data integration and functional association networks
DESCRIPTION
Exploring Modular Protein Architecture, European Molecular Biology Laboratory, Heidelberg, Germany, December 3-5, 2008TRANSCRIPT
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Lars Juhl Jensen
Data integration and functional association
networks
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Lars Juhl Jensen
Data integration and functional association
networks
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if this is your plan
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STRING
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Jensen, Kuhn et al., Nucleic Acids Research, 2009
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data integration
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functional associations
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Frishman et al., Modern Genome Annotation, 2009
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the basis
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630 genomes
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model organism databases
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Ensembl
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RefSeq
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genomic context methods
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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conserved neighborhood
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Korbel et al., Nature Biotechnology, 2004
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phylogenetic profiles
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Korbel et al., Nature Biotechnology, 2004
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primary experimental data
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gene coexpression
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GEOGene Expression Omnibus
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protein interactions
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Jensen & Bork, Science, 2008
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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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PDBProtein Data Bank
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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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Letunic & Bork, Trends in Biochemical Sciences, 2008
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KEGGKyoto Encyclopedia of Genes and Genomes
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MetaCyc
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Reactome
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PIDNCI-Nature Pathway Interaction Database
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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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thesaurus
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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 630 genomes
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raw quality scores
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reproducibility
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von Mering et al., Nucleic Acids Research, 2005
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intergenic distances
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Korbel et al., Nature Biotechnology, 2004
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benchmarking
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calibrate vs. gold standard
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von Mering et al., Nucleic Acids Research, 2005
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raw quality scores
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probabilistic scores
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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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COG mode
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von Mering et al., Nucleic Acids Research, 2005
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protein mode
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von Mering et al., Nucleic Acids Research, 2005
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combine all evidence
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visualize
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Frishman et al., Modern Genome Annotation, 2009
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related resources
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STITCH
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protein–chemical network
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Reflect
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eggNOG
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orthologous groups
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NetworKIN
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Linding, Jensen, Ostheimer et al., Cell, 2007
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Acknowledgments
NetworKIN.info– Rune Linding
– Gerard Ostheimer
– Francesca Diella
– Karen Colwill
– Jing Jin
– Pavel Metalnikov
– Vivian Nguyen
– Adrian Pasculescu
– Jin Gyoon Park
– Leona D. Samson
– Rob Russell
– Peer Bork
– Michael Yaffe
– Tony Pawson
STRING.embl.de– Michael Kuhn– Manuel Stark– Samuel Chaffron– Chris Creevey– Jean Muller– Tobias Doerks– Philippe Julien– Alexander Roth– Milan Simonovic– Peer Bork– Christian von Mering
STITCH.embl.de– Michael Kuhn– Christian von Mering– Monica Campillos– Peer Bork
eggNOG.embl.de– Philippe Julien– Michael Kuhn– Christian von Mering– Jean Muller– Tobias Doerks– Peer Bork
Reflect.ws– Sean O’Donoghue– Evangelos Pafilis– Heiko Horn– Michael Kuhn– Peer Bork– Reinhardt Schneider