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As a demonstration, view the Stanford Microarray Database website. Under the Public Data section, click on the "Public Login" link. Limit the data set search to the organism Arabidopsis thaliana and the author Gutierrez. Click on the button entitled "Display data", and a table of microarray datasets should be returned. Choose one of the experiments, making note of the Experiment ID number from the table and select the clickable image icon. (There is a legend for the icons at the top of the web page, if there is uncertainty as to which is the clickable image icon.) This yields the qualitative visualization of the microarray experiment, as described previously in this module. Take a look at the array image and note that it is difficult to draw many conclusions fromthis kind of visualization.

What is the Experiment ID number for the viewed microarray image?

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Is it possible to get a feeling for which color dot, green, red, or yellow, is most predominant just by viewing the image? (If so, which color?)

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Are all of the dots, over the entire grid, well-shaped? (Give a brief explanation.)

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Click on one of the individual spots in the microarray grid. This will open a new window that contains a close up of the individual spot and all the experimental information about that spot.

Retrieve and list the following information about the chosen spot: a. spot number, b. description (under biological information), c. the Channel 1 intensity (mean), d. the Channel 1 background (median), e. the Channel 1 net intensity (mean), and f. the Log(base2) of R/G Normalized Ratio (Mean).

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Return to the table of Arabidopsis thaliana data sets and forExperiment ID #11374, select the "Data" icon, which is the first icon under the "Options" column. Next to "Sort By", select "Log(base2) of R/G NormalizedRatio (Mean)", and "Descending". Under "Display:", click on "Spot", then scroll down and hold down the control key (or the apple key on macintoshes) while selecting "Log(base2) ofR/G Normalized Ratio (Mean)". (The control key allows selection of additional choices without deselecting the previous choice.) Accept the default values for allremaining options and select "Display" at the bottom of the page. Recall that the data are converted to numbers representingthe fluorescence intensity of red dye, green dye, and the ratios of red to green. Scientists commonly use a log transformation of the ratio data, because thelogs are more mathematically tractable in reference to statistical analysis. The results page will show the top ranking spots from this chip, ranked from highest log red/green value to lowest.

What are the spot numbers of the three highest ranking spots?

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What are the "Log(base2) of R/G Normalized Ratio (Mean)" values for the three highest ranking spots?

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Use the browser's back button to go back and select new data for display. Chage the sortingselection to R/G Normalized (Mean), in descending order. under the "Display:" window select "Spot", then scroll down and hold down the control key while selecting "R/G Normalized (Mean)".

Questions & Answers

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.
what is biological synthesis of nanoparticles
Sanket Reply
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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Source:  OpenStax, Bios 533 bioinformatics. OpenStax CNX. Sep 24, 2008 Download for free at http://cnx.org/content/col10152/1.16
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