To identify potential interactions between and within villi and decidua, we used a list of ligand-receptor pairs, which was obtained and manually curated from the Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu) and the IUPHAR/BPS guide to pharmacology (www.guidetopharmacology.org), as described earlier (30). The list of interactions was intersected with TPM-normalized expression table (data file S1) of genes for each cell type, and only ligands and receptors expressed by >15% cells and with expression >5 and >1.5 TPM, respectively, were used. Receptor-ligand pairs where both partners pass the filtering criteria were considered for graphical representation. Custom Perl and R scripts were used for analyses and to draw the interaction diagrams.

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