DAStk - Differential ATAC-seq toolkit

DAStk - Differential ATAC-seq toolkit analyzes differential ATAC-seq data to detect changes in chromatin accessibility and infer altered transcription factor (TF) activity.

Key Features:

• Transcription Factor Activity Analysis: Examines genome-wide TF recognition motif profiles relative to regions of open chromatin from ATAC-seq to identify TFs with altered activity.
• Versatility in Data Comparison: Compares any pair of bedGraphs, including regions such as transcription regulatory elements (TRE) from nascent transcription assays like PRO-seq or ChIP-seq peaks.
• Comprehensive Data Integration: Integrates a graph linking all human proteins listed in Uniprot with their annotations and all human Reactome data on pathways, biochemical reactions, and complex formation to enable queries about significantly changing TFs and shared aspects among factors.

Scientific Applications:

• Transcription factor activity profiling: Identifies TFs altered by perturbations, including drug treatments and disease states, to reveal changes in chromatin regulatory dynamics.
• Mechanistic insight and target prioritization: Links altered TFs to curated protein and pathway data to provide mechanistic hypotheses and support prioritization of potential therapeutic targets.

Methodology:

Analyzes chromatin accessibility (ATAC-seq) by examining genome-wide TF recognition motif profiles relative to regions of open chromatin, supports comparison of pairs of bedGraphs (e.g., TRE from PRO-seq or ChIP-seq peaks), and integrates Uniprot human protein annotations with Reactome pathway, reaction, and complex data into a queryable graph.