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Biomed Mater Eng. 2015;26 Suppl 1:S1917-27. doi: 10.3233/BME-151494.

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

Lee KE1,2, Park HS1,2,3.

Author information

1
Bioinformatics Laboratory, Ewha Womans University, Seoul, Korea.
2
Ewha Information and Telecommunication Institute, Ewha Womans University, Seoul, Korea.
3
Center for Convergence Research of Advanced Technologies, Ewha Womans University, Seoul, Korea.

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.

KEYWORDS:

Chromatin maps; Markov chain; computational epigenetics; noncoding DNA; nucleotide frequency patterns

PMID:
26405965
DOI:
10.3233/BME-151494
[Indexed for MEDLINE]

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