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Orbitrap User Meeting, University of Southern Denmark, Odense, Denmark, December 2, 2009.
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From phosphoproteomicsto signaling networks
Lars Juhl Jensen
Orbitrap
in vivo phosphosites
kinases are unknown
functions are unknown
sequence motifs
machine-learning methods
Miller, Jensen et al., Science Signaling, 2008
peptide assays
Miller, Jensen et al., Science Signaling, 2008
domain-specific
group-specific
no context
in vitro
in vivo
context
co-activators
protein scaffolds
localization
expression
NetworKIN
Linding, Jensen, Ostheimer et al., Cell, 2007
functional associations
Jensen, Kuhn et al., Nucleic Acids Research, 2009
data integration
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
protein interactions
Jensen & Bork, Science, 2008
gene coexpression
genomic context methods
Korbel et al., Nature Biotechnology, 2004
literature mining
different formats
different identifiers
variable quality
not comparable
spread over 630 genomes
confidence scores
von Mering et al., Nucleic Acids Research, 2005
transfer by orthology
von Mering et al., Nucleic Acids Research, 2005
Linding, Jensen, Ostheimer et al., Cell, 2007
does it work?
Linding, Jensen, Ostheimer et al., Cell, 2007
context is crucial
much context missing
many motifs missing
NetPhorest
automated pipeline
Miller, Jensen et al., Science Signaling, 2008
data organization
Miller, Jensen et al., Science Signaling, 2008
compilation of datasets
redundancy reduction
training and evaluation
classifier selection
motif atlas
179 kinases
89 SH2 domains
8 PTB domains
BRCT domains
WW domains
14-3-3 proteins
use case
cell-cycle kinases
Olsen et al., Science Signaling, 2009
coming soon(ish)
new web interface
new scoring scheme
path length penalty
Linding, Jensen, Ostheimer et al., Cell, 2007
model organisms
S. cerevisiae
D. melanogaster
C. elegans
other modifications
phosphatases
acetylation
ubiquitylation
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– 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
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 B. Yaffe– Tony Pawson
larsjuhljensen
