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Open Access Research article

Comparative modular analysis of gene expression in vertebrate organs

Barbara Piasecka123, Zoltán Kutalik23, Julien Roux13, Sven Bergmann23 and Marc Robinson-Rechavi13*

Author affiliations

1 Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1005 Lausanne, Switzerland

2 Department of Medical Genetics, University of Lausanne, Rue de Bungon 27, CH-1015 Lausanne, Switzerland

3 Swiss Institute of Bioinformatics, Lausanne, Switzerland

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Citation and License

BMC Genomics 2012, 13:124  doi:10.1186/1471-2164-13-124

Published: 29 March 2012

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.