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Genomic Variations Explorer (GenVarX): a toolset for annotating promoter and CNV regions using genotypic and
Yen On Chan1, Jana Biová2, Anser Mahmood3
1MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States.
Frontiers in Genetics
|November 6, 2023
Summary
Genomic variations drive phenotype changes. The GenVarX toolset analyzes whole genome re-sequencing data, including copy number variations and SNPs, to understand plant trait differences.
Area of Science:
- Genomics and Phenomics
- Bioinformatics and Computational Biology
- Plant Science Research
Background:
- Whole genome re-sequencing (WGRS) data is increasingly abundant, offering opportunities to link genomic variations to phenotypic changes.
- Genomic variations, such as allele and structural changes, impact gene expression and organism phenotypes.
- Understanding these variations is crucial for advancing plant research and addressing complex biological questions.
Purpose of the Study:
- To develop an integrated toolset, GenVarX, for analyzing WGRS data to uncover genotype-phenotype relationships.
- To provide researchers with an interactive and visualization-enhanced platform for exploring genomic variations in plants.
- To facilitate the study of phenotypic differences by integrating diverse genomic and phenotypic datasets.
Main Methods:
- Developed the GenVarX toolset, integrating data on transcription factor binding sites, copy number variations, SNPs, Indels, and phenotypes.
- Employed efficient data processing scripts, libraries, and frameworks for WGRS data mining.
- Designed user-friendly interfaces for data querying, visualization, and interaction, including tabular displays and interactive figures.
Main Results:
- The GenVarX toolset provides accessible analysis of WGRS data, focusing on promoter regions and copy number variations.
- Interactive visualizations and tabular data outputs enhance the interpretation of genomic variation impacts.
- The toolset currently supports major plant models: soybean, rice, and *Arabidopsis*.
Conclusions:
- GenVarX offers a powerful, user-friendly solution for exploring genomic variations and their phenotypic consequences in plants.
- The toolset bridges the gap between genomics and phenomics, enabling deeper insights into plant biology.
- Accessible via SoyKB and KBCommons, GenVarX empowers researchers to investigate plant traits and variations effectively.
Keywords:
IndelsSNPscopy number variationgenomic variationsphenotypespromotertranscription factorwhole genome re-sequencing dataMore Related Videos
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