Gene regulatory network identification from the yeast cell cycle based on a neuro-fuzzy system

• Published in: Genetics and molecular research Vol. 15; no. 3
• Main Authors: Wang, B H, Lim, J W, Lim, J S
• Format: Journal Article
• Language: English
• Published: Brazil 30.08.2016
• Subjects: Cell Cycle; Computational Biology; Fuzzy Logic; Gene Expression Regulation, Fungal; Gene Regulatory Networks; Models, Genetic; Neural Networks (Computer); Saccharomyces cerevisiae - genetics
• ISSN: 1676-5680; 1676-5680
• DOI: 10.4238/gmr.15039002

Many studies exist for reconstructing gene regulatory networks (GRNs). In this paper, we propose a method based on an advanced neuro-fuzzy system, for gene regulatory network reconstruction from microarray time-series data. This approach uses a neural network with a weighted fuzzy function to model the relationships between genes. Fuzzy rules, which determine the regulators of genes, are very simplified through this method. Additionally, a regulator selection procedure is proposed, which extracts the exact dynamic relationship between genes, using the information obtained from the weighted fuzzy function. Time-series related features are extracted from the original data to employ the characteristics of temporal data that are useful for accurate GRN reconstruction. The microarray dataset of the yeast cell cycle was used for our study. We measured the mean squared prediction error for the efficiency of the proposed approach and evaluated the accuracy in terms of precision, sensitivity, and F-score. The proposed method outperformed the other existing approaches.