GOToolBox: functional analysis of gene datasets based on Gene Ontology

Table 3 Summary of the functionalities offered by GOToolBox and other GO processing tools

Program	References	Statistics	Multiple testing correction	Output	Ontology options
eGOn	[18]	Fisher exact test	-	TAB/RANK/TREE	ALL/EVID
CLENCH	[14]	Hypergeometric Binomial Chi Square	-	TAB/RANK	ALL/SLIM
FatiGO	[19]	Fisher exact test	Westfall/Benjamini/Yekutieli	TAB/RANK/TREE	LEVEL
FuncAssociate	[20]	Fisher exact test	P-value adjustment	TAB/RANK	ALL
FuncSpec	[21]	Hypergeometric	Bonferroni	TAB/RANK	ALL
GeneMerge	[22]	Hypergeometric	Bonferroni	TAB/RANK	ALL
GFINDer	[13]	Hypergeometric Fisher exact test Binomial	-	TAB/RANK	ALL
GoMiner	[15]	Fisher exact test	-	TAB/DAG/TREE	ALL
Gostat	[23]	Fisher exact test	Holm/Benjamini/Yekutieli	TAB/RANK	LEVEL
GO Term-Finder (CPAN)	[17]	Hypergeometric	Bonferroni/Benjamini	TAB/RANK/DAG	ALL
GO Term-Finder (SGD)	[17]	Binomial	-	TAB/RANK/DAG	ALL
GOTM	[16]	Hypergeometric	-	TAB/TREE/DAG	ALL
GOToolBox	This paper	Hypergeometric Fisher exact test Binomial	Bonferroni	TAB/RANK	ALL/SLIM/ LEVEL/EVID

In the output column, TREE, DAG, RANK and TAB refer respectively to tree-based output, directed acyclic graph visualization, P-value based ranking of terms, and results organized in a table. In the Ontology options column, terms listed refer to the way a gene set-GO term association can be built: ALL stands for 'all terms are taken into account (including parent terms)'; SLIM for 'mapping of the terms on a slim ontology'; LEVEL for 'fit the terms to a given depth of the ontology'; and EVID for 'filter terms according to the type of evidence which indicates how annotation has been associated to the gene'. See text for more details.

ISSN: 1474-760X