20,781 research outputs found
Principles of microRNA regulation of a human cellular signaling network
MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs, which suppress gene
expression by selectively binding to the 3-noncoding region of specific message
RNAs through base-pairing. Given the diversity and abundance of miRNA targets,
miRNAs appear to functionally interact with various components of many cellular
networks. By analyzing the interactions between miRNAs and a human cellular
signaling network, we found that miRNAs predominantly target positive
regulatory motifs, highly connected scaffolds and most downstream network
components such as signaling transcription factors, but less frequently target
negative regulatory motifs, common components of basic cellular machines and
most upstream network components such as ligands. In addition, when an adaptor
has potential to recruit more downstream components, these components are more
frequently targeted by miRNAs. This work uncovers the principles of miRNA
regulation of signal transduction networks and implies a potential function of
miRNAs for facilitating robust transitions of cellular response to
extracellular signals and maintaining cellular homeostasis
Global network structure of dominance hierarchy of ant workers
Dominance hierarchy among animals is widespread in various species and
believed to serve to regulate resource allocation within an animal group.
Unlike small groups, however, detection and quantification of linear hierarchy
in large groups of animals are a difficult task. Here, we analyse
aggression-based dominance hierarchies formed by worker ants in Diacamma sp. as
large directed networks. We show that the observed dominance networks are
perfect or approximate directed acyclic graphs, which are consistent with
perfect linear hierarchy. The observed networks are also sparse and random but
significantly different from networks generated through thinning of the perfect
linear tournament (i.e., all individuals are linearly ranked and dominance
relationship exists between every pair of individuals). These results pertain
to global structure of the networks, which contrasts with the previous studies
inspecting frequencies of different types of triads. In addition, the
distribution of the out-degree (i.e., number of workers that the focal worker
attacks), not in-degree (i.e., number of workers that attack the focal worker),
of each observed network is right-skewed. Those having excessively large
out-degrees are located near the top, but not the top, of the hierarchy. We
also discuss evolutionary implications of the discovered properties of
dominance networks.Comment: 5 figures, 2 tables, 4 supplementary figures, 2 supplementary table
Directed network modules
A search technique locating network modules, i.e., internally densely
connected groups of nodes in directed networks is introduced by extending the
Clique Percolation Method originally proposed for undirected networks. After
giving a suitable definition for directed modules we investigate their
percolation transition in the Erdos-Renyi graph both analytically and
numerically. We also analyse four real-world directed networks, including
Google's own webpages, an email network, a word association graph and the
transcriptional regulatory network of the yeast Saccharomyces cerevisiae. The
obtained directed modules are validated by additional information available for
the nodes. We find that directed modules of real-world graphs inherently
overlap and the investigated networks can be classified into two major groups
in terms of the overlaps between the modules. Accordingly, in the
word-association network and among Google's webpages the overlaps are likely to
contain in-hubs, whereas the modules in the email and transcriptional
regulatory networks tend to overlap via out-hubs.Comment: 21 pages, 10 figures, version 2: added two paragaph
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