networks of proteins and diseases
TRANSCRIPT
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
STRINGChristian 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 miningSune Frankild
Evangelos Pafilis
Janos Binder
Kalliopi Tsafou
Alberto Santos
Heiko Horn
Michael Kuhn
Nigel Brown
Reinhardt Schneider
Sean O’Donoghue
EHR miningAnders Boeck Jensen
Peter Bjødstrup 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
Thank you!