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. 2021 Aug 23;80(12):1575–1583. doi: 10.1136/annrheumdis-2021-220687

Figure 3.

Figure 3

MWAS results of the SLE case-control pathway association tests. (A) A quantile-quantile plot of the MWAS p values of pathways based on KEGG pathways (P pathway). The x-axis indicates log-transformed empirically estimated median P pathway. The y-axis indicates observed −log10(P pathway). The diagonal dashed line represents y=x, which corresponds to the null hypothesis. The horizontal red dashed line indicates the Bonferroni-corrected threshold (α=0.05), and the brown dashed line indicates the FDR threshold (FDR=0.05) calculated with Benjamini-Hochberg method. Pathways with p values less than the Bonferroni thresholds are plotted as red dots. Pathways with FDR<0.05 are plotted as brown dots, and other pathways are plotted as black dots. (B) System diagram of KEGG pathways. The three levels are defined as A, B and C and described from the inside layer out. The size and the colour of dots represent set sizes and P pathway, respectively. The seven pathways with significant enrichment (FDR<0.05) are outlined in red. (C) Comparison of P pathway between the SLE MWAS and GWAS data. The x-axis indicates the P pathway of the GWAS data (left, SLE GWAS; right, RA GWAS). The y-axis indicates the P pathway of the SLE MWAS. The horizontal and vertical black lines indicate P pathway of 0.05. The overlap of the pathway enrichment was evaluated by classifying the pathways based on the significance threshold of P pathway<0.05 or P pathway≥0.05 and using Fisher’s exact test. FDR, false discovery rate; GWAS, genome-wide association study; KEGG, Kyoto Encyclopedia of Genes and Genomes; MWAS, metagenome-wide association study; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus.