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@@ -657,7 +657,7 @@ LatexCommand tableofcontents
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\begin_layout Standard
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\begin_inset Note Note
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-status open
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+status collapsed
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\begin_layout Plain Layout
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To create a new abbreviation:
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@@ -746,7 +746,7 @@ addcontentsline{toc}{chapter}{Abstract}
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\begin_layout Standard
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\begin_inset Note Note
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-status open
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+status collapsed
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\begin_layout Plain Layout
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It is included as an integral part of the thesis and should immediately
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@@ -792,9 +792,12 @@ Transplant rejection mediated by adaptive immune response is the major challenge
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are heavily used in the study of immunology and transplant rejection.
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Here we present 3 analyses of such assays in this context.
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First, we re-analyze a large data set consisting of H3K4me2, H3K4me3, and
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- H3K27me3 ChIP-seq data and RNA-seq data in naïve and memory CD4 T-cells
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- using modern bioinformatics methods designed to address deficiencies in
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- the data and extend the analysis in several new directions.
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+ H3K27me3 ChIP-seq data and RNA-seq data in naïve and memory CD4
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+\begin_inset Formula $^{+}$
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+\end_inset
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+
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+ T-cells using modern bioinformatics methods designed to address deficiencies
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+ in the data and extend the analysis in several new directions.
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All 3 histone marks are found to occur in broad regions and are enriched
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near promoters, but the radius of promoter enrichment is found to be larger
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for H3K27me3.
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@@ -805,7 +808,7 @@ Transplant rejection mediated by adaptive immune response is the major challenge
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to be important, with asymmetric associations with gene expression for
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peaks located the same distance up- or downstream of the TSS.
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Second, we demonstrate the effectiveness of fRMA as a single-channel normalizat
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-ion for using expression arrays to diagnost transplant rejection in a clinical
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+ion for using expression arrays to diagnose transplant rejection in a clinical
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diagnostic setting, and we develop a custom fRMA normalization for a previously
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unsupported array platform.
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For methylation arrays, we adapt methods designed for RNA-seq to improve
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@@ -1647,8 +1650,8 @@ HTS
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\end_inset
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- are powerful methods for interrogating gene expression and empigenetic
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- state across the entire genome.
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+ are powerful methods for interrogating gene expression and epigenetic state
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+ across the entire genome.
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However, these data present many unique analysis challenges, and proper
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analysis requires identifying and exploiting genome-wide trends in the
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data to make up for the small sample sizes.
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@@ -23178,6 +23181,19 @@ Reintroduce all abbreviations
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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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+Present or past tense for talking about previous chapters?
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+\end_layout
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+
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+\end_inset
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+
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\end_layout
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\begin_layout Standard
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@@ -23309,7 +23325,7 @@ ChIP-seq
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\end_inset
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- data required choosing a
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+ data required choosing an
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\begin_inset Quotes eld
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\end_inset
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