ArticleCommunications biology2024
Rummagene: massive mining of gene sets from supporting materials of biomedical research publications.
Article in Communications biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed.
- Molecular programs in human locus coeruleus link APOE and neuromelanin to Alzheimer's vulnerability.Acta neuropathologica · 2026Article
- Literature-informed gene extraction and ranking for multimodal data fusion.Briefings in bioinformatics · 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
- Spatially resolved molecular sex differences at single-cell resolution in the adult human ventromedial and arcuate hypothalamus.Cell reports · 2026Article
- Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells.Oncology letters · 2026Article
- Functional Genomic Screening Identifies lncRNA CNPY2-AS1 as a Regulator of Redox Metabolism and Antiviral Immunity.International journal of biological sciences · 2026Article
- Conserved small RNA networks link inflammation to pain signaling in mice and men.Translational psychiatry · 2025Article
- Gene module-trait network analysis uncovers cell type specific systems and genes relevant to Alzheimer's Disease.Acta neuropathologica communications · 2025Article
- Impact of Alzheimer's disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus.bioRxiv : the preprint server for biology · 2025Article
- Cetacean loss of the master adipose tissue regulator βNature communications · 2025Article
- Article
- Targeting long non-coding RNAMolecular therapy. Nucleic acids · 2025Article
- Review
- Identifying motor resilience proteins associated with motor decline in older adults.The journals of gerontology. Series A, Biological sciences and medical sciences · 2025Article
- L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine.Nucleic acids research · 2025Article
- A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets.bioRxiv : the preprint server for biology · 2025Article
- Potential Adaptive Introgression From Dogs in Iberian Grey Wolves (Canis lupus).Molecular ecology · 2025Article
- Tyrosinase-induced neuromelanin accumulation triggers rapid dysregulation and degeneration of the mouse locus coeruleus.bioRxiv : the preprint server for biology · 2025Article
- Chromosomal and gonadal sex have differing effects on social motivation in mice.Biology of sex differences · 2025Article
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
Many biomedical research publications contain gene sets in their supporting tables, and these sets are currently not available for search and reuse. By crawling PubMed Central, the Rummagene server provides access to hundreds of thousands of such mammalian gene sets. So far, we scanned 5,448,589 articles to find 121,237 articles that contain 642,389 gene sets. These sets are served for enrichment analysis, free text, and table title search. Investigating statistical patterns within the Rummagene database, we demonstrate that Rummagene can be used for transcription factor and kinase enrichment analyses, and for gene function predictions. By combining gene set similarity with abstract similarity, Rummagene can find surprising relationships between biological processes, concepts, and named entities. Overall, Rummagene brings to surface the ability to search a massive collection of published biomedical datasets that are currently buried and inaccessible. The Rummagene web application is available at https://rummagene.com .
Indexed as
Identifiers
What Socratic 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 Socratic graph.