Dataset Information

FSEM: Functional Structural Equation Models for Twin Functional Data.

ABSTRACT: The aim of this paper is to develop a novel class of functional structural equation models (FSEMs) for dissecting functional genetic and environmental effects on twin functional data, while characterizing the varying association between functional data and covariates of interest. We propose a three-stage estimation procedure to estimate varying coefficient functions for various covariates (e.g., gender) as well as three covariance operators for the genetic and environmental effects. We develop an inference procedure based on weighted likelihood ratio statistics to test the genetic/environmental effect at either a fixed location or a compact region. We also systematically carry out the theoretical analysis of the estimated varying functions, the weighted likelihood ratio statistics, and the estimated covariance operators. We conduct extensive Monte Carlo simulations to examine the finite-sample performance of the estimation and inference procedures. We apply the proposed FSEM to quantify the degree of genetic and environmental effects on twin white-matter tracts obtained from the UNC early brain development study.

SUBMITTER: Luo S

PROVIDER: S-EPMC6497081 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

FSEM: Functional Structural Equation Models for Twin Functional Data.

Luo S S Song R R Styner M M Gilmore J H JH Zhu H H

Journal of the American Statistical Association 20180709 525

The aim of this paper is to develop a novel class of functional structural equation models (FSEMs) for dissecting functional genetic and environmental effects on twin functional data, while characterizing the varying association between functional data and covariates of interest. We propose a three-stage estimation procedure to estimate varying coefficient functions for various covariates (e.g., gender) as well as three covariance operators for the genetic and environmental effects. We develop a ...[more]

PMID: 31057192

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Project description:BACKGROUND:It is currently accepted that the perturbation of complex intracellular networks, rather than the dysregulation of a single gene, is the basis for phenotypical diversity. High-throughput gene expression data allow to investigate changes in gene expression profiles among different conditions. Recently, many efforts have been made to individuate which biological pathways are perturbed, given a list of differentially expressed genes (DEGs). In order to understand these mechanisms, it is necessary to unveil the variation of genes in relation to each other, considering the different phenotypes. In this paper, we illustrate a pipeline, based on Structural Equation Modeling (SEM) that allowed to investigate pathway modules, considering not only deregulated genes but also the connections between the perturbed ones. RESULTS:The procedure was tested on microarray experiments relative to two neurological diseases: frontotemporal lobar degeneration with ubiquitinated inclusions (FTLD-U) and multiple sclerosis (MS). Starting from DEGs and dysregulated biological pathways, a model for each pathway was generated using databases information biological databases, in order to design how DEGs were connected in a causal structure. Successively, SEM analysis proved if pathways differ globally, between groups, and for specific path relationships. The results confirmed the importance of certain genes in the analyzed diseases, and unveiled which connections are modified among them. CONCLUSIONS:We propose a framework to perform differential gene expression analysis on microarray data based on SEM, which is able to: 1) find relevant genes and perturbed biological pathways, investigating putative sub-pathway models based on the concept of disease module; 2) test and improve the generated models; 3) detect a differential expression level of one gene, and differential connection between two genes. This could shed light, not only on the mechanisms affecting variations in gene expression, but also on the causes of gene-gene relationship modifications in diseased phenotypes.

Dataset Information

FSEM: Functional Structural Equation Models for Twin Functional Data.

Publications

FSEM: Functional Structural Equation Models for Twin Functional Data.

Similar Datasets

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