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Experimental technologies have advanced to identify in vitro and in vivo rG4s across diverse transcriptomes. Building on these recent advances, here we present G4Atlas, the first transcriptome-wide G-quadruplex database, in which we have collated, classified, and visualized transcriptome rG4 experimental data, generated from rG4-seq, chemical profiling and ligand-binding methods. Our comprehensive database includes transcriptome-wide rG4s generated from 82 experimental treatments and 238 samples across ten species. In addition, we have also included RNA secondary structure prediction information across both experimentally identified and unidentified rG4s to enable users to display any potential competitive folding between rG4 and RNA secondary structures. As such, G4Atlas will enable users to explore the general functions of rG4s in diverse biological processes. In addition, G4Atlas lays the foundation for further data-driven deep learning algorithms to examine rG4 structural features.<\/jats:p>","DOI":"10.1093\/nar\/gkac896","type":"journal-article","created":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T10:06:56Z","timestamp":1665914816000},"page":"D126-D134","source":"Crossref","is-referenced-by-count":29,"title":["G4Atlas: a comprehensive transcriptome-wide G-quadruplex database"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5184-2430","authenticated-orcid":false,"given":"Haopeng","family":"Yu","sequence":"first","affiliation":[{"name":"Department of Cell and Developmental Biology , John Innes Centre, Norwich Research Park, Norwich \u00a0NR4 7UH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiman","family":"Qi","sequence":"additional","affiliation":[{"name":"Department of Cell and Developmental Biology , John Innes Centre, Norwich Research Park, Norwich \u00a0NR4 7UH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bibo","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Cell and Developmental Biology , John Innes Centre, Norwich Research Park, Norwich \u00a0NR4 7UH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaofei","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Cell and Developmental Biology , John Innes Centre, Norwich Research Park, Norwich \u00a0NR4 7UH, UK"},{"name":"National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai ,\u00a0 China"},{"name":"CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai ,\u00a0 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4161-6365","authenticated-orcid":false,"given":"Yiliang","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Cell and Developmental Biology , John Innes Centre, Norwich Research Park, Norwich \u00a0NR4 7UH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,16]]},"reference":[{"key":"2023010804324881100_B1","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/nrg3681","article-title":"Insights into RNA structure and function from genome-wide studies","volume":"15","author":"Mortimer","year":"2014","journal-title":"Nat. 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Plant Sci."},{"key":"2023010804324881100_B5","doi-asserted-by":"crossref","first-page":"2908","DOI":"10.1093\/nar\/gki609","article-title":"Prevalence of quadruplexes in the human genome","volume":"33","author":"Huppert","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023010804324881100_B6","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s13059-020-02142-9","article-title":"RNA G-quadruplex structures exist and function in vivo in plants","volume":"21","author":"Yang","year":"2020","journal-title":"Genome Biol."},{"key":"2023010804324881100_B7","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1038\/nmeth.3965","article-title":"rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome","volume":"13","author":"Kwok","year":"2016","journal-title":"Nat. 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