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Fortunately, the results were very promising. By using binary gene expression data, generated via cDNA microarrays, and the Hamming distance as a similarity metric, a clear separation between different sub-types of gliomas as well as between different sarcomas was showed. This seems to suggest that a good deal of meaningful biological information, to the extent that it is contained in the measured continuous-domain gene expression data, is retained when it is binarized.

Biological example

Below an example id presented, borrowed from (Shmulevich et al., 2002), showing the logical representation of cell cycle regulation. This process of cellular growth and division is highly regulated. A disbalance in this process results in unregulated cell growth in diseases such as cancer. In order for cells to move from the G1 phase to the S phase, when the genetic material, DNA, is replicated for the daughter cells, a series of molecules such as cyclin E and cyclin dependent kinase 2 (cdk2) work together to phosphorylate the retinoblastoma (Rb) protein and inactivate it, thus releasing cells into the S phase. Cdk2/cyclin E is regulated by two switches: the positive switch complex called cdk activating kinase (CAK) and the negative switch p21/WAF1. The CAK complex can be composed of two gene products: cyclin H and cdk7. When cyclin H and cdk7 are present, the complex can activate cdk2/cyclin E. A negative regulator of cdk2/cyclin E is p21/WAF1, which in turn can be activated by p53. When p21/WAF1 binds to cdk2/cyclin E, the kinase complex is turned off (Gartel and Tyner, 1999). Further, p53 can inhibit cyclin H, a positive regulator of cyclin E/cdk2 (Schneider et al., 1998). This negative regulation is an important defensive system in the cells.For example, when cells are exposed to mutagen, DNA damage occurs. It is to the benefit of cells to repair the damage before DNA replication so that the damaged genetic materials do not pass onto the next generation. Extensive amount of work has demonstrated that DNA damage triggers switches that turn on p53, which then turns on p21/WAF1. p21/WAF1 then inhibits cdk2/cyclin E, thus Rb becomes activated and DNA synthesis stops. As an extra measure, p53 also inhibits cyclin H, thus turning off the switch that turns on cdk2/cyclin E. Such delicate genetic switch networks in the cells are the basis for cellular homeostasis—the ability of an organism to maintain equilibrium.

For purposes of illustration, let consider a simplified diagram, shown in Figure3 , illustrating the effects of cdk7/cyclin H, cdk2/cyclin E, and p21/WAF1 on Rb. Thus, p53 and other known regulatory factors are not considered. While this diagram represents the above relationships from a pathway perspective, one may also represent the activity of Rb in terms of the other variables in a logic-based fashion. Figure4 contains a logic circuit diagram of the activity of Rb (‘on’or‘off’) as a Boolean function of four input variables: cdk7, cyclin H, cyclin E, and p21/WAF1. Note that cdk2 is shown to be completely determined by the values of cdk7 and cyclin H using the AND operation and thus, cdk2 is not an independent input variable. Also, in Figure3 , p21/WAF1 is shown to have an inhibitive effect on the cdk2/cyclin E complex, which in turn regulates Rb, while in Figure4 , we see that from a logic-based perspective, the value of p21/WAF1 works together with cdk2 and cyclin E to determine the value of Rb.

A diagram illustrating the cell cycle regulation example. Arrowed lines represent activation and lines with bars at the end represent inhibition.

The logic diagram describing the activity of retinoblastoma (Rb) protein in terms of 4 inputs: cdk7, cyclin H, cyclin E, and p21. The gate with inputs cdk7 and cyclin H is an AND gate, the gate with input p21/WAF1 is a NOT gate, and the gate whose output is Rb is a NAND (negated AND) gate.

Probabilistic Boolean Networks
Bayesian Networks

Questions & Answers

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 .?
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
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
for teaching engĺish at school how nano technology help us
Do somebody tell me a best nano engineering book for beginners?
s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
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.
what is the Synthesis, properties,and applications of carbon nano chemistry
Abhijith Reply
Mostly, they use nano carbon for electronics and for materials to be strengthened.
is Bucky paper clear?
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
so some one know about replacing silicon atom with phosphorous in semiconductors device?
s. Reply
Yeah, it is a pain to say the least. You basically have to heat the substarte up to around 1000 degrees celcius then pass phosphene gas over top of it, which is explosive and toxic by the way, under very low pressure.
Do you know which machine is used to that process?
how to fabricate graphene ink ?
for screen printed electrodes ?
What is lattice structure?
s. Reply
of graphene you mean?
or in general
in general
Graphene has a hexagonal structure
On having this app for quite a bit time, Haven't realised there's a chat room in it.
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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