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. 2014 Sep 11;10(9):e1004585. doi: 10.1371/journal.pgen.1004585

Figure 4. The expression and binding of Tet enzymes correlates with C to G rates.

Figure 4

(A) Expression levels of Tet1 and Tet3, but not Tet2, correlate with C to G somatic mutation rates across 346 cancer genomes. (B) For different upstream contexts, correlation coefficients (Spearman's rho) between C to G rates and expression levels were computed for the three Tet genes (red dots) and their respective set of control genes (grey/black, see main text). Whiskers extend to approximately 1.5*IQR (interquartile range) below/above the bottom/top quartile of the data, (see R documentation [69] for details). (C) Distribution of correlation coefficients (C to G rates ∼ Tet expression) calculated independently for 44 different cancer type-upstream context combinations. (D) C to G SNP rates at 5hmC and 5mC sites as a function of Tet1-binding in mESCs. (E) Rates of cytosine loss for the matched set of sites as a function of location inside or outside 5fC-enriched regions in mESC as defined by [32]. Error bars are 95% confidence intervals, calculated using Wilson's interval score for single proportions. TPM: transcripts per million.