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GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data



GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data



Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2008: 539-550



We present GSE, the Genomic Spatial Event database, a system to store, retrieve, and analyze all types of high-throughput microarray data. GSE handles expression datasets, ChIP-chip data, genomic annotations, functional annotations, the results of our previously published Joint Binding Deconvolution algorithm for ChIP-chip, and precomputed scans for binding events. GSE can manage data associated with multiple species; it can also simultaneously handle data associated with multiple 'builds' of the genome from a single species. The GSE system is built upon a middle software layer for representing streams of biological data; we outline this layer, called GSEBricks, and show how it is used to build an interactive visualization application for ChIP-chip data. The visualizer software is written in Java and communicates with the GSE database system over the network. We also present a system to formulate and record binding hypotheses--simple descriptions of the relationships that may hold between different ChIP-chip experiments. We provide a reference software implementation for the GSE system.

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Accession: 053343662

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PMID: 18229714


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