Pathway enrichment analysis of genes showing higher SEM burden in JIA patients than healthy controls revealed enrichment in key inflammatory pathways, including ‘TNF-alpha signaling via NF-kB’ and ‘TGF-beta signaling’, which has been previously implicated in JIA and rheumatoid arthritis (Zhang et al. 2023; Singh et al. 2012; Bira et al. 2005), further supporting the biological relevance of our findings (Supplementary Table S14). Here, NFKB1 is linked to rheumatoid arthritis.