TEMBLOR mid-term review Participation in DESPRAD project Bernd Drescher Robert Wagner
TEMBLOR mid-term review
Participation in DESPRAD project
Bernd DrescherRobert Wagner
History
• 1995: Central infrastructure unit of the German Human Genome Project (@ MPI MG & DKFZ)
• 7/2000: Non-profit company: „RZPD Deutsches Ressourcenzentrum für Genomforschung GmbH“
• Today: Europe's largest resource center for genome research
Clones
Clone related products/services
Primary database
Range of products & services
MicroArrays @ RZPD
• Certified Affymetrix service provider• cDNA microarrays
– OncoChip RZPD1– ImmunoChip RZPD1.2– Custom-made microarrays
• DESPRAD
TranscriptProfiler
• Public database and analysis tool for gene expression data
• Based on MAGE-OM• Standard query and analysis (web-)
interface• Available as of 11/2003
Structure
AffyFiles
Primary db
MIAMExpress
MAGE-ML Geneexp
WWWInterface
Query Interface
• Query for experiments by certain criteria (name, type, species, ...)
Query Interface
• Query for experiments by certain criteria (name, type, species, ...)
• Display of hybridizations, samples, arrays, reporters
Query Interface
• Query for experiments by certain criteria (name, type, species, ...)
• Display of hybridizations, samples, arrays, reporters
• Simple statistic analysis– Distribution– Normalized ratios– T-test
Current Content
• 19 experiments, 103 hybridizations• 79 arrays of 42 array designs• 64 bio sources• 370 protocols• Sources: inhouse, collaborations
Implementation
• Oracle• Tomcat• Java, Perl
– Generated APIs from Oracle data dictionary•Object-relational mapping•Database interface
• R, Bioconductor
Problems
• Data aquisition• Data not MIAME compatible• Performance
Next Steps
• Automated analysis pipeline• Further cooperations with new partners• User training• Integration into RZPD system (clone
ordering)• Use functional annotations for analysis• Combine text mining with analysis
Thank you!