START-R

START-R analyzes DNA replication timing (RT) data to identify Constant Timing Regions (CTR), Temporal Transition Regions (TTR), and differential replication timing between experimental conditions.

Key Features:

• Replication Timing Region Detection: Identifies Constant Timing Regions (CTR) and Temporal Transition Regions (TTR) from high-throughput RT datasets.
• Differential RT Analysis: Detects significant replication timing differences between two experimental conditions for comparative studies.

Scientific Applications:

• Spatio-Temporal Genome Regulation Studies: Investigates relationships between DNA replication timing, transcriptional activity, epigenomic modifications, nuclear organization, mutation rates, and cell fate determination.

Methodology:

START-R implements an optimized replication timing protocol with partially automated processing, integrating R-based analytical scripts to segment RT profiles, classify CTR and TTR regions, and perform statistical comparisons across multiple high-throughput samples.