Table 1.
Pathway analysis for genes with DNA methylation changes that negatively or positively correlated with disease activity in naïve CD4+ T cells in lupus
| Genes with negative correlation between
methylation status and disease activity in lupus | |||
|---|---|---|---|
| Pathway | Odds Ratio |
P value (FDR adjusted) |
Genes |
| Asthma | 8.49 | 2.67E-06 | IL13,IL4,IL5,HLA-DMB,HLA-DPA1,HLA-DRB1,HLA-DQA2,HLA-DMA,FCER1G,RNASE3,FCER1A,IL9,HLA-DQA1,HLA-DPB1,HLA-DRB5,IL3,CD40 |
| Allograft rejection | 5.81 | 1.69E-05 | IL12B,IL4,IL5,HLA-DMB,HLA-DPA1,HLA-DRB1,HLA-DQA2,HLA-A,CD86,HLA-DMA,HLA-DQA1,PRF1,HLA-DPB1,HLA-DRB5,GZMB,FAS,CD40,CD80 |
| Autoimmune thyroid disease | 4.11 | 2.94E-04 | IL4,IL5,HLA-DMB,HLA-DPA1,HLA-DRB1,HLA-DQA2,HLA-A,CD86,TPO,HLA-DMA,HLA-DQA1,PRF1,HLA-DPB1,HLA-DRB5,GZMB,FAS,CD40,CD80 |
| Graft-versus-host disease | 4.17 | 4.98E-04 | HLA-DMB,HLA-DPA1,HLA-DRB1,HLA-DQA2,HLA-A,CD86,IL6,HLA-DMA,KLRD1,HLA-DQA1,PRF1,HLA-DPB1,HLA-DRB5,GZMB,FAS,CD80 |
| Type I diabetes mellitus | 3.88 | 4.98E-04 | IL12B,HLA-DMB,HLA-DPA1,HLA-DRB1,HLA-DQA2,PTPRN2,HLA-A,CD86,HLA-DMA,CPE,HLA-DQA1,PRF1,HLA-DPB1,HLA-DRB5,GZMB,FAS,CD80 |
| Regulation of actin cytoskeleton | 1.93 | 5.47E-04 | DOCK1,VCL,TIAM2,CHRM2,FGFR2,LIMK2,FGF11,ITGB2,MYLK,CRK,ARHGEF6,FGF1,PIP5K1C,PIK3CD,ITGAD,ITGAX,FGF12,ITGB4,PDGFA,FGFR4,PIK3R1,DIAPH1, GNA12,FGF21,ITGAE,ITGB1,MYL7,MYL9,PXN,CHRM3,CYFIP1,VAV2,FGFR1,FGFR3,ITGA3,PIP4K2A,PDGFRB,MYLK2,ITGA11,BAIAP2,MYH9,NCKAP1L,ACTN4,MYH10,EGFR,GSN,ARHGEF7,PPP1CA,IQGAP2,SSH1,VAV3,PDGFD,DIAPH3,PIK3CB |
| Genes with positive correlation between
methylation status and disease activity in lupus | |||
|---|---|---|---|
| Pathway | Odds Ratio |
P value (FDR adjusted) |
Genes |
| Pathways in cancer | 2.39 | 7.62E-04 | TPM3,ARNT2,WNT10A,SMAD3,TCF7,CTNNA2,FGF12,KITLG,PIK3CD,CBL,ETS1,HDAC1,PDGFRA,BMP4,LAMA3,AXIN2,GLI3,TGFBR2,COL4A6,FGF13,BCR,FGF4,BIRC2,VEGFB,RASSF5,APC2,APC,TGFB2,MMP2,PLCG1,FGFR2,TGFBR1 |
| Neuroactive ligand-receptor interaction | 2.31 | 2.80E-03 | GALR1,MTNR1A,MC4R,GRM6,CHRM2,F2RL1,P2RX1,ADRA2A,GRM7,KISS1R,NPY1R,OPRM1,TSHR,NTSR2,GABRA5,GABRB2,HCRTR2,CHRNA3,GABRG2,CRHR1, GABBR2,GRIN1,PTGFR,PTGDR,S1PR1,MCHR1 |
| TGF-beta signaling pathway | 3.15 | 1.03E-02 | SMAD3,PPP2R1B,SMURF2,BMP4,TGFBR2,BMPR1A,ID4,ID3,PITX2,TGFB2,TGFBR1 |
| Colorectal cancer | 3.53 | 1.03E-02 | SMAD3,TCF7,PIK3CD,AXIN2,TGFBR2,APC2,APC,TGFB2,TGFBR1 |
| Glycosaminoglycan biosynthesis -chondroitin sulfate | 6.07 | 1.03E-02 | B3GAT1,CHST11,DSE,CHSY1,CHST13 |
| Phosphatidylinositol signaling system | 3.06 | 1.03E-02 | DGKZ,INPP5A,ITPR3,PIK3CD,PIP4K2A,ITPKB,DGKA,PLCB1,INPP4A,PLCG1 |