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

3. http://web.wi.mit.edu/young/chipdb.html Whitehead Institute 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

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

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

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

7. http://web.wi.mit.edu/young/chipdb.html Whitehead Institute 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) Rescaled dataPrimary result Analysis tool Search & Comparison Conclusions Classifications Stored results

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

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

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

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

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

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

14. http://web.wi.mit.edu/young/chipdb.html Whitehead Institute 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

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

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