ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.

Bart Hj van den Berg, Jay H. Konieczka, Fiona M McCarthy, Shane C Burgess

Research output: Contribution to journalArticle

9 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)30
Number of pages1
JournalBMC Bioinformatics
Volume10
DOIs
StatePublished - 2009
Externally publishedYes

Fingerprint

DNA Microarray
Systems Biology
Expressed Sequence Tags
Microarrays
Oligonucleotide Array Sequence Analysis
Names
Annotation
Chickens
DNA
Clone Cells
Pipelines
Databases
Pseudogenes
Microarray Analysis
Microarray
Entire
Clone
Research
Neoplasms
Functional analysis

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

ArrayIDer : automated structural re-annotation pipeline for DNA microarrays. / van den Berg, Bart Hj; Konieczka, Jay H.; McCarthy, Fiona M; Burgess, Shane C.

In: BMC Bioinformatics, Vol. 10, 2009, p. 30.

Research output: Contribution to journalArticle

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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.",
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