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Numerous databases that collate m$^{6}$A profiles of distinct cell types have been created to facilitate quick and easy mining of m$^{6}$A signatures associated with cell-specific phenotypes. However, these databases contain inherent complexities that have not been explicitly reported, which may lead to inaccurate identification and interpretation of m$^{6}$A-associated biology by end-users who are unaware of them. Here, we review various m$^{6}$A-related databases, and highlight several critical matters. In particular, differences in peak-calling pipelines across databases drive substantial variability in both peak number and coordinates with only moderate reproducibility, and the inclusion of peak calls from early m$^{6}$A sequencing protocols may lead to the reporting of false positives or negatives. The awareness of these matters will help end-users avoid the inclusion of potentially unreliable data in their studies and better utilize m$^{6}$A databases to derive biologically meaningful results.<\/jats:p>","DOI":"10.1093\/bib\/bbae434","type":"journal-article","created":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T11:27:33Z","timestamp":1726054053000},"source":"Crossref","is-referenced-by-count":2,"title":["Variable calling of m6A and associated features in databases: a guide for end-users"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8228-7281","authenticated-orcid":false,"given":"Renhua","family":"Song","sequence":"first","affiliation":[{"name":"Epigenetics and RNA Biology Laboratory , School of Medical Sciences, , Camperdown, NSW 2050,","place":["Australia"]},{"name":"The University of Sydney , School of Medical Sciences, , Camperdown, NSW 2050,","place":["Australia"]},{"name":"Faculty of Medicine and Health, The University of Sydney , Camperdown, NSW 2050,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5266-8772","authenticated-orcid":false,"given":"Gavin","family":"J Sutton","sequence":"additional","affiliation":[{"name":"Epigenetics and RNA Biology Laboratory , School of Medical Sciences, , Camperdown, NSW 2050,","place":["Australia"]},{"name":"The University of Sydney , School of Medical Sciences, , Camperdown, NSW 2050,","place":["Australia"]},{"name":"Faculty of Medicine and Health, The University of Sydney , Camperdown, NSW 2050,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5216-3213","authenticated-orcid":false,"given":"Fuyi","family":"Li","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Northwest A&F University , Yangling 712100, Shaanxi,","place":["China"]},{"name":"South Australian immunoGENomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6737-4969","authenticated-orcid":false,"given":"Qian","family":"Liu","sequence":"additional","affiliation":[{"name":"Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas , Maryland Pkwy, NV 89154,","place":["United States"]},{"name":"School of Life Sciences , College of Sciences, , Maryland Pkwy, NV 89154,","place":["United States"]},{"name":"University of Nevada, Las Vegas , College of Sciences, , Maryland Pkwy, NV 89154,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7038-5079","authenticated-orcid":false,"given":"Justin J-L","family":"Wong","sequence":"additional","affiliation":[{"name":"Epigenetics and RNA Biology Laboratory , School of Medical Sciences, , Camperdown, NSW 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