MEAP

MEAP preprocesses and quantifies exon array data to estimate exon-, alternatively spliced variant-, and gene-level expression for genome-wide analysis of alternative splicing.

Key Features:

• PM-BayesBG sequence-based background estimation: Implements the PM-BayesBG algorithm to estimate sequence-based backgrounds for exon array probes.
• Robust expression estimates: Generates robust expression estimates at the exon and alternatively spliced variant levels and aggregates to gene-level expression.
• Computationally efficient pre-processing: Provides a pre-processing methodology tailored for large-scale exon array data to improve processing efficiency.
• Validation with comparisons and qPCR: Demonstrates reliability via comparisons to existing methods and qPCR validation of six exons and two alternatively spliced variants.
• Application to HNSCC and 11q13 amplification: Has been applied to head and neck squamous cell carcinoma (HNSCC) cell lines to identify transcripts associated with 11q13 amplification.

Scientific Applications:

• Alternative splicing analysis: Enables genome-wide detection and quantification of alternative splicing events at exon and variant resolution.
• Oncology research: Supports analysis of cancer-related transcriptomic alterations, exemplified by studies in HNSCC and 11q13 amplification.
• Biomarker and target discovery: Facilitates identification and characterization of alternatively spliced variants associated with disease progression and drug response.

Methodology:

Sequence-based background estimation using PM-BayesBG; exon array pre-processing, quantification at exon, alternatively spliced variant, and gene levels; visualization of expression levels; and method comparisons for validation.