Modeling of pathway cross-talk - Githubissues

saezlab / footprints

Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"

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Modeling of pathway cross-talk #24

Closed mschubert closed 7 years ago

mschubert commented 7 years ago

Fit using pathway factors:

That's how we do it now for speed_linear (w/o intercept)

Fit using perturbed vs basal for each pathway:

That's how we do it now for speed_matrix; VEGF surv increase?!
MAPK += EGFR - MAPK drug assocs > EGFR for MEKi

Fit using one matrix with 1/-1 coefficients:

MAPK += EGFR EGFR MEKi resistance (because non-MEK EGFR targets, esp. PI3K)
MAPK, PI3K += EGFR - mut assocs good (TP53, BRAF); EGFR survival increase (why?)
intercept but no xtalk - drug assocs good (MAPK>EGFR; good pvals: Trametinib<1e-15)
no intercept, no xtalk - ??