Systematic discovery of phosphorylation networks - Combining linear motifs and protein interactions

Systematic discovery ofphosphorylation networks

Combining linear motifs and protein interactions

Lars Juhl Jensen

EMBL Heidelberg

Lars Juhl Jensen

promoter analysis

genome visualization

protein function prediction

data integration

dynamic interactions

prediction of interactions

http://string.embl.de

prediction of interactions

http://networkin.info

the starting point

phosphoproteomics

mass spectrometry

phosphorylation sites

in vivo

kinases are unknown

HTP kinase assays

in vitro

no context

what a kinase could do

not what it actually does

computational methods

sequence motifs

kinase families

phosphorylation sites

overprediction

no context

what a kinase could do

not what it actually does

in vitro

in vivo

context

localization

expression

co-activators

scaffolders

protein networks

the idea

mass spectrometry

phosphorylation sites

sequence motifs

kinase families

protein networks

context

in vitro

in vivo

“shake and bake”

NetworKIN

the context network

STRING

functional interactions

373 genomes

genomic context methods

gene neighborhood

gene fusion

phylogenetic profiles

primary experimental data

protein interactions

genetic interactions

gene coexpression

literature mining

curated knowledge

many sources

different formats

different gene identifiers

redundancy

variable quality

spread over many species

benchmarking

transfer by orthology

combine all evidence

the results

7797 predictions

1790 substrates

69 kinases

benchmarking

Phospho.ELM

2.5-fold better accuracy

context is crucial

localization

visualization

ATM signaling

small-scale validation

ATM phosphorylates Rad50

Cdk1 phosphorylates 53BP1

high-throughput validation

multiple reaction monitoring

the future

NetPhorest

sequence motifs

in vivo

in vitro

automatic pipeline

data organization

benchmarking

selection

~200 kinases

~100 SH2 domains

~15 PTB domains

upstream signaling

downstream signaling

ordered signaling events

signaling pathways

Acknowledgments

The NetworKIN method– 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

The STRING database– Christian von Mering

– Michael Kuhn

– Berend Snel

– Martijn Huynen

– Samuel Chaffron

– Peer Bork

• The NetPhorest method– Martin Lee Miller– Rune Linding– Nikolaj Blom– Søren Brunak