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RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication
Recent advances in epitranscriptomics have unveiled functional associations between RNA modifications (RMs) and multiple human diseases, but distinguishing the functional or disease-related single nucleotide variants (SNVs) from the majority of ‘silent’ variants remains a major challenge. We previou...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825452/ https://www.ncbi.nlm.nih.gov/pubmed/36062570 http://dx.doi.org/10.1093/nar/gkac750 |
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author | Song, Bowen Wang, Xuan Liang, Zhanmin Ma, Jiongming Huang, Daiyun Wang, Yue de Magalhães, João Pedro Rigden, Daniel J Meng, Jia Liu, Gang Chen, Kunqi Wei, Zhen |
author_facet | Song, Bowen Wang, Xuan Liang, Zhanmin Ma, Jiongming Huang, Daiyun Wang, Yue de Magalhães, João Pedro Rigden, Daniel J Meng, Jia Liu, Gang Chen, Kunqi Wei, Zhen |
author_sort | Song, Bowen |
collection | PubMed |
description | Recent advances in epitranscriptomics have unveiled functional associations between RNA modifications (RMs) and multiple human diseases, but distinguishing the functional or disease-related single nucleotide variants (SNVs) from the majority of ‘silent’ variants remains a major challenge. We previously developed the RMDisease database for unveiling the association between genetic variants and RMs concerning human disease pathogenesis. In this work, we present RMDisease v2.0, an updated database with expanded coverage. Using deep learning models and from 873 819 experimentally validated RM sites, we identified a total of 1 366 252 RM-associated variants that may affect (add or remove an RM site) 16 different types of RNA modifications (m(6)A, m(5)C, m(1)A, m(5)U, Ψ, m(6)Am, m(7)G, A-to-I, ac(4)C, Am, Cm, Um, Gm, hm(5)C, D and f(5)C) in 20 organisms (human, mouse, rat, zebrafish, maize, fruit fly, yeast, fission yeast, Arabidopsis, rice, chicken, goat, sheep, pig, cow, rhesus monkey, tomato, chimpanzee, green monkey and SARS-CoV-2). Among them, 14 749 disease- and 2441 trait-associated genetic variants may function via the perturbation of epitranscriptomic markers. RMDisease v2.0 should serve as a useful resource for studying the genetic drivers of phenotypes that lie within the epitranscriptome layer circuitry, and is freely accessible at: www.rnamd.org/rmdisease2. |
format | Online Article Text |
id | pubmed-9825452 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98254522023-01-10 RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication Song, Bowen Wang, Xuan Liang, Zhanmin Ma, Jiongming Huang, Daiyun Wang, Yue de Magalhães, João Pedro Rigden, Daniel J Meng, Jia Liu, Gang Chen, Kunqi Wei, Zhen Nucleic Acids Res Database Issue Recent advances in epitranscriptomics have unveiled functional associations between RNA modifications (RMs) and multiple human diseases, but distinguishing the functional or disease-related single nucleotide variants (SNVs) from the majority of ‘silent’ variants remains a major challenge. We previously developed the RMDisease database for unveiling the association between genetic variants and RMs concerning human disease pathogenesis. In this work, we present RMDisease v2.0, an updated database with expanded coverage. Using deep learning models and from 873 819 experimentally validated RM sites, we identified a total of 1 366 252 RM-associated variants that may affect (add or remove an RM site) 16 different types of RNA modifications (m(6)A, m(5)C, m(1)A, m(5)U, Ψ, m(6)Am, m(7)G, A-to-I, ac(4)C, Am, Cm, Um, Gm, hm(5)C, D and f(5)C) in 20 organisms (human, mouse, rat, zebrafish, maize, fruit fly, yeast, fission yeast, Arabidopsis, rice, chicken, goat, sheep, pig, cow, rhesus monkey, tomato, chimpanzee, green monkey and SARS-CoV-2). Among them, 14 749 disease- and 2441 trait-associated genetic variants may function via the perturbation of epitranscriptomic markers. RMDisease v2.0 should serve as a useful resource for studying the genetic drivers of phenotypes that lie within the epitranscriptome layer circuitry, and is freely accessible at: www.rnamd.org/rmdisease2. Oxford University Press 2022-09-05 /pmc/articles/PMC9825452/ /pubmed/36062570 http://dx.doi.org/10.1093/nar/gkac750 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Issue Song, Bowen Wang, Xuan Liang, Zhanmin Ma, Jiongming Huang, Daiyun Wang, Yue de Magalhães, João Pedro Rigden, Daniel J Meng, Jia Liu, Gang Chen, Kunqi Wei, Zhen RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication |
title | RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication |
title_full | RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication |
title_fullStr | RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication |
title_full_unstemmed | RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication |
title_short | RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication |
title_sort | rmdisease v2.0: an updated database of genetic variants that affect rna modifications with disease and trait implication |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825452/ https://www.ncbi.nlm.nih.gov/pubmed/36062570 http://dx.doi.org/10.1093/nar/gkac750 |
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