CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs

• Published in: BMC bioinformatics Vol. 25; no. 1; p. 31
• Main Authors: Nguyen, Thi-Hau, Nguyen, Ha-Nam, Vu, Trung Nghia
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 17.01.2024; BioMed Central; BMC
• Subjects: Animals; Applications programs; Binding sites; Biological research; Biology, Experimental; Cancer; Chromosomes; Circular RNA; Databases, Factual; Gene expression; Gene Regulatory Networks; Genomes; Humans; Installation procedures; Interaction network; Linux; Medicin och hälsovetenskap; Methods; Mice; MicroRNAs; MicroRNAs - genetics; MicroRNAs - metabolism; miRNA; Networks; Protein-protein interactions; RNA; RNA, Circular; RNA, Messenger - genetics; RNA-binding protein; Software; Visualization; Visualization (Computers); Web applications; Vietnam; Visualization; Circular RNA; Interaction network
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05646-4

Analyzing the interactions of circular RNAs (circRNAs) is a crucial step in understanding their functional impacts. While there are numerous visualization tools available for investigating circRNA interaction networks, these tools are typically limited to known circRNAs from specific databases. Moreover, these existing tools usually require complex installation procedures which can be time-consuming and challenging for users. There is a lack of a user-friendly web application that facilitates interactive exploration and visualization of circRNA interaction networks. CircNetVis is an interactive online web application to enhance the analysis of human/mouse circRNA interactions. The tool allows three different input formats of circRNAs including circRNA IDs from CircBase, circRNA coordinates (chromosome, start position, end position), and circRNA sequences in the FASTA format. It integrates multiple interaction networks for visualization and investigation of the interplay between circRNA, microRNAs, mRNAs and RNA binding proteins. CircNetVis also enables users to interactively explore the interactions of unknown circRNAs which are not reported from previous databases. The tool can generate interactive plots and allows users to save results as output files for offline usage. CircNetVis is implemented as a web application using R-shiny and freely available for academic use at https://www.meb.ki.se/shiny/truvu/CircNetVis/ .