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A Review on Computational Methods for Protein Complex Detection

D. Ramyachitra, A. Brindhadevi, R. Ranjani Rani

Abstract


In cell biology, the protein complex plays a vital role. The initial step for understanding the protein function is the identification of protein complexes. Protein complex is a form of quaternary structure. It is similar to phosphorylation, and the   complex pattern frequently serve to trigger or reduce one or more of the connected proteins. The protein complexes are predicted from high through-put Protein-Protein Interaction (PPI) dataset. From PPI data, there are three sections of complexes such as Sparse complexes, embedded complexes and Small complexes remains challenging in nature. This paper discussed about the numerous computational methods to solve protein complex detection, tools, protein-protein interaction databases and various performance measures to assess the accuracy of the predicted result.


Keywords


Protein-Protein Interaction, Protein Complex Detection, Protein Complex Algorithm methods, Tools, Databases.

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References


William Andreopoulos, Dirk Labudde, “Protein-Protein Interaction Networks”, Protein Purification and Analysis: Methods and Applications(Book);Iconcept Press,ISBN:978-1-477555-057.

D. Ramyachitra, D. Banupriya, “Protein Complex Detection: A Study”, International Journal of Computer Science and Information Technology & Security. 2014; Vol. 4, Issue.4: ISNN: 2249-9555.

Xiaoyun Sun, Pengyu Hong, Meghana Kulkarni, Young Kwon, Norbert Perrimon, “PPIRank - an advanced method for ranking protein-protein interations in TAP/MS data”, Proteome Sci. 2013;Vol.11: Issue.1:Pages: S16.Doi:10.1186/1477-5956-11-S1-S16.

M. Mary Sujatha, “A Novel Survey on Protein Interaction Networks”, International Journal of Research Studies in Computer Science and Engineering.2015;Vol.2: Issue.3: Pages:53-58.

Bader G,Hogue C, “An automated method for finding molecular complexes in large protein interaction networks”, BMC Bioinformatics 2003, Vol.4: Issue.2:Doi:10.1186/1471-2105-4-2.

Guimin Qinab,Lin Gaoa, “Spectral clustering for detecting protein complexes in protein_protein interaction (PPI) networks”, Mathematical and Computer Modelling.2010;Vol.52:Issues 11-12: Pages 2066-2074.Doi:10.1016/j.mcm.2010.06.015.

Min Wu, Xiaoli Li, Chee-Keong Kwoh: ”Algorithms for Detecting Protein Complexes in PPI Networks: An Evaluation Study”, Suppl(http://www.ntu.edu.sg/home2006/wumi0002/PRIB08.html).

Spirin V,Mirny L, “Protein complexes and functional modules in molecular networks”, Proc Natl Acad Sci USA .2003, Vol.100: Issue.21: Pages:12123–12128.

Tamas Nepusz,Haiyuan Yu, Alberto Paccanaro, “Detecting overlapping protein complexes in ppi networks”, Nat Methods.2012; Vol.9: Issue.5: Pages:471-472.Doi:10.1038/nmeth.1938.

Chern Han Yong, Limsoon Wong, “Prediction of problematic complexes from PPI networks: sparse, embedded, and small Complexes”,Biology Direct.2015;Vol.10:Issue.40: Doi:10.1186/s13062-015-0067-4.

Sriganesh Srihari ,Chern Han Yong , Ashwini Patil , Limsoon Wong, “Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes”,FEBS Letters.2015;Vol.589:Issue.19:Pages:2590–2602.Doi:10.1016/j.febslet.2015.04.026.

Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K and Kanaya S, “Development and implementation of an algorithm for detection of protein complexes in large interaction networks”, BMC Bioinformatics 2006; Vol.7: Pages:207.Doi:10.1186/1471-2105-7-207.

Van Dongen S, “Graph Clustering by Flow Simulation”, Pages:169: ISBN:9039324085,9789039324080,2000.

Ucar D, Asur S, Çatalyürek ÜV, Parthasarathy S, “Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-Induced Subgraphs”, Part of Lecture notes in computer Science.2006; Vol. 4213: Pages:371–382.

Mete M, Tang F, Xu X ,Yuruk N, “A structural approach for finding functional modules from large biological networks”,BMC Bioinformatics.2008; Vol.9: Issue.9:Pages:S19.Doi:10.1186/1471-2105-9-S9-S19.

Navlakha S, Schatz MC,Kingsford C, “Revealing Biological Modules via Graph Summarization”, Journal of Computational Biology.2009; Vol.16: Issue.2: Pages:253–264.Doi:10.1089/cmb.2008.11TT.

Liu GM, Chua HN,Wong L, “Complex discovery from weighted PPI networks”,Bioinformatics.2009;Vol.25:Issue.15:Pages:1891-1897.Doi:10.1093/bioinformatics/btp311.

Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walter T, Krogan NJ, Koller D, “A complex-based reconstruction of the Saccharomyces cerevisiae interactome”, Mol Cell Proteomics.2009;Vol.8:Issue.6:Pages1361-1381.Doi:10.1074/mcp.M800490-MCP200.

Leung HC, Yiu SM, Xiang Q Chin FY, “Predicting Protein Complexes from PPI Data:A Core-Attachment Approach”,Journal of Computational Biology.2009;Vol.16:Issue.2:Pages:133144.Doi:10.1089/cmb.2008011TT.

Henry C.M. Leung, Qian Xiang, S.M. Yiu, And Francis Y.L. Chin:” Predicting Protein Complexes From Ppi Data, “A Core-Attachment Approach”, Journal of Biology.2009; Vol. 16: Pages:133-144, 2009.Doi: 10.1089/cmb.2008011TT.

Wu M, Li XL, Kwoh CK, Ng SK: “A Core-Attachment based Method to Detect Protein Complexes in PPI Networks”, BMC Bioinformatics 2009; Vol.10: Pages:169.Doi:10.1186/1471-2105-10-169.

Sriganesh Srihari, Kang Ning, Hon Wai Leong, MCL-CAW, “A refinement of MCL for detecting yeast complexes from weighted PPi networks by incorporating core attachment structure”,BMC Bioinformatics 2010;Vol.11: Pages:504.Doi:10.1186/147-2105-11-504.

Jung SK, Jang WH , Hur HY, “Protein complex prediction based on mutually exclusive interactions in protein interaction network”, Genome Inform. 2008; Vol.21 Pages:77-88.

Li XL, Tan SH, Foo CS ,Ng SK, “Interaction Graph Mining for Protein Complexes Using Local Clique Merging”,Genome Inform.2005; Vol.16: Issue.2: Pages:260-269.

Eileen Marie Hanna,Nazar Zaki, ”Detecting overlapping protein complexes using a protein ranking algorithm”, Innovations in InformationTechnology(IIT)2013;Doi:10.1109/Innovations.2013.6544424.

Feng J, Jiang R,Jiang T, “A Max-Flow Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data”, Comput Syst Bioinformatics Conf.2008; Vol.7: Pages:51-62.

Maraziotis I, Dimitrakopoulou K , Bezerianos A, “Growing functional modules from a seed protein via integration of protein interaction and gene expression data”,BMC Bioinformatics 2007; Vol.8: Pages:408.Doi:10.1186/1471-2105-8-408.

Ulitsky I, Shamir R, “Identification of functional modules using network topology and high-throughput data”, BMC Systems Biology 2007; Vol.1: Pages:8. Doi:10.1186/1752-0509-1-8.

Suk Hoon Jung, Bora Hyun, Woo-Hyuk Jang, Hee-Young Hur, Dong-Soo Han, “Protein complex prediction based on simultaneous protein interaction network”, Bioinformatics.2010;Vol.26: Issue.3: Pages:385-391. Doi:10.1093/bioinformatics/btp668.

Thorsten Will,Volkhard Helms, “Mutual exclusion of proteins” , ECCB.2014;Vol.30:Pages:i415-421.Doi:10.1093/bioinformatics/btu448.

Kalaev M1, Smoot M, Ideker T, Sharan R, “NetworkBLAST: comparative analysis of protein networks”, Bioinformatics.2008; Vol.24: Issue.4: Pages:594-596. Doi:10.1093/bioinformatics/btr.

Roded Sharan, Amiram Wingarten,Stas Levin:“Protein-protein Interaction: Network Alignment”, 2009.

Phi-Vu Nguyen, Sriganesh Srihari, Hon Wai Leong, “Identifying conserved protein complexes between species by constructing interolog networks”,BMC Bioinformatics.2013;Vol.14:Issue.16: Pages:S8. Doi:10.1186/1471-2105-14-S16-S8.

Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V ,Sharan R, “QNet: A Tool for Querying Protein Interaction Networks”, J Comput Biol. 2008; Vol.15: Issue.7: Pages:913-925.Doi:10.1089/cmb.2007.0172.

King A, Przulj N and Jurisica I, “Protein complex prediction via cost-based clustering”, Bioinformatics 2004; Vol.20: Issue.17: Pages:3013–3020.Doi:10.1093/bioinformatics/bth.

Hon Nian Chua, Kang Ning, Wing-Kin Sung,Hon Wai Leong, Limsoon Wong, “Using Indirect Protein-Protein Interactions for Protein Complex Prediction”, J Bioinform Comput Biol. 2008; Vol.6: Issue.3: Pages:435-466.

Chua HN, Ning K, Sung WK, Leong HW,Wong L, “Using indirect protein-protein interactions for protein complex prediction”, Comput Syst Bioinformatics Conf. 2007; Vol.6: Pages:97–109.

Li X, Foo CS, Ng SK, “ Discovering protein complexes in dense reliable neighborhoods of protein interaction networks”, Comput Syst Bioinformatics Conf. 2007; Vol.6: Pages:157–168.

Min Li, Jian-er Chen,Jian-Xin Wang,Bin Hu and Gang Chen, “Modifying the DPClus algorithm for identifying protein complexes based on new topologicalstructures”, BMC Bioinformatics. 2008 Vol.9: Pages:398.Doi:10.1186/1471-2105-9-398.

Lubovac Z, Gamalielsson J,Olsson B, “Combining Functional and Topological Properties to Identify Core Modules in Protein Interaction Networks”,Proteins.2006;Vol.64:Issue.4:Pages:948-959. Doi:10.1002/prot.21071.

Cho Y, Hwang W, Ramanathan M and Zhang A, “Semantic integration to identify overlapping functional modules in protein interaction networks”, BMC Bioinformatics.2007, Vol.8: Pges:265.Doi:10.1186/1471-2105-8-265.

Chern Han Yong, Guimei Liu,Hon Nian Chua ND Limsoon Wong, ”Supervised maximum-likelihood weighting of composite protein networks for complex prediction”, BMC System Biology.2012; Vol.6: Issue.2:Pages:S13.Doi:10.1186/1752-0509-6-S2-S13.

Chern Han Yong, Osamu Mruyama,Limsoon Wong, “Discovery of small protein complexes from PPI networks with size-specific supervised weighting”, BMC Syst Biol.2014; Vol.8: Issue.5: Pages:S3.

Le Ou-Yang,Dao-Qing Dai,Xiao-Li Li,Min Wu,Xiao-Fei Zhang, Peng Yang, “Detecting temporal protein complexes from dynamic protein-protein interaction networks”, BMC Bioinformatics.2014; Vol.15: Pages:335.Doi:10.1186/1471-2105-15-335.

Le Ou-Yang,Min Wu,Xiao-Fei Zhang,Dao-Qing Dai,Xiao-Li, Yan, “A two-layer integration framework for protein complex detection”,BMCBioinformatic.2016;Vol.17:Pages:100.Doi:10.1186/s12859-016-0939-3.

Pizzuti C, Rombo SE, “A coclustering approach for mining large protein-protein interaction networks”, IEEE/ACM Trans Comput BioL Bioinform.2012 May-Jun; Vol.9: Issue.3 Pages:717-730. Doi: 10.1109/TCBB.2011.158.

Becker E1, Robisson B, Chapple CE, Guénoche A, Brun C, “Multifunctional proteins revealed by overlapping clustering in protein interaction network”, Bioinformatics. 2012 Jan ; Vol.28: Issue.1 Pages:84-90.Doi:10.1093/bioinformatics/btr621.

Tadaka S, Kinoshita K, “NCMine: Core-peripheral based functional module detection using near-clique mining”, Bioinformatics. 2016 Nov ; Vol.32: Issue.22: Pages:3554-3460.Doi:10.1093/bioinformatics/btw488.

Yanjun Qi, Fernanda Balem,Christos Faloutsos,Judith Klein-Seetharaman, Ziv Bar-Joseph, “Protein complex identification by supervised graph local clustering”, ISMB 2008; Vol.24: Issue.13: Pages:i250-i258. Doi: 10.1093/bioinformatics/btn164.

Mario Cannataro, Pietro H. Guzzi , Pierangelo Veltri, “IMPRECO: Distributed prediction of protein complexes”, Future Generation Computer Systems. 2010 Mar; Vol.26: Issue.3: Pages:434-440. Doi:10.1016/j.fiture.2009.08.001.

Charalampos N Moschopoulos, Georgios A Pavlopoulos,Reinhard Schneider, Spiridon D Likothanassis and Sophia Kossida, “GIBA: a clustering tool for detecting protein complexes”, BMC Bioinformatics 2009; Vol.10: Issue.6: Pages:S11. Doi:10.1186/1471-2105-10-S6-S11.

Jan Krumsiek, Caroline C. Friedel and Ralf Zimmer, “ProCope:protein complex prediction and evaluation” , Bioinformatics 2008; Vol.24: Issue.18: Pages:2115–2116. Doi:10.1093/bioinforatics/btn376.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T, “ Cytoscape: a software environment for integrated models of biomolecular interaction networks”, Genome Res. 2003 Nov; Vol.13: Issue.11:Pages:2498-2504. Doi:10.1101/gr.1239303.

Brian P. Kelley, Bingbing Yuan, Fran Lewitter, Roded Sharan, Brent R. Stockwell, Trey Ideker, “PathBLAST: a tool for alignment of protein interaction networks”, Nucleic Acids Res.2004; Vol. 32: Pages: W83-W88.Doi:10.1093/nar/gkh411.

Balazs Adamcsek,Gergely Palla.Illes J.Farkas,Imre Derenyi,Tamas Vicsek, “CFinder: locating cliques and overlapping modules in biological networks”, Bioinformatics 2006 Apr; Vol.22: Issue.8: Pages:1021-1023.Doi:10.1093/bioinformatics/btl039.

Mehmet E Turanalp,Tolga Can, “Discovering functional interaction patterns in protein-protein interaction networks”, BMC Bioinformatics 2008 Jun; Vol.9: Issue.276: Doi: 10.1186/1471-2105-9-276.

He M, Wang Y, Li W, “PPI finder: a mining tool for human protein-protein interactions”,PLoS One.2009;Vol.4: Isuue.2:Pages:e4554.Doi: 10.1371/journal.pone.0004554.

William E. Payne, James L. Garrels, “The Yeast Protein Database (YPD): Curated proteome database for Saccharomyces cerevisiae”, Nucleic Acids Res. 1997; Vol.25: Issue.1: Pages:57-62.Doi:10.1093/nar/25.1.57.

Luana Licata,Leonardo Briganti,Daniele Peluso,Livia Perfetto,Marta Lannuccelli et al., “MINT: The molecular interaction database”, Nucleic Acids Res. 2012 Jan; Vol.40: Pages:D857-D861.Doi:10.1093/nar/gkr930.

Orchard S, Ammari M et al., “The INTACT project-intact as a common curation platform for moleculer interaction databases”, Nucleic Acids Res. 2014 jan; Vol.42: Pages:D358-363.Doi:10.1093/nar/gkt1115.

http://www.ihop-net.org/

Carlos Prieto, Javier De Las Rivas, “APID:Agile Protein Interaction Data Analyzer”, Nucleic Acids Res.2006 Vol.34: Pages:W298-W302.Doi:10.1093/nar/gkl128.

WWW.dip.doe-mbi.ucla.edu

WWW.bind.ca/‎

WWW.thebiogrid.org/‎

Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, Warfsmann J,Ruepp A, “MIPS: analysis and annotation of proteins from whole genomes.” Nucleic Acids Res 2004 Jan; Vol. 32: Pages:D41-D44.

wilab.inha.ac.kr/hpid/‎

www.droidb.org/‎

WWW.string-db.org/‎

http://www.ncbi.nlm.nih.gov/projects/RefSeq/HIVInteractions /

Mark J. Cowley,Mark Pinese,Karin S.Kassahn,Nic Waddell,John V.Pearson,Sean M.Grimmond,Andrew V.Biankin,Sampsa Hautaniemi,Jianmin Wu, “PINA V2.0:Mining Interactome Modules”, Nucleic Acids Res.2012 Jan; Vol.40:Pages:D862-D865, Doi:10.1093/nar/gkr967.


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