networks of proteins and diseases
TRANSCRIPT
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Networks of proteins and diseases
Lars Juhl Jensen
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three parts
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protein networks
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localization & disease
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disease networks
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protein networks
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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computational predictions
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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experimental data
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physical interactions
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Jensen & Bork, Science, 2008
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curated knowledge
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metabolic pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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text mining
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dictionary-based approach
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co-mentioning
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many databases
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different formats
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different identifiers
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variable quality
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not comparable
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hard work
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quality scores
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von Mering et al., Nucleic Acids Research, 2005
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calibrate vs. gold standard
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von Mering et al., Nucleic Acids Research, 2005
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localization & disease
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general approach
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suite of web resources
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curated knowledge
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experimental data
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text mining
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computational predictions
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quality scores
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data visualization
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compartments
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Gene Ontology
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compartments.jensenlab.org
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tissues
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BRENDA Tissue Ontology
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tissues.jensenlab.org
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diseases
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Disease Ontology
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removal of gene symbols
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addition of links
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evidence viewers
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web services
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diseases.jensenlab.org
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download files
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disease networks
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electronic health records
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Jensen et al., Nature Reviews Genetics, 2012
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structured data
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Jensen et al., Nature Reviews Genetics, 2012
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unstructured data
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comorbidity
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Jensen et al., Nature Reviews Genetics, 2012
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Roque et al., PLoS Computational Biology, 2011
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in Danish
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multiple testing
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confounding factors
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age and gender
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reporting bias
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molecular basis
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protein–disease links
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protein networks
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Acknowledgments
STRINGChristian von MeringDamian SzklarczykMichael KuhnManuel StarkSamuel ChaffronChris CreeveyJean MullerTobias DoerksPhilippe JulienAlexander RothMilan SimonovicJan KorbelBerend SnelMartijn HuynenPeer Bork
Text miningSune FrankildEvangelos PafilisAlberto SantosKalliopi TsafouJanos BinderLucia FaniniSarah FaulwetterChristina PavloudiJulia SchnetzerAikaterini VasileiadouHeiko HornMichael KuhnNigel BrownReinhard SchneiderSean O’Donoghue
EHR miningRobert ErikssonPeter Bjødstrup JensenAnders Boeck JensenFrancisco S. RoqueHenriette SchmockMarlene DalgaardMassimo AndreattaThomas HansenKaren SøebySøren BredkjærAnders JuulTudor OpreaPope MoseleyThomas WergeSøren Brunak
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