Ela Hunt, MRC research fellowDepartment of Computing Science
SyntenyVistaSyntenyVista
BIOINFORMATICSBIOINFORMATICSRESEARCH CENTRERESEARCH CENTRE
Rat Chr. a
Mouse Chr. b
Human Chr. c
gene1 gene2
gene2
gene3
gene4
gene2
gene3
gene3
gene4gene4
CONSERVED SYNTENYCONSERVED SYNTENY
gene1
gene1
gene3
Mouse Chromosome b
Human Chromosome c
gene2gene3
gene4
gene1
Hypertensionsusceptibility
Obesity
Obesity
Renal disease
QTL:area correlatedwith disease
Research paradigm in hypertension
• QTLs are being studied in three species (human, mouse, rat)
• A syntenic area containing QTLs for blood pressure in more than one species may harbour novel hypertension genes
• Micro array experiments and proteomics will lead to the identification of a candidate gene
• Verification: the faulty gene can be repaired using transgenic technology
• Drugs can be developed to repair the faulty pathway which leads to hypertension
• Hypertension• Schizophrenia• Cancer• Parasitology• Plants• etc
Application areas:
QTLs synteny micro arrays proteomics patient datasequence datastructurespathways
COMBINING
Synteny Representation - visualization issues
• Vertical or horizontal
• Showing relationships
• Use of colour
• Size of objects, labelling
• Searching and viewing data (zooming, inversion, selection, filtering)
E. Hunt, N. Hanlon, D. Leader, H. Bryce and A. F. Dominiczak, The Visual Language of Synteny, OMICS - A Journal of Integrative Biology, 2004, 8(4),to appear
Recent additions
• Saving of all data in view to a spreadsheet or web page including all references
• Query for gene names and QTL names
• Centering of display on a selected gene and its syntenic area
Ongoing work
• Preparation of a public release
• Publishing the information on how to connect to data sources other than Ensembl (configuration options in XML)
• Adding the display of micro array positions and results
• Interaction with proteomics, metabolomics and pathways datasets
Future work
• Combing visualisation with our data integration work (XTECT project, XML-based data integration)
• Database support for sequence searching, and display of results in SyntenyVista (database research – stringology)
• Usability study and improvements (human-computer interaction studies)
Funding
Medical Research Council
Wellcome Trust
British Heart Foundation
Engineering and Physical
Sciences Research Council
National e-Science Centre
REFERENCESE. Hunt and N. Hanlon, SyntenyVista, 2004, Proceedings of NordiCHI 04, ACM, 455-456E. Hunt, N. Hanlon, D. Leader, H. Bryce and A. F. Dominiczak, The Visual Language of Synteny, OMICS - A Journal of Integrative Biology, 2004, 8(4), to appear
http://www.dcs.gla.ac.uk/~ela/Synteny
Asia JakubowskaNeil HanlonWillem LigtenbergDavid LeaderHunter Bryce Anna DominiczakMagnus FerrierRichard Sinnott
CONTRIBUTORS
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