Putting a gene in front of an inducible promoter, and then inducing that promoter is typically considered over-expression of a gene. Artificially inducing expression of a gene in a context in which it would normally not be expressed, and expressing it at higher levels than considered normal for that gene, would be considered over-expression of a gene (and is also up-regulation). However, up-regulation of a gene in its native context is not over-expression. There are myriad ways of measuring gene expression profiles, regardless of whether they are over-expressed. Like any gene expression measurement, you might have to calibrate your linear range across various orders of magnitude.
Thank you for your reply, sir. I have some PDAC samples, how can I say a certain number of genes are over-expressed in this condition?
I understand that Up/downregulation of a gene is a natural process, while over-expression is induced artificially but does these two terms Up-regulation and over-expression are similar? If some genes are up-regulated does that mean those genes are also over-expressed?
You'll have to explain what PDAC samples are. Even those committed to a life of acronyms don't know them all. Regarding up-regulation and over-expression, you have the answer in your sentence and in the answer above. Over-expression is a result of up-regulation, but not all up-regulation results in over-expression. Over-expression refers to artificially high levels of expression.
In your case, if PDAC is a condition, and you're referring to several genes, perhaps you mean they are enriched in a given condition? This would mean they show higher expression in one condition than the other. However, when you use terms like up-regulated or down-regulated, you begin to impose mechanism unnecessarily. If you were to measure genes in two conditions, and find that some are expressed higher in one condition than the other, you can simply say this - expressed higher or enriched under condition X, but I would avoid the term up-regulated, and the term over-expressed doesn't apply - unless you are explicitly testing such a scenario (i.e. we have 10 genes under an inducible promoter, and when we add the inducer we find that they are indeed over-expressed - if their expression level surpasses an otherwise baseline level for a given context).
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This reads like assignment questions. Please provide some real life context that would convince us this is not the case.