Table 1.

Comparison of GOLEM with other gene ontology navigation and analysis tools.

	Availability	Finds statistically enriched GO terms	Supports gene-based queries	Visualization As Tree	Visualization As DAG	Visualization As Interactively Expandable DAG	Accepts Local Annotations Files	Requires Internet Connection
AmiGO	Freely available; HTML-based application	No	Yes	Yes	Yes	No	No	Yes
Gene InfoViz	Freely available; web-based application	No	Yes	No	Yes	No	No	Yes
GOFish	Freely available; Java applet	No	Yes	Yes	No	No	No	Yes
FatiGO	Freely available; web-based application	Yes	Yes	No	No	No	No	Yes
GO Term Finder	Freely available; yeast-only web-based version, downloadable generic version	Yes	Yes	Yes	Yes	No	No	Yes
TO-GO	Freely available; Java application	No	Yes	Yes	No	No	Yes	Yes (at program startup only)
DynGO	Freely available; standalone Java package	No	Yes	Yes	No	No	Yes	No
GenNav	Freely available; web-based application	No	Yes	No	Yes	No	No	Yes
GoMiner	Freely available; Java application	Yes	Yes	Yes	Yes	No	Yes	No
GOLEM	Freely available; application version, applet version	Yes	Yes	No	Yes	Yes	Yes	No