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Development of a Zebrafish S1500+ Sentinel Gene Set for High Throughput Transcriptomics
Citation:
Balik-Meisner, M., D. Mav, D. Phadke, L. Everett, R. Shah, T. Tal, P. Shepard, B. Merrick, AND R. Paules. Development of a Zebrafish S1500+ Sentinel Gene Set for High Throughput Transcriptomics. Zebrafish. Mary Ann Liebert, Inc., New Rochelle, NY, 16(4):331-347, (2019). https://doi.org/10.1089/zeb.2018.1720
Impact/Purpose:
This paper describes the gene set developed to enable targeted high-throughput RNA sequencing in zebrafish and obtain pathway-level perturbation information.
Description:
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. Here 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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DOI: Development of a Zebrafish S1500+ Sentinel Gene Set for High Throughput Transcriptomics