Dataset Information

NEASE: a method for gene ontology subclassification of high-throughput gene expression data.

ABSTRACT:

Unlabelled

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 http://www.tm4.org/mev.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Chittenden TW

PROVIDER: S-EPMC6903781 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature

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Publications

nEASE: a method for gene ontology subclassification of high-throughput gene expression data.

Chittenden Thomas W TW Howe Eleanor A EA Taylor Jennifer M JM Mar Jessica C JC Aryee Martin J MJ Gómez Harold H Sultana Razvan R Braisted John J Nair Sarita J SJ Quackenbush John J Holmes Chris C

Bioinformatics (Oxford, England) 20120113 5

<h4>Unlabelled</h4>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 ope ...[more]

PMID: 22247278