Graphlet-based measures are suitable for biological network comparison

Bioinformatics

Volumn 29, Issue 4, 2013, Pages 483-491

  Hayes, Wayne ^a   Sun, Kai ^b   Pržulj, Nataša ^b  

^a Irvine   (United States)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN;

ARTICLE; BIOLOGICAL MODEL; METABOLISM; METHODOLOGY; NONPARAMETRIC TEST; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION;

MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; STATISTICS, NONPARAMETRIC; VIRAL PROTEINS;

MLCS; MLOWN;

EID: 84874289423     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts729     Document Type: Article

References (45)

1. Arabidopsis Interactome Mapping Consortium (2011). Evidence for network evolution in an Arabidopsis interactome map. Science, 333, 601-607.
2. Barabasi, A.-L. and Albert, R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
3. Colak, R. et al. (2009) Dense graphlet statistics of protein interaction and random networks. Pac. Symp. Biocomput., 14, 178-189.
4. Collins, S. et al. (2007) Toward a comprehensive atlas of the phyisical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics, 6, 439-450.
5. Erdos, P. and Re?nyi, A. (1959) On random graphs. Publ. Math., 6, 290-297.
6. Erdos, P. and Renyi, A. (1960) On the evolution of random graphs. Publ.Math. Inst. Hung. Acad. Sci., 5, 17-61.
7. Feynman, R.P. (1963) Feynman Lectures on Physics, Vol. 1. Addison-Wesley, Reading, MA.
8. Fossum, E. et al. (2009) Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog., 5, 13.
9. Gavin, A.C. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
10. Gavin, A.-C. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature, 440, 631-636.
11. Gibson, T.A. and Goldberg, D.S. (2011) Improving evolutionary models of protein interaction networks. Bioinformatics, 27, 376-382.
12. Hakes, L. et al. (2008) Protein-protein interaction networks and biology-what's the connection? Nat. Biotechnol., 26, 69-72.
13. Han, J.D. et al. (2005) Effect of sampling on topology predictions of protein-protein interaction networks. Nat. Biotechnol., 23, 839-844.
14. Hartuv, E. and Shamir, R. (2000) A clustering algorithm based on graph connectivity. Inform. Process. Lett., 76, 175-181.
15. Ho, H. et al. (2010) Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. BMC Syst. Biol., 4, 84.
16. Ito, T. et al. (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.
17. Krogan, N.J. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
18. Kuchaiev, O. and Przulj, N. (2011) Integrative network alignment reveals large regions of global network similarity in yeast and human. Bioinformatics, 27, 1390-1396.
19. Kuchaiev, O. et al. (2009) Geometric de-noising of protein-protein interaction networks. PLoS Comput. Biol., 5, e1000454.
20. Kuchaiev, O. et al. (2010) Topological network alignment uncovers biological function and phylogeny. J. R. Soc. Interface, 7, 1341-1354.
21. Memisevic, V. and Przulj, N. (2012) C-graal: common-neighbors-based global graph alignment of biological networks. Integr. Biol., 4, 734-743.
22. Milenkovic, T. et al. (2010a) Optimal network alignment with graphlet degree vectors. Cancer Inform., 9, 121-137.
23. Milenkovic, T. et al. (2010b) Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. J. R. Soc. Interface, 44, 353-350.
24. Parrish, J.R. et al. (2007) A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol., 8, R130.
25. Penrose, M. (2003) Geometric Random Graphs. Oxford University Press, Oxford, UK.
26. Peregrn-Alvarez, J.M. et al. (2009) The modular organization of protein interactions in Escherichia coli. PLoS Comput. Biol., 5, e1000523.
27. Peri, S. et al. (2004) Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res, 32 (Database issue), D497-D501.
28. Przulj, N. (2007) Biological network comparison using graphlet degree distribution. Bioinformatics, 23, e177-e183.
29. Przulj, N. and Higham, D. (2006) Modelling protein-protein interaction networks via a stickiness index. J. R. Soc. Interface, 3, 711-716.
30. Przulj, N. et al. (2004) Modeling interactome: scale-free or geometric? Bioinformatics, 20, 3508-3515.
31. Przulj, N. et al. (2010) Geometric evolutionary dynamics of protein interaction networks. In: Proceedings of the 2010 Pacific Symposium on Biocomputing (PSB). Big Island, Hawaii, January 4-8, 2010.
32. Przulj, N. (2010) Erratum to Biological network comparison using graphlet degree distribution. Bioinformatics, 26, 853-854.
33. Radivojac, P. et al. (2008) An integrated approach to inferring gene-disease associations in humans. Proteins, 72, 1030-1037.
34. Rigaut, G. et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol., 17, 1030-1032.
35. Rito, T. et al. (2010) How threshold behaviour affects the use of subgraphs for network comparison. Bioinformatics, 26, i611-i617.
36. Rual, J.-F. et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
37. Sato, S. et al. (2007) A large-scale protein-protein interaction analysis in Synechocystis sp PCC6803. DNA Res., 14, 207-216.
38. Shimoda, Y. et al. (2008) A large scale analysis of protein-protein interactions in the nitrogen-fixing bacterium Mesorhizobium loti. DNA Res., 15, 13-23.
39. Simonis, N. et al. (2009) Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat. Methods, 6, 47-54.
40. Stark, C. et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res., 34, D535-D539.
41. Stelzl, U. et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122, 957-968.
42. Stumpf, M.P.H. et al. (2005) Subnets of scale-free networks are not scale-free: sampling properties of networks. Proc. Natl. Acad. Sci. USA, 102, 4221-4224.
43. Uetz, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
44. Vazquez, A. et al. (2003) Modeling of protein interaction networks. Complexus, 1, 38-44.
45. von Mering, C. et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.