PRES: a webserver for decoding the functional perturbations of RNA editing sites. Issue 4 (19th June 2022)

• Record Type: Journal Article
• Authors: Lv, Dezhong; Xu, Kang; Yang, Changbo; Liu, Yujie; Luo, Ya; Zhou, Weiwei; Zou, Haozhe; Cai, Yangyang; Ding, Na; Li, Xia; Shao, Tingting; Li, Yongsheng; Xu, Juan
• Is Part Of: Briefings in bioinformatics. Volume 23:Issue 4(2022)
• Publication Date: 2022-06-19
• Subjects: RNA editing -- webserver -- functional consequence -- regulation perturbation -- user-friendly; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbac242
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Rapid progresses in RNA-Seq and computational methods have assisted in quantifying A-to-I RNA editing and altered RNA editing sites have been widely observed in various diseases. Nevertheless, functional characterization of the altered RNA editing sites still remains a challenge. Here, we developed perturbations of RNA editing sites (PRES; http://bio-bigdata.hrbmu.edu.cn/PRES/ ) as the webserver for decoding functional perturbations of RNA editing sites based on editome profiling. After uploading an editome profile among samples of different groups, PRES will first annotate the editing sites to various genomic elements and detect differential editing sites under the user-selected method and thresholds. Next, the downstream functional perturbations of differential editing sites will be characterized from gain or loss miRNA/RNA binding protein regulation, RNA and protein structure changes, and the perturbed biological pathways. A prioritization module was developed to rank genes based on their functional consequences of RNA editing events. PRES provides user-friendly functionalities, ultra-efficient calculation, intuitive table and figure visualization interface to display the annotated RNA editing events, filtering options and elaborate application notebooks. We anticipate PRES will provide an opportunity for better understanding the regulatory mechanisms of RNA editing in human complex diseases.