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Protocols

circBase specifications

Information


Unique identifier OMICS_10188
Name circBase
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Petar Glažar

Publication for circBase

circBase citations

 (33)
library_books

Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects

2018
BMC Genomics
PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] the 20 samples by two, three or all four algorithms in each sample (Additional file : Table S1). Furthermore, 548 circRNAs detected in our dataset were also reported in the four studies deposited in circBase [] (Additional file : Table S1); various cell lines and tissue types were evaluated in these studies, including cerebellum, diencephalon, SH-SY5Y cells, Hs68 cells, HeLa cells and HEK293 cell […]

library_books

Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

2018
BMC Genomics
PMCID: 5954272
PMID: 29764361
DOI: 10.1186/s12864-018-4456-9

[…] ets were obtained from the NCBI Sequence Read Archive (SRA). The back-spliced junction sites in each RNA-seq sample were identified using a circRNA discovery pipeline adapting the scripts provided on circBase [, ], which was referred as find_circ []. Detected back-spliced junction sites, along with the collected junction sites from previous reports, were further compared with the hg19 human genome […]

library_books

CircRNAs in the tree shrew (Tupaia belangeri) brain during postnatal development and aging

2018
PMCID: 5940110
PMID: 29723158
DOI: 10.18632/aging.101437

[…] data on the calculation of circRNA expression levels. Therefore, the calculated expression levels could be used directly to compare differential expression among samples. circRNAs were compared with circBase [] using BLAST for annotation. The circRNAs that could not be annotated were defined as novel circRNAs. Box plots and Venn diagrams were generated using online tools (www.omicshare.com/tools/ […]

library_books

Downregulation of hsa_circ_0011946 suppresses the migration and invasion of the breast cancer cell line MCF 7 by targeting RFC3

2018
PMCID: 5865555
PMID: 29593432
DOI: 10.2147/CMAR.S155923

[…] genome with Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml). The junctions of the unmapped reads were then chosen using a back splice algorithm. Finally, circRNAs were verified using circbase (http://www.circbase.org). “Mapped backsplicing junction reads per million mapped reads” (RPM) was used to measure the expression level of each circRNA. […]

library_books

Signature of circular RNAs in human induced pluripotent stem cells and derived cardiomyocytes

2018
PMCID: 5845222
PMID: 29523209
DOI: 10.1186/s13287-018-0793-5

[…] rther analysis. We totally identified 5602 circRNAs, including 1612 in the hiPSC group and 4260 in the hiPSC-CM group with 270 in common. Among these, more than 3500 circRNAs were not yet included in circBase, a database for circRNAs (Fig. ) []. Furthermore, there were 614 and 2918 new circRNAs exclusively expressed in hiPSCs and hiPSC-CMs, respectively, indicating the cell type specificity of cir […]

call_split

Luminal breast cancer specific circular RNAs uncovered by a novel tool for data analysis

2018
Oncotarget
PMCID: 5865691
PMID: 29581865
DOI: 10.18632/oncotarget.24522
call_split See protocol

[…] The Control gene set was defined by selecting genes lacking circRNA predictions considering the union between circBase [], circRNADb [] annotations and circRNAs predicted in this study. To select control genes expressed in MCF-7, a public Poly(A)+ MCF-7 RNA-Seq experiment performed in full medium (GSE48213, [ […]

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circBase institution(s)
Max Delbrück Center for Molecular Medicine, Berlin, Germany

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