Ela Hunt, MRC research fellow Department of Computing Science [email protected] SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

Ela Hunt, MRC research fellowDepartment of Computing Science

[email protected]

SyntenyVistaSyntenyVista

BIOINFORMATICSBIOINFORMATICSRESEARCH CENTRERESEARCH CENTRE

SYNTENYSYNTENY

Chromosome

gene1

gene2

gene3

gene4

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

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

barchartChromosome synopses

SYNTENYVISTA

QTLs

Cartoon scaling

Physicalscale

Cartoonscale

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, 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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