Kober Kord M, Berger Liam, Roy Ritu, Olshen Adam
School of Nursing, University of California San Francisco, San Francisco, California, USA.
Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
bioRxiv. 2023 Mar 10:2023.03.07.531597. doi: 10.1101/2023.03.07.531597.
Gene expression may be regulated by the DNA methylation of regulatory elements in , , and 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 18x 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.
基因表达可能受基因间、基因内及基因上游区域调控元件的DNA甲基化作用影响。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）位点图谱（也称为表达相关CpG位点，即eCpG）。然而，目前尚无开源工具可用于进行eQTM图谱绘制。此外，eQTM图谱绘制可能涉及大量比较，这可能因计算资源的限制而阻碍分析。在此，我们介绍Torch - eCpG，这是一种用于执行eQTM图谱绘制的开源工具，它包含一种优化实现，可使用图形处理单元（GPU）来减少运行时间。
我们证明使用该工具进行的分析具有可重复性，使用GPU时速度可提高18倍，并且随着甲基化位点数量的增加呈线性扩展。
Torch - eCpG是一种用于执行eQTM图谱绘制的快速、可靠且可扩展的工具。Torch - eCpG的源代码可在https://github.com/kordk/torch - ecpg获取。
