Consistent with the downregulation of pathways involved in energy metabolism that we observe, mitochondrial ATP is known to be reduced in HD brain50 and blood51, and PGC-1α, a member of the dysregulated ATP metabolic process pathway (Tables 3, S14 and S18), is a key protective regulator of mitochondrial genes that is repressed HD mouse models52, 53. Here, PPARGC1A is linked to Huntington disease.