TAPAS

TAPAS detects novel alternative polyadenylation (APA) sites from RNA-Seq data to analyze 3' untranslated region (3' UTR) shortening and lengthening events that influence mRNA stability, sub-cellular localization, translation efficiency, and protein binding.

Key Features:

• Comprehensive Detection of APA Sites: Identifies multiple APA sites per gene, including sites occurring before the last exon, rather than limiting analysis to only up to two sites or the terminal exon.
• Integration with Shortening/Lengthening Analysis: Couples APA site detection with analysis of 3' UTR shortening and lengthening to correlate APA events with changes in 3' UTR length.
• Advanced Methodology: Builds on an existing change-point detection method for time series data and applies additional filtration techniques to remove false-positive APA calls, improving reliability.
• Comparative Analysis Capability: Identifies APA sites that are differentially expressed between two biological samples to support comparative studies across conditions or disease states.

Scientific Applications:

• Post-transcriptional regulation studies: Profiles APA-mediated changes in 3' UTR length to investigate effects on mRNA stability, localization, translation efficiency, and protein binding.
• Disease and condition comparisons: Enables investigation of APA alterations across biological conditions or diseases, including cancer, to assess impacts on mRNA regulation.
• Comprehensive transcriptomic analysis: Supports analysis of complex datasets containing genes with multiple APA sites for detailed transcriptome-wide APA profiling.

Methodology:

Processes RNA-Seq data, applies an existing change-point detection method from time series analysis, employs filtration techniques to remove false-positive APA sites, and performs comparisons of APA site expression between two biological samples.