Definition of the Subject
In cell biology, networks are systems of interacting molecules that implement cellular functions, such as the regulation of gene expression , metabolism or intracellular signaling. While on a molecular level a biological network is a mesh of chemical reactions between, for example, enzymes and their substrates, or DNA-binding proteins and the genes that they regulate, the collective effect of these reactions can often be thought of as the enabling and regulating the flow of matter and energy (in metabolic networks), or of information (in signaling and transcriptional regulatory networks). The field is concerned primarily with the description and properties of such flows and with their emergence from network constituent parts – the molecules and their physical interactions. An important focus is also the question of how network function and operating principles can be inferred despite the limited experimental access to network...
Abbreviations
- Dynamical system:
-
is a set of components the properties of which (e. g. their quantity, activity level etc.) change in time because the components interact among themselves and are also influenced by external forces.
- Network node:
-
is a constituent component of the network, in biological networks most often identified with a molecular species.
- Interaction:
-
is a connection between network nodes; in biological networks an interaction means that two nodes chemically react, regulate each other, or effectively influence each other's activities. Interactions are mostly pairwise, but can be higher-order as well; they can be directed or undirected, and are usually characterized by an interaction strength.
- Network:
-
is a system of interacting nodes. A network can be represented mathematically as a graph, where vertices denote the nodes and edges denote the interactions. Biological networks often are understood to be dynamical systems as well, because the activities of network nodes evolve in time due to the graph of interactions.
- Network state:
-
is the vector of activities of all nodes that fully characterizes the network at any point in time; since a biological network is a dynamical system, this state generally changes through time according to a set of dynamical equations.
- Biological function :
-
refers to the role that a specific network plays in the life of the organism; the network can be viewed as existing to perform a task that enables the cell to survive and reproduce, such as the detection or transduction of a specific chemical signal.
- Pathway:
-
is a subset of nodes and interactions in a network along which information or energy and matter flow in a directed fashion; pathways can be coupled through interactions or unwanted cross-talk.
- Curse of dimensionality:
-
is the rapid increase of complexity encountered when analyzing or experimentally observing network states, as more and more network nodes are added. If there are N network nodes each of which only has two states (for example on and off), the number of states that the network can be in grows as 2N.
- Design principle :
-
is an (assumed) constraint on the network architecture, stating that a biological network, in addition to performing a certain function, implements that function in a particular way, usually to maximize or minimize some further objective measure, for instance robustness, information transmission, or designability.
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Acknowledgments
We thank our colleagues and collaborators who have helped us learn about these issues: MJ Berry, CG Callan, T Gregor, JB Kinney, P Mehta, SE Palmer, E Schneidman, JJ Hopfield, T Mora, S Setayeshgar, N Slonim, GJ Stephens, DW Tank, N Tishby, A Walczak, EF Wieschaus, CH Wiggins and NS Wingreen. Our work was supported in part by NIH grants P50 GM071508 and R01 GM077599, by NSF Grants IIS–0613435 and PHY–0650617, by the Swartz Foundation, and by the Burroughs Wellcome Fund.
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Tkačik, G., Bialek, W. (2009). Cell Biology: Networks , Regulation and Pathways . In: Meyers, R. (eds) Encyclopedia of Complexity and Systems Science. Springer, New York, NY. https://doi.org/10.1007/978-0-387-30440-3_48
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