Skin Cutaneous Melanoma: Mutation Analysis (MutSig v2.0)
(NF1_Any_Mutants 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-NF1_Any_Mutants

  • Number of patients in set: 31

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-NF1_Any_Mutants.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 46

  • Mutations seen in COSMIC: 140

  • Significantly mutated genes in COSMIC territory: 10

  • Genes with clustered mutations (≤ 3 aa apart): 602

  • Significantly mutated genesets: 0

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

Mutation Preprocessing

  • Read 31 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 56688

  • After removing 2 mutations outside chr1-24: 56686

  • After removing 123 blacklisted mutations: 56563

  • After removing 1039 noncoding mutations: 55524

Mutation Filtering

  • Number of mutations before filtering: 55524

  • After removing 675 mutations outside gene set: 54849

  • After removing 46 mutations outside category set: 54803

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 236
Frame_Shift_Ins 64
In_Frame_Del 125
In_Frame_Ins 9
Missense_Mutation 33301
Nonsense_Mutation 2150
Nonstop_Mutation 17
Silent 18387
Splice_Site 500
Translation_Start_Site 14
Total 54803
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 25919 247926384 0.0001 100 2.6 1.6
(A/G)p*C->T 2673 208118093 0.000013 13 0.32 1.9
A->G 1443 439863049 3.3e-06 3.3 0.081 2.3
transver 3279 895907526 3.7e-06 3.7 0.09 5
indel+null 3057 895907526 3.4e-06 3.4 0.084 NaN
double_null 45 895907526 5e-08 0.05 0.0012 NaN
Total 36416 895907526 0.000041 41 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-NF1_Any_Mutants.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: 46. 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 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 265976 38 31 36 1 12 0 1 3 18 4 3.7e-15 0.000024 1 1 1.2e-13 2.3e-09
2 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 18116 9 9 6 0 1 0 1 7 0 0 3.2e-11 0.14 0.17 0.00054 5.7e-13 5.1e-09
3 TPTE transmembrane phosphatase with tensin homology 53920 29 15 27 1 24 0 1 0 4 0 1.4e-10 0.00033 0.58 0.57 1.9e-09 0.000012
4 TP53 tumor protein p53 37759 11 10 10 0 4 0 0 2 5 0 9.7e-08 0.025 0.2 0.0072 1.5e-08 0.000069
5 GRXCR1 glutaredoxin, cysteine rich 1 26704 12 10 11 1 5 1 2 1 3 0 1e-09 0.052 0.73 0.87 2e-08 0.000071
6 BRAF v-raf murine sarcoma viral oncogene homolog B1 68906 9 9 6 0 6 0 1 2 0 0 0.00016 0.057 0.079 0.000025 8.1e-08 0.00024
7 TRAT1 T cell receptor associated transmembrane adaptor 1 18135 9 7 6 1 7 1 1 0 0 0 1.9e-06 0.11 0.078 0.0081 2.9e-07 0.00073
8 ZNF585B zinc finger protein 585B 70432 11 9 10 1 7 2 1 0 1 0 0.00022 0.051 0.086 0.000079 3.2e-07 0.00073
9 TPTE2 transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 50530 15 12 14 1 11 2 0 1 1 0 3.4e-08 0.035 0.86 0.66 4.2e-07 0.00085
10 OR51S1 olfactory receptor, family 51, subfamily S, member 1 30128 11 11 9 1 8 0 0 1 2 0 1.3e-07 0.0089 0.89 0.2 4.7e-07 0.00085
11 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 19060 5 5 2 0 5 0 0 0 0 0 0.0023 0.08 0.19 0.000017 7.2e-07 0.0012
12 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 27643 6 6 4 0 2 0 0 1 3 0 0.00022 0.14 0.00013 0.00037 1.4e-06 0.0021
13 C7 complement component 7 65059 19 14 17 1 17 1 0 0 1 0 3.6e-06 0.013 0.51 0.03 1.8e-06 0.0025
14 C15orf23 chromosome 15 open reading frame 23 31624 7 6 3 0 7 0 0 0 0 0 0.0058 0.042 1 0.000023 2.3e-06 0.0029
15 GLRB glycine receptor, beta 45005 10 9 9 1 7 0 1 0 2 0 0.000018 0.05 0.093 0.01 3e-06 0.0036
16 FAM58A family with sequence similarity 58, member A 18604 5 5 4 0 0 0 0 0 5 0 0.000012 0.26 0.085 0.017 3.3e-06 0.0038
17 EPHA6 EPH receptor A6 95264 24 15 19 2 21 0 0 2 1 0 0.00017 0.0043 0.49 0.0019 5e-06 0.0053
18 NAP1L2 nucleosome assembly protein 1-like 2 42424 10 9 10 0 5 0 2 1 2 0 2.3e-06 0.033 0.46 0.19 6.9e-06 0.0069
19 SLC9A11 solute carrier family 9, member 11 105541 17 13 15 1 13 0 2 2 0 0 0.000012 0.012 0.85 0.043 8.2e-06 0.0076
20 OR4K5 olfactory receptor, family 4, subfamily K, member 5 30194 11 10 11 3 3 0 1 5 2 0 8.5e-07 0.27 0.36 0.64 8.4e-06 0.0076
21 ADAMTS20 ADAM metallopeptidase with thrombospondin type 1 motif, 20 153071 32 18 31 1 28 1 0 1 2 0 6.8e-06 0.0015 0.097 0.2 2e-05 0.017
22 SLC38A4 solute carrier family 38, member 4 47556 15 13 13 2 13 0 0 2 0 0 4.4e-06 0.046 0.95 0.44 0.000028 0.023
23 OR2T2 olfactory receptor, family 2, subfamily T, member 2 27909 10 8 9 1 7 1 1 0 1 0 0.000013 0.007 0.48 0.21 0.000038 0.03
24 PRB2 proline-rich protein BstNI subfamily 2 38658 12 11 12 1 11 0 0 1 0 0 0.000035 0.5 0.79 0.1 0.000048 0.036
25 COL21A1 collagen, type XXI, alpha 1 63654 22 12 22 1 19 1 0 0 2 0 3.9e-06 0.042 0.46 1 0.000053 0.037
26 PROX1 prospero homeobox 1 69130 8 7 7 0 7 0 0 1 0 0 0.021 0.031 0.8 0.00019 0.000054 0.037
27 OR4N2 olfactory receptor, family 4, subfamily N, member 2 28702 12 10 9 3 12 0 0 0 0 0 0.000011 0.017 0.18 0.39 0.000055 0.037
28 C8A complement component 8, alpha polypeptide 52887 13 11 12 0 10 0 0 1 2 0 7.4e-06 0.0061 0.88 0.73 7e-05 0.044
29 ANGPT1 angiopoietin 1 47231 12 10 11 1 9 0 0 2 1 0 0.000012 0.079 0.52 0.44 0.000071 0.044
30 SERPINB11 serpin peptidase inhibitor, clade B (ovalbumin), member 11 29826 8 7 8 1 5 2 0 0 1 0 8.4e-06 0.1 0.48 0.75 0.000082 0.049
31 THEMIS thymocyte selection associated 57922 15 10 13 3 12 0 1 2 0 0 0.0009 0.12 0.48 0.0082 0.000094 0.053
32 LPPR1 31143 5 5 5 1 4 0 0 0 1 0 0.0043 0.18 0.47 0.0017 0.000094 0.053
33 C18orf34 chromosome 18 open reading frame 34 76034 11 11 11 1 8 1 0 2 0 0 2e-05 0.097 0.4 0.38 0.000099 0.053
34 FRG2B FSHD region gene 2 family, member B 16484 7 7 5 2 5 1 0 1 0 0 0.000049 0.33 0.97 0.16 0.000099 0.053
35 SNAP91 synaptosomal-associated protein, 91kDa homolog (mouse) 49635 13 10 13 0 10 2 1 0 0 0 0.000015 0.013 0.95 0.6 0.00011 0.057
NF1

Figure S1.  This figure depicts the distribution of mutations and mutation types across the NF1 significant gene.

NRAS

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

TPTE

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

TP53

Figure S4.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

GRXCR1

Figure S5.  This figure depicts the distribution of mutations and mutation types across the GRXCR1 significant gene.

BRAF

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

TRAT1

Figure S7.  This figure depicts the distribution of mutations and mutation types across the TRAT1 significant gene.

ZNF585B

Figure S8.  This figure depicts the distribution of mutations and mutation types across the ZNF585B significant gene.

TPTE2

Figure S9.  This figure depicts the distribution of mutations and mutation types across the TPTE2 significant gene.

OR51S1

Figure S10.  This figure depicts the distribution of mutations and mutation types across the OR51S1 significant gene.

RAC1

Figure S11.  This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.

CDKN2A

Figure S12.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

C7

Figure S13.  This figure depicts the distribution of mutations and mutation types across the C7 significant gene.

C15orf23

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

GLRB

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

FAM58A

Figure S16.  This figure depicts the distribution of mutations and mutation types across the FAM58A significant gene.

EPHA6

Figure S17.  This figure depicts the distribution of mutations and mutation types across the EPHA6 significant gene.

NAP1L2

Figure S18.  This figure depicts the distribution of mutations and mutation types across the NAP1L2 significant gene.

SLC9A11

Figure S19.  This figure depicts the distribution of mutations and mutation types across the SLC9A11 significant gene.

OR4K5

Figure S20.  This figure depicts the distribution of mutations and mutation types across the OR4K5 significant gene.

ADAMTS20

Figure S21.  This figure depicts the distribution of mutations and mutation types across the ADAMTS20 significant gene.

SLC38A4

Figure S22.  This figure depicts the distribution of mutations and mutation types across the SLC38A4 significant gene.

OR2T2

Figure S23.  This figure depicts the distribution of mutations and mutation types across the OR2T2 significant gene.

COL21A1

Figure S24.  This figure depicts the distribution of mutations and mutation types across the COL21A1 significant gene.

PROX1

Figure S25.  This figure depicts the distribution of mutations and mutation types across the PROX1 significant gene.

OR4N2

Figure S26.  This figure depicts the distribution of mutations and mutation types across the OR4N2 significant gene.

C8A

Figure S27.  This figure depicts the distribution of mutations and mutation types across the C8A significant gene.

ANGPT1

Figure S28.  This figure depicts the distribution of mutations and mutation types across the ANGPT1 significant gene.

SERPINB11

Figure S29.  This figure depicts the distribution of mutations and mutation types across the SERPINB11 significant gene.

THEMIS

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

LPPR1

Figure S31.  This figure depicts the distribution of mutations and mutation types across the LPPR1 significant gene.

C18orf34

Figure S32.  This figure depicts the distribution of mutations and mutation types across the C18orf34 significant gene.

FRG2B

Figure S33.  This figure depicts the distribution of mutations and mutation types across the FRG2B 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: 10. 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 9 33 7 1023 8434 8.2e-14 2.5e-10
2 BRAF v-raf murine sarcoma viral oncogene homolog B1 9 89 9 2759 28833 1.1e-13 2.5e-10
3 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 38 285 10 8835 24 7.3e-12 1.1e-08
4 TP53 tumor protein p53 11 356 10 11036 732 6.1e-11 6.8e-08
5 EPHA6 EPH receptor A6 24 8 4 248 4 4.2e-10 3.8e-07
6 CNTN5 contactin 5 23 1 2 31 2 7.7e-07 0.00058
7 CTNNA3 catenin (cadherin-associated protein), alpha 3 13 2 2 62 2 3.1e-06 0.0018
8 STK19 serine/threonine kinase 19 4 2 2 62 4 3.1e-06 0.0018
9 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 6 332 6 10292 217 5.2e-06 0.0026
10 PDGFRA platelet-derived growth factor receptor, alpha polypeptide 9 69 3 2139 3 0.0001 0.046

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
6179 MUC16 mucin 16, cell surface associated 203 0 14 26 46 14 26 46
6612 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 9 0 10 10 12 10 10 12
10471 TTN titin 324 0 8 14 32 8 14 32
7310 PCLO piccolo (presynaptic cytomatrix protein) 101 0 8 13 32 8 13 32
1166 C15orf23 chromosome 15 open reading frame 23 7 0 7 11 11 7 11 11
2850 DNAH5 dynein, axonemal, heavy chain 5 69 0 7 10 22 7 10 22
670 ARMC4 armadillo repeat containing 4 29 0 7 7 14 7 7 14
4947 KCNB2 potassium voltage-gated channel, Shab-related subfamily, member 2 21 0 6 8 10 6 8 10
3210 EPHA6 EPH receptor A6 24 0 6 6 19 6 6 19
8151 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 5 0 6 6 10 6 6 10

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: 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 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 MYC(2), SP1(2), TP53(11), WT1(3) 324396 18 14 17 1 8 1 1 3 5 0 0.01 0.012 1
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(1), CDKN1B(1), CDKN2A(6), E2F1(2), E2F2(1), PRB1(8), TP53(11) 386767 33 19 30 5 17 1 1 5 9 0 0.0051 0.019 1
3 RECKPATHWAY RECK is a membrane-anchored inhibitor of matrix metalloproteinases, which are expressed by tumor cells and promote metastasis. HRAS, MMP14, MMP2, MMP9, RECK, TIMP1, TIMP2, TIMP3, TIMP4 9 HRAS(2), MMP14(2), MMP2(3), MMP9(4), RECK(2), TIMP1(1), TIMP3(1), TIMP4(2) 340497 17 15 17 2 10 2 1 4 0 0 0.019 0.038 1
4 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(4) 32727 4 4 4 0 3 1 0 0 0 0 0.13 0.039 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(2), DCN(6), FMOD(2), KERA(8), LUM(4) 161484 22 15 22 5 16 2 3 1 0 0 0.016 0.045 1
6 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(2), CCND1(1), CCNE1(1), CCNE2(3), CDK4(2), CDKN1B(1), CDKN2A(6), E2F1(2), E2F2(1), E2F4(1), PRB1(8) 412938 28 19 26 5 16 0 2 5 5 0 0.024 0.067 1
7 BOTULINPATHWAY Blockade of Neurotransmitter Relase by Botulinum Toxin CHRM1, CHRNA1, SNAP25, STX1A, VAMP2 5 CHRM1(2), CHRNA1(3), SNAP25(2), STX1A(1) 149636 8 7 8 1 3 1 0 1 3 0 0.089 0.15 1
8 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 FOSB(2), GRIA2(5), PPP1R1B(1) 168715 8 8 7 1 6 0 0 0 2 0 0.11 0.22 1
9 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 CCNE1(1), CDC34(1), CUL1(2), E2F1(2), FBXW7(4), RB1(2), TFDP1(1) 373766 13 10 13 2 5 1 2 1 3 1 0.071 0.27 1
10 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(1), CDKN2A(6), E2F1(2), MYC(2), PIK3CA(3), POLR1A(5), POLR1B(4), RAC1(5), RB1(2), TBX2(2), TP53(11) 926877 43 19 37 4 27 2 0 3 10 1 5e-05 0.31 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 RECKPATHWAY RECK is a membrane-anchored inhibitor of matrix metalloproteinases, which are expressed by tumor cells and promote metastasis. HRAS, MMP14, MMP2, MMP9, RECK, TIMP1, TIMP2, TIMP3, TIMP4 9 HRAS(2), MMP14(2), MMP2(3), MMP9(4), RECK(2), TIMP1(1), TIMP3(1), TIMP4(2) 340497 17 15 17 2 10 2 1 4 0 0 0.019 0.038 1
2 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(4) 32727 4 4 4 0 3 1 0 0 0 0 0.13 0.039 1
3 SLRPPATHWAY Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. BGN, DCN, DSPG3, FMOD, KERA, LUM 5 BGN(2), DCN(6), FMOD(2), KERA(8), LUM(4) 161484 22 15 22 5 16 2 3 1 0 0 0.016 0.045 1
4 BOTULINPATHWAY Blockade of Neurotransmitter Relase by Botulinum Toxin CHRM1, CHRNA1, SNAP25, STX1A, VAMP2 5 CHRM1(2), CHRNA1(3), SNAP25(2), STX1A(1) 149636 8 7 8 1 3 1 0 1 3 0 0.089 0.15 1
5 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 FOSB(2), GRIA2(5), PPP1R1B(1) 168715 8 8 7 1 6 0 0 0 2 0 0.11 0.22 1
6 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 CCNE1(1), CDC34(1), CUL1(2), E2F1(2), FBXW7(4), RB1(2), TFDP1(1) 373766 13 10 13 2 5 1 2 1 3 1 0.071 0.27 1
7 RIBOFLAVIN_METABOLISM ACP1, ACP2, ACP5, ACPP, ACPT, ENPP1, ENPP3, FLAD1, RFK, TYR 10 ACP5(1), ACPP(2), ENPP1(4), ENPP3(7), FLAD1(2), TYR(3) 440888 19 13 19 2 12 1 1 1 4 0 0.013 0.37 1
8 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(1) 23498 1 1 1 0 1 0 0 0 0 0 0.68 0.38 1
9 FLUMAZENILPATHWAY Flumazenil is a benzodiazepine receptor antagonist that may induce protective preconditioning in ischemic cardiomyocytes. GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GPX1, PRKCE, SOD1 9 GABRA1(6), GABRA2(4), GABRA3(6), GABRA4(3), GABRA5(1), GABRA6(8), PRKCE(2) 352674 30 17 28 8 21 2 1 4 2 0 0.035 0.4 1
10 EOSINOPHILSPATHWAY Recruitment of eosinophils in the inflammatory response observed in asthma occurs via the chemoattractant eotaxin binding to the CCR3 receptor. CCL11, CCL5, CCR3, CSF2, HLA-DRA, HLA-DRB1, IL3, IL5 8 CCR3(3), HLA-DRA(3), HLA-DRB1(2) 138490 8 7 8 3 7 0 0 0 1 0 0.18 0.44 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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