Extended Data Fig. 3: Regulon profiles of current and additional SCENIC predictions.
From: Gene regulatory networks and essential transcription factors for de novo-originated genes
(a) and (bb) Current SCENIC predictions. (a) The ratio of de novo genes and testis-specific genes in each regulon. (b) Number of de novo genes and de novo and non-de novo genes in each regulon. (c)–(e) Additional SCENIC analysis with a lower TF expression cutoff of 10 (Methods). (c) Top regulons from this additional SCENIC analysis were similar to the current SCENIC analysis (Fig. 2a). (d) The ratio of de novo genes and testis-specific genes in each regulon. (e) Number of de novo genes and de novo and non-de novo genes in each regulon. (g)–(h) Additional SCENIC analysis with two additional gene sets except for de novo genes and TF genes, which are non-testis tissue specific genes and non-tissue specific genes, with the same cutoff as the original SCENIC analysis. (f) Top regulons from this additional SCENIC analysis were also similar to the current SCENIC analysis (Fig. 2a). (g) The ratio of de novo genes and non-testis tissue-specific genes in each regulon (n = 83). (h) The ratio of de novo genes and non-tissue specific genes in each regulon (n = 83). In (g) and (h), p-values were calculated by Kendall’s Tau and Spearman rank correlations, and shaded areas indicate 95% confident intervals.
