methGraph: A genome visualization tool for PCR-based methylation assays

Steve Lefever, Jasmien Hoebeeck, Filip Pattyn, Gábor Tusnády, Anne de Paepe, Frank Speleman, Tamás Aarányi, Jo Vandesompele

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Abnormalities in DNA methylation of CpG islands that play a role in gene regulation affect gene expression and hence play a role in disease, including cancer. Bisulfite-based DNA methylation analysis methods such as methylation-specific PCR (MSP) and bisulfite sequencing (BiSeq) are most commonly used to study gene-specific DNA methylation. Assessing specificity and visualizing the position of PCR primers in their genomic context is a laborious and tedious task, primarily due to the sequence changes induced during the bisulfite conversion. For this purpose, we developed methGraph, a web application for easy, fast and flexible visualization and accurate in silico quality evaluation of PCR-based methylation assays. The visualization process starts by submitting PCR primer sequences for specificity assessment and mapping on the genome using the BiSearch ePCR primer-search algorithm. The next step comprises the selection of relevant UCSC genome annotation tracks for display in the final graph. A custom track showing all individual CpG dinucleotides, representing their distribution in the CpG island is also provided. Finally, methGraph creates a BED file that is automatically uploaded to the UCSC genome browser, after which the resulting image files are extracted and made available for visualization and download. The generated high-quality figures can easily be customized and exported for use in publications or presentations. methGraph is available at http://mellfire.ugent.be/methgraph/.

Original languageEnglish
Pages (from-to)159-163
Number of pages5
JournalEpigenetics
Volume5
Issue number2
DOIs
Publication statusPublished - Feb 2010

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Keywords

  • Assay visualization
  • Bisulfite sequencing (BiSeq)
  • CpG dinucleotides
  • CpG island
  • DNA methylation
  • Graphics tool
  • Methylation-specific PCR (MSP)
  • Primer specificity
  • UCSC genome browser

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research

Cite this

Lefever, S., Hoebeeck, J., Pattyn, F., Tusnády, G., de Paepe, A., Speleman, F., Aarányi, T., & Vandesompele, J. (2010). methGraph: A genome visualization tool for PCR-based methylation assays. Epigenetics, 5(2), 159-163. https://doi.org/10.4161/epi.5.2.11161