TF and neoplasm: Since the model captures relationships between signaling proteins, TFs, and gene expression, we can use the trained W to obtain different views of a tumor data set: to infer the TF activities in each sample, we can right-multiply the protein expression profiles through the model by WPT; To infer protein activities in each sample, we can left-multiply the gene expression profile and motif-hit matrix through the model by YTDW. We refer to these operations as “mappings” onto the TF space and the protein space, respectively.