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Series GSE4008 Query DataSets for GSE4008
Status Public on Jan 11, 2006
Title Genome-Wide Identification of Direct Targets of the Drosophila Retinal Determination Protein Eyeless
Organism Drosophila melanogaster
Experiment type Expression profiling by array
Summary The discovery of direct downstream targets of transcription factors (TFs) is necessary for understanding the genetic mechanisms underlying complex, highly regulated processes such as development. In this report, we have used a combinatorial strategy to conduct a genome-wide search for novel direct targets of Eyeless (Ey), a key transcription factor controlling early eye development in Drosophila. Like many other TFs, little is known for Ey direct downstream targets. To date, only one gene, sine oculis (so), has been identified as Ey direct targets in Drosophila. Therefore, it is crucial to identify additional targets in order to gain a better understanding of ey function. To overcome the lack of high quality consensus binding site sequences, phylogenetic shadowing of Ey binding sites in so was used to construct a position weight matrix (PWM) of the Ey protein. This PWM was then used for in silico prediction of potential binding sites in the Drosophila melanogaster genome. To reduce the false positive rate, conservation of these potential binding sites was assessed by comparing the genomic sequences from seven Drosophila species. In parallel, microarray analysis of wild-type versus ectopic ey-expressing tissue, followed by microarray-based epistasis experiments in an atonal (ato) mutant background, identified 188 genes induced by ey. Intersection of in silico predicted conserved Ey binding sites with the candidate gene list produced through expression profiling yields a list of 20 putative ey-induced, eye-enriched, ato-independent, direct targets of Ey, including so. The accuracy of this list of genes was confirmed using both in vitro and in vivo methods. Initial analysis reveals three genes, eyes absent, shifted, and Optix, as novel direct targets of Ey. These results suggest that the integrated strategy of computational biology, genomics, and genetics is a powerful approach that can be applied to systematically identify direct downstream targets for any transcription factor genome-wide.
Keywords: genetic modification, cell type comparison
 
Overall design biological triplicates were done for all samples
 
Citation(s) 16533912
Submission date Jan 10, 2006
Last update date May 04, 2018
Contact name rui chen
E-mail(s) ruichen@bcm.tmc.edu
Phone 7137985194
Organization name Baylor College of Medicine
Department HGSC, Department of Molecular and Human Gentics
Street address One Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL1322 [Drosophila_2] Affymetrix Drosophila Genome 2.0 Array
Samples (25)
GSM91472 ato_mutant_UASey_legdisc_rep1
GSM91473 ato_mutant_UASey_legdisc_rep2
GSM91474 ato_mutant_UASey_legdisc_rep3
Relations
BioProject PRJNA95229

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

Supplementary data files not provided

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