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How to analyze the KEGG Brite database, I believe that many inexperienced people are at a loss about it. Therefore, this paper summarizes the causes and solutions of the problem. Through this article, I hope you can solve this problem.

KEGG, known as the Kyoto Encyclopedia of Genome, is a comprehensive database. For such a large database, it is necessary to sort out the data. In addition to splitting all kinds of data into different sub-databases, KEGG also makes a more detailed functional classification of all the data, and the functional classification information is stored in the brite database.

Birte mainly contains the following five categories of classified information:

Genes and protein

Compounds and reactions

Drugs

Diseases

Organisms and cells

In the brite database, the classification information is stored as a file. Contains files in two formats:

Table format, such as the classification of drugs

Htext files, such as the classification of kegg orthology

Http://www.kegg.jp/kegg-bin/get_htext?ko00000.keg

Files in two formats are provided for download, with the suffix keg for htext and json for json.

Json format is a new standard for network data legends, which is mainly used for program parsing; `keg files are plain text files and can be opened with a text editor.

Take all ko classification files, ko00000.keg files, as an example:

The classification levels are arranged in alphabetical order. In the sample file, An is the first level of classification, and B, C and D are the second level.

We can see intuitively that K00844 belongs to the category of Glycolysis / Gluconeogenesis, corresponding to a higher level of classification is Carbohydrate metabolism, and then a higher level of Metabolism.

Keg file format is still very easy to understand, but not intuitive enough to use, when we want to query the specific classification of a KO, if there are too many nodes in the same category with this KO, we need to look up a lot of lines in order to find the corresponding classification; sometimes accidentally flipped over, it will be a mistake.

Of course, you can format the file through a program, such as changing the file to the following format:

KONameCBAK00844HK... Glycolysis... Carbo..bolismMetabolism

This makes it easy to view the detailed classification information of items

For people who have no programming foundation, kegg provides a keggHier program specifically for viewing classification information in brite. The software is developed in java and provides a graphical interface, which is easy to use.

Download address:

Http://www.kegg.jp/kegg/download/kegtools.html

Usage

Double-add batch file startup

Click the File button from the menu bar and select Import data from the kegg website

Select the classification structure of the first kegg pathway map here to view it.

The downward triangle represents the meaning of expansion. Here are three, indicating that pathway has three layers of classification. The mouse can click on any record to expand the details.

The search box in the upper right corner can be searched, and you can quickly find the records you are interested in through the search box.

Brite is a database that stores classification information, providing a classification of all records such as pathway, ko, module, drug, disease,organism, etc.

The classification information is separated by files, and there are two formats: keg and table.

Through the KEGGHier tool, you can easily browse the KEGG classification system.

After reading the above, have you mastered the method of how to analyze KEGG Brite database? If you want to learn more skills or want to know more about it, you are welcome to follow the industry information channel, thank you for reading!

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