Fig. 3

The number of cells substantially influences the identification of DEGs by scRNA-seq. A Overlap of DEGs identified by bulk and pseudo-bulk RNA-seq. B Characteristics of DEGs identified by both bulk and pseudo-bulk RNA-seq or by one method only. C Overlap of DEGs identified by bulk RNA-seq and by scRNA-seq analyzed with Seurat with BH adjustment. D Overlap of DEGs identified by bulk RNA-seq and by scRNA-seq analyzed with Seurat with Bonferroni adjustment. The bulk RNA-seq data were analyzed using BH adjustment. scRNA-seq analyzed using Bonferroni adjustment was plotted here for reference only as it was the default setting in Seurat. E Spearman correlation coefficients of p values of DEGs for bulk vs. pseudo-bulk RNA-seq data and bulk vs. scRNA-seq data. 100% to 1% corresponded to scRNA-seq data from approximately 5,000 to 50 cells, randomly sampled three time at each level below 100%. DEG, differentially expressed gene; Log₂FC, log₂ fold change; TPM, transcript per million; Q1 to Q4, first to fourth quartile. N = 3