Ranking of network elements based on functional substructures

Journal of Theoretical Biology

Volumn 248, Issue 3, 2007, Pages 471-479

  Koschützki, Dirk ^a   Schwöbbermeyer, Henning ^a   Schreiber, Falk ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

Gene regulatory network; Network analysis; Network centrality; Network motif

Indexed keywords

BACTERIUM; GENE; METABOLISM; NETWORK ANALYSIS; PROTEIN;

ARTICLE; ARTIFICIAL NEURAL NETWORK; ESCHERICHIA COLI; GENE CONTROL; GENE STRUCTURE; NONHUMAN; PRIORITY JOURNAL; SYSTEMS BIOLOGY;

ALGORITHMS; DNA, BACTERIAL; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; GENES, BACTERIAL; GENES, REGULATOR; METABOLIC NETWORKS AND PATHWAYS; MODELS, GENETIC; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 34548419326     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2007.05.038     Document Type: Article

References (30)

1. Bae W., Xia B., Inouye M., and Severinov K. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc. Nat. Acad. Sci. 97 14 (2000) 7784-7789
2. Barabási A.-L., and Oltvai Z.N. Network biology: understanding the cell's functional organization. Nature Rev. Genetics 5 2 (2004) 101-113
3. Browning D.F., and Busby S.J. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2 1 (2004) 57-65
4. Busby S., and Ebright R.H. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293 2 (1999) 199-213
5. Conant G.C., and Wagner A. Convergent evolution of gene circuits. Nature Genet. 34 3 (2003) 264-266
6. Darwin A.J., Ziegelhoffer E.C., Kiley P.J., and Stewart V. Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro. J. Bacteriol. 180 16 (1998) 4192-4198
7. Engelfriet J., and Rozenberg G. Node replacement graph grammars. In: Rozenberg G. (Ed). Handbook of Graph Grammars and Computing by Graph Transformation vol. 1 (1997), World Scientific, Singapore 1-94 (Chapter 1)
8. Garey M.R., and Johnson D.S. Computers and Intractability (2003), W. H. Freeman and Company, New York
9. Goosen N., and van de Putte P. The regulation of transcription initiation by integration host factor. Mol. Microbiol. 16 1 (1995) 1-7
10. Jeong H., Mason S.P., Barabási A.-L., and Oltvai Z.N. Lethality and centrality in protein networks. Nature 411 (2001) 41-42
11. Karp P.D., Krummenacker M., Paley S., and Wagg J. Integrated pathway-genome databases and their role in drug discovery. Trends Biotechnol. 17 7 (1999) 275-281
12. Kashtan N., Itzkovitz S., Milo R., and Alon U. Topological generalizations of network motifs. Phys. Rev. E 70 3 (2004) 031909
13. Keseler I.M., Collado-Vides J., Gama-Castro S., Ingraham J., Paley S., Paulsen I.T., Peralta-Gil M., and Karp P.D. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33 (2005) D334-D337
14. Koschützki, D., Lehmann, K.A., Peeters, L., Richter, S., Tenfelde-Podehl, D., Zlotowski, O., 2005. Network Analysis: Methodological Foundations, Lecture Notes in Computer Science, Tutorial, vol. 3418, Centrality Indices, Springer, Berlin, pp. 16-61.
15. Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I., Zeitlinger J., Jennings E.G., Murray H.L., Gordon D.B., Ren B., Wyrick J.J., Tagne J.-B., Volkert T.L., Fraenkel E., Gifford D.K., and Young R.A. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 5594 (2002) 799-804
16. Levanon S.S., San K.-Y., and Bennett G.N. Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses. Biotechnol. Bioeng. 89 5 (2005) 556-564
17. Ma Z., Masuda N., and Foster J.W. Characterization of EvgAS-YdeO-GadE branched regulatory circuit governing glutamate-dependent acid resistance in Escherichia coli. J. Bacteriol. 186 21 (2004) 7378-7389
18. Mangan S., and Alon U. Structure and function of the feed-forward loop network motif. Proc. Nat. Acad. Sci. 100 21 (2003) 11980-11985
19. Mangan S., Zaslaver A., and Alon U. The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J. Mol. Biol. 334 2 (2003) 197-204
20. Martínez-Antonio A., and Collado-Vides J. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opinion Microbiol. 6 5 (2003) 482-489
21. Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., and Alon U. Network motifs: simple building blocks of complex networks. Science 298 5594 (2002) 824-827
22. Phadtare S., and Inouye M. Role of CspC and CspE in regulation of expression of RpoS and UspA the stress response proteins in Escherichia coli. J. Bacteriol. 183 4 (2001) 1205-1214
23. Potapov A.P., Voss N., Sasse N., and Wingender E. Topology of mammalian transcription networks. Genome Inf. 16 2 (2005) 270-278
24. Salgado H., Gama-Castro S., Peralta-Gil M., Díaz-Peredo E., Sánchez-Solano F., Santos-Zavaleta A., Martínez-Flores I., Jiménez-Jacinto V., Bonavides-Martínez C., Segura-Salazar J., Martínez-Antonio A., and Collado-Vides J. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 34 Suppl. 1 (2006) D394-D397
25. Schreiber F., and Schwöbbermeyer H. Frequency concepts and pattern detection for the analysis of motifs in networks. Trans. Comput. Systems Biol. 3 LNBI 3737 (2005) 89-104
26. Shen-Orr S., Milo R., Mangan S., and Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31 1 (2002) 64-68
27. Sporns O., and Kötter R. Motifs in brain networks. PLoS Biol. 2 11 (2004) e369
28. Stavans J., and Oppenheim A. DNA-protein interactions and bacterial chromosome architecture. Phys. Biol. 3 4 (2006) R1-R10
29. Wuchty S., Oltvai Z.N., and Barabási A.-L. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet. 35 2 (2003) 176-179
30. Wuchty S., and Stadler P.F. Centers of complex networks. J. Theor. Biol. 223 (2003) 45-53