Mutation Analysis (MutSig v2.0)
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1FQ9VSD
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C1FQ9VSD
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: DLBC-TP

  • Number of patients in set: 48

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:DLBC-TP.final_analysis_set.maf

  • Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt

  • Significantly mutated genes (q ≤ 0.1): 640

  • Mutations seen in COSMIC: 117

  • Significantly mutated genes in COSMIC territory: 19

  • Significantly mutated genesets: 0

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

Mutation Preprocessing

  • Read 48 MAFs of type "maf1"

  • Total number of mutations in input MAFs: 76860

  • After removing 89 mutations outside chr1-24: 76771

  • After removing 3669 blacklisted mutations: 73102

  • After removing 1917 noncoding mutations: 71185

  • After collapsing adjacent/redundant mutations: 71167

Mutation Filtering

  • Number of mutations before filtering: 71167

  • After removing 4183 mutations outside gene set: 66984

  • After removing 94 mutations outside category set: 66890

  • After removing 18 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 62595

Results
Breakdown of Mutations by Type

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

type count
De_novo_Start_InFrame 2
De_novo_Start_OutOfFrame 13
Frame_Shift_Del 303
Frame_Shift_Ins 151
In_Frame_Del 362
In_Frame_Ins 127
Missense_Mutation 32075
Nonsense_Mutation 593
Nonstop_Mutation 26
Silent 32021
Splice_Site 1154
Start_Codon_Del 1
Start_Codon_Ins 3
Start_Codon_SNP 44
Stop_Codon_Del 10
Stop_Codon_Ins 5
Total 66890
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
*CpG->T 7561 89487814 0.000084 84 3.7 2.1
*Np(A/C/T)->transit 12409 1218829196 1e-05 10 0.45 2
*ApG->G 1794 237296330 7.6e-06 7.6 0.34 2.2
transver 10347 1545613340 6.7e-06 6.7 0.3 5
indel+null 2664 1545613340 1.7e-06 1.7 0.076 NaN
double_null 86 1545613340 5.6e-08 0.056 0.0025 NaN
Total 34861 1545613340 0.000023 23 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). If the figure is unpopulated, then full coverage is assumed (e.g. MutSig CV doesn't use WIGs and assumes full coverage).

Figure 1. 

Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

Figure 2.  Patients counts and rates file used to generate this plot: DLBC-TP.patients.counts_and_rates.txt

Lego Plots

The mutation spectrum is depicted in the lego plots below in which the 96 possible mutation types are subdivided into six large blocks, color-coded to reflect the base substitution type. Each large block is further subdivided into the 16 possible pairs of 5' and 3' neighbors, as listed in the 4x4 trinucleotide context legend. The height of each block corresponds to the mutation frequency for that kind of mutation (counts of mutations normalized by the base coverage in a given bin). The shape of the spectrum is a signature for dominant mutational mechanisms in different tumor types.

Figure 3.  Get High-res Image SNV Mutation rate lego plot for entire set. Each bin is normalized by base coverage for that bin. Colors represent the six SNV types on the upper right. The three-base context for each mutation is labeled in the 4x4 legend on the lower right. The fractional breakdown of SNV counts is shown in the pie chart on the upper left. If this figure is blank, not enough information was provided in the MAF to generate it.

Figure 4.  Get High-res Image SNV Mutation rate lego plots for 4 slices of mutation allele fraction (0<=AF<0.1, 0.1<=AF<0.25, 0.25<=AF<0.5, & 0.5<=AF) . The color code and three-base context legends are the same as the previous figure. If this figure is blank, not enough information was provided in the MAF to generate it.

CoMut Plot

Figure 5.  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: *CpG->T

  • n2 = number of nonsilent mutations of type: *Np(A/C/T)->transit

  • n3 = number of nonsilent mutations of type: *ApG->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: 640. 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_clust p_cons p_joint p q
1 MUC6 mucin 6, oligomeric mucus/gel-forming 353866 49 27 16 31 4 19 0 25 1 0 1 0.94 0 1 0 <1.00e-15 <4.67e-13
2 FLG filaggrin 585076 172 22 77 53 29 44 8 90 1 0 1 0.28 0 0.95 0 <1.00e-15 <4.67e-13
3 MUC2 mucin 2, oligomeric mucus/gel-forming 385696 59 19 36 48 16 15 4 16 5 3 1 1 0 1 0 <1.00e-15 <4.67e-13
4 IGLL5 immunoglobulin lambda-like polypeptide 5 29626 38 18 32 25 1 15 0 13 8 1 1 0.99 0 0.98 0 <1.00e-15 <4.67e-13
5 MUC17 mucin 17, cell surface associated 646492 121 18 79 43 7 49 17 48 0 0 0.29 0.036 0 1 0 <1.00e-15 <4.67e-13
6 NBPF10 neuroblastoma breakpoint family, member 10 250908 25 14 12 2 0 6 2 17 0 0 1.9e-06 0.05 0 0.99 0 <1.00e-15 <4.67e-13
7 BTG2 BTG family, member 2 23234 20 13 17 5 0 5 0 11 4 0 1.2e-07 0.38 0 0.98 0 <1.00e-15 <4.67e-13
8 KRTAP4-7 keratin associated protein 4-7 21336 23 13 9 7 4 1 0 18 0 0 1 0.9 0 1 0 <1.00e-15 <4.67e-13
9 TPTE2 transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 78852 13 13 3 0 0 0 0 13 0 0 1.9e-13 0.13 0 0.95 0 <1.00e-15 <4.67e-13
10 KCNN3 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3 107269 12 11 3 11 0 0 0 11 1 0 1 1 0 1 0 <1.00e-15 <4.67e-13
11 ZNF814 zinc finger protein 814 123757 27 11 7 8 0 11 0 12 4 0 0.00013 0.54 0 0.91 0 <1.00e-15 <4.67e-13
12 ATXN1 ataxin 1 111295 14 10 5 3 0 1 0 9 4 0 0.000017 0.69 0 1 0 <1.00e-15 <4.67e-13
13 DMKN dermokine 82246 22 10 13 4 3 7 0 3 9 0 1.5e-06 0.4 0 0.98 0 <1.00e-15 <4.67e-13
14 PCMTD1 protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 52343 11 10 4 3 0 2 1 8 0 0 1 0.62 0 1 0 <1.00e-15 <4.67e-13
15 COL6A3 collagen, type VI, alpha 3 454925 15 9 7 28 3 6 0 3 3 0 1 1 0 0.9 0 <1.00e-15 <4.67e-13
16 CR1 complement component (3b/4b) receptor 1 (Knops blood group) 365815 18 9 8 2 1 8 2 3 4 0 0.066 0.062 0 0.66 0 <1.00e-15 <4.67e-13
17 TPRX1 tetra-peptide repeat homeobox 1 56647 13 9 7 7 6 5 0 0 2 0 0.027 0.8 0 0.34 0 <1.00e-15 <4.67e-13
18 OR51G1 olfactory receptor, family 51, subfamily G, member 1 46199 12 8 5 1 1 7 0 4 0 0 0.000036 0.068 0 0.84 0 <1.00e-15 <4.67e-13
19 UBXN11 UBX domain protein 11 75360 15 8 10 9 4 0 1 9 1 0 0.6 0.93 0 1 0 <1.00e-15 <4.67e-13
20 FAM120B family with sequence similarity 120B 130683 15 7 11 5 0 9 1 5 0 0 0.24 0.45 0 1 0 <1.00e-15 <4.67e-13
21 KIAA0040 KIAA0040 14592 12 7 4 1 0 5 0 1 3 3 3.8e-14 0.25 0 0.79 0 <1.00e-15 <4.67e-13
22 OVGP1 oviductal glycoprotein 1, 120kDa (mucin 9, oviductin) 99723 20 7 10 4 0 6 2 9 3 0 0.047 0.3 0 1 0 <1.00e-15 <4.67e-13
23 SIRPA signal-regulatory protein alpha 71388 24 7 8 3 3 9 0 11 1 0 0.0098 0.027 0 1 0 <1.00e-15 <4.67e-13
24 KRTAP5-1 keratin associated protein 5-1 40236 9 6 4 1 0 1 0 8 0 0 0.000093 0.3 0 1 0 <1.00e-15 <4.67e-13
25 TREML2 triggering receptor expressed on myeloid cells-like 2 46993 10 6 7 5 2 6 0 2 0 0 1 0.69 2e-07 0.013 0 <1.00e-15 <4.67e-13
26 ARHGAP25 Rho GTPase activating protein 25 96697 6 5 3 4 0 3 0 3 0 0 1 0.89 0 0.98 0 <1.00e-15 <4.67e-13
27 DEFA3 defensin, alpha 3, neutrophil-specific 14063 5 5 1 0 0 0 0 5 0 0 4.2e-06 0.36 0 1 0 <1.00e-15 <4.67e-13
28 FOXD4L4 forkhead box D4-like 4 100725 5 5 2 0 0 0 0 0 5 0 0.023 1 0 1 0 <1.00e-15 <4.67e-13
29 SPATA22 spermatogenesis associated 22 53742 8 5 3 5 0 8 0 0 0 0 1 0.82 0 1 0 <1.00e-15 <4.67e-13
30 TPPP tubulin polymerization promoting protein 31571 5 5 1 3 0 5 0 0 0 0 0.084 0.75 0 0.32 0 <1.00e-15 <4.67e-13
31 C8orf44 chromosome 8 open reading frame 44 19500 4 4 1 0 0 4 0 0 0 0 0.0024 0.17 1.8e-06 0.0049 0 <1.00e-15 <4.67e-13
32 KRT84 keratin 84 86887 9 4 4 24 5 3 0 1 0 0 1 1 9.6e-06 0.0031 0 <1.00e-15 <4.67e-13
33 LRRC43 leucine rich repeat containing 43 90099 5 4 2 3 0 0 1 4 0 0 0.53 0.9 2e-07 0.054 0 <1.00e-15 <4.67e-13
34 SGK1 serum/glucocorticoid regulated kinase 1 94332 24 4 19 5 0 9 0 12 1 2 0.013 0.29 0 0.034 0 <1.00e-15 <4.67e-13
35 CLDN16 claudin 16 45024 6 3 2 0 0 0 0 3 0 3 0.00058 0.55 0 1 0 <1.00e-15 <4.67e-13
MUC6

Figure S1.  This figure depicts the distribution of mutations and mutation types across the MUC6 significant gene.

FLG

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

MUC2

Figure S3.  This figure depicts the distribution of mutations and mutation types across the MUC2 significant gene.

MUC17

Figure S4.  This figure depicts the distribution of mutations and mutation types across the MUC17 significant gene.

NBPF10

Figure S5.  This figure depicts the distribution of mutations and mutation types across the NBPF10 significant gene.

BTG2

Figure S6.  This figure depicts the distribution of mutations and mutation types across the BTG2 significant gene.

KRTAP4-7

Figure S7.  This figure depicts the distribution of mutations and mutation types across the KRTAP4-7 significant gene.

TPTE2

Figure S8.  This figure depicts the distribution of mutations and mutation types across the TPTE2 significant gene.

KCNN3

Figure S9.  This figure depicts the distribution of mutations and mutation types across the KCNN3 significant gene.

ZNF814

Figure S10.  This figure depicts the distribution of mutations and mutation types across the ZNF814 significant gene.

ATXN1

Figure S11.  This figure depicts the distribution of mutations and mutation types across the ATXN1 significant gene.

DMKN

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

PCMTD1

Figure S13.  This figure depicts the distribution of mutations and mutation types across the PCMTD1 significant gene.

COL6A3

Figure S14.  This figure depicts the distribution of mutations and mutation types across the COL6A3 significant gene.

CR1

Figure S15.  This figure depicts the distribution of mutations and mutation types across the CR1 significant gene.

TPRX1

Figure S16.  This figure depicts the distribution of mutations and mutation types across the TPRX1 significant gene.

OR51G1

Figure S17.  This figure depicts the distribution of mutations and mutation types across the OR51G1 significant gene.

UBXN11

Figure S18.  This figure depicts the distribution of mutations and mutation types across the UBXN11 significant gene.

FAM120B

Figure S19.  This figure depicts the distribution of mutations and mutation types across the FAM120B significant gene.

KIAA0040

Figure S20.  This figure depicts the distribution of mutations and mutation types across the KIAA0040 significant gene.

OVGP1

Figure S21.  This figure depicts the distribution of mutations and mutation types across the OVGP1 significant gene.

SIRPA

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

KRTAP5-1

Figure S23.  This figure depicts the distribution of mutations and mutation types across the KRTAP5-1 significant gene.

TREML2

Figure S24.  This figure depicts the distribution of mutations and mutation types across the TREML2 significant gene.

ARHGAP25

Figure S25.  This figure depicts the distribution of mutations and mutation types across the ARHGAP25 significant gene.

DEFA3

Figure S26.  This figure depicts the distribution of mutations and mutation types across the DEFA3 significant gene.

FOXD4L4

Figure S27.  This figure depicts the distribution of mutations and mutation types across the FOXD4L4 significant gene.

SPATA22

Figure S28.  This figure depicts the distribution of mutations and mutation types across the SPATA22 significant gene.

TPPP

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

C8orf44

Figure S30.  This figure depicts the distribution of mutations and mutation types across the C8orf44 significant gene.

KRT84

Figure S31.  This figure depicts the distribution of mutations and mutation types across the KRT84 significant gene.

LRRC43

Figure S32.  This figure depicts the distribution of mutations and mutation types across the LRRC43 significant gene.

SGK1

Figure S33.  This figure depicts the distribution of mutations and mutation types across the SGK1 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: 19. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 ZC3H3 zinc finger CCCH-type containing 3 14 1 4 48 4 4.8e-14 2.2e-10
2 ABHD12B abhydrolase domain containing 12B 6 1 3 48 3 2e-10 3e-07
3 SFT2D1 SFT2 domain containing 1 3 1 3 48 3 2e-10 3e-07
4 PITPNM3 PITPNM family member 3 4 2 3 96 3 1.6e-09 1.9e-06
5 MAPK6 mitogen-activated protein kinase 6 3 3 3 144 3 5.6e-09 5.1e-06
6 ATM ataxia telangiectasia mutated 8 245 6 11760 32 3.9e-07 0.00029
7 TNFAIP3 tumor necrosis factor, alpha-induced protein 3 8 138 5 6624 9 5.5e-07 0.00029
8 CNKSR1 connector enhancer of kinase suppressor of Ras 1 2 1 2 48 2 5.7e-07 0.00029
9 USP6 ubiquitin specific peptidase 6 (Tre-2 oncogene) 13 1 2 48 2 5.7e-07 0.00029
10 SOCS1 suppressor of cytokine signaling 1 9 67 4 3216 14 1.1e-06 0.00049

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)

Geneset Analyses

Table 5.  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 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(2) 51556 2 2 2 0 1 0 0 1 0 0 0.59 0.088 1
2 TUBBYPATHWAY Tubby is activated by phospholipase C activity and hydrolysis of PIP2, after which it enters the nucleus and regulates transcription. CHRM1, GNAQ, GNB1, GNGT1, HTR2C, PLCB1, TUB 7 GNGT1(1), HTR2C(1), PLCB1(8), TUB(2) 517190 12 9 10 7 2 1 0 3 6 0 0.9 0.22 1
3 TCRMOLECULE T Cell Receptor and CD3 Complex CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@ 3 CD3D(1), CD3G(2) 84242 3 3 3 3 0 1 0 1 1 0 0.94 0.59 1
4 ALKALOID_BIOSYNTHESIS_II ABP1, AOC2, AOC3, CES1, ESD 5 AOC2(2), AOC3(4), CES1(12), ESD(2) 444881 20 8 13 5 6 9 0 2 3 0 0.21 0.62 1
5 HSA00471_D_GLUTAMINE_AND_D_GLUTAMATE_METABOLISM Genes involved in D-glutamine and D-glutamate metabolism GLS, GLS2, GLUD1, GLUD2 4 GLS(1), GLS2(2) 330026 3 3 2 1 0 0 2 1 0 0 0.64 0.66 1
6 RNAPATHWAY dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation. CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53 9 CHUK(1), EIF2S2(1), NFKB1(3), NFKBIA(3), TP53(6) 751321 14 13 13 6 4 4 0 1 5 0 0.74 0.74 1
7 INOSITOL_METABOLISM ALDH6A1, ALDOA, ALDOB, ALDOC, TPI1 5 ALDOB(1), ALDOC(1) 284076 2 2 2 0 1 1 0 0 0 0 0.47 0.75 1
8 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(1) 120022 1 1 1 1 1 0 0 0 0 0 0.88 0.76 1
9 FOLATE_BIOSYNTHESIS ALPI, ALPL, ALPP, ALPP, ALPPL2, ALPPL2, DHFR, FPGS, GCH1, GGH, SPR 9 ALPL(2), ALPP(13), ALPPL2(5), FPGS(2), GCH1(1), GGH(3) 518717 26 12 18 8 6 9 3 7 1 0 0.2 0.77 1
10 HSA00300_LYSINE_BIOSYNTHESIS Genes involved in lysine biosynthesis AADAT, AASDHPPT, AASS, KARS 4 AASDHPPT(2), AASS(2) 342070 4 4 4 2 0 2 0 1 1 0 0.86 0.79 1

Table 6.  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(2) 51556 2 2 2 0 1 0 0 1 0 0 0.59 0.088 1
2 TUBBYPATHWAY Tubby is activated by phospholipase C activity and hydrolysis of PIP2, after which it enters the nucleus and regulates transcription. CHRM1, GNAQ, GNB1, GNGT1, HTR2C, PLCB1, TUB 7 GNGT1(1), HTR2C(1), PLCB1(8), TUB(2) 517190 12 9 10 7 2 1 0 3 6 0 0.9 0.22 1
3 TCRMOLECULE T Cell Receptor and CD3 Complex CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@ 3 CD3D(1), CD3G(2) 84242 3 3 3 3 0 1 0 1 1 0 0.94 0.59 1
4 HSA00471_D_GLUTAMINE_AND_D_GLUTAMATE_METABOLISM Genes involved in D-glutamine and D-glutamate metabolism GLS, GLS2, GLUD1, GLUD2 4 GLS(1), GLS2(2) 330026 3 3 2 1 0 0 2 1 0 0 0.64 0.66 1
5 INOSITOL_METABOLISM ALDH6A1, ALDOA, ALDOB, ALDOC, TPI1 5 ALDOB(1), ALDOC(1) 284076 2 2 2 0 1 1 0 0 0 0 0.47 0.75 1
6 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(1) 120022 1 1 1 1 1 0 0 0 0 0 0.88 0.76 1
7 ALKALOID_BIOSYNTHESIS_II ABP1, AOC2, AOC3, CES1, ESD 4 AOC2(2), AOC3(4), ESD(2) 360646 8 6 6 0 3 5 0 0 0 0 0.037 0.76 1
8 FOLATE_BIOSYNTHESIS ALPI, ALPL, ALPP, ALPP, ALPPL2, ALPPL2, DHFR, FPGS, GCH1, GGH, SPR 9 ALPL(2), ALPP(13), ALPPL2(5), FPGS(2), GCH1(1), GGH(3) 518717 26 12 18 8 6 9 3 7 1 0 0.2 0.77 1
9 HSA00300_LYSINE_BIOSYNTHESIS Genes involved in lysine biosynthesis AADAT, AASDHPPT, AASS, KARS 4 AASDHPPT(2), AASS(2) 342070 4 4 4 2 0 2 0 1 1 0 0.86 0.79 1
10 IL18PATHWAY Pro-inflammatory IL-18 is activated in macrophages by caspase-1 cleavage and, in conjunction with IL-12, stimulates Th1 cell differentiation. CASP1, IFNG, IL12A, IL12B, IL18, IL2 6 CASP1(1), IL12B(2) 222942 3 3 2 9 2 0 0 0 1 0 1 0.86 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
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