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Title: Identification of putative targets of Nkx2-5 in Xenopus laevis using gene expression analysis and cross-species annotation      
dateReleased:
12-01-2011
description:
While the heart is the first organ to form during development, the earliest molecular mechanisms surrounding specification and differentiation are not clear. In vertebrates, the first marker of cardiac specification is the expression of the homeobox transcription factor Nkx2-5 and its paralogs. While some downstream targets of Nkx2-5 have been discovered, they alone are not sufficient to completely rescue Nkx2-5 knock-downs, suggesting that other targets of Nkx2-5 regulation remain unknown. In order to identify early targets of Nkx2-5, Xenopus laevis embryos were injected with synthetic Nkx2-5 mRNA and changes in gene expression measured using Affymetrix GeneChips. To interpret the data, X. laevis genomic annotation was augmented using cross-species information from the CrossGene database followed by gene ontology enrichment, network analysis, spatial expression, and Nkx2-5 binding site predictions. This allowed us to compile a list of 99 UniGene clusters representing likely early targets of Nkx2-5. Nkx2-5+GFP or GFP mRNA was injected into 8 cell Xenopus embryos. Total RNA was collected at St. 11.5. comparison of gene expression profiles for treated vs, control
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-29791
refinement:
raw
alternateIdentifiers:
29791
keywords:
functional genomics
dateModified:
12-13-2011
availability:
available
types:
gene expression
name:
Xenopus laevis
ID:
A-AFFY-62
name:
Affymetrix GeneChip Xenopus laevis Genome Array [Xenopus_laevis]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-29791/E-GEOD-29791.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-29791/E-GEOD-29791.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29791
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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