What kind of analysis can be done with differential expression of transcription factors? I have two different stem cell types and their respective gene expressions from RNAseq. 

I noticed that there is differential expression in some of the genes coding for histones as well as transcription factors?

What kind of interesting downstream analysis might be available?

Is it feasible to survey ENCODE for downstream TF binding sites?
Can anything interesting be investigated with regard to the histone gene data?

Thanks in advance.
Expanding my comment. 

TF usually bind in the upper region of the genes it regulates, so you could see which genes are in the region below the binding site. Perhaps there are some databases for TF. 
I found a website base on the ENCODE project with the genes regulated by each TF.You can use them for pathway or gene set enrichment analysis, but I am not aware of any specific analysis for genes regulated by a single TF. 

The histone data is harder if it was methylation I would say to look if different states of the histones are in different spatial state, but with gene expression is harder to conclude anything. Nevertheless you can check methylation studies to see if gene expression is associated with methylation changes.