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Editor to share with you what the use of PathVisio tools, I believe that most people do not know much about it, so share this article for your reference, I hope you will learn a lot after reading this article, let's go to understand it!

PathVisio is a free and open source pathway visualization tool, through which we can not only create and edit road maps, but also conduct enrichment analysis.

The official website of the software is as follows

Https://www.pathvisio.org/

Download and install

This software is a GUI graphical interface tool for java language development. The official website provides two ways to download it:

Choose Binary Installation to download, because the software is developed with java program, you must ensure that the java runtime environment (JRE) is installed on your computer, unzip it after download, and then double-click the pathvisio.bat file to start the software.

The initial interface is as follows:

Edit the road diagram

The gpml path file we downloaded from wikipathway can be imported directly into this software. Take the WP554 pathway as an example.

Https://www.wikipathways.org/index.php/Pathway:WP554

Download the gpml file for the path from the link above, then click File-> Import to import the file. After the import is successful, you can see the road map. Each element in the diagram can be edited.

For the connection between elements, mouse click can drag; for elements in the box, click to select, you can change its size and move its position, double-click will pop up the edit box, edit the label information marked on the node.

You can not only edit the original elements, but also insert new elements through the options in the toolbar shown below, without expanding the specific usage.

For the edited road map, you can select File-> Export to export, you can export to pictures, support PDF, PNG,SVG, TIFF four formats, can also be saved as gpml and other file formats.

Retrieve gene-related pathway information

On the right panel, there is a Search function that can query the pathway information corresponding to genes.

The first thing you need is a database for retrieval, that is, a folder under which all the pathway gpml files can be obtained from wikipathway's official website. Then enter the name of the gene to be retrieved, providing two formats: Symbol and ID. Through the Search function, we can easily query the gene-related pathway information.

This software can also install plug-ins to make it more powerful.

These are all the contents of this article entitled "what are PathVisio tools for?" Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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