Table 1.
List of biological processes GO categories enriched among genes differentially expressed in mineralizing VSa13 and VSa16 cells
| VSa13 (CHONDROCYTIC LINEAGE) | VSa16 (OSTEOBLASTIC LINEAGE) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| BP | TERM | COUNT | % | P | FE | TERM | COUNT | % | P | FE |
| protein homotetramerization | 6 | 0.5 | 0.006 | 3.8 | ||||||
| PROT. INTER. | protein tetramerization | 7 | 0.5 | 0.013 | 2.9 | |||||
| protein homooligomerization | 9 | 0.7 | 0.024 | 2.3 | ||||||
| rRNA transcription | 5 | 0.4 | 0.019 | 3.8 | ||||||
| DNA/RNA METAB. | DNA replication | 37 | 2.9 | 0.000 | 2.1 | |||||
| DNA-dependent DNA replication | 19 | 1.5 | 0.001 | 2.1 | ||||||
| serine family amino acid biosynt. process | 6 | 0.4 | 0.025 | 2.9 | vitamin biosynthetic process | 10 | 0.8 | 0.003 | 2.7 | |
| hexose/alcohol/monosaccharide biosynthetic process | 12 | 0.8 | 0.005 | 2.3 | water-soluble vitamin biosynthetic process | 9 | 0.7 | 0.008 | 2.6 | |
| BIOSYN. PROC. | amino acid biosynthetic process | 15 | 1.0 | 0.043 | 1.7 | hexose/alcohol/monosaccharide biosynthetic process | 10 | 0.8 | 0.028 | 2.1 |
| carbohydrate biosynthetic process | 21 | 1.5 | 0.016 | 1.6 | coenzyme biosynthetic process | 21 | 1.6 | 0.012 | 1.7 | |
| nitrogen compound biosynthetic process | 21 | 1.5 | 0.027 | 1.6 | cofactor biosynthetic process | 24 | 1.9 | 0.035 | 1.5 | |
| amine biosynthetic process | 19 | 1.3 | 0.040 | 1.5 | ||||||
| pigmentation | 7 | 0.5 | 0.026 | 2.6 | ||||||
| inner ear morphogenesis | 7 | 0.5 | 0.045 | 2.4 | ||||||
| fertilization | 9 | 0.7 | 0.024 | 2.3 | ||||||
| DEV. | tissue remodeling | 14 | 1.1 | 0.009 | 2.0 | |||||
| embryonic morphogenesis | 14 | 1.1 | 0.013 | 2.0 | ||||||
| tissue development | 33 | 2.5 | 0.005 | 1.6 | ||||||
| embryonic development | 33 | 2.5 | 0.010 | 1.5 | ||||||
| mitochondrion organization and biogenesis | 15 | 1.0 | 0.016 | 1.8 | mitotic cell cycle checkpoint | 9 | 0.7 | 0.024 | 2.3 | |
| cell motility/localization of the cell | 59 | 4.1 | 0.002 | 1.4 | cell cycle checkpoint | 12 | 0.9 | 0.015 | 2.1 | |
| mitosis/M phase of mitotic cell cycle | 35 | 2.4 | 0.024 | 1.4 | regulation of mitosis | 14 | 1.1 | 0.009 | 2.0 | |
| cell projection: morphogenesis, | 28 | 2.0 | 0.040 | 1.4 | growth | 38 | 2.9 | 0.001 | 1.6 | |
| CELL CYCLE | organization and biogenesis | regulation of cell growth | 18 | 1.4 | 0.042 | 1.6 | ||||
| AND | M phase | 40 | 2.8 | 0.034 | 1.3 | regulation of growth | 25 | 1.9 | 0.018 | 1.5 |
| GROWTH | cell division | 36 | 2.5 | 0.041 | 1.3 | cell growth | 24 | 1.9 | 0.023 | 1.5 |
| cell proliferation | 89 | 6.2 | 0.013 | 1.2 | regulation of cell size | 24 | 1.9 | 0.035 | 1.5 | |
| cell motility/localization of the cell | 52 | 4.0 | 0.007 | 1.4 | ||||||
| mitosis/M phase of mitotic cell cycle | 33 | 2.5 | 0.018 | 1.4 | ||||||
| cell migration | 31 | 2.4 | 0.027 | 1.4 | ||||||
| mitotic cell cycle | 43 | 3.3 | 0.039 | 1.3 | ||||||
| cell proliferation | 78 | 6.0 | 0.047 | 1.2 | ||||||
| SIGNAL. | DNA damage response. signal transduction resulting in induction of apoptosis | 5 | 0.3 | 0.028 | 3.4 | phosphoinositide-mediated signaling | 16 | 1.2 | 0.010 | 1.9 |
| PROT. | tRNA modification | 6 | 0.4 | 0.010 | 3.4 | tRNA aminoacylation for protein translation/aminoacid activation | 14 | 1.1 | 0.025 | 1.8 |
| SYNT. | RNA modification | 9 | 0.6 | 0.001 | 3.1 | |||||
| response to virus | 14 | 1.0 | 0.003 | 2.2 | response to wounding | 50 | 3.9 | 0.006 | 1.4 | |
| STRESS | cell redox homeostasis | 17 | 1.2 | 0.003 | 2.0 | inflammatory response | 32 | 2.5 | 0.049 | 1.4 |
| RESP. | response to oxidative stress | 19 | 1.3 | 0.040 | 1.5 | response to stress | 112 | 8.6 | 0.028 | 1.2 |
| response to stimulus | 216 | 15.1 | 0.011 | 1.1 | response to stimulus | 194 | 15.0 | 0.026 | 1.1 | |
| ADH. | biological/cell adhesion | 65 | 5.0 | 0.026 | 1.3 | |||||
| BIOL. REG. | regulation of biological quality | 103 | 7.2 | 0.018 | 1.2 | regulation of biological quality | 97 | 7.5 | 0.008 | 1.2 |
| isoprenoid metabolic process | 9 | 0.6 | 0.015 | 2.4 | purine ribonucleoside metabolic process | 5 | 0.4 | 0.019 | 3.8 | |
| glutathione metabolic process | 8 | 0.6 | 0.033 | 2.3 | ribonucleoside/glycine metabolic process | 6 | 0.5 | 0.017 | 3.2 | |
| pyruvate metabolic process | 11 | 0.8 | 0.017 | 2.1 | retinoid/diterpenoid metabolic process | 5 | 0.4 | 0.046 | 3.1 | |
| gluconeogenesis | 9 | 0.6 | 0.043 | 2.1 | aldehyde metabolic process | 6 | 0.5 | 0.035 | 2.8 | |
| mitochondrial transport | 12 | 0.8 | 0.032 | 1.9 | serine family amino acid metabolic process | 12 | 0.9 | 0.002 | 2.5 | |
| sulfur metabolic process | 17 | 1.2 | 0.010 | 1.8 | glutamine family amino acid metab. process | 12 | 0.9 | 0.004 | 2.4 | |
| water-soluble vitamin metabolic process | 13 | 0.9 | 0.049 | 1.7 | nucleoside/pyridine nucleotide metab. process | 10 | 0.8 | 0.011 | 2.4 | |
| glucose metabolic process | 26 | 1.8 | 0.010 | 1.6 | water-soluble vitamin metabolic process | 16 | 1.2 | 0.001 | 2.3 | |
| glucose catabolic process | 17 | 1.2 | 0.037 | 1.6 | gluconeogenesis | 9 | 0.7 | 0.024 | 2.3 | |
| vitamin/alcohol metabolic process | 18 | 1.3 | 0.039 | 1.6 | oxygen and ROS metabolic process | 8 | 0.6 | 0.033 | 2.3 | |
| nucleotide metabolic process | 47 | 3.3 | 0.001 | 1.5 | vitamin metabolic process | 23 | 1.8 | 0.000 | 2.2 | |
| nucleobase. nucleoside and nucleotide metabolic process | 49 | 3.4 | 0.002 | 1.5 | pyruvate metabolic process | 10 | 0.8 | 0.028 | 2.1 | |
| monosaccharide metabolic process | 32 | 2.2 | 0.016 | 1.5 | glucose metabolic process | 26 | 2.0 | 0.002 | 1.8 | |
| carboxylic/organic acid metab. process | 102 | 7.1 | 0.000 | 1.4 | glucose catabolic process | 17 | 1.3 | 0.015 | 1.8 | |
| amino acid and derivative metabolic process | 67 | 4.7 | 0.002 | 1.4 | amino acid catabolic process | 15 | 1.2 | 0.025 | 1.8 | |
| amino acid metabolic process | 54 | 3.8 | 0.008 | 1.4 | alcohol catabolic process | 18 | 1.4 | 0.015 | 1.7 | |
| monocarboxylic acid metabolic process | 45 | 3.1 | 0.015 | 1.4 | hexose/monosaccharide catabolic process | 17 | 1.3 | 0.026 | 1.7 | |
| hexose metabolic process | 31 | 2.2 | 0.023 | 1.4 | amine/nitrogen compound catabolic process | 16 | 1.2 | 0.034 | 1.7 | |
| fatty acid metabolic process | 31 | 2.2 | 0.034 | 1.4 | monosaccharide metabolic process | 31 | 2.4 | 0.007 | 1.6 | |
| METAB. | lipid biosynthetic process | 32 | 2.2 | 0.040 | 1.4 | aromatic compound metabolic process | 23 | 1.8 | 0.012 | 1.6 |
| amine metabolic process | 74 | 5.2 | 0.006 | 1.3 | carbohydrate catabolic process | 21 | 1.6 | 0.025 | 1.6 | |
| nitrogen compound metabolic process | 75 | 5.2 | 0.010 | 1.3 | tRNA metabolic process | 19 | 1.5 | 0.026 | 1.6 | |
| alcohol metabolic process | 47 | 3.3 | 0.021 | 1.3 | cellular carbohydrate catabolic process | 20 | 1.5 | 0.032 | 1.6 | |
| cellular carbohydrate metabolic process | 52 | 3.6 | 0.036 | 1.3 | amino acid metabolic process | 54 | 4.2 | 0.001 | 1.5 | |
| catabolic process | 106 | 7.4 | 0.012 | 1.2 | nucleobase. nucleoside and nucleotide metabolic process | 46 | 3.5 | 0.001 | 1.5 | |
| lipid metabolic process | 85 | 5.9 | 0.012 | 1.2 | nucleotide metabolic process | 42 | 3.2 | 0.003 | 1.5 | |
| cellular lipid metabolic process | 69 | 4.8 | 0.037 | 1.2 | coenzyme metabolic process | 37 | 2.9 | 0.011 | 1.5 | |
| hexose metabolic process | 30 | 2.3 | 0.011 | 1.5 | ||||||
| carboxylic/organic acid metabolic process | 97 | 7.5 | 0.000 | 1.4 | ||||||
| amine metabolic process | 72 | 5.6 | 0.001 | 1.4 | ||||||
| amino acid and derivative metabolic process | 62 | 4.8 | 0.002 | 1.4 | ||||||
| nitrogen compound metabolic process | 73 | 5.6 | 0.002 | 1.4 | ||||||
| cofactor metabolic process | 46 | 3.5 | 0.007 | 1.4 | ||||||
| cellular carbohydrate metabolic process | 51 | 3.9 | 0.009 | 1.4 | ||||||
| carbohydrate metabolic process | 67 | 5.2 | 0.009 | 1.3 | ||||||
| alcohol metabolic process | 43 | 3.3 | 0.026 | 1.3 | ||||||
| cellular catabolic process | 84 | 6.5 | 0.017 | 1.2 | ||||||
| catabolic process | 95 | 7.3 | 0.027 | 1.2 | ||||||
| lipid metabolic process | 75 | 5.8 | 0.037 | 1.2 | ||||||
| cellular lipid metabolic process | 63 | 4.9 | 0.043 | 1.2 | ||||||
| bone mineralization | 6 | 0.5 | 0.035 | 2.8 | ||||||
| BONE | ossification/biomineral formation/bone remodelling | 13 | 1.0 | 0.011 | 2.0 | |||||
| skeletal development | 28 | 2.2 | 0.009 | 1.6 | ||||||
Functional annotation tool from the database for annotation, visualization and integrated discovery (DAVID; v6.7) has been used to identify significant biological processes among differentially expressed genes. p < 0.05 (P) and fold enrichment (FE) was higher than 1.1.