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Old 02-03-2014, 11:00 AM   #6
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Location: Research Triangle Park, NC

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Originally Posted by HGENETIC View Post
Apparently the pituitary is a bag of growth hormone so I'm not sure if normal pituitary is a good or bad thing to compare against, my gut instinct is that it is a good comparison but I wonder if there is a whole brain transcriptome dataset out there somewhere?

Cheers H
For DGE, that is the very crux of your problem. If the intent is to characterize genes that are differentially expressed in abnormal pituitary tissue, then really, the only valid baseline comparison is against normal pituitary tissue. And if pituitary tissue is normally highly biologically active, then not only may "normal" gene expression be wildly different from other brain tissues, it may also be wildly variable, so the need for large scale replication is essential in order to have any statistical power to discriminate truly differentially expressed genes in the actual tumor samples.

Differentially expression is a purely subjective condition, and as such you absolutely have to properly characterize what you are considering your target tissue against as the baseline. Otherwise, you leave your results entirely open to valid outright dismissal as an inadequate comparison to even address differential expression.

I'm not trying to make your life harder, but seriously, if you do not properly characterize a biologically relevant and legitimate baseline for determination of DGE in your target tissue, you will have nothing that will pass peer review for publication (at the least), and nothing really of any value to anyone. So I would say you absolutely have to get hold of some "normal" pituitary tissue for your controls. At least for the differential gene expression aspect, as the only way to determine if a gene in a cancerous pituitary cell is up or down regulated is to compare it to a normal pituitary cell. Any other comparison is simply invalid for determining DGE in cancerous pituitary cells.
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.

Last edited by mbblack; 02-03-2014 at 11:04 AM.
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