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Statistics in Biosciences

, Volume 10, Issue 1, pp 59–85 | Cite as

A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD

  • Elin Shaddox
  • Francesco C. StingoEmail author
  • Christine B. Peterson
  • Sean Jacobson
  • Charmion Cruickshank-Quinn
  • Katerina Kechris
  • Russell Bowler
  • Marina Vannucci
Article

Abstract

In this paper, we propose a Bayesian hierarchical approach to infer network structures across multiple sample groups where both shared and differential edges may exist across the groups. In our approach, we link graphs through a Markov random field prior. This prior on network similarity provides a measure of pairwise relatedness that borrows strength only between related groups. We incorporate the computational efficiency of continuous shrinkage priors, improving scalability for network estimation in cases of larger dimensionality. Our model is applied to patient groups with increasing levels of chronic obstructive pulmonary disease severity, with the goal of better understanding the break down of gene pathways as the disease progresses. Our approach is able to identify critical hub genes for four targeted pathways. Furthermore, it identifies gene connections that are disrupted with increased disease severity and that characterize the disease evolution. We also demonstrate the superior performance of our approach with respect to competing methods, using simulated data.

Keywords

Gaussian graphical model Bayesian inference Markov random field prior Spike-and-slab prior Gene network Chronic obstructive pulmonary disease (COPD) 

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Copyright information

© International Chinese Statistical Association 2016

Authors and Affiliations

  1. 1.Department of StatisticsRice UniversityHoustonUSA
  2. 2.Dipartimento di Statistica, Informatica, Applicazioni “G.Parenti”University of FlorenceFlorenceItaly
  3. 3.Department of BiostatisticsUT MD Anderson Cancer CenterHoustonUSA
  4. 4.Department of MedicineNational Jewish HealthDenverUSA
  5. 5.Department of Pharmaceutical Sciences, School of PharmacyUniversity of Colorado DenverDenverUSA
  6. 6.Department of Biostatistics and Informatics, Colorado School of Public HealthUniversity of Colorado DenverDenverUSA

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