Transcript isoforms and exon array data. Probe-level exon array data is plotted in the top graphic. The data of the exon array is intentionally not plotted on the exact chromosomal location of the probes in order to clearly visualize alternative splicing events. Each line in the top track represents a different sample. Usually, there are four probes per exon on the Affymetrix GeneChip® Human Exon 1.0 ST platform, vertical gray lines group these four probes belonging to the same exon together. The blue connecting lines map these exons to gene models as defined by Affymetrix (green) and Ensembl (orange). Transcript isoforms known for this gene are plotted in dark blue. The region highlighted in the plot by an RectangleOverlay object shows the exon that is not expressed in the samples. One can see that this is a known alternatively spliced exon as annotated by Ensembl.
Durinck et al. BMC Bioinformatics 2009 10:2 doi:10.1186/1471-2105-10-2