Related Experiment Video
Updated: Feb 22, 2026

06:24
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
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PETScan: score-based genome-wide association analysis of RNA-Seq and ATAC-Seq data
Yajing Hao1, Tal Kafri2,3,4, Fei Zou1,5
1Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Bioinformatics (Oxford, England)
|February 20, 2026
Summary
PETScan efficiently analyzes gene expression and chromatin accessibility data, improving systems biology insights. This tool enhances genome-wide association studies by considering distant gene-regulatory element interactions.
Area of Science:
- Systems biology
- Genomics
- Bioinformatics
Background:
- High-dimensional sequencing data like RNA-Seq (gene expression) and ATAC-Seq (chromatin accessibility) are crucial for systems biology.
- Current methods often overlook long-range cis-regulatory interactions and fail to adequately model count-based sequencing data.
- Understanding gene regulation requires analyzing associations between gene expression and chromatin accessibility.
Purpose of the Study:
- To develop a computationally efficient method for genome-wide association analysis of RNA-Seq and ATAC-Seq data.
- To address limitations of existing tools by incorporating distant regulatory element interactions and accommodating count-based data.
- To provide a robust tool for uncovering gene regulatory mechanisms.
Main Methods:
- Introduced PETScan, a PEak-Transcript Score-based association analysis method.
- Utilized negative binomial models to accurately represent RNA-Seq count data.
- Employed score tests and matrix calculations for computational efficiency, combined with empirical permutation and genomic control for valid p-value calculations.
Main Results:
- PETScan demonstrated computational efficiency, achieving speeds three orders of magnitude faster than Wald tests.
- The method identified significant gene-peak pairs comparable to existing approaches.
- PETScan effectively analyzes genome-wide associations between gene expression and chromatin accessibility.
Conclusions:
- PETScan offers a computationally efficient and statistically robust approach for analyzing high-dimensional sequencing data.
- The tool enhances the study of gene regulatory mechanisms by considering both local and distant interactions.
- PETScan provides valuable insights for systems biology research and is available as an R package.
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