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Lars Juhl Jensen
Network visualizationA crash course on using Cytoscape
STRING & STITCH
network database
Cytoscape
network tool
stringApp
STRING → Cytoscape
Cytoscape basics
three examples
live demo
Cytoscape
networks
tables
visual styles
load/save sessions
import network
local file
public database
import table
property mappings
passthrough
discrete
continuous
default & bypass
selection filters
select by attributes
layout algorithms
clustering
app store
stringApp
import from STRING
import from STITCH
visual style
node attributes
subcellular localization
tissue expression
drug target classifications
enrichment analysis
protein query
proteomics experiment
Emdal et al., Scienc Signaling, 2015
list of proteins
import network
organic layout
import table
gene names from study
passthrough mapping
color by log-ratio
continuous mapping
Szklarczyk et al., Nucleic Acids Research, 2017
enrichment analysis
very easy example
PubMed query
angiogenesis regulation
~20 thousand abstracts
named entity recognition
foreground count
background count
top-100 genes
functional associations
ridiculogram
physical interactions
color by target development
discrete mapping
fairly easy example
disease query
DISEASES
major depressive disorder
Alzheimer’s disease
Parkinson’s disease
three networks
merge
combined network
ridiculogram
clustering
intra-cluster interactions
color by disease
Boolean select & bypass
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