Cytokine signaling

Use this workflow to summarize immune signaling between sender and receiver cell populations. It combines ligand-receptor scoring, pathway aggregation, permutation-aware evidence, sender/receiver role summaries, and optional ligand-to-target follow-up when signaling needs a mechanistic hypothesis.

Research question

Which sender/receiver pairs and cytokine pathways dominate immune signaling, and which signaling axes differ by disease, treatment, timepoint, or response group?

Use case

Use this after immune annotation when the study needs interpretable cell-cell signaling evidence rather than only population proportions. The workflow is useful for ranking communication axes, comparing conditions, identifying sender/receiver roles, and deciding whether to run ligand-to-target hypothesis analysis.

Suggested path

1. Register expression and metadata inputs.
2. Run cell_communication.
3. Review signaling bubbles, complex-aware interactions, communication matrix, pathway heatmap table, p/q-values, specificity scores, sender/receiver roles, and comparative deltas.
4. Run Ligand Activity Inference when you have receiver target genes or want to infer receiver targets from a two-condition comparison.
5. Generate interpretation from completed communication and ligand activity runs.

Outputs to cite

• interaction score
• pathway score
• ligand activity score
• ligand ranking score
• ligand-receptor-target path score
• comparative delta
• p-value and adjusted p-value when permutations are requested
• sender/receiver role score