ReviewFrontiers in genetics2017
A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.
Review in Frontiers in genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- A Narrative Review on Integrative Bioinformatics Approaches for microRNA Research in Familial Mediterranean Fever: Current Insights and Future Directions.Health science reports · 2026Article
- Circulating metabolites, genetics and lifestyle factors in relation to future risk of type 2 diabetes.Nature medicine · 2026Article
- A multi-layered systems biology framework reveals dual-phased regulators and hormonal crosstalk underlying soybean cold tolerance.Plant cell reports · 2025Article
- Comparative Analysis of Genetic Risk for Viral-Induced Axonal Loss in Genetically Diverse Mice.International journal of molecular sciences · 2025Article
- Coactosin-like F-actin binding protein (Cotl1) plays a key role in adipocyte differentiation and obesity.Communications biology · 2025Article
- Fructose induces inflammatory activation in macrophages and microglia through the nutrient-sensing ghrelin receptor.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Orphan nuclear receptor NR4A1 regulates both osteoblastogenesis and adipogenesis in human mesenchymal stem cells.Molecular medicine reports · 2025Article
- Gene-environment interactions within a precision environmental health framework.Cell genomics · 2024Review
- The Histogenetic Origin of Malignant Cells Predicts Their Susceptibility towards Synthetic Lethality Utilizing theCancers · 2024Article
- Quantitative proteomic profiling in brain subregions of mice exposed to open-field low-intensity blast reveals position-dependent blast effects.Shock waves · 2024Article
- The alteration of cortical microstructure similarity in drug-resistant epilepsy correlated with mTOR pathway genes.EBioMedicine · 2023Article
- Basal forebrain cholinergic neurons are vulnerable in a mouse model of Down syndrome and their molecular fingerprint is rescued by maternal choline supplementation.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2023Article
- Applications of Genomics and Transcriptomics in Precision Medicine for Myopia Control or Prevention.Biomolecules · 2023Review
- Occupational exposure to diesel engine exhaust and serum levels of microRNAs in a cross-sectional molecular epidemiology study in China.Environmental and molecular mutagenesis · 2023Article
- A Drug Repurposing Pipeline Based on Bladder Cancer Integrated Proteotranscriptomics Signatures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Application of Multiple Omics to Understand Postoperative Delirium Pathophysiology in Humans.Gerontology · 2023Review
- Analytical Approaches to Uncover Genetic Associations for Rare Outcomes: Lessons from West Nile Neuroinvasive Disease.Methods in molecular biology (Clifton, N.J.) · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological processes in which the affected genes and proteins are involved. Such analyses support an interactive evaluation of the possible effects of variations on function, regulation or interaction of gene products. Current pathway analysis software often does not support data visualization of variants in pathways as an alternate method to interpret genetic association results, and specific statistical methods for pathway analysis of SNP data are not combined with these visualization features. In this review, we first describe the visualization options of the tools that were identified by a literature review, in order to provide insight for improvements in this developing field. Tool evaluation was performed using a computational epistatic dataset of gene-gene interactions for obesity risk. Next, we report the necessity to include in these tools statistical methods designed for the pathway-based analysis with SNP data, expressly aiming to define features for more comprehensive pathway-based analysis tools. We conclude by recognizing that pathway analysis of genetic variations data requires a sophisticated combination of the most useful and informative visual aspects of the various tools evaluated.
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