Shulou(Shulou.com)06/01 Report--

In this issue, the editor will bring you about how to analyze IMex and IntAct databases. The article is rich in content and analyzes and narrates it from a professional point of view. I hope you can get something after reading this article.

There are many databases of protein-protein interaction, such as DIP, MINT, IntAct, BioGRID and so on. There is a lot of redundancy in different databases, and it is very laborious to search between different databases.

In order to reduce the redundancy of different databases and maximize the efficiency of data storage and retrieval, a committee called international molecular exchange consortium, or IMEx, was set up with the participation of development teams and maintainers of multiple databases. The committee is committed to merging information in different databases, reducing redundancy and providing a unified query tool.

The members of the committee indicate as follows

The address of the project is as follows

Http://www.imexconsortium.org/

Through the search box of the official website, you can easily retrieve the contents of each member database, as shown below

Take tp53 as an example, the search results are as follows

Click on the link to IMEx and you can see the table shown below

The MITAB format is used to display the protein interaction information, which can be downloaded through the Download button in the upper left corner. Through the official website of IMEx, we can easily query the network information about the interaction of a protein, but it is not very convenient to download the data. If you want to download the data, you still need to use the IntAct database.

IntAct database is one of the member databases of IMEx. At present, this data also integrates all the data of IMEx. The website is as follows.

Https://www.ebi.ac.uk/intact/

There must be online retrieval functions, as shown below, supporting a variety of query methods

On the page of the search results, you can customize the column information displayed, or you can choose the corresponding format to download, as shown below

Through the Graph button, you can also display the interaction network of query proteins.

Compared with string database, the retrieval function of IntAct also has its limitations. It is only suitable for querying the interaction network of a single protein, but can not query the interaction network of multiple proteins input. If you want to query the interaction network between multiple proteins, you can only write your own script to extract information from the entire interaction network. The official website provides a download function, as shown below.

Provide a variety of formats for download, mainly XML and TAB two formats, PSI-MI format is xml format files, PSI-MI TAB is\ t separated files, the content of TAB format is relatively intuitive, and XML format is suitable for program processing.

For protein-protein interaction network, the use of String database is simpler and more humanized, so it is more well-known, while the use of IMEx and IntAct has a certain technical threshold, but it can be used as a supplement to String database to get more abundant information.

The above is the editor for you to share how to parse IMex and IntAct database, if you happen to have similar doubts, you might as well refer to the above analysis to understand. If you want to know more about it, you are welcome to follow the industry information channel.

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