Paper Titles

Emotional Expression System Based on Expression Intensity Recognition and Affective Model
p.618

Review of Current Available Dental Articular Simulators
p.623

Study on Optimization of CPG Model for Lower Limb Prosthesis
p.633

Succulent Intracalvarium Enclosing and Protecting the Brain of a Falling Gecko
p.641

Topology Analysis of a Metabolic Functional Gene Transcriptional Regulatory Network of Escherichia Coli
p.648

Tracking Time Variant Neuron Tuning Properties of Brain Machine Interfaces
p.654

Design and Realization of an Early Pre-Impact Fall Alarm System Based on MEMS Inertial Sensing Units
p.659

Design and Realization of a Wearable Hip-Airbag System for Fall Protection
p.667

Controllable Adjustment of Bio-Replicated Shark Skin Drag Reduction Riblets
p.677

HomeApplied Mechanics and MaterialsApplied Mechanics and Materials Vol. 461Topology Analysis of a Metabolic Functional Gene...

Topology Analysis of a Metabolic Functional Gene Transcriptional Regulatory Network of Escherichia Coli

Article Preview

Abstract:

Under the perspectives of network science and systems biology, the characterizations of transcriptional regulatory networks (TRNs) beyond the context of model organisms have been studied extensively. However, little is still known about the structure and functionality of TRNs that control metabolic physiological processes. In this study, we present a newly version of the TRN of E.coli controlling metabolism based on functional annotations from GeneProtEC and Gene Ontology (GO). We also present an exhaustive topological analysis of the metabolic transcriptional regulatory network (MTRN), focusing on the main statistical characterization describing the topological structure and the comparison with TRN. From the results in this paper we infer that TRN and MTRN have very similar characteristic distribution.

You might also be interested in these eBooks

Advances in Bionic Engineering

Info:

Periodical:

Applied Mechanics and Materials (Volume 461)

Pages:

648-653

DOI:

https://doi.org/10.4028/www.scientific.net/AMM.461.648

Citation:

Cite this paper

Online since:

November 2013

Authors:

Qing Yu Zou, Fu Liu, Hou Tao

Keywords:

Metabolic Functional, Module, Motif, Topology

Export:

RIS, BibTeX

Price:

Permissions CCC:

Request Permissions

Permissions PLS:

Request Permissions

Сopyright:

© 2014 Trans Tech Publications Ltd. All Rights Reserved

Share:

Citation:

[1] M. Carey, S.T. Smale, Transcriptional regulation in eukaryotes concepts, strategies, and techniques, Cold Spring Harbor. (2000).

[2] A. Ma'ayan, Introduction to network analysis in systems biology, Science Signaling. 4(2011).

[3] H. -Y. Chuang, M. Hofree, T. Ideker, A decade of systems biology, Annual Review of Cell and Developmental Biology. 26(2010) 721-744.

DOI: 10.1146/annurev-cellbio-100109-104122

[4] S.B.T. de-Leon, E.H. Davidson, Modeling the dynamics of transcriptional gene regulatory networks for animal development, Developmental Biology. 325(2009) 317-328.

DOI: 10.1016/j.ydbio.2008.10.043

[5] M.M. Babu, N.M. Luscombe, L. Aravind, M. Gerstein, S.A. Teichmann, Structure and evolution of transcriptional regulatory networks, Current Opinion in Structural Biology. 14(2004) 283-291.

DOI: 10.1016/j.sbi.2004.05.004

[6] E.H. Davidson, J.P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.H. Yuh, T. Minokawa, G. Amore, V. Hinman, C. Arenas-Mena, O. Otim, C.T. Brown, C.B. Livi, P.Y. Lee, R. Revilla, A.G. Rust, Z.J. Pan, M.J. Schilstra, P.J.C. Clarke, M.I. Arnone, L. Rowen, R.A. Cameron, D.R. McClay, L. Hood, H. Bolouri, A genomic regulatory network for development, Science. 295(2002).

DOI: 10.1126/science.1069883

[7] M.M. Babu, Structure, evolution and dynamics of transcriptional regulatory networks, Biochemical Society Transactions. 38(2010) 1155-1178.

DOI: 10.1042/bst0381155

[8] T.M. Kim, P.J. Park, Advances in analysis of transcriptional regulatory networks, Wiley Interdiscip Rev-Syst Biol. 3(2011) 21-35.

[9] M.M. Babu, S.A. Teichmann, L. Aravind, Evolutionary dynamics of prokaryotic transcriptional regulatory networks, Journal of Molecular Biology. 358(2006) 614-633.

DOI: 10.1016/j.jmb.2006.02.019

[10] M.E. Wall, Structure-function relations are subtle in genetic regulatory networks, Mathematical Biosciences. 231(2011) 61-68.

DOI: 10.1016/j.mbs.2011.02.003

[11] A. Martinez-Antonio, S.C. Janga, D. Thieffry, Functional organisation of escherichia coli transcriptional regulatory network, Journal of Molecular Biology. 381(2008) 238-247.

DOI: 10.1016/j.jmb.2008.05.054

[12] L. Guzman-Vargas, M. Santillan, Comparative analysis of the transcription-factor gene regulatory networks of e. Coli and s. Cerevisiae, Bmc Systems Biology. 2(2008) 13.

DOI: 10.1186/1752-0509-2-13

[13] R. Dobrin, Q.K. Beg, A.L. Barabasi, Z.N. Oltvai, Aggregation of topological motifs in the escherichia coli transcriptional regulatory network, Bmc Bioinformatics. 5(2004).

[14] O. Resendis-Antonio, J.A. Freyre-Gonzalez, R. Menchaca-Mendez, R.M. Gutierrez-Rios, A. Martinez-Antonio, C. Avila-Sanchez, J. Collado-Vides, Modular analysis of the transcriptional regulatory network of e-coli, Trends in Genetics. 21(2005) 16-20.

DOI: 10.1016/j.tig.2004.11.010

[15] D.S. Lee, H. Rieger, Comparative study of the transcriptional regulatory networks of e-coli and yeast: Structural characteristics leading to marginal dynamic stability, J Theor Biol. 248(2007) 618-626.

DOI: 10.1016/j.jtbi.2007.07.001

[16] N. Guelzim, S. Bottani, P. Bourgine, F. Kepes, Topological and causal structure of the yeast transcriptional regulatory network, Nat Genet. 31(2002) 60-63.

DOI: 10.1038/ng873

[17] S.C. Janga, H. Salgado, A. Martinez-Antonio, J. Collado-Vides, Coordination logic of the sensing machinery in the transcriptional regulatory network of escherichia coli, Nucleic Acids Research. 35(2007) 6963-6972.

DOI: 10.1093/nar/gkm743

[18] C. Marr, F.J. Theis, L.S. Liebovitch, M.T. Hutt, Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of escherichia coli, Plos Computational Biology. 6(2010) e1000836.

DOI: 10.1371/journal.pcbi.1000836

[19] H.W. Ma, J. Buer, A.P. Zeng, Hierarchical structure and modules in the escherichia coli transcriptional regulatory network revealed by a new top-down approach, Bmc Bioinformatics. 5(2004) 199.

[20] A. Martinez-Antonio, J. Collado-Vides, Identifying global regulators in transcriptional regulatory networks in bacteria, Current Opinion in Microbiology. 6(2003) 482-489.

DOI: 10.1016/j.mib.2003.09.002

[21] N.D. Price, J.L. Reed, B.O. Palsson, Genome-scale models of microbial cells: Evaluating the consequences of constraints, Nat Rev Microbiol. 2(2004) 886-897.

DOI: 10.1038/nrmicro1023

[22] K.J. Kauffman, P. Prakash, J.S. Edwards, Advances in flux balance analysis, Curr Opin Biotechnol. 14(2003) 491-496.

[23] M.W. Covert, B.O. Palsson, Transcriptional regulation in constraints-based metabolic models of escherichia coli, J Biol Chem. 277(2002) 28058-28064.

DOI: 10.1074/jbc.m201691200

[24] L.D.F. Costa, F.A. Rodrigues, G. Travieso, P.R.V. Boas, Characterization of complex networks: A survey of measurements, Advances in Physics. 56(2007) 167-242.

DOI: 10.1080/00018730601170527

[25] S. Gama-Castro, H. Salgado, M. Peralta-Gil, A. Santos-Zavaleta, L. Muniz-Rascado, H. Solano-Lira, V. Jimenez-Jacinto, V. Weiss, J.S. Garcia-Sotelo, A. Lopez-Fuentes, L. Porron-Sotelo, S. Alquicira-Hernandez, A. Medina-Rivera, I. Martinez-Flores, K. Alquicira-Hernandez, R. Martinez-Adame, C. Bonavides-Martinez, J. Miranda-Rios, A.M. Huerta, A. Mendoza-Vargas, L. Collado-Torres, B. Taboada, L. Vega-Alvarado, M. Olvera, L. Olvera, R. Grande, E. Morett, J. Collado-Vides, Regulondb version 7. 0: Transcriptional regulation of escherichia coli k-12 integrated within genetic sensory response units (gensor units), Nucleic Acids Research. 39(2011).

DOI: 10.1093/nar/gkq1110

[26] H. Salgado, I. Martinez-Flores, A. Lopez-Fuentes, J.S. Garcia-Sotelo, L. Porron-Sotelo, H. Solano, L. Muniz-Rascado, J. Collado-Vides, Extracting regulatory networks of escherichia coli from regulondb, Methods Mol Biol. 804(2012) 179-195.

DOI: 10.1007/978-1-61779-361-5_10

[27] M.H. Serres, S. Goswami, M. Riley, Genprotec: An updated and improved analysis of functions of escherichia coli k-12 proteins, Nucleic Acids Research. 32(2004) D300-D302.

DOI: 10.1093/nar/gkh087

[28] T.G.O. Consortium, The gene ontology: Enhancements for 2011, Nucleic Acids Res. 40(2012) D559-564.

DOI: 10.1093/nar/gkr1028

[29] F.R. Blattner, G. Plunkett, 3rd, C.A. Bloch, N.T. Perna, V. Burland, M. Riley, J. Collado-Vides, J.D. Glasner, C.K. Rode, G.F. Mayhew, J. Gregor, N.W. Davis, H.A. Kirkpatrick, M.A. Goeden, D.J. Rose, B. Mau, Y. Shao, The complete genome sequence of escherichia coli k-12, Science. 277(1997).

DOI: 10.1126/science.277.5331.1453

[30] Z. Du, L. Li, C.F. Chen, P.S. Yu, J.Z. Wang, G-sesame: Web tools for go-term-based gene similarity analysis and knowledge discovery, Nucleic Acids Res. 37(2009) W345-349.

DOI: 10.1093/nar/gkp463

[31] J.B. Axelsen, S. Bernhardsson, M. Rosvall, K. Sneppen, A. Trusina, Degree landscapes in scale-free networks, Phys Rev E. 74(2006).

DOI: 10.1103/physreve.74.036119

[32] M. Girvan, M.E.J. Newman, Community structure in social and biological networks, Proceedings of the National Academy of Sciences of the United States of America. 99(2002) 7821-7826.

DOI: 10.1073/pnas.122653799

[33] D.J. Watts, S.H. Strogatz, Collective dynamics of small-world, networks, Nature. 393(1998) 440-442.

DOI: 10.1038/30918