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Davidson Group including Editorial Office (Jamie Davies) and Database Core (GUDMAP1) | ATLAS-D2K Center
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Davidson Group including Editorial Office (Jamie Davies) and Database Core (GUDMAP1)

The time and location where a gene is expressed give clues to its function.  But the pattern of expression of any particular gene becomes much more meaningful when compared with the expression of other genes. Such comparisons suggest networks of gene interaction and implicate genetic pathways in developmental and functional processes. This, in the longer term, may lead us to a better understanding of disease.  A key part of the GUDMAP project is therefore to bring together information about gene expression from different experiments, labs and approaches and to make this data accessible to researchers worldwide.  Additional value comes from linking GUDMAP gene expression data to information from other sources concerning the function of genes and their role in disease. To satisfy these requirements, we are building a public database that integrates and stores the data generated by GUDMAP and presents it on the Web for query and analysis.

An important first step in building the GUDMAP database is to devise convenient mechanisms for the laboratories to prepare their results in a consistent, database-ready format. For example, this information will contain annotations that describe which tissues express the gene as well as images of the original data, description of the experiment, etc. We are working closely with our GUDMAP partners to achieve this. Once submitted to the database, the information is curated by the GUDMAP editorial office before being made accessible on the public database website. The database will have interactive web-pages to browse and query the data and will provide programmatic access so that other bioinformatics databases can tap into data from the GUDMAP project.

The GUDMAP database will help project partners, as well as other researchers, to explore gene expression in the genitourinary system. Data can be browsed to see the latest results, to look at which genes or which tissues have been assayed and to examine the expression of any particular gene. A query interface will allow researchers to ask which genes are expressed in any particular tissue in the genitourinary system, which tissues express any particular gene and to identify patterns of expression that are common to several genes. An important aspect of this will be to make data from in situ and microarray experiments accessible to the same query. Co-expression patterns suggest interactions between genes. The database interface will help researchers to explore these by linking to other bioinformatics databases (containing information about DNA sequence, protein interactions, gene functions, etc.).This will help researchers to identify the molecular pathways that underlie normal development and function in the genitourinary system.