Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression?
If you overexpress a gene for a protein involved in signal transduction (e.g., a kinase, scaffold, or receptor) by vector cell transfection, then you overdrive the cell using this signaling pathway, it's useful to isolate the pathway and study them.
Is there any way to modify the overall gene expression or cell differential expression pattern by gene transfection? I think this would work if you delivered a gene for overexpression in proteins involved for RNA processing (e.g., splicing, ribosomal proteins, etc.), RNA transcription (e.g., TFs) or protein translation.
Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression
This is a very relevant question and the field of experimental biology needs to revisit the experimental strategies.
One of the explanations that you gave is correct- that the overexpressed protein might override the cellular processes.
Another problem that this practice gives rise to is incorrect inference. We are mostly interested in knowing what a protein does in a cell at general physiological conditions. If the stoichiometry is altered wrong results will definitely pop up. For example in the case of a repressor/activator with multiple targets: At its general physiological concentration it may not really activate gene-X because of low affinity but in high concentrations it just may, and we end up concluding that gene-x is a target of repressor-1 by an OVEREXPRESSION experiment.
A synthetic biological approach is very good in studying small signaling/transcriptional modules. The entire module can be cloned and expressed in a cell under an inducible/constitutive promoter. This can be implemented in a heterologous cell also. A mathematical model generally helps in making certain predictions.
Other strategies which can be used instead of overexpression:
- using sensor constructs harboring a functional or non-functional target sites instead of overexpressing the upstream protein
- downregulation experiments
There are lots of different overexpression vectors (usually they're promoters/regulatory elements upstream of the transfected gene). Here's an example of an overexpression vector (overexpression vector pCAMBIA1300S) that was used to overexpress a transcription factor called NAC in rice, resulting in large phenotypic changes (drought and salt tolerance): http://www.ncgr.ac.cn/articles/2009ZhenXN_NAC.pdf