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