A Transcript-level View Of Affymetrix Probe Sets Enhances The Interpretation And Exploitation Of Gene Expression Data

The wide use of Affymetrix Microarray in broad fields of biological research has made the probe set annotation a key issue. Standard Affymetrix probe set annotation is gene-centered, i.e. probe set is precisely linked to gene, and probe set expression is interpreted as gene expression. The exponentially increased sequence information and knowledge of one gene bearing multiple transcript variants clearly brings up the necessity of updating the gene-centered annotation to transcript-centered.This paper performed rigorous alignments of the Affymetrix probe sequences against a comprehensive pool of currently available transcript sequences. The hit transcript accessions were merged into non-redundant conceptual transcripts and linked to the International Protein Index. The alignment and association work resulted in the transcript or protein-level annotation tables for two popular Affymetrix expression arrays, Mouse Genome 430A 2.0 Array and Human Genome U133A Array, of which application in expression data analysis reveals increased expression...