JCVI: NEASE: a Method for Gene Ontology Subclassification of High-throughput Gene Expression Data.
 
 
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Chittenden TW, Howe EA, Taylor JM, Mar JC, Aryee MJ, Gómez H, Sultana R, Braisted J, Nair SJ, Quackenbush J, Holmes C

NEASE: a Method for Gene Ontology Subclassification of High-throughput Gene Expression Data.

Bioinformatics (Oxford, England). 2012 Mar 01; 28: 726-728.

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Abstract

SUMMARY: High-throughput technologies can identify genes whose expression profiles correlate with specific phenotypes; however, placing these genes into a biological context remains challenging. To help address this issue, we developed nested Expression Analysis Systematic Explorer (nEASE). nEASE complements traditional gene ontology enrichment approaches by determining statistically enriched gene ontology subterms within a list of genes based on co-annotation. Here, we overview an open-source software version of the nEASE algorithm. nEASE can be used either stand-alone or as part of a pathway discovery pipeline. AVAILABILITY: nEASE is implemented within the Multiple Experiment Viewer software package available at www.tm4.org/mev. CONTACT: cholmes@stats.ox.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.