Table 2.

Overlapping genes between significant gene lists from the present study and gene categories known to be involved in the embryogenesis

CategoryCommon genes within 687 interhistologic subtype-regulated genesPCommon genes within the 68 genes with specific expression changes in the undifferentiated histologyP
Homeobox genes (209)EMX2, HESX1, I_1221473, NANOG, PAX3, PAX5, PCBD, POU5F1, SHOX2, TCF8, TLX20.30HESX1, MOX2, NANOG, POU5F10.01
Specifically expressed in embryonic stem cells (83)CYP26A1, DNMT3B, FABP5, GAL, GDF3, HMGB2, MGST1, NANOG, POU5F1, SEMA6A, SPS, TK13 × 10−4DNMT3B, EIF4A1, GAL, GDF3, NANOG, POU5F1, SEMA6A1 × 10−7
WNT signaling components (79)AES, DKK1, FRAT2, FZD4, FZD7, TCF7L1, TCF7L20.26FRAT2, WNT5A0.05
WNT signaling target genes (52)FZD7, ID2, SLC2A10.401.00
TGF-β signaling (102)BMP2, GDF10, GDF3, ID2, INHA, MAPK4, TGFBI0.16GDF30.36
Notch signaling (9)1.001.00
DNA methylation (16)DNMT3B, DNMT3L0.15DNMT3B, DNMT3L2 × 10−3
Genomic imprinting (6)DNMT3B, DNMT3L0.03DNMT3B, DNMT3L3 × 10−4
Imprinted genes (32)1.001.00
  • NOTE: Enrichment analyses were also done (Fisher's exact Ps). In parentheses are the numbers of genes present on the microarray within each category. The actual genes making up each category list can be found in Supplementary Table S3.