Treffer: ncPlantDB: a plant ncRNA database with potential ncPEP information and cell type-specific interaction.

Title:
ncPlantDB: a plant ncRNA database with potential ncPEP information and cell type-specific interaction.
Authors:
Liu L; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Liu E; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Hu Y; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Li S; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Zhang S; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Chao H; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Hu Y; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Zhu Y; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Chen Y; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Xie L; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Shen Y; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Wu L; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China., Chen M; Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Source:
Nucleic acids research [Nucleic Acids Res] 2025 Jan 06; Vol. 53 (D1), pp. D1587-D1594.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
Imprint Name(s):
Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
MeSH Terms:
RNA, Untranslated*/genetics , RNA, Untranslated*/metabolism , RNA, Plant*/genetics , RNA, Plant*/metabolism , Databases, Nucleic Acid*, Plants/genetics ; Plants/metabolism ; Gene Expression Regulation, Plant ; User-Computer Interface ; Databases, Genetic
Grant Information:
32070677 National Natural Sciences Foundation of China; 2023YFE0112300 National Key Research and Development Program of China; 2022R52035 151 Talent Project, and Science and Technology Innovation Leader of Zhejiang Province; Jiangsu Collaborative Innovation Center for Modern Crop Production
Substance Nomenclature:
0 (RNA, Untranslated)
0 (RNA, Plant)
Entry Date(s):
Date Created: 20241029 Date Completed: 20250108 Latest Revision: 20250116
Update Code:
20250117
PubMed Central ID:
PMC11701631
DOI:
10.1093/nar/gkae1017
PMID:
39470718
Database:
MEDLINE

Weitere Informationen

The field of plant non-coding RNAs (ncRNAs) has seen significant advancements in recent years, with many ncRNAs recognized as important regulators of gene expression during plant development and stress responses. Moreover, the coding potential of these ncRNAs, giving rise to ncRNA-encoded peptides (ncPEPs), has emerged as an essential area of study. However, existing plant ncRNA databases lack comprehensive information on ncRNA-encoded peptides (ncPEPs) and cell type-specific interactions. To address this gap, we present ncPlantDB (https://bis.zju.edu.cn/ncPlantDB), a comprehensive database integrating ncRNA and ncPEP data across 43 plant species. ncPlantDB encompasses 353 140 ncRNAs, 3799 ncPEPs and 4 647 071 interactions, sourced from established databases and literature mining. The database offers unique features including translational potential data, cell-specific interaction networks derived from single-cell RNA sequencing and Ribo-seq analyses, and interactive visualization tools. ncPlantDB provides a user-friendly interface for exploring ncRNA expression patterns at the single-cell level, facilitating the discovery of tissue-specific ncRNAs and potential ncPEPs. By integrating diverse data types and offering advanced analytical tools, ncPlantDB serves as a valuable resource for researchers investigating plant ncRNA functions, interactions, and their potential coding capacity. This database significantly enhances our understanding of plant ncRNA biology and opens new avenues for exploring the complex regulatory networks in plant genomics.
(© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)