ArticleNature methods2015
Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 3 of them syntheses that pooled it.
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
45 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Neural crest-derived tumor neuroblastoma and melanoma share 1p13.2 as susceptibility locus that shows a long-range interaction with the SLC16A1 gene.Carcinogenesis · 2020Pooled it
- Pooled it
- Pooled it
- Discovery and validation of ASG1 as a novel determinant of NaCl tolerance in the yeast Saccharomyces cerevisiae through iterative crossing.G3 (Bethesda, Md.) · 2026Article
- Integrating omics and functional data via representation learning to prioritize candidate genes for pleiotropic effect in dairy sheep.PNAS nexus · 2025Article
- The Importance of Regulatory Network Structure for Complex Trait Heritability and Evolution.Molecular biology and evolution · 2025Article
- Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci.PLoS computational biology · 2025Article
- A unifying statistical framework to discover disease genes from GWASs.Cell genomics · 2023Article
- A novel candidate disease gene prioritization method using deep graph convolutional networks and semi-supervised learning.BMC bioinformatics · 2022Article
- Prostate cancer in omics era.Cancer cell international · 2022Article
- Human Genomics and Drug Development.Cold Spring Harbor perspectives in medicine · 2022Review
- Triangulating Molecular Evidence to Prioritize Candidate Causal Genes at Established Atopic Dermatitis Loci.The Journal of investigative dermatology · 2021Article
- Rare genetic coding variants associated with human longevity and protection against age-related diseases.Nature aging · 2021Article
- An Integrative Analysis of Transcriptome and GWAS Data to Identify Potential Candidate Genes Influencing Meat Quality Traits in Pigs.Frontiers in genetics · 2021Article
- Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling.Cancers · 2020Article
- Genetics of extreme human longevity to guide drug discovery for healthy ageing.Nature metabolism · 2020Review
- Dynamic rewiring of the human interactome by interferon signaling.Genome biology · 2020Article
- The Integrated Landscape of Biological Candidate Causal Genes in Coronary Artery Disease.Frontiers in genetics · 2020Article
- Cross-population analysis for functional characterization of type II diabetes variants.BMC bioinformatics · 2019Article
- Benchmarker: An Unbiased, Association-Data-Driven Strategy to Evaluate Gene Prioritization Algorithms.American journal of human genetics · 2019Article
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
Genome-wide association (GWA) studies have linked thousands of loci to human diseases, but the causal genes and variants at these loci generally remain unknown. Although investigators typically focus on genes closest to the associated polymorphisms, the causal gene is often more distal. Reliance on published work to prioritize candidates is biased toward well-characterized genes. We describe a 'prix fixe' strategy and software that uses genome-scale shared-function networks to identify sets of mutually functionally related genes spanning multiple GWA loci. Using associations from ∼100 GWA studies covering ten cancer types, our approach outperformed the common alternative strategy in ranking known cancer genes. As more GWA loci are discovered, the strategy will have increased power to elucidate the causes of human disease.
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.