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

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.

Pubmed ID: 17916571

Authors

  • Haudry Y
  • Berube H
  • Letunic I
  • Weeber PD
  • Gagneur J
  • Girardot C
  • Kapushesky M
  • Arendt D
  • Bork P
  • Brazma A
  • Furlong EE
  • Wittbrodt J
  • Henrich T

Journal

Nucleic acids research

Publication Data

January 15, 2008

Associated Grants

None

Mesh Terms

  • Animals
  • Databases, Genetic
  • Drosophila
  • Gene Expression
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Internet
  • Mice
  • Oligonucleotide Array Sequence Analysis
  • Oryzias
  • Systems Integration
  • User-Computer Interface
  • Zebrafish