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Unraveling cellular phosphorylation networks using computational biology

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Lars Juhl Jensen
Lars Juhl Jensen

BRIC/LEO Minisymposium on Protein Kinases in Health and Disease, Copenhagen Biocenter, Copenhagen, September 26, 2008

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Unraveling cellular phosphorylation networks using computational biology Lars Juhl Jensen EMBL Heidelberg
the problem
Oda & Kitano, Molecular Systems Biology , 2006
a good start
long way to go
the toolbox
mass spectrometry
Linding, Jensen, Ostheimer et al., Cell , 2007
phosphorylation sites
in vivo
kinases are unknown
peptide assays
Miller, Jensen et al., Science Signaling , 2008
sequence specificity
kinase-specific
in vitro
no context
what a kinase could do
not what it actually does
computational methods
sequence specificity
Miller, Jensen et al., Science Signaling , 2008
kinase-specific
no context
what a kinase could do
not what it actually does
in vitro
in vivo
context
localization
expression
co-activators
scaffolders
association networks
Linding, Jensen, Ostheimer et al., Cell , 2007
the idea
mass spectrometry
phosphorylation sites
sequence motifs
sequence specificity
association network
context
in vitro
in vivo
Linding, Jensen, Ostheimer et al., Cell , 2007
the sequence motifs
NetPhorest
Miller, Jensen et al., Science Signaling , 2008
pipeline
data organization
Miller, Jensen et al., Science Signaling , 2008
compilation of datasets
Miller, Jensen et al., Science Signaling , 2008
redundancy reduction
Miller, Jensen et al., Science Signaling , 2008
cross-validation partitioning
Miller, Jensen et al., Science Signaling , 2008
training and evaluation
classifier selection
Miller, Jensen et al., Science Signaling , 2008
motif atlas
 
179 kinases
93 SH2 domains
8 PTB domains
BRCT domains
WW domains
14-3-3 proteins
benchmarking
Miller, Jensen et al., Science Signaling , 2008
low-specificity kinases
disease-related kinases
Miller, Jensen et al., Science Signaling , 2008
docking domains
Miller, Jensen et al., Science Signaling , 2008
the context network
STRING
functional associations
373 genomes
Jensen et al., Nucleic Acids Research , 2008
genomic context methods
gene fusion
Korbel et al., Nature Biotechnology , 2004
conserved neighborhood
Korbel et al., Nature Biotechnology , 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology , 2004
primary experimental data
protein interactions
Jensen & Bork, Science , 2008
gene coexpression
 
literature mining
 
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences , 2008
different formats
parsers
different gene identifiers
thesaurus
redundancy
bookkeeping
variable reliability
benchmarking
von Mering et al., Nucleic Acids Research , 2005
spread over many species
transfer by orthology
von Mering et al., Nucleic Acids Research , 2005
combine all evidence
Linding, Jensen, Ostheimer et al., Cell , 2007
the results
NetworKIN
123 kinases
5515 substrates
21,702 sites
benchmarking
Phospho.ELM
Linding, Jensen, Ostheimer et al., Cell , 2007
2.5-fold better accuracy
context is crucial
localization
Linding, Jensen, Ostheimer et al., Cell , 2007
ATM signaling
Linding, Jensen, Ostheimer et al., Cell , 2007
Linding, Jensen, Ostheimer et al., Cell , 2007
small-scale validation
ATM phosphorylates Rad50
Linding, Jensen, Ostheimer et al., Cell , 2007
Cdk1 phosphorylates 53BP1
Linding, Jensen, Ostheimer et al., Cell , 2007
high-throughput validation
multiple reaction monitoring
Linding, Jensen, Ostheimer et al., Cell , 2007
systematic validation
design optimal experiments
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