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)

[eshinesimida]

Hello, very interesting work, I have a question, when I use import function, There is also an error. Like this,

b = import('base') Error in import("base") : could not find function "import" would you help me? thank you very much

[mschubert]

Hi eshinesimida,

Thank you for your interest.

The reason you see this error is that we use the modules package to cross-reference scripts, and the ebits toolkit for utility functions.

But you're right, we should probably document this better. Can you please open a new issue? (I will delete this comment here)