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figure3_test.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=edge"/>
<title>Juicebox</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<link rel="icon" type="image/png" href="https://aidenlab.org/favicon.ico">
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<!-- DataTables CSS -->
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href="https://cdn.datatables.net/v/dt/dt-1.10.15/sc-1.4.2/se-1.2.2/datatables.min.css"/>
<!-- Bootstrap CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<!-- Font Awesome CSS-->
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</head>
<body style="margin:30px">
<h1 style="text-align: center; font:Helvetica Neue;font-size:36px;line-height: 40px; color: #333333
">Figure 3</h1>
<div class="row">
<div class="col-md-8">
<div>
<p style="font-size:30px" class="panelID">A</p>
</div>
<br>
</div>
<div class="col-md-4">
<div>
<p style="font-size:30px" class="panelID">B</p>
</div>
<br>
</div>
</div>
<div class="row">
<div class="col-md-4">
<div>
<img class="img-responsive"
src="https://theaidenlab.github.io/figures/css/img/figure2_static_components/Fig2A_untreated_header.png"
alt="Untreated" width="400">
</div>
<br>
<div id="app-container-1">
</div>
<br>
</div>
<div class="col-md-4">
<div>
<img class="img-responsive"
src="https://theaidenlab.github.io/figures/css/img/figure2_static_components/Fig2A_treated_header.png"
alt="6hr Auxin Treated" width="400">
</div>
<br>
<div id="app-container-2">
</div>
<br>
</div>
<div class="col-md-4">
<div>
<img src="https://theaidenlab.github.io/figures/css/img/figure3_static_components/3B_corner_scores.png"
alt="corner scores" width="600">
</div>
</div>
</div>
<div class="row">
<div class="col-md-2.5">
<div>
<p style="font-size:30px" class="panelID">C</p>
</div>
<br>
<div id="app-container-3">
</div>
<br>
</div>
<div class="col-md-1.5">
<div>
<p style="font-size:30px; color:white" class="panelID">C</p>
</div>
<br>
<div id="app-container-4">
</div>
<br>
</div>
<div class="col-md-1.5">
<div>
<p style="font-size:30px; color:white" class="panelID">C</p>
</div>
<br>
<div id="app-container-5">
</div>
<br>
</div>
<div class=col-md-2.5">
<div>
<p style="font-size:30px; color:white" class="panelID">C</p>
</div>
<br>
<div id="app-container-6">
</div>
<br>
</div>
<div class="col-md-4">
<div>
<p style="font-size:30px" class="panelID">E</p>
</div>
<br>
<div>
<img src="https://theaidenlab.github.io/figures/css/img/figure3_static_components/3E_loopdomains_vs_compartmentalization.png"
width="500">
</div>
<br>
</div>
</div>
<div class="row">
<div class="col-md-2.5">
<div>
<p style="font-size:30px" class="panelID">D</p>
</div>
<br>
<div id="app-container-7">
</div>
<br>
</div>
<div class="col-md-1.5">
<div>
<p style="font-size:30px; color:white" class="panelID">C</p>
</div>
<br>
<div id="app-container-8">
</div>
<br>
</div>
<div class="col-md-1.5">
<div>
<p style="font-size:30px; color:white" class="panelID">C</p>
</div>
<br>
<div id="app-container-9">
</div>
<br>
</div>
<div class=col-md-2.5">
<div>
<p style="font-size:30px; color:white" class="panelID">C</p>
</div>
<br>
<div id="app-container-10">
</div>
<br>
</div>
<div class="col-md-4">
<div>
<p style="font-size:30px" class="panelID">F</p>
</div>
<br>
<div>
<img src="https://theaidenlab.github.io/figures/css/img/figure3_static_components/3F_histone_vs_compartmentalization.png"
width="500">
</div>
<br>
</div>
</div>
<br>
<div>
<p class="legend">(A) Contact matrices of chromosome 8 at 500kb resolution. The plaid pattern in the Hi-C map is
preserved after auxin treatment, indicating that the genome compartments still form.</p>
</div>
<div>
<p class="legend">(B) Strength of contact domains called in untreated cells versus random intervals measured using
the corner score (see Methods) in untreated (top) and treated cells (middle). Contact domain strength is
significantly reduced, but does not disappear. The remaining signal in treated cells comes from compartment
domains (contact domains where both boundaries of the domain are also boundaries of a compartment interval),
which are preserved after cohesin loss (bottom). Contact domains where both boundaries are contained completely
inside a compartment interval (‘other domains’) show corner scores in treated cells comparable to random
pixels.</p>
</div>
<div>
<p class="legend">(C,D) Examples (C: chr21:32.4-39Mb and D: chr1:167-177Mb) showing that the loss of
cohesin-associated loops after auxin treatment results in increased fine-scale compartmentalization. Top:
Sliding correlation scores; valleys imply strong differences in long-range contact pattern observed at a locus
as compared to neighboring loci, indicating a change in compartment (see Methods). Middle: Observed contact
matrices. Bottom: Pearson’s correlation maps for the local region shown (see Methods). Deeper valleys in the
sliding correlation score and increased plaid patterning in the observed and Pearson’s correlation maps indicate
strengthened fine-scale compartment interactions after auxin treatment. Blowouts: loss of a loop domain results
in strengthening of a compartment boundary spanned by the loop. Blown-out regions are indicated on zoomed out
maps for both the observed (black upper triangle) and Pearson’s correlation maps (white rectangle). Observed and
Pearson’s correlation maps are both shown at 25kb resolution for the zoomed out matrices and 10kb and 25kb
resolution respectively for the blown-out matrices.</p>
</div>
<div>
<p class="legend">(E) Sliding correlation scores before and after auxin treatment for compartment boundaries which
either coincide with loop domain anchors (left) or are located in the interior of a loop domain (right). For
compartment boundaries that lie in the interior of a loop domain in untreated cells, the difference in
long-range contact pattern on opposite sides of the boundary increases greatly after cohesin treatment.</p>
</div>
<div>
<p class="legend">(F) Sliding correlation scores before and after auxin treatment for H3K27ac boundaries in
untreated cells which either coincide with loop domain anchors (left) or are located in the interior of a loop
domain (right). H3K27Ac modification patterns are unchanged after auxin treatment (top and middle). For H3K27ac
boundaries that lie in the interior of a loop domain in untreated cells, the difference in long-range contact
pattern on opposite sides of the boundary increases greatly after cohesin treatment. This indicates that loop
domains facilitate mixing of chromatin with different histone modifications.</p>
</div>
<style type="text/css">
.row {
display: flex;
}
.legend {
text-align: left;
font: Helvetica Neue;
font-size: 36;
px color: #333333;
}
.col-md-2 {
display: inline-flex;
flex-direction: column;
justify-content: center;
}
</style>
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igv.xhr.loadJson("config/hicFileConfigs.txt", {})
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hic.loadDataset({
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