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Table 1 List of important bioinformatics tools and databases useful for circRNA research

From: Circular RNAs and their role in renal cell carcinoma: a current perspective

Tool/database name Important features Ref
Circ2Traits It contains information of 1951 human circRNAs potentially associated with 105 different diseases. It also stores a putative miRNA-circRNA-mRNA-lncRNA interaction network for all these diseases [28]
CircAtlas It is a comprehensive database that contains 1070 RNA-seq samples from 6 different species with the integration of 1,007,087 circRNAs [29]
CircBank It is a human circRNA database that contains 12,348 conserved circRNAs and 4388 circRNAs with m6A modifications [30]
Circbase merged and unified data sets of circRNAs from multiple species [31]
CIRCexplorer3 A comprehensive pipeline to quantitatively evaluate circRNA expression across samples [32]
CircInteractome A web-based tool for the analysis of circRNAs and their interacting proteins and miRNAs [33]
CircNet It provides tissue-specific circRNA expression profiles and circRNA-miRNA-gene regulatory networks [34]
CIRCpedia v2 An updated database containing 180 RNA-seq datasets for circRNA annotations across 6 different species with computational tools to compare circRNA expression among different samples [35]
CircPro An integrated tool for the identification of circRNAs with protein-coding potential from high-throughput sequencing data [36]
CircRNA disease It provides a user-friendly interface for searching experimentally supported disease-associated circRNAs [37]
CircRNADb A comprehensive database comprising 32,914 non-redundant human exonic circRNAs with protein-encoding feature annotation [38]
CircRNAFisher A circRNA identification pipeline for robust circRNA identification [39]
CIRI A de novo circular RNA identification tool [40]
CSCD A comprehensive cancer-specific circRNA database [41]
ExoRBase It is a database containing 58,330 circRNAs, 15,501 lncRNAs and 18,333 mRNAs characterized from derived from RNA-seq data analyses of human blood exosomes [42]
StarBase v2.0 A tool to identify the RNA–RNA and RNA–protein interactions including miRNAs, ncRNAs (lncRNAs, pseudogenes and circRNAs) [43]