A new method for predicting essential proteins based on participation degree in protein complex and subgraph density.
Essential proteins are crucial to living cells. Identification of essential proteins from protein-protein interaction (PPI) networks can be applied to pathway analysis and function prediction, furthermore, it can contribute to disease diagnosis and drug design. There have been some experimental and...
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| _version_ | 1849716961789870080 |
|---|---|
| author | Xiujuan Lei Xiaoqin Yang |
| author_facet | Xiujuan Lei Xiaoqin Yang |
| author_sort | Xiujuan Lei |
| collection | DOAJ |
| description | Essential proteins are crucial to living cells. Identification of essential proteins from protein-protein interaction (PPI) networks can be applied to pathway analysis and function prediction, furthermore, it can contribute to disease diagnosis and drug design. There have been some experimental and computational methods designed to identify essential proteins, however, the prediction precision remains to be improved. In this paper, we propose a new method for identifying essential proteins based on Participation degree of a protein in protein Complexes and Subgraph Density, named as PCSD. In order to test the performance of PCSD, four PPI datasets (DIP, Krogan, MIPS and Gavin) are used to conduct experiments. The experiment results have demonstrated that PCSD achieves a better performance for predicting essential proteins compared with some competing methods including DC, SC, EC, IC, LAC, NC, WDC, PeC, UDoNC, and compared with the most recent method LBCC, PCSD can correctly predict more essential proteins from certain numbers of top ranked proteins on the DIP dataset, which indicates that PCSD is very effective in discovering essential proteins in most case. |
| format | Article |
| id | doaj-art-5cd23af0e1ac4ebba1956549c0fcecdf |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-5cd23af0e1ac4ebba1956549c0fcecdf2025-08-20T03:12:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01136e019899810.1371/journal.pone.0198998A new method for predicting essential proteins based on participation degree in protein complex and subgraph density.Xiujuan LeiXiaoqin YangEssential proteins are crucial to living cells. Identification of essential proteins from protein-protein interaction (PPI) networks can be applied to pathway analysis and function prediction, furthermore, it can contribute to disease diagnosis and drug design. There have been some experimental and computational methods designed to identify essential proteins, however, the prediction precision remains to be improved. In this paper, we propose a new method for identifying essential proteins based on Participation degree of a protein in protein Complexes and Subgraph Density, named as PCSD. In order to test the performance of PCSD, four PPI datasets (DIP, Krogan, MIPS and Gavin) are used to conduct experiments. The experiment results have demonstrated that PCSD achieves a better performance for predicting essential proteins compared with some competing methods including DC, SC, EC, IC, LAC, NC, WDC, PeC, UDoNC, and compared with the most recent method LBCC, PCSD can correctly predict more essential proteins from certain numbers of top ranked proteins on the DIP dataset, which indicates that PCSD is very effective in discovering essential proteins in most case.https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pone.0198998/1/pone.0198998.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210220%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210220T175550Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=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 |
| spellingShingle | Xiujuan Lei Xiaoqin Yang A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. PLoS ONE |
| title | A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. |
| title_full | A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. |
| title_fullStr | A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. |
| title_full_unstemmed | A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. |
| title_short | A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. |
| title_sort | new method for predicting essential proteins based on participation degree in protein complex and subgraph density |
| url | https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pone.0198998/1/pone.0198998.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210220%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210220T175550Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=556e62128296c547cc1695b57a88fcd174c4fcddeb0b467309931241969f8b4491f2cd3daa0a32abde9f7a9802281aab1db3d76b4fed42a98c4558ec2189dbb9c5eb988f40f169e14c810dc636fcfd4bdb2ab71d1f688028f4fc19245e27a82d705616809461353fcf4c7380a8f2364727e592a1b41dcbf54d26654e216884405c866947c075d1989f3ff38f022c53ed9155d74fc051a5c06f479b842b78dac1ba7bda025afe67777da5e3d43f73bd87e674e1c144cefa0d671d03a52eca0dd143feb0312b8524179ce89d2698f9f4229a85cb6929082ceedad6c50bd426d1c0c17293776d19901930069334e99289e324eb3c43b29006c71faf06de075e084b |
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