Unraveling signaling networks by data integration
May 10, 2015
Unraveling signalingnetworks by data integration
Lars Juhl Jensen
promoter analysis
Jensen & Knudsen, Bioinformatics, 2000
genome visualization
Pedersen, Jensen et al., Journal of Molecular Biology, 2000
function prediction
Jensen, Gupta et al., Journal of Molecular Biology, 2002
data integration
Jensen & Bork, Drug Discovery Today: TARGETS, 2004
Gavin, Aloy et al., Nature, 2006
cell-cycle regulation
de Lichtenberg, Jensen et al., Science, 2005
Jensen, Jensen, de Lichtenberg et al., Nature, 2006
drug repurposing
Campillos, Kuhn et al., Science, 2008
signaling networks
phosphoproteomics
Linding, Jensen, Ostheimer et al., Cell, 2007
in vivo phosphosites
kinases are unknown
peptide assays
Miller, Jensen et al., Science Signaling, 2008
kinase-specific
in vitro
no context
machine-learning methods
Phospho.ELM
Miller, Jensen et al., Science Signaling, 2008
kinase-specific
no context
context
association networks
Linding, Jensen, Ostheimer et al., Cell, 2007
NetworKIN
Linding, Jensen, Ostheimer et al., Cell, 2007
sequence motifs
NetPhorest
Miller, Jensen et al., Science Signaling, 2008
data organization
Miller, Jensen et al., Science Signaling, 2008
automated pipeline
compilation of datasets
redundancy reduction
training and evaluation
classifier selection
motif atlas
179 kinases
93 SH2 domains
8 PTB domains
BRCT domains
WW domains
14-3-3 proteins
comparison
Miller, Jensen et al., Science Signaling, 2008
association networks
STRING
functional associations
630 genomes
genomic context
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
benchmarking
von Mering et al., Nucleic Acids Research, 2005
transfer by orthology
combine all evidence
Frishman et al., Modern Genome Annotation, 2009
small molecules
STITCH
Kuhn et al., Nucleic Acids Research, 2008
kinase inhibitor screens
Fedorov et al., PNAS, 2007
design optimal experiments
multiple reaction monitoring
Linding, Jensen, Ostheimer et al., Cell, 2007
high-throughput validation
NetworKIN predictions
augmented browsing
Reflect
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
STITCH.embl.de– Michael Kuhn– Christian von Mering– Monica Campillos– Peer Bork
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
Reflect.ws– Sean O’Donoghue– Evangelos Pafilis– Heiko Horn– Michael Kuhn– Nigel Brown– Reinhardt Schneider