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PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication

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 e...

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Autores principales: Xu, Chaoqun, Ma, Dongna, Ding, Qiansu, Zhou, Ying, Zheng, Hai‐Lei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9616517/
https://www.ncbi.nlm.nih.gov/pubmed/35842742
http://dx.doi.org/10.1111/pbi.13893
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author Xu, Chaoqun
Ma, Dongna
Ding, Qiansu
Zhou, Ying
Zheng, Hai‐Lei
author_facet Xu, Chaoqun
Ma, Dongna
Ding, Qiansu
Zhou, Ying
Zheng, Hai‐Lei
author_sort Xu, Chaoqun
collection PubMed
description 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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spelling pubmed-96165172022-10-31 PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication Xu, Chaoqun Ma, Dongna Ding, Qiansu Zhou, Ying Zheng, Hai‐Lei Plant Biotechnol J Research Articles 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. John Wiley and Sons Inc. 2022-07-30 2022-11 /pmc/articles/PMC9616517/ /pubmed/35842742 http://dx.doi.org/10.1111/pbi.13893 Text en © 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Research Articles
Xu, Chaoqun
Ma, Dongna
Ding, Qiansu
Zhou, Ying
Zheng, Hai‐Lei
PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication
title PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication
title_full PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication
title_fullStr PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication
title_full_unstemmed PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication
title_short PlantPhoneDB: A manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication
title_sort plantphonedb: a manually curated pan‐plant database of ligand‐receptor pairs infers cell–cell communication
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9616517/
https://www.ncbi.nlm.nih.gov/pubmed/35842742
http://dx.doi.org/10.1111/pbi.13893
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