title: Single-species microarrays and comparative transcriptomics.
abstract: BACKGROUND
  Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes.
  
  
  RESULTS
  Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes.
  
  
  CONCLUSIONS
  Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species.
authors.affiliation: Department of Biology, Center for Environmental Genomics, McMaster University, Hamilton, Ontario, Canada.
authors.forename: Frédéric J J
authors.initials: FJ
authors.lastname: Chain
authors.forename: Dora
authors.initials: D
authors.lastname: Ilieva
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Evans
mesh_terms: D000818:Animals; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D016678:Genome; D023281:Genomics / Q000379:methods; D009693:Nucleic Acid Hybridization / Q000235:genetics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D011123:Polyploidy; D015203:Reproducibility of Results; D013045:Species Specificity; D014158:Transcription, Genetic; D014981:Xenopus / Q000378:metabolism* / Q000502:physiology; D014982:Xenopus laevis / Q000378:metabolism* / Q000502:physiology