Data Integration & Data Mining Tool

Donald DunbarBHF CoRE Bioinformatics Team

Edinburgh Bioinformatics MeetingApril 2013

BHF CoRE Bioinformatics

Data Integration and our Data Mining Tool

Our strategy is to help biologists make the most of their ‘-omics’ data

We analyse array and sequence data using current methods

Biologists mine their results in a custom built, secure web based platform

We help integrate other relevant data from biologist’s lab and the literature

Data Mining Tool

• Wish list– Web accessible– Secure– Complex queries across datasets– Technology agnostic– Query cross species– Annotation, statistics and graphs– Links to external databases– Include downstream tools

Data Mining Tool

• Login via EASE or htaccess (+ vpn)• Built in PHP with mySQL back end• Generic database structure for statistics

– counts, intensity, fold change, p-value• Separate annotation tables• Includes experiment details and QC info• Query builder type interface• Output as tables with links• Gene set enrichment, heat-map and literature

Data Integration

• Across technologies– array, sequencing– gene expression, methylation, proteomics, genetics

• Across species– Human, mouse, rat, fly, fish

• At the gene level– Probe level for within array– Entrez gene within species– orthologous groups across species

Development• New platform: Drupal

– Some nice features– New look and feel

• Web services– interactions, diseases, TF binding sites, miRNA…

• More use of literature data– Top 10 co-cited on gene detail page– Better visualisation– Better text mining

• Correlation data (expression profiles)– searchable with other stats

• Cross experiment gene sets

Thanks• Jon Manning• John Mullins• Our collaborators• British Heart Foundation

qmri.bioinf@ed.ac.uk | www.bioinf.mvm.ed.ac.uk

“Providing bioinformatics services to biology teamsthroughout the research process”