ArticleNucleic acids research2019
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 220 papers, 1 of them a synthesis that pooled it.
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Who cites it
220 citing papers in PubMed, 1 synthesis or guideline pooled it, 461 citations in OpenAlex.
- Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum.BMC genomics · 2022Pooled it
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- Circadian clock-related transcription factors Reveille 1 and Reveille 8 regulate the O-acetylserine cluster genes and sulfur homeostasis.Plant physiology · 2026Article
- Designing and testing CRISPRi-based synthetic gene circuits in plants.Nature protocols · 2026Review
- Nitrogen Status Rewires Transcriptional Regulation of Dhurrin, a Dual-Purpose Defense Metabolite inPlant direct · 2026Article
- Fruit-Specific Promoters in Plants: Advances, Regulatory Mechanisms and Applications in Plant Biotechnology.Plants (Basel, Switzerland) · 2026Review
- Article
- Loss-of-function of MIR172b and prime editing of SNB reveal a regulatory module underlying cleistogamy in rice.Plant physiology · 2026Article
- Genome wide identification, structural characterization, expression analysis, and regulatory network inferring of BAG gene family in barley.Scientific reports · 2026Article
- Haplotype-resolved genome assembly provides insights into the evolutionary origin of waterlogging-tolerantHorticulture research · 2026Article
- A transposon insertion in the 5' UTR of OsPT1 reprograms its expression pattern and promotes cadmium accumulation in rice grains.Plant communications · 2026Article
- Genome-wide identification of tomato B-RRs gene family and expression analysis in response to ABA and drought.PloS one · 2026Article
- Standardized Protocols and Bioinformatic Pipelines for Conducting DAP-seq Experiments in Non-model Plant Crops.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The bHLH transcription factor PIL1 orchestrates starch synthesis in key cereal crops.Nature communications · 2025Article
- Characterization of trehalose-6-phosphate synthase gene family in linseed (Linum usitatissimum L.) and its potential implications in flowering time regulation.BMC plant biology · 2025Article
- Evaluation of the Global White Lupin Collection Reveals Significant Associations Between HomologousInternational journal of molecular sciences · 2025Article
- Natural variation of AcEGY3 mediates chloroplastic ROS homeostasis to confer kiwifruit thermotolerance.Nature communications · 2025Article
- Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan.BMC plant biology · 2025Article
- Genome-wide identification of the cotton ANK gene family and functional study of GhANK169 in response to heat stress.BMC plant biology · 2025Article
- Harnessing promoter elements to enhance gene editing in plants: perspectives and advances.Plant biotechnology journal · 2025Review
160 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional regulatory networks for plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 plant species. To explore regulatory landscapes, genomic locations of TFBSs have been captured from 662 public ChIP-seq samples using standard data processing. A total of 1 233 999 regulatory linkages were identified from 99 regulatory factors (TFs, histones and other DNA-binding proteins) and their target genes across seven species. Additionally, this new version added 2449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. In addition to integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events, including (i) 1107 experimentally verified TF matrices from the literature, (ii) gene regulation network comparison between two species, (iii) 3D structures of TFs and TF-DNA complexes and (iv) condition-specific co-expression networks of TFs and their target genes extended to four species. The PlantPAN 3.0 can not only be efficiently used to investigate critical cis- and trans-regulatory elements in plant promoters, but also to reconstruct high-confidence relationships among TF-targets under specific conditions.
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