ATAC-DEA: A Web-Based ATAC-Seq Data Differential Peak and Annotation Analysis Application

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) is crucial for studying gene regulation by identifying open chromatin sites.
• Biologists often face challenges in analyzing and interpreting ATAC-seq data due to limited bioinformatics expertise.
• Existing tools for ATAC-seq analysis have limitations in user-friendliness and comprehensive visualization.

Purpose of the Study:

• To develop a user-friendly web application, ATAC-DEA, for the exploration and visualization of ATAC-seq data.
• To facilitate differential peak analysis and annotation for biologists with limited programming experience.
• To provide an interactive platform for customizing ATAC-seq data analysis based on experimental needs.

Main Methods:

• Developed ATAC-seq Data Differential Expression Analysis (ATAC-DEA), a web application accessible at www.atac-dea.xyz:3838/ATAC-DEA.
• Utilized DiffBind and ChIPpeakAnno for differential peak and annotation analysis.
• Implemented a user-friendly interface for interactive data exploration and parameter modification.

Main Results:

• ATAC-DEA simplifies the input process by consolidating three files into a single input file.
• The application offers multifactor analysis, customized contrast models, and annotation of individual, overlapped, and differential peaks.
• Provides various downloadable plots for comprehensive data visualization.

Conclusions:

• ATAC-DEA empowers biologists to effectively analyze and visualize ATAC-seq downstream results without extensive bioinformatics training.
• The web application enhances the accessibility and interpretability of ATAC-seq data for gene regulation studies.
• ATAC-DEA offers a valuable, interactive solution for exploring chromatin accessibility and its regulatory roles.