ArticleNucleic acids research2018
Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 2 of them syntheses that pooled it.
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Who cites it
52 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Large-scale cross-ancestry genome-wide meta-analysis of serum urate.Nature communications · 2024Pooled it
- Shared genetic architectures of educational attainment in East Asian and European populations.Nature human behaviour · 2024Pooled it
- Neurobehavioural genes exert indirect genetic effects on blood lipid profiles through behavioural traits.Communications biology · 2026Article
- SNPWay: streamlined SNP-to-function and pathway over-representation analysis.bioRxiv : the preprint server for biology · 2026Article
- A resource of "bottom-line" variant associations for 1,281 complex traits by integrating data across published genome-wide association studies.Research square · 2026Article
- A Self-Adapting Polygenic Risk Score Model Improves Risk Prediction of Venous Thromboembolism in Han Chinese Cohorts.Phenomics (Cham, Switzerland) · 2025Article
- In Silico Analysis Reveals MDM2 as a Potential Target of Ursolic Acid for Overcoming Tamoxifen Resistance in Breast Cancer.Asian Pacific journal of cancer prevention : APJCP · 2025Article
- Genetic Nurture Effects on Type 2 Diabetes Among Chinese Han Adults: A Family-Based Design.Biomedicines · 2025Article
- Transcriptomic profiling of murine GnRH neurons reveals developmental trajectories linked to human reproduction and infertility.Theranostics · 2025Article
- Cross-modal embedding integrator for disease-gene/protein association prediction using a multi-head attention mechanism.Pharmacology research & perspectives · 2024Article
- Integrative Multiomics in the Lung Reveals a Protective Role of Asporin in Pulmonary Arterial Hypertension.Circulation · 2024Article
- A comprehensive framework for trans-ancestry pathway analysis using GWAS summary data from diverse populations.PLoS genetics · 2024Article
- CYP1B1-RMDN2 Alzheimer's disease endophenotype locus identified for cerebral tau PET.Nature communications · 2024Article
- The goldmine of GWAS summary statistics: a systematic review of methods and tools.BioData mining · 2024Article
- A deep learning framework for predicting disease-gene associations with functional modules and graph augmentation.BMC bioinformatics · 2024Article
- Omics-driven investigation of the biology underlying intrinsic submaximal working capacity and its trainability.Physiological genomics · 2023Article
- Genome-wide association study of brain biochemical phenotypes reveals distinct genetic architecture of Alzheimer's disease related proteins.Molecular neurodegeneration · 2023Article
- Hierarchical association of COPD to principal genetic components of biological systems.PloS one · 2023Article
- HetIG-PreDiG: A Heterogeneous Integrated Graph Model for Predicting Human Disease Genes based on gene expression.PloS one · 2023Article
- A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies.BMC bioinformatics · 2022Article
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9 authors.
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Abstract
Pathway-based analysis in genome-wide association study (GWAS) is being widely used to uncover novel multi-genic functional associations. Many of these pathway-based methods have been used to test the enrichment of the associated genes in the pathways, but exhibited low powers and were highly affected by free parameters. We present the novel method and software GSA-SNP2 for pathway enrichment analysis of GWAS P-value data. GSA-SNP2 provides high power, decent type I error control and fast computation by incorporating the random set model and SNP-count adjusted gene score. In a comparative study using simulated and real GWAS data, GSA-SNP2 exhibited high power and best prioritized gold standard positive pathways compared with six existing enrichment-based methods and two self-contained methods (alternative pathway analysis approach). Based on these results, the difference between pathway analysis approaches was investigated and the effects of the gene correlation structures on the pathway enrichment analysis were also discussed. In addition, GSA-SNP2 is able to visualize protein interaction networks within and across the significant pathways so that the user can prioritize the core subnetworks for further studies. GSA-SNP2 is freely available at https://sourceforge.net/projects/gsasnp2.
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