國家衛生研究院 NHRI:Item 3990099045/12133
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    Please use this identifier to cite or link to this item: http://ir.nhri.org.tw/handle/3990099045/12133


    Title: pWGBSSimla: A profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions
    Authors: Chung, RH;Kang, CY
    Contributors: Institute of Population Health Sciences
    Abstract: MOTIVATION: DNA methylation plays an important role in regulating gene expression. DNA methylation is commonly analyzed using bisulfite sequencing (BS-seq)-based designs, such as whole-genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and oxidative bisulfite sequencing (oxBS-seq). Furthermore, there has been growing interest in investigating the roles that genetic variants play in changing the methylation levels (i.e., methylation quantitative trait loci or meQTLs), how methylation regulates the imprinting of gene expression (i.e., allele-specific methylation or ASM), and the differentially methylated regions (DMRs) among different cell types. However, none of the current simulation tools can generate different BS-seq data types (e.g., WGBS, RRBS, and oxBS-seq) while modeling meQTLs, ASM, and DMRs. RESULTS: We developed pWGBSSimla, a profile-based bisulfite sequencing data simulator, which simulates WGBS, RRBS, and oxBS-seq data for different cell types based on real data. meQTLs and ASM are modeled based on the block structures of the methylation status at CpGs, whereas the simulation of DMRs is based on observations of methylation rates in real data. We demonstrated that pWGBSSimla adequately simulates data and allows performance comparisons among different methylation analysis methods. AVAILABILITY: pWGBSSimla is available at https://omicssimla.sourceforge.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    Date: 2020-02
    Relation: Bioinformatics. 2020 Feb;36(3):660-665.
    Link to: http://dx.doi.org/10.1093/bioinformatics/btz635
    JIF/Ranking 2023: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=NHRI&SrcApp=NHRI_IR&KeyISSN=1367-4803&DestApp=IC2JCR
    Cited Times(WOS): https://www.webofscience.com/wos/woscc/full-record/WOS:000515095200002
    Cited Times(Scopus): https://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=85079076167
    Appears in Collections:[Ren-Hua Chung] Periodical Articles

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