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cytoscape / network-ptm-integration

This repo tracks the work of data-driven addition of phosphorylation sites to proteins in networks (and pathways).
MIT License
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Choose pathways as test cases #1

Open AlexanderPico opened 9 months ago

AlexanderPico commented 9 months ago

Let's pick one or a handful of pathways to use as test cases and compose a pathways.tsv file listing the WPIDs per row. These should be CPTAC-related pathways that we understand well and can manually verify and interpret the final output without too much trouble.

For example, we might pick a pathway that has been manually annotated with PTMs already. Then we could used a "stripped" version as the input to this new pipeline and compare it with the manual version. It shouldn't necessarily be the same, but the manual work already done can help in evaluating the output.

khanspers commented 9 months ago

Making a list here for now: Hippo-Merlin signaling dysregulation Wnt Signaling Cell Cycle ErbB signaling pathway TCA cycle nutrient use and invasiveness of ovarian cancer - would be nice if we could get a dataset with both low and high invasiveness ovarian cancer.