{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T12:08:38Z","timestamp":1778501318079,"version":"3.51.4"},"reference-count":40,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,11,8]],"date-time":"2019-11-08T00:00:00Z","timestamp":1573171200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["1470330"],"award-info":[{"award-number":["1470330"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"China 863 Program","award":["2015AA020108"],"award-info":[{"award-number":["2015AA020108"]}]},{"DOI":"10.13039\/501100011253","name":"State Key Laboratory of Protein and Plant Gene Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011253","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2014M560017"],"award-info":[{"award-number":["2014M560017"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2015T80015"],"award-info":[{"award-number":["2015T80015"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Peking University and Peking-Tsinghua Center for Life Sciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>With the goal of charting plant transcriptional regulatory maps (i.e.\u00a0transcription factors (TFs), cis-elements and interactions between them), we have upgraded the TF-centred database PlantTFDB (http:\/\/planttfdb.cbi.pku.edu.cn\/) to a plant regulatory data and analysis platform PlantRegMap (http:\/\/plantregmap.cbi.pku.edu.cn\/) over the past three years. In this version, we updated the annotations for the previously collected TFs and set up a new section, \u2018extended TF repertoires\u2019 (TFext), to allow users prompt access to the TF repertoires of newly sequenced species. In addition to our regular TF updates, we are dedicated to updating the data on cis-elements and functional interactions between TFs and cis-elements. We established genome-wide conservation landscapes for 63 representative plants and then developed an algorithm, FunTFBS, to screen for functional regulatory elements and interactions by coupling the base-varied binding affinities of TFs with the evolutionary footprints on their binding sites. Using the FunTFBS algorithm and the conservation landscapes, we further identified over 20 million functional TF binding sites (TFBSs) and two million functional interactions for 21 346 TFs, charting the functional regulatory maps of these 63 plants. These resources are publicly available at PlantRegMap (http:\/\/plantregmap.cbi.pku.edu.cn\/) and a cloud-based mirror (http:\/\/plantregmap.gao-lab.org\/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems.<\/jats:p>","DOI":"10.1093\/nar\/gkz1020","type":"journal-article","created":{"date-parts":[[2019,10,21]],"date-time":"2019-10-21T15:20:39Z","timestamp":1571671239000},"source":"Crossref","is-referenced-by-count":333,"title":["PlantRegMap: charting functional regulatory maps in plants"],"prefix":"10.1093","author":[{"given":"Feng","family":"Tian","sequence":"first","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing\u00a0100871, China"},{"name":"Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing\u00a0100871, China"},{"name":"Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"}]},{"given":"De-Chang","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing\u00a0100871, China"},{"name":"Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing\u00a0100871, China"}]},{"given":"Yu-Qi","family":"Meng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing\u00a0100871, China"},{"name":"Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing\u00a0100871, China"}]},{"given":"Jinpu","family":"Jin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing\u00a0100871, China"},{"name":"Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing\u00a0100871, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6470-8815","authenticated-orcid":false,"given":"Ge","family":"Gao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing\u00a0100871, China"},{"name":"Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing\u00a0100871, China"}]}],"member":"286","published-online":{"date-parts":[[2019,11,8]]},"reference":[{"key":"2019110802583051900_B1","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1038\/nature14099","article-title":"An Arabidopsis gene regulatory network for secondary cell wall synthesis","volume":"517","author":"Taylor-Teeples","year":"2015","journal-title":"Nature"},{"key":"2019110802583051900_B2","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/molbev\/msv058","article-title":"An arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors","volume":"32","author":"Jin","year":"2015","journal-title":"Mol. 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