TY - JOUR
T1 - Utilizing microarray spot characteristics to improve cross-species hybridization results
AU - Bar-Or, Carmiya
AU - Novikov, Eugene
AU - Reiner, Anat
AU - Czosnek, Henryk
AU - Koltai, Hinanit
PY - 2007/11
Y1 - 2007/11
N2 - 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.
AB - 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.
KW - cDNA microarrays
KW - Gene expression
KW - Image quantification
KW - Species diversity
KW - Transcriptome
UR - http://www.scopus.com/inward/record.url?scp=35548990220&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2007.06.008
DO - 10.1016/j.ygeno.2007.06.008
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C2 - 17888623
AN - SCOPUS:35548990220
SN - 0888-7543
VL - 90
SP - 636
EP - 645
JO - Genomics
JF - Genomics
IS - 5
ER -