Calculating pathway activity from TCGA RPPA data
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14 months ago
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Is it possible to infer pathway activity from RPPA (reverse-phase protein array) data from for instance TCGA? I've read some papers where they say it is possible, but unfortunately they don't explain how.

R TCGA RPPA Pathway • 389 views
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14 months ago

Sure, just use any standard pathway analysis program. However, performing pathway analysis in this way is immediately biased by the fact that only certain genes were profiled via RPPA.

Check the input distribution of the RPPA data. While some pathway analysis tools may only take a list of genes / proteins, others may want, in addition, the expression data, which one would usually have following a normal distribution.

An idea: try STRINGdb

Kevin

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Thanks, I also thought about this procedure. What could be a way to make use of measurements where they measured both (non)-phosphorylated proteins? Manually checking databases like KEGG to see what influence the phosphorylated protein has?

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Your educated guess is as good as mine.

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