Network biology An introduction to STRING and Cytoscape Lars Juhl Jensen jensenlab.org
core concepts
STRING
Cytoscape
stringApp
core concepts
nodes / vertices
things to be connected
proteins
diseases
edges
connections between things
undirected
directed
weighted
topology
degree
centrality
clustering coefficient
robustness
protein networks
physical interactions
functional associations
guilt by association
STRING
5090 genomes
24.6 million proteins
functional associations
string-db.org Szklarczyk et al., Nucleic Acids Res., 2017
heavily used
4000 users daily
easy to use
works well
Huang et al., Cell Syst., 2018
data integration
genomic context
gene fusion
Korbel et al., Nat. Biotechnol., 2004
gene neighborhood
Korbel et al., Nat. Biotechnol., 2004
phylogenetic profiles
Korbel et al., Nat. Biotechnol., 2004
experimental data
gene coexpression
physical interactions
von Mering et al., Nucleic Acids Res., 2005
curated knowledge
pathways
Letunic & Bork, Trends Biochem. Sci., 2008
many databases
different formats
different identifiers
varying quality
not comparable
not same species
hard work
parsers
mapping files
quality scores
von Mering et al., Nucleic Acids Res., 2005
score calibration
gold standard
von Mering et al., Nucleic Acids Res., 2005
common identifiers
common scale
orthology transfer
Franceschini et al., Nucleic Acids Res., 2013
cross-species integration
missing most of the data
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
dictionary
synonyms
cyclin dependent kinase 1
CDC2
orthographic variation
cyclin dependent kinase 1
cyclin-dependent kinase 1
CDC2
hCDC2
black list
SDS
a
co-mentioning
counting
documents
paragraphs
sentences
weighted count
quality score
score calibration
orthology transfer
combine all evidence
Cytoscape
network tool
analysis
visualization
not a database
user interface
networks
tables
visual styles
load/save sessions
import network
local file
public database
import table
property mappings
passthrough mapping
discrete mapping
continuous mapping
default & bypass
selection filters
select by attributes
layout algorithms
clustering
app store
stringApp
STRING Cytoscape
protein query
disease query
PubMed query
visualize your own data
proteomics experiment
Emdal et al., Science Signaling, 2015
protein query
STRING network
import table
user data
new node attributes
color by log-ratio
Szklarczyk et al., Nucleic Acids Research, 2017
term enrichment analysis
select terms of interest
visualize on network
easy example
typical omics dataset
100–1000 proteins
1000–10000 interactions
Doncheva et al., J. Proteome Res., 2018
ridiculogram
clustering
functional modules
intra-cluster interactions
re-layout network
Doncheva et al., J. Proteome Res., 2018
compare diseases
disease query
merged STRING network
ridiculogram
clustering
color by diseases
highlight drug targets
summarize literature
topic of interest
PubMed query
retrieve abstracts
enriched proteins
STRING network
color by literature support
highlight physical interactions
visualize enriched terms
summary
networks
nodes & edges
useful abstraction
lends itself to visualization
STRING
protein network database
functional associations
curated knowledge
experimental data
genomic context
text mining
unified identifiers
scored
transferred
web interface
Cytoscape
network analysis
network visualization