circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations

By Xiaoping Chen, P. Han, Tao Zhou, Xuejiang Guo, Xiaofeng Song, Yan Li. Scientific Reports, 2016

443 citations recorded by the source corpus.

It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8963825c900a946fcb52fa7660eeb0904956c5d7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

1. Wanying Wu
2. Peifeng Ji
3. Fangqing Zhao
4. Burton B. Yang

In Molecular Biology

1. Wanying Wu
2. Peifeng Ji
3. Feizhe Xiao
4. Nu Zhang
5. Kun Zhao
6. Fangqing Zhao
7. Xuesong Yang
8. Sheng Yan

Citations in the corpus

• CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes (2020, background): “…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 circRNAs.”
• Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis (2017, background): “Furthermore, a computational analysis– based database suggests the coding potential of human circRNAs (20).”
• CSCD: a database for cancer-specific circular RNAs (2017, methodology): “The minimal length of ORF length was set as 300nt according to a previous work (26).”
• Circbank: a comprehensive database for circRNA with standard nomenclature (2019, methodology): “Recent studies have suggested the potential of circRNAs in proteins translation [22 – 24].”
• The bioinformatics toolbox for circRNA discovery and analysis (2020, background): “CircRNADb [101] is also a comprehensive database, but features human circRNA with annotated exonic circRNAs and circRNA with protein-coding potential.”
• A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis (2018, background): “As circ-SHPRH was annotated in circRNADb [13], we analyzed the putative ORF of circ-SHPRH.”