Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Zhang, Minlu ^a,b   Su, Shengchang ^c   Bhatnagar, Raj K ^b   Hassett, Daniel J ^c   Lu, Long J ^a,b,c  

^a CINCINNATI CHILDREN S HOSPITAL RESEARCH FOUNDATION   (United States)

^b University of Cincinnati   (United States)

^c UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; INTERACTOME; PROTEIN MUCA; PROTEIN MUCB; PROTEIN RHIR; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; DRUG TARGETING; MACHINE LEARNING; NONHUMAN; OPEN READING FRAME; PREDICTION; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PSEUDOMONAS AERUGINOSA; VALIDATION PROCESS;

BACTERIAL PROTEINS; DRUG DELIVERY SYSTEMS; DRUG DISCOVERY; HUMANS; INTERNET; MODELS, BIOLOGICAL; PROTEOME; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS INFECTIONS;

PSEUDOMONAS AERUGINOSA;

EID: 84864259146     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041202     Document Type: Article

References (72)

1. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406: 959-964.
2. Foundation CF (2009) Cystic Fibrosis Foundation Patient Registry. 2008 Annual Data Report. Bethesda, MD.
3. Livermore DM, (1995) beta-Lactamases in laboratory and clinical resistance. Clin Microbiol Rev 8: 557-584.
4. Vicens Q, Westhof E, (2002) Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site. Chemistry & Biology 9: 747-755.
5. Kola I, Landis J, (2004) Can the pharmaceutical industry reduce attrition rates? Nat Rev Drug Discov 3: 711-715.
6. Kipnis E, Sawa T, Wiener-Kronish J, (2006) Targeting mechanisms of Pseudomonas aeruginosa pathogenesis. Med Mal Infect 36: 78-91.
7. Huang S, (2002) Rational drug discovery: what can we learn from regulatory networks? Drug Discov Today 7: S163-169.
8. Lu LJ, Sboner A, Huang YJ, Lu HX, Gianoulis TA, et al. (2007) Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem Sci 32: 320-331.
9. Hopkins AL, (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4: 682-690.
10. Lee CK, Boyle MP, Diener-West M, Brass-Ernst L, Noschese M, et al. (2007) Levofloxacin pharmacokinetics in adult cystic fibrosis. Chest 131: 796-802.
11. Goll J, Rajagopala SV, Shiau SC, Wu H, Lamb BT, et al. (2008) MPIDB: the microbial protein interaction database. Bioinformatics 24: 1743-1744.
12. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302: 449-453.
13. Lu LJ, Xia Y, Yu H, Rives A, Lu H, et al. (2005) Protein interaction prediction by integrating genomic features and protein interaction network analysis. Data analysis and visualization in genomics and proteomics pp. 61-81.
14. Shen J, Zhang J, Luo X, Zhu W, Yu K, et al. (2007) Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A 104: 4337-4341.
15. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37: D412-416.
16. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, et al. (2004) Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 14: 1107-1118.
17. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
18. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
19. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-4574.
20. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
21. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
22. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
23. Han JD, Dupuy D, Bertin N, Cusick ME, Vidal M, (2005) Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol 23: 839-844.
24. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968.
25. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
26. Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M, (2005) Assessing the limits of genomic data integration for predicting protein networks. Genome Res 15: 945-953.
27. Xia Y, Lu LJ, Gerstein M, (2006) Integrated prediction of the helical membrane protein interactome in yeast. J Mol Biol 357: 339-349.
28. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-568.
29. Yoon SS, Coakley R, Lau GW, Lymar SV, Gaston B, et al. (2006) Anaerobic killing of mucoid Pseudomonas aeruginosa by acidified nitrite derivatives under cystic fibrosis airway conditions. J Clin Invest 116: 436-446.
30. Yoon SS, Hennigan RF, Hilliard GM, Ochsner UA, Parvatiyar K, et al. (2002) Pseudomonas aeruginosa anaerobic respiration in biofilms: relationships to cystic fibrosis pathogenesis. Dev Cell 3: 593-603.
31. Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T, (2006) A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics 7: 360.
32. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691.
33. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
34. Sprinzak E, Sattath S, Margalit H, (2003) How reliable are experimental protein-protein interaction data? J Mol Biol 327: 919-923.
35. Deng M, Mehta S, Sun F, Chen T, (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res 12: 1540-1548.
36. Park D, Lee S, Bolser D, Schroeder M, Lappe M, et al. (2005) Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Bioinformatics 21: 3234-3240.
37. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34: D247-251.
38. Qi Y, Bar-Joseph Z, Klein-Seetharaman J, (2006) Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 63: 490-500.
39. McDowall MD, Scott MS, Barton GJ, (2009) PIPs: human protein-protein interaction prediction database. Nucleic Acids Res 37: D651-656.
40. Bowie JU, (2005) Solving the membrane protein folding problem. Nature 438: 581-589.
41. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2010) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res.
42. Liu H, Setiono R, (1995) Chi2: Feature selection and discretization of numeric attributes. Seventh International Conference on Tools with Artificial Intelligence, Proceedings pp. 388-391.
43. Quinlan JR, (1996) Improved use of continuous attributes in C4.5. Journal of Artificial Intelligence Research 4: 77-90.
44. Shannon CE, (1997) The mathematical theory of communication (Reprinted). M D Computing 14: 306-317.
45. Attneave F, (1980) Citation Classic- Applications of Information-Theory to Psychology- a Summary of Basic Concepts, Methods, and Results. Current Contents/Social & Behavioral Sciences pp. 10-10.
46. Zhang M, Deng J, Fang C, Zhang X, Lu LJ, (2010) Biomolecular Network Analysis and Applications. In: Alterovitz G, Ramoni M, editors. pp. 253-288 editors. Knowledge-Based Bioinformatics: from analysis to interpretation: John Wiley and Sons.
47. Jeong H, Mason SP, Barabasi AL, Oltvai ZN, (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
48. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36: D901-906.
49. Hartwell LH, Hopfield JJ, Leibler S, Murray AW, (1999) From molecular to modular cell biology. Nature 402: C47-52.
50. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO, (2000) Protein function in the post-genomic era. Nature 405: 823-826.
51. Bader GD, Hogue CW, (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2.
52. Driscoll T, Dyer MD, Murali TM, Sobral BW, (2009) PIG-the pathogen interaction gateway. Nucleic Acids Res 37: D647-650.
53. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: D767-772.
54. Hassett DJ, Sutton MD, Schurr MJ, Herr AB, Caldwell CC, et al. (2009) Pseudomonas aeruginosa hypoxic or anaerobic biofilm infections within cystic fibrosis airways. Trends Microbiol 17: 130-138.
55. Florez AF, Park D, Bhak J, Kim BC, Kuchinsky A, et al. (2010) Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. BMC Bioinformatics 11: 484.
56. Park SJ, Choi JS, Kim BC, Jho SW, Ryu JW, et al. (2009) PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. BMC Genomics 10: S18.
57. Hwang S, Son SW, Kim SC, Kim YJ, Jeong H, et al. (2008) A protein interaction network associated with asthma. J Theor Biol 252: 722-731.
58. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, et al. (2009) ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 37: D868-872.
59. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-484.
60. Zhang R, Lin Y, (2009) DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 37: D455-458.
61. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, et al. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305.
62. Peregrin-Alvarez JM, Xiong X, Su C, Parkinson J, (2009) The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol 5: e1000523.
63. Hu P, Janga SC, Babu M, Diaz-Mejia JJ, Butland G, et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7: e96.
64. Retief JD, (2000) Phylogenetic analysis using PHYLIP. Methods Mol Biol 132: 243-258.
65. Deng J, Deng L, Su S, Zhang M, Lin X, et al. (2011) Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res 39: 795-807.
66. Raghavachari B, Tasneem A, Przytycka TM, Jothi R, (2008) DOMINE: a database of protein domain interactions. Nucleic Acids Res 36: D656-661.
67. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-222.
68. Mao F, Dam P, Chou J, Olman V, Xu Y, (2009) DOOR: a database for prokaryotic operons. Nucleic Acids Res 37: D459-463.
69. Breiman L, (2001) Random forests. Machine Learning 45: 5-32.
70. Frank E, Hall M, Trigg L, Holmes G, Witten IH, (2004) Data mining in bioinformatics using Weka. Bioinformatics 20: 2479-2481.
71. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
72. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.