APAlyzer

APAlyzer analyzes alternative polyadenylation (APA) isoforms from RNA-seq data to quantify and characterize 3'UTR and intronic APA and to relate APA to gene expression using PolyA_DB and GTEx annotations.

Key Features:

• Implementation: Implemented as an R/Bioconductor package for analysis of APA from RNA-seq data.
• 3'UTR APA: Performs detailed analysis of alternative polyadenylation events occurring in 3' untranslated regions (3'UTRs) of genes.
• Intronic APA: Supports investigation of intronic APA events occurring within gene introns.
• Gene Expression Analysis: Integrates gene expression analysis from RNA-seq to relate transcriptional changes to APA isoform usage.
• Integration with PolyA_DB: Uses annotated polyadenylation sites from PolyA_DB to identify and characterize APA events.
• Cross-Tissue APA Profiling: Supports profiling of APA events across human tissues using GTEx data.

Scientific Applications:

• Regulation Under Different Conditions: Enables analysis of dynamic APA regulation across growth and differentiation conditions.
• Tissue-Specific Studies: Facilitates identification of tissue-specific APA patterns using GTEx-derived profiles.
• Gene Expression Correlation: Allows correlation of APA isoform usage with gene expression changes measured from RNA-seq.

Methodology:

Uses RNA-seq data as input and maps reads to annotated polyadenylation sites to quantify and characterize APA isoforms.