Update Thursday/String_DB_HandsOn_Diabetes.md

Thursday/String_DB_HandsOn_Diabetes.md

+
+# Hands-On: STRING DB - Diabetes
+
+Here, we will explore the intractions of genes associzated to diabetes.
+
+# Input:
+
+
+<!-- <img src="images/ATAC-seq_PE.png" width="700" align="center" > -->
+
+We will use The Human Protein Atlas to find the 126 genes associated to diabetes.
+
+https://www.proteinatlas.org/
+
+*	In the search bar, type diabetes
+
+*	Download the table as a .tsv file   
+
+*	Open in Excel and choose one column as gene identifier : copy it to clipboard
+
+
+## Looking for the gene interactors
+
+We will find our interacting proteins in  the String DB.
+https://string-db.org/
+
+
+*	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
+
+ 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
+
+
+4. What types of networks can you display ?
+
+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 structure preview
+
+### Check the analysis tab to explore the network's main statistics
+
+What kind of infomration can you give about this network ?
+
+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 Insulin metabolic process GO term ?
+How many genes are there annotated with this term for Human?
+
+12. Examine the Reactome pathways and choose to visualize the proteins in the two pathways related to GABA synthesis.
+
+
+
+<details>
+  <summary markdown="span">13. Save a figure of the network in file</summary>
+Exports -> svg
+
+</details>
+
+<details>
+  <summary markdown="span">14. Save a table of the protein interactions </summary>
+Exports -> tsv
+
+15. What protein is the biggest hub in the network ?
+
+</details>
+
+<details>
+  <summary markdown="span">16. Save a table of the number of interactors per protein i</summary>
+Exports -> tsv
+
+</details>
+
+
+
+