{"doi":"10.1093/nar/gkac969","title":"MethBank 4.0: an updated database of DNA methylation across a variety of species","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>DNA methylation, as the most intensively studied epigenetic mark, regulates gene expression in numerous biological processes including development, aging, and disease. With the rapid accumulation of whole-genome bisulfite sequencing data, integrating, archiving, analyzing, and visualizing those data becomes critical. Since its first publication in 2015, MethBank has been continuously updated to include more DNA methylomes across more diverse species. Here, we present MethBank 4.0 (https://ngdc.cncb.ac.cn/methbank/), which reports an increase of 309% in data volume, with 1449 single-base resolution methylomes of 23 species, covering 236 tissues/cell lines and 15 biological contexts. Value-added information, such as more rigorous quality evaluation, more standardized metadata, and comprehensive downstream annotations have been integrated in the new version. Moreover, expert-curated knowledge modules of featured differentially methylated genes associated with biological contexts and methylation analysis tools have been incorporated as new components of MethBank. In addition, MethBank 4.0 is equipped with a series of new web interfaces to browse, search, and visualize DNA methylation profiles and related information. With all these improvements, we believe the updated MethBank 4.0 will serve as a fundamental resource to provide a wide range of data services for the global research community.</jats:p>","journal":"Nucleic Acids Research","year":2023,"id":650251,"datarank":0.5101796072493234,"base_score":3.4011973816621555,"endowment":3.4011973816621555,"self_citation_contribution":0.5101796072493234,"citation_network_contribution":0.0,"self_endowment_contribution":0.5101796072493234,"citer_contribution":0.0,"corpus_percentile":62.6,"corpus_rank":5092,"citation_count":29,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1695427,"name":"Wenting Zong","orcid":"0000-0003-1834-9684","position":1,"is_corresponding":false},{"id":1658339,"name":"Dong Zou","orcid":null,"position":2,"is_corresponding":false},{"id":1058770,"name":"Guoliang Wang","orcid":"0000-0002-9191-6166","position":3,"is_corresponding":false},{"id":525139,"name":"Wei Zhao","orcid":"0000-0001-9437-3198","position":4,"is_corresponding":false},{"id":719435,"name":"Fei Yang","orcid":"0000-0002-6965-8447","position":5,"is_corresponding":false},{"id":232519,"name":"Song Wu","orcid":"0000-0003-3504-1630","position":6,"is_corresponding":false},{"id":1120074,"name":"Xinran Zhang","orcid":"0009-0003-4982-1694","position":7,"is_corresponding":false},{"id":1169805,"name":"Xutong Guo","orcid":"0000-0002-3614-4298","position":8,"is_corresponding":false},{"id":1519039,"name":"Yingke Ma","orcid":"0000-0002-9460-4117","position":9,"is_corresponding":false},{"id":1693825,"name":"Zhuang Xiong","orcid":"0000-0001-8360-9417","position":10,"is_corresponding":false},{"id":50353,"name":"Zhang Zhang","orcid":"0000-0001-6603-5060","position":11,"is_corresponding":false},{"id":752,"name":"Yiming Bao","orcid":null,"position":12,"is_corresponding":false},{"id":1695428,"name":"Rujiao Li","orcid":null,"position":13,"is_corresponding":false},{"id":1169808,"name":"Mochen Zhang","orcid":"0000-0001-9136-451X","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"MethBank 4.0: an updated database of DNA methylation across a variety of species","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>DNA methylation, as the most intensively studied epigenetic mark, regulates gene expression in numerous biological processes including development, aging, and disease. With the rapid accumulation of whole-genome bisulfite sequencing data, integrating, archiving, analyzing, and visualizing those data becomes critical. Since its first publication in 2015, MethBank has been continuously updated to include more DNA methylomes across more diverse species. Here, we present MethBank 4.0 (https://ngdc.cncb.ac.cn/methbank/), which reports an increase of 309% in data volume, with 1449 single-base resolution methylomes of 23 species, covering 236 tissues/cell lines and 15 biological contexts. Value-added information, such as more rigorous quality evaluation, more standardized metadata, and comprehensive downstream annotations have been integrated in the new version. Moreover, expert-curated knowledge modules of featured differentially methylated genes associated with biological contexts and methylation analysis tools have been incorporated as new components of MethBank. In addition, MethBank 4.0 is equipped with a series of new web interfaces to browse, search, and visualize DNA methylation profiles and related information. With all these improvements, we believe the updated MethBank 4.0 will serve as a fundamental resource to provide a wide range of data services for the global research community.</jats:p>","is_dataset_classified":null,"base_score":3.4011973816621555,"endowment":3.4011973816621555,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"36318250","pmcid":"PMC9825483","openalex_id":"https://openalex.org/W4307844551","authors":[],"funders":[{"funder_name":"National Key Research and Development Program of China","grant_id":"2021YFF0703704","title":null},{"funder_name":"Strategic Priority Research Program of the Chinese Academy of Sciences","grant_id":"XDB38030200","title":null},{"funder_name":"Strategic Priority Research Program of the Chinese Academy of Sciences","grant_id":"XDB38030100","title":null},{"funder_name":"Genomics Data Center Construction of Chinese Academy of Sciences","grant_id":"WX145XQ07-04","title":null},{"funder_name":"Professional Association of the Alliance of International Science Organizations","grant_id":"ANSO-PA-2020–07","title":null}],"total_grants":5,"fwci":1.4107,"citation_percentile":0.81326865,"influential_citations":1,"citation_trend":[{"year":2022,"count":2},{"year":2023,"count":3},{"year":2024,"count":5},{"year":2025,"count":8},{"year":2026,"count":11}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/51/D1/D208/48441017/gkac969.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/51/D1/D208/48441017/gkac969.pdf","host_type":"GOLD"},{"url":"https://academic.oup.com/nar/article-pdf/51/D1/D208/48441017/gkac969.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkac969","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/36318250","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825483","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC9825483","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9825483?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Epigenetics and DNA Methylation","Cancer-related gene regulation","RNA modifications and cancer","Computer Science","Medicine","Biology","Environmental Science"],"mesh_terms":["Whole Genome Sequencing","Epigenome","Databases, Factual","Sequence Analysis, DNA","DNA Methylation","Databases, Genetic","Epigenomics"],"keywords":["Biology","DNA methylation","Computational biology","Methylation","Metadata","Epigenetics","DNA","Database","Genetics","Gene","World Wide Web","Computer science","Gene expression"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-10T05:08:46.043455Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}