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. 2020 Mar 3;10:3920. doi: 10.1038/s41598-020-60845-2

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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GeneEXPLORE modeling: (a) Several methylation probes are associated with gene expression, and they can be located far from the gene due to chromatin looping structure. (b) Straightened genome, upstream and downstream $L_{g}$ Mb from the promoter region of the gene g. There are M_g numbers of probes in the range. (c) Predicting gene expression from the methylation probes. Methylation data to predict the expression of gene, g consist of n samples and M_g probes. The shaded columns are an example of probes that are associated with gene expression. Our model, geneEXPLORE, identifies the associated probes and estimates the weights of them. Gene expression of g is predicted by summing the weighted methylation values. The procedure is repeated for each gene. (d) Application of geneEXPLORE: Predicting phenotypes from the predicted gene expression. After predicting gene expression on the entire genome, we estimated the effects of the predicted gene expression on several binary phenotypes (see Methods).