ReviewRegulatory toxicology and pharmacology : RTP2017
A generic Transcriptomics Reporting Framework (TRF) for 'omics data processing and analysis.
Review in Regulatory toxicology and pharmacology : RTP, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-omics time-series analysis in microbiome research: a systematic review.Briefings in bioinformatics · 2025Pooled it
- Fungal ecology in the age of 'omics.The New phytologist · 2026Review
- Value-based health care frameworks for the health technology assessments of "omics" technologies: an international survey.International journal of technology assessment in health care · 2025Article
- Computational Strategies for Assessing Adverse Outcome Pathways: Hepatic Steatosis as a Case Study.International journal of molecular sciences · 2024Review
- Effects of Deoxynivalenol and Its Acetylated Derivatives on Lipid Metabolism in Human Normal Hepatocytes.Toxins · 2024Article
- Next generation risk assessment: anFrontiers in pharmacology · 2024Article
- Applying genomics in regulatory toxicology: a report of the ECETOC workshop on omics threshold on non-adversity.Archives of toxicology · 2023Article
- Multiomics Point of Departure (moPOD) Modeling Supports an Adverse Outcome Pathway Network for Ionizing Radiation.Environmental science & technology · 2023Article
- Application of AOPs to assist regulatory assessment of chemical risks - Case studies, needs and recommendations.Environmental research · 2023Review
- Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay.Current research in toxicology · 2023Article
- Toxicoepigenetics for Risk Assessment: Bridging the Gap Between Basic and Regulatory Science.Epigenetics insights · 2022Article
- Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology.Regulatory toxicology and pharmacology : RTP · 2021Article
- Methodological considerations for measuring biofluid-based microRNA biomarkers.Critical reviews in toxicology · 2021Article
- Article
- Drivers of and Obstacles to the Adoption of Toxicogenomics for Chemical Risk Assessment: Insights from Social Science Perspectives.Environmental health perspectives · 2020Article
- Mode of action-based risk assessment of genotoxic carcinogens.Archives of toxicology · 2020Review
- Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects.Nanomaterials (Basel, Switzerland) · 2020Review
- A cross-sector call to improve carcinogenicity risk assessment through use of genomic methodologies.Regulatory toxicology and pharmacology : RTP · 2020Article
- Use cases, best practice and reporting standards for metabolomics in regulatory toxicology.Nature communications · 2019Review
- Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials.Frontiers in genetics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
A generic Transcriptomics Reporting Framework (TRF) is presented that lists parameters that should be reported in 'omics studies used in a regulatory context. The TRF encompasses the processes from transcriptome profiling from data generation to a processed list of differentially expressed genes (DEGs) ready for interpretation. Included within the TRF is a reference baseline analysis (RBA) that encompasses raw data selection; data normalisation; recognition of outliers; and statistical analysis. The TRF itself does not dictate the methodology for data processing, but deals with what should be reported. Its principles are also applicable to sequencing data and other 'omics. In contrast, the RBA specifies a simple data processing and analysis methodology that is designed to provide a comparison point for other approaches and is exemplified here by a case study. By providing transparency on the steps applied during 'omics data processing and analysis, the TRF will increase confidence processing of 'omics data, and regulatory use. Applicability of the TRF is ensured by its simplicity and generality. The TRF can be applied to all types of regulatory 'omics studies, and it can be executed using different commonly available software tools.
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.