. Author manuscript; available in PMC: 2011 Oct 1.

Published in final edited form as: Mol Genet Metab. 2010 Jun 22;101(2-3):134–140. doi: 10.1016/j.ymgme.2010.06.005

Table 2. Percent of Entrez Gene IDs that are eligible for network and functional analysis.

Entrez Gene IDs were analyzed because the percentage of Entrez Gene IDs annotated were similar between PAS and Affymetrix. GeneGO had nearly 50% and 20% more network annotations than its proprietary and public functional annotations, respectively. IPA had 7.6% more network annotations than proprietary function annotations, and Pathway Studio had 3.9% more. GeneGO had fewer proprietary functional annotations (31.1%) than its Gene Ontology annotations because the manual curation process removes many of GO’s inferred annotations (http://www.geneontology.org). We used Pathway Studio’s ResNet Mammalian demo database, which contains about 10% of the full database’s network and proprietary functional information (personal correspondence from Pathway Studio, February 2010).

Software	Version	#Entrez Gene IDs	A. % Network Info. (#)	B. % Functional Annotations
Software	Version	#Entrez Gene IDs	A. % Network Info. (#)	Proprietary	Public (GO)^*
IPA	7.6 build 76537	20979	63.2% (13257)	55.6% (11669)	---
GeneGO	5.4 build 19940	21446	75.3% (16144)	25.5% (5462)	56.6% (12137)
PStudio	7.0 demo	21447	37.5% (8038)	33.6% (7206)	72.1% (15456)
Affymetrix	na29	21450	---	---	74.5% (15975)

IPA does not allow a separate analysis of public functional annotations from GO.