DocumentCode :
2657330
Title :
Reconstruction of Gene Regulatory Networks using Differential Evolution
Author :
Mondal, Briti Sundar ; Sarkar, Arup Kumar ; Hasan, Md Mahmudul ; Noman, Nasimul
Author_Institution :
Dept. of Comput. Sci. & Eng., Dhaka Univ., Dhaka, Bangladesh
fYear :
2010
fDate :
23-25 Dec. 2010
Firstpage :
440
Lastpage :
445
Abstract :
Gene Regulatory Network (GRN) is an abstract mapping of gene regulations in living cells that can help to predict the system behavior of living organisms. In this research, we use a model based inference method to reconstruct GRN from gene expression data. We use linear time variant model which is of particular interest among all other models because of its capability of discovering the non-linear interactions among genes in a reasonably short time even while dealing with noisy time-series data. Here, Differential Evolution (DE), a versatile, robust and well-known Evolutionary Algorithm (EA) has been used. The potency of the proposed method has been verified in gene network reconstruction experiments, varying the network dimension and characteristics, the amount of gene expression data used for inference, and the noise level present in gene expression profiles. Real expression dataset of SOS DNA repair system in Escherichia coli is used to reconstruct the regulatory network. All these experiments have proved the efficacy of the proposed reconstruction method.
Keywords :
bioinformatics; evolutionary computation; genetic engineering; inference mechanisms; living systems; microorganisms; time series; Escherichia coli; SOS DNA repair system; abstract mapping; differential evolution; evolutionary algorithm; gene expression data; gene regulatory network reconstruction; inference; linear time variant model; living cells; living organisms; noisy time-series data; nonlinear interactions; DNA; Data models; Gene expression; Mathematical model; Noise; Noise measurement; Differential evolution; Global optimization; Linear time variant model; Reverse engineering;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Computer and Information Technology (ICCIT), 2010 13th International Conference on
Conference_Location :
Dhaka
Print_ISBN :
978-1-4244-8496-6
Type :
conf
DOI :
10.1109/ICCITECHN.2010.5723898
Filename :
5723898
Link To Document :
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