analysis and practical guideline of constraint-based boolean method in genetic network inference基于布尔方法的分析和实际指导基因网络推理.pdfVIP

Analysis and Practical Guideline of Constraint-Based Boolean Method in Genetic Network Inference 1,2 2 2,3 2,4 Treenut Saithong *, Somkid Bumee , Chalothorn Liamwirat , Asawin Meechai 1 Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand, 2 Systems Biology and Bioinformatics Research Laboratory, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand, 3 Division of Biotechnology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand, 4 Department of Chemical Engineering, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand Abstract Boolean-based method, despite of its simplicity, would be a more attractive approach for inferring a network from high- throughput expression data if its effectiveness has not been limited by high false positive prediction. In this study, we explored factors that could simply be adjusted to improve the accuracy of inferring networks. Our work focused on the analysis of the effects of discretisation methods, biological constraints, and stringency of Boolean function assignment on the performance of Boolean network, including accuracy, precision, specificity and sensitivity, using three sets of microarray time-series data. The study showed that biological constraints have pivotal influence on the network performance over the other factors. It can reduce the variation in network performance resulting from the arbitrary selection of discretisation methods and stringency settings. We also presented the master Boolean network as an appr