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

Whitehead Institute Expression analysis motivation objectives analysis architecture data mining platform future enhancements

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

Whitehead Institute Motivation LIMS chipDB Publication/Web Public RepositoriesLIMS chipDB Publication/Web Public RepositoriesExternal Analyses

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

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)

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

Whitehead Institute Analysis Architecture Currently supported tools: –GeneCluster self organizing map –rule-based analysis Future tools: –differential display –nearest-neighbor analysis Genecluster output

Whitehead Institute Analysis Architecture

Whitehead Institute Rescaled data Analysis tool Primary result Search & Comparison Classifications Stored results Data mining Querying results Multiset comparisons Conclusions

Whitehead Institute Rescaled data Analysis tool Primary result Search & Comparison Classifications Stored results Data mining Querying results –by gene –by conditions Multiset comparisons Conclusions

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

Whitehead Institute Platform Oracle DBMS WebDB - Web/Oracle middleware Perl Java Solaris 2.6 on 4 x 400Mhz Sparc

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

Whitehead Institute Future Enhancements Microarray data Human array data Additional analysis tools

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