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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]](https://image.slidesharecdn.com/jensen2015talk3-150415235400-conversion-gate02/75/Systems-biology-Bioinformatics-on-complete-biological-systems-118-2048.jpg)
Uploaded byLars Juhl Jensen
Systems biology: Bioinformatics on complete biological systems
Systems biology uses mathematical modeling and computational analysis to study complete biological systems and molecular networks. It requires integrating diverse experimental data, literature knowledge and computational predictions. Several web resources can be used together to analyze gene and protein interaction networks, find related diseases and compounds, while accounting for tissue specificity and other contextual factors. These resources include STRING, STITCH, COMPARTMENTS and DISEASES.
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Systems biology: Bioinformatics on complete biological systems
- 1. Lars Juhl Jensen Systemsbiology Bioinformatics on complete biological systems
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- 42. BioGRID General Repository forInteraction Datasets
- 43. DIP Database of InteractingProteins
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- 46. 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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- 86. calibrate vs. goldstandard
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- 89. Franceschini et al.,Nucleic Acids Research, 2013
- 90. Exercise 2 Query STRINGfor human TYMS Show network in confidence mode Show up to 20 interaction partners Show only experimental evidence Show also low-confidence links
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- 93. too much toread
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- 95. as smart asa dog
- 96. teach it specifictricks
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- 118. 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]
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- 123. suite of webresources
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- 132. STRING + 300kchemicals
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- 139. Exercise 3 Find TYMS-relateddiseases http://diseases.jensenlab.org Find some inhibitors of TYMS http://stitch-db.org Assess their tissue specificity http://tissues.jensenlab.org
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