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!