12,733 research outputs found
One Hub-One Process: A Tool Based View on Regulatory Network Topology
The relationship between the regulatory design and the functionality of
molecular networks is a key issue in biology. Modules and motifs have been
associated to various cellular processes, thereby providing anecdotal evidence
for performance based localization on molecular networks. To quantify
structure-function relationship we investigate similarities of proteins which
are close in the regulatory network of the yeast Saccharomyces Cerevisiae. We
find that the topology of the regulatory network show weak remnants of its
history of network reorganizations, but strong features of co-regulated
proteins associated to similar tasks. This suggests that local topological
features of regulatory networks, including broad degree distributions, emerge
as an implicit result of matching a number of needed processes to a finite
toolbox of proteins.Comment: 18 pages, 3 figures, 5 supplementary figure
Degree Landscapes in Scale-Free Networks
We generalize the degree-organizational view of real-world networks with
broad degree-distributions in a landscape analogue with mountains (high-degree
nodes) and valleys (low-degree nodes). For example, correlated degrees between
adjacent nodes corresponds to smooth landscapes (social networks), hierarchical
networks to one-mountain landscapes (the Internet), and degree-disassortative
networks without hierarchical features to rough landscapes with several
mountains. We also generate ridge landscapes to model networks organized under
constraints imposed by the space the networks are embedded in, associated to
spatial or, in molecular networks, to functional localization. To quantify the
topology, we here measure the widths of the mountains and the separation
between different mountains.Comment: 4 pages, 5 figure
- …