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