• Decrease font size
  • Return font size to normal
  • Increase font size
U.S. Department of Health and Human Services

Science & Research

  • Print
  • Share
  • E-mail

Gene Ontology for Functional Analysis (GOFFA)

GOFFA is a tool developed for ArrayTrack™ that takes a list of genes and identifies terms in Gene Ontology (GO)disclaimer icon associated with those genes. GOFFA provides tools to view/access the following:

  • GO term hierarchy
  • Full listing of GO terms annotated with the genes associated with a given term
  • Fisher's exact test p-value providing the probability of identifying that many genes for a given term by chance alone
  • Relative enrichment factor (E-value) giving the enrichment of a GO term for genes in the submitted list relative to the frequency of genes assigned to that term from the full set of GOFFA annotated genes for a particular species  


GOFFA also provides two novel methods to visualize and interpret results—GOPath and GO TreePrune.

  • GO Path—simultaneously displays the ranks that order GOFFA Tree Paths based on statistical analysis
  • GO TreePrune—provides a visual display of a reduced GO term set based on a user's statistical cut-offs

A more complete description of GOFFA's abilities and functions has been published in BMC Bioinformatics disclaimer icon  2006, 7(Suppl 2):S23.

Running GOFFA requires an Internet connection and Java Runtime Environment (JRE) 1.6 or greater installed. To install or upgrade Java please visit the Oracle Java websitedisclaimer icon.  

Launch GOFFA for FDA users

Launch GOFFA for non-FDA users


Citation - Please cite the following for publications that incorporate analysis using GOFFA:
Sun, H., Fang, H., Chen, T., Perkings, R., and Tong, W., "GOFFA: Gene Ontology For Functional Analysis - Software for gene ontology-based functional analysis of genomic and proteomic data." BMC Bioinformatics, 7(Suppl 2):S23, 2006.

Contact Information

Please e-mail NCTRBioinformaticsSupport@fda.hhs.gov with any questions or problems running GOFFA.