Gamage, Hasini Nakulugamuwa, Chetty, Madhu, Shatte, Adrian, and Hallinan, Jennifer (2021) An Efficient Boolean Modelling Approach for Genetic Network Inference. In: Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. From: CIBCB 2021: IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 13-15 October 2021, Melbourne, VIC, Australia.

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Abstract

The inference of Gene Regulatory Networks (GRNs) from time series gene expression data is an effective approach for unveiling important underlying gene-gene relationships and dynamics. While various computational models exist for accurate inference of GRNs, many are computationally inefficient, and do not focus on simultaneous inference of both network topology and dynamics. In this paper, we introduce a simple, Boolean network model-based solution for efficient inference of GRNs. First, the microarray expression data are discretized using the average gene expression value as a threshold. This step permits an experimental approach of defining the maximum indegree of a network. Next, regulatory genes, including the self-regulations for each target gene, are inferred using estimated multivariate mutual information-based Min-Redundancy Max-Relevance Criterion, and further accurate inference is performed by a swapping operation. Subsequently, we introduce a new method, combining Boolean network regulation modelling and Pearson correlation coefficient to identify the interaction types (inhibition or activation) of the regulatory genes. This method is utilized for the efficient determination of the optimal regulatory rule, consisting AND, OR, and NOT operators, by defining the accurate application of the NOT operation in conjunction and disjunction Boolean functions. The proposed approach is evaluated using two real gene expression datasets for an Escherichia coli gene regulatory network and a fission yeast cell cycle network. Although the Structural Accuracy is approximately the same as existing methods (MIBNI, REVEAL, Best-Fit, BIBN, and CST), the proposed method outperforms all these methods with respect to efficiency and Dynamic Accuracy.

Item ID:	81636
Item Type:	Conference Item (Research - E1)
ISBN:	978-1-6654-0112-8
Keywords:	Correlation coefficient; Computational modeling; Biological system modeling; Search methods; Time series analysis; Reverse engineering; Regulation
Copyright Information:	© 2021 IEEE
Date Deposited:	26 Mar 2024 22:12
FoR Codes:	31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310201 Bioinformatic methods development @ 50% 31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310202 Biological network analysis @ 50%
SEO Codes:	28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280102 Expanding knowledge in the biological sciences @ 100%
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