Matrix formalism to describe functional states of transcriptional regulatory systems.

TitleMatrix formalism to describe functional states of transcriptional regulatory systems.
Publication TypeJournal Article
Year of Publication2006
AuthorsGianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO
JournalPLoS Comput Biol
Date Published2006 Aug 11
KeywordsComputational Biology, Escherichia coli, Gene Expression Regulation, Genome, Genomics, Lac Operon, Models, Genetic, Transcription, Genetic

Complex regulatory networks control the transcription state of a genome. These transcriptional regulatory networks (TRNs) have been mathematically described using a Boolean formalism, in which the state of a gene is represented as either transcribed or not transcribed in response to regulatory signals. The Boolean formalism results in a series of regulatory rules for the individual genes of a TRN that in turn can be used to link environmental cues to the transcription state of a genome, thereby forming a complete transcriptional regulatory system (TRS). Herein, we develop a formalism that represents such a set of regulatory rules in a matrix form. Matrix formalism allows for the systemic characterization of the properties of a TRS and facilitates the computation of the transcriptional state of the genome under any given set of environmental conditions. Additionally, it provides a means to incorporate mechanistic detail of a TRS as it becomes available. In this study, the regulatory network matrix, R, for a prototypic TRS is characterized and the fundamental subspaces of this matrix are described. We illustrate how the matrix representation of a TRS coupled with its environment (R*) allows for a sampling of all possible expression states of a given network, and furthermore, how the fundamental subspaces of the matrix provide a way to study key TRS features and may assist in experimental design.

PubMed URL
Alternate TitlePLoS Comput. Biol.
PubMed ID16895435