title: PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.
abstract: Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands and tandem repeats) in a promoter or a set of plant promoters. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between similar gene promoters are also identified. The current PlantPAN release (version 2.0) contains 16 960 TFs and 1143 TF binding site matrices among 76 plant species. In addition to updating of the annotation information, adding experimentally verified TF matrices, and making improvements in the visualization of transcriptional regulatory networks, several new features and functions are incorporated. These features include: (i) comprehensive curation of TF information (response conditions, target genes, and sequence logos of binding motifs, etc.), (ii) co-expression profiles of TFs and their target genes under various conditions, (iii) protein-protein interactions among TFs and their co-factors, (iv) TF-target networks, and (v) downstream promoter elements. Furthermore, a dynamic transcriptional regulatory network under various conditions is provided in PlantPAN 2.0. The PlantPAN 2.0 is a systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.
authors.affiliation: College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Chi-Nga
authors.initials: CN
authors.lastname: Chow
authors.affiliation: College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Han-Qin
authors.initials: HQ
authors.lastname: Zheng
authors.affiliation: College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Nai-Yun
authors.initials: NY
authors.lastname: Wu
authors.affiliation: College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Chia-Hung
authors.initials: CH
authors.lastname: Chien
authors.affiliation: Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
authors.affiliation: Department of Computer Science and Engineering, Yuan Ze University, Chung-Li 320, Taiwan.
authors.forename: Tzong-Yi
authors.initials: TY
authors.lastname: Lee
authors.affiliation: College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Yi-Fan
authors.initials: YF
authors.lastname: Chiang-Hsieh
authors.affiliation: College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan College of Biosciences and Biotechnology, Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Ping-Fu
authors.initials: PF
authors.lastname: Hou
authors.affiliation: College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Tien-Yi
authors.initials: TY
authors.lastname: Yang
authors.affiliation: College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan sarah321@mail.ncku.edu.tw.
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Chang
mesh_terms: D001665:Binding Sites; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000378:metabolism; D010944:Plants / Q000235:genetics*; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors