Mesodermal commitment pathway (Homo sapiens)

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PBX3PIAS1BCORL1CRTC1DIP2AELK4ZFHX4NLKAHDC176643NucleusEctoderm SpecificationPLCH1WDFY2C2orf44PRKACAEOMESNOGGDF3RARGPARP8TEAD2NODALWDFY2GRHL2HES7SMAD1SESN1RGS10SMAD3FOXC1KLF5JAK2ZIC2CSRP2CUL4BSMAD4DLL1YAP1EXT1DDAH1SESN1TRIM28ATP8B2CCND1PAX6ASCC3ZNF462NABP2MEIS1BMP4MIR302CHTTTEAD1BMPR2CEP250C11orf30MACF1PBX1MIR125B1ARID5BTBX6CCDC6ELP4ASCC3TACVR2ASCHIP1HNF4AADAM19PLCH1C9orf72TBX3PARP8GATA6TRIM5SMAD6WNT3AFOXC1CEP250TCF7L1PHF6ZNF462FGFR1MIR373LATS1TBX1CCDC88AKDM6AAXIN1HPRT1ARL4AEPB41L5MBTD1PBX1BMP7ACVR2BNANOGFOXA1TCF4SNAI1FOXA2TOX3POU5F1CSRP2MIXL1RPL38SLC2A12ARL4AFOXH1PITX2CHRDFOXC2WNT3ACACAC11orf30KLF4C11orf30SETD2BMPR1ATOXINHBATRERF1CCND1C6orf201SOX2MSGN1LEF1PRKAR1AMIR200AHMGA2SRFTWSG1FOXA2HAND1PPP2CAATP8B2HPRT1ACVR1SMAD2DKK1EXT2RARBLEFTY1BHLHE40TRERF1VAV3TCF4AMHGATA3MIR653MIR372MIR141-5pSOX17MIR200A 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)LEFTY2NANOGFZD42FZD5FZD8FGF8AXIN2Mesoderm SpecificationNFE2L25SOX2MIR375MIR375 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.

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Quality Tags

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

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CompareRevisionActionTimeUserComment
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

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NameTypeDatabase referenceComment
ACACAGeneProductENSG00000278540 (Ensembl)
ACVR1ENSG00000115170 (Ensembl)
ACVR2AENSG00000121989 (Ensembl)
ACVR2BENSG00000114739 (Ensembl)
ADAM19GeneProductENSG00000135074 (Ensembl)
AEBP2GeneProductENSG00000139154 (Ensembl)
AHDC1GeneProductENSG00000126705 (Ensembl)
AMHENSG00000104899 (Ensembl)
ARID5BGeneProductENSG00000150347 (Ensembl)
ARL4AGeneProductENSG00000122644 (Ensembl)
ASCC3GeneProductENSG00000112249 (Ensembl)
ATP8B2GeneProductENSG00000143515 (Ensembl)
AXIN1ENSG00000103126 (Ensembl)
AXIN2GeneProductENSG00000168646 (Ensembl)
BCORL1GeneProductENSG00000085185 (Ensembl)
BHLHE40GeneProductENSG00000134107 (Ensembl)
BMP4ENSG00000125378 (Ensembl)
BMP7ENSG00000101144 (Ensembl)
BMPR1AENSG00000107779 (Ensembl)
BMPR2ENSG00000204217 (Ensembl)
C11orf30GeneProductENSG00000158636 (Ensembl)
C1QBPGeneProductENSG00000108561 (Ensembl)
C2orf44GeneProductENSG00000163026 (Ensembl)
C6orf201GeneProductENSG00000185689 (Ensembl)
C9orf72GeneProductENSG00000147894 (Ensembl)
CCDC6GeneProductENSG00000108091 (Ensembl)
CCDC88AGeneProductENSG00000115355 (Ensembl)
CCND1GeneProductENSG00000110092 (Ensembl)
CEP250GeneProductENSG00000126001 (Ensembl)
CHRDENSG00000090539 (Ensembl)
CRTC1GeneProductENSG00000105662 (Ensembl)
CSRP2GeneProductENSG00000175183 (Ensembl)
CTBP2GeneProductENSG00000175029 (Ensembl)
CUL4BGeneProductENSG00000158290 (Ensembl)
DDAH1GeneProductENSG00000153904 (Ensembl)
DIP2AGeneProductENSG00000160305 (Ensembl)
DKK1ENSG00000107984 (Ensembl)
DLL1GeneProductENSG00000198719 (Ensembl)
DNMT3BGeneProductENSG00000088305 (Ensembl)
ELK4GeneProductENSG00000158711 (Ensembl)
ELP4GeneProductENSG00000109911 (Ensembl)
EOMESENSG00000163508 (Ensembl)
EPB41L5ENSG00000115109 (Ensembl)
EXT1ENSG00000182197 (Ensembl)
EXT2ENSG00000151348 (Ensembl)
FGF8GeneProductENSG00000107831 (Ensembl)
FGFR1ENSG00000077782 (Ensembl)
FOXA1GeneProductENSG00000129514 (Ensembl)
FOXA2GeneProductENSG00000125798 (Ensembl)
FOXC1GeneProductENSG00000054598 (Ensembl)
FOXC2ENSG00000176692 (Ensembl)
FOXH1ENSG00000160973 (Ensembl)
FZD4GeneProductENSG00000174804 (Ensembl)
FZD5GeneProductENSG00000163251 (Ensembl)
FZD8GeneProductENSG00000177283 (Ensembl)
GATA3GeneProductENSG00000107485 (Ensembl)
GATA6GeneProductENSG00000141448 (Ensembl)
GDF3ENSG00000184344 (Ensembl)
GRHL2GeneProductENSG00000083307 (Ensembl)
HAND1ENSG00000113196 (Ensembl)
HES7GeneProductENSG00000179111 (Ensembl)
HMGA2ENSG00000149948 (Ensembl)
HNF4AGeneProductENSG00000101076 (Ensembl)
HPRT1GeneProductENSG00000165704 (Ensembl)
HTTENSG00000197386 (Ensembl)
INHBAENSG00000122641 (Ensembl)
JAK2ENSG00000096968 (Ensembl)
JARID2GeneProductENSG00000008083 (Ensembl)
KDM6AENSG00000147050 (Ensembl)
KLF4ENSG00000136826 (Ensembl)
KLF5GeneProductENSG00000102554 (Ensembl)
LATS1GeneProductENSG00000131023 (Ensembl)
LEF1ENSG00000138795 (Ensembl)
LEFTY1GeneProductENSG00000243709 (Ensembl)
LEFTY2GeneProductENSG00000143768 (Ensembl)
MACF1ENSG00000127603 (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)
NODALENSG00000156574 (Ensembl)
NOGENSG00000183691 (Ensembl)
PARP8GeneProductENSG00000151883 (Ensembl)
PAX6GeneProductENSG00000007372 (Ensembl)
PBX1GeneProductENSG00000185630 (Ensembl)
PBX3GeneProductENSG00000167081 (Ensembl)
PHF6GeneProductENSG00000156531 (Ensembl)
PIAS1GeneProductENSG00000033800 (Ensembl)
PITX2GeneProductENSG00000164093 (Ensembl)
PLCH1GeneProductENSG00000114805 (Ensembl)
POU5F1GeneProductENSG00000204531 (Ensembl)
PPP2CAENSG00000113575 (Ensembl)
PRKACAENSG00000072062 (Ensembl)
PRKAR1AENSG00000108946 (Ensembl)
RARBGeneProductENSG00000077092 (Ensembl)
RARGGeneProductENSG00000172819 (Ensembl)
RGS10GeneProductENSG00000148908 (Ensembl)
RPL38ENSG00000172809 (Ensembl)
SCHIP1GeneProductENSG00000151967 (Ensembl)
SESN1GeneProductENSG00000080546 (Ensembl)
SETD2ENSG00000181555 (Ensembl)
SLC2A12GeneProductENSG00000146411 (Ensembl)
SMAD1ENSG00000170365 (Ensembl)
SMAD2ENSG00000175387 (Ensembl)
SMAD3ENSG00000166949 (Ensembl)
SMAD4ENSG00000141646 (Ensembl)
SMAD6GeneProductENSG00000137834 (Ensembl)
SNAI1ENSG00000124216 (Ensembl)
SOX17GeneProductENSG00000164736 (Ensembl)
SOX21GeneProductENSG00000125285 (Ensembl)
SOX2GeneProductENSG00000181449 (Ensembl)
SRFENSG00000112658 (Ensembl)
TGeneProduct
TBX1ENSG00000184058 (Ensembl)
TBX3ENSG00000135111 (Ensembl)
TBX6GeneProductENSG00000149922 (Ensembl)
TCF4GeneProductENSG00000196628 (Ensembl)
TCF7L1ENSG00000152284 (Ensembl)
TEAD1ENSG00000187079 (Ensembl)
TEAD2ENSG00000074219 (Ensembl)
TET1GeneProductENSG00000138336 (Ensembl)
TOX3GeneProductENSG00000103460 (Ensembl)
TOXGeneProductENSG00000198846 (Ensembl)
TRERF1GeneProductENSG00000124496 (Ensembl)
TRIM28GeneProductENSG00000130726 (Ensembl)
TRIM5GeneProductENSG00000132256 (Ensembl)
TRIM71GeneProductENSG00000206557 (Ensembl)
TWSG1ENSG00000128791 (Ensembl)
UBR5GeneProductENSG00000104517 (Ensembl)
VAV3GeneProductENSG00000134215 (Ensembl)
WDFY2GeneProductENSG00000139668 (Ensembl)
WDHD1GeneProductENSG00000198554 (Ensembl)
WNT3AENSG00000154342 (Ensembl)
WNT3ENSG00000108379 (Ensembl)
YAP1ENSG00000137693 (Ensembl)
ZFHX4GeneProductENSG00000091656 (Ensembl)
ZIC2GeneProductENSG00000043355 (Ensembl)
ZIC3GeneProductENSG00000156925 (Ensembl)
ZIC5GeneProductENSG00000139800 (Ensembl)
ZNF281GeneProductENSG00000162702 (Ensembl)
ZNF462GeneProductENSG00000148143 (Ensembl)

Annotated Interactions

No annotated interactions
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