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Preliminary testing for the Markov property of the fifteen chromatin states of the Broad Histone Track

Title
Preliminary testing for the Markov property of the fifteen chromatin states of the Broad Histone Track
Authors
Lee K.-E.Park H.-S.
Ewha Authors
박현석
SCOPUS Author ID
박현석scopus
Issue Date
2015
Journal Title
Bio-medical materials and engineering
ISSN
1878-3619JCR Link
Citation
vol. 26, pp. S1917 - S1927
Keywords
Chromatin mapscomputational epigeneticsMarkov chainnoncoding DNAnucleotide frequency patterns
Indexed
SCIE; SCOPUS WOS scopus
Abstract
Epigenetic computational analyses based on Markov chains can integrate dependencies between regions in the genome that are directly adjacent. In this paper, the BED files of fifteen chromatin states of the Broad Histone Track of the ENCODE project are parsed, and comparative nucleotide frequencies of regional chromatin blocks are thoroughly analyzed to detect the Markov property in them. We perform various tests to examine the Markov property embedded in a frequency domain by checking for the presence of the Markov property in the various chromatin states. We apply these tests to each region of the fifteen chromatin states. The results of our simulation indicate that some of the chromatin states possess a stronger Markov property than others. We discuss the significance of our findings in statistical models of nucleotide sequences that are necessary for the computational analysis of functional units in noncoding DNA.
DOI
10.3233/BME-151494
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엘텍공과대학 > 컴퓨터공학과 > Journal papers
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