Increased methylation in OA cluster 3 and downregulated in OA cluster B | Decreased methylation in OA cluster 3 and upregulated in OA cluster B | ||||||||
---|---|---|---|---|---|---|---|---|---|
Gene symbol | Mean ß value difference (cluster 3−non-cluster 3) | Adjusted p value for methylation | Log Fc (cluster B vs non-cluster B) | Adjusted p value for expression | Gene symbol | Mean ß value difference (cluster 3−non-cluster 3) | Adjusted p value for methylation | Log Fc (cluster B vs non-cluster B) | Adjusted p value for expression |
Inflammatory/immune/defence response | Inflammatory/immune/defence response | ||||||||
CCL28 | 0.1447 | 9.88×10−6 | −0.6227 | 0.00130 | CD28 | −0.2863 | 6.97×10−6 | 0.7635 | 0.00162 |
IL16 | 0.1474 | 7.32×10−7 | −0.7627 | 0.00111 | FCGR2B | −0.1698 | 1.69×10−5 | 1.9550 | 0.00058 |
Cellular adhesion and migration | FCGR1A | −0.1612 | 3.82×10−5 | 1.5853 | 0.00064 | ||||
DDR2 | 0.0980 | 6.48×10−5 | −0.8365 | 0.00188 | LCP2 | −0.1489 | 5.68×10−5 | 2.6111 | 0.00007 |
DCC | 0.0122 | 0.00147 | −1.9390 | 0.00145 | KYNU | −0.1431 | 0.00012 | 1.3398 | 0.00019 |
Cell surface receptor-linked signal transduction | MX2 | −0.1218 | 0.00021 | 1.3058 | 0.00008 | ||||
GPR75 | 0.2761 | 0.00045 | −0.8595 | 0.00049 | HLA-DPB1 | −0.1140 | 0.00023 | 1.3535 | 0.00126 |
Carboxylic acid catabolic process | LCP1 | −0.1054 | 0.00034 | 2.4059 | 0.00020 | ||||
AMT | 0.1696 | 6.19×10−6 | −0.7351 | 0.00021 | LST1 | −0.1018 | 0.00027 | 1.6268 | 0.00027 |
DDAH1 | 0.0452 | 6.28×10−6 | −0.7000 | 0.00142 | NCF2 | −0.0966 | 0.00206 | 2.4497 | 0.00004 |
Other categories | TREM1 | −0.0861 | 0.00169 | 3.4118 | 0.00034 | ||||
SLC44A2 | 0.2959 | 0.00016 | −0.6322 | 0.00149 | IGSF6 | −0.0810 | 0.00096 | 2.7235 | 0.00005 |
PLSCR4 | 0.1241 | 7.09×10−5 | −0.7997 | 0.00012 | NCF4 | −0.0784 | 0.00105 | 1.2456 | 0.00022 |
CRIM1 | 0.1206 | 6.70×10−6 | −0.7080 | 0.00113 | LILRB5 | −0.0764 | 0.00012 | 1.8094 | 0.00019 |
CYGB | 0.0803 | 0.00043 | −0.8646 | 0.00040 | CD86 | −0.0758 | 0.00053 | 1.0675 | 0.00050 |
RHOJ | 0.0439 | 0.00017 | −0.8414 | 0.00142 | Cellular adhesion and migration | ||||
ABCA5 | 0.0375 | 0.00012 | −1.0671 | 0.00122 | PLEK | −0.2917 | 4.07×10−5 | 2.147 | 0.00005 |
PLA2R1 | 0.0195 | 0.00097 | −0.8952 | 3.48×10−5 | SELPLG | −0.1268 | 0.00143 | 2.687 | 0.00005 |
ZNF134 | 0.0188 | 0.00203 | −0.7573 | 0.00027 | CD33 | −0.1212 | 8.65×10−6 | 1.185 | 0.00158 |
PECAM1 | −0.1200 | 0.00021 | 2.332 | 0.00185 | |||||
SIGLEC10 | −0.1124 | 0.00026 | 0.618 | 0.00005 | |||||
ITGAX | −0.1087 | 0.00097 | 1.756 | 0.00090 | |||||
ITGAM | −0.1086 | 2.55×10−5 | 2.257 | 0.00003 | |||||
CD84 | −0.0959 | 0.00097 | 2.246 | 0.00022 | |||||
FERMT3 | −0.0834 | 0.00046 | 1.549 | 0.00011 | |||||
Cell surface receptor-linked signal transduction | |||||||||
GNA15 | −0.2186 | 8.91×10−5 | 1.977 | 0.00002 | |||||
MARCO | −0.1419 | 0.00117 | 2.430 | 0.00004 | |||||
Other categories | |||||||||
LAPTM5 | −0.2020 | 4.99×10−6 | 3.255 | 0.00017 | |||||
CYTIP | −0.1109 | 9.09×10−5 | 1.977 | 0.00011 | |||||
KCNMB1 | −0.1094 | 0.00127 | 0.613 | 0.00014 | |||||
MSR1 | −0.1001 | 0.00032 | 2.532 | 0.00023 | |||||
CTSZ | −0.0960 | 0.00101 | 0.840 | 0.00059 | |||||
NCKAP1L | −0.0855 | 0.00016 | 1.663 | 0.00039 |
Adjusted p values calculated by Benjamini & Hochberg's method for false discovery rate control. Log Fc, log fold change.
AMT, aminomethyltransferase; ABCA5, ATP-binding cassette, subfamily A (ABC1), member 5; DDAH1, dimethylarginine dimethylaminohydrolase 1; DDR2, discoidin domain receptor tyrosine kinase 2; CCL28, chemokine C–C motif ligand 28; CD86, CD86 molecule; CD84, CD84 molecule; CD28, CD28 molecule; CD33, CD33 molecule; CRIM1, cysteine-rich transmembrane BMP regulator 1; CTSZ, cathepsin Z; CYGB, cytoglobin; CYTIP, cytohesin 1 interacting protein; DCC, deleted in colorectal carcinoma; FCGR1A, Fc fragment of IgG high-affinity Ia receptor CD64; FCGR2B, Fc fragment of IgG low-affinity IIb receptor CD32; FERMT3, fermitin family member 3; GNA15, guanine nucleotide-binding protein (G protein) α15; GPR75, G protein-coupled receptor 75; HLA-DPB1, major histocompatibility complex, class II, DP β1; IL16, interleukin 16; IGSF6, immunoglobulin superfamily,member 6; ITGAX, integrin α X; ITGAM, integrin α M; KCNMB1, potassium large conductance calcium-activated channel, subfamily M, β member 1; KYNU, kynureninase; LAPTM5, lysosomal protein transmembrane-5; LCP2, lymphocyte cytosolic protein 2; LILRB5, leucocyte immunoglobin-like receptor, subfamily B (with TM and ITIM domains), member 5; LCP1, lymphocyte cytosolic protein 1 (L-plastin); LST1, leucocyte-specific transcript 1; MARCO, macrophage receptor with collagenous structure; MSR1, macrophage scavenger receptor 1; MX2, myxovirus (influenza virus) resistance 2 (mouse); NCF2, neutrophil cytosolic factor 2; NCF4, neutrophil cytosolic factor 4; NCKAP1L, NCK-associated protein 1-like; OA, osteoarthritis; PECAM1, platelet/endothelial cell adhesion molecule 1; PLA2R1, phospholipase A2, receptor 1; PLEK, pleckstrin; PLSCR4, phospholipid scramblase 4; RHOJ, ras homologue family member J; SLC44A2, solute carrier family 44, member 2; SIGLEC10, sialic acid binding Ig-like lectin 10; SELPLG, selectin P ligand; TREM1, triggered receptor expressed on myeloid cells 1; ZNF134, zinc finger protein 134.