Fig. 1: Memory genes drive the transcriptomic similarity of related cells across cell types.
From: Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets
a UMAP of the lineage-annotated mESC scRNA-seq dataset with 25 random colored lineages. b Boxplot of the correlation distance for related cells (blue), and randomly sampled cells (gray; 100 repetitions) in different cell types (n = 1 dataset for each cell type). c Boxplot as in b for lineages encompassing one single cell type (symmetric; sym.) and lineages encompassing several cell types (asymmetric, asym.) for one HSPC dataset. d Illustration of the temporal pattern of expression levels and variability of quantitative memory genes, qualitative memory genes, and non-memory genes across cell generations and lineages, respectively. e Percentage of expressed genes (gray) that are categorized as quantitative (green) and qualitative (blue) memory genes across cell types (n = 1 dataset for each). f Relation of CV2 and mean gene expression in the mESC dataset. The different memory gene categories are colored as in e. g Mean gene expression for different memory gene categories and all genes across cell types as in (b; n = 7 datasets, qual=qualitative, quant=quantitative). h Same representation as in g for CV2 of gene expression. i Memory genes as a percentage of expressed genes for lineages being composed of one cell type (symmetric; sym.) and lineages encompassing several cell types (asymmetric; asym) at day 4 of HSPC differentiation (n = 22 datasets). j The overlap between memory genes of day 2 and day 5–30 over the course of MEF reprogramming. Overlap is the percentage of the memory gene number at day 5–30, respectively (n = 2 dataset for each timepoint). Boxes: intervals between the 25th and 75th percentile and median (horizontal line). Error bars: 1.5-fold the interquartile range or the closest data point when no data point is outside this range. Source data are provided as a Source Data file.
