ArticlePloS one2017
A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 143 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
143 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity.Toxicological sciences : an official journal of the Society of Toxicology · 2022Pooled it
- Advancing genotoxicity assessment with transcriptomic biomarkers: from 2D to 3D HepaRG spheroid models.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Detection ofInternational journal of molecular sciences · 2026Article
- Systematic comparison of temporal hepatotoxicant-induced gene network responses across 3 liver test systems.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Transplatformer: translating toxicogenomic profiles between generations of platforms.BMC bioinformatics · 2026Article
- ARACRA: Automated RNA-seq Analysis for Chemical Risk Assessment.Computational and structural biotechnology journal · 2026Article
- Article
- Article
- Eosinophils and Bioactive Lipid Mediators Regulate Skin Inflammation and Cancer Growth.The Journal of investigative dermatology · 2025Article
- Stromal transcriptomics uncover LIF as a key effector in high tumor budding triple-negative breast cancer.Scientific reports · 2025Article
- Assessing the impact of in vitro xenobiotic metabolism on estrogenic chemical bioactivity in high-throughput profiling assays.Toxicology · 2025Article
- Comparison of whole transcriptome and targeted RNA sequencing for ecological high-throughput transcriptomics.Regulatory toxicology and pharmacology : RTP · 2025Article
- Differential Responses of Human iPSC-Derived Microglia to Stimulation with Diverse Inflammogens.Cells · 2025Article
- The important role of standards for the uptake of transcriptomics and metabolomics based in vitro methods in regulatory toxicology.Archives of toxicology · 2025Review
- Identifying Gene Predictors of Chemicals Linked With Breast Cancer: A Machine Learning Analysis of MCF7 Cellular Transcriptomic Screening Data.Environmental and molecular mutagenesis · 2025Article
- High-throughput profiling of chemical-induced gene expression across 93,644 perturbations.Nature methods · 2025Article
- Article
- Decoding Cellular Stress States for Toxicology Using Single-Cell Transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and Ppara-null mouse livers.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Dose-response modeling of effects in mice after exposure to a polyfluoroalkyl substance (Nafion byproduct 2).Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
83 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3' end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression.
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.