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Perturbation-response genes reveal signaling footprints in cancer gene expression

GSE97979 Homo sapiens Expression profiling by high throughput sequencing 24 samples Submitted 2017/04/20 Platform GPL11154
Summary
Aberrant cell signaling can cause cancer and other diseases and is a focal point of drug research. A common approach is to infer signaling activity of pathways from gene expression. However, mapping gene expression to pathway components disregards the effect of post-translational modifications, and downstream signatures represent very specific experimental conditions. Here we present PROGENy, a method that overcomes both limitations by leveraging a large compendium of publicly available perturbation experiments to yield a common core of Pathway RespOnsive GENes. 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 accurately infers pathway activity from gene expression.
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Direct links to NCBI, no account and no request form: the whole study as GSE97979_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 24 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA383562 and SRA study SRP104287. Searching any of these in the dataset finder brings you back here.

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