PceRBase


28053167	PceRBase: a database of plant competing endogenous RNA. [PMID: 28053167] Yuan C, Meng X, Li X, Illing N, Ingle RA, Wang J, Chen M. Abstract Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants. We have developed a Plant ceRNA database (PceRBase, http://bis.zju.edu.cn/pcernadb/index.jsp) which contains potential ceRNA target-target, and ceRNA target-mimic pairs from 26 plant species. For example, in Arabidopsis lyrata, 311 candidate ceRNAs are identified which could affect 2646 target-miRNA-target interactions. Predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated GO annotations are also stored in the database. A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for the visualization and enrichment analysis of genes in the ceRNA networks. Moreover, users can use PceRBase to predict novel competing mimic-target and target-target interactions from their own data. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2017:45(D1) \| 31 Citations (from Europe PMC, 2025-03-08)

PceRBase: a database of plant competing endogenous RNA. [PMID: 28053167]

Yuan C, Meng X, Li X, Illing N, Ingle RA, Wang J, Chen M.

Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants. We have developed a Plant ceRNA database (PceRBase, http://bis.zju.edu.cn/pcernadb/index.jsp) which contains potential ceRNA target-target, and ceRNA target-mimic pairs from 26 plant species. For example, in Arabidopsis lyrata, 311 candidate ceRNAs are identified which could affect 2646 target-miRNA-target interactions. Predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated GO annotations are also stored in the database. A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for the visualization and enrichment analysis of genes in the ceRNA networks. Moreover, users can use PceRBase to predict novel competing mimic-target and target-target interactions from their own data. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2017:45(D1) | 31 Citations (from Europe PMC, 2025-03-08)

URL:	http://bis.zju.edu.cn/pcernadb/index.jsp
Full name:	plant ceRNA database
Description:	PceRBase integrates gene annotations for 26 species from Phytozome10, TAIR10, MSU RGCP7, and also predicts novel lncRNAs for four species. Based on this, it predicts 696,756 potential ceRNA target-target, and 167,608 ceRNA target-mimic pairs from 28 plant species. Users can submit their own sequence information and expression data to PceRBase to predict significant ceRNA interactions and their biological significance.
Year founded:	2017
Last update:	2018-10-11
Version:	v1.2
Accessibility:	Unaccessible
Country/Region:	China

Data type:	RNA
Data object:	Plant
Database category:	Interaction
Major species:	Arabidopsis lyrata Arabidopsis thaliana Brachypodium distachyon Brassica napus Brassica rapa Carica papaya Chlamydomonas reinhardtii Citrus clementina Citrus sinensis Glycine max Gossypium raimondii Helianthus annuus Linum usitatissimum Manihot esculenta Medicago truncatula Oryza sativa Physcomitrella patens Populus trichocarpa Prunus persica Ricinus communis Selaginella moellendorffii Solanum lycopersicum Solanum tuberosum Sorghum bicolor Theobroma cacao Vitis vinifera Zea mays
Keywords:	miRNA lncRNA lncRNA prediction ceRNA

University/Institution:	Zhejiang University
Address:	Department of Bioinformatics, College of Life Sciences, Zhejiang University, Yuhangtang Road 866, Xihu District, Hangzhou, Zhejiang, P. R. China, 310058.
City:	Hangzhou
Province/State:	Zhejiang
Country/Region:	China
Contact name (PI/Team):	Ming Chen
Contact email (PI/Helpdesk):	mchen@zju.edu.cn

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Database Commons a catalog of worldwide biological databases