title: Reverse engineering of gene regulatory networks based on S-systems and Bat algorithm.
abstract: The correct inference of gene regulatory networks for the understanding of the intricacies of the complex biological regulations remains an intriguing task for researchers. With the availability of large dimensional microarray data, relationships among thousands of genes can be simultaneously extracted. Among the prevalent models of reverse engineering genetic networks, S-system is considered to be an efficient mathematical tool. In this paper, Bat algorithm, based on the echolocation of bats, has been used to optimize the S-system model parameters. A decoupled S-system has been implemented to reduce the complexity of the algorithm. Initially, the proposed method has been successfully tested on an artificial network with and without the presence of noise. Based on the fact that a real-life genetic network is sparsely connected, a novel Accumulative Cardinality based decoupled S-system has been proposed. The cardinality has been varied from zero up to a maximum value, and this model has been implemented for the reconstruction of the DNA SOS repair network of Escherichia coli. The obtained results have shown significant improvements in the detection of a greater number of true regulations, and in the minimization of false detections compared to other existing methods.
authors.affiliation: * Electronics and Communication Engineering Department, Global Institute of Management and Technology Krishnanagar, West Bengal 741102, India.
authors.forename: Sudip
authors.initials: S
authors.lastname: Mandal
authors.affiliation: † Computer Science and Engineering Department, University of Calcutta, Acharya Prafulla Chandra Siksha Prangan, JD-2, Sector - III, Salt Lake Kolkata 700098, India.
authors.forename: Abhinandan
authors.initials: A
authors.lastname: Khan
authors.affiliation: ‡ Information Technology Department, North Eastern Hill University, Umshing, Mawkynroh, Shillong, Meghalaya 793022, India.
authors.forename: Goutam
authors.initials: G
authors.lastname: Saha
authors.affiliation: † Computer Science and Engineering Department, University of Calcutta, Acharya Prafulla Chandra Siksha Prangan, JD-2, Sector - III, Salt Lake Kolkata 700098, India.
authors.forename: Rajat Kumar
authors.initials: RK
authors.lastname: Pal
mesh_terms: D000465:Algorithms; D000818:Animals; D002685:Chiroptera / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D013014:SOS Response, Genetics / Q000235:genetics
keywords: Bat algorithm; DREAM4; GNW; S-system; cardinality; gene regulatory network; microarray data; regularization