Mutation Analysis (MutSig vS2N)
Lung Squamous Cell Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1X34VP9
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig vS2N). Broad Institute of MIT and Harvard. doi:10.7908/C1X34VP9
- Overview
+ Introduction
- Summary
- Results
- Significantly Mutated Genes

Column Descriptions:

  • N = number of sequenced bases in this gene across the individual set

  • nnon = number of (nonsilent) mutations in this gene across the individual set

  • nnull = number of (nonsilent) null mutations in this gene across the individual set

  • nflank = number of noncoding mutations from this gene's flanking region, across the individual set

  • nsil = number of silent mutations in this gene across the individual set

  • p = p-value (overall)

  • q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Table 1.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 29. 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).

gene N nflank nsil nnon nnull p q
PTEN 28658 0 0 16 8 4.1e-57 7.7e-53
CDKN2A 10680 0 1 26 12 1.7e-56 1.6e-52
TP53 22428 0 7 147 47 1.8e-50 1.2e-46
PIK3CA 74938 0 1 29 0 7.8e-39 3.7e-35
EYS 40050 0 1 14 4 1e-22 3.9e-19
NFE2L2 38270 0 0 28 1 2.1e-16 6.6e-13
HLA-A 19224 0 0 7 6 6.4e-16 1.7e-12
KEAP1 32752 0 0 24 2 6.8e-15 1.6e-11
WHSC1L1 93628 0 1 16 2 3.9e-14 8.1e-11
MLL2 222678 0 6 41 18 1.2e-11 2.3e-08
RB1 86686 0 0 12 8 1.5e-09 2.5e-06
CPS1 99680 0 3 29 2 2.2e-07 0.00035
ZNF221 41296 0 0 5 0 2.8e-07 0.00041
NOTUM 16732 0 1 6 1 1.5e-06 0.0021
EBF1 33464 0 1 8 1 3.8e-06 0.0048
PRR23B 9612 0 2 9 0 9.8e-06 0.012
AKAP13 169812 0 4 19 0 0.000014 0.015
KIAA0319 65148 0 0 8 0 0.000026 0.027
DCAF5 54112 0 0 7 2 0.000037 0.037
DPP8 61054 0 0 8 0 0.000039 0.037
COL22A1 61054 0 5 35 6 0.000041 0.037
COL19A1 56604 0 5 19 2 0.000058 0.05
CD109 98968 0 1 8 0 0.000082 0.067
REG3A 10858 0 2 14 1 0.000085 0.067
TRIOBP 96298 0 1 20 1 0.000094 0.071
SPHKAP 103062 0 3 36 1 0.0001 0.076
FAM58B 14596 0 1 5 3 0.00011 0.076
FAM47C 50374 0 5 21 1 0.00014 0.091
PDGFRA 73514 0 3 10 0 0.00014 0.094
FSCB 40940 0 2 19 1 0.00017 0.11
NNT 65326 0 1 10 1 0.00023 0.14
SCN1A 140798 0 9 33 3 0.00023 0.14
PI16 21894 0 1 7 1 0.00025 0.15
PIK3CG 71556 0 4 18 1 0.0003 0.17
ASCL4 3204 0 0 6 2 0.00036 0.19
+ Methods & Data
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