Mammalian development is complicated; each of the thousands of embryological events that operate in sequence to make a mature body typically involves the concerted action of many cells in response to a multitude of simultaneous environmental signals that regulate hundreds of different genes. Traditional gene-by-gene analyses have served developmental biology well in the era when its main goal was discovering basic developmental principles from whatever organism might illustrate a principle best. Now that the focus of many developmental biologists has moved on to understanding in detail the development of specific, clinically relevant body systems with a view to preventing or repairing malformation, the gene-by-gene approach is no longer sufficient and it is necessary to consider the genome as a whole and to take a systems biology approach (Bard, 2007
; Davidson, 2009
; Rumballe et al., 2010
). This requires comprehensive databases of the expression of thousands of transcripts, annotated at high resolution and made easily accessible to manual and automated queries.
The development of the genitourinary (GU) system is attracting much attention for two reasons. First, humans suffer from a wide range of congenital abnormalities of urogenital organs, which can damage this system directly (kidney failures and infertility syndromes) (Schedl, 2007
) and also cause indirect damage to other organs, for example because failing kidneys can raise systemic blood pressure (Hoy et al., 2005
). Second, damage to the GU tract from non-developmental causes, for example infection, is repaired poorly and there is an urgent need to develop novel approaches to GU tract organ regeneration (Unbekandt and Davies, 2009
). A comprehensive description of gene expression during urogenital development will be central to understanding the mechanisms of congenital urogenital abnormalities and to the development of better ways to treat them.
GUDMAP aims to provide a fundamental description of gene expression in the developing mouse GU system, generating gene expression data that will ‘enable, facilitate and stimulate research’ into understanding the GU system (McMahon et al., 2008
). In addition, microarray analyses and the generation of transgenic mouse strains with genetic markers will bolster the overall aim of defining molecular and cellular anatomy through developmental time. The specific focus on the GU system combined with the range of data (in situ and microarray across a range of developmental time points) distinguishes GUDMAP from other gene expression databases.
Some gene expression data for the developing murine GU system are already publicly available, but they are dispersed across various resources that cover a range of species, organ systems and data types [GEO (Barrett et al., 2009
), ArrayExpress (Parkinson et al., 2009
), GXD (Smith et al., 2007
), EMAGE (Richardson et al., 2010
)]. The EuReGene database (http://www.euregene.org
) holds in situ gene expression data for the developing [17.5 days post-coitum (dpc)] and adult mouse kidney, but not for other components of the GU system or time points of development. Although funding for the EuReGene project ended in 2009, there are plans to assimilate the data into the GUDMAP database and make it available once again. Additionally, the Kidney Development Database (Davies, 1999
) holds text descriptions from published developmental studies that have a bearing on kidney development.
Here, we present an overview of the GUDMAP database. Our goals are to describe how the data are generated by expert GUDMAP consortium laboratories, how the quality of the data and its annotation are maintained by a dedicated editorial team and how the data are made available via the GUDMAP website (www.gudmap.org