ReviewEuropean journal of human genetics : EJHG2011
Gene set analysis of SNP data: benefits, challenges, and future directions.
Review in European journal of human genetics : EJHG, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers, 4 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
94 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Statistical genomics in rare cancer.Seminars in cancer biology · 2020Pooled it
- Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2015Pooled it
- Genome-wide pathway analysis in major depressive disorder.Journal of molecular neuroscience : MN · 2013Pooled it
- Systematic testing of literature reported genetic variation associated with coronary restenosis: results of the GENDER Study.PloS one · 2012Pooled it
- Utilising genomic association data for causal inference in anorexia nervosa.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Review
- RNA-Seq and Gene Set Enrichment Analysis (GSEA) in Peripheral Blood Mononuclear Cells (PBMCs).Methods in molecular biology (Clifton, N.J.) · 2025Article
- The genomic response to urbanization in the damselflyEvolutionary applications · 2023Article
- Article
- Working memory dysfunction in fibromyalgia is associated with genotypes of the catechol- O-methyltransferase gene: an event-related potential study.European archives of psychiatry and clinical neuroscience · 2023Article
- Genomic regions associated with pseudorabies virus infection status in naturally infected feral swine (Frontiers in genetics · 2023Article
- Genomic architecture of phenotypic extremes in a wild cervid.BMC genomics · 2022Article
- IPRS: Leveraging Gene-Environment Interaction to Reconstruct Polygenic Risk Score.Frontiers in genetics · 2022Article
- Genetic variants of SDCCAG8 and MAGI2 in mitosis-related pathway genes are independent predictors of cutaneous melanoma-specific survival.Cancer science · 2021Article
- Review
- A powerful subset-based method identifies gene set associations and improves interpretation in UK Biobank.American journal of human genetics · 2021Article
- Genetic Pathways and Functional Subnetworks for the Complex Nature of Bipolar Disorder in Genome-Wide Association Study.Frontiers in molecular neuroscience · 2021Article
- Genetic variants ofAmerican journal of cancer research · 2021Article
- Mood-Stabilizing Antiepileptic Treatment Response in Bipolar Disorder: A Genome-Wide Association Study.Clinical pharmacology and therapeutics · 2020Article
- Novel Variants ofCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2020Article
- Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges.Entropy (Basel, Switzerland) · 2020Review
34 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
2 authors.
Funding
Abstract
The last decade of human genetic research witnessed the completion of hundreds of genome-wide association studies (GWASs). However, the genetic variants discovered through these efforts account for only a small proportion of the heritability of complex traits. One explanation for the missing heritability is that the common analysis approach, assessing the effect of each single-nucleotide polymorphism (SNP) individually, is not well suited to the detection of small effects of multiple SNPs. Gene set analysis (GSA) is one of several approaches that may contribute to the discovery of additional genetic risk factors for complex traits. Complex phenotypes are thought to be controlled by networks of interacting biochemical and physiological pathways influenced by the products of sets of genes. By assessing the overall evidence of association of a phenotype with all measured variation in a set of genes, GSA may identify functionally relevant sets of genes corresponding to relevant biomolecular pathways, which will enable more focused studies of genetic risk factors. This approach may thus contribute to the discovery of genetic variants responsible for some of the missing heritability. With the increased use of these approaches for the secondary analysis of data from GWAS, it is important to understand the different GSA methods and their strengths and weaknesses, and consider challenges inherent in these types of analyses. This paper provides an overview of GSA, highlighting the key challenges, potential solutions, and directions for ongoing research.
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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.