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@@ -5424,20 +5424,6 @@ Focus on what hypotheses were tested, then select figures that show how
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\end_inset
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-\end_layout
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-
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-\begin_layout Standard
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-\begin_inset Flex TODO Note (inline)
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-status open
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-
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-\begin_layout Plain Layout
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-Maybe reorder these sections to do RNA-seq, then ChIP-seq, then combined
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- analyses?
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-\end_layout
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-
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-\end_inset
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-
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-
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\end_layout
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\begin_layout Subsection
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@@ -5681,7 +5667,7 @@ H3K4 and H3K27 methylation occur in broad regions and are enriched near
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\begin_inset Float table
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wide false
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sideways false
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-status collapsed
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+status open
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\begin_layout Plain Layout
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\align center
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@@ -7836,20 +7822,6 @@ cloud
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distribution of promoter coverage landscapes.
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While the clusters are a useful abstraction that aids in visualization,
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they are ultimately not an accurate representation of the data.
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- A better representation might be something like a polar coordinate system
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- with the origin at the center of Cluster 5, where the radius represents
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- the peak height above the background and the angle represents the peak's
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- position upstream or downstream of the
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-\begin_inset Flex Glossary Term
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-status open
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-
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-\begin_layout Plain Layout
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-TSS
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-\end_layout
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-
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-\end_inset
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-
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-.
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The continuous nature of the distribution also explains why different values
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of
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\begin_inset Formula $K$
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@@ -10240,6 +10212,24 @@ For H3K4, define polar coordinates based on PC1 & 2: R = peak size, Theta
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Then correlate with expression.
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\end_layout
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+\begin_layout Standard
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+A better representation might be something like a polar coordinate system
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+ with the origin at the center of Cluster 5, where the radius represents
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+ the peak height above the background and the angle represents the peak's
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+ position upstream or downstream of the
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+\begin_inset Flex Glossary Term
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+status open
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+
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+\begin_layout Plain Layout
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+TSS
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+\end_layout
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+
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+\end_inset
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+
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+.
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+
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+\end_layout
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+
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\begin_layout Itemize
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Current analysis only at Day 0.
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Need to study across time points.
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