SyntenyVista

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SyntenyVista
Ela Hunt, MRC research fellow Department of
Computing Science ela_at_dcs.gla.ac.uk
BIOINFORMATICSRESEARCH CENTRE
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Chromosome
gene1
SYNTENY
gene2
gene3
gene4
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Rat Chr. a
Mouse Chr. b
Human Chr. c
gene2
gene1
gene1
gene3
gene3
gene2
gene2
gene1
gene3
gene3
gene4
gene4
gene4
CONSERVED SYNTENY
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Mouse Chromosome b
Human Chromosome c
QTL area correlated with disease
gene1
gene3
gene2
Obesity
gene4
Obesity
Hypertension susceptibility
Renal disease
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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

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Application areas

• Hypertension
• Schizophrenia
• Cancer
• Parasitology
• Plants
• etc

QTLs synteny micro arrays proteomics patient
data sequence data structures pathways
COMBINING
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www.ensembl.org
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www.ensembl.org
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Horizontal representation, Apollo, label overlap
problem
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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
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SYNTENYVISTA
Chromosome synopses
barchart
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SYNTENYVISTA
QTLs
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Cartoon scaling
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Physical scale
Cartoon scale
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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

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VIEW
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SAVED DATA
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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

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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)

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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