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SyntenyVista Ela Hunt, MRC research fellow Department of Computing Science [email protected] BIOINFORMATICS RESEARCH CENTRE Chromosome gene1 SYNTENY gene2 gene3 gene4 Rat Chr. a gene1 gene2 Mouse Chr. b gene2 Human Chr. c gene1 gene3 gene2 gene1 gene3 gene3 gene4 gene4 gene4 CONSERVED SYNTENY Mouse Chromosome b Human Chromosome c QTL: area correlated with disease gene1 gene3 gene2 Obesity Obesity Hypertension susceptibility gene4 Renal 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 Application areas: • • • • • • Hypertension Schizophrenia Cancer Parasitology Plants etc COMBINING QTLs synteny micro arrays proteomics patient data sequence data structures pathways www.ensembl.org www.ensembl.org Horizontal representation, Apollo, label overlap problem 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 SYNTENYVISTA Chromosome synopses barchart SYNTENYVISTA QTLs Cartoon scaling Physical scale Cartoon scale 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 VIEW SAVED DATA 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, XMLbased data integration) • Database support for sequence searching, and display of results in SyntenyVista (database research – stringology) • Usability study and improvements (humancomputer interaction studies) Funding Medical Research Council Wellcome Trust British Heart Foundation Engineering and Physical Sciences Research Council National e-Science Centre CONTRIBUTORS Asia Jakubowska Neil Hanlon Willem Ligtenberg David Leader Hunter Bryce Anna Dominiczak Magnus Ferrier Richard Sinnott REFERENCES E. Hunt and N. Hanlon, SyntenyVista, 2004, Proceedings of NordiCHI 04, ACM, 455-456 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 Access via BRIDGES portal http://www.dcs.gla.ac.uk/~ela/Synteny