1. Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE

2. SYNTENY Chromosome gene1 gene2 gene3 gene4

3. Rat Chr. a Mouse Chr. b Human Chr. c gene1 gene2 gene3 gene4 gene2 gene3 gene4 CONSERVED SYNTENY gene1 gene3

4. Mouse Chromosome b Human Chromosome c gene2 gene3 gene4 gene1 Hypertension susceptibility Obesity Renal disease QTL: area correlated with disease

5. 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

6. Hypertension Schizophrenia Cancer Parasitology Plants etc Application areas: QTLs synteny micro arrays proteomics patient data sequence data structures pathways COMBINING

9. www.ensembl.org

11. Horizontal representation, Apollo, label overlap problem

12. 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

13. SYNTENYVISTA barchart Chromosome synopses

14. SYNTENYVISTA QTLs

15. Cartoon scaling

16. Physical scale Cartoon scale

17. 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

18. VIEW

19. SAVED DATA

20. 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

21. 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)

22. Funding Medical Research Council Wellcome Trust British Heart Foundation Engineering and Physical Sciences Research Council National e-Science Centre 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 http://www.dcs.gla.ac.uk/~ela/Synteny Asia Jakubowska Neil Hanlon Willem Ligtenberg David Leader Hunter Bryce Anna Dominiczak Magnus Ferrier Richard Sinnott CONTRIBUTORS Access via BRIDGES portal