Computer Science ›› 2014, Vol. 41 ›› Issue (Z11): 399-402.

Previous Articles     Next Articles

Link Prediction in Uncertain Protein-Protein Interaction Network

ZHANG Yue-yang and LIU Wei   

  • Online:2018-11-14 Published:2018-11-14

Abstract: Prediction of protein-protein interaction network is an important research content in post-genomic era.So far,the forecast for the PPI network interactions are assuming that the interaction is determined.However,protein-protein interaction networks and other biological data because of the limitations of the experiment test and presents the uncertainty.Put forward a kind of based on the uncertainty of information dissemination PPI network link prediction algorithm.We according to their appearance on each vertex to link the probability that defines the link information,the algorithm will be on the edge of the link information to spread at a certain probability on the diagram.We set for testing using the standard data,the experimental results show that the proposed algorithm,has good accuracy and good biometric features.

Key words: Protein-protein interaction network,Uncertain PPI network,Information dissemination,Link information

[1] 沈瑶瑶,严庆丰.蛋白质相互作用研究进展[J].生命科学,2013,5(3):269-274
[2] Sehaerer M T,Kannenberg K,Hunziker P,et al.Interaction between GABA(A) receptor beta subunits and the multifunctional protein gC1q-R[J].Biol.Chem,2001,6(28):26597-2660
[3] Gavin AC,Aloy P,Grandi P,et al.Superti-Furga G.Proteome Survey Reveals Modularity of the Yeast Cell Machinery[J].Nature,2006,0(7084):631-636
[4] Tong A H,Drees B,et al.A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules[J].Science,2002,5(5553):321-324 (下转第418页)(上接第402页)
[5] Dandekar T,Snel B,Huynen M,et al.Conservation of Gene Order:A Fingerprint of Proteins that Physically Interact[J].Science,1998,3(9):324-328
[6] Marcotte E M,Pellegrini M,Ng H L,et al.Detecting ProteinFunction and Protein-Protein Interactions from Genome Sequences [J].Science,1999,5(5428):751-753
[7] Enright A J,Iliopoulos I,Kyrpides N C,et al.Protein Interactions Maps for Complete Genomes Based on Gene Fusion Events[J].Nature,1999,2(6747):86-90
[8] Pellegrini M,Marcotte E M,Thompson M J,et al.AssigningProtein Functions by Comparative Genome Analysis:Protein Phylogenetic Profiles[J].Proc.Natl.Acad.Sci.USA,1999,96(8):4285-4288
[9] Pazos F,Valencia A.In Silico Two-Hybrid System for the Selection of Physically Interacting Protein Pairs[J].Proteins:Structure,Function and Genetics,2002,7(2):219-227
[10] Goh C S,Bogan A A,Joachimiak M,et al.Co-evolution of Proteins with their interaction Partners[J].J Mol Biol,2000,299(2):283-293
[11] Martin S,Roe D,Faulon J L.Predicting Protein-Protein Interactions Using Signature Products[J].Bioinformatics,2005,1(2):218-226
[12] Shen J,Zhang J,Luo X,et al.Predicting Protein-Protein Interactions Based Only on Sequences Information[J].PNAS,2007,4(11):4337-4341
[13] Guo Y,Yu L,Wen Z,et al.Using Support Vector Machine Combined with Auto Covariance to Predict Protein-Protein Interactions from Protein Sequences[J].Nucleic.Acids.Res.,2008,6(9):3025-3030
[14] Gomez S M,Lo S H,Rzhetsky A.Probabilistic Prediction of Unknown Metabolic and Signal-Transduction Networks[J].Gene-tics,2001,9(3):1291-1298
[15] Gomez S M,Noble W S,Rzhetsky A.Learning to Predict Protein-Protein Interactions from Protein Sequences[J].Bioinformaties,2003,9(15):1875-1881
[16] Deng M,Mehta S,Sun F,et al.Inferring Domain-Domain Interactions from Protein-Protein Interactions[J].Genome Research,2002,2(10):1540-1548
[17] Ryan N.Lichtenwalter.New Precepts and Method in Link Prediction[C]∥Proceedings of ACM KDD’10.2010:243-252
[18] Lv Lin-yuan,ZhouTao.Link Prediction in Complex Networks:A survey[J].Physica A,2011,390:1150-1170
[19] 吕琳媛.复杂网络链路预测[J].电子科技大学学报,2010,39(5):651-661
[20] Bader J S,Chaudhuri A,Rithberg J M,et al.Gaining Confidence in High-Throughput Protein Interaction Networks [J].Nature Biotechnology,2003,22(1):78-75
[21] Asthana S,King O D,Gibbons F D,et al.Predicting ProteinComplex Membership using Probabilistic Network Reliability [J].Genome Research,2004,14(6):1170-1175
[22] Suthram S,Shlomi T,Ruppin E,et al.A Direct Comparison of Protein Interaction Confidence Assignment Schemes [J].BMC Bioinformatics,2006,7(1):360
[23] Jensen L J,Kuhn M,Stark M,et al.STRING 8-a Global View on Proteins and Their Functional Interactions in 630 Organisms [J].Nucleic Acids Research,2009,37:412-416
[24] Erdos P,Renyi A.On the Evolution of Random Graphs[J].Publ.Math.Inst.Hung.Acad.Sci.,1960,5:17-60
[25] Zou Z,Li J,Gao H,et al.Mining Frequent Subgraph Patterns from Uncertain Graph Data [J].IEEE Transactions on Know-ledge and Data Engineering,2010,2(9):1203-1218
[26] Zou Z,Gao H,Li J.Discovering Frequent Subgraph over Uncer-tain Graph Database under Probabilistic Semantics[C]∥ACM SIGKDD Conf.on Knowledge Discovery and Data Mining (KDD).New York,USA,ACM,2010:633-642
[27] Li J,Zou Z,Gao H.Finding Top-k Maximum Cliques in an Uncertain Graph[C]∥Proceedings of 26th International Conf.on Data Engineering.2010:649-652
[28] Parapetrou O,Ioannou E,Skoutas D.Efficient Discovery of Frequent Subgraph Patterns in Uncertain Graph[C]∥Proceedings of the 14th International Conf.on Extending Database Technology.New York,USA,CAN,2011,5-366
[29] Jin R,Liu L,Aggarwal C C.Discovering Highly Reliable Subgraphs in Uncertain Graphs[C]∥ACM SIGKDD Conf.on Knowledge Discovery and Data Mining (KDD).New York,USA,ACM,2011,992-1000
[30] Kollios G,Potamias M,Terzi E.Clustering Large Probabilistic Graph[J].IEEE Transactions on Knowledge and Data Engineering,2012
[31] Yan Xi-feng,Zhou X J,Han Jia-wei.Mining Closed RelationalGraphs with Connectivity Constraints[C]∥Proc of the 11th ACM SIGKDD International Conference on Knowledge Disco-very in Data Mining.New York:ACM Press,2005,324-333
[32] Krogan N J,Cagney G,et al.Global Landscape of Protein Complexes in theYeastSaccharomyces Cerevisiae[J].Nature,2006,440(7084):637-643

No related articles found!
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!