search

cytoscape / network-ptm-integration

This repo tracks the work of data-driven addition of phosphorylation sites to proteins in networks (and pathways).
MIT License
0 stars 0 forks source link

PTM datasets #3

Closed AlexanderPico closed 3 months ago

AlexanderPico commented 9 months ago

@khanspers and Bing are collecting PTM datasources. Let's capture that table here in folder called datasets, as a README, along with some sample datasets.

At first, let's get our hands on a few datasets that will likely relate to the handful of test pathways we have selected (see #1)

AlexanderPico commented 4 months ago

From Sarah: CPTAC pancancer, harmonizing 10 cancer datasets. https://kb.linkedomics.org/download

AlexanderPico commented 4 months ago

Yuxing will send correlated PROGENy:EGFR and pathway activity score (linear model) values per phosphosite.

khanspers commented 3 months ago

From Yuxing we got the following:

CPTAC_phospho_tn.txt (The p-values and statistics (“val”) are from Wilcoxon rank sum test. Positive values mean abundance is higher in tumor.) CPTAC_protein_tn.txt (The p-values and statistics (“val”) are from Wilcoxon rank sum test. Positive values mean abundance is higher in tumor.) CPTAC_PROGENy__EGFR.txt (EGFR pathway set correlation from PROGENy. The cohort.val is the Spearman correlation coefficient and cohort.pval is the p-value)