Spotlight: Assembly of protein complexes by integrating graph clustering methods

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Please use this identifier to cite or link to this item: https://ir.lib.ncu.edu.tw/handle/987654321/107299

Title:	Spotlight: Assembly of protein complexes by integrating graph clustering methods
Authors:	何錦文;Chin, Chia-Hao;Chen, Shu-Hwa;Chen, Chun-Yu;Hsiung, Chao A.;Ho, Chin-Wen;Ko, Ming-Tat;Lin, Chung-Yen
Contributors:	資訊電機學院資訊工程學系
Keywords:	Algorithm;Algorithms;Cluster Analysis;Fungal Proteins;Fungal Proteins - genetics;Fungal Proteins - metabolism;genetics;Internet;metabolism;methods;Network biology;Protein complex;Protein Interaction Mapping;Protein Interaction Mapping - methods;proteins;RNA Splicing;Software;Topology;yeasts
Date:	2013-04-10
Issue Date:	2026-04-23 14:06:42 (UTC+8)
Publisher:	Elsevier;Netherlands: Elsevier B.V
Abstract:	摘要： As is generally assumed, clusters in protein–protein interaction (PPI) networks perform specific, crucial functions in biological systems. Various network community detection methods have been developed to exploit PPI networks in order to identify protein complexes and functional modules. Due to the potential role of various regulatory modes in biological networks, a single method may just apply a single graph property and neglect communities highlighted by other network properties. This work presents a novel integration method to capture protein modules/protein complexes by multiple network features detected by different algorithms. The integration method is further implemented in a web-based platform with a highly effective interactive network analyzer. Conventionally adopted methods with different perspectives on network community detection (e.g., CPM, FastGreedy, HUNTER, MCL, LE, SpinGlass, and WalkTrap) are also executed simultaneously. Analytical results indicate that the proposed method performs better than the conventional ones. The proposed approach can capture the transcription and RNA splicing machineries from the yeast protein network. Meanwhile, proteins that are highly associated with each other, yet not described in both machineries are also identified. In sum, a protein that is closely connected to components of a known module or a complex in the network view implies the functional association among them. Importantly, our method can detect these unique network features, thus facilitating efforts to discover unknown components of functional modules/protein complexes. Availability: Spotlight is freely accessible at http://hub.iis.sinica.edu.tw/spotlight. Video clips for a quick view of usage are available in the website online help page. [Display omitted] ► Capture protein modules/complexes by different topological algorithms. ► Discover unknown components of functional modules/protein complexes. ► The integration method is further implemented in a web-based platform. ► Website: http://hub.iis.sinica.edu.tw/spotlight. 其他題名： Gene 出版者： Netherlands: Elsevier B.V 出版日期： 2013-04-10 出處： Gene, 2013-04, Vol.518 (1), p.42-51 版權： 2012 版權： Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved. 識別號： ISSN: 0378-1119 識別號： ISSN: 1879-0038 識別號： EISSN: 1879-0038 識別號： DOI: 10.1016/j.gene.2012.11.087 識別號： PMID: 23274651
Appears in Collections:	[Department of Computer Science and information Engineering] journal & Dissertation

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