通过分析ENCODE的15个不同染色质区域的200碱基对单元构建人类基因组的SeqChromMM马尔可夫性质图谱。

Building the SeqChromMM Markov property atlas of the human genome by analyzing the 200-bp units of the 15 different chromatin regions of ENCODE.

作者信息

Lee K-E, Park H-S

机构信息

Bioinformatics Laboratory, Engineering School, Ewha Womans University, Seoul, Korea.

Bioinformatics Laboratory, Engineering School, Ewha Womans University, Seoul, Korea

出版信息

Genet Mol Res. 2016 Aug 30;15(3):gmr8992. doi: 10.4238/gmr.15038992.

DOI:10.4238/gmr.15038992

PMID:27706663

Abstract

We analyzed the publicly available ChromHMM BED files of the ENCODE project and tested the Markov properties of the different chromatin states in the human genome. Nucleotide frequency profiles of regional chromatin segmentations were analyzed, and Markov chains were built to detect Markov properties in the chromatin states of different ChromHMM regions. By estimating the transition probabilities of 200-base pair nucleotide sequences of the human genome, we constructed a nucleotide-sequence-based Markovian chromatin map called SeqChromMM.

摘要

我们分析了ENCODE项目中公开可用的ChromHMM BED文件，并测试了人类基因组中不同染色质状态的马尔可夫性质。分析了区域染色质分割的核苷酸频率谱，并构建了马尔可夫链以检测不同ChromHMM区域染色质状态中的马尔可夫性质。通过估计人类基因组200个碱基对核苷酸序列的转移概率，我们构建了一个基于核苷酸序列的马尔可夫染色质图谱，称为SeqChromMM。