A New Method for Recognizing Protein Complexes Based on Protein Interaction Networks and GO Terms
Motivation: A protein complex is the combination of proteins which interact with each other. Protein–protein interaction (PPI) networks are composed of multiple protein complexes. It is very difficult to recognize protein complexes from PPI data due to the noise of PPI.Results: We proposed a new met...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-12-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.792265/full |
| _version_ | 1818400260621336576 |
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| author | Xiaoting Wang Nan Zhang Yulan Zhao Juan Wang |
| author_facet | Xiaoting Wang Nan Zhang Yulan Zhao Juan Wang |
| author_sort | Xiaoting Wang |
| collection | DOAJ |
| description | Motivation: A protein complex is the combination of proteins which interact with each other. Protein–protein interaction (PPI) networks are composed of multiple protein complexes. It is very difficult to recognize protein complexes from PPI data due to the noise of PPI.Results: We proposed a new method, called Topology and Semantic Similarity Network (TSSN), based on topological structure characteristics and biological characteristics to construct the PPI. Experiments show that the TSSN can filter the noise of PPI data. We proposed a new algorithm, called Neighbor Nodes of Proteins (NNP), for recognizing protein complexes by considering their topology information. Experiments show that the algorithm can identify more protein complexes and more accurately. The recognition of protein complexes is vital in research on evolution analysis.Availability and implementation: https://github.com/bioinformatical-code/NNP. |
| first_indexed | 2024-12-14T07:33:45Z |
| format | Article |
| id | doaj.art-df2458ed21e2495a8c44c5730620e1b8 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T07:33:45Z |
| publishDate | 2021-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-df2458ed21e2495a8c44c5730620e1b82022-12-21T23:11:17ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-12-011210.3389/fgene.2021.792265792265A New Method for Recognizing Protein Complexes Based on Protein Interaction Networks and GO TermsXiaoting WangNan ZhangYulan ZhaoJuan WangMotivation: A protein complex is the combination of proteins which interact with each other. Protein–protein interaction (PPI) networks are composed of multiple protein complexes. It is very difficult to recognize protein complexes from PPI data due to the noise of PPI.Results: We proposed a new method, called Topology and Semantic Similarity Network (TSSN), based on topological structure characteristics and biological characteristics to construct the PPI. Experiments show that the TSSN can filter the noise of PPI data. We proposed a new algorithm, called Neighbor Nodes of Proteins (NNP), for recognizing protein complexes by considering their topology information. Experiments show that the algorithm can identify more protein complexes and more accurately. The recognition of protein complexes is vital in research on evolution analysis.Availability and implementation: https://github.com/bioinformatical-code/NNP.https://www.frontiersin.org/articles/10.3389/fgene.2021.792265/fullprotein interaction networkprotein complexGO termsNNPfunction of proteins |
| spellingShingle | Xiaoting Wang Nan Zhang Yulan Zhao Juan Wang A New Method for Recognizing Protein Complexes Based on Protein Interaction Networks and GO Terms Frontiers in Genetics protein interaction network protein complex GO terms NNP function of proteins |
| title | A New Method for Recognizing Protein Complexes Based on Protein Interaction Networks and GO Terms |
| title_full | A New Method for Recognizing Protein Complexes Based on Protein Interaction Networks and GO Terms |
| title_fullStr | A New Method for Recognizing Protein Complexes Based on Protein Interaction Networks and GO Terms |
| title_full_unstemmed | A New Method for Recognizing Protein Complexes Based on Protein Interaction Networks and GO Terms |
| title_short | A New Method for Recognizing Protein Complexes Based on Protein Interaction Networks and GO Terms |
| title_sort | new method for recognizing protein complexes based on protein interaction networks and go terms |
| topic | protein interaction network protein complex GO terms NNP function of proteins |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.792265/full |
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