omimIds: Entrez identifiers for disease-related genes in the OMIM...

In goProfiles: goProfiles: an R package for the statistical analysis of functional profiles

Description

Entrez identifiers for several lists of genes related with human disease.

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.

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').

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.

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.

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.

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.

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.

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.

Usage

data(omimIds)

Format

Each dataset is a character vector with a different number of elements which (should) correspond to valid Entrez identifiers

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 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 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 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.

Examples

data(omimIds)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: GO.db

goProfiles documentation built on Nov. 8, 2020, 8:12 p.m.