Classical oncogenes and tumor suppressor genes: a comparative genomics perspective

Abstract

We have curated a reference set of cancer- related genes and reanalyzed their sequences in the light of molecular information and resources that have become available since they were first cloned. Homology studies were carried out for human oncogenes and tumor suppressors, compared with the complete proteome of the nematode, Caenorhabditis elegans, and partial proteomes of mouse and rat and the fruit fly, Drosophila melanogaster. Our results demonstrate that simple, semi-automated bioinformatics approaches to identifying putative functionally equivalent gene products in different organisms may often be misleading. An electronic supplement to this article provides an integrated view of our comparative genomics analysis as well as mapping data, physical cDNA resources and links to published literature and reviews, thus creating a "window" into the genomes of humans and other organisms for cancer biology.

Figure 1

Neighbor joining tree for the proteins that share fly and nematode matches with the human SRC family of genes. Seven human, seven rodent, one D. melanogaster and one C. elegans gene products belong to this “cluster.” Numeric values at branch points indicate the bootstrap values for 1000 tree replications.

Figure 2

Neighbor joining tree for the proteins that share fly and nematode matches with the human EGFR/ERBB-1 genes. Numeric values at branch points indicate the bootstrap values for 1000 tree replications.