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

Yannick Haudry1, Hugo Berube, Ivica Letunic

  • 1European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Nucleic Acids Research
|October 6, 2007
PubMed
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A new resource, 4DXpress, integrates gene expression patterns across mouse, zebrafish, medaka, and Drosophila. This tool enables cross-species comparisons of gene regulation and evolution, facilitating developmental biology research.

Area of Science:

  • Developmental Biology
  • Comparative Genomics
  • Bioinformatics

Background:

  • Whole mount in situ hybridization provides spatial gene expression data in model organisms.
  • Existing model organism databases (ZFIN, MEPD, BDGP, GXD) store species-specific gene expression data.
  • A centralized resource for cross-species gene expression comparison is lacking.

Purpose of the Study:

  • To establish a central public repository, 4DXpress, for querying and comparing gene expression patterns across multiple species.
  • To facilitate research in gene regulation and evolution by enabling cross-species analysis.
  • To link gene expression data with public microarray datasets.

Main Methods:

  • Integration of gene expression data from zebrafish, Drosophila, medaka, and mouse into a single database.

Related Experiment Videos

  • Development of an anatomy ontology for querying expression annotations across species.
  • Mapping of developmental stages between species for temporal comparisons.
  • Linking gene entries to public microarray data in ArrayExpress.

    • Main Results:

    • 4DXpress is a central repository for four-dimensional (4D) gene expression data.
    • The database contains the largest collection of annotated gene expression patterns to date (16,505 genes).
    • Users can query expression patterns across species and identify orthologous genes.

    Conclusions:

    • 4DXpress provides an invaluable tool for developmental and computational biologists.
    • The resource supports comparative analysis of gene regulation and evolutionary processes.
    • 4DXpress enhances the accessibility and utility of gene expression data for cross-species research.