mining heterogeneous data: understanding systems at the level of complexes and networks
TRANSCRIPT
Mining heterogeneous dataUnderstanding systems at the level of complexes and networks
Lars Juhl Jensen
the 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
regulation
gene expression
protein complexes
phosphorylation
targeted degradation
gene expression
cell cultures
S. cerevisiae
synchronization
microarrays
time courses
Gauthier et al., Nucleic Acids Research, 2007
cycling genes
scoring scheme
shape
magnitude
benchmarking
Gauthier et al., Nucleic Acids Research, 2007
protein complexes
interaction data
Jensen & Bork, Science, 2008
high error rate
scoring scheme
von Mering et al., Nucleic Acids Research, 2005
von Mering et al., Nucleic Acids Research, 2005
quality threshold
time of peak mRNA level
temporal network
de Lichtenberg, Jensen et al., Science, 2005
hypothesis
just-in-time assembly
de Lichtenberg, Jensen et al., Cell Cycle, 2007
how can we test it?
evolution
microarray time courses
S. pombe
H. sapiens
A. thaliana
cross-species comparison
orthologous genes
sequence similarity
Jensen, Jensen, de Lichtenberg et al., Nature, 2006
protein complexes
all cell-cycle complexes
Jensen, Jensen, de Lichtenberg et al., Nature, 2006
time of peak mRNA level
time of action
just-in-time assembly
pathways
generalize to metabolism
deoxynucleotide synthesis
just-in-time flux
phenotypes
H. sapiens
siRNA screen
comparison with expression
summary
reanalysis
integration
high-throughput data
biological insights
Acknowledgments
Thomas Skøt JensenUlrik de Lichtenberg
Søren BrunakPeer Bork
larsjuhljensen