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GUDMAP - For Biologists

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).

The primary entry point for developmental biologists is the GUDMAP gene expression database page. From here the user can query, browse and download the data held in the database.

Features

  • Database of Gene Expression
    • access the database via the menu bar item at the top of the page or click on the image below
    • query the database :
      • for specific genes and perform batch queries
      • by anatomy - an interactive anatomy tree allowing users to search gene expression in anatomical components and to perform boolean anatomy search.
      • by gene function.
      • by disease - a searchable database of gene-disease associations and gene-phenotype associations.
    • browse database to show gene expression data by :
      • Theiler stage (TS) - view ISH and microarray entries
      • gene - search an alphabetical list of all genes in GUDMAP database
      • searches can be restricted to particular organs/systems of interest using the focus options
    • All microarray data is accessed by clicking Browse > Array > Series (red boxes)
    • All ISH data is accessed by clicking Browse > In Situ > RNA and Protein (red boxes)

GUDMAP gene expression query page
  • Molecular Anatomy
    • Access the organ summaries via the gene expression section of the menu bar at the top of the page.
    • A refined view of anatomy based on gene expression patterns.
    • Helps to understand the developmental genetic basis of genitourinary disease and the relationship between anatomy and function
 
  • Mouse Strains
    • We are genetically marking or labelling the different types of cells in the mouse GU tract through knocking fluorescent protein markers and/or the Cre recombinase, or epitope tags, into genes that are specifically expressed in those cell types. For details got to the Zhang group page.
    • An up-to-date list of genes being targeted can be found on the mouse strains page.
 

Examples