Skip to content

Commit

Permalink
Changed instructions in stringApp disease exercise
Browse files Browse the repository at this point in the history
  • Loading branch information
scaramonche committed Sep 29, 2024
1 parent 19a059f commit 0daa93d
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion _pages/training_stringapp_diseases.md
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ _How many big clusters are there (with more than 10 nodes)? Are any of the clust

### 2.2 Group-wise functional enrichment

Now we will perform functional enrichment analysis on each of the bigger clusters separately. Sometimes stringApp does not detect the clustered network as STRING network, so switch to the unclustered network and back to the clustered one. Now, select the menu **Apps → STRING Enrichment → Retrieve group-wise functional enrichment**. In the resulting dialog, press **Advanced** to show the advanced options and set the **minimum group size** to **10**, in order to retrieve enrichment results only for clusters with at least 10 nodes. Press **OK** and the **STRING enrichment** table will be populated with several tables, one for each cluster. You can explore the results of each of them separately. Note that if you only see enriched DISEASES, you need to reset the filter by pressing the filter icon, choosing **Select all** for including all categories, and pressing **OK**.
Now we will perform functional enrichment analysis on each of the bigger clusters separately. Sometimes stringApp does not detect the clustered network as STRING network, so switch to the unclustered network and back to the clustered one. Now, select the menu **Apps → STRING Enrichment → Retrieve group-wise functional enrichment**. In the resulting dialog, press **Advanced** to show the advanced options and set the **minimum group size** to **10**, in order to retrieve enrichment results only for clusters with at least 10 nodes. Press **OK** and the **STRING enrichment** table will be populated with several tables, one for each cluster (look at the bottom right, next to the *Node* and *Edge Table*). You can explore the results of each of them separately. Note that if you only see enriched DISEASES, you need to reset the filter by pressing the filter icon, choosing **Select all** for including all categories, and pressing **OK**.

_Can you briefly characterize the three largest clusters in terms of their functionality? What distinguishes them?_

Expand Down

0 comments on commit 0daa93d

Please sign in to comment.