Table 1. Categorized deregulated genes in Tfap2−/−PGCLCs based on gene ontology analysis.
| Category | Upregulatedgenes | FC | Function | Downregulated genes | FC | Function |
| I: | Bcl11a | 1.93 | leukemogenesis and hematopoiesis | Gata2 | −1.87 | hematopoiesis |
| Somatic | Cited2 | 1.87 | CNS development | Lhx1 | −1.59 | mesodem formation |
| differentiation | Chd7 | 1.67 | CNS development | Slit2 | −2.34 | neurogenesis |
| Cobl | 2.43 | neural tube closure | Kctd15 | −3.20 | inhibit neural crest formation | |
| Ehna | 2.01 | neural tube closure | Pecam1/CD31 | −1.50 | mesoderm development | |
| Epha2 | 1.53 | neural tube development | ||||
| Gbx2 | 2.36 | gastrulation-brain specific | ||||
| Gli2 | 3.48 | neural tube development | ||||
| Hck | 2.83 | hemopoietic cell kinase | ||||
| Hhex | 1.52 | hematopoietically expressed homeobox gene | ||||
| Hoxa5 | 1.97 | mammary gland- lung development | ||||
| Hoxa1 | 1.13 | central nervous system neuron differentiation | ||||
| Hoxa3 | 1.13 | cartilage- and thymus development | ||||
| Hoxb1 | 1.03 | CNS development | ||||
| Mtap1b | 1.70 | CNS development | ||||
| Ncam1 | 2.42 | neuron-neuron adhesion | ||||
| Nefl | 3.56 | neurogenesis | ||||
| Neurod1 | 1.57 | neurogenesis | ||||
| Pou4f2 | 1.58 | expressed in brain | ||||
| Pten | 1.63 | CNS development | ||||
| Robo1 | 1.79 | neurogenesis | ||||
| Sfrp1 | 3.12 | neural tube closure and development | ||||
| Sfrp2 | 1.66 | neural tube development | ||||
| Smarca1 | 2.06 | neuron differentiation, brain development | ||||
| Tcf7l2 | 2.56 | neural tube development | ||||
| Zic2 | 3.71 | CNS development; neural tube closure | ||||
| Zic5 | 3.14 | neural tube closure | ||||
| II: | Cited2 | 1.87 | sex determination | Aurkc | −2.06 | key regulator mitosis; meiosis |
| Germ cell | Pten | 1.63 | tumor suppressor; apoptosis | Bik | −2.20 | spermatogenesis, apoptosis |
| maintenance | Sprink3 | 2.54 | inhibits calcium uptake in spermatozoa | Cdk16 | −1.00 | required for spermatogenesis |
| and | Ceacam10 | −2.98 | sperm surface protein | |||
| maturation | Chdh | −4.80 | localized in mitochondrial | |||
| Cxcr4 | −1.94 | germ cell migration | ||||
| Dazl | −1.40 | gametogenesis; spermatogenesis | ||||
| Dmrt1 | −2.68 | male sex determination and differentiation | ||||
| Hk1 | −3.04 | expressed in meiosis and postmeiotic germ cells | ||||
| Immp2l | −1.57 | spermatogenesis | ||||
| Kit | −1.91 | cell survival, migration and proliferation | ||||
| Phf13/Spoc1 | −1.85 | spermatogenesis | ||||
| Rhox5 | −4.29 | spermatogenesis, sperm maturation | ||||
| Rhox4a | −2.70 | in fetal germ cells expressed | ||||
| Rhox6 | −6.11 | germ cell lineage determination | ||||
| Rhox9/Psx2 | −5.59 | oogenesis | ||||
| Sept4 | −1.63 | sperm capacitation; mitochondrion organization | ||||
| Slco4c1 | −2.32 | sperm maturation | ||||
| Spa17 | −2.30 | sperm surface protein | ||||
| Stella/Dppa3 | −4.27 | PGC specific protein | ||||
| Stk31 | −2.40 | male germ cell specific expression | ||||
| Tes | −2.04 | cell adhesion, cell proliferation | ||||
| III: | Ccnd1 | 2.33 | interacts with Cdk4/Cdk6 | Urgcp | −3.17 | regulation of Ccnd1 |
| Cell cycle | Ccnt2 | 1.88 | interacts with Cdk9 | |||
| Cdc14a | 1.57 | cell cycle; cell division | ||||
| Cdk6 | 1.50 | promotes G1/S transition | ||||
| Cdk7 | 1.17 | cell cycle; cell division | ||||
| Cdkn1a/p21 | 1.02 | bind and inhibit cyclin-dependent kinase | ||||
| Plk2 | 1.68 | involved in G1/S phase transition | ||||
| S100a10 | 2.15 | cell cycle progression and differentiation | ||||
| IV: | Eras | 3.52 | maintenance of ESC pluripotency | |||
| Pluripotency | Fgf4 | 2.94 | regulation cell proliferation, differentiation | |||
| FoxD3 | 1.03 | early direct response gene of Oct3/4 | ||||
| Gbx2 | 2.36 | cell pluripotency and differentiation | ||||
| Jam2 | 2.47 | early direct response gene of Oct3/4 | ||||
| Klf4 | 2.22 | maintenance of ESC pluripotency | ||||
| Msi2 | 2.31 | RNA binding protein; self-renewal of ESC | ||||
| Nr0b1 | 1.62 | maintenance of ESC pluripotency | ||||
| Tdgf1 | 1.36 | early direct response gene of Oct3/4 | ||||
| V: | Dnmt3b | 1.34 | genome-wide de novo methylation | Pcgf5 | −2.40 | chromatin remodeling; histone modification |
| Epigenetics | Dnmt3l | 3.21 | DNA methyltransferase like enzyme | |||
| Smarca6/Hells | 1.09 | de novo or maintenance of DNA methylation | ||||
| Mbd2 | 1.54 | recruits Hdacs and Dnmts; gene silencing | ||||
| Tet2 | 1.27 | conversion of 5mC to 5hmC | ||||
| Uhrf1 | 1.45 | major role in the G1/S transition |
bold: genes with fold-change >1.5 in log2 scale; regular: genes with fold-change ≤1.5 in log2 scale.