Analysis ideas

[mschubert]

• [x] relationship between signalling footprints and pathway expression
  • [x] overlap
  • [x] which signal activates transcription of which pathway?
  • [x] ~~which pathways are more posttranslationally controlled, which more by expression? (would need phospho for this, but could probably do drug/survival response)~~
  • [x] ~~is the effect the same for cell lines and primary tumors?~~
  • [ ] for each cancer type, where do pathway expression/footprints correlate more? less?
    • [ ] should do a pancan and tissue-specific correlation plot here (resp<->resp and resp<->expr)
• [ ] TCGA pathway activation + enrichment of variants that activate those
  • [ ] e.g., we find PI3K_variantTP53_R282W and enrichment of this variant in some cancers (BRCA)
    • [ ] does the same cancer need to have PI3K activated?
    • [ ] does p53 bind more PI3K-responsive genes with modified motif?
• [x] tcga_pathway_per_mutation: use GISTIC scores as regression coeffs? (= include +/-1)