Fig. 5: Dynamics of isoform switching during human ESC differentiation to PE and PGC. | Nature Biotechnology

Fig. 5: Dynamics of isoform switching during human ESC differentiation to PE and PGC.

From: Improving gene isoform quantification with miniQuant

Fig. 5

a, Number of long reads and short-read pairs. b, Number of gene isoforms with TPM ≥ 1. Known, annotated by GENCODE annotation; New, not annotated by GENCODE annotation. c,d, Left, expression heatmap of 151 genes with isoform switches from ESC to PE (c) and 161 genes from ESC to PGC (d). Right, for each gene, the maximal difference of the usage ratios (ranging from 0 to 100%) of its isoforms between ESC and PE (c) and between ESC and PGC (d). Results by cDNA-ONT and Illumina data are shown. e, GO analysis of 151 (ESC to PE) and 161 (ESC to PGC) isoform-switching genes identified in both differentiation trajectories (see Methods, ‘Analyses of isoform switching’). Only the GO terms with one-sided exact P value < 0.05 are shown. f, Three example genes with isoform switches. For each gene isoform, the usage ratios (ranging from 0 to 100%) in three samples by cDNA-ONT and Illumina data are specified within parentheses. Certain intron regions are condensed for readability. g, Ternary and contour plots showing the relative enrichment of the isoform usage ratios across ESC, PE and PGC for four genes with isoform switches (Fig. 5f and Extended Data Fig. 10d) and corresponding density. Each gene has two isoforms, where one is used predominantly in ESC (Down, deep color), and the other is used mainly in PE and/or PGC (Up, light color); 100 bootstrap sampling of cDNA-ONT reads for four genes was conducted, with sizes corresponding to real abundances of four genes (Real data) and quartiles (Q3, Q2, Q1) of all gene abundances in ESC. Isoforms used solely in one of the ESC, PE and PGC will be located at the triangle vertices without contour. The contour plot is not generated for extremely sparse points such as LIQA at the 25th percentile. The distribution of all gene abundances in ESC are shown on the right and the bootstrap sampling sizes are indicated correspondingly. Due to technological issues, the FLAMES and TALON are not shown here (Supplementary Note 13).

Back to article page