ArticleGenomics, proteomics & bioinformatics2023
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database.
Article in Genomics, proteomics & bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Deciphering Cell-Type-Specific Transcriptional Regulation in Tomato Leaves Through Ensemble Machine Learning and Single-Cell Transcriptomics.Plants (Basel, Switzerland) · 2026Article
- Design and implementation of a web-based platform for biodiversity valorization data management: from process modeling to user-centred evaluation.Database : the journal of biological databases and curation · 2026Article
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- Calm in the midst of the storm: inferring gene expression stability in flowering plants.Frontiers in plant science · 2026Article
- Epigenetic crop improvement: Integrating ENCODE strategies into horticultural breeding.Horticulture research · 2025Article
- Review
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- IRGL-RRI: interpretable graph representation learning for plant RNA-RNA interaction discovery.Frontiers in plant science · 2025Article
- A BERT-based rice enhancer identification model combined with sequence-representation differential entropy interpretation.Frontiers in plant science · 2025Article
- Identification of DNA N6-methyladenine modifications in the rice genome with a fine-tuned large language model.Frontiers in plant science · 2025Article
- SaGP: identifying plant saline-alkali tolerance genes based on machine learning techniques.Frontiers in plant science · 2025Article
- Omics-Driven Strategies for Developing Saline-Smart Lentils: A Comprehensive Review.International journal of molecular sciences · 2024Review
- Integrating omics databases for enhanced crop breeding.Journal of integrative bioinformatics · 2023Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin accessibility landscapes are essential for detecting regulatory elements, illustrating the corresponding regulatory networks, and, ultimately, understanding the molecular basis underlying key biological processes. With the advancement of sequencing technologies, a large volume of chromatin accessibility data has been accumulated and integrated for humans and other mammals. These data have greatly advanced the study of disease pathogenesis, cancer survival prognosis, and tissue development. To advance the understanding of molecular mechanisms regulating plant key traits and biological processes, we developed a comprehensive plant chromatin accessibility database (PlantCADB) from 649 samples of 37 species. These samples are abiotic stress-related (such as heat, cold, drought, and salt; 159 samples), development-related (232 samples), and/or tissue-specific (376 samples). Overall, 18,339,426 accessible chromatin regions (ACRs) were compiled. These ACRs were annotated with genomic information, associated genes, transcription factor footprint, motif, and single-nucleotide polymorphisms (SNPs). Additionally, PlantCADB provides various tools to visualize ACRs and corresponding annotations. It thus forms an integrated, annotated, and analyzed plant-related chromatin accessibility resource, which can aid in better understanding genetic regulatory networks underlying development, important traits, stress adaptations, and evolution.PlantCADB is freely available at https://bioinfor.nefu.edu.cn/PlantCADB/.
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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.