ArticleNucleic acids research2020
PlantRegMap: charting functional regulatory maps in plants.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 648 papers, 3 of them syntheses that pooled it.
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Who cites it
648 citing papers in PubMed, 3 syntheses or guidelines pooled it, 1,038 citations in OpenAlex.
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- Meta-analysis, WGCNA, and machine learning converge on a four-gene biomarker panel for heat stress tolerance in Solanum lycopersicum.Scientific reports · 2026Pooled it
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- Cross-species transcriptomics uncovers shared responses to water deficiency in plants.The plant genome · 2026Article
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- Signaling by a tyrosine-sulfated peptide balances growth and osmotic stress response in rice.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The miR167-ARF8 module coordinates stamen-pistil development and fruit set in tomato.The New phytologist · 2026Article
- Mutual antagonism between auxin and diacylglycerol acyltransferase 2 regulates high-temperature-induced hypocotyl elongation.The New phytologist · 2026Article
- Functional and regulatory complexity: challenges and prospects for understanding rice WRKY transcription factors.Journal of experimental botany · 2026Review
- Decoding the landscape of cell-type-specific co-expressed transcription factors in soybean.Nature plants · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Comprehensive Characterization of Cytochrome P450s Reveals Candidate Enzymes Involved in the Metabolic Fate of Absorbed Volatile Organic Compounds in Potato.Antioxidants (Basel, Switzerland) · 2026Article
- From knowledge graph to topological data analysis: a novel framework to analyze gene regulatory networks for tomato-multi-pathogen interactions.The New phytologist · 2026Article
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- Distinct processes contributing to post-submergence recovery determine leaf age-specific flood resilience in Arabidopsis.Plant physiology · 2026Article
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Genome-Wide Analysis ofInternational journal of molecular sciences · 2026Article
- Genome-Wide Identification of the Maize TALE Gene Family and Their Expression Analysis Under Low-Phosphorus Response in Maize (Plants (Basel, Switzerland) · 2026Article
588 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the goal of charting plant transcriptional regulatory maps (i.e. transcription factors (TFs), cis-elements and interactions between them), we have upgraded the TF-centred database PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) to a plant regulatory data and analysis platform PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) over the past three years. In this version, we updated the annotations for the previously collected TFs and set up a new section, 'extended TF repertoires' (TFext), to allow users prompt access to the TF repertoires of newly sequenced species. In addition to our regular TF updates, we are dedicated to updating the data on cis-elements and functional interactions between TFs and cis-elements. We established genome-wide conservation landscapes for 63 representative plants and then developed an algorithm, FunTFBS, to screen for functional regulatory elements and interactions by coupling the base-varied binding affinities of TFs with the evolutionary footprints on their binding sites. Using the FunTFBS algorithm and the conservation landscapes, we further identified over 20 million functional TF binding sites (TFBSs) and two million functional interactions for 21 346 TFs, charting the functional regulatory maps of these 63 plants. These resources are publicly available at PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) and a cloud-based mirror (http://plantregmap.gao-lab.org/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.