Distribution of Clique Sizes in Control and IR

<p>Maximum clique and average clique sizes were larger in IR (red bars) than control (blue bars).</p

Impact of Normalization on the Correlation Distributions

<p>Normalization results in a distribution approximately centered around zero.</p

Comparison of Pearson's and Spearman's Correlation Coefficients

<p>Comparison of Pearson's and Spearman's Correlation Coefficients</p

The Distributions of Correlations in Control and IR Are Highly Similar

<p>Control (blue dashed) and IR (red solid) lines overlay each other across the entire distribution. The vertical lines in each tail of the distribution delineate the edges that were included in the graph after applying the threshold of |0.875| to the correlation matrix.</p

Differential Correlation Identifies Edges Impacted by IR

<p>The graph was filtered to identify edges that exceeded r = |0.875| in one condition but were less than |0.25| in the other. Vertices with > 8 differential correlations are represented in (A). Red indicates edges that are present only in IR, while blue edges are only found in control. Dark edges for each color represent the subset of edges that are differentially correlated and of opposite direction (+ vs. −) in the two conditions, while bright edges are of the same direction. The portion of the graph containing three connected sub-graphs centered around <i>Top3a</i>, <i>Notch3,</i> and an unannotated gene is shown in (B).</p

Overall Schema of Our Approach

<p>Overall Schema of Our Approach</p

Genes Co-Expressed with Tulp4 in HSCs

<p>Gene expression data from HSCs [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020089#pcbi-0020089-b043" target="_blank">43</a>] were used in WebQTL (webqtl.org) to identify genes most highly correlated with <i>Tulp4</i>. The majority of genes encode proteins involved in immune function (e.g., immunoglobulins).</p

Scale Free Properties of Gene Connectivity

<p>Gene lists were sorted in order of abundance for each condition, and the 400 genes most abundant in control (blue bars) and IR (red bars) were plotted against clique membership (A) and vertex degree (B). Although average vertex degree and clique membership were not markedly different between control and IR, the genes most abundant in IR cliques were more highly connected and present in more cliques than in control.</p