Comparison (Fig. 3 and Additional file 1: Table S4) of Alc-DEs (regions 1, 2, 4, and 5) to TII-DEs (regions 2, 3, 5, and 6) shows that 225 of the 312 Alc-DEs are present in both groups (regions 2 and 5). The remaining 87 Alc-DEs (regions 1 and 4) are not induced by a robust inflammatory stimulus; therefore, these represent a non-canonical type of microglial activation; we refer to this group as Alc*-DEs. Further comparison to the AlcTII-DE group shows that 21 DEs (“AlcOnly-DEs”, region 1) are found only in the Alc-DE group. Comparison of AlcTII-DEs to TII-DEs shows considerable overlap (2601 DEs, regions 5 and 6) between these two groups; as well as an additional 951 (“AlcInf-DEs”, regions 4 and 7) that are not detected in the TII group. Of those 951 AlcInf-DEs, 885 (“Alc*TII-DEs”, region 7) are increased by alcohol only in the context of inflammation but not by alcohol or by TII alone.
