TSRexploreR

TSRexploreR analyzes and processes global transcription start site (TSS) mapping data from technologies such as Cap Analysis of Gene Expression (CAGE) and Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq) to identify TSSs and transcription start regions (TSRs) and characterize TSS heterogeneity relevant to transcript stability, translation, and gene regulation.

Key Features:

• Data compatibility and import: Imports mapped reads from BAM/SAM or pre-aggregated TSSs from GRanges, bigWig, bedGraph, or CTSS formats and accepts TSS/TSR sets from CAGEr.
• TSS and TSR detection: Detects individual TSSs and clusters them into transcription start regions (TSRs) for promoter identification.
• Normalization and correlation analysis: Provides normalization methods for TSS data and tools for correlation analysis across samples or conditions.
• Visualization: Generates graphical representations of TSS distributions and shifts across genomic regions.
• Differential analysis: Performs differential TSS and TSR analyses to identify changes in transcription initiation between conditions.
• TSS shift detection: Implements a novel approach for detecting shifts in TSS distribution to characterize dynamic changes in initiation sites.

Scientific Applications:

• Promoter atlas construction: Enables creation and refinement of promoter atlases by aggregating and clustering TSSs and TSRs genome-wide.
• Differential gene expression studies: Identifies condition-specific changes in transcription initiation that contribute to differential gene expression.
• Transcription initiation regulation: Facilitates analysis of TSS heterogeneity to investigate mechanisms affecting transcript stability and translation.
• Context-specific regulatory studies: Supports investigation of transcription initiation dynamics across biological contexts such as development, metabolism, and disease.

Methodology:

Implements import of BAM/SAM or pre-aggregated TSSs (GRanges, bigWig, bedGraph, CTSS), detection of TSSs and clustering into TSRs, normalization, correlation analysis, differential TSS/TSR analysis, visualization, and a novel TSS shift-detection method.