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Networks of proteins and diseases

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Lars Juhl Jensen
Lars Juhl Jensen
1 of 93
Networks of proteins and diseases Lars Juhl Jensen
three parts
protein networks
localization and diseases
disease networks
protein networks
STRING
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
computational predictions
gene fusion
Korbel et al., Nature Biotechnology, 2004
experimental data
Jensen & Bork, Science, 2008
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
many databases
different formats
different identifiers
variable quality
not comparable
hard work
quality scores
von Mering et al., Nucleic Acids Research, 2005
calibrate vs. gold standard
missing most of the data
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
comprehensive lexicon
cyclin dependent kinase 1
CDK1
CDC2
orthographic variation
cyclin-dependent kinase 1
hCdc2
“black list”
SDS
information extraction
co-mentioning
localization and disease
proteins
compartments
tissues
diseases
suite of web resources
jensenlab.org
text mining
curated knowledge
experimental data
computational predictions
quality scores
visualization
compartments.jensenlab.org
tissues.jensenlab.org
project onto networks
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
compartments.jensenlab.org
tissues.jensenlab.org
diseases.jensenlab.org
disease networks
medical data
electronic health records
Jensen et al., Nature Reviews Genetics, 2012
structured data
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
comorbidity
Jensen et al., Nature Reviews Genetics, 2012
in Danish
multiple testing
confounding factors
age and gender
reporting bias
comorbidity matrix
Roque et al., PLoS Computational Biology, 2011
comorbidity network
temporal correlation
Jensen et al., in preparation, 2012
disease trajectories
Jensen et al., in preparation, 2012
molecular basis
protein networks
Acknowledgments STRING Text EHR mining Christian von Mering Damian Szklarczyk mining Anders Boeck Jensen Peter Bjødstrup Jensen Sune Frankild Michael Kuhn Francisco S. Roque Manuel Stark Evangelos Pafilis Henriette Schmock Janos Binder Samuel Chaffron Marlene Dalgaard Chris Creevey Kalliopi Tsafou Massimo Andreatta Jean Muller Alberto Santos Thomas Hansen Heiko Horn Tobias Doerks Karen Søeby Philippe Julien Michael Kuhn Søren Bredkjær Nigel Brown Alexander Roth Anders Juul Milan Simonovic Reinhardt Schneider Tudor Oprea Jan Korbel Sean O’Donoghue Pope Moseley Berend Snel Thomas Werge Martijn Huynen Søren Brunak Peer Bork
Thank you!

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Networks of proteins and diseases