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What is Transcriptional Regulatory Network

Handbook of Research on Computational Methodologies in Gene Regulatory Networks
A network model of transcription factor-target relationships. Directed edges run from transcription factor nodes to target nodes.
Published in Chapter:
What are Gene Regulatory Networks?
Alberto de la Fuente (CRS4 Bioinformatica, Italy)
DOI: 10.4018/978-1-60566-685-3.ch001
Abstract
This book deals with algorithms for inferring and analyzing Gene Regulatory Networks using mainly gene expression data. What precisely are the Gene Regulatory Networks that are inferred by such algorithms from this type of data? There is still much confusion in the current literature and it is important to start a book about computational methods for Gene Regulatory Networks with a definition that is as unambiguous as possible. In this chapter, I provide a definition and try to clearly explain what Gene Regulatory Networks are in terms of the underlying biochemical processes. To do the latter in a formal way, I will use a linear approximation to the in general non-linear kinetics underlying interactions in biochemical systems and show how a biochemical system can be ‘condensed’ into the more compact description of Gene Regulatory Networks. Important differences between the defined Gene Regulatory Networks and other network models for gene regulation, such as Transcriptional Regulatory Networks and Co-Expression Networks, will be highlighted.
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Methodologies for Modeling Gene Regulatory Networks
The networks that are only directed; they have directed edges between source and target genes.
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