We did not detect any Gene Ontology term that was significantly enriched among the 49 DEGs. A comparison of our DEG set with 8 different protein interaction databases, including BIND, DIP, MINT and REACTOME INTERACTION using DAVID, also showed no significant enrichment (data not shown). Notably, 48 of 49 DEGs were downregulated in hiPSCs relative to hESCs (Fig. 3C). This raised the possibility that the DEGs were silenced in fibroblast-like cells and were not properly reactivated in derivative hiPSCs. However, the expression levels of the DEGs in fibroblast-like cells did not show a consistent pattern, excluding incomplete reprogramming or the retention of ‘epigenetic memory’ (Fig. 3C).
