10.6084/m9.figshare.7504715.v1
Nasibeh Khayer
Nasibeh
Khayer
Mehdi Mirzaie
Mehdi
Mirzaie
Sayed-Amir Marashi
Sayed-Amir
Marashi
Mostafa Rezaei-Tavirani
Mostafa
Rezaei-Tavirani
Fatemeh Goshadrou
Fatemeh
Goshadrou
Three-way interaction model with switching mechanism as an effective strategy for tracing functionally-related genes
Taylor & Francis Group
2018
Three-way interaction model
switching mechanism
functionally-related genes
differential co-expression
2018-12-24 08:41:27
Dataset
https://tandf.figshare.com/articles/dataset/Three-way_interaction_model_with_switching_mechanism_as_an_effective_strategy_for_tracing_functionally-related_genes/7504715
<p><b>Introduction</b>: Identification of functionally-related genes is an important step in understanding biological systems. The most popular strategy to infer functional dependence is to study pairwise correlations between gene expression levels. However, certain functionally-related genes may have a low expression correlation due to their nonlinear interactions. The use of a three-way interaction (3WI) model with switching mechanism (SM) is a relatively new strategy to trace functionally-related genes. The 3WI model traces the dynamic and nonlinear nature of the co-expression relationship of two genes by introducing their link to the expression level of a third gene.</p> <p><b>Areas covered</b>: In this paper, we reviewed a variety of existing methods for tracing the 3WIs. Furthermore, we provide a comprehensive review of the previous biological studies based on 3WI models.</p> <p><b>Expert commentary</b>: Comparison of features of these methods indicates that the modified liquid association algorithm has the best efficiency for tracing 3WI between others. The limited number of biological studies based on the 3WI suggests that high computational demand of the available algorithms is a major challenge to apply this approach for analyzing high-throughput omics data.</p>