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Table 3 Classification of genes that are differentially expressed in chondrocyte monolayer (baseline) and scaffold culture
| Functional annotation Gene title (Gene symbol) | Accession number | Fold change Scaffold vs Monolayer | |
|---|---|---|---|
| Normal donors | OA donors | ||
| Extracellular matrix | |||
| Aggrecan (ACAN) | [GenBank:X17406] | 2.0 | 3.4 ** |
| Asporin (ASPN) | [GenBank:NM_017680] | 18.8 * | 6.0 * |
| Biglycan (BGN) | [GenBank:NM_001711] | 12.5 | 12.7 * |
| Cartilage intermediate layer protein 2 (CILP2) | [GenBank:BC034926] | 78.2 * | 71.3 * |
| Collagen, type II, alpha 1 (COL2A1) | [GenBank:X06268] | 87.1 | 519.9 ** |
| Collagen, type XI, alpha 1 (COL11A1) | [GenBank:BG028597] | 10.4 ** | 5.9 * |
| Collagen, type IX, alpha 2 (COL9A2) | [GenBank:AI733465] | 4.3 | 8.1 |
| Cartilage link protein 1 (CRTL1) | [GenBank:NM_001884] | 2.5 | 1.8 |
| Cartilage oligomeric matrix protein (COMP) | [GenBank:NM_000095] | 128.0 ** | 794.2 *** |
| Dermatopontin (DPT) | [GenBank:AL049798] | 69.7 ** | 44.2 *** |
| Fibromodulin (FMOD) | [GenBank:NM_002023] | 5.1 | 8.4 * |
| Fibronectin 1 (FN1) | [GenBank:AJ276395] | 5.7 * | 34.6 *** |
| TIMP metalloproteinase inhibitor 4 (TIMP4) | [GenBank:NM_003256] | 14.1 * | 25.4 * |
| Tenascin C (TNC) | [GenBank:BF434846] | 3.3 | 3.5 * |
| Cell adhesion and receptors | |||
| Epidermal growth factor receptor (EGFR) | [GenBank:AW157070] | -3.0 ** | -1.9 |
| Fibroblast growth factor receptor 2 (FGFR2) | [GenBank:NM_022969] | -7.4 * | -4.3 |
| Laminin, alpha 2 (LAMA2) | [GenBank:AK026829] | 5.7 * | 4.8 |
| Laminin, alpha 4 (LAMA4) | [GenBank:NM_002290] | -6.6 * | -8.6 ** |
| Transforming growth factor, beta receptor I (TGFBR1) | [GenBank:AV700621] | 4.2 | 20.0 *** |
| Thrombospondin 3 (THBS3) | [GenBank:L38969] | 8.2 ** | 8.5 * |
| Growth factors | |||
| Bone morphogenetic protein 1 (BMP1) | [GenBank:NM_001199] | 2.1 * | 1.8 |
| Fibroblast growth factor 9 (FGF9) | [GenBank:NM_002010] | -9.0 | -3.0 |
| Insulin-like growth factor 1 (IGF1) | [GenBank:AI972496] | 8.3 | 6.0 |
| Insulin-like growth factor 2 (IGF2) | [GenBank:X07868] | 114.9 ** | 43.5 ** |
| Transforming growth factor, beta 1 (TGFB1) | [GenBank:BC000125] | 3.0 * | 2.4 * |
| Transcription factors | |||
| Distal-less homeobox 5 (DLX5) | [GenBank:NM_005221] | 5.1 * | 25.6 * |
| Homeobox A11 (HOXA11) | [GenBank:H94842] | 6.5 | 2.3 * |
| Homeobox A13 (HOXA13) | [GenBank:BG289306] | 5.2 | 2.0 |
| Runt-related transcription factor 2 (RUNX2) | [GenBank:AL353944] | 4.0 | 4.2 * |
| SIX homeobox 1 (SIX1) | [GenBank:N79004] | 1.6 * | 1.3 |
| SIX homeobox 4 (SIX4) | [GenBank:AI554514] | 1.8 | 2.3 |
| SRY (sex determining region Y)-box 9 (SOX9) | [GenBank:NM_000346] | 4.4 ** | 11.8 ** |
| Wingless-type MMTV integration site family, member 5B (WNT5B) | [GenBank:AW007350] | 3.0 | 7.0 |
| Enzymes | |||
| ADAM metalloproteinase with thrombospondin type 1 motif, 12 (ADAMTS12) | [GenBank:W74476] | -13.7 ** | -2.4 |
| ADAM metalloproteinase with thrombospondin type 1 motif, 2 (ADAMTS2) | [GenBank:NM_021599] | 3.1 | 4.7 ** |
| ADAM metalloproteinase with thrombospondin type 1 motif, 5 (ADAMTS5) | [GenBank:BF060767] | -8.8 * | -7.6 ** |
| Matrix metalloproteinase 1 (MMP1) | [GenBank:NM_002421] | -10.6 ** | -59.7 |
| Matrix metalloproteinase 2 (MMP2) | [GenBank:NM_004530] | 1.9 * | 3.4 * |
| Matrix metalloproteinase 7 (MMP7) | [GenBank:NM_002423] | 109.7 *** | 107.2 ** |
