GUDMAP - For Bioinformaticians
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 cell types of particular interest are marked and can be genetically manipulated.
3) a public database that reports the annotated and collated data (determined by in situ hybridization, immuno-staining, microarrays)arising from the project as soon as it becomes available.
The primary entry point for bioinformaticians is the GUDMAP gene expression query page. From here the data can be browsed and there are links to parts of the site where data can be downloaded.
The most informative way of downloading microarray data is to go via Browse > Array > Series.
Step 1: Go to the GUDMAP gene expression page and click on Browse > Array > Series.
Step 2: This page lists the microarray series that are available. Click on the series name of interest. For example 'Gene expression in whole ovary at gd 11, 12, 14, 16, 18 and pnd2'.
Step 3: A full description of the series is given along with a list of the samples available. Click on the sample you wish to download. In this example GUDMAP:2217 (pnd 2 whole ovary).
Step 4: Download data from the individual sample page by clicking on the 'Supplemental Data Files' section. Files are available in .CEL, .CHP, .RPT and .TXT format.