PathVisio is an application for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as you would in any drawing program, like PowerPoint or Photoshop. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological entities (genes or proteins) in your pathways to biological data using database identifiers.

This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing. Note: mapping experimental data is not yet a feature of PathVisio 1.1, but you can do this in combination with GenMAPP or with additional plug-ins for PathVisio).


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Here are some key features of "PathVisio":

Creating a new pathway:

· Create a new pathway by pressing Ctrl+N or selecting File > New. A blank drawing area will open where you can start editing the pathway. To save a pathway, click Ctrl+S or select File > Save.
Opening an existing pathway:

· Open an existing pathway file by pressing Ctrl+O or selecting File > Open. A file browser will open where you can navigate to the desired pathway file.
Searching for pathways:

PathVisio allows you to search for pathways that contain a given gene product. You can search pathways in two ways:

· Gene symbol (gene name)
· Gene identifier (as defined in the synonym database)

Search by gene symbol:

· This method searches for all pathways containing one or more gene products for which the gene symbol contains the specified search text. To find only gene products where the symbol exactly matches the search text, add "" before and after the text (e.g. "TP53" to search for exact matches of "TP53").

· To start the search, go to the Pathway search tab in the side panel or select Edit > Search pathways. In the search interface, choose Symbol in the Search by drop-down list.
· Type the gene symbol you want to search for in the Symbol text field.
· Choose the directory you want to search (sub directories will be included) using the Browse button.
· Click the Search button to start the search.

Search by gene identifier:

· This method searches for all pathways containing one or more gene products that correspond to the given identifier. Gene products that are linked via cross references in the synonym database are also included.

· To start the search, go to the Search tab in the side panel or select Edit > Search pathways. In the search interface, choose ID in the Search by drop-down list.
· Type the gene identifier you want to search for in the Id text field.
· Choose the database system the id belongs to (also see LINK TO DATABASES).
· Choose the directory that contains the pathway files you want to search (sub directories will be included) using the Browse button.
· Click the Search button to start the search.

Browsing search results:

· The search results will be displayed in the side panel. The results table shows pathways that have one or more gene-products matching the symbol or identifier searched. If you double-click on a pathway in the table, PathVisio will open this pathway and highlight the relevant gene products with a green outline. You can disable this highlighting by un-checking Highlight matches.

Requirements:

· Java 2 Standard Edition Runtime Environment

What's New in This Release: [ read full changelog ]

· Autosave
· Zoom using scroll wheel
· Selection of lines is easier: no longer necessary to click on the exact pixel
· Now with two methods for over-representation analysis; one pathway-oriented and one data-oriented