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Networks of proteins and diseases

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Lars Juhl Jensen
Lars Juhl Jensen
Technologie
1  sur  75
Networks of proteins and diseases Lars Juhl Jensen
three parts
protein networks
localization & disease
disease networks
protein networks
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
computational predictions
gene fusion
Korbel et al., Nature Biotechnology, 2004
experimental data
physical interactions
Jensen & Bork, Science, 2008
curated knowledge
metabolic pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
text mining
dictionary-based approach
co-mentioning
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
von Mering et al., Nucleic Acids Research, 2005
localization & disease
general approach
suite of web resources
curated knowledge
experimental data
text mining
computational predictions
quality scores
data visualization
compartments
Gene Ontology
compartments.jensenlab.org
tissues
BRENDA Tissue Ontology
tissues.jensenlab.org
diseases
Disease Ontology
removal of gene symbols
addition of links
evidence viewers
web services
diseases.jensenlab.org
download files
disease networks
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
Roque et al., PLoS Computational Biology, 2011
in Danish
multiple testing
confounding factors
age and gender
reporting bias
molecular basis
protein–disease links
protein networks
Acknowledgments 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 Text mining Sune Frankild Evangelos Pafilis Alberto Santos Kalliopi Tsafou Janos Binder Lucia Fanini Sarah Faulwetter Christina Pavloudi Julia Schnetzer Aikaterini Vasileiadou Heiko Horn Michael Kuhn Nigel Brown Reinhard Schneider Sean O’Donoghue EHR mining Robert Eriksson Peter Bjødstrup Jensen Anders Boeck Jensen Francisco S. Roque Henriette Schmock Marlene Dalgaard Massimo Andreatta Thomas Hansen Karen Søeby Søren Bredkjær Anders Juul Tudor Oprea Pope Moseley Thomas Werge Søren Brunak
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Networks of proteins and diseases