Table 2.
Databases for identifying circRNAs and their basic properties or associations. The table summarises for each database what species the data are based on, as well as data sources, integrations or predictions of circRNA genes or transcripts. A link to the hosting website is provided followed by the latest known version as well as the most recent publication describing the database. IRES and MRE correspond to Internal Ribosome Entry Sites and miRNA Response Elements. See Section 3.2 for more information on CLIP and PAR-CLIP techniques.
| Database/Version/Ref. | Link | Species | Data Sources | Integrations | Predictions |
|---|---|---|---|---|---|
| CircAtlas (2020) [103] |
http://159.226.67.237:8080/new/index.php (accessed on 8 March 2021) | H. sapiens, M. mulatta, M. musculus, R norvegicus, S. scrofa and G gallus | 1070 RNA-seq samples across 6 species | Integrates circR2Disease and circRNADIsease for disease associations | Co-expression network; Functional inference from GO/KEGG; RBP and miRNA binding |
| circRNAdb (2016) [104] |
http://reprod.njmu.edu.cn/cgi-bin/circrnadb/circRNADb.php (accessed on 8 March 2021) | H. sapiens | Literature and RNA-seq dataset | UniProt | Protein domains, post-translational modifications, half-lifes |
| CircFunBase (2019) [105] |
http://bis.zju.edu.cn/CircFunBase/ (accessed on 8 March 2021) | H. sapiens, M. musculus + 13 more. | Literature search | CircInteractome (CLIP data), miRBase | miRNA-circRNA interactions |
| circBase (2017) [106] |
http://www.circbase.org/ (accessed on 8 March 2021) | H. sapiens, C. elegans, D. melanogaster, M. musculus, L. chalumnae, L. menadoensis | Various publications [18,107,108,109,110,111] | doRiNA | NA |
| Circbank (2019) [112] |
http://www.circbank.cn/ (accessed on 8 March 2021) | M. musculus, R. norvegicus, D. melanogaster | circBase, miRBase | m6A literature, COSMIC somatic mutations | IRES, circRNA-miRNA prediction |
| CIRCpedia v2 (2018) [113] |
https://www.picb.ac.cn/rnomics/circpedia/ (accessed on 8 March 2021) | H. sapiens, M. musculus, R. norvegicus, D. rerio, D. melanogaster, C | 180 RNA-seq samples across 6 species | NA | Putative circRNAs |
| CircRNADisease (2018) [114] |
http://cgga.org.cn:9091/circRNADisease/ (accessed on 8 March 2021) | H. sapiens | Manual curation of 800 publications | NA | Association to diseases |
| CircR2Disease (2018) [115] |
http://bioinfo.snnu.edu.cn/CircR2Disease/ (accessed on 8 March 2021) | H. sapiens | Manual curation of literature | NA | Association to diseases |
| TSCD (2017) [116] |
http://gb.whu.edu.cn/tscd/ (accessed on 8 March 2021) | H. sapiens, M. musculus | ENCODE + NCBI GEO RNA-seq | Starbase, Gene Ontology | MRE, Protein binding sites |
| circad (2020) [117] |
http://clingen.igib.res.in/circad/ (accessed on 8 March 2021) | H. sapiens, M. musculus, R. rattus | Manual curation of literature | NA | Asssociation to diseases |
| circVAR (2020) [118] |
http://soft.bioinfo-minzhao.org/circvar/ (accessed on 8 March 2021) | H. sapiens | circBase, circNet, circRNAdb | 1000 Genomes, ClinVAR, GWASCatalog, ClinVAR, COSMIC | Association to diseases/cancer |
| CSCD (2018) [119] |
http://gb.whu.edu.cn/cscd/ (accessed on 8 March 2021) | H. sapiens | 228 RNA-seq samples from ENCODE | Starbase | Cancer Association, MRE, RBP, ORFs |
| Circ2Traits (2013) [120] |
http://gyanxet-beta.com/circdb/ (accessed on 8 March 2021) | H. sapiens | RNA-seq [107] | Starbase, TargetScan, miRCode, dbSNP, GWAS catalog, PAR-CLIP Data [121] | miRNA interactions |
| Circ2Disease (2018) [122] |
http://bioinformatics.zju.edu.cn/Circ2Disease/index.html (accessed on 8 March 2021) | H. sapiens | Manual curation of literature | HMDD, OncomiRDB, miRTarBase, dbDEMC, miRecords | miRNA interactions |
| CircInteractome (2016) [123] |
https://circinteractome.nia.nih.gov/ (accessed on 8 March 2021) | H. sapiens | circBase | Starbase, miRBase | IRES, RBP and miRNA binding sites |