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.

Martin et al. Genome Biology 2004 5:R101   doi:10.1186/gb-2004-5-12-r101