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