Biological network querying techniques: Analysis and comparison

Journal of Computational Biology

Volumn 18, Issue 4, 2011, Pages 595-625

  Fionda, Valeria ^a   Palopoli, Luigi ^b  

^a FREE UNIVERSITY OF BOZEN BOLZANO   (Italy)

^b UNIVERSITY OF CALABRIA   (Italy)

Author keywords

algorithms; computational molecular biology; proteins

Indexed keywords

PROTEIN;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; HUMAN; METABOLISM; METHODOLOGY; SYSTEMS BIOLOGY;

ALGORITHMS; ANIMALS; HUMANS; MODELS, BIOLOGICAL; PROTEINS; SYSTEMS BIOLOGY;

EID: 79957500684     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0144     Document Type: Article

References (47)

1. Albert, R. 2005. Scale-free networks in cell biology. J. Cell Sci. 118, 4947-4957. (Pubitemid 41672427)
2. Alon, N., Yuster, R., and Zwick, U. 1995. Color-coding. J. ACM 42, 844-856.
3. Bairoch, A., Boeckmann, B., Ferro, S. et al. 2004. Swiss-prot: juggling between evolution and stability. Brief.Bioinform. 5, 39-58.
4. Berg, J. Lässig, M. and Wagner, A. 2004. Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol. Biol. 4, 51.
5. Bruckner, S. Hüffner, F. Karp, R.M. et al. 2009. Topology-free querying of protein interaction networks. Lect. Notes Bioinform. 5541.
6. Carbon, S., Ireland, A., Mungall, C.J., et al. 2008. Amigo: online access to ontology and annotation data. Bioinformatics 25, 288-289.
7. Chang, A., Scheer, M., Grote, A., et al. 2008. Brenda, amenda and frenda the enzyme information system: new content and tools in 2009. Nucleic Acids Res. 36, D588-D592.
8. Chatraryamontri, A., Ceol, A., Montecchi-Palazzi, L., et al. 2007. Mint: the molecular interaction database. Nucleic Acids Res. 35, 572-574.
9. Cherry, J.M., Adler, C., Ball, C., et al. 1998. Sgd: Saccharomyces genome database. Nucleic Acids Res. 26, 73-79. (Pubitemid 28295265)
10. Dost, B., Shlomi, T., Gupta, N., et al. 2008. Qnet: a tool for querying protein interaction networks. J. Comput. Biol. 15, 913-925.
11. Durand, P., Labarre, L., Meil, A., et al. 2006. Genolink: a graph-based querying and browsing system for investigating the function of genes and proteins. BMC Bioinform. 7, 21.
12. Ferro, A., Giugno, R., Pigola, G., et al. 2007. Netmatch: a cytoscape plugin for searching biological networks. Bioinformatics 23, 910-912. (Pubitemid 47049930)
13. Fionda, V., Palopoli, L., Panni, S., et al. 2008. Protein-protein interaction network querying by a "focus and zoom" approach. Proc. 2nd Int. Conf. Bioinform. Res. Dev. (BIRD 08) 331-346.
14. Consortium Flybase. 1999. The flybase database of the Drosophila genome projects and community literature. The flybase consortium. Nucleic Acids Res. 27, 85-88.
15. Garey, M.R., and Johnson, D.S. 1979. Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman, New York.
16. Hattori, M., Okuno, Y., Goto, S., et al. 2003. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc. 125, 11853-11865. (Pubitemid 37175419)
17. Hunter, S., Apweiler, R., Attwood, T.K., et al. 2008. Interpro: the integrative protein signature database. Nucleic Acids Res. 36, D211-D215.
18. Janes, K.A., and Yaffe, M.B. 2008. Data-driven modelling of signal-transduction networks. Nat. Rev. Mol. Cell Biol. 7, 820-828. (Pubitemid 44627475)
19. Kalaev, M., Smoot, M., Ideker, T., et al. 2008. Networkblast: comparative analysis of protein networks. Bioinformatics 24, 594-596. (Pubitemid 351256310)
20. Kanehisa, M., and Goto, S. 2000. Kegg: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30. (Pubitemid 30047706)
21. Karp, P.D., Ouzounis, C.A., Moore-Kochlacs, C., et al. 2005. Expansion of the biocyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33, 6083-6089. (Pubitemid 41742547)
22. Kelley, B.P., Sharan, R., Karp, R.M., et al. 2003. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. USA 100, 11394-11399. (Pubitemid 37205946)
23. Kelley, R., and Ideker, T. 2005. Systematic interpretation of genetic interactions using protein networks. Nat. Bio-technol. 23, 561-566. (Pubitemid 41724894)
24. Keseler, I.M., Bonavides-Martinez, C., Collado-Vides, J., et al. 2009. Ecocyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res. 37, D464-D470.
25. Lee, T.I., Rinaldi, N.J., Robert, F., et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804. (Pubitemid 35231527)
26. Matthews, L., Gopinath, G., Gillespie, M., et al. 2008. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 36, D619-D622.
27. Pearson, W.R., and Lipman, D.J. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444-2448.
28. Pinter, R.Y., Rokhlenko, O., Yeger Lotem, E. et al. 2005. Alignment of metabolic pathways. Bioinformatics 21, 3401-3408. (Pubitemid 41222445)
29. Prasad, K.T.S., Goel, R., Kandasamy, K., et al. 2008. Human protein reference database-2009 update. Nucleic Acids Res. 36, D767-D772.
30. Qian X., Sze, S.-H., and Yoon, B.-J. 2009. Querying pathways in protein interaction networks based on hidden markov models. J. Comput. Biol. 16, 145-157.
31. Robertson, N., and Seymour, P.D. 1986. Graph minors. II. Algorithmic aspects of tree-width. J. Algorithms 7, 309-322.
32. Ruepp, A., Brauner, B., Dunger-Kaltenbach, I., et al. 2008. Corum: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res. 36, D646-D650. (Pubitemid 351149800)
33. Salwinski, L., Miller, C.S., Smith, A.J., et al. 2004. The database of interacting proteins: 2004 update. Nucleic Acids Res. 32, D449-D451. (Pubitemid 38081696)
34. Sharan, R., and Ideker, T. 2006. Modeling cellular machinery through biological network comparison. Nat. Biotechnol. 24, 427-433.
35. Sharan, R., Suthram, S., Kelley, R.M., et al. 2005. Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA 102, 1974-1979. (Pubitemid 40261997)
36. Shlomi, T., Segal, D., Ruppin, E., et al. 2006. Qpath: a method for querying pathways in a protein-protein interaction network. BMC Bioinform. 7.
37. Singh, R., Xu, J., and Berger, B. 2007. Pairwise global alignment of protein interaction networks by matching neighborhood topology. Proc. RECOMB '07 16-31. (Pubitemid 47164529)
38. Stark, C., Breitkreutz, B.-J., Reguly, T., et al. 2006. Biogrid: a general repository for interaction datasets. Nucleic Acids Res. 34 D535-D539.
39. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278, 631-637. (Pubitemid 27464953)
40. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., et al. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22-28. (Pubitemid 32054398)
41. Tatusova, T.A., and Madden, T.L. 1999. Blast 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174, 247-250. (Pubitemid 29217013)
42. Tian, Y., McEachin, R.C., Santos, C., et al. 2007. Saga: a subgraph matching tool for biological graphs. Bioinformatics 23, 232-239. (Pubitemid 46189614)
43. Tohsato, Y., Matsuda, H., and Hashimoto, A. 2000. A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. Proc. ISMB '00 376-383.
44. Wernicke, S., and Rasche, F. 2007. Simple and fast alignment of metabolic pathways by exploiting local diversity. Bioinformatics 23, 1978-1985. (Pubitemid 47299839)
45. Yang, Q., and Sze, S.-H. 2007. Path matching and graph matching in biological networks. J. Comput. Biol. 14, 56-67. (Pubitemid 46535306)
46. Zhang, L.V., King, O.D., Wong, S.L., et al. 2005. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J. Biol. 4, 2.
47. Zhang, S., Zhang, X.-S., and Chen, L. 2008. Biomolecular network querying: a promising approach in system biology. BMC Syst. Biol. 5, 2.