{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:07:15Z","timestamp":1792786035942,"version":"4.5.0"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,11,5]],"date-time":"2020-11-05T00:00:00Z","timestamp":1604534400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771460"],"award-info":[{"award-number":["31771460"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91629103"],"award-info":[{"award-number":["91629103"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2016YFC0902100"],"award-info":[{"award-number":["2016YFC0902100"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Health Commission","award":["2020YJZX0108"],"award-info":[{"award-number":["2020YJZX0108"]}]},{"name":"Clinical Research Plan of SHDC","award":["SHDC12018X01"],"award-info":[{"award-number":["SHDC12018X01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Gene regulatory networks (GRNs) formed by transcription factors (TFs) and their downstream target genes play essential roles in gene expression regulation. Moreover, GRNs can be dynamic changing across different conditions, which are crucial for understanding the underlying mechanisms of disease pathogenesis. However, no existing database provides comprehensive GRN information for various human and mouse normal tissues and diseases at the single-cell level. Based on the known TF-target relationships and the large-scale single-cell RNA-seq data collected from public databases as well as the bulk data of The Cancer Genome Atlas and the Genotype-Tissue Expression project, we systematically predicted the GRNs of 184 different physiological and pathological conditions of human and mouse involving &amp;gt;633 000 cells and &amp;gt;27 700 bulk samples. We further developed GRNdb, a freely accessible and user-friendly database (http:\/\/www.grndb.com\/) for searching, comparing, browsing, visualizing, and downloading the predicted information of 77 746 GRNs, 19 687 841 TF-target pairs, and related binding motifs at single-cell\/bulk resolution. GRNdb also allows users to explore the gene expression profile, correlations, and the associations between expression levels and the patient survival of diverse cancers. Overall, GRNdb provides a valuable and timely resource to the scientific community to elucidate the functions and mechanisms of gene expression regulation in various conditions.<\/jats:p>","DOI":"10.1093\/nar\/gkaa995","type":"journal-article","created":{"date-parts":[[2020,10,13]],"date-time":"2020-10-13T08:32:32Z","timestamp":1602577952000},"page":"D97-D103","source":"Crossref","is-referenced-by-count":109,"title":["GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions"],"prefix":"10.1093","volume":"49","author":[{"given":"Li","family":"Fang","sequence":"first","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunjin","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Ma","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiyue","family":"Xu","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Tan","sequence":"additional","affiliation":[{"name":"Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai\u00a0200443, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3452-9434","authenticated-orcid":false,"given":"Geng","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China"},{"name":"Shanghai Applied Protein Technology Co., Ltd. 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