The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Comparison of circular RNA prediction tools
Open accessAbstract
CircRNAs are novel members of the non-coding RNA family. For several decades circRNAs have been known to exist, however only recently the widespread abundance has become appreciated. Annotation of circRNAs depends on sequencing reads spanning the backsplice junction and therefore map as non-linear reads in the genome. Several pipelines have been developed to specifically identify these non-linear reads and consequently predict the landscape of circRNAs based on deep sequencing datasets. Here, we use common RNAseq datasets to scrutinize and compare the output from five different algorithms; circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice and evaluate the levels of bona fide and false positive circRNAs based on RNase R resistance. By this approach, we observe surprisingly dramatic differences between the algorithms specifically regarding the highly expressed circRNAs and the circRNAs derived from proximal splice sites. Collectively, this study emphasizes that circRNA annotation should be handled with care and that several algorithms should ideally be combined to achieve reliable predictions.
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Cites
Circular RNAs are a large class of animal RNAs with regulatory potency
Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., et al. (2013) · Nature · doi:10.1038/nature11928 · Cited by 7,990
Natural RNA circles function as efficient microRNA sponges
Hansen, T. B., Jensen, T. I., Clausen, B. H., Bramsen, J. B., Finsen, B., Damgaard, C. K., & Kjems, J. (2013) · Nature · doi:10.1038/nature11993 · Cited by 7,985
Self-citationCircular RNAs are abundant, conserved, and associated with ALU repeats
Jeck, W. R., Sorrentino, J. A., Wang, K., Slevin, M. K., Burd, C. E., Liu, J., Marzluff, W. F., & Sharpless, N. E. (2013) · RNA · doi:10.1261/rna.035667.112 · Cited by 4,388
Circular intronic long noncoding RNAs
Zhang, Y., Zhang, X.-O., Chen, T., Xiang, J.-F., Yin, Q.-F., Xing, Y.-H., Zhu, S., Yang, L., & Chen, L.-L. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.08.017 · Cited by 2,221
Complementary Sequence-Mediated Exon Circularization
Zhang, X.-O., Wang, H.-B., Zhang, Y., Lu, X., Chen, L.-L., & Yang, L. (2014) · Cell · doi:10.1016/j.cell.2014.09.001 · Cited by 1,999 · cited 2×
“…of two non-treated RNA samples derived from Hs68 fibroblast (SRR444655 and SRR444975) and two RNase R treated samples (SRR444974 and SRR445016), we compared five different circRNA predicting algorithms: find circ (7), MapSplice (17), CIRCexplorer (10), cir-cRNA finder (11), and CIRI (12).”
MethodMapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., He, X., Mieczkowski, P., Grimm, S. A., Perou, C. M., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq622 · Cited by 1,193
Cited by
The biogenesis, biology and characterization of circular RNAs
Kristensen, L. S., Andersen, M. S., Stagsted, L. V. W., Ebbesen, K. K., Hansen, T. B., & Kjems, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0158-7 · Cited by 4,823
Self-citationThe Biogenesis, Functions, and Challenges of Circular RNAs
Li, X., Yang, L., & Chen, L.-L. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.034 · Cited by 2,062
The Landscape of Circular RNA in Cancer
Vo, J. N., Cieslik, M., Zhang, Y., Shukla, S., Xiao, L., Zhang, Y., Wu, Y.-M., Dhanasekaran, S. M., Engelke, C. G., Cao, X., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.021 · Cited by 1,738
Circular RNAs: analysis, expression and potential functions
Barrett, S. P., & Salzman, J. (2016) · Development · doi:10.1242/dev.128074 · Cited by 859
Circular RNA and its mechanisms in disease: From the bench to the clinic
Han, B., Chao, J., & Yao, H. (2018) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2018.01.010 · Cited by 788
Metadata
- Authors
- Hansen, T. B., Venø, M. T., Damgaard, C. K., & Kjems, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-12-10
- Volume
- 44
- Issue
- 6
- Pages
- e58-e58
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2194134194
- Cited by
- 395
- References
- 6
- FWCI
- 11.84
- Type
- journal article
- Language
- en
- Open access
- gold
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