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closewhere is IKBKAP within the microarray results?
Posted by elcherif on 31 Dec 2010 at 07:51 GMT
It is shown that PS increases the level of IKBKAP mRNA by semiquantitative and quantitative RT-PCR. However, I could not find IKBKAP among the upregulated genes by PS treatment (microarray analysis). Why?
RE: where is IKBKAP within the microarray results?
gast replied to elcherif on 04 Jan 2011 at 14:04 GMT
IKBKAP is not found within the up-regulated genes in the microarray data because the level it had changed due to PS treatment was not statistically significant when analyzing the results. However, on the same RNA samples that were sent to microarray we preformed RT-PCR and QPCR analysis that showed elevation in IKBKAP levels as expected.
We can presume that the reason for this discrepancy involves DNA microarray technology and its reliability. It has been suggested that for relatively abundant transcripts the existence and direction of expression changes can be reliably detected. However, it is hard to achieve accurate and reliable measurements of expression levels in low abundant genes (Draghici S., et al. Reliability and reproducibility issues in DNA microarray measurements. Trends Genet. 2006 Feb;22(2):101-9).
As demonstrated, IKBKAP is very low abundant in FD derived cells, which may cause difficulties in the microarray technology in this case.