AffyProbeMiner

AffyProbeMiner redefines Affymetrix chip definition files (CDFs) by remapping probes to verified coding sequences and mRNA transcripts to increase the accuracy of gene expression measurements.

Key Features:

• Regrouping and Remapping: Regroups individual probes into probe sets and remaps them to mRNA transcripts based on non-redundant, verified complete coding sequences.
• Use of Reference Databases: Leverages sequence information from GenBank and RefSeq to align probes with validated coding sequences and transcripts.
• Transcript-Consistency: Produces transcript-consistent probe sets that hybridize to the same mRNA transcript(s) and represent identical biological entities.
• CDF Redefinition: Rewrites Affymetrix-format CDF files to reflect updated probe-to-transcript mappings.
• Correction of Probe Set Inaccuracies: Corrects original Affymetrix probe groupings and mappings using updated genomic sequences, affecting approximately 65.6% of probe sets on chips such as HG-U133A.
• Splice Variant Handling and Customization: Supports consideration of splice variants and customization for commercial and custom short-oligo arrays with Affymetrix-format CDFs.
• Computational Efficiency and Extensibility: Implements platform-independent, computationally efficient procedures and an extensible framework for updates as new genomic data become available.

Scientific Applications:

• Gene Expression Analysis: Improves accuracy of microarray-based gene expression measurements by ensuring correct probe-to-transcript assignments.
• Genomics and Transcriptomics: Enables more reliable interpretation of microarray data in genomics and transcriptomics studies that depend on precise transcript-level measurement.
• Gene Function and Regulation Studies: Enhances validity of results for studies investigating gene function, regulation, and alternative splicing by providing updated probe mappings.

Methodology:

Integrates current genomic sequence information; regroups individual probes into probe sets using non-redundant verified complete coding sequences from GenBank and RefSeq; remaps probe sets to corresponding mRNA transcripts to generate transcript-consistent probe sets and updated Affymetrix-format CDFs.