Abstract
Circular RNA (or circRNA) is a type of single-stranded covalently closed circular RNA molecule and play important roles in diverse biological pathways. A comprehensive functionally annotated circRNA database will help to understand the circRNAs and their functions. CircFunBase is such a web-accessible database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions. CircFunBase provides visualized circRNA–miRNA interaction networks. In addition, a genome browser is provided to visualize the genome context of circRNA. In this chapter, we illustrate examples of searching for circRNA and getting detailed information of circRNA. Moreover, other circRNA related databases are outlined.
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References
Wilusz JE (2018) A 360° view of circular RNAs: from biogenesis to functions. Wiley Interdiscip Rev RNA 9
Wang PL, Bao Y, Yee MC et al (2014) Circular RNA is expressed across the eukaryotic tree of life. PLoS One 9
Ye C-Y, Chen L, Liu C et al (2015) Widespread noncoding circular RNAs in plants. New Phytol 208:88–95
Salzman J, Gawad C, Wang PL et al (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7
Vo JN, Cieslik M, Zhang Y et al (2019) The landscape of circular RNA in cancer. Cell 176:869–881
Meng X, Li X, Zhang P et al (2017) Circular RNA: an emerging key player in RNA world. Brief Bioinform 18:547–557
Piwecka M, Glažar P, Hernandez-Miranda LR et al (2017) Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science 357
Ashwal-Fluss R, Meyer M, Pamudurti NR et al (2014) CircRNA biogenesis competes with pre-mRNA splicing. Mol Cell 56:55–66
Du WW, Fang L, Yang W et al (2017) Induction of tumor apoptosis through a circular RNA enhancing Foxo3 activity. Cell Death Differ 24:357–370
Legnini I, Di Timoteo G, Rossi F et al (2017) Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis. Mol Cell 66:22–37
Patop IL, Wüst S, Kadener S (2019) Past, present, and future of circ RNA s. EMBO J 38
Kristensen LS, Andersen MS, Stagsted LVW et al (2019) The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet 20:675–691
Gao Y, Zhang J, Zhao F (2018) Circular RNA identification based on multiple seed matching. Brief Bioinform 19:803–810
Szabo L, Morey R, Palpant NJ et al (2015) Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biol 16
Li X, Chu C, Pei J et al (2018) CircMarker: a fast and accurate algorithm for circular RNA detection. BMC Genomics 19:572
Glažar P, Papavasileiou P, Rajewsky N (2014) CircBase: a database for circular RNAs. RNA 20:1666–1670
Ji P, Wu W, Chen S et al (2019) Expanded expression landscape and prioritization of circular RNAs in mammals. Cell Rep 26:3444–3460
Zhang P, Meng X, Chen H et al (2017) PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks. Database 2017
Down TA, Piipari M, Hubbard TJP (2011) Dalliance: interactive genome viewing on the web. Bioinformatics 27:889–890
Priyam A, Woodcroft BJ, Rai V et al (2019) Sequenceserver: a modern graphical user Interface for custom BLAST databases. Mol Biol Evol 36:2922–2924
Ghosal S, Das S, Sen R et al (2013) Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Front Genet 4
Dudekula DB, Panda AC, Grammatikakis I et al (2016) Circinteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol 13:34–42
Liu YC, Li JR, Sun CH et al (2016) CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res 44:D209–D215
Chen X, Han P, Zhou T et al (2016) CircRNADb: a comprehensive database for human circular RNAs with protein-coding annotations. Sci Rep 6:34985
Xia S, Feng J, Lei L et al (2017) Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes. Brief Bioinform 18:984–992
Chu Q, Zhang X, Zhu X et al (2017) PlantcircBase: a database for plant circular RNAs. Mol. Plant 10:1126–1128
Ye J, Wang L, Li S et al (2019) AtCircDB: a tissue-specific database for Arabidopsis circular RNAs. Brief Bioinform 20:58–65
Xia S, Feng J, Chen K et al (2018) CSCD: a database for cancer-specific circular RNAs. Nucleic Acids Res 46:D925–D929
Li S, Li Y, Chen B et al (2018) ExoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. Nucleic Acids Res 46:D106–D112
Fan C, Lei X, Fang Z et al (2018) CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases. Database 2018
Dong R, Ma XK, Li GW, Yang L (2018) CIRCpedia v2: an updated database for comprehensive circular RNA annotation and expression comparison. Genom Proteom Bioinf 16:226–233
Tang Z, Li X, Zhao J et al (2019) TRCirc: a resource for transcriptional regulation information of circRNAs. Brief Bioinform 20:2327–2333
Meng X, Hu D, Zhang P et al (2019) CircFunBase: a database for functional circular RNAs. Database 2019
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Hu, D., Zhang, P., Chen, M. (2021). Database Resources for Functional Circular RNAs. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 2284. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1307-8_24
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DOI: https://doi.org/10.1007/978-1-0716-1307-8_24
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