Alignment-free protein interaction network comparison

Bioinformatics

Volumn 30, Issue 17, 2014, Pages

  Ali, Waqar ^a   Rito, Tiago ^a   Reinert, Gesine ^a   Sun, Fengzhu ^b   Deane, Charlotte M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; EVOLUTION; HUMAN; PHYLOGENY; PROCEDURES; PROTEIN ANALYSIS;

ALGORITHMS; ANIMALS; BIOLOGICAL EVOLUTION; HUMANS; PHYLOGENY; PROTEIN INTERACTION MAPPING;

EID: 84907030076     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu447     Document Type: Conference Paper

References (46)

1. Ali, W. and Deane, C.M. (2010) Evolutionary analysis reveals low coverage as the major challenge for protein interaction network alignment. Mol. Biosyst., 6, 2296-2304.
2. Alkan, F. and Erten, C. (2014) Beams: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. Bioinformatics, 30, 531-539.
3. Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
4. Chung, F. and Lu, L. (2002) The average distances in random graphs with given expected degrees. Proc. Natl Acad. Sci. USA, 99, 15879-15882.
5. Cootes, A.P. et al. (2007) The identification of similarities between biological networks: application to the metabolome and interactome. J. Mol. Biol., 369, 1126-1139.
6. Deane, C.M. et al. (2002) Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. Cell. Proteomics, 1, 349-356.
7. Erdös, P. and Renyi, A. (1961) On the evolution of random graphs. Bull. Inst. Internat. Statist., 38, 343-347.
8. Flannick, J. et al. (2009) Automatic parameter learning for multiple network alignment. J. Comput. Biol., 16, 1001-1022.
9. Gonnet, G. (2012) Surprising results on phylogenetic tree building methods based on molecular sequences. BMC Bioinformatics, 13, 148.
10. Hoevar, T. and Demar, J. (2014) A combinatorial approach to graphlet counting. Bioinformatics, 30, 559-565.
11. Hu, J. et al. (2014) Netcoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics, 30, 540-548.
12. Hubert, L. and Arabie, P. (1985) Comparing partitions. J. Classif., 2, 193-218.
13. Huelsenbeck, J.P. and Hillis, D.M. (1993) Success of phylogenetic methods in the four-taxon case. Syst. Biol., 42, 247-264.
14. Ideker, T. and Krogan, N.J. (2012) Differential network biology. Mol. Systems Biol., 8, 565.
15. Keshava Prasad, T.S. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
16. Kuchaiev, O. and Przulj, N. (2011) Integrative network alignment reveals large regions of global network similarity in yeast and human. Bioinformatics, 27, 1390-1396.
17. Lewis, A.C.F. et al. (2012) What evidence is there for the homology of proteinprotein interactions? PLoS Comput. Biol., 8, e1002645.
18. Liao, C.-S. et al. (2009) IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics, 25, i253-i258.
19. Liu, X. et al. (2011a) New powerful statistics for alignment-free sequence comparison under a pattern transfer model. J. Theor. Biol., 284, 106-116.
20. Liu, Z. et al. (2011b) Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. BMC Evol. Biol., 11, 133.
21. Matthews, L.R. et al. (2001) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or interologs. Genome Res., 11, 2120-2126.
22. Middendorf, M. et al. (2005) Inferring network mechanisms: the drosophila melanogaster protein interaction network. Proc. Natl Acad. Sci. USA, 102, 3192-3197.
23. Newman, M. (2010) Networks: An Introduction. 1st edn. Oxford University Press, USA.
24. Onnela, J.-P. et al. (2012) Taxonomies of networks from community structure. Phys. Rev. E, 86, 036104.
25. Patro, R. and Kingsford, C. (2012) Global network alignment using multiscale spectral signatures. Bioinformatics, 28, 3105-3114.
26. Pattison, P. (1993) Algebraic Models for Social Networks. Structural Analysis in the Social Sciences. Cambridge University Press, USA.
27. Penrose, M. (2003) Random Geometric Graphs (Oxford Studies in Probability). Oxford University Press, USA.
28. Phan, H.T.T. and Sternberg, M.J.E. (2012) Pinalog: a novel approach to align protein interaction networks-implications for complex detection and function prediction. Bioinformatics, 28, 1239-1245.
29. Pržulj, N. (2007) Biological network comparison using graphlet degree distribution. Bioinformatics, 23, e177-e183.
30. Pržulj, N. et al. (2010) Geometric Evolutionary Dynamics of Protein Interaction Networks. Chapter 20, pp 178-189.
31. R Core Team. (2013) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
32. Ratmann, O. et al. (2009) From evidence to inference: probing the evolution of protein interaction networks. HFSP J., 3, 290-306.
33. Reinert, G. et al. (2009) Alignment-free sequence comparison (I): statistics and power. J. Comput. Biol., 16, 1615-1634.
34. Rice, J.J. et al. (2005) Lasting impressions: Motifs in protein-protein maps may provide footprints of evolutionary events. Proc. Natl Acad. Sci. USA, 102, 3173-3174.
35. Rito, T. et al. (2010) How threshold behaviour affects the use of subgraphs for network comparison. Bioinformatics, 26, i611-i617.
36. Rito, T. et al. (2012) The importance of age and high degree, in protein-protein interaction networks. J. Comput. Biol., 19, 785-795.
37. Salwinski, L. et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32 (Suppl. 1), D449-D451.
38. Sayers, E.W. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37 (Suppl. 1), D5-D15.
39. Schliep, K. (2011) phangorn: phylogenetic analysis in r. Bioinformatics, 27, 592-593.
40. Sharan, R. and Ideker, T. (2006) Modeling cellular machinery through biological network comparison. Nat. Biotechnol., 24, 427-433.
41. Shou, C. et al. (2011) Measuring the evolutionary rewiring of biological networks. PLoS Comput. Biol., 7, e1001050.
42. Singh, R. et al. (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl Acad. Sci. USA, 105, 12763-12768.
43. Sokal, R.R. andMichener, C.D. (1958) A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull., 28, 1409-1438.
44. Song, K. et al. (2013) Alignment-free sequence comparison based on next-generation sequencing reads. J. Comput. Biol., 20, 64-79.
45. Wagner, G.P. et al. (2007) The road to modularity. Nat. Rev. Genet., 8, 921-931.
46. Zhu, X. et al. (2007) Getting connected: analysis and principles of biological networks. Genes Dev., 21, 1010-1024.