circBase: a database for circular RNAs

By Petar Glažar, Panagiotis Papavasileiou, Nikolaus Rajewsky. RNA: A publication of the RNA Society, 2014

1,604 citations recorded by the source corpus.

Recently, several laboratories have reported thousands of circular RNAs (circRNAs) in animals. Numerous circRNAs are highly stable and have specific spatiotemporal expression patterns. Even though a function for circRNAs is unknown, these features make circRNAs an interesting class of RNAs as possible biomarkers and for further research. We developed a database and website, “circBase,” where merged and unified data sets of circRNAs and the evidence supporting their expression can be accessed, downloaded, and browsed within the genomic context. circBase also provides scripts to identify known and novel circRNAs in sequencing data. The database is freely accessible through the web server at http://www.circbase.org/.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d90293c06067d1a3718b4fb8c167285bfd099702

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Citations in the corpus

Circular RNAs: Promising Biomarkers for Human Diseases (2018, background): “[2] Universality: circRNAs are suggested to be the most universal molecules distributed in human cells [35]; and in some circumstances circRNAs are way more abundant than their linear isoforms [8].”
Circular RNA cSMARCA5 inhibits growth and metastasis in hepatocellular carcinoma. (2018, methodology): “Characterization of cSMARCA5 in HCC We chose the circRNA derived from exons 15 and 16 of the SMARCA5 gene [CircBase [36] ID: hsa_circ_0001445, termed cSMARCA5] for further study (Fig.”
CSCD: a database for cancer-specific circular RNAs (2017, methodology): “Cir-cBase integrates several circRNAs datasets into a standardized database, which allows users to explore circR-NAs or download customized python scripts to identify cir-cRNAs from their own RNA-seq data (24).”
A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis (2018, methodology): “found that circRNAs comprise more than 14% of all transcribed genes in fibroblasts; both studies suggest the abundance of circRNAs in the transcriptome [10, 20].”
CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes (2020, background): “…accumulation of large circRNA datasets and the imperative requirement of delineating their functional importance, various databases (e.g., circBase [17], CIRCpedia v2 [18], circRNADb [19], TSCD [20], CircRiC [21], and MiOncoCirc [7]) have been established to extend the catalog of the annotated…”
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs (2016, methodology): “48 The mature sequences of all of the reported circRNAs were downloaded from the UCSC browser mirror (http://genome.mdc-berlin.de) at the Max-Delbr € uck-Centrum f € ur Molekulare Medizin (MDC), Berlin, Germany.”