Part 3.  Many investigators would like to discover the set of downstream targets of a gene of interest.

In a genetic and functional sense, that question can only be addressed effectively if there is genetic variation in the particular gene.  We know that Fos is an important transcription factor, but unless it is polymorphic between C57BL/6J and DBA/2J, then it cannot generate a genetic variance signal with which we can work. We can still study covariance of Fos and hundreds of other transcripts (an interesting exercise), but there are no genetic causes-and-effects.