title: Estimating the efficiency of fish cross-species cDNA microarray hybridization.
abstract: Using an available cross-species cDNA microarray is advantageous for examining multigene expression patterns in non-model organisms, saving the need for construction of species-specific arrays. The aim of the present study was to estimate relative efficiency of cross-species hybridizations across bony fishes, using bioinformatics tools. The methodology may serve also as a model for similar evaluations in other taxa. The theoretical evaluation was done by substituting comparative whole-transcriptome sequence similarity information into the thermodynamic hybridization equation. Complementary DNA sequence assemblages of nine fish species belonging to common families or suborders and distributed across the bony fish taxonomic branch were selected for transcriptome-wise comparisons. Actual cross-species hybridizations among fish of different taxonomic distances were used to validate and eventually to calibrate the theoretically computed relative efficiencies.
authors.affiliation: National Institute for Biotechnology in Negev, Ben Gurion University of Negev, Beer-Sheva 84105, Israel.
authors.forename: Raphael
authors.initials: R
authors.lastname: Cohen
authors.forename: Vered
authors.initials: V
authors.lastname: Chalifa-Caspi
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Williams
authors.forename: Meirav
authors.initials: M
authors.lastname: Auslander
authors.forename: Stephen G
authors.initials: SG
authors.lastname: George
authors.forename: James K
authors.initials: JK
authors.lastname: Chipman
authors.forename: Moshe
authors.initials: M
authors.lastname: Tom
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D004526:Efficiency; D005399:Fishes / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods / Q000662:veterinary*; D008297:Male; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards / Q000662:veterinary*; D013045:Species Specificity