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This article is to share with you about the use of TSCD databases. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

TSCD is the abbreviation of Tissue-Specific CircRNA Database, which predicts circular RNA in different tissues of human and mice by software, and then looks for tissue-specific circular RNA. The web address of the database is as follows

Http://gb.whu.edu.cn/TSCD/

The transcriptome sequencing data of human and mouse tissues were collected from two public databases, ENCODE and GEO, and then the circular RNA was identified by the following three softwares

Find_circ

CIRI

CircRNA_finder

The merging of the three softwares was selected as the final result. As an example, the false positive rate was reduced, and only the circular RNA with more than 2 junction reads was retained. After the circular RNA in all tissues is detected using the above strategy, the tissue-specific circular RNA can then be identified.

In this database, a circular RNA expressed only in a certain tissue is defined as a tissue-specific circular RNA, referred to as TS circRNA, as follows

After the TS circRNA was identified, the following three kinds of analysis were carried out

TS circRNA with high expression was screened and its source genes were analyzed by GO enrichment analysis.

To predict miRNA binding sites, 50bp sequences were taken from the head and tail of circular RNA, and targetscan was used to predict miRNA binding sites on this 100bp sequence.

Predict the protein binding sites, download CLIP-Seq data from the starbase database, and also analyze the protein binding sites in the head-tail 50bp region

All the above results are integrated to build a TSCD database, and the whole database construction process is as follows

Different versions of the genome are available on the official website, as shown below

Click Gene Symbol to view the expression of the circular RNA in different tissues, as shown below

Click MRE to view the miRNA that the ring RNA can combine with, as shown below

Click RBP to view the proteins that annular RNA can bind, as shown below

The database not only provides a collection of annular RNA, but also provides the corresponding functional annotation information such as MRE,RBP.

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