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9 weeks ago
Anst ▴ 40
How to understand that the gene is “turned on” by its expression?
For example, if we use the gene BAX which is the gene of MOP Cell Death, is 0.001 expression strong enough to cause cell death? Or is there any confidence interval to make sure that the gene is enough expressed?
If there are 3 genes that referred to one death pathway, how can I calculate their sum (overall) expression? Can I just use the Euclidean norm?
There are no universal units of gene expression, so when you say I have 0.001, it's like saying I have 0.001 happiness. It could be a lot or a little depending on many things. Also, you're asking about causation and mechanism. Different genes have different mechanisms depending on many different components, and expression can be expressed at transcription or translation and you haven't defined either. To know the expression level you have to define some relationship between your measurements and the number of molecules in the cell. You can calculate a confidence interval if you have replicates, but you haven't mentioned anything about the system you're using. What did you measure? How did you measure it? What is known about the mechanism of action for this gene?
On the other hand, they way you are mentioning "confidence interval" sounds like an assay-based threshold for an apoptotic response. This may be an established threshold, or a control experiment based threshold you need to define. Rather than calculate the sum of genes, you might calculate their ratios relative to a control.
I am studying cell death pathways, for example, external apoptosis. I have the list of the genes that cause the cell death (IRAK3, PIK3R5, FAS, FADD, CASP8, DIABLO, TRADD). And I want to understand the common gene expression in different cell types in order to understand which cell type is more likely to use the death pathway of my interest.