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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]