Fig. 4: Specifically methylated isoforms are cell line-specific.
From: Isoform characterization of m6A in single cells identifies its role in RNA surveillance
a Volcano plot showing the correlation between m6A methylation level and isoforms expression at single-cell level in HeLa. P values based on a two-tailed t test are shown. b Comparing the m6A level for isoforms (n = 516) with negative correlation between m6A level and expression and other isoforms (n = 3140) in single cells of HeLa. P value of two-tailed Wilcoxon test is indicated. c Box plot demonstrating the correlation between normalized isoforms expression and the m6A-isoSC-seq determined m6A levels of ISG15-203 in single-cell level. P values of two-tailed Wilcoxon tests are indicated. d Box plot comparing the number of exons for isoforms (n = 516) with negative correlation between m6A level and expression and other isoforms (n = 3140) in single cells of HeLa. P value of two-tailed Wilcoxon test is indicated. e Volcano plot showing the differential m6A levels of the isoforms in the same genes in HeLa. f Comparing the mean expression of highly methylated isoforms (n = 507) and lowly methylated isoforms (n = 354) in single cells of HeLa. g, h The overlaps of highly methylated isoforms (g) and lowly methylated isoforms (h) identified in different cells. P values from one-tailed Fisher’s exact tests are indicated. Comparing the m6A levels (i) and expression (j) between HeLa-specific highly methylated and lowly methylated isoforms in indicated cell lines. k C-to-U mutations on all the ONT reads of the different isoforms in indicated cell lines. l Violin plots comparing the m6A levels between EEF1D-202 and EEF1D-223 in different cell lines. m UMAP comparing the transcript expression level of the isoform EEF1D-202 (left) and isoform EEF1D-223 (right) in ONT single-cell data. The UMAP_1 and UMAP_2 values for each cell were identical to those presented in Fig. 3f. For box plots and violin plots, P values of two-tailed Wilcoxon tests are indicated, the horizontal line represents the median value, the lower and upper quartiles represent the 25th and 75th percentiles, and the whiskers are extended to 1.5 × IQR. Source data are provided as a Source Data file.
