Fig. 7

Identification of transcription factor binding sites in differentially methylated DNA regions. A DNA sequences within Genomic regions with (1) significantly higher methylation in lens fiber cells compared to lens epithelial cells and (2) found in the genebodies or promoters of genes with decreased expression levels in fiber cells compared to epithelial cells were analyzed to find significantly enriched transcription factor binding motifs. Scatterplot shows a plot of the − log10 (adjusted p value) of significantly detected transcription factor motifs identified using the AME tool versus the number of downregulated/epithelial cell genes that have at least one binding site within a methylated region identified by the FIMO tool. Only transcription factors encoded by genes that have a total transcript expression level (sum of average Epi and Fiber FPKM) of at least 1 FPKM are reported (Additional file 13: Table S9A). The color of each datapoint also indicates whether the gene encoding the transcription factor is more highly expressed in epithelial cells (blue) (log2-fold change FPKM < − 0.4, q < 0.05), fiber cells (red) (log2-fold change FPKM > 0.4, q < 0.05), or there is no significant differences in gene expression levels between epithelial and fiber cells (grey) (Additional file 13: Table S9A). The size of each datapoint corresponds to the total transcript expression level for each transcription factor. Select transcription factor consensus sequence logos from JASPAR database are shown. B Same as A but for DNA sequences in genomic regions with (1) significantly lower methylation in lens fiber cells compared to lens epithelial cells and (2) found in the genebodies or promoters of genes with increased expression levels in fiber cells compared to epithelial cells