Supplementary Materials

Supplementary Materials for:

Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks

Mark Grimes,* Benjamin Hall, Lauren Foltz, Tyler Levy, Klarisa Rikova, Jeremiah Gaiser, William Cook, Ekaterina Smirnova, Travis Wheeler, Neil R. Clark, Alexander Lachmann, Bin Zhang, Peter Hornbeck, Avi Ma'ayan, Michael Comb

*Corresponding author. Email: mark.grimes{at}mso.umt.edu

This PDF file includes:

  • Text S1. Data analysis considerations and network development.
  • Fig. S1. Example t-SNE embeddings.
  • Fig. S2. Initial evaluation of clusters derived from t-SNE embeddings.
  • Fig. S3. Correlation between replicates.
  • Fig. S4. Number of edges per gene in clusters.
  • Fig. S5. Correlation between degree and betweenness.
  • Fig. S6. CFN betweenness is not biased by overrepresentation in PPI databases.
  • Fig. S7. The number of posttranslational modifications per protein weakly correlates with CFN betweenness.
  • Fig. S8. The effect of applying PTM correlation threshold on CFNs.
  • Fig. S9. Network density as a function of PTM correlation threshold defines a minimum for construction of a PTM CCCN.
  • Fig. S10. Relative network density of drug-affected proteins.
  • Fig. S11. EP300 interactions with PTM-modifying enzymes.
  • Fig. S12. Combined EP300 CCCN and CFN.
  • Fig. S13. Comparison of tyrosine phosphorylation, serine/threonine phosphorylation, and acetylation.
  • Fig. S14. Western blot data from cell fractionation experiments.
  • Fig. S15. Separation of tyrosine and serine/threonine phosphorylation and relative abundance compared to paxDB.
  • Legends for tables S1 and S2
  • Legend for data file S1
  • References (8991)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Proteins with PTMs that have negative correlations.
  • Table S2 (Microsoft Excel format). Amount of proteins in cell fractions.
  • Data file S1 (.cys format). Cytoscape file: Complete cocluster correlation network.

[Download Tables S1 and S2]

[Download Data file S1]


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