Transcriptome data for chromosomes 21 and 22 from Affymetrix, as described in P. Kapranov et al. Large-Scale Transcriptional Activity in Chromosomes 21 and 22. Science, 296(5569):916-9). In general, the data presented is the perfect match - mis-match value. Different experiments were normalized by setting the average value to be the same for each chip. Replicates for different cell types were averaged together to produce the data seen in "full" mode for each cell type. In dense mode, or at the top of the track in full mode, "Transcriptome" displays the maximum value over all experiments for that probe, the idea being to paint as many transcribed regions as possible.
To present a more interpretable display when zoomed out, averages have been precalculated over the chromosome at two different resolutions in addition to the raw data. For example, when zoomed out, there may appear to be a peak at the center of a gene rather than a signal at every exon. Zooming in will reveal the "raw" data for that region.
NOTE: Affymetrix transcriptome annotations appear only on chromosomes 21 and 22.
Thanks to Affymetrix for providing these data. Questions/Comments? Email sugnet@soe.ucsc.edu.