Dataset Information

A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.

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.

SUBMITTER: Cirillo E

PROVIDER: S-EPMC5681904 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.

Cirillo Elisa E Parnell Laurence D LD Evelo Chris T CT

Frontiers in genetics 20171107

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 inte ...[more]

PMID: 29163640

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Project description:BackgroundObesity and dyslipidemias are risk factors for developing cardiovascular diseases, the leading causes of morbidity and mortality worldwide. The pathogenesis of these diseases involves environmental factors, such as nutrition, but other aspects like genetic polymorphisms confer susceptibility to developing obesity and dyslipidemias. In this sense, nutrigenetics is being used to study the influence of genetic variations on the circulating lipid responses promoted by certain nutrients or foods to provide specific dietary strategies considering the genetic factors in personalized nutrition interventions.ObjectiveTo identify throughout a systematic review the potential nutrigenetic recommendations that demonstrate a strong interaction between gene-diet and circulating lipid variations.MethodsThis systematic review used the PRISMA-Protocol for manuscript research and preparation using PubMed and ScienceDirect databases. Human studies published in English from January 2010 to December 2020 were included. The main results were outcomes related to gene-diet interactions and plasmatic lipids variation.ResultsAbout 1,110 articles were identified, but only 38 were considered to fulfill the inclusion criteria established based on the reported data. The acquired information was organized based on gene-diet interaction with nutrients and components of the diet and dietary recommendation generated by each interaction: gene-diet interaction with dietary fats, carbohydrates or dietary fiber, gene-diet interaction with nutraceutical or dietary supplementation, and gene-diet interaction with proteins.ConclusionFindings included in this systematic review indicated that a certain percentage of dietary macronutrients, the consumption of specific amounts of polyunsaturated or monounsaturated fatty acids, as well as the ingestion of nutraceuticals or dietary supplements could be considered as potential strategies for the development of a wide range of nutrigenetic interventions since they have a direct impact on the blood levels of lipids. In this way, specific recommendations were identified as potential tools in developing precision diets and highlighted the importance of personalized nutrition. These recommendations may serve as a possible strategy to implement as dietary tools for the preventive treatment and control alterations in lipid metabolism.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021248816, identifier [CRD42021248816].

Dataset Information

A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.

Publications

A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.

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