A novel method for cross-species gene expression analysis

作者：Kristiansson Erik^*; Osterlund Tobias; Gunnarsson Lina; Arne Gabriella; Larsson D G Joakim; Nerman Olle

来源：BMC Bioinformatics, 2013, 14: 70.

DOI：10.1186/1471-2105-14-70

• Gene expression
• Evolution
• Meta-analysis
• Orthologs
• Paralogs
• Microarray
• RNA-seq

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. %26lt;br%26gt;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. %26lt;br%26gt;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/.

• 出版日期2013-2-27