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circNet is a circular RNA database, which not only contains basic information of cirRNA, but also provides expression profile data of circular RNA in different tissues and circRNA-miRNA-gene ceRNA regulatory network. The website is as follows

http://syslab5.nchu.edu.tw/CircNet/

The process of database construction is as follows

RNA_seq data from 464 samples from 26 different tissues were collected from SRA database, and circular RNAs were predicted by find_circ software. A total of 212950 circular RNAs were predicted, of which 53687 were new circular RNAs compared with circBase database. To reduce false positives, circular RNAs with junction reads greater than 3 were selected as highly reliable circular RNAs, resulting in 34000 circular RNAs.

The software predicts that circular RNA will only give the position of the junction on the genome, which means that we can only determine the head and tail of circular RNA, and cannot directly determine the sequence information in the middle. Therefore, the database annotates the sequence information of circular RNA according to the strategy shown in the figure below.

Figure A shows circular RNA corresponding to exon at both ends, and all combinations of oxn are listed as multiple isoforms of circRNA when annotating the sequence; Figure B shows circular RNA with splice sites on introns, and the intron sequences on both sides of exon are included when annotating the sequence; Figure C shows that when circular RNA is located at the antisense strand of a known gene at both ends, the sequence is directly truncated according to the chromosomal position of the head and tail; Figure D shows that for circular RNA in the head-to-tail intergenic region, the sequence is cut directly from the head-to-tail chromosome position in the same way as Figure C.

According to the sequence of circular RNA, the interaction with miRNA was predicted by targetScan software, and then the regulatory relationship between miRNA and gene in miRTarBase and miRBase database was combined to construct circRNA-miRNA-gene ceRNA regulatory network.

On the homepage of the official website, you can search for the corresponding ceRNA regulatory network by gene unit. Take ZEB1 as an example, the following is shown.

The legend is as follows

Purple nodes represent circular RNA, yellow nodes represent miRNA, blue nodes represent gene; red lines connect miRNA to target gene, green lines connect gene to circular RNA, blue lines connect circRNA to miRNA.

The right panel displays information such as expression levels in different tissues and the interaction network between circular RNA and miRNA.

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