Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their different DNA.
However two types of cells in an adult organism may have clearly different phenotypes (e.g. morphology), but the same DNA, with a different set of genes expressed.
To explain this it would seem that there must be some molecules to modulate the expression of the DNA in different cell types. In my reading I have found one such type of molecules the presence of which is prerequisite for one type of differentiation – modification of histons – methyl, phosphate, acetyl, ubiquitin. Another class of molecules is the transcription factors.
What would one look at to tell the differentiated type of a cell (ignoring its phenotype)?
Addendum: After having delved a little bit deeper into the topic of epigenetics, I'd like to suggest as a possible answer: it's the histone code one has to look at, something like: how the DNA is wrapped around which sequence (!) of (modified) histones.