Abstract:
BACKGROUND:Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedical model organisms, are often dated. In addition, most microarray analysis tools do not readily accept EST clone names, which are abundantly represented on arrays. Manual re-annotation of microarrays is impracticable and so we developed a computational re-annotation tool (ArrayIDer) to retrieve the most recent accession mapping files from public databases based on EST clone names or accessions and rapidly generate database accessions for entire microarrays. RESULTS:We utilized the Fred Hutchinson Cancer Research Centre 13K chicken cDNA array - a widely-used non-commercial chicken microarray - to demonstrate the principle that ArrayIDer could markedly improve annotation. We structurally re-annotated 55% of the entire array. Moreover, we decreased non-chicken functional annotations by 2 fold. One beneficial consequence of our re-annotation was to identify 290 pseudogenes, of which 66 were previously incorrectly annotated. CONCLUSION:ArrayIDer allows rapid automated structural re-annotation of entire arrays and provides multiple accession types for use in subsequent functional analysis. This information is especially valuable for systems biology modeling in the non-traditional biomedical model organisms.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
van den Berg BH,Konieczka JH,McCarthy FM,Burgess SCdoi
10.1186/1471-2105-10-30subject
Has Abstractpub_date
2009-01-23 00:00:00pages
30issn
1471-2105pii
1471-2105-10-30journal_volume
10pub_type
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