Table_2

Table 2: 44 different phenotypes used in our example data, defined based on the expressed markers

Number	Shortened phenotype name	Full phenotype name
1	Apoptotic_Bcat+_HLA-DR+_tum	apoptotic β-catenin positive HLA-DR positive tumor cells
2	Apoptotic_Bcat+_Prol_tum	apoptotic β-catenin positive proliferating tumor cells
3	Apoptotic_Bcat+_tum	apoptotic β-catenin positive tumor cells
4	Bcat+_CD15+_tum	β-catenin positive CD15 positive tumor cells
5	Bcat+_FOXP3+_PDL1+_tum	β-catenin positive FOXP3 positive PDL1 positive tumor cells
6	Bcat+_HLA-DR+_Prol_tum	β-catenin positive HLA-DR positive proliferating tumor cells
7	Bcat+_HLA-DR+_TGFb+_tum	β-catenin positive HLA-DR positive TGFβ positive tumor cells
8	Bcat+_HLA-DR+_tum	β-catenin positive HLA-DR positive tumor cells
9	Bcat+_Prol_TGFb+_tum	β-catenin positive TGFβ positive proliferating tumor cells
10	Bcat+_Prol_tum	β-catenin positive proliferating tumor cells
11	Bcat+_TGFb+_tum	β-catenin positive TGFβ positive tumor cells
12	Bcat+_tum	β-catenin positive tumor cells
13	CD11c+_cells	CD11c positive cells
14	CD11c+_HLA-DR+_macrophages	CD11c positive HLA-DR positive macrophages
15	CD163+_HLA-DR+_macrophages	CD163 positive HLA-DR positive macrophages
16	CD38+_cells	CD38 positive cells
17	CD4+_Tcells	CD4 positive T cells
18	CD45RO_undefined	undefined CD45RO positive cells
19	CD57+_cells	CD57 positive cells
20	CD8-_Tcells	CD8 negative T cells
21	CD8+_Tcells	CD8 positive T cells
22	D2-40+_fibroblasts	D2-40 positive fibroblasts
23	D2-40+_TGFb+_fibroblasts	D2-40 positive TGFβ positive fibroblasts
24	D2-40+_vessels	D2-40 positive vessels
25	Fibroblasts	fibroblasts
26	Granulocytes	granulocytes
27	HLA-DR+_fibroblasts	HLA-DR positive fibroblasts
28	HLA-DR+_macrophages	HLA-DR positive macrophages
29	HLA-DR+_monocytes	HLA-DR positive monocytes
30	ICOS+_Tregs	ICOS positive regulatory T cells
31	ILC	innate lymphoid cells
32	Intraepithelial_CD4+_PD1+_Tcells	intraepithelial CD4 positive PD1 positive T cells
33	Intraepithelial_CD8+_Tcells	intraepithelial CD8 positive T cells
34	Macrophages_undefined	undefined macrophages
35	Monocytes	monocytes
36	Prol_Tcells	proliferating T cells
37	Tcells_undefined	undefined T cells
38	TGFb+_tum	TGFβ positive tumor cells
39	TGFb+_vessels	TGFβ positive vessels
40	Tregs	regulatory T cells
41	Unknown	unknown cells
42	Vessels	vessels
43	VISTA+_CD31+_CD38+_cells	VISTA positive CD31 positive CD38 positive cells
44	VISTA+_vessels	VISTA positive vessels