title: Comparative modular analysis of gene expression in vertebrate organs.
abstract: BACKGROUND
  The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity.
  
  
  RESULTS
  Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human.
  
  
  CONCLUSIONS
  Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1005 Lausanne, Switzerland.
authors.forename: Barbara
authors.initials: B
authors.lastname: Piasecka
authors.forename: Zoltán
authors.initials: Z
authors.lastname: Kutalik
authors.forename: Julien
authors.initials: J
authors.lastname: Roux
authors.forename: Sven
authors.initials: S
authors.lastname: Bergmann
authors.forename: Marc
authors.initials: M
authors.lastname: Robinson-Rechavi
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D051379:Mice; D009928:Organ Specificity; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014714:Vertebrates / Q000235:genetics*