Networks in Cell Biology by Mark Buchanan, Guido Caldarelli, Paolo De Los Rios

By Mark Buchanan, Guido Caldarelli, Paolo De Los Rios

The technological know-how of complicated organic networks is remodeling examine in components starting from evolutionary biology to drugs. this can be the 1st e-book at the topic, supplying a accomplished creation to advanced community technological know-how and its organic purposes. With contributions from key leaders in either community concept and smooth cellphone biology, this ebook discusses the community technology that's more and more foundational for platforms biology and the quantitative realizing of dwelling platforms. It surveys experiences within the quantitative constitution and dynamics of genetic regulatory networks, molecular networks underlying mobile metabolism, and different primary organic techniques. The e-book balances empirical experiences and concept to offer a unified evaluate of this interdisciplinary technology. it's a key introductory textual content for graduate scholars and researchers in physics, biology and biochemistry, and offers rules and strategies from fields open air the reader's personal region of specialization.

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In addition, location data were obtained for 84 TFs in at least one of the 12 different environmental conditions. By investigating the resulting network, the authors addressed questions on the organization of regulatory elements in promoters in the context of their environment-dependent usage (Fig. 3). By compiling information from TF binding data, phylogenetically conserved sequences, and prior knowledge, they were able to infer a detailed transcriptional regulatory network for 102 TFs. In contrast to the previous approach, this approach experimentally identified all promoters that are bound by TFs in the different conditions.

The authors demonstrate experimentally that certain networks consistently survive over the wild-type, suggesting that addition of new links to the network is often not a barrier for evolution and that sometimes such events can offer a fitness advantage to the cell. 3 Transcriptional network evolution across organisms From a cross-genome perspective one could ask how the networks evolve across genomes and if parts of the regulatory networks are conserved across organisms. This points to an important question: if there is a regulatory interaction between a transcription factor and target gene in one organism, does the orthologous transcription factor regulate the orthologous target gene in another organism?

Structure of the transcriptional regulatory network. Nodes represent transcription factors or target genes and directed edge indicates a regulatory interaction between the two. (a) Components of a regulatory interaction (b) Local structure of the network consists of patterns of inter-connections called network motifs. The three frequently occurring motifs are the feed-forward motif (top), single input motif (middle) and multiple input motif (bottom) (c) Motifs are interconnected to form groups of highly connected genes, referred to as regulatory modules (dashed circles) (d) the set of all regulatory interactions in a cell is referred to as the transcriptional network.

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