ArticleNucleic acids research2005
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
34 citing papers in PubMed, 64 citations in OpenAlex.
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- MicroRNA bioinformatics in precision oncology: an integrated pipeline from NGS to AI-based target discovery.Journal of applied genetics · 2025Review
- Non-coding single-nucleotide and structural variants affecting the EYS putative promoter cause autosomal recessive retinitis pigmentosa.Genetics in medicine : official journal of the American College of Medical Genetics · 2025Article
- Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development.Nature communications · 2025Article
- Boolean implication analysis of single-cell data predicts retinal cell type markers.BMC bioinformatics · 2022Article
- Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.Genome biology · 2022Article
- DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring.BMC bioinformatics · 2020Article
- Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing.Frontiers in genetics · 2020Article
- TF-ChIP Method for Tissue-Specific Gene Targets.Frontiers in cellular neuroscience · 2019Article
- Isolation of photoreceptors from mature, developing, and regenerated zebrafish retinas, and of microglia/macrophages from regenerating zebrafish retinas.Experimental eye research · 2018Article
- Co-expression networks reveal the tissue-specific regulation of transcription and splicing.Genome research · 2017Article
- Transcriptomics resources of human tissues and organs.Molecular systems biology · 2016Review
- Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease.Progress in retinal and eye research · 2015Review
- Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers.Genome research · 2013Article
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- CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors.Genome research · 2010Article
- Computational analysis of tissue-specific gene networks: application to murine retinal functional studies.Bioinformatics (Oxford, England) · 2010Article
- SOX9, through interaction with microphthalmia-associated transcription factor (MITF) and OTX2, regulates BEST1 expression in the retinal pigment epithelium.The Journal of biological chemistry · 2010Article
- Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina.Nature reviews. Neuroscience · 2010Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Identification of tissue-specific gene regulatory networks can yield insights into the molecular basis of a tissue's development, function and pathology. Here, we present a computational approach designed to identify potential regulatory target genes of photoreceptor cell-specific transcription factors (TFs). The approach is based on the hypothesis that genes related to the retina in terms of expression, disease and/or function are more likely to be the targets of retina-specific TFs than other genes. A list of genes that are preferentially expressed in retina was obtained by integrating expressed sequence tag, SAGE and microarray datasets. The regulatory targets of retina-specific TFs are enriched in this set of retina-related genes. A Bayesian approach was employed to integrate information about binding site location relative to a gene's transcription start site. Our method was applied to three retina-specific TFs, CRX, NRL and NR2E3, and a number of potential targets were predicted. To experimentally assess the validity of the bioinformatic predictions, mobility shift, transient transfection and chromatin immunoprecipitation assays were performed with five predicted CRX targets, and the results were suggestive of CRX regulation in 5/5, 3/5 and 4/5 cases, respectively. Together, these experiments strongly suggest that RP1, GUCY2D, ABCA4 are novel targets of CRX.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.