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MEPD: a resource for medaka gene expression patterns.

Thorsten Henrich1, Mirana Ramialison, Beate Wittbrodt

  • 1EMBL Heidelberg Meyerhofstrasse 1, D-69117 Heidelberg, Germany. henrich@embl.de

Bioinformatics (Oxford, England)
|May 10, 2005
PubMed
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The Medaka Expression Pattern Database (MEPD) centralizes gene expression data for medaka fish (Oryzias latipes) using in situ hybridization. This resource aids bioinformatics analysis and cross-species gene expression pattern comparisons.

Area of Science:

  • Developmental Biology
  • Genomics
  • Bioinformatics

Background:

  • The Medaka Expression Pattern Database (MEPD) serves as a repository for gene expression patterns in medaka (Oryzias latipes).
  • Data is compiled from multiple research groups, establishing MEPD as a central hub for the medaka research community.
  • Gene expression data is crucial for understanding organismal development and function.

Purpose of the Study:

  • To enhance the Medaka Expression Pattern Database (MEPD) with advanced features for data analysis.
  • To facilitate bioinformatics approaches and cross-species comparisons of gene expression patterns.
  • To establish a comprehensive resource for medaka gene expression studies.

Main Methods:

  • Gene expression patterns were determined using in situ hybridization.

Related Experiment Videos

  • A detailed medaka anatomy ontology with over 4000 terms was developed and submitted to Open Biological Ontologies.
  • Sequence data was annotated using BLAST results and Gene Ontology (GO) terms.

    • Main Results:

    • MEPD currently contains 19,757 entries, with expression patterns determined for 1024 genes.
    • The database integrates images and anatomical terms for comprehensive gene expression descriptions.
    • New annotation features enable advanced bioinformatics analyses and comparative studies.

    Conclusions:

    • The enhanced MEPD facilitates sophisticated data analysis and cross-species comparisons.
    • MEPD is a valuable and growing resource for the medaka research community.
    • The database supports a deeper understanding of gene function and regulation in medaka.