In situ Analysis of Cross-Hybridisation on Microarrays and the Inference of Expression Correlation

Background
Microarray co-expression signatures are an important tool for studying gene function and relationsbetween genes. In addition to genuine biological co-expression, correlated signals can result from technicaldeficiencies like hybridization of reporters with otarget transcripts. An approach that is able to distinguishthese factors permits the detection of more biologically relevant co-expression signatures.
Results
We demonstrate a positive relation between otarget reporter alignment strength and expressioncorrelation in data from oligonucleotide genechips. Furthermore, we describe a method that allows theidentification, from their expression data, of individual probe sets acted by otarget hybridization.
Conclusions
The ects of otarget hybridization on expression correlation coecients can be substantial, andcan be alleviated by more accurate mapping between microarray reporters and the target transcriptome. Werecommend attention to the mapping for any microarray analysis of gene expression patterns.

Casneuf, T., Van de Peer, Y., Huber, H. (2007) In situ Analysis of Cross-Hybridisation on Microarrays and the Inference of Expression Correlation. BMC Bioinformatics 8:461.

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