Analysis ideas

[mschubert]

• relationship between signalling footprints and pathway expression
  • overlap
  • which signal activates transcription of which pathway?
  • which pathways are more posttranslationally controlled, which more by expression? (would need phospho for this, but could probably do drug/survival response)
  • 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?
• 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)