Networks of proteins and diseases
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Networks of proteins and diseases

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    Networks of proteins and diseases Networks of proteins and diseases Presentation 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
    • AcknowledgmentsSTRING Text EHR miningChristian von MeringDamian Szklarczyk mining Anders Boeck Jensen Peter Bjødstrup Jensen Sune FrankildMichael Kuhn Francisco S. RoqueManuel Stark Evangelos Pafilis Henriette Schmock Janos BinderSamuel Chaffron Marlene DalgaardChris Creevey Kalliopi Tsafou Massimo AndreattaJean Muller Alberto Santos Thomas Hansen Heiko HornTobias Doerks Karen SøebyPhilippe Julien Michael Kuhn Søren Bredkjær Nigel BrownAlexander Roth Anders JuulMilan Simonovic Reinhardt Schneider Tudor OpreaJan Korbel Sean O’Donoghue Pope MoseleyBerend Snel Thomas WergeMartijn Huynen Søren BrunakPeer Bork
    • Thank you!