1. Does STRING only contain interaction data for human?

2. Can you download the whole content (all protein associations) of the database?

3. What are your search options?

4. Use the given list of 28 proteins (STRING_input_28_genes.txt) as input and the search option “multiple proteins” to generate a network in STRING revolving around these proteins. How many interactions are returned? What do the different colors of the edges mean? Try to understand what the different sources of evidence mean (you can also explore the help pages to get more information). Which of these evidences are based on predictions and which ones are based on experiments?

5. Is there a confidence score for each protein association and if yes, how should you interpret it? (Bonus question: Try to understand how the confidence score is calculated.)

6. Using your query results from point 4, explore the information provided under the Analysis panel. What do the network stats tell you? For which cellular processes or protein complexes is this network enriched for? Take a screen short or copy/paste the enriched functional terms.

7. Play with the different settings under the Settings panel and try to understand how they can help you further expand or reduce the network. Select as confidence cutoff 0.7 and set the 2nd shell parameter to “no more than 50 interactors”. Explain how the network has changed. What are the white nodes compared to the colored nodes?

8. Explore again which functional terms are now enriched in this expanded network. Which differences do you observe compared to the previously enriched terms?

9. Inspect the network a little more. Find cases where the expansion was helpful to understand functional relationships between your proteins of interest (your query proteins) and where it maybe wasn’t so helpful. 

10. Click on the edge between the two proteins HNRNPD and U2AF2. What is the source of evidence for this interaction? Try to understand if a physical association has been detected experimentally between both proteins by further exploring the information provided. In case it was, by which assays was this interaction detected?

11. Which options do you have to download/export your network (hint: do not use the Downloads button but the Exports panel)?