D'Addabbo Pietro, Cohen-Fultheim Roni, Twersky Itamar, Fonzino Adriano, Silvestris Domenico Alessandro, Prakash Ananth, Mazzacuva Pietro Luca, Vizcaino Juan Antonio, Green Andrew, Sweeney Blake, Yates Andy, Lussi Yvonne, Luo Jie, Martin Maria-Jesus, Eisenberg Eli, Levanon Erez Y, Pesole Graziano, Picardi Ernesto
Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, via Orabona 4, 70125, Bari, Italy.
Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 52900, Israel.
Nucleic Acids Res. 2025 Jan 6;53(D1):D233-D242. doi: 10.1093/nar/gkae1083.
A-to-I RNA editing is the most common non-transient epitranscriptome modification. It plays several roles in human physiology and has been linked to several disorders. Large-scale deep transcriptome sequencing has fostered the characterization of A-to-I editing at the single nucleotide level and the development of dedicated computational resources. REDIportal is a unique and specialized database collecting ∼16 million of putative A-to-I editing sites designed to face the current challenges of epitranscriptomics. Its running version has been enriched with sites from the TCGA project (using data from 31 studies). REDIportal provides an accurate, sustainable and accessible tool enriched with interconnections with widespread ELIXIR core resources such as Ensembl, RNAcentral, UniProt and PRIDE. Additionally, REDIportal now includes information regarding RNA editing in putative double-stranded RNAs, relevant for the immune-related roles of editing, as well as an extended catalog of recoding events. Finally, we report a reliability score per site calculated using a deep learning model trained using a huge collection of positive and negative instances. REDIportal is available at http://srv00.recas.ba.infn.it/atlas/.
A-to-I RNA编辑是最常见的非瞬时表观转录组修饰。它在人类生理学中发挥多种作用，并与多种疾病相关。大规模深度转录组测序促进了单核苷酸水平上A-to-I编辑的表征以及专用计算资源的开发。REDIportal是一个独特的专门数据库，收集了约1600万个假定的A-to-I编辑位点，旨在应对表观转录组学当前面临的挑战。其运行版本已通过TCGA项目的位点（使用31项研究的数据）得到了扩充。REDIportal提供了一个准确、可持续且易于访问的工具，该工具与诸如Ensembl、RNAcentral、UniProt和PRIDE等广泛的ELIXIR核心资源相互关联。此外，REDIportal现在包括有关假定双链RNA中RNA编辑的信息，这与编辑的免疫相关作用有关，以及一个扩展的重新编码事件目录。最后，我们报告了使用深度学习模型计算的每个位点的可靠性得分，该模型使用大量正负实例进行训练。可通过http://srv00.recas.ba.infn.it/atlas/访问REDIportal。
