Evidence for the relationship between the regulatory effects of microRNAs and attack robustness of biological networks

Computers in Biology and Medicine

Volumn 63, Issue , 2015, Pages 83-91

  Ahmadi, Mehdi ^a   Jafari, Rahim ^b   Marashi, Sayed Amir ^a   Farazmand, Ali ^a  

^a UNIVERSITY OF TEHRAN   (Iran)

^b TARBIAT MODARES UNIVERSITY   (Iran)

Author keywords

Attack robustness; Biological networks; Centrality measures; Vulnerability

Indexed keywords

NETWORK COMPONENTS; PROTEINS; SIGNALING;

BETWEENNESS CENTRALITY; BIOLOGICAL NETWORKS; CENTRALITY MEASURES; EIGENVECTOR CENTRALITIES; NETWORK STRUCTURES; REGULATORY EFFECTS; SIGNALING NETWORKS; VULNERABILITY;

RNA;

MICRORNA;

ARTICLE; BIOLOGY; DISEASE TRANSMISSION; ESSENTIAL GENE; HUMAN; INTERNET; METABOLISM; ONCOGENE; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; SIGNAL TRANSDUCTION; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; PHYSIOLOGY;

GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS; MODELS, BIOLOGICAL;

EID: 84930645174     PISSN: 00104825     EISSN: 18790534     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2015.05.010     Document Type: Article

References (40)

1. Ambros V. The functions of animal microRNAs. Nature 2004, 431:350-355.
2. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
3. Lim L.P., Glasner M.E., Yekta S., Burge C.B., Bartel D.P. Vertebrate microRNA genes. Science 2003, 299. 1540-1540.
4. Pasquinelli A.E. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat. Rev. Genet. 2012, 13:271-282.
5. Witkos T., Koscianska E., Krzyzosiak W. Practical aspects of microRNA target prediction. Curr. Mol. Med. 2011, 11:93.
6. Re A., Corá D., Taverna D., Caselle M. Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human. Mol. BioSyst. 2009, 5:854-867.
7. Shalgi R., Lieber D., Oren M., Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol. 2007, 3:e131.
8. Tsang J., Zhu J., van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell 2007, 26:753-767.
9. F. Emmert-Streib, G.V. Glazko, Network Biology: A Direct Approach to Study Biological Function, Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 3 (2011) 379-391.
10. Barabasi A.-L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 2004, 5:101-113.
11. Liang H., Li W.-H. MicroRNA regulation of human protein-protein interaction network. RNA 2007, 13:1402-1408.
12. Iyer S., Killingback T., Sundaram B., Wang Z. Attack robustness and centrality of complex networks. PLoS One 2013, 8:e59613.
13. Marashi S.-A., Kouhestani H., Mahdavi M. Studying the relationship between robustness against mutations in metabolic networks and lifestyle of organisms. Sci. World J. 2013, 2013:615697.
14. Scott J., Carrington P.J. The SAGE Handbook of Social Network Analysis 2011, SAGE Publications.
15. Crucitti P., Latora V., Marchiori M., Rapisarda A. Efficiency of scale-free networks: error and attack tolerance. Physica A 2003, 320:622-642.
16. Albert R., Jeong H., Barabási A.-L. Error and attack tolerance of complex networks. Nature 2000, 406:378-382.
17. Friedel C.C., Zimmer R. Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinf. 2007, 8:297.
18. Callaway D.S., Newman M.E., Strogatz S.H., Watts D.J. Network robustness and fragility: percolation on random graphs. Phys. Rev. Lett. 2000, 85:5468.
19. Crucitti P., Latora V., Marchiori M., Rapisarda A. Error and attack tolerance of complex networks. Physica A 2004, 340:388-394.
20. Holme P., K1im B.J., Yoon C.N., Han S.K. Attack vulnerability of complex networks. Phys. Rev. E 2002, 65:056109.
21. Tibiche C., Wang E. MicroRNA regulatory patterns on the human metabolic network. Open Syst. Biol. J. 2008, 1:1-8.
22. Cui Q., Yu Z., Purisima E.O., Wang E. Principles of microRNA regulation of a human cellular signaling network. Mol. Syst. Biol. 2006, 2:46.
23. Cui Q., Yu Z., Pan Y., Purisima E.O., Wang E. MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem. Biophys. Res. Commun. 2007, 352:733-738.
24. Gusev Y., Schmittgen T.D., Lerner M., Postier R., Brackett D. Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer. BMC Bioinf. 2007, 8:S16.
25. Pelaez N., Carthew R.W. Biological robustness and the role of microRNAs: a network perspective. Curr. Top. Dev. Biol. 2012, 99:237.
26. Li X., Cassidy J.J., Reinke C.A., Fischboeck S., Carthew R.W. A microRNA imparts robustness against environmental fluctuation during development. Cell 2009, 137:273-282.
27. Osella M., Bosia C., Corá D., Caselle M. The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput. Biol. 2011, 7:e1001101.
28. Rual J.-F., Venkatesan K., Hao T., Hirozane-Kishikawa T., Dricot A., Li N., Berriz G.F., Gibbons F.D., Dreze M., Ayivi-Guedehoussou N. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437:1173-1178.
29. 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. Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science 2005, 309:1078-1083.
30. Simonis N., Rual J.-F., Carvunis A.-R., Tasan M., Lemmens I., Hirozane-Kishikawa T., Hao T., Sahalie J.M., Venkatesan K., Gebreab F. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat. Methods 2009, 6:47-54.
31. Lewis B.P., Burge C.B., Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
32. Krek A., Grün D., Poy M.N., Wolf R., Rosenberg L., Epstein E.J., MacMenamin P., da Piedade I., Gunsalus K.C., Stoffel M. Combinatorial microRNA target predictions. Nat. Genet. 2005, 37:495-500.
33. Luo H., Lin Y., Gao F., Zhang C.-T., Zhang R. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucl. Acids Res. 2014, 42:D574-D580.
34. Liao B.-Y., Zhang J. Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc. Natl. Acad. Sci. 2008, 105:6987-6992.
35. Georgi B., Voight B.F., Bućan M. From mouse to human: evolutionary genomics analysis of human orthologs of essential genes. PLoS Genet. 2013, 9:e1003484.
36. Khosravi P., Gazestani V.H., Asgari Y., Law B., Sadeghi M., Goliaei B. Network-based approach reveals Y chromosome influences prostate cancer susceptibility. Comput. Biol. Med. 2014, 54:24-31.
37. Schneider C.M., Moreira A.A., Andrade J.S., Havlin S., Herrmann H.J. Mitigation of malicious attacks on networks. Proc. Natl. Acad. Sci. 2011, 108:3838-3841.
38. A.A. Hagberg, D.A. Schult, P.J. Swart, Exploring network structure, dynamics, and function using Network X. in: Proceedings of the 7th Python in Science Conference (SciPy2008), 2008, pp. 11-15.
39. Csárdi G., Nepusz T. The igraph software package for complex network research. InterJ. Complex Syst. 2006, 1695.
40. Wang Z., Yang B. MicroRNA Expression Detection Methods 2010, Springer, Berlin.