Matrix formalism to describe functional states of transcriptional regulatory systems.
|Title||Matrix formalism to describe functional states of transcriptional regulatory systems.|
|Publication Type||Journal Article|
|Year of Publication||2006|
|Authors||Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO|
|Journal||PLoS Comput Biol|
|Date Published||2006 Aug 11|
|Keywords||Computational 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.
|Alternate Title||PLoS Comput. Biol.|