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Protein Association Networks with STRING Database

Explore protein association networks using STRING. Learn about interaction networks, curated knowledge, pathways, and types of evidence supporting interactions.

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Protein Association Networks with STRING Database

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  1. Protein associationnetworks with STRING Lars Juhl Jensen

  2. interaction networks

  3. association networks

  4. guilt by association

  5. protein networks

  6. STRING

  7. 9.6 million proteins

  8. common foundation

  9. Exercise 1 Go to http://string-db.org/ Query for human insulin receptor (INSR) 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 proteins?

  10. curated knowledge

  11. (what we know)

  12. protein complexes

  13. 3D structures

  14. pathways

  15. metabolic pathways

  16. Letunic & Bork, Trends in Biochemical Sciences, 2008

  17. signaling pathways

  18. very incomplete

  19. experimental data

  20. (what we measured)

  21. physical interactions

  22. Jensen & Bork, Science, 2008

  23. genetic interactions

  24. Beyer et al., Nature Reviews Genetics, 2007

  25. gene coexpression

  26. microarrays

  27. RNAseq

  28. Exercise 2 (Continue from where exercise 1 ended) Which types of evidence support the interaction between INSR and IRS1? Click on the interaction to view the popup, which has buttons linking to full details Which types of experimental assays support the INSR–IRS1 interaction?

  29. predictions

  30. (what we infer)

  31. genomic context

  32. evolution

  33. gene fusion

  34. Korbel et al., Nature Biotechnology, 2004

  35. gene neighborhood

  36. Korbel et al., Nature Biotechnology, 2004

  37. phylogenetic profiles

  38. Korbel et al., Nature Biotechnology, 2004

  39. a real example

  40. Cell Cellulosomes Cellulose

  41. complications

  42. many databases

  43. different formats

  44. different identifiers

  45. variable quality

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