TY - JOUR
T1 - PlantPAN 2.0
T2 - An update of Plant Promoter Analysis Navigator for reconstructing transcriptional regulatory networks in plants
AU - Chow, Chi Nga
AU - Zheng, Han Qin
AU - Wu, Nai Yun
AU - Chien, Chia Hung
AU - Huang, Hsien Da
AU - Lee, Tzong Yi
AU - Chiang-Hsieh, Yi Fan
AU - Hou, Ping Fu
AU - Yang, Tien Yi
AU - Chang, Wen Chi
N1 - Funding Information:
Ministry of Science and Technology [MOST 103-2311-B-006-001, MOST 104-2627-M-009-008, MOST 103-2628-B-009-001-MY3, MOST 104-2319-B-400-002 and MOST 103-2911-I-009-101]; Academia Sinica [Innovative Translational Agricultural Research Grant] of the Republic of China. Funding for open access charge: Academia Sinica [Innovative Translational Agricultural Research Grant]. Conflict of interest statement. None declared.
Publisher Copyright:
© The Author(s) 2015.
PY - 2016
Y1 - 2016
N2 - 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 PlantPANrelease (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) TFtarget 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.
AB - 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 PlantPANrelease (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) TFtarget 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.
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U2 - 10.1093/nar/gkv1035
DO - 10.1093/nar/gkv1035
M3 - Article
C2 - 26476450
AN - SCOPUS:84976899061
SN - 0305-1048
VL - 44
SP - D1154-D1164
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -