title: Novel definition files for human GeneChips based on GeneAnnot.
abstract: BACKGROUND
  Improvements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective alignments of probes and transcription products. In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence.
  
  
  RESULTS
  We developed a novel set of custom Chip Definition Files (CDF) and the corresponding Bioconductor libraries for Affymetrix human GeneChips, based on the information contained in the GeneAnnot database. GeneAnnot-based CDFs are composed of unique custom-probesets, including only probes matching a single gene.
  
  
  CONCLUSIONS
  GeneAnnot-based custom CDFs solve the problem of a reliable reconstruction of expression levels and eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the same transcript when gene differential expression is the focus of the analysis. GeneAnnot CDFs are freely distributed and fully compliant with Affymetrix standards and all available software for gene expression analysis. The CDF libraries are available from http://www.xlab.unimo.it/GA_CDF, along with supplementary information (CDF libraries, installation guidelines and R code, CDF statistics, and analysis results).
authors.affiliation: Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100, Modena, Italy. ferrari.francesco@unimore.it
authors.forename: Francesco
authors.initials: F
authors.lastname: Ferrari
authors.forename: Stefania
authors.initials: S
authors.lastname: Bortoluzzi
authors.forename: Alessandro
authors.initials: A
authors.lastname: Coppe
authors.forename: Alexandra
authors.initials: A
authors.lastname: Sirota
authors.forename: Marilyn
authors.initials: M
authors.lastname: Safran
authors.forename: Michael
authors.initials: M
authors.lastname: Shmoish
authors.forename: Sergio
authors.initials: S
authors.lastname: Ferrari
authors.forename: Doron
authors.initials: D
authors.lastname: Lancet
authors.forename: Gian Antonio
authors.initials: GA
authors.lastname: Danieli
authors.forename: Silvio
authors.initials: S
authors.lastname: Bicciato
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors