EcoToxXplorer: Leveraging Design Thinking to Develop a Standardized Web‐Based Transcriptomics Analytics Platform for Diverse Users

Soufan, Othman; Ewald, Jessica; Zhou, Guohui; Haçarız, Orçun; Boulanger, Emily; Alcaraz, Alper James; Hickey, Gordon M.; Maguire, Steve; Pain, Guillaume; Hogan, Natacha S.; Hecker, Markus; Crump, Doug; Head, Jessica; Basu, Niladri; Xia, Jianguo

doi:10.1002/etc.5251

Cited by 9 publications

(6 citation statements)

References 9 publications

(15 reference statements)

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“…Data are normalized using either delta C t (default) or quantile normalization ahead of differential expression analysis between control and treated samples (Soufan et al, 2022). Given the nature of the initial 24 samples tested/species, it was not possible to perform differential gene expression analysis because the samples were from various exposure studies and did not have sufficient sample sizes to perform such analyses.…”

Section: Methodsmentioning

confidence: 99%

“…This cloud-based tool serves as the main portal for analyzing and interpreting Eco-ToxChip results (Soufan et al, 2022). A detailed tutorial describing data upload, analysis, and report generation can be found at EcoToxXplorer (n.d.) and Soufan et al (2022).…”

Section: Ecotoxchip Data Analysis: Ecotoxxplorermentioning

confidence: 99%

“…The EcoToxXplorer is an intuitive data evaluation tool designed to help overcome existing barriers to the adoption of novel toxicogenomics tools that are associated with the challenges of managing and analyzing big omics data sets (e.g., lack of standardization, methods, tools). This cloud-based tool serves as the main portal for analyzing and interpreting Eco-ToxChip results (Soufan et al, 2022). A detailed tutorial describing data upload, analysis, and report generation can be found at EcoToxXplorer (n.d.) and Soufan et al (2022).…”

Section: Ecotoxchip Data Analysis: Ecotoxxplorermentioning

confidence: 99%

“…EcoToxChips were developed for three laboratory model species that are among the most commonly used vertebrate test species in ecological risk assessment—fathead minnow ( Pimephales promelas ), African clawed frog ( Xenopus laevis ), and Japanese quail ( Coturnix japonica ). Similar to the approach our team used to develop a standardized web‐based transcriptomics analytics platform, EcoToxXplorer (http://www.ecotoxxplorer.ca; Soufan et al, 2022), we took a design thinking approach (Dam & Siang, 2020) to develop a toxicogenomics tool to support chemical management and environmental monitoring (Basu et al, 2019). Our study is part of a larger effort aimed at improving chemical prioritization and environmental management via harnessing NAMs and novel tools (Basu et al, 2019; EcoToxChip, n.d.).…”

Section: Introductionmentioning

confidence: 99%

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Development and Initial Testing of EcoToxChip, a Novel Toxicogenomics Tool for Environmental Management and Chemical Risk Assessment

Crump

Hickey

Boulanger

et al. 2023

Enviro Toxic and Chemistry

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New approach methods (NAMs) are increasingly important to help accelerate the pace of ecological risk assessment and offer more ethical, affordable, and efficient alternatives to traditional toxicity tests. In the present study, we describe the development, technical characterization, and initial testing of a toxicogenomics tool, EcoToxChip (384‐well quantitative polymerase chain reaction [qPCR] array), to support chemical management and environmental monitoring for three laboratory model species—fathead minnow (Pimephales promelas), African clawed frog (Xenopus laevis), and Japanese quail (Coturnix japonica). Chip design, including gene selection, was informed by a diverse end‐user group and quality control metrics (e.g., primer assay, reverse transcription, and PCR efficiency) performed well based on a priori established criteria. Correlation with RNA sequencing (seq) data provided additional confidence in this novel toxicogenomics tool. Although the present study represents an initial testing of only 24 EcoToxChips for each of the model species, the results provide increased confidence in the robustness/reproducibility of EcoToxChips for evaluating perturbations in gene expression associated with chemical exposure and thus, this NAM, combined with early‐life stage toxicity testing, could augment current efforts for chemical prioritization and environmental management. Environ Toxicol Chem 2023;42:1763–1771. © 2023 SETAC

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Section: Methodsmentioning

confidence: 99%

Section: Ecotoxchip Data Analysis: Ecotoxxplorermentioning

confidence: 99%

Section: Ecotoxchip Data Analysis: Ecotoxxplorermentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Development and Initial Testing of EcoToxChip, a Novel Toxicogenomics Tool for Environmental Management and Chemical Risk Assessment

Crump

Hickey

Boulanger

et al. 2023

Enviro Toxic and Chemistry

Self Cite

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“…Also in recent WoE applications, transcriptional evidence was evaluated qualitatively without taking part in the weighted integrative process (e.g., Mezzelani et al, 2021;Schmitz et al, 2022;Lucia et al, 2023). This represents a missed opportunity for transcriptomics, and -omics data in general, to be considered within QWoE approaches for environmental risk assessment (ERA) and regulatory purposes (Soufan et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment

Cecchetto

Peruzza

Giubilato

et al. 2023

Environmental Research

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Comparing Transcriptomic Responses to Chemicals Across Six Species Using the EcoToxChip RNASeq Database

Mittal,

Ewald,

Crump

et al. 2024

Enviro Toxic and Chemistry

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The EcoToxChip project includes RNA‐sequencing data from experiments involving model (Japanese quail, fathead minnow, African clawed frog) and ecological (double‐crested cormorant, rainbow trout, northern leopard frog) species, at multiple life stages (whole embryo and adult), exposed to eight chemicals of environmental concern known to perturb a wide range of biological systems (ethinyl estradiol, hexabromocyclododecane, lead, selenomethionine, 17β trenbolone, chlorpyrifos, fluoxetine, and benzo[a]pyrene). The objectives of this short communication were to: 1) present and make available this RNA‐sequencing database (i.e., 724 samples from 49 experiments) under the FAIR principles, while also summarizing key meta‐data attributes; and 2) use ExpressAnalyst (including the Seq. 2Fun algorithm and EcoOmicsDB) to perform a comparative transcriptomics analysis of this database focusing on baseline and differential transcriptomic changes across species‐life stage‐chemical combinations. The database is available in NCBI GEO under accession number GSE239776. Across all species, the number of raw reads per sample ranged between 13 and 58 million, with 30 to 79% of clean reads mapped to the ‘vertebrate’ sub‐group database in EcoOmicsDB. Principal component analyses of the reads illustrated separation across the three taxonomic groups as well as some between tissue types. The most common differentially expressed gene was CYP1A1 followed by CTSE, FAM20CL, MYC, ST1S3, RIPK4, VTG1, and VIT2. The most common enriched pathways were metabolic pathways, biosynthesis of cofactors and biosynthesis of secondary metabolites, and chemical carcinogenesis, drug metabolism and metabolism of xenobiotics by Cytochrome P450. The RNA‐sequencing database presented here may be used by the research community for multiple purposes, including for example, cross‐species investigations, in depth analyses of a particular test compound, and transcriptomic meta‐analyses.

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EcoToxXplorer: Leveraging Design Thinking to Develop a Standardized Web‐Based Transcriptomics Analytics Platform for Diverse Users

Abstract: Focus articles are part of a regular series intended to sharpen understanding of current and emerging topics of interest to the scientific community.

Cited by 9 publications

References 9 publications

Development and Initial Testing of EcoToxChip, a Novel Toxicogenomics Tool for Environmental Management and Chemical Risk Assessment

Development and Initial Testing of EcoToxChip, a Novel Toxicogenomics Tool for Environmental Management and Chemical Risk Assessment

An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment

Comparing Transcriptomic Responses to Chemicals Across Six Species Using the EcoToxChip RNASeq Database

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