JustRNA: a database of plant long noncoding RNA expression profiles and functional network

Kuan Chieh Tseng, Nai Yun Wu, Chi Nga Chow, Han Qin Zheng, Chin Yuan Chou, Chien Wen Yang, Ming Jun Wang, Song Bin Chang, Wen Chi Chang

研究成果: Article同行評審

2 引文 斯高帕斯(Scopus)

摘要

Long noncoding RNAs (lncRNAs) are regulatory RNAs involved in numerous biological processes. Many plant lncRNAs have been identified, but their regulatory mechanisms remain largely unknown. A resource that enables the investigation of lncRNA activity under various conditions is required because the co-expression between lncRNAs and protein-coding genes may reveal the effects of lncRNAs. This study developed JustRNA, an expression profiling resource for plant lncRNAs. The platform currently contains 1 088 565 lncRNA annotations for 80 plant species. In addition, it includes 3692 RNA-seq samples derived from 825 conditions in six model plants. Functional network reconstruction provides insight into the regulatory roles of lncRNAs. Genomic association analysis and microRNA target prediction can be employed to depict potential interactions with nearby genes and microRNAs, respectively. Subsequent co-expression analysis can be employed to strengthen confidence in the interactions among genes. Chromatin immunoprecipitation sequencing data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs in several plant species. The JustRNA platform provides researchers with valuable insight into the regulatory mechanisms of plant lncRNAs. JustRNA is a free platform that can be accessed at http://JustRNA.itps.ncku.edu.tw.

原文English
頁(從 - 到)4949-4958
頁數10
期刊Journal of experimental botany
74
發行號17
DOIs
出版狀態Published - 2023 9月 13

All Science Journal Classification (ASJC) codes

  • 生理學
  • 植物科學

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