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ChipDB: An interactive database system for high-throughput expression analysis

ChipDB: An interactive database system for high-throughput expression analysis. Peter Young, John Barnett, Bing Ren, Ezra Jennings and Richard Young Whitehead Institute for Biomedical Research. Expression analysis. motivation objectives analysis architecture data mining platform

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ChipDB: An interactive database system for high-throughput expression analysis

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  1. ChipDB: An interactive database system for high-throughput expression analysis Peter Young, John Barnett, Bing Ren, Ezra Jennings and Richard Young Whitehead Institute for Biomedical Research

  2. Expression analysis • motivation • objectives • analysis architecture • data mining • platform • future enhancements http://web.wi.mit.edu/young/chipdb http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  3. Motivation 1) Analyze individual experiments 2) Integrate results across experiments 3) Compare results to external data sources 4) Allow outside users to analyze data 5) Publish findings http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  4. LIMS Public Repositories LIMS Public Repositories chipDB External Analyses chipDB Publication/Web Publication/Web Motivation http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  5. Objectives LIMS Public Repositories • Accessible: • web-based interface • Interactive: • iterative analysis process • Extensible: • “pluggable” tools • Integrated: • links to external data • Queryable: • search across datasets chipDB Publication/Web http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  6. Analysis tool Classifications Search & Comparison Rescaled data Primary result Stored results Conclusions Analysis Architecture • Rescaling datasets • Direct analysis • Result storage • Data mining (result search & comparison) http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  7. Analysis tool Classifications Search & Comparison Rescaled data Primary result Stored results Conclusions Analysis Architecture • Direct analysis • “pluggable” interface • Analysis has access to samples (inputs) • Analysis stores parameters into database • Analysis produces lists of genes and profiles (outputs) http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  8. Analysis Architecture Genecluster output • Currently supported tools: • GeneCluster self organizing map • http://www.genome.wi.mit.edu/MPR/ • rule-based analysis • Future tools: • differential display • nearest-neighbor analysis http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  9. Analysis Architecture http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  10. Stored results Analysis tool Rescaled data Data mining • Querying results • Multiset comparisons Classifications Search & Comparison Primary result Conclusions http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  11. Stored results Analysis tool Rescaled data Data mining • Querying results • by gene • by conditions • Multiset comparisons Classifications Search & Comparison Primary result Conclusions http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  12. Analysis tool Classifications Search & Comparison Search & Comparison Rescaled data Primary result Primary result Stored results Conclusions Analysis tool Analysis tool Analysis tool Classifications Classifications Search & Comparison Search & Comparison Rescaled data Rescaled data Rescaled data Primary result Primary result Stored results Stored results Conclusions Conclusions Data mining • Querying results • Multiset comparisons: • Classifications • MIPS • User defined • Primary results • Internal results • External results http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  13. Platform • Oracle DBMS • WebDB - Web/Oracle middleware • Perl • Java • Solaris 2.6 on 4 x 400Mhz Sparc http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  14. chipDB is: • A Web-based system for interactive analysis and integration of experimental results. • Flexible normalization scheme • Extensible analysis framework • Searching of analysis results • Web-based public access http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  15. Future Enhancements • Microarray data • Human array data • Additional analysis tools http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

  16. Acknowledgements • Young Lab • Helen Causton • Tony Lee • Rhonda Harrison • Design & • Development • John Barnett • Bing Ren • Ezra Jennings • WICGR/MPR • Michael Angelo • Pablo Tamayo • Eric Lander Richard Young http://web.wi.mit.edu/young/chipdb.html Whitehead Institute

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