Abstract:
BACKGROUND:Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures. RESULTS:We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization. CONCLUSION:The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Casneuf T,Van de Peer Y,Huber Wdoi
10.1186/1471-2105-8-461subject
Has Abstractpub_date
2007-11-26 00:00:00pages
461issn
1471-2105pii
1471-2105-8-461journal_volume
8pub_type
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