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Series GSE4448 Query DataSets for GSE4448
Status Public on Mar 11, 2006
Title Global analysis of the transcriptional network controlling Xenopus endoderm formation
Organism Xenopus laevis
Experiment type Expression profiling by array
Summary A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc finger factors and Sox17 HMG domain proteins. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. Here we used a combination of microarray analysis and loss-of-function experiments to examine the global regulatory network controlling Xenopus endoderm formation. We identified over 300 transcripts enriched in the gastrula endoderm, including most of the known endoderm regulators as well as over a hundred uncharacterized genes. Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodals, Mixer and Sox17 have both shared and distinct sets of downstream targets and that a number of unexpected autoregulatory loops exist between Sox17 and Gata4-6, Sox17 and Bix1, 2, 4 and between Sox17 and Xnr4. We find that Mixer does not function primarily via Sox17 as previously proposed. This data provides a new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network.
Keywords: Embryonic, Development. Endoderm, Xenopus, nodal, Sox17, Mixer, microarray, gene regulatory network
Overall design Define a set of transcripts with enriched expression in the gastrula endoderm of the Xenopus laevis embryo and determine how these are regulated by nodal signaling, Mixer and Sox17 using loss-of-function experiments. For more specific details see Sinner et al., (2006) Global analysis of the transcriptional network controlling Xenopus endoderm formation.
Contributor(s) Sinner D, Kirilenko P, Rankin S, Wei E, Howard L, Kofron M, Heasman J, Woodland HR, Zorn AM
Citation(s) 16651540
Submission date Mar 10, 2006
Last update date Mar 16, 2012
Contact name Aaron M Zorn
Phone 636 3770
Organization name Cincinnati Children's Hospital Medical Center
Department Develpomental Biology
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45236
Country USA
Platforms (1)
GPL1318 [Xenopus_laevis] Affymetrix Xenopus laevis Genome Array
Samples (31)
GSM99967 Zorn_f4a_Xenopus_laevis.txt
GSM99968 Zorn_H_1_Xenopus_laevis.txt
GSM99969 Zorn_D2_Xenopus_laevis.txt
BioProject PRJNA94719

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE4448_MIAME_checkList.txt 5.6 Kb (ftp)(http) TXT
GSE4448_RAW.tar 100.4 Mb (http)(custom) TAR (of CEL)

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