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A common approach is to infer its activity on the level of pathways using gene expression. However, mapping gene expression to pathway components disregards the effect of post-translational modifications, and downstream signatures represent very specific experimental conditions. Unlike existing methods, PROGENy can i recover the effect of known driver mutations, ii provide or improve strong markers for drug indications, and iii distinguish between oncogenic and tumor suppressor pathways for patient survival. Collectively, these results show that PROGENy more accurately infers pathway activity from gene expression than other methods.


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This is an R package for using the method described in Nature Communications. Skip to content.

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