CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison

Abstract

Circular RNAs (circRNAs) from back-splicing of exon(s) have been recently identified to be broadly expressed in eukaryotes, in tissue- and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at http://www.picb.ac.cn/rnomics/circpedia.

Keywords: Back-splicing; CIRCpedia; CircRNA; Circular RNA; Database.

Figure 1

Homepage of CIRCpedia v2 A. Summary of annotated circRNAs in CIRCpedia v2. B. Datasets used in CIRCpedia v2.

Figure 2

Screenshots of web interface in CIRCpedia v2 A. Search circRNAs with query. The result table shows the annotation of circRNAs originating from human SMARCA5 locus. B. Browse circRNAs by JBrowse visualization. C. Download circRNAs for further analysis.

Figure 3

Screenshots of a new “Tool” interface for direct online analysis A. Heatmap to show differential circRNA expression among selected samples. B. Point plot to show differential circRNA expression among selected samples.