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The GUDMAP database--an online resource for genitourinary research.

The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is an international consortium working to generate gene expression data and transgenic mice. GUDMAP includes data from large-scale in situ hybridisation screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of the developing mouse genitourinary (GU) system. These expression data are annotated using a high-resolution anatomy ontology specific to the developing murine GU system. GUDMAP data are freely accessible at www.gudmap.org via easy-to-use interfaces. This curated, high-resolution dataset serves as a powerful resource for biologists, clinicians and bioinformaticians interested in the developing urogenital system. This paper gives examples of how the data have been used to address problems in developmental biology and provides a primer for those wishing to use the database in their own research.

Pubmed ID: 21652655 RIS Download

Mesh terms: Animals | Databases, Genetic | Humans | Internet | Mice | Software | Urogenital System

Research resources used in this publication

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Data used in this publication

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Associated grants

  • Agency: NIDDK NIH HHS, Id: R01 DK061459-02
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-04
  • Agency: NIDDK NIH HHS, Id: DK070136
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-08
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-05
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-07S1
  • Agency: NIDDK NIH HHS, Id: U01 DK070200
  • Agency: NIDDK NIH HHS, Id: DK070200
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-09
  • Agency: NIDDK NIH HHS, Id: R01 DK061459
  • Agency: NIDDK NIH HHS, Id: R56 DK082963-01
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-06
  • Agency: NIDDK NIH HHS, Id: DK070181
  • Agency: NIDDK NIH HHS, Id: R56 DK082963
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-03
  • Agency: Medical Research Council, Id: MC_U127527203
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-07
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-01A1S1
  • Agency: NIDDK NIH HHS, Id: U01 DK070136
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-01A1
  • Agency: NIDDK NIH HHS, Id: U01 DK070181

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This is a list of tools and resources that we have found mentioned in this publication.


GenitoUrinary Development Molecular Anatomy Project

International consortium providing a molecular atlas of gene expression for the developing organs of the GenitoUrinary (GU) tract; a high resolution molecular anatomy highlighting development of the GU system; mouse strains to facilitate developmental and functional studies within the GU system; experimental protocols and standard specifications; tutorials describing GU organogenesis and primary data via the database. The data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of the developing mouse genitourinary (GU) system. These expression data are annotated using a high-resolution anatomy ontology specific to the developing murine GU system.

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GUDMAP Ontology

A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system.

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Edinburgh Mouse Atlas Project

A digital atlas of mouse development and database for spatially mapped data such as in situ gene expression and cell lineage. Resources provided by EMAP are the EMA Anatomy Atlas of Mouse Development and the EMAGE Gene Expression Database. EMA, the e-Mouse Atlas is a 3-D anatomical atlas of mouse embryo development including detailed histology. EMA includes the EMAP ontology of anatomical structure. EMAGE, the e-Mouse Atlas of Gene Expression, is a database of mouse gene expression where, uniquely, the gene expression is mapped into the EMA 3-D space and can be queried spatially. The e-Mouse Atlas (EMA) is a detailed model of the developing mouse. Its purpose is not only to provide information about the shape, gross anatomy and detailed histological structure of the mouse, but also to provide a framework into which information about gene function can be mapped. The spatial, temporal and anatomical integration achieved by mapping diverse data to the organism itself rather than simply to database tables, allows powerful computational analyses. An example of data mapped to the atlas is EMAGE where gene expression patterns can be queried and analyzed on a spatial basis. The website presents 3D volumetric models of the embryo linked, in most cases, to comprehensive and detailed images of histological structure. It also contains a detailed anatomy ontology that gives the names and structural relationships between the parts, the "EMAP anatomy ontology". The embryo models and anatomy in EMA are organized by standard developmental stage (TS. after Theiler, 1989) and age of the embryo in days post coitum (dpc.). EMAGE is a database of in situ gene expression data in the mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. These are sourced from the community and our curators take this data and describe it in a standardized way that allows data query and exchange. The description includes a text-based component but the unique aspect of EMAGE is its spatial annotation focus.

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Jackson Laboratory

An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels.

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PubChem Substance

As one of three primary databases of PubChem (Pcsubstance, Pccompound, and PCBioAssay), PubChem Substance Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound. A PubChem FTP is available and new data is accepted into the repository. Pcsubstance contains more than 81 million records (2011).

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Kidney Development Database

The Kidney Development Database was created to collect in one place the data from a large number of developmental studies that have a bearing on the study of kidney development. With its oldest parts dating back to 1993/4, it is, as far as we know, the earliest computer database in the field of vertebrate organogenesis. Data are displayed in tables, arranged according to a standard scheme of kidney development explained in the key. Many of the entries are derived from low-power in situs or published text-only descriptions, and should therefore be interpreted with mild caution.

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