Table 2.

Gene ontology analysis of genes associated with increased chromatin accessibility in CD4+CD28+KIR+CD11a^hi compared to the CD4+CD28+KIR-CD11a^low T cells isolated from lupus patients (derived from ATAC-seq). Gene ontologies with fold enrichment of at least 3 and false discovery rate of <10% are shown.

Gene Ontology Term	Genes	Fold Enrichment	P Value	FDR
GO:0033634~positive regulation of cell-cell adhesion mediated by integrin	CXCL13, PODXL, CCL5, PIEZO1	14.24	0.0016	2.95
GO:0032740~positive regulation of interleukin-17 production	PRKCQ, NOD2, IL23R, IL15, LY9, IL21, IL2	9.59	3.75E-05	0.07
GO:0042523~positive regulation of tyrosine phosphorylation of Stat5 protein	IL3, CSF2, IL23R, ERBB4, FYN, GHR, IL2	7.33	2.23E-04	0.41
GO:2000484~positive regulation of interleukin-8 secretion	HYAL2, CD58, F2RL1, CD2, F2R	6.85	0.0047	8.32
GO:0048008~platelet-derived growth factor receptor signaling pathway	PTPRJ, NRP1, BCR, CSRNP1, ARID5B, TIPARP, PDGFC, RAPGEF1, IQGAP1	5.52	1.42E-04	0.26
GO:0015026~coreceptor activity	RGMA, ACVR2A, CD86, NRP1, CD80, CXCR4, CXCR6, TGFBR3, ITGB1	5.34	1.85E-04	0.29
GO:0045672~positive regulation of osteoclast differentiation	FOS, IL23R, KLF10, IFNG, CCL5, TMEM64	5.09	0.0053	9.32
GO:0005164~tumor necrosis factor receptor binding	TRAF2, TNFSF10, TNFSF15, TNFSF14, FASLG, TNFSF9, EDA, TRAF3	4.91	9.03E-04	1.43
GO:0030032~lamellipodium assembly	ARHGEF4, CDH13, GOLPH3, NCK1, RAC1, CAPZB, PARVB, FGD4	4.59	0.0014	2.51
GO:0032266~phosphatidylinositol-3-phosphate binding	DAB2IP, PARD3, PLEKHA5, ZFYVE26, NCF4, ZFYVE28, DENND1A, PHLDA3	4.45	0.0017	2.64
GO:0042110~T cell activation	CD86, CD80, NEDD4, FYN, NCK1, CD2, CD276, TNFSF14, PPP3CA, WAS, DPP4	4.26	1.89E-04	0.35
GO:0005251~delayed rectifier potassium channel activity	KCNC2, KCNQ3, KCNA2, KCNA4, KCNA3, KCNA6, KCNV2, KCNG1	3.95	0.0034	5.32
GO:0032467~positive regulation of cytokinesis	KIF14, CUL3, KIF3B, CXCR5, SVIL, KIF20B, PRKCE, CDC25B	3.75	0.0047	8.33
GO:0007223~Wnt signaling pathway, calcium modulating pathway	GNAO1, GNG2, AGO4, PPP3CA, TNRC6B, PLCB1, TCF7L2, CTNNB1	3.65	0.0054	9.61
GO:0010811~positive regulation of cell-substrate adhesion	LIMS1, HSD17B12, RAC1, CCDC80, NID1, EDIL3, PRKCE, ITGB1	3.65	0.0054	9.61
GO:0045785~positive regulation of cell adhesion	PTPRJ, PTGER4, TNFRSF18, ITGA2, CCL5, NRG1, ADAM8, ADGRG1, TNFSF18	3.41	0.0043	7.60
GO:0014068~positive regulation of phosphatidylinositol 3-kinase signaling	ERBB4, NEDD4, FYN, F2RL1, PDGFC, SEMA4D, CCL5, PRR5L, NRG1, TGFB2, F2R	3.01	0.0032	5.72