*2.2. Identification of the Common OA-Responsive Genes in Both Cartilage and Synovium*

Heatmaps of the differential expression genes (DEGs) in cartilage and synovium samples were generated, respectively, visualizing the gene expression changes between healthy and OA samples (Figure 2). In both cartilage and synovium, healthy samples could be easily distinguished from OA samples. Interestingly, cartilage displays more gene alteration in response to OA than synovium: 761 DEGs (414 increased, 347 decreased) were identified when comparing OA cartilage samples to their healthy counterparts and 372 OA-responsive DEGs (188 increased, 184 decreased) in synovium samples (Figures 2 and 3). Then, by comparing the OA-responsive DEGs in cartilage and synovium, we recognized 24 upregulated and 11 downregulated genes shared by these two tissues (Figure 3). In addition, there were 3 genes that exhibited different expression trends in cartilage and synovium in OA (Figure 3).

**Figure 2.** Heatmaps visualize the osteoarthritis (OA)-responsive differential expressed genes (DEGs) in cartilage and synovium, respectively.

**Figure 3.** Venn diagrams visualize the osteoarthritis (OA)-responsive differential expressed genes (DEGs) with the same or different expression trends in cartilage and synovium. *AMTN*—*Amelotin*; *ANLN*—*Anillin*; *ASPM*—*Abnormal spindle-like microcephaly-associated protein*; *C1QB*—*complement C1q subcomponent subunit B*; *CDK1*—*cyclin-dependent kinase 1*; *CHI3L2*—*Chitinase-3-like protein 2*; *CKAP2L*—*cytoskeleton-associated protein 2 like*; *FAP*—*fibroblast activation protein alpha*; *FPR3*—*N-formyl peptide receptor 3*; *GJB2*—*Gap junction beta-2 protein*; *H1ST1H3B*—*histone cluster 1 H3 family member b*; *IFNE*—*Interferon epsilon*; *KCNJ6*—*G protein-activated inward rectifier potassium channel 2*/*Potassium voltage-gated channel subfamily J member 6*; *LINC01411*—*long intergenic non-protein coding RNA 1411*; *LRRC15*—*Leucine-rich repeat-containing protein 15*; *MIR31HG*—*MIR31 host gene*; *MMP13*—*Matrix metallopeptidase-13*; *MSR1*—*Macrophage scavenger receptor types I and II*; *PBK*—*Lymphokine-activated killer T-cell-originated protein kinase*; *ST6GALNAC5*—*Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5*; *TNFAIP6*—*Tumor necrosis factor-inducible gene 6 protein*; *TOP2A*—*DNA topoisomerase 2-alpha*; *TREM1*—*Triggering receptor expressed on myeloid cell 1*; *VSIG4*—*V-set and immunoglobulin domain containing 4*; *ALDH1L1-AS2*—*ALDH1L1 antisense RNA 2*; *APOD*—*Apolipoprotein*; *CLDN5*—*Claudin-5*; *FOXI2*—*forkhead box I2*; *GPT2*—*Glutamate pyruvate transaminase 2*/*Alanine aminotransferase 2*; *IQCN*—*IQ motif containing N*; *KLF15*—*Krueppel-like factor 15*; *MYOC*—*Myocilin*; *PEAK3*—*PEAK family member 3*; *PFKFB3*—*6-phosphofructo-2-kinase*/*fructose-2,6-biphosphatase 3*; *TMEM211*—*transmembrane protein 211*; *RUN12*-*RNA U12 small nuclear*; *RUN6-2*—*RNA U6 small nuclear 2*; *PHACTR3*—*Phosphatase and actin regulator 3*.
