ArticleJournal of biomolecular screening2015
A Data Analysis Pipeline Accounting for Artifacts in Tox21 Quantitative High-Throughput Screening Assays.
Article in Journal of biomolecular screening, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed.
- Prioritizing chemicals for developmental neurotoxicity by integrating data from a new approach methods (NAMs) battery covering key cellular events in neurodevelopment.Neurotoxicology · 2026Article
- Development of machine learning-based multi-task quantitative structure-activity relationship models for predicting toxicities in six human organ systems.Computational toxicology (Amsterdam, Netherlands) · 2026Article
- Bayesian matrix completion for hypothesis testing.Journal of the Royal Statistical Society. Series C, Applied statistics · 2023Article
- Predicting Endocrine Disruption Using Conformal Prediction - A Prioritization Strategy to Identify Hazardous Chemicals with Confidence.Chemical research in toxicology · 2023Article
- ALOHA: Aggregated local extrema splines for high-throughput dose-response analysis.Computational toxicology (Amsterdam, Netherlands) · 2022Article
- Accounting for Artifacts in High-Throughput Toxicity Assays.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Harnessing In Silico, In Vitro, and In Vivo Data to Understand the Toxicity Landscape of Polycyclic Aromatic Compounds (PACs).Chemical research in toxicology · 2021Article
- The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology.Chemical research in toxicology · 2021Review
- A Gene Expression Biomarker Identifies Chemical Modulators of Estrogen Receptor α in an MCF-7 Microarray Compendium.Chemical research in toxicology · 2021Article
- Selecting a minimal set of androgen receptor assays for screening chemicals.Regulatory toxicology and pharmacology : RTP · 2020Article
- Endocrine-disrupting chemicals: economic, regulatory, and policy implications.The lancet. Diabetes & endocrinology · 2020Review
- Navigating the Minefield of Computational Toxicology and Informatics: Looking Back and Charting a New Horizon.Frontiers in toxicology · 2020Article
- Identifying Compounds with Genotoxicity Potential Using Tox21 High-Throughput Screening Assays.Chemical research in toxicology · 2019Article
- Using Tox21 High-Throughput Screening Assays for the Evaluation of Botanical and Dietary Supplements.Applied in vitro toxicology · 2019Article
- Quality Control of Quantitative High Throughput Screening Data.Frontiers in genetics · 2019Article
- Identifying Attributes That Influence In Vitro-to-In Vivo Concordance by Comparing In Vitro Tox21 Bioactivity Versus In Vivo DrugMatrix Transcriptomic Responses Across 130 Chemicals.Toxicological sciences : an official journal of the Society of Toxicology · 2019Article
- Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial Pharmaceutical Research.Frontiers in pharmacology · 2019Review
- Application of Benchmark Concentration (BMC) Analysis on Zebrafish Data: A New Perspective for Quantifying Toxicity in Alternative Animal Models.Toxicological sciences : an official journal of the Society of Toxicology · 2019Article
- Screening for Developmental Neurotoxicity at the National Toxicology Program: The Future Is Here.Toxicological sciences : an official journal of the Society of Toxicology · 2019Article
- Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure-Activity Relationship (QSAR) Analysis.Frontiers in bioengineering and biotechnology · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
A main goal of the U.S. Tox21 program is to profile a 10K-compound library for activity against a panel of stress-related and nuclear receptor signaling pathway assays using a quantitative high-throughput screening (qHTS) approach. However, assay artifacts, including nonreproducible signals and assay interference (e.g., autofluorescence), complicate compound activity interpretation. To address these issues, we have developed a data analysis pipeline that includes an updated signal noise-filtering/curation protocol and an assay interference flagging system. To better characterize various types of signals, we adopted a weighted version of the area under the curve (wAUC) to quantify the amount of activity across the tested concentration range in combination with the assay-dependent point-of-departure (POD) concentration. Based on the 32 Tox21 qHTS assays analyzed, we demonstrate that signal profiling using wAUC affords the best reproducibility (Pearson's r = 0.91) in comparison with the POD (0.82) only or the AC(50) (i.e., half-maximal activity concentration, 0.81). Among the activity artifacts characterized, cytotoxicity is the major confounding factor; on average, about 8% of Tox21 compounds are affected, whereas autofluorescence affects less than 0.5%. To facilitate data evaluation, we implemented two graphical user interface applications, allowing users to rapidly evaluate the in vitro activity of Tox21 compounds.
Indexed as
Identifiers
What OpenQuestion holds
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.