The "Pathway" mode provides a pathway-based search. Users can narrow their search to studies of interest by refining the search box with keywords and finally search for pathways to see which studies have cellular communication mediated through that pathway

  • Note: Users can also search for all information in a relevant category, such as All Organisms, by selecting all information in the corresponding dropdowns box. Except for Study Type, in this category, users should select one of the Single or Comparison, as the corresponding results are different.

  • Single Dataset: Users can obtain the results of the cell communication analysis related to the current search, including basic information about the source and target cell, ligand and receptor, and the probability of communication. By clicking on the icons, users can also view a chord diagram of the total communication strength, a bubble diagram of individual communications, and the contribution of each cell as different roles in the communication network under the current pathway.

  • Comparison Dataset: Users can compare differences in the results of the same communication under disease and control. Attention: P-value = 3 means p value < 0.01; P-value = 2 means 0.01 < p value < 0.05; P-value = 1 means p value > 0.05

    • Note: The maximum record limit is 50,000.


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    The "L-R Pairs" mode provides a ligand‒receptor pair-based search. Users can select different analysis tools (including CellChat and CellPhoneDB) and narrow their search to studies of interest by refining the search box with keywords and finally search for ligands and receptors to see which studies have cellular communication mediated through those L-R pairs.

  • Note: Users can also search for all information in a relevant category, such as All Organisms, by selecting all information in the corresponding dropdowns box. Except for Study Type, in this category, users should select one of the Single or Comparison, as the corresponding results are different. Additionally, please note that using the CellPhoneDB analysis tool will only yield Single study results for Homo sapiens.

  • Single Dataset: Users can obtain the results of the cell communication analysis related to the current search, including basic information about the source and target cell, ligand and receptor, and the probability of communication. By clicking on the icons, users can also view a bubble diagram of individual communications under the current L-R pairs.

  • Comparison Dataset: Users can compare differences in the results of the same communication under disease and control. Attention: P-value = 3 means p value < 0.01; P-value = 2 means 0.01 < p value < 0.05; P-value = 1 means p value > 0.05

    • Note: The maximum record limit is 50,000.


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    The "Cell Types" mode provides a source and target cell-based search. Users can select different analysis tools (including CellChat and CellPhoneDB) and narrow their search to studies of interest by refining the search box with keywords and finally search for source cells and target cells to see which studies have cellular communication between the query cells.

  • Note: Users can also search for all information in a relevant category, such as All Organisms, by selecting all information in the corresponding dropdowns box. Except for Study Type, in this category, users should select one of the Single or Comparison, as the corresponding results are different. Additionally, please note that using the CellPhoneDB analysis tool will only yield Single study results for Homo sapiens.

  • Single Dataset: Users can obtain the results of the cell communication analysis related to the current search, including basic information about the source and target cell, ligand and receptor, and the probability of communication. By clicking on the icons, users can also view a bubble diagram of individual communications under the current source and target cells.

  • Comparison Dataset: Users can compare differences in the results of the same communication under disease and control. Attention: P-value = 3 means p value < 0.01; P-value = 2 means 0.01 < p value < 0.05; P-value = 1 means p value > 0.05

    • Note: The maximum record limit is 50,000.


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    The "L-R expression" mode allows users to query the expression levels of interested ligand-receptor genes in the relevant datasets. Users can narrow their search to studies of interest by refining the search box with keywords and finally input the ligands or receptors gene they want to query and retrieve its expression profile in the selected datasets.

    To perform the gene expression query in the L-R expression module, users need to follow these steps:

  • 1. Select the desired datasets using the options provided in Selection Boxes 1 to 4. These options help narrow down the datasets for the analysis.
  • 2. Choose one of the five available resolutions (provided as options) to annotate the cells. This step is crucial as different resolutions can impact the cell annotation results.
  • 3. Input the query genes for the gene expression analysis. It is essential to use semicolons as the separators between multiple genes.

    • By following these steps, users can obtain the dotplot about expression levels of their selected ligand or receptor genes in the specified datasets, at the chosen resolution.


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