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The GUDMAP Database: An Online Resource for the Genitourinary Research Community Chris Armit

The GUDMAP Database: An Online Resource for the Genitourinary Research Community Chris Armit Deputy Senior Editor, GUDMAP University of Edinburgh. GUDMAP Genitourinary Development Molecular Anatomy Project. International consortium UK USA Australia

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The GUDMAP Database: An Online Resource for the Genitourinary Research Community Chris Armit

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  1. The GUDMAP Database: An Online Resource for the Genitourinary Research Community Chris Armit Deputy Senior Editor, GUDMAP University of Edinburgh

  2. GUDMAP Genitourinary Development Molecular Anatomy Project • International consortium • UK • USA • Australia • Provide scientific community with gene expression data and tools to facilitate research • Key Components • Maps of gene expression within the developing genitourinary system of the mouse • High resolution molecular anatomy highlighting the development of the GU system • Funded by NIH, NIDDK

  3. GUDMAP Gene Expression Database • Why GUDMAP? • Generate a resource for the community to enhance existing research and stimulate new research • New level of understanding benefits treatment of disorders and disease of GU system • Why GUDMAP Database? • Prompt assemblage and release of information through a web database • Raw data is made available to the research community • Easy-to-use window onto this data

  4. GUDMAP Gene Expression Database • In situ data • In situ hybridisation (section & wholemount) • In situ analysis of transgenic reporter knock-ins (wholemount) • Immunohistochemistry (section) GUDMAP:7156 GUDMAP:11296

  5. GUDMAP Gene Expression Database • Microarray data • Array analysis of laser-captured components of developing GU system • Array analysis of FACS-isolated cells (transgenic reporter mice)

  6. GUDMAP Gene Expression Database • What has GUDMAP accomplished?

  7. GUDMAP Gene Expression Database • What has GUDMAP accomplished? • Statistics

  8. GUDMAP Gene Expression Database • What has GUDMAP accomplished? • Statistics

  9. GUDMAP Gene Expression Database • Using the Database • Browse • Query - standard and advanced Boolean Query • Download • Data Integration • Gene Strip • Disease Resource • Associations between genes and OMIM diseases • Associations between genes and mammalian renal/urinary/reproductive phenotypes (MGI) • Tools • Online Annotation Tool • Collections

  10. GUDMAP Gene Expression Database • Using the Database • Browse • Query - standard and advanced Boolean Query • Download • Data Integration • Gene Strip • Disease Resource • Associations between genes and OMIM diseases • Associations between genes and mammalian renal/urinary/reproductive phenotypes (MGI) • Tools • Online Annotation Tool • Collections

  11. GUDMAP Using the Database • Query/Browse • Live Demo

  12. GUDMAP Gene Expression Database • Using the Database • Browse • Query - standard and advanced Boolean Query • Download • Data Integration • Gene Strip • Disease Resource • Associations between genes and OMIM diseases • Associations between genes and mammalian renal/urinary/reproductive phenotypes (MGI) • Tools • Online Annotation Tool • Collections

  13. GUDMAP Data Integration • Gene Strip • Integration of in situ data, microarray expression profiles, and disease associations

  14. GUDMAP Gene Expression Database • Using the Database • Browse • Query - standard and advanced Boolean Query • Download • Data Integration • Gene Strip • Disease Resource • Associations between genes and OMIM diseases • Associations between genes and mammalian renal/urinary/reproductive phenotypes (MGI) • Tools • Online Annotation Tool • Collections

  15. GUDMAP Disease Resource • Why?

  16. GUDMAP Disease Resource • Why? • Studying gene expression in the genitourinary (GU) system is useful to understand GU disease. • If we know that a particular disease affects the GU system we can look at which genes are expressed (or not expressed) in the affected GU tissues and structures. • This helps us to better understand the aetiology of the disease.

  17. GUDMAP Disease Resource • Why? • Studying gene expression in the genitourinary (GU) system is useful to understand GU disease. • If we know that a particular disease affects the GU system we can look at which genes are expressed (or not expressed) in the affected GU tissues and structures. • This helps us to better understand the aetiology of the disease. • Disease-gene associations are searchable with results presented in a simple table.

  18. GUDMAP Gene Expression Database • Using the Database • Browse • Query - standard and advanced Boolean Query • Download • Data Integration • Gene Strip • Disease Resource • Associations between genes and OMIM diseases • Associations between genes and mammalian renal/urinary/reproductive phenotypes (MGI) • Tools • Online Annotation Tool • Collections

  19. GUDMAP Online Annotation Tool • Simple method of annotating in situ data • Ontology-based graphical user interface

  20. GUDMAP Online Annotation Tool • High Resolution Ontology • Developed by GUDMAP consortium • Describes sub-compartments of developing murine GU tract • Used to describe gene expression patterns

  21. GUDMAP Collections • Genes, Entries and Images • Collections allow the user to: • Build, edit and view collections. • Collections can be viewed on a clipboard. • Advanced functions are available.

  22. GUDMAP Tools • Login • Save personal collections of genes, images and database entries • Submit new gene expression annotations using the online annotation tool

  23. Harvard University Andy McMahon et al Cincinnati Children's Hospital Medical Center Bruce Aronow et al Steve Potter et al Jim Lessard et al University of Queensland Melissa Little et al Peter Koopman et al Sean Grimmond et al Kylie Georgas (illustrations) Columbia University Cathy Mendelsohn et al Vanderbilt University Michelle Southard-Smith et al Research Triangle, NC Kevin Gaido et al Acknowledgements University of Edinburgh & MRC Human Genetics Unit GUDMAP Editorial Office Duncan Davidson Jamie Davies Jane Armstrong Jane Brennan Sue Lloyd-MacGilp Simon Harding Chris Armit GUDMAP Database Development Team Derek Houghton Mehran Sharghi Xingjun Pi Ying Cheng Koosum Roochun

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