Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
Epigenetics. 2010 Feb 16;5(2):159-63. doi: 10.4161/epi.5.2.11161. Epub 2010 Feb 11.
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/.
在基因调控中发挥作用的 CpG 岛的 DNA 甲基化异常会影响基因表达，从而在疾病（包括癌症）中发挥作用。基于亚硫酸氢盐的 DNA 甲基化分析方法，如甲基化特异性 PCR（MSP）和亚硫酸氢盐测序（BiSeq），是最常用于研究基因特异性 DNA 甲基化的方法。评估特异性并在其基因组背景中可视化 PCR 引物的位置是一项繁琐而乏味的任务，主要是由于在亚硫酸氢盐转化过程中诱导的序列变化。为此，我们开发了 methGraph，这是一种用于轻松、快速和灵活地可视化以及准确进行基于 PCR 的甲基化检测的计算机模拟质量评估的网络应用程序。可视化过程首先通过提交 PCR 引物序列来进行特异性评估，并使用 BiSearch ePCR 引物搜索算法在基因组上进行映射。下一步包括选择相关的 UCSC 基因组注释轨道以在最终图形中显示。还提供了一个自定义轨道，显示所有单个 CpG 二核苷酸，代表它们在 CpG 岛中的分布。最后，methGraph 创建一个 BED 文件，该文件会自动上传到 UCSC 基因组浏览器，之后提取生成的图像文件并提供可视化和下载。生成的高质量图形可以轻松自定义并导出，用于出版物或演示。methGraph 可在 http://mellfire.ugent.be/methgraph/ 获得。
