the gudmap database: an online resource for genitourinary research dr. simon harding
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The GUDMAP Database:
An Online Resource for Genitourinary Research
Dr. Simon Harding
Stem Cells & Bioinformatics
22nd September 2009
Overview
• GUDMAP: Introduction• The Data
• In Situ, Microarray and statistics• The Website
• Basic features – browsing and querying
• Additional tools – gene expression summaries, disease resource• Examples of Use
• Complex Boolean anatomy querykidney
Reproductive system
GUDMAP: Introduction
• GenitoUrinary Development Molecular Anatomy Project
• Goal: Provide the scientific research community with tools to facilitate research through a molecular atlas of gene expression in developing organs of mouse GU system
• Worldwide consortium based project• USA• Australia• UK – Edinburgh
• Funded by NIH, NIDDK
GUDMAP: Introduction
• Why GUDMAP?• Community resource to enhance existing research and stimulate
new research• High resolution molecular anatomy of the developing GU system
• Markers for anatomically defined cell types• Describe developmental processes that establish function domains• Understand genesis of organ anatomy at molecular/cellular level
• New level of understanding to benefits treatment of disorders and disease of GU system
• GUDMAP Edinburgh• Human Genetics Unit & University of Edinburgh• Curating data and making it accessible through a website• Raw data available to research community• Easy-to-use window onto this data – web-interface
GUDMAP: In Situ Data
• In situ data• In situ hydbridisation (section & wholemount)
• Immunohistochemistry (section)• In situ analysis of transgenic reporter screens (wholemount)
GUDMAP:11296GUDMAP:7156
GUDMAP: Microarray Data
• Microarray data• Array analysis of laser-captured components of developing GU
system - enrichment
• Array analysis of FACS-isolated cells from transgenic reporter mice - purification
GUDMAP: Statistics
ISH MA IHC TgGenes Entries Genes Entries Genes Entries Genes Entries
Metanephros2785 5449 - 129 7 9 1 6
Lower Urinary System
2689 4902 - 54 0 0 1 6
Early Reproductive System
227 253 - 11 0 0 0 0
Male Reproductive System
2364 2831 - 33 2 2 1 3
Female Reproductive System
2292 2741 - 15 1 1 1 3
Total2907 7728 - 259 9 12 1 6
GUDMAP: The Website
BROWSEMicroarrays, in situs,
by stage, genes
QUERYgene
anatomyfunction
boolean anatomyFOCUSFocus query to
distinct anatomical groups
Annotation in a GUDMAP entry Annotation Notes
High resolution ontology
Signal is strongest on the side of the vesicle furthest from the
ureteric tip
GUDMAP: Gene strip
• Summarising gene expression
Gene PageGene Page
Disease Associations
Disease Associations
In situ expression
entries
In situ expression
entries
In situ image matrix
In situ image matrix
Microarray expressionMicroarray expression
GUDMAP: Linking to disease
• Why?• Link between gene expression, GU development and GU disease• 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.
• Help to better understand aetiology of disease.• Some diseases occur as a consequence of events taking place
during development, e.g. incorrect formation of structures.
• Disease Resource• Associations between genes and OMIM disease• Associations between genes and mammalian
renal/urinary/reproductive phenotypes (MGI)• Disease-gene associations are searchable with results presented in a
simple table.
GUDMAP: Linking to disease
OMIM: Online Mendelian Inheritance in Man (www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM)NCBI: National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/)MGI: Mouse Genome Informatics (www.informatics.jax.org)
• What genes specifically mark the structure I am interested in examining?
• Ureteric Tip
• Looking for gene expressed in ureteric tip but not in surrounding structures
• Strategy - use Boolean Anatomy Query
GUDMAP: Example
• Boolean Query syntax – to build complex query
• Save larger queries to a file or in collections
Query for ureteric tip at TS23 (E15.5)
GENE: nd{in cap mesenchyme TS23..TS23} AND | nd{in early tubule TS23..TS23} AND | nd{in late tubule TS23..TS23} AND | nd{in renal vasculature TS23..TS23} AND | nd{in ureter TS23..TS23} AND | p{in ureteric tip TS23..TS23} AND | nd{in ureteric trunk TS23..TS23} AND | nd{in renal interstitium group TS23..TS23}
What genes specifically mark the structure I am interested in examining?
University of Edinburgh & MRC Human Genetics Unit
GUDMAP Editorial OfficeDuncan DavidsonJamie DaviesJane ArmstrongJane BrennanSue Lloyd-MacGilpChris Armit
GUDMAP Database Development TeamDerek HoughtonMehran SharghiXingjun PiYing ChengKoosum Roochun
Harvard UniversityAndy McMahon et al University of QueenslandMelissa Little et alPeter Koopman et alSean Grimmond et al
Cincinnati Children's Hospital Medical CenterBruce Aronow et al Steve Potter et alJim Lessard et al Columbia UniversityCathy Mendelsohn et al
Vanderbilt UniversityMichelle Southard-Smith et al
Research Triangle, NCKevin Gaido et al
Acknowledgements
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