PLATA

PLATA analyzes probe-level Affymetrix exon array data to investigate 3'UTR-mediated regulation of mRNA expression.

Key Features:

• Probe-Level Analysis: Performs probe-level examination and quantification of exon-specific signals from Affymetrix exon arrays.
• Raw Data Handling: Processes raw probe-level Affymetrix exon array data for accurate downstream analysis.
• Python Implementation: Implemented as a suite of Python scripts for data processing and analytical workflows.
• Visualization: Produces visualizations for interpreting probe-level and exon-level expression patterns.
• 3'UTR and Alternative Polyadenylation Analysis: Analyzes 3'UTR dynamics and alternative polyadenylation to assess impacts on mRNA stability, localization, and translation.

Scientific Applications:

• Gene Expression Programs: Identifies conserved expression patterns such as upregulation of mRNAs terminating at upstream polyadenylation sites after cellular activation, including in primary murine CD4+ T lymphocytes.
• Proliferation Correlations: Correlates changes in 3'UTR length and exon-level expression with cellular proliferation across cell types and tissues.
• Regulatory Capacity Analysis: Assesses how full-length versus truncated 3'UTRs alter protein expression, including effects of microRNA target site inclusion within variably included regions.

Methodology:

Uses Python scripts to process raw probe-level Affymetrix exon array data; identifies changes in mRNA expression associated with alternative polyadenylation events; and evaluates how 3'UTR length variation influences mRNA stability, localization, and translation, including consideration of microRNA target sites.