ArticleBMC bioinformatics2024
Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units.
Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Expression quantitative trait methylation across multiple cancer types with functional and therapeutic characterization using Onco-eQTM.NAR genomics and bioinformatics · 2026Article
- Adverse and adaptive placental DNA methylation changes linking prenatal air pollution exposure to child lung function: findings from the SEPAGES cohort.EBioMedicine · 2026Article
- Epigenome-wide analysis identifies DNA methylation mediators of treatment-related cardiometabolic risk in survivors of childhood cancer.Nature communications · 2026Article
- Article
- Placental PFAS concentrations are associated with perturbations of placental DNA methylation.Environmental pollution (Barking, Essex : 1987) · 2025Article
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4 authors.
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Abstract
backgroundGene 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.
resultsWe demonstrate the analyses using the tool are reproducible, up to 18 × faster using the GPU, and scale linearly with increasing methylation loci.
conclusionsTorch-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 .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.