6. 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.
7. Human Interactome
Protein
Y2H (Rual et al.)
Literature
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.
21. Assortativity
• A preference for a network's nodes to attach
to others that are similar or different in
degree. Maslov and Sneppen, 2002.
P(K0,K1)/PR(K0,K1)
Yeast interactome Yeast transcriptome
22.
23.
24. Non-Hub Bottleneck in Yeast Interactome
Cak1p is a cyclin-
dependent kinase-
activating kinase
involved in two key
signaling pathways.
25. Hubs, bottlenecks: which are more
essential?
NH-NB: Non-hub, non-bottleneck; H-NB: Hub, non-bottleneck;
B-NH: Bottleneck, non-hub; BH: Bottleneck, hub. Yu et al. 2007.
29. 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.
42. Date hubs vs. party hubs
Non-hubs
Hubs
Hubs (random)
43. Date hubs vs. party hubs
Date hubs organize the proteome, connecting
biological processes—or modules—to each
other, whereas party hubs function inside modules.
46. Further References
• 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.
Notas do Editor
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.