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

22
Ela Hunt, MRC research fellow Department of Computing Science [email protected] SyntenyVista SyntenyVista BIOINFORMATICS BIOINFORMATICS RESEARCH CENTRE RESEARCH CENTRE

TAGS:

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

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

Ela Hunt, MRC research fellowDepartment of Computing Science

[email protected]

SyntenyVistaSyntenyVista

BIOINFORMATICSBIOINFORMATICSRESEARCH CENTRERESEARCH CENTRE

Page 2: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

SYNTENYSYNTENY

Chromosome

gene1

gene2

gene3

gene4

Page 3: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

Rat Chr. a

Mouse Chr. b

Human Chr. c

gene1 gene2

gene2

gene3

gene4

gene2

gene3

gene3

gene4gene4

CONSERVED SYNTENYCONSERVED SYNTENY

gene1

gene1

gene3

Page 4: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

Mouse Chromosome b

Human Chromosome c

gene2gene3

gene4

gene1

Hypertensionsusceptibility

Obesity

Obesity

Renal disease

QTL:area correlatedwith disease

Page 5: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

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

Page 6: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

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

Application areas:

QTLs synteny micro arrays proteomics patient datasequence datastructurespathways

COMBINING

Page 7: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.
Page 8: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.
Page 9: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

www.ensembl.org

Page 10: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

www.ensembl.org

Page 11: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

Horizontal representation, Apollo, label overlap problem

Page 12: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

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

Page 13: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

SYNTENYVISTA

barchartChromosome synopses

Page 14: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

SYNTENYVISTA

QTLs

Page 15: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

Cartoon scaling

Page 16: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

Physicalscale

Cartoonscale

Page 17: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

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

Page 18: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

VIEW

Page 19: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

SAVED DATA

Page 20: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

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

Page 21: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

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)

Page 22: Ela Hunt, MRC research fellow Department of Computing Science ela@dcs.gla.ac.uk SyntenyVista BIOINFORMATICS RESEARCH CENTRE.

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

Access via BRIDGES portal


MRC Stratified Medicine Initiative Open...MRC Stratified Medicine Initiative • Set up in 2010/11 and represented a new way of funding from the MRC • Builds on the MRC/ABPI Inflammation

MRC Stratified Medicine Initiative Open...MRC Stratified Medicine Initiative • Set up in 2010/11 and represented a new way of funding from the MRC • Builds on the MRC/ABPI Inflammation

MRC March Newsletter

MRC March Newsletter

MRC - curs 9

MRC - curs 9

MRC Engineering Handbook - SKF · 2020. 8. 20. · 4 MRC® history he historical perspectie of MRC MRC is the outgrowth of three of America’s oldest bearing companies—Standard

MRC Engineering Handbook - SKF · 2020. 8. 20. · 4 MRC® history he historical perspectie of MRC MRC is the outgrowth of three of America’s oldest bearing companies—Standard

MRC Funded Research Opportunities Harriet Warburton Programme Manager, Research Career Awards, MRC

MRC Funded Research Opportunities Harriet Warburton Programme Manager, Research Career Awards, MRC

MRC Network of Hubs for Trials Methodology …...MRC Network of Hubs for Trials Methodology Research Gordon Murray, University of Edinburgh Edinburgh Midlands MRC- MRC-CTUMRC MRC-CTSU

MRC Network of Hubs for Trials Methodology …...MRC Network of Hubs for Trials Methodology Research Gordon Murray, University of Edinburgh Edinburgh Midlands MRC- MRC-CTUMRC MRC-CTSU

Austel MRC 1

Austel MRC 1

Mrc happy 20th

Mrc happy 20th

MRC Working Papers

MRC Working Papers

Circuit Parallelism in Haskell - dcs.gla.ac.uk

Circuit Parallelism in Haskell - dcs.gla.ac.uk

MRC Location-Based Advertising Measurement Guidelines ...mediaratingcouncil.org/MRC Location-Based Advertising Measurement... · MRC Location-Based Advertising Measurement Guidelines

MRC Location-Based Advertising Measurement Guidelines ...mediaratingcouncil.org/MRC Location-Based Advertising Measurement... · MRC Location-Based Advertising Measurement Guidelines

MRC Corporate Office, Nigdi MRC LOGISTICS (I) PVT. LTD. PRESENTATION OF.

MRC Corporate Office, Nigdi MRC LOGISTICS (I) PVT. LTD. PRESENTATION OF.

What Is MRC? - The Arc of Massachusettsthearcofmass.org/wp-content/uploads/2015/06/A4-MRC.pdf · What is MRC? MRC is a state ... MRC tuition waiver for state college ... What can

What Is MRC? - The Arc of Massachusettsthearcofmass.org/wp-content/uploads/2015/06/A4-MRC.pdf · What is MRC? MRC is a state ... MRC tuition waiver for state college ... What can

MRC Annual Meeting December 12, 2012 Welcome MRC BOD election results Preliminary FY2013 budget PERC facility performance PERC partnership outlook MRC.

MRC Annual Meeting December 12, 2012 Welcome MRC BOD election results Preliminary FY2013 budget PERC facility performance PERC partnership outlook MRC.

AnglePose: Robust, Precise Capacitive Touch Tracking via ...ftp.dcs.glasgow.ac.uk/~rod/publications/RogWilSteMur11b.pdf · John Williamson jhw@dcs.gla.ac.uk Craig Stewart craig@dcs.gla.ac.uk

AnglePose: Robust, Precise Capacitive Touch Tracking via ...ftp.dcs.glasgow.ac.uk/~rod/publications/RogWilSteMur11b.pdf · John Williamson [email protected] Craig Stewart [email protected]

MRC September

MRC September

MRC Framework for Stratified Medicine - MRC

MRC Framework for Stratified Medicine - MRC

The Brain MRC

The Brain MRC

Comités familles mrc

Comités familles mrc

12.25) MRC Expenses Policy - UCL MRC Expenses Policy.pdf · 3.1.2 MRC Employees should submit their expenses via Employee Self Service on Oracle, using the “MRC iExpenses User ...

12.25) MRC Expenses Policy - UCL MRC Expenses Policy.pdf · 3.1.2 MRC Employees should submit their expenses via Employee Self Service on Oracle, using the “MRC iExpenses User ...