AN INTEGRATED VIEW FOR THE HUMAN VARIOME
PEDRO LOPES pedrolopes@ua.pt 14.ยบ 14ยบ SPGH - Coimbra, Portugal November 18th, 2010
PREVIOUSLY... ‣ GENOTYPE TO PHENOTYPE • Understanding changes in our genetic sequence
‣ GENETIC VARIATION SOFTWARE • Genome Wide Association Studies, GWAS ‣ Huge databases, huge statistics
‣ Causes
• Locus-specific Databases, LSDBs
‣ Consequences
‣ Publish genomic variation datasets
‣ GEN2PHEN • Unify human and model organism genetic variation databases • Link biomedical knowledge
http://bioinformatics.ua.pt/
WHAT IS WAVe?
http://bioinformatics.ua.pt/
WEB ANALYSIS OF THE VARIOME ‣ INTEGRATE • Integrate genomic variation datasets from multiple distributed and heterogeneous sources
‣ ENRICH • Enrich available data with connections to miscellaneous (yet relevant) resources • Display original applications/content to maintain authorship and ownership
‣ INNOVATE • Use “card” metaphor to provide a holistic view over human variome research
‣ ADD VALUE • Extract and combine true added value from LSDBs • One step forward for personalized medicine research
http://bioinformatics.ua.pt/
HIGHLIGHT | RESOURCES ‣ LSDB
‣ PHARMACOGENOMICS
• LOVD + MUTbase + UMD + misc legacy
‣ LOCUS
• PharmGKB
‣ GENOME
• GeneCards + GeneNames + Entrez
• MapViewer + Ensembl
‣ PUBLICATION
‣ PATHWAY
‣ DISEASE
‣ PROTEIN
~ 1350 Genes, 1550 LSDBs, 80k Variants, 100k Links ! • QuExT • KEGG + Reactome • OMIM
• UniProt + PDB + Expasy + InterPro
‣ GENE ONTOLOGY • AmiGO
http://bioinformatics.ua.pt/
HIGHLIGHT | FEATURES ‣ GENE SEARCH
‣ API
• Direct access to genes
• RSSaccess to data
‣ Auto-suggest engine
• Genes ‣ Access navigation tree data
• Curated genes
‣ Google Chrome Extension
‣ GENE ANALYSIS WORKSPACE
• Variants ‣ Only platform that publishes variants from multiple sources
• Navigation tree ‣ Holistic perspective on all data • “Live view” mode ‣ Shows original applications/content
http://bioinformatics.ua.pt/
DEMO
http://bioinformatics.ua.pt/
YOUR FEEDBACK IS HIGHLY APPRECIATED! QUESTIONS? THANK YOU!