Fig. 3

Analysis of differentially expressed genes in SGPs and hmcs. (a) In total, we detected transcripts from 11,330 genes (mean FPKM > 1). Differential gene expression analysis identified 5912 genes with differential expression between SGPs and hmcs (FDR ≤ 0.01, fold-change ≥2). Of these genes, 2749 have higher expression in SGPs and 3163 have higher expression in hmcs. 5418 genes show expression in at least one of the two cell types, but do not have significantly different expression between the two sample types. (b) Volcano plot shows genes that are differentially expressed in SGPs (red) and hmcs (blue). Dashed lines indicate the FDR and fold change cutoffs (FDR ≤ 0.1 and fold change ≥2). (c) MA plot showing genes that are differentially expressed in SGPs (red) and hmcs (blue). A cluster of genes has a high average level of expression and is differentially expressed in SGPs (dashed oval). This cluster includes genes involved in ribosomal biogenesis, such as ribosomal protein-encoding genes