diff --git a/Friday/StringDB-HandsOn.md b/Friday/StringDB-HandsOn.md new file mode 100644 index 0000000000000000000000000000000000000000..0d050b14dca54bb9c89dc90c8342df122abaa5ae --- /dev/null +++ b/Friday/StringDB-HandsOn.md @@ -0,0 +1,58 @@ + +# Hands-On: STRING DB + +Here, we will explore the intractions of genes associzated to large deletiomns in cancer. + + +# Input: + + +<!-- <img src="images/ATAC-seq_PE.png" width="700" align="center" > --> + +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 + +2. Download the table as a .tsv file + +3. 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/ + + +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 + +## 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 ? + + +Check the settings tab to change the network options + + +6. What types of networks can you display ? + +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 + +7. In the analysis tab + +How many nodes does the network have ? + How many interactions does the network have ? + + + +