Inferring dynamic genetic networks with low order independencies

DOI10.2202/1544-6115.1294zbMATH Open1276.62080arXiv0704.2551OpenAlexW1990552935WikidataQ33409970 ScholiaQ33409970MaRDI QIDQ2864047FDOQ2864047

Authors: Sophie Lèbre 

Publication date: 5 December 2013

Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Abstract: In this paper, we propose a novel inference method for dynamic genetic networks which makes it possible to face with a number of time measurements n much smaller than the number of genes p. The approach is based on the concept of low order conditional dependence graph that we extend here in the case of Dynamic Bayesian Networks. Most of our results are based on the theory of graphical models associated with the Directed Acyclic Graphs (DAGs). In this way, we define a minimal DAG G which describes exactly the full order conditional dependencies given the past of the process. Then, to face with the large p and small n estimation case, we propose to approximate DAG G by considering low order conditional independencies. We introduce partial qth order conditional dependence DAGs G(q) and analyze their probabilistic properties. In general, DAGs G(q) differ from DAG G but still reflect relevant dependence facts for sparse networks such as genetic networks. By using this approximation, we set out a non-bayesian inference method and demonstrate the effectiveness of this approach on both simulated and real data analysis. The inference procedure is implemented in the R package 'G1DBN' freely available from the CRAN archive.

Full work available at URL: https://arxiv.org/abs/0704.2551

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zbMATH Keywords

conditional independencetime series modelingdynamic Bayesian networksdirected acyclic graphsgraphical modelingsoftware Rnetworks inferenceR package G1DBN

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Graphical methods in statistics (62A09)

Cited In (7)

• Inferring dynamic gene regulatory networks with low-order conditional independencies -- an evaluation of the method
• Low-Order Conditional Independence Graphs for Inferring Genetic Networks
• Inferring stable genetic networks from steady-state data
• G1DBN
• Title not available (Why is that?)
• Operator-valued kernel-based vector autoregressive models for network inference
• Invalidation of the structure of genetic network dynamics: a geometric approach

Uses Software

• R
• CRAN
• BNT
• MGraph

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