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Functional association networks The STRING and STITCH web resources
Lars Juhl Jensen
EMBL Heidelberg
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functional associations
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data integration
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STRING
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STITCH
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373 genomes
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model organism databases
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Ensembl
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Genome Reviews
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RefSeq
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genomic context methods
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gene fusion
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conserved neighborhood
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operons
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bidirectional promoters
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phylogenetic profiles
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primary experimental data
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gene coexpression
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GEOGene Expression Omnibus
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expression compendia
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protein interactions
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genetic interactions
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BINDBiomolecular Interaction Network Database
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BioGRIDGeneral Repository for Interaction Datasets
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DIPDatabase of Interacting Proteins
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IntAct
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MINTMolecular Interactions Database
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HPRDHuman Protein Reference Database
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curated knowledge
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complexes
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MIPSMunich Information center
for Protein Sequences
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Gene Ontology
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pathways
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KEGGKyoto Encyclopedia of Genes and Genomes
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Reactome
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PIDNCI-Nature Pathway Interaction Database
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STKESignal Transduction Knowledge Environment
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literature mining
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MEDLINE
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SGDSaccharomyces Genome Database
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The Interactive Fly
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OMIMOnline Mendelian Inheritance in Man
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synonyms lists
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co-mentioning
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NLPNatural Language Processing
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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]
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too easy …
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… to be true
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many data types
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not comparable
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different error rates
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many sources
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different file formats
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different gene identifiers
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redundancy
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spread over many species
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raw quality scores
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reproducibility
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intergenic distances
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benchmarking
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calibrate vs. gold standard
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raw quality scores
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probabilistic scores
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transfer by orthology
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two modes
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COG mode
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protein mode
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combine all evidence
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Bayesian scoring scheme
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Acknowledgments
Christian von Mering
Michael Kuhn
Manuel Stark
Samuel Chaffron
Philippe Julien
Tobias Doerks
Berend Snel
Jasmin Saric
Isabel Rojas
Peer Bork