Summary of method comparison.

<p>Summary of method comparison.</p

Regions with similar epigenetic and transcriptional status occupy the same nuclear space.

<p>(<b>A</b>) Normalized ATAC-Seq signal across the Eβand MiEκ enhancer in T and B cells. (<b>B</b>) Enrichment of ATAC-Seq peaks in 4C interacting domains (<b>C</b>) Normalized RNA-Seq data for the <i>Tcrb</i> gene and the 3’ end of the <i>Igk</i> gene. (<b>D</b>). DESeq2 normalized expression values (log₁₀) of genes that overlap with 4C-ker identified domains of interaction for each cell type.</p

Identification of differentially interacting regions.

<p>(<b>A-C</b>) Windows located within Dataset-specific Interacting Domains (DIDs) are represented as small circles with the normalized read count for each condition. Large filled circles represent windows with an FDR adjust p-value smaller than 0.05 for the difference between the two cell-types. The red arrow above the plots represents the bait region. Lines represent the average of the replicates for each window across the displayed region. Large filled circles represent windows with an FDR adjusted p-value smaller than 0.05 for the difference between the two cell-types. (<b>A</b>) Whole chromosome, (<b>B</b>) Near the bait, (<b>C</b>) Far <i>cis</i> (region around <i>Cd69)</i>.</p

Workflow of 4C-ker.

<p>The key features of the method are outlined in the figure. A more detailed explanation of each section can be found in the materials and methods section.</p

4C-ker outperforms other methods in the region near the bait when the similarity of interacting regions between replicates is examined for four methods.

<p>(<b>A-B</b>) Example datasets for 6bp and 4bp cutter experiments. Raw 4C-Seq reads are shown for a 10MB region around the bait in (<b>A</b>) and 2 MB in (<b>B</b>). Experiment in <b>A</b> was performed using activated B cells digested with HindIII and a bait near the <i>Cd83</i> locus. Experiment in <b>B</b> was performed in double negative T cells digested with NlaIII and a bait near the Eβ enhancer of <i>Tcrb</i>. Significant interactions determined by each method for 2 replicates are shown below the raw 4C-Seq profile. Domainograms generated using 4cseqpipe are displayed for the same region. (<b>C-D</b>) Each dot represents the distance of the midpoint of each interacting domain to the bait plotted against its size. Plots only contain domains that overlap by 50% between replicates.</p

4C-ker identifies the most reproducible interactions across the <i>cis</i> chromosome and exhibits stable performance for 4bp and 6bp cutters.

<p>(<b>A</b>) Example datasets of 6bp and 4bp cutter experiments. Raw 4C-Seq reads are shown for the entire bait chromosome. Experiment shown in the top panel in <b>A</b> was performed in activated B cells digested with HindIII using a bait near the <i>Cd83</i> gene. Experiment shown in the bottom panel in <b>A</b> was performed in immature B cells digested with NlaIII using a bait near the MiEκ enhancer of <i>Igk</i>. Significant interactions determined by each method for 2 replicates are shown below the raw 4C-Seq profiles. (<b>B</b>) Similarity index between replicates in far-<i>cis</i>. Example datasets shown in <b>A</b> are denoted with an asterisk (*) (<b>C</b>) Boxplot of the size of domains identified in far-<i>cis</i> by each method using all fourteen datasets. (<b>D</b>) Similarity index between replicates for domains identified across all <i>trans</i> chromosomes. (<b>E</b>) Boxplot of the size of all domains in trans identified by the four methods.</p

Comparisons of HER-2 assessment by different sites using ACCEPT versus CellTracks Analyzer II^® (Menarini Silicon Biosystems Inc) visualization.

<p>Indicated are the percentages of scored CTCs where all, five, four or only three out of six investigators agreed on the HER-2 status. In the case of 3 agree indifferent means that three investigators vote for HER-2 positive and the other three for HER-2 negative.</p

Number of manually scored HER-2+ cells versus number of automatically scored HER-2+ cells using a threshold of >0.

<p>Samples of 132 patients were investigated.</p

Sample Visualizer of ACCEPT.

<p>In the scatter plots 3 of the 158 objects are depicted blue and the corresponding thumbnail images are highlighted. In this example ‘Marker1’ represents signals for HER-2. The corresponding HER-2 images are shown below the Sample Visualizer, in the right image the red line indicates the boundary detected by ACCEPT of the identified CTC and the number indicates the median value of the HER-2 staining within this boundary. Size bar in overlay: 6.4μm.</p

Cytokeratin and HER-2 mean intensities of cells in breast cancer cell lines MDA-MB 231, MDA-MB 453 and SKBR-3.

<p>Panel A, 373 MDA-MB 231 cells (magenta), 496 MDA-MB 453 cells (cyan), 361 SKBR-3 cells (orange). Average number of HER-2 antigens included for each cell line. Panel B classification of the MDA-MB 231, MDA-MB 453 and SKBR-3 into 428 negative HER-2 (green), 462 dim HER-2 (blue) and 340 bright HER-2 (red) expressing cells identified by cluster analysis.</p