Predicting essential proteins by integrating orthology, gene expressions, and PPI networks.
Identifying essential proteins is very important for understanding the minimal requirements of cellular life and finding human disease genes as well as potential drug targets. Experimental methods for identifying essential proteins are often costly, time-consuming, and laborious. Many computational...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5892885?pdf=render |
| _version_ | 1819163398966870016 |
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| author | Xue Zhang Wangxin Xiao Xihao Hu |
| author_facet | Xue Zhang Wangxin Xiao Xihao Hu |
| author_sort | Xue Zhang |
| collection | DOAJ |
| description | Identifying essential proteins is very important for understanding the minimal requirements of cellular life and finding human disease genes as well as potential drug targets. Experimental methods for identifying essential proteins are often costly, time-consuming, and laborious. Many computational methods for such task have been proposed based on the topological properties of protein-protein interaction networks (PINs). However, most of these methods have limited prediction accuracy due to the noisy and incomplete natures of PINs and the fact that protein essentiality may relate to multiple biological factors. In this work, we proposed a new centrality measure, OGN, by integrating orthologous information, gene expressions, and PINs together. OGN determines a protein's essentiality by capturing its co-clustering and co-expression properties, as well as its conservation in the evolution process. The performance of OGN was tested on the species of Saccharomyces cerevisiae. Compared with several published centrality measures, OGN achieves higher prediction accuracy in both working alone and ensemble. |
| first_indexed | 2024-12-22T17:43:30Z |
| format | Article |
| id | doaj.art-748d540819e340dd8307f7b50d244945 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T17:43:30Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-748d540819e340dd8307f7b50d2449452022-12-21T18:18:21ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01134e019541010.1371/journal.pone.0195410Predicting essential proteins by integrating orthology, gene expressions, and PPI networks.Xue ZhangWangxin XiaoXihao HuIdentifying essential proteins is very important for understanding the minimal requirements of cellular life and finding human disease genes as well as potential drug targets. Experimental methods for identifying essential proteins are often costly, time-consuming, and laborious. Many computational methods for such task have been proposed based on the topological properties of protein-protein interaction networks (PINs). However, most of these methods have limited prediction accuracy due to the noisy and incomplete natures of PINs and the fact that protein essentiality may relate to multiple biological factors. In this work, we proposed a new centrality measure, OGN, by integrating orthologous information, gene expressions, and PINs together. OGN determines a protein's essentiality by capturing its co-clustering and co-expression properties, as well as its conservation in the evolution process. The performance of OGN was tested on the species of Saccharomyces cerevisiae. Compared with several published centrality measures, OGN achieves higher prediction accuracy in both working alone and ensemble.http://europepmc.org/articles/PMC5892885?pdf=render |
| spellingShingle | Xue Zhang Wangxin Xiao Xihao Hu Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. PLoS ONE |
| title | Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. |
| title_full | Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. |
| title_fullStr | Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. |
| title_full_unstemmed | Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. |
| title_short | Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. |
| title_sort | predicting essential proteins by integrating orthology gene expressions and ppi networks |
| url | http://europepmc.org/articles/PMC5892885?pdf=render |
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