Editing Gene regulatory network (section)

=== Boolean network ===
The following example illustrates how a [[Boolean network]] can model a GRN together with its gene products (the outputs) and the substances from the environment that affect it (the inputs). [[Stuart Kauffman]] was amongst the first biologists to use the metaphor of Boolean networks to model genetic regulatory networks.<ref name="kauffmanRBN">{{cite book | title=The Origins of Order| vauthors = Kauffman SA | year=1993 | publisher = Oxford University Press | isbn=978-0-19-505811-6}}</ref><ref>{{cite journal | vauthors = Kauffman SA | title = Metabolic stability and epigenesis in randomly constructed genetic nets | journal = Journal of Theoretical Biology | volume = 22 | issue = 3 | pages = 437–467 | date = March 1969 | pmid = 5803332 | doi = 10.1016/0022-5193(69)90015-0 | bibcode = 1969JThBi..22..437K }}</ref>

# Each gene, each input, and each output is represented by a node in a [[directed graph]] in which there is an arrow from one node to another if and only if there is a causal link between the two nodes.
# Each node in the graph can be in one of two states: on or off.
# For a gene, "on" corresponds to the gene being expressed; for inputs and outputs, "on" corresponds to the substance being present.
# Time is viewed as proceeding in discrete steps. At each step, the new state of a node is a [[Boolean function]] of the prior states of the nodes with arrows pointing towards it.

The validity of the model can be tested by comparing simulation results with time series observations. A partial validation of a Boolean network model can also come from testing the predicted existence of a yet unknown regulatory connection between two particular transcription factors that each are nodes of the model.<ref name="pmid25398016">{{cite journal | vauthors = Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács KA | title = Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord | journal = PLOS ONE | volume = 9 | issue = 11 | pages = e111430 | date = November 2014 | pmid = 25398016 | pmc = 4232242 | doi = 10.1371/journal.pone.0111430 | doi-access = free | bibcode = 2014PLoSO...9k1430L }}</ref>