Out of twenty thousand genes,
you find the one in command
A KAIST team led by Prof. Kwang-Hyun Cho showed that lung cancer cells disguise themselves as fetal tissue to slip past the immune system, and found DDX54, the master regulator directing that disguise, through a three-stage ARACNe โ VIPER โ DIGGIT analysis.
Over these 20 lessons you rerun all three stages yourself on public TCGA raw data. Python runs right inside this page. There is nothing to install.
How you'll learn
Mutual information is a game of twenty questions, a regulon is the staff list under one boss, VIPER is reading the boss from how the staff move. You get a picture of the meaning before you memorise the formula.
Not a stand-in dataset. You work with the expression, mutation and copy-number data of 515 TCGA lung adenocarcinoma patients and the raw GEO GSE285342 data, exactly as deposited.
You put the regulator-score ranking you computed side by side with the actual values in the paper's supplementary Table S2A and argue out whether it matches.
Every lesson has a laboratory widget โ turn the DPI tolerance, the regulon size and the regulator quantile cut-off yourself.