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\name{PolyPhenDbColumns}
\alias{PolyPhenDbColumns}
\title{PolyPhenDb Columns}
\description{
Description of the PolyPhen Sqlite Database Columns
}
\section{Column descriptions}{
These column names are displayed when \code{columns} is called on a
\code{PolyPhenDb} object.
\itemize{
\item rsid : rsid
}
Original query :
\itemize{
\item OSNPID : original SNP identifier from user input
\item OSNPACC : original protein identifier from user input
\item OPOS : original substitution position in the protein sequence
from user input
\item OAA1 : original wild type (reference) aa residue from user input
\item OAA2 : original mutant (reference) aa residue from user input
}
Mapped query :
\itemize{
\item SNPID : SNP identifier mapped to dbSNP rsID if available,
otherwise same as o_snp_id. This value was used as the
rsid column
\item ACC : protein UniProtKB accession if known protein, otherwise
same as o_acc
\item POS : substitution position mapped to UniProtKB protein sequence
if known, otherwise same as o_pos
\item AA1 : wild type aa residue
\item AA2 : mutant aa residue
\item NT1 : wild type allele nucleotide
\item NT2 : mutant allele nucleotide
}
PolyPhen-2 prediction :
\itemize{
\item PREDICTION : qualitative ternary classification FPR thresholds
}
PolyPhen-1 prediction :
\itemize{
\item BASEDON : prediction basis
\item EFFECT : predicted substitution effect on the protein structure or
function
}
PolyPhen-2 classifiers :
\itemize{
\item PPH2CLASS : binary classifier outcome ("damaging" or "neutral")
\item PPH2PROB : probability of the variation being dammaging
\item PPH2FPR : false positive rate at the pph2_prob level
\item PPH2TPR : true positive rate at the pph2_prob level
\item PPH2FDR : false discovery rate at the pph2_prob level
}
UniProtKB-SwissProt derived protein sequence annotations :
\itemize{
\item SITE : substitution SITE annotation
\item REGION : substitution REGION annotation
\item PHAT : PHAT matrix element for substitution in the
TRANSMEM region
}
Multiple sequence alignment scores :
\itemize{
\item DSCORE : difference of PSIC scores for two aa variants
(Score1 - Score2)
\item SCORE1 : PSIC score for wild type aa residue (aa1)
\item SCORE2 : PSIC score for mutant aa residue (aa2)
\item NOBS : number of residues observed at the substitution position
in the multiple alignment (sans gaps)
}
Protein 3D structure features :
\itemize{
\item NSTRUCT : initial number of BLAST hits to similar proteins with
3D structures in PDB
\item NFILT : number of 3D BLAST hits after identity threshold filtering
\item PDBID : protein structure identifier from PDB
\item PDBPOS : position of substitution in PDB protein sequence
\item PDBCH : PDB polypeptide chain identifier
\item IDENT : sequence identity between query and aligned PDB sequences
\item LENGTH : PDB sequence alignment length
\item NORMACC : normalized accessible surface
\item SECSTR : DSSP secondary structure assignment
\item MAPREG : region of the phi-psi (Ramachandran) map derived from the
residue dihedral angles
\item DVOL : change in residue side chain volume
\item DPROP : change in solvent accessible surface propensity resulting
from the substitution
\item BFACT : normalized B-factor (temperature factor) for the residue
\item HBONDS : number of hydrogen sidechain-sidechain and
sidechain-mainchain bonds formed by the residue
\item AVENHET : average number of contacts with heteroatoms per residue
\item MINDHET : closest contact with heteroatom
\item AVENINT : average number of contacts with other chains per residue
\item MINDINT : closest contact with other chain
\item AVENSIT : average number of contacts with critical sites per
residue
\item MINDSIT : closest contact with a critical site
}
Nucleotide sequence features (CpG/codon/exon junction) :
\itemize{
\item TRANSV : whether substitution is a transversion
\item CODPOS : position of the substitution within the codon
\item CPG : whether or not the substitution changes CpG context
\item MINDJNC : substitution distance from exon/intron junction
}
Pfam protein family :
\itemize{
\item PFAMHIT : Pfam identifier of the query protein
}
Substitution scores :
\itemize{
\item IDPMAX : maximum congruency of the mutant aa residue to all
sequences in multiple alignment
\item IDPSNP : maximum congruency of the mutant aa residue to the
sequence in alignment with the mutant residue
\item IDQMIN : query sequence identity with the closest homologue
deviating from the wild type aa residue
}
Comments :
\itemize{
\item COMMENTS : Optional user comments
}
}
\seealso{
\code{?PolyPhenDb}
}
\author{Valerie Obenchain <vobencha@fhcrc.org>}
\keyword{classes}
\keyword{methods}
|
