Update Friday/StringDB-HandsOn.md

Friday/StringDB-HandsOn.md

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+# 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 ?
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+What kind of interaction sources do you have in this netwrok ? 
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+Choose to see both functional and physical associations and that the edges represent the confidence of the data
+
+7.	In the analysis tab
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+How many nodes does the network have ? 
+       How many interactions does the network have ?
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