Additional file 2 of Large-scale integrative analysis of juvenile idiopathic arthritis for new insight into its pathogenesis

Additional file 2: Table S1. The list of 12 reference eQTL panels used in the TWAS for JIA. Table S2. The list of the total TWAS associations for JIA from the connective tissues. Table S3. The list of 35 significant TWAS associations for JIA (PTWAS < 7.55 × 10−07). Table S4. The list of the total PWAS associations for JIA. Asterisks represent significant PWAS associations after Bonferroni correction (PPWAS < 2.16 × 10−05). Table S5. The result of fine-mapping of TWAS/PWAS signals by using the FOCUS. Table S6. Biological pathways significantly involved in JIA, identified by the MAGMA (FDR < 0.05). Table S7. The list of Entrez IDs of genes in 11 co-expression modules identified by WGCNA. Table S8. The result of gene set enrichment analysis with TWAS associations using co-expression modules as reference gene sets. Table S9. Functional annotation of the 11 modules with GO terms using DAVID, respectively. Table S10. HLA allele types having significantly imbalanced distribution between healthy controls and JIA patients (P < 0.05). Table S11. HLA allele types having significantly imbalanced distribution between healthy controls, oligo-JIA, poly-JIA, and sJIA patients (P < 0.05). Table S12. HLA allele types having significantly imbalanced distribution between healthy controls, African JIA, and European JIA patients (P < 0.05). Table S13. The P-values calculated by comparing the alpha diversity of TCRs. Table S14. Expression profiles of gene markers in each T cell cluster.