Elucidating regulatory mechanisms downstream
We further split the peaks if the read coverage goes below 5% of the peak summit, which is defined as the midpoint of the region of maximumcoverage in the peak.Chapter 5 PREDICTIVE MODELS OF GENE REGULATION FROM HIGH-THROUGHPUT EPIGENOMICS DATA This article has been submitted for publication to the special issue ”Epigenetic Control of Reprogramming and Cellular Differentiation“ of ”Comparative and Functional Genomics“ Thus, they effectively compare the properties of different genes in a direct way; hence, the accuracy of the predictive model will be dependent on theaccuracy of the estimation of the significance of the Ch IP-Seq signals and, more importantly, they rely on the premise that signals in two different genes should be comparable. 2011 Wang et al., “Combinatorial patterns of histone acetylations and methylations in the human genome,” Nature genetics, vol.Conversely, weak PRbs and PREs that do not bind PRare not enriched in nucleosomes, suggesting a crucial role of nucleosomes for PR binding and hormonal gene regulation.
16 Figure 1.9: Profile of Ch IP-Seq data near TSS (A)(L) Profiles of the methylated histones and RNA Polymerase II (Pol II) indicated above each panel across the TSS for highly active, two stagesof intermediately active and silent genes. Eyras 25 Althammer S, Gonzalez-Vallinas J, Ballare C, Beato M, Eyras E.1.5 CLIP-Seq Being able to determine the location of specific RNA-binding proteins can give insight into the regulation of alternative splicing.Thus, alignment of these tagsto the genome results into two peaks, one on each strand, flanking the location where the protein or nucleosome of interest was bound.Chapter 3 PYICOS: A VERSATILE TOOLKIT FOR THE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA S. We calculated the peak densities in different regions related to genes and found that the region around the proximal promoter and the first exon were the most 36 Figure 4.2: Distribution of PRbs in breast cancer cells A) We describe the distribution of PRbs in different regions related to genes.4.2 Methods A block-like cluster was defined as such if the ratio between the length covered by the maximum of the peak and the length of the peak was greaterthan 0.25.