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This article mainly introduces the use of the Co-LncRNA database, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

Many studies have shown that lncRNA is related to many biological processes and complex diseases. In order to further explore the specific role of lncRNA in these life activities, we need to analyze the function of lncRNA.

In bioinformatics, the usual way to mine gene function is to use functional databases such as GO and KEGG, but these databases are all protein coding genes. In order to make use of the information in these databases, we need to establish a relationship between lncRNA and mRNA. The common ideas are as follows.

Through the interaction between lncRNA and mRNA

The interaction between lncRNA and mRNA has been reported in many literatures and databases, and the combination of them can also be predicted by software, and the function of lncRNA can be studied through mRNA, the target of lncRNA.

Through co-expression of lncRNA and mRNA

It is generally believed that the set of co-expressed genes participate in the same pathway or are subject to the same regulation and have similar biological functions. We use expression profile data to find mRNA co-expressed with lncRNA, so as to study the function of lncRNA.

Through ceRNA regulation mechanism

CeRNA is a very popular concept in recent years, which means that all kinds of RNA molecules play a regulatory role through competitive binding of miRNA. For lncRNA, through the ceRNA mechanism of lncRNA-miRNA-mRNA, lncRNA is associated with mRNA, so as to explore the function of lncRNA.

Co-LncRNA analyzes and finds the mRNA co-expressed with lncRNA, constructs the co-expression network between lncRNA and mRNA, and studies the function of lncRNA through the corresponding GO and KEGG of the co-expressed mRNA. The website of the database is as follows

Http://bio-bigdata.hrbmu.edu.cn/Co-LncRNA/

The RNA-seq data of 6500 samples from 28 tissue / cell lines were collected from GEO and TCGA, and then mRNA and lncRNA were quantified by classical tophat+cufflinks+RSEM strategy. Spelman correlation analysis and linear regression were used to analyze the co-expression between lncRNA and mRNA, and the co-expression network of lncRNA and mRNA was constructed. For lncRNA, the co-expressed mRNA is analyzed by GO and KEGG enrichment analysis, the method is Fisher test, and the result of functional enrichment is regarded as the annotation of the lncRNA. The complete process is as follows

CEGs stands for co-expression gene Co-Expressed Genes, and the results of co-expression analysis can be viewed through this menu, as shown below

Select the data set and the method of co-expression analysis, set the threshold, find the corresponding co-expression genes by the name of mRNA or lncRNA, click pattern to view the detailed analysis results, as shown below

View the functional enrichment results of the coexpression mRNA of lncRNA through CEGsFuncs, as shown below

For the results of KEGG enrichment, click to view the specific road map, on which the co-expressed protein coding genes will be marked in red, as shown below

Through CEGsNet, you can view the co-expression network of lncRNA and mRNA, as shown below

The site also supports uploading its own lncRNA and mRNA expression profiles, and then carries out co-expression analysis. The interface is as follows

The data in this database is downloaded for free. Through this database, we can not only find the existing co-expression analysis results of lncRNA and mRNA, but also carry on the co-expression analysis of our own data.

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