Skin Cutaneous Melanoma: Mutation Analysis (MutSig v1.5)
(All_Samples 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 v1.5 was used to generate the results found in this report.

  • Working with individual set: SKCM-All_Samples

  • Number of patients in set: 264

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-All_Samples.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 76

  • Mutations seen in COSMIC: 719

  • Significantly mutated genes in COSMIC territory: 48

  • Genes with clustered mutations (≤ 3 aa apart): 1817

  • Significantly mutated genesets: 2

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

Mutation Preprocessing

  • Read 264 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 217724

  • After removing 5 mutations outside chr1-24: 217719

  • After removing 921 blacklisted mutations: 216798

  • After removing 4051 noncoding mutations: 212747

Mutation Filtering

  • Number of mutations before filtering: 212747

  • After removing 2697 mutations outside gene set: 210050

  • After removing 182 mutations outside category set: 209868

  • After removing 7 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 206982

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 1021
Frame_Shift_Ins 304
In_Frame_Del 371
In_Frame_Ins 52
Missense_Mutation 128287
Nonsense_Mutation 7849
Nonstop_Mutation 52
Silent 69854
Splice_Site 2014
Translation_Start_Site 64
Total 209868
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 96950 2101461636 0.000046 46 2.5 1.6
(A/G)p*C->T 10787 1763455192 6.1e-06 6.1 0.33 1.9
A->G 5550 3732811328 1.5e-06 1.5 0.081 2.3
transver 15056 7597728156 2e-06 2 0.11 5
indel+null 11505 7597728156 1.5e-06 1.5 0.082 NaN
double_null 162 7597728156 2.1e-08 0.021 0.0012 NaN
Total 140010 7597728156 0.000018 18 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-All_Samples.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_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)

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 76. 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_ns_s p q
1 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 239438 34 34 16 1 10 0 1 1 22 0 0.00032 <1.00e-15 <1.00e-11
2 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 154647 73 73 9 1 2 1 28 42 0 0 1.1e-07 1.11e-15 1.00e-11
3 BRAF v-raf murine sarcoma viral oncogene homolog B1 585625 147 140 18 3 14 1 6 125 1 0 1.2e-10 2.55e-15 1.54e-11
4 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 299528 23 23 20 0 2 0 4 3 14 0 0.014 4.77e-15 1.92e-11
5 TP53 tumor protein p53 320589 43 39 34 1 18 1 4 4 16 0 2.4e-06 5.33e-15 1.92e-11
6 PPP6C protein phosphatase 6, catalytic subunit 265045 24 23 15 2 17 0 0 2 5 0 0.017 1.17e-10 3.52e-07
7 PRB2 proline-rich protein BstNI subfamily 2 328896 50 39 46 2 44 1 1 3 1 0 0.017 3.87e-10 9.98e-07
8 NAP1L2 nucleosome assembly protein 1-like 2 360760 30 26 27 2 22 1 3 2 2 0 0.0014 1.63e-08 3.68e-05
9 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 162300 17 17 8 1 15 0 0 2 0 0 0.0025 5.56e-08 0.000111
10 RBM11 RNA binding motif protein 11 172319 16 16 14 0 11 0 0 2 3 0 0.03 8.99e-08 0.000162
11 LCE1B late cornified envelope 1B 95164 12 12 12 1 8 0 0 2 2 0 0.18 1.10e-07 0.000180
12 GFRAL GDNF family receptor alpha like 316087 40 33 37 9 32 2 0 2 4 0 0.032 7.33e-07 0.00110
13 MUC7 mucin 7, secreted 300191 22 19 17 1 14 1 6 0 1 0 0.0013 9.36e-07 0.00130
14 CDH9 cadherin 9, type 2 (T1-cadherin) 618104 46 37 41 6 35 2 1 5 3 0 0.0058 1.81e-06 0.00227
15 DDX3X DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked 519948 20 20 19 0 7 1 2 3 7 0 0.012 1.89e-06 0.00227
16 HIST1H2AA histone cluster 1, H2aa 105598 10 10 8 0 5 1 0 3 1 0 0.037 3.21e-06 0.00362
17 DEFB118 defensin, beta 118 99490 10 10 8 1 8 0 0 1 1 0 0.18 7.68e-06 0.00815
18 ACSM2B acyl-CoA synthetase medium-chain family member 2B 459165 51 40 37 10 41 4 0 2 4 0 0.00038 1.08e-05 0.0109
19 TFEC transcription factor EC 272153 17 16 17 1 13 1 0 2 1 0 0.044 1.42e-05 0.0131
20 GIMAP7 GTPase, IMAP family member 7 234940 24 24 23 6 15 6 0 3 0 0 0.022 1.45e-05 0.0131
21 FAM19A1 family with sequence similarity 19 (chemokine (C-C motif)-like), member A1 107987 10 10 9 1 6 0 0 2 2 0 0.17 1.69e-05 0.0139
22 FUT9 fucosyltransferase 9 (alpha (1,3) fucosyltransferase) 265158 25 25 24 5 19 2 1 3 0 0 0.048 1.70e-05 0.0139
23 ARID2 AT rich interactive domain 2 (ARID, RFX-like) 1440915 45 38 36 5 19 1 0 2 18 5 0.018 1.92e-05 0.0151
24 OR4N2 olfactory receptor, family 4, subfamily N, member 2 244025 28 25 20 8 25 1 1 1 0 0 0.0012 2.07e-05 0.0155
25 FGF16 fibroblast growth factor 16 86225 8 8 8 0 5 0 0 3 0 0 0.055 2.59e-05 0.0178
26 SNAP91 synaptosomal-associated protein, 91kDa homolog (mouse) 411005 33 28 32 4 25 3 2 1 2 0 0.012 2.63e-05 0.0178
27 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 332700 15 15 4 1 13 0 0 2 0 0 0.012 2.67e-05 0.0178
28 KLHL4 kelch-like 4 (Drosophila) 557440 27 23 25 2 18 3 1 1 4 0 0.0074 3.19e-05 0.0206
29 SPINK13 serine peptidase inhibitor, Kazal type 13 (putative) 79193 9 9 8 1 5 0 0 3 1 0 0.18 3.52e-05 0.0219
30 ANXA10 annexin A10 266162 18 14 18 1 12 0 1 4 1 0 0.013 4.31e-05 0.0259
31 PARM1 prostate androgen-regulated mucin-like protein 1 234441 18 18 15 2 14 2 0 1 1 0 0.018 4.86e-05 0.0280
32 GML glycosylphosphatidylinositol anchored molecule like protein 129090 10 10 10 1 7 0 0 2 1 0 0.088 4.96e-05 0.0280
33 ZNF479 zinc finger protein 479 399294 29 27 22 5 21 0 1 6 1 0 0.064 5.77e-05 0.0316
34 HBG2 hemoglobin, gamma G 94917 10 9 8 2 5 3 0 2 0 0 0.086 6.22e-05 0.0330
35 NOTCH2NL Notch homolog 2 (Drosophila) N-terminal like 190171 13 13 12 2 6 0 1 3 3 0 0.26 6.52e-05 0.0336
CDKN2A

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

NRAS

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

BRAF

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

PTEN

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

TP53

Figure S5.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

PPP6C

Figure S6.  This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.

NAP1L2

Figure S7.  This figure depicts the distribution of mutations and mutation types across the NAP1L2 significant gene.

RAC1

Figure S8.  This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.

RBM11

Figure S9.  This figure depicts the distribution of mutations and mutation types across the RBM11 significant gene.

LCE1B

Figure S10.  This figure depicts the distribution of mutations and mutation types across the LCE1B significant gene.

GFRAL

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

MUC7

Figure S12.  This figure depicts the distribution of mutations and mutation types across the MUC7 significant gene.

CDH9

Figure S13.  This figure depicts the distribution of mutations and mutation types across the CDH9 significant gene.

DDX3X

Figure S14.  This figure depicts the distribution of mutations and mutation types across the DDX3X significant gene.

HIST1H2AA

Figure S15.  This figure depicts the distribution of mutations and mutation types across the HIST1H2AA significant gene.

ACSM2B

Figure S16.  This figure depicts the distribution of mutations and mutation types across the ACSM2B significant gene.

TFEC

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

GIMAP7

Figure S18.  This figure depicts the distribution of mutations and mutation types across the GIMAP7 significant gene.

FAM19A1

Figure S19.  This figure depicts the distribution of mutations and mutation types across the FAM19A1 significant gene.

FUT9

Figure S20.  This figure depicts the distribution of mutations and mutation types across the FUT9 significant gene.

ARID2

Figure S21.  This figure depicts the distribution of mutations and mutation types across the ARID2 significant gene.

OR4N2

Figure S22.  This figure depicts the distribution of mutations and mutation types across the OR4N2 significant gene.

FGF16

Figure S23.  This figure depicts the distribution of mutations and mutation types across the FGF16 significant gene.

SNAP91

Figure S24.  This figure depicts the distribution of mutations and mutation types across the SNAP91 significant gene.

IDH1

Figure S25.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

KLHL4

Figure S26.  This figure depicts the distribution of mutations and mutation types across the KLHL4 significant gene.

SPINK13

Figure S27.  This figure depicts the distribution of mutations and mutation types across the SPINK13 significant gene.

ANXA10

Figure S28.  This figure depicts the distribution of mutations and mutation types across the ANXA10 significant gene.

PARM1

Figure S29.  This figure depicts the distribution of mutations and mutation types across the PARM1 significant gene.

GML

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

ZNF479

Figure S31.  This figure depicts the distribution of mutations and mutation types across the ZNF479 significant gene.

HBG2

Figure S32.  This figure depicts the distribution of mutations and mutation types across the HBG2 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: 48. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 STK19 serine/threonine kinase 19 13 2 6 528 12 0 0
2 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 15 5 12 1320 17904 0 0
3 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 73 33 71 8712 88771 0 0
4 BRAF v-raf murine sarcoma viral oncogene homolog B1 147 89 139 23496 1824289 0 0
5 TP53 tumor protein p53 43 356 41 93984 4732 0 0
6 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 34 332 34 87648 1344 0 0
7 EPHA6 EPH receptor A6 69 8 6 2112 6 4.6e-12 3e-09
8 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 23 767 23 202488 585 1.6e-11 8.8e-09
9 EPHA7 EPH receptor A7 44 13 6 3432 6 8.4e-11 4.2e-08
10 NAP1L2 nucleosome assembly protein 1-like 2 30 1 3 264 3 1.9e-08 8.6e-06

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
1360 BRAF v-raf murine sarcoma viral oncogene homolog B1 147 0 4869 5485 5595 4869 5485 5595
9400 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 73 0 1959 1963 1969 1959 1963 1969
8810 MUC16 mucin 16, cell surface associated 835 0 130 279 716 130 279 716
14817 TTN titin 1177 0 101 174 463 101 174 463
4036 DNAH5 dynein, axonemal, heavy chain 5 336 0 91 139 391 91 139 391
6565 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 15 0 67 67 67 67 67 67
10273 PCLO piccolo (presynaptic cytomatrix protein) 293 0 61 114 274 61 114 274
11496 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 17 0 55 55 67 55 55 67
14078 THSD7B thrombospondin, type I, domain containing 7B 136 0 48 94 215 48 94 215
11991 RP1 retinitis pigmentosa 1 (autosomal dominant) 168 0 39 76 196 39 76 196

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 BFAR(1), BRAF(147), CAMP(1), CREB3(1), CREB5(11), MAPK1(4), RAF1(8), SNX13(1), SRC(1), TERF2IP(2) 4346750 177 155 48 31 31 4 7 131 4 0 0.0029 1.7e-12 1e-09
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(34), CFL1(1), E2F1(7), E2F2(4), MDM2(4), NXT1(2), PRB1(34), TP53(43) 3283462 140 88 108 17 69 4 8 17 42 0 1.4e-10 0.000022 0.0066
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(18), CCND1(1), CCNE1(4), CCNE2(14), CDK4(5), CDKN1B(1), CDKN2A(34), E2F1(7), E2F2(4), E2F4(1), PRB1(34) 3498413 123 84 95 18 71 0 6 20 26 0 1.5e-07 0.029 1
4 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(10) 279111 10 10 10 2 7 1 1 1 0 0 0.12 0.16 1
5 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(12), CDKN2A(34), E2F1(7), MDM2(4), MYC(5), PIK3CA(9), PIK3R1(7), POLR1A(11), POLR1B(9), POLR1C(1), RAC1(17), RB1(8), TBX2(6), TP53(43), TWIST1(1) 7859836 174 108 137 25 87 9 9 18 48 3 7.2e-11 0.43 1
6 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(4) 200024 4 4 4 1 4 0 0 0 0 0 0.48 0.53 1
7 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(4), FOSB(6), GRIA2(38), JUND(1), PPP1R1B(2) 1422676 51 43 48 16 33 3 2 6 7 0 0.038 0.77 1
8 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(5), SP1(5), SP3(1), TP53(43), WT1(6) 2756180 61 49 52 11 27 3 7 6 18 0 0.0023 0.85 1
9 HSA00785_LIPOIC_ACID_METABOLISM Genes involved in lipoic acid metabolism LIAS, LIPT1, LOC387787 2 LIAS(2), LIPT1(3) 601922 5 4 5 0 0 2 1 1 1 0 0.21 0.9 1
10 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(6), GOT2(7), TAT(17) 1024012 30 20 29 8 23 2 2 1 2 0 0.015 0.93 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(10) 279111 10 10 10 2 7 1 1 1 0 0 0.12 0.16 1
2 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(4) 200024 4 4 4 1 4 0 0 0 0 0 0.48 0.53 1
3 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(4), FOSB(6), GRIA2(38), JUND(1), PPP1R1B(2) 1422676 51 43 48 16 33 3 2 6 7 0 0.038 0.77 1
4 HSA00785_LIPOIC_ACID_METABOLISM Genes involved in lipoic acid metabolism LIAS, LIPT1, LOC387787 2 LIAS(2), LIPT1(3) 601922 5 4 5 0 0 2 1 1 1 0 0.21 0.9 1
5 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(6), GOT2(7), TAT(17) 1024012 30 20 29 8 23 2 2 1 2 0 0.015 0.93 1
6 SLRPPATHWAY Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. BGN, DCN, DSPG3, FMOD, KERA, LUM 5 BGN(6), DCN(17), FMOD(5), KERA(15), LUM(12) 1368273 55 41 51 18 44 4 3 1 3 0 0.0024 0.94 1
7 HSA00031_INOSITOL_METABOLISM Genes involved in inositol metabolism ALDH6A1, TPI1 2 ALDH6A1(5) 644527 5 5 3 1 4 0 0 1 0 0 0.27 0.96 1
8 BOTULINPATHWAY Blockade of Neurotransmitter Relase by Botulinum Toxin CHRM1, CHRNA1, SNAP25, STX1A, VAMP2 5 CHRM1(5), CHRNA1(5), SNAP25(6), STX1A(3) 1271830 19 16 16 4 13 1 0 1 4 0 0.016 0.98 1
9 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(7) 668513 12 12 12 5 6 1 0 4 1 0 0.49 0.99 1
10 INOSITOL_METABOLISM ALDH6A1, ALDOA, ALDOB, ALDOC, TPI1 5 ALDH6A1(5), ALDOA(2), ALDOB(13), ALDOC(3) 1534583 23 18 19 5 18 2 0 1 2 0 0.01 0.99 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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
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