Figure 4.

Examples of tiling results for known genes. The colored bars across the bottom of the data window are color matched with the corresponding exon annotations shown in the genome viewer. (a) The KDELR3 gene shows strong agreement between the public transcript annotations and the tiling results. The top panel represents a screen shot from the UCSC genome browser [60] highlighting KDLER3. The bottom panel represents transcription activity as raw intensities (y-axis) for each probe used to tile through KDLER3 (x-axis), in one of the eight conditions monitored by the genomic tiling arrays. (b) The EWRS1 gene potentially contains a larger number of false-positive predictions, but more probably lends additional experimental support to previously predicted alternative splice forms (EWSR.b and EWSR.g), giving a more accurate representation of the putative structure of this gene. The top panel represents a screen shot from the UCSC genome browser [60] highlighting EWRS1. The bottom panel represents transcription activity as raw intensities (y-axis) for each probe used to tile through EWSR1 (x-axis), in one of the eight conditions monitored by the genomic tiling arrays. (c) Conserved regions between mouse and human upstream of the beta-actin gene. The tiling data readily detect all of the transcribed parts of the gene, but not the conserved regulatory regions. The green bars in the probe-intensity plot represent the annotated transcribed regions for the beta-actin gene, while the blue bars indicate regions that are not known to be transcribed. The lower section shows the sequence conservation between human and mouse as obtained through the program rVISTA [36,61]. Conserved coding (blue peaks) and non-coding regions (red peaks) are shown where the two genomic sequences align with 75% identity over 100-bp windows. The rows marked ELK, ETF, and SRF show binding sites for these transcription factors predicted using TRANSFAC matrix models and the MATCHTM program, which are part of the rVISTA suite. The exons for the gene are shown in blue.