Extended Data Fig. 5: Gene ontology analysis and CellPhoneDB results for bulk and single-nucleus assays showing immune and angiogenesis dysregulation.
a, GO analysis for upregulated (top) and downregulated genes (bottom) from the bulk RNA-seq. The colour scale represents the ratio of dysregulated genes to total genes under each GO term; P values were calculated using a one-tailed hypergeometric test. b,c, GREAT analysis of decreased peaks from the H3K27me3 CUT&Tag (b) and increased (c,top) and decreased (c,bottom) peaks from the bulk ATAC-seq. P values were calculated using a one-tailed binomial test. d, Expression of selected interferon genes from the bulk RNA-seq. The fold change (patient/control) and Padj using the two-tailed Wald test were calculated by DESeq2. Significantly dysregulated genes (|log2(fold change)| > 1 and Padj < 0.05) are marked by red stars. e, RT–qPCR results of selected interferon genes in our patient and control samples. Each dot represents a sample (n = 7 for both patient and control); P values were calculated using a one-tailed Wilcoxon test. The centre and bounds of boxes indicate the median and quartile of all data points, respectively. The minima and maxima of whiskers indicate quartile 1 − 1.5× the interquartile range and quartile 3 + 1.5× the interquartile range, respectively. f, GO analysis of significant patient-specific receptor–ligand interactions, defined by CellPhoneDB, in which the ligand is differentially expressed (|log2(fold change)| > 0.25 and one-tailed MAST model Padj < 0.05) in given cell types from Seurat. The colour scale represents the ratio of dysregulated genes to total genes under each GO term; P values were calculated using a one-tailed hypergeometric test. g, Significant patient-specific receptor–ligand pairs under the GO term regulation of cytokine production defined by CellPhoneDB (see Methods). Only interactions between immune and trophoblast cell types are shown. The mean expression and P values (one-tailed Wilcoxon test) were calculated by CellPhoneDB.
