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This article will explain in detail what is the use of STRING 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 study of protein-protein interaction network is helpful to mine the core regulatory genes. At present, there are many databases of protein-protein interaction, among which string is definitely the one with the largest number of species and larger interaction information.

Https://string-db.org/

The latest version of the database, version 10.5, was updated on May 14, 2017. it stores 1380838440 interactions of 2031 species and 9643763 proteins.

Through the SEARCH function provided on the official website, the database can be easily retrieved, as shown in the following diagram

You can use the protein name, sequence and other formats to search, it should be noted that although the search is shown here according to the protein name, in fact, you can enter the gene sysmbol.

Searching for a single protein will give a network of all the proteins that interact with that protein, which is more suitable for exploring the interaction of a protein, while inputting multiple proteins at a time will only give the interaction network between the input proteins, which is more suitable for mining the interactions between the input proteins, such as all the differential genes identified by the input transcriptome data. The interaction between these differential genes was analyzed.

After the retrieval is complete, you will get the results shown below

The above networks are called protein interaction networks, protein-protein interaction network, or PPI networks. To understand the picture above, you need to understand the following two aspects

1. Node (node)

Each node in the figure represents a protein. Due to variable splicing and post-transcriptional modification in eukaryotes, a protein coding gene may produce multiple proteins. Here, different isoform produced by the same gene are merged, and the letters marked on the node are actually the gene symbol of the corresponding gene.

Some of the nodes in the picture have a spiral structure inside, which means that the three-dimensional structure of the protein is known, if unknown, the interior of the node is empty.

By default, the color of the node is divided into red and white, red represents your query protein, and white represents other proteins that interact with the query protein. Because white is not very good-looking, string maps colors according to the score values that interact with them. On the Legend page, you can see the color of each protein and the corresponding score value, as shown below

two。 Edge (edge)

The lines between the nodes represent the interaction between the two proteins, and different colors correspond to different types of interaction, as shown below

As can be seen from the figure, there is more than one line between the two proteins, which indicates that there are multiple interactions between the two proteins. Among all the relationships, there are both experimental verification and data prediction results, so it seems that there are many connections and is very complex. This can be set through the Settings of the results page, showing only the types of interactions you are interested in, as shown below.

On the Analysis page, the results of GO and KEGG enrichment analysis are provided for the genes in the protein-protein interaction network, as shown below

On the Exports page, you can export pictures of the interaction network, supporting PNG and SVG formats, and you can also export the corresponding interaction tables, protein sequences, comments and other information, as shown below

For a protein-protein interaction network with many nodes, you can also mine the subnet sub network, or module, through the Cluster page, which is essentially clustering genes. The interaction network formed by genes belonging to the same class is a module, as shown below.

Kmeans and MCL clustering are supported, and the result of clustering is TSV format, from which we can see which genes belong to the same group.

STRING database provides download function, because the whole database is very large, so you can select a species, and then download the corresponding data for that species, as shown below

This is the end of this article on "what is the use of STRING 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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