ReviewGenomics2011
Gene set analysis of genome-wide association studies: methodological issues and perspectives.
Review in Genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers, 6 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
116 citing papers in PubMed, 6 syntheses or guidelines pooled it, 212 citations in OpenAlex.
- Pathway Analysis of Renal Cell Carcinoma Genome-Wide Association Studies Identifies Novel Associations.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2020Pooled it
- Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer.Journal of the National Cancer Institute · 2019Pooled it
- A pathway analysis of genome-wide association study highlights novel type 2 diabetes risk pathways.Scientific reports · 2017Pooled it
- Systems Genetics Analysis of Genome-Wide Association Study Reveals Novel Associations Between Key Biological Processes and Coronary Artery Disease.Arteriosclerosis, thrombosis, and vascular biology · 2015Pooled it
- Network-based multiple sclerosis pathway analysis with GWAS data from 15,000 cases and 30,000 controls.American journal of human genetics · 2013Pooled it
- Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia.PLoS computational biology · 2012Pooled it
- Trial
- Multi-trait GWAS for growth under contrasting thermal rearing conditions in rainbow trout (Oncorhynchus mykiss).Molecular genetics and genomics : MGG · 2025Article
- A best-match approach for gene set analyses in embedding spaces.Genome research · 2024Article
- Novel insights into the genetic architecture of pregnancy glycemic traits from 14,744 Chinese maternities.Cell genomics · 2024Article
- The goldmine of GWAS summary statistics: a systematic review of methods and tools.BioData mining · 2024Article
- Uncertainty quantification in high-dimensional linear models incorporating graphical structures with applications to gene set analysis.Bioinformatics (Oxford, England) · 2024Article
- A high-dimensional omnibus test for set-based association analysis.Briefings in bioinformatics · 2024Article
- A genome-wide association study of Chinese and English language phenotypes in Hong Kong Chinese children.NPJ science of learning · 2024Article
- A gene regulatory network approach harmonizes genetic and epigenetic signals and reveals repurposable drug candidates for multiple sclerosis.Human molecular genetics · 2023Article
- Article
- The shared genetic architecture of suicidal behaviour and psychiatric disorders: A genomic structural equation modelling study.Frontiers in genetics · 2023Article
- Translational relevance of forward genetic screens in animal models for the study of psychiatric disease.Neuroscience and biobehavioral reviews · 2022Review
- MEF2C gene variations are associated with ADHD in the Chinese Han population: a case-control study.Journal of neural transmission (Vienna, Austria : 1996) · 2022Article
- Article
56 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Recent studies have demonstrated that gene set analysis, which tests disease association with genetic variants in a group of functionally related genes, is a promising approach for analyzing and interpreting genome-wide association studies (GWAS) data. These approaches aim to increase power by combining association signals from multiple genes in the same gene set. In addition, gene set analysis can also shed more light on the biological processes underlying complex diseases. However, current approaches for gene set analysis are still in an early stage of development in that analysis results are often prone to sources of bias, including gene set size and gene length, linkage disequilibrium patterns and the presence of overlapping genes. In this paper, we provide an in-depth review of the gene set analysis procedures, along with parameter choices and the particular methodology challenges at each stage. In addition to providing a survey of recently developed tools, we also classify the analysis methods into larger categories and discuss their strengths and limitations. In the last section, we outline several important areas for improving the analytical strategies in gene set analysis.
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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.