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

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

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
  1. 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.