Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics

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.

Keywords: S1500; S1500+; transcriptomics; zebrafish.

FIG. 1.

Creation of Zf S1500+: diagram describes selection process for the zebrafish orthologs of each human S1500+ gene for inclusion on the Zf S1500+ gene set. The workflow proceeds until there is only one ortholog to add to the list, unless otherwise stated. If at any step only one gene remains, then it is selected for inclusion, and the next iteration of workflow for the next human gene begins.

FIG. 2.

Venn Diagram of human-zebrafish ortholog gene pairs present in each of three databases (HomoloGene, ZFIN, and Ensembl “high confidence”) after filtering out genes with no current NCBI Entrez ID or Ensembl ID. A gene pair designates an orthologous relationship between one human and one zebrafish gene; therefore, genes with one-to-many or many-to-one orthologous relationships are counted for each unique pairing. ZFIN, Zebrafish Information Network.

FIG. 3.

Venn Diagram of human, rat, mouse, and zebrafish S1500+ gene sets in human ortholog space. HomoloGene was used to determine human orthologs of rat and mouse S1500+ genes. CZfO db was used to determine human orthologs of zebrafish Zf S1500+ genes. CZfO db, Combined Zebrafish Ortholog Database.