8.8. How can I create a heat map for a specific list of genes?
This FAQ addressed how to create a heat map to visualize only a specific list of genes.
The FAQ is divided into three sections:
- How to create a heat map for a specific list of genes
- Example showing how to create a heat map visualizing differential expressed genes for a specific GO term
- How to create a filtered feature track
You can create a heat map for only a specific list of genes using the "Specify features" option in the Create Heat Map for RNA-Seq tool wizard. This functionality is also described on the following manual page:
In the wizard you can either enter the list of gene names by typing or coping/pasting your list of gene names into the text box:
Here, any white-space characters, and ",", and ";" are accepted as separators.
By specifying a filtered feature track only containing the listed genes:
The latter option is preferable if wishing to visualize the same set of genes on a routine basis or for saving the gene list in the Navigation Area for later use. Furthermore, the feature track option can be used if the list of features contain more than 10000 characters.
For information on how to create the filtered feature track see section 3.
Example showing how to create a heat map visualizing differential expressed genes for a specific GO term
In this example 39 differential expressed genes involved in the GO biological process cornification were identified by a Gene Set Test. In this example we will visualize these 39 genes on a heat map.
The steps are:
- First open the resulting table from the Gene Set Test
- Select to show DE Genes (Names) in the side panel
- Right click the cell with the DE Gene names and select the option to Copy Cell
- Launch Create Heat Map for RNA-Seq tool and follow the wizard to the Set filtering step
- Select Specify features as the filter setting
- Paste the DE gene names in the Keep these features text box by clicking Ctrl+V or ⌘+V on Mac
- Follow the wizard to save the heat map
You can now edit the layout of the heat map by setting different side panel settings:
To create a filtered feature track please follow the steps below:
- Open the feature track used for the RNA-Seq Analysis in the table view
- Click the arrow in the top right corner to open the Advanced filter option
- Set the filter to Name | is in list |
- Type or copy/paste the list of gene names and click the button labelled "Filter"
- Select all rows of the table by clicking a single row, then pressing Ctrl+A or ⌘+A on Mac
- Click the button labelled "Create Track from Selection"