MethReg

"MethReg" is an R package designed for the comprehensive analysis of epigenome-wide association studies (EWAS) data, mainly focusing on the functional impact of CpG methylation. The tool utilizes matched DNA-methylation and gene-expression data, incorporating external transcription factor (TF) binding information. By simultaneously modeling CpG methylation, target gene expression, and TF activity, MethReg evaluates, prioritizes, and annotates CpG sites with high regulatory potential. The unique approach identifies associations between TFs and target genes specific to subsets of samples with distinct methylation levels, providing a more nuanced understanding of regulatory roles in complex diseases.

Topic

Epigenetics;Transcription factors and regulatory sites;Gene transcripts;Methylated DNA immunoprecipitation;DNA polymorphism

Detail

  • Operation: Gene methylation analysis;DMR identification;DNA transcription;Gene regulatory network analysis;Regression analysis

  • Software interface: Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.12.0

  • Credit: National Institutes of Health, National Institute on Aging, Illinois Department of Public Health, Translational Genomics Research Institute.

  • Input: -

  • Output: -

  • Contact: Tiago Silva tiagochst@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • MethReg: estimating the regulatory potential of DNA methylation in gene transcription
  • Silva TC, Young JI, Martin ER, Chen XS, Wang L. MethReg: estimating the regulatory potential of DNA methylation in gene transcription. Nucleic Acids Res. 2022 May 20;50(9):e51. doi: 10.1093/nar/gkac030. PMID: 35100398; PMCID: PMC9122535.
  • https://doi.org/10.1093/nar/gkac030
  • PMID: 35100398
  • PMC: PMC9122535

Download and documentation

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