ArticleNucleic acids research2024
PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 2 of them syntheses that pooled it.
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Who cites it
85 citing papers in PubMed, 2 syntheses or guidelines pooled it, 120 citations in OpenAlex.
- Integrative meta-analysis of RNA-Seq data reveals conserved orthologous gene modules and pathways in wheat and rice in response to plant growth-promoting bacteria.Functional & integrative genomics · 2026Pooled it
- Genome-wide transcriptional analysis of rapeseed (Brassica napus L.) responses to heat stress: an integrated RNA-Seq meta-analysis, gene co-expression, and gene regulatory network study.BMC plant biology · 2025Pooled it
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- SRF6, a heat-inducible receptor-like kinase, regulates thermotolerance in Arabidopsis thaliana.Plant cell reports · 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 saltmarsh cordgrass Spartina anglica has novel genomic features that contribute to abiotic stress tolerance.Journal of experimental botany · 2026Article
- Functional and regulatory complexity: challenges and prospects for understanding rice WRKY transcription factors.Journal of experimental botany · 2026Review
- Molecular Cloning, In Silico Characterization, and Promoter Analysis of a PutativeCurrent issues in molecular biology · 2026Article
- The OsUVR8-OsNAC3-OsERF117 signaling module mediates metabolic acclimation and climate adaptation in rice.Science advances · 2026Article
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- OsIDD7 integrates signaling networks for arbuscular mycorrhizal symbiosis.Nature communications · 2026Article
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Functional divergence of MADS-box genes and the dual regulatory role of a long noncoding RNA underlie sex determination in Ginkgo biloba.BMC plant biology · 2026Article
- Loss-of-function of MIR172b and prime editing of SNB reveal a regulatory module underlying cleistogamy in rice.Plant physiology · 2026Article
- Two LEAFY homologs regulate floral patterning and development without affecting flowering time in kiwifruit.Journal of experimental botany · 2026Article
- Peanut genome resource: a functional genomics platform for Arachis hypogaea.Plant & cell physiology · 2026Article
- VERNALIZATION2 alters early tiller development in a facultative spring hexaploid bread wheat.The New phytologist · 2026Article
- Modular control of orchid beauty: co-expression networks orchestrate organ development and evolution in Phalaenopsis flower.Plant molecular biology · 2026Article
- AMF-induced salinity tolerance in durum wheat is associated with transcriptomic modulation of the Cation/Calcium Exchanger 1 (CCX1).Mycorrhiza · 2026Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions' binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.
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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.