2.6. Functional annotation of a cluster¶
In this section, you will perform a GO Over-representation analysis for genes in Cluster 3
and visually annotate the cluster with representative functions via the Visual Editor UI.
- Make sure you select the Network tab of
Cluster 3
.
- Select the .
Before going to remaining steps, you need to import
symbol2uniprot_all.csv
into the node table. The reason is that our in-house GO over-representation analysis tool expects IDs of gene set to be UniProt Accessions.- Select as described in previous section.
- In the Import Attributes dialog,
- Choose a CSV file to import:
symbol2uniprot_all.csv
- Key Column in Annotation File:
HGNC.symbol
- Key Attribute in Network:
hgnc_symbol
In the Enrichment Analysis window,
- Choose
Gene Ontology
in the drop-down list. - Set Gene ID column to
UniProt.Ac
. - Set the multiple testing Correction method to
Bonferroni
. - Click the Run button.
- Choose
After a little, the result is shown in the Enrichment window at the bottom of main application.
- You can see that GO terms of
cell cycle checkpoint
andDNA damage checkpoint
are listed in first and second rows respectively. - Select the
cell cycle checkpoint
GO term, the click icon to see the details about the term.
- You can see that GO terms of
Next you will visually annotate the group node of
Cluster 3
with two representative functions.Caution
Now be sure to switch to the original network tab named
tcga_gbm_edges
.- Click the group node of cluster
3
in the original GBM-altered network. - In the Editor window,
- Click the
...
icon in Name property to edit a group name. - Enter
DNA damage response
andCell Cycle
. - Set the Font property to
Droid Serif 80 Bold
or what you want. (You can open the font chooser by clicking...
button in the Font property)
- Click the group node of cluster
The result is shown below:
Tip
How to define a group node that contains nodes (genes or proteins) with a same function after GO over-representation analysis.
After GO over-representation analysis of Cluster 3
:
- Select the TreeTable view tab in the Enrichment result window.
- Select a GO term named kinase binding at
molecular_function > binding > protein binding > enzyme binding > kinase binding
. - Click the button.
- After clicking the group node named
kinase binding
, edit its visual properties in the Editor window.
- Set Font to
Droid Serif 80 Bold
.- Set Text Color to
Orange
.- Set Shape to
Convex hull of the lines
.
- Manually adjust the positions of nodes like below:
- Select a GO term named cell cycle at
biological_process > cellular process > single-organism cellular process > cell cycle
. - Click the button.
- After clicking the group node named
cell cycle
, edit its visual properties in the Editor window.
- Set Font to
Droid Serif 100 Bold
.- Set Text Color to
Blue
.- Set Shape to
Rectangle
.
- Now you can see that
cell cycle
contains all genes inkinase binding
. The final result looks like below: