<< Chapter < Page Chapter >> Page >

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

Application of nanotechnology in medicine
what is variations in raman spectra for nanomaterials
Jyoti Reply
I only see partial conversation and what's the question here!
Crow Reply
what about nanotechnology for water purification
RAW Reply
please someone correct me if I'm wrong but I think one can use nanoparticles, specially silver nanoparticles for water treatment.
Damian
yes that's correct
Professor
I think
Professor
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
Rafiq
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
Damian
How we are making nano material?
LITNING Reply
what is a peer
LITNING Reply
What is meant by 'nano scale'?
LITNING Reply
What is STMs full form?
LITNING
scanning tunneling microscope
Sahil
how nano science is used for hydrophobicity
Santosh
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
Rafiq
what is differents between GO and RGO?
Mahi
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
Rafiq
if virus is killing to make ARTIFICIAL DNA OF GRAPHENE FOR KILLED THE VIRUS .THIS IS OUR ASSUMPTION
Anam
analytical skills graphene is prepared to kill any type viruses .
Anam
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
Bob
The nanotechnology is as new science, to scale nanometric
brayan
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Damian
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
Renato
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
?
Kyle
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
Adin
why?
Adin
what school?
Kyle
biomolecules are e building blocks of every organics and inorganic materials.
Joe
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
research.net
kanaga
sciencedirect big data base
Ernesto
Introduction about quantum dots in nanotechnology
Praveena Reply
hi
Loga
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
Bharti
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
Privacy Information Security Software Version 1.1a
Good
Got questions? Join the online conversation and get instant answers!
Jobilize.com Reply

Get the best Algebra and trigonometry course in your pocket!





Source:  OpenStax, Introduction to bioinformatics. OpenStax CNX. Oct 09, 2007 Download for free at http://cnx.org/content/col10240/1.3
Google Play and the Google Play logo are trademarks of Google Inc.

Notification Switch

Would you like to follow the 'Introduction to bioinformatics' conversation and receive update notifications?

Ask