Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions

Bioinformatics
Hon Nian ChuaLimsoon Wong

Abstract

Most approaches in predicting protein function from protein-protein interaction data utilize the observation that a protein often share functions with proteins that interacts with it (its level-1 neighbours). However, proteins that interact with the same proteins (i.e. level-2 neighbours) may also have a greater likelihood of sharing similar physical or biochemical characteristics. We speculate that functional similarity between a protein and its neighbours from the two different levels arise from two distinct forms of functional association, and a protein is likely to share functions with its level-1 and/or level-2 neighbours. We are interested in finding out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction. We made a statistical study on recent interaction data and observed that functional association between level-2 neighbours is clearly observable. A substantial number of proteins are observed to share functions with level-2 neighbours but not with level-1 neighbours. We develop an algorithm that predicts the functions of a protein in two steps: (1) assign a weight to each of its level-1 and level-2 neighbours by estimating its functional simi...Continue Reading

References

Dec 2, 2000·Nature Biotechnology·B SchwikowskiS Fields
Aug 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Xianghong ZhouWing Hung Wong
Mar 7, 2003·Genome Biology·Bobby-Joe BreitkreutzMike Tyers
Mar 29, 2003·Journal of Molecular Biology·Einat SprinzakHanah Margalit
May 13, 2003·Nature Biotechnology·Alexei VazquezAlessandro Vespignani
Oct 21, 2003·Proceedings of the National Academy of Sciences of the United States of America·Manoj Pratim Samanta, Shoudan Liang
Jan 31, 2004·Bioinformatics·Minghua DengTing Chen
Jun 22, 2005·Expert Review of Proteomics·Björn TitzPeter Uetz

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Citations

Apr 23, 2008·Amino Acids·Xing-Ming ZhaoKazuyuki Aihara
Jan 17, 2013·Bulletin of Mathematical Biology·Ashish Saini, Jingyu Hou
Dec 2, 2010·Journal of Proteome Research·Mathieu Lavallée-AdamMathieu Blanchette
Dec 15, 2006·Nature Reviews. Cancer·Pingzhao HuAndrew Emili
Apr 26, 2008·Molecular BioSystems·Troy HawkinsDaisuke Kihara
Oct 30, 2012·IET Systems Biology·S MadaniM Aminghafari
Nov 8, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Aleksandar Stojmirović, Yi-Kuo Yu
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mathieu Lavallée-AdamMathieu Blanchette
Jun 16, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ofer LaviRon Shamir
Apr 9, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hua WangChris Ding
Mar 6, 2012·Omics : a Journal of Integrative Biology·Joan Planas-IglesiasBaldo Oliva
Feb 26, 2009·Briefings in Bioinformatics·Bill AndreopoulosMichael Schroeder
Feb 23, 2007·Bioinformatics·Bill AndreopoulosMichael Schroeder
Jul 25, 2007·Bioinformatics·Sitaram AsurSrinivasan Parthasarathy
Apr 25, 2008·Bioinformatics·Yong LiDilip Rajagopalan
May 14, 2009·Bioinformatics·Guimei LiuHon Nian Chua
Feb 1, 2011·Bioinformatics·Michael SmootSteven Maere
May 10, 2011·Bioinformatics·Jesse Gillis, Paul Pavlidis
Jan 15, 2013·Bioinformatics·Christopher L PoirelT M Murali
Jul 3, 2013·Bioinformatics·Carlo Vittorio CannistraciTimothy Ravasi
May 30, 2012·Nucleic Acids Research·Mark N WassMichael J E Sternberg
Mar 8, 2008·Journal of Bioinformatics and Computational Biology·Cao NguyenKrzysztof J Cios
Jun 25, 2008·Journal of Bioinformatics and Computational Biology·Hon Nian ChuaLimsoon Wong
Dec 18, 2008·Journal of Bioinformatics and Computational Biology·Yonghui Wu, Stefano Lonardi
Feb 20, 2009·Journal of Bioinformatics and Computational Biology·Lin GaoJia Song
Dec 2, 2010·Journal of Bioinformatics and Computational Biology·Nassim Sohaee, Christian V Forst
Nov 16, 2011·Journal of Bioinformatics and Computational Biology·Jingyan Wang, Yongping Li
Oct 7, 2011·Journal of Bioinformatics and Computational Biology·Kaushal DesaiAnastasia Christianson
Apr 23, 2013·Journal of Bioinformatics and Computational Biology·Sriganesh Srihari, Hon Wai Leong
Jul 19, 2013·Journal of Bioinformatics and Computational Biology·Jingyu Hou, Yongqing Jiang
Jun 3, 2009·BMC Bioinformatics·Min WuSee-Kiong Ng
Jan 2, 2010·BMC Bioinformatics·Marcelo M BrandãoMarcio C Silva-Filho
Jan 5, 2010·BMC Bioinformatics·Leander SchietgatSaso Dzeroski
Aug 5, 2010·BMC Bioinformatics·Chia-Ying Cheng, Yuh-Jyh Hu

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