Fig. 4

Canonical pathway and cell-type enrichment of identified RA GWAS-associated genes and enrichment with RA gene expression disease profiles. Genes identified as associated with RA GWAS SNPs in monocytes, B cells, or T cells were tested for enrichment with the MSigDB term database a or a database of cell type-specific gene expression b. c The genes identified were compared to genes differentially expressed in three publicly available RA synovial tissue datasets with the GEO IDs indicated. The enrichment p value is the unadjusted p value from one-sided Fisher’s exact test. d The enrichment with the increased genes in the same RA synovial tissue datasets were compared with gene lists generated by choosing the closest genes to the RA GWAS SNPs (“closest genes”; the same number of genes are selected per SNP as with our method) or choosing any gene(s) within 5000 bp of the GWAS SNP (“within 5000 bp”)