Fig. 4: scMORE identifies key eRegulons associated with five autoimmune diseases in a cell type- and state-specific manner.

a, UMAP embedding of seven immune cell types from a single-cell multiomic dataset. The dataset includes monocytes (n = 3,313 cells), CD4⁺ T cells (n = 2,283 cells), CD8⁺ T cells (n = 997 cells), NK (n = 1,130 cells), mDC (n = 101 cells) and pDC (n = 121 cells). b, Proportion of autoimmune disease-associated eRegulons in each immune cell type. c, Heatmap illustrating scMORE-identified cell type-specific eRegulons associated with five autoimmune diseases across seven immune cell types. **Denotes P_CTS < 0.05, P_GRS < 0.05, P_TRS < 0.05 and TRS > 3. *Denotes P_CTS < 0.05, P_GRS < 0.05, P_TRS < 0.05 and TRS > 1.5. Significance was assessed by an MC permutation test (one-sided, upper tail; n = 1,000 iterations; no multiple correction). d, Scatter-plots highlighting significant eRegulons associated with IBD in CD8⁺ T cells, RA in CD4⁺ T cells, SLE in monocytes and UC in mDCs. Each dot indicates an eRegulon, with the −log-transformed GRS P values (−log₁₀(P)) shown on the y axis and the −log-transformed CTS P values (−log₁₀(P)) shown on the x axis. Gray dots represent nonsignificant eRegulons, while red dots indicate significant eRegulons. Significance was assessed by an MC permutation test (one-sided, upper tail; n = 1,000 iterations; no multiple correction). e, The UMAP visualization of 3,313 monocyte cells, highlighting two subtypes: CD14⁺ and FCGR3A⁺ monocytes. f, Feature plot displaying the expression of two marker genes. g, Heatmap showing scMORE-identified monocyte subtype-specific eRegulons associated with five autoimmune diseases. The color bar represents the TRS of each eRegulon, and * denotes P_CTS < 0.05, P_GRS < 0.05 and P_TRS < 0.05. Significance was assessed by an MC permutation test (one-sided, upper tail; n = 1,000 iterations; no multiple correction). h, TRS distributions for four eRegulon-disease pairs (HES5-IBD, KLF4-RA, BCL11B-SLE and UBTF-UC) across 50 monocyte cell states. Color bar indicates the TRS of each eRegulon.

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