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The STRING database and related tools

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Lars Juhl Jensen
Lars Juhl Jensen

The STRING database and related tools

Science
1 of 90
The STRING database and related tools Lars Juhl Jensen
association networks
guilt by association
molecular networks
computational predictions
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
protein interactions
Jensen & Bork, Science, 2008
gene coexpression
curated knowledge
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
many databases
different formats
different identifiers
variable quality
not comparable
not same species
hard work
scoring schemes
von Mering et al., Nucleic Acids Research, 2005
score calibration
gold standard
von Mering et al., Nucleic Acids Research, 2005
orthology-based transfer
Franceschini et al., Nucleic Acids Research, 2013
missing most of the data
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
comprehensive lexicon
CDC2
cyclin dependent kinase 1
orthographic variation
expansion rules
CDC2
hCdc2
flexible matching
cyclin dependent kinase 1
cyclin-dependent kinase 1
“black list”
SDS
information extraction
co-mentioning
counting
within documents
within paragraphs
within sentences
scoring scheme
score calibration
natural language processing
Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]
general approach
computational predictions
experimental data
curated knowledge
text mining
common identifiers
quality scores
score calibration
visualization
web resource
STRING
protein networks
string-db.org
STITCH
chemical networks
stitch-db.org
COMPARTMENTS
subcellular localization
compartments.jensenlab.org
TISSUES
tissue expression
tissues.jensenlab.org
DISEASES
disease associations
Acknowledgments STRING and STITCH Michael Kuhn Damian Szklarczyk Andrea Franceschini Milan Simonovic Alexander Roth Sune Pletscher- Frankild Jianyi Lin Pablo Minguez Christian von Mering Peer Bork Localization and disease Sune Pletscher-Frankild Alberto Santos Janos Binder Kalliopi Tsafou Christian Stolte Albert Palleja Heiko Horn Evangelos Pafilis Reinhardt Schneider Sean O’ Donoghue

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