In addition to the positive regulation of those genes that are important to maintain the proliferation, Oct4, Sox2, and Nanog inhibit the activity of a number of prodifferentiation transcription factors active in the embryonic period, for example, ESX1I, HOXB1, MEIS1, LHX5, LBX1, MYF5, and ONECUT1
Genes over-expressed in a variety of cancers include FAM149A (family with sequence similarity 149, member A), ONECUT1
(one cut homeobox 1), TOX2 (tox high mobility group box family member 2), and GDAPIL1 (ganglioside induced differentiation associated protein 1-like 1).
Among transcriptionally inactive genes co-occupied by Oct4, SOX2, and NANOG, genes that specify transcription factors important for differentiation into extraembryonic, endodermal, mesodermal, and ectodermal lineages (e.g., ESX1L (Extraembryonic, Spermatogenesis, Homeobox-1 Homolog (Mouse)), HOXB1 (Homeobox-B1), HAND1 (Heart And Neural Crest Derivatives Expressed-1), MEIS1 (Meis Homeobox-1), PAX6 (Paired Box-6), LHX5 (LIM Homeobox-5), MYF5 (Myogenic Factor-5), and ONECUT1
(One Cut Homeobox-1)) are present.