2.5. Import expression log2FCs in normal vs. tumor

You will import gene expression log2FCs between normal vs. tumor condition in all TCGA GBM patients. and map them to the colors of nodes.

  • Select the Network tab of previously created network from Cluster 3 in the original network.
../_images/new_graph_tp53.png
  • Select File ‣ Import ‣ Attributes from CSV File.
../_images/import_attr_menu.png

  • In the Import Attributes dialog,

    1. Be sure Attributes for: Node to be checked.
    2. Choose a CSV file to import: tcga_gbm_exp_log2fc.csv
    3. Check The first line in a CSV file contains column names
    4. Key Column in Annotation File: Gene_Symbol
    5. Key Attribute in Network: hgnc_symbol
    6. Click the OK button.
    ../_images/import_attr_dialog.png

  • Now you can see a newly added column log2FC in the node table as shown in below:

../_images/import_attr_col.png

  • In the Visual Mapping (Nodes) window,

    1. Click color-icon icon.
    2. Choose log2FC in the drop-down list.
    3. Click pallet-icon to show up a palette chooser.
    4. Select ryb-icon (Red-Yellow-Blue).
    5. Click invert-icon to map Red to the maximum and Blue to the minimum value.
    6. Check list-icon to show a list of node names with their mapped colors ranked by values.
    7. Click the Apply button.
    ../_images/log2fc_to_color.png

  • The final network of Cluster 3 is shown below:

../_images/tp53_network_log2fc.png
  • Repeat above steps on the network of Cluster 5.

Tip

How to add more gradation points and colors.

  • You can add any number of gradation points by clicking desired positions on the color bar.
  • Once you have a gradation point, you can edit its color by double-clicking the point.
  • You can also move the points by dragging them.
../_images/gradation_points.png