affyGG: computational protocols for genetical genomics with Affymetrix arrays

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Affymetrix arrays measure mRNA abundance using multiple probes per gene.
• Standard analysis averages probe data, potentially losing information due to sequence polymorphisms affecting hybridization.
• Genetical genomics experiments require sophisticated analysis to account for probe-level variations.

Purpose of the Study:

• To develop and present custom software for analyzing genetical genomics experiments.
• To enable quantitative trait loci (QTL) analysis at the individual probe level.
• To facilitate the identification of sequence polymorphisms impacting probe hybridization.

Main Methods:

• Development of an R package for probe-level QTL analysis.
• Creation of Perl scripts for generating custom tracks in the UCSC Genome Browser.
• Application of the software to analyze genetical genomics data in humans, mice, and other organisms.

Main Results:

• The R package provides functions for detailed QTL analysis, considering individual probe performance.
• Perl scripts allow visualization of probe regions within the UCSC Genome Browser, aiding polymorphism detection.
• The custom software enhances the analysis of genetical genomics experiments by accounting for sequence variations.

Conclusions:

• The presented software improves the accuracy and depth of genetical genomics data analysis.
• Individual probe-level analysis overcomes limitations of averaging probe data.
• This approach is valuable for understanding gene expression regulation influenced by genetic variation.