{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T01:11:46Z","timestamp":1773796306148,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,2,3]],"date-time":"2021-02-03T00:00:00Z","timestamp":1612310400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Zhejiang Provincial Natural Science Foundation of China","award":["LQ20C060004"],"award-info":[{"award-number":["LQ20C060004"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["K20200099"],"award-info":[{"award-number":["K20200099"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Alibaba Cloud. J.J.L. is supported by the Sloan Research Fellowship, Johnson and Johnson WiSTEM2D Award"},{"name":"UCLA DGSOM W. M. Keck Foundation Junior Faculty Award"},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"crossref","award":["PJT-166169"],"award-info":[{"award-number":["PJT-166169"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>With the advance of genomic sequencing techniques, chromatin accessible regions, transcription factor binding sites and epigenetic modifications can be identified at genome-wide scale. Conventional analyses focus on the gene regulation at proximal regions; however, distal regions are usually less focused, largely due to the lack of reliable tools to link these regions to coding genes. In this study, we introduce RAD (Region Associated Differentially expressed genes), a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes (DEGs). With DEGs and genomic regions of interest (gROI) as input, RAD maps the up- and down-regulated genes associated with any gROI and helps researchers to infer the regulatory function of these regions based on the distance of gROI to differentially expressed genes. RAD includes visualization of the results and statistical inference for significance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>RAD is implemented with Python 3.7 and run on a Nginx server. RAD is freely available at https:\/\/labw.org\/rad as online web service.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab075","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T13:40:40Z","timestamp":1611841240000},"page":"2741-2743","source":"Crossref","is-referenced-by-count":20,"title":["RAD: a web application to identify region associated differentially expressed genes"],"prefix":"10.1093","volume":"37","author":[{"given":"Yixin","family":"Guo","sequence":"first","affiliation":[{"name":"Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine , Haining 314400, China"}]},{"given":"Ziwei","family":"Xue","sequence":"additional","affiliation":[{"name":"Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine , Haining 314400, China"}]},{"given":"Ruihong","family":"Yuan","sequence":"additional","affiliation":[{"name":"Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine , Haining 314400, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9288-5648","authenticated-orcid":false,"given":"Jingyi Jessica","family":"Li","sequence":"additional","affiliation":[{"name":"University of California Department of Statistics, , Los Angeles, CA 90095-1554, USA"}]},{"given":"William A.","family":"Pastor","sequence":"additional","affiliation":[{"name":"McGill University Department of Biochemistry, , Montreal, QC H3G 1Y6, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5963-2908","authenticated-orcid":false,"given":"Wanlu","family":"Liu","sequence":"additional","affiliation":[{"name":"Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine , Haining 314400, China"},{"name":"Zhejiang University Department of Orthopedic, The Second Affiliated Hospital of Zhejiang University School of Medicine, , Hangzhou 310029, China"},{"name":"Zhejiang University Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, , Hangzhou 310029, China"}]}],"member":"286","published-online":{"date-parts":[[2021,2,3]]},"reference":[{"key":"2023051609213685400_btab075-B1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2023051609213685400_btab075-B2","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.cell.2007.12.014","article-title":"High-resolution mapping and characterization of open chromatin across the genome","volume":"132","author":"Boyle","year":"2008","journal-title":"Cell"},{"key":"2023051609213685400_btab075-B3","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"Buenrostro","year":"2013","journal-title":"Nat. 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