Fig. 4

Transcriptome analyses of PyMT-R221A cells. Murine PyMT-R221A cells were treated with vehicle (control), 200 μmol·L⁻¹ SAM, 100 nmol·L⁻¹ 25(OH)D and a combination of SAM and 25(OH)D every other day for three times (on days 0, 2, 4) using the in vitro treatment protocol described in Fig. 1a. At the end of the experiment, RNA extracted from control and different treatment groups were subjected to RNA-Seq analyses. a The volcano plots of the significantly differentially expressed genes are shown [log₁₀(FDR) versus log₂FC]. b Venn diagrams representing the frequency of common and unique genes among different treatment groups. c Circos plot further representing the commonality and uniqueness of the functionalities of the up- and downregulated genes from each group. Each gene from the up- or downregulated gene lists has a spot on the arc. The dark orange color represents genes that are present in multiple treatment groups, and the light orange color shows genes that are unique for a treatment. In addition, the purple lines indicate the common genes that are found in different treatment groups, and the blue lines represent genes that are different but have similar functions. d Comparative heatmap of the Gene Ontology (GO) enrichment for biological processes for the different treatment groups, as determined by Metascape⁵²