4DXpress: a database for cross-species expression pattern comparisons - PubMed (original) (raw)
. 2008 Jan;36(Database issue):D847-53.
doi: 10.1093/nar/gkm797. Epub 2007 Oct 4.
Hugo Berube, Ivica Letunic, Paul-Daniel Weeber, Julien Gagneur, Charles Girardot, Misha Kapushesky, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E M Furlong, Joachim Wittbrodt, Thorsten Henrich
Affiliations
- PMID: 17916571
- PMCID: PMC2238840
- DOI: 10.1093/nar/gkm797
4DXpress: a database for cross-species expression pattern comparisons
Yannick Haudry et al. Nucleic Acids Res. 2008 Jan.
Abstract
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.
Figures
Figure 1.
Mapping of developmental species was done via a list of stages common to all bilaterian animals.
Figure 2.
Comparison of the number of genes annotated at species-specific developmental stages in zebrafish, Drosophila, mouse and medaka. Corresponding developmental stages have the same colour. Colour legend for all panels is shown in the mouse panel.
Figure 3.
The comparative view shows expression patterns of a list of selected genes (medaka Six3 and its Drosophila orthologue Optix). Expression annotation and images can be easily compared between the genes on a single page.
References
- Henrich T, Ramialison M, Wittbrodt B, Assouline B, Bourrat F, Berger A, Himmelbauer H, Sasaki T, Shimizu N, et al. MEPD: a resource for medaka gene expression patterns. Bioinformatics. 2005;21:3195–3197. - PubMed
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