Databases

• Gene Expression Omnibus at NCBI GEO is a gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval.
• ArrayExpressfrom EBI ArrayExpress is a public repository for microarray data, which is aimed at storing well annotated data in accordance with MGED recommendations.
• Dragon Database- Database Referencing of Array Genes ONline DRAGON can rapidly supply information pertaining to a range of the biological characteristics of a majority of the genes in any microarray data set. The subsequent inclusion of this information during the analysis of microarray data allows for deeper insight into gene expression patterns.
• Stanford Microarray Database SMD is fee based microarray repository and analysis tool.

Links to Microarry Data from the Whitehead Institute

• Expression and Location Analysis/Young Lab
• Galitski et al (1999)(Fink Lab)
• Madhani et al (1999)(Fink Lab)
• Rubin-Bejerano et al (2003)(Fink Lab)
• Broad Institute: Cancer Program publications and data

Analysis tools

• Bioconductor Project - an open source and open development software project for the analysis and comprehension of genomic data, emphasizing microarray data. It is a collection of packages created for the R Project for Statistical Computing.
• Cluster 3.0 and Java TreeView: clustering and visualization tools for all operating systems
• Clustering software from Stanford
• Expression Profiler at EBI
• List of Microarray Tools gathered at EBI
• GenePattern, GeneCluster and other tools from the Broad Institute
• Gene Ontology tools from the the GO Consortium and other groups
• VERA and SAM - Testing for differentially-expressed genes in DNA microarray data
• Terry Speed's Group Microarray Page - Tools for Affy data analysis
• Software from TIGR - the TM4 package
• GeneX from NCGR - Open source software
• MAExplorer from NCI - data exploratory tool
• NOMAD relational database for storing microarray data
• SNOMAD: a collection of algorithms for normalization and standardization
• GEPAS: Gene expression pattern analysis suite
• GEDA: integrated analysis of global gene expression patterns in cancer