Fig. 3

Trajectory analysis of CD4⁺ T populations. a The developmental trajectory of CD4⁺ T cells, coloured-coded by the associated cell subpopulations (left) and states (right). b Gene set enrichment analysis of the CD4-C4-GZMA population with different cell fates. NES, normalised enrichment score. c Boxplots showing infiltrating score of cell fate2 cells in paired early (n = 32) and advanced (n = 32) lesions (left). Kaplan–Meier survival curve of the ischemic event (IE)–free survival in patients undergoing endarterectomy, stratified high and low according to the mean infiltration score of cell fate2 (right). *, P ≤ 0.05. Paired Student’s t test (left) and two-sided log-rank test (right). d The gene regulatory network constructed by Cytoscape, coloured for the associated gene type (red: top 30 upregulated genes from cell fate2 cells, blue: the upstream transcription factors predicted by RegNetwork, green: the targeted genes predicted by GeneMANIA). e Scatter plots showing the expression of selected transcription factors in different cell states as the pseudotime progresses