PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
| Autor: | Hsien Da Huang, Han Qin Zheng, Tzong-Yi Lee, Chi Nga Chow, Nai Yun Wu, Tien Yi Yang, Wen Chi Chang, Yi Fan Chiang-Hsieh, Chia Hung Chien, Ping Fu Hou |
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| Rok vydání: | 2015 |
| Předmět: |
0106 biological sciences
0301 basic medicine Transcription Genetic Gene regulatory network Biology 01 natural sciences 03 medical and health sciences Epigenetics of physical exercise Tandem repeat Gene Expression Regulation Plant Databases Genetic Genetics Database Issue Gene Regulatory Networks Promoter Regions Genetic Transcription factor Gene Plant Proteins Regulation of gene expression Binding Sites Molecular Sequence Annotation Promoter Plants DNA binding site 030104 developmental biology Transcription Factors 010606 plant biology & botany |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkv1035 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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