DMEAS: DNA Methylation Entropy Analysis Software

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2013 Jun 11

PMID 23749987

Citations 12

Authors

Jianlin He

Xinxi Sun

Xiaojian Shao

Liji Liang

Hehuang Xie

Affiliations

Soon will be listed here.

Abstract

Summary: DMEAS is the first user-friendly tool dedicated to analyze the distribution of DNA methylation patterns for the quantification of epigenetic heterogeneity. It supports the analysis of both locus-specific and genome-wide bisulfite sequencing data. DMEAS progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. It determines the DNA methylation level and calculates methylation entropy for genomic segments to enable the quantitative assessment of DNA methylation variations observed in cell populations.

Availability And Implementation: DMEAS program, user guide and all the testing data are freely available from http://sourceforge.net/projects/dmeas/files/

Citing Articles

Low-pass nanopore sequencing for measurement of global methylation levels in plants.

Liau Y, Whibley A, Hill A, Vanga B, Pither-Joyce M, Hilario E BMC Genomics. 2024; 25(1):1235.

PMID: 39716067 PMC: 11668104. DOI: 10.1186/s12864-024-11145-w.

Methylation entropy landscape of Chinese long-lived individuals reveals lower epigenetic noise related to human healthy aging.

Wang H, Xiao F, Gao Z, Guo L, Yang L, Li G Aging Cell. 2024; 23(7):e14163.

PMID: 38566438 PMC: 11258444. DOI: 10.1111/acel.14163.

Estimating genome-wide DNA methylation heterogeneity with methylation patterns.

Lin P, Chang Y, Huang Y, Chen P Epigenetics Chromatin. 2023; 16(1):44.

PMID: 37941029 PMC: 10634068. DOI: 10.1186/s13072-023-00521-7.

msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data.

Kim H, Sim M, Park N, Kwon K, Kim J, Kim J BMC Bioinformatics. 2022; 23(1):383.

PMID: 36123620 PMC: 9487059. DOI: 10.1186/s12859-022-04925-2.

Ten Years of EWAS.

Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N Adv Sci (Weinh). 2021; 8(20):e2100727.

PMID: 34382344 PMC: 8529436. DOI: 10.1002/advs.202100727.

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