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

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Presentation transcript:

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

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 Affy Files Primary db MIAMExpress MAGE-ML Geneexp WWW Interface

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!