Skin Cutaneous Melanoma: Mutation Analysis (MutSig v2.0)
(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 v2.0 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): 79

  • 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_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: 79. 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 27223512 1177 204 1077 409 907 76 37 110 38 9 1.000 0.0029 1 0 <1.00e-15 <2.01e-12
2 BRAF v-raf murine sarcoma viral oncogene homolog B1 585625 147 140 18 3 14 1 6 125 1 0 2.55e-15 1.2e-10 0 0 <1.00e-15 <2.01e-12
3 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 154647 73 73 9 1 2 1 28 42 0 0 1.11e-15 1.1e-07 8e-07 0 <1.00e-15 <2.01e-12
4 TP53 tumor protein p53 320589 43 39 34 1 18 1 4 4 16 0 5.33e-15 2.4e-06 0.032 0 <1.00e-15 <2.01e-12
5 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 239438 34 34 16 1 10 0 1 1 22 0 <1.00e-15 0.00032 0 0 <1.00e-15 <2.01e-12
6 UGT2B15 UDP glucuronosyltransferase 2 family, polypeptide B15 796877 29 24 28 13 17 2 1 3 6 0 1.000 0.5 0.65 0 <1.00e-15 <2.01e-12
7 C15orf23 chromosome 15 open reading frame 23 268948 15 14 7 4 15 0 0 0 0 0 0.0243 0.14 1 0 <1.00e-15 <2.01e-12
8 STK19 serine/threonine kinase 19 285691 13 11 8 1 11 1 0 1 0 0 0.0200 0.018 0.96 0 <1.00e-15 <2.01e-12
9 OXA1L oxidase (cytochrome c) assembly 1-like 402552 8 8 3 3 8 0 0 0 0 0 0.924 0.39 1 0 <1.00e-15 <2.01e-12
10 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 299528 23 23 20 0 2 0 4 3 14 0 4.77e-15 0.014 0.9 0.11 1.94e-14 3.51e-11
11 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 5.56e-08 0.0025 0.17 0.000045 6.93e-11 1.14e-07
12 PPP6C protein phosphatase 6, catalytic subunit 265045 24 23 15 2 17 0 0 2 5 0 1.17e-10 0.017 0.3 0.026 8.48e-11 1.28e-07
13 PRB2 proline-rich protein BstNI subfamily 2 328896 50 39 46 2 44 1 1 3 1 0 3.87e-10 0.017 0.73 0.021 2.16e-10 3.00e-07
14 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 332700 15 15 4 1 13 0 0 2 0 0 2.67e-05 0.012 0.99 4.4e-06 2.80e-09 3.61e-06
15 NAP1L2 nucleosome assembly protein 1-like 2 360760 30 26 27 2 22 1 3 2 2 0 1.63e-08 0.0014 0.26 0.64 2.03e-07 0.000245
16 FIGLA folliculogenesis specific basic helix-loop-helix 95076 4 4 1 0 0 0 0 3 1 0 0.0107 0.42 0.033 5.4e-06 1.02e-06 0.00115
17 RBM11 RNA binding motif protein 11 172319 16 16 14 0 11 0 0 2 3 0 8.99e-08 0.03 0.32 0.8 1.25e-06 0.00133
18 HBG2 hemoglobin, gamma G 94917 10 9 8 2 5 3 0 2 0 0 6.22e-05 0.086 0.62 0.0014 1.53e-06 0.00154
19 LCE1B late cornified envelope 1B 95164 12 12 12 1 8 0 0 2 2 0 1.10e-07 0.18 0.68 1 1.87e-06 0.00178
20 MUC7 mucin 7, secreted 300191 22 19 17 1 14 1 6 0 1 0 9.36e-07 0.0013 0.085 0.21 3.21e-06 0.00289
21 DDX3X DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked 519948 20 20 19 0 7 1 2 3 7 0 1.89e-06 0.012 0.89 0.28 8.07e-06 0.00694
22 CDH9 cadherin 9, type 2 (T1-cadherin) 618104 46 37 41 6 35 2 1 5 3 0 1.81e-06 0.0058 0.13 0.32 8.80e-06 0.00704
23 HIST1H2AA histone cluster 1, H2aa 105598 10 10 8 0 5 1 0 3 1 0 3.21e-06 0.037 0.67 0.18 8.97e-06 0.00704
24 GFRAL GDNF family receptor alpha like 316087 40 33 37 9 32 2 0 2 4 0 7.33e-07 0.032 0.88 0.85 9.55e-06 0.00718
25 TBC1D3B TBC1 domain family, member 3B 168135 6 6 4 1 4 0 0 1 1 0 0.0755 0.21 0.067 1e-05 1.18e-05 0.00853
26 HHLA2 HERV-H LTR-associating 2 297719 23 18 17 3 19 1 0 0 3 0 0.000157 0.032 0.0087 0.0076 1.75e-05 0.0121
27 COPG2 coatomer protein complex, subunit gamma 2 321853 12 10 8 1 1 1 0 4 6 0 0.00147 0.24 0.0048 0.0011 2.30e-05 0.0153
28 FGF16 fibroblast growth factor 16 86225 8 8 8 0 5 0 0 3 0 0 2.59e-05 0.055 0.028 0.077 2.81e-05 0.0176
29 IL32 interleukin 32 131437 10 10 6 3 2 1 0 1 6 0 0.000346 0.72 0.93 0.0058 2.82e-05 0.0176
30 PRB4 proline-rich protein BstNI subfamily 4 199584 21 19 16 2 18 0 1 1 1 0 0.000291 0.14 0.55 0.0099 3.97e-05 0.0239
31 NBPF7 neuroblastoma breakpoint family, member 7 342408 18 16 12 1 7 0 0 10 1 0 0.000109 0.036 0.86 0.03 4.52e-05 0.0257
32 POM121 POM121 membrane glycoprotein (rat) 657357 20 18 17 2 10 4 0 0 6 0 0.00774 0.012 0.013 0.00043 4.55e-05 0.0257
33 MAP2K1 mitogen-activated protein kinase kinase 1 301351 13 13 5 2 10 0 0 2 1 0 0.00174 0.05 0.76 0.0022 5.18e-05 0.0280
34 ARID2 AT rich interactive domain 2 (ARID, RFX-like) 1440915 45 38 36 5 19 1 0 2 18 5 1.92e-05 0.018 0.47 0.2 5.27e-05 0.0280
35 DEFB118 defensin, beta 118 99490 10 10 8 1 8 0 0 1 1 0 7.68e-06 0.18 0.83 0.59 6.00e-05 0.0309
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.

TP53

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

CDKN2A

Figure S5.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

UGT2B15

Figure S6.  This figure depicts the distribution of mutations and mutation types across the UGT2B15 significant gene.

C15orf23

Figure S7.  This figure depicts the distribution of mutations and mutation types across the C15orf23 significant gene.

STK19

Figure S8.  This figure depicts the distribution of mutations and mutation types across the STK19 significant gene.

OXA1L

Figure S9.  This figure depicts the distribution of mutations and mutation types across the OXA1L significant gene.

PTEN

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

RAC1

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

PPP6C

Figure S12.  This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.

IDH1

Figure S13.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

NAP1L2

Figure S14.  This figure depicts the distribution of mutations and mutation types across the NAP1L2 significant gene.

FIGLA

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

RBM11

Figure S16.  This figure depicts the distribution of mutations and mutation types across the RBM11 significant gene.

HBG2

Figure S17.  This figure depicts the distribution of mutations and mutation types across the HBG2 significant gene.

LCE1B

Figure S18.  This figure depicts the distribution of mutations and mutation types across the LCE1B significant gene.

MUC7

Figure S19.  This figure depicts the distribution of mutations and mutation types across the MUC7 significant gene.

DDX3X

Figure S20.  This figure depicts the distribution of mutations and mutation types across the DDX3X significant gene.

CDH9

Figure S21.  This figure depicts the distribution of mutations and mutation types across the CDH9 significant gene.

HIST1H2AA

Figure S22.  This figure depicts the distribution of mutations and mutation types across the HIST1H2AA significant gene.

GFRAL

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

TBC1D3B

Figure S24.  This figure depicts the distribution of mutations and mutation types across the TBC1D3B significant gene.

HHLA2

Figure S25.  This figure depicts the distribution of mutations and mutation types across the HHLA2 significant gene.

COPG2

Figure S26.  This figure depicts the distribution of mutations and mutation types across the COPG2 significant gene.

FGF16

Figure S27.  This figure depicts the distribution of mutations and mutation types across the FGF16 significant gene.

IL32

Figure S28.  This figure depicts the distribution of mutations and mutation types across the IL32 significant gene.

PRB4

Figure S29.  This figure depicts the distribution of mutations and mutation types across the PRB4 significant gene.

NBPF7

Figure S30.  This figure depicts the distribution of mutations and mutation types across the NBPF7 significant gene.

POM121

Figure S31.  This figure depicts the distribution of mutations and mutation types across the POM121 significant gene.

MAP2K1

Figure S32.  This figure depicts the distribution of mutations and mutation types across the MAP2K1 significant gene.

ARID2

Figure S33.  This figure depicts the distribution of mutations and mutation types across the ARID2 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 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 12 CCNA1(18), CCND1(1), CCNE1(4), CCNE2(14), CDK4(5), CDKN1B(1), E2F1(7), E2F2(4), E2F4(1), PRB1(34) 3258975 89 61 79 17 61 0 5 19 4 0 0.00014 0.95 1
8 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
9 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
10 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
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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