Determining the minimum number of protein-protein interactions required to support known protein complexes.
The prediction of protein complexes from protein-protein interactions (PPIs) is a well-studied problem in bioinformatics. However, the currently available PPI data is not enough to describe all known protein complexes. In this paper, we express the problem of determining the minimum number of (addit...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5919440?pdf=render |
| _version_ | 1818306565958008832 |
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| author | Natsu Nakajima Morihiro Hayashida Jesper Jansson Osamu Maruyama Tatsuya Akutsu |
| author_facet | Natsu Nakajima Morihiro Hayashida Jesper Jansson Osamu Maruyama Tatsuya Akutsu |
| author_sort | Natsu Nakajima |
| collection | DOAJ |
| description | The prediction of protein complexes from protein-protein interactions (PPIs) is a well-studied problem in bioinformatics. However, the currently available PPI data is not enough to describe all known protein complexes. In this paper, we express the problem of determining the minimum number of (additional) required protein-protein interactions as a graph theoretic problem under the constraint that each complex constitutes a connected component in a PPI network. For this problem, we develop two computational methods: one is based on integer linear programming (ILPMinPPI) and the other one is based on an existing greedy-type approximation algorithm (GreedyMinPPI) originally developed in the context of communication and social networks. Since the former method is only applicable to datasets of small size, we apply the latter method to a combination of the CYC2008 protein complex dataset and each of eight PPI datasets (STRING, MINT, BioGRID, IntAct, DIP, BIND, WI-PHI, iRefIndex). The results show that the minimum number of additional required PPIs ranges from 51 (STRING) to 964 (BIND), and that even the four best PPI databases, STRING (51), BioGRID (67), WI-PHI (93) and iRefIndex (85), do not include enough PPIs to form all CYC2008 protein complexes. We also demonstrate that the proposed problem framework and our solutions can enhance the prediction accuracy of existing PPI prediction methods. ILPMinPPI can be freely downloaded from http://sunflower.kuicr.kyoto-u.ac.jp/~nakajima/. |
| first_indexed | 2024-12-13T06:44:31Z |
| format | Article |
| id | doaj.art-79306497edd946d78d751c31e38f22f7 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T06:44:31Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-79306497edd946d78d751c31e38f22f72022-12-21T23:56:20ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01134e019554510.1371/journal.pone.0195545Determining the minimum number of protein-protein interactions required to support known protein complexes.Natsu NakajimaMorihiro HayashidaJesper JanssonOsamu MaruyamaTatsuya AkutsuThe prediction of protein complexes from protein-protein interactions (PPIs) is a well-studied problem in bioinformatics. However, the currently available PPI data is not enough to describe all known protein complexes. In this paper, we express the problem of determining the minimum number of (additional) required protein-protein interactions as a graph theoretic problem under the constraint that each complex constitutes a connected component in a PPI network. For this problem, we develop two computational methods: one is based on integer linear programming (ILPMinPPI) and the other one is based on an existing greedy-type approximation algorithm (GreedyMinPPI) originally developed in the context of communication and social networks. Since the former method is only applicable to datasets of small size, we apply the latter method to a combination of the CYC2008 protein complex dataset and each of eight PPI datasets (STRING, MINT, BioGRID, IntAct, DIP, BIND, WI-PHI, iRefIndex). The results show that the minimum number of additional required PPIs ranges from 51 (STRING) to 964 (BIND), and that even the four best PPI databases, STRING (51), BioGRID (67), WI-PHI (93) and iRefIndex (85), do not include enough PPIs to form all CYC2008 protein complexes. We also demonstrate that the proposed problem framework and our solutions can enhance the prediction accuracy of existing PPI prediction methods. ILPMinPPI can be freely downloaded from http://sunflower.kuicr.kyoto-u.ac.jp/~nakajima/.http://europepmc.org/articles/PMC5919440?pdf=render |
| spellingShingle | Natsu Nakajima Morihiro Hayashida Jesper Jansson Osamu Maruyama Tatsuya Akutsu Determining the minimum number of protein-protein interactions required to support known protein complexes. PLoS ONE |
| title | Determining the minimum number of protein-protein interactions required to support known protein complexes. |
| title_full | Determining the minimum number of protein-protein interactions required to support known protein complexes. |
| title_fullStr | Determining the minimum number of protein-protein interactions required to support known protein complexes. |
| title_full_unstemmed | Determining the minimum number of protein-protein interactions required to support known protein complexes. |
| title_short | Determining the minimum number of protein-protein interactions required to support known protein complexes. |
| title_sort | determining the minimum number of protein protein interactions required to support known protein complexes |
| url | http://europepmc.org/articles/PMC5919440?pdf=render |
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