The STRING database
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The STRING database
Lars Juhl Jensen
EMBL Heidelberg
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data integration
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Jensen et al., Drug Discovery Today: Targets, 2004
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functional interactions
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Bork et al., Current Opinion in Structural Biology, 2005
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373 proteomes
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Genome Reviews
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RefSeq
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Ensembl
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model organism databases
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genomic context methods
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gene fusion
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gene neighborhood
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phylogenetic profiles
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Cell
Cellulosomes
Cellulose
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automation
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scoring scheme
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correct interactions
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wrong associations
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gene fusion
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sequence similarity
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gene neighborhood
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sum of intergenic distances
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phylogenetic profiles
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SVDSingular Value Decomposition
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Euclidian distance
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raw quality scores
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not comparable
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sequence similarity
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sum of intergenic distances
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Euclidian distance
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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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curated knowledge
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KEGGKyoto Encyclopedia of Genes and Genomes
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Reactome
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MIPSMunich Information center
for Protein Sequences
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STKESignal Transduction Knowledge Environment
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primary experimental data
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many sources
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many parsers
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physical protein interactions
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BINDBiomolecular Interaction Network Database
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GRIDGeneral Repository for Interaction Datasets
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MINTMolecular Interactions Database
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DIPDatabase of Interacting Proteins
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HPRDHuman Protein Reference Database
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merge data by publication
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topology-based scores
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von Mering et al., Nucleic Acids Research, 2005
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co-expression
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GEOGene Expression Omnibus
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correlation coefficient
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literature mining
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different gene identifiers
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synonyms lists
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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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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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calibrate vs. gold standard
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combine all evidence
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spread over many species
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transfer by orthology
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von Mering et al., Nucleic Acids Research, 2005
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two modes
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orthologous groups
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von Mering et al., Nucleic Acids Research, 2005
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fuzzy orthology
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von Mering et al., Nucleic Acids Research, 2005
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Bayesian scoring scheme
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Bork et al., Current Opinion in Structural Biology, 2005
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Acknowledgments
The STRING team (EMBL)– Christian von Mering
– Berend Snel
– Martijn Huynen
– Sean Hooper
– Samuel Chaffron
– Julien Lagarde
– Mathilde Foglierini
– Peer Bork
Literature mining project(EML Research)– Jasmin Saric
– Rossitza Ouzounova
– Isabel Rojas