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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!


WAVe: An Integrated View for the Human Variome