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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:
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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
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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