XHM: A system for detection of potential cross hybridizations in DNA microarrays

doi:10.1186/1471-2105-5-117

BMC Bioinformatics

Volume 5

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Yadetie F
Laegreid A
Jonassen I

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XHM: A system for detection of potential cross hybridizations in DNA microarrays

Kristian Flikka¹ , Fekadu Yadetie²^,3 , Astrid Laegreid² and Inge Jonassen¹^,4

¹Computational Biology Unit, Bergen Center for Computational Science, UNIFOB/UiB, Thormoehlensgt.55, N-5008 Bergen, Norway

²Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway

³Sars International Centre for Marine Molecular Biology, Bergen High Technology Centre, Thormoehlensgt. 55, N-5008 Bergen, Norway

⁴Department of Informatics, University of Bergen, PB. 7800, N-5020 Bergen, Norway

author email corresponding author email

BMC Bioinformatics 2004, 5:117doi:10.1186/1471-2105-5-117


Published:	27 August 2004

Abstract

Background

Microarrays have emerged as the preferred platform for high throughput gene expression analysis. Cross-hybridization among genes with high sequence similarities can be a source of error reducing the reliability of DNA microarray results.

Results

We have developed a tool called XHM (cross hybridization on microarrays) for assessment of the reliability of hybridization signals by detecting potential cross-hybridizations on DNA microarrays. This is done by comparing the sequences of the probes against an extensive database representing the transcriptome of the organism in question. XHM is available online at http://www.bioinfo.no/tools/xhm/ webcite.

Conclusions

Using XHM with its user-adjustable parameters will enable scientists to check their lists of differentially expressed genes from microarray experiments for potential cross-hybridizations. This provides information that may be useful in the validation of the microarray results.