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Nucleic Acids Research Advance Access first published online on October 4, 2007
This version published online on December 17, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm797
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

4DXpress: a database for cross-species expression pattern comparisons

Yannick Haudry1, Hugo Berube2, Ivica Letunic1, Paul-Daniel Weeber1, Julien Gagneur1, Charles Girardot1, Misha Kapushesky2, Detlev Arendt1, Peer Bork1, Alvis Brazma2, Eileen E. M. Furlong1, Joachim Wittbrodt1 and Thorsten Henrich1,*

1European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany and 2European Bioinformatics Institute, EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK

*To whom correspondence should be addressed. Tel: +49 6221 387 516; Fax: +49 6221 387 166; Email: henrich{at}embl.de

Received August 14, 2007. Revised September 14, 2007. Accepted September 17, 2007.

In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these species, expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for Drosophila or GXD for mouse. However, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. Therefore, we have integrated expression patterns for zebrafish, Drosophila, medaka and mouse into a central public repository called 4DXpress (expression database in four dimensions). Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species. Genes are linked to public microarray data in ArrayExpress. We have mapped developmental stages between the species to be able to compare developmental time phases. We store the largest collection of gene expression patterns available to date in an individual resource, reflecting 16 505 annotated genes. 4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at http://ani.embl.de/4DXpress.


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