Principal Component Analysis (PCA).

<p>Two-dimensional (2D) projections of the data on (A) the plane defined by the first (PC1) and second (PC2) principal components, and (B) the plane defined by the second (PC2) and the third (PC3) principal components. The densities were computed by a kernel density estimation. The density values are indicated by a color (white: high density, yellow: moderate density, green: low density) and a contour plot.</p

Sequence composition in the four chromatin states.

<p>(A) Boxplots of GC content computed in 100 kb non-overlapping windows per chromatin state. (B) Boxplots of CpG o/e computed in 100 kb non-overlapping windows per chromatin states. Same color coding as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi-1003233-g003" target="_blank">Fig. 3A</a>.</p

Gene expression in the four chromatin states.

<p>(A) c.d.f. of gene expression (measured in , see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#s3" target="_blank">Materials and Methods</a>) in the four chromatin states. (B) Density of promoters in the 4 chromatin states as a function of gene expression (genes were grouped into bins of width 0.05 in unit). Same color coding as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi-1003233-g003" target="_blank">Fig. 3A</a>.</p

Spearman correlation matrix between epigenetics marks and mean replication timing (MRT).

<p>For each pair of variables we computed the Spearman correlation over all 100-overlapping windows with a valid score. Spearman correlation value is color coded using the color map shown on the right. A white line separates the MRT from epigenetics marks. Correlations with MRT (from late to early) are placed at the top and the right of the matrix. Lines for the thirteen epigenetic marks were reorganized by a hierarchical clustering using Spearman correlation distances (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi.1003233.e037" target="_blank">Equation 1</a>) as illustrated by the dendrogram on the left of the graph. This ordering implies that highly correlated epigenetic marks are close to each other.</p

MRT in the four chromatin states.

<p>(A) Boxplots of MRT computed in 100 kb non-overlapping windows per chromatin state. (B) Empirical cumulative distribution function (c.d.f.) of MRT in the four chromatin states. Same color coding as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi-1003233-g003" target="_blank">Fig. 3A</a>.</p

Repartition of transcription factors in the four chromatin states.

<p>Boxplots of the decimal logarithm of transcription factor ChiP-seq read density in 100 kb non-overlapping windows per chromatin state. Same color coding as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi-1003233-g003" target="_blank">Fig. 3A</a>.</p

Distribution of the four chromatin states inside replication timing U-domains.

<p>(A) The 876 K562 U-domains were centered and ordered vertically from the smallest (top) to the largest (bottom). All transcriptionally active chromatin state C1 100-kb-windows were represented by an horizontal segment of the corresponding length. (B) Same as (A) for the Pc repressed by chromatin state C2. (C) Same as (A) for the silent unmarked chromatin state C3. (D) Same as (A) for the HP1 heterochromatin state C4. (E) Mean coverage of chromatin state with respect to the distance to the closest U-domain border for U-domains smaller than 0.8 Mb. Error bars represent the standard deviation of the mean. (F) Same as (E) for U-domains of size between 0.8 Mb and 1.2 Mb. (G) Same as (E) for U-domains of size between 1.2 Mb and 1.8 Mb. (H) Same as (E) for U-domains of size between 1.8 Mb and 3.0 Mb. Same color coding as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi-1003233-g003" target="_blank">Fig. 3A</a>.</p

Defining the four prevalent chromatin states.

<p>(A) Scatterplot of the data points onto the first three principal components. Color dots indicate the four chromatin states as found by our clustering procedure (pink: transcriptionally active chromatin, orange: chromatin repressed by polycomb, green: silent unmarked chromatin, blue: HP1 heterochromatin). Points in dark grey are not classified in any chromatin state (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#s3" target="_blank">Materials and Methods</a>). (B) Within-cluster sum of squares (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi.1003233.e045" target="_blank">Eq. 2</a>) with respect to the number of clusters (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#s3" target="_blank">Materials and Methods</a>). (C) Gap statistics (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi.1003233.e049" target="_blank">Eq. 4</a>) with respect to the number of clusters (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#s3" target="_blank">Materials and Methods</a>).</p

Repartition of histone marks in the four chromatin states.

<p>Boxplots of the decimal logarithm of histone mark ChiP-seq read density in 100 kb non-overlapping windows per chromatin state. Same color coding as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#pcbi-1003233-g003" target="_blank">Fig. 3A</a>.</p

Transition matrix between chromatin states.

<p>The first line is the probability of each chromatin state. The matrix below the first line is the Markov transition matrix between states (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003233#s3" target="_blank">Materials and Methods</a> for its estimation). A value at the row and the column is the probability to find the chromatin state j in a 100 kb window next to a 100 kb window of chromatin state i. D corresponds to 100 kb windows that are not classified in any chromatin state.</p