Atlas of Gene Human Gene Expression Proposal

1. Atlas of Gene Human Gene Expression Proposal Alvis Brazma, Tom Freeman and Helen Parkinson

2. EBI Microarray Informatics Team • ArrayExpress public database, major international effort with core funding • Data annotation, submission tools and analysis tools • Genetic network research

3. Existing EBI Resources for this project • Co-developers of MIAME annotation standard • ArrayExpress Database • MIAMExpress data submission tool • Data analysis tools, Expression Profiler • Interoperability within EBI databases • Expertise in data mining

4. Overview of the database ArrayExpress MAGE-ML MAGE-ML MIAMExpress Expression Profiler Internet www

5. Lack of reference data • We have started to solve the problem of data availability • Now there is a problem of quality data • Most researchers are tied to a particular project, these typically focus on disease • Human data is being generated, but we have no common reference set

6. Existing reference data • Lacking input in experimental design • Poorly annotated, lack of provenance on samples • Data not fully available, e.g. cel file for Affy data, image data not available Novartis data • Experiments done without input of bioinformaticians until after completion

7. Advantages of joint project • Influence on experimental design, replicate numbers, data file availability • Data analysis while project is in progress • Structured data annotation during expt • Control and access of sample annotation • Pilot project can be extended and recombined with other data if we do this systematically

8. History of the collaboration • MIAME compliant mouse tissue profiling pilot project in progress with HGMP • Limited by funding – chips and facility capacity, staff etc.

9. Data Display possibilities