Gene regulatory networks represent the regulatory relationships between genes and their products and are important for exploring and defining the underlying biological processes of cellular systems. We develop a novel framework to recover the structure of nonlinear gene regulatory networks using semiparametric spline-based directed acyclic graphical models. Our use of splines allows the model to have both flexibility in capturing nonlinear dependencies as well as control of overfitting via shrinkage, using mixed model representations of penalized splines. We propose a novel discrete mixture prior on the smoothing parameter of the splines that allows for simultaneous selection of both linear and nonlinear functional relationships as well as inducing sparsity in the edge selection. Using simulation studies, we demonstrate the superior performance of our methods in comparison with several existing approaches in terms of network reconstruction and functional selection. We apply our methods to a gene expression dataset in glioblastoma multiforme, which reveals several interesting and biologically relevant nonlinear relationships.

Bayesian nonlinear model selection for gene regulatory networks / Ni, Yang; Stingo, Francesco C.; Baladandayuthapani, Veerabhadran. - In: BIOMETRICS. - ISSN 0006-341X. - STAMPA. - 71:(2015), pp. 585-595. [10.1111/biom.12309]

Bayesian nonlinear model selection for gene regulatory networks

STINGO, FRANCESCO CLAUDIO;
2015

Abstract

Gene regulatory networks represent the regulatory relationships between genes and their products and are important for exploring and defining the underlying biological processes of cellular systems. We develop a novel framework to recover the structure of nonlinear gene regulatory networks using semiparametric spline-based directed acyclic graphical models. Our use of splines allows the model to have both flexibility in capturing nonlinear dependencies as well as control of overfitting via shrinkage, using mixed model representations of penalized splines. We propose a novel discrete mixture prior on the smoothing parameter of the splines that allows for simultaneous selection of both linear and nonlinear functional relationships as well as inducing sparsity in the edge selection. Using simulation studies, we demonstrate the superior performance of our methods in comparison with several existing approaches in terms of network reconstruction and functional selection. We apply our methods to a gene expression dataset in glioblastoma multiforme, which reveals several interesting and biologically relevant nonlinear relationships.
2015
71
585
595
Ni, Yang; Stingo, Francesco C.; Baladandayuthapani, Veerabhadran
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Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/1054625
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