Single-cell VIPER activity matrix (internal signature)

Single-cell protein activity was computed on the SCTransform-scaled and Anchor-Integrated gene expression signatures across metaCells by the metaVIPER function in the VIPER package (Bioconductor). Briefly, metaVIPER was developed as an adaptation of VIPER to single-cell data. Protein activity is inferred for a given gene expression signature using multiple networks which are integrated on a protein-by-protein basis using the square of the NES generated by each individual network. Since a non-relevant network would generate a protein activity score close to zero under the null model, networks that generate more extreme NES can be interpreted to more accurately match the given biological context and are thus weighted more heavily for each protein. VIPER-inferred protein activity was computed on the gene expression signatures of all the single cells using the gene expression cluster-based single-cell ARACNe networks, and on the gene expression signatures of the tumor compartment single cells using the six patient-specific tumor single-cell ARACNe networks. The VIPER matrix includes all significant Master Regulators (MR).