IsoSCM

IsoSCM applies change-point analysis to RNA-seq-based transcript assemblies to improve annotation of 3' untranslated regions (3' UTRs) and detection of alternative cleavage and polyadenylation (APA) events.

Key Features:

• Change-Point Analysis Integration: Integrates change-point analysis to detect transcript termini and partition RNA-seq signal into distinct 3' UTR isoforms.
• Improved 3' UTR Annotation: Reduces fragmentation of long 3' UTRs and distinguishes tandem isoforms for more accurate 3' end annotation.
• Alternative Cleavage and Polyadenylation Detection: Identifies APA events by resolving subtle variations in transcript ends indicative of alternative cleavage and polyadenylation.
• Evaluated Sensitivity and Specificity: Demonstrates superior sensitivity and specificity in annotating 3' termini based on evaluations with simulated and genuine RNA-seq datasets.
• Support for Genome-Wide APA Analysis: Enables genome-wide investigations of APA and 3' UTR regulation across genes and conditions.

Scientific Applications:

• Gene Expression Studies: Assess how changes in 3' UTR length and isoform composition affect gene regulation.
• RNA Processing Research: Investigate mechanisms and consequences of alternative cleavage and polyadenylation (APA).
• Cellular Identity and Disease Analysis: Examine APA pattern differences related to cellular differentiation, environmental responses, and disease progression.

Methodology:

Performs transcript assembly from RNA-seq data and applies change-point analysis to identify transcript ends and alternative cleavage and polyadenylation (APA) events.