ArticleBMC bioinformatics2009
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations.BMC bioinformatics · 2011Article
- AgBase: supporting functional modeling in agricultural organisms.Nucleic acids research · 2011Article
- Re-annotation is an essential step in systems biology modeling of functional genomics data.PloS one · 2010Article
- Structural and functional-annotation of an equine whole genome oligoarray.BMC bioinformatics · 2009Article
- The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays.BMC bioinformatics · 2009Article
- Pathway analysis software: annotation errors and solutions.Molecular genetics and metabolismArticle
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Authors and funding
4 authors.
Funding
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Abstract
backgroundSystems 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.
resultsWe 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.
conclusionArrayIDer 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.
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