Dynamic properties of network motifs contribute to biological network organization

PLoS Biology

Volumn 3, Issue 11, 2005, Pages 1881-1892

  Prill, Robert J ^a   Iglesias, Pablo A ^a,b   Levchenko, Andre ^a  

^a the United States of America   (United States)

^b Departments of Orthopaedic Surgery   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CORRELATION ANALYSIS; GENE CONTROL; MATHEMATICAL ANALYSIS; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PHYSICAL CHEMISTRY; SIGNAL TRANSDUCTION; SYNAPSE; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CAENORHABDITIS ELEGANS; COMPARATIVE STUDY; COMPUTER SIMULATION; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; METHODOLOGY; NERVE CELL NETWORK; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; STATISTICS; SYSTEMS THEORY;

ANIMALS; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; MODELS, BIOLOGICAL; NERVE NET; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; STATISTICS; SYSTEMS THEORY; TRANSCRIPTION, GENETIC;

EID: 27844551326     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030343     Document Type: Article

References (33)

1. White JG, Southgate E, Thomson JN, Brenner S (1986) The structure of the nervous system of the nematode C. elegans. Philos Trans R Soc Lond B Biol Sci 275: 1-340.
2. Barabasi AL, Oltvai ZN (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
3. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: Simple building blocks of complex networks. Science 298: 824-827.
4. Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
5. Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100: 11980-11985.
6. Mangan S, Zaslaver A, Alon U (2003) The coherent feed-forward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334: 197-204.
7. Kalir S, Mangan S, Alon U (2005) A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol DOI: 10.1038/msb4100010.
8. Sporns O, Kotter R (2004) Motifs in brain networks. PLoS Biol 2: e369.
9. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
10. Song S, Sjostrom PJ, Reigl M, Nelson S, Chklovskii DB (2005) Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol 3: e68.
11. Levchenko A, Bruck J, Sternberg PW (2004) Regulatory modules that generate biphasic response in biological systems. IEE Proc Sys Biol 1: 139-148.
12. Wolf DM, Arkin AP (2003) Motifs, modules and games in bacteria. Curr Opin Microbiol 6: 125-134.
13. Savageau MA (2001) Design principles for elementary gene circuits: Elements, methods, and examples. Chaos 11: 142-159.
14. Spirin V, Mirny LA (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100: 12123-12128.
15. Rao CV, Arkin AP (2001) Control motifs for intracellular regulatory networks. Annu Rev Biomed Eng 3: 391-419.
16. Francois P, Hakim V (2004) Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci U S A 101: 580-585.
17. Ozbudak EM, Thattai M, Lim HN, Shraiman BI, Van Oudenaarden A (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427: 737-740.
18. Alon U, Surette MG, Barkai N, Leibler S (1999) Robustness in bacterial chemotaxis. Nature 397: 168-171.
19. Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387: 913-917.
20. Guet CC, Elowitz MB, Hsing W, Leibler S (2002) Combinatorial synthesis of genetic networks. Science 296: 1466-1470.
21. Stelling J, Sauer U, Szallasi Z, Doyle FJ 3rd, Doyle J (2004) Robustness of cellular functions. Cell 118: 675-685.
22. Hoffmann A, Levchenko A, Scott ML, Baltimore D (2002) The IkappaB-NFkappaB signaling module: Temporal control and selective gene activation. Science 298: 1241-1245.
23. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
24. Itzkovitz S, Milo R, Kashtan N, Ziv G, Alon U (2003) Subgraphs in random networks. Phys Rev E Stat Nonlin Soft Matter Phys 68: 026127.
25. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, et al. (2004) Superfamilies of evolved and designed networks. Science 303: 1538-1542.
26. Kashtan N, Itzkovitz S, Milo R, Alon U (2004) Topological generalizations of network motifs. Phys Rev E Stat Nonlin Soft Matter Phys 70: 031909.
27. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
28. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312.
29. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338.
30. El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M (2005) Surviving heat shock: Control strategies for robustness and performance. Proc Natl Acad Sci U S A 102: 2736-2741.
31. Variano EA, McCoy JH, Lipson H (2004) Networks, dynamics, and modularity. Phys Rev Lett 92: 188701.
32. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
33. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.