circVAR database: genome-wide archive of genetic variants for human circular RNAs
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RESEARCH ARTICLE
Open Access
circVAR database: genome-wide archive of genetic variants for human circular RNAs Min Zhao1 and Hong Qu2*
Abstract Background: Circular RNAs (circRNAs) play important roles in regulating gene expression through binding miRNAs and RNA binding proteins. Genetic variation of circRNAs may affect complex traits/diseases by changing their binding efficiency to target miRNAs and proteins. There is a growing demand for investigations of the functions of genetic changes using large-scale experimental evidence. However, there is no online genetic resource for circRNA genes. Results: We performed extensive genetic annotation of 295,526 circRNAs integrated from circBase, circNet and circRNAdb. All pre-computed genetic variants were presented at our online resource, circVAR, with data browsing and search functionality. We explored the chromosome-based distribution of circRNAs and their associated variants. We found that, based on mapping to the 1000 Genomes and ClinVAR databases, chromosome 17 has a relatively large number of circRNAs and associated common and health-related genetic variants. Following the annotation of genome wide association studies (GWAS)-based circRNA variants, we found many non-coding variants within circRNAs, suggesting novel mechanisms for common diseases reported from GWAS studies. For cancer-based somatic variants, we found that chromosome 7 has many highly complex mutations that have been overlooked in previous research. Conclusion: We used the circVAR database to collect SNPs and small insertions and deletions (INDELs) in putative circRNA regions and to identify their potential phenotypic information. To provide a reusable resource for the circRNA research community, we have published all the pre-computed genetic data concerning circRNAs and associated genes together with data query and browsing functions at http://soft.bioinfo-minzhao.org/circvar. Keywords: Bioinformatics database, Circular RNA, Genetic variant, Systems biology
Background Circular RNAs (circRNA) are long non-coding RNAs (lncRNAs) that form covalently linked continuous loops and are abundant in eukaryotic cells [12]. circRNAs are generated by back-splicing events in which an upstream splice acceptor is linked to a downstream splice donor [12]. Most circRNAs have independent gene expression regulatory mechanisms which are different from their * Correspondence: [email protected] 2 Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, P. R. China Full list of author information is available at the end of the article
cognate linear forms. Rather than being regarded as byproducts of transcription, there is emerging evidence that circRNAs play important regulatory roles at the transcriptional and post-transcriptional levels by acting as microRNA sponges and by modulating RNA binding protein genes [2]. Accumulated evidence revealed that circRNAs are associated with a broad range of diseases, including cancers, n
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