Network biology: A basis for large-scale biomedical data mining
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Transcript of Network biology: A basis for large-scale biomedical data mining
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Network biologyA basis for large-scale biomedical data mining
Lars Juhl Jensen
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sequence analysis
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Jensen, Gupta et al., Journal of Molecular Biology, 2002
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data mining
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de Lichtenberg, Jensen et al., Science, 2005
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data mining
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text mining
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
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signaling networks
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phosphoproteomics
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in vivo phosphosites
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kinases are unknown
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sequence motifs
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Miller, Jensen et al., Science Signaling, 2008
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NetPhorest
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data organization
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Miller, Jensen et al., Science Signaling, 2008
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automated pipeline
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Miller, Jensen et al., Science Signaling, 2008
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compilation of datasets
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training and evaluation
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motif atlas
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179 kinases
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89 SH2 domains
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8 PTB domains
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BRCT domains
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WW domains
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14-3-3 proteins
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phosphatases
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sequence specificity
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in vitro
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network context
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Linding, Jensen, Ostheimer et al., Cell, 2007
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STRING
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Jensen, Kuhn et al., Nucleic Acids Research, 2009
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630 genomes
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2.5 million proteins
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genomic context
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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phylogenetic profiles
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Korbel et al., Nature Biotechnology, 2004
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primary experimental data
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physical interactions
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Jensen & Bork, Science, 2008
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gene coexpression
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curated knowledge
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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literature mining
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not comparable
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confidence scores
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von Mering et al., Nucleic Acids Research, 2005
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cross-species integration
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Linding, Jensen, Ostheimer et al., Cell, 2007
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putting it all together
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NetworKIN
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Linding, Jensen, Ostheimer et al., Cell, 2007
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>2x better accuracy
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use case
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DNA damage response
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Linding, Jensen, Ostheimer et al., Cell, 2007
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experimental validation
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ATM phosphorylates Rad50
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Linding, Jensen, Ostheimer et al., Cell, 2007
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drug repositioning
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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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phenotypic similarity
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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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no database
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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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confidence scores
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drug–drug network
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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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experimental validation
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20 drug–drug pairs
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in vitro binding assays
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Ki<10 µM for 11 of 20
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cell assays
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9 of 9 showed activity
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work in progress
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link side-effects to targets
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direct target prediction
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STITCH
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Kuhn et al., Nucleic Acids Research, 2010
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thank you!
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AcknowledgmentsNetPhorest.info
– Rune Linding– Martin Lee Miller– Francesca Diella– Claus Jørgensen– Michele Tinti– Lei Li– Marilyn Hsiung– Sirlester A. Parker– Jennifer Bordeaux– Thomas Sicheritz-Pontén– Marina Olhovsky– Adrian Pasculescu– Jes Alexander– Stefan Knapp– Nikolaj Blom– Peer Bork– Shawn Li– Gianni Cesareni– Tony Pawson– Benjamin E. Turk– Michael B. Yaffe– Søren Brunak
STRING-DB.org– Christian von Mering– Damian Szklarczyk– Michael Kuhn– Manuel Stark– Samuel Chaffron– Chris Creevey– Jean Muller– Tobias Doerks– Philippe Julien– Alexander Roth– Milan Simonovic– Jan Korbel– Berend Snel– Martijn Huynen– Peer Bork
Side effect– Monica Campillos– Michael Kuhn– Christian von Mering– Anne-Claude Gavin– Peer Bork
NetworKIN.info– Rune Linding– Gerard Ostheimer– Heiko Horn– Martin Lee Miller– Francesca Diella– Karen Colwill– Jing Jin– Pavel Metalnikov– Vivian Nguyen– Adrian Pasculescu– Jin Gyoon Park– Leona D. Samson– Rob Russell– Peer Bork– Michael Yaffe– Tony Pawson
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larsjuhljensen