Glioblastoma Multiforme: Mutation Analysis (MutSig v2.0)
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: GBM-TP

  • Number of patients in set: 291

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:GBM-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 116

  • Mutations seen in COSMIC: 0

  • Significantly mutated genes in COSMIC territory: 0

  • Genes with clustered mutations (≤ 3 aa apart): 1

  • Significantly mutated genesets: 190

  • Significantly mutated genesets: (excluding sig. mutated genes):16

Mutation Preprocessing

  • Read 291 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 21540

  • After removing 126 blacklisted mutations: 21414

Mutation Filtering

  • Number of mutations before filtering: 21414

  • After removing 234 mutations outside gene set: 21180

  • After removing 5581 mutations outside category set: 15599

  • After removing 62 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 15537

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 537
Frame_Shift_Ins 206
In_Frame_Del 206
In_Frame_Ins 26
Missense_Mutation 9859
Nonsense_Mutation 591
Nonstop_Mutation 9
Silent 3837
Splice_Site 283
Translation_Start_Site 45
Total 15599
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
A->T 2819 4185997415 6.7e-07 0.67 0.49
C->(A/T) 4383 4350488149 1e-06 1 0.73
A->(C/G) 1952 4185997415 4.7e-07 0.47 0.34
C->G 711 4350488149 1.6e-07 0.16 0.12
indel+null 1854 8536485735 2.2e-07 0.22 0.16
double_null 0 8536485735 0 0 0
Total 11719 8536485735 1.4e-06 1.4 1
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: GBM-TP.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: A->T

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

  • n3 = number of nonsilent mutations of type: A->(C/G)

  • n4 = number of nonsilent mutations of type: C->G

  • 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_ks = p-value for clustering of mutations (Kolmogorov-Smirnoff test)

  • 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: 116. 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_ks p_cons p_joint p q
1 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 1157577 73 60 39 5 39 19 9 1 5 0 <1.00e-15 4e-07 1 0.000019 <0.000 <0.000
2 TP53 tumor protein p53 366862 69 59 48 0 17 20 7 7 18 0 <1.00e-15 NaN NaN NaN <1.00e-15 <8.99e-12
3 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 345600 69 67 59 0 11 8 12 3 35 0 3.22e-15 NaN NaN NaN 3.22e-15 1.93e-11
4 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 681132 32 31 28 0 1 4 4 3 20 0 5.55e-15 NaN NaN NaN 5.55e-15 2.08e-11
5 RB1 retinoblastoma 1 (including osteosarcoma) 778931 20 20 20 1 0 0 0 1 19 0 5.77e-15 NaN NaN NaN 5.77e-15 2.08e-11
6 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 2521044 27 26 27 1 2 2 1 1 21 0 7.44e-15 NaN NaN NaN 7.44e-15 2.23e-11
7 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 369059 15 15 2 0 0 13 0 2 0 0 1.21e-14 NaN NaN NaN 1.21e-14 2.55e-11
8 SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2) 2163316 28 26 26 1 3 12 7 2 4 0 1.27e-14 NaN NaN NaN 1.27e-14 2.55e-11
9 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 943754 28 26 22 0 9 4 6 3 6 0 1.28e-14 NaN NaN NaN 1.28e-14 2.55e-11
10 GABRA6 gamma-aminobutyric acid (GABA) A receptor, alpha 6 405492 10 10 9 1 6 3 1 0 0 0 2.43e-10 NaN NaN NaN 2.43e-10 4.23e-07
11 FLG filaggrin 3451129 24 24 23 13 7 12 2 0 3 0 2.59e-10 NaN NaN NaN 2.59e-10 4.23e-07
12 RPL5 ribosomal protein L5 267625 8 8 8 0 0 1 1 0 6 0 3.45e-10 NaN NaN NaN 3.45e-10 5.17e-07
13 KEL Kell blood group, metallo-endopeptidase 655925 11 11 9 2 6 1 1 0 3 0 9.29e-10 NaN NaN NaN 9.29e-10 1.29e-06
14 RIMS2 regulating synaptic membrane exocytosis 2 1243358 10 10 9 2 3 2 2 0 3 0 4.09e-06 0.000026 0.41 0.000031 3.06e-09 3.87e-06
15 PCLO piccolo (presynaptic cytomatrix protein) 4271304 23 23 23 6 9 6 3 0 5 0 1.78e-08 0.0012 0.53 0.0076 3.23e-09 3.87e-06
16 RBM47 RNA binding motif protein 47 480608 9 9 9 3 5 3 1 0 0 0 1.65e-08 NaN NaN NaN 1.65e-08 1.85e-05
17 TCHH trichohyalin 1639471 14 14 14 0 7 4 2 0 1 0 2.20e-08 NaN NaN NaN 2.20e-08 2.33e-05
18 SEMA3C sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C 670293 9 9 9 1 1 3 2 2 1 0 5.55e-08 NaN NaN NaN 5.55e-08 5.55e-05
19 OR8K3 olfactory receptor, family 8, subfamily K, member 3 273493 7 7 7 1 0 5 1 0 1 0 7.01e-08 NaN NaN NaN 7.01e-08 6.63e-05
20 PRB2 proline-rich protein BstNI subfamily 2 344124 6 6 2 0 0 0 0 0 6 0 6.26e-07 NaN NaN NaN 6.26e-07 0.000563
21 RYR2 ryanodine receptor 2 (cardiac) 4070819 21 20 21 4 7 7 5 1 1 0 6.97e-07 NaN NaN NaN 6.97e-07 0.000597
22 TPTE2 transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 473916 7 7 5 0 2 1 0 1 3 0 1.14e-06 NaN NaN NaN 1.14e-06 0.000929
23 LZTR1 leucine-zipper-like transcription regulator 1 637471 8 9 9 0 0 3 2 2 1 0 1.68e-06 NaN NaN NaN 1.68e-06 0.00131
24 DCAF12L2 DDB1 and CUL4 associated factor 12-like 2 391480 6 6 5 0 4 2 0 0 0 0 3.86e-06 NaN NaN NaN 3.86e-06 0.00289
25 PSPH phosphoserine phosphatase 202218 5 5 3 0 3 0 1 0 1 0 4.89e-06 NaN NaN NaN 4.89e-06 0.00352
26 PDGFRA platelet-derived growth factor receptor, alpha polypeptide 973191 10 9 9 1 2 3 3 0 2 0 7.40e-06 NaN NaN NaN 7.40e-06 0.00512
27 SPRYD5 SPRY domain containing 5 260718 5 5 5 1 2 1 0 1 1 0 8.65e-06 NaN NaN NaN 8.65e-06 0.00576
28 LRFN5 leucine rich repeat and fibronectin type III domain containing 5 626196 7 7 7 0 3 2 1 1 0 0 9.16e-06 NaN NaN NaN 9.16e-06 0.00588
29 MUC16 mucin 16, cell surface associated 12550554 37 36 37 15 9 16 6 3 3 0 9.53e-06 NaN NaN NaN 9.53e-06 0.00591
30 CALN1 calneuron 1 198851 5 5 5 3 3 2 0 0 0 0 9.92e-06 NaN NaN NaN 9.92e-06 0.00594
31 HCN1 hyperpolarization activated cyclic nucleotide-gated potassium channel 1 710195 8 7 8 3 2 3 0 2 1 0 1.17e-05 NaN NaN NaN 1.17e-05 0.00672
32 KIF2B kinesin family member 2B 585575 7 7 7 1 2 2 0 1 2 0 1.20e-05 NaN NaN NaN 1.20e-05 0.00672
33 MUC17 mucin 17, cell surface associated 3928199 18 17 17 5 4 5 4 3 2 0 1.67e-05 NaN NaN NaN 1.67e-05 0.00903
34 AZGP1 alpha-2-glycoprotein 1, zinc-binding 264723 5 5 5 0 2 1 1 0 1 0 1.71e-05 NaN NaN NaN 1.71e-05 0.00903
35 AFM afamin 535897 6 6 6 1 1 1 3 1 0 0 1.81e-05 NaN NaN NaN 1.81e-05 0.00923
EGFR

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

TP53

Figure S2.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

PTEN

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

PIK3R1

Figure S4.  This figure depicts the distribution of mutations and mutation types across the PIK3R1 significant gene.

RB1

Figure S5.  This figure depicts the distribution of mutations and mutation types across the RB1 significant gene.

NF1

Figure S6.  This figure depicts the distribution of mutations and mutation types across the NF1 significant gene.

IDH1

Figure S7.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

SPTA1

Figure S8.  This figure depicts the distribution of mutations and mutation types across the SPTA1 significant gene.

PIK3CA

Figure S9.  This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

GABRA6

Figure S10.  This figure depicts the distribution of mutations and mutation types across the GABRA6 significant gene.

FLG

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

RPL5

Figure S12.  This figure depicts the distribution of mutations and mutation types across the RPL5 significant gene.

KEL

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

RIMS2

Figure S14.  This figure depicts the distribution of mutations and mutation types across the RIMS2 significant gene.

PCLO

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

RBM47

Figure S16.  This figure depicts the distribution of mutations and mutation types across the RBM47 significant gene.

TCHH

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

SEMA3C

Figure S18.  This figure depicts the distribution of mutations and mutation types across the SEMA3C significant gene.

OR8K3

Figure S19.  This figure depicts the distribution of mutations and mutation types across the OR8K3 significant gene.

RYR2

Figure S20.  This figure depicts the distribution of mutations and mutation types across the RYR2 significant gene.

TPTE2

Figure S21.  This figure depicts the distribution of mutations and mutation types across the TPTE2 significant gene.

LZTR1

Figure S22.  This figure depicts the distribution of mutations and mutation types across the LZTR1 significant gene.

DCAF12L2

Figure S23.  This figure depicts the distribution of mutations and mutation types across the DCAF12L2 significant gene.

PSPH

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

PDGFRA

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

SPRYD5

Figure S26.  This figure depicts the distribution of mutations and mutation types across the SPRYD5 significant gene.

LRFN5

Figure S27.  This figure depicts the distribution of mutations and mutation types across the LRFN5 significant gene.

MUC16

Figure S28.  This figure depicts the distribution of mutations and mutation types across the MUC16 significant gene.

CALN1

Figure S29.  This figure depicts the distribution of mutations and mutation types across the CALN1 significant gene.

HCN1

Figure S30.  This figure depicts the distribution of mutations and mutation types across the HCN1 significant gene.

KIF2B

Figure S31.  This figure depicts the distribution of mutations and mutation types across the KIF2B significant gene.

MUC17

Figure S32.  This figure depicts the distribution of mutations and mutation types across the MUC17 significant gene.

AZGP1

Figure S33.  This figure depicts the distribution of mutations and mutation types across the AZGP1 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: 0. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 A4GNT alpha-1,4-N-acetylglucosaminyltransferase 0 0 0 0 0 1 1
2 AACS acetoacetyl-CoA synthetase 2 0 0 0 0 1 1
3 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 2 0 0 0 0 1 1
4 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 0 0 0 0 0 1 1
5 ABCF2 ATP-binding cassette, sub-family F (GCN20), member 2 1 0 0 0 0 1 1
6 ABHD2 abhydrolase domain containing 2 0 0 0 0 0 1 1
7 ABHD4 abhydrolase domain containing 4 0 0 0 0 0 1 1
8 ACADS acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain 4 0 0 0 0 1 1
9 ACOT11 acyl-CoA thioesterase 11 1 0 0 0 0 1 1
10 ACRBP acrosin binding protein 0 0 0 0 0 1 1

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
1678 DST dystonin 5 0 3 3 3 3 3 3

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: 190. 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 q
1 HSA04510_FOCAL_ADHESION Genes involved in focal adhesion ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, ARHGAP5, BAD, BCAR1, BCL2, BIRC2, BIRC3, BIRC4, BRAF, CAPN2, CAV1, CAV2, CAV3, CCND1, CCND2, CCND3, CDC42, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, CRK, CRKL, CTNNB1, DIAPH1, DOCK1, EGF, EGFR, ELK1, ERBB2, FARP2, FIGF, FLNA, FLNB, FLNC, FLT1, FN1, FYN, GRB2, GRLF1, GSK3B, HGF, HRAS, IBSP, IGF1, IGF1R, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, JUN, KDR, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LOC653852, MAP2K1, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MET, MLCK, MRCL3, MRLC2, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PARVA, PARVB, PARVG, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP5K1C, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PRKCA, PRKCB1, PRKCG, PTEN, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF1, RELN, RHOA, ROCK1, ROCK2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SPP1, SRC, THBS1, THBS2, THBS3, THBS4, TLN1, TLN2, TNC, TNN, TNR, TNXB, VASP, VAV1, VAV2, VAV3, VCL, VEGFA, VEGFB, VEGFC, VTN, VWF, ZYX 191 ACTN1(2), ACTN3(1), AKT1(1), ARHGAP5(3), BCL2(2), BIRC3(1), BRAF(5), CAV3(1), CCND2(1), CCND3(1), COL11A1(1), COL11A2(5), COL1A1(1), COL1A2(9), COL2A1(1), COL3A1(4), COL4A1(1), COL4A2(1), COL4A4(5), COL4A6(2), COL5A1(1), COL5A2(1), COL5A3(1), COL6A3(13), COL6A6(5), CRKL(1), DOCK1(1), EGF(3), EGFR(73), ELK1(2), ERBB2(1), FIGF(2), FLNB(1), FLNC(3), FLT1(5), FN1(2), FYN(1), GRLF1(1), GSK3B(1), HGF(1), IGF1(2), IGF1R(2), ITGA1(2), ITGA10(2), ITGA11(1), ITGA2(1), ITGA2B(1), ITGA3(1), ITGA4(3), ITGA5(1), ITGA7(2), ITGA8(1), ITGA9(1), ITGAV(1), ITGB1(1), ITGB3(1), ITGB4(2), ITGB6(2), ITGB7(1), ITGB8(1), KDR(6), LAMA1(3), LAMA2(6), LAMA3(4), LAMA4(1), LAMA5(5), LAMB1(2), LAMB3(3), LAMB4(3), LAMC1(1), LAMC3(3), MAP2K1(1), MAPK1(1), MAPK3(1), MAPK8(1), MET(1), MYLK(2), PAK1(1), PAK3(1), PAK4(3), PDGFD(1), PDGFRA(10), PDGFRB(2), PIK3CA(28), PIK3CB(4), PIK3CG(5), PIK3R1(32), PIK3R2(3), PIK3R3(1), PIK3R5(3), PRKCA(1), PRKCG(2), PTEN(69), PXN(1), RAF1(1), RELN(12), ROCK1(1), ROCK2(1), SHC4(1), SOS1(3), SRC(2), THBS3(1), THBS4(1), TLN2(2), TNC(1), TNN(2), TNXB(2), VASP(1), VAV1(3), VAV2(2), VAV3(1), VEGFA(2), VEGFB(1), VWF(5), ZYX(2) 160724111 454 215 393 89 117 134 73 27 103 0 <1.00e-15 <3.24e-14
2 HSA04012_ERBB_SIGNALING_PATHWAY Genes involved in ErbB signaling pathway ABL1, ABL2, AKT1, AKT2, AKT3, ARAF, AREG, BAD, BRAF, BTC, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CBL, CBLB, CBLC, CDKN1A, CDKN1B, CRK, CRKL, EGF, EGFR, EIF4EBP1, ELK1, ERBB2, ERBB3, ERBB4, EREG, FRAP1, GAB1, GRB2, GSK3B, HBEGF, HRAS, JUN, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MYC, NCK1, NCK2, NRAS, NRG1, NRG2, NRG3, NRG4, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCG, PTK2, RAF1, RPS6KB1, RPS6KB2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SRC, STAT5A, STAT5B, TGFA 85 ABL1(1), ABL2(1), AKT1(1), BRAF(5), CAMK2A(1), CBL(1), CBLB(1), CDKN1A(1), CRKL(1), EGF(3), EGFR(73), ELK1(2), ERBB2(1), ERBB4(1), GSK3B(1), KRAS(2), MAP2K1(1), MAPK1(1), MAPK3(1), MAPK8(1), MYC(1), PAK1(1), PAK3(1), PAK4(3), PIK3CA(28), PIK3CB(4), PIK3CG(5), PIK3R1(32), PIK3R2(3), PIK3R3(1), PIK3R5(3), PLCG1(6), PLCG2(2), PRKCA(1), PRKCG(2), RAF1(1), SHC4(1), SOS1(3), SRC(2), STAT5B(1), TGFA(3) 44683890 204 142 155 25 73 48 32 11 40 0 <1.00e-15 <3.24e-14
3 ST_FAS_SIGNALING_PATHWAY The Fas receptor induces apoptosis and NF-kB activation when bound to Fas ligand. ADPRT, ALG2, BAK1, BAX, BFAR, BIRC4, BTK, CAD, CASP10, CASP3, CASP8, CASP8AP2, CD7, CDK2AP1, CSNK1A1, DAXX, DEDD, DEDD2, DFFA, DIABLO, EGFR, EPHB2, FADD, FAF1, FAIM2, FREQ, HRB, HSPB1, IL1A, IL8, MAP2K4, MAP2K7, MAP3K1, MAP3K5, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MCP, MET, NFAT5, NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBIE, NFKBIL1, NFKBIL2, NR0B2, PFN1, PFN2, PTPN13, RALBP1, RIPK1, ROCK1, SMPD1, TNFRSF6, TNFRSF6B, TP53, TPX2, TRAF2, TUFM, VIL2 59 CAD(1), CASP8AP2(1), DAXX(2), DEDD(1), DEDD2(1), EGFR(73), EPHB2(1), FAF1(1), IL1A(1), MAP3K1(2), MAP3K5(1), MAPK1(1), MAPK8(1), MAPK8IP1(1), MAPK8IP2(2), MAPK8IP3(2), MET(1), NFKB1(1), NFKB2(1), NFKBIA(1), NFKBIE(2), NFKBIL2(2), NR0B2(1), PTPN13(1), RALBP1(1), RIPK1(1), ROCK1(1), TP53(69), TPX2(2) 31809563 176 127 121 13 66 51 20 12 27 0 <1.00e-15 <3.24e-14
4 HSA00562_INOSITOL_PHOSPHATE_METABOLISM Genes involved in inositol phosphate metabolism CARKL, FN3K, IMPA1, IMPA2, INPP1, INPP4A, INPP4B, INPP5A, INPP5B, INPP5E, INPPL1, IPMK, ISYNA1, ITGB1BP3, ITPK1, ITPKA, ITPKB, MINPP1, MIOX, OCRL, PI4KA, PI4KB, PIB5PA, PIK3C3, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PTEN, PTPMT1, SKIP, SYNJ1, SYNJ2 47 INPP1(1), INPP4B(1), INPP5A(1), INPP5B(1), INPP5E(1), INPPL1(3), OCRL(2), PI4KB(2), PIK3CA(28), PIK3CB(4), PIK3CG(5), PIP4K2C(3), PIP5K1B(2), PLCB1(1), PLCB2(3), PLCB4(1), PLCD1(1), PLCE1(2), PLCG1(6), PLCG2(2), PLCZ1(1), PTEN(69), SYNJ2(2) 32143184 142 114 126 16 30 26 26 11 49 0 <1.00e-15 <3.24e-14
5 HSA04370_VEGF_SIGNALING_PATHWAY Genes involved in VEGF signaling pathway AKT1, AKT2, AKT3, BAD, CASP9, CDC42, CHP, HRAS, KDR, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPKAPK2, MAPKAPK3, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NOS3, NRAS, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCG1, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKCA, PRKCB1, PRKCG, PTGS2, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, SH2D2A, SHC2, SPHK1, SPHK2, SRC, VEGFA 69 AKT1(1), CASP9(1), KDR(6), KRAS(2), MAP2K1(1), MAPK1(1), MAPK13(1), MAPK3(1), NFATC2(2), NFATC4(2), NOS3(4), PIK3CA(28), PIK3CB(4), PIK3CG(5), PIK3R1(32), PIK3R2(3), PIK3R3(1), PIK3R5(3), PLA2G2F(1), PLA2G3(1), PLA2G4A(2), PLA2G6(1), PLCG1(6), PLCG2(2), PPP3CB(1), PPP3R2(1), PRKCA(1), PRKCG(2), PXN(1), RAF1(1), SRC(2), VEGFA(2) 31232956 122 97 111 17 23 34 18 12 35 0 <1.00e-15 <3.24e-14
6 PPARAPATHWAY Peroxisome proliferators regulate gene expression via PPAR/RXR heterodimers which bind to peroxisome-proliferator response elements (PPREs). ACOX1, APOA1, APOA2, CD36, CITED2, CPT1B, CREBBP, DUSP1, DUT, EHHADH, EP300, FABP1, FAT, FRA8B, HSD17B4, HSPA1A, HSPCA, INS, JUN, LPL, MAPK1, MAPK3, ME1, MRPL11, MYC, NCOA1, NCOR1, NCOR2, NFKBIA, NOS2A, NR0B2, NR1H3, NR2F1, NRIP1, PDGFA, PIK3CA, PIK3R1, PPARA, PPARBP, PPARGC1, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PTGS2, RB1, RELA, RXRA, SP1, SRA1, STAT5A, STAT5B, TNF 48 CREBBP(4), EHHADH(1), HSD17B4(1), MAPK1(1), MAPK3(1), MYC(1), NCOA1(1), NCOR1(1), NCOR2(1), NFKBIA(1), NR0B2(1), NR1H3(1), NRIP1(1), PIK3CA(28), PIK3R1(32), PPARA(1), PRKAR1B(1), PRKAR2B(1), PRKCA(1), RB1(20), RXRA(2), STAT5B(1) 26846850 103 92 93 11 16 15 10 9 53 0 <1.00e-15 <3.24e-14
7 HSA04150_MTOR_SIGNALING_PATHWAY Genes involved in mTOR signaling pathway AKT1, AKT2, AKT3, BRAF, CAB39, DDIT4, EIF4B, EIF4EBP1, FIGF, FRAP1, GBL, HIF1A, IGF1, INS, KIAA1303, LYK5, MAPK1, MAPK3, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PRKAA1, PRKAA2, RHEB, RICTOR, RPS6, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA6, RPS6KB1, RPS6KB2, STK11, TSC1, TSC2, ULK1, ULK2, ULK3, VEGFA, VEGFB, VEGFC 44 AKT1(1), BRAF(5), EIF4B(1), FIGF(2), IGF1(2), MAPK1(1), MAPK3(1), PIK3CA(28), PIK3CB(4), PIK3CG(5), PIK3R1(32), PIK3R2(3), PIK3R3(1), PIK3R5(3), RICTOR(2), RPS6KA2(2), RPS6KA3(1), RPS6KA6(2), TSC2(2), ULK2(1), VEGFA(2), VEGFB(1) 22950463 102 86 88 11 21 24 16 10 31 0 <1.00e-15 <3.24e-14
8 APOPTOSIS APAF1, BAD, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BCL2L11, BID, BIRC2, BIRC3, BIRC4, BIRC5, BNIP3L, CASP1, CASP10, CASP1, COPl, CASP2, CASP3, CASP4, CASP6, CASP7, CASP8, CASP9, CHUK, CYCS, DFFA, DFFB, FADD, FAS, FASLG, GZMB, HELLS, HRK, IKBKB, IKBKG, IRF1, IRF2, IRF3, IRF4, IRF5, IRF6, IRF7, JUN, LTA, MAP2K4, MAP3K1, MAPK10, MDM2, MYC, NFKB1, NFKBIA, NFKBIB, NFKBIE, PRF1, RELA, RIPK1, TNF, TNFRSF10B, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF25, PLEKHG5, TNFSF10, TP53, TP73, TRADD, TRAF1, TRAF2, TRAF3 66 BCL2(2), BIRC3(1), CASP1(1), CASP9(1), CHUK(1), IKBKB(1), IRF1(1), IRF2(1), IRF4(2), IRF5(1), IRF6(2), MAP3K1(2), MDM2(2), MYC(1), NFKB1(1), NFKBIA(1), NFKBIE(2), PLEKHG5(1), RIPK1(1), TNFRSF1A(1), TNFSF10(2), TP53(69) 24836757 97 79 76 9 22 34 10 8 23 0 <1.00e-15 <3.24e-14
9 FCER1PATHWAY In mast cells, Fc epsilon receptor 1 activates BTK, PKC, and the MAP kinase pathway to promote degranulation and arachnidonic acid release. BTK, CALM1, CALM2, CALM3, ELK1, FCER1A, FCER1G, FOS, GRB2, HRAS, JUN, LYN, MAP2K1, MAP2K4, MAP2K7, MAP3K1, MAPK1, MAPK3, MAPK8, NFATC1, NFATC2, NFATC3, NFATC4, PAK2, PIK3CA, PIK3R1, PLA2G4A, PLCG1, PPP3CA, PPP3CB, PPP3CC, PRKCB1, RAF1, SHC1, SOS1, SYK, SYT1, VAV1 37 ELK1(2), FCER1A(1), FOS(1), LYN(2), MAP2K1(1), MAP3K1(2), MAPK1(1), MAPK3(1), MAPK8(1), NFATC2(2), NFATC4(2), PIK3CA(28), PIK3R1(32), PLA2G4A(2), PLCG1(6), PPP3CB(1), RAF1(1), SOS1(3), VAV1(3) 18589718 92 79 82 9 17 17 18 10 30 0 <1.00e-15 <3.24e-14
10 AT1RPATHWAY Binding of angiotensin II to AT1-R activates Ca2+ signaling and the JNK pathway. AGT, AGTR1, ATF2, CALM1, CALM2, CALM3, EGFR, ELK1, GNAQ, GRB2, HRAS, JUN, MAP2K1, MAP2K2, MAP2K4, MAP3K1, MAPK1, MAPK3, MAPK8, MEF2A, MEF2B, MEF2C, MEF2D, PAK1, PRKCA, PRKCB1, PTK2, PTK2B, RAC1, RAF1, SHC1, SOS1, SRC, SYT1 33 AGTR1(1), EGFR(73), ELK1(2), MAP2K1(1), MAP3K1(2), MAPK1(1), MAPK3(1), MAPK8(1), MEF2A(2), MEF2D(1), PAK1(1), PRKCA(1), PTK2B(2), RAF1(1), SOS1(3), SRC(2) 14612734 95 78 61 9 49 21 14 3 8 0 <1.00e-15 <3.24e-14

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 16. 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 q
1 DCPATHWAY Dendritic cells internalize and present antigen, after which they migrate to lymphocyte-rich tissues and induce T and B cell differentiation. ANPEP, CD2, CD33, CD5, CD7, CSF2, IFNA1, IFNB1, IFNG, IL10, IL12A, IL12B, IL13, IL3, IL4, IL5, ITGAX, TLR2, TLR4, TLR7, TLR9, TNFRSF5 21 ANPEP(2), CD2(1), CD33(4), CD5(2), CSF2(2), IFNB1(1), IFNG(2), IL12B(1), IL3(1), ITGAX(6), TLR2(3), TLR4(1), TLR7(3), TLR9(2) 8029007 31 31 31 8 2 20 4 1 4 0 3.9e-07 0.00024
2 HSA04640_HEMATOPOIETIC_CELL_LINEAGE Genes involved in hematopoietic cell lineage ANPEP, CD14, CD19, CD1A, CD1B, CD1C, CD1D, CD1E, CD2, CD22, CD24, CD33, CD34, CD36, CD37, CD38, CD3D, CD3E, CD3G, CD4, CD44, CD5, CD55, CD59, CD7, CD8A, CD8B, CD9, CR1, CR2, CSF1, CSF1R, CSF2, CSF2RA, CSF3, CSF3R, DNTT, EPO, EPOR, FCER2, FCGR1A, FLT3, FLT3LG, GP1BA, GP1BB, GP5, GP9, GYPA, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, IL11, IL11RA, IL1A, IL1B, IL1R1, IL1R2, IL2RA, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL7, IL7R, IL9R, ITGA1, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGAM, ITGB3, KIT, KITLG, MME, MS4A1, TFRC, THPO, TNF, TPO 81 ANPEP(2), CD19(1), CD1B(1), CD1D(3), CD1E(2), CD2(1), CD22(3), CD33(4), CD37(1), CD38(1), CD3E(2), CD3G(1), CD44(3), CD5(2), CD55(1), CD59(1), CR2(3), CSF1R(1), CSF2(2), DNTT(1), EPO(1), FCER2(1), FLT3(4), HLA-DRA(1), IL1A(1), IL1B(1), IL1R1(2), IL3(1), IL4R(4), IL5RA(1), IL6(1), IL7(1), IL7R(1), ITGA1(2), ITGA2(1), ITGA2B(1), ITGA3(1), ITGA4(3), ITGA5(1), ITGAM(4), ITGB3(1), KIT(3), KITLG(1), MME(1), THPO(1), TPO(3) 34897969 79 70 78 28 18 36 9 2 14 0 0.00011 0.034
3 HSA04650_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY Genes involved in natural killer cell mediated cytotoxicity ARAF, BID, BRAF, CASP3, CD244, CD247, CD48, CHP, CSF2, FAS, FASLG, FCER1G, FCGR3A, FCGR3B, FYN, GRB2, GZMB, HCST, HLA-A, HLA-B, HLA-C, HLA-E, HLA-G, HRAS, ICAM1, ICAM2, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNG, IFNGR1, IFNGR2, ITGAL, ITGB2, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DS1, KIR2DS2, KIR3DL1, KIR3DL2, KLRC1, KLRC2, KLRC3, KLRD1, KLRK1, KRAS, LAT, LCK, LCP2, LOC652578, MAP2K1, MAP2K2, MAPK1, MAPK3, MICA, MICB, NCR1, NCR2, NCR3, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NRAS, PAK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRF1, PRKCA, PRKCB1, PRKCG, PTK2B, PTPN11, PTPN6, RAC1, RAC2, RAC3, RAF1, SH2D1A, SH2D1B, SH3BP2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SYK, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFSF10, TYROBP, ULBP1, ULBP2, ULBP3, VAV1, VAV2, VAV3, ZAP70 123 BRAF(5), CD244(1), CSF2(2), FYN(1), ICAM1(1), ICAM2(1), IFNA10(4), IFNA21(1), IFNB1(1), IFNG(2), IFNGR2(3), ITGB2(4), KIR2DL1(2), KIR2DL3(1), KIR2DL4(1), KIR3DL1(3), KLRC3(2), KLRD1(1), KLRK1(1), KRAS(2), MAP2K1(1), MAPK1(1), MAPK3(1), NCR1(1), NFATC2(2), NFATC4(2), PAK1(1), PIK3CB(4), PIK3CG(5), PIK3R2(3), PIK3R3(1), PIK3R5(3), PLCG1(6), PLCG2(2), PPP3CB(1), PPP3R2(1), PRKCA(1), PRKCG(2), PTK2B(2), PTPN11(4), RAF1(1), SH2D1A(1), SH2D1B(1), SHC4(1), SOS1(3), TNFSF10(2), ULBP1(1), VAV1(3), VAV2(2), VAV3(1), ZAP70(3) 47276775 102 78 95 34 30 30 19 9 14 0 0.00024 0.049
4 ERYTHPATHWAY Erythropoietin selectively stimulates erythrocyte differentiation from CFU-GEMM cells in bone marrow. CCL3, CSF2, CSF3, EPO, FLT3, IGF1, IL11, IL1A, IL3, IL6, IL9, KITLG, TGFB1, TGFB2, TGFB3 15 CCL3(1), CSF2(2), EPO(1), FLT3(4), IGF1(2), IL1A(1), IL3(1), IL6(1), KITLG(1) 3629573 14 14 14 1 1 6 5 0 2 0 0.00043 0.053
5 TH1TH2PATHWAY Helper T subtype Th1 produces pro-inflammatory cytokines that stimulate phagocytosis, while Th2 cells promote antibody production and activate eosinophils. CD28, CD86, HLA-DRA, HLA-DRB1, IFNG, IFNGR1, IFNGR2, IL12A, IL12B, IL12RB1, IL12RB2, IL18, IL18R1, IL2, IL2RA, IL4, IL4R, TNFRSF5, TNFSF5 17 CD28(1), CD86(2), HLA-DRA(1), IFNG(2), IFNGR2(3), IL12B(1), IL12RB1(2), IL12RB2(1), IL18R1(2), IL4R(4) 5517896 19 18 19 4 3 8 3 2 3 0 0.00052 0.053
6 TOLLPATHWAY Toll-like receptors are activated by bacterial lipoproteins, lipopolysaccharides, and other surface molecules, and activate pro-inflammatory factors such as NF-kB. CD14, CHUK, ELK1, FOS, IKBKB, IKBKG, IRAK1, JUN, LY96, MAP2K3, MAP2K4, MAP2K6, MAP3K1, MAP3K14, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAPK14, MAPK8, MYD88, NFKB1, NFKBIA, PGLYRP, PPARA, PRKR, RELA, SITPEC, TIRAP, TLR10, TLR2, TLR3, TLR4, TLR6, TLR7, TLR9, TOLLIP, TRAF6 31 CHUK(1), ELK1(2), FOS(1), IKBKB(1), IRAK1(2), LY96(2), MAP2K3(3), MAP3K1(2), MAP3K7(2), MAPK8(1), NFKB1(1), NFKBIA(1), PPARA(1), TLR10(2), TLR2(3), TLR3(1), TLR4(1), TLR6(5), TLR7(3), TLR9(2), TRAF6(1) 15827389 38 37 38 9 9 16 5 2 6 0 0.00052 0.053
7 HSA04610_COMPLEMENT_AND_COAGULATION_CASCADES Genes involved in complement and coagulation cascades A2M, BDKRB1, BDKRB2, C1QA, C1QB, C1QC, C1R, C1S, C2, C3, C3AR1, C4A, C4B, C4BPA, C4BPB, C5, C5AR1, C6, C7, C8A, C8B, C8G, C9, CD46, CD55, CD59, CFB, CFD, CFH, CFI, CPB2, CR1, CR2, F10, F11, F12, F13A1, F13B, F2, F2R, F3, F5, F7, F8, F9, FGA, FGB, FGG, KLKB1, KNG1, MASP1, MASP2, MBL2, PLAT, PLAU, PLAUR, PLG, PROC, PROS1, SERPINA1, SERPINA5, SERPINC1, SERPIND1, SERPINE1, SERPINF2, SERPING1, TFPI, THBD, VWF 67 A2M(3), BDKRB1(1), C1QC(1), C1S(2), C2(2), C3(3), C4BPB(1), C5(1), C5AR1(3), C6(1), C8A(1), C8B(3), C9(2), CD46(2), CD55(1), CD59(1), CFB(1), CFH(2), CFI(1), CR2(3), F10(1), F13A1(3), F2(2), F5(4), F8(6), F9(4), FGA(4), FGB(2), FGG(3), KLKB1(1), KNG1(2), MASP2(1), MBL2(1), PLAT(1), PLG(2), SERPINA5(1), SERPINC1(1), SERPING1(2), VWF(5) 39287991 81 70 81 25 24 29 14 2 12 0 0.00066 0.055
8 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(4) 312623 4 4 4 0 2 2 0 0 0 0 0.00071 0.055
9 ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS Rat-derived PC12 cells respond to nerve growth factor (NGF) and PACAP to differentiate into neuronal cells. AKT1, ASAH1, ATF1, BRAF, CAMP, CREB1, CREB3, CREB5, CREBBP, CRKL, DAG1, EGR1, EGR2, EGR3, EGR4, ELK1, FRS2, GAS, GNAQ, GRF2, JUN, MAP1B, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, NTRK1, OPN1LW, PACAP, PIK3C2G, PIK3CA, PIK3CD, PIK3R1, PTPN11, RPS6KA3, SH2B, SHC1, SRC, TERF2IP, TH, TUBA3 40 AKT1(1), BRAF(5), CREB1(1), CREBBP(4), CRKL(1), DAG1(2), EGR1(3), EGR2(1), EGR3(1), ELK1(2), MAP1B(2), MAPK1(1), MAPK3(1), MAPK8(1), MAPK8IP1(1), MAPK8IP2(2), MAPK8IP3(2), NTRK1(1), PIK3C2G(6), PTPN11(4), RPS6KA3(1), SRC(2), TERF2IP(1) 20692311 46 42 42 14 12 14 6 4 10 0 0.00095 0.065
10 BADPATHWAY When phosphorylated, BAD is inhibited by sequestration; when non-phosphorylated, it promotes apoptosis by inactivating pro-survival BCL-XL and BCL-2. ADCY1, AKT1, BAD, BAX, BCL2, BCL2L1, CSF2RB, IGF1, IGF1R, IL3, IL3RA, KIT, KITLG, PIK3CA, PIK3R1, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, YWHAH 19 ADCY1(3), AKT1(1), BCL2(2), CSF2RB(2), IGF1(2), IGF1R(2), IL3(1), KIT(3), KITLG(1), PRKAR1B(1), PRKAR2B(1), YWHAH(1) 7358109 20 20 20 4 4 7 5 1 3 0 0.0012 0.068
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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