Table of Contents

  1. Overview
  2. Main Features and Workflows
    1. Creating a new pathway
    2. Opening an existing pathway
    3. Searching for pathways
      1. Search by gene symbol
      2. Search by gene identifier
      3. Browsing search results
    4. Displaying experimental data
  3. Editing and Viewing Pathways
    1. Manipulating objects
      1. Placing new objects
      2. Selecting objects
      3. Moving objects
      4. Changing the size of objects
      5. Deleting objects
      6. Editing object properties
      7. Grouping objects
      8. Aligning, scaling and stacking objects
      9. Changing line and arrow type
      10. Using Molecular Interaction Map styles
      11. Changing the drawing order
      12. Copy and paste
    2. Annotating pathways
      1. Creating links between biological entities
      2. Creating links between lines
      3. Adding Literature References
      4. Adding Comments
      5. Changing general pathway information
    3. Manipulating pathways
      1. Zoom
      2. Import and export pathways
        1. Import/export between PathVisio and GenMAPP
        2. Export DataNode list
        3. Export to Eu.Gene
        4. Export to graphics formats
  4. Using experimental data in PathVisio
    1. Preparing raw data for PathVisio
    2. Creating an expression dataset
    3. Creating color sets
      1. Threshold color set
      2. Gradient color sets
  5. Retrieving Pathways and Databases
    1. Retrieving pathways
    2. Retrieving synonym databases
    3. Available synonym databases
    4. Supported database systems
  6. Pathway Statistics
    1. Running statistical analysis
    2. Results
        1. positive (r)
        2. measured (n)
        3. total
        4. %
        5. Z Score
  7. Other Features
    1. Setting Preferences
      1. Display
      2. Directories
      3. Files
      4. Database
    2. Keyboard shortcuts
  8. Tutorials
    9. Error: Page PathVisioTroubleshooting does not exist

Overview

PathVisio is a tool 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).

Main Features and Workflows

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 "\b" before and after the text (e.g. "\bTP53\b" 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.

Displaying experimental data

  1. Select the right synonym database.
  2. Create an expression dataset.
  3. Create a color set.
  4. Create a visualization.
  5. Open the pathway on which the data has to be displayed.

Attachments