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

Other Features

Setting Preferences

Several preferences can be set in PathVisio to customize the appearance and usage of the program. The Preferences menu can be accessed from the Edit menu. Options in the Preferences menu are:

Display

  • The initial size of the right side panel when PathVisio is first opened can be set. The default value for this is 30.
  • Gene product rectangles (data nodes) can be displayed with rounded or squared edges. The default is squared edge display.
  • Movement of lines on the drawing board can be either be free or lines can be set to "snap-to-angles" to facilitate drawing. The default is free movement. The degree of angles for "snap-to-angle" is user-defined as well, the default is 15.
  • Support for MIMs (Molecular Interaction Maps) can be loaded automatically when PathVisio starts. MIMs support is not loaded by default.
  • Advanced object attributes, such as references, can be displayed. Advanced attributes are hidden by default.
  • Coloring preferences for managing the coloring of highlighted and selected objects, as well as options for coloring related to displaying data.
    • Default color for "no criteria met"
    • Default color for "gene not found"
    • Default color for "no data found"
    • Outline color for selected objects
    • Outline color for highlighted objects

NOTE: You need additional plug-ins for displaying data on pathways with PathVisio 1.1

Directories

Preferences for file locations determine in which directories PathVisio will look for files by default. The following file locations can be set:

  • gpml pathways
  • Gene databases
  • Expression Datasets

NOTE: You need additional plug-ins to display data on pathways in PathVisio 1.1

Files

The location of where the PathVisio log file will be stored can be set as a preference.

Database

The type of database connector for gene databases and expression datasets can be stored as a preference.

NOTE: PathVisio 1.1 requires additional plug-ins to support display of microarray data on pathways.

Keyboard shortcuts

Ctrl + N: Create a new pathway
Ctrl + O: Open a pathway
Ctrl + S: Save pathway
Ctrl + C: Copy
Ctrl + V: Paste
Ctrl + left mouse click: Add or remove object from selection
Ctrl + A: Select all gene products on the pathway
Ctrl + G: Create a group of selected objects
Ctrl + Z: Undo