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

doi:10.1093/bioinformatics/bti478

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

Center for Supercentenarian Medical Research

Research output: Contribution to journal › Article › peer-review

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 language	English
Pages (from-to)	3195-3197
Number of pages	3
Journal	Bioinformatics
Volume	21
Issue number	14
DOIs	https://doi.org/10.1093/bioinformatics/bti478
Publication status	Published - 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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title = "MEPD: A resource for medaka gene expression patterns",

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.",

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

note = "Funding Information: We would like to thank MEPD users for their constructive feedback on the interfaces and the Medaka ontologies. We thank Geo Pertea from TIGR for his help with the tgicl software. We thank Daniel Barrell and Wolfgang Fleischmann for their help with the UniProt GO annotation. This work was supported by grants from the HFSPO (J.W., H.H. and H.K.) and the EU (J.W.).",

year = "2005",

month = jul,

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doi = "10.1093/bioinformatics/bti478",

language = "English",

volume = "21",

pages = "3195--3197",

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T1 - MEPD

T2 - A resource for medaka gene expression patterns

AU - Henrich, Thorsten

AU - Ramialison, Mirana

AU - Wittbrodt, Beate

AU - Assouline, Beatrice

AU - Bourrat, Franck

AU - Berger, Anja

AU - Himmelbauer, Heinz

AU - Sasaki, Takashi

AU - Shimizu, Nobuyoshi

AU - Westerfield, Monte

AU - Kondoh, Hisato

AU - Wittbrodt, Joachim

N1 - Funding Information: We would like to thank MEPD users for their constructive feedback on the interfaces and the Medaka ontologies. We thank Geo Pertea from TIGR for his help with the tgicl software. We thank Daniel Barrell and Wolfgang Fleischmann for their help with the UniProt GO annotation. This work was supported by grants from the HFSPO (J.W., H.H. and H.K.) and the EU (J.W.).

PY - 2005/7/15

Y1 - 2005/7/15

N2 - 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.

AB - 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.

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MEPD: A resource for medaka gene expression patterns

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