Update Thursday/StringDB-HandsOn.md

Thursday/StringDB-HandsOn.md

@@ -12,11 +12,11 @@ Here, we will explore the intractions of genes associzated to large deletiomns i
 We will use The Human Protein Atlas to find the 41 genes associated to large deletions in cancer
 https://www.proteinatlas.org/
 
-1.	Choose : The tissue -> Go to the Human Subproteomes and choose The cancer proteome  -> Select the   large deletions genes
+*	Choose : The tissue -> Go to the Human Subproteomes and choose The cancer proteome  -> Select the   large deletions genes
 
-2.	Download the table as a .tsv file   
+*	Download the table as a .tsv file   
 
-3.	Open in Excel and choose one column as gene identifier : copy it to clipboard
+*	Open in Excel and choose one column as gene identifier : copy it to clipboard
 
 
 ## Looking for the gene interactors
@@ -25,36 +25,58 @@ We will find our interacting proteins in  the String DB.
 https://string-db.org/
 
 
-1.	Search -> Multiple proteins and paste list
-2.	Select  organism and click  the search button
-3.	Check the mapping, are they your prots ? How many ?
-4.	Click the continue button
+*	Search -> Multiple proteins and paste list
+*	Select  organism and click  the search button
+*	Check the mapping, are they your prots ? How many ?
+*	Click the continue button
 
 ## Exploring your network
 
 ### Check the legend tab to understand the network components
 
-5. What do nodes represent? 
-What do edges represent ?
-What are the figures inside the nodes ?
+ 1. What do nodes represent? 
+
+ 2. What do edges represent ?
+
+ 3. What are the figures inside the nodes ?
 
 
 ### Check the settings tab to change the network options
 
 
-6. What types of networks can you display ?
+4. What types of networks can you display ?
 
-What kind of interaction sources do you have in this netwrok ? 
+5. What kind of interaction sources do you have in this netwrok ? 
 
 Choose to see both functional and physical associations and that the edges represent the confidence of the data
 
-Remove the protein structures previews
+Remove the protein structure preview
+
+### Check the analysis tab to explore the network's main statistics
+
+7. How many proteins does the network have ? 
+
+8. How many interactions does the network have ?
+
+9. How many interactions is this network expected to have if it were a random list of proteins ? 
+
+10. How many interactions does each protein have on average ?
+
+### Check the analysis tab to explore the functional enrichment of the network
+
+11. Which proteins belong to the Fanconi anemia KEGG pathway ?
+
+12. How many proteins are described in Uniprot with the Hereditary nonpolyposis colorectal cancer keyword ?
+
+13. How many drug compounds can we find associated to the PTEN protein ?
+
+14. Save a figure of the network in file
+
+15. Save a table of the protein interactions in a table
+
 
-### Check the analysis tab
 
-7.How many nodes does the network have ? 
 
-       How many interactions does the network have ?