Patent Document ID: 20110015869
Application ID: 12933936
Patent Flag: 0

Claim One:
1. A method for classifying an isolated cell sample as having a deregulated or regulated growth factor signaling pathway, comprising: (i) calculating a measure of similarity between a first expression profile and a regulated growth factor signaling pathway template, said first expression profile comprising the expression levels of a first plurality of genes in the tumor cell sample, said regulated growth factor signaling pathway template comprising expression levels of said first plurality of genes that are average expression levels of the respective genes in a plurality of control cell samples not having at least one or more components of said growth factor signaling pathway with abnormal activity, said first plurality of genes consisting of at least 5 of the genes for which biomarkers are listed in Tables 5a and 5b; (ii) classifying said tumor cell sample as having said regulated growth factor signaling pathway if said first expression profile has a high similarity to said regulated growth factor signaling pathway template, or classifying said tumor cell sample as having said deregulated growth factor signaling pathway if said first expression profile has a low similarity to said regulated growth factor signaling pathway template; wherein said first expression profile has a high similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is above a predetermined threshold, or has a low similarity to said regulated growth factor signaling pathway template if the similarity to said regulated growth factor signaling pathway template is below said predetermined threshold; and (iii) displaying; or outputting to a user interface device, a computer readable storage medium, or a local or remote computer system; the classification produced by said classifying step (ii).