Mesodermal commitment pathway (Bos taurus)

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PIAS1AHDC1CRTC1NLKDIP2APBX3ZFHX4BCORL1ELK412254NucleusEctodermSpecificationPLCH1WDFY2C2orf44PRKACAEOMESNOGGDF3RARGPARP8TEAD2NODALWDFY2GRHL2HES7SMAD1SESN1RGS10SMAD3FOXC1KLF5JAK2ZIC2CSRP2CUL4BSMAD4DLL1YAP1EXT1DDAH1SESN1TRIM28ATP8B2CCND1PAX6ASCC3ZNF462NABP2MEIS1BMP4bta-mir-302cHTTTEAD1BMPR2CEP250C11orf30MACF1PBX1bta-mir-125b-1ARID5BTBX6CCDC6ELP4ASCC3TACVR2ASCHIP1HNF4AADAM19PLCH1C9orf72TBX3PARP8GATA6TRIM5SMAD6WNT3AFOXC1CEP250TCF7L1PHF6ZNF462FGFR1MIR373LATS1TBX1CCDC88AKDM6AAXIN1HPRT1ARL4AEPB41L5MBTD1PBX1BMP7ACVR2BNANOGFOXA1TCF4SNAI1FOXA2TOX3POU5F1CSRP2MIXL1RPL38SLC2A12ARL4AFOXH1PITX2CHRDFOXC2WNT3ACACAC11orf30KLF4C11orf30SETD2BMPR1ATOXINHBATRERF1CCND1C6orf201SOX2MSGN1LEF1PRKAR1Abta-mir-200aHMGA2SRFTWSG1FOXA2HAND1PPP2CAATP8B2HPRT1ACVR1SMAD2DKK1EXT2RARBLEFTY1BHLHE40TRERF1VAV3TCF4AMHGATA3MIR653MIR372bta-mir-141SOX17MIR200A and MIR141 Targets(Induced in Endoderm)MIR653 Targets(Induced in Ectoderm)MIR653 Targets(Induced in Stem Cells)MIR372 Targets(Induced in Stem Cells)MIR372 Targets(Induced in Ectoderm)MIR373 Targets(Induced in Stem Cells)MIR373 Targets(Induced in Ectoderm)LEFTY2NANOGFZD47FZD5FZD8FGF8AXIN2MesodermSpecificationNFE2L26SOX2bta-mir-375MIR375 Targets(Induced in Ectoderm)UBR5SOX21C1QBPZIC3TRIM71DNMT3BWDHD1JARID2CTBP2MTF2ZIC5AEBP2NCAPG2ZNF281GRHL2TET1MIR375 Targets(Induced in Stem Cells)


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: https://www.synapse.org/#!Synapse:syn1773109

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.
HomologyConvert 
This pathway was inferred from Homo sapiens pathway WP2857(80151) with a 19.0% conversion rate.

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Quality Tags

Ontology Terms

 

Bibliography

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  1. White PH, Chapman DL; ''Dll1 is a downstream target of Tbx6 in the paraxial mesoderm.''; Genesis, 2005 PubMed Europe PMC Scholia
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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

History

CompareRevisionActionTimeUserComment
117550view11:17, 21 May 2021EweitzModified title
87781view11:12, 25 July 2016ElisaOntology Term : 'regulatory pathway' added !
80763view15:25, 30 June 2015MkutmonNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
ACACAGeneProduct
ACVR1ENSG00000115170 (Ensembl)
ACVR2AENSG00000121989 (Ensembl)
ACVR2BENSG00000114739 (Ensembl)
ADAM19GeneProduct
AEBP2GeneProduct
AHDC1GeneProduct
AMHENSG00000104899 (Ensembl)
ARID5BGeneProduct
ARL4AGeneProduct
ASCC3GeneProduct
ATP8B2GeneProduct
AXIN1ENSG00000103126 (Ensembl)
AXIN2GeneProductENSBTAG00000030162 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000168646
BCORL1GeneProduct
BHLHE40GeneProduct
BMP4ENSG00000125378 (Ensembl)
BMP7ENSG00000101144 (Ensembl)
BMPR1AENSG00000107779 (Ensembl)
BMPR2ENSG00000204217 (Ensembl)
C11orf30GeneProduct
C1QBPGeneProduct
C2orf44GeneProduct
C6orf201GeneProduct
C9orf72GeneProduct
CCDC6GeneProduct
CCDC88AGeneProduct
CCND1GeneProduct
CEP250GeneProduct
CHRDENSG00000090539 (Ensembl)
CRTC1GeneProduct
CSRP2GeneProduct
CTBP2GeneProduct
CUL4BGeneProduct
DDAH1GeneProduct
DIP2AGeneProduct
DKK1ENSG00000107984 (Ensembl)
DLL1GeneProductENSBTAG00000031476 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000198719
DNMT3BGeneProduct
ELK4GeneProduct
ELP4GeneProduct
EOMESENSG00000163508 (Ensembl)
EPB41L5ENSG00000115109 (Ensembl)
EXT1ENSG00000182197 (Ensembl)
EXT2ENSG00000151348 (Ensembl)
FGF8GeneProductENSBTAG00000001530 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000107831
FGFR1ENSG00000077782 (Ensembl)
FOXA1GeneProduct
FOXA2GeneProduct
FOXC1GeneProduct
FOXC1ENSG00000054598 (Ensembl)
FOXC2ENSG00000176692 (Ensembl)
FOXH1ENSG00000160973 (Ensembl)
FZD4GeneProductENSBTAG00000040128 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000174804
FZD5GeneProductENSBTAG00000020957 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000163251
FZD8GeneProductENSBTAG00000015072 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000177283
GATA3GeneProduct
GATA6GeneProduct
GDF3ENSG00000184344 (Ensembl)
GRHL2GeneProduct
HAND1ENSG00000113196 (Ensembl)
HES7GeneProductENSBTAG00000012436 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000179111
HMGA2ENSG00000149948 (Ensembl)
HNF4AGeneProduct
HPRT1GeneProduct
HTTENSG00000197386 (Ensembl)
INHBAENSG00000122641 (Ensembl)
JAK2ENSG00000096968 (Ensembl)
JARID2GeneProduct
KDM6AENSG00000147050 (Ensembl)
KLF4ENSG00000136826 (Ensembl)
KLF5GeneProduct
LATS1GeneProductENSBTAG00000015076 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000131023
LEF1ENSG00000138795 (Ensembl)
LEFTY1GeneProductENSBTAG00000002855 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000243709
LEFTY2GeneProductENSBTAG00000002855 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000143768
MACF1ENSG00000127603 (Ensembl)
MBTD1GeneProduct
MEIS1GeneProduct
MIR372Rna
MIR373Rna
MIR653Rna
MIXL1GeneProductENSBTAG00000002139 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000185155
MSGN1GeneProduct
MTF2GeneProduct
NABP2GeneProduct
NANOGGeneProductENSBTAG00000020916 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000111704
NANOGENSG00000111704 (Ensembl)
NCAPG2GeneProduct
NFE2L2GeneProductENSBTAG00000019255 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000116044
NLKGeneProduct
NODALENSG00000156574 (Ensembl)
NOGENSG00000183691 (Ensembl)
PARP8GeneProduct
PAX6GeneProduct
PBX1GeneProduct
PBX3GeneProduct
PHF6GeneProduct
PIAS1GeneProduct
PITX2GeneProduct
PLCH1GeneProduct
POU5F1GeneProductENSBTAG00000001873 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000204531
PPP2CAENSG00000113575 (Ensembl)
PRKACAENSG00000072062 (Ensembl)
PRKAR1AENSG00000108946 (Ensembl)
RARBGeneProduct
RARGGeneProduct
RGS10GeneProduct
RPL38ENSG00000172809 (Ensembl)
SCHIP1GeneProduct
SESN1GeneProduct
SETD2ENSG00000181555 (Ensembl)
SLC2A12GeneProduct
SMAD1ENSG00000170365 (Ensembl)
SMAD2ENSG00000175387 (Ensembl)
SMAD3ENSG00000166949 (Ensembl)
SMAD4ENSG00000141646 (Ensembl)
SMAD6GeneProductENSBTAG00000000625 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000137834
SNAI1ENSG00000124216 (Ensembl)
SOX17GeneProductENSBTAG00000005748 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000164736
SOX21GeneProduct
SOX2GeneProductENSBTAG00000011598 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000181449
SRFENSG00000112658 (Ensembl)
TGeneProduct
TBX1ENSG00000184058 (Ensembl)
TBX3ENSG00000135111 (Ensembl)
TBX6GeneProductENSBTAG00000009046 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000149922
TCF4GeneProduct
TCF7L1ENSG00000152284 (Ensembl)
TEAD1ENSG00000187079 (Ensembl)
TEAD2ENSG00000074219 (Ensembl)
TET1GeneProduct
TOXGeneProduct
TOX3GeneProduct
TRERF1GeneProduct
TRIM28GeneProduct
TRIM5GeneProduct
TRIM71GeneProduct
TWSG1ENSG00000128791 (Ensembl)
UBR5GeneProduct
VAV3GeneProduct
WDFY2GeneProduct
WDHD1GeneProduct
WNT3AENSG00000154342 (Ensembl)
WNT3ENSG00000108379 (Ensembl)
YAP1ENSG00000137693 (Ensembl)
ZFHX4GeneProduct
ZIC2GeneProduct
ZIC3GeneProduct
ZIC5GeneProduct
ZNF281GeneProduct
ZNF462GeneProduct
bta-mir-125b-1RnaENSBTAG00000029925 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000207971
bta-mir-141RnaENSBTAG00000036410 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000207708
bta-mir-200aRnaENSBTAG00000029998 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000207607
bta-mir-302cGeneProductENSBTAG00000036429 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000199102
bta-mir-375RnaENSBTAG00000029763 (Ensembl) HomologyConvert: Homo sapiens to Bos taurus: Original ID = En:ENSG00000198973

Annotated Interactions

No annotated interactions
Retrieved from "https://classic.wikipathways.org/index.php/Pathway:WP3183"
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