BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

  • Authors:

  • Steffen Durinck;Yves Moreau;Arek Kasprzyk;Sean Davis;Bart De Moor;Alvis Brazma;Wolfgang Huber

  • Affiliations:

  • Department of Electronical Engineering ESAT-SCD, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium;Department of Electronical Engineering ESAT-SCD, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium;EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK;Cancer Genetics Branch, National Human Genome Research Institute, National Institute of Health 50 South Drive, Bethesda, MD 20892-8000, USA;Department of Electronical Engineering ESAT-SCD, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium;EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK;EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK

  • Venue:
  • Bioinformatics
  • Year:
  • 2005

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Abstract

Summary:biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. Entrez-Gene and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Furthermore biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SQL queries to the BioMart databases (e.g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining. Availability:http://www.bioconductor.org. LGPL Contact: steffen.durinck@esat.kuleuven.ac.be