Skin Cutaneous Melanoma: Mutation Analysis (MutSig v2.0)
(metastatic tumor 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-TM

  • Number of patients in set: 225

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-TM.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 98

  • Mutations seen in COSMIC: 595

  • Significantly mutated genes in COSMIC territory: 41

  • Genes with clustered mutations (≤ 3 aa apart): 1213

  • Significantly mutated genesets: 2

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

Mutation Preprocessing

  • Read 225 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 172938

  • After removing 4 mutations outside chr1-24: 172934

  • After removing 790 blacklisted mutations: 172144

  • After removing 3204 noncoding mutations: 168940

Mutation Filtering

  • Number of mutations before filtering: 168940

  • After removing 2144 mutations outside gene set: 166796

  • After removing 110 mutations outside category set: 166686

  • After removing 7 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 164425

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 907
Frame_Shift_Ins 264
In_Frame_Del 335
In_Frame_Ins 49
Missense_Mutation 102037
Nonsense_Mutation 6390
Nonstop_Mutation 44
Silent 54926
Splice_Site 1686
Translation_Start_Site 48
Total 166686
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 75410 1788133353 0.000042 42 2.4 1.6
(A/G)p*C->T 8509 1500436990 5.7e-06 5.7 0.33 1.9
A->G 4906 3176808123 1.5e-06 1.5 0.089 2.3
transver 13254 6465378466 2e-06 2 0.12 5
indel+null 9574 6465378466 1.5e-06 1.5 0.086 NaN
double_null 103 6465378466 1.6e-08 0.016 0.00092 NaN
Total 111756 6465378466 0.000017 17 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-TM.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: 98. 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 TP53 tumor protein p53 272813 37 34 31 1 15 0 4 4 14 0 2.8e-15 0.000028 0.055 2e-05 0.000 0.000
2 BRAF v-raf murine sarcoma viral oncogene homolog B1 498822 120 115 16 2 11 1 5 103 0 0 2.4e-15 2.3e-09 0 0 <1.00e-15 <2.58e-12
3 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 131798 65 65 9 1 2 1 22 40 0 0 2.3e-15 1.4e-06 1.6e-06 0 <1.00e-15 <2.58e-12
4 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 206066 31 31 15 1 9 0 0 1 21 0 6.8e-15 0.00083 0 0 <1.00e-15 <2.58e-12
5 C15orf23 chromosome 15 open reading frame 23 229072 15 14 7 4 15 0 0 0 0 0 0.01 0.14 1 0 <1.00e-15 <2.58e-12
6 STK19 serine/threonine kinase 19 243376 12 10 7 0 10 1 0 1 0 0 0.024 0.0052 0.92 0 <1.00e-15 <2.58e-12
7 OXA1L oxidase (cytochrome c) assembly 1-like 343046 6 6 3 2 6 0 0 0 0 0 0.78 0.41 1 0 <1.00e-15 <2.58e-12
8 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 254423 18 18 16 0 1 0 3 3 11 0 8.8e-14 0.046 0.71 0.12 3.37e-13 7.60e-10
9 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 138204 16 16 8 1 14 0 0 2 0 0 5.1e-08 0.004 0.2 0.00031 4.07e-10 8.17e-07
10 ACSM2B acyl-CoA synthetase medium-chain family member 2B 390509 42 36 32 5 34 2 0 2 4 0 6e-10 0.000053 0.68 1 1.33e-08 2.39e-05
11 CADM2 cell adhesion molecule 2 289047 28 22 26 3 18 9 0 1 0 0 1.9e-08 0.0067 0.72 0.044 1.84e-08 3.01e-05
12 OR51S1 olfactory receptor, family 51, subfamily S, member 1 218336 27 26 18 6 21 3 0 1 2 0 1.7e-07 0.0023 0.99 0.0063 2.32e-08 3.50e-05
13 LCE1B late cornified envelope 1B 81085 13 13 13 0 8 0 0 3 2 0 1.3e-09 0.042 0.68 1 2.88e-08 4.00e-05
14 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 283623 11 11 4 1 10 0 0 1 0 0 0.00073 0.044 0.98 0.000015 2.14e-07 0.000261
15 TAF1A TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa 313386 14 14 7 0 1 0 0 13 0 0 5.6e-07 0.13 0.37 0.02 2.17e-07 0.000261
16 NAP1L2 nucleosome assembly protein 1-like 2 307024 23 21 22 1 16 1 2 2 2 0 5.5e-08 0.003 0.19 0.28 2.95e-07 0.000333
17 MUC7 mucin 7, secreted 255653 22 19 17 1 14 1 6 0 1 0 1.2e-07 0.0013 0.085 0.2 4.26e-07 0.000453
18 PPP6C protein phosphatase 6, catalytic subunit 225775 18 17 13 2 12 0 0 2 4 0 2.3e-07 0.078 0.38 0.15 6.36e-07 0.000638
19 FRG2B FSHD region gene 2 family, member B 117951 17 17 11 4 13 1 1 2 0 0 5.3e-06 0.092 0.96 0.0093 8.81e-07 0.000837
20 USP29 ubiquitin specific peptidase 29 623157 43 35 38 4 31 1 4 2 5 0 2.2e-07 0.000071 0.16 0.41 1.51e-06 0.00137
21 PRB4 proline-rich protein BstNI subfamily 4 170100 18 18 13 2 15 0 1 1 1 0 0.000098 0.2 0.71 0.00095 1.60e-06 0.00137
22 RPTN repetin 531666 47 38 42 4 35 2 4 6 0 0 3e-07 0.0015 0.98 0.48 2.46e-06 0.00198
23 HIST1H2AA histone cluster 1, H2aa 89998 10 10 8 0 5 1 0 3 1 0 8.3e-07 0.037 0.67 0.18 2.52e-06 0.00198
24 ZNF479 zinc finger protein 479 338455 23 22 18 3 16 0 1 5 1 0 2.4e-06 0.051 0.99 0.067 2.63e-06 0.00198
25 C8A complement component 8, alpha polypeptide 384948 29 26 25 2 24 1 0 1 3 0 1.4e-06 0.00048 0.97 0.15 3.39e-06 0.00245
26 FUT9 fucosyltransferase 9 (alpha (1,3) fucosyltransferase) 224540 22 22 21 4 15 2 1 4 0 0 2.2e-07 0.058 0.63 1 3.67e-06 0.00255
27 ZNF679 zinc finger protein 679 176141 19 18 15 2 15 0 1 3 0 0 7.3e-07 0.032 0.43 0.46 5.34e-06 0.00357
28 NRK Nik related kinase 548842 29 28 28 4 22 0 0 3 4 0 0.000012 0.017 0.0041 0.03 5.60e-06 0.00361
29 CDH9 cadherin 9, type 2 (T1-cadherin) 525372 37 32 34 4 30 1 0 3 3 0 8.1e-07 0.0061 0.26 0.5 6.35e-06 0.00396
30 PRAMEF11 PRAME family member 11 279205 24 21 19 7 8 2 4 6 4 0 0.000017 0.067 0.92 0.029 7.53e-06 0.00453
31 DDX3X DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked 442121 18 18 17 0 6 1 2 2 7 0 4.1e-06 0.019 0.86 0.14 9.04e-06 0.00526
32 GRXCR1 glutaredoxin, cysteine rich 1 195954 20 18 18 3 11 2 2 1 4 0 7.9e-07 0.04 0.72 1 1.19e-05 0.00670
33 PRB2 proline-rich protein BstNI subfamily 2 280074 37 29 35 2 33 1 1 1 1 0 1e-05 0.07 0.78 0.083 1.25e-05 0.00682
34 IL32 interleukin 32 111539 9 9 6 2 2 1 0 1 5 0 4e-05 0.57 0.9 0.022 1.33e-05 0.00695
35 ELF5 E74-like factor 5 (ets domain transcription factor) 183331 7 7 6 2 5 0 0 0 2 0 0.05 0.32 0.2 0.000018 1.35e-05 0.00695
TP53

Figure S1.  This figure depicts the distribution of mutations and mutation types across the TP53 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.

C15orf23

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

STK19

Figure S6.  This figure depicts the distribution of mutations and mutation types across the STK19 significant gene.

OXA1L

Figure S7.  This figure depicts the distribution of mutations and mutation types across the OXA1L significant gene.

PTEN

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

RAC1

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

ACSM2B

Figure S10.  This figure depicts the distribution of mutations and mutation types across the ACSM2B significant gene.

CADM2

Figure S11.  This figure depicts the distribution of mutations and mutation types across the CADM2 significant gene.

OR51S1

Figure S12.  This figure depicts the distribution of mutations and mutation types across the OR51S1 significant gene.

LCE1B

Figure S13.  This figure depicts the distribution of mutations and mutation types across the LCE1B significant gene.

IDH1

Figure S14.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

TAF1A

Figure S15.  This figure depicts the distribution of mutations and mutation types across the TAF1A significant gene.

NAP1L2

Figure S16.  This figure depicts the distribution of mutations and mutation types across the NAP1L2 significant gene.

MUC7

Figure S17.  This figure depicts the distribution of mutations and mutation types across the MUC7 significant gene.

PPP6C

Figure S18.  This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.

FRG2B

Figure S19.  This figure depicts the distribution of mutations and mutation types across the FRG2B significant gene.

USP29

Figure S20.  This figure depicts the distribution of mutations and mutation types across the USP29 significant gene.

PRB4

Figure S21.  This figure depicts the distribution of mutations and mutation types across the PRB4 significant gene.

RPTN

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

HIST1H2AA

Figure S23.  This figure depicts the distribution of mutations and mutation types across the HIST1H2AA significant gene.

ZNF479

Figure S24.  This figure depicts the distribution of mutations and mutation types across the ZNF479 significant gene.

C8A

Figure S25.  This figure depicts the distribution of mutations and mutation types across the C8A significant gene.

FUT9

Figure S26.  This figure depicts the distribution of mutations and mutation types across the FUT9 significant gene.

ZNF679

Figure S27.  This figure depicts the distribution of mutations and mutation types across the ZNF679 significant gene.

NRK

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

CDH9

Figure S29.  This figure depicts the distribution of mutations and mutation types across the CDH9 significant gene.

PRAMEF11

Figure S30.  This figure depicts the distribution of mutations and mutation types across the PRAMEF11 significant gene.

DDX3X

Figure S31.  This figure depicts the distribution of mutations and mutation types across the DDX3X significant gene.

GRXCR1

Figure S32.  This figure depicts the distribution of mutations and mutation types across the GRXCR1 significant gene.

IL32

Figure S33.  This figure depicts the distribution of mutations and mutation types across the IL32 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: 41. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 STK19 serine/threonine kinase 19 12 2 6 450 12 0 0
2 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 65 33 63 7425 78387 0 0
3 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 11 5 9 1125 13428 0 0
4 BRAF v-raf murine sarcoma viral oncogene homolog B1 120 89 114 20025 1479650 0 0
5 TP53 tumor protein p53 37 356 35 80100 3367 0 0
6 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 31 332 31 74700 1172 0 0
7 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 18 767 18 172575 374 3.3e-09 2.1e-06
8 EPHA6 EPH receptor A6 58 8 4 1800 4 3.8e-08 0.000021
9 EPHA7 EPH receptor A7 36 13 4 2925 4 2.6e-07 0.00011
10 RIPK4 receptor-interacting serine-threonine kinase 4 8 3 3 675 3 2.6e-07 0.00011

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
1330 BRAF v-raf murine sarcoma viral oncogene homolog B1 120 0 3582 4024 4117 3582 4024 4117
9126 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 65 0 1491 1495 1501 1491 1495 1501
8549 MUC16 mucin 16, cell surface associated 665 0 95 184 469 95 184 469
14404 TTN titin 914 0 74 113 275 74 113 275
3917 DNAH5 dynein, axonemal, heavy chain 5 274 0 74 105 254 74 105 254
9980 PCLO piccolo (presynaptic cytomatrix protein) 240 0 53 93 194 53 93 194
11166 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 16 0 45 45 56 45 45 56
6375 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 11 0 36 36 36 36 36 36
3083 CNTN5 contactin 5 65 0 32 42 69 32 42 69
13685 THSD7B thrombospondin, type I, domain containing 7B 111 0 31 62 129 31 62 129

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(120), CAMP(1), CREB3(1), CREB5(7), MAPK1(4), RAF1(7), SNX13(1), SRC(1), TERF2IP(1) 3702957 143 127 39 25 24 4 6 106 3 0 0.0069 1.7e-15 1e-12
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(5), CDKN1A(4), CDKN1B(1), CDKN2A(31), CFL1(1), E2F1(4), E2F2(4), MDM2(3), NXT1(1), PRB1(26), TP53(37) 2797685 118 78 92 14 54 3 6 16 39 0 6e-09 8.9e-07 0.00028
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(13), CCND1(1), CCNE1(3), CCNE2(12), CDK4(5), CDKN1B(1), CDKN2A(31), E2F1(4), E2F2(4), E2F4(1), PRB1(26) 2981654 101 74 77 14 55 0 4 18 24 0 1.5e-06 0.0093 1
4 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(9) 237556 9 9 9 1 6 1 1 1 0 0 0.073 0.04 1
5 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(4), SP1(3), TP53(37), WT1(4) 2347608 49 41 43 7 22 1 7 5 14 0 0.0016 0.23 1
6 ARFPATHWAY Cyclin-dependent kinase inhibitor 2A is a tumor suppressor that induces G1 arrest and can activate the p53 pathway, leading to G2/M arrest. ABL1, CDKN2A, E2F1, MDM2, MYC, PIK3CA, PIK3R1, POLR1A, POLR1B, POLR1C, POLR1D, RAC1, RB1, TBX2, TP53, TWIST1 16 ABL1(10), CDKN2A(31), E2F1(4), MDM2(3), MYC(4), PIK3CA(6), PIK3R1(3), POLR1A(11), POLR1B(8), RAC1(16), RB1(8), TBX2(6), TP53(37), TWIST1(1) 6692195 148 92 118 20 74 7 6 16 42 3 8.5e-10 0.25 1
7 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(3) 170466 3 3 3 1 3 0 0 0 0 0 0.61 0.49 1
8 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(3), GOT2(4), TAT(12) 871759 19 16 18 4 12 2 2 1 2 0 0.033 0.53 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(15), FMOD(4), KERA(13), LUM(10) 1162061 47 37 44 14 36 4 3 1 3 0 0.0024 0.66 1
10 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(4), FOSB(5), GRIA2(31), JUND(1), PPP1R1B(2) 1208725 43 38 40 14 26 3 2 5 7 0 0.076 0.68 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 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(9) 237556 9 9 9 1 6 1 1 1 0 0 0.073 0.04 1
2 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(3) 170466 3 3 3 1 3 0 0 0 0 0 0.61 0.49 1
3 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(3), GOT2(4), TAT(12) 871759 19 16 18 4 12 2 2 1 2 0 0.033 0.53 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(15), FMOD(4), KERA(13), LUM(10) 1162061 47 37 44 14 36 4 3 1 3 0 0.0024 0.66 1
5 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(4), FOSB(5), GRIA2(31), JUND(1), PPP1R1B(2) 1208725 43 38 40 14 26 3 2 5 7 0 0.076 0.68 1
6 BOTULINPATHWAY Blockade of Neurotransmitter Relase by Botulinum Toxin CHRM1, CHRNA1, SNAP25, STX1A, VAMP2 5 CHRM1(3), CHRNA1(5), SNAP25(5), STX1A(2) 1083206 15 14 13 2 9 1 0 1 4 0 0.013 0.89 1
7 HSA03060_PROTEIN_EXPORT Genes involved in protein export OXA1L, SEC61A2, SRP19, SRP54, SRP68, SRP72, SRP9, SRPR 7 SEC61A2(7), SRP19(5), SRP54(3), SRP68(6), SRP72(1), SRP9(1), SRPR(2) 2191823 25 21 25 4 6 0 3 10 6 0 0.2 0.94 1
8 BBCELLPATHWAY Fas ligand expression by T cells induces apoptosis in Fas-expressing, inactive B cells. CD28, CD4, HLA-DRA, HLA-DRB1, TNFRSF5, TNFRSF6, TNFSF5, TNFSF6 4 CD28(1), CD4(6), HLA-DRA(10), HLA-DRB1(3) 777496 20 18 20 8 15 1 0 3 1 0 0.14 0.96 1
9 INOSITOL_METABOLISM ALDH6A1, ALDOA, ALDOB, ALDOC, TPI1 5 ALDH6A1(3), ALDOA(1), ALDOB(9), ALDOC(3) 1307091 16 14 13 4 11 2 0 1 2 0 0.061 0.96 1
10 HSA00785_LIPOIC_ACID_METABOLISM Genes involved in lipoic acid metabolism LIAS, LIPT1, LOC387787 2 LIPT1(2) 512888 2 2 2 0 0 1 0 1 0 0 0.63 0.97 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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