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Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units

BACKGROUND: 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 expre...

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Detalles Bibliográficos
Autores principales: Kober, Kord M., Berger, Liam, Roy, Ritu, Olshen, Adam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10028892/
https://www.ncbi.nlm.nih.gov/pubmed/36945384
http://dx.doi.org/10.1101/2023.03.07.531597
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author Kober, Kord M.
Berger, Liam
Roy, Ritu
Olshen, Adam
author_facet Kober, Kord M.
Berger, Liam
Roy, Ritu
Olshen, Adam
author_sort Kober, Kord M.
collection PubMed
description BACKGROUND: 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. RESULTS: We demonstrate the analyses using the tool are reproducible, up to 18x faster using the GPU, and scale linearly with increasing methylation loci. CONCLUSIONS: 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.
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spelling pubmed-100288922023-03-22 Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units Kober, Kord M. Berger, Liam Roy, Ritu Olshen, Adam bioRxiv Article BACKGROUND: 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. RESULTS: We demonstrate the analyses using the tool are reproducible, up to 18x faster using the GPU, and scale linearly with increasing methylation loci. CONCLUSIONS: 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. Cold Spring Harbor Laboratory 2023-03-10 /pmc/articles/PMC10028892/ /pubmed/36945384 http://dx.doi.org/10.1101/2023.03.07.531597 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Kober, Kord M.
Berger, Liam
Roy, Ritu
Olshen, Adam
Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units
title Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units
title_full Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units
title_fullStr Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units
title_full_unstemmed Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units
title_short Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units
title_sort torch-ecpg: a fast and scalable eqtm mapper for thousands of molecular phenotypes with graphical processing units
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10028892/
https://www.ncbi.nlm.nih.gov/pubmed/36945384
http://dx.doi.org/10.1101/2023.03.07.531597
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