Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks
Figure 2
Human interactome: overlap of six databases and coverage of 3-D structural data.
Analysis of human interactome PPI data showing the coverage of six major primary databases (BIND, BioGRID, DIP, HPRD, IntAct, and MINT), according to the integration provided by the meta-database APID. (A) Growth of the total number of human PPIs during the last 3 years. (B) Number of PPIs obtained from each primary repository showing the % (with respect to the total number of PPIs: 80,032 in December 2009) and the number of PPIs only reported by each database (shown inside the corresponding sector of the Venn diagram). Coverage and intersection of PPIs with 3-D structural information: (C) Intersection between the PPIs of all human proteins that have at least one Pfam annotated (69,079 interactions, called ppihs_all) and the PPIs that include proteins with 3-D structural information (9,879 interactions, called ppihsxsdd); (D) intersection between the PPIs with 3-D structural information and a more stringent interactome constituted by PPIs proven at least by two experimental methods (16,959 interactions, called ppihsx2meth); (E) intersection between the PPIs with 3-D structural information and more stringent interactome constituted by interactions between proteins that are annotated to the same KEGG functional pathway (7,693 interactions, called ppihsxKEGG).