Table 1.
List of genes whose expression altered more than two-fold by thalidomide treatment.
| Gene | hiPSC | mesoderm | marker | Descriptions and [References] |
|---|---|---|---|---|
| ACTC1 | down | down | ES/iPSCs | Actin alpha cardiac muscle 1. Sarcomere gene |
| AICDA | up | up | ES/iPSCs (reprogramming-related) | Activation-induced cytidine deaminase. Genes associated with DNA demethylation |
| BMP2 | up | ES/iPSCs | Bone morphogenetic protein-2 encodes a TGF-β super family morphogen. Related to limb growth [38]. | |
| CD34 | down | mesoderm (blood stem cells) | Protein localized to hematopoietic progenitor cells and stem cells | |
| CDH1 | down | E-cadherin and keratinocyte | Intercellular adhesion factor. Association of E-cadherin expression | |
| EMX2 | up | ectoderm (neural stem cells) | Encodes empty spiracles homolog 2, which is associated with neural differentiation and cell proliferation in the brain, and limb formation [39] | |
| FABP7 | down | up | ectoderm (neural stem cells) | Encodes fatty acid binding protein 7, which localizes in the brain and is involved in neural development [21,22]. |
| FGF4 | down | ES/iPSCs (pluripotency markers) | Encodes fibroblast growth factor 4, which plays various roles in development, including limb bud development [38] | |
| FOXA2 | down | endoderm | Encodes forkhead box A2 | |
| FOXD3 | down | ES/iPSCs (pluripotency markers) | Encodes forkhead box protein D3, which acts as a transcriptional repressor. | |
| GJB2 | up | keratinocytes (CX26) | Encode the gap junction structural component connexin 26 (GJB2), which is a component of gap junctions and is related to hearing loss [42,47,48] | |
| HAND1 | down | mesoderm | essential gene for cardiovascular development and is involved in mammalian heart chamber formation [41]. | |
| HNF4A | down | mesoderm | Hepatocyte nuclear factor 4, alpha | |
| LEFTY1 | up | ES/iPSCs (pluripotency markers) | TGF-β super family related genes that determine the left-right asymmetry of the body | |
| LEFTY2 | up | down | ES/iPSCs (pluripotency markers) | TGF-β super family related genes that determine the left-right asymmetry of the body |
| MYC | up | ES/iPSCs (reprogramming factors) | oncogene. MYC can induce DNA breaks in vivo and in vitro, independent of reactive oxygen species. | |
| NR5A2 | down | ES/iPSCs (reprogramming factors) | Encodes nuclear receptor subfamily 5, group A, member 2, which is responsible for transcriptional activation of OCT3/4. | |
| OTX2 | up | ES/iPSCs | Encodes orthodenticle Homeobox 2, a marker gene for ectoderm and neural differentiation. | |
| PODXL | down | ES/iPSCs (pluripotency markers) | Encodes podocalyxin-like 1, which is related to cell adhesion. | |
| RUNX1 | down | mesoderm | Encodes Runt-related transcription factor 1 | |
| RUNX2 | up | ES/iPSC | Runt-related transcription factor 2 related to osteoblast differentiation. | |
| SOX17 | up | down | endoderm | Encodes sex-determining region Y-box 17 (SOX17). |
| TBX3 | up | ES/iPSCs (ESC related) | Encodes T-box transcription factor TBX3, which is essential for embryonic development and is involved in heart and angiogenesis. | |
| TUBB3 | up | ectoderm | Encodes tubulin beta 3 class III (TUB-β3), which is used for microtubule formation and is a neural differentiation marker. |
up: upregulated genes, down: downregulated genes.