Inference of Gene Regulatory Network using Fuzzy Logic – A Review
Raviajot Kaur1 , Abhishek 2 , Shailendra Singh3
Section:Review Paper, Product Type: Journal Paper
Volume-4 ,
Issue-1 , Page no. 22-29, Jan-2016
Online published on Jan 31, 2016
Copyright © Raviajot Kaur, Abhishek , Shailendra Singh . This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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IEEE Style Citation: Raviajot Kaur, Abhishek , Shailendra Singh, “Inference of Gene Regulatory Network using Fuzzy Logic – A Review,” International Journal of Computer Sciences and Engineering, Vol.4, Issue.1, pp.22-29, 2016.
MLA Style Citation: Raviajot Kaur, Abhishek , Shailendra Singh "Inference of Gene Regulatory Network using Fuzzy Logic – A Review." International Journal of Computer Sciences and Engineering 4.1 (2016): 22-29.
APA Style Citation: Raviajot Kaur, Abhishek , Shailendra Singh, (2016). Inference of Gene Regulatory Network using Fuzzy Logic – A Review. International Journal of Computer Sciences and Engineering, 4(1), 22-29.
BibTex Style Citation:
@article{Kaur_2016,
author = {Raviajot Kaur, Abhishek , Shailendra Singh},
title = {Inference of Gene Regulatory Network using Fuzzy Logic – A Review},
journal = {International Journal of Computer Sciences and Engineering},
issue_date = {1 2016},
volume = {4},
Issue = {1},
month = {1},
year = {2016},
issn = {2347-2693},
pages = {22-29},
url = {https://www.ijcseonline.org/full_paper_view.php?paper_id=774},
publisher = {IJCSE, Indore, INDIA},
}
RIS Style Citation:
TY - JOUR
UR - https://www.ijcseonline.org/full_paper_view.php?paper_id=774
TI - Inference of Gene Regulatory Network using Fuzzy Logic – A Review
T2 - International Journal of Computer Sciences and Engineering
AU - Raviajot Kaur, Abhishek , Shailendra Singh
PY - 2016
DA - 2016/01/31
PB - IJCSE, Indore, INDIA
SP - 22-29
IS - 1
VL - 4
SN - 2347-2693
ER -
VIEWS | XML | |
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Abstract
Cellular processes like metabolism, responses to the actions or surroundings and reproduction of cells are controlled by proteins. Genes are responsible for the synthesis of a protein. Some genes synthesize proteins which control the rate at which other genes synthesize protein and form the network of interactions between the genes named as Gene Regulatory Networks (GRNs). GRNs are the control systems which represents the causal relationships between genes, protein-protein interactions, etc. They provide a very useful contribution to cellular biology, mechanics of various harmful diseases like cancer, help in drug discovery and impact of those drugs on the individuals. Large amount of microarray gene expression datasets are available that can be used to analyse the relationships between the genes. These datasets are imprecise and uncertain because of the noisy and missing values in gene expression datasets. Fuzzy logic based models are capable of handling uncertainty of data which provide the valuable contribution in the inference of GRNs. To address this most challenging area of cellular biology, this paper reviews various fuzzy logic based techniques to infer GRNs from microarray gene expression datasets. The main objective of this review paper is to present, analyse and compare contributions given by researchers in this field.
Key-Words / Index Term
Fuzzy Logic, Genetic Regulatory Networks, Microarray gene expression data, Clustering, GRN Inference
References
[1] T. Al-Quzlan, A. Hamdi-Cherif, and C. Kara-Mohamed, “Big data fuzzy management methods in gene regulatory networks inference: a review”, in Proceedings of the 6th International Conference on Management of Emergent Digital EcoSystems, ACM, ISBN: 978-1-4503-2767-1, Page No (201-203), Sept 2014.
[2] S. Vineetha, C. Bhat, and S.M. Idicula, “Gene regulatory network from microarray data using dynamic neural fuzzy approach” in Proceedings of the International Symposium on Biocomputing, ACM, ISBN: 978-1-60558-722-6, Article No (17), Feb 2010.
[3] S. Mandai, G. Saha, and R.K. Pal "Neural network based gene regulatory network reconstruction." Computer, Communication, Control and Information Technology (C3IT), 2015 Third International Conference, IEEE, Page No. (1-5), Feb 2015.
[4] J.F. Al-Shobaili, and A. Hamdi-Cherif. "Gene regulatory networks estimation using uniting Bayesian subnetworks" Proceedings of the 6th International Conference on Management of Emergent Digital EcoSystem, ACM, Page No(95-100) 2014.
[5] G.A. Ruz, T. Timmermann, and E. Goles, “Reconstruction of a GRN model of salt stress response in arabidopsis using genetic algorithms” in Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2015 IEEE Conference, Page No (1-8), Aug 2015.
[6] R. Duenas Jimenez, D. Correa Martins, and C. Silva Santos, “Gene networks inference through one genetic algorithm per gene” in Bioinformatics and Bioengineering (BIBE), 2014 IEEE International Conference, Page No. (1-8), Nov 2014.
[7] Y. Xiao, “A tutorial on analysis and simulation of boolean gene regulatory network models”. Current genomics, Volume-10, Issue-7, Page No (511-525), Nov 2009.
[8] R. Albert, “Boolean modelling of genetic regulatory networks”, in Complex networks, Springer Berlin Heidelberg, Page No. (459-481), Jan 2004.
[9] D.C. Nguyen, and F. Azadivar, “Application of Computer Simulation and Genetic Algorithms to Gene Interactive Rules for Early Detection and Prevention of Cancer” Systems Journal, IEEE, Volume-8, Issue-3, Page No (1005-1013), 2014.
[10] S. Marshall, and L. Yu, “A method for analysing gene expression data temporal sequence using Probabilistic Boolean Networks” in Signal Processing Conference, 2006 14th European, IEEE, Page No (1-5), Sept 2006.
[11] I. Shmulevich, E.R. Dougherty, S. Kim and W. Zhang, “Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks” Bioinformatics, Volume-18, Issue-2, Page No (261-274), 2002.
[12] I. Shmulevich, E.R. Dougherty, and W. Zhang, “From Boolean to probabilistic Boolean networks as models of genetic regulatory networks” Proceedings of the IEEE, Volume-90, Issue-11, Page No (1778-1792), 2002.
[13] H. Kim, and E. Gelenbe, “Reconstruction of large-scale gene regulatory networks using bayesian model averaging”, in Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference, Page No (202-207), Nov 2011.
[14] G.F. Cooper, and E. Herskovits, “A Bayesian method for the induction of probabilistic networks from data”, Machine learning, Volume-9, Issue-4, Page No (309-347), 1992.
[15] Y. Watanabe, S. Seno, Y. Takenaka, and H. Matsuda, “An estimation method for inference of gene regulatory network using Bayesian network with uniting of partial problems”, BMC genomics, Volume-13, Suppl-1, p.S12, Jan 2012.
[16] K.P. Murphy, “Dynamic bayesian networks: representation, inference and learning “, Doctoral dissertation, University of California, Berkeley, 2002.
[17] A. Shermin, and M. Orgun, “A 2-stage approach for inferring gene regulatory networks using dynamic bayesian networks” in Bioinformatics and Biomedicine, 2009 BIBM'09, IEEE International Conference, Page No (166-169), Nov 2009.
[18] M. Zou, and S.D. Conzen, “A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data” Bioinformatics, Volume-21, Issue-1, Page No (71-79), 2005.
[19] E. Keedwell, and A. Narayanan, “Discovering gene networks with a neural-genetic hybrid”, Computational Biology and Bioinformatics, IEEE/ACM Transactions, Volume-2, Issue-3, Page No (231-242), 2005.
[20] L. Liu, M. Liu, and M. Ma, “Construction of linear dynamic gene regulatory network based on feedforward neural network”, in Natural Computation (ICNC), 2014 10th International Conference, IEEE, Page No (99-107), Aug 2014.
[21] H.W. Ressom, Y. Zhang, J. Xuan, Y. Wang, and R. Clarke, “Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence”, in Computational Intelligence and Bioinformatics and Computational Biology, 2006. CIBCB'06. 2006 IEEE Symposium, Page No (1-8), Sept 2006.
[22] N. Kennedy, A. Mizeranschi, P. Thompson, H. Zheng, and W. Dubitzky, “Reverse engineering of gene regulation models from multi-condition experiments”, in Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2013 IEEE Symposium, Page No (112-119), April 2013.
[23] Y. Gao, and D. Wang, “Least squares identification method for differential equations of gene regulatory networks” in Proceedings of the 33rd Chinese Control Conference, July 2014.
[24] E. Sakamoto, and H. Iba, “Inferring a system of differential equations for a gene regulatory network by using genetic programming”, in Evolutionary Computation, Proceedings of the 2001 Congress, Volume-1, Page No (720-726), 2001.
[25] J. Gebert, N. Radde, and G.W. Weber, “Modeling gene regulatory networks with piecewise linear differential equations”, European Journal of Operational Research, Voulme-181, Issue-3, Page No (1148-1165), 2007.
[26] R. Ji, L. Ding, X. Yan, and M. Xin, “Modelling gene regulatory network by fractional order differential equations”, in Bio-Inspired Computing: Theories and Applications (BIC-TA), 2010 IEEE Fifth International Conference, Page No (431-434), Sept 2010.
[27] I. Chebil, R. Nicolle, G. Santini, C. Rouveirol, and M. Elati, “Hybrid method inference for the construction of cooperative regulatory network in human”, Nano Bioscience, IEEE Transactions, Voulme-13, Issue-2, Page No (97-103), 2014.
[28] Y. Lu, Q. Tian, M. Sanchez, and Y. Wang, “Hybrid PCA and LDA analysis of microarray gene expression data”, in Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'05, Proceedings of the 2005 IEEE Symposium, Page No (1-6), Nov 2005.
[29] Y. Li, and A. Ngom, “The max-min high-order dynamic Bayesian network learning for identifying gene regulatory networks from time-series microarray data”, in Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2013 IEEE Symposium, Page No (83-90), April 2013.
[30] N. Vijesh, S.K. Chakrabarti, and J. Sreekumar, “Modeling of gene regulatory networks: A review”, Journal of Biomedical Science and Engineering, Volume-6, Issue-02, p.223, 2013.
[31] H. Xu, and S. Wang, “Fuzzy Logical on Boolean Networks as Model of Gene Regulatory Networks”, in 2009 International Joint Conference on Artificial Intelligence, Page No (501-505), April 2009.
[32] M.J. Heller, “DNA microarray technology: devices, systems, and applications”, Annual review of biomedical engineering, Volume-4, Issue-1, Page No (129-153), 2002.
[33] O. ElBakry, M.O. Ahmad, and M.N.S. Swamy, “Inference of gene regulatory networks from time-series microarray data”, in NEWCAS Conference (NEWCAS), 2010 8th IEEE International, Page No (141-144), June 2010.
[34] D. Ramot, M. Friedman, G. Langholz, and A. Kandel, “Complex fuzzy logic” Fuzzy Systems, IEEE Transactions, Volume-11, Issue-4, Page No (450-461), 2003.
[35] F.M. Alakwaa, “Modeling of Gene Regulatory Networks: A Literature Review”, Journal of Computational Systems Biology, Volume-1, Issue-1, p.1, 2014.
[36] J. Kacprzyk, “Studies in Fuzziness and Soft Computing”, Volume- 242, 2009.
[37] P.J. Woolf and Y. Wang, “A fuzzy logic approach to analyzing gene expression data”, Physiological Genomics, Volume-3, 2000.
[38] R. Ram, M. Chetty, and T. Dix, “Fuzzy model for gene regulatory network” in Evolutionary Computation, CEC 2006. IEEE Congress, Page No (1450-1455), July 2006.
[39] H. Ressom, D. Wang, R.S. Varghese, and R. Reynolds, “Fuzzy logic-based gene regulatory network”, in Fuzzy Systems, FUZZ'03, 12th IEEE International Conference, Volume-2, Page No (1210-1215), May 2003.
[40] J. Bordon, M. Moskon, N. Zimic, and M. Mraz, “Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data”, IEEE Computational Intelligence Society, Volume-12, Issue-5, Page No (1199-1205), April 2015.
[41] Sehgal, B. Muhammad Shoaib, I. Gondal, and L.S. Dooley, "CF-GeNe: Fuzzy Framework for Robust Gene Regulatory Network Inference", JCP, Voulme-1, Issue-7, Page No (1-8), 2006.
[42] B.A. Sokhansansanj, J.P. Fitch, J.N. Quong, and A.A. Quong, “Exhaustive search for fuzzy gene networks from microarray data” in Engineering in Medicine and Biology Society, Proceedings of the 25th Annual International Conference of the IEEE, Volume-4, Page No (3571-3574), Sept 2003.