MEPD: A resource for medaka gene expression patterns

Thorsten Henrich, Mirana Ramialison, Beate Wittbrodt, Beatrice Assouline, Franck Bourrat, Anja Berger, Heinz Himmelbauer, Takashi Sasaki, Nobuyoshi Shimizu, Monte Westerfield, Hisato Kondoh, Joachim Wittbrodt

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Summary: The Medaka Expression Pattern Database (MEPD) is a database for gene expression patterns determined by in situ hybridization in the small freshwater fish medaka (Oryzias latipes). Data have been collected from various research groups and MEPD is developing into a central expression pattern depository within the medaka community. Gene expression patterns are described by images and terms of a detailed medaka anatomy ontology of over 4000 terms, which we have developed for this purpose and submitted to Open Biological Ontologies. Sequences have been annotated via BLAST match results and using Gene Ontology terms. These new features will facilitate data analyses using bioinformatics approaches and allow cross-species comparisons of gene expression patterns. Presently, MEPD has 19 757 entries, for 1024 of them the expression pattern has been determined.

Original languageEnglish
Pages (from-to)3195-3197
Number of pages3
JournalBioinformatics
Volume21
Issue number14
DOIs
Publication statusPublished - 2005 Jul 15

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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    Henrich, T., Ramialison, M., Wittbrodt, B., Assouline, B., Bourrat, F., Berger, A., Himmelbauer, H., Sasaki, T., Shimizu, N., Westerfield, M., Kondoh, H., & Wittbrodt, J. (2005). MEPD: A resource for medaka gene expression patterns. Bioinformatics, 21(14), 3195-3197. https://doi.org/10.1093/bioinformatics/bti478