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DESPRAD Project Mid-Term Review: Advancements in Genome Research and Analysis Tools

This mid-term review of the DESPRAD project highlights the key achievements and future directions of Europe's largest resource center for genome research, the RZPD. Established as a non-profit company in 2000, RZPD specializes in providing a diverse range of products and services, including clones, microarrays, and a public database for gene expression analysis. The review covers the development of various tools and methodologies, including the DESPRAD TranscriptProfiler and standard query interfaces, emphasizing user training, automated analysis pipelines, and ongoing collaborations.

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DESPRAD Project Mid-Term Review: Advancements in Genome Research and Analysis Tools

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Presentation Transcript

  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

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

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

  9. 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

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

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

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

  13. 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

  14. Thank you!

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