Circular RNA (circRNA) databases and resources

In molecular biology, Circular RNAs (circRNAs) refer to a class of circular RNA molecules found across all kingdoms of life.[1][2][3] Studies in 2013 have suggested that circRNAs play important regulatory roles in miRNA activity. Researchers found that CDR1as circRNA acts as a miR-7 super-sponge that contains about 70 target sites from the same miR-7 at the same transcript.[4][5] The other testis-specific circRNA, sex-determining region Y (Sry), also was found as a miR-138 sponge.[6] About-mentioned examples suggesting that miRNA sponge effects achieved by circRNA formation may be a general phenomenon. As miR-7 modulates the expression of several oncogenes, ciRS-7/miR-7 interactions may play an important roles in cancer-related pathways.[7]

This Circular RNA (circRNA) databases and resources is a compilation of databases and web portals and servers used for circRNAs.

Name DescriptiontypeLinkReferences
circRNABase circRNABase is designed for decoding miRNA-circRNA interaction networks from thousands of circRNAs and 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets.databasewebsite[8]
circBase circBase explore public circRNA datasets and download the custom python scripts needed to discover circRNAs in your own (ribominus) RNA-seq data.databasewebsite[9]
CircNet CircNet records public and novel circRNAs and putative circRNA-miRNA interactions. All the information is presented in an interactive user interface and available for download. database website [10]
Circ2Traits Circ2Traits a comprehensive database for circular RNA potentially associated with disease and traits.databasedatabase[11]
Gokool et al. 2019 The Landscape of Circular RNA Expression in the Human Brain resource resource[12]

References
  1. Memczak, S; Jens, M; Elefsinioti, A; Torti, F; Krueger, J; Rybak, A; Maier, L; Mackowiak, SD; Gregersen, LH; Munschauer, M; Loewer, A; Ziebold, U; Landthaler, M; Kocks, C; le Noble, F; Rajewsky, N (Mar 21, 2013). "Circular RNAs are a large class of animal RNAs with regulatory potency". Nature. 495 (7441): 333–338. Bibcode:2013Natur.495..333M. doi:10.1038/nature11928. PMID 23446348.
  2. Hansen, TB; Jensen, TI; Clausen, BH; Bramsen, JB; Finsen, B; Damgaard, CK; Kjems, J (Mar 21, 2013). "Natural RNA circles function as efficient microRNA sponges". Nature. 495 (7441): 384–388. Bibcode:2013Natur.495..384H. doi:10.1038/nature11993. PMID 23446346.
  3. Kosik, KS (Mar 21, 2013). "Molecular biology: Circles reshape the RNA world". Nature. 495 (7441): 322–324. Bibcode:2013Natur.495..322K. doi:10.1038/nature11956. PMID 23446351.
  4. Memczak, S; Jens, M; Elefsinioti, A; Torti, F; Krueger, J; Rybak, A; Maier, L; Mackowiak, SD; Gregersen, LH; Munschauer, M; Loewer, A; Ziebold, U; Landthaler, M; Kocks, C; le Noble, F; Rajewsky, N (Mar 21, 2013). "Circular RNAs are a large class of animal RNAs with regulatory potency". Nature. 495 (7441): 333–338. Bibcode:2013Natur.495..333M. doi:10.1038/nature11928. PMID 23446348.
  5. Hansen, TB; Jensen, TI; Clausen, BH; Bramsen, JB; Finsen, B; Damgaard, CK; Kjems, J (Mar 21, 2013). "Natural RNA circles function as efficient microRNA sponges". Nature. 495 (7441): 384–388. Bibcode:2013Natur.495..384H. doi:10.1038/nature11993. PMID 23446346.
  6. Hansen, TB; Jensen, TI; Clausen, BH; Bramsen, JB; Finsen, B; Damgaard, CK; Kjems, J (Mar 21, 2013). "Natural RNA circles function as efficient microRNA sponges". Nature. 495 (7441): 384–388. Bibcode:2013Natur.495..384H. doi:10.1038/nature11993. PMID 23446346.
  7. Hansen, TB; Kjems, J; Damgaard, CK (Sep 15, 2013). "Circular RNA and miR-7 in Cancer". Cancer Research. 73 (18): 5609–5612. doi:10.1158/0008-5472.CAN-13-1568. PMID 24014594.
  8. Li, JH; Liu, S; Zhou, H; Qu, LH; Yang, JH (Jan 1, 2014). "starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data". Nucleic Acids Research. 42 (1): D92–7. doi:10.1093/nar/gkt1248. PMC 3964941. PMID 24297251.
  9. Memczak, S; Jens, M; Elefsinioti, A; Torti, F; Krueger, J; Rybak, A; Maier, L; Mackowiak, SD; Gregersen, LH; Munschauer, M; Loewer, A; Ziebold, U; Landthaler, M; Kocks, C; le Noble, F; Rajewsky, N (Mar 21, 2013). "Circular RNAs are a large class of animal RNAs with regulatory potency". Nature. 495 (7441): 333–338. Bibcode:2013Natur.495..333M. doi:10.1038/nature11928. PMID 23446348.
  10. Liu, Yu-Chen; Li, Jian-Rong; Sun, Chuan-Hu; Andrews, Erik; Chao, Rou-Fang; Lin, Feng-Mao; Weng, Shun-Long; Hsu, Sheng-Da; Huang, Chieh-Chen (2016-01-04). "CircNet: a database of circular RNAs derived from transcriptome sequencing data". Nucleic Acids Research. 44 (D1): D209–215. doi:10.1093/nar/gkv940. ISSN 1362-4962. PMC 4702939. PMID 26450965.
  11. Ghosal, S; Das, S; Sen, R; Basak, P; Chakrabarti, J (2013). "Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits". Frontiers in Genetics. 4: 283. doi:10.3389/fgene.2013.00283. PMC 3857533. PMID 24339831.
  12. Gokool, A; Anwar, F; Voineagu, I (2019). "The Landscape of Circular RNA Expression in the Human Brain". Biological Psychiatry. doi:10.1016/j.biopsych.2019.07.029. PMID 31570194.

circbase.org original paper [1]

  1. RNA. 2014 Nov;20(11):1666-70. doi: 10.1261/rna.043687.113. Epub 2014 Sep 18. circBase: a database for circular RNAs. Glažar P1, Papavasileiou P1, Rajewsky N2.
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