BMC Cancer 2008, 8:19 http://www.biomedcentral.com/1471-2407/8/19 FGiegnuersefr4om distinct chromosome locations are differentially enriched between the RGP and Met libraries Genes from distinct chromosome locations are differentially enriched between the RGP and Met libraries. Chromosome locations of all genes/ESTs were obtained from GenBank accession number reports or through BLAT alignment. (A) Represents the total number of genes per human chromosome for each library; (B and C) Represent the chromosome locations for all genes identified in the RGP (B) and Met (C) libraries, along the length (bp) of all human chromosomes. The absence of genes mapping to Y chromosome in the RGP library is not explained by lack of this chromosome since the RGP cell line WM1552C was obtained from a male patient. by other methods confirmed the differential expression between the metastatic and the WM1552C cells (Fig. 3). Although some subtracted genes might reflect only indi- vidual genetic variations due to the use of a single cell line representing the RGP stage, we believe many of them truly represent cancer associated genes, since among them we have several known genes with characterized cancer related functions (Additional files 2 and 4). Potential metastasis suppressor pathways Genes involved in DNA packaging, DNA repair and response to DNA damage are particularly enriched in the RGP library (Table 2), in accordance to the fact that early tumorigenic lesions have an activated DNA damage response and, in contrast to advanced tumors, are not marked by gross genomic instability [44,45]. The dispro- portion in the number of genes mapping to different chro- mosomes between the two libraries (Fig. 4) may be explained at least in part by chromosome abnormalities, which have been described for two of the cell lines used here, WM1552C (translocations involving 1p22, 5q34, 11p11, 12q11) and WM9 (loss of the long arm of chro- mosome 6 and gain of an extra copy of the entire chromo- some 7) [7]. Since no extra copy of chromosome 1 occurs Page 11 of 18 (page number not for citation purposes)