By Pook, M
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2 DNA Methylation Profiling from High-Throughput Sequencing Data Michael Hackenberg, Guillermo Barturen and José L. Oliver Dpto. de Genética, Facultad de Ciencias, Universidad de Granada,Granada, Lab. de Bioinformática, Inst. de Biotecnología, Centro de Investigación Biomédica, Granada, Spain 1. Introduction The methylation of a cytosine at the carbon 5 position (5meC) is a common epigenetic mark in eukaryotic cells that is normally found in CpG and CpHpG (H=A,C,T) sequence contexts. , 1999). , 2006).
Zhu, H. & Ruan, J. (2010). De novo assembly of human genomes with massively parallel short read sequencing, Nucleic Acid Research 20(2): 265–272. Matsumoto, M. & Nishimura, T. (1998). Mersenne twister: A 623-dimensionally equidistributed uniform pseudo-random number generator, ACM Transactions on Modeling and Computer Simulation 8(1): 3–30. Meng, C. , Zhu, X. , Peng, G. & Dai, D. (2009). Promoter histone H3 lysine 9 di-methylation is associated with DNA methylation and aberrant expression of p16 in gastric cancer cells, Oncology Report 22(5): 1221–1227.
Outputs namely, Histone states, progress in transcription rate and DNA methylation, for the whole dataset were recorded every 1,000 time-steps (total number of time steps being 10,000). Although the system can trace and report evolution of all 4 types of histone, we discuss here only 2 types namely H4 and H2A. The following Figures 5 and 6 show the expected values of each histone node being chosen during several iterations over the 3 independent simulation trials. 0], for the 3 simulation runs (results not shown here).
DNA methylation and trinucleotide repeat expansion diseases by Pook, M