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Unraveling cellular phosphorylation networks using computational biology
Lars Juhl Jensen
EMBL Heidelberg
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the problem
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Oda & Kitano, Molecular Systems Biology, 2006
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a good start
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long way to go
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the toolbox
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mass spectrometry
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Linding, Jensen, Ostheimer et al., Cell, 2007
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phosphorylation sites
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in vivo
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kinases are unknown
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peptide assays
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Miller, Jensen et al., Science Signaling, 2008
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sequence specificity
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kinase-specific
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in vitro
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no context
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what a kinase could do
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not what it actually does
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computational methods
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sequence specificity
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Miller, Jensen et al., Science Signaling, 2008
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kinase-specific
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no context
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what a kinase could do
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not what it actually does
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in vitro
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in vivo
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context
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localization
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expression
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co-activators
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scaffolders
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association networks
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Linding, Jensen, Ostheimer et al., Cell, 2007
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the idea
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mass spectrometry
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phosphorylation sites
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sequence motifs
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sequence specificity
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association network
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context
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in vitro
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in vivo
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Linding, Jensen, Ostheimer et al., Cell, 2007
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the sequence motifs
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NetPhorest
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Miller, Jensen et al., Science Signaling, 2008
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pipeline
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data organization
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Miller, Jensen et al., Science Signaling, 2008
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compilation of datasets
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Miller, Jensen et al., Science Signaling, 2008
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redundancy reduction
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Miller, Jensen et al., Science Signaling, 2008
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cross-validation partitioning
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Miller, Jensen et al., Science Signaling, 2008
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training and evaluation
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classifier selection
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Miller, Jensen et al., Science Signaling, 2008
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motif atlas
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179 kinases
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93 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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benchmarking
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Miller, Jensen et al., Science Signaling, 2008
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low-specificity kinases
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disease-related kinases
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Miller, Jensen et al., Science Signaling, 2008
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docking domains
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Miller, Jensen et al., Science Signaling, 2008
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the context network
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STRING
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functional associations
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373 genomes
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Jensen et al., Nucleic Acids Research, 2008
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genomic context methods
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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conserved neighborhood
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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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protein interactions
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Jensen & Bork, Science, 2008
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gene coexpression
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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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parsers
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different gene identifiers
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thesaurus
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redundancy
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bookkeeping
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variable reliability
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benchmarking
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von Mering et al., Nucleic Acids Research, 2005
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spread over many species
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transfer by orthology
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von Mering et al., Nucleic Acids Research, 2005
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combine all evidence
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Linding, Jensen, Ostheimer et al., Cell, 2007
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the results
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NetworKIN
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123 kinases
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5515 substrates
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21,702 sites
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benchmarking
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Phospho.ELM
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Linding, Jensen, Ostheimer et al., Cell, 2007
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2.5-fold better accuracy
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context is crucial
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localization
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Linding, Jensen, Ostheimer et al., Cell, 2007
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ATM signaling
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Linding, Jensen, Ostheimer et al., Cell, 2007
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Linding, Jensen, Ostheimer et al., Cell, 2007
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small-scale validation
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ATM phosphorylates Rad50
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Linding, Jensen, Ostheimer et al., Cell, 2007
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Cdk1 phosphorylates 53BP1
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Linding, Jensen, Ostheimer et al., Cell, 2007
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high-throughput validation
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multiple reaction monitoring
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Linding, Jensen, Ostheimer et al., Cell, 2007
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systematic validation
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design optimal experiments
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Acknowledgments
NetworKIN.info– Rune Linding– Gerard Ostheimer– 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
NetPhorest.info– 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.embl.de– Christian von Mering– Michael Kuhn– Manuel Stark– Samuel Chaffron– Philippe Julien– Tobias Doerks– Jan Korbel– Berend Snel– Martijn Huynen– Peer Bork
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