Inferring gene regulatory networks from temporal expression profiles under time-delay and noise

Computational Biology and Chemistry

Volumn 31, Issue 4, 2007, Pages 239-245

  Kim, Shinuk ^a   Kim, Junil ^a   Cho, Kwang Hyun ^a  

^a Seoul National University   (South Korea)

Author keywords

Gene networks; Inference; Noise; Optimization; Ordinary differential equations; Time delay

Indexed keywords

GENE NETWORKS; REGULATORY NETWORKS; TEMPORAL EXPRESSION;

BIOLOGY; COMPUTER SIMULATION; OPTIMIZATION; ORDINARY DIFFERENTIAL EQUATIONS; SPURIOUS SIGNAL NOISE; TIME DELAY;

GENE EXPRESSION;

ARTICLE; GENE EXPRESSION PROFILING; THEORETICAL MODEL;

GENE EXPRESSION PROFILING; MODELS, THEORETICAL;

SACCHAROMYCETALES;

EID: 34447651339     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2007.03.013     Document Type: Article

References (21)

1. Andrec M., Kholodenko B., Levy R., and Sontag E. Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. J. Theor. Biol. 232 (2005) 427-441
2. Bahler J. Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet. 39 (2005) 69-94
3. Bansal M., Gatta G., and Bernardo D. Inference of gene regulatory networks and compound mode of action from time course gene expression profile. Syst. Biol. 22 (2006) 815-822
4. Brazhnik P. Inferring gene networks from steady-state response to single-gene perturbations. J. Theor. Biol. 237 (2005) 427-440
5. Chen T., He H.L., and Church G.M. Modeling gene expression with differential equations. Pac. Symp. Biocomput. 4 (1999) 29-40
6. Dasika M.S., Gupta A., and Maranas C.D. A mixed integer linear programming (MILP) framework for inferring time delay in gene regulatory networks. Pac. Symp. Biocomput. (2004) 474-486
7. de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 1 (2002) 67-103
8. Draghici S. Data Analysis Tools for DNA Microarrays (2003), Chapman & Hall/CRC
9. Gardner T., Bernardo D., Lorenz D., and Collins J. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301 (2003) 102-105
10. Kholodenko B.N., Kiyatkin A., Bruggeman F.J., Sontag E., Westerhoff H.V., and Hoek J.B. Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. PNAS 99 20 (2002) 12841-12846
11. Kimura S., Ide K., Kashihara A., Kano M., Hatakeyama M., Masui R., Nakagawa N., Yokoyama S., Kuramitsu S., and Konagaya A. Inference of S-System models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics 21 (2005) 1157-1163
12. Liu Q., and Cao J. Improved global exponential stability criteria of cellular neural networks with time-varying delays. Math Comp. Model. 43 (2006) 423-432
13. Press W.H., Flannery B.P., Teukolsky S.A., and Vetterling W.T. Numerical Recipes in Fortran. second ed. (1992), Cambridge University Press
14. Schroeder A., Mueller O., Stocker S., Salowsky R., Leiber M., Gassmann M., Lightfoot S., Menzel W., Granzow M., and Ragg T. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol. 7 3 (2006)
15. Smolen P., Baxtes D.A., and Byrne J.H. Modeling transcriptional control in gene networks-methods, recent results and future directions. Bull. Math Biol. 62 2 (2000) 247-292
16. Sontag E., Kiyatkin A., and Kholodenko B. Inferring dynamic architecture of cellular network using time series of gene expression, protein and metabolite data. Informatics 20 (2004) 1877-1886
17. Spell man P.T., Sherlock G., Hang M., Ayer V.R., Anders K., Essen M.B., Brown P.O., Bot stein D., and Fetcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharides cerevisiae by microarray hybridization 9 (1998) 3273-3297
18. Tegner J., Stephen Yeung M.K., and Collins J. Reverse engineering gene networks: integrating genetic perturbations with dynamical modelling. PNAS 100 (2003) 5944-5949
19. Wahde M., and Hertz J. Coarse-grained reverse engineering of genetic regulatory networks. Biosystems 55 (2000) 129-136
20. Yeung M.K., Tegner J., and Collins J.J. Reverse engineering gene networks using singular value decomposition and robust regression. PNAS 99 (2002) 6163-6168
21. Xu S., Lam J., Ho D., and Zou Y. Delay-dependent exponential stability for a class of neural networks with timedelays. J. Comput. Appl. Math. 183 (2005) 16-28