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Statistical Applications in Genetics and Molecular Biology

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Volume 13, Issue 3 (Jun 2014)

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Statistical inference of regulatory networks for circadian regulation

Andrej Aderhold
  • School of Mathematics and Statistics, University of Glasgow, 15 University Gardens, Glasgow G12 8QW, UK
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Dirk Husmeier
  • Corresponding author
  • School of Biology, Sir Harold Mitchell Building, University of St Andrews, St Andrews, Fife KY16 9TH, UK
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Marco Grzegorczyk
  • Johann Bernoulli Institute (JBI), Groningen University, Nijenborgh 9, 9747 AG Groningen, The Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2014-05-26 | DOI: https://doi.org/10.1515/sagmb-2013-0051

Abstract

We assess the accuracy of various state-of-the-art statistics and machine learning methods for reconstructing gene and protein regulatory networks in the context of circadian regulation. Our study draws on the increasing availability of gene expression and protein concentration time series for key circadian clock components in Arabidopsis thaliana. In addition, gene expression and protein concentration time series are simulated from a recently published regulatory network of the circadian clock in A. thaliana, in which protein and gene interactions are described by a Markov jump process based on Michaelis-Menten kinetics. We closely follow recent experimental protocols, including the entrainment of seedlings to different light-dark cycles and the knock-out of various key regulatory genes. Our study provides relative network reconstruction accuracy scores for a critical comparative performance evaluation, and sheds light on a series of highly relevant questions: it quantifies the influence of systematically missing values related to unknown protein concentrations and mRNA transcription rates, it investigates the dependence of the performance on the network topology and the degree of recurrency, it provides deeper insight into when and why non-linear methods fail to outperform linear ones, it offers improved guidelines on parameter settings in different inference procedures, and it suggests new hypotheses about the structure of the central circadian gene regulatory network in A. thaliana.

Keywords: regulatory network inference; circadian clock; hierarchical Bayesian models; comparative method evaluation; ANOVA

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About the article

Corresponding author: Dirk Husmeier, School of Mathematics and Statistics, University of Glasgow, 15 University Gardens, Glasgow G12 8QW, UK, e-mail:


Published Online: 2014-05-26

Published in Print: 2014-06-01


https://www.agronomics.ethz.ch/.

Note that the sets of potential regulators are defined for each gene g specifically. That is, the potential regulators for two target variables yg and yg can be different, e.g., if certain (biologically-motivated) restrictions are imposed.

For consistency with the fundamental equation of transcription, equation (1), we will enforce that each regulator set πg for yg contains the concentration xg of g, symbolically xg∈πg.

Note that vector x·,t includes every available regulator without any dependency on the target gene g.

Note that the repeated bi-partitioning of the genes into targets and putative regulators renders Glasso equivalent to Lasso, as discussed on page 4 of Friedman et al. (2008). Lasso will be discussed in Section 2.3.

We set: ν=0.005, Aδ=2, and Bδ=0.2, as in Grzegorczyk and Husmeier (2012).

We note that the coupled variant of the non-homogeneous Bayesian regression model cannot be represented properly as a graphical model, as the regression parameter vectors are sequentially coupled among adjacent segments via equations (21–22).

For each yg we apply exactly the same permutation to order the realizations of the explanatory variables (covariates) and thereby ensure that the segment-specific design matrices are built properly.

In our study we follow Rogers and Girolami (2005) and use a slightly modified version of the fast marginal likelihood algorithm from Tipping et al. (2003) for optimization.

We use the authors’ terminology, although the model is not a proper Bayesian network.

More precisely, μg,h* is obtained by deleting the element corresponding to the target variable yg,t in μg,h, and Σg,h* is obtained by deleting the row and the column corresponding to yg,t in Σg,h.

Note that the abbreviation “BGe” was introduced by Geiger and Heckerman (1994) and stands for Bayesian metric for Gaussian networks having score equivalence; see Geiger and Heckerman (1994) for more details.

http://www.biopepa.org.

We turned off the translation of those proteins contributing to interactions we like to surpress.

In the model equations defined by Guerriero et al. (2012) the concentration of P only appears in a product with the binary light indicator L, where the light variable L is equal to zero in the absence of light.

For the Bayesian methods this can be enforced by setting the prior P(πg) to zero for all πg with xg∉πg.

Matlab software for Disciplined Convex Programming: http://cvxr.com/cvx/.

Note that the maximal number of hidden nodes n is restricted by the number of regulators, Gg. In our simulation study we analyzed various data sets, and we employed the lowest Gg as an upper bound on the number of hidden nodes n.

In our study we initialized the EM-algorithm with allocations obtained by the k-means cluster algorithm. Thereby the initial 𝕂g centers of the k-means algorithms were sampled from a multivariate Gaussian N(μ, I) distribution, where I is the identity matrix and μ is a random expectation vector with entries sampled independently from continuous uniform distributions on the interval [–1, +1]. To avoid that the EM-algorithm is initialized with allocations that possess unoccupied (empty) mixture components, we re-sampled the initial centers and re-ran the k-means algorithm whenever we obtained k-means outputs with empty components.

Loosely speaking, this setting (μ0=0 and T0=I) reflects our “prior belief” that all domain variables, i.e., the potential regulators and the target variable, are i.i.d. standard normally distributed.

The sensitivity is the proportion of true interactions that have been detected, the specificity is the proportion of non-interactions that have been avoided.


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: https://doi.org/10.1515/sagmb-2013-0051.

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