Additional file 3: Table S7. of Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

The overlap between RMD modules and published protein-protein interactions. (XLS 25 kb

Additional file 2: Tables S1-S6. of Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

The RMD module matrix and summary for K562, GM12878, and K562 direct versus indirect binding, respectively. (XLS 181 kb

Additional file 4: Table S8. of Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

TF diversification scores and random forest prediction accuracies. (CSV 609 bytes

Additional file 1: Figures S1-S6. of Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

(PDF 1964 kb

Corrected DNase-capture and DNase-seq appear concordant.

<p>A one kilobase capture region in chromosome 10, starting at base 127508639. The reads are smoothed in a 5bp window, and only the forward reads are shown for visualization purpose. The DNase-capture reads counts were scaled so they could be shown on the same plot as the DNase-seq reads. Data normalization was used here.</p

DNase-seq and DNase-capture appear concordant.

<p>A one kilobase capture region in chromosome 10, starting at base 127508639. The reads are smoothed in a 5bp window, and only the forward reads are shown for visualization purpose. The DNase-capture reads counts were scaled so they could be shown on the same plot as the DNase-seq reads. The data pre-correction was used here.</p

DNase-capture protocol.

<p>This figure shows the stages of the DNase-capture protocol.</p

Increased tiling density produces more coverage.

<p>Log enrichment of the DNase-capture reads at a given tiling density compared to the number of DNase-seq reads over the same regions. Data pre-normalization data was used.</p

Enhancer usage reflects cell-type appropriate motif enrichment.

<p>1 kb windows centered on Med1 binding events involved in interactions with TSSs in one or both cell types were scanned for matches to known transcription factor motifs. Med1 binding events were categorized based on whether they interact with TSSs in one or both cell types. The bar graphs reflect the percentages of Med1 binding events in each group that have a motif match within 500 bp for several important transcription factors.</p

DNase-capture has more reads per base.

<p>Reads per base, excluding bases with no reads, for the forward reads. The x- and y-axes are in log 10 scale. The DNase-capture reads were truncated at 1000 reads for visualization purposes. Reads from all tiling densities were aggregated in this plot.</p