GSE

GSE is a database system that stores, retrieves, and analyzes high-throughput microarray data. This software tool enables researchers to handle complex datasets, including expression datasets, ChIP-chip data, genomic annotations, and functional annotations. Moreover, the system includes precomputed scans for binding events, which makes it easier for users to identify and analyze relevant data. One of the most impressive features of GSE is its ability to manage data associated with multiple species and multiple genomes built into a single species. This flexibility allows researchers to work with diverse datasets and make cross-species comparisons.

To build an interactive visualization application for ChIP-chip data, GSE uses a middle software layer called GSEBricks. This layer represents biological data streams and is essential for visualizing complex datasets. The visualizer software is written in Java and communicates with the GSE database system over the network. This visualization feature gives users a clear understanding of the data, making it easier to identify patterns and draw conclusions.

In addition, GSE includes a system for formulating and recording binding hypotheses. These hypotheses are simple descriptions of the relationships that may hold between different ChIP-chip experiments. This system provides researchers a powerful tool for analyzing complex datasets and identifying key relationships between experiments. A reference software implementation is also provided, making it easier for users to understand and apply the system.