Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript...

Area of Science:

• Transcriptomics
• Molecular Biology
• Genomics

Background:

• Isoform-sensitive microarrays enable detailed human transcriptome studies.
• The Affymetrix GeneChip Human Exon 1.0 ST Array (Exon Array) profiles gene expression at the isoform level.
• The newer Affymetrix GeneChip Human Gene 1.0 ST Array (Gene Array) contains a subset of Exon Array probes.

Purpose of the Study:

• To explore the Gene Array's potential for assessing sub-transcript expression variation.
• To compare the Gene Array's performance against the Exon Array in detecting isoform variations.
• To evaluate the Gene Array's utility for alternative splicing analysis.

Main Methods:

• Utilized high-quality Microarray Quality Control (MAQC) RNA samples.
• Compared expression measurements from both Exon Array and Gene Array platforms.
• Modified Gene Array probe set definitions to enable exon-level summarization.
• Analyzed gene expression calls and splicing index for differentially spliced genes.

Main Results:

• Gene Array demonstrated comparable gene expression calls to the Exon Array.
• Highly correlated expression profiles between platforms after modifying Gene Array for exon-level analysis.
• Concordant results for expression calls of known differentially spliced genes.
• Good correlation in splicing index analysis, indicating comparable exon inclusion level estimates.

Conclusions:

• The Gene Array is effective for gene and exon expression profiling, capable of detecting alternative splicing and isoform variation.
• While having reduced gene content coverage compared to the Exon Array, it offers comparable selectivity and sensitivity for monitored splicing events.
• The Gene Array is suitable for researchers interested in gene expression with potential for splicing analysis, but not a substitute for the Exon Array.