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Q: What do the different fields for significantly mutated genes mean?

A: Many of these field fields depend on what version of MutSig was used. The following table covers the majority of them:

Fields
Description
MutSig_1.5MutSig_2.0MutSig_CVMutSig_2CV
genegenegenegeneHUGO Symbol
descriptiondescription longnameFull description/name of the gene
NN  number of sequenced bases in this gene across the individual set
nn  number of (nonsilent) mutations in this gene across the individual set
  nnonnnonnumber of nonsense mutations
npatnpatnpatnpatnumber of patients (individuals) with at least one nonsilent mutation
nsitensitensitensitenumber of unique sites having a nonsilent mutation
nsilnsilnsilnsilnumber of silent mutations in this gene across the individual set
n1n1  number of nonsilent mutations of type "*CpG->T"
n2n2  number of nonsilent mutations of type "*Cp(A/C/T)->T*"
n3n3  number of nonsilent mutations of type "A->G"
n4n4  number of nonsilent mutations of type "transver"
n5n5  number of nonsilent mutations of type "indel+null"
n6n6  number of nonsilent mutations of type "double_null"
p_ns_sp_ns_s  p-value for the observed nonsilent/silent ratio being elevated in this gene
ppppp-value (overall)
qqqqq-value, False Discovery Rate (Benjamini-Hochberg procedure)
 p_classic  p-value for the observed amount of nonsilent mutations being elevated in this gene
 p_clust pCLp-value for clustering
 p_cons pFNp-value for conservation
 p_joint  p-value for joint model of clustering and conservation
   pCVp-value from covariates
   codelenthe gene's coding length
   nncdnumber of noncoding mutations
   nmisnumber of missense mutations
   nstpnumber of readthrough mutations
   nsplnumber of splice site mutations
   nindnumber of indels

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