ArticleG3 (Bethesda, Md.)2022
GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships.
Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- Article
- Genome-Wide Annotation of Promoter-Enhancer Interactions via Chromatin Loops in the Hybrid Rat Diversity Panel.bioRxiv : the preprint server for biology · 2026Article
- Genetic Loci Influencing Cue-Reactivity in Heterogeneous Stock Rats.Genes, brain, and behavior · 2025Article
- Twenty-first century mouse genetics is again at an inflection point.Lab animal · 2025Review
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.Cell genomics · 2024Article
- Genomic Loci Influencing Cue-Reactivity in Heterogeneous Stock Rats.bioRxiv : the preprint server for biology · 2024Article
- An approach for prioritizing candidate genes from RNA-seq using preclinical cocaine self-administration datasets as a test case.G3 (Bethesda, Md.) · 2023Article
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.bioRxiv : the preprint server for biology · 2023Article
- Divergent risky decision-making and impulsivity behaviors in Lewis rat substrains with low genetic difference.Behavioral neuroscience · 2023Article
- The effects of Phycocyanobilin on experimental arthritis involve the reduction in nociception and synovial neutrophil infiltration, inhibition of cytokine production, and modulation of the neuronal proteome.Frontiers in immunology · 2023Article
- The Wistar Kyoto Rat: A Model of Depression Traits.Current neuropharmacology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Interpreting and integrating results from omics studies typically requires a comprehensive and time consuming survey of extant literature. GeneCup is a literature mining web service that retrieves sentences containing user-provided gene symbols and keywords from PubMed abstracts. The keywords are organized into an ontology and can be extended to include results from human genome-wide association studies. We provide a drug addiction keyword ontology that contains over 300 keywords as an example. The literature search is conducted by querying the PubMed server using a programming interface, which is followed by retrieving abstracts from a local copy of the PubMed archive. The main results presented to the user are sentences where gene symbol and keywords co-occur. These sentences are presented through an interactive graphical interface or as tables. All results are linked to the original abstract in PubMed. In addition, a convolutional neural network is employed to distinguish sentences describing systemic stress from those describing cellular stress. The automated and comprehensive search strategy provided by GeneCup facilitates the integration of new discoveries from omic studies with existing literature. GeneCup is free and open source software. The source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup.
Indexed as
Identifiers
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.