TCIA

Immunophenogram

The immunophenogram [1] was constructed, similar to the recently proposed metabologram [2], to visualize the immunophenotypes of a tumor sample. The immunophenogram enables the calculation of an aggregated score -  immunophenoscore  - based on the expression of major determinants, identified by a random forest approach [ Supplementary Tables S4    ]. These factors were classified into four categories:

• MHC molecules (MHC)
• Immunomodulators (CP)
• Effector cells (EC)
• Suppressor cells (SC)

Samplewise z-score from gene expression of all factors (cell types) included in any of the ten best predictors within each cancer type are color coded and divided into the four categories. The outer part of the wheel includes individual factors, whereas the inner wheel illustrates the weighted average z-scores of the factors included in the particular category. The immunophenscore (IPS) was calculated on a 0-10 scale based on the expression of the representative genes or gene sets of the immunophenogram. Samplewise z-scores are positively weighted according to stimulatory factors (cell types) and negatively weighted according to inhibitory factors (cell types) and averaged. Z-scores ≥ 3 were designated as IPS10 and z-scores ≤ 0 are designated as IPS0.