Prediction of protein-small molecule networks through large-scale data integration
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Prediction of protein–small moleculenetworks through large-scale data integration
Lars Juhl Jensen
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function prediction
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cell-cycle regulation
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de Lichtenberg & Jensen et al., Science, 2005
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data integration
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the problem
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new uses for old drugs
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drug–drug network
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shared target(s)
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chemical similarity
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Tanimoto coefficients
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Campillos & Kuhn et al., Science, 2008
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Campillos & Kuhn et al., Science, 2008
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similar drugs share targets
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only trivial predictions
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the idea
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chemical perturbations
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phenotypic readouts
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drug treatment
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side effects
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the implementation
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information on side effects
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package inserts
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Campillos & Kuhn et al., Science, 2008
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text mining
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side-effect ontology
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backtracking
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Campillos & Kuhn et al., Science, 2008
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side-effect correlations
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Campillos & Kuhn et al., Science, 2008
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GSC weighting
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side-effect frequencies
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Campillos & Kuhn et al., Science, 2008
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raw similarity score
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Campillos & Kuhn et al., Science, 2008
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p-values
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Campillos & Kuhn et al., Science, 2008
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side-effect similarity
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chemical similarity
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Campillos & Kuhn et al., Science, 2008
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reference set
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drug–target pairs
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Campillos & Kuhn et al., Science, 2008
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drug–drug pairs
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score bins
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benchmark
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Campillos & Kuhn et al., Science, 2008
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fit calibration function
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Campillos & Kuhn et al., Science, 2008
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probabilistic scores
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the results
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drug–drug network
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ATC codes
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Campillos & Kuhn et al., Science, 2008
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categorization
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Campillos & Kuhn et al., Science, 2008
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Campillos & Kuhn et al., Science, 2008
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Campillos & Kuhn et al., Science, 2008
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map onto score space
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Campillos & Kuhn et al., Science, 2008
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the experiments
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20 drug–drug relations
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in vitro binding assays
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Campillos & Kuhn et al., Science, 2008
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Campillos & Kuhn et al., Science, 2008
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Campillos & Kuhn et al., Science, 2008
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Ki<10 µM for 11 of 20
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cell assays
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Campillos & Kuhn et al., Science, 2008
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9 of 9 showed activity
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the bigger picture
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STITCH
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protein–chemical network
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Kuhn et al., Nucleic Acids Research, 2008
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primary experimental data
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activity screens
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Fedorov et al., PNAS, 2007
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protein interactions
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Jensen & Bork, Science, 2008
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gene coexpression
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genomic context
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Korbel et al., Nature Biotechnology, 2004
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literature mining
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curated knowledge
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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different formats
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different identifiers
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different reliability
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benchmarking
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von Mering et al., Nucleic Acids Research, 2005
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373 genomes
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Jensen et al., Nucleic Acids Research, 2008
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transfer by orthology
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combine all evidence
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Kuhn et al., Nucleic Acids Research, 2008
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Acknowledgments
Monica Campillos
Michael Kuhn
Christian von Mering
Anne-Claude Gavin
Peer Bork
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