Alternative mapping of probes to genes for Affymetrix chips

Background: Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results using an updated mapping of probes to genes, taking into account the latest biological knowledge available. Methods: We investigated how probes found on recent commercial microarrays for human genes (Affymetrix HG-U133A) were matching a recent curated collection of human transcripts: the NCBI RefSeq database. We also built mappings and used them in place of the original probe to genes associations provided by the manufacturer of the arrays. Results: In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that c...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Laurent Gautier, Morten Møller, Lennart Friis-Hansen, Steen Knudsen
• Keywords: Biological Knowledge, BMCBI 2004, Expression Levels, Short Oligonucleotide Arrays