Insights into the organization of biochemical regulatory networks using graph theory analyses

Journal of Biological Chemistry

Volumn 284, Issue 9, 2009, Pages 5451-5455

  Ma'ayan, Avi ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL NETWORK; BIOLOGICAL RESPONSE; BOW TIE; CELL SIGNALING; CLASSIFICATION SYSTEM; DYNAMICAL STABILITY; EXTRACELLULAR SIGNALS; FEEDFORWARD LOOPS; GAIN INSIGHT; GLOBAL ORGANIZATION; GRAPH ANALYSIS; IN-NETWORK; INTRACELLULAR SIGNALING; MATHEMATICAL MODELING; MICROARRAY DATA SETS; MULTIPLE PATHWAYS; NEGATIVE FEEDBACK LOOP; NETWORK MOTIF; POSITIVE FEEDBACK LOOP; PRIOR KNOWLEDGE; REGULATORY NETWORK; SCALE-FREE; SIGNALING NETWORKS; SMALL WORLDS;

CELL MEMBRANES; ENZYME ACTIVITY; FEEDBACK; LAWS AND LEGISLATION; LOCATION; PROTEINS; SIGNALING; STABILITY;

GRAPH THEORY;

TRANSCRIPTION FACTOR;

BAYES THEOREM; BIOCHEMISTRY; COMPUTER NETWORK; GENE REGULATORY NETWORK; INFORMATION SYSTEM; MATHEMATICAL MODEL; MICROARRAY ANALYSIS; MOLECULAR INTERACTION; PLOTS AND CURVES; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SHORT SURVEY; SIGNAL TRANSDUCTION; ANIMAL; BIOLOGICAL MODEL; COMPUTER GRAPHICS; HUMAN; MATHEMATICS; METABOLISM; REVIEW;

ANIMALS; COMPUTER GRAPHICS; GENE REGULATORY NETWORKS; HUMANS; MATHEMATICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION;

EID: 65549162694     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.R800056200     Document Type: Short Survey

References (49)

1. Pagliarini, D. J., Calvo, S. E., Chang, B., Sheth, S. A., Vafai, S. B., Ong, S.-E., Walford, G. A., Sugiana, C., Boneh, A., Chen, W. K., Hill, D. E., Vidal, M., Evans, J. G., Thorburn, D. R., Carr, S. A., and Mootha, V. K. (2008) Cell 134, 112-123
2. Euler, L. (1736) Commetarii Academiae Scientiarum Imperialis Petropolitanae 8, 128-140
3. Watts, D. J., and Strogatz, S. H. (1998) Nature 393, 440-442
4. Barabási, A.-L., and Albert, R. (1999) Science 286, 509-512
5. Eisenberg, D., Marcotte, E. M., Xenarios, I., and Yeates, T. O. (2000) Nature 405, 823-826
6. Ma'ayan, A., Blitzer, R. D., and Iyengar, R. (2005) Annu. Rev. Biophys. Biomol. Struct. 34, 319-349
7. Ma'ayan, A., Jenkins, S. L., Neves, S., Hasseldine, A., Grace, E., Dubin-Thaler, B., Eungdamrong, N. J., Weng, G., Ram, P. T., Rice, J. J., Kershenbaum, A., Stolovitzky, G. A., Blitzer, R. D., and Iyengar, R. (2005) Science 309, 1078-1083
8. Bhalla, U. S., and Iyengar, R. (1999) Science 283, 381-387
9. Gene Ontology Consortium (2004) Nucleic Acids Res. 32, D258-D261
10. Goh, K.-I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., and Barabási, A.-L. (2007) Proc. Natl. Acad. Sci. U. S. A. 104, 8685-8690
11. Yildirim, M. A., Goh, K.-I., Cusick, M. E., Barabási, A.-L., and Vidal, M. (2007) Nat. Biotechnol. 25, 1119-1126
12. Ma'ayan, A., Jenkins, S. L., Goldfarb, J., and Iyengar, R. (2007) Mt. Sinai J. Med. 74, 27-32
13. Tanay, A., Sharan, R., Kupiec, M., and Shamir, R. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 2981-2986
14. Friedman, N., Linial, M., Nachman, I., and Pe'er, D. (2000) J. Comput. Biol. 7, 601-620
15. Sachs, K., Perez, O., Pe'er, D., Lauffenburger, D. A., and Nolan, G. P. (2005) Science 308, 523-529
16. White, A. G., and Ma'ayan, A. (2007) Connecting Seed Lists of Mammalian Proteins Using Steiner Trees, in Proceedings of the 41st Asilomar Conference on Signals, Systems and Computers, November 4-7, 2007, Pacific Grove, CA, IEEE, Washington, D. C.
17. Jeong, H., Mason, S. P., Barabási, A.-L., and Oltvai, Z. N. (2001) Nature 411, 41-42
18. Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., and Barabási, A.-L. (2002) Science 297, 1551-1555
19. Han, J.-D. J., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J. M., Cusick, M. E., Roth, F. P., and Vidal, M. (2004) Nature 430, 88-93
20. Kim, P. M., Lu, L. J., Xia, Y., and Gerstein, M. B. (2006) Science 314, 1938-1941
21. Newman, M. E. J. (2002) Phys. Rev. Lett. 89, 208701
22. Eguiluz, V. M., Chialvo, D. R., Cecchi, G. A., Baliki, M., and Apkarian, A. V. (2005) Phys. Rev. Lett. 94, 018102-018104
23. Dijkstra, E. W. (1959) Numer. Math. 1, S269-S271
24. Floyd, R. W. (1962) Commun. ACM 5, 345
25. Bromberg, K. D., Ma'ayan, A., Neves, S. R., and Iyengar, R. (2008) Science 320, 903-909
26. Ma'ayan, A., Lipshtat, A., and Iyengar, R. (2006) Phys. Rev. E 73, 061912
27. Oda, K., and Kitano, H. (2006) Mol. Syst. Biol. 2, 2006.0015
28. Neves, S. R., Ram, P. T., and Iyengar, R. (2002) Science 296, 1636-1639
29. Berger, S., Posner, J., and Ma'ayan, A. (2007) BMC Bioinformatics 8, 372
30. Yu, H., Paccanaro, A., Trifonov, V., and Gerstein, M. (2006) Bioinformatics 22, 823-829
31. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., and Alon, U. (2002) Science 298, 824-827
32. Maslov, S., and Sneppen, K. (2002) Science 296, 910-913
33. Lipshtat, A., Purushothaman, S. P., Iyengar, R., and Ma'ayan, A. (2008) Biophys. J. 94, 2566-2579
34. Ingram, P., Stumpf, M., and Stark, J. (2006) BMC Genomics 7, 108
35. Shen-Orr, S. S., Milo, R., Mangan, S., and Alon, U. (2002) Nat. Genet. 31, 64-68
36. Hayot, F., and Jayaprakash, C. (2005) J. Theor. Biol. 234, 133-143
37. Ferrell, J. E. (2002) Curr. Opin. Cell Biol. 14, 140-148
38. Mangan, S., and Alon, U. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 11980-11985
39. Angeli, D., Ferrell, J. E., Jr., and Sontag, E. D. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 1822-1827
40. Ma'ayan, A., Lipshtat, A., Iyengar, R., and Sontag, E. D. (2008) IET Syst. Biol. 2, 103-112
41. Kwon, Y.-K., and Cho, K.-H. (2008) Bioinformatics, btn337
42. Stryer, L. (1981) Biochemistry, 2nd Ed., W. H. Freeman & Co., San Francisco
43. Girvan, M., and Newman, M. E. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 7821-7826
44. Eungdamrong, N. J., and Iyengar, R. (2004) Trends Cell Biol. 14, 661-669
45. Li, S., Assmann, S. M., and Albert, R. (2006) PLoS Biol. 4, e312
46. Hardy, S., and Robillard, P. N. (2008) Bioinformatics 24, 209-217
47. Kashtan, N., Itzkovitz, S., Milo, R., and Alon, U. (2004) Bioinformatics 20, 1746-1758
48. Chin, G., Chavarria, D., Nakamura, G., and Sofia, H. (2008) BMC Bioinformatics 9, S6
49. Anderson, C. (2008) Wired Magazine, Issue 16.07