Table 3 FlowSOM clusters differentially abundant between PBC and Control.

FlowSOM cluster ID	FlowSOM metacluster ID	Immune cell subset	PBC		Control		Fold-change^†	p value^‡
FlowSOM cluster ID	FlowSOM metacluster ID	Immune cell subset	Mean (%)	SD (%)	Mean (%)	SD (%)	Fold-change^†	p value^‡
9	3	Gamma-delta T cells (CXCR3⁺)	0.19	± 0.32	0.37	± 0.47	2.0(−)	0.014
10	4	CD8⁺ T cells (CD161⁺PD1⁺CD56⁺)	0.16	± 0.21	0.56	± 0.64	3.5(−)	0.003
11	4	CD8⁺ T cells (CD161⁺PD1⁺CTLA4⁺)	0.16	± 0.15	0.32	± 0.28	2.0(−)	0.002
27	4	CD8⁺ T cells (CD161⁺PD1⁺)	0.31	± 0.38	0.75	± 0.57	2.4(−)	< 0.001
50	9	Monocytes (IL3R⁺TIM3⁺)	0.52	± 0.60	0.26	± 0.45	2.0(+)	0.032
68	9	Monocytes	0.63	± 1.08	0.26	± 0.42	2.4(+)	0.035
113	9	CD66b⁺ Granulocytes (contaminant)	0.90	± 0.84	0.37	± 0.50	2.4(+)	0.006
177	16	Memory B cells	0.25	± 0.29	0.71	± 0.25	2.9(−)	0.004
196	18	CD45⁻ cells	0.59	± 0.60	0.26	± 0.25	2.3(+)	0.007

^†Ratio of larger mean to smaller mean. Positive and negative signs indicate higher mean in PBC and in Control, respectively.
^‡P-values from Mann–Whitney U test. FlowSOM clusters were considered to be associated with PBC if fold-change was ≥ 2.0 and p < 0.05.

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