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Bioinformatics Advance Access published online on May 6, 2005
Bioinformatics, 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@oupjournals.org
Received February 4, 2005
Revised April 13, 2005
Accepted April 28, 2005

Applications note

MEPD: a resource for medaka gene expression patterns

Thorsten Henrich 1*, Mirana Ramialison 1, Beate Wittbrodt 1, Beatrice Assouline 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

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

* To whom correspondence should be addressed.
Thorsten Henrich, E-mail: henrich{at}embl.de


  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) (Henrich et al., 2003). 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 which we submitted to Open Biological Ontologies (OBO). 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. MEPD has now 19757 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.

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


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