ArticleNucleic acids research2016
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 195 papers, 1 of them a synthesis that pooled it.
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195 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach.PloS one · 2019Pooled it
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- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Transgenic validation of a promoter strongly inducible by Agrobacterium tumefaciens.Scientific reports · 2025Article
- Fine-tuning wheat development for the winter to spring transition.Plant communications · 2025Article
- Characterization of the VOC Promoter That Is Active Under Low-Salinity Conditions in the DiatomMarine drugs · 2025Article
- Promoter of Vegetable PeaInternational journal of molecular sciences · 2024Article
- Identification of CAP genes in finger lime (Citrus australasica) and their role in plant responses to abiotic and biotic stress.Scientific reports · 2024Article
- SUMOylation of rice DELLA SLR1 modulates transcriptional responses and improves yield under salt stress.Planta · 2024Article
- Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean.BMC genomics · 2024Article
- Genetic variability of aquaporin expression in maize: From eQTLs to a MITE insertion regulating PIP2;5 expression.Plant physiology · 2024Article
- Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages.Molecular biology reports · 2024Article
- The Putative GATA Transcription FactorLife (Basel, Switzerland) · 2024Article
- Pungency related gene network in Allium sativum L., response to sulfur treatments.BMC genomic data · 2024Article
- Isolation and Functional Characterization of a Constitutive Promoter in Upland Cotton (International journal of molecular sciences · 2024Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- A telomere-to-telomere reference genome of ficus (Horticulture research · 2024Article
- Pectin methylesterase 31 is transcriptionally repressed by ABI5 to negatively regulate ABA-mediated inhibition of seed germination.Frontiers in plant science · 2024Article
- Comprehensive analysis of transcription factor binding sites and expression profiling of rice pathogenesis related genes (Frontiers in plant science · 2024Article
135 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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