TEMBLOR mid-term review

1. TEMBLOR mid-term review Participation in DESPRAD project Bernd Drescher Robert Wagner

2. 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

3. Range of products & services Clones Clone related products/services Primary database

4. MicroArrays @ RZPD • Certified Affymetrix service provider • cDNA microarrays • OncoChip RZPD1 • ImmunoChip RZPD1.2 • Custom-made microarrays • DESPRAD

5. 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

6. Structure Primary db Geneexp MAGE-ML Affy Files MIAMExpress WWW Interface

9. Query Interface • Query for experiments by certain criteria (name, type, species, ...)

11. Query Interface • Query for experiments by certain criteria (name, type, species, ...) • Display of hybridizations, samples, arrays, reporters

17. 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

20. Current Content • 19 experiments, 103 hybridizations • 79 arrays of 42 array designs • 64 bio sources • 370 protocols • Sources: inhouse, collaborations

21. Implementation • Oracle • Tomcat • Java, Perl • Generated APIs from Oracle data dictionary • Object-relational mapping • Database interface • R, Bioconductor

22. Problems • Data aquisition • Data not MIAME compatible • Performance

23. 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

24. Thank you!