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Advanced bioinformatics methods for proteomics

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Lars Juhl Jensen
Lars Juhl Jensen
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Advanced bioinformatics methods for proteomics Lars Juhl Jensen
phosphoproteomics
in vivo phosphosites
kinases are unknown
sequence motifs
Miller, Jensen et al., Science Signaling, 2008
NetPhorest
data organization
Miller, Jensen et al., Science Signaling, 2008
automated pipeline
Miller, Jensen et al., Science Signaling, 2008
compilation of datasets
training and evaluation
motif atlas
179 kinases
89 SH2 domains
8 PTB domains
BRCT domains
WW domains
14-3-3 proteins
sequence specificity
protein-specific
no context
association networks
Linding, Jensen, Ostheimer et al., Cell, 2007
guilt by association
STRING
Jensen, Kuhn et al., Nucleic Acids Research, 2009
computational predictions
gene fusion
Korbel et al., Nature Biotechnology, 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology, 2004
experimental data
physical interactions
Jensen & Bork, Science, 2008
genetic interactions
Beyer et al., Nature Reviews Genetics, 2007
gene coexpression
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
>10 km
literature mining
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
co-mentioning
NLP Natural Language Processing
different formats
different names
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
integration
NetworKIN
Linding, Jensen, Ostheimer et al., Cell, 2007
>2x better accuracy
use case
DNA damage response
Linding, Jensen, Ostheimer et al., Cell, 2007
experimental validation
ATM phosphorylates Rad50
Linding, Jensen, Ostheimer et al., Cell, 2007
summary
computational biology
network analysis
testable predictions
save much time in the lab
thank you! NetPhorest – 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 – Christian von Mering – Damian Szklarczyk – 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 Reflect – Sune Frankild – Heiko Horn – Evangelos Pafilis – Michael Kuhn – Nigel Brown – Reinhardt Schneider – Sean O’Donoghue NetworKIN – Rune Linding – Heiko Horn – Gerard Ostheimer – 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 Yaffe – Tony Pawson
larsjuhljensen

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Advanced bioinformatics methods for proteomics

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