Topological network alignment uncovers biological function and phylogeny

Journal of the Royal Society Interface

Volumn 7, Issue 50, 2010, Pages 1341-1354

  Kuchaiev, Oleksii ^a   Milenković, Tijana ^a   Memišević, Vesna ^a   Hayes, Wayne ^a,b   Pržulj, Nataša ^b  

^a Irvine   (United States)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Network alignment; Network topology; Phylogeny; Protein function; Protein interaction networks

Indexed keywords

ACTIVE NETWORKS; ALGORITHMS; BIOLOGICAL SYSTEMS; ELECTRIC NETWORK TOPOLOGY; PROTEINS;

NETWORK ALIGNMENT; NETWORK TOPOLOGY; PHYLOGENY; PROTEIN FUNCTION; PROTEIN INTERACTION NETWORKS;

ALIGNMENT;

ARTICLE; BIOLOGICAL ACTIVITY; GENETIC ALGORITHM; HUMAN; METABOLISM; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SPECIES COMPARISON;

EID: 77956576710     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2010.0063     Document Type: Article

References (76)

1. Agrafioti, I., Swire, J., Abbott, J., Huntley, D., Butcher, S. & Stunpf, M. P. 2005 Comparative analysis of the Saccharomyces cerevisiae and Caenorhabdits elegans protein interaction networks. BMC Evol. Biol. 5.
2. Altschul, S. F., Gish, W., Miller, W. & Lipman, D. J. 1990 Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Barabási, A. & Albert, R. 1999 Emergence of scaling in random networks. Science 286, 509-512. (doi:10.1126/science.286.5439.509)
4. Berg, J. & Lassig, M. 2004 Local graph alignment and motif search in biological networks. Proc. Natl Acad. Sci. USA 101, 14 689-14 694. (doi:10.1073/pnas.0305199101)
5. Berg, J. & Lassig, M. 2006 Cross-species analysis of biological networks by Bayesian alignment. Proc. Natl Acad. Sci. USA 103, 10 967-10 972. (doi:10.1073/pnas.0602294103)
6. Colizza, V., Flammini, A., Serrano, M. A. & Vespignani, A. 2006 Detecting rich-club ordering in complex networks. Nat. Phys. 2, 110-115. (doi:10.1038/nphys209)
7. Collins, S., Kemmeren, P., Zhao, X., Greenblatt, J., Spencer, F., Holstege, F., Weissman, J. & Krogan, N. 2008 Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteom. 6, 439-450. (doi:10.1074/mcp.M600381-MCP200)
8. Collins, L. & Penny, D. 2005 Complex spliceosomal organization ancestral to extant eukaryotes. Mol. Biol. Evol. 22, 1053-1066. (doi:10.1093/molbev/msi091)
9. Cook, S. 1971 The complexity of theorem-proving procedures. Proc. 3rd Annu. ACM Symp. Theory of Computing, pp. 151-158. New York, NY: Association for Computing Machinery.
10. de Silva, E., Thorne, T., Ingram, P., Agrafioti, I., Swire, J., Wiuf, C. & Stumpf, M. P. 2006 The effects of incomplete protein interaction data on structural and evolutionary inferences. BMC Biol. 4.
11. Doolittle, R. F. 1981 Similar amino-acid sequences: chance or common ancestry? Science 214, 149-159. (doi:10.1126/science.7280687)
12. Flannick, J., Novak, A., Balaji, S., Harley, H. & Batzglou, S. 2006 GRAEMLIN general and robust alignment of multiple large interaction networks. Genome Res. 16, 1169-1181. (doi:10.1101/gr.5235706)
13. Flannick, J., Novak, A. F., Do, C. B., Srinivasan, B. S. & Batzoglou, S. 2008 Automatic parameter learning for multiple network alignment. In Proc. Int. Conf. Research in Computational Molecular Biology - RECOMB, pp. 214-231.
14. Forst, C. & Schulten, K. 2001 Phylogenetic analysis of metabolic pathways. J. Mol. Evol. 52, 471-489.
15. Gavin, A. C. et al. 2002 Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147. (doi:10.1038/415141a)
16. Gavin, A. C. et al. 2006 Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636. (doi:10.1038/nature04532)
17. Guimera, R., Sales-Pardo, M. & Amaral, L. A. N. 2007 Classes of complex networks defined by role-to-role connectivity profiles. Nat. Phys. 3, 63-69. (doi:10.1038/nphys489)
18. Han, J. D. H., Dupuy, D., Bertin, N., Cusick, M. E. & Vidal, M. 2005 Effect of sampling on topology predictions of protein-protein interaction networks. Nat. Biotechnol. 23, 839-844. (doi:10.1038/nbt1116)
19. Heymans, M. & Singh, A. 2003 Deriving phylogenetic trees from the similarity analysis of metabolic pathways. Bioinformatics 19, i138-i146. (doi:10.1093/bioinformatics/btg1018)
20. Higham, D., Rašajski, M. & Pržulj, N. 2008 Fitting a geometric graph to a protein-protein interaction network. Bioinformatics 24, 1093-1099. (doi:10.1093/bioinformatics/btn079)
21. Ho, Y. et al. 2002 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183. (doi:10.1038/415180a)
22. Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S. & Sakaki, Y. 2000 Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl Acad. Sci. USA 97, 1143-1147. (doi:10.1073/pnas.97.3.1143)
23. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. & Sakaki, Y. 2001 A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569-4574. (doi:10.1073/pnas. 061034498)
24. Jeong, H., Mason, S. P., Barabási, A. L. & Oltvai, Z. N. 2001 Lethality and centrality in protein networks. Nature 411, 41-42. (doi:10.1038/35075138)
25. Kanehisa, M. & Goto, S. 2000 KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30. (doi:10.1093/nar/28.1.27)
26. Keeling, P., Luker, M. & Palmer, J. 2000 Evidence from β-tubulin phylogeny that microsporidia evolved from within the fungi. Mol. Biol. Evol. 17, 23-31.
27. Kelley, B. P., Bingbing, Y., Lewitter, F., Sharan, R., Stockwell, B. R. & Ideker, T. 2004 PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. 32, W83-W88.
28. Komili, S., Farny, N. G., Roth, F. P. & Silver, P. A. 2007 Functional specificity among ribosomal proteins regulates gene expression. Cell 131, 557-571. (doi:10.1016/j.cell.2007.08.037)
29. Kosloff, M. & Kolodny, R. 2008 Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 71, 891-902. (doi:10.1002/prot.21770)
30. Koyuturk, M., Kim, Y., Topkara, U., Subramaniam, S., Szpankowski, W. & Grama, A. 2006 Pairwise alignment of protein interaction networks. J. Comput. Biol. 13, 182-199. (doi:10.1089/cmb.2006.13.182)
31. Krogan, N. J. et al. 2006 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643. (doi:10.1038/nature04670)
32. Kuchaiev, O. & Pržulj, N. 2009 Learning the structure of protein-protein interaction networks. In Proc. 2009 Pacific Symp. Biocomputing (PSB), Big Island, Hawaii, 4-8 January 2010, pp. 39-50.
33. Kuchaiev, O., Wang, P. T., Nenadić, Z. & Pržulj, N. 2009 Structure of brain functional networks. In 31st Annu. Int. Conf. IEEE Engineering in Medicine and Biology Society (EMBC '09), Minneapolis, Minnesota, USA, 2-6 September 2009.
34. Labarga, A., Valentin, F., Andersson, M. & Lopez, R. 2007 Web services at the European bioinformatics institute. Nucleic Acids Res. 35, W6-W11. (doi:10.1093/nar/gkm291)
35. Liang, Z., Xu, M., Teng, M. & Niu, L. 2006 NETALIGN: a web-based tool for comparison of protein interaction networks. Bioinformatics 22, 2175-2177. (doi:10.1093/bioinformatics/btl287)
36. Liao, C. S., Lu, K., Baym, M., Singh, R. & Berger, B. 2009 ISORANKN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25, i253-i258. (doi:10.1093/bioinformatics/btp203)
37. Lorkovic, Z. J., Lehner, R., Forstner, C. & Barta, A. 2005 Evolutionary conservation of minor u12-type spliceosome between plants and humans. RNA 11, 1095-1107. (doi:10.1261/rna.2440305)
38. Memišević, V., Milenković, T. & Pržulj, N. In press. Complementarity of network and sequence structure in homologous proteins. J. Integr. Bioinformatics.
39. Milenković, T., Filippis, I., Lappe, M. & Pržulj, N. 2009 Optimized null model for protein structure networks. PLoS ONE 4, e5967. (doi:10.1371/journal.pone.0005967)
40. Milenković, T. & Pržulj, N. 2008 Uncovering biological network function via graphlet degree signatures. Cancer Inform. 6, 257-273.
41. Milenković, T., Lai, J. & Pržulj, N. 2008 GRAPHCRUNCH: a tool for large network analyses. BMC Bioinformatics 9.
42. Ohno, S. 1970 Evolution by gene duplication. Berlin, Germany: Springer.
43. Out, H. & Sayood, K. 2003 A new sequence distance measure for phylogenetic tree construction. Bioinformatics 19, 2122-2130. (doi:10.1093/bioinformatics/btg295)
44. Pennisi, E. 2003 Modernizing the tree of life. Science 300, 1692-1697. (doi:10.1126/science.300.5626.1692)
45. Peri, S. 2004 Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 32, D497-D501.
46. Pržulj, N. 2007 Biological network comparison using graphlet degree distribution. Bioinformatics 23, e177-e183.
47. Pržulj, N. & Higham, D. 2006 Modelling protein-protein interaction networks via a stickiness index. J. R. Soc. Interface 3, 711-716. (doi:10.1098/rsif.2006.0147)
48. Pržulj, N., Corneil, D. G. & Jurisica, I. 2004 Modeling interactome: scale-free or geometric? Bioinformatics 20, 3508-3515. (doi:10.1093/bioinformatics/bth436)
49. Pržulj, N., Corneil, D. G. & Jurisica, I. 2006 Efficient estimation of graphlet frequency distributions in protein-protein interaction networks. Bioinformatics 22, 974-980.
50. Pržulj, N., Kuchaiev, O., Stevanović, A. & Hayes, W. 2010 Geometric evolutionary dynamics of protein interaction networks. In Proc. 2009 Pacific Symp. Biocomputing (PSB), Big Island, Hawaii, 4-8 January 2010, pp. 178-189.
51. Radivojac, P., Peng, K., Clark, W. T., Peters, B. J., Mohan, A., Boyle, S. M. & Mooney, S. D. 2008 An integrated approach to inferring gene-disease associations in humans. Proteins 72, 1030-1037. (doi:10.1002/prot.21989)
52. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M. & Seraphin, B. 1999 A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030-1032. (doi:10.1038/13732)
53. Rost, B. 1999 Twilight zone of protein sequence alignments. Protein Eng. 12, 85-94. (doi:10.1093/protein/12.2.85)
54. Rual, J. et al. 2005 Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178. (doi:10.1038/ nature04209)
55. Sharan, R. & Ideker, T. 2006 Modeling cellular machinery through biological network comparison. Nat. Biotechnol. 24, 427-433. (doi:10.1038/nbt1196)
56. Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M. & Ideker, T. 2005 Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA 102, 1974-1979. (doi:10.1073/pnas.0409522102)
57. Simonis, N. et al. 2008 Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat. Meth. 6, 47-54. (doi:10.1038/nmeth.1279)
58. Singh, R., Xu, J. & Berger, B. 2007 Pairwise global alignment of protein interaction networks by matching neighborhood topology. In Research in computational molecular biology, pp. 16-31. Berlin, Germany: Springer.
59. Singh, R., Xu, J. & Berger, B. 2008 Global alignment of multiple protein interaction networks. Proc. Pacific Symp. Biocomputing 13, 303-314. (doi:10.1142/9789812776136-0030)
60. Snijders, T. A. 2002 Markov chain Monte Carlo estimation of exponential random graph models. J. Soc. Struct. 3, 2-40.
61. Stark, C., Breitkreutz, B., Reguly, T., Boucher, L., Breitkreutz, A. & Tyers, M. 2006 BIOGRID: a general repository for interaction datasets. Nucleic Acids Res. 34, D535-D539.
62. Stelzl, U. et al. 2005 A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957-968. (doi:10.1016/j.cell. 2005.08.029)
63. Suthram, S., Sittler, T. & Ideker, T. 2005 The plasmodium protein network diverges from those of other eukaryotes. Nature 438, 108-112. (doi:10.1038/nature04135)
64. Tanriverdi, S. & Widmer, G. 2006 Differential evolution of repetitive sequences in Cryptosporidium parvum and Cryptosporidium hominis. Infect. Genet. Evol. 6, 113-122. (doi:10.1016/j.meegid.2005.02.002)
65. The Gene Ontology Consortium 2000 Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-29.
66. Thorne, T. & Stumpf, M. 2007 Generating confidence intervals on biological networks. BMC Bioinformatics 8, 467. (doi:10.1186/1471-2105-8-467)
67. Uetz, P. et al. 2000 A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627. (doi:10.1038/35001009)
68. Venkatesan, K. et al. 2009 An empirical framework for binary interactome mapping. Nat. Meth. 6, 83-90. (doi:10.1038/nmeth.1280)
69. Watson, J. D., Laskowski, R. A. & Thornton, J. M. 2005 Predicting protein function from sequence and structural data. Curr. Opin. Struct. Biol. 15, 275-284. (doi:10.1016/j.sbi.2005.04.003)
70. Watts, D. J. & Strogatz, S. H. 1998 Collective dynamics of 'small-world' networks. Nature 393, 440-442. (doi:10.1038/30918)
71. Webb, E. C. 1990 Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes, the University of Michigan.
72. Wentz-Hunter, K. & Potashkin, J. 1995 The evolutionary conservation of the splicing apparatus between fission yeast and man. Nucleic Acids Symp. 33, 226-228.
73. Whisstock, J. C. & Lesk, A. M. 2003 Prediction of protein function from protein sequence and structure. Q. Rev. Biophys. 36, 307-340. (doi:10.1017/S0033583503003901)
74. Xu, P. et al. 2004 The genome of Cryptosporidium hominis. Nature 431, 1107-1112. (doi:10.1038/nature02977)
75. Zhang, Y. et al. 2006 Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. BMC Bioinformatics 7. (doi:10.1186/1471-2105-7-7)
76. Zaslavskiy, M., Bach, F. & Vert, J. P. 2009 Global alignment of protein-protein interaction networks by graph matching methods. Bioinformatics 25, i259-i267.