Table 1.

Genes analyzed and their functions.

CATEGORY	GENE	FUNCTION AND REFERENCE
iPS genes	KLF2	Transcriptional activator or repressor depending on the promoter context and/or cooperation with other transcription factors. Involved in the differentiation of epithelial cells. iPS inducing factor (Ghaleb et al., 2005; Park et al., 2008; Takahashi et al., 2006; Takahashi and Yamanaka, 2006; Yoon et al., 2005).
	KLF4
	LIN28	Acts as a 'translational enhancer', driving specific mRNAs to polysomes and thus increasing the efficiency of protein synthesis. Its association with the translational machinery and target mRNAs results in an increased number of initiation events per molecule of mRNA and, indirectly, in stabilizing the mRNAs. iPS inducing factor. (Takahashi and Yamanaka, 2006; Viswanathan et al., 2008; Viswanathan et al., 2009; West et al., 2009; Wu and Belasco, 2005; Yu and Thomson, 2008; Yu et al., 2007)
	MYC	Encodes a DNA-binding factor that can activate and repress transcription. It regulates expression of numerous target genes that control key cellular functions, including cell growth and cell cycle progression. Involved in the induction of iPS cells.
	NANOG	Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. iPS inducing factor (Mitsui et al., 2003; Takahashi et al., 2006; Takahashi and Yamanaka, 2006; Wernig et al., 2007).
	POU5F1	Critical for early embryogenesis and for embryonic stem cell pluripotency. iPS inducing factor.(Niwa, 2000; Stadtfeld et al., 2008; Takahashi et al., 2006; Takahashi and Yamanaka, 2006)
	SOX2	Involved in the regulation of embryonic development and in the determination of cell fate. Critical for early embryogenesis and for embryonic stem cell pluripotency (Mitsui et al., 2003; Takahashi et al., 2006; Takahashi and Yamanaka, 2006).
Pluripotency maintenance, growth regulatorsand self-renewal	DPPA4	Play a role in maintaining cell pluripotentiality (Bortvin et al., 2003; Chakravarthy et al., 2008; Madan et al., 2009).
	ID1	May play a role in cell growth, senescence; Negatively regulates cell differentiation. (Caldon et al., 2008) Alani et al., 2001)
	ID2
	SALL4	Transcription factor that plays a diverse role in regulating stem cell pluripotency during early embryonic development through integration of transcriptional and epigenetic controls. Sakaki-Yumoto et al., 2006; Tsubooka et al., 2009, Lu et al., 2009; Yang et al., 2008; Lim et al., 2008
	SOX17	Critical for early embryogenesis and for embryonic stem cell pluripotency (Qu et al., 2008; Wei et al., 2008; Séguin et al., 2008
	CTNNB1	Involved in the regulation of cell adhesion and in signal transduction through the Wnt pathway (Cajánek et al., 2009; Hierholzer and Kemler 2009)
	FBXO15	Regulate the abundance of proteins that promote and inhibit cell cycle progression at the transition between G1 and S phases. Indespensable for ES cell self-renewal, development, and fertility. (Okita et al., 2007; Tokuzawa et al., 2003).
	CDH1	Involved in the compartmentalization, proliferation, survival, and differentiation of cells. Regulates stem cells self-renewal.
	FDZ7	Receptor for Wnt proteins. They are coupled to the beta-catenin canonical signaling pathway. May be involved in transduction and intercellular transmission of polarity information during tissue morphogenesis and/or in differentiated tissues
	GATA2	Promotes proliferation at the expense of differentiation (Stainier, 2002).
	GDF3	Regulators of cell growth and differentiation in both embryonic and adult tissues.
	KIT	Receptor for stem cell factor (mast cell growth factor).
	LIF	Is a pleiotropic cytokine with roles in several different system. It is used in mouse ES to maintain the stem cells in an undifferentiated state. It is not required in hES and rat. (Brenin et al., 1997; Buehr et al., 2003; Daheron et al., 2004; Iannaccone et al., 1994).
	ZFP42/REX1	Involved in self-renewal property of ES cells (Masui et al., 2008; Sharov et al., 2008; Zhang et al., 2006).
Ectoderm marker	LIMK1	Protein kinase, which regulates actin filament dynamics. May be involved in brain development.
	NES	Play a role in the trafficking and distribution of intermediate filament proteins and potentially other cellular factors to daughter cells during progenitor cell division It is expressed predominantly in stem cells of the central nervous system in the neural tube (Kleeberger et al., 2007; Zulewski et al., 2001).
	BMP4	Induces cartilage and bone formation. Also act in mesoderm induction, tooth development, limb formation and fracture repair. It induces the differentiation of human ES cells to trophoblast. In mouse, it maintains self-renewal with leukemia inhibitory factor (LIF). In Monkey induces differentiation into the primitive endoderm lineage (Schulz et al., 2008; Xu et al., 2002).
Mesoderm marker	GSC	Play a role in spatial programming within discrete embryonic fields or lineage compartments during organogenesis (Steinbeisser et al., 1995; Tada et al., 2005).
	NODAL	Essential for mesoderm formation and axial patterning during embryonic development (Pfendler et al., 2005).
	T(BRACHYURY	Involved in the transcriptional regulation of genes required for mesoderm formation and differentiation (Vidricaire et al., 1994).
	TCF3	Play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation (Merrill et al., 2004).
Endoderm marker	FOXA1	Transcription activator for a number of liver genes such as AFP, albumin, tyrosine aminotransferase, PEPCK, etc Review by (Stainier, 2002).
	GRB2	Required during embyrogenesis for the differentiation of endodermal cells and formation of the epiblast (Hamazaki et al., 2006).
	HEY2	Required for embryonic cardiovascular development, and are also implicated in neurogenesis and somitogenesis (Fischer et al., 2004).
	LEFTY1	Required for left-right axis determination (Meno et al., 1998).
	LEFTY2
	PAX6	Required for the differentiation of pancreatic islet alpha cells (Mansouri et al., 1999; St-Onge et al., 1997).
	PDX1	DNA binding protein. Function as regulators of gene transcription. Required for the differentiation of pancreatic islet alpha cells, development of eye, nose and nervous system.
	ZIC3	Functions as a transcription factor in the earliest stages of the left-right (LR) body axis formation. Mutation of ZIC3 cause x-link abnormalities. (Gebbia et al., 1997).
Early differentiation marker	KRT7	Plays a role in maintaining cellular structural integrity and also functions in signal transduction and cellular differentiation. Stem cell markers (Cauffman et al., 2009; Maurer et al., 2008).
	KRT8
	KRT18
Trophoblast markers	AFP	Ensure specific transport and the modulation of the activities of a number of ligands which are essential for the differentiation of embryonic organs and fetal development. It is expressed in trophoblastic cells during early pregnancy (Duc-Goiran et al., 2006).
	ASCL2/HASH1	Involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system. Expressed in extravillus trophoblast, which is paternally imprinted (van Wijk et al., 2001a).
	BMP4	See above.
	CDX2	Necessary for trophoblastic development, vasculogenesis in the yolk sac mesoderm, allantoic growth, and chorioallantoic fusion (Niwa et al., 2005; Strumpf et al., 2005; Tolkunova et al., 2006).
	CGB	Stimulates the ovaries to synthesize the steroids that are essential for the maintenance of pregnancy. Is a trophoblast marker (Bonduelle et al., 1988).
	EOMES	Essential during trophoblast development and gastrulation (Russ et al., 2000).
	HAND1	Plays an essential role in early trophoblast differentiation; Review by Cross (Cross, 2005) and in cardiac morphogenesis (Thattaliyath et al., 2002).
	HLA-G	Involved in the presentation of foreign antigens to the immune system. It is expressed in fetal-derived placental cells (van Wijk et al., 2001b).