ArticleZebrafish2019
Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics.
Article in Zebrafish, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
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.
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Who cites it
8 citing papers in PubMed, 19 citations in OpenAlex.
- Zebrafish cell lines and high-throughput transcriptomics: advancing in vitro and bioinformatics methods for supporting environmental risk assessment.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Comparison of whole transcriptome and targeted RNA sequencing for ecological high-throughput transcriptomics.Regulatory toxicology and pharmacology : RTP · 2025Article
- Chemical structure drives developmental toxicity of alkyl-substituted naphthalenes in zebrafish.Environment international · 2025Article
- Bioinformatic workflows for deriving transcriptomic points of departure: current status, data gaps, and research priorities.Toxicological sciences : an official journal of the Society of Toxicology · 2025Review
- Progress in toxicogenomics to protect human health.Nature reviews. Genetics · 2025Review
- High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution.Scientific reports · 2024Article
- Toward Sustainable Environmental Quality: Priority Research Questions for Asia.Environmental toxicology and chemistry · 2020Review
- Translational Toxicology in Zebrafish.Current opinion in toxicologyArticle
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
Sentinel gene sets have been developed with the purpose of maximizing the information from targeted transcriptomic platforms. We recently described the development of an S1500+ sentinel gene set, which was built for the human transcriptome, utilizing a data- and knowledge-driven hybrid approach to select a small subset of genes that optimally capture transcriptional diversity, correlation with other genes based on large-scale expression profiling, and known pathway annotation within the human genome. While this detailed bioinformatics approach for gene selection can in principle be applied to other species, the reliability of the resulting gene set depends on availability of a large body of transcriptomics data. For the model organism zebrafish, we aimed to create a similar sentinel gene set (Zf S1500+ gene set); however, there is insufficient standardized expression data in the public domain to train the gene correlation model. Therefore, our strategy was to use human-zebrafish ortholog mapping of the human S1500+ genes and nominations from experts in the zebrafish scientific community. In this study, we present the bioinformatics curation and refinement process to produce the final Zf S1500+ gene set, explore whole transcriptome extrapolation using this gene set, and assess pathway-level inference. This gene set will add value to targeted high-throughput transcriptomics in zebrafish for toxicogenomic screening and other research domains.
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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 Socratic graph.