Estimating the efficiency of fish cross-species cDNA microarray hybridization

Raphael Cohen, Vered Chalifa-Caspi, Timothy D. Williams, Meirav Auslander, Stephen G. George, James K. Chipman, Moshe Tom

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

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.

Original languageEnglish
Pages (from-to)491-499
Number of pages9
JournalMarine Biotechnology
Volume9
Issue number4
DOIs
StatePublished - 3 Oct 2007

Keywords

  • Bony fish
  • Cross-species
  • Microarray
  • Transcriptome sequence comparisons
  • cDNA hybridization

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