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Network biology An introduction to STRING and Cytoscape
Lars Juhl Jensen jensenlab.org
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core concepts
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STRING
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Cytoscape
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stringApp
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core concepts
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nodes / vertices
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things to be connected
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proteins
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diseases
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edges
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connections between things
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undirected
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directed
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weighted
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topology
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degree
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centrality
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clustering coefficient
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robustness
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protein networks
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physical interactions
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functional associations
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guilt by association
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STRING
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5090 genomes
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24.6 million proteins
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functional associations
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string-db.org Szklarczyk et al., Nucleic Acids Res., 2017
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heavily used
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4000 users daily
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easy to use
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works well
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Huang et al., Cell Syst., 2018
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data integration
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genomic context
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gene fusion
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Korbel et al., Nat. Biotechnol., 2004
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gene neighborhood
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Korbel et al., Nat. Biotechnol., 2004
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phylogenetic profiles
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Korbel et al., Nat. Biotechnol., 2004
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experimental data
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gene coexpression
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physical interactions
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von Mering et al., Nucleic Acids Res., 2005
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curated knowledge
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pathways
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Letunic & Bork, Trends Biochem. Sci., 2008
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many databases
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different formats
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different identifiers
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varying quality
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not comparable
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not same species
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hard work
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parsers
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mapping files
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quality scores
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von Mering et al., Nucleic Acids Res., 2005
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score calibration
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gold standard
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von Mering et al., Nucleic Acids Res., 2005
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common identifiers
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common scale
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orthology transfer
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Franceschini et al., Nucleic Acids Res., 2013
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cross-species integration
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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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synonyms
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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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a
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co-mentioning
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counting
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documents
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paragraphs
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sentences
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weighted count
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quality score
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score calibration
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orthology transfer
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combine all evidence
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Cytoscape
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network tool
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analysis
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visualization
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not a database
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user interface
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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 mapping
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discrete mapping
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continuous mapping
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default & bypass
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selection filters
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select by attributes
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layout algorithms
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clustering
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app store
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stringApp
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STRING Cytoscape
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protein query
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disease query
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PubMed query
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visualize your own data
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proteomics experiment
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Emdal et al., Science Signaling, 2015
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protein query
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STRING network
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import table
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user data
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new node attributes
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color by log-ratio
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Szklarczyk et al., Nucleic Acids Research, 2017
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term enrichment analysis
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select terms of interest
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visualize on network
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easy example
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typical omics dataset
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100–1000 proteins
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1000–10000 interactions
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Doncheva et al., J. Proteome Res., 2018
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ridiculogram
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clustering
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functional modules
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intra-cluster interactions
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re-layout network
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Doncheva et al., J. Proteome Res., 2018
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compare diseases
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disease query
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merged STRING network
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ridiculogram
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clustering
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color by diseases
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highlight drug targets
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summarize literature
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topic of interest
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PubMed query
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retrieve abstracts
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enriched proteins
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STRING network
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color by literature support
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highlight physical interactions
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visualize enriched terms
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summary
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networks
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nodes & edges
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useful abstraction
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lends itself to visualization
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STRING
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protein network database
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functional associations
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curated knowledge
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experimental data
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genomic context
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text mining
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unified identifiers
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scored
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transferred
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web interface
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Cytoscape
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network analysis
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network visualization
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