Criteria for assigning amplified and overexpressed genes

To be considered in this analysis, genes must lie within a minimal region of amplification and overexpression of the normal gene must accompany the amplification. Genes that meet this criteria are classified as class IV genes. Genes were further classified according to their scores as determined by the evidence shown in the table.

Supporting evidence Criteria Assigned score
Clinical correlation Expression correlated with clinical outcome 1 point
Knowledge of cancer genes and control pathways Mutation and amplification mutually exclusive 1 point
Sole identified gene within the amplicon 1 point
Inherited mutation predisposed to the same cancer type 1 point
Mutation or amplification and overexpression of other genes in the same pathway 1 point
Biological evidence Overexpression causes biological effect 1 point*
siRNA knockdown or targeted drug causes biological effect in the cell containing the amplified and overexpressed gene, but not in cells lacking the amplified and overexpressed gene 1 point*
Animal studies Substantial evidence from animal experiments 1 point

* Modulation of gene expression affecting biological properties can only be counted once.

Integrated datasets methodology

This methodology is used to screen for additional Class III genes using integrated datasets of DNA copy number and gene expression. We cross reference reported recurrent gene amplifications and overexpression found in these studies, with mutations in established cancer genes.

Pubmed search

"2009"[Publication Date]
    	(amplification[Title/Abstract] OR
	copy number[Title/Abstract] OR
	CGH[Title/Abstract] OR
	(microarray[Title/Abstract] OR
	SNP[Title/Abstract] OR