Figure 5.

Expression of genes mapping to the amplicon from methotrexate resistant colony 1M-89_6. (a) Chromosome 19 copy number profile at approximately 1.4 Mb resolution (HumArray3.0) shows four discrete regions of amplification. (b) Chromosome 19 copy number profile from the 32K BAC genome tiling path array in the amplified region showing the four regions of amplification detected on the lower resolution array and an additional small region distal to the others. The regions, ranging in size from 0.2 to 1.2 Mb, were amplified together in some cells as double minutes, while in others the amplified DNA was integrated into different chromosomes and present as a homogeneously staining region. Both copies of chromosome 19 were retained without rearrangement. As all regions are included together on the double minutes, their formation may have occurred by joining of broken pieces of DNA subsequent to resolution of stalled replication forks [63]. (c) Expression levels of genes mapping to the five amplified regions plotted according to position on the human genome sequence. Expression levels are shown as the log₂ ratios of the signal intensities after hybridization of Cy3 labeled cDNA from the methotrexate resistant colony and Cy5 labeled cDNA from the untreated parent 1M-89 as reference. Shown is the list of genes in genomic order that map to the amplified regions according to the RefSeq database [64]. Genes that are expressed in this cell line with or without exposure to methotrexate are labeled in black and expression levels denoted by black dots. Genes present on the array, but not expressed in untreated or resistant cells, are colored by dark gray and represented by dots of the same color with zero change in expression. Genes not present on the array are listed in the upper line in light gray. Genes with log₂ fold change >0.8 are indicated with an asterisk.