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

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