Pre-implantation embryo (Homo sapiens)

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3, 56single-cellRNA-SeqDefinedOocyteDNA-binding1-cell2-cell4-cell8-16-cell16-32-cellEarly blastocystLate blastocystTEICMPEEPIESCDDIT3GATA3BARX2MIR290DLX2DPRXMYBL1ZFP36L2NR3C2HNRNPABESRRATEAD4ARGFXCELF3NKX2-1MOSIRF4LEUTXPADI6NLRP5ELAVL1EGR1ZFP36BATF3NANOGNBDPPA3KHSRPZAR1FOXD1E2F5SIX3ZSCAN4GATA2H2AFY2TPRX1IRX51MXD1FOXQ1TFAP2BDNA-binding8-cell pattern 18-cell pattern 28-cell pattern 3Morulae pattern 1Morulae pattern 2Late blastocysthESC Early PassageHMGA1PBX1hESC Late PassageSOX11TCF7L1FOSBMTA3SOX8Core PluripotencySOX2POU5F1NANOGKLF4DPPA3DNMT3LNaive PSCKLF44ZFP42TBX3CDX26Maternal2SMARCA4CDH1ATP1A1Embryonic GenomeActivation2AQP3AQP9RNA Stabilizationby RBPs2MIR302AMIR2957


The source of this pathway is RNA-Seq data from single-cell pre-implantation embryos (Supplemental Table 1):

Analysis options for running the single-cell analysis workflow in AltAnalyze (ICGS):

  • For optimal filtering (not too restrictive), change the Fold change filter cutoff from 10 to 100 and the Minimum number of samples differing from 3 to 2.
  • Change the Select the column clustering method to hopach.
  • The final ICGS cell cluster groups (hopach) were further analyzed to identify genes with restricted expression in one of the identified sub-populations using the MarkerFinder algorithm in AltAnalyze (RPKM>1).
  • MarkerFinder identified genes for each sub-population (e.g., 8-cell pattern 1) were further filtered for DNA-binding and RNA-binding factors, that are reported in this pathway.
This pathway is part the CPTAC Assay Portal.

Quality Tags

Ontology Terms



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  1. Houbaviy HB, Murray MF, Sharp PA; ''Embryonic stem cell-specific MicroRNAs.''; Dev Cell, 2003 PubMed Europe PMC Scholia
  2. Bell CE, Calder MD, Watson AJ; ''Genomic RNA profiling and the programme controlling preimplantation mammalian development.''; Mol Hum Reprod, 2008 PubMed Europe PMC Scholia
  3. Zernicka-Goetz M, Morris SA, Bruce AW; ''Making a firm decision: multifaceted regulation of cell fate in the early mouse embryo.''; Nat Rev Genet, 2009 PubMed Europe PMC Scholia
  4. Theunissen TW, Powell BE, Wang H, Mitalipova M, Faddah DA, Reddy J, Fan ZP, Maetzel D, Ganz K, Shi L, Lungjangwa T, Imsoonthornruksa S, Stelzer Y, Rangarajan S, D'Alessio A, Zhang J, Gao Q, Dawlaty MM, Young RA, Gray NS, Jaenisch R; ''Systematic identification of culture conditions for induction and maintenance of naive human pluripotency.''; Cell Stem Cell, 2014 PubMed Europe PMC Scholia
  5. Yan L, Yang M, Guo H, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Qiao J, Tang F; ''Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.''; Nat Struct Mol Biol, 2013 PubMed Europe PMC Scholia
  6. Deb K, Sivaguru M, Yong HY, Roberts RM; ''Cdx2 gene expression and trophectoderm lineage specification in mouse embryos.''; Science, 2006 PubMed Europe PMC Scholia
  7. Lin SL, Chang DC, Lin CH, Ying SY, Leu D, Wu DT; ''Regulation of somatic cell reprogramming through inducible mir-302 expression.''; Nucleic Acids Res, 2011 PubMed Europe PMC Scholia


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120810view12:37, 11 January 2022SusanOntology Term : 'signaling pathway pertinent to development' added !
120809view12:34, 11 January 2022SusanOntology Term : 'altered regulatory pathway pertinent to the brain' added !
116646view11:38, 9 May 2021EweitzModified title
106534view23:59, 5 September 2019KhanspersModified description
105790view19:48, 15 August 2019KhanspersModified description
94671view13:41, 4 October 2017Marvin M2Connected unconnected lines
88345view16:10, 1 August 2016FehrhartOntology Term : 'regulatory pathway' added !
87387view11:05, 22 July 2016MaintBotadded missing graphids
84571view12:27, 3 March 2016Mkutmonadded missing graph ids
83782view15:38, 4 December 2015SusanChanged IDs of POU5F1 and PADI6
82555view18:28, 6 October 2015KhanspersModified description
82554view18:07, 6 October 2015KhanspersAdded literature reference
82553view18:05, 6 October 2015KhanspersModified description
82552view18:04, 6 October 2015KhanspersModified description
82551view18:01, 6 October 2015KhanspersUpdating to latest version per Nathan
82539view11:32, 6 October 2015Mkutmonadded Ensembl identifier for FOXD1
82473view16:43, 30 September 2015NsalomonisNew pathway

External references


View all...
NameTypeDatabase referenceComment
AQP3GeneProductENSG00000165272 (Ensembl)
AQP9GeneProductENSG00000103569 (Ensembl)
ARGFXGeneProductENSG00000186103 (Ensembl)
ATP1A1GeneProductENSG00000163399 (Ensembl)
BARX2GeneProductENSG00000043039 (Ensembl)
BATF3GeneProductENSG00000123685 (Ensembl)
CDH1GeneProductENSG00000039068 (Ensembl)
CDX2GeneProductENSG00000165556 (Ensembl)
CELF3GeneProductENSG00000159409 (Ensembl)
DDIT3GeneProductENSG00000175197 (Ensembl)
DLX2GeneProductENSG00000115844 (Ensembl)
DNMT3LGeneProductENSG00000142182 (Ensembl)
DPPA3GeneProductENSG00000187569 (Ensembl)
DPRXGeneProductENSG00000204595 (Ensembl)
E2F5GeneProductENSG00000133740 (Ensembl)
EGR1GeneProductENSG00000120738 (Ensembl)
ELAVL1GeneProductENSG00000066044 (Ensembl)
ESRRAGeneProductENSG00000173153 (Ensembl)
FOSBGeneProductENSG00000125740 (Ensembl)
FOXD1GeneProductENSG00000251493 (Ensembl)
FOXQ1GeneProductENSG00000164379 (Ensembl)
GATA2GeneProductENSG00000179348 (Ensembl)
GATA3GeneProductENSG00000107485 (Ensembl)
H2AFY2GeneProductENSG00000099284 (Ensembl)
HMGA1GeneProductENSG00000137309 (Ensembl)
HNRNPABGeneProductENSG00000197451 (Ensembl)
IRF4GeneProductENSG00000137265 (Ensembl)
IRX5GeneProductENSG00000176842 (Ensembl)
KHSRPGeneProductENSG00000088247 (Ensembl)
KLF4GeneProductENSG00000136826 (Ensembl)
LEUTXGeneProductENSG00000213921 (Ensembl)
MIR302ARnaENSG00000207927 (Ensembl)
MOSGeneProductENSG00000172680 (Ensembl)
MTA3GeneProductENSG00000057935 (Ensembl)
MXD1GeneProductENSG00000059728 (Ensembl)
MYBL1GeneProductENSG00000185697 (Ensembl)
NANOGGeneProductENSG00000111704 (Ensembl)
NANOGNBGeneProductENSG00000205857 (Ensembl)
NKX2-1GeneProductENSG00000136352 (Ensembl)
NLRP5GeneProductENSG00000171487 (Ensembl)
NR3C2GeneProductENSG00000151623 (Ensembl)
PADI6GeneProductENSG00000276747 (Ensembl)
PBX1GeneProductENSG00000185630 (Ensembl)
POU5F1GeneProductENSG00000204531 (Ensembl)
SIX3GeneProductENSG00000138083 (Ensembl)
SMARCA4GeneProductENSG00000127616 (Ensembl)
SOX11GeneProductENSG00000176887 (Ensembl)
SOX2GeneProductENSG00000181449 (Ensembl)
SOX8GeneProductENSG00000005513 (Ensembl)
TBX3GeneProductENSG00000135111 (Ensembl)
TCF7L1GeneProductENSG00000152284 (Ensembl)
TEAD4GeneProductENSG00000197905 (Ensembl)
TFAP2BGeneProductENSG00000008196 (Ensembl)
TPRX1GeneProductENSG00000178928 (Ensembl)
ZAR1GeneProductENSG00000182223 (Ensembl)
ZFP36GeneProductENSG00000128016 (Ensembl)
ZFP36L2GeneProductENSG00000152518 (Ensembl)
ZFP42GeneProductENSG00000179059 (Ensembl)
ZSCAN4GeneProductENSG00000180532 (Ensembl)

Annotated Interactions

No annotated interactions

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