A method for developing regulatory gene set networks to characterize complex biological systems

BMC Genomics

Table 1 Summary of co-membership gene set networks and regulatory gene set networks for five gene set collections.

Collection	Number of gene sets	co-membership edges (M)	Regulatory edges (R)	Regulatory relationships	Shared edges ^a	Number of genes	Normalized proportion of R edges to nodes
KEGG	186	2,230	4,452	3,274	1,461	5,267	50.49
Reactome	674	15,859	25,569	20,917	7,437	6,025	69.96
GO BP	825	33,055	32,607	27,513	10,354	6,178	71.08
GO CC	223	4,186	1,446	1,122	793	5,270	13.67
GO MF	396	3,178	2,620	2,404	503	5,314	13.83

^aFor regulatory edges, a pair of gene set can have a loop if both incoming and outgoing edges are significant. The number of regulatory edges is always greater than or equal to the number of regulatory relationships because one pair of gene sets either have or do not have regulatory relationship.

ISSN: 1471-2164