Pathway Human Homo sapiens

Gastrulation

R-HSA-9758941 in Reactome release 97: under Developmental Biology, with 120 genes placed in it by the mapping files and 10 child pathways in the hierarchy.

The same number in the other species

Reactome writes the mouse and rat events it infers from a human pathway under the human number with the species token. A door opens only where that species' own list in this release holds the id: R-MMU-9758941 (mouse), R-RNO-9758941 (rat). Whether the event was inferred from this one is what the record says.

The record
The genes
Parents and children

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01The record

Reactome's own record of this pathway

What this tells you

The pathway list, the hierarchy and the genes on this page are read from the files Reactome publishes for Reactome release 97, built into this site on 2026-09-09: the pathway list, the hierarchy relationship file and the two gene mapping files. The record card is the one live read, Reactome's own record of this pathway.

Reactome's download page describes the mapping files: Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway, all levels of the pathway hierarchy or database identifier to all reactions. [R13] The gene list here is the all-levels mapping of NCBI Gene ids, filled from the all-levels mapping of Ensembl ids where the NCBI file has no row for a gene; each row names which file it came from by the shape of its source id. Each row carries the evidence codes the file writes for it, as written and unranked, and both where the file writes both; no page of Reactome's documentation the survey read defines the codes, so this page does not expand them. A gene id the identity files do not name is kept as the source's own id with no door rather than turned into a symbol.

On citing what a search finds, Reactome says: It should be remembered that while we strive to contain the most current and accurate data, Reactome should not be used in citations where other primary sources of information are available. [R12] The record card prints the literature Reactome attaches to a curated pathway for that reason. The data are public domain: All data in the Reactome database and files derived from that data are licensed under the Creative Commons Public Domain Dedication (CC0). User may copy, modify, and distribute these data, even for commercial purposes, without asking for permission. Attribution is encouraged but not required. [R10] The pathway illustrations are licensed apart, under CC BY 4.0, and none is shown here.

A gene on this list is one Reactome places in this pathway in this release, and that is all the row says: it does not say the gene is expressed in a tissue or associated with a disease, which are the other two explorers' questions, read from other sources. Reactome's papers of record are [R01] [R02].

[R01] Ragueneau E, Gong C, Sinquin P, Sevilla C, Beavers D, Grentner A, et al. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Research 54:D673-D681. PMID 41251150, doi 10.1093/nar/gkaf1223.
[R02] Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, et al. (2024). The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research 52:D672-D678. PMID 37941124, doi 10.1093/nar/gkad1025.
[R10] Reactome, reactome.org. License Agreement. https://reactome.org/license, read 2026-09-09.
[R12] Reactome, reactome.org. Citing us. https://reactome.org/cite, read 2026-09-09.
[R13] Reactome, reactome.org. Download. https://reactome.org/download-data, read 2026-09-09.

Stable id: R-HSA-9758941.6
Class: Pathway
Species: Homo sapiens (human)
Inferred: no: a curated human pathway
Disease pathway: no
Released: 2022-06-09
Last updated: 2023-09-13
Events inside: 10, counted from the record

Gastrulation is the reorganization of the blastula to form the multilayered gastrula. During gastrulation, a portion of cells from the exterior of the epithelial epiblast layer migrate to the interior, where they form mesoderm and endoderm which, together with the outer layer of ectoderm (arising from epiblast cells that have not migrated), comprise the three cell layers that are characteristic of triploblastic metazoans (reviewed in Technau and Scholz 2003). In the human peri-implantation embryo, epiblast cells ingress through the primitive streak located in the posterior region of the embryonic disc to form the mesoderm and endoderm of the embryo proper (reviewed in Bardot and Hadjantonakis 2020, Ghimire et al. 2021, Zhai et al. 2021, Rossant and Tam 2022). In the mouse, a mammalian model organism, the embryo is cup-shaped instead of being disc-shaped (reviewed in Kojima et al. 2014). However, the morphogenetic process of germ layer formation is broadly conserved in both species.

The primitive streak forms at the posterior region of the epiblast where there is high signaling activity of NODAL, BMP, FGF and WNT pathways, which drive the allocation of cells to the mesoderm and endoderm lineages. In the primitive streak, the ingressing cells undergo epithelial-to-mesenchymal transition (reviewed in Amack 2021). Cells allocated to the mesoderm acquire a mesenchymal phenotype. Endodermal cells are reputed to revert back to an epithelial architecture through a mesenchymal-to-epithelial transition as they are integrated into the pre-existing layer of hypoblast. A recent study in mouse, however, revealed that ingressing cells that are destined for the endoderm undergo an incomplete or partial-EMT and retain some epithelial features prior to re-acquiring epithelialization (Scheibner et al. 2021).

During gastrulation in mice, extraembryonic mesoderm is formed first and is followed by mesoderm that populates the anterior structures, the head, face and heart of the embryo and next the mesoderm to the trunk. Endoderm is also formed in an anterior to posterior sequence, with endoderm emerging early in gastrulation populating the foregut, followed by the mid- and hind-gut. Along the anterior-posterior axis of the primitive streak, endoderm and axial mesoderm emerge from the anterior region, whereas mesoderm emerging from the mid- to posterior regions is allocated in a medial-lateral order to paraxial, intermediate and lateral plate mesoderm. Cells remaining in the overlying epiblast contribute to the ectoderm. Cells of the ectoderm are allocated to the neural ectoderm and to the surface ectoderm and the neural border cells that give rise to the neural crest cells. Patterning of the neuroectoderm is facilitated by the inductive interaction with prechordal plate and the notochord derived from the axial mesoderm.

Reading this pathway's record from Reactome (the pathway record).Still reading. A first read of a pathway can take a while; this page waits up to 35 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.

02The genes

Genes Reactome places in this human pathway

The mapping files place 120 genes in this human pathway; showing 101 to 120, in pages of 100, sorted by symbol for reading. The order carries no ranking. 1 of the rows shown carries an id the identity file does not name, kept as the source wrote it.

Genes Reactome places in this human pathway, page 2 of 2
Gene	Authority id	Mapping file id	Evidence codes
GeneSOX2	AuthorityHGNC:11195	Mapping file id6657 NCBI file	EvidenceIEA, TAS
GeneTBPL2	AuthorityHGNC:19841	Mapping file id387332 NCBI file	EvidenceIEA
GeneTBX6	AuthorityHGNC:11605	Mapping file id6911 NCBI file	EvidenceIEA
GeneTBXT	AuthorityHGNC:11515	Mapping file id6862 NCBI file	EvidenceIEA
GeneTCF7	AuthorityHGNC:11639	Mapping file id6932 NCBI file	EvidenceIEA
GeneTCF7L1	AuthorityHGNC:11640	Mapping file id83439 NCBI file	EvidenceIEA
GeneTCF7L2	AuthorityHGNC:11641	Mapping file id6934 NCBI file	EvidenceIEA
GeneTEAD2	AuthorityHGNC:11715	Mapping file id8463 NCBI file	EvidenceIEA
GeneTEAD4	AuthorityHGNC:11717	Mapping file id7004 NCBI file	EvidenceIEA
GeneTFAP2A	AuthorityHGNC:11742	Mapping file id7020 NCBI file	EvidenceIEA, TAS
GeneTFAP2B	AuthorityHGNC:11743	Mapping file id7021 NCBI file	EvidenceIEA, TAS
GeneTFAP2C	AuthorityHGNC:11744	Mapping file id7022 NCBI file	EvidenceIEA, TAS
GeneTRIM33	AuthorityHGNC:16290	Mapping file id51592 NCBI file	EvidenceIEA
GeneWNT3A	AuthorityHGNC:15983	Mapping file id89780 NCBI file	EvidenceIEA
GeneYAP1	AuthorityHGNC:16262	Mapping file id10413 NCBI file	EvidenceIEA
GeneZEB2	AuthorityHGNC:14881	Mapping file id9839 NCBI file	EvidenceIEA
GeneZIC1	AuthorityHGNC:12872	Mapping file id7545 NCBI file	EvidenceIEA
GeneZIC2	AuthorityHGNC:12873	Mapping file id7546 NCBI file	EvidenceIEA
GeneZNF521	AuthorityHGNC:24605	Mapping file id25925 NCBI file	EvidenceIEA
Geneno symbol in the identity file	Authoritynone	Mapping file idNR_144432 as written	EvidenceIEA

Evidence codes on this page: IEA, TAS, as the mapping file writes them; a row carrying two was written twice by the file, once under each. The mapping file id says which file placed the gene: an NCBI Gene id from NCBI2Reactome_All_Levels.txt, an Ensembl gene id from Ensembl2Reactome_All_Levels.txt. The two files can disagree about a code, so a row's codes are the one file's view. Measured by this site's build over this release on 2026-09-09: of the 138,908 human pathway-gene pairs both files place, 207 (0.149 per cent, over 47 genes) carry TAS in the Ensembl file where the NCBI rows carry IEA alone.

Reactome mapping files, the human rows for this pathway · Reactome release 97 · read 2026-09-09 · Reactome downloads"NCBI2Reactome_All_Levels.txt" and "Ensembl2Reactome_All_Levels.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.

03The hierarchy

Parents and children in this release's hierarchy

Parents

Developmental BiologyR-HSA-12667381,589 genes

Children

Reactome's hierarchy is a graph rather than a tree: a pathway can sit under more than one parent, and the gene counts are each pathway's own placements at every level under it, so a parent's count is not the sum of its children's.

Reactome, the human pathway list and hierarchy relationship file · Reactome release 97 · read 2026-09-09 · Reactome downloads"ReactomePathways.txt" and "ReactomePathwaysRelation.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.