Structural characterization and modeling of ncRNA-protein interactions

BioSystems

Volumn 101, Issue 1, 2010, Pages 10-19

  Nacher, J C ^a   Araki, N ^a  

^a FUTURE UNIVERSITY HAKODATE   (Japan)

Author keywords

Complex networks; Noncoding RNA; Transcriptional regulation

Indexed keywords

UNTRANSLATED RNA; PROTEIN;

GENETICS; MODELING; MOLECULAR ANALYSIS; NETWORK ANALYSIS; PROTEIN; RNA;

ARTICLE; GENE REGULATORY NETWORK; NONHUMAN; PROTEIN ANALYSIS; PROTEIN MOTIF; PROTEIN RNA BINDING; PROTEIN TARGETING; RNA STRUCTURE; SIMULATION; TRANSCRIPTION REGULATION; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM; MOLECULAR EVOLUTION; OPEN READING FRAME; PROCEDURES; SIGNAL TRANSDUCTION;

EUKARYOTA; HOMO SAPIENS;

ANIMALS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HUMANS; MODELS, GENETIC; OPEN READING FRAMES; PROTEIN INTERACTION MAPPING; PROTEINS; RNA, UNTRANSLATED; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 77953614905     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2010.02.005     Document Type: Article

References (29)

1. Amaral P.P., Dinger M.E., Mercer T.R., Mattick J.S. The eukaryotic genome as an RNA machine. Science 2008, 319:1787-1789.
2. Barabási A.-L., Oltvai Z.N. Network biology: understanding the cell functional organization. Nat. Rev. Genet. 2004, 5:101-103.
3. Bray D. Molecular networks: the top-down view. Science 2003, 301:1864-1865.
4. Dorogotvsev S.N., Mendes J.F.F. Evolution of Networks: From Biological Nets to the Internet and WWW 2003, Oxford University Press.
5. Ergün G. Human sexual contact network as a bipartite graph. Physica A 2002, 308:483-489.
6. Foster D.V., Kauffman S.A., Socolar J.E.S. Network growth models and genetic regulatory networks. Phys. Rev. E 2006, 73:031912.
7. Guelzim N., Bottani S., Bourgine P., Kepes F. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 2002, 31:60-63.
8. Harbison C.T., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104.
9. Hartwell L.H., Hopfield J.J., Leibler S., Murray A.W. From molecular to modular cell biology. Nature 1999, 402:C47-C52.
10. Krapivsky P.L., Redner S. Rate equation approach for growing networks. Lect. Notes Phys. 2003, 625:3-20.
11. Lee T.I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
12. Liang H., Li W.-H. MicroRNA regulation of human protein-protein interaction network. RNA 2007, 13:1402-1408.
13. Luscombe M.L., et al. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312.
14. Mattick J.S., Makunin I.V. Small regulatory RNAs in mammals. Hum. Mol. Genet. 2005, 14:R121-R132.
15. Mattick J.S., Gagen M.J. Accelerating networks. Science 2005, 307:856-858.
16. Mattick J.S. RNA regulation: a new genetics?. Nat. Rev. Genet. 2004, 5:316-322.
17. McAdams H.H., Srinivasan B., Arkin A.P. The evolution of genetic regulatory systems in bacteria. Nat. Rev. Genet. 2004, 5:169-178.
18. Milo R., et al. Network motifs: simple building blocks of complex networks. Science 2002, 298:824-829.
19. Newman M.E.J., Barabási A.-L., Watts D.J. The Structure and Dynamics of Networks 2007, Princeton University Press.
20. Nacher J.C., Ochiai T., Hayashida M., Akutsu T. A bipartite graph based model for protein domain networks. Springer Lect. Notes Inst. Comput. Sci. Soc. Inform. Telecommun. Eng. (Complex '09) 2009, 4:525-535.
21. Regulon Database Version 6.3, 2009. http://regulondb.ccg.unam.mx/.
22. Seitz H., et al. Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat. Genet. 2003, 34:261-262.
23. Shen-Orr S., Milo R., Mangan S., Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 2002, 31:64-69.
24. Shimoni Y. Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol. Syst. Biol. 2007, 3:1-9.
25. Solé R.V., Pastor-Satorras R., Smith E.D., Kepler T. A model of large-scale proteome evolution. Adv. Complex Syst. 2002, 5:43-54.
26. Teichman S.A., Madan Babu M. Gene regulatory network growth by duplication. Nat. Genet. 2004, 36:492-496.
27. Vogelstein B., Lane D., Levine A. Surfing the p53 network. Nature 2000, 408:307-310.
28. Wu T., et al. NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. Nuclei Acid Res. 2006, 34:D150-D152.
29. Zhao Y., et al. MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. Trends Genet. 2008, 24:323-327.