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

BMC Bioinformatics. 2004 Aug 27;5:117. doi: 10.1186/1471-2105-5-117.


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/.

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.

MeSH terms

  • Animals
  • Computational Biology / methods
  • DNA Probes / genetics
  • DNA, Complementary / genetics
  • Databases, Genetic
  • Gene Expression Profiling / standards*
  • Humans
  • Internet
  • Mice
  • Nucleic Acid Hybridization / methods*
  • Oligonucleotide Array Sequence Analysis / standards*
  • Rats
  • Software*
  • User-Computer Interface


  • DNA Probes
  • DNA, Complementary