in silico and text-based analysis of cellular networks
TRANSCRIPT
In Silico and Text-Based Analysisof Cellular Networks
Lars Juhl Jensen
association networks
guilt by association
protein networks
STRING
2000+ genomes
computational predictions
gene fusion
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
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
many databases
different formats
different identifiers
variable quality
not comparable
hard work
parsers
mapping files
quality scores
von Mering et al., Nucleic Acids Research, 2005
score calibration
gold standard
von Mering et al., Nucleic Acids Research, 2005
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
comprehensive lexicon
cyclin dependent kinase 1
CDC2
orthographic variation
spaces and hyphens
cyclin dependent kinase 1
cyclin-dependent kinase 1
prefixes and suffixes
CDC2
hCdc2
“black list”
SDS
co-mentioning
within documents
within paragraphs
within sentences
quality score
protein networks
Szklarczyk et al., Nucleic Acids Research, 2015string-db.org
general approach
chemical networks
Kuhn et al., Nucleic Acids Research, 2014stitch-db.org
space
subcellular localization
Binder et al., Database, 2014compartments.jensenlab.org
tissue expression
tissues.jensenlab.org Santos et al., submitted, 2015
time
cell-cycle expression
Santos et al., Nucleic Acids Research, 2015cyclebase.org
disease associations
diseases.jensenlab.org Frankild et al., Methods, 2015
AcknowledgmentsMolecular networks
Michael KuhnDamian Szklarczyk
Andrea Franceschini Milan SimonovicAlexander Roth
Sune Pletscher-FrankildJianyi Lin
Pablo MinguezChristian von Mering
Peer Bork
Time and spaceAlberto SantosSune Pletscher-FrankildJanos BinderKalliopi TsafouChristian StolteAlbert PallejaHeiko HornRasmus WernerssonReinhardt SchneiderSean O’ Donoghue