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Advanced bioinformatics methods for proteomics

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Lars Juhl Jensen
Lars Juhl Jensen
1 of 93
Advanced bioinformatics methods for proteomics Lars Juhl Jensen
three parts
signaling networks
association networks
text mining
Part 1 signaling networks
phosphoproteomics
Linding, Jensen, Ostheimer et al., Cell, 2007
in vivo phosphosites
kinases are unknown
sequence specificity
Miller, Jensen et al., Science Signaling, 2008
NetPhorest
Miller, Jensen et al., Science Signaling, 2008
motif atlas
kinases
phospho-binding proteins
phosphatases
protein-specific
no context
co-activators
protein scaffolds
localization
expression
association network
Linding, Jensen, Ostheimer et al., Cell, 2007
NetworKIN
Linding, Jensen, Ostheimer et al., Cell, 2007
web interface
Part 2 association networks
guilt by association
STRING
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
>1100 genomes
computational predictions
genomic context
gene fusion
Korbel et al., Nature Biotechnology, 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology, 2004
experimental data
physical interactions
Jensen & Bork, Science, 2008
gene coexpression
curated knowledge
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
many databases
different formats
different identifiers
variable quality
not comparable
quality scores
von Mering et al., Nucleic Acids Research, 2005
calibrate vs. gold standard
von Mering et al., Nucleic Acids Research, 2005
missing most of the data
Part 3 text mining
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
comprehensive lexicon
proteins
cellular components
compartments.jensenlab.org
tissues
tissues.jensenlab.org
diseases
orthographic variation
singular vs. plural
spaces and hyphens
“black list”
information extraction
co-mentioning
NLP Natural Language Processing
Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]
summary
bioinformatics
more than BLAST
data/text mining
save you much time
Acknowledgments NetPhorest NetworKIN STRING Text- Rune Linding Martin Lee Miller Rune Linding Heiko Horn Christian von Mering Damian Szklarczyk mining Erwin Schoof Gerard Ostheimer Michael Kuhn Sune Frankild Francesca Diella Martin Lee Miller Manuel Stark Evangelos Pafilis Claus Jørgensen Francesca Diella Samuel Chaffron Janos Binder Michele Tinti Karen Colwill Chris Creevey Heiko Horn Lei Li Jing Jin Jean Muller Michael Kuhn Marilyn Hsiung Pavel Metalnikov Tobias Doerks Nigel Brown Sirlester A. Parker Vivian Nguyen Philippe Julien Reinhardt Schneider Jennifer Bordeaux Adrian Pasculescu Alexander Roth Sean O’Donoghue Thomas Sicheritz-Pontén Jin Gyoon Park Milan Simonovic Marina Olhovsky Leona D. Samson Jan Korbel Adrian Pasculescu Rob Russell Berend Snel Jes Alexander Peer Bork Martijn Huynen Stefan Knapp Michael Yaffe Peer Bork Nikolaj Blom Tony Pawson Peer Bork Shawn Li Gianni Cesareni Tony Pawson Benjamin E. Turk Michael B. Yaffe Søren Brunak
larsjuhljensen
Advanced bioinformatics methods for proteomics

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