ArticleDatabase : the journal of biological databases and curation2021
Curation of over 10 000 transcriptomic studies to enable data reuse.
Article in Database : the journal of biological databases and curation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 2 of them syntheses that pooled it.
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The trial behind it
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Who cites it
40 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A Meta-Analysis of the Effects of Acute Sleep Deprivation on the Cortical Transcriptome in Rodent Models.Journal of sleep research · 2026Pooled it
- A Meta-Analysis of the Effects of Early Life Stress on the Prefrontal Cortex Transcriptome Reveals Long-Term Downregulation of Myelin-Related Gene Expression.Brain and behavior · 2025Pooled it
- A Meta-Analysis of the Converging Effects of Different Classes of Antipsychotics on the Frontal Cortex Transcriptome in Laboratory Rodents and Non-Human Primates.bioRxiv : the preprint server for biology · 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 Meta-Analysis as a Framework for Robust Cross-Study Biological Inference.International journal of molecular sciences · 2026Review
- The Converging Effects of Different Categories of Antidepressants on the Brain: A Systematic Meta-Analysis of Public Transcriptional Profiling Data from the Hippocampus and Cortex.bioRxiv : the preprint server for biology · 2026Article
- Effects of feeding strategies on culture performance and product quality in NISTCHO.NPJ systems biology and applications · 2026Article
- Application of large language models to the annotation of cell lines and mouse strains in genomics data.bioRxiv : the preprint server for biology · 2026Article
- Using semantic search to find publicly available gene-expression datasets.Bioinformatics (Oxford, England) · 2026Article
- Application of large language models to the annotation of cell lines and mouse strains in genomics data.Database : the journal of biological databases and curation · 2026Article
- A Meta-Analysis of the Effects of Chronic Stress on the Prefrontal Transcriptome in Animal Models and Convergence with Existing Human Data.bioRxiv : the preprint server for biology · 2025Article
- EGFR-STAT3 activation provides a therapeutic rationale for targeting aggressive ETV1-positive prostate cancer.Molecular oncology · 2025Article
- Translatability of Animal Models for Alzheimer's Disease Using a Machine Learning Based Workflow.Clinical and translational science · 2025Article
- How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO.Briefings in bioinformatics · 2025Review
- CORESH: a gene signature-based search engine for public gene expression datasets.Nucleic acids research · 2025Article
- Effect of Chronic Stress on Whole Blood Transcriptome: A Meta-Analysis of Publicly Available Datasets from Rodent Models.bioRxiv : the preprint server for biology · 2025Article
- Investigating the role of necroptosis in the immunological microenvironment of periodontitis.Molecular biology reports · 2025Article
- GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data.PLoS computational biology · 2025Article
- Bioenergetic-related gene expression in the hippocampus predicts internalizing vs. externalizing behavior in an animal model of temperament.Frontiers in molecular neuroscience · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface and web services. Here we present an update on Gemma's holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10 811 manually curated datasets (primarily human, mouse and rat), over 395 000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA sequencing). Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service and an R package. Database URL: https://gemma.msl.ubc.ca/home.html.
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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.