ArticleGenes2015
JAG: A Computational Tool to Evaluate the Role of Gene-Sets in Complex Traits.
Article in Genes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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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
10 citing papers in PubMed.
- Pathway-Informed Machine Learning Identifies Genetic Predictors of High-Dose Methotrexate-Induced Mucositis in Pediatric Acute Lymphoblastic Leukemia.Clinical pharmacology and therapeutics · 2026Article
- Pathway analysis for genome-wide genetic variation data: Analytic principles, latest developments, and new opportunities.Journal of genetics and genomics = Yi chuan xue bao · 2021Review
- Decreased microglial Wnt/β-catenin signalling drives microglial pro-inflammatory activation in the developing brain.Brain : a journal of neurology · 2019Article
- Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic.PLoS genetics · 2019Article
- Integrative genomics of microglia implicates DLG4 (PSD95) in the white matter development of preterm infants.Nature communications · 2017Article
- Examination of the Involvement of Cholinergic-Associated Genes in Nicotine Behaviors in European and African Americans.Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco · 2017Article
- Molecular genetic aetiology of general cognitive function is enriched in evolutionarily conserved regions.Translational psychiatry · 2016Article
- Test for association of common variants in GRM7 with alcohol consumption.Alcohol (Fayetteville, N.Y.) · 2016Article
- Beyond main effects of gene-sets: harsh parenting moderates the association between a dopamine gene-set and child externalizing behavior.Brain and behavior · 2016Article
- Functional gene group analysis indicates no role for heterotrimeric G proteins in cognitive ability.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Gene-set analysis has been proposed as a powerful tool to deal with the highly polygenic architecture of complex traits, as well as with the small effect sizes typically found in GWAS studies for complex traits. We developed a tool, Joint Association of Genetic variants (JAG), which can be applied to Genome Wide Association (GWA) data and tests for the joint effect of all single nucleotide polymorphisms (SNPs) located in a user-specified set of genes or biological pathway. JAG assigns SNPs to genes and incorporates self-contained and/or competitive tests for gene-set analysis. JAG uses permutation to evaluate gene-set significance, which implicitly controls for linkage disequilibrium, sample size, gene size, the number of SNPs per gene and the number of genes in the gene-set. We conducted a power analysis using the Wellcome Trust Case Control Consortium (WTCCC) Crohn's disease data set and show that JAG correctly identifies validated gene-sets for Crohn's disease and has more power than currently available tools for gene-set analysis. JAG is a powerful, novel tool for gene-set analysis, and can be freely downloaded from the CTG Lab website.
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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.