AlignNemo: A local network alignment method to integrate homology and topology

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Ciriello, Giovanni ^a,d   Mina, Marco ^a   Guzzi, Pietro H ^b   Cannataro, Mario ^b   Guerra, Concettina ^a,c  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

^c Georgia Institute of Technology   (United States)

^d MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ALIGNEMO; ARTICLE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EVOLUTIONARY HOMOLOGY; HUMAN; INFORMATION PROCESSING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS;

CONSERVED SEQUENCE; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84862164356     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038107     Document Type: Article

References (38)

1. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. (2003) A Protein interaction map of Drosophila melanogaster. Science 302: 1727-36.
2. Uetz P, Giot L, Cagney G, Mansfi TA, Judson RS, et al. (2002) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-7.
3. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. (2008) High-Quality Binary Protein Interaction Map of the Yeast Interactome Network. Science 322: 104-110.
4. Kiemer L, Cesareni G, (2007) Comparative interactomics: comparing apples and pears? Trends in biotechnology 10 25: 448-454.
5. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, et al. (2005) Conserved patterns of protein interaction in multiple species. Proc. Nat. Acad. Sci. USA 102: 1974-1979.
6. Kalaev M, Bafna V, Sharan R, (2008) Fast and accurate alignment of multiple protein networks. Proc. RECOMB, 246-256.
7. Kelley BP, Yuan B, Lewitter F, Sharan R, Brent R, et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Nat. Acad. Sci. USA 100: 11394-11399.
8. de Silva E, Thorne T, Ingram P, Agrafioti I, Swire J, et al. (2006) The effects of incomplete protein interaction data on structural and evolutionary inferences. BMC Biology 4: 39.
9. Hakes L, Pinney JW, Robertson D, Lovell SC, (2008) Protein-protein interaction networks and biology- what is the connection? Nature Biotechnology, 26 1: 69-72.
10. Koyuturk M, Grama A, Szpankowski W, (2006) Pairwise alignment of protein interaction networks. J. Comput. Biol. 13: 182-199.
11. Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S, (2006) Graemlin: General and robust alignment of multiple large interaction networks. Genome Res., 16 9: 1169-1181.
12. Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S, et al. (2009) Automatic parameter learning for multiple local network alignment. J. Comput. Biol., 16 8: 1001-1022.
13. O'Brien KP, Remm M, Sonnhammer EL, (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33: D476-D480.
14. Kanehisa M, Goto S, (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28: 27-30.
15. Cootes AP, Muggleton SH, Sternberg MJ, (2007) The Identification of Similarities between Biological Networks: Application to the Metabolome and Interactome. J Mol Biol, 369 4: 1126-39.
16. Pache RA, Aloy P, (2012) A Novel Framework fro the Comparative Analysis of Biological Networks. PLoS ONE, 7 2: e31220.
17. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, et al. (2004) The Database of Interacting Proteins: 2004 update Nucleic Acids Res., 32 (Suppl 1), D449-451.
18. Human Integrated Protein-Protein Interaction rEference. Available:http://cbdm.mdc-berlin.de/tools/hippie/information.php (Accessed 2011).
19. Ortholog Resources from the Gerstein Lab. Available:http://info.gersteinlab.org/Ortholog_Resources (Accessed 2011).
20. Deng M, Sun F, Chen T, (2003) Assessment of the reliability of protein-protein interactions and protein function prediction. Proc. of Pacific Symposium on Biocomputing 8: 140-151.
21. Engel S, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, et al. (2010) SGD: Saccharomyces Genome Database. Nucl. Acid Res., 38 (Suppl 1), D433-D436.
22. Pu S, Wong J, Turner B, Cho E, Wodak SJ, (2009) Up-to-date catalogues of yeast protein complexes. Nucl. Acids Res 37 3: 825-831.
23. Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, et al. (2007) CORUM: the comprehensive resource of mammalian protein complexes. Nucl. Acids Res. 36 (suppl 1), D646-D650.
24. Guzzi PH, Mina M, Guerra C, Cannataro M, (2011) Semantic similarity analysis of protein data: assessment with biological features and issues. Brief Bioinform, doi:10.1093/bib/bbr066.
25. Resnik P, (1999) Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language. J. of Artificial Intelligence Res. 11: 95-130.
26. Faria D, Pesquita C, Couto FM, Falcao A, (2007) ProteinOn: A web tool for protein semantic similarity. Department of Informatics, University of Lisbon, Technical Reports, di-fcul-tr-07-6.
27. Library and tools for semantic similarity measures. Available:http://sourceforge.net/p/fastsemsim (Version 0.4).
28. Gavin AC, Aloy P, Grandi P, Krause P, Boesche P, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature, 440 7084: 631-636.
29. Generic Gene Ontology Term Finder. Available:http://go.princeton.edu/cgi-bin/GOTermFinder (Accessed 2011).
30. Burley SK, Roeder RG, (1996) Biochemistry and Structural Biology of Transcription Factor IID (TFIID). Annu. Rev. Biochem. 65: 769-799.
31. Veltman DM, Insall RH, (2010) WASP family proteins: their evolution and its physiological implications. Mol. Biol. Cell, 21 16: 2880-93.
32. Liben-Nowell D, Kleinberg J, (2003) The link prediction problem for social networks. In Proceedings of the Twelfth International Conference on Information and Knowledge Management, 556-559 New York, NY.
33. Singh R, Xu J, Berger B, (2007) Pairwise global alignment of protein interaction networks by matching neighborhood topology. Research in Computational Molecular Biology, 16-31, Springer.
34. Singh R, Xu J, Berger B, (2008) Global alignment of multiple protein interaction networks. Proc. of Pacific Symposium on Biocomputing 13: 303-314.
35. Kuchaiev O, Milenkovic T, Memisevic V, Hayes W, Przulj N, (2010) Topological network alignment uncovers biological function and phylogeny. J. R. Soc. Interface, 7 50: 1341-1354.
36. Kuchaiev O, Przulj N, (2011) Integrative Network Alignment Reveals Large Regions of Global Network Similarity in Yeast and Human. Bioinformatics, 27 10: 1390-1396.
37. Milenkovic T, Leong W, Przulj N, (2010) Optimal network Alignment with Graphlet Degree Vectors. Cancer Informatics, 9, 121-137.
38. Tian W, Samatova NF, (2009) Pairwise Alignment of interaction networks by fast identification of maximal conserved patterns. Pacific Symposium on Biocomputing 14: 99-110.