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Lars Juhl Jensen
STRING & STITCH
Network integration of heterogeneous
data
interaction networks
association networks
guilt by association
molecular networks
web resources
STRING
string-db.org
STITCH
stitch-db.org
9.6 million proteins
430 thousand chemicals
common foundation
data integration
curated knowledge
protein complexes
3D structures
pathways
signaling pathways
metabolic pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
known drug targets
text mining
text corpus
PubMed abstracts
open access articles
dictionary
genes/proteins
chemical compounds
“black list”
co-mentioning
natural language processing
experimental data
physical interactions
high-throughput assays
Jensen & Bork, Science, 2008
genetic interactions
synthetic lethality
Beyer et al., Nature Reviews Genetics, 2007
transcriptomics
microarrays
RNAseq
gene coexpression
chemical screens
binding assays
Campillos et al., Science, 2008
activity assays
genomic context
genome comparison
gene fusion
Korbel et al., Nature Biotechnology, 2004
operons
Korbel et al., Nature Biotechnology, 2004
bidirectional promoters
Korbel et al., Nature Biotechnology, 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology, 2004
a real example
Cell
Cellulosomes
Cellulose
complications
many databases
different formats
different identifiers
variable quality
not comparable
not same species
hard work
parsers
mapping files
quality scores
text mining
co-mention score
affinity purification
von Mering et al., Nucleic Acids Research, 2005
phylogenetic profiles
score calibration
gold standard
von Mering et al., Nucleic Acids Research, 2005
implicit weighting by quality
common scale
orthology-based transfer
orthologous groups
Franceschini et al., Nucleic Acids Research, 2013
access
web interface
evidence viewers
good for small networks
not for big networks
Cytoscape
stringApp
handles large networks
great for visualization
steep learning curve
download files
R/Bioconductor
REST API
payload mechanism
requires programming
related resources
RAIN
ncRNA networks
Junge et al., Database, 2017rth.dk/resources/rain
COMPARTMENTS
subcellular localization
Binder et al., Database, 2014compartments.jensenlab.org
TISSUES
tissue expression
tissues.jensenlab.org Santos et al., PeerJ, 2015
DISEASES
disease associations
heterogeneous data
common identifiers
quality scores
STRING & STITCH: Network integration of heterogeneous data

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