ArticlePloS one2010
Ontology-based meta-analysis of global collections of high-throughput public data.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 papers, 7 of them syntheses 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
236 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- Meta-analysis of global and high throughput public gene array data for robust vascular gene expression discovery in chronic rhinosinusitis: Implications in controlled release.Journal of controlled release : official journal of the Controlled Release Society · 2021Pooled it
- Meta-Analysis of Gene Expression Changes in the Blood of Patients with Mild Cognitive Impairment and Alzheimer's Disease Dementia.International journal of molecular sciences · 2019Pooled it
- Transcriptomic immaturity of the hippocampus and prefrontal cortex in patients with alcoholism.Scientific reports · 2017Pooled it
- Modeling vascular inflammation and atherogenicity after inhalation of ambient levels of ozone: exploratory lessons from transcriptomics.Inhalation toxicology · 2017Pooled it
- Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues.Toxicological sciences : an official journal of the Society of Toxicology · 2015Pooled it
- Meta-analysis of gene expression profiles indicates genes in spliceosome pathway are up-regulated in hepatocellular carcinoma (HCC).Medical oncology (Northwood, London, England) · 2015Pooled it
- Global meta-analysis of transcriptomics studies.PloS one · 2014Pooled it
- Pharmacokinetics and Pharmacodynamics with Extended Dosing of CC-486 in Patients with Hematologic Malignancies.PloS one · 2015Trial
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- ToxCompl completion of the DrugMatrix toxicogenomics database: an integrated resource for hypothesis generation.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Sleep Deprivation and Neuronal Hyperexcitation Share Transcriptomic Signatures.Neuropsychopharmacology reports · 2026Article
- Menopausal timing and senescent-immune coupling in age-related lobular involution of the human breast: a longitudinal cohort study.EBioMedicine · 2026Article
- Repetitive neuronal activation regulates cellular maturation state via nuclear reprogramming.Nature communications · 2026Article
- Chemicals in plastics differentially affect the transcriptome of MCF-7 breast cancer cells.Archives of toxicology · 2026Article
- Hyper-maturity and accelerated aging in the hippocampus of mouse models of neuropsychiatric disorders with anxiety-like behavior.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- MetaOmixTools: A User-Friendly Web Suite for Meta-analysis of Ranked Features and Functional Enrichment.Computational and structural biotechnology journal · 2026Article
- Nucleophosmin 1 induction is an early event in a Phenobarbital induced proliferation response in rat but not human liver 3D microtissues.Toxicology reports · 2025Article
- High-throughput transcriptomics analysis of equipotent and human relevant mixtures of BPA alternatives reveal additive effects in vitro.Archives of toxicology · 2025Article
- Impacts of Inorganic Arsenic Exposure on Genetic Stability of Human Mesenchymal Stromal Cells.Journal of applied toxicology : JAT · 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
176 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
15 authors.
Funding
Abstract
backgroundThe investigation of the interconnections between the molecular and genetic events that govern biological systems is essential if we are to understand the development of disease and design effective novel treatments. Microarray and next-generation sequencing technologies have the potential to provide this information. However, taking full advantage of these approaches requires that biological connections be made across large quantities of highly heterogeneous genomic datasets. Leveraging the increasingly huge quantities of genomic data in the public domain is fast becoming one of the key challenges in the research community today. METHODOLOGY/
resultsWe have developed a novel data mining framework that enables researchers to use this growing collection of public high-throughput data to investigate any set of genes or proteins. The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. As an example of our strategy and the utility of this framework, we apply our data mining approach to explore the biology of brown fat within the context of the thousands of publicly available gene expression datasets.
conclusionsOur work presents a practical strategy for organizing, mining, and correlating global collections of large-scale genomic data to explore normal and disease biology. Using a hypothesis-free approach, we demonstrate how a data-driven analysis across very large collections of genomic data can reveal novel discoveries and evidence to support existing hypothesis.
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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.