There's still an enormous gap in understanding of expression from gene sequence, especially in multicelled organisms. At each major level, starting with transcription through RNA processing, through translation and post-translational processing, there is an amplification of possibilities, cascading of effects, networked feedback loops, and so forth. You can see how this becomes complicated very quickly and how it's difficult to tease out one aspect of it.
Identical sequences end up affected differently in different cell types. The brain expresses different proteins than the liver. We already know about the differences between different cell types. This study shows that there is a species expression difference between same cell type.
All this can't be separated from development. The signals at the unicellular stage start the program of expression patters with morphogenic gradient fields.
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A fascinating book is Calvin's Throwing Madonna
The idea is that our ancestors adopted throwing stones to hunt for food. In order to get accuracy it is necessary to release the stone at a precise time. This requires lots of neurons working together. Hence our large brains. He also discusses handedness.