Bar-Or, C., Department of Ornamental Horticulture, ARO Volcani Center, Bet Dagan, 50250, Israel, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agricultural, Food and Environmental Quality Sciences, Rehovot, Israel
Novikov, E., Service Bioinformatique, Institut Curie, Paris, France
Reiner, A., Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
Czosnek, H., The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agricultural, Food and Environmental Quality Sciences, Rehovot, Israel
Koltai, H., Department of Ornamental Horticulture, ARO Volcani Center, Bet Dagan, 50250, Israel

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. © 2007 Elsevier Inc. All rights reserved.