Formulating and testing hypotheses in functional genomics
Artificial Intelligence in Medicine
Text-mining approach to evaluate terms for ontology development
Journal of Biomedical Informatics
TreeHugger: A New Test for Enrichment of Gene Ontology Terms
INFORMS Journal on Computing
CarGene: Characterisation of sets of genes based on metabolic pathways analysis
International Journal of Data Mining and Bioinformatics
The multi-reference contrast method: Facilitating set enrichment analysis
Computers in Biology and Medicine
Annotation concept synthesis and enrichment analysis
AI'10 Proceedings of the 23rd Canadian conference on Advances in Artificial Intelligence
Mining dense structures to uncover anomalous behaviour in financial network data
MSM'11 Proceedings of the 2011 international conference on Modeling and Mining Ubiquitous Social Media
Curbing false discovery rates in interpretation of genome-wide expression profiles
Journal of Biomedical Informatics
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Motivation: A number of available program packages determine the significant enrichments and/or depletions of GO categories among a class of genes of interest. Whereas a correct formulation of the problem leads to a single exact null distribution, these GO tools use a large variety of statistical tests whose denominations often do not clarify the underlying P-value computations. Summary: We review the different formulations of the problem and the tests they lead to: the binomial, χ2, equality of two probabilities, Fisher's exact and hypergeometric tests. We clarify the relationships existing between these tests, in particular the equivalence between the hypergeometric test and Fisher's exact test. We recall that the other tests are valid only for large samples, the test of equality of two probabilities and the χ2-test being equivalent. We discuss the appropriateness of one- and two-sided P-values, as well as some discreteness and conservatism issues. Contact: isabelle.rivals@espci.fr Supplementary information: Supplementary data are available at Bioinformatics online.