Using surveys of Affymetrix GeneChips to study antisense expression

Abstract

We have used large surveys of Affymetrix GeneChip HG-U133_Plus_2 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.