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Protein interactions
This document discusses protein-protein interaction data and resources. It introduces common interaction detection methods like yeast two-hybrid and affinity purification. Several curated interaction databases are described, including BioGRID, DIP, IntAct, and MINT. The document also discusses the STRING database, which integrates interaction data with genomic context predictions. It notes challenges like errors, biased assays, different formats between databases, and difficulty in comparing data across species. Quality scores and calibration to gold standards are presented as ways to assess confidence in interactions. The related STITCH database is also introduced, which integrates protein-protein and chemical-protein interactions.
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Protein interactions
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- 2. what is aninteraction?
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- 22. BioGRID General Repository forInteraction Datasets
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- 26. Exercise 1 Go tohttp://thebiogrid.org Query for human TYMS Find the interaction partners Check their sources Think of possible problems
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- 36. Exercise 2 Go tohttp://string-db.org Query for human TYMS Show only highest confidence Show network in confidence view Show network in evidence view
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- 80. Exercise 3 Query STRINGfor human TYMS Show only experimental evidence Show up to 50 interaction partners Show also low-confidence links Redo exercise for mouse TYMS
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- 83. STRING + 300kchemicals
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- 90. Exercise 4 Go tohttp://stitch-db.org Query for human TYMS What is the role of thymidylate? What is the role of dUMP? What is the role of Permetrexed?
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Editor's Notes
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