Expression levels for genes associated with different types of nucleosome predictions.

<p>RNA-seq data for mouse adult islets are from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#pone.0032095-Kim1" target="_blank">[29]</a>. Nucleosomes were predicted from H3K4me1 data for (A,B) mouse adult islets and (C,D) mouse adult liver <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#pone.0032095-Hoffman1" target="_blank">[19]</a>. Dashed horizontal lines show medians. In islets, genes categorized as bimodal and NoNuc respectively have significantly higher and lower expression levels than those in the monomodal group. Nucleosome prediction groups are outlined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#pone-0032095-g003" target="_blank">Fig. 3</a>'s caption and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#s4" target="_blank">Methods</a>.</p

Model-based nucleosome occupancy profiles for sonicated H3K4me1 ChIP-Seq data.

<p>Panels show nucleosome positioning within bp from the top-ranked <i>in vivo</i> transcription factor binding sites that PICS detected for (A) SPI1 and (B) CEBPB from sonicated H3K4me1 ChIP-Seq data for 0 hour (blue) and 1 hour (red) after tamoxifen stimulation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#pone.0032095-Heinz1" target="_blank">[20]</a>. The heatmaps show nucleosome prediction profiles for each region as pairs of blue/red horizontal lines, with darker colors indicating higher scoring, i.e. better positioned, nucleosomes. The lower part of each heatmap shows genomic regions that lack detectable nucleosome positioning. Curves below each heatmap show average occupancy profiles across all TF regions.</p

Modality and nucleosome occupancy for Foxa2 and Pdx1 binding sites in mouse adult islet tissue.

<p>Panels show the modality and nucleosome profiles for <i>in vivo</i> binding sites of the transcription factors Foxa2 (left) and Pdx1 (right) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#pone.0032095-Hoffman1" target="_blank">[19]</a>. (A) The number of binding sites in bimodal(bi), monomodal(mono) and NoNuc(No) groups. A NoNuc transcription factor binding site had no H3K4me1-marked nucleosome within 1 kb of its peak summit, a monomodal site had at least one H3K4me1 nucleosome within 50 bp of its summit, and all other sites were bimodal. (B) Average model-based nucleosome positioning profiles for the three classes of binding sites.</p

Truncated AUC statistics for PING, TpF and NPS.

<p>Panels show the area under ROC curves (AUC), truncated at a specificity of 0.8, as a function of number of reads in random subsets for PING, TpF and NPS. A larger AUC value corresponds to a more accurate method; the maximum possible AUC value for the truncated curves is 0.2. Datasets are (A) MNase-Seq data from budding yeast <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#pone.0032095-Kaplan1" target="_blank">[21]</a>, (B) sonicated H3K4me1 ChIP-Seq data from a mouse cell line <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#pone.0032095-Heinz1" target="_blank">[20]</a>, and (C) sonicated H3K4me1 ChIP-Seq data from mouse adult islet tissue <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032095#pone.0032095-Hoffman1" target="_blank">[19]</a>.</p

Supplementary document for Heimdallr, Baldr and Solarstein: designing the next generation of VLTI instruments in the Asgard suite - 6870111.pdf

Supplementary documen