networks of proteins and diseases

Networks of proteins and diseases

Lars Juhl Jensen

association networks

proteins

diseases

protein networks

STRING

Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

computational predictions

gene fusion

Korbel et al., Nature Biotechnology, 2004

conserved neighborhood

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

integrate it all

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

text mining

>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

CDC2

expansion rules

CDC2

hCdc2

flexible matching

cyclin dependent kinase 1

cyclin-dependent kinase 1

“black list”

SDS

co-mentioning

within documents

within paragraphs

within sentences

weighted counts

localization and disease

general approach

suite of web resources

curated knowledge

experimental data

text mining

computational predictions

quality scores

proteins

compartments

compartments.jensenlab.org

tissues

tissues.jensenlab.org

diseases

evidence viewers

web services

compartments.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

temporal correlation

diagnosis trajectories

Jensen et al., in preparation, 2013

diabetes progression

Jensen et al., in preparation, 2013

molecular basis

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 BinderHeiko HornMichael KuhnNigel BrownReinhardt SchneiderSean O’Donoghue

EHR miningAnders Boeck JensenPeter Bjødstrup JensenFrancisco S. RoqueHenriette SchmockMarlene DalgaardMassimo AndreattaThomas HansenKaren SøebySøren BredkjærAnders JuulTudor OpreaPope MoseleyThomas WergeSøren Brunak