title: GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data.
abstract: BACKGROUND
  Gene Ontology (GO) characterizes and categorizes the functions of genes and their products according to biological processes, molecular functions and cellular components, facilitating interpretation of data from high-throughput genomics and proteomics technologies. The most effective use of GO information is achieved when its rich and hierarchical complexity is retained and the information is distilled to the biological functions that are most germane to the phenomenon being investigated.
  
  
  RESULTS
  Here we present a FDA GO tool named Gene Ontology for Functional Analysis (GOFFA). GOFFA first ranks GO terms in the order of prevalence for a list of selected genes or proteins, and then it allows the user to interactively select GO terms according to their significance and specific biological complexity within the hierarchical structure. GOFFA provides five interactive functions (Tree view, Terms View, Genes View, GO Path and GO TreePrune) to analyze the GO data. Among the five functions, GO Path and GO TreePrune are unique. The GO Path simultaneously displays the ranks that order GOFFA Tree Paths based on statistical analysis. The GO TreePrune provides a visual display of a reduced GO term set based on a user's statistical cut-offs. Therefore, the GOFFA visual display can provide an intuitive depiction of the most likely relevant biological functions.
  
  
  CONCLUSIONS
  With GOFFA, the user can dynamically interact with the GO data to interpret gene expression results in the context of biological plausibility, which can lead to new discoveries or identify new hypotheses.
  
  
  BACKGROUND
  GOFFA is available through ArrayTrack softwarehttp://edkb.fda.gov/webstart/arraytrack/.
authors.affiliation: National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA.
authors.forename: Hongmei
authors.initials: H
authors.lastname: Sun
authors.forename: Hong
authors.initials: H
authors.lastname: Fang
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.forename: Roger
authors.initials: R
authors.lastname: Perkins
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
mesh_terms: D023281:Genomics / Q000379:methods*; D020407:Internet; D040901:Proteomics / Q000379:methods*; D012985:Software Design; D014481:United States; D014486:United States Food and Drug Administration