{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T18:03:11Z","timestamp":1776362591281,"version":"3.51.2"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2018,11,5]],"date-time":"2018-11-05T00:00:00Z","timestamp":1541376000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007225","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["MOST 105-2311-B-006-004-MY3"],"award-info":[{"award-number":["MOST 105-2311-B-006-004-MY3"]}],"id":[{"id":"10.13039\/100007225","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,8]]},"DOI":"10.1093\/nar\/gky1081","type":"journal-article","created":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T07:26:10Z","timestamp":1540193170000},"page":"D1155-D1163","source":"Crossref","is-referenced-by-count":402,"title":["PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants"],"prefix":"10.1093","volume":"47","author":[{"given":"Chi-Nga","family":"Chow","sequence":"first","affiliation":[{"name":"Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan"}]},{"given":"Tzong-Yi","family":"Lee","sequence":"additional","affiliation":[{"name":"School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China"}]},{"given":"Yu-Cheng","family":"Hung","sequence":"additional","affiliation":[{"name":"Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan"}]},{"given":"Guan-Zhen","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan"}]},{"given":"Kuan-Chieh","family":"Tseng","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan"}]},{"given":"Ya-Hsin","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan"}]},{"given":"Po-Li","family":"Kuo","sequence":"additional","affiliation":[{"name":"Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan"}]},{"given":"Han-Qin","family":"Zheng","sequence":"additional","affiliation":[{"name":"Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan"}]},{"given":"Wen-Chi","family":"Chang","sequence":"additional","affiliation":[{"name":"Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan"},{"name":"Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan"},{"name":"Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan"}]}],"member":"286","published-online":{"date-parts":[[2018,11,5]]},"reference":[{"key":"key\n\t\t\t\t2019010803580712300_B1","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1016\/j.cell.2016.04.038","article-title":"Cistrome and epicistrome features shape the regulatory DNA landscape","volume":"165","author":"O\u2019Malley","year":"2016","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803580712300_B2","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1016\/j.cell.2014.08.009","article-title":"Determination and inference of eukaryotic transcription factor sequence specificity","volume":"158","author":"Weirauch","year":"2014","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803580712300_B3","doi-asserted-by":"crossref","first-page":"2015","DOI":"10.1016\/j.celrep.2014.08.019","article-title":"Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana","volume":"8","author":"Sullivan","year":"2014","journal-title":"Cell Rep."},{"key":"key\n\t\t\t\t2019010803580712300_B4","doi-asserted-by":"crossref","first-page":"D658","DOI":"10.1093\/nar\/gkw983","article-title":"Cistrome data browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse","volume":"45","author":"Mei","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B5","doi-asserted-by":"crossref","first-page":"D267","DOI":"10.1093\/nar\/gkx1092","article-title":"ReMap 2018: An updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments","volume":"46","author":"Cheneby","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B6","doi-asserted-by":"crossref","first-page":"D171","DOI":"10.1093\/nar\/gks1221","article-title":"Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium","volume":"41","author":"Wang","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B7","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkw951","article-title":"GTRD: A database of transcription factor binding sites identified by ChIP-seq experiments","volume":"45","author":"Yevshin","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B8","doi-asserted-by":"crossref","first-page":"D1040","DOI":"10.1093\/nar\/gkw982","article-title":"PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants","volume":"45","author":"Jin","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B9","doi-asserted-by":"crossref","first-page":"D43","DOI":"10.1093\/nar\/gkw965","article-title":"ChIPBase v2.0: Decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data","volume":"45","author":"Zhou","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B10","doi-asserted-by":"crossref","first-page":"372","DOI":"10.12688\/f1000research.10041.1","article-title":"Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data [version 1; referees: 2 approved, 1 approved with reservations]","volume":"6","author":"Aghamirzaie","year":"2017","journal-title":"F1000Research"},{"key":"key\n\t\t\t\t2019010803580712300_B11","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.cell.2013.12.027","article-title":"Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors","volume":"156","author":"Boer","year":"2014","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803580712300_B12","doi-asserted-by":"crossref","first-page":"6726","DOI":"10.1093\/nar\/gku269","article-title":"DNA-protein pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar","volume":"42","author":"Wilson","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B13","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.tplants.2004.12.010","article-title":"NAC transcription factors: structurally distinct, functionally diverse","volume":"10","author":"Olsen","year":"2005","journal-title":"Trends Plant Sci."},{"key":"key\n\t\t\t\t2019010803580712300_B14","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B15","first-page":"D271","article-title":"The RCSB protein data bank: Integrative view of protein, gene and 3D structural information","volume":"45","author":"Rose","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B16","doi-asserted-by":"crossref","first-page":"4062","DOI":"10.1073\/pnas.0711034105","article-title":"Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway","volume":"105","author":"Taketa","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t2019010803580712300_B17","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.bbagrm.2016.08.005","article-title":"Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families","volume":"1860","author":"Lehti-Shiu","year":"2017","journal-title":"Biochim. Biophys. Acta"},{"key":"key\n\t\t\t\t2019010803580712300_B18","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.1105\/tpc.17.00073","article-title":"ePlant: visualizing and exploring multiple levels of data for hypothesis generation in plant biology","volume":"29","author":"Waese","year":"2017","journal-title":"Plant Cell"},{"key":"key\n\t\t\t\t2019010803580712300_B19","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene expression omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B20","doi-asserted-by":"crossref","first-page":"D54","DOI":"10.1093\/nar\/gkr854","article-title":"The sequence read archive: explosive growth of sequencing data","volume":"40","author":"Kodama","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B21","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"key\n\t\t\t\t2019010803580712300_B22","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t2019010803580712300_B23","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803580712300_B24","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1038\/nbt.1508","article-title":"Design and analysis of ChIP-seq experiments for DNA-binding proteins","volume":"26","author":"Kharchenko","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t2019010803580712300_B25","doi-asserted-by":"crossref","first-page":"i225","DOI":"10.1093\/bioinformatics\/btx243","article-title":"Denoising genome-wide histone ChIP-seq with convolutional neural networks","volume":"33","author":"Koh","year":"2017","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803580712300_B26","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t2019010803580712300_B27","doi-asserted-by":"crossref","first-page":"1696","DOI":"10.1093\/bioinformatics\/btr189","article-title":"MEME-ChIP: Motif analysis of large DNA datasets","volume":"27","author":"Machanick","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803580712300_B28","doi-asserted-by":"crossref","first-page":"baw014","DOI":"10.1093\/database\/baw014","article-title":"HistoneDB 2.0: A histone database with variants\u2013an integrated resource to explore histones and their variants","volume":"2016","author":"Draizen","year":"2016","journal-title":"Database (Oxford)"},{"key":"key\n\t\t\t\t2019010803580712300_B29","doi-asserted-by":"crossref","first-page":"D1154","DOI":"10.1093\/nar\/gkv1035","article-title":"PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants","volume":"44","author":"Chow","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B30","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: A hub for protein information","volume":"43","author":"UniProt Consortium","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B31","doi-asserted-by":"crossref","first-page":"D234","DOI":"10.1093\/nar\/gku1203","article-title":"InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic","volume":"43","author":"Sonnhammer","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B32","doi-asserted-by":"crossref","first-page":"2040","DOI":"10.1093\/bioinformatics\/btx120","article-title":"ProtVista: visualization of protein sequence annotations","volume":"33","author":"Watkins","year":"2017","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803580712300_B33","doi-asserted-by":"crossref","first-page":"D117","DOI":"10.1093\/nar\/gku1045","article-title":"UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein\u2013DNA interactions","volume":"43","author":"Hume","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B34","doi-asserted-by":"crossref","first-page":"3576","DOI":"10.1093\/nar\/gkg585","article-title":"MATCH: a tool for searching transcription factor binding sites in DNA sequences","volume":"31","author":"Kel","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B35","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: a next-generation genome browser","volume":"19","author":"Skinner","year":"2009","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010803580712300_B36","doi-asserted-by":"crossref","first-page":"D1229","DOI":"10.1093\/nar\/gkt1064","article-title":"CottonGen: a genomics, genetics and breeding database for cotton research","volume":"42","author":"Yu","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B37","doi-asserted-by":"crossref","first-page":"D802","DOI":"10.1093\/nar\/gkx1011","article-title":"Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species","volume":"46","author":"Kersey","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B38","doi-asserted-by":"crossref","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: a comparative platform for green plant genomics","volume":"40","author":"Goodstein","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B39","doi-asserted-by":"crossref","first-page":"D1036","DOI":"10.1093\/nar\/gku1195","article-title":"The Sol Genomics Network (SGN)\u2013from genotype to phenotype to breeding","volume":"43","author":"Fernandez-Pozo","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B40","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1002\/dvg.22877","article-title":"The Arabidopsis information resource: Making and mining the \u201cgold standard\u201d annotated reference plant genome","volume":"53","author":"Berardini","year":"2015","journal-title":"Genesis"},{"key":"key\n\t\t\t\t2019010803580712300_B41","doi-asserted-by":"crossref","first-page":"D1181","DOI":"10.1093\/nar\/gkx1111","article-title":"Gramene 2018: unifying comparative genomics and pathway resources for plant research","volume":"46","author":"Tello-Ruiz","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B42","doi-asserted-by":"crossref","first-page":"D843","DOI":"10.1093\/nar\/gkp798","article-title":"SoyBase, the USDA-ARS soybean genetics and genomics database","volume":"38","author":"Grant","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803580712300_B43","doi-asserted-by":"crossref","first-page":"R41","DOI":"10.1186\/gb-2014-15-3-r41","article-title":"Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development","volume":"15","author":"Pajoro","year":"2014","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t2019010803580712300_B44","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1104\/pp.112.202614","article-title":"Characterization of SOC1\u2019s central role in flowering by the identification of its upstream and downstream regulators","volume":"160","author":"Immink","year":"2012","journal-title":"Plant Physiol."},{"key":"key\n\t\t\t\t2019010803580712300_B45","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/nrg3291","article-title":"The genetic basis of flowering responses to seasonal cues","volume":"13","author":"Andres","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t2019010803580712300_B46","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1186\/s12864-015-1952-z","article-title":"Comprehensive analysis of the endoplasmic reticulum stress response in the soybean genome: Conserved and plant-specific features","volume":"16","author":"Silva","year":"2015","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t2019010803580712300_B47","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1111\/j.1467-7652.2008.00336.x","article-title":"Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants","volume":"6","author":"Zhou","year":"2008","journal-title":"Plant Biotechnol. J."},{"key":"key\n\t\t\t\t2019010803580712300_B48","doi-asserted-by":"crossref","first-page":"e222","DOI":"10.1371\/journal.pbio.0050222","article-title":"The circadian clock regulates auxin signaling and responses in Arabidopsis","volume":"5","author":"Covington","year":"2007","journal-title":"PLoS Biol."},{"key":"key\n\t\t\t\t2019010803580712300_B49","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1007\/s11103-016-0477-4","article-title":"Circadian regulation of hormone signaling and plant physiology","volume":"91","author":"Atamian","year":"2016","journal-title":"Plant Mol. Biol."},{"key":"key\n\t\t\t\t2019010803580712300_B50","doi-asserted-by":"crossref","first-page":"16883","DOI":"10.1073\/pnas.0813035106","article-title":"REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways","volume":"106","author":"Rawat","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t2019010803580712300_B51","doi-asserted-by":"crossref","first-page":"D1157","DOI":"10.1093\/nar\/gkx919","article-title":"PCSD: A plant chromatin state database","volume":"46","author":"Liu","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/D1\/D1155\/27437370\/gky1081.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,27]],"date-time":"2019-10-27T08:09:36Z","timestamp":1572163776000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/D1\/D1155\/5160978"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,11,5]]},"references-count":51,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2018,11,5]]},"published-print":{"date-parts":[[2019,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky1081","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,1,8]]},"published":{"date-parts":[[2018,11,5]]}}}