\name{omimIds}
\alias{omimIds}
\alias{diseaseIds}
\alias{morbidmapIds}
\alias{dominantIds}
\alias{recessiveIds}
\alias{dominantIdsEBI}
\alias{recessiveIdsEBI}
\alias{dominantIdsNCBI}
\alias{recessiveIdsNCBI}
\docType{data}                                                  
\title{Entrez identifiers for disease-related genes in the OMIM database}
\description{Entrez identifiers for several lists of genes related with human
disease.
 
\describe{
\item{\code{diseaseIds}}{contains the Entrez identifiers corresponding to
  disease-related genes found in the OMIM database. This list has been manually
  curated by Nuria Lopez-Bigas et al. who kindly provided it to us.}
\item{\code{morbidmapIds}}{contains the Entrez identifiers for all the genes
  in the morbidmap table. This list would correspond to disease-related genes
  if there had been no manual curation, as in the previous list
  ('diseaseIds').}
\item{\code{dominantIds}}{ontains the Entrez identifiers for dominant genes
after manual curation by Nuria Lopez-Bigas who has kindly allowed us to
include them in the package.}
\item{\code{recessiveIds}}{contains the Entrez identifiers for recessive genes
after manual curation by Nuria Lopez-Bigas who has kindly allowed us to
include them in the package.}
\item{\code{dominantIdsEBI}}{contains the Entrez identifiers for dominant
genes in the EBI version of the OMIM database recovered using SRS with the
term 'dominant' in the KEYWORDS field.}
\item{\code{recessiveIdsEBI}}{contains the Entrez identifiers for recessive genes in the EBI version of the OMIM database recovered using SRS with the term 'recessive' in the KEYWORDS field.}
\item{\code{dominantIdsNCBI}}{contains the Entrez identifiers for dominant
genes in the NCBI version of the OMIM database recovered using ENTREZ with the
term 'dominant' in the CLINICAL field.}
\item{\code{recessiveIdsNCBI}}{contains the Entrez identifiers for recessive
genes in the NCBI version of the OMIM database recovered using ENTREZ with the
term 'recessive' in the CLINICAL field.}
}
}
\details{Lopez-Bigas et al. analyzed the distribution of functional categories in genes causing disease in human.
They did several comparisosn which can also be done using \code{goProfiles}. In order to perform these comparisons
we first tried to obtain the same lists of genes using standard database browsers, such as 'SRS', at the European Bioinformatics Institute, or 'Entrez', at the National Center for Biotechnological Information. Curiously both approaches provided very different lists so we asked the authors for their data and they kindly provided them to us. In order to facilitat the use of functions included in \code{goProfiles} we have trimmed the list of recessive and dominant genes so that (i) They become exclussive (no gene belows to both lists) (2) They are both included in the \code{diseaseIds} list. This eliminated 39 genes (out of 639) from the list of recessive genes and  52 genes (out of 414) from the list of dominant genes}
\references{
Lopez-Bigas, N., Blencowe, B.J. and Ouzounis, C.A.,
Highly consistent patterns for inherited human diseases at the molecular level,
Bioinformatics, 2006, 22 (3), 269-277.
}
\usage{data(omimIds)}
\format{Each dataset is a character vector with a different number of elements which (should) correspond to valid Entrez identifiers}
\examples{
data(omimIds)
}
\keyword{datasets}