Identification of potential host proteins for influenza A virus based on topological and biological characteristics by proteome-wide network approach

Journal of Proteomics

Volumn 75, Issue 8, 2012, Pages 2500-2513

  Lai, Yan Hua ^a   Li, Zhan Chao ^a   Chen, Li Li ^a   Dai, Zong ^a   Zou, Xiao Yong ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

Influenza A virus infection; Potential targets; Prediction; Proteome wide network approach; Topological and biological features

Indexed keywords

ANTIVIRUS AGENT; HOST FACTOR; PHOSPHORUS; PROTEOME; VIRUS PROTEIN;

ALGORITHM; APOPTOSIS; ARTICLE; CELL DEATH; GENE IDENTIFICATION; GENETIC ANALYSIS; INFLUENZA; INFLUENZA VIRUS A; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION;

ALGORITHMS; CLUSTER ANALYSIS; HOST-PATHOGEN INTERACTIONS; HUMANS; INFLUENZA A VIRUS; INFLUENZA, HUMAN; METABOLIC NETWORKS AND PATHWAYS; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOME; SEQUENCE ANALYSIS, PROTEIN; SUPPORT VECTOR MACHINES; VALIDATION STUDIES AS TOPIC;

INFLUENZA A VIRUS;

EID: 84862826823     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.02.034     Document Type: Article

References (51)

1. Rambaut A., Pybus O.G., Nelson M.I., Viboud C., Taubenberger J.K., Holmes E.C. The genomic and epidemiological dynamics of human influenza A virus. Nature 2008, 453:615-620.
2. Konig R., Stertz S., Zhou Y., Inoue A., Hoffmann H.H., Bhattacharyya S., et al. Human host factors required for influenza virus replication. Nature 2010, 463:813-817.
3. Ge Q., Pastey M., Kobasa D., Puthavathana P., Lupfer C., Bestwick R.K., et al. Inhibition of multiple subtypes of influenza A virus in cell cultures with morpholino oligomers. Antimicrob Agents Chemother 2006, 50:3724-3733.
4. ElHefnawi M., Alaidi O., Mohamed N., Kamar M., El-Azab I., Zada S., et al. Identification of novel conserved functional motifs across most influenza A viral strains. Virol J 2011, 8:44.
5. Das K., Aramini J.M., Ma L.C., Krug R.M., Arnold E. Structures of influenza A proteins and insights into antiviral drug targets. Nat Struct Mol Biol 2010, 17:530-538.
6. Navratil V., de Chassey B., Combe C.R., Lotteau V. When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases. BMC Syst Biol 2011, 5:13.
7. Chatr-Aryamontri A., Ceol A., Peluso D., Nardozza A., Panni S., Sacco F., et al. VirusMINT: a viral protein interaction database. Nucleic Acids Res 2009, 37:D669-D673.
8. Xu J., Li Y. Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics 2006, 22:2800-2805.
9. Gandhi T.K., Zhong J., Mathivanan S., Karthick L., Chandrika K.N., Mohan S.S., et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 2006, 38:285-293.
10. Brunner H.G., van Driel M.A. From syndrome families to functional genomics. Nat Rev Genet 2004, 5:545-551.
11. Shapira S.D., Gat-Viks I., Shum B.O., Dricot A., de Grace M.M., Wu L., et al. A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 2009, 139:1255-1267.
12. MacPherson J.I., Dickerson J.E., Pinney J.W., Robertson D.L. Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PLoS Comput Biol 2010, 6:e1000863.
13. de Chassey B., Navratil V., Tafforeau L., Hiet M.S., Aublin-Gex A., Agaugue S., et al. Hepatitis C virus infection protein network. Mol Syst Biol 2008, 4:230.
14. van Dijk D., Ertaylan G., Boucher C.A., Sloot P.M. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. BMC Syst Biol 2010, 4:96.
15. Dyer M.D., Murali T.M., Sobral B.W. The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 2008, 4:e32.
16. Navratil V., de Chassey B., Meyniel L., Delmotte S., Gautier C., Andre P., et al. VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res 2009, 37:D661-D668.
17. Colizza V., Flammini A., Maritan A., Vespignani A. Characterization and modeling of protein-protein interaction networks. Physica A 2005, 352:1-27.
18. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
19. Li Z., Zhou X., Dai Z., Zou X. Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm. BMC Bioinformatics 2010, 11:325.
20. Stark C., Breitkreutz B.J., Reguly T., Boucher L., Breitkreutz A., Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, 34:D535-D539.
21. Xenarios I., Salwinski L., Duan X.J., Higney P., Kim S.M., Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30:303-305.
22. Peri S., Navarro J.D., Kristiansen T.Z., Amanchy R., Surendranath V., Muthusamy B., et al. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 2004, 32:D497-D501.
23. Ceol A., Chatr Aryamontri A., Licata L., Peluso D., Briganti L., Perfetto L., et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 2010, 38:D532-D539.
24. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
25. Assenov Y., Ramirez F., Schelhorn S.E., Lengauer T., Albrecht M. Computing topological parameters of biological networks. Bioinformatics 2008, 24:282-284.
26. Bader G.D., Hogue C.W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2.
27. Maere S., Heymans K., Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449.
28. Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
29. Karchin R., Karplus K., Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics 2002, 18:147-159.
30. Guo J., Chen H., Sun Z., Lin Y. A novel method for protein secondary structure prediction using dual-layer SVM and profiles. Proteins 2004, 54:738-743.
31. Kumar M., Bhasin M., Natt N.K., Raghava G.P. BhairPred: prediction of β-hairpins in a protein from multiple alignment information using ANN and SVM techniques. Nucleic Acids Res 2005, 33:W154-W159.
32. Adie E.A., Adams R.R., Evans K.L., Porteous D.J., Pickard B.S. Speeding disease gene discovery by sequence based candidate prioritization. BMC Bioinformatics 2005, 6:55.
33. Holland J.H. Adaptation in natural and artificial systems 1975, The University of Michigan Press.
34. Torreira E., Schoehn G., Fernandez Y., Jorba N., Ruigrok R.W., Cusack S., et al. Three-dimensional model for the isolated recombinant influenza virus polymerase heterotrimer. Nucleic Acids Res 2007, 35:3774-3783.
35. Coloma R., Valpuesta J.M., Arranz R., Carrascosa J.L., Ortin J., Martin-Benito J. The structure of a biologically active influenza virus ribonucleoprotein complex. PLoS Pathog 2009, 5:e1000491.
36. Nemeroff M.E., Barabino S.M., Li Y., Keller W., Krug R.M. Influenza virus NS1 protein interacts with the cellular 30kDa subunit of CPSF and inhibits 3' end formation of cellular pre-mRNAs. Mol Cell 1998, 1:991-1000.
37. Shimizu K., Iguchi A., Gomyou R., Ono Y. Influenza virus inhibits cleavage of the HSP70 pre-mRNAs at the polyadenylation site. Virology 1999, 254:213-219.
38. Portela A., Digard P. The influenza virus nucleoprotein: a multifunctional RNA binding protein pivotal to virus replication. J Gen Virol 2002, 83:723-734.
39. Newcomb L.L., Kuo R.L., Ye Q., Jiang Y., Tao Y.J., Krug R.M. Interaction of the influenza a virus nucleocapsid protein with the viral RNA polymerase potentiates unprimed viral RNA replication. J Virol 2009, 83:29-36.
40. Kosik I., Krejnusova I., Bystricka M., Polakova K., Russ G. N-terminal region of the PB1-F2 protein is responsible for increased expression of influenza A viral protein PB1. Acta Virol 2011, 55:45-53.
41. Sharan R., Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol 2006, 24:427-433.
42. Jonsson P.F., Bates P.A. Global topological features of cancer proteins in the human interactome. Bioinformatics 2006, 22:2291-2297.
43. Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
44. Brydon E.W., Smith H., Sweet C. Influenza A virus-induced apoptosis in bronchiolar epithelial [NCI-H292] cells limits pro-inflammatory cytokine release. J Gen Virol 2003, 84:2389-2400.
45. Hunter T., Karin M. The regulation of transcription by phosphorylation. Cell 1992, 70:375-387.
46. Jans D.A., Hubner S. Regulation of protein transport to the nucleus: central role of phosphorylation. Physiol Rev 1996, 76:651-685.
47. Dickerson J.E., Pinney J.W., Robertson D.L. The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. BMC Syst Biol 2010, 4:80.
48. Chen J., Xu H., Aronow B.J., Jegga A.G. Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics 2007, 8:392.
49. Hao L., Sakurai A., Watanabe T., Sorensen E., Nidom C.A., Newton M.A., et al. Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature 2008, 454:890-893. [Suppl.].
50. Stevens T.H., Forgac M. Structure, function and regulation of the vacuolar [H+]-ATPase. Annu Rev Cell Dev Biol 1997, 13:779-808.
51. Wu T.F., Lin C.J., Weng R.C. Probability estimates for multi-class classification by pairwise coupling. J Mach Learn Res 2004, 5:975-1005.