Pre-implantation embryo (WP3527)

Homo sapiens

The source of this pathway is RNA-Seq data from single-cell pre-implantation embryos, Supplemental Table 1 from [ Yan et al.] 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. Proteins on this pathway have targeted assays available via the [ CPTAC Assay Portal]


Nathan Salomonis , Martina Summer-Kutmon , Kristina Hanspers , Susan Coort , Friederike Ehrhart , Marvin Martens , and Eric Weitz


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Homo sapiens



Pathway Ontology

regulatory pathway signaling pathway pertinent to development


Label Type Compact URI Comment
H2AFY2 GeneProduct ensembl:ENSG00000099284
BARX2 GeneProduct ensembl:ENSG00000043039
TEAD4 GeneProduct ensembl:ENSG00000197905
DDIT3 GeneProduct ensembl:ENSG00000175197
IRX5 GeneProduct ensembl:ENSG00000176842
NR3C2 GeneProduct ensembl:ENSG00000151623
SIX3 GeneProduct ensembl:ENSG00000138083
E2F5 GeneProduct ensembl:ENSG00000133740
KHSRP GeneProduct ensembl:ENSG00000088247
DPPA3 GeneProduct ensembl:ENSG00000187569
ZFP36L2 GeneProduct ensembl:ENSG00000152518
NLRP5 GeneProduct ensembl:ENSG00000171487
CELF3 GeneProduct ensembl:ENSG00000159409
NANOGNB GeneProduct ensembl:ENSG00000205857
BATF3 GeneProduct ensembl:ENSG00000123685
FOXD1 GeneProduct ensembl:ENSG00000251493
PADI6 GeneProduct ensembl:ENSG00000276747
NKX2-1 GeneProduct ensembl:ENSG00000136352
GATA3 GeneProduct ensembl:ENSG00000107485
ELAVL1 GeneProduct ensembl:ENSG00000066044
ZAR1 GeneProduct ensembl:ENSG00000182223
ZSCAN4 GeneProduct ensembl:ENSG00000180532
EGR1 GeneProduct ensembl:ENSG00000120738
ARGFX GeneProduct ensembl:ENSG00000186103
HNRNPAB GeneProduct ensembl:ENSG00000197451
ESRRA GeneProduct ensembl:ENSG00000173153
GATA2 GeneProduct ensembl:ENSG00000179348
MYBL1 GeneProduct ensembl:ENSG00000185697
IRF4 GeneProduct ensembl:ENSG00000137265
TPRX1 GeneProduct ensembl:ENSG00000178928
DPRX GeneProduct ensembl:ENSG00000204595
MOS GeneProduct ensembl:ENSG00000172680
LEUTX GeneProduct ensembl:ENSG00000213921
ZFP36 GeneProduct ensembl:ENSG00000128016
DLX2 GeneProduct ensembl:ENSG00000115844
MXD1 GeneProduct ensembl:ENSG00000059728
FOXQ1 GeneProduct ensembl:ENSG00000164379
TFAP2B GeneProduct ensembl:ENSG00000008196
HMGA1 GeneProduct ensembl:ENSG00000137309
PBX1 GeneProduct ensembl:ENSG00000185630
SOX11 GeneProduct ensembl:ENSG00000176887
TCF7L1 GeneProduct ensembl:ENSG00000152284
FOSB GeneProduct ensembl:ENSG00000125740
MTA3 GeneProduct ensembl:ENSG00000057935
SOX8 GeneProduct ensembl:ENSG00000005513
SOX2 GeneProduct ensembl:ENSG00000181449
POU5F1 GeneProduct ensembl:ENSG00000204531
NANOG GeneProduct ensembl:ENSG00000111704
KLF4 GeneProduct ensembl:ENSG00000136826
DPPA3 GeneProduct ensembl:ENSG00000187569
DNMT3L GeneProduct ensembl:ENSG00000142182
KLF4 GeneProduct ensembl:ENSG00000136826
ZFP42 GeneProduct ensembl:ENSG00000179059
TBX3 GeneProduct ensembl:ENSG00000135111
CDX2 GeneProduct ensembl:ENSG00000165556
SMARCA4 GeneProduct ensembl:ENSG00000127616
CDH1 GeneProduct ensembl:ENSG00000039068
ATP1A1 GeneProduct ensembl:ENSG00000163399
AQP3 GeneProduct ensembl:ENSG00000165272
AQP9 GeneProduct ensembl:ENSG00000103569


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  2. Cdx2 gene expression and trophectoderm lineage specification in mouse embryos. Deb K, Sivaguru M, Yong HY, Roberts RM. Science. 2006 Feb 17;311(5763):992–6. PubMed Europe PMC Scholia
  3. Genomic RNA profiling and the programme controlling preimplantation mammalian development. Bell CE, Calder MD, Watson AJ. Mol Hum Reprod. 2008 Dec;14(12):691–701. PubMed Europe PMC Scholia
  4. Making a firm decision: multifaceted regulation of cell fate in the early mouse embryo. Zernicka-Goetz M, Morris SA, Bruce AW. Nat Rev Genet. 2009 Jul;10(7):467–77. PubMed Europe PMC Scholia
  5. Regulation of somatic cell reprogramming through inducible mir-302 expression. Lin SL, Chang DC, Lin CH, Ying SY, Leu D, Wu DTS. Nucleic Acids Res. 2011 Feb;39(3):1054–65. PubMed Europe PMC Scholia
  6. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Yan L, Yang M, Guo H, Yang L, Wu J, Li R, et al. Nat Struct Mol Biol. 2013 Sep;20(9):1131–9. PubMed Europe PMC Scholia
  7. Systematic identification of culture conditions for induction and maintenance of naive human pluripotency. Theunissen TW, Powell BE, Wang H, Mitalipova M, Faddah DA, Reddy J, et al. Cell Stem Cell. 2014 Oct 2;15(4):471–87. PubMed Europe PMC Scholia