title: A novel method for cross-species gene expression analysis.
abstract: BACKGROUND
  Analysis of gene expression from different species is a powerful way to identify evolutionarily conserved transcriptional responses. However, due to evolutionary events such as gene duplication, there is no one-to-one correspondence between genes from different species which makes comparison of their expression profiles complex.
  
  
  RESULTS
  In this paper we describe a new method for cross-species meta-analysis of gene expression. The method takes the homology structure between compared species into account and can therefore compare expression data from genes with any number of orthologs and paralogs. A simulation study shows that the proposed method results in a substantial increase in statistical power compared to previously suggested procedures. As a proof of concept, we analyzed microarray data from heat stress experiments performed in eight species and identified several well-known evolutionarily conserved transcriptional responses. The method was also applied to gene expression profiles from five studies of estrogen exposed fish and both known and potentially novel responses were identified.
  
  
  CONCLUSIONS
  The method described in this paper will further increase the potential and reliability of meta-analysis of gene expression profiles from evolutionarily distant species. The method has been implemented in R and is freely available at http://bioinformatics.math.chalmers.se/Xspecies/.
authors: Department of Mathematical Statistics, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden. erik.kristiansson@chalmers.se
authors: Erik
authors: E
authors: Kristiansson
authors: Tobias
authors: T
authors: Österlund
authors: Lina
authors: L
authors: Gunnarsson
authors: Gabriella
authors: G
authors: Arne
authors: D G Joakim
authors: DG
authors: Larsson
authors: Olle
authors: O
authors: Nerman
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D004967:Estrogens / Q000494:pharmacology; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D018869:Heat-Shock Response / Q000235:genetics; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D004967:Estrogens