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STRING & related databases: Large-scale integration of heterogeneous data
The document discusses the STRING database, which integrates heterogeneous biological data to generate association networks for proteins. It describes how STRING collects and connects curated knowledge, experimental data, and predicted interactions from genomic context, co-expression and text mining. The document also outlines exercises for users to explore protein-protein associations in STRING and related databases that integrate data on subcellular localization, tissue expression, and disease associations.
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STRING & related databases: Large-scale integration of heterogeneous data
- 1. Lars Juhl Jensen STRING& related databases Large-scale integration of heterogeneous data
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- 10. Exercise 1 Go tohttps://string-db.org/ Query for human SORCS2 using the search by name functionality Make sure you are in evidence view (check the buttons below the network) Why are there multiple lines connecting the same to two
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- 30. Exercise 2 (Continue fromwhere exercise 1 ended) Which types of evidence support the interaction between SORCS2 and NGFR? Click on the interaction to view the popup, which has buttons linking to full details
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- 70. Exercise 3 (Continue fromwhere exercise 2 ended) Change the network to the confidence view Change the confidence cutoff to 0.15; any changes in proteins or interactions shown? Increase the number of interactors
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- 125. Exercise 4 Open https://diseases.jensenlab.org Searchfor Parkinson’s disease What is the strongest associated gene? Inspect the underlying text-mining evidence Open https://tissues.jensenlab.org