Often i see and hear researches explain gene expression as either up regulated or down regulated. if genes are said to be up regulated to what extend can it be considered hazardous, and how can that be measured.
Hazardous up regulation is completely dependent on which gene is being up regulated. There are many ways to measure gene expression...real-time PCR, RNA seq, northern blot (technique choice is completely dependent on the question you want to answer).
Thanks Johnson, I know a little bit about the techniques you mentioned in measuring gene expression. However to what extend is it appropriate to say there is over expression of a gene/s. Thank you.
Usually, upregulation and downregulation refer to changes in gene expression that occur during development or in response to environmental cues such as hormones. For example, when a precursor cell becomes a muscle cell, muscle cell specific genes become upregulated. Alternatively, when cells are deprived of oxygen, genes for growth are downregulated to allow the cell to survive. Overexpression usually (probably not always) refers to an experiment when DNA is added to the cell to force expression of the gene to a much higher than normal level (such as a transfection or transgenic mouse). This could certainly have a detrimental effect on the cell, though I'm not sure if that's what you mean by hazardous.
Dear Colleagues, your explanations certainly is leading to me finding the answer to my query. However, taking some clues from Michael's submission, 'when a gene is expressed much higher than the normal level such genes are said to be over expressed'. Does anyone know how to tell if the expression profiles of genes are over expressed or not. Put differently, how can one tell if there is over expression?
How to determine significant fold differences in gene expression? Usually, 2-fold change or higher (above background values) is "deemed" to be significant but this sounds somewhat arbitrary to me. What if the fold change is 1.99? So, I would rather avoid such a "yes/no", "black/white" interpretation.
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Besides, to assess the significance (for the living thing) of the fold difference for a particular gene, one needs to have such data on all relevant genes. No gene product acts in isolation. There can be compensatory changes in the expression of other genes etc.
Thanks Martin, your response meets my expectation. However, if any one has a review or any related material on cytokines and/or other immune relevant genes of Oreochromis niloticus with regards to their normal expression in healthy fish, I would delight in reading such stuff. Thanks
I would search PubMed for:
"Oreochromis niloticus"[title/abstract] AND "gene expression"[title/abstract]
This query returns 98 papers.
Adding "cytokine"[title/abstract] to the query returns 1 paper:
http://www.ncbi.nlm.nih.gov/pubmed/23871840
I'll note one thing just to be completely clear. Genes can only be overexpressed, upregulated, or downregulated in a comparison between two conditions. If a gene was expressed at a higher level in a sick fish than in a healthy fish, it would be considered upregulated as a result of illness. Expression profiles can be produced in a variety of ways, but they always have at least two samples that are compared.
I agree, I think that genes can be express when stimulants are fed to fish, in which case can cause some genes to be upregulated, down regulated or over expressed. However, my concern is when the use of stimulants for what ever reason causes some genes to be over expressed. This can be detrimental to the fish. Therefore my interest is to know at which point can genes be said to be over expressed. I gather from all your valuable contribution the answer to my query. Thank you guys.
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