TY - GEN
T1 - Regularizing predicted complexes by mutually exclusive protein-protein interactions
AU - Maruyama, Osamu
AU - Wong, Limsoon
N1 - Publisher Copyright:
© 2015 ACM.
Copyright:
Copyright 2018 Elsevier B.V., All rights reserved.
PY - 2015/8/25
Y1 - 2015/8/25
N2 - Protein complexes are key entities in the cell responsible for various cellular mechanisms and biological processes. We propose here a method for predicting protein complexes from a protein-protein interaction (PPI) network, using information on mutually exclusive PPIs. If two interactions are mutually exclusive, they are not allowed to exist simultaneously in the same predicted complex. We introduce a new regularization term which checks whether predicted complexes are connected by mutually exclusive PPIs. This regularization term is added into the scoring function of our earlier protein complex prediction tool, PPSampler2. We show that PPSampler2 with mutually exclusive PPIs outperforms the original one. Furthermore, the performance is superior to well-known representative conventional protein complex prediction methods. Thus, it is is effective to use mutual exclusiveness of PPIs in protein complex prediction.
AB - Protein complexes are key entities in the cell responsible for various cellular mechanisms and biological processes. We propose here a method for predicting protein complexes from a protein-protein interaction (PPI) network, using information on mutually exclusive PPIs. If two interactions are mutually exclusive, they are not allowed to exist simultaneously in the same predicted complex. We introduce a new regularization term which checks whether predicted complexes are connected by mutually exclusive PPIs. This regularization term is added into the scoring function of our earlier protein complex prediction tool, PPSampler2. We show that PPSampler2 with mutually exclusive PPIs outperforms the original one. Furthermore, the performance is superior to well-known representative conventional protein complex prediction methods. Thus, it is is effective to use mutual exclusiveness of PPIs in protein complex prediction.
UR - http://www.scopus.com/inward/record.url?scp=84962545115&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84962545115&partnerID=8YFLogxK
U2 - 10.1145/2808797.2808817
DO - 10.1145/2808797.2808817
M3 - Conference contribution
AN - SCOPUS:84962545115
T3 - Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015
SP - 1068
EP - 1075
BT - Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015
A2 - Pei, Jian
A2 - Tang, Jie
A2 - Silvestri, Fabrizio
PB - Association for Computing Machinery, Inc
T2 - IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015
Y2 - 25 August 2015 through 28 August 2015
ER -