Supplementary Figure 6: VGLL3 targets in autoimmune diseases.

a, log₂(FC) of autoimmune disease genes upon VGLL3 RNAi. b, density plot of log₂(FC) levels upon VGLL3 knockdown for plaque psoriasis (PP) and non-PP genes. c, density plot of log₂(FC) levels upon VGLL3 knockdown for SCLE and PP genes. d, density plot of log₂(FC) levels upon Fez knockdown for SCLE and non-SCLE genes. e, density plot of log₂(FC) levels upon Fyn knockdown for SCLE and non-SCLE genes. b-e, Wilcoxon-Matt-Whitney test. f, gene expression levels in female (F) and male (M) SCLE patients by RNA-Seq. Mean+s.e.m. g, associations of VGLL3 targets with various autoimmune conditions, with (*) indicating the observed mean of VGLL3 target gene expression and box indicating 1st and 3rd percentile for the null distribution for the mean signed log₁₀ P-value (2000 simulations). h, expression of VGLL3 targets and non-targets in Sjögren’s syndrome, showing higher percentage of Vgll3 targets that have increased expression in disease (red boxed region) compared to non-targets (grey boxed region). Mann-Whitney U test.