Online Databases in Circular RNAs

Circular RNAs (circRNAs) have been attracting attention as biomarkers of various diseases, including cancer, because, as non-coding RNA (ncRNA)/protein sponges, they regulate gene expression and can be detected in various body fluids. Several comprehensive databases have been published to allow easy identification of target circRNAs.In all, 43 circRNA-related databases have been established and are listed in Database Commons since the development of the first comprehensive database of circRNAs, Circ2Traits, in 2013. Some of these databases, including Circ2Traits, provide annotation, ncRNA/protein-circRNA interactions and disease associations, and information on protein synthesis potentials and conservation among species. Additionally, databases that include analyzed RNA sequencing (RNA-seq) data or manually curated literature reporting the expression of circRNAs in specific tissues, organs, and body fluids have been established, making the exploration of target circRNAs easier. Currently, in addition to animals, plant circRNAs are being analyzed, and they cover a surprisingly large number of species.In this chapter, we summarize a selection of popular databases [circBase, CircInteractome, CircNet, CircR2Disease, the tissue-specific circular RNA database (TSCD), and the cancer-specific circRNA database (CSCD)] discussed in the previous edition and introduce some new circRNA databases listed in Database Commons. Furthermore, we discuss some reported challenges related to the nomenclature and updating of those databases.