title: MEPD: medaka expression pattern database, genes and more.
abstract: The Medaka Expression Pattern Database (MEPD; http://mepd.cos.uni-heidelberg.de/) is designed as a repository of medaka expression data for the scientific community. In this update we present two main improvements. First, we have changed the previous clone-centric view for in situ data to a gene-centric view. This is possible because now we have linked all the data present in MEPD to the medaka gene annotation in ENSEMBL. In addition, we have also connected the medaka genes in MEPD to their corresponding orthologous gene in zebrafish, again using the ENSEMBL database. Based on this, we provide a link to the Zebrafish Model Organism Database (ZFIN) to allow researches to compare expression data between these two fish model organisms. As a second major improvement, we have modified the design of the database to enable it to host regulatory elements, promoters or enhancers, expression patterns in addition to gene expression. The combination of gene expression, by traditional in situ, and regulatory element expression, typically by fluorescence reporter gene, within the same platform assures consistency in terms of annotation. In our opinion, this will allow researchers to uncover new insights between the expression domain of genes and their regulatory landscape.
authors.affiliation: Department of Computing Systems, University of Castilla-La Mancha, Albacete, 02071, Spain.
authors.forename: Juan I
authors.identifier: http://orcid.org/0000-0001-9902-6048
authors.initials: JI
authors.lastname: Alonso-Barba
authors.affiliation: Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany.
authors.forename: Raza-Ur
authors.initials: RU
authors.lastname: Rahman
authors.affiliation: Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany juan.mateo@cos.uni-heidelberg.de.
authors.forename: Joachim
authors.initials: J
authors.lastname: Wittbrodt
authors.affiliation: Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany juan.mateo@cos.uni-heidelberg.de.
authors.forename: Juan L
authors.initials: JL
authors.lastname: Mateo
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D015870:Gene Expression; D058977:Molecular Sequence Annotation; D009990:Oryzias / Q000235:genetics* / Q000378:metabolism