Overview of the detection of immune–tumor cross talk genes. First, the ExSeq images were segmented using InSituSeg. Next, cell typing was performed using the cell's expression profiles, clustered after dimension reduction, and displayed via uniform manifold approximation and projection (UMAP). Finally, cross talk genes were detected using a differential expression, tree-based machine learning methods, and matrix factorization using cNMF (Kotliar et al. 2019). In the cNMF panel, gene expression program (GEP) can define cell type (blue = T cells, brown = tumor cells), or be proximity-related (yellow). In the schema, two GEPs represent cell types, and one GEP is triggered by proximity. The pie chart inside each cell describes its GEP usage.
