Preparing data file for PathVisio


To visualize data on PathVisio pathways you need to convert your data file into a PathVisio expression data set (.pgex). Such a data set can be created from a text file, which can be prepared with most spreadsheet programs (e.g. Microsoft Excel). The PathVisio input file must have the following structure:

  • It can contain a header line, which provides a name for every column, but this is not necessary. The names of the columns define the names of the samples (variables) in your dataset.
  • It must contain two columns that contain respectively the gene identifier and System Code. If no System Code is present, it can also be manually selected during the wizard. Every other column contains data associated with the gene-products. The names of the columns containing the id and code is arbitrary, you can specify which column contains the id/code while creating the dataset.

An example of the structure of a raw data file:


Creating an expression dataset


Start data import wizard

  1. Go to Data -> Import Expression data
  2. Be sure your raw data is in the right format for import to PathVisio.
  3. Select a gene database before importing the data (with Data -> Select Gene Database). The choice of gene database can also be changed during the import wizard.

Pages during wizard

  1. File Locations: select location for the text file with expression data, select location to save expression dataset and, if necessary, change location of gene database.
  2. Header and Delimiter Information: select the line at which the header starts and the line at which the data starts. If more headers are present, for example at row 1 and 2, select header at line 1 and data at line 3. Also select delimiter present in the data.
  3. Column Information: Select column with gene ID’s and column with system code. If no system code is present in the data, select the appropriate system code manually.
  4. Create expression dataset: Finish the import.

Creating color sets


Color sets are used to color genes and proteins on pathways according to user-defined criteria based on the parameters available in the dataset. Color sets are stored together with your dataset, so before you can create a color-set you have to import your data or select an existing expression dataset.

Threshold color set

A threshold color set colors data nodes based on threshold-type criteria, for example “If the value is above 2, then color red, if the value is below 2 then color blue”. Two data nodes with values 2.1 and 5 will both be colored blue, a threshold color set does not produce a gradient based on the magnitude of the value.

  1. To create or edit a color-set, go to Data -> Visualization options or click the color-set button on the toolbar.
  2. The Visualization options window will open with a new, empty color set selected, named “untitled”. Click on the Icon in the upper right corner and select Rename to enter a descriptive name for your color set. For example, the name could describe a comparison between normal and transgenic animals.
  3. First, select if you want to display a text label on the data nodes in the pathway. You can select either a Text label, which is the gene symbol, or the Identifier, which is the gene or protein ID assigned to the data node.
  4. NOTE: For most pathways, the gene symbol is already used as a label on the data nodes, so adding an additional option here will obscure the original data node label.

  5. Selecting the Expression as color check box will open an interface for defining coloring criteria. Select the Basic radio button and click the icon to the right of the Color Set drop-down to select New.
  6. In the Edit Color Set window, click the Add rule button to activate the Rules interface. Build your criteria by clicking on the parameters and logical operators in the two lists. For example, a criteria may be: [24hrs-v14 fold] > 1.2
  7. When you have finished a criteria, select a color by clicking the Color button.
  8. Repeat steps 5 and 6 for additional criteria. Click OK when you are finished.
  9. TIP: A typical color set usually contains several criteria all dealing with the same comparison. For example, it could include criteria for both both up- and down-regulation.

  10. In the Visualization options window, you can also select to display a numerical next to each data node on the pathways. Check the Expression as numerical value check box and select a parameter from your dataset to display. Click OK when finished.

Gradient color sets

A gradient color set defines a color gradient based on an experimental parameters value. If the gradient is defined from -1 to 1 with colors ranging from blue to yellow, the color of the data nodes will be progressively darker blue as their values reach -1. For example, a data node with value -1 will be a darker blue than a data node with value -0.5 This is different from a threshold color set where all values past a certain threshold will be colored with the same exact color.

  1. To create or edit a color-set, go to Data -> Visualization options or click the color-set button on the toolbar.
  2. The Visualization options window will open with a new, empty color set selected, named “untitled”. Click on the Icon in the upper right corner and select Rename to enter a descriptive name for your color set. For example, the name could describe a comparison between normal and transgenic animals.
  3. First, select if you want to display a text label on the data nodes in the pathway. You can select either a Text label, which is the gene symbol, or the Identifier, which is the gene or protein ID assigned to the data node.
  4. NOTE: For most pathways, the gene symbol is already used as a label on the data nodes, so adding an additional option here will obscure the original data node label.

  5. Selecting the Expression as color check box will open an interface for defining coloring criteria. In the list of available parameters (data you imported), select the parameter you want to use for the criteria.
  6. Select the Basic radio button and click the icon to the right of the Color Set drop-down to select New.
  7. In the Edit Color Set window, select the Gradient check box. This will bring up the default gradient color set, ranging from -1 (blue) to 1 (yellow).
  8. In the gradient drop-down menu, select a color scheme and then select upper and lower gradient limits by typing into the entry fields for the gradient.
  9. Click OK when you are finished.