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.
Highlights
Medaka (Oryzias latipes) is already an established model organism in developmental biology [1,2]
At that time the medaka genome sequence was not yet available and all the information was based on expressed sequence tags (EST)
We have replicated the structure containing the information of gene expression pattern with new tables for regulatory elements
Summary
Medaka (Oryzias latipes) is already an established model organism in developmental biology [1,2]. The availability of the genome sequence together with the gene annotation accomplished by the ENSEMBL team [6] implies a major change in the structure of MEPD. Medaka is as well a good model organism to study transcriptional regulation and the expression domain of regulatory elements, namely promoters and enhancers.
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