Fig. 6: Total RNA sequencing reveals signaling alterations after Mkx knockdown in calvarial suture cells.

A Volcano plot summarizing differentially expressed genes (DEGs) (FDR < 0.05). DEGs with fold change (Log2FC) over 1 and p-value less than 0.05 were colored red or blue. Red dots are significantly upregulated DEGs after Mkx KD, while blue dots are significantly downregulated DEGs in comparison to scramble control. N = 3 biological replicates. B Ingenuity Pathway Analysis (IPA) showing top canonical pathways upregulated and downregulate among Mkx KD cells in comparison to control. C, D Bubble plot showing GO enrichment analysis identified representative pathways that were upregulated (C) or downregulated (D) among Mkx KD cells. E–J Heatmaps and corresponding module scores among Mkx KD cells versus control in key biological processes and signaling pathways, including E Ossification, F Tenogenesis, G Mechanical stress, H BMP signaling, I Hedgehog signaling, and J Canonical Wnt signaling. Gene module scores are shown as a boxplot with center line as the median, box limits as upper and lower quartiles of the modulus score. *p < 0.05; **p < 0.01. A two-tailed Student t-test was used for all comparisons.