Estimated correlation coefficients, obtained using the general linear model with different variance-covariance structures, for the five metabolic subsets defined for apolipoprotein B.

<p>A. GLM with metabolic-subset specific correlation coefficients defined by Eqs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150257#pone.0150257.e003" target="_blank">2</a>) and (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150257#pone.0150257.e009" target="_blank">3</a>); B. GLM with common correlation coefficients across the first three metabolic-subsets; C. GLM with no metabolic-subset dependent correlation coefficients, i.e., the null model defined by Eqs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150257#pone.0150257.e003" target="_blank">2</a>) and (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150257#pone.0150257.e011" target="_blank">4</a>).</p

Power of the linear regression and GLM-based test statistics for different co-expression dynamics and sample sizes.

<p>Power of the linear regression and GLM-based test statistics for different co-expression dynamics and sample sizes.</p

Box-plots of the core LL module expression.

<p>Heterogeneous mean expression values and variances are observed.</p

Histograms of the observed values for 3-hydroxybutyrate, linoleic acid, large HDL particles, small HDL particles, small LDL particles, and total cholesterol in large HDL.

<p>Histograms of the observed values for 3-hydroxybutyrate, linoleic acid, large HDL particles, small HDL particles, small LDL particles, and total cholesterol in large HDL.</p

The six simulated co-expression dynamics for a four gene module.

<p>The four genes of the simulated module generate six gene-pair correlations. Each trajectory of dots captures the metabolite-co-expression association for one of the module gene pairs.</p

Co-expression dynamics by mean metabolic concentration based on sliding-window correlation estimates (<i>w</i> = 0.2).

<p>The <i>G</i> = 7 genes of the core LL module result in 21 gene-pair correlations. Each trajectory roughly captures the co-expression dynamics of one of the module’s gene pairs.</p

GLM based gene-pair correlation estimates for the five metabolic subsets.

<p>The estimates corresponding to a particular pair of genes are connected by a line. Benjamini and Yekutieli adjusted Larntz & Perlman test <i>p</i>-values are reported.</p

Scatter-plot matrix of the core LL module gene expression values.

<p>Scatter-plots of the expression values for each gene pair appear in the lower triangular matrix. Points are colour coded by gender: red represents males and blue represents females. Pairwise Spearman’s correlation coefficients are indicated in the upper triangular matrix. The distribution of gene expression values for each gene is illustrated on the main diagonal.</p

Type I error probabilities for the linear regression and the GLM-based test statistics by module size and sample size.

<p>Type I error probabilities for the linear regression and the GLM-based test statistics by module size and sample size.</p

Cohort-wise effects of risk allele count on SBP.

<p>The higher median age in HBCS is reflected as higher systolic blood pressure (SBP) and less consistent association. Error bars show standard error.</p