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This article mainly introduces the use of the SomamiR 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.

MiRNA can combine with multi-search RNA molecules and play an important role in ceRNA regulatory network. CeRNA as an endogenous regulatory mechanism, when the binding of miRNA is abnormal, its regulatory function is also affected, which may lead to the occurrence of disease.

For complex diseases such as tumors, scientists try to analyze and mine effective information from genomes, transcriptome and other groups at different levels. At the genome level, it includes a variety of genomic variation studies with somatic mutation as the main body, and at the transcriptome level, including a number of analyses based on the ceRNA regulatory network. Due to the complexity of life activities, the information that can be explained by a single group of science is limited. It is the trend of future research to combine multiple groups of data to analyze the experimental phenomena from all levels and angles.

The developers of SomamiR database associate genomic variation with transcriptome data based on the idea that genomic variation at miRNA binding site may affect the ceRNA regulatory network. The database collects somatic mutation sites of various tumors, which are located on miRNA or miRNA binding sites, which may affect the binding of miRNA to target molecules. The database website is as follows.

Http://compbio.uthsc.edu/SomamiR/

As shown in the following figure, we can retrieve and view the information in the database from six aspects

For tumor-related somatic mutation sites, they can be simply divided into two categories, the first type is directly located on miRNA, and the second type is located in the region of miRNA binding sites. For the second category, according to the method of miRNA binding region analysis, they are subdivided into three subcategories, namely, miRNA binding regions verified by CLASH experiments. The miRNA binding regions verified by RAP-CLIP,HIS-CLIP experiments and the miRNA binding regions predicted by software. These correspond to the four boxes shown on the left side of the image above.

Taking the somatic mutation site directly located in the miRNA gene region as an example, the search box is as follows

You can select the corresponding tumor type, and the search results are as follows

The retrieval method of the second type of loci is the same, except that the specific information displayed is slightly different for different detection methods. Take CLASH as an example, as shown below

The miRNA binding sites obtained by CLASH data analysis and the details of somatic mutations located in this region are given.

In addition to providing tumor-related somatic mutation sites directly, in order to better study their functions, the pathway information of the corresponding genes involved in these mutation sites is also provided, as shown below.

At the same time, the information of mutation sites that increase the risk of disease was collected from the literature, and the results are as follows.

The analysis idea of linking genomic variation with transcriptome in this database is worthy of our reference.

Thank you for reading this article carefully. I hope the article "what's the use of SomamiR database" shared by the editor will be helpful to you? at the same time, I also hope you will support us and pay attention to the industry information channel. More related knowledge is waiting for you to learn!

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