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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...

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Detalles Bibliográficos
Autores principales: Zhang, Fengyu, Peng, Wei, Yang, Yunfei, Dai, Wei, Song, Junrong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
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.
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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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