Abstract
ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics.
Highlights
Centralized storage of microarray data is provided by a number of databases, such as ArrayExpress, Gene Expression Omnibus, Stanford Microarray Database/Longhorn Array Database, Bioarray Software Environment, and TM4 [1,2,3,4,5,6], many common downstream analysis procedures remain challenging, especially when reference to large-scale data in external databases is required
In an attempt to address this pervasive set of challenges in functional genomics analysis, we developed ArrayPlex, a network-centric software environment chartered with the goal of streamlining the acquisition and up-to-date maintenance of these resources and the ease by which they can be associated with primary microarray data
The ArrayPlex client serves as a normalization intermediary without interfering in the process of storing final results in one of many possible microarray databases that supports the GenePix Results files (GPR) file-format
Summary
Centralized storage of microarray data is provided by a number of databases, such as ArrayExpress, Gene Expression Omnibus, Stanford Microarray Database/Longhorn Array Database, Bioarray Software Environment, and TM4 [1,2,3,4,5,6], many common downstream analysis procedures remain challenging, especially when reference to large-scale data in external databases is required. Data analysis typically involves association of gene names with systematic and custom annotations, gene ontology information, and genomic DNA sequence, followed by a battery of analyses such as enrichment of functional annotations in gene sets, statistical tests for significance, analysis of cis-regulatory motifs and regulator-target relationships. Resources for these tasks are difficult to manually assemble while ensuring they remain error free. In an attempt to address this pervasive set of challenges in functional genomics analysis, we developed ArrayPlex, a network-centric software environment chartered with the goal of streamlining the acquisition and up-to-date maintenance of these resources and the ease by which they can be associated with primary microarray data. We demonstrate how ArrayPlex has been indispensable in the large-scale analysis of a transcriptional regulatory network
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