TY - JOUR
T1 - REDIportal
T2 - Toward an integrated view of the A-To-I editing
AU - D'Addabbo, Pietro
AU - Cohen-Fultheim, Roni
AU - Twersky, Itamar
AU - Fonzino, Adriano
AU - Silvestris, Domenico Alessandro
AU - Prakash, Ananth
AU - Mazzacuva, Pietro Luca
AU - Vizcaino, Juan Antonio
AU - Green, Andrew
AU - Sweeney, Blake
AU - Yates, Andy
AU - Lussi, Yvonne
AU - Luo, Jie
AU - Martin, Maria Jesus
AU - Eisenberg, Eli
AU - Levanon, Erez Y.
AU - Pesole, Graziano
AU - Picardi, Ernesto
N1 - Publisher Copyright:
© 2025 The Author(s) 2024.
PY - 2025/1/6
Y1 - 2025/1/6
N2 - 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/.
AB - 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/.
UR - http://www.scopus.com/inward/record.url?scp=85212437498&partnerID=8YFLogxK
U2 - 10.1093/nar/gkae1083
DO - 10.1093/nar/gkae1083
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C2 - 39588754
AN - SCOPUS:85212437498
SN - 0305-1048
VL - 53
SP - D233-D242
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -