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. Author manuscript; available in PMC: 2024 Apr 19.
Published in final edited form as: Cell Syst. 2023 Apr 19;14(4):285–301.e4. doi: 10.1016/j.cels.2023.03.004

Figure 3.

Figure 3.

Residual mode can help to mitigate the confounding effects of other cell types present in the interaction region

A. Tissue regions annotated by CODA based on morphological features show clusters of acinar cells in close proximity to the neoplasia duct.

B. CoGAPS analysis reveals two patterns representing the stromal region (Pattern 6, orange), the neoplasia region (Pattern 9, blue) and all Other patterns (white).

C. Scatterpie chart showing the overlap between Pattern 6 and Pattern 9 also illustrated how the acinar cells coincide with the interaction region between the two patterns.

D. Two markers of acinar cells identified among the top SpaceMarkers of interaction between Patterns 6 and 9 also show overexpression in their interaction region.

E. Overrepresented pathways associated with neoplasia-stromal interactions identified by SpaceMarkers analysis in DE mode demonstrate overrepresentation of acinar cell markers.

F. Other relevant pathways are overrpresented in comparison to acinar markers with SpaceMarkers analysis in residual mode.