GSE: A COMPREHENSIVE DATABASE SYSTEM FOR THE REPRESENTATION, RETRIEVAL, AND ANALYSIS OF MICROARRAY DATA

Pacific Symposium on Biocomputing 2008

TIMOTHY DANFORD ; ALEX ROLFE ; DAVID GIFFORD

Others  :  http://psb.stanford.edu/psb-online/proceedings/psb08/danford.pdf
PID  :  19784

来源: CEUR

【 摘 要 】

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 visualizationapplication 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 providea reference software implementation for the GSE system.