title: A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus.
abstract: The recent sequencing of a large number of Xenopus tropicalis expressed sequences has allowed development of a high-throughput approach to study Xenopus global RNA gene expression. We examined the global gene expression similarities and differences between the historically significant Xenopus laevis model system and the increasingly used X.tropicalis model system and assessed whether an X.tropicalis microarray platform can be used for X.laevis. These closely related species were also used to investigate a more general question: is there an association between mRNA sequence divergence and differences in gene expression levels? We carried out a comprehensive comparison of global gene expression profiles using microarrays of different tissues and developmental stages of X.laevis and X.tropicalis. We (i) show that the X.tropicalis probes provide an efficacious microarray platform for X.laevis, (ii) describe methods to compare interspecies mRNA profiles that correct differences in hybridization efficiency and (iii) show independently of hybridization bias that as mRNA sequence divergence increases between X.laevis and X.tropicalis differences in mRNA expression levels also increase.
authors.affiliation: University of Cincinnati, Department of Environmental Health Cincinnati, OH 45267-0056, USA.
authors.forename: Maureen A
authors.initials: MA
authors.lastname: Sartor
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Zorn
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Schwanekamp
authors.forename: Danielle
authors.initials: D
authors.lastname: Halbleib
authors.forename: Saikumar
authors.initials: S
authors.lastname: Karyala
authors.forename: Michael L
authors.initials: ML
authors.lastname: Howell
authors.forename: Gary E
authors.initials: GE
authors.lastname: Dean
authors.forename: Mario
authors.initials: M
authors.lastname: Medvedovic
authors.forename: Craig R
authors.initials: CR
authors.lastname: Tomlinson
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D014644:Genetic Variation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism*; D013045:Species Specificity; D014981:Xenopus / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D014982:Xenopus laevis / Q000196:embryology / Q000235:genetics* / Q000378:metabolism
chemical_list: D015345:Oligonucleotide Probes; D012333:RNA, Messenger