just-in-time assembly - co-evolution of transcriptional and post-translational cell-cycle regulation...
TRANSCRIPT
Just-in-time assemblyCo-evolution of transcriptional and post-translational
cell-cycle regulation of protein complexes
Lars Juhl JensenEMBL Heidelberg
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
phosphorylation
targeted degradation
protein interactions
molecular biology
one gene
one postdoc
many types of data
a single gene
high-throughput biology
one lab
one technology
all the relevant genes
a single type of data
systems biology
many types of data
all the relevant genes
data integration
expression data
cell cultures
synchronization
microarrays
time courses
expression profiles
list of genes
periodically expressed
S. cerevisiae
expression data
Cho et al.
Spellman et al.
computational methods
Zhao et al.
Langmead et al.
Johansson et al.
Wichert et al.
Luan and Li
Lu et al.
Ahdesmäki et al.
Willbrand et al.
Chen
Qiu et al.
Ahnert et al.
Glynn et al.
Andersson et al.
Lu et al.
Xu et al.
Liew et al.
no benchmarking
reanalysis
benchmarking
no progress
no benchmarking
S. pombe
H. sapiens
A. thaliana
reanalysis
benchmarking
list of genes
periodically expressed
four organisms
orthologous groups
sequence similarity
not conserved
others had seen this before
Ota et al.
Rustici et al.
Dyczkowski and Vingron
technical issues
orthology definitions
no reanalysis
different analysis methods
no error estimates
no biological explanation
turn back time …
temporal network
S. cerevisiae cell cycle
dynamic and static subunits
just-in-time assembly
evolutionary flexibility
different organisms
different dynamic subunits
manual curation
protein complexes
different time scales
time warping
same color = same phase
DNA polymerases
dynamic subunits
time of peak expression
time of action
just-in-time assembly
CDK substrates
Übersax et al.
Loog et al.
Phospho.ELM
NetPhosK
correlation
Fisher’s exact test
cell cycle vs. non-cell cycle
correlated changes
Fisher’s exact test
co-evolution
transcriptional regulation
phosphorylation
targeted degradation
just-in-time assembly
Acknowledgments
Thomas Skøt JensenUlrik de Lichtenberg
Søren BrunakPeer Bork
Thank you!
Questions?