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Database Commons - 4DXpress

4DXpress

Citations: 36

z-index 0.00

Short name 4DXpress
Full name Expression Database in Four Dimensions
Description 4DXpress is a central public repository of expression patterns for zebrafish, Drosophila, medaka and mouse.
URL http://ani.embl.de/4DXpress
Year founded 2008
Last update & version     
Availability Not Available
University/Institution hosted European Molecular Biology Laboratory
Address Meyerhofstrasse 1, 69117 Heidelberg, Germany
City Heidelberg
Province/State
Country/Region Germany
Contact name Thorsten Henrich
Contact email henrich@embl.de
Data type(s)
Major organism(s)
Keyword(s)
  • spatio-temporal gene expression
Publication(s)
  • 4DXpress: a database for cross-species expression pattern comparisons. [PMID: 17916571]

    Yannick Haudry, 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
    Nucleic acids research 2008:36(Database issue)
    36 Citations (Google Scholar as of 2016-03-01)

    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.

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Tags

Expression
Danio rerio Drosophila melanogaster Mus musculus Oryzias latipes
spatio-temporal gene expression

Record metadata

  • Created on: 2015-07-28
  • Curated by:
    • Lina Ma [2016-04-11]
    • Mengwei Li [2016-03-31]
    • Lina Ma [2016-03-30]
    • Lina Ma [2016-03-28]
    • Mengwei Li [2016-03-24]
    • Mengwei Li [2016-02-20]
    • Lina Ma [2015-12-31]
    • Mengwei Li [2015-11-21]
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