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Here, we described a database, IEAtlas (http:\/\/bio-bigdata.hrbmu.edu.cn\/IEAtlas), which aims to provide and visualize the comprehensive atlas of human leukocyte antigen (HLA)-presented immunogenic epitopes derived from non-coding regions. IEAtlas reanalyzed publicly available mass spectrometry-based HLA immunopeptidome datasets against our integrated benchmarked non-canonical open reading frame information. The current IEAtlas identified 245 870 non-canonical epitopes binding to HLA-I\/II allotypes across 15 cancer types and 30 non-cancerous tissues, greatly expanding the cancer immunopeptidome. IEAtlas further evaluates the immunogenicity via several commonly used immunogenic features, including HLA binding affinity, stability and T-cell receptor recognition. In addition, IEAtlas provides the biochemical properties of epitopes as well as the clinical relevance of corresponding genes across major cancer types and normal tissues. Several flexible tools were also developed to aid retrieval and to analyze the epitopes derived from non-coding regions. Overall, IEAtlas will serve as a valuable resource for investigating the immunogenic capacity of non-canonical epitopes and the potential as therapeutic cancer vaccines.<\/jats:p>","DOI":"10.1093\/nar\/gkac776","type":"journal-article","created":{"date-parts":[[2022,9,13]],"date-time":"2022-09-13T18:35:21Z","timestamp":1663094121000},"page":"D409-D417","source":"Crossref","is-referenced-by-count":32,"title":["IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions"],"prefix":"10.1093","volume":"51","author":[{"given":"Yangyang","family":"Cai","sequence":"first","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]},{"given":"Dezhong","family":"Lv","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]},{"given":"Donghao","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]},{"given":"Jiaqi","family":"Yin","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]},{"given":"Yingying","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]},{"given":"Ya","family":"Luo","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]},{"given":"Limei","family":"Fu","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]},{"given":"Na","family":"Ding","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6047-9592","authenticated-orcid":false,"given":"Yongsheng","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University , Haikou , Hainan \u00a0571199,\u00a0 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1011-0954","authenticated-orcid":false,"given":"Zhenwei","family":"Pan","sequence":"additional","affiliation":[{"name":"Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin , Heilongjiang \u00a0150086,\u00a0 China"},{"name":"NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University , Harbin , Heilongjiang \u00a0150001,\u00a0 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9794-2648","authenticated-orcid":false,"given":"Xia","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"},{"name":"Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University , Haikou , Hainan \u00a0571199,\u00a0 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3709-4165","authenticated-orcid":false,"given":"Juan","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin , Heilongjiang \u00a0150081,\u00a0 China"}]}],"member":"286","published-online":{"date-parts":[[2022,9,13]]},"reference":[{"key":"2023010804181334800_B1","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1016\/j.ccell.2020.07.013","article-title":"Identifying and targeting human tumor antigens for T cell-based immunotherapy of solid tumors","volume":"38","author":"Leko","year":"2020","journal-title":"Cancer Cell"},{"key":"2023010804181334800_B2","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1038\/s41587-021-01038-8","article-title":"Identification of tumor antigens with immunopeptidomics","volume":"40","author":"Chong","year":"2022","journal-title":"Nat. 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