GeneRegionScan

GeneRegionScan performs probe-level analysis of Affymetrix microarray and exon-array data to map probe sequences to mRNA or DNA targets and quantify expression and genotype–expression relationships.

Key Features:

• Probe-Level Analysis: Analyzes expression at individual probe resolution instead of summarizing probes into single gene-level values.
• Sequence Matching and Visualization: Matches probe sequences to mRNA or DNA target sequences and visualizes probe-level expression along the gene sequence.
• Linear Regression Modeling: Fits linear regression models based on various genetic models to assess genotype–expression relationships.
• R Package Implementation: Implemented as an R package.

Scientific Applications:

• Variable Splicing: Detects alternative splicing and exon-specific expression differences by analyzing probe-level signals across exons.
• Gene Expression Regulation: Investigates how genetic variation affects gene expression by relating genotype to probe-level expression measurements.

Methodology:

Matches probe sequences to target mRNA or DNA sequences, visualizes probe-level expression along gene sequences, and fits linear regression models under various genetic models.