Affy exon tissues: exon levels in normal tissues in human, mouse and rat

Abstract

Summary: Most genes in human, mouse and rat produce more than one transcript isoform. The Affymetrix Exon Array is a tool for studying the many processes that regulate RNA production, with separate probesets measuring RNA levels at known and putative exons. For insights on how exons levels vary between normal tissues, we constructed the Affy Exon Tissues track from tissue data published by Affymetrix. This track reports exon probeset intensities as log ratios relative to median values across the dataset and renders them as colored heat maps, to yield quick visual identification of exons with intensities that vary between normal tissues.

Availability: Affy Exon Tissues track is freely available under the UCSC Genome Browser (http://genome.ucsc.edu/) for human (hg18), mouse (mm8 and mm9), and rat (rn4).

Fig. 1.

(a) The Affy Exon Tissues track demonstrates tissue-dependent splicing of two mutually exclusive exons (third and fourth from the left) in the mm9 TPM2 locus. Red indicates probesets that are up-regulated relative to median levels, while blue indicates down-regulated probesets. The constitutive exons (those included in all transcripts: first, second and fifth from the left) offer perspectives on overall gene expression, and indicate that the gene is up-regulated (red) in embryo, muscle and ovary. The leftmost mutually-exclusive exon appears upregulated in embryo and muscle, while the second appears upregulated in ovary. The remaining two probesets, which map to no known exons, are rendered mostly white. This indicates no variation in their expression levels, and suggests that they are not expressed in these tissues. (b) A probeset was designed for this unannotated region in mm9 based on more-speculative evidence such as genomic conservation or ab initio exon prediction. This region shows evidence of up-regulation (red) in brain, suggesting production of a brain-specific transcript.