Using surveys of Affymetrix GeneChips to study antisense expression

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doi doi:10.2390/biecoll-jib-2010-114
submission December 15, 2009
last revision February 05, 2010
published February 19, 2010
NCBI PubMed PubMed ID 20167985

Olivia Sanchez-Graillet, Maria A Stalteri, Joanna Rowsell, Graham JG Upton and Andrew P Harrison

Correspondence should be addressed to:
Andrew P Harrison
Departments of Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom
ku.ca.xesse@nullyrrah


Abstract

We have used large surveys of Affymetrix GeneChip data in the public domain to conduct a study of antisense expression across diverse conditions. We derive correlations between groups of probes which map uniquely to the same exon in the antisense direction. When there are no probes assigned to an exon in the sense direction we find that many of the antisense groups fail to detect a coherent block of transcription. We find that only a minority of these groups contain coherent blocks of antisense expression suggesting transcription. We also derive correlations between groups of probes which map uniquely to the same exon in both sense and antisense direction. In some of these cases the locations of sense probes overlap with the antisense probes, and the sense and antisense probe intensities are correlated with each other. This configuration suggests the existence of a Natural Antisense Transcript (NAT) pair. We find the majority of such NAT pairs detected by GeneChips are formed by a transcript of an established gene and either an EST or an mRNA. In order to determine the exact antisense regulatory mechanism indicated by the correlation of sense probes with antisense probes, a further investigation is necessary for every particular case of interest. However, the analysis of microarray data has proved to be a good method to reconfirm known NATs, discover new ones, as well as to notice possible problems in the annotation of antisense transcripts.

Reference

Olivia Sanchez-Graillet, Maria A Stalteri, Joanna Rowsell, Graham JG Upton and Andrew P Harrison. Using surveys of Affymetrix GeneChips to study antisense expression. Journal of Integrative Bioinformatics, 7(2):114, 2010. Online Journal: http://journal.imbio.de/index.php?paper_id=114
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