Bayesian methods for elucidating genetic regulatory networks intimidating job interview questions
The nodes may represent the set of genes that share a common regulatory TF or that are expressed under the same specific set of conditions. Network motifs describe how single nodes connect with their neighbors.
Studies of the regulatory networks governing cell cycle progression and myogenesis provide examples (see below). Examples include the single-input motif, which describes the connection between a target gene and its sole transcriptional regulator; the multiple-input motif, in which a target gene is regulated by a group of factors; and the feed-forward loop, in which the product of one TF regulates the expression of a second TF, and both factors together regulate the expression of a third gene.
The dynamics of a global network have recently been examined computationally in yeast, where a majority of TF hubs were identified as active in more than one specific physiological setting, although few were active in all settings (Luscombe et al. The terms “endogenous” and “exogenous” have been introduced to describe network components that regulate processes in very different ways.
Endogenous subnetworks are defined as regulatory structures controlling processes that are temporally complex and intrinsic to the cell (examples include cell cycle and sporulation).
In addition, the process of gene expression is often the , the origin and effector of a response, wherein the information contained within a genome is interpreted and then ultimately used to produce the building blocks (proteins) required for a given response.
The TF hubs that regulate them have a relatively small number of targets, which often tend to be other TFs, and this tendency generates high local interconnectivity.One important characteristic of biological networks is their scale-free structure: The number of nodes that make a large number of connections with other nodes (referred to as “hubs”) is much lower than the number of nodes with few connections.This is thought to confer a hierarchical structure, whereby hubs play a central role in directing the cellular response to a given stimulus.For an extensive discussion of the principles underlying biological networks, we refer the reader to a recent review (Barabasi and Oltvai 2004).Biological networks are usually depicted as nodes connected by edges.