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![Gene and protein names
Cue words for entity
recognition
Verbs for relation extraction
[nxexpr The expression of
[nxgene the cytochrome
genes
[nxpg CYC1 and CYC7]]]
is controlled by
[nxpg HAP1]
Saric et al., Proceedings of ACL, 2004](https://image.slidesharecdn.com/jensen2016talk8-160619152956/85/Protein-association-networks-with-STRING-101-320.jpg)
Uploaded byLars Juhl Jensen
Protein association networks with STRING
The document discusses the STRING protein association network database. It provides information from multiple sources, including curated databases, experiments, and predictions, to assign confidence scores and generate protein interaction networks. The document guides the reader through exercises exploring the human insulin receptor network on STRING, examining the evidence supporting its interaction with IRS1 and how confidence view and cutoffs alter the network displayed.
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Protein association networks with STRING
- 1. Protein association networks withSTRING Lars Juhl Jensen
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- 10. Exercise 1 Go tohttp://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
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- 30. Exercise 2 (Continue fromwhere 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
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- 70. Exercise 3 (Continue fromwhere exercise 2 ended) Change the network to the confidence view Change the confidence cutoff to 0.9; any changes in proteins or interactions shown? Turn off all but experiments; what
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- 101. Gene and proteinnames Cue words for entity recognition Verbs for relation extraction [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1] Saric et al., Proceedings of ACL, 2004
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- 125. Exercise 4 Open http://tissues.jensenlab.org Lookup tissue associations for insulin (INS) Open http://diseases.jensenlab.org Search for insulin receptor (INSR) What is the strongest associated disease?