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This article shows you how the metabolic pathway database wikipathway is, concise and easy to understand, which will definitely brighten your eyes. I hope you can get something through the detailed introduction of this article.

In order to prevent and treat diseases, it is important to understand cell activity. Cell activity is usually a dynamic process of changes in a series of proteins and metabolites, called pathway. Our commonly used pathway database is KEGG pathway, in addition to KEGG pathway, there are many pathway databases can be used.

When we query a gene on NCBI, we will give the corresponding pathway annotation information, such as human's TP53 gene.

From the figure, we can see that there are KEGG pathway, Wikipathway, REACTOME, Pathway Interaction Database and other databases.

Pathway is the embodiment of our known information about cell activity. With the continuous efforts of researchers, there will be a substantial increase in new pathway information every year. Wikipathway contains this information and provides a free, easy-to-use web service.

The information in wikipathway is different from that in kegg pathway. Pathway in kegg is a cross-species concept, while wikipathway contains its specific pathway information for each species.

The link to the official website is as follows:

Https://www.wikipathways.org/index.php/WikiPathways

We can search through the Search function or browse through Browse.

For example, retrieve the pathway information that the tp53 gene participates in, enter the gene name as shown above, and then click the Search button to see the page shown below

On this page, select the corresponding species and all relevant pathway information will be given. Of course, we can also download all the pathway information directly.

Click the picture below the Download button, and you can download it by species when you jump to the page.

However, this method downloads files in gpml format and is suitable for programming or importing into other files for processing. The kgml format of gpml is similar to that of KEGG, which preserves the information of protein interaction (interaction) and molecular reaction (reaction) in pathway. At the bottom of this page, there are other ways to download.

The two most commonly used methods are Gene lists per pathway (GMT) and Pathway image files (SVG).

Gene lists per pathway (GMT) can download files in .gmt format, which preserves the correspondence between genes and pathway, but gene ID gives Entrez ID; Pathway image files (SVG) the road map of all pathway that can be downloaded in svg format.

For the path map of wikipathway, there are two core concepts, gene products (gene product) and metabolites (Metabolites). Pathway is simply understood as a series of enzymatic reactions. Enzymes are products of genes, and the substrates and products of enzymatic reactions can be regarded as metabolites.

In the road map, metabolites are shown in blue, gene products in black, metabolite A to metabolite B linked with black arrows, and catalytic proteases (gene products) linked with arrows with rounded ends.

For example, the following:

Summary

Wikipathway is a database of metabolic pathways and can be used as a supplement to kegg pathway.

Wikipathway uses gpml format to store interaction and reaction information in pathway. Blue represents metabolites and black represents gene products in the metabolic pathway map.

The above is what the metabolic pathway database wikipathway is like. Have you learned any knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

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