TSIS

TSIS detects significant transcript isoform switches in time-series gene expression data, identifying reversals in relative expression between transcript isoforms of the same gene over time.

Key Features:

• Implementation: Implemented as an R package for analysis of transcript-level time-series expression data.
• Switch detection: Identifies potential isoform switch points within time-series datasets.
• Switch characterization: Characterizes detected isoform switches to describe their nature and implications.
• Parameter filtering: Supports refinement of results by applying specific input parameters that filter the data.
• Time-series focus: Tailored to detect isoform switches across time rather than relying solely on pairwise comparisons.
• Biological scope: Targets alternative splicing isoform switches defined as reversals in relative expression between two transcript isoforms of the same gene.

Scientific Applications:

• Gene regulation: Analysis of isoform switching to investigate temporal regulation of gene expression mechanisms.
• Cellular responses to stimuli: Detection of isoform switches that occur in response to external or internal stimuli across time.
• Disease progression: Characterization of temporal changes in isoform usage relevant to disease progression studies.
• Genomics and molecular biology: Study of transcript-level expression dynamics and alternative splicing in genomics and molecular biology research.
• Personalized medicine: Identification of time-dependent isoform changes that may inform individualized biomarkers or therapeutic responses.

Methodology:

Identifies potential isoform switch points in time-series gene expression data, characterizes detected switches, and applies input parameters to filter and refine results.