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

CSCD included tumor-specific circular RNA, analyzed circRNA from 87 tumor samples by bioinformatics, and screened out circular RNA expressed only in tumor patients. The website of this database is as follows

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

At present, a total of 272152 tumor-specific circular RNA are included. In the process of analyzing circular RNA using RNA_seq data, the following four softwares are used to identify circular RNA.

CIRI

Find_circ

CircRNA_finder

Circexplorer

On the home page of the official website, you can screen the results according to the sample, source gene and cell location, as shown below

In the search results, one circRNA for each behavior will give the name of the circRNA source gene, the corresponding sample name, the name of the software used and the corresponding expression level. Click on the ring RNA of each row, and the details of the source gene and the ring RNA will be given in the right panel. For the source gene, the details are as follows

1. Overview

In this part, the gene structure is visualized. The rectangular region represents the exon and the black solid line represents the intron. At the same time, the position of the circular RNA on the source gene is marked with a curve, and the variable cutting event is represented by a broken line, as shown below.

2. Gene

This section gives the chromosome location of the gene, as shown below

3. Transcript

This section gives the chromosome location of the transcript, as shown below

4. CircRNA

This section gives the chromosome location of the circular RNA, as shown below

5. Splice

This section gives the chromosome location of the variable cutting event, as shown below

For ring RNA, the details are as follows

1. Overview

This part visualizes the structure of the annular RNA and provides the visualization of the corresponding miRNA binding sites, protein binding sites and ORF regions, as shown below.

2. CircRNA

This section gives the chromosome location of the circular RNA, as shown below

3. MRE

MRE represents the binding site of miRNA and is predicted by targetscan software. The results are as follows.

4. RBP

RBP stands for RNA binding protein, which is obtained using HITS_CLIP sequencing data, as shown below

5. ORF

ORF stands for the development reading frame, which is used to analyze the coding potential of circRNA. The results are as follows

The data of this database can be downloaded free of charge, and the idea of analyzing tumor specificity and the analysis content of circular RNA should be used for reference.

Thank you for reading! This is the end of this article on "what's the use of CSCD database?". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, you can share it for more people to see!

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