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This article mainly introduces "brief introduction of ceRNA database". In daily operation, I believe many people have doubts about the brief introduction of ceRNA database. The editor consulted all kinds of materials and sorted out simple and easy-to-use operation methods. I hope it will be helpful for you to answer the doubts of "brief introduction of ceRNA database"! Next, please follow the editor to study!

In the ceRNA regulatory network, miRNA acts as a bridge and mediates the occurrence of this regulatory mechanism by combining with various RNA molecules. The starBase database provides information about the interaction between miRNA and various RNA molecules, and on this basis, a ceRNA network is constructed at the following URL

Http://starbase.sysu.edu.cn/index.php

The database provides the following types of information

MiRNA target

RNA-RNA interaction

CeRNA regulatory network

Binding information of RNA and protein

According to the different research methods, there are 5 different navigation bar menus.

1. MiRNA target

Firstly, the CLIP-seq sequencing results of AGO protein were downloaded from GEO database, and the miRNA binding sites were obtained by peak calling analysis. Then the prediction results of targetscan and other software were used to intersect with the results of CLIP data analysis, and the final miRNA binding site information was obtained, thus the interaction information between miRNA and other RNA molecules was determined.

Through the miRNA target menu of the navigation bar, you can view the following four types of miRNA target information

MiRNA-mRNA

MiRNA-lncRNA

MiRNA-circRNA

MiRNA-pseudogene

MiRNA-sncRNA

The results are as follows

2. Degradome-RNA

The target information of miRNA is analyzed by using the sequence data of degradation group in GEO database. The results are as follows.

3. RNA-RNA

Download LIGR-seq and other sequencing data on RNA-RNA interaction from GEO database, and analyze the interaction information between RNA molecules. Through the RNA-RNA menu in the navigation bar, you can view the following four types of RNA molecular interaction information.

MiRNA-RNA

MRNA-RNA

LncRNA-RNA

Pseudigene-RNA

SncRNA-RNA

The search results are as follows

4. CeRNA network

Through the ceRNA-network menu of the navigation bar, you can view ceRNA network information, which can be divided into the following three types

MRNA-ceRNA

LncRNA-ceRNA

Pseudogene-ceRNA

For each ceRNA relation pair, the p value is calculated using hypergeometric distribution, and the formula is as follows

N represents the total number of miRNA in the ceRNA network, K represents the number of miRNA bound by the gene, n represents the number of miRNA bound by another gene that constitutes the ceRNA relationship, c represents the number of miRNA bound by the two genes, v2 version of the database can view the specific miRNA number information, as shown below

The results of ceRNA retrieval are shown below

5. RBP-RNA

Similar to miRNA target, the RBP CLIP-seq sequencing results of RNA binding protein are downloaded from GEO database, and the binding site information is obtained by peak calling analysis. At the same time, the motif of binding site is analyzed by homer software, and the disease annotation information of COSMIC database is provided according to the target gene, corresponding to the menus of the following three navigation bars.

RBP-target

RBP-motfi

RBP-disease

The results are as follows

In addition to the above five basic information, the following two kinds of analysis are provided.

1. Pathway

Through kegg enrichment analysis of target genes, the results of the following four types of enrichment analysis can be viewed through the pathway menu in the navigation bar.

MirTarPathway

RbpTarPathway

RnaTarPathway

CeRnaPathway

The search results are as follows

2. Pan-Cancer

Using the transcriptome data corresponding to 32 cancer types in TCGA, pan-cancer analysis is carried out. The detailed information can be viewed from the pan-cancer column in the search results, as shown below.

The results of co-expression analysis of the two genes are provided, and two display forms of scatter plot and box diagram are provided, as shown below.

Through the starbase database, we can query the interaction information between various RNA molecules to regulate the network information by ceRNA.

At this point, the study of "A brief introduction to ceRNA Database" is over. I hope to be able to solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!

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