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SyntenyVista

SyntenyVista. Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk. BIOINFORMATICS RESEARCH CENTRE. Chromosome. gene1. SYNTENY. gene2. gene3. gene4. Rat Chr. a. Mouse Chr. b. Human Chr. c. gene2. gene1. gene1. gene3. gene3. gene2. gene2. gene1.

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SyntenyVista

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

  2. Chromosome gene1 SYNTENY gene2 gene3 gene4

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

  4. Mouse Chromosome b Human Chromosome c QTL: area correlated with disease gene1 gene3 gene2 Obesity gene4 Obesity Hypertension susceptibility Renal 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. Application areas: • Hypertension • Schizophrenia • Cancer • Parasitology • Plants • etc QTLs synteny micro arrays proteomics patient data sequence data structures pathways COMBINING

  7. www.ensembl.org

  8. www.ensembl.org

  9. Horizontal representation, Apollo, label overlap problem

  10. 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

  11. SYNTENYVISTA Chromosome synopses barchart

  12. SYNTENYVISTA QTLs

  13. Cartoon scaling

  14. Physical scale Cartoon scale

  15. 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

  16. VIEW

  17. SAVED DATA

  18. 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

  19. 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)

  20. Funding CONTRIBUTORS Asia Jakubowska Neil Hanlon Willem Ligtenberg David Leader Hunter Bryce Anna Dominiczak Magnus Ferrier Richard Sinnott 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 Access via BRIDGES portal http://www.dcs.gla.ac.uk/~ela/Synteny

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