Figure 1.
Venn diagram of DEGs identified between the analysed primary MSC, ADM and CDM cells
Table 1.
The identified overrepresented GO terms and KEGG pathways based on DEGs modified during differentiation of MSCs to ADMs
| Accession number | Number of DEGs* | FDR | |
|---|---|---|---|
| Biological process | |||
| regulation of signalling | GO:0023051 | 393 | 0.00001 |
| fat cell differentiation | GO:0045444 | 47 | 0.0001 |
| positive regulation of cell differentiation | GO:0045597 | 125 | 0.001 |
| regulation of cell differentiation | GO:0045595 | 207 | 0.001 |
| regulation of cell communication | GO:0010646 | 390 | 0.001 |
| negative regulation of apoptotic process | GO:0043066 | 40 | 0.01 |
| response to growth factor | GO:0070848 | 88 | 0.01 |
| positive regulation of metabolic process | GO:0009893 | 370 | 0.02 |
| cell development | GO:0048468 | 241 | 0.03 |
| KEGG pathway | |||
| biosynthesis of amino acids | ecb01230 | 21 | 0.001 |
| metabolic pathways | ecb01100 | 200 | 0.01 |
| AGE-RAGE signalling pathway in diabetic complications | ecb04933 | 24 | 0.02 |
| aldosterone-regulated sodium reabsorption | ecb04960 | 13 | 0.02 |
| HIF-1 signalling pathway | ecb04066 | 25 | 0.02 |
| MAPK signalling pathway | ecb04010 | 50 | 0.02 |
| cAMP signalling pathway | ecb04024 | 40 | 0.02 |
Figure 2.
The detailed protein‒protein interaction (PPI) network of the identified DEGs associated with fat cell differentiation: the upregulated genes are marked with a blue halo; the downregulated genes are marked with a red halo; the additional GO terms are highlighted: blue, regulation of fat cell differentiation; yellow, regulation of cell differentiation; green‒brown, fat cell differentiation; and red, adipocyte fat development (String software v12.0)
Figure 3.
The involvement of the identified top DEGs (MSC vs. ADM cells) with significant GO terms (FC values according to the RNA-seq results) (R package)
Figure 4.
Heatmap of the DEGs between MSC and ADM primary cells identified as the top DEGs and showing their expression in only one group. A unit variance scale was used with no logarithmic transformation. (R software, ClustVis package)
Table 2.
The identified overrepresented GO terms and KEGG pathways based on DEGs modified during differentiation of MSCs to CDMs
| Accession number | Number of DEGs* | FDR | |
|---|---|---|---|
| Biological process | |||
| regulation of cell differentiation | GO:0045595 | 96 | 0.00006 |
| ossification | GO:0001503 | 35 | 0.00006 |
| negative regulation of developmental process | GO:0051093 | 62 | 0.00007 |
| regulation of signalling | GO:0023051 | 159 | 0.0001 |
| regulation of cell communication | GO:0010646 | 158 | 0.0001 |
| response to growth factor | GO:0070848 | 48 | 0.0004 |
| regulation of cell proliferation | GO:0042127 | 82 | 0.0005 |
| cell adhesion | GO:0007155 | 16 | 0.0006 |
| regulation of cell death | GO:0010941 | 79 | 0.001 |
| apoptotic process | GO:0006915 | 79 | 0.003 |
| KEGG pathway | |||
| cGMP-PKG signalling pathway | ecb04022 | 17 | 0.05 |
| fluid shear stress and atherosclerosis | ecb05418 | 15 | 0.05 |
Figure 5.
The detailed PPI network between the identified DEGs associated with ossification: the upregulated genes are marked with a blue halo; the downregulated genes are marked with a red halo; the additional GO terms are highlighted: blue, regulation of ossification; yellow, mesenchymal cell proliferation; purple, bone development; green, negative regulation of ossification; red, negative regulation of chondrocyte proliferation; pink, positive regulation of astrocyte differentiation; deep green, response to fluid shear stress; and orange, cell population proliferation (String software v12.0)
Figure 6.
Heatmap of the DEGs between MSCs and CDM primary cells identified as the top DEGs and showing their expression in only one group. A unit variance scale was used with no logarithmic transformation. (R software, ClustVis package)
Table 3.
The Pearson correlation coefficients obtained during RNA-seq result validation using qPCR
| Gene | Pearson correlation coefficient | P value |
|---|---|---|
| MSC vs. CDM comparison | ||
| BMP7 | 0.99 | <0.0001 |
| BMPR1B | 0.89 | 0.021 |
| CLDN1 | 0.99 | <0.0001 |
| IHH | 0.99 | <0.0001 |
| SOX9 | 0.95 | 0.003 |
| PHOSPHO1 | 0.99 | <0.0001 |
| MSC vs. ADM comparison | ||
| LEP | 0.75 | 0.084 |
| SOX9 | 0.98 | 0.008 |
| FABP4 | 0.99 | 0.001 |
| GERP1 | 0.66 | 0.153 |