Various signalling pathways, as FGF, WNT and TGF-β pathways, regulate the processes involved in embryogenesis.
FGF (Fibroblast Growth Factor) ligands bind to receptors tyrosine kinase, FGFR (Fibroblast Growth Factor Receptors), and form a stable complex with co-receptors HSPG (Heparan Sulphate Proteoglycans) that will promote autophosphorylation of the intracellular domain of FGFR and consequent activation of four main pathways: MAPK/ERK, PI3K, PLCγ and JAK/STAT.
* MAPK/ERK (Mitogen-Activated Protein Kinase/Extracellular Signal-Regulated Kinase) regulates gene transcription through successive kinase phosphorylation and in human embryonic stem cells it helps maintaining pluripotency. However, in the presence of Activin A, a TGF-β ligand, it causes the formation of mesoderm and neuroectoderm. 
* Phosphorylation of membrane phospholipids by PI3K (Phosphatidylinositol 3-Kinase) results in activation of AKT/PKB (Protein Kinase B). This kinase is involved in cell survival and inhibition of apoptosis, cellular growth and maintenance of pluripotency, in embryonic stem cells. 
* PLCγ (Phosphoinositide Phospholipase C γ) hydrolyzes membrane phospholipids to form IP3 (Inositoltriphosphate) and DAG (Diacylglycerol), leading to activation of kinases and regulating morphogenic movements during gastrulation and neurulation.
* STAT (Signal Trandsducer and Activator of Transcription) is phosphorylated by JAK (Janus Kinase) and regulates gene transcription, determining cell fates. In mouse embryonic stem cells, this pathway helps maintaining pluripotency.
The WNT pathway allows β-catenin function in gene transcription, once the interaction between WNT ligand and G protein-coupled receptor Frizzled inhibits GSK-3 (Glycogen Synthase Kinase-3) and thus formation of β-catenin destruction complex. Although there is some controversy about the effects of this pathway in embryogenesis, it is thought that WNT signalling induces primitive streak, mesoderm and endoderm formation.
In TGF-β (Transforming Growth Factor β) pathway, BMP (Bone Morphogenic Protein), Activin and Nodal ligands bind to their receptors and activate Smads that bind to DNA and promote gene transcription. Activin is necessary for mesoderm and specially endoderm differentiation, and Nodal and BMP are involved in embryo patterning. BMP is also responsible for formation of extra-embryonic tissues before and during gastrulation, and for early mesoderm differentiation, when Activin and FGF pathways are activated.