GUDMAP - For Clinicians
Given the importance of the genitourinary system for human health and reproduction, the need for a systematic molecular and cellular description of its developmental program is clearly a high priority. In late 2004, the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) and the National Institute of Child Health and Human Development (NICHD) established an International Consortium of research groups charged with the task of producing a high quality molecular anatomy of the developing mammalian urogenital tract. The information obtained through this initiative is anticipated to enable the highest level of basic and clinical research grounded on a 21st century view of the developing anatomy.
There are three components to GUDMAP, all intended to provide resources that support research on the kidney and urogenital tract.
1) a description of genitourinary development that includes a tutorial, an ontology of anatomical parts and the molecular hallmarks of those structures.
2) novel mouse strains in which tissues of particular interest are marked and can be genetically manipulated.
3) a public database that reports the gene expression data arising from the project as soon as it becomes available (determined by in situ hybridization, immuno-staining, microarrays.)
From a clinical researcher’s perspective, the primary entry point is a table of genes associated with diseases of the urogenital system.
Features
- Diseases
- A simple table provides associations between genes and diseases of the urogenital system.
- From here, users can move directly to data describing the anatomical expression of each gene. Click on the icon to the right to go to the disease pages.
- Links to external data resources are provided in the table.
- Database of Gene Expression
- This can be accessed via the menu bar item at the top of the page or via the database icon to the right.
- Users can search the raw gene expression data.
- Molecular Anatomy
- A refined view of anatomy based on gene expression patterns.
- This will advance the understaning of the developmental genetic basis of genitourinary disease and the relationship between anatomy and function
Examples - 1. Finding GUDMAP expression data relating to a disease/gene of interest
1. GUDMAP Disease Page
The primary entry point is a table of genes associated with diseases of the urogenital system. e.g. Pax2 (Renal-Coloboma Syndrome)
From here navigate to gene expression data by clicking the gene name.
There are also links to external data and references such as OMIM, MGI and PubMed.
2. GUDMAP Gene Pages
Information about Pax2 with details of the expression data in the database. Click the GUDMAP ID link for details of that entry.
3. GUDMAP Gene Expression Data Page
Shows in-situ hydridisation data stored within GUDMAP for Pax2
Examples - 2. Batch query to get gene expression patterns
Batch query
The batch function of the GUDMAP gene expression query can be used to obtain gene expression data for a set of genes.
Select Query > Gene > click Options
An example use would be to upload a set of genes from a specific chromosomal location linked to a disease of interest. All expression data/patterns in the GUDMAP database for the genes in the uploaded set will be returned. This information can be used to select candidate genes for further investigation.
