If a Transcription Factor is discovered to bind to a few genes, is it possible that those genes have a relation between them? Is there a possibility that just because there is TF binding to 2 genes, can we say that those genes may regulate each other? If it is possible to assume that they can regulate each other, how can we find out those 2 genes have a realtion between them?
1. Of course it's possible, these two genes may involved in a same or related pathways and regulated by this TF, which may regulated a biological process. But it's only a possibility and need more stronger evidences (e.g. co-expression, functional, or pathway, even the functional experiments).
2. No, there is no direct evidence that these genes could regulate each other only because of binding with a same TF, at least in my opinion.
3. If assuming that they can regulate each other, maybe you can check their co-expression, or directly knock down one genes and measure another gene expression/protein level. I'm not expert in the experiments, so no more advice could be given on this subject.
The estrogen and androgen receptor TFs are probably the best example to look at. They have binding sites in genes for common pathways but also in unrelated ones. If genes have TF binding sites in common at most you can predict is that they may express in the same cell type.
Although possible that a TF can cause expression of regulatory proteins and RNAs for other genes that it binds to, this is not a necessity. This means you cannot infer regulation based purely on sharing common TF binding sites.
As for validation that the two genes regulate each other you would have to do knockdown and overexpression experiments to check for transcriptional regulation and yeast two hybrid assays followed by deletion mutagenesis to check for regulation at the protein level.
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