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Bioinformatics Advance Access originally published online on May 6, 2005
Bioinformatics 2005 21(14):3195-3197; doi:10.1093/bioinformatics/bti478
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

MEPD: a resource for medaka gene expression patterns

Thorsten Henrich 1,*,{dagger}, Mirana Ramialison 1,{dagger}, Beate Wittbrodt 1, Beatrice Assouline 1,2, Franck Bourrat 3, Anja Berger 4, Heinz Himmelbauer 4, Takashi Sasaki 5, Nobuyoshi Shimizu 5, Monte Westerfield 6, Hisato Kondoh 7 and Joachim Wittbrodt 1

1EMBL Heidelberg Meyerhofstrasse 1, D-69117 Heidelberg, Germany
2INSERM E363, Faculty of Medicine Necker 75730 Paris Cedex 15, France
3UPR CNRS 2197, Institut de Neurobiologie A. Fessard 91198, Gif/Yvette, France
4Max-Planck-Institut für Molekulare Genetik D-14195 Berlin-Dahlem, Germany
5Department of Molecular Biology, Keio University School of Medicine Tokyo, Japan
6ZFIN, University of Oregon Eugene, OR 97403-5274, USA
7Japan Science and Technology Agency, ERATO Kondoh Differentiation Signaling Project/SORST Kondoh Research Group, Kinki-chihou Hatsumei Center Building Yoshida-Kawaracho 14, Sakyo-ku, Kyoto 606-8305, Japan

*To whom correspondence should be addressed.

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.

Availability: A new version has been implemented at the EMBL in Heidelberg and is now accessible at http://www.embl.de/mepd

Contact: henrich{at}embl.de

Supplementary information: http://www.embl.de/mepd/supplement.html

Received on February 4, 2005; revised on April 13, 2005; accepted on April 28, 2005

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