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Characterizing gene sets with FuncAssociate
Gabriel F Berriz1, Oliver D King, Barbara Bryant
1Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, Boston, MA 02115, USA.
Bioinformatics (Oxford, England)
|December 12, 2003
Summary
FuncAssociate is a web tool that uses Gene Ontology attributes to analyze large gene sets from experiments. It offers a more accurate significance determination using Monte Carlo simulations for 10 different organisms.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- FuncAssociate is a freely accessible web-based tool.
- Source code is available for academic users.
Purpose of the Study:
- To provide researchers with a tool for characterizing large gene sets using Gene Ontology (GO) attributes.
- To offer a more statistically robust method for determining significance in gene set analysis.
Main Methods:
- Utilizes Gene Ontology attributes for gene set characterization.
- Employs a Monte Carlo simulation approach for significance testing.
- Handles ranked input lists.
Main Results:
- FuncAssociate supports the analysis of gene sets across 10 different organisms.
- The tool provides a more appropriate method for determining statistical significance compared to traditional corrections like Bonferroni or Šidák.
Conclusions:
- FuncAssociate is a valuable web-based tool for researchers analyzing large gene sets.
- Its unique features, including ranked list handling and Monte Carlo simulations, enhance the accuracy of biological interpretation.