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<li class="chapter" data-level="6.3.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-5"><i class="fa fa-check"></i><b>6.3.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.3.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-5"><i class="fa fa-check"></i><b>6.3.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="6.4" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#comparison-to-random-peaks"><i class="fa fa-check"></i><b>6.4</b> Comparison to random peaks</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html"><i class="fa fa-check"></i><b>7</b> POE HPTM enrichment-POE transcription dynamics</a>
<ul>
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<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-gene-body"><i class="fa fa-check"></i>H3K4me3 (gene body)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-promoter"><i class="fa fa-check"></i>H3K4me3 (promoter)</a></li>
</ul></li>
<li class="chapter" data-level="7.4" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#comparison-to-random-peaks"><i class="fa fa-check"></i><b>7.4</b> Comparison to random peaks</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html"><i class="fa fa-check"></i><b>8</b> GO enrichment analyses</a>
<ul>
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<meta charset="utf-8" />
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<title>S6 HPTM-transcription dynamics | Supplementary Materials</title>
<meta name="description" content="S6 HPTM-transcription dynamics | Supplementary Materials" />
<title>S6 HPTM-transcription dynamics | Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)</title>
<meta name="description" content="S6 HPTM-transcription dynamics | Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)" />
<meta name="generator" content="bookdown 0.38 and GitBook 2.6.7" />

<meta property="og:title" content="S6 HPTM-transcription dynamics | Supplementary Materials" />
<meta property="og:title" content="S6 HPTM-transcription dynamics | Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)" />
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<meta name="twitter:title" content="S6 HPTM-transcription dynamics | Supplementary Materials" />
<meta name="twitter:title" content="S6 HPTM-transcription dynamics | Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)" />




<meta name="author" content="Sean T. Bresnahan, Shaun Mahony, Kate Anton, Brock Harpur, Christina M. Grozinger" />


<meta name="date" content="2024-05-07" />
<meta name="date" content="2024-06-09" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
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<li><a href="./">Appendix D</a></li>

<li class="divider"></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>About</a></li>
<li><a href="index.html#section" id="toc-section"></a></li>
<li class="chapter" data-level="1" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html"><i class="fa fa-check"></i><b>1</b> WGS, mRNA-seq, and ChIP-seq</a>
<ul>
<li class="chapter" data-level="1.1" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#wgs"><i class="fa fa-check"></i><b>1.1</b> WGS</a></li>
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<li class="chapter" data-level="6.3.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-5"><i class="fa fa-check"></i><b>6.3.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.3.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-5"><i class="fa fa-check"></i><b>6.3.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="6.4" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#comparison-to-random-peaks"><i class="fa fa-check"></i><b>6.4</b> Comparison to random peaks</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html"><i class="fa fa-check"></i><b>7</b> POE HPTM enrichment-POE transcription dynamics</a>
<ul>
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<div class="body-inner">
<div class="book-header" role="navigation">
<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Supplementary Materials</a>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)</a>
</h1>
</div>

Expand All @@ -234,11 +235,11 @@ <h3><span class="header-section-number">6.1.1</span> Gene bodies<a href="hptm-tr
##
## Coefficients:
## Estimate Std. Error z value Pr(&gt;|z|)
## (Intercept) 0.23129 0.01836 12.601 &lt;2e-16 ***
## Transcription 1.51770 0.94366 1.608 0.108
## Groupb1W -0.48790 0.02589 -18.843 &lt;2e-16 ***
## (Intercept) 0.23128 0.01836 12.600 &lt;2e-16 ***
## Transcription 1.52362 0.94428 1.614 0.107
## Groupb1W -0.48789 0.02589 -18.843 &lt;2e-16 ***
## Groupb2Q -0.46453 0.02586 -17.960 &lt;2e-16 ***
## Groupb2W -0.53713 0.02593 -20.717 &lt;2e-16 ***
## Groupb2W -0.53712 0.02593 -20.717 &lt;2e-16 ***
## ---
## Signif. codes: 0 &#39;***&#39; 0.001 &#39;**&#39; 0.01 &#39;*&#39; 0.05 &#39;.&#39; 0.1 &#39; &#39; 1
##
Expand All @@ -250,12 +251,12 @@ <h3><span class="header-section-number">6.1.1</span> Gene bodies<a href="hptm-tr
##
## Number of Fisher Scoring iterations: 3</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (Intercept) 1.2602237 1.2157175 1.3064186
## Transcription 4.5617258 0.8228371 36.8689768
## Groupb1W 0.6139173 0.5835236 0.6458607
## Groupb2Q 0.6284289 0.5973503 0.6610918
## Groupb2W 0.5844257 0.5554530 0.6148742</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-17-1.png" width="672" /></p>
## (Intercept) 1.2602085 1.2157024 1.3064034
## Transcription 4.5887869 0.8272917 37.1403134
## Groupb1W 0.6139213 0.5835273 0.6458649
## Groupb2Q 0.6284311 0.5973523 0.6610940
## Groupb2W 0.5844272 0.5554545 0.6148758</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-14-1.png" width="672" /></p>
</div>
<div id="promoters-3" class="section level3 hasAnchor" number="6.1.2">
<h3><span class="header-section-number">6.1.2</span> Promoters<a href="hptm-transcription-dynamics.html#promoters-3" class="anchor-section" aria-label="Anchor link to header"></a></h3>
Expand All @@ -266,11 +267,11 @@ <h3><span class="header-section-number">6.1.2</span> Promoters<a href="hptm-tran
##
## Coefficients:
## Estimate Std. Error z value Pr(&gt;|z|)
## (Intercept) -0.19268 0.01842 -10.46 &lt;2e-16 ***
## Transcription -3.51111 1.53339 -2.29 0.022 *
## Groupb1W -0.43184 0.02643 -16.34 &lt;2e-16 ***
## Groupb2Q -0.37462 0.02629 -14.25 &lt;2e-16 ***
## Groupb2W -0.43267 0.02641 -16.38 &lt;2e-16 ***
## (Intercept) -0.19269 0.01842 -10.462 &lt;2e-16 ***
## Transcription -3.50202 1.53037 -2.288 0.0221 *
## Groupb1W -0.43184 0.02643 -16.341 &lt;2e-16 ***
## Groupb2Q -0.37462 0.02629 -14.249 &lt;2e-16 ***
## Groupb2W -0.43267 0.02641 -16.384 &lt;2e-16 ***
## ---
## Signif. codes: 0 &#39;***&#39; 0.001 &#39;**&#39; 0.01 &#39;*&#39; 0.05 &#39;.&#39; 0.1 &#39; &#39; 1
##
Expand All @@ -282,12 +283,12 @@ <h3><span class="header-section-number">6.1.2</span> Promoters<a href="hptm-tran
##
## Number of Fisher Scoring iterations: 4</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (Intercept) 0.82474921 0.795497195 0.8550560
## Transcription 0.02986382 0.001111175 0.4037698
## Groupb1W 0.64931138 0.616519170 0.6838102
## Groupb2Q 0.68755063 0.653002319 0.7238935
## Groupb2W 0.64877440 0.616031517 0.6832205</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-20-1.png" width="672" /></p>
## (Intercept) 0.82474140 0.795490181 0.8550473
## Transcription 0.03013634 0.001127849 0.4054232
## Groupb1W 0.64931347 0.616521187 0.6838123
## Groupb2Q 0.68755015 0.653001844 0.7238930
## Groupb2W 0.64877540 0.616032490 0.6832215</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-17-1.png" width="672" /></p>
</div>
</div>
<div id="h3k27ac-3" class="section level2 hasAnchor" number="6.2">
Expand All @@ -301,11 +302,11 @@ <h3><span class="header-section-number">6.2.1</span> Gene bodies<a href="hptm-tr
##
## Coefficients:
## Estimate Std. Error z value Pr(&gt;|z|)
## (Intercept) 0.26670 0.01852 14.403 &lt; 2e-16 ***
## Transcription 5.84046 1.65205 3.535 0.000407 ***
## Groupb1W -0.22908 0.02585 -8.862 &lt; 2e-16 ***
## Groupb2Q -0.42431 0.02586 -16.410 &lt; 2e-16 ***
## Groupb2W -0.73402 0.02616 -28.057 &lt; 2e-16 ***
## (Intercept) 0.26665 0.01852 14.400 &lt; 2e-16 ***
## Transcription 5.86657 1.65313 3.549 0.000387 ***
## Groupb1W -0.22906 0.02585 -8.861 &lt; 2e-16 ***
## Groupb2Q -0.42429 0.02586 -16.410 &lt; 2e-16 ***
## Groupb2W -0.73401 0.02616 -28.057 &lt; 2e-16 ***
## ---
## Signif. codes: 0 &#39;***&#39; 0.001 &#39;**&#39; 0.01 &#39;*&#39; 0.05 &#39;.&#39; 0.1 &#39; &#39; 1
##
Expand All @@ -317,12 +318,12 @@ <h3><span class="header-section-number">6.2.1</span> Gene bodies<a href="hptm-tr
##
## Number of Fisher Scoring iterations: 4</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (Intercept) 1.3056481 1.2591417 1.353938e+00
## Transcription 343.9371567 17.1230492 1.030419e+04
## Groupb1W 0.7952628 0.7559666 8.365813e-01
## Groupb2Q 0.6542232 0.6218807 6.882166e-01
## Groupb2W 0.4799744 0.4559652 5.052074e-01</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-23-1.png" width="672" /></p>
## (Intercept) 1.3055858 1.2590807 1.353875e+00
## Transcription 353.0366507 17.5064483 1.059278e+04
## Groupb1W 0.7952834 0.7559861 8.366032e-01
## Groupb2Q 0.6542313 0.6218882 6.882252e-01
## Groupb2W 0.4799784 0.4559689 5.052116e-01</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-20-1.png" width="672" /></p>
</div>
<div id="promoters-4" class="section level3 hasAnchor" number="6.2.2">
<h3><span class="header-section-number">6.2.2</span> Promoters<a href="hptm-transcription-dynamics.html#promoters-4" class="anchor-section" aria-label="Anchor link to header"></a></h3>
Expand All @@ -333,9 +334,9 @@ <h3><span class="header-section-number">6.2.2</span> Promoters<a href="hptm-tran
##
## Coefficients:
## Estimate Std. Error z value Pr(&gt;|z|)
## (Intercept) -0.12083 0.01825 -6.620 3.59e-11 ***
## Transcription 0.63365 0.83094 0.763 0.44571
## Groupb1W -0.08052 0.02579 -3.123 0.00179 **
## (Intercept) -0.12084 0.01825 -6.620 3.58e-11 ***
## Transcription 0.63709 0.83078 0.767 0.44317
## Groupb1W -0.08051 0.02579 -3.122 0.00179 **
## Groupb2Q -0.32665 0.02604 -12.546 &lt; 2e-16 ***
## Groupb2W -0.58884 0.02654 -22.187 &lt; 2e-16 ***
## ---
Expand All @@ -349,12 +350,12 @@ <h3><span class="header-section-number">6.2.2</span> Promoters<a href="hptm-tran
##
## Number of Fisher Scoring iterations: 4</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (Intercept) 0.8861842 0.8550308 0.9184490
## Transcription 1.8844851 0.3607992 10.4949961
## Groupb1W 0.9226399 0.8771650 0.9704639
## Groupb2Q 0.7213345 0.6854346 0.7590862
## Groupb2W 0.5549713 0.5268214 0.5845819</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-26-1.png" width="672" /></p>
## (Intercept) 0.8861782 0.8550249 0.9184428
## Transcription 1.8909677 0.3623550 10.5315474
## Groupb1W 0.9226433 0.8771682 0.9704675
## Groupb2Q 0.7213358 0.6854358 0.7590876
## Groupb2W 0.5549721 0.5268221 0.5845828</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-23-1.png" width="672" /></p>
</div>
</div>
<div id="h3k4me3-3" class="section level2 hasAnchor" number="6.3">
Expand All @@ -368,10 +369,10 @@ <h3><span class="header-section-number">6.3.1</span> Gene bodies<a href="hptm-tr
##
## Coefficients:
## Estimate Std. Error z value Pr(&gt;|z|)
## (Intercept) 0.34155 0.01865 18.311 &lt; 2e-16 ***
## Transcription 6.90333 1.80531 3.824 0.000131 ***
## Groupb1W -0.06428 0.02606 -2.467 0.013629 *
## Groupb2Q -0.31405 0.02590 -12.125 &lt; 2e-16 ***
## (Intercept) 0.34155 0.01865 18.310 &lt; 2e-16 ***
## Transcription 6.89945 1.80374 3.825 0.000131 ***
## Groupb1W -0.06428 0.02606 -2.467 0.013635 *
## Groupb2Q -0.31404 0.02590 -12.124 &lt; 2e-16 ***
## Groupb2W -0.27871 0.02591 -10.758 &lt; 2e-16 ***
## ---
## Signif. codes: 0 &#39;***&#39; 0.001 &#39;**&#39; 0.01 &#39;*&#39; 0.05 &#39;.&#39; 0.1 &#39; &#39; 1
Expand All @@ -384,12 +385,12 @@ <h3><span class="header-section-number">6.3.1</span> Gene bodies<a href="hptm-tr
##
## Number of Fisher Scoring iterations: 4</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (Intercept) 1.4071244 1.3566526 1.459570e+00
## Transcription 995.5844895 35.2006129 3.996824e+04
## Groupb1W 0.9377424 0.8910494 9.868753e-01
## Groupb2Q 0.7304846 0.6943134 7.685136e-01
## Groupb2W 0.7567564 0.7192760 7.961652e-01</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-29-1.png" width="672" /></p>
## (Intercept) 1.4071207 1.3566493 1.459566e+00
## Transcription 991.7309448 35.1738630 3.969657e+04
## Groupb1W 0.9377463 0.8910530 9.868794e-01
## Groupb2Q 0.7304884 0.6943170 7.685177e-01
## Groupb2W 0.7567566 0.7192762 7.961654e-01</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-26-1.png" width="672" /></p>
</div>
<div id="promoters-5" class="section level3 hasAnchor" number="6.3.2">
<h3><span class="header-section-number">6.3.2</span> Promoters<a href="hptm-transcription-dynamics.html#promoters-5" class="anchor-section" aria-label="Anchor link to header"></a></h3>
Expand All @@ -400,11 +401,11 @@ <h3><span class="header-section-number">6.3.2</span> Promoters<a href="hptm-tran
##
## Coefficients:
## Estimate Std. Error z value Pr(&gt;|z|)
## (Intercept) -0.03695 0.01822 -2.028 0.04259 *
## Transcription 0.47954 0.83142 0.577 0.56410
## (Intercept) -0.03695 0.01822 -2.028 0.04257 *
## Transcription 0.48051 0.83121 0.578 0.56321
## Groupb1W 0.07629 0.02570 2.968 0.00299 **
## Groupb2Q -0.11694 0.02573 -4.545 5.5e-06 ***
## Groupb2W -0.02362 0.02570 -0.919 0.35799
## Groupb2W -0.02362 0.02570 -0.919 0.35800
## ---
## Signif. codes: 0 &#39;***&#39; 0.001 &#39;**&#39; 0.01 &#39;*&#39; 0.05 &#39;.&#39; 0.1 &#39; &#39; 1
##
Expand All @@ -416,14 +417,21 @@ <h3><span class="header-section-number">6.3.2</span> Promoters<a href="hptm-tran
##
## Number of Fisher Scoring iterations: 3</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (Intercept) 0.9637236 0.9299061 0.9987623
## Transcription 1.6153293 0.3176644 9.2686175
## Groupb1W 1.0792787 1.0262594 1.1350464
## Groupb2Q 0.8896384 0.8458808 0.9356480
## Groupb2W 0.9766554 0.9286808 1.0271056</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-32-1.png" width="672" /></p>

## (Intercept) 0.9637213 0.9299038 0.9987600
## Transcription 1.6168956 0.3181529 9.2732218
## Groupb1W 1.0792802 1.0262608 1.1350481
## Groupb2Q 0.8896392 0.8458815 0.9356488
## Groupb2W 0.9766560 0.9286814 1.0271063</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-29-1.png" width="672" /></p>
</div>
</div>
<div id="comparison-to-random-peaks" class="section level2 hasAnchor" number="6.4">
<h2><span class="header-section-number">6.4</span> Comparison to random peaks<a href="hptm-transcription-dynamics.html#comparison-to-random-peaks" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div class="float">
<img src="resources/figures/fig3_RANDOMIZED.png" alt="Randomized peaks of the same quantity and average length in each sample group as the true peak set were generated with bedtools random for comparison." />
<div class="figcaption">Randomized peaks of the same quantity and average length in each sample group as the true peak set were generated with bedtools random for comparison.</div>
</div>

</div>
</div>
</section>
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<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-gene-body"><i class="fa fa-check"></i>H3K4me3 (gene body)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-promoter"><i class="fa fa-check"></i>H3K4me3 (promoter)</a></li>
</ul></li>
<li class="chapter" data-level="7.4" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#comparison-to-random-peaks"><i class="fa fa-check"></i><b>7.4</b> Comparison to random peaks</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html"><i class="fa fa-check"></i><b>8</b> GO enrichment analyses</a>
<ul>
Expand Down Expand Up @@ -1210,15 +1209,8 @@ <h3>H3K4me3 (promoter)<a href="poe-hptm-enrichment-poe-transcription-dynamics.ht
## Groupb2Q 1.675221e+00 7.069031e-01 4.063030e+00
## Groupb2W 2.114952e+00 8.439543e-01 5.373705e+00</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-162-1.png" width="672" /></p>
</div>
</div>
<div id="comparison-to-random-peaks" class="section level2 hasAnchor" number="7.4">
<h2><span class="header-section-number">7.4</span> Comparison to random peaks<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#comparison-to-random-peaks" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div class="float">
<img src="resources/figures/fig3_RANDOMIZED.png" alt="Randomized peaks of the same quantity and average length in each sample group as the true peak set were generated with bedtools random for comparison." />
<div class="figcaption">Randomized peaks of the same quantity and average length in each sample group as the true peak set were generated with bedtools random for comparison.</div>
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