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From phosphoproteomics to signaling networks

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Lars Juhl Jensen
Lars Juhl Jensen

Orbitrap User Meeting, University of Southern Denmark, Odense, Denmark, December 2, 2009.

TecnologiaEspiritual
1 de 90
From phosphoproteomics to 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
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From phosphoproteomics to signaling networks

Notas do Editor

  1. Integration Automation Collaboration
  2. Atlas of human kinases Atlases for phospho-binding proteins Atlases for model organisms Ubiquitination would be welcome