Table 6.
Top regulated soloculture enriched pathways at 24 h (top), 48 h (middle) and 96 h (bottom) for (A) the comparison of soloculture vs. coculture with human pericytes (CHP); and for (B) the comparison of soloculture vs. coculture with bovine pericytes (CBP)
| A. | B. | ||||
|---|---|---|---|---|---|
| 24 h | 24 h | ||||
| Pathway | Ratio | p-value | Pathway | Ratio | p-value |
| Post-Golgi vesicle mediated transport | 1.7 | 1.10E−06 | Regulation of cell morphogenesis involved in differentiation | 2.1 | 6.90E−04 |
| Regulation of programmed cell death | 1.7 | 6.50E−06 | Salivary gland morphogenesis | 3.0 | 7.60E−04 |
| Regulation of cell death | 1.7 | 8.70E−06 | Salivary gland development | 3.0 | 1.44E−03 |
| Regulation of apoptotic process | 1.7 | 1.40E−05 | Lysosomal transport | 2.0 | 1.72E−03 |
| Golgi vesicle transport | 1.8 | 1.90E−05 | Establishment of protein localization to plasma membrane | 3.3 | 2.66E−03 |
| Protein folding | 1.7 | 4.10E−05 | Protein localization to plasma membrane | 2.0 | 2.94E−03 |
| Regulation of transcription from RNA polymerase II promotor in response to hypoxia | 3.8 | 4.60E−05 | Positive regulation of osteoblast proliferation | 2.0 | 3.27E−03 |
| Negative regulation of cell death | 1.9 | 5.40E−05 | Plasma membrane organization | 2.0 | 4.00E−03 |
| Negative regulation of programmed cell death | 1.9 | 5.70E−05 | Toll-like receptor 3 signaling pathway | 1.6 | 5.24E−03 |
| De novo protein folding | 2.0 | 6.60E−05 | Exocrine system development | 3.0 | 5.72E−03 |
| 48 h | 48 h | ||||
| RNA export from nucleus | 1.5 | 2.30E−05 | RNA splicing, via transesterification reactions | 4.3 | 9.20E−08 |
| mRNA export from nucleus | 1.6 | 7.00E−05 | mRNA splicing, via spliceosome | 4.1 | 2.70E−07 |
| Post-Golgi vesicle-mediated transport | 1.5 | 3.40E−04 | RNA splicing, via transesterification reactions with bulged adenosine | 4.1 | 2.70E−07 |
| Protein localization to endosome | 7.0 | 5.80E−04 | Regulation of cellular protein catabolic process | 1.8 | 4.00E−07 |
| Type I interferon production | 1.8 | 7.00E−04 | Regulation of proteolysis involved in cellular protein catabolic process | 1.9 | 5.80E−07 |
| Regulation of type I interferon production | 1.8 | 7.00E−04 | Positive regulation of cellular protein catabolic process | 2.5 | 1.70E−06 |
| Regulation of monocyte differentiation | 2.0 | 7.60E−04 | mRNA metabolic process | 2.2 | 2.50E−06 |
| Golgi localization | 2.0 | 7.60E−04 | Ribonucleoside triphosphate biosynthetic process | 1.6 | 2.80E−06 |
| Protein K48-linked ubiquitination | 1.6 | 1.00E−03 | Positive regulation of proteolysis involved in cellular protein catabolic process | 2.7 | 3.40E−06 |
| Pyrimidine nucleotide metabolic process | 1.8 | 1.46E−03 | mRNA processing | 2.6 | 4.20E−06 |
| 96 h | 96 h | ||||
| Arp2/3 complex-mediated actin nucleation | 2.0 | 7.50E−04 | Positive regulation of protein ubiquitination | 2.8 | 1.00E−05 |
| Pyrimidine nucleoside triphosphate metabolic process | 1.8 | 1.01E−03 | Positive regulation of ligase activity | 3.9 | 1.90E−05 |
| Programmed necrotic cell death | 4.5 | 1.88E−03 | Positive regulation of protein modification by small protein conjugation or removal | 2.6 | 2.00E−05 |
| Necroptotic process | 9.0 | 2.59E−03 | Nucleoside monophosphate metabolic process | 2.2 | 2.70E−05 |
| Sprouting angiogenesis | 2.0 | 3.53E−03 | Positive regulation of ubiquitin-protein transferase activity | 4.3 | 4.40E−05 |
| Regulation of necroptotic process | 5.0 | 3.74E−03 | Regulation of protein modification by small protein conjugation or removal | 2.1 | 8.00E−05 |
| Fibroblast apoptotic process | 2.0 | 3.74E−03 | Regulation of protein ubiquitination | 2.1 | 8.60E−05 |
| Deoxyribonucleotide biosynthetic process | 4.0 | 4.17E−03 | Ribonucleoside monophosphate metabolic process | 1.9 | 1.10E−04 |
| Positive regulation of protein catabolic process | 2.0 | 5.23E−03 | Regulation of ligase activity | 4.0 | 2.30E−04 |
| Positive regulation of protein modification by small protein conjugation or removal | 1.8 | 5.81E−03 | Positive regulation of execution phase of apoptosis | 4.0 | 3.50E−04 |
Pathways in italic are soloculture enriched pathways identified in both comparisons for that specific time point. The 2nd column represents the ratio of upregulated and downregulated genes in the pathway under study (ratio ≥ 1.5)