December 16th 2015
The normalized read counts spanning back spliced junction sites are now available on the top- right panel. The value SRPBM stands for spliced reads per billion mapping as mentioned in the work of Jeck et al. 2013. SRPBM represents the count of reads spanning the site normalized by read length and number of reads mapped on human genome for each run.
November 4th 2015
Displaying issue fixed: the sponge panel didn’t change dynamically with user search and would have been fixed in the displaying of ZEB1 circRNAs before user clicked on searched nodes of new circRNAs. The issue was fixed now. The sponge panel will change accroding to user query.
November 2nd 2015
Noticed that expression levels of circRNAs within poly-A enriched samples should be depleted and biased, we removed a portion of expression level data from the database.
We are currently working on the ENCODE nonpoly-A selection and whole cell data sets. The database will be updated soon.
August 9th 2016
All the data including the fasta file, gtf file of the annotation and the source of the back spliced junction sites is available for user to download.
Published back spliced junction sites from the following studies has been collected into this database:
1. Salzman, J., et al., Cell-type specific features of circular RNA expression. PLoS Genet, 2013. 9(9): p. e1003777.
2. Salzman, J., et al., Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types. Plos One, 2012. 7(2).
3. Jeck, W.R., et al., Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA, 2013. 19(2): p. 141-57.
4. Gao, Y., J. Wang, and F. Zhao, CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome biology, 2015. 16(1): p. 1.
5. Kelly, S., et al., Exon skipping is correlated with exon circularization. Journal of molecular biology, 2015. 427(15): p. 2414-2417.
6. Bachmayr-Heyda, A., et al., Correlation of circular RNA abundance with proliferation-exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues. Scientific reports, 2015. 5.
7. Zhang, X.-O., et al., Complementary sequence-mediated exon circularization. Cell, 2014. 159(1): p. 134-147.
8. Guo, J.U., et al., Expanded identification and characterization of mammalian circular RNAs. Genome biology, 2014. 15(7): p. 1.
9. Caiment, F., et al., High-throughput data integration of RNA–miRNA–circRNA reveals novel insights into mechanisms of benzo [a] pyrene-induced carcinogenicity. Nucleic acids research, 2015. 43(5): p. 2525-2534.
10. Rybak-Wolf, A., et al., Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Molecular cell, 2015. 58(5): p. 870-885.
11. Boeckel, J.-N., et al., Identification and characterization of hypoxia-regulated endothelial circular RNA. Circulation research, 2015. 117(10): p. 884-890.
12. Bahn, J.H., et al., The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clinical chemistry, 2015. 61(1): p. 221-230.
13. Conn, S.J., et al., The RNA binding protein quaking regulates formation of circRNAs. Cell, 2015. 160(6): p. 1125-1134.
14. Memczak, S., et al., Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood. PloS one, 2015. 10(10): p. e0141214.
15. Alhasan, A.A., et al., Circular RNA enrichment in platelets is a signature of transcriptome degradation. Blood, 2016. 127(9): p. e1-e11.
16. Cheng, J., F. Metge, and C. Dieterich, Specific identification and quantification of circular RNAs from sequencing data. Bioinformatics, 2015: p. btv656.
17. Zhang, X.-O., et al., Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Research, 2016: p. gr. 202895.115.
18. Song, X., et al., Circular RNA profile in gliomas revealed by identification tool UROBORUS. Nucleic acids research, 2016: p. gkw075.
19. Dang, Y., et al., Tracing the expression of circular RNAs in human pre-implantation embryos. Genome Biology, 2016. 17(1): p. 1.
20. Zheng, Q., et al., Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nature communications, 2016. 7.