Management and Analysis of Protein-to-Protein Interaction Data

  • Mario Cannataro
  • Pietro Hiram Guzzi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6685)

Abstract

This paper introduces technologies, standards and databases for generating, representing and storing Protein-to-Protein Interaction (PPI) data. Emerging algorithms for the analysis, comparison and knowledge extraction from Protein-to-Protein Interaction Networks (PINs) are also presented. Finally, the paper presents a methodology for the ontology-based analysis of Protein-to-Protein Interaction data by discussing a real case study.

Keywords

Protein-to-Protein Interaction Data Protein-to-Protein Interaction Networks Protein Complex Prediction Motifs Extraction Network Alignment Gene Ontology 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Alfarano, C., Andrade, C.E., Anthony, K., Bahroos, N., Bajec, M., Bantoft, K., Bete, D., Bobechko, B., Boutilier, K., Burgess, E., Buzadzija, K., Cavero, R., D’Abreo, C., Donaldson, I., Dorairajoo, D., Dumontie, M.J., Dumontier, M.R., Earles, V., Farral, R., Feldman, H., Garderman, E., Gong, Y., Gonzaga, R., Grytsan, V., Gryz, E., Gu, V., Haldorsen, E., Halupa, A., Haw, R., Hrvojic, A., Hurrell, L., Isserlin, R., Jack, F., Juma, F., Khan, A., Kon, T., Konopinsky, S., Le, V., Lee, E., Ling, S., Magidin, M., Moniakis, J., Montojo, J., Moore, S., Muskat, B., Ng, I., Paraiso, J.P., Parker, B., Pintilie, G., Pirone, R., Salama, J.J., Sgro, S., Shan, T., Shu, Y., Siew, J., Skinner, D., Snyder, K., Stasiuk, R., Strumpf, D., Tuekam, B., Tao, S., Wang, Z., White, M., Willis, R., Wolting, C., Wong, S., Wrong, A., Xin, C., Yao, R., Yates, B., Zhang, S., Zheng, K., Pawson, T., Ouellette, B.F., Hogue, C.W.: The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res. 33(database issue), 418–424 (2005)CrossRefGoogle Scholar
  2. 2.
    Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A.T., Kerrien, S., Khadake, J., Kerssemakers, J., Leroy, C., Menden, M., Michaut, M., Montecchi-Palazzi, L., Neuhauser, S.N., Orchard, S., Perreau, V., Roechert, B., van Eijk, K., Hermjakob, H.: The IntAct molecular interaction database in 2010. Nucleic Acids Research  38(database issue), gkp878–531 (2010)Google Scholar
  3. 3.
    Assenov, Y., Ramirez, F., Schelhorn, S.-E., Lengauer, T., Albrecht, M.: Computing topological parameters of biological networks. Bioinformatics 24(2), 282–284 (2008)CrossRefGoogle Scholar
  4. 4.
    Bader, G., Hogue, C.: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4(1), 2 (2003)CrossRefGoogle Scholar
  5. 5.
    Berg, J., Lassig, M.: Local graph alignment and motif search in biological networks. Proc. Natl. Acad. Sci. 41(101), 14689–14694 (2004)CrossRefGoogle Scholar
  6. 6.
    Brown, K., Jurisica, I.: Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biology 8(5), R95+ (2007)Google Scholar
  7. 7.
    Cannataro, M., Guzzi, P.H., Veltri, P.: Protein-to-protein interactions: Technologies, databases, and algorithms. ACM Comput. Surv. 43, 1:1–1:36 (2010)Google Scholar
  8. 8.
    Chatr-Aryamontri, A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L., Cesareni, G.: Mint: the molecular interaction database. Nucleic Acids Res. 35, D572–D574 (2007)CrossRefGoogle Scholar
  9. 9.
    Chaurasia, G., Iqbal, Y., Hanig, C., Herzel, H., Wanker, E.E., Futschik, M.E.: UniHI: an entry gate to the human protein interactome. Nucl. Acids Res. 35(suppl. 1), D590–D594 (2007)CrossRefGoogle Scholar
  10. 10.
    Deng, M., Sun, F., Chen, T.: Assessment of the reliability of proteinprotein interactions and protein function prediction. In: Proc. of Pacific Symposium Biocomputing, Grand Wailea, Maui, Hawaii, pp. 140–151. World Scientific, Singapore (2003)Google Scholar
  11. 11.
    Enright, S., Van Dongen, A.J., Ouzounis, C.A.: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 30(7), 1575–1584 (2002)CrossRefGoogle Scholar
  12. 12.
    Fell, D.A., Wagner, A.: The small world of metabolism. Nat. Biotechnol. 18(11), 1121–1122 (2000)CrossRefGoogle Scholar
  13. 13.
    Flannick, J., Novak, A., Srinivasan, B.S., McAdams, H.H., Batzoglou, S.: Graemlin: general and robust alignment of multiple large interaction networks. Genome Res. 16(9), 1169–1181 (2006)CrossRefGoogle Scholar
  14. 14.
    Golumbic, M.C.: Algorithmic graph theory and perfect graphs. Academic Press, New York (1980)MATHGoogle Scholar
  15. 15.
    Harris, M.A., et al.: The gene ontology (go) database and informatics resource. Nucleic Acids Res. 32(database issue), 258–261 (2004)Google Scholar
  16. 16.
    Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., Apweiler, R.: Intact: an open source molecular interaction database. Nucleic Acids Res. 1(32)(database issue), 452–455 (2004)Google Scholar
  17. 17.
    Huang, D.W., Sherman, B.T., Lempicki, R.A.: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research 37(1), 1–13 (2009)CrossRefGoogle Scholar
  18. 18.
    Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattor, M., Sakaki, Y.: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569–4574 (2001)CrossRefGoogle Scholar
  19. 19.
    Kelley, B.P., Yuan, B., Lewitter, F., Sharan, R., Stockwell, B.R., Ideker, T.: PathBLAST: a tool for alignment of protein interaction networks. Nucl. Acids Res. 32(suppl. 2), W83–W88 (2004)CrossRefGoogle Scholar
  20. 20.
    Kerrien, S., Orchard, S., Montecchi-Palazzi, L., Aranda, B., Quinn, A., Vinod, N., Bader, G., Xenarios, I., Wojcik, J., Sherman, D., Tyers, M., Salama, J., Moore, S., Ceol, A., Chatraryamontri, A., Oesterheld, M., Stumpflen, V., Salwinski, L., Nerothin, J., Cerami, E., Cusick, M., Vidal, M., Gilson, M., Armstrong, J., Woollard, P., Hogue, C., Eisenberg, D., Cesareni, G., Apweiler, R., Hermjakob, H.: Broadening the horizon - level 2.5 of the hupo-psi format for molecular interactions. BMC Biology 44(1), 44 (2007)CrossRefGoogle Scholar
  21. 21.
    King, A.D.: Graph clustering with restricted neighbourhood search, Master’s thesis, University of Toronto (2004)Google Scholar
  22. 22.
    Koyutürk, M., Kim, Y., Subramaniam, S., Szpankowski, W., Grama, A.: Detecting conserved interaction patterns in biological networks. J. Comput. Biol. 13(7), 1299–1322 (2006)MathSciNetCrossRefGoogle Scholar
  23. 23.
    Liao, C.-S., Lu, K., Baym, M., Singh, R., Berger, B.: IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25(12), i253–i258 (2009)CrossRefGoogle Scholar
  24. 24.
    Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., Alon, U.: Network motifs: simple building blocks of complex networks. Science 298(5594), 824–827 (2002)CrossRefGoogle Scholar
  25. 25.
    Nassa, G., Tarallo, R., Ambrosino, C., Bamundo, A., Ferraro, L., Paris, O., Ravo, M., Guzzi, P.H., Cannataro, M., Baumann, M., Nyman, T.A., Nola, E., Weisz, A.: A large set of estrogen receptor interacting proteins identified by tandem affinity purification in hormone-responsive human breast cancer cell nuclei. Proteomics 43, 159–165 (2011)CrossRefGoogle Scholar
  26. 26.
    Nassa, G., Tarallo, R., Guzzi, P.H., Ferraro, L., Cirillo, F., Ravo, M., Nola, E., Baumann, M., Nyman, T.A., Cannataro, M., Ambrosino, C., Weisz, A.: Comparative analysis of nuclear estrogen receptor alpha and beta interactomes in breast cancer cells. Mol. BioSyst. 7(3), 667–676 (2011)CrossRefGoogle Scholar
  27. 27.
    Orchard, S., Kerrien, S., Jones, P., Ceol, A., Chatr-Aryamontri, A., Salwinski, L., Nerothin, J., Hermjakob, H.: Submit your interaction data the imex way: a step by step guide to trouble-free deposition. Proteomics 7(S1), 28–34 (2007)CrossRefGoogle Scholar
  28. 28.
    Pavlopoulos, G., Wegener, A.L., Schneider, R.: A survey of visualization tools for biological network analysis. BioData Mining 1(1), 12+ (2008)Google Scholar
  29. 29.
    Nucleic Acids Res. (Nar. database issue) (January 2007)Google Scholar
  30. 30.
    Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U., Eisenberg, D.: The Database of Interacting Proteins: 2004 update. Nucl. Acids Res. 32(suppl. 1), D449–D451 (2004)CrossRefGoogle Scholar
  31. 31.
    Singh, R., Xu, J., Berger, B.: Global alignment of multiple protein interaction networks with application to functional orthology detection. Proceedings of the National Academy of Sciences 105(35), 12763–12768 (2008)CrossRefGoogle Scholar
  32. 32.
    Siuzdak, G.: The expanding role of mass spectrometry in biotechnology. MCC Press (2006)Google Scholar
  33. 33.
    Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., Jensen, L.J., von Mering, C.: The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research 39(database issue), D561–D568 (2011)CrossRefGoogle Scholar
  34. 34.
    Xia, K., Dong, D., Han, J.-D.D.: IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics 7, 508 (2006)CrossRefGoogle Scholar
  35. 35.
    Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M., Cesareni, G.: Mint: a molecular interaction database. FEBS Lett. 513(1), 135–140 (2002)CrossRefGoogle Scholar
  36. 36.
    Zhang, S., Zhang, X.-S., Chen, L.: Biomolecular network querying: a promising approach in systems biology. BMC Systems Biology 2(1), 5 (2008)MathSciNetCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Mario Cannataro
    • 1
  • Pietro Hiram Guzzi
    • 1
  1. 1.Department of Experimental Medicine and ClinicUniversity Magna Græcia of CatanzaroItaly

Personalised recommendations