Title: FUNCTIONAL CENTRALITY: DETECTING LETHALITY OF PROTEINS IN PROTEIN INTERACTION NETWORKS
Abstract: Genome Informatics 2007, pp. 166-177 (2007) Free AccessFUNCTIONAL CENTRALITY: DETECTING LETHALITY OF PROTEINS IN PROTEIN INTERACTION NETWORKSKar Leong Tew, Xiao-Li Li and Soon-Heng TanKar Leong TewKnowledge Discovery Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore, Xiao-Li LiKnowledge Discovery Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore and Soon-Heng TanKnowledge Discovery Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canadahttps://doi.org/10.1142/9781860949852_0015Cited by:10 PreviousNext AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsRecommend to Library ShareShare onFacebookTwitterLinked InRedditEmail Abstract: Identifying lethal proteins is important for understanding the intricate mechanism governing life. Researchers have shown that the lethality of a protein can be computed based on its topological position in the protein-protein interaction (PPI) network. Performance of current approaches has been less than satisfactory as the lethality of a protein is a functional characteristic that cannot be determined solely by network topology. Furthermore, a significant number of lethal proteins have low connectivity in the interaction networks but are overlooked by most current methods. Our work reveals that a protein's lethality correlates more strongly with its "functional centrality" than pure topological centrality. We define functional centrality as the topological centrality within a subnetwork of proteins with similar functions. Evaluation experiments on four Saccharomyces cerevisiae PPI datasets showed that NFC performed significantly better than all the other existing computational techniques. Our method was able to detect low connectivity lethal proteins that were previously undetected by conventional methods. The results and an online version of NFC is available at http://lethalproteins.i2r.a-star.edu.sg Keywords: Lethal proteinsFunctional centralityProtein similarityProtein-protein interaction FiguresReferencesRelatedDetailsCited By 10An Experimental Study on the Scalability of Recent Node Centrality Metrics in Sparse Complex NetworksAlexander J. Freund and Philippe J. Giabbanelli16 February 2022 | Frontiers in Big Data, Vol. 5Network analysis and the impact of Aflibercept on specific mediators of angiogenesis in HUVEC cellsHamid Latifi‐Navid, Zahra‐Soheila Soheili, Shahram Samiei, Mehdi Sadeghi and Sepideh Taghizadeh et al.11 July 2021 | Journal of Cellular and Molecular Medicine, Vol. 25, No. 17Identification of essential proteins based on a new combination of topological and biological features in weighted protein–protein interaction networksAbdolkarim Elahi and Seyed Morteza Babamir1 December 2018 | IET Systems Biology, Vol. 12, No. 6The Features of Low-Connectivity Essential ProteinsYun-Yuan Dong1 Sep 2016Evolution of Centrality Measurements for the Detection of Essential Proteins in Biological NetworksMahdi Jalili, Ali Salehzadeh-Yazdi, Shailendra Gupta, Olaf Wolkenhauer and Marjan Yaghmaie et al.26 August 2016 | Frontiers in Physiology, Vol. 7Identification of important interacting proteins (IIPs) in Plasmodium falciparum using large-scale interaction network analysis and in-silico knock-out studiesMadhumita Bhattacharyya and Saikat Chakrabarti8 February 2015 | Malaria Journal, Vol. 14, No. 1CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality AnalysisMahdi Jalili, Ali Salehzadeh-Yazdi, Yazdan Asgari, Seyed Shahriar Arab and Marjan Yaghmaie et al.16 November 2015 | PLOS ONE, Vol. 10, No. 11Computational approaches to predicting essential proteins: A surveyJianxin Wang, Wei Peng and Fang-Xiang Wu22 January 2013 | PROTEOMICS - Clinical Applications, Vol. 7, No. 1-2Network Analysis to Interpret Complex PhenotypesHong Yu, Jialiang Huang, Wei Zhang and Jing-Dong J. Han21 April 2011A Unified Scoring Scheme for Detecting Essential Proteins in Protein Interaction NetworksHon Nian Chua, Kar Leong Tew, Xiao-Li Li and See-Kiong Ng1 Nov 2008 Genome Informatics 2007Metrics History KeywordsLethal proteinsFunctional centralityProtein similarityProtein-protein interactionPDF download