School of Nursing, University of California San Francisco, San Francisco, CA, USA.
Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
BMC Bioinformatics. 2024 Feb 14;25(1):71. doi: 10.1186/s12859-024-05670-4.
Gene expression may be regulated by the DNA methylation of regulatory elements in cis, distal, and trans regions. One method to evaluate the relationship between DNA methylation and gene expression is the mapping of expression quantitative trait methylation (eQTM) loci (also called expression associated CpG loci, eCpG). However, no open-source tools are available to provide eQTM mapping. In addition, eQTM mapping can involve a large number of comparisons which may prevent the analyses due to limitations of computational resources. Here, we describe Torch-eCpG, an open-source tool to perform eQTM mapping that includes an optimized implementation that can use the graphical processing unit (GPU) to reduce runtime.
We demonstrate the analyses using the tool are reproducible, up to 18 × faster using the GPU, and scale linearly with increasing methylation loci.
Torch-eCpG is a fast, reliable, and scalable tool to perform eQTM mapping. Source code for Torch-eCpG is available at https://github.com/kordk/torch-ecpg .
基因表达可能受到顺式、远端和反式调控元件的 DNA 甲基化的调节。评估 DNA 甲基化与基因表达之间关系的一种方法是绘制表达数量性状甲基化 (eQTM) 基因座（也称为与表达相关的 CpG 基因座，eCpG）。然而，目前没有开源工具可用于提供 eQTM 图谱绘制。此外，eQTM 图谱绘制可能涉及大量比较，这可能会由于计算资源的限制而阻止分析。在这里，我们描述了 Torch-eCpG，这是一种用于进行 eQTM 图谱绘制的开源工具，它包含了一个经过优化的实现，可以使用图形处理单元 (GPU) 来减少运行时间。
我们证明了使用该工具进行的分析是可重复的，使用 GPU 可以快 18 倍，并且随着甲基化基因座数量的增加呈线性扩展。
Torch-eCpG 是一种快速、可靠和可扩展的工具，可用于进行 eQTM 图谱绘制。Torch-eCpG 的源代码可在 https://github.com/kordk/torch-ecpg 上获得。
