Software
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays
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* Corresponding author: Bart HJ van den Berg bvandenberg@cvm.msstate.edu
1 Department of Basic Science, PO Box 6100, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
2 Instistute for Digital Biology, Mississippi State University, Mississippi State, MS 39762, USA
3 Department of Molecular & Cellular Biology, University of Arizona, 1656 E. Mabel, MRB 317, Tucson, AZ 85724, USA
4 Life Sciences and Biotechnology Institute, Mississippi State University, Mississippi State, Mississippi 39762, USA
BMC Bioinformatics 2009, 10:30 doi:10.1186/1471-2105-10-30
Published: 23 January 2009Abstract
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.