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 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.


CONCLUSIONS
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.
Casneuf
Tineke
T
Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. tineke.casneuf@psb.ugent.be
Van de Peer
Yves
Y
Huber
Wolfgang
W
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D016477:Artifacts; D016000:Cluster Analysis; D003626:Data Display; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards*; D015345:Oligonucleotide Probes / Q000009:adverse effects / Q000737:chemistry*; D010363:Pattern Recognition, Automated / Q000592:standards
D015345:Oligonucleotide Probes