ReviewBiophysical reviews2019
Mining data and metadata from the gene expression omnibus.
Review in Biophysical reviews, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 2 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
63 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Discovering Promising Biomarkers and Therapeutic Targets for Duchenne Muscular Dystrophy: a Multiomics Meta-Analysis Approach.Molecular neurobiology · 2024Pooled it
- Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies.Biology of sex differences · 2023Pooled it
- Trial
- Article
- Identification of Markers on the Basis of Transcriptomic Analysis for Molecular Assignment of Medulloblastoma.International journal of molecular sciences · 2026Article
- FAIR in practice: minimum metadata schema for bioinformatics analytics by machines.Journal of biomedical semantics · 2026Article
- CistromeMeta: a large language model powered tool for automated ChIP-seq metadata extraction.Bioinformatics (Oxford, England) · 2026Article
- Transcriptomic data and biomedical literature synergize in finding pharmacologic gene regulators.bioRxiv : the preprint server for biology · 2026Article
- Semantic alignment of the German Human Genome-Phenome Archive metadata model in Europe's genomics field.Scientific data · 2026Article
- The impact of epigenetics on tumor metabolism: Friend or foe in drug response?Frontiers in epigenetics and epigenomics · 2026Review
- Concordant Shared Transcriptomic Signatures and Candidate Regulatory Features in Chronic Lymphocytic Leukemia and Multiple Myeloma.Oncology research · 2026Article
- PBX1 promotes osteoporosis by upregulating HMGB1 to suppress osteogenic differentiation of bone marrow mesenchymal stem cells.Stem cell research & therapy · 2025Article
- How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO.Briefings in bioinformatics · 2025Review
- Publicly available imaging datasets for age-related macular degeneration: Evaluation according to the Findable, Accessible, Interoperable, Reusable (FAIR) principles.Experimental eye research · 2025Review
- Expression and prognosis of NR3C1 in uterine corpus endometrial carcinoma based on multiple datasets.Discover oncology · 2025Article
- Competing Endogenous RNA Networks Reveal Long Non-coding RNAs as Potential Prognostic Biomarkers in Gastric Cancer: A Systematic Review and Meta-Analysis.Advanced biomedical research · 2025Review
- Exploring the molecular mechanisms of phthalates in the comorbidity of preeclampsia and depression by integrating multiple datasets.Frontiers in psychiatry · 2025Article
- Therapeutic role of aripiprazole in cartilage defects explored through a drug repurposing approach.Scientific reports · 2024Article
- Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata.Briefings in bioinformatics · 2024Article
- RummaGEO: Automatic mining of human and mouse gene sets from GEO.Patterns (New York, N.Y.) · 2024Article
3 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
3 authors.
Funding
Abstract
Publicly available gene expression datasets deposited in the Gene Expression Omnibus (GEO) are growing at an accelerating rate. Such datasets hold great value for knowledge discovery, particularly when integrated. Although numerous software platforms and tools have been developed to enable reanalysis and integration of individual, or groups, of GEO datasets, large-scale reuse of those datasets is impeded by minimal requirements for standardized metadata both at the study and sample levels as well as uniform processing of the data across studies. Here, we review methodologies developed to facilitate the systematic curation and processing of publicly available gene expression datasets from GEO. We identify trends for advanced metadata curation and summarize approaches for reprocessing the data within the entire GEO repository.
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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.