Prediction of Intra- and Interspecies Protein-Protein Interactions Facilitating Systems Biology Studies

Protein-Protein Interactions in Drug Discovery

Volumn 56, Issue , 2013, Pages 21-53

  Schleker, Sylvia ^a,b   Ananthasubramanian, Seshan ^b   Klein Seetharaman, Judith ^a,b   Ganapathiraju, Madhavi K ^b  

^a Institute of Complex Systems   (Germany)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

Computational prediction; Disease; Drug discovery; Interactome; Protein protein interaction; Systems biology

Indexed keywords

DISEASES; PATHOGENS; VIRUSES;

COMPUTATIONAL PREDICTIONS; DRUG DISCOVERY; INTERACTOME; PROTEIN-PROTEIN INTERACTIONS; SYSTEMS BIOLOGY;

PROTEINS;

EID: 85016477726     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527648207.ch2     Document Type: Chapter

References (161)

1. Kitano, H. (2002) Computational systems biology. Nature, 420, 206-210.
2. Chautard, E., Thierry-Mieg, N., and Ricard-Blum, S. (2009) Interaction networks: from protein functions to drug discovery. A review. Pathologie-Biologie, 57, 324-333.
3. Pujana, M.A., Han, J.D., Starita, L.M., Stevens, K.N., Tewari, M., Ahn, J.S., Rennert, G., Moreno, V., Kirchhoff, T., Gold, B., Assmann, V., Elshamy, W.M., Rual, J.F., Levine, D., Rozek, L.S., Gelman, R.S., Gunsalus, K.C., Greenberg, R.A., Sobhian, B., Bertin, N., Venkatesan, K., Ayivi-Guedehoussou, N., Sole, X., Hernandez, P., Lazaro, C., Nathanson, K. L., Weber, B.L., Cusick, M.E., Hill, D.E., Offit, K., Livingston, D.M., Gruber, S.B., Parvin, J.D., and Vidal, M. (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nature Genetics, 39, 1338-1349.
4. Dawber, T.R., Kannel,W.B., and Lyell, L.P. (1963) An approach to longitudinal studies in a community: the Framingham Study. Annals of the New York Academy of Sciences, 107, 539-556.
5. International HapMap Consortium (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
6. Cerami, E., Demir, E., Schultz, N., Taylor, B.S., and Sander, C. (2010) Automated network analysis identifies core pathways in glioblastoma. PLoS ONE, 5, e8918.
7. Wachi, S., Yoneda, K., and Wu, R. (2005) Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics, 21, 4205-4208.
8. Balakrishnan, S., Tastan, O., Carbonell, J., and Klein-Seetharaman, J. (2009) Alternative paths in HIV-1 targeted human signal transduction pathways. BMC Genomics, 10 (Suppl. 3), S30.
9. Schwikowski, B., Uetz, P., and Fields, S. (2000) A network of protein-protein interactions in yeast. Nature Biotechnology, 18, 1257-1261.
10. Prasad, T.S.K., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D.S., Sebastian, A., Rani, S., Ray, S., Kishore, C.J.H., Kanth, S., Ahmed, M., Kashyap, M.K., Mohmood, R., Ramachandra, Y.L., Krishna, V., Rahiman, B.A., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R., and Pandey, A. (2009) Human protein reference database-2009 update. Nucleic Acids Research, 37, D767-D772.
11. Hishigaki, H., Nakai, K., Ono, T., Tanigami, A., and Takagi, T. (2001) References j43 Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast, 18, 523-531.
12. Brun, C., Chevenet, F., Martin, D.,Wojcik, J., Guenoche, A., and Jacq, B. (2003) Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biology, 5, R6.
13. Vazquez, A., Flammini, A., Maritan, A., and Vespignani, A. (2003) Global protein function prediction from protein-protein interaction networks. Nature Biotechnology, 21, 697-700.
14. Nabieva, E., Jim, K., Agarwal, A., Chazelle, B., and Singh, M. (2005) Whole-proteome prediction of protein function via graphtheoretic analysis of interaction maps. Bioinformatics, 21 (Suppl. 1), i302-i310.
15. Chua, H.N., Sung, W.K., and Wong, L. (2006) Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics, 22, 1623-1630.
16. Deng, M., Chen, T., and Sun, F. (2004) An integrated probabilistic model for functional prediction of proteins. Journal of Computational Biology, 11, 463-475.
17. Deng, M.H., Zhang, K., Mehta, S., Chen, T., and Sun, F.Z. (2003) Prediction of protein function using protein-protein interaction data. Journal of Computational Biology, 10, 947-960.
18. Nguyen, C.D., Gardiner, K.J., Nguyen, D., and Cios, K.J. (2008) Prediction of protein functions from protein interaction networks: a naive Bayes approach. Pricai 2008: Trends in Artificial Intelligence, 5351, 788-798.
19. Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature, 340, 245-246.
20. Chen, Y. and Xu, D. (2003) Computational analyses of highthroughput protein-protein interaction data. Current Protein & Peptide Science, 4, 159-181.
21. Stelzl, U.,Worm, U., Lalowski, M., Haenig, C., Brembeck, F.H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksoz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H., and Wanker, E.E. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122, 957-968.
22. Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D.S., Zhang, L.V., Wong, S.L., Franklin, G., Li, S., Albala, J.S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R.S., Vandenhaute, J., Zoghbi, H.Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M.E., Hill, D.E., Roth, F.P., and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
23. Barrios-Rodiles, M., Brown, K.R., Ozdamar, B., Bose, R., Liu, Z., Donovan, R. S., Shinjo, F., Liu, Y., Dembowy, J., Taylor, I.W., Luga, V., Przulj, N., Robinson, M., Suzuki, H., Hayashizaki, Y., Jurisica, I., and Wrana, J.L. (2005) High-throughput mapping of a dynamic signaling network in mammalian cells. Science, 307, 1621-1625.
24. Vidal, M., Cusick, M.E., and Barabasi, A.L. (2011) Interactome networks and human disease. Cell, 144, 986-998.
25. Braun, P., Tasan, M., Dreze, M., Barrios- Rodiles, M., Lemmens, I., Yu, H., Sahalie, J.M., Murray, R.R., Roncari, L., de Smet, A. S., Venkatesan, K., Rual, J.F., Vandenhaute, J., Cusick, M.E., Pawson, T., Hill, D.E., Tavernier, J.,Wrana, J.L., Roth, F.P., and Vidal, M. (2009) An experimentally derived confidence score for binary protein- protein interactions. Nature Methods, 6, 91-97.
26. Venkatesan, K., Rual, J.F., Vazquez, A., Stelzl, U., Lemmens, I., Hirozane- Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K.I., Yildirim, M.A., Simonis, N., Heinzmann, K., Gebreab, F., Sahalie, J.M., Cevik, S., Simon, C., de Smet, A.S., Dann, E., Smolyar, A., Vinayagam, A., Yu, H., Szeto, D., Borick, H., Dricot, A., Klitgord, N., Murray, R.R., Lin, C., Lalowski, M., Timm, J., Rau, K., Boone, C., Braun, P., Cusick, M.E., Roth, F.P., Hill, D.E., Tavernier, J.,Wanker, E.E., Barabasi, A.L., and Vidal, M. (2009) An empirical framework for binary interactome mapping. Nature Methods, 6, 83-90.
27. Collins, S.R., Kemmeren, P., Zhao, X.C., Greenblatt, J.F., Spencer, F., Holstege, F. C., Weissman, J.S., and Krogan, N.J. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Molecular & Cellular Proteomics, 6, 439-450.
28. Ramirez, F., Schlicker, A., Assenov, Y., Lengauer, T., and Albrecht, M. (2007) Computational analysis of human protein interaction networks. Proteomics, 7, 2541-2552.
29. Yu, H., Braun, P., Yildirim, M.A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., Hao, T., Rual, J.F., Dricot, A., Vazquez, A., Murray, R.R., Simon, C., Tardivo, L., Tam, S., Svrzikapa, N., Fan, C., de Smet, A.S., Motyl, A., Hudson, M.E., Park, J., Xin, X., Cusick, M.E., Moore, T., Boone, C., Snyder, M., Roth, F.P., Barabasi, A.L., Tavernier, J., Hill, D.E., and Vidal, M. (2008) High-quality binary protein interaction map of the yeast interactome network. Science, 322, 104-110.
30. von Mering, C. and Bork, P. (2002) Teamed up for transcription. Nature, 417, 797-798.
31. Collins, F.S., Green, E.D., Guttmacher, A. E., and Guyer, M.S. (2003) A vision for the future of genomics research. Nature, 422, 835-847.
32. Smialowski, P., Pagel, P., Wong, P., Brauner, B., Dunger, I., Fobo, G., Frishman, G., Montrone, C., Rattei, T., Frishman, D., and Ruepp, A. (2010) The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Research, 38 (Database issue), D540-D544.
33. Persico, M., Ceol, A., Gavrila, C., Hoffmann, R., Florio, A., and Cesareni, G. (2005) HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics, 6 (Suppl. 4), S21.
34. Schwartz, A.S., Yu, J., Gardenour, K.R., Finley, R.L.Jr., and Ideker, T. (2009) Costeffective strategies for completing the interactome. Nature Methods, 6, 55-61.
35. Dandekar, T., Snel, B., Huynen, M., and Bork, P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends in Biochemical Sciences, 23, 324-328.
36. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D., and Maltsev, N. (1999) The use of gene clusters to infer functional coupling. Proceedings of the National Academy of Sciences of the United States of America, 96, 2896-2901.
37. Enright, A.J., Iliopoulos, I., Kyrpides, N.C., and Ouzounis, C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
38. Valencia, A. and Pazos, F. (2002) Computational methods for the prediction of protein interactions. Current Opinion in Structural Biology, 12, 368-373.
39. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., and Eisenberg, D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
40. Tsoka, S. and Ouzounis, C.A. (2000) Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nature Genetics, 26, 141-142.
41. Tan, S.H., Zhang, Z., and Ng, S.K. (2004) ADVICE: automated detection and validation of interaction by co-evolution. Nucleic Acids Research, 32 (Web Server issue), W69-W72.
42. Pazos, F. and Valencia, A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering, 14, 609-614.
43. Sun, J.C., Li, Y.X., and Zhao, Z.M. (2007) Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochemical and Biophysical Research Communications, 353, 985-991.
44. Grigoriev, A. (2001) A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Research, 29, 3513-3519.
45. Bhardwaj, N. and Lu, H. (2005) Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics, 21, 2730-2738.
46. Ogmen, U., Keskin, O., Aytuna, A.S., Nussinov, R., and Gursoy, A. (2005) PRISM: protein interactions by structural matching. Nucleic Acids Research, 33 (Web Server issue), W331-W336.
47. Ramani, A.K., Bunescu, R.C., Mooney, R.J., and Marcotte, E.M. (2005) Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biology, 6, R40.
48. Jansen, R. and Gerstein, M. (2004) Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Current Opinion in Microbiology, 7, 535-545.
49. Lee, I., Date, S.V., Adai, A.T., and Marcotte, E.M. (2004) A probabilistic functional network of yeast genes. Science, 306, 1555-1558.
50. Yamanishi, Y., Vert, J.P., and Kanehisa, M. (2004) Protein network inference from multiple genomic data: a supervised approach. Bioinformatics, 20 (Suppl. 1), i363-i370.
51. Lin, N., Wu, B., Jansen, R., Gerstein, M., and Zhao, H. (2004) Information assessment on predicting protein- protein interactions. BMC Bioinformatics, 5, 154.
52. Zhang, L.V., Wong, S.L., King, O.D., and Roth, F.P. (2004) Predicting cocomplexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics, 5, 38.
53. Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N.J., Chung, S., Emili, A., Snyder, M., Greenblatt, J.F., and Gerstein, M. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 302, 449-453.
54. Qi, Y.J., Bar-Joseph, Z., and Klein- Seetharaman, J. (2006) Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins-Structure Function and Bioinformatics, 63, 490-500.
55. Stein, A., Ceol, A., and Aloy, P. (2011) 3did: identification and classification of domainbased interactions of known threedimensional structure. Nucleic Acids Research, 39 (Database issue), D718-D723.
56. Qi, Y., Dhiman, H.K., Bhola, N., Budyak, I., Kar, S., Man, D., Dutta, A., Tirupula, K., Carr, B.I., Grandis, J., Bar-Joseph, Z., and Klein-Seetharaman, J. (2009) Systematic prediction of human membrane receptor interactions. Proteomics, 9, 5243-5255.
57. Tastan, O., Qi, Y.J., Carbonell, J.G., and Klein-Seetharaman, J. (2009) Prediction of interactions between HIV-1 and human proteins by information integration. Pacific Symposium on Biocomputing, 2009, 516-527.
58. Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M., and Eisenberg, D. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Research, 30, 303-305.
59. Stark, C., Breitkreutz, B.J., Reguly, T., Boucher, L., Breitkreutz, A., and Tyers, M. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Research, 34 (Database issue), D535-D539.
60. Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer- Citterich, M., and Cesareni, G. (2002) MINT: a Molecular INTeraction database. FEBS Letters, 513, 135-140.
61. Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U., Jandrasits, C., Jimenez, R.C., Khadake, J., Mahadevan, U., Masson, P., Pedruzzi, I., Pfeiffenberger, E., Porras, P., Raghunath, A., Roechert, B., Orchard, S., and Hermjakob, H. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Research, 40 (Database issue), D841-D846.
62. Bader, G.D., Betel, D., and Hogue, C.W. (2003) BIND: the biomolecular interaction network database. Nucleic Acids Research, 31, 248-250.
63. Joshi-Tope, G., Gillespie, M., Vastrik, I., D'Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G.R., Wu, G.R., Matthews, L., Lewis, S., Birney, E., and Stein, L. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Research, 33 (Database issue), D428-D432.
64. Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research, 28, 27-30.
65. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel- Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25, 25-29.
66. Ostlund, G., Schmitt, T., Forslund, K., Kostler, T., Messina, D.N., Roopra, S., Frings, O., and Sonnhammer, E.L. (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Research, 38 (Database issue), D196-D203.
67. Bowers, P.M., Pellegrini, M., Thompson, M.J., Fierro, J., Yeates, T.O., and Eisenberg, D. (2004) Prolinks: a database of protein functional linkages derived from coevolution. Genome Biology, 5, R35.
68. von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., and Snel, B. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Research, 31, 258-261.
69. Kuhn, M., von Mering, C., Campillos, M., Jensen, L.J., and Bork, P. (2008) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research, 36 (Database issue), D684-D688.
70. Dyer, M.D., Murali, T.M., and Sobral, B.W. (2008) The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathogens, 4, e32.
71. Dyer, M.D., Neff, C., Dufford, M., Rivera, C.G., Shattuck, D., Bassaganya-Riera, J., Murali, T.M., and Sobral, B.W. (2010) The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS ONE, 5, e12089.
72. Adams, L.G., Khare, S., Lawhon, S.D., Rossetti, C.A., Lewin, H.A., Lipton, M.S., Turse, J.E., Wylie, D.C., Bai, Y., and Drake, K.L. (2011) Enhancing the role of veterinary vaccines reducing zoonotic diseases of humans: linking systems biology with vaccine development. Vaccine, 29, 7197-7206.
73. Adams, L.G., Khare, S., Lawhon, S.D., Rossetti, C.A., Lewin, H.A., Lipton, M.S., Turse, J.E., Wylie, D.C., Bai, Y., and Drake, K.L. (2011) Multi-comparative systems biology analysis reveals time-course biosignatures of in vivo bovine pathway responses to B. melitensis, S. enterica typhimurium and M. avium paratuberculosis. BMC Proceedings, 5 (Suppl. 4), S6.
74. Rajagopala, S.V., Titz, B., Goll, J., Parrish, J.R., Wohlbold, K., McKevitt, M.T., Palzkill, T., Mori, H., Finley, R.L.Jr., and Uetz, P. (2007) The protein network of bacterial motility. Molecular Systems Biology, 3, 128.
75. Rashid, M., Ramasamy, S., and Raghava, G.P. (2010) A simple approach for predicting protein-protein interactions. Current Protein & Peptide Science, 11, 589-600.
76. Di Lallo, G., Fagioli, M., Barionovi, D., Ghelardini, P., and Paolozzi, L. (2003) Use of a two-hybrid assay to study the assembly of a complex multicomponent protein machinery: bacterial septosome differentiation. Microbiology, 149, 3353-3359.
77. Maggi, S., Massidda, O., Luzi, G., Fadda, D., Paolozzi, L., and Ghelardini, P. (2008) Division protein interaction web: identification of a phylogenetically conserved common interactome between Streptococcus pneumoniae and Escherichia coli. Microbiology, 154, 3042-3052.
78. Krishnadev, O. and Srinivasan, N. (2011) Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria. International Journal of Biological Macromolecules, 48, 613-619.
79. Selbach, M., Paul, F.E., Brandt, S., Guye, P., Daumke, O., Backert, S., Dehio, C., and Mann, M. (2009) Host cell interactome of tyrosine-phosphorylated bacterial proteins. Cell Host & Microbe, 5, 397-403.
80. Davis, F.P., Barkan, D.T., Eswar, N., McKerrow, J.H., and Sali, A. (2007) Host References j47 pathogen protein interactions predicted by comparative modeling. Protein Science, 16, 2585-2596.
81. Verkhedkar, K.D., Raman, K., Chandra, N.R., and Vishveshwara, S. (2007) Metabolome based reaction graphs of M. tuberculosis and M. leprae: a comparative network analysis. PLoS ONE, 2, e881.
82. Noirot-Gros, M.F., Dervyn, E., Wu, L.J., Mervelet, P., Errington, J., Ehrlich, S.D., and Noirot, P. (2002) An expanded view of bacterial DNA replication. Proceedings of the National Academy of Sciences of the United States of America, 99, 8342-8347.
83. Marchadier, E., Carballido-Lopez, R., Brinster, S., Fabret, C., Mervelet, P., Bessieres, P., Noirot-Gros, M.F., Fromion, V., and Noirot, P. (2011) An expanded protein-protein interaction network in Bacillus subtilis reveals a group of hubs: exploration by an integrative approach. Proteomics, 11, 2981-2991.
84. Hoebeke, M., Chiapello, H., Noirot, P., and Bessieres, P. (2001) SPiD: a subtilis protein interaction database. Bioinformatics, 17, 1209-1212.
85. Noirot, P. and Noirot-Gros, M.F. (2004) Protein interaction networks in bacteria. Current Opinion in Microbiology, 7, 505-512.
86. Costes, A., Lecointe, F., McGovern, S., Quevillon-Cheruel, S., and Polard, P. (2010) The C-terminal domain of the bacterial SSB protein acts as a DNA maintenance hub at active chromosome replication forks. PLoS Genetics, 6, e1001238.
87. Parrish, J.R., Yu, J., Liu, G., Hines, J.A., Chan, J.E., Mangiola, B.A., Zhang, H., Pacifico, S., Fotouhi, F., DiRita, V.J., Ideker, T., Andrews, P., and Finley, R.L.Jr. (2007) A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biology, 8, R130.
88. Wang, A., Johnston, S.C., Chou, J., and Dean, D. (2010) A systemic network for Chlamydia pneumoniae entry into human cells. Journal of Bacteriology, 192, 2809-2815.
89. Diaz-Mejia, J.J., Babu, M., and Emili, A. (2009) Computational and experimental approaches to chart the Escherichia coli cellenvelope- associated proteome and interactome. FEMS Microbiology Reviews, 33, 66-97.
90. Vinogradov, A.E. (2008) Modularity of cellular networks shows general centerperiphery polarization. Bioinformatics, 24, 2814-2817.
91. Rooney, J.P., George, A.D., Patil, A., Begley, U., Bessette, E., Zappala, M.R., Huang, X., Conklin, D.S., Cunningham, R.P., and Begley, T.J. (2009) Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks. Genomics, 93, 42-51.
92. Su, C., Peregrin-Alvarez, J.M., Butland, G., Phanse, S., Fong, V., Emili, A., and Parkinson, J. (2008) Bacteriome.org-an integrated protein interaction database for E. coli. Nucleic Acids Research, 36 (Database issue), D632-D636.
93. Pazos, F., Ranea, J.A., Juan, D., and Sternberg, M.J. (2005) Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. Journal of Molecular Biology, 352, 1002- 1015.
94. Peregrin-Alvarez, J.M., Xiong, X., Su, C., and Parkinson, J. (2009) The modular organization of protein interactions in Escherichia coli. PLoS Computational Biology, 5, e1000523.
95. Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H.C., Hirai, A., Tsuzuki, K., Nakamura, S., Altaf-Ul-Amin, M., Oshima, T., Baba, T., Yamamoto, N., Kawamura, T., Ioka-Nakamichi, T., Kitagawa, M., Tomita, M., Kanaya, S., Wada, C., and Mori, H. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Research, 16, 686-691.
96. Butland, G., Peregrin-Alvarez, J.M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J., and Emili, A. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature, 433, 531-537.
97. Karimova, G., Dautin, N., and Ladant, D. (2005) Interaction network among Escherichia coli membrane proteins involved in cell division as revealed by bacterial two-hybrid analysis. Journal of Bacteriology, 187, 2233-2243.
98. Hu, P., Janga, S.C., Babu, M., Diaz-Mejia, J.J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., Chandran, S., Christopoulos, C., Nazarians-Armavil, A., Nasseri, N.K., Musso, G., Ali, M., Nazemof, N., Eroukova, V., Golshani, A., Paccanaro, A., Greenblatt, J.F., Moreno- Hagelsieb, G., and Emili, A. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biology, 7, e96.
99. Kim,W.K., Kim, K., Lee, E., Marcotte, E. M., Kim, H.H., and Suh, J.K. (2007) Identification of disease specific protein interactions between the gastric cancer causing pathogen, H. pylori, and human hosts using protein network modeling and gene chip analysis. Biochip Journal, 1, 179-187.
100. Costa, A.C., Figueiredo, C., and Touati, E. (2009) Pathogenesis of Helicobacter pylori infection. Helicobacter, 14 (Suppl. 1), 15-20.
101. Tyagi, N., Krishnadev, O., and Srinivasan, N. (2009) Prediction of protein-protein interactions between Helicobacter pylori and a human host. Molecular bioSystems, 5, 1630-1635.
102. Ricci, V., Romano, M., and Boquet, P. (2011) Molecular cross-talk between Helicobacter pylori and human gastric mucosa. World Journal of Gastroenterology, 17, 1383-1399.
103. Stingl, K., Schauer, K., Ecobichon, C., Labigne, A., Lenormand, P., Rousselle, J. C., Namane, A., and de Reuse, H. (2008) In vivo interactome of Helicobacter pylori urease revealed by tandem affinity purification. Molecular & Cellular Proteomics, 7, 2429-2441.
104. Terradot, L., Durnell, N., Li, M., Ory, J., Labigne, A., Legrain, P., Colland, F., and Waksman, G. (2004) Biochemical characterization of protein complexes from the Helicobacter pylori protein interaction map: strategies for complex formation and evidence for novel interactions within type IV secretion systems. Molecular & Cellular Proteomics, 3, 809-819.
105. Rain, J.C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F.,Wojcik, J., Schachter, V., Chemama, Y., Labigne, A., and Legrain, P. (2001) The protein-protein interaction map of Helicobacter pylori. Nature, 409, 211-215.
106. Legrain, P. and Strosberg, D. (2002) Protein interaction domain mapping for the selection of validated targets and lead compounds in the anti-infectious area. Current Pharmaceutical Design, 8, 1189- 1198.
107. Busler, V.J., Torres, V.J., McClain, M.S., Tirado, O., Friedman, D.B., and Cover, T. L. (2006) Protein-protein interactions among Helicobacter pylori cag proteins. Journal of Bacteriology, 188, 4787-4800.
108. Ewing, R.M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., McBroom- Cerajewski, L., Robinson, M.D., O'Connor, L., Li, M., Taylor, R., Dharsee, M., Ho, Y., Heilbut, A., Moore, L., Zhang, S., Ornatsky, O., Bukhman, Y.V., Ethier, M., Sheng, Y., Vasilescu, J., Abu-Farha, M., Lambert, J.P., Duewel, H.S., Stewart, II., Kuehl, B., Hogue, K., Colwill, K., Gladwish, K., Muskat, B., Kinach, R., Adams, S.L., Moran, M.F., Morin, G.B., Topaloglou, T., and Figeys, D. (2007) Large-scale mapping of human protein- protein interactions by mass spectrometry. Molecular Systems Biology, 3, 89.
109. Jeronimo, C., Forget, D., Bouchard, A., Li, Q., Chua, G., Poitras, C., Therien, C., Bergeron, D., Bourassa, S., Greenblatt, J., Chabot, B., Poirier, G.G., Hughes, T.R., Blanchette, M., Price, D.H., and Coulombe, B. (2007) Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Molecular Cell, 27, 262-274.
110. Wang, J., Huo, K., Ma, L., Tang, L., Li, D., Huang, X., Yuan, Y., Li, C., Wang, W., Guan, W., Chen, H., Jin, C., Wei, J., Zhang, W., Yang, Y., Liu, Q., Zhou, Y., Zhang, C., Wu, Z., Xu, W., Zhang, Y., Liu, T., Yu, D., Chen, L., Zhu, D., Zhong, X., Kang, L., Gan, X., Yu, X., Ma, Q., Yan, J., Zhou, L., Liu, Z., Zhu, Y., Zhou, T., He, F., and Yang, X. (2011) Toward an understanding of the protein interaction network of the human liver. Molecular Systems Biology, 7, 536.
111. Lim, J., Hao, T., Shaw, C., Patel, A.J., Szabo, G., Rual, J.F., Fisk, C.J., Li, N., Smolyar, A., Hill, D.E., Barabasi, A.L., Vidal, M., and Zoghbi, H.Y. (2006) A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell, 125, 801-814.
112. Lehner, B. and Fraser, A.G. (2004) A firstdraft human protein-interaction map. Genome Biology, 5, R63.
113. Brown, K.R. and Jurisica, I. (2005) Online predicted human interaction database. Bioinformatics, 21, 2076-2082.
114. Xia, K., Dong, D., and Han, J.D. (2006) IntNetDB v1.0: an integrated protein- protein interaction network database generated by a probabilistic model. BMC Bioinformatics, 7, 508.
115. Futschik, M.E., Chaurasia, G., and Herzel, H. (2007) Comparison of human protein- protein interaction maps. Bioinformatics, 23, 605-611.
116. Bossi, A. and Lehner, B. (2009) Tissue specificity and the human protein interaction network. Molecular Systems Biology, 5, 260.
117. Ramani, A.K., Li, Z., Hart, G.T., Carlson, M.W., Boutz, D.R., and Marcotte, E.M. (2008) A map of human protein interactions derived from coexpression of human mRNAs and their orthologs. Molecular Systems Biology, 4, 180.
118. Lima, A., Duran, R., Schujman, G.E., Marchissio, M.J., Portela, M.M., Obal, G., Pritsch, O., de Mendoza, D., and Cervenansky, C. (2011) Serine/threonine protein kinase PrkA of the human pathogen Listeria monocytogenes: biochemical characterization and identification of interacting partners through proteomic approaches. Journal of Proteomics, 74, 1720-1734.
119. Raman, K., Bhat, A.G., and Chandra, N. (2010) A systems perspective of host- pathogen interactions: predicting disease outcome in tuberculosis. Molecular bioSystems, 6, 516-530.
120. Chandra, N., Kumar, D., and Rao, K. (2011) Systems biology of tuberculosis. Tuberculosis, 91, 487-496.
121. Mazandu, G.K., Opap, K., and Mulder, N. J. (2011) Contribution of microarray data to the advancement of knowledge on the Mycobacterium tuberculosis interactome: use of the random partial least squares approach. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 11, 181-189.
122. Mazandu, G.K., Opap, K., and Mulder, N. J. (2011) Contribution of microarray data to the advancement of knowledge on the Mycobacterium tuberculosis interactome: use of the random partial least squares approach. Infection, Genetics And Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 11, 725-733.
123. Raman, K. and Chandra, N. (2008) Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance. BMC Microbiology, 8, 234.
124. Raman, K., Yeturu, K., and Chandra, N. (2008) targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Systems Biology, 2, 109.
125. Cui, T., Zhang, L., Wang, X., and He, Z.G. (2009) Uncovering new signaling proteins and potential drug targets through the interactome analysis of Mycobacterium tuberculosis. BMC Genomics, 10, 118.
126. Wang, Y., Cui, T., Zhang, C., Yang, M., Huang, Y., Li, W., Zhang, L., Gao, C., He, Y., Li, Y., Huang, F., Zeng, J., Huang, C., Yang, Q., Tian, Y., Zhao, C., Chen, H., Zhang, H., and He, Z.G. (2010) Global protein-protein interaction network in the human pathogen Mycobacterium tuberculosis H37Rv. Journal of Proteome Research, 9, 6665-6677.
127. Strong, M., Graeber, T.G., Beeby, M., Pellegrini, M., Thompson, M.J., Yeates, T. O., and Eisenberg, D. (2003) Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Research, 31, 7099-7109.
128. Park, S.J., Choi, J.S., Kim, B.C., Jho, S.W., Ryu, J.W., Park, D., Lee, K.A., Bhak, J., and Kim, S.I. (2009) PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. BMC Genomics, 10 (Suppl. 3), S18.
129. Cherkasov, A., Hsing, M., Zoraghi, R., Foster, L.J., See, R.H., Stoynov, N., Jiang, J., Kaur, S., Lian, T., Jackson, L., Gong, H., Swayze, R., Amandoron, E., Hormozdiari, F., Dao, P., Sahinalp, C., Santos-Filho, O., Axerio-Cilies, P., Byler, K., McMaster, W. R., Brunham, R.C., Finlay, B.B., and Reiner, N.E. (2011) Mapping the protein interaction network in methicillinresistant Staphylococcus aureus. Journal of Proteome Research, 10, 1139-1150.
130. Hsing, M., Byler, K.G., and Cherkasov, A. (2008) The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. BMC Systems Biology, 2, 80.
131. Sun, X., Jia, H.L., Xiao, C.L., Yin, X.F., Yang, X.Y., Lu, J., He, X., Li, N., Li, H., and He, Q.Y. (2011) Bacterial proteome of Streptococcus pneumoniae through multidimensional separations coupled with LC-MS/MS. Omics: A Journal of Integrative Biology, 15, 477-482.
132. Hauser, R., Sabri, M., Moineau, S., and Uetz, P. (2011) The proteome and interactome of Streptococcus pneumoniae phage Cp-1. Journal of Bacteriology, 193, 3135-3138.
133. Sabri, M., Hauser, R., Ouellette, M., Liu, J., Dehbi, M., Moeck, G., Garcia, E., Titz, B., Uetz, P., and Moineau, S. (2011) Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1. Journal of Bacteriology, 193, 551-562.
134. Shea, P.R., Virtaneva, K., Kupko, J.J. 3rd, Porcella, S.F., Barry, W.T.,Wright, F.A., Kobayashi, S.D., Carmody, A., Ireland, R. M., Sturdevant, D.E., Ricklefs, S.M., Babar, I., Johnson, C.A., Graham, M.R., Gardner, D.J., Bailey, J.R., Parnell, M.J., Deleo, F.R., and Musser, J.M. (2010) Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus. Proceedings of the National Academy of Sciences of the United States of America, 107, 4693-4698.
135. Shelburne, S.A., Davenport, M.T., Keith, D.B., and Musser, J.M. (2008) The role of complex carbohydrate catabolism in the pathogenesis of invasive streptococci. Trends in Microbiology, 16, 318-325.
136. Titz, B., Rajagopala, S.V., Goll, J., Hauser, R., McKevitt, M.T., Palzkill, T., and Uetz, P. (2008) The binary protein interactome of Treponema pallidum-the syphilis spirochete. PLoS ONE, 3, e2292.
137. Ruepp, A., Brauner, B., Dunger- Kaltenbach, I., Frishman, G., Montrone, C., Stransky, M.,Waegele, B., Schmidt, T., Doudieu, O.N., Stumpflen, V., and Mewes, H.W. (2008) CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Research, 36 (Database issue), D646-D650.
138. Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stumpflen, V., Mewes, H.W., Ruepp, A., and Frishman, D. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-834.
139. Stumpf, M.P., Thorne, T., de Silva, E., Stewart, R., An, H.J., Lappe, M., and Wiuf, C. (2008) Estimating the size of the human interactome. Proceedings of the National Academy of Sciences of the United States of America, 105, 6959-6964.
140. Hart, G.T., Ramani, A.K., and Marcotte, E. M. (2006) How complete are current yeast and human protein-interaction networks? Genome Biology, 7, 120.
141. Camargo, L.M., Collura, V., Rain, J.C., Mizuguchi, K., Hermjakob, H., Kerrien, S., Bonnert, T.P., Whiting, P.J., and Brandon, N.J. (2007) Disrupted in schizophrenia 1 interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia. Molecular Psychiatry, 12, 74-86.
142. Park, Y.U., Jeong, J., Lee, H., Mun, J.Y., Kim, J.H., Lee, J.S., Nguyen, M.D., Han, S.S., Suh, P.G., and Park, S.K. (2010) Disrupted-in-schizophrenia 1 (DISC1) plays essential roles in mitochondria in collaboration with Mitofilin. Proceedings of the National Academy of Sciences References j51 of the United States of America, 107, 17785-17790.
143. Camargo, L.M.,Wang, Q., and Brandon, N.J. (2008) What can we learn from the disrupted in schizophrenia 1 interactome: lessons for target identification and disease biology? Novartis Foundation Symposium, 289, 208-216, discussion 216-221, 238-240.
144. Wang, Q., Jaaro-Peled, H., Sawa, A., and Brandon, N.J. (2008) How has DISC1 enabled drug discovery? Molecular and Cellular Neurosciences, 37, 187-195.
145. Kaidanovich-Beilin, O. and Woodgett, J.R. (2011) GSK-3: functional insights from cell biology and animal models. Frontiers in Molecular Neuroscience, 4, 40.
146. Goehler, H., Lalowski, M., Stelzl, U., Waelter, S., Stroedicke, M., Worm, U., Droege, A., Lindenberg, K.S., Knoblich, M., Haenig, C., Herbst, M., Suopanki, J., Scherzinger, E., Abraham, C., Bauer, B., Hasenbank, R., Fritzsche, A., Ludewig, A. H., Bussow, K., Coleman, S.H., Gutekunst, C.A., Landwehrmeyer, B.G., Lehrach, H., and Wanker, E.E. (2004) A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Molecules and Cells, 15, 853-865.
147. Enokido, Y., Tamura, T., Ito, H., Arumughan, A., Komuro, A., Shiwaku, H., Sone, M., Foulle, R., Sawada, H., Ishiguro, H., Ono, T., Murata, M., Kanazawa, I., Tomilin, N., Tagawa, K., Wanker, E.E., and Okazawa, H. (2010) Mutant huntingtin impairs Ku70- mediated DNA repair. The Journal of Cell Biology, 189, 425-443.
148. Soler-Lopez, M., Zanzoni, A., Lluis, R., Stelzl, U., and Aloy, P. (2011) Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. Genome Research, 21, 364-376.
149. Behrends, C., Sowa, M.E., Gygi, S.P., and Harper, J.W. (2010) Network organization of the human autophagy system. Nature, 466, 68-76.
150. Dervyn, E., Noirot-Gros, M.F., Mervelet, P., McGovern, S., Ehrlich, S.D., Polard, P., and Noirot, P. (2004) The bacterial condensin/cohesin-like protein complex acts in DNA repair and regulation of gene expression. Molecular Microbiology, 51, 1629-1640.
151. Schleker, S., Sun, J., Raghavan, B., Srnec, M., Muller, N., Koepfinger, M., Murthy, L., Zhao, Z., and Klein-Seetharaman, J. (2012) The current Salmonella-host interactome. Proteomics. Clinical Applications, 6, 117-133.
152. Schleker, S., Garcia-Garcia, J., Klein- Seetharaman, J., and Oliva, B. (2012) Prediction and comparison of Salmonella- human and Salmonella-Arabidopsis interactomes. Chemistry and Biodiversity, 9, 991-1018.
153. Chatr-aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., Tinti, M., Smolyar, A., Castagnoli, L., Vidal, M., Cusick, M.E., and Cesareni, G. (2009) VirusMINT: a viral protein interaction database. Nucleic Acids Research, 37 (Database issue), D669-D673.
154. Ptak, R.G., Fu, W., Sanders-Beer, B.E., Dickerson, J.E., Pinney, J.W., Robertson, D.L., Rozanov, M.N., Katz, K.S., Maglott, D.R., Pruitt, K.D., and Dieffenbach, C.W. (2008) Cataloguing the HIV type 1 human protein interaction network. AIDS Research and Human Retroviruses, 24, 1497-1502.
155. Fu, W., Sanders-Beer, B.E., Katz, K.S., Maglott, D.R., Pruitt, K.D., and Ptak, R.G. (2009) Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Research, 37, D417-D422.
156. Evans, P., Dampier, W., Ungar, L., and Tozeren, A. (2009) Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. BMC Medical Genomics, 2, 27.
157. Puntervoll, P., Linding, R., Gemund, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M., Ausiello, G., Brannetti, B., Costantini, A., Ferre, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, L., Kuster, B., Helmer-Citterich, M., Hunter, W.N., Aasland, R., and Gibson, T.J. (2003) ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research, 31, 3625-3630.
158. Doolittle, J.M. and Gomez, S.M. (2010) Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virology Journal, 7, 82.
159. Dyer, M.D., Murali, T.M., and Sobral, B. W. (2011) Supervised learning and prediction of physical interactions between human and HIV proteins. Infection Genetics and Evolution, 11, 917-923.
160. Nouretdinov, I., Gammerman, A., Qi, Y., and Klein-Seetharaman, J. (2012) Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method. Pacific Symposium on Biocomputing, 2012, 311-322.
161. Jager, S., Cimermancic, P., Gulbahce, N., Johnson, J.R., McGovern, K.E., Clarke, S. C., Shales, M., Mercenne, G., Pache, L., Li, K., Hernandez, H., Jang, G.M., Roth, S.L., Akiva, E., Marlett, J., Stephens, M., D'Orso, I., Fernandes, J., Fahey, M., Mahon, C., O'Donoghue, A.J., Todorovic, A., Morris, J.H., Maltby, D.A., Alber, T., Cagney, G., Bushman, F.D., Young, J.A., Chanda, S.K., Sundquist,W.I., Kortemme, T., Hernandez, R.D., Craik, C. S., Burlingame, A., Sali, A., Frankel, A.D., and Krogan, N.J. (2012) Global landscape of HIV-human protein complexes. Nature, 481, 365-370.