Predicting protein-protein interactions between human and hepatitis C virus via an ensemble learning method

Molecular BioSystems

Volumn 10, Issue 12, 2014, Pages 3147-3154

  Emamjomeh, Abbasali ^a   Goliaei, Bahram ^a   Zahiri, Javad ^a,b   Ebrahimpour, Reza ^c  

^a UNIVERSITY OF TEHRAN   (Iran)

^b K N TOOSI UNIVERSITY OF TECHNOLOGY   (Iran)

^c SHAHID RAJAEE TEACHER TRAINING UNIVERSITY   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

HEPATITIS C VIRUS;

AMINO ACID; PROTEIN; VIRUS PROTEIN;

ALGORITHM; BAYES THEOREM; BIOLOGY; CHEMISTRY; HEPACIVIRUS; HOST PATHOGEN INTERACTION; HUMAN; PROCEDURES; PROTEIN ANALYSIS; PROTEIN PROCESSING; SUPPORT VECTOR MACHINE;

ALGORITHMS; AMINO ACIDS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; HEPACIVIRUS; HOST-PATHOGEN INTERACTIONS; HUMANS; PROTEIN INTERACTION MAPPING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; SUPPORT VECTOR MACHINES; VIRAL PROTEINS;

EID: 84908405706     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c4mb00410h     Document Type: Article

References (58)

1. J. E. McDermott D. L. Diamond C. Corley A. L. Rasmussen M. G. Katze K. M. Waters Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis BMC Syst. Biol. 2012 6 28
2. T. Wilkins J. K. Malcolm D. Raina R. R. Schade Hepatitis C: Diagnosis and Treatment Am. Fam. Physician 2010 81 1351 1357
3. B. De Chassey V. Navratil L. Tafforeau M. Hiet A. Aublin-Gex S. Agaugue et al., Hepatitis C virus infection protein network Mol. Syst. Biol. 2008 4 10.1038/msb.2008.66
4. A. S. Nishiya C. de Almeida-Neto S. C. Ferreira C. S. Alencar C. Di-Lorenzo-Oliveira J. E. Levi et al., HCV Genotypes, Characterization of Mutations Conferring Drug Resistance to Protease Inhibitors, and Risk Factors among Blood Donors in São Paulo, Brazil PLoS One 2014 9 e86413
5. X. Fan B. Xue P. T. Dolan D. J. LaCount L. Kurgan V. N. Uversky The intrinsic disorder status of the human hepatitis C virus proteome Mol. BioSyst. 2014 10 1345 1363
6. P. Evans W. Dampier L. Ungar A. Tozeren Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs BMC Med. Genomics 2009 2 27
7. J.-N. Tournier A. Quesnel-Hellmann Host-Pathogen Interactions: A Biological Rendez-Vous of the Infectious Nonself and Danger Models? PLoS Pathog. 2006 2 e44
8. P. T. Dolan C. Zhang S. Khadka V. Arumugaswami A. D. Vangeloff N. S. Heaton et al., Identification and comparative analysis of hepatitis C virus-host cell protein interactions Mol. BioSyst. 2013 9 3199 3209
9. J. M. Doolittle S. M. Gomez Mapping protein interactions between Dengue virus and its human and insect hosts PLoS Neglected Trop. Dis. 2011 5 e954
10. C. Zhao and A. Sacan, Prediction of HIV-1 and human protein interactions based on a novel evolution-aware structure alignment method, Biocomp2013, 2013
11. M. R. Arkin J. A. Wells Small-molecule inhibitors of protein-protein interactions: progressing towards the dream Nat. Rev. Drug Discovery 2004 3 301 317
12. A. Mukhopadhyay S. Ray U. Maulik Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach BMC Bioinf. 2014 15 26
13. H. Zhou J. Jin L. Wong Progress in computational studies of host-pathogen interactions J. Bioinf. Comput. Biol. 2013 11 10.1142/S0219720012300018
14. J. Zahiri J. Hannon Bozorgmehr A. Masoudi-Nejad Computational Prediction of Protein-Protein Interaction Networks: Algorithms and Resources Curr. Genomics 2013 14 397 414
15. O. Krishnadev N. Srinivasan Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria Int. J. Biol. Macromol. 2011 48 613 619
16. S. Wuchty Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens PLoS One 2011 6 e26960
17. J. M. Doolittle S. M. Gomez Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens Virol. J. 2010 7 82
18. M. D. Dyer T. Murali B. W. Sobral Computational prediction of host-pathogen protein-protein interactions Bioinformatics 2007 23 i159 i166
19. M. D. Dyer T. Murali B. W. Sobral Supervised learning and prediction of physical interactions between human and HIV proteins Infect., Genet. Evol. 2011 11 917 923
20. Y. Qi O. Tastan J. G. Carbonell J. Klein-Seetharaman J. Weston Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins Bioinformatics 2010 26 i645 i652
21. G. Cui C. Fang K. Han Prediction of protein-protein interactions between viruses and human by an SVM model BMC Bioinf. 2012 13 S5
22. S. Kerrien B. Aranda L. Breuza A. Bridge F. Broackes-Carter C. Chen et al., The IntAct molecular interaction database in 2012 Nucleic Acids Res. 2012 40 D841 D846
23. J. Yu M. Guo C. Needham Y. Huang L. Cai D. Westhead Simple sequence-based kernels do not predict protein-protein interactions Bioinformatics 2010 26 2610 2614
24. Y. Park E. M. Marcotte Revisiting the negative example sampling problem for predicting protein-protein interactions Bioinformatics 2011 27 3024 3028
25. S. Kawashima P. Pokarowski M. Pokarowska A. Kolinski T. Katayama M. Kanehisa AAindex: amino acid index database, progress report 2008 Nucleic Acids Res. 2008 36 D202 D205
26. J. C. Dunn Well-separated clusters and optimal fuzzy partitions Journal of Cybernetics 1974 4 95 104
27. K. C. Chou Prediction of protein cellular attributes using pseudo-amino acid composition Proteins: Struct., Funct., Bioinf. 2001 43 246 255
28. K.-C. Chou Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology Curr. Proteomics 2009 6 262 274
29. Y. Xu X. Wen X.-J. Shao N.-Y. Deng K.-C. Chou iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition Int. J. Mol. Sci. 2014 15 7594 7610
30. C. Chen L. Chen X. Zou P. Cai Prediction of protein secondary structure content by using the concept of Chou's pseudo amino acid composition and support vector machine Protein Pept. Lett. 2009 16 27 31
31. J. Guo N. Rao G. Liu Y. Yang G. Wang Predicting protein folding rates using the concept of Chou's pseudo amino acid composition J. Comput. Chem. 2011 32 1612 1617
32. L. Yu Y. Guo Y. Li G. Li M. Li J. Luo et al., SecretP: Identifying bacterial secreted proteins by fusing new features into Chou's pseudo-amino acid composition J. Theor. Biol. 2010 267 1 6
33. H.-B. Shen K.-C. Chou PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition Anal. Biochem. 2008 373 386 388
34. J. Zahiri O. Yaghoubi M. Mohammad-Noori R. Ebrahimpour A. Masoudi-Nejad PPIevo: Protein-Protein Interaction Prediction from PSSM Based Evolutionary Information Genomics 2013 237 242 10.1016/j.ygeno.2013.05.006
35. S. Altschul T. Madden A. Schffer J. Zhang Z. Zhang W. Miller D. Lipman Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res. 1997 25 3389 3402
36. Y. Assenov F. Ramírez S.-E. Schelhorn T. Lengauer M. Albrecht Computing topological parameters of biological networks Bioinformatics 2008 24 282 284
37. M. E. Smoot K. Ono J. Ruscheinski P. L. Wang T. Ideker Cytoscape 2.8: new features for data integration and network visualization Bioinformatics 2011 27 431 432
38. A. Chatr-aryamontri B.-J. Breitkreutz S. Heinicke L. Boucher A. Winter C. Stark et al., The BioGRID interaction database: 2013 update Nucleic Acids Res. 2013 41 D816 D823
39. A. Zhang, Protein interaction networks: computational analysis, Cambridge University Press, 2009
40. L. C. Freeman A set of measures of centrality based on betweenness Sociometry 1977 35 41
41. O. Tastan, Y. Qi, J. G. Carbonell and J. Klein-Seetharaman, Prediction of interactions between HIV-1 and human proteins by information integration, Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing, NIH Public Access, 2009. p. 516
42. T. S. Keshava Prasad R. Goel K. Kandasamy S. Keerthikumar S. Kumar S. Mathivanan et al., Human Protein Reference Database7#x2013;2009 update Nucleic Acids Res. 2009 37 D767 D772
43. H. Kontaki I. Talianidis Cross-talk between post-translational modifications regulates life or death decisions by E2F1 Cell Cycle 2010 9 3836 3837
44. J. Woodsmith A. Kamburov U. Stelzl Dual Coordination of Post Translational Modifications in Human Protein Networks PLoS Comput. Biol. 2013 9 e1002933
45. L. Kuncheva, Combining Pattern Classifiers: Methods and Algorithms, 2004
46. I. Saha J. Zubek T. Klingström S. Forsberg J. Wikander M. Kierczak et al., Ensemble learning prediction of protein-protein interactions using proteins functional annotations Mol. BioSyst. 2014 10 820 830
47. I. H. Witten, E. Frank and M. A. Hall, Data Mining: Practical machine learning tools and techniques, Morgan Kaufmann Publishers Inc, San Francisco, 2011
48. M. Ashburner C. A. Ball J. A. Blake D. Botstein H. Butler J. M. Cherry et al., Gene Ontology: tool for the unification of biology Nat. Genet. 2000 25 1 25 29
49. M. Kanehisa S. Goto Y. Sato M. Kawashima M. Furumichi M. Tanabe Data, information, knowledge and principle: back to metabolism in KEGG Nucleic Acids Res. 2014 42 D1 D199 D205
50. D. Croft A. F. Mundo R. Haw M. Milacic J. Weiser G. Wu et al., The Reactome pathway knowledgebase Nucleic Acids Res. 2014 42 D1 D472 D477
51. Z. Lu, X. Wu, X. Zhu and J. Bongard, Ensemble pruning via individual contribution ordering, Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining, ACM, 2010
52. B. T. S. Da Wei Huang R. A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 2008 4 1 44 57
53. Y. Benjamini Y. Hochberg Controlling the false discovery rate: a practical and powerful approach to multiple testing Journal of the Royal Statistical Society. Series B (Methodological) 1995 289 300
54. R. M. Memmott P. A. Dennis Akt-dependent and-independent mechanisms of mTOR regulation in cancer Cell. Signalling 2009 21 5 656 664
55. I. Letunic T. Doerks P. Bork SMART 7: recent updates to the protein domain annotation resource Nucleic Acids Res. 2012 40 D1 D302 D305
56. S. Pietrokovski J. G. Henikoff S. Henikoff The Blocks database-a system for protein classification Nucleic Acids Res. 1996 24 1 197 200
57. R. D. Finn A. Bateman J. Clements P. Coggill R. Y. Eberhardt S. R. Eddy et al., Pfam: the protein families database Nucleic Acids Res. 2013 gkt1223
58. N. Hulo A. Bairoch V. Bulliard L. Cerutti E. De Castro P. S. Langendijk-Genevaux et al., The PROSITE database Nucleic Acids Res. 2006 34 suppl 1 D227 D230