Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II: Analysis Beyond Single Gene

Table 1

Recapitulative list of GO annotations tools.

Tool name	Statistical model	GO abstraction level	GO visualization	Multiple testing	Type of array	Other annotation	OS
Onto-Express	hypergeometric, Fisher’s exact test, binomial, 𝒳^2	Available	DAG	Bonferroni, Holm, Sidak, FDR	172 commercial arrays	Chromosomal position	Any
FatiGO+	Fisher’s exact test	Available	One level at a time	FDR	User-provided	KEGG pathways, SwissPROT keywords	Any
FuncAssociate	Fisher’s exact test	Not available	Not available	Monte Carlo simulation	User-provided	Not available	Web-based
GoToolBox	hypergeometric test, Fisher’s exact test or binomial	Available	One level at a time	Bonferroni	User-provided	Not available	Any
CLENCH2	Hypergeometric, binomial, 𝒳^2	Static global	DAG	None	User-provided	Not available	Windows
BiNGO	Hypergeometric, binomial	Available, GOSlim	DAG	FDR, Bonferroni	commercial arrays	Not available
GoSurfer	𝒳^2	Lowest level	DAG	FDR	Affymetrix only	Not available	Windows