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

From: GOToolBox: functional analysis of gene datasets based on Gene Ontology

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
  1. 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.