RT-PCR may give you an indiciation, but is definately not the best tool too use in this case. You will need to either block the action of the transcription factor (there are loads of blockers available)..or design a reporter-construct. Another approach is western blot and specifically look at the presence (or absence) of phoshorylated residues on the transcription factor, depending on the current knowledge on this specific factor ab's might be available.
As seeing is always beliving, thus its best to go for western blotting approach and see if the desired factor is upregulated or not. To get the picture crystal clear you can use knock outs, if available and then go for cytokine evaluation. You can also use inhibitors of the the particular factors, if available, and then again go for cytokine profiling.
Sir,
if i am going for western blotting some many proteins will be there in the cell, transcription factor will be meager one..how to get-rid off these cellular proteins...
I think the best solution could be to perform transcriptome analysis using the NGS technology and then confirm with RT PCR or EMSA for the differentially expressed genes or transcription factors .
As suggested by Dereje Damte, do transcriptome analysis and confirm with RT PCR .lalitha kabilan
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