Table 3 |
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|
Summary of the functionalities offered by GOToolBox and other GO processing tools |
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| Program |
References |
Statistics |
Multiple testing correction |
Output |
Ontology options |
|
|
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| 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 |
|
|
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|
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. |
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|
Martin et al. Genome Biology 2004 5:R101 doi:10.1186/gb-2004-5-12-r101 |
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