Fig. 4

DGCA analysis identified significantly correlated DEGs that share potential transcription factor binding sites. a Matrix highlighting the number of significantly correlated gene pairs from the filtered list of DEGs. Each axis represents a condition (GF or SPF), with + indicating a significant positive correlation between the gene pair, − indicating a significant negative correlation, and 0 indicating the lack of a significant correlation. Gene pairs that are positively correlated in both SPF and GF skin are highlighted in the uppermost left corner. b The Loricrin and Serpina12 gene pair is positively correlated in both colonization conditions, but a significant loss of correlation is observed in SPF compared to GF skin (q < 0.05). The x- and y-axes indicate the TMM normalized, batch effect-corrected gene counts, and each dot represents a single mouse, colored by their microbial condition. Colored lines and shaded areas represent the linear regression lines and their respective 95% confidence interval for each microbial condition. c Analysis with oppossum3 identified enriched transcription factors in positively correlated DGCA gene sets, using Fisher scores to assess significance. The y-axis identifies significant transcription factors, while x-axis represents the significance metric. Higher values indicate greater significance and the shape indicates whether the metric score was 1 or 2 standard deviations (SD) above the mean. Fisher scores are significant when greater than 1 SD above the mean. Size of each point reflects the percentage of all DGCA +/+ DEGs containing a binding region for each TF and color indicates colonization status of the DGCA +/+ DEGs