Global alignment of pairwise protein interaction networks for maximal common conserved patterns

International Journal of Genomics

Volumn 2013, Issue , 2013, Pages

  Tian, Wenhong ^a   Samatova, Nagiza F ^b,c  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c North Carolina State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; COST BENEFIT ANALYSIS; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENOME; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; SALMONELLA TYPHIMURIUM; SENSITIVITY ANALYSIS; SPECIES; YEAST;

EID: 84877945298     PISSN: 2314436X     EISSN: 23144378     Source Type: Journal    
DOI: 10.1155/2013/670623     Document Type: Article

References (32)

1. Sharan R., Suthram S., Kelley R. M., Kuhn T., McCuine S., Uetz P., Sittler T., Karp R. M., Ideker T., Conserved patterns of protein interaction in multiple species. Proceedings of the National Academy of Sciences of the United States of America 2005 102 6 1974 1979 2-s2.0-13844314048 10.1073/pnas. 0409522102 (Pubitemid 40261997)
2. Sharan R., Ideker T., Modeling cellular machinery through biological network comparison. Nature Biotechnology 2006 24 4 427 433 2-s2.0-33645732240 10.1038/nbt1196
3. DIP,. http://dip.doe-mbi.ucla.edu/
4. IntAct,. http://www.ebi.ac.uk/intact/site/index.jsf
5. Biogrid,. http://www.thebiogrid.org/
6. HPRD (Human Protein Reference Database),. http://www.hprd.org/
7. InterPro,. http://www.ebi.ac.uk/interpro/
8. Flannick J., Novak A., Srinivasan B. S., McAdams H. H., Batzoglou S., General and robust alignment of multiple large interaction networks. Genome Research 2006 16 9 1169 1181 2-s2.0-33748257786 10.1101/gr.5235706 (Pubitemid 44320404)
9. Flannick J., Novak A., Do C. B., Srinivasan B. S., Batzoglou S., Automatic parameter learning for multiple local network alignment. Journal of Computational Biology 2009 16 8 1001 1022 2-s2.0-70349215207 10.1089/cmb.2009.0099
10. Kalaev M., Bafna V., Sharan R., Fast and accurate alignment of multiple protein networks. Journal of Computational Biology 2009 16 8 989 999 2-s2.0-70349193233 10.1089/cmb.2009.0136
11. Kelley B. P., Sharan R., Karp R. M., Sittler T., Root D. E., Stockwell B. R., Ideker T., Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proceedings of the National Academy of Sciences of the United States of America 2003 100 20 11394 11399 2-s2.0-0141593601 10.1073/pnas.1534710100 (Pubitemid 37205946)
12. Koyutürk M., Grama A., Szpankowski W., Pairwise local alignment of protein interaction networks guided by models of evolution. 3500 Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB '05) May 2005 48 65 2-s2.0-26444593028
13. Singh R., Xu J., Berger B., Pairwise global alignment of protein interaction networks by matching neighborhood topology. Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB '07) April 2007 16 31 2-s2.0-34547416529
14. Singh R., Xu J., Berger B., Global alignment of multiple protein interaction networks. Pacific Symposium on Biocomputing 2008 13 303 314 2-s2.0-40549129437
15. Bandyopadhyay S., Sharan R., Ideker T., Systematic identification of functional orthologs based on protein network comparison. Genome Research 2006 16 3 428 435 2-s2.0-33644656793 10.1101/gr.4526006 (Pubitemid 43327512)
16. Maslov S., Sneppen K., Specificity and stability in topology of protein networks. Science 2002 296 5569 910 913 2-s2.0-0037012880 10.1126/science. 1065103 (Pubitemid 34464896)
17. Wagner A., The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Molecular Biology and Evolution 2001 18 7 1283 1292 2-s2.0-0034943378 (Pubitemid 32660673)
18. Zhang B., Park B. H., Karpinets T., Samatova N. F., From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics 2008 24 7 979 986 2-s2.0-41349108025 10.1093/bioinformatics/ btn036 (Pubitemid 351448033)
19. Ashburner M., Ball C. A., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A. P., Dolinski K., Dwight S. S., Eppig J. T., Harris M. A., Hill D. P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J. C., Richardson J. E., Ringwald M., Rubin G. M., Sherlock G., Gene ontology: tool for the unification of biology. Nature Genetics 2000 25 1 25 29 2-s2.0-0034069495 10.1038/75556 (Pubitemid 30257031)
20. Kanehisa M., Goto S., KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 2000 28 1 27 30 2-s2.0-0033982936 (Pubitemid 30047706)
21. Remm M. R., Storm C. E. V., Sonnhammer E. L. L., Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 2001 314 5 1041 1052 2-s2.0-0035861990 10.1006/jmbi.2000.5197 (Pubitemid 34073068)
22. Towfic F., Greenlee M. H. W., Honavar V., Aligning Biomolecular Networks Using Modular Graph Kernels 2009 5724 Lecture Notes in Computer Science
23. Chen W., Schmidt M. C., Tian W., Samatova N. F., A fast and accurate algorithm for identifying functional modules through pairwise local alignment of protein interaction. Proceedings of the International Conference on Bioinformatics and Computational Biology July 2009 Las Vegas, Nev, USA
24. Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejs M., Tetko I., Güldener U., Mannhaupt G., Münsterkötter M., Mewes H. W., The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research 2004 32 18 5539 5545 2-s2.0-9144257282 10.1093/nar/gkh894 (Pubitemid 39545671)
25. Mewes H. W., Amid C., Arnold R., Munich information center for protein sequences. Nucleic Acids Research 2004 32 D41 D44
26. Stanford Network Database (SNDB),. ftp://ftp-networks.stanford.edu/pub/ graemlin
27. UniProt,. http://www.pir.uniprot.org/
28. Yu G. X., Park B. H., Chandramohan P., Munavalli R., Geist A., Samatova N. F., In silico discovery of enzyme-substrate specificity-determining residue clusters. Journal of Molecular Biology 2005 352 5 1105 1117 2-s2.0-24944451493 10.1016/j.jmb.2005.08.008 (Pubitemid 41316719)
29. North B. V., Curtis D., Sham P. C., A note on the calculation of empirical P values from Monte Carlo procedures. American Journal of Human Genetics 2002 71 2 439 441 2-s2.0-0036071235 10.1086/341527 (Pubitemid 34800261)
30. GO termFinder,. http://go.princeton.edu/cgi-bin/GOTermFinder
31. Cormen T. H., Leiserson C. E., Rivest R. L., Stein C., Introduction to Algorithms 2001 2nd The MIT Press
32. AlgoWiki,. http://algowiki.net/wiki/index.php?title=Tarjan's-algorithm