Regularizing predicted complexes by mutually exclusive protein-protein interactions

Osamu Maruyama, Limsoon Wong

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationProceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015
EditorsJian Pei, Jie Tang, Fabrizio Silvestri
PublisherAssociation for Computing Machinery, Inc
Pages1068-1075
Number of pages8
ISBN (Electronic)9781450338547
DOIs
Publication statusPublished - Aug 25 2015
EventIEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015 - Paris, France
Duration: Aug 25 2015Aug 28 2015

Publication series

NameProceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015

Other

OtherIEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015
CountryFrance
CityParis
Period8/25/158/28/15

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Proteins

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Computer Networks and Communications

Cite this

Maruyama, O., & Wong, L. (2015). Regularizing predicted complexes by mutually exclusive protein-protein interactions. In J. Pei, J. Tang, & F. Silvestri (Eds.), Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015 (pp. 1068-1075). (Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015). Association for Computing Machinery, Inc. https://doi.org/10.1145/2808797.2808817

Regularizing predicted complexes by mutually exclusive protein-protein interactions. / Maruyama, Osamu; Wong, Limsoon.

Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015. ed. / Jian Pei; Jie Tang; Fabrizio Silvestri. Association for Computing Machinery, Inc, 2015. p. 1068-1075 (Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Maruyama, O & Wong, L 2015, Regularizing predicted complexes by mutually exclusive protein-protein interactions. in J Pei, J Tang & F Silvestri (eds), Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015. Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015, Association for Computing Machinery, Inc, pp. 1068-1075, IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015, Paris, France, 8/25/15. https://doi.org/10.1145/2808797.2808817
Maruyama O, Wong L. Regularizing predicted complexes by mutually exclusive protein-protein interactions. In Pei J, Tang J, Silvestri F, editors, Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015. Association for Computing Machinery, Inc. 2015. p. 1068-1075. (Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015). https://doi.org/10.1145/2808797.2808817
Maruyama, Osamu ; Wong, Limsoon. / Regularizing predicted complexes by mutually exclusive protein-protein interactions. Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015. editor / Jian Pei ; Jie Tang ; Fabrizio Silvestri. Association for Computing Machinery, Inc, 2015. pp. 1068-1075 (Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2015).
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