16 3 12 1 2 63 0 0 4.3e-15 0.000025 1.2e-06 0 <1.00e-15 <3.01e-12
4 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 80273 39 39 6 0 1 1 12 25 0 0 3.8e-15 0.000069 0.0001 0 <1.00e-15 <3.01e-12
5 C15orf23 chromosome 15 open reading frame 23 139470 11 10 6 2 11 0 0 0 0 0 0.0051 0.094 1 0 <1.00e-15 <3.01e-12
6 ERVFRDE1 103278 3 3 2 0 3 0 0 0 0 0 0.36 0.36 0.76 0 <1.00e-15 <3.01e-12
7 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 153968 12 12 12 0 0 0 2 3 7 0 2e-10 0.16 0.4 0.4 1.91e-09 4.91e-06
8 PPP6C protein phosphatase 6, catalytic subunit 137456 15 14 11 1 12 0 0 0 3 0 4.1e-08 0.036 0.33 0.066 5.70e-08 0.000129
9 PRB4 proline-rich protein BstNI subfamily 4 103572 18 16 14 1 16 0 0 1 1 0 2.4e-07 0.16 0.28 0.027 1.31e-07 0.000264
10 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 84034 9 9 5 0 8 0 0 1 0 0 0.00014 0.015 0.075 0.000086 2.30e-07 0.000415
11 STK19 serine/threonine kinase 19 148453 11 9 7 0 9 1 0 1 0 0 0.0024 0.0083 0.94 0.000038 1.57e-06 0.00246
12 CDH9 cadherin 9, type 2 (T1-cadherin) 318377 32 23 31 2 25 2 0 2 3 0 1.5e-07 0.0017 0.21 0.64 1.63e-06 0.00246
13 ADH1C alcohol dehydrogenase 1C (class I), gamma polypeptide 155776 22 20 18 4 15 2 0 4 1 0 2.4e-07 0.027 0.23 0.72 2.83e-06 0.00393
14 TCEB3C transcription elongation factor B polypeptide 3C (elongin A3) 138189 23 19 17 7 15 2 0 2 4 0 0.00043 0.11 0.99 0.00059 4.06e-06 0.00523
15 TRAT1 T cell receptor associated transmembrane adaptor 1 80007 13 9 10 2 11 1 1 0 0 0 0.00026 0.087 0.3 0.0015 6.05e-06 0.00685
16 TTN titin 13942638 717 108 674 232 562 49 22 58 19 7 1 0.00088 1 4e-07 6.29e-06 0.00685
17 DDX3X DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked 268460 14 14 14 0 4 1 1 1 7 0 1.2e-06 0.063 0.79 0.33 6.45e-06 0.00685
18 GH2 growth hormone 2 136692 10 10 8 1 9 0 0 0 1 0 0.0023 0.069 0.14 0.00039 1.35e-05 0.0135
19 TFEC transcription factor EC 139819 14 13 14 0 11 1 0 1 1 0 4.2e-06 0.018 0.088 0.24 1.50e-05 0.0143
20 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 172490 7 7 3 1 5 0 0 2 0 0 0.0056 0.24 0.87 0.00022 1.76e-05 0.0158
21 WDR12 WD repeat domain 12 181304 9 9 7 1 2 0 1 5 1 0 0.00027 0.37 0.00066 0.0047 1.84e-05 0.0158
22 RGS18 regulator of G-protein signaling 18 89490 7 7 5 0 4 0 0 2 1 0 0.00021 0.2 0.15 0.0068 2.10e-05 0.0172
23 POF1B premature ovarian failure, 1B 201955 21 17 20 2 15 3 1 1 1 0 1.8e-06 0.014 0.46 0.87 2.21e-05 0.0173
24 OR5AC2 olfactory receptor, family 5, subfamily AC, member 2 127342 18 16 16 4 17 0 0 0 1 0 2.7e-06 0.026 0.28 0.6 2.34e-05 0.0176
25 VEGFC vascular endothelial growth factor C 161178 14 13 13 1 9 1 0 0 4 0 2.4e-06 0.018 0.87 0.84 2.81e-05 0.0203
26 RERG RAS-like, estrogen-regulated, growth inhibitor 83497 11 9 10 0 9 0 1 1 0 0 0.00036 0.0052 0.43 0.0058 2.97e-05 0.0206
27 CCNE2 cyclin E2 172467 10 10 7 0 2 0 0 7 1 0 0.000014 0.14 0.51 0.16 3.12e-05 0.0209
28 GPR141 G protein-coupled receptor 141 126217 12 12 9 2 9 0 1 1 1 0 0.000012 0.0048 0.3 0.26 4.35e-05 0.0280
29 GK2 glycerol kinase 2 227421 21 17 19 2 14 1 1 2 3 0 4.2e-06 0.026 0.9 1 5.62e-05 0.0350
30 NAP1L2 nucleosome assembly protein 1-like 2 186787 15 12 15 0 8 1 2 2 2 0 6.7e-06 0.007 0.45 0.8 7.00e-05 0.0421
31 SNAP91 synaptosomal-associated protein, 91kDa homolog (mouse) 211873 21 18 21 2 15 2 1 1 2 0 5.8e-06 0.033 0.81 1 7.62e-05 0.0444
32 PRB2 proline-rich protein BstNI subfamily 2 170586 29 20 28 2 26 1 0 1 1 0 0.00014 0.21 0.74 0.051 8.90e-05 0.0499
33 TLL1 tolloid-like 1 406878 39 27 34 4 33 1 1 1 3 0 0.000015 0.008 0.6 0.47 9.13e-05 0.0499
34 HBD hemoglobin, delta 61670 8 8 7 0 7 1 0 0 0 0 5e-05 0.0059 0.47 0.15 9.48e-05 0.0503
35 GRXCR2 glutaredoxin, cysteine rich 2 103416 12 11 12 2 8 2 0 1 1 0 0.00011 0.066 0.12 0.069 9.89e-05 0.0510
CDKN2A

Figure S1.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

TP53

Figure S2.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

BRAF

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

NRAS

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

C15orf23

Figure S5.  This figure depicts the distribution of mutations and mutation types across the C15orf23 significant gene.

PTEN

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

PPP6C

Figure S7.  This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.

PRB4

Figure S8.  This figure depicts the distribution of mutations and mutation types across the PRB4 significant gene.

RAC1

Figure S9.  This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.

STK19

Figure S10.  This figure depicts the distribution of mutations and mutation types across the STK19 significant gene.

CDH9

Figure S11.  This figure depicts the distribution of mutations and mutation types across the CDH9 significant gene.

ADH1C

Figure S12.  This figure depicts the distribution of mutations and mutation types across the ADH1C significant gene.

TCEB3C

Figure S13.  This figure depicts the distribution of mutations and mutation types across the TCEB3C significant gene.

TRAT1

Figure S14.  This figure depicts the distribution of mutations and mutation types across the TRAT1 significant gene.

TTN

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

DDX3X

Figure S16.  This figure depicts the distribution of mutations and mutation types across the DDX3X significant gene.

GH2

Figure S17.  This figure depicts the distribution of mutations and mutation types across the GH2 significant gene.

TFEC

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

IDH1

Figure S19.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

WDR12

Figure S20.  This figure depicts the distribution of mutations and mutation types across the WDR12 significant gene.

RGS18

Figure S21.  This figure depicts the distribution of mutations and mutation types across the RGS18 significant gene.

POF1B

Figure S22.  This figure depicts the distribution of mutations and mutation types across the POF1B significant gene.

OR5AC2

Figure S23.  This figure depicts the distribution of mutations and mutation types across the OR5AC2 significant gene.

RERG

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

CCNE2

Figure S25.  This figure depicts the distribution of mutations and mutation types across the CCNE2 significant gene.

GPR141

Figure S26.  This figure depicts the distribution of mutations and mutation types across the GPR141 significant gene.

GK2

Figure S27.  This figure depicts the distribution of mutations and mutation types across the GK2 significant gene.

NAP1L2

Figure S28.  This figure depicts the distribution of mutations and mutation types across the NAP1L2 significant gene.

SNAP91

Figure S29.  This figure depicts the distribution of mutations and mutation types across the SNAP91 significant gene.

TLL1

Figure S30.  This figure depicts the distribution of mutations and mutation types across the TLL1 significant gene.

HBD

Figure S31.  This figure depicts the distribution of mutations and mutation types across the HBD 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: 30. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 7 5 6 685 8952 3.4e-14 1.5e-10
2 STK19 serine/threonine kinase 19 11 2 5 274 10 7.2e-14 1.6e-10
3 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 39 33 39 4521 49232 1.1e-13 1.6e-10
4 BRAF v-raf murine sarcoma viral oncogene homolog B1 78 89 72 12193 890854 2.5e-13 2.8e-10
5 TP53 tumor protein p53 26 356 24 48772 2841 4.4e-13 3.3e-10
6 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 23 332 23 45484 1003 4.4e-13 3.3e-10
7 EPHA7 EPH receptor A7 29 13 4 1781 4 9.7e-08 0.000062
8 RIPK4 receptor-interacting serine-threonine kinase 4 6 3 3 411 3 1.2e-07 7e-05
9 EPHA4 EPH receptor A4 11 5 3 685 3 5.7e-07 0.00029
10 TTN titin 717 65 5 8905 5 2.1e-06 0.00095

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
1252 BRAF v-raf murine sarcoma viral oncogene homolog B1 78 0 1282 1451 1507 1282 1451 1507
8535 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 39 0 562 562 562 562 562 562
3654 DNAH5 dynein, axonemal, heavy chain 5 203 0 53 65 168 53 65 168
13457 TTN titin 717 0 51 79 184 51 79 184
7993 MUC16 mucin 16, cell surface associated 522 0 50 102 277 50 102 277
9361 PCLO piccolo (presynaptic cytomatrix protein) 182 0 25 43 102 25 43 102
13204 TPTE transmembrane phosphatase with tensin homology 57 0 21 36 94 21 36 94
12184 SPTLC3 serine palmitoyltransferase, long chain base subunit 3 17 0 21 21 29 21 21 29
2878 CNTN5 contactin 5 55 0 20 31 56 20 31 56
10914 RP1 retinitis pigmentosa 1 (autosomal dominant) 114 0 17 37 88 17 37 88

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: 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_ns_s p q
1 ST_G_ALPHA_S_PATHWAY The G-alpha-s protein activates adenylyl cyclases, which catalyze cAMP formation. ASAH1, BF, BFAR, BRAF, CAMP, CREB1, CREB3, CREB5, EPAC, GAS, GRF2, MAPK1, RAF1, SNX13, SRC, TERF2IP 12 BRAF(78), CAMP(1), CREB5(7), MAPK1(3), RAF1(2), SNX13(1), SRC(1) 2251916 93 80 31 23 25 3 2 63 0 0 0.13 0.000068 0.04
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), CDK4(2), CDKN1A(2), CDKN1B(1), CDKN2A(23), CFL1(1), E2F1(5), E2F2(3), MDM2(2), NXT1(2), PRB1(18), TP53(26) 1704325 86 52 72 14 40 3 4 10 29 0 2e-05 0.00013 0.04
3 SA_REG_CASCADE_OF_CYCLIN_EXPR Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1 13 CCNA1(12), CCND1(1), CCNE1(3), CCNE2(10), CDK4(2), CDKN1B(1), CDKN2A(23), E2F1(5), E2F2(3), PRB1(18) 1815524 78 54 64 13 41 0 4 12 21 0 0.00011 0.00092 0.19
4 PEPIPATHWAY Proepithelin (PEPI) induces epithelial cells to secrete IL-8, which promotes elastase secretion by neutrophils. ELA1, ELA2, ELA2A, ELA2B, ELA3B, GRN, IL8, SLPI 3 GRN(4), IL8(1), SLPI(5) 346525 10 10 10 2 4 1 0 4 1 0 0.23 0.14 1
5 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(3), FOSB(5), GRIA2(22), PPP1R1B(1) 731255 31 25 28 8 22 1 0 4 4 0 0.033 0.15 1
6 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(8) 144360 8 8 8 2 7 1 0 0 0 0 0.17 0.22 1
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 HDAC1(1), MYC(2), SP1(4), SP3(1), TP53(26), WT1(4) 1428799 38 29 35 5 18 2 5 4 9 0 0.0032 0.22 1
8 1_AND_2_METHYLNAPHTHALENE_DEGRADATION ADH1A, ADH1A, ADH1B, ADH1C, ADH1B, ADH1C, ADH4, ADH6, ADH7, ADHFE1 7 ADH1A(10), ADH1B(17), ADH1C(22), ADH4(7), ADH6(7), ADH7(12), ADHFE1(3) 1133089 78 50 71 20 59 5 4 8 2 0 0.0013 0.51 1
9 SLRPPATHWAY Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. BGN, DCN, DSPG3, FMOD, KERA, LUM 5 BGN(5), DCN(14), FMOD(3), KERA(13), LUM(7) 704012 42 28 41 13 34 3 2 1 2 0 0.0046 0.64 1
10 HSA00830_RETINOL_METABOLISM Genes involved in retinol metabolism ALDH1A1, ALDH1A2, BCMO1, RDH5 4 ALDH1A1(3), ALDH1A2(9), BCMO1(10), RDH5(1) 785999 23 20 22 7 15 2 1 3 2 0 0.066 0.78 1

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 PEPIPATHWAY Proepithelin (PEPI) induces epithelial cells to secrete IL-8, which promotes elastase secretion by neutrophils. ELA1, ELA2, ELA2A, ELA2B, ELA3B, GRN, IL8, SLPI 3 GRN(4), IL8(1), SLPI(5) 346525 10 10 10 2 4 1 0 4 1 0 0.23 0.14 1
2 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(3), FOSB(5), GRIA2(22), PPP1R1B(1) 731255 31 25 28 8 22 1 0 4 4 0 0.033 0.15 1
3 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(8) 144360 8 8 8 2 7 1 0 0 0 0 0.17 0.22 1
4 SLRPPATHWAY Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. BGN, DCN, DSPG3, FMOD, KERA, LUM 5 BGN(5), DCN(14), FMOD(3), KERA(13), LUM(7) 704012 42 28 41 13 34 3 2 1 2 0 0.0046 0.64 1
5 HSA00830_RETINOL_METABOLISM Genes involved in retinol metabolism ALDH1A1, ALDH1A2, BCMO1, RDH5 4 ALDH1A1(3), ALDH1A2(9), BCMO1(10), RDH5(1) 785999 23 20 22 7 15 2 1 3 2 0 0.066 0.78 1
6 BOTULINPATHWAY Blockade of Neurotransmitter Relase by Botulinum Toxin CHRM1, CHRNA1, SNAP25, STX1A, VAMP2 5 CHRM1(4), CHRNA1(3), SNAP25(5), STX1A(2) 659260 14 11 12 3 10 0 0 1 3 0 0.052 0.82 1
7 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(1) 103800 1 1 1 1 1 0 0 0 0 0 0.9 0.88 1
8 HSA03060_PROTEIN_EXPORT Genes involved in protein export OXA1L, SEC61A2, SRP19, SRP54, SRP68, SRP72, SRP9, SRPR 7 SEC61A2(4), SRP19(4), SRP54(2), SRP68(5), SRP72(1), SRPR(2) 1333237 18 16 18 4 6 0 1 6 5 0 0.34 0.88 1
9 1_AND_2_METHYLNAPHTHALENE_DEGRADATION ADH1A, ADH1A, ADH1B, ADH1C, ADH1B, ADH1C, ADH4, ADH6, ADH7, ADHFE1 6 ADH1A(10), ADH1B(17), ADH4(7), ADH6(7), ADH7(12), ADHFE1(3) 977313 56 41 53 16 44 3 4 4 1 0 0.013 0.89 1
10 BETAOXIDATIONPATHWAY Beta-Oxidation of Fatty Acids ACADL, ACADM, ACADS, ACAT1, ECHS1, HADHA 6 ACADL(2), ACADM(5), ACADS(2), HADHA(7) 1105580 16 14 16 4 10 1 1 4 0 0 0.2 0.91 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)
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