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

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

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

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

Motivation

LIMS

chipDB

Publication/Web

Public RepositoriesLIMS

chipDB

Publication/Web

Public Repositories

External Analyses

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

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

Analysis Architecture

Rescaled data Primary result

Analysis tool

Search &Comparison

Conclusions

Classifications

Stored results

• Rescaling datasets• Direct analysis• Result storage• Data mining (result search & comparison)

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 data Primary result

Analysis tool

Search &Comparison

Conclusions

Classifications

Stored results

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

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

Analysis Architecture

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

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

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 resultsRescaled data Primary result

Analysis tool

Search &Comparison

Conclusions

Classifications

Stored resultsRescaled data

Analysis tool

Primary result

Search &Comparison

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

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

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

Future Enhancements

• Microarray data

• Human array data

• Additional analysis tools

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

Acknowledgements

Young Lab

Helen Causton Tony LeeRhonda Harrison

WICGR/MPR

Michael Angelo Pablo TamayoEric Lander

Design & Development

John Barnett Bing RenEzra Jennings

Richard Young