Table 1.
Genes with cross-omics significant differences between osteophytic and low-grade articular chondrocytes
| Gene | Gene DMPs in DMRs | Prop BetaFC >0 DMPs | RNA logFC | RNA FDR | Protein logFC | Protein FDR | ENSG | O vs H 5% FDR |
|---|---|---|---|---|---|---|---|---|
| ACTB | 4 | 0 | −0.9 | 9.48E-06 | 0.34 | 3.93E-04 | 075624 | |
| ALDH1A2* | 4 | 1 | −2.89 | 1.08E-07 | −3.29 | 1.44E-09 | 128918 | Y |
| ALDH1A3 | 10 | 1 | −1.89 | 3.02E-08 | −2.79 | 2.93E-08 | 184254 | Y |
| ARHGDIA | 4 | 1 | −0.48 | 2.35E-05 | −0.37 | 6.60E-05 | 141522 | Y |
| BLVRA | 3 | 1 | −0.63 | 3.85E-06 | −0.33 | 4.50E-04 | 106605 | Y |
| CASP4 | 2 | 0 | 0.87 | 1.53E-06 | 0.61 | 9.85E-04 | 196954 | |
| CHDH | 3 | 1 | −1.68 | 3.09E-06 | −1.32 | 8.92E-05 | 016391 | Y |
| CHI3L2 | 4 | 0.25 | −0.84 | 7.07E-05 | −0.97 | 7.33E-04 | 064886 | Y |
| CHST6 | 2 | 1 | −0.72 | 8.75E-05 | −0.73 | 9.80E-05 | 183196 | Y |
| CILP | 7 | 1 | −4.44 | 2.55E-08 | −3.55 | 1.07E-06 | 138615 | Y |
| COMP* | 13 | 1 | −1.16 | 3.10E-05 | −2.72 | 2.88E-06 | 105664 | Y |
| CPPED1 | 1 | 1 | −0.9 | 1.15E-05 | −0.69 | 1.18E-05 | 103381 | Y |
| CPT1A | 8 | 0.625 | 0.8 | 9.15E-04 | 0.91 | 4.64E-05 | 110090 | |
| CSRP1 | 5 | 0 | −0.39 | 5.37E-04 | −0.36 | 3.66E-04 | 159176 | Y |
| CYR61 | 5 | 1 | −2.09 | 2.83E-06 | −1.82 | 4.75E-07 | 142871 | Y |
| DCN | 3 | 1 | −1.06 | 1.15E-04 | −1.85 | 8.29E-05 | 011465 | |
| EFHD1 | 3 | 1 | −2.56 | 1.79E-06 | −0.79 | 3.98E-04 | 115468 | |
| EMILIN1 | 2 | 1 | −0.91 | 3.67E-05 | −1.73 | 5.11E-08 | 138080 | Y |
| EMILIN3 | 3 | 1 | −2.65 | 1.15E-06 | −2.96 | 4.11E-06 | 183798 | Y |
| FAM162A | 1 | 0 | 0.39 | 1.77E-04 | −0.74 | 1.24E-05 | 114023 | |
| FGF1 | 14 | 1 | −3.61 | 9.36E-08 | −2.15 | 1.01E-08 | 113578 | Y |
| FIBIN | 3 | 1 | −1.22 | 1.04E-05 | −2.73 | 1.53E-05 | 176971 | Y |
| GALE | 3 | 1 | −1.31 | 7.84E-06 | −1.42 | 2.54E-08 | 117308 | Y |
| GNAS | 2 | 1 | −0.37 | 4.49E-04 | −0.45 | 5.76E-05 | 087460 | Y |
| IDUA | 1 | 1 | 0.57 | 9.82E-05 | 0.34 | 9.73E-04 | 127415 | |
| IFI16 | 5 | 0 | 1.67 | 7.71E-05 | 1.21 | 3.55E-06 | 163565 | Y |
| IL6 | 4 | 0.5 | 4.27 | 2.62E-04 | 1.61 | 2.40E-04 | 136244 | Y |
| KRT8 | 9 | 1 | −2.29 | 8.55E-09 | −2.73 | 2.54E-08 | 170421 | Y |
| MMP13 | 4 | 0 | 3.16 | 1.95E-05 | 2.51 | 6.43E-08 | 137745 | Y |
| NEBL | 3 | 1 | −2.22 | 1.49E-07 | −1.49 | 8.84E-07 | 078114 | Y |
| NME2 | 6 | 1 | −0.53 | 4.07E-04 | −0.41 | 1.05E-04 | 243678 | |
| OSBPL10 | 4 | 1 | −1.51 | 1.08E-07 | -0.51 | 2.84E-04 | 144645 | |
| OSBPL3 | 2 | 0 | 1.36 | 1.19E-05 | 1.28 | 6.86E-06 | 070882 | Y |
| PAPSS2 | 2 | 1 | −0.95 | 1.82E-06 | −0.62 | 6.16E-05 | 198682 | |
| PDLIM4 | 3 | 1 | −1.3 | 4.22E-05 | −0.63 | 1.19E-05 | 131435 | |
| PGM1 | 1 | 1 | −0.57 | 2.82E-07 | −0.84 | 4.10E-06 | 079739 | Y |
| PRKCZ | 29 | 1 | −1.46 | 1.56E-06 | −0.83 | 4.52E-05 | 067606 | Y |
| PSTPIP1 | 3 | 1 | −1.51 | 2.99E-04 | −0.56 | 2.39E-04 | 140368 | Y |
| PTPRE | 2 | 0.5 | −0.77 | 5.24E-04 | −0.74 | 7.21E-05 | 132334 | Y |
| S100A1 | 2 | 1 | −1.97 | 1.75E-05 | −1.26 | 3.61E-05 | 160678 | Y |
| SCRN1 | 2 | 1 | −0.74 | 7.21E-05 | −0.95 | 3.52E-05 | 136193 | Y |
| SERPINA5 | 3 | 1 | −1.76 | 4.16E-08 | −1.58 | 1.19E-05 | 188488 | Y |
| SFN | 6 | 1 | −4.07 | 1.46E-07 | −1.68 | 3.03E-04 | 175793 | Y |
| SH3PXD2B | 5 | 0 | 1.28 | 1.83E-05 | 0.86 | 3.39E-04 | 174705 | Y |
| SLC25A22 | 2 | 0.5 | −0.53 | 5.48E-04 | 0.53 | 1.51E-05 | 177542 | |
| SLC29A1 | 4 | 0 | −1.28 | 6.39E-04 | −0.58 | 6.90E-05 | 112759 | Y |
| SMOC2 | 14 | 1 | −2.09 | 8.54E-07 | −2.29 | 6.23E-06 | 112562 | Y |
| SOD3 | 5 | 1 | −1.53 | 1.20E-06 | −1.69 | 2.42E-05 | 109610 | Y |
| TES | 1 | 1 | −1.59 | 6.30E-07 | −1.38 | 2.16E-07 | 135269 | Y |
| TF | 7 | 1 | −4.77 | 3.16E-09 | −0.94 | 7.82E-04 | 091513 | Y |
| TNFAIP2 | 8 | 0.625 | 1.84 | 3.75E-05 | 1.26 | 1.46E-04 | 185215 | Y |
| TPM3 | 0 | 0 | −0.5 | 2.83E-05 | 1.32 | 6.05E-04 | 143549 | Y |
| TRPV4 | 4 | 1 | −0.96 | 6.16E-04 | −0.69 | 1.65E-04 | 111199 | |
| TUBB2B | 5 | 0 | −2.14 | 8.00E-06 | −1.01 | 3.01E-05 | 137285 | Y |
| TYMP | 2 | 0 | 1.31 | 2.96E-04 | 0.84 | 4.55E-04 | 025708 | |
| UPP1 | 5 | 1 | −1.75 | 8.31E-07 | −0.93 | 1.86E-05 | 183696 | Y |
Only genes with significant differences on all three omics levels (methylation, gene expression and protein abundance) are shown. Gene DMPs in DMRs: differentially methylated probes at 0.1% FDR located in DMRs that overlap gene; Prop PosBetaFC DMPs: proportion of gene DMPs in DMRs that show increased methylation in osteophytic cartilage; DMR: differentially methylated region; logFC: log2-fold change (increase means higher value in osteophytic cartilage); FDR: false discovery rate; ENSG: Ensembl gene ID, prefix with ENSG00000; O vs H 5% FDR: genes with significant differences between chondrocytes from osteophytic and high-grade articular cartilage across all three molecular levels at 5% or lower FDR (Y = yes).
Genes associated with OA in genome-wide association studies.