Table 5

Drug target predictive power of degree and centralities for different reliable subsets
Network Number of proteins in network AUC – Degree AUC - BC AUC - CC
Full PIN, spoke 16078 0.6139 0.6294 0.5795
B subset 14408 0.6114 0.6171 0.5764
Non-predicted interactions 14928 0.5916 0.6128 0.5647
LTP subset 10591 0.5794 0.6066 0.5482
BioGRID only 8642 0.5082 0.5467 0.4874
MI score, IntAct > 0.6 219 0.6353 0.5347 0.4382
MI score, PSICQUIC > 0.7 747 0.5719 0.5725 0.5414
Rual+Stelzl only 3575 0.5004 0.5045 0.5011

The AUC was evaluated for degree and centrality ranks of the full PIN, five reliable subsets and two small subsets used in the literature. The best degree performance is achieved by the MI-IntAct score greater than 0.6; however, this subset contains 219 proteins only, making it of limited applicability. The second best performance is achieved by the full PIN and the B subset. Other reliable subsets (non-predicted, PSICQUIC, LTP) have a slightly inferior performance, while BioGRID and Rual+Stelzl perform close to randomness.

The best centrality performance is achieved by the full PIN, followed by three reliable subsets (B, non-predicted and LTP). Both MI-scores and both limited data sets perform close to randomness.

Mora and Donaldson

Mora and Donaldson BMC Bioinformatics 2012 13:294   doi:10.1186/1471-2105-13-294

Open Data