Utilizing microarray spot characteristics to improve cross-species hybridization results

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• 作者：Carmiya Bar-Or ; Eugene Novikov ; Anat Reiner ; Henryk Czosnek ; Hinanit Koltai
• 关键词：cDNA microarrays ; Gene expression ; Image quantification ; Species diversity ; Transcriptome
• 刊名：Genomics
• 出版年：2007
• 出版时间：November 2007
• 年：2007
• 卷：90
• 期：5
• 页码：636-645
• 全文大小：2110 K

文摘

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.