Download Powerpoint of Chris Armit`s Talk

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
•
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
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
GUDMAP
Gene Expression Database
•
In situ data
• In situ hybridisation (section & wholemount)
GUDMAP:7156
GUDMAP:11296
• In situ analysis of transgenic reporter knock-ins (wholemount)
• Immunohistochemistry (section)
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)
GUDMAP
Gene Expression Database
• What has GUDMAP accomplished?
GUDMAP
Gene Expression Database
• What has GUDMAP accomplished?
• Statistics
GUDMAP
Gene Expression Database
• What has GUDMAP accomplished?
• Statistics
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
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
GUDMAP
Using the Database
• Query/Browse
• Live Demo
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
GUDMAP
Data Integration
• Gene Strip
• Integration of in situ data, microarray expression profiles, and disease
associations
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
GUDMAP
Disease Resource
• Why?
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.
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.
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
GUDMAP
Online Annotation Tool
• Simple method of annotating in situ data
• Ontology-based graphical user interface
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
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.
GUDMAP
Tools
• Login
• Save personal collections of genes, images and database entries
• Submit new gene expression annotations using the online annotation
tool
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
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