title: Consistent annotation of gene expression arrays.
abstract: BACKGROUND
  Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome. Effectively translating the results from the microarray into a biological interpretation requires an accurate mapping between the probesets on the array and the genes that they are targeting. Although major array manufacturers provide annotations of their gene expression arrays, the methods used by various manufacturers are different and the annotations are difficult to keep up to date in the rapidly changing world of biological sequence databases.
  
  
  RESULTS
  We have created a consistent microarray annotation protocol applicable to all of the major array manufacturers. We constantly keep our annotations updated with the latest Ensembl Gene predictions, and thus cross-referenced with a large number of external biomedical sequence database identifiers. We show that these annotations are accurate and address in detail reasons for the minority of probesets that cannot be annotated. Annotations are publicly accessible through the Ensembl Genome Browser and programmatically through the Ensembl Application Programming Interface. They are also seamlessly integrated into the BioMart data-mining tool and the biomaRt package of BioConductor.
  
  
  CONCLUSIONS
  Consistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles.
authors.affiliation: European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Benoît
authors.initials: B
authors.lastname: Ballester
authors.forename: Nathan
authors.initials: N
authors.lastname: Johnson
authors.forename: Glenn
authors.initials: G
authors.lastname: Proctor
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
mesh_terms: D000483:Alleles; D000818:Animals; D019295:Computational Biology; D057225:Data Mining; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D006801:Humans; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D011381:Programming Languages; D011786:Quality Control; D012333:RNA, Messenger / Q000235:genetics; D051381:Rats
chemical_list: D012333:RNA, Messenger
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