Multiple FLR models for fixed vs. <i>in vitro</i> HERV-K.

<p>See explanations for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004956#pcbi.1004956.t003" target="_blank">Table 3</a>.</p

Multiple FLR models for polymorphic ETn vs. control.

<p>See explanations for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004956#pcbi.1004956.t003" target="_blank">Table 3</a>.</p

Multiple FLR models for <i>in vitro</i> HERV-K vs. control.

<p>See explanations for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004956#pcbi.1004956.t003" target="_blank">Table 3</a>.</p

Multiple FLR models for fixed vs. polymorphic ETn.

<p>See explanations for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004956#pcbi.1004956.t003" target="_blank">Table 3</a>.</p

Workflow of the methodology employed to compare the flanking regions of ERVs versus control regions.

<p>The comparison between the flanking regions of two different ERV types utilizes an analogous pipeline. (A) Generation of windows and data. (B) Schematic of the nine comparisons implemented in our study. (C) Schematic of the statistical analysis, including Functional Data Analysis techniques. FLR: Functional Logistic Regression, ITP: interval testing procedure, IDL: invariant differential landscape, LDL: localized differential landscape.</p

Multiple FLR models for fixed HERV-K vs. control.

<p>See explanations for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004956#pcbi.1004956.t003" target="_blank">Table 3</a>.</p

Multiple FLR models for fixed ETn vs. control.

<p>The "Predictor" column reports predictors included in the logistic regression. The "Coefficient" column reports coefficient estimates (a positive coefficient means that an increase in the feature increases the likelihood of, e.g., fixed vs. control; a negative coefficient means an increase in the feature decreases such likelihood). The "p-value" column reports p-values for the coefficients. They both are in bold if p-value<0.05. For functional predictors, several rows are listed corresponding to the intervals where the feature was considered—as indicated in the "Range of windows" column. The "RCDE" column reports the relative contribution to the deviance explained for each feature. "DE" at the bottom of each panel is the total deviance explained by the model.</p

The Distribution of Correctly and Incorrectly Classified Genes along the X Chromosome

<p>Dark green indicates correctly classified genes; light green indicates misclassified genes. X inactivation expression patterns [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020151#pgen-0020151-b006" target="_blank">6</a>] for genes included in this study: yellow indicates inactivated genes, and blue indicates escape genes. Not all genes were analyzed at all distances because sequences that included adjacent genes with <i>different</i> inactivation patterns were excluded from analysis (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020151#s4" target="_blank">Methods</a>). These gene distances remain uncolored.</p

Complete list of genomic features analyzed in this study.

<p>H and L marks indicate features analyzed in mouse, human or both using high- and low-resolution datasets, respectively. The nature of the measures used is explained in more detail in the Methods.</p

LDA Classification Success Rates for Different Values of the Tuning Parameter τ

<div><p>(A) Training set derived largely, but not exclusively, from Xp22 (See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020151#pgen-0020151-st003" target="_blank">Table S3</a>).</p><p>(B) Test set of Xp22 genes, with training performed on genes in (A).</p><p>(C) Test set of X genes outside of Xp22, with training performed on genes in (A).</p><p>(D) Training set of all X genes, including genes in Xp22. Dots indicate optimal values of τ (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020151#pgen-0020151-t004" target="_blank">Table 4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020151#s4" target="_blank">Methods</a>).</p></div