ArticleBMC genomics2014
Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 28 citations in OpenAlex.
- Article
- A gal4 insertion in the rx3 locus as a tool for visualization and manipulation of eye fated cells in zebrafish.Biological research · 2025Article
- Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina.Nature communications · 2023Article
- Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina.Research square · 2023Article
- Zebrafish as a Model to Study Retinoic Acid Signaling in Development and Disease.Biomedicines · 2023Review
- An Overview towards Zebrafish Larvae as a Model for Ocular Diseases.International journal of molecular sciences · 2023Review
- Foxd1-dependent induction of a temporal retinal character is required for visual function.Development (Cambridge, England) · 2022Article
- Article
- Sex-dependent dominance maintains migration supergene in rainbow trout.Nature ecology & evolution · 2019Article
- Fishing forward and reverse: Advances in zebrafish phenomics.Mechanisms of development · 2018Review
- Magnetic nanoparticles: a strategy to target the choroidal layer in the posterior segment of the eye.Scientific reports · 2017Article
- The zebrafish eye-a paradigm for investigating human ocular genetics.Eye (London, England) · 2017Review
- Rx3 and Shh direct anisotropic growth and specification in the zebrafish tuberal/anterior hypothalamus.Development (Cambridge, England) · 2016Article
- Global Transcriptomic Analysis of Interactions between Pseudomonas aeruginosa and Bacteriophage PaP3.Scientific reports · 2016Article
- Conserved genetic pathways associated with microphthalmia, anophthalmia, and coloboma.Birth defects research. Part C, Embryo today : reviews · 2015Review
- Watching eyes take shape.Current opinion in genetics & development · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe genetic cascades underpinning vertebrate early eye morphogenesis are poorly understood. One gene family essential for eye morphogenesis encodes the retinal homeobox (Rx) transcription factors. Mutations in the human retinal homeobox gene (RAX) can lead to gross morphological phenotypes ranging from microphthalmia to anophthalmia. Zebrafish rx3 null mutants produce a similar striking eyeless phenotype with an associated expanded forebrain. Thus, we used zebrafish rx3-/- mutants as a model to uncover an Rx3-regulated gene network during early eye morphogenesis.
resultsRx3-regulated genes were identified using whole transcriptomic sequencing (RNA-seq) of rx3-/- mutants and morphologically wild-type siblings during optic vesicle morphogenesis. A gene co-expression network was then constructed for the Rx3-regulated genes, identifying gene cross-talk during early eye development. Genes highly connected in the network are hub genes, which tend to exhibit higher expression changes between rx3-/- mutants and normal phenotype siblings. Hub genes down-regulated in rx3-/- mutants encompass homeodomain transcription factors and mediators of retinoid-signaling, both associated with eye development and known human eye disorders. In contrast, genes up-regulated in rx3-/- mutants are centered on Wnt signaling pathways, associated with brain development and disorders. The temporal expression pattern of Rx3-regulated genes was further profiled during early development from maternal stage until visual function is fully mature. Rx3-regulated genes exhibited synchronized expression patterns, and a transition of gene expression during the early segmentation stage when Rx3 was highly expressed. Furthermore, most of these deregulated genes are enriched with multiple RAX-binding motif sequences on the gene promoter.
conclusionsHere, we assembled a comprehensive model of Rx3-regulated genes during early eye morphogenesis. Rx3 promotes optic vesicle morphogenesis and represses brain development through a highly correlated and modulated network, exhibiting repression of genes mediating Wnt signaling and concomitant enhanced expression of homeodomain transcription factors and retinoid-signaling genes.
Indexed as
Identifiers
What OpenQuestion holds
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.