The gene family that best distinguished CNS neuron classes was homeodomain transcription factors (Figure S7), consistent with an important role in specifying and maintaining neuronal cell types. Many homeodomain transcription factors are involved in dorsoventral and anteroposterior patterning (as well as the specification of, for example, the neural crest). Although patterning takes place during embryogenesis, we reasoned that significant traces of patterning gene expression might remain and could explain the observation that the nervous system was molecularly organized according to developmental origin. In agreement with this prediction, we found that Hox genes were expressed in cell types derived from the hindbrain, spinal cord, and the PNS (Figure 7B). For example, spinal cord cell types expressed Hoxa1 (rhombomere 1) through Hoxd10 (thoracic bordering on lumbar), with additional expression of lumbar Hox genes in some cell types. Enteric neurons and glia of the small intestine both expressed a Hox code consistent with a major vagal and minor thoracic origin of these cells. Sensory and sympathetic neurons, as well as satellite glia, expressed Hox genes from all rostrocaudal levels (lumbar cells were not
