ArticlePatterns (New York, N.Y.)2024
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
Article in Patterns (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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
9 citing papers in PubMed.
- ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow.Nucleic acids research · 2026Article
- The Common Fund Data Ecosystem (CFDE).bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic data and biomedical literature synergize in finding pharmacologic gene regulators.bioRxiv : the preprint server for biology · 2026Article
- CORESH: a gene signature-based search engine for public gene expression datasets.Nucleic acids research · 2025Article
- L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine.Nucleic acids research · 2025Article
- Genomic ncRNAs regulating mitochondrial function in neurodegeneration: a neglected clue in the complex etiopathogenesis of multiple sclerosis.Cell & bioscience · 2025Article
- A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets.bioRxiv : the preprint server for biology · 2025Article
- Light and sex modifybioRxiv : the preprint server for biology · 2025Article
- GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.GigaScience · 2025Article
Corrections and comments
- Update of
Authors and funding
5 authors.
Funding
Abstract
The Gene Expression Omnibus (GEO) has millions of samples from thousands of studies. While users of GEO can search the metadata describing studies, there is a need for methods to search GEO at the data level. RummaGEO is a gene expression signature search engine for human and mouse RNA sequencing perturbation studies extracted from GEO. To develop RummaGEO, we automatically identified groups of samples and computed differential expressions to extract gene sets from each study. The contents of RummaGEO are served for gene set, PubMed, and metadata search. Next, we analyzed the contents of RummaGEO to identify patterns and perform global analyses. Overall, RummaGEO provides a resource that is enabling users to identify relevant GEO studies based on their own gene expression results. Users of RummaGEO can incorporate RummaGEO into their analysis workflows for integrative analyses and hypothesis generation.
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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.