Mesodermal commitment pathway (Homo sapiens)

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ArcPathVisio Brace Ellipse EndoplasmicReticulum GolgiApparatus HexagonPathVisio MimDegradation Mitochondria Octagon PentagonPathVisio Rectangle RoundedRectangle SarcoplasmicReticulum TriangleEquilateralEast TrianglePathVisio none PIAS1NLKBCORL1DIP2AAHDC1CRTC1ELK4PBX3ZFHX4MIR375 Targets (Induced in Ectoderm)EXT1EXT2NucleusEctoderm SpecificationPLCH1WDFY2SESN1DDAH1PBX1PARP8HPRT1TCF4ACACATRERF1MIR653 Targets (Induced in Stem Cells)WDFY2PARP8RGS10CUL4BSESN1SCHIP1PLCH1TRIM5CEP250PBX1SLC2A12C11orf30ATP8B2HPRT1VAV3TCF4MIR653 Targets (Induced in Ectoderm)C2orf44CSRP2CCND1CCDC6ASCC3CCDC88AARL4AC6orf201MIR372 Targets (Induced in Stem Cells)PRKACAEOMESNOGGDF3RARGGRHL2ASCC3NABP2ZNF462MBTD1TOXTRERF1MIR373 Targets (Induced in Stem Cells)TEAD2NODALHES7SMAD1SMAD3FOXC1KLF5PAX6ARID5BHNF4AGATA6FOXC1FOXA1PITX2FOXA2RARBBHLHE40GATA3SOX17MIR200A and MIR141 Targets (Induced in Endoderm)JAK2ZIC2TRIM28MEIS1ADAM19FOXA2MSGN1FGF8AXIN2SMAD4DLL1YAP1ATP8B2CEP250C11orf30C9orf72CSRP2ARL4ACCND1MIR372 Targets (Induced in Ectoderm)ZNF462ELP4PHF6TOX3C11orf30MIR373 Targets (Induced in Ectoderm)BMP4MIR302CHTTTEAD1BMPR2MACF1MIR125B1TBX6TACVR2ATBX3SMAD6WNT3ATCF7L1FGFR1MIR373LATS1TBX1KDM6AAXIN1EPB41L5BMP7ACVR2BNANOGSNAI1POU5F1NANOGMIXL1RPL38FOXH1CHRDFOXC2WNT3KLF4SETD2BMPR1AINHBASOX2LEF1PRKAR1AMIR200AMIR141-5pHMGA2SRFTWSG1HAND1PPP2CAACVR1SMAD2DKK1LEFTY1LEFTY2AMHMIR653MIR372FZD4FZD5FZD8Mesoderm SpecificationNFE2L2SOX2MIR375UBR5SOX21C1QBPZIC3TRIM71DNMT3BWDHD1JARID2CTBP2MTF2ZIC5AEBP2NCAPG2ZNF281GRHL2TET1MIR375 Targets (Induced in Stem Cells)Name: Mesodermal commitment pathwayOrganism: Homo sapiens


Description

Model depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lines, following differentiation to multiple lineages (ectoderm, mesoderm, endoderm, embryoid body). The underlying genomic data can be obtained from [www.synapse.org](https://www.synapse.org/#!Synapse:syn1773109). Proteins on this pathway have targeted assays available via the [CPTAC Assay Portal](https://assays.cancer.gov/available_assays?wp_id=WP2857).

Comments

 
Developed using Gene Ontology mesoderm process associated genes and interactions from the software NetPerspective (AltAnalyze). A preliminary layout was obtained using the exported SIF file in Cytoscape's Cerebral plugin.

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Quality Tags

Image:Featured.pngFeatured version
Image:Curated.pngApproved version
Image:MissingXref.pngAnnotate nodes

Ontology Terms

 

Bibliography

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  1. Takemoto T, Uchikawa M, Yoshida M, Bell DM, Lovell-Badge R, Papaioannou VE, Kondoh H; ''Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells.''; Nature, 2011 PubMed Europe PMC Scholia
  2. Wong SS, Ritner C, Ramachandran S, Aurigui J, Pitt C, Chandra P, Ling VB, Yabut O, Bernstein HS; ''miR-125b promotes early germ layer specification through Lin28/let-7d and preferential differentiation of mesoderm in embryonic stem cells.''; PLoS One, 2012 PubMed Europe PMC Scholia
  3. White PH, Chapman DL; ''Dll1 is a downstream target of Tbx6 in the paraxial mesoderm.''; Genesis, 2005 PubMed Europe PMC Scholia
  4. Yamaguchi TP, Takada S, Yoshikawa Y, Wu N, McMahon AP; ''T (Brachyury) is a direct target of Wnt3a during paraxial mesoderm specification.''; Genes Dev, 1999 PubMed Europe PMC Scholia
  5. Chen YL, Liu B, Zhou ZN, Hu RY, Fei C, Xie ZH, Ding X; ''Smad6 inhibits the transcriptional activity of Tbx6 by mediating its degradation.''; J Biol Chem, 2009 PubMed Europe PMC Scholia
  6. Bessho Y, Miyoshi G, Sakata R, Kageyama R; ''Hes7: a bHLH-type repressor gene regulated by Notch and expressed in the presomitic mesoderm.''; Genes Cells, 2001 PubMed Europe PMC Scholia
  7. Barroso-delJesus A, Lucena-Aguilar G, Sanchez L, Ligero G, Gutierrez-Aranda I, Menendez P; ''The Nodal inhibitor Lefty is negatively modulated by the microRNA miR-302 in embryonic stem cells.''; FASEB J, 2011 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
137825
Featured
Approved
view06:48, 8 March 2025EgonwModified description
118395view14:06, 27 May 2021Mkutmonpublication ref fix
116397view00:00, 7 May 2021EweitzModified title
110685view13:26, 28 May 2020Marvin M2changed types unknown to geneproducts
106642view21:04, 12 September 2019KhanspersModified description
105645view05:10, 10 August 2019KhanspersModified description
102044view18:49, 26 November 2018Khanspersfixed labels
101908view17:03, 16 November 2018EgonwRemoved "undefined" as data source.
87780view11:11, 25 July 2016ElisaOntology Term : 'regulatory pathway' added !
85459view15:25, 18 May 2016Mshel016Adding Ensembl annotations
85452view06:44, 17 May 2016Mkutmonfix broken annotations
85446view13:46, 16 May 2016Mshel016Quick edit to datanode annotation or property
85445view13:34, 16 May 2016Mshel016Quick edit to datanode annotation or property
85444view13:26, 16 May 2016Mshel016Quick edit to datanode annotation or property
80151view18:50, 14 May 2015KhanspersChanged color and type for miRNA nodes
79850view03:35, 20 April 2015NsalomonisModified description
78577view14:50, 7 January 2015MaintBotadded missing graphIds
77690view18:30, 8 October 2014NsalomonisSpecify description
77685view19:42, 7 October 2014NsalomonisNew pathway

External references

DataNodes

View all...
Name  â†“Type  â†“Database reference  â†“Comment  â†“
ACACAGeneProductENSG00000278540 (Ensembl)
ACVR1GeneProductENSG00000115170 (Ensembl)
ACVR2AGeneProductENSG00000121989 (Ensembl)
ACVR2BGeneProductENSG00000114739 (Ensembl)
ADAM19GeneProductENSG00000135074 (Ensembl)
AEBP2GeneProductENSG00000139154 (Ensembl)
AHDC1GeneProductENSG00000126705 (Ensembl)
AMHGeneProductENSG00000104899 (Ensembl)
ARID5BGeneProductENSG00000150347 (Ensembl)
ARL4AGeneProductENSG00000122644 (Ensembl)
ASCC3GeneProductENSG00000112249 (Ensembl)
ATP8B2GeneProductENSG00000143515 (Ensembl)
AXIN1GeneProductENSG00000103126 (Ensembl)
AXIN2GeneProductENSG00000168646 (Ensembl)
BCORL1GeneProductENSG00000085185 (Ensembl)
BHLHE40GeneProductENSG00000134107 (Ensembl)
BMP4GeneProductENSG00000125378 (Ensembl)
BMP7GeneProductENSG00000101144 (Ensembl)
BMPR1AGeneProductENSG00000107779 (Ensembl)
BMPR2GeneProductENSG00000204217 (Ensembl)
C11orf30GeneProductENSG00000158636 (Ensembl)
C1QBPGeneProductENSG00000108561 (Ensembl)
C2orf44GeneProductENSG00000163026 (Ensembl)
C6orf201GeneProductENSG00000185689 (Ensembl)
C9orf72GeneProductENSG00000147894 (Ensembl)
CCDC6GeneProductENSG00000108091 (Ensembl)
CCDC88AGeneProductENSG00000115355 (Ensembl)
CCND1GeneProductENSG00000110092 (Ensembl)
CEP250GeneProductENSG00000126001 (Ensembl)
CHRDGeneProductENSG00000090539 (Ensembl)
CRTC1GeneProductENSG00000105662 (Ensembl)
CSRP2GeneProductENSG00000175183 (Ensembl)
CTBP2GeneProductENSG00000175029 (Ensembl)
CUL4BGeneProductENSG00000158290 (Ensembl)
DDAH1GeneProductENSG00000153904 (Ensembl)
DIP2AGeneProductENSG00000160305 (Ensembl)
DKK1GeneProductENSG00000107984 (Ensembl)
DLL1GeneProductENSG00000198719 (Ensembl)
DNMT3BGeneProductENSG00000088305 (Ensembl)
ELK4GeneProductENSG00000158711 (Ensembl)
ELP4GeneProductENSG00000109911 (Ensembl)
EOMESGeneProductENSG00000163508 (Ensembl)
EPB41L5GeneProductENSG00000115109 (Ensembl)
EXT1GeneProductENSG00000182197 (Ensembl)
EXT2GeneProductENSG00000151348 (Ensembl)
FGF8GeneProductENSG00000107831 (Ensembl)
FGFR1GeneProductENSG00000077782 (Ensembl)
FOXA1GeneProductENSG00000129514 (Ensembl)
FOXA2GeneProductENSG00000125798 (Ensembl)
FOXC1GeneProductENSG00000054598 (Ensembl)
FOXC2GeneProductENSG00000176692 (Ensembl)
FOXH1GeneProductENSG00000160973 (Ensembl)
FZD4GeneProductENSG00000174804 (Ensembl)
FZD5GeneProductENSG00000163251 (Ensembl)
FZD8GeneProductENSG00000177283 (Ensembl)
GATA3GeneProductENSG00000107485 (Ensembl)
GATA6GeneProductENSG00000141448 (Ensembl)
GDF3GeneProductENSG00000184344 (Ensembl)
GRHL2GeneProductENSG00000083307 (Ensembl)
HAND1GeneProductENSG00000113196 (Ensembl)
HES7GeneProductENSG00000179111 (Ensembl)
HMGA2GeneProductENSG00000149948 (Ensembl)
HNF4AGeneProductENSG00000101076 (Ensembl)
HPRT1GeneProductENSG00000165704 (Ensembl)
HTTGeneProductENSG00000197386 (Ensembl)
INHBAGeneProductENSG00000122641 (Ensembl)
JAK2GeneProductENSG00000096968 (Ensembl)
JARID2GeneProductENSG00000008083 (Ensembl)
KDM6AGeneProductENSG00000147050 (Ensembl)
KLF4GeneProductENSG00000136826 (Ensembl)
KLF5GeneProductENSG00000102554 (Ensembl)
LATS1GeneProductENSG00000131023 (Ensembl)
LEF1GeneProductENSG00000138795 (Ensembl)
LEFTY1GeneProductENSG00000243709 (Ensembl)
LEFTY2GeneProductENSG00000143768 (Ensembl)
MACF1GeneProductENSG00000127603 (Ensembl)
MBTD1GeneProductENSG00000011258 (Ensembl)
MEIS1GeneProductENSG00000143995 (Ensembl)
MIR125B1RnaENSG00000207971 (Ensembl)
MIR141-5pRnaENSG00000207708 (Ensembl)
MIR200ARnaENSG00000207607 (Ensembl)
MIR302CGeneProductENSG00000199102 (Ensembl)
MIR372RnaENSG00000199095 (Ensembl)
MIR373RnaENSG00000199143 (Ensembl)
MIR375RnaENSG00000198973 (Ensembl)
MIR653RnaENSG00000199143 (Ensembl)
MIXL1GeneProductENSG00000185155 (Ensembl)
MSGN1GeneProductENSG00000151379 (Ensembl)
MTF2GeneProductENSG00000143033 (Ensembl)
NABP2GeneProductENSG00000139579 (Ensembl)
NANOGGeneProductENSG00000111704 (Ensembl)
NCAPG2GeneProductENSG00000146918 (Ensembl)
NFE2L2GeneProductENSG00000116044 (Ensembl)
NLKGeneProductENSG00000087095 (Ensembl)
NODALGeneProductENSG00000156574 (Ensembl)
NOGGeneProductENSG00000183691 (Ensembl)
PARP8GeneProductENSG00000151883 (Ensembl)
PAX6GeneProductENSG00000007372 (Ensembl)
PBX1GeneProductENSG00000185630 (Ensembl)
PBX3GeneProductENSG00000167081 (Ensembl)
PHF6GeneProductENSG00000156531 (Ensembl)
PIAS1GeneProductENSG00000033800 (Ensembl)
PITX2GeneProductENSG00000164093 (Ensembl)
PLCH1GeneProductENSG00000114805 (Ensembl)
POU5F1GeneProductENSG00000204531 (Ensembl)
PPP2CAGeneProductENSG00000113575 (Ensembl)
PRKACAGeneProductENSG00000072062 (Ensembl)
PRKAR1AGeneProductENSG00000108946 (Ensembl)
RARBGeneProductENSG00000077092 (Ensembl)
RARGGeneProductENSG00000172819 (Ensembl)
RGS10GeneProductENSG00000148908 (Ensembl)
RPL38GeneProductENSG00000172809 (Ensembl)
SCHIP1GeneProductENSG00000151967 (Ensembl)
SESN1GeneProductENSG00000080546 (Ensembl)
SETD2GeneProductENSG00000181555 (Ensembl)
SLC2A12GeneProductENSG00000146411 (Ensembl)
SMAD1GeneProductENSG00000170365 (Ensembl)
SMAD2GeneProductENSG00000175387 (Ensembl)
SMAD3GeneProductENSG00000166949 (Ensembl)
SMAD4GeneProductENSG00000141646 (Ensembl)
SMAD6GeneProductENSG00000137834 (Ensembl)
SNAI1GeneProductENSG00000124216 (Ensembl)
SOX17GeneProductENSG00000164736 (Ensembl)
SOX21GeneProductENSG00000125285 (Ensembl)
SOX2GeneProductENSG00000181449 (Ensembl)
SRFGeneProductENSG00000112658 (Ensembl)
T
TBX1GeneProductENSG00000184058 (Ensembl)
TBX3GeneProductENSG00000135111 (Ensembl)
TBX6GeneProductENSG00000149922 (Ensembl)
TCF4GeneProductENSG00000196628 (Ensembl)
TCF7L1GeneProductENSG00000152284 (Ensembl)
TEAD1GeneProductENSG00000187079 (Ensembl)
TEAD2GeneProductENSG00000074219 (Ensembl)
TET1GeneProductENSG00000138336 (Ensembl)
TOX3GeneProductENSG00000103460 (Ensembl)
TOXGeneProductENSG00000198846 (Ensembl)
TRERF1GeneProductENSG00000124496 (Ensembl)
TRIM28GeneProductENSG00000130726 (Ensembl)
TRIM5GeneProductENSG00000132256 (Ensembl)
TRIM71GeneProductENSG00000206557 (Ensembl)
TWSG1GeneProductENSG00000128791 (Ensembl)
UBR5GeneProductENSG00000104517 (Ensembl)
VAV3GeneProductENSG00000134215 (Ensembl)
WDFY2GeneProductENSG00000139668 (Ensembl)
WDHD1GeneProductENSG00000198554 (Ensembl)
WNT3AGeneProductENSG00000154342 (Ensembl)
WNT3GeneProductENSG00000108379 (Ensembl)
YAP1GeneProductENSG00000137693 (Ensembl)
ZFHX4GeneProductENSG00000091656 (Ensembl)
ZIC2GeneProductENSG00000043355 (Ensembl)
ZIC3GeneProductENSG00000156925 (Ensembl)
ZIC5GeneProductENSG00000139800 (Ensembl)
ZNF281GeneProductENSG00000162702 (Ensembl)
ZNF462GeneProductENSG00000148143 (Ensembl)

Annotated Interactions

No annotated interactions
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