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greenelab / connectivity-search-analyses

hetnet connectivity search research notebooks (previously hetmech)
BSD 3-Clause "New" or "Revised" License
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DWPC degree effect analyses for mansucript #176

Closed dhimmel closed 2 years ago

dhimmel commented 3 years ago

Some analyses that would be helpful for the manuscript:

  1. Show how DWPC measures are affected by source/target node degree.
  2. Show that the null distributions can remove these effects.
  3. Show that corrected DWPCs (either p-values or some other metric) provide superior prediction in certain domains (where avoiding recapitulating study bias is critical).
dhimmel commented 3 years ago

The HuRI gene/protein interaction data at http://www.interactome-atlas.org/download might be a good dataset for 3, since it's should not be subject to study bias.

A reference map of the human binary protein interactome
Katja Luck, Dae-Kyum Kim, Luke Lambourne, Kerstin Spirohn, Bridget E. Begg, Wenting Bian, Ruth Brignall, Tiziana Cafarelli, Francisco J. Campos-Laborie, Benoit Charloteaux, … Michael A. Calderwood
Nature (2020-04-08) https://doi.org/ggrjmp
DOI: 10.1038/s41586-020-2188-x · PMID: 32296183 · PMCID: PMC7169983

dhimmel commented 3 years ago

I'm envisioning a multi-panel figure that can illustrate some of the core concepts of degree-grouping:

  1. heatmap: degree-group versus number of samples
  2. heatmap: degree-group versus mean PC
  3. heatmap: degree-group versus mean DWPC
  4. heatmap: degree-group versus mean null DWPC
  5. heatmap: null gamma hurdle parameters?
  6. heatmap: mean DWPC p-value?