Functional association networks The STRING and STITCH web resources

Lars Juhl Jensen

EMBL Heidelberg

functional associations

data integration

STRING

STITCH

373 genomes

model organism databases

Ensembl

Genome Reviews

RefSeq

genomic context methods

gene fusion

conserved neighborhood

operons

bidirectional promoters

phylogenetic profiles

primary experimental data

gene coexpression

GEOGene Expression Omnibus

expression compendia

protein interactions

genetic interactions

BINDBiomolecular Interaction Network Database

BioGRIDGeneral Repository for Interaction Datasets

DIPDatabase of Interacting Proteins

IntAct

MINTMolecular Interactions Database

HPRDHuman Protein Reference Database

curated knowledge

complexes

MIPSMunich Information center

for Protein Sequences

Gene Ontology

pathways

KEGGKyoto Encyclopedia of Genes and Genomes

Reactome

PIDNCI-Nature Pathway Interaction Database

STKESignal Transduction Knowledge Environment

literature mining

MEDLINE

SGDSaccharomyces Genome Database

The Interactive Fly

OMIMOnline Mendelian Inheritance in Man

synonyms lists

co-mentioning

NLPNatural Language Processing

Gene and protein namesCue words for entity recognitionVerbs for relation extraction

[nxgene The GAL4 gene]

[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]

too easy …

… to be true

many data types

not comparable

different error rates

many sources

different file formats

different gene identifiers

redundancy

spread over many species

raw quality scores

reproducibility

intergenic distances

benchmarking

calibrate vs. gold standard

raw quality scores

probabilistic scores

transfer by orthology

two modes

COG mode

protein mode

combine all evidence

Bayesian scoring scheme

Acknowledgments

Christian von Mering

Michael Kuhn

Manuel Stark

Samuel Chaffron

Philippe Julien

Tobias Doerks

Berend Snel

Jasmin Saric

Isabel Rojas

Peer Bork