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Inference of Gene Regulatory Networks with Variable Time Delay from Time-Series Microarray Data
May-June 2013 (vol. 10 no. 3)
pp. 671-687
Ola ElBakry, Dept. of Electr. & Comput. Eng., Concordia Univ., Montreal, QC, Canada
M. Omair Ahmad, Dept. of Electr. & Comput. Eng., Concordia Univ., Montreal, QC, Canada
M. N. S. Swamy, Dept. of Electr. & Comput. Eng., Concordia Univ., Montreal, QC, Canada
Regulatory interactions among genes and gene products are dynamic processes and hence modeling these processes is of great interest. Since genes work in a cascade of networks, reconstruction of gene regulatory network (GRN) is a crucial process for a thorough understanding of the underlying biological interactions. We present here an approach based on pairwise correlations and lasso to infer the GRN, taking into account the variable time delays between various genes. The proposed method is applied to both synthetic and real data sets, and the results on synthetic data show that the proposed approach outperforms the current methods. Further, the results using real data are more consistent with the existing knowledge concerning the possible gene interactions.
Index Terms:
genetics,gene regulatory network,gene interactions,pairwise correlation,biological interaction,dynamic process,time-series microarray data,variable time delay,Correlation,Delays,Delay effects,Gene expression,Time series analysis,Mathematical model,Pairwise error probability,correlation,genetics,gene regulatory network,gene interactions,pairwise correlation,biological interaction,dynamic process,time-series microarray data,variable time delay,Correlation,Delays,Delay effects,Gene expression,Time series analysis,Mathematical model,Pairwise error probability,lasso,Gene regulatory network
Citation:
Ola ElBakry, M. Omair Ahmad, M. N. S. Swamy, "Inference of Gene Regulatory Networks with Variable Time Delay from Time-Series Microarray Data," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 3, pp. 671-687, May-June 2013, doi:10.1109/TCBB.2013.73
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