title: A tutorial to identify nonlinear associations in gene expression time series data.
abstract: The study of gene regulatory networks is the basis to understand the biological complexity of several diseases and/or cell states. It has become the core of research in the field of systems biology. Several mathematical methods have been developed in the last decade, especially in the analysis of time series gene expression data derived from microarrays and sequencing-based methods. Most of the models available in the literature assumes linear associations among genes and do not infer directionality in these connections or uses a priori biological knowledge to set the directionality. However, in several cases, a priori biological information is not available. In this context, we describe a statistical method, namely nonlinear vector autoregressive model to estimate nonlinear relationships and also to infer directionality at the edges of the network by using the temporal information of the time series gene expression data without a priori biological information.
authors.affiliation: Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, Rua do Matão, 1010 - Building C, Cidade Universitária, São Paulo, SP, 05508-090, Brazil, fujita@ime.usp.br.
authors.forename: André
authors.initials: A
authors.lastname: Fujita
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000465:Algorithms; D000818:Animals; D015870:Gene Expression; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D023281:Genomics; D006801:Humans; D008957:Models, Genetic; D017711:Nonlinear Dynamics; D049490:Systems Biology