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This article mainly introduces what pathway common is a database, the article introduces in great detail, has a certain reference value, interested friends must read it!

Network based analysis, network-based data analysis, is the most common method to study gene function, the most typical is the analysis of pathway and protein interaction network, the interaction between genes constitutes a network, through the network-based data mining algorithm to mine potential hub genes.

The functional annotation of genes comes from the database. For pathway, there are kegg pathway, reactome and other databases. For ppi, there are string, IntAct and other databases. The contents and formats of data collected in different databases are different. In order to retrieve various databases more conveniently, some scientists have integrated the information from multiple pathway and ppi databases to build a comprehensive website, pathway common.

The web address of the database is as follows

Https://www.pathwaycommons.org/

The initial version integrates information from a database of nine pathway and gene interactions, including BioGRID, HPRD, IncAct, etc., as detailed below

Later, the information in the following databases was further integrated

Kegg pathway

PANTHER pathway

Wikipathways

NCI Pathway Interaction Database:Pathway

NetPath

Through the Search function of the front page, the information in the database can be retrieved according to pathway or gene name. Take TP53 as an example, the results are as follows

Contains two kinds of information about the interaction of the gene, interactions and pathway, as shown below

1. Interactions

Using the gene interaction information collected in each database, the following gene interaction network is drawn.

2. Enrichment

If more than five genes are searched at a time, the pathways enriched by the entered gene list will be displayed in Enrichment, as shown below

3. Pathway

Click on each pathway to view a detailed road map, as shown below

Through the PCViz function of the official website, you can view the functional interaction network among multiple genes, and the results are as follows

The pathway common database provides a unified data exchange format BioPAX, and all data can be downloaded from the following FTP address

Https://www.pathwaycommons.org/archives/

Through this database, we can easily carry out network-based gene function research, of course, this integrated database is convenient, but also has the limitation of the source database, there is no one database can cover all the related databases, such as the most commonly used string database of ppi is not included, but for pathway, the database is very comprehensive.

The above is all the contents of the article "what database is pathway common?" Thank you for reading! Hope to share the content to help you, more related knowledge, welcome to follow the industry information channel!

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