CellPhoneDB[1] addresses the challenges of studying cell-cell communication in scRNA-seq and spatial data. It allows researchers to move beyond just measuring gene expression and delve into the complicated cellular communication world. By analyzing the scRNA-seq or spatial data through the lens of CellPhoneDB, researchers can identify potential signaling pathways and communication networks between different cell types within the tissue sample. Partek^® Flow^® wrapped the statistical analysis pipeline (method 2) from CellPhoneDB v5 for the purpose. 

CellPhoneDB task in Flow can be invoked in Exploratory analysis section by clicking the normalized counts data node (Figure 1). We recommend running CellPhoneDB on the normalized data directly, particularly the log normalized data.  

Figure 1. CellPhoneDB task in Flow

To run CellPhoneDB task, 

• Click a Normalized counts data node
• Click the Exploratory analysis section in the toolbox
• Click CellPhoneDB

The GUI is simple and easy to understand. For each option, the grey colored description explains more details (Figure 2).  If the dataset working on is single cell RNA-Seq, no Micro environment file is needed. However, if the dataset is spatial, most likely you would like to provide the Micro environment file because of its spatial contents. By default 0.10 will be used as threshold to select which cells are used for the analysis in the cluster. However, the number could be adjusted manually or typed in directly.  Simply click the Finish button if you want to run the task as default.

Figure 2. Interface of CellPhoneDB task in Partek Flow.

Double click the CellPhoneDB result data node will open the task report in Data Viewer. It is a heatmap that summarizes how many significant interactions identified in the cell type pairs (Figure 3).

Figure 3. CellPhoneDB task report in Data Viewer.

To explore more, the task of Explore CellPhoneDB results allows users to filter CellPhoneDB results by specifying the cell type pairs and genes of interest.  See Figure 4 on how to run the task. Its GUI is simple and easy to understand. For each option, the grey colored description explains more details (Figure 2).  If the dataset working on is single cell RNA-Seq, no Micro environment file is needed. However, if the dataset is spatial, most likely you would like to provide the Micro environment file because of its spatial contents. By default 0.10 will be used as threshold to select which cells are used for the analysis in the cluster. However, the number could be adjusted manually or typed in directly.  Simply click the Finish button if you want to run the task as default.

Figure 4. Task of Explore CellPhoneDB results in Partek Flow.

Double click the CellPhoneDB result data node will open the task report in Data Viewer. It is a heatmap that summarizes how many significant interactions identified in the cell type pairs (Figure 3).

References

1. Cusanovich, D., Reddington, J., Garfield, D. et al. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature 555, 538–542 (2018). https://doi.org/10.1038/nature25981

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