CircView: a visualization and exploration tool for circular RNAs

Abstract

Circular RNAs (circRNAs) are novel rising stars of noncoding RNAs, which are highly abundant and evolutionarily conserved across species. Number of publications related to circRNAs increased sharply in recent years, representing emerging focuses in the field. Therefore, tools, pipelines and databases have been developed to identify and store circRNAs. However, there is no existing tool to visualize and explore circRNAs. Therefore, we introduce CircView, a user-friendly visualization tool for circRNAs detected from existing tools. CircView enables users to visualize circRNAs and to quantify number of samples with detected circRNAs. CircView allows users to explore circRNAs detected by unique or multiple tools. Furthermore, CircView allows users to view the regulatory elements, such as microRNA response elements and RNA-binding protein binding sites. CircView is a unique tool to visualize and explore circRNAs, which helps users to better understand potential functions of circRNAs and design the functional experiments.

Hsa_circ_0033155: A potential novel biomarker for non‑small cell lung cancer

“…Notably, it is the unique circular structure that protects them from the degradation of exonuclease RNase R and confers these RNAs excellent stability (15). In addition, the expression level of circRNAs, including circular ANRIL, is higher compared with that of linear RNAs (16,17). In addition, their expression level and function are independent of linear RNA isomers (16,17).…”

“…In addition, the expression level of circRNAs, including circular ANRIL, is higher compared with that of linear RNAs (16,17). In addition, their expression level and function are independent of linear RNA isomers (16,17). The aforementioned advantages indicate that, circRNAs may serve as ideal diagnostic biomarkers for cancer, and be superior to other non-coding RNAs such as long non-coding RNAs and miRNAs (18,19).…”

The Regulatory Functions of Circular RNAs in Digestive System Cancers

“…Following the application of high-throughput RNA sequencing and various modern computational approaches, a large number of human circRNA-related datasets have been established ( Table 6). The circRNA basic information integration and analysis databases are circBase [111], CIRCpedia v2 [112], circView [113], and circBank [114]. It is worth noting that circBase and circBank provide the system nomenclature for circRNAs.…”

CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms

“…The miARma-Seq (Andres-Leon & Rojas, 2019) with CIRI predictor (Gao, Wang & Zhao, 2015), circRNA_finder (Westholm et al, 2014), find_circ (Memczak et al, 2013), CIRCexplorer2 (Zhang et al, 2016), and other tools are very popular today for prediction of circRNAs sequences based on transcriptomic data (Hansen et al, 2016;Szabo & Salzman, 2016), despite significant output differences. Several circRNA predictors (CIRI, CIRI2, and CircExplorer2) can use genome annotation files for host gene prediction but they are definitely useful only for well-annotated genomes, and even, such as CircView (Feng et al, 2018) or circMeta (Chen et al, 2019), have been designed specifically for them.…”