compendiumdb

compendiumdb provides systematic retrieval, parsing, and MySQL storage of Gene Expression Omnibus (GEO) microarray expression data to enable large-scale comparative and meta-analyses of gene expression across over 1 million samples from more than 40,000 microarray-based experiments.

Key Features:

• Data retrieval from GEO: Downloads microarray expression datasets and associated metadata from the Gene Expression Omnibus (GEO).
• Data parsing and storage: Parses GEO data and loads processed tables into local or remote MySQL databases for structured storage.
• Integration with R/Bioconductor: Provides dedicated R functions to query and interact with stored databases for downstream analyses within R/Bioconductor.
• Implementation and platform support: Implemented using R, MySQL, and Perl and stated to operate on Linux, MS Windows, and OS X.

Scientific Applications:

• Comparative genomics studies: Enables comparison of gene expression profiles across different conditions or species using assembled GEO datasets.
• Disease mechanism exploration: Facilitates identification of gene expression patterns associated with diseases across multiple studies.
• Data integration and meta-analyses: Supports integration of data from multiple GEO studies to perform meta-analyses and validate findings across datasets.

Methodology:

Data are downloaded from GEO, parsed, and loaded into local or remote MySQL databases and accessed via dedicated R functions; implementation uses R, MySQL, and Perl.