EINVis: a visualization tool for analyzing and exploring genetic interactions in large-scale association studies
Yubao Wu1, Xiaofeng Zhu, Jian Chen
1Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio.
Genetic Epidemiology
|August 13, 2013
Summary
EINVis is a new tool that visualizes gene-gene interactions detected in genetic studies. This network-based approach helps researchers explore complex genetic patterns and identify interactions among single nucleotide polymorphisms (SNPs).
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Complex traits are often influenced by multiple genetic factors, necessitating the study of gene-gene interactions (epistasis).
- Detecting epistasis in large genetic association studies presents significant statistical and computational challenges.
- Existing methods for epistasis detection typically output results in flat files, limiting further exploration.
Purpose of the Study:
- To develop an effective visualization tool for analyzing and exploring detected genetic interactions.
- To facilitate the investigation of hidden interaction patterns within large-scale genetic data.
- To provide a user-friendly platform for researchers studying epistasis.
Main Methods:
- Developed EINVis, a novel visualization tool for genetic interaction analysis.
- Employed a network-based approach to display interactions among genetic markers.
- Utilized a circular layout, specifically a tree ring view, for hierarchical visualization.
Main Results:
- EINVis visualizes interactions among single nucleotide polymorphisms (SNPs), genes, and chromosomes in a network structure.
- The tool enables users to differentiate marginal effects from interactions and track multi-marker interactions.
- EINVis aids in visualizing interactions at various levels and identifying proxy SNPs through linkage disequilibrium.
Conclusions:
- EINVis is an effective and user-friendly free visualization tool for analyzing and exploring genetic interactions.
- The tool enhances the understanding of complex genetic architectures underlying various traits.
- EINVis is publicly available with comprehensive documentation and an online tutorial.
Related Concept Videos
01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
02:46Genetic Screens
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
01:09Epistasis Analysis
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
01:12Statistical Software for Data Analysis and Clinical Trials
Statistical software is pivotal in data analysis and clinical trials by providing tools to analyze data, draw conclusions, and make predictions. These software packages range from simple data management applications to complex analytical platforms, supporting various statistical tests, models, and simulation techniques. Their significance lies in their ability to handle vast amounts of data with precision and efficiency, enabling researchers to validate hypotheses, identify trends, and make...
01:23Behavioral Genetics and Its Designs
Behavior genetics explores how genetic inheritance influences human behavior. It focuses on how genes, passed from parents to offspring, contribute to the development of behavioral traits and tendencies. This branch of genetics seeks to understand the complex interplay between inherited genetic factors and environmental influences in shaping our behaviors.
The primary methodologies used in behavior genetics include family studies, twin studies, and adoption studies, each providing unique...
The primary methodologies used in behavior genetics include family studies, twin studies, and adoption studies, each providing unique...