Utilizing microarray spot characteristics to improve cross-species hybridization results.
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.
Bar-Or
Carmiya
C
Department of Ornamental Horticulture, ARO Volcani Center, Bet Dagan 50250, Israel.
Novikov
Eugene
E
Reiner
Anat
A
Czosnek
Henryk
H
Koltai
Hinanit
H
D020869:Gene Expression Profiling; D018551:Solanum lycopersicum / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins / Q000235:genetics*; D011198:Solanum tuberosum / Q000235:genetics*; D013045:Species Specificity
D010940:Plant Proteins