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Currently available in silico methods have facilitated the identification, positioning and quantitative comparisons of individual modification sites. However, the essential challenge to link specific \u2018epi-marks\u2019 to gene expression in the particular context of cellular and biological processes is unmet. To fast-track exploration, we generated epidecodeR implemented in R, which allows biologists to quickly survey whether an epigenomic or epitranscriptomic status of their interest potentially influences gene expression responses. The evaluation is based on the cumulative distribution function and the statistical significance in differential expression of genes grouped by the number of \u2018epi-marks\u2019. This tool proves useful in predicting the role of H3K9ac and H3K27ac in associated gene expression after knocking down deacetylases FAM60A and SDS3 and N6-methyl-adenosine-associated gene expression after knocking out the reader proteins. We further used epidecodeR to explore the effectiveness of demethylase FTO inhibitors and histone-associated modifications in drug abuse in animals. epidecodeR is available for downloading as an R package at https:\/\/bioconductor.riken.jp\/packages\/3.13\/bioc\/html\/epidecodeR.html.<\/jats:p>","DOI":"10.1093\/bib\/bbad521","type":"journal-article","created":{"date-parts":[[2024,1,25]],"date-time":"2024-01-25T18:10:11Z","timestamp":1706206211000},"source":"Crossref","is-referenced-by-count":2,"title":["epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2153-0110","authenticated-orcid":false,"given":"Kandarp","family":"Joshi","sequence":"first","affiliation":[{"name":"Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University , Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501 , Japan"}]},{"given":"Dan O","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University , Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501 , Japan"},{"name":"Center for Biosystems Dynamics Research , RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 , Japan"},{"name":"New York University Abu Dhabi ,Saadiyat Campus C1-031, Abu Dhabi, United Arab Emirates"}]}],"member":"286","published-online":{"date-parts":[[2024,1,23]]},"reference":[{"key":"2024012518094899000_ref1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2024012518094899000_ref2","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open 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