CircNet – a database of circular RNAs derived from transcriptome sequencing data

in Databases October 13, 2015 17,527 Views

Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression.

In this study, researchers from the National Chiao Tung University, Taiwan utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by the pipeline) in 464 RNA-seq samples, and then constructed the CircNet database that provides the following resources:

novel circRNAs,
integrated miRNA-target networks,
expression profiles of circRNA isoforms,
genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and
sequences of circRNA isoforms.

Framework of the database construction in CircNet. The graph illustrates how the network in CircNet was constructed. For circRNA identification, transcriptome sequencing data sets 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 we developed (scripts provided on circBase). Detected back-spliced junction sites were further compared with hg19 human genome annotation to define circRNA isoforms. Only isoforms with an average expression level (those with an average FPKM in the 464 examined samples greater than 0.01) were included in the database. To predict circRNA–miRNA interactions, the occurrence of miRNA target seeds in circRNA isoforms were examined and normalized by isoform length. The significance of interactions was evaluated by referring to the background distribution of miRNA seeds in all transcripts and only circRNA–miRNA interactions with P-values < 0.001 were reported.

The CircNet database is the first public database that provides tissue-specific circRNA expression profiles and circRNA-miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.

Availability – The CircNet database can be accessed at: http://circnet.mbc.nctu.edu.tw/

Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, Liu CC, Huang HD. (2015) CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res [Epub ahead of print]. [article]