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” and organism "Homo sapiens" to generate a network in STRING revolving around these proteins. What do the nodes and edges mean (hint: use the viewers panel)? How many interactions are returned? How many of the 28 proteins are connected with at least 1 interaction? What do the different colours 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?

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. For example, switch the network type from full STRING network to physical subnetwork and click update. What happened to the network? Which interaction evidences are now used (use the legend panel to understand)? Now, in the settings panel switch the 2nd shell option and set it to "no more than 20 interactors" and click update. What has changed in the network? What are the white nodes compared to the colored nodes? How many of the 28 starting proteins are now connected to at least one protein in the network?

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. If experiments were done, which assays were used to detect the interaction?

11. Which options do you have to download/export your network (hint: do not use the Downloads button but the Exports panel)? Use the export to short tabular text output and save the network as a .tsv file. Open the file with a text editor or excel or any other software to manipulate tabular data and inspect its content. What is in each row and each column?