Global regulators: CRP (glucose starvation) and RpoS (general stress in bacteria) ; q: do you think any striking feature exists in this network? Does it look homogeneous?
The ratio P(K0,K1)/Pr(K0,K1), whereP(K0,K1) is the probability that a pair of proteins with total numbers of interaction partners given by K0,K1 correspondingly, directly interact with each other in the full set of (2), whilePr(K0,K1) is the same probability in a randomized version of the same network. (B) The same as in (A) but for a protein with the in-degree Kin to be regulated by that with the out-degree Kout in the transcription regulatory network (3).
Cak1p is a cyclin-dependent kinase-activating kinase involved in two key signaling-transduction pathways: cell cycle and sporulation.
GLEaM is a discrete stochastic epidemic computational model based on a meta-population approach in which the world is defined in geographical census areas connected in a network of interactions by human travel fluxes corresponding to transportation infrastructures and mobility patterns. The GLEaM 2.0 simulation engine includes a multiscale mobility model integrating different layer of transportation networks ranging from the long range airline connections to the short range daily commuting pattern.
Graph properties of biological networks
Graph properties of biological
Modeling of Biological Systems
UCSF, May 8 2009
Transcription factor binding networks
Sea urchin: Davidson et al. 2002
Large scale identification of TF-binding sites using ChIP-chip or DNA sequencing
Yeast and mammalian cells: Horak and Snyder 2005; Kim et al.; Wei et al 2006.
Y2H (Rual et al.)
Yeast: Yu et al. 2008; Krogan et al.
Human: Rual et al 2005; Stelzl et al 2005.
2006; Gavin et al. 2006; Ito et al
Drosophila: Giot et al. 2003.
2001; Uetz et al 2000.
C. elegans: Li et al 2004.
How to randomize a network
Network randomization is used to determine the
statistical significance of a quantity, or how happy
you should be about a research result.
• Shuffle everything.
• Conserve the degree.
• Conserve the connectedness of the network.
Palla et al. Nature (2005).
Error and attack tolerance
Albert et al. Nature (2000).
Date hubs vs. party hubs
Date hubs vs. party hubs
Date hubs organize the proteome, connecting
biological processes—or modules—to each
other, whereas party hubs function inside modules.
• Barabasi and Oltvai, “Network biology:
understanding the cell’s functional
organization,” Nature Reviews Genetics, 2004.
• Zhu, Gerstein and Snyder, “Getting connected:
analysis and principles of biological networks,”
Genes and Development, 2007.