Visualization of large-scale protein and disease networks Lars Juhl Jensen
Jul 07, 2015
Visualization of large-scale
protein and disease networks
Lars Juhl Jensen
the mitotic cell cycle
grow and divide
one cell
two cells
four phases
G1 phase
growth
S phase
DNA replication
G2 phase
growth
M phase
cell division
cell culture
synchronization
microarrays
time courses
Gauthier et al., Nucleic Acids Research, 2007
cycling genes
single-number summary
time of peak expression
circular color scale
system-level visualization
gene expression
protein interactions
temporal network
de Lichtenberg, Jensen et al., Science, 2005
discovery
just-in-time assembly
de Lichtenberg, Jensen et al., Cell Cycle, 2007
protein networks
STRING
web resource
functional associations
heterogeneous evidence
computational predictions
genomic context
Korbel et al., Nature Biotechnology, 2004
experimental data
physical interactions
Jensen & Bork, Science, 2008
curated knowledge
pathways
Letunic & Bork, Trends in Biochemical Sciences, 2008
text mining
biomedical literature
>10 km
common identifiers
quality scores
cross-species transfer
complex information
interactive visualization
string-db.org
inspect evidence
explorative analysis
disease networks
central health registries
CPR number
established in 1968
national discharge registry
14 years
6.2 million patients
45 million admissions
68 million records
119 million diagnosis
distributions
gender
age
type of hospital encounter
Jensen et al., Nature Communications, 2014
temporal correlations
too many to visualize
trajectories
Jensen et al., Nature Communications, 2014
trajectory networks
Jensen et al., Nature Communications, 2014
discovery
key diagnoses
Jensen et al., Nature Communications, 2014
direct medical implications
summary
visualization is important
publishing results
exploring data
making discoveries
Acknowledgments
STRING
Michael Kuhn
Damian Szklarczyk
Andrea Franceschini
Milan Simonovic
Alexander Roth
Sune Pletscher-
Frankild
Jianyi Lin
Pablo Minguez
Christian von Mering
Peer Bork
Cell cycle
Ulrik de Lichtenberg
Thomas Skøt Jensen
Søren Brunak
Peer Bork
Disease networks
Anders Bøck Jensen
Tudor Oprea
Pope Moseley
Søren Brunak