Utilizing microarray spot characteristics to improve cross-species hybridization results

Carmiya Bar-Or, Eugene Novikov, Anat Reiner-Benaim, Henryk Czosnek, Hinanit Koltai

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

Cross-species hybridization (CSH), i.e., the hybridization of a (target) species RNA to a DNA microarray that represents another (reference) species, is often used to study species diversity. However, filtration of CSH data has to be applied to extract valid information. We present a novel approach to filtering the CSH data, which utilizes spot characteristics (SCs) of image-quantification data from scanned spotted cDNA microarrays. Five SCs that were affected by sequence similarity between probe and target sequences were identified (designated as BS-SCs). Filtration by all five BS-SC thresholds demonstrated improved clustering for two of the three examined experiments, suggesting that BS-SCs may serve for filtration of data obtained by CSH, to improve the validity of the results. This CSH data-filtration approach could become a promising tool for studying a variety of species, especially when no genomic information is available for the target species.
Original languageEnglish
Pages (from-to)636-645
Number of pages10
JournalGenomics
Volume90
Issue number5
DOIs
StatePublished - 1 Dec 2007
Externally publishedYes

Keywords

  • Gene expression
  • Image quantification
  • Species diversity
  • Transcriptome
  • cDNA microarrays

ASJC Scopus subject areas

  • Genetics

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