title: XHM: a system for detection of potential cross hybridizations in DNA microarrays.
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/.
  
  
  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.
authors.affiliation: Computational Biology Unit, Bergen Center for Computational Science, UNIFOB/UiB, Thormoehlensgt,55, N-5008 Bergen, Norway. flikka@ii.uib.no
authors.forename: Kristian
authors.initials: K
authors.lastname: Flikka
authors.forename: Fekadu
authors.initials: F
authors.lastname: Yadetie
authors.forename: Astrid
authors.initials: A
authors.lastname: Laegreid
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D015342:DNA Probes / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000592:standards*; D006801:Humans; D020407:Internet; D051379:Mice; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D051381:Rats; D012984:Software; D014584:User-Computer Interface
chemical_list: D015342:DNA Probes; D018076:DNA, Complementary