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Atlas of Gene Human Gene Expression Proposal

Atlas of Gene Human Gene Expression Proposal. Alvis Brazma, Tom Freeman and Helen Parkinson. EBI Microarray Informatics Team. ArrayExpress public database, major international effort with core funding Data annotation, submission tools and analysis tools Genetic network research.

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Atlas of Gene Human Gene Expression Proposal

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  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

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