diff --git a/Thursday/String_DB_HandsOn_Diabetes.md b/Thursday/String_DB_HandsOn_Diabetes.md new file mode 100644 index 0000000000000000000000000000000000000000..8d319eda3f852b85827eeabe02b19a7232aa78fa --- /dev/null +++ b/Thursday/String_DB_HandsOn_Diabetes.md @@ -0,0 +1,98 @@ + +# 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> + + + +