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Boolean networks

The Boolean network model, introduced by Kauffman (Kauffman, 1969, 1974; Kauffman and Glass, 1973)and recently developed by Shmulevich(Shmulevich, 2002), has received the most attention, not only from the biology community, but also in physics. In this model, gene expression is quantized to only two levels: ON and OFF. The expression level (state) of each gene is functionally related to the expression states of some other genes, using logical rules. A Boolean network G(V,F) is defined by a set of nodes corresponding to genes V = {x1, . . . , xn} and a list of Boolean functions F = (f1, . . . , fn) . The state of a node (gene) is completely determined by the values of other nodes at time t by means of underlying logical Boolean functions. The model is represented in the form of directed graph.Each xi represents the state (expression) of gene i, where xi=1 represents the fact that gene i is expressed and xi=0 means it is not expressed. The list of Boolean functions F represents the rules of regulatory interactions between genes. That is, any given gene transforms its inputs (regulatory factors that bind to it) into an output, which is the state or expression of the gene itself. The maximum connectivity of a Boolean network is defined by K= maxi (ki) . All genes are assumed to update synchronously in accordance with the functions assigned to them and this process is then repeated. The artificial synchrony simplifies computation while preserving the qualitative, generic properties of global network dynamics (Kauffman, 1993; Huang, 1999; Wuensche, 1998).

Below the example is presented. Consider a Boolean network consisting of 5 genes {x1, . . . , x5} with the corresponding Boolean functions given by the truth tables shown in Figure1. The maximum connectivity is K=3, although we allow some input variables to duplicate, essentially reducing the connectivity.The dynamics of this Boolean network are shown in Figure2. Since there are 5 genes, there are 2^5 = 32 possible states that the network can be in. Each state is represented by a circle and the arrows between states show the transitions of the network according to the functions in Table 1., Figure1. . It is easy to see that because of the inherent deterministic directionality in Boolean networks as well as only a finite number of possible states.

Truth tables of the functions in a Boolean network with 5 genes. The indices j1, j2, and j3 indicate the input connections for each of the functions.

The state-transition diagram for the Boolean network defined in table 1. (Figure1).

In the context of Boolean networks as models of genetic regulatory networks, there is no doubt that the binary approximation of gene expression is an oversimplification (Huang, 1999). However, even though most biological phenomena manifest themselves in the continuous domain, they are often described in a binary logical language such as‘on and off,’‘upregulated and downregulated’, and‘responsive and nonresponsive.’There is a several examples showing that a Boolean formalism is meaningful in biology, in (Shmulevich and Zhang, 2002), one reasoned that if the genes, when quantized to only two levels (1 or 0), would not be informative in separating known sub-classes of tumors, then there would be little hope for Boolean modeling of realistic genetic networks based on gene expression data.

Questions & Answers

what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
How we are making nano material?
what is a peer
What is meant by 'nano scale'?
What is STMs full form?
scanning tunneling microscope
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Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
what is differents between GO and RGO?
what is simplest way to understand the applications of nano robots used to detect the cancer affected cell of human body.? How this robot is carried to required site of body cell.? what will be the carrier material and how can be detected that correct delivery of drug is done Rafiq
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
The nanotechnology is as new science, to scale nanometric
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
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Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
what school?
biomolecules are e building blocks of every organics and inorganic materials.
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
sciencedirect big data base
Introduction about quantum dots in nanotechnology
Praveena Reply
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
Damian Reply
absolutely yes
how to know photocatalytic properties of tio2 nanoparticles...what to do now
Akash Reply
it is a goid question and i want to know the answer as well
characteristics of micro business
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s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
how can I make nanorobot?
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
what is the actual application of fullerenes nowadays?
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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Source:  OpenStax, Introduction to bioinformatics. OpenStax CNX. Oct 09, 2007 Download for free at http://cnx.org/content/col10240/1.3
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