Network visualization: A crash course on using Cytoscape
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Transcript of Network visualization: A crash course on using Cytoscape
![Page 1: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/1.jpg)
Lars Juhl Jensen
Network visualizationA crash course on using Cytoscape
![Page 2: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/2.jpg)
STRING & STITCH
![Page 3: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/3.jpg)
network database
![Page 4: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/4.jpg)
Cytoscape
![Page 5: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/5.jpg)
network tool
![Page 6: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/6.jpg)
stringApp
![Page 7: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/7.jpg)
STRING → Cytoscape
![Page 8: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/8.jpg)
Cytoscape basics
![Page 9: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/9.jpg)
three examples
![Page 10: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/10.jpg)
live demo
![Page 11: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/11.jpg)
Cytoscape
![Page 12: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/12.jpg)
networks
![Page 13: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/13.jpg)
tables
![Page 14: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/14.jpg)
visual styles
![Page 15: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/15.jpg)
![Page 16: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/16.jpg)
load/save sessions
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import network
![Page 18: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/18.jpg)
local file
![Page 19: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/19.jpg)
public database
![Page 20: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/20.jpg)
import table
![Page 21: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/21.jpg)
property mappings
![Page 22: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/22.jpg)
passthrough
![Page 23: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/23.jpg)
discrete
![Page 24: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/24.jpg)
continuous
![Page 25: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/25.jpg)
default & bypass
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selection filters
![Page 27: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/27.jpg)
select by attributes
![Page 28: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/28.jpg)
layout algorithms
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clustering
![Page 30: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/30.jpg)
app store
![Page 31: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/31.jpg)
stringApp
![Page 32: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/32.jpg)
import from STRING
![Page 33: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/33.jpg)
import from STITCH
![Page 34: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/34.jpg)
visual style
![Page 35: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/35.jpg)
![Page 36: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/36.jpg)
node attributes
![Page 37: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/37.jpg)
subcellular localization
![Page 38: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/38.jpg)
tissue expression
![Page 39: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/39.jpg)
drug target classifications
![Page 40: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/40.jpg)
enrichment analysis
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protein query
![Page 42: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/42.jpg)
proteomics experiment
![Page 43: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/43.jpg)
Emdal et al., Scienc Signaling, 2015
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list of proteins
![Page 45: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/45.jpg)
import network
![Page 46: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/46.jpg)
organic layout
![Page 47: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/47.jpg)
import table
![Page 48: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/48.jpg)
gene names from study
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passthrough mapping
![Page 50: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/50.jpg)
color by log-ratio
![Page 51: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/51.jpg)
continuous mapping
![Page 52: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/52.jpg)
Szklarczyk et al., Nucleic Acids Research, 2017
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enrichment analysis
![Page 54: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/54.jpg)
![Page 55: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/55.jpg)
very easy example
![Page 56: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/56.jpg)
PubMed query
![Page 57: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/57.jpg)
angiogenesis regulation
![Page 58: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/58.jpg)
~20 thousand abstracts
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named entity recognition
![Page 60: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/60.jpg)
foreground count
![Page 61: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/61.jpg)
background count
![Page 62: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/62.jpg)
top-100 genes
![Page 63: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/63.jpg)
functional associations
![Page 64: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/64.jpg)
![Page 65: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/65.jpg)
ridiculogram
![Page 66: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/66.jpg)
physical interactions
![Page 67: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/67.jpg)
color by target development
![Page 68: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/68.jpg)
discrete mapping
![Page 69: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/69.jpg)
![Page 70: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/70.jpg)
fairly easy example
![Page 71: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/71.jpg)
disease query
![Page 72: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/72.jpg)
DISEASES
![Page 73: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/73.jpg)
major depressive disorder
![Page 74: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/74.jpg)
Alzheimer’s disease
![Page 75: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/75.jpg)
Parkinson’s disease
![Page 76: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/76.jpg)
three networks
![Page 77: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/77.jpg)
merge
![Page 78: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/78.jpg)
combined network
![Page 79: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/79.jpg)
![Page 80: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/80.jpg)
ridiculogram
![Page 81: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/81.jpg)
clustering
![Page 82: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/82.jpg)
intra-cluster interactions
![Page 83: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/83.jpg)
color by disease
![Page 84: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/84.jpg)
Boolean select & bypass
![Page 85: Network visualization: A crash course on using Cytoscape](https://reader030.fdocuments.us/reader030/viewer/2022021422/5a6d52bc7f8b9af8418b5363/html5/thumbnails/85.jpg)
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