Skin Cutaneous Melanoma: Mutation Analysis (MutSig v2.0)
(Regional_LN 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_LN

  • Number of patients in set: 105

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_LN.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 49

  • Mutations seen in COSMIC: 342

  • Significantly mutated genes in COSMIC territory: 26

  • Genes with clustered mutations (≤ 3 aa apart): 1490

  • Significantly mutated genesets: 3

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

Mutation Preprocessing

  • Read 105 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 112221

  • After removing 374 blacklisted mutations: 111847

  • After removing 2027 noncoding mutations: 109820

Mutation Filtering

  • Number of mutations before filtering: 109820

  • After removing 1378 mutations outside gene set: 108442

  • After removing 122 mutations outside category set: 108320

  • After removing 4 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 106816

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 393
Frame_Shift_Ins 142
In_Frame_Del 172
In_Frame_Ins 25
Missense_Mutation 65862
Nonsense_Mutation 3857
Nonstop_Mutation 22
Silent 36854
Splice_Site 968
Translation_Start_Site 25
Total 108320
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 51881 832515348 0.000062 62 2.6 1.6
(A/G)p*C->T 5494 698460898 7.9e-06 7.9 0.33 1.9
A->G 2500 1479553456 1.7e-06 1.7 0.071 2.3
transver 6007 3010529702 2e-06 2 0.084 5
indel+null 5477 3010529702 1.8e-06 1.8 0.077 NaN
double_null 104 3010529702 3.5e-08 0.035 0.0015 NaN
Total 71463 3010529702 0.000024 24 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_LN.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 TTN titin 10637202 589 83 561 183 462 41 18 49 13 6 1.000 0.00051 1 0 <1.00e-15 <3.61e-12
2 BRAF v-raf murine sarcoma viral oncogene homolog B1 232855 64 59 14 3 11 1 2 50 0 0 <1.00e-15 0.00025 8e-06 0 <1.00e-15 <3.61e-12
3 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 61521 29 29 5 0 0 1 8 20 0 0 5.44e-15 0.0011 0.00076 0 <1.00e-15 <3.61e-12
4 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 99076 16 16 12 1 4 0 0 1 11 0 1.39e-13 0.038 6e-07 0 <1.00e-15 <3.61e-12
5 STK19 serine/threonine kinase 19 113742 9 7 6 0 8 1 0 0 0 0 0.00586 0.016 0.98 0 <1.00e-15 <3.61e-12
6 TP53 tumor protein p53 127717 20 18 18 1 9 0 1 3 7 0 2.12e-12 0.0087 0.28 0.019 1.29e-12 3.88e-09
7 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 119866 11 11 11 0 0 0 2 3 6 0 1.07e-10 0.18 0.5 0.62 1.62e-09 4.17e-06
8 TPTE transmembrane phosphatase with tensin homology 182369 48 29 38 9 38 1 1 1 7 0 6.12e-09 0.014 0.8 0.19 2.46e-08 5.56e-05
9 PRB4 proline-rich protein BstNI subfamily 4 79380 17 15 13 1 16 0 0 1 0 0 1.55e-07 0.19 0.27 0.035 1.08e-07 0.000217
10 CDH9 cadherin 9, type 2 (T1-cadherin) 243959 31 22 30 2 25 2 0 2 2 0 4.55e-08 0.0022 0.24 0.82 6.76e-07 0.00122
11 SERPINB4 serpin peptidase inhibitor, clade B (ovalbumin), member 4 114440 23 17 21 4 18 0 1 3 1 0 4.67e-08 0.0078 0.75 1 8.36e-07 0.00137
12 PRB2 proline-rich protein BstNI subfamily 2 130664 27 19 26 0 25 1 0 0 1 0 4.56e-07 0.024 0.75 0.17 1.37e-06 0.00205
13 TCEB3C transcription elongation factor B polypeptide 3C (elongin A3) 102780 17 14 13 4 11 0 0 2 4 0 2.33e-05 0.093 0.99 0.0038 1.53e-06 0.00213
14 ADH1C alcohol dehydrogenase 1C (class I), gamma polypeptide 119581 19 17 16 3 13 2 0 3 1 0 2.44e-07 0.026 0.27 0.74 3.00e-06 0.00367
15 C15orf23 chromosome 15 open reading frame 23 106996 7 7 5 1 7 0 0 0 0 0 0.00839 0.15 0.98 0.000022 3.05e-06 0.00367
16 CCNE2 cyclin E2 132180 10 10 7 0 2 0 0 7 1 0 1.26e-06 0.14 0.51 0.16 3.32e-06 0.00374
17 SDR16C5 short chain dehydrogenase/reductase family 16C, member 5 99998 18 16 15 3 14 2 0 2 0 0 2.99e-07 0.06 0.91 0.74 3.61e-06 0.00383
18 PDE1A phosphodiesterase 1A, calmodulin-dependent 176744 21 19 18 4 16 1 0 3 1 0 3.95e-06 0.1 0.21 0.087 5.49e-06 0.00550
19 TLL1 tolloid-like 1 311157 35 24 31 3 29 1 1 1 3 0 9.00e-07 0.006 0.74 0.84 1.15e-05 0.0109
20 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 64503 7 7 4 0 6 0 0 1 0 0 0.000459 0.04 0.1 0.0024 1.60e-05 0.0145
21 RERG RAS-like, estrogen-regulated, growth inhibitor 63976 10 8 9 0 8 0 1 1 0 0 0.000241 0.0089 0.54 0.0057 2.01e-05 0.0172
22 OR52L1 olfactory receptor, family 52, subfamily L, member 1 98341 12 12 10 3 9 1 0 1 1 0 2.24e-05 0.046 0.95 0.068 2.19e-05 0.0179
23 HBD hemoglobin, delta 47334 8 8 7 0 7 1 0 0 0 0 1.07e-05 0.0059 0.47 0.15 2.35e-05 0.0185
24 VEGFC vascular endothelial growth factor C 123714 13 12 12 1 9 1 0 0 3 0 1.89e-06 0.026 0.88 1 2.68e-05 0.0202
25 BAGE2 B melanoma antigen family, member 2 36273 8 7 8 2 5 1 0 0 1 1 5.10e-06 0.17 0.38 0.41 2.94e-05 0.0212
26 PPP6C protein phosphatase 6, catalytic subunit 105553 11 10 9 0 9 0 0 0 2 0 8.71e-06 0.027 0.41 0.32 3.79e-05 0.0255
27 OR1N2 olfactory receptor, family 1, subfamily N, member 2 103311 15 13 15 3 14 0 0 1 0 0 4.96e-05 0.018 0.012 0.056 3.82e-05 0.0255
28 HNF4G hepatocyte nuclear factor 4, gamma 138428 16 12 15 2 9 3 1 2 1 0 1.01e-05 0.082 0.61 0.37 4.99e-05 0.0321
29 TRAT1 T cell receptor associated transmembrane adaptor 1 61363 10 6 9 1 8 1 1 0 0 0 0.00126 0.083 0.57 0.0036 6.09e-05 0.0379
30 AREG amphiregulin (schwannoma-derived growth factor) 70577 6 5 4 0 4 0 2 0 0 0 0.00881 0.12 0.0017 0.00056 6.57e-05 0.0395
31 TAF1A TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa 146252 8 8 6 1 0 0 0 8 0 0 2.46e-05 0.62 0.45 0.25 7.98e-05 0.0452
32 ST18 suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein) 336674 31 24 29 4 22 2 1 2 4 0 7.38e-05 0.0061 0.9 0.084 8.01e-05 0.0452
33 OR9K2 olfactory receptor, family 9, subfamily K, member 2 104834 11 11 10 1 8 2 1 0 0 0 8.58e-06 0.032 0.98 0.76 8.46e-05 0.0455
34 GRXCR2 glutaredoxin, cysteine rich 2 79277 10 9 10 0 6 2 0 1 1 0 4.95e-05 0.01 0.17 0.13 8.56e-05 0.0455
35 OXA1L oxidase (cytochrome c) assembly 1-like 160118 4 4 2 2 4 0 0 0 0 0 0.748 0.59 0.97 0.000011 0.000103 0.0530
TTN

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

BRAF

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

NRAS

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

CDKN2A

Figure S4.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

STK19

Figure S5.  This figure depicts the distribution of mutations and mutation types across the STK19 significant gene.

TP53

Figure S6.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

PTEN

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

TPTE

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

PRB4

Figure S9.  This figure depicts the distribution of mutations and mutation types across the PRB4 significant gene.

CDH9

Figure S10.  This figure depicts the distribution of mutations and mutation types across the CDH9 significant gene.

SERPINB4

Figure S11.  This figure depicts the distribution of mutations and mutation types across the SERPINB4 significant gene.

TCEB3C

Figure S12.  This figure depicts the distribution of mutations and mutation types across the TCEB3C significant gene.

ADH1C

Figure S13.  This figure depicts the distribution of mutations and mutation types across the ADH1C significant gene.

C15orf23

Figure S14.  This figure depicts the distribution of mutations and mutation types across the C15orf23 significant gene.

CCNE2

Figure S15.  This figure depicts the distribution of mutations and mutation types across the CCNE2 significant gene.

SDR16C5

Figure S16.  This figure depicts the distribution of mutations and mutation types across the SDR16C5 significant gene.

PDE1A

Figure S17.  This figure depicts the distribution of mutations and mutation types across the PDE1A significant gene.

TLL1

Figure S18.  This figure depicts the distribution of mutations and mutation types across the TLL1 significant gene.

RAC1

Figure S19.  This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.

RERG

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

OR52L1

Figure S21.  This figure depicts the distribution of mutations and mutation types across the OR52L1 significant gene.

HBD

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

PPP6C

Figure S23.  This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.

OR1N2

Figure S24.  This figure depicts the distribution of mutations and mutation types across the OR1N2 significant gene.

HNF4G

Figure S25.  This figure depicts the distribution of mutations and mutation types across the HNF4G significant gene.

TRAT1

Figure S26.  This figure depicts the distribution of mutations and mutation types across the TRAT1 significant gene.

AREG

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

TAF1A

Figure S28.  This figure depicts the distribution of mutations and mutation types across the TAF1A significant gene.

ST18

Figure S29.  This figure depicts the distribution of mutations and mutation types across the ST18 significant gene.

OR9K2

Figure S30.  This figure depicts the distribution of mutations and mutation types across the OR9K2 significant gene.

GRXCR2

Figure S31.  This figure depicts the distribution of mutations and mutation types across the GRXCR2 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: 26. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 29 33 29 3465 36255 0 0
2 BRAF v-raf murine sarcoma viral oncogene homolog B1 64 89 59 9345 718347 0 0
3 TP53 tumor protein p53 20 356 19 37380 1309 0 0
4 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 16 332 16 34860 638 0 0
5 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 6 5 5 525 7460 2.4e-12 2.2e-09
6 STK19 serine/threonine kinase 19 9 2 4 210 8 2.5e-11 1.9e-08
7 EPHA4 EPH receptor A4 9 5 3 525 3 3.2e-07 0.00021
8 MSTN myostatin 6 1 2 105 2 3.1e-06 0.0015
9 SYK spleen tyrosine kinase 9 1 2 105 2 3.1e-06 0.0015
10 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 11 767 11 80535 329 5.5e-06 0.0023

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
1199 BRAF v-raf murine sarcoma viral oncogene homolog B1 64 0 785 917 962 785 917 962
8123 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 29 0 301 301 301 301 301 301
3464 DNAH5 dynein, axonemal, heavy chain 5 179 0 48 59 143 48 59 143
12817 TTN titin 589 0 32 51 123 32 51 123
7606 MUC16 mucin 16, cell surface associated 437 0 28 65 181 28 65 181
8928 PCLO piccolo (presynaptic cytomatrix protein) 139 0 15 26 60 15 26 60
11605 SPTLC3 serine palmitoyltransferase, long chain base subunit 3 16 0 15 15 22 15 15 22
12574 TPTE transmembrane phosphatase with tensin homology 48 0 13 23 66 13 23 66
9870 PTPRT protein tyrosine phosphatase, receptor type, T 59 0 13 22 40 13 22 40
10397 RP1 retinitis pigmentosa 1 (autosomal dominant) 96 0 11 26 66 11 26 66

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: 3. 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 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(7), CCNE1(1), CCNE2(10), CDK4(2), CDKN2A(16), E2F1(5), E2F2(1), PRB1(14) 1394347 56 41 49 8 29 0 1 12 14 0 0.00051 0.000022 0.01
2 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(64), CREB5(7), MAPK1(2), RAF1(2), SNX13(1) 1725227 76 63 26 18 21 3 2 50 0 0 0.13 0.000033 0.01
3 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 CDK4(2), CDKN1A(1), CDKN2A(16), E2F1(5), E2F2(1), MDM2(2), NXT1(2), PRB1(14), TP53(20) 1308030 63 38 57 10 29 2 2 9 21 0 0.00027 0.00039 0.08
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) 265596 10 10 10 2 4 1 0 4 1 0 0.23 0.044 1
5 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(3), FOSB(5), GRIA2(19) 561071 27 21 24 7 21 1 0 3 2 0 0.044 0.15 1
6 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(6) 110886 6 6 6 2 6 0 0 0 0 0 0.33 0.33 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(3), SP3(1), TP53(20), WT1(4) 1095688 31 23 29 5 14 1 4 4 8 0 0.024 0.33 1
8 HSA00830_RETINOL_METABOLISM Genes involved in retinol metabolism ALDH1A1, ALDH1A2, BCMO1, RDH5 4 ALDH1A1(3), ALDH1A2(8), BCMO1(9), RDH5(1) 601941 21 18 20 5 13 2 1 3 2 0 0.037 0.38 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(11), FMOD(3), KERA(10), LUM(7) 538277 36 22 36 13 30 3 1 1 1 0 0.021 0.5 1
10 1_AND_2_METHYLNAPHTHALENE_DEGRADATION ADH1A, ADH1A, ADH1B, ADH1C, ADH1B, ADH1C, ADH4, ADH6, ADH7, ADHFE1 7 ADH1A(9), ADH1B(13), ADH1C(19), ADH4(6), ADH6(6), ADH7(8), ADHFE1(3) 869053 64 39 58 17 49 4 4 5 2 0 0.004 0.61 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) 265596 10 10 10 2 4 1 0 4 1 0 0.23 0.044 1
2 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(3), FOSB(5), GRIA2(19) 561071 27 21 24 7 21 1 0 3 2 0 0.044 0.15 1
3 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(6) 110886 6 6 6 2 6 0 0 0 0 0 0.33 0.33 1
4 HSA00830_RETINOL_METABOLISM Genes involved in retinol metabolism ALDH1A1, ALDH1A2, BCMO1, RDH5 4 ALDH1A1(3), ALDH1A2(8), BCMO1(9), RDH5(1) 601941 21 18 20 5 13 2 1 3 2 0 0.037 0.38 1
5 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(11), FMOD(3), KERA(10), LUM(7) 538277 36 22 36 13 30 3 1 1 1 0 0.021 0.5 1
6 CAPROLACTAM_DEGRADATION AKR1A1, ECHS1, EHHADH, HADHA, SDS 5 EHHADH(5), HADHA(7) 747324 12 11 11 4 8 1 0 3 0 0 0.29 0.64 1
7 BOTULINPATHWAY Blockade of Neurotransmitter Relase by Botulinum Toxin CHRM1, CHRNA1, SNAP25, STX1A, VAMP2 5 CHRM1(4), CHRNA1(1), SNAP25(5), STX1A(2) 505419 12 9 10 3 8 0 0 1 3 0 0.11 0.69 1
8 TCRMOLECULE T Cell Receptor and CD3 Complex CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@ 3 CD3D(4), CD3E(2) 173837 6 4 6 2 5 0 0 0 1 0 0.42 0.7 1
9 BETAOXIDATIONPATHWAY Beta-Oxidation of Fatty Acids ACADL, ACADM, ACADS, ACAT1, ECHS1, HADHA 6 ACADL(2), ACADM(3), HADHA(7) 847363 12 10 12 2 6 1 1 4 0 0 0.18 0.76 1
10 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(1) 79550 1 1 1 1 1 0 0 0 0 0 0.9 0.82 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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