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Table 1 Interaction networks used in the study

From: A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

Network name Ref Type Screen Nodes Edges D MND MNDSD MCC
Ito-Core [42] PI PPI 426 568 0.006 2.667 3.919 0.093
VonMering [49] PI PPI 573 2097 0.013 7.319 9.017 0.450
Schwikowski [50] PI PPI 1297 1862 0.002 2.871 3.109 0.125
Y2H-CCSB [43] PI PPI 964 1598 0.003 3.315 5.456 0.095
Y2H-Union [43] PI PPI 1647 2682 0.002 3.257 5.334 0.086
AP/MS-Combined [45] PI CCA 1004 8319 0.017 16.57 18.63 0.648
LC-Multiple [48] MT LCI 1213 2621 0.004 4.322 4.533 0.337
Secretory-Map [53] GI E-MAP 409 4175 0.050 20.42 23.82 0.251
Chromosome-Map [54] GI E-MAP 735 17,185 0.064 46.76 43.61 0.233
Costanzo [55] GI SGA 4319 74,984 0.007 29.96 41.86 0.062
Costanzo-Stringent [55] GI SGA 3811 35,924 0.004 16.07 22.92 0.046
  1. Network types: PI, physical interactions; GI, genetic interactions; MT, mixed type. Screening methods: PPI, protein-protein interaction screen; CCA, protein co-complex association mapping; LCI, literate-curated interactions; E-MAP, epistatic miniarray profiling; SGA, synthetic genetic array mapping. Topological parameters: D, density; MND, mean node degree; MNDSD, standard deviation of MND; MCC, mean clustering coefficient of the network. Costanzo-Stringent sub-network was constructed using the interaction score cut-offs ε < -0.17 or ε > 0.21. In each network, we extracted the largest connected component to be used in the evaluations.