Interested in gene arrays?

G

Gagarin

Registered Member
You have to read an article in Science, 22 OCTOBER 2004 VOL 306, page 630. Only a short piece of text:
.........She was taken aback by what she found.
Not only was she unable to pick a clear
winner (Amersham-Affymetrix-Agilent), but she had a hard time figuring out
whether any of the arrays produced trustworthy
results. As she delved deeper, she
found that the devices produced wildly
incompatible data, largely because they
were measuring different things. Although
the samples she tested were all the same—
RNAs from a single batch of cells—each
brand identified a different set of genes as
being highly up- or down-regulated.
The disharmony appears in a striking
illustration in Cam’s 2003 paper in Nucleic
Acids Research. It shows a Venn diagram of
overlapping circles representing the number
of genes that were the most or least active
on each device. From a set of 185 common
genes that Cam selected, only four behaved
consistently on all three platforms—“very
low concordance,” she said at an August
forum in Washington, D.C., run by the
Cambridge Healthtech Institute, based in
Newton Upper Falls, Massachusetts. Using........etc

Is anybody here on this forum that is working with gene arrays? I'm interested in his/her opinion.
 
This is a known problem with microarray experiments. The obtained data sets are not only subject to wide variations due to the biological samples (medium, shaker etc.), but also due to the microarray platform and normalization.
At this point only experiments conduccted under precisely the same conditions following identical protocols are comparable. Therefore the MIAME standards for publishing microarray data has been established.
 
Microarray expression data for any given gene should be used as a guide only. Microarrays are a fantastic technique for determining lots of candidate genes for your biological process of interest, but accurate expression data for each of the individual candidate genes (once they have been identified via microarray) needs to be assessed and confirmed by more accurate means – northen blot, quantitative RT-PCR, in situ hybridization etc etc.<P>
 
Or my favourite, reporter gene fusion. The reason is that this is a technique that doesn't actually measure mRNA concentrations but if you still see the same tendencies you have a good validation of the data.
THat's basically true for most biological experiments. It is often necessary to tackle the same question with different approaches to get a significant answer...
 
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