visualization of large-scaleprotein and disease networks

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