GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data.
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.
Danford
Timothy
T
MIT Computer Science and Artificial Intelligence Laboratory 32-G538, 77 Massachusetts Ave, Cambridge, MA 02139, USA.
Rolfe
Alex
A
Gifford
David
D
D000465:Algorithms; D047369:Chromatin Immunoprecipitation / Q000706:statistics & numerical data; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D016247:Information Storage and Retrieval; D046228:Microarray Analysis / Q000706:statistics & numerical data*; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D012984:Software