Gene Set: NRL_DN.V1_DN

Standard name NRL_DN.V1_DN
Systematic name M2797
Brief description Genes down-regulated in retina cells from NRL [GeneID=4901] knockout mice.
Full description or abstract The photoreceptor cells of the retina are subject to a greater number of genetic diseases than any other cell type in the human body. The majority of more than 120 cloned human blindness genes are highly expressed in photoreceptors. In order to establish an integrative framework in which to understand these diseases, we have undertaken an experimental and computational analysis of the network controlled by the mammalian photoreceptor transcription factors, Crx, Nrl, and Nr2e3. Using microarray and in situ hybridization datasets we have produced a model of this network which contains over 600 genes, including numerous retinal disease loci as well as previously uncharacterized photoreceptor transcription factors. To elucidate the connectivity of this network, we devised a computational algorithm to identify the photoreceptor-specific cis-regulatory elements (CREs) mediating the interactions between these transcription factors and their target genes. In vivo validation of our computational predictions resulted in the discovery of 19 novel photoreceptor-specific CREs near retinal disease genes. Examination of these CREs permitted the definition of a simple cis-regulatory grammar rule associated with high-level expression. To test the generality of this rule, we used an expanded form of it as a selection filter to evolve photoreceptor CREs from random DNA sequences in silico. When fused to fluorescent reporters, these evolved CREs drove strong, photoreceptor-specific expression in vivo. This study represents the first systematic identification and in vivo validation of CREs in a mammalian neuronal cell type and lays the groundwork for a systems biology of photoreceptor transcriptional regulation.
Collection C6: oncogenic signature gene sets
Source publication Pubmed 17653270   Authors: Hsiau TH,Diaconu C,Myers CA,Lee J,Cepko CL,Corbo JC
Exact source Nrl-/- mouse retina cells vs Controls; bottom 150 genes (diff. of means)
Related gene sets (show 5 additional gene sets from the source publication)

(show 78 gene sets from the same authors)
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Organism Mus musculus
Contributed by Pablo Tamayo (Broad Institute)
Source platform HUMAN_GENE_SYMBOL
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Version history 7.1: Fixed RIKEN identifiers.

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