We used archetypal analysis to determine the similarity between the monkeys P and F, and the relationships between MSN subtypes.28-30 Archetypal analysis decomposes the expression matrix into gene loading vectors, or ‘archetypes,’ that correspond to cell states.28-30 We found the archetypes that defined the transition from one MSN subtype to another using the data from Monkey P. When projected onto monkey F, these archetypes maintained the same transitions between subtype clusters (Figure S3G). This result illustrates the high level of consistency between the two experimental subjects and validates the archetypes. We subsequently found all genes that were significantly correlated with the archetypes that defined the transitions between subtypes (p < 0.05, Benjamini-Hochberg corrected, Pearson’s correlation). Each subtype pair contained genes where transitions included a significant discontinuity (Figure 3A, p < 0.05, Regression discontinuity test, Methods) and other genes without significant discontinuity (Figure 3B, p > 0.05, Regression discontinuity test). The p-value distributions demonstrated the degree of discontinuity between subtype pairs (Figure 3C). For every pair, except for D1S and D2S – the subtypes for which we had the lowest sample
