You are studying a transcription factor that you hypothesise is necessary for expression of protein X in organ Y. Which two experiments would you carry out to test this?
I suppose one thing you would do, is to delete or knock down the gene of your transcription factor.
Then, you can extract total protein only from organ Y and check by western blot the levels of your protein X using an anti-X antibody. (Or tag protein X with an epitope and use an antibody against this epitope). As a control, you should extract total protein from organ Y and check the levels of protein X in a wild-type background (=wt gene for the transcription factor). You compare the expression levels in both cases (wt vs deletion/knock-down). If your transcription factor is necessary, then the levels of protein X should be significantly reduced in the deletion/knock-down background.
If you do not have a specific antibody for protein X, then you could do RT-PCR/ Northern checking the mRNA expression levels of the gene X. Again, if your transcription factor is necessary for transcription of gene x, then the mRNA levels of gene x will be significantly reduced in the deletion/knock-down background vs wt.
The experiment that was suggested above would be a good first step where you wcould use a lentiviral shRNA knockdown or an siren knockdown. Most transcription factors have DNA binding motif of a specific sequence. Look at the promoter of protein x. You could subclone this promoter and place it 5' to a reporter (e.g Lucifer's) and overexposes your TF of interest to see if there is a direct link to this promoter.
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