4DXpress: a database for cross-species expression pattern comparisons

Abstract

In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these species, expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for Drosophila or GXD for mouse. However, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. Therefore, we have integrated expression patterns for zebrafish, Drosophila, medaka and mouse into a central public repository called 4DXpress (expression database in four dimensions). Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species. Genes are linked to public microarray data in ArrayExpress. We have mapped developmental stages between the species to be able to compare developmental time phases. We store the largest collection of gene expression patterns available to date in an individual resource, reflecting 16 505 annotated genes. 4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at http://ani.embl.de/4DXpress.

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

“…A Document Type Definition (DTD) was developed for three expression databases, ANISEED 20 , COMPARE 21 and 4DXpress 22 . It defines a format that follows the MISFISHIE specification.…”

Adding a spatial dimension to postnatal ventricular-subventricular zone neurogenesis

“…Introducing this germinal region and progenitor domains into current brain development databases (Thompson et al, 2014), together with the homogenization of the ontological nomenclature across species (Haudry et al, 2008), represent important steps for screening databases or sampling subregions of the postnatal V-SVZ to identify regionally enriched genes.…”

Evolutionary crossroads in developmental biology: annelids

“…This is made possible by colabelling the embryo with an anti-tubulin antibody, which labels the nervous system and provides a 3D expression scaffold upon which distinct WMISH experiments can be aligned and directly compared (cellular profiling by image registration, PrimR) . Work is well underway to integrate all of this data and make it publicly available via the 4DXpress database (Haudry et al, 2008), and further databases are appearing that will facilitate comparisons of expression data between various animals, including annelids [e.g. the KahiKai database (Ormestad et al, 2011)].…”