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Lars Juhl Jensen
Network BiologyA crash course on STRING and
Cytoscape
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STRING
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protein network database
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Cytoscape
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network visualization tool
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stringApp
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gene/protein list
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STRING network
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map external data
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Szklarczyk et al., Nucleic Acids Research, 2017
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STRING
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string-db.org
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2000+ genomes
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functional associations
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genomic context
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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gene 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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experimental data
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gene coexpression
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physical interactions
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Jensen & Bork, Science, 2008
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curated knowledge
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3D structures
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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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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quality scores
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affinity purification
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von Mering et al., Nucleic Acids Research, 2005
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score calibration
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gold standard
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von Mering et al., Nucleic Acids Research, 2005
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implicit weighting by quality
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common scale
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missing most of the data
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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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dictionary
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cyclin dependent kinase 1
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CDC2
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orthographic variation
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cyclin dependent kinase 1
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cyclin-dependent kinase 1
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CDC2
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hCdc2
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“black list”
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SDS
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co-mentioning
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scoring scheme
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Cytoscape
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networks
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tables
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visual styles
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load/save sessions
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import network
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local file
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public database
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import table
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property mappings
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passthrough
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discrete
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continuous
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default & bypass
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layouts
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force-directed
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grid
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circle attribute
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clustering
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clusterMaker2
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new node attribute
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clustered network
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selection filters
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stringApp
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import from STRING
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protein query
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Szklarczyk et al., Nucleic Acids Research, 2017
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disease query
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PubMed query
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import from STITCH
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Kuhn et al., Nucleic Acids Research, 2016stitch-db.org
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subcellular localization
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Binder et al., Database, 2014compartments.jensenlab.org
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tissue expression
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tissues.jensenlab.org Santos et al., PeerJ, 2015
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target classification
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STRING visual style
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enrichment analysis
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