TP53andP53

[leslielay-123]

It's a very good tool. I would like to ask: When the TP53 gene is upregulated or downregulated in the P53 pathway, how do you define the upregulation or downregulation of the P53 pathway?

[deeenes]

The scores are calculated based on transcriptomics in perturbation experiments; the list of these can be found in the supplement of the original publication, with the perturbation types and search terms used to find these perturbation studies. The "pathway activities" inferred from transcriptomics are about the pathway as a whole, the activity of specific proteins, such as TP53 in the p53 pathway, depends on their position in network topology, and looking at the perturbation experiments and a pathway diagram, or even your own data and results, should be fairly easy to find out the relation between the pathway and a specific protein in it.