ArticleInvestigative ophthalmology & visual science2012
iSyTE: integrated Systems Tool for Eye gene discovery.
Article in Investigative ophthalmology & visual science, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 3 of them syntheses that pooled it.
What it found
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Who cites it
82 citing papers in PubMed, 3 syntheses or guidelines pooled it, 104 citations in OpenAlex.
- Transcriptome Meta-Analysis Uncovers Cell-Specific Regulatory Relationships in Embryonic, Juvenile, Adult, and Aged Mouse Lens Epithelium and Fibers.Investigative ophthalmology & visual science · 2025Pooled it
- A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects.Nature communications · 2021Pooled it
- Common variants in SOX-2 and congenital cataract genes contribute to age-related nuclear cataract.Communications biology · 2020Pooled it
- RNA-binding proteins in the mouse lens: Functional classifications, expression profiling, and interaction studies of Carhsp1 with crystallin mRNAs.Developmental biology · 2026Article
- Lens tissue transcriptome analysis in patients with total congenital cataract.Human genomics · 2026Article
- Loss of cyclase-associated protein 2 alters actin cytoskeleton organization and biomechanical properties of the ocular lens.Journal of cell science · 2026Article
- Candidate Genes for Non-Syndromic Pediatric Cataracts.Clinical ophthalmology (Auckland, N.Z.) · 2026Review
- Cyclase associated actin cytoskeleton regulatory protein 2 (CAP2) organizes the actin cytoskeleton to influence the biomechanical properties of the ocular lens.bioRxiv : the preprint server for biology · 2025Article
- Artificial Intelligence in Ocular Transcriptomics: Applications of Unsupervised and Supervised Learning.Cells · 2025Review
- Whole Exome Sequencing Study Uncovers Novel Candidate Genes and Protein-Coding Variants for Cataract.Investigative ophthalmology & visual science · 2025Article
- LIRTS Viewer: A Web-Based Resource to View the Transcriptional Response of Lens Epithelial Cells to Injury.Investigative ophthalmology & visual science · 2025Article
- CD24 is required for sustained transparency of the adult lens.Experimental eye research · 2025Article
- Lens Regeneration: The Application of iSyTE and In Silico Approaches to Evaluate Gene Expression in Lens Organoids.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Multi-tissue transcriptome-wide association study identifies novel candidate susceptibility genes for cataract.Frontiers in ophthalmology · 2024Article
- Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology.Development (Cambridge, England) · 2024Article
- Article
- Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery.Human genetics · 2023Article
- High-Throughput Transcriptomics ofCells · 2023Article
- Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery.Research square · 2023Article
- Variant analyses of candidate genes in orofacial clefts in multi-ethnic populations.Oral diseases · 2022Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
purposeTo facilitate the identification of genes associated with cataract and other ocular defects, the authors developed and validated a computational tool termed iSyTE (integrated Systems Tool for Eye gene discovery; http://bioinformatics.udel.edu/Research/iSyTE). iSyTE uses a mouse embryonic lens gene expression data set as a bioinformatics filter to select candidate genes from human or mouse genomic regions implicated in disease and to prioritize them for further mutational and functional analyses.
methodsMicroarray gene expression profiles were obtained for microdissected embryonic mouse lens at three key developmental time points in the transition from the embryonic day (E)10.5 stage of lens placode invagination to E12.5 lens primary fiber cell differentiation. Differentially regulated genes were identified by in silico comparison of lens gene expression profiles with those of whole embryo body (WB) lacking ocular tissue.
resultsGene set analysis demonstrated that this strategy effectively removes highly expressed but nonspecific housekeeping genes from lens tissue expression profiles, allowing identification of less highly expressed lens disease-associated genes. Among 24 previously mapped human genomic intervals containing genes associated with isolated congenital cataract, the mutant gene is ranked within the top two iSyTE-selected candidates in approximately 88% of cases. Finally, in situ hybridization confirmed lens expression of several novel iSyTE-identified genes.
conclusionsiSyTE is a publicly available Web resource that can be used to prioritize candidate genes within mapped genomic intervals associated with congenital cataract for further investigation. Extension of this approach to other ocular tissue components will facilitate eye disease gene discovery.
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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.