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A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks
Essential genes play an indispensable role in supporting the life of an organism. Identification of essential genes helps us to understand the underlying mechanism of cell life. The essential genes of bacteria are potential drug targets of some diseases genes. Recently, several computational methods...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356314/ https://www.ncbi.nlm.nih.gov/pubmed/30626157 http://dx.doi.org/10.3390/genes10010031 |
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author | Zhang, Fengyu Peng, Wei Yang, Yunfei Dai, Wei Song, Junrong |
author_facet | Zhang, Fengyu Peng, Wei Yang, Yunfei Dai, Wei Song, Junrong |
author_sort | Zhang, Fengyu |
collection | PubMed |
description | Essential genes play an indispensable role in supporting the life of an organism. Identification of essential genes helps us to understand the underlying mechanism of cell life. The essential genes of bacteria are potential drug targets of some diseases genes. Recently, several computational methods have been proposed to detect essential genes based on the static protein–protein interactive (PPI) networks. However, these methods have ignored the fact that essential genes play essential roles under certain conditions. In this work, a novel method was proposed for the identification of essential proteins by fusing the dynamic PPI networks of different time points (called by FDP). Firstly, the active PPI networks of each time point were constructed and then they were fused into a final network according to the networks’ similarities. Finally, a novel centrality method was designed to assign each gene in the final network a ranking score, whilst considering its orthologous property and its global and local topological properties in the network. This model was applied on two different yeast data sets. The results showed that the FDP achieved a better performance in essential gene prediction as compared to other existing methods that are based on the static PPI network or that are based on dynamic networks. |
format | Online Article Text |
id | pubmed-6356314 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-63563142019-02-04 A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks Zhang, Fengyu Peng, Wei Yang, Yunfei Dai, Wei Song, Junrong Genes (Basel) Article Essential genes play an indispensable role in supporting the life of an organism. Identification of essential genes helps us to understand the underlying mechanism of cell life. The essential genes of bacteria are potential drug targets of some diseases genes. Recently, several computational methods have been proposed to detect essential genes based on the static protein–protein interactive (PPI) networks. However, these methods have ignored the fact that essential genes play essential roles under certain conditions. In this work, a novel method was proposed for the identification of essential proteins by fusing the dynamic PPI networks of different time points (called by FDP). Firstly, the active PPI networks of each time point were constructed and then they were fused into a final network according to the networks’ similarities. Finally, a novel centrality method was designed to assign each gene in the final network a ranking score, whilst considering its orthologous property and its global and local topological properties in the network. This model was applied on two different yeast data sets. The results showed that the FDP achieved a better performance in essential gene prediction as compared to other existing methods that are based on the static PPI network or that are based on dynamic networks. MDPI 2019-01-08 /pmc/articles/PMC6356314/ /pubmed/30626157 http://dx.doi.org/10.3390/genes10010031 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Zhang, Fengyu Peng, Wei Yang, Yunfei Dai, Wei Song, Junrong A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks |
title | A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks |
title_full | A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks |
title_fullStr | A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks |
title_full_unstemmed | A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks |
title_short | A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks |
title_sort | novel method for identifying essential genes by fusing dynamic protein–protein interactive networks |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356314/ https://www.ncbi.nlm.nih.gov/pubmed/30626157 http://dx.doi.org/10.3390/genes10010031 |
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