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.
../_images/tp53_network_log2fc.png
  • Select the Window ‣ Enrichment Analysis.
../_images/enrich_analysis_win.png

  • 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.

    1. Select File ‣ Import ‣ Attributes from CSV File as described in previous section.
    2. 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
    ../_images/import_uniprot.png

  • In the Enrichment Analysis window,

    1. Choose Gene Ontology in the drop-down list.
    2. Set Gene ID column to UniProt.Ac.
    3. Set the multiple testing Correction method to Bonferroni.
    4. Click the Run button.
    ../_images/enrich_analysis_run.png

  • 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 and DNA damage checkpoint are listed in first and second rows respectively.
    • Select the cell cycle checkpoint GO term, the click info-icon icon to see the details about the term.
    ../_images/enrich_analysis_result.png

  • 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 and Cell 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)
    ../_images/group_name_edit.png

  • The result is shown below:

../_images/group_name_result.png

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:

  1. Select the TreeTable view tab in the Enrichment result window.
  2. Select a GO term named kinase binding at molecular_function > binding > protein binding > enzyme binding > kinase binding.
  3. Click the group-icon button.
../_images/kinase_binding_tree.png
  1. 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.
../_images/kinase_binding_edit.png
  1. Manually adjust the positions of nodes like below:
../_images/GO_kinase_binding.png
  1. Select a GO term named cell cycle at biological_process > cellular process > single-organism cellular process > cell cycle.
  2. Click the group-icon button.
../_images/cell_cycle_tree.png
  1. 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.
../_images/cell_cycle_edit.png
  1. Now you can see that cell cycle contains all genes in kinase binding. The final result looks like below:
../_images/GO_cell_cycle.png