diff --git a/Thursday/StringDB-HandsOn.md b/Thursday/StringDB-HandsOn.md index 76035550d90568918248406bbb1d3128f71aa619..62a6253a790c7eee30d0e043940c0aa632bbeed6 100644 --- a/Thursday/StringDB-HandsOn.md +++ b/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 ?