Enrichment or depletion of a GO category within a class of genes: which test?

• Published in: Bioinformatics Vol. 23; no. 4; pp. 401 - 407
• Main Authors: Rivals, Isabelle, Personnaz, Léon, Taing, Lieng, Potier, Marie-Claude
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.02.2007; Oxford Publishing Limited (England); Oxford University Press (OUP)
• Subjects: Bioinformatics; Biological and medical sciences; Computer Science; Data Interpretation, Statistical; Database Management Systems; Databases, Protein; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; General aspects; Information Storage and Retrieval - methods; Life Sciences; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Methodology; Multigene Family - physiology; Oligonucleotide Array Sequence Analysis - methods; Proteins - classification; Proteins - metabolism; Quantitative Methods; Statistics; Gene; Ontology; Computer program; Test; Distribution; DNA chip; Database; Hypergeometric function; Probability; Review; Gene expression; Bioinformatics; hypergeometric test; p-value; Fisher's exact test; GO category

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 te...