Figure 2

Detection of increased copy number on chromosomes 8q and 12p by DGS in HSC45 gastric cancer cells. (a) A whole-genome view of the tag density ratio (using a window of 1000 virtual tags) in HSC45 cells as determined by DGS. Values on the y-axis indicate fold-changes in tag density relative to the average tag density of the whole genome, and represent DNA content per haploid genome, in windows. The x-axis represents chromosome number. (b and c) Expanded view of tag density ratios on chromosomes 8 (b) and 12 (c). In each panel, the upper graph shows a whole-chromosome view of the tag density ratio (based on a window of 1000 virtual tags). The lower graph shows an expanded view of 8q24.21 and 12p12.1, in which increased tag density was detected using windows of 1000 and 500 virtual tags. Unique real tags are indicated as black vertical bars, and unique virtual tags are indicated in blue (60 bp or shorter) or light blue (longer than 60 bp) bars in dense mode. The positions of refseq genes, with some splicing isoforms omitted, are shown at the bottom of the lower panels.