Correlation of expression changes

Question

[marina-orlova]

Hi

There is list of genes which expression are supposed to be controlled in similar way by two proteins (knockdown of these proteins leads to reduction in expression levels of these genes). How can I confirm this?(which experiments and analysis can help me?) Should I look at binding sites of these proteins or smth like that?

Answer 1

[Manvendra Singh]

I think that you should perform Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA (ChIP-qPCR). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2681100/

even if binding site is there, this necessarily does not mean that protein would bind there.

If you intend to show the direct binding of these prteins over the regulatory sequence of your genes then EMSA would be validation.