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<!DOCTYPE html>
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<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)" />
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<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: 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="2024-06-09" />
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<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
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<nav role="navigation">
<ul class="summary">
<li><a href="./">Appendix D</a></li>
<li class="divider"></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>
<li class="chapter" data-level="1.2" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#mrna-seq"><i class="fa fa-check"></i><b>1.2</b> mRNA-seq</a></li>
<li class="chapter" data-level="1.3" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#chip-seq"><i class="fa fa-check"></i><b>1.3</b> ChIP-seq</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html"><i class="fa fa-check"></i><b>2</b> Transcriptomic Analyses</a>
<ul>
<li class="chapter" data-level="2.1" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html#differential-gene-expression-analysis"><i class="fa fa-check"></i><b>2.1</b> Differential gene expression analysis</a></li>
<li class="chapter" data-level="2.2" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html#wgcna"><i class="fa fa-check"></i><b>2.2</b> WGCNA</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html"><i class="fa fa-check"></i><b>3</b> Allele-Specific Transcriptomic Analyses</a>
<ul>
<li class="chapter" data-level="3.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#snps-and-transcripts"><i class="fa fa-check"></i><b>3.1</b> SNPs and transcripts</a></li>
<li class="chapter" data-level="3.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#poe-gene-lists"><i class="fa fa-check"></i><b>3.2</b> POE gene lists</a></li>
<li class="chapter" data-level="3.3" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#hpf-wl-ql---allelic-transcriptomics"><i class="fa fa-check"></i><b>3.3</b> 192hpf WL & QL - allelic transcriptomics</a>
<ul>
<li class="chapter" data-level="3.3.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-1"><i class="fa fa-check"></i><b>3.3.1</b> Block 1</a></li>
<li class="chapter" data-level="3.3.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-2"><i class="fa fa-check"></i><b>3.3.2</b> Block 2</a></li>
</ul></li>
<li class="chapter" data-level="3.4" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#hpf-eggs---allelic-transcriptomics"><i class="fa fa-check"></i><b>3.4</b> 24hpf eggs - allelic transcriptomics</a>
<ul>
<li class="chapter" data-level="3.4.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-3"><i class="fa fa-check"></i><b>3.4.1</b> Block 3</a></li>
<li class="chapter" data-level="3.4.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-4"><i class="fa fa-check"></i><b>3.4.2</b> Block 4</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html"><i class="fa fa-check"></i><b>4</b> ChIP-seq Analysis</a>
<ul>
<li class="chapter" data-level="4.1" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#enrichment-across-promoters-and-gene-bodies"><i class="fa fa-check"></i><b>4.1</b> Enrichment across promoters and gene bodies</a></li>
<li class="chapter" data-level="4.2" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#differential-enrichment-analysis"><i class="fa fa-check"></i><b>4.2</b> Differential enrichment analysis</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k27me3"><i class="fa fa-check"></i><b>4.2.1</b> H3K27me3</a></li>
<li class="chapter" data-level="4.2.2" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k27ac"><i class="fa fa-check"></i><b>4.2.2</b> H3K27ac</a></li>
<li class="chapter" data-level="4.2.3" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k4me3"><i class="fa fa-check"></i><b>4.2.3</b> H3K4me3</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html"><i class="fa fa-check"></i><b>5</b> Allele-Specific ChIP-seq Analyses</a>
<ul>
<li class="chapter" data-level="5.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#snps-and-peaks"><i class="fa fa-check"></i><b>5.1</b> SNPs and peaks</a></li>
<li class="chapter" data-level="5.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#poe-peak-lists"><i class="fa fa-check"></i><b>5.2</b> POE peak lists</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27me3-1"><i class="fa fa-check"></i><b>5.2.1</b> H3K27me3</a></li>
<li class="chapter" data-level="5.2.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27ac-1"><i class="fa fa-check"></i><b>5.2.2</b> H3K27ac</a></li>
<li class="chapter" data-level="5.2.3" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k4me3-1"><i class="fa fa-check"></i><b>5.2.3</b> H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27me3-2"><i class="fa fa-check"></i><b>5.3</b> H3K27me3</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies"><i class="fa fa-check"></i><b>5.3.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.3.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters"><i class="fa fa-check"></i><b>5.3.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27ac-2"><i class="fa fa-check"></i><b>5.4</b> H3K27ac</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies-1"><i class="fa fa-check"></i><b>5.4.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.4.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters-1"><i class="fa fa-check"></i><b>5.4.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k4me3-2"><i class="fa fa-check"></i><b>5.5</b> H3K4me3</a>
<ul>
<li class="chapter" data-level="5.5.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies-2"><i class="fa fa-check"></i><b>5.5.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.5.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters-2"><i class="fa fa-check"></i><b>5.5.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="5.6" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#combined-results"><i class="fa fa-check"></i><b>5.6</b> Combined results</a>
<ul>
<li class="chapter" data-level="5.6.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#block-1-7"><i class="fa fa-check"></i><b>5.6.1</b> Block 1</a></li>
<li class="chapter" data-level="5.6.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#block-2-7"><i class="fa fa-check"></i><b>5.6.2</b> Block 2</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html"><i class="fa fa-check"></i><b>6</b> HPTM-transcription dynamics</a>
<ul>
<li class="chapter" data-level="6.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k27me3-3"><i class="fa fa-check"></i><b>6.1</b> H3K27me3</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-3"><i class="fa fa-check"></i><b>6.1.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.1.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-3"><i class="fa fa-check"></i><b>6.1.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k27ac-3"><i class="fa fa-check"></i><b>6.2</b> H3K27ac</a>
<ul>
<li class="chapter" data-level="6.2.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-4"><i class="fa fa-check"></i><b>6.2.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.2.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-4"><i class="fa fa-check"></i><b>6.2.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k4me3-3"><i class="fa fa-check"></i><b>6.3</b> H3K4me3</a>
<ul>
<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>
<li class="chapter" data-level="7.1" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#block-1-8"><i class="fa fa-check"></i><b>7.1</b> Block 1</a>
<ul>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-4"><i class="fa fa-check"></i>H3K27me3</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#h3k27ac-4"><i class="fa fa-check"></i>H3K27ac</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#h3k4me3-4"><i class="fa fa-check"></i>H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="7.2" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#block-2-8"><i class="fa fa-check"></i><b>7.2</b> Block 2</a>
<ul>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-5"><i class="fa fa-check"></i>H3K27me3</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#h3k27ac-5"><i class="fa fa-check"></i>H3K27ac</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#h3k4me3-5"><i class="fa fa-check"></i>H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="7.3" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#logistic-regression"><i class="fa fa-check"></i><b>7.3</b> Logistic regression</a>
<ul>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-gene-body"><i class="fa fa-check"></i>H3K27me3 (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#h3k27me3-promoter"><i class="fa fa-check"></i>H3K27me3 (promoter)</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#h3k27ac-gene-body"><i class="fa fa-check"></i>H3K27ac (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#h3k27ac-promoter"><i class="fa fa-check"></i>H3K27ac (promoter)</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-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>
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<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>
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<li class="chapter" data-level="8.1" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#degs-poe-genes"><i class="fa fa-check"></i><b>8.1</b> DEGs & POE genes</a></li>
<li class="chapter" data-level="8.2" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#wgcna-modules"><i class="fa fa-check"></i><b>8.2</b> WGCNA modules</a></li>
<li class="chapter" data-level="8.3" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#hptm-differentially-enriched-regions"><i class="fa fa-check"></i><b>8.3</b> HPTM differentially enriched regions</a></li>
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<li class="chapter" data-level="9" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html"><i class="fa fa-check"></i><b>9</b> POE gene feature assessment</a>
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<li class="chapter" data-level="9.1" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#spatial-clustering"><i class="fa fa-check"></i><b>9.1</b> Spatial clustering</a></li>
<li class="chapter" data-level="9.2" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-feature-analyses"><i class="fa fa-check"></i><b>9.2</b> Intron feature analyses</a>
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<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#recombination-rate"><i class="fa fa-check"></i>Recombination rate</a></li>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron"><i class="fa fa-check"></i>% intron</a></li>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-gc"><i class="fa fa-check"></i>Intron GC</a></li>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-cpg-density"><i class="fa fa-check"></i>Intron CpG density</a></li>
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<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>
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<div id="hptm-transcription-dynamics" class="section level1 hasAnchor" number="6">
<h1><span class="header-section-number">S6</span> HPTM-transcription dynamics<a href="hptm-transcription-dynamics.html#hptm-transcription-dynamics" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="h3k27me3-3" class="section level2 hasAnchor" number="6.1">
<h2><span class="header-section-number">6.1</span> H3K27me3<a href="hptm-transcription-dynamics.html#h3k27me3-3" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="gene-bodies-3" class="section level3 hasAnchor" number="6.1.1">
<h3><span class="header-section-number">6.1.1</span> Gene bodies<a href="hptm-transcription-dynamics.html#gene-bodies-3" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<pre><code>##
## Call:
## glm(formula = H3K27me3_GB ~ Transcription + Group, family = "binomial",
## data = corrdat, na.action = na.exclude)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.23128 0.01836 12.600 <2e-16 ***
## Transcription 1.52362 0.94428 1.614 0.107
## Groupb1W -0.48789 0.02589 -18.843 <2e-16 ***
## Groupb2Q -0.46453 0.02586 -17.960 <2e-16 ***
## Groupb2W -0.53712 0.02593 -20.717 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 66993 on 48491 degrees of freedom
## Residual deviance: 66423 on 48487 degrees of freedom
## AIC: 66433
##
## Number of Fisher Scoring iterations: 3</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (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>
<pre><code>##
## Call:
## glm(formula = H3K27me3_P ~ Transcription + Group, family = "binomial",
## data = corrdat, na.action = na.exclude)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.19269 0.01842 -10.462 <2e-16 ***
## Transcription -3.50202 1.53037 -2.288 0.0221 *
## Groupb1W -0.43184 0.02643 -16.341 <2e-16 ***
## Groupb2Q -0.37462 0.02629 -14.249 <2e-16 ***
## Groupb2W -0.43267 0.02641 -16.384 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 64247 on 48491 degrees of freedom
## Residual deviance: 63863 on 48487 degrees of freedom
## AIC: 63873
##
## Number of Fisher Scoring iterations: 4</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (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">
<h2><span class="header-section-number">6.2</span> H3K27ac<a href="hptm-transcription-dynamics.html#h3k27ac-3" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="gene-bodies-4" class="section level3 hasAnchor" number="6.2.1">
<h3><span class="header-section-number">6.2.1</span> Gene bodies<a href="hptm-transcription-dynamics.html#gene-bodies-4" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<pre><code>##
## Call:
## glm(formula = H3K27ac_GB ~ Transcription + Group, family = "binomial",
## data = corrdat, na.action = na.exclude)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.26665 0.01852 14.400 < 2e-16 ***
## Transcription 5.86657 1.65313 3.549 0.000387 ***
## Groupb1W -0.22906 0.02585 -8.861 < 2e-16 ***
## Groupb2Q -0.42429 0.02586 -16.410 < 2e-16 ***
## Groupb2W -0.73401 0.02616 -28.057 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 67163 on 48491 degrees of freedom
## Residual deviance: 66279 on 48487 degrees of freedom
## AIC: 66289
##
## Number of Fisher Scoring iterations: 4</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (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>
<pre><code>##
## Call:
## glm(formula = H3K27ac_P ~ Transcription + Group, family = "binomial",
## data = corrdat, na.action = na.exclude)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (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 < 2e-16 ***
## Groupb2W -0.58884 0.02654 -22.187 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 65645 on 48491 degrees of freedom
## Residual deviance: 65037 on 48487 degrees of freedom
## AIC: 65047
##
## Number of Fisher Scoring iterations: 4</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (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">
<h2><span class="header-section-number">6.3</span> H3K4me3<a href="hptm-transcription-dynamics.html#h3k4me3-3" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="gene-bodies-5" class="section level3 hasAnchor" number="6.3.1">
<h3><span class="header-section-number">6.3.1</span> Gene bodies<a href="hptm-transcription-dynamics.html#gene-bodies-5" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<pre><code>##
## Call:
## glm(formula = H3K4me3_GB ~ Transcription + Group, family = "binomial",
## data = corrdat, na.action = na.exclude)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.34155 0.01865 18.310 < 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 < 2e-16 ***
## Groupb2W -0.27871 0.02591 -10.758 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 66811 on 48491 degrees of freedom
## Residual deviance: 66571 on 48487 degrees of freedom
## AIC: 66581
##
## Number of Fisher Scoring iterations: 4</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (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>
<pre><code>##
## Call:
## glm(formula = H3K4me3_P ~ Transcription + Group, family = "binomial",
## data = corrdat, na.action = na.exclude)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (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 0.35800
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 67191 on 48491 degrees of freedom
## Residual deviance: 67133 on 48487 degrees of freedom
## AIC: 67143
##
## Number of Fisher Scoring iterations: 3</code></pre>
<pre><code>## OR 2.5 % 97.5 %
## (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>
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<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>
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