An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data

• Published in: Statistical Applications in Genetics and Molecular Biology Vol. 9; no. 1; pp. 9 - Article 9
• Main Authors: Rau, Andrea, Jaffrézic, Florence, Foulley, Jean-Louis, Doerge, Rebecca W
• Format: Journal Article
• Language: English
• Published: Germany bepress 01.01.2010; De Gruyter
• Subjects: Algorithms; Bayes Theorem; Biostatistics; Computer Simulation; Gene Expression Profiling - statistics & numerical data; Gene Regulatory Networks; Humans; Life Sciences; Lymphocyte Activation - genetics; Models, Genetic; Models, Statistical; Oligonucleotide Array Sequence Analysis - statistics & numerical data; ROC Curve; T-Lymphocytes - immunology; T-Lymphocytes - metabolism; microarray; bayesian method
• ISSN: 1544-6115; 1544-6115
• DOI: 10.2202/1544-6115.1513

Abstract Gene regulatory networks refer to the interactions that occur among genes and other cellular products. The topology of these networks can be inferred from measurements of changes in gene expression over time. However, because the measurement device (i.e., microarrays) typically yields information on thousands of genes over few biological replicates, these systems are quite difficult to elucidate. An approach with proven effectiveness for inferring networks is the Dynamic Bayesian Network. We have developed an iterative empirical Bayesian procedure with a Kalman filter that estimates the posterior distributions of network parameters. We compare our method to similar existing methods on simulated data and real microarray time series data. We find that the proposed method performs comparably on both model-based and data-based simulations in considerably less computational time. The R and C code used to implement the proposed method are publicly available in the R package ebdbNet. Submitted: September 11, 2009 · Accepted: December 15, 2009 · Published: January 15, 2010 Recommended Citation Rau, Andrea; Jaffrézic, Florence; Foulley, Jean-Louis; and Doerge, Rebecca W. (2010) "An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data," Statistical Applications in Genetics and Molecular Biology: Vol. 9 : Iss. 1, Article 9. DOI: 10.2202/1544-6115.1513 Available at: http://www.bepress.com/sagmb/vol9/iss1/art9