Fig. 6

Distinct co-expression and correlation patterns identified two classes of lineage specific transcriptional regulators. a Expression of transcriptional regulators in ectoderm-like and XEN-like cells identified in the SMART-seq2 data set. Genes that were significantly differentially expressed after 48 h of RA exposure are shown in red or pink (overexpressed in ectoderm-like cells) and blue or cyan (overexpressed in XEN-like cells), respectively. The two panels contain genes, which are present in the pluripotent state (early, left panel) or absent in the pluripotent state (late, right panel). A list of all identified genes is given in Supplementary Fig. 9b. b Co-expression of transcriptional regulators in the pluripotent state. The gene set comprised the differentially expressed transcriptional regulators identified here (see a), as well as pluripotency related transcription factors⁵¹ (see Supplementary Fig. 9b). Co-expression was calculated using gene expression measured by SMART-seq2. Co-expression of two genes was quantified as the fraction of cells in which the expression of both genes exceeded a certain threshold value (see Methods). c Co-expression network in the pluripotent state. Two genes are connected by an edge if their co-expression exceeds 0.8. The gene set comprised XEN specific regulators (cyan nodes) and ectoderm specific regulators (pink nodes) that are expressed in the pluripotent state (early factors), as well as pluripotency factors⁵¹ (orange nodes). The radius of solid nodes is proportional to the number of connections to other nodes. Nodes without any connections are depicted as open nodes. d Pearson correlation between transcriptional regulators after 48 h of RA exposure. The gene set is the same as in b. Pearson correlation was calculated using gene expression measured by SMART-seq2