ArticlePlant biotechnology journal2022
PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication.
Article in Plant biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 27 citations in OpenAlex.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- PlantCCC prioritizes context-specific candidate ligand-receptor communication patterns in plant spatial transcriptomics.Plant molecular biology · 2026Article
- Advances in single-cell and spatial multi-omics for plant development and stress responses.Plant diversity · 2026Review
- A spatiotemporal atlas of giant-cell formation during Meloidogyne incognita infection in tomato roots.Molecular horticulture · 2026Article
- Exploring specialized metabolic pathways in medicinal plants with single-cell and spatial omics.Acta pharmaceutica Sinica. B · 2026Review
- Integrated Single-Cell and Spatial Transcriptomics Reveal Cell-Type-Specific Immune Regulatory Networks in Maize Responding to Southern Corn Rust.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The OsRALF5-FLR1 Module Regulates Rice Root Development and Provides a Target for Studying Cell-Cell Communication.Rice (New York, N.Y.) · 2026Article
- Comprehensive insights into the development of arabidopsis trichomes by single-nucleus RNA-seq.BMC plant biology · 2026Article
- Spatiotemporal transcriptomic and metabolomic landscapes of wild soybean seed development reveal regulatory mechanisms of nutrient accumulation.Plant communications · 2026Article
- A voyage of reprogrammable metabolic bioengineering reshapes plant defense: from editing tools to synthetic systems.Frontiers in plant science · 2026Review
- Single-Cell/Nucleus RNA-Sequencing for Phytohormone Signaling in Plants.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Integrated single-cell transcriptomics and spatial metabolomics unveil cellular differentiation and ginsenosides biosynthesis inHorticulture research · 2025Article
- Hi-C3: a statistical inference-based model for reconstructing higher-order cell-cell communication networks.Briefings in bioinformatics · 2025Article
- Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions.Briefings in bioinformatics · 2025Review
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- Single-cell analysis reveals cellular heterogeneity, gene expression profiles, and pathway dynamics in acne vulgaris.Archives of dermatological research · 2025Article
- Single-Cell Transcriptomics Applied in Plants.Cells · 2024Review
- Cell-cell communication: new insights and clinical implications.Signal transduction and targeted therapy · 2024Review
- Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb.BMC biology · 2024Article
- The diversification of methods for studying cell-cell interactions and communication.Nature reviews. Genetics · 2024Review
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Authors and funding
5 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Ligand-receptor pairs play important roles in cell-cell communication for multicellular organisms in response to environmental cues. Recently, the emergence of single-cell RNA-sequencing (scRNA-seq) provides unprecedented opportunities to investigate cellular communication based on ligand-receptor expression. However, so far, no reliable ligand-receptor interaction database is available for plant species. In this study, we developed PlantPhoneDB (https://jasonxu.shinyapps.io/PlantPhoneDB/), a pan-plant database comprising a large number of high-confidence ligand-receptor pairs manually curated from seven resources. Also, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell types but also provided visualization functions to present analysis results. At the PlantPhoneDB web interface, the processed datasets and results can be searched, browsed, and downloaded. To uncover novel cell-cell communication events in plants, we applied the PlantPhoneDB R package on GSE121619 dataset to infer significant cell-cell interactions of heat-shocked root cells in Arabidopsis thaliana. As a result, the PlantPhoneDB predicted the actively communicating AT1G28290-AT2G14890 ligand-receptor pair in atrichoblast-cortex cell pair in Arabidopsis thaliana. Importantly, the downstream target genes of this ligand-receptor pair were significantly enriched in the ribosome pathway, which facilitated plants adapting to environmental changes. In conclusion, PlantPhoneDB provided researchers with integrated resources to infer cell-cell communication from scRNA-seq datasets.
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