Gene regulatory network modeling somitogenesis (WP2854)

Homo sapiens

Reaction scheme of the proposed gene regulatory network (GRN). The scheme details the full GRN for one cell and part of a neighboring cell for those reactions that involve ligand-receptor interactions like in Delta-Notch signaling or input from the Fgf8 or Wnt3a signal transduction pathways. Color-coded circular areas for each gene symbolize mRNA and protein. For fast changing gene products the transport of mRNA or protein between cytoplasm and nucleus or between cytoplasm and membrane is explicitly simulated, which is indicated by dividing each half-area of the circle again. Regulatory interactions are shown as activating or repressing arrows. Broken lines indicate that the interaction is simulated only in an even more course-grained manner than the other gene regulatory reactions. NICD, which originates through cleavage reactions following DLL1 ligand binding to the NOTCH1 receptor, was assigned a separate symbol to clarify that only the intracellular domain of the Notch receptor acts in the nucleus as a transcription (co)-factor. The (weak) modulating action of LFNG on D/N signaling is shown as dashed lines - (red for the case of inhibiting action, green for the case of a positive effect on the D/N reaction rate.) Arrows pointing to the symbol for the empty set designate decay reactions of a species. We suppressed them for all species' decays except for those decay rates that we assume as controlled by signal transduction pathways. This applies also to the removal of DLL1 and NOTCH1 from the membrane after their binding, resulting in NOTCH1 cleavage and NICD split-off. Proteins on this pathway have targeted assays available via the [ CPTAC Assay Portal]


Nathan Salomonis , Zahra Roudbari , Alex Pico , Kristina Hanspers , and Eric Weitz


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Homo sapiens



Pathway Ontology

regulatory pathway


Label Type Compact URI Comment
NOTCH1 GeneProduct ensembl:ENSG00000148400
RIPPLY2 GeneProduct ensembl:ENSG00000203877
WNT3A GeneProduct ensembl:ENSG00000154342
HES7 GeneProduct ensembl:ENSG00000179111
TBX6 GeneProduct ensembl:ENSG00000149922
FGF8 GeneProduct ensembl:ENSG00000107831
NOTCH1 GeneProduct ensembl:ENSG00000148400
MESP2 GeneProduct ensembl:ENSG00000188095
NICD GeneProduct ncbigene:4851
DLL1 GeneProduct ensembl:ENSG00000198719
LFNG GeneProduct ensembl:ENSG00000106003
EPHA4 GeneProduct ensembl:ENSG00000116106
HES1 GeneProduct ensembl:ENSG00000114315
DLL1 GeneProduct ensembl:ENSG00000198719
WNT3A GeneProduct ensembl:ENSG00000154342
FGF8 GeneProduct ensembl:ENSG00000107831
FGF8 GeneProduct ensembl:ENSG00000107831


  1. From dynamic expression patterns to boundary formation in the presomitic mesoderm. Tiedemann HB, Schneltzer E, Zeiser S, Hoesel B, Beckers J, Przemeck GKH, et al. PLoS Comput Biol. 2012;8(6):e1002586. PubMed Europe PMC Scholia