… With respect to intracellular regulation, we now expect that regulatory networks may … of
regulatory networks as ‘‘black-box’’ modules and relate intrinsic properties of the modules and …

… of hierarchical systems, for example hierarchical control analysis and modular response
analysis. The authors, here, review these methods and illustrate the strength of these types of …

… Gene regulatory networks control the cellular phenotype by changing the RNA and protein …
the structure of these networks. Particularly, we focus on modular response analysis (MRA), a …

… network of Escherichia coli is currently the best-understood regulatory network of a single
cell. … , suggesting a hierarchical modular architecture in this network, we identified eight …

… , Cell differentiation, Cell signaling and communication, Cell processes The dynamical analysis
of comprehensive biological regulatory networks … large networks into functional modules …

… shared biological processes, including cell cycle and immune-related … regulatory network
level, but share a common regulatory network that includes histones and regulators of the cell …

… cellular process that appears in more than one module. In our analysis, we found that
different sets of regulatory … in the CMCS cell and Cell differentiation modules. Sporulation is …

… A cellular network that is composed of 4 modules and … the response of E21 upon a perturbation
in S will be analyzed. A perturbation of module 1 through S is spread through the network …

… that clustering does not necessarily identify the corresponding regulators. Therefore, genes
clustered together may not fully represent modules in transcriptional regulatory networks. …

… regulatory networks based on systematic perturbation data. That is, given a biological system
of interest, which could be the whole cell… in a steady state, modular response analysis [10] (…