Twelve genes implicated in the early stages of phagosome maturation were also downregulated, including those encoding the early endosome markers EEA1 (early endosome antigen1) and ALS2 (amyotrophic lateral sclerosis 2) (Fig. 5a; Table 2; Supplementary Table S20); ALS2 is a Rab5 effector protein, which localizes with Rab5 on early endosomal compartments. Here, ALS2 is linked to amyotrophic lateral sclerosis type 2, juvenile.