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

Pathway Statistics

Running statistical analysis

Before running PathVisio statistical analysis, you will need the following:

Once you have these prerequisites in place you are ready to run statistical analysis.

  1. Select Data > Statistics... to open the Pathway statistics interface.
  2. Use the Expression field to enter a criterion for running the analysis. This is similar to entering a criterion for a color set. For example, you could specify a criteria based on a fold change threshold. You can either type the expression in the Expression field or you can use the available parameters and operators listed by clicking on them.
  3. Select the correct pathway archive under Pathway directory.
  4. Click Calculate to start the analysis.

Results

When the analysis is finished, the results will be displayed in the statistics interface. The results are formatted as a list of all pathways in the designated pathway archive, with a set of metrics reported for each pathway, explained below. Clicking on any pathway in the list opens the pathway in PathVisio. It is also possible to save the results table as a tab-delimited text file by clicking the Save results button.

Metrics in the results table:

positive (r)

The number of genes on the pathway that pass the criterion.

measured (n)

The number of genes on the pathway that were measured in the experiment.

total

The total number of genes on the pathway.

%

The percentage of genes measured that passed the criterion (positive/measured).

Z Score

The standard statistical test under the hypergeometric distribution. A high Z score indicates that the pathway has more genes that pass the criterion than would be expected by chance.