Finding alignments of conserved graphlets in protein interaction networks

Journal of Computational Biology

Volumn 21, Issue 3, 2014, Pages 234-246

  Hsieh, Mu Fen ^a   Sze, Sing Hoi ^a,b  

^a Department of Electrical and Computer Engineering   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

graphlet alignment; protein interaction networks

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT; THEORETICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; MODELS, THEORETICAL; PROTEIN INTERACTION MAPS; PROTEINS; SEQUENCE ALIGNMENT;

EID: 84896758867     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2013.0130     Document Type: Article

References (42)

1. Alon, N., Dao, P., Hajirasouliha, I., et al. 2008. Biomolecular network motif counting and discovery by color coding. Bioinformatics 24, I241-I249. (Pubitemid 351911679)
2. Altschul, S.F., Gish, W., Miller, W., et al. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Ashburner, M., Ball, C.A., Blake, J.A., et al. 2000. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-29. (Pubitemid 30257031)
4. Bae, W., Xia, B., Inouye, M., and Severinov, K. 2000. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc. Natl. Acad. Sci. USA 97, 7784-7789. (Pubitemid 30460725)
5. Berg, J., and Lässig, M. 2004. Local graph alignment and motif search in biological networks. Proc. Natl. Acad. Sci. USA 101, 14689-14694. (Pubitemid 39410736)
6. Boyle, E.I., Weng, S., Gollub, J., et al. 2004. GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20, 3710-3715. (Pubitemid 40136825)
7. Delgado, A., Zaman, S., Muthaiyan, A., et al. 2008. The fusidic acid stimulon of Staphylococcus aureus. J. Antimicrob. Chemother. 62, 1207-1214.
8. Dost, B., Shlomi, T., Gupta, N., et al. 2008. QNet: a tool for querying protein interaction networks. J. Comput. Biol. 15, 913-925.
9. Dutkowski, J., and Tiuryn, J. 2007. Identification of functional modules from conserved ancestral protein-protein interactions. Bioinformatics 23, I149-I158. (Pubitemid 47244396)
10. Flannick, J., Novak, A., Srinivasan, B.S., et al. 2006. Græmlin: general and robust alignment of multiple large interaction networks. Genome Res. 16, 1169-1181. (Pubitemid 44320404)
11. Flannick, J., Novak, A., Do, C.B., et al. 2009. Automatic parameter learning for multiple local network alignment. J. Comput. Biol. 16, 1001-1022.
12. Grochow, J.A., and Kellis, M. 2007. Network motif discovery using subgraph enumeration and symmetry-breaking. Lect. Notes Bioinformatics 4453, 92-106. (Pubitemid 47164534)
13. Guo, X., and Hartemink, A.J. 2009. Domain-oriented edge-based alignment of protein interaction networks. Bioinformatics 25, I240-I246.
14. Gustin, M.C., Albertyn, J., Alexander, M., and Davenport, K. 1998. MAP kinase pathways in the yeast Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 62, 1264-1300. (Pubitemid 28558299)
15. Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., et al. 2004. IntAct: an open source molecular interaction database. Nucleic Acids Res. 32, D452-D455. (Pubitemid 38081697)
16. Hsieh, M.-F., and Sze, S.-H. 2014. A software program implementing the algorithm GraphletAlign: http://faculty .cse.tamu.edu/shsze/graphletalign
17. Jiang, R., Tu, Z., Chen, T., and Sun, F. 2006. Network motif identification in stochastic networks. Proc. Natl. Acad. Sci. USA 103, 9404-9409. (Pubitemid 43955839)
18. Kalaev, M., Bafna, V., and Sharan, R. 2009. Fast and accurate alignment of multiple protein networks. J. Comput. Biol. 16, 989-999.
19. Kanehisa, M., Goto, S., Kawashima, S., et al. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-D280. (Pubitemid 38081656)
20. Kashtan, N., Itzkovitz, S., Milo, R., and Alon, U. 2004. Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 20, 1746-1758. (Pubitemid 39162051)
21. 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)
22. Koyutürk, M., Grama, A., and Szpankowski, W. 2004. An efficient algorithm for detecting frequent subgraphs in biological networks. Bioinformatics 20, SI200-SI207.
23. Koyutürk, M., Kim, Y., Topkara, U., et al. 2006. Pairwise alignment of protein interaction networks. J. Comput. Biol. 13, 182-199.
24. Kuchaiev, O., and Pr-zulj, N. 2011. Integrative network alignment reveals large regions of global network similarity in yeast and human. Bioinformatics 27, 1390-1396.
25. Li, H., Pellegrini, M., and Eisenberg, D. 2005. Detection of parallel functional modules by comparative analysis of genome sequences. Nat. Biotechnol. 23, 253-260. (Pubitemid 40255337)
26. Liao, C.-S., Lu, K., Baym, M., et al. 2009. IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25, I253-I258.
27. McKay, B.D. 1998. Isomorph-free exhaustive generation. J. Algorithms 26, 306-324. (Pubitemid 128638721)
28. Milo, R., Shen-Orr, S., Itzkovitz, S., et al. 2002. Network motifs: simple building blocks of complex networks. Science 298, 824-827. (Pubitemid 35231534)
29. Parida, L. 2007. Discovering topological motifs using a compact notation. J. Comput. Biol. 14, 300-323. (Pubitemid 46742187)
30. Pellegrini, M., Marcotte, E.M., Thompson, M.J., et al. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96, 4285-4288. (Pubitemid 29190328)
31. Pr-zulj, N., Corneil, D.G., and Jurisica, I. 2006. Efficient estimation of graphlet frequency distributions in protein-protein interaction networks. Bioinformatics 22, 974-980.
32. Remm, M., Storm, C.E.V., and Sonnhammer, E.L.L. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041-1052. (Pubitemid 34073068)
33. 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)
34. Shen-Orr, S.S., Milo, R., Mangan, S., and Alon, U. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68.
35. Shlomi, T., Segal, D., Ruppin, E., and Sharan, R. 2006. QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics 7, 199.
36. Singh, R., Xu, J., and Berger, B. 2008. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl. Acad. Sci. USA 105, 12763-12768.
37. Srinivasan, B.S., Novak, A.F., Flannick, J.A., et al. 2006. Integrated protein interaction networks for 11 microbes. Lect. Notes Bioinformatics 3909, 1-14. (Pubitemid 44019140)
38. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278, 631-637. (Pubitemid 27464953)
39. Tian, Y., McEachin, R.C., Santos, C., et al. 2007. SAGA: a subgraph matching tool for biological graphs. Bioinformatics 23, 232-239. (Pubitemid 46189614)
40. Wernicke, S. 2006. Efficient detection of network motifs. IEEE/ACM Trans. Comput. Biol. Bioinformatics 3, 347-359. (Pubitemid 44950084)
41. Wuchty, S., Oltvai, Z.N., and Barabási, A.-L. 2003. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet. 35, 176-179. (Pubitemid 37187637)
42. Xenarios, I., Rice, D.W., Salwinski, L., et al. 2000. DIP: the Database of Interacting Proteins. Nucleic Acids Res. 28, 289-291. (Pubitemid 30047782)