Table 2.

Topological parameters for HCM models obtained with Network Analyzer

	Manual HCM model	Tabular manual HCM model	INDRA-assembled PubMed HCM model	INDRA-assembled PubMed+PathwayCommons HCM model	Truncated INDRA DB HCM model	INDRA DB HCM model
Average number of neighbors	2.309a	2.789	1.917	3.582	1.455	2.059
Network diameter	1a	12	6	8	3	9
Network radius	1a	1	1	1	1	1
Characteristic path length	1.000a	4.334	2.541	2.395	1.299	3.900
Clustering coefficient	0.000a	0.054	0.007	0.006	0.014	0.028
Network density	0.003a	0.009	0.002	0.001	0.010	0.002
Connected components	26a	11	58	51	23	101
Multi-edge node pairs	1a	24	21	213	3	48
Number of self-loops	0a	4	7	14	0	6

^a Due to the CellDesigner XML file incompatibility, we suggest that some or all topological measures for the Manual HCM model are calculated falsely by Cytoscape