Fig. 5
Demethylation in Il6ra during mouse T-cell development and analysis of genome-wide BS-seq, TAB-seq, and fCAB-seq data. a A locus close to the 3’ UTR of Il6ra (top) with the canonical E-box motif (middle) is depicted. The posterior means of methylation proportions of the cytosines within the locus are visualized in DP, CD4 SP, and naïve CD4 cells (bottom). The error bars (mean ± standard deviation is depicted) show the standard deviations of the posterior distributions. The different methylation modifications are distinguished with different colors (p(C) in green, p(5mC) in yellow, and p(5hmC) in red). b The bar plot shows the gene expression (RPKM) of Il6ra in DP, CD4 SP, CD8 SP, naïve CD4, and naïve CD8 cells. c The marginal distributions of the posterior means of θ among the common cytosines. The panels, from left to right, correspond to the marginal distributions of the posteriors means of p(C), p(5mC), p(5hmC) and p(5fC). d Comparison of the Lux and frequency method estimates (5fCfrequency = NBS,T/NBS − NfCAB,T/NfCAB) of the 5fC levels. Almost half (47 %) of the frequency method estimates are negative. e The estimated posterior means of C, 5mC, 5hmC, and 5fC levels (from top to bottom) across the locus chr2:130,637,802 − 130,638,418 are depicted in the bar charts