title: nEASE: a method for gene ontology subclassification of high-throughput gene expression data.
abstract: 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.
  
  
  BACKGROUND
  nEASE is implemented within the Multiple Experiment Viewer software package available at http://www.tm4.org/mev.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA.
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Chittenden
authors.forename: Eleanor A
authors.initials: EA
authors.lastname: Howe
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Taylor
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Mar
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Aryee
authors.forename: Harold
authors.initials: H
authors.lastname: Gómez
authors.forename: Razvan
authors.initials: R
authors.lastname: Sultana
authors.forename: John
authors.initials: J
authors.lastname: Braisted
authors.forename: Sarita J
authors.initials: SJ
authors.lastname: Nair
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Chris
authors.initials: C
authors.lastname: Holmes
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D018875:Vocabulary, Controlled