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This article will explain in detail what is the use of lncRNASNP database for you. The editor thinks it is very practical, so I share it with you as a reference. I hope you can get something after reading this article.

The lncRNASNP database collects the information of SNP loci located on the lncRNA gene in humans and mice, and combines lncRNA with SNP through the following two ideas

To explore the effect of SNP loci on the structure of lncRNA

Analysis of the effect of SNP locus on the binding of lncRNA to miRNA

In addition, it also provides the relevant information of lncRNA,SNP in TCGA database, such as the expression profile of lncRNA in various tumors and the mutation of SNP site in various diseases. The web address of the database is as follows

Http://bioinfo.life.hust.edu.cn/lncRNASNP2

For a lncRNA, it contains the following types of information

1. Basic information

two。 SNP locus on lncRNA

Contains SNP loci from the following three sources

Dbsnp

TCGA

Cosmic

Taking the dbsnp database as an example, the results are as follows

3. LncRNA-related diseases

Contains the related diseases supported by the experimental evidence provided in the lncDisease database and the information predicted using TAM software, as shown below

4. Information of binding sites of lncRNA and miRNA

Using the software to predict the binding region information of lncRNA and miRNA, there will be multiple miRNA binding sites in a lncRNA, as shown below.

Click on each miRNA to see the detailed results of the software prediction.

Pita, MiRanda and TargetScan3 softwares are used for prediction.

4. Effect of SNP locus on lncRNA-miRNA binding.

It includes the following two effects

Gain

Loss

Gain refers to the fact that there is no binding site between lncRNA and miRNA, but there is a binding site between lncRNA and miRNA after mutation, while loss is the opposite, as shown below

5. Expression profile of lncRNA in TCGA database

The expression profile data in different tumors are displayed in the form of a histogram, as shown below.

The official website also provides online tools to analyze the effects of mutation sites on lncRNA-miRNA binding and SNP on the secondary structure of lncRNA, as described below

1. Effect of mutation site on lncRNA-miRNA binding

We only need to input the wild type sequence and mutant sequence of lncRNA, and use the above three kinds of software to predict the binding sites of miRNA and the two sequences, so as to analyze the effect of mutation on lncRNA-miRNA binding, as shown below.

2. The effect of SNP on the secondary structure of lncRNA

The effect of snp loci on the secondary structure of lncRNA is predicted by RNAsnp software, as shown below.

The official website also provides a lot of functions, please move to the official website to explore the specific usage.

This is the end of this article on "what is the use of lncRNASNP 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, please share it out for more people to see.

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