title: Learning gene regulatory networks from next generation sequencing data.
abstract: In recent years, next generation sequencing (NGS) has gradually replaced microarray as the major platform in measuring gene expressions. Compared to microarray, NGS has many advantages, such as less noise and higher throughput. However, the discreteness of NGS data also challenges the existing statistical methodology. In particular, there still lacks an appropriate statistical method for reconstructing gene regulatory networks using NGS data in the literature. The existing local Poisson graphical model method is not consistent and can only infer certain local structures of the network. In this article, we propose a random effect model-based transformation to continuize NGS data and then we transform the continuized data to Gaussian via a semiparametric transformation and apply an equivalent partial correlation selection method to reconstruct gene regulatory networks. The proposed method is consistent. The numerical results indicate that the proposed method can lead to much more accurate inference of gene regulatory networks than the local Poisson graphical model and other existing methods. The proposed data-continuized transformation fills the theoretical gap for how to transform discrete data to continuous data and facilitates NGS data analysis. The proposed data-continuized transformation also makes it feasible to integrate different types of data, such as microarray and RNA-seq data, in reconstruction of gene regulatory networks.
authors.affiliation: Department of Biostatistics, University of Florida, Gainesville, Florida, U.S.A.
authors.forename: Bochao
authors.initials: B
authors.lastname: Jia
authors.affiliation: Department of Biostatistics, University of Florida, Gainesville, Florida, U.S.A.
authors.forename: Suwa
authors.initials: S
authors.lastname: Xu
authors.affiliation: Department of Clinical Sciences, University of Texas, Southwestern Medical Center, Dallas, Taxes, U.S.A.
authors.forename: Guanghua
authors.initials: G
authors.lastname: Xiao
authors.affiliation: Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, Florida, U.S.A.
authors.forename: Vishal
authors.initials: V
authors.lastname: Lamba
authors.affiliation: Department of Biostatistics, University of Florida, Gainesville, Florida, U.S.A.
authors.forename: Faming
authors.initials: F
authors.lastname: Liang
mesh_terms: D053263:Gene Regulatory Networks / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data*; D006801:Humans; D013223:Statistics as Topic
keywords: Data-continuized transformation; Gaussian graphical model; Gene regulatory network; Poisson graphical model; RNA-seq