making gene networks through data integration
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Making gene networks through data integration
Lars Juhl Jensen
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association networks
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guilt by association
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molecular networks
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proteins
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string-db.org
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small molecules
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stitch-db.org
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non-coding RNAs
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compartments
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compartments.jensenlab.org
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tissues
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tissues.jensenlab.org
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diseases
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data integration
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computational predictions
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gene neighborhood
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Korbel et al., Nature Biotechnology, 2004
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TargetScan
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experimental data
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gene expression
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protein interactions
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Jensen & Bork, Science, 2008
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miRTarBase
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curated knowledge
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metabolic pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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signaling pathways
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many databases
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different formats
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different identifiers
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variable quality
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not comparable
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hard work
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(Ph.D. students)
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common identifiers
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quality scores
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von Mering et al., Nucleic Acids Research, 2005
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score calibration
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von Mering et al., Nucleic Acids Research, 2005
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homology-based transfer
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Franceschini et al., Nucleic Acids Research, 2013
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missing most of the data
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text mining
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>10 km
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too much to read
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computer
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as smart as a dog
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teach it specific tricks
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named entity recognition
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comprehensive lexicon
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let-7a-3p
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let-7a*
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flexible matching
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let-7a
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let7a
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name expansions
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let-7a
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miR-let-7a
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“black list”
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SDS
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co-mentioning
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counting
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within documents
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within paragraphs
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within sentences
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high recall
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high precision
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fuzzy associations
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NLPNatural Language Processing
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Gene and protein namesCue words for entity recognitionVerbs for relation extraction
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
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extract stated facts
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high precision
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poor recall
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Jensen et al., Nature Reviews Genetics, 2006
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questions?