Transcript Making sense of Sequences: Comparative Genomics and the New GIS

Xin-Yi Chua
Peter Ansell,
Chris Bowles,
Lawrence Buckingham,
James M. Hogan,
Scott Mann,
Paul Roe,
Jiro Sumitomo,
Jan M. Weinert
www.mquter.qut.edu.au/bio
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Overview
 Another Genomic Revolution
 Bio 2.0: Navigate and Share the graph
 Bringing ‘GIS’ to Comparative Genomics
 Future Directions
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Another Genomic Revolution
 An explosion in genomic data
 The rise of population genomics & proteomics
 Alignment does not scale to the new BioScience
 Comparative genomics
 Gene regulation
 Protein characterisation
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Searching for similar genes
Results “Hits”
3e-56
Reference gene
BLAST
5e-56
9e -45
…
9.9
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Example ClustalW alignment
mammalian sulfatases: first 110 residues of the catalytic domain
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Bio2.0: Navigate & Share the Graph
 We allow scientists to visualise the graph
 Make the topology fit the question
 Visualisation is navigation
 Let the graph answer the question
 Refine and test hypotheses
 And then make the answer available
 Peer communities & link-based publication
 Sharing the vision…
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Bringing ‘GIS’ to Comparative Genomics
 The new ‘GIS’ – Genomic Information System
 All about distances and what works for the user
 Linking to data sources via Bio2RDF
 Combining a collection of data sources together
 Exploiting tags and ontologies
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SilverMap Model
Tags
Bio2RDF
Bio2RDF
TRN
SilverMap
Blast
component
BlastDB
Protein-protein
interactions
User defined
distance measures
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Demo
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Future directions
 Future applications
 Support user defined distances
 Transcriptional Regulatory Network analyses
 Protein-Protein interactions
 Bringing our tools to the community
 Making SilverMap the lingua franca of genomic publication
 The lab wiki and public web site
 Integration, tagging and sharing of views
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Acknowledgements
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