Lars Juhl Jensen Network Biology A crash course on STRING and Cytoscape
Lars Juhl Jensen
Network BiologyA crash course on STRING and
Cytoscape
STRING
protein network database
Cytoscape
network visualization tool
stringApp
gene/protein list
STRING network
map external data
Szklarczyk et al., Nucleic Acids Research, 2017
STRING
string-db.org
2000+ genomes
functional associations
genomic context
gene fusion
Korbel et al., Nature Biotechnology, 2004
gene neighborhood
Korbel et al., Nature Biotechnology, 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology, 2004
experimental data
gene coexpression
physical interactions
Jensen & Bork, Science, 2008
curated knowledge
3D structures
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
many databases
different formats
different identifiers
variable quality
not comparable
hard work
quality scores
affinity purification
von Mering et al., Nucleic Acids Research, 2005
score calibration
gold standard
von Mering et al., Nucleic Acids Research, 2005
implicit weighting by quality
common scale
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
cyclin dependent kinase 1
CDC2
orthographic variation
cyclin dependent kinase 1
cyclin-dependent kinase 1
CDC2
hCdc2
“black list”
SDS
co-mentioning
scoring scheme
Cytoscape
networks
tables
visual styles
load/save sessions
import network
local file
public database
import table
property mappings
passthrough
discrete
continuous
default & bypass
layouts
force-directed
grid
circle attribute
clustering
clusterMaker2
new node attribute
clustered network
selection filters
stringApp
import from STRING
protein query
Szklarczyk et al., Nucleic Acids Research, 2017
disease query
PubMed query
import from STITCH
Kuhn et al., Nucleic Acids Research, 2016stitch-db.org
subcellular localization
Binder et al., Database, 2014compartments.jensenlab.org
tissue expression
tissues.jensenlab.org Santos et al., PeerJ, 2015
target classification
STRING visual style
enrichment analysis
Thank youSTRING & STITCH
Damian SzklarczykNadezhda Donche
vaJohn
"Scooter" MorrisHelen Cook
Michael KuhnStefan Wyder
Milan SimonovicAlexander Roth
Peer BorkChristian von Merin
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COMPARTMENTS,TISSUES & DISEASESAlberto SantosOana PalascaSune Pletscher-FrankildChristian StolteJanos BinderKalliopi TsafouJan GorodkinSean I. O’Donoghue