Table 3.
Transcriptional Changes During Human Mesenchymal Stem Cell Three-Dimensional Chondrogenesis
| d0 → d3 | d3 → d7 | d7 → d10 | d10 → d14 | d14 → d21 | d21 → d28 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Fold change | Gene | Fold change | Gene | Fold change | Gene | Fold change | Gene | Fold change | Gene | Fold change |
| Significant upregulated genes comparing each time point during chondrogenesis | |||||||||||
| RHBDL2 | 56.0 | APOD | 11.6 | None | EPYC | 5.10 | CXCL14 | 4.07 | ORM1 | 6.17 | |
| SERPINA3 | 44.0 | GPAM | 9.3 | LECT1 | 4.75 | MMP10 | 3.80 | SLC38A4 | 2.36 | ||
| IL8 | 43.1 | RASL11B | 7.1 | KLK4 | 4.26 | ANGPTL7 | 3.40 | MT1H | 2.19 | ||
| PTGR2 | 42.5 | ANGPTL2 | 6.9 | CLEC3A | 4.05 | COL9A1 | 2.96 | APOD | 2.15 | ||
| RN7SK | 41.3 | MAT2A | 6.7 | MATN3 | 3.86 | FOXA2 | 2.79 | CXCL13 | 2.07 | ||
| CYCSL1 | 39.1 | COL10A1 | 6.2 | ANGPTL7 | 3.43 | IBSP | 2.64 | FTHL3 | 2.04 | ||
| LOC389765 | 38.2 | SCRG1 | 6.2 | OGN | 2.78 | COL11A2 | 2.59 | ORM1 | 6.17 | ||
| LOC729120 | 36.8 | CXCL13 | 6.1 | EPYC | 5.10 | F13A1 | 2.55 | SLC38A4 | 2.36 | ||
| FLJ40722 | 35.9 | PSAT1 | 5.5 | FMOD | 2.48 | MT1H | 2.19 | ||||
| LOC730993 | 35.5 | HAPLN1 | 5.3 | CSPG4 | 2.47 | ||||||
| GSTTP2 | 34.5 | FOXO1 | 5.3 | C2orf82 | 2.45 | ||||||
| C11orf63 | 33.8 | ID3 | 5.2 | PTH1R | 2.44 | ||||||
| TPR | 31.5 | AKR1C2 | 5.2 | COL9A2 | 2.44 | ||||||
| FAM73A | 31.4 | ID1 | 4.9 | ENPP1 | 2.38 | ||||||
| MBTD1 | 30.8 | SPP1 | 4.8 | IFITM5 | 2.36 | ||||||
| ZNF557 | 29.6 | PCNA | 4.7 | AEBP1 | 2.35 | ||||||
| MIR1974 | 29.1 | SPP1 | 4.7 | EFHD1 | 2.31 | ||||||
| RN7SK | 28.1 | RNU4-1 | 4.1 | CAPN6 | 2.31 | ||||||
| EEF1A2 | 26.8 | NOP56 | 4.1 | PRELP | 2.25 | ||||||
| ANKRD44 | 24.8 | HNRNPAB | 4.0 | MIA | 2.23 | ||||||
| GCLM | 24.0 | HNRPM | 3.9 | NGF | 2.21 | ||||||
| PRO1853 | 23.1 | MRFAP1 L1 | 3.8 | PMP2 | 2.21 | ||||||
| PRG4 | 22.7 | HSPA6 | 3.8 | CHST3 | 2.20 | ||||||
| Significant downregulated genes comparing each time point during chondrogenesis | |||||||||||
| FOSB | 0.06 | IL8 | 0.08 | PTGR2 | 0.09 | RN7SK | 0.09 | AKR1C3 | 0.40 | IL11 | 0.28 |
| CCL2 | 0.08 | PRG4 | 0.09 | FAM73A | 0.10 | RN5S9 | 0.18 | HSPE1 | 0.40 | IER3 | 0.28 |
| ARHGEF3 | 0.10 | TPR | 0.09 | RHBDL2 | 0.10 | HSPA6 | 0.21 | ANGPT1 | 0.43 | TUBB3 | 0.29 |
| ODZ4 | 0.10 | LBP | 0.11 | MBTD1 | 0.10 | RNU4-2 | 0.23 | C7orf10 | 0.44 | IFITM5 | 0.32 |
| CD248 | 0.11 | CHI3 L1 | 0.12 | GSTTP2 | 0.10 | RNU4-1 | 0.25 | GPAM | 0.45 | DBNDD1 | 0.33 |
| THBS1 | 0.12 | SFRP4 | 0.12 | FLJ40722 | 0.12 | RHBDL2 | 0.27 | TMSL3 | 0.46 | CRYGS | 0.33 |
| PDE7B | 0.12 | IER3 | 0.12 | KIAA1751 | 0.12 | KIAA1666 | 0.28 | CA12 | 0.34 | ||
| ANGPTL2 | 0.13 | C20orf186 | 0.13 | ZNF557 | 0.12 | FLJ46309 | 0.32 | CDC20 | 0.36 | ||
| ID1 | 0.13 | MIR1974 | 0.13 | IL17RD | 0.13 | FOXQ1 | 0.32 | TOP2A | 0.41 | ||
| MAT2A | 0.14 | MT3 | 0.13 | MIR886 | 0.13 | ARL16 | 0.33 | MATN4 | 0.41 | ||
| THBS2 | 0.15 | PTGS2 | 0.14 | FCAR | 0.13 | CAMK2 N1 | 0.35 | PTGS2 | 0.41 | ||
| NRP1 | 0.16 | STC1 | 0.15 | SLC5A8 | 0.14 | ZNF682 | 0.35 | ANGPTL4 | 0.42 | ||
| ID3 | 0.17 | C7orf68 | 0.15 | CYCSL1 | 0.14 | RNU6-1 | 0.36 | TAGLN | 0.44 | ||
| FASN | 0.17 | ANXA2P1 | 0.16 | ANKRD44 | 0.14 | RNU6-15 | 0.36 | MATN4 | 0.44 | ||
| KIAA1644 | 0.18 | SLC2A1 | 0.16 | XRCC2 | 0.14 | CYCSL1 | 0.37 | TYMS | 0.45 | ||
| PDGFRA | 0.18 | EFEMP1 | 0.16 | PRO1853 | 0.14 | FLJ40722 | 0.38 | KCNS1 | 0.46 | ||
| SFRS5 | 0.20 | LOX | 0.16 | SSTR2 | 0.15 | PNPT1 | 0.39 | PANX3 | 0.46 | ||
| STEAP1 | 0.20 | LOC387763 | 0.16 | CREB1 | 0.15 | RNU1G2 | 0.39 | BAPX1 | 0.46 | ||
| C14orf4 | 0.21 | HLA-DRA | 0.16 | DTWD2 | 0.15 | RNU1-5 | 0.39 | BEND5 | 0.46 | ||
| H3F3B | 0.22 | LOC730167 | 0.16 | DENR | 0.16 | RNU1-3 | 0.40 | SLC13A5 | 0.47 | ||
| SLC1A3 | 0.22 | PTGS2 | 0.17 | DEM1 | 0.16 | TMEM158 | 0.40 | PHLDA1 | 0.47 | ||
| EPDR1 | 0.23 | PPIB | 0.17 | LEP | 0.16 | CCBE1 | 0.41 | PRC1 | 0.47 | ||
Analysis of the filtered data showing changes in gene expression accumulated between each time point during the chondrogenic program. Significant up- and downregulated genes were analyzed for each time frame. Gene names in bold letters have or may have a role during chondrogenesis.